Rank ID GeneSet BroadUrl Description PubMedID NumGenes Contributor p.value p.adj vote.rank avg.rank med.rank min.pvalue min.rank avg.logfc avg.logfc.dir direction significance camera safe gage padog plage zscore gsva ssgsea globaltest ora fry 1 M2574 LIM_MAMMARY_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_STEM_CELL_DN.html Genes consistently down-regulated in mammary stem cells both in mouse and human species. 20346151 572/695 Daniel Hollern 1.00908210748472e-22 7.00506818210122e-21 5 628.727272727273 37 1.00908210748472e-23 1 2.22245003731901 -2.26255349666242 -1 17.9638142919967 2 1116 4715 1 800 1 77 2 156 37 9 2 M2575 LIM_MAMMARY_LUMINAL_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_PROGENITOR_UP.html Genes consistently up-regulated in mammary luminal progenitor cells both in mouse and human species. 20346151 79/91 Daniel Hollern 1.17567825973176e-32 1.69392828430092e-30 5 173.272727272727 47 1.06879841793796e-33 2 3.85019410676735 -4.03286882817977 -1 46.0475541352917 3 85 17 2 1237 6 39 94 47 50 326 3 M11629 MONTERO_THYROID_CANCER_POOR_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MONTERO_THYROID_CANCER_POOR_SURVIVAL_UP.html Up-regulated genes predicting poor survival of patients with thyroid carcinoma. 17873908 14/14 Arthur Liberzon 5.71577893215653e-07 1.20368443390297e-06 60 386.272727272727 58 5.19616401560266e-08 19 2.77017363594539 2.91571042327607 1 6.54461270734302 58 834 427 57 2081 30 19 57 23 508 155 4 M13072 SMID_BREAST_CANCER_LUMINAL_A_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_A_DN.html Genes down-regulated in the luminal A subtype of breast cancer. 18451135 23/24 Jessica Robertson 2.68390117294949e-07 8.34415403671576e-07 40 371.181818181818 62 2.43991045488494e-08 2 2.65314379028721 2.65314379028721 1 6.43580343274359 37 701 666 62 1619 20 2 58 34 710 174 5 M2761 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP.html Top 100 probe sets contrubuting to the positive side of the 2nd principal component; associated with adipocytic differentiation. 17464315 132/209 Nikolaos Papanikolaou 2.14438354462529e-22 1.4459271900902e-20 15 391.909090909091 70 1.94943958602299e-23 4 2.63936446192135 2.77584697094157 1 21.0089985612403 11 1472 45 47 1507 4 70 196 717 59 183 6 M683 REACTOME_LATENT_INFECTION_OF_HOMO_SAPIENS_WITH_MYCOBACTERIUM_TUBERCULOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LATENT_INFECTION_OF_HOMO_SAPIENS_WITH_MYCOBACTERIUM_TUBERCULOSIS.html Genes involved in Latent infection of Homo sapiens with Mycobacterium tuberculosis 26/38 Reactome 4.53295863334218e-08 4.72308272613136e-07 5 849.090909090909 73 4.12087156976443e-09 3 1.95546041215468 -1.93635324429808 -1 4.92462261385071 73 1817 1956 1393 42 5 3 24 1708 2308 11 7 M991 REACTOME_TRANSFERRIN_ENDOCYTOSIS_AND_RECYCLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSFERRIN_ENDOCYTOSIS_AND_RECYCLING.html Genes involved in Transferrin endocytosis and recycling 24/29 Reactome 6.55042224665308e-08 5.92246664446794e-07 80 803.363636363636 79 5.95492949244509e-09 5 1.93505873844863 -1.93505873844863 -1 4.79624123749404 79 1834 2324 996 114 11 5 8 19 3415 32 8 M17333 FARMER_BREAST_CANCER_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_2.html Cluster 2: selected proliferation and 8q amplicon genes clustered together across breast cancer samples. 15897907 45/72 Leona Saunders 1.03759762686201e-07 6.84002904858752e-07 45 191.636363636364 104 9.43270614362519e-09 18 2.26577997514466 2.48477700976201 1 5.56751852732169 42 361 481 59 324 18 37 104 65 352 265 9 M16848 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION.html Epithelial cell signaling in Helicobacter pylori infection 82/91 KEGG 6.4061110297286e-08 5.85985350006182e-07 30 451.818181818182 107 5.82373746933286e-09 8 1.91573369132849 -1.9768508079103 -1 4.75139864013207 30 185 1373 610 107 8 40 59 942 1570 46 10 M6875 LANDIS_BREAST_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_BREAST_CANCER_PROGRESSION_UP.html Genes up-regulated in preneoplastic mammary tissues and whose expression is maintained in tumors. 16434967 55/57 Lauren Kazmierski 5.16620745738352e-08 5.19978203455085e-07 110 326.090909090909 107 4.69655234427305e-09 41 2.24765392495008 -2.35872168185997 -1 5.63021086861233 41 377 1114 61 57 101 107 81 107 1350 191 11 M506 REACTOME_INSULIN_RECEPTOR_RECYCLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INSULIN_RECEPTOR_RECYCLING.html Genes involved in Insulin receptor recycling 20/27 Reactome 8.54516841692069e-08 6.48443648357969e-07 110 928.363636363636 110 7.76833522620852e-09 4 1.37050859568381 -1.37050859568381 -1 3.36064844219627 110 827 2979 2320 211 10 4 43 49 3636 23 12 M6744 COLDREN_GEFITINIB_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/COLDREN_GEFITINIB_RESISTANCE_DN.html Genes down-regulated in NSCLC (non-small cell lung carcinoma) cell lines resistant to gefitinib [PubChem=123631] compared to the sensitive ones. 16877703 320/386 Arthur Liberzon 4.09536215749181e-17 1.77340453058361e-15 80 246.181818181818 122 3.72305650681074e-18 11 2.46329346634993 -2.47208184059564 -1 14.5631157921793 76 1232 74 11 202 67 365 122 385 134 40 13 M2580 LIM_MAMMARY_LUMINAL_MATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_MATURE_DN.html Genes consistently down-regulated in mature mammary luminal cells both in mouse and human species. 20346151 161/176 Daniel Hollern 1.39675694866604e-14 4.36602172033358e-13 75 748.727272727273 123 1.26977904424186e-15 67 2.69609414247409 2.89603235345255 1 13.3513933680662 75 1452 108 336 3027 79 1489 123 1366 114 67 14 M2573 LIM_MAMMARY_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_STEM_CELL_UP.html Genes consistently up-regulated in mammary stem cells both in mouse and human species. 20346151 691/782 Daniel Hollern 3.69896359832591e-85 8.72955409204915e-82 5 687.090909090909 134 3.69896359832596e-86 1 3.06913022354112 3.2150594211085 1 100 1 1095 4714 213 887 2 134 1 492 2 17 15 M17299 CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP.html Genes up-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. 16288205 583/712 Arthur Liberzon 3.18507357130846e-16 1.20268378052607e-14 125 678.636363636364 142 3.18507357130848e-17 3 2.24513318516343 -2.24473536278162 -1 12.5182840909492 123 1126 4294 6 828 3 572 142 278 71 22 16 M19164 RICKMAN_HEAD_AND_NECK_CANCER_D http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_D.html Cluster d: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 19/70 Jessica Robertson 8.89411532787748e-09 1.18758139528968e-07 395 261.090909090909 149 8.08555942166766e-10 7 4.72580020919251 -5.3225815410996 -1 13.1118116755862 392 790 274 21 13 445 149 7 45 680 56 17 M7357 LEE_EARLY_T_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_EARLY_T_LYMPHOCYTE_UP.html Genes up-regulated at early stages of progenitor T lymphocyte maturation compared to the late stages. 15210650 123/177 Arthur Liberzon 4.08136185496084e-17 1.77340453058361e-15 15 459.272727272727 152 3.71032895905531e-18 14 2.26763870058232 2.38938940995677 1 13.4024205444057 14 1494 152 40 1661 32 78 406 460 65 650 18 M4491 CROONQUIST_NRAS_VS_STROMAL_STIMULATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_VS_STROMAL_STIMULATION_DN.html Genes down-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing an activated form of NRAS [GeneID=4893] off a plasmid vector compared to those co-cultured with bone marrow stromal cells. 12791645 148/194 Arthur Liberzon 1.13430773363784e-16 4.57601068612873e-15 165 619.454545454545 165 1.03118884876167e-17 62 2.56994480271331 2.79817504986869 1 14.7703261628815 165 1456 80 63 2009 62 736 720 1195 164 164 19 M636 REACTOME_HS_GAG_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HS_GAG_DEGRADATION.html Genes involved in HS-GAG degradation 19/21 Reactome 5.18074076822687e-08 5.20278647362358e-07 245 398.727272727273 166 4.70976444566111e-09 6 2.13324523804997 2.40820302456436 1 5.34086318572481 245 785 1342 343 59 95 166 161 87 1097 6 20 M12942 MAINA_VHL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAINA_VHL_TARGETS_UP.html Genes up-regulated in RCC4 cells (renal cell carcinoma) engineered to stably express VHL [GeneID=7428] off a plasmid vector. 15824735 17/18 Leona Saunders 4.89475104078383e-07 1.099106798882e-06 170 467.818181818182 170 4.44977466346444e-08 21 3.42605711913785 3.44292197946432 1 8.16038958593725 170 819 541 326 1924 103 108 129 167 838 21 21 M737 LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_DN.html Genes down-regulated between two breast carcinoma subtypes: metaplastic (MCB) and ductal (DCB). 17603561 148/223 Arthur Liberzon 1.73455773585615e-11 3.60665749481984e-10 255 331.454545454545 174 1.57687066897257e-12 30 2.55872975962959 -2.68189684384861 -1 9.66691890289693 253 1458 174 30 88 74 719 70 509 238 33 22 M2483 REICHERT_MITOSIS_LIN9_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/REICHERT_MITOSIS_LIN9_TARGETS.html Genes with known mitosis function that were down-regulated in MEF cells (embryonic fibroblast) upon knockout of LIN9 [GeneID=286826]. 20404087 33/33 Arthur Liberzon 1.48936328569141e-07 7.26289540930751e-07 30 269.454545454545 183 1.35396671501712e-08 27 2.49978764038276 2.69970411867264 1 6.12150409021202 63 529 533 86 624 27 30 183 84 510 295 23 M10605 BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN.html Genes down-regulated in medullary breast cancer (MBC) relative to ductal breast cancer (DBD). 16651414 229/309 Arthur Liberzon 4.61153590546228e-18 2.1766449473782e-16 195 318.363636363636 184 4.19230536860205e-19 7 2.59028013393426 2.76054591418787 1 16.2654669889438 195 1324 69 243 184 7 671 53 608 113 35 24 M1735 GAVIN_FOXP3_TARGETS_CLUSTER_P6 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P6.html Cluster P6 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 94/126 Jessica Robertson 1.74678537291703e-13 4.76579593073316e-12 40 449.636363636364 195 1.58798670265197e-14 17 2.29916156022247 2.39793872950026 1 10.4185506121326 36 50 195 920 2315 17 81 398 277 95 562 25 M1967 MIKKELSEN_IPS_WITH_HCP_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_WITH_HCP_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV8.1 (induced pluripotent cells, iPS). 18509334 80/196 Jessica Robertson 9.09570975588287e-15 2.92052721413382e-13 195 641.636363636364 195 8.26882705080263e-16 36 3.39929937350747 3.63591717072796 1 17.0855276962633 150 193 104 2044 1401 66 625 36 1995 249 195 26 M12895 CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN.html Genes down-regulated in basal-like breast cancer cell lines as compared to the mesenchymal-like ones. 16288205 87/104 Arthur Liberzon 1.95176913502008e-07 7.60722569553657e-07 90 513.272727272727 201 1.77433573470434e-08 35 2.28672388584686 2.35949192857119 1 5.5769869066641 87 158 566 1157 921 35 201 56 1710 603 152 27 M19977 SU_SALIVARY_GLAND http://www.broadinstitute.org/gsea/msigdb/cards/SU_SALIVARY_GLAND.html Genes up-regulated specifically in human salivary gland tissue. 11904358 18/35 John Newman 1.19500758516071e-07 7.06112554001409e-07 90 478.363636363636 204 1.08637059097433e-08 65 2.91125600472193 -2.73780243225485 -1 7.15167366202332 409 864 924 87 415 198 90 65 153 1853 204 28 M4888 ZHAN_MULTIPLE_MYELOMA_PR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_PR_UP.html Top 50 up-regulated genes in cluster PR of multiple myeloma samples characterized by increased expression of proliferation and cell cycle genes. 16728703 48/61 Kevin Vogelsang 1.87984508199794e-10 3.46596436993369e-09 10 432.727272727273 216 1.7089500746896e-11 9 2.48466455659691 2.47559817461021 1 8.40368191061917 9 348 260 532 2499 13 9 216 185 215 474 29 M15664 ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER http://www.broadinstitute.org/gsea/msigdb/cards/ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER.html The 'Cervical Cancer Proliferation Cluster' (CCPC): genes whose expression in cervical carcinoma positively correlates with that of the HPV E6 and E7 oncogenes; they are also differentially expressed according to disease outcome. 16007141 173/219 Leona Saunders 5.44152463704075e-18 2.54296992938934e-16 10 605.818181818182 223 4.94684057912795e-19 6 2.08114425300192 2.13021766832918 1 13.0020124020985 6 1395 223 45 2807 88 75 480 578 55 912 30 M7012 SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN.html Genes down-regulated in invasive ductal carcinoma (IDC) relative to ductal carcinoma in situ (DCIS, non-invasive). 16707453 123/148 Arthur Liberzon 6.00067410767576e-19 3.18237997620557e-17 680 434.636363636364 224 5.45515827970522e-20 13 2.93312066437388 -2.54137845847059 -1 19.4099292235441 676 1493 60 13 224 403 1071 304 206 137 194 31 M19391 LIU_PROSTATE_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_PROSTATE_CANCER_DN.html Genes down-regulated in prostate cancer samples. 16618720 646/808 Arthur Liberzon 1.36463520322718e-34 2.14702605307743e-32 210 789.090909090909 227 1.36463520322717e-35 18 2.58694010064753 2.86133573952379 1 32.8965090553593 209 1110 4276 227 465 37 1245 188 798 18 107 32 M1637 NIELSEN_LEIOMYOSARCOMA_CNN1_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_CNN1_UP.html Top 20 positive significant genes associated with leiomyosarcoma tumors expressing muscle gene cluster with CNN1 [GeneID=1264]. 11965276 26/32 John Newman 1.72002885692348e-08 2.15918516081883e-07 115 497.636363636364 227 1.56366260942837e-09 3 3.89738650154182 4.18087361787248 1 10.3976594552257 112 689 297 356 2532 57 168 34 227 999 3 33 M2571 ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_DN.html Genes down-regulated during prostate cancer progression in the JOCK1 model due to inducible activation of FGFR1 [GeneID=2260] gene in prostate. 18068632 392/587 Yujin Hoshida 2.34937438340512e-41 5.83634057351166e-39 40 440 232 2.13579489400468e-42 11 2.87574275543075 3.36752476543141 1 44.1679355024319 307 1199 11 232 729 36 1427 37 718 41 103 34 M1796 ZHENG_GLIOBLASTOMA_PLASTICITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_GLIOBLASTOMA_PLASTICITY_UP.html The glioblastoma multiforme (GBM) plasticity signature: genes up-regulated in neural stem cells (NSC) with double knockout of TP53 and PTEN [GeneID=7157;5728] vs those with knockout of TP53 alone. 18948956 342/447 Jessica Robertson 7.27176086630035e-29 8.37139299730187e-27 25 391.636363636364 235 6.6106916966367e-30 21 2.42072288639051 2.50626765811138 1 25.3366905975684 81 1216 24 235 1081 21 278 192 800 29 351 35 M13387 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_6.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 6. 12554760 85/111 Arthur Liberzon 3.8081353875297e-08 4.22927035979769e-07 410 255 237 3.46194132131584e-09 33 2.38029042929519 -2.6117409447219 -1 6.051293695455 408 121 381 33 99 225 392 573 237 242 94 36 M6906 SENESE_HDAC2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC2_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC2 [GeneID=3066] by RNAi. 17470557 169/210 Leona Saunders 1.53351545187338e-24 1.2268123614987e-22 240 429.636363636364 238 1.39410495624853e-25 37 3.13359879285983 3.15630454468482 1 27.5627751801396 238 1416 37 245 1066 152 721 119 499 96 137 37 M13202 FOURNIER_ACINAR_DEVELOPMENT_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_LATE_DN.html Genes down-regulated late in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 40/50 Arthur Liberzon 1.26618578308511e-06 2.09184350583189e-06 170 605.181818181818 242 1.15107864711362e-07 117 2.27205725466495 2.60686578308597 1 5.13949008134528 169 512 895 162 2741 242 222 117 311 1107 179 38 M2533 BOSCO_EPITHELIAL_DIFFERENTIATION_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_EPITHELIAL_DIFFERENTIATION_MODULE.html Genes representing epithelial differentiation module in sputum during asthma exacerbations. 20336062 54/95 Antony Bosco 6.72460176337884e-20 3.87074638087172e-18 250 263.090909090909 243 6.11327433034441e-21 14 3.61744331364529 -3.62115931113595 -1 25.2811863507851 249 302 54 14 521 243 423 118 670 147 153 39 M6171 TANG_SENESCENCE_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TANG_SENESCENCE_TP53_TARGETS_DN.html Genes down-regulated in WI-38 cells (senescent primary fibroblasts) after inactivation of TP53 [GeneID=7157] by GSE56 polypeptide. 17533371 65/94 Leona Saunders 4.26108435120733e-08 4.58360044171859e-07 260 420.181818181818 247 3.87371312158038e-09 15 2.29123721627933 2.29460695986995 1 5.79082953775715 28 242 477 535 2430 15 43 88 247 260 257 40 M8448 BENPORATH_PRC2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_PRC2_TARGETS.html Set 'PRC2 targets': Polycomb Repression Complex 2 (PRC) targets; identified by ChIP on chip on human embryonic stem cells as genes that: posess the trimethylated H3K27 mark in their promoters and are bound by SUZ12 [GeneID=23512] and EED [GeneID=8726] Polycomb proteins. 18443585 489/952 Jessica Robertson 5.62278566438915e-73 6.63488708397919e-70 5 458.727272727273 250 5.11162333126296e-74 2 2.98693383966135 3.18693593015042 1 83.0488684408145 250 1151 2 220 679 23 1117 251 1115 5 233 41 M6470 VERRECCHIA_RESPONSE_TO_TGFB1_C5 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C5.html Cluster 5: ECM related genes up-regulated in dermal fibroblasts later than 30 min after TGFB1 [GeneID=7040] addition; decreased slowly after the peak at 120 min time point. 11279127 43/50 John Newman 6.70247503998879e-08 6.00297574739034e-07 255 634.181818181818 251 6.09315931289548e-09 16 2.06497507035558 2.35273740865655 1 5.1167418225571 251 513 1226 1713 119 31 165 78 1720 1144 16 42 M1037 KANG_DOXORUBICIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_DOXORUBICIN_RESISTANCE_UP.html Genes up-regulated in gastric cancer cell lines: doxorubicin [PubChem=31703] resistant vs sensitive. 14734480 67/71 John Newman 8.90179718061452e-10 1.43892064015413e-08 20 503.818181818182 253 8.09254289474221e-11 16 2.14661657136444 2.21446746410428 1 6.71982659769819 18 216 436 534 2844 16 49 253 501 177 498 43 M15973 SHEPARD_BMYB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_BMYB_TARGETS.html Human orthologs of BMYB [GeneID=4605] target genes in zebra fish, identified as commonly changed in the BMYB loss of function mutant crb ('crush and burn') and after knockdown of BMYB by morpholino. 16150706 100/158 Jennifer Shepard 5.3364116714304e-08 5.26942742450868e-07 245 542.545454545455 258 4.85128345533874e-09 56 2.38422252008455 2.46398358384085 1 5.96980515684331 244 78 332 552 2347 56 258 199 1218 250 434 44 M5505 HUPER_BREAST_BASAL_VS_LUMINAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUPER_BREAST_BASAL_VS_LUMINAL_DN.html Genes down-regulated in basal mammary epithelial cells compared to the luminal ones. 17409405 85/112 Jessica Robertson 3.29825187792128e-10 5.70247211127782e-09 225 481.181818181818 263 2.99841079855978e-11 135 2.65473653512887 -2.58981365652807 -1 8.75146369644558 222 135 213 263 1836 256 419 320 1077 367 185 45 M12795 CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP.html Genes up-regulated in basal-like breast cancer cell lines as compared to the mesenchymal-like ones. 16288205 173/215 Arthur Liberzon 2.01474362271322e-14 6.13521928981059e-13 545 401.181818181818 265 1.83158511155748e-15 17 2.65628368098711 -2.39586253308623 -1 12.9956796241101 544 1407 112 17 104 265 1065 324 407 127 41 46 M2128 CHICAS_RB1_TARGETS_GROWING http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_GROWING.html Genes up-regulated in growing IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 343/431 Arthur Liberzon 3.27647654149772e-24 2.57749487931154e-22 265 542.363636363636 265 2.9786150377252e-25 38 2.5505618988895 2.56726219636111 1 22.0944215333886 80 1231 38 264 1559 52 304 265 1676 75 422 47 M12432 PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN.html Genes down-regulated in unstable ateroslerotic plaques compared to the stable ones. 16741146 61/71 Arthur Liberzon 5.69300898080555e-08 5.517659628214e-07 75 351.090909090909 273 5.17546284375032e-09 1 2.93423324051624 3.08260680161382 1 7.33491784671813 71 310 334 1142 822 25 183 10 273 691 1 48 M2070 YAGUE_PRETUMOR_DRUG_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAGUE_PRETUMOR_DRUG_RESISTANCE_DN.html Down-regulated genes common to all pretumorigenic cells with acquired drug resistance. 17283147 25/27 Jessica Robertson 8.56249640327132e-07 1.57073389131133e-06 120 583 274 7.78409066894024e-08 25 3.16492376261171 3.26321513638688 1 7.3372270468554 119 727 536 1135 2444 82 274 108 240 723 25 49 M9192 CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN.html Genes down-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. 16288205 657/762 Arthur Liberzon 1.00920473809933e-22 7.00506818210122e-21 120 842.181818181818 279 1.00920473809933e-23 38 2.31719502072681 2.54290894010274 1 18.7317604907299 116 1113 4295 246 537 166 867 68 1539 38 279 50 M2391 WANG_THOC1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_THOC1_TARGETS_DN.html Genes down-regulated in testis tissue expressing hypomorphic allele of THOC1 [GeneID=9984]. 19307311 18/47 Arthur Liberzon 4.21130171459091e-07 1.00849031419935e-06 285 449.818181818182 279 3.82845683702756e-08 8 2.69729102938627 -3.06674192971529 -1 6.45446199494753 282 830 722 66 1777 279 94 237 71 582 8 51 M1642 SIMBULAN_PARP1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_PARP1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) from PARP1 [GeneID=142] knockout mice. 11016956 21/25 John Newman 1.48046106027703e-07 7.26289540930751e-07 90 322.454545454545 283 1.34587378172974e-08 10 3.51849758325512 3.22424816632188 1 8.63652190402233 88 749 547 283 619 87 27 207 10 555 375 52 M10169 WU_APOPTOSIS_BY_CDKN1A_VIA_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/WU_APOPTOSIS_BY_CDKN1A_VIA_TP53.html Genes downstream of both CDKN1A and TP53 [GeneID=1026;7157] in 2774qw1 cells (ovarian cancer). 12138103 98/116 Arthur Liberzon 2.42636977529384e-07 8.07627467909088e-07 145 599.090909090909 288 2.20579094808825e-08 96 2.29742114413767 2.34729164040888 1 5.57930179743503 144 96 623 134 2377 173 236 351 1375 288 793 53 M6679 BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_DN.html Genes down-regulated in SaOS-2 cells (osteosarcoma) upon expression of PAX3-FOXO1 [GeneID=5077;2308] fusion protein off an adenoviral vector. 15688035 78/91 Leona Saunders 2.06418527571003e-09 3.11276501640618e-08 155 647.727272727273 289 1.87653207058798e-10 100 2.72165867938552 3.11376983937753 1 8.16656507343266 154 215 243 429 2963 144 760 911 917 289 100 54 M5618 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_DN.html Genes down-regulated in ductal carcinoma vs normal lobular breast cells. 17389037 90/118 Arthur Liberzon 2.89270760077121e-17 1.30034094053715e-15 880 502 290 2.62973418251927e-18 4 3.43231596845009 4.09261654847309 1 20.4977121959801 877 119 71 244 755 420 2352 85 305 290 4 55 M10117 VERHAAK_AML_WITH_NPM1_MUTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_AML_WITH_NPM1_MUTATED_DN.html Genes down-regulated in acute myeloid leukemia (AML) patients with mutated NPM1 [GeneID=4869]. 16109776 298/470 Kevin Vogelsang 9.07494622172544e-28 9.7349423105782e-26 600 571.181818181818 290 8.24995111065952e-29 23 2.59063787287321 2.79103765995676 1 26.0084977960845 600 1255 23 238 587 167 1637 203 1220 63 290 56 M1003 REACTOME_IKK_COMPLEX_RECRUITMENT_MEDIATED_BY_RIP1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IKK_COMPLEX_RECRUITMENT_MEDIATED_BY_RIP1.html Genes involved in IKK complex recruitment mediated by RIP1 12/22 Reactome 2.25288052918965e-07 7.85927279953817e-07 280 618.818181818182 292 2.04807341808445e-08 38 2.32569805937248 -2.40013797539367 -1 5.6596518054314 277 941 1542 604 1078 165 38 112 211 1547 292 57 M19867 ALCALAY_AML_BY_NPM1_LOCALIZATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/ALCALAY_AML_BY_NPM1_LOCALIZATION_DN.html Genes down-regulated in acute myeloid leukemia (AML) with respect to cellular localization of NPM1 [GeneID=4869]: cytoplasmic vs. nucleolar. 15831697 218/279 Kevin Vogelsang 2.570335634777e-11 5.18460863083224e-10 250 651.454545454545 293 2.33666875891548e-12 55 2.19901572795895 2.27544008628303 1 8.16149468964604 246 1344 230 55 2178 162 293 456 1225 138 839 58 M13186 MCBRYAN_PUBERTAL_BREAST_3_4WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_3_4WK_UP.html Genes up-regulated during pubertal mammary gland development between weeks 3 and 4. 17486082 310/374 Arthur Liberzon 4.6036776521185e-32 6.03593292166647e-30 965 528.909090909091 298 4.18516150192594e-33 10 2.879599590164 -3.06363550453039 -1 33.7877461123846 962 1244 18 10 241 298 1374 1086 329 44 212 59 M695 REACTOME_GLYCOSAMINOGLYCAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSAMINOGLYCAN_METABOLISM.html Genes involved in Glycosaminoglycan metabolism 99/122 Reactome 4.35513208283864e-08 4.64023102279873e-07 185 472.636363636364 302 3.95921106277552e-09 71 2.36248957222714 2.58949414110257 1 5.96740068080198 185 71 324 706 277 215 816 259 1652 302 392 60 M1259 SASAI_RESISTANCE_TO_NEOPLASTIC_TRANSFROMATION http://www.broadinstitute.org/gsea/msigdb/cards/SASAI_RESISTANCE_TO_NEOPLASTIC_TRANSFROMATION.html Genes down-regulated in MEF and REF cells (mouse and rat fibroblasts) but not in TIG3/T cells (human lung fibroblasts expressing TERT [GeneID=7015]) by co-expression of the SV40 early region and the activated HRAS (H-RasV12) [GeneID=3265]. 16832346 79/80 Arthur Liberzon 9.89367406318149e-13 2.34664028031239e-11 85 797.090909090909 308 8.99424914835086e-14 85 2.97540190976234 3.09689357623259 1 12.6692072418434 85 202 146 1130 3467 250 935 1054 904 308 287 61 M17163 CAIRO_LIVER_DEVELOPMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_LIVER_DEVELOPMENT_UP.html Genes up-regulated at early fetal liver stage (embryonic days E11.5 - E12.5) compared to the late fetal liver stage (embryonic days E14.5 - E16.5). 19061838 230/273 Arthur Liberzon 4.78552429722719e-07 1.08334171141066e-06 50 661.727272727273 308 4.35047758017554e-08 26 2.0317251847832 2.10082670596911 1 4.82404831103185 48 1332 405 308 1911 26 281 114 2250 407 197 62 M16376 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC.html Arrhythmogenic right ventricular cardiomyopathy (ARVC) 67/95 KEGG 4.48441085502135e-08 4.70636656673264e-07 225 398.818181818182 309 4.07673722402744e-09 120 2.8768904378252 3.36664767088545 1 7.27050726731845 225 261 327 309 1230 190 523 120 444 515 243 63 M1591 BURTON_ADIPOGENESIS_PEAK_AT_24HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_24HR.html Cluster 5: genes progressively up-regulated (peak at 24 h time point) during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 59/99 John Newman 2.00574296233139e-07 7.65527859584926e-07 100 408.363636363636 309 1.82340285926843e-08 97 2.39279031560943 2.29702666201779 1 5.83535683273729 98 309 604 114 937 97 147 431 304 693 758 64 M10331 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FGF3 http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FGF3.html Genes whose expression is coregulated with that of FGF3 [GeneID=2248] in hematopoietic stem cells (HSC). 15711547 7/12 Jean Junior 2.28955363247612e-08 2.72896291547659e-07 630 993.272727272727 311 2.28955365606537e-09 8 1.97101699220945 2.17841000410506 1 5.15303381854695 630 1027 4474 1800 8 311 52 45 140 2402 37 65 M5319 APPEL_IMATINIB_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/APPEL_IMATINIB_RESPONSE.html Genes up-regulated by imatinib [PubChem=5291] during dendritic cell differentiation. 15756019 36/65 Kevin Vogelsang 4.28495323261006e-08 4.58360044171859e-07 680 376 312 3.8954121055167e-09 33 2.05457649261008 -2.30349534790861 -1 5.18752939385128 678 493 1124 81 33 412 312 271 76 568 88 66 M2448 SWEET_KRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_KRAS_TARGETS_UP.html Genes upregulated in KRAS [GeneID=3845] knockdown vs control in a human cell line. 15608639 129/150 Aravind Subramanian 8.76771795814321e-13 2.10731692325516e-11 140 653.090909090909 314 7.97065268922426e-14 90 2.65353504250668 3.01302477500926 1 11.3431448465824 140 1539 142 367 2041 205 1323 187 836 314 90 67 M1916 ZHANG_TLX_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_DN.html Genes down-regulated in neural stem cells (NSC) at both 36 h and 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 100/112 Jessica Robertson 2.60246183756807e-10 4.61790220801553e-09 10 717.272727272727 326 2.36587439806902e-11 10 1.84370478021886 1.81571738592623 1 6.13050495913845 10 56 1109 1766 2912 33 29 326 657 287 705 68 M10748 YANG_BREAST_CANCER_ESR1_BULK_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_BULK_UP.html Genes up-regulated in bulk samples from early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative samples. 16261164 34/39 Leona Saunders 9.94023774129103e-08 6.71132834037269e-07 335 624.272727272727 332 9.0365801731089e-09 158 1.98835579483381 -2.13483167525779 -1 4.88629645181175 332 583 1499 556 306 197 327 663 170 2076 158 69 M19875 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP.html Genes up-regulated in nsopharyngeal carcinoma relative to the normal tissue. 16912175 405/518 Leona Saunders 5.9498626058093e-12 1.31846720654553e-10 130 605.636363636364 336 5.40896600529582e-13 127 2.16678477979975 2.31385381804623 1 8.55931210685528 127 1203 246 714 1403 201 489 277 1538 128 336 70 M1461 PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP.html Genes up-regulated in LEC (lymphatic endothelial cells) compared to BEC (blood endothelial cells). 12198161 171/224 Kevin Vogelsang 8.42112615230635e-15 2.72244626293739e-13 245 463.545454545455 336 7.65556922936943e-16 39 2.52715429368072 2.48539543455606 1 12.7201220301255 243 1417 103 52 507 39 336 386 1463 91 462 71 M1429 REACTOME_SMOOTH_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SMOOTH_MUSCLE_CONTRACTION.html Genes involved in Smooth Muscle Contraction 34/38 Reactome 2.11153769833641e-07 7.70763712250053e-07 285 505.545454545455 342 1.91957990999972e-08 2 2.99817670285545 3.50555644750061 1 7.32081785036565 281 608 774 819 1007 212 342 48 155 1313 2 72 M629 GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_DN.html Genes down-regulated in quiescent (G0) vs dividing (M) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients. 17717066 8/35 Arthur Liberzon 8.24182500346631e-08 6.34342404134915e-07 455 786.545454545455 342 8.24182530914089e-09 32 2.48970771873479 2.66668812857804 1 6.15547892388608 453 990 4315 138 250 342 161 32 68 1538 365 73 M6302 LIANG_SILENCED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_SILENCED_BY_METHYLATION_DN.html Genes down-regulated in LD419 cells (fibroblast) after treatment with decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 11861364 12/16 John Newman 7.23401373706986e-07 1.39981369640702e-06 75 724 344 6.57637828704611e-08 20 2.27697976531702 2.27697976531702 1 5.31048791215965 126 933 1194 1810 2292 71 20 71 344 896 207 74 M6451 ODONNELL_TFRC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TFRC_TARGETS_DN.html Genes down-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) upon knockdown of TFRC [GeneID=7037] by RNAi. 16508012 145/184 Leona Saunders 3.22046384872324e-08 3.69844023503009e-07 65 586.818181818182 345 2.92769445078719e-09 43 2.37416863602233 2.42596440357715 1 6.09121593815378 64 1465 313 530 2025 43 142 645 345 324 559 75 M19248 REACTOME_CELL_JUNCTION_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_JUNCTION_ORGANIZATION.html Genes involved in Cell junction organization 76/101 Reactome 6.0016494681437e-10 1.00810624518286e-08 1730 1105.18181818182 353 5.45604497252816e-11 34 2.84657583618504 2.59550729416012 1 9.10421794987188 1729 171 218 34 167 893 1921 3076 232 353 3363 76 M16948 CROMER_TUMORIGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_TUMORIGENESIS_DN.html Tumorigenesis markers of head and neck squamous cell carcinoma (HNSCC): down-regulated in the 'early' tumors vs normal samples. 14676830 47/90 Arthur Liberzon 2.12415907918e-11 4.35914384944765e-10 470 369.454545454545 359 1.9310537083641e-12 29 3.34402302915497 -3.54919206894737 -1 12.53845010424 466 403 176 29 90 890 1028 79 395 359 149 77 M12804 LE_EGR2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LE_EGR2_TARGETS_UP.html Genes up-regulated in P14 nerves of transgenic mice having hypomorhic (reduced function) allele of EGR2 [GeneID=1959]. 15695336 158/189 Kate Stafford 1.01834683851085e-09 1.63489696522831e-08 45 614.909090909091 360 9.25769853620209e-11 45 2.17853482533669 2.26343894928016 1 6.77190423575813 45 1441 360 93 2471 69 148 532 740 180 685 78 M11504 TOMLINS_PROSTATE_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_PROSTATE_CANCER_DN.html Genes down-regulated in prostate cancer vs benign prostate tissue, based on a meta-analysis of five gene expression profiling studies. 17173048 57/67 Leona Saunders 1.50799338900534e-07 7.2629885674543e-07 635 572.454545454545 364 1.37090317488272e-08 204 2.60315358193354 2.66191311643664 1 6.37669080491823 318 364 634 1573 641 204 631 208 302 1173 249 79 M16108 CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN.html Genes down-regulated in SH-SY5Y cells (neuroblastoma) after treatment with epoxomicin [PubChem=3035402], a protease inhibitor causing apoptosis. 16983338 203/279 Leona Saunders 2.80892358306447e-10 4.92866888924323e-09 155 573.272727272727 365 2.553566894021e-11 59 2.31755070755796 2.40890575524456 1 7.69258815743514 152 1369 209 525 379 59 196 365 2061 261 730 80 M205 WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP.html Top up-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 27/28 Arthur Liberzon 2.10449745602153e-07 7.70763712250053e-07 270 496.818181818182 366 1.91317968848694e-08 127 2.1640909239588 2.25683812989351 1 5.27026314279398 269 665 953 591 1004 176 184 127 230 900 366 81 M8556 OSADA_ASCL1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OSADA_ASCL1_TARGETS_UP.html Genes up-regulated in A549 cells (lung cancer) upon expression of ASCL1 [GeneID=429] off a viral vector. 18339843 56/87 Jessica Robertson 1.2201783201014e-09 1.93913860972343e-08 425 552 370 1.10925301888922e-10 49 3.11942295057753 3.54481339252182 1 9.62525223762365 424 370 228 694 2606 85 439 49 832 267 78 82 M13007 GLINSKY_CANCER_DEATH_UP http://www.broadinstitute.org/gsea/msigdb/cards/GLINSKY_CANCER_DEATH_UP.html Genes whose over-expression is associated with the risk of death in multiple cancer types 15931389 9/12 Yujin Hoshida 4.78268754596351e-07 1.08321906031419e-06 375 1162.09090909091 371 4.78268857529833e-08 38 2.39206266273353 2.66336406813445 1 5.68854110260605 371 984 4627 1437 1998 362 85 275 38 2326 280 83 M12602 WOO_LIVER_CANCER_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WOO_LIVER_CANCER_RECURRENCE_UP.html Genes positively correlated with recurrence free survival in patients with hepatitis B-related (HBV) hepatocellular carcinoma (HCC). 18381945 176/200 Yujin Hoshida 1.3024283473498e-14 4.09830786632735e-13 380 622.727272727273 378 1.184025770318e-15 103 2.4934588138426 2.64759130854695 1 12.371714825202 378 1406 107 334 586 366 1850 641 866 103 213 84 M6100 SENESE_HDAC1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC1 [GeneID=3065] by RNAi. 17470557 364/452 Leona Saunders 2.39716833330973e-10 4.31856279893967e-09 380 552.363636363636 379 2.17924393960994e-11 14 2.2662095690072 2.44974477791081 1 7.57336893026755 379 1224 205 337 943 14 966 483 1242 154 129 85 M19636 MCBRYAN_PUBERTAL_BREAST_6_7WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_6_7WK_DN.html Genes down-regulated during pubertal mammary gland development between week 6 and 7. 17486082 98/121 Arthur Liberzon 1.02833278334426e-12 2.42686536869245e-11 510 407 379 9.34847984858853e-14 83 3.22392258031936 3.29375903432755 1 13.7126547275113 507 83 147 290 963 258 670 233 427 379 520 86 M129 PID_PLK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PLK1_PATHWAY.html PLK1 signaling events 18832364 63/65 Pathway Interaction Database 1.35720219306389e-07 7.20206492018647e-07 255 557.909090909091 380 1.23382025162825e-08 108 2.05819906516243 2.3656544421162 1 5.03432213181599 189 282 1146 1382 530 108 252 380 601 1016 251 87 M1758 SANSOM_WNT_PATHWAY_REQUIRE_MYC http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_WNT_PATHWAY_REQUIRE_MYC.html Wnt target genes up-regulated after Cre-lox knockout of APC [GeneID=324] in the small intestine that require functional MYC [GeneID=4609]. 17377531 80/97 Jessica Robertson 1.80217250365729e-08 2.24439425257583e-07 245 569 380 1.63833865310921e-09 160 3.27125025871204 3.30460800987138 1 8.69706664271988 242 218 298 380 2391 160 337 494 425 592 722 88 M915 REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE.html Genes involved in Nitric oxide stimulates guanylate cyclase 14/27 Reactome 7.21197609986972e-07 1.39624803902318e-06 385 810.727272727273 381 6.55634405825441e-08 284 3.37866490879838 3.21290994427325 1 7.90560883602589 381 908 575 1577 2291 284 308 376 1542 375 301 89 M17956 ZERBINI_RESPONSE_TO_SULINDAC_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZERBINI_RESPONSE_TO_SULINDAC_DN.html Selected genes down-regulated in DU145 and PC-3 cells (prostate cancer) after treatment with the NSAID (non-steroid anti-inflammatory drug) sulindac [PubChem=5352]. 17178890 7/8 Arthur Liberzon 3.25898368470824e-06 4.56026661303158e-06 335 1147.36363636364 382 3.25898846415669e-07 35 3.00927126446026 3.00927126446026 1 6.41372493556141 333 1024 4281 167 3350 348 138 382 35 1807 756 90 M14228 RICKMAN_HEAD_AND_NECK_CANCER_A http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_A.html Cluster a: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 120/228 Jessica Robertson 1.20448146256067e-18 6.1130672078348e-17 360 748.272727272727 383 1.09498314778243e-19 28 2.88324087061254 3.00657765673973 1 18.7502639951126 356 1529 64 28 1345 383 2136 1291 755 116 228 91 M2608 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_24HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_24HR.html Cell cycle genes significantly (p =< 0.05) changed in fibroblast cells at 24 h after exposure to ionizing radiation. 17404513 153/213 Itai Pashtan 1.19522652252194e-12 2.79280652787306e-11 5 605.090909090909 391 1.08656956592963e-13 5 2.04183079750104 2.03926292060953 1 8.61630461799703 5 1430 391 527 2777 9 22 308 459 187 541 92 M5688 CADWELL_ATG16L1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CADWELL_ATG16L1_TARGETS_UP.html Genes up-regulated in Paneth cell (part of intestiinal epithelium) of mice with hypomorphic (reduced function) form of ATG16L1 [GeneID=55054]. 18849966 80/138 Jessica Robertson 1.63427611811013e-08 2.05700887399462e-07 920 688.272727272727 393 1.48570557295491e-09 43 3.09242641538678 -3.17637456569416 -1 8.2659921774048 916 221 296 935 43 824 676 252 2788 393 227 93 M1954 MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 345/697 Jessica Robertson 2.53237037959309e-69 2.39055763833587e-66 545 510.909090909091 395 2.30215489053917e-70 3 3.14767931173837 3.28705364873713 1 83.0186395727139 545 1207 3 219 454 118 1553 347 768 11 395 94 M10156 BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP.html Genes up-regulated in SaOS-2 cells (osteosarcoma) upon expression of PAX3-FOXO1 [GeneID=5077;2308] fusion protein off an adenoviral vector. 15688035 96/118 Leona Saunders 3.17006742557502e-07 8.94262307705344e-07 220 413.727272727273 396 2.88187989305702e-08 59 2.47993836224966 2.82347318499607 1 5.98238523270786 217 112 420 396 1445 72 551 154 437 688 59 95 M236 PID_DELTA_NP63_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_DELTA_NP63_PATHWAY.html Validated transcriptional targets of deltaNp63 isoforms 18832364 80/93 Pathway Interaction Database 8.90563909093809e-09 1.18758139528968e-07 470 596.818181818182 397 8.09603556998935e-10 126 2.72833441597947 3.45795595323152 1 7.54866010674612 470 181 276 397 1017 214 1761 1095 636 392 126 96 M2025 NAKAMURA_ADIPOGENESIS_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_EARLY_DN.html Genes down-regulated in mesenchymal stem cells during early phase of adipogenesis, defined as days 1 to 5 of culturing with adipogenic hormones. 12646203 54/62 Arthur Liberzon 2.01830866349475e-08 2.47297695028127e-07 280 767.272727272727 397 1.83482607455543e-09 97 3.358423108056 3.88691998490405 1 8.87327125990672 276 397 302 763 2839 361 1144 297 1206 758 97 97 M8645 MCCLUNG_DELTA_FOSB_TARGETS_2WK http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_DELTA_FOSB_TARGETS_2WK.html Genes up-regulated in the nucleus accumbens (a major reward center in brain) 2 weeks after induction of deltaFosB, a FOSB [GeneID=2354] splice variant. 14566342 79/105 John Newman 3.47427223261592e-09 5.01485166298077e-08 225 650 400 3.15842930736594e-10 158 2.77582246046169 2.88689149939344 1 8.09887890246963 158 222 254 400 2219 257 666 869 1469 413 223 98 M1249 YU_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YU_MYC_TARGETS_UP.html Genes up-regulated in B cell lymphoma tumors expressing an activated form of MYC [GeneID=4609]. 16382050 49/54 Kevin Vogelsang 1.60423572562307e-08 2.02459695854034e-07 25 611.545454545455 404 1.45839612483738e-09 21 2.04495439302256 1.91785130865477 1 5.45484492694631 21 392 1053 975 2467 60 31 404 275 542 507 99 M9678 STEIN_ESR1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESR1_TARGETS.html Genes regulated by ESR1 [GeneID=2099] in MCF-7 cells (breast cancer). 18974123 97/113 Arthur Liberzon 4.20928530587059e-07 1.00849031419935e-06 265 682.454545454545 410 3.82662373748928e-08 110 2.00557637000958 2.21084853222944 1 4.7863967485872 265 110 1110 1195 1776 123 410 359 1310 577 272 100 M1253 INAMURA_LUNG_CANCER_SCC_UP http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_UP.html Up-regulated genes characteristic to the squamous cell carcinoma (SCC) type of non-small cell lung cancer (NSCLC). 16007138 28/33 Arthur Liberzon 3.96977719726027e-07 9.84888613642883e-07 220 546.181818181818 411 3.60888901234963e-08 143 3.61254169981125 4.20320081144354 1 8.67652458090687 220 645 411 699 1700 143 213 901 146 663 267 101 M5485 REACTOME_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MUSCLE_CONTRACTION.html Genes involved in Muscle contraction 51/77 Reactome 2.49136755299104e-07 8.17750684987324e-07 295 510.454545454545 413 2.26487985011224e-08 34 2.81762968858886 3.25478926696582 1 6.8478314194015 294 413 602 422 1189 364 983 103 265 946 34 102 M12084 WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP.html Genes up-regulated in non-neoplastic rectal mucosa samples from patients having cancer associated with ulcerative collitis, compared to those who did not have the cancer. 17255260 32/34 Arthur Liberzon 2.97881035771358e-07 8.70294688256627e-07 415 572.090909090909 415 2.70800978276907e-08 20 2.27457369989957 2.62707337486705 1 5.49363070182897 359 585 988 412 1379 236 633 130 415 1136 20 103 M5329 KIM_MYCL1_AMPLIFICATION_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCL1_AMPLIFICATION_TARGETS_UP.html Genes positively correlated with amplifications of MYCL1 [GeneID=4610] in SCLC (small cell lung cancer) cell lines. 16116477 10/19 Arthur Liberzon 5.26018354261336e-07 1.14309697611119e-06 420 651.272727272727 416 4.78198618210885e-08 75 3.82585104828886 4.19047913060589 1 9.09225901651344 416 955 538 1348 1997 252 187 175 396 825 75 104 M7876 CHEBOTAEV_GR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEBOTAEV_GR_TARGETS_DN.html Genes down-regulated in follicular epithelial stem cells after transgenic expression of GR [GeneID=2908] under control of the keratin5 (K5) [GeneID=3852] promoter. 17146443 176/216 Leona Saunders 1.19931928820989e-18 6.1130672078348e-17 275 687.454545454545 422 1.09029026200899e-19 63 2.72345034851649 2.9935227473273 1 17.7083427426708 273 1408 63 256 1333 422 1441 248 1535 83 500 105 M12457 LY_AGING_MIDDLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_MIDDLE_DN.html Genes down-regulated in fibroblasts from middle-age individuals, compared to those from the young donors. 10741968 24/36 John Newman 8.59733173710516e-07 1.57310167253419e-06 115 599.363636363636 424 7.81575917894491e-08 23 2.59243827922398 2.76477511759439 1 6.00030381393823 114 735 855 607 2450 45 23 184 370 786 424 106 M1991 MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_DN.html Genes down-regulated in derivatives of MCF-7aro cells (breast cancer) that developed resistance to tamoxifen [PubChem=5376] or inhibitors of aromatase (CYP19A1) [GeneID=1588]. 18559539 31/34 Leona Saunders 3.36074676107521e-10 5.78689468470119e-09 585 525.727272727273 424 3.05522432871691e-11 60 3.90114992506698 4.3135222146054 1 12.8738033989403 585 576 214 269 424 678 2256 149 142 430 60 107 M2452 PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_UP.html Genes up-regulated after 10 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 90/119 Arthur Liberzon 9.33565049669184e-11 1.76257081377542e-09 290 689.090909090909 425 8.48695499735272e-12 149 2.92918751210423 3.24488018441186 1 10.2620624181503 288 149 193 404 1913 547 1435 425 1451 320 455 108 M540 LOPEZ_MESOTELIOMA_SURVIVAL_TIME_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTELIOMA_SURVIVAL_TIME_UP.html Top genes higher expressed in short term mesothelioma survivors. 16540645 30/57 Arthur Liberzon 4.05239853458922e-07 9.96733771926062e-07 260 603.818181818182 426 3.68399934640087e-08 61 2.05943315963935 2.25066044806586 1 4.92048981837036 256 623 1088 605 1722 157 405 61 320 979 426 109 M4455 EGUCHI_CELL_CYCLE_RB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/EGUCHI_CELL_CYCLE_RB1_TARGETS.html RB1 [GeneID=5925] target genes involved in cell cycle regulation: genes down-regulated by doxorubicin [PubChem=31703] only in cells expressing RB1. 16862181 24/25 Leona Saunders 1.89705226512683e-08 2.35015398724373e-07 25 768.272727272727 428 1.72459298316822e-09 7 2.34702476577236 2.34702476577236 1 6.20687465822021 23 690 683 2260 3140 44 7 337 428 276 563 110 M2124 HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN.html Down-regulated genes in the cancer gene signature, representing a gene signature of cellular transformation. 20385360 155/181 Arthur Liberzon 1.35821388177823e-07 7.20206492018647e-07 430 602 429 1.2347399687548e-08 73 2.42922396499914 2.85103051564297 1 5.95086316675876 429 1468 397 357 531 203 1331 935 389 509 73 111 M1471 AFFAR_YY1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/AFFAR_YY1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) expressing ~25% of YY1 [GeneID=7528]. 16611997 284/397 Kevin Vogelsang 7.77487525059699e-10 1.26980661532241e-08 215 776.454545454545 430 7.06806841213152e-11 119 2.2550443744172 2.36533860418149 1 7.11102293664858 212 1291 222 945 1223 119 409 430 2767 188 735 112 M3672 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN.html Genes down-regulated in lobular carcinoma vs normal ductal breast cells. 17389037 112/150 Arthur Liberzon 4.23730764975846e-16 1.56250719584843e-14 775 572 434 3.85209786341678e-17 19 3.24884346323107 3.797962732148 1 17.9885661451534 775 19 89 252 464 933 2498 107 228 434 493 113 M1522 ONGUSAHA_TP53_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ONGUSAHA_TP53_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblast) lacking TP53 and BRCA1 [GeneID=7157;672] by expression of TP53; most genes are further up-regulated by simultaneous expression of BRCA1. 12802282 45/47 John Newman 1.35072668369589e-07 7.20206492018647e-07 615 393.363636363636 434 1.22793342420547e-08 77 2.7912646632853 3.18706982489015 1 6.84521057159499 615 434 402 286 526 260 605 77 436 540 146 114 M16966 BIOCARTA_STATHMIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STATHMIN_PATHWAY.html Stathmin and breast cancer resistance to antimicrotubule agents 17/22 BioCarta 6.90161394605936e-07 1.35901617961619e-06 455 705.727272727273 436 6.2741964646943e-08 43 2.39670267651209 2.4132487423351 1 5.60472410411446 455 851 1147 436 2249 296 159 136 43 1667 324 115 M15057 HENDRICKS_SMARCA4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HENDRICKS_SMARCA4_TARGETS_UP.html Genes up-regulated in ALAB cells (breast cancer) upon reintroduction of SMARCA4 [GeneID=6597] expressed off adenoviral vector. 14673169 82/109 John Newman 6.32603989539842e-08 5.82044996223792e-07 1320 962.727272727273 437 5.75094552481999e-09 103 2.47529942397972 2.84497461391354 1 6.15676464364208 1317 157 462 317 103 2278 4518 378 149 474 437 116 M7339 FURUKAWA_DUSP6_TARGETS_PCI35_DN http://www.broadinstitute.org/gsea/msigdb/cards/FURUKAWA_DUSP6_TARGETS_PCI35_DN.html Genes down-regulated in PCI-35 cells (pancreatic cancer, lack endogenous DUSP6 [GeneID=1848]) upon expression of DUSP6 off an adenoviral vector. 16532023 84/97 Arthur Liberzon 7.05542556463917e-07 1.37666840285642e-06 155 613.727272727273 440 6.41402529756668e-08 69 2.00662347757155 2.22480707381164 1 4.67985140347164 69 153 952 967 2273 102 153 341 440 732 569 117 M820 REACTOME_CELL_CELL_JUNCTION_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CELL_JUNCTION_ORGANIZATION.html Genes involved in Cell-cell junction organization 46/69 Reactome 3.82798208335399e-09 5.4421913956117e-08 2095 1042.45454545455 441 3.47998371819514e-10 39 3.23912098146755 -3.34167523030668 -1 9.41270880652186 2095 425 258 39 1487 2477 2005 1780 267 441 193 118 M11790 ONDER_CDH1_TARGETS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_3_DN.html Genes down-regulated in HMLE cells (immortalized nontransformed mammary epithelial) cells after loss of function of E-cadhedrin (CDH1) [GeneID=999], which was achieved either by RNAi knockdown or by expression of a dominan-negative form of CDH1. 18483246 60/94 Jessica Robertson 3.27774992683012e-17 1.4458859490316e-15 785 548.272727272727 444 2.97977266075464e-18 36 3.77001577518925 -3.6100366666721 -1 22.4495111578424 783 290 73 36 444 870 754 198 1383 271 929 119 M17906 KEGG_VIBRIO_CHOLERAE_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIBRIO_CHOLERAE_INFECTION.html Vibrio cholerae infection 55/73 KEGG 2.16431796835969e-07 7.73907637171042e-07 450 869.272727272727 446 1.9675619829829e-08 143 1.80132308972011 -1.60456108064636 -1 4.37713738459046 446 394 2124 455 1039 149 246 825 209 3532 143 120 M19130 BROWNE_HCMV_INFECTION_16HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_16HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 16 h time point that were not down-regulated at the previous time point, 14 h. 11711622 142/194 John Newman 8.16710946900099e-10 1.3246995427383e-08 265 729.818181818182 447 7.42464497457535e-11 169 2.60222775701335 2.79684455581862 1 8.19429467279121 263 1516 225 756 1315 217 737 447 2068 315 169 121 M14767 AMUNDSON_GAMMA_RADIATION_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_GAMMA_RADIATION_RESPONSE.html Genes down-regulated across the entire panel of NCI-60 cell lines in response to gamma radiation. 18199535 53/62 Jessica Robertson 2.45344388063287e-06 3.58632862080742e-06 65 677.181818181818 447 2.23040601520189e-07 29 2.25664437911435 2.54819932388844 1 4.89181296989332 62 356 841 985 3150 29 65 295 447 708 511 122 M2030 NAKAMURA_ADIPOGENESIS_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_LATE_DN.html Genes down-regulated in mesenchymal stem cells during late phase of adipogenesis, defined as days 7 to 14 of culturing with adipogenic hormones. 12646203 53/61 Arthur Liberzon 2.09242241273389e-08 2.54542107940824e-07 285 809.909090909091 447 1.90220221148631e-09 80 3.27478465708788 3.81052727843962 1 8.63452991719106 284 401 304 755 3151 447 1488 282 906 811 80 123 M14590 AIGNER_ZEB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/AIGNER_ZEB1_TARGETS.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of ZEB1 [GeneID=6935] by RNAi. 17486063 43/55 Leona Saunders 2.75553027374537e-10 4.87119958504799e-09 210 711 448 2.50502752190045e-11 26 3.64473505372253 -3.54626176078512 -1 12.1339988576322 914 448 207 242 1929 1544 1668 26 98 536 209 124 M1369 SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_DN.html Predicted targets of SOX9 [GeneID=6662] that are down-regulated during early prostate development. 18794802 64/77 Jessica Robertson 2.10200088486902e-07 7.70763712250053e-07 385 695.909090909091 448 1.91091007791433e-08 306 2.26143233042854 2.07028059670223 1 5.50957171791706 383 324 1352 407 1001 567 484 329 448 2054 306 125 M10739 CROONQUIST_NRAS_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_SIGNALING_DN.html Genes down-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing a constantly active form of NRAS [GeneID=4893] off a plasmid vector compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 90/102 Arthur Liberzon 3.37160177604413e-10 5.78689468470119e-09 90 605 451 3.06509252414622e-11 29 2.01679292047221 2.17003123917441 1 6.63125185049167 29 67 451 938 3057 86 86 482 469 160 830 126 M9326 VALK_AML_CLUSTER_9 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_9.html Top 40 genes from cluster 9 of acute myeloid leukemia (AML) expression profile; 87% of the samples are FAB M4 or M5 subtype, all have inv(16) inversion producing the CBFB-MYH11 fusion [GeneID=865;4629]; indicate good survival. 15084694 37/49 Jessica Robertson 3.70896236843742e-07 9.54542114450634e-07 520 515.636363636364 451 3.37178453975324e-08 39 2.84284254887805 3.0891452298476 1 6.83275624030621 518 551 613 311 1624 222 451 39 343 869 131 127 M2194 OHGUCHI_LIVER_HNF4A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OHGUCHI_LIVER_HNF4A_TARGETS_DN.html Genes down-regulated in liver samples of liver-specific knockout of HNF4A [GeneID=3172]. 18426912 90/243 Arthur Liberzon 2.02869337684371e-10 3.68970417681311e-09 1980 756.454545454545 451 1.84426670639163e-11 26 2.69980527586707 -3.25672045815075 -1 9.10617043851778 1977 95 202 26 233 1696 2074 451 550 230 787 128 M678 REACTOME_CHONDROITIN_SULFATE_DERMATAN_SULFATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHONDROITIN_SULFATE_DERMATAN_SULFATE_METABOLISM.html Genes involved in Chondroitin sulfate/dermatan sulfate metabolism 43/50 Reactome 2.74369291250305e-07 8.38703759494626e-07 95 508.818181818182 452 2.49426659516195e-08 92 2.32332397292768 2.60897747919892 1 5.62745009562567 92 452 715 720 1295 133 288 185 706 735 276 129 M3268 CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP.html Top 200 marker genes up-regulated in the 'proliferation' subclass of hepatocellular carcinoma (HCC); characterized by increased proliferation, high levels of serum AFP [GeneID=174], and chromosomal instability. 18701503 212/260 Yujin Hoshida 1.81303096188819e-13 4.86322662005742e-12 60 521.909090909091 462 1.64820996535304e-14 19 2.04033405694713 2.1913613007264 1 9.23284030102627 60 1339 245 520 1555 19 177 462 673 98 593 130 M602 REACTOME_REGULATION_OF_COMPLEMENT_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_COMPLEMENT_CASCADE.html Genes involved in Regulation of Complement cascade 12/20 Reactome 6.9208753564677e-08 6.06161982149702e-07 375 1018.54545454545 466 6.29170506744385e-09 121 3.12271686403242 -3.15429096651143 -1 7.75801778310408 375 2420 1115 2276 129 466 352 131 1857 1962 121 131 M366 LANDIS_ERBB2_BREAST_TUMORS_324_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_324_UP.html Up-regulated genes from the 324 genes identified by two analytical methods as changed in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 205/218 Leona Saunders 4.57226141718361e-08 4.74962050738399e-07 250 548.545454545455 467 4.15660137473541e-09 44 1.8825721007771 -2.0185499792118 -1 4.73735363226475 247 1374 1150 83 44 467 447 281 679 661 601 132 M1945 ISHIDA_E2F_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ISHIDA_E2F_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblast) after expression of E2F1 or E2F2 [GeneID=1869;1870]. 11416145 57/63 Arthur Liberzon 2.64801420101749e-09 3.91806489931114e-08 15 775.727272727273 470 2.40728564018614e-10 15 2.11338516143385 2.13652965192692 1 6.24527764111513 15 289 738 1351 3834 117 34 523 266 470 896 133 M692 REACTOME_HEPARAN_SULFATE_HEPARIN_HS_GAG_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HEPARAN_SULFATE_HEPARIN_HS_GAG_METABOLISM.html Genes involved in Heparan sulfate/heparin (HS-GAG) metabolism 43/53 Reactome 7.31530809618111e-08 6.11119543610174e-07 350 672.363636363636 471 6.65028030856851e-09 62 2.25488067084947 2.69232359070842 1 5.58486847691657 347 471 942 1581 155 280 1110 273 863 1312 62 134 M8519 DAVICIONI_MOLECULAR_ARMS_VS_ERMS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_MOLECULAR_ARMS_VS_ERMS_DN.html Genes down-regulated in mARMS (molecular ARMS) compared to the mERMS (molecular ERMS) class of rhabdomyosarcoma tumors. 16849537 255/354 Arthur Liberzon 1.20927920244372e-11 2.57108010609655e-10 475 804.636363636364 471 1.09934472950033e-12 124 2.32691239229822 2.62468556802631 1 8.92412799504806 471 1316 169 726 786 154 2131 247 2493 234 124 135 M1490 GREENBAUM_E2A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GREENBAUM_E2A_TARGETS_UP.html Genes up-regulated in pre-B lymphocytes upon Cre-Lox knockout of E2A [GeneID=6929]. 15310760 45/58 Kevin Vogelsang 5.30635316116978e-07 1.1483717065897e-06 170 651.181818181818 472 4.8239585827739e-08 97 2.45244245639402 2.4854719945195 1 5.80837460758772 167 472 859 1011 2008 138 97 484 463 1007 457 136 M9940 HONRADO_BREAST_CANCER_BRCA1_VS_BRCA2 http://www.broadinstitute.org/gsea/msigdb/cards/HONRADO_BREAST_CANCER_BRCA1_VS_BRCA2.html Genes distinguishing between breast cancer tumors bearing mutations in BRCA1 [GeneID=672] and those with mutated BRCA2 [GeneID=675]. 16998498 32/36 Arthur Liberzon 1.79948226458551e-07 7.47800341964416e-07 1165 726.181818181818 473 1.63589310161231e-08 130 3.28081015980134 3.84368861850498 1 8.03298821652184 1163 571 368 130 1465 341 198 1725 456 473 1098 137 M7081 FARMER_BREAST_CANCER_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_8.html Cluster 8: selected ERBB2 [GeneID=2064] amplicon genes clustered together across breast cancer samples. 15897907 11/12 Leona Saunders 1.28262373380944e-07 7.20206492018647e-07 455 689.181818181818 475 1.16602164417072e-08 37 2.30738755804946 -2.75524744145135 -1 5.64989127358255 451 968 1708 620 475 576 211 52 37 2244 239 138 M19439 DOANE_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_ESR1_UP.html Genes up-regulated in breast cancer samples positive for ESR1 [GeneID=2099] compared to the ESR1 negative tumors. 16491124 125/174 Arthur Liberzon 4.72574923768495e-14 1.41174281024513e-12 2105 1004.18181818182 477 4.29613567062276e-15 22 2.69676150021093 -2.83220672306415 -1 12.8019564537285 2102 1511 115 22 477 2300 3166 349 330 179 495 139 M7169 REACTOME_NCAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NCAM1_INTERACTIONS.html Genes involved in NCAM1 interactions 43/60 Reactome 7.84001208923801e-12 1.69747050739465e-10 255 924.454545454545 479 7.12728371751451e-13 38 3.39362267385851 3.4936552298124 1 13.284181147978 38 479 166 566 3931 310 964 1524 1687 252 252 140 M14693 VANTVEER_BREAST_CANCER_POOR_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_POOR_PROGNOSIS.html The optimal set of 70 prognostic markers predicting poor breast cancer clinical outcome (defined as developing metastases with 5 years). 11823860 82/129 Arthur Liberzon 3.56997276259978e-07 9.41752134134615e-07 155 592.545454545455 479 3.24543031082247e-08 120 2.18191115733683 2.27841318228886 1 5.23771890283681 153 209 723 435 1578 120 479 807 1070 746 198 141 M19768 LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT http://www.broadinstitute.org/gsea/msigdb/cards/LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT.html Genes downregulated in MCF10A cells (breast cancer) co-cultured with cancer-associated fibroblasts (CAF). 19074894 132/209 Jessica Robertson 9.6090186095019e-17 4.01367856963265e-15 1360 791.818181818182 481 8.73547146318352e-18 37 2.748678872387 -2.7782570304527 -1 15.863997326345 1358 1497 77 37 74 1543 1956 429 1106 152 481 142 M11951 HINATA_NFKB_TARGETS_KERATINOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HINATA_NFKB_TARGETS_KERATINOCYTE_UP.html Genes up-regulated in primary keratinocytes by expression of p50 (NFKB1) and p65 (RELA) [GeneID=4790;5970] components of NFKB. 12673201 122/152 Arthur Liberzon 3.84822112807722e-11 7.56816821855186e-10 485 610.454545454545 481 3.49838284376775e-12 13 2.64984074099314 -2.45188773137598 -1 9.66989696373842 481 13 185 784 473 309 499 899 2185 169 718 143 M14985 BASAKI_YBX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BASAKI_YBX1_TARGETS_UP.html Genes up-regulated in SKOC-3 cells (ovarian cancer) after YB-1 (YBX1) [GeneID=4904] knockdown by RNAi. 17072343 348/437 Arthur Liberzon 8.22375502160733e-09 1.11540585350536e-07 25 620.272727272727 486 7.4761409566803e-10 24 1.99210687502599 2.09651927911053 1 5.52000490871351 24 1230 486 952 2122 40 115 224 895 213 522 144 M2293 PASINI_SUZ12_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PASINI_SUZ12_TARGETS_DN.html Genes down-regulated in ES (embryonic stem cells) with defficient SUZ12 [GeneID=23512]. 17339329 456/529 Arthur Liberzon 4.41421162827578e-17 1.89409808049652e-15 495 638.727272727273 493 4.01291966206888e-18 75 2.30029021279203 2.49909499868308 1 13.5696686107378 493 1177 75 282 275 430 1611 928 1114 76 565 145 M2299 VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP.html Genes up-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout compared to normal 9.5 dpc embryos. 17371845 96/143 Arthur Liberzon 1.30994163028146e-07 7.20206492018647e-07 475 696.272727272727 496 1.19085609843551e-08 49 2.43835732071603 -2.43700334359972 -1 5.97342525168874 763 93 552 49 496 473 475 2813 376 608 961 146 M962 REACTOME_IRON_UPTAKE_AND_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IRON_UPTAKE_AND_TRANSPORT.html Genes involved in Iron uptake and transport 37/51 Reactome 2.0065604178772e-07 7.65527859584926e-07 100 972.272727272727 497 1.82414600080924e-08 38 1.72036725090881 -1.72844499598697 -1 4.18144062972368 96 2269 2580 1012 939 38 41 62 497 2996 165 147 M4680 DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_UP.html Genes up-regulated in RD cells (embryonal rhabdomyosarcoma, ERMS) by expression of PAX3- or PAX7-FOXO1 [GeneID=5077;5081;2308] fusions off retroviral vectors. 16849537 366/462 Arthur Liberzon 3.35839004101845e-11 6.66033655193575e-10 925 827.909090909091 497 3.05308185551792e-12 183 2.2780837554454 2.60343583971589 1 8.3570895044408 925 1227 183 358 1387 262 2210 446 1412 200 497 148 M11840 SHEPARD_BMYB_MORPHOLINO_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_BMYB_MORPHOLINO_DN.html Human orthologs of genes down-regulated in zebra fish after knockdown of BMYB [GeneID=4605] by morpholino. 16150706 250/360 Jennifer Shepard 3.03877514332747e-13 7.9683437091698e-12 280 689.727272727273 497 2.76252285757081e-14 49 2.38982598557586 2.43460982774121 1 10.6168176069366 280 1322 133 538 1620 49 471 497 1877 151 649 149 M9325 MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_DN.html Down-regulated 'cooperation response genes': responded synergystically to the combination of mutant TP53 and HRAS [GeneID=7157;3265] in YAMC cells (colon). 18500333 99/122 Jessica Robertson 7.58195543371684e-13 1.85424811223886e-11 2135 1213.81818181818 498 6.89268675792678e-14 31 2.790897818009 3.0525492745814 1 11.9952861525678 2131 43 139 31 498 1956 4473 1322 238 144 2377 150 M10952 KAAB_HEART_ATRIUM_VS_VENTRICLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_HEART_ATRIUM_VS_VENTRICLE_UP.html Genes up-regulated in the atria of healthy hearts, compared to venticles. 15103417 389/507 John Newman 9.92277205137143e-14 2.8558222001508e-12 595 660.818181818182 500 9.02070186488353e-15 121 2.39218720231224 2.71939842680886 1 11.0560799356137 593 1215 121 369 515 500 1669 330 1287 257 413 151 M5198 GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN.html Genes down-regulated in quiescent vs dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors. 17717066 105/155 Arthur Liberzon 4.33811969759821e-10 7.36544063764877e-09 50 915.363636363636 502 3.94374518041239e-11 13 1.97017953037489 2.01367687923408 1 6.39383054890464 13 47 609 1776 3572 81 48 502 2118 297 1006 152 M15025 LIAO_HAVE_SOX4_BINDING_SITES http://www.broadinstitute.org/gsea/msigdb/cards/LIAO_HAVE_SOX4_BINDING_SITES.html Genes up-regulated in the samples with intrahepatic metastatic hepatocellular carcinoma (HCC) vs primary HCC that also have putative binding sites for SOX4 [GeneID=6659]. 18504433 63/66 Jessica Robertson 1.29422557721406e-07 7.20206492018647e-07 835 623.636363636364 502 1.17656877577394e-08 333 2.84349255711013 2.9678339724191 1 6.97422888783243 832 333 739 393 484 502 1077 411 619 1017 453 153 M19675 FARMER_BREAST_CANCER_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_3.html Cluster 3: selected apocrine, basal and hypoxia genes clustered together across breast cancer samples. 15897907 22/23 Arthur Liberzon 1.56338119201836e-07 7.30242482708713e-07 505 765.909090909091 503 1.42125573010599e-08 69 2.57938440495785 -2.98099905790413 -1 6.31556936747602 503 823 1429 991 674 345 366 69 168 2826 231 154 M17967 REACTOME_TIGHT_JUNCTION_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TIGHT_JUNCTION_INTERACTIONS.html Genes involved in Tight junction interactions 23/35 Reactome 2.77069745239523e-07 8.41009130244725e-07 390 513.272727272727 504 2.51881618303557e-08 12 3.51664461358581 -3.76021487265629 -1 8.54187174802327 387 771 692 43 1384 504 562 12 77 1092 122 155 M9066 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_DN.html Genes down-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 46/67 John Newman 6.22171565540896e-07 1.26798350144777e-06 370 726.454545454545 506 5.65610674085778e-08 24 2.38437485938824 2.73131504902698 1 5.60451153591717 367 506 1029 1194 2161 164 329 153 842 1222 24 156 M10773 LI_WILMS_TUMOR http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR.html 'Wilm's tumor signature': genes highly expressed in Wilm's tumor samples compared to normal fetal kidney and a heterologous tumor, Burkit lymphoma. 12057921 40/109 Arthur Liberzon 2.10326712469663e-09 3.16159898998984e-08 230 989 509 1.91206102427947e-10 227 2.9589470910621 3.13714396622731 1 8.87488658714533 227 509 244 406 2992 514 1462 2151 1751 268 355 157 M902 REACTOME_CGMP_EFFECTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CGMP_EFFECTS.html Genes involved in cGMP effects 9/21 Reactome 1.25520318864936e-06 2.07806350418274e-06 510 1093.72727272727 510 1.25520389764069e-07 138 3.8561330390552 3.6046765633693 1 8.76207404230886 510 973 4250 1124 2792 432 367 413 138 636 396 158 M16515 CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP.html Genes in the AKT1 [GeneID=207] pathway which are independent of MTOR [GeneID=2475], insensitive to RAD001 (everolimus) [PubChem=6442177]. 17213801 52/58 Arthur Liberzon 1.3316594091286e-07 7.20206492018647e-07 1335 1094.81818181818 511 1.21059953612174e-08 18 2.02784829779007 -2.31604544810983 -1 4.95934677638564 1335 415 1479 111 511 2354 3479 156 57 2128 18 159 M2530 SHIRAISHI_PLZF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHIRAISHI_PLZF_TARGETS_DN.html Genes down-regulated in A375 and 397 cells (melanoma) by forced expression of PLZF [GeneID=7704] off adenovirus vector. 16862184 8/12 Arthur Liberzon 9.36653063838319e-08 6.56909726792996e-07 670 978 512 9.36653103317675e-09 55 2.50347735902319 2.73644651063198 1 6.17451408252719 668 1005 4349 118 321 705 512 476 55 2067 482 160 M3155 GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_UP.html Genes up-regulated in quiescent CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors compared to the dividing cells from CML (chronic myeloid leukemia) patients. 17717066 228/341 Arthur Liberzon 2.17075525129155e-08 2.61376652706534e-07 195 783.272727272727 515 1.97341388428231e-09 40 1.96603609665129 2.05366211126251 1 5.15469510866651 40 1337 532 117 2732 195 192 515 1764 232 960 161 M7184 GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_UP.html Genes up-regulated in glioblastoma cell lines displaying spherical growth (cluster-1) compared to those displaying semiadherent or adherent growth phenotype (cluster-2). 18037961 23/35 Jessica Robertson 1.68548200898472e-07 7.33971845416521e-07 515 570.454545454545 515 1.53225648919478e-08 97 2.74801645418349 3.31695120654189 1 6.72928780228557 515 752 846 1169 763 367 440 97 325 885 116 162 M17761 ST_WNT_BETA_CATENIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_WNT_BETA_CATENIN_PATHWAY.html Wnt/beta-catenin Pathway 42/54 Signaling Transduction KE 1.14018007113854e-07 7.05613393308323e-07 385 615.545454545455 516 1.03652739111812e-08 179 2.2406936457718 2.7666435505289 1 5.49314878220568 699 516 1090 788 381 381 659 179 229 1634 215 163 M4288 SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_UP.html Genes up-regulated in MCF10A cells (breast cancer) grown at low (mesenchymal phenotype) compared to those grown at high (epithelial, basal-like phenotype) confluency. 18281472 224/277 Jessica Robertson 2.12404103675641e-11 4.35914384944765e-10 60 829.818181818182 516 1.93094639706992e-12 56 2.00698933236452 2.0570343482055 1 7.50522170457329 56 1338 454 937 3005 112 151 516 1600 135 824 164 M16010 KOBAYASHI_EGFR_SIGNALING_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_24HR_DN.html Genes down-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 24h. 17145885 303/370 Arthur Liberzon 3.16810715766858e-15 1.06052948824083e-13 15 823.272727272727 516 2.88009741606234e-16 12 1.83843301663134 1.90628548514544 1 9.54260697549269 12 1251 516 1347 3000 93 99 448 1344 81 865 165 M16643 VERRECCHIA_DELAYED_RESPONSE_TO_TGFB1 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_DELAYED_RESPONSE_TO_TGFB1.html ECM related genes up-regulated later than 30 min following addition of TGFB1 [GeneID=7040] in dermal fibroblasts. 11279127 84/98 John Newman 3.1532622402095e-07 8.93979952731796e-07 215 748 519 2.86660244742453e-08 148 2.20822511724547 2.45086288482969 1 5.32156758941032 213 180 580 482 1435 148 689 1355 2457 519 170 166 M1720 LEIN_MIDBRAIN_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_MIDBRAIN_MARKERS.html Top 100 ranked genes most specific to midbrain region of adult mouse brain. 17151600 102/141 Jessica Robertson 7.01195852232495e-08 6.06161982149702e-07 1595 928.727272727273 519 6.37450795073991e-09 64 2.5330731653276 2.97204730517959 1 6.28367009047777 1592 64 348 332 136 1159 2622 2008 1060 376 519 167 M1157 KONG_E2F3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KONG_E2F3_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblasts) at 16 hr after serum stimulation and knockdown of E2F3 [GeneID=1871] by RNAi. 16909124 118/175 Arthur Liberzon 6.07054203236105e-09 8.42734070374828e-08 30 749.636363636364 520 5.51867459010156e-10 12 2.06267242732644 2.18703232398424 1 5.8182988055346 26 1548 520 946 3025 12 58 290 988 208 625 168 M13766 NIKOLSKY_BREAST_CANCER_5P15_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_5P15_AMPLICON.html Genes within amplicon 5p15 identified in a copy number alterations study of 191 breast tumor samples. 19010930 27/36 Jessica Robertson 9.10070371220992e-08 6.55522041874465e-07 830 899.909090909091 520 8.27336735334298e-09 91 2.54527435229584 2.73668606387445 1 6.27937662093616 826 1831 1601 1200 252 513 305 520 91 2437 323 169 M11771 DOANE_BREAST_CANCER_CLASSES_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_CLASSES_DN.html Genes down-regulated in ER(-) / PR(-) breast tumors (do not express ESR1 and PGR [GeneID=2099;5241]) with molecular similarity to ER(+) (class A) relative to the rest of the ER(-) / PR(-) samples (class B). 16491124 51/53 Arthur Liberzon 6.15473476502239e-07 1.25922618512812e-06 525 838.636363636364 522 5.5952149880689e-08 110 2.33778215042141 2.27953795866869 1 5.49684661956797 522 443 1177 2064 2149 199 684 110 184 1402 291 170 M14 PID_AURORA_B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AURORA_B_PATHWAY.html Aurora B signaling 18832364 47/52 Pathway Interaction Database 7.26482728512001e-07 1.40302720072694e-06 70 868.454545454545 523 6.60439062191653e-08 53 2.1377078353749 2.26736393567449 1 4.98175416801872 70 1708 1655 1005 2298 136 53 245 523 1450 410 171 M990 CORRE_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CORRE_MULTIPLE_MYELOMA_DN.html Genes down-regulated in multiple myeloma (MM) bone marrow mesenchymal stem cells. 17344918 83/104 Leona Saunders 2.5796591434187e-08 3.04824847556035e-07 240 909.181818181818 525 2.34514470333371e-09 119 2.49350075978004 2.55868014188292 1 6.48409443841307 236 187 308 119 2583 525 1497 965 2471 239 871 172 M9898 BENPORATH_SUZ12_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_SUZ12_TARGETS.html Set 'Suz12 targets': genes identified by ChIP on chip as targets of the Polycomb protein SUZ12 [GeneID=23512] in human embryonic stem cells. 18443585 834/1473 Jessica Robertson 1.28295914227214e-63 8.65081021646355e-61 525 983.272727272727 525 1.28295914227214e-64 4 2.79352679710568 3.00312319626085 1 67.4276371147114 525 1088 4451 218 427 34 1582 838 1276 4 373 173 M14098 BROWNE_HCMV_INFECTION_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_24HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 24 h time point that were not down-regulated at the previous time point, 20 h. 11711622 223/276 John Newman 6.26886620914748e-11 1.20280684988521e-09 390 840.727272727273 530 5.69896928120554e-12 191 2.52239322975676 2.9129018042418 1 8.99829973732209 389 1370 191 372 1989 530 1296 547 1919 243 402 174 M1714 LEIN_OLIGODENDROCYTE_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_OLIGODENDROCYTE_MARKERS.html Genes enriched in oligodendrocytes in the adult mouse brain identified through correlation-based searches seeded with the oligodendrocyte cell-type specific gene expression patterns. 17151600 82/114 Jessica Robertson 4.40575799631167e-08 4.68359859067366e-07 4410 1935.90909090909 531 4.00523462231104e-09 36 2.41484520176899 -2.19461626283676 -1 6.09683084943744 4408 141 396 531 36 3496 2756 4707 359 325 4140 175 M1486 KAMMINGA_EZH2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KAMMINGA_EZH2_TARGETS.html Putative targets or partners of EZH2 [GeneID=2146] in hematopoietic stem cells. 16293602 49/56 Kevin Vogelsang 1.16799480656254e-07 7.06112554001409e-07 35 962.363636363636 533 1.0618135168838e-08 25 1.67191677186618 1.69541433139248 1 4.08586194179789 34 430 2169 1843 2949 80 25 305 1389 829 533 176 M4241 BENPORATH_ES_2 http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_2.html Set 'Set 'ES exp2': genes overexpressed in human embryonic stem cells according to a meta-analysis of 8 profiling studies. 18443585 39/66 Jessica Robertson 3.18916726816279e-07 8.98142571940833e-07 535 782.454545454545 534 2.89924339133765e-08 217 2.07471578462743 2.26141667925516 1 4.99511691752184 423 534 1510 1443 1449 338 351 217 433 1374 535 177 M5372 REACTOME_XENOBIOTICS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_XENOBIOTICS.html Genes involved in Xenobiotics 4/46 Reactome 4.09457051538499e-07 1.00046055710989e-06 540 988 537 4.09457126983303e-08 13 4.40714387270331 -4.40714387270331 -1 10.5839139135405 536 1054 4224 537 1851 363 13 146 183 1387 574 178 M2470 MALIK_REPRESSED_BY_ESTROGEN http://www.broadinstitute.org/gsea/msigdb/cards/MALIK_REPRESSED_BY_ESTROGEN.html Genes consistently and robustly repressed by estradiol [PubChem=5757] in MCF7 cells (breast cancer); this reperession was prevented by fulvestrant [PubChem=3478439]. 19917725 13/15 Arthur Liberzon 3.44918104337121e-07 9.25433439442563e-07 540 610.272727272727 540 3.13561962194294e-08 31 4.35333407546909 -3.84531464728368 -1 10.5133478789685 540 926 560 90 1538 376 227 1113 31 1053 259 179 M5549 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_UP.html Genes up-regulated in lobular carcinoma vs normal lobular breast cells. 17389037 126/168 Arthur Liberzon 3.24782677289671e-18 1.56425942531352e-16 1820 1064.81818181818 543 2.95256979354246e-19 68 3.28803035473774 3.85743229593248 1 20.8501399038979 1819 1520 68 248 194 2188 3498 543 202 380 1053 180 M15549 CERVERA_SDHB_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/CERVERA_SDHB_TARGETS_1_UP.html Genes turned on in Hep3B cells (hepatocellular carcinoma, HCC) upon knockdown of SDHB [GeneID=6390] by RNAi. 18519664 133/199 Jessica Robertson 5.22297317336217e-11 1.0145034312045e-09 335 853.363636363636 543 4.74815743044198e-12 188 2.65435320227857 2.72582421186637 1 9.55059889938343 334 1537 188 338 941 359 1341 1042 2453 311 543 181 M13944 GOZGIT_ESR1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOZGIT_ESR1_TARGETS_UP.html Genes up-regulated in TMX2-28 cells (breast cancer) which do not express ESR1 [GeneID=2099]) compared to the parental MCF7 cells which do. 17726467 191/244 Arthur Liberzon 6.96269749892373e-13 1.72062472224712e-11 1630 808.909090909091 546 6.32972499902356e-14 138 2.51591854029336 3.01516602191097 1 10.8413596376306 1626 1390 138 253 325 546 2442 808 857 157 356 182 M2687 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_15 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_15.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 15. 12554760 63/75 Arthur Liberzon 2.62291387232728e-08 3.08732006917325e-07 145 992.090909090909 546 2.38446718508958e-09 141 2.76564068400533 3.10710880953984 1 7.1910755072894 141 329 309 616 3360 388 657 1668 2478 421 546 183 M1842 LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP.html Up-regulated genes in NMuMG cells (mammary epithelium) after stimulation with both TGFB1 and WNT3A [GeneID=7040;89780]. 17210685 152/219 Jessica Robertson 2.97901233133118e-14 8.95601159483006e-13 1215 729.181818181818 548 2.70819302848293e-15 113 2.74249414346823 2.94925037018956 1 13.2378884676582 1214 1455 113 276 316 435 2016 569 881 198 548 184 M1236 OXFORD_RALA_OR_RALB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_OR_RALB_TARGETS_DN.html Genes down-regulated after knockdown of RALA or RALB [GeneiD=5898;5899], which were also differentially expressed in bladder cancer compared to normal bladder urothelium tissue. 17496927 38/43 Arthur Liberzon 6.95929292459136e-08 6.06161982149702e-07 540 761.090909090909 550 6.32663013157793e-09 97 2.97926671805831 3.39899164013889 1 7.39933440840103 538 550 711 330 131 1356 2251 452 97 1116 840 185 M489 REACTOME_INHIBITION_OF_THE_PROTEOLYTIC_ACTIVITY_OF_APC_C_REQUIRED_FOR_THE_ONSET_OF_ANAPHASE_BY_MITOTIC_SPINDLE_CHECKPOINT_COMPONENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_THE_PROTEOLYTIC_ACTIVITY_OF_APC_C_REQUIRED_FOR_THE_ONSET_OF_ANAPHASE_BY_MITOTIC_SPINDLE_CHECKPOINT_COMPONENTS.html Genes involved in Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components 20/22 Reactome 2.5043389578884e-06 3.64451671271203e-06 230 1327.90909090909 552 2.27667437151987e-07 16 1.32372779210548 1.38809227883679 1 2.84508768770227 229 835 3124 2424 3163 107 16 345 552 3332 480 186 M12004 SENESE_HDAC1_AND_HDAC2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_AND_HDAC2_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of both HDAC1 and HDAC2 [GeneID=3065;3066] by RNAi. 17470557 306/422 Leona Saunders 4.85261974534187e-22 3.09518448621805e-20 555 571.818181818182 552 4.41147249576531e-23 48 2.79096218998122 2.79975788082819 1 21.8475666347592 552 1262 48 258 899 193 1198 373 723 132 652 187 M1215 LI_WILMS_TUMOR_ANAPLASTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_ANAPLASTIC_UP.html Selected up-regulated genes distinguishing between Wilms tumors of different histological types: anaplastic vs favorable histology. 15531917 21/24 Leona Saunders 2.5385150726782e-06 3.68217306178276e-06 105 928.363636363636 552 2.30774363800051e-07 102 2.00738778014952 2.09415742024092 1 4.33671638275651 102 784 1551 1812 3173 115 122 221 164 1616 552 188 M18983 GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_UP.html Genes up-regulated in quiescent (G0) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the quiescent cells from normal donors. 17717066 124/198 Arthur Liberzon 4.15919974545485e-07 1.0045025695513e-06 650 749.363636363636 553 3.78109139251875e-08 5 2.23088403554967 2.27704246824447 1 5.33126842021364 649 5 553 150 1760 313 537 226 2672 701 677 189 M2446 PLASARI_TGFB1_TARGETS_10HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_10HR_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 10 h. 19752192 326/413 Arthur Liberzon 4.89593021705325e-13 1.22919099066443e-11 555 835.090909090909 554 4.45084565186759e-14 111 2.24557791528055 2.4926410579871 1 9.80296740947648 554 1250 170 931 1193 183 1334 371 2754 111 335 190 M16201 WONG_ENDMETRIUM_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ENDMETRIUM_CANCER_UP.html Genes up-regulated in cancer endometrium samples compared to the normal endometrium. 17043662 32/52 Arthur Liberzon 2.93273358726911e-10 5.12685278959636e-09 660 574.090909090909 556 2.66612144332733e-11 21 3.91942826604577 -3.59014718936937 -1 13.0172585233439 659 584 210 526 21 574 794 1491 537 556 363 191 M14340 FUJII_YBX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FUJII_YBX1_TARGETS_DN.html Genes down-regulated in MCF-7 cells (breast cancer) after knockdown of YBX1 [GeneID=4904] by RNAi. 18316615 266/317 Jessica Robertson 1.3138180443699e-06 2.15544705228569e-06 60 862 557 1.19438075360871e-07 42 1.87693483471053 1.96521742809881 1 4.22718568103387 57 1303 993 1373 2765 42 181 537 1279 395 557 192 M2009 MIKKELSEN_NPC_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in neural progenitor cells (NPC). 17603471 247/551 Arthur Liberzon 7.25586558452426e-55 4.28096069486932e-52 1485 853.727272727273 557 6.59624144047661e-56 4 3.37589892891022 3.70953743015608 1 69.690714740679 1482 1293 4 221 263 424 2350 1114 557 27 1656 193 M11187 REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH.html Genes involved in NCAM signaling for neurite out-growth 78/96 Reactome 9.69678046526092e-07 1.71547240614811e-06 220 948.272727272727 558 8.81525885385742e-08 218 2.862791876373 3.16717623245795 1 6.58794626443069 218 239 415 451 2546 558 1836 1648 1322 845 353 194 M1395 MORI_PRE_BI_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PRE_BI_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Pre-BI stage. 18922927 112/185 Jessica Robertson 1.03172064102811e-06 1.79165615366177e-06 180 864 559 9.37928295334722e-08 39 1.86380430439598 1.82672135848684 1 4.25743932481218 180 39 1019 151 2592 336 314 1049 1508 559 1757 195 M2296 BERGER_MBD2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BERGER_MBD2_TARGETS.html Genes strongly up-regulated in colon tissue upon MBD2 [GeneID=8932] knockout. 17353267 4/23 Arthur Liberzon 1.88808685573754e-06 2.88033935329062e-06 595 1120.27272727273 559 1.88808845993184e-07 8 3.50639043183186 -3.50639043183186 -1 7.7628994663708 595 1056 4680 559 3062 407 8 51 186 1390 329 196 M3102 SMID_BREAST_CANCER_ERBB2_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_ERBB2_UP.html Genes up-regulated in the erbb2 subype of breast cancer samples, characterized by higher expression of ERBB2 [GeneID=2064]. 18451135 187/290 Jessica Robertson 5.34340711290298e-09 7.48394111955551e-08 560 565.181818181818 560 4.85764284171015e-10 60 2.47275510687892 -2.59033356489574 -1 7.03626446450842 560 1402 265 60 283 632 995 414 644 326 636 197 M1377 HE_PTEN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HE_PTEN_TARGETS_UP.html Genes up-regulated in the intestine after the tissue specific knockout of PTEN [GeneID=5728] by Cre-lox. 17237784 23/26 Jessica Robertson 4.26131125031553e-07 1.01522971616225e-06 750 657.181818181818 565 3.87392006883141e-08 80 2.8324506561848 2.92749386443783 1 6.77710356770559 749 730 891 131 1788 527 390 565 80 886 492 198 M1187 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN.html Genes down-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 57/85 Arthur Liberzon 3.64669464882364e-07 9.47297674322927e-07 515 744.272727272727 566 3.31517750299607e-08 210 2.06819218759578 2.21430546444546 1 4.96000564596981 513 341 983 618 1606 210 306 356 1516 1172 566 199 M11816 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY.html Fc epsilon RI signaling pathway 65/94 KEGG 1.09127356304719e-07 7.0366273464245e-07 820 876.636363636364 567 9.92066924707285e-09 174 1.80891383498583 -1.81562418028822 -1 4.42585605510576 816 298 1893 174 346 733 464 567 1976 1933 443 200 M13788 MCBRYAN_PUBERTAL_BREAST_5_6WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_5_6WK_UP.html Genes up-regulated during pubertal mammary gland development between week 5 and 6. 17486082 150/174 Arthur Liberzon 3.84367171331375e-08 4.24874250277305e-07 650 593.090909090909 569 3.49424707315222e-09 46 2.77736188561256 -3.09265645383956 -1 7.06686741394725 650 1506 319 46 569 516 1052 164 709 909 84 201 M11410 LUCAS_HNF4A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LUCAS_HNF4A_TARGETS_UP.html Genes up-regulated in Tet-On HEK293 cells (embryonic kidney) by expression of HNF4A [GeneID=3172]. 16007190 79/96 Leona Saunders 1.75529344980159e-07 7.39730810987813e-07 570 582.272727272727 570 1.59572144531778e-08 72 2.13461885807078 -2.20555122930907 -1 5.21312910726395 570 225 1156 562 810 680 798 72 315 1119 98 202 M6787 SCIBETTA_KDM5B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCIBETTA_KDM5B_TARGETS_DN.html Genes down-regulated in HB2 cells (mammary epithelium) upon expression of KDM5B [GeneID=10765] off an adenoviral vector. 17709396 100/109 Leona Saunders 2.52604101757877e-06 3.6685888009144e-06 510 969 571 2.29640356180445e-07 75 2.06608706338042 2.21660811647465 1 4.46632592012705 509 75 1017 571 3170 532 461 1225 536 809 1754 203 M13108 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN.html Genes down-regulated in Wilm's tumor samples compared to fetal kidney. 12057921 229/287 Kevin Vogelsang 1.89167312610124e-07 7.49827400961101e-07 35 699.727272727273 572 1.71970298977913e-08 35 2.02530228915964 2.15309803261855 1 4.93880017054765 35 1343 654 993 2019 48 156 572 948 423 506 204 M11288 SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER.html Genes bearing H3K27me3 mark or whose promoters are bound by the polycomb proteins SUZ12 or EED [GeneID=23512;8726]; their DNA is methylated de novo in cancer. 17200670 88/126 Leona Saunders 3.49977832851306e-09 5.03626637517733e-08 915 886.727272727273 573 3.18161666734594e-10 173 2.72097988665462 3.18473666886538 1 7.93585379669685 915 173 255 1153 1343 448 2167 302 2104 321 573 205 M2603 VALK_AML_CLUSTER_13 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_13.html Top 40 genes from cluster 13 of acute myeloid leukemia (AML) expression profile; 91% of the samples are FAB M2 subtype, all bear the t(8;21) translocation producing the AML1-ETO fusion [GeneID=861;862]; indicate good survival. 15084694 37/50 Jessica Robertson 1.09537618979789e-07 7.03739764799127e-07 810 650.909090909091 573 9.9579658576044e-09 209 2.59291638358796 2.69273071750675 1 6.36570634302038 810 573 872 576 348 209 364 298 371 2141 598 206 M1281 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5.html Cluster PAM5: genes changed exclusively in hepatocellular carcinoma (HCC) samples from 27 month old mice deficient for TXNIP [GeneID=10628]. 16607285 108/185 Leona Saunders 9.60671307233291e-08 6.64473403617636e-07 1210 718.545454545455 574 8.73337590166193e-09 53 2.43557495825637 2.5980974984889 1 6.00081416574722 1206 53 507 1126 285 550 1749 1016 642 574 196 207 M2062 NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_DN.html Top 20 negative significant genes associated with malignant fibrous histiocytoma tumors. 11965276 46/48 Arthur Liberzon 4.4632088834748e-06 5.9881597299605e-06 450 969.272727272727 576 4.05747085286556e-07 224 2.89464360704634 3.3390455217908 1 6.02979211814547 306 450 468 449 3618 729 2018 1044 780 576 224 208 M16817 KEGG_OOCYTE_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OOCYTE_MEIOSIS.html Oocyte meiosis 104/119 KEGG 1.41736750820477e-07 7.20206492018647e-07 465 985.909090909091 578 1.28851599956346e-08 94 1.6379421685351 1.84274867734091 1 3.99616353074593 462 94 2933 657 578 211 290 1053 898 3181 488 209 M3766 SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP.html Up-regulated genes whose expression correlated with histologic grade of invasive breast cancer tumors: comparison of grade 1 vs grade 3. 16478745 183/229 Arthur Liberzon 7.62127402064278e-13 1.85424811223886e-11 580 815.272727272727 578 6.92843092785948e-14 4 1.91628490867702 1.9472351607318 1 8.22051689786474 4 1386 576 1340 3004 141 101 578 656 189 993 210 M5539 KEGG_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AXON_GUIDANCE.html Axon guidance 133/153 KEGG 6.470287894182e-08 5.87303055010366e-07 580 671.363636363636 579 5.88208007679614e-09 112 2.17615326967452 2.49962969625922 1 5.40323891694724 579 1527 694 781 112 368 1322 261 935 456 350 211 M14383 SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_UP.html Genes up-regulated in brain relapse of breast cancer. 18451135 42/112 Jessica Robertson 2.03246416519366e-10 3.68970417681311e-09 815 627.363636363636 579 1.8476946958013e-11 42 3.70465213963976 3.92079708163782 1 12.5140408443468 814 442 203 42 1113 754 967 579 82 373 1532 212 M15107 JAATINEN_HEMATOPOIETIC_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAATINEN_HEMATOPOIETIC_STEM_CELL_UP.html Genes up-regulated in CD133+ [GeneID=8842] cells (hematopoietic stem cells, HSC) compared to the CD133- cells. 16210406 410/523 Arthur Liberzon 7.63294999041387e-08 6.22237028579507e-07 825 782.181818181818 580 6.93904568658258e-09 283 2.04727274916883 2.21857554123992 1 5.05961362345117 822 1202 344 325 580 491 1451 518 1984 283 604 213 M9402 SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_DN.html Cell cycle genes down-regulated in H1299 cells (lung cancer) after overexpression of either P53 or P73 [GeneID=7157;7161]. 17982488 26/31 Jessica Robertson 6.72162436516575e-08 6.00568928582638e-07 35 755.909090909091 581 6.11056779139133e-09 31 2.32790977462878 2.32790977462878 1 5.77444761841559 31 643 725 982 3734 105 33 581 181 364 936 214 M14780 KUNINGER_IGF1_VS_PDGFB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUNINGER_IGF1_VS_PDGFB_TARGETS_DN.html Genes down-regulated in C2AS12 cells (myoblast) by IGF1 [GeneID=3479] vs PDGFB [GeneID=5155]. 15475267 53/67 John Newman 1.60029534920061e-07 7.31918027928963e-07 585 747.272727272727 581 1.45481405964293e-08 312 2.32192991525397 2.48637383187221 1 5.67927359660788 517 399 756 581 698 312 584 791 2795 466 321 215 M1551 ULE_SPLICING_VIA_NOVA2 http://www.broadinstitute.org/gsea/msigdb/cards/ULE_SPLICING_VIA_NOVA2.html Genes whose splicing in neocortex was most affected by knock out of NOVA2 [GeneID=4858]. 16041372 78/102 John Newman 2.23756039754143e-07 7.84059768106575e-07 540 738.727272727273 583 2.03414602283425e-08 204 2.13014303215986 2.50654493636663 1 5.18044088262041 539 211 1153 583 1073 1032 1575 529 204 950 277 216 M9826 VANTVEER_BREAST_CANCER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_METASTASIS_DN.html Genes whose expression is significantly and negatively correlated with poor breast cancer clinical outcome (defined as developing distant metastases in less than 5 years). 11823860 162/263 Jean Junior 2.44651834112786e-07 8.09787277007258e-07 90 633.181818181818 588 2.22410783017627e-08 28 1.9515464265965 2.02912110489472 1 4.73089949630428 90 1451 898 588 1171 28 280 405 1138 602 314 217 M4001 DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_DN.html Genes down-regulated in RD cells (embryonal rhabdomyosarcoma, ERMS) by expression of PAX3- or PAX7-FOXO1 [GeneID=5077;5081;2308] fusions off retroviral vectors. 16849537 111/139 Arthur Liberzon 2.03469795693285e-08 2.48159544101371e-07 590 702.181818181818 589 1.84972543250092e-09 52 2.65159254254756 3.05050338296898 1 6.99361583670034 589 52 303 764 1516 425 1771 968 858 327 151 218 M5740 JAEGER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAEGER_METASTASIS_UP.html Genes up-regulated in metastases from malignant melanoma compared to the primary tumors. 17289871 57/79 Leona Saunders 7.04303497030534e-07 1.37538788000998e-06 475 920.454545454545 590 6.40276111368106e-08 127 2.49249997853836 2.20363118475207 1 5.82553451406747 474 351 590 127 2271 564 729 985 1681 534 1819 219 M1129 MCBRYAN_TERMINAL_END_BUD_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_TERMINAL_END_BUD_UP.html The 'TEB profile genes': up-regulated during pubertal mammary gland development specifically in the TEB (terminal end bud) structures. 17486082 16/17 Arthur Liberzon 2.12923802761719e-07 7.70763712250053e-07 805 572.363636363636 592 1.93567112153856e-08 78 3.99561016075089 3.65256343843415 1 9.77295397871748 804 867 592 365 1019 456 302 87 78 944 782 220 M15015 FARMER_BREAST_CANCER_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_1.html Cluster 1: interferon, T and B lymphocyte genes clustered together across breast cancer samples. 15897907 32/84 Leona Saunders 3.42386054663497e-07 9.21518482625961e-07 475 754.363636363636 592 3.11260098135508e-08 272 2.70402445927833 -2.74809284045524 -1 6.51329270431028 397 607 471 1353 1534 479 272 592 1155 472 966 221 M14829 HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN http://www.broadinstitute.org/gsea/msigdb/cards/HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN.html Genes down-regulated in hematopoietic precursor cells conditionally expressing HOXA9 and MEIS1 [GeneID=3205;4211]. 16507773 97/178 Kevin Vogelsang 7.07820871834323e-08 6.06397110828564e-07 595 912.727272727273 592 6.43473540552292e-09 140 2.63870112475014 -2.66824351821828 -1 6.54760396961574 592 1595 392 1606 140 234 310 789 3239 517 626 222 M6379 KUMAMOTO_RESPONSE_TO_NUTLIN_3A_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUMAMOTO_RESPONSE_TO_NUTLIN_3A_DN.html Genes down-regulated in response to nutlin-3a [PubChem=216345], an inhibitor of MDM2 [GeneID=4193], in skin fibroblast cultures after knockdown of TP53 [GeneID=7157] by RNAi. 18451145 15/17 Jessica Robertson 1.57959462187763e-06 2.48771658834248e-06 65 692.272727272727 593 1.43599614183986e-07 6 2.77568039345591 2.77568039345591 1 6.20577452418141 61 866 593 1384 2898 47 6 338 191 619 612 223 M176 PID_FOXM1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FOXM1_PATHWAY.html FOXM1 transcription factor network 18832364 45/51 Pathway Interaction Database 5.56537539874439e-07 1.18540486832462e-06 235 748.909090909091 594 5.05943346056988e-08 147 2.24630733603712 2.37671691344657 1 5.30350521041969 233 453 931 147 2056 563 594 749 313 1006 1193 224 M1373 GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP.html Genes up-regulated in MMH-RT cells (hepatocytes displaying an invasive, metastatic phenotype) during epithelial to mesenchymal transition (EMT). 16607286 113/135 Jessica Robertson 6.45612972737446e-10 1.07678206053737e-08 200 843.181818181818 595 5.86920884479007e-11 189 2.63637695556043 2.57700428793534 1 8.39789697859795 196 1566 219 1160 2339 189 956 595 1490 266 299 225 M2597 GHANDHI_BYSTANDER_IRRADIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_BYSTANDER_IRRADIATION_UP.html Genes significantly (FDR < 10%) up-regulated in IMR-90 cells (fibroblast) in response to bystander irradiation. 19108712 82/108 Itai Pashtan 1.83893979499363e-08 2.28415679799209e-07 270 838.818181818182 597 1.67176346396817e-09 205 2.63283846853893 -2.75359340106249 -1 6.98192090674982 266 205 329 1379 1013 406 597 797 3074 226 935 226 M16801 SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES.html Genes related to regulation of the actin cytoskeleton 45/63 Signaling Gateway 7.09387843890834e-08 6.06397110828564e-07 910 950.636363636364 602 6.44898060695433e-09 141 2.16745010853783 2.69957153418267 1 5.36931778052721 906 459 1213 461 141 1628 1817 496 309 2425 602 227 M11362 REACTOME_THE_ROLE_OF_NEF_IN_HIV1_REPLICATION_AND_DISEASE_PATHOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THE_ROLE_OF_NEF_IN_HIV1_REPLICATION_AND_DISEASE_PATHOGENESIS.html Genes involved in The role of Nef in HIV-1 replication and disease pathogenesis 57/79 Reactome 4.63644182551407e-07 1.06078552672935e-06 325 1327.72727272727 602 4.21494800239292e-08 161 1.29226749973843 -1.24444346762587 -1 3.05484674113528 321 358 3303 1082 1885 161 255 602 3266 3052 320 228 M1351 SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN.html Genes down-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 48 h. 18794802 534/749 Jessica Robertson 1.09110974264977e-17 5.00003687893874e-16 945 1152 602 1.09110974264977e-18 62 2.42356047345219 2.73705717255571 1 14.8633087139279 942 1149 4443 254 602 171 1824 528 2308 62 389 229 M835 KEGG_DILATED_CARDIOMYOPATHY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DILATED_CARDIOMYOPATHY.html Dilated cardiomyopathy 80/122 KEGG 2.70257675488413e-07 8.3538310137901e-07 365 607 603 2.45688826080054e-08 200 2.65479254397365 3.07582615635894 1 6.43929652525809 361 200 386 746 1279 603 1145 310 708 666 273 230 M1238 DAWSON_METHYLATED_IN_LYMPHOMA_TCL1 http://www.broadinstitute.org/gsea/msigdb/cards/DAWSON_METHYLATED_IN_LYMPHOMA_TCL1.html Genes hypermethylated in at least one of the lymphoma tumors of transgenic mice overexpressing TCL1 [GeneID=8115] in germinal center B lymphocytes. 17260020 65/94 Arthur Liberzon 2.99387398430206e-07 8.72827992952795e-07 1730 1046.54545454545 605 2.72170399247638e-08 274 2.53015554196487 2.91782330206438 1 6.1152589387001 1730 274 460 551 1388 1648 2502 562 605 593 1199 231 M9389 FINETTI_BREAST_CANCER_KINOME_RED http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCER_KINOME_RED.html Genes in the red cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 29/55 Jessica Robertson 2.76564627602243e-07 8.4037418352842e-07 165 572.090909090909 606 2.51422420335926e-08 89 2.11367272273612 2.13323458607388 1 5.1143925688384 164 630 1059 606 1308 89 163 200 250 899 925 232 M4965 VALK_AML_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_6.html Top 40 genes from cluster 6 of acute myeloid leukemia (AML) expression profile; all samples are FAB M1 or M2 subtypes and all samples have internal tundem duplication of FLT3 [GeneID=2322]. 15084694 42/55 Jessica Robertson 2.33874976422773e-07 7.98113405922816e-07 660 539.272727272727 608 2.12613637532072e-08 18 2.36563278718948 2.62287510708579 1 5.75133602029538 656 474 789 737 1122 347 608 18 287 782 112 233 M19166 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_CHONDROITIN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_CHONDROITIN_SULFATE.html Glycosaminoglycan biosynthesis - chondroitin sulfate 20/24 KEGG 9.79446259527411e-07 1.72692803323473e-06 410 1164.09090909091 609 8.90406086890857e-08 80 2.27566445740071 2.50132844019035 1 5.22392284884771 410 860 1518 3050 2552 433 344 80 439 2510 609 234 M8560 BIOCARTA_G2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G2_PATHWAY.html Cell Cycle: G2/M Checkpoint 38/43 BioCarta 4.02892522778127e-06 5.47821438072748e-06 395 1011.81818181818 611 3.66266600553674e-07 196 2.35921479063453 2.49275578581237 1 4.94186695386351 393 611 1828 196 3400 283 202 737 254 2229 997 235 M17079 VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP.html Up-regulated genes distinguishing between two subtypes of gastric cancer: advanced (AGC) and early (EGC). 17297478 251/324 Arthur Liberzon 2.32832478920839e-27 2.38906369675296e-25 190 789.818181818182 611 2.11665889928034e-28 26 2.78986438105219 2.90749298861691 1 27.5750117917403 188 1313 26 262 1749 679 1913 461 1401 85 611 236 M19779 FARMER_BREAST_CANCER_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_6.html Cluster 6: selected luminal genes clustered together across breast cancer samples. 15897907 22/26 Leona Saunders 4.68352438627689e-07 1.06845022248559e-06 625 826.272727272727 614 4.25775034849169e-08 66 2.20378765648407 -2.54166232310044 -1 5.24215178683826 622 799 1702 401 1895 600 614 66 100 2088 202 237 M17466 SANA_TNF_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/SANA_TNF_SIGNALING_UP.html Genes up-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by TNF [GeneID=7124]. 15749026 120/173 Yujin Hoshida 2.81385267814249e-07 8.49189526890862e-07 180 982 615 2.55804821640095e-08 11 1.97780527713564 -2.03951047947693 -1 4.77881696643376 178 11 615 1009 1321 337 387 2019 3488 333 1104 238 M14555 ZHU_CMV_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_ALL_DN.html Down-regulated at any timepoint following infection of primary human foreskin fibroblasts with CMV 9826724 186/248 John Newman 8.90496163478468e-09 1.18758139528968e-07 220 1006.54545454545 615 8.09541970075401e-10 176 2.44756358870236 2.88863392818269 1 6.76668392795077 216 2069 275 792 2295 556 1490 499 2089 615 176 239 M19432 MCBRYAN_PUBERTAL_BREAST_4_5WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_4_5WK_UP.html Genes up-regulated during pubertal mammary gland development between week 4 and 5. 17486082 397/469 Arthur Liberzon 3.74247506037512e-54 1.96272025388562e-51 5 590.818181818182 616 3.40225005488649e-55 3 3.07093279117765 -3.06637289208834 -1 62.5738606852311 985 1186 5 3 384 616 1257 1058 236 33 736 240 M158 PID_INTEGRIN4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN4_PATHWAY.html Alpha6 beta4 integrin-ligand interactions 18832364 12/12 Pathway Interaction Database 7.714224342041e-07 1.46053505392834e-06 165 864.181818181818 617 7.0129336790987e-08 54 2.34294624554172 2.34294624554172 1 5.44841130975933 161 1923 1259 739 2349 299 458 617 54 1545 102 241 M13608 ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP.html The v1LDG up-regulated set: most variable late differentiation genes (LDG) with similar expression patterns in tonsil plasma cells (TPC) and multiple myeloma (MM) samples. 12393520 43/48 Arthur Liberzon 6.79760549470648e-08 6.04231599529465e-07 565 687.363636363636 617 6.17964154976392e-09 122 2.18748106650579 -2.34184915119673 -1 5.42076873230004 564 476 1006 1401 122 617 453 163 809 1146 804 242 M2604 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_2HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_2HR.html Cell cycle genes significantly (p =< 0.05) changed in fibroblast cells at 2 h after exposure to ionizing radiation. 17404513 9/9 Itai Pashtan 2.68615045352279e-06 3.86425789107819e-06 265 1279.09090909091 618 2.68615370046022e-07 26 2.22749351430106 2.22749351430106 1 4.79893649790336 264 1000 4716 1415 3263 227 26 618 256 1802 483 243 M2185 PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP http://www.broadinstitute.org/gsea/msigdb/cards/PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP.html Genes up-regulated in ovarian tumors from mouse models for the BMP SMAD signaling (gonad specific double knockout of SMAD1 and SMAD5 [GeneID=4086, 4090]). 17967875 184/227 Arthur Liberzon 6.7618628736021e-11 1.29214545600817e-09 735 651.636363636364 620 6.14714806709995e-12 137 2.35487573903118 2.4651084664862 1 8.36791281229521 735 1403 217 698 137 289 1555 316 1050 148 620 244 M18789 LY_AGING_OLD_DN http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_OLD_DN.html Genes down-regulated in fibroblasts from old individuals, compared to those from young donors. 10741968 77/99 Arthur Liberzon 1.02502238409714e-06 1.78462030724401e-06 110 1014.54545454545 621 9.31838965159208e-08 107 2.28885130988447 2.40543875247135 1 5.24134717178095 107 251 1131 2359 2586 285 132 467 1968 1253 621 245 M2733 NOJIMA_SFRP2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NOJIMA_SFRP2_TARGETS_DN.html Cellular proliferation, growth, apoptosis and Wnt signaling genes down-regulated in SNU638 cells (gastric cancer) by overexpression of SFRP2 [GeneID=6423] off a plasmid vector. 17297461 33/40 Arthur Liberzon 1.19547284047567e-07 7.06112554001409e-07 1265 986.363636363636 622 1.08679355039753e-08 137 2.22202375019016 -2.67021742986386 -1 5.44668743397347 1265 614 1277 622 418 1880 2035 137 573 1684 345 246 M10457 LUCAS_HNF4A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LUCAS_HNF4A_TARGETS_DN.html Genes down-regulated in Tet-On HEK293 cells (embryonic kidney) by expression of HNF4A [GeneID=3172]. 16007190 13/18 Leona Saunders 3.06965629965283e-07 8.82385976514091e-07 640 565.181818181818 622 2.79059702541959e-08 105 3.18569248775784 3.21389723753416 1 7.70656312632715 639 907 622 105 1413 443 638 286 257 772 135 247 M18400 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_16 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_16.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 16. 12554760 119/149 Arthur Liberzon 1.39056225912542e-10 2.59992766082461e-09 65 914.181818181818 622 1.26414750837574e-11 65 2.66267002636031 2.89358264708136 1 9.14302638430511 65 1557 196 1159 3363 170 622 945 1233 406 340 248 M1523 NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN.html Top 20 genes whose down-regulation correlated with gastrointestinal stromal tumors (GIST) and synovial sarcoma compared to other tumors. 11965276 24/32 John Newman 1.15544410440285e-07 7.06112554001409e-07 610 1027.45454545455 626 1.05040378644272e-08 91 3.32311050106127 -3.78651213094306 -1 8.17049749042355 607 2335 626 1392 389 1062 415 91 3089 1002 294 249 M3518 WU_HBX_TARGETS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_3_DN.html Genes down-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] both in SK-Hep-1 cells (hepatocellular carcinoma) and normal primary hepatocytes. 11439330 18/23 John Newman 1.49390668346755e-07 7.26289540930751e-07 720 1255 628 1.35809707719188e-08 170 2.39086249200301 2.589328314036 1 5.85258682827328 716 2830 2295 2223 628 395 301 170 494 3412 341 250 M1778 ZHANG_GATA6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_GATA6_TARGETS_DN.html Genes down-regulated after cre-lox knockout of GATA6 [GeneID=2627] in airway epithelium. 18536717 108/129 Jessica Robertson 2.17054584432632e-12 4.97328950738845e-11 630 864.545454545455 628 1.97322349484406e-13 51 2.6975706713269 2.8805492128169 1 11.1276564623144 628 51 153 331 2080 758 1948 1432 1378 280 471 251 M8365 RHODES_UNDIFFERENTIATED_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/RHODES_UNDIFFERENTIATED_CANCER.html Genes commonly up-regulated in undifferentiated cancer relative to well-differentiated cancer, based on the meta-analysis of the OncoMine gene expression database. 15184677 117/172 John Newman 7.27969250443996e-07 1.40431223245242e-06 50 723.454545454545 629 6.61790446659615e-08 17 2.04205781547805 2.06613554070778 1 4.75628419240087 49 17 660 629 2300 248 179 927 1446 478 1025 252 M2156 DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP.html Genes up-regulated in MCF7 cells (breast cancer) at 24 h of estradiol [PubChem=5757] treatment. 20406972 375/447 Jessica Robertson 8.04829884161429e-22 4.99841717531835e-20 115 807.363636363636 629 7.31663531055844e-23 20 2.00055282864791 2.04861268072498 1 15.4786327284954 20 1200 114 1762 2865 84 114 629 991 40 1062 253 M11537 CHANG_CYCLING_GENES http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_CYCLING_GENES.html Fibroblast serum response genes showing periodic expression during the cell cycle; excluded from the core serum response signature. 14737219 202/262 Arthur Liberzon 7.56080729498957e-10 1.23913230667885e-08 50 853 632 6.87346117962547e-11 41 1.97504920221936 2.04214269189239 1 6.23031284393532 50 1373 632 1352 3200 41 129 556 972 174 904 254 M2313 DELPUECH_FOXO3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELPUECH_FOXO3_TARGETS_UP.html Genes up-regulated in DL23 cells (colon cancer) upon expression of an activated form of FOXO3 [GeneID=2309]. 17452451 117/143 Arthur Liberzon 1.1647029473304e-07 7.06112554001409e-07 1460 896.636363636364 633 1.05882091726454e-08 33 2.5472511955399 -2.49035807972934 -1 6.25121785410283 1458 33 465 113 391 1146 1862 2253 1111 633 398 255 M2879 BLUM_RESPONSE_TO_SALIRASIB_DN http://www.broadinstitute.org/gsea/msigdb/cards/BLUM_RESPONSE_TO_SALIRASIB_DN.html Selected genes down-regulated in response to the Ras inhibitor salirasib [PubChem=5469318] in a panel of cancer cell lines with constantly active HRAS [GeneID=3265]. 17409441 494/576 Jessica Robertson 1.40765088805929e-06 2.27538088754789e-06 80 1056.81818181818 635 1.27968344430299e-07 77 1.86194889424357 1.99805158481625 1 4.17542576648985 77 1175 1223 1905 2810 126 226 400 2667 381 635 256 M2576 LIM_MAMMARY_LUMINAL_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_PROGENITOR_DN.html Genes consistently down-regulated in mammary luminal progenitor cells both in mouse and human species. 20346151 28/33 Daniel Hollern 4.12122379556164e-07 1.00046055710989e-06 115 803.272727272727 636 3.74656778871265e-08 77 3.05298994005171 3.21283676399803 1 7.31649013579077 115 1804 636 1603 1746 77 95 83 1445 799 433 257 M10959 REACTOME_OTHER_SEMAPHORIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OTHER_SEMAPHORIN_INTERACTIONS.html Genes involved in Other semaphorin interactions 24/29 Reactome 2.37495668906979e-07 8.0069968374353e-07 190 893.363636363636 640 2.1590517685932e-08 9 2.60553335949795 2.91945142290425 1 6.33818529388294 186 743 806 1178 2762 329 595 9 2203 640 376 258 M5888 RASHI_RESPONSE_TO_IONIZING_RADIATION_2 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_2.html Cluster 2: late ATM [GeneID=472] dependent genes induced by ionizing radiation treatment. 16314843 181/231 Arthur Liberzon 2.30039019613972e-07 7.92543191662735e-07 1440 832.545454545455 642 2.09126403334172e-08 411 2.31159034520694 -2.34006501918306 -1 5.62163235964643 411 1436 469 589 1101 554 621 642 1437 713 1185 259 M8821 REACTOME_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AXON_GUIDANCE.html Genes involved in Axon guidance 271/342 Reactome 3.56798474897718e-12 8.01947048341538e-11 490 774.727272727273 643 3.24362249907542e-13 157 2.35129164663565 2.68140814758608 1 9.49659588017357 487 1284 157 324 337 643 1974 1384 1029 223 680 260 M1610 CUI_TCF21_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_2_UP.html All significantly up-regulated genes in kidney glomeruli isolated from TCF21 [Gene ID=6943] knockout mice. 16207825 543/664 John Newman 4.4451483884176e-19 2.38421595378762e-17 85 898.181818181818 644 4.44514838841761e-20 46 2.34177180059439 2.42814702627952 1 15.6046935596679 82 1147 4496 683 663 55 295 415 1354 46 644 261 M12522 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1.html The 'group 1 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [GeneID=2099;2064]. 18794137 663/837 Jessica Robertson 1.98289462169107e-07 7.65527859584926e-07 645 1018.36363636364 645 1.98289479862529e-08 76 2.07102579533493 2.17486402800687 1 5.04393312707688 645 1127 4509 349 1044 76 1169 473 964 485 361 262 M9709 TAVOR_CEBPA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAVOR_CEBPA_TARGETS_UP.html Genes up-regulated in KCL22 cells (chronic myelogenous leukemia, CML, with BCR-ABL1 [GeneID=613;25] fusion) by expression of CEBPA [GeneID=1050]. 14517214 51/67 Kevin Vogelsang 1.38905762861831e-07 7.20206492018647e-07 730 877.545454545455 646 1.26277974211092e-08 276 2.28739548561415 -2.0879086683683 -1 5.60050495269525 729 437 798 2100 559 320 369 276 2703 716 646 263 M17204 CHIARETTI_T_ALL_RELAPSE_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/CHIARETTI_T_ALL_RELAPSE_PROGNOSIS.html Genes whose expression predicted relapse in less than 2 years after chemotherapy for adult patients with T-ALL (T cell lymphoblastic leukemia). 14684422 32/68 Arthur Liberzon 8.49089256526518e-07 1.56298478827681e-06 940 986.818181818182 646 7.71899622029462e-08 190 1.88147117613053 2.00140638004081 1 4.34313920517532 939 646 1793 638 2433 511 424 190 604 1861 816 264 M2129 CHICAS_RB1_TARGETS_CONFLUENT http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_CONFLUENT.html Genes up-regulated in confluent IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 721/968 Arthur Liberzon 1.18431426656632e-32 1.69392828430092e-30 625 1135.90909090909 646 1.18431426656631e-33 20 2.45709354746628 2.73077076417304 1 29.3682443521155 623 1102 4662 230 646 375 2153 460 1483 20 741 265 M18506 CROONQUIST_IL6_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_IL6_DEPRIVATION_DN.html Genes down-regulated in the ANBL-6 cell line (multiple myeloma, MM) after withdrawal of IL6 [GeneID=3569]. 12791645 121/145 Arthur Liberzon 3.72004111056094e-13 9.49113191451225e-12 35 755.363636363636 647 3.38185555505597e-14 33 2.16532151865604 2.16894248025628 1 9.54861653928129 33 1508 338 928 2850 68 93 647 816 106 922 266 M233 PID_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPO_PATHWAY.html EPO signaling pathway 18832364 47/58 Pathway Interaction Database 1.94095649560295e-07 7.601476063939e-07 665 1208.54545454545 649 1.76450606076767e-08 189 1.50968382882168 -1.49793479032798 -1 3.66509573121142 665 500 2840 189 914 601 303 649 3377 2886 370 267 M1495 PETROVA_PROX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_PROX1_TARGETS_UP.html Genes specific to LEC (lymphatic endothelium cells) induced in BEC (blood endothelium cells) by expression of PROX1 [GeneID=5629] off adenovirus vector. 12198161 33/37 Kevin Vogelsang 7.23632504074815e-07 1.39981369640702e-06 260 1173.09090909091 649 6.57847947359022e-08 66 1.86941738987106 1.81736778760432 1 4.35099394999405 258 649 1985 3310 2293 100 66 493 2303 889 558 268 M19826 ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP.html Genes up-regulated in BxPC3 cells (pancreatic cancer) after treatment with TNF [GeneID=7124] or IKI-1, an inhibitor of IkappaB kinase (IKK). 19010928 261/341 Jessica Robertson 1.58048206713515e-07 7.31918027928963e-07 150 1096 650 1.43680198243377e-08 149 2.17827222782175 -2.22696019388365 -1 5.32480142665077 149 2045 385 2315 1459 264 361 650 3364 273 791 269 M4594 GENTILE_UV_LOW_DOSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_LOW_DOSE_DN.html Selected genes down-regulated in WS1 (fibroblast) in response to irradiation with low dose UV-C. 12907719 102/123 John Newman 1.70036730844414e-07 7.33971845416521e-07 1640 1084.18181818182 653 1.54578858169506e-08 65 2.70143922127867 3.13970906240973 1 6.61438230462463 1638 65 363 299 1203 1971 4359 264 334 653 777 270 M3578 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION.html Progesterone-mediated oocyte maturation 80/92 KEGG 2.37426746497726e-07 8.0069968374353e-07 460 869.181818181818 655 2.1584252011011e-08 163 1.76342053243269 1.89397247718137 1 4.27350089413761 460 212 2013 655 1141 163 240 742 779 2686 470 271 M4038 PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN.html Genes down-regulated in CD38+ [GeneID=952] CLL (chronic lymphocytic leukemia) cells. 17287849 16/31 Arthur Liberzon 4.42861417182816e-08 4.68840158031105e-07 1125 643 657 4.02601296452404e-09 37 2.04207746776749 2.03970546271924 1 5.14760360761292 1124 856 1293 953 37 657 411 623 122 943 54 272 M12671 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN.html Genes down-regulated in nsopharyngeal carcinoma relative to the normal tissue. 16912175 302/528 Leona Saunders 4.08087687627706e-19 2.21399297195721e-17 660 673.545454545455 658 3.70988806934279e-20 59 2.70250300109317 -2.8929534410038 -1 18.0511425529639 658 1269 59 918 261 998 1502 95 1121 101 427 273 M2316 WIEDERSCHAIN_TARGETS_OF_BMI1_AND_PCGF2 http://www.broadinstitute.org/gsea/msigdb/cards/WIEDERSCHAIN_TARGETS_OF_BMI1_AND_PCGF2.html Genes up-regulated in DAOY cells (medulloblastoma) upon knockdown of both BMI1 and PCGF2 [GeneID=648, 7703] by RNAi. 17452456 95/110 Arthur Liberzon 7.38627161499569e-15 2.4043587601917e-13 175 867.636363636364 658 6.71479237726884e-16 102 3.24947069802458 3.49001014352279 1 16.4406306907523 174 1593 102 712 2520 288 658 1821 820 269 587 274 M2148 SHEPARD_CRUSH_AND_BURN_MUTANT_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_CRUSH_AND_BURN_MUTANT_DN.html Human orthologs of genes down-regulated in the crb ('crash and burn') zebrafish mutant that represents a loss-of-function mutation in BMYB [GeneID=4605]. 16150706 255/352 Jennifer Shepard 1.33783480564407e-06 2.18573218506058e-06 450 1032.54545454545 663 1.21621419926465e-07 213 2.09042246784964 2.27095319252446 1 4.70859432904601 449 1327 663 1377 2776 659 903 213 1960 455 576 275 M11885 NIELSEN_SCHWANNOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SCHWANNOMA_DN.html Top 20 negative significant genes associated with schwannoma tumors. 11965276 28/31 Arthur Liberzon 1.08668514296159e-06 1.86514686355589e-06 1220 1009.54545454545 664 9.87896072479718e-08 104 2.79851770035336 3.12782284092068 1 6.39802606186016 1220 639 540 104 2629 1289 2574 106 454 664 886 276 M10 PID_BCR_5PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BCR_5PATHWAY.html BCR signaling pathway 18832364 85/107 Pathway Interaction Database 1.49253434663033e-07 7.26289540930751e-07 685 1172.45454545455 665 1.3568494980796e-08 174 1.64156655472921 -1.67627004027866 -1 4.00270537453408 683 174 2715 178 627 665 532 560 3128 2656 979 277 M1501 SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A.html Genes basally silent, with hypermethylated promoters, up-regulated by the combination of TSA and decitabine [PubChem=5562;451668] in RKO cells (colorectal cancer). 11992124 29/38 John Newman 2.02151788300291e-07 7.65527859584926e-07 485 646 667 1.83774369886773e-08 141 3.2404599196462 3.03193629735822 1 7.92031579163729 482 667 562 703 954 353 835 522 817 1070 141 278 M1579 BURTON_ADIPOGENESIS_8 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_8.html Progressively down-regulated 8-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 145/182 John Newman 5.39885430733988e-07 1.16482288679751e-06 125 774.181818181818 667 4.90805057475683e-08 122 2.16867954760777 2.48477687018628 1 5.12513208688005 122 1481 667 433 2021 206 833 533 1247 828 145 279 M631 REACTOME_COLLAGEN_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COLLAGEN_FORMATION.html Genes involved in Collagen formation 57/64 Reactome 1.54701913229771e-11 3.24530235753119e-10 70 995.545454545455 668 1.40638102937144e-12 68 2.85328300374864 2.95511761677401 1 10.8381172482672 68 336 172 722 4073 668 1444 1413 1293 246 516 280 M1007 FERRANDO_TAL1_NEIGHBORS http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_TAL1_NEIGHBORS.html Nearest neighbors of TAL1 [GeneID=6886], based on the close agreement of their expression profiles with that of TAL1 in pediatric T cell acute lymphoblastic leukemia (T-ALL) 12086890 24/40 Jean Junior 1.54232972209146e-07 7.28175281873995e-07 4450 1823.09090909091 668 1.40211802747079e-08 93 3.04693783209663 2.66773496912153 1 7.47094289604414 4448 668 367 266 659 3890 4587 878 93 346 3852 281 M778 BIERIE_INFLAMMATORY_RESPONSE_TGFB1 http://www.broadinstitute.org/gsea/msigdb/cards/BIERIE_INFLAMMATORY_RESPONSE_TGFB1.html Inflammatory genes down-regulated in mammary carcinoma cells after stimulation with TGFB1 [GeneID=7040] for 1 hr. 18339861 10/10 Jessica Robertson 8.97134926078012e-08 6.54205957136183e-07 670 1330.09090909091 669 8.15577238783774e-09 212 3.65699261905774 -4.0974018270935 -1 9.0452050397387 669 2903 1300 1995 243 595 212 343 4177 1565 629 282 M7552 BIOCARTA_CARDIACEGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARDIACEGF_PATHWAY.html Role of EGF Receptor Transactivation by GPCRs in Cardiac Hypertrophy 31/34 BioCarta 4.70972039149005e-07 1.07280143849385e-06 675 1068.27272727273 671 4.28156490885347e-08 316 2.2060046452206 -2.46004313343208 -1 5.24590977374777 671 1797 1035 647 1899 316 414 468 3136 892 476 283 M211 PID_HEDGEHOG_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HEDGEHOG_2PATHWAY.html Signaling events mediated by the Hedgehog family 18832364 30/34 Pathway Interaction Database 4.68471228158691e-08 4.82791309368782e-07 655 1062.18181818182 672 4.25882943758533e-09 48 2.1704422517881 2.47447228637227 1 5.46321111565441 651 672 1864 2152 48 350 569 2046 564 1883 885 284 M8124 SMID_BREAST_CANCER_BASAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_BASAL_UP.html Genes up-regulated in basal subtype of breast cancer samles. 18451135 828/1212 Jessica Robertson 1.88893267817664e-38 4.05261920045171e-36 570 992.727272727273 672 1.88893267817662e-39 14 2.54671204006467 2.5988531115312 1 36.1983629376265 566 1089 4553 223 672 127 1520 753 849 14 554 285 M7678 CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_DN.html Marker genes down-regulated in the 'chromosome 7 polysomy' subclass of hepatocellular carcinoma (HCC); characterized by polysomy of chromosome 7 and by a lack of gains of chromosome 8q. 18701503 31/39 Yujin Hoshida 4.17242687450062e-07 1.00504816968881e-06 300 1173.63636363636 673 3.7931160598415e-08 27 1.81895160818383 1.80200730271513 1 4.33743858102518 296 673 2087 3636 1765 121 84 27 2558 1455 208 286 M1050 REACTOME_PHOSPHORYLATION_OF_THE_APC_C http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHORYLATION_OF_THE_APC_C.html Genes involved in Phosphorylation of the APC/C 22/24 Reactome 2.81930018503386e-06 4.02391801432108e-06 165 1245.18181818182 674 2.56300345270343e-07 11 1.59505027569559 1.6678026159638 1 3.41090803841911 163 793 2587 1960 3234 96 11 664 318 3197 674 287 M15008 PIEPOLI_LGI1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PIEPOLI_LGI1_TARGETS_UP.html Up-regulated genes in U87 cells (glioblastoma multiforme, GBM) engineered to stably express LGI1 [GeneID=9211]. 16533756 23/33 Arthur Liberzon 1.15453075077616e-07 7.06112554001409e-07 675 893.181818181818 674 1.04957346487673e-08 72 2.63070043335894 3.02558728821805 1 6.45765015654835 674 1842 1129 1661 388 641 573 105 846 1894 72 288 M2118 SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN.html Genes down-regulated in pleura relapse of breast cancer. 18451135 26/84 Jessica Robertson 3.40316848804283e-08 3.8799408849184e-07 2460 1397 678 3.09378958244207e-09 18 3.39418004972279 -4.14424849479867 -1 8.70127457216154 2459 678 459 550 18 2317 1458 4104 450 652 2222 289 M258 PID_BARD1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BARD1_PATHWAY.html BARD1 signaling events 18832364 34/36 Pathway Interaction Database 8.75525828453324e-06 1.09382792755418e-05 165 1590.27272727273 679 7.95935738882142e-07 21 1.98894443845413 2.07953799108292 1 3.91819429231924 162 2736 2779 3170 3721 54 21 517 152 3502 679 290 M5636 LEE_LIVER_CANCER_MYC_E2F1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_E2F1_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) from MYC and E2F1 [GeneID=4609;1869] double transgenic mice. 15565109 54/107 Yujin Hoshida 3.64443314047716e-07 9.47297674322927e-07 685 1044.81818181818 682 3.31312158563609e-08 295 2.56659081222601 -2.52394838489523 -1 6.16733950237646 682 405 759 1623 1602 295 406 1555 3192 655 319 291 M684 REACTOME_SYNTHESIS_OF_PC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PC.html Genes involved in Synthesis of PC 14/19 Reactome 2.97889899442455e-07 8.70294688256627e-07 610 866.818181818182 683 2.70809036161905e-08 103 1.9230729029001 -1.8768588001319 -1 4.63694108306035 608 915 1975 1369 1380 282 110 683 103 1911 199 292 M13422 HUPER_BREAST_BASAL_VS_LUMINAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUPER_BREAST_BASAL_VS_LUMINAL_UP.html Genes up-regulated in basal mammary epithelial cells compared to the luminal ones. 17409405 61/100 Jessica Robertson 2.72977548788091e-19 1.49820236079045e-17 690 686.818181818182 686 2.48161407989172e-20 58 3.83525297283586 4.34311961845177 1 25.8998226750364 344 278 58 689 1865 589 1215 723 686 167 941 293 M8728 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM.html Hypertrophic cardiomyopathy (HCM) 79/137 KEGG 4.31269086241258e-07 1.02188257382467e-06 785 849.636363636364 687 3.92062882530514e-08 220 2.69567390928729 3.20878654301481 1 6.4443512472025 685 220 455 398 1799 988 1949 687 784 784 597 294 M12661 MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN.html Genes commonly down-regulated in SK-N-BE cells (neuroblastoma) after RNAi knockdown of CCND1 and CDK4 [GeneID=595;1019]. 18413728 72/103 Jessica Robertson 1.60894989090003e-06 2.52636177147311e-06 55 765.181818181818 688 1.46268278872003e-07 24 1.83295659393168 1.90295301035538 1 4.07613440359609 51 235 1123 1360 2908 24 50 250 1033 695 688 295 M1233 OHM_METHYLATED_IN_ADULT_CANCERS http://www.broadinstitute.org/gsea/msigdb/cards/OHM_METHYLATED_IN_ADULT_CANCERS.html Genes showing frequent DNA methylation and which are silenced in adult cancers but remain unmethylated in embryonic carcinoma and embryonic stem (ES) cells. 17211412 33/42 Leona Saunders 2.43785291359383e-07 8.08620221515313e-07 760 986.909090909091 690 2.21623016703273e-08 221 2.15521897533411 2.34792509597595 1 5.2304033840571 760 631 1544 2147 1167 271 508 391 690 2526 221 296 M2899 LINDGREN_BLADDER_CANCER_HIGH_RECURRENCE http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_HIGH_RECURRENCE.html Genes up-regulated among the high recurrence rate urothelial cell carcinoma (UCC) tumors. 16532037 83/87 Arthur Liberzon 4.28403046231241e-12 9.58323401995951e-11 140 870 692 3.89457314756433e-13 139 2.91152406866336 3.06258550299491 1 11.6806436156868 139 170 158 734 3091 692 2011 839 969 240 527 297 M1935 MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 trimethylation marks at k4 (H3K4me3) and K27 ((H3K27me3) in neural precursor cells (NPC). 18600261 159/261 Jessica Robertson 8.80899003101779e-19 4.61982588293377e-17 1675 995.545454545455 692 8.00817275547072e-20 61 2.83616428424308 3.27619313344821 1 18.5820338233197 1673 1444 61 692 596 976 3488 466 786 115 654 298 M7047 MCCOLLUM_GELDANAMYCIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCOLLUM_GELDANAMYCIN_RESISTANCE_UP.html Genes up-regulated in A549GARS cells (lung cancer) resistant to the geldanamycin and 17-AAG [PubChem=5476289;6440175]. 18794130 19/28 Jessica Robertson 3.10043988211081e-07 8.87599861826974e-07 435 1059 701 2.81858210823004e-08 14 3.38782060423268 3.51243922893725 1 8.19522349353914 434 841 550 2081 3046 396 674 14 1814 1098 701 299 M2059 FERRANDO_HOX11_NEIGHBORS http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_HOX11_NEIGHBORS.html Nearest neighbors of HOX11 [GeneID=3195], based on the close agreement of their expression profiles with that of HOX11 in pediatric T cell acute lymphoblastic leukemia (T-ALL). 12086890 23/28 Arthur Liberzon 1.60998658449664e-07 7.3358205358541e-07 215 829 702 1.46362427483402e-08 117 1.634512220565 1.7275645515284 1 3.98243731966196 214 767 2037 1431 702 153 117 463 1627 1096 512 300 M10394 FARMER_BREAST_CANCER_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_7.html Cluster 7: selected apocrine and luminal genes clustered together across breast cancer samples. 15897907 29/31 Leona Saunders 1.27341034636478e-07 7.19819980220572e-07 335 1078.81818181818 704 1.15764583642972e-08 70 1.9931855070778 -1.85283460516291 -1 4.87390632694942 331 704 1751 3848 470 186 164 1733 839 1771 70 301 M10504 SEMBA_FHIT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SEMBA_FHIT_TARGETS_DN.html Genes down-regulated in H1299 cells (non-small cell lung cancer, NSCLC) expressing the Y144F mutant form of FHIT [GeneID=2272]. 16407838 9/9 Leona Saunders 1.15680703804003e-06 1.95493348354778e-06 300 1189.18181818182 704 1.15680764023161e-07 105 2.11028808700014 2.26133148072128 1 4.79494746127407 298 989 4404 1808 2744 202 105 235 641 951 704 302 M6862 NADERI_BREAST_CANCER_PROGNOSIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NADERI_BREAST_CANCER_PROGNOSIS_UP.html Up-regulated genes in the breast cancer prognostic signature of 70 genes that significantly correlated with survival. 16936776 58/147 Arthur Liberzon 1.71476720843892e-07 7.35006487528071e-07 530 791.636363636364 706 1.55887940190427e-08 295 1.8909765892912 2.03340827769579 1 4.61451507783235 529 295 992 1356 784 568 902 706 542 646 1388 303 M5840 SMID_BREAST_CANCER_RELAPSE_IN_LUNG_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LUNG_UP.html Genes up-regulated in lung relapse of breast cancer. 18451135 39/105 Jessica Robertson 1.06649097637128e-08 1.39056282002001e-07 280 1095.90909090909 706 9.69537255946626e-10 278 3.31323522462134 3.07616395965376 1 9.08636063044381 278 523 284 366 3229 954 1591 2506 1086 532 706 304 M9399 BOYLAN_MULTIPLE_MYELOMA_PCA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA1_UP.html Top up-regulated genes from principal component 1 (PCA1) which captures variation between normal plasma cells and tumors arising from aberrant expression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 112/199 Arthur Liberzon 4.38537406239712e-10 7.41898407688688e-09 840 894.454545454545 707 3.98670369388299e-11 27 2.56340993761528 -2.59351429112861 -1 8.33086677882703 837 27 216 695 206 1345 1287 707 2350 279 1890 305 M8231 HEIDENBLAD_AMPLICON_12P11_12_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_12P11_12_UP.html Up-regulated genes whose expression is associated with amplification of the 12p11-12 chromosome in pancreatic cancer cell lines. 15688027 44/48 Arthur Liberzon 5.30379896356952e-08 5.25922922437986e-07 1400 920.545454545455 709 4.82163553766766e-09 66 2.24056100149073 2.35898601406745 1 5.60783716889693 1398 519 1609 129 66 1367 1907 709 374 1845 203 306 M5756 REACTOME_E2F_ENABLED_INHIBITION_OF_PRE_REPLICATION_COMPLEX_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_E2F_ENABLED_INHIBITION_OF_PRE_REPLICATION_COMPLEX_FORMATION.html Genes involved in E2F-enabled inhibition of pre-replication complex formation 13/13 Reactome 5.51403194400965e-06 7.20748567591403e-06 240 1197.90909090909 710 5.01276887664306e-07 14 2.06731539416363 2.06731539416363 1 4.22517552223476 239 940 2014 2404 3541 114 14 394 166 2641 710 307 M17966 VALK_AML_WITH_T_8_21_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_T_8_21_TRANSLOCATION.html Genes that best predicted acute myeloid leukemia (AML) with the t(8;21) translocation producing the AML1-ETO fusion [GeneID=861;862]. 15084694 7/9 Jessica Robertson 2.25717962430839e-07 7.86164283892477e-07 715 1449.63636363636 711 2.25717985357711e-08 56 4.63889979921587 5.60216676696629 1 11.3384174883361 711 1980 4620 3645 1181 287 56 176 336 2404 550 308 M5885 NABA_MATRISOME_ASSOCIATED http://www.broadinstitute.org/gsea/msigdb/cards/NABA_MATRISOME_ASSOCIATED.html Ensemble of genes encoding ECM-associated proteins including ECM-affilaited proteins, ECM regulators and secreted factors 22159717 391/882 Alexandra Naba 5.51023314734298e-53 2.60083004554588e-50 700 999.272727272727 711 5.00930286122088e-54 6 2.94622908232138 3.03396893176668 1 58.7011305698452 697 1201 6 680 711 926 2205 441 2328 24 1773 309 M2465 DELACROIX_RAR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RAR_TARGETS_DN.html Genes bound by RARG [GeneID=5916] and down-regulated by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] in MEF cells (embryonic fibroblast). 19884340 29/35 Arthur Liberzon 1.09779916034113e-07 7.03739764799127e-07 555 788.090909090909 712 9.97999286473883e-09 172 2.63465537006702 2.82176636146222 1 6.46898257418111 551 692 1073 1173 349 1016 731 712 172 1775 425 310 M15975 LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP.html Genes up-regulated between two breast carcinoma subtypes: metaplastic (MCB) and ductal (DCB). 17603561 100/130 Arthur Liberzon 1.81825701321953e-07 7.47800341964416e-07 345 842.181818181818 713 1.65296105772267e-08 88 2.39942789813842 2.49343363839697 1 5.8615016474432 343 88 384 2055 843 323 1066 1255 1647 547 713 311 M264 PID_TOLL_ENDOGENOUS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TOLL_ENDOGENOUS_PATHWAY.html Endogenous TLR signaling 18832364 29/47 Pathway Interaction Database 3.23574753187094e-07 9.02643519529009e-07 485 920.090909090909 715 2.9415890979845e-08 225 2.87383579557083 -3.02829889811164 -1 6.93585402057719 483 715 1214 1872 1468 261 225 362 1308 1768 445 312 M7250 MA_PITUITARY_FETAL_VS_ADULT_UP http://www.broadinstitute.org/gsea/msigdb/cards/MA_PITUITARY_FETAL_VS_ADULT_UP.html Up-regulated in human fetal pituitary tissue, compared to adult pituitary tissue 15894316 38/42 John Newman 3.68330174927903e-08 4.1294974481228e-07 720 1229.09090909091 718 3.34845619176901e-09 24 1.73333318138607 2.05673686924455 1 4.40019405149723 718 600 2411 2472 24 437 482 892 1898 3367 219 313 M17471 SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP.html Genes up-regulated in invasive ductal carcinoma (IDC) relative to ductal carcinoma in situ (DCIS, non-invasive). 16707453 439/604 Arthur Liberzon 6.53509331651142e-38 1.34111480234495e-35 110 1138 719 5.9409939241013e-39 12 2.62821827700567 2.73222787865004 1 36.8091362800236 109 2018 12 688 2588 719 1613 657 2986 32 1096 314 M203 PID_ALK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK2_PATHWAY.html ALK2 signaling events 18832364 9/13 Pathway Interaction Database 1.25043304463563e-05 1.52271516271418e-05 720 1658.27272727273 720 1.25044008081395e-06 136 1.77333499202972 1.97124923982777 1 3.38556179052603 720 1962 4204 3660 3844 517 136 172 307 2315 404 315 M18647 REACTOME_STRIATED_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_STRIATED_MUSCLE_CONTRACTION.html Genes involved in Striated Muscle Contraction 24/48 Reactome 1.66160057914328e-07 7.3358205358541e-07 535 706 721 1.51054609512682e-08 222 2.76192743919508 2.97288075274336 1 6.76386229345063 532 755 1024 599 737 721 1447 285 253 1191 222 316 M685 REACTOME_HS_GAG_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HS_GAG_BIOSYNTHESIS.html Genes involved in HS-GAG biosynthesis 24/30 Reactome 1.84246888455593e-07 7.47950348864313e-07 300 679.272727272727 723 1.67497185350919e-08 35 2.30208538229149 2.5465589335733 1 5.62159547298666 299 723 986 1575 862 470 1033 35 438 1000 51 317 M2368 GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP.html Genes up-regulated during later stage of differentiation of Oli-Neu cells (oligodendroglial precursor) in response to PD174265 [PubChem=4709]. 19139271 661/745 Arthur Liberzon 7.69464936204167e-18 3.56066127341536e-16 10 1190.36363636364 725 7.69464936204168e-19 8 1.79578943535053 1.8574083631441 1 11.1068109647394 8 1115 4692 1764 2830 22 67 402 1409 60 725 318 M564 REACTOME_MEMBRANE_BINDING_AND_TARGETTING_OF_GAG_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEMBRANE_BINDING_AND_TARGETTING_OF_GAG_PROTEINS.html Genes involved in Membrane binding and targetting of GAG proteins 14/17 Reactome 1.17164002729625e-07 7.06112554001409e-07 730 2014.18181818182 726 1.06512735426686e-08 63 0.947578639753406 -0.880975368280116 -1 2.29403265408903 726 3782 3507 4232 398 321 63 140 4500 3998 489 319 M873 REACTOME_ROLE_OF_SECOND_MESSENGERS_IN_NETRIN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ROLE_OF_SECOND_MESSENGERS_IN_NETRIN1_SIGNALING.html Genes involved in Role of second messengers in netrin-1 signaling 8/13 Reactome 2.24679473658823e-08 2.69159166413616e-07 2385 1173.72727272727 728 2.24679475930462e-09 7 2.50662773150934 -2.89367082151574 -1 6.57297048758756 2381 996 4246 728 7 2167 442 50 20 1537 337 320 M6967 HU_ANGIOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HU_ANGIOGENESIS_UP.html Up-regulated genes that separate angiogenic from non-angiogenic non-small cell lung carcinoma (NSCLC) samples. 15592519 45/48 Leona Saunders 8.12200161436304e-06 1.02174433954674e-05 590 1405.72727272727 729 7.38366509043383e-07 465 2.44473185799516 2.9657055257256 1 4.85666473852162 586 465 594 627 3695 1079 2020 2853 2238 729 577 321 M18679 SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_UP.html Cell cycle genes up-regulated in H1299 cells (lung cancer) after overexpression of either P53 or P73 [GeneID=7157;7161]. 17982488 16/17 Jessica Robertson 9.48236242669774e-07 1.68829689377644e-06 705 1013.72727272727 730 8.62033319432237e-08 25 3.4671740841984 4.04069181880647 1 7.99900298178643 702 903 984 440 3563 730 1414 25 26 2281 83 322 M11980 REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS.html Genes involved in Adherens junctions interactions 23/34 Reactome 4.99426472295982e-07 1.11141872398347e-06 1980 1307.18181818182 731 4.5402416879258e-08 22 3.01710207577294 3.26087155798899 1 7.17447302027436 1980 731 551 568 1947 2131 2036 22 632 709 3072 323 M3045 CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_UP.html Genes up-regulated in CD4+ [GeneID=920] T lymphocytes after stimulation with prostaglandin E2 [PubChem=5280360]. 16424048 177/192 Arthur Liberzon 5.43973829257554e-07 1.16813306373779e-06 100 920.545454545455 731 4.94521785237293e-08 99 1.8205579915629 1.9507820518385 1 4.2934993832978 99 1422 1381 971 2035 116 197 399 2056 731 719 324 M8760 MCGARVEY_SILENCED_BY_METHYLATION_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/MCGARVEY_SILENCED_BY_METHYLATION_IN_COLON_CANCER.html Genes silenced in HCT116 cells (colon cancer) by methylation of CpG islands in their promoters. 18632628 53/86 Jessica Robertson 5.94522587258428e-07 1.23104631893713e-06 715 864.454545454545 732 5.40475225382555e-08 177 2.66707047479257 3.099776131786 1 6.28869588137929 714 439 732 1217 2118 819 1469 177 692 810 322 325 M7854 WHITEFORD_PEDIATRIC_CANCER_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/WHITEFORD_PEDIATRIC_CANCER_MARKERS.html Differentially expressed genes in a panel of xenografts representing 8 common pediatric tumors compared to the normal tissues. 17210681 148/222 Jessica Robertson 3.19112063408653e-08 3.67368033972889e-07 855 827.545454545455 734 2.90101880034003e-09 25 1.91497581614099 2.0021312852106 1 4.90567024688191 25 1466 853 961 3275 53 83 420 851 382 734 326 M2590 SMIRNOV_RESPONSE_TO_IR_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_6HR_DN.html Genes down-regulated in B lymphocytes at 6 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 130/177 Itai Pashtan 8.9398003428309e-08 6.54205957136183e-07 990 873.545454545455 736 8.12709155100344e-09 238 2.21805252888693 2.31036833840933 1 5.46644237569138 988 1545 407 951 238 461 1352 736 1894 345 692 327 M2342 FEVR_CTNNB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FEVR_CTNNB1_TARGETS_UP.html Genes up-regulated in intestinal crypt cells upon deletion of CTNNB1 [GeneID=1499]. 17785439 861/1201 Arthur Liberzon 3.62236901900819e-13 9.29582881596852e-12 740 1060 737 3.62236901900878e-14 35 2.08586966411862 -2.0049192950569 -1 9.20398920132595 737 1093 4685 35 728 70 925 1011 1691 107 578 328 M17673 KEGG_CARDIAC_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CARDIAC_MUSCLE_CONTRACTION.html Cardiac muscle contraction 71/118 KEGG 2.56740565646319e-07 8.25487377282443e-07 480 1137.09090909091 741 2.33400541461831e-08 311 2.56404427103803 2.85891974794564 1 6.2228093664288 385 2623 1002 2589 1217 478 311 479 741 2199 484 329 M6387 WINNEPENNINCKX_MELANOMA_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WINNEPENNINCKX_MELANOMA_METASTASIS_UP.html Genes from the 254-gene classifier which were up-regulated in melanoma patients with a reported distant metastasis within 4 years. 16595783 211/263 Arthur Liberzon 6.45497452342588e-09 8.8311535508899e-08 20 980.454545454545 741 5.86815867487754e-10 17 1.8690431508622 1.94974900063864 1 5.25214156921328 17 1388 1661 2292 2646 106 103 279 915 741 637 330 M15535 KIM_WT1_TARGETS_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_12HR_UP.html Genes up-regulated in UB27 cells (osteosarcoma) at 12 hr after inducing the expression of a mutated form of WT1 [GeneID=7490]. 17430890 223/253 Arthur Liberzon 1.27203245610214e-07 7.19819980220572e-07 1035 886.727272727273 742 1.1563932087733e-08 113 2.13260018473832 2.4649163292939 1 5.21831480937023 1032 1377 742 768 468 442 2429 255 1537 591 113 331 M4336 OSADA_ASCL1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OSADA_ASCL1_TARGETS_DN.html Genes down-regulated in A549 cells (lung cancer) upon expression of ASCL1 [GeneID=429] off a viral vector. 18339843 37/45 Jessica Robertson 7.07257529532645e-08 6.06397110828564e-07 2315 1280.81818181818 742 6.42961411154192e-09 16 3.0609541311967 3.44635500314323 1 7.60337863891202 2315 542 340 425 1956 2421 3756 16 1053 523 742 332 M2358 RAFFEL_VEGFA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAFFEL_VEGFA_TARGETS_DN.html Genes down-regulated in hearts of E18.5 embryos upon knockout of VEGFA [GeneID=7422]. 18981216 3/5 Arthur Liberzon 4.03704072016293e-07 9.94511075113206e-07 620 1285.90909090909 742 4.03704145355951e-08 1 3.24175457650302 -3.24175457650302 -1 7.77533540145879 619 1993 4689 1818 1835 462 1 174 742 1695 117 333 M6225 WANG_BARRETTS_ESOPHAGUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_UP.html Genes up-regulated in Barrett's esophagus compared to the normal tissue. 16449976 62/102 Arthur Liberzon 4.68370368063394e-08 4.82791309368782e-07 815 734 744 4.25791252758903e-09 47 2.27974609429688 -2.83763215051029 -1 5.74085924105871 815 321 1081 744 47 1244 943 549 409 1213 708 334 M2948 SESTO_RESPONSE_TO_UV_C8 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C8.html Cluster 8: genes changed in primary keratinocytes by UVB irradiation. 11867738 146/168 John Newman 3.03167038163887e-07 8.77601760597774e-07 220 776.181818181818 746 2.75606436310257e-08 46 2.21701574234462 2.60122286365484 1 5.35011097164501 219 1512 802 474 1399 46 690 746 1090 1483 77 335 M12347 REACTOME_NEF_MEDIATES_DOWN_MODULATION_OF_CELL_SURFACE_RECEPTORS_BY_RECRUITING_THEM_TO_CLATHRIN_ADAPTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEF_MEDIATES_DOWN_MODULATION_OF_CELL_SURFACE_RECEPTORS_BY_RECRUITING_THEM_TO_CLATHRIN_ADAPTERS.html Genes involved in Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters 41/60 Reactome 3.41415499388626e-07 9.20320478077849e-07 340 1394.36363636364 748 3.1037777488411e-08 129 1.20806569545857 -1.14693913403595 -1 2.88250874058222 340 489 3233 1508 1529 129 266 748 3515 3370 211 336 M2108 VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_DN.html Down-regulated genes distinguishing between two subtypes of gastric cancer: advanced (AGC) and early (EGC). 17297478 114/210 Arthur Liberzon 7.90412989937907e-07 1.48694671682221e-06 230 880.636363636364 748 7.18557521742315e-08 206 2.68318799998207 -2.75016724948138 -1 6.23849498967476 230 1565 458 924 2368 704 815 206 435 748 1234 337 M9167 ROZANOV_MMP14_TARGETS_SUBSET http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_TARGETS_SUBSET.html Genes linked to the ECM maintenance and angiogenesis that were changed in HT1080 cells (fibrosarcoma) over-expressing MMP14 [GeneID=4323] compared to those with knockdown of the gene by RNAi. 18519667 66/72 Jessica Robertson 1.70474913817231e-09 2.62954769025271e-08 95 1185.27272727273 749 1.54977194499391e-10 93 2.94312593375796 3.14282406572383 1 8.92188547138799 93 1650 236 749 3757 734 2091 1317 1512 491 408 338 M2523 ZHAN_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_DN.html Genes most significantly down-regulated in multiple myeloma samples, compared to normal bone marrow plasma cells. 11861292 63/90 Kevin Vogelsang 7.96876470758682e-10 1.29698515240723e-08 445 1216.72727272727 749 7.24433155497569e-11 224 2.86816582416569 2.84158483866022 1 9.04742651047284 445 340 224 821 3056 489 1539 2437 2910 374 749 339 M13308 MURAKAMI_UV_RESPONSE_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_1HR_UP.html Genes up-regulated in primary keratinocytes at 1 h after UVB irradiation. 11532376 29/39 Arthur Liberzon 1.16707626625559e-06 1.96724659298497e-06 1125 1055.72727272727 749 1.06097898670674e-07 369 3.18437577106091 4.17129577769544 1 7.25744019696123 1121 702 749 1146 2678 512 648 1830 595 1263 369 340 M3238 SMID_BREAST_CANCER_RELAPSE_IN_BONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BONE_UP.html Genes up-regulated in bone relapse of breast cancer. 18451135 119/168 Jessica Robertson 1.2530548271396e-07 7.16209778122308e-07 3985 2044.63636363636 750 1.13914081682718e-08 25 2.42959883437535 -2.35061049782823 -1 5.95415062565556 3983 25 446 750 457 4672 4219 3164 541 567 3667 341 M1542 YAMAZAKI_TCEB3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMAZAKI_TCEB3_TARGETS_UP.html Genes up-regulated in embryonic stem cells from TCEB3 [GeneID=6924] knockout mice. 12604609 245/290 John Newman 4.36611802555282e-07 1.02629865939289e-06 615 937.363636363636 751 3.96919899277495e-08 297 2.18695070346472 2.42388641873779 1 5.21709368915273 612 1336 440 751 1816 297 1839 823 1529 417 451 342 M15592 NGUYEN_NOTCH1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NGUYEN_NOTCH1_TARGETS_UP.html Genes up-regulated in primary keratinocytes by expression of constantly active NOTCH1 [GeneID=4851]. 16618808 41/56 Kevin Vogelsang 1.79352243181832e-06 2.75567248638752e-06 1200 960.909090909091 753 1.63047626724243e-07 363 2.30582093428957 2.69612637400827 1 5.10561067115189 753 522 1199 1197 2978 386 513 363 877 1336 446 343 M2441 LE_NEURONAL_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LE_NEURONAL_DIFFERENTIATION_DN.html Genes down-regulated during neuronal differentiation of SH-SY5Y cells (neuroblastoma) in response to stimulation by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] and BDNF [GeneID=627]. 19635812 22/25 Arthur Liberzon 4.44995421942997e-06 5.97547195326016e-06 1000 951.181818181818 754 4.04542110946056e-07 115 2.27673549769139 2.48172028009967 1 4.73279846518174 234 754 997 1357 3444 560 1013 350 115 996 643 344 M708 REACTOME_A_TETRASACCHARIDE_LINKER_SEQUENCE_IS_REQUIRED_FOR_GAG_SYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_A_TETRASACCHARIDE_LINKER_SEQUENCE_IS_REQUIRED_FOR_GAG_SYNTHESIS.html Genes involved in A tetrasaccharide linker sequence is required for GAG synthesis 22/26 Reactome 7.89324045091562e-07 1.48566831691645e-06 300 972.454545454545 756 7.17567571171157e-08 300 2.44464292315515 2.86795737517044 1 5.6797890792764 300 756 899 2049 2366 501 643 449 1215 1203 316 345 M10660 YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP.html Genes up-regulated in the uteri of ovariectomized mice 6 h after progesterone [PubChem=5994] injection: HOXA10 [GeneID=3206] knockout vs wild type animals. 12554760 92/127 Kevin Vogelsang 1.68009140583726e-07 7.33971845416521e-07 1790 935.818181818182 757 1.52735594012923e-08 161 2.8459289469657 3.09522418903238 1 6.9708367954032 1788 161 437 329 757 1460 2735 289 1232 859 247 346 M3063 DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN http://www.broadinstitute.org/gsea/msigdb/cards/DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN.html Genes down-regulated in HEK293 cells (embryonic kidney) at 6 h, 12 h or 24 h after infection with reovirus strain T3A (known as a strong inducer of apoptosis). 12885910 434/538 John Newman 9.95902656301583e-08 6.71132834037269e-07 850 900.727272727273 757 9.05366092167642e-09 155 2.06267715202018 2.3076563139195 1 5.07080820537896 849 1196 691 432 307 155 2200 1973 980 757 368 347 M19467 SANA_TNF_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/SANA_TNF_SIGNALING_DN.html Genes down-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by TNF [GeneID=7124]. 15749026 122/138 Yujin Hoshida 3.31767885433883e-07 9.06217835212921e-07 875 870.181818181818 758 3.01607214059709e-08 20 2.22416447995897 2.34360320901445 1 5.35505907988623 871 20 476 758 1506 292 1025 86 3285 489 764 348 M8245 REACTOME_CRMPS_IN_SEMA3A_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CRMPS_IN_SEMA3A_SIGNALING.html Genes involved in CRMPs in Sema3A signaling 26/29 Reactome 1.85396092180119e-06 2.83285708996491e-06 515 910.181818181818 763 1.68542044013957e-07 116 2.77199235986859 3.16636502546078 1 6.13456186372925 514 698 763 823 2998 633 890 116 1341 794 442 349 M521 BROWNE_HCMV_INFECTION_2HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_2HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 2 h time point that were not down-regulated at the previous time point, 1 h. 11711622 67/89 Arthur Liberzon 1.59804463950462e-07 7.31918027928963e-07 980 1067.27272727273 763 1.45276795962184e-08 269 2.46323334225333 2.62479002436241 1 6.0279366809588 978 2187 773 2122 696 393 763 385 2587 587 269 350 M610 REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION.html Genes involved in Extracellular matrix organization 71/134 Reactome 5.92090307925785e-13 1.47087697547879e-11 105 1141.18181818182 764 5.38263916296312e-14 105 2.82258708683416 2.89198516074805 1 12.2462399169935 105 1629 137 709 3971 764 1612 1441 1448 181 556 351 M11581 COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_UP.html Genes up-regulated in pilocytic astrocytoma compared to glioblastoma samples. 16314830 65/104 Jessica Robertson 1.19230919548111e-07 7.06112554001409e-07 1780 1107.45454545455 765 1.08391750918123e-08 256 2.39590965706143 -1.97940884167314 -1 5.87683717597717 1778 256 570 1136 410 765 1554 3740 781 520 672 352 M4034 YEGNASUBRAMANIAN_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/YEGNASUBRAMANIAN_PROSTATE_CANCER.html Genes expressed in at least one prostate cancer cell line but not in normal prostate epithelial cells or stromal cells 18974140 116/278 Leona Saunders 4.65158278951708e-08 4.8147962207282e-07 3405 1497.18181818182 766 4.22871171624372e-09 31 2.31012709458464 -2.54741340320382 -1 5.81912922721456 3405 31 721 82 46 4618 4491 766 244 1166 899 353 M994 REACTOME_DSCAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DSCAM_INTERACTIONS.html Genes involved in DSCAM interactions 15/19 Reactome 5.53183291687328e-08 5.39468003463675e-07 75 781.363636363636 767 5.02893914179048e-09 71 1.86701988922747 -2.08229225946659 -1 4.65627752314363 767 899 1953 816 71 972 496 314 74 2103 130 354 M6724 REACTOME_NA_CL_DEPENDENT_NEUROTRANSMITTER_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NA_CL_DEPENDENT_NEUROTRANSMITTER_TRANSPORTERS.html Genes involved in Na+/Cl- dependent neurotransmitter transporters 10/23 Reactome 1.29841482802363e-07 7.20206492018647e-07 1125 762.454545454545 769 1.18037718604963e-08 408 3.05418000844317 2.63218049564647 1 7.49468909085173 1122 965 769 950 489 905 408 619 559 1152 449 355 M589 GOUYER_TATI_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOUYER_TATI_TARGETS_UP.html Genes up-regulated in constitutively invasive HT-29 5M21 cells (colon cancer) vs those expressing functionally inactive TATI [GeneID=6690]. 18317448 10/14 Jessica Robertson 1.07533010460101e-07 6.98151044527752e-07 1220 677.727272727273 769 9.77572870146985e-09 4 2.5460983240446 -3.23664302397911 -1 6.25340839125968 1219 969 1234 1006 610 769 349 4 310 826 159 356 M1079 REACTOME_APC_CDC20_MEDIATED_DEGRADATION_OF_NEK2A http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_CDC20_MEDIATED_DEGRADATION_OF_NEK2A.html Genes involved in APC-Cdc20 mediated degradation of Nek2A 26/31 Reactome 2.29845734486069e-06 3.40567166137415e-06 530 1757.36363636364 772 2.08950886016835e-07 205 1.25570464609194 1.43864891664872 1 2.71117993586387 528 772 3305 3437 3109 314 205 512 2774 3625 750 357 M16975 NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP.html Up-regulated genes in peripheral zone of human pancreatic cancer growing in the pancreas of nude mice compared to that of the tumor from the central zone. 17699763 373/439 Arthur Liberzon 2.91578605031839e-07 8.63936607501744e-07 185 950 772 2.65071494251299e-08 183 2.08444279309389 2.23732250636701 1 5.03290670702736 183 2026 577 1218 1361 294 559 1331 1559 570 772 358 M4621 ROSS_AML_OF_FAB_M7_TYPE http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_OF_FAB_M7_TYPE.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtype FAB M7 (also known as acute megakaryoblastic leukemia, AMKL). 15226186 94/126 Jean-Pierre Bourquin 3.6199075323549e-07 9.43951209799063e-07 610 775.545454545455 772 3.29082557089014e-08 136 2.13077999213456 2.25760071017617 1 5.11293699728366 772 136 1036 608 1597 508 827 238 1356 846 607 359 M45 PID_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD40_PATHWAY.html CD40/CD40L signaling 18832364 37/44 Pathway Interaction Database 1.18526473153894e-07 7.06112554001409e-07 325 1109.63636363636 773 1.07751345035988e-08 323 1.56520045988303 -1.83878558467443 -1 3.82187278423423 323 577 2244 1078 406 642 738 1396 2822 1207 773 360 M16050 KAYO_AGING_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_AGING_MUSCLE_UP.html Upregulated in the vastus lateralis muscle of aged vs young adult rhesus monkeys 11309484 319/538 John Newman 1.64105414431499e-07 7.3358205358541e-07 1825 1182.81818181818 773 1.49186751520615e-08 403 2.31365326145712 2.70524957994684 1 5.65793346398176 1821 1271 403 773 721 1262 3530 555 1500 644 531 361 M19062 DODD_NASOPHARYNGEAL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DODD_NASOPHARYNGEAL_CARCINOMA_UP.html Genes up-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. 17119049 1758/2621 Arthur Liberzon 3.95530421296359e-32 5.3340102529109e-30 775 1049.36363636364 774 3.95530421296359e-33 23 2.23202270153389 -2.21349486760094 -1 26.2263526035703 774 1067 4318 517 343 172 1511 1121 1253 23 444 362 M2395 SERVITJA_ISLET_HNF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_ISLET_HNF1A_TARGETS_UP.html Genes up-regulated in pancreatic islets upon knockout of HNF1A [GeneID=6927]. 19289501 229/327 Arthur Liberzon 1.11551046061823e-24 9.40215959663935e-23 360 917.818181818182 774 1.01410041874384e-25 34 2.53776837097314 2.84070113628633 1 22.4303350779415 357 1329 34 277 1933 400 1915 932 2102 43 774 363 M10994 BIOCARTA_SRCRPTP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SRCRPTP_PATHWAY.html Activation of Src by Protein-tyrosine phosphatase alpha 17/18 BioCarta 4.36232151686256e-07 1.02591716789194e-06 680 1054 775 3.96574761986903e-08 235 2.22234926491448 2.50294240572722 1 5.30249316737883 677 1894 1730 636 1815 775 564 374 235 2042 852 364 M9387 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION.html Vascular smooth muscle contraction 97/140 KEGG 1.89345845316321e-07 7.49827400961101e-07 1030 793.181818181818 776 1.72132601466017e-08 48 2.59444363672827 3.09456178685346 1 6.34074082056141 1029 133 556 795 897 776 2700 169 746 876 48 365 M2066 WHITFIELD_CELL_CYCLE_LITERATURE http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_LITERATURE.html A list of known cell cycle regulated genes that was compiled from the literature by the authors. 12058064 49/52 Jessica Robertson 1.78554612804071e-08 2.22957082654818e-07 25 1089 776 1.62322376593856e-09 22 2.06697783816454 2.12982890311278 1 5.47931521136061 22 2206 936 1414 4051 150 46 776 565 720 1093 366 M15822 OZANNE_AP1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OZANNE_AP1_TARGETS_UP.html Cancer motility and invasion genes up-regulated by the AP-1 transcription factor. 16799638 26/40 Arthur Liberzon 2.91036480152558e-07 8.62871976331704e-07 780 886.818181818182 777 2.64578653321436e-08 414 2.78633886576827 -2.82874669838918 -1 6.74509049795429 777 674 764 414 1359 807 613 1377 584 1174 1212 367 M16123 EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION.html Muscle development genes up-regulated in Rh4 cells (alveolar rhabdomyosarcoma, ARMS) but not in the RD cells (embryonal rhabdomyosarcoma, ERMS) after knockdown of PAX3-FOXO1 [GeneID=5077;2308] fusion by RNAi for 72 hr. 17525748 59/86 Leona Saunders 9.06279444319417e-07 1.63518309525522e-06 835 1109.36363636364 778 8.23890743324637e-08 225 3.07005787793383 3.82781351581258 1 7.09423830047024 834 363 426 2073 2493 1312 2690 225 655 778 354 368 M4717 LI_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_CISPLATIN_RESISTANCE_UP.html Genes consistently up-regulated in ACRP cells (ovarian cancer, resistant to cisplatin [PubChem=2767]) compared to the parental sensitive A2780 cells, regardless of cisplatin exposure. 17072341 58/69 Arthur Liberzon 4.53073108613604e-08 4.72308272613136e-07 295 883.272727272727 778 4.11884652676632e-09 292 2.72610545465919 3.01077878428472 1 6.88513118667224 292 337 328 813 2437 778 1848 890 1230 452 311 369 M11266 KEGG_LYSOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSOSOME.html Lysosome 120/155 KEGG 2.97634197941852e-07 8.70294688256627e-07 295 1354.18181818182 781 2.70576580189342e-08 40 1.38887860018355 -1.47683746246845 -1 3.33498467940732 295 40 3732 2403 1377 109 655 781 1396 3872 236 370 M6813 IVANOVA_HEMATOPOIESIS_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL.html Genes in the expression cluster 'HSC Shared': up-regulated in hematopoietic stem cells (HSC) from adult bone marrow and fetal liver. 12228721 340/530 John Newman 1.86324188170522e-07 7.48468228225416e-07 1490 1061.54545454545 782 1.69385639955312e-08 357 2.1731314130232 2.48244307035741 1 5.30362971547545 1490 1247 434 752 878 712 2751 782 1671 357 603 371 M13135 ENGELMANN_CANCER_PROGENITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ENGELMANN_CANCER_PROGENITORS_UP.html Up-regulated genes in the cancer progenitor (stem) cells corresponding to side population (SP) MCF7 cells (breast cancer) positive for MUC1 [GeneID=4582]. 18381450 58/66 Jessica Robertson 8.09590288227326e-08 6.29674606547497e-07 4270 1598.90909090909 783 7.35991198199901e-09 58 2.37959825910207 2.13469293297762 1 5.88410423629308 4267 314 783 58 191 4466 3388 1254 231 647 1989 372 M1404 LEI_HOXC8_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEI_HOXC8_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) by overexpression of HOXC8 [GeneID=3224]. 15699330 26/30 Kate Stafford 7.27715015378218e-07 1.40431223245242e-06 4280 1906.09090909091 785 6.61559323719615e-08 470 3.3576998882738 -2.5627320831557 -1 7.85286576516185 4278 709 470 733 2299 3968 2746 785 483 651 3845 373 M10371 BENPORATH_ES_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_WITH_H3K27ME3.html Set 'H3K27 bound': genes posessing the trimethylated H3K27 (H3K27me3) mark in their promoters in human embryonic stem cells, as identified by ChIP on chip. 18443585 889/1630 Jessica Robertson 4.04420333793467e-69 3.18143995917527e-66 790 1087.63636363636 788 4.04420333793472e-70 3 2.75186745955854 3.07861828180528 1 72.4356182231239 788 1084 4453 216 443 50 2128 1144 1156 3 499 374 M18153 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 9. 12554760 77/91 Arthur Liberzon 2.88204320369847e-07 8.58790651607119e-07 500 1013.72727272727 788 2.62003961931987e-08 244 1.9879089423678 -2.10116303230716 -1 4.79958177238261 496 244 1896 2281 1350 302 652 788 891 1555 696 375 M11640 LEE_LIVER_CANCER_CIPROFIBRATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_CIPROFIBRATE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by ciprofibrate [PubChem=2763]. 15565109 57/117 Yujin Hoshida 2.03927201339103e-06 3.07716237314758e-06 800 1409.27272727273 790 1.85388536698182e-07 408 2.96126696954318 -2.91060443412591 -1 6.51406865503161 800 408 563 2567 3044 551 751 2041 3328 790 659 376 M2176 ROY_WOUND_BLOOD_VESSEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROY_WOUND_BLOOD_VESSEL_DN.html Genes down-regulated in blood vessel cells from wound site. 17728400 38/64 Leona Saunders 9.30567527614664e-07 1.6643723873972e-06 850 944.363636363636 792 8.45970837482932e-08 32 3.09952172133959 -2.91935429792965 -1 7.15322475623376 847 511 449 292 2517 910 917 2728 32 792 393 377 M16130 RICKMAN_HEAD_AND_NECK_CANCER_C http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_C.html Cluster c: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 120/231 Jessica Robertson 1.09394652863104e-24 9.38805020934277e-23 580 952.545454545455 792 9.94496844210036e-26 16 3.46471706583556 3.79532081944793 1 30.6424549196838 576 16 33 705 1184 792 1689 1174 2594 122 1593 378 M16478 LEE_TARGETS_OF_PTCH1_AND_SUFU_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_TARGETS_OF_PTCH1_AND_SUFU_DN.html Genes down-regulated in medulloblastoma tumors from animals with inactivating mutations of one copy of PTCH1 or SUFU [GeneID=5727;51684] in conjunction with TP53 [GeneID=7157] loss. 17452975 112/167 Jessica Robertson 1.76812260728315e-09 2.70959048908326e-08 1350 948.545454545455 793 1.60738418973106e-10 60 2.50361356616968 2.96348015542666 1 7.5689494946367 1346 60 238 565 1055 1170 2122 793 2277 229 579 379 M1430 BROWN_MYELOID_CELL_DEVELOPMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWN_MYELOID_CELL_DEVELOPMENT_UP.html Genes defining differentiation potential of the bipotential myeloid cell line FDB. 16769770 167/326 Kevin Vogelsang 7.13095045970408e-08 6.06397110828564e-07 1045 1060.63636363636 794 6.48268244622047e-09 125 2.34290310291817 -2.45448262561883 -1 5.8080093334372 1041 2080 607 1378 144 794 1753 125 2656 343 746 380 M1869 VILIMAS_NOTCH1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VILIMAS_NOTCH1_TARGETS_UP.html Genes up-regulated in bone marrow progenitors by constitutively active NOTCH1 [GeneID=4851]. 17173050 44/80 Jessica Robertson 2.2235577181716e-07 7.8190759646174e-07 490 966.727272727273 794 2.02141631173491e-08 219 2.18512940926549 -2.15283499317303 -1 5.31650668268482 433 490 794 1405 1063 486 219 830 3044 500 1370 381 M5369 POOLA_INVASIVE_BREAST_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/POOLA_INVASIVE_BREAST_CANCER_UP.html Genes up-regulated in atypical ductal hyperplastic tissues from patients with (ADHC) breast cancer vs those without the cancer (ADH). 15864312 286/518 Jessica Robertson 4.1602732491828e-33 6.33435152778801e-31 275 829.090909090909 794 3.78206659016618e-34 16 2.58401527963887 2.60371099233175 1 31.3317877850614 271 1265 16 521 966 440 814 794 2852 28 1153 382 M2606 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_6HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_6HR.html Cell cycle genes significantly (p =< 0.05) changed in fibroblast cells at 6 h after exposure to ionizing radiation. 17404513 98/110 Itai Pashtan 8.99913391943929e-11 1.70585992368488e-09 10 1006.90909090909 795 8.18103083618853e-12 7 1.91878724264346 1.89171210928077 1 6.71594458961992 7 1578 795 1770 3713 99 36 682 1036 251 1109 383 M17937 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_DN.html Top 100 probe sets contrubuting to the negative side of the 1st principal component; predominantly associated with synovial sarcoma and myxoid/round cell liposarcoma samples. 17464315 105/190 Nikolaos Papanikolaou 2.97744908979472e-16 1.15193112326484e-14 325 975.090909090909 797 2.70677189981337e-17 35 2.82129121764084 3.24948270538263 1 15.7648792172284 322 35 84 707 2799 797 2497 1000 1478 156 851 384 M77 PID_WNT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_SIGNALING_PATHWAY.html Wnt signaling network 18832364 28/34 Pathway Interaction Database 1.80749901357293e-06 2.7744375102648e-06 690 1149.45454545455 798 1.64318227145326e-07 223 2.84225176685777 2.95154487727108 1 6.30166203360736 686 712 907 2090 2981 315 223 1705 1524 798 703 385 M2438 TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA.html Genes whose DNA methylation differed between primary ALL cells (acute lymphoblastic leukemia) and normal peripheral blood samples. 17363581 108/146 Jessica Robertson 1.33971078192603e-07 7.20206492018647e-07 500 1209.63636363636 800 1.21791896682635e-08 111 1.89959723113566 2.04984189116081 1 4.64252878003102 500 111 1752 2195 519 253 800 1653 2184 2731 608 386 M2440 LE_NEURONAL_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LE_NEURONAL_DIFFERENTIATION_UP.html Genes up-regulated during neuronal differentiation of SH-SY5Y cells (neuroblastoma) in response to stimulation by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] and BDNF [GeneID=627]. 19635812 20/34 Arthur Liberzon 1.20500493359907e-07 7.07415831665123e-07 1200 892.909090909091 801 1.09545909054613e-08 5 3.00893656192098 3.21864015315989 1 7.39234156620217 1196 801 670 1132 1077 1369 2530 5 342 604 96 387 M9694 REACTOME_ACTIVATION_OF_THE_PRE_REPLICATIVE_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_THE_PRE_REPLICATIVE_COMPLEX.html Genes involved in Activation of the pre-replicative complex 30/30 Reactome 1.36364509703692e-06 2.21890986133675e-06 45 1279.27272727273 802 1.23967812934331e-07 17 1.49618976197912 1.49618976197912 1 3.35194794455719 44 637 2317 1866 4031 147 17 729 2201 802 1281 388 M1296 BIOCARTA_IL7_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL7_PATHWAY.html IL-7 Signal Transduction 25/27 BioCarta 6.58159783800129e-07 1.31687756656914e-06 840 1015.45454545455 803 5.98327255179655e-08 171 2.13812458351329 -2.1259172366031 -1 5.00639938448452 839 766 1899 171 2209 803 492 214 386 2162 1229 389 M16114 SIMBULAN_UV_RESPONSE_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_UV_RESPONSE_NORMAL_DN.html Genes down-regulated in HFK cells (primary keratinocytes) in response to UVB irradiation. 16007217 54/56 Leona Saunders 1.4139223845864e-07 7.20206492018647e-07 950 699.363636363636 804 1.28538406859824e-08 318 2.48674000373753 2.59092613601709 1 6.09294476207564 950 411 822 842 575 318 1084 397 804 866 624 390 M1577 BURTON_ADIPOGENESIS_3 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_3.html Strongly up-regulated at 16-24 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 132/152 John Newman 4.24465869353235e-08 4.58360044171859e-07 30 909.727272727273 804 3.8587807049349e-09 27 2.06114991374857 2.16561966715844 1 5.20428648753932 27 1515 804 1370 3409 92 112 558 992 293 835 391 M662 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE.html Genes involved in Synthesis of PIPs at the plasma membrane 33/36 Reactome 6.45491381697964e-07 1.30536389100874e-06 805 1248.54545454545 805 5.86810519171412e-08 74 1.62519442864464 -1.75237133876964 -1 3.79586695260253 805 636 2365 1886 2180 582 963 605 484 3154 74 392 M18876 MAHADEVAN_IMATINIB_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_IMATINIB_RESISTANCE_UP.html Top genes up-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] compared to the parental cell line sensitive to the drug. 17325667 20/31 Arthur Liberzon 1.0656554865989e-06 1.83706862554669e-06 750 932.181818181818 805 9.68778184355362e-08 79 3.59362739280316 3.42663795724851 1 8.23955851026934 750 816 474 805 2614 630 962 148 1994 982 79 393 M19837 RICKMAN_HEAD_AND_NECK_CANCER_E http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_E.html Cluster e: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 87/189 Jessica Robertson 6.84328444867633e-16 2.42416750495948e-14 475 776.363636363636 805 6.22116768061484e-17 93 3.03736980312868 -3.14863980289321 -1 16.5814054574545 473 146 93 922 676 1227 1016 805 1466 191 1525 394 M5880 NABA_ECM_AFFILIATED http://www.broadinstitute.org/gsea/msigdb/cards/NABA_ECM_AFFILIATED.html Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins 22159717 89/185 Alexandra Naba 1.92504144268039e-10 3.52447873537516e-09 955 827.818181818182 805 1.75003767531712e-11 131 2.77405171618376 2.72631554989485 1 9.38016928506768 953 131 200 691 999 805 1477 469 1844 270 1267 395 M12848 CASTELLANO_NRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_NRAS_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) isolated from NRAS [GeneID=4893] knockout mice. 16909116 22/24 Leona Saunders 7.7139101541785e-07 1.46053505392834e-06 205 916.363636363636 806 7.01264805356885e-08 76 2.14553683705714 2.23984653792785 1 4.9851290366968 201 806 1294 1214 2348 110 146 76 2567 1204 114 396 M1180 OHASHI_AURKA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OHASHI_AURKA_TARGETS.html Candidate substrate proteins of AURKA [GeneID=6790]. 16785988 8/8 Arthur Liberzon 8.81320070049557e-05 9.71696036120978e-05 725 1793.81818181818 806 8.81355024628596e-06 91 2.08916033974313 2.08916033974313 1 3.32116019071593 724 2465 4380 2369 4316 503 91 806 662 2664 752 397 M977 REACTOME_KINESINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KINESINS.html Genes involved in Kinesins 28/32 Reactome 2.64706887411313e-07 8.3155405373626e-07 280 940.727272727273 807 2.40642653873817e-08 51 2.0705415754794 2.38761507846499 1 5.01282391297952 279 1813 1758 2296 1254 51 64 232 807 1638 156 398 M11615 CHANDRAN_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_DN.html Genes down-regulated in metastatic tumors from the whole panel of patients with prostate cancer. 17430594 387/480 Arthur Liberzon 1.13134582717921e-13 3.23633472987022e-12 965 745.818181818182 810 1.02849620652661e-14 122 2.4001256900664 2.85811419692825 1 11.0405017073198 961 1218 122 1127 256 218 1816 810 1078 291 307 399 M1171 RASHI_NFKB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_NFKB1_TARGETS.html Known and putative targets of NFKB1 [GeneID=4790] identified among the ATM [GeneID=472] dependent, late responders to ionizing radiation. 16314843 28/29 Arthur Liberzon 1.30970284287232e-06 2.1509385589274e-06 115 1201 811 1.19063965687689e-07 113 2.47461874893677 -2.55841495971444 -1 5.59011307166538 113 729 932 2441 2760 278 113 358 3690 986 811 400 M1246 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_DN.html Genes down-regulated in Wilm's tumor vs fetal kidney. 15531917 89/104 Arthur Liberzon 7.11732129533911e-12 1.54809937852537e-10 405 1030.18181818182 812 6.47029208669284e-13 140 2.83636158965897 2.90343048635113 1 11.1402224486258 401 140 164 395 3082 1061 2112 1400 1544 221 812 401 M16673 VALK_AML_CLUSTER_16 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_16.html Top 40 genes from cluster 16 of acute myeloid leukemia (AML) expression profile; 81% of the samples are FAB M5 subtype, 45% have 11q23 abnormalities. 15084694 23/39 Jessica Robertson 1.29916919423822e-07 7.20206492018647e-07 780 1093.09090909091 812 1.18106297359841e-08 65 2.20130450183725 2.6267088009433 1 5.3878348073631 779 812 1670 2767 491 597 467 1745 1041 1590 65 402 M13867 ONDER_CDH1_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_2_UP.html Genes up-regulated in HMLE cells (immortalized nontransformed mammary epithelium) after E-cadhedrin (CDH1) [GeneID=999] knockdown by RNAi. 18483246 369/443 Jessica Robertson 3.71589206466245e-26 3.50780210904135e-24 1120 1000.90909090909 814 3.37808369514767e-27 29 2.60479158769498 2.73293100952266 1 24.5201475971158 159 2025 29 1116 2609 483 1118 628 1955 74 814 403 M2840 CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP.html Genes up-regulated in luminal-like breast cancer cell lines compared to the basal-like ones. 16288205 502/589 Arthur Liberzon 2.7668251720406e-07 8.4037418352842e-07 1355 1185.09090909091 817 2.76682551653013e-08 50 2.011653937862 -1.86910701764264 -1 4.86512557446176 1352 1168 4292 50 1405 553 1868 817 753 712 66 404 M12705 SIG_CD40PATHWAYMAP http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CD40PATHWAYMAP.html Genes related to CD40 signaling 33/36 Signaling Gateway 2.34842662855019e-07 7.98113405922816e-07 600 1432.45454545455 820 2.13493352657904e-08 413 1.38368379845503 -1.40032053240413 -1 3.34324776164831 597 640 3161 2464 1129 413 700 820 2817 2525 491 405 M1541 DELASERNA_MYOD_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELASERNA_MYOD_TARGETS_DN.html Genes down-regulated in NIH 3T3 cells (fibroblasts) 24 h after inducing MyoD [GeneID=4654] differentiation program. 15870273 117/154 John Newman 2.59187336175916e-07 8.27068974676848e-07 765 1079.72727272727 820 2.35624878828555e-08 45 2.40295505235417 2.72144924285522 1 5.82790676536807 761 45 376 797 2486 892 2460 1338 1270 632 820 406 M1759 WANG_LSD1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LSD1_TARGETS_UP.html Genes up-regulated after Cre-lox knockout of LSD1 [GeneID=23028] in pituitary. 17392792 24/34 Jessica Robertson 8.96494609175604e-07 1.62186836155954e-06 825 913.727272727273 821 8.14995431359243e-08 38 2.45857264375962 3.02073810911271 1 5.67477302667587 821 720 862 1141 2485 1056 1902 38 241 641 144 407 M1469 BIOCARTA_LYM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LYM_PATHWAY.html Adhesion and Diapedesis of Lymphocytes 10/14 BioCarta 3.49195191860205e-06 4.84195448172786e-06 730 1384.09090909091 824 3.17450678292554e-07 100 2.37184298417933 2.11661069647632 1 5.01973177280358 730 1001 1201 3363 3331 434 100 293 3496 824 452 408 M1229 OXFORD_RALB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALB_TARGETS_UP.html Genes up-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALB [GeneID=5899] by RNAi. 17496927 26/28 Arthur Liberzon 1.1631896007304e-06 1.96220690330504e-06 125 1424.18181818182 826 1.05744565066857e-07 124 3.45631973741027 3.34595545148237 1 7.88304326959041 124 1814 412 826 4264 930 2365 2789 803 650 689 409 M912 MUELLER_METHYLATED_IN_GLIOBLASTOMA http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_METHYLATED_IN_GLIOBLASTOMA.html Genes up-regulated in short-term cultured glioblastomas after azacitidine [PubChem=9444] treatment. 16909125 46/104 Leona Saunders 1.3263223019236e-07 7.20206492018647e-07 3200 1602.45454545455 827 1.20574761989463e-08 328 2.81549322484688 -2.81806979462772 -1 6.90506227130194 3200 440 365 328 505 3773 2790 3899 827 442 1058 410 M10010 VALK_AML_WITH_FLT3_ITD http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_FLT3_ITD.html Genes that best predicted acute myeloid leukemia (AML) with internal tandem duplications (IDT) in FLT3 [GeneID=2322]. 15084694 58/73 Jessica Robertson 6.56918080233062e-06 8.4124299247111e-06 585 1451.27272727273 827 5.97200037993561e-07 528 2.48777443645769 2.56125556455833 1 5.02751532914244 583 1669 528 827 3622 683 1624 2975 2307 563 583 411 M17372 LEE_LIVER_CANCER_MYC_TGFA_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_TGFA_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) tissue of MYC and TGFA [GeneID=4609;7039] double transgenic mice. 15565109 60/113 Yujin Hoshida 2.31533270196959e-07 7.95369021346178e-07 745 1152 828 2.10484813240072e-08 344 2.5067089221197 -2.56682523651287 -1 6.09881294673686 1289 344 681 1639 1107 743 828 1435 3146 743 717 412 M10381 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN.html Genes down-regulated in transformed NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845]) vs normal cells. 16607279 215/252 Lauren Kazmierski 1.39146405199428e-07 7.20206492018647e-07 800 1108.63636363636 829 1.26496740000192e-08 447 2.13603341288697 2.29153460522546 1 5.22659594861089 798 1380 616 447 560 829 1965 1996 2259 454 891 413 M4913 IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_DN.html Genes down-regulated in adipose tissue mesenchymal stem cells (ASC) vs bone marrow mesenchymal stem cells (rBMSC) 18519682 192/245 Leona Saunders 3.40807620551766e-09 4.9495752892441e-08 685 1348.45454545455 829 3.09825110072473e-10 252 2.44223526181625 2.63817343269891 1 7.12516360593062 684 2067 252 811 2200 921 2384 783 3504 398 829 414 M8697 NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_UP.html Top 20 genes whose up-regulation correlated with gastrointestinal stromal tumors (GIST) and synovial sarcoma compared to other tumors. 11965276 44/52 John Newman 2.63549491511559e-06 3.79601342671516e-06 160 1387.72727272727 831 2.39590733847082e-07 157 2.68168536209623 2.55313103982745 1 5.79600071642414 157 1714 439 831 3984 596 895 2925 2776 378 570 415 M10967 VICENT_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VICENT_METASTASIS_UP.html The metastasis gene signature: genes up-regulated during metastasis of NSCLC (non-small cell lung carcinoma) tumors to bone. 18381434 20/23 Jessica Robertson 7.75027654893975e-08 6.27525965386533e-07 240 888.636363636364 831 7.04570620179145e-09 61 2.4838517376757 2.49941505256672 1 6.1455700087778 1344 831 1736 109 170 1259 1967 240 61 1821 237 416 M2302 VANDESLUIS_COMMD1_TARGETS_GROUP_4_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_4_DN.html Genes down-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout and in normal 8.5 dpc embryos compared to normal 9.5 dpc embryos. 17371845 27/41 Arthur Liberzon 3.09869782092137e-06 4.37506841601821e-06 140 1475.09090909091 831 2.81700198676617e-07 138 2.8497799316416 2.73308259302394 1 6.0917811104326 138 2312 447 798 4227 831 1636 2685 2127 487 538 417 M19957 FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP.html Genes up-regulated in genomically unstable Ewing's sarcoma tumors compared to the stable ones. 17952124 245/318 Jessica Robertson 9.66558927324295e-07 1.71252182318719e-06 130 1201.36363636364 833 8.78690319979414e-08 128 1.76180215627772 1.90940099140313 1 4.03560037792555 128 1345 1997 1830 2542 385 493 701 2204 833 757 418 M6768 REACTOME_E2F_MEDIATED_REGULATION_OF_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_E2F_MEDIATED_REGULATION_OF_DNA_REPLICATION.html Genes involved in E2F mediated regulation of DNA replication 38/40 Reactome 2.89454098803163e-06 4.10277281186466e-06 135 972.272727272727 834 2.6314043603523e-07 119 1.8339662848924 1.84524831273316 1 3.92309242862145 131 524 1750 1030 3258 128 119 834 393 1279 1249 419 M1588 MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_4 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_4.html Cluster 4: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate and sulindac [PubChem=5222465;5352]. 10969808 25/34 John Newman 2.03927608434198e-07 7.66608353710733e-07 815 1118.18181818182 835 1.85388752124674e-08 269 1.65727635960395 1.59712517236696 1 4.02585172272844 811 778 2573 2149 968 606 577 269 835 1871 863 420 M7890 WAESCH_ANAPHASE_PROMOTING_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/WAESCH_ANAPHASE_PROMOTING_COMPLEX.html Subunits of the anaphase promoting complex (APC). 15637585 16/18 Leona Saunders 9.35214102471895e-07 1.67141634368321e-06 840 1510.18181818182 836 8.50195000026491e-08 96 1.5621534604823 1.61054395959478 1 3.57924180970446 836 1908 2687 3440 2519 290 96 319 540 3558 419 421 M393 VANTVEER_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_ESR1_UP.html Up-regulated genes from the optimal set of 550 markers discriminating breast cancer samples by ESR1 [GeneID=2099] expression: ER(+) vs ER(-) tumors. 11823860 217/252 Arthur Liberzon 1.80330889301183e-07 7.47800341964416e-07 400 744.909090909091 836 1.63937185529685e-08 61 1.8897679565964 -1.7965294991771 -1 4.60583794056551 398 1367 1284 939 836 61 527 1173 495 930 184 422 M1039 REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B.html Genes involved in APC/C:Cdc20 mediated degradation of Cyclin B 27/32 Reactome 1.78608818860974e-06 2.74872391595631e-06 2940 1541.18181818182 837 1.62371785332896e-07 204 1.44662709442692 1.66373286632388 1 3.18515366546735 448 746 2936 2940 2972 281 204 611 1285 3693 837 423 M2700 SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN.html Genes down-regulated in bone relapse of breast cancer. 18451135 400/649 Jessica Robertson 5.93975302863785e-31 7.57719845815423e-29 1455 927.636363636364 838 5.39977548057988e-32 19 2.67617248651026 2.83645048828857 1 30.2147525100172 1455 1197 19 251 490 1002 3035 757 1113 47 838 424 M2171 FIGUEROA_AML_METHYLATION_CLUSTER_4_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_4_DN.html Cluster 4 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 21/34 Arthur Liberzon 8.11728389304714e-08 6.30157565381291e-07 1000 797 839 7.37934926595318e-09 38 2.7956835747968 3.41334245320846 1 6.92134581383115 998 839 1326 458 193 1018 868 536 188 2305 38 425 M14981 REACTOME_GAP_JUNCTION_ASSEMBLY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_ASSEMBLY.html Genes involved in Gap junction assembly 7/18 Reactome 1.94049307713354e-06 2.946004285645e-06 575 1244.36363636364 841 1.94049477161664e-07 270 4.08990469472223 3.99883374198812 1 9.04698337441294 573 1019 4271 1122 3066 423 270 584 473 841 1046 426 M8696 VALK_AML_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_7.html Top 40 genes from cluster 7 of acute myeloid leukemia (AML) expression profile; 61% of the samples are FAB M1 or M2 subtype. 15084694 33/47 Jessica Robertson 8.63025323009929e-08 6.48643236402367e-07 1825 913.636363636364 843 7.8456850624096e-09 28 2.56320948353034 -2.32908066062305 -1 6.32869910116558 1824 597 896 303 217 1026 843 3038 28 1235 43 427 M1555 RUAN_RESPONSE_TO_TNF_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_DN.html Adipocyte abundant genes down-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to TNF [GeneID=7124]. 12732648 104/126 John Newman 4.57855366707567e-08 4.74962050738399e-07 845 747.363636363636 845 4.16232160214796e-09 45 1.90788680949329 -1.62877000822845 -1 4.80172907034844 845 82 1519 1167 45 251 436 1100 1194 1272 310 428 M1349 SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_DN.html Genes down-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 12 h. 18794802 67/94 Jessica Robertson 6.50727811069059e-07 1.30791290081906e-06 720 1297.18181818182 846 5.91570912313549e-08 384 2.54626356654928 2.52682171905216 1 5.97464234326949 719 2634 771 1421 2194 384 793 846 2967 586 954 429 M4065 ZHU_CMV_24_HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_24_HR_DN.html Down-regulated at 24 h following infection of primary human foreskin fibroblasts with CMV 9826724 136/180 John Newman 4.78483797420325e-09 6.72155810661885e-08 285 1271.90909090909 847 4.34985271328174e-10 263 2.64331692253013 3.1652837141449 1 7.57465415110195 285 2096 263 803 3318 937 2176 847 2355 645 266 430 M11884 GOLDRATH_ANTIGEN_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/GOLDRATH_ANTIGEN_RESPONSE.html Genes up-regulated at the peak of an antigen response of naive CD8+ [GeneID=925;926] T-cells. 15548615 401/541 Arthur Liberzon 2.5095371971032e-10 4.50380820164528e-09 605 1088 849 2.28139745217223e-11 155 1.83691465091913 1.96375399026469 1 6.11576907003753 602 1205 849 573 1983 389 623 1438 2666 155 1485 431 M7617 BENPORATH_EED_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_EED_TARGETS.html Set 'Eed targets': genes identified by ChIP on chip as targets of the Polycomb protein EED [GeneID=8726] in human embryonic stem cells. 18443585 848/1581 Jessica Robertson 5.01283466905828e-43 1.47878622737219e-40 680 1075.81818181818 852 5.01283466905828e-44 9 2.69494679363699 2.95150197011013 1 43.1179886106659 679 1092 4452 225 907 65 1709 852 1394 9 450 432 M15285 BIOCARTA_NFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NFKB_PATHWAY.html NF-kB Signaling Pathway 28/37 BioCarta 4.05858475595083e-07 9.97185221109921e-07 215 1028.81818181818 854 3.68962318607574e-08 188 1.91266754013045 -2.03412364050377 -1 4.56611366288598 215 722 2066 1909 1723 188 195 222 1830 1393 854 433 M18597 BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_AND_PAX3 http://www.broadinstitute.org/gsea/msigdb/cards/BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_AND_PAX3.html Genes up-regulated in SaOS-2 cells (osteosarcoma) upon expression of PAX3-FOXO1 [GeneID=5077;2308] but down-regulated by PAX3 expression off adenoviral vectors. 15688035 9/10 Leona Saunders 3.16152647292966e-07 8.94262307705344e-07 855 1217.54545454545 854 3.16152692271599e-08 42 4.35262568668165 4.55644579711344 1 10.5376762609945 851 1009 4383 360 1544 770 1409 854 42 1318 853 434 M2895 MARKEY_RB1_CHRONIC_LOF_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_CHRONIC_LOF_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) isolated from RB1 [GeneID=5925] knockout mice: chronic loss of function (LOF) of RB1. 17452985 148/168 Arthur Liberzon 3.71476196108507e-07 9.54993271041478e-07 410 1105.72727272727 855 3.37705689848476e-08 378 1.97032145460297 2.13529996247655 1 4.7201366999975 406 1522 1235 1625 1627 378 450 727 2494 844 855 435 M5315 TAKAYAMA_BOUND_BY_AR http://www.broadinstitute.org/gsea/msigdb/cards/TAKAYAMA_BOUND_BY_AR.html Genes whose promoters bound AR [GeneID=367] in LNCaP cells (prostate cancer) after exposure to the synthetic androgen R1881 [PubChem=13766], based on ChIP-chip analysis. 17297473 15/26 Leona Saunders 3.94239090636449e-07 9.80113872773632e-07 2185 1309.45454545455 855 3.58399237530862e-08 115 2.93965437142819 3.5025945368863 1 7.05357336450828 2185 855 658 754 1693 2505 2447 115 358 617 2217 436 M5624 KIM_MYCL1_AMPLIFICATION_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCL1_AMPLIFICATION_TARGETS_DN.html Genes negatively correlated with amplifications of MYCL1 [GeneID=4610] in SCLC (small cell lung cancer) cell lines. 16116477 32/37 Arthur Liberzon 1.29048342316005e-07 7.20206492018647e-07 1560 1023.81818181818 855 1.17316681714333e-08 406 2.02092910160534 1.86797940367776 1 4.94225431915456 1557 641 2240 1022 481 855 806 944 730 1580 406 437 M1116 CAIRO_PML_TARGETS_BOUND_BY_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_PML_TARGETS_BOUND_BY_MYC_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) after knockout of PML [GeneID=5371] and whose promoters were bound by MYC [GeneID=4609]. 15735755 31/35 Lauren Kazmierski 6.30633929570533e-07 1.28025468712814e-06 440 1146.90909090909 856 5.73303736675406e-08 384 2.38849438901111 2.66047419126817 1 5.6102632000425 437 680 1474 1511 2170 404 384 856 734 2944 1022 438 M1120 JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP.html Genes up-regulated in brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 77/90 Arthur Liberzon 1.55587071951138e-07 7.2854263850136e-07 835 908.636363636364 856 1.41442802685885e-08 253 2.18575165223855 2.41263189646939 1 5.34502135861273 831 253 1435 1440 670 968 856 331 627 1554 1030 439 M16003 LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_DN.html Top genes associated with unfavorable overall survival of mesothelioma patients after surgery. 16540645 37/40 Arthur Liberzon 8.27394799004706e-06 1.03836837311944e-05 200 1232.54545454545 856 7.52179918871046e-07 197 2.60905250926298 2.961161325986 1 5.17911020096977 197 1747 519 856 3702 528 1121 2292 1642 744 210 440 M18359 RODRIGUES_DCC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_DCC_TARGETS_UP.html Genes up-regulated in HCT8/S1 cells (colon cancer) which normally lack DCC [GeneID=9423] compared to those stably expressing wild type DCC off a plasmid vector. 17334389 7/7 Arthur Liberzon 3.0352956273611e-08 3.52004800028117e-07 2595 1283.18181818182 857 3.03529566881968e-09 3 3.73616855195039 -4.01556217978348 -1 9.64655565706877 2595 1023 4297 278 16 3166 857 11 3 1808 61 441 M1721 LEIN_PONS_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_PONS_MARKERS.html Top 100 ranked genes most specific to pons region (P) of the adult mouse brain. 17151600 109/143 Jessica Robertson 7.86785444829269e-08 6.28391550069647e-07 1155 862.636363636364 857 7.15259520879143e-09 62 2.27838304999973 2.34117972010536 1 5.63250971106278 1154 62 549 958 178 710 2197 857 1349 459 1016 442 M10427 TSENG_IRS1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_IRS1_TARGETS_UP.html Up-regulated in brown preadipocytes with IRS1 [GeneID=3667] knockout vs wild type controls; the knockouts have severe defects in adipocyte differentiation. 15895078 155/177 John Newman 5.81109315664277e-07 1.21525740803517e-06 700 1235.27272727273 858 5.28281335598997e-08 608 2.36142277570011 2.68334193712579 1 5.567597673748 696 2543 608 807 2097 858 1747 1279 1365 837 751 443 M1974 MIKKELSEN_IPS_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 12/30 Jessica Robertson 9.59780675787446e-08 6.64473403617636e-07 670 841.818181818182 858 8.72527925144744e-09 3 3.28587288239052 3.38001162437242 1 8.11326252788518 666 959 858 2062 980 663 1022 3 485 1550 12 444 M509 REACTOME_DEVELOPMENTAL_BIOLOGY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEVELOPMENTAL_BIOLOGY.html Genes involved in Developmental Biology 398/520 Reactome 1.20749489026588e-07 7.07997003981982e-07 990 964.636363636364 861 1.09772268776419e-08 371 2.17260120847374 2.53879593975047 1 5.3234172301479 990 1208 371 427 425 861 2518 1211 1400 493 707 445 M1350 SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP.html Genes up-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 48 h. 18794802 601/800 Jessica Robertson 2.3688595878025e-25 2.19235632439761e-23 695 1189.90909090909 861 2.36885958780251e-26 7 2.44219592802345 -2.33309416118794 -1 22.2047578947744 1164 1119 4442 7 499 695 1673 1902 693 34 861 446 M2000 MIKKELSEN_ES_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 K27 trimethylation mark (H327me3) in embryonic stem cells (ES). 17603471 39/81 Arthur Liberzon 7.34823654498882e-07 1.41105274582373e-06 145 906.272727272727 861 6.68021727216362e-08 142 2.54079797326455 2.42565853397096 1 5.9280268491202 291 1734 976 1592 2311 145 936 454 527 861 142 447 M808 REACTOME_CYCLIN_A_B1_ASSOCIATED_EVENTS_DURING_G2_M_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYCLIN_A_B1_ASSOCIATED_EVENTS_DURING_G2_M_TRANSITION.html Genes involved in Cyclin A/B1 associated events during G2/M transition 16/17 Reactome 2.87261378878213e-06 4.08149821885962e-06 160 882.272727272727 862 2.61147049059742e-07 87 2.36259767909633 2.4355468752253 1 5.07047199362179 156 862 1163 1035 3248 169 87 596 220 1224 945 448 M1158 CROSBY_E2F4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CROSBY_E2F4_TARGETS.html Putative E2F4 [GeneID=1874] target genes identified as mitotic genes down-regulated in the LNCaP C4-2 cells (prostate cancer) at both 6 and 24 h following irradiation. 17043659 10/10 Leona Saunders 1.39428600028318e-06 2.25999006138431e-06 865 1046 864 1.26753353085048e-07 167 2.16716197538784 2.22868095828123 1 4.87063809825112 864 976 1760 624 2800 841 167 311 457 1563 1143 449 M1348 SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP.html Genes up-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 12 h. 18794802 178/214 Jessica Robertson 1.39360529277251e-10 2.59992766082461e-09 1260 1038.09090909091 864 1.26691390260072e-11 149 2.53261564821921 2.89614918621055 1 8.69400410510979 1260 1438 197 149 1648 864 3003 444 1357 394 665 450 M13398 OHM_EMBRYONIC_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/OHM_EMBRYONIC_CARCINOMA_DN.html Genes with low to medium basal transcription state in undifferentiated embryonic carcinoma cells. 17211412 11/14 Leona Saunders 3.20018238185281e-06 4.4914840447057e-06 870 1180.90909090909 870 2.9092609426712e-07 86 3.49528211475975 3.49528211475975 1 7.46692953720607 867 972 1353 1650 3286 708 870 272 86 2746 180 451 M606 REACTOME_AMINE_COMPOUND_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINE_COMPOUND_SLC_TRANSPORTERS.html Genes involved in Amine compound SLC transporters 15/33 Reactome 5.75360083021003e-08 5.54224406501864e-07 2495 1554.45454545455 871 5.23054634607491e-09 76 2.92753499672396 2.72313551846424 1 7.31578638877789 2494 871 628 545 76 1676 505 3094 3472 616 3122 452 M9719 CAVARD_LIVER_CANCER_MALIGNANT_VS_BENIGN http://www.broadinstitute.org/gsea/msigdb/cards/CAVARD_LIVER_CANCER_MALIGNANT_VS_BENIGN.html Genes identified by subtractive hybridization comparing malignant and benign components of a hepatocellular carcinoma (HCC) in a pre-existing liver adenoma in a morphologically normal liver. 16314847 56/108 Arthur Liberzon 1.41665682248531e-06 2.28820310400138e-06 670 1279.18181818182 872 1.28787066792812e-07 375 2.21062232629081 -1.9964644681007 -1 4.9645273954703 667 375 854 634 2813 644 872 3168 1760 1121 1163 453 M15425 VANTVEER_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_ESR1_DN.html Down-regulated genes from the optimal set of 550 markers discriminating breast cancer samples by ESR1 [GeneID=2099] expression: ER(+) vs ER(-) tumors. 11823860 317/450 Arthur Liberzon 1.40892272430728e-09 2.20202492010939e-08 1860 959.545454545455 872 1.28083884109962e-10 184 2.15879943928668 2.43952924039507 1 6.59782000718125 1859 1253 289 293 393 924 2130 872 766 184 1592 454 M10263 LOPEZ_MESOTHELIOMA_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_DN.html Top genes associated with unfavorable survival after surgery of patients with epithelioid mesothelioma. 16540645 34/37 Arthur Liberzon 1.87113953501238e-05 2.21347834718256e-05 210 1298.09090909091 872 1.70105040870898e-06 206 2.69027009829965 3.15898443635074 1 4.98623509817975 206 1759 583 872 3928 693 1436 1918 1848 801 235 455 M11592 MAHADEVAN_RESPONSE_TO_MP470_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_RESPONSE_TO_MP470_UP.html Top genes up-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] after treatment with MP470, a protein kinase inhibitor. 17325667 21/29 Arthur Liberzon 6.46949443728118e-07 1.3066330228484e-06 425 1305.36363636364 873 5.88136030886618e-08 106 2.62424690410812 -2.93656419983793 -1 6.15960639232421 425 2355 923 2807 2183 307 189 732 3459 873 106 456 M3261 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY.html Toll-like receptor signaling pathway 95/144 KEGG 4.08781119799658e-07 1.00023166690222e-06 440 1098.90909090909 874 3.71619268868304e-08 436 2.03414797557245 -2.11567933007165 -1 4.85821836977071 436 1605 1726 874 1732 671 733 440 1336 1737 798 457 M10158 LEE_SP4_THYMOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_SP4_THYMOCYTE.html Genes enriched in the single positive 4 (SP4) thymocytes compared to all other T lymphocyte differentiation stages. 15210650 21/31 Arthur Liberzon 8.02243686270608e-07 1.50261515841161e-06 1580 1105.81818181818 875 7.29312708012643e-08 293 2.58530800910401 -3.28120125881517 -1 6.00436254014327 1578 791 713 947 2380 1596 1651 811 293 875 529 458 M4210 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3.html The 'group 3 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [GeneID=2099;2064]. 18794137 885/1090 Jessica Robertson 2.18204005988865e-14 6.60206992479131e-13 860 1016.81818181818 877 2.18204005988867e-15 25 2.06334800799864 -2.07887048827169 -1 10.0571854383377 857 1090 4510 25 189 583 934 1064 968 88 877 459 M6767 POOLA_INVASIVE_BREAST_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/POOLA_INVASIVE_BREAST_CANCER_DN.html Genes down-regulated in atypical ductal hyperplastic tissues from patients with (ADHC) breast cancer vs those without the cancer (ADH). 15864312 185/269 Jessica Robertson 3.75810266712028e-24 2.90790894898487e-22 1195 924.545454545455 878 3.41645697010935e-25 39 2.9688789401822 3.48812018618221 1 25.663785176746 1195 1393 39 260 1271 894 2920 688 491 141 878 460 M3412 BIOCARTA_CACAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CACAM_PATHWAY.html Ca++/ Calmodulin-dependent Protein Kinase Activation 15/15 BioCarta 6.80309313407469e-05 7.56789997474253e-05 790 1625.63636363636 879 6.18482137841481e-06 328 2.00647258531069 1.93391182997048 1 3.27532608039352 790 1919 2243 3105 4196 811 879 675 404 2532 328 461 M11792 BIOCARTA_SHH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SHH_PATHWAY.html Sonic Hedgehog (Shh) Pathway 16/19 BioCarta 4.73802719907786e-07 1.07723932464583e-06 880 1655.54545454545 879 4.30729838134798e-08 487 1.59014890629425 1.75699801385108 1 3.7662807249685 879 2405 2590 3122 1903 833 774 841 487 3551 826 462 M3432 LEE_LIVER_CANCER_MYC_TGFA_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_TGFA_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) tissue of MYC and TGFA [GeneID=4609;7039] double transgenic mice. 15565109 81/124 Yujin Hoshida 7.79790909975967e-08 6.27525965386533e-07 1420 848.545454545455 881 7.08900852377897e-09 97 2.37758649110354 -2.39346840936578 -1 5.88050679477599 1420 190 698 97 173 1066 854 1464 945 881 1546 463 M8156 BENPORATH_CYCLING_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_CYCLING_GENES.html Genes showing cell-cycle stage-specific expression [PMID=12058064]. 18443585 832/1017 Jessica Robertson 3.42838188814898e-07 9.21518482625961e-07 310 1222.45454545455 886 3.4283824170702e-08 78 1.7916745847599 1.97614553794443 1 4.29879602392403 308 1098 4455 1460 1645 78 431 886 1996 505 585 464 M1402 LEI_HOXC8_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEI_HOXC8_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) by overexpression of HOXC8 [GeneID=3224]. 15699330 17/28 Kate Stafford 8.3519062740362e-07 1.54406128769991e-06 435 1306.09090909091 887 7.59264494971785e-08 23 3.26401745031403 3.0658202498903 1 7.57828580340165 431 887 878 2593 3289 809 1175 23 2306 1343 633 465 M583 REACTOME_RIP_MEDIATED_NFKB_ACTIVATION_VIA_DAI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RIP_MEDIATED_NFKB_ACTIVATION_VIA_DAI.html Genes involved in RIP-mediated NFkB activation via DAI 22/35 Reactome 6.7550546870237e-07 1.34078461407703e-06 405 1215.72727272727 888 6.14096069195473e-08 176 1.89526265031304 -2.01253844784952 -1 4.4261012645832 404 805 1937 1699 2231 351 176 280 3157 1445 888 466 M1450 WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_UP.html Up-regulated genes in myeloid progenitors immortalized by HOXA9 [GeneID=3205] vs those immortalized by HOXA9 and MEIS1 [GeneID=4211]. 15755900 39/63 Kevin Vogelsang 1.11041030803287e-07 7.03739764799127e-07 2355 1329.54545454545 888 1.00946396734439e-08 357 2.67626594676047 -2.41363363637633 -1 6.57194107652714 2351 539 693 381 357 2178 1763 3336 888 742 1397 467 M3058 WALLACE_JAK2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_JAK2_TARGETS_UP.html Genes up-regulated more than 7-fold by expressing JAK2 [GeneID=3717] in the JAK2 null cell line. 15189810 29/50 Arthur Liberzon 3.55153013917982e-07 9.40697096348413e-07 890 1230.27272727273 888 3.22866428410434e-08 313 1.65416045734802 1.76486508427305 1 3.95906447230437 888 688 2694 2364 1570 460 647 511 1625 1773 313 468 M17844 KEGG_OTHER_GLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OTHER_GLYCAN_DEGRADATION.html Other glycan degradation 16/17 KEGG 3.2474356739085e-07 9.03906004064471e-07 615 1407.45454545455 890 2.95221468478627e-08 99 1.34363360266075 -1.39380881888015 -1 3.21581940601278 611 890 3175 4139 1471 717 394 99 1185 2700 101 469 M3642 DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_DN.html 'PAX-FKHR signature': genes down-regulated by PAX3- or PAX7-FOXO1 [GeneID=5081;5077;2308] fusion in primary alveolar rhabdomyosarcoma(ARMS) tumors. 16849537 23/28 Arthur Liberzon 3.12474734204539e-07 8.90628469471876e-07 1430 1059.54545454545 891 2.84067980533251e-08 60 2.58783683481567 3.00738436627768 1 6.24668743899991 1497 815 1426 2784 1426 891 876 60 381 1307 192 470 M658 REACTOME_CHONDROITIN_SULFATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHONDROITIN_SULFATE_BIOSYNTHESIS.html Genes involved in Chondroitin sulfate biosynthesis 16/21 Reactome 1.41336552743088e-06 2.28383611416425e-06 255 1294.72727272727 892 1.28487857766606e-07 252 3.85036685333968 3.85036685333968 1 8.68540029754852 252 2400 908 3046 2812 415 353 491 892 1878 795 471 M12617 KEGG_TYPE_I_DIABETES_MELLITUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYPE_I_DIABETES_MELLITUS.html Type I diabetes mellitus 33/78 KEGG 2.12727017079992e-06 3.19158143870809e-06 245 1459.18181818182 894 1.93388384340675e-07 241 1.62480205456062 -1.64017272768236 -1 3.54122713476937 241 617 1983 2414 3065 306 535 786 3977 1233 894 472 M1845 RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN.html Down-regulated genes in breast tumors from transgenic mice overexpressing ERBB2 and CDC25A [GeneID=2064;993] compared to those from mice overexpressing ERBB2 only. 17283130 228/267 Jessica Robertson 8.26526649455451e-08 6.34342404134915e-07 1320 862.545454545455 894 7.51387891370505e-09 199 2.03204720780548 -2.0775092173971 -1 5.01477487839026 1318 1353 940 541 199 773 1482 1125 894 516 347 473 M198 PID_SYNDECAN_1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_1_PATHWAY.html Syndecan-1-mediated signaling events 18832364 52/61 Pathway Interaction Database 3.82119260502974e-07 9.66043336675971e-07 185 1289.36363636364 895 3.4738120624864e-08 181 2.70503746825864 2.89420957060772 1 6.49345844214438 181 1686 383 824 3964 895 1790 1816 1192 573 879 474 M6023 BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_DN http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_DN.html Genes down-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes are independent of ATM [GeneID=472] signaling. 18849970 74/95 Jessica Robertson 1.21605756296892e-07 7.10527676861612e-07 1990 1227.18181818182 897 1.10550693653357e-08 252 2.71444095756186 3.07313873868344 1 6.66184787469145 1988 252 897 1590 428 1947 3140 309 813 1507 628 475 M6362 NAKAMURA_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_LUNG_CANCER.html Genes up-regulated in lung adenocarcinoma cell lines and not expressed in non-cancerous lung epithelial cells. 16491115 23/26 Arthur Liberzon 1.66105870063021e-05 1.97884832583911e-05 135 1560 898 1.51006476563561e-06 134 2.763923299621 2.65939004443206 1 5.17820707118649 134 2336 524 883 4354 898 1599 2568 2600 566 698 476 M16424 BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_UP.html Genes up-regulated in the invasive ductal carcinoma (IDC) compared to the invasive lobular carcinoma (ILC), the two major pathological types of breast cancer. 18490921 43/48 Jessica Robertson 1.02469904507299e-06 1.78462030724401e-06 1090 1352.90909090909 899 9.31545020317936e-08 384 2.18275662146416 -2.22259954383429 -1 4.99607664205977 1087 3087 1722 625 2585 738 724 546 899 2485 384 477 M362 LE_SKI_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LE_SKI_TARGETS_UP.html Selected genes implicated in metastasis and epithelial-to-mesenchymal transition (EMT) which were up-regulated in MDA-MB-231 cells (breast cancer) upon knockdown of SKI [GeneID=6497] by RNAi. 18451154 36/54 Jessica Robertson 1.13039620875837e-08 1.46578849047789e-07 900 1158.27272727273 899 1.02763292233322e-09 286 3.3568315084151 3.68252029106266 1 9.17569069592377 899 570 286 747 2822 1514 2263 419 1095 483 1643 478 M768 REN_ALVEOLAR_RHABDOMYOSARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/REN_ALVEOLAR_RHABDOMYOSARCOMA_UP.html Genes commonly up-regulated in human alveolar rhabdomyosarcoma (ARMS) and its mouse model overexpressing PAX3-FOXO1 [GeneID=5077;2308] fusion. 18701482 121/192 Jessica Robertson 5.85448493619844e-07 1.22123997631427e-06 815 1157.09090909091 900 5.32226044923026e-08 6 2.20576557149591 2.47399539967255 1 5.19540981058723 1403 6 627 570 2102 813 2422 2065 900 813 1007 479 M15103 DOUGLAS_BMI1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOUGLAS_BMI1_TARGETS_UP.html Genes up-regulated in A4573 cells (Ewing's sarcoma, ESFT) after knockdown of BMI1 [GeneID=648] by RNAi. 18701473 766/940 Jessica Robertson 1.12882231407049e-07 7.05613393308323e-07 900 1131.27272727273 900 1.12882237141128e-08 94 2.12380451126812 2.30071329254688 1 5.20398019828893 900 1107 4500 385 452 94 1616 904 1677 531 278 480 M10279 HORIUCHI_WTAP_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HORIUCHI_WTAP_TARGETS_DN.html Genes down-regulated in primary endothelial cells (HUVEC) after knockdown of WTAP [GeneID=9589] by RNAi. 17088532 419/539 Leona Saunders 6.23495791317237e-07 1.27013385197124e-06 150 1128.63636363636 901 5.66814516382265e-08 148 1.88867783501954 2.01900190095641 1 4.42840632064356 148 2021 1420 1792 2162 229 358 648 1977 759 901 481 M15346 LEE_LIVER_CANCER_E2F1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_E2F1_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by overexpression of E2F1 [GeneID=1869]. 15565109 61/118 Yujin Hoshida 5.9065657624769e-07 1.22706823938781e-06 765 1321.81818181818 902 5.36960668024893e-08 332 2.13196298045126 -2.35613772779449 -1 5.01812984776649 762 332 1120 2131 2111 781 875 1728 3060 902 738 482 M5200 VALK_AML_WITH_EVI1 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_EVI1.html Genes that best predicted acute myeloid leukemia (AML) with the up-regulated expression of EVI1 [GeneID=2122]. 15084694 29/41 Jessica Robertson 6.38034892530148e-08 5.85899745669708e-07 1265 884.909090909091 902 5.80031737303795e-09 56 2.17588602474032 2.30474582207098 1 5.4034783631038 1264 578 902 71 105 1006 1615 2198 56 1501 438 483 M1804 WANG_SMARCE1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_SMARCE1_TARGETS_UP.html Genes up-regulated in BT549 cells (breast cancer) by expression of SMARCE1 [GeneID=6605] off a retroviral vector. 16135788 377/460 John Newman 2.45631884959265e-23 1.81153515157458e-21 575 957.818181818182 903 2.2330171359933e-24 40 2.48036824600485 2.71433553393906 1 20.6402475784471 574 1209 40 684 1094 747 2901 903 1289 56 1039 484 M1732 GAVIN_FOXP3_TARGETS_CLUSTER_P2 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P2.html Cluster P2 of genes with similar expression profiles in peripheral T ymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 91/145 Jessica Robertson 1.28446339421987e-07 7.20206492018647e-07 3575 1803.90909090909 905 1.16769406292081e-08 126 2.27776761637671 2.46159436143746 1 5.57672127338138 3706 126 674 943 478 3571 4650 621 905 595 3574 485 M13022 BIOCARTA_PTC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTC1_PATHWAY.html Sonic Hedgehog (SHH) Receptor Ptc1 Regulates cell cycle 14/16 BioCarta 1.55431259446657e-06 2.45527290692176e-06 195 951.090909090909 906 1.41301244781673e-07 125 2.72012290275973 2.72012290275973 1 6.08679602008684 192 906 1272 1028 2890 244 251 696 125 1910 948 486 M1941 MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation at K4 (H3K4me2) and trimethylation at K27 (H3K27me3) in brain. 18600261 1102/1553 Jessica Robertson 6.40872651692949e-92 3.02491891599072e-88 1325 1216 907 6.40872651692948e-93 1 2.63493727119027 2.87491341579571 1 92.6915879837431 1323 1073 4613 214 411 184 2950 662 1038 1 907 487 M1080 REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT.html Genes involved in G2/M DNA damage checkpoint 16/16 Reactome 1.81654153717543e-06 2.78650505540073e-06 910 1165.72727272727 908 1.65140276099708e-07 319 2.19753897406476 2.32196804642233 1 4.85922952173786 908 889 1786 653 2983 997 635 488 319 1879 1286 488 M19982 WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP.html Genes up-regulated in mucinous ovarian carcinoma tumors of low malignant potential (LMP) compared to normal ovarian surface epithelium tissue. 16467078 345/404 Arthur Liberzon 5.59291599417665e-07 1.18659903470788e-06 375 1240.72727272727 908 5.08447037820689e-08 200 1.90655017981238 -2.03597561599603 -1 4.49343908237105 372 2950 1918 1365 2062 233 908 587 796 2257 200 489 M37 PID_NFKAPPAB_CANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFKAPPAB_CANONICAL_PATHWAY.html Canonical NF-kappaB pathway 18832364 33/38 Pathway Interaction Database 2.45285185137906e-06 3.58632862080742e-06 405 1180.36363636364 914 2.22986780558906e-07 315 1.72828978588096 -1.98349340635368 -1 3.73476348282259 405 599 1778 1483 3148 674 315 914 1890 747 1031 490 M9702 SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_2 http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_2.html 50 most interesting genes up-regulated in the pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 12839967 43/61 John Newman 3.38008837204748e-07 9.13746684768849e-07 755 1038.36363636364 914 3.07280808305969e-08 404 2.99899325233948 2.99115354024114 1 7.23369048241501 752 473 450 721 1525 914 1085 1588 2105 404 1405 491 M15606 MARKEY_RB1_ACUTE_LOF_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_ACUTE_LOF_UP.html Genes up-regulated in adult fibroblasts with inactivated RB1 [GeneID=5925] by Cre-lox: acute loss of function (LOF) of RB1. 17452985 299/356 Arthur Liberzon 2.25219355570967e-06 3.35448203942873e-06 75 1105.27272727273 916 2.04745078303486e-07 74 1.88473371353966 1.89626707972062 1 4.09936146198882 74 1280 1316 2351 3090 124 160 606 1735 506 916 492 M7669 LEE_TARGETS_OF_PTCH1_AND_SUFU_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_TARGETS_OF_PTCH1_AND_SUFU_UP.html Genes up-regulated in medulloblastoma tumors from animals with inactivating mutations of one copy of PTCH1 or SUFU [GeneID=5727;51684] in conjunction with TP53 [GeneID=7157] loss. 17452975 73/93 Jessica Robertson 1.94729070501317e-07 7.60600386859923e-07 645 1148.36363636364 917 1.7702644339765e-08 237 2.03334764447303 2.35852507840207 1 4.9535518804433 641 286 1437 2826 917 237 1269 526 3187 927 379 493 M2542 GENTLES_LEUKEMIC_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/GENTLES_LEUKEMIC_STEM_CELL_UP.html Genes up-regulated in LSC (leukemic stem) cells compared to LPC (leukemia progenitor) cells from AML (acute myeloid leukemia) tumor samples. 21177505 37/51 Andrew Gentles 1.37750110765753e-07 7.20206492018647e-07 745 1125.36363636364 917 1.2522738126436e-08 549 2.59851052205392 2.75372272064893 1 6.36905093872007 1940 588 797 2280 549 1114 1206 917 1498 745 745 494 M12641 JIANG_TIP30_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_TIP30_TARGETS_UP.html Up-regulated genes in HepG2 cells (liver cancer) overexpressing an oncogenic variant of tumor suppressor TIP30 [GeneID=10553] compared to its wild type form. 17440068 63/76 Jessica Robertson 2.07215010292406e-07 7.68728418959517e-07 1400 971.181818181818 918 1.88377299827008e-08 219 2.24172740755207 2.70809044609863 1 5.46216348787212 1400 322 918 825 985 1005 2613 219 1329 770 297 495 M11290 SOUCEK_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SOUCEK_MYC_TARGETS.html Chemokine genes up-regulated within 2 hr of c-Myc [GeneID=4609] activation in a mouse model of Myc-induced pancreatic beta-cell tumorigenesis. 17906636 10/13 Jessica Robertson 1.39849218094695e-06 2.26445389161908e-06 740 1304.36363636364 919 1.27135733630802e-07 325 3.26428439320519 -3.57702253152875 -1 7.36059740568874 736 992 919 1935 2804 675 325 464 3915 1154 429 496 M1801 GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_UP.html Up-regulated genes from the set D (Fig. 5a): specific signature shared by cells expressing MLL-AF4 [GeneID=4297;4299] alone and those expressing both MLL-AF4 and AF4-MLL fusion proteins. 17130830 36/59 Arthur Liberzon 1.0889730926661e-07 7.03139944922573e-07 935 848.272727272727 920 9.89975587789951e-09 101 2.45828714606246 2.49530516745209 1 6.0329546312349 934 603 1118 1607 344 523 920 101 1920 953 308 497 M14811 LEE_LIVER_CANCER_ACOX1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_ACOX1_DN.html Genes down-regulated in hepatocellular carcinoma of ACOX1 [GeneID=51] knockout mice. 15565109 65/128 Yujin Hoshida 1.94987456674231e-07 7.60612227687911e-07 1045 1352.63636363636 920 1.77261339960092e-08 323 2.63310758851604 -2.5216164022911 -1 6.42941250886846 1042 323 656 2287 920 602 1185 3839 2429 863 733 498 M13256 RIGGI_EWING_SARCOMA_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIGGI_EWING_SARCOMA_PROGENITOR_DN.html Genes down-regulated in mesenchymal stem cells (MSC) engineered to express EWS-FLI1 [GeneID=2130;2321] fusion protein. 18381423 216/259 Jessica Robertson 2.85109259279782e-18 1.41654284610586e-16 695 948.545454545455 920 2.59190235708892e-19 66 2.52188286113007 2.57871990801565 1 16.0238581226202 692 1354 66 274 1344 802 1751 920 1533 86 1612 499 M40 PID_E2F_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_E2F_PATHWAY.html E2F transcription factor network 18832364 85/115 Pathway Interaction Database 2.87864633213407e-06 4.08637915418732e-06 315 1369.18181818182 921 2.61695463525407e-07 210 1.71114358776497 1.81868732663048 1 3.65820423281431 314 210 2681 1964 3252 524 516 921 713 2268 1698 500 M1478 LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS http://www.broadinstitute.org/gsea/msigdb/cards/LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS.html Granule constituents expressed during mouse promyelocytic cell line differentiation to neutrophils. 11468144 23/68 Kevin Vogelsang 7.01856472596453e-07 1.37329085443823e-06 925 1056.90909090909 921 6.38051542278894e-08 115 2.77660115348627 -3.37696108196123 -1 6.49598634326242 921 738 909 115 2264 1173 998 2375 563 1095 475 501 M10861 LI_PROSTATE_CANCER_EPIGENETIC http://www.broadinstitute.org/gsea/msigdb/cards/LI_PROSTATE_CANCER_EPIGENETIC.html Genes affected by epigenetic aberrations in prostate cancer. 15657340 35/46 Jessica Robertson 3.29758664687377e-07 9.06126045087621e-07 945 1145.36363636364 921 2.99780649195467e-08 136 2.13708875185821 2.43611518679328 1 5.14348812692364 944 634 1775 2632 1497 392 714 478 921 2476 136 502 M10867 OHASHI_AURKB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OHASHI_AURKB_TARGETS.html Candidate substrate proteins of AURKB [GeneID=9212]. 16785988 10/17 Arthur Liberzon 5.25805649594036e-07 1.14309697611119e-06 205 1014.27272727273 926 4.78005250239071e-08 69 2.93471352381821 2.93471352381821 1 6.96278688331554 202 979 926 1807 1995 156 69 234 2979 1153 657 503 M4151 HINATA_NFKB_TARGETS_FIBROBLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/HINATA_NFKB_TARGETS_FIBROBLAST_UP.html Genes up-regulated in primary fibroblast cells by expression of p50 (NFKB1) and p65 (RELA) [GeneID=4790;5970] components of NFKB. 12673201 114/141 Arthur Liberzon 1.06085367792911e-10 1.99491209554796e-09 1810 1162.72727272727 926 9.6441243452751e-12 46 2.59524183777224 -2.52598715857679 -1 9.03029103287453 1806 46 194 132 926 1994 2111 853 2713 338 1677 504 M1089 REACTOME_FGFR4_LIGAND_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FGFR4_LIGAND_BINDING_AND_ACTIVATION.html Genes involved in FGFR4 ligand binding and activation 3/13 Reactome 9.87466263172588e-07 1.73782280468852e-06 845 1511.36363636364 927 9.87466701963192e-08 28 3.44505767446264 3.44505767446264 1 7.93026287384409 844 1065 4268 3842 2628 669 28 202 927 1691 461 505 M15374 VERRECCHIA_RESPONSE_TO_TGFB1_C6 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C6.html Cluster 6: ECM related genes up-regulated in dermal fibroblasts later than 30 min after TGFB1 [GeneID=7040] addition; slowly increased up to 120 min time point, then reached a plateau. 11279127 14/19 Arthur Liberzon 2.38437235865437e-07 8.00711660757103e-07 1015 906.454545454545 928 2.1676114700673e-08 128 2.50422044201846 2.78152759110241 1 6.089780682436 1011 928 1514 873 1146 1155 786 622 128 1533 275 506 M6900 MAHADEVAN_GIST_MORPHOLOGICAL_SWITCH http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_GIST_MORPHOLOGICAL_SWITCH.html Genes up-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] that may correlate with the morphological switch in these cells. 17325667 23/32 Arthur Liberzon 9.09334642853815e-07 1.63569341245046e-06 930 1104.54545454545 930 8.26668198829901e-08 211 3.8534896934495 3.74213925705437 1 8.91713812045352 930 795 644 1601 2501 1105 1487 211 887 1308 681 507 M7098 KEGG_ECM_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ECM_RECEPTOR_INTERACTION.html ECM-receptor interaction 85/94 KEGG 5.83619889432368e-09 8.14995821929224e-08 120 1506.09090909091 931 5.30563537255095e-10 117 2.71252596368496 2.81686415512721 1 7.68299852608893 117 2139 266 790 3848 931 1527 2493 3127 408 921 508 M19620 COLLER_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/COLLER_MYC_TARGETS_DN.html Genes down-regulated in 293T (transformed fetal renal cell) upon expression of MYC [GeneID=4609]. 10737792 29/34 Yujin Hoshida 5.61225721838361e-05 6.2906326456354e-05 130 1531.90909090909 932 5.10218217603486e-06 129 3.09200810305567 3.17028324424843 1 5.1742321580684 129 2320 589 887 4356 932 1354 2303 2627 738 616 509 M2045 MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_1 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_1.html Cluster 1: genes up-regulated in SW260 cells (colon cancer) by sodium butyrate, curcumin, sulindac and TSA [PubChem=5222465;969516;5352;5562]. 10969808 14/24 Arthur Liberzon 1.81538251025793e-07 7.47800341964416e-07 1690 1179 932 1.65034787278052e-08 252 2.40507926246878 2.80344067275517 1 5.87542507462584 1689 932 1763 635 842 1307 1657 530 252 2838 524 510 M17427 DOANE_BREAST_CANCER_CLASSES_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_CLASSES_UP.html Genes up-regulated in ER(-) / PR(-) breast tumors (do not express ESR1 and PGR [GeneID=2099;5241]) with molecular similarity to ER(+) (class A) relative to the rest of the ER(-) / PR(-) samples (class B). 16491124 90/126 Arthur Liberzon 2.49662636132962e-07 8.18104459972526e-07 1080 965.272727272727 933 2.26966058604941e-08 33 2.67268103675843 -2.62473033454482 -1 6.49277921122177 1080 1609 642 933 1191 1682 2029 33 512 774 133 511 M10480 GU_PDEF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GU_PDEF_TARGETS_DN.html Integrin, VEGF, Wnt and TGFbeta signaling pathway genes down-regulated in PC-3 cells (prostate cancer) after knockdown of PDEF [GeneID=25803] by RNAi. 17483333 53/92 Jessica Robertson 2.32873807778361e-07 7.97250262911913e-07 3150 1570.63636363636 933 2.11703484025873e-08 412 2.73687569596674 -2.22586124776906 -1 6.66227294726301 3147 412 649 417 1114 4619 3557 803 1027 933 599 512 M15847 MORI_MATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_MATURE_B_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the mature B 18922927 92/109 Jessica Robertson 1.32610536090876e-07 7.20206492018647e-07 570 1223.27272727273 937 1.20555040076646e-08 165 1.79620184789762 1.88360547755672 1 4.3871116595008 567 165 2462 2425 504 744 937 874 1454 1703 1621 513 M12890 ROZANOV_MMP14_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_TARGETS_UP.html Genes up-regulated in HT1080 cells (fibrosarcoma) over-expressing MMP14 [GeneID=4323] compared to those with knockdown of the gene by RNAi. 18519667 375/525 Jessica Robertson 7.36320574018087e-16 2.5743948958262e-14 1210 980.272727272727 939 6.69382340016443e-17 95 2.38586452383615 2.64759181611595 1 12.9889636791064 1209 1220 95 296 758 959 2767 726 1629 185 939 514 M12868 KEGG_PATHWAYS_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PATHWAYS_IN_CANCER.html Pathways in cancer 338/425 KEGG 1.42164775009571e-07 7.21524449510942e-07 1655 1288.63636363636 942 1.29240712905736e-08 488 2.04193516213608 2.32789291633095 1 4.99349345001982 1651 1259 830 488 582 718 3603 2038 1504 942 560 515 M13678 JEON_SMAD6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JEON_SMAD6_TARGETS_DN.html Genes down-regulated in H1299 cells (lung cancer) upon knockdown of SMAD6 [GeneID=4091] by RNAi. 19047146 27/32 Jessica Robertson 2.01029396455138e-07 7.65527859584926e-07 2375 1264.90909090909 942 1.82754013476912e-08 152 2.38651391383078 2.36164714044167 1 5.81991916686401 2371 666 835 152 942 2022 1467 2185 500 594 2180 516 M19948 HOQUE_METHYLATED_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HOQUE_METHYLATED_IN_CANCER.html Genes whose DNA was methylated both in primary tumors and across a panel of cancer cell lines. 18413733 48/73 Jessica Robertson 1.94823277057976e-07 7.60600386859923e-07 995 943.272727272727 943 1.7711208573705e-08 370 2.44297894016767 2.41022478692043 1 5.96155790051744 994 455 949 2082 918 459 823 370 943 1348 1035 517 M1416 HAHTOLA_CTCL_PATHOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_CTCL_PATHOGENESIS.html Differentially expressed genes relevant to pathogenesis of cutaneous T cell lymphoma (CTCL). 16914566 11/46 Arthur Liberzon 6.40382101756398e-08 5.85985350006182e-07 2665 1360.72727272727 945 5.82165563997108e-09 39 4.14113334578434 5.33689924269241 1 10.3289555024438 2663 945 680 542 106 2657 2224 3305 39 1026 781 518 M13273 DELYS_THYROID_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELYS_THYROID_CANCER_DN.html Genes down-regulated in papillary thyroid carcinoma (PTC) compared to normal tissue. 17621275 292/388 Aravind Subramanian 5.61449646366973e-23 4.01521565280623e-21 870 1038.54545454545 948 5.10408769424521e-24 42 2.64374149466002 2.7104970176201 1 21.6355329222684 866 1273 42 690 1499 187 2047 948 2545 57 1270 519 M14308 GRASEMANN_RETINOBLASTOMA_WITH_6P_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/GRASEMANN_RETINOBLASTOMA_WITH_6P_AMPLIFICATION.html Genes changed in retinoblastoma tumors with respect to chromosome 6p amplifications. 16007192 16/23 Leona Saunders 1.15749340435827e-05 1.41795195135505e-05 530 1963 949 1.05227226760194e-06 144 1.68156671679743 1.68156671679743 1 3.22870819045033 530 3772 3162 3696 4409 676 144 155 248 3852 949 520 M19048 RUIZ_TNC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUIZ_TNC_TARGETS_DN.html Genes down-regulated in T98G cells (glioblastoma) by TNC [GeneID=3371]. 15492259 190/241 Arthur Liberzon 2.89755225287864e-09 4.2605752752608e-08 125 981.454545454545 949 2.6341384151772e-10 121 1.98522095929114 1.93866281410488 1 5.83444603213906 121 1387 501 949 2709 179 248 1404 1541 194 1563 521 M6335 AUJLA_IL22_AND_IL17A_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/AUJLA_IL22_AND_IL17A_SIGNALING.html Genes changed in HBE cells (bronchial epithelium) after treatment with IL22 and IL17A [GeneID=50616;3605]. 18264110 9/19 Jessica Robertson 8.19858708753316e-08 6.33344207089305e-07 490 1514.81818181818 952 8.19858739000891e-09 111 3.72280062872963 -3.68067649160737 -1 9.22994715975952 486 1961 4563 2393 246 967 686 111 3605 952 693 522 M96 BIOCARTA_FREE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FREE_PATHWAY.html Free Radical Induced Apoptosis 13/19 BioCarta 3.25408633359332e-06 4.55494884180322e-06 275 1259.27272727273 953 2.95826467892772e-07 18 1.97870293386823 -2.01008714350306 -1 4.20051964594346 274 2869 1879 1703 3296 139 18 301 953 2166 254 523 M644 FOURNIER_ACINAR_DEVELOPMENT_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_LATE_UP.html Genes up-regulated late in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 17/24 Arthur Liberzon 8.49138413547894e-07 1.56298478827681e-06 755 1188.90909090909 955 7.71944310265206e-08 534 3.45617297786118 3.69075999209027 1 8.02001868314552 751 1890 877 1346 2434 713 955 813 534 1089 1676 524 M14134 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN.html Genes down-regulated in ductal carcinoma vs normal ductal breast cells. 17389037 245/315 Arthur Liberzon 2.3110709282744e-27 2.38906369675296e-25 2585 1207.72727272727 955 2.10097357115855e-28 25 2.90533757268228 3.38169779360487 1 28.7184195481907 2581 1306 25 233 142 2073 4287 955 378 73 1232 525 M1932 MEISSNER_NPC_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the H3K27 tri-methylation (H3K27me3) mark in neural precursor cells (NPC). 18600261 36/125 Jessica Robertson 1.32717666746233e-07 7.20206492018647e-07 4145 1947.09090909091 955 1.20652431593261e-08 354 3.24124617501465 3.32622090583071 1 7.95679774713776 4142 569 480 711 508 4622 4283 1388 354 955 3406 526 M2154 DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN.html Genes down-regulated in MCF7 cells (breast cancer) at 6 h of estradiol [PubChem=5757] treatment. 20406972 128/150 Jessica Robertson 1.90336974888705e-07 7.51162643373486e-07 850 1034.63636363636 955 1.73033628505504e-08 296 2.12238606781307 -2.21489384125095 -1 5.1772828279564 850 1541 792 955 904 740 1416 1471 1252 296 1164 527 M8604 HALMOS_CEBPA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HALMOS_CEBPA_TARGETS_DN.html Genes down-regulated in H358 cells (lung cancer) by inducible expression of CEBPA [GeneID=1050] off plasmid vector. 15205324 55/78 Kevin Vogelsang 9.1106453277468e-08 6.55522041874465e-07 1520 1257.54545454545 956 8.28240518639733e-09 254 2.30290762541268 -2.51890746534633 -1 5.67667565763356 1516 362 603 956 254 2257 2665 2141 764 471 1844 528 M1464 VALK_AML_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_2.html Top 40 genes from cluster 2 of acute myeloid leukemia (AML) expression profile; 71% of the samples are FAB M4 or M5 subtypes, and 82% bear internal tundem duplications in FLT3 [GeneID=2322]. 15084694 36/51 Jessica Robertson 6.78479995671147e-07 1.34422242460247e-06 3665 1830.81818181818 956 6.16800186285878e-08 79 2.53842742687041 -2.59157233081531 -1 5.94396099562369 3661 555 832 79 2235 4395 4716 1967 143 956 600 529 M7963 KEGG_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CELL_CYCLE.html Cell cycle 132/142 KEGG 8.74440192323067e-07 1.59295936231759e-06 120 1140.63636363636 957 7.94945945354058e-08 120 1.7327068976291 1.88760901467638 1 3.99003047043028 120 1552 2604 1514 2464 135 157 700 773 1571 957 530 M12338 GERY_CEBP_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GERY_CEBP_TARGETS.html Genes changed in NIH 3T3 cells (embryonic fibroblast) by expression of one or more of C/EBP proteins: CEBPA, CEBPB, CEBPG, and CEBPD [GeneID=1050;1051;1054;1052]. 15985538 170/229 Kevin Vogelsang 2.02664181852509e-07 7.65527859584926e-07 905 1687.90909090909 957 1.84240182292685e-08 140 2.25124815704159 -1.95479819179572 -1 5.4872145964666 902 3584 914 3747 957 196 866 1863 3966 1432 140 531 M2306 SUMI_HNF4A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SUMI_HNF4A_TARGETS.html Genes up-regulated in HepG2 cells (hepatocellular carcinoma, HCC) upon expression of HNF4A [GeneID=3172] and down-regulated upon knockdown of HNF4A [GeneID=3172] in these cells by RNAi. 17403900 24/60 Arthur Liberzon 1.80692347597142e-07 7.47800341964416e-07 335 1327.54545454545 957 1.6426578403448e-08 147 2.37161517045411 -2.13155490559962 -1 5.79297863848001 499 2347 1620 3294 838 334 332 957 2199 2036 147 532 M11216 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_14 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_14.html Amplification hot spot 14: colocolized fragile sites and cancer genes in the 8q24.1-q24.3 region. 16751803 4/4 Arthur Liberzon 1.14737856640737e-07 7.06112554001409e-07 1060 1137.27272727273 958 1.14737862564887e-08 73 1.83958066910849 1.83958066910849 1 4.50062000609291 1060 1061 4367 1452 463 958 128 73 614 2147 187 533 M4263 CHEBOTAEV_GR_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEBOTAEV_GR_TARGETS_UP.html Genes up-regulated in follicular epithelial stem cells after transgenic expression of GR [GeneID=2908] under control of the keratin5 (K5) [GeneID=3852] promoter. 17146443 106/124 Leona Saunders 2.16187157839457e-08 2.61376652706534e-07 4320 2167.63636363636 960 1.96533781785328e-09 37 2.26296625445883 2.35281415372931 1 5.94076509994113 4319 37 351 295 585 4584 3480 4383 960 231 4619 534 M10387 NIELSEN_SYNOVIAL_SARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SYNOVIAL_SARCOMA_UP.html Top 20 positive significant genes associated with synovial sarcoma tumors. 11965276 37/100 Arthur Liberzon 1.61890647032385e-05 1.93351177629771e-05 525 1440.81818181818 960 1.47174398494383e-06 345 2.61486870965785 3.05249418906655 1 4.90684010995044 345 1745 522 630 4038 960 2566 2424 1692 524 403 535 M17788 LINDGREN_BLADDER_CANCER_CLUSTER_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_1_DN.html Down-regulated genes whose expression profile is specific to Custer I of urothelial cell carcinoma (UCC) tumors. 16532037 527/653 Leona Saunders 3.0753346706841e-13 8.01965726277841e-12 800 1117 963 3.07533467068452e-14 68 2.15322575786171 2.17682504953468 1 9.55835167112225 799 1154 4334 68 805 208 1228 1241 1382 105 963 536 M3010 HECKER_IFNB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HECKER_IFNB1_TARGETS.html Genes transcriptionally modulated in the blood of multiple sclerosis patients in response to subcutaneous treatment with recombinant IFNB1 [GeneID = 3456]. 23636981 87/145 Michael Hecker 3.73516725275373e-07 9.57631147908614e-07 260 1318.36363636364 963 3.39560716991983e-08 259 2.11252769294566 -2.10833263542813 -1 5.06340209966646 259 1617 963 2275 1635 492 382 2144 3003 936 796 537 M197 PID_HIV_NEF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIV_NEF_PATHWAY.html HIV-1 Nef: Negative effector of Fas and TNF-alpha 18832364 43/52 Pathway Interaction Database 4.04968386135789e-07 9.96585392367531e-07 265 1479.72727272727 964 3.68153146073625e-08 254 1.56304346347079 -1.66143497005513 -1 3.72247342741972 262 540 3042 3187 1721 339 254 964 2582 2484 902 538 M19256 SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_UP.html Genes up-regulated in pleura relapse of breast cancer. 18451135 9/11 Jessica Robertson 3.43031350418181e-07 9.21518482625961e-07 1420 1153.09090909091 964 3.4303140336992e-08 90 4.32807215904281 5.45087163193091 1 10.4552543797209 1417 964 4550 700 1646 995 1244 139 90 637 302 539 M19002 STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_DN.html Genes down-regulated by estradiol [PubChem=5757] and down-regulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 49/58 Leona Saunders 4.85792073636733e-06 6.43911384418421e-06 130 1184.63636363636 965 4.41630133036156e-07 125 1.98453372603307 2.16216930573355 1 4.09305614632541 130 1701 1740 1656 3493 140 125 760 1663 965 658 540 M15209 LANDIS_ERBB2_BREAST_PRENEOPLASTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_PRENEOPLASTIC_UP.html Up-regulated genes from top 82 genes out of the 324-gene signature identified in the pre-neoplastic tissue adjacent to the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 27/27 Leona Saunders 6.52806734823809e-08 5.91410324063029e-07 1270 1021.18181818182 968 5.93460685631425e-09 113 2.33830158784557 -2.64827634812375 -1 5.80672420319462 1269 685 1350 968 113 2409 2072 360 223 1274 510 541 M18784 VALK_AML_CLUSTER_10 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_10.html Top 40 genes from cluster 10 of acute myeloid leukemia (AML) expression profile; 41% of the samples are FAB M1 subtype, 45% have up-regulated EVI1 [GeneID=2122] expression; indicate poor survival. 15084694 38/54 Jessica Robertson 2.16956313068153e-08 2.61376652706534e-07 1625 1097.45454545455 968 1.97233013825183e-09 3 2.33236705112971 2.7314814151138 1 6.1244914146959 1623 528 968 102 3 1807 3256 1709 116 1474 486 542 M1295 GALIE_TUMOR_STEMNESS_GENES http://www.broadinstitute.org/gsea/msigdb/cards/GALIE_TUMOR_STEMNESS_GENES.html Stemness-related genes changed in A17 carcinomas (MTC, mesenchymal tumor cells) compared with the mesenchymal stem cells (MSC). 17998939 11/11 Jessica Robertson 1.26870474266107e-05 1.54377065876779e-05 1135 1192.54545454545 969 1.15337459921551e-06 27 4.8579959805305 5.41324443075216 1 9.35002710434073 1132 975 969 729 3823 865 844 762 27 1762 1230 543 M17500 CHESLER_BRAIN_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_QTL_CIS.html Best cis-regulated quantitative trait loci (QTLs) in the mouse genome which modulate transcription in brain tissue. 15711545 84/108 Jean Junior 1.54036407589659e-07 7.28175281873995e-07 975 1462.27272727273 971 1.40033107613416e-08 39 1.89744398819027 2.16057079944783 1 4.63356295448901 971 2607 2819 1967 656 223 397 218 2523 3665 39 544 M2323 DORMOY_ELAVL1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/DORMOY_ELAVL1_TARGETS.html Genes down-regulated in HeLa cells upon knockdown of ELAVL1 [GeneID=1994] by RNAi. 17548472 21/31 Arthur Liberzon 1.21353527236409e-06 2.02470360040951e-06 1355 1212.27272727273 972 1.10321449250826e-07 535 2.46299844589825 3.06874057255529 1 5.58964571622085 1351 838 1254 1061 2708 951 861 535 856 1948 972 545 M1053 KEGG_HEDGEHOG_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEDGEHOG_SIGNALING_PATHWAY.html Hedgehog signaling pathway 40/61 KEGG 2.04683651338271e-07 7.67360472054519e-07 1060 974.545454545455 973 1.86076063983305e-08 150 2.7099036477736 2.99699480053192 1 6.61420861279579 1057 554 1168 2083 973 274 627 1203 187 2444 150 546 M4493 REN_BOUND_BY_E2F http://www.broadinstitute.org/gsea/msigdb/cards/REN_BOUND_BY_E2F.html Genes whose promoters were bound by E2F1 and E2F4 [GeneID=1869;1874] in the primary fibroblasts WI-38, by ChIP on chip assay. 11799067 76/110 Yujin Hoshida 4.61551783223207e-06 6.16098534166725e-06 75 1034.09090909091 975 4.19593410494959e-07 72 1.80123772327371 1.78898732923419 1 3.72428154628093 72 236 1880 1891 3466 98 82 321 1025 1329 975 547 M1519 KEGG_ENDOCYTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOCYTOSIS.html Endocytosis 203/231 KEGG 1.6334357197551e-07 7.3358205358541e-07 575 1509.54545454545 977 1.48494167366631e-08 419 1.4650760552529 -1.34416780450474 -1 3.56442452909958 571 1404 3427 1515 713 419 818 977 2623 3498 640 548 M7439 DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_DN.html Genes down-regulated in fibroblasts expressing different mutant forms of ERCC3 [GeneID=2071]: XP/CS (xeroderma pigmentosum (XP) and Cockraine's syndrome (CS)) vs TTD (trichothiodystrophy). 15608684 63/72 Arthur Liberzon 2.59177741567391e-07 8.27068974676848e-07 230 1291.72727272727 978 2.35616156455113e-08 226 2.74799353169069 2.80409417842794 1 6.67191624264354 226 2183 375 1203 3362 402 978 1387 2804 527 762 549 M8493 BASSO_CD40_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_CD40_SIGNALING_UP.html Gene up-regulated by CD40 [GeneID=958] signaling in Ramos cells (EBV negative Burkitt lymphoma). 15331443 126/201 Kevin Vogelsang 2.06293921787367e-07 7.68728418959517e-07 690 1216.27272727273 979 1.87539946483221e-08 9 1.72948073296679 -1.68422995563148 -1 4.20259622381741 688 9 1764 1490 979 771 830 1434 3123 823 1468 550 M2053 ZEMBUTSU_SENSITIVITY_TO_VINBLASTINE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_VINBLASTINE.html Top genes associated with chemosensitivity to vinblastine [PubChem=13342] across 85 tumor xenografts. 11809704 27/47 Arthur Liberzon 9.03228016669229e-08 6.55310251195451e-07 2995 1659.36363636364 981 8.21116412501814e-09 102 2.19888309228865 -2.32985563416104 -1 5.4181186804965 2995 707 1662 981 247 3893 3510 962 102 2440 754 551 M5681 MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP.html Genes up-regulated in apoptotic tissues (neuroepithelium) after MDM4 [GeneID=4194] knockout. 15608685 227/276 Arthur Liberzon 1.64549775769937e-07 7.3358205358541e-07 1455 1140.36363636364 983 1.49590716434088e-08 725 2.16583976642797 2.45302235526562 1 5.2932655583661 1452 2057 776 757 725 800 1565 827 1150 1452 983 552 M242 PID_AURORA_A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AURORA_A_PATHWAY.html Aurora A signaling 18832364 44/47 Pathway Interaction Database 1.09552747827698e-06 1.8775924827405e-06 520 1056 984 9.95934567103572e-08 126 1.88957263375637 2.05820850221364 1 4.30153132730347 519 496 1986 1051 2634 239 249 996 126 2336 984 553 M19944 GEISS_RESPONSE_TO_DSRNA_DN http://www.broadinstitute.org/gsea/msigdb/cards/GEISS_RESPONSE_TO_DSRNA_DN.html Genes down-pregulated by dsRNA in GRE cells (glioma; no interferon system). 11487589 19/25 John Newman 4.34721446060912e-07 1.02542989775487e-06 2390 1187.81818181818 984 3.9520139269289e-08 44 2.73943325261047 3.05901427251978 1 6.54811775199972 984 2388 1665 2162 1809 561 420 368 279 2386 44 554 M1327 MANTOVANI_VIRAL_GPCR_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_VIRAL_GPCR_SIGNALING_UP.html Up-regulated genes in the expression signature of direct and paracrine viral GPCR signaling in endothelial cells. 17906691 109/156 Jessica Robertson 6.28361746197412e-09 8.6217076803831e-08 2000 1475.36363636364 985 5.71237952720121e-10 63 2.74215644316621 -2.51325492638769 -1 7.74052102925103 1998 63 269 352 488 2449 2004 4428 985 549 2644 555 M679 REICHERT_G1S_REGULATORS_AS_PI3K_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/REICHERT_G1S_REGULATORS_AS_PI3K_TARGETS.html G1 to S phase regulators significantly changed in DanG cells (pancreatic cancer) treated with Ly294002 [PubChem=3973], a phosphoinositide 3-kinase (PI3K) inhibitor. 17483325 10/11 Jessica Robertson 1.49930437961955e-05 1.80252589704643e-05 400 1211.18181818182 988 1.36301327046022e-06 136 2.75215697530941 2.75215697530941 1 5.20081005367931 400 988 1749 1068 3867 539 241 396 136 2549 1390 556 M19612 LEE_LIVER_CANCER_ACOX1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_ACOX1_UP.html Genes up-regulated in hepatocellular carcinoma of ACOX1 [GeneID=51] knockout mice. 15565109 86/148 Yujin Hoshida 9.44841316108193e-12 2.02711409637758e-10 3785 1927.18181818182 989 8.58946651011136e-13 128 2.68658969844777 2.84295390298831 1 10.4228317874049 3782 128 168 288 701 4551 3483 2829 989 146 4134 557 M17770 BIOCARTA_CELLCYCLE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELLCYCLE_PATHWAY.html Cyclins and Cell Cycle Regulation 26/30 BioCarta 3.17420054686087e-06 4.46298081059973e-06 340 1115.36363636364 990 2.88564102424106e-07 260 2.27600594896154 2.31442616347301 1 4.84728040400356 337 713 1512 1477 3281 520 260 990 276 1407 1496 558 M265 ODONNELL_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_METASTASIS_UP.html Up-regulated genes in the signature set for lymph node metastasis in head and neck squamous cell carcinoma (HNSCC). 15558013 119/204 Leona Saunders 4.22087541881171e-07 1.00930518493669e-06 765 1282 992 3.83716020783685e-08 175 2.60164965980515 2.44231332594455 1 6.2234564679328 765 1563 414 992 1779 175 1547 3960 1718 514 675 559 M11367 MAHADEVAN_IMATINIB_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_IMATINIB_RESISTANCE_DN.html Top genes down-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] compared to the parental cell line sensitive to the drug. 17325667 26/33 Arthur Liberzon 2.0464060840351e-07 7.67360472054519e-07 3720 1759.27272727273 992 1.86036934035333e-08 89 3.09824846198007 2.32510251493557 1 7.56923345034415 3720 686 388 89 972 4428 3494 992 2400 649 1534 560 M2270 STEGER_ADIPOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEGER_ADIPOGENESIS_UP.html Genes up-regulated during adipogenesis of 3T3-L1 cells (fibroblast). 18285465 22/32 Arthur Liberzon 8.61325099702421e-08 6.48643236402367e-07 1135 1077.18181818182 993 7.83022848567529e-09 214 2.69315788292372 -2.9290542983684 -1 6.65208529887236 1135 803 1138 959 214 1261 821 2811 1091 993 623 561 M4275 GOLUB_ALL_VS_AML_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOLUB_ALL_VS_AML_UP.html Up-regulated genes highly correlated with acute lymphoblastic leukemia (ALL) vs acute myeloid leukemia (AML). 10521349 33/38 Jean Junior 6.56239418444223e-08 5.92246664446794e-07 415 1490.18181818182 994 5.96581307290211e-09 115 1.65309554163196 1.68214486116579 1 4.09007551458615 412 2750 2731 2922 115 399 433 822 3129 1685 994 562 M1040 REACTOME_G1_S_SPECIFIC_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_S_SPECIFIC_TRANSCRIPTION.html Genes involved in G1/S-Specific Transcription 20/22 Reactome 2.56811916376546e-05 2.97972528342502e-05 180 1121.54545454545 995 2.3346810387282e-06 179 1.75553126512322 1.83876669447454 1 3.14522767897206 179 761 1570 1020 4013 300 203 995 502 1217 1577 563 M8795 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP.html Genes up-regulated in transformed NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845]) vs normal cells. 16607279 163/210 Lauren Kazmierski 4.3699576636287e-07 1.02668990404816e-06 370 1048.27272727273 995 3.97268957423003e-08 369 1.98000586479498 1.78595910341994 1 4.71854847588026 369 1453 995 1191 1817 370 556 681 1836 687 1576 564 M6998 FURUKAWA_DUSP6_TARGETS_PCI35_UP http://www.broadinstitute.org/gsea/msigdb/cards/FURUKAWA_DUSP6_TARGETS_PCI35_UP.html Genes up-regulated in PCI-35 cells (pancreatic cancer, lack endogenous DUSP6 [GeneID=1848]) upon expression of DUSP6 off an adenoviral vector. 16532023 99/159 Arthur Liberzon 7.19573698589485e-08 6.06397110828564e-07 345 934.545454545455 995 6.54157929204754e-09 84 2.55890764552135 -2.20633314837246 -1 6.34809340874673 995 84 341 342 1016 1223 1705 1727 731 569 1547 565 M2346 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_UP http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_UP.html Top 20 up-regulated genes in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 22/36 Arthur Liberzon 8.89314255653316e-08 6.53462771551776e-07 1810 1231.90909090909 995 8.08467537820365e-09 235 2.80959136815011 3.01458227004066 1 6.93820602248307 1808 818 785 1343 235 1571 771 883 3346 995 996 566 M2578 LIM_MAMMARY_LUMINAL_MATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_MATURE_UP.html Genes consistently up-regulated in mature mammary luminal cells both in mouse and human species. 20346151 153/201 Daniel Hollern 2.5268711463575e-06 3.66866558314592e-06 50 1332.45454545455 995 2.29715822606386e-07 47 2.15579734719792 -2.24671255215406 -1 4.66242023788723 47 2541 635 1338 4056 213 1461 778 2113 480 995 567 M9487 FRIDMAN_SENESCENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_SENESCENCE_DN.html Genes down-regulated in senescent cells. 18711403 36/38 Jessica Robertson 8.87883799727941e-07 1.61371256631339e-06 160 1625.72727272727 996 8.07167416421305e-08 160 3.01824645049975 3.1344782767867 1 6.98063647241154 160 2276 406 1286 4314 815 996 2936 3312 796 586 568 M1722 LEIN_MEDULLA_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_MEDULLA_MARKERS.html Top 100 ranked genes most specific to medulla (myelencephalon) hindbrain region of adult mouse brain. 17151600 89/121 Jessica Robertson 1.83432904682252e-07 7.47950348864313e-07 2130 1369.63636363636 996 1.66757199978756e-08 189 2.30103905322177 2.27643380427179 1 5.61901763892606 2127 189 996 578 856 1963 2405 1757 974 923 2298 569 M17641 FRASOR_RESPONSE_TO_ESTRADIOL_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_ESTRADIOL_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by estradiol (E2) [PubChem=5757]. 14973112 42/51 Arthur Liberzon 2.09231278661927e-07 7.70763712250053e-07 1085 1021.36363636364 997 1.90210271418997e-08 47 2.14299448089942 2.11350711829637 1 5.21839868026154 1085 520 906 1162 997 935 2190 47 1888 1419 86 570 M7600 DOANE_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in MDA-MB-453 cells (class A ER(-) [GeneID=2099] breast cancer) after exposure to the androgen R1881 [PubChem=13766]. 16491124 231/341 Arthur Liberzon 7.05225277882517e-08 6.06397110828564e-07 1485 994.727272727273 998 6.41113909535456e-09 138 1.93043378721446 -1.86927990172882 -1 4.77669718471702 1483 1364 1287 998 138 454 1132 767 1653 699 967 571 M19384 YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP.html Genes up-regulated in mouse stroma of pancreatic adenocarcinoma zenografts after treatment with HhAntag, a hedgehog (Hh) pathway inhibitor. 18754008 165/243 Jessica Robertson 1.4809716702814e-07 7.26289540930751e-07 1000 1216.45454545455 1000 1.3463379727053e-08 42 2.5042066094495 2.80902982157271 1 6.13241375689319 1000 2540 487 3063 620 122 1150 698 2226 1433 42 572 M1938 MEISSNER_BRAIN_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the H3K27 tri-methylation (H3K27me3) mark in brain. 18600261 140/357 Jessica Robertson 1.1332082598478e-22 7.75180142968353e-21 4180 1699.09090909091 1000 1.03018932713436e-23 20 2.96805414100202 3.00278494876896 1 23.9547270071486 4176 1475 43 20 554 4711 4251 1510 873 77 1000 573 M2077 WHITFIELD_CELL_CYCLE_G2_M http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_G2_M.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the G2/M phase of cell cycle. 12058064 297/356 Jessica Robertson 2.80180418799337e-07 8.47725369700557e-07 550 1044.54545454545 1003 2.54709504074223e-08 174 1.90076994318965 2.02347181605828 1 4.5913064324848 549 1285 1651 1003 1318 174 692 1517 1586 884 831 574 M16463 MANN_RESPONSE_TO_AMIFOSTINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANN_RESPONSE_TO_AMIFOSTINE_DN.html Genes down-regulated in HCT116 cells (colon cancer) after treatment with amifostine [PubChem=2141] depending on the presence of TP53 [GeneID=7157]: TP53-positive vs TP53-null cells. 15750621 19/24 Leona Saunders 5.92785779841626e-06 7.67191905909645e-06 390 1443.90909090909 1004 5.3889761554324e-07 242 1.75274816807635 1.91313501524952 1 3.55553309697212 386 2375 2359 1510 3582 572 242 1004 529 2775 549 575 M2539 KUMAR_AUTOPHAGY_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/KUMAR_AUTOPHAGY_NETWORK.html Genes defining the Mycobacterium tuberculosis strain-independent regulatory axis of the host macrophage cells. 20211141 86/126 Arthur Liberzon 9.32244981529101e-07 1.66674102758233e-06 1005 1367.81818181818 1004 8.47495796878199e-08 219 1.95181265446455 2.29574698674527 1 4.4854739165827 1004 219 2094 2422 2518 340 606 694 1695 3124 330 576 M196 PID_IL23_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL23_PATHWAY.html IL23-mediated signaling events 18832364 37/54 Pathway Interaction Database 3.81171673194299e-07 9.64463514816902e-07 495 1361.63636363636 1007 3.46519762941874e-08 361 2.36368501085965 -2.35524865614528 -1 5.66840126911891 494 1748 865 1482 1658 949 1007 361 3923 868 1623 577 M2414 PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2.html Genes up-regulated in MCF7 cells (breast cancer) more than three-fold by the truncated form 611-CTF of ERBB2 [GeneID=2064] and less than two-fold by the full-length ERBB2 [GeneID=2064]. 19364815 103/133 Arthur Liberzon 2.11511154015169e-07 7.70763712250053e-07 3715 1779 1008 1.9228288577287e-08 101 2.36681672750776 2.7359618297404 1 5.76865354978961 3713 101 687 2561 1008 4175 3363 312 930 925 1794 578 M13449 CAIRO_HEPATOBLASTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_DN.html Genes down-regulated in hepatoblastoma samples compared to normal liver tissue. 19061838 267/467 Arthur Liberzon 2.35476725828308e-09 3.52841316161782e-08 1415 904.181818181818 1009 2.14069750982136e-10 247 2.44200752092991 -2.25268000044582 -1 7.26884923948431 1415 1308 247 926 383 495 1128 1324 1009 638 1073 579 M16530 ZHAN_MULTIPLE_MYELOMA_CD1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_DN.html Top 50 down-regulated genes in cluster CD-1 of multiple myeloma samples with the characteristic expression spike of CCND1 [GeneID=595]. 16728703 66/101 Kevin Vogelsang 8.53540418034194e-08 6.48443648357969e-07 1495 1183.54545454545 1011 7.75945864681141e-09 209 1.76539060027567 -1.36840681492241 -1 4.34336272539718 1494 299 1633 1001 209 1175 1011 3318 1331 804 744 580 M10619 KAAB_FAILED_HEART_ATRIUM_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_FAILED_HEART_ATRIUM_DN.html Genes down-regulated in atria of failing hearts (DCM and ICM) compared to healthy controls. 15103417 216/274 John Newman 2.20450536829679e-07 7.7970890443293e-07 560 1388.72727272727 1012 2.00409599018074e-08 545 1.92657374367591 2.1118588305358 1 4.68245734606242 558 2532 2477 878 1053 651 758 545 1071 3741 1012 581 M9126 BEIER_GLIOMA_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BEIER_GLIOMA_STEM_CELL_UP.html Genes up-regulated in cancer stem cells derived from glyoblastoma tumors: CD133+ [GeneID=8842] vs. CD133- cells. 17483311 54/71 Jessica Robertson 6.6502779458357e-08 5.96754979170047e-07 3340 1840.27272727273 1014 6.0457074062399e-09 118 2.61193788376834 2.96997032470837 1 6.48799891526209 3340 418 947 141 118 4168 2865 4335 997 1014 1900 582 M2151 DUTERTRE_ESTRADIOL_RESPONSE_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_6HR_UP.html Genes up-regulated in MCF7 cells (breast cancer) at 6 h of estradiol [PubChem=5757] treatment. 20406972 271/303 Jessica Robertson 2.08341287587636e-07 7.70063333918279e-07 1070 1177 1014 1.89401188470619e-08 339 1.92336507541302 1.88103077313081 1 4.67875707402011 1066 1302 879 724 992 1014 1667 1775 896 339 2293 583 M872 REACTOME_L1CAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_L1CAM_INTERACTIONS.html Genes involved in L1CAM interactions 100/131 Reactome 1.25943668610491e-07 7.16209778122308e-07 2465 1604 1015 1.14494250745822e-08 73 2.25665800629613 2.67369558032095 1 5.52676763760103 2463 73 741 403 462 2819 3794 2888 423 1015 2563 584 M12272 MISSIAGLIA_REGULATED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/MISSIAGLIA_REGULATED_BY_METHYLATION_UP.html Genes up-regulated in PaCa44 and CFPAC1 cells (pancreatic cancer) after treatment with decitabine [PubChem=451668], a DNA hypomethylating agent similar to azacitidine [PubChem=9444]. 15637593 191/288 Leona Saunders 3.27910126756822e-07 9.05922275783096e-07 505 1196.18181818182 1015 2.98100159665323e-08 478 2.21826499140741 -2.13551506836305 -1 5.34084870478286 505 1410 478 1015 1486 639 874 2559 2294 535 1363 585 M2397 SERVITJA_LIVER_HNF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_LIVER_HNF1A_TARGETS_UP.html Genes up-regulated in liver tissue upon knockout of HNF1A [GeneID=6927]. 19289501 165/232 Arthur Liberzon 1.8134065362926e-13 4.86322662005742e-12 2190 1218.45454545455 1017 1.64855139662977e-14 99 2.40815318772451 2.47091643415633 1 10.9063015224801 2189 1428 149 528 808 1017 2642 755 1713 99 2075 586 M8191 ALONSO_METASTASIS_EMT_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_EMT_UP.html EMT (epithelial-mesenchymal transition) genes up-regulated genes in melanoma tumous that developed metastatic disease compared to primary melanoma that did not. 17409456 56/69 Jessica Robertson 2.20239895284664e-07 7.7970890443293e-07 1055 902.363636363636 1018 2.00218106666066e-08 342 2.64416543476375 3.103512644257 1 6.44517146753142 1054 342 445 394 1052 1073 2063 553 1018 501 1431 587 M2143 HOELZEL_NF1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOELZEL_NF1_TARGETS_DN.html Genes down-regulated in SH-SY5Y cells (neuroblastoma) after knockdown of NF1 [GeneID=4763] by RNAi. 20655465 134/179 Arthur Liberzon 2.97688240231411e-13 7.84965639045955e-12 430 1204.18181818182 1018 2.70625672937684e-14 132 2.61341001186577 2.99459301987658 1 11.6216223047165 428 1531 132 1578 2961 696 2489 1018 1798 142 473 588 M16774 WILCOX_RESPONSE_TO_PROGESTERONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILCOX_RESPONSE_TO_PROGESTERONE_DN.html Genes down-regulated in primary cultures of ovarian surface epithlium cells exposed to progesterone [PubChem=5994] for 5 days. 18070364 97/163 Arthur Liberzon 1.29335713528192e-08 1.65887110829638e-07 265 1003.54545454545 1021 1.17577922080494e-09 261 2.7159923251387 3.02904021475427 1 7.35574420705861 261 1591 291 1174 1879 783 1810 1021 1199 362 668 589 M13220 OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_DN.html Genes down-regulated in pirmary cultures of epithelial ovarian cancer (EOC): invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 83/134 Leona Saunders 2.21347019896137e-12 5.04713977734186e-11 185 1147.18181818182 1021 2.01224563542144e-13 154 3.0910461505051 3.26971965960722 1 12.7501094439169 184 1615 154 760 3616 506 1203 2085 1021 409 1066 590 M1663 SASSON_FSH_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_FSH_RESPONSE.html Genes up-regulated in rFSH-17 cells (primary granulosa) after stimulation with FSH. 12832290 11/12 John Newman 2.67318206766338e-07 8.3338304883561e-07 1050 948.727272727273 1023 2.43016581134288e-08 68 2.59931503985585 -3.01825184721103 -1 6.30477640339378 1047 1943 1676 1023 1267 953 412 84 198 1765 68 591 M9377 ALCALAY_AML_BY_NPM1_LOCALIZATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALCALAY_AML_BY_NPM1_LOCALIZATION_UP.html Genes up-regulated in acute myeloid leukemia (AML) with respect to cellular localization of NPM1 [GeneID=4869]: cytoplasmic vs. nucleolar. 15831697 186/271 Kevin Vogelsang 1.13487950356909e-07 7.05613393308323e-07 1415 1253.63636363636 1024 1.0317086928294e-08 91 2.33099186197497 2.48040868643019 1 5.71653487724822 1616 1412 359 91 371 746 2770 3376 1024 614 1411 592 M19695 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP.html Genes up-regulated in kidney biopsies from patients with acute transplant rejection compared to the biopsies from patients with well functioning kidneys more than 1-year post transplant. 15307835 117/208 Jean Junior 3.33177398844254e-07 9.09015793378542e-07 1030 1107.90909090909 1026 3.02888590274612e-08 32 2.24982185595234 -2.03973219640679 -1 5.41619949058755 1026 32 586 442 1510 749 1083 2770 2062 521 1406 593 M2464 DELACROIX_RAR_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RAR_TARGETS_UP.html Genes bound by RARG [GeneID=5916] and up-regulated by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] in MEF cells (embryonic fibroblast). 19884340 62/85 Arthur Liberzon 1.08006663375443e-07 6.98688397397428e-07 1590 1043.09090909091 1027 9.81878806162868e-09 341 2.07819639740621 -2.10436803485257 -1 5.09473147427069 652 360 1587 1027 341 782 1031 1771 1588 939 1396 594 M6792 ODONNELL_TARGETS_OF_MYC_AND_TFRC_DN http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TARGETS_OF_MYC_AND_TFRC_DN.html Genes up-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) by MYC [GeneID=4609] and down-regulated by RNAi knockdown of TFRC [GeneID=7037]. 16508012 53/59 Leona Saunders 5.38511751738391e-06 7.05656709662744e-06 100 1160.63636363636 1028 4.89557336274159e-07 97 2.05314410004244 2.03443036676288 1 4.20345765813094 97 1678 1112 2288 3533 182 155 1028 621 932 1141 595 M15969 VERNELL_RETINOBLASTOMA_PATHWAY_UP http://www.broadinstitute.org/gsea/msigdb/cards/VERNELL_RETINOBLASTOMA_PATHWAY_UP.html Cluster 1: genes up-regulated by RB1, CDNK2A [GeneID=1029;5925], and one of the E2Fs (E2F1, E2F2, or E2F3 [GeneID=1869;1870;1871]). 12923195 91/123 Kevin Vogelsang 1.27970943122607e-06 2.10968214747388e-06 135 953.272727272727 1029 1.16337288692352e-07 104 1.70391518058233 1.7859616401016 1 3.83928936731157 104 134 2049 1429 2748 131 126 477 1208 1029 1051 596 M17294 BIOCARTA_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAS_PATHWAY.html Ras Signaling Pathway 42/44 BioCarta 1.45284418268206e-07 7.26289540930751e-07 570 1508.18181818182 1031 1.32076752602322e-08 515 1.28760920465661 -1.35876709533304 -1 3.12884618920832 1473 567 3540 515 600 1031 568 1397 1737 4133 1029 597 M2650 CAIRO_HEPATOBLASTOMA_POOR_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_POOR_SURVIVAL.html Genes whose expression classifies hepatoblastoma tumors as belonging to either rC1 or rC2 subtypes and whose expression predicts poor survival. 19061838 15/25 Yujin Hoshida 6.14153143381271e-06 7.91806292477356e-06 640 1296.72727272727 1031 5.58322598055526e-07 207 2.83156380230513 2.83761044995164 1 5.7591419874036 637 929 1096 1031 3596 904 207 1845 1467 1702 850 598 M19232 EPPERT_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_PROGENITOR.html Genes up-regulated in human hematopoietic lineage committed progenitor cells versus hematopoietic stem cells (HSC) and mature cells. 21873988 164/189 Kolja Eppert 6.50908348310162e-07 1.30791290081906e-06 395 1190 1032 5.91735037175293e-08 391 1.8717787160298 1.87606017598071 1 4.37875293282839 391 1477 2584 1032 2196 739 592 677 705 1620 1077 599 M143 PID_IL2_PI3K_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_PI3K_PATHWAY.html IL2 signaling events mediated by PI3K 18832364 52/58 Pathway Interaction Database 2.15545114823035e-07 7.72948789223918e-07 605 1416.63636363636 1033 1.95950123582801e-08 256 1.67930036060948 -1.63800997766525 -1 4.07760148536268 604 2240 2862 1089 1033 662 585 256 2440 2847 965 600 M5465 MCCABE_HOXC6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_DN.html Genes with promoters bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and down-regulated upon loss of function (LOF) of HOXC6. 18339881 30/38 Jessica Robertson 1.8016203820901e-07 7.47800341964416e-07 735 1036.72727272727 1033 1.63783684511647e-08 223 2.11924100678905 2.50711022660879 1 5.17119722691955 732 681 1317 2124 835 1033 819 223 1180 1157 1303 601 M18968 HAHTOLA_SEZARY_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_SEZARY_SYNDROM_DN.html Genes down-regulated in monocytes isolated from peripheral blood samples of Sezary syndrom patients compared to those from healthy normal donors. 16914566 40/79 Arthur Liberzon 2.07491526642887e-07 7.68728418959517e-07 3980 1985 1034 1.88628678374831e-08 347 2.84560800684229 -1.97470429522256 -1 6.94705010988777 3976 515 545 1128 988 4641 4574 3403 347 684 1034 602 M1999 WONG_ADULT_TISSUE_STEM_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ADULT_TISSUE_STEM_MODULE.html The 'adult tissue stem' module: genes coordinately up-regulated in a compendium of adult tissue stem cells. 18397753 955/1207 Arthur Liberzon 2.80768795386452e-35 5.09703351624637e-33 1035 1284.09090909091 1034 2.80768795386452e-36 16 2.30550427797331 2.48779218334982 1 29.8912667289358 1034 1083 4642 236 527 224 2913 1426 1555 16 469 603 M2581 DURAND_STROMA_S_UP http://www.broadinstitute.org/gsea/msigdb/cards/DURAND_STROMA_S_UP.html Genes up-regulated in the HSC supportive stromal cell lines. 439/546 Charles Durand 3.35874708775415e-22 2.17168304852049e-20 755 1133.81818181818 1034 3.05340644341285e-23 47 2.44790647497557 2.68167531248429 1 19.307484331534 755 1189 47 1567 989 1034 3027 408 2292 64 1100 604 M12824 SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4.html Cluster 4 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts good survival outcome. 18641660 278/338 Arthur Liberzon 1.06587449968252e-07 6.9392105358641e-07 1765 1145.54545454545 1035 9.68976864839e-09 72 2.13985472640323 -2.24735626287022 -1 5.24993127679842 1761 1295 557 72 335 2148 2195 1662 1035 583 958 605 M2180 PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_UP.html The XPRSS-Int network genes up-regulated in breast tumors from patients with germline mutations in BRCA1 [GeneID=672] compared to those with the wild type allele. 17922014 68/75 Arthur Liberzon 2.40376101463787e-06 3.52790795680682e-06 50 1429.90909090909 1035 2.18523967366907e-07 46 1.54157213775178 1.60786478119562 1 3.33029055014028 46 2169 2777 2362 3620 104 61 665 2022 1035 868 606 M17990 BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_DN.html Genes from cluster 2: down-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 38/69 Jessica Robertson 5.10497501404571e-07 1.12648350006058e-06 1090 1402.81818181818 1036 4.64088745329686e-08 565 2.31436620345942 -2.56788153217419 -1 5.48631596019761 1090 565 838 1805 1965 945 1036 4162 1240 793 992 607 M6031 BIOCARTA_SKP2E2F_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SKP2E2F_PATHWAY.html E2F1 Destruction Pathway 13/15 BioCarta 3.33651416440965e-06 4.65376680142245e-06 695 1339.63636363636 1040 3.03319929506266e-07 176 1.94511549958446 1.90109857988977 1 4.12107724620475 693 927 1897 1040 3308 774 945 1541 176 1729 1706 608 M2100 STAMBOLSKY_BOUND_BY_MUTATED_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_BOUND_BY_MUTATED_TP53.html Gene promoters preferentially bound by a mutated form of TP53 [GeneID=7157] in SKBR3 cells (breast cancer). 20227041 24/32 Arthur Liberzon 6.96017047774813e-08 6.06161982149702e-07 1585 1175 1040 6.32742790722546e-09 132 2.04547622234969 2.41957935858137 1 5.06448055383013 1583 1845 2016 1207 132 1040 706 475 299 2725 897 609 M769 REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS.html Genes involved in Elevation of cytosolic Ca2+ levels 6/9 Reactome 1.25857761735513e-07 7.16209778122308e-07 1095 1268.81818181818 1041 1.25857768863592e-08 185 1.9227890852796 -1.93603072328198 -1 4.70168833928047 1094 1041 4234 2801 555 735 185 1167 369 1487 289 610 M4932 GAJATE_RESPONSE_TO_TRABECTEDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAJATE_RESPONSE_TO_TRABECTEDIN_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) by trabectedin [PubChem=3199]. 12198119 100/142 John Newman 9.03103182001965e-07 1.63102462931498e-06 620 1161.27272727273 1041 8.21003229752128e-08 180 2.16979083475408 -2.13004472305196 -1 5.00020833812719 618 1596 1041 612 2490 697 1295 180 2220 1441 584 611 M5056 REACTOME_HDL_MEDIATED_LIPID_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HDL_MEDIATED_LIPID_TRANSPORT.html Genes involved in HDL-mediated lipid transport 15/27 Reactome 6.47795921956277e-07 1.30722392117727e-06 1260 1197 1045 5.88905557001462e-08 508 2.94583046540708 3.44370966881719 1 6.92032323911344 1256 909 1045 965 2185 728 989 1891 1619 1072 508 612 M11105 NIELSEN_LEIOMYOSARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_DN.html Top 20 negative significant genes associated with CNN1 [GeneID=1264] negative leiomyosarcoma tumors. 11965276 29/32 John Newman 1.23855973961052e-06 2.05555624858005e-06 645 1303.54545454545 1045 1.12596403354322e-07 226 1.79100822222495 1.87166257187442 1 4.04621661691185 643 1816 2079 1660 2728 372 899 814 1045 2057 226 613 M1245 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_UP.html Genes up-regulated in Wilm's tumor vs fetal kidney. 15531917 35/44 Arthur Liberzon 4.1337591577627e-06 5.60426437478643e-06 490 1569.27272727273 1046 3.7579699318544e-07 326 2.15970345994572 2.35788031626466 1 4.51113649782785 488 1773 1380 2817 3406 452 326 1025 3612 1046 937 614 M2115 VERHAAK_GLIOBLASTOMA_PRONEURAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_PRONEURAL.html Genes correlated with proneural type of glioblastoma multiforme tumors. 20129251 232/333 Arthur Liberzon 5.60420072902868e-07 1.18755717431014e-06 950 1065.36363636364 1047 5.09472923329371e-08 409 2.20170221477422 2.33658992396298 1 5.19650188251562 949 1350 409 1143 2066 577 1384 1408 907 479 1047 615 M2309 AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_UP http://www.broadinstitute.org/gsea/msigdb/cards/AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_UP.html Genes up-regulated in RWPE-1 cells (prostate cancer) upon expression of constitutively active form of STAT3 [GeneID=6774]. 17438134 175/256 Arthur Liberzon 1.41000261933664e-16 5.59261543131845e-15 305 930.909090909091 1048 1.28182056303331e-17 81 2.85274012543091 2.93791437548476 1 16.3011922328892 301 1423 81 318 1311 908 1418 1686 1048 411 1335 616 M9823 REN_MIF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/REN_MIF_TARGETS_DN.html Genes down-regulated in SK-N-DZ cells (neuroblastoma) after knockdown of MIF [GeneID=4282] by antisense RNA. 16449971 7/9 Leona Saunders 4.46668316565825e-06 5.98941606304174e-06 605 1779 1049 4.46669214374996e-07 74 1.69379730677499 -1.69379730677499 -1 3.50750573617191 605 3246 4403 2460 3652 401 74 98 1049 3063 518 617 M1435 GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN http://www.broadinstitute.org/gsea/msigdb/cards/GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN.html Genes up-regulated in macrophages by aerolysin-related cytotoxic enterotoxin (Act) from Aeromonas hydrophila. 12824169 110/135 Kevin Vogelsang 9.33141221766594e-08 6.56798957981166e-07 1050 1510.09090909091 1050 8.48310237587504e-09 271 2.38239614085921 -2.40013458998334 -1 5.87353249852337 1050 2574 618 1936 271 731 717 2715 3046 1033 1920 618 M2699 BIOCARTA_SODD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SODD_PATHWAY.html SODD/TNFR1 Signaling Pathway 14/15 BioCarta 3.50482669991151e-07 9.34092717311256e-07 745 1243.90909090909 1052 3.18620659842423e-08 335 2.15372765372602 -2.32498939435375 -1 5.17248944516515 741 942 1711 3089 1553 620 335 1052 1515 1208 917 619 M1655 HAN_JNK_SINGALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAN_JNK_SINGALING_DN.html Genes down-regulated in 3T3 cells (fibroblast) upon activation of JNK pathway. 12354774 56/65 John Newman 1.73478041629861e-07 7.37919956089047e-07 875 1187.09090909091 1053 1.577073230084e-08 492 2.80854722596716 2.72426224672966 1 6.87598497260255 875 1676 492 1139 792 1053 2041 668 1821 1004 1497 620 M5223 BRUNEAU_SEPTATION_ATRIAL http://www.broadinstitute.org/gsea/msigdb/cards/BRUNEAU_SEPTATION_ATRIAL.html Genes for which mutations result in atrial septation defects, a major class of congenital heart disease. 18288184 4/18 Jessica Robertson 5.62235046568281e-07 1.18895583324475e-06 1875 1355.90909090909 1053 5.62235188817042e-08 30 3.4367569356849 3.76395814957796 1 8.13886493133297 1872 1053 4604 133 2153 1521 581 656 30 2149 163 621 M3069 LENAOUR_DENDRITIC_CELL_MATURATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LENAOUR_DENDRITIC_CELL_MATURATION_DN.html Genes down-regulated during in vitro maturation of CD14+ [GeneID=929] monocytes (day 0) into immature (day 7) and mature dendritic cells (day 14). 11279020 145/235 Kevin Vogelsang 1.50643529782035e-07 7.26289540930751e-07 1015 1394.90909090909 1054 1.36948672815683e-08 510 2.09477735674367 -2.35593839623851 -1 5.12160408407621 1015 2550 1054 2161 639 510 599 812 3497 1335 1172 622 M1664 CHEN_ETV5_TARGETS_TESTIS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_ETV5_TARGETS_TESTIS.html Genes down-regulated in testis from 4 week old ETV5 [GeneID=2119] knockout mice. 16107850 24/41 John Newman 1.28035498118204e-06 2.10968214747388e-06 430 1313.36363636364 1054 1.16395975120277e-07 237 1.65687129084071 1.68351465380061 1 3.73190781983014 427 751 2342 2366 2749 305 237 831 2192 1193 1054 623 M12095 BIOCARTA_IL1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL1R_PATHWAY.html Signal transduction through IL1R 34/52 BioCarta 4.29448985172042e-07 1.02013045295019e-06 315 1278.18181818182 1055 3.90408244547509e-08 315 1.79768971768891 -1.97782767913121 -1 4.28147625737088 315 633 2241 1919 1794 540 651 487 2601 1824 1055 624 M17175 MURAKAMI_UV_RESPONSE_24HR http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_24HR.html Genes down-regulated in primary keratinocytes at 24 h after UVB irradiation. 11532376 35/40 John Newman 6.68439739513607e-07 1.33123863734356e-06 1055 1454.54545454545 1055 6.07672675099921e-08 457 2.70174551171955 3.02352018832496 1 6.3341846004959 1055 622 948 2069 2223 457 905 2316 2930 1047 1428 625 M1291 THEODOROU_MAMMARY_TUMORIGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/THEODOROU_MAMMARY_TUMORIGENESIS.html Candidate mammary tumorigenesis genes from the common insertion sites (CIS) of MMTV virus that induced breast tumors in mice. 17468756 33/53 Leona Saunders 1.73819772587021e-07 7.37919956089047e-07 2870 1639.63636363636 1056 1.58017987563952e-08 125 2.38882549986923 3.11197496385905 1 5.84092957367581 2867 598 951 419 796 2908 4631 2020 1665 1056 125 626 M1915 ZHANG_TLX_TARGETS_60HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_60HR_DN.html Genes down-regulated in neural stem cells (NSC) at 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 324/374 Jessica Robertson 3.9280963257198e-09 5.56775214936861e-08 20 1033 1056 3.57099666612128e-10 16 1.74764691248472 1.75771985325647 1 5.04856426043703 16 1249 1576 2259 2786 130 109 638 1281 263 1056 627 M1952 MEISSNER_BRAIN_HCP_WITH_H3K4ME2 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K4ME2.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark (H3K4me2) in brain. 18600261 20/29 Arthur Liberzon 4.43001238153966e-07 1.03461941815276e-06 3355 1683 1056 4.02728479416891e-08 29 2.50320205541632 -2.9147176910138 -1 5.97523450736228 3354 811 1056 54 1830 3906 4331 885 29 766 1491 628 M2435 WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP.html Genes up-regulated in mucinous ovarian carcinoma tumors of grades 1 and 2 compared to the normal ovarian survace epithelium tissue. 16467078 194/221 Arthur Liberzon 8.25847683535601e-08 6.34342404134915e-07 760 944.272727272727 1057 7.50770649578829e-09 198 1.9551433851376 -2.140695143638 -1 4.82309458363812 757 1399 1057 1129 198 1160 1187 1273 579 848 800 629 M9841 TURJANSKI_MAPK8_AND_MAPK9_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK8_AND_MAPK9_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK8 and MAPK9 [GeneID=5599;5601]. 17496919 11/11 Arthur Liberzon 4.22976099211935e-07 1.01085933583814e-06 1785 1267.45454545455 1057 3.84523800485572e-08 95 2.50046643462889 2.80609575225033 1 5.97879611635254 1681 993 1782 2651 1781 624 540 495 95 2243 1057 630 M10487 HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN.html Genes down-regulated during differentiation from small pre-BII to immature B lymphocyte. 11779835 78/114 Arthur Liberzon 3.73781454623774e-07 9.57789612282418e-07 1955 982.727272727273 1059 3.39801380117732e-08 53 1.94833899288927 2.48780642721822 1 4.66592191730377 1954 197 1093 413 1636 1059 1976 548 703 1178 53 631 M9483 SUNG_METASTASIS_STROMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SUNG_METASTASIS_STROMA_UP.html Genes up-regulated in metastatic vs non-metastatic stromal cells originated from either bone or prostate tissues. 19047182 174/236 Jessica Robertson 6.96796129247787e-07 1.36922470027042e-06 985 1270.63636363636 1060 6.33451227219087e-08 483 2.28583129546777 2.46362186729478 1 5.34014731809661 982 1443 483 1199 2256 767 2177 1031 1973 606 1060 632 M259 MANALO_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANALO_HYPOXIA_UP.html Genes up-regulated in response to both hypoxia and overexpression of an active form of HIF1A [GeneID=3091]. 15374877 342/437 Kate Stafford 1.57580474438734e-10 2.92826708405836e-09 1250 1108.36363636364 1060 1.43254976772746e-11 198 2.22316091938475 2.53352203638053 1 7.57941075597717 1250 1240 198 387 1100 1060 3350 554 2129 222 702 633 M17033 LINDSTEDT_DENDRITIC_CELL_MATURATION_A http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_A.html Maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli: genes up-regulated only at 8 hr after the stimulation (cluster A). 12356685 73/96 Arthur Liberzon 6.1967796723624e-07 1.26483853347944e-06 975 1604.09090909091 1061 5.63343765256472e-08 565 2.18099108676311 -2.68782642856981 -1 5.12313257820398 973 2175 956 3104 2156 565 640 1226 3968 821 1061 634 M5360 KANG_IMMORTALIZED_BY_TERT_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_IMMORTALIZED_BY_TERT_UP.html Up-regulated genes in the signature of adipose stromal cells (ADSC) immortalized by forced expression of telomerase (TERT) [GeneID=7015]. 15579653 137/177 Kevin Vogelsang 1.06288630313732e-08 1.38970175922664e-07 1545 992.818181818182 1062 9.66260280247682e-10 221 2.62335117380284 3.01170609630319 1 7.18425758382182 293 1542 283 1183 1545 221 1062 1509 2311 674 298 635 M11318 MITSIADES_RESPONSE_TO_APLIDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/MITSIADES_RESPONSE_TO_APLIDIN_DN.html Genes down-regulated in the MM1S cells (multiple myeloma) after treatment with aplidin [PubChem=44152164], a marine-derived compound with potential anti-cancer properties. 18593922 353/406 Jessica Robertson 1.87595429476188e-07 7.48978540381421e-07 380 1175.81818181818 1062 1.70541314065977e-08 357 1.64367902019815 1.6989623283499 1 3.99908966978927 377 1245 3146 1062 889 357 663 1212 1267 1726 990 636 M2347 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_DN http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_DN.html Top 20 down-regulated genes in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 23/32 Arthur Liberzon 4.12018260508644e-08 4.48093592073917e-07 1310 1037 1063 3.74562062022694e-09 29 2.46142787519677 2.55031797605708 1 6.23442146851114 1631 792 1307 2768 29 1063 1173 244 430 1310 660 637 M6641 BROWNE_HCMV_INFECTION_18HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_18HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 18 h time point that were not down-regulated at the previous time point, 16 h. 11711622 254/356 John Newman 3.34668815854744e-07 9.11504218600341e-07 1110 1133.45454545455 1064 3.04244424332098e-08 382 2.26744547159398 2.60265620657895 1 5.45793573851891 1107 1340 382 405 1568 1064 2798 980 1601 585 638 638 M1860 ZHOU_PANCREATIC_EXOCRINE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_PANCREATIC_EXOCRINE_PROGENITOR.html Transcription factors expressed in progenitors of exocrine pancreatic cells. 18754011 3/14 Jessica Robertson 1.75042519437272e-06 2.70619289794931e-06 765 1446 1064 1.75042657316901e-07 12 2.16689932621453 -2.16689932621453 -1 4.80184932384937 764 1064 4581 1403 3017 636 12 2650 36 1693 50 639 M18483 NAKAMURA_METASTASIS_MODEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_METASTASIS_MODEL_UP.html Top genes up-regulated in orthotopic tumors from highly metastatic pancreatic cancer cells. 17210693 50/65 Jessica Robertson 2.23662773047048e-07 7.84059768106575e-07 805 1176.18181818182 1065 2.0332981435064e-08 466 2.36416858811036 2.57906003345494 1 5.75508094953472 802 466 1387 3052 1072 838 745 894 1065 1328 1289 640 M15590 DORN_ADENOVIRUS_INFECTION_32HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_32HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 32 h after infection with adenovirus Ad12. 15681441 73/90 Arthur Liberzon 1.98680569313107e-06 3.00953879062217e-06 895 1497.09090909091 1065 1.80618862491331e-07 168 2.42006489707376 2.87832089269154 1 5.32380302063503 894 3039 1044 897 3030 1051 2247 1065 1250 1783 168 641 M952 OLSSON_E2F3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OLSSON_E2F3_TARGETS_DN.html Genes down-regulated in the 5637 cell line (bladder cancer) after knockdown of E2F3 [GeneID=1871] by RNAi. 16909110 61/100 Arthur Liberzon 1.35362062367622e-06 2.20617725958279e-06 1845 1567.36363636364 1068 1.2305649604868e-07 331 2.50508898206954 2.36098038381236 1 5.64846636807784 1845 331 653 1044 2784 1025 1068 1943 3639 1027 1882 642 M2427 NAKAMURA_CANCER_MICROENVIRONMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_CANCER_MICROENVIRONMENT_DN.html Genes down-regulated in pancreatic cancer cells grown in orthotopic xenograft tumors compared to those grown in vitro. 17210693 54/56 Arthur Liberzon 4.38295500454983e-06 5.89724846678313e-06 105 1242.45454545455 1069 3.98451248775115e-07 102 1.82742757643374 1.85277363165902 1 3.79312389531811 103 1684 1823 1838 3434 151 102 1069 732 1865 866 643 M12784 RHEIN_ALL_GLUCOCORTICOID_THERAPY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RHEIN_ALL_GLUCOCORTICOID_THERAPY_UP.html Genes up-regulated in ALL (acute lymphoblastic leukemia) blasts after 1 week of treatment with glucocorticoids. 17330098 104/190 Arthur Liberzon 6.02601404638989e-07 1.24278871853236e-06 415 1404.18181818182 1069 5.47819608815856e-08 133 2.35430369674737 -2.4066886487323 -1 5.54145041284162 414 3006 1122 2389 2126 847 805 133 2780 1069 755 644 M10728 BASSO_HAIRY_CELL_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_HAIRY_CELL_LEUKEMIA_DN.html Genes down-regulated in hairy cell leukemia (HCL) compared with normal and other neoplastic B cell populations. 14707115 101/147 Arthur Liberzon 1.54055601906359e-07 7.28175281873995e-07 2215 1544.18181818182 1069 1.40050556994678e-08 99 2.02182297374283 2.5273839755137 1 4.94057672461805 2213 99 1069 434 657 3222 4698 471 979 1252 1892 645 M18855 VECCHI_GASTRIC_CANCER_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_EARLY_UP.html Up-regulated genes distinguishing between early gastric cancer (EGC) and normal tissue samples. 17297478 529/656 Arthur Liberzon 4.07835260213564e-07 9.99471665736252e-07 325 1237.36363636364 1070 4.07835335061902e-08 270 2.06091248846403 1.90932050859579 1 4.92307285544158 324 1158 4298 954 1847 270 485 1070 1480 331 1394 646 M18608 MURATA_VIRULENCE_OF_H_PILORI http://www.broadinstitute.org/gsea/msigdb/cards/MURATA_VIRULENCE_OF_H_PILORI.html Selected genes up-regulated in WT-A10 cells (gastric epithelium) expressing the H. pilori virulence gene CagA. 17237808 26/38 Arthur Liberzon 4.98870074697853e-06 6.58279774272817e-06 890 1549.63636363636 1070 4.53519278122599e-07 348 2.89600353453688 -3.07277899323734 -1 5.98476092534692 923 2333 1070 2788 3510 585 887 887 2540 1175 348 647 M882 BIOCARTA_CXCR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CXCR4_PATHWAY.html CXCR4 Signaling Pathway 41/45 BioCarta 1.03133186906338e-07 6.8232212069871e-07 1575 1356.54545454545 1072 9.37574470373549e-09 322 1.92010557107051 -1.88118761886899 -1 4.71131193141518 1575 563 2343 493 322 1586 1072 2138 533 3369 928 648 M11190 KEGG_DORSO_VENTRAL_AXIS_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DORSO_VENTRAL_AXIS_FORMATION.html Dorso-ventral axis formation 25/28 KEGG 2.62190983499209e-07 8.29211725993449e-07 1875 1289.45454545455 1074 2.38355467951398e-08 239 1.81509595934674 -1.99581202967822 -1 4.38910588516441 1874 777 2364 656 1243 1717 1074 458 239 2863 919 649 M8716 HEDVAT_ELF4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEDVAT_ELF4_TARGETS_UP.html Genes up-regulated in HEL cells (erythroleukemia) upon expression of ELF4 [GeneID=2000]. 14625302 17/21 Kevin Vogelsang 1.7456535242179e-07 7.37919956089047e-07 805 1328.90909090909 1074 1.58695787521076e-08 123 3.29134279743461 -3.65869535899591 -1 8.06658372352045 1928 878 803 123 803 2933 2588 128 1074 1344 2016 650 M5218 SILIGAN_BOUND_BY_EWS_FLT1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/SILIGAN_BOUND_BY_EWS_FLT1_FUSION.html Genes bound by EWSR1-FLT1 [GeneID=2130;2321] fusion but whose expression did not change in STA-ET-7.2 cells (Ewing's sarcoma) after knockdown of EWSR1-FLT1 by RNAi. 15735734 62/89 Leona Saunders 2.15836123770577e-07 7.72948789223918e-07 4005 2225.27272727273 1075 1.96214677223351e-08 346 2.78061738460433 2.73948426635448 1 6.78458519625588 4005 346 836 574 1036 4158 4220 4185 576 1075 3467 651 M3210 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 3 days after transduction. 16818636 27/55 Arthur Liberzon 4.30891696975394e-07 1.02188257382467e-06 935 1308 1077 3.91719801245278e-08 682 3.24217096893362 -3.15083748136436 -1 7.76096605097239 932 708 682 1768 1797 1099 831 3274 754 1077 1466 652 M2408 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_3 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_3.html Genes regulated in MCF7 cells (breast cancer) by expression of the truncated (611-CTF) form of ERBB2 [GeneID=2064] at both 15 h and 60 h time points. 19364815 24/27 Arthur Liberzon 4.43540604297571e-07 1.03485499371455e-06 1030 1409.90909090909 1077 4.03218812472306e-08 509 2.11896517469089 -2.45004964538376 -1 5.05028220309566 1027 2349 1703 2328 1832 1077 901 993 1068 1722 509 653 M7327 LIN_NPAS4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIN_NPAS4_TARGETS_DN.html Genes down-regulated in neurons after NPAS4 [GeneID=266743] knockdown by RNAi. 18815592 71/113 Jessica Robertson 1.54737247398224e-07 7.28175281873995e-07 670 1303.90909090909 1081 1.40670234801533e-08 297 2.38639287466601 2.78021756220374 1 5.84047134315628 1466 297 668 2754 667 903 1579 1605 2743 580 1081 654 M2092 KAMIKUBO_MYELOID_CEBPA_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/KAMIKUBO_MYELOID_CEBPA_NETWORK.html Network of differentially expressed myeloid genes centered around CEBPA [GeneID=1050]. 20478528 27/48 Arthur Liberzon 4.67546415113588e-07 1.06712721437917e-06 1360 1052.09090909091 1081 4.25042285888268e-08 331 3.13897580166556 -3.5851251665931 -1 7.48859751629117 1359 670 638 970 1893 1331 1635 1118 331 1081 547 655 M8831 BRUECKNER_TARGETS_OF_MIRLET7A3_UP http://www.broadinstitute.org/gsea/msigdb/cards/BRUECKNER_TARGETS_OF_MIRLET7A3_UP.html Genes up-regulated in A549 cells (lung cancer) expressing MIRLET7A3 [GeneID=406883] microRNA off a plasmid vector. 17308078 156/201 Jessica Robertson 8.70705262459095e-08 6.50173706444736e-07 2425 1264.90909090909 1084 7.91550269926768e-09 222 2.23468442483667 -2.20265190596901 -1 5.51022037651181 2425 1470 408 549 222 1735 1628 2972 1084 401 1020 656 M2450 PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_UP.html Genes up-regulated after 1 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 42/57 Arthur Liberzon 6.96753942914972e-07 1.36922470027042e-06 750 1602.72727272727 1085 6.33412875983145e-08 264 2.41340085722888 2.55055353868693 1 5.64096718810707 747 2697 966 3072 2254 542 1216 644 4143 1085 264 657 M11106 BIOCARTA_GSK3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GSK3_PATHWAY.html Inactivation of Gsk3 by AKT causes accumulation of b-catenin in Alveolar Macrophages 44/55 BioCarta 6.05844170131748e-07 1.24654946949514e-06 1090 1381.54545454545 1086 5.50767579064936e-08 362 1.73161382846069 -1.67292513182908 -1 4.06164385090198 1086 487 2218 643 2132 839 739 2616 362 2335 1740 658 M979 REACTOME_N_GLYCAN_ANTENNAE_ELONGATION_IN_THE_MEDIAL_TRANS_GOLGI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_N_GLYCAN_ANTENNAE_ELONGATION_IN_THE_MEDIAL_TRANS_GOLGI.html Genes involved in N-glycan antennae elongation in the medial/trans-Golgi 17/19 Reactome 7.8511224255084e-07 1.48051529558129e-06 920 1210.72727272727 1088 7.13738657030325e-08 323 2.36500360578237 2.70801545510117 1 5.49456329187485 919 859 1025 1608 2361 990 1506 323 1387 1088 1252 659 M12166 KRASNOSELSKAYA_ILF3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRASNOSELSKAYA_ILF3_TARGETS_DN.html Down-regulated in GHOST(3)CXCR4 cells (osteosarcoma) upon ectopic expression of ILF3 [GeneID=3609]. 12036489 77/90 John Newman 1.35770863528121e-06 2.21131289114123e-06 270 1128.18181818182 1093 1.2342813392533e-07 270 2.60695787559877 2.80903783359505 1 5.87913607690687 270 1633 422 1216 2989 356 1093 1281 2037 719 394 660 M4551 SANA_RESPONSE_TO_IFNG_UP http://www.broadinstitute.org/gsea/msigdb/cards/SANA_RESPONSE_TO_IFNG_UP.html Genes up-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by IFNG [GeneID=3458]. 15749026 105/166 Yujin Hoshida 7.89418673480181e-07 1.48566831691645e-06 135 1197.90909090909 1094 7.17653597040724e-08 70 1.83977859777109 -1.79757496384403 -1 4.26209021740696 133 70 1094 2271 2367 549 519 1790 2417 613 1354 661 M15066 LIU_CMYB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CMYB_TARGETS_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by overexpression of CMYB [GeneID=4602] off adenovirus vector. 16205643 227/304 Arthur Liberzon 1.19247133613011e-07 7.06112554001409e-07 1940 1116.72727272727 1096 1.08406490978721e-08 326 1.94662158612641 2.03784990391627 1 4.76541215439039 1938 1351 1079 731 412 326 1812 1293 1096 579 1667 662 M1298 GROSS_ELK3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_ELK3_TARGETS_UP.html Genes up-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 39/43 Jessica Robertson 9.66483339268118e-08 6.64473403617636e-07 2680 1657.45454545455 1101 8.78621256115237e-09 288 2.11225445388467 -1.94823100072947 -1 5.19756879665956 2678 530 1101 598 288 2398 1725 3510 823 629 3952 663 M2513 ELVIDGE_HIF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) after knockdown of HIF1A [GeneID=3091] by RNAi. 16565084 124/150 Arthur Liberzon 1.10400456956364e-07 7.03739764799127e-07 2925 1446.45454545455 1103 1.00364056814984e-08 21 2.45862458829431 2.73184813904019 1 6.03342346641776 2924 21 600 344 352 2716 4167 1989 585 1110 1103 664 M1172 IWANAGA_E2F1_TARGETS_INDUCED_BY_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_E2F1_TARGETS_INDUCED_BY_SERUM.html Genes up-regulated in REF52 cells (embryonic fibroblast) by expression of E2F1 [GeneID=1869] that were also induced at 16 hr after serum stimulation. 16288221 35/37 Arthur Liberzon 3.28981330515808e-07 9.05922275783096e-07 1105 1507.90909090909 1103 2.99073981555172e-08 408 1.95018531659737 2.00450368242235 1 4.68935443412985 1102 568 1901 1783 1492 1103 985 4292 408 879 2074 665 M9032 MOHANKUMAR_TLX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOHANKUMAR_TLX1_TARGETS_DN.html Down-regulated in MCF7 cells (breast cancer) by TLX1 (HOX11) [GeneID=3195]. 17213808 226/353 Arthur Liberzon 9.95405139459525e-20 5.59322887886781e-18 3245 1538 1103 9.0491376314502e-21 56 2.68041631439068 2.98890732156321 1 18.5473036380364 3244 1342 56 261 1103 2442 4662 974 939 143 1752 666 M1829 MATZUK_SPERMATOGONIA http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATOGONIA.html Genes important for spermatogonia, based on mouse models with male reproductive defects. 18989307 18/32 Jessica Robertson 1.74687203689809e-06 2.70335607021606e-06 1105 1439.72727272727 1103 1.58806674906657e-07 229 2.05801659424029 1.7216985611482 1 4.55842788755649 1103 874 1289 2268 2954 609 691 3469 1598 753 229 667 M863 LEI_MYB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LEI_MYB_TARGETS.html Myb-regulated genes in MCF7 (breast cancer) and lung epithelial cell lines overexpressing MYBL2, MYBL1 or MYB [GeneID=4605;4603;4602]. 15105423 440/532 Kevin Vogelsang 1.70173721764312e-09 2.62954769025271e-08 1890 1149.63636363636 1104 1.54703383541768e-10 235 2.22597545366818 2.33186540439463 1 6.73570017874331 1888 1194 235 361 439 655 2509 2200 1104 310 1751 668 M1170 HUMMERICH_SKIN_CANCER_PROGRESSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_SKIN_CANCER_PROGRESSION_DN.html Selected genes down-regulated during progression through benign to malignant skin tumors formed by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 155/194 Arthur Liberzon 2.31149285777202e-07 7.94929240715632e-07 480 1004.45454545455 1105 2.10135736421423e-08 382 2.39830391227756 2.66034332491747 1 5.83313175286606 477 1488 515 611 1105 382 1181 1126 2477 1247 440 669 M11594 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_22 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_22.html Amplification hot spot 22: colocolized fragile sites and cancer genes in the 22q11.1-q13s region. 16751803 16/25 Arthur Liberzon 2.31236832098e-07 7.94929240715632e-07 1250 1308.81818181818 1106 2.10215324002513e-08 209 2.07429438519303 2.35221239849729 1 5.03831889731746 1246 1910 2172 2822 1106 964 752 209 289 2707 220 670 M2970 WILLIAMS_ESR1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR1_TARGETS_UP.html The 'ER-alpha profile': genes up-regulated in T47D cells (breast cancer, ESR2 [GeneID=2100] Tet-Off) upon activation of ESR1 [GeneID=2099] by estradiol (E2) [PubChem=5757]. 17700529 31/50 Jessica Robertson 2.25451634410049e-06 3.35688237985941e-06 745 1206.63636363636 1107 2.04956241317038e-07 341 2.53322594164813 2.30637308277089 1 5.52675476375449 742 1803 1107 833 3092 623 341 598 1370 1454 1310 671 M11262 MORI_IMMATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_IMMATURE_B_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature based on expression profiling of lymphomas from the Emu-myc transgenic mice: the immature B stage. 18922927 68/84 Jessica Robertson 4.92430314777022e-07 1.10364249085828e-06 790 1358.81818181818 1107 4.4766402272609e-08 308 1.90202447833106 -1.87804497033596 -1 4.50673027902647 789 308 1705 2799 1928 673 1107 918 3069 1273 378 672 M178 CROMER_TUMORIGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_TUMORIGENESIS_UP.html Tumorigenesis markers of head and neck squamous cell carcinoma (HNSCC): up-regulated in the 'early' tumors vs normal samples. 14676830 72/110 Arthur Liberzon 1.34934631582173e-13 3.77136523757706e-12 2155 1154.09090909091 1108 1.22667846892892e-14 124 3.1453246187957 3.02941638914635 1 14.3998803380258 316 247 124 354 2885 1318 2152 2154 1752 285 1108 673 M2222 ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_DN.html Genes down-regulated in K562 cells (lymphoblast) by MYC [GeneID=4609] in the presence of CKN1B [GeneID=1027]. 18838534 140/188 Arthur Liberzon 1.50421250445635e-07 7.26289540930751e-07 695 1316.90909090909 1108 1.36746600664029e-08 322 1.88429051824787 -1.80202801563163 -1 4.60194865900308 691 2097 1687 1016 636 322 1147 1108 3435 1442 905 674 M999 HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_DN.html Genes down-regulated in hematopoietic progenitor cells (HPC) of T lymphocyte and NK (natural killer) lineage. 15331438 51/109 Kevin Vogelsang 2.03627362491331e-09 3.08051650948425e-08 1865 1482.45454545455 1110 1.85115784254367e-10 28 2.85732928995901 3.07541527394481 1 8.58134757679973 1864 368 242 929 28 3111 4602 1515 1110 205 2333 675 M4388 BIOCARTA_CDMAC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CDMAC_PATHWAY.html Cadmium induces DNA synthesis and proliferation in macrophages 26/29 BioCarta 2.32517506587256e-07 7.97009899122621e-07 1045 1906.63636363636 1111 2.11379573783621e-08 438 1.410660354219 -1.56985155176586 -1 3.40974476669047 1043 3446 3258 1104 1111 742 438 1698 4086 3002 1045 676 M12289 REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS.html Genes involved in Peptide ligand-binding receptors 69/226 Reactome 7.62759589694397e-14 2.23616475984941e-12 2250 1351.90909090909 1111 6.93417808813111e-15 118 3.14604529923251 -2.99972020694185 -1 14.6903892863419 2247 279 118 1769 1608 1111 984 961 2964 265 2565 677 M1204 TERAMOTO_OPN_TARGETS_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_8.html Cluster 8: genes showing sustained pattern of down-regulation after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 8/8 Arthur Liberzon 1.62468331043128e-07 7.3358205358541e-07 2980 2016.45454545455 1111 1.6246834292131e-08 5 3.56660891804192 3.10520429617165 1 8.74907690136537 2977 980 4388 38 832 2665 4572 455 5 1111 4158 678 M13809 LIAO_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/LIAO_METASTASIS.html Genes up-regulated in the samples with intrahepatic metastatic hepatocellular carcinoma (HCC) vs primary HCC. 18504433 725/853 Jessica Robertson 2.34444338343811e-07 7.98113405922816e-07 1840 1472.36363636364 1111 2.34444363077681e-08 108 1.92776557824639 2.10477356240467 1 4.67752984828496 1840 1111 4436 108 1221 722 2954 1316 1069 596 823 679 M16963 RAMASWAMY_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMASWAMY_METASTASIS_DN.html Down-regulated genes in metastatic vs primary solid tumors. 12469122 74/105 John Newman 3.39154689099432e-07 9.15271659547923e-07 2620 1289.18181818182 1111 3.08322492167222e-08 15 2.50389749806638 2.87810365038882 1 6.03051016559869 582 2617 1039 2618 2986 371 1111 15 1453 1362 27 680 M4995 LINDGREN_BLADDER_CANCER_CLUSTER_2B http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_2B.html Genes specifically up-regulated in Cluster IIb of urothelial cell carcinom (UCC) tumors. 16532037 508/674 Arthur Liberzon 3.13954500707695e-18 1.52769612715497e-16 2015 1586.36363636364 1112 3.13954500707695e-19 51 2.46734089290126 2.79033253683196 1 15.6436666335931 701 2014 4362 1112 2014 897 2689 624 2181 51 805 681 M2017 MIKKELSEN_NPC_WITH_LCP_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_WITH_LCP_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing histone H3 trimethylation mark at K27 in neural progenitor cells (NPC). 17603471 8/11 Arthur Liberzon 5.82374879461032e-08 5.56439156084225e-07 2065 1432.18181818182 1112 5.82374894723254e-09 108 3.66314350014622 -3.90758734837864 -1 9.16406235168464 2062 1003 4648 558 108 1768 1125 2353 594 1112 423 682 M8583 STEIN_ESTROGEN_RESPONSE_NOT_VIA_ESRRA http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESTROGEN_RESPONSE_NOT_VIA_ESRRA.html Genes up-regulated by estradiol [PubChem=5757] and not modulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 21/24 Arthur Liberzon 1.77351829078262e-07 7.4119215967118e-07 1115 1455.81818181818 1114 1.61228948523079e-08 346 1.81392192262304 2.11685243292566 1 4.42178597606403 1114 1866 2116 3085 821 1044 1060 346 1791 2303 468 683 M1004 REACTOME_LIGAND_GATED_ION_CHANNEL_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIGAND_GATED_ION_CHANNEL_TRANSPORT.html Genes involved in Ligand-gated ion channel transport 4/24 Reactome 2.1207140250938e-07 7.70763712250053e-07 1580 1455.72727272727 1116 2.12071422747808e-08 9 3.17780157732197 3.19380977913583 1 7.76241587451794 1579 1050 4255 323 1116 1680 1054 3420 9 1388 139 684 M4217 REACTOME_MITOTIC_PROMETAPHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_PROMETAPHASE.html Genes involved in Mitotic Prometaphase 102/108 Reactome 4.39419919590998e-07 1.02957416944572e-06 55 1146 1117 3.99472733962857e-08 55 1.80000551709482 1.88193725795822 1 4.28415918346074 55 2577 2458 1839 1823 83 73 741 1117 1296 544 685 M1399 KHETCHOUMIAN_TRIM24_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KHETCHOUMIAN_TRIM24_TARGETS_UP.html Retinoic acid-responsive genes up-regulated in hepatocellular carcinoma (HCC) samples of TRIM24 [GeneID=8805] knockout mice. 18026104 73/82 Leona Saunders 1.02445209176486e-08 1.34317052031392e-07 1070 1248.18181818182 1117 9.31320087759383e-10 259 2.91852133133315 3.09485595524985 1 8.0155945526421 1070 259 281 459 2602 1139 3012 1455 1761 575 1117 686 M2496 PHONG_TNF_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_TARGETS_UP.html Genes up-regulated in Calu-6 cells (lung cancer) at 1 h time point after TNF [GeneID=7124] treatment. 20516219 89/104 Arthur Liberzon 1.66535133986153e-07 7.3358205358541e-07 1120 1489.27272727273 1118 1.5139558781136e-08 176 2.5365508320823 -2.30503466034116 -1 6.20783988646826 1118 176 401 1266 742 1477 848 4035 3185 546 2588 687 M759 REACTOME_PKA_MEDIATED_PHOSPHORYLATION_OF_CREB http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PKA_MEDIATED_PHOSPHORYLATION_OF_CREB.html Genes involved in PKA-mediated phosphorylation of CREB 14/16 Reactome 5.46459053001602e-07 1.17240305916707e-06 1120 1281.54545454545 1119 4.96781080669887e-08 5 2.26073477606875 2.19831488301008 1 5.34224436344578 1119 1929 1689 1646 2038 934 1005 1010 363 2359 5 688 M566 VERRECCHIA_RESPONSE_TO_TGFB1_C4 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C4.html Cluster 4: ECM related genes up-regulated in dermal fibroblasts later than 30 min after TGFB1 [GeneID=7040] addition; kept increasing with time. 11279127 45/55 John Newman 5.87645004896921e-06 7.61791931643359e-06 575 1545 1119 5.34224158699446e-07 466 2.44095074689391 2.78759697663928 1 4.97424285864534 575 1722 770 891 3576 1119 1935 2803 2130 1008 466 689 M5650 REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE.html Genes involved in Cytochrome P450 - arranged by substrate type 21/99 Reactome 1.11717955068127e-07 7.04017019921975e-07 4385 2138.45454545455 1120 1.01561782492058e-08 362 3.22953037719932 3.2487821451897 1 7.94068038799325 4384 762 473 1120 362 4486 4206 3844 1064 554 2268 690 M2164 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION.html Leukocyte transendothelial migration 100/141 KEGG 2.54614990544134e-07 8.22189102913976e-07 3375 1881.36363636364 1121 2.31468200010702e-08 81 2.38758364224799 -2.516139137306 -1 5.79277398840406 3373 81 404 98 1211 4520 4378 4246 665 598 1121 691 M16189 BERENJENO_TRANSFORMED_BY_RHOA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector. 17213802 675/796 Leona Saunders 8.93419119096224e-07 1.61940792708686e-06 95 1456.54545454545 1123 8.934194782854e-08 95 1.72852828581739 1.76696853988188 1 3.97531601236819 95 1123 4341 2353 2554 333 253 711 2380 545 1334 692 M11542 YE_METASTATIC_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/YE_METASTATIC_LIVER_CANCER.html Genes up-regulated in hepatocellular carcinoma (HCC) with intra-hepatic metastasis compared to the non-metastatic tumors. 12640447 40/71 Yujin Hoshida 2.34074453591915e-07 7.98113405922816e-07 1105 1322.45454545455 1123 2.12794980451682e-08 99 2.37605814086109 2.28603582361133 1 5.77690269642303 1101 2710 1774 2409 1123 521 1069 113 1444 2184 99 693 M8570 DOANE_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_ESR1_DN.html Genes down-regulated in breast cancer samples positive for ESR1 [GeneID=2099] compared to the ESR1 negative tumors. 16491124 54/77 Arthur Liberzon 4.43067413650982e-13 1.11833058418857e-11 4490 2060.63636363636 1125 4.0278855786461e-14 136 3.569031363879 3.86168844172527 1 15.6688516458239 4488 350 136 255 1125 4546 3682 3621 193 264 4007 694 M18917 MORI_IMMATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_IMMATURE_B_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature based on expression profiling of lymphomas from the Emu-myc transgenic mice: the immature B stage. 18922927 137/197 Jessica Robertson 3.57104418355395e-07 9.41752134134615e-07 40 976.909090909091 1125 3.24640433018787e-08 39 1.88472511230822 1.91885562209735 1 4.51750290798819 39 1504 1125 1448 2946 134 106 625 1179 513 1127 695 M576 REACTOME_GLYCOSPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSPHINGOLIPID_METABOLISM.html Genes involved in Glycosphingolipid metabolism 32/36 Reactome 1.33904120605994e-07 7.20206492018647e-07 1125 1881.09090909091 1127 1.21731026141943e-08 518 1.39269502768173 -1.2743861671723 -1 3.39033069205121 1123 1800 3536 3730 518 752 1127 1002 2949 3361 794 696 M16523 REACTOME_GENERATION_OF_SECOND_MESSENGER_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GENERATION_OF_SECOND_MESSENGER_MOLECULES.html Genes involved in Generation of second messenger molecules 17/33 Reactome 1.57126620429165e-08 1.98830468746825e-07 4290 2090.90909090909 1127 1.42842383228529e-09 1 2.64188267754012 -3.0214755116214 -1 7.07008276260912 4289 863 1127 964 1 4519 3790 2630 210 1087 3520 697 M1723 LEIN_CEREBELLUM_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_CEREBELLUM_MARKERS.html Top 100 ranked genes most specific to the cerebellum region of adult mouse brain. 17151600 84/121 Jessica Robertson 1.17213177689683e-07 7.06112554001409e-07 2320 1400.45454545455 1127 1.06557439940592e-08 168 2.12476649672488 2.20084131890908 1 5.20609759412494 2316 168 812 716 401 1776 3089 2438 844 1127 1718 698 M1417 JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN http://www.broadinstitute.org/gsea/msigdb/cards/JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN.html Genes down-regulated during epithelial to mesenchymal transition (EMT) induced by TGFB1 [GeneID=7040] in the EpH4 cells (mammary epithelium cell line transformed by HRAS [GeneID=3265]). 14562044 102/124 Arthur Liberzon 2.14393882838541e-07 7.71883392065533e-07 3175 2026.54545454545 1130 1.94903548846915e-08 104 2.44598738444499 -2.05328461994746 -1 5.96267017177868 3172 104 621 738 1028 3434 3023 4190 1130 543 4309 699 M8544 GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_UP.html Up-regualted genes from the set F (Fig. 5a): specific signature shared by cells expressing AF4-MLL [GeneID=4299;4297] alone and those expressing both AF4-MLL and MLL-AF4 fusion proteins. 17130830 283/339 Arthur Liberzon 1.56230241002108e-14 4.85136011532863e-13 885 1168.09090909091 1131 1.42027491820099e-15 109 2.44311427420979 2.68128895119685 1 12.0489327800943 883 1298 109 1131 1786 1020 3009 438 1840 159 1176 700 M17807 KEGG_BASAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_CELL_CARCINOMA.html Basal cell carcinoma 45/60 KEGG 3.58048556543303e-06 4.94004439311427e-06 935 1227.72727272727 1132 3.25499217514825e-07 219 2.65748504147836 3.07459528506896 1 5.62097732614835 931 480 815 2061 3348 751 1353 1188 219 1132 1227 701 M16498 REACTOME_SEMA3A_PAK_DEPENDENT_AXON_REPULSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA3A_PAK_DEPENDENT_AXON_REPULSION.html Genes involved in Sema3A PAK dependent Axon repulsion 32/35 Reactome 6.49875554554566e-07 1.30791290081906e-06 760 1359.72727272727 1135 5.90796133205973e-08 342 2.17900408200377 2.5701556068828 1 5.10567468325634 756 1788 1557 875 2190 975 1696 342 2628 1135 1015 702 M12225 PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP.html Up-regulated genes in angioimmunoblastic lymphoma (AILT) compared to normal T lymphocytes. 18006812 277/361 Arthur Liberzon 2.72070353237862e-25 2.46956166785136e-23 335 1330 1135 2.47336684761693e-26 30 2.70476040365505 2.96334668070395 1 24.5411610623553 335 2035 30 1568 2475 916 2416 1135 2738 48 934 703 M2240 JOHNSTONE_PARVB_TARGETS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_3_UP.html Genes up-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D Matrigel only. 17998334 613/767 Arthur Liberzon 1.11163577981522e-07 7.03739764799127e-07 1320 1506.90909090909 1135 1.11163583542325e-08 411 1.85421893684058 -1.73546808516574 -1 4.53792146601065 1316 1135 4670 411 437 709 1576 2514 1744 1021 1043 704 M7416 ST_GAQ_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GAQ_PATHWAY.html G alpha q Pathway 31/35 Signaling Transduction KE 9.68444147642813e-08 6.64473403617636e-07 1085 1450.18181818182 1136 8.80403809339916e-09 291 1.47957838465539 -1.79008442193613 -1 3.62577203193357 1081 677 3165 2461 291 1265 1136 672 1897 2297 1010 705 M10845 GOLDRATH_IMMUNE_MEMORY http://www.broadinstitute.org/gsea/msigdb/cards/GOLDRATH_IMMUNE_MEMORY.html 'Memory genes' expressed uniquely in CD8+ [GeneID=925] memory T lymphocytes (compared with effector or naive cells) 15548615 78/90 Kate Stafford 1.5795433325082e-07 7.31918027928963e-07 4230 2135.72727272727 1137 1.43594858719577e-08 214 2.015891707039 -1.64086505891927 -1 4.92413107903863 4229 214 1128 1137 682 3929 2967 3197 531 949 4530 706 M5053 EHRLICH_ICF_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/EHRLICH_ICF_SYNDROM_UP.html Up-regulated in B lymphocytes from patients with ICF syndrom caused by mutations in DNMT3B [GeneID=1789] compared to normals. 11741835 18/23 John Newman 2.07230022901908e-07 7.68728418959517e-07 1140 1602.36363636364 1137 1.88390947656399e-08 159 2.44532736279023 2.67994612759059 1 5.96279697424586 1137 3481 2078 3110 986 1342 507 159 993 3047 786 707 M750 REACTOME_ADENYLATE_CYCLASE_INHIBITORY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADENYLATE_CYCLASE_INHIBITORY_PATHWAY.html Genes involved in Adenylate cyclase inhibitory pathway 12/14 Reactome 4.48700202336798e-08 4.70636656673264e-07 1805 1148.54545454545 1138 4.07909283171135e-09 10 2.36496400705553 2.81326145346886 1 5.9678576645881 1801 948 1404 444 39 1946 2741 1138 200 1963 10 708 M1794 WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_DN.html Protease genes down-regulated at tumor-bone interface compared to the tumor alone area. 18632634 4/7 Jessica Robertson 2.15355690949418e-07 7.72948789223918e-07 1990 1604.72727272727 1138 2.15355711819554e-08 4 3.55784839802504 -3.34161977342974 -1 8.69498124670382 1990 1048 4557 64 1138 1531 216 4411 4 2148 545 709 M2075 WHITFIELD_CELL_CYCLE_S http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_S.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the S phase of cell cycle. 12058064 199/285 Jessica Robertson 1.33615598089689e-06 2.18450163832121e-06 430 1123.90909090909 1139 1.214687993094e-07 64 1.94456264004144 2.07348792437776 1 4.37675071271718 426 2064 1139 1206 2774 64 434 1356 1859 781 260 710 M10091 WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN.html Genes down-regulated in mucinous ovarian carcinoma tumors of low malignant potential (LMP) compared to normal ovarian surface epithelium tissue. 16467078 255/317 Arthur Liberzon 1.26921213888282e-07 7.19819980220572e-07 475 910.727272727273 1140 1.1538292837323e-08 81 1.90661729930345 2.09184129496883 1 4.66004918101782 475 1331 1203 1598 466 230 1308 613 1573 1140 81 711 M16488 DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY.html The lung adenocarcinoma TSP (tumor sequencing project) genes that were found significantly mutated by at least one method. 18948947 50/58 Jessica Robertson 2.26355352078364e-07 7.86164283892477e-07 2215 1367.09090909091 1141 2.05777613970724e-08 173 2.7172893637281 3.03410987756022 1 6.62088223948095 2215 444 699 173 1084 2349 3695 1141 518 1327 1393 712 M19245 COULOUARN_TEMPORAL_TGFB1_SIGNATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/COULOUARN_TEMPORAL_TGFB1_SIGNATURE_DN.html 'Early-TGFB1 signature': genes overexpressed in primary hepatocytes at an early phase of TGFB1 [GeneID=7040] treatment; is associated with a less invasive phenotype. 18506891 182/254 Yujin Hoshida 4.06531886160549e-07 9.97313151079934e-07 1150 1192.09090909091 1141 3.69574510256788e-08 121 2.17869645145032 -2.16637360987118 -1 5.20811557331405 1148 1433 920 121 1727 1110 1500 1815 1079 1141 1119 713 M3126 KEGG_LEISHMANIA_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEISHMANIA_INFECTION.html Leishmania infection 68/98 KEGG 2.42699111541335e-06 3.55757703874256e-06 310 1796.54545454545 1142 2.20635799347287e-07 249 1.83815670244568 -1.89068077650282 -1 3.97794644037259 309 3355 2200 2957 3141 249 363 1127 4062 1142 857 714 M156 PID_ECADHERIN_NASCENT_AJ_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ECADHERIN_NASCENT_AJ_PATHWAY.html E-cadherin signaling in the nascent adherens junction 18832364 67/73 Pathway Interaction Database 2.08848717452161e-07 7.70426069813627e-07 1575 1566 1142 1.89862488434937e-08 306 1.48483507231609 -1.38353735990012 -1 3.60046305500143 1574 306 2965 495 995 1142 795 3454 1407 3169 924 715 M7804 ROSS_ACUTE_MYELOID_LEUKEMIA_CBF http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_ACUTE_MYELOID_LEUKEMIA_CBF.html Top 100 probe sets for core-binding factor (CBF) acute myeloid leukemia (AML): contains CBFB MYH11 [GeneID=865;4629] or AML1 ETO [GeneID=861;862] fusions. 15226186 98/176 Kate Stafford 2.75244093952791e-07 8.38703759494626e-07 1145 1216.81818181818 1142 2.50221934898952e-08 346 2.2139425246376 2.46262890355228 1 5.36015556968811 1286 1598 990 2570 1302 346 912 1142 977 1120 1142 716 M1424 LEE_LIVER_CANCER_DENA_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_DENA_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by diethylnitrosamine (DENA) [PubChem=5921]. 15565109 74/159 Yujin Hoshida 2.83918288229622e-07 8.51178263306103e-07 1385 1167.72727272727 1143 2.58107568063958e-08 207 2.54421285471136 -2.50239455985089 -1 6.16067380531144 1382 207 380 932 1335 1112 1143 2064 2289 322 1679 717 M8520 SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6.html Cluster 6 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts poor survival outcome. 18641660 580/733 Arthur Liberzon 1.02128582790883e-06 1.78074218977824e-06 90 1341.90909090909 1144 1.02128629727027e-07 89 1.82112804989433 1.84730788662616 1 4.16075283159843 89 1144 4603 1386 2647 255 372 951 1348 694 1272 718 M15243 REACTOME_GAP_JUNCTION_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_DEGRADATION.html Genes involved in Gap junction degradation 10/11 Reactome 3.95098159861029e-07 9.81507007654768e-07 1040 1431.81818181818 1145 3.59180209833413e-08 441 1.74931682282226 -1.35070002393638 -1 4.17671472377306 1040 994 2743 1461 1695 929 617 2146 441 2539 1145 719 M2668 KEGG_BETA_ALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BETA_ALANINE_METABOLISM.html beta-Alanine metabolism 24/30 KEGG 6.80741735906949e-07 1.34664752450998e-06 1055 1368.90909090909 1147 6.18856315043307e-08 536 2.25095335857245 2.21140759400516 1 5.2644387757618 1051 780 1255 2365 2239 884 536 858 2227 1716 1147 720 M1680 SUZUKI_RESPONSE_TO_TSA http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_RESPONSE_TO_TSA.html Genes up-regulated by TSA alone [PubChem=5562], with non-hypermethylated promoters, in RKO cells (colorectal cancer). 11992124 23/32 John Newman 3.50482940802315e-08 3.96709707574802e-07 1275 1199.72727272727 1147 3.18620860350794e-09 20 2.10867314962502 1.84721169102452 1 5.37863374126683 1271 800 2108 2789 20 711 610 1357 1147 1897 487 721 M1189 DING_LUNG_CANCER_BY_MUTATION_RATE http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_BY_MUTATION_RATE.html The lung adenocarcinoma TSP (tumor sequencing project) genes mutations in which show positive correlation with the higher overall mutation rate. 18948947 43/47 Arthur Liberzon 5.10148518882697e-07 1.12623994814141e-06 2450 1410.54545454545 1147 4.63771488344434e-08 145 2.78514049892353 3.69627242780501 1 6.61259242123429 2450 505 709 145 1964 2445 3187 1475 478 1147 1011 722 M1616 BURTON_ADIPOGENESIS_7 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_7.html Down-regulated at 48-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 74/94 John Newman 4.23425856379894e-07 1.01142208608963e-06 715 1036.54545454545 1149 3.84932670795567e-08 132 2.00557098751109 2.07509055772046 1 4.7853669326529 715 257 1242 1649 1782 263 1149 474 2376 1363 132 723 M15380 KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_DN.html Top 25 most highly expressed genes in seminoma relative to embryonic carcinoma tumors. 16424014 24/90 Arthur Liberzon 1.22858336704085e-07 7.12872631945934e-07 1870 1449.63636363636 1149 1.11689403240975e-08 91 2.2214069161613 2.5845748240175 1 5.44146479156065 1868 742 1062 1149 442 1809 3370 4026 192 1195 91 724 M4502 GAL_LEUKEMIC_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAL_LEUKEMIC_STEM_CELL_DN.html Genes down-regulated in leukemic stem cells (LSC), defined as CD34+CD38- [GeneID=947;952] cells from AML (acute myeloid leukemia patients) compared to the CD34+CD38+ cells. 17039238 251/464 Leona Saunders 1.73429374642057e-13 4.75922469947970e-12 1120 1271.09090909091 1150 1.57663067856428e-14 102 2.36177895172976 2.55387088679163 1 10.7042305156904 1120 1326 128 2263 435 1150 2260 339 3196 102 1663 725 M7735 BOYLAN_MULTIPLE_MYELOMA_C_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_DN.html Genes down-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 78/102 Jessica Robertson 2.39674942452774e-07 8.03455772995096e-07 3495 1998.90909090909 1150 2.1788633505793e-08 76 2.33903863192655 -2.39647207714075 -1 5.6833922167923 3494 224 716 76 1150 3916 3314 4306 544 671 3577 726 M88 PID_CD8_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD8_TCR_PATHWAY.html TCR signaling in naïve CD8+ T cells 18832364 74/109 Pathway Interaction Database 1.47140131429558e-07 7.26289540930751e-07 855 1370.72727272727 1151 1.33763764791424e-08 179 1.60053343773029 -1.32812858006622 -1 3.90140173954896 855 246 2326 179 613 1151 1014 1383 3259 2038 2014 727 M1044 REACTOME_CONVERSION_FROM_APC_C_CDC20_TO_APC_C_CDH1_IN_LATE_ANAPHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CONVERSION_FROM_APC_C_CDC20_TO_APC_C_CDH1_IN_LATE_ANAPHASE.html Genes involved in Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase 19/21 Reactome 2.73701977311366e-06 3.92905514875197e-06 895 1811.72727272727 1151 2.48820288931419e-07 104 1.0595625446831 1.10434344774857 1 2.25342002157344 893 872 3443 2927 3213 398 104 1151 2146 3829 953 728 M16644 PARENT_MTOR_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARENT_MTOR_SIGNALING_DN.html Genes down-regulated in HepaRG cells (liver cancer) expressing constituvely active form of MTOR [GeneID=2475]. 17483347 51/81 Arthur Liberzon 2.00688468870157e-07 7.65527859584926e-07 3580 2042.27272727273 1151 1.82444079252154e-08 417 2.94034578186908 -2.87351207697973 -1 7.18214415345288 3578 422 417 1151 940 4135 2943 4005 932 715 3227 729 M6386 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_4 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_4.html The 'group 4 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 but not ERBB2 [GeneID=2099;2064]. 18794137 396/488 Jessica Robertson 6.12372631676439e-07 1.25560331082224e-06 1240 1152.81818181818 1151 5.56702547391964e-08 421 2.11186772705613 2.30080949073355 1 4.9618794926129 1238 1222 561 789 2142 421 1969 893 1292 1003 1151 730 M11636 GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN.html Genes down-regulated in quiescent (G0) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the quiescent cells from normal donors. 17717066 52/82 Arthur Liberzon 1.54323372245258e-07 7.28175281873995e-07 4595 2077.63636363636 1153 1.40293984609617e-08 375 2.53782209974586 2.72005438450687 1 6.21425520296947 4591 380 579 375 660 3787 4483 1740 1153 449 4657 731 M1549 LINDVALL_IMMORTALIZED_BY_TERT_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDVALL_IMMORTALIZED_BY_TERT_UP.html Genes up-regulated in BJ cells (foreskin fibroblasts) immortalized by expression of TERT [GeneID=7015]. 12702554 102/119 John Newman 2.93098457510458e-07 8.66807468326668e-07 1995 1386.18181818182 1154 2.66453178689971e-08 98 2.19451432314248 2.63316169687187 1 5.30004617508755 1995 98 978 1154 1362 2263 3718 318 1298 1005 1059 732 M2619 ZWANG_EGF_INTERVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_INTERVAL_UP.html Genes induced in the time interval between two pulses of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 85/171 Yaara Zwang 2.40785745283019e-07 8.0442878985801e-07 2935 1982.54545454545 1154 2.18896156033234e-08 227 2.53026967093423 2.38758254676816 1 6.15160106341922 2934 227 752 2752 1154 3505 4603 800 982 960 3139 733 M649 REACTOME_PHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHOLIPID_METABOLISM.html Genes involved in Phospholipid metabolism 180/208 Reactome 2.41067930885089e-07 8.0442878985801e-07 630 1602.90909090909 1156 2.19152688454939e-08 111 1.54587458751333 -1.56521382278309 -1 3.73886922780315 627 2076 3454 2845 1156 111 974 774 1962 3398 255 734 M6250 KORKOLA_YOLK_SAC_TUMOR http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_YOLK_SAC_TUMOR.html Genes predicting the yolk sac tumor (YS) subtype of nonseminomatous male germ cell tumors (NSGCT). 15870693 95/124 Leona Saunders 9.82537601619584e-17 4.06805042074073e-15 785 1146.45454545455 1156 8.93216001472348e-18 78 2.88966341572844 2.9942047064954 1 16.6734648930549 781 89 78 304 2334 1313 2912 1685 1762 197 1156 735 M2361 TERAO_AOX4_TARGETS_HG_DN http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_HG_DN.html Genes down-regulated in Harderian gland tissue upon knockout of AOX4 [GeneID=71872]. 18981221 9/10 Arthur Liberzon 4.88396704168471e-07 1.099106798882e-06 1160 1659.90909090909 1157 4.88396811507606e-08 145 2.33306742404641 -2.59020882462253 -1 5.54107778631269 1157 1969 4690 2286 2018 720 145 721 950 2903 700 736 M6315 IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_DN.html Cluster 2: genes down-regulated in lung tissue samples from mice with oncogenic form of KRAS [GeneID=3845] and inactivated PTEN [GeneID=5728]. 18281487 443/575 Jessica Robertson 3.84024587721486e-08 4.24874250277305e-07 1160 1214.63636363636 1158 3.4911326765899e-09 318 2.18254774948174 2.54074316107916 1 5.54267444689586 1158 1198 318 1580 1707 613 2219 1046 2228 705 589 737 M1951 MEISSNER_NPC_HCP_WITH_H3K4ME2 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K4ME2.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark at K4 (H3K4me2) in neural precursor cells (NPC). 18600261 559/753 Arthur Liberzon 9.81355879769568e-29 1.10285708393151e-26 1165 1322.72727272727 1161 9.81355879769558e-30 30 2.50185216528916 2.7470379207497 1 26.0670560103837 1161 1137 4625 228 601 444 2286 1381 1468 30 1189 738 M976 REACTOME_GABA_RECEPTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_RECEPTOR_ACTIVATION.html Genes involved in GABA receptor activation 29/59 Reactome 1.25338706132106e-07 7.16209778122308e-07 2690 1742.63636363636 1162 1.13944284793564e-08 458 2.31855207295333 2.7753127074199 1 5.67972441157162 2688 657 1162 812 458 3592 3811 2476 1105 1498 910 739 M7057 LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_DN.html Genes higher expressed in the best 25 mesothelioma survivors compared to the 25 worst ones. 16540645 5/8 Arthur Liberzon 5.02657441672668e-07 1.11649088220941e-06 2305 1719.81818181818 1163 5.02657555371731e-08 58 3.21843840221716 -3.95511606286281 -1 7.65401730330313 2305 1049 4305 725 2047 3355 2675 1063 58 1163 173 740 M1702 CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS.html High-grade amplification (copy number, CN >= 5) detected in primary neuroblastoma samples. 18923524 52/69 Jessica Robertson 1.62169021684317e-07 7.3358205358541e-07 1070 1217.81818181818 1163 1.47426394216649e-08 87 2.72587090130695 2.92538546101156 1 6.67490788402529 1067 1706 1347 2099 706 562 1163 472 1599 2588 87 741 M2019 MIKKELSEN_MEF_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in MEF cells (embryonic fibroblast). 17603471 427/986 Arthur Liberzon 9.03478647738612e-76 1.42147307244208e-72 4170 2006.81818181818 1163 8.21344225216928e-77 1 3.12030260900764 3.32958499413617 1 90.1086516045355 4167 1163 1 215 336 2548 4164 4272 558 7 4644 742 M1472 PETROVA_PROX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_PROX1_TARGETS_DN.html Genes specific to BEC (blood endothelium cells) repressed in BEC by expression of PROX1 [GeneID=5629] off adenovirus vector. 12198161 93/111 Kevin Vogelsang 5.26447779306512e-08 5.23122845963524e-07 2270 1507.36363636364 1164 4.78588901731016e-09 65 2.32555320468251 2.41781195667461 1 5.8246281401425 2267 137 569 1164 65 2408 3416 676 2638 481 2760 743 M970 REACTOME_ACTIVATION_OF_IRF3_IRF7_MEDIATED_BY_TBK1_IKK_EPSILON http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_IRF3_IRF7_MEDIATED_BY_TBK1_IKK_EPSILON.html Genes involved in Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon 18/31 Reactome 1.52486393277718e-06 2.42009339701018e-06 465 1270.27272727273 1165 1.38624089971986e-07 72 1.96543885578767 -2.04268307797816 -1 4.38911745220256 461 1905 2165 1890 2875 158 72 263 1165 2612 407 744 M14353 CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN.html All marker genes down-regulated in the 'interferon' subclass of hepatocellular carcinoma (HCC). 18701503 55/68 Yujin Hoshida 3.2777587083884e-07 9.05922275783096e-07 3215 1651.90909090909 1166 2.97978108794418e-08 357 2.51222667719663 -1.95631723376436 -1 6.05524211867699 3213 357 737 713 1484 2295 1166 2487 729 610 4380 745 M6939 HOSHIDA_LIVER_CANCER_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SURVIVAL_UP.html Survival signature genes defined in adjacent liver tissue: genes correlated with poor survival of hepatocellular carcinoma (HCC) patients. 18923165 120/169 Yujin Hoshida 4.47470938979117e-08 4.70636656673264e-07 705 1127.81818181818 1168 4.06791770982267e-09 18 2.43684300487219 2.79683238398441 1 6.15076118806854 705 18 326 1168 1871 1101 2270 1187 2028 495 1237 746 M7923 REACTOME_SEMAPHORIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMAPHORIN_INTERACTIONS.html Genes involved in Semaphorin interactions 85/106 Reactome 8.98147161492048e-08 6.54205957136183e-07 1300 1199.09090909091 1169 8.1649745287163e-09 244 2.27451451585478 2.48071013925874 1 5.60686799332391 1298 1608 843 800 244 1616 3000 500 1169 553 1559 747 M1871 BENPORATH_ES_1 http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_1.html Set 'ES exp1': genes overexpressed in human embryonic stem cells according to 5 or more out of 20 profiling studies. 18443585 502/629 Jessica Robertson 5.09023568755001e-07 1.12428228569191e-06 860 1523.63636363636 1170 5.09023685352285e-08 541 1.908258058243 2.04013619608585 1 4.51548889245293 858 1170 4448 1010 2065 818 1051 1540 1574 541 1685 748 M6455 MORI_PRE_BI_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PRE_BI_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Pre-BI stage. 18922927 103/138 Jessica Robertson 8.12479992632625e-07 1.51522021873402e-06 330 1465.54545454545 1171 7.38618447899114e-08 113 1.65366094690125 -1.56428413915965 -1 3.8201734990333 330 113 2182 2874 2394 344 880 1171 3627 1467 739 749 M19287 MORI_LARGE_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_LARGE_PRE_BII_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Large Pre-BII stage. 18922927 126/203 Jessica Robertson 7.53261917861091e-08 6.16173757276429e-07 35 1120.90909090909 1171 6.84783585138326e-09 32 1.77063390755712 1.81096016600933 1 4.3721975203076 32 1547 1597 1458 3347 178 137 671 1438 754 1171 750 M16859 SENESE_HDAC3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC3_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC3 [GeneID=8841] by RNAi. 17470557 657/789 Leona Saunders 1.03360236504148e-07 6.8232212069871e-07 2185 1633.09090909091 1172 1.0336024131165e-08 301 1.97278403419482 2.13254573637341 1 4.84194045357918 2184 1122 4309 307 374 1172 3057 2162 996 301 1980 751 M8626 SIG_BCR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/SIG_BCR_SIGNALING_PATHWAY.html Members of the BCR signaling pathway 52/63 Signaling Gateway 1.35905883124137e-07 7.20206492018647e-07 1480 1571.45454545455 1174 1.23550810472525e-08 409 1.49366305837017 -1.40647093393515 -1 3.6397515351915 1478 409 3029 885 532 1174 680 1249 3736 3095 1019 752 M1719 LEIN_CHOROID_PLEXUS_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_CHOROID_PLEXUS_MARKERS.html Genes enriched in choroid plexus cells in the brain identified through correlation-based searches seeded with the choroid plexus cell-type specific gene expression patterns. 17151600 115/154 Jessica Robertson 1.55806631325799e-07 7.28847670820387e-07 1640 1092.36363636364 1174 1.41642402145647e-08 36 2.580316205751 -2.41843144939682 -1 6.31873056977796 1637 36 362 1115 820 2142 1543 1352 1174 323 1512 753 M8513 SMID_BREAST_CANCER_NORMAL_LIKE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_NORMAL_LIKE_UP.html Genes up-regulated in the normal-like subtype of breast cancer. 18451135 492/820 Jessica Robertson 3.52155274666359e-43 1.10811526428348e-40 1300 1436.36363636364 1174 3.20141158787603e-44 9 2.71980279014163 2.96543971750324 1 43.6532109234954 1297 1159 9 1109 1174 1797 3431 690 2897 21 2216 754 M1887 WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_UP http://www.broadinstitute.org/gsea/msigdb/cards/WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_UP.html Genes up-regulated in gastric mucosal tissue of mice on 2% cholesterol [PubChem=5997] diet and infected with H. pylori vs those infected with H. pylori while on 0% cholesterol diet. 16951684 84/197 Jessica Robertson 5.06409356177055e-07 1.12165751344707e-06 205 1116.09090909091 1174 4.6037224795043e-08 188 1.83498298482188 -1.65196105313676 -1 4.34092666436019 203 188 1409 1457 1958 471 588 1155 2428 1246 1174 755 M16826 ZUCCHI_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZUCCHI_METASTASIS_DN.html The 50 most down-regulated genes in primary invasive breast dutcal carcinoma (IDC) or lymph node metastases, compared to normal mammary epithelium. 15608061 57/65 Kate Stafford 4.34142409396959e-07 1.02508863049207e-06 740 1197 1175 3.94674995517765e-08 253 2.63371617411749 -3.12364538732763 -1 6.29364240905831 738 2217 1175 633 1807 1427 933 422 1464 2098 253 756 M5236 ROSS_AML_WITH_CBFB_MYH11_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_CBFB_MYH11_FUSION.html Top 63 probe sets for pediatric acute myeloid leukemia (AML) subtype inv(16); has a CBFB-MYH11 fusion [GeneID=865;4629]. 15226186 59/91 Kate Stafford 1.49640467582525e-06 2.3829386200726e-06 1175 1515.18181818182 1175 1.36036881241514e-07 758 2.6866831834941 3.08350475620509 1 6.02538522798855 1175 2201 821 2075 2862 909 2349 758 1482 1161 874 757 M7918 SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_UP.html Genes that were inversely correlated in H1299 cells (lung cancer): up-regulated by P53 [GeneID=7157] and down-regulated by P73 [GeneID=7161]. 17982488 10/20 Jessica Robertson 1.23515326815248e-05 1.50527328316027e-05 1180 1511.72727272727 1177 1.12287291160799e-06 372 2.95225470200535 3.77630837067853 1 5.67550113980956 1177 985 1421 2128 3818 1094 1154 372 434 2548 1498 758 M1539 MCCLUNG_COCAINE_REWARD_5D http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_COCAINE_REWARD_5D.html Genes up-regulated in the nucleus accumbens (a major reward center in the brain) after 5 days of cocaine [PubChem=5760] treatment. 14566342 121/143 John Newman 2.47644070296162e-07 8.15687377388613e-07 2170 1234.36363636364 1180 2.25130998338492e-08 26 2.02067616374528 2.32971647302004 1 4.89769280008366 2167 26 1202 794 1180 1846 2892 426 1200 1082 763 759 M1919 COLINA_TARGETS_OF_4EBP1_AND_4EBP2 http://www.broadinstitute.org/gsea/msigdb/cards/COLINA_TARGETS_OF_4EBP1_AND_4EBP2.html Genes up-regulated in MEF cells (embryonic fibroblast) with double knockout of the translation repressors 4EBP1 [GeneID=1978] and 4EBP2 [GeneID=1979]. 18272964 480/630 Jessica Robertson 2.64736500169765e-09 3.91806489931114e-08 1180 1132.81818181818 1180 2.40669545898487e-10 193 1.95503484491166 2.13375481934386 1 5.77358648353561 1180 1165 395 575 1561 497 1184 1651 2231 193 1829 760 M5014 TSUNODA_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSUNODA_CISPLATIN_RESISTANCE_DN.html Genes down-regulated in bladder cancer cells resistant to cisplatin [PubChem=2767] compared to the parental cells sensitive to the drug. 15608674 64/80 Leona Saunders 3.14612698524666e-07 8.93484919997849e-07 2280 1269.81818181818 1181 2.86011585014643e-08 312 2.37938459781239 -2.21488422981178 -1 5.73815074148952 2277 312 661 774 1434 1225 1755 2937 1181 494 918 761 M856 REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE.html Genes involved in Phospholipase C-mediated cascade 39/61 Reactome 1.25711833645079e-07 7.16209778122308e-07 1775 1308 1182 1.14283491662248e-08 119 2.17411832142559 2.45459754093168 1 5.32279002546141 1775 541 1182 450 460 1539 3102 3425 422 1373 119 762 M1240 JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_DN.html Genes down-regulated in early vs late brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 70/85 Leona Saunders 1.39807196924948e-07 7.20206492018647e-07 2850 1915.45454545455 1183 1.27097459826835e-08 258 2.15564576742495 2.2548759659832 1 5.2750442541931 2849 258 1183 969 567 2443 3786 3228 612 904 4271 763 M5652 FARMER_BREAST_CANCER_BASAL_VS_LULMINAL http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_BASAL_VS_LULMINAL.html Genes which best discriminated between two groups of breast cancer according to the status of ESR1 and AR [GeneID=2099;367]: basal (ESR1- AR-) and luminal (ESR1+ AR+). 15897907 450/582 Leona Saunders 2.53430123126172e-10 4.53102341346792e-09 3280 1871.54545454545 1184 2.30391021050333e-11 206 2.24243318975536 2.29977727715029 1 7.47457714641803 3276 1184 206 265 951 1885 3321 4481 624 313 4081 764 M2121 VERHAAK_GLIOBLASTOMA_CLASSICAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_CLASSICAL.html Genes correlated with classical type of glioblastoma multiforme tumors. 20129251 272/331 Arthur Liberzon 2.70327600869941e-07 8.3538310137901e-07 1035 1136.81818181818 1184 2.45752394624337e-08 118 1.95189759643915 2.23672187419776 1 4.72115102316381 1033 1317 1184 1665 1281 304 1793 1078 1842 890 118 765 M815 REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS.html Genes involved in Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds 57/102 Reactome 7.7288587622141e-08 6.27525965386533e-07 4215 2224.72727272727 1186 7.02623548521638e-09 169 2.73127324145297 -2.69399463898879 -1 6.76272699208031 4212 374 493 930 169 4549 3869 4114 1186 700 3876 766 M2214 CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN.html Genes down-regulated in CD4+ [GeneID=920] T lymphocytes after stimulation with prostaglandin E2 [PubChem=5280360]. 16424048 428/562 Arthur Liberzon 8.79536936189124e-13 2.10731692325516e-11 2980 1650.63636363636 1187 7.99579032899523e-14 23 2.29229768192476 -2.08897583449669 -1 9.7921410215085 2980 1187 143 23 797 3545 4023 3045 702 161 1551 767 M5519 PAL_PRMT5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PAL_PRMT5_TARGETS_DN.html Genes down-regulated in NIH-3T3 cells (fibroblast) after knockdown of PRMT5 [GeneID=10419] by RNAi. 15485929 26/42 John Newman 1.71407032266041e-07 7.35006487528071e-07 2335 1314.36363636364 1187 1.5582458692796e-08 178 2.69990407180012 3.3712915321402 1 6.60993084848402 2334 1829 1187 1150 783 2014 1991 1024 178 1680 288 768 M11457 GHO_ATF5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GHO_ATF5_TARGETS_DN.html Genes down-regulated in HEP3B cells (liver cancer) overexpressing ATF5 [GeneID=22809] off a plasmid vector. 18701499 28/32 Jessica Robertson 3.25505280243928e-07 9.04287770895433e-07 1190 1396.27272727273 1187 2.95913934913368e-08 49 2.2473408452042 2.8824189070047 1 5.41221843744399 1187 3438 1891 2662 1475 416 664 63 951 2563 49 769 M15955 KEGG_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPHINGOLIPID_METABOLISM.html Sphingolipid metabolism 39/46 KEGG 6.94232773556556e-07 1.36646317397287e-06 1360 1378.72727272727 1190 6.31120902389992e-08 172 1.76532504221112 -1.84308290003229 -1 4.11337180576615 1356 572 2690 2579 2251 656 514 1190 569 2617 172 770 M18274 VANHARANTA_UTERINE_FIBROID_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_UP.html Genes up-regulated in uterine fibroids vs normal myometrium samples. 15940248 69/88 Leona Saunders 2.19609286121368e-06 3.27712877171311e-06 410 1316.63636363636 1190 1.99645004855401e-07 407 2.46569028044482 2.58064763298388 1 5.38843276723515 407 1651 587 1190 3084 901 2332 1748 1455 665 463 771 M4605 FONTAINE_FOLLICULAR_THYROID_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_FOLLICULAR_THYROID_ADENOMA_UP.html Genes up-regulated in follicular thyroid adenoma (FTA) compared to other thyroid tumors. 17968324 98/122 Arthur Liberzon 2.20697266169999e-07 7.7970890443293e-07 1140 1287.27272727273 1190 2.00633898463342e-08 130 2.02968846933455 2.11840653350807 1 4.93575150387845 1139 130 1600 2335 1056 537 1190 1940 1363 2265 605 772 M881 REACTOME_TRANSPORT_OF_VITAMINS_NUCLEOSIDES_AND_RELATED_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_VITAMINS_NUCLEOSIDES_AND_RELATED_MOLECULES.html Genes involved in Transport of vitamins, nucleosides, and related molecules 24/37 Reactome 4.29226990516868e-08 4.58360044171859e-07 2350 1608.90909090909 1192 3.90206362628383e-09 35 2.52256393193669 -2.6850248998412 -1 6.38053212415001 2349 739 1113 1772 35 3144 3402 1056 405 1192 2491 773 M2631 FARMER_BREAST_CANCER_APOCRINE_VS_BASAL http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_APOCRINE_VS_BASAL.html Genes which best discriminate between two groups of breast cancer according the status of ESR1 and AR [GeneID=2099;367]: apocrine (ESR1- AR+) vs basal (ESR1- AR-). 15897907 439/571 Leona Saunders 1.09435105536235e-08 1.42295784609099e-07 4535 2053.72727272727 1193 9.94864600732734e-10 51 2.21258371954701 2.18603904602722 1 6.04236429265961 4531 1193 285 51 1183 2936 3346 4283 681 299 3803 774 M1867 WANG_NEOPLASTIC_TRANSFORMATION_BY_CCND1_MYC http://www.broadinstitute.org/gsea/msigdb/cards/WANG_NEOPLASTIC_TRANSFORMATION_BY_CCND1_MYC.html Selected genes changed in NMuMG cells (mammary epithelium) transformed by overexpression of CCND1 [GeneID=595] vs those transformed by overexpression of CCND1 and MYC [GeneID=4609]. 17440082 36/42 Jessica Robertson 1.68893472741174e-09 2.62229339256033e-08 340 1473.54545454545 1193 1.53539520791666e-10 234 3.22859313849798 3.39048980580385 1 9.79367096215249 339 2265 234 1193 4183 1071 1879 2305 1617 306 817 775 M12751 MIZUKAMI_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIZUKAMI_HYPOXIA_DN.html Genes down-regulated in DLD-1 cells (colon cancer) in response to hypoxia; might not be direct targets of HIF1A [GeneID=3091]. 16127434 11/13 Jessica Robertson 1.95824036764756e-06 2.96912770166928e-06 1555 1340.09090909091 1194 1.78022010063419e-07 257 3.5155501899788 2.81725525099824 1 7.76466771385086 1555 1945 1030 761 3024 872 257 1194 383 1340 2380 776 M6311 ODONNELL_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_METASTASIS_DN.html Down-regulated genes in the signature set for lymph node metastasis in head and neck squamous cell carcinoma (HNSCC). 15558013 31/40 Leona Saunders 3.29325118611617e-07 9.05922275783096e-07 2060 1469.81818181818 1195 2.99386516281245e-08 655 2.55762106283017 2.94852273398324 1 6.1655607475735 2057 655 1186 2283 1495 1195 701 2376 822 1063 2335 777 M8417 CROMER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_METASTASIS_DN.html Metastatic propensity markers of head and neck squamous cell carcinoma (HNSCC): down-regulated in metastatic vs non-metastatic tumors. 14676830 119/149 Kevin Vogelsang 1.8250351903702e-07 7.47800341964416e-07 1275 1109.27272727273 1195 1.659123037971e-08 390 2.15574098037076 2.60242870706218 1 5.26112325090699 1272 1573 1195 1248 850 906 1324 513 840 2091 390 778 M8809 BIOCARTA_PTDINS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTDINS_PATHWAY.html Phosphoinositides and their downstream targets. 39/42 BioCarta 6.82827520272794e-08 6.05242275488957e-07 2475 1655 1197 6.20752310423754e-09 123 1.67288274153173 -1.61262135842419 -1 4.13328982910481 2473 532 2450 177 123 1900 1197 4103 675 3446 1129 779 M571 REACTOME_NUCLEAR_SIGNALING_BY_ERBB4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEAR_SIGNALING_BY_ERBB4.html Genes involved in Nuclear signaling by ERBB4 42/70 Reactome 7.53789801337433e-06 9.54369061779154e-06 1200 1724.63636363636 1198 6.85265803702585e-07 465 2.16358647252373 -2.05420982804167 -1 4.31816939285807 1198 564 1972 3890 3671 853 1097 1271 465 3202 788 780 M1275 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2.html Cluster PAM2: genes up-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 222/290 Leona Saunders 1.91898325244499e-09 2.9218067585614e-08 1735 1228.54545454545 1198 1.74453023101714e-10 240 2.34596185393137 2.49666253939492 1 7.05828830915439 1734 1366 240 314 699 944 1896 2621 1198 248 2254 781 M1188 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment with 2 nM docetaxel [PubChem=148124]. 17099726 120/163 Arthur Liberzon 6.97694953957829e-08 6.06161982149702e-07 780 1341.27272727273 1200 6.34268160076467e-09 339 2.52638477685842 2.63019016484968 1 6.26694641458912 710 1560 339 779 2524 1198 1796 1545 2327 776 1200 782 M2002 MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) without H3 methylation marks at K4 and K27 in embryonic stem cells (ES). 17603471 70/135 Arthur Liberzon 6.18554968283233e-07 1.26388720792072e-06 1200 1374.36363636364 1200 5.62322856542774e-08 664 2.59017685921646 2.57559632669878 1 6.09403514266677 1200 1652 731 1847 2154 788 1925 868 2586 703 664 783 M2007 MIKKELSEN_ES_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in embryonic stem cells (ES). 17603471 137/229 Arthur Liberzon 5.55814497574509e-11 1.07518214284905e-09 1405 1183.90909090909 1202 5.05285906898682e-12 189 2.57781736610323 -2.47842682955891 -1 9.24761898654091 1404 1514 189 921 282 1547 2381 2282 1202 275 1026 784 M1949 MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark at K4 (H3K4me2) and trimethylation mark at K27 (H3K27me3) in neural precursor cells (NPC). 18600261 251/536 Arthur Liberzon 2.48956098070489e-52 1.06824798444792e-49 1725 1225.27272727273 1203 2.26323725518627e-53 7 3.14684849472702 3.46465006219181 1 61.9252244831863 1721 1283 7 224 506 1203 3072 1833 1062 25 2542 785 M2402 KOHOUTEK_CCNT2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KOHOUTEK_CCNT2_TARGETS.html Genes down-regulated in E14 ES (embryonic stem) cells upon knockdown of CYCT2 [GeneID=905] by RNAi. 19364821 64/179 Arthur Liberzon 4.28835559893029e-08 4.58360044171859e-07 4540 2194.63636363636 1203 3.89850516592833e-09 34 2.41424649255099 2.76998069443754 1 6.10440718987389 4536 305 598 940 34 4588 3482 2999 1203 816 4640 786 M984 BIOCARTA_TOLL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TOLL_PATHWAY.html Toll-Like Receptor Pathway 56/78 BioCarta 3.23398039468485e-07 9.02643519529009e-07 775 1435.90909090909 1204 2.93998260916107e-08 735 2.0157232482481 -2.00561995952184 -1 4.84990293891825 773 2657 1993 1493 1467 1194 845 735 1204 2253 1181 787 M7137 WEINMANN_ADAPTATION_TO_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEINMANN_ADAPTATION_TO_HYPOXIA_DN.html Genes most down-regulated in hypoxia tolerant NCI H460 cells (lung cancer). 15897868 65/74 Arthur Liberzon 2.94514988679275e-09 4.31711411977074e-08 565 1433.54545454545 1205 2.67740899157767e-10 249 3.13857723143832 3.30086520847322 1 9.24593496090367 565 2182 249 1205 3036 1038 2282 2073 1965 462 712 788 M12110 KANG_FLUOROURACIL_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_FLUOROURACIL_RESISTANCE_DN.html Genes down-regulated in gastric cancer cell lines resistant to 5-fluorouracil [PubChem=3385]. 14734480 22/26 John Newman 1.62531501765003e-07 7.3358205358541e-07 805 1383 1205 1.47755921611362e-08 314 2.11493851716999 2.57339202724461 1 5.16768803950377 1705 802 1299 801 709 1606 1567 4560 314 1205 645 789 M7396 SWEET_LUNG_CANCER_KRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_LUNG_CANCER_KRAS_DN.html Genes down-regulated in the Kras2LA mouse lung cancer model with mutated KRAS [GeneID=3845]. 15608639 543/758 Arthur Liberzon 1.07738101987184e-16 4.38382621878888e-15 1210 1685.45454545455 1207 1.07738101987185e-17 69 2.41565042724251 2.5291876296566 1 13.8986433230684 1207 1153 4602 702 1202 1028 2784 1495 2661 69 1637 790 M2354 VANLOO_SP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANLOO_SP3_TARGETS_DN.html Genes down-regulated in E12.5 hearts from mice with SP3 [GeneID=6670] knockout compared to the wild type organ. 17923686 94/134 Arthur Liberzon 1.19620905313923e-07 7.06112554001409e-07 4490 2024.72727272727 1207 1.08746283470989e-08 132 2.13086231218526 -2.37258016226532 -1 5.22117709938653 4490 132 1207 544 420 4379 4410 2865 617 847 2361 791 M2084 WANG_METASTASIS_OF_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METASTASIS_OF_BREAST_CANCER.html Genes whose expression in primary ER(-) [GeneID=2099] breast cancer tumors negatively correlates with developing distant metastases. 15721472 31/45 Arthur Liberzon 9.21029798745356e-06 1.14733719980947e-05 650 1601.54545454545 1209 8.37303322416696e-07 648 2.8188630432124 3.12231280169244 1 5.550487784794 648 1786 688 1021 3732 1324 2238 2918 1209 893 1160 792 M1677 WENG_POR_TARGETS_LIVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_LIVER_DN.html Genes down-regulated in liver from mice with liver specific knockout of POR [GeneID=5447]. 16006652 27/35 John Newman 3.00382528116152e-08 3.49213185396117e-07 1210 1360.36363636364 1210 2.73075029288636e-09 12 1.92683165997214 -1.50823497520152 -1 4.953407689908 1210 2334 2187 2375 12 727 263 659 3416 1525 256 793 M3955 GU_PDEF_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GU_PDEF_TARGETS_UP.html Integrin, VEGF, Wnt and TGFbeta signaling pathway genes up-regulated in PC-3 cells (prostate cancer) after knockdown of PDEF [GeneID=25803] by RNAi. 17483333 109/138 Jessica Robertson 2.71999331287029e-08 3.18569936395726e-07 350 1255 1211 2.4727212240902e-09 311 2.57549955225437 2.8196866669565 1 6.67912988612733 349 1579 311 844 2763 822 1780 1558 2090 498 1211 794 M4008 FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL.html Genes which best discriminate between two groups of breast cancer according to the status of ESR1 and AR [GeneID=2099;367]: apocrine (ESR1- AR+) and luminal (ESR1+ AR+). 15897907 406/551 Leona Saunders 1.54623031387966e-07 7.28175281873995e-07 3440 2009.09090909091 1212 1.40566402050334e-08 557 2.05524678940943 -2.04836611262365 -1 5.02307917962934 3439 1212 809 557 665 3637 3255 3525 910 924 3167 795 M75 TSENG_ADIPOGENIC_POTENTIAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_ADIPOGENIC_POTENTIAL_UP.html Genes showing increasing expression in brown preadipocytes with decreasing ability of the cells to differentiate. 15895078 47/52 John Newman 4.42000845208211e-07 1.03381763596767e-06 350 1347.54545454545 1212 4.0181903091854e-08 348 2.90707697257815 3.3793996809931 1 6.94776544010712 348 1704 389 780 3653 1212 2229 1660 1433 463 952 796 M854 LINDGREN_BLADDER_CANCER_CLUSTER_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_3_UP.html Genes whose expression profile is specific to Cluster III of urothelial cell carcinoma (UCC) tumors. 16532037 397/547 Leona Saunders 4.46765845099284e-07 1.03872096525265e-06 820 1450.27272727273 1213 4.06150850751323e-08 801 1.70025950555145 1.75287362616522 1 4.04135623567573 818 1213 2340 1007 1843 801 1104 2050 1384 855 2538 797 M3854 MARTINEZ_RB1_AND_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_AND_TP53_TARGETS_DN.html Genes down-regulated in mice with skin specific double knockout of both RB1 and TP53 [GeneID=5925;7157] by Cre-lox. 18245467 760/992 Jessica Robertson 1.01642314797175e-07 6.77615431981167e-07 365 1598.72727272727 1213 1.01642319446197e-08 363 2.02490707180935 2.37696302632622 1 4.97363970762276 2192 1105 4537 363 363 1234 3620 1534 1213 657 768 798 M12816 DOANE_RESPONSE_TO_ANDROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_RESPONSE_TO_ANDROGEN_DN.html Genes down-regulated in MDA-MB-453 cells (class A ER(-) [GeneID=2099] breast cancer) after exposure to the androgen R1881 [PubChem=13766]. 16491124 396/480 Arthur Liberzon 4.12266055842953e-07 1.00046055710989e-06 1910 1298.72727272727 1214 3.74787393726381e-08 430 1.85958811798817 2.12437112935097 1 4.43694343449005 1909 1214 1140 430 1747 1344 2807 884 1796 476 539 799 M18159 BIOCARTA_RB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RB_PATHWAY.html RB Tumor Suppressor/Checkpoint Signaling in response to DNA damage 20/23 BioCarta 1.21886795134199e-06 2.03288223686721e-06 1220 1355 1216 1.10806238784819e-07 72 2.59838189681821 2.82298003814591 1 5.89781224562683 1939 809 1218 165 2710 1655 750 1156 72 1216 3215 800 M16864 REACTOME_METABOLISM_OF_CARBOHYDRATES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_CARBOHYDRATES.html Genes involved in Metabolism of carbohydrates 218/287 Reactome 1.46832328025028e-07 7.26289540930751e-07 755 1296.45454545455 1216 1.33483943477188e-08 428 1.94948566656623 2.01402803707967 1 4.76290415034969 754 1391 1561 2565 609 428 1177 986 1545 2029 1216 801 M16692 COWLING_MYCN_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/COWLING_MYCN_TARGETS.html Genes down-regulated by MYCN [GeneID=4613] but not by its transactivation-defficient, trunkated form N-Myc-delta-73. 17704800 71/86 Jessica Robertson 3.54367132802629e-08 4.00146618858471e-07 510 1273.36363636364 1216 3.22151944100575e-09 303 2.82625170537606 3.02828870638275 1 7.22174483395635 506 1641 314 785 3786 1216 2007 1574 1224 303 651 802 M1712 LEIN_NEURON_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_NEURON_MARKERS.html Genes enriched in neurons in the adult mouse brain identified through correlation-based searches seeded with neuron cell-type specific gene expression patterns. 17151600 78/110 Jessica Robertson 2.05034536708765e-07 7.67989556725435e-07 1800 1380.63636363636 1216 1.86395050743161e-08 243 2.08277250924715 2.14300088165655 1 5.07165787837801 1799 243 1216 577 974 1055 1786 3678 1229 1177 1453 803 M2570 ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP.html Genes up-regulated during prostate cancer progression in the JOCK1 model due to inducible activation of FGFR1 [GeneID=2260] gene in prostate. 18068632 356/499 Yujin Hoshida 9.61302557637117e-24 7.3183033420116e-22 1330 968.090909090909 1217 8.73911416033741e-25 18 2.44931862425743 -2.47448154883603 -1 20.7689839714727 1327 1217 44 18 203 1786 1952 1364 975 35 1728 804 M605 KEGG_ASCORBATE_AND_ALDARATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASCORBATE_AND_ALDARATE_METABOLISM.html Ascorbate and aldarate metabolism 11/30 KEGG 1.08708231074082e-05 1.33864557962345e-05 750 1742.36363636364 1218 9.88261529417797e-07 174 2.73134661238383 2.50170819315493 1 5.30304219786801 748 977 1197 2434 3774 552 174 3104 2748 2240 1218 805 M9936 PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_UP.html Genes up-regulated in unstable ateroslerotic plaques compared to the stable ones. 16741146 76/108 Arthur Liberzon 2.5699021481201e-07 8.25727579246215e-07 600 1593.81818181818 1218 2.3362749530182e-08 599 1.70026106841911 -1.58642852404929 -1 4.10950693182902 599 1634 2059 3201 1218 661 1020 678 4133 1469 860 806 M10702 JAEGER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAEGER_METASTASIS_DN.html Genes down-regulated in metastases from malignant melanoma compared to the primary tumors. 17289871 327/478 Leona Saunders 1.22983788826462e-47 4.46525756354539e-45 4095 1921.72727272727 1219 1.11803444387693e-48 8 2.95448513092084 3.2969312428694 1 52.6459554858552 4093 1219 8 226 423 3216 4610 2211 707 19 4407 807 M2413 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7.html Genes regulated in MCF7 cells (breast cancer) by expression of the truncated (611-CTF) form of ERBB2 [GeneID=2064] at 60 h time point. 19364815 508/662 Arthur Liberzon 4.0711062953942e-07 9.98214115026527e-07 2375 1682.72727272727 1219 4.07110704122018e-08 345 2.01739374942638 2.2358340668807 1 4.81850304394839 2372 1162 4697 345 1846 878 2762 1045 1219 460 1724 808 M154 SCHAVOLT_TARGETS_OF_TP53_AND_TP63 http://www.broadinstitute.org/gsea/msigdb/cards/SCHAVOLT_TARGETS_OF_TP53_AND_TP63.html Genes up-regulated by TP53 [GeneID=7157] and down-regulated by an isoform of TP63 [GeneID=8626] in primary HEK cells (epidermal keratinocytes). 17404570 24/30 Leona Saunders 9.48956991763914e-05 0.000104431732364786 1145 1825.36363636364 1220 8.6272538812243e-06 255 2.49060457592407 2.80339997323904 1 3.93760231461432 1144 3455 1946 2699 4243 1220 570 626 255 3100 821 809 M1303 GROSS_HYPOXIA_VIA_ELK3_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_UP.html Genes up-regulated in SEND cells (skin endothelium) at hypoxia with ELK3 [GeneID=2004] knockdown by RNAi. 17704799 314/372 Jessica Robertson 1.64716721816063e-07 7.3358205358541e-07 745 1263.63636363636 1220 1.49742485589645e-08 394 1.75677814318174 1.85551977114029 1 4.28407728778545 743 1270 1991 1065 727 394 1220 1559 2578 985 1368 810 M3697 GOUYER_TATI_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOUYER_TATI_TARGETS_DN.html Genes down-regulated in constitutively invasive HT-29 5M21 cells (colon cancer) vs those expressing functionally inactive TATI [GeneID=6690]. 18317448 19/22 Jessica Robertson 8.69472442106955e-07 1.58635868834357e-06 1310 1043.18181818182 1223 7.9042980521407e-08 82 3.30540663893627 3.682939846068 1 7.6594144259897 1306 836 565 1576 2460 1228 1223 82 1319 528 352 811 M4077 FOURNIER_ACINAR_DEVELOPMENT_LATE_2 http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_LATE_2.html Genes identified by method 2 as coordinately down-regulated late in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 391/454 Arthur Liberzon 4.54915684242455e-07 1.04588506070355e-06 85 1179.63636363636 1223 4.13559798463529e-08 84 1.66710986160092 1.80447962333384 1 3.95958576994753 84 1223 2839 1305 1867 194 284 828 1414 2160 778 812 M7182 KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) with early recurrence. 15288478 24/42 Yujin Hoshida 1.14137563830431e-05 1.40075221341558e-05 235 1635.81818181818 1226 1.03761959989569e-06 235 1.31268955905685 -1.32803265866052 -1 2.51226372319936 235 728 2556 1954 3789 387 359 799 3583 2378 1226 813 M5436 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY.html B cell receptor signaling pathway 76/110 KEGG 1.23528491962796e-07 7.12872631945934e-07 1230 1105.45454545455 1228 1.12298635362578e-08 166 1.70634773673625 -1.76881107831914 -1 4.16819582206009 1228 229 2136 166 450 1148 612 1342 1604 1986 1259 814 M17726 KEGG_DRUG_METABOLISM_OTHER_ENZYMES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DRUG_METABOLISM_OTHER_ENZYMES.html Drug metabolism - other enzymes 28/80 KEGG 7.07036440964766e-07 1.3784725468932e-06 1755 1412.81818181818 1229 6.4276060744762e-08 615 2.30306171854559 2.26402013094428 1 5.37807046161748 1751 703 1031 2769 2274 1229 1304 615 978 1170 1717 815 M2043 RICKMAN_HEAD_AND_NECK_CANCER_F http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_F.html Cluster f: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 53/93 Jessica Robertson 2.50806659774246e-07 8.19243899054975e-07 1540 1631.27272727273 1229 2.28006080333608e-08 46 3.22628919918461 3.8525105804902 1 7.84724702396025 1538 2230 614 1618 1196 3001 4339 46 1034 1229 1099 816 M202 YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) samples from patients with early recurrence (within 2 years after surgery) after resection. 19167881 41/52 Yujin Hoshida 2.59860866408001e-07 8.27068974676848e-07 1760 1888.36363636364 1233 2.36237179184002e-08 647 2.03671339793866 2.45802503588737 1 4.9320315345992 1756 3950 2658 3103 1233 647 859 1017 889 3590 1070 817 M16586 LAIHO_COLORECTAL_CANCER_SERRATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/LAIHO_COLORECTAL_CANCER_SERRATED_UP.html Genes up-regulated in serrated vs conventional colorectal carcinoma (CRC) samples. 16819509 156/175 Arthur Liberzon 1.98884260941804e-07 7.65527859584926e-07 1235 1322.36363636364 1235 1.80803889928481e-08 472 1.86868886574391 2.02428119788683 1 4.54625786296676 1235 2088 2581 472 932 979 1285 669 1248 2251 806 818 M16407 IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM.html Genes in the expression cluster 'LT-HSC Shared': up-regulated in long term hematopoietic stem cells (LT-HSC) from adult bone marrow and fetal liver. 12228721 348/476 John Newman 1.41209534233654e-07 7.20206492018647e-07 3055 1786.27272727273 1236 1.28372312088501e-08 272 2.14635345727385 2.3914490368384 1 5.25208950488479 3054 1236 358 272 789 2420 4046 2996 1197 544 2737 819 M1844 RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP.html Up-regulated genes in breast tumors from transgenic mice overexpressing ERBB2 and CDC25A [GeneID=2064;993] compared to those from mice overexpressing ERBB2 only. 17283130 133/174 Jessica Robertson 5.07810116101905e-13 1.2681818772492e-11 1475 1106.36363636364 1236 4.61645560092746e-14 112 2.55771251249086 2.65517051848457 1 11.1585815892585 1474 1496 165 693 1236 1087 1719 1557 929 112 1702 820 M2061 NIELSEN_LEIOMYOSARCOMA_CNN1_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_CNN1_DN.html Top 20 negative significant genes associated with leiomyosarcoma tumors expressing muscle gene cluster with CNN1 [GeneID=1264]. 11965276 33/43 John Newman 9.24685197962038e-07 1.6576202561264e-06 1005 1423 1236 8.40623260561859e-08 191 2.89939761331721 3.15916260261304 1 6.69019661314357 1002 1783 775 2558 2511 1171 2175 191 1263 1236 988 821 M6712 ROVERSI_GLIOMA_LOH_REGIONS http://www.broadinstitute.org/gsea/msigdb/cards/ROVERSI_GLIOMA_LOH_REGIONS.html Genes in the most frequently heterozygous deleted loci of a panel of glioma cell lines. 16247447 63/83 Arthur Liberzon 3.60339905560829e-07 9.41752134134615e-07 1465 1118.81818181818 1238 3.27581785982935e-08 320 2.58287124385447 2.64055459575246 1 6.2094262640559 1462 320 659 759 1594 1238 2348 1274 424 769 1460 822 M1223 DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_DN.html Genes that classify skin lesions into low risk papilloma. 17525749 47/58 Arthur Liberzon 3.11119312924674e-06 4.390084176396e-06 1215 1948.36363636364 1238 2.82836139003499e-07 865 1.92786589175847 2.12574067420846 1 4.10372717838323 865 1718 1238 3441 3272 1211 1214 3001 3173 1124 1175 823 M2086 LI_INDUCED_T_TO_NATURAL_KILLER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_INDUCED_T_TO_NATURAL_KILLER_UP.html Genes up-regulated in ITNK cells (T-lymphocyte progenitors (DN3 cells) reprogrammed to natural killer (NK) cells by ablation of BCL11B [GeneID=64919] gene), compared to the parental DN3 cells. 20538915 347/480 Arthur Liberzon 9.47573897405424e-08 6.60267713309408e-07 2565 1550.54545454545 1238 8.61430852926269e-09 279 2.06587756180817 -1.93175750033758 -1 5.08464279196699 2561 1238 651 302 279 2001 1960 3452 1160 356 3096 824 M72 PID_NECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NECTIN_PATHWAY.html Nectin adhesion pathway 18832364 51/55 Pathway Interaction Database 6.57802452235867e-08 5.92524346288796e-07 1570 1190.36363636364 1239 5.98002247185667e-09 116 2.04702487284317 -1.76231158086792 -1 5.07648842075768 1570 402 1279 420 116 1271 509 4331 194 1239 1763 825 M4383 BIOCARTA_NO1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NO1_PATHWAY.html Actions of Nitric Oxide in the Heart 37/50 BioCarta 2.42172854342768e-05 2.81749044243989e-05 255 1503 1240 2.20159563807277e-06 137 2.25690734629339 2.41473882034662 1 4.0798568730548 255 2721 1240 2191 4004 137 141 388 3070 2140 246 826 M544 REACTOME_SIGNALING_BY_ERBB4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ERBB4.html Genes involved in Signaling by ERBB4 105/137 Reactome 1.89611920930204e-07 7.50182956236849e-07 1240 1786 1240 1.72374488429394e-08 469 1.4910356870516 -1.40552847659533 -1 3.62264147789798 1240 2586 3599 1758 900 469 780 1148 2157 4448 561 827 M904 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP.html Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs poorly differentiated tumors. 18679425 304/403 Jessica Robertson 2.61423169700251e-07 8.29211725993449e-07 620 1735.81818181818 1240 2.37657455240759e-08 219 1.67682002346956 1.78929407623082 1 4.05092725746554 620 2951 3541 2881 1240 219 820 916 1928 3450 528 828 M15908 BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_UP.html Genes up-regulated in D-341 MED (OBR) cells (medulloblastoma) resistant to both carmustine and O6-BG [PubChem=2578;4578]. 12479369 45/57 John Newman 3.80134778729025e-06 5.21428699680616e-06 910 1494.63636363636 1240 3.45577668690848e-07 128 3.07290663859248 3.34526117260775 1 6.47848082530881 909 2690 704 1680 3371 694 1240 168 3160 1697 128 829 M1319 HESS_TARGETS_OF_HOXA9_AND_MEIS1_UP http://www.broadinstitute.org/gsea/msigdb/cards/HESS_TARGETS_OF_HOXA9_AND_MEIS1_UP.html Genes up-regulated in hematopoietic precursor cells conditionally expressing HOXA9 and MEIS1 [GeneID=3205;4211]. 16507773 72/85 Kevin Vogelsang 2.40011680812952e-06 3.52475150416034e-06 270 1448.09090909091 1241 2.18192675142745e-07 267 1.66285543656642 1.61099714847429 1 3.59649804236004 555 268 2551 2824 3136 267 323 1153 2173 1241 1438 830 M33 PID_GLYPICAN_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_GLYPICAN_1PATHWAY.html Glypican 1 network 18832364 30/37 Pathway Interaction Database 2.6218412769252e-07 8.29211725993449e-07 1440 1390.72727272727 1242 2.38349235398377e-08 443 2.36726368966442 2.66170801329514 1 5.73953120764637 1436 658 958 443 1242 2633 3055 949 625 1370 1929 831 M1015 REACTOME_INHIBITION_OF_REPLICATION_INITIATION_OF_DAMAGED_DNA_BY_RB1_E2F1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_REPLICATION_INITIATION_OF_DAMAGED_DNA_BY_RB1_E2F1.html Genes involved in Inhibition of replication initiation of damaged DNA by RB1/E2F1 13/13 Reactome 7.19245019631453e-08 6.06397110828564e-07 1110 1359.63636363636 1242 6.53859130132453e-09 150 1.48180777981603 1.24435513038447 1 3.6549811344638 1108 1931 2797 1878 150 826 1242 855 918 1730 1521 832 M1614 DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_DN.html Genes down-regulated in RMS cells (rhabdomyosarcoma) expressing PAX3 or PAX7 fusions with FOXO1 [GeneID=5077;5081;2308] compared to the fusion negative cell lines. 16849537 34/41 Arthur Liberzon 1.55077456273355e-05 1.85872420926926e-05 180 1306.72727272727 1247 1.40980499473908e-06 176 2.9771750536815 3.2550734801314 1 5.61415840633869 176 1764 518 1247 4178 745 1491 1799 1256 677 523 833 M7337 ROY_WOUND_BLOOD_VESSEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROY_WOUND_BLOOD_VESSEL_UP.html Genes up-regulated in blood vessel cells from wound site. 17728400 79/92 Leona Saunders 1.5541677711062e-07 7.28467912574107e-07 375 1407.81818181818 1247 1.4128798917262e-08 240 2.72169196285494 2.88519940935546 1 6.6679236739374 374 240 361 771 3353 1247 2242 2569 2288 370 1671 834 M11428 GAURNIER_PSMD4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GAURNIER_PSMD4_TARGETS.html Inflammatory cytokines, chemokines and their cognate receptors up-regulated in THP-1 cells (monocyte) after treatment with PSMD4 [GeneID=5710]. 18632645 62/115 Jessica Robertson 9.97863253142419e-07 1.7476491854665e-06 145 1591.81818181818 1247 9.07148823407035e-08 145 1.91837525121204 -2.04272677673008 -1 4.39189184425585 145 2190 1247 2470 2568 575 822 975 4232 938 1348 835 M2398 SERVITJA_LIVER_HNF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_LIVER_HNF1A_TARGETS_DN.html Genes down-regulated in liver tissue upon knockout of HNF1A [GeneID=6927]. 19289501 148/290 Arthur Liberzon 5.80289133290483e-08 5.56439156084225e-07 1255 1137.27272727273 1251 5.27535589633311e-09 77 2.30007962212116 -2.4241593911214 -1 5.73547533938673 1251 1486 342 1344 77 1123 1855 1670 2241 350 771 836 M7880 SPIRA_SMOKERS_LUNG_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SPIRA_SMOKERS_LUNG_CANCER_UP.html Up-regulated genes that distinguished smokers with and without lung cancer. 17334370 49/72 Jessica Robertson 1.3224571281791e-07 7.20206492018647e-07 1295 1285.36363636364 1252 1.2022338251584e-08 456 2.33377850327834 -2.24325474144958 -1 5.71508469931715 1293 456 1252 852 501 1502 1038 1130 2503 1426 2186 837 M2256 MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN.html Genes commonly down-regulated in UET-13 cells (mesenchymal progenitor) by expression of EWSR1 [GeneID=2130] fusions with ETS transcription factors FLI1 and ERG [GeneID=2313 ,2078]. 18212050 323/415 Arthur Liberzon 1.13659650074206e-24 9.41181663772375e-23 770 1121 1252 1.03326954612915e-25 35 2.58115707900555 2.86347685225306 1 22.8142234741784 766 1252 35 281 1876 1272 2854 815 1609 53 1518 838 M6239 NEWMAN_ERCC6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NEWMAN_ERCC6_TARGETS_DN.html Genes down-regulated in Cockayne syndrome fibroblasts rescued by expression of ERCC6 [GeneID=2074] off a plasmid vector. 16772382 63/82 Leona Saunders 1.3503405193867e-13 3.77136523757706e-12 565 1520.54545454545 1254 1.22758229035162e-14 125 3.61019440692811 3.86952390950591 1 16.5355359238158 563 347 125 392 3959 2010 3157 2664 1254 336 1919 839 M10761 PEREZ_TP63_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/PEREZ_TP63_TARGETS.html Genes up-regulated in the HMEC cells (primary mammary epithelium) upon expression of the transcriptionally active isoform of TP63 [GeneID=8626] off adenoviral vector. 17563751 486/644 Leona Saunders 1.27530262562363e-18 6.40364722653565e-17 2990 1852.54545454545 1255 1.15936602329421e-19 65 2.34510822610682 2.5631052538118 1 15.222325086642 2987 1171 65 522 859 2064 4457 2953 1255 108 3937 840 M13061 BILD_E2F3_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_E2F3_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing E2F3 [GeneID=1871] from control cells expressing GFP. 16273092 332/390 Arthur Liberzon 5.58933281977209e-07 1.18659903470788e-06 1700 1488.72727272727 1257 5.08121294527431e-08 652 1.91569581183033 2.03123021806664 1 4.51523392540302 1698 1257 1228 1152 2061 652 2329 2051 1097 822 2029 841 M666 REACTOME_HYALURONAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HYALURONAN_METABOLISM.html Genes involved in Hyaluronan metabolism 20/23 Reactome 2.03112677532902e-06 3.06683249505853e-06 1290 1521.90909090909 1258 1.84648059140709e-07 333 2.19897780800467 2.02563011966795 1 4.82562839486713 1290 842 1447 2791 3042 614 333 383 3760 981 1258 842 M676 REACTOME_PI_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI_METABOLISM.html Genes involved in PI Metabolism 47/51 Reactome 1.15883524314011e-06 1.95695969503446e-06 850 1662.27272727273 1258 1.05348713959023e-07 45 1.46956408054985 -1.58196014762682 -1 3.32365115441823 846 2260 3304 1527 2673 453 1045 1258 792 4082 45 843 M11948 WEINMANN_ADAPTATION_TO_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEINMANN_ADAPTATION_TO_HYPOXIA_UP.html Genes most up-regulated in hypoxia tolerant NCI H460 cells (lung cancer). 15897868 56/64 Arthur Liberzon 6.41069890109018e-06 8.22465311583193e-06 230 1615.54545454545 1258 5.82792507422581e-07 228 2.75281880280262 2.9877844031778 1 5.57932505000275 228 3060 700 2188 3613 533 1113 1752 2952 1258 374 844 M2206 CHYLA_CBFA2T3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHYLA_CBFA2T3_TARGETS_DN.html Genes down-regulated in immature bone marrow progenitor cells upon knock out of CBFA2T3 [GeneID=863]. 18710942 295/395 Arthur Liberzon 2.58203986264236e-12 5.85924430368844e-11 4245 1978.18181818182 1258 2.34730896604126e-13 24 2.25498646428486 -2.37183996628551 -1 9.22919086979088 4245 1258 159 24 259 4476 3847 4054 749 121 2568 845 M25 ASTON_MAJOR_DEPRESSIVE_DISORDER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ASTON_MAJOR_DEPRESSIVE_DISORDER_UP.html Genes up-regulated in the temporal cortex samples from patients with major depressive disorder. 15303102 65/77 Jean Junior 3.62237452084259e-07 9.43951209799063e-07 1345 1224 1260 3.29306828843543e-08 95 2.36392278386902 2.76886162007342 1 5.67785229395496 1345 2184 1260 1602 1598 715 1999 743 806 1117 95 846 M11616 ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP.html Genes whose promoters display higher levels of histone H3 trimethylation mark at K27 (H3K27me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 307/615 Jessica Robertson 1.69438483809302e-16 6.6095011866108e-15 1490 1160.54545454545 1260 1.54034985281184e-17 83 2.49511923996337 2.67262719465059 1 14.1785907805141 1486 1260 83 289 749 1525 2923 988 1655 272 1536 847 M16389 ZEMBUTSU_SENSITIVITY_TO_METHOTREXATE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_METHOTREXATE.html Top genes associated with chemosensitivity to methotrexate [PubChem=4112] across 85 tumor xenografts. 11809704 32/41 Arthur Liberzon 2.32149312746566e-05 2.70955676598366e-05 360 1581.27272727273 1260 2.11047056798515e-06 358 2.46093943427416 2.78161584020202 1 4.47000270802137 358 1782 833 865 3990 1260 1930 2905 1549 971 951 848 M14435 TIAN_TNF_SIGNALING_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/TIAN_TNF_SIGNALING_VIA_NFKB.html Genes modulated in HeLa cells (cervical carcinoma) by TNF [GeneID=7124] via NFKB pathway. 15722553 29/31 Arthur Liberzon 4.50826017960557e-06 6.04039880348692e-06 205 1814.72727272727 1262 4.09842674363653e-07 204 2.82928727684231 -2.82810894426939 -1 5.88822732460136 204 3432 929 3442 3450 450 322 981 4074 1262 1416 849 M5410 KEGG_ARACHIDONIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARACHIDONIC_ACID_METABOLISM.html Arachidonic acid metabolism 39/108 KEGG 1.1373008445137e-07 7.05613393308323e-07 1485 1284.45454545455 1263 1.0339099120973e-08 376 2.49494961230017 -2.17113424502364 -1 6.12214512224686 1484 538 766 2264 376 1263 906 1627 2599 860 1446 850 M1036 REACTOME_INNATE_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INNATE_IMMUNE_SYSTEM.html Genes involved in Innate Immune System 233/416 Reactome 2.66528442461397e-07 8.32746245638274e-07 785 1575.63636363636 1263 2.42298613410123e-08 669 1.99672093442932 -2.21609332458526 -1 4.83181902224427 784 2957 1810 1952 1263 1023 968 775 3150 1981 669 851 M5588 HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_UP.html Genes up-regulated during differentiation from large pre-BII to small pre-BII lymphocyte. 11779835 223/286 Arthur Liberzon 1.38169551510661e-06 2.24418542026951e-06 60 1077.90909090909 1263 1.25608762079286e-07 59 1.85346486772599 1.8927763975556 1 4.16064121988149 59 1362 1263 1427 2793 180 172 967 1867 484 1283 852 M762 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_29 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_29.html Amplification hot spot 29: colocolized fragile sites and cancer genes in the 7p22-p13 region. 16751803 8/11 Arthur Liberzon 5.38610912695037e-08 5.28532953829642e-07 2265 1569.45454545455 1264 5.38610925749615e-09 11 2.70383483058787 -3.8129631321285 -1 6.77536041554127 2261 1006 4366 146 81 3024 2635 401 11 2069 1264 853 M828 MASSARWEH_TAMOXIFEN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MASSARWEH_TAMOXIFEN_RESISTANCE_DN.html Genes down-regulated in breast cancer tumors (formed by MCF-7 xenografts) resistant to tamoxifen [PubChem=5376]. 18245484 305/377 Jessica Robertson 2.64717654176503e-08 3.10812768087834e-07 3760 2039.45454545455 1264 2.40652415783408e-09 75 2.20729973518032 2.36697025719607 1 5.72661500677994 3758 1264 310 75 629 3853 3894 3674 843 385 3749 854 M2281 ISSAEVA_MLL2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ISSAEVA_MLL2_TARGETS.html Genes down-regulated in HeLa cells upon knockdown of MLL2 [GeneID=8085] by RNAi. 17178841 90/125 Arthur Liberzon 1.94037383046329e-13 5.17433021456879e-12 130 1079 1264 1.76397620951224e-14 127 2.98788476660603 3.40550837118583 1 13.5115386644748 603 127 130 280 2406 1435 2673 1264 1393 254 1304 855 M16369 HUANG_DASATINIB_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_DASATINIB_RESISTANCE_DN.html Genes whose expression negatively correlated with resistance of breast cancer cell lines to dasatinib [PubChem=3062316]. 17332353 82/100 Jessica Robertson 1.62044302274158e-07 7.3358205358541e-07 1325 1012.72727272727 1265 1.47313012917978e-08 26 2.12399658147233 -2.18525803473953 -1 5.19003502032185 1322 201 1324 1345 704 1393 2679 284 597 1265 26 856 M16441 REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS.html Genes involved in Integrin cell surface interactions 97/114 Reactome 1.61170877405746e-06 2.52817062597248e-06 880 1666.36363636364 1266 1.46519086798936e-07 468 2.46583748825709 2.6338255832449 1 5.50050536675053 468 2587 578 877 2910 1149 1994 2411 3213 877 1266 857 M3444 REACTOME_TRANSMEMBRANE_TRANSPORT_OF_SMALL_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSMEMBRANE_TRANSPORT_OF_SMALL_MOLECULES.html Genes involved in Transmembrane transport of small molecules 304/475 Reactome 7.01357157138572e-10 1.15748453905387e-08 2670 1528.27272727273 1266 6.37597415783787e-11 220 2.3221512203257 -2.28512139058536 -1 7.36168857558907 2667 1266 220 1111 433 2708 2389 1826 1103 372 2716 858 M3695 SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP.html Genes up-regulated in prostate cancer samples bearing the fusion of TMPRSS2 with ERG [GeneID=7113;2078]. 18505969 108/126 Jessica Robertson 2.66937514756506e-07 8.32746245638274e-07 835 1153.63636363636 1266 2.42670497404943e-08 66 1.87938373599761 2.02961230529232 1 4.54493700530298 835 66 1755 384 1266 1264 1301 1617 790 2061 1351 859 M1277 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM3 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM3.html Cluster PAM3: genes most highly up-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 114/153 Leona Saunders 3.18305239702892e-13 8.25494907361346e-12 795 1057.36363636364 1267 2.89368399729943e-14 48 2.78865726019045 2.72323213428461 1 12.3797679386471 792 48 134 423 2139 1267 1303 2109 1606 228 1582 860 M945 MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP.html Genes up-regulated in normal bone marrow plasma cells (BMPC) compared to polyclonal plasmablasts (PPC) that also distinguished multiple myeloma (MM) samples by expression of levels of TACI (TNFRSF13B) [GeneID=23495]. 15827134 142/185 Kevin Vogelsang 2.55926495403814e-07 8.24554988604781e-07 1445 1358.18181818182 1268 2.32660477432551e-08 481 2.22199992247351 2.42459218158781 1 5.38644816858736 1444 1524 506 481 1214 1268 3017 1430 2396 572 1088 861 M2212 TAKADA_GASTRIC_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKADA_GASTRIC_CANCER_COPY_NUMBER_UP.html Candidate genes in the regions of copy number gain in gastric cancer cell lines. 16103878 14/14 Arthur Liberzon 6.33360350668704e-06 8.13458736096948e-06 1535 1456.09090909091 1270 5.75783794603576e-07 281 1.86616678519121 2.03075751860206 1 3.76975964693651 1532 934 2122 1271 3610 1270 1115 946 575 2361 281 862 M7013 KAYO_CALORIE_RESTRICTION_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_CALORIE_RESTRICTION_MUSCLE_UP.html Upregulated in the vastus lateralis muscle of middle aged rhesus monkeys subjected to caloric restriction since young adulthood vs age matched controls 11309484 137/232 John Newman 2.18309173958409e-06 3.26185280494996e-06 615 1549.63636363636 1272 1.98463082354594e-07 362 2.45619587677717 2.79836392835207 1 5.36949572555615 614 2555 582 1272 3079 923 2640 1942 2116 961 362 863 M12985 BIOCARTA_TALL1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TALL1_PATHWAY.html TACI and BCMA stimulation of B cell immune responses. 17/23 BioCarta 5.2994525310193e-07 1.14793097505329e-06 770 1439.27272727273 1274 4.81768527961286e-08 749 1.47296146395255 -1.49943133290468 -1 3.46868228083651 770 881 2688 1464 2006 899 749 1626 1014 2461 1274 864 M18058 WILCOX_RESPONSE_TO_PROGESTERONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILCOX_RESPONSE_TO_PROGESTERONE_UP.html Genes up-regulated in primary cultures of ovarian surface epithlium cells exposed to progesterone [PubChem=5994] for 5 days. 18070364 188/235 Arthur Liberzon 7.38059203105307e-07 1.41635501657579e-06 1275 1360.72727272727 1274 6.70963137009636e-08 817 2.04493229064671 2.20074381971047 1 4.75999994437625 1069 1424 1274 1820 2312 875 1256 1272 1413 817 1436 865 M5443 HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_DN.html Genes down-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 31/43 Arthur Liberzon 5.38170621545523e-06 7.05405535599797e-06 1770 1463.54545454545 1274 4.89247216399276e-07 176 3.04557302398796 -2.71097464023754 -1 6.25966019258106 1768 682 1111 176 3532 2201 1274 1787 316 1996 1256 866 M13968 BIOCARTA_HIVNEF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HIVNEF_PATHWAY.html HIV-I Nef: negative effector of Fas and TNF 75/87 BioCarta 2.6909631991572e-07 8.3451683968607e-07 550 1441.45454545455 1275 2.44633048027862e-08 271 1.82195114119125 -1.52528569981162 -1 4.40384207379457 547 271 2344 1994 1275 621 428 2399 1207 2928 1842 867 M251 PID_SYNDECAN_3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_3_PATHWAY.html Syndecan-3-mediated signaling events 18832364 22/26 Pathway Interaction Database 6.60527864303677e-05 7.35825234721113e-05 1180 1580.54545454545 1275 6.0049790620167e-06 208 2.05997446344055 -2.0832234451772 -1 3.37410329518044 1176 1869 2160 1275 4185 587 234 1798 208 3195 699 868 M1098 GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN.html Genes down-regulated in ME-A cells (breast cancer) undergoing apoptosis upon serum starvation (5% to 0% FCS) for 22 hr. 17160024 299/346 Arthur Liberzon 6.18070621523511e-09 8.53009746664027e-08 270 1485 1275 5.61882384781749e-10 267 2.27329378037849 2.37986064529746 1 6.41270791223889 3044 1275 268 267 717 1924 3022 1650 767 438 2963 869 M596 HASINA_NOL7_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HASINA_NOL7_TARGETS_DN.html Genes down-regulated in SiHa cells (cervical carcinoma) by stable expression of NOL7 [GeneID=51406] off a plasmid vector. 16205646 23/25 Leona Saunders 1.78751162075376e-06 2.74912181490967e-06 3125 1992.63636363636 1276 1.62501188465277e-07 40 3.05910621934171 2.44886188727916 1 6.79117337271183 3125 745 758 341 2974 4714 4096 2756 40 1094 1276 870 M10593 MACLACHLAN_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MACLACHLAN_BRCA1_TARGETS_DN.html Genes down-regulated in SW480 cells (colon cancer with mutated p53 [GeneID=7157]) upon expression of BRCA1 [GeneID=672] off an adenovirus vector. 10644742 44/51 John Newman 1.05648267044221e-06 1.82592391229851e-06 350 1549.27272727273 1276 9.60439252532744e-08 350 3.2325800773971 3.77773540851898 1 7.41014861539785 350 2261 410 2207 3677 766 1276 2517 1843 1068 667 871 M1124 MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP.html Pubertal genes up-regulated by TGFB1 [GeneID=7040]. 17486082 292/366 Arthur Liberzon 1.49040944078255e-13 4.13807797676096e-12 2120 1560 1277 1.35491767343877e-14 126 2.50830847646915 2.70301790787611 1 11.4327156693747 2120 1277 126 312 1136 2081 4109 2377 620 369 2633 872 M16718 DING_LUNG_CANCER_MUTATED_FREQUENTLY http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_MUTATED_FREQUENTLY.html The lung adenocarcinoma TSP (tumor sequencing project) genes with significantly higher frequencies of nonsense, splice site, and frame-shift mutations. 18948947 24/25 Jessica Robertson 1.40769545101869e-07 7.20206492018647e-07 2635 1591 1278 1.2797232191743e-08 159 2.70819514234799 -2.67059001669789 -1 6.64000433145966 2634 783 1210 159 570 2886 1876 4426 251 1428 1278 873 M1787 WORSCHECH_TUMOR_REJECTION_UP http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_REJECTION_UP.html Up-regulated genes defining rejection of mammary carcinoma (MMC) tumors. 18381452 53/115 Jessica Robertson 4.91144449872515e-07 1.10164133334149e-06 530 1584.63636363636 1281 4.46495054108463e-08 258 2.61331698416674 -2.81226547049271 -1 6.21163479207613 526 2229 706 2405 1926 1281 897 258 4388 1230 1585 874 M6729 REACTOME_RECRUITMENT_OF_NUMA_TO_MITOTIC_CENTROSOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECRUITMENT_OF_NUMA_TO_MITOTIC_CENTROSOMES.html Genes involved in Recruitment of NuMA to mitotic centrosomes 13/13 Reactome 3.22553096111209e-06 4.52302618432831e-06 665 1571.90909090909 1282 2.9323051729413e-07 201 2.14687722289637 2.37385598439186 1 4.56442090926582 663 1935 2287 2448 3290 845 575 1123 201 2642 1282 875 M10150 LI_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_CISPLATIN_RESISTANCE_DN.html Genes consistently down-regulated in ACRP cells (ovarian cancer, resistant to cisplatin [PubChem=2767]) compared to the parental sensitive A2780 cells, regardless of cisplatin exposure. 17072341 39/61 Arthur Liberzon 3.17349441823401e-07 8.94262307705344e-07 840 1100 1282 2.88499534182715e-08 132 2.89595291336818 2.71087537074572 1 6.99433598797968 840 557 488 1600 1448 1282 1882 132 1789 628 1454 876 M12107 MAHAJAN_RESPONSE_TO_IL1A_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAHAJAN_RESPONSE_TO_IL1A_DN.html Genes down-regulated in corneal fibroblasts after treatment with IL1A [GeneID=3552]. 12091409 134/175 John Newman 5.61763520462408e-07 1.18849117731177e-06 1285 1547.36363636364 1282 5.10694239915563e-08 483 2.250321769547 2.61702622846517 1 5.3120506948962 1282 2104 1134 483 2069 1612 3385 1268 1040 1519 1125 877 M3034 BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 43/52 Leona Saunders 2.71144416245006e-07 8.37018734255349e-07 365 1323.90909090909 1283 2.46494954238976e-08 7 2.15909615657559 2.3421452755769 1 5.22688634890059 365 3097 1355 2178 1283 113 277 21 3647 2220 7 878 M12948 CHUANG_OXIDATIVE_STRESS_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHUANG_OXIDATIVE_STRESS_RESPONSE_DN.html Genes down-regulated in MCF7 cells (breast cancer) after treatment with the oxydants: hydrogen peroxyde, menadione, and t-butyl hydroperoxyde [PubChem=784;4055;6410]. 12414654 21/38 John Newman 6.60611934808021e-06 8.45468636739115e-06 1045 1590.27272727273 1285 6.00558107717882e-07 557 2.63156141991483 2.72359036620797 1 5.31868191028708 1045 2371 1693 1285 3625 1245 924 557 1149 1944 1655 879 M5887 NABA_BASEMENT_MEMBRANES http://www.broadinstitute.org/gsea/msigdb/cards/NABA_BASEMENT_MEMBRANES.html Genes encoding structural components of basement membranes 22159717 49/56 Alexandra Naba 4.26346600286526e-11 8.35002470270707e-10 95 1477.18181818182 1285 3.87587818449809e-12 91 3.14646194296249 3.22837721521435 1 11.4375350070758 91 1691 186 727 4284 1285 2162 2774 1786 414 849 880 M4381 LUI_THYROID_CANCER_PAX8_PPARG_UP http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_PAX8_PPARG_UP.html Top up-regulated genes distinguishing between follicular thyroid carcinoma (FTC) samples by the presence or absence of the PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 67/84 Leona Saunders 4.06057202324845e-07 9.97185221109921e-07 1170 1237.72727272727 1286 3.69142979337667e-08 165 2.09598186118338 2.10303373095946 1 5.00853584988724 1169 318 1759 1653 1725 1286 1791 165 379 2956 414 881 M14566 PEREZ_TP53_AND_TP63_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/PEREZ_TP53_AND_TP63_TARGETS.html Genes up-regulated in HMEC cells (primary mammary epithelium) upon expression of both of TP53 [GeneID=7157] and the transcriptionally active isoform of TP63 [GeneID=8626] off adenoviral vectors. 17563751 283/385 Leona Saunders 5.97962523137901e-12 1.31887061178079e-10 2665 1792.72727272727 1286 5.43602293763204e-13 161 2.30567744211332 2.51393682836929 1 9.11105518651344 2664 1286 161 524 685 2112 3992 3167 854 196 4079 882 M16734 KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3.html Genes with high histone H3 trimethylation mark at K27 (H3K27me3) in PC3 cells (prostate cancer) by ChIP-chip assay on a 12K CpG array (high-CpG-density promoters, HCP). 18488029 97/143 Jessica Robertson 4.44922760320636e-07 1.03654265977957e-06 1620 1122.90909090909 1286 4.04475318455256e-08 123 2.32544976212236 2.47115637193551 1 5.54662587320424 1618 123 793 1774 1838 634 1470 1758 580 1286 478 883 M3115 KEGG_LONG_TERM_POTENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_POTENTIATION.html Long-term potentiation 65/89 KEGG 1.39398380589169e-07 7.20206492018647e-07 2130 1658.63636363636 1287 1.26725808565324e-08 352 1.64783890273351 1.79298481617163 1 4.02061138588651 2128 352 2908 895 562 1664 3331 1287 924 3221 973 884 M1021 REACTOME_SIGNALING_BY_INSULIN_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_INSULIN_RECEPTOR.html Genes involved in Signaling by Insulin receptor 100/149 Reactome 9.59920741485732e-08 6.64473403617636e-07 1290 1737.18181818182 1287 8.7265525760884e-09 284 1.31670037702677 -1.15772588732279 -1 3.22112400131097 1287 2135 3833 1557 284 541 994 1047 2785 4241 405 885 M19511 WANG_CISPLATIN_RESPONSE_AND_XPC_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CISPLATIN_RESPONSE_AND_XPC_UP.html Genes up-regulated in fibroblasts with defective XPC [GeneID=7508] in response to cisplatin [PubChem=2767]. 15107491 253/404 John Newman 1.73769139257073e-07 7.37919956089047e-07 1365 1144.63636363636 1289 1.57971957256727e-08 140 2.25336975609961 2.18258998296206 1 5.50688873140673 1362 1334 364 140 1289 559 1270 1566 2346 360 2001 886 M11480 REACTOME_MEMBRANE_TRAFFICKING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEMBRANE_TRAFFICKING.html Genes involved in Membrane Trafficking 151/177 Reactome 1.85839579461669e-07 7.48271685670965e-07 545 1987.72727272727 1290 1.68945086509101e-08 120 1.3902545092557 -1.17826448467001 -1 3.37501943921962 543 3589 3924 3231 873 181 474 1290 3245 4395 120 887 M18334 REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS.html Genes involved in Class A/1 (Rhodopsin-like receptors) 108/346 Reactome 1.70273144922095e-19 9.45516757685047e-18 2695 1416.45454545455 1290 1.54793768110995e-20 57 3.18452614954102 -3.02753343646949 -1 21.7529260521851 2693 74 57 2750 905 1468 1290 1014 2674 130 2526 888 M1848 MATTHEWS_SKIN_CARCINOGENESIS_VIA_JUN http://www.broadinstitute.org/gsea/msigdb/cards/MATTHEWS_SKIN_CARCINOGENESIS_VIA_JUN.html Genes up-regulated by skin tumor promoters but completely blocked by expression of TAM67, a dominan-negative form of JUN [GeneID=3725]. 17363560 20/23 Jessica Robertson 2.73508740023232e-07 8.38703759494626e-07 1310 1479.54545454545 1290 2.4864434002403e-08 320 3.49461857789944 -3.6478929512786 -1 8.48973287815794 1308 3185 1573 1899 1290 1190 320 643 1144 2934 789 889 M1627 JACKSON_DNMT1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JACKSON_DNMT1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon Cre-lox knockout of DNMT1 [GeneID=1786]. 11137995 49/53 John Newman 1.11435220496206e-05 1.37008137729121e-05 420 1768 1293 1.01305259041858e-06 418 2.3041063089329 2.15987876980626 1 4.45636645183667 418 1717 884 1074 3780 1274 1293 2666 3533 1255 1554 890 M7715 FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_DN.html Top 100 genes negatively associated with T-cell acute lymphoblastic leukemia MLL T-ALL) expressing MLL-ENL fusion [GeneID=4297;4298]. 12637319 106/152 Kevin Vogelsang 2.74430716508707e-07 8.38703759494626e-07 610 1407.27272727273 1296 2.49482500674126e-08 117 1.69019872898701 1.56981885428781 1 4.08028725783421 609 117 3018 2391 1296 837 662 1749 1152 1942 1707 891 M8646 BOYLAN_MULTIPLE_MYELOMA_C_D_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_D_DN.html Genes down-regulated both in group C and D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 288/419 Jessica Robertson 3.53945665310293e-09 5.07788310110815e-08 1375 1172.90909090909 1296 3.21768787163396e-10 204 2.28054349390671 -2.31788532529365 -1 6.63992503964306 1375 1279 256 696 204 1296 1380 2223 1961 212 2020 892 M12802 SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS http://www.broadinstitute.org/gsea/msigdb/cards/SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS.html Genes from the recurrent amplicons in 89 samples of oral squamous cell carcinoma (SCC). 15824737 54/61 Leona Saunders 4.61938353259514e-07 1.05842185795384e-06 2070 1307.54545454545 1297 4.19944045685139e-08 386 2.05495657756116 2.2008595163474 1 4.88813255435142 2067 386 1297 626 1881 1791 2115 1089 391 1283 1457 893 M9893 RODWELL_AGING_KIDNEY_NO_BLOOD_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_NO_BLOOD_UP.html Genes whose expression increases with age in normal kidney, excluding those with higher expression in blood. 15562319 279/355 John Newman 1.47829222244381e-24 1.203024015506e-22 900 1195.90909090909 1297 1.34390202040346e-25 36 2.88273920903515 2.94526040977021 1 25.3620961094603 896 1297 36 687 1420 1362 2227 1913 1231 140 1946 894 M735 REACTOME_NEURONAL_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEURONAL_SYSTEM.html Genes involved in Neuronal System 192/338 Reactome 8.00375068684122e-08 6.29674606547497e-07 2120 1555.54545454545 1298 7.27613725274834e-09 345 2.2903911255816 2.42820178588452 1 5.6616432629406 2117 1400 345 743 781 1249 3456 2971 2274 477 1298 895 M651 REACTOME_CS_DS_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CS_DS_DEGRADATION.html Genes involved in CS/DS degradation 11/13 Reactome 2.61669037848069e-06 3.77468783203816e-06 885 1732.18181818182 1299 2.37881226435432e-07 884 2.52415828788602 2.96799155056233 1 5.45507751316651 884 971 1522 4134 3193 963 1090 994 2245 1759 1299 896 M2001 WU_CELL_MIGRATION http://www.broadinstitute.org/gsea/msigdb/cards/WU_CELL_MIGRATION.html Genes associated with migration rate of 40 human bladder cancer cells. 18724390 257/340 Jessica Robertson 2.23960247946581e-30 2.78182202712595e-28 4490 2234.36363636364 1299 2.03600225405985e-31 20 2.84624217942608 3.08277221737344 1 31.4915461286745 4486 1299 20 241 1124 4669 3731 3716 1129 42 4121 897 M13661 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5.html The 'group 5 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 but not ERBB2 [GeneID=2099;2064]. 18794137 609/708 Jessica Robertson 8.08585375402361e-08 6.29674606547497e-07 1300 1377.72727272727 1300 8.08585404823826e-09 92 1.87266749669667 -1.77512574925107 -1 4.61994175985683 1300 1132 4511 92 236 1021 1765 1496 1582 503 1517 898 M15835 RIGGINS_TAMOXIFEN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIGGINS_TAMOXIFEN_RESISTANCE_DN.html Genes down-regulated SUM44/LCCTam cells (breast cancer) resistant to 4-hydroxytamoxifen [PubChem=63062] relative to the parental SUM44 cells sensitive to the drug. 18974135 319/395 Leona Saunders 1.33455307707381e-07 7.20206492018647e-07 3065 2089.54545454545 1300 1.21323014366347e-08 514 2.13526735596831 2.28836676109855 1 5.22470356186982 3062 1267 647 782 514 3409 4589 2519 1300 984 3912 899 M5731 BIOCARTA_AKAP95_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAP95_PATHWAY.html AKAP95 role in mitosis and chromosome dynamics 20/20 BioCarta 1.44799617756191e-07 7.26289540930751e-07 1270 1874.36363636364 1301 1.31636024806013e-08 498 1.88234815642138 2.10018056038986 1 4.59715330520423 1270 3472 2984 2968 594 1637 1010 1301 498 3633 1251 900 M7375 DORN_ADENOVIRUS_INFECTION_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_48HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 48 h after infection with adenovirus Ad12. 15681441 76/94 Arthur Liberzon 3.3126254901735e-06 4.62865373404941e-06 640 1495.54545454545 1301 3.01148225284813e-07 248 2.5144473118228 2.96714569489569 1 5.34433121980747 640 3343 962 1301 3302 772 1572 863 1460 1988 248 901 M17400 BIOCARTA_ALK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ALK_PATHWAY.html ALK in cardiac myocytes 38/51 BioCarta 8.61842332097653e-08 6.48643236402367e-07 1305 1426.36363636364 1302 7.83493059872752e-09 215 1.74454229075765 1.9500449424758 1 4.29138527587864 1189 1761 2386 2160 215 1138 1302 636 1304 2507 1092 902 M16496 CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP.html Top 200 marker genes up-regulated in the 'CTNNB1' subclass of hepatocellular carcinoma (HCC); characterized by activated CTNNB1 [GeneID=1499]. 18701503 198/302 Yujin Hoshida 1.50728144620595e-08 1.9176195218577e-07 4285 1959.90909090909 1302 1.37025586957523e-09 294 2.36567358371438 2.70991416010864 1 6.3406297369087 4283 1398 294 925 777 3306 4356 1302 1055 298 3565 903 M13537 KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP.html Genes up-regulated in MEWO cells (melanoma) after 48h of methionine [PubChem=876] deprivation. 16908595 161/209 Arthur Liberzon 2.5017772784843e-07 8.18539112849675e-07 2335 1614.54545454545 1303 2.27434323907211e-08 885 2.20350265796315 2.36738272584595 1 5.34400976119405 2332 2086 885 1303 1194 1106 2959 1485 2413 1038 959 904 M2532 BOSCO_INTERFERON_INDUCED_ANTIVIRAL_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_INTERFERON_INDUCED_ANTIVIRAL_MODULE.html Genes representing interferon-induced antiviral module in sputum during asthma exacerbations. 20336062 90/139 Antony Bosco 5.94664645615973e-06 7.68990993782847e-06 905 1821.36363636364 1303 5.40605684557409e-07 663 2.13832242448719 -2.25145086745629 -1 4.34782136473461 903 1614 1196 1597 3585 1290 860 4523 663 1303 2501 905 M1574 LEE_AGING_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_MUSCLE_DN.html Downregulated in the gastrocnemius muscle of aged adult mice (30-month) vs young adult (5-month) 10464095 80/102 John Newman 7.2808113387826e-07 1.40431223245242e-06 580 1532.90909090909 1304 6.61892158939899e-08 477 2.13209065413326 2.31407358815606 1 4.96819139336977 580 3022 1304 1298 2301 545 977 2080 2372 1906 477 906 M7094 MARKEY_RB1_ACUTE_LOF_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_ACUTE_LOF_DN.html Genes down-regulated in adult fibroblasts with inactivated RB1 [GeneID=5925] by Cre-lox: acute loss of function (LOF) of RB1. 17452985 297/446 Arthur Liberzon 3.55149771326779e-07 9.40697096348413e-07 1100 1438.09090909091 1305 3.22863480599298e-08 650 2.05090530698519 -2.09816061185679 -1 4.92063408415494 1096 1288 650 1640 1569 1305 1698 1165 3186 692 1530 907 M14601 CAIRO_HEPATOBLASTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_UP.html Genes up-regulated in hepatoblastoma samples compared to normal liver tissue. 19061838 299/338 Arthur Liberzon 1.87415286182173e-07 7.48978540381421e-07 920 1707.90909090909 1305 1.70377547407138e-08 371 1.86455705335908 1.95808818373538 1 4.54321243449324 917 3850 2545 3183 888 451 1305 525 2491 2261 371 908 M1344 FUJIWARA_PARK2_IN_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_IN_LIVER_CANCER_DN.html Genes down-regulated in tumorous liver tissues from PARK2 [GeneID=5071] knockout mice compared to the normal, non-tumorous tissue from wild type mice. 18574468 11/16 Jessica Robertson 3.76547033097801e-06 5.17108523777021e-06 1650 1806.09090909091 1306 3.42316070535224e-07 987 3.12115551354682 -3.53655408083065 -1 6.5855229323938 1648 987 1064 2654 3367 2003 1070 1136 3607 1025 1306 909 M2442 STEINER_ERYTHROCYTE_MEMBRANE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/STEINER_ERYTHROCYTE_MEMBRANE_GENES.html Major erythrocyte membrane genes. 19687298 17/27 Arthur Liberzon 4.56710540098268e-07 1.04898965900916e-06 2760 1684 1308 4.15191486281309e-08 173 2.64956460548083 3.60952004558427 1 6.32114964284491 2759 886 1308 840 1872 3534 4354 173 195 2050 553 910 M9611 MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_UP.html Genes up-regulated in derivatives of MCF-7aro cells (breast cancer) that developed resistance to tamoxifen [PubChem=5376] or inhibitors of aromatase (CYP19A1) [GeneID=1588]. 18559539 21/31 Leona Saunders 2.73889712159286e-06 3.93055470170821e-06 1800 1474.09090909091 1309 2.48990957399785e-07 305 2.91097347252401 2.95967535391138 1 6.27813784478168 1796 813 933 1147 3214 1309 2408 2324 348 1618 305 911 M2512 FOSTER_KDM1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_KDM1A_TARGETS_UP.html Genes up-regulated in ES cells (embryonic stem) heterozygotic for KDM1A [GeneID=23028] loss of function mutant compared to the homozygotic loss of the gene. 20713442 254/576 Arthur Liberzon 3.0063924310945e-18 1.47814294528813e-16 3140 1798.27272727273 1310 2.73308402826773e-19 67 2.61848104186696 2.67510997790493 1 16.6200849886746 3137 1310 67 259 397 3281 4274 2532 893 94 3537 912 M4737 VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_EARLY_RESPONSE_TO_TGFB1.html ECM related genes up-regulated early (within 30 min) in dermal fibroblasts after addition of TGFB1 [GeneID=7040]. 11279127 137/173 John Newman 1.28371673921727e-07 7.20206492018647e-07 740 1356.18181818182 1311 1.16701528556648e-08 352 2.51737386129705 2.78878992349613 1 6.16861943384092 740 1544 352 460 2411 1311 2495 2321 1288 620 1376 913 M5883 NABA_SECRETED_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_SECRETED_FACTORS.html Genes encoding secreted soluble factors 22159717 161/379 Alexandra Naba 5.63613385420538e-27 5.66011740252115e-25 1315 1330 1313 5.12375804927761e-28 27 3.09339547660326 3.16404334808705 1 30.1145398112745 1313 1454 27 2043 318 980 2662 566 2726 84 2457 914 M630 REACTOME_GLUTAMATE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUTAMATE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Glutamate Neurotransmitter Release Cycle 18/28 Reactome 4.92952957411061e-07 1.10376563518985e-06 1550 1246.36363636364 1314 4.4813915260621e-08 292 2.14923875240836 -1.99584147586116 -1 5.09895099383208 1547 884 1721 2564 1931 857 330 292 1314 1852 418 915 M1084 REACTOME_TRYPTOPHAN_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRYPTOPHAN_CATABOLISM.html Genes involved in Tryptophan catabolism 5/11 Reactome 3.51999726993944e-06 4.8736835183673e-06 1075 1619.45454545455 1314 3.52000284562322e-07 391 2.56160752370767 -3.06231504787704 -1 5.42242760921926 1073 1044 4264 1388 3383 1314 1067 607 1499 1784 391 916 M14722 GAUTSCHI_SRC_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/GAUTSCHI_SRC_SIGNALING.html Genes down-regulated in A549 cells (lung cancer) after treatment with AZD0530 [PubChem=10302451], a SRC [GeneID=6714] kinase inhibitor. 18381431 8/8 Jessica Robertson 1.74305693373009e-06 2.69922202336155e-06 1315 1604.54545454545 1314 1.74305830094296e-07 76 2.2012393636396 2.43570661356056 1 4.87973142934732 1314 1973 4543 1449 3014 925 677 1280 328 2071 76 917 M15472 VECCHI_GASTRIC_CANCER_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_EARLY_DN.html Down-regulated genes distinguishing between early gastric cancer (EGC) and normal tissue samples. 17297478 383/696 Arthur Liberzon 8.50745601866903e-30 1.00387981020295e-27 3230 1828.36363636364 1315 7.73405092606274e-31 21 2.66869654534145 2.85934734026991 1 28.9258378935359 3227 1211 21 237 745 3528 4539 1623 1315 54 3612 918 M4047 BIOCARTA_NKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NKT_PATHWAY.html Selective expression of chemokine receptors during T-cell polarization 9/30 BioCarta 1.39197795108819e-05 1.68249319568149e-05 1020 1844.72727272727 1316 1.39198667037683e-06 273 1.96528398163959 -2.29274495993019 -1 3.72318719176152 1017 1959 4196 2818 3876 913 273 498 2363 1316 1063 919 M4991 DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP.html 'PAX-FKHR signature': genes up-regulated by PAX3- or PAX7-FOXO1 [GeneID=5081;5077;2308] fusion in primary alveolar rhabdomyosarcoma(ARMS) tumors. 16849537 76/95 Arthur Liberzon 5.8746510625257e-07 1.22366959466555e-06 2085 1381.90909090909 1316 5.34059330111997e-08 260 2.21916987614831 2.50132373774891 1 5.22651573899696 2081 260 1051 1622 2106 1540 2445 710 1316 968 1102 920 M16973 BIOCARTA_CBL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CBL_PATHWAY.html CBL mediated ligand-induced downregulation of EGF receptors 20/21 BioCarta 5.58779774801511e-07 1.18659903470788e-06 1355 1249.72727272727 1317 5.07981742478625e-08 342 2.1033323436836 -2.69419246626943 -1 4.96238823368669 1353 2382 1984 649 2060 1317 1155 457 587 1461 342 921 M10778 CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY http://www.broadinstitute.org/gsea/msigdb/cards/CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY.html Genes down-regulated in T cell acute lymphocytic leukemia (T-ALL) patients refractory to chemotherapy treatment. 14684422 36/69 Arthur Liberzon 2.79965525027702e-07 8.47618523496314e-07 2875 1533.90909090909 1317 2.5451414605027e-08 594 2.06428082398411 2.14361428727715 1 4.99061649300911 2874 594 1675 1256 1317 1869 1832 923 1294 1299 1940 922 M17026 RIZKI_TUMOR_INVASIVENESS_3D_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_3D_UP.html Genes up-regulated in three-dimentional (3D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 276/374 Jessica Robertson 3.03027739091378e-07 8.77601760597774e-07 1520 1342.18181818182 1319 2.75479800754901e-08 813 2.03696035925071 2.19800168439468 1 4.91153684511377 1517 1319 1104 870 1397 1350 2295 958 1979 1162 813 923 M9951 WANG_METHYLATED_IN_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METHYLATED_IN_BREAST_CANCER.html Genes up-regulated in MDA468 cells (breast cancer) vs DU99 cells (normal breast) after treatment with azacytidine [PubChem=9444]. 15735726 67/88 Leona Saunders 1.11572977474193e-07 7.04017019921975e-07 1270 1404.27272727273 1320 1.01429984666015e-08 360 2.19428575497548 2.70199423480333 1 5.37920970490783 1662 2188 1270 879 360 1656 2236 1270 1320 1371 1235 924 M18843 JI_METASTASIS_REPRESSED_BY_STK11 http://www.broadinstitute.org/gsea/msigdb/cards/JI_METASTASIS_REPRESSED_BY_STK11.html Adenocarcinoma metastatic program genes up-regulated in A549 and H2126 cells (lung cancer) lacking functional STK11 [GeneID=6794] but down-regulated by the normal gene. 17676035 33/42 Jessica Robertson 4.91304026839797e-07 1.10164133334149e-06 2725 1563.27272727273 1320 4.46640124143502e-08 402 2.49422484692877 -2.21745989497819 -1 5.92628253616489 2722 615 876 600 1927 2422 1320 2338 402 1057 2917 925 M559 REACTOME_SIGNALING_BY_CONSTITUTIVELY_ACTIVE_EGFR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_CONSTITUTIVELY_ACTIVE_EGFR.html Genes involved in Signaling by constitutively active EGFR 30/35 Reactome 8.11294929486674e-07 1.51475952024411e-06 1545 1723.90909090909 1321 7.37541116971274e-08 418 1.56428239531444 -1.58373094933422 -1 3.61107595990749 1541 2767 3010 669 2392 1303 418 655 1321 3898 989 926 M9331 YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN.html Genes down-regulated in mouse stroma of pancreatic adenocarcinoma zenografts after treatment with HhAntag, a hedgehog (Hh) pathway inhibitor. 18754008 263/465 Jessica Robertson 2.3379254163257e-11 4.75646895045574e-10 2000 1355 1321 2.12538674213686e-12 178 2.49723009967978 2.81621459629926 1 9.31267426543701 1996 1321 178 1123 865 936 3381 1998 1327 389 1391 927 M2544 ROESSLER_LIVER_CANCER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROESSLER_LIVER_CANCER_METASTASIS_UP.html Genes up-regulated in liver samples containing tumor thrombi in the major branches of the portal vein at surgery (PT) compared to those from metastasis-free HCC patients (PN) at the time of surgery and at follow-up. 21159642 158/214 Yujin Hoshida 1.7377938540527e-07 7.37919956089047e-07 2420 1600.54545454545 1321 1.57981271938377e-08 136 2.32866823488109 2.29658308330938 1 5.69257865915558 2420 1489 777 136 794 1321 3344 2511 884 928 3002 928 M4479 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_UP.html Genes up-regulated in ductal carcinoma vs normal lobular breast cells. 17389037 105/146 Arthur Liberzon 3.90645641859945e-07 9.76357383103197e-07 725 1277.18181818182 1323 3.55132464750386e-08 723 2.33338012175672 2.6128241569866 1 5.59008987492002 723 1586 778 830 1681 1218 1687 1939 1369 915 1323 929 M11513 SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_DN.html Genes down-regulated in MCF10A cells (breast cancer) grown at low (mesenchymal phenotype) compared to those grown at high (epithelial, basal-like phenotype) confluency. 18281472 237/351 Jessica Robertson 1.45893396722668e-16 5.73847360442495e-15 1325 1339 1323 1.32630360656971e-17 82 2.55773559959556 -2.04983129267965 -1 14.5987948197647 2174 1323 82 313 722 1323 1944 2994 1123 233 2498 930 M7346 KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_UP.html Top 25 most highly expressed genes in embryonic carcinoma relative to seminoma tumors. 16424014 21/29 Arthur Liberzon 1.22474993225096e-06 2.03819039301383e-06 2795 1667.18181818182 1325 1.11340964915937e-07 212 2.40296322732727 2.86682736301883 1 5.44939293201194 2795 794 1087 979 2716 2980 3588 212 339 1325 1524 931 M2890 KEGG_CALCIUM_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CALCIUM_SIGNALING_PATHWAY.html Calcium signaling pathway 114/193 KEGG 6.25985868775438e-09 8.61414956448999e-08 2115 1251.72727272727 1327 5.69078064142376e-10 22 2.4064227814002 2.49365332812018 1 6.78705907373895 2115 22 280 362 568 1327 3084 2239 2011 209 1552 932 M1797 ZHENG_GLIOBLASTOMA_PLASTICITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_GLIOBLASTOMA_PLASTICITY_DN.html The glioblastoma multiforme (GBM) plasticity signature: genes down-regulated in neural stem cells (NSC) with double knockout of TP53 and PTEN [GeneID=7157;5728] vs those with knockout of TP53 alone. 18948956 98/115 Jessica Robertson 4.43014217122612e-08 4.68840158031105e-07 1185 1247.18181818182 1327 4.02740205494176e-09 103 2.61550762611202 3.02819541344342 1 6.60713882217504 1185 103 325 110 2159 1410 3870 1399 1487 344 1327 933 M9118 IWANAGA_CARCINOGENESIS_BY_KRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_UP.html Cluster 3: genes up-regulated in lung tissue samples from mice with tumor-bearing genotypes (activated KRAS [GeneID=3845] alone or together with inactivated PTEN [GeneID=5728]). 18281487 249/309 Jessica Robertson 2.20998166922148e-07 7.79888761522542e-07 3760 2266.36363636364 1328 2.0090744465658e-08 298 2.3222054491301 2.5935070633601 1 5.65420558967172 3760 1328 475 298 1059 3349 4529 4440 762 511 4419 934 M2311 AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_DN http://www.broadinstitute.org/gsea/msigdb/cards/AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_DN.html Genes down-regulated in RWPE-1 cells (prostate cancer) upon expression of constitutively active form of STAT3 [GeneID=6774]. 17438134 17/19 Arthur Liberzon 4.02922727321009e-07 9.93104581177629e-07 1330 1812.90909090909 1329 3.66293455559084e-08 373 2.89814046225715 -2.81446849893287 -1 6.94659093832807 1329 900 903 3622 1718 950 373 2894 3696 1090 2467 935 M674 REACTOME_ALPHA_LINOLENIC_ACID_ALA_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ALPHA_LINOLENIC_ACID_ALA_METABOLISM.html Genes involved in alpha-linolenic acid (ALA) metabolism 15/17 Reactome 9.44042715644697e-07 1.68146476145018e-06 915 1682.09090909091 1330 8.58221018857651e-08 287 1.45736110570818 -1.22729067765501 -1 3.33425689376314 912 914 2724 3669 2529 687 287 1330 2770 2100 581 936 M1571 YAMAZAKI_TCEB3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMAZAKI_TCEB3_TARGETS_DN.html Genes down-regulated in embryonic stem cells from TCEB3 [GeneID=6924] knockout mice. 12604609 301/568 John Newman 4.26310444371519e-07 1.01522971616225e-06 1535 1478.63636363636 1330 3.87555024528094e-08 389 2.04996155046739 2.0881693564788 1 4.89104661554649 1535 1281 881 389 1789 1330 1558 2610 1323 973 2596 937 M8779 LI_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LI_LUNG_CANCER.html Proteins showing significant overexpression in lung cancer cell lines relative to normal bronchial epithelial cell lines. 16369491 69/87 Arthur Liberzon 1.57306790335583e-07 7.31918027928963e-07 2200 1517.90909090909 1331 1.43006183257732e-08 264 2.53534509687144 2.58611952036683 1 6.20587084233779 2198 284 825 409 678 2857 2630 1473 264 1331 3748 938 M2431 KAUFFMANN_MELANOMA_RELAPSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_MELANOMA_RELAPSE_UP.html DNA repair and replication genes up-regulated in melanoma patients who will relapse vs patients who will not. 17891185 69/74 Jessica Robertson 1.18568606804659e-06 1.98878402316272e-06 45 1577.72727272727 1332 1.07789700642769e-07 43 1.48410619081932 1.49641098671184 1 3.35285419573281 43 2614 3049 2382 4028 231 44 631 1686 1332 1315 939 M11620 WIELAND_UP_BY_HBV_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/WIELAND_UP_BY_HBV_INFECTION.html Genes induced in the liver during hepatitis B (HBV) viral clearance in chimpanzees. 15100412 120/193 Kate Stafford 1.08173604191622e-06 1.8586800574607e-06 640 1562.81818181818 1335 9.83396885276589e-08 24 1.7477527408653 -1.58820594624963 -1 3.97801926370388 638 24 1335 1454 2625 1120 1048 2255 3873 590 2229 940 M9990 REACTOME_APOPTOTIC_CLEAVAGE_OF_CELL_ADHESION_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOTIC_CLEAVAGE_OF_CELL_ADHESION_PROTEINS.html Genes involved in Apoptotic cleavage of cell adhesion proteins 15/19 Reactome 1.46970462782714e-07 7.26289540930751e-07 2275 1307 1336 1.33609520546401e-08 24 2.91800880041298 -2.30020349567745 -1 7.15401945432309 2275 921 1336 124 611 1998 992 2537 24 2101 1458 941 M512 REACTOME_DAG_AND_IP3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DAG_AND_IP3_SIGNALING.html Genes involved in DAG and IP3 signaling 32/37 Reactome 1.89882585160256e-07 7.5062462475411e-07 2590 1756.27272727273 1337 1.72620546862795e-08 242 2.14035131715366 2.36724000660295 1 5.22179809601139 2590 627 1357 437 901 2602 4401 4487 242 1337 338 942 M2546 DUNNE_TARGETS_OF_AML1_MTG8_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/DUNNE_TARGETS_OF_AML1_MTG8_FUSION_UP.html Genes up-regulated in Kasumi-1 cells (acute myeloid leukaemia (AML) with the t(8;21) translocation) after knockdown of the AML1 MTG8 fusion [GeneID=861;862] by RNAi. 16652140 47/93 Leona Saunders 6.76843168521106e-07 1.34257275111063e-06 980 1469.63636363636 1337 6.15312160687317e-08 463 2.46687649802797 -2.91392935284238 -1 5.77553660551534 2015 463 893 980 2232 2327 1512 997 2433 977 1337 943 M2390 WANG_THOC1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_THOC1_TARGETS_UP.html Genes up-regulated in testis tissue expressing hypomorphic allele of THOC1 [GeneID=9984]. 19307311 3/13 Arthur Liberzon 1.16664506411326e-07 7.06112554001409e-07 2855 1718.63636363636 1338 1.166645125361e-08 7 5.0417368064933 5.00861535556881 1 12.4219441728143 2852 1058 4696 100 476 2395 1338 1209 7 1696 3078 944 M7061 CROMER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_METASTASIS_UP.html Metastatic propensity markers of head and neck squamous cell carcinoma (HNSCC): up-regulated in metastatic vs non-metastatic tumors. 14676830 124/157 Kevin Vogelsang 2.33679252235107e-07 7.98113405922816e-07 1605 1542.90909090909 1339 2.12435706414561e-08 23 2.11969669723574 2.50242815197452 1 5.1482132334809 1601 23 928 868 1120 1986 3491 2585 1339 1199 1832 945 M1439 ABBUD_LIF_SIGNALING_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_2_UP.html Genes up-regulated in GH3 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 38/45 Kevin Vogelsang 5.55189620899266e-05 6.2274120975393e-05 415 1701.81818181818 1340 5.04730574635929e-06 413 2.60847787701968 2.68898552209297 1 4.36185934115552 413 2270 726 462 4158 1273 2028 3174 1595 1281 1340 946 M4042 NIKOLSKY_BREAST_CANCER_10Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_10Q22_AMPLICON.html Genes within amplicon 10q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 14/19 Jessica Robertson 5.90610754751332e-07 1.22706823938781e-06 1450 1469 1346 5.36919012096745e-08 12 3.40199493126131 5.00990626218114 1 8.03728829738354 1449 930 1179 736 2110 1346 1379 4070 12 2837 111 947 M14808 SESTO_RESPONSE_TO_UV_C7 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C7.html Cluster 7: genes changed in primary keratinocytes by UVB irradiation. 11867738 86/113 John Newman 4.51825146730439e-07 1.04185917010687e-06 1025 1397.81818181818 1346 4.1075021774917e-08 196 2.02013847899914 1.94043476524534 1 4.81002773018969 1022 196 1444 1224 1859 882 1073 1452 2771 1346 2107 948 M2230 BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP.html Genes bound by ESR1 [GeneID=2099] and up-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer). 18838536 238/310 Arthur Liberzon 1.70625749309684e-07 7.34141783720791e-07 3885 2051.54545454545 1346 1.55114329584485e-08 496 2.13801514540199 2.14358412379211 1 5.22433514368743 3882 1346 508 708 779 3475 2787 4207 853 496 3526 949 M9806 ZHU_CMV_8_HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_8_HR_DN.html Down-regulated at 8 h following infection of primary human foreskin fibroblasts with CMV 9826724 72/93 John Newman 1.13445280132444e-07 7.05613393308323e-07 745 1126.72727272727 1347 1.03132078165789e-08 41 2.00320143317008 2.27975579192277 1 4.90562379880242 745 1648 1807 1871 370 518 1347 41 1717 2272 58 950 M1836 LABBE_WNT3A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_WNT3A_TARGETS_UP.html Up-regulated genes in NMuMG cells (mammary epithelium) after stimulation with WNT3A [GeneID=89780]. 17210685 148/192 Jessica Robertson 1.79110493417814e-07 7.46161984935643e-07 1685 1155.54545454545 1348 1.62827734545357e-08 143 2.27891437923339 2.36325314483728 1 5.56546205574455 1684 1478 435 143 834 688 1348 2522 1667 383 1529 951 M3911 GEISS_RESPONSE_TO_DSRNA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GEISS_RESPONSE_TO_DSRNA_UP.html Genes up-pregulated by dsRNA in GRE cells (glioma; no interferon system). 11487589 48/55 John Newman 2.87648768693996e-07 8.57676682397763e-07 1350 1875.72727272727 1349 2.61498914821744e-08 632 1.87790737429472 -2.09080605403185 -1 4.53165230185377 632 3083 1926 3933 1349 981 1109 1444 3886 1347 943 952 M11536 XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_DN.html Genes down-regulated in DU-145 cells (prostate cancer) in the absence and presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 31/57 Arthur Liberzon 1.15317393704128e-07 7.06112554001409e-07 2620 1363.63636363636 1350 1.04833999771564e-08 292 3.30283499658546 3.02108668863362 1 8.1203410218736 2620 669 1027 602 387 2326 2468 1536 292 1723 1350 953 M764 REACTOME_INSULIN_SYNTHESIS_AND_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INSULIN_SYNTHESIS_AND_PROCESSING.html Genes involved in Insulin Synthesis and Processing 29/35 Reactome 3.62712427761492e-07 9.44292696654297e-07 875 1546.63636363636 1352 3.2973862505604e-08 207 1.95149421806579 -1.58661210257147 -1 4.67839635503937 874 3137 2540 1831 1599 977 316 1149 207 3031 1352 954 M7883 CUI_TCF21_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_UP.html Genes most strongly up-regulated in kidney glomeruli isolated from TCF21 [GeneID=6943] knockout mice. 16207825 71/87 John Newman 1.76900655815439e-13 4.79868445660271e-12 370 1355.27272727273 1353 1.60818778014048e-14 129 2.97103458370232 3.24475549423019 1 13.4741674418937 366 248 129 787 3742 1353 1869 2196 2368 236 1614 955 M3005 NABA_COLLAGENS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_COLLAGENS.html Genes encoding collagen proteins 22159717 38/45 Alexandra Naba 1.32844790830584e-09 2.09708164789417e-08 210 1476.36363636364 1353 1.20767991737092e-10 210 3.14549984245909 3.43986870017717 1 9.66311486961731 210 1733 231 778 4323 1413 2487 2246 1353 316 1150 956 M16637 LIU_CDX2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CDX2_TARGETS_UP.html Genes up-regulated in HET1A cells (esophagus epithelium) engineered to stably express CDX2 [GeneID=1045]. 16990345 34/58 Arthur Liberzon 8.694640713419e-08 6.50173706444736e-07 2510 1401.09090909091 1354 7.90421914276433e-09 220 2.77312947868636 -2.56382102929994 -1 6.84995906250402 2507 589 637 1354 220 3326 2030 1791 847 561 1550 957 M12486 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_RUNX1 http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_RUNX1.html Genes whose expression is coregulated with that of RUNX1 [GeneID=861] in hematopoietic stem cells (HSC). 15711547 15/22 Jean Junior 7.11791220330793e-08 6.06397110828564e-07 4280 2266.54545454545 1354 6.47082948509267e-09 51 2.78704391536876 -2.62164850441395 -1 6.91851088636185 4280 922 1258 628 143 4509 3330 4574 51 1354 3883 958 M2396 SERVITJA_ISLET_HNF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_ISLET_HNF1A_TARGETS_DN.html Genes down-regulated in pancreatic islets upon knockout of HNF1A [GeneID=6927]. 19289501 97/171 Arthur Liberzon 7.40487665445678e-08 6.11670596203388e-07 3730 1938 1355 6.7317062760855e-09 122 2.64908224380739 -2.88122018058007 -1 6.56955399932138 3730 122 343 1355 1173 4572 4656 465 1654 578 2670 959 M9440 DUTTA_APOPTOSIS_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/DUTTA_APOPTOSIS_VIA_NFKB.html NF-kB target genes involved in the regulation of programmed cell death. 17072329 38/51 Arthur Liberzon 2.90277386196225e-07 8.62110332351922e-07 1005 1681.45454545455 1356 2.63888567724244e-08 671 2.59337476948294 -2.09390491554403 -1 6.27490319153688 1001 3405 1461 3426 1356 1137 776 2310 1241 1712 671 960 M16338 NIELSEN_LEIOMYOSARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_UP.html Top 20 positive significant genes associated with CNN1 [GeneID=1264] negative leiomyosarcoma tumors. 11965276 38/41 John Newman 8.55236377205202e-06 1.0713152071148e-05 315 1593.81818181818 1357 7.77490638092505e-07 311 2.81544063762688 2.72568666316275 1 5.57739989550823 311 1742 543 621 3709 1193 1739 2717 2915 685 1357 961 M19133 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_UP.html Genes from the grey module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 26/29 Arthur Liberzon 2.73622243633029e-06 3.92905514875197e-06 2125 1557.54545454545 1358 2.48747803588962e-07 199 3.02397986035749 -2.47900953294161 -1 6.52400434808477 2124 1822 856 1358 3212 1914 1055 1084 199 997 2512 962 M18837 BIOCARTA_EGFR_SMRTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EGFR_SMRTE_PATHWAY.html Map Kinase Inactivation of SMRT Corepressor 17/18 BioCarta 6.86895742259369e-07 1.35484659568083e-06 1035 1574.09090909091 1359 6.24450869750652e-08 268 1.9085413281195 -2.36731721940276 -1 4.4539843796668 1031 2391 2440 1507 2245 1226 1359 942 268 2873 1033 963 M6891 HOUSTIS_ROS http://www.broadinstitute.org/gsea/msigdb/cards/HOUSTIS_ROS.html Genes known to modulate ROS or whose expression changes in response to ROS 16612386 39/53 Nick Houstis 2.04625094967689e-07 7.67360472054519e-07 1270 2046.36363636364 1359 1.86022830909236e-08 915 1.55947963965161 -1.69328455460562 -1 3.78506435419804 1268 2278 2944 3702 971 1319 915 1083 3224 3447 1359 964 M1681 BURTON_ADIPOGENESIS_PEAK_AT_16HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_16HR.html Cluster 4: genes maximally expressed at 16 h time point during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 58/73 John Newman 1.19915817783282e-05 1.46518938632433e-05 700 1607.81818181818 1360 1.09014974014268e-06 447 2.00972897753091 2.16548428864563 1 3.85706113791944 447 2202 1360 2129 3807 700 698 591 3166 1115 1471 965 M15327 AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_2G http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_2G.html Genes with basal expression distinguishing NCI-60 cell lines with poor survival after 2 Gy gamma irradiation. 18199535 228/292 Jessica Robertson 1.03346507783236e-07 6.8232212069871e-07 1430 1110.72727272727 1360 9.39513751254634e-09 323 1.8141286750721 1.94281497277709 1 4.4485175276542 1426 1360 1612 410 323 862 1982 1547 720 1596 380 966 M13479 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 10 days after transduction. 16818636 226/350 Arthur Liberzon 5.67972859790258e-12 1.26454334821227e-10 4450 2083.90909090909 1361 5.16338963447023e-13 160 2.37673755391679 2.51695699772531 1 9.41085820887107 4450 1361 160 268 1097 4359 3668 2560 1217 219 3564 967 M1914 ZHANG_TLX_TARGETS_60HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_60HR_UP.html Genes up-regulated in neural stem cells (NSC) at 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 395/528 Jessica Robertson 2.49261387523779e-09 3.71139983947078e-08 2840 1874.81818181818 1361 2.26601261641994e-10 190 2.16526900101548 2.40700919263559 1 6.42032134103531 2837 1210 264 1333 1089 2526 4567 2915 1361 190 2331 968 M1587 YIH_RESPONSE_TO_ARSENITE_C4 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C4.html Genes in cluster 4: immediate down-regulation in HFW cells (fibroblast) by sodium arsenite [PubChem=26435]. 12016162 24/28 John Newman 2.86277341339287e-06 4.07263753735392e-06 695 1315.09090909091 1362 2.6025246714673e-07 190 1.92775027564947 -2.00983880204379 -1 4.12874952683149 695 1847 1856 1941 3243 544 389 367 1362 2032 190 969 M10196 WILLIAMS_ESR1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR1_TARGETS_DN.html The 'ER-alpha profile': genes down-regulated in T47D cells (breast cancer, ESR2 [GeneID=2100] Tet-Off) upon activation of ESR1 [GeneID=2099] by estradiol (E2) [PubChem=5757]. 17700529 8/10 Jessica Robertson 1.47092756034984e-06 2.35348409655975e-06 1785 1562.72727272727 1363 1.4709285339833e-07 221 2.85190281454879 -3.74778646163207 -1 6.40519318251096 1781 1012 4427 623 2911 2033 1363 754 221 1539 526 970 M1960 MIKKELSEN_MCV6_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K4 (H3K4me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 186/271 Jessica Robertson 3.75035100487113e-08 4.19470538933454e-07 1365 1346.90909090909 1363 3.40941006254868e-09 315 2.3717764771315 -2.44632087433488 -1 6.03286958600334 1363 1409 315 1335 455 1830 2717 2432 928 354 1678 971 M16021 KORKOLA_TERATOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_TERATOMA_UP.html Genes from the 12p region that up-regulated in teratoma cells compared to normal testis. 16424014 19/25 Arthur Liberzon 1.82812832689475e-07 7.47800341964416e-07 1365 1406.54545454545 1364 1.66193498073298e-08 303 2.09121284231151 2.69412192019005 1 5.10214344019586 1364 1891 1783 2622 853 750 309 325 2499 2773 303 972 M1524 RUAN_RESPONSE_TO_TNF_TROGLITAZONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_TROGLITAZONE_DN.html Adipocyte abundant genes down-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591] and TNF [GeneID=7124]. 12732648 53/67 John Newman 2.93558592107002e-07 8.6694222517255e-07 1065 1661 1364 2.66871482980192e-08 617 2.01835638930797 -1.8374889330718 -1 4.87052977743456 1065 2232 2090 2833 1364 1046 804 1292 2486 2442 617 973 M7514 BERENJENO_TRANSFORMED_BY_RHOA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector. 17213802 558/655 Leona Saunders 2.55876968915613e-07 8.24554988604781e-07 1475 1989.54545454545 1365 2.55876998378477e-08 1196 1.97297387207416 2.40749618366335 1 4.77716530649519 1471 2496 4342 1228 1323 1335 3279 1365 2626 1196 1224 974 M2076 WHITFIELD_CELL_CYCLE_G2 http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_G2.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the G2 phase of cell cycle. 12058064 236/299 Jessica Robertson 4.69250687256646e-07 1.06998224340646e-06 520 1192.18181818182 1365 4.26591624859873e-08 90 1.795219643167 1.99456714232888 1 4.26056483342414 516 1365 2215 1883 1896 90 534 798 1776 1504 537 975 M1167 HUMMERICH_SKIN_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_SKIN_CANCER_PROGRESSION_UP.html Selected genes up-regulated during progression through benign to malignant skin tumors formed by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 128/168 Arthur Liberzon 5.91748338790837e-07 1.22825512712962e-06 980 1424.09090909091 1366 5.37953179961187e-08 475 2.50349077891468 2.58501520048716 1 5.90091426281603 979 2562 702 475 2113 753 1366 1528 2840 1367 980 976 M997 REACTOME_ION_CHANNEL_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ION_CHANNEL_TRANSPORT.html Genes involved in Ion channel transport 33/63 Reactome 2.85593864809137e-07 8.53706802976014e-07 2655 1656.72727272727 1367 2.59630819894203e-08 616 2.26620394942799 -2.16513545772395 -1 5.48084860682019 2653 616 1108 783 1341 2599 1877 1854 1367 1055 2971 977 M15305 PUJANA_BRCA_CENTERED_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BRCA_CENTERED_NETWORK.html Genes constituting the BRCA-centered network (BCN). 17922014 143/153 Leona Saunders 2.54863722793334e-06 3.69231667153019e-06 70 1568.90909090909 1369 2.31694561860149e-07 66 1.50861600990696 1.51798287550133 1 3.24602332686352 66 2546 3550 1951 3177 277 200 934 2004 1369 1184 978 M1458 ABBUD_LIF_SIGNALING_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_1_UP.html Genes up-regulated in AtT20 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 51/73 Kevin Vogelsang 1.02937148415963e-05 1.27389444290337e-05 1250 1622.90909090909 1371 9.35796636891371e-07 1041 2.37661822480456 -2.27033741514122 -1 4.62840142546515 1247 2227 1423 1371 3756 1451 1229 1041 1143 1104 1860 979 M13883 BIOCARTA_MPR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MPR_PATHWAY.html How Progesterone Initiates Oocyte Membrane 56/66 BioCarta 2.95678646427182e-07 8.6953471098835e-07 1960 1528.90909090909 1372 2.68798805605652e-08 429 1.92810910418128 2.38747243294327 1 4.6495096815355 1305 429 1958 499 1372 1599 1959 1852 878 3776 1191 980 M19784 BIOCARTA_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCR_PATHWAY.html T Cell Receptor Signaling Pathway 61/73 BioCarta 1.81889953618197e-07 7.47800341964416e-07 1685 1600 1372 1.65354516960328e-08 193 1.70151816567085 -1.60978503600235 -1 4.14204157160359 1682 359 2515 193 845 1372 741 3306 1273 2679 2635 981 M6175 CAIRO_LIVER_DEVELOPMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_LIVER_DEVELOPMENT_DN.html Genes down-regulated at early fetal liver stage (embryonic days E11.5 - E12.5) compared to the late fetal liver stage (embryonic days E14.5 - E16.5). 19061838 233/344 Arthur Liberzon 2.19237570924852e-11 4.47965945785846e-10 1700 1220.45454545455 1372 1.99306882660943e-12 177 2.56626192930081 -2.80935658519462 -1 9.5983653569612 1697 1347 177 519 365 2249 2121 1372 1765 330 1483 982 M19118 BIOCARTA_KERATINOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KERATINOCYTE_PATHWAY.html Keratinocyte Differentiation 58/63 BioCarta 3.36537102267593e-07 9.13746684768849e-07 345 1293.81818181818 1373 3.05942867043781e-08 341 1.54747049417422 -1.53358834563568 -1 3.70834195223575 341 384 2817 1088 1518 649 399 1373 2069 2196 1398 983 M188 REACTOME_AMINO_ACID_TRANSPORT_ACROSS_THE_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINO_ACID_TRANSPORT_ACROSS_THE_PLASMA_MEMBRANE.html Genes involved in Amino acid transport across the plasma membrane 24/36 Reactome 4.41567525096578e-06 5.93619686259142e-06 1195 1724.72727272727 1373 4.01425828527579e-07 775 2.23312716890613 2.22533327572424 1 4.64376060515058 1191 775 1046 3044 3438 1719 1294 2074 1373 1190 1828 984 M11067 KENNY_CTNNB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KENNY_CTNNB1_TARGETS_UP.html Genes up-regulated in HC11 cells (mammary epithelium) by expression of constantly active CTNNB1 [GeneID=1499]. 15642117 63/72 Yujin Hoshida 1.41673395313949e-07 7.20206492018647e-07 4270 2308.27272727273 1374 1.28794004033901e-08 258 2.46003740331828 2.03984137721117 1 6.02698145601533 4266 319 1071 1374 577 3882 4015 4590 258 883 4156 985 M19218 LIU_CDX2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CDX2_TARGETS_DN.html Genes down-regulated in HET1A cells (esophagus epithelium) engineered to stably express CDX2 [GeneID=1045]. 16990345 13/19 Arthur Liberzon 1.92337002144966e-07 7.55266763830481e-07 3095 1495.18181818182 1375 1.74851835418369e-08 70 4.563972253804 -2.51924188010861 -1 11.1864317342586 3091 919 372 686 2593 2124 1375 1756 70 564 2897 986 M1126 HUMMERICH_MALIGNANT_SKIN_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_MALIGNANT_SKIN_TUMOR_UP.html Genes up-regulated in malignant skin tumors (squamous cell carcinoma, SCC) formed by treatment with DMBA and TPA [PubChem=6001;4792] in the two stage skin carcinogenesis model. 16247483 34/40 Leona Saunders 4.01680292324923e-09 5.67644005920251e-08 565 1517.45454545455 1375 3.6516390278029e-10 259 3.65997060644752 3.55709280559819 1 10.615236964184 561 1756 259 373 3926 1950 3078 2201 535 678 1375 987 M9016 PROVENZANI_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PROVENZANI_METASTASIS_DN.html Genes down-regulated in polysomal and total RNA samples from SW480 cells (primary colorectal carcinoma, CRC) compared to the SW620 cells (lymph node metastasis from the same individual). 16531451 205/239 Arthur Liberzon 8.65846817126784e-08 6.49549484309567e-07 2280 1557.81818181818 1379 7.87133501094213e-09 218 2.34961518436652 2.59127904143669 1 5.79658094493602 2279 1379 356 351 218 1840 3190 2882 799 660 3182 988 M9775 HAHTOLA_MYCOSIS_FUNGOIDES_CD4_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_CD4_UP.html Genes up-regulated in T helper cells (defines as CD4+) isolated from patients with mucosis fungoides compared to those from normal control donors. 16914566 78/116 Arthur Liberzon 8.04677034986461e-08 6.29674606547497e-07 1120 1588.81818181818 1380 7.31524604016830e-09 187 2.16173609041775 -2.13041685902009 -1 5.3408087823362 1116 1636 1170 1236 187 1340 1395 3243 3164 1610 1380 989 M14650 NGUYEN_NOTCH1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NGUYEN_NOTCH1_TARGETS_DN.html Genes down-regulated in primary keratinocytes by expression of constantly active NOTCH1 [GeneID=4851]. 16618808 137/163 Kevin Vogelsang 1.52285721243701e-06 2.41772150780446e-06 1005 1589.54545454545 1380 1.38441660597428e-07 639 2.05345839123496 2.44223645814722 1 4.58827069962136 1003 2986 1516 1297 2874 912 2452 761 1380 1665 639 990 M5863 BOYLAN_MULTIPLE_MYELOMA_D_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_UP.html Genes up-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 103/121 Jessica Robertson 1.17329534655081e-07 7.06112554001409e-07 405 1862.72727272727 1380 1.06663219011322e-08 402 1.42314687923924 1.57833631182065 1 3.47046816402044 1380 2130 3463 4374 402 405 660 715 3759 2575 627 991 M11857 RODRIGUES_NTN1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_NTN1_TARGETS_DN.html Genes down-regulated in HCT8/S11 cells (colon cancer) engineered to stably express NTN1 [GeneID=1630] off a plasmid vector. 17334389 222/305 Arthur Liberzon 3.04183215681543e-07 8.79206845080762e-07 1445 1363.36363636364 1381 2.76530234308612e-08 727 2.30200201110795 -2.19908434647709 -1 5.55638359775862 1442 1381 727 963 1404 1996 2303 801 1269 760 1951 992 M6041 DAIRKEE_CANCER_PRONE_RESPONSE_E2 http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_CANCER_PRONE_RESPONSE_E2.html 'Cancer prone response profile' (CPRP): genes changed in response to estradiol [PubChem=5757] in epithelial cell cultures from patients at high risk of breast cancer. 18381411 46/58 Jessica Robertson 8.29420516076645e-06 1.0406339276666e-05 1210 1496.18181818182 1381 7.54021493714403e-07 364 2.26152463958438 2.56764965792159 1 4.48172274436301 1708 1712 1206 1430 3703 1209 2292 586 867 1381 364 993 M2010 MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the bivalent histone H3 trimethylation mark at K4 and K27 (H3K4me3 and H3K27me3) in neural progenitor cells (NPC). 17603471 196/329 Arthur Liberzon 5.66414773634182e-25 4.95088468806174e-23 3045 1784.81818181818 1382 5.1492252148562e-26 32 2.84617900660073 3.24592136670922 1 25.4811652284792 3045 1382 32 240 874 2836 4530 2507 1183 89 2915 994 M11654 LIEN_BREAST_CARCINOMA_METAPLASTIC http://www.broadinstitute.org/gsea/msigdb/cards/LIEN_BREAST_CARCINOMA_METAPLASTIC.html Genes up-regulated in metaplastic carcinoma of the breast (MCB) subclass 2 compared to the MCB subclass 1. 17603561 64/78 Arthur Liberzon 2.28408993888277e-07 7.89313577332338e-07 135 1794.81818181818 1383 2.07644561456565e-08 135 2.91448214014141 2.98675144680682 1 7.10295355789981 135 2640 373 1225 4278 1383 1831 2807 3427 450 1194 995 M7581 NAKAMURA_CANCER_MICROENVIRONMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_CANCER_MICROENVIRONMENT_UP.html Genes up-regulated in pancreatic cancer cells grown in orthotopic xenograft tumors compared to those grown in vitro. 17210693 35/63 Arthur Liberzon 8.41720065247104e-05 9.29772690841641e-05 380 1838.90909090909 1384 7.65229337440353e-06 380 2.868292233623 2.90581900223319 1 4.60050929771751 380 2720 624 1072 4224 1384 1744 3123 2732 878 1347 996 M1322 INGRAM_SHH_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/INGRAM_SHH_TARGETS_DN.html Genes down-regulated in 10T1/2 cells (multipotent mesoderma) by expression of SHH [GeneID=6469]. 17873912 117/144 Jessica Robertson 3.89810175230742e-08 4.29884118478762e-07 715 1266.18181818182 1384 3.54372892852409e-09 320 2.56180374973833 2.82702415382526 1 6.50926126784703 712 1567 320 817 2423 787 2361 1499 1607 451 1384 997 M12892 SMID_BREAST_CANCER_LUMINAL_B_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_B_UP.html Genes up-regulated in the luminal B subtype of breast cancer. 18451135 189/288 Jessica Robertson 6.88217045899512e-16 2.42416750495948e-14 3220 1835 1384 6.25651859908645e-17 82 2.57052882930462 2.70080425756253 1 14.0251678649584 3219 1384 94 247 82 2105 4191 4211 468 186 3998 998 M16842 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_DN.html Genes down-regulated in reverted NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845] which then reverted to normal cells upon stable over-expression of a dominant negative form of CDC25 [GeneID=5923]) vs normal fibroblasts. 16607279 223/271 Lauren Kazmierski 1.39316969206222e-07 7.20206492018647e-07 1415 1292.81818181818 1387 1.26651798207813e-08 399 2.06685196778839 2.24712432484933 1 5.05569735577412 1412 1358 605 399 561 1387 2419 2063 1804 432 1781 999 M5354 FIRESTEIN_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/FIRESTEIN_PROLIFERATION.html Genes required for proliferation of DLD-1 cell (colon cancer with APC [GeneID=324] deletions), based on shRNA screen. 18794900 216/296 Jessica Robertson 9.61605921643678e-08 6.64473403617636e-07 2600 1640 1388 8.74187239704419e-09 161 1.92669925559626 2.02456426413434 1 4.73658240167371 2598 1376 1388 161 286 2149 3014 1866 1007 1261 2934 1000 M2424 YANG_BCL3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BCL3_TARGETS_UP.html Genes up-regulated in neonatal cardiac myocytes upon knockdown of BCL3 [GeneID=602] by RNAi. 19451226 458/593 Arthur Liberzon 8.2474477595197e-14 2.40296008795883e-12 2085 1406.27272727273 1390 7.49767978138179e-15 92 2.17050513012886 2.39324920567756 1 10.0923385666147 2084 1180 155 1114 1090 1714 2755 1390 1953 92 1942 1001 M4665 BAELDE_DIABETIC_NEPHROPATHY_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAELDE_DIABETIC_NEPHROPATHY_DN.html Genes down-regulated in glomeruli of kidneys from patients with diabetic nephropathy (type 2 diabetes mellitus). 15042541 639/758 John Newman 1.61646753782672e-07 7.3358205358541e-07 1900 1604.09090909091 1391 1.61646765541026e-08 144 2.05964555547796 2.15721584207357 1 5.03127580913506 1899 1131 4498 144 825 1391 3245 865 1511 461 1675 1002 M1650 MCDOWELL_ACUTE_LUNG_INJURY_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCDOWELL_ACUTE_LUNG_INJURY_DN.html Genes down-regulated in the mouse model of acute lung injury induced by inhaling nickel sulfate [PubChem=24586]. 12540486 57/75 John Newman 1.61296949045616e-07 7.3358205358541e-07 2010 1585.81818181818 1392 1.46633600792175e-08 406 2.50530217102688 2.6326076598896 1 6.13074689994409 2008 406 754 2063 703 1703 3514 833 3155 913 1392 1003 M15 PID_LYSOPHOSPHOLIPID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LYSOPHOSPHOLIPID_PATHWAY.html LPA receptor mediated events 18832364 91/103 Pathway Interaction Database 3.01694893210165e-07 8.77129148999025e-07 2145 1497.18181818182 1393 2.74268122348013e-08 881 2.05681956662752 -1.92407730414609 -1 4.96010288643085 2144 1612 1531 881 1393 1333 1058 1257 986 2497 1777 1004 M1733 GAVIN_FOXP3_TARGETS_CLUSTER_P3 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P3.html Cluster P3 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 196/250 Jessica Robertson 5.96270004840368e-08 5.64006898366039e-07 3585 1993 1394 5.4206365545562e-09 84 2.12820182064017 -1.86962261381803 -1 5.29812074501961 3582 1394 695 704 84 2780 2583 4273 919 391 4518 1005 M17123 YAGI_AML_WITH_11Q23_REARRANGED http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_11Q23_REARRANGED.html Genes specifically expressed in samples from patients with pediatric acute myeloid leukemia (AML) bearing 11q23 rearrangements. 12738660 471/627 Arthur Liberzon 1.49611356460181e-07 7.26289540930751e-07 2805 1806.72727272727 1395 1.36010333304115e-08 630 2.04792920518045 2.39451970611298 1 5.00594413930984 2804 1190 1152 818 630 2529 3796 2557 1395 1664 1339 1006 M177 PID_EPHA_FWDPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHA_FWDPATHWAY.html EPHA forward signaling 18832364 37/45 Pathway Interaction Database 6.23840026175197e-08 5.79630890461994e-07 3585 1962.18181818182 1396 5.67127312604574e-09 96 2.57089125618715 2.5308961135178 1 6.39832697256271 3581 579 1121 452 96 3913 3807 2298 137 1396 4204 1007 M18559 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP.html Genes up-rgulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 6h. 16818636 84/135 Arthur Liberzon 2.32016356631121e-07 7.96239411200756e-07 1400 1394.18181818182 1397 2.10923982818208e-08 194 2.39863132222192 2.73949912709959 1 5.83324500075468 1397 194 657 2751 1109 1453 2474 891 1534 1030 1846 1008 M5133 GRANDVAUX_IRF3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRANDVAUX_IRF3_TARGETS_UP.html Genes up-regulated in Jurkat cells (T lymphocyte) by expression of a constitutively active form of IRF3 [GeneID=3661]. 11991981 22/30 Yujin Hoshida 7.87769979574331e-07 1.48374872449754e-06 1150 1640.45454545455 1398 7.16154783324537e-08 990 2.09184994640283 -2.34133266911068 -1 4.85337485682466 1147 1864 1398 1424 2365 1283 1172 3322 1784 990 1296 1009 M3698 SEIKE_LUNG_CANCER_POOR_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/SEIKE_LUNG_CANCER_POOR_SURVIVAL.html The 'CLASS-11' set of pro- and anti-inflammatory cytokines whose expression identifies stage I lung adenocarcinoma patients with poor prognosis. 17686824 4/10 Jessica Robertson 1.87701958492459e-05 2.21987783534053e-05 1375 1772.81818181818 1399 1.87703543952442e-06 271 3.01595240402897 -3.48894847833416 -1 5.59440213292143 1372 2485 4629 1856 3962 1399 271 403 1410 1389 325 1010 M3462 REACTOME_LIPOPROTEIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIPOPROTEIN_METABOLISM.html Genes involved in Lipoprotein metabolism 26/44 Reactome 8.09223563980835e-07 1.51268721662952e-06 1300 1621.45454545455 1400 7.35658056033452e-08 845 2.68884693639158 2.93117449298272 1 6.24369762196669 1258 2777 1298 1400 2388 1039 1298 2230 1895 1408 845 1011 M6139 STARK_BRAIN_22Q11_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/STARK_BRAIN_22Q11_DELETION.html Genes located outside the microdeletion region in 22q11 which were differentially expressed in the same manner both in hyppocampus and prefrontal cortex. 18469815 11/17 Jessica Robertson 8.95088134339427e-08 6.54205957136183e-07 1085 1379.72727272727 1400 8.13716518869844e-09 240 2.47568278601139 2.61926533838392 1 6.107190070209 1084 978 1748 2285 240 1380 1760 1809 246 2247 1400 1012 M17363 KIM_LRRC3B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KIM_LRRC3B_TARGETS.html Immune response genes up-regulated in zenograft tumors formed by SNU-601 cells (gastric cancer) made to express LRRC3B [GeneID=116135]. 18757430 58/111 Jessica Robertson 2.74057006006828e-06 3.93056538545192e-06 170 1580 1400 2.49143043094527e-07 166 1.92972324833117 -2.01124020584658 -1 4.144993768068 166 2203 1432 2002 3216 519 477 784 4212 1400 969 1013 M13714 LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_DN.html Down-regulated genes displaying alternative splicing in MDA-MB-435 cells (breast cancer) whose metastatic potential has been reduced by expression of NME1 [GeneID=4830]. 18245461 69/87 Jessica Robertson 1.32777933125135e-07 7.20206492018647e-07 2805 1763.72727272727 1400 1.20707219217057e-08 293 2.2039951247139 1.8576091960915 1 5.39448144018233 2802 293 1400 1404 509 3262 4553 651 539 1333 2655 1014 M2506 LEE_NEURAL_CREST_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_NEURAL_CREST_STEM_CELL_UP.html Genes up-regulated in the neural crest stem cells (NCS), defined as p75+/HNK1+ [GeneID=4804;27087]. 18037878 188/284 Arthur Liberzon 8.14599046857303e-20 4.63241867610418e-18 970 1352.63636363636 1401 7.40544588052094e-21 55 2.71363202403932 3.14253376520514 1 18.8670914836041 966 1401 55 350 1941 1879 2862 1201 1990 120 2114 1015 M15148 LE_EGR2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LE_EGR2_TARGETS_DN.html Genes down-regulated in P14 nerves of transgenic mice having hypomorhic (reduced function) allele of EGR2 [GeneID=1959]. 15695336 132/159 Kate Stafford 1.84590316841002e-07 7.47950348864313e-07 3405 1933.72727272727 1402 1.67809393026362e-08 3 2.15911781721181 2.49313019386185 1 5.26936722139028 3402 3 915 1155 867 3859 4335 1402 1557 1042 2734 1016 M11509 HASLINGER_B_CLL_WITH_11Q23_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_11Q23_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 11q23 region. 15459216 35/49 Kevin Vogelsang 9.14940603065953e-08 6.55893974641757e-07 1120 2239.36363636364 1402 8.31764219196995e-09 257 1.73018127505734 -1.78446526606297 -1 4.25228761951083 1117 3966 2938 4026 257 1310 522 1344 3939 3812 1402 1017 M11355 KEGG_TIGHT_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TIGHT_JUNCTION.html Tight junction 114/153 KEGG 1.17188541389596e-07 7.06112554001409e-07 2800 1287.63636363636 1404 1.06535043301763e-08 49 2.42262921787746 -2.42063534687988 -1 5.94293460962358 2797 49 701 74 400 2929 2158 2100 131 1404 1421 1018 M10276 LEE_NEURAL_CREST_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_NEURAL_CREST_STEM_CELL_DN.html Genes down-regulated in the neural crest stem cells (NCS), defined as p75+/HNK1+ [GeneID=4804;27087]. 18037878 178/239 Arthur Liberzon 1.71775449463815e-13 4.74140421911817e-12 3290 1766.45454545455 1405 1.56159499512572e-14 123 2.47598180799116 2.94522059124096 1 11.2258710313797 3286 1405 127 297 1252 4002 3739 1407 1167 123 2626 1019 M16104 ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_DN.html The vEDG down-regulated set: most variable early differentiation genes (EDG) with similar expression patterns in tonsil B lymphocytes (TBC) and multiple myeloma (MM) cells compared to the plasma cells from tonsil (TPC) and bone marrow (BPC). 12393520 45/48 Arthur Liberzon 3.04986370944575e-07 8.80674477121123e-07 1495 1711.72727272727 1406 2.77260375658995e-08 147 1.7001625723416 1.91469191693053 1 4.09013586274724 1493 2688 2921 2445 1406 1076 1017 531 147 4118 987 1020 M6754 ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_UP.html Genes whose promoters display higher histone H3 trimethylation mark at K9 (H3K9me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 105/208 Jessica Robertson 2.01053538160886e-07 7.65527859584926e-07 1560 1438.09090909091 1407 1.82775960486148e-08 105 2.72106748825848 3.10563387989786 1 6.64279929482103 1559 105 558 1583 945 1407 2584 2843 1159 1326 1750 1021 M9270 VALK_AML_WITH_11Q23_REARRANGED http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_11Q23_REARRANGED.html Genes that best predicted acute myeloid leukemia (AML) with the 11q23 rearrangements. 15084694 19/39 Jessica Robertson 3.57703502777367e-07 9.41752134134615e-07 1315 1730.54545454545 1407 3.25185055397533e-08 844 2.15956948978014 2.06356374326112 1 5.18357495296067 1315 844 1332 3621 1580 1517 1029 3366 1926 1099 1407 1022 M2096 ABDULRAHMAN_KIDNEY_CANCER_VHL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABDULRAHMAN_KIDNEY_CANCER_VHL_DN.html Genes down-regulated in the RCC4 cells (renal cell carcinoma, RCC) expressing VHL [GeneID=7428] mutants Type 1 and 2B (associated with RCC) but not those of Type 2A and 2C (not associated with RCC). 17001320 26/40 Arthur Liberzon 1.17509941616099e-06 1.9752383348575e-06 3125 1573.36363636364 1409 1.06827276711316e-07 538 2.53634750737501 2.6899429200429 1 5.76855471010718 3122 719 851 597 2685 2446 2321 538 760 1409 1859 1023 M10654 REACTOME_PYRIMIDINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_CATABOLISM.html Genes involved in Pyrimidine catabolism 10/16 Reactome 4.95075815835677e-07 1.10641943690549e-06 1730 1428.54545454545 1410 4.50069024768029e-08 64 3.2746276074989 3.19582111844625 1 7.79370139806114 1727 1015 1410 3629 1938 1808 862 64 588 1559 1114 1024 M16597 REACTOME_EGFR_DOWNREGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EGFR_DOWNREGULATION.html Genes involved in EGFR downregulation 32/36 Reactome 1.01032656464479e-07 6.74503731983509e-07 1385 1622.63636363636 1410 9.18478737311783e-09 314 1.45300725496045 -1.31076568352882 -1 3.55595752944793 1383 2297 3093 1522 314 757 549 1990 526 4008 1410 1025 M8834 WHITESIDE_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WHITESIDE_CISPLATIN_RESISTANCE_DN.html Genes down-regulated in NCI-H2170 cells (lung cancer) upon induction of resistance to cisplatin [PubChem=2767]. 14737109 41/64 John Newman 8.8890122046748e-07 1.61493986166532e-06 1415 1768.54545454545 1411 8.0809234511334e-08 634 2.74290571108993 -2.17682708351806 -1 6.33889624624357 1411 3402 1141 2141 2474 1409 1079 1633 634 2845 1285 1026 M16384 XU_GH1_AUTOCRINE_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_AUTOCRINE_TARGETS_DN.html Genes down-regulated in MFCF-7 cells (breast cancer) upon stable autocrine expression of HG1 [GeneID=2688]. 15845533 198/237 John Newman 2.81923726406352e-07 8.49189526890862e-07 1425 1889.18181818182 1411 2.56294329576436e-08 802 1.99749533813132 2.46387556406376 1 4.82689067400109 2978 1411 1204 802 1326 4316 3391 1392 1423 1114 1424 1027 M2821 BIOCARTA_NTHI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NTHI_PATHWAY.html NFkB activation by Nontypeable Hemophilus influenzae 32/42 BioCarta 1.13692544464616e-07 7.05613393308323e-07 465 1673.72727272727 1412 1.03356863945517e-08 373 1.58813224857202 -1.7055380356039 -1 3.87879637940764 465 2757 3063 2016 373 608 545 704 2862 3606 1412 1028 M8582 RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_DN.html Genes down-regulated in peripheral blood monocytes by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 364/541 Arthur Liberzon 2.38517075217052e-07 8.00711660757103e-07 2325 1877.72727272727 1412 2.16833728251206e-08 908 1.88339465321196 -1.78465799011887 -1 4.567647407572 2323 1235 1320 1252 1147 1412 1941 4218 2247 908 2652 1029 M4235 GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN.html Genes down-regulated in quiescent CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors compared to the dividing cells from CML (chronic myeloid leukemia) patients. 17717066 118/196 Arthur Liberzon 1.16742748028621e-06 1.96724659298497e-06 1245 1597.09090909091 1414 1.06129827252793e-07 54 2.50712563614095 -2.48624896023983 -1 5.70329257443759 1243 54 438 990 2679 2254 2118 1414 3101 550 2727 1030 M14812 SEMBA_FHIT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SEMBA_FHIT_TARGETS_UP.html Genes up-regulated in H1299 cells (non-small cell lung cancer, NSCLC) expressing the Y144F mutant form of FHIT [GeneID=2272]. 16407838 30/40 Leona Saunders 7.36174805989366e-06 9.34322421153485e-06 405 1409.72727272727 1414 6.69252063113821e-07 163 2.43910381944763 2.45980437768179 1 4.88347304280982 403 629 664 163 3661 1430 2023 2605 1846 669 1414 1031 M19025 MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP.html Up-regulated genes distinguishing in multiple myeloma (MM) samples with higher expression of TACI [GeneID=23495]. 15827134 500/758 Kevin Vogelsang 7.4765496452003e-17 3.15083163619155e-15 2855 1592.72727272727 1414 6.79686331381844e-18 76 2.25565603815934 2.43618576144039 1 13.1048975290483 2851 1161 76 112 831 1414 3646 1962 2502 109 2856 1032 M16955 ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN.html Genes whose promoters display lower levels of histone H3 trimethylation mark at K27 (H3K27me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 171/413 Jessica Robertson 4.59630532157635e-07 1.05466996197571e-06 1415 1395.90909090909 1414 4.17846025622763e-08 541 2.35301914644514 2.52650403095043 1 5.60585212402364 1414 2538 707 1584 1877 586 2559 541 1221 1588 740 1033 M2091 NOUSHMEHR_GBM_SILENCED_BY_METHYLATION http://www.broadinstitute.org/gsea/msigdb/cards/NOUSHMEHR_GBM_SILENCED_BY_METHYLATION.html Top 50 most differentially hypermethylated and down-regulated genes in proneural G-CIMP (a CpG island methylator phenotype) GBM (glyoblastoma multiforme) tumors. 20399149 51/75 Arthur Liberzon 4.07877565468e-08 4.47398945165397e-07 4590 2255 1415 3.70797793663641e-09 321 2.83910321416071 2.87121684968588 1 7.1994623941504 4586 396 321 735 1415 4020 4642 2546 1109 465 4570 1034 M2223 KANG_AR_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_AR_TARGETS_UP.html Genes up-regulated in osteoblasts from wild type male mice compared to those with AR [GeneID=367] knockout. 18838539 29/35 Arthur Liberzon 1.43783080506385e-05 1.73480608381937e-05 330 1846.09090909091 1415 1.30712745657185e-06 326 2.62994619206598 2.93443010913051 1 4.98523334622262 326 2298 513 1279 4422 1415 2519 3122 2581 601 1231 1035 M1000 REACTOME_TRAF6_MEDIATED_INDUCTION_OF_TAK1_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_INDUCTION_OF_TAK1_COMPLEX.html Genes involved in TRAF6 mediated induction of TAK1 complex 18/31 Reactome 1.97893201127532e-06 2.99857434774302e-06 260 1422.72727272727 1416 1.79903071941428e-07 10 2.09762046882592 -2.09762046882592 -1 4.60914088040581 260 2835 2410 1938 3029 132 10 167 1416 3044 409 1036 M6866 MISSIAGLIA_REGULATED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/MISSIAGLIA_REGULATED_BY_METHYLATION_DN.html Genes down-regulated in PaCa44 and CFPAC1 cells (pancreatic cancer) after treatment with decitabine [PubChem=451668], a DNA hypomethylating agent similar to azacitidine [PubChem=9444]. 15637593 152/203 Leona Saunders 9.98845064940972e-09 1.31324476504774e-07 20 1257.36363636364 1416 9.0804097225085e-10 19 1.81006941094053 1.87102645368102 1 4.9593977231639 19 2542 1962 2345 2513 91 55 381 1724 1416 783 1037 M675 REACTOME_SIGNALING_BY_ACTIVATED_POINT_MUTANTS_OF_FGFR1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ACTIVATED_POINT_MUTANTS_OF_FGFR1.html Genes involved in Signaling by activated point mutants of FGFR1 6/15 Reactome 4.13433232055219e-06 5.60426437478643e-06 1275 1925.45454545455 1417 4.13434001228901e-07 524 2.34970674363966 2.80402767824664 1 4.91241287246535 1274 1982 4215 3141 3456 1128 524 667 1417 2786 590 1038 M1087 REACTOME_FGFR2C_LIGAND_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FGFR2C_LIGAND_BINDING_AND_ACTIVATION.html Genes involved in FGFR2c ligand binding and activation 6/16 Reactome 4.13433232055219e-06 5.60426437478643e-06 1275 1940.45454545455 1418 4.13434001228901e-07 525 2.34970674363966 2.80402767824664 1 4.91241287246535 1275 1983 4267 3142 3457 1129 525 770 1418 2788 591 1039 M2114 BENPORATH_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_PROLIFERATION.html Set 'Proliferation Cluster': genes defined in human breast tumor expression data. 18443585 178/210 Jessica Robertson 2.05886670328794e-06 3.09979293126605e-06 55 1337.54545454545 1418 1.87169875461616e-07 53 1.51047307383853 1.65009028947344 1 3.29622671793533 53 1418 2892 1845 3052 254 232 632 1698 1659 978 1040 M1521 WESTON_VEGFA_TARGETS_6HR http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS_6HR.html Genes up-regulated in MMEC cells (myometrial endothelium) at 6 h after VEGFA [GeneID=7422] stimulation. 12200464 75/93 John Newman 1.5858025242639e-10 2.93528937824533e-09 110 1524.45454545455 1418 1.44163865852564e-11 108 2.92191972029236 3.13236969264385 1 9.97619018931523 108 2159 199 1223 4096 1102 1620 1695 2809 340 1418 1041 M1878 HUNSBERGER_EXERCISE_REGULATED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HUNSBERGER_EXERCISE_REGULATED_GENES.html Exercise regulated genes in hyppocampus. 18059283 40/53 Jessica Robertson 3.08955806434037e-07 8.85948606542316e-07 945 1524.09090909091 1418 2.80868954383715e-08 181 2.14734159185132 2.11021994147366 1 5.17685031525236 945 2273 1569 2637 1418 842 1360 181 3372 1907 261 1042 M1092 REACTOME_FGFR1_LIGAND_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FGFR1_LIGAND_BINDING_AND_ACTIVATION.html Genes involved in FGFR1 ligand binding and activation 6/18 Reactome 4.13433232055219e-06 5.60426437478643e-06 1280 1941.63636363636 1419 4.13434001228901e-07 526 2.34970674363966 2.80402767824664 1 4.91241287246535 1276 1984 4270 3143 3458 1130 526 771 1419 2789 592 1043 M14877 BASAKI_YBX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BASAKI_YBX1_TARGETS_DN.html Genes down-regulated in SKOC-3 cells (ovarian cancer) after YB-1 (YBX1) [GeneID=4904] knockdown by RNAi. 17072343 525/667 Arthur Liberzon 1.69720646233902e-07 7.33971845416521e-07 1050 1701.90909090909 1420 1.69720659196197e-08 881 1.95880198458826 -1.87001913152752 -1 4.7823047864551 1046 1166 4296 986 881 1704 1634 1351 1870 1420 2367 1044 M2182 WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG.html Classic adipogenic genes (group 1) that are induced by PPARG [GeneID=5468] during adipogenesis in 3T3-L1 preadipocytes. 17954559 22/34 Arthur Liberzon 1.83284472741927e-06 2.80695234049933e-06 670 1699.09090909091 1420 1.66622386762236e-07 57 1.77028592470751 -1.78748971405622 -1 3.90249252926615 670 1860 2141 3626 2991 581 472 1420 3880 992 57 1045 M619 REACTOME_TRIGLYCERIDE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRIGLYCERIDE_BIOSYNTHESIS.html Genes involved in Triglyceride Biosynthesis 37/42 Reactome 6.98167720679694e-07 1.37020858278925e-06 1295 1744.27272727273 1424 6.3469812931145e-08 384 1.61441951713062 -1.54829624577077 -1 3.75669873351967 1291 2728 2669 2621 2259 1424 939 384 876 2995 1001 1046 M660 REACTOME_HYALURONAN_UPTAKE_AND_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HYALURONAN_UPTAKE_AND_DEGRADATION.html Genes involved in Hyaluronan uptake and degradation 12/13 Reactome 1.17466130084877e-06 1.97520532241046e-06 1985 1732.72727272727 1425 1.06787448004029e-07 550 1.90353856239327 1.83968392428509 1 4.31684397811168 1981 946 1806 2757 2684 978 550 1082 3670 1181 1425 1047 M2322 KASLER_HDAC7_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/KASLER_HDAC7_TARGETS_2_DN.html Genes down-regulated in DO11.10 cells (hybridoma) by expression of transciptionally activating and by transcriptionally repressive forms of HDAC7 [GeneID=51564]. 17470548 49/62 Arthur Liberzon 3.21756753762989e-07 9.00232292686014e-07 1310 1719 1427 2.92506182564464e-08 938 2.30376057466816 2.49666331866245 1 5.55115750382991 1213 2248 1310 3305 1462 999 938 2430 2268 1427 1309 1048 M2387 KATSANOU_ELAVL1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KATSANOU_ELAVL1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) with ELAVL1 [GeneID=1994] knocked out. 19307312 185/232 Arthur Liberzon 1.78223527686054e-09 2.72237880478374e-08 1430 1346 1427 1.62021388936759e-10 239 2.37516211071256 2.57694162519076 1 7.17609326303184 485 1427 239 2559 1278 915 1428 1607 2992 396 1480 1049 M2543 GENTLES_LEUKEMIC_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/GENTLES_LEUKEMIC_STEM_CELL_DN.html Genes down-regulated in LSC (leukemic stem) cells compared to LPC (leukemia progenitor) cells from AML (acute myeloid leukemia) tumor samples. 21177505 12/40 Andrew Gentles 4.5316027377218e-07 1.04337389863643e-06 1885 1413.09090909091 1427 4.11963970104582e-08 308 2.7378369889535 2.45172042146078 1 6.53597769179702 1882 1930 1180 1787 1863 2240 1321 421 308 1185 1427 1050 M7528 KEGG_PANTOTHENATE_AND_COA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PANTOTHENATE_AND_COA_BIOSYNTHESIS.html Pantothenate and CoA biosynthesis 17/20 KEGG 1.58947977443617e-06 2.49994819571434e-06 1745 1605.18181818182 1428 1.44498265711078e-07 364 2.68751957846088 2.80328536977265 1 6.00477595546155 1744 891 1488 1211 2901 1428 976 3393 364 2041 1220 1051 M19744 GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_UP.html Genes up-regulated in quiescent (G0) vs dividing (M) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients. 17717066 24/59 Arthur Liberzon 3.58653429399203e-06 4.94549864669657e-06 460 1703.27272727273 1428 3.26049103720663e-07 71 2.73846674798994 -2.66728087166001 -1 5.79326271743299 457 3171 1428 3212 3351 303 175 684 4167 1717 71 1052 M16257 BIOCARTA_MITOCHONDRIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MITOCHONDRIA_PATHWAY.html Role of Mitochondria in Apoptotic Signaling 24/28 BioCarta 1.75345898679022e-06 2.70999555260309e-06 930 1737.36363636364 1429 1.59405489485964e-07 141 1.75614248760349 -2.04486889587001 -1 3.88169636490432 927 1851 2510 3681 2957 1429 834 141 1137 2721 923 1053 M1437 WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_DN.html Down-regulated genes in myeloid progenitors immortalized by HOXA9 [GeneID=3205] vs those immortalized by HOXA9 and MEIS1 [GeneID=4211]. 15755900 24/33 Kevin Vogelsang 1.90998519204472e-06 2.90810648595197e-06 935 2053.54545454545 1429 1.73635168204391e-07 705 2.15398489765021 2.11063086557644 1 4.74586106951758 933 2344 1399 3298 3011 848 705 3778 3930 1429 914 1054 M19097 SWEET_LUNG_CANCER_KRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_LUNG_CANCER_KRAS_UP.html Genes up-regulated in the Kras2LA mouse lung cancer model with mutated KRAS [GeneID=3845]. 15608639 627/808 Arthur Liberzon 1.11199913280965e-07 7.03739764799127e-07 1565 1602.45454545455 1430 1.11199918845405e-08 438 1.93987175815816 -1.91526161597286 -1 4.7498552315419 1561 2009 4601 730 438 1660 1652 991 1430 1244 1311 1055 M2142 HOELZEL_NF1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOELZEL_NF1_TARGETS_UP.html Genes up-regulated in SH-SY5Y cells (neuroblastoma) after knockdown of NF1 [GeneID=4763] by RNAi. 20655465 170/230 Arthur Liberzon 1.95764000268514e-09 2.97108064716201e-08 245 1716.72727272727 1431 1.77967273129738e-10 241 2.30681933277775 2.59376076165009 1 6.93294750779915 2719 1429 241 1117 339 4131 3412 1527 1431 241 2297 1056 M3001 CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP.html Genes up-regulated in type 1 (soleus) vs type 2B (EDL) myofibers. 21364395 40/85 Emmanuelle Fouilloux-Meugnier 1.49237268739095e-06 2.37848871910874e-06 1435 1600.81818181818 1431 1.35670336340432e-07 147 2.72477709860307 3.35976967557821 1 6.112416890098 1431 3101 1158 2420 2859 1425 1821 147 845 1908 494 1057 M4707 IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_DN.html Genes down-regulated during transition from G2 (moderately differentiated tumor, infected with HCV) to G3 (poorly differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 11/11 Yujin Hoshida 3.14354303772159e-07 8.93484919997849e-07 1115 2166.45454545455 1432 2.85776680627025e-08 661 1.05251525296879 -1.05970742368978 -1 2.5103543141277 1115 1947 3236 4568 1432 1015 1207 1289 4059 3302 661 1058 M14233 MARSON_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_UP.html Genes up-regulated by FOXP3 [GeneID=50943] in both ex vivo and hybridoma cells. 17237765 84/108 Arthur Liberzon 2.28432700558469e-07 7.89313577332338e-07 1430 1576.90909090909 1434 2.07666112979396e-08 603 1.98550636681352 -1.91755991067905 -1 4.82297558065683 1427 2144 1875 1408 1093 1434 1711 3021 603 1864 766 1059 M10184 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP.html Genes up-regulated in monocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 286/354 Arthur Liberzon 3.94329712796002e-07 9.80113872773632e-07 800 1496.81818181818 1436 3.58481621341803e-08 417 1.82297596313229 1.8259937303407 1 4.3551443982428 796 2038 1628 1720 1694 417 1388 1176 3201 1436 971 1060 M15171 SASAKI_ADULT_T_CELL_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/SASAKI_ADULT_T_CELL_LEUKEMIA.html Genes up-regulated in adult T-cell leukemia (ATL) cells compared to T lymphocytes from healthy controls. 15471956 234/286 Kate Stafford 3.94001906084744e-07 9.80113872773632e-07 1305 1503.18181818182 1436 3.58183615133875e-08 578 1.75264563149765 1.85525882000285 1 4.18519268906667 1301 1355 2019 1436 1692 578 1037 1937 2263 1266 1651 1061 M15410 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 16 days after transduction. 16818636 177/287 Arthur Liberzon 1.88138260501642e-07 7.48978540381421e-07 1850 1496.72727272727 1437 1.7103479690067e-08 69 2.54624939118577 -2.62724601232405 -1 6.22252981262985 1848 1437 370 69 892 3006 2569 2738 862 627 2046 1062 M18325 OLSSON_E2F3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OLSSON_E2F3_TARGETS_UP.html Genes up-regulated in the 5637 cell line (bladder cancer) after knockdown of E2F3 [GeneID=1871] by RNAi. 16909110 33/42 Arthur Liberzon 4.0233270825474e-07 9.93104581177629e-07 1445 1450.63636363636 1437 3.6575707439342e-08 220 2.23679581274122 -2.4331947089997 -1 5.34998696918066 1445 652 1278 1432 1714 522 220 2291 2844 1437 2122 1063 M7404 FRIDMAN_IMMORTALIZATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_IMMORTALIZATION_DN.html Genes down-regulated in immortalized cell lines. 18711403 51/63 Jessica Robertson 9.89993388664662e-07 1.74032357336954e-06 1440 1614.45454545455 1438 8.99994394689993e-08 145 3.16500542946917 3.67670853571495 1 7.2807412553247 1438 2668 491 1241 2559 1777 3578 145 2466 1103 293 1064 M19068 CERVERA_SDHB_TARGETS_2 http://www.broadinstitute.org/gsea/msigdb/cards/CERVERA_SDHB_TARGETS_2.html Genes present but differentially expressed between Hep3B cells (hepatocellular carcinoma, HCC) with RNAi knockdown of SDHB [GeneID=6390] and control cells. 18519664 159/210 Jessica Robertson 3.16297668450665e-17 1.40841980668598e-15 1395 1342.63636363636 1439 2.87543334955149e-18 72 2.69596077835111 2.99069548917854 1 16.0518861961872 1391 1439 72 284 1029 1513 2952 2066 1882 119 2022 1065 M1676 SHEN_SMARCA2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHEN_SMARCA2_TARGETS_DN.html Genes whose expression negatively correlated with that of SMARCA2 [GeneID=6595] in prostate cancer samples. 19074882 283/664 Jessica Robertson 3.98942561454488e-25 3.55284696238713e-23 1935 1497.72727272727 1440 3.62675055867715e-26 31 2.72053488296182 2.73541674812179 1 24.5117602872009 1934 1287 31 44 877 1440 2918 3141 1771 79 2953 1066 M6145 LEE_LIVER_CANCER_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_SURVIVAL_UP.html Genes highly expressed in hepatocellular carcinoma with good survival. 15349906 170/349 Yujin Hoshida 1.45095625435293e-07 7.26289540930751e-07 2710 1623.54545454545 1440 1.31905122731565e-08 538 2.13041904839469 -1.94434399410493 -1 5.209597226819 2706 1440 646 1337 598 2512 2145 2382 1127 538 2428 1067 M16101 BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transfrormed by expression of constitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression did NOT reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 65/71 Leona Saunders 2.64103440491451e-07 8.31045492746432e-07 830 1351.81818181818 1441 2.40094065632988e-08 377 2.71710024580655 3.04437277525082 1 6.59407100699642 828 1656 377 864 1441 1480 2875 1878 2389 419 663 1068 M17275 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 8 days after transduction. 16818636 168/298 Arthur Liberzon 2.05256217041264e-11 4.24916379138055e-10 2525 1493.36363636364 1442 1.86596560948345e-12 73 2.39245356900397 2.51527626564636 1 8.96696946062861 2522 1442 175 73 1198 2368 3608 915 1785 207 2134 1069 M501 REACTOME_SIGNALING_BY_RHO_GTPASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_RHO_GTPASES.html Genes involved in Signaling by Rho GTPases 115/130 Reactome 5.36341760875997e-08 5.28503781071964e-07 4350 2320.63636363636 1443 4.87583430865058e-09 12 1.83778785973736 -1.72752369913298 -1 4.58918138800191 4350 12 1443 553 68 4055 4499 4074 1355 1126 3992 1070 M16431 DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP.html Genes up-regulated in T-PLL cells (T-cell prolymphocytic leukemia) bearing the inv(14)/t(14:14) chromosomal aberration. 17713554 485/702 Leona Saunders 1.59749101691388e-07 7.31918027928963e-07 4335 2528 1443 1.45226466628443e-08 694 1.95045842838581 -1.87534720403073 -1 4.76267590955772 4332 1179 1230 1033 694 4705 4036 4603 1443 1113 3440 1071 M13941 DIRMEIER_LMP1_RESPONSE_EARLY http://www.broadinstitute.org/gsea/msigdb/cards/DIRMEIER_LMP1_RESPONSE_EARLY.html Clusters 1 and 2: genes up-regulated in B2264-19/3 cells (primary B lymphocytes) within 30-60 min after activation of LMP1 (an oncogene encoded by Epstein-Barr virus, EBV). 15674340 78/103 Arthur Liberzon 7.50013219854881e-07 1.43364609476926e-06 630 2049.09090909091 1443 6.81830432314395e-08 629 2.07297533277352 -2.20045159564501 -1 4.82156876033179 629 2622 1346 3921 2323 952 728 3932 3227 1443 1417 1072 M1133 DARWICHE_PAPILLOMA_RISK_LOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_LOW_UP.html Genes up-regulated during skin tumor progression from low risk papilloma vs normal skin. 17525749 179/307 Arthur Liberzon 1.7043075054587e-07 7.33971845416521e-07 1470 1385.63636363636 1445 1.54937057953536e-08 593 2.13586726404204 2.16991624689328 1 5.2191227935636 1467 1445 1160 1215 776 1315 2138 593 1481 1941 1711 1073 M16518 ST_WNT_CA2_CYCLIC_GMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_WNT_CA2_CYCLIC_GMP_PATHWAY.html Wnt/Ca2+/cyclic GMP signaling. 17/28 Signaling Transduction KE 3.7790294497433e-07 9.60480334359217e-07 3085 1651.90909090909 1446 3.43548190807519e-08 104 2.4851494245067 -3.15321650102096 -1 5.96405516016265 3084 880 1554 1004 1652 2789 2953 1446 104 1341 1364 1074 M2909 REACTOME_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_METABOLISM.html Genes involved in Pyrimidine metabolism 22/29 Reactome 3.8942712358223e-07 9.76357383103197e-07 1045 1374.54545454545 1446 3.54024720468771e-08 412 2.26871480365585 2.2699279043879 1 5.43378417650635 1044 822 1436 2319 1675 1647 1631 412 716 1446 1972 1075 M3258 LIU_TARGETS_OF_VMYB_VS_CMYB_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_TARGETS_OF_VMYB_VS_CMYB_DN.html Gene regulated in the opposite directions by v-MYB (DN) and c-MYB (UP) variants of CMYB [GeneID=4602] overexpressed in primary monocyte cultures off adenoviral vectors. 16205643 64/80 Arthur Liberzon 1.74605333923719e-06 2.70297532345017e-06 790 1724.63636363636 1446 1.58732247728408e-07 399 2.72461527166404 2.9653762706508 1 6.05119265240031 787 1664 429 1444 3251 1446 2599 2309 3446 399 1197 1076 M4577 MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN.html Top genes down-regulated in mesenchyme stem cells (MSC) grown in a tumor conditioned medium, which leads to carcinoma-associated fibroblast phenotype. 18519693 38/40 Leona Saunders 5.88766936343146e-07 1.22475977943572e-06 1450 1654 1446 5.35242812645271e-08 319 3.08586840376443 -2.5678555384651 -1 7.28679763774504 1446 1749 595 319 2109 1736 1330 3665 3198 1282 765 1077 M16473 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION.html Aldosterone-regulated sodium reabsorption 40/55 KEGG 1.82973401031879e-07 7.47800341964416e-07 1970 1448.54545454545 1447 1.66339469317936e-08 545 1.8079008283464 -2.02442387554033 -1 4.40413956611842 1967 545 1796 1669 854 1658 1291 608 3094 1447 1005 1078 M11825 BRUECKNER_TARGETS_OF_MIRLET7A3_DN http://www.broadinstitute.org/gsea/msigdb/cards/BRUECKNER_TARGETS_OF_MIRLET7A3_DN.html Genes down-regulated in A549 cells (lung cancer) expressing MIRLET7A3 [GeneID=406883] microRNA off a plasmid vector. 17308078 110/144 Jessica Robertson 1.93649851728914e-08 2.38649425629367e-07 830 1304.54545454545 1447 1.76045321303155e-09 42 2.48269035852846 2.47578381121513 1 6.56189062219569 827 42 300 745 2755 1685 2732 1835 1447 440 1542 1079 M10290 KOBAYASHI_EGFR_SIGNALING_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_24HR_UP.html Genes up-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 24h. 17145885 138/193 Arthur Liberzon 1.77812691820016e-06 2.7411772276752e-06 1285 1634.09090909091 1449 1.61648032304928e-07 846 2.05663823455023 -2.30875817793527 -1 4.55035074685923 1283 2103 1424 1426 2967 1449 1828 1035 2148 1466 846 1080 M2437 HUANG_GATA2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_GATA2_TARGETS_UP.html Genes up-regulated in G1ME cells (megakaryocyte/erythroid progenitor lacking GATA1 [GeneID=2623]) upon knockdown of GATA2 [GeneID=2624] by RNAi. 19620289 178/247 Arthur Liberzon 3.20437233614489e-07 8.98683416254527e-07 420 1423.81818181818 1450 2.91306618442942e-08 335 1.73135816448365 -1.74968982718931 -1 4.15998094537608 420 1450 2376 2813 1455 335 990 552 2422 2269 580 1081 M2583 TOMIDA_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOMIDA_METASTASIS_DN.html Down-regulated genes associated with the acquision of metastatic potential in LNM35 cells (large cell lung cancer). 17260014 26/37 Arthur Liberzon 3.39174485140834e-06 4.71686378864094e-06 1455 1561.36363636364 1451 3.08340916407285e-07 28 2.73145282592807 -3.04121627516704 -1 5.80087781002015 1030 2337 1452 1451 3317 409 300 3901 300 2650 28 1082 M11193 AMIT_SERUM_RESPONSE_20_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_20_MCF10A.html Genes whose expression peaked at 20 min after stimulation of MCF10A cells with serum. 17322878 25/33 Leona Saunders 5.36304456951604e-05 6.03134867002996e-05 810 1778.81818181818 1451 4.87561391951337e-06 225 1.48681307321649 -1.65887303394505 -1 2.4730184402067 809 2789 3200 1971 4148 571 338 1451 546 3519 225 1083 M16701 HUANG_FOXA2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_FOXA2_TARGETS_DN.html Genes down-regulated in H358 cells (lung cancer) by inducible expression of FOXA2 [GeneID=3170] in a Tet-off system. 18593902 45/57 Leona Saunders 3.19881153363301e-07 8.98528442785416e-07 3000 1994.27272727273 1453 2.90801090794725e-08 488 2.96605453410826 -2.85350939054904 -1 7.16239192742229 3000 488 546 1175 1453 3209 2062 4140 1371 1009 3484 1084 M12175 BENNETT_SYSTEMIC_LUPUS_ERYTHEMATOSUS http://www.broadinstitute.org/gsea/msigdb/cards/BENNETT_SYSTEMIC_LUPUS_ERYTHEMATOSUS.html Genes significantly up-regulated in the blood mononuclear cells from patients with systemic lupus erythematosus compared to those from healthy persons. 12642603 33/109 Kevin Vogelsang 2.71837007711792e-07 8.37744283366146e-07 825 1516.45454545455 1454 2.47124583000542e-08 734 2.0493391019698 -2.36184834282362 -1 4.95832527560655 825 2288 1928 2313 1285 1042 734 1454 1486 1952 1374 1085 M14183 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_17 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_17.html Amplification hot spot 17: colocalized fragile sites and cancer genes in the 1q11-q44 region. 16751803 24/31 Arthur Liberzon 2.81042725938541e-07 8.49189526890862e-07 1175 1509.27272727273 1455 2.55493419855297e-08 73 2.4753336867858 2.40905549865915 1 5.99354328328971 1173 2787 1813 2116 1319 869 1455 1793 73 3099 105 1086 M144 PID_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CERAMIDE_PATHWAY.html Ceramide signaling pathway 18832364 64/69 Pathway Interaction Database 3.2047367039828e-07 8.98683416254527e-07 675 1598.54545454545 1456 2.91339742801492e-08 319 1.65403384967635 -1.735745596336 -1 3.97195701543295 672 2199 3172 2014 1456 319 407 1248 2566 2936 595 1087 M8395 REACTOME_HEMOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HEMOSTASIS.html Genes involved in Hemostasis 435/615 Reactome 2.13285736827078e-07 7.70833597108584e-07 1460 1779.18181818182 1456 1.93896143186109e-08 672 2.08161622854131 2.22138975203062 1 5.06747060843001 1456 3271 672 1283 1021 1275 2478 2227 3082 739 2067 1088 M6370 KEGG_P53_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_P53_SIGNALING_PATHWAY.html p53 signaling pathway 79/91 KEGG 9.1695605666345e-07 1.64593206000409e-06 1460 1618.18181818182 1457 8.33596762590284e-08 631 2.31813999003645 2.97934776266667 1 5.34181117122034 1457 2610 1529 1733 2506 631 1027 1308 981 2812 1206 1089 M2088 LI_INDUCED_T_TO_NATURAL_KILLER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_INDUCED_T_TO_NATURAL_KILLER_DN.html Genes down-regulated in ITNK cells (T-lymphocyte progenitors (DN3 cells) reprogrammed to natural killer (NK) cells by ablation of BCL11B [GeneID=64919] gene), compared to the parental DN3 cells. 20538915 159/199 Arthur Liberzon 8.01028086124865e-09 1.0895828721929e-07 2650 1876.72727272727 1457 7.28207353674032e-10 271 2.35022390583212 2.69433714358286 1 6.53093501177132 2646 1457 271 753 2314 2154 4569 3327 1408 444 1301 1090 M12144 BROWNE_HCMV_INFECTION_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_48HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 48 h time point that were not down-regulated at the previous time point, 24 h. 11711622 630/965 John Newman 1.33685471741659e-07 7.20206492018647e-07 2325 1787.90909090909 1458 1.33685479783972e-08 306 2.19868147256919 2.42375148693493 1 5.38135515071179 2321 1129 4494 306 612 1458 3867 2148 1742 424 1166 1091 M1737 GAVIN_PDE3B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_PDE3B_TARGETS.html Genes changed in peripheral regulatory T lymphocytes that depend on PDE3B [GeneID=5140]. 17220874 17/35 Jessica Robertson 6.52461513303572e-07 1.30936154030309e-06 710 1741.27272727273 1459 5.93147006187629e-08 355 2.53042333965071 2.80734262804899 1 5.9366737613906 707 3476 1459 3058 2199 1012 355 510 3780 2047 551 1092 M2451 PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_DN.html Genes down-regulated after 1 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 161/189 Arthur Liberzon 1.36332398947062e-09 2.13783695358847e-08 2425 1564.09090909091 1459 1.23938544574132e-10 232 2.62299698272126 2.86084361321606 1 8.04083329839868 1406 1459 232 333 741 2423 3802 2421 2188 405 1795 1093 M15588 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 16 days after transduction. 16818636 160/276 Arthur Liberzon 7.29489500979295e-14 2.15199402788892e-12 3150 1934.18181818182 1460 6.6317227361756e-15 117 2.69910556976156 2.72173778526879 1 12.6143925898268 3149 1460 117 685 205 3554 4670 2814 860 292 3470 1094 M5968 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_UP.html Genes from the green module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 45/79 Arthur Liberzon 9.21079443236473e-08 6.56798957981166e-07 1645 1223 1461 8.37344983454124e-09 260 1.91053635750757 2.07539304018539 1 4.70030431312674 1643 494 1920 1041 260 1724 1789 1087 1461 1479 555 1095 M1139 DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP.html Genes up-regulated in squamous cell carcinoma (SCC) compared to normal skin. 17525749 167/272 Arthur Liberzon 2.87383847665813e-07 8.57471256032483e-07 3240 2013.09090909091 1462 2.61258077460446e-08 864 2.22604351812992 2.10405951873571 1 5.3811226337695 3236 1462 864 1156 1348 2813 4158 987 962 1745 3413 1096 M18320 WINNEPENNINCKX_MELANOMA_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WINNEPENNINCKX_MELANOMA_METASTASIS_DN.html Genes from the 254-gene classifier which were down-regulated in melanoma patients with a reported distant metastasis within 4 years. 16595783 32/51 Arthur Liberzon 1.49034541008373e-07 7.26289540930751e-07 2045 1771.54545454545 1462 1.3548595554947e-08 625 2.51787904000798 -2.38521433764483 -1 6.16616861189707 2044 2746 1285 3070 625 1462 1217 2732 869 1338 2099 1097 M4085 KEGG_PRIMARY_IMMUNODEFICIENCY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_IMMUNODEFICIENCY.html Primary immunodeficiency 21/48 KEGG 2.10653177793119e-07 7.70763712250053e-07 2150 1934.54545454545 1463 1.91502907239516e-08 262 2.17540204985403 -2.2505581872876 -1 5.29807093311873 2146 826 1341 2279 1005 3414 3332 262 4111 1101 1463 1098 M1234 OXFORD_RALA_AND_RALB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_AND_RALB_TARGETS_DN.html Genes down-regulated in the UMUC-3 cells (bladder cancer) after knockdown of both RALA and RALB [GeneID=5898;5899] by RNAi. 17496927 24/25 Arthur Liberzon 3.72308860339148e-05 4.25392839700019e-05 175 1686.54545454545 1464 3.38468328290617e-06 175 3.33409417642113 3.20229525719042 1 5.81107685870663 175 2338 568 861 4450 1191 2049 2725 1730 1001 1464 1099 M11680 HATADA_METHYLATED_IN_LUNG_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/HATADA_METHYLATED_IN_LUNG_CANCER_DN.html Genes with unmethylated DNA in lung cancer samples. 16407832 61/217 Arthur Liberzon 6.75348758894804e-07 1.34078461407703e-06 1135 1742.27272727273 1464 6.13953605646574e-08 645 2.1825490701515 -1.79830090633582 -1 5.10460025037508 1134 2193 1464 1817 2228 1354 1564 4143 645 1440 1183 1100 M18834 FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_DN http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_DN.html Genes down-regulated in thyroid tumors of uncertain malignancy (T-UM) compared to other thyroid tumors. 17968324 27/65 Arthur Liberzon 5.8455557196275e-07 1.22123997631427e-06 1355 1390.18181818182 1464 5.31414297530328e-08 54 2.59462313137303 2.8319098841809 1 6.1201371435078 1354 1809 991 2072 2099 2037 1464 54 940 1526 946 1101 M18107 WILENSKY_RESPONSE_TO_DARAPLADIB http://www.broadinstitute.org/gsea/msigdb/cards/WILENSKY_RESPONSE_TO_DARAPLADIB.html Atherosclerotic process genes whose coronary expression changed after darapladib [PubChem=9939609] treatment. 18806801 20/39 Jessica Robertson 1.82989278595106e-07 7.47800341964416e-07 1380 1844.18181818182 1465 1.66353903468725e-08 396 2.20916100636561 -2.08950463369673 -1 5.39273568970146 1376 2828 1898 4360 855 1202 396 1635 3815 1465 456 1102 M3837 WEST_ADRENOCORTICAL_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_DN.html Down-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 681/905 Jessica Robertson 2.11798965532415e-07 7.70763712250053e-07 1610 1787.63636363636 1466 2.11798985718878e-08 286 2.17018773248712 2.6020517400797 1 5.28525181631562 1610 2003 4572 1145 1430 531 3506 1466 2406 286 709 1103 M8268 AMBROSINI_FLAVOPIRIDOL_TREATMENT_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/AMBROSINI_FLAVOPIRIDOL_TREATMENT_TP53.html Genes down-regulated by flavopiridol [PubChem=5287969] in the HCT116 cells (colon cancer) depending on their TP53 [GeneID=7157] status: wild-type vs loss of the gene's function (LOF). 18381438 165/209 Jessica Robertson 7.82918066886477e-08 6.28391550069647e-07 3350 1674.54545454545 1467 7.11743722498478e-09 176 2.12737758990589 2.70653507721167 1 5.25588489087335 3349 1467 994 1645 176 2100 3922 1306 1985 1159 317 1104 M12228 BOYAULT_LIVER_CANCER_SUBCLASS_G12_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G12_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G12, defined by unsupervised clustering 17187432 16/33 Yujin Hoshida 2.57335353289518e-05 2.98506480099907e-05 1470 1681.81818181818 1468 2.33943966732971e-06 321 1.88979376346953 -2.21981793596463 -1 3.38900963455662 1468 917 2312 2373 4014 796 321 702 1685 2709 1203 1105 M1617 KEEN_RESPONSE_TO_ROSIGLITAZONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KEEN_RESPONSE_TO_ROSIGLITAZONE_DN.html Genes down-regulated in aorta biopsies from mice treated with rosiglitazone [PubChem=77999]. 15054141 154/202 John Newman 7.5848252309937e-13 1.85424811223886e-11 2190 1799.90909090909 1469 6.89529566454211e-14 140 2.7958813853636 2.86778172746581 1 12.0167948870356 2186 1469 140 348 1032 2628 4373 3019 1003 371 3230 1106 M1325 MANTOVANI_NFKB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_NFKB_TARGETS_UP.html NF-kB-controlled genes up-regulated in endothelial cells in response to viral GPCR protein. 17906691 66/77 Jessica Robertson 6.43176164245651e-08 5.87193712812277e-07 1470 1315.09090909091 1470 5.84705620953717e-09 109 2.57927211627792 -3.03918191700759 -1 6.41350824359803 1470 294 581 977 109 2448 2221 1640 1978 803 1945 1107 M11038 GEORGES_CELL_CYCLE_MIR192_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GEORGES_CELL_CYCLE_MIR192_TARGETS.html Experimentally validated direct targets of MIR192 [GeneID=406967] microRNA; MIR192 caused cell cycle arrest in HCT116 cells (colon cancer). 19074876 76/85 Jessica Robertson 5.42236467812832e-07 1.1665251267441e-06 1145 1542.45454545455 1470 4.92942364962279e-08 264 1.97657814266909 2.13085595616281 1 4.66621201117509 1145 264 2055 1841 2030 1179 1209 3241 455 1470 2078 1108 M4592 JEON_SMAD6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JEON_SMAD6_TARGETS_UP.html Genes up-regulated in H1299 cells (lung cancer) upon knockdown of SMAD6 [GeneID=4091] by RNAi. 19047146 29/36 Jessica Robertson 3.29823499693102e-07 9.06126045087621e-07 1645 1258 1470 2.99839590127433e-08 364 2.77297319875514 3.09833247133181 1 6.68880624207305 1642 651 625 364 1498 1795 2304 1950 802 737 1470 1109 M4448 BOYAULT_LIVER_CANCER_SUBCLASS_G23_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G23_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G23, defined by unsupervised clustering. 17187432 61/68 Yujin Hoshida 2.77384435174364e-06 3.96864060025159e-06 290 1514.90909090909 1472 2.52167986283557e-07 286 1.81712412651059 1.90533474643845 1 3.89715463191932 297 2192 2374 2329 3225 286 289 1472 1324 1626 1250 1110 M11250 FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN.html Genes down-regulated in MCF-7 cells (breast cancer) by selective estrogen receptor modulators (SERM) 4-hydroxytamoxifen, raloxifene, or ICI 182780 but not by estradiol [PubChem=44959;5035;3478439;5757]. 14973112 61/71 Arthur Liberzon 2.93217797580831e-05 3.38880510426426e-05 275 1567.90909090909 1473 2.66565186985926e-06 272 1.67580551496573 1.88423656178663 1 2.96246428602723 272 2637 1788 1473 4034 515 343 1328 2455 773 1629 1111 M3603 OUILLETTE_CLL_13Q14_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUILLETTE_CLL_13Q14_DELETION_DN.html Genes down-regulated in chronic lymphocytic leukemia (CLL) samples bearing deletions in the 13q14 region. 18281475 81/98 Jessica Robertson 1.1561143743917e-07 7.06112554001409e-07 1570 1322.09090909091 1474 1.05101312286025e-08 390 2.10939610295339 2.13962162723432 1 5.16807512850788 1568 1621 1142 989 390 889 1474 1655 865 1979 1971 1112 M5825 VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_DN.html Angiogenic markers down-regulated in lymph endothelial cells upon infection with KSHV (Kaposi's sarcoma herpes virus). 17483315 155/220 Jessica Robertson 5.89152460050186e-16 2.12274779498998e-14 1385 1397.36363636364 1474 5.35593145500169e-17 91 2.70388543590249 2.74136505943575 1 14.8180802260106 1381 1474 91 125 1800 1436 3645 1487 2074 136 1722 1113 M1550 SIMBULAN_PARP1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_PARP1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) from PARP1 [GeneID=142] knockout mice. 11016956 48/53 John Newman 5.79117176099123e-05 6.48655213855686e-05 1475 1679 1475 5.26484019142334e-06 370 2.71847706199794 3.00726999184403 1 4.52855073852499 370 2237 617 866 4162 1474 2253 2343 1628 1044 1475 1114 M1800 ZHENG_IL22_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_IL22_SIGNALING_UP.html Genes up-regulated in ex-vivo colonic tissue after treatment with IL22 [GeneID=50616]. 18264109 74/114 Jessica Robertson 1.03366575632816e-12 2.42731461187508e-11 1750 1322.54545454545 1475 9.39696142116949e-14 148 3.42818376320549 -3.94429578779428 -1 14.5845200903001 1749 245 148 927 1532 2956 2314 1195 1475 443 1564 1115 M18009 KEGG_CIRCADIAN_RHYTHM_MAMMAL http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CIRCADIAN_RHYTHM_MAMMAL.html Circadian rhythm - mammal 14/14 KEGG 1.88643820332902e-06 2.87875471054413e-06 400 1577.09090909091 1477 1.71494529172612e-07 228 1.66035436417552 -1.75492305215038 -1 3.64972281362012 396 1937 2624 2800 3003 591 228 1477 1145 2357 790 1116 M7343 LUI_THYROID_CANCER_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_2.html Cluster 2: genes with similar expression profiles across follicular thyroid carcinoma (FTC) samples. 15608688 64/74 Leona Saunders 1.48339786421493e-07 7.26289540930751e-07 4090 2335 1478 1.34854360385115e-08 335 2.18373759855288 -1.78622143058678 -1 5.34123146126681 4086 335 1266 596 621 4361 3746 4038 688 1478 4470 1117 M2262 KIM_GLIS2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GLIS2_TARGETS_DN.html Partial list of genes down-regulated in the kidney of GLIS2 [GeneID=84662] knockout mice compared to the wild type. 18227149 7/9 Arthur Liberzon 2.96576798820476e-07 8.70294688256627e-07 2410 1998.45454545455 1478 2.96576838401492e-08 109 1.56819822968393 0.928021304474851 1 3.77202853918168 2408 1025 4675 2847 1478 1095 636 4692 613 2405 109 1118 M53 PID_INTEGRIN3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN3_PATHWAY.html Beta3 integrin cell surface interactions 18832364 66/73 Pathway Interaction Database 3.73469334836062e-06 5.13330011772339e-06 525 1871.90909090909 1479 3.39518153485989e-07 400 2.52058634256498 2.60228087950652 1 5.31194467520884 524 2631 453 1230 4007 1343 2163 2820 3541 400 1479 1119 M18311 REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS.html Genes involved in Metabolism of vitamins and cofactors 55/56 Reactome 2.0277467504547e-07 7.65527859584926e-07 1480 1675.18181818182 1480 1.84340630668433e-08 400 1.59689700947146 -1.48581050740322 -1 3.87774873748591 1569 400 2863 3633 959 1476 1480 1470 1518 1939 1120 1120 M1193 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 25/33 Arthur Liberzon 1.63514659933314e-07 7.3358205358541e-07 2140 1424 1480 1.48649701896834e-08 475 2.71615072531858 2.8269378202506 1 6.6509274198654 2136 721 641 1636 715 1952 2133 1480 2512 475 1263 1121 M7054 SU_LIVER http://www.broadinstitute.org/gsea/msigdb/cards/SU_LIVER.html Genes up-regulated specifically in human liver tissue. 11904358 45/140 John Newman 1.79985512382558e-05 2.13342947876865e-05 1480 1655.54545454545 1480 1.63624531717851e-06 427 2.70644721785612 -3.09381366131527 -1 5.0339307752415 662 2254 930 1480 3921 427 602 2267 3152 1480 1036 1122 M17778 DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_DN.html Genes down-regulated in CD34+ [GeneID=947] cells isolated from bone marrow of CML (chronic myelogenous leukemia) patients, compared to those from normal donors. 17252012 160/301 Leona Saunders 3.27301661386116e-07 9.05922275783096e-07 1440 1931 1481 2.97547009163577e-08 799 2.01857123021881 -1.56468791161555 -1 4.8555476785424 1437 2083 801 2109 1481 799 1135 4602 2867 1083 2844 1123 M1316 GROSS_HYPOXIA_VIA_ELK3_ONLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_ONLY_DN.html Genes specifically down-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 55/59 Jessica Robertson 7.2494740920075e-07 1.40178278223168e-06 1140 1361 1481 6.59043316442412e-08 407 2.05254696220265 1.91877660686987 1 4.78161843360181 1140 407 1507 1779 2294 1188 1578 2027 651 919 1481 1124 M5622 DAZARD_UV_RESPONSE_CLUSTER_G2 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G2.html Cluster G2: genes increasingly up-regulated in NHEK cells (normal keratinocyte) and reaching maximum levels at 12 h and 24 h after UV-B irradiation. 12771951 45/79 John Newman 5.26227686554719e-06 6.90326481528147e-06 565 1861.72727272727 1481 4.78389950241915e-07 562 2.24711954645012 -2.4556377899759 -1 4.61393662344739 562 3090 1334 1532 3530 1022 1064 1658 3931 1481 1275 1125 M929 SABATES_COLORECTAL_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_UP.html Genes up-regulated in colorectal adenoma compared to normal mucosa samples. 18171984 130/249 Leona Saunders 1.12039225828391e-34 1.82353498589658e-32 15 1635.81818181818 1482 1.01853841662174e-35 12 3.54286417627521 -3.15365273848514 -1 45.1719426459209 3301 1482 15 12 301 3775 3234 2431 721 58 2664 1126 M2318 KASLER_HDAC7_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/KASLER_HDAC7_TARGETS_1_DN.html Genes down-regulated in DO11.10 cells (hybridoma) by expression of transciptionally activating form of HDAC7 [GeneID=51564] and up-regulated by its transcriptionally repressing form. 17470548 26/28 Arthur Liberzon 6.35822167405642e-07 1.28912398202518e-06 810 1332.09090909091 1482 5.78020319240663e-08 208 2.46406327736268 -1.92216470466623 -1 5.78637663486885 808 1837 1482 1651 2172 505 208 2034 488 2309 1159 1127 M1318 GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN.html Genes down-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] and HIF1A [GeneID=3091] by RNAi. 17704799 169/214 Jessica Robertson 2.81833583349447e-07 8.49189526890862e-07 1230 1530.81818181818 1483 2.56212381321887e-08 275 1.87905506010852 2.07291063523791 1 4.53771618687743 1229 2077 1483 1497 1324 275 1691 2474 2708 1054 1027 1128 M9524 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN.html Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs moderately differentiated tumors. 18679425 152/229 Jessica Robertson 2.46727131180086e-09 3.68529132648737e-08 3845 2095.45454545455 1483 2.24297392233444e-10 60 2.62928550714597 2.86010386991484 1 7.81015915210747 3841 1483 248 1119 60 3245 4719 2895 1335 348 3757 1129 M17082 HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP.html Genes up-regulated in hematopoietic progenitor cells (HPC) of T lymphocyte and NK (natural killer) lineage. 15331438 137/161 Kevin Vogelsang 4.17895663700616e-07 1.00504816968881e-06 895 1582 1483 3.79905220982723e-08 844 2.0876026137595 2.35993746580393 1 4.98544909850773 892 2098 965 1898 1767 1483 2102 1275 3029 1049 844 1130 M7245 SEKI_INFLAMMATORY_RESPONSE_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SEKI_INFLAMMATORY_RESPONSE_LPS_UP.html Genes up-regulated in hepatic stellar cells after stimulation with bacterial lipopolysacharide (LPS). 17952090 96/123 Jessica Robertson 3.27490265228391e-07 9.05922275783096e-07 450 1651.54545454545 1483 2.9771846725304e-08 416 2.27601634383691 -2.36478007489277 -1 5.48119755911857 450 2591 512 2397 1483 1189 889 2264 3818 416 2158 1131 M81 PID_CDC42_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CDC42_PATHWAY.html CDC42 signaling events 18832364 97/107 Pathway Interaction Database 1.37601517682934e-07 7.20206492018647e-07 1720 1882.81818181818 1484 1.25092296626708e-08 151 1.46284698822987 -1.29384525048681 -1 3.56362674455967 1720 151 3413 1090 545 1484 1337 4300 1306 3264 2101 1132 M3284 KUMAR_TARGETS_OF_MLL_AF9_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/KUMAR_TARGETS_OF_MLL_AF9_FUSION.html Myeloid leukemia model in mice with germ-line MLL-AF9 fusion knock-in [GeneID=4297;4300]: genes changed in comparison among the leukemic, preleukemic and wild-type animals. 14615372 448/605 Kevin Vogelsang 8.62805224269247e-08 6.48643236402367e-07 4720 2242.63636363636 1484 7.84368416461003e-09 77 2.1688623999017 2.14602800477918 1 5.34733723332621 4716 1195 572 77 216 4327 4170 3352 1484 807 3753 1133 M19128 HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS.html Genes down-regulated in tumor-conditioned vs quiescent endothelial cells and up-regulated upon treatment with decitabine and TSA [PubChem=451668;5562]. 17483324 138/176 Jessica Robertson 9.18342773172264e-15 2.928768844171e-13 1945 1569.63636363636 1484 8.34857066520243e-16 105 2.67472348065577 3.30296702756884 1 13.4316888167737 1944 1484 105 723 1957 2740 4449 1075 1022 168 1599 1134 M2777 AMIT_SERUM_RESPONSE_240_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_240_MCF10A.html Genes whose expression peaked at 240 min after stimulation of MCF10A cells with serum. 17322878 104/123 Leona Saunders 1.21697331884183e-07 7.10527676861612e-07 110 1599.72727272727 1485 1.10633944196465e-08 107 2.62931050019933 -2.13672145832216 -1 6.45134934011548 2809 107 482 107 430 3483 2598 2844 1485 453 2799 1135 M9904 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY.html T cell receptor signaling pathway 103/137 KEGG 1.16784846229225e-07 7.06112554001409e-07 1705 1450.09090909091 1486 1.06168047662395e-08 90 1.61180296707831 -1.54373932977146 -1 3.93715559701338 1239 90 2649 486 395 1486 1255 1703 2526 2421 1701 1136 M657 REACTOME_GASTRIN_CREB_SIGNALLING_PATHWAY_VIA_PKC_AND_MAPK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GASTRIN_CREB_SIGNALLING_PATHWAY_VIA_PKC_AND_MAPK.html Genes involved in Gastrin-CREB signalling pathway via PKC and MAPK 135/232 Reactome 1.58740642128569e-07 7.31918027928963e-07 3540 1822.54545454545 1486 1.44309685074978e-08 8 2.38429304978555 -2.12939652622283 -1 5.83315325329638 3536 8 768 1486 687 3488 2334 864 2149 1330 3398 1137 M11184 REACTOME_ENDOGENOUS_STEROLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOGENOUS_STEROLS.html Genes involved in Endogenous sterols 6/15 Reactome 7.34425976711552e-07 1.41086308916505e-06 940 1996.36363636364 1486 7.34426219433347e-08 531 2.34562062135117 2.62404169277623 1 5.46886291654012 937 1040 4226 3839 2387 828 531 1827 4175 1486 684 1138 M1481 ABBUD_LIF_SIGNALING_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_2_DN.html Genes down-regulated in GH3 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 7/16 Kevin Vogelsang 4.82918408716779e-07 1.09217771401207e-06 1490 1492.72727272727 1487 4.82918513661396e-08 20 4.03642504108808 5.55069137157535 1 9.62757360445553 1487 1979 4485 1628 2203 1463 468 20 301 1811 575 1139 M930 REACTOME_TRANSPORT_OF_ORGANIC_ANIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_ORGANIC_ANIONS.html Genes involved in Transport of organic anions 6/16 Reactome 5.19124241378562e-07 1.13438260153093e-06 3410 1964.63636363636 1488 5.19124362649091e-08 25 3.82362294379156 2.21221638974164 1 9.09204533655802 3409 1037 4253 536 2079 2666 1246 1453 25 1488 3419 1140 M18841 MULLIGHAN_MLL_SIGNATURE_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_1_DN.html The 'MLL signature 1': genes down-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to all AML cases with the intact gene. 17597811 296/408 Arthur Liberzon 2.02520683665597e-07 7.65527859584926e-07 960 1630.72727272727 1488 1.84109729371466e-08 599 2.17311706047324 2.26401204485619 1 5.29504051238583 2175 2034 599 960 956 1385 2919 2731 2057 634 1488 1141 M5669 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY.html Natural killer cell mediated cytotoxicity 99/188 KEGG 1.78294331957889e-07 7.43418062580597e-07 1490 1335.63636363636 1489 1.62085769461251e-08 109 1.66760216784445 -1.45004415282356 -1 4.06019361918903 1489 109 2222 186 829 1196 1596 1119 2787 1528 1631 1142 M2348 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP.html Genes up-regulated in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 345/424 Arthur Liberzon 9.344633008717e-08 6.56798957981166e-07 2335 1573.72727272727 1490 8.49512127785084e-09 273 2.09507938329813 2.3056275055038 1 5.15915053591346 2335 1248 596 548 273 1490 3267 3315 1614 377 2248 1143 M2920 KEGG_LINOLEIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LINOLEIC_ACID_METABOLISM.html Linoleic acid metabolism 18/62 KEGG 2.18537207041853e-07 7.77552820877664e-07 1500 1632.27272727273 1491 1.98670207954791e-08 882 2.9944698018323 -2.60839339199028 -1 7.30711803687376 1499 882 955 2765 1046 1397 1139 2678 2324 1491 1779 1144 M1515 JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_DN.html Genes down-regulated in H460 cells (non-small cell lung carcinoma, NSCLC) after treatment with sodium butyrate [PubChem=5222465]. 15318170 93/171 John Newman 3.28835741084586e-07 9.05922275783096e-07 1340 1925.27272727273 1491 2.98941627487214e-08 907 2.03082880641133 2.08452033833931 1 4.88533636232522 1336 1611 1229 3385 1491 907 1153 3258 3556 1778 1474 1145 M15514 REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES.html Genes involved in Transmission across Chemical Synapses 149/243 Reactome 1.4323688236847e-07 7.24081202656879e-07 2350 1789.18181818182 1492 1.30215356085718e-08 588 2.10503754550014 2.23254827860514 1 5.14805430402597 2347 1492 805 799 588 1729 3885 3324 2447 1125 1140 1146 M14899 BIOCARTA_AT1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AT1R_PATHWAY.html Angiotensin II mediated activation of JNK Pathway via Pyk2 dependent signaling 50/56 BioCarta 2.10323437631278e-07 7.70763712250053e-07 1225 1669.81818181818 1493 1.91203143398663e-08 208 1.72519448607678 -1.84983378890403 -1 4.19126002392302 1224 2673 2910 208 1003 1621 893 1561 1493 3580 1202 1147 M17812 TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_DN.html Genes down-regulated in plasma cells compared with B lymphocytes. 12663452 46/64 Kate Stafford 1.62391466180483e-06 2.54647083180026e-06 345 1510.09090909091 1493 1.47628714589759e-07 269 1.84292951370933 -1.64479100419071 -1 4.09603253867007 342 2680 2081 1926 2913 436 269 1425 1826 1220 1493 1148 M12314 KANG_GIST_WITH_PDGFRA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_GIST_WITH_PDGFRA_UP.html Genes up-regulated in gastrointestinal stromal tumors (GIST) with PDGFRA [GeneID=5156] mutations. 15690055 68/116 Arthur Liberzon 7.39251635959739e-09 1.00845887911271e-07 270 1380.45454545455 1495 6.72046944039815e-10 270 2.61664219035126 2.85789936506265 1 7.31230524874279 1495 280 270 1588 1383 2195 3445 270 1945 351 1963 1149 M8215 IVANOVA_HEMATOPOIESIS_STEM_CELL_AND_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL_AND_PROGENITOR.html Genes in the expression cluster 'HSC and Progenitors Shared': up-regulated in hematopoietic stem cells (HSC) and progenitors from adult bone marrow and fetal liver. 12228721 826/1015 John Newman 2.14936456958057e-07 7.72658093558287e-07 1890 1662.36363636364 1495 2.14936477747017e-08 619 1.82468886725891 1.95363031291144 1 4.43507924654757 1890 1100 4497 966 1135 619 2276 1625 1777 906 1495 1150 M1736 GAVIN_FOXP3_TARGETS_CLUSTER_P7 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P7.html Cluster P7 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 130/177 Jessica Robertson 1.75861185224059e-07 7.39808194525452e-07 2055 1339 1495 1.59873817528962e-08 1 2.4000688526377 2.7805354531055 1 5.86758498528387 2055 1 457 1579 812 2110 3302 481 1495 670 1767 1151 M3468 NABA_ECM_REGULATORS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_ECM_REGULATORS.html Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix 22159717 142/319 Alexandra Naba 2.73109049869233e-17 1.23949491863729e-15 860 1230.09090909091 1495 2.48280954426574e-18 70 2.88205993630624 3.07985097255784 1 17.2276968221702 856 1495 70 250 1937 1609 2668 616 2021 166 1843 1152 M18615 KEGG_ALLOGRAFT_REJECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALLOGRAFT_REJECTION.html Allograft rejection 29/70 KEGG 3.55820125943657e-06 4.91504534519772e-06 305 1818 1496 3.23473364941542e-07 304 1.48420509095372 -1.43575380501819 -1 3.11853891726667 304 1805 2383 2453 3343 474 927 1468 3964 1496 1381 1153 M8323 KRASNOSELSKAYA_ILF3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRASNOSELSKAYA_ILF3_TARGETS_UP.html Up-regulated in GHOST(3)CXCR4 cells (osteosarcoma) upon ectopic expression of ILF3 [GeneID=3609]. 12036489 82/150 John Newman 5.71305874286739e-06 7.42061557801729e-06 1500 1854.54545454545 1496 5.19370325349881e-07 438 1.85996549644101 -1.76558037019918 -1 3.78690860352231 438 2149 1318 1496 3566 1168 1059 1498 4046 1264 2398 1154 M2003 MIKKELSEN_ES_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 K27 trimethylation mark (H3K27me3) in embryonic stem cells (ES). 17603471 63/100 Arthur Liberzon 3.45407173156031e-09 5.00098729232045e-08 375 1432.36363636364 1497 3.14006521543938e-10 253 3.03632382822153 2.96512489259176 1 8.86509475050267 373 1658 253 1610 2815 666 2479 3614 1497 337 454 1155 M2006 MIKKELSEN_ES_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters bearing H3 trimethylation mark at K27 (H3K27me3) in embryonic stem cells (ES). 17603471 8/24 Arthur Liberzon 5.13151387353453e-06 6.74860559573223e-06 1500 1875.36363636364 1498 5.13152572316862e-07 99 3.32830241512831 2.82399749135295 1 6.87114044402565 1498 1026 4644 1172 3555 2214 3819 197 99 2074 331 1156 M19381 REACTOME_G2_M_CHECKPOINTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G2_M_CHECKPOINTS.html Genes involved in G2/M Checkpoints 46/46 Reactome 2.53115659246538e-05 2.93972911329641e-05 90 1465.36363636364 1499 2.30107792231106e-06 47 1.61833459968863 1.62086054012461 1 2.89933395482905 86 2234 2377 1499 4010 232 47 966 1656 1379 1633 1157 M8224 ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_DN.html Genes in discrete regions of loss within 16q region detected in individual invasive breast cancer tumors. 16702952 29/64 Arthur Liberzon 4.15843885626573e-07 1.0045025695513e-06 1585 1613.72727272727 1500 3.78039967481257e-08 693 2.64094380614543 2.81254716215833 1 6.32040855539841 1584 693 1043 3061 1758 1921 3053 1145 970 1500 1023 1158 M15356 PUJANA_BREAST_CANCER_LIT_INT_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BREAST_CANCER_LIT_INT_NETWORK.html Genes constituting the LIT-Int network of proteins interacting with breast cancer reference proteins BRCA1, BRCA2, ATM, and CHEK2 [GeneID=672;675;472;11200]; the interactions were manually curated from the literature. 17922014 130/143 Leona Saunders 1.0623121095528e-06 1.83331376858838e-06 495 1731.09090909091 1501 9.65738747737162e-08 273 1.51333470406644 1.61565539698224 1 3.44138663785137 492 2991 3315 2028 2610 273 334 1238 1501 3073 1187 1159 M1496 KIM_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/KIM_HYPOXIA.html Genes up-regulated in normal fibroblasts under hypoxia conditions. 14499499 38/42 John Newman 8.57536264320631e-06 1.07362630440143e-05 1440 2032 1501 7.79581460838828e-07 666 2.12933174773345 2.12797610107046 1 4.20522003016789 1501 3702 2203 2194 3711 1178 951 666 1440 3366 1440 1160 M67 PID_ARF6_TRAFFICKING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_TRAFFICKING_PATHWAY.html Arf6 trafficking events 18832364 64/75 Pathway Interaction Database 6.6111367387348e-08 5.94372674415777e-07 2265 1843.54545454545 1502 6.0101244885487e-09 117 1.69439146102851 -1.3164395878747 -1 4.19243908594821 2263 327 2152 857 117 2312 1277 4086 1502 1477 3909 1161 M18517 MATSUDA_NATURAL_KILLER_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/MATSUDA_NATURAL_KILLER_DIFFERENTIATION.html Genes changed between developmental stages of Valpha14i natural killer T lymphocyte cells (NKT). 16357323 614/792 Kevin Vogelsang 1.7508199028296e-08 2.19200794200416e-07 1715 1476.72727272727 1502 1.75081991662376e-09 227 2.2080319261335 2.28287608276145 1 5.86320021500432 1712 1136 4482 340 826 685 2226 1502 1602 227 1506 1162 M10770 ZHAN_MULTIPLE_MYELOMA_MF_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MF_UP.html Top 50 up-regulated genes in cluster MF of multiple myeloma samples with characteristic expression spike of MAF family transcription factors. 16728703 65/98 Kevin Vogelsang 3.30989507622186e-07 9.06126045087621e-07 4270 2430.72727272727 1502 3.00899597654085e-08 339 2.41667623263833 2.42437803854967 1 5.82293798754988 4269 339 938 838 1502 4505 4326 4060 752 1118 4091 1163 M7815 RADMACHER_AML_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/RADMACHER_AML_PROGNOSIS.html The 'Bullinger validation signature' [PMID=15084693] used to validate prediction of prognostic outcome of acute myeloid leukemia (AML) patients with a normal karyotype. 16670265 143/181 Kevin Vogelsang 4.09349353161315e-08 4.47398945165397e-07 1620 1588.36363636364 1502 3.72135782525448e-09 322 2.47505725788925 2.70646791003991 1 6.26989034169462 1617 1502 322 368 1614 2018 4332 2891 937 437 1434 1164 M1931 MEISSNER_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone trimethylation marks at K4 (H3K4me3) and K27 (H3K27me3)ES cells (embryonic stem). 18600261 15/23 Jessica Robertson 7.66438673499121e-07 1.4528476059903e-06 1570 1522.09090909091 1502 6.96762673192807e-08 720 2.19140734691064 -2.19488809805423 -1 5.09479825597771 1567 916 1502 1459 2346 1799 1608 1231 2239 1356 720 1165 M46 PID_ATR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATR_PATHWAY.html ATR signaling pathway 18832364 50/52 Pathway Interaction Database 4.34490246441571e-06 5.85941132344062e-06 225 1536.18181818182 1503 3.94991913220834e-07 223 1.62218116970021 1.63026494623946 1 3.36330530526877 223 2224 2887 1503 3425 317 230 867 1201 2413 1608 1166 M971 REACTOME_ION_TRANSPORT_BY_P_TYPE_ATPASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ION_TRANSPORT_BY_P_TYPE_ATPASES.html Genes involved in Ion transport by P-type ATPases 29/39 Reactome 3.31183221821666e-07 9.06126045087621e-07 1665 1696 1503 3.01075701524799e-08 706 2.10045892617453 -2.09623249242706 -1 5.05447080080414 1661 706 1627 3638 1503 1771 1433 1120 2603 1497 1097 1167 M7534 YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) samples from patients with early recurrence (within 2 years after surgery) after resection. 19167881 96/124 Yujin Hoshida 1.35013094663745e-07 7.20206492018647e-07 1460 1524.45454545455 1503 1.22739184499494e-08 525 1.98360515563931 2.14142402078395 1 4.8500531540066 1459 1604 1969 2609 525 1201 1758 1910 1119 1503 1112 1168 M50 PID_PTP1B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PTP1B_PATHWAY.html Signaling events mediated by PTP1B 18832364 74/115 Pathway Interaction Database 9.68470182728771e-08 6.64473403617636e-07 3095 1970.27272727273 1505 8.80427477601962e-09 182 2.31174545802807 -2.23863810888839 -1 5.69317678652156 3095 265 1086 182 292 3616 3515 3244 1280 1505 3593 1169 M128 PID_TNF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TNF_PATHWAY.html TNF receptor signaling pathway 18832364 57/60 Pathway Interaction Database 2.84124092826957e-07 8.51178263306103e-07 400 1827.18181818182 1505 2.58294663200752e-08 399 1.63636905204729 -1.70728948217926 -1 3.94452453142866 399 3059 3036 3188 1336 622 422 1482 2954 2096 1505 1170 M8273 CROONQUIST_NRAS_VS_STROMAL_STIMULATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_VS_STROMAL_STIMULATION_UP.html Genes up-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing an activated form of NRAS [GeneID=4893] off a plasmid vector compared to those co-cultured with bone marrow stromal cells. 12791645 47/67 Arthur Liberzon 8.3562703900054e-08 6.40285653260154e-07 1860 1497.18181818182 1508 7.59660973400187e-09 200 2.17054084792369 2.12874155253336 1 5.35643050227015 1856 483 1508 1655 200 885 2146 4135 1374 1888 339 1171 M244 SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_DN.html Genes down-regulated in brain relapse of breast cancer. 18451135 156/196 Jessica Robertson 5.14642366366412e-07 1.12935898771536e-06 1335 1568.45454545455 1509 4.67856806141719e-08 595 2.23050334637401 -2.08039031513746 -1 5.28470874041902 1332 2084 782 595 1975 2094 1798 2619 1268 1197 1509 1172 M1839 LABBE_TGFB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TGFB1_TARGETS_DN.html Down-regulated genes in NMuMG cells (mammary epithelium) after stimulation with TGFB1 [GeneID=7040]. 17210685 140/235 Jessica Robertson 1.11403467283523e-09 1.78245547653637e-08 3950 2314.09090909091 1509 1.01275879399941e-10 227 2.63951835134066 2.51250080437835 1 8.17560765539446 3948 1509 227 374 1149 3189 4601 3967 1477 427 4587 1173 M6319 KIM_MYC_AMPLIFICATION_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYC_AMPLIFICATION_TARGETS_DN.html Genes negatively correlated with amplifications of MYC [GeneID=4609] in SCLC (small cell lung cancer) cell lines. 16116477 152/196 Arthur Liberzon 1.96853585879829e-07 7.64036221497417e-07 1180 1622 1510 1.78957821358249e-08 922 2.18989444495131 -1.9759528329918 -1 5.33705276869406 1178 1510 1349 1165 922 2127 1783 2878 1214 1542 2174 1174 M26 PID_NFKAPPAB_ATYPICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFKAPPAB_ATYPICAL_PATHWAY.html Atypical NF-kappaB pathway 18832364 27/30 Pathway Interaction Database 1.55796146460481e-06 2.45939067322232e-06 780 1585.36363636364 1512 1.41632960718055e-07 503 1.89170065663517 -1.89766877558171 -1 4.21724993158837 776 2766 2521 1512 2892 793 654 503 1015 2434 1573 1175 M2456 WANG_MLL_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WANG_MLL_TARGETS.html Genes requiring MLL [GeneID=4297] for H3K4me3 and expression in MEF cells (embryonic fibroblast). 19703992 344/461 Arthur Liberzon 3.80392455134449e-23 2.76223444343784e-21 1245 1637.72727272727 1512 3.45811322849499e-24 41 2.62776847880549 2.74586256254779 1 21.676185973209 1245 1241 41 2042 1512 1326 3251 3078 2580 90 1609 1176 M12353 FONTAINE_PAPILLARY_THYROID_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_PAPILLARY_THYROID_CARCINOMA_UP.html Genes up-regulated in papillary thyroid carcinoma (PTC) compared to other thyroid tumors. 17968324 87/119 Arthur Liberzon 4.13692104002441e-07 1.00297161701715e-06 3950 2072.36363636364 1513 3.76083801630816e-08 183 2.51833357559561 2.34550062306083 1 6.02532083689569 3949 183 677 585 1748 3969 4549 3478 739 1406 1513 1177 M2225 KANG_AR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_AR_TARGETS_DN.html Genes down-regulated in osteoblasts from wild type male mice compared to those with AR [GeneID=367] knockout. 18838539 31/38 Arthur Liberzon 0.000175556284266655 0.000189313607890933 185 1749.81818181818 1514 1.59609359024448e-05 182 2.74378632371246 2.46869340240733 1 4.05789028675266 182 2747 800 1715 4338 835 1514 2849 2222 1065 981 1178 M749 REACTOME_CA_DEPENDENT_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CA_DEPENDENT_EVENTS.html Genes involved in Ca-dependent events 28/33 Reactome 4.4035564652849e-07 1.03048024373548e-06 1515 1333.72727272727 1515 4.003233951553e-08 63 2.1121150915974 2.39180425165833 1 5.0353569223343 1515 705 1548 463 1826 1169 1966 3131 357 1928 63 1179 M875 REACTOME_NETRIN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NETRIN1_SIGNALING.html Genes involved in Netrin-1 signaling 43/54 Reactome 3.50142878605959e-07 9.33714342949225e-07 3080 1765.27272727273 1515 3.18311758484782e-08 326 2.26928411321661 2.46179429828427 1 5.4528603321847 3076 504 1315 806 1552 3813 3001 2315 326 1515 1195 1180 M1975 MIKKELSEN_IPS_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_LCP_WITH_H3K4ME3.html Table 2S. Genes in MEF, MCV6, MCV8.1 and ES cells by epigenetic mark of their promoter 18509334 179/284 Jessica Robertson 8.06306293774825e-08 6.29674606547497e-07 350 1738.36363636364 1517 7.33005748478348e-09 347 2.36022006790749 -2.24287273238449 -1 5.83577972338887 1963 1426 347 1336 434 3028 3478 2979 1517 349 2265 1181 M2232 BHAT_ESR1_TARGETS_NOT_VIA_AKT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_NOT_VIA_AKT1_DN.html Genes bound by ESR1 [GeneID=2099] and down-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer). 18838536 135/157 Arthur Liberzon 1.44427918890062e-07 7.26289540930751e-07 4025 2049.54545454545 1518 1.31298116701472e-08 387 2.35077217291458 -2.02845852456702 -1 5.75361079748629 4025 1518 413 546 593 3492 2806 3210 859 387 4696 1182 M522 REACTOME_CELL_CELL_COMMUNICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CELL_COMMUNICATION.html Genes involved in Cell-Cell communication 124/162 Reactome 1.42017710192656e-09 2.21228908286909e-08 4345 2038.63636363636 1519 1.29107009349393e-10 32 2.4976755682855 2.49534261559728 1 7.63933436352489 4345 1519 233 32 50 3668 4528 4161 180 329 3380 1183 M13671 COATES_MACROPHAGE_M1_VS_M2_UP http://www.broadinstitute.org/gsea/msigdb/cards/COATES_MACROPHAGE_M1_VS_M2_UP.html Up-regulated genes distinguishing between M1 (pro-inflammatory) and M2 (anti-inflammatory) macrophage subtypes. 18199539 102/119 Jessica Robertson 8.38088733609726e-08 6.41131089568543e-07 2475 1495.54545454545 1519 7.61898877760609e-09 92 2.07259060684137 2.15834144648499 1 5.11197456699737 2471 92 1244 941 201 2496 2493 2210 1519 1188 1596 1184 M15422 BIOCARTA_VITCB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VITCB_PATHWAY.html Vitamin C in the Brain 22/24 BioCarta 0.000139950442224972 0.00015188918999813 290 1780.09090909091 1520 1.27235768911456e-05 290 3.11488722587356 3.4445988851428 1 4.73331901365784 290 2798 648 876 4512 1520 2425 2837 1646 988 1041 1185 M69 PID_REELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_REELIN_PATHWAY.html Reelin signaling pathway 18832364 42/47 Pathway Interaction Database 1.32420102610425e-07 7.20206492018647e-07 1540 1620.90909090909 1520 1.20381918709926e-08 389 1.41949120996565 1.67122990325455 1 3.45652517294406 1540 1740 2919 1306 502 1507 1853 389 1520 3670 884 1186 M16884 BIOCARTA_ACH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACH_PATHWAY.html Role of nicotinic acetylcholine receptors in the regulation of apoptosis 18/21 BioCarta 1.91814365979225e-07 7.53841638153156e-07 2125 1822.45454545455 1521 1.74376711548368e-08 144 1.98262728460834 -2.56294878873988 -1 4.83183184747355 2123 3760 2875 1521 912 2517 1423 144 341 4016 415 1187 M913 REACTOME_NEPHRIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEPHRIN_INTERACTIONS.html Genes involved in Nephrin interactions 27/33 Reactome 1.70218237389643e-07 7.33971845416521e-07 2960 1932.81818181818 1521 1.54743864145234e-08 53 2.23575628550465 2.49110551332384 1 5.46554786019395 2959 710 1663 424 774 3716 4617 3576 53 1521 1248 1188 M6189 ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) after knockdown of both HIF1A and HIF2A [GeneID=3091;2034] by RNAi. 16565084 141/165 Arthur Liberzon 6.8486835196451e-08 6.05242275488957e-07 3675 1876.54545454545 1521 6.22607612077023e-09 125 2.35844949974212 2.59120766838792 1 5.84766577383794 3674 1521 534 346 125 4045 4343 2943 870 654 1587 1189 M2255 MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP.html Genes commonly up-regulated in UET-13 cells (mesenchymal progenitor) by expression of EWSR1 [GeneID=2130] fusions with ETS transcription factors FLI1 and ERG [GeneID=2313 ,2078]. 18212050 357/464 Arthur Liberzon 6.81632380056878e-11 1.29730033623728e-09 3115 1921.81818181818 1522 6.19665800070907e-12 192 2.27565651349326 2.48384797790393 1 8.08314620032559 3112 1226 192 1113 380 2058 4065 3169 1522 202 4101 1190 M8510 POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_DN.html Top down-regulated marker genes for medulloblastoma classification: desmoplastic vs classic morphology. 11807556 84/113 Jean Junior 8.86866328068321e-06 1.10682418521483e-05 320 1511.18181818182 1523 8.0624536657584e-07 319 2.79383488447258 2.94786754108144 1 5.51830348291442 319 2598 564 1679 3724 939 1987 2052 1523 733 505 1191 M8673 MARTINEZ_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_TP53_TARGETS_DN.html Genes down-regulated in mice with skin specific knockout of TP53 [GeneID=7157]. 18245467 748/997 Jessica Robertson 7.96456168667587e-08 6.29674606547497e-07 2625 1789 1523 7.96456197212997e-09 225 2.01602493884347 2.30259910053454 1 4.97744048062873 2625 1106 4535 339 225 1661 3742 2119 1274 530 1523 1192 M2132 WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN.html Genes down-regulated in RS4;11 cells (MLL, mixed lineage leukemia) in response to SB216763 [PubChem=176158], an inhibitor of GSK3B [GeneID=2932]. 20541704 463/609 Arthur Liberzon 1.15278483583197e-06 1.95093023489671e-06 355 1455.45454545455 1523 1.04798676353066e-07 352 1.74868992606096 1.77133259517362 1 3.96538473274354 352 1181 1714 1849 2668 736 792 1523 2660 599 1936 1193 M532 REACTOME_G0_AND_EARLY_G1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G0_AND_EARLY_G1.html Genes involved in G0 and Early G1 26/29 Reactome 1.37339772801306e-05 1.66173731766768e-05 490 1839.81818181818 1526 1.24855118347387e-06 489 1.38232452071347 1.58360994904556 1 2.60693780574404 489 1825 3034 2897 3842 590 603 1001 1428 3003 1526 1194 M777 REACTOME_METABOLISM_OF_NUCLEOTIDES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_NUCLEOTIDES.html Genes involved in Metabolism of nucleotides 74/85 Reactome 2.49585348134512e-07 8.18104459972526e-07 1055 1724.27272727273 1526 2.26895796772224e-08 262 1.53513575286124 1.60154569470107 1 3.70802868642005 1053 262 2650 2642 1190 1526 1801 1346 1492 2850 2155 1195 M515 LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_UP.html Up-regulated genes displaying alternative splicing in MDA-MB-435 cells (breast cancer) whose metastatic potential has been reduced by expression of NME1 [GeneID=4830]. 18245461 127/152 Jessica Robertson 1.92651591891269e-10 3.52447873537516e-09 2235 1656.72727272727 1526 1.75137810825581e-11 201 2.36782014925264 2.53238781565715 1 7.99921177694078 2234 1526 201 335 1232 2546 4515 2328 1459 258 1590 1196 M3228 KEGG_SMALL_CELL_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SMALL_CELL_LUNG_CANCER.html Small cell lung cancer 112/124 KEGG 9.77636994478814e-07 1.72546377095256e-06 1680 1568.81818181818 1527 8.88761299019868e-08 57 2.15320640352453 2.41613351008899 1 4.94043952307921 1676 57 787 871 2549 1527 3857 2166 2172 752 843 1197 M4861 VERHAAK_AML_WITH_NPM1_MUTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_AML_WITH_NPM1_MUTATED_UP.html Genes up-regulated in acute myeloid leukemia (AML) patients with mutated NPM1 [GeneID=4869]. 16109776 199/356 Kevin Vogelsang 6.1004938277265e-16 2.18138870203554e-14 1715 1518.36363636364 1527 5.54590347975136e-17 92 2.55263354187427 -2.47469300884808 -1 13.9742276259472 1714 1397 92 732 1527 1243 1577 3171 3066 153 2030 1198 M6946 SHI_SPARC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHI_SPARC_TARGETS_DN.html Genes down-regulated in glioma cell lines after knockdown of SPARC [GeneID=6678] by RNAi. 17213807 15/16 Arthur Liberzon 1.82327124682592e-07 7.47800341964416e-07 1530 1678.27272727273 1529 1.65751945266482e-08 391 2.34309321597749 2.07266831169281 1 5.72270828727848 1529 1925 1530 3083 847 817 391 3607 2162 1353 1217 1199 M5202 BIOCARTA_P53HYPOXIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P53HYPOXIA_PATHWAY.html Hypoxia and p53 in the Cardiovascular system 40/44 BioCarta 0.000814482723078287 0.000852596685058664 1530 2214.45454545455 1530 7.40713106164437e-05 661 2.5462027172797 2.96733752209958 1 3.09283556684031 1530 4534 2486 2244 4476 1132 661 1180 1337 3508 1271 1200 M4710 ZHU_CMV_8_HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_8_HR_UP.html Up-regulated at 8 h following infection of primary human foreskin fibroblasts with CMV 9826724 82/121 John Newman 1.25620069568959e-06 2.07898572358166e-06 595 1735.45454545455 1530 1.14200128452833e-07 459 1.6558676093965 -1.78072671902431 -1 3.73385580303774 591 2602 2398 1530 2736 557 1367 1429 3715 1706 459 1201 M2116 VERHAAK_GLIOBLASTOMA_NEURAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_NEURAL.html Genes correlated with neural type of glioblastoma multiforme tumors. 20129251 140/198 Arthur Liberzon 7.78681032530385e-08 6.27525965386533e-07 4630 2338.09090909091 1530 7.07891872810442e-09 172 2.2649691778687 -2.39321172444547 -1 5.59959927363258 4629 1530 998 322 172 4371 4697 2964 272 1242 4522 1202 M601 REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS.html Genes involved in Antigen Activates B Cell Receptor Leading to Generation of Second Messengers 38/47 Reactome 8.8213750709254e-08 6.51622504172635e-07 3040 1609.36363636364 1532 8.01943220421589e-09 229 2.02654042179251 -2.1011452167032 -1 4.99153647943848 3037 535 1532 415 229 2594 1627 3165 515 1278 2776 1203 M2410 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4.html Genes regulated in MCF7 cells (breast cancer) by expression of the full-length and truncated (611-CTF) forms of ERBB2 [GeneID=2064] at 60 h time point. 19364815 131/188 Arthur Liberzon 8.92586838239446e-09 1.18758139528968e-07 2950 1841.72727272727 1535 8.11442583509875e-10 94 2.28937056480141 2.38760532329348 1 6.32609977773186 2948 1535 399 94 487 2322 3738 4429 1258 216 2833 1204 M145 PID_P53_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P53_DOWNSTREAM_PATHWAY.html Direct p53 effectors 18832364 160/185 Pathway Interaction Database 6.1272028858973e-07 1.2557706305443e-06 2575 1728.36363636364 1538 5.57018599307316e-08 821 2.22776748718436 2.40216658126133 1 5.23688272245306 2572 1490 964 1045 2143 1538 2161 1350 821 1661 3267 1205 M1125 MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN.html Pubertal genes down-regulated by TGFB1 [GeneID=7040]. 17486082 86/106 Arthur Liberzon 8.55197564292988e-07 1.56941388159522e-06 3060 1914.18181818182 1538 7.77452633391673e-08 142 2.59357562119904 -2.93376930412096 -1 6.00402136079002 3056 195 573 142 2443 4568 4563 1538 2133 905 940 1206 M8759 ROPERO_HDAC2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ROPERO_HDAC2_TARGETS.html Genes up-regulated genes in cell lines with HDAC2 [GeneID=3066] loss of function (LOS). 18264134 143/222 Jessica Robertson 3.45076875724346e-07 9.25433439442563e-07 1540 2576.36363636364 1539 3.13706299864313e-08 584 2.26692315500992 -2.18748728733682 -1 5.45066223514965 4042 1536 922 584 1539 4088 4695 4615 952 1460 3907 1207 M210 PID_IL8_CXCR2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL8_CXCR2_PATHWAY.html IL8- and CXCR2-mediated signaling events 18832364 57/67 Pathway Interaction Database 2.03652213752774e-07 7.66537838048718e-07 1555 1416.45454545455 1541 1.85138393276996e-08 192 1.86912757160329 -1.89414665609358 -1 4.54690650355687 1554 426 2572 192 965 1541 1230 1645 967 2803 1686 1208 M1293 YANG_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_DN.html Genes down-regulated in early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 46/54 Leona Saunders 2.27166454458942e-06 3.37708870880695e-06 2060 1553.63636363636 1541 2.06515171841487e-07 462 2.29891723249641 2.57893931188819 1 5.00852419013106 2056 462 1091 1024 3098 1859 1541 1831 874 1219 2035 1209 M2205 CHYLA_CBFA2T3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHYLA_CBFA2T3_TARGETS_UP.html Genes up-regulated in immature bone marrow progenitor cells upon knock out of CBFA2T3 [GeneID=863]. 18710942 461/721 Arthur Liberzon 3.01723147809897e-09 4.39547301747751e-08 4090 2280.72727272727 1541 2.74293771112455e-10 237 2.21938258995689 2.31808472271133 1 6.5164523165542 4087 1185 251 279 1541 3292 3826 4498 1352 237 4540 1210 M17370 BIOCARTA_RANMS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RANMS_PATHWAY.html Role of Ran in mitotic spindle regulation 11/15 BioCarta 0.00071706078035744 0.000751782959415174 795 1888.09090909091 1543 6.52086003180151e-05 517 1.40258579281517 1.40258579281517 1 1.71205352621642 791 2432 2882 2634 4467 808 517 1196 757 2742 1543 1211 M10351 BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN.html Genes down-regulated in T24 (bladder cancer) cells in response to the photodynamic therapy (PDT) stress. 17952126 810/943 Jessica Robertson 1.62143492572401e-07 7.3358205358541e-07 1095 1737.09090909091 1543 1.62143504403133e-08 761 1.81474545503228 1.9631040242367 1 4.42708735735007 1092 1104 4433 2181 830 761 1595 1543 2262 1508 1799 1212 M14863 BIOCARTA_P53_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P53_PATHWAY.html p53 Signaling Pathway 21/22 BioCarta 2.54584810677401e-06 3.69054148156428e-06 1545 1558.18181818182 1546 2.31441004803963e-07 81 2.56461151607292 2.91908782167145 1 5.55340308146466 1542 1861 1546 640 3175 1495 841 2359 81 1614 1986 1213 M1459 PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN.html Genes down-regulated in BEC (blood endothelial cells) compared to LEC (lymphatic endothelial cells). 12198161 237/274 Kevin Vogelsang 3.83502856847401e-16 1.42530195615727e-14 1600 1425.27272727273 1546 3.48638960770365e-17 88 2.47823701052467 2.51096830284309 1 13.7496976404046 1598 1333 88 305 819 1546 3429 2175 2073 176 2136 1214 M3015 HUANG_DASATINIB_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_DASATINIB_RESISTANCE_UP.html Genes whose expression positively correlated with sensitivity of breast cancer cell lines to dasatinib [PubChem=3062316]. 17332353 131/159 Jessica Robertson 3.48260408572291e-07 9.30654820258927e-07 1065 1562.63636363636 1546 3.16600421547264e-08 2 2.29401101705731 2.61096028410912 1 5.51413682567913 1061 2 419 1687 1546 2115 4349 1158 2694 490 1668 1215 M16402 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_24 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_24.html Amplification hot spot 24: colocalized fragile sites and cancer genes in the 1q21-q24 region. 16751803 18/23 Arthur Liberzon 6.19824476258042e-07 1.26483853347944e-06 1030 1521.54545454545 1547 5.63476955351333e-08 48 2.73639412344463 2.67954946352613 1 6.44051264718989 1028 2385 1547 2087 2157 1164 2246 960 48 3046 69 1216 M9858 VALK_AML_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_3.html Top 40 genes from cluster 3 of acute myeloid leukemia (AML) expression profile; 84% of the samples are FAB M1 or M2 subtypes, 52% bear intern tandem duplication in FLT3 [GeneID=2322]. 15084694 55/76 Jessica Robertson 2.881388464638e-06 4.08658460128947e-06 1550 1644.90909090909 1549 2.6194474895117e-07 530 2.51548358448727 2.6895130248786 1 5.40127775665844 1110 1677 530 1192 3255 1549 2695 2755 1173 609 1549 1217 M3002 FRASOR_RESPONSE_TO_ESTRADIOL_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_ESTRADIOL_DN.html Genes down-regulated in MCF-7 cells (breast cancer) by estradiol (E2) [PubChem=5757]. 14973112 122/178 Arthur Liberzon 1.95793803990872e-08 2.40663217405446e-07 2095 1635.45454545455 1550 1.77994368848528e-09 99 2.44804222001569 -2.55934097564828 -1 6.46602253306549 2091 1550 301 99 795 2478 2363 4532 984 355 2442 1218 M2338 KIM_TIAL1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KIM_TIAL1_TARGETS.html Top scoring genes whose transcripts bound TIAR1 [GeneID=7073] in extracts from RKO cells (colon cancer). 17682065 48/66 Arthur Liberzon 1.06426854977464e-07 6.93852357637273e-07 1465 1487.90909090909 1550 9.67516910235944e-09 333 1.5389482949945 1.66299315789167 1 3.76163950388985 1465 458 2621 1221 333 1742 1860 777 1550 1971 2369 1219 M5686 MARKEY_RB1_CHRONIC_LOF_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_CHRONIC_LOF_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) isolated from RB1 [GeneID=5925] knockout mice: chronic loss of function (LOF) of RB1. 17452985 127/188 Arthur Liberzon 2.24342329681532e-08 2.69159166413616e-07 3580 2265.45454545455 1551 2.03947574517487e-09 305 2.62352092972454 2.59470519066834 1 6.88182550317691 3579 1551 305 715 1428 3191 4202 3430 1509 775 4235 1220 M1038 BOYLAN_MULTIPLE_MYELOMA_PCA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA1_DN.html Top down-regulated genes from principal component 1 (PCA1) which captures variation between normal plasma cells and tumors arising from aberrant expression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 8/9 Arthur Liberzon 4.55938296465513e-06 6.09809244584997e-06 1555 1833.09090909091 1551 4.55939231927001e-07 288 3.30998831216418 4.05632337803749 1 6.89165371410509 1551 1011 4638 2080 3512 1951 2178 288 303 1541 1111 1221 M12210 YOKOE_CANCER_TESTIS_ANTIGENS http://www.broadinstitute.org/gsea/msigdb/cards/YOKOE_CANCER_TESTIS_ANTIGENS.html Genes up-regulated in both colorectal cancer cells and normal testis relative to normal colon epithelium. 18281482 48/74 Jessica Robertson 4.51075046314366e-07 1.04185917010687e-06 1190 1683.18181818182 1552 4.1006830800015e-08 664 1.98773363540287 2.0880986432681 1 4.73206790483661 1188 3076 1889 2865 1855 664 756 779 2760 1552 1131 1222 M8689 CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN.html Top 200 marker genes down-regulated in the 'CTNNB1' subclass of hepatocellular carcinoma (HCC); characterized by activated CTNNB1 [GeneID=1499]. 18701503 218/315 Yujin Hoshida 2.35280509417091e-20 1.42374872365214e-18 3460 2047.36363636364 1552 2.13891372197356e-21 51 2.6814266415914 3.04928457392656 1 19.1951107035256 3459 1357 51 270 1386 4502 3876 2596 1552 125 3347 1223 M1769 JI_CARCINOGENESIS_BY_KRAS_AND_STK11_UP http://www.broadinstitute.org/gsea/msigdb/cards/JI_CARCINOGENESIS_BY_KRAS_AND_STK11_UP.html Cluster A: genes up-regulated in primary lung tumors driven by KRAS [GeneID=3845] activation and loss of STK11 [GeneID=6794]; also up-regulated in human squamous cell carcinoma (SCC) vs adenocarcinoma subtype of NSCLC (non-small cell lung cancer). 17676035 21/24 Jessica Robertson 7.56565581172279e-07 1.43952717492005e-06 1940 1388.36363636364 1553 6.87787128500317e-08 464 4.07620405448171 5.4906015203738 1 9.52635180591463 1936 808 464 1616 2335 1553 1643 1307 805 874 1931 1224 M10668 DORN_ADENOVIRUS_INFECTION_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_12HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 12 h after infection with adenovirus Ad12. 15681441 48/77 Arthur Liberzon 6.44484947648909e-08 5.87252693610589e-07 2570 1528.72727272727 1553 5.85895424117225e-09 110 2.7580760440251 3.20795145027909 1 6.86153484208006 2568 1721 845 809 110 2460 3644 658 431 1553 2017 1225 M8353 BIOCARTA_HCMV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HCMV_PATHWAY.html Human Cytomegalovirus and Map Kinase Pathways 25/25 BioCarta 1.68431392655432e-06 2.62548273888256e-06 1395 1759.54545454545 1554 1.53119565096527e-07 660 1.45310396459047 -1.6149348819613 -1 3.21128037685551 1392 768 2881 660 2931 1554 1174 2213 710 3209 1863 1226 M2429 SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12.html Cluster 12 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts good survival outcome. 18641660 317/534 Arthur Liberzon 1.3847962458827e-07 7.20206492018647e-07 3495 2066.54545454545 1554 1.25890575731736e-08 558 2.17570504002957 -2.05610340550567 -1 5.32459657933712 3493 1278 753 1397 558 3477 3129 3066 1554 827 3200 1227 M10253 BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins; the changes did not depend on expression of constitutively active (Q63L) form of RHOA [GeneID=387]. 17213802 91/107 Leona Saunders 1.15175378394249e-06 1.95093023489671e-06 1015 1718 1557 1.04704944264927e-07 334 2.36275742231388 2.8143702577126 1 5.37543464409866 1013 2140 974 1081 2664 1557 3202 1474 2126 2333 334 1228 M12090 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_DN.html Genes down-regulated in erythroid lineage cells by RUNX1-RUNX1T1 [GeneID=861;862] fusion . 17898786 14/25 Arthur Liberzon 2.6149228204614e-06 3.77439758251123e-06 1560 1806.54545454545 1558 2.37720538960654e-07 923 3.10575358941319 3.17567435229934 1 6.72356140249292 1558 1914 1083 3625 3191 1816 1336 1806 923 1530 1090 1229 M1963 MIKKELSEN_MEF_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MEF cells (embryonic fibroblasts). 18509334 169/379 Jessica Robertson 5.2154525769315e-20 3.07711702038959e-18 2040 1380.18181818182 1558 4.74132052448316e-21 48 2.93605046145555 -2.85798569859455 -1 20.6273827049788 2039 1434 52 48 1360 1773 1746 2942 1558 97 2133 1230 M1123 HUMMERICH_BENIGN_SKIN_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_BENIGN_SKIN_TUMOR_DN.html Genes down-regulated in benign skin tumors (papilloma) induced by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 22/41 Leona Saunders 8.50842563817437e-07 1.56507283757533e-06 2465 1816.27272727273 1559 7.7349353898009e-08 40 2.36638195498082 3.20056102148862 1 5.47483893438455 2462 843 1559 1442 2436 2967 4645 40 808 1753 1024 1231 M2295 BAKKER_FOXO3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAKKER_FOXO3_TARGETS_DN.html Genes down-regulated in I/11 erythroblast cells upon expression of an activated form of FOXO3 [GeneID=2309]. 17353275 224/308 Arthur Liberzon 2.18286369909736e-07 7.77552820877664e-07 1955 1714.09090909091 1561 1.98442174153044e-08 1045 1.96332118112604 2.02108148319953 1 4.77367440656941 1955 2061 2223 1066 1045 1141 1561 2307 1372 2635 1489 1232 M16647 REACTOME_CELL_CYCLE_CHECKPOINTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE_CHECKPOINTS.html Genes involved in Cell Cycle Checkpoints 125/137 Reactome 1.47440777463241e-05 1.77394970590491e-05 125 1989.36363636364 1562 1.34037968726369e-06 125 1.3861630463611 1.49877732136201 1 2.59849569678053 125 2563 3779 1562 3864 526 379 1550 1411 4109 2015 1233 M8729 AMIT_EGF_RESPONSE_480_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_480_HELA.html Genes whose expression peaked at 480 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 249/275 Leona Saunders 2.89335203314254e-07 8.60199355114146e-07 3130 2207.54545454545 1562 2.63032037605882e-08 1061 1.97645804518563 2.39523045389807 1 4.77108086411204 3126 2524 1245 1281 1354 3612 4424 1562 1386 1061 2708 1234 M10450 REACTOME_GAB1_SIGNALOSOME http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAB1_SIGNALOSOME.html Genes involved in GAB1 signalosome 46/46 Reactome 3.54034092555098e-07 9.39877005182141e-07 770 2212.90909090909 1563 3.21849226843546e-08 347 1.25871289726181 -1.42593653209984 -1 3.00083077314213 768 3938 3733 3574 1563 494 347 912 3594 4340 1079 1235 M214 PID_ERBB1_INTERNALIZATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_INTERNALIZATION_PATHWAY.html Internalization of ErbB1 18832364 57/64 Pathway Interaction Database 5.7698896416023e-07 1.21093281940253e-06 1565 1769.90909090909 1564 5.24535559532601e-08 417 1.31197981840445 -1.25392485198652 -1 3.0718741769549 1564 417 3485 1100 2090 1732 1684 1461 934 4169 833 1236 M4420 LEE_LIVER_CANCER_MYC_E2F1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_E2F1_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) from MYC and E2F1 [GeneID=4609;1869] double transgenic mice. 15565109 83/125 Yujin Hoshida 2.5631678764516e-11 5.18460863083224e-10 3695 2081.72727272727 1564 2.33015261498316e-12 95 2.83980391166291 2.795589094447 1 10.5543164052555 3693 172 179 95 788 4503 3387 3784 1564 217 4517 1237 M19848 ENK_UV_RESPONSE_EPIDERMIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_EPIDERMIS_UP.html Genes up-regulated in epidermis after to UVB irradiation. 16434974 377/554 Lauren Kazmierski 1.3841275394645e-07 7.20206492018647e-07 1240 1755.36363636364 1566 1.25829784231522e-08 553 1.95571961600131 2.04562337183049 1 4.78116763885385 2512 1239 1533 1238 553 873 2278 2640 1566 2594 2283 1238 M7281 KONDO_PROSTATE_CANCER_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_PROSTATE_CANCER_WITH_H3K27ME3.html Top 200 genes with high histone H3 trimethylation mark at K27 (H3K27me3) in PC3 cells (prostate cancer), by ChIP-chip assay on an 88K microarray (all promoters). 18488029 102/442 Jessica Robertson 1.59362559016734e-14 4.91628286639861e-13 110 1874.63636363636 1566 1.44875053651578e-15 106 3.5494057570819 -3.57939958439284 -1 17.5193496367353 2910 106 110 1566 1159 3820 3214 3287 1222 410 2817 1239 M1873 VILIMAS_NOTCH1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VILIMAS_NOTCH1_TARGETS_DN.html Genes down-regulated in bone marrow progenitors by constitutively active NOTCH1 [GeneID=4851]. 17173050 10/42 Jessica Robertson 1.02858906759485e-06 1.78819167552402e-06 940 1762.09090909091 1566 9.35081407729271e-08 29 2.46316816437446 -2.8002745375503 -1 5.64347416842378 938 2451 1998 3623 2927 1236 619 29 3005 1566 991 1240 M2243 REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING.html Genes involved in Sema4D in semaphorin signaling 41/55 Reactome 6.16703640017026e-08 5.75735672118533e-07 3525 2285.45454545455 1567 5.60639688458595e-09 93 2.1411558752174 2.19885801206095 1 5.32297715154902 3522 537 1503 1050 93 3393 4387 3626 1125 1567 4337 1241 M19752 REACTOME_COMPLEMENT_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMPLEMENT_CASCADE.html Genes involved in Complement cascade 22/39 Reactome 1.90257847097082e-07 7.51162643373486e-07 1000 1882.36363636364 1567 1.72961694137039e-08 714 3.05805796049023 -3.37254979200244 -1 7.48179116969293 996 3467 1233 2811 903 1659 807 1567 4094 2455 714 1242 M10082 BIOCARTA_TNFR2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR2_PATHWAY.html TNFR2 Signaling Pathway 21/22 BioCarta 3.87637621923338e-06 5.29565723727396e-06 330 1610.81818181818 1568 3.52398459034839e-07 329 1.55664066656866 -1.70201455563874 -1 3.25290073344466 329 1855 2360 1948 3384 690 376 836 3051 1322 1568 1243 M2515 YU_BAP1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/YU_BAP1_TARGETS.html Genes deregulated in U2OS cells (osteosarcoma) upon knockdown of BAP1 [GeneID=8314] by RNAi. 20805357 41/46 Arthur Liberzon 4.50854342895856e-06 6.04039880348692e-06 1570 1813.90909090909 1568 4.09868424410372e-07 972 2.10407249912684 2.1350141447733 1 4.36610647038018 1233 1732 1811 1494 3451 1156 972 2142 1567 1568 2827 1244 M6384 LANDIS_ERBB2_BREAST_TUMORS_65_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_65_UP.html Up-regulated genes from the 65 most significantly changed (p<0.01) genes identified by two analytical methods in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 29/32 Leona Saunders 2.5654815167904e-07 8.25430999267259e-07 1705 1607.81818181818 1569 2.33225619632584e-08 108 1.65277387045659 -1.50709082539048 -1 3.993437241253 1704 1808 2597 1447 1216 1569 779 1297 108 3032 2129 1245 M2369 GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN.html Genes down-regulated during differentiation of Oli-Neu cells (oligodendroglial precursor) in response to PD174265 [PubChem=4709]. 19139271 1433/1785 Arthur Liberzon 8.62281078015816e-08 6.48643236402367e-07 2990 1957.09090909091 1569 8.62281111474608e-09 262 1.93371032714854 2.26657630210927 1 4.76214391778325 2986 1070 4693 287 769 2304 4456 1955 1569 262 1177 1246 M5988 REACTOME_SLC_MEDIATED_TRANSMEMBRANE_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SLC_MEDIATED_TRANSMEMBRANE_TRANSPORT.html Genes involved in SLC-mediated transmembrane transport 170/268 Reactome 9.66013964520597e-08 6.64473403617636e-07 4255 2273.72727272727 1571 8.78194551761825e-09 287 2.41415729926281 2.24628803815057 1 5.94760493474992 4254 1449 400 1571 287 3686 4304 2712 1151 537 4660 1247 M9972 NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_UP.html Top 20 genes whose up-regulation correlated with gastrointestinal stromal tumors (GIST) compared to synovial sarcoma. 11965276 37/110 John Newman 2.70437580276934e-07 8.3538310137901e-07 200 1696.90909090909 1572 2.45852375927996e-08 200 3.18712164748621 3.4607922705539 1 7.74051352509876 200 2275 378 1251 4484 1572 2576 1735 2361 522 1312 1248 M1880 PIONTEK_PKD1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PIONTEK_PKD1_TARGETS_DN.html Genes down-regulated during later stages of renal maturation (days P14-P16) in kidney specific knockout of PKD1 [GeneID=5310]. 17965720 24/48 Jessica Robertson 5.65026798378487e-07 1.19272204308876e-06 915 1547.36363636364 1572 5.13660857722342e-08 776 2.17969874045202 2.36396961102773 1 5.14241664843682 911 776 1476 1058 2075 1804 1629 1572 2418 1194 2108 1249 M1936 MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) that have no histone H3 methylation marks in neural precursor cells (NPC). 18600261 525/913 Jessica Robertson 3.31123265711879e-36 6.25160725664028e-34 4265 2195.54545454545 1573 3.31123265711877e-37 4 2.66973853213624 2.76652026013763 1 35.5999926696126 4265 1143 4612 4 221 4085 4714 1573 909 15 2610 1250 M2125 CHICAS_RB1_TARGETS_SENESCENT http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_SENESCENT.html Genes up-regulated in senescent IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 733/946 Arthur Liberzon 1.18561084220411e-09 1.89056864027142e-08 1480 1775.81818181818 1574 1.18561084283666e-10 182 1.88484128401677 1.90785179537786 1 5.80438978884722 1479 1109 4661 1398 1574 573 1840 1941 3022 182 1755 1251 M1666 BURTON_ADIPOGENESIS_9 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_9.html Strongly down-regulated at 8-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 129/142 John Newman 7.54551762088508e-08 6.16173757276429e-07 2100 1566.36363636364 1575 6.85956170879982e-09 166 2.0351383097326 2.20247323190445 1 5.03280869378819 2098 1553 1103 1852 166 1575 2981 1808 2067 707 1320 1252 M1131 DARWICHE_SKIN_TUMOR_PROMOTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SKIN_TUMOR_PROMOTER_UP.html Genes up-regulated during skin tumor progression: epidermis treated with the carcinogen DMBA [PubChem=6001] followed by 20 weekly applications of the tumor promoter TPA [PubChem=4792], compared to the untreated skin. 17525749 163/260 Arthur Liberzon 4.33263312088254e-07 1.02352494146975e-06 3750 2066.27272727273 1576 3.9387581583112e-08 476 2.27302792791371 2.41104352240498 1 5.42547957702391 3747 1480 892 777 1806 4116 3779 1394 476 1576 2686 1253 M6920 MCCLUNG_CREB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_CREB1_TARGETS_UP.html Genes up-regulated in the nucleus accumbens (a major reward center in the brain) 8 weeks after induction of CREB1 [GeneID=1385] expression in a transgenic Tet-Off system. 14566342 112/159 John Newman 2.67907762031319e-07 8.34119153553974e-07 2945 2153.36363636364 1576 2.4355254059648e-08 120 2.08821010444019 2.18863045706655 1 5.05490344686554 2941 1576 989 120 1268 2668 3353 4320 1312 1305 3835 1254 M19387 TCGA_GLIOBLASTOMA_MUTATED http://www.broadinstitute.org/gsea/msigdb/cards/TCGA_GLIOBLASTOMA_MUTATED.html Genes significantly mutated in 91 glioblastoma samples. 18772890 14/14 Arthur Liberzon 3.56770867691427e-07 9.41752134134615e-07 3455 2054.09090909091 1576 3.24337205044058e-08 16 3.06997338125256 -2.78223643822664 -1 7.38989471588135 3455 898 1209 170 1576 4695 4557 2686 16 2365 968 1255 M2235 BHAT_ESR1_TARGETS_VIA_AKT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_VIA_AKT1_DN.html Genes bound by ESR1 [GeneID=2099] and down-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer) expressing constitutevly active form of AKT1 [GeneID=207]. 18838536 108/125 Arthur Liberzon 8.78961600600051e-08 6.51622504172635e-07 2555 1869.45454545455 1576 7.99056032470025e-09 87 2.17040739901399 -2.06807883325525 -1 5.34944493950263 2555 87 999 1390 227 3311 3474 3926 1576 768 2251 1256 M5889 NABA_MATRISOME http://www.broadinstitute.org/gsea/msigdb/cards/NABA_MATRISOME.html Ensemble of genes encoding extracellular matrix and extracellular matrix-associated proteins 22159717 595/1178 Alexandra Naba 9.63058411728485e-50 3.78802975279871e-47 440 1632.18181818182 1576 9.63058411728478e-51 6 3.09913411248522 3.22185102989885 1 57.8076413955073 439 1128 4720 217 1883 1576 2800 1099 2284 6 1802 1257 M19708 KEGG_TYPE_II_DIABETES_MELLITUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYPE_II_DIABETES_MELLITUS.html Type II diabetes mellitus 46/67 KEGG 1.30519977804614e-07 7.20206492018647e-07 495 1606.27272727273 1577 1.18654532316371e-08 164 2.33138299288214 -1.74671619242097 -1 5.70916708144645 3110 492 1049 164 494 2941 3313 2280 2008 1577 241 1258 M11520 BIOCARTA_TPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TPO_PATHWAY.html TPO Signaling Pathway 37/42 BioCarta 3.56957511708647e-07 9.41752134134615e-07 1425 2049.09090909091 1577 3.24506881478395e-08 211 1.3293016843055 -1.26134681180361 -1 3.17146111547168 1424 3110 3482 211 1577 1375 975 1877 3058 4086 1365 1259 M18161 KORKOLA_YOLK_SAC_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_YOLK_SAC_TUMOR_UP.html Genes from the 12p region that were up-regulated in yolk sac tumor cells compared to normal testis. 16424014 31/42 Arthur Liberzon 4.38219379011596e-06 5.89724846678313e-06 535 1647.18181818182 1577 3.98382047187235e-07 178 2.69196342166871 2.95575684965571 1 5.6112810383164 535 3979 2011 2638 3433 327 214 1577 284 2943 178 1260 M3434 NIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLICON.html Genes within amplicon 17q11-q21 identified in a copy number alterations study of 191 breast tumor samples. 19010930 119/185 Jessica Robertson 1.7679234051488e-07 7.40425773939871e-07 1680 1704.09090909091 1577 1.60720322474493e-08 818 1.82751368183848 -1.74338465191518 -1 4.45562365848078 1677 1577 2366 2384 818 941 1095 1721 1565 3378 1223 1261 M966 REACTOME_N_GLYCAN_ANTENNAE_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_N_GLYCAN_ANTENNAE_ELONGATION.html Genes involved in N-Glycan antennae elongation 12/14 Reactome 5.71642535725793e-07 1.20368443390297e-06 1375 1491.63636363636 1578 5.19675167509113e-08 379 2.5095688589584 2.82178967769356 1 5.92421937216653 1374 952 1032 2566 2082 1578 1904 379 1659 1182 1700 1262 M3804 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP.html Genes up-regulated in normal hematopoietic progenitors by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 262/368 Arthur Liberzon 3.62284183445916e-09 5.18176165413552e-08 1615 1566 1579 3.29349258220459e-10 257 2.377343423006 2.58110055168018 1 6.91547867950339 1611 1325 257 791 1340 1579 3030 2530 2366 402 1995 1263 M4333 LUI_THYROID_CANCER_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_4.html Cluster 4: genes with similar expression profiles across follicular thyroid carcinoma (FTC) samples. 15608688 13/15 Leona Saunders 5.23250397333994e-07 1.13983544520085e-06 1535 1445.90909090909 1579 4.75682292531346e-08 217 2.50895100116224 2.36934155857387 1 5.94663211791385 1531 2416 1579 2591 1990 1082 239 1860 217 2168 232 1264 M13251 BROWNE_HCMV_INFECTION_14HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_14HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 14 h time point that were not down-regulated at the previous time point, 12 h. 11711622 388/510 John Newman 8.06729590038755e-08 6.29674606547497e-07 2130 1439.27272727273 1579 7.33390563291953e-09 188 2.12358811450045 2.27313228032454 1 5.24567697483291 2130 1225 750 594 188 1651 3337 1579 2064 492 1822 1265 M3362 MARKS_HDAC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARKS_HDAC_TARGETS_DN.html Genes whose transcription is down-regulated by histone deacetylase inhibitors. 17322921 18/23 Arthur Liberzon 2.54989040693129e-07 8.22657738941605e-07 2490 2049.45454545455 1580 2.31808245679465e-08 861 1.91078987466448 -1.96631141564296 -1 4.62579079263751 2490 861 1504 1481 1213 3303 2860 3552 2733 967 1580 1266 M11238 LINDGREN_BLADDER_CANCER_CLUSTER_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_3_DN.html Genes whose expression profile is specific to Cluster III of urothelial cell carcinoma (UCC) tumors. 16532037 315/375 Leona Saunders 7.53178471385127e-08 6.16173757276429e-07 3995 2206.09090909091 1581 6.84707724700439e-09 165 1.95650521810549 2.22689395026944 1 4.83641914976945 3994 1276 1333 592 165 4419 4277 2097 1581 1301 3232 1267 M8976 WATANABE_COLON_CANCER_MSI_VS_MSS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_COLON_CANCER_MSI_VS_MSS_DN.html Down-regulated genes discriminating between MSI (microsatellite instability) and MSS (microsatellite stability) colon cancers. 17047040 80/123 Leona Saunders 1.23353022967513e-07 7.12872631945934e-07 3725 1858.36363636364 1582 1.12139118076239e-08 223 2.65641710773935 2.69643471038944 1 6.5168460302197 3722 223 652 321 448 3102 3647 2866 332 1582 3547 1268 M11778 BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_DN.html Genes down-regulated in B lymphocytes from patients with primary immunodefiency syndrom. 17195838 74/103 Jessica Robertson 2.23447959664827e-07 7.84059768106575e-07 2505 1720.36363636364 1582 2.03134529418023e-08 617 2.30144661263645 -2.15821925611686 -1 5.60106973466147 2505 2621 1582 617 1071 2759 1544 751 933 2429 2112 1269 M1987 GYORFFY_DOXORUBICIN_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/GYORFFY_DOXORUBICIN_RESISTANCE.html Genes associated with resistance to doxorubicin [PubChem=31703]. 16044152 64/77 Arthur Liberzon 1.82411885708475e-07 7.47800341964416e-07 2440 1648.18181818182 1582 1.65829000757333e-08 338 2.9048800672756 2.78464566027498 1 7.10679854566103 2440 338 497 1582 849 2362 3119 2388 623 725 3207 1270 M1273 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1.html Cluster PAM1: genes up-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 307/408 Leona Saunders 1.59850102211423e-07 7.31918027928963e-07 4235 2352.54545454545 1584 1.45318285296359e-08 312 2.05909224510106 -1.81959857114602 -1 5.03072745229152 4235 1268 503 560 697 4650 3851 4073 1584 312 4145 1271 M2197 THILLAINADESAN_ZNF217_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/THILLAINADESAN_ZNF217_TARGETS_UP.html Genes bound and activated by ZNF217 [GeneID=7764] in MCF7 cells (breast cancer). 18625718 55/58 Arthur Liberzon 1.74630633676158e-07 7.37919956089047e-07 1585 1917.54545454545 1585 1.58755134125375e-08 398 1.57057120925999 1.65644951130495 1 3.82307233987502 1585 398 2813 2323 804 1379 965 4387 1101 2623 2715 1272 M8599 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by activated KRAS [GeneID=3845] vs those reverted to normal cells upon over-expression of a dominant negative form of CDC25 [GeneID=5923]. 16607279 64/102 Lauren Kazmierski 3.59518676186707e-07 9.41752134134615e-07 2470 1654.81818181818 1586 3.26835213580356e-08 317 2.05932929535264 1.70548502385131 1 4.94064769388809 2466 317 1151 383 1586 2040 2827 2868 582 1059 2924 1273 M2234 BHAT_ESR1_TARGETS_VIA_AKT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_VIA_AKT1_UP.html Genes bound by ESR1 [GeneID=2099] and up-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer) expressing constitutevly active form of AKT1 [GeneID=207]. 18838536 338/425 Arthur Liberzon 2.20602561336439e-07 7.7970890443293e-07 4580 2625.36363636364 1586 2.00547803142836e-08 673 1.97424373616252 2.03177095450065 1 4.79955536986907 4578 1256 905 1586 1054 4686 3966 4220 1261 673 4694 1274 M1504 RUAN_RESPONSE_TO_TROGLITAZONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TROGLITAZONE_UP.html Adipocyte abundant genes up-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591]. 12732648 33/38 John Newman 7.75263862400485e-06 9.78247753242543e-06 1375 1748.81818181818 1587 7.04787813079042e-07 385 1.50783737014914 -1.19567197026292 -1 2.98772641033397 1371 632 2655 2619 3683 1081 385 1345 1587 1953 1926 1275 M1557 DELASERNA_MYOD_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELASERNA_MYOD_TARGETS_UP.html Genes up-regulated in NIH 3T3 cells (fibroblasts) 24 h after inducing MyoD [GeneID=4654] differentiation program. 15870273 114/146 John Newman 2.3097066862933e-07 7.94929240715632e-07 2005 1585.72727272727 1587 2.09973357161977e-08 464 2.06302040969111 2.35463163224529 1 5.01066322699599 2004 1587 1691 847 1104 1085 3526 685 2325 2125 464 1276 M19618 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_UP http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_UP.html Hepatic graft versus host disease (GVHD), day 35: genes up-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 144/220 Arthur Liberzon 1.43282170186764e-07 7.24081202656879e-07 2485 1858.45454545455 1587 1.30256526834985e-08 335 2.26472768832321 -2.61744459499043 -1 5.54238644880526 2484 1503 466 1587 589 3369 3715 1221 2814 335 2360 1277 M19437 ALONSO_METASTASIS_NEURAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_NEURAL_UP.html Neural-related genes up-regulated in melanoma tumors that developed metastases compared to primary melanoma that did not. 17409456 25/34 Jessica Robertson 1.87435811872214e-06 2.86124525238308e-06 1440 1652.63636363636 1588 1.70396337785589e-07 776 1.96387891418796 -2.11729978164708 -1 4.32815779799734 1440 1821 1874 1399 3002 1588 808 2550 776 1091 1830 1278 M2613 ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF.html Class III of genes transiently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 305/365 Yaara Zwang 4.23370438565756e-10 7.21411000010963e-09 1590 1360.45454545455 1588 3.84882216952026e-11 215 2.35725790797052 -2.22854814479709 -1 7.66839523065508 1588 1282 215 563 315 1878 1721 2753 1694 259 2697 1279 M9160 ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN.html Genes down-regulated in BxPC3 cells (pancreatic cancer) after treatment with TNF [GeneID=7124] or IKI-1, an inhibitor of IkappaB kinase (IKK). 19010928 151/182 Jessica Robertson 2.03995782258619e-07 7.66608353710733e-07 1530 1761.09090909091 1589 1.85450728340184e-08 331 1.91491996253991 2.10380775762885 1 4.65949782153913 1526 2548 2036 2623 969 331 1239 3073 2054 1384 1589 1280 M3576 MCCLUNG_CREB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_CREB1_TARGETS_DN.html Genes down-regulated in the nucleus accumbens (a major reward center in the brain) 8 weeks after induction of CREB1 [GeneID=1385] expression in a transgenic Tet-Off system. 14566342 90/118 John Newman 1.65975958667541e-07 7.3358205358541e-07 3400 1995.63636363636 1589 1.5088724653579e-08 142 2.07668846353411 2.32135233445634 1 5.07332204845315 3398 142 871 390 736 3256 3448 2871 1589 870 4381 1281 M223 PID_BETA_CATENIN_NUC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BETA_CATENIN_NUC_PATHWAY.html Regulation of nuclear beta catenin signaling and target gene transcription 18832364 96/123 Pathway Interaction Database 1.33237733832504e-06 2.17907866836251e-06 1195 1546.63636363636 1591 1.21125285931652e-07 148 2.22697172836777 2.6696158805933 1 5.02062047231572 1194 2590 1365 2179 2773 1010 2257 257 1591 1649 148 1282 M7738 PYEON_HPV_POSITIVE_TUMORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_HPV_POSITIVE_TUMORS_UP.html Up-regulated genes in cervical carcinoma and head and neck tumors positive for human papilloma virus (HPV) compared to those negative for HPV. 17510386 105/125 Arthur Liberzon 1.49600263954721e-06 2.3829386200726e-06 700 1798.45454545455 1591 1.36000332439252e-07 108 1.64356306404344 1.74328577653843 1 3.66656771717886 698 108 2955 2831 2861 1497 1478 2056 2584 1591 1124 1283 M556 REACTOME_TERMINATION_OF_O_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TERMINATION_OF_O_GLYCAN_BIOSYNTHESIS.html Genes involved in Termination of O-glycan biosynthesis 10/22 Reactome 5.67851704062092e-06 7.3872821002858e-06 2700 1871.27272727273 1594 5.16230154340427e-07 261 2.88696596231112 -3.23075272705492 -1 5.90779063594072 2700 1960 1455 1594 3559 2020 261 1437 1046 1151 3401 1284 M15343 REACTOME_ACTIVATED_TLR4_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_TLR4_SIGNALLING.html Genes involved in Activated TLR4 signalling 104/124 Reactome 3.28984119366552e-07 9.05922275783096e-07 1595 2063.18181818182 1594 2.99076516874789e-08 1064 1.67605003483462 -1.8620039570123 -1 4.02314366832363 1064 3007 3295 2013 1493 1591 1225 1252 3143 3018 1594 1285 M12605 CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN.html Genes specifically down-regulated in pediadric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490]. 12704389 19/25 Jean Junior 0.000196519647725184 0.000211388499832012 1240 2249 1594 1.78670185866848e-05 93 2.17714310874048 2.37530366519227 1 3.16758732934999 1236 4045 3037 4209 4430 482 542 1594 994 4077 93 1286 M523 KEGG_THYROID_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_THYROID_CANCER.html Thyroid cancer 36/43 KEGG 3.53893728573632e-06 4.89559905881461e-06 1575 1785.27272727273 1595 3.21722088955588e-07 88 2.55606390260942 3.39868308928026 1 5.40858156799744 1573 3106 1595 894 3339 2141 3169 135 88 3177 421 1287 M12898 REACTOME_GAP_JUNCTION_TRAFFICKING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_TRAFFICKING.html Genes involved in Gap junction trafficking 16/27 Reactome 2.28724498619955e-07 7.89743696771168e-07 4110 2584.72727272727 1595 2.07931383999506e-08 689 2.82565638512876 -1.82007579353503 -1 6.88468034228504 4107 877 1016 1595 1096 4305 4450 4418 689 1225 4654 1288 M16033 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_8.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 8. 12554760 63/77 Arthur Liberzon 9.98601015628618e-08 6.71132834037269e-07 2345 1661.36363636364 1595 9.07819146323702e-09 308 2.28424282971033 2.24817475976032 1 5.62087178425587 2341 2196 1501 1185 308 2762 2878 1873 520 1595 1116 1289 M4629 KEGG_NITROGEN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NITROGEN_METABOLISM.html Nitrogen metabolism 16/23 KEGG 2.54684112136038e-06 3.69084743408689e-06 3500 1990.54545454545 1597 2.31531279066242e-07 765 2.6066722636599 -3.25594027205615 -1 5.6452642045811 3500 875 1200 1387 3176 3646 2531 1710 765 1509 1597 1290 M34 PID_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_PATHWAY.html TCR signaling in naïve CD4+ T cells 18832364 66/94 Pathway Interaction Database 9.71456123804271e-08 6.64473403617636e-07 1705 1360.18181818182 1597 8.83141969728142e-09 283 1.84172306410631 -1.55344838282221 -1 4.52547072958953 1702 283 1848 454 293 2038 1170 564 1597 1840 3173 1291 M15912 HAMAI_APOPTOSIS_VIA_TRAIL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAMAI_APOPTOSIS_VIA_TRAIL_DN.html Genes down-regulated in T1 cells (primary melanoma, sensitive to TRAIL [GeneID=8743]) compared to G1 cells (metastatic melanoma, resistant to TRAIL). 16983347 213/337 Leona Saunders 1.98224785402604e-07 7.65527859584926e-07 2120 1662.36363636364 1599 1.8020436660281e-08 676 2.20067054267496 2.45344857071604 1 5.36281205838889 2119 1389 712 1599 929 2198 3864 1310 1697 676 1793 1292 M1972 MIKKELSEN_IPS_LCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_LCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the bivalent tri-methylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 8/17 Jessica Robertson 0.000301805373446695 0.000322217001282153 1600 2337.81818181818 1599 3.0184637020072e-05 1116 3.97527944976854 4.25071360428128 1 5.53240315889362 1599 2909 4626 3076 4397 1444 1586 1116 1560 2072 1331 1293 M11725 REACTOME_CD28_CO_STIMULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CD28_CO_STIMULATION.html Genes involved in CD28 co-stimulation 35/41 Reactome 1.04585359668911e-07 6.87524927071391e-07 2455 1844.81818181818 1600 9.50776042188853e-09 194 1.47010935521026 -1.41961567685598 -1 3.59349103705019 2453 621 2823 194 327 1600 1204 4045 1301 2472 3253 1294 M14507 CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN.html Genes down-regulated in luminal-like breast cancer cell lines compared to the basal-like ones. 16288205 644/782 Arthur Liberzon 5.05615295871501e-17 2.15000378064278e-15 2280 1925.09090909091 1600 5.05615295871502e-18 66 2.26908546040366 2.5170664386776 1 13.3346863139873 2276 1121 4293 271 386 2730 4318 1600 1456 66 2659 1295 M9834 DORN_ADENOVIRUS_INFECTION_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_24HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 24 h after infection with adenovirus Ad12. 15681441 19/21 Arthur Liberzon 1.80316484236661e-05 2.13627963252269e-05 2025 1737.90909090909 1602 1.63925420149344e-06 22 3.20648884179584 3.53437920536002 1 5.97249407685901 2025 2816 1225 1589 3923 1602 948 1783 22 1645 1539 1296 M1754 ZHENG_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_DN.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are down-regulated both in developing (located in the thymus) and mature (from peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 9/11 Jessica Robertson 3.31465858037458e-07 9.06126045087621e-07 3685 1924 1604 3.31465907478795e-08 60 2.44626227810911 -2.73385826409018 -1 5.89483761057845 3684 991 4521 116 1604 3774 3156 74 60 2322 862 1297 M2055 DAZARD_UV_RESPONSE_CLUSTER_G28 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G28.html Cluster G28: genes differentially up-regulated in NHEK (normal keratinocyte) compared to SCC12B2 cells (squamous cell carcinoma) by UV-B radiation. 12771951 27/41 Arthur Liberzon 1.20173745012599e-05 1.46720143936748e-05 970 2095 1604 1.09249455872587e-06 969 2.57006171290135 -2.60618920043413 -1 4.94578361123097 969 2785 1604 1536 3810 1115 1080 2402 4172 2113 1459 1298 M15569 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY.html NOD-like receptor signaling pathway 56/72 KEGG 1.69649073132863e-06 2.6409750171079e-06 195 1653.36363636364 1605 1.54226549049872e-07 193 2.03968187150128 -2.21037872635384 -1 4.52568820577267 193 2658 1977 2950 2935 411 416 639 3721 1605 682 1299 M19508 HATADA_METHYLATED_IN_LUNG_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/HATADA_METHYLATED_IN_LUNG_CANCER_UP.html Genes with hypermethylated DNA in lung cancer samples. 16407832 450/744 Arthur Liberzon 1.88802058704866e-14 5.78666050056471e-13 2410 1573.63636363636 1605 1.71638235186243e-15 111 2.38521694507251 2.74401523698761 1 11.6887654399013 2410 1188 111 1569 955 1650 3618 2010 1605 277 1917 1300 M15913 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY.html RIG-I-like receptor signaling pathway 56/79 KEGG 2.84340061004174e-06 4.05218927518025e-06 385 1476.72727272727 1606 2.58491298637747e-07 344 1.84793666181049 -2.05628238076328 -1 3.957362051195 382 2214 2170 3106 3239 365 371 344 1832 1606 615 1301 M10880 STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN.html Down-regulated genes classifying non-tumor lung tissues by age after incution of lung cancer by urethane injection [PubChem=5641]: early (24-26 weeks) vs late (46 weeks). 18172294 70/107 Jessica Robertson 3.34085478177136e-08 3.81811975059584e-07 2045 1801.09090909091 1607 3.03714075682234e-09 17 2.19269329790891 2.03519597236519 1 5.60959800102883 2043 296 1425 1784 17 1607 2101 4685 1449 1405 3000 1302 M2351 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN.html Genes down-regulated in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 430/516 Arthur Liberzon 6.67375687281597e-10 1.10915959294688e-08 4050 2155.45454545455 1608 6.06705170440042e-11 172 1.91591690013589 2.099792192564 1 6.07936096265741 4050 1191 729 923 378 4012 4465 2716 1608 172 3466 1303 M2285 CHENG_TAF7L_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CHENG_TAF7L_TARGETS.html Genes down-regulated in testis tissues upon knockout of TAF7L [GeneID=54457]. 17242199 8/8 Arthur Liberzon 7.22171816955875e-06 9.18031504452391e-06 1900 1708.09090909091 1610 7.22174163861209e-07 69 2.74146410599102 3.7972073647449 1 5.50347141834124 1896 1974 4679 561 3691 1610 960 407 69 2671 271 1304 M12899 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GLOBO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GLOBO_SERIES.html Glycosphingolipid biosynthesis - globo series 10/15 KEGG 2.96818596564082e-07 8.70294688256627e-07 1615 1608.72727272727 1613 2.69835124191023e-08 604 2.23027881399374 -2.23317400606482 -1 5.38567370928732 1613 1953 2021 3296 1375 1325 877 604 1858 2004 770 1305 M9556 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_DN.html Genes down-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 184/308 John Newman 2.13856867102511e-07 7.7139268662581e-07 2995 1786.81818181818 1613 1.9441535262822e-08 521 1.98051817657226 2.13352064759453 1 4.81867732502539 2991 1432 950 1613 1025 2299 3587 521 2189 911 2137 1306 M14238 BALLIF_DEVELOPMENTAL_DISABILITY_P16_P12_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/BALLIF_DEVELOPMENTAL_DISABILITY_P16_P12_DELETION.html Candidate genes in the pericentromeric microdeletion in 16p11.2-p12.2 associated with developmental disabilities. 17704777 21/28 Leona Saunders 1.62980489351265e-05 1.94505160490005e-05 1615 1658.09090909091 1614 1.48165178869555e-06 83 2.86098455710331 -3.21601770795656 -1 5.37041630193665 1614 3173 1402 2048 3896 1626 1397 409 83 1617 974 1307 M9138 CHANG_POU5F1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_POU5F1_TARGETS_UP.html Genes up-regulated by POU5F1 [GeneID=5460] in bladder cancer cell lines. 18676852 33/36 Jessica Robertson 6.37236759552038e-05 7.11053783708185e-05 510 1790.54545454545 1615 5.79322925508267e-06 508 2.70949726223633 2.94638751957264 1 4.46996175326827 508 2280 639 1268 4177 1615 2820 2479 1728 888 1294 1308 M19727 NIELSEN_LIPOSARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LIPOSARCOMA_DN.html Top 20 negative significant genes associated with liposarcomas, versus other soft-tissue tumors. 11965276 26/28 John Newman 1.38246046699783e-06 2.24465545381141e-06 1615 1632.27272727273 1615 1.2567830324768e-07 416 2.1615894640151 2.2639673489425 1 4.86055577363154 1615 2330 1773 1862 2794 1276 1158 416 2390 1410 931 1309 M16458 RIZ_ERYTHROID_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION.html Selected gradually up-regulated genes in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 93/104 Leona Saunders 5.64088004530915e-07 1.19180634797937e-06 550 1639.54545454545 1616 5.12807408331984e-08 245 1.31822971031651 1.41780119104518 1 3.09041164490875 550 1616 3757 2912 2072 245 445 599 2693 2842 304 1310 M15412 OSAWA_TNF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OSAWA_TNF_TARGETS.html Genes up-regulated in Hc cells (normal hepatocyte) by TNF [GeneID=7124]. 12682234 26/29 Yujin Hoshida 2.46692137780865e-05 2.86794800572828e-05 705 1954.54545454545 1616 2.24268094592779e-06 544 3.43113251372316 3.50513603001388 1 6.21792356119397 703 2771 544 1287 4322 1831 2699 3192 1616 998 1537 1311 M2621 ZWANG_EGF_PERSISTENTLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_PERSISTENTLY_DN.html Genes persistently repressed by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 83/110 Yaara Zwang 6.02307332570871e-08 5.6744323547595e-07 4185 2174.54545454545 1619 5.4755213550964e-09 86 2.30563516064971 -1.98727861524509 -1 5.74156356237956 4183 1619 916 1395 86 4648 4068 2094 659 862 3390 1312 M648 BIOCARTA_G1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G1_PATHWAY.html Cell Cycle: G1/S Check Point 34/39 BioCarta 4.94486170326462e-07 1.10573202865232e-06 1620 1413.54545454545 1620 4.49532983154903e-08 157 1.87155740681557 2.10085354622058 1 4.4331206158374 1401 574 1831 641 1935 1620 1617 1858 157 1823 2092 1313 M12621 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP.html Genes up-regulated in Wilm's tumor samples compared to fetal kidney. 12057921 277/342 Kevin Vogelsang 1.76345562098614e-09 2.70959048908326e-08 4510 2158 1621 1.6031414749088e-10 84 2.2563171582912 2.40053622064119 1 6.81637806759764 4510 1289 237 84 644 4566 3427 4006 1621 256 3098 1314 M16355 BIOCARTA_NKCELLS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NKCELLS_PATHWAY.html Ras-Independent pathway in NK cell-mediated cytotoxicity 41/65 BioCarta 2.51407577538568e-07 8.19318755885969e-07 625 1749.72727272727 1622 2.28552369334971e-08 531 1.26390633820498 -1.16544359211662 -1 3.04372220951637 625 531 3168 1097 1199 852 1738 1647 3924 2844 1622 1315 M18635 CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN.html Genes down-regulated in APL (acute promyeolocytic leukemia) blasts expressing PML-RARA fusion [GeneID=5371;5914] compared to normal promyeloblasts. 16990782 874/1119 Leona Saunders 3.37573242263609e-07 9.13746684768849e-07 730 1857.63636363636 1622 3.37573293543682e-08 728 1.70854891925339 1.7813046357065 1 4.09955703026471 728 1097 4289 904 1626 1144 1088 1622 2150 3524 2262 1316 M19457 GRABARCZYK_BCL11B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRABARCZYK_BCL11B_TARGETS_DN.html Genes down-regulated in Jurkat cells (transformed T lymphocytes) after knockdown of BCL11B [GeneID=64919] by RNAi. 17173069 61/97 Arthur Liberzon 3.48381301613486e-07 9.30654820258927e-07 1720 1908 1622 3.16710324346788e-08 1053 2.23357728819948 2.21564023301629 1 5.3675534918712 1718 1673 1602 1053 1547 1535 1622 3395 1615 2003 3225 1317 M17454 MASSARWEH_TAMOXIFEN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MASSARWEH_TAMOXIFEN_RESISTANCE_UP.html Genes up-regulated in breast cancer tumors (formed by MCF-7 xenografts) resistant to tamoxifen [PubChem=5376]. 18245484 763/965 Jessica Robertson 5.5034169651355e-08 5.38923818992522e-07 2200 1716.81818181818 1622 5.50341710142968e-09 247 1.96173510615204 -1.88168175913124 -1 4.89537793936552 2200 1103 4538 533 666 1622 2483 2095 1610 247 1788 1318 M16026 VERRECCHIA_RESPONSE_TO_TGFB1_C1 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C1.html Cluster 1: ECM related genes up-regulated in dermal fibroblasts within 30 min after TGFB1 [GeneID=7040] addition, and which kept increasing with time. 11279127 58/82 John Newman 4.16748904751876e-07 1.00504816968881e-06 1880 1461.90909090909 1624 3.78862712451992e-08 349 2.49627695420858 2.7855999513153 1 5.97120856093292 1879 1681 917 468 1763 2075 3045 699 349 1581 1624 1319 M1985 KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS http://www.broadinstitute.org/gsea/msigdb/cards/KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS.html Inflammatory cytokines and their receptors modulated in brain tumors after treatment with an oncocytic virus, a potential anticancer therapy. 18042934 27/57 Jessica Robertson 7.25770568252546e-07 1.40279978794104e-06 950 1937.63636363636 1625 6.59791643346596e-08 767 3.07708783461716 -3.62857338941402 -1 7.19297793763828 946 2780 767 3662 2296 1754 1346 924 3938 1276 1625 1320 M1135 DARWICHE_PAPILLOMA_RISK_HIGH_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_UP.html Genes up-regulated during skin tumor progression from normal skin to high risk papilloma. 17525749 151/262 Arthur Liberzon 1.45044923960902e-07 7.26289540930751e-07 1965 1689.09090909091 1626 1.3185903047604e-08 597 2.14021478291797 2.1548180719365 1 5.23378119301838 1961 1505 1257 1626 597 1868 3101 875 1196 2130 2464 1321 M1202 TERAMOTO_OPN_TARGETS_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_6.html Cluster 6: genes exhibiting prolonged up-regulation (>72 h) after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 38/44 Arthur Liberzon 5.55204015562444e-07 1.18470296268297e-06 1625 1608.90909090909 1626 5.04731050615283e-08 575 2.07089086353397 2.11340587149118 1 4.88565575777308 1625 575 1626 2309 2052 984 1938 759 2312 2231 1287 1322 M1805 WILLERT_WNT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/WILLERT_WNT_SIGNALING.html Genes up-regulated in NCCIT cell line (embryonic teratocarcinoma) after stimulation with WNT3A [GeneID=89780]. 12095419 36/43 Yujin Hoshida 2.58280309646127e-06 3.73493585027488e-06 1050 1741.09090909091 1626 2.34800557152793e-07 134 2.36499775533568 2.90357154599454 1 5.11232620143906 1049 2735 2106 2185 3183 1359 1626 134 653 3178 944 1323 M6951 ELLWOOD_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELLWOOD_MYC_TARGETS_DN.html Genes down-regulated in transgenic mice expressing human MYC [GeneID=4609] in prostate. 14522256 55/73 Arthur Liberzon 2.55596393842909e-05 2.9663510669745e-05 890 1978.27272727273 1626 2.32363057649717e-06 887 1.97467273808953 -1.80370705920537 -1 3.54564135842484 887 3061 2100 2412 4012 1469 1137 913 1282 2862 1626 1324 M12596 SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_DN.html Genes down-regulated in prostate cancer samples bearing the fusion of TMPRSS2 with ERG [GeneID=7113;2078]. 18505969 15/42 Jessica Robertson 3.85732512672886e-06 5.27421048614143e-06 2100 1674.54545454545 1628 3.50666535446163e-07 121 2.57749774216654 2.39486707278438 1 5.42082000426981 2096 1909 1491 1791 3380 1765 1281 1628 121 1357 1601 1325 M209 PID_P38_GAMMA_DELTA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_GAMMA_DELTA_PATHWAY.html Signaling mediated by p38-gamma and p38-delta 18832364 12/12 Pathway Interaction Database 5.37658190572659e-08 5.28532953829642e-07 4145 2100.36363636364 1629 4.88780185193176e-09 69 1.9954102567742 -1.81833717324726 -1 4.98705614409905 4143 938 1629 586 69 4186 3019 3264 89 1546 3635 1326 M5301 KONDO_EZH2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_EZH2_TARGETS.html Genes up-regulated in PC3 cells (prostate cancer) after EZH2 [GeneID=2146] knockdown by RNAi. 18488029 276/457 Jessica Robertson 1.15939720938644e-08 1.49517891483715e-07 2115 1623.90909090909 1629 1.05399746863313e-09 288 2.36124950811485 2.68608100023476 1 6.43130149002024 2113 1305 288 386 1629 2558 3849 1680 1624 341 2090 1327 M63 PID_AVB3_OPN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AVB3_OPN_PATHWAY.html Osteopontin-mediated events 18832364 48/54 Pathway Interaction Database 3.72380909866058e-07 9.56797982889382e-07 595 1403.36363636364 1630 3.38528157178886e-08 441 1.83709339246624 -1.84216062138568 -1 4.39698405020937 594 2246 2251 1745 1630 484 441 646 2047 2712 641 1328 M18085 LIANG_SILENCED_BY_METHYLATION_2 http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_SILENCED_BY_METHYLATION_2.html Genes up-regulated in T24 cells (bladder carcinoma) after treatment with decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 11861364 65/108 John Newman 9.94702019106584e-07 1.74397258284237e-06 1125 1827.09090909091 1630 9.0427497168067e-08 467 2.85775647656388 -2.8479538093052 -1 6.56804648180796 1125 2189 467 1630 2565 1442 922 3946 3134 675 2003 1329 M5493 WNT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/WNT_SIGNALING.html Genes related to Wnt-mediated signal transduction 98/137 SuperArray 3.73077750725611e-07 9.57025534470045e-07 2635 1839.45454545455 1634 3.39161649084043e-08 214 2.30800726563062 3.07042796374346 1 5.53682152140859 2633 1606 1442 1694 1634 3055 4279 740 674 2263 214 1330 M2144 DEMAGALHAES_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/DEMAGALHAES_AGING_UP.html Genes consistently overexpressed with age, based on meta-analysis of microarray data. 19189975 85/116 Joao Pedro de Magalhaes 2.28353363056656e-06 3.38939582901703e-06 665 2093.72727272727 1634 2.07594181891729e-07 664 2.05312677510771 -2.17631911919887 -1 4.46637987283681 664 2157 1361 3668 3103 1634 1618 1598 3764 1586 1878 1331 M14614 SAKAI_TUMOR_INFILTRATING_MONOCYTES_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_TUMOR_INFILTRATING_MONOCYTES_UP.html Selected genes up-regulated in inflammatory monocytes infiltrating hepatocellular carcinoma (HCC). 19074895 42/47 Jessica Robertson 2.36500924032724e-06 3.48729884859249e-06 1730 1547.90909090909 1635 2.15001071156903e-07 148 2.27903696059647 2.89321233521685 1 4.95199670941625 1726 536 1657 1635 3125 1197 2271 1606 148 2659 467 1332 M1491 LY_AGING_PREMATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_PREMATURE_DN.html Genes down-regulated in fibroblasts from patients with Hutchinson-Gilford progeria (premature aging), compared to those from normal young individuals. 10741968 42/57 Arthur Liberzon 9.69545008095688e-07 1.71547240614811e-06 480 1652.54545454545 1636 8.81404941251493e-08 143 1.8683683231196 1.78275663076923 1 4.28216667583298 478 2698 1914 2406 2545 276 143 1038 4067 1636 977 1333 M7409 MODY_HIPPOCAMPUS_NEONATAL http://www.broadinstitute.org/gsea/msigdb/cards/MODY_HIPPOCAMPUS_NEONATAL.html Genes highly expressed in the neonatal hippocampus (clusters 4 and 8). 11438693 69/85 John Newman 6.91137105612297e-06 8.80714670218694e-06 815 1745.72727272727 1636 6.2830843350126e-07 690 2.51954319546513 2.7650308117961 1 5.07217752834146 813 2624 690 898 3644 1465 1979 2848 1636 962 1644 1334 M11064 HALMOS_CEBPA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HALMOS_CEBPA_TARGETS_UP.html Genes up-regulated in H358 cells (lung cancer) by inducible expression of CEBPA [GeneID=1050] off plasmid vector. 15205324 77/99 Kevin Vogelsang 1.70311270073056e-07 7.33971845416521e-07 2745 1744 1637 1.54828439325064e-08 498 2.96237846341924 -2.61556143790559 -1 7.25811641263195 2744 1637 498 613 775 1873 1192 4674 2048 635 2495 1335 M11548 AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_8G http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_8G.html Genes with basal expression distinguishing NCI-60 cell lines with poor survival after 8 Gy gamma irradiation. 18199535 134/152 Jessica Robertson 5.41926926249043e-07 1.16639083077769e-06 2090 1689.72727272727 1637 4.92660963401978e-08 930 1.89001819803949 2.08039802564879 1 4.45971213203823 2089 1540 1637 1189 2029 1677 2730 1134 2337 1295 930 1336 M13618 REACTOME_CD28_DEPENDENT_VAV1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CD28_DEPENDENT_VAV1_PATHWAY.html Genes involved in CD28 dependent Vav1 pathway 17/22 Reactome 8.58839832825756e-07 1.57310167253419e-06 1640 1613.36363636364 1639 7.80763789183026e-08 130 1.96601642139476 -1.67911651342468 -1 4.5383342576845 1639 883 1902 473 2447 1118 417 3574 130 2044 3120 1337 M1711 DASU_IL6_SIGNALING_SCAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_SCAR_DN.html Genes down-regulated in hypertrophic scar fibroblasts in response to IL6 [GeneID=3569]. 15095275 28/34 John Newman 1.54142182857775e-07 7.28175281873995e-07 3080 1974 1640 1.40129266961537e-08 658 2.95779011936933 3.04173939599482 1 7.25089305996292 3079 736 1060 1212 658 3506 3999 1729 1403 1640 2692 1338 M9726 KEGG_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PANCREATIC_CANCER.html Pancreatic cancer 83/90 KEGG 1.46275192627085e-07 7.26289540930751e-07 1645 1498.09090909091 1641 1.32977456684306e-08 200 1.71518649657062 -1.57184733048025 -1 4.18446021699763 1641 231 2422 200 605 1691 1009 3053 926 2911 1790 1339 M18 PID_INTEGRIN1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN1_PATHWAY.html Beta1 integrin cell surface interactions 18832364 79/86 Pathway Interaction Database 3.59237028652277e-11 7.09455554493199e-10 170 1696.72727272727 1642 3.26579116961948e-12 168 2.97126931739073 2.93836205118836 1 10.8824720153587 168 2152 184 776 4155 1431 2119 2747 2983 307 1642 1340 M10183 BIOCARTA_RELA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RELA_PATHWAY.html Acetylation and Deacetylation of RelA in The Nucleus 19/19 BioCarta 1.08031589525183e-06 1.85691588695872e-06 270 1354.90909090909 1643 9.82105841585647e-08 120 1.72613568006378 -1.78331665659087 -1 3.9284845786575 268 2373 2678 1707 2624 235 120 268 1938 1643 1050 1341 M48 PID_MET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MET_PATHWAY.html Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met) 18832364 101/111 Pathway Interaction Database 1.71994390079046e-07 7.36005005596643e-07 1555 2011 1643 1.56358548659494e-08 677 1.43719816119174 -1.3264310041131 -1 3.49481978241828 1553 3011 3647 677 787 1643 1263 1879 1076 4441 2144 1342 M18532 KIM_MYCN_AMPLIFICATION_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCN_AMPLIFICATION_TARGETS_UP.html Genes positively correlated with amplifications of MYCN [GeneID=4613] in the SCLC (small cell lung cancer) cell lines. 16116477 122/163 Arthur Liberzon 1.53250283343547e-07 7.28175281873995e-07 2715 1952 1644 1.39318449108039e-08 648 2.02122695326429 2.1605413287757 1 4.93910552356765 2711 1570 1414 1034 648 2879 4386 1644 1265 1686 2235 1343 M1484 IGLESIAS_E2F_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IGLESIAS_E2F_TARGETS_UP.html Genes up-regulated in pancreatic cells from mice with double knockout of E2F1 [GeneID=1869] and E2F2 [GeneID=1870] compared to wild type. 15146237 217/271 Kevin Vogelsang 8.90972608939337e-07 1.61749143019345e-06 545 1520.09090909091 1646 8.09975427065777e-08 418 2.23985996407762 2.37104999337169 1 5.16655560945398 542 2058 418 854 2476 1157 2069 1646 3036 706 1759 1344 M7761 KEGG_MELANOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOGENESIS.html Melanogenesis 86/110 KEGG 4.35785800178605e-07 1.02591716789194e-06 2600 1845.18181818182 1647 3.96168987728201e-08 191 2.13292260151811 2.25119295260864 1 5.08710896269778 2599 191 1393 456 1811 2516 4598 3217 503 1647 1366 1345 M2288 BIOCARTA_NFAT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NFAT_PATHWAY.html NFAT and Hypertrophy of the heart (Transcription in the broken heart) 72/91 BioCarta 2.01679198616403e-07 7.65527859584926e-07 2105 1596.90909090909 1647 1.83344742822558e-08 490 2.0656710073707 2.28139036042967 1 5.03076229602917 2104 1647 1698 490 952 1904 2873 905 554 3924 515 1346 M9464 WONG_ENDOMETRIAL_CANCER_LATE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ENDOMETRIAL_CANCER_LATE.html Genes down-regulated in late stage (stage 3) endometrial cancers compared to the earlier stages (stage 1 and 2). 17043662 13/28 Arthur Liberzon 4.54847753525734e-05 5.15333988632132e-05 1650 1909.27272727273 1647 4.13506507026179e-06 334 3.51154239243075 4.41125915684867 1 6.00538398627973 1647 2873 927 2269 4193 1127 708 334 3826 1359 1739 1347 M3340 PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP.html Genes up-regulated in CD38+ [GeneID=952] CLL (chronic lymphocytic leukemia) cells. 17287849 39/87 Arthur Liberzon 3.76545294136504e-08 4.20164016152317e-07 2970 1651.90909090909 1648 3.42313909619398e-09 25 2.68011715092949 -3.04478116494433 -1 6.82289918999132 2968 470 316 65 25 3086 1708 4632 1648 458 2795 1348 M2412 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_6 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_6.html Genes regulated in MCF7 cells (breast cancer) by expression of the full-length form of ERBB2 [GeneID=2064] at 60 h time point. 19364815 36/65 Arthur Liberzon 9.13695931522251e-07 1.64103683287101e-06 1775 1468.63636363636 1649 8.30633009995742e-08 675 3.12041615526906 3.15763717067678 1 7.20947857766215 733 1771 675 1775 2505 1043 1540 1649 1726 797 1941 1349 M1748 ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_UP.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are up-regulated only in mature (peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 11/14 Jessica Robertson 2.58306295528704e-07 8.26284126785448e-07 1650 1770.36363636364 1650 2.34823932597232e-08 377 1.43382095598084 1.59216057148757 1 3.45751512379649 1650 2428 2696 3352 1224 1125 377 1027 3076 1766 753 1350 M18415 REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE.html Genes involved in Sema4D induced cell migration and growth-cone collapse 35/48 Reactome 6.16519942938572e-08 5.75735672118533e-07 3905 2128.36363636364 1652 5.60472691105185e-09 92 2.20452833419387 2.39553044462748 1 5.48200393410043 3903 593 1517 168 92 4178 4477 2199 203 1652 4430 1351 M9128 KIM_WT1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_UP.html Genes up-regulated in UB27 cells (osteosarcoma) at any time point after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 289/336 Arthur Liberzon 8.52858434036419e-08 6.48443648357969e-07 3260 2030.45454545455 1652 7.75325879180527e-09 208 2.06623454924319 2.45926280232561 1 5.09205130129345 3258 2036 730 1652 208 3945 4045 1385 1547 867 2662 1352 M12027 RODRIGUES_NTN1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_NTN1_TARGETS_UP.html Genes up-regulated in HCT8/S11 cells (colon cancer) engineered to stably express NTN1 [GeneID=1630] off a plasmid vector. 17334389 35/43 Arthur Liberzon 3.78527925110892e-06 5.19526550312128e-06 835 1556.54545454545 1653 3.44116887636907e-07 236 2.22193361336736 2.19289654636109 1 4.67197150041036 833 2717 1642 1846 3369 737 2051 236 1706 1653 332 1353 M1725 LEIN_LOCALIZED_TO_DISTAL_AND_PROXIMAL_DENDRITES http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_LOCALIZED_TO_DISTAL_AND_PROXIMAL_DENDRITES.html Transcripts showing subcellular localization to both distal and proximal dendrites in the adult mouse brain. 17151600 29/31 Jessica Robertson 1.02629127432546e-06 1.78531198550712e-06 2810 1783.54545454545 1653 9.32992502805987e-08 626 2.32268878495449 -1.58249770663914 -1 5.31941571192631 2810 718 1411 1013 2589 2853 1653 1966 626 898 3082 1354 M1009 REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT.html Genes involved in Endosomal Sorting Complex Required For Transport (ESCRT) 29/32 Reactome 3.78845798550168e-07 9.60855544952602e-07 350 2102.27272727273 1654 3.44405330716753e-08 80 0.859106873227377 -0.818642096181163 -1 2.02895347800363 346 3734 3912 4052 1654 159 80 124 4463 4396 205 1355 M54 PID_IL12_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL12_2PATHWAY.html IL12-mediated signaling events 18832364 65/119 Pathway Interaction Database 1.08900241379839e-06 1.8677657678519e-06 395 1659.36363636364 1657 9.90002684414686e-08 395 1.52497462490951 -1.32978335180183 -1 3.46328237610364 395 1657 2460 1523 2631 446 518 959 4178 1739 1747 1356 M12313 KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_UP.html Genes up-regulated in MEWO cells (melanoma) after 96 h of methionine [PubChem=876] deprivation. 16908595 147/191 Arthur Liberzon 3.81163740621665e-07 9.64463514816902e-07 1785 1521.63636363636 1657 3.4651255150971e-08 431 2.10511003492243 2.28337858157551 1 5.04283353254371 1784 2092 1133 1727 1657 762 2942 1382 1856 972 431 1357 M15626 OUYANG_PROSTATE_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUYANG_PROSTATE_CANCER_PROGRESSION_UP.html Genes up-regulated during prostate cancer progression in mice heterozygotic for both NKX3.1 and PTEN [GeneID=4824;5728]. 18381418 26/29 Jessica Robertson 2.75220819068568e-07 8.38703759494626e-07 605 2005.54545454545 1657 2.50200775908e-08 425 1.46280112764674 -1.47530279903024 -1 3.52459765050344 601 3742 3072 2505 1301 645 425 1140 3623 3350 1657 1358 M11159 SMID_BREAST_CANCER_RELAPSE_IN_LIVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LIVER_UP.html Genes up-regulated in liver relapse of breast cancer. 18451135 5/6 Jessica Robertson 2.41011535465231e-06 3.53503557301396e-06 1640 1945.18181818182 1661 2.41011796855151e-07 550 5.34236294581517 -5.65105325948016 -1 11.6627033247236 1640 1055 4549 2773 3202 1499 620 550 1661 1788 2060 1359 M2287 CHANGOLKAR_H2AFY_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANGOLKAR_H2AFY_TARGETS_UP.html Genes up-regulated in liver tissue upon knockout of H2AFY [GeneID=9555]. 17242180 67/73 Arthur Liberzon 1.41244555635513e-07 7.20206492018647e-07 1090 1804.90909090909 1662 1.28404149730642e-08 573 1.6141578192159 -1.56960760670791 -1 3.93740916641604 1088 1662 3015 3121 573 969 1018 1975 2215 2957 1261 1360 M1315 SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES.html Genes related to PIP3 signaling in B lymphocytes 46/60 Signaling Gateway 3.30691181410638e-07 9.06126045087621e-07 1945 1972.90909090909 1663 3.00628391925654e-08 486 1.59390937624888 -1.69162938366601 -1 3.82346067067627 1943 486 2473 1273 1500 2833 1663 873 3979 3059 1620 1361 M12170 AMIT_EGF_RESPONSE_480_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_480_MCF10A.html Genes whose expression peaked at 480 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 50/56 Leona Saunders 8.84475496152861e-08 6.51764353986912e-07 2170 1760.36363636364 1663 8.04068665192554e-09 231 2.05619994133603 2.47707750460288 1 5.06524447833089 2166 2669 1553 1663 231 2382 3457 1088 1245 1709 1201 1362 M9630 KOMMAGANI_TP63_GAMMA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KOMMAGANI_TP63_GAMMA_TARGETS.html Genes changed in H1299 cells (non-small cell lung cancer, NSCLC) transiently transfected to express the TP63 [GeneID=8626] gamma splice variant. 16462763 14/16 Arthur Liberzon 4.724225492501e-06 6.29323436734499e-06 2760 1686.45454545455 1664 4.29475967019661e-07 129 2.90311883768527 3.60284821491191 1 6.0223974922195 2760 2408 1521 1664 3473 1706 1411 204 129 1917 1358 1363 M10508 HARRIS_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/HARRIS_HYPOXIA.html Genes known to be induced by hypoxia 11902584 116/148 John Newman 2.13692114319635e-06 3.20402407747356e-06 1605 1889.90909090909 1665 1.94265747168188e-07 514 2.65603430909033 2.48378985164084 1 5.81873213315575 1602 2569 514 848 3068 1563 3307 1665 2160 1165 2328 1364 M6750 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_DN.html Genes down-regulated in nasopharyngeal carcinoma (NPC) positive for LMP1 [GeneID=9260], a latent gene of Epstein-Barr virus (EBV). 16912175 150/300 Arthur Liberzon 5.67069759620573e-20 3.30440650050507e-18 3050 1973.36363636364 1666 5.15517963291428e-21 53 3.25064505098599 -3.04611370308024 -1 22.8024858338921 3049 1479 53 239 1666 3713 3029 4492 782 199 3006 1365 M3003 MEINHOLD_OVARIAN_CANCER_LOW_GRADE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MEINHOLD_OVARIAN_CANCER_LOW_GRADE_UP.html Genes up-regulated in low grade (LMP and G1) serous ovarian carcinomas vs the higher grade invasive tumors (G2 and G3). 15558012 24/31 Arthur Liberzon 5.81289612618014e-08 5.56439156084225e-07 2200 1598.81818181818 1666 5.28445116342725e-09 79 1.67890247912256 2.03951585381259 1 4.17299545920155 2199 770 2478 1666 79 2307 4194 835 1067 1718 274 1366 M626 REACTOME_ACYL_CHAIN_REMODELLING_OF_PI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PI.html Genes involved in Acyl chain remodelling of PI 8/16 Reactome 1.09867269951464e-06 1.88139659102166e-06 1670 2037.72727272727 1667 1.09867324270178e-07 559 2.31630924667124 -2.24147184023555 -1 5.28346043192348 1667 1021 4210 2778 2701 1608 601 559 4193 2063 1014 1367 M1545 WESTON_VEGFA_TARGETS_12HR http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS_12HR.html Genes up-regulated in MMEC cells (myometrial endothelium) at 12 h after VEGFA [GeneID=7422] stimulation. 12200464 49/62 John Newman 1.20019157736084e-07 7.07228994399893e-07 195 1806.81818181818 1667 1.09108331166935e-08 194 3.00544555273522 3.31827627180608 1 7.38384547341137 194 2241 350 2175 4292 1598 2104 1667 3204 624 1426 1368 M673 REACTOME_SIGNALING_BY_FGFR1_FUSION_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR1_FUSION_MUTANTS.html Genes involved in Signaling by FGFR1 fusion mutants 27/36 Reactome 1.01831561508221e-06 1.77621940250851e-06 1155 2110.54545454545 1668 9.25741896755463e-08 591 1.42438456754789 -1.43345754188501 -1 3.24404006281295 1151 3994 3406 1091 2580 1668 591 738 2383 4104 1510 1369 M954 REACTOME_GABA_B_RECEPTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_B_RECEPTOR_ACTIVATION.html Genes involved in GABA B receptor activation 26/42 Reactome 1.66189273244165e-07 7.3358205358541e-07 3100 1974.72727272727 1668 1.51081168907454e-08 738 2.22776506112836 2.7670405193618 1 5.44604029330199 3098 741 1481 1668 738 4108 3274 1795 1632 1974 1213 1370 M6984 GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_UP.html Genes up-regulated in common hematopoietic progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 64/87 Arthur Liberzon 3.70651122741613e-07 9.54490445253898e-07 1300 2014.09090909091 1668 3.36955622898278e-08 1123 1.41071105502461 -1.24881666277584 -1 3.36544240729393 1299 1668 3171 2190 1622 1291 1903 1163 3182 3543 1123 1371 M3941 HASLINGER_B_CLL_WITH_13Q14_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_13Q14_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 13q14 region. 15459216 36/43 Kevin Vogelsang 3.62506087464371e-08 4.08360079434804e-07 3020 2031.81818181818 1669 3.29550994034167e-09 22 2.10649087588872 2.28956817670271 1 5.36236653315847 3020 592 1669 175 22 3456 3654 4356 738 1297 3371 1372 M11788 CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_DN.html Selected genes down-regulated during invasion of lymphatic vessels during metastasis. 18794116 70/84 Jessica Robertson 3.70340325904118e-16 1.38730661767257e-14 150 1572.45454545455 1669 3.36673023549198e-17 87 3.389971582148 3.54900136482547 1 18.8425686730302 146 1638 87 834 4221 1669 1988 2037 2608 224 1845 1373 M15394 BIOCARTA_AMI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AMI_PATHWAY.html Acute Myocardial Infarction 24/34 BioCarta 5.857096070235e-08 5.58055700841083e-07 290 1821.09090909091 1670 5.3246329328813e-09 287 3.22773607586665 3.14749314784739 1 8.06722352164965 287 1826 335 1242 4317 1670 3114 2977 2178 512 1574 1374 M1360 ZEMBUTSU_SENSITIVITY_TO_FLUOROURACIL http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_FLUOROURACIL.html Top genes associated with chemosensitivity to 5-fluorouracil [PubChem=3385] across 85 tumor xenografts. 11809704 29/41 Arthur Liberzon 2.45412160109016e-07 8.11734685153857e-07 2240 1632.54545454545 1670 2.23101988622716e-08 716 2.08643596508733 -1.77064787219144 -1 5.06047923541533 2236 716 2097 1670 1172 1712 1288 2205 966 2691 1205 1375 M159 PID_AMB2_NEUTROPHILS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AMB2_NEUTROPHILS_PATHWAY.html amb2 Integrin signaling 18832364 53/76 Pathway Interaction Database 4.63528062546241e-07 1.06078552672935e-06 1080 1720.72727272727 1671 4.21389236553742e-08 642 2.32375074896921 2.24537914904739 1 5.53315386213927 1076 2222 1205 642 1884 1663 1671 1981 3571 931 2082 1376 M1973 HORIUCHI_WTAP_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HORIUCHI_WTAP_TARGETS_UP.html Genes up-regulated in primary endothelial cells (HUVEC) after knockdown of WTAP [GeneID=9589] by RNAi. 17088532 417/531 Leona Saunders 3.88102812418762e-07 9.75943140445688e-07 2225 1931.54545454545 1672 3.52820800803762e-08 342 2.12513924390277 -1.69898440273744 -1 5.08689819015162 2223 2022 425 1629 1672 1467 1552 4078 2331 342 3506 1377 M2432 VERNOCHET_ADIPOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/VERNOCHET_ADIPOGENESIS.html Genes up-regulated during adipogenic differentiation of 3T3-L1 cells (preadipocyte) and down-regulated by troglitazone [PubChem=5591]. 19564408 17/26 Arthur Liberzon 1.81597877912014e-06 2.78650505540073e-06 3800 2007.45454545455 1672 1.65089116192027e-07 462 3.613077156376 2.89639226357721 1 8.02151903453087 3800 1903 959 543 2982 4637 3451 941 462 1672 732 1378 M19590 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_DN.html Genes from the turquoise module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphocholine (oxPAPC). 16912112 79/90 Arthur Liberzon 3.05205587597544e-05 3.52131599477e-05 970 1725.45454545455 1673 2.77463474355615e-06 325 1.94106713260846 2.26229818695728 1 3.42630626690629 968 2606 2277 1918 4039 325 541 603 3412 1673 618 1379 M5516 VALK_AML_CLUSTER_12 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_12.html Top 40 genes from cluster 12 of acute myeloid leukemia (AML) expression profile; 89% of the samples are FAB M3 subtype, 95% bear the t(15;17) translocation, all have the PML-RARA fusion [GeneID=5371;5914]; indicate good survival. 15084694 36/47 Jessica Robertson 3.88570083938203e-07 9.76357383103197e-07 2880 2308.45454545455 1673 3.5324559324413e-08 591 2.31052362611142 3.14660734138137 1 5.53484232306303 2879 591 1286 2571 1673 3079 4117 4700 1612 1513 1372 1380 M17428 GAL_LEUKEMIC_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAL_LEUKEMIC_STEM_CELL_UP.html Genes up-regulated in leukemic stem cells (LSC), defined as CD34+CD38- [GeneID=947;952] cells from AML (acute myeloid leukemia patients) compared to the CD34+CD38+ cells. 17039238 161/232 Leona Saunders 2.09400582465429e-07 7.70763712250053e-07 1675 1746.72727272727 1674 1.90364183996923e-08 998 2.04999258874079 2.29463973364374 1 4.98975856601428 1674 2087 1246 1863 998 2145 3551 1578 1853 1198 1021 1381 M4767 VERRECCHIA_RESPONSE_TO_TGFB1_C2 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C2.html Cluster 2: ECM related genes up-regulated in dermal fibroblasts within 30 min after TGFB1 [GeneID=7040] addition; reached a plateau after that. 11279127 64/76 John Newman 1.09956363503077e-05 1.35295629753525e-05 460 1761.81818181818 1674 9.99608300642216e-07 459 2.66652109623227 2.82298089027595 1 5.17104034204403 459 2186 531 839 3777 1482 2019 3408 2281 724 1674 1382 M1605 BURTON_ADIPOGENESIS_4 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_4.html Progressively up-regulated from 8-48 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 87/108 John Newman 7.40617580456251e-06 9.38951109254231e-06 585 2023.45454545455 1675 6.73290976104796e-07 581 2.09089069596729 2.32346791500023 1 4.17734695377172 581 3332 1509 2727 3665 971 1675 1592 2856 2418 932 1383 M11153 REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS.html Genes involved in Activation of ATR in response to replication stress 40/40 Reactome 3.75812631920583e-05 4.29188391644121e-05 100 1730.63636363636 1676 3.41653683502682e-06 51 1.44513372799089 1.43542054908611 1 2.48816897317809 100 2693 2897 1505 4081 301 51 1040 2781 1676 1912 1384 M2072 BAE_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAE_BRCA1_TARGETS_UP.html Genes concordantly up-regulated in DU-145 and MCF-7 cells (lprostate, breast cancer) upon expression of BRCA1. 15520196 108/139 Arthur Liberzon 3.89644441774809e-07 9.76357383103197e-07 3550 2000.27272727273 1676 3.54222282531987e-08 76 2.11983123531413 2.05508144312102 1 5.07391043250543 3547 76 970 849 1676 2689 2444 3039 1452 767 4494 1385 M19828 PASTURAL_RIZ1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PASTURAL_RIZ1_TARGETS_UP.html Genes up-regulated in K562 (chronic myelogenous leukemia, CML) cells engineered to stably express RIZ1 [GeneID=7799]. 16953217 28/43 Aravind Subramanian 4.72659233733856e-06 6.29323436734499e-06 660 1921.54545454545 1678 4.29691135656494e-07 657 1.62930333518696 -1.33623385157694 -1 3.35796594627834 657 694 2123 2674 3475 970 1678 1371 3619 2235 1641 1386 M16944 WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN.html Genes down-regulated in esophageal adenocarcinoma (EAC) and Barret's esophagus (BE) relative to normal esophagi. 16449976 44/80 Leona Saunders 3.89856903047474e-07 9.76357383103197e-07 2940 1880.90909090909 1678 3.54415429211935e-08 467 2.85638195579462 -1.97501161298293 -1 6.85426314958644 2938 467 484 948 1678 3403 2917 1888 925 499 4543 1387 M1394 BIOCARTA_GATA3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GATA3_PATHWAY.html GATA3 participate in activating the Th2 cytokine genes expression 14/17 BioCarta 1.21032296210244e-06 2.02274165108136e-06 1680 1886.09090909091 1679 1.10029420723478e-07 230 1.47771252830242 1.62135869554428 1 3.33382462081004 1679 1934 2612 3664 2703 1666 839 470 1640 3310 230 1388 M1387 SHIN_B_CELL_LYMPHOMA_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_3.html Cluster 3 of genes distinguishing among different B lymphocyte neoplasms. 19010892 34/44 Jessica Robertson 7.1969777890034e-07 1.3944883072289e-06 3290 2170.45454545455 1679 6.54270922126396e-08 158 2.32410696933896 2.44654500577353 1 5.42298321486545 3289 625 1339 158 2289 4194 4542 1582 1679 1131 3047 1389 M212 PID_INTEGRIN5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN5_PATHWAY.html Beta5 beta6 beta7 and beta8 integrin cell surface interactions 18832364 23/26 Pathway Interaction Database 7.80808699459691e-05 8.6390460887242e-05 1610 2386.18181818182 1680 7.09851284323672e-06 963 2.22202819516964 2.53743915662341 1 3.58119602219026 1609 3170 1680 4154 4218 1445 1601 963 4195 1891 1322 1390 M239 PID_A6B1_A6B4_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_A6B1_A6B4_INTEGRIN_PATHWAY.html a6b1 and a6b4 Integrin signaling 18832364 56/64 Pathway Interaction Database 1.02884633863771e-07 6.8232212069871e-07 1875 1659.90909090909 1680 9.35314897047706e-09 320 1.96777301727405 2.19442161249581 1 4.82951446967464 1871 1680 1611 867 320 2574 4013 2018 401 1836 1068 1391 M11896 LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN.html Genes whose expression profile is specific to Cluster IIa of urothelial cell carcinoma (UCC) tumors. 16532037 193/246 Leona Saunders 3.05747387269064e-07 8.80936447462993e-07 2650 1970.90909090909 1682 2.77952208873315e-08 1256 2.04196641484999 2.032436195788 1 4.92237786897181 2648 2068 1682 1643 1410 2250 3049 1590 1388 1256 2696 1392 M17836 AMUNDSON_DNA_DAMAGE_RESPONSE_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_DNA_DAMAGE_RESPONSE_TP53.html Genes discriminating TP53 [GeneID=7157] status across various genotoxic stress agents. 15824734 27/35 Leona Saunders 4.19808243494184e-07 1.00788143911116e-06 2400 1503.90909090909 1682 3.81643930548022e-08 538 2.55715751194488 -1.98337057573641 -1 6.11680069113054 2398 684 1063 587 1772 1922 1682 2654 538 1523 1720 1393 M18328 POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP.html Top marker genes in medulloblastoma associated with good response to treatment (good outcome). 11807556 64/80 Jean Junior 2.56202244138544e-07 8.2488034947744e-07 2530 1748.27272727273 1683 2.32911158158842e-08 291 2.03696040319593 2.56575826031224 1 4.9335784396917 2528 1660 1683 2096 1215 2587 3386 291 452 2266 1067 1394 M12717 LOPES_METHYLATED_IN_COLON_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPES_METHYLATED_IN_COLON_CANCER_DN.html Genes un-methylated aberrantly in HCT116 and Colo320 (colon cancer) cells. 18794111 34/46 Jessica Robertson 3.90749808619055e-07 9.76357383103197e-07 845 1448.90909090909 1683 3.55227161837756e-08 67 2.11081185692222 2.35631249583745 1 5.05210925251887 841 1794 1959 3683 1683 328 703 67 1773 2980 127 1395 M19043 ST_ADRENERGIC http://www.broadinstitute.org/gsea/msigdb/cards/ST_ADRENERGIC.html Adrenergic Pathway 44/55 Signaling Transduction KE 1.64694903666486e-07 7.3358205358541e-07 2685 1900 1684 1.49722650905241e-08 544 1.65051881799353 -1.86966212811029 -1 4.0219268964367 2681 544 2980 907 726 2806 2910 1684 1296 3380 986 1396 M19496 ZEMBUTSU_SENSITIVITY_TO_CISPLATIN http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_CISPLATIN.html Top genes associated with chemosensitivity to cisplatin [PubChem=2767] across 85 tumor xenografts. 11809704 19/28 Arthur Liberzon 6.4901200637647e-07 1.30791290081906e-06 1075 1513.63636363636 1684 5.90011088944213e-08 104 2.31156253574412 -2.14609689309956 -1 5.41931943365473 1071 2377 1712 3066 2189 1008 696 355 1684 2388 104 1397 M15493 CHEN_HOXA5_TARGETS_9HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_9HR_DN.html Genes down-regulated 9 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 59/69 Arthur Liberzon 2.24659951288983e-07 7.84896350913396e-07 1405 1803.81818181818 1685 2.04236340209861e-08 1076 2.07896057278181 2.27771450215387 1 5.05437725049183 1402 1685 1615 2316 1076 1376 1805 2327 2472 1458 2310 1398 M8342 CROONQUIST_IL6_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_IL6_DEPRIVATION_UP.html Genes up-regulated in the ANBL-6 cell line (multiple myeloma, MM) after withdrawal of IL6 [GeneID=3569]. 12791645 26/42 Arthur Liberzon 8.77760852753551e-08 6.51622504172635e-07 3815 2069.90909090909 1686 7.97964443431498e-09 226 2.0012676285593 1.57659178239723 1 4.92866349300122 3815 740 1686 1364 226 3205 4310 610 461 1976 4376 1399 M17243 REACTOME_ACTIVATED_TAK1_MEDIATES_P38_MAPK_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_TAK1_MEDIATES_P38_MAPK_ACTIVATION.html Genes involved in activated TAK1 mediates p38 MAPK activation 17/17 Reactome 3.76782054543518e-07 9.5981847370948e-07 1690 1714 1687 3.42529199157228e-08 674 1.70246150328154 -1.79059931440811 -1 4.07014568410773 1687 1907 2888 2392 1644 1978 1157 674 812 2045 1670 1400 M1956 MIKKELSEN_MCV6_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 57/125 Jessica Robertson 6.12409352971524e-09 8.47675116136538e-08 875 2005.63636363636 1687 5.5673577697843e-10 267 3.28567526931103 3.51354634314724 1 9.29440660127516 873 1687 267 2118 3257 1638 3154 3248 3716 605 1499 1401 M13907 TSENG_IRS1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_IRS1_TARGETS_DN.html Down-regulated in brown preadipocytes with IRS1 [GeneID=3667] knockout vs wild type controls; the knockouts have severe defects in adipocyte differentiation. 15895078 194/236 John Newman 1.84090146785088e-06 2.81563672334937e-06 1550 1802.63636363636 1688 1.67354818933641e-07 418 2.31981127472628 2.61994242834009 1 5.12816998711365 1546 2534 525 2597 2995 911 2768 1688 2360 418 1487 1402 M6034 REACTOME_SEROTONIN_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEROTONIN_RECEPTORS.html Genes involved in Serotonin receptors 3/12 Reactome 7.8168891455048e-07 1.47641923836665e-06 2790 1747.72727272727 1689 7.81689189517518e-08 15 4.20968400723631 3.96276021691795 1 9.8213361028053 2786 1060 4236 67 2451 2482 1061 1663 15 1689 1715 1403 M1466 AFFAR_YY1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/AFFAR_YY1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) expressing ~25% of YY1 [GeneID=7528]. 16611997 280/415 Kevin Vogelsang 1.97864560893538e-12 4.55571086545120e-11 3140 1638.09090909091 1689 1.79876873539742e-13 151 2.48657315376731 2.7313774171867 1 10.2914517897708 3140 1300 151 320 1698 1689 3709 1785 1092 244 2891 1404 M2098 MARTENS_TRETINOIN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTENS_TRETINOIN_RESPONSE_UP.html Genes up-regulated in NB4 cells (acute promyelocytic leukemia, APL) in response to tretinoin [PubChem=444795]; based on Chip-seq data. 20159609 683/1518 Arthur Liberzon 9.03161818412043e-41 2.02996370614516e-38 3045 2048.54545454545 1689 9.0316181841204e-42 8 2.77824882677016 2.93499801090823 1 42.0639996352827 3041 1108 4656 8 436 1116 3628 3257 1689 13 3582 1405 M943 REACTOME_GABA_A_RECEPTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_A_RECEPTOR_ACTIVATION.html Genes involved in GABA A receptor activation 3/15 Reactome 1.43986041208194e-07 7.26289540930751e-07 2730 1844 1690 1.43986050537586e-08 17 2.9237988184531 2.82080974173945 1 7.16831400265363 2726 1059 4254 572 686 2767 2179 3531 17 1690 803 1406 M5466 WINTER_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WINTER_HYPOXIA_UP.html Genes up-regulated in head and neck tumor samples which clustered around known hypoxia genes. 17409455 141/174 Arthur Liberzon 3.20005574644552e-07 8.98528442785416e-07 600 1592.81818181818 1690 2.90914201083306e-08 596 1.97486637514207 2.16966138101221 1 4.75216169120292 596 2557 1690 2203 1454 612 881 2040 1900 2291 1297 1407 M834 CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_UP.html Marker genes up-regulated in the 'chromosome 7 polysomy' subclass of hepatocellular carcinoma (HCC); characterized by polysomy of chromosome 7 and by a lack of gains of chromosome 8q. 18701503 90/144 Yujin Hoshida 2.18604362988276e-07 7.77552820877664e-07 1050 2138.63636363636 1690 1.98731258827306e-08 591 2.33953968447932 2.02053481744375 1 5.69801096851931 4066 1613 1050 1781 1047 4127 4676 1908 591 976 1690 1408 M600 REACTOME_G_ALPHA_I_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_I_SIGNALLING_EVENTS.html Genes involved in G alpha (i) signalling events 84/229 Reactome 3.16373113513268e-12 7.14488562575418e-11 160 2079.63636363636 1691 2.87611921376112e-13 156 2.8177138632913 -2.79055444294266 -1 11.4471765048858 4709 160 156 1574 684 4414 2831 1691 2414 204 4039 1409 M1035 REACTOME_MYD88_MAL_CASCADE_INITIATED_ON_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MYD88_MAL_CASCADE_INITIATED_ON_PLASMA_MEMBRANE.html Genes involved in MyD88:Mal cascade initiated on plasma membrane 95/113 Reactome 3.93343561935187e-07 9.79209711146668e-07 1095 2275.63636363636 1691 3.57585120238268e-08 982 1.61481634209606 -1.77932364794311 -1 3.85239152609657 1091 3884 3453 2523 1691 1613 1280 982 3616 3470 1429 1410 M19632 ZHAN_MULTIPLE_MYELOMA_MS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MS_UP.html Top 50 up-regulated genes in cluster MS of multiple myeloma samples with characteristic expression spike of WHSC1 [GeneID=7468]. 16728703 67/75 Kevin Vogelsang 5.13926912466276e-07 1.12877386079145e-06 1695 1677.63636363636 1691 4.67206393201143e-08 288 1.92267968763005 2.01311898874804 1 4.54865387874862 1691 288 1799 1177 1974 2136 3924 2131 715 1372 1247 1411 M9065 KUNINGER_IGF1_VS_PDGFB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUNINGER_IGF1_VS_PDGFB_TARGETS_UP.html Genes up-regulated in C2AS12 cells (myoblast) by IGF1 [GeneID=3479] vs PDGFB [GeneID=5155]. 15475267 94/160 John Newman 3.74823496108476e-07 9.58740773617983e-07 2635 1861.90909090909 1692 3.40748690880717e-08 156 2.33481222924225 2.4218846197898 1 5.60097652244384 2635 156 760 1813 1638 2889 4708 933 2495 762 1692 1412 M17609 WU_ALZHEIMER_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_ALZHEIMER_DISEASE_UP.html Genes up-regulated in brain endothelial cells from patients with Alzheimer disease. 16116430 23/45 Jessica Robertson 4.54014207669121e-06 6.07928244027872e-06 2985 1822.72727272727 1693 4.12741040564888e-07 227 2.47971457586816 2.97771874384342 1 5.15174578699672 2982 814 1457 1682 3453 1832 1693 227 1052 1898 2960 1413 M10389 FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN.html Genes down-regulated in B-CLL (B-cell chronic lymphocytic leukemia) patients with mutated immunoglobulin variable heavy chain (VH) genes. 15817677 66/76 Kevin Vogelsang 4.30554284894573e-07 1.02188257382467e-06 1695 1864.54545454545 1694 3.91413062869877e-08 326 1.31138418925602 1.49156347229802 1 3.10933542977225 1694 326 3588 2689 1795 1316 1602 1286 1004 3317 1893 1414 M1979 KEGG_GNRH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GNRH_SIGNALING_PATHWAY.html GnRH signaling pathway 90/116 KEGG 9.72811696652649e-08 6.64473403617636e-07 2015 1306.54545454545 1695 8.84374308790121e-09 162 1.88994810459298 -1.85194073521253 -1 4.64527921658994 2012 162 1704 467 295 1695 916 2636 1005 1742 1738 1415 M153 PID_P75_NTR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P75_NTR_PATHWAY.html p75(NTR)-mediated signaling 18832364 88/106 Pathway Interaction Database 2.20095854643422e-07 7.7970890443293e-07 4370 2310.63636363636 1695 2.00087160602363e-08 164 1.918396610908 2.41440892535948 1 4.66237078767255 4366 164 1695 484 1051 4512 4353 1284 1187 2295 4026 1416 M5601 BROWNE_HCMV_INFECTION_20HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_20HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 20 h time point that were not down-regulated at the previous time point, 18 h. 11711622 161/203 John Newman 1.81309504878829e-07 7.47800341964416e-07 1695 1762.27272727273 1695 1.6482683620106e-08 841 2.01077596792039 2.38614939892126 1 4.90396882289708 1695 2081 1181 1658 841 1756 2869 1584 2859 948 1913 1417 M18095 GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP.html Up-regulated genes from the set G (Fig. 5a): specific to cells expressing both MLL-AF4 [GeneID=4297;4299] and AF4-MLL fusion proteins. 17130830 257/379 Arthur Liberzon 1.68202217563631e-11 3.51289587124043e-10 4010 2026.27272727273 1696 1.52911106877197e-12 173 2.50569687802421 2.66067797971037 1 9.4770504632028 4009 1330 173 301 1696 2920 4264 1450 2026 525 3595 1418 M8364 TSENG_ADIPOGENIC_POTENTIAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_ADIPOGENIC_POTENTIAL_DN.html Genes showing decreasing expression in brown preadipocytes with increasing ability of the cells to differentiate. 15895078 73/93 John Newman 7.58070162912726e-06 9.58502858009126e-06 415 1807 1696 6.89157068239437e-07 415 2.75046377934466 2.812195621521 1 5.50097818631442 415 2625 485 1696 3997 1143 1389 2273 3057 819 1978 1419 M18550 BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP.html Up-regulated genes in MDA-MB-435 cells (breast cancer) undergoing G2/M arrest after treatment with 2-methoxyestradiol (2ME2)[PubChem=1573]. 17234781 161/205 Jessica Robertson 5.21536546946406e-07 1.13754736672229e-06 1780 1769.63636363636 1697 4.74124245984526e-08 631 2.07726427320935 2.24418798200847 1 4.91558230549815 1777 1498 1169 631 1987 1049 1697 3310 3228 1383 1737 1420 M141 PID_PI3KCI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PI3KCI_PATHWAY.html Class I PI3K signaling events 18832364 54/68 Pathway Interaction Database 1.96877132235696e-07 7.64036221497417e-07 1760 1602.27272727273 1698 1.78979227140141e-08 478 1.80196232295703 -1.86572951267934 -1 4.38274867575041 1757 1698 2585 478 923 2186 725 1542 1099 2762 1870 1421 M19667 CHENG_RESPONSE_TO_NICKEL_ACETATE http://www.broadinstitute.org/gsea/msigdb/cards/CHENG_RESPONSE_TO_NICKEL_ACETATE.html Genes down-regulated in HPL1D cells (lung epithelium) upon exposure to nickel acetate [PubChem=9756]. 12915101 58/71 John Newman 6.52456877673894e-07 1.30936154030309e-06 1465 1622 1699 5.9314279197633e-08 410 1.64944789629747 -1.80244197576452 -1 3.85238010355908 1464 410 2664 1910 2198 2071 1699 686 1342 2655 743 1422 M6937 CUI_TCF21_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_DN.html Genes most strongly down-regulated in kidney glomeruli isolated from TCF21 [GeneID=6943] knockout mice. 16207825 63/82 John Newman 1.55763546175137e-08 1.97635467189959e-07 1700 1681 1700 1.41603224798153e-09 295 3.06488778131293 3.04494492065809 1 8.21334788350173 1700 345 295 439 2470 1993 3777 3202 2313 597 1360 1423 M2136 QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2 http://www.broadinstitute.org/gsea/msigdb/cards/QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2.html Genes up-regulated by hypoxia in TRAMP-C cells (prostatic cancer) expressing HIF1A and FOXA2 [GeneID=3091,3170] off plasmid vectors. 20609350 53/57 Arthur Liberzon 8.2190683629125e-07 1.52792448495262e-06 1325 1894.18181818182 1700 7.47188312137169e-08 686 1.76947960187806 2.27200035536946 1 4.0886538420373 1325 1700 2298 2867 2404 850 1316 1283 2932 3175 686 1424 M2275 ZHU_SKIL_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_SKIL_TARGETS_DN.html Genes down-regulated in A549 cells (lung adenocarcinoma) upon SKIL [GeneID=6498] knockdown by RNAi. 17074815 10/11 Arthur Liberzon 3.76735707553491e-05 4.2993049798174e-05 1700 1734.36363636364 1700 3.42492871874912e-06 303 2.84154393331465 3.75393038990285 1 4.93994062647498 1696 2902 1925 1700 4399 1939 702 303 528 2552 432 1425 M14511 NAKAMURA_BRONCHIAL_AND_BRONCHIOLAR_EPITHELIA http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_BRONCHIAL_AND_BRONCHIOLAR_EPITHELIA.html Differentiation markers for normal bronchiolar and bronchial epithelial cells. 16491115 6/18 Arthur Liberzon 4.11399809084063e-08 4.48093592073917e-07 1705 2006.45454545455 1701 4.11399816700304e-09 41 2.88127809628075 -3.39964647415996 -1 7.30637298740488 1701 3534 4364 2926 41 1657 285 157 3171 2792 1443 1426 M8236 KANG_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_CISPLATIN_RESISTANCE_DN.html Genes down-regulated in gastric cancer cell lines resistant to cisplatin [PubChem=2767]. 14734480 15/15 Arthur Liberzon 3.53449892481057e-06 4.8908926781313e-06 1165 1771.45454545455 1701 3.21318600301405e-07 931 2.66576056202715 2.96122820077595 1 5.64329278839014 1165 931 1720 2810 3338 1308 1063 2176 1457 1701 1817 1427 M1843 LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN.html Down-regulated genes in NMuMG cells (mammary epithelium) after stimulation with both TGFB1 and WNT3A [GeneID=7040;89780]. 17210685 134/200 Jessica Robertson 4.14644855464312e-07 1.00337562730974e-06 1925 1694.54545454545 1701 3.7694993964954e-08 597 2.26487286194445 -2.12850615613389 -1 5.41369980737513 1924 2095 597 994 1753 1701 1592 3206 2556 929 1293 1428 M9945 UDAYAKUMAR_MED1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/UDAYAKUMAR_MED1_TARGETS_DN.html Genes down-regulated in HeLa cells after knockdown of MED1 [GeneID=5469] by RNAi. 16574658 346/406 Leona Saunders 3.51767989981347e-07 9.35932870750822e-07 2725 2111.81818181818 1702 3.19789132933764e-08 907 2.08477845037884 2.56008457401628 1 5.00457943714452 2724 2510 982 1055 1557 2608 4200 3672 1702 907 1313 1429 M1713 LEIN_ASTROCYTE_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_ASTROCYTE_MARKERS.html Genes enriched in astrocytes in the adult mouse brain identified through correlation-based searches seeded with the astrocyte cell-type specific gene expression patterns. 17151600 49/75 Jessica Robertson 9.15750273917198e-08 6.55893974641757e-07 3170 1813.72727272727 1702 8.32500283668467e-09 258 2.7908442493233 2.33257980089736 1 6.88976652130928 3166 1702 823 554 258 2193 3025 3416 1479 830 2505 1430 M3169 RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_UP.html ES/PNET (Ewing sarcoma; primitive neuroectodermal tumors) markers up-regulated in neuroblastoma cell lines expressing ESWR1-FLI1 [GeneID=2130;2313] fusion protein. 14973077 52/73 Kevin Vogelsang 1.24223158396921e-06 2.06020136202905e-06 2640 1854.45454545455 1703 1.12930207763339e-07 139 2.09313026635846 -1.66368791689039 -1 4.73638130567466 2640 379 960 139 2730 2670 2889 4043 1223 1023 1703 1431 M1983 SCHOEN_NFKB_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SCHOEN_NFKB_SIGNALING.html Genes down-regulated in A375 cells (melanoma) treated with KINK-1, a small molecule inhibitor of NFKB. 18544741 51/67 Jessica Robertson 5.08168912402352e-08 5.1804692581838e-07 3485 1956.45454545455 1703 4.61971749218486e-09 331 3.33330564933959 -2.91899476747592 -1 8.37602516111864 3481 1703 331 808 994 3836 2346 1677 2007 622 3716 1432 M274 PID_LYMPH_ANGIOGENESIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LYMPH_ANGIOGENESIS_PATHWAY.html VEGFR3 signaling in lymphatic endothelium 18832364 53/57 Pathway Interaction Database 3.76267702401583e-05 4.29500255220187e-05 445 1925.18181818182 1704 3.42067398083007e-06 444 2.15167771719035 2.5574197469611 1 3.72885679081668 444 2225 1417 1324 4083 1295 1704 2155 3167 2205 1158 1433 M1645 LI_ADIPOGENESIS_BY_ACTIVATED_PPARG http://www.broadinstitute.org/gsea/msigdb/cards/LI_ADIPOGENESIS_BY_ACTIVATED_PPARG.html Adipocyte genes induced in 3T3-L1 cells (adipocyte) by constitutively active PPARG [GeneID=5468] or its agonist, TZD [PubChem=5437]. 11981038 15/22 John Newman 5.96124714473254e-07 1.23354171517482e-06 990 1721.18181818182 1704 5.41931705457013e-08 520 2.0836501785471 -1.77262346248519 -1 4.90136433729921 986 2861 1974 3335 2120 1083 520 1244 1704 2107 999 1434 M12653 HUTTMANN_B_CLL_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUTTMANN_B_CLL_POOR_SURVIVAL_DN.html Down-regulated genes in B-CLL (B-cell chronic leukemia) patients expressing high levels of ZAP70 and CD38 [GeneID=7535;952], which are associated with poor survival. 16932341 82/112 Leona Saunders 1.80538855258627e-07 7.47800341964416e-07 2450 1856.72727272727 1705 1.64126245522009e-08 230 2.12645139757723 -1.83601739858166 -1 5.18896167196838 2448 230 1268 1202 837 3061 2006 3631 758 1705 3278 1435 M17977 BIOCARTA_P27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P27_PATHWAY.html Regulation of p27 Phosphorylation during Cell Cycle Progression 16/17 BioCarta 1.54662487757475e-05 1.8542213416695e-05 575 1660.81818181818 1707 1.40603250057232e-06 547 1.55541145892222 1.44854233541525 1 2.90985475997531 572 1895 2494 1470 3878 626 604 1707 547 2701 1775 1436 M16664 SIMBULAN_UV_RESPONSE_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_UV_RESPONSE_NORMAL_UP.html Genes up-regulated in HFK cells (primary keratinocytes) in response to UVB irradiation. 16007217 11/12 Leona Saunders 6.48687962383695e-06 8.31560886054057e-06 1075 2148.54545454545 1707 5.89718068273646e-07 360 2.96164736093745 -3.82990309165121 -1 6.00067884426201 1072 3790 1707 3943 3617 1503 767 508 4121 2246 360 1437 M13903 NELSON_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/NELSON_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in LNCaP cells (prostate cancer) in response to synthetic androgen R1881 [PubChem=13766]. 12185249 123/158 Broad Institute 1.82683372488185e-07 7.47800341964416e-07 3490 2327.18181818182 1707 1.66075806961663e-08 851 2.05049647903495 -2.02245577141261 -1 5.00182937688586 3488 1564 1265 1644 851 3880 4089 3515 1707 974 2622 1438 M15456 MCCABE_HOXC6_TARGETS_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_CANCER_UP.html Genes whose promoters were bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and which were up-regulated in comparison of tumor vs normal prostate tissue samples. 18339881 33/50 Jessica Robertson 1.96998322364906e-07 7.64036221497417e-07 1710 1674.45454545455 1707 1.79089400004602e-08 477 1.92203678749014 2.20272818470931 1 4.67812909532716 2014 606 1798 2110 925 1707 1706 4059 477 2527 490 1439 M2469 KRIEG_HYPOXIA_NOT_VIA_KDM3A http://www.broadinstitute.org/gsea/msigdb/cards/KRIEG_HYPOXIA_NOT_VIA_KDM3A.html Genes induced under hypoxia independently of KDM3A [GeneID=55818] in RCC4 cells (renal carcinoma) expressing VHL [GeneID=7428]. 19858293 951/1187 Arthur Liberzon 1.86015619056707e-07 7.48271685670965e-07 1945 1765.54545454545 1709 1.86015634627523e-08 564 1.86933273661198 1.96058775916693 1 4.55528538247387 1941 1087 4705 564 970 881 2977 2132 1709 714 1741 1440 M7494 REACTOME_TOLL_RECEPTOR_CASCADES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TOLL_RECEPTOR_CASCADES.html Genes involved in Toll Receptor Cascades 141/182 Reactome 2.79589134074123e-07 8.470222803786e-07 1410 1778.09090909091 1714 2.54171972369078e-08 190 1.86635062995546 -2.03778550245024 -1 4.50753103132547 1407 2558 2711 190 1316 2163 1714 1183 1899 2904 1514 1441 M17004 LU_TUMOR_ENDOTHELIAL_MARKERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_ENDOTHELIAL_MARKERS_UP.html Genes specifically up-regulated in tumor endothelium. 17308118 43/48 Jessica Robertson 3.59589585246842e-06 4.95695923587936e-06 285 1983.63636363636 1714 3.26900157269715e-07 283 3.14924613542942 3.37428699645425 1 6.66850453758497 283 3095 452 1714 4483 1400 1803 2521 3522 852 1695 1442 M6303 SCHEIDEREIT_IKK_INTERACTING_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/SCHEIDEREIT_IKK_INTERACTING_PROTEINS.html Genes encoding IkappaB kinase (IKK) interacting proteins. 17072322 81/88 Arthur Liberzon 2.1182951837936e-07 7.70763712250053e-07 3345 1857.18181818182 1715 1.92572307977828e-08 778 1.5587074844517 -1.7390508699662 -1 3.78196074851348 926 3341 3345 1957 1010 1365 778 1128 1715 2978 1886 1443 M15123 MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN.html Genes down-regulated in at least 8 of 11 sarcoma cell lines by trabectedin [PubChem=3199]. 15897246 377/435 John Newman 1.86921464971672e-07 7.48955275608059e-07 1715 2183.81818181818 1715 1.69928618957569e-08 885 1.60610012611255 1.83615981314464 1 3.90652452500788 1715 3278 3819 1559 885 1834 2333 1131 1514 4302 1652 1444 M1686 ZHONG_SECRETOME_OF_LUNG_CANCER_AND_ENDOTHELIUM http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_SECRETOME_OF_LUNG_CANCER_AND_ENDOTHELIUM.html Proteins secreted in co-culture of LKR-13 tumor cells (non-small cell lung cancer, NSCLC) and MEC stroma cells (endothelium). 18757440 124/177 Jessica Robertson 4.29421516221607e-07 1.02013045295019e-06 1720 1698.36363636364 1717 3.90383272764638e-08 28 2.63208853417169 2.73471587690404 1 6.29195094785327 1717 28 431 464 1793 2648 3599 2450 1066 1200 3286 1445 M165 PID_SYNDECAN_4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_4_PATHWAY.html Syndecan-4-mediated signaling events 18832364 49/62 Pathway Interaction Database 3.20906820381497e-07 8.98919995371315e-07 2220 1916.09090909091 1719 2.91733515628306e-08 481 2.32464274793142 2.87785798279812 1 5.60252118156181 2219 481 1010 1719 1458 2470 3720 1914 2971 1421 1694 1446 M1984 NAKAYAMA_FGF2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_FGF2_TARGETS.html Genes down-regulated in S-17 cells (bone marrow stroma) after stimulation with FGF2 [GeneID=2247]. 17284717 48/57 Jessica Robertson 8.57072422435444e-06 1.07333028227522e-05 550 1654 1719 7.79159783111328e-07 546 2.55161275246398 3.01356627760584 1 5.04922941036631 546 1719 708 2208 3710 1302 2058 2218 1790 1045 890 1447 M607 REACTOME_PRE_NOTCH_EXPRESSION_AND_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRE_NOTCH_EXPRESSION_AND_PROCESSING.html Genes involved in Pre-NOTCH Expression and Processing 51/53 Reactome 2.06976216052668e-07 7.68728418959517e-07 2275 1695.27272727273 1721 1.88160214113648e-08 457 1.82803391066368 2.19468344030724 1 4.44492938585515 2274 457 2271 3153 983 1721 2505 1242 973 2259 810 1448 M3652 DER_IFN_ALPHA_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_ALPHA_RESPONSE_UP.html Genes up-regulated in HT1080 cells (fibrosarcoma) by treatment with interferon alpha for 6 h. 9861020 144/205 Yujin Hoshida 1.18214917787414e-06 1.98450355880301e-06 1295 2182 1722 1.07468164826481e-07 1239 1.74612931457716 -1.66262434940595 -1 3.95430134265859 1292 2091 1644 1722 2689 1239 1610 4250 3502 1517 2446 1449 M9143 FRIDMAN_SENESCENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_SENESCENCE_UP.html Genes up-regulated in senescent cells. 18711403 122/146 Jessica Robertson 8.73585541525075e-07 1.59201689420786e-06 1460 1933.72727272727 1723 7.94168989465822e-08 463 2.59203882374074 3.05456748450961 1 5.99396047884258 1460 2116 463 901 2463 2499 4064 1723 3013 1034 1535 1450 M1647 WENG_POR_TARGETS_LIVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_LIVER_UP.html Genes up-regulated in liver from mice with liver specific knockout of POR [GeneID=5447]. 16006652 46/96 John Newman 9.75506039929729e-08 6.64473403617636e-07 2385 1663.09090909091 1723 8.86823711986201e-09 298 2.63162679228713 2.20771689908719 1 6.48787801000409 2383 1723 979 1381 298 1889 2307 1987 466 1579 3302 1451 M18519 WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_DN.html Down-regulated genes in pediatric adrenocortical carcinoma (ACC) compared to the adenoma (ACA) tumors. 17234769 24/38 Jessica Robertson 3.13926788873234e-06 4.42039983623536e-06 2670 1875.81818181818 1723 2.85388397117096e-07 482 2.85774902851022 -3.11888524808422 -1 6.10381105650099 2670 782 1157 942 3277 2976 1723 3178 482 1720 1727 1452 M2843 REACTOME_ACTIVATION_OF_NMDA_RECEPTOR_UPON_GLUTAMATE_BINDING_AND_POSTSYNAPTIC_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_NMDA_RECEPTOR_UPON_GLUTAMATE_BINDING_AND_POSTSYNAPTIC_EVENTS.html Genes involved in Activation of NMDA receptor upon glutamate binding and postsynaptic events 38/49 Reactome 1.53898760127602e-06 2.43622335387917e-06 1185 1804.36363636364 1724 1.39908061623653e-07 216 1.56417471029968 1.63069222626662 1 3.48100451150653 1184 1758 2586 1724 2882 821 1102 969 3241 3365 216 1453 M8780 MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_DN.html Down-regulated target genes shared by acute myeloid leukemia (AML) translocation products PML RARA [GeneID=5371;5914], AML1 ETO [GeneID=861;862], and PLZF RARA [GeneID=5914;7704]. 15024077 46/71 Arthur Liberzon 2.82229641492189e-07 8.49446700978142e-07 2960 1893.72727272727 1724 2.56572434271239e-08 1017 2.38139849748983 2.45781023746086 1 5.76407255458706 2957 1724 1066 1419 1327 1961 2499 3976 1017 1805 1080 1454 M14765 REACTOME_PLC_BETA_MEDIATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLC_BETA_MEDIATED_EVENTS.html Genes involved in PLC beta mediated events 39/48 Reactome 1.99234396195792e-07 7.65527859584926e-07 2230 1551.36363636364 1725 1.81122194762435e-08 157 1.93282053227542 2.32763938357959 1 4.70399844024744 2230 566 1725 859 934 1967 3162 3220 403 1842 157 1455 M5542 SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER.html 50 genes up-regulated in the pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by the combination of decitabine and TSA [PubChem=451668;5562]. 12839967 47/66 John Newman 2.06102564489648e-07 7.68728418959517e-07 3475 2038.72727272727 1725 1.87365985270867e-08 376 3.04600012048747 3.10369688746316 1 7.43979581004591 3473 1725 606 376 978 2527 3626 2281 1057 1271 4506 1456 M74 REACTOME_POST_NMDA_RECEPTOR_ACTIVATION_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_NMDA_RECEPTOR_ACTIVATION_EVENTS.html Genes involved in Post NMDA receptor activation events 36/45 Reactome 2.83603305558214e-06 4.04396767993855e-06 1410 1953.45454545455 1726 2.57821519230526e-07 245 1.48537723023025 1.52263916921945 1 3.17164967553349 1409 1769 2790 1726 3237 1163 1371 1066 3035 3677 245 1457 M1074 REACTOME_NUCLEOTIDE_BINDING_DOMAIN_LEUCINE_RICH_REPEAT_CONTAINING_RECEPTOR_NLR_SIGNALING_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEOTIDE_BINDING_DOMAIN_LEUCINE_RICH_REPEAT_CONTAINING_RECEPTOR_NLR_SIGNALING_PATHWAYS.html Genes involved in Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways 49/56 Reactome 4.5000540809626e-07 1.04185917010687e-06 710 1765.63636363636 1728 4.09095909221776e-08 709 1.84041969554593 -2.02153360185993 -1 4.37765887986466 709 1728 2306 3395 1849 1231 812 1305 3180 1863 1044 1458 M1784 KAN_RESPONSE_TO_ARSENIC_TRIOXIDE http://www.broadinstitute.org/gsea/msigdb/cards/KAN_RESPONSE_TO_ARSENIC_TRIOXIDE.html Genes changed in U373-MG cells (malignant glioma) upon treatment with arsenic trioxide [PubChem=14888], a chemical that can cause autophagic cell death. 15592527 141/179 Arthur Liberzon 1.72429306224949e-06 2.67631149418533e-06 1730 1838.09090909091 1728 1.56754037609037e-07 607 2.24901090655346 2.3090266791375 1 4.99006610616911 1728 2552 834 2650 2944 607 1449 1277 3151 1109 1918 1459 M15267 FUJII_YBX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FUJII_YBX1_TARGETS_UP.html Genes up-regulated in MCF-7 cells (breast cancer) after knockdown of YBX1 [GeneID=4904] by RNAi. 18316615 55/70 Jessica Robertson 5.34283871881748e-07 1.15415097266904e-06 2365 1661.45454545455 1728 4.85712728759999e-08 416 2.61479498700308 -2.3779765318932 -1 6.19391090562308 2363 416 784 976 2015 1824 1728 3520 913 1062 2675 1460 M12073 HAHTOLA_MYCOSIS_FUNGOIDES_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_DN.html Genes down-regulated in monocytes isolated from peripheral blood samples of patients with mucosis fungoides compared to those from normal healthy donors. 16914566 13/24 Arthur Liberzon 6.89953313577935e-08 6.06161982149702e-07 4065 2159.36363636364 1731 6.27230304741741e-09 118 2.19438275303984 -2.35479115742354 -1 5.43680709682931 4064 949 2105 1420 128 3734 4604 1285 118 1731 3615 1461 M12224 MARTINEZ_RB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_TARGETS_UP.html Genes up-regulated in mice with skin specific knockout of RB1 [GeneID=5925] by Cre-lox. 18245467 873/1078 Jessica Robertson 1.00029688201705e-07 6.71132834037269e-07 2730 1892.63636363636 1731 1.00029692704377e-08 351 2.03537339742247 2.27502700575732 1 5.00302333397035 2729 1096 4532 438 351 1810 3638 1599 1854 1041 1731 1462 M1911 OKUMURA_INFLAMMATORY_RESPONSE_LPS http://www.broadinstitute.org/gsea/msigdb/cards/OKUMURA_INFLAMMATORY_RESPONSE_LPS.html Genes up-regulated in mast cells (MC) after stimulation with a bacterial lipopolysaccharide (LPS). 12855579 242/375 Kate Stafford 2.65352435096181e-07 8.31648157220804e-07 4570 2627.54545454545 1732 2.41229515546911e-08 1237 1.97224828262298 -1.84865615905692 -1 4.77243946379657 4569 1363 1344 1237 1258 4665 3782 2784 1732 1535 4634 1463 M1421 PEART_HDAC_PROLIFERATION_CLUSTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/PEART_HDAC_PROLIFERATION_CLUSTER_DN.html Cell proliferation genes down-regulated by histone deacetylase (HDAC) inhibitors SAHA and depsipeptide [PubChem=5311;5352062]. 15738394 98/131 Kate Stafford 6.78661448692304e-07 1.34422242460247e-06 1060 1632.45454545455 1732 6.16965143679599e-08 856 1.7734468605092 1.82111438858389 1 4.13760952611489 1058 2133 2048 1732 2236 856 1000 1110 2622 1920 1242 1464 M15409 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_3 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_3.html Amplification hot spot 3: colocolized fragile sites and cancer genes in the 15q21-q26 region. 16751803 6/7 Arthur Liberzon 2.1012610675739e-05 2.46408751278232e-05 1735 2375 1733 2.10128093667966e-06 230 2.85607885968587 2.85607885968587 1 5.24313142458653 1733 4109 4372 4580 4382 1552 1309 230 443 2793 622 1465 M1419 MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_UP.html Up-regulated genes discriminating multiple myeloma samples by type of immunoglobulin they produce: IgG vs IgA. 12623842 41/51 Kate Stafford 5.15048840305019e-06 6.77167277504092e-06 1265 1874.63636363636 1733 4.68227314641659e-07 548 2.89106442409023 3.10072829704907 1 5.96018463531303 1261 1738 548 1250 3523 1863 3518 3204 1126 857 1733 1466 M1432 SANSOM_APC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS_DN.html Top genes down-regulated at day 5 of Cre-Lox induced APC [GeneID=324] knockout in the intestine. 15198980 423/653 Kevin Vogelsang 1.29291755783361e-13 3.67624751384014e-12 2170 1502.63636363636 1733 1.17537959803062e-14 93 2.12724976391367 -1.94024663662155 -1 9.73223934691208 2216 1192 145 1110 767 2200 2739 2167 1733 93 2167 1467 M16009 ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN.html Genes whose DNA is hyper-methylated in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 780/1587 Jessica Robertson 1.30373887557473e-11 2.75948318058866e-10 2690 1984.90909090909 1734 1.30373887558238e-12 133 2.30023485393113 2.63468835383311 1 8.79283039975231 2687 1101 4547 523 429 2688 4707 1906 1379 133 1734 1468 M2301 VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP.html Genes up-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout and in normal 8.5 dpc embryos compared to normal 9.5 dpc embryos. 17371845 13/23 Arthur Liberzon 7.80418944241302e-08 6.27525965386533e-07 4360 2210.81818181818 1734 7.09471792659602e-09 13 3.7510348486152 -3.45947408149888 -1 9.30637411876862 4356 936 819 56 175 4479 3748 4131 13 1734 3872 1469 M14827 FERRARI_RESPONSE_TO_FENRETINIDE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FERRARI_RESPONSE_TO_FENRETINIDE_UP.html Genes up-regulated in HUVEC cells (umbilical vein endothelium) by fenretinide [PubChem=1744]. 15958647 31/31 Arthur Liberzon 1.1709405844053e-06 1.9724623691624e-06 1740 1908.54545454545 1736 1.06449200693989e-07 615 2.91657403120519 -2.84826211580507 -1 6.6415423458613 1736 2754 689 2378 2680 1048 615 2494 4179 1251 1170 1470 M1913 ZHANG_TLX_TARGETS_36HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_36HR_DN.html Genes down-regulated in neural stem cells (NSC) at 36 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 247/272 Jessica Robertson 1.01397753753121e-06 1.77127090197903e-06 155 1985.63636363636 1736 9.21798186247842e-08 151 1.77345931854102 1.84584562739657 1 4.05218562812856 151 3853 3224 2894 2576 1213 777 1736 2323 1520 1575 1471 M16956 YAMASHITA_LIVER_CANCER_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_STEM_CELL_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) cells with hepatic stem cell properties. 19150350 81/95 Yujin Hoshida 5.08531043003945e-07 1.12395348044995e-06 4135 1875.27272727273 1736 4.62301055046523e-08 126 2.40149361318666 2.35189541441191 1 5.69568246623414 4132 213 733 126 1962 3693 3666 2831 654 882 1736 1472 M16962 IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN.html Genes down-regulated during transition from L0 (non-tumor, not infected with HCV) to L1 (non-tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 41/61 Yujin Hoshida 2.23806076825773e-06 3.33659091161607e-06 550 1892.45454545455 1737 2.03460276821906e-07 220 1.02035612723327 -1.01203732072067 -1 2.19731507262525 548 1737 3682 2021 3087 220 711 660 4300 3589 262 1473 M2339 DUAN_PRDM5_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/DUAN_PRDM5_TARGETS.html Direct targets of PRDM5 [GeneID=11107]. 17636019 95/174 Arthur Liberzon 3.78558670838642e-07 9.60855544952602e-07 3710 2127.90909090909 1738 3.44144305434592e-08 154 2.48475863548297 2.28483789906723 1 5.9629399453977 3710 154 925 1406 1653 2610 4261 2039 774 1738 4137 1474 M114 CHEOK_RESPONSE_TO_HD_MTX_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_HD_MTX_UP.html Genes specifically up-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by high-dose methotrexate (HDMTX) [PubChem=4112]. 12704389 15/79 Jean Junior 4.17523450333235e-08 4.51997863663503e-07 4215 2361.72727272727 1739 3.79566780233761e-09 31 3.17808396189983 2.85698270768854 1 8.05935516275006 4211 2843 1102 1648 31 4470 4094 1318 1739 1073 3450 1475 M11215 REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK.html Genes involved in NRAGE signals death through JNK 56/60 Reactome 9.93868294138616e-08 6.71132834037269e-07 3770 2028.81818181818 1740 9.0351667185222e-09 305 2.14715626042435 -2.02863988312004 -1 5.28053780426617 3766 369 1327 1385 305 2380 2258 3498 1740 1257 4032 1476 M1235 OXFORD_RALA_OR_RALB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_OR_RALB_TARGETS_UP.html Genes up-regulated after knockdown of RALA or RALB [GeneiD=5898;5899], which were also differentially expressed in bladder cancer compared to normal bladder urothelium tissue. 17496927 65/75 Arthur Liberzon 7.31650196453087e-06 9.29079614543602e-06 355 1616.45454545455 1740 6.65138754273477e-07 353 1.57408968865471 1.75639179595188 1 3.13537908577533 353 2177 2578 1939 3659 414 629 582 2258 1740 1452 1477 M1352 NIKOLSKY_BREAST_CANCER_15Q26_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_15Q26_AMPLICON.html Genes within amplicon 15q26 identified in a copy number alterations study of 191 breast tumor samples. 19010930 31/44 Jessica Robertson 2.67327721539125e-06 3.84808431126767e-06 840 1678.09090909091 1741 2.43025496705949e-07 483 2.31194929961539 2.31236380230784 1 4.98447974864064 838 2313 1808 2631 3204 883 483 826 1741 2947 785 1478 M2083 WANG_METASTASIS_OF_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METASTASIS_OF_BREAST_CANCER_ESR1_DN.html Genes whose expression in primary ER(+) [GeneID=2099] breast cancer tumors negatively correlates with developing distant metastases. 15721472 34/46 Arthur Liberzon 2.69734250918724e-07 8.3538310137901e-07 1660 2090.09090909091 1741 2.4521298544536e-08 650 1.61696924864189 -1.85324621042925 -1 3.90245736729071 1660 650 2675 2866 1277 1741 1211 2983 2999 3247 1682 1479 M3218 MOSERLE_IFNA_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/MOSERLE_IFNA_RESPONSE.html Top 50 genes up-regulated in ovarian cancer progenitor cells (also known as side population, SP, cells) in response to interferon alpha (IFNA). 18632618 49/74 Jessica Robertson 4.74990823586566e-05 5.37381756310784e-05 150 1836 1742 4.31819162892843e-06 147 2.06263357459113 -2.20168338261812 -1 3.49174490428316 147 2671 1023 1865 4122 1133 649 1742 3833 966 2045 1480 M19492 GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN.html Genes exclusively down-regulated in B lymphocytes from CLL (chronic lymphocytic leukemia) patients but with a similiar expression pattern in the normal cells and in the cells from WM (Waldenstroem's macroblobulinemia) patients. 17252022 71/90 Arthur Liberzon 2.19617750924973e-07 7.78809755346262e-07 2920 1899.81818181818 1742 1.99652520771448e-08 304 2.14610272949398 2.59589220484294 1 5.22214754307868 2916 304 1523 1785 1050 3063 4228 1073 1216 1998 1742 1481 M987 REACTOME_NFKB_AND_MAP_KINASES_ACTIVATION_MEDIATED_BY_TLR4_SIGNALING_REPERTOIRE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NFKB_AND_MAP_KINASES_ACTIVATION_MEDIATED_BY_TLR4_SIGNALING_REPERTOIRE.html Genes involved in NFkB and MAP kinases activation mediated by TLR4 signaling repertoire 82/99 Reactome 2.27816159696253e-07 7.89211097089284e-07 1225 1944.54545454545 1743 2.07105621170235e-08 1088 1.67388883871234 -1.83610794277198 -1 4.05821307819485 1225 2605 3197 1544 1088 1743 1165 1112 2650 3037 2024 1482 M7952 GALLUZZI_PREVENT_MITOCHONDIAL_PERMEABILIZATION http://www.broadinstitute.org/gsea/msigdb/cards/GALLUZZI_PREVENT_MITOCHONDIAL_PERMEABILIZATION.html Proteins acting on mitochondria to prevent membrane permeabilization. 16892093 33/38 Arthur Liberzon 5.16673257246684e-08 5.19978203455085e-07 2215 1660.36363636364 1743 4.69702972164394e-09 58 1.54608183151593 -1.68648883029867 -1 3.85720504035952 2214 638 2905 1069 58 2481 1743 2410 726 3156 864 1483 M1412 PARK_HSC_VS_MULTIPOTENT_PROGENITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_VS_MULTIPOTENT_PROGENITORS_UP.html Genes up-regulated in long term hematopoietic stem cells (LT-HSC) compared to multipotent progenitor (MPP) cells. 11781229 27/30 Kate Stafford 2.47415285242814e-07 8.15502895493072e-07 1910 1751.18181818182 1743 2.24923011879555e-08 630 1.57419451105719 1.51685616582532 1 3.80452159924622 1906 753 2692 2615 1179 1590 1992 630 1725 2438 1743 1484 M10219 DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN.html Genes down-regulated in multiple myeloma (MM) compared to monoclonal gammopathy of uncertain significance (MGUS). 12947006 35/123 Arthur Liberzon 6.3143677034019e-08 5.82044996223792e-07 4285 2019.72727272727 1743 5.74033444057711e-09 100 2.39840420024539 2.56330427147891 1 5.9639502270758 4281 1743 1008 1000 100 4240 3776 2061 555 1048 2405 1485 M568 REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING.html Genes involved in PI3K events in ERBB4 signaling 44/44 Reactome 2.3829879768765e-07 8.00711660757103e-07 1645 2066.63636363636 1744 2.1663529409056e-08 982 1.6252165435063 -1.58005642572952 -1 3.93464939313714 1644 1744 3044 3544 1144 1153 982 1802 2379 4089 1208 1486 M18667 DITTMER_PTHLH_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DITTMER_PTHLH_TARGETS_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PTHLH [GeneID=5744] by RNAi. 16551631 117/141 Leona Saunders 2.11426280934843e-06 3.17408411581571e-06 1025 1767.63636363636 1744 1.92205894656189e-07 434 2.17203177792937 2.5868659518722 1 4.75284247630243 1023 3316 2132 1744 3061 1013 1378 434 1817 2779 747 1487 M12369 RICKMAN_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_METASTASIS_DN.html Genes down-regulated in metastatic vs non-metastatic HNSCC (head and neck squamous cell carcinoma) samples. 18679425 335/416 Jessica Robertson 1.57850331502576e-07 7.31918027928963e-07 2510 1973.90909090909 1744 1.43500311662147e-08 681 1.9721963439919 -1.74272130544767 -1 4.81631373606715 2510 1263 1348 1171 681 3042 3058 2806 1326 1744 2764 1488 M3582 ALONSO_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_UP.html Up-regulated genes in melanoma tumous that developed metastatic disease compared to primary melanoma that did not. 17409456 260/333 Jessica Robertson 3.69495392225694e-07 9.53941705852328e-07 1235 2007.36363636364 1744 3.35904958439423e-08 1069 1.79966968346358 1.84509365016451 1 4.3073328425238 1232 2523 2766 1735 1618 1069 1151 1744 2136 3870 2237 1489 M16927 BOYLAN_MULTIPLE_MYELOMA_C_D_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_D_UP.html Genes up-regulated both in group C and D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 176/197 Jessica Robertson 4.12010006627447e-07 1.00046055710989e-06 1390 2105.36363636364 1744 3.74554621625072e-08 902 1.77737309907008 1.96482993479622 1 4.23856768028381 1387 2971 2750 4361 1744 902 1413 1593 1808 3125 1105 1490 M1195 PATIL_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/PATIL_LIVER_CANCER.html Genes up-regulated in hepatocellular carcinoma (HCC) compared to normal liver samples. 15735714 912/1154 Arthur Liberzon 2.10817233996846e-07 7.70763712250053e-07 1225 1886.18181818182 1746 2.10817253996606e-08 499 1.61319008256116 1.69754644058577 1 3.91590326481185 1223 1094 4384 1973 1108 499 1318 2713 2358 2332 1746 1491 M9538 GRADE_COLON_VS_RECTAL_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_VS_RECTAL_CANCER_UP.html Genes up-regulated in rectal but down-regulated in colon carcinoma compared to normal mucosa samples. 17210682 44/52 Jessica Robertson 6.51524956705932e-07 1.30859480666043e-06 1205 2100 1746 5.92295590594213e-08 748 1.78131430514158 2.10928173145207 1 4.16454415811329 1205 1746 2805 4368 2197 1058 810 1074 3953 3136 748 1492 M10775 REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS.html Genes involved in G alpha (z) signalling events 36/47 Reactome 1.59760475448158e-07 7.31918027928963e-07 4255 2444.18181818182 1747 1.45236806408826e-08 605 2.20004927015982 2.72665592946077 1 5.37853579750695 4251 605 1413 1220 695 4506 3161 4583 1364 1747 3341 1493 M1023 REACTOME_LIPID_DIGESTION_MOBILIZATION_AND_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIPID_DIGESTION_MOBILIZATION_AND_TRANSPORT.html Genes involved in Lipid digestion, mobilization, and transport 38/63 Reactome 5.41173841299013e-07 1.1656955988727e-06 1510 1814.09090909091 1748 4.91976340383081e-08 1232 2.41497710999955 2.69567948604986 1 5.71256165613728 1510 1765 1232 2098 2026 1466 1748 3303 1815 1472 1520 1494 M5547 LU_AGING_BRAIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_AGING_BRAIN_UP.html Age up-regulated genes in the human frontal cortex. 15190254 372/458 John Newman 3.47512131866246e-07 9.30378481230108e-07 2115 1782 1751 3.15920169781178e-08 420 2.07263640427726 2.20224549776819 1 4.97729535512612 2114 1237 645 829 1543 2121 4030 1751 2720 420 2192 1495 M11690 KORKOLA_CHORIOCARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CHORIOCARCINOMA.html Genes predicting the choriocarcinoma (CC) of nonseminomatous male germ cell tumors (NSGCT). 15870693 2/12 Leona Saunders 1.42022520053422e-05 1.71575708894843e-05 1325 2128.6 1751.5 1.57803796137213e-06 194 4.58420203692966 4.58420203692966 1 8.73567367341405 1324 2934 4385 NA 4058 1000 486 194 3402 2136 1367 1496 M653 REACTOME_SYNTHESIS_OF_PA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PA.html Genes involved in Synthesis of PA 22/29 Reactome 8.01116093405671e-07 1.50169498049038e-06 1280 1920.90909090909 1752 7.28287622842893e-08 940 1.78657992635452 -1.96741895246162 -1 4.13405351447422 1277 2357 2180 2781 2378 1746 1179 940 3379 1752 1161 1497 M1091 REACTOME_DIGESTION_OF_DIETARY_CARBOHYDRATE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DIGESTION_OF_DIETARY_CARBOHYDRATE.html Genes involved in Digestion of dietary carbohydrate 3/13 Reactome 4.73699543640654e-05 5.36049351710354e-05 1755 1922.81818181818 1752 4.73709641550197e-06 46 3.71648967940425 -3.71648967940425 -1 6.33321988046675 1752 2930 4269 2312 4139 1277 331 1102 46 2606 387 1498 M15762 RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN.html Neuroblastoma markers down-regulated in neuroblastoma cell lines expressing ESWR1-FLI1 [GeneID=2130;2313] fusion protein. 14973077 22/43 Kevin Vogelsang 1.40513654957276e-06 2.27209472901111e-06 1755 1968.72727272727 1754 1.27739767912007e-07 807 2.3545660619214 2.73924581772812 1 5.29395390924344 1754 807 1034 1833 2809 1727 2382 3850 2805 991 1664 1499 M7371 LOPES_METHYLATED_IN_COLON_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPES_METHYLATED_IN_COLON_CANCER_UP.html Genes methylated aberrantly in HCT116 and Colo320 (colon cancer) cells. 18794111 27/42 Jessica Robertson 4.41240465797178e-06 5.93349002439511e-06 980 1725.36363636364 1754 4.01128500698655e-07 241 2.83880202041435 3.09344244892641 1 5.91705139909447 976 2327 1239 2399 3437 1047 1754 241 2443 2112 1004 1500 M1708 HOWLIN_CITED1_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_2_DN.html Genes down-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs wild type (WT) animals. 16278680 22/26 Arthur Liberzon 2.1174050349287e-05 2.48178588648212e-05 380 1628 1754 1.92493219482979e-06 299 2.12541178527842 -2.13818887516855 -1 3.88632999051239 376 3176 2127 2427 3970 476 317 299 2482 1754 504 1501 M797 REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS.html Genes involved in Class B/2 (Secretin family receptors) 50/92 Reactome 4.14836107727873e-07 1.00337562730974e-06 3530 2347.45454545455 1755 3.77123805409241e-08 454 2.76048731870124 3.1543365993427 1 6.60931086361629 3529 454 748 1363 1755 3000 4303 4286 885 1036 4463 1502 M6206 HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2 http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2.html Genes differentially expressed in hereditary breast cancer tumors with mutated BRCA1 [GeneID=672] compared to those with mutated BRCA2 [GeneID=675]. 11207349 232/254 John Newman 1.41576402456993e-07 7.20206492018647e-07 1660 2167.72727272727 1755 1.28705828698043e-08 576 1.44327173033384 1.42199748712794 1 3.51527007863456 1657 2054 3703 1549 576 1368 1688 2576 1755 4224 2695 1503 M1837 LABBE_WNT3A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_WNT3A_TARGETS_DN.html Down-regulated genes in NMuMG cells (mammary epithelium) after stimulation with WNT3A [GeneID=89780]. 17210685 120/248 Jessica Robertson 9.01536003595978e-09 1.19194676105687e-07 3605 1869.27272727273 1755 8.19578188445796e-10 29 2.67923649176903 2.46520797686825 1 7.41020029772485 3605 29 279 772 1827 4485 3717 1755 1527 425 2141 1504 M3737 PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP http://www.broadinstitute.org/gsea/msigdb/cards/PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP.html Genes up-regulated in OV-90 cells (ovarian cancer) exposed to ascites which inhibited invasion. 17971902 122/157 Arthur Liberzon 1.91561005685296e-07 7.53743535490661e-07 1700 1801.36363636364 1757 1.74146383968295e-08 55 1.5961343965177 1.56087174103296 1 3.88019775126808 1699 55 3207 1525 909 1097 1757 1963 2170 3231 2202 1505 M1857 MALONEY_RESPONSE_TO_17AAG_UP http://www.broadinstitute.org/gsea/msigdb/cards/MALONEY_RESPONSE_TO_17AAG_UP.html Up-regulated genes in A2780 cells (ovarian cancer) treated with 17AAG [PubChem=6440175], a chemical with anticancer properties. 17409432 73/107 Jessica Robertson 1.23653633015865e-06 2.05343161212006e-06 1760 2137.27272727273 1758 1.12412456833568e-07 343 2.3533948368991 2.75393897804978 1 5.33288832210497 1758 3897 1470 1710 2725 1582 3747 717 2803 2758 343 1506 M4377 KEGG_GALACTOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GALACTOSE_METABOLISM.html Galactose metabolism 29/39 KEGG 7.85166066585357e-08 6.28391550069647e-07 1760 1886 1759 7.13787358734032e-09 177 1.93425555561654 -2.05282787298643 -1 4.77421653667183 1759 2324 2747 3390 177 1672 1649 1198 346 3609 1875 1507 M16756 MURAKAMI_UV_RESPONSE_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_6HR_DN.html Genes down-regulated in primary keratinocytes at 6 h after UVB irradiation. 11532376 28/31 John Newman 1.02655439166659e-06 1.78531198550712e-06 1405 1782.63636363636 1761 9.33231700612031e-08 863 2.73131112742238 3.02656568676072 1 6.26404438076485 1405 1820 1224 1615 2590 863 1053 2306 3042 1930 1761 1508 M256 PID_TAP63_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TAP63_PATHWAY.html Validated transcriptional targets of TAp63 isoforms 18832364 63/73 Pathway Interaction Database 3.44650819172505e-07 9.25342358642903e-07 3030 2090.27272727273 1762 3.13318975604845e-08 685 2.44405062477991 2.80566824401088 1 5.88050486530582 3029 3642 1732 3682 1537 2469 1762 725 685 2848 882 1509 M1431 NADLER_OBESITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/NADLER_OBESITY_UP.html Genes up-regulated in adipose tissue from obese mouse strains compared to the lean ones. 11027337 87/125 Kevin Vogelsang 7.83737097801786e-07 1.47910399905015e-06 1765 1770.45454545455 1762 7.1248852454879e-08 159 2.44066886147886 2.56153915388176 1 5.6723622119176 1762 159 539 408 2359 2642 2737 3640 1436 839 2954 1510 M508 REACTOME_SIGNALING_BY_SCF_KIT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_SCF_KIT.html Genes involved in Signaling by SCF-KIT 97/107 Reactome 1.54336451918479e-07 7.28175281873995e-07 1765 1913.54545454545 1764 1.40305875223304e-08 205 1.48776557725808 -1.53780473011027 -1 3.62232369311385 1764 1610 3525 205 662 1684 1183 2340 1797 3930 2349 1511 M232 PID_ECADHERIN_STABILIZATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ECADHERIN_STABILIZATION_PATHWAY.html Stabilization and expansion of the E-cadherin adherens junction 18832364 70/82 Pathway Interaction Database 4.99023512103847e-08 5.11493068309462e-07 2335 1556.36363636364 1765 4.53657748566493e-09 51 2.03988430187874 -1.72583264837473 -1 5.11099941194355 2333 285 1765 652 51 2319 1722 2643 633 2338 2379 1512 M2213 WIERENGA_STAT5A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_DN.html Genes down-regulated in CD34+ [GeneID=947] cells by intermediate activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 247/340 Arthur Liberzon 1.14136429586199e-07 7.05613393308323e-07 2920 2006.36363636364 1765 1.03760395916018e-08 332 2.18045656887818 2.13892512187928 1 5.3441300534883 2917 1348 424 1765 382 1623 3340 3990 2946 332 3003 1513 M2445 PLASARI_TGFB1_TARGETS_10HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_10HR_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 10 h. 19752192 268/318 Arthur Liberzon 1.14491331628537e-18 5.93845148666696e-17 1625 1459.81818181818 1766 1.04083028753215e-19 62 2.64341800969844 3.04348435042832 1 17.199868191481 1622 2040 62 718 520 1772 3496 1840 2083 139 1766 1514 M1696 WOOD_EBV_EBNA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WOOD_EBV_EBNA1_TARGETS_UP.html Genes up-regulated in the Ad/AH cells (adenocarcinoma) engineered to stably express the Epstein-Barr virus (EBV) gene EBNA1. 17486072 150/175 Arthur Liberzon 1.31320745072072e-06 2.1551944253831e-06 1610 1888.27272727273 1767 1.19382566781026e-07 876 1.7121196256774 1.78429421714588 1 3.85163423452873 1606 2090 2492 1690 2764 1004 1767 876 2987 1937 1558 1515 M10454 MCLACHLAN_DENTAL_CARIES_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCLACHLAN_DENTAL_CARIES_UP.html Genes up-regulated in pulpal tissue extracted from carious teeth. 15869869 225/455 John Newman 3.15491473662289e-16 1.20090302877904e-14 1580 1859.27272727273 1767 2.86810430602081e-17 86 2.58609235883972 -2.45679361749174 -1 14.4276527935454 1576 2526 86 1767 756 2358 1742 3209 3769 149 2514 1516 M14043 PETRETTO_CARDIAC_HYPERTROPHY http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_CARDIAC_HYPERTROPHY.html Genes that correlated most highly with left ventricular mass (LVM) index. 18443592 66/74 Jessica Robertson 1.69820831697009e-06 2.64277720280211e-06 560 1893.72727272727 1768 1.54382693440033e-07 428 3.08630932091023 3.55927391749261 1 6.87327477108256 557 2185 428 1258 4351 2392 2909 2413 1768 1167 1403 1517 M507 REACTOME_GPCR_LIGAND_BINDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPCR_LIGAND_BINDING.html Genes involved in GPCR ligand binding 162/454 Reactome 2.98215159200884e-22 1.95496604365024e-20 3565 1621.72727272727 1769 2.71104690182622e-23 46 3.06596383863501 -2.86809077839632 -1 24.251245892168 3563 1461 46 1763 534 2029 1769 2193 2208 104 2169 1518 M11787 GRADE_COLON_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_CANCER_DN.html Down-regulated genes in colon carcinoma tumors compared to the matched normal mucosa samples. 17210682 44/64 Jessica Robertson 9.50351490286663e-06 1.18168046210565e-05 2005 2085.54545454545 1769 8.63959632382162e-07 1061 2.39226184299763 2.37282868458757 1 4.69059211836492 2005 3393 1769 2661 3739 1649 1656 1105 1061 2577 1326 1519 M13166 REACTOME_DOWNSTREAM_TCR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_TCR_SIGNALING.html Genes involved in Downstream TCR signaling 32/42 Reactome 3.4744231212121e-07 9.30378481230108e-07 2145 1676.09090909091 1770 3.1585669726564e-08 548 1.85225657752472 -1.74153680234671 -1 4.44274782474797 2143 620 1982 1054 1542 2338 1598 1770 548 1857 2985 1520 M4661 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_UP.html Genes up-regulated in granulocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 78/109 Arthur Liberzon 1.21940166328745e-07 7.10564919841578e-07 1280 2031.27272727273 1770 1.10854702806878e-08 432 2.10593612065036 2.12786345048333 1 5.15720404166042 1278 2616 1383 4165 432 1205 1580 2401 3732 1782 1770 1521 M1175 IWANAGA_E2F1_TARGETS_NOT_INDUCED_BY_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_E2F1_TARGETS_NOT_INDUCED_BY_SERUM.html Genes up-regulated in REF52 cells (embryonic fibroblast) by expression of E2F1 [GeneID=1869] that were not induced at all at 16 hr after serum stimulation. 16288221 6/8 Arthur Liberzon 0.000356994949506981 0.000380021687341666 1770 2410.09090909091 1770 3.57052312904374e-05 864 1.90384883807562 1.90384883807562 1 2.56864960808102 1770 2920 4361 3148 4412 1713 1745 1172 864 2791 1615 1522 M10814 BECKER_TAMOXIFEN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BECKER_TAMOXIFEN_RESISTANCE_UP.html Genes up-regulated in a breast cancer cell line resistant to tamoxifen [PubChem=5376] compared to the parental line sensitive to the drug. 15657362 58/83 Jean Junior 1.37296641588137e-07 7.20206492018647e-07 3470 2003.09090909091 1770 1.24815136505897e-08 419 2.02944751867193 -1.51059493839231 -1 4.96329732407883 3468 419 1738 2145 539 2709 2279 1080 1770 1399 4488 1523 M83 PID_CDC42_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CDC42_REG_PATHWAY.html Regulation of CDC42 activity 18832364 40/42 Pathway Interaction Database 3.41495132332318e-08 3.88399283038203e-07 3620 1872.54545454545 1771 3.10450125121071e-09 19 1.7991521745001 -1.68253807590214 -1 4.58844047403362 3618 495 1610 974 19 2861 2552 4117 398 2183 1771 1524 M18120 GEORGES_TARGETS_OF_MIR192_AND_MIR215 http://www.broadinstitute.org/gsea/msigdb/cards/GEORGES_TARGETS_OF_MIR192_AND_MIR215.html Genes down-regulated in HCT116 cells (colon cancer) by expression of MIR192 or MIR215 [GeneID=406967;406997] at 24 h. 19074876 1117/1300 Jessica Robertson 1.94001407264262e-07 7.601476063939e-07 2065 1897.45454545455 1771 1.94001424200709e-08 584 1.74810269817241 1.89208108281359 1 4.25181314135892 2065 1078 4458 1771 1022 1603 2563 2026 1937 584 1765 1525 M3879 LEE_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER.html Genes down-regulated in tumor compared to non-tumor liver samples from patients with hepatocellular carcinoma (HCC). 18519680 29/95 Leona Saunders 1.04082092305258e-07 6.85170816849119e-07 2435 1737.90909090909 1772 9.46200883903515e-09 326 2.44453714335365 -2.23638219510453 -1 6.00998336998448 2433 695 1250 1804 326 2248 1645 3848 1020 1772 2076 1526 M1529 SA_G1_AND_S_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/SA_G1_AND_S_PHASES.html Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. 20/30 SigmaAldrich 6.48418490550099e-07 1.30791290081906e-06 1775 1742.72727272727 1773 5.89471528783855e-08 150 1.94522403501418 2.40483832851279 1 4.552530900893 1773 837 2302 1519 2186 1843 1521 1321 150 3331 2387 1527 M17321 REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES.html Genes involved in Synthesis and interconversion of nucleotide di- and triphosphates 21/22 Reactome 4.98536600991868e-07 1.11141872398347e-06 1595 1760.27272727273 1773 4.53215194512782e-08 532 1.41537091822973 1.76851867958477 1 3.33909629725492 1595 798 2501 2602 1942 1688 878 1773 532 3077 1977 1528 M13519 KEGG_GRAFT_VERSUS_HOST_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GRAFT_VERSUS_HOST_DISEASE.html Graft-versus-host disease 29/73 KEGG 3.77257857557498e-06 5.17933998740951e-06 390 1944 1774 3.42962276803646e-07 390 1.50217712499302 -1.45398606839949 -1 3.14316495933248 390 2304 2353 1976 3368 635 1224 1774 4115 1767 1478 1529 M1278 MCLACHLAN_DENTAL_CARIES_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCLACHLAN_DENTAL_CARIES_DN.html Genes down-regulated in pulpal tissue extracted from carious teeth. 15869869 125/178 John Newman 1.40458262417015e-07 7.20206492018647e-07 1630 1740 1774 1.27689337622296e-08 7 2.35097562444966 2.64030727325346 1 5.75756666546912 1627 7 357 1611 2785 2337 3945 2447 1819 431 1774 1530 M2449 PLASARI_NFIC_TARGETS_BASAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_NFIC_TARGETS_BASAL_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon knockout of NFIC [GeneID=4782]. 19752192 29/37 Arthur Liberzon 1.15458215284132e-05 1.41475279372042e-05 1005 2035.81818181818 1774 1.04962564749931e-06 315 3.12147406074005 3.4036802423161 1 6.0374937163711 1005 3719 954 2606 3797 1208 2070 315 4131 1774 815 1531 M76 PID_P38_ALPHA_BETA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_ALPHA_BETA_PATHWAY.html Regulation of p38-alpha and p38-beta 18832364 35/37 Pathway Interaction Database 1.4557820330333e-07 7.26289540930751e-07 2320 1777 1776 1.3234382994229e-08 603 1.94734937601385 -1.75427481795372 -1 4.75763002022826 2317 1776 2031 1254 603 1811 1195 3124 1171 1413 2852 1532 M871 REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE.html Genes involved in Deposition of New CENPA-containing Nucleosomes at the Centromere 36/81 Reactome 1.61389874083436e-05 1.92899520302309e-05 325 1611.45454545455 1777 1.46719143669197e-06 63 1.77387434457942 1.83542664853217 1 3.31333325335716 325 1777 2387 3345 3892 63 76 423 2922 1999 517 1533 M15844 DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP.html Genes exclusively up-regulated in fibroblasts expressing the TTD mutant form of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 112/131 Arthur Liberzon 7.54775911768676e-07 1.43766840336891e-06 1455 1742.81818181818 1777 6.86160155197537e-08 80 1.96512275318337 2.29226143568562 1 4.56714766102898 1453 80 1777 1307 2333 1423 2723 2326 2592 2310 847 1534 M3732 SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN.html Genes down-regulated in response to UVB radiation in HFK cells (keratinocytes) immortalized by overexpression of HPV E6 and E7 viral oncogenes. 16007217 58/61 Leona Saunders 9.01901239591376e-07 1.62977559374858e-06 1215 1750.45454545455 1777 8.19910553936918e-08 442 2.374602695187 2.76959284473843 1 5.47723108470318 1211 2208 1296 886 2489 2414 3079 442 1235 1777 2218 1535 M7578 REACTOME_SEMA3A_PLEXIN_REPULSION_SIGNALING_BY_INHIBITING_INTEGRIN_ADHESION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA3A_PLEXIN_REPULSION_SIGNALING_BY_INHIBITING_INTEGRIN_ADHESION.html Genes involved in SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion 32/34 Reactome 4.21705782889062e-07 1.00930518493669e-06 3040 2087.72727272727 1778 3.83368967021385e-08 970 2.19253207866275 2.71118406414855 1 5.2369298872054 3039 1770 1185 1227 1778 3809 3686 1224 2225 970 2052 1536 M19541 REN_ALVEOLAR_RHABDOMYOSARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/REN_ALVEOLAR_RHABDOMYOSARCOMA_DN.html Genes commonly down-regulated in human alveolar rhabdomyosarcoma (ARMS) and its mouse model overexpressing PAX3-FOXO1 [GeneID=5077;2308] fusion. 18701482 575/636 Jessica Robertson 1.3775614385498e-07 7.20206492018647e-07 2100 1962.18181818182 1778 1.37756152394521e-08 377 1.91899439387126 2.21341822698409 1 4.69044549833338 2100 1139 4487 377 642 2575 3939 1778 1743 446 2358 1537 M17843 NIELSEN_SCHWANNOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SCHWANNOMA_UP.html Top 20 positive significant genes associated with schwannoma tumors. 11965276 15/25 John Newman 2.95876403655827e-07 8.69574486460463e-07 4595 2533.81818181818 1778 2.68978584952761e-08 618 2.42460987148984 2.40050823560953 1 5.8596545144837 4592 893 1076 1778 1373 4434 4600 3872 691 618 3945 1538 M7603 BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_UP.html Genes up-regulated in B lymphocytes from patients with primary immunodefiency syndrom. 17195838 56/84 Jessica Robertson 2.48627522271456e-06 3.62645829765535e-06 1130 1944.81818181818 1778 2.26025275683731e-07 1130 1.68540349055459 1.65873599999384 1 3.63757075437176 1130 2213 2717 1924 3157 1778 1252 1726 1662 1607 2227 1539 M78 EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP.html Genes up-regulated in Rh4 cells (alveolar rhabdomyosarcoma, ARMS) after knockdown of the PAX3-FOXO1 [GeneiD=5077;2308] fusion protein by RNAi for 72 hr. 17525748 268/388 Leona Saunders 4.09483780320871e-08 4.47398945165397e-07 2355 1634.45454545455 1779 3.72257989038683e-09 323 2.26346103730493 2.69662709964493 1 5.72959060845493 2352 1314 323 850 1067 2056 3672 2101 1779 439 2026 1540 M15804 TURJANSKI_MAPK1_AND_MAPK2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK1_AND_MAPK2_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK1 and MAPK3 [GeneID=5594;5595] phosphorylation. 17496919 17/17 Arthur Liberzon 8.66983421853871e-08 6.49549484309567e-07 3000 1607.54545454545 1779 7.88166778200228e-09 138 2.13561037097427 2.85625279825421 1 5.2640663326111 2998 913 1779 2447 219 2465 2412 1037 399 2876 138 1541 M925 REACTOME_SIGNAL_REGULATORY_PROTEIN_SIRP_FAMILY_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_REGULATORY_PROTEIN_SIRP_FAMILY_INTERACTIONS.html Genes involved in Signal regulatory protein (SIRP) family interactions 10/15 Reactome 3.06411448360622e-05 3.53436470249788e-05 845 2142.18181818182 1781 2.78559741890088e-06 60 1.19923132530993 -1.19923132530993 -1 2.0969448094292 842 4350 3344 3743 4508 569 60 274 1781 3985 108 1542 M6562 CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_UP.html Genes up-regulated by 2-methoxyestradiol (2ME2) [PubChem=1573] in the MM.1S cell line (multiple myeloma) sensitive to dexamethasone [PubChem=5743]. 12480690 73/89 Arthur Liberzon 1.16929361597017e-05 1.43092192568815e-05 390 2105.09090909091 1781 1.06299984616186e-06 388 1.90885736400432 1.90306408190397 1 3.66884739738207 388 4195 2996 1728 3802 684 811 1781 2655 3190 926 1543 M13746 ZHAN_MULTIPLE_MYELOMA_HP_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_HP_UP.html Top 50 up-regulated genes in cluster HP of multiple myeloma samples characterized by a hyperploid signature. 16728703 66/96 Kevin Vogelsang 2.19333613293896e-07 7.78436449348851e-07 2670 1928.27272727273 1782 1.99394213782568e-08 480 2.42265106053387 -2.23073194658371 -1 5.90172790020289 2666 1674 1566 619 1048 2306 1782 4129 480 2653 2288 1544 M15326 HUANG_FOXA2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_FOXA2_TARGETS_UP.html Genes up-regulated in H358 cells (lung cancer) by inducible expression of FOXA2 [GeneID=3170] in a Tet-off system. 18593902 65/77 Leona Saunders 9.59216373699693e-07 1.70334886526055e-06 3415 2102.63636363636 1783 8.7201526538675e-08 315 2.58374203803642 2.80649165087087 1 5.94411119226829 3414 315 526 810 2537 3653 4717 1178 1783 864 3332 1545 M4364 PASTURAL_RIZ1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PASTURAL_RIZ1_TARGETS_DN.html Genes down-regulated in K562 (chronic myelogenous leukemia, CML) cells engineered to stably express RIZ1 [GeneID=7799]. 16953217 5/6 Aravind Subramanian 5.99299239888098e-07 1.23793978655222e-06 930 2272.90909090909 1785 5.99299401509969e-08 928 3.8749655154722 3.8749655154722 1 9.15567852221471 928 2481 4325 4562 2211 1338 1261 1059 3837 1785 1215 1546 M2257 SONG_TARGETS_OF_IE86_CMV_PROTEIN http://www.broadinstitute.org/gsea/msigdb/cards/SONG_TARGETS_OF_IE86_CMV_PROTEIN.html Cellular genes up-regulated in forskin fibroblasts by expression of CMV EI86 protein off an adenovirus vector. 11867723 71/80 John Newman 1.82776227588045e-05 2.16433465683787e-05 145 1630 1785 1.66161587374998e-06 143 1.5317683228558 1.63668243547495 1 2.82348917508357 143 2163 2752 1880 3924 536 283 1335 2295 834 1785 1547 M2399 MADAN_DPPA4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MADAN_DPPA4_TARGETS.html Genes differentially expressed in ES cells with DPPA4 [GeneID=55211] knockout. 19332562 38/76 Arthur Liberzon 2.66880038659855e-07 8.32746245638274e-07 3185 2291.72727272727 1786 2.42618246395309e-08 1189 2.52487898944952 -2.43256031429107 -1 6.1231320083488 3183 1766 1189 1786 1265 3575 3354 2314 1747 1476 3554 1548 M1059 REACTOME_NOD1_2_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOD1_2_SIGNALING_PATHWAY.html Genes involved in NOD1/2 Signaling Pathway 36/37 Reactome 4.64759860327733e-07 1.06230825217767e-06 320 1514.72727272727 1787 4.2250905319124e-08 317 1.79865217309549 -1.91947170724771 -1 4.27106807233041 317 1787 2499 3400 1888 570 401 925 2293 2000 582 1549 M1113 GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP.html Up-regulated genes from the set C (Fig. 5a): specific to cells expressing AF4-MLL [GeneID=4299;4297] fusion protein alone. 17130830 226/262 Arthur Liberzon 2.29410374921043e-07 7.91532872534593e-07 1790 1861.18181818182 1787 2.08554908039431e-08 850 2.07920699457789 2.48175487845486 1 5.05192467874318 1787 2527 1005 2103 1098 2483 3357 1672 1580 850 2011 1550 M18299 YANG_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_UP.html Genes up-regulated in early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 51/67 Leona Saunders 4.25699523475936e-07 1.01481223304284e-06 2900 1848.36363636364 1787 3.86999641680659e-08 145 2.33812341799467 -2.21065136042473 -1 5.58577976857652 2896 383 972 740 1787 3077 3244 3692 145 947 2449 1551 M15902 KEGG_GLYCEROLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROLIPID_METABOLISM.html Glycerolipid metabolism 53/70 KEGG 7.18278376820048e-08 6.06397110828564e-07 2485 1656.90909090909 1788 6.52980363882847e-09 148 2.24437695240674 -2.35403821600335 -1 5.56166078793214 2483 436 1312 1788 148 3106 2911 747 1133 1972 2190 1552 M15484 ONDER_CDH1_SIGNALING_VIA_CTNNB1 http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_SIGNALING_VIA_CTNNB1.html Genes changed in HMLE cells (mmortalized nontransformed mammary epithelium) after RNAi knockdown of both CDH1 and CTNNB1 [GeneID=999;1499], compared to the knockdown of CDH1 alone. 18483246 144/178 Jessica Robertson 2.91670083798616e-26 2.80955672557034e-24 1790 1737.54545454545 1789 2.65154621635104e-27 28 3.13469093181151 3.40948379585432 1 29.6400459292147 1789 1473 28 294 2723 2208 4097 2637 1140 78 2646 1553 M2785 EHLERS_ANEUPLOIDY_DN http://www.broadinstitute.org/gsea/msigdb/cards/EHLERS_ANEUPLOIDY_DN.html Down-regulated genes in the expression signature of aneuploidy in uveal melanoma tumors: low vs high aneuploidy. 18172260 14/18 Jessica Robertson 2.85388874675219e-07 8.53634656823216e-07 1790 1902 1789 2.5944446517864e-08 135 2.20446321290826 2.30761096470749 1 5.33019702025078 2090 1916 1789 1789 1339 1882 1640 3709 135 1532 3101 1554 M17228 SASAI_TARGETS_OF_CXCR6_AND_PTCH1_DN http://www.broadinstitute.org/gsea/msigdb/cards/SASAI_TARGETS_OF_CXCR6_AND_PTCH1_DN.html Down-regulated genes in medulloblastoma tumors from heterozygotic CXCR6 [GeneID=10663] knockout mice compared to those from PTCH1 [GeneID=5727] heterozygotic knockout mice. 17413002 5/9 Jessica Robertson 3.18275944288546e-06 4.47235027401589e-06 3260 2049.45454545455 1789 3.1827640013756e-07 169 3.25235899183916 -2.66793379006497 -1 6.94692321684953 3256 2475 4586 1620 3332 2562 1008 1137 169 1789 610 1555 M5785 KEGG_TASTE_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TASTE_TRANSDUCTION.html Taste transduction 33/88 KEGG 4.17919675819129e-07 1.00504816968881e-06 4465 2406.45454545455 1790 3.79927050189663e-08 796 2.4115018256321 2.42385391131447 1 5.76672328524679 4463 1790 1251 796 1768 3771 2067 4369 1748 1683 2765 1556 M2193 OHGUCHI_LIVER_HNF4A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OHGUCHI_LIVER_HNF4A_TARGETS_UP.html Genes up-regulated in liver samples of liver-specific knockout of HNF4A [GeneID=3172]. 18426912 65/91 Arthur Liberzon 3.28250061959322e-07 9.05922275783096e-07 2410 1670.36363636364 1790 2.98409191759765e-08 353 2.25737436997311 -2.33169995035609 -1 5.43589334433788 2409 353 850 1790 1489 2427 1838 1823 3252 1011 1132 1557 M13910 CLIMENT_BREAST_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/CLIMENT_BREAST_CANCER_COPY_NUMBER_UP.html Genes from the most frequent genomic gains and amplifications in a panel of patients with lymph node negative breast cancer (NNBC). 17234794 34/41 Jessica Robertson 4.28614903128564e-07 1.01917498376162e-06 4620 2451.27272727273 1792 3.89649987848606e-08 154 2.342162127168 -1.91494283220005 -1 5.59375981127799 4618 587 1085 154 1792 4567 4374 3205 647 1314 4621 1558 M3624 KEGG_GLYCOSAMINOGLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_DEGRADATION.html Glycosaminoglycan degradation 22/28 KEGG 6.07911017524215e-08 5.71581673847469e-07 1795 1493 1793 5.52646394838368e-09 89 1.62058005706576 2.086912312431 1 4.01869434033768 1793 774 2526 1815 89 1636 1971 1982 127 1751 1959 1559 M137 PID_VEGF_VEGFR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGF_VEGFR_PATHWAY.html VEGF and VEGFR signaling network 18832364 9/10 Pathway Interaction Database 1.07045908721462e-05 1.31989730711938e-05 725 2184 1793 1.07046424372153e-06 133 2.49645150051802 2.49645150051802 1 4.84882856446628 725 3520 4203 3873 4084 431 133 160 4215 1793 887 1560 M18658 WIKMAN_ASBESTOS_LUNG_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WIKMAN_ASBESTOS_LUNG_CANCER_UP.html Genes positively correlated with the asbestos exposure of lung cancer patients. 17297452 22/26 Arthur Liberzon 6.73095261059779e-08 6.00568928582638e-07 3485 1775.63636363636 1793 6.11904801502992e-09 120 1.77046979324552 0.975089234105992 1 4.37971972632673 3483 789 2249 1793 120 1145 683 4318 124 2456 2372 1561 M707 WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_DN.html Genes down-regulated in mucinous ovarian carcinoma tumors of grades 1 and 2 compared to the normal ovarian survace epithelium tissue. 16467078 86/119 Arthur Liberzon 1.36521188488226e-07 7.20206492018647e-07 2685 1920.09090909091 1794 1.241101790546e-08 234 2.34382817444913 2.39302486828836 1 5.7399103539289 2682 234 904 2074 538 2662 4039 1764 1794 1345 3085 1562 M17019 REACTOME_NEF_MEDIATED_DOWNREGULATION_OF_MHC_CLASS_I_COMPLEX_CELL_SURFACE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEF_MEDIATED_DOWNREGULATION_OF_MHC_CLASS_I_COMPLEX_CELL_SURFACE_EXPRESSION.html Genes involved in Nef mediated downregulation of MHC class I complex cell surface expression 30/45 Reactome 8.74956221118493e-07 1.59328447672812e-06 225 1827 1795 7.95415062813842e-08 216 1.0331713030894 -1.00807454892373 -1 2.35892082860959 224 1795 3391 2493 2465 216 313 881 4401 3143 775 1563 M19522 REACTOME_ADENYLATE_CYCLASE_ACTIVATING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADENYLATE_CYCLASE_ACTIVATING_PATHWAY.html Genes involved in Adenylate cyclase activating pathway 9/11 Reactome 2.53179972395459e-07 8.22189102913976e-07 2425 2076.09090909091 1795 2.53180001240508e-08 218 2.33675404357517 2.5979309066422 1 5.66838557279783 2421 1004 4228 1208 1312 2823 4665 2677 486 1795 218 1564 M99 PID_TXA2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TXA2PATHWAY.html Thromboxane A2 receptor signaling 18832364 74/89 Pathway Interaction Database 2.70266208648859e-07 8.3538310137901e-07 2350 1817.09090909091 1796 2.45696583500548e-08 184 2.06614005345018 -2.035911710087 -1 5.00040351224513 2350 275 1571 184 1280 2280 2671 3061 3014 1506 1796 1565 M1467 BIOCARTA_CTLA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTLA4_PATHWAY.html The Co-Stimulatory Signal During T-cell Activation 13/29 BioCarta 9.34104859034569e-08 6.56798957981166e-07 3365 1608.90909090909 1797 8.49186271541838e-09 33 2.05006673001236 -1.84492467359015 -1 5.04723145444558 3361 925 1797 155 272 3207 2541 220 33 2167 3020 1566 M9230 LIU_CMYB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CMYB_TARGETS_DN.html Genes down-regulated in MCF-7 cells (breast cancer) by overexpression of CMYB [GeneID=4602] off adenovirus vector. 16205643 9/9 Arthur Liberzon 2.49361049702125e-06 3.63463233559836e-06 3660 2082.09090909091 1797 2.49361329516766e-07 21 3.47108371510397 -3.44275712531662 -1 7.54321596270767 3658 981 4291 315 3218 3535 1524 2356 21 1797 1207 1567 M286 PID_TGFBR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TGFBR_PATHWAY.html TGF-beta receptor signaling 18832364 79/85 Pathway Interaction Database 3.12385166851714e-08 3.60503175437675e-07 2205 1919.54545454545 1798 2.83986519352157e-09 14 1.67976508262728 -1.61338558031524 -1 4.30250975653252 2205 1640 3081 880 14 1798 1724 2383 652 3564 3174 1568 M10172 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN.html Genes from the yellow module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 31/32 Arthur Liberzon 4.31142973055937e-07 1.02188257382467e-06 1090 1750.27272727273 1798 3.91948234135279e-08 322 1.63386405277319 1.57781582205551 1 3.88625042817896 1089 2316 2772 3356 1798 917 478 322 2768 2298 1139 1569 M14437 VALK_AML_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_5.html Top 40 genes from cluster 5 of acute myeloid leukemia (AML) expression profile; 96% of the samples are FAB M4 or M5 subtype. 15084694 32/69 Jessica Robertson 2.47317242040537e-06 3.60846176949408e-06 1015 1597.54545454545 1799 2.24834109152201e-07 217 1.93228430518739 -1.66981317322679 -1 4.17941689918661 1012 1799 1866 2627 3156 308 217 2335 1521 1859 873 1570 M8617 WEI_MIR34A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WEI_MIR34A_TARGETS.html Potential direct target genes for MIR34A [GeneID=407040] microRNA in IMR32 cells (neuroblastoma). 18504438 188/211 Jessica Robertson 2.03096811002534e-07 7.65651554540509e-07 1955 1871 1800 1.84633481592519e-08 872 1.6802458286577 1.91510086426909 1 4.08270910693297 1952 1431 2503 2385 962 1731 2990 1800 2197 1758 872 1571 M2485 GUILLAUMOND_KLF10_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUILLAUMOND_KLF10_TARGETS_UP.html Genes up-regulated in the liver tissue from 10 week old male mice with KLF10 [GeneID=7071] compared to wild-type littermates. 20385766 69/96 Arthur Liberzon 1.10087947092707e-06 1.88402868120949e-06 1265 1891 1800 1.0008000198248e-07 751 2.58848157269761 2.74706380321278 1 5.90952814845526 1262 1655 751 2173 2637 1800 2259 3077 2359 1215 1613 1572 M277 PID_INTEGRIN_A4B1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_A4B1_PATHWAY.html Alpha4 beta1 integrin signaling events 18832364 46/61 Pathway Interaction Database 1.11226666216133e-07 7.03739764799127e-07 3985 2069 1803 1.01115156217713e-08 148 2.54185754542253 2.45844796141794 1 6.23936967751897 3982 503 1072 148 359 3641 4406 2540 510 1803 3795 1573 M18496 LEE_LIVER_CANCER_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by overexpression of MYC [GeneID=4609]. 15565109 69/119 Yujin Hoshida 2.3577153589783e-06 3.47980503263839e-06 1805 1863.81818181818 1803 2.1433798961084e-07 802 2.40012651786003 -2.13986108371104 -1 5.21866603760227 1803 2179 943 1858 3122 1418 1588 2126 3579 1084 802 1574 M17487 RIGGINS_TAMOXIFEN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIGGINS_TAMOXIFEN_RESISTANCE_UP.html Genes up-regulated SUM44/LCCTam cells (breast cancer) resistant to 4-hydroxytamoxifen [PubChem=63062] relative to the parental SUM44 cells sensitive to the drug. 18974135 93/145 Leona Saunders 9.95025035083582e-07 1.74397258284237e-06 4680 1912.90909090909 1803 9.04568622834431e-08 147 2.28128034974026 -1.79658955927171 -1 5.23302466912811 4680 147 685 793 2566 3782 2524 1374 1883 805 1803 1575 M814 REACTOME_PURINE_SALVAGE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_SALVAGE.html Genes involved in Purine salvage 15/15 Reactome 2.35739736426598e-07 7.99922038773217e-07 1510 2430.81818181818 1806 2.14308874261053e-08 931 1.05529273405877 1.0385285972527 1 2.53749883581624 1509 2867 3459 4411 1132 1457 931 1327 4420 3420 1806 1576 M1989 WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_UP.html Selected genes with immunologic function which were reciprocally changed in evasion and tolerogenic tumor models. 18381452 23/40 Arthur Liberzon 2.55534367539091e-06 3.70089663941243e-06 1380 1976.09090909091 1806 2.32304240316195e-07 611 2.25783025983162 -2.35775216710801 -1 4.88200932744784 1379 3172 1794 2343 3178 1806 611 1504 2956 2227 767 1577 M1562 YIH_RESPONSE_TO_ARSENITE_C2 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C2.html Genes in cluster 2: moderately up-regulated in HFW cells (fibroblast) upon treatment with sodium arsenite [PubChem=26435] at all time points. 12016162 31/36 John Newman 1.07571192946737e-06 1.85102453776376e-06 1810 1987.36363636364 1807 9.77920414043458e-08 1164 2.39219692806456 -1.81151125946827 -1 5.46499816399949 1807 3131 1948 3138 2619 2028 1164 1339 1421 1725 1541 1578 M215 LIU_VAV3_PROSTATE_CARCINOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_VAV3_PROSTATE_CARCINOGENESIS_UP.html Selected genes up-regulated in prostate tumors developed by transgenic mice overexpressing VAV3 [GeneID=10451] in prostate epithelium. 18676865 118/208 Jessica Robertson 2.3055997521385e-10 4.16951372800526e-09 4565 2258.81818181818 1807 2.09599977489102e-11 59 2.96716844562513 -2.65177509561003 -1 9.9495586932566 4562 59 204 775 1562 3838 3835 4024 1807 659 3522 1579 M6161 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_DN.html Genes down-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing granulocytes. 17898786 7/10 Arthur Liberzon 1.38022231077373e-05 1.66956671113582e-05 620 2162.63636363636 1809 1.38023088340999e-06 29 1.9447037635784 1.9447037635784 1 3.68629406455346 616 3247 4303 4152 3872 507 173 1085 3996 1809 29 1580 M2421 PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_UP.html Genes up-regulated in M2-10B4 cells (osteoblast) in response to phenylamil [PubChem=4755]. 19433444 16/19 Arthur Liberzon 6.98109105587095e-07 1.37020858278925e-06 2615 1767.27272727273 1809 6.34644842829813e-08 110 3.34056896147341 3.28827688328286 1 7.82688928668311 2611 2394 880 1359 2258 1718 1809 3399 1957 945 110 1581 M1266 SHANK_TAL1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHANK_TAL1_TARGETS_DN.html Genes down-regulated in preleukemic thymocytes from transgenic mice which overexpress TAL1 [GeneID=6886] in thymus. 16407836 7/16 Leona Saunders 3.13212104019316e-06 4.41170137562272e-06 1145 1837.27272727273 1810 3.13212545478391e-07 152 2.28337133415569 -2.14023578724374 -1 4.86773740676362 1141 1978 4405 3300 3324 760 152 439 2473 1810 428 1582 M8349 MARCHINI_TRABECTEDIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARCHINI_TRABECTEDIN_RESISTANCE_DN.html Genes down-regulated in chondrosarcoma and ovarian carcinoma cell lines which developed resistance to trabectedin [PubChem=3199]. 15661559 117/164 John Newman 1.74248054565375e-06 2.69921502313281e-06 1365 1962.81818181818 1810 1.58407447796697e-07 564 2.09759796833357 2.79802857769436 1 4.64762309377646 1361 2998 1211 1319 2953 1284 3232 1810 3011 1848 564 1583 M9371 MILICIC_FAMILIAL_ADENOMATOUS_POLYPOSIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MILICIC_FAMILIAL_ADENOMATOUS_POLYPOSIS_UP.html Top genes up-regulated in colon epithelium biopsies from FAP (familial adenomatous polyposis) patients with mutated APC [GeneID=324]. 18829530 10/58 Jessica Robertson 1.53193127512492e-05 1.8370720575685e-05 1810 1902.27272727273 1810 1.39267449323881e-06 338 2.79164786887158 -2.31991493777671 -1 5.26689858027412 1810 2435 1378 2368 3877 1917 1199 1511 338 1564 2528 1584 M570 REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING.html Genes involved in PI3K events in ERBB2 signaling 47/47 Reactome 2.15751232386498e-07 7.72948789223918e-07 1345 2010.54545454545 1813 1.96137503222684e-08 682 1.54301321661181 -1.46907454699121 -1 3.74261431021884 1343 2255 3104 2998 1035 851 682 1813 2689 4081 1265 1585 M13254 GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_DN.html Genes down-regulated in quescent CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloblastic leukemia) patients compared to the dividing cells from normal donors. 17717066 9/24 Arthur Liberzon 2.16228648666122e-06 3.23655703962543e-06 3430 2467.72727272727 1813 2.16228859063139e-07 712 2.09725918388678 -2.26232371677291 -1 4.58036290414659 3428 982 4316 1794 3129 4513 3285 1375 712 1798 1813 1586 M9575 WAKASUGI_HAVE_ZNF143_BINDING_SITES http://www.broadinstitute.org/gsea/msigdb/cards/WAKASUGI_HAVE_ZNF143_BINDING_SITES.html DNA repair genes whose promoters contain putative ZNF143 [GeneID=7702] binding sites. 17297437 65/67 Leona Saunders 1.9769842132272e-05 2.32876603105375e-05 780 2260.81818181818 1813 1.79727452655262e-06 268 1.69823540214362 1.77325348256824 1 3.11405441896476 778 3909 3434 3557 3947 441 268 809 1813 4115 1798 1587 M19428 KEGG_WNT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_WNT_SIGNALING_PATHWAY.html Wnt signaling pathway 144/178 KEGG 6.13977119053006e-07 1.25698601298786e-06 1815 1742.45454545455 1814 5.58161173092835e-08 458 1.88089509471381 2.4118312155125 1 4.413370157385 1814 2093 2260 1723 2146 1422 2997 870 643 2741 458 1588 M1493 NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON.html Genes within amplicon 11q12-q14 identified in a copy number alterations study of 191 breast tumor samples. 19010930 157/230 Jessica Robertson 5.23450213159285e-08 5.22119909633759e-07 1690 1704.18181818182 1814 4.75863841467125e-09 62 1.93926440246392 -1.88812702305144 -1 4.8494598102504 1686 2089 2213 1814 62 1253 1906 2705 1350 2859 809 1589 M17096 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_2 http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_2.html Genes exclusively up-regulated in B lymphocytes from WM (Waldenstroem's macroglobulinemia) but with a similar expression profile in MM (macroglobulinemia) and normal cells. 17252022 7/24 Arthur Liberzon 1.70323276908137e-05 2.02500218389523e-05 1095 1986.36363636364 1814 1.70324582373058e-06 276 1.89248065263055 1.87057966584964 1 3.52216325894362 1095 2915 4640 1870 3929 638 276 752 2498 1814 1423 1590 M243 PID_ARF_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF_3PATHWAY.html Arf1 pathway 18832364 30/33 Pathway Interaction Database 4.19434247009397e-07 1.00749600299458e-06 1820 2251.81818181818 1816 3.81303933613971e-08 561 0.985912481484698 -0.991946124609972 -1 2.32765400181558 1816 717 3881 2981 1771 1294 561 2260 3354 4327 1808 1591 M5316 MODY_HIPPOCAMPUS_PRENATAL http://www.broadinstitute.org/gsea/msigdb/cards/MODY_HIPPOCAMPUS_PRENATAL.html Genes highly expressed in prenatal hippocampus (cluster 1). 11438693 63/88 John Newman 1.01819251360444e-05 1.26237684901837e-05 1135 2457 1816 9.25633841800363e-07 792 1.6311899637122 2.02300653304974 1 3.16359285999909 1131 4210 3357 4106 3752 1251 1087 792 1816 4233 1292 1592 M1688 YANG_MUC2_TARGETS_DUODENUM_3MO_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_DUODENUM_3MO_DN.html Genes down-regulated in duodenum of 3 month old MUC2 [GeneID=4583] knockout mice. 18794118 21/66 Jessica Robertson 5.28500584707628e-07 1.1469070160092e-06 1820 2196.63636363636 1819 4.80455192425514e-08 602 2.26070799438401 -2.95662806250377 -1 5.35086190663578 3655 820 1667 1819 2002 4623 4172 1818 602 1945 1040 1593 M4974 REACTOME_BASIGIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASIGIN_INTERACTIONS.html Genes involved in Basigin interactions 22/30 Reactome 4.50652710145133e-06 6.04039880348692e-06 1565 1932.09090909091 1820 4.09685121158581e-07 772 1.94859671795358 2.00375788161895 1 4.03978530853674 1565 781 1575 3049 3449 1820 2105 2796 772 989 2352 1594 M3146 MARSON_FOXP3_TARGETS_STIMULATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_STIMULATED_UP.html Genes with promoters bound by FOXP3 [GeneID=50943], dependent on it, and up-regulated in hybridoma cells stimulated by PMA [PubChem=4792] and ionomycin [PubChem=3733]. 17237765 25/41 Arthur Liberzon 7.3123538041577e-07 1.40702445803605e-06 2865 1985.81818181818 1821 6.64759657694265e-08 769 2.1672218628519 -2.13390766841808 -1 5.05014816241898 2863 769 1469 1821 2307 3098 3516 1233 1082 1294 2392 1595 M2599 GHANDHI_BYSTANDER_IRRADIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_BYSTANDER_IRRADIATION_DN.html Genes significantly (FDR < 10%) down-regulated in IMR-90 cells (fibroblast) in response to bystander irradiation. 19108712 20/32 Itai Pashtan 2.49423078754811e-06 3.63463233559836e-06 1985 1871.45454545455 1822 2.26748510487724e-07 110 3.03090999255222 3.42448934841028 1 6.5803032896759 1983 1876 1033 1231 3159 3173 4307 509 110 1822 1383 1596 M1687 ZHONG_SECRETOME_OF_LUNG_CANCER_AND_FIBROBLAST http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_SECRETOME_OF_LUNG_CANCER_AND_FIBROBLAST.html Proteins secreted in co-culture of LKR-13 tumor cells (non-small cell lung cancer, NSCLC) and MLg stroma cells (fibroblasts). 18757440 192/257 Jessica Robertson 2.08037869427896e-07 7.70063333918279e-07 1825 1895.27272727273 1823 1.89125353727741e-08 831 2.2906803633058 2.42083717190654 1 5.58184013502502 1823 1419 831 853 990 2091 3040 3063 1012 2053 3673 1597 M19233 EPPERT_CE_HSC_LSC http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_CE_HSC_LSC.html Shared human hematopoietic stem cell (HSC) and acute myeloid leukemia (AML) stem cell (LSC) genes: HSC genes that are highly expressed in LSC versus other leukemic cells. 21873988 54/67 Kolja Eppert 4.39532193100238e-07 1.02957416944572e-06 2445 1794.18181818182 1824 3.99574800830218e-08 393 2.81025686452922 2.83839863125596 1 6.71672267630079 2442 393 584 936 1824 2391 2693 2617 638 656 4562 1598 M16121 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS.html Fc gamma R-mediated phagocytosis 96/116 KEGG 4.278686486959e-08 4.58360044171859e-07 2480 1632.90909090909 1825 3.88971506379395e-09 32 1.79539658173526 -1.89906326256046 -1 4.52682289763171 2480 129 2245 632 32 2934 2380 1928 1825 1648 1729 1599 M1111 GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN.html Down-regulated genes from the set A (Fig. 5a): specific to cells expressing MLL-AF4 [GeneID=4297;4299] fusion protein alone. 17130830 148/206 Arthur Liberzon 3.7761944823263e-07 9.60325320936429e-07 2205 1755.09090909091 1825 3.43290466408375e-08 309 2.35611188358015 2.60295343000884 1 5.65184913547381 2202 1500 387 1180 1650 1987 3432 2687 2147 309 1825 1600 M14091 KEGG_OLFACTORY_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OLFACTORY_TRANSDUCTION.html Olfactory transduction 29/833 KEGG 4.89338804199324e-07 1.099106798882e-06 2025 1648.90909090909 1826 4.44853557310353e-08 367 1.96635234948204 2.03672972669331 1 4.66225786127552 2023 676 1826 2307 1923 1433 2933 922 2234 1494 367 1601 M1847 LIN_TUMOR_ESCAPE_FROM_IMMUNE_ATTACK http://www.broadinstitute.org/gsea/msigdb/cards/LIN_TUMOR_ESCAPE_FROM_IMMUNE_ATTACK.html Genes up-regulated in highly immune-resistant cancer cell line developed from a susceptible cancer using an in vivo selection strategy. 17308126 23/33 Jessica Robertson 1.34540904053259e-07 7.20206492018647e-07 2180 1784.72727272727 1826 1.22309920255548e-08 6 2.96494165855357 3.24712561904764 1 7.27424402206958 1826 810 888 3643 2352 2180 2792 6 2177 1589 1369 1602 M2455 PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_DN.html Genes down-regulated after 10 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 38/51 Arthur Liberzon 2.66231306280913e-06 3.83347091411199e-06 3150 2231.45454545455 1826 2.4202875314475e-07 662 2.79020490091371 2.27868707849853 1 6.0277866691226 3148 1757 662 1361 3203 3879 2936 769 4064 941 1826 1603 M11718 BOYLAN_MULTIPLE_MYELOMA_D_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_DN.html Genes down-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 95/120 Jessica Robertson 2.84480299643025e-07 8.51456572171893e-07 4250 2432 1827 2.5861848766269e-08 155 1.96053809848922 1.94126339108201 1 4.73574584978011 4249 155 1827 2298 1338 4259 4171 4157 1347 1311 1640 1604 M2461 DELACROIX_RARG_BOUND_MEF http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RARG_BOUND_MEF.html Genes with DNA sequences bound by RARG [GeneID=5916] in MEF cells (embryonic fibroblast). 19884340 484/602 Arthur Liberzon 1.74549223012469e-07 7.37919956089047e-07 3800 2291.45454545455 1827 1.58681124419366e-08 611 1.96570438507143 -1.66061721755829 -1 4.79749110709241 3798 1183 1095 1002 802 3051 3004 4474 1827 611 4359 1605 M941 REACTOME_FACTORS_INVOLVED_IN_MEGAKARYOCYTE_DEVELOPMENT_AND_PLATELET_PRODUCTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FACTORS_INVOLVED_IN_MEGAKARYOCYTE_DEVELOPMENT_AND_PLATELET_PRODUCTION.html Genes involved in Factors involved in megakaryocyte development and platelet production 112/159 Reactome 6.75439322269156e-07 1.34078461407703e-06 1550 2058.36363636364 1828 6.14035936037445e-08 567 1.79808189982194 1.96490949749914 1 4.19658453113028 1548 3604 2967 2945 2229 867 1680 939 1828 3468 567 1606 M12112 VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP.html Angiogenic markers up-regulated in lymph endothelial cells upon infection with KSHV (Kaposi's sarcoma herpes virus). 17483315 186/272 Jessica Robertson 9.85342376316163e-16 3.41971765897962e-14 1150 1795.27272727273 1828 8.95765796651059e-17 96 2.69252916393603 2.79431272293158 1 14.5313887116322 1150 2536 96 1188 2205 1762 3453 1828 2741 129 2660 1607 M187 PID_TRKR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TRKR_PATHWAY.html Neurotrophic factor-mediated Trk receptor signaling 18832364 89/98 Pathway Interaction Database 3.37543306389938e-07 9.13746684768849e-07 1830 1865.36363636364 1829 3.06857598344369e-08 192 1.74120378071643 -1.49979235393439 -1 4.17886668436029 1829 192 2623 659 1522 1847 980 3471 1644 3744 2008 1608 M4779 IGARASHI_ATF4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IGARASHI_ATF4_TARGETS_DN.html Genes down-regulated in A549 cells (lung cancer) after knockdown of ATF4 [GeneID=468] by RNAi. 17297441 121/145 Leona Saunders 1.40941394326131e-07 7.20206492018647e-07 2860 2086 1829 1.28128548504945e-08 30 1.80278877506452 -1.92522176460072 -1 4.40338331416684 2858 30 1821 851 571 3295 2656 4524 1829 1385 3126 1609 M11675 KEGG_HOMOLOGOUS_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HOMOLOGOUS_RECOMBINATION.html Homologous recombination 27/27 KEGG 2.17802402782015e-05 2.55030350069737e-05 455 2019.18181818182 1830 1.98004144617706e-06 191 1.29102399865414 1.36476040255087 1 2.33486189991426 454 3157 3358 2459 3975 207 191 1220 4030 1830 1330 1610 M2894 AMIT_EGF_RESPONSE_240_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_240_MCF10A.html Genes whose expression peaked at 240 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 27/28 Leona Saunders 4.06524295216391e-07 9.97313151079934e-07 1730 2281.36363636364 1830 3.69567609395912e-08 889 2.34147397439785 2.50562973292905 1 5.60096932700481 2792 1830 1728 3649 1726 3955 3868 889 1019 2111 1528 1611 M10679 REACTOME_INHIBITION_OF_INSULIN_SECRETION_BY_ADRENALINE_NORADRENALINE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_INSULIN_SECRETION_BY_ADRENALINE_NORADRENALINE.html Genes involved in Inhibition of Insulin Secretion by Adrenaline/Noradrenaline 27/36 Reactome 3.58746002944084e-07 9.41752134134615e-07 3610 2285.45454545455 1831 3.26132783130458e-08 734 2.28196577290731 3.10627834373554 1 5.48019642053234 3609 734 1526 2599 1584 4096 3125 2959 1313 1831 1764 1612 M5914 LANDEMAINE_LUNG_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/LANDEMAINE_LUNG_METASTASIS.html Genes associated with metastasis of breast cancer in the lung compared to the non-lung metastasis. 18676831 27/31 Jessica Robertson 6.28852988563738e-07 1.27828859001759e-06 1835 1564.36363636364 1831 5.71684698469613e-08 226 2.41945974909854 2.5277414720366 1 5.68429496140525 2508 726 1374 1604 2167 1910 2273 756 226 1833 1831 1613 M2130 KEGG_ETHER_LIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ETHER_LIPID_METABOLISM.html Ether lipid metabolism 26/37 KEGG 4.50939203392988e-07 1.04185917010687e-06 2160 1917.90909090909 1832 4.09944814384627e-08 1035 2.29662273699455 -2.22875507460542 -1 5.47519571355503 2159 1832 1524 2584 1854 1248 1035 2002 3598 1678 1583 1614 M19141 WONG_IFNA2_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WONG_IFNA2_RESISTANCE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) cell lines resistant to IFNA2 [GeneID=3440]. 15709204 30/37 Yujin Hoshida 2.39534998527959e-06 3.51994144785792e-06 3265 1870.54545454545 1833 2.17759326666338e-07 670 1.84063249021747 1.97200934196829 1 3.98679071314743 3264 691 1833 1282 3134 2017 1713 670 1473 2487 2012 1615 M757 REACTOME_ACETYLCHOLINE_BINDING_AND_DOWNSTREAM_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACETYLCHOLINE_BINDING_AND_DOWNSTREAM_EVENTS.html Genes involved in Acetylcholine Binding And Downstream Events 2/14 Reactome 0.000142794694471345 0.000154833668252871 1970 2212.6 1833.5 1.58670841836412e-05 614 3.58158519007477 -3.58158519007477 -1 5.43799005818071 1969 2936 4231 NA 4358 1698 667 614 769 3268 1616 1616 M275 PID_ALPHA_SYNUCLEIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALPHA_SYNUCLEIN_PATHWAY.html Alpha-synuclein signaling 18832364 41/48 Pathway Interaction Database 1.57763281240786e-07 7.31918027928963e-07 1835 1864.63636363636 1834 1.43421175049167e-08 680 2.25705197155005 2.14265389834659 1 5.51918870384545 1834 1752 1945 1047 680 1747 2065 4159 1377 2020 1885 1617 M883 REACTOME_HIGHLY_CALCIUM_PERMEABLE_POSTSYNAPTIC_NICOTINIC_ACETYLCHOLINE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIGHLY_CALCIUM_PERMEABLE_POSTSYNAPTIC_NICOTINIC_ACETYLCHOLINE_RECEPTORS.html Genes involved in Highly calcium permeable postsynaptic nicotinic acetylcholine receptors 2/11 Reactome 0.000149454883854588 0.000161758094885039 1970 2216.9 1834.5 1.66072013598654e-05 633 3.58158519007477 -3.58158519007477 -1 5.41062201669997 1970 2937 4247 NA 4359 1699 668 633 770 3269 1617 1618 M886 REACTOME_PRESYNAPTIC_NICOTINIC_ACETYLCHOLINE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRESYNAPTIC_NICOTINIC_ACETYLCHOLINE_RECEPTORS.html Genes involved in Presynaptic nicotinic acetylcholine receptors 2/12 Reactome 0.000149454883854588 0.000161758094885039 1975 2217.9 1835.5 1.66072013598654e-05 634 3.58158519007477 -3.58158519007477 -1 5.41062201669997 1971 2938 4248 NA 4360 1700 669 634 771 3270 1618 1619 M234 PID_IL2_STAT5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_STAT5_PATHWAY.html IL2 signaling events mediated by STAT5 18832364 34/46 Pathway Interaction Database 2.89406054220607e-07 8.60199355114146e-07 1840 1474.90909090909 1836 2.63096447537692e-08 619 2.05434467046948 -1.67803639754935 -1 4.96106749945462 1904 619 1836 644 1355 1839 1888 1370 756 2075 1938 1620 M2042 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_UP.html Genes up-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 26/39 John Newman 3.19763285156339e-07 8.98528442785416e-07 3555 2199.72727272727 1836 2.90693937848151e-08 600 2.36854129007881 2.4490838308257 1 5.70944429656743 3551 1836 1577 1209 1452 3009 2549 4063 600 1411 2940 1621 M2110 KIM_ALL_DISORDERS_CALB1_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_CALB1_CORR_UP.html Genes whose expression significantly and positively correlated with the density of CALB1-positive [GeneID=793] GABAergic interneurons in the BA9 brain region across all subjects with psychiatric disorders. 18762803 697/844 Jessica Robertson 1.47483669018261e-07 7.26289540930751e-07 1840 2225.45454545455 1836 1.47483678806406e-08 707 1.63247280351339 1.74991411679647 1 3.98025448312757 1836 1124 4660 900 707 1522 2156 3579 1611 4001 2384 1622 M17814 REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS.html Genes involved in Activation of BH3-only proteins 24/26 Reactome 2.58561748423675e-06 3.7378604978859e-06 430 1783.18181818182 1837 2.35056411188001e-07 426 2.02195603020002 2.12381058305407 1 4.36325158712097 1078 2359 2311 3192 3184 426 426 1537 543 2722 1837 1623 M15381 REACTOME_TCR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TCR_SIGNALING.html Genes involved in TCR signaling 47/65 Reactome 1.11113583763484e-07 7.03739764799127e-07 2835 1694.36363636364 1838 1.01012353977642e-08 358 1.92251801261469 -1.87735708123529 -1 4.70691625320444 2020 449 1838 1026 358 2832 2204 1235 2187 1657 2832 1624 M14791 SABATES_COLORECTAL_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_DN.html Genes down-regulated in colorectal adenoma compared to normal mucosa samples. 18171984 280/566 Leona Saunders 3.60859227192257e-35 6.08305554409805e-33 1840 1671.45454545455 1838 3.28053842902055e-36 14 3.10772301126845 3.45023077659273 1 40.2135933915434 1838 1292 14 249 1840 2943 4403 1107 2086 68 2546 1625 M19261 YAGI_AML_WITH_T_8_21_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_T_8_21_TRANSLOCATION.html Genes specifically expressed in samples from patients with pediatric AML (acute myeloid leukemia ) bearing t(8;21) translocation. 12738660 488/708 Arthur Liberzon 1.75209738612269e-07 7.39704799865751e-07 3215 1955.54545454545 1838 1.5928159324192e-08 122 1.95716344268005 2.04922216592408 1 4.77560289662012 3215 1174 1022 122 807 2691 4044 3222 1838 662 2714 1626 M2701 ST_MYOCYTE_AD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_MYOCYTE_AD_PATHWAY.html Myocyte Adrenergic Pathway is a specific case of the generalized Adrenergic Pathway. 39/54 Signaling Transduction KE 5.13295126460989e-08 5.19978203455085e-07 3880 2212 1841 4.66631944033623e-09 54 2.01775659438489 -1.44201713109641 -1 5.04921668311583 3877 549 1696 480 54 4060 3878 3584 296 1841 4017 1627 M1685 ZHONG_SECRETOME_OF_LUNG_CANCER_AND_MACROPHAGE http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_SECRETOME_OF_LUNG_CANCER_AND_MACROPHAGE.html Proteins secreted in co-culture of LKR-13 tumor cells (non-small cell lung cancer, NSCLC) and MHS stroma cells (macrophages). 18757440 104/143 Jessica Robertson 3.03699814554096e-07 8.78347502877042e-07 4365 2384.27272727273 1844 2.76090778616779e-08 571 2.35889192814454 2.21979402562044 1 5.69533927700108 4361 1592 1007 603 1402 4373 4026 2879 571 1844 3569 1628 M409 LOPEZ_EPITHELIOID_MESOTHELIOMA http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_EPITHELIOID_MESOTHELIOMA.html Top 20 genes expressed higher in epithelioid than in sarcomatoid mesothelioma samples. 16540645 27/30 Arthur Liberzon 4.47118216471084e-07 1.03872096525265e-06 4300 2086.63636363636 1844 4.06471188492207e-08 321 2.86964400744273 2.7370503686406 1 6.85528671278526 4297 675 714 547 1844 3143 3875 2856 321 1277 3404 1629 M1950 MEISSNER_BRAIN_HCP_WITH_H3K4ME2_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K4ME2_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing bivalent histone H3 dimethylation mark at K4 (H3K4me2) and trimethlation mark at K27 (H3K27me3) in brain. 18600261 63/106 Arthur Liberzon 1.34078641795464e-13 3.77136523757706e-12 690 1586.27272727273 1845 1.2188967435952e-14 123 3.0880361371798 3.16499515253254 1 14.13669165834 690 300 123 710 2905 1845 2250 3390 2988 295 1953 1630 M5311 HOSHIDA_LIVER_CANCER_SUBCLASS_S1 http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SUBCLASS_S1.html Genes from 'subtype S1' signature of hepatocellular carcinoma (HCC): aberrant activation of the WNT signaling pathway. 19723656 326/406 Jessica Robertson 8.31787783684015e-09 1.12493935214572e-07 275 1541.54545454545 1847 7.56170715298986e-10 272 2.18045291859715 2.39324557904539 1 6.0433897966355 1851 1254 272 416 773 2139 3577 2172 2382 274 1847 1631 M17331 ALONSO_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_DN.html Down-regulated genes in melanoma tumors that developed metastatic disease compared to primary melanoma that did not. 17409456 25/41 Jessica Robertson 3.14016962942736e-06 4.42039983623536e-06 2210 1993.63636363636 1848 2.85470373777901e-07 576 2.75384943073071 3.74646053571724 1 5.88007469990626 2208 1848 1013 3661 3278 1559 2141 576 3443 1573 630 1632 M1613 MILI_PSEUDOPODIA_CHEMOTAXIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_CHEMOTAXIS_DN.html Transcripts depleted in pseudopodia of NIH/3T3 cells (fibroblast) in response to the chemotactic migration stimulus by lysophosphatidic acid (LPA) [PubChem=3988]. 18451862 650/764 Jessica Robertson 1.25007240285464e-07 7.16209778122308e-07 3105 2116.09090909091 1848 1.25007247317529e-08 479 1.83052006318958 2.14923091996997 1 4.47366693563807 3101 1133 4616 479 543 1848 4371 1898 1738 2732 818 1633 M4844 KEGG_CHEMOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHEMOKINE_SIGNALING_PATHWAY.html Chemokine signaling pathway 161/239 KEGG 1.11592329591714e-07 7.04017019921975e-07 1455 1724.36363636364 1849 1.01447577501909e-08 361 1.8718214887539 -1.81994132415182 -1 4.58134729969685 1454 1485 1970 506 361 1855 1221 2721 2966 1849 2580 1634 M14573 BENPORATH_NOS_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_NOS_TARGETS.html Set 'NOS targets': genes upregulated and identified by ChIP on chip as targets of the transcription factors NANOG , OCT4, and Sox2 [GeneID=79923;5460;6657] (NOS) in human embryonic stem cells. 18443585 243/323 Jessica Robertson 4.20878630505665e-07 1.00849031419935e-06 2150 2165.18181818182 1849 3.82617010021212e-08 1192 1.99709072106387 2.20354519468278 1 4.76593366325673 2150 3569 1849 1730 1775 1937 3236 1192 3009 1656 1714 1635 M752 REACTOME_NEUROTRANSMITTER_RECEPTOR_BINDING_AND_DOWNSTREAM_TRANSMISSION_IN_THE_POSTSYNAPTIC_CELL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEUROTRANSMITTER_RECEPTOR_BINDING_AND_DOWNSTREAM_TRANSMISSION_IN_THE_POSTSYNAPTIC_CELL.html Genes involved in Neurotransmitter Receptor Binding And Downstream Transmission In The Postsynaptic Cell 94/156 Reactome 1.46549316850118e-07 7.26289540930751e-07 2485 1952.81818181818 1850 1.33226660556597e-08 138 1.84220356654249 1.9652923105268 1 4.49804328926698 2485 138 1747 1255 607 2080 3382 3794 2524 1850 1619 1636 M12294 KEGG_VIRAL_MYOCARDITIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIRAL_MYOCARDITIS.html Viral myocarditis 70/116 KEGG 1.11584589965487e-06 1.90411881647541e-06 2540 2126.36363636364 1851 1.01440587783209e-07 272 1.97726120706278 -1.52655048335103 -1 4.49862787888189 2538 272 1241 1487 2642 1851 1993 3945 1802 1129 4490 1637 M16697 BIOCARTA_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CD40_PATHWAY.html CD40L Signaling Pathway 18/19 BioCarta 3.89642411708426e-06 5.31996581794553e-06 315 1665.81818181818 1851 3.5422100164231e-07 312 1.50646112800669 -1.67024327177426 -1 3.1452229252822 312 1892 2615 2454 3386 538 345 764 3091 1851 1076 1638 M5589 HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_UP.html Genes up-regulated during differentiation from pre-BI to large pre-BII lymphocyte. 11779835 46/61 Arthur Liberzon 1.69846707748893e-07 7.33971845416521e-07 3705 2353.18181818182 1851 1.54406109874161e-08 482 1.88988492378251 1.9661910738163 1 4.61228719040344 3701 482 1776 1425 771 3830 4062 3514 1851 1382 3091 1639 M9746 SU_TESTIS http://www.broadinstitute.org/gsea/msigdb/cards/SU_TESTIS.html Genes up-regulated specifically in human testis tissue. 11904358 79/176 John Newman 7.87286112950269e-07 1.4834293226049e-06 1205 1972.72727272727 1852 7.15714904260466e-08 1122 1.79369374421542 2.04209209602439 1 4.15454766634278 1204 2161 2956 2907 2364 1122 1264 1632 1424 2814 1852 1640 M18938 SENESE_HDAC1_AND_HDAC2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_AND_HDAC2_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of both HDAC1 and HDAC2 [GeneID=3065;3066] by RNAi. 17470557 285/454 Leona Saunders 2.59777132668623e-10 4.61790220801553e-09 2900 1897.18181818182 1853 2.36161029726634e-11 101 2.27343370278518 2.25412836829669 1 7.57105972649335 2899 1301 282 388 101 3283 4663 1853 2163 158 3778 1641 M17162 NAKAMURA_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_METASTASIS.html Genes up-regulated in highly metastatic pancreatic cancer cells. 17210693 51/70 Jessica Robertson 5.61070444642291e-07 1.18755717431014e-06 2175 1755.36363636364 1855 5.1006417066661e-08 445 2.2076020397325 2.49909830339479 1 5.21056085100311 2171 445 1467 2123 2068 1304 2025 2805 1806 1240 1855 1642 M11090 DITTMER_PTHLH_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DITTMER_PTHLH_TARGETS_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PTHLH [GeneID=5744] by RNAi. 16551631 174/198 Leona Saunders 2.26744197645249e-07 7.86490142806441e-07 1345 1867.45454545455 1856 2.06131110013424e-08 1085 1.7522965377206 1.93035877021694 1 4.25170724770966 1342 1463 2301 1312 1085 1481 2140 2847 2120 2595 1856 1643 M9516 PUJANA_BRCA2_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BRCA2_PCC_NETWORK.html Genes constituting the BRCA2-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC >= 0.4) with that of BRCA2 [GeneID=675] across a compendium of normal tissues. 17922014 585/743 Leona Saunders 2.08245429839153e-06 3.13131070035298e-06 500 1936.09090909091 1856 2.08245624987126e-07 498 1.59790391923219 1.69487240344645 1 3.48709548594349 498 2940 4420 2017 3104 810 743 1062 2501 1856 1346 1644 M940 REACTOME_TRAF6_MEDIATED_NFKB_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_NFKB_ACTIVATION.html Genes involved in TRAF6 mediated NF-kB activation 23/29 Reactome 4.21070383386616e-06 5.69797078436017e-06 340 1581.36363636364 1857 3.82791990271894e-07 71 1.89669640149188 -1.89068959043813 -1 3.95018697966157 336 1857 2115 2899 3415 291 71 166 3568 1893 784 1645 M12828 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP.html Genes up-regulated in reverted NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845] which then reverted to normal cells upon stable over-expression of a dominant negative form of CDC25 [GeneID=5923]) vs normal fibroblasts. 16607279 177/214 Lauren Kazmierski 8.9584753877389e-07 1.62131916526563e-06 995 2061.54545454545 1858 8.1440718506026e-08 750 2.09573692580243 2.05820863780741 1 4.83003051274232 992 3581 1119 2157 2484 1646 3007 750 3460 1623 1858 1646 M9546 BIOCARTA_TID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TID_PATHWAY.html Chaperones modulate interferon Signaling Pathway 30/35 BioCarta 1.85303813557556e-06 2.8323639896103e-06 620 1667.45454545455 1859 1.68458154215727e-07 259 2.33229908353699 -1.85718705556233 -1 5.15363201505886 617 3127 1859 1965 2997 439 259 1530 2230 2186 1133 1647 M14174 NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_DN.html Genes down-regulated in K562 cells (bone marrow) after treatment with dasatinib [PubChem=3062316] or imatinib [PubChem=5291]. 17213809 17/18 Arthur Liberzon 4.51852315762577e-07 1.04185917010687e-06 400 1852 1860 4.10774916879439e-08 109 1.72510328985062 -1.77685193049111 -1 4.10022977203256 1388 3480 2948 3701 1860 900 400 109 1865 3321 400 1648 M1572 LEE_CALORIE_RESTRICTION_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_MUSCLE_UP.html Up-regulated in the gastrocnemius muscle of aged (30-month) mice subjected to caloric restriction diet since young adulthood. 10464095 47/68 John Newman 1.84575336937963e-07 7.47950348864313e-07 1820 1773.09090909091 1861 1.67795774930404e-08 465 2.27167844466126 -1.91208546546004 -1 5.54668210034913 1820 3670 1987 2167 866 965 465 1861 2015 2887 801 1649 M95 PID_CIRCADIAN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CIRCADIAN_PATHWAY.html Circadian rhythm pathway 18832364 21/21 Pathway Interaction Database 1.41869518929967e-06 2.28883831480239e-06 1295 1766.36363636364 1862 1.28972373105667e-07 865 1.70767485665887 -1.75308365644875 -1 3.82356109952978 952 2809 2773 1927 2817 1293 865 1862 1291 1943 898 1650 M494 REACTOME_PTM_GAMMA_CARBOXYLATION_HYPUSINE_FORMATION_AND_ARYLSULFATASE_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PTM_GAMMA_CARBOXYLATION_HYPUSINE_FORMATION_AND_ARYLSULFATASE_ACTIVATION.html Genes involved in PTM: gamma carboxylation, hypusine formation and arylsulfatase activation 22/27 Reactome 8.92440611272631e-07 1.61887766533698e-06 1510 1988.90909090909 1863 8.11309975723342e-08 287 1.83779671990113 2.04485588841781 1 4.22988271312266 1506 1863 2330 3650 2479 1829 2922 287 1332 2822 858 1651 M2776 IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP.html Cluster 1: genes up-regulated in lung tissue samples from mice with oncogenic form of KRAS [GeneID=3845] and inactivated PTEN [GeneID=5728]. 18281487 226/300 Jessica Robertson 3.9771907119677e-07 9.84907668441108e-07 2600 1945.54545454545 1864 3.61562857360906e-08 686 2.28270107654168 2.46583843567322 1 5.46411482915726 2600 2050 686 995 1703 2551 3913 1864 1474 1417 2148 1652 M1937 MEISSNER_NPC_ICP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_ICP_WITH_H3_UNMETHYLATED.html Genes with intermediate-CpG-density promoters (ICP) that have no histone H3 methylation marks in neural precursor cells (NPC). 18600261 30/45 Jessica Robertson 7.51725711823184e-06 9.52522244243068e-06 1670 2070 1864 6.83389345848552e-07 944 2.83216364188462 -2.65652636637608 -1 5.66896181459267 1666 1815 944 1864 3668 2177 2310 1875 3531 1158 1762 1653 M2467 KRIEG_HYPOXIA_VIA_KDM3A http://www.broadinstitute.org/gsea/msigdb/cards/KRIEG_HYPOXIA_VIA_KDM3A.html Genes dependent on KDM3A [GeneID=55818] for hypoxic induction in RCC4 cells (renal carcinoma) expressing VHL [GeneID=7428]. 19858293 87/103 Arthur Liberzon 3.6026745821562e-07 9.41752134134615e-07 2575 1963.36363636364 1865 3.27515924738444e-08 179 2.37248944758111 2.43992265994122 1 5.69957616430956 2575 179 521 1675 1593 2992 3634 3005 3010 548 1865 1654 M126 KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP.html Genes up-regulated in glioma cell lines treated with both decitabine [PubChem=451668] and TSA [PubChem=5562]. 16885346 147/241 Arthur Liberzon 4.59675444823312e-11 8.96557065936377e-10 4635 2361.63636363636 1869 4.17886768029923e-12 187 2.70220586879696 2.56028012753705 1 9.78200964016351 4631 1491 187 291 1869 4030 4085 4025 1158 428 3783 1655 M15055 MATTIOLI_MULTIPLE_MYELOMA_SUBGROUPS http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MULTIPLE_MYELOMA_SUBGROUPS.html Genes differentially expressed in multiple myeloma (MM) patients: comparison of MGUS-like vs PCL-like samples; MGUS=monoclonal gammopathy of undetermined significance, PCL=plasma cell leukemia. 15735737 17/41 Leona Saunders 9.56497482058493e-07 1.69979974221238e-06 1870 1987.36363636364 1869 8.6954354356061e-08 481 1.47993006144543 1.37288311254705 1 3.38386342997115 1869 2392 2710 3402 2535 1334 481 947 1849 2877 1465 1656 M16297 SCHLESINGER_H3K27ME3_IN_NORMAL_AND_METHYLATED_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SCHLESINGER_H3K27ME3_IN_NORMAL_AND_METHYLATED_IN_CANCER.html Genes bearing the H3K27me3 mark in normal cells; their DNA is methylated in cancer cells. 17200670 36/73 Leona Saunders 1.84418430557054e-07 7.47950348864313e-07 535 2010.36363636364 1869 1.67653132742017e-08 369 2.86848468762148 2.7789754834791 1 7.0170297234797 533 1763 369 1869 3936 2093 2716 2703 3753 683 1696 1657 M4435 YAO_HOXA10_TARGETS_VIA_PROGESTERONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAO_HOXA10_TARGETS_VIA_PROGESTERONE_DN.html Genes down-regulated in the uteri of ovariectomized mice 6 h after progesterone [PubChem=5994] injection: HOXA10 [GeneID=3206] knockout vs wild type animals. 12554760 25/36 Kevin Vogelsang 3.33097844714276e-06 4.64879310186689e-06 2370 1697.54545454545 1869 3.02816680956818e-07 402 3.27915608133971 3.86082791450375 1 6.98241229111412 2367 750 585 402 3306 2539 3221 2021 999 1869 614 1658 M14386 MCCOLLUM_GELDANAMYCIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCOLLUM_GELDANAMYCIN_RESISTANCE_DN.html Genes down-regulated in A549GARS cells (lung cancer) resistant to the geldanamycin and 17-AAG [PubChem=5476289;6440175]. 18794130 8/13 Jessica Robertson 7.61394438261483e-07 1.44597311199533e-06 1310 2022.45454545455 1869 7.61394699136278e-08 563 1.8711953171935 -1.99037871298939 -1 4.34457655978323 1307 1977 4508 2859 2421 1733 907 563 2563 1540 1869 1659 M1925 BOYAULT_LIVER_CANCER_SUBCLASS_G56_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G56_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G56, defined by unsupervised clustering. 17187432 19/34 Yujin Hoshida 1.24482501283188e-05 1.51627717692038e-05 2755 2431.27272727273 1871 1.13166550588678e-06 1037 2.72220474982319 -3.11216709142426 -1 5.22588427163905 2752 1871 1037 1368 3820 3138 1585 4144 1649 1644 3736 1660 M13380 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION.html Neuroactive ligand-receptor interaction 89/344 KEGG 3.62379767402163e-13 9.29582881596852e-12 3715 2112.09090909091 1873 3.29436152183839e-14 135 3.12806391533304 3.36819311838919 1 13.8277167776014 3714 166 135 1334 1411 2803 4432 2584 1873 220 4561 1661 M4281 REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Neurotransmitter Release Cycle 37/61 Reactome 9.03984365731087e-07 1.63166585325076e-06 3600 2407.54545454545 1873 8.21804306527517e-08 1126 2.27655378801183 -2.19227449052844 -1 5.2485456449045 3598 1774 1419 1637 2492 1858 1126 3804 3142 1873 3760 1662 M773 REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE.html Genes involved in GPVI-mediated activation cascade 49/59 Reactome 2.1240023837755e-06 3.18769197183478e-06 1995 1943.36363636364 1873 1.93091312218939e-07 427 2.33977817771715 2.5055896295439 1 5.12202148177264 1994 427 761 476 3063 3197 4205 3229 1188 964 1873 1663 M1110 GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP.html Up-regulated genes from the set A (Fig. 5a): specific to cells expressing MLL-AF4 [GeneID=4297;4299] fusion protein alone. 17130830 281/360 Arthur Liberzon 1.63853068800296e-07 7.3358205358541e-07 4200 2725.54545454545 1874 1.48957346367142e-08 718 1.8921478950648 2.18627927468123 1 4.61804546770823 4196 1309 1555 1418 718 4522 4357 4409 1874 1699 3924 1664 M513 ZHAN_MULTIPLE_MYELOMA_MF_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MF_DN.html Top 50 down-regulated genes in cluster MF of multiple myeloma samples with characteristic expression spike of MAF family transcription factors. 16728703 55/66 Arthur Liberzon 6.98849917718306e-08 6.06161982149702e-07 3735 2219.27272727273 1874 6.35318127198096e-09 134 2.32740256530073 2.65596376612438 1 5.76941041932933 3732 435 1394 1874 134 3379 4075 2988 1284 1201 3916 1665 M17987 CAFFAREL_RESPONSE_TO_THC_8HR_5_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_5_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 22/32 Jessica Robertson 6.84500368813564e-06 8.73672726014068e-06 2245 1988.18181818182 1875 6.22274998685041e-07 571 1.95077035980062 -2.1317475922195 -1 3.91860131353052 2241 832 2253 1875 3638 1516 997 4399 725 2823 571 1666 M6670 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 3 days after transduction. 16818636 207/331 Arthur Liberzon 1.2725504327076e-14 4.03116647139588e-13 4700 2490.72727272727 1878 1.15686402973418e-15 53 2.43541498057441 2.72509313016807 1 12.0895820913701 4697 1375 106 53 1494 4685 3892 4502 1878 162 4554 1667 M2207 FUKUSHIMA_TNFSF11_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/FUKUSHIMA_TNFSF11_TARGETS.html Genes up-regulated in RAW 264.7 cells (macrophage) upon stimulation with TNFSF11 [GeneID=8600]. 18710934 14/16 Arthur Liberzon 4.61768034479876e-07 1.05842185795384e-06 4530 2424.72727272727 1880 4.19789210365912e-08 847 2.8231916085508 -2.3563240210718 -1 6.73424210912795 4526 920 847 1367 1880 4070 3535 1610 4149 1211 2557 1668 M3656 REACTOME_UNWINDING_OF_DNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNWINDING_OF_DNA.html Genes involved in Unwinding of DNA 11/11 Reactome 0.000190998181641818 0.000205683645299881 195 1711.27272727273 1881 1.73649786922305e-05 169 1.73248089713918 1.73248089713918 1 2.51869435400829 191 2875 1951 1881 4343 498 169 1412 2815 727 1962 1669 M19918 ABE_VEGFA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ABE_VEGFA_TARGETS.html Genes most profoundly induced in HUVEC cells (endothelium) by VEGFA [GeneID=7422]. 12197474 20/29 John Newman 5.23656402774616e-08 5.22119909633759e-07 3495 2041.27272727273 1881 4.76051286580893e-09 63 2.48711235699753 2.2345045081201 1 6.23358226223123 3495 3469 1323 2293 63 1504 645 2566 3395 1820 1881 1670 M1782 POS_RESPONSE_TO_HISTAMINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/POS_RESPONSE_TO_HISTAMINE_UP.html Genes gradually up-regulated by histamine [PubChem=774] in B16-F10 melanoma tumors. 18339882 16/17 Jessica Robertson 9.94654697561179e-07 1.74397258284237e-06 1040 2008.63636363636 1881 9.04231952055036e-08 166 1.28204485869408 1.38431388781161 1 2.91896322845601 1039 3210 3318 4393 2564 615 459 597 1881 3853 166 1671 M4230 ZHAN_LATE_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_LATE_DIFFERENTIATION_GENES_DN.html B lymphocyte late differentiation genes (LDG): top genes down-regulated in plasma cells from tonsils (TPC) compared to those from bone marrow (BPC). 12393520 16/37 Arthur Liberzon 1.56305911445207e-05 1.87186039376703e-05 4615 2589.63636363636 1882 1.42097292709733e-06 133 1.92586269257015 1.40425870418616 1 3.61162541800445 4613 897 1847 1834 3882 4429 4614 1266 133 1882 3089 1672 M18437 REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS.html Genes involved in G alpha (q) signalling events 104/199 Reactome 1.55084633938402e-07 7.28467912574107e-07 3515 1813.09090909091 1885 1.40986040791624e-08 120 2.62236819276065 -2.23860006031575 -1 6.42276249933129 3515 120 509 2762 668 2935 2093 1177 1885 783 3497 1673 M15411 BARIS_THYROID_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARIS_THYROID_CANCER_DN.html Genes down-regulated in oncocytic follicular carcinoma (FTC) vs mitochondrial-rich papillary carcinoma (PTC) types of thyroid cancer. 15806164 91/108 Arthur Liberzon 4.12120484983304e-07 1.00046055710989e-06 2815 2173.81818181818 1885 3.74655056531656e-08 169 2.08300319699177 -2.09929677034279 -1 4.97601932818464 2815 169 1885 1076 1745 4043 3904 2472 1044 2883 1876 1674 M1127 HUMMERICH_MALIGNANT_SKIN_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_MALIGNANT_SKIN_TUMOR_DN.html Genes down-regulated in malignant skin tumors (squamous cell carcinoma, SCC) formed by treatment with DMBA and TPA [PubChem=6001;4792] in the two stage skin carcinogenesis model. 16247483 25/49 Leona Saunders 2.6246337343128e-07 8.29211725993449e-07 2040 1919.81818181818 1885 2.38603095221426e-08 102 2.26276077459474 2.77436234237132 1 5.48395056605024 2037 3735 1850 1885 1245 2535 4006 102 680 2163 880 1675 M1276 XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_UP.html Genes up-regulated synergistically in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin and NSC682994 [PubChem=444795;388304]. 16140955 30/48 Kevin Vogelsang 1.73644852391816e-07 7.37919956089047e-07 4515 2321.18181818182 1885 1.57858969179559e-08 648 1.9532337989614 -1.9434678065604 -1 4.76673799931081 4512 648 1395 1046 793 4009 4189 1991 868 1885 4197 1676 M1838 LABBE_TGFB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TGFB1_TARGETS_UP.html Up-regulated genes in NMuMG cells (mammary epithelium) after stimulation with TGFB1 [GeneID=7040]. 17210685 144/206 Jessica Robertson 1.36198547610429e-09 2.13783695358847e-08 3885 2053.63636363636 1886 1.2381686154068e-10 183 2.25663420851633 -1.96997984021262 -1 6.91075431978529 3884 1507 390 371 1610 3255 2719 2518 1886 183 4267 1677 M17923 BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP.html Genes up-regulated in cultured stromal stem cells from adipose tissue, compared to the freshly isolated cells. 15635089 593/758 Arthur Liberzon 4.67508850563826e-20 2.79321743628007e-18 2040 1946.09090909091 1887 4.67508850563828e-21 45 2.48830567617043 2.77378953397962 1 17.5161654108335 2040 1138 4571 275 1131 1887 3937 1505 2824 45 2054 1678 M2385 KATSANOU_ELAVL1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KATSANOU_ELAVL1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) with ELAVL1 [GeneID=1994] knocked out. 19307312 212/297 Arthur Liberzon 1.24812852131445e-09 1.97690155053832e-08 1785 1836.18181818182 1887 1.13466229274778e-10 229 2.52318119844519 2.91906338501353 1 7.76743261246351 1783 2060 229 1605 2455 1692 3812 2090 2304 281 1887 1679 M12322 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_3.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 3. 12554760 19/24 Arthur Liberzon 2.30954131498237e-05 2.69694087251776e-05 3120 2407.90909090909 1888 2.09960505518844e-06 1134 3.3781679222861 3.18069042672921 1 6.15744194375599 3119 2381 1155 1441 3987 1888 1659 4271 1134 1646 3806 1680 M16300 HAEGERSTRAND_RESPONSE_TO_IMATINIB http://www.broadinstitute.org/gsea/msigdb/cards/HAEGERSTRAND_RESPONSE_TO_IMATINIB.html Genes with the highest differential expression in primary tissue cultures of high grade glioma: responders vs non-responders to imatinib [PubChem=5291] treatment. 16547494 30/32 Arthur Liberzon 8.79671632887839e-06 1.09842595429381e-05 210 2043.63636363636 1889 7.99704682073711e-07 207 3.25540187302536 3.48131764471843 1 6.44257474955837 207 3123 494 1725 4571 1805 2319 2495 2872 980 1889 1681 M2195 LEE_LIVER_CANCER_CIPROFIBRATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_CIPROFIBRATE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by ciprofibrate [PubChem=2763]. 15565109 72/99 Yujin Hoshida 6.97784458568913e-12 1.52478826131725e-10 3375 1958 1889 6.34349507791931e-13 163 2.9774996937796 3.33057929553782 1 11.7049429939092 3371 232 163 300 1889 3860 4545 2366 724 284 3804 1682 M625 REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES.html Genes involved in Chemokine receptors bind chemokines 21/74 Reactome 1.91426928731319e-06 2.91275017282987e-06 1895 2073.72727272727 1892 1.74024632087619e-07 593 2.92110682286504 -3.04981123921132 -1 6.45306212521463 1892 2803 786 3091 3013 1337 593 3273 3940 698 1385 1683 M811 REACTOME_ADP_SIGNALLING_THROUGH_P2RY1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADP_SIGNALLING_THROUGH_P2RY1.html Genes involved in ADP signalling through P2Y purinoceptor 1 23/29 Reactome 2.40870445931119e-07 8.0442878985801e-07 1870 1933.09090909091 1892 2.18973156639273e-08 644 2.00864882368453 -1.54521775536817 -1 4.87311923688792 2489 1868 2446 1892 1155 2413 644 1431 1866 2579 2481 1684 M1144 OZANNE_AP1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OZANNE_AP1_TARGETS_DN.html Cancer motility and invasion genes down-regulated by the AP-1 transcription factor. 16799638 8/8 Arthur Liberzon 7.0751363556158e-05 7.8594124731717e-05 1445 2234.63636363636 1892 7.07536162470501e-06 721 2.30180688316139 2.33814068711091 1 3.74959388493099 1443 2906 4348 2102 4215 1352 1712 1227 1892 2663 721 1685 M2271 STEGER_ADIPOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEGER_ADIPOGENESIS_DN.html Genes down-regulated during adipogenesis of 3T3-L1 cells (fibroblast). 18285465 33/34 Arthur Liberzon 2.84650916004331e-06 4.05539487938558e-06 385 1906.63636363636 1892 2.58773894823321e-07 384 3.58258720587012 3.70563522359505 1 7.71859641907351 384 1779 444 2065 4353 1892 2593 1750 2544 1058 2111 1686 M3029 ALONSO_METASTASIS_EMT_DN http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_EMT_DN.html EMT (epithelial-mesenchymal transition) genes down-regulated genes in melanoma tumous that developed metastatic disease compared to primary melanoma that did not. 17409456 9/19 Jessica Robertson 1.24141861191046e-05 1.51251828813046e-05 1895 2143.18181818182 1893 1.24142554700575e-06 171 4.28754513440857 5.02709957406676 1 8.26153862922963 1893 997 4580 2573 4283 1705 2099 171 1746 1320 2208 1687 M10412 ZHAN_MULTIPLE_MYELOMA_PR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_PR_DN.html Top 50 down-regulated genes in cluster PR of multiple myeloma samples characterized by increased expression of proliferation and cell cycle genes. 16728703 57/69 Arthur Liberzon 2.47391168370634e-07 8.15502895493072e-07 1665 2450 1893 2.24901087445369e-08 1177 1.50783232883635 -1.10931571144453 -1 3.64202774620684 1665 1692 2985 4355 1177 1850 1425 3546 1893 3262 3100 1688 M4785 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_DN.html Genes down-regulated in monocyte-derived dendritic cells (MDDC) after stimulation with galecin-1 (lectin, LGALS1) [GeneID=3956] compared to that with bacterial lipopolysaccharide (LPS). 16785517 556/774 Arthur Liberzon 4.50241095940084e-07 1.04185917010687e-06 2500 2184.72727272727 1894 4.5024118716278e-08 1193 1.80928779283779 -1.88433020269129 -1 4.30276150562412 1193 2498 4284 1894 1939 1341 1799 2498 3353 1654 1579 1689 M2987 ROZANOV_MMP14_CORRELATED http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_CORRELATED.html Genes whose expression most uniformly correlated with that of MMP14 [GeneID=4323] both in HT1080 cells (fibrosarcoma) and in 190 human tumors. 18519667 21/23 Jessica Robertson 3.35700864511505e-07 9.12209603047959e-07 2160 1894.90909090909 1894 3.05182650669589e-08 178 2.20993835450716 2.99839110805367 1 5.31794354618482 2156 1887 2651 3181 1515 1894 2335 178 312 3406 1329 1690 M2008 MIKKELSEN_ES_LCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_LCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the bivalent histone H3 trimethylation mark at K4 and K27 (H3K4me3 and H3K27me3) in embryonic stem cells (ES). 17603471 3/8 Arthur Liberzon 1.32838274012577e-06 2.1748062897654e-06 1895 1969.90909090909 1894 1.32838353419676e-07 134 2.3641665442594 2.3641665442594 1 5.33381377193736 1894 3265 4645 3309 2841 1124 386 589 871 2611 134 1691 M427 CHESLER_BRAIN_HIGHEST_GENETIC_VARIANCE http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_HIGHEST_GENETIC_VARIANCE.html Neurologically relevant transcripts with highest variance accounted for by mouse strain (genotype) differences. 15711545 54/64 Jean Junior 1.55631703234758e-05 1.86442040423365e-05 1120 2061.27272727273 1895 1.41484367464116e-06 606 2.44156236615269 2.78882768101059 1 4.59382883024653 606 3067 1354 1746 3881 1117 1895 2363 3449 2078 1118 1692 M3323 KANG_DOXORUBICIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_DOXORUBICIN_RESISTANCE_DN.html Genes down-regulated in gastric cancer cell lines: doxorubicin [PubChem=31703] resistant vs sensitive. 14734480 30/32 John Newman 5.40636909591458e-06 7.08048338865617e-06 1320 1876.63636363636 1895 4.91489307435514e-07 213 1.68148068724734 -1.7473364388258 -1 3.43248958386407 1319 2318 2877 1895 3535 1536 882 433 213 3430 2205 1693 M1918 WEST_ADRENOCORTICAL_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_UP.html Up-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 429/516 Jessica Robertson 2.9860224448457e-07 8.71077004924084e-07 640 1929.54545454545 1896 2.71456622739409e-08 636 1.75161093442299 1.87487251472453 1 4.21877329984368 636 3273 3137 2518 1385 1192 1105 1776 2053 2254 1896 1694 M647 REACTOME_ACTIVATED_POINT_MUTANTS_OF_FGFR2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_POINT_MUTANTS_OF_FGFR2.html Genes involved in Activated point mutants of FGFR2 7/20 Reactome 7.54466334650088e-05 8.35346258397471e-05 1545 2333.72727272727 1897 7.54491950749364e-06 437 2.34970674363966 2.80402767824664 1 3.80364374690739 1544 2471 4211 3156 4232 1897 1299 437 1758 3060 1606 1695 M17859 KIM_WT1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_DN.html Genes down-regulated in UB27 cells (osteosarcoma) at any time point after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 592/683 Arthur Liberzon 4.26965758783156e-07 1.01576531323412e-06 1085 2189.45454545455 1897 4.26965840818069e-08 360 1.69085104455789 1.87341676689428 1 4.02531603852771 1083 3839 4313 3569 1897 360 1238 708 2891 3499 687 1696 M276 PID_FGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FGF_PATHWAY.html FGF signaling pathway 18832364 68/84 Pathway Interaction Database 1.33180460982254e-07 7.20206492018647e-07 3260 1700.27272727273 1898 1.21073153676857e-08 156 2.18325346572714 -2.10608133762688 -1 5.3432434192233 3260 277 1292 156 512 2798 1898 4186 262 2161 1901 1697 M3661 REACTOME_FGFR_LIGAND_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FGFR_LIGAND_BINDING_AND_ACTIVATION.html Genes involved in FGFR ligand binding and activation 7/24 Reactome 7.94440592287896e-05 8.78369546872539e-05 1545 2345.63636363636 1898 7.94468994830429e-06 505 2.34970674363966 2.80402767824664 1 3.7830334289741 1545 2472 4265 3157 4233 1898 1300 505 1759 3061 1607 1698 M2333 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION.html Pathogenic Escherichia coli infection 82/116 KEGG 4.99260548542573e-07 1.11141872398347e-06 2210 1695.63636363636 1899 4.5387332894828e-08 361 2.5272120196372 -2.41553051203873 -1 6.0014216568835 2210 2164 1345 477 1946 2396 1549 1675 361 2630 1899 1699 M319 RAY_TARGETS_OF_P210_BCR_ABL_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TARGETS_OF_P210_BCR_ABL_FUSION_DN.html Genes down-regulated in HL-60 cells (acute myeloid leukemia, AML) by expression of p210 BCR-ABL [GeneID=613;25] fusion protein. 15155749 18/21 Arthur Liberzon 3.60004763099413e-07 9.41752134134615e-07 2535 2068 1900 3.27277110918251e-08 353 1.63718974047725 1.95900868702244 1 3.91761291629528 2532 1900 2517 3677 1590 1792 1167 353 3191 2211 1818 1700 M18030 ST_TUMOR_NECROSIS_FACTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_TUMOR_NECROSIS_FACTOR_PATHWAY.html Tumor Necrosis Factor Pathway. 35/37 Signaling Transduction KE 4.12742448602967e-06 5.60294609550189e-06 215 1742 1902 3.752211117745e-07 125 1.83517037034538 -1.87822947029244 -1 3.82581605557514 211 3710 2563 3198 3404 125 127 317 3222 1902 383 1701 M10322 REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS.html Genes involved in Glucagon-type ligand receptors 17/36 Reactome 3.70038780289186e-07 9.5441696336883e-07 1905 1961.09090909091 1902 3.36398947754108e-08 369 2.0075981912425 -1.45637670248413 -1 4.81059582826384 2907 1901 2270 1676 1621 2673 1213 369 1902 2875 2165 1702 M9664 BIOCARTA_GPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GPCR_PATHWAY.html Signaling Pathway from G-Protein Families 51/55 BioCarta 9.25190905723429e-08 6.56798957981166e-07 2035 1862.09090909091 1903 8.41082676937754e-09 264 1.4210322980638 1.51694336993446 1 3.48320554847631 2034 469 3211 500 264 1903 3127 2433 1164 4098 1280 1703 M17122 NUYTTEN_EZH2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_EZH2_TARGETS_DN.html Genes down-regulated in PC3 cells (prostate cancer) after knockdown of EZH2 [GeneID=2146] by RNAi. 17724462 1197/1509 Jessica Robertson 3.65256944544389e-07 9.47640282569729e-07 975 2121.72727272727 1904 3.65257004580089e-08 592 1.61054544685105 1.72809848629489 1 3.85128850198856 974 2492 4431 2916 1712 592 1106 1654 2175 3383 1904 1704 M2200 LEE_DIFFERENTIATING_T_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_DIFFERENTIATING_T_LYMPHOCYTE.html Genes enriched at every T lymphocyte differentiation stage compared to the early passage fetal thymic stromal cultures (TSC). 15210650 264/361 Arthur Liberzon 4.3288349944928e-07 1.02326646843649e-06 1050 1878.09090909091 1904 3.9353053147793e-08 1048 1.92579298794938 -1.72796165510827 -1 4.58910726009367 1048 1335 2162 1465 1803 2002 1420 1904 2833 2480 2207 1705 M15226 LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_UP.html Genes higher expressed in the worst 25 mesothelioma survivors compared to the 25 best ones. 16540645 22/24 Arthur Liberzon 5.75586731372619e-07 1.20852730074678e-06 1275 1662.72727272727 1905 5.2326080178511e-08 31 1.92402639145346 2.48432855569771 1 4.52893304356041 1273 1865 2047 2134 2089 1589 2811 89 1905 2457 31 1706 M14127 HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP.html Genes up-regulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562]. 18172295 587/881 Jessica Robertson 5.87715758934034e-09 8.18294508014348e-08 3070 2187.18181818182 1905 5.87715760488378e-10 210 2.13440623955513 2.27365496233922 1 6.03335348180165 3069 1141 4530 1140 1833 1905 4120 1595 2272 210 2244 1707 M11773 REACTOME_PECAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PECAM1_INTERACTIONS.html Genes involved in PECAM1 interactions 16/17 Reactome 5.81309468371331e-06 7.54200299811073e-06 3250 2296.54545454545 1906 5.28464549436533e-07 306 2.4297344855573 -2.37021744306943 -1 4.9554063619131 3246 1906 1535 453 3571 3268 1372 4430 306 1511 3664 1708 M15368 ROSS_AML_WITH_PML_RARA_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_PML_RARA_FUSION.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtype t(15;17): has PML RARA fusion [GeneID=5371;5914]. 15226186 112/135 Kate Stafford 1.51722995279075e-06 2.41122066571459e-06 1425 1961 1906 1.3793009083176e-07 736 2.25548910610243 2.65668585341404 1 5.04567400861825 1425 2119 736 1249 2871 1744 3650 2129 2723 1019 1906 1709 M950 ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN.html Genes up-regulated in A549 cells (lung carcinoma) upon infection with RSV (respiratory syncytial virus) and down-regulated by further treatment with ribavirin [PubChem=5064]. 12719586 73/97 John Newman 2.63885883531435e-07 8.30914856750082e-07 3075 1993.90909090909 1906 2.39896286530962e-08 270 1.89953382022058 2.25404107003602 1 4.59493311351923 3075 270 1723 1906 1251 2749 3539 1206 2890 1051 2273 1710 M19312 REACTOME_DNA_STRAND_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_STRAND_ELONGATION.html Genes involved in DNA strand elongation 30/31 Reactome 3.20570941070528e-05 3.68687826962206e-05 85 1918.45454545455 1907 2.91432374850262e-06 83 1.39656100929633 1.4405401663256 1 2.4399191216008 83 2737 2592 1907 4363 555 218 1747 3615 978 2308 1711 M4872 TARTE_PLASMA_CELL_VS_PLASMABLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_PLASMABLAST_UP.html Genes up-regulated in mature plasma cells compared with plasmablastic B lymphocytes. 12663452 493/952 Kate Stafford 8.01393825454925e-22 4.99841717531835e-20 4325 2133.63636363636 1907 7.28539841322656e-23 49 2.42637227472352 2.57141704024613 1 18.7839239062545 4324 1164 49 701 708 4213 3989 2337 1907 117 3961 1712 M1640 YIH_RESPONSE_TO_ARSENITE_C1 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C1.html Genes in cluster 1: strongly up-regulated in HFW cells (fibroblast) upon treatment with sodium arsenite [PubChem=26435] at all time points. 12016162 47/53 John Newman 1.24082553964157e-06 2.05859281093434e-06 1755 2261.36363636364 1907 1.12802385407466e-07 160 2.40454076559204 3.09799316200496 1 5.44882027730488 1755 3673 1892 3216 2729 1396 1632 1907 3366 3149 160 1713 M1648 HU_GENOTOXIC_DAMAGE_4HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIC_DAMAGE_4HR.html Genes most consistently regulated at 4 h by all six genotoxins tested: cisplatin, methyl methanesulfonate, mitomycin C, taxol, hydroxyurea and etoposide [PubChem=2767;4156;5746;4666;3657;36462]. 15120960 47/65 John Newman 5.90532396846951e-06 7.65324797670953e-06 1910 2379.09090909091 1907 5.36849074529552e-07 533 1.51992265722866 1.79441344094041 1 3.07723564574955 1907 533 3007 4378 3577 1838 1607 1433 3603 2626 1661 1714 M8123 BERNARD_PPAPDC1B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERNARD_PPAPDC1B_TARGETS_DN.html Genes down-regulated in ZR-75-1 cells (breast cancer, amplified 8p11-12 region) upon knockdown of PPAPDC1B [GeneID=84513] by RNAi. 18757432 75/91 Jessica Robertson 1.5432438697622e-07 7.28175281873995e-07 3445 2132.90909090909 1907 1.40294907092439e-08 255 1.88099238390993 -1.96212408348458 -1 4.5929542533299 3441 255 1907 1025 661 4243 3477 989 1505 2127 3832 1715 M9673 ZHOU_INFLAMMATORY_RESPONSE_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_LPS_UP.html Genes up-regulated in macrophages by P.gingivalis LPS (lipopolysaccharide). 18025224 433/673 Arthur Liberzon 1.92960715720592e-15 6.59981578406661e-14 3765 2111.63636363636 1908 1.75418832473265e-16 98 2.42168512055839 -2.25670921179164 -1 12.7865378904091 3763 1204 98 1121 564 3631 2528 4252 1908 145 4014 1716 M12135 MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN.html Genes down-regulated in apoptotic tissues (neuroepithelium) after MDM4 [GeneID=4194] knockout. 15608685 144/231 Arthur Liberzon 1.20461299570973e-07 7.07415831665123e-07 2420 1931.54545454545 1908 1.09510278333499e-08 422 2.23762263221637 2.55234922368774 1 5.4845544552045 2418 1525 717 1362 422 1908 3401 4191 2510 791 2002 1717 M18181 HUMMEL_BURKITTS_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMEL_BURKITTS_LYMPHOMA_DN.html Down-regulated genes constituting the molecular signature of Burkitt 's lymphoma. 16760442 18/23 Arthur Liberzon 1.12861803083353e-05 1.3865375079475e-05 870 2114.36363636364 1910 1.02602165525283e-06 734 2.2860869093795 -1.99927157205121 -1 4.41635665067114 869 4046 2283 2870 3784 1619 803 734 1910 3045 1295 1718 M4623 KORKOLA_TERATOMA http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_TERATOMA.html Genes predicting the teratoma (T) subtype of nonseminomatous male germ cell tumors (NSGCT). 15870693 63/87 Leona Saunders 1.35645034704898e-07 7.20206492018647e-07 2090 1784.45454545455 1910 1.23313675516675e-08 354 2.97214410100066 2.8084364135648 1 7.2920361811874 2088 1659 354 719 1910 1448 2475 3806 2339 689 2142 1719 M702 REACTOME_ACYL_CHAIN_REMODELLING_OF_PE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PE.html Genes involved in Acyl chain remodelling of PE 13/22 Reactome 8.27104523917028e-06 1.03828014704478e-05 775 1729.81818181818 1911 7.51916030443141e-07 152 2.43576916504851 -2.21503115367968 -1 4.83184626944582 771 1938 1911 2336 3701 599 586 152 3558 2640 836 1720 M1895 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_OLD http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_OLD.html Human environmental etress response genes not changed in primary fibroblasts from old donors in response to 4NQO treatment. 15897889 17/20 Jessica Robertson 9.78183903792388e-07 1.72546377095256e-06 1915 1960.18181818182 1912 8.89258489746943e-08 323 2.53294502784297 -2.09419984392162 -1 5.82055800668 1912 892 1624 1434 2550 2281 1977 3950 323 1670 2949 1721 M18719 BIOCARTA_HER2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HER2_PATHWAY.html Role of ERBB2 in Signal Transduction and Oncology 35/37 BioCarta 7.45477179360325e-07 1.42860425764545e-06 1915 2018.27272727273 1913 6.77706756334381e-08 210 1.51990770830623 -1.75710792446487 -1 3.52276467452197 1913 654 3190 210 2318 2384 2368 1639 1368 4255 1902 1722 M7030 ELVIDGE_HYPOXIA_BY_DMOG_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_BY_DMOG_DN.html Genes down-regulated in MCF7 cells (breast cancer) treated with hypoxia mimetic DMOG [PubChem=3080614]. 16565084 76/89 Arthur Liberzon 3.42601820965787e-07 9.21518482625961e-07 1915 2064.63636363636 1914 3.11456249380482e-08 956 1.68207981085942 1.94704392989204 1 4.03278265584152 1914 2165 2977 3139 1535 1802 2212 956 1714 2574 1723 1723 M7330 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE.html Glycosaminoglycan biosynthesis - heparan sulfate 22/28 KEGG 9.30008877616497e-08 6.56798957981166e-07 2590 2125.72727272727 1915 8.4546265175535e-09 268 2.18507948659543 2.36585049645035 1 5.38292603364075 2586 1870 1621 2759 268 4056 3270 1915 664 2821 1553 1724 M13103 KEGG_AUTOIMMUNE_THYROID_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AUTOIMMUNE_THYROID_DISEASE.html Autoimmune thyroid disease 29/87 KEGG 4.35736650303781e-06 5.86951195614682e-06 500 2065.81818181818 1915 3.96125012123086e-07 497 1.47210352092843 -1.29899559731153 -1 3.04707381107071 497 1807 2304 2936 3429 703 1271 2219 4148 1495 1915 1725 M127 PID_ERBB1_RECEPTOR_PROXIMAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_RECEPTOR_PROXIMAL_PATHWAY.html EGF receptor (ErbB1) signaling pathway 18832364 52/54 Pathway Interaction Database 1.07661976820525e-06 1.85191155463877e-06 1810 1874 1915 9.78745722794412e-08 202 1.71939919335616 -1.69545638221829 -1 3.91376824302881 1809 2667 2876 202 2621 1915 1092 1923 747 3714 1048 1726 M5082 FRASOR_TAMOXIFEN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_TAMOXIFEN_RESPONSE_DN.html Genes preferentially down-regulated in MCF-7 cells (breast cancer) by tamoxifen [PubChem=5376] but not by estradiol or fulvestrant (ICI 182780) [PubChem=5757;3478439]. 16849584 17/18 Arthur Liberzon 5.0795052986703e-07 1.12395348044995e-06 1605 1735.81818181818 1915 4.61773315587311e-08 265 2.08968933453252 -1.45292303975036 -1 4.94967175140153 1605 888 1915 3844 1960 1235 265 1985 677 2462 2258 1727 M8804 GILMORE_CORE_NFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/GILMORE_CORE_NFKB_PATHWAY.html Genes encoding the NF-kB core signaling proteins. 17072321 14/14 Arthur Liberzon 1.30193372744297e-05 1.58053682961184e-05 270 1774 1915 1.18358312017739e-06 54 1.74232699826713 -1.66942323161904 -1 3.31414651019601 267 2856 2467 2883 3831 293 54 722 2982 1915 1244 1728 M4276 NIKOLSKY_BREAST_CANCER_6P24_P22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_6P24_P22_AMPLICON.html Genes within amplicon 6p24-p22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 25/26 Jessica Robertson 3.9645805737116e-08 4.36196277573863e-07 4270 2204 1917 3.60416422286964e-09 27 2.21596672244636 2.50621579446746 1 5.61813092412849 4268 763 1917 1827 27 2491 2248 3619 1094 1868 4122 1729 M1364 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_UP.html Early prostate development genes (up-regulated at 48 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 14/15 Jessica Robertson 0.000354904232562539 0.00037788133943045 1150 2263.54545454545 1918 3.22692271531562e-05 718 3.03507197286153 2.97442061197463 1 4.12760701328618 1197 2868 1026 4173 4401 1147 718 1147 4079 1918 2225 1730 M638 KEGG_ADHERENS_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADHERENS_JUNCTION.html Adherens junction 96/111 KEGG 1.68209850657966e-07 7.33971845416521e-07 3385 1778.63636363636 1919 1.52918057744662e-08 125 2.090870305985 -1.4938870889208 -1 5.10811581576956 3385 125 1313 446 761 2035 1919 2922 400 1961 4298 1731 M18660 ROETH_TERT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROETH_TERT_TARGETS_UP.html Genes up-regulated in T lymphocytes overexpressing TERT [GeneID=7015] off a retrovirus vector. 15741219 14/19 Kevin Vogelsang 1.65822103978797e-05 1.97596650032801e-05 1010 1956.90909090909 1919 1.50748503503879e-06 748 2.10989227717516 -2.073705551366 -1 3.94157740207529 1008 1924 1634 2333 3902 1161 748 1189 3482 1919 2226 1732 M1823 HOEGERKORP_CD44_TARGETS_DIRECT_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_DIRECT_DN.html Genes directly down-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 21/39 Kevin Vogelsang 3.10849734717577e-07 8.88142099193076e-07 2210 1799.90909090909 1920 2.8259070785382e-08 615 2.69776835210464 3.12800350214727 1 6.51549005050279 2206 824 1362 615 1422 2128 1920 2490 2706 2302 1824 1733 M12627 REACTOME_DOPAMINE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOPAMINE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Dopamine Neurotransmitter Release Cycle 14/20 Reactome 8.51275144407428e-07 1.56525854367085e-06 770 1815.54545454545 1921 7.73886794366159e-08 62 1.53508997607714 -1.53112963606687 -1 3.53396017643056 769 1932 2537 3338 2438 332 62 1921 3819 1912 911 1734 M1982 ONO_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONO_FOXP3_TARGETS_DN.html Genes down-regulated in CD4+ [GeneID=920] T lymphocytes transduced with FOXP3 [GeneID=50943]. 17377532 30/53 Jessica Robertson 8.15235103576259e-07 1.51791309226033e-06 1295 2017.72727272727 1921 7.41123096064623e-08 1011 2.31583575015858 2.02625894464648 1 5.36920223419991 1295 3136 1921 3112 2399 1011 1043 2947 2123 1887 1321 1735 M19476 GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_UP.html Genes up-regulated in dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the dividing cells from normal donors. 17717066 15/54 Arthur Liberzon 4.25373113647635e-05 4.82983184127216e-05 1590 2474.09090909091 1922 3.86710307745119e-06 1251 2.57247793379016 -2.53093446095313 -1 4.41515947225727 1590 1922 1275 2842 4106 1867 1251 3612 3848 1352 3550 1736 M10991 NIKOLSKY_OVERCONNECTED_IN_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_OVERCONNECTED_IN_BREAST_CANCER.html Overconnected mutated transcription factors regulating genes within the breast cancer amplicome. 19010930 26/38 Leona Saunders 1.89922874744876e-06 2.89596696650906e-06 2890 2215.27272727273 1922 1.72657307911631e-07 360 2.22834417032787 2.77125783356281 1 4.91305179133622 2888 744 1803 1922 3006 3679 4555 1334 360 1412 2665 1737 M16650 KEGG_PHENYLALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHENYLALANINE_METABOLISM.html Phenylalanine metabolism 20/27 KEGG 5.2122052818567e-06 6.83947982495514e-06 2300 2162.45454545455 1923 4.73837966415651e-07 1317 2.41632120786146 2.137905781714 1 4.96903806186758 2296 1879 1328 1888 3529 1923 1317 1689 2836 2152 2950 1738 M15193 GRUETZMANN_PANCREATIC_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRUETZMANN_PANCREATIC_CANCER_UP.html Genes up-regulated in pancreatic ductal adenocarcinoma (PDAC) identified in a meta analysis across four independent studies. 15897887 515/686 Leona Saunders 1.20384609188223e-07 7.07415831665123e-07 2160 1894.72727272727 1924 1.20384615709828e-08 465 1.94279638717585 2.0105960831873 1 4.75532386748834 2160 1169 4401 465 503 1766 2938 2319 1924 588 2609 1739 M903 REACTOME_REGULATION_OF_SIGNALING_BY_CBL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_SIGNALING_BY_CBL.html Genes involved in Regulation of signaling by CBL 23/26 Reactome 3.61260725017611e-07 9.43114282125621e-07 4555 2312.09090909091 1925 3.2841889485458e-08 172 1.87329148809998 -1.9461961094774 -1 4.48932117882562 4552 804 2056 172 1596 4425 3701 1925 282 1892 4028 1740 M1760 WANG_LSD1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LSD1_TARGETS_DN.html Genes down-regulated after Cre-lox knockout of LSD1 [GeneID=23028] in pituitary. 17392792 31/76 Jessica Robertson 3.76463798505783e-07 9.5981847370948e-07 1930 2353.81818181818 1926 3.422398753875e-08 714 2.04135354156434 -1.7682609824177 -1 4.8903094078654 1926 714 1853 3365 1642 1653 1193 4269 3335 1995 3947 1741 M308 TSAI_RESPONSE_TO_RADIATION_THERAPY http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_RESPONSE_TO_RADIATION_THERAPY.html Genes up-regulated in response to both single dose and fractionated radiation that were common to all three cell lines studied. 17440099 57/76 Jessica Robertson 5.63568847630185e-08 5.47334354077052e-07 905 1795.45454545455 1927 5.12335329151814e-09 333 2.68658439602662 2.95553117693798 1 6.71541267253998 901 388 333 1232 3436 1927 2752 2718 3188 469 2406 1742 M4625 AMIT_EGF_RESPONSE_20_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_20_MCF10A.html Genes whose expression peaked at 20 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 28/30 Leona Saunders 2.956326240148e-07 8.6953471098835e-07 1410 2149.36363636364 1929 2.68756967037696e-08 1101 2.66315095537978 2.28961909459172 1 6.44109067208638 1408 3149 1390 2400 1371 1617 1101 2797 3450 1929 3031 1743 M1213 KANG_GIST_WITH_PDGFRA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_GIST_WITH_PDGFRA_DN.html Genes down-regulated in gastrointestinal stromal tumors (GIST) with PDGFRA [GeneID=5156] mutations. 15690055 8/10 Arthur Liberzon 0.000225115771334895 0.000241707561578869 1390 2284.90909090909 1930 2.25138579286495e-05 158 1.5573432181575 1.31543701281664 1 2.2151216009397 1386 2905 4390 2383 4371 1089 158 1624 1618 3280 1930 1744 M1634 WENG_POR_DOSAGE http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_DOSAGE.html Genes up-regulated in liver from mice with liver specific knockout of POR [GeneID=5447] vs mice with reduced expression of POR in all tissues. 16006652 28/69 John Newman 2.69446592477692e-07 8.35054442872428e-07 3855 2067 1931 2.44951477707604e-08 182 2.93352945933727 -2.28323823306968 -1 7.12083832938715 3854 3132 1001 1376 1276 3898 2796 333 182 1931 2958 1745 M15377 CREIGHTON_AKT1_SIGNALING_VIA_MTOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_AKT1_SIGNALING_VIA_MTOR_DN.html Genes in the AKT1 [GeneID=207] pathway which depend on MTOR [GeneID=2475], sensitive to RAD001 (everolimus) [PubChem=6442177]. 17213801 38/43 Arthur Liberzon 1.00857420282462e-06 1.76313712493786e-06 1150 2155.09090909091 1932 9.1688605927138e-08 1146 1.46256940153878 -1.54841435243021 -1 3.33423592260132 1146 3114 3408 2010 2574 1390 1236 1570 1351 3975 1932 1746 M12398 MAINA_HYPOXIA_VHL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAINA_HYPOXIA_VHL_TARGETS_UP.html Genes up-regulated by hypoxia in RCC4 cells (renal cell carcinoma) engineered to stably express VHL [GeneID=7428] off a plasmid vector. 15824735 7/8 Leona Saunders 2.44376054752841e-07 8.09442090128709e-07 4020 2289.72727272727 1933 2.4437608162669e-08 52 3.01168422427633 2.23514165452381 1 7.32827011140532 4019 1017 4395 101 1273 4247 4106 1933 52 842 3202 1747 M13095 SU_THYMUS http://www.broadinstitute.org/gsea/msigdb/cards/SU_THYMUS.html Genes up-regulated specifically in human thymus. 11904358 12/22 John Newman 2.34709077028845e-06 3.46737666221017e-06 490 1824.09090909091 1933 2.13372115846194e-07 486 1.85200843013018 -2.01961442118313 -1 4.01660701067201 1903 1940 2531 1933 3119 2714 1098 486 489 2448 1404 1748 M17374 SASAKI_TARGETS_OF_TP73_AND_TP63 http://www.broadinstitute.org/gsea/msigdb/cards/SASAKI_TARGETS_OF_TP73_AND_TP63.html Genes up-regulated in DLD1 cells (colon cancer) by p73 beta [GeneID=7161] or by and p63 gamma [GeneID=8626] but not by p53 [GeneID=7157]. 15856012 12/13 Arthur Liberzon 2.03634385637383e-05 2.39271670452688e-05 1765 1946 1934 1.8512388229433e-06 210 2.78446034196513 3.17554879494018 1 5.12469499999976 1765 2878 1863 2183 4273 1934 2034 210 668 1964 1634 1749 M1311 WONG_ENDMETRIUM_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ENDMETRIUM_CANCER_DN.html Genes down-regulated in cancer endometrium samples compared to the normal endometrium. 17043662 124/156 Arthur Liberzon 3.13518075401724e-10 5.46053622101896e-09 315 1831.72727272727 1935 2.85016432224003e-11 211 2.74663573947146 2.92317646787026 1 9.07694299582222 313 2112 211 2572 3911 1726 2291 1739 2924 415 1935 1750 M1363 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_DN.html Early prostate development genes (down-regulated at 12 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 17/20 Jessica Robertson 5.93751829497983e-06 7.68021001707448e-06 3090 2249.90909090909 1935 5.39775847240179e-07 904 2.18253539288594 -2.13247912619315 -1 4.43923470853416 3087 904 1935 1060 3584 3804 2845 1804 1182 1669 2875 1751 M11673 KEGG_BIOSYNTHESIS_OF_UNSATURATED_FATTY_ACIDS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BIOSYNTHESIS_OF_UNSATURATED_FATTY_ACIDS.html Biosynthesis of unsaturated fatty acids 27/33 KEGG 4.56064003790207e-07 1.04801465330564e-06 1425 1998.27272727273 1936 4.14603725757393e-08 725 1.48589456863032 -1.62904167079694 -1 3.5232107810529 1422 725 2541 3330 1870 1574 1400 2325 1936 2433 2425 1752 M5149 MARTINELLI_IMMATURE_NEUTROPHIL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINELLI_IMMATURE_NEUTROPHIL_DN.html Neutrophil-specific genes down-regulated in comparison of immature with mature neutrophils. 15302890 11/19 Arthur Liberzon 2.11094056533947e-07 7.70763712250053e-07 2395 1650.54545454545 1937 1.91903706171649e-08 728 2.8431855070584 3.01044048377941 1 6.93978039089208 2394 961 829 2340 1006 2316 1937 1945 1712 728 1988 1753 M18501 DANG_REGULATED_BY_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/DANG_REGULATED_BY_MYC_UP.html Genes up-regulated by MYC [GeneID=4609], according to the MYC Target Gene Database. 14519204 97/109 Chi Dang 1.28937578773697e-06 2.1219852573635e-06 655 2277.72727272727 1937 1.17216049401348e-07 654 1.42149065253901 1.52527864947726 1 3.19318849841828 654 3325 3563 3532 2752 1086 1431 1445 1081 4249 1937 1754 M16325 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_4.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 4. 12554760 12/18 Arthur Liberzon 1.28585855304665e-06 2.11693490421353e-06 420 1591.90909090909 1939 1.16896300418851e-07 182 1.46362699557623 1.55793117501551 1 3.28993450650621 417 1939 2695 2616 2751 354 182 193 3466 2451 447 1755 M257 PID_EPHRINB_REV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHRINB_REV_PATHWAY.html Ephrin B reverse signaling 18832364 44/52 Pathway Interaction Database 7.6036647680251e-06 9.61148840521652e-06 3410 2513 1940 6.91244640729458e-07 694 2.0704303592795 -1.78911178795376 -1 4.12753060496223 3407 1729 1543 888 3676 3147 1940 4678 694 1603 4338 1756 M499 REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM.html Genes involved in Bile acid and bile salt metabolism 25/53 Reactome 4.95995977740787e-07 1.1074271593834e-06 4710 2524.27272727273 1940 4.50905535967694e-08 779 3.07514019414207 -3.18534833315942 -1 7.31537883196308 4710 1823 779 1366 1940 3324 2341 4337 1682 1289 4176 1757 M2029 KOYAMA_SEMA3B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOYAMA_SEMA3B_TARGETS_DN.html Genes down-regulated in NCI-H1299 cells (large cell neuroendocrine carcinoma) stably expressing SEMA3B [GeneID=7869]. 18985860 488/616 Jessica Robertson 3.51581719131876e-07 9.35932870750822e-07 3140 2183.18181818182 1940 3.19619795743745e-08 1178 1.87621926149502 2.15042722238811 1 4.49892055533037 3136 1178 1724 1647 1556 3072 4050 2233 1940 1227 2252 1758 M17143 SASSON_RESPONSE_TO_GONADOTROPHINS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_GONADOTROPHINS_DN.html Genes down-regulated in primary granulosa cells after stimulation with LH or FSH gonadotrophic hormones for 24 h. 15026540 151/168 Arthur Liberzon 1.67289857059499e-07 7.3358205358541e-07 1540 1787.63636363636 1941 1.52081699800329e-08 666 1.99698976290762 2.3820146842802 1 4.87669887658362 1537 2547 2234 666 751 1941 2740 1766 2065 2260 1157 1759 M12275 BROWNE_HCMV_INFECTION_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_24HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 24 h time point that were not up-regulated at the previous time point, 20 h. 11711622 209/260 John Newman 3.72817988615312e-07 9.57025534470045e-07 2500 2091.45454545455 1943 3.38925501630981e-08 1029 1.93093362293934 1.98572304916221 1 4.62406132781477 2497 1396 1188 1029 1631 2685 4127 2252 1943 1284 2974 1760 M5929 CROONQUIST_STROMAL_STIMULATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_STROMAL_STIMULATION_UP.html Genes up-regulated in ANBL-6 cell line (multiple myeloma, MM) co-cultured with bone marrow stromal cells compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 104/137 Arthur Liberzon 8.61015172105569e-14 2.4932463879376e-12 1360 1824.36363636364 1944 7.82741065550549e-15 119 2.89859095034363 3.14397968815232 1 13.4758782286439 1360 1580 119 742 3076 2096 3846 2834 1944 318 2153 1761 M5002 DAZARD_UV_RESPONSE_CLUSTER_G24 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G24.html Cluster G24: genes induced in NHEK (normal keratinocyte) but not in SCC12B2 cells (squamous cell carcinoma) by UV-B radiation. 12771951 34/102 Arthur Liberzon 4.87302189035585e-05 5.50386774885848e-05 1450 2246.90909090909 1944 4.43011802874808e-06 1448 2.29010648089529 -2.6759011478209 -1 3.8727777993735 1448 3120 1904 1944 4128 1911 1508 2435 2330 2352 1636 1762 M2466 DELACROIX_RAR_BOUND_ES http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RAR_BOUND_ES.html Genes with DNA sequences bound by RARA and RARG [GeneID=5914, 5916] in ES cells. 19884340 510/658 Arthur Liberzon 1.36992267201831e-07 7.20206492018647e-07 4030 2389.72727272727 1944 1.36992275646928e-08 103 2.01769431917868 2.21764936268747 1 4.93426345160241 4027 1167 4704 103 640 1944 4199 3862 1311 626 3704 1763 M6761 GOLUB_ALL_VS_AML_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOLUB_ALL_VS_AML_DN.html Down-regulated genes highly correlated with acute lymphoblastic leukemia (ALL) vs acute myeloid leukemia (AML). 10521349 20/35 Jean Junior 1.06887897586422e-06 1.84074926531728e-06 1245 1603.09090909091 1947 9.71708631985264e-08 96 1.97481501810181 -2.51470791811257 -1 4.50467464642218 1242 2369 1947 2381 2616 1485 528 96 2434 2154 382 1764 M12494 REACTOME_PHOSPHORYLATION_OF_CD3_AND_TCR_ZETA_CHAINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHORYLATION_OF_CD3_AND_TCR_ZETA_CHAINS.html Genes involved in Phosphorylation of CD3 and TCR zeta chains 10/18 Reactome 1.19591233834961e-07 7.06112554001409e-07 2810 2092.81818181818 1948 1.08719309396272e-08 419 3.37820979274709 -3.84524730062394 -1 8.30679919842101 2806 1948 1011 1389 419 3145 2828 950 3588 1560 3377 1765 M802 RIZ_ERYTHROID_DIFFERENTIATION_HBZ http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_HBZ.html Selected gradually up-regulated genes whose expression profile follows that of HBZ [GeneID=3050] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 42/65 Leona Saunders 8.67150132327514e-07 1.58395844604716e-06 1950 2044.72727272727 1948 7.88318612838966e-08 1550 1.86990646608947 1.68666135584416 1 4.31178258911694 1946 1755 2193 2282 2457 1997 1550 2593 1948 1876 1895 1766 M5884 NABA_CORE_MATRISOME http://www.broadinstitute.org/gsea/msigdb/cards/NABA_CORE_MATRISOME.html Ensemble of genes encoding core extracellular matrix including ECM glycoproteins, collagens and proteoglycans 22159717 207/301 Alexandra Naba 5.26231633422111e-42 1.37989628319576e-39 1950 1740.90909090909 1948 4.78392394020102e-43 10 3.40415821233444 3.57790689294077 1 53.1503634502501 394 2053 10 681 3749 2563 3579 1947 2165 61 1948 1767 M889 REACTOME_DCC_MEDIATED_ATTRACTIVE_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DCC_MEDIATED_ATTRACTIVE_SIGNALING.html Genes involved in DCC mediated attractive signaling 20/22 Reactome 1.38435096651409e-06 2.24695205018793e-06 2245 1956.45454545455 1949 1.2585016705621e-07 562 1.78688439412245 -1.91264418178477 -1 4.00900002085115 2242 2374 2787 1701 2795 1949 765 1927 562 2512 1907 1768 M3900 MUNSHI_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MUNSHI_MULTIPLE_MYELOMA_DN.html Genes down-regulated in multiple myeloma (MM) compared to normal plasma cells from the patient's identical twin. 12969976 11/14 Kevin Vogelsang 6.99177453387546e-07 1.37161994180765e-06 1950 2470.90909090909 1949 6.35616068719806e-08 1246 0.942951399951624 1.06868023561433 1 2.17323452803009 1947 1949 3440 4380 2260 1459 1775 1514 3487 3723 1246 1769 M1626 BURTON_ADIPOGENESIS_PEAK_AT_0HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_0HR.html Cluster 1: genes progressively down-regulated over 24 h (peak at 0 h timepoint) during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 118/149 John Newman 7.61893035917879e-07 1.44597311199533e-06 2205 2043.63636363636 1949 6.92630272520914e-08 703 2.24904041671738 2.89174800594031 1 5.23196829674672 2203 1571 703 1949 2343 2843 4154 1885 2519 788 1522 1770 M2582 DURAND_STROMA_NS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DURAND_STROMA_NS_UP.html Genes up-regulated in the HSC non-supportive stromal cell lines. 212/268 Charles Durand 3.15476945528144e-07 8.93979952731796e-07 3700 2262 1949 2.86797264333736e-08 366 2.23090285305054 2.62404513696584 1 5.37673217959147 3700 1392 555 1349 1436 2241 3804 4391 1949 366 3699 1771 M1130 MCBRYAN_TERMINAL_END_BUD_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_TERMINAL_END_BUD_DN.html The 'TEB profile genes': down-regulated during pubertal mammary gland development specifically in the TEB (terminal end bud) structures. 17486082 11/15 Arthur Liberzon 6.40817582279793e-06 8.2236514093546e-06 3195 2143.18181818182 1951 5.82563135332243e-07 1049 2.74391013148026 -3.17276755808423 -1 5.56116568174372 3195 1951 1713 1049 3612 3335 2512 1076 1190 2744 1198 1772 M1452 NEMETH_INFLAMMATORY_RESPONSE_LPS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NEMETH_INFLAMMATORY_RESPONSE_LPS_DN.html Genes down-regulated in RAW 264.7 cells (macrophage) 3 hr after stimulation with bacterial lipopolysaccharide (LPS). 12766259 43/60 Kevin Vogelsang 2.42295775309076e-06 3.55276812506629e-06 2085 2058.18181818182 1951 2.20269129236901e-07 1143 2.14649120848922 2.13125271947161 1 4.65411212289058 2083 1731 1505 1476 3139 2386 2753 1951 1767 1143 2706 1773 M7363 ELVIDGE_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_UP.html Genes up-regulated in MCF7 cells (breast cancer) under hypoxia conditions. 16565084 225/258 Arthur Liberzon 1.21783239529882e-07 7.10527676861612e-07 3550 2113.54545454545 1952 1.10712042064835e-08 431 2.14375553697657 2.37165140013057 1 5.25073781539152 3548 1378 676 769 431 3489 4544 3545 1952 551 2366 1774 M311 KEGG_ALPHA_LINOLENIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALPHA_LINOLENIC_ACID_METABOLISM.html alpha-Linolenic acid metabolism 10/21 KEGG 5.05164443577005e-07 1.11952927170486e-06 480 1684.63636363636 1954 4.5924050870273e-08 32 1.75753922720569 -1.75753922720569 -1 4.15619309442055 480 1964 2513 3859 1954 266 32 294 4392 2537 240 1775 M1965 MIKKELSEN_MEF_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MEF cells (embryonic fibroblasts). 18509334 42/127 Jessica Robertson 3.10005207390535e-08 3.58633475216501e-07 3015 1908.18181818182 1954 2.81822919780784e-09 312 3.68863215812563 3.5774738725757 1 9.5111639211607 3015 1727 312 529 2698 1954 2234 4141 356 682 3342 1776 M13088 KEGG_PPAR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PPAR_SIGNALING_PATHWAY.html PPAR signaling pathway 52/91 KEGG 5.15931273794817e-08 5.19978203455085e-07 2120 1709.36363636364 1955 4.69028441721943e-09 56 2.01261198088437 -1.83694919159272 -1 5.03621526842744 2645 433 1596 2120 56 1955 1131 3157 2444 1149 2117 1777 M1570 MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP.html Genes up-regulated in non-apoptotic tissues (fetal liver) after MDM4 [GeneID=4194] knockout. 15608685 286/354 Arthur Liberzon 2.97981064001691e-07 8.70294688256627e-07 1835 2166.63636363636 1955 2.70891913056385e-08 1162 2.00952678841092 2.1847209896746 1 4.84764941388512 1833 3561 1955 2803 1381 1162 1726 2266 2419 3036 1691 1778 M2591 GHANDHI_DIRECT_IRRADIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_DIRECT_IRRADIATION_UP.html Genes significantly (FDR < 10%) up-regulated in IMR-90 cells (fibroblast) in response to direct irradiation. 19108712 113/143 Itai Pashtan 1.19272941774061e-07 7.06112554001409e-07 2125 1422.45454545455 1955 1.08429952945856e-08 77 2.39663385241264 -2.63753968949812 -1 5.87862865206106 2125 77 496 999 413 1992 1955 2330 2740 486 2034 1779 M17636 KEGG_RENIN_ANGIOTENSIN_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENIN_ANGIOTENSIN_SYSTEM.html Renin-angiotensin system 10/30 KEGG 6.50395378435564e-07 1.30791290081906e-06 960 1553.45454545455 1958 5.91268700649821e-08 124 1.9815554919715 -2.05697771708236 -1 4.63849426594033 959 1958 2075 2349 2192 429 124 580 3557 2538 327 1780 M9221 BROWNE_INTERFERON_RESPONSIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_INTERFERON_RESPONSIVE_GENES.html Genes up-regulated in primary fibroblast culture after treatment with interferon alpha for 6 h. 11711622 114/192 John Newman 5.6094528068962e-07 1.18755717431014e-06 200 1625.81818181818 1958 5.0995038519706e-08 199 1.64911861417382 -1.68205535111892 -1 3.87972460819265 199 2124 2444 1979 2067 629 723 1551 3104 1958 1106 1781 M1922 MIKKELSEN_PLURIPOTENT_STATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_PLURIPOTENT_STATE_UP.html Genes up-regulated in the induced pluripotent cells (iPS) and embryonic stem cells (ES) compared to the parental lineage-committed and partially reprogrammed cell lines. 18509334 11/22 Jessica Robertson 5.69733995040375e-07 1.2010470998618e-06 2610 1934.09090909091 1958 5.17940129622218e-08 141 1.84583004889514 2.57175078425826 1 4.34483600565887 2608 1952 2484 1958 2078 2457 1820 1629 141 3307 841 1782 M957 REACTOME_NFKB_ACTIVATION_THROUGH_FADD_RIP1_PATHWAY_MEDIATED_BY_CASPASE_8_AND10 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NFKB_ACTIVATION_THROUGH_FADD_RIP1_PATHWAY_MEDIATED_BY_CASPASE_8_AND10.html Genes involved in NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 12/15 Reactome 3.71252073818177e-07 9.54937214398798e-07 1960 2128.27272727273 1959 3.37501942243027e-08 239 1.83002931081971 -1.44858244724134 -1 4.38050635711685 1959 2884 2595 4156 1625 1614 678 239 3622 2967 1072 1783 M16853 KEGG_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DNA_REPLICATION.html DNA replication 35/36 KEGG 0.000118939474587186 0.00012986220681275 110 2077.63636363636 1962 1.08132641223659e-05 106 1.29364684143768 1.3280180179767 1 1.97194342181209 106 3109 3238 1962 4332 598 154 1580 3731 1901 2143 1784 M8713 REACTOME_AMINE_DERIVED_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINE_DERIVED_HORMONES.html Genes involved in Amine-derived hormones 3/15 Reactome 1.01874203736601e-05 1.26272647488644e-05 1965 2028.18181818182 1962 1.01874670765517e-06 160 3.08245807227493 -4.0881913627466 -1 6.02260725684374 1962 1063 4233 2270 3782 2901 1715 348 160 1688 2188 1785 M14515 COATES_MACROPHAGE_M1_VS_M2_DN http://www.broadinstitute.org/gsea/msigdb/cards/COATES_MACROPHAGE_M1_VS_M2_DN.html Down-regulated genes distinguishing between M1 (pro-inflammatory) and M2 (anti-inflammatory) macrophage subtypes. 18199539 98/138 Jessica Robertson 1.36062444526341e-07 7.20206492018647e-07 1645 2112.63636363636 1964 1.23693139037579e-08 535 2.10339850351169 -2.05054556446904 -1 5.14597808811892 1645 3883 1964 3125 535 1121 1376 2048 3640 2264 1638 1786 M7253 KEGG_FOCAL_ADHESION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOCAL_ADHESION.html Focal adhesion 214/245 KEGG 3.91358973459982e-07 9.77362092450325e-07 1420 1800.36363636364 1965 3.55780948253654e-08 571 2.16046693350038 2.39826832156522 1 5.17174486558613 1418 2062 571 902 1685 2309 3328 1999 2437 1128 1965 1787 M5076 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_UP.html Genes specifically up-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and high dose methotrexate (HDMTX) [PubChem=4112]. 12704389 9/9 Arthur Liberzon 4.36292047449787e-06 5.87531658762623e-06 1710 1997.54545454545 1965 4.36292904030531e-07 117 1.72235438835238 -2.12350369008446 -1 3.57327116840183 1709 1965 4614 2314 3486 2399 837 983 117 2901 648 1788 M6682 BIOCARTA_MCM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCM_PATHWAY.html CDK Regulation of DNA Replication 19/19 BioCarta 8.02938551546423e-05 8.87557368454126e-05 2385 1879.54545454545 1966 7.29970780053015e-06 88 1.532747587516 1.532747587516 1 2.44754437932133 257 2384 2686 1966 4220 324 88 1488 3097 2381 1784 1789 M17572 SMID_BREAST_CANCER_LUMINAL_B_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_B_DN.html Genes down-regulated in the luminal B subtype of breast cancer. 18451135 617/967 Jessica Robertson 5.13339005312556e-45 1.73068578933948e-42 1970 1925.90909090909 1966 5.13339005312557e-46 8 2.69518337166783 2.79911185397773 1 45.2155326982653 1966 1118 4551 229 500 2044 3809 1965 2286 8 2709 1790 M15125 FARMER_BREAST_CANCER_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_4.html Cluster 4: selected stromal genes clustered together across breast cancer samples. 15897907 44/55 Leona Saunders 2.90234343150711e-11 5.80468686301423e-10 80 1898.27272727273 1966 2.63849402867764e-12 78 3.44945843829468 3.45532696870828 1 12.7628173826125 78 2682 181 1681 4528 1635 2126 2525 3043 436 1966 1791 M840 REACTOME_CELL_EXTRACELLULAR_MATRIX_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_EXTRACELLULAR_MATRIX_INTERACTIONS.html Genes involved in Cell-extracellular matrix interactions 20/22 Reactome 7.17429424240286e-07 1.39158880803028e-06 470 1490.18181818182 1967 6.52208780179274e-08 469 1.9488602651844 1.85786185637745 1 4.54002631449839 469 2358 1967 2101 2286 481 802 2418 763 2153 594 1792 M19829 BIOCARTA_AGPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGPCR_PATHWAY.html Attenuation of GPCR Signaling 18/21 BioCarta 1.52352249762297e-07 7.28175281873995e-07 1815 2047 1968 1.38502054829861e-08 539 1.07089579988415 1.1910425445326 1 2.59333345464356 1815 2829 3353 2705 645 1269 539 1968 2497 3748 1149 1793 M527 GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_DN.html Down-regulated genes from the set D (Fig. 5a): specific signature shared by cells expressing MLL-AF4 [GeneID=4297;4299] alone and those expressing both MLL-AF4 and AF4-MLL fusion proteins. 17130830 15/17 Arthur Liberzon 2.65162548093087e-07 8.31648157220804e-07 2685 2099.18181818182 1968 2.41056890957017e-08 902 2.10694835030839 2.16961571468255 1 5.10180363915384 2685 902 1472 2390 1256 2490 1404 4027 2797 1700 1968 1794 M17534 LEE_DOUBLE_POLAR_THYMOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_DOUBLE_POLAR_THYMOCYTE.html Genes enriched in the double polar (DP) thymocyte compared to all other T lymphocyte differentiation stages. 15210650 21/34 Arthur Liberzon 1.82047150924025e-06 2.79162622599545e-06 1970 1957.09090909091 1968 1.65497546878054e-07 847 1.83001111502884 -1.83206501614656 -1 4.03759132087864 1968 847 2158 3342 2984 1976 913 1416 1699 1619 2606 1795 M7970 PENG_GLUCOSE_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUCOSE_DEPRIVATION_DN.html Genes down-regulated in BJAB cells (B-lymphoma) after glucose [PubChem=206] deprivation. 12101249 225/285 Broad Institute 4.74449323662911e-07 1.07819008555077e-06 1530 2198.18181818182 1969 4.31317659983733e-08 1527 1.68719976262443 1.83956858418045 1 3.99894040321886 1527 2530 3019 1731 1904 1969 2461 1718 2438 2939 1944 1796 M10544 BOYAULT_LIVER_CANCER_SUBCLASS_G56_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G56_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G56, defined by unsupervised clustering. 17187432 24/27 Yujin Hoshida 5.12294624418072e-07 1.12712781758131e-06 2690 2026.45454545455 1970 4.65722494283317e-08 909 2.36302168765688 -2.16392850569215 -1 5.60247206464291 2686 1849 1359 1782 1970 3115 2940 909 1309 2035 2337 1797 M1928 MIKKELSEN_PARTIALLY_REPROGRAMMED_TO_PLURIPOTENCY http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_PARTIALLY_REPROGRAMMED_TO_PLURIPOTENCY.html Genes up-regulated in cells that have been partially reprogrammed to pluripotency: comparison with the parental lineage-committed cell lines, fully reprogrammed stem cells, and embryonic stem cells. 18509334 8/12 Jessica Robertson 1.17413799069167e-06 1.97502897935306e-06 2365 2029.27272727273 1972 1.17413861106214e-07 283 2.40080378497608 3.33354771199334 1 5.45765059669288 2364 1972 4610 1659 2754 2729 1089 1216 283 3288 358 1798 M1969 MIKKELSEN_IPS_ICP_WITH_H3K4ME3_AND_H327ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_ICP_WITH_H3K4ME3_AND_H327ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the bivalent tri-methylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 149/250 Jessica Robertson 3.04229842325655e-15 1.02568918269792e-13 3380 2340.45454545455 1972 2.76572583932413e-16 99 2.86027315953819 2.88437648753636 1 14.8910897230979 3376 1499 99 1138 1571 3553 4174 4233 1972 173 3957 1799 M2371 WACKER_HYPOXIA_TARGETS_OF_VHL http://www.broadinstitute.org/gsea/msigdb/cards/WACKER_HYPOXIA_TARGETS_OF_VHL.html Genes down-regulated by VHL [GeneID=7428] and re-expressed under hypoxia conditions in renal carcinoma cells. 19158274 21/23 Arthur Liberzon 5.13198571425268e-07 1.12806520559919e-06 2165 2044.72727272727 1972 4.66544264672913e-08 489 1.98449517106337 2.19166018235711 1 4.69672265107564 2161 1878 1865 1672 1972 2944 2364 489 794 3082 3271 1800 M2131 WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP.html Genes up-regulated in RS4;11 cells (MLL, mixed lineage leukemia) in response to SB216763 [PubChem=176158], an inhibitor of GSK3B [GeneID=2932]. 20541704 458/675 Arthur Liberzon 7.58654682163943e-07 1.44272767921588e-06 445 1847.81818181818 1973 6.89686312528048e-08 408 1.69700160911443 -1.63853513154068 -1 3.9361382434911 441 2947 3363 2413 2338 408 775 1359 3147 1973 1162 1801 M830 REACTOME_RECEPTOR_LIGAND_BINDING_INITIATES_THE_SECOND_PROTEOLYTIC_CLEAVAGE_OF_NOTCH_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECEPTOR_LIGAND_BINDING_INITIATES_THE_SECOND_PROTEOLYTIC_CLEAVAGE_OF_NOTCH_RECEPTOR.html Genes involved in Receptor-ligand binding initiates the second proteolytic cleavage of Notch receptor 15/18 Reactome 1.23684450704605e-06 2.05343161212006e-06 2585 1813.45454545455 1974 1.12440472945737e-07 324 2.23399174606771 -1.2379365812176 -1 5.05977735424194 2585 2409 1785 1446 2726 1974 574 585 324 2533 3007 1802 M1203 TERAMOTO_OPN_TARGETS_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_7.html Cluster 7: genes down-regulated early (within 24 h) after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 22/27 Arthur Liberzon 0.000258795612827974 0.000276799295841386 870 2116.18181818182 1974 2.35296419182996e-05 421 2.5468464900842 2.17173534712339 1 3.59405395294596 868 3182 1940 3678 4375 816 421 2318 1620 2086 1974 1803 M1382 PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_DN.html Down-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that were identified as candidate genes for the regulation of left ventricle mass (LVM). 18443592 10/12 Jessica Robertson 7.42955023087141e-07 1.42492795976079e-06 1870 2184.36363636364 1974 6.75413885443858e-08 115 1.20773933372301 -1.35546382168164 -1 2.78950328162039 1866 4095 3471 4182 2316 1336 357 327 1974 3989 115 1804 M1017 REACTOME_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPLICATION.html Genes involved in DNA Replication 206/224 Reactome 3.8464553893595e-06 5.26392271318551e-06 55 1813.81818181818 1975 3.4967837404323e-07 54 1.52728721835766 1.61435782248856 1 3.19222082609194 54 3295 3608 1975 3431 246 210 1253 2244 2201 1435 1805 M1581 RUAN_RESPONSE_TO_TNF_TROGLITAZONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_TROGLITAZONE_UP.html Adipocyte abundant genes up-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591] and TNF [GeneID=7124]. 12732648 32/42 John Newman 5.15487470569978e-07 1.13009793826767e-06 2940 2047.72727272727 1978 4.68625083050153e-08 656 2.71533048356501 -1.6753797781907 -1 6.44397069750153 2937 656 1077 770 1978 3359 2269 3870 735 1137 3737 1806 M3062 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2.html The 'group 2 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [GeneID=2099;2064]. 18794137 456/685 Jessica Robertson 1.94385203584203e-07 7.601476063939e-07 2035 1897.72727272727 1978 1.76713837054073e-08 490 1.86303433874014 1.95616445596765 1 4.53464475901376 2035 2019 2236 3647 916 490 1781 1978 2533 1482 1758 1807 M9131 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROPHOSPHOLIPID_METABOLISM.html Glycerophospholipid metabolism 64/81 KEGG 5.15992667203566e-07 1.13030335934061e-06 965 1707.45454545455 1979 4.69084352932382e-08 397 1.74551307315123 -1.56466285375652 -1 4.1244915796949 963 2644 2757 3312 1979 397 488 453 2329 2935 525 1808 M1221 YAN_ESCAPE_FROM_ANOIKIS http://www.broadinstitute.org/gsea/msigdb/cards/YAN_ESCAPE_FROM_ANOIKIS.html Genes up-regulated in IEC-18 cells (intestinal epithelial cells) which avoided anoikis (a form of apoptosis) after detachment. 16007176 46/64 Arthur Liberzon 4.23551073535727e-06 5.72713227875401e-06 240 2088.27272727273 1980 3.85047171792791e-07 240 1.85375394217239 -1.77894978876161 -1 3.85796647281643 240 3388 1980 3561 3417 418 515 2137 4381 1804 1130 1809 M12710 AMIT_EGF_RESPONSE_120_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_120_HELA.html Genes whose expression peaked at 120 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 99/122 Leona Saunders 1.3753765001855e-07 7.20206492018647e-07 1590 2175.27272727273 1980 1.25034235106371e-08 544 2.08535408903516 -1.72582993826524 -1 5.10140305736886 1586 3013 1795 2974 544 1693 1123 3796 2354 1980 3070 1810 M1436 GUO_HEX_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUO_HEX_TARGETS_UP.html Genes up-regulated in day 6 embryoid bodies derived from embryonic stem cells (ES) with HEX [GeneID=3087] knockout. 12791650 122/141 Kevin Vogelsang 5.16060114275215e-07 1.13030335934061e-06 1905 1767.72727272727 1980 4.69145668480827e-08 58 1.90783299999039 2.41514056503799 1 4.51269216777923 1901 58 2166 2154 1980 2800 3625 787 1028 2587 359 1811 M12924 SASSON_RESPONSE_TO_FORSKOLIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_FORSKOLIN_DN.html Genes down-regulated in primary granulosa cells in response to forskolin [PubChem=47936]. 15026540 142/157 Arthur Liberzon 1.35934609563257e-07 7.20206492018647e-07 1800 1797.54545454545 1980 1.23576925420407e-08 533 1.98436642017951 2.5102221361558 1 4.85193370215807 1797 2099 2209 1087 533 2047 2979 1479 1980 2802 761 1812 M8492 KEGG_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_APOPTOSIS.html Apoptosis 90/107 KEGG 2.25654543760147e-07 7.86164283892477e-07 2065 1799.27272727273 1981 2.0514051536872e-08 186 2.0326455648026 -1.91453454665872 -1 4.94008825819654 2064 186 1888 1310 1079 2699 2503 2531 1981 2441 1110 1813 M15693 GENTILE_UV_RESPONSE_CLUSTER_D8 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D8.html Cluster d8: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 62/67 John Newman 7.77049132687691e-07 1.46941983424916e-06 1065 1902.90909090909 1981 7.06408551949824e-08 519 1.53069194929922 1.45015031223211 1 3.54058382098952 1063 2651 3170 1981 2354 798 1373 519 3807 2313 903 1814 M3389 LIU_TARGETS_OF_VMYB_VS_CMYB_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_TARGETS_OF_VMYB_VS_CMYB_UP.html Genes regulated in the opposite directions by v-MYB (UP) and c-MYB (DN) variants of CMYB [GeneID=4602] overexpressed in primary monocyte cultures off adenoviral vectors. 16205643 19/25 Arthur Liberzon 2.88614655972245e-07 8.59470773620819e-07 4215 2584.54545454545 1983 2.62376994395609e-08 876 2.81571894070396 -2.52361059177852 -1 6.81868286919634 4213 876 1392 1621 1352 4011 4667 3201 1212 1983 3902 1815 M15821 AMIT_SERUM_RESPONSE_120_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_120_MCF10A.html Genes whose expression peaked at 120 min after stimulation of MCF10A cells with serum. 17322878 95/127 Leona Saunders 9.42681233362394e-07 1.68146476145018e-06 1515 2235.81818181818 1983 8.56983306630458e-08 1467 1.90291479505716 -2.0213155218172 -1 4.3689247607595 1514 3613 2139 3424 2525 1983 1795 1805 2430 1899 1467 1816 M1623 SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_DN.html Down-regulated in murine dorsal skin cells at 6 h after treatment with the phorbol ester carcinogen TPA [PubChem=4792]. 12640676 47/68 John Newman 1.90459649584364e-05 2.24967353863413e-05 485 2008.45454545455 1985 1.73146634965859e-06 484 2.34884556975996 2.56604190551298 1 4.34042330231351 484 2676 1012 2688 3935 1405 1985 2704 2853 835 1516 1817 M8873 ST_FAS_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_FAS_SIGNALING_PATHWAY.html Fas Signaling Pathway 84/100 Signaling Transduction KE 1.16898433201023e-07 7.06112554001409e-07 2505 1962.36363636364 1986 1.06271308556816e-08 228 1.85513201871526 -1.71619041795993 -1 4.53909011066622 2501 228 1832 1986 396 2323 1875 4608 815 2569 2453 1818 M123 MUELLER_PLURINET http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_PLURINET.html Genes constituting the PluriNet protein-protein network shared by the pluripotent cells (embryonic stem cells, embryonical carcinomas and induced pluripotent cells). 18724358 364/443 Arthur Liberzon 2.7171826694437e-06 3.90651909831687e-06 200 1956.81818181818 1986 2.4701691139961e-07 198 1.55699794870779 1.53783530915952 1 3.33639393864632 198 2948 3726 2521 3208 380 294 1405 1986 3193 1666 1819 M1214 PATTERSON_DOCETAXEL_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/PATTERSON_DOCETAXEL_RESISTANCE.html Genes up-regulated in DU145-RD cells (prostate cancer) resistant to docetaxel [PubChem=148124] vs the parental, docetaxel-sensitive cells. 16652143 53/80 Arthur Liberzon 3.79573911901057e-06 5.20810716329357e-06 1875 2342.90909090909 1987 3.450677879956e-07 806 1.5921472856295 -1.62365478922083 -1 3.33287574262017 806 1709 2647 1987 3370 1875 2198 1333 4390 3583 1874 1820 M86 PID_ARF6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_PATHWAY.html Arf6 signaling events 18832364 55/66 Pathway Interaction Database 1.13385847171269e-07 7.05613393308323e-07 2655 2134.63636363636 1988 1.03078048195514e-08 369 1.98631066799789 -1.74547315154788 -1 4.86383823278851 2651 2656 1929 1988 369 2298 1499 4239 1525 1727 2600 1821 M8601 BIOCARTA_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAC1_PATHWAY.html Rac 1 cell motility signaling pathway 35/38 BioCarta 7.77067013025618e-08 6.27525965386533e-07 3760 2193.45454545455 1989 7.06424582247798e-09 171 1.85004865455127 -1.60917925055329 -1 4.5646403287892 3759 595 1989 1064 171 4119 3824 2419 998 1228 3962 1822 M2103 STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP.html Genes induced in SKBR3 cells (breast cancer) by 25-hydroxyvitamin D3 [PubChem=1593]. 20227041 127/173 Arthur Liberzon 6.27185156029405e-08 5.80453713031135e-07 4195 2181.81818181818 1989 5.70168339917691e-09 4 2.24232253020507 -2.46419908970965 -1 5.57364834548045 4194 4 679 555 98 4335 3210 4714 1989 856 3366 1823 M16289 REACTOME_CYTOSOLIC_SULFONATION_OF_SMALL_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOSOLIC_SULFONATION_OF_SMALL_MOLECULES.html Genes involved in Cytosolic sulfonation of small molecules 5/18 Reactome 2.36582599621695e-06 3.48741371085073e-06 1105 2059.63636363636 1990 2.36582851493041e-07 79 1.5956610510283 -1.5956610510283 -1 3.45211301639673 1104 1990 4260 4359 3187 706 79 763 2865 3251 92 1824 M12480 LINDSTEDT_DENDRITIC_CELL_MATURATION_B http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_B.html Maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli: genes up-regulated both at 8 hr and 48 hr after the stimulation (cluster B). 12356685 70/83 Arthur Liberzon 1.28055918485438e-06 2.10968214747388e-06 515 2063.36363636364 1990 1.16414539112099e-07 511 1.75539955063181 -2.00744150823839 -1 3.95680667630504 511 3045 2420 3523 2750 919 563 1261 3792 1923 1990 1825 M71 PID_ILK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ILK_PATHWAY.html Integrin-linked kinase signaling 18832364 60/68 Pathway Interaction Database 1.32949166969329e-07 7.20206492018647e-07 1925 2247.72727272727 1991 1.20862886366944e-08 510 1.5244061295242 1.75325239841469 1 3.71569599677678 1887 2207 3107 3175 510 1991 2879 1922 1922 3471 1654 1826 M7933 SESTO_RESPONSE_TO_UV_C1 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C1.html Cluster 1: genes changed in primary keratinocytes by UVB irradiation. 11867738 97/129 John Newman 7.80399928385111e-07 1.47457472457075e-06 955 2205.81818181818 1991 7.09454732013057e-08 954 1.9269008930355 -1.8451587196923 -1 4.46881246706061 954 3015 2635 1991 2356 1734 1200 1938 3604 3265 1572 1827 M2508 KINNEY_DNMT1_METHYLATION_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KINNEY_DNMT1_METHYLATION_TARGETS.html Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. 20584988 4/18 Arthur Liberzon 8.35494179827452e-07 1.54406128769991e-06 1540 2450.90909090909 1991 8.35494493950354e-08 1310 2.59370004469567 -2.71402935257022 -1 6.01168950185205 1539 1991 4711 3653 2509 2463 1310 1734 4187 1391 1472 1828 M12730 KORKOLA_EMBRYONAL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONAL_CARCINOMA_UP.html Genes from the 12p region that were up-regulated in embryonic carcinoma tumors compared to normal testis. 16424014 53/69 Arthur Liberzon 5.23655254844056e-07 1.14003873451315e-06 1115 1909 1992 4.76050344988364e-08 820 2.11285735889248 2.41847979314687 1 4.99985886798465 1111 3660 2232 3159 1992 820 846 2062 1283 2942 892 1829 M4732 BIOCARTA_LECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LECTIN_PATHWAY.html Lectin Induced Complement Pathway 10/15 BioCarta 0.00543277015793508 0.00558177517315054 900 2572.45454545455 1994 0.000495112057176764 897 3.01834080049613 -3.01834080049613 -1 2.68506782178418 897 4100 1994 3913 4705 1152 1039 1824 4235 3105 1333 1830 M2314 DELPUECH_FOXO3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELPUECH_FOXO3_TARGETS_DN.html Genes down-regulated in DL23 cells (colon cancer) upon expression of an activated form of FOXO3 [GeneID=2309]. 17452451 46/50 Arthur Liberzon 5.10428670551366e-06 6.71841418015184e-06 910 2015.27272727273 1994 4.64027140742044e-07 632 1.63153370891198 1.51114410274595 1 3.34400149962672 907 2679 2689 2840 3519 832 632 2629 1641 1806 1994 1831 M8813 SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN.html Top 50 down-regulated markers distinguishing diffuse large B-cell lymphoma (DLBCL) from follicular lymphoma (FL) samples. 11786909 71/124 Jean Junior 3.23872486750685e-06 4.5374833406448e-06 635 1927.63636363636 1996 2.94429966854358e-07 633 1.89932564911634 -1.60919698011765 -1 4.03127951636366 633 2629 1996 2008 3293 691 954 1621 3959 2412 1008 1832 M2514 FOSTER_KDM1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_KDM1A_TARGETS_DN.html Genes down-regulated in ES cells (embryonic stem) heterozygotic for KDM1A [GeneID=23028] loss of function mutant compared to the homozygotic loss of the gene. 20713442 274/326 Arthur Liberzon 4.43854081378412e-07 1.03507473523029e-06 1835 2540.54545454545 1996 4.03503791751655e-08 488 1.41813807614205 1.47134936520656 1 3.36334864478732 1835 3286 4014 4075 1834 488 1355 1546 3474 4043 1996 1833 M4345 LIAN_LIPA_TARGETS_6M http://www.broadinstitute.org/gsea/msigdb/cards/LIAN_LIPA_TARGETS_6M.html Genes up-regulated at 6 months of age in lungs from LIPA [GeneID=3988] knockout mice, which display pulmonary pathology. 16127159 79/156 John Newman 2.05687971147827e-07 7.6868347095625e-07 980 1904.63636363636 1997 1.869890821623e-08 443 3.04321515934594 -3.0041714034974 -1 7.43297892685889 2821 1635 443 2059 976 3562 2589 979 1997 1237 2653 1834 M5314 MILI_PSEUDOPODIA_HAPTOTAXIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_HAPTOTAXIS_DN.html Transcripts depleted from pseudopodia of NIH/3T3 cells (fibroblast) in response to haptotactic migratory stimulus by fibronectin, FN1 [GeneID=2335]. 18451862 878/998 Jessica Robertson 8.07803579357188e-08 6.29674606547497e-07 2515 2239.72727272727 1997 8.07803608721786e-09 234 1.71160635251247 1.94071761465592 1 4.21829429635819 2511 1997 4618 1270 234 2009 4084 1926 1778 2252 1958 1835 M888 REACTOME_ORGANIC_CATION_ANION_ZWITTERION_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ORGANIC_CATION_ANION_ZWITTERION_TRANSPORT.html Genes involved in Organic cation/anion/zwitterion transport 5/14 Reactome 0.00358336848400186 0.00369209763031844 1020 2555.72727272727 1999 0.000358915987004657 949 2.61709167077097 -2.61709167077097 -1 2.51039298172095 1020 3819 4249 3320 4554 1654 949 1843 1999 3250 1456 1836 M14958 PRAMOONJAGO_SOX4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PRAMOONJAGO_SOX4_TARGETS_UP.html Genes up-regulated in ACC3 cells (adenoid cystic carcinoma) after knockdown of SOX4 [GeneID=6659] by RNAi. 16636670 66/71 Leona Saunders 8.02335798447603e-08 6.29674606547497e-07 2360 1989.36363636364 2000 7.2939620700785e-09 186 1.99744529733768 -2.09771941636334 -1 4.93110735713511 2359 2643 1734 3862 186 2068 1890 1262 2579 1300 2000 1837 M13763 RADAEVA_RESPONSE_TO_IFNA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/RADAEVA_RESPONSE_TO_IFNA1_UP.html Genes up-regulated in primary hepatocytes and Hep3B (hepatocyte) cells in response to IFNA [GeneID=3439]. 11910354 85/136 Yujin Hoshida 1.67309482085814e-06 2.61144429710662e-06 865 1768.18181818182 2000 1.52099644840379e-07 272 1.75158640492327 -1.60811982173819 -1 3.88282858527104 863 2597 2393 2000 2926 272 722 1642 3282 2470 283 1838 M2226 PILON_KLF1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PILON_KLF1_TARGETS_UP.html Genes up-regulated in erythroid progenitor cells from fetal livers of E13.5 embryos with KLF1 [GeneID=10661] knockout compared to those from the wild type embryos. 18852285 672/853 Arthur Liberzon 3.31458346823971e-07 9.06126045087621e-07 1525 2048.36363636364 2005 3.31458396263066e-08 690 2.08322885742644 2.26522370703153 1 5.01259851175598 1521 2005 4668 767 1603 2246 2778 1476 2514 690 2264 1839 M4956 BIOCARTA_MONOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MONOCYTE_PATHWAY.html Monocyte and its Surface Molecules 10/16 BioCarta 0.000538956365779371 0.000567955804080962 785 2436.72727272727 2006 4.90080404273719e-05 229 2.03859929820885 2.03859929820885 1 2.61092655342809 785 3515 1625 4584 4448 942 229 2171 4619 2006 1880 1840 M180 PID_HIF1A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF1A_PATHWAY.html Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 18832364 25/30 Pathway Interaction Database 5.11761954838391e-06 6.73408538287484e-06 1635 2283.45454545455 2006 4.65239222998336e-07 298 2.05343088220744 2.38172608064692 1 4.22082801945128 1635 4023 2811 3522 3520 1473 1026 1007 298 3797 2006 1841 M10372 CHIBA_RESPONSE_TO_TSA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIBA_RESPONSE_TO_TSA_UP.html Cancer related genes up-regulated in any of four hepatoma cell lines following 24 h treatment with TSA [PubChem=5562]. 15452378 89/110 John Newman 1.22253318819408e-06 2.03640334472471e-06 2010 2043.72727272727 2006 1.11139442504774e-07 502 2.22658235721441 3.06653420050916 1 5.04606817043478 2006 1599 502 1213 2713 2732 3611 1920 2940 922 2323 1842 M16932 CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_DN.html Top 200 marker genes down-regulated in the 'proliferation' subclass of hepatocellular carcinoma (HCC); characterized by increased proliferation, high levels of serum AFP [GeneID=174], and chromosomal instability. 18701503 146/313 Yujin Hoshida 5.01014295880953e-07 1.11441445643643e-06 1840 1906.90909090909 2006 4.55467645435331e-08 726 2.357246941001 -2.16334677701686 -1 5.59332870501954 1837 2549 755 2258 1949 2540 2360 1765 2006 726 2231 1843 M10791 ENK_UV_RESPONSE_KERATINOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_KERATINOCYTE_UP.html Genes up-regulated in NHEK cells (normal epidermal keratinocytes) after UVB irradiation. 16434974 663/936 Lauren Kazmierski 1.02947706489122e-07 6.8232212069871e-07 2010 2130.90909090909 2008 1.02947711258326e-08 368 1.72694468631864 -1.67746126887806 -1 4.23232451571399 1607 2008 4327 1084 368 1438 2010 3103 2606 3356 1533 1844 M2041 GERHOLD_RESPONSE_TO_TZD_DN http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_RESPONSE_TO_TZD_DN.html Genes down-regulated in 3T3-L1 cells (fibroblast) induced to differentiate to mature adipocytes and then treated with a TZD derivative AD-5075 [PubChem=128440], a PPARG [GeneID=5468] activator. 12021175 12/13 Arthur Liberzon 5.49133076030038e-07 1.17653568718192e-06 4255 2181.90909090909 2008 4.99212011906332e-08 340 2.29834584228588 -2.25230541631779 -1 5.43054140496643 4253 2418 1605 1806 2042 3584 2008 1568 340 1184 3193 1845 M47 PID_INTEGRIN_CS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_CS_PATHWAY.html Integrin family cell surface interactions 18832364 22/27 Pathway Interaction Database 3.74233544902582e-06 5.14081004639169e-06 1690 2264.36363636364 2009 3.40212892271272e-07 1444 2.0113801607737 2.25616241233217 1 4.22820921338678 1690 2363 1741 3109 3366 1730 1716 2106 3634 1444 2009 1846 M12971 KYNG_DNA_DAMAGE_BY_GAMMA_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_GAMMA_RADIATION.html Genes specifically responding to gamma radiation. 15897889 118/154 Jessica Robertson 4.44690977858008e-07 1.03651427925422e-06 4325 2824.63636363636 2009 4.04264607040388e-08 1468 1.94968546467061 2.12455744496044 1 4.64228276093367 4325 1569 1800 1717 1837 4369 3655 4473 2009 1468 3849 1847 M253 BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING.html Genes whose expression in suboptimally debulked ovarian tumors is associated with survival prognosis. 18593951 632/779 Jessica Robertson 2.67663269231387e-07 8.33908007110328e-07 1595 2097.90909090909 2011 2.67663301471023e-08 670 1.704172831473 1.94902567894825 1 4.11614248906 1594 2011 4556 2885 1368 946 2450 1043 2926 2628 670 1848 M3008 NABA_ECM_GLYCOPROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_ECM_GLYCOPROTEINS.html Genes encoding structural ECM glycoproteins 22159717 150/221 Alexandra Naba 1.94135319095583e-28 2.13097373518873e-26 1025 1903.54545454545 2011 1.76486653723256e-29 22 3.42183798691432 3.56241450410758 1 35.2772282781129 1021 1476 22 682 3432 3121 4278 2011 2340 163 2393 1849 M9670 BIOCARTA_STRESS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STRESS_PATHWAY.html TNF/Stress Related Signaling 32/35 BioCarta 1.57263886147061e-07 7.31918027928963e-07 1290 2016.09090909091 2012 1.42967179444408e-08 659 1.40095682748182 -1.533385514491 -1 3.40679284928473 1288 659 3115 3154 677 1966 1289 2012 3179 2423 2415 1850 M2520 RAO_BOUND_BY_SALL4_ISOFORM_B http://www.broadinstitute.org/gsea/msigdb/cards/RAO_BOUND_BY_SALL4_ISOFORM_B.html Loci bound exclusively by SALL4 [GeneID=57167] isoform b in ES cells (embryonic stem). 20837710 608/939 Arthur Liberzon 2.36306125969141e-07 8.00344136252823e-07 2565 2353.36363636364 2012 2.36306151097408e-08 1219 1.90822371976005 2.12122848215299 1 4.62867602872329 2563 2012 4712 1219 1234 2679 3614 2003 1585 2287 1979 1851 M12143 CHESLER_BRAIN_D6MIT150_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_D6MIT150_QTL_CIS.html Cis-regulatory QTLs (quantitative trait loci) found at the D6Mit150 region. 15711545 10/16 Jean Junior 1.29919537294327e-06 2.13665580497987e-06 2120 2052.09090909091 2013 1.18108740015917e-07 186 2.02729595535579 2.4794313702604 1 4.57293412878615 2116 999 1890 2140 2756 1577 1116 4420 3360 2013 186 1852 M9634 SESTO_RESPONSE_TO_UV_C4 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C4.html Cluster 4: genes changed in primary keratinocytes by UVB irradiation. 11867738 32/37 John Newman 2.30102028314948e-06 3.40784930544888e-06 2015 2257.09090909091 2013 2.09183880893841e-07 578 1.95695771515496 1.81956728493773 1 4.25297372522944 2013 1793 2003 1953 3111 1561 578 3427 3124 2134 3131 1853 M17607 DER_IFN_BETA_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_BETA_RESPONSE_DN.html Genes down-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon beta for 6 h. 9861020 10/11 Yujin Hoshida 1.52054412366338e-06 2.41486146153807e-06 1435 2065.63636363636 2014 1.3823137950893e-07 435 1.56905343684064 -1.73937203341024 -1 3.49443152896387 1432 2897 2705 3860 2873 759 755 1442 3550 2014 435 1854 M3961 KYNG_DNA_DAMAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_UP.html Genes with GO annotation and up-regulated after DNA damage in cell lines from young donors. 15897889 300/392 Jessica Robertson 3.87515575709792e-07 9.75657802563599e-07 3930 2547.27272727273 2014 3.52286949061943e-08 779 1.86751338354259 2.0290807590213 1 4.46425442458075 3929 1274 1164 1017 1669 4449 3915 3887 2014 779 3923 1855 M2056 RUAN_RESPONSE_TO_TROGLITAZONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TROGLITAZONE_DN.html Adipocyte abundant genes down-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591]. 12732648 24/31 Arthur Liberzon 1.53016743654792e-06 2.42753554823548e-06 795 1805.45454545455 2014 1.39106227347938e-07 233 2.34841869722491 -2.26596924681907 -1 5.25285914356116 795 2793 1957 3324 2876 660 233 2014 2398 2380 430 1856 M7189 CHESLER_BRAIN_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_QTL_TRANS.html Best trans-regulated quantitative trait loci (QTLs) in the mouse genome which modulate transcription in brain tissue. 15711545 10/19 Jean Junior 4.35182368889742e-06 5.86539343563559e-06 3940 2242.72727272727 2015 3.95621117933727e-07 134 2.85190410227115 3.41208056730449 1 5.9503412570132 3940 2433 1656 1008 3427 3666 4042 1393 134 2015 956 1857 M80 KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP.html Genes up-regulated in TC71 and EWS502 cells (Ewing's sarcoma) by EWSR1-FLI1 [GeneID=2130;2314] as inferred from RNAi knockdown of this fusion protein. 17114343 1535/1883 Leona Saunders 4.87349056708046e-07 1.09746543304484e-06 535 2193.90909090909 2017 4.87349163587175e-08 534 1.56323070375848 1.65845729265774 1 3.69659888992448 534 2939 4312 2535 2017 947 969 1353 2529 4041 1957 1858 M2263 MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_UP.html Proteins significantly induced by oxidative stress (hydrogen peroxide [PubChem=784] in 786-O cells (renal clear cell carcinoma, RCC) expressing VHL [GeneID=7428]. 18285459 9/9 Arthur Liberzon 2.49059507236242e-05 2.89475713901763e-05 1605 2407.90909090909 2017 2.4906229865899e-06 319 1.72960936271226 1.92734687733984 1 3.1067862571877 1604 2910 4676 1942 4025 1551 319 2178 2017 3883 1382 1859 M916 REACTOME_PLATELET_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_HOMEOSTASIS.html Genes involved in Platelet homeostasis 64/91 Reactome 1.58185428455311e-07 7.31918027928963e-07 2550 2021 2018 1.43804945299304e-08 683 2.0986441487429 2.5128191688539 1 5.1283209007206 2548 1663 1219 1654 683 2947 3774 2628 2018 815 2282 1860 M17044 WANG_HCP_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WANG_HCP_PROSTATE_CANCER.html Genes with the high-CpG-density promoters (HCP) that were up-regulated in 1542-CP3TX cells (prostate cancer) compared to 1542-NPTX (normal prostate). 17486081 166/220 Arthur Liberzon 9.0114946667792e-07 1.62904078235151e-06 1150 2043.36363636364 2018 8.19227123455476e-08 876 2.0734200644528 -1.94464221005807 -1 4.77634356514644 1149 4154 2536 2018 2488 876 919 1124 2893 2907 1413 1861 M746 REACTOME_SIGNALING_BY_GPCR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_GPCR.html Genes involved in Signaling by GPCR 358/1438 Reactome 5.80344365217076e-16 2.10709646448046e-14 4550 2192.72727272727 2019 5.27585786560978e-17 90 2.42531811773474 -2.33293464296773 -1 13.289429883804 4550 1228 90 540 239 4345 3147 3944 2019 192 3826 1862 M12678 BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_DN.html Genes from cluster 4: down-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 56/61 Jessica Robertson 1.17164197718245e-07 7.06112554001409e-07 3600 2569.90909090909 2019 1.06512912689086e-08 399 2.27106745795854 2.41524346693949 1 5.56800915936834 3599 1689 1534 1822 399 3794 4061 4194 556 2019 4602 1863 M2187 TSUTSUMI_FBXW8_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TSUTSUMI_FBXW8_TARGETS.html Genes differentially expressed in E18.5 whole embryos upon knockout of FBXW8 [GeneID=26259]. 17998335 10/15 Arthur Liberzon 2.36159631952914e-06 3.4844434598867e-06 1845 2018.36363636364 2019 2.14690804963209e-07 530 2.21739204057158 2.30322141847875 1 4.8170155778616 1843 1020 2339 3836 3123 2019 2345 1501 530 2551 1095 1864 M1463 TIEN_INTESTINE_PROBIOTICS_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_24HR_UP.html Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 24h. 16394013 673/786 Arthur Liberzon 4.89266367959438e-07 1.099106798882e-06 465 2352.45454545455 2020 4.89266475681182e-08 463 1.53965059379063 1.57809475523554 1 3.63968194073171 463 3550 4310 3033 2020 1230 1133 1716 1987 4166 2269 1865 M10582 STAEGE_EWING_FAMILY_TUMOR http://www.broadinstitute.org/gsea/msigdb/cards/STAEGE_EWING_FAMILY_TUMOR.html Genes up-regulated in Ewing family tumors (EFT) compared with normal bone marrow samples. 15548687 28/44 Kevin Vogelsang 3.24997393815421e-07 9.03940894996339e-07 3715 2332.45454545455 2020 2.9545221984184e-08 748 2.50401327140969 2.61475953482764 1 6.03623926166363 3711 748 1322 3304 1473 3533 3327 1090 2020 1639 3490 1866 M5459 NEWMAN_ERCC6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NEWMAN_ERCC6_TARGETS_UP.html Genes up-regulated in Cockayne syndrome fibroblasts rescued by expression of ERCC6 [GeneID=2074] off a plasmid vector. 16772382 29/44 Leona Saunders 5.2331004443861e-07 1.13983544520085e-06 2185 1967.63636363636 2021 4.75736517197701e-08 600 2.37195757387571 -2.49675291274391 -1 5.61920273491648 2182 2305 882 2113 1991 1877 1012 3357 3304 600 2021 1867 M1333 RAHMAN_TP53_TARGETS_PHOSPHORYLATED http://www.broadinstitute.org/gsea/msigdb/cards/RAHMAN_TP53_TARGETS_PHOSPHORYLATED.html Proteins phosporylated in HCT116 cells (colon cancer) upon p53 [GeneID=7157] activation. 18438429 35/44 Jessica Robertson 1.7027139407651e-05 2.02489538937044e-05 820 2063.45454545455 2022 1.54793374477066e-06 504 1.89997922887573 2.23343015847137 1 3.5363348902405 817 2734 2380 2215 3909 1667 2022 1200 504 3811 1439 1868 M19872 TAVOR_CEBPA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAVOR_CEBPA_TARGETS_DN.html Genes down-regulated in KCL22 cells (chronic myelogenous leukemia, CML, with BCR-ABL1 [GeneID=613;25] fusion) by expression of CEBPA [GeneID=1050]. 14517214 41/60 Kevin Vogelsang 1.76655825230388e-07 7.40425773939871e-07 2150 2000 2022 1.6059621765047e-08 817 1.99134081136628 1.95212463044147 1 4.85953279894946 2148 2266 1979 3114 817 962 1279 1389 3295 2022 2729 1869 M5077 MARTINEZ_RESPONSE_TO_TRABECTEDIN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RESPONSE_TO_TRABECTEDIN.html Genes down-regulated by trabectedin [PubChem=3199] and its synthetic analog phthalascidin Pt 650 in HCT116 cells (colon cancer). 11755394 72/76 John Newman 3.75168264591613e-07 9.58740773617983e-07 2025 2059.72727272727 2022 3.41062116881326e-08 276 1.43818270347264 -1.35878405559487 -1 3.43083809966497 2022 276 3489 1070 1640 2151 1292 3132 1745 2915 2925 1870 M877 REACTOME_INTERACTION_BETWEEN_L1_AND_ANKYRINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERACTION_BETWEEN_L1_AND_ANKYRINS.html Genes involved in Interaction between L1 and Ankyrins 16/27 Reactome 5.40211292203337e-07 1.16482288679751e-06 3070 2239.72727272727 2023 4.91101295320531e-08 365 3.07863453355336 3.27973441866495 1 7.29657833632986 3068 850 620 717 2023 3464 3912 4493 365 730 4395 1871 M16867 MULLIGHAN_MLL_SIGNATURE_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_2_DN.html The 'MLL signature 2': genes down-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to the AML cases with intact MLL and NPM1 [GeneID=4869]. 17597811 404/552 Arthur Liberzon 1.30088729373582e-07 7.20206492018647e-07 4380 2467.54545454545 2023 1.18262488241719e-08 493 2.18098917955636 2.37959242448609 1 5.33764996392884 4379 2023 504 1144 493 4433 4153 3458 1969 623 3964 1872 M1718 SIG_IL4RECEPTOR_IN_B_LYPHOCYTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_IL4RECEPTOR_IN_B_LYPHOCYTES.html Genes related to IL4 rceptor signaling in B lymphocytes 33/36 Signaling Gateway 1.42985445697261e-07 7.24081202656879e-07 2025 2283.63636363636 2024 1.29986777263973e-08 584 1.24364688576703 -1.11142363039865 -1 3.02097231674414 2024 2301 3572 1550 584 1360 1438 1448 3676 4053 3114 1873 M11319 GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP.html Up-regulated genes from the set E (Fig. 5a): specific signature shared by cells expressing either MLL-AF4 [GeneID=4297;4299] or AF4-MLL fusion proteins alone, and those expressing both fusion proteins. 17130830 133/170 Arthur Liberzon 5.84109618212293e-11 1.12530506039266e-09 3540 2138.45454545455 2024 5.31008743843457e-12 190 2.73074092378213 3.02941968593562 1 9.77745133498696 3540 1546 190 327 1873 3279 4615 2180 2024 358 3591 1874 M1834 BOQUEST_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_UP.html Genes up-regulated in freshly isolated CD31- [GeneID=5175] (stromal stem cells from adipose tissue) versus the CD31+ (non-stem) counterparts. 15635089 381/494 Arthur Liberzon 6.46432562110069e-37 1.2713173721498e-34 590 1875.81818181818 2024 5.87665965554613e-38 13 2.86782371040616 3.00921440109124 1 39.0429000429653 588 2024 13 1570 3593 2343 3098 1638 2914 49 2804 1875 M7602 ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN.html Genes down-regulated in CD-1 compared to CD-2 cluster of multiple myeloma samples. 16728703 70/81 Kevin Vogelsang 4.25142097756168e-07 1.01449479343231e-06 3645 2177.09090909091 2025 3.8649289083034e-08 292 2.00650360414916 -2.07204388578603 -1 4.78655240581194 3642 292 1715 1799 1785 3202 2850 2483 2025 1922 2233 1876 M879 REACTOME_FATTY_ACID_TRIACYLGLYCEROL_AND_KETONE_BODY_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FATTY_ACID_TRIACYLGLYCEROL_AND_KETONE_BODY_METABOLISM.html Genes involved in Fatty acid, triacylglycerol, and ketone body metabolism 185/250 Reactome 2.83833788663836e-07 8.51178263306103e-07 3590 2402.81818181818 2026 2.58030750257056e-08 1179 1.61010713656239 -1.55486700940968 -1 3.88041622913938 2026 3580 3587 3150 1334 2239 2017 1841 1891 3587 1179 1877 M17074 AIYAR_COBRA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/AIYAR_COBRA1_TARGETS_UP.html Genes up-regulated in T47D cells (breast cancer) after COBRA1 [GeneID=25920] knockdown by RNAi. 17043641 46/63 Arthur Liberzon 5.80060841911252e-07 1.21467931402889e-06 3420 1953.72727272727 2026 5.27328177138618e-08 281 2.6064410604314 2.47372196876687 1 6.15069306934827 3416 497 1097 569 2093 2088 1764 4279 281 2026 3381 1878 M6890 HELLER_HDAC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_DN.html Genes down-regulated in at least one of three multiple myeloma (MM) cell lines by TSA [PubChem=5562]. 18172295 358/493 Jessica Robertson 3.60988291824177e-07 9.42924591815227e-07 1935 2342.63636363636 2027 3.28171228233787e-08 1595 1.84256462430029 2.0235542892777 1 4.41492860240304 1932 2027 1913 3685 1595 1665 2306 2736 3261 1711 2938 1879 M19745 TARTE_PLASMA_CELL_VS_PLASMABLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_PLASMABLAST_DN.html Genes down-regulated in mature plasma cells compared with plasmablastic B lymphocytes. 12663452 408/494 Kate Stafford 9.38315135153933e-07 1.67505576320974e-06 2030 2071.09090909091 2028 8.53014123047301e-08 354 1.64483882180508 1.66518640542286 1 3.7707160296007 354 3275 3633 2027 2523 840 665 1490 2320 3627 2028 1880 M9802 BROWNE_HCMV_INFECTION_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_1HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 1 h time point that were not down-regulated at the previous time point, 30 min. 11711622 282/402 Arthur Liberzon 1.27150872748365e-07 7.19819980220572e-07 3475 2292.45454545455 2028 1.15591709179235e-08 157 2.19855019790946 2.23598925366986 1 5.38123699470291 3474 1318 985 157 467 2232 3675 4643 1719 2028 4519 1881 M852 REACTOME_TAK1_ACTIVATES_NFKB_BY_PHOSPHORYLATION_AND_ACTIVATION_OF_IKKS_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TAK1_ACTIVATES_NFKB_BY_PHOSPHORYLATION_AND_ACTIVATION_OF_IKKS_COMPLEX.html Genes involved in TAK1 activates NFkB by phosphorylation and activation of IKKs complex 24/27 Reactome 7.54692586030297e-06 9.54999733528955e-06 445 1844.36363636364 2030 6.86086522687191e-07 235 1.85246600834859 -2.07875171917069 -1 3.68981415551423 442 2362 2734 3449 3672 726 235 352 3203 2030 1083 1882 M16845 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_12 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_12.html Amplification hot spot 12: colocolized fragile sites and cancer genes in the 17q11.1-q21; 17q25 region. 16751803 14/14 Arthur Liberzon 5.51570229823387e-08 5.39008588978548e-07 2030 1941.81818181818 2030 5.01427494229101e-09 70 2.23949759706559 -2.4166104020105 -1 5.59553879678017 2030 3212 2268 2442 70 3136 3484 1984 212 1916 606 1883 M1422 MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP.html Up-regulated genes discriminating multiple myeloma samples by the ype of immunoglobulin light chain they produce: Ig lambda (IGLL) vs Ig kappa (IGLK). 12623842 63/77 Kate Stafford 4.14751658705884e-08 4.50029385998109e-07 3725 2116.72727272727 2030 3.77046969568114e-09 30 2.02063981115417 2.28806928816486 1 5.10749060544592 3721 334 2030 160 30 4603 3734 3513 414 1594 3151 1884 M1368 SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_UP.html Predicted targets of SOX9 [GeneID=6662] that are up-regulated during early prostate development. 18794802 24/29 Jessica Robertson 2.01800064164139e-06 3.04958900089323e-06 2450 2202.09090909091 2031 1.83454772063755e-07 508 2.19017746763147 2.0764014886351 1 4.80827277873165 2447 779 1672 1243 3038 2227 1951 4580 508 2031 3747 1885 M18850 JIANG_VHL_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_VHL_TARGETS.html Genes up-regulated in 786-0 cells (renal carcinoma, RCC) upon expression of VHL [GeneID=7428] off a retroviral vector under normoxia (normal oxygen) condition. 12692265 185/212 John Newman 5.42954835511228e-07 1.1675384162246e-06 995 2512.45454545455 2031 4.93595426828411e-08 487 1.44242887085915 1.57547712456697 1 3.39147696729904 991 4420 3982 4519 2031 487 852 1664 3041 4218 1432 1886 M1544 LEE_AGING_CEREBELLUM_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_CEREBELLUM_DN.html Downregulated in the cerebellum of aged adult mice (30-month) vs young adult (5-month) 10888876 118/167 John Newman 9.89917298404516e-07 1.74032357336954e-06 4185 2044.27272727273 2031 8.9992522166397e-08 151 2.21130646408135 -1.56611048157791 -1 5.07178586580255 4181 2565 1173 1678 2558 2474 2151 151 2031 1604 1921 1887 M10664 XU_GH1_AUTOCRINE_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_AUTOCRINE_TARGETS_UP.html Genes up-regulated in MFCF-7 cells (breast cancer) upon stable autocrine expression of HG1 [GeneID=2688]. 15845533 268/405 John Newman 2.9674920846166e-07 8.70294688256627e-07 2035 1776.72727272727 2032 2.69772044080893e-08 511 2.26369481694877 2.39106068728088 1 5.4671163207314 2032 2044 511 1591 1374 1496 3086 2086 2302 704 2318 1888 M10319 WALLACE_PROSTATE_CANCER_RACE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_RACE_UP.html Genes up-regulated in prostate cancer samples from African-American patients compared to those from the European-American patients. 18245496 291/525 Jessica Robertson 5.62342400282797e-15 1.84633949095459e-13 3255 2199.81818181818 2032 5.1122036389345e-16 100 2.26417781416156 2.48251331923007 1 11.5448200293602 3254 2032 101 957 1757 3614 4524 860 3678 100 3321 1889 M2343 FEVR_CTNNB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FEVR_CTNNB1_TARGETS_DN.html Genes down-regulated in intestinal crypt cells upon deletion of CTNNB1 [GeneID=1499]. 17785439 720/1027 Arthur Liberzon 9.80102368048072e-07 1.72743957325874e-06 275 2003.18181818182 2032 9.80102800318634e-08 275 1.63062992885383 1.6316688604439 1 3.72894046907816 275 3268 4686 2509 2622 604 589 900 2032 3035 1515 1890 M5058 FUNG_IL2_TARGETS_WITH_STAT5_BINDING_SITES_T1 http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_TARGETS_WITH_STAT5_BINDING_SITES_T1.html Genes with putative STAT5 [GeneID=6777] binding sites; up-regulated by IL2 [GeneID=3558] only in T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 6/11 Arthur Liberzon 6.19813768573274e-06 7.98668028300807e-06 2035 2103.36363636364 2033 6.19815497341046e-07 340 2.48593815430981 2.84942279524314 1 5.04631697227881 2033 3257 4393 3418 3637 1347 788 340 882 2115 927 1891 M14072 WINTER_HYPOXIA_METAGENE http://www.broadinstitute.org/gsea/msigdb/cards/WINTER_HYPOXIA_METAGENE.html Genes regulated by hypoxia, based on literature searches. 17409455 311/364 Jessica Robertson 3.01791893638648e-07 8.77129148999025e-07 3135 2067.90909090909 2033 2.74356304579913e-08 393 2.33463293048466 2.46354479167723 1 5.63681944704435 3132 2033 393 860 1394 1550 4099 2722 2624 721 3219 1892 M7079 WONG_EMBRYONIC_STEM_CELL_CORE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_EMBRYONIC_STEM_CELL_CORE.html The 'core ESC-like gene module': genes coordinately up-regulated in a compendium of mouse embryonic stem cells (ESC) which are shared with the human ESC-like module. 18397753 414/477 Nikolaos Papanikolaou 4.54816830102243e-06 6.08485101497332e-06 70 2105.45454545455 2033 4.13470700336534e-07 67 1.45942995632433 1.54142252192419 1 3.01122610339933 67 3274 4003 2033 3459 654 370 1481 2079 3846 1894 1893 M272 PID_CD8_TCR_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD8_TCR_DOWNSTREAM_PATHWAY.html Downstream signaling in naïve CD8+ T cells 18832364 62/117 Pathway Interaction Database 7.00240346797883e-07 1.37256413491944e-06 1145 2324.72727272727 2034 6.36582336071118e-08 955 1.36220542563357 -1.06493678711529 -1 3.16157945131961 1143 3360 3280 2034 2262 955 1538 1456 4266 3892 1386 1894 M2540 KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION.html Gamma and UV responding genes. 15897889 131/185 Jessica Robertson 2.50397374209037e-07 8.18539112849675e-07 4405 2659.09090909091 2037 2.27634002462288e-08 14 1.88203084564612 1.79700035420059 1 4.55706537655361 4401 14 1668 1916 1195 3083 4057 4187 2005 2037 4687 1895 M11575 REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION.html Genes involved in Glucagon signaling in metabolic regulation 27/36 Reactome 1.49775727808928e-07 7.26289540930751e-07 2165 2244.81818181818 2039 1.36159761823311e-08 631 1.90561245870407 2.16049265538548 1 4.65458882458461 2163 1824 2039 1686 631 2919 4655 3279 1680 2765 1052 1896 M848 REACTOME_MITOTIC_G1_G1_S_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_G1_G1_S_PHASES.html Genes involved in Mitotic G1-G1/S phases 141/159 Reactome 5.73551642022052e-06 7.4474931233675e-06 255 2063.36363636364 2040 5.21411943006356e-07 254 1.37978269004242 1.52317428886188 1 2.79546228206644 254 2556 3814 2029 3568 637 727 1507 2040 3469 2096 1897 M2058 NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_DN.html Top 20 genes whose down-regulation correlated with gastrointestinal stromal tumors (GIST) compared to synovial sarcoma. 11965276 27/45 Arthur Liberzon 5.474747870123e-07 1.17351543810084e-06 3660 2113.81818181818 2040 4.97704475684218e-08 527 3.16208014822836 2.8807165323836 1 7.49160039965102 3660 711 527 1133 2040 3691 3011 3081 1043 1080 3275 1898 M543 REACTOME_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE.html Genes involved in Cell Cycle 434/635 Reactome 2.30574319271129e-06 3.41377285746465e-06 105 1980.63636363636 2041 2.09613237207616e-07 101 1.50094897232942 1.6200160412984 1 3.24983424411433 101 3272 3990 2041 3112 241 224 954 2931 3565 1356 1899 M8776 HELLER_SILENCED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_SILENCED_BY_METHYLATION_UP.html Genes up-regulated in at least one of three multiple myeloma (MM) cell lines treated with the DNA hypomethylating agent decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 18172295 311/565 Jessica Robertson 1.02371757963131e-16 4.20169302248675e-15 80 2353 2041 9.30652345119366e-18 79 2.43511716794054 -2.37191358725683 -1 14.0290977728249 4220 1261 79 80 1887 4046 3825 3664 2041 124 4656 1900 M847 BOYLAN_MULTIPLE_MYELOMA_C_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_UP.html Genes up-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 61/69 Jessica Robertson 2.94246907004552e-07 8.67486196790435e-07 1740 2126.18181818182 2042 2.67497223963336e-08 397 1.80154839756915 2.02276635000348 1 4.34177449578108 1739 2209 2902 4347 1367 1605 2648 1673 2042 2459 397 1901 M5793 CHANG_CORE_SERUM_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_CORE_SERUM_RESPONSE_DN.html Down-regulated genes in the canonical gene expression signature of the fibroblast core serum response (CSR) defined by the Stanford group. 14737219 276/325 Arthur Liberzon 1.39427420502839e-07 7.20206492018647e-07 2445 2032.09090909091 2042 1.26752208490187e-08 563 1.95970961998444 -1.96966183372202 -1 4.79102412660366 2444 2042 1692 1797 563 2415 3135 2535 1917 2094 1719 1902 M1406 JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP http://www.broadinstitute.org/gsea/msigdb/cards/JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP.html Genes up-regulated during epithelial to mesenchymal transition (EMT) induced by TGFB1 [GeneID=7040] in the EpH4 cells (mammary epithelium cell line transformed by HRAS [GeneID=3265]). 14562044 107/132 Arthur Liberzon 5.0469441090948e-08 5.15618532357737e-07 795 1804.45454545455 2043 4.58813111352274e-09 330 2.60646908680072 2.5864903848737 1 6.54083783053183 794 2576 330 1234 2923 1979 2794 2055 2695 426 2043 1903 M11403 KANNAN_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANNAN_TP53_TARGETS_DN.html Primary down-regulated targets of TP53 [GeneID=7157] in the H1299 (lung cancer) cell line. 11402317 31/37 Broad Institute 4.56064964700221e-06 6.09809244584997e-06 2625 1859.72727272727 2043 4.14605372850844e-07 90 2.04402618737365 2.26584790100493 1 4.23668429591302 2621 2294 1370 1244 3460 2043 2098 90 2462 1248 1527 1904 M2069 BILD_MYC_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_MYC_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing c-Myc [GeneID=4609] from control cells expressing GFP. 16273092 275/338 Arthur Liberzon 7.15321820433143e-07 1.38943168413351e-06 1935 2089.18181818182 2043 6.50292775470437e-08 535 1.83016030032476 1.89435142933366 1 4.26095347035269 1931 2043 2250 1748 2283 535 2014 3189 2569 2929 1490 1905 M7585 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_UP.html Genes up-regulated in ductal carcinoma vs normal ductal breast cells. 17389037 88/114 Arthur Liberzon 2.08353539482337e-06 3.1319385552759e-06 940 1955.81818181818 2045 1.89412488005658e-07 554 2.58205641056561 2.73699540608063 1 5.66553275043178 936 2596 554 2135 3055 1681 2725 2974 2045 891 1922 1906 M12746 KOYAMA_SEMA3B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOYAMA_SEMA3B_TARGETS_UP.html Genes up-regulated in NCI-H1299 cells (large cell neuroendocrine carcinoma) stably expressing SEMA3B [GeneID=7869]. 18985860 347/474 Jessica Robertson 7.94744428336159e-08 6.29674606547497e-07 4535 2499.54545454545 2046 7.22494960951003e-09 183 2.01498884419959 2.22679354026928 1 4.97485671166468 4535 1246 808 2046 183 4611 3690 3918 1630 658 4170 1907 M2040 GERHOLD_RESPONSE_TO_TZD_UP http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_RESPONSE_TO_TZD_UP.html Genes up-regulated in 3T3-L1 cells (fibroblast) induced to differentiate to mature adipocytes and then treated with a TZD derivative AD-5075 [PubChem=128440], a PPARG [GeneID=5468] activator. 12021175 6/8 Arthur Liberzon 9.74796698124751e-06 1.21111882472988e-05 2080 2211.90909090909 2046 9.74800974179863e-07 650 3.28904110912735 4.26157015208116 1 6.45356052642184 2080 3531 4652 1475 3769 2046 789 1406 650 2799 1134 1908 M823 REACTOME_TRANSPORT_OF_INORGANIC_CATIONS_ANIONS_AND_AMINO_ACIDS_OLIGOPEPTIDES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_INORGANIC_CATIONS_ANIONS_AND_AMINO_ACIDS_OLIGOPEPTIDES.html Genes involved in Transport of inorganic cations/anions and amino acids/oligopeptides 62/101 Reactome 2.82901752488108e-07 8.50336182209636e-07 3945 2305.09090909091 2047 2.57183444424485e-08 316 2.55445961617611 2.35515236317224 1 6.18612891084391 3944 316 495 2047 1329 3619 4703 2799 938 558 4608 1909 M1047 YAGI_AML_WITH_INV_16_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_INV_16_TRANSLOCATION.html Genes specifically expressed in samples from patients with pediatric acute myeloid leukemia (AML) bearing inv(16) translocation. 12738660 561/770 Arthur Liberzon 2.05176870981096e-07 7.67989556725435e-07 1585 2261.63636363636 2048 2.05176889924995e-08 1080 2.01434100345907 2.3713967021226 1 4.90337963247996 2048 2942 4624 1288 1080 1583 3149 2669 2103 1585 1807 1910 M1280 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4.html Cluster PAM4: genes down-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 242/403 Leona Saunders 1.67006885003202e-07 7.3358205358541e-07 2920 2214.36363636364 2049 1.51824452437334e-08 747 1.86249336837628 -1.74812714939646 -1 4.54488534022868 2920 2049 1903 1780 747 1973 2435 4000 2301 1439 2811 1911 M17557 DANG_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DANG_MYC_TARGETS_DN.html Genes down-regulated by MYC [GeneID=4609] and whose promoters are bound by MYC, according to MYC Target Gene Database. 14519204 39/42 Chi Dang 2.98522577512046e-06 4.22370073698099e-06 2015 2158.45454545455 2049 2.71384529622102e-07 630 1.76120555278621 1.51863836527443 1 3.75652704026906 2011 1767 2868 1729 3264 2049 2056 2855 630 3449 1065 1912 M986 SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_UP.html Genes up-regulated in circulating endothelial cells (CEC) from cancer patients compared to those from healthy donors. 16540638 227/329 Arthur Liberzon 1.54689282871317e-11 3.24530235753119e-10 3355 1881.36363636364 2050 1.40626620793095e-12 171 2.46052361665726 2.69678035803529 1 9.33934378243698 3351 1371 171 391 1011 3462 3523 2924 2050 211 2230 1913 M1367 BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP.html Genes from cluster 1: up-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 45/52 Jessica Robertson 1.02186993634934e-05 1.2662709633943e-05 1350 2093.72727272727 2050 9.28976984387656e-07 485 2.1415794963372 2.45770092009837 1 4.16796632984282 1347 2685 2050 3699 3753 1674 2615 1032 1264 2427 485 1914 M3649 BROWNE_HCMV_INFECTION_2HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_2HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 2 h time point that were not up-regulated at the previous time point, 1 h. 11711622 38/49 Arthur Liberzon 1.11570249423879e-06 1.90411881647541e-06 2090 2528.36363636364 2050 1.01427550913978e-07 1463 2.04211820289153 -2.28276467114069 -1 4.64783059886392 2087 3698 1463 4407 2641 2050 1886 2028 4569 1475 1508 1915 M15047 MULLIGHAN_NPM1_SIGNATURE_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_SIGNATURE_3_DN.html The 'NPM1 signature 3': genes down-regulated in pediatric AML (acute myeloid leukemia) with mutated NPM1 [GeneID=4869] compared to the AML cases with intact NPM1 and MLL [GeneID=4297]. 17597811 229/372 Arthur Liberzon 9.06605072098791e-08 6.55310251195451e-07 2055 1985.18181818182 2051 8.24186463144882e-09 251 2.37630749277076 2.7266782876356 1 5.85933553154792 3243 2051 673 1186 251 3427 4510 2053 814 1434 2195 1916 M2020 MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) with unmethylated histone H3 in MEF cells (embryonic fibroblast). 17603471 171/480 Arthur Liberzon 1.25728071507511e-08 1.61699318124101e-07 2625 1840.27272727273 2051 1.14298247478214e-09 235 2.46379649121049 2.50826828175107 1 6.67907671167534 2623 2078 290 2051 1095 1154 3128 3428 2143 235 2018 1917 M7987 LEE_LIVER_CANCER_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_SURVIVAL_DN.html Genes highly expressed in hepatocellular carcinoma with poor survival. 15349906 237/330 Yujin Hoshida 1.33143965805017e-06 2.17829989116007e-06 430 1901.45454545455 2052 1.21040042167084e-07 430 1.45856035921702 1.52479008434616 1 3.27109301079677 430 2052 3699 2499 2772 658 634 1208 2216 3192 1556 1918 M9450 REACTOME_PLATELET_ADHESION_TO_EXPOSED_COLLAGEN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_ADHESION_TO_EXPOSED_COLLAGEN.html Genes involved in Platelet Adhesion to exposed collagen 29/34 Reactome 0.000824021467810903 0.000862199363349028 455 2256.63636363636 2053 7.49391155716972e-05 452 2.80108582168471 2.94268084248174 1 3.40196795547928 452 3139 818 1738 4478 2053 3415 3188 3018 897 1627 1919 M160 PID_AVB3_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AVB3_INTEGRIN_PATHWAY.html Integrins in angiogenesis 18832364 104/117 Pathway Interaction Database 1.90848792885879e-05 2.25370603558006e-05 1205 2288.63636363636 2055 1.73500407735266e-06 839 2.41128488562798 2.61002453258039 1 4.45638060544912 1202 3320 839 1290 3937 2055 3152 2950 2944 1534 1952 1920 M853 REACTOME_MYOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MYOGENESIS.html Genes involved in Myogenesis 29/38 Reactome 3.03100336249003e-07 8.77601760597774e-07 3625 2097.09090909091 2055 2.75545798189107e-08 446 1.94963863280309 2.22879361955284 1 4.69884089986679 3624 687 1844 2130 1398 3282 3787 1256 446 2055 2559 1921 M1851 QI_PLASMACYTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/QI_PLASMACYTOMA_UP.html Up-regulated genes that best disciminate plasmablastic plasmacytoma from plasmacytic plasmacytoma tumors. 17363561 277/394 Jessica Robertson 5.95304492324074e-08 5.64006898366039e-07 2640 1704.90909090909 2055 5.41185916756902e-09 83 2.1176703823083 -2.14593265281331 -1 5.27165530610199 2676 1304 537 567 83 2639 2055 2688 3111 457 2637 1922 M13183 ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP.html Genes down-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) by MYC [GeneID=4609] and up-regulated by RNAi knockdown of TFRC [GeneID=7037]. 16508012 123/186 Leona Saunders 3.44912912180874e-05 3.9514294793537e-05 590 2209.36363636364 2057 3.13562108905266e-06 587 2.19991472942688 -2.09648711393575 -1 3.84560831072341 587 3873 1870 2489 4070 1402 1148 765 3701 2341 2057 1923 M13656 NAKAMURA_LUNG_CANCER_DIFFERENTIATION_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_LUNG_CANCER_DIFFERENTIATION_MARKERS.html 14 candidate differentiation markers in lung adenocarcinoma cells, noncancerous lung cells and peripheral blood cells. 16491115 10/27 Arthur Liberzon 5.568384664272e-07 1.18551085319638e-06 2415 2120.72727272727 2057 5.06216915788854e-08 150 2.81760463774535 -3.76320309741174 -1 6.6650132452614 2415 3800 1666 3340 2057 2724 1078 150 3373 2009 716 1924 M851 REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE.html Genes involved in Regulation of mitotic cell cycle 85/99 Reactome 1.76949270233484e-05 2.09902125031929e-05 440 2222.81818181818 2058 1.60864266798904e-06 440 1.2549691193215 1.46239657945552 1 2.31094304503486 440 2600 3890 1558 3916 943 784 2058 1716 4380 2166 1925 M16088 LIAN_LIPA_TARGETS_3M http://www.broadinstitute.org/gsea/msigdb/cards/LIAN_LIPA_TARGETS_3M.html Genes up-regulated at 3 months of age in lungs from LIPA [GeneID=3988] knockout mice, which display pulmonary pathology. 16127159 59/122 John Newman 4.42559149831258e-07 1.03461079108645e-06 2255 2098.81818181818 2058 4.02326580779928e-08 490 2.99260605073495 -3.07008658574515 -1 7.15324685996351 2251 3057 816 3053 1828 2917 1914 490 2664 2058 2039 1926 M18895 SA_TRKA_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/SA_TRKA_RECEPTOR.html The TrkA receptor binds nerve growth factor to activate MAP kinase pathways and promote cell growth. 25/28 SigmaAldrich 5.80993317085585e-07 1.21525740803517e-06 1805 2306.90909090909 2059 5.28175882289936e-08 705 1.5238751972729 1.91636879161929 1 3.57513935172805 1802 3741 3143 1752 2094 2059 1815 705 2839 4300 1126 1927 M142 PID_AJDISS_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AJDISS_2PATHWAY.html Posttranslational regulation of adherens junction stability and dissassembly 18832364 75/87 Pathway Interaction Database 4.51364267957718e-07 1.04185917010687e-06 3380 2189.72727272727 2059 4.10331236874686e-08 281 1.96945618246192 -1.32791029075174 -1 4.68809586605967 3379 281 1746 1742 1857 2191 2061 1899 2059 2501 4371 1928 M2510 ZHANG_RESPONSE_TO_CANTHARIDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_CANTHARIDIN_DN.html Genes down-regulated in HL-60 cells (promyeloid leukemia) by cantharidin [PubChem=6708701]. 14639605 95/114 John Newman 1.98986838741096e-06 3.01224464033987e-06 560 2157.63636363636 2059 1.80897289747327e-07 178 1.25477355582564 1.24567100937039 1 2.73603519347474 559 178 3834 3563 3032 686 740 1533 3703 3847 2059 1929 M9583 SANA_RESPONSE_TO_IFNG_DN http://www.broadinstitute.org/gsea/msigdb/cards/SANA_RESPONSE_TO_IFNG_DN.html Genes down-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by IFNG [GeneID=3458]. 15749026 119/144 Yujin Hoshida 3.1559693837126e-06 4.43999269482071e-06 880 2251.81818181818 2061 2.86906719187209e-07 876 1.68334679898984 1.71490529253715 1 3.57356474820047 876 3315 3013 1737 3280 1687 1419 1325 2678 3379 2061 1930 M116 BILD_SRC_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_SRC_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing c-Src (CSK) [GeneID=1445] from control cells expressing GFP. 16273092 100/109 Arthur Liberzon 1.15744908031028e-06 1.95531841770384e-06 1070 2186.18181818182 2061 1.05222699023636e-07 1068 1.8869789071635 2.22835807791257 1 4.28218975604508 1068 3008 2061 3221 2672 1683 2139 1512 3287 2052 1345 1931 M2267 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_UP http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_UP.html Genes up-regulated more than two-fold in lymphoblastoid cell lines from European population compared to those from Asian population. 17206142 19/37 Leona Saunders 3.83918396276403e-07 9.69034668676269e-07 2475 1817.18181818182 2063 3.49016784793991e-08 161 2.69243594608005 2.98661474147349 1 6.46152143931902 2472 2378 1525 1201 1664 2566 2529 246 161 3184 2063 1932 M2157 DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN.html Genes down-regulated in MCF7 cells (breast cancer) at 24 h of estradiol [PubChem=5757] treatment. 20406972 682/817 Jessica Robertson 1.71229532690694e-12 3.98129750886737e-11 2065 1890.72727272727 2063 1.71229532690825e-13 41 2.08332736927904 -1.97537484695226 -1 8.66341966402801 2063 1114 4664 41 304 2511 2355 3661 1039 118 2928 1933 M703 REACTOME_ACYL_CHAIN_REMODELLING_OF_PS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PS.html Genes involved in Acyl chain remodelling of PS 8/16 Reactome 4.24985485983035e-06 5.74436281168363e-06 580 1900.81818181818 2064 4.24986298742207e-07 92 2.65475828737425 -2.65475828737425 -1 5.5452161886935 578 2460 4220 2308 4036 605 275 92 3735 2064 536 1934 M9112 LU_AGING_BRAIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_AGING_BRAIN_DN.html Age down-regulated genes in the human frontal cortex. 15190254 222/295 John Newman 1.06341760548848e-06 1.83455083987779e-06 1670 1888.72727272727 2064 9.66743745013404e-08 539 1.89709981673498 2.14622476243532 1 4.32654998648938 1668 2531 2064 1321 2612 1210 2446 539 2617 2677 1091 1935 M594 REACTOME_SIGNALING_BY_NOTCH4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH4.html Genes involved in Signaling by NOTCH4 16/16 Reactome 4.89683201154229e-06 6.47605690514979e-06 2315 1886.27272727273 2065 4.45167537373203e-07 62 2.12482497763401 -1.19092404513003 -1 4.38381783034321 2311 894 1841 2304 3500 2065 1233 1361 62 2703 2475 1936 M16596 WATTEL_AUTONOMOUS_THYROID_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATTEL_AUTONOMOUS_THYROID_ADENOMA_UP.html Up-regulated genes characteristic for autonomous thyroid adenoma. 16027733 94/124 Arthur Liberzon 7.54041966001936e-10 1.23913230667885e-08 3035 1827 2065 6.85492696600346e-11 88 2.69856311576918 2.96308037368521 1 8.53097482903046 3032 115 221 88 2381 3949 4098 2934 959 255 2065 1937 M604 REACTOME_SIGNALING_BY_NOTCH2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH2.html Genes involved in Signaling by NOTCH2 16/16 Reactome 4.89683201154229e-06 6.47605690514979e-06 2315 1887.27272727273 2066 4.45167537373203e-07 63 2.12482497763401 -1.19092404513003 -1 4.38381783034321 2312 895 1842 2305 3501 2066 1234 1362 63 2704 2476 1938 M2134 REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS.html Genes involved in Metabolism of lipids and lipoproteins 453/619 Reactome 2.01038753862916e-07 7.65527859584926e-07 2165 2066.90909090909 2066 1.8276252021281e-08 944 1.75725664702363 -1.68154621299103 -1 4.27217512881591 1800 2946 3140 1917 944 1441 2066 2164 2164 2926 1228 1939 M16941 DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_UP.html Genes up-regulated in fibroblasts expressing different mutant forms of ERCC3 [GeneID=2071]: XP/CS (xeroderma pigmentosum (XP) and Cockraine's syndrome (CS)) vs TTD (trichothiodystrophy). 15608684 25/33 Arthur Liberzon 4.61034781221566e-06 6.15582508448597e-06 4405 2478.45454545455 2066 4.19123406704288e-07 336 3.32441321206973 3.87149386467759 1 6.91643437915692 4402 1843 813 2066 3465 4196 3450 336 1139 1290 4263 1940 M618 REACTOME_SIGNALING_BY_NOTCH3 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH3.html Genes involved in Signaling by NOTCH3 16/16 Reactome 4.89683201154229e-06 6.47605690514979e-06 2315 1901 2067 4.45167537373203e-07 64 2.12482497763401 -1.19092404513003 -1 4.38381783034321 2313 896 1843 2306 3502 2067 1235 1503 64 2705 2477 1941 M2526 BOSCO_ALLERGEN_INDUCED_TH2_ASSOCIATED_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_ALLERGEN_INDUCED_TH2_ASSOCIATED_MODULE.html Genes representing a co-expression network in atopic CD4 [GeneID=920] T lymphocyte responses. 19414752 168/248 Antony Bosco 4.34495736008191e-07 1.02540993697933e-06 3695 2262.63636363636 2068 3.949962016548e-08 826 2.20590643292298 -2.04001538693164 -1 5.26308112489556 3692 1471 826 2068 1808 2771 2277 3486 1465 1031 3994 1942 M8637 STREICHER_LSM1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STREICHER_LSM1_TARGETS_DN.html Genes down-regulated in MCF10A cells (breast cancer) by expression of LSM1 [GeneID=27257] off a letiviral vector. 17001308 26/29 Arthur Liberzon 3.21840871903272e-06 4.51438013486907e-06 2070 2334.36363636364 2069 2.92583038844954e-07 834 2.07869312668808 2.4239394286899 1 4.41856194894688 2069 2784 2208 3726 3288 1629 1953 1575 3933 1679 834 1943 M15981 RIGGI_EWING_SARCOMA_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIGGI_EWING_SARCOMA_PROGENITOR_UP.html Genes up-regulated in mesenchymal stem cells (MSC) engineered to express EWS-FLI1 [GeneID=2130;2321] fusion protein. 18381423 564/830 Jessica Robertson 1.24924582188436e-16 4.99698328753744e-15 2075 1992.09090909091 2071 1.24924582188436e-17 70 2.51269331336873 2.86159516228514 1 14.4015456225276 2071 1145 4542 257 1070 2169 3882 1909 2485 70 2313 1944 M2133 QI_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/QI_HYPOXIA.html Genes up-regulated by hypoxia in TRAMP-C cells (prostatic cancer). 20609350 187/201 Arthur Liberzon 2.42015668496637e-07 8.06149580313428e-07 3605 2624.18181818182 2071 2.20014268290989e-08 1160 1.92893367495977 2.15462428444049 1 4.6770191579849 3601 1435 1449 2071 1160 3108 4560 3732 1696 1715 4339 1945 M2137 GREGORY_SYNTHETIC_LETHAL_WITH_IMATINIB http://www.broadinstitute.org/gsea/msigdb/cards/GREGORY_SYNTHETIC_LETHAL_WITH_IMATINIB.html Genes identified as synthetic lethal with imatinib [PubChem=5291] in RNAi screen in K562 cells (CML, chronic myelogenous leukemia). 20609354 197/291 Arthur Liberzon 4.36096087139303e-07 1.02591716789194e-06 3820 2393.09090909091 2071 3.96451066895172e-08 1171 2.18583284707425 -2.03546582467463 -1 5.21454333993801 3820 2071 1171 1695 1814 3510 2154 2898 1793 1597 3801 1946 M2304 VANDESLUIS_NORMAL_EMBRYOS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_NORMAL_EMBRYOS_DN.html Genes down-regulated in normal 9.5 days post coitus (dpc) embryos compared to normal 8.5 dpc and 9.5 dpc embryos. 17371845 21/62 Arthur Liberzon 1.70430207576206e-06 2.65051261864809e-06 1835 2005.81818181818 2072 1.54936672368812e-07 377 3.08201243757999 -3.64194536945158 -1 6.86206257327389 1832 2808 1132 2052 2937 2997 2305 377 2072 2685 867 1947 M13339 CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP.html Genes up-regulated in secondary APL (acute promyelocytic leukemia) compared to the de novo tumors. 16990782 50/65 Leona Saunders 9.08068899922454e-07 1.63528622954368e-06 2075 1960.90909090909 2075 8.25517522487192e-08 701 2.27264708314827 2.21425012106893 1 5.23857320669963 2075 2239 1303 2067 2497 1722 2157 2317 701 1936 2556 1948 M11837 RODWELL_AGING_KIDNEY_NO_BLOOD_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_NO_BLOOD_DN.html Genes whose expression decreases with age in normal kidney, excluding those with higher expression in blood. 15562319 189/251 John Newman 9.10340482882623e-08 6.55522041874465e-07 2405 1995.09090909091 2075 8.27582291410643e-09 253 1.76167134013542 -1.85749351364329 -1 4.33076636263288 2401 2075 3086 1914 253 1975 1986 2574 2121 2415 1146 1949 M19056 REACTOME_AMINO_ACID_AND_OLIGOPEPTIDE_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINO_ACID_AND_OLIGOPEPTIDE_SLC_TRANSPORTERS.html Genes involved in Amino acid and oligopeptide SLC transporters 34/55 Reactome 5.68163833814504e-07 1.19827225004667e-06 3340 2359.36363636364 2076 5.16512709587673e-08 604 2.49890237429699 2.39492421416511 1 5.90079369194072 3339 604 684 2050 2076 4080 4616 2992 828 800 3884 1950 M2011 MIKKELSEN_NPC_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in neural progenitor cells (NPC). 17603471 7/16 Arthur Liberzon 7.63716006048833e-07 1.44885030086435e-06 1850 2075.54545454545 2077 7.63716268516921e-08 357 3.22609599996782 -2.3897051315775 -1 7.52552151624307 1846 1036 4646 3835 2424 2077 1019 357 2139 3071 381 1951 M4095 SHI_SPARC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHI_SPARC_TARGETS_UP.html Genes up-regulated in glioma cell lines after knockdown of SPARC [GeneID=6678] by RNAi. 17213807 29/35 Arthur Liberzon 9.00108957064587e-06 1.12246083945703e-05 1995 2307.54545454545 2078 8.18284217995804e-07 333 2.45559318010533 2.76277051294155 1 4.83814351796232 1993 3436 1963 2668 3727 2078 3046 693 3390 2056 333 1952 M16468 SEIDEN_MET_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SEIDEN_MET_SIGNALING.html Genes down-regulated both in vivo and in vitro upon activation of MET [GeneID=4233] signaling. 16158056 33/41 Arthur Liberzon 3.81418569294951e-06 5.22733927721304e-06 1040 1968.36363636364 2079 3.46744755063501e-07 511 1.76371796157527 1.80475423361603 1 3.69628488692575 1038 663 2605 2691 3374 653 511 1544 2812 3682 2079 1953 M885 GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP.html Genes exclusively up-regulated in B lymphocytes from CLL (chronic lymphocytic leukemia) patients but with a similiar expression pattern in the normal cells and in the cells from WM (Waldenstroem's macroblobulinemia) patients. 17252022 10/17 Arthur Liberzon 7.20738938929713e-08 6.06397110828564e-07 2785 2233.81818181818 2080 6.55217238674312e-09 75 2.00440843371726 -1.97383188677461 -1 4.96165870483751 2783 1957 2080 1413 152 3747 4253 3599 75 3112 1401 1954 M12674 WANG_LMO4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LMO4_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) engineered to conditionally express LMO4 [GeneID=8543] by a Tet Off system. 17452977 465/560 Arthur Liberzon 2.09744450164739e-07 7.70763712250053e-07 790 2478 2081 1.90676791055853e-08 786 1.48182093165437 -1.32529037727416 -1 3.59293932316791 786 3840 4062 3801 1000 1627 1243 1423 2820 4575 2081 1955 M2292 ITO_PTTG1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ITO_PTTG1_TARGETS_DN.html Genes down-regulated in HSA/c and KYSE140 cells (esophageal squamous cell carcinoma, ESCC) after knockdown of PTTG1 [GeneID=9232] by RNAi. 18451147 16/17 Jessica Robertson 7.18179851058585e-08 6.06397110828564e-07 2075 1977.27272727273 2083 6.52890795002944e-09 147 1.61394704935837 2.07213892152101 1 3.98537379353837 2073 2395 2606 2643 147 1812 2083 724 1286 3854 2127 1956 M4013 KEGG_GAP_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GAP_JUNCTION.html Gap junction 85/107 KEGG 3.90725411155967e-07 9.76357383103197e-07 3920 2684.72727272727 2084 3.5520498231798e-08 195 1.98858727123586 2.05034425859353 1 4.75667423742737 3918 1624 1886 195 1682 4079 4187 4169 1272 2084 4436 1957 M5522 ROZANOV_MMP14_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_TARGETS_DN.html Genes down-regulated in HT1080 cells (fibrosarcoma) over-expressing MMP14 [GeneID=4323] compared to those with knockdown of the gene by RNAi. 18519667 34/48 Jessica Robertson 1.13635442836034e-06 1.9300442252108e-06 4105 2420 2085 1.03305001392359e-07 647 2.12654449624325 -1.96657699372634 -1 4.837029386549 4102 647 1873 2085 2657 3127 2555 1417 1805 1825 4527 1958 M1909 BIOCARTA_EGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EGF_PATHWAY.html EGF Signaling Pathway 49/53 BioCarta 5.74166092511243e-07 1.20715543726195e-06 1110 2154.63636363636 2086 5.21969311236181e-08 1057 1.34639048857037 -1.38952859500263 -1 3.15449051056429 1106 3080 3449 1107 2086 1401 1057 2143 3255 3715 1302 1959 M1194 NAISHIRO_CTNNB1_TARGETS_WITH_LEF1_MOTIF http://www.broadinstitute.org/gsea/msigdb/cards/NAISHIRO_CTNNB1_TARGETS_WITH_LEF1_MOTIF.html Genes regulated by CTNNB1 [GeneID=1499] and whose promoters contain binding sites for LEF1 [GeneID=51176]. 15735679 8/11 Leona Saunders 5.01905007047896e-06 6.6209939442875e-06 2770 2181.90909090909 2086 5.01906140640362e-07 274 3.3966538048321 2.88509803501201 1 7.02460194219481 2768 1031 4382 1617 3542 2698 2155 1378 274 2070 2086 1960 M184 PID_ECADHERIN_KERATINOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ECADHERIN_KERATINOCYTE_PATHWAY.html E-cadherin signaling in keratinocytes 18832364 34/40 Pathway Interaction Database 6.16115318058094e-08 5.75735672118533e-07 2370 1486.72727272727 2087 5.60104850284138e-09 91 1.76186965205679 -1.96242150970805 -1 4.37119669818667 2368 596 2159 183 91 2087 2183 3060 123 2350 1154 1961 M12029 BILD_HRAS_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_HRAS_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing activated HRAS [GeneID=3265] oncogene from control cells expressing GFP. 16273092 373/465 Arthur Liberzon 1.53622244315832e-07 7.28175281873995e-07 4330 2238.18181818182 2087 1.39656595493648e-08 368 2.14406160145517 2.42351042387125 1 5.24230729254831 4328 1233 421 1811 652 4596 3334 2087 2202 368 3588 1962 M1970 MIKKELSEN_IPS_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 70/120 Jessica Robertson 3.90244925133454e-07 9.76357383103197e-07 2915 2190.72727272727 2088 3.54768176687909e-08 488 2.76222011075322 2.88923043499069 1 6.62665995539574 2911 2172 591 3045 1680 2045 4059 1936 3083 488 2088 1963 M19170 MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP.html The 'NPM1-mutated signature 1': genes up-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to all AML cases with the intact gene. 17597811 317/448 Arthur Liberzon 3.52107656997552e-07 9.36308811847011e-07 2090 1829.27272727273 2089 3.20097921229109e-08 439 1.90488480617681 2.15918258172873 1 4.56828753736963 1399 3280 2089 2900 1558 682 2090 731 2620 2334 439 1964 M4723 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN.html Genes down-regulated in normal hematopoietic progenitors by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 182/303 Arthur Liberzon 3.78678508732089e-09 5.39988689188961e-08 2470 1669.72727272727 2090 3.44253190348997e-10 95 2.24665427460044 2.45692947262033 1 6.51638548453849 2467 1413 307 748 95 2090 3729 2652 2399 201 2266 1965 M219 PID_HEDGEHOG_GLI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HEDGEHOG_GLI_PATHWAY.html Hedgehog signaling events mediated by Gli proteins 18832364 65/86 Pathway Interaction Database 1.76130774565894e-06 2.7194545500524e-06 990 1924.27272727273 2091 1.60119014159426e-07 168 1.51008163552415 1.53475142527482 1 3.32988489903065 989 2197 3326 3233 2960 168 368 2091 1578 4023 234 1966 M13206 KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN.html Genes down-regulated in TC71 and EWS502 cells (Ewing's sarcoma) by EWSR1-FLI1 [GeneID=2130;2314] as inferred from RNAi knockdown of this fusion protein. 17114343 485/623 Leona Saunders 8.93758582100658e-10 1.43977491724065e-08 2465 1787.81818181818 2091 8.12507802239771e-11 225 2.12913142395016 2.53011967668998 1 6.66446233487503 2464 1176 226 741 1117 2779 4492 2250 2091 225 2105 1967 M17312 ZIRN_TRETINOIN_RESPONSE_WT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_WT1_UP.html Genes up-regulated in MZ128 cells (Wilms tumor with mutated WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 31/34 Leona Saunders 3.50681294139034e-07 9.3409464353061e-07 4415 2473.72727272727 2093 3.18801227307137e-08 593 2.2194426241852 1.96715195402086 1 5.33183942618142 4411 2311 1565 2093 1554 4133 3018 1974 593 1992 3567 1968 M18117 XU_AKT1_TARGETS_48HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_AKT1_TARGETS_48HR.html Genes up-regulated in DU-145 cells (prostate cancer) expressing a dominant negative form of AKT1 [GeneID=207] upon sham-treatment for 48 h (as a control for the HGF [GeneID=3082] experiments). 17099727 10/13 Arthur Liberzon 3.96524656750933e-06 5.40455206429224e-06 2095 2070 2093 3.60477610402502e-07 111 2.11965415886459 1.7055115464612 1 4.43998818168859 2093 995 2363 2139 3393 1508 1044 3970 111 3107 2047 1969 M10153 CLAUS_PGR_POSITIVE_MENINGIOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CLAUS_PGR_POSITIVE_MENINGIOMA_UP.html Genes up-regulated in meningioma samples positive for PGR [GeneID=5241] compared to those without the receptor. 18172325 9/18 Jessica Robertson 5.78226064884619e-07 1.21245092237024e-06 905 1790.63636363636 2093 5.78226215340096e-08 28 2.43140786899378 2.73742269005317 1 5.73506841830224 904 2461 4531 3628 2173 689 118 28 2093 2897 175 1970 M208 MIZUKAMI_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIZUKAMI_HYPOXIA_UP.html Genes up-regulated in DLD-1 cells (colon cancer) in response to hypoxia; might not be direct targets of HIF1A [GeneID=3091]. 16127434 14/20 Jessica Robertson 7.89122222597191e-06 9.94037067162727e-06 2240 2065.54545454545 2093 7.173864119355e-07 366 2.72687731442767 2.73356094758467 1 5.43603867934327 2240 2403 697 3308 3690 1767 1593 366 4057 507 2093 1971 M13008 DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN.html Genes exclusively down-regulated in fibroblasts expressing the TTD mutant form of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 144/151 Arthur Liberzon 1.9162971241288e-07 7.53743535490661e-07 1200 2148.27272727273 2094 1.74208844640614e-08 910 1.97507029002817 2.42485933802403 1 4.81326897977559 1199 2094 2010 2680 910 2374 4055 1911 2778 2312 1308 1972 M1802 ZHENG_IL22_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_IL22_SIGNALING_DN.html Genes down-regulated in ex-vivo colonic tissue after treatment with IL22 [GeneID=50616]. 18264109 73/105 Jessica Robertson 1.48225689549098e-06 2.36807068277938e-06 1320 1785.90909090909 2094 1.34750717651559e-07 269 2.66656204362605 2.67687747739458 1 5.98280006390142 1320 269 472 2094 2852 2367 3130 1746 2299 820 2276 1973 M16524 LEE_LIVER_CANCER_DENA_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_DENA_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by diethylnitrosamine (DENA) [PubChem=5921]. 15565109 87/123 Yujin Hoshida 6.21570748235276e-10 1.04035955023777e-08 3750 2231.27272727273 2095 5.65064316737173e-11 144 2.57035132086563 2.62557783701843 1 8.20177417117401 3748 144 262 379 1651 4346 3890 3286 2095 171 4572 1974 M5958 VARELA_ZMPSTE24_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VARELA_ZMPSTE24_TARGETS_DN.html Top genes down-regulated in liver tissue from mice with knockout of ZMPSTE24 [GeneID=10269]. 16079796 48/80 John Newman 3.84419424575977e-07 9.6978069695276e-07 1430 2269.18181818182 2095 3.49472265225406e-08 1143 2.06643203082417 -2.13035805477784 -1 4.94727594114398 1428 3085 2246 3197 1665 2095 1717 1143 3687 2988 1710 1975 M16646 WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN.html Unmethylated germline-specific genes with high-CpG-density promoters (HCP) in primary fibroblasts. 17334365 29/79 Jessica Robertson 2.11612138499507e-07 7.70763712250053e-07 4145 2270.63636363636 2096 1.92374689867197e-08 737 2.14766606729449 -2.38862309569783 -1 5.22988352236843 4141 737 2096 1823 1009 4317 3076 3282 811 2369 1316 1976 M2401 KOHOUTEK_CCNT1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KOHOUTEK_CCNT1_TARGETS.html Genes down-regulated in E14 ES (embryonic stem) cells upon knockdown of CYCT1 [GeneID=904] by RNAi. 19364821 71/86 Arthur Liberzon 6.18427935940882e-08 5.75735672118533e-07 4130 2182.36363636364 2096 5.62207230295558e-09 241 2.60799914155963 3.00922764837431 1 6.49447315787829 4129 241 337 316 2096 4696 3469 3512 549 304 4357 1977 M1910 VANASSE_BCL2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANASSE_BCL2_TARGETS_DN.html Genes down-regulated in primary B lymphocytes engineered to overexpress BCL2 [GeneID=12043]. 15561778 103/141 Arthur Liberzon 5.24509274123559e-07 1.14086809855447e-06 2760 1987.36363636364 2098 4.76826726521446e-08 102 2.3776690655872 2.69748703275304 1 5.63247777365708 2757 102 762 1226 1994 2983 4169 2850 2098 625 2295 1978 M11048 RIZ_ERYTHROID_DIFFERENTIATION_CCNE1 http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_CCNE1.html Selected gradually up-regulated genes whose expression profile follows that of CCNE1 [GeneID=898] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 46/57 Leona Saunders 3.40137846919848e-06 4.72747537532887e-06 1360 2234.09090909091 2099 3.09216702546991e-07 976 1.33531125518318 1.55713339776968 1 2.80974536793195 1357 3089 3695 2919 3320 1140 1282 1368 2099 3330 976 1979 M5407 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_DN.html Genes down-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 13/20 John Newman 6.7934545107374e-06 8.67797166188919e-06 4290 2316.27272727273 2099 6.1758868077876e-07 8 2.59811933104688 -3.64075193916781 -1 5.23862718883985 4288 960 2045 128 3634 3142 2053 2099 8 2648 4474 1980 M9948 KIM_WT1_TARGETS_8HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_8HR_DN.html Genes down-regulated in UB27 cells (osteosarcoma) at 8 hr after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 144/204 Arthur Liberzon 5.05211302697322e-07 1.11952927170486e-06 2470 2195 2100 4.59283107922583e-08 635 1.79338995080411 1.9611493303568 1 4.24199282868874 2003 2100 2469 3735 1955 1443 2809 635 3027 2469 1500 1981 M17359 XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_UP.html Genes up-regulated in DU-145 cells (prostate cancer) in the absence but not in the presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 27/37 Arthur Liberzon 5.84773093683812e-07 1.22123997631427e-06 1845 2181.18181818182 2100 5.31612044654581e-08 416 2.26368797059068 2.75577833655945 1 5.33315285883397 1844 3442 1784 3723 2100 1556 2254 1612 2826 2436 416 1982 M9874 OUYANG_PROSTATE_CANCER_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/OUYANG_PROSTATE_CANCER_MARKERS.html Mouse orthologs of human prostate cancer tumor markers which were deregulated in mice heterozygotic for both NKX3.1 and PTEN [GeneID=4824;5728]. 18381418 25/27 Jessica Robertson 2.05418338929327e-07 7.68284120242806e-07 4175 2243.54545454545 2100 1.86743961917859e-08 291 2.10687302748052 -1.8930633307447 -1 5.13078176270378 4175 759 2086 1467 975 4225 3168 2927 291 2506 2100 1983 M19971 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP.html Genes up-regulated in peripheral blood mononucleocytes by HGF [GeneID=3082] compared to those regulated by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 480/678 Arthur Liberzon 2.19347558820757e-07 7.78436449348851e-07 2555 2066.54545454545 2100 1.99406891536786e-08 832 1.87820664636826 -1.85122745283226 -1 4.56418272063335 2551 1182 1515 1673 1049 2251 2100 4196 2273 832 3110 1984 M1366 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_DN.html Early prostate development genes (down-regulated at 48 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 6/7 Jessica Robertson 0.000241550912108356 0.000258589318473904 2000 2599 2101 2.41577172205187e-05 1046 2.71221147579456 -1.99147938171391 -1 3.86289866144149 1997 1046 4445 2608 4380 2949 1560 4136 2101 1490 1877 1985 M13333 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN.html Genes down-regulated in peripheral blood mononucleocytes by HGF [GeneID=3082] compared to those regulated by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 291/368 Arthur Liberzon 2.83025030137995e-07 8.50336182209636e-07 3230 2459.45454545455 2101 2.57295515044121e-08 821 1.84023486598582 2.16960153135576 1 4.442502143676 3226 2521 2101 3680 1331 2918 4649 821 2043 2060 1704 1986 M13767 LEE_EARLY_T_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_EARLY_T_LYMPHOCYTE_DN.html Genes down-regulated at early stages of progenitor T lymphocyte maturation compared to the late stages. 15210650 73/109 Arthur Liberzon 9.83623218102339e-07 1.73235133934442e-06 1620 2076.63636363636 2102 8.94203325347266e-08 1288 1.75163797324156 -1.55910563285256 -1 4.00850742099397 1620 1642 1819 2155 2555 2119 2544 1659 3340 1288 2102 1987 M2551 KEGG_ARGININE_AND_PROLINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARGININE_AND_PROLINE_METABOLISM.html Arginine and proline metabolism 51/66 KEGG 2.01425798905647e-07 7.65527859584926e-07 2730 2130 2103 1.83114379406934e-08 428 1.97879652663835 1.69355478361402 1 4.8170826665602 2728 428 1549 1837 950 2103 2249 3494 3260 1598 3234 1988 M525 REACTOME_ENDOSOMAL_VACUOLAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOSOMAL_VACUOLAR_PATHWAY.html Genes involved in Endosomal/Vacuolar pathway 22/38 Reactome 4.20131024055392e-05 4.7737564601383e-05 290 2355.36363636364 2103 3.81944588595671e-06 289 1.00534005377663 -0.992813544474424 -1 1.69703944444463 289 1859 3286 2978 4103 830 840 1871 4554 3196 2103 1989 M11011 ASTON_MAJOR_DEPRESSIVE_DISORDER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ASTON_MAJOR_DEPRESSIVE_DISORDER_DN.html Genes down-regulated in the temporal cortex samples from patients with major depressive disorder. 15303102 240/304 Jean Junior 5.85522471694746e-07 1.22123997631427e-06 4620 2457.18181818182 2103 5.32293297754187e-08 470 2.24580586893066 2.49815253431998 1 5.29062811486266 4619 1359 643 470 2103 4069 3303 3886 1530 831 4216 1990 M11545 KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN.html Down-regulated genes predicting response of patients with hepatocellular carcinoma (HCC) to combination chemotherapy with 5-fluorouracil (5-FU) [PubChem=3385] and IFN1@ [GeneID=3438]. 15447987 55/68 Yujin Hoshida 2.01340538218184e-07 7.65527859584926e-07 2540 1882.09090909091 2103 1.83036869676869e-08 306 1.55714170414183 1.57498454396103 1 3.77996514395361 2540 424 2720 2869 948 2025 2103 306 2934 3119 715 1991 M18090 NUYTTEN_NIPP1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_NIPP1_TARGETS_DN.html Genes down-regulated in PC3 cells (prostate cancer) after knockdown of NIPP1 [GeneID=5511] by RNAi. 17724462 1112/1300 Jessica Robertson 1.51134877359953e-07 7.27172906359816e-07 2765 2130.90909090909 2104 1.51134887638742e-08 739 1.80793784022921 1.95119218832624 1 4.41306333920188 2762 1079 4429 815 739 2104 3358 2773 1678 1186 2517 1992 M1290 DIERICK_SEROTONIN_FUNCTION_GENES http://www.broadinstitute.org/gsea/msigdb/cards/DIERICK_SEROTONIN_FUNCTION_GENES.html Genes involved in serotonin [PubChem=5202] function, orthologs computed from D. melanogaster genes using InsParanoid resource. 17450142 3/7 Leona Saunders 1.83547649968422e-06 2.8082492961133e-06 2105 1927.09090909091 2105 1.83547801572427e-07 18 3.88438004282662 3.88438004282662 1 8.62233177751001 2105 2931 4416 1809 3040 2244 685 882 18 2608 460 1993 M14314 KEGG_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PURINE_METABOLISM.html Purine metabolism 139/171 KEGG 2.33811642043665e-07 7.98113405922816e-07 690 2050.27272727273 2106 2.12556060811552e-08 689 1.54595670495265 1.49122337911587 1 3.74119865860586 689 2106 3246 4167 1121 1242 1250 1674 2305 2632 2121 1994 M17148 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_DN.html Genes down-regulated in granulocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 17/30 Arthur Liberzon 1.62795076146821e-05 1.94333019578401e-05 1590 2347.18181818182 2106 1.47996618914936e-06 1342 2.00128655796106 1.77085320248724 1 3.74193230239946 1589 2837 2028 2871 3895 1392 1677 2262 3820 1342 2106 1995 M2259 KIM_GLIS2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GLIS2_TARGETS_UP.html Partial list of genes up-regulated in the kidney of GLIS2 [GeneID=84662] knockout mice compared to the wild type. 18227149 123/190 Arthur Liberzon 2.76743410579313e-11 5.55842084227386e-10 865 1730.09090909091 2106 2.51584918711631e-12 15 2.46429649844818 2.98613656899203 1 9.12213749679139 862 15 180 1222 3195 2106 2948 2203 3714 319 2267 1996 M2089 NOUSHMEHR_GBM_SOMATIC_MUTATED http://www.broadinstitute.org/gsea/msigdb/cards/NOUSHMEHR_GBM_SOMATIC_MUTATED.html Genes showing significantly elevated somatic mutation frequencies in proneural G-CIMP (a CpG island methylator phenotype) GBM (glyoblastoma multiforme) tumors. 20399149 23/29 Arthur Liberzon 2.82462311961362e-06 4.03029659146805e-06 1425 1897.45454545455 2107 2.56784249655375e-07 250 2.89570206020405 3.65771857577129 1 6.23226538867438 1421 3459 1617 3206 3235 2107 2311 527 511 2228 250 1997 M2090 NOUSHMEHR_GBM_GERMLINE_MUTATED http://www.broadinstitute.org/gsea/msigdb/cards/NOUSHMEHR_GBM_GERMLINE_MUTATED.html Genes with significantl germline mutation differences in proneural G-CIMP (a CpG island methylator phenotype) GBM (glyoblastoma multiforme) tumors. 20399149 9/17 Arthur Liberzon 1.96293244475485e-05 2.31394633847225e-05 1755 2251.27272727273 2107 1.96294978393743e-06 279 2.86825067495002 3.18039460755631 1 5.29718328263996 1753 2454 4654 2836 3972 1542 279 1030 2107 2327 1810 1998 M15258 BIOCARTA_AKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKT_PATHWAY.html AKT Signaling Pathway 30/33 BioCarta 7.61646100041503e-07 1.44597311199533e-06 925 2067 2108 6.9240578520511e-08 624 1.40339473773887 -1.51967683001759 -1 3.24591901657874 922 3148 3462 2524 2342 1091 624 1259 2108 3896 1361 1999 M14804 REACTOME_EXTENSION_OF_TELOMERES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTENSION_OF_TELOMERES.html Genes involved in Extension of Telomeres 27/29 Reactome 6.8301371785165e-05 7.59619403454239e-05 120 2106.90909090909 2108 6.20940839700521e-06 98 1.22091115440352 1.25653873611525 1 1.97260518082736 118 3140 3213 2877 4197 391 98 1395 3812 2108 1827 2000 M10332 MODY_HIPPOCAMPUS_POSTNATAL http://www.broadinstitute.org/gsea/msigdb/cards/MODY_HIPPOCAMPUS_POSTNATAL.html Genes up-regulated in hyppocampus at late postnatal stages (clusters 11 and 15). 11438693 95/117 John Newman 7.34435915456945e-08 6.11382278828356e-07 2130 1642.72727272727 2110 6.67669036340863e-09 157 1.97946571947809 -1.80607472890665 -1 4.8964629348915 2129 2594 2185 841 157 1639 2160 795 683 2777 2110 2001 M14698 HOEBEKE_LYMPHOID_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOEBEKE_LYMPHOID_STEM_CELL_UP.html Genes up-regulated in the common lymphoid progenitor (CLP, defined as CD34+CD38-CD7+ [GeneID=947;952;924]) compared to a multipotent cord blood cell (defined as CD34+CD38+CD7-). 17170726 127/163 Arthur Liberzon 1.90615471316224e-07 7.51633270353031e-07 4205 2726.27272727273 2111 1.73286807119817e-08 906 2.07840413826162 -1.6363498060816 -1 5.06873039362672 4203 2111 2046 1879 906 4039 2316 4635 1318 2095 4441 2002 M924 REACTOME_PLATELET_CALCIUM_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_CALCIUM_HOMEOSTASIS.html Genes involved in Platelet calcium homeostasis 13/19 Reactome 8.61263692249652e-08 6.48643236402367e-07 4085 2451.36363636364 2112 7.82967023606098e-09 213 2.26286938378659 -1.74575216228526 -1 5.58128056174221 4084 1921 1477 2112 213 4352 4009 4093 380 1052 3272 2003 M1448 NEMETH_INFLAMMATORY_RESPONSE_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NEMETH_INFLAMMATORY_RESPONSE_LPS_UP.html Genes up-regulated in RAW 264.7 cells (macrophage) 3 hr after stimulation with bacterial lipopolysaccharide (LPS). 12766259 111/147 Kevin Vogelsang 3.01995789534033e-07 8.77181616369622e-07 2115 2345.72727272727 2112 2.7454166453568e-08 1141 2.06060059264405 -2.0484887211292 -1 4.96929143764746 2112 3318 1591 3130 1395 2041 1141 2985 3463 1259 3368 2004 M19629 MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN.html The 'NPM1-mutated signature 1': genes down-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to all AML cases with the intact gene. 17597811 169/259 Arthur Liberzon 1.10869058709201e-07 7.03739764799127e-07 3590 2362.27272727273 2113 1.00790058451319e-08 356 2.23275812120117 2.46626874134704 1 5.47455418293204 3589 2082 1311 1691 356 4017 4624 2113 897 2629 2676 2005 M5635 BUSA_SAM68_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BUSA_SAM68_TARGETS_DN.html Genes down-regulated in LNCaP cells (prostate cancer) after knockdown of SAM68 [GeneID=10657] by RNAi. 17237817 6/7 Arthur Liberzon 2.06355615186324e-06 3.10487250136898e-06 4275 2272.27272727273 2114 2.06355806808454e-07 683 2.32058108332685 1.64687530075702 1 5.09025591545111 4272 1042 4347 1433 3097 3090 2199 1889 829 2114 683 2006 M1582 BURTON_ADIPOGENESIS_2 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_2.html Strongly up-regulated at 8 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 116/131 John Newman 1.08500544900217e-06 1.86361925738364e-06 1330 2100.81818181818 2114 9.86369076463806e-08 668 2.10924465002902 2.22275400924376 1 4.81017421932608 1328 2114 788 1184 2626 2692 4137 2887 2077 668 2608 2007 M17173 MCCLUNG_DELTA_FOSB_TARGETS_8WK http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_DELTA_FOSB_TARGETS_8WK.html Genes up-regulated in the nucleus accumbens (a major reward center in brain) 8 weeks after induction of deltaFosB, a FOSB [GeneID=2354] splice variant. 14566342 74/99 John Newman 2.57344468994759e-07 8.25741600037569e-07 3755 2277.18181818182 2115 2.33949544634155e-08 266 1.83490352880887 -1.35552183677024 -1 4.43889281872385 3751 266 1753 1472 1219 2955 2835 3271 2115 2039 3373 2008 M2109 KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN.html Genes whose expression significantly and negatively correlated with oligodendrocyte density in layer VI of BA9 brain region in patients with bipolar disorder. 18762803 70/174 Jessica Robertson 5.93167852636145e-07 1.22925373509314e-06 4645 2588.81818181818 2116 5.39243647788328e-08 267 2.47876922883192 -2.58367801398723 -1 5.84179777429679 4641 267 499 1803 2116 3627 4074 4463 1901 552 4534 2009 M7778 EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_DN.html Genes down-regulated in Rh4 cells (alveolar rhabdomyosarcoma, ARMS) after knockdown of the PAX3-FOXO1 [GeneiD=5077;2308] fusion protein by RNAi for 72 hr. 17525748 51/71 Leona Saunders 1.26958701523023e-06 2.09672873054117e-06 3140 1982.63636363636 2117 1.15417067990041e-07 372 2.13186251826883 2.9904864671797 1 4.81840759529336 3138 446 1599 2117 2742 2855 3637 2609 467 1827 372 2010 M1270 CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_DN http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_DN.html Genes down-regulated in neuroblastoma xenografts: sensitive vs resistant to the topoisomerase inhibitor irinotecan [GeneID=3750]. 16501609 6/7 Arthur Liberzon 1.58472589594154e-06 2.49413345409939e-06 1330 2115.36363636364 2117 1.58472702605295e-07 42 4.03439619176408 4.62986445227151 1 9.04084537675931 1330 2476 4409 2158 4261 2039 2000 42 261 2117 2176 2011 M1968 MIKKELSEN_IPS_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) without H3 methylation marks at either H3K4 or H3K27 in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 79/162 Jessica Robertson 8.30717221467635e-07 1.53643624033199e-06 1720 1824.09090909091 2118 7.55197759223249e-08 612 2.59953440325955 2.47273529856908 1 6.02757263227528 1719 2154 612 2581 2419 1126 2526 2118 2648 785 1377 2012 M2291 PASINI_SUZ12_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PASINI_SUZ12_TARGETS_UP.html Genes up-regulated in ES (embryonic stem cells) with defficient SUZ12 [GeneID=23512]. 17339329 117/167 Arthur Liberzon 5.59434610871085e-07 1.18659903470788e-06 3295 2487.90909090909 2118 5.08577048299002e-08 1448 2.10730335516188 -2.09466506270929 -1 4.9718515022369 3291 2118 1448 2111 2063 3459 2898 3234 1983 1977 2785 2013 M2568 ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION http://www.broadinstitute.org/gsea/msigdb/cards/ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION.html Genes up-regulated in lung tissue upon LPS aspiration with mechanical ventilation (MV) compared to control (PBS aspiration without MV). 16116230 137/218 Jernej Godec 1.74316984093924e-07 7.37919956089047e-07 1495 1961 2118 1.584699980963e-08 384 2.25398394670716 -2.40255912510656 -1 5.50840335708556 1492 2559 500 3382 799 1758 2148 2268 4163 384 2118 2014 M2891 ROETH_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROETH_TERT_TARGETS_DN.html Genes down-regulated in T lymphocytes overexpressing TERT [GeneID=7015] off a retrovirus vector. 15741219 6/14 Kevin Vogelsang 2.02239216696731e-08 2.47297695028127e-07 5 2100.27272727273 2119 2.02239218537262e-09 2 2.91022199303093 2.0050252527762 1 7.68240380215771 4574 1032 4484 106 4 4220 3858 19 2 2119 2685 2015 M1679 ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP.html Genes up-regulated in CD-1 compared to CD-2 cluster of multiple myeloma samples. 16728703 70/94 Kevin Vogelsang 6.43363219438527e-05 7.17720254254278e-05 1555 2352.54545454545 2120 5.84892758711851e-06 1130 1.98806338437225 2.38562224793841 1 3.2632213399845 1552 3041 1489 3646 4179 2120 2457 1916 2439 1130 1909 2016 M1988 GYORFFY_MITOXANTRONE_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/GYORFFY_MITOXANTRONE_RESISTANCE.html Genes associated with resistance to mitoxantrone [PubChem=4212]. 16044152 85/111 Arthur Liberzon 5.93055560009687e-07 1.22925373509314e-06 2125 2173.63636363636 2121 5.39141563527413e-08 729 1.99263734016432 2.11233079566575 1 4.68630140267999 2121 2141 1614 3057 2115 2222 3930 3096 1818 1067 729 2017 M13314 LUI_TARGETS_OF_PAX8_PPARG_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/LUI_TARGETS_OF_PAX8_PPARG_FUSION.html Genes down-regulated in follicular thyroid carcinoma (FTC) samples that bear PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 61/93 Leona Saunders 2.77759989453415e-06 3.97234830739423e-06 910 2260.90909090909 2122 2.52509400126031e-07 47 1.25236630390724 -1.30944675224559 -1 2.67017262425602 910 3649 3683 2023 3226 358 673 2122 4185 3994 47 2018 M10280 ZHAN_LATE_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_LATE_DIFFERENTIATION_GENES_UP.html B lymphocyte late differentiation genes (LDG): top genes up-regulated in plasma cells from tonsils (TPC) compared to those from bone marrow (BPC). 12393520 37/48 Arthur Liberzon 6.87160224047889e-05 7.6369113668614e-05 2055 2250.54545454545 2123 6.24710625573395e-06 1239 2.1351761669932 2.41989445866521 1 3.48524359551034 2051 2282 1943 2652 4201 2123 1442 1239 1391 2409 3023 2019 M11472 RIZKI_TUMOR_INVASIVENESS_3D_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_3D_DN.html Genes down-regulated in three-dimentional (3D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 377/565 Jessica Robertson 2.626422733814e-07 8.29211725993449e-07 3650 2171.27272727273 2124 2.38765731578535e-08 153 2.01928798304288 -1.60416585909883 -1 4.88849414041332 3646 1221 574 153 1247 3399 3378 2877 2124 589 4676 2020 M97 BAELDE_DIABETIC_NEPHROPATHY_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAELDE_DIABETIC_NEPHROPATHY_UP.html Genes up-regulated in glomeruli of kidneys from patients with diabetic nephropathy (type 2 diabetes mellitus). 15042541 108/162 John Newman 3.21456030882193e-06 4.51032243092732e-06 3260 2426.63636363636 2126 2.92233182348238e-07 935 2.02838034137623 2.00744733621519 1 4.31072234269214 3257 2126 1302 2104 3287 2042 3736 1132 3375 935 3397 2021 M16312 REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL.html Genes involved in Cell surface interactions at the vascular wall 99/131 Reactome 1.21337398970829e-06 2.02470360040951e-06 1415 2043.54545454545 2127 1.10306787175034e-07 416 2.29874943904086 2.33504086025107 1 5.21355440570218 1413 2127 416 1204 2904 1895 3417 3136 3194 433 2340 2022 M1703 HOWLIN_CITED1_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_1_DN.html Genes down-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs. heterozygotic animals. 16278680 56/75 Arthur Liberzon 4.86898877558811e-07 1.09697503679121e-06 2790 2135.18181818182 2127 4.42635441198337e-08 420 2.34422829558252 -2.03074555755049 -1 5.5686193135451 2790 420 1369 2127 1920 3518 2996 1837 2246 1123 3141 2023 M2572 ANASTASSIOU_CANCER_MESENCHYMAL_TRANSITION_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/ANASTASSIOU_CANCER_MESENCHYMAL_TRANSITION_SIGNATURE.html Genes in the 'mesenchymal transition signature' common to all invasive cancer types. 22208948 105/125 Dimitris Anastassiou 3.13887910719423e-16 1.20090302877904e-14 175 1967.81818181818 2128 2.85352646108566e-17 85 3.27663739658101 3.52274164999986 1 18.2935228307268 173 2128 85 2115 4443 2125 2482 2441 3015 390 2249 2024 M8043 ROSS_AML_WITH_AML1_ETO_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_AML1_ETO_FUSION.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtype t(8;21) ; has AML1 ETO fusion [GeneID=861;862]. 15226186 86/177 Kate Stafford 6.05404514230255e-07 1.24618809732525e-06 3870 2273 2131 5.50367891661705e-08 206 1.94351425327979 2.01494372356044 1 4.56489542207786 3867 206 1727 1014 2131 1630 2514 4364 961 2715 3874 2025 M94 PID_FAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FAS_PATHWAY.html FAS (CD95) signaling pathway 18832364 47/54 Pathway Interaction Database 5.99080410414559e-08 5.65531907431344e-07 1285 1996.09090909091 2132 5.44618569752796e-09 85 1.51220073594472 -1.53833157588164 -1 3.74940068211968 1285 1726 2949 2216 85 1739 1262 2801 3599 2132 2163 2026 M11405 TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN.html Candidate genes in the regions of copy number loss in gastric cancer cell lines. 16103878 28/41 Arthur Liberzon 3.58582016198981e-07 9.41752134134615e-07 1885 2310.27272727273 2133 3.25983704222665e-08 1135 2.24702253435586 1.81064881229938 1 5.39551317332893 1883 3437 2133 2815 1582 1135 1471 3791 2229 3228 1709 2027 M18757 ONDER_CDH1_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_1_UP.html Genes up-regulated in HMLE cells (mmortalized nontransformed mammary epithelial) by expression of a dominant-negative form of E-cadhedrin (CDH1) [GeneID=999]. 18483246 200/263 Jessica Robertson 3.77393997572336e-07 9.60325320936429e-07 2770 2145.90909090909 2133 3.43085511192316e-08 961 2.22192731566732 -2.04302043511038 -1 5.32711703945516 2770 2070 961 1052 1647 2133 2533 4080 2206 1028 3125 2028 M2407 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_1 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_1.html Genes regulated in MCF7 cells (breast cancer) by expression of full-length and truncated (611-CTF) forms of ERBB2 [GeneID=2064] at both 15 h and 60 h time points. 19364815 69/82 Arthur Liberzon 1.38458647647375e-07 7.20206492018647e-07 2135 1908.54545454545 2133 1.25871505783068e-08 325 2.16020940443406 2.42803683428729 1 5.28631778486253 2133 325 1055 3344 557 2379 3282 2776 1570 1334 2239 2029 M659 KOBAYASHI_EGFR_SIGNALING_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_6HR_DN.html Genes down-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 6h. 17145885 28/34 Leona Saunders 8.08133387386985e-08 6.29674606547497e-07 4655 2338 2134 7.34666742793112e-09 190 1.82487623065318 -1.26467151342054 -1 4.50076192364629 4653 2770 1868 1540 190 3815 2134 2272 1660 1394 3422 2030 M2662 SINGH_NFE2L2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SINGH_NFE2L2_TARGETS.html Selected electrophile and drug detoxication genes down-regulated in A549 and H460 cells (lung cancer) upon knockdown of NFE2L2 [GeneID=4780] by RNAi. 18829555 32/38 Jessica Robertson 3.92442675406798e-07 9.79032467188206e-07 2550 2372.90909090909 2135 3.56766132192664e-08 1215 1.57756831541466 1.38895102504719 1 3.76242635741611 2550 1780 2404 1245 1687 1215 1847 4332 2518 2135 4389 2031 M4780 WANG_SMARCE1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_SMARCE1_TARGETS_DN.html Genes down-regulated in BT549 cells (breast cancer) by expression of SMARCE1 [GeneID=6605] off a retroviral vector. 16135788 488/682 John Newman 1.50521528343741e-07 7.26289540930751e-07 2150 1942.63636363636 2137 1.36837762402051e-08 637 1.96215238641016 2.15764210546535 1 4.79417608037541 2147 2943 1248 2177 637 2076 2508 1299 2137 1431 2766 2032 M6868 HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP.html Genes up-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with low risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 41/55 Arthur Liberzon 7.862842357122e-06 9.90991079455696e-06 925 2463.45454545455 2137 7.14806405382962e-07 924 1.89923443774548 -1.48508063223619 -1 3.77196103072209 924 3683 2137 3881 3688 1092 1249 2111 4023 2277 2033 2033 M11932 REACTOME_TIE2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TIE2_SIGNALING.html Genes involved in Tie2 Signaling 21/24 Reactome 4.77007324770927e-07 1.08181093402886e-06 4230 2356.54545454545 2138 4.33643116542189e-08 469 1.75012712091175 -1.98236930634406 -1 4.14892999954149 4228 848 2275 469 1908 4579 4168 1199 1429 2681 2138 2034 M2005 MIKKELSEN_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing bivalent histone H3 methylation mark (H3K4me3 and H3K27me3) in embryonic stem cells (ES). 17603471 153/277 Arthur Liberzon 5.62058822436685e-14 1.66850166157305e-12 3650 2513.18181818182 2138 5.10962565851543e-15 116 2.72163002151522 2.89543160043526 1 12.8410411301914 3650 1487 116 1350 2073 3448 4358 4644 2138 206 4175 2035 M14971 BIOCARTA_DEATH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DEATH_PATHWAY.html Induction of apoptosis through DR3 and DR4/5 Death Receptors 41/48 BioCarta 1.33534517119457e-07 7.20206492018647e-07 545 1825.09090909091 2140 1.21395022931518e-08 449 1.66078697581009 -1.60295474472896 -1 4.0525969488591 541 2703 2929 2973 517 716 449 2140 3454 2553 1101 2036 M19861 REACTOME_ENERGY_DEPENDENT_REGULATION_OF_MTOR_BY_LKB1_AMPK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENERGY_DEPENDENT_REGULATION_OF_MTOR_BY_LKB1_AMPK.html Genes involved in Energy dependent regulation of mTOR by LKB1-AMPK 21/41 Reactome 5.41201880789315e-07 1.1656955988727e-06 2145 2300.90909090909 2141 4.92001830841352e-08 1075 1.39138489063564 -1.43184933372461 -1 3.27007418947995 2141 3187 3607 2503 2027 2258 1710 1513 1075 3732 1557 2037 M7 PID_FCER1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FCER1_PATHWAY.html Fc-epsilon receptor I signaling in mast cells 18832364 78/97 Pathway Interaction Database 9.48435401745294e-08 6.60267713309408e-07 2040 2040.09090909091 2142 8.62214038757279e-09 188 1.55980818102724 -1.46606547940246 -1 3.8268217295119 2036 1632 2893 188 281 2811 2142 2695 3205 1956 2602 2038 M2102 STAMBOLSKY_TARGETS_OF_MUTATED_TP53_DN http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_TARGETS_OF_MUTATED_TP53_DN.html Genes repressed in SKBR3 cells (breast cancer) by mutated TP53 [GeneID=7157]. 20227041 86/125 Arthur Liberzon 1.17327032905305e-06 1.97427306706966e-06 1010 2307.90909090909 2142 1.06660995887645e-07 1007 1.64633629464227 -1.3357436607803 -1 3.72693560525634 1007 2142 2535 1705 2683 1370 1594 4711 1476 3316 2848 2039 M1840 KEGG_GLUTATHIONE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLUTATHIONE_METABOLISM.html Glutathione metabolism 43/58 KEGG 1.8682142499e-07 7.48955275608059e-07 4290 2544.45454545455 2143 1.69837673504235e-08 475 1.70745300784885 -1.57607414404458 -1 4.15620318650847 4287 475 2143 1633 884 3607 4221 4394 714 1514 4117 2040 M6413 RUTELLA_RESPONSE_TO_HGF_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_DN.html Genes down-regulated in peripheral blood monocytes by HGF [GeneID=3082]. 16527888 281/404 Arthur Liberzon 2.12912367667944e-07 7.70763712250053e-07 3635 2362.90909090909 2145 1.93556716612049e-08 1018 1.81670303145261 -1.67158922430775 -1 4.41622882599476 3634 1315 2145 1063 1018 2994 2617 3687 2052 1982 3485 2041 M6110 BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN.html Genes down-regulated in patients at the incipient stage of Alzheimer's disease. 14769913 259/311 John Newman 1.99391196633106e-07 7.65527859584926e-07 2060 2296.63636363636 2146 1.81264740640367e-08 935 1.81211902507116 2.24961724258627 1 4.40711662733378 2060 3851 2898 1327 935 2146 2870 1367 2347 4042 1420 2042 M4960 SMID_BREAST_CANCER_BASAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_BASAL_DN.html Genes down-regulated in basal subtype of breast cancer samles. 18451135 858/1156 Jessica Robertson 1.98417554702987e-23 1.48655691777476e-21 2770 1985.54545454545 2147 1.98417554702988e-24 36 2.31949215531134 -2.15392209511903 -1 19.3783766693816 2767 1091 4554 234 407 3053 3286 2627 1639 36 2147 2043 M12315 TSAI_DNAJB4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_DNAJB4_TARGETS_DN.html Genes down-regulated in CL1-5 cells (lung cancer) overexpressing DNAJB4 [GeneID=11080] off a plasmid vector. 16788156 8/9 Jessica Robertson 1.11520968913387e-06 1.90411881647541e-06 1895 2630.27272727273 2150 1.11521024879596e-07 1112 3.28481411565679 4.1435810372556 1 7.50663723839267 1891 1976 4630 3065 2719 3485 3990 1842 1112 2073 2150 2044 M1192 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 80/123 Arthur Liberzon 3.75124468112653e-07 9.58740773617983e-07 4330 2617.54545454545 2151 3.41022301886875e-08 226 2.00464341162467 2.22052730994314 1 4.80185936588983 4327 226 1281 987 1639 4571 3714 3971 2151 1418 4508 2045 M2904 SUNG_METASTASIS_STROMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SUNG_METASTASIS_STROMA_DN.html Genes down-regulated in metastatic vs non-metastatic stromal cells originated from either bone or prostate tissues. 19047182 60/67 Jessica Robertson 4.82762069369108e-06 6.40786548768895e-06 890 2026 2151 4.38875571574939e-07 804 1.69299161877331 1.70327615987606 1 3.4858447520635 890 2212 2698 3447 3489 804 1042 1516 2659 2151 1378 2046 M5536 TCGA_GLIOBLASTOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/TCGA_GLIOBLASTOMA_COPY_NUMBER_UP.html Genes up-regulated and displaying increased copy number in glioblastoma samples. 18772890 89/106 Jessica Robertson 4.99432015586642e-07 1.11141872398347e-06 4125 2612.90909090909 2151 4.54029208150012e-08 263 1.89304001980972 -1.95118023535973 -1 4.48288434487933 4122 2151 2915 1999 1948 4064 4512 1993 1157 3618 263 2047 M1821 MATZUK_EMBRYONIC_GERM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_EMBRYONIC_GERM_CELL.html Genes important for embryonic germ cell, based on mouse models with female fertility defects. 18989307 21/31 Jessica Robertson 0.00216352511331591 0.00224091255976543 2140 2426.36363636364 2151 0.00019687779111146 609 2.52050275726491 2.21539463694938 1 2.63570341953982 2138 3183 2151 2360 4520 2051 1936 2930 609 1947 2865 2048 M278 PID_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAC1_PATHWAY.html RAC1 signaling pathway 18832364 73/83 Pathway Interaction Database 8.82175381708292e-08 6.51622504172635e-07 1525 1979.54545454545 2152 8.01977651893217e-09 230 1.43012066761705 -1.16414955814928 -1 3.5077791927322 1525 291 3291 2487 230 1601 1286 3762 2796 2354 2152 2049 M6285 REACTOME_OPSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OPSINS.html Genes involved in Opsins 4/8 Reactome 5.61040887672636e-07 1.18755717431014e-06 3940 2636 2152 5.61041029317781e-08 1226 3.00150970305711 -3.19588870203102 -1 7.10240050719423 3938 1992 4242 3301 2152 2968 1226 1700 2111 2145 3221 2050 M1121 JOHANSSON_GLIOMAGENESIS_BY_PDGFB_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_GLIOMAGENESIS_BY_PDGFB_DN.html Genes down-regulated in brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 29/35 Arthur Liberzon 7.20457099959926e-06 9.16098467621458e-06 2315 2139.72727272727 2153 6.5496314484296e-07 697 1.92186075136511 -1.52586720774578 -1 3.84387114036327 2314 697 2153 1859 3655 2219 1603 4206 711 1769 2351 2051 M2493 PEDRIOLI_MIR31_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PEDRIOLI_MIR31_TARGETS_UP.html Genes up-regulated in primary LEC cells (lymphatic endothelum) upon overexpression of MIR31 [GeneID=407035]. 20479124 252/454 Arthur Liberzon 4.11560257218321e-07 1.00046055710989e-06 2310 2094.36363636364 2153 3.74145758372808e-08 818 2.1416511585041 -1.7741691314041 -1 5.1175303775132 2306 2048 860 3048 1742 1437 2193 3856 2153 818 2577 2052 M7871 ST_GRANULE_CELL_SURVIVAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GRANULE_CELL_SURVIVAL_PATHWAY.html Granule Cell Survival Pathway is a specific case of more general PAC1 Receptor Pathway. 37/47 Signaling Transduction KE 5.79995960514877e-07 1.21467931402889e-06 2155 2368.54545454545 2155 5.27269194019905e-08 1099 2.08967662164767 -1.91574479899917 -1 4.92130908991225 2155 2723 2053 2020 2092 1509 1099 3462 2591 3274 3076 2053 M19993 HUTTMANN_B_CLL_POOR_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUTTMANN_B_CLL_POOR_SURVIVAL_UP.html Up-regulated genes in B-CLL (B-cell chronic leukemia) patients expressing high levels of ZAP70 and CD38 [GeneID=7535;952], which are associated with poor survival. 16932341 364/551 Leona Saunders 3.64224531135505e-07 9.47297674322927e-07 3100 2206.09090909091 2155 3.31113264941178e-08 764 1.89898373029935 -1.65523289862988 -1 4.55011065591865 3099 1234 1003 1196 1601 2710 3311 4123 2155 764 3071 2054 M19877 KEGG_ENDOMETRIAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOMETRIAL_CANCER.html Endometrial cancer 56/61 KEGG 1.50009564650704e-07 7.26289540930751e-07 4000 2319.36363636364 2157 1.36372340799348e-08 171 1.73233655505243 1.99873307584174 1 4.22680073098931 3999 385 2157 503 634 3360 4257 1796 171 3775 4476 2055 M17283 REACTOME_G1_S_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_S_TRANSITION.html Genes involved in G1/S Transition 113/126 Reactome 9.83748554048892e-06 1.22159778350717e-05 205 2081.90909090909 2157 8.94320866355505e-07 205 1.3392101795687 1.42452722742418 1 2.59603998596305 205 2571 3811 1548 3745 580 679 1834 2403 3368 2157 2056 M1850 MATTHEWS_AP1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MATTHEWS_AP1_TARGETS.html Known targets of AP1 that were down-regulated by overexpression of TAM67, a dominant-negative form of JUN [GeneID=3725]. 17363560 20/22 Jessica Robertson 2.68533262325662e-07 8.34415403671576e-07 2485 2027.90909090909 2157 2.44121177366356e-08 1148 3.06247110392481 3.30547106057418 1 7.43643962931798 2482 3466 1148 2278 1270 2877 2861 1240 1251 2157 1277 2057 M11572 BROWNE_HCMV_INFECTION_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_12HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 12 h time point that were not up-regulated at the previous time point, 10 h. 11711622 174/220 John Newman 4.35625375121262e-06 5.86951195614682e-06 1105 2294.72727272727 2158 3.96023852465583e-07 1105 1.87583989261714 -1.87206671053462 -1 3.89648170467603 1105 3305 2672 1972 3428 1593 1201 2945 2158 2882 1981 2058 M18762 COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP.html 'Late-TGFB1 signature': genes overexpressed in primary hepatocytes at a late phase of TGFB1 [GeneID=7040] treatment; is associated with a more invasive phenotype. 18506891 138/156 Yujin Hoshida 7.00565375532108e-08 6.06161982149702e-07 3850 2462 2159 6.36877634400756e-09 135 1.86294998219775 1.57948701122201 1 4.60809114171079 3848 1538 1458 1396 135 4702 4337 3749 2159 910 2850 2059 M6590 MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP.html The 'NPM1-mutated signature 2': genes up-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to the AML cases with the intact gene and without recurring cytogenetic anomalities or M7 phenotype. 17597811 180/214 Arthur Liberzon 6.21823567445162e-07 1.26782170122728e-06 780 1891.90909090909 2160 5.65294312001677e-08 465 1.873487581658 2.09289399757856 1 4.39298331486044 780 3303 2388 2473 2160 777 1415 1294 3002 2754 465 2060 M16639 KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_DN.html Genes down-regulated in MEWO cells (melanoma) after 48h of methionine [PubChem=876] deprivation. 16908595 82/93 Arthur Liberzon 6.4290418592714e-07 1.30068913740939e-06 980 1702.18181818182 2160 5.84458521638705e-08 377 1.51303558379271 1.67663169602317 1 3.53139929285377 980 2160 3350 2504 2179 377 712 1077 2507 2430 448 2061 M15694 WATTEL_AUTONOMOUS_THYROID_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATTEL_AUTONOMOUS_THYROID_ADENOMA_DN.html Down-regulated genes characteristic for autonomous thyroid adenoma. 16027733 59/85 Arthur Liberzon 8.03496392147239e-08 6.29674606547497e-07 4640 2417.45454545455 2161 7.30451292266351e-09 329 3.00045482113332 3.14138323487166 1 7.43237004925128 4637 372 346 1341 329 4026 4711 4296 2161 533 3840 2062 M5125 KHETCHOUMIAN_TRIM24_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KHETCHOUMIAN_TRIM24_TARGETS_DN.html Retinoic acid-responsive genes down-regulated in hepatocellular carcinoma (HCC) samples of TRIM24 [GeneID=8805] knockout mice. 18026104 9/13 Leona Saunders 1.37613643470725e-06 2.23669558258204e-06 3020 2291.36363636364 2161 1.37613728689616e-07 469 2.89696881693022 2.24460709570186 1 6.53295197429559 3018 1013 4423 1056 2868 2161 469 1386 2981 1319 4511 2063 M19766 WU_SILENCED_BY_METHYLATION_IN_BLADDER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WU_SILENCED_BY_METHYLATION_IN_BLADDER_CANCER.html Genes silenced by DNA methylation in bladder cancer cell lines. 17456585 78/106 Jessica Robertson 3.03008527754374e-07 8.77601760597774e-07 1060 2257.81818181818 2162 2.75462335898268e-08 379 2.8113039912561 2.97559361924665 1 6.79766252603639 1056 2162 379 2153 3960 2176 3219 3790 3145 756 2040 2064 M18394 ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP.html Genes in discrete regions of gain within 16q region detected in individual invasive breast cancer tumors. 16702952 66/97 Arthur Liberzon 3.31542305056424e-07 9.06126045087621e-07 2690 2054.36363636364 2164 3.01402140927461e-08 330 1.79357009366167 1.91877989126339 1 4.30867355016618 2690 330 2384 2164 1505 2352 3165 1409 1822 2652 2125 2065 M11519 AMIT_SERUM_RESPONSE_40_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_40_MCF10A.html Genes whose expression peaked at 40 min after stimulation of MCF10A cells with serum. 17322878 40/49 Leona Saunders 8.52803308812718e-07 1.56721853588047e-06 1885 2173.27272727273 2166 7.75276035810686e-08 1028 2.57044666034413 -2.63253249635124 -1 5.95066098124938 1885 2711 1028 1509 2439 2632 2166 2780 3552 1448 1756 2066 M15743 ST_GA12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA12_PATHWAY.html G alpha 12 Pathway 44/52 Signaling Transduction KE 1.41335643453968e-07 7.20206492018647e-07 4195 2596.81818181818 2167 1.28486956848965e-08 527 1.95874297826478 2.16882840293176 1 4.78863623618839 4192 527 1840 1075 574 3618 4702 4199 2167 1602 4069 2067 M6382 KEGG_REGULATION_OF_AUTOPHAGY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_REGULATION_OF_AUTOPHAGY.html Regulation of autophagy 23/60 KEGG 2.42657732526319e-05 2.82243592292811e-05 1815 2756.54545454545 2168 2.20600371870391e-06 1373 1.27675592159523 -1.39557528822538 -1 2.28589570122839 1812 4025 3660 2983 4005 1957 2009 2168 2096 4234 1373 2068 M16702 REACTOME_ACTIVATED_AMPK_STIMULATES_FATTY_ACID_OXIDATION_IN_MUSCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_AMPK_STIMULATES_FATTY_ACID_OXIDATION_IN_MUSCLE.html Genes involved in Activated AMPK stimulates fatty-acid oxidation in muscle 23/44 Reactome 3.83185845551739e-05 4.37185687939137e-05 1925 2362.09090909091 2168 3.48356836244257e-06 916 1.36545426862452 -1.26729809261994 -1 2.34381851064952 1925 1872 3381 2920 4088 2339 1529 1215 916 3630 2168 2069 M838 REACTOME_UNBLOCKING_OF_NMDA_RECEPTOR_GLUTAMATE_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNBLOCKING_OF_NMDA_RECEPTOR_GLUTAMATE_BINDING_AND_ACTIVATION.html Genes involved in Unblocking of NMDA receptor, glutamate binding and activation 10/19 Reactome 1.36655529692426e-06 2.22188804735877e-06 1960 2094 2168 1.24232376888776e-07 1107 1.92898331547413 2.02679294100868 1 4.33556723479058 1956 2442 2168 2828 2790 1737 1421 2232 2792 1561 1107 2070 M2181 FIGUEROA_AML_METHYLATION_CLUSTER_7_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_7_DN.html Cluster 7 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 3/6 Arthur Liberzon 1.84686319381144e-05 2.18585613710883e-05 2760 2100.27272727273 2169 1.84687854305743e-06 36 4.0326858331032 3.96604118827541 1 7.50812535813397 2169 1062 4666 2756 3957 2757 2440 249 1317 1694 36 2071 M17386 REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY.html Genes involved in Costimulation by the CD28 family 55/72 Reactome 4.8242754196275e-08 4.96091067116379e-07 2660 2188.90909090909 2170 4.38570502310612e-09 49 1.59024349598335 -1.61536818073187 -1 3.98187163823329 2656 1699 2903 1311 49 2170 1863 3268 1472 2860 3827 2072 M2023 YIH_RESPONSE_TO_ARSENITE_C5 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C5.html Genes in cluster 5: slowly down-regulated in HFW cells (fibroblast) by sodium arsenite [PubChem=26435]. 12016162 13/17 Arthur Liberzon 2.33260081051404e-08 2.76773781599054e-07 2740 2201.36363636364 2170 2.12054621385998e-09 5 2.16544920438162 2.28588644865688 1 5.66095799610938 2736 2872 1936 3635 5 2683 1922 2170 3845 1733 678 2073 M155 PID_S1P_META_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_META_PATHWAY.html Sphingosine 1-phosphate (S1P) pathway 18832364 25/30 Pathway Interaction Database 4.76034113106735e-07 1.08023125666528e-06 1870 2571.90909090909 2173 4.32758378282381e-08 1830 1.9408113310525 1.89881931666425 1 4.60692167066926 3071 1841 1830 2641 1907 1870 2173 4197 2717 1867 4177 2074 M13438 STEARMAN_TUMOR_FIELD_EFFECT_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEARMAN_TUMOR_FIELD_EFFECT_UP.html Up-regulated genes in the 'Field Effect' signature of normal lung tissue adjacent to the tumor. 18172294 33/69 Jessica Robertson 5.92289797654219e-08 5.62496548275234e-07 2190 1834.54545454545 2173 5.38445285090911e-09 80 2.19467212662213 -2.48356468255705 -1 5.4661880603902 2187 644 1564 3067 80 2277 1787 2510 2657 1234 2173 2075 M17837 DASU_IL6_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_DN.html Genes down-regulated in normal fibroblasts in response to IL6 [GeneID=3569]. 15095275 13/15 Arthur Liberzon 2.05417179589252e-06 3.09469865196703e-06 3330 2056.18181818182 2174 1.86743064900447e-07 179 3.28501317459107 4.06885904121054 1 7.22844171777148 3330 2423 1701 1657 3050 4348 2302 1265 179 2174 189 2076 M7634 REACTOME_MITOTIC_M_M_G1_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_M_M_G1_PHASES.html Genes involved in Mitotic M-M/G1 phases 187/203 Reactome 2.33166278911456e-06 3.44566323250493e-06 55 1806.81818181818 2176 2.11969569120308e-07 52 1.52322157725445 1.62789172455931 1 3.29632735638111 52 3298 3620 2455 3118 226 206 1139 2176 2328 1257 2077 M7141 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP.html Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs moderately differentiated tumors. 18679425 145/165 Jessica Robertson 6.86026731751254e-08 6.05242275488957e-07 3360 2351.81818181818 2176 6.23660684676044e-09 126 1.87679981453726 1.94687886602303 1 4.64321905261858 3357 1513 2176 1383 126 2601 4129 4612 818 1949 3206 2078 M19751 MORI_SMALL_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_SMALL_PRE_BII_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Small Pre-BII stage. 18922927 115/144 Jessica Robertson 3.29356488399109e-07 9.05922275783096e-07 4230 2671.09090909091 2176 2.99415034278412e-08 1210 2.13448069052926 -1.91157224167261 -1 5.13723389500116 4227 3000 1416 1210 1496 4139 4088 1822 1711 2176 4097 2079 M12950 BIOCARTA_ACE2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACE2_PATHWAY.html Angiotensin-converting enzyme 2 regulates heart function 19/27 BioCarta 6.07424968103119e-06 7.83988474007853e-06 685 2204.81818181818 2177 5.52206041112414e-07 479 3.20766784049988 3.20888095106245 1 6.5363084065642 681 1881 479 1277 4506 2405 3741 3718 2709 679 2177 2080 M4113 SENESE_HDAC2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC2_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC2 [GeneID=3066] by RNAi. 17470557 137/166 Leona Saunders 2.21559773568249e-07 7.81002338493005e-07 1990 2204.63636363636 2177 2.01417996255739e-08 1061 2.00524903297894 2.02623325791549 1 4.87513722298587 1989 2108 2177 2672 1061 3112 3964 1091 1405 2218 2454 2081 M1583 VISALA_AGING_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_AGING_LYMPHOCYTE_DN.html Genes down-regulated in peripheral lymphocytes from old individuals compared to those from young donors. 12618007 26/31 John Newman 3.18540000557763e-06 4.47405970205427e-06 2995 2385.27272727273 2178 2.89582237977874e-07 1442 1.87909399403333 -1.87363289303073 -1 3.99242504296531 2992 1835 2178 1860 3283 2659 2164 3307 1442 1681 2837 2082 M8857 KIM_WT1_TARGETS_8HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_8HR_UP.html Genes up-regulated in UB27 cells (osteosarcoma) at 8 hr after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 244/284 Arthur Liberzon 6.13923928041538e-07 1.25698601298786e-06 1920 2348.09090909091 2179 5.58112817600876e-08 1302 1.87061286044653 2.27335223259269 1 4.38897017892986 1917 2956 2179 1302 2145 2747 3704 1439 2276 3236 1928 2083 M1492 BRUNO_HEMATOPOIESIS http://www.broadinstitute.org/gsea/msigdb/cards/BRUNO_HEMATOPOIESIS.html Genes that are rapidly down-regulated as multipotential cells of the FDCP-mix hematopoiesis model undergo differentiation and loose their self-renewal and proliferation properties. 14701746 81/112 Kevin Vogelsang 1.04901199662845e-07 6.88642089580849e-07 2780 1879.90909090909 2179 9.53647315134393e-09 328 2.06935237621146 -2.19914050534488 -1 5.07807187712395 2778 1630 1671 2299 328 2183 2202 2817 1278 2179 1314 2084 M1428 SANSOM_APC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS_UP.html Top genes up-regulated at day 5 of Cre-Lox induced APC [GeneID=324] knockout in the intestine. 15198980 181/216 Kevin Vogelsang 2.61858650313089e-06 3.77626895654684e-06 2650 2227.81818181818 2180 2.38053601813829e-07 1347 2.01938627177366 2.01443541415124 1 4.35403694636958 2650 2968 1379 2180 3194 1491 2388 1347 2030 1682 3197 2085 M11333 WEIGEL_OXIDATIVE_STRESS_BY_TBH_AND_H2O2 http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_BY_TBH_AND_H2O2.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to tert-butyl hydroperoxide (tBH) and H2O2 [PubChem=6410;784]. 12419474 81/118 John Newman 1.72361741275233e-06 2.67614282506283e-06 3515 2294.36363636364 2180 1.56692614831214e-07 1427 2.05465010242266 2.58330550598689 1 4.55452012584861 3512 2599 1427 1531 2942 1842 1981 1682 2530 2180 3012 2086 M4144 SAGIV_CD24_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAGIV_CD24_TARGETS_UP.html Genes up-regulated in HT29 cells (colon cancer) after knockdown of CD24 [GeneID=100133941] by both RNAi and monoclonal antibodies. 18413748 30/39 Jessica Robertson 1.87123726785179e-07 7.48978540381421e-07 1280 2482.81818181818 2180 1.70112493364746e-08 886 1.94788423138223 2.29075691270047 1 4.74848506315662 1279 3990 2828 4414 886 1920 2180 1313 4241 2818 1442 2087 M7405 HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_DN.html Genes down-regulated during differentiation from pre-BI to large pre-BII lymphocyte. 11779835 90/132 Arthur Liberzon 1.8557600834207e-07 7.48271685670965e-07 875 2171.27272727273 2180 1.68705476359923e-08 184 2.13698535510624 1.94518825564184 1 5.21467930228285 3626 184 1174 2598 872 3911 2821 1597 2180 871 4050 2088 M1226 OXFORD_RALA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_TARGETS_DN.html Genes down-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALA [GeneID=5898] by RNAi. 17496927 30/32 Arthur Liberzon 0.000118271381622804 0.000129162637959194 975 2311.27272727273 2181 1.07525218488747e-05 807 3.03880606312394 3.48303837210198 1 4.70250842866169 972 2756 807 1721 4285 2581 3641 3291 2033 1156 2181 2089 M1726 LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES.html Transcripts showing subcellular localization only to proximal dendrites in the adult mouse brain. 17151600 38/54 Jessica Robertson 9.45005234740371e-08 6.60267713309408e-07 2845 2060.09090909091 2182 8.59095704848064e-09 165 2.04663728952309 2.12916708996922 1 5.03682164204837 2843 559 1377 962 278 2182 3293 4627 165 2232 4143 2090 M1032 REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS.html Genes involved in APC/C:Cdc20 mediated degradation of mitotic proteins 73/85 Reactome 4.98326918710874e-05 5.62434972815716e-05 495 2464.72727272727 2183 4.53034733439355e-06 491 1.14663599002186 1.31031581463281 1 1.90974482273111 491 3354 3989 2547 4131 1080 838 1886 2125 4488 2183 2091 M19929 BROWNE_HCMV_INFECTION_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_48HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 48 h time point that were not up-regulated at the previous time point, 24 h. 11711622 261/381 John Newman 5.43712650827185e-07 1.16813306373779e-06 3135 2455.09090909091 2184 4.94284350183205e-08 1575 1.77191737463898 -1.80015862858206 -1 4.17745128230714 3133 2046 2083 1873 2033 3018 3063 3284 2714 1575 2184 2092 M19610 CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_UP.html Marker genes up-regulated in the 'unannotated' subclass of hepatocellular carcinoma (HCC) samples. 18701503 102/161 Yujin Hoshida 9.82670192397095e-08 6.68315649405766e-07 2055 2088 2185 8.93336578445327e-09 300 2.11819852122647 -2.04657252205244 -1 5.2102029381708 2052 3322 2212 2330 300 2571 2185 1519 2013 1872 2592 2093 M1624 DELASERNA_TARGETS_OF_MYOD_AND_SMARCA4 http://www.broadinstitute.org/gsea/msigdb/cards/DELASERNA_TARGETS_OF_MYOD_AND_SMARCA4.html Genes up-regulated in NIH 3T3 cells (fibroblasts) 24 h after inducing MYOD [GeneID=4654] which were down-regulated by dominant negative form of SMARCA4 [GeneID=6597]. 15870273 12/24 John Newman 1.94702815214357e-05 2.29691898978197e-05 3650 2303.27272727273 2186 1.77004125800488e-06 205 2.48892027482448 -1.10256578141329 -1 4.59321610408253 3648 2880 1688 2186 4236 2915 1476 205 949 1966 3187 2094 M2186 PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_DN http://www.broadinstitute.org/gsea/msigdb/cards/PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_DN.html Genes down-regulated in ovarian tumors from mouse models for the BMP SMAD signaling (gonad specific double knockout of SMAD1 and SMAD5 [GeneID=4086, 4090]). 17967875 192/257 Arthur Liberzon 7.74348681430913e-07 1.46548748049475e-06 1920 2296.54545454545 2187 7.03953594530654e-08 1811 1.75345614218408 1.76904059410916 1 4.06395364730618 1918 2072 2763 1868 2351 1938 2187 1811 3409 2296 2649 2095 M2252 CERIBELLI_PROMOTERS_INACTIVE_AND_BOUND_BY_NFY http://www.broadinstitute.org/gsea/msigdb/cards/CERIBELLI_PROMOTERS_INACTIVE_AND_BOUND_BY_NFY.html Transcriptionally inactive genes whose promoters (regions between -2 kb to +0.5 kb relative to trascription start sites) where bound by NF-Y transcription factor. 18212061 30/92 Arthur Liberzon 2.12418715576964e-07 7.70763712250053e-07 3745 2528.18181818182 2188 1.93107941897123e-08 661 2.69848289992627 -2.57923645425906 -1 6.58403686935023 3745 3135 1567 2159 1014 4284 4361 2174 661 2188 2522 2096 M2254 CERIBELLI_GENES_INACTIVE_AND_BOUND_BY_NFY http://www.broadinstitute.org/gsea/msigdb/cards/CERIBELLI_GENES_INACTIVE_AND_BOUND_BY_NFY.html Transcriptionally inactive genes which where bound by NF-Y transcription factor. 18212061 30/65 Arthur Liberzon 1.757341255933e-06 2.71510662127783e-06 4245 2651.09090909091 2189 1.59758423607617e-07 830 2.01688983779199 1.9084485455152 1 4.46480592365344 4244 1810 1681 1777 2958 3974 4035 1855 830 2189 3809 2097 M9291 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_16 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_16.html Amplification hot spot 16: colocolized fragile sites and cancer genes in the 8q11.1-q24.3 region. 16751803 12/15 Arthur Liberzon 8.41485304497395e-06 1.05464966469137e-05 2190 2169.63636363636 2190 7.64989566490646e-07 324 1.64675629247276 1.34134790602812 1 3.24597026691801 2190 2886 2871 3394 3707 1381 324 1459 2186 2972 496 2098 M1342 FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_DN.html Genes commonly down-regulated in both non-tumorous and tumorous liver tissues of PARK2 [GeneID=5071] knockout mice. 18574468 10/15 Jessica Robertson 2.4154005230593e-05 2.81220781175133e-05 1165 2519.63636363636 2190 2.19584276579508e-06 1162 1.70558329723063 -1.80999028427395 -1 3.07155310757705 1162 2895 2190 3346 4001 1529 1460 3014 3984 2012 2123 2099 M14365 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP.html All common up-regulated stress response genes (Human Environmental Stress Response, H-ESR). 15897889 96/114 Jessica Robertson 2.49495948460565e-06 3.63463233559836e-06 1775 2257.09090909091 2190 2.26814755825006e-07 857 2.43738174623458 2.73795105672959 1 5.28191621907019 1774 2134 857 893 3160 2874 3571 2719 2190 1826 2830 2100 M19270 PARK_TRETINOIN_RESPONSE_AND_PML_RARA_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/PARK_TRETINOIN_RESPONSE_AND_PML_RARA_FUSION.html Genes up-regulated by tretinoin (ATRA) [PubChem=444795] in U937 cells (acute promyelocytic leukemia, APL) made sensitive to the drug by expression of the PML-RARA fusion [GeneID=5371;5914]. 12893766 35/43 Arthur Liberzon 1.00524214151462e-06 1.75861486580764e-06 1560 2111 2190 9.13856909853128e-08 513 2.17426752624626 -2.37880253998318 -1 4.98202590929648 1556 3967 2316 4149 2572 1534 850 713 2861 2190 513 2101 M17395 KEGG_LIMONENE_AND_PINENE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LIMONENE_AND_PINENE_DEGRADATION.html Limonene and pinene degradation 13/14 KEGG 6.76975243144766e-07 1.34257275111063e-06 1705 2169.18181818182 2191 6.15432228600893e-08 448 1.70474318407063 1.4885945114371 1 3.97574490453519 1703 956 2191 2456 2233 1177 448 3959 3677 3137 1924 2102 M2527 BOSCO_TH1_CYTOTOXIC_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_TH1_CYTOTOXIC_MODULE.html Genes representing Th1 / cytotoxic module in sputum during asthma exacerbations. 20336062 104/233 Antony Bosco 2.24355042197138e-07 7.84779759379662e-07 3620 2035.09090909091 2191 2.03959150069791e-08 100 2.34366453221617 2.71150541016102 1 5.70435837336557 3616 100 432 1342 1509 4165 3768 2197 2191 282 2784 2103 M11650 BIOCARTA_NOS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NOS1_PATHWAY.html Nitric Oxide Signaling Pathway 21/27 BioCarta 6.50511163855139e-07 1.30791290081906e-06 2145 2236.36363636364 2193 5.91373960184403e-08 849 1.4684929392456 1.52650785272732 1 3.42454395384877 2145 849 2659 3176 2193 1406 944 3746 4292 2301 889 2104 M13334 WU_ALZHEIMER_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_ALZHEIMER_DISEASE_DN.html Genes down-regulated in brain endothelial cells from patients with Alzheimer disease. 16116430 29/44 Jessica Robertson 1.2013547972023e-05 1.46711374975288e-05 1865 2586.09090909091 2193 1.09214668863177e-06 1863 2.20757788906482 2.08821828820243 1 4.24119158334043 1863 3155 2062 2193 3809 1953 2057 3249 3749 2370 1987 2105 M549 REACTOME_DOWNREGULATION_OF_ERBB2_ERBB3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNREGULATION_OF_ERBB2_ERBB3_SIGNALING.html Genes involved in Downregulation of ERBB2:ERBB3 signaling 16/19 Reactome 5.11705038333675e-07 1.12704049506997e-06 3180 2247.90909090909 2194 4.65186506684387e-08 666 1.76091895653851 -1.90669901713225 -1 4.16222504546307 3177 918 2194 1977 1968 3014 2391 2735 666 3552 2135 2106 M8825 DORN_ADENOVIRUS_INFECTION_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_24HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 24 h after infection with adenovirus Ad12. 15681441 76/104 Arthur Liberzon 1.53058173549763e-06 2.42753554823548e-06 1210 2062.54545454545 2194 1.39143890941219e-07 401 2.16477377525464 2.51428426017343 1 4.83817585851746 1208 3037 1445 2241 2877 1257 3222 1714 3092 2194 401 2107 M2439 HUANG_GATA2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_GATA2_TARGETS_DN.html Genes down-regulated in G1ME cells (megakaryocyte/erythroid progenitor lacking GATA1 [GeneID=2623]) upon knockdown of GATA2 [GeneID=2624] by RNAi. 19620289 82/97 Arthur Liberzon 6.75472884303014e-07 1.34078461407703e-06 1860 2215.18181818182 2194 6.14066446996051e-08 1589 2.07023354151578 2.24727199565144 1 4.83933893969126 1858 2603 1589 2367 2230 1929 2194 2007 2080 2631 2879 2108 M2616 ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY.html Genes transiently induced only by the second pulse of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 1222/2731 Yaara Zwang 3.58066216376811e-32 4.97080159205456e-30 3255 2311.27272727273 2196 3.58066216376812e-33 22 2.48253672666449 2.61650032010006 1 29.2060958574093 3102 1074 4718 518 913 2196 4208 3252 2169 22 3252 2109 M836 OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_UP.html Genes up-regulated in pirmary cultures of epithelial ovarian cancer (EOC): invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 84/95 Leona Saunders 5.81046086371494e-07 1.21525740803517e-06 3720 2327 2197 5.28223854393374e-08 217 1.69411481819487 1.48099597780616 1 3.98012571689726 3717 217 2518 1887 2095 2484 1647 3246 1239 2197 4350 2110 M220 PID_CASPASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CASPASE_PATHWAY.html Caspase cascade in apoptosis 18832364 63/81 Pathway Interaction Database 2.74848377588219e-07 8.38703759494626e-07 1940 2235.36363636364 2198 2.4986219265939e-08 1299 1.91431903186365 -1.72716827357143 -1 4.62796815845202 1937 2198 2291 2687 1299 1796 1507 3781 1462 3091 2540 2111 M1386 KEGG_PENTOSE_PHOSPHATE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_PHOSPHATE_PATHWAY.html Pentose phosphate pathway 28/33 KEGG 0.000521344396537014 0.000550010181415893 1580 2634.54545454545 2200 4.74061802714484e-05 1577 1.28460897318642 -1.38510140019927 -1 1.63395401592429 1577 2332 3571 3178 4441 2023 1910 1850 1921 3977 2200 2112 M12428 MCBRYAN_PUBERTAL_BREAST_4_5WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_4_5WK_DN.html Genes down-regulated during pubertal mammary gland development between week 4 and 5. 17486082 257/319 Arthur Liberzon 2.93762480126744e-07 8.6694222517255e-07 3860 2657.18181818182 2200 2.67056835774896e-08 1352 1.90726247958682 -1.61125159633255 -1 4.59969305934343 3856 1352 2111 2151 1365 3435 2536 4041 2023 2200 4159 2113 M2349 BIOCARTA_CCR5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CCR5_PATHWAY.html Pertussis toxin-insensitive CCR5 Signaling in Macrophage 20/27 BioCarta 1.04681660675366e-05 1.29480460793429e-05 3955 2435.72727272727 2201 9.51655988917822e-07 466 2.04300992486119 -2.46451210833562 -1 3.96587476883755 3952 825 1761 466 3759 4432 4043 2708 831 1815 2201 2114 M2145 DEMAGALHAES_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/DEMAGALHAES_AGING_DN.html Genes consistently underexpressed with age, based on meta-analysis of microarray data. 19189975 28/35 Joao Pedro de Magalhaes 0.000305754067833296 0.000326358932648837 525 2163.54545454545 2201 2.77996881395392e-05 523 2.33838150257663 2.65986189037366 1 3.22850924782084 523 2765 1367 1535 4390 1750 2201 2893 2801 2238 1336 2115 M2238 JOHNSTONE_PARVB_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_2_UP.html Genes up-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D collagen I and 3D Matrigel only. 17998334 206/250 Arthur Liberzon 2.0669343213503e-07 7.68728418959517e-07 3020 2460.63636363636 2203 1.87903137776548e-08 981 1.77542185160467 -1.34667785877542 -1 4.31556119163721 3016 2063 1739 1711 981 2332 2267 4515 2092 2203 4148 2116 M2620 ZWANG_EGF_INTERVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_INTERVAL_DN.html Genes repressed in the time interval between two pulses of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 255/310 Yaara Zwang 6.83569641227597e-08 6.05242275488957e-07 2835 2262.90909090909 2203 6.21426965879115e-09 124 1.89652339865068 -1.72856270946784 -1 4.69254121963295 2832 1349 1607 3289 124 2552 3591 3785 1933 1627 2203 2117 M19888 KEGG_ACUTE_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ACUTE_MYELOID_LEUKEMIA.html Acute myeloid leukemia 64/71 KEGG 1.77886140855278e-06 2.7411772276752e-06 2125 2460.36363636364 2204 1.61714804263124e-07 1323 1.42468741682459 -1.37928164690822 -1 3.13677257928586 2122 2204 3433 1323 2969 2083 1439 2772 2034 3701 2984 2118 M6487 BIOCARTA_PLATELETAPP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLATELETAPP_PATHWAY.html Platelet Amyloid Precursor Protein Pathway 21/29 BioCarta 0.000123802410850377 0.00013495320536115 140 1955.27272727273 2204 1.12553980212969e-05 137 2.83794450395894 2.83794450395894 1 4.3666328952267 137 2800 640 2204 4458 1204 2274 2783 2950 872 1186 2119 M3618 BIOCARTA_TNFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR1_PATHWAY.html TNFR1 Signaling Pathway 33/35 BioCarta 6.53487829727398e-07 1.3097505546978e-06 1840 2125.63636363636 2204 5.9408002167223e-08 1243 1.56338351985026 -1.44844610239779 -1 3.64867988220216 1839 2306 3308 2902 2204 1492 1443 1548 1243 2851 2246 2120 M5955 COLLER_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/COLLER_MYC_TARGETS_UP.html Genes up-regulated in 293T (transformed fetal renal cell) upon expression of MYC [GeneID=4609]. 10737792 29/35 Yujin Hoshida 6.72278174309507e-05 7.48208673129185e-05 600 2488.09090909091 2204 6.11180653392112e-06 598 1.53119867010898 1.63756400445015 1 2.49069582371612 598 3987 3225 3746 4191 1394 1180 1246 1982 3616 2204 2121 M1168 SHIRAISHI_PLZF_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHIRAISHI_PLZF_TARGETS_UP.html Genes up-regulated in A375 and 397 cells (melanoma) by forced expression of PLZF [GeneID=7704] off adenovirus vector. 16862184 15/17 Arthur Liberzon 4.65884498590445e-06 6.21354855424385e-06 1155 2138.81818181818 2205 4.23532259251684e-07 309 1.77184495747328 -1.8551493175449 -1 3.66006282525128 1155 2857 2205 3840 3469 1113 1642 492 3434 3011 309 2122 M6815 AMIT_EGF_RESPONSE_60_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_60_MCF10A.html Genes whose expression peaked at 60 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 56/58 Leona Saunders 3.3501488552565e-07 9.11513192862964e-07 3990 2579.09090909091 2205 3.04559033219598e-08 724 2.74312293001998 -2.56199714474013 -1 6.61342454396706 3987 1694 724 2148 1513 3684 2313 4620 2205 1122 4360 2123 M11350 KYNG_DNA_DAMAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_DN.html Genes with GO annotation and down-regulated after DNA damage in cell lines from young donors. 15897889 289/346 Jessica Robertson 7.02334080471112e-07 1.37329085443823e-06 1525 2069.36363636364 2205 6.38485731532986e-08 870 2.1817211206559 2.411451607827 1 5.09351675249319 1523 3282 870 2205 2266 1783 2432 2179 2739 1169 2315 2124 M18356 XU_HGF_TARGETS_INDUCED_BY_AKT1_6HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_INDUCED_BY_AKT1_6HR.html Genes changed in DU-145 cells (prostate cancer) in the absence but not presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 6 h. 17099727 27/36 Arthur Liberzon 6.80470798206135e-07 1.34664752450998e-06 980 2296.72727272727 2206 6.18610007890167e-08 977 2.17134904767801 -2.31077084959866 -1 5.07649387945927 977 3737 2206 3371 2238 1411 1056 2828 3857 2110 1473 2125 M1445 GUO_HEX_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUO_HEX_TARGETS_DN.html Genes down-regulated in day 6 embryoid bodies derived from embryonic stem cells (ES) with HEX [GeneID=3087] knockout. 12791650 80/106 Kevin Vogelsang 1.4736844291114e-06 2.35709607096096e-06 1395 2301.09090909091 2206 1.33971401479046e-07 1191 2.23123038614553 2.31680689732093 1 4.99971475891378 1394 3344 1743 3128 2848 1246 1191 2206 3901 2092 2219 2126 M17728 BLALOCK_ALZHEIMERS_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_DN.html Genes down-regulated in brain from patients with Alzheimer's disease. 14769913 1572/1930 John Newman 2.51919303441965e-07 8.19550616410033e-07 1395 2521 2207 2.51919332000469e-08 1309 1.68165272129151 1.83134277799072 1 4.0661886012312 1393 4124 4490 2257 1309 1592 1856 1520 2207 4613 2370 2127 M1122 HUMMERICH_BENIGN_SKIN_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_BENIGN_SKIN_TUMOR_UP.html Genes up-regulated in benign skin tumors (papilloma) induced by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 18/33 Leona Saunders 9.08640118000518e-07 1.63552999490983e-06 4465 2056.18181818182 2208 8.26036812077884e-08 649 3.06512943736258 -2.69752894602769 -1 7.08265585670927 4462 869 1038 1148 2498 3806 2490 832 649 2208 2618 2128 M1337 RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_DN http://www.broadinstitute.org/gsea/msigdb/cards/RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_DN.html Angiogenic genes down-regulated in hepatocytes after knockout of VHL and HIF2A [GeneID=7428;2034]. 18490920 18/22 Jessica Robertson 5.0093554482079e-05 5.65108932015805e-05 1385 1966.36363636364 2209 4.55406319441199e-06 388 1.87462619165499 2.21819687284615 1 3.15244211870496 1384 3197 2308 2220 4133 994 829 392 3576 2209 388 2129 M1362 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_UP.html Early prostate development genes (up-regulated at 12 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 18/20 Jessica Robertson 0.000126347908065004 0.000137569117893154 1215 2284.36363636364 2210 1.14868331744025e-05 395 2.34265337320216 2.196260391482 1 3.58796011229875 1212 2831 1697 3451 4294 1070 395 3006 4054 2210 908 2130 M7739 BIOCARTA_PYK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PYK2_PATHWAY.html Links between Pyk2 and Map Kinases 43/47 BioCarta 1.64545804095985e-07 7.3358205358541e-07 2380 2199.18181818182 2211 1.49587105820864e-08 509 1.34802415127809 -1.4395756180204 -1 3.27564796872934 2380 1753 3461 509 724 2963 1571 2873 2211 3893 1853 2131 M1835 KEGG_GLIOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLIOMA.html Glioma 66/75 KEGG 1.98251656187454e-07 7.65527859584926e-07 2860 1915.81818181818 2213 1.80228794593439e-08 185 1.93702518192987 1.97666869693938 1 4.71434034931714 2860 287 1910 185 930 2242 2886 3223 472 2213 3866 2132 M13014 ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN.html Genes down-regulated in liver tumor compared to the normal adjacent tissue. 18413731 287/408 Jessica Robertson 1.09287632367761e-07 7.03734822340835e-07 2755 1982.72727272727 2214 9.93523979970503e-09 347 2.17563170001238 -2.07876994098545 -1 5.33320695368322 2755 2520 867 590 347 1662 2327 4390 2669 2214 1469 2133 M3346 RODRIGUES_NTN1_AND_DCC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_NTN1_AND_DCC_TARGETS.html Genes down-regulated in HCT8/S11 cells (colon cancer) which lack DCC [GeneID=9423] and stably express NTN1 [GeneID=1630]. 17334389 48/49 Leona Saunders 5.70766608192254e-08 5.52052948907262e-07 2200 2229.90909090909 2215 5.18878748181991e-09 73 1.80818411318058 -1.83457498066844 -1 4.5006837126398 2196 517 2369 3341 73 2079 1523 3761 3368 2215 3087 2134 M18761 SMITH_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SMITH_LIVER_CANCER.html Potential marker genes specifically up-regulated in the majority of hepatocellular carcinoma (HCC) tumors. 12591738 57/66 Yujin Hoshida 3.05699765094792e-07 8.80936447462993e-07 2005 2423.45454545455 2215 2.77908915975582e-08 1409 1.58468872825807 1.76226317178394 1 3.80885590797654 2262 2215 3011 2001 1409 1871 2001 4051 2407 3654 1776 2135 M12922 REACTOME_REGULATION_OF_RHEB_GTPASE_ACTIVITY_BY_AMPK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_RHEB_GTPASE_ACTIVITY_BY_AMPK.html Genes involved in Regulation of Rheb GTPase activity by AMPK 13/32 Reactome 0.00011017851556298 0.000120603569911239 1975 2389.72727272727 2216 1.00167303469027e-05 678 1.7208138192832 -1.73591560711817 -1 2.66183920772444 1973 3504 3253 2481 4271 2216 1344 1552 678 3571 1444 2136 M13831 BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G123, defined by unsupervised clustering. 17187432 58/69 Yujin Hoshida 1.13244103063075e-06 1.92547610395431e-06 820 2136.72727272727 2216 1.02949237595507e-07 444 1.48492716075207 1.34435798314801 1 3.36312667360881 819 2216 3217 3919 2653 618 444 2152 2700 3357 1409 2137 M8565 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN.html Genes from the grey module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 77/102 Arthur Liberzon 1.46398259311724e-06 2.34396127527591e-06 1930 2227 2217 1.33089415210949e-07 695 1.90851844011064 1.8593517982323 1 4.27121124107724 1930 1645 2217 3321 2846 1566 2895 695 3352 2262 1768 2138 M14553 LIANG_SILENCED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_SILENCED_BY_METHYLATION_UP.html Genes up-regulated in LD419 cells (fibroblast) after treatment with decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 11861364 48/98 John Newman 1.80283303949886e-05 2.13627963252269e-05 4130 2509.63636363636 2217 1.63895255757854e-06 448 3.20893094581297 3.49714642240134 1 5.97708091576004 4128 510 719 448 3922 4047 4474 1093 1551 2217 4497 2139 M656 REACTOME_SYNTHESIS_OF_PE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PE.html Genes involved in Synthesis of PE 9/12 Reactome 9.92274487186689e-07 1.74238674833377e-06 1130 2160.54545454545 2219 9.92274930260862e-08 244 1.47659099849728 -1.68257147885452 -1 3.36973400571619 1129 3805 4212 4350 2632 961 244 445 2219 3454 315 2140 M12123 REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS.html Genes involved in Effects of PIP2 hydrolysis 20/25 Reactome 1.37974483910461e-06 2.24178851654863e-06 2255 1993.18181818182 2219 1.25431427674696e-07 884 1.93292735400923 -1.3960481810658 -1 4.34152387106697 2254 3464 2219 2868 2791 1801 884 973 920 2511 1240 2141 M1376 GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN.html Genes down-regulated in MMH-RT cells (hepatocytes displaying an invasive, metastatic phenotype) during epithelial to mesenchymal transition (EMT). 16607286 271/350 Jessica Robertson 2.08515796005031e-07 7.70105287279928e-07 4360 2447.63636363636 2219 1.89559832516493e-08 457 2.13721475796907 2.16177516010142 1 5.20450855408816 4357 1320 973 457 993 3395 3737 3830 1234 2219 4409 2142 M5823 BROWNE_HCMV_INFECTION_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_1HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 1 h time point that were not up-regulated at the previous time point, 30 min. 11711622 81/179 Arthur Liberzon 1.05217397625278e-07 6.89758495543491e-07 2225 1754.63636363636 2220 9.56521842340141e-09 208 2.20703501362656 2.27755105462014 1 5.41864193141525 2224 208 790 828 330 2220 2718 2622 2392 1010 3959 2143 M19927 TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C http://www.broadinstitute.org/gsea/msigdb/cards/TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C.html Genes down-regulated in HCT116 cells (colon cancer) upon expression of MIR34B or MIR34C [GeneID=407041;407042] microRNAs. 18519671 589/723 Leona Saunders 1.10191016182277e-06 1.88510908437967e-06 1495 2393.90909090909 2221 1.10191070821586e-07 1491 1.57684274369703 1.65795226330015 1 3.58023346320712 1491 2494 4560 1959 2706 1512 1776 2221 1988 3345 2281 2144 M12763 RAMALHO_STEMNESS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMALHO_STEMNESS_DN.html Genes depleted in embryonic, neural and hematopoietic stem cells. 12228720 103/149 John Newman 6.68139120923664e-07 1.33120162547898e-06 2085 2227.81818181818 2222 6.07399385306666e-08 91 2.05291947992643 2.32120894582551 1 4.80101934600974 2085 91 811 2133 2222 2260 3522 3861 3517 836 3168 2145 M14371 NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN.html Down-regulated genes in peripheral zone of human pancreatic cancer growing in the pancreas of nude mice compared to that of the tumor from the central zone. 17699763 846/1057 Arthur Liberzon 3.7681009147959e-07 9.5981847370948e-07 2300 2404.54545454545 2223 3.76810155373236e-08 1558 1.91713962659492 -1.77073700139971 -1 4.58969524307104 2298 1998 4274 1702 1752 1558 2223 3942 2266 2024 2413 2146 M10236 BORCZUK_MALIGNANT_MESOTHELIOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BORCZUK_MALIGNANT_MESOTHELIOMA_UP.html Genes up-regulated in biphasic (mixed) vs epithelial subtypes of malignant peritoneal mesothelioma. 16862182 420/473 Arthur Liberzon 6.69996098374878e-07 1.33377544678592e-06 880 2744.45454545455 2224 6.09087547652767e-08 880 1.21117087770859 1.313705299738 1 2.81155559961973 880 4134 4174 3281 2224 1585 1630 1724 3853 4600 2104 2147 M14954 KIM_RESPONSE_TO_TSA_AND_DECITABINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_RESPONSE_TO_TSA_AND_DECITABINE_DN.html Genes down-regulated in glioma cell lines treated with both decitabine [PubChem=451668] and TSA [PubChem=5562]. 16885346 13/19 Arthur Liberzon 4.47076701690825e-08 4.70636656673264e-07 2225 1993.18181818182 2225 4.06433373432882e-09 38 0.945889546830732 -0.904957038506497 -1 2.35687633846801 2225 947 3209 2855 38 2353 1545 861 3787 3573 532 2148 M4163 PALOMERO_GSI_SENSITIVITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/PALOMERO_GSI_SENSITIVITY_UP.html Up-regulated genes associated with sensitivity and resistance to gamma-secretase (GSI) in T-cell acute lymphoblastic leukemia (T-ALL) cell lines. 17873882 9/9 Jessica Robertson 3.55062260568149e-06 4.90744910653488e-06 2295 2024.45454545455 2225 3.55062827880865e-07 14 2.18498312797855 2.46118685931162 1 4.61519500968541 2295 1007 4594 1410 3389 2225 1398 2257 14 2900 780 2149 M1998 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS.html Genes trans-regulated by the hematopoietic stem cell (HSC) proliferation QTL (quantitative trait locus) Scp2. 15711547 45/62 Arthur Liberzon 4.21010997263845e-05 4.78260386783478e-05 1010 2375.72727272727 2225 3.82744594826999e-06 1006 2.58753205188463 2.81119690554827 1 4.4457306538971 1006 3096 1161 2225 4104 1912 3175 2944 3272 1698 1540 2150 M1513 LEE_CALORIE_RESTRICTION_NEOCORTEX_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_NEOCORTEX_UP.html Up-regulated in the neocortex of aged (30-month) mice subjected to caloric restriction since young adulthood. 10888876 123/187 John Newman 5.31659844829339e-07 1.15006162584532e-06 4520 2731 2226 4.83327248465633e-08 38 1.64878538063258 -1.26866932113233 -1 3.88816947491777 4517 38 2226 1524 2010 4385 4470 1851 3929 2185 2906 2151 M15940 NAKAMURA_METASTASIS_MODEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_METASTASIS_MODEL_DN.html Bottom genes down-regulated in subcutaneous tumors from highly metastatic pancreatic cancer cells. 17210693 51/63 Jessica Robertson 2.17808830181567e-07 7.76784911772201e-07 3820 2467.18181818182 2226 1.98008047041381e-08 1042 2.06352135969241 2.23414423155274 1 5.02021375593709 3817 2226 1574 1631 1042 4581 2947 3754 2256 1403 1908 2152 M19891 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_12 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_12.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 12. 12554760 97/134 Arthur Liberzon 6.72920627633139e-07 1.33846833646372e-06 1675 2109.36363636364 2226 6.11746212237716e-08 152 1.80217301123353 1.99028121870693 1 4.20679095502205 1671 152 2697 2648 2226 1221 1494 3378 1916 3266 2534 2153 M2334 BILANGES_SERUM_SENSITIVE_VIA_TSC2 http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_SENSITIVE_VIA_TSC2.html Genes translationally up-regulated by serum in MEF cells (embryonic fibroblast) lacking TSC2 [GeneID=7249]. 17562867 74/98 Arthur Liberzon 3.94794591309157e-06 5.38252591270717e-06 1175 2336.18181818182 2226 3.58904817980064e-07 1174 2.1259444350592 2.24600660435752 1 4.45482912069064 1174 3038 1237 2226 3392 1977 2771 3397 3669 1231 1586 2154 M14833 GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP.html Up-regulated genes from the set B (Fig. 5a): specific signature shared by cells expressing either AF4-MLL or MLL-AF4 [GeneID=4299;4297] fusion proteins. 17130830 46/59 Arthur Liberzon 3.12042509253203e-06 4.3991656023749e-06 825 2111.18181818182 2228 2.83675410770353e-07 386 2.46352572868079 2.53060932919172 1 5.25696640740081 823 2228 448 1235 3958 2361 3273 3208 3090 386 2213 2155 M10462 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY.html Adipocytokine signaling pathway 70/102 KEGG 9.6779578926139e-07 1.71342690371859e-06 1140 2134.27272727273 2229 8.79814740910877e-08 1072 1.73600176649191 -1.37288952457562 -1 3.97560880198635 1138 3046 2804 2229 2544 1072 1108 1157 3202 3179 1998 2156 M2104 STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_DN http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_DN.html Genes repressed in SKBR3 cells (breast cancer) by 25-hydroxyvitamin D3 [PubChem=1593]. 20227041 52/61 Arthur Liberzon 1.74865464787597e-06 2.70509901010904e-06 1315 2150.90909090909 2231 1.58968730707587e-07 842 2.46949047040155 2.80326497091445 1 5.47955305013027 1312 2231 842 2679 2955 1940 2421 3080 3537 1024 1639 2157 M6698 RAMASWAMY_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMASWAMY_METASTASIS_UP.html Up-regulated genes in metastatic vs primary solid tumors. 12469122 92/101 John Newman 5.59375348617062e-06 7.29754462540777e-06 515 1953.09090909091 2232 5.08524337180364e-07 512 1.95937711642593 2.07733636502853 1 3.99770934324231 512 3018 2740 2232 3549 701 871 1872 2279 2566 1144 2158 M19 PID_P73PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P73PATHWAY.html p73 transcription factor network 18832364 102/123 Pathway Interaction Database 5.74930532706777e-07 1.20768674427058e-06 2235 1977 2233 5.22664257231467e-08 684 1.98683876604747 2.27768591356673 1 4.67866099453392 2233 2579 2068 1517 2088 2371 2414 938 684 2347 2508 2159 M4359 SWEET_KRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_KRAS_TARGETS_DN.html Genes upregulated in control vs KRAS [GeneID=3845] knockdown in a human cell line. 15608639 95/144 Aravind Subramanian 2.21078636211263e-07 7.79888761522542e-07 3595 2444 2233 2.00980598570475e-08 1060 2.01858565718225 -2.28290611513861 -1 4.908396901185 3591 1603 1541 1484 1060 3705 2824 4224 1295 2233 3324 2160 M10154 SA_G2_AND_M_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/SA_G2_AND_M_PHASES.html Cdc25 activates the cdc2/cyclin B complex to induce the G2/M transition. 13/13 SigmaAldrich 1.2850830840906e-05 1.5608832107328e-05 2235 2174.18181818182 2235 1.16826417335525e-06 824 1.85398603288614 1.94685017308922 1 3.53379585941327 2235 2417 2666 1978 3829 1899 1311 824 1340 2637 2780 2161 M65 PID_FRA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FRA_PATHWAY.html Validated transcriptional targets of AP1 family members Fra1 and Fra2 18832364 54/66 Pathway Interaction Database 6.27005082634017e-06 8.06613243399444e-06 1725 2153.18181818182 2235 5.70006245109198e-07 489 3.04027546036226 2.98803223011843 1 6.17749242417225 1722 3063 489 614 3604 2603 4348 2235 2640 865 1502 2162 M3898 ENK_UV_RESPONSE_KERATINOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_KERATINOCYTE_DN.html Genes down-regulated in NHEK cells (normal epidermal keratinocytes) after UVB irradiation. 16434974 649/741 Lauren Kazmierski 3.76499855408875e-07 9.5981847370948e-07 1285 2594.54545454545 2236 3.76499919197353e-08 1281 1.66806011664361 1.88840021093553 1 3.98688976133552 1281 3551 4328 2742 1750 2117 2517 2236 1871 4369 1778 2163 M16912 BALDWIN_PRKCI_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BALDWIN_PRKCI_TARGETS_UP.html Genes up-regulated in U87MG cells (glioblastoma multiforme) after knockdown of PRKCI [GeneID=5584] by RNAi. 16331246 49/80 Jessica Robertson 5.20369154676968e-08 5.21473972415136e-07 3325 2275.81818181818 2236 4.73062879077576e-09 61 1.80974130226556 2.19069257786494 1 4.52261462209639 3325 2236 2309 2150 61 4256 4069 2428 936 1425 1839 2164 M18149 RUTELLA_RESPONSE_TO_HGF_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_UP.html Genes up-regulated in peripheral blood monocytes by HGF [GeneID=3082]. 16527888 489/649 Arthur Liberzon 2.347362142267e-07 7.98113405922816e-07 4030 2627.81818181818 2236 2.13396581156958e-08 808 1.9028294080196 -1.75087915503403 -1 4.61637748759448 4028 2017 1415 2144 1127 4044 3110 3276 2236 808 4701 2165 M91 PID_TCPTP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCPTP_PATHWAY.html Signaling events mediated by TCPTP 18832364 64/71 Pathway Interaction Database 5.51477242336791e-07 1.17941666689155e-06 1800 2245.54545454545 2237 5.01343073251321e-08 1098 1.70390342948891 -1.61623757434527 -1 4.01232091233787 1798 2645 2739 1098 2046 2237 2078 2104 2562 2478 2916 2166 M14557 DORSEY_GAB2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/DORSEY_GAB2_TARGETS.html Genes up-regulated by expression of GAB2 [GeneID=9846] in K562 cells (chronic myeloid leukemia (CML) cell line with p210 BCR-ABL [GeneID=613;25]). 11830491 48/76 Kevin Vogelsang 5.17370742881371e-07 1.131848467036e-06 865 2118.18181818182 2238 4.70337149591566e-08 394 2.86696339128187 2.93335919750001 1 6.80584223102142 861 2238 394 1269 3890 1789 3042 4132 2715 447 2523 2167 M16992 ZHANG_PROLIFERATING_VS_QUIESCENT http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_PROLIFERATING_VS_QUIESCENT.html Genes up-regulated in HDMEC cells (microvascular endothelium): proliferating vs quiescent cells. 14517420 83/97 John Newman 2.81386889098584e-07 8.49189526890862e-07 1935 2216.36363636364 2240 2.55806295535323e-08 1322 1.93511261638953 2.21301208354674 1 4.67458191665767 1935 3336 1900 2240 1322 2030 2609 1341 2675 2696 2296 2168 M2370 GOBERT_CORE_OLIGODENDROCYTE_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/GOBERT_CORE_OLIGODENDROCYTE_DIFFERENTIATION.html Oligodendrocyte core differentiation genes: up-regulated in Oli-neo cells (oligodendroglial precursor) at 10 h after treatment with PD174265, dexamethasone or isotretinoin [PubChem=4709, 5743, 5282379]. 19139271 54/66 Arthur Liberzon 6.81579359985726e-07 1.3471752843939e-06 4495 2570.72727272727 2241 6.19617791950092e-08 196 2.52895726364341 3.02896468271078 1 5.92062984558445 4494 1693 1343 1596 2241 4215 3008 4254 196 1866 3372 2169 M495 REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS.html Genes involved in Apoptotic cleavage of cellular proteins 51/60 Reactome 1.99093313183048e-07 7.65527859584926e-07 2930 2186.36363636364 2242 1.809939374549e-08 838 2.30186416364551 -1.91666634359292 -1 5.61171156548614 2926 2242 1636 1059 933 2805 1784 4255 838 2738 2834 2170 M5392 BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins; the changes did not depend on expression of constitutively active (Q63L) form of RHOA [GeneID=387]. 17213802 36/41 Leona Saunders 1.21064516192899e-06 2.02274165108136e-06 2195 2140.63636363636 2242 1.10058711649034e-07 795 2.54385884271376 -2.95369135648614 -1 5.77522760644537 2191 1768 1009 3059 2704 2459 2285 2242 3200 795 1835 2171 M1852 QI_PLASMACYTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/QI_PLASMACYTOMA_DN.html Down-regulated genes that best disciminate plasmablastic plasmacytoma from plasmacytic plasmacytoma tumors. 17363561 149/179 Jessica Robertson 6.81967801223676e-07 1.34737882870479e-06 1980 2138 2242 6.19970920567096e-08 747 2.31827552021353 2.54179395991465 1 5.42316582914073 1976 2544 747 1170 2242 2631 3447 2976 1700 1043 3042 2172 M5291 BIOCARTA_CDC42RAC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CDC42RAC_PATHWAY.html Role of PI3K subunit p85 in regulation of Actin Organization and Cell Migration 26/29 BioCarta 8.0174944621866e-07 1.50228558402226e-06 2145 2521.27272727273 2246 7.28863398546924e-08 1023 1.13283690560216 -1.07043942213196 -1 2.60293865062035 2142 2342 3741 2246 2379 1745 1023 2149 3942 3838 2187 2173 M15351 SUZUKI_AMPLIFIED_IN_ORAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_AMPLIFIED_IN_ORAL_CANCER.html High-level amplifications detected in oral squamous cell carcinoma (OSCC) lines by array-CGH analysis. 17599052 17/24 Leona Saunders 1.67449667069618e-06 2.61190491926172e-06 1485 2142.90909090909 2247 1.52227085928664e-07 366 2.26757249880106 -2.06203232525791 -1 5.04131079551066 1485 2833 2247 2465 2929 2172 790 2854 366 3322 2109 2174 M13424 JAZAG_TGFB1_SIGNALING_VIA_SMAD4_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_VIA_SMAD4_UP.html Genes up-regulated in PANC-1-S4KD cells (pancreatic cancer; SMAD4 [GeneID=4089] knocked down by RNAi) after stimulation by TGF1B [GeneID=7040] for 2 h. 15592526 142/199 Leona Saunders 3.30932947257401e-07 9.06126045087621e-07 3430 2320.36363636364 2247 3.00848179125173e-08 1234 2.03096560692675 2.31657369876146 1 4.88558903991265 3427 2101 1767 2423 1501 2513 3865 1234 1645 2801 2247 2175 M1207 NIKOLSKY_BREAST_CANCER_1Q32_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_1Q32_AMPLICON.html Genes within amplicon 1q32 identified in a copy number alterations study of 191 breast tumor samples. 19010930 11/15 Jessica Robertson 3.66786475115864e-08 4.12198133939732e-07 4720 2402.72727272727 2248 3.33442255664518e-09 23 2.79077966212934 -3.06270550956149 -1 7.11601381229012 4717 970 1578 1391 23 4413 3953 2707 190 2248 4240 2176 M14427 DODD_NASOPHARYNGEAL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DODD_NASOPHARYNGEAL_CARCINOMA_DN.html Genes down-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. 17119049 1648/1982 Arthur Liberzon 6.28784185518129e-07 1.27828859001759e-06 190 2114.09090909091 2250 6.28784363434497e-08 190 1.66698803979297 1.73650717767536 1 3.90087091250617 190 3826 4319 3250 2250 465 565 1008 2378 4006 998 2177 M12212 WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN.html Down-regulated genes specific to esophageal adenocarcinoma (EAC) relative to normal tissue. 16449976 140/168 Arthur Liberzon 9.47865140539228e-08 6.60267713309408e-07 4390 2768.09090909091 2250 8.61695619434355e-09 280 1.97522311728927 -1.54117468717404 -1 4.85932374669087 4386 1543 1729 2137 280 3851 4467 3882 1471 2250 4453 2178 M5042 CHANG_CORE_SERUM_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_CORE_SERUM_RESPONSE_UP.html Up-regulated genes in the canonical gene expression signature of the fibroblast core serum response (CSR) defined by the Stanford group. 14737219 273/318 Arthur Liberzon 1.83407428428483e-06 2.80701382030622e-06 175 2185.72727272727 2251 1.66734164845414e-07 171 1.46602975369052 1.50862837488319 1 3.22317205120369 171 3562 3845 2713 2994 836 742 1421 2251 3703 1805 2179 M19148 TOMLINS_PROSTATE_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_PROSTATE_CANCER_UP.html Genes up-regulated in prostate cancer vs benign prostate tissue, based on a meta-analysis of five gene expression profiling studies. 17173048 58/64 Leona Saunders 2.93481866327292e-07 8.6694222517255e-07 2255 2444.45454545455 2252 2.66801732252754e-08 1363 1.83151316650651 1.84451501992517 1 4.41502321196995 2252 3368 2874 3656 1363 2247 2073 2611 1572 2891 1982 2180 M8943 TING_SILENCED_BY_DICER http://www.broadinstitute.org/gsea/msigdb/cards/TING_SILENCED_BY_DICER.html Epigenetically silenced genes up-regulated in HCT116 cells (colon cancer) hypomorphic for DICER1 [GeneID=23405]. 18413723 43/68 Jessica Robertson 3.36380266833613e-06 4.68905747033271e-06 4570 2355.90909090909 2252 3.05800710145955e-07 312 2.43689349262283 2.7447558966586 1 5.17243278227047 4566 547 1042 2772 3310 4527 3975 1467 2252 1145 312 2181 M6917 BIOCARTA_EPONFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPONFKB_PATHWAY.html Erythropoietin mediated neuroprotection through NF-kB 15/18 BioCarta 1.2008600030285e-05 1.46688903061452e-05 1040 2293.72727272727 2253 1.09169687083486e-06 781 1.65718135215252 -1.55409830923018 -1 3.17134051237221 1037 3496 2745 2484 3808 1027 781 2158 3343 2099 2253 2182 M563 REACTOME_SIGNALING_BY_EGFR_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_EGFR_IN_CANCER.html Genes involved in Signaling by EGFR in Cancer 132/143 Reactome 2.16198305145289e-07 7.73658832665478e-07 2960 2413.27272727273 2253 1.96543933083203e-08 516 1.55751223962996 -1.24875264409791 -1 3.77800242770878 2956 2110 3478 516 1038 2253 1773 3027 1970 4229 3196 2183 M1791 NADELLA_PRKAR1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NADELLA_PRKAR1A_TARGETS_DN.html Epithelial and mesenchymal markers down-regulated in MEF cells (embryonic fibroblasts) after knockout of PRKAR1A [GeneID=5573]. 18413734 16/22 Jessica Robertson 1.02478094488254e-05 1.26887881947681e-05 2255 2168.63636363636 2253 9.31623380400797e-07 143 3.64383811664378 5.67846846597678 1 7.12546945519266 2253 2838 941 2659 3813 3104 4087 143 1172 1881 964 2184 M16763 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NEUROTROPHIN_SIGNALING_PATHWAY.html Neurotrophin signaling pathway 139/152 KEGG 1.50064903468621e-07 7.26289540930751e-07 3250 2214.27272727273 2254 1.36422648822497e-08 492 1.79659309630574 -1.47424866802674 -1 4.38543896460687 3250 1533 2254 492 635 3196 2159 3706 778 3492 2862 2185 M1482 IGLESIAS_E2F_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IGLESIAS_E2F_TARGETS_DN.html Genes down-regulated in pancreatic cells from mice with double knockout of E2F1 [GeneID=1869] and E2F2 [GeneID=1870] compared to wild type. 15146237 15/36 Kevin Vogelsang 2.69664530184104e-05 3.12347627599748e-05 1525 2414.63636363636 2255 2.45152577861862e-06 1305 2.66046075697466 -3.08758816882081 -1 4.77040839060729 1522 2404 1305 2786 4022 2255 2846 1449 3654 2106 2212 2186 M18377 MELLMAN_TUT1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MELLMAN_TUT1_TARGETS_UP.html Genes up-regulated in HEK293 cells (embryo kidney) after knockdown of TUT1 [GeneID=64852] by RNAi. 18288197 24/26 Jessica Robertson 5.93271188250461e-07 1.22925373509314e-06 1955 2687.90909090909 2256 5.3933758930655e-08 1361 1.02777907950404 -1.07410394413837 -1 2.39291097652797 1953 1852 3480 4381 2117 2256 1361 2096 3585 4130 2356 2187 M2174 FIGUEROA_AML_METHYLATION_CLUSTER_5_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_5_DN.html Cluster 5 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 44/119 Arthur Liberzon 4.17989312944732e-07 1.00504816968881e-06 2500 2214.27272727273 2256 3.79990356691539e-08 594 2.29118775103768 2.66519086580177 1 5.47651485825317 2499 2256 1273 3659 1769 2824 3938 594 2614 1847 1084 2188 M13 PID_ERBB4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB4_PATHWAY.html ErbB4 signaling events 18832364 51/81 Pathway Interaction Database 6.7377622845977e-07 1.33960564377848e-06 2260 2102.54545454545 2257 6.12524031647147e-08 1030 1.89813585858068 -1.74727954643799 -1 4.43317870706491 2738 1707 2164 1513 2227 2276 2410 2548 1030 2258 2257 2189 M10953 BOYAULT_LIVER_CANCER_SUBCLASS_G2 http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G2.html Genes in hepatocellular carcinoma (HCC) subclass G2, defined by unsupervised clustering. 17187432 41/52 Yujin Hoshida 2.24260018819294e-07 7.84779759379662e-07 4645 2410.45454545455 2258 2.03872765163227e-08 132 2.79464217105935 2.81143044260114 1 6.8116430039892 4642 2258 1264 426 1074 3907 2522 3933 132 2023 4334 2190 M16834 BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 10/10 Leona Saunders 0.00195304713538172 0.00202557294638578 1790 2564.27272727273 2259 0.000177707555306129 502 1.29093617616049 -1.422695025157 -1 1.34830895531609 1786 1967 3226 3952 4562 1420 809 2259 4132 3592 502 2191 M13337 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN.html Hepatic graft versus host disease (GVHD), day 35: genes down-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 47/96 Arthur Liberzon 2.16989137183989e-07 7.74726722774909e-07 2575 2126.63636363636 2259 1.97262871441764e-08 934 2.79851102400957 -2.89258454389754 -1 6.82744389720726 2573 2259 934 3078 1041 2604 2714 3447 2255 1451 1037 2192 M2201 PHESSE_TARGETS_OF_APC_AND_MBD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/PHESSE_TARGETS_OF_APC_AND_MBD2_UP.html Genes up-regulated in small intestine upon loss of both APC and MBD2 [GeneID=324, 8932]. 18644872 15/31 Arthur Liberzon 3.51443531420655e-06 4.86883906165393e-06 1915 2176.45454545455 2260 3.19494629856927e-07 479 2.08795793927998 -1.99688878468894 -1 4.41091369473173 2260 1912 1988 1913 3335 2439 2454 4122 479 2536 503 2193 M6489 ZHANG_BREAST_CANCER_PROGENITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_BREAST_CANCER_PROGENITORS_DN.html Genes down-regulated in cancer stem cells isolated from mammary tumors compared to the non-tumorigenic cells. 18559513 206/242 Leona Saunders 3.68669436594132e-07 9.52968094591624e-07 2985 2745.27272727273 2261 3.35154089431519e-08 1616 1.93162792722811 2.09486528978595 1 4.62717536289678 2984 2066 1871 2192 1616 3520 3967 4606 2261 2202 2913 2194 M1980 SEKI_INFLAMMATORY_RESPONSE_LPS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SEKI_INFLAMMATORY_RESPONSE_LPS_DN.html Genes down-regulated in hepatic stellar cells after stimulation with bacterial lipopolysacharide (LPS). 17952090 23/30 Jessica Robertson 1.12393794346563e-06 1.91515779536381e-06 2385 2269.36363636364 2261 1.02176228878586e-07 797 2.38732880075447 -2.74110063967032 -1 5.43957299858604 2385 797 946 2261 2648 4038 4384 1146 3887 887 1584 2195 M1763 TESAR_ALK_AND_JAK_TARGETS_MOUSE_ES_D4_UP http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_AND_JAK_TARGETS_MOUSE_ES_D4_UP.html Genes up-regulated in mES cells (mouse embryonic stem cells) after tratment with the ALK [GeneID=238] inhibitor SB-431542 and JAK inhibitor I [PubChem=4521392;5494425]. 17597760 2/6 Jessica Robertson 7.44278971337666e-05 8.25422167460946e-05 1565 2412.9 2261.5 8.27003991715819e-06 162 3.2886627788042 3.2886627788042 1 5.35046101748692 1563 2933 4526 NA 4241 871 162 2009 3301 2137 2386 2196 M14262 LU_TUMOR_VASCULATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_VASCULATURE_DN.html Genes down-regulated in endothelial cells derived from invasive ovarian cancer tissue. 17308118 14/17 Arthur Liberzon 0.00116711191209124 0.00121740734255705 1525 2847.45454545455 2263 0.000106157411956812 1219 2.04201598874646 2.24611456677461 1 2.34346265881032 1524 3218 2085 4574 4605 2205 1998 1219 4319 3312 2263 2197 M2447 PLASARI_NFIC_TARGETS_BASAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_NFIC_TARGETS_BASAL_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon knockout of NFIC [GeneID=4782]. 19752192 43/64 Arthur Liberzon 1.17036931399024e-07 7.06112554001409e-07 1025 2319.36363636364 2263 1.06397216022932e-08 349 3.45449607778222 3.28067428261362 1 8.49551216784283 1025 2263 349 2084 3744 1989 2992 3738 2939 736 3654 2198 M15181 BIOCARTA_PGC1A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PGC1A_PATHWAY.html Regulation of PGC-1a 29/30 BioCarta 1.34401283319529e-06 2.19430666644129e-06 2265 2089.09090909091 2264 1.22183059479408e-07 522 1.89879108828141 2.45460342212278 1 4.27106678329381 2264 2319 2228 1265 2779 2761 4162 1019 522 3029 632 2199 M204 PID_RHODOPSIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHODOPSIN_PATHWAY.html Visual signal transduction: Rods 18832364 12/35 Pathway Interaction Database 3.72973791132187e-07 9.57025534470045e-07 2525 2006.27272727273 2264 3.390671403307e-08 162 1.87947626640731 -1.94359054165948 -1 4.49950150343995 2524 1941 2528 3332 1632 2264 1501 162 3020 2964 201 2200 M1506 WEBER_METHYLATED_HCP_IN_SPERM_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_SPERM_UP.html Methylated germline-specific genes with high-CpG-density promoters (HCP) in sperm. 17334365 10/41 Jessica Robertson 1.42961760545584e-07 7.24081202656879e-07 2140 1687.81818181818 2265 1.29965245305104e-08 13 1.91032849062106 -2.50730231734075 -1 4.66724792574195 2139 2445 2310 2265 583 2755 2840 55 50 3111 13 2201 M1978 ONO_AML1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONO_AML1_TARGETS_DN.html Genes down-regulated in CD4+ [GeneID=920] T lymphocytes by expression of AML1 [GeneID=861] off a viral vector. 17377532 31/54 Jessica Robertson 1.75433492406617e-07 7.39730810987813e-07 3360 2059.63636363636 2266 1.59485005814658e-08 660 2.80957649168568 2.71321076199554 1 6.87732046559751 3356 660 866 2266 809 2664 3359 2446 727 1064 4439 2202 M15542 BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP.html Genes up-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes are independent of ATM [GeneID=472] signaling. 18849970 74/103 Jessica Robertson 2.32124031739882e-07 7.96239411200756e-07 4225 2605.54545454545 2267 2.11021869301369e-08 263 2.14216677860321 2.15356699571588 1 5.20419740042231 4636 273 1648 2267 1110 4224 3764 4031 263 2224 4221 2203 M15545 VALK_AML_CLUSTER_15 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_15.html Top 40 genes from cluster 15 of acute myeloid leukemia (AML) expression profile; 88% of the samples are FAB M1 or M2 subtype, 63% have mutations in CEBPA [GeneID=1050]. 15084694 45/59 Jessica Robertson 2.39789354663389e-06 3.52258248991969e-06 2830 2131.63636363636 2267 2.17990560020529e-07 1023 1.81865832088626 -1.81632010126619 -1 3.93835929044611 2826 1736 2267 1904 3135 2373 2320 1508 1023 1927 2429 2204 M4957 FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP.html Genes up-regulated in thyroid tumors of uncertain malignancy (T-UM) compared to other thyroid tumors. 17968324 40/58 Arthur Liberzon 6.46960557603271e-08 5.87303055010366e-07 4160 2162.45454545455 2267 5.88145978753302e-09 111 2.44715923223286 2.16355739032719 1 6.08235943482677 4159 2267 1253 1593 111 3814 3759 2392 426 2446 1567 2205 M15150 ZHANG_BREAST_CANCER_PROGENITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_BREAST_CANCER_PROGENITORS_UP.html Genes up-regulated in cancer stem cells isolated from mammary tumors compared to the non-tumorigenic cells. 18559513 606/696 Leona Saunders 6.39234790028564e-07 1.2949305617746e-06 175 2134.72727272727 2269 6.39234973908141e-08 172 1.56931390020818 1.68682983528614 1 3.66582927412124 172 3838 4561 3590 2269 472 506 692 2297 4072 1013 2206 M10941 PENG_RAPAMYCIN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_RAPAMYCIN_RESPONSE_UP.html Genes up-regulated in BJUB cells (B-lymphoma) in response to rapamycin (sirolimus) [PubChem=6610346] treatment. 12101249 278/380 Broad Institute 5.29808184798874e-07 1.14793097505329e-06 2985 2582.72727272727 2270 4.81643920353029e-08 1312 1.75013165020101 -1.60150526769144 -1 4.13080695270987 2981 1312 2175 1921 2005 3644 4260 3543 1809 2490 2270 2207 M812 REACTOME_GPCR_DOWNSTREAM_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPCR_DOWNSTREAM_SIGNALING.html Genes involved in GPCR downstream signaling 266/1312 Reactome 1.57353860772706e-15 5.42124250253411e-14 4000 1920.90909090909 2271 1.43048964338823e-16 87 2.48107848582146 -2.34775383471282 -1 13.1866076112111 3996 1307 97 934 87 3370 2866 2497 2271 126 3579 2208 M9526 ST_T_CELL_SIGNAL_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/ST_T_CELL_SIGNAL_TRANSDUCTION.html T Cell Signal Transduction 55/72 Signaling Transduction KE 1.55307090683485e-07 7.28467912574107e-07 2905 2323.36363636364 2272 1.41188274224778e-08 669 2.00525710069424 -1.67166118879364 -1 4.89954524680616 2904 2223 2272 1309 669 2678 1806 3332 2134 2622 3608 2209 M2881 REACTOME_LYSOSOME_VESICLE_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LYSOSOME_VESICLE_BIOGENESIS.html Genes involved in Lysosome Vesicle Biogenesis 40/42 Reactome 7.80358613268629e-08 6.27525965386533e-07 955 2079.18181818182 2272 7.09416946316917e-09 174 1.26137172294428 -1.09213541747413 -1 3.09627127555852 955 2272 3356 3172 174 723 918 2558 3699 3737 1307 2210 M15699 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_0 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_0.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 0. 12554760 92/110 Arthur Liberzon 1.45653763011483e-07 7.26289540930751e-07 3870 2512.63636363636 2273 1.32412520595158e-08 604 2.14777252194338 2.41413129869981 1 5.25243993726058 3869 1607 1208 2273 604 4569 3852 3823 1736 630 3468 2211 M9815 AKL_HTLV1_INFECTION_DN http://www.broadinstitute.org/gsea/msigdb/cards/AKL_HTLV1_INFECTION_DN.html Genes down-regulated in WE17/10 cells (CD4+ [GeneID=920] T lymphocytes) infected by HTLV1 (and thus displaying low CD7 [GeneID=924]) compared to the uninfected (i.e., CD7+) cells. 17287851 93/136 Arthur Liberzon 2.44069196890279e-06 3.57322149293461e-06 1325 2423.63636363636 2274 2.2188133423854e-07 1321 2.08125569960638 2.43433753235386 1 4.50905834038847 1321 3614 1869 1749 3145 2701 3549 1934 2374 2274 2130 2212 M12595 FOSTER_TOLERANT_MACROPHAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_TOLERANT_MACROPHAGE_UP.html Class T (tolerizeable) genes: induced during the first LPS stimulation and either not re-induced or induced to a much lesser degree in tolerant macrophages. 17538624 195/269 Jessica Robertson 3.07207512255648e-07 8.82543796619999e-07 2050 2104.27272727273 2274 2.79279595594587e-08 806 1.92479590366299 -1.82747279279965 -1 4.63644182987592 2047 1420 1220 2274 1414 2921 2534 2889 2621 806 3001 2213 M16061 STANELLE_E2F1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/STANELLE_E2F1_TARGETS.html Genes up-regulated by induction of E2F1 expression in Saos2 (osteosarcoma) cells. 11937641 41/59 Yujin Hoshida 2.61568951110047e-06 3.77439758251123e-06 2825 2467.72727272727 2276 2.37790238275374e-07 826 1.98432836066903 2.02504452054091 1 4.27775103417448 2824 2702 2022 1501 3192 1573 1387 4326 826 2276 4516 2214 M2380 IKEDA_MIR30_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR30_TARGETS_DN.html Genes down-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-30 microRNA. 19188439 43/48 Arthur Liberzon 6.94577770382156e-08 6.06161982149702e-07 2530 1957.09090909091 2277 6.31434356646517e-09 130 2.122714679817 2.22698351493541 1 5.25760793193844 2527 2686 1742 2277 130 2480 4080 673 260 1516 3157 2215 M87 PID_LKB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LKB1_PATHWAY.html LKB1 signaling events 18832364 68/103 Pathway Interaction Database 9.29912240084958e-08 6.56798957981166e-07 2775 1821.45454545455 2278 8.45374799446526e-09 197 1.7598797540457 2.16908525895987 1 4.32571300500105 2774 343 2951 501 267 2589 3339 1039 197 3758 2278 2216 M1876 JU_AGING_TERC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JU_AGING_TERC_TARGETS_DN.html Cytokines, growth factors, and secreted proteins that show decreased expression on a protein array of samples from aged TERC [GeneID=7012] knockout mice. 17486088 6/7 Jessica Robertson 1.80890873098516e-05 2.14254685326223e-05 2280 2427.81818181818 2278 1.80892345583244e-06 970 2.59320142785093 -3.60755099256859 -1 4.81927099355895 2278 1045 4593 3355 3949 2194 1266 970 2431 2122 2503 2217 M1921 REACTOME_REGULATION_OF_INSULIN_SECRETION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_SECRETION.html Genes involved in Regulation of Insulin Secretion 96/133 Reactome 1.29241586291416e-07 7.20206492018647e-07 3380 2111.27272727273 2279 1.17492358076242e-08 145 1.96474401112707 2.36293831406112 1 4.80346055895687 3378 145 1117 1239 482 3327 4623 3065 2643 926 2279 2218 M4371 MARTINEZ_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_TP53_TARGETS_UP.html Genes up-regulated in mice with skin specific knockout of TP53 [GeneID=7157]. 18245467 770/969 Jessica Robertson 1.62571690980253e-07 7.3358205358541e-07 3070 2399.72727272727 2279 1.62571702873554e-08 833 2.07345778760325 2.27266387566549 1 5.06535170836208 3067 2000 4534 837 833 2266 3980 2279 2448 1076 3077 2219 M9400 REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING.html Genes involved in p75 NTR receptor-mediated signalling 103/116 Reactome 1.63982062501439e-07 7.3358205358541e-07 2740 2118.54545454545 2281 1.49074613385655e-08 114 1.84894430271152 -1.6032273852649 -1 4.51145869404837 2740 114 2281 1469 719 1935 2396 4154 1837 2422 3237 2220 M11814 GRANDVAUX_IRF3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRANDVAUX_IRF3_TARGETS_DN.html Genes down-regulated in Jurkat cells (T lymphocyte) by expression of a constitutively active form of IRF3 [GeneID=3661]. 11991981 20/33 Yujin Hoshida 7.10908757176991e-07 1.38199725447916e-06 3270 2467.36363636364 2281 6.46280897182177e-08 1591 2.26804095221146 2.95897999363767 1 5.29451809713232 3269 1874 1664 2827 2281 3250 3092 2920 2218 2155 1591 2221 M252 PID_IL8_CXCR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL8_CXCR1_PATHWAY.html IL8- and CXCR1-mediated signaling events 18832364 44/52 Pathway Interaction Database 1.59446654030655e-07 7.31918027928963e-07 2550 1696.72727272727 2282 1.44951514169702e-08 187 1.99604212729835 -2.04565052664471 -1 4.87515267955878 2549 548 2293 187 690 2282 2097 2485 890 2337 2306 2222 M15798 KEGG_MELANOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOMA.html Melanoma 67/89 KEGG 3.25733118311573e-07 9.04388422606248e-07 2895 1979.81818181818 2283 2.96121060490721e-08 301 2.29415429447415 2.68836915198498 1 5.52595588119825 2891 301 1215 1086 1476 2283 3242 2702 607 2499 3476 2223 M16141 CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_UP.html All marker genes up-regulated in the 'interferon' subclass of hepatocellular carcinoma (HCC). 18701503 16/132 Yujin Hoshida 1.63584001503118e-05 1.95126734165963e-05 1450 2267.54545454545 2283 1.48713834424492e-06 473 2.72328167849929 -2.16747406680922 -1 5.10800532111778 1447 4054 1745 2370 3897 1823 473 3763 648 2283 2440 2224 M3896 KEGG_INOSITOL_PHOSPHATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INOSITOL_PHOSPHATE_METABOLISM.html Inositol phosphate metabolism 50/55 KEGG 1.16144938337828e-06 1.9606727788074e-06 1880 2279.90909090909 2284 1.05586363322227e-07 285 1.68901129782593 -1.93059133495843 -1 3.82687844520124 1876 3079 3111 3411 2674 1837 2284 1637 958 3927 285 2225 M8773 HO_LIVER_CANCER_VASCULAR_INVASION http://www.broadinstitute.org/gsea/msigdb/cards/HO_LIVER_CANCER_VASCULAR_INVASION.html Gene expression signature of vascular invasion of hepatocellular carcinoma (HCC). 17009164 18/40 Yujin Hoshida 9.28538709634847e-07 1.66263380480898e-06 2380 2068.45454545455 2284 8.4412645594269e-08 351 2.44466245612659 2.14165054706328 1 5.63178368114648 2378 885 1511 2284 2515 1981 1364 4495 351 2614 2375 2226 M14512 BIOCARTA_RACCYCD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RACCYCD_PATHWAY.html Influence of Ras and Rho proteins on G1 to S Transition 44/48 BioCarta 1.6772469499184e-06 2.61533055950275e-06 2260 2103.45454545455 2285 1.52477111693422e-07 204 1.34978630760692 -1.36015463318771 -1 2.98030964689088 2259 508 3342 204 2930 1548 1268 3346 2314 3134 2285 2227 M14139 FUNG_IL2_SIGNALING_1 http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_SIGNALING_1.html Genes up-regulated by IL2 [GeneID=3558] in both primary thymocytes and T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 10/14 Arthur Liberzon 0.000116451710922097 0.000127204831185442 1650 2562.72727272727 2285 1.05870795882075e-05 943 2.37640738060943 1.88686783813818 1 3.67288839476602 1649 3233 2285 3433 4282 1587 1396 943 1131 3987 4264 2228 M10797 AMIT_EGF_RESPONSE_60_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_60_HELA.html Genes whose expression peaked at 60 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 60/71 Leona Saunders 2.42884223476657e-07 8.07627467909088e-07 2285 2313.18181818182 2285 2.20803863901405e-08 930 1.88280648001541 -1.85116647298724 -1 4.56337727186293 2285 3916 2334 2963 1163 1280 930 3250 3626 1938 1760 2229 M748 REACTOME_RECRUITMENT_OF_MITOTIC_CENTROSOME_PROTEINS_AND_COMPLEXES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECRUITMENT_OF_MITOTIC_CENTROSOME_PROTEINS_AND_COMPLEXES.html Genes involved in Recruitment of mitotic centrosome proteins and complexes 93/115 Reactome 6.09908346960217e-07 1.252328823352e-06 1035 2765.36363636364 2286 5.54462287314385e-08 1035 1.38894852171735 1.47793743807578 1 3.24687009496099 1035 4454 3916 3808 2137 1206 1152 2286 3906 4348 2171 2230 M18788 REACTOME_PHASE_II_CONJUGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHASE_II_CONJUGATION.html Genes involved in Phase II conjugation 38/95 Reactome 2.80554441406233e-06 4.00670790752623e-06 2235 2379.90909090909 2287 2.55049817439283e-07 558 1.66908711213533 1.78854578710306 1 3.57280288239768 2660 558 2196 3073 3232 2235 3335 2231 2287 1280 3092 2231 M3815 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_27 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_27.html Amplification hot spot 27: colocalized fragile sites and cancer genes in the 5p15.3-p15.1; 5p12-q35 region. 16751803 16/22 Arthur Liberzon 5.66517929310444e-06 7.37238661799089e-06 1925 2648 2287 5.15017625586855e-07 1243 1.43995410044088 -1.30591255418268 -1 2.92210180921695 1921 2846 3070 3894 3558 2215 1692 1243 4122 2280 2287 2232 M12300 CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP.html Up-regulated genesin the left ventricle myocardium of patients with heart failure following implantation of LVAD (left ventricular assist device). 12824457 116/140 John Newman 7.17611686174936e-07 1.39158880803028e-06 3525 2585.81818181818 2287 6.52374472955219e-08 791 2.31509755246734 -1.78633984128844 -1 5.40260862973908 3523 2120 791 3075 2287 4126 3950 1694 3817 901 2160 2233 M18811 PUJANA_XPRSS_INT_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_XPRSS_INT_NETWORK.html Genes constituting the XPRSS-Int network: intersection of genes whose expression correlates with BRCA1, BRCA2, ATM, and CHEK2 [GeneID=672;675;472;11200] in a compendium of normal tissues. 17922014 243/283 Leona Saunders 5.91555335245355e-06 7.66229742688824e-06 290 2058.72727272727 2288 5.37779023524835e-07 286 1.51049576379693 1.53524434749021 1 3.05752785158335 286 3568 3904 2515 3579 610 437 1012 3311 2288 1136 2234 M670 REACTOME_KERATAN_SULFATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_BIOSYNTHESIS.html Genes involved in Keratan sulfate biosynthesis 20/27 Reactome 2.40145955120734e-07 8.03892842673661e-07 2290 1950.45454545455 2289 2.18314528485827e-08 765 2.58705363889011 2.80356375870858 1 6.291078526287 2289 840 810 2753 1152 2731 2885 1616 2737 765 2877 2235 M961 REACTOME_TRANSPORT_TO_THE_GOLGI_AND_SUBSEQUENT_MODIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_TO_THE_GOLGI_AND_SUBSEQUENT_MODIFICATION.html Genes involved in Transport to the Golgi and subsequent modification 36/38 Reactome 1.21276010499276e-06 2.02470360040951e-06 2210 2319.45454545455 2289 1.10250979412078e-07 624 1.81884031204153 2.03910105515802 1 4.11467620877179 1974 624 2210 3651 2707 2426 2785 2207 1633 2289 3008 2236 M4740 BENPORATH_ES_CORE_NINE http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_CORE_NINE.html Set 'Core 9': 'embryonic stem cell' transcription regulators that are preferentially and coordinately overexpressed in the high-grade, ER-negative breast cancer tumors. 18443585 12/16 Jessica Robertson 7.60914351842413e-07 1.44585979899203e-06 3290 2263.72727272727 2289 6.91740559109191e-08 695 1.94861254166642 -2.08225010883154 -1 4.52642219723639 3288 954 1867 2289 2341 3383 1794 2778 695 1549 3963 2237 M3559 ZHANG_INTERFERON_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_INTERFERON_RESPONSE.html Interferon-inducible genes up-regulated in A549 cells (lung cancer) infected with a respiratory syncytial virus (RSV) that had its NS1 [GeneID=1494468] gene knocked down by RNAi. 15619625 36/61 Jessica Robertson 0.000156211706789027 0.000168800195980817 2290 2357.81818181818 2289 1.42020727049266e-05 631 1.75475534789769 -1.92473271512276 -1 2.6122880318698 631 3117 2289 2479 4325 1254 926 2043 4340 2290 2242 2238 M9362 IWANAGA_CARCINOGENESIS_BY_KRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_DN.html Cluster 4: genes down-regulated in lung tissue samples from mice with tumor-bearing genotypes (activated KRAS [GeneID=3845] alone or together with inactivated PTEN [GeneID=5728]). 18281487 183/239 Jessica Robertson 7.20788703848581e-07 1.3960290037609e-06 1675 2084.27272727273 2290 6.55262672728708e-08 760 1.85814882606594 2.10255560544544 1 4.32534384884219 1675 3299 2338 1943 2290 812 2491 3032 2718 1569 760 2239 M6349 SU_PLACENTA http://www.broadinstitute.org/gsea/msigdb/cards/SU_PLACENTA.html Genes up-regulated specifically in human placenta. 11904358 25/52 John Newman 4.04927929633628e-07 9.96585392367531e-07 725 2206.45454545455 2291 3.68116367421757e-08 490 3.07565423696326 -3.34259132221016 -1 7.37326133487544 4106 724 490 1798 1720 4254 2703 2993 2470 722 2291 2240 M13796 THUM_MIR21_TARGETS_HEART_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/THUM_MIR21_TARGETS_HEART_DISEASE_UP.html Genes up-regulated in a mouse model of heart disease whose expression reverted to normal by silencing of MIR21 [GeneID=406991] microRNA. 19043405 32/34 Jessica Robertson 2.9658689912794e-09 4.33402527518228e-08 405 2188 2291 2.69624454116159e-10 250 3.50542307435587 3.54301909503692 1 10.3300810271251 402 2291 250 1662 4535 2455 3407 3281 2858 672 2255 2241 M2063 HOFFMAN_CLOCK_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMAN_CLOCK_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) upon knockdown of CLOCK [GeneID=9575] by RNAi that also belong to the highest confidence network (according to Ingenuity Pathway Analysis). 20124474 10/23 Jessica Robertson 2.43773084127462e-05 2.83471041409614e-05 3180 2263.63636363636 2292 2.21614350291016e-06 1130 3.39568961131952 -2.78556076579719 -1 6.1600903323315 3178 2449 1407 2165 4006 2292 1130 1217 1193 2550 3313 2242 M19275 LAU_APOPTOSIS_CDKN2A_DN http://www.broadinstitute.org/gsea/msigdb/cards/LAU_APOPTOSIS_CDKN2A_DN.html Genes down-regulated by UV-irradiation in cervical cancer cells after knockdown of CDKN2A [GeneID=1029]. 17369842 7/8 Leona Saunders 1.41651528280293e-07 7.20206492018647e-07 2295 1971 2293 1.41651537309613e-08 177 1.28369125061262 1.63473143966217 1 3.12105918307281 2293 2917 4329 2682 673 2711 1356 283 177 3647 613 2243 M285 PID_HNF3A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HNF3A_PATHWAY.html FOXA1 transcription factor network 18832364 35/84 Pathway Interaction Database 6.20987555655795e-07 1.26666433132902e-06 1770 2277.90909090909 2294 5.6453430085473e-08 282 1.76915762735595 -1.63400302208601 -1 4.14584454415802 1767 2741 2361 3896 2158 1180 735 2294 4280 3363 282 2244 M8818 BIDUS_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BIDUS_METASTASIS_DN.html Genes down-regulated in endometroid endometrial tumors from patients with lymph node metastases compared to those without the metastases. 16397028 216/275 Arthur Liberzon 1.13712252457173e-07 7.05613393308323e-07 2305 1987.81818181818 2294 1.03374780304238e-08 375 2.03410513552221 -1.90194441475827 -1 4.98207555699959 2469 3292 1645 2294 375 2303 2301 2461 1855 1260 1611 2245 M5497 NIKOLSKY_BREAST_CANCER_1Q21_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_1Q21_AMPLICON.html Genes within amplicon 1q21 identified in a copy number alterations study of 191 breast tumor samples. 19010930 39/50 Jessica Robertson 7.86820775616867e-08 6.28391550069647e-07 2770 2053.09090909091 2294 7.15291639779260e-09 179 1.92447901940651 -1.7929465983062 -1 4.74983274160978 2769 1750 2294 2318 179 2875 2687 1583 1721 2342 2066 2246 M11358 BIOCARTA_ARF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARF_PATHWAY.html Tumor Suppressor Arf Inhibits Ribosomal Biogenesis 25/28 BioCarta 9.55366582585952e-07 1.6984294801528e-06 3040 2035.36363636364 2295 8.68515452237584e-08 288 2.60528132833652 2.77879781844007 1 5.99539729264738 3038 2343 1757 1071 2534 2027 1258 2295 288 2864 2914 2247 M2935 LAMB_CCND1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LAMB_CCND1_TARGETS.html The cyclin D1 signature: genes whose expression correlated with the levels of CCND1 [GeneID=595]. 12914697 33/36 Jean Junior 2.74940568004817e-07 8.38703759494626e-07 2375 2282.72727272727 2296 2.49946002149969e-08 551 1.46296006594933 1.73517028776281 1 3.52498604669776 2375 2296 2818 2199 1300 2230 2680 551 3811 3157 1693 2248 M7899 WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_TBH http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_TBH.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to HNE and tBH [PubChem=5283344;6410]. 12419474 98/117 John Newman 2.74219882307083e-07 8.38703759494626e-07 2955 2125.45454545455 2296 2.49290833170305e-08 139 1.77424362381672 -2.01386932286998 -1 4.28566706101072 2954 139 2296 869 1292 3091 3631 4127 963 3159 859 2249 M1186 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_UP.html Genes up-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 39/141 Arthur Liberzon 2.54345557214645e-07 8.22189102913976e-07 4065 2482.36363636364 2297 2.31223260563592e-08 580 2.69245687351152 2.46860308407781 1 6.53884909400792 4065 580 1065 2297 1208 4576 3710 3470 1162 1583 3590 2250 M17183 BENPORATH_OCT4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_OCT4_TARGETS.html Set 'Oct4 targets': genes upregulated and identified by ChIP on chip as OCT4 [GeneID=5460] transcription factor targets in human embryonic stem cells. 18443585 372/499 Jessica Robertson 3.97517327404939e-07 9.84907668441108e-07 2300 2404.18181818182 2297 3.61379453847493e-08 1214 1.93145712560599 2.08824537183082 1 4.61564081969228 2297 3557 2381 3211 1702 2062 3463 1214 2712 1843 2004 2251 M454 ROSS_AML_WITH_MLL_FUSIONS http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_MLL_FUSIONS.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtypes with chimeric MLL fusions [GeneID=4297]. 15226186 88/138 Kate Stafford 5.11298902109875e-07 1.12704049506997e-06 2925 2156.72727272727 2297 4.64817291763792e-08 182 1.69699040460852 1.74821770327687 1 4.00930271880544 2921 182 2522 3343 1967 2297 2578 1169 2280 2481 1984 2252 M15926 BIOCARTA_TFF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TFF_PATHWAY.html Trefoil Factors Initiate Mucosal Healing 34/40 BioCarta 4.73503678087938e-07 1.07707824606027e-06 3675 2263.81818181818 2299 4.30457981817878e-08 209 1.41574613132347 -1.76346268821928 -1 3.34775537164488 3675 653 3244 209 1902 3366 3601 2299 294 4099 1560 2253 M56 PID_LPA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LPA4_PATHWAY.html LPA4-mediated signaling events 18832364 16/19 Pathway Interaction Database 4.51439635688679e-07 1.04185917010687e-06 3070 2559.90909090909 2299 4.10399753021858e-08 586 1.96903051573374 1.9772595661077 1 4.6870717937265 3070 1911 2299 1685 1858 3472 4669 4346 586 2702 1561 2254 M7999 RIZ_ERYTHROID_DIFFERENTIATION_HEMGN http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_HEMGN.html Selected gradually up-regulated genes whose expression profile follows that of HEMGN [GeneID=55363] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 33/47 Leona Saunders 1.02177341090629e-06 1.78093445327833e-06 2020 2450.81818181818 2300 9.28885350419598e-08 1903 2.09152122313286 1.89082684207816 1 4.78591318122806 2016 2742 2155 2300 2581 2052 2761 3563 1903 1951 2935 2255 M11028 ROVERSI_GLIOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROVERSI_GLIOMA_COPY_NUMBER_UP.html Genes in the most frequently gained loci in a panel of glioma cell lines. 16247447 101/137 Arthur Liberzon 4.85362102935061e-07 1.09541410640518e-06 3895 2955.27272727273 2301 4.41238372741148e-08 1916 2.05691266016953 -1.71048592088401 -1 4.8804915201583 3893 2131 1950 2301 1916 4336 3872 3913 2087 2129 3980 2256 M13696 DAUER_STAT3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAUER_STAT3_TARGETS_DN.html Top 50 genes down-regulated in A549 cells (lung cancer) expressing STAT3 [GeneID=6774] off an adenovirus vector. 15735721 71/106 Arthur Liberzon 3.90078486904456e-06 5.32374103863799e-06 425 1930.09090909091 2301 3.54617435043735e-07 238 1.85320746853189 -2.07172167535322 -1 3.88045520467405 421 3048 2379 1974 3387 238 346 2301 3800 3053 284 2257 M2310 DANG_REGULATED_BY_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/DANG_REGULATED_BY_MYC_DN.html Genes down-regulated by MYC [GeneID=4609], according to the MYC Target Gene Database. 14519204 334/435 Chi Dang 3.54246015300642e-07 9.39877005182141e-07 2405 2305.72727272727 2301 3.22041883946975e-08 1566 1.96899587969162 2.28327247850304 1 4.72241445401186 2402 2512 1580 2719 1566 2301 3622 1946 2786 1968 1961 2258 M4406 GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP.html Genes up-regulated in quiescent vs dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors. 17717066 83/142 Arthur Liberzon 2.47160087778685e-06 3.60728390326344e-06 2305 2308.45454545455 2302 2.24691241320314e-07 744 2.58969637272743 -2.53881303213428 -1 5.61853197621006 2302 2156 744 1466 3155 3107 2627 2188 3163 1086 3399 2259 M18227 BOYLAN_MULTIPLE_MYELOMA_PCA3_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA3_UP.html Top up-regulated genes from principal component 3 (PCA3) which captures variation among different plasma cell tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 90/124 Arthur Liberzon 2.72173036480404e-07 8.37744283366146e-07 3060 2024.36363636364 2302 2.47430063774819e-08 163 2.06041741480316 2.26441396247005 1 4.98539947036535 3060 163 1433 2302 1286 2854 3145 2675 1631 1302 2417 2260 M1330 MANTOVANI_VIRAL_GPCR_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_VIRAL_GPCR_SIGNALING_DN.html Down-regulated genes in the expression signature of direct and paracrine viral GPCR signaling in endothelial cells. 17906691 76/105 Jessica Robertson 7.29297275787086e-07 1.40501352723063e-06 3825 2318.90909090909 2304 6.62997743225766e-08 135 1.91722308836979 -1.68438154935968 -1 4.46229780084587 3825 237 1371 135 2304 3909 4008 2591 1305 1633 4190 2261 M6154 MAHAJAN_RESPONSE_TO_IL1A_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAHAJAN_RESPONSE_TO_IL1A_UP.html Genes up-regulated in corneal fibroblasts after treatment with IL1A [GeneID=3552]. 12091409 111/143 John Newman 5.86431414443172e-08 5.58055700841083e-07 2305 2471.81818181818 2304 5.3311948188643e-09 294 2.48565333010464 2.50589081448102 1 6.20099934415639 2304 2122 336 1048 2240 2702 4441 4647 3630 294 3426 2262 M14162 REACTOME_CHYLOMICRON_MEDIATED_LIPID_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHYLOMICRON_MEDIATED_LIPID_TRANSPORT.html Genes involved in Chylomicron-mediated lipid transport 12/19 Reactome 4.20781151602856e-06 5.69701262706411e-06 2070 2428.81818181818 2305 3.82529051280495e-07 1360 2.38221413797649 2.14762021701855 1 4.97423726405821 2066 3789 2305 1889 3412 2826 2962 1690 1360 2969 1449 2263 M661 REACTOME_SIGNALING_BY_FGFR1_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR1_MUTANTS.html Genes involved in Signaling by FGFR1 mutants 33/51 Reactome 5.84530041362276e-07 1.22123997631427e-06 2430 2347.45454545455 2308 5.313910878812e-08 1231 1.65571511157083 -1.36414719291014 -1 3.88735578962648 2429 2308 2966 1743 2098 2772 1231 1762 1927 3866 2720 2264 M14933 KEGG_STEROID_HORMONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_HORMONE_BIOSYNTHESIS.html Steroid hormone biosynthesis 21/88 KEGG 1.17858458048308e-06 1.97968655511749e-06 2310 2198.09090909091 2309 1.07144110170473e-07 1014 2.55629141687234 -2.25621336172905 -1 5.8133033719508 2309 2364 1014 2396 2688 2209 1664 1343 3296 1613 3283 2265 M16334 BIOCARTA_EPHA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPHA4_PATHWAY.html Eph Kinases and ephrins support platelet aggregation 30/36 BioCarta 1.30565326707812e-06 2.14578113530944e-06 2705 2121.45454545455 2309 1.18695821996022e-07 489 2.54311429570495 3.54338339157389 1 5.74729439312986 2705 2309 1165 489 2758 4147 3569 1029 2618 1609 938 2266 M2244 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B.html Category B genes: p53-dependent genes whose expression in the absence of S389 phosphorylation is dissimilar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 677/874 Arthur Liberzon 9.33971619072921e-09 1.23138157598441e-07 3285 2384.18181818182 2310 9.33971622998284e-10 218 2.16583785413256 2.40035807195062 1 5.96834777531 3284 1125 4673 1585 447 1709 4272 3400 2310 218 3203 2267 M17787 REACTOME_GLUCURONIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCURONIDATION.html Genes involved in Glucuronidation 6/23 Reactome 1.35291461517371e-05 1.63821369513082e-05 1985 2370.45454545455 2311 1.35292285194509e-06 182 2.53267017841944 3.25056185590295 1 4.82433133199799 1985 2468 4257 3081 4187 2311 2710 182 1593 1489 1812 2268 M2612 ZWANG_CLASS_2_TRANSIENTLY_INDUCED_BY_EGF http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_CLASS_2_TRANSIENTLY_INDUCED_BY_EGF.html Class II of genes transiently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 49/64 Yaara Zwang 7.51338606789953e-07 1.43364609476926e-06 1425 2258.54545454545 2311 6.83035330350358e-08 186 1.99735129827212 2.38290325884455 1 4.64384812407874 1423 3668 1995 4575 2327 1533 2398 186 3894 2311 534 2269 M2246 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D.html Category D genes: p53-independent genes whose expression in the absence of S389 phosphorylation is similar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 324/496 Arthur Liberzon 1.53603345664223e-07 7.28175281873995e-07 4360 2507.54545454545 2313 1.39639414898876e-08 651 2.20402297934346 -1.82968119463073 -1 5.39031435825828 4358 2030 980 1632 651 4652 3925 2313 2367 1223 3452 2270 M1286 HOSHIDA_LIVER_CANCER_SUBCLASS_S3 http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SUBCLASS_S3.html Genes from 'subtype S3' signature of hepatocellular carcinoma (HCC): hepatocyte differentiation. 19723656 294/490 Jessica Robertson 1.76238714860966e-07 7.40077165608328e-07 2535 1976.72727272727 2315 1.60217026344717e-08 815 2.01991984193789 -2.05611885997627 -1 4.93015938050833 2531 1294 1098 1438 815 2696 2315 3618 2409 917 2613 2271 M12484 REACTOME_GAMMA_CARBOXYLATION_TRANSPORT_AND_AMINO_TERMINAL_CLEAVAGE_OF_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAMMA_CARBOXYLATION_TRANSPORT_AND_AMINO_TERMINAL_CLEAVAGE_OF_PROTEINS.html Genes involved in Gamma-carboxylation, transport, and amino-terminal cleavage of proteins 9/13 Reactome 4.11686806202811e-07 1.00046055710989e-06 730 2245.36363636364 2316 4.11686882471543e-08 17 2.32407522623667 2.21366270733347 1 5.55769949135693 2212 1016 4207 3631 3795 2958 3091 17 728 2316 728 2272 M1457 GREENBAUM_E2A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GREENBAUM_E2A_TARGETS_DN.html Genes down-regulated in pre-B lymphocytes upon Cre-Lox knockout of E2A [GeneID=6929]. 15310760 27/36 Kevin Vogelsang 2.53947160885452e-07 8.22189102913976e-07 4550 2795.72727272727 2316 2.30861081998829e-08 1078 2.05814274429605 1.79266805518423 1 4.98657774837648 4549 1818 1480 2097 1205 4288 4660 4098 2316 1078 3164 2273 M6910 BIOCARTA_INFLAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INFLAM_PATHWAY.html Cytokines and Inflammatory Response 13/44 BioCarta 6.28561108108926e-07 1.27828859001759e-06 4380 2489.81818181818 2317 5.71419352449942e-08 771 2.394602331456 -3.12751838480631 -1 5.62538069809277 4380 937 967 2317 2166 4142 2369 2182 2889 771 4268 2274 M710 REACTOME_VEGF_LIGAND_RECEPTOR_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VEGF_LIGAND_RECEPTOR_INTERACTIONS.html Genes involved in VEGF ligand-receptor interactions 9/10 Reactome 0.000126269627559297 0.000137547344121829 760 2305.72727272727 2317 1.26276802941604e-05 140 2.19893144419442 2.19893144419442 1 3.36482954605493 758 3241 4221 3403 4309 594 140 844 4245 2317 1291 2275 M2683 WINTER_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WINTER_HYPOXIA_DN.html Genes down-regulated in head and neck tumor samples which clustered around known hypoxia genes. 17409455 70/115 Arthur Liberzon 3.15544618909147e-07 8.93979952731796e-07 4385 2481.45454545455 2317 2.86858785606838e-08 307 2.57823648796242 2.39367560352406 1 6.22163652942344 4382 307 799 2272 1438 3648 4460 2939 2317 780 3954 2276 M6705 BIOCARTA_TH1TH2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TH1TH2_PATHWAY.html Th1/Th2 Differentiation 7/21 BioCarta 5.17484955903323e-07 1.131848467036e-06 2320 2381.09090909091 2318 5.17485076409167e-08 93 1.84786895587794 -1.87326600127589 -1 4.3688426619622 2318 2470 4199 4349 2077 2613 1849 93 3298 1267 1659 2277 M271 PID_PI3K_PLC_TRK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PI3K_PLC_TRK_PATHWAY.html Trk receptor signaling mediated by PI3K and PLC-gamma 18832364 54/60 Pathway Interaction Database 5.02638276315934e-07 1.11649088220941e-06 3850 2607 2320 4.56943991958831e-08 1294 1.86650906885737 2.4322810836103 1 4.41787109546664 3849 1697 2320 1294 1951 4422 2645 3049 2248 3815 1387 2278 M2384 SCHMIDT_POR_TARGETS_IN_LIMB_BUD_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHMIDT_POR_TARGETS_IN_LIMB_BUD_DN.html Genes down-regulated in E12.5 forelimb buds with POR [GeneID=5447] knockout. 19273610 22/35 Arthur Liberzon 1.01459199835111e-06 1.77168858017656e-06 2320 2181.72727272727 2320 9.22356787508278e-08 1067 2.44326274085853 -2.23365439870149 -1 5.6014201698395 2320 1850 1080 1067 2577 2986 3246 1897 2402 1756 2818 2279 M1398 ZEILSTRA_CD44_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZEILSTRA_CD44_TARGETS_UP.html Genes implicated in apoptosis that were up-regulated in duodenum of CD44 [GeneID=960] knockout mice. 18483247 9/12 Jessica Robertson 2.39300562711987e-06 3.51759157894917e-06 2835 2381.18181818182 2321 2.39300820403794e-07 151 3.9249305755192 3.32876743961345 1 8.55847751445281 2831 1971 4471 1614 3199 3131 2268 1711 151 2321 2525 2280 M1512 RUAN_RESPONSE_TO_TNF_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_UP.html Adipocyte abundant genes up-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to TNF [GeneID=7124]. 12732648 27/34 John Newman 7.26225222865037e-07 1.40302720072694e-06 3580 2325.72727272727 2321 6.6020496599438e-08 750 2.80974449156159 -1.85903916043688 -1 6.56361122564925 3580 2321 1092 973 2297 3912 2343 3445 750 1079 3791 2281 M3335 HELLER_HDAC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_UP.html Genes up-regulated in at least one of three multiple myeloma (MM) cell lines by TSA [PubChem=5562]. 18172295 445/635 Jessica Robertson 3.59567750648489e-07 9.41752134134615e-07 3465 2431.54545454545 2321 3.26879826742013e-08 934 1.89242436136032 2.029280240468 1 4.53616166538414 3464 2020 1572 2176 1587 2849 4340 2374 3110 934 2321 2282 M12692 FINETTI_BREAST_CANCER_KINOME_GREEN http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCER_KINOME_GREEN.html Genes in the green cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 21/27 Jessica Robertson 1.04060669281905e-06 1.80252127078677e-06 2625 1959.45454545455 2321 9.46006531845004e-08 524 2.23973952069775 -1.97990814707197 -1 5.123905846683 2624 2365 1485 1462 2600 2568 1382 524 2321 1324 2899 2283 M12836 BIOCARTA_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPO_PATHWAY.html EPO Signaling Pathway 31/36 BioCarta 7.4949330120501e-07 1.43339075433049e-06 2075 2479.72727272727 2322 6.81357778674172e-08 864 1.0897739992131 -0.962042706216377 -1 2.51102550727789 2074 3150 3731 913 2322 1890 864 3068 3729 4354 1182 2284 M103 PID_S1P_S1P1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P1_PATHWAY.html S1P1 pathway 18832364 38/45 Pathway Interaction Database 2.37439702991438e-06 3.49568121684214e-06 3400 2614.36363636364 2322 2.15854508412455e-07 1308 1.87096013368093 1.90561183049266 1 4.05556452934737 3397 1772 2008 1308 3128 2252 2322 3466 3505 1471 4129 2285 M19208 RADAEVA_RESPONSE_TO_IFNA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/RADAEVA_RESPONSE_TO_IFNA1_DN.html Genes down-regulated in primary hepatocytes and Hep3B (hepatocyte) cells in response to IFNA [GeneID=3439]. 11910354 15/16 Yujin Hoshida 3.93279321779987e-07 9.79209711146668e-07 3425 2237.27272727273 2322 3.57526720076296e-08 418 1.89634056582862 -2.13080280555373 -1 4.53273404008094 3421 3205 2322 2344 1690 3529 1897 418 947 2105 2732 2286 M5389 RODWELL_AGING_KIDNEY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_UP.html Genes whose expression increases with age in normal kidney. 15562319 568/819 John Newman 3.92257235554152e-10 6.70816721672318e-09 3115 2327.63636363636 2322 3.92257235623391e-11 165 2.29971627961627 2.46618326031017 1 7.50919111347667 3115 1148 4495 1118 689 2223 3610 3029 2322 165 3690 2287 M1163 BAKER_HEMATOPOIESIS_STAT3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BAKER_HEMATOPOIESIS_STAT3_TARGETS.html STAT3 [GeneID=6774] targets in hematopoietic signaling. 17934481 18/20 Arthur Liberzon 1.94170732115812e-05 2.29121463896658e-05 2310 2458.18181818182 2324 1.76520405342435e-06 971 1.95363724143986 2.45953811524247 1 3.59545696160969 2308 3478 2121 2708 3942 2324 1307 971 3658 1492 2731 2288 M11361 KYNG_DNA_DAMAGE_BY_4NQO http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_4NQO.html Genes specifically responding to 4NQO treatment of primary fibroblasts. 15897889 57/66 Jessica Robertson 7.32482978586679e-06 9.29886944305843e-06 1690 2402.54545454545 2325 6.6589583397886e-07 1500 2.24321837202722 2.33897715244447 1 4.48912514869342 2325 1690 1500 3108 3660 2190 2397 2743 2254 1687 2874 2289 M1879 PIONTEK_PKD1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PIONTEK_PKD1_TARGETS_UP.html Genes up-regulated during later stages of renal maturation (days P14-P16) in kidney specific knockout of PKD1 [GeneID=5310]. 17965720 36/67 Jessica Robertson 4.58520451106067e-07 1.05263449864817e-06 2725 2288.36363636364 2325 4.16836860609262e-08 635 2.17326922694348 -1.89900279718295 -1 5.17452531310938 2725 635 1632 3866 1875 2419 2272 3099 2575 1749 2325 2290 M9911 WOO_LIVER_CANCER_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WOO_LIVER_CANCER_RECURRENCE_DN.html Genes negatively correlated with recurrence free survival in patients with hepatitis B-related (HBV) hepatocellular carcinoma (HCC). 18381945 78/146 Yujin Hoshida 1.70058966389368e-06 2.64561081528615e-06 1185 2126 2325 1.54599179858448e-07 866 1.96227641780691 -2.15044447819442 -1 4.35143942032226 1181 3032 2325 2594 2936 866 1247 1944 2597 3145 1519 2291 M1462 BIOCARTA_CTL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTL_PATHWAY.html CTL mediated immune response against target cells 26/57 BioCarta 1.46581550996596e-05 1.76541189258467e-05 995 2580.36363636364 2326 1.33256843317216e-06 993 1.08999490152145 -1.03093340006369 -1 2.03352758006137 993 2326 3151 2980 3860 1478 2147 2077 4561 2307 2504 2292 M9703 BIOCARTA_ATRBRCA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ATRBRCA_PATHWAY.html Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility 27/27 BioCarta 2.01213361927491e-06 3.04204698365713e-06 1185 2128.90909090909 2326 1.82921405417012e-07 295 2.1310011928759 2.29153675630271 1 4.67792801228231 1182 4272 2835 3537 3037 714 626 902 295 3692 2326 2293 M12399 BIOCARTA_CFTR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CFTR_PATHWAY.html Cystic Fibrosis Transmembrane Conductance Regulator And Beta 2 Adrenergic Receptor Pathway 15/17 BioCarta 1.47549598069755e-07 7.26289540930751e-07 2330 1974.09090909091 2327 1.34136007241466e-08 171 1.35341872885834 1.39018930348845 1 3.29131846784247 2327 1920 2765 1708 616 2485 2930 3270 516 3007 171 2294 M19529 RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN.html Genes down-regulated in anaplastic thyroid carcinoma (ATC) compared to normal thyroid tissue. 17406368 645/761 Arthur Liberzon 1.14213693323635e-07 7.05613393308323e-07 3625 2623 2327 1.14213699193781e-08 459 1.76677117742059 2.10154422002225 1 4.32072595914903 3625 2010 4323 2327 459 2273 4626 3681 1992 2906 631 2295 M193 PID_NEPHRIN_NEPH1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NEPHRIN_NEPH1_PATHWAY.html Nephrin/Neph1 signaling in the kidney podocyte 18832364 39/46 Pathway Interaction Database 8.15876413817836e-08 6.31301093970522e-07 3475 2085.18181818182 2328 7.41705858249868e-09 196 1.88882480788873 -1.78844415480936 -1 4.65938313679215 3471 610 2300 471 196 3310 2328 4378 269 2618 2986 2296 M2013 MIKKELSEN_NPC_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in neural progenitor cells (NPC). 17603471 625/901 Arthur Liberzon 1.9652266918981e-07 7.64036221497417e-07 2330 2163.45454545455 2330 1.96522686569334e-08 628 1.93434044646529 2.12381632196957 1 4.70839581327205 2330 1142 4647 3086 1037 628 3069 3530 2539 958 832 2297 M12645 ST_GA13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA13_PATHWAY.html G alpha 13 Pathway 47/53 Signaling Transduction KE 1.13844153561276e-07 7.05613393308323e-07 1745 2435.63636363636 2331 1.03494690411281e-08 377 1.37524955004531 -1.41137059810889 -1 3.35215214737759 1741 2687 3546 4017 377 2331 1844 1191 3717 3147 2194 2298 M1408 KIM_GERMINAL_CENTER_T_HELPER_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GERMINAL_CENTER_T_HELPER_DN.html Genes down-regulated in germinal center T helper cells compared to other CD4+ [GeneID=920] T lymphocyte types. 15213097 29/40 Kate Stafford 9.04282325658413e-08 6.55310251195451e-07 1930 2080.45454545455 2331 8.22074875298002e-09 248 1.81807989808722 -1.92433189712501 -1 4.47114190751983 1927 2761 2279 2795 248 2060 2331 745 2864 2368 2507 2299 M8526 CHEN_LUNG_CANCER_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LUNG_CANCER_SURVIVAL.html Protein profiles associated with survival in lung adenocarcinoma. 14573703 45/62 Kate Stafford 7.52845626854558e-07 1.43514998334148e-06 4645 2755.54545454545 2331 6.84405349527619e-08 1405 2.31920275847285 -2.05540931306815 -1 5.39979205201364 4643 1741 1405 1677 2331 3718 4192 3219 1441 1924 4020 2300 M18387 KORKOLA_SEMINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_SEMINOMA_UP.html Genes from the 12p region that were up-regulated in seminoma tumors compared to normal testis. 16424014 63/79 Arthur Liberzon 2.89280630099424e-07 8.60199355114146e-07 2215 2208.27272727273 2332 2.62982425579352e-08 697 1.99256571192431 2.43662958110531 1 4.81037183859897 2211 3361 2332 3145 1353 2111 2664 2539 1262 2616 697 2301 M2051 ZEMBUTSU_SENSITIVITY_TO_CYCLOPHOSPHAMIDE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_CYCLOPHOSPHAMIDE.html Top genes associated with chemosensitivity to cyclophosphamide [PubChem=2907] across 85 tumor xenografts. 11809704 20/29 Arthur Liberzon 1.05710873937189e-05 1.30650778995426e-05 2490 2051 2333 9.61012562595953e-07 242 2.86520689452481 -2.70277619335511 -1 5.57755137705446 2488 2386 1635 3319 3762 2175 923 780 2333 2518 242 2302 M13283 HSIAO_LIVER_SPECIFIC_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HSIAO_LIVER_SPECIFIC_GENES.html Liver selective genes 11773596 212/467 Kevin Vogelsang 6.59159288885576e-12 1.44708457839066e-10 2545 2066.36363636364 2334 5.99235717170499e-13 162 2.59748833374479 -2.7045202235593 -1 10.228411191351 2542 1383 162 944 1162 3478 3116 4160 2334 365 3084 2303 M292 DASU_IL6_SIGNALING_SCAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_SCAR_UP.html Genes up-regulated in hypertrophic scar fibroblasts in response to IL6 [GeneID=3569]. 15095275 45/49 John Newman 3.4184002315149e-07 9.20938875156981e-07 4525 2474.18181818182 2334 3.10763705697481e-08 507 2.12856698218585 2.82214160738707 1 5.11675031914862 4524 507 1802 2334 1533 4424 4180 2369 1107 1926 2510 2304 M2462 DE_YY1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DE_YY1_TARGETS_UP.html Genes up-regulated in SaOS-2 cells (osteosarcoma) upon knockdown of YY1 [GeneID=7528] by RNAi. 18339860 14/26 Jessica Robertson 2.40246485581933e-05 2.79783718713724e-05 3850 2666.63636363636 2335 2.1840828107681e-06 957 2.50388024499799 2.39953043687709 1 4.53485150004479 3846 957 1493 3847 3999 3118 2218 1820 2335 1531 4169 2305 M295 SIG_PIP3_SIGNALING_IN_CARDIAC_MYOCTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_PIP3_SIGNALING_IN_CARDIAC_MYOCTES.html Genes related to PIP3 signaling in cardiac myocytes 81/93 Signaling Gateway 1.25075055146978e-07 7.16209778122308e-07 2240 2451.72727272727 2336 1.13704602052529e-08 456 1.36655055714377 -1.32035633777903 -1 3.3270743347908 2237 2615 3770 2253 456 2336 1265 2067 3383 4185 2402 2306 M1185 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_DN.html Genes down-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment wiht 4 nM docetaxel [PubChem=148124]. 17099726 11/11 Arthur Liberzon 9.17467637684486e-07 1.64593206000409e-06 1020 1917.81818181818 2336 8.34061836633565e-08 411 1.75589849890458 1.89821130027536 1 4.03407269758122 1016 2892 2336 4183 2508 1029 454 450 3072 2745 411 2307 M1443 REACTOME_GLUTATHIONE_CONJUGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUTATHIONE_CONJUGATION.html Genes involved in Glutathione conjugation 20/32 Reactome 3.60113564292727e-07 9.41752134134615e-07 1820 2350.45454545455 2338 3.27376021126367e-08 845 1.56571438863372 1.50429549818326 1 3.74439586086394 2346 845 2701 3637 1592 1932 2338 3602 1820 1816 3226 2308 M5899 LOPEZ_MESOTELIOMA_SURVIVAL_TIME_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTELIOMA_SURVIVAL_TIME_DN.html Top genes higher expressed in long term mesothelioma survivors. 16540645 10/13 Arthur Liberzon 1.61821145662289e-05 1.93317086187296e-05 2340 2509.27272727273 2338 1.47111214500959e-06 1015 2.82063720781846 2.03105255122997 1 5.29699214445612 2338 1954 1015 1455 3894 2650 1492 3483 2725 2008 4588 2309 M20 PID_P38_MKK3_6PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_MKK3_6PATHWAY.html p38 MAPK signaling pathway 18832364 34/36 Pathway Interaction Database 9.49839847259109e-07 1.69051435862104e-06 2080 2663.72727272727 2339 8.63491143043935e-08 2004 1.4136677670183 -1.40978311754804 -1 3.23146663941214 2078 3421 3539 2006 2530 2290 2339 2004 3755 3244 2095 2310 M9564 SMID_BREAST_CANCER_NORMAL_LIKE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_NORMAL_LIKE_DN.html Genes down-regulated in the normal-like subtype of breast cancer. 18451135 23/24 Jessica Robertson 0.000394885316895362 0.000419032980158747 900 2171.63636363636 2339 3.59051103627857e-05 711 2.87107811547704 3.04699523240246 1 3.85004175757008 898 2339 728 1274 4413 2383 3138 3571 2088 711 2345 2311 M3270 ST_INTEGRIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTEGRIN_SIGNALING_PATHWAY.html Integrin Signaling Pathway 109/127 Signaling Transduction KE 6.31726300938332e-08 5.82044996223792e-07 3595 2232.72727272727 2342 5.74296653707499e-09 97 1.93174526033745 2.17434409168666 1 4.79380510148697 3592 97 2156 485 102 3915 4536 2342 1142 2467 3726 2312 M2862 FINETTI_BREAST_CANCERS_KINOME_BLUE http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCERS_KINOME_BLUE.html Genes in the blue cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 39/50 Jessica Robertson 2.40507245570345e-07 8.0442878985801e-07 4205 2315.36363636364 2343 2.18642974420868e-08 271 1.93765740250036 -1.81928209804325 -1 4.69912074295859 4202 552 1882 1498 1153 3175 2551 4680 271 2343 3162 2313 M5967 REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS.html Genes involved in Synthesis of bile acids and bile salts 17/32 Reactome 1.93109340953689e-06 2.93551075459391e-06 2990 2361.36363636364 2344 1.75554100417665e-07 1269 2.72296083775686 3.38667419549006 1 6.00823880870243 2988 1898 1269 1854 3018 2706 2344 1846 2975 2043 3034 2314 M11213 SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER.html 50 most interesting genes up-regulated in pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by TSA [PubChem=5562]. 12839967 56/89 John Newman 1.45615609580977e-08 1.85758291141139e-07 3930 2288.81818181818 2344 1.32377827767992e-09 293 3.06922995372318 3.23152347469242 1 8.25827898502968 3930 391 293 1773 2344 2089 3866 2794 3308 347 4042 2315 M9197 ELVIDGE_HYPOXIA_BY_DMOG_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_BY_DMOG_UP.html Genes up-regulated in MCF7 cells (breast cancer) treated with hypoxia mimetic DMOG [PubChem=3080614]. 16565084 178/201 Arthur Liberzon 1.88196726460247e-07 7.48978540381421e-07 4485 2623.09090909091 2345 1.71087947781221e-08 643 2.16907166338525 2.37109413315775 1 5.29337001752222 4485 2079 848 1423 893 4351 4063 4282 2345 643 3442 2316 M1709 HILLION_HMGA1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HILLION_HMGA1_TARGETS.html Genes changed in Rat1a cells (fibroblasts) by overexpression of HMGA1 isoform a [GeneID=3159] off a plasmid vector. 19074878 116/175 Leona Saunders 7.28871621570216e-07 1.40476686558245e-06 2330 2578.18181818182 2345 6.62610784590315e-08 1661 1.8813711929526 -2.30896943483014 -1 4.37797524429221 2329 3603 2652 2709 2303 2345 1661 2190 2951 3756 1861 2317 M988 RUIZ_TNC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUIZ_TNC_TARGETS_UP.html Genes up-regulated in T98G cells (glioblastoma) by TNC [GeneID=3371]. 15492259 231/287 Arthur Liberzon 7.64167357491591e-07 1.44912411705918e-06 605 2449.54545454545 2345 6.94697839022122e-08 601 2.19650970814712 2.54838914906035 1 5.10776170490077 3816 1372 601 601 2345 4032 4472 2454 2235 912 4105 2318 M2529 BIOCARTA_PDGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PDGF_PATHWAY.html PDGF Signaling Pathway 48/52 BioCarta 5.28747746777147e-07 1.1469160683769e-06 1795 2481.63636363636 2346 4.80679885323966e-08 676 1.32527066876392 -1.24278218275935 -1 3.11607230424564 1791 3086 3513 676 2003 2092 1495 2912 3718 3666 2346 2319 M4342 BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G6, defined by unsupervised clustering. 17187432 102/123 Yujin Hoshida 2.66145238855511e-07 8.32475498607032e-07 2585 2230.18181818182 2346 2.41950246411332e-08 124 2.00738319448034 2.43751348765576 1 4.85800158103016 2582 124 1267 2630 1262 2346 4247 4021 2152 1189 2712 2320 M19946 LI_CYTIDINE_ANALOG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/LI_CYTIDINE_ANALOG_PATHWAY.html The 'cytidine analog pathway': genes involved in transport and metabolism of the anti-cancer analogs of cytidine: gemcitabine and cytarabine [PubChem=596;3461;6253]. 18757419 13/18 Jessica Robertson 4.0065562000016e-06 5.45298306343931e-06 2535 2220 2347 3.64233045146158e-07 474 2.56356661331369 2.23667704655603 1 5.37632553662996 2535 943 1816 2347 3398 2763 3211 1440 474 2171 3322 2321 M17316 WU_HBX_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_2_UP.html Genes up-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in primary hepatocytes. 11439330 41/42 John Newman 2.98149684515035e-07 8.70294688256627e-07 2350 2635.72727272727 2348 2.7104520447369e-08 1269 1.82736544432619 -2.27652862060197 -1 4.40367963131145 2348 3946 2988 2977 1382 1865 1880 1269 4199 3805 2334 2322 M1102 GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN.html Genes down-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) upon serum deprivation for 22 hr in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 110/129 Arthur Liberzon 1.6405775828526e-06 2.564930835066e-06 2780 2142.81818181818 2349 1.49143527841873e-07 234 2.1882256929122 2.13778400713819 1 4.87009061314609 2779 2125 1401 382 2920 1968 2702 2416 234 2349 4295 2323 M201 PID_ERBB_NETWORK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB_NETWORK_PATHWAY.html ErbB receptor signaling network 18832364 16/18 Pathway Interaction Database 1.41816783121425e-06 2.28883831480239e-06 3295 2386.54545454545 2350 1.28924431399718e-07 615 2.94193230031739 -2.97638568832085 -1 6.6232846425116 3295 912 945 2350 2816 3735 3442 4443 615 1510 2189 2324 M874 REACTOME_SIGNALING_BY_ILS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ILS.html Genes involved in Signaling by Interleukins 118/135 Reactome 4.9855374786931e-07 1.11141872398347e-06 1595 2359.27272727273 2350 4.53230782590249e-08 1096 1.756121466455 -1.70754916633521 -1 4.15503017908308 1591 2996 2856 1096 1943 2350 1759 2577 3439 3025 2320 2325 M8 PID_ENDOTHELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ENDOTHELIN_PATHWAY.html Endothelins 18832364 88/104 Pathway Interaction Database 4.85509811567722e-07 1.09541410640518e-06 4175 2767.63636363636 2351 4.41372653375553e-08 505 2.10497646293618 2.38351999530084 1 4.99570300344939 4172 2143 1337 505 1917 4602 3160 4489 2351 1940 3828 2326 M17068 BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_DN.html Down-regulated genes in tumor samples from colon cancer patients who developed recurrence of the disease. 16091735 14/17 Leona Saunders 1.06593150109169e-05 1.31500174729555e-05 1855 2221.45454545455 2352 9.69033332470425e-07 793 1.64848303591927 2.24783346731196 1 3.18590311523497 1852 1933 2465 2352 3767 2675 2646 1315 793 3314 1324 2327 M1813 MATZUK_IMPLANTATION_AND_UTERINE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_IMPLANTATION_AND_UTERINE.html Genes important for implantation and uterine, based on mouse models with female fertility defects. 18989307 20/32 Jessica Robertson 1.69641110507598e-06 2.6409750171079e-06 1855 2270.27272727273 2353 1.54219310288467e-07 576 2.4784627063548 2.56641814095098 1 5.51002827822134 1854 3474 1990 3383 2934 927 576 4034 2353 2515 933 2328 M11733 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_DN.html Genes exclusively down-regulated in B lymphocytes from WM (Waldenstroem's macroblobulinemia) patients but with a similiar expression pattern in the normal cells and in the cells from CLL (chronic lymphocytic leukemia) patients. 17252022 12/15 Arthur Liberzon 2.44102155299356e-07 8.09102649587753e-07 2925 2071.63636363636 2354 2.21911074894403e-08 967 2.46496014812542 -2.98442949332644 -1 5.98903462394263 2925 967 1261 2354 1168 2764 1219 3404 2690 1551 2485 2329 M14265 APPIERTO_RESPONSE_TO_FENRETINIDE_DN http://www.broadinstitute.org/gsea/msigdb/cards/APPIERTO_RESPONSE_TO_FENRETINIDE_DN.html Genes down-regulated in A2780 cells (ovarian carcinoma) exposed to fenretinide [PubChem=1744]. 17213814 81/108 Arthur Liberzon 5.50501469374344e-06 7.19769234195818e-06 225 2057.63636363636 2355 5.00457133534235e-07 221 1.78142907225915 1.76700468129895 1 3.63438504564163 221 2604 2355 2516 3540 627 596 2183 3524 3151 1317 2330 M12533 WALLACE_PROSTATE_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_DN.html Genes down-regulated in prostate tumor vs normal tissue samples. 18245496 9/10 Jessica Robertson 0.000583819534382041 0.000614409855581546 1790 2509.45454545455 2356 5.83972971480736e-05 432 1.82940131432381 2.25016902583484 1 2.31274248762724 1790 3237 4539 2356 4706 2573 3466 1003 432 2324 1178 2331 M1568 APRELIKOVA_BRCA1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/APRELIKOVA_BRCA1_TARGETS.html Genes down-regulated in embryonic stem cells with BRCA1 [GeneID=672] loss of function (LOF). 11384963 70/85 John Newman 1.76889576464956e-05 2.09884062572799e-05 2030 2330.45454545455 2357 1.60809998863782e-06 570 2.29524446883324 2.89987160711181 1 4.26805320502613 2028 4196 2357 903 3915 2737 2914 1267 570 3699 1049 2332 M18810 REACTOME_PD1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PD1_SIGNALING.html Genes involved in PD-1 signaling 11/21 Reactome 1.59529624215107e-07 7.31918027928963e-07 3320 2259.54545454545 2358 1.45026941621049e-08 692 3.0483965830195 -3.26807418360066 -1 7.47181404973087 3319 2436 1639 2358 692 3232 2867 1363 861 2241 3847 2333 M9379 REACTOME_SIGNAL_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_AMPLIFICATION.html Genes involved in Signal amplification 28/36 Reactome 6.65057054125837e-07 1.32618052195773e-06 3545 2603.36363636364 2358 6.04597504701616e-08 944 2.08480325062311 -1.4524355886252 -1 4.877736840171 3541 2329 2358 1698 2220 3411 1597 3577 944 2909 4053 2334 M827 REACTOME_REPAIR_SYNTHESIS_FOR_GAP_FILLING_BY_DNA_POL_IN_TC_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REPAIR_SYNTHESIS_FOR_GAP_FILLING_BY_DNA_POL_IN_TC_NER.html Genes involved in Repair synthesis for gap-filling by DNA polymerase in TC-NER 14/15 Reactome 7.12433406425588e-05 7.91220159606771e-05 475 2090.36363636364 2360 6.47687707674953e-06 186 1.26281965710657 1.33845567722951 1 2.03304384691676 472 2410 2865 2851 4204 648 186 1447 3672 2360 1879 2335 M6434 FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP.html Top 100 genes positively associated with T-cell acute lymphoblastic leukemia MLL T-ALL) expressing MLL-ENL fusion [GeneID=4297;4298]. 12637319 133/194 Kevin Vogelsang 2.62588005845481e-07 8.29211725993449e-07 2110 2405.18181818182 2360 2.38716397443194e-08 863 1.76968690289614 2.07489313271906 1 4.2780498847248 3656 2107 2107 863 1246 3430 4136 2360 1536 2443 2573 2336 M13167 FREDERICK_PRKCI_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/FREDERICK_PRKCI_TARGETS.html Genes down-regulated in H1703 cells (non-small cell lung cancer, NSCLC) after knockdown of PRKCI [GeneID=5584] by RNAi. 18427549 13/23 Jessica Robertson 7.85429736507537e-07 1.4805225065158e-06 3350 2446.63636363636 2362 7.14027288106099e-08 950 2.68734704717673 2.10258883570883 1 6.25027469276894 3348 950 1040 1877 2362 2851 1829 3871 3992 1360 3433 2337 M1218 BORLAK_LIVER_CANCER_EGF_UP http://www.broadinstitute.org/gsea/msigdb/cards/BORLAK_LIVER_CANCER_EGF_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) developed by transgenic mice overexpressing a secretable form of EGF [GeneID=1950] in liver. 15674348 100/134 Leona Saunders 1.90956350658369e-12 4.4182057603309e-11 4430 2153.54545454545 2363 1.7359668241685e-13 70 2.80872540062794 2.57330899027737 1 11.6462958262447 4427 79 150 70 2363 4357 3600 4667 1051 412 2513 2338 M1615 WENG_POR_TARGETS_GLOBAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_GLOBAL_DN.html Genes down-regulated in liver from transgenic mice with reduced expression of POR [GeneID=5447] in all tissues. 16006652 31/39 John Newman 1.12267937221934e-07 7.05613393308323e-07 2455 2368.27272727273 2365 1.02061766319152e-08 364 1.60631731839097 -1.30441480000087 -1 3.92378388753062 2454 2314 2571 3865 364 2365 1081 2237 3948 1994 2858 2339 M2817 STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP.html Genes up-regulated in prefrontal cortex (PFC) of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 285/347 Jessica Robertson 7.3743780005476e-08 6.11670596203388e-07 2370 2541.36363636364 2366 6.70398022521455e-09 159 1.85040828105508 2.18647631491156 1 4.57380806705428 2366 2039 2052 2600 159 3487 4585 3708 1510 2344 3105 2340 M12695 ROSS_LEUKEMIA_WITH_MLL_FUSIONS http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_LEUKEMIA_WITH_MLL_FUSIONS.html Top 100 probe sets associated with MLL fusions [GeneID=4297] irrespective of the lineage of the pediatric acute leukemia. 15226186 95/157 Arthur Liberzon 1.46319086382526e-07 7.26289540930751e-07 3480 2281.09090909091 2366 1.3301736010365e-08 606 2.03308958894519 2.18678548779074 1 4.9693077057078 3476 2136 1558 1416 606 2366 3531 3237 2616 1592 2558 2341 M7176 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP.html Genes up-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing monocytes. 17898786 23/30 Arthur Liberzon 8.68200403388674e-07 1.58465038824228e-06 1695 2401.81818181818 2368 7.89273405465885e-08 883 2.10899758326639 2.10982245399363 1 4.86933536230835 1692 2796 1814 3438 2459 918 883 4260 3897 1895 2368 2342 M17552 MAINA_VHL_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAINA_VHL_TARGETS_DN.html Genes down-regulated in RCC4 cells (renal cell carcinoma) engineered to stably express VHL [GeneID=7428] off a plasmid vector. 15824735 23/27 Leona Saunders 9.26332302836832e-07 1.65931251210241e-06 3670 2454.36363636364 2368 8.42120629889698e-08 1016 3.13813228104159 2.64757752207998 1 7.24462417475365 3667 2368 1116 2355 2514 3428 3899 1697 1016 2225 2713 2343 M552 REACTOME_PROLACTIN_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROLACTIN_RECEPTOR_SIGNALING.html Genes involved in Prolactin receptor signaling 14/41 Reactome 5.42773404643452e-05 6.09973921408832e-05 1995 2600.45454545455 2369 4.93442541954577e-06 364 1.28616440124966 -1.39960037034562 -1 2.12999370729197 1991 4069 3380 4436 4716 2369 1947 364 744 4212 377 2344 M6322 REACTOME_ACTIVATION_OF_RAC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_RAC.html Genes involved in Activation of Rac 16/20 Reactome 7.90925552878651e-07 1.48705212576209e-06 3660 2435.54545454545 2369 7.19023488387016e-08 759 2.3892793934795 3.55125408367136 1 5.54963789247572 3659 924 1812 2174 2369 3878 4390 926 759 2706 3194 2345 M4562 LENAOUR_DENDRITIC_CELL_MATURATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LENAOUR_DENDRITIC_CELL_MATURATION_UP.html Genes up-regulated during in vitro maturation of CD14+ [GeneID=929] monocytes (day 0) into immature (day 7) and mature dendritic cells (day 14). 11279020 133/177 Kevin Vogelsang 2.01913181976989e-07 7.65527859584926e-07 4455 2324.54545454545 2370 1.83557455007568e-08 334 2.27049532465023 2.26123165630085 1 5.53455562927934 4453 1532 456 582 953 3910 3345 3329 2370 334 4306 2346 M2242 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A.html Category A genes: p53-dependent genes whose expression in the absence of S389 phosphorylation is similar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 992/1481 Arthur Liberzon 4.78924454810296e-16 1.75234374163147e-14 3740 2324.18181818182 2370 4.78924454810297e-17 19 2.30096394327815 2.56341985047429 1 12.6795597897542 3739 1082 4672 19 827 2370 4613 3256 1333 72 3583 2347 M167 PID_AP1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AP1_PATHWAY.html AP-1 transcription factor network 18832364 106/143 Pathway Interaction Database 4.39683700621935e-06 5.91424071511979e-06 4420 2603 2371 3.99713253963319e-07 1020 2.0759292687989 2.73403232467355 1 4.3146907364976 4417 2129 1020 1103 3435 4463 3047 2278 2993 1377 2371 2348 M1499 WHITESIDE_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WHITESIDE_CISPLATIN_RESISTANCE_UP.html Genes up-regulated in NCI-H2170 cells (lung cancer) upon induction of resistance to cisplatin [PubChem=2767]. 14737109 19/25 John Newman 2.16673370608105e-08 2.61376652706534e-07 3245 2145 2372 1.96975793401887e-09 2 2.06474394082409 -2.56569630881323 -1 5.41600663990526 3241 2372 1709 1262 2 3578 3810 2121 470 2385 2645 2349 M250 ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN.html Genes down-regulated in macrophages by P.gingivalis FimA pathogen. 18025224 355/510 Arthur Liberzon 4.37797986533302e-07 1.02755171379273e-06 3275 2360.18181818182 2373 3.97998248777023e-08 789 1.85078609486201 2.07469798082641 1 4.40706830300087 3275 2028 2373 4354 1820 789 2685 3098 2577 1401 1562 2350 M1530 SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1B http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1B.html Genes with some basal expression and partially methylated promoters, up-regulated by the combination of TSA and decitabine [PubChem=5562;451668] in RKO cells (colorectal cancer). 11992124 31/44 John Newman 6.84833878494067e-07 1.35134444251338e-06 3575 2537.81818181818 2373 6.22576446977105e-08 868 2.83656215615727 -2.61440580093069 -1 6.64532969651624 3573 1801 868 2604 2244 3776 2169 2373 3294 1249 3965 2351 M13336 PETRETTO_HEART_MASS_QTL_CIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_HEART_MASS_QTL_CIS_DN.html Down-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that colocalize with previously mapped cardiac mass QTLs. 18443592 39/74 Jessica Robertson 1.09888139252657e-07 7.03739764799127e-07 2830 1927.09090909091 2374 9.98983134013431e-09 350 2.0671651169302 2.46661224022379 1 5.06482163237592 2830 613 2252 2374 350 2464 2775 1323 995 2619 2603 2352 M706 REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS.html Genes involved in Glycerophospholipid biosynthesis 69/85 Reactome 9.43142374374158e-07 1.68146476145018e-06 610 1630.18181818182 2375 8.57402526091413e-08 296 1.69151220316347 -1.73940847497345 -1 3.87800419594104 610 2630 2758 2780 2526 369 538 375 2375 2675 296 2353 M866 REACTOME_ROLE_OF_DCC_IN_REGULATING_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ROLE_OF_DCC_IN_REGULATING_APOPTOSIS.html Genes involved in Role of DCC in regulating apoptosis 14/16 Reactome 6.0650424730157e-07 1.24736385501674e-06 3250 2472.90909090909 2375 5.5136764955e-08 722 1.76871404870309 2.13463576437829 1 4.14953579867925 3247 1918 2375 3087 2133 3469 3907 2714 722 1914 1716 2354 M18367 PYEON_HPV_POSITIVE_TUMORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_HPV_POSITIVE_TUMORS_DN.html Down-regulated genes in cervical carcinoma and head and neck tumors positive for human papilloma virus (HPV) compared to those negative for HPV. 17510386 8/17 Arthur Liberzon 1.12623695611981e-05 1.3839725157213e-05 2730 2543.72727272727 2375 1.12624266400409e-06 855 4.19451793337483 -3.99550494147479 -1 8.14626980664611 2727 2455 4273 1857 3819 2375 1517 4648 855 2066 1389 2355 M13158 BIOCARTA_LONGEVITY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LONGEVITY_PATHWAY.html The IGF-1 Receptor and Longevity 22/25 BioCarta 2.66118437838798e-07 8.32475498607032e-07 2380 2374.45454545455 2376 2.41925881844789e-08 854 1.20408678320404 -1.18632073749679 -1 2.89394712083861 2376 854 3260 2520 1261 1728 1892 2899 3281 4191 1857 2356 M2191 SUBTIL_PROGESTIN_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SUBTIL_PROGESTIN_TARGETS.html Genes responding to progestin R5020 [PubChem=36709] treatment of T47D-MTVL cells (breast cancer). 18378698 56/62 Arthur Liberzon 7.98542499134895e-07 1.49746547314927e-06 2280 2389 2376 7.25947989986452e-08 703 1.40851681531656 1.39163947960017 1 3.24934038476898 2280 3372 3319 4058 2376 1255 1086 703 4144 2960 726 2357 M3456 FERNANDEZ_BOUND_BY_MYC http://www.broadinstitute.org/gsea/msigdb/cards/FERNANDEZ_BOUND_BY_MYC.html Genes identified by ChIP within the high-affinity group of MYC [GeneID=4609] targets. 12695333 251/334 Yujin Hoshida 4.1881940805199e-07 1.00653136761985e-06 2380 2556.36363636364 2377 3.80744988894264e-08 1770 1.90695120826667 2.05792841350546 1 4.54921042086333 2377 3289 1973 2245 1770 2157 3648 2883 2879 2624 2275 2358 M1217 SMITH_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMITH_TERT_TARGETS_DN.html Genes consistently down-regulated in HMEC cells (primary mammary epithelium) upon expression of TERT [GeneID=7015] off a retroviral vector. 12717449 127/169 Broad Institute 5.56222680042615e-08 5.413136185157e-07 2850 2008.63636363636 2377 5.05656994641373e-09 34 2.16764038515797 2.25239336394284 1 5.41277753077964 2848 34 1166 2184 72 2377 2683 2572 3056 1960 3143 2359 M4857 UROSEVIC_RESPONSE_TO_IMIQUIMOD http://www.broadinstitute.org/gsea/msigdb/cards/UROSEVIC_RESPONSE_TO_IMIQUIMOD.html Interferon cluster genes up-regulated in skin tumors treated with imiquimod [PubChem=57469]. 16077073 32/44 Jessica Robertson 2.74023394194423e-06 3.93056538545192e-06 1255 2287.18181818182 2377 2.49112486825308e-07 1255 2.1667539102829 -2.10861403428079 -1 4.66027540827687 1255 2743 1674 2377 3215 2069 2086 2671 2602 1860 2607 2360 M2064 BIOCARTA_41BB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_41BB_PATHWAY.html The 4-1BB-dependent immune response 19/25 BioCarta 3.18912894696116e-06 4.47730179347314e-06 355 2052.63636363636 2379 2.89921233631349e-07 209 1.24634624665648 -1.30540564723751 -1 2.63104813853678 355 2379 3159 2946 3285 584 209 1560 3900 2769 1433 2361 M8334 ZEMBUTSU_SENSITIVITY_TO_DOXORUBICIN http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_DOXORUBICIN.html Top genes associated with chemosensitivity to doxorubicin [PubChem=31703] across 85 tumor xenografts. 11809704 24/24 Arthur Liberzon 1.08573091897518e-05 1.33733035948926e-05 4035 2740.54545454545 2379 9.87032979315341e-07 1336 2.00463073486049 2.47858973577276 1 3.8791190230273 4032 1858 2093 3387 3773 4145 3096 1336 1757 2379 2290 2362 M16120 BIOCARTA_SALMONELLA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SALMONELLA_PATHWAY.html How does salmonella hijack a cell 20/24 BioCarta 7.32575152407185e-07 1.40845406083988e-06 2710 2461.45454545455 2380 6.65977633042318e-08 646 1.96977634139305 -0.995491041428955 -1 4.58514457929558 2709 2380 2408 2221 2309 2108 1024 3382 646 3634 4255 2363 M18438 LEE_LIVER_CANCER_E2F1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_E2F1_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by overexpression of E2F1 [GeneID=1869]. 15565109 90/147 Yujin Hoshida 8.93202108745413e-09 1.18758139528968e-07 4400 2355.72727272727 2381 8.12001920338022e-10 253 2.68587565657575 3.01516016730309 1 7.43040801212183 4397 1602 277 804 1892 4128 3184 2744 2381 253 4251 2364 M17915 KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP.html Genes up-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 24 h. 18701491 940/1166 Jessica Robertson 2.59634911030139e-07 8.27068974676848e-07 1490 2554.63636363636 2381 2.59634941364773e-08 1342 1.62222954100365 -1.49964956221922 -1 3.91814953481897 1488 3546 4503 2975 1342 1479 1908 2381 2905 3542 2032 2365 M10382 IIZUKA_LIVER_CANCER_EARLY_RECURRENCE http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_EARLY_RECURRENCE.html Genes down-regulated in hepatocellular carcinoma (HCC) tumors with higher risk of early intrahepatic recurrence. The single up-regulated gene (GenBank Accession=AC000063) has been excluded from the signature. 12648972 20/27 Yujin Hoshida 1.27081727409443e-05 1.54594266333137e-05 2385 2260.90909090909 2382 1.1552951045057e-06 1118 2.72667366885347 -2.25943901934628 -1 5.22531816426968 2382 2812 1325 2649 3824 2171 2230 2400 1118 1463 2496 2366 M16617 GAJATE_RESPONSE_TO_TRABECTEDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAJATE_RESPONSE_TO_TRABECTEDIN_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) by trabectedin [PubChem=3199]. 12198119 25/37 John Newman 2.9999987750033e-07 8.74073717161454e-07 4715 2665.36363636364 2382 2.72727198553996e-08 658 1.98426032730585 -1.54485105519251 -1 4.78456753416442 4712 773 2382 1422 1389 4239 3278 4547 658 2164 3755 2367 M17300 KARAKAS_TGFB1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/KARAKAS_TGFB1_SIGNALING.html Genes up-regulated by TGFB1 [GeneID=7040] in MCF10A cells (breast cancer): both wild-type and those lacking p21 [GeneID=1026]. 16619041 25/28 Arthur Liberzon 3.3963379262359e-06 4.7218600918508e-06 2530 2367.54545454545 2383 3.08758469952695e-07 824 3.11601717474339 3.08953678379951 1 6.62405861272001 2529 1846 824 2338 3319 2651 2383 2103 3574 1291 3185 2368 M1959 HINATA_NFKB_TARGETS_KERATINOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HINATA_NFKB_TARGETS_KERATINOCYTE_DN.html Genes down-regulated in primary keratinocytes by expression of p50 (NFKB1) and p65 (RELA) [GeneID=4790;5970] components of NFKB. 12673201 29/44 Arthur Liberzon 8.03680477514365e-07 1.50411255109746e-06 3105 2415.36363636364 2383 7.30618882824066e-08 844 2.8206642819636 -2.83949689167424 -1 6.55504058641232 3105 1796 844 1402 2383 4201 4399 1518 3257 1071 2593 2369 M9946 LU_TUMOR_ANGIOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_ANGIOGENESIS_UP.html Up-regulated genes of putative pathways stimulated in tumor endothelial cells by papillary serous ovarian epithelial tumor cells. 17308118 37/40 Jessica Robertson 1.14100722681831e-06 1.93655307823892e-06 4560 2280.72727272727 2386 1.03727983508212e-07 368 3.01752532734738 3.13712391944165 1 6.88284097205705 4560 561 629 820 2659 4174 3292 2386 368 1039 4600 2370 M1489 FIRESTEIN_CTNNB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/FIRESTEIN_CTNNB1_PATHWAY.html Genes required for CTNNB1 [GeneID=1499] activity in DLD-1 cell (colon cancer with APC [GeneID=324] deletions), based on shRNA screen. 18794900 62/72 Jessica Robertson 2.74569979684578e-07 8.38703759494626e-07 1300 2239.36363636364 2387 2.49609103592876e-08 366 1.79222391785146 1.66570371289881 1 4.32960535443582 2387 366 2405 1956 1297 2867 4076 2254 1299 2749 2977 2371 M5882 NABA_PROTEOGLYCANS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_PROTEOGLYCANS.html Genes encoding proteoglycans 22159717 19/35 Alexandra Naba 1.44205403776296e-05 1.7390125340422e-05 2390 2017.45454545455 2387 1.31096680928423e-06 535 3.85826396351697 4.01299756075581 1 7.33532714334867 970 2387 535 3042 3854 2447 2766 1309 2387 1100 1395 2372 M19469 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_DN http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_DN.html Hepatic graft versus host disease (GVHD), day 7: down-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 43/66 Arthur Liberzon 2.02742542522912e-07 7.65527859584926e-07 4245 2585.72727272727 2388 1.84311419278905e-08 958 2.47144928761173 -2.02928698566708 -1 6.0288292984162 4242 2262 1154 2770 958 4077 3052 1463 2388 1736 4341 2373 M3397 KEGG_BUTANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BUTANOATE_METABOLISM.html Butanoate metabolism 36/48 KEGG 8.09902300037447e-07 1.51335663348248e-06 3180 2457 2389 7.36275089266305e-08 1189 2.03769073099079 1.78433588268465 1 4.71939075247493 1908 2731 2395 2212 2389 1472 1189 4048 3178 3176 2329 2374 M16651 RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN.html Genes down-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to normal thyroid tissue. 17406368 1047/1230 Arthur Liberzon 1.44993229764763e-07 7.26289540930751e-07 2495 2497.27272727273 2389 1.4499323922513e-08 691 1.77826740283977 -1.52377045672439 -1 4.34019601214545 2492 1085 4321 2430 691 2144 2377 4376 2110 2389 3055 2375 M11736 SA_MMP_CYTOKINE_CONNECTION http://www.broadinstitute.org/gsea/msigdb/cards/SA_MMP_CYTOKINE_CONNECTION.html Cytokines can induce activation of matrix metalloproteinases, which degrade extracellular matrix. 10/15 SigmaAldrich 2.5832614199664e-08 3.04824847556035e-07 2775 2252.72727272727 2390 2.3484195002721e-09 9 2.33680839831657 -2.54437138059865 -1 6.07348758053341 2773 1956 1762 3648 9 3443 2390 1205 3021 1558 3015 2376 M13015 REACTOME_NOREPINEPHRINE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOREPINEPHRINE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Norepinephrine Neurotransmitter Release Cycle 14/21 Reactome 8.10323688585263e-07 1.51354483977936e-06 2230 2394.36363636364 2390 7.36658170046446e-08 256 1.52676000081643 -1.447934676373 -1 3.52347086843642 2228 1928 2427 3314 2390 1107 256 4062 3406 1913 3307 2377 M9375 DAZARD_UV_RESPONSE_CLUSTER_G1 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G1.html Cluster G1: genes most highly up-regulated in NHEK cells (normal keratinocyte) between 6 h and 12 h after UV-B irradiation. 12771951 114/137 John Newman 6.07983445482083e-07 1.24986143844749e-06 1765 2726.72727272727 2390 5.52712375910991e-08 1763 2.02043526094152 1.89765747391376 1 4.74650800255943 1763 3605 1861 3505 2134 2390 2379 3312 3511 2126 3408 2378 M19703 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_WS http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_WS.html Human environmental stress response genes not changed in primary fibroblasts from patients with Warner syndrom (WS) . 15897889 17/19 Jessica Robertson 5.54453805490474e-07 1.18363725097921e-06 3350 2467.90909090909 2390 5.04049041114948e-08 566 2.36885092901541 -1.76183215847802 -1 5.59617629039068 3347 2390 1909 1253 2050 2987 2376 4184 566 2464 3621 2379 M6977 BROWNE_HCMV_INFECTION_30MIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_30MIN_UP.html Genes up-regulated in primary fibroblast cell culture at 30 min time point after infection with HCMV (AD169 strain). 11711622 70/94 Arthur Liberzon 7.56580195245587e-06 9.56875273729681e-06 1080 2317.18181818182 2390 6.87802542852797e-07 890 2.43471658667575 2.38544895487945 1 4.86445652243955 1079 3352 890 1982 3674 1907 2459 3147 3589 1020 2390 2380 M724 REACTOME_RESPONSE_TO_ELEVATED_PLATELET_CYTOSOLIC_CA2_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESPONSE_TO_ELEVATED_PLATELET_CYTOSOLIC_CA2_.html Genes involved in Response to elevated platelet cytosolic Ca2+ 100/153 Reactome 4.0958069790826e-07 1.00046055710989e-06 2295 2881.72727272727 2392 3.72346158328332e-08 1647 2.19228487885651 2.00861697846369 1 5.23970394866064 2291 3885 1647 3767 1733 1836 2059 4314 4114 2392 3661 2381 M1420 MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_DN.html Down-regulated genes discriminating multiple myeloma samples by the ype of immunoglobulin light chain they produce: Ig lambda (IGLL) vs Ig kappa (IGLK). 12623842 29/32 Kate Stafford 4.52060928046371e-07 1.04185917010687e-06 2395 1935.18181818182 2393 4.10964564488081e-08 428 1.70452733689439 2.06187106578245 1 4.05072798399968 2393 2759 2643 1456 1861 2753 2597 428 795 2689 913 2382 M14181 YAMASHITA_METHYLATED_IN_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_METHYLATED_IN_PROSTATE_CANCER.html Genes up-regulated in prostate cancer cell lines after treatment with 5-aza-2'-deoxycytidine (decitabine) [PubChem=451668]. 18381416 72/104 Jessica Robertson 2.7010492818297e-13 7.16233292709897e-12 3075 1967.45454545455 2393 2.45549934711821e-14 131 3.38178316019278 3.13211294204909 1 15.1073505620664 1653 1643 131 762 2797 2393 3075 2998 3071 397 2722 2383 M14146 BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G1, defined by unsupervised clustering 17187432 194/241 Yujin Hoshida 1.68706330130282e-07 7.33971845416521e-07 3125 2142.54545454545 2393 1.53369402788615e-08 560 1.86616642753617 -1.67999491435613 -1 4.55377393306753 3121 1425 2216 609 764 2911 2580 4400 560 2393 2589 2384 M2247 BRUINS_UVC_RESPONSE_LATE http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_LATE.html Late response genes: differentially expressed only 12 h after UV-C irradiation of MEF cells (embryonic fibroblast). 18195040 1444/1740 Arthur Liberzon 1.24816267130739e-07 7.16209778122308e-07 1400 2411.81818181818 2394 1.24816274141334e-08 540 1.8080587472882 2.05371780521536 1 4.41815902341059 2286 3543 4674 2692 540 1398 2636 1398 2394 2735 2234 2385 M16794 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450.html Metabolism of xenobiotics by cytochrome P450 40/110 KEGG 8.12504740172842e-07 1.51522021873402e-06 4220 2758.36363636364 2395 7.38640945679564e-08 633 2.76957490886224 2.46131327221689 1 6.4318467874655 4217 2257 633 988 2395 4411 4576 3297 2298 1106 4164 2386 M9251 SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_UP.html Genes bound by EWSR1-FLT1 [GeneID=2130;2321] fusion and up-regulated in STA-ET-7.2 cells (Ewing's sarcoma) after knockdown of EWSR1-FLT1 by RNAi. 15735734 19/24 Arthur Liberzon 8.13228470646232e-07 1.51597092474337e-06 3980 2774.09090909091 2396 7.39298882959751e-08 504 2.5051587438344 1.5628866877067 1 5.81279325466883 3978 3191 2255 2138 2396 4136 4654 504 1266 2384 3613 2387 M6782 BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP.html Genes up-regulated in T24 (bladder cancer) cells in response to the photodynamic therapy (PDT) stress. 17952126 1112/1329 Jessica Robertson 3.67539212185912e-07 9.51088312235473e-07 960 2829 2396 3.67539272974207e-08 958 1.56326067440532 -1.43282295313904 -1 3.7357559774625 958 4390 4432 4130 1719 1371 1319 2357 3521 4526 2396 2388 M8472 REACTOME_FACILITATIVE_NA_INDEPENDENT_GLUCOSE_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FACILITATIVE_NA_INDEPENDENT_GLUCOSE_TRANSPORTERS.html Genes involved in Facilitative Na+-independent glucose transporters 7/11 Reactome 1.43672462264013e-05 1.73391465580706e-05 2665 2383 2397 1.43673391152404e-06 44 3.0382761039455 3.87516201755777 1 5.76729074405626 2661 1981 4243 1627 3887 3081 3583 1912 44 2397 797 2389 M8445 KIM_MYC_AMPLIFICATION_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYC_AMPLIFICATION_TARGETS_UP.html Genes positively correlated with amplifications of MYC [GeneID=4609] in SCLC (small cell lung cancer) cell lines. 16116477 234/298 Arthur Liberzon 2.74725718776536e-06 3.93515256239949e-06 690 2234.45454545455 2397 2.49750965310705e-07 600 1.72263241235943 1.76333606465541 1 3.69444747662314 687 3855 3396 3196 3220 702 855 600 2397 3891 1780 2390 M5718 NIKOLSKY_BREAST_CANCER_21Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_21Q22_AMPLICON.html Genes within amplicon 21q22 identified in a copy alterations study of 191 breast tumor samples. 19010930 17/21 Jessica Robertson 1.38414383679916e-05 1.67345258957276e-05 1060 2434.18181818182 2397 1.2583204957308e-06 1059 1.80957492839764 1.99784398753239 1 3.4259382322359 1059 2397 2941 3432 3845 1306 1403 1657 3993 3324 1419 2391 M1757 SANSOM_APC_TARGETS_REQUIRE_MYC http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS_REQUIRE_MYC.html Genes up-regulated after Cre-lox knockout of APC [GeneID=324] in the small intestine that require functional MYC [GeneID=4609]. 17377531 255/287 Jessica Robertson 8.14171898344305e-07 1.51654095166464e-06 1130 2521.90909090909 2397 7.40156545137892e-08 973 1.59384512980576 1.84506130405955 1 3.67993865168683 1126 4141 3738 3586 2397 973 1365 1772 2505 4162 1976 2392 M3812 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS.html Amyotrophic lateral sclerosis (ALS) 50/69 KEGG 1.83475244749148e-07 7.47950348864313e-07 1920 2056.90909090909 2398 1.66795690955081e-08 461 1.69996183766821 -1.47073832007981 -1 4.13814764865347 1920 461 2475 3709 857 2519 1569 2398 2565 2920 1233 2393 M1150 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_UP.html Apoptotic genes dependent on SMAD4 [GeneID=4089] and up-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 7/7 Arthur Liberzon 3.12715850398117e-06 4.4060263100869e-06 1230 2294.63636363636 2398 3.12716290459403e-07 190 1.52398886879966 -1.72974827853473 -1 3.23257215705612 1227 3528 4352 4382 3322 763 190 243 4189 2398 647 2394 M6889 KEGG_RIBOFLAVIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOFLAVIN_METABOLISM.html Riboflavin metabolism 17/19 KEGG 4.32250914366273e-07 1.02326646843649e-06 4095 2583.27272727273 2399 3.92955453903597e-08 1801 1.79860760794861 1.45477769929244 1 4.28272368142149 4095 1899 2399 2612 1801 4154 3020 1856 1868 2040 2672 2395 M1827 MATZUK_PREOVULATORY_FOLLICLE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_PREOVULATORY_FOLLICLE.html Genes important for preovulatory follicle, based on mouse models with female fertility defects. 18989307 16/19 Jessica Robertson 8.14176858372497e-07 1.51654095166464e-06 2400 2576.18181818182 2399 7.40161054257767e-08 1226 2.28776186878773 2.85553401966208 1 5.30386848740849 3285 2399 1430 3657 2398 3322 3258 3956 1359 1226 2048 2396 M19943 BIOCARTA_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CERAMIDE_PATHWAY.html Ceramide Signaling Pathway 29/33 BioCarta 8.17274630640698e-07 1.5211105112871e-06 1520 2482.54545454545 2400 7.42977212953598e-08 590 1.17423188453834 -1.23534037215297 -1 2.69732705451801 1519 3731 3821 3249 2400 1300 590 1539 4352 3611 1196 2397 M906 REACTOME_AMINO_ACID_SYNTHESIS_AND_INTERCONVERSION_TRANSAMINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINO_ACID_SYNTHESIS_AND_INTERCONVERSION_TRANSAMINATION.html Genes involved in Amino acid synthesis and interconversion (transamination) 19/20 Reactome 6.76881593934448e-06 8.6488389912577e-06 1720 2180.81818181818 2401 6.15348796843984e-07 553 1.7889638496959 1.26402990778353 1 3.59258196603822 1716 868 2425 2628 3633 1240 553 2729 2401 2382 3414 2398 M1264 WANG_RESPONSE_TO_BEXAROTENE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_BEXAROTENE_DN.html Genes down-regulated in the mouse lung cancer model and which reverted to normal levels upon treatment with bexarotene [PubChem=82146]. 16247446 35/51 Leona Saunders 1.29491853084222e-07 7.20206492018647e-07 4425 2347.63636363636 2401 1.17719873369186e-08 486 2.20016015713843 -1.70642822902147 -1 5.38500793812859 4422 609 1136 2095 486 3239 2401 4139 2538 1904 2855 2399 M8232 KEGG_LONG_TERM_DEPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_DEPRESSION.html Long-term depression 61/94 KEGG 6.17375711597216e-08 5.75735672118533e-07 4560 2413.09090909091 2403 5.61250662656675e-09 94 2.03897338976294 -1.80506396892704 -1 5.06656052897543 4558 378 1598 1263 94 3954 2403 3069 2960 1624 4643 2400 M2241 JOHNSTONE_PARVB_TARGETS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_3_DN.html Genes down-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D Matrigel only. 17998334 1117/1358 Arthur Liberzon 7.46024043965869e-07 1.42907203227228e-06 930 2840.90909090909 2403 7.4602429441433e-08 929 1.44496182390311 1.5824859835763 1 3.34650899116943 929 4126 4671 3812 2403 1959 1901 1930 2729 4552 2238 2401 M254 PID_MYC_REPRESS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_REPRESS_PATHWAY.html Validated targets of C-MYC transcriptional repression 18832364 88/110 Pathway Interaction Database 9.91227827015007e-07 1.7411966295165e-06 3000 2550.63636363636 2404 9.01116612382743e-08 1094 1.92959909492537 2.09379713025755 1 4.41912686695307 2999 2147 1905 1094 2561 3983 3706 3441 2404 1621 2196 2402 M2049 REACTOME_SIGNALING_BY_PDGF http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_PDGF.html Genes involved in Signaling by PDGF 143/154 Reactome 8.22656565250083e-07 1.52871613700015e-06 2310 2470.81818181818 2405 7.47869884427422e-08 905 1.89946152266049 2.22468215551474 1 4.39250076500866 2310 2982 1839 905 2405 2629 4640 3496 2283 2411 1279 2403 M920 REACTOME_AQUAPORIN_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AQUAPORIN_MEDIATED_TRANSPORT.html Genes involved in Aquaporin-mediated transport 37/54 Reactome 1.02036577389635e-07 6.79284408009984e-07 4005 2304.54545454545 2406 9.27605292019264e-09 317 2.25187438456448 2.26520684388491 1 5.53576490908905 4001 581 1314 1163 317 4398 3471 2792 761 2406 4146 2404 M8179 BIOCARTA_RAB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAB_PATHWAY.html Rab GTPases Mark Targets In The Endocytotic Machinery 24/29 BioCarta 1.73485704000776e-06 2.69001255539921e-06 2445 2273.18181818182 2407 1.57714400733444e-07 381 1.95222026993467 -1.00018978215218 -1 4.32320798030855 2445 3456 2407 1996 2950 991 381 1462 1205 3708 4004 2405 M12138 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP.html Genes up-regulated in erythroid lineage cells by RUNX1-RUNX1T1 [GeneID=861;862] fusion . 17898786 228/342 Arthur Liberzon 9.20763568027982e-12 1.98447673109227e-10 3535 2138.63636363636 2408 8.37057789119852e-13 150 2.25251379832031 2.39165454900234 1 8.7390795066746 3532 1356 167 378 590 4321 3767 3673 2408 150 3183 2406 M15866 BIDUS_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BIDUS_METASTASIS_UP.html Genes up-regulated in endometroid endometrial tumors from patients with lymph node metastases compared to those without the metastases. 16397028 283/314 Arthur Liberzon 8.25019702180576e-07 1.53096141410712e-06 145 2108.18181818182 2408 7.50018192336833e-08 142 1.43247547429937 1.59367903898983 1 3.29992758920594 142 3284 4030 3025 2408 611 500 1161 2744 3997 1288 2407 M17535 CAMPS_COLON_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAMPS_COLON_CANCER_COPY_NUMBER_DN.html Genes from chromosomal copy number losses in a panel of 51 primary colon carcinoma samples. 18316590 63/215 Jessica Robertson 4.87144516778013e-06 6.45152109762128e-06 860 2048.45454545455 2408 4.42859632238342e-07 328 1.49950923856059 -1.48217005408529 -1 3.0799707032319 860 328 2529 2408 3497 1001 1498 3062 2896 3092 1362 2408 M169 PID_INTEGRIN2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN2_PATHWAY.html Beta2 integrin cell surface interactions 18832364 24/38 Pathway Interaction Database 8.25121453053598e-07 1.53096141410712e-06 2745 2487.45454545455 2409 7.5011069319987e-08 639 2.30127754086902 2.09374451108469 1 5.33169452650052 2741 2346 874 3849 2409 1990 1963 3018 3967 639 3566 2409 M1662 REACTOME_SIGNALING_BY_BMP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_BMP.html Genes involved in Signaling by BMP 23/27 Reactome 1.91389613331944e-07 7.53743535490661e-07 1735 2452.54545454545 2410 1.73990572710853e-08 908 1.49019170483867 1.59154769169797 1 3.61933020303828 1735 1856 2927 3864 908 2410 3081 2187 3387 3339 1284 2410 M18219 BREUHAHN_GROWTH_FACTOR_SIGNALING_IN_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/BREUHAHN_GROWTH_FACTOR_SIGNALING_IN_LIVER_CANCER.html Growth factor signaling components up-regulated in hepatocellular carcinoma (HCC). 16799620 29/31 Arthur Liberzon 2.95067952748095e-07 8.68821420443549e-07 2800 2315.36363636364 2411 2.68243629384678e-08 699 1.93934112899199 1.97947894051646 1 4.67716443507981 2800 699 1454 1934 1370 2411 2637 3023 3235 1770 4136 2411 M14275 FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN.html Genes down-regulated in papillary thyroid carcinoma (PTC) compared to other thyroid tumors. 17968324 76/137 Arthur Liberzon 1.66139734407458e-06 2.59404414953094e-06 3010 2674.90909090909 2411 1.5103623624827e-07 1466 2.19409929822215 -2.194370527247 -1 4.87897197354312 3007 2166 1466 2295 2925 3400 2641 4379 2411 2390 2344 2412 M1263 WANG_RESPONSE_TO_BEXAROTENE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_BEXAROTENE_UP.html Genes up-regulated in the mouse lung cancer model and which reverted to normal levels upon treatment with bexarotene [PubChem=82146]. 16247446 36/53 Leona Saunders 8.26162765233581e-07 1.5322154231444e-06 4720 2582.45454545455 2412 7.51057341346757e-08 233 2.53722990017549 -2.64858270960291 -1 5.88312619688983 4718 626 1178 978 2412 4356 4254 3477 233 1748 4427 2413 M104 SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP.html Top 50 up-regulated markers distinguishing diffuse large B-cell lymphoma (DLBCL) from follicular lymphoma (FL) samples. 11786909 81/118 Jean Junior 8.07503234158703e-07 1.51006943947269e-06 1690 2209.72727272727 2412 7.34094118682212e-08 421 1.77565610461354 1.69811077843148 1 4.10674572142737 1688 1627 2412 645 2386 2440 3068 3072 421 3152 3396 2414 M2067 ONGUSAHA_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONGUSAHA_BRCA1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) lacking TP53 and BRCA1 [GeneID=7157;672] by expression of BRCA1. 12802282 17/20 Arthur Liberzon 0.000323135155716378 0.000344599623809604 2840 2691.18181818182 2412 2.93802388587282e-05 1262 2.58680391127649 2.5037865064493 1 3.55224039822301 2412 2840 1262 2357 4394 2387 1584 3683 4173 1671 2840 2415 M4229 SESTO_RESPONSE_TO_UV_C6 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C6.html Cluster 6: genes changed in primary keratinocytes by UVB irradiation. 11867738 50/61 John Newman 2.141241956058e-07 7.71500918518607e-07 1920 2469.72727272727 2414 1.94658378587577e-08 1027 1.55571564889813 1.65287485371553 1 3.77434572103363 1916 3663 3417 3453 1027 1461 1412 2076 3540 2414 2788 2416 M6972 MONTERO_THYROID_CANCER_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MONTERO_THYROID_CANCER_POOR_SURVIVAL_DN.html Down-regulated genes predicting poor survival of patients with thyroid carcinoma. 17873908 15/16 Arthur Liberzon 1.72256632831068e-06 2.67539094097611e-06 4095 2710.18181818182 2414 1.56597061550475e-07 449 1.82606836545344 2.14911492207624 1 4.04234845915514 4092 1917 2231 3654 2941 3947 2353 2024 449 3790 2414 2417 M8719 BIOCARTA_MCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCALPAIN_PATHWAY.html mCalpain and friends in Cell motility 39/49 BioCarta 8.29398800959435e-07 1.53614043097655e-06 2535 2142 2415 7.5399919422045e-08 551 2.26308204171788 2.4903394100321 1 5.24103627183844 2534 2708 1475 1300 2415 2777 3552 1604 551 3191 1455 2418 M579 REACTOME_PPARA_ACTIVATES_GENE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PPARA_ACTIVATES_GENE_EXPRESSION.html Genes involved in PPARA Activates Gene Expression 115/156 Reactome 1.59721399627134e-07 7.31918027928963e-07 2415 2280.90909090909 2415 1.4520128293001e-08 693 1.69209518915747 -1.60452262340206 -1 4.12517032469561 2379 2999 3325 2861 693 2592 2413 907 2415 2841 1665 2419 M587 REACTOME_DEGRADATION_OF_THE_EXTRACELLULAR_MATRIX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEGRADATION_OF_THE_EXTRACELLULAR_MATRIX.html Genes involved in Degradation of the extracellular matrix 14/70 Reactome 1.78164584843977e-06 2.74457193362784e-06 3570 2510.63636363636 2415 1.61967935571612e-07 1209 2.68138586902752 2.471102120575 1 5.94723686935358 3566 2415 1231 2088 2970 3770 3437 2633 2364 1209 1934 2420 M22 PID_GMCSF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_GMCSF_PATHWAY.html GMCSF-mediated signaling events 18832364 50/57 Pathway Interaction Database 1.54875159717537e-06 2.44894724913492e-06 1950 2491.09090909091 2416 1.40795698860317e-07 609 1.28950592872119 -1.09821961544914 -1 2.85978104316493 1949 3081 3583 1564 2887 1945 953 609 4347 4068 2416 2421 M17083 MORI_MATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_MATURE_B_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the mature B 18922927 119/156 Jessica Robertson 3.8881775349693e-07 9.76357383103197e-07 1850 2322.18181818182 2417 3.53470747467987e-08 1572 1.63425167046027 -1.40222337169385 -1 3.90019235225888 1847 1572 2780 1932 1674 2430 2451 2528 3597 2417 2316 2422 M6162 BOWIE_RESPONSE_TO_EXTRACELLULAR_MATRIX http://www.broadinstitute.org/gsea/msigdb/cards/BOWIE_RESPONSE_TO_EXTRACELLULAR_MATRIX.html Genes up-regulated by growing HMEC-E6 cells (mammary epithelial cells damaged by expression of HPV-16 E6 [GeneID=1489078]) in extracellular matrix (ECM). 17016442 31/52 Arthur Liberzon 3.11536942752393e-05 3.58910024357163e-05 890 2470.90909090909 2418 2.83219413129898e-06 847 1.64876040460362 -1.83864056222893 -1 2.8973105548739 889 3425 2418 2929 4042 1470 847 1977 4400 2598 2185 2423 M11893 RAY_ALZHEIMERS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/RAY_ALZHEIMERS_DISEASE.html A biomarker of plasma signaling proteins that predicts clinical Alzheimer's diagnosis. 17934472 13/20 Jessica Robertson 2.74792844001095e-06 3.93515256239949e-06 2570 2480.18181818182 2418 2.49811988394545e-07 1282 3.09720625357382 -2.85585268642155 -1 6.68235749701737 2566 3497 1282 3675 3221 2418 1945 1768 3273 1732 1905 2424 M115 PID_REG_GR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_REG_GR_PATHWAY.html Glucocorticoid receptor regulatory network 18832364 95/143 Pathway Interaction Database 1.23544451892325e-07 7.12872631945934e-07 3335 1917.18181818182 2419 1.12313144391053e-08 167 2.50317379106603 2.68268685331266 1 6.13801585361497 3333 167 977 445 451 2476 3521 2701 1088 2419 3511 2425 M11516 ADDYA_ERYTHROID_DIFFERENTIATION_BY_HEMIN http://www.broadinstitute.org/gsea/msigdb/cards/ADDYA_ERYTHROID_DIFFERENTIATION_BY_HEMIN.html Selected genes changed in K562 (immortalized erythroleukemia) cells induced by hemin [PubChem=26945] treatment to express erythroid properties. 15252187 91/129 Kevin Vogelsang 2.76969215355016e-06 3.96390144474128e-06 2155 2488.72727272727 2419 2.51790512769359e-07 1319 2.20789541591461 -2.37602674261692 -1 4.74645627307364 2151 3617 1319 2419 3224 1645 1522 3565 3827 1651 2436 2426 M766 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM.html Glycine, serine and threonine metabolism 26/34 KEGG 8.53005173448501e-07 1.56721853588047e-06 1890 2447.27272727273 2420 7.75459549258232e-08 739 2.07871278878627 1.98881770610893 1 4.80271008995174 1889 2341 2067 4138 2440 2621 3194 739 2765 2306 2420 2427 M3206 SANCHEZ_MDM2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANCHEZ_MDM2_TARGETS.html Genes up-regulated in BJ cells (forskin fibroblasts) upon overexpression of the most abundant alternative splicing forms of MDM2 [GeneID=4193], HDM2-A and HDM2-B, off a retroviral vector. 16331255 21/48 Arthur Liberzon 8.72802414157117e-05 9.62979755685271e-05 1010 2435.36363636364 2420 7.93488220571256e-06 863 2.01356679658148 -1.76064433115451 -1 3.2023466976898 1010 3471 2709 2201 4231 1322 863 2699 2420 4158 1705 2428 M9052 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM.html Phosphatidylinositol signaling system 67/77 KEGG 5.987867120293e-07 1.23742262731099e-06 2545 2208.63636363636 2421 5.44351704549637e-08 642 1.64170718319024 -1.65698555349952 -1 3.85026949781744 2544 1666 2894 2421 2124 2744 3347 1903 1056 2954 642 2429 M17200 SA_B_CELL_RECEPTOR_COMPLEXES http://www.broadinstitute.org/gsea/msigdb/cards/SA_B_CELL_RECEPTOR_COMPLEXES.html Antigen binding to B cell receptors activates protein tyrosine kinases, such as the Src family, which ultimate activate MAP kinases. 33/37 SigmaAldrich 2.61197101790704e-07 8.29211725993449e-07 3735 2547.81818181818 2421 2.37451938910532e-08 662 1.60932788977217 -1.3619639855186 -1 3.8858631267514 3735 1791 2421 662 1238 3761 2170 2475 1906 3438 4429 2430 M3686 SA_REG_CASCADE_OF_CYCLIN_EXPR http://www.broadinstitute.org/gsea/msigdb/cards/SA_REG_CASCADE_OF_CYCLIN_EXPR.html Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. 13/24 SigmaAldrich 1.07901860642715e-05 1.32975661157602e-05 1925 2477.90909090909 2421 9.80930816955047e-07 1702 1.86727583132716 2.09382563729025 1 3.61175017804903 1922 2421 2480 2928 3771 2181 2215 1702 2242 2638 2757 2431 M2541 PARK_APL_PATHOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARK_APL_PATHOGENESIS_DN.html Genes down-regulated in U937 cells (acute promyelocytic leukemia, APL) expressing RARA [GeneID=5914] fused with either PML or PLZF [GeneID=5371;7704]. 12893766 72/116 Arthur Liberzon 6.96760797618726e-07 1.36922470027042e-06 2395 2520.18181818182 2421 6.3341910753596e-08 696 2.09420907755412 2.21798120398217 1 4.88828584042024 2392 1654 939 2471 2255 2990 4468 3300 4136 696 2421 2432 M2428 WELCSH_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WELCSH_BRCA1_TARGETS_DN.html Down-regulated by induction of exogenous BRCA1 in EcR-293 cells 12032322 189/216 John Newman 2.84206979442885e-07 8.51178263306103e-07 1750 2679.18181818182 2422 2.58370014689243e-08 1337 1.34826388509018 1.4811823089139 1 3.24122727403677 1748 3300 3963 2741 1337 1759 1983 2422 3620 4358 2240 2433 M2479 SUZUKI_CTCFL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_CTCFL_TARGETS_UP.html Genes up-regulated in testis tissue upon knockout of CTCFL [GeneID=140690]. 20231363 12/17 Arthur Liberzon 2.34784901368886e-07 7.98113405922816e-07 2800 1877.45454545455 2422 2.13440842204755e-08 66 2.16491244484835 2.30480965854877 1 5.25909833258589 2798 2422 2495 1641 1128 3419 3422 570 66 2453 238 2434 M1694 HARRIS_BRAIN_CANCER_PROGENITORS http://www.broadinstitute.org/gsea/msigdb/cards/HARRIS_BRAIN_CANCER_PROGENITORS.html Genes from the brain cancer stem (cancer stem cell, CSC) signature. 19074870 38/60 Leona Saunders 1.07462002191197e-05 1.32468177159167e-05 1880 2550.54545454545 2424 9.76932064614555e-07 571 2.49712175064845 2.75034302320636 1 4.84856572691165 1880 1754 678 3290 3770 2394 3594 3693 4008 571 2424 2435 M2363 TERAO_AOX4_TARGETS_SKIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_SKIN_DN.html Genes down-regulated in skin upon knockout of AOX4 [GeneID=71872]. 18981221 32/39 Arthur Liberzon 3.89508769707449e-05 4.4418492220806e-05 435 2147.72727272727 2424 3.54105151008524e-06 259 1.67274528743907 -1.58058903835451 -1 2.87790760727066 435 3424 2562 4366 4090 259 264 1202 4250 2424 349 2436 M5574 CAFFAREL_RESPONSE_TO_THC_24HR_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_3_DN.html Genes down-regulated in EVSA-T cells (breast cancer) after treatment with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 19/26 Jessica Robertson 8.40618820094607e-07 1.55170935895446e-06 3285 2245.18181818182 2425 7.64199219358891e-08 413 2.07127869904543 2.2917700909139 1 4.78895306395793 3282 846 1952 1435 2425 2667 1807 3865 413 3186 2819 2437 M643 REACTOME_ACYL_CHAIN_REMODELLING_OF_PC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PC.html Genes involved in Acyl chain remodelling of PC 14/23 Reactome 1.19624907019194e-05 1.46239202572026e-05 1225 2086.54545454545 2426 1.08750506803701e-06 332 1.91407956597161 -1.79744769116314 -1 3.6717487417003 1221 2871 2426 2864 3805 779 533 332 4214 2829 1078 2438 M8512 TSAI_RESPONSE_TO_IONIZING_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_RESPONSE_TO_IONIZING_RADIATION.html Genes up-regulated in TK6, WTK1, and NH32 cell lines (lymphoblast) in response to ionizing radiation. 16247478 215/274 Arthur Liberzon 4.11487417491865e-07 1.00046055710989e-06 2430 2496.36363636364 2426 3.74079540414893e-08 1067 2.05878502320116 2.35346076823197 1 4.91758355143202 3726 2961 1067 1291 1741 4117 4404 2059 2426 1238 2430 2439 M1761 TESAR_ALK_TARGETS_EPISC_3D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_EPISC_3D_UP.html Genes up-regulated in EpiSC cells (mouse epiblast embryonic stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=4521392]. 17597760 5/11 Jessica Robertson 5.69064232720269e-05 6.37697810645696e-05 2390 2749.36363636364 2426 5.69078805780039e-06 490 2.57383352333714 3.0025556530397 1 4.2925939059043 2389 1989 4524 2426 4174 1652 490 4277 3643 1787 2892 2440 M8701 KRISHNAN_FURIN_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRISHNAN_FURIN_TARGETS_DN.html Genes down-regulated in naive T lymphocytes lacking FURIN [GeneID=5045]: Cre-Lox knockout of FURIN in CD4+ [GeneID=920] cells. 18690214 17/23 Jessica Robertson 8.23960386829682e-06 1.03460841336422e-05 2430 2238 2426 7.49057702548797e-07 126 2.7523515235257 4.07059249256611 1 5.46805856313425 2426 2844 1366 3632 4021 2783 3845 126 445 2048 1082 2441 M122 PID_IL2_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_1PATHWAY.html IL2-mediated signaling events 18832364 74/87 Pathway Interaction Database 2.02779211042831e-07 7.65527859584926e-07 2430 2305.90909090909 2428 1.84344754303157e-08 674 1.65777232408762 -1.57140920067699 -1 4.02747987327326 2428 2626 3234 674 960 2204 2026 1403 3199 3441 3170 2442 M5098 CLIMENT_BREAST_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/CLIMENT_BREAST_CANCER_COPY_NUMBER_DN.html Genes from the most frequent genomic losses and homozygous deletions in a panel of patients with lymph node negative breast cancer (NNBC). 17234794 10/12 Jessica Robertson 3.12574368140351e-05 3.59929499297989e-05 2900 2482.36363636364 2431 2.84162553874661e-06 1342 2.1997405885581 2.62639139939041 1 3.88116086626321 2897 2431 1540 1840 4044 2118 1342 2662 3300 2016 3116 2443 M11720 BEIER_GLIOMA_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BEIER_GLIOMA_STEM_CELL_DN.html Genes down-regulated in cancer stem cells derived from glyoblastoma tumors: CD133+ [GeneID=8842] vs. CD133- cells. 17483311 82/103 Jessica Robertson 1.15443908802929e-05 1.41475279372042e-05 2005 2267.90909090909 2431 1.04949558721422e-06 243 2.24649590718191 -1.5537091471682 -1 4.33110230241658 2486 3337 1934 2764 3796 2004 1370 2001 243 2431 2581 2444 M14857 REACTOME_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPHINGOLIPID_METABOLISM.html Genes involved in Sphingolipid metabolism 65/73 Reactome 7.70873384385947e-08 6.27331443845116e-07 2435 2325.18181818182 2432 7.0079401036102e-09 168 1.43558974861774 -1.31034537824794 -1 3.53091055678685 2432 1667 3521 3698 168 1694 2463 2270 2697 3222 1745 2445 M10546 REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_CAMKII http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_CAMKII.html Genes involved in CREB phosphorylation through the activation of CaMKII 12/19 Reactome 3.72596245952342e-05 4.25618170594157e-05 1890 2297.54545454545 2433 3.38729596785364e-06 588 1.48540420385783 1.43535412552028 1 2.56106644408985 1886 2876 3040 2433 4080 1849 1927 2818 810 2966 588 2446 M231 PID_KIT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_KIT_PATHWAY.html Signaling events mediated by Stem cell factor receptor (c-Kit) 18832364 74/85 Pathway Interaction Database 1.47471817669796e-07 7.26289540930751e-07 2435 2356.54545454545 2435 1.34065297777475e-08 206 1.38671632433278 -1.34040285974428 -1 3.37352444449087 2435 1649 3497 206 615 2721 2094 3043 1810 4318 3534 2447 M9461 REACTOME_LAGGING_STRAND_SYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LAGGING_STRAND_SYNTHESIS.html Genes involved in Lagging Strand Synthesis 19/20 Reactome 0.000274814161469837 0.00029366602719892 305 2293.63636363636 2435 2.49862269118673e-05 302 1.19896107527112 1.24591301244988 1 1.65307957946979 302 2814 3098 2435 4383 768 388 2045 4052 2383 2562 2448 M1514 KANG_IMMORTALIZED_BY_TERT_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_IMMORTALIZED_BY_TERT_DN.html Down-regulated genes in the signature of adipose stromal cells (ADSC) immortalized by forced expression of telomerase (TERT) [GeneID=7015]. 15579653 126/211 Kevin Vogelsang 8.49376267358055e-07 1.56298478827681e-06 2535 1909.09090909091 2435 7.72160541168658e-08 44 2.49884946572391 2.4828006018608 1 5.78469821060441 2533 44 567 835 2435 3056 3660 1340 2973 1012 2545 2449 M9246 ENGELMANN_CANCER_PROGENITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ENGELMANN_CANCER_PROGENITORS_DN.html Down-regulated genes in the cancer progenitor (stem) cells corresponding to side population (SP) MCF7 cells (breast cancer) positive for MUC1 [GeneID=4582]. 18381450 84/118 Jessica Robertson 1.84569297252846e-07 7.47950348864313e-07 735 2220.27272727273 2435 1.67790284306649e-08 734 2.56328437421528 2.25652735456624 1 6.2651097147853 3716 1625 734 997 864 2435 2907 3048 2977 734 4386 2450 M7732 RAGHAVACHARI_PLATELET_SPECIFIC_GENES http://www.broadinstitute.org/gsea/msigdb/cards/RAGHAVACHARI_PLATELET_SPECIFIC_GENES.html Genes in this set correspond to the most abuntant transcripts that are also specific to platelets. 17353439 105/163 Arthur Liberzon 4.33788278310163e-06 5.85234389157779e-06 1910 2235.90909090909 2435 3.94353757855478e-07 1317 1.85980215439392 1.98874049711973 1 3.86369192199474 1910 2585 2706 1317 3423 1363 2618 1678 2435 3232 1328 2451 M1075 REACTOME_INWARDLY_RECTIFYING_K_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INWARDLY_RECTIFYING_K_CHANNELS.html Genes involved in Inwardly rectifying K+ channels 21/39 Reactome 4.08086200699478e-07 9.99567652984709e-07 3975 2783 2436 3.70987523997207e-08 1615 2.21406413783231 2.21015241744599 1 5.2926001754809 3972 2367 1658 1940 1730 3862 3926 2436 3757 1615 3350 2452 M8240 REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL.html Genes involved in Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell 45/119 Reactome 4.84655552256222e-06 6.42757574220108e-06 1520 2370.72727272727 2437 4.40596927223543e-07 485 1.60696288985075 -1.37154327620129 -1 3.30530825846439 1520 485 1770 2463 3492 1943 2437 4147 4016 843 2962 2453 M19202 CHENG_IMPRINTED_BY_ESTRADIOL http://www.broadinstitute.org/gsea/msigdb/cards/CHENG_IMPRINTED_BY_ESTRADIOL.html Genes whose CpG islands became hypermethylated in breast progenitor cells pre-exposed to estradiol [PubChem=5757]. 18339859 159/198 Jessica Robertson 9.84269605595939e-07 1.73284316986678e-06 2425 2697 2437 8.94790950867078e-08 1148 1.91883255914076 -1.75277229321248 -1 4.39580208516915 2423 4155 2843 3922 2556 2437 2237 2417 1833 3696 1148 2454 M9884 BRUNEAU_HEART_GREAT_VESSELS_AND_VALVULOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/BRUNEAU_HEART_GREAT_VESSELS_AND_VALVULOGENESIS.html Genes for which mutations result in developmental defects in the great vessels formation and valvulogenesis, a major class of congenital heart disease. 18288184 11/14 Jessica Robertson 2.81178030449543e-07 8.49189526890862e-07 4165 2664.81818181818 2437 2.55616423987643e-08 139 2.74921959176632 -1.85098144917633 -1 6.66224161315933 4162 2437 1922 2625 1320 4642 4391 2082 139 2249 3344 2455 M8751 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_14 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_14.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 14. 12554760 186/227 Arthur Liberzon 8.84151528323519e-06 1.1037279062912e-05 320 2513 2437 8.03777346940072e-07 320 1.39685111640145 1.40314348255813 1 2.73468440959469 320 3302 3861 3246 3723 1292 785 2049 2344 4284 2437 2456 M117 PID_CONE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CONE_PATHWAY.html Visual signal transduction: Cones 18832364 11/34 Pathway Interaction Database 3.18098769236516e-06 4.4711917534138e-06 1845 2112.72727272727 2438 2.89181117434154e-07 30 1.75726369329031 -1.94359054165948 -1 3.73053043928095 1842 2438 2788 3392 3282 1524 783 121 3745 3295 30 2457 M553 REACTOME_SIGNALING_BY_ERBB2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ERBB2.html Genes involved in Signaling by ERBB2 118/128 Reactome 3.05064146206152e-07 8.80674477121123e-07 3100 2399 2438 2.77331080461853e-08 508 1.67057650042461 -1.44070483408836 -1 4.01808895432968 3097 2121 3021 508 1407 2438 1690 3518 1540 3916 3133 2458 M7547 JIANG_HYPOXIA_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_HYPOXIA_CANCER.html Genes up-regulated in 786-0 cells (renal carcinoma, RCC) by hypoxia and in the absensce of VHL [GeneID=7428]. 12692265 107/138 John Newman 7.92785567349534e-07 1.4886566923604e-06 2440 2552.18181818182 2438 7.20714411850516e-08 1571 1.3386485443008 1.37703129562617 1 3.08705698769958 2438 1594 3698 3174 2372 1925 2400 1571 2516 3632 2754 2459 M17670 REACTOME_RAS_ACTIVATION_UOPN_CA2_INFUX_THROUGH_NMDA_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAS_ACTIVATION_UOPN_CA2_INFUX_THROUGH_NMDA_RECEPTOR.html Genes involved in Ras activation uopn Ca2+ infux through NMDA receptor 16/23 Reactome 3.94428731674867e-05 4.49578269380675e-05 2440 2680.54545454545 2439 3.58578003089937e-06 807 1.60193708456321 1.36981138133716 1 2.75058936750615 2439 2393 2512 2436 4092 2321 2255 3042 4026 3163 807 2460 M914 REACTOME_IL_3_5_AND_GM_CSF_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_3_5_AND_GM_CSF_SIGNALING.html Genes involved in Interleukin-3, 5 and GM-CSF signaling 53/66 Reactome 4.46618322063844e-07 1.03872096525265e-06 2905 2611.54545454545 2439 4.06016738846463e-08 1073 1.8988832360056 -1.91370380271862 -1 4.51931140585129 2902 2219 1961 1073 1842 3589 2439 3758 3315 2206 3423 2461 M16830 NELSON_RESPONSE_TO_ANDROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/NELSON_RESPONSE_TO_ANDROGEN_DN.html Genes down-regulated in LNCaP cells (prostate cancer) in response to synthetic androgen R1881 [PubChem=13766]. 12185249 28/30 Broad Institute 2.07340154250019e-07 7.68728418959517e-07 4455 2562.18181818182 2439 1.88491067082638e-08 524 1.51878488535276 1.23747168436403 1 3.68451459343542 4452 700 2439 1450 987 4638 3909 3036 524 2237 3812 2462 M10142 KALMA_E2F1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KALMA_E2F1_TARGETS.html DNA replication genes up-regulated in a Rat-1a cell line (fibroblast) by expression of E2F1 [GeneID=1869]. 11313881 12/13 John Newman 1.68100113910797e-05 2.00058632793485e-05 365 2078.45454545455 2439 1.5281945305736e-06 24 1.47994921790559 1.47994921790559 1 2.74661448150689 362 3221 2806 2439 4372 480 24 1581 3445 2449 1684 2463 M16812 KERLEY_RESPONSE_TO_CISPLATIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/KERLEY_RESPONSE_TO_CISPLATIN_UP.html Genes genes up-regulated in NT2/D1 cells (embryonal carcinoma) in response to treatment with cisplatin [PubChem=2767]. 15940259 65/77 Leona Saunders 1.16440930753963e-06 1.96356267652271e-06 1935 2825.27272727273 2440 1.05855447621373e-07 1278 2.15651161003903 -1.47997647487197 -1 4.89941259059734 4527 2195 1351 2440 2677 4464 4720 1278 1935 1934 3557 2464 M10395 DAIRKEE_TERT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_TERT_TARGETS_UP.html Genes up-regulated in non-spontaneously immortalizing (NSI) primary breast cancer tumor cultures upon expression of TERT [GeneID=7015] off a retroviral vector. 17471242 468/574 Arthur Liberzon 2.08929103678272e-07 7.70426069813627e-07 985 2565 2441 1.89935566836188e-08 981 1.75187519281163 1.90545251324227 1 4.2569871623377 981 4130 3544 4305 996 1167 1329 2341 2704 4277 2441 2465 M1388 SHIN_B_CELL_LYMPHOMA_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_5.html Cluster 5 of genes distinguishing among different B lymphocyte neoplasms. 19010892 11/25 Jessica Robertson 2.788213379002e-07 8.45238737886283e-07 4530 2756.63636363636 2441 2.53473975670161e-08 1314 2.37393378985022 1.52170351366108 1 5.74790675689072 4529 2441 1966 4348 1314 3389 2068 1497 2841 1764 4166 2466 M18825 KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN.html Genes down-regulated in AIDS-related primary effusion lymphoma (PEL) samples compared to other tumor subtypes and normal B lymphocytes. 12531789 58/78 Kate Stafford 8.54505828100614e-07 1.5693647893521e-06 3780 2398.18181818182 2441 7.76823781818989e-08 381 2.08391344968524 -1.78976846892317 -1 4.8143529107556 3777 381 1376 1825 2441 3834 3699 3448 1651 975 2973 2467 M12227 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_5 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_5.html Amplification hot spot 5: colocolized fragile sites and cancer genes in the 17q22-q25 region. 16751803 7/7 Arthur Liberzon 6.83976580392167e-07 1.35078220060712e-06 4440 2696.18181818182 2442 6.83976790913039e-08 6 2.41359362899519 -1.43531507701486 -1 5.64713833057707 4439 1028 4374 765 2330 4720 4638 2442 6 2400 2516 2468 M1684 DURCHDEWALD_SKIN_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DURCHDEWALD_SKIN_CARCINOGENESIS_DN.html Genes down-regulated upon skin specific knockout of FOS [GeneID=2353] by cre-lox in the K5-SOS-F mice (express a constitutively active form of SOS1 [GeneID=6654] in the skin). 18757399 374/460 Jessica Robertson 7.3702675981047e-08 6.11670596203388e-07 4005 2600.45454545455 2442 6.70024349547056e-09 158 1.94355129222489 2.16550291695096 1 4.80655608981522 4004 1229 1082 1181 158 4399 3910 4708 2442 1285 4207 2469 M1197 TERAMOTO_OPN_TARGETS_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_1.html Cluster 1: genes whose up-regulation peaked one day after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 17/19 Arthur Liberzon 3.34238115737525e-05 3.84032109610788e-05 3905 2632 2443 3.0385744891404e-06 163 2.82892400780956 -3.83855526834067 -1 4.97356052810077 3905 2401 2263 2443 4057 4396 3389 1175 163 3323 1437 2470 M12050 STARK_HYPPOCAMPUS_22Q11_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/STARK_HYPPOCAMPUS_22Q11_DELETION_UP.html Genes up-regulated in hyppocampus of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 76/98 Jessica Robertson 8.58185267134958e-07 1.57306192655417e-06 3500 2399 2446 7.80168728999695e-08 254 1.75456139789568 -1.67395331135894 -1 4.04483941426742 3496 254 2112 2303 2446 3387 2709 3551 1128 1987 3016 2471 M2471 TIAN_BHLHA15_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TIAN_BHLHA15_TARGETS.html Genes up-regulated in both AGS and HGC-27 cells (gastric cancer) by BHLHA15 [GeneID=168620] transfection. 20038531 18/22 Arthur Liberzon 3.59745833430645e-07 9.41752134134615e-07 3035 2453.54545454545 2447 3.27041720233269e-08 728 1.73142214400849 -1.65795175089714 -1 4.14598058493766 3033 1897 2447 3306 1589 3432 2624 728 3543 2212 2178 2472 M5193 SIG_CHEMOTAXIS http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CHEMOTAXIS.html Genes related to chemotaxis 50/63 Signaling Gateway 9.75593365904707e-08 6.64473403617636e-07 3995 2451.27272727273 2448 8.86903099243227e-09 299 1.64199603283579 -1.47036925076005 -1 4.02927636276014 3991 432 2448 1485 299 4192 3503 3587 1178 1935 3914 2473 M645 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_GOLGI_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_GOLGI_MEMBRANE.html Genes involved in Synthesis of PIPs at the Golgi membrane 18/19 Reactome 0.000233642246319492 0.000250577460265395 1635 2713.81818181818 2448 2.12424602776798e-05 188 1.295428782945 -1.43142861199202 -1 1.82601241163104 1632 4601 3564 4487 4366 1050 1188 2448 1850 4478 188 2474 M5091 EINAV_INTERFERON_SIGNATURE_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/EINAV_INTERFERON_SIGNATURE_IN_CANCER.html A gene expression signature found in a subset of cancer patients suggestive of a deregulated immune or inflammatory response. 16007187 37/53 Leona Saunders 2.06922765551421e-05 2.43014544265416e-05 950 2201 2449 1.88113374368842e-06 521 1.74244397731018 -1.82239340796865 -1 3.18345400060122 947 2729 2906 2449 3963 625 521 3504 3526 2407 634 2475 M19259 IYENGAR_RESPONSE_TO_ADIPOCYTE_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/IYENGAR_RESPONSE_TO_ADIPOCYTE_FACTORS.html Genes up-regulated in MCF-7 cells (breast cancer) in response to growth medium from L3T3-L1 cells (differentiated to pre-adipocytes). 14508521 15/17 John Newman 8.94793837687483e-07 1.62127712625141e-06 1385 2301.45454545455 2449 8.13449274202037e-08 782 2.38036133192351 -1.92331879305138 -1 5.492808813481 1385 3208 1497 3672 2481 1233 782 2449 4269 1074 3266 2476 M13859 BASSO_HAIRY_CELL_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_HAIRY_CELL_LEUKEMIA_UP.html Genes up-regulated in hairy cell leukemia (HCL) compared with normal and other neoplastic B cell populations. 14707115 4/6 Arthur Liberzon 6.52873546456093e-05 7.27813684287378e-05 2450 2599.45454545455 2449 6.52892728223281e-06 411 2.20473231145166 2.20473231145166 1 3.61893895232191 2449 3539 4559 3388 4498 2444 2433 417 411 3762 694 2477 M14019 DING_LUNG_CANCER_MUTATED_RECURRENTLY http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_MUTATED_RECURRENTLY.html The lung adenocarcinoma TSP (tumor sequencing project) genes bearing recurrent somatic mutations. 18948947 12/13 Arthur Liberzon 1.22984767486661e-05 1.49958176837261e-05 4410 2497.45454545455 2450 1.1180495909413e-06 94 3.03206867242347 3.1261088449991 1 5.83229674042746 4410 958 1249 181 3816 4660 3749 4475 94 2450 1430 2478 M2122 VERHAAK_GLIOBLASTOMA_MESENCHYMAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_MESENCHYMAL.html Genes correlated with mesenchymal type of glioblastoma multiforme tumors. 20129251 280/399 Arthur Liberzon 2.26555203172516e-08 2.70719128854247e-07 3460 2247.09090909091 2450 2.0595927773234e-09 245 2.09727078330529 -1.83062508653583 -1 5.4892513895246 3457 1290 306 353 483 3832 3343 4589 2450 245 4370 2479 M677 REACTOME_ABACAVIR_TRANSPORT_AND_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABACAVIR_TRANSPORT_AND_METABOLISM.html Genes involved in Abacavir transport and metabolism 9/16 Reactome 0.000656593817465105 0.000689306676698242 2420 2532.09090909091 2451 6.56787900126342e-05 577 3.04013544008547 3.04013544008547 1 3.8154015616486 2416 3521 4216 3102 4468 1833 616 1197 577 3456 2451 2480 M93 REACTOME_ACETYLCHOLINE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACETYLCHOLINE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Acetylcholine Neurotransmitter Release Cycle 10/18 Reactome 1.6362170342389e-06 2.55980921498429e-06 1100 2236.18181818182 2453 1.48747113741097e-07 35 1.24129114353223 -1.13548074437788 -1 2.74138388697335 1097 2453 2986 4185 2918 534 35 1870 4391 2541 1588 2481 M1897 RASHI_RESPONSE_TO_IONIZING_RADIATION_1 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_1.html Cluster 1: ATM [GeneID=472] dependent genes induced at 30 min after ionizing radiation treatment. 16314843 65/89 Arthur Liberzon 5.3267144733913e-07 1.15119470304061e-06 3815 2640.36363636364 2453 4.84246887555807e-08 1670 1.66382068770897 -1.1693111934876 -1 3.92379589593179 3813 1670 2453 2206 2012 3258 2935 2135 3563 2345 2654 2482 M18134 COLDREN_GEFITINIB_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/COLDREN_GEFITINIB_RESISTANCE_UP.html Genes up-regulated in NSCLC (non-small cell lung carcinoma) cell lines resistant to gefitinib [PubChem=123631] compared to the sensitive ones. 16877703 105/123 Arthur Liberzon 1.00983072368282e-06 1.764680124318e-06 625 1817.45454545455 2454 9.18028352008657e-08 386 1.79421938376424 1.86550191015427 1 4.1013743449532 624 3005 2454 2848 2575 438 715 1232 2632 3083 386 2483 M111 BIOCARTA_BARRESTIN_SRC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARRESTIN_SRC_PATHWAY.html Roles of fl-arrestin-dependent Recruitment of Src Kinases in GPCR Signaling 30/35 BioCarta 1.23370777588089e-06 2.05038757118232e-06 2605 2471.63636363636 2456 1.1215531524686e-07 672 1.33667897562001 -1.3030672064054 -1 3.0076981051112 2603 3143 3460 672 2722 2456 1496 2208 2081 3897 2450 2484 M17268 SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN.html Genes down-regulated in 293 cells (embryonic kidney) upon expression of KHSV (Kaposi sarcoma-associated herpesvirus) microRNAs. 17500590 84/111 Arthur Liberzon 4.38963152746944e-07 1.0292628320743e-06 2460 2491.81818181818 2456 3.99057491211562e-08 1144 2.13911864020466 -2.15386579338488 -1 5.10081571021501 2456 3026 1144 2380 1822 2804 2217 3819 3885 1378 2479 2485 M2160 MARSON_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_DN.html Genes down-regulated by FOXP3 [GeneID=50943] in both ex vivo and hybridoma cells. 17237765 61/84 Arthur Liberzon 8.65129463241579e-07 1.58087923596603e-06 2605 2494.90909090909 2456 7.8648163949623e-08 903 2.10004265760756 -2.22035880633512 -1 4.84932134071695 2605 1675 1439 2331 2456 2850 2085 4550 4072 903 2478 2486 M15188 KAAB_FAILED_HEART_VENTRICLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_FAILED_HEART_VENTRICLE_DN.html Genes down-regulated in the ventricles of failing hearts (DCM and ICM) compared to the healthy controls. 15103417 62/95 Arthur Liberzon 6.16114027916262e-07 1.2599905596901e-06 2590 2422.18181818182 2457 5.60103818600173e-08 1166 2.10012355644638 2.32783501831168 1 4.93272863137176 2587 3647 2457 2446 2150 2593 2168 1619 1166 3207 2604 2487 M2282 ITO_PTTG1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ITO_PTTG1_TARGETS_UP.html Genes up-regulated in HSA/c and KYSE140 cells (esophageal squamous cell carcinoma, ESCC) after knockdown of PTTG1 [GeneID=9232] by RNAi. 18451147 18/30 Jessica Robertson 8.46299557483347e-07 1.55975552960617e-06 2460 2255.54545454545 2457 7.69363530035821e-08 100 3.26907317719379 4.6233603216273 1 7.58432738038548 2457 3192 837 2620 2431 2712 3188 100 2249 1854 3171 2488 M2337 BILANGES_SERUM_RESPONSE_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_RESPONSE_TRANSLATION.html Genes translationally repressed upon serum deprivation in MEF cells (embryonic fibroblast). 17562867 43/69 Arthur Liberzon 6.47284130344593e-07 1.30674982687189e-06 965 2158.09090909091 2457 5.88440291626044e-08 501 1.52036378961266 -1.34417937038944 -1 3.54751110620888 964 2700 3275 2457 2184 699 501 3495 687 3895 2882 2489 M517 REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_EXPRESSION.html Genes involved in BMAL1:CLOCK/NPAS2 Activates Circadian Expression 38/44 Reactome 5.92312247449697e-07 1.22888519031322e-06 1215 2634.18181818182 2458 5.38465824472423e-08 1100 1.54386872387162 -1.59919747824813 -1 3.61969537763287 1215 4245 3519 3495 2114 1595 1100 2136 3293 3806 2458 2490 M12769 LU_TUMOR_VASCULATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_VASCULATURE_UP.html Genes up-regulated in endothelial cells derived from invasive ovarian cancer tissue. 17308118 51/59 Arthur Liberzon 8.55070598408152e-09 1.15312377842471e-07 745 2166.45454545455 2458 7.77336910665036e-10 273 3.44028820354629 3.4260585423074 1 9.54921813019052 744 3065 273 1638 4257 2011 2692 3290 2458 621 2782 2491 M305 CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70 http://www.broadinstitute.org/gsea/msigdb/cards/CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70.html Differentially expressed genes between high vs low ZAP70 [GeneID=7535] acute lymphoblastic leukemia (ALL) cases with no known molecular aberrations. 16160012 73/90 Kevin Vogelsang 5.16388498755146e-07 1.13049801211702e-06 4190 2329.27272727273 2458 4.69444199966317e-08 263 1.91775456557365 -1.58468916507484 -1 4.53636267741213 4190 263 1894 579 1981 3754 2458 3542 493 2756 3712 2492 M1502 SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP.html Up-regulated in murine dorsal skin cells at 6 h after treatment with the phorbol ester carcinogen TPA [PubChem=4792]. 12640676 45/82 John Newman 5.87793213106498e-07 1.2238129536227e-06 2700 2393.45454545455 2459 5.34357609229456e-08 521 2.31240493936236 2.13959404046463 1 5.44815480908796 2699 521 1396 3064 2107 3386 3893 1801 2576 2426 2459 2493 M1592 SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP.html Genes up-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] which continued to respond normally to insulin in the insulin resistant cells. 14530283 47/52 John Newman 2.84701413489182e-05 3.29279752920593e-05 1420 2579.63636363636 2459 2.5882281624485e-06 1185 1.71971690320612 1.983759989871 1 3.05003362538744 1416 3391 2459 2710 4030 1185 1984 2153 4211 2888 1949 2494 M2038 CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_UP.html Genes up-regulated in APL (acute promyeolocytic leukemia) blasts expressing PML-RARA fusion [GeneID=5371;5914] compared to normal promyeloblasts. 16990782 260/396 Leona Saunders 1.39560021812478e-07 7.20206492018647e-07 2460 2406.90909090909 2460 1.268727551506e-08 566 1.94008537070395 -1.49708218890677 -1 4.74254643749592 2460 3564 1877 2513 566 2302 1814 3550 3012 1365 3453 2495 M15510 NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP.html Genes up-regulated in K562 cells (bone marrow) after treatment with dasatinib [PubChem=3062316] or imatinib [PubChem=5291]. 17213809 36/39 Arthur Liberzon 7.11500322389111e-07 1.38257781872236e-06 2285 2932.27272727273 2461 6.46818684086355e-08 1929 1.85795502990647 -1.31552433298467 -1 4.32802937847993 4274 2284 2461 1993 2282 4536 3323 2489 1929 2001 4683 2496 M1454 NUMATA_CSF3_SIGNALING_VIA_STAT3 http://www.broadinstitute.org/gsea/msigdb/cards/NUMATA_CSF3_SIGNALING_VIA_STAT3.html Target genes for STAT3 [GeneID=20848] in CSF3 [GeneID=12985] signaling during myeloblast differentiation to neutrophils. 15664994 26/36 Kevin Vogelsang 3.66707523617356e-07 9.49977777976905e-07 2840 2551.09090909091 2462 3.33370531583728e-08 1609 2.19812377448806 2.33132936138124 1 5.27367067101679 2836 3444 2070 2805 1609 1988 1918 3958 2997 1975 2462 2497 M15687 LE_SKI_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LE_SKI_TARGETS_DN.html Selected genes implicated in metastasis and epithelial-to-mesenchymal transition (EMT) which were down-regulated in MDA-MB-231 cells (breast cancer) upon knockdown of SKI [GeneID=6497] by RNAi. 18451154 8/11 Jessica Robertson 9.69766345275383e-05 0.00010662234217796 730 2334.36363636364 2462 9.69808667979203e-06 727 3.98632270979609 3.98632270979609 1 6.31790253952727 727 2462 4555 2587 4265 1494 1884 1222 2686 2668 1128 2498 M2352 WINZEN_DEGRADED_VIA_KHSRP http://www.broadinstitute.org/gsea/msigdb/cards/WINZEN_DEGRADED_VIA_KHSRP.html Transcripts (mRNA molecules) rapidly degraded upon interaction with KHSRP [GeneID=8570]. 17908789 110/146 Arthur Liberzon 4.25163179547675e-09 5.99035882825381e-08 4580 2470.36363636364 2462 3.86511982153935e-10 261 2.64472845017895 2.55685347619047 1 7.63192435229403 4580 1583 261 2079 1783 3870 3077 2462 3099 403 3977 2499 M5109 KEGG_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRIMIDINE_METABOLISM.html Pyrimidine metabolism 93/106 KEGG 5.26681418197945e-07 1.14401117988693e-06 1585 2391.36363636364 2464 4.78801403896235e-08 704 1.31080584776464 1.45111594114539 1 3.08209602669488 704 3016 3645 3959 1999 1581 1581 1366 2464 3501 2489 2500 M14092 OXFORD_RALA_AND_RALB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_AND_RALB_TARGETS_UP.html Genes up-regulated in the UMUC-3 cells (bladder cancer) after knockdown of both RALA and RALB [GeneID=5898;5899] by RNAi. 17496927 9/12 Arthur Liberzon 0.000118987057439506 0.000129884114503808 975 2377.45454545455 2464 1.18993428983588e-05 150 1.49030070449066 1.61943789059414 1 2.2792711108953 975 2464 4398 3414 4297 888 150 1532 3125 2896 2013 2501 M1803 GEORGANTAS_HSC_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/GEORGANTAS_HSC_MARKERS.html Genes up-regulated in HSC (hematopoietic stem cells) compared to HPC (hematopoietic progenitor cells). 15231652 102/161 John Newman 3.33613758874675e-06 4.65376680142245e-06 1630 2580.09090909091 2464 3.0328569525126e-07 1415 1.80391954834392 -1.75118965027038 -1 3.81829601388825 1629 1597 1791 2431 3307 3247 3916 2464 3934 1415 2650 2502 M11078 YANG_BREAST_CANCER_ESR1_LASER_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_LASER_DN.html Genes down-regulated in laser microdissected (LCM) samples of early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 69/75 Leona Saunders 1.34293937958047e-07 7.20206492018647e-07 2900 1922.81818181818 2466 1.22085405596102e-08 303 1.97672413494153 1.9333490138563 1 4.83305500149828 2898 303 2227 814 522 2906 2619 2503 418 2466 3475 2503 M969 SCHUHMACHER_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHUHMACHER_MYC_TARGETS_DN.html Genes down-regulated in P493-6 cells (Burkitt's lymphoma) induced to express MYC [GeneID=4609]. 11139609 7/8 Yujin Hoshida 3.45536319031541e-05 3.95761083676019e-05 1580 2402.90909090909 2466 3.45541691939772e-06 290 2.27803776662586 2.27803776662586 1 3.98332795828486 1580 2466 4475 3348 4087 1715 1563 3444 290 3065 399 2504 M10336 OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_DN.html Genes down-regulated in epithelial ovarian cancer (EOC) biopsies: invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 14/15 Leona Saunders 7.78824296023699e-05 8.619914572922e-05 575 2518.81818181818 2467 7.08047153300395e-06 571 1.55203439583985 -1.48300418648637 -1 2.48689471601302 1849 4066 3138 4160 4216 1770 571 2467 574 3686 1210 2505 M1384 SHIN_B_CELL_LYMPHOMA_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_2.html Cluster 2 of genes distinguishing among different B lymphocyte neoplasms. 19010892 36/41 Jessica Robertson 4.98907347627613e-07 1.11141872398347e-06 4040 2720.63636363636 2467 4.53552237061723e-08 1611 2.00820902064765 -1.46629318408183 -1 4.75865877990043 4036 2293 2229 3753 1945 2467 2209 1611 2513 2870 4001 2506 M11302 SMID_BREAST_CANCER_RELAPSE_IN_LUNG_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LUNG_DN.html Genes down-regulated in lung relapse of breast cancer. 18451135 44/60 Jessica Robertson 4.00243902759506e-06 5.44895073846226e-06 1330 2495.72727272727 2467 3.63858755382979e-07 796 2.97239440059293 3.07095887283447 1 6.24208512042967 1326 3678 796 3634 3397 2334 2467 1656 3465 1846 2854 2507 M5374 BIOCARTA_SARS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SARS_PATHWAY.html The SARS-coronavirus Life Cycle 11/14 BioCarta 0.000107819255597966 0.000118130660729434 2355 2297.18181818182 2468 9.80223091343315e-06 327 2.06277651313543 1.8606941242886 1 3.20821141220877 2354 2888 2616 2341 4266 2661 1260 796 327 3292 2468 2508 M671 REACTOME_REVERSIBLE_HYDRATION_OF_CARBON_DIOXIDE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REVERSIBLE_HYDRATION_OF_CARBON_DIOXIDE.html Genes involved in Reversible Hydration of Carbon Dioxide 6/12 Reactome 3.16889813521595e-06 4.45685315799145e-06 3455 2225.63636363636 2468 3.16890265408694e-07 144 3.29658205426344 -4.4906182550538 -1 7.04406103446455 3451 1035 4214 972 3329 2468 957 3808 144 1485 2619 2509 M5408 RODWELL_AGING_KIDNEY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_DN.html Genes whose expression decreases with age in normal kidney. 15562319 171/233 John Newman 2.22879338585767e-07 7.8273101050954e-07 2670 2352.36363636364 2468 2.0261760105946e-08 1068 1.89395530344974 -2.00246659117406 -1 4.60105276320711 2668 2970 2544 2806 1068 2359 2252 3040 1834 2468 1867 2510 M241 PID_RAC1_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAC1_REG_PATHWAY.html Regulation of RAC1 activity 18832364 48/51 Pathway Interaction Database 1.5450767673512e-07 7.28175281873995e-07 3325 2416.09090909091 2471 1.40461534169375e-08 441 1.9601421654823 -2.1285751905769 -1 4.78832546284305 3323 441 1583 1375 664 4575 3906 4223 1422 2471 2594 2511 M3506 MOREIRA_RESPONSE_TO_TSA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOREIRA_RESPONSE_TO_TSA_DN.html Down-regulated in CD4+ [GeneID=920] T lymphocytes after 4 h treatment with 100 nM TSA [PubChem=5562]. 14606959 16/24 John Newman 2.16341895339369e-06 3.23655703962543e-06 2475 2104.18181818182 2471 1.96674643712981e-07 432 1.56171265483498 -1.97949096499664 -1 3.39796508333068 2617 905 2471 2812 3074 3590 2471 432 1432 1880 1462 2512 M16587 SASSON_RESPONSE_TO_GONADOTROPHINS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_GONADOTROPHINS_UP.html Genes up-regulated in primary granulosa cells after stimulation with LH or FSH gonadotrophic hormones for 24 h. 15026540 126/157 Arthur Liberzon 7.38949869482876e-08 6.11670596203388e-07 4225 2284.18181818182 2471 6.71772631184719e-09 160 1.63824682966712 -1.32926807303103 -1 4.04365386979928 4222 1559 2891 651 160 2471 2300 2933 1116 3683 3140 2513 M12026 LUND_SILENCED_BY_METHYLATION http://www.broadinstitute.org/gsea/msigdb/cards/LUND_SILENCED_BY_METHYLATION.html Genes up-regulated in FE-8 cells (fibroblasts) upon treatment with azacitidine [PubChem=9444]. 16568090 24/29 Arthur Liberzon 7.5461177871192e-07 1.43766840336891e-06 4015 2660.81818181818 2472 6.86010943225386e-08 441 1.99608734313839 1.55448148279602 1 4.63990099659484 4013 2797 2472 1684 2332 4329 2902 3710 2214 2375 441 2514 M16097 NOUZOVA_METHYLATED_IN_APL http://www.broadinstitute.org/gsea/msigdb/cards/NOUZOVA_METHYLATED_IN_APL.html Genes whose CpG islands are hyper-methylated in the NB4 cell line (APL, acute promyelocytic leukemia) compared to PBMC (normal peripheral peripheral blood mononuclear cells). 15302897 73/112 Kevin Vogelsang 2.49764518394155e-07 8.18104459972526e-07 3360 2400.27272727273 2472 2.27058678863415e-08 783 1.99707715720061 2.30427501583506 1 4.83887735360855 3359 2632 2319 3116 1192 2472 3946 2134 783 3381 1069 2515 M14744 ZHAN_MULTIPLE_MYELOMA_LB_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_LB_UP.html Top 50 up-regulated genes in cluster LB of multiple myeloma samples belonging to the low bone disease group. 16728703 59/68 Kevin Vogelsang 1.39712800709156e-06 2.26302134298975e-06 2095 2219.72727272727 2474 1.27011717668175e-07 376 2.10500560254969 2.03452485504557 1 4.72901541466057 2094 376 1403 1411 2803 2560 2965 3555 2474 1457 3319 2516 M4619 LIU_PROSTATE_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_PROSTATE_CANCER_UP.html Genes up-regulated in prostate cancer samples. 16618720 133/169 Arthur Liberzon 2.74295340234369e-07 8.38703759494626e-07 2340 2455.54545454545 2475 2.49359431303123e-08 1293 1.99422450772653 -1.91250638995254 -1 4.82323249828725 2339 2560 2091 3353 1293 3502 3405 2668 2475 1599 1726 2517 M1651 RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP.html Genes up-regulated in the brain cortex of mice that were exposed to an enriched learning environment for 2 or 14 days. 11070096 31/38 John Newman 6.60445925336955e-07 1.32080237532945e-06 2870 2766.27272727273 2475 6.00405566913348e-08 2035 1.87306818717847 2.35925924947743 1 4.37859571625566 2866 2317 2424 2475 2212 2555 2357 3737 2035 3507 3944 2518 M13515 KEGG_MISMATCH_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MISMATCH_REPAIR.html Mismatch repair 22/23 KEGG 0.000289996480207361 0.000309749578316077 3530 2411 2476 2.63667921461863e-05 231 1.07190093745841 1.10191152292882 1 1.46260897657172 360 3184 3527 2476 4388 672 231 1789 4107 3527 2260 2519 M1096 KOINUMA_COLON_CANCER_MSI_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOINUMA_COLON_CANCER_MSI_UP.html Genes up-regulated in colorectal carcinoma samples positive for MSI (microsatellite instability) compared to the MSI negative ones. 16247484 18/21 Arthur Liberzon 2.32301324297021e-06 3.43610858878703e-06 2660 2504.90909090909 2476 2.11183245079875e-07 1886 1.51839362827787 1.46297966736899 1 3.28645723840605 2657 1886 2516 2834 3115 2187 2476 2006 3262 2207 2408 2520 M2778 TAVAZOIE_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/TAVAZOIE_METASTASIS.html Putative metastasis genes: up-regulated in metastatic cell lines LM2 (lung) and BoM2 (bone) relative to the parental MDA-MB-231 line (breast adenocarcinoma). 18185580 140/262 Jessica Robertson 1.13792315912801e-08 1.47150611262581e-07 2865 2098.81818181818 2476 1.03447560455798e-09 287 2.49873189813942 -2.10930010662579 -1 6.81563870868513 2861 1528 287 593 880 3437 3205 3138 2476 317 4365 2521 M8535 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIO_SERIES.html Glycosphingolipid biosynthesis - ganglio series 12/16 KEGG 5.71217682084586e-06 7.42061557801729e-06 2480 2350.45454545455 2477 5.19290150204279e-07 267 1.73281620509546 -1.7137162324396 -1 3.52461076134303 2477 2425 2576 2586 3565 3650 2455 267 3532 1543 779 2522 M19436 FUNG_IL2_TARGETS_WITH_STAT5_BINDING_SITES http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_TARGETS_WITH_STAT5_BINDING_SITES.html Genes with putative STAT5 [GeneID=6777] binding sites; up-regulated by IL2 [Gene D=3558] in both primary thymocytes and T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 6/9 Arthur Liberzon 3.39140818043104e-06 4.71686378864094e-06 2425 2431.27272727273 2478 3.39141335618441e-07 354 3.16858390853904 2.61674351373016 1 6.73723547870259 2422 2478 4394 2876 3364 1960 1030 354 490 3481 3895 2523 M868 REACTOME_CHROMOSOME_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHROMOSOME_MAINTENANCE.html Genes involved in Chromosome Maintenance 96/251 Reactome 6.85741278411696e-06 8.75019960557773e-06 115 1857.18181818182 2479 6.23403105345975e-07 58 1.48821997189846 1.55036899937443 1 2.97719036686279 111 3014 3401 2488 3639 58 111 637 4019 2479 472 2524 M17406 BIOCARTA_CYTOKINE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CYTOKINE_PATHWAY.html Cytokine Network 5/34 BioCarta 8.15199462602268e-05 9.00899429520652e-05 1865 2202.09090909091 2482 8.15229368903693e-06 154 2.81607110408062 -3.48894847833416 -1 4.53135582888449 1862 2482 4188 2613 4239 2189 713 568 2724 2491 154 2525 M17941 BIOCARTA_VIP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VIP_PATHWAY.html Neuropeptides VIP and PACAP inhibit the apoptosis of activated T cells 32/34 BioCarta 3.40619745092217e-07 9.18700112477295e-07 4130 2529.90909090909 2482 3.09654361663105e-08 661 1.66191485831418 -1.82507620442514 -1 3.98472647964829 4126 661 2482 1276 1528 3436 1866 4137 1918 2727 3672 2526 M12993 KLEIN_PRIMARY_EFFUSION_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KLEIN_PRIMARY_EFFUSION_LYMPHOMA_UP.html Genes up-regulated in AIDS-related primary effusion lymphoma (PEL) samples compared to other tumor subtypes and normal B lymphocytes. 12531789 59/72 Kate Stafford 3.58642316278484e-07 9.41752134134615e-07 2235 2750.09090909091 2482 3.2603852249463e-08 1263 1.51126919199688 1.58831340433061 1 3.61245056223205 2232 4207 3359 4247 1583 1933 1720 1263 3828 3397 2482 2527 M17730 GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_UP.html Genes up-regulated in quescent CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloblastic leukemia) patients compared to the dividing cells from normal donors. 17717066 80/146 Arthur Liberzon 6.53942708294672e-05 7.28833431676706e-05 1220 2808.36363636364 2483 5.94511043030803e-06 1100 2.10571011553873 -2.26103462431775 -1 3.45363753996606 1217 4473 2349 4543 4182 1100 1390 3609 4431 2483 1115 2528 M5487 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_UP http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_UP.html Hepatic graft versus host disease (GVHD), day 7: up-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 138/204 Arthur Liberzon 5.59612171877065e-07 1.18659903470788e-06 2325 2492.36363636364 2484 5.08738467477453e-08 702 2.14431228469453 -2.22396013991473 -1 5.06004702643488 2324 2102 869 2675 2064 3378 2484 3442 3869 702 3507 2529 M4862 REACTOME_RECYCLING_OF_BILE_ACIDS_AND_SALTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECYCLING_OF_BILE_ACIDS_AND_SALTS.html Genes involved in Recycling of bile acids and salts 9/27 Reactome 9.7805817605744e-07 1.72546377095256e-06 3505 2246.09090909091 2485 9.78058606526715e-08 85 4.17135404165545 -4.92483107844571 -1 9.61789113112225 3505 1002 4205 85 2620 4031 2485 3218 120 1317 2119 2530 M18175 REACTOME_P75NTR_SIGNALS_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P75NTR_SIGNALS_VIA_NFKB.html Genes involved in p75NTR signals via NF-kB 20/23 Reactome 8.62548920383806e-06 1.07875752628817e-05 680 2127.63636363636 2485 7.84138456525459e-07 121 1.71509101350272 -1.43968314880189 -1 3.37597297359917 680 3470 2746 2485 3716 477 121 1526 3868 3333 982 2531 M1199 TERAMOTO_OPN_TARGETS_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_4.html Cluster 4: genes whose up-regulation peaked 4 days after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 30/33 Arthur Liberzon 0.000581011364450211 0.000611590909947591 250 2350.81818181818 2486 5.28331694570943e-05 248 2.55000628996013 2.55000628996013 1 3.24549440905069 248 3986 1498 3779 4452 985 1350 2824 3336 2486 915 2532 M1902 SCHRAETS_MLL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAETS_MLL_TARGETS_UP.html Genes up-regulated in fibroblasts from MLL [GeneID=4297] knockout mice. 12789274 59/77 Arthur Liberzon 1.47296694820487e-05 1.77266802537658e-05 875 2210.09090909091 2486 1.33906982750842e-06 611 2.65963674183995 2.95438493904504 1 5.03204948281594 872 2653 611 2676 3863 2486 3208 2116 3667 1037 1122 2533 M18312 KEGG_MATURITY_ONSET_DIABETES_OF_THE_YOUNG http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MATURITY_ONSET_DIABETES_OF_THE_YOUNG.html Maturity onset diabetes of the young 4/27 KEGG 1.61084056319012e-06 2.5276487560696e-06 4295 2902.36363636364 2487 1.61084173085461e-07 1386 2.96573811890435 -2.67230031926851 -1 6.62587693404592 4292 2487 4184 2324 2962 3935 2107 1931 2319 1386 3999 2534 M2849 TIMOFEEVA_GROWTH_STRESS_VIA_STAT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIMOFEEVA_GROWTH_STRESS_VIA_STAT1_DN.html Genes down-regulated in SK-NEP-1 cells (Wilm's tumor ) stably expressing inactivated forms of STAT1 [GeneID=6772] under growth stress (hypoxia or nutritional deprivation). 16799645 25/33 Arthur Liberzon 1.01761555060983e-06 1.77565449126744e-06 1990 2293.81818181818 2487 9.2510547391889e-08 387 1.29103470373714 1.32672671984654 1 2.93572263545295 1986 2788 3364 3765 2579 1217 1536 387 2487 3798 1325 2535 M2012 DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP.html Genes up-regulated in mARMS (molecular ARMS) compared to the mERMS (molecular ERMS) class of rhabdomyosarcoma tumors. 16849537 444/551 Arthur Liberzon 1.84209732397499e-07 7.47950348864313e-07 3885 2509.72727272727 2488 1.67463407110631e-08 861 1.80308228455852 2.08913564068053 1 4.3922048167375 3883 1206 2488 1900 861 3233 4379 3127 1991 2809 1730 2536 M1888 WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_DN http://www.broadinstitute.org/gsea/msigdb/cards/WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_DN.html Genes down-regulated in gastric mucosal tissue of mice on 2% cholesterol [PubChem=5997] diet and infected with H. pylori vs those infected with H. pylori while on 0% cholesterol diet. 16951684 30/52 Jessica Robertson 7.75102467466813e-06 9.78247753242543e-06 1600 2796 2488 7.04641089378088e-07 1596 1.76683909964806 -0.984403288532621 -1 3.50952407705765 1596 2303 1825 2004 3682 2150 2906 4537 3507 2488 3758 2537 M14560 CHO_NR4A1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CHO_NR4A1_TARGETS.html Genes up-regulated in RKO cells (colon cancer) after treatment with the NR4A1 [GeneID=3164] agonist, DIM-C-pPhOCH3. 17234778 38/54 Jessica Robertson 4.05981120950077e-07 9.97185221109921e-07 2495 2555.63636363636 2493 3.69073814425984e-08 764 2.31044085971767 -2.03547461612071 -1 5.52612453913233 2493 3692 1486 3851 1724 1861 764 2556 3337 1713 4635 2538 M593 REACTOME_TRAFFICKING_AND_PROCESSING_OF_ENDOSOMAL_TLR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAFFICKING_AND_PROCESSING_OF_ENDOSOMAL_TLR.html Genes involved in Trafficking and processing of endosomal TLR 34/64 Reactome 9.0708987009881e-07 1.63524808786642e-06 3710 2650.27272727273 2494 8.24627494640452e-08 743 2.52756522240341 -2.91197666441722 -1 5.83179602940494 3709 3705 1654 1893 2494 4557 4400 919 743 3245 1834 2539 M672 CHIN_BREAST_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIN_BREAST_CANCER_COPY_NUMBER_UP.html Genes from common regions of gains observed in more than 15% of 148 primary breast cancer tumors. 17001317 34/37 Arthur Liberzon 9.07537502321232e-07 1.63524808786642e-06 4055 2430.36363636364 2495 8.25034433360125e-08 159 2.25745665597389 2.03193168243818 1 5.20323320545386 4052 1785 2054 858 2495 3552 2791 2555 159 2351 4082 2540 M8066 BIOCARTA_IL22BP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL22BP_PATHWAY.html IL22 Soluble Receptor Signaling Pathway 12/17 BioCarta 9.47066112826962e-06 1.17821614458178e-05 1350 2465.18181818182 2496 8.60972899841155e-07 567 1.35199850925199 -1.24808760627929 -1 2.62984600578109 1348 3509 3147 2496 3738 1633 567 1410 4138 2961 2170 2541 M821 SCHLESINGER_METHYLATED_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SCHLESINGER_METHYLATED_IN_COLON_CANCER.html Genes expressed in normal colon; they undergo down-regulation in tumors through DNA methylation. 17200670 5/11 Leona Saunders 2.53836487377461e-05 2.94737569599414e-05 2500 2506.54545454545 2496 2.53839386907379e-06 254 2.67024563770175 3.03749837273667 1 4.81520190478188 2589 1057 4417 4564 4438 2500 2456 254 458 2496 2343 2542 M17256 HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC.html Genes distinguishing between sporadic breast cancer tumors and hereditary breast cancer tumors that have mutated BRCA1 and BRCA2 [GeneID=672;675]. 11207349 76/83 John Newman 9.07701269112294e-07 1.63524808786642e-06 460 2199.90909090909 2496 8.25183312383932e-08 457 1.22027762859004 1.29873363867895 1 2.78964008246297 956 2619 3642 2976 2496 458 457 1995 3135 3962 1503 2543 M7657 AMUNDSON_GAMMA_RADIATION_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_GAMMA_RADIATION_RESISTANCE.html Gene predicting resistance of the NCI-60 cell lines to gamma radiation. 18199535 42/64 Jessica Robertson 1.17642224710775e-05 1.43927242258906e-05 1620 2514.36363636364 2496 1.06948048902219e-06 743 2.81750501511609 3.01957334659566 1 5.43623451146726 1619 3093 743 1734 3803 3150 4209 3417 2496 920 2474 2544 M1820 MATZUK_CENTRAL_FOR_FEMALE_FERTILITY http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_CENTRAL_FOR_FEMALE_FERTILITY.html Genes central for female fertility pathways, based on mouse models with female fertility defects. 18989307 24/37 Jessica Robertson 3.53052732456716e-07 9.38293297970552e-07 2895 2728.90909090909 2497 3.20957081012825e-08 828 1.65784249947685 1.79941020756109 1 3.96872929686118 2892 828 2497 3884 1560 3963 3360 2451 4220 2033 2330 2545 M10850 CHUNG_BLISTER_CYTOTOXICITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHUNG_BLISTER_CYTOTOXICITY_DN.html Genes down-regulated in blister cells from patients with adverse drug reactions (ADR). 19029983 65/120 Jessica Robertson 3.24341527362968e-06 4.54135867443847e-06 1715 2767.54545454545 2497 2.94856368667341e-07 1713 1.62746645149414 -2.05058557263143 -1 3.44685926232319 1713 3359 3278 2497 3295 2275 1735 2245 4100 3764 2182 2546 M2494 PEDRIOLI_MIR31_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PEDRIOLI_MIR31_TARGETS_DN.html Genes down-regulated in primary LEC cells (lymphatic endothelum) upon overexpression of MIR31 [GeneID=407035]. 20479124 547/811 Arthur Liberzon 1.7447665145891e-07 7.37919956089047e-07 2525 2383.54545454545 2497 1.74476665157857e-08 278 2.21681217645013 -2.0990085740131 -1 5.41673585669216 2521 2497 4708 1572 1351 2458 2856 2863 2727 278 2388 2547 M11685 SHIPP_DLBCL_CURED_VS_FATAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_CURED_VS_FATAL_DN.html Top 50 down-regulated markers for the diffused large B-cell lymphoma (DLBCL) that distinguished between cured and fatal/refractory clinical outcomes. 11786909 63/90 Jean Junior 1.2760279769774e-06 2.10535997801613e-06 4075 2715.90909090909 2498 1.16002610644587e-07 367 1.74011044091933 -1.38581775697592 -1 3.92253131827694 4075 367 2498 2437 2745 4547 4145 3128 2198 1779 1956 2548 M2300 VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN.html Genes down-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout compared to normal 9.5 dpc embryos. 17371845 35/54 Arthur Liberzon 6.1078341547105e-06 7.87892244062136e-06 1475 2535.90909090909 2499 5.55259191989511e-07 1295 2.2376883788275 2.25358500141917 1 4.54269587499112 1472 3415 1295 3389 3595 1690 1873 2499 4576 1414 2677 2549 M2341 REACTOME_APOPTOTIC_EXECUTION_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOTIC_EXECUTION_PHASE.html Genes involved in Apoptotic execution phase 67/78 Reactome 1.70846322284741e-07 7.34421348983585e-07 2945 2504.45454545455 2500 1.55314850502024e-08 780 2.13537232562689 -1.90596991020216 -1 5.21767344757231 2944 1672 1881 1506 780 3567 2602 4681 2168 2500 3248 2550 M16128 XU_GH1_EXOGENOUS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_EXOGENOUS_TARGETS_UP.html Genes up-regulated in MFCF-7 cells (breast cancer) by exogenous HG1 [GeneID=2688]. 15845533 63/121 John Newman 1.28918250503122e-07 7.20206492018647e-07 3325 2302.18181818182 2500 1.17198416416027e-08 365 1.99804896820581 2.37566856736734 1 4.88573363508495 3324 365 1771 2578 479 3585 4678 1111 3153 1780 2500 2551 M18702 MARSON_FOXP3_TARGETS_STIMULATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_STIMULATED_DN.html Genes with promoters bound by FOXP3 [GeneID=50943], dependent on it, and down-regulated in hybridoma cells stimulated by PMA [PubChem=4792] and ionomycin [PubChem=3733]. 17237765 15/21 Arthur Liberzon 9.08897283188241e-07 1.63552999490983e-06 1220 1853.72727272727 2500 8.2627059880532e-08 242 1.68234118619079 -1.84137882147044 -1 3.86484586845757 1216 2860 2801 2843 2500 1200 398 242 3059 2535 737 2552 M9177 BIOCARTA_DC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DC_PATHWAY.html Dendritic cells in regulating TH1 and TH2 Development 25/83 BioCarta 1.53345443956584e-06 2.43034905384331e-06 2520 2161.18181818182 2502 1.39405046220234e-07 588 2.74612376080314 -2.74710975630564 -1 6.15034987507211 2516 3738 1527 2808 2879 3017 1859 588 801 2502 1538 2553 M19104 REACTOME_REGULATION_OF_AMPK_ACTIVITY_VIA_LKB1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_AMPK_ACTIVITY_VIA_LKB1.html Genes involved in Regulation of AMPK activity via LKB1 18/38 Reactome 3.85458426453722e-06 5.27199006914392e-06 2505 2500.81818181818 2502 3.50417365282569e-07 971 1.42249813892815 -1.4959460692689 -1 2.96938498949091 2502 3759 3483 1534 3379 2564 2228 1529 971 3749 1811 2554 M58 PID_AR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_PATHWAY.html Coregulation of Androgen receptor activity 18832364 87/113 Pathway Interaction Database 9.13171568066803e-07 1.6407193761992e-06 2465 2400.36363636364 2504 8.3015631554949e-08 619 1.44536645915681 1.39397031850668 1 3.31259539118234 2465 3335 3505 3225 2504 1329 1732 829 2613 4248 619 2555 M837 REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_RAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_RAS.html Genes involved in CREB phosphorylation through the activation of Ras 28/35 Reactome 6.796697433329e-06 8.67976512048509e-06 2505 2795.36363636364 2504 6.17883493744612e-07 1155 1.34671842201173 1.27443589064129 1 2.69125933185239 2504 2322 3187 2005 3635 2179 2208 3492 4084 3978 1155 2556 M19488 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP.html Genes up-regulated in nasopharyngeal carcinoma (NPC) positive for LMP1 [GeneID=9260], a latent gene of Epstein-Barr virus (EBV). 16912175 474/643 Arthur Liberzon 1.75842271043979e-07 7.39808194525452e-07 1105 2287.63636363636 2504 1.5985662281705e-08 811 2.10940159347753 -2.17790918262833 -1 5.15091429010321 2560 2504 840 2057 811 3626 2843 4032 1102 1105 3684 2557 M1701 HOWLIN_CITED1_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_1_UP.html Genes up-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs. heterozygotic animals. 16278680 42/50 Arthur Liberzon 5.09094745092125e-06 6.70272579312365e-06 1500 2601.72727272727 2505 4.62814475613912e-07 1500 1.76481073147515 -2.1301648890889 -1 3.62197496149397 1500 2701 2505 3876 3518 2364 1644 1784 3844 2660 2223 2558 M3710 WALLACE_PROSTATE_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_UP.html Genes up-regulated in prostate tumor vs normal tissue samples. 18245496 25/27 Jessica Robertson 4.50433811391715e-08 4.71407447842327e-07 2555 2125.54545454545 2505 4.09485291467288e-09 40 1.5199992399972 -1.63115249016222 -1 3.81732323177725 2552 787 2987 3852 40 3163 3458 1081 1787 2505 1169 2559 M1584 LIU_VMYB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_VMYB_TARGETS_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by overexpression of v-MYB oncogenic varian of CMYB [GeneID=4602] off adenovirus vector. 16205643 179/224 Arthur Liberzon 4.2669994148695e-07 1.01564484307534e-06 2510 2481.09090909091 2506 3.8790911295214e-08 1259 1.72653904520631 1.72465419684436 1 4.11136837522048 2506 1447 2886 1259 1790 2268 2733 4452 2572 2331 3048 2560 M19613 BIOCARTA_IGF1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1R_PATHWAY.html Multiple antiapoptotic pathways from IGF-1R signaling lead to BAD phosphorylation 40/44 BioCarta 3.5885931113391e-07 9.41752134134615e-07 2180 2514.81818181818 2507 3.26235790609354e-08 822 1.06237923663773 1.28529551194532 1 2.52458748391889 2178 2715 3736 1330 1585 1931 2507 2726 3762 4371 822 2561 M12636 RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP.html Genes up-regulated in peripheral blood monocytes by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 407/507 Arthur Liberzon 2.26087223365115e-07 7.86164283892477e-07 3935 2748.72727272727 2507 2.05533860544914e-08 1083 1.84839922819822 2.03009752313369 1 4.48776526319628 3932 2507 2221 3099 1083 4109 4066 1954 2066 1663 3536 2562 M1401 BYSTROEM_CORRELATED_WITH_IL5_DN http://www.broadinstitute.org/gsea/msigdb/cards/BYSTROEM_CORRELATED_WITH_IL5_DN.html Genes whose expression in bone marrow samples correlated inversely with increased levels of serum IL5 [GeneID=3567]. 14525773 87/136 Kate Stafford 6.4670381197614e-07 1.3066330228484e-06 1635 2403.81818181818 2508 5.87912729162602e-08 1260 1.73823852056935 -1.88069298412342 -1 4.06308252947594 1633 3333 3256 2933 2181 2508 1325 1260 1958 3494 2561 2563 M744 REACTOME_PROCESSIVE_SYNTHESIS_ON_THE_LAGGING_STRAND http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSIVE_SYNTHESIS_ON_THE_LAGGING_STRAND.html Genes involved in Processive synthesis on the lagging strand 15/16 Reactome 0.000139995969194202 0.000151903672321065 495 2301.72727272727 2509 1.2727716233258e-05 432 1.25744314218965 1.33210161414588 1 1.88092622184755 495 2845 2990 2879 4310 825 432 1972 3960 2102 2509 2564 M5736 BARRIER_COLON_CANCER_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_COLON_CANCER_RECURRENCE_DN.html Down-regulated genes from the 70-gene prognosis predictor for stage 2 colon cancer, based on non-neoplastic mucosa gene expression profiles. 17043639 40/56 Arthur Liberzon 6.24509812749905e-06 8.03841373378661e-06 460 2514.72727272727 2509 5.67737805037336e-07 458 0.843120437079771 -0.849221705315422 -1 1.67747031377631 458 1751 3865 4067 3602 496 1034 2509 4535 3904 1441 2565 M6510 PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_UP.html Genes up-regulated in post-GC, BCL6 [GeneID=604] dependent B cell non-Hodgkin's lymphoma (B-NHL) vs MYC [GeneID=4609] driven pre-GC lymphoma. 18066064 361/414 Jessica Robertson 4.40001698587537e-07 1.0301627070105e-06 1825 2906.45454545455 2509 4.00001624171128e-08 1634 1.8840602778173 -1.62641266992641 -1 4.48636486779787 4250 2509 2321 1634 1825 4078 3015 4539 1824 1889 4087 2566 M10688 PAL_PRMT5_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PAL_PRMT5_TARGETS_UP.html Genes up-regulated in NIH-3T3 cells (fibroblast) after knockdown of PRMT5 [GeneID=10419] by RNAi. 15485929 279/323 John Newman 1.03288513014353e-06 1.79170077702221e-06 135 1805.18181818182 2510 9.38986922796757e-08 132 1.52706807236093 1.62973349978491 1 3.47919464413615 132 2953 3705 2510 2596 240 245 435 2911 3188 942 2567 M4290 LUI_THYROID_CANCER_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_3.html Cluster 3: genes with similar expression profiles across follicular thyrorid carcinoma (FTC) samples; genes in this cluster correlated well with the presence of PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 37/55 Leona Saunders 2.45875956035422e-06 3.59076272427967e-06 1610 2753.27272727273 2512 2.2352384621022e-07 1273 1.51966308967668 -1.76689505416362 -1 3.2775616459858 1608 4541 3597 2512 3153 1866 1510 2092 3831 4303 1273 2568 M19818 KEGG_NON_SMALL_CELL_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NON_SMALL_CELL_LUNG_CANCER.html Non-small cell lung cancer 58/64 KEGG 1.53643341303132e-07 7.28175281873995e-07 3945 2437.36363636364 2514 1.39675774575689e-08 201 1.77187874313078 -1.73794046601603 -1 4.32362105303654 3941 404 2514 201 653 4533 3954 4362 355 3535 2359 2569 M6663 HOLLMANN_APOPTOSIS_VIA_CD40_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLMANN_APOPTOSIS_VIA_CD40_DN.html Genes down-regulated in DLBCL (diffuse large B-cell lymphoma) cell lines sensitive to stimulation of CD40 [GeneID=958] relative to the resistant ones. 16585179 390/543 Arthur Liberzon 8.82939087141906e-07 1.60596242439684e-06 2155 2696.63636363636 2514 8.02672219543002e-08 1379 1.6050684204466 -1.45690993519142 -1 3.69014305184523 2154 3277 3768 2514 2469 1515 2465 3653 2635 3834 1379 2570 M4716 CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP.html Genes up-regulated in SH-SY5Y cells (neuroblastoma) after treatment with epoxomicin [PubChem=3035402], a protease inhibitor causing apoptosis. 16983338 322/404 Leona Saunders 3.1009579918489e-07 8.87599861826974e-07 2840 2356.81818181818 2514 2.81905311721562e-08 1221 1.85827630926154 2.1005986646037 1 4.47262631846062 2840 2514 1699 2697 1421 2532 4409 1868 3137 1587 1221 2571 M12367 LEE_NAIVE_T_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_NAIVE_T_LYMPHOCYTE.html Genes enriched in the naive circulating T lymphocytes compared to the earlier differentiation stages. 15210650 20/30 Arthur Liberzon 1.53441529246887e-06 2.43034905384331e-06 1825 2419.09090909091 2516 1.39492396605955e-07 970 1.96634747579563 1.83670600441834 1 4.3897173624692 1822 1880 1781 3297 2881 1708 970 3374 3638 2516 2743 2572 M1744 MARSON_BOUND_BY_E2F4_UNSTIMULATED http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_BOUND_BY_E2F4_UNSTIMULATED.html Genes with promoters bound by E2F4 [GeneID=1874] in unstimulated hybridoma cells. 17237765 788/969 Jessica Robertson 1.06896053733785e-06 1.84074926531728e-06 190 2052.72727272727 2519 1.06896105154268e-07 187 1.56644682139354 1.6613360547369 1 3.56281455592133 187 3547 4520 2519 2686 373 470 1057 3103 2570 1548 2573 M14132 SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP http://www.broadinstitute.org/gsea/msigdb/cards/SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP.html Genes up-regulated in head and neck squamous cell carcinoma (HNSCC) samples positive for HPV compared to the HPV-negative tumors. 16467079 86/105 Leona Saunders 1.79345853827315e-06 2.75567248638752e-06 2375 2547.45454545455 2520 1.63041818210666e-07 1628 1.53457083323081 1.56734368814566 1 3.38115155958208 2373 1628 3230 3908 2977 2008 1865 1779 3139 2520 2595 2574 M170 KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN.html Genes down-regulated in MEWO cells (melanoma) after 96 h of methionine [PubChem=876] deprivation. 16908595 95/107 Arthur Liberzon 2.61316898692104e-06 3.77329494725722e-06 2710 2510.54545454545 2520 2.37561099169e-07 1930 1.83369181986997 1.80768211813332 1 3.949308738841 2707 2592 2397 2007 3189 1930 2520 2032 2901 2420 2921 2575 M14859 COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_DN.html Genes down-regulated in pilocytic astrocytoma compared to glioblastoma samples. 16314830 49/60 Jessica Robertson 1.99927717449195e-05 2.35326390613516e-05 2045 2574.27272727273 2520 1.81754122127398e-06 780 2.75777833816188 2.77275179538441 1 5.08311651474231 2045 1716 780 1293 3951 2971 4267 3879 2520 1424 3471 2576 M17772 MACLACHLAN_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MACLACHLAN_BRCA1_TARGETS_UP.html Genes up-regulated in SW480 cells (colon cancer with mutated p53 [GeneID=7157]) upon expression of BRCA1 [GeneID=672] off an adenovirus vector. 10644742 35/51 John Newman 3.62666592828482e-06 4.99354235166405e-06 2490 2532.18181818182 2520 3.2969744607284e-07 947 2.06190780958186 2.2347774754544 1 4.34614964426349 2487 3970 2520 3519 3356 2135 1437 1020 3376 3087 947 2577 M347 WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_H2O2 http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_H2O2.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to HNE and H2O2 [PubChem=5283344;784]. 12419474 54/62 John Newman 1.47926214445577e-06 2.36441494135836e-06 2760 2002.36363636364 2521 1.3447846719096e-07 286 1.93662094457425 2.15971506019902 1 4.33190190350146 2758 414 1744 1267 2851 2940 2795 1814 286 2521 2636 2578 M2210 WIERENGA_STAT5A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_UP.html Genes up-regulated in CD34+ [GeneID=947] cells by intermediate activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 269/369 Arthur Liberzon 3.16018715314682e-07 8.94262307705344e-07 4605 2819.81818181818 2522 2.87289782462871e-08 464 2.18282227170087 2.27093376498641 1 5.25965365655058 4603 2522 705 1612 1439 4110 4302 4462 2488 464 4311 2579 M10570 BIOCARTA_RNA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RNA_PATHWAY.html Double Stranded RNA Induced Gene Expression 17/17 BioCarta 8.41436521585188e-06 1.05464966469137e-05 1540 2488.54545454545 2523 7.64945218049391e-07 225 2.3231005497299 -1.47917990074222 -1 4.59968345030876 1536 2396 2084 3195 3706 2523 1208 4449 225 3319 2733 2580 M16743 KEGG_TYROSINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYROSINE_METABOLISM.html Tyrosine metabolism 33/53 KEGG 8.6229458268918e-06 1.07872526644392e-05 1870 2403.09090909091 2524 7.8390723862664e-07 772 2.29181431679476 1.92201447567856 1 4.52802869710324 1870 3118 1933 2901 3715 1555 772 2098 3113 2524 2835 2581 M6564 HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP.html Genes up-regulated in lesional skin biopsies from mycosis fundoides patients compared to the normal skin samples. 16914566 217/264 Arthur Liberzon 5.01587697097036e-07 1.11516435718229e-06 1600 2656.81818181818 2526 4.55988919505694e-08 1560 1.73939018246217 1.78038647226794 1 4.11394467831065 1597 3574 3397 3230 1950 1560 1852 2526 3214 3915 2410 2582 M12139 GALE_APL_WITH_FLT3_MUTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/GALE_APL_WITH_FLT3_MUTATED_DN.html Genes down-regulated in acute promyelocytic leukemia (APL) patients with mutated FLT3 [GeneID=2322]. 16105978 34/50 Kevin Vogelsang 1.65668476861448e-05 1.97463437067181e-05 715 2507 2527 1.50608840383696e-06 464 0.970401408909861 -0.957978762368278 -1 1.78593787347871 713 2726 3744 2527 3901 464 1702 2334 4451 3940 1075 2583 M2488 FORTSCHEGGER_PHF8_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FORTSCHEGGER_PHF8_TARGETS_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) upon knockdown of PHF8 [GeneID=23133] by RNAi. 20421419 984/1186 Arthur Liberzon 1.29120085567548e-07 7.20206492018647e-07 3900 2482.81818181818 2527 1.29120093069947e-08 581 1.78255504063912 1.94300757529572 1 4.35340001682163 3897 1086 4707 766 581 3113 4620 3031 1548 1435 2527 2584 M389 NAKAJIMA_MAST_CELL http://www.broadinstitute.org/gsea/msigdb/cards/NAKAJIMA_MAST_CELL.html Top 50 most-increased mast cell specific genes. 11493461 48/75 Kevin Vogelsang 9.43711630864163e-07 1.68146476145018e-06 3030 2328 2528 8.57920032435263e-08 1176 2.21922675659431 1.87883872596291 1 5.103466591234 3026 1715 1495 1176 2528 2834 2897 3054 1191 1970 3722 2585 M4357 XU_CREBBP_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_CREBBP_TARGETS_DN.html Genes down-regulated in pro-B lymphocytes after knockout of CREBBP [GeneID=1387]. 16424387 67/87 Kevin Vogelsang 4.00209317838708e-07 9.8899894251241e-07 2030 2307.09090909091 2530 3.63826718765578e-08 1537 1.81446510121007 -1.45923269859392 -1 4.331718147429 2027 3357 2565 2530 1710 1570 1537 2000 2789 2717 2576 2586 M980 KEGG_TRYPTOPHAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TRYPTOPHAN_METABOLISM.html Tryptophan metabolism 31/53 KEGG 3.12546860789368e-06 4.40496023566981e-06 3205 2471.27272727273 2531 2.84133913468577e-07 664 2.1596283891458 1.5417895629759 1 4.60180481067377 3201 664 1556 1474 3276 2637 1672 4178 2531 1990 4005 2587 M110 PID_IL1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL1_PATHWAY.html IL1-mediated signaling events 18832364 40/47 Pathway Interaction Database 9.51521666252075e-07 1.69286930445149e-06 445 2122.09090909091 2531 8.65020070722559e-08 360 1.50021631403513 -1.57686331062435 -1 3.43200438545788 443 3407 3436 4029 2531 463 360 612 3946 3308 808 2588 M4270 KAYO_CALORIE_RESTRICTION_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_CALORIE_RESTRICTION_MUSCLE_DN.html Downregulated in the vastus lateralis muscle of middle aged rhesus monkeys subjected to caloric restriction since young adulthood vs age matched controls 11309484 132/169 John Newman 5.5599353269364e-07 1.18518124301653e-06 2155 2699.36363636364 2531 5.05448793824349e-08 2054 2.01655065448897 2.24076744246776 1 4.75600093648186 2152 3312 2065 2247 2054 2453 2971 3635 3361 2531 2912 2589 M18322 ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION.html Genes up-regulated in RD-EF cells (rhabdomyosarcoma) engineered to express EWSR1-FLI1 fusion [GeneID=2130;2313] and which are also highly expressed in Ewing's famliy tumors. 15930281 128/188 Kevin Vogelsang 1.488732988717e-07 7.26289540930751e-07 3300 2376.72727272727 2532 1.35339371769009e-08 623 1.66013274141854 -1.42031005234879 -1 4.04854206297017 3299 1554 2074 1674 623 2638 3043 4259 2532 1368 3080 2590 M2379 IKEDA_MIR30_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR30_TARGETS_UP.html Genes up-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-30 microRNA. 19188439 209/261 Arthur Liberzon 1.37448446360234e-07 7.20206492018647e-07 1545 2237.63636363636 2532 1.24953140861402e-08 542 1.94650943507532 2.16038465339852 1 4.75841577297736 1543 2962 2532 1500 542 2996 3497 1556 1503 3405 2578 2591 M18467 MATTIOLI_MULTIPLE_MYELOMA_WITH_14Q32_TRANSLOCATIONS http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MULTIPLE_MYELOMA_WITH_14Q32_TRANSLOCATIONS.html Genes expressed in multiple myeloma (MM) patients carrying specific translocations involving the immunoglobulin heavy chain (IGH) locus at 14q32. 15735737 61/80 Leona Saunders 2.6195679134141e-07 8.29211725993449e-07 3700 2265.27272727273 2533 2.38142565939039e-08 406 2.45248717224382 2.25314051652062 1 5.94796053559551 3698 2648 1290 428 1241 3058 4710 2684 406 2222 2533 2592 M5071 IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_UP.html Genes up-regulated during transition from G1 (well differentiated tumor, infected with HCV) to G2 (moderately differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 18/22 Yujin Hoshida 2.36690566825128e-05 2.75846784052989e-05 1255 2732.45454545455 2533 2.15175557579384e-06 1253 1.93716912912568 -1.93747194730989 -1 3.50193388619292 1253 3193 2533 2835 3996 1755 2342 4669 1930 3411 2140 2593 M5336 REACTOME_CELL_CYCLE_MITOTIC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE_MITOTIC.html Genes involved in Cell Cycle, Mitotic 361/409 Reactome 2.50242501037253e-06 3.64325911442268e-06 270 1976.63636363636 2534 2.27493441527292e-07 94 1.47261723379089 1.59343158816044 1 3.17081253075398 94 2949 3948 2534 3162 268 267 1348 2609 3117 1447 2594 M844 ONDER_CDH1_TARGETS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_3_UP.html Genes up-regulated in HMLE cells (immortalized nontransformed mammary epithelial) cells after loss of function of E-cadhedrin (CDH1) [GeneID=999], which was achieved either by RNAi knockdown or by expression of a dominan-negative form of CDH1. 18483246 24/28 Jessica Robertson 2.26801080263394e-06 3.37271927801896e-06 2860 2361.09090909091 2534 2.06183012796491e-07 673 2.10901064126703 2.2552941750905 1 4.59112865376302 2856 3164 1694 4146 3096 2084 1408 2598 2534 1719 673 2595 M1865 WANG_TUMOR_INVASIVENESS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TUMOR_INVASIVENESS_UP.html Up-regulated genes in the subpopulation of invasive PyMT cells (breast cancer) compared to the general population of PyMT cells. 17440055 520/637 Jessica Robertson 4.16754948549862e-07 1.00504816968881e-06 4585 3061.63636363636 2534 4.16755026707992e-08 1373 1.51565682876478 1.62898269951883 1 3.60586414846366 1373 4677 4585 4333 1874 1827 2265 2534 3429 4582 2199 2596 M7239 BIOCARTA_DNAFRAGMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DNAFRAGMENT_PATHWAY.html Apoptotic DNA fragmentation and tissue homeostasis 9/18 BioCarta 1.50295920335478e-05 1.80554019848169e-05 2540 2555.63636363636 2536 1.50296936844019e-06 1049 1.26895367688227 1.48957730273903 1 2.37063242824747 2536 3234 4186 2918 3900 2287 1049 1230 2275 2892 1605 2597 M2842 BIOCARTA_FIBRINOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FIBRINOLYSIS_PATHWAY.html Fibrinolysis Pathway 10/15 BioCarta 5.4425402458564e-05 6.11346738706383e-05 2270 2698.36363636364 2536 4.947886265945e-06 1412 3.03157121440812 2.83555285661438 1 5.08724379930592 2268 3801 1412 3107 4152 2048 1811 2696 4295 1556 2536 2598 M722 REACTOME_TRANSLOCATION_OF_ZAP_70_TO_IMMUNOLOGICAL_SYNAPSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSLOCATION_OF_ZAP_70_TO_IMMUNOLOGICAL_SYNAPSE.html Genes involved in Translocation of ZAP-70 to Immunological synapse 7/16 Reactome 2.57260076480034e-07 8.25741600037569e-07 4055 2683 2536 2.57260106262274e-08 419 3.30756838758724 2.66681868884618 1 8.04163778408487 4051 2452 4223 984 1330 3904 4157 2536 419 840 4617 2599 M10633 BASSO_B_LYMPHOCYTE_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_B_LYMPHOCYTE_NETWORK.html Genes which comprise the top 1% of highly interconnected genes (major hubs) that account for most of gene interactions in the reconstructed regulatory networks from expression profiles in B lymphocytes. 15778709 193/235 Jean Junior 2.17502671357319e-06 3.25186128858583e-06 1860 2440.63636363636 2536 1.97729896719371e-07 886 1.3863304729684 1.46772027239652 1 3.00960810833201 1857 2966 3829 2536 3077 886 1082 1894 3614 3131 1975 2600 M19231 EPPERT_HSC_R http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_HSC_R.html Genes up-regulated in human hematopoietic stem cell (HSC) enriched populations compared to committed progenitors and mature cells. 21873988 169/206 Kolja Eppert 9.57995195153201e-07 1.70182059507833e-06 1825 2681 2536 8.70905102104295e-08 981 2.35851311763872 2.64860725271459 1 5.42196146063833 1825 3861 981 2838 2536 2432 3553 4454 2436 1397 3178 2601 M14418 MARTINELLI_IMMATURE_NEUTROPHIL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINELLI_IMMATURE_NEUTROPHIL_UP.html Neutrophil-specific genes up-regulated in comparison of immature with mature neutrophils. 15302890 2/65 Arthur Liberzon 0.000147236875047057 0.000159540415569814 1450 2641.7 2536.5 1.63607234352189e-05 123 2.16615312356016 -2.16615312356016 -1 3.25780813446158 1450 2935 4597 NA 4379 1266 123 3948 3498 2138 2083 2602 M1824 MATZUK_LUTEAL_GENES http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_LUTEAL_GENES.html Luteal genes, based on mouse models with female fertility defects. 18989307 7/34 Jessica Robertson 1.76421993605072e-05 2.09424057804417e-05 1950 2745.54545454545 2537 1.76423394233114e-06 719 2.28206313259932 -2.6432264153799 -1 4.24412941173563 1950 2473 4569 3358 3941 2502 2537 719 2875 3068 2209 2603 M2535 PECE_MAMMARY_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PECE_MAMMARY_STEM_CELL_DN.html The '3/3 signature': genes consistently down-regulated in all three pools of normal mammary stem cells (defined by their ability to retain the dye PKH26). 20074520 195/217 Arthur Liberzon 2.5942308792662e-07 8.27068974676848e-07 1280 2457.72727272727 2537 2.35839198652444e-08 1229 1.68835004709431 1.85526160278979 1 4.07988898454668 1280 2537 3106 4178 1229 2197 2839 2304 2663 2977 1725 2604 M11682 BONCI_TARGETS_OF_MIR15A_AND_MIR16_1 http://www.broadinstitute.org/gsea/msigdb/cards/BONCI_TARGETS_OF_MIR15A_AND_MIR16_1.html Potential targets of MIR15A and MIR16-1 [GeneID=406948;406950] microRNAs in prostate cancer. 18931683 115/140 Jessica Robertson 2.51523914677705e-07 8.19318755885969e-07 2455 2612.27272727273 2539 2.28658130394728e-08 1200 1.89711661328312 2.42418171216623 1 4.59367901371747 2539 3001 2452 3751 1200 3120 4184 1298 2454 2674 2062 2605 M1859 RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN.html Genes down-regulated in ALL (acute lymphoblastic leukemia) blasts after 1 week of treatment with glucocorticoids. 17330098 474/606 Arthur Liberzon 9.62453366426636e-07 1.70717019524003e-06 240 2146.72727272727 2540 8.74957988618038e-08 237 1.53189258712446 1.57933549921824 1 3.50327511104658 237 2945 3894 3011 2540 748 766 1428 2908 3132 2005 2606 M8511 SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_DN.html Genes that were inversely correlated in H1299 cells (lung cancer): down-regulated by P53 [GeneID=7157] and up-regulated by P73 [GeneID=7161]. 17982488 43/63 Jessica Robertson 5.47210864834921e-06 7.15863437367192e-06 2545 2401.63636363636 2541 4.97465659935769e-07 1483 1.64734239079206 -1.93136501140082 -1 3.35862720367472 2541 3400 3017 1489 3538 2636 1483 1494 1513 3516 1791 2607 M13760 HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_UP.html Genes up-regulated during differentiation from small pre-BII to immature B lymphocyte. 11779835 67/90 Arthur Liberzon 7.31589674196719e-07 1.40713254368725e-06 3270 2892.27272727273 2542 6.65081743163837e-08 2033 1.99525760928272 2.10367555553623 1 4.64543298598243 3266 2191 2033 2884 2308 2542 3284 4406 2371 2294 4236 2608 M2477 ALFANO_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ALFANO_MYC_TARGETS.html Genes up-regulated hT-RPE cells (immortalized retinal pigment epithelium) by MYC [GeneID=4609]. 20123981 362/489 Arthur Liberzon 3.15520548060645e-07 8.93979952731796e-07 3230 2506.45454545455 2542 2.86836903011015e-08 1338 1.81597482610741 1.9831140503515 1 4.36740149694568 3228 3279 3009 2690 1437 1864 3567 2542 2243 2374 1338 2609 M5409 MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_UP.html Genes up-regulated in FSHD (facioscapulohumeral muscular dystrophy) mesoangioblasts. 17761758 29/36 Arthur Liberzon 0.000479118421033205 0.000506027958665636 1395 2756.72727272727 2543 4.35657087086154e-05 1309 2.47083158039678 2.79065645362463 1 3.22493795250791 1395 3433 1309 4157 4435 2466 2516 2543 3872 1499 2699 2610 M4100 PROVENZANI_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PROVENZANI_METASTASIS_UP.html Genes up-regulated in polysomal and total RNA samples from SW480 cells (primary colorectal carcinoma, CRC) compared to the SW620 cells (lymph node metastasis from the same individual). 16531451 261/336 Arthur Liberzon 7.92898924702131e-07 1.4886566923604e-06 2085 2542.27272727273 2543 7.20817464063517e-08 1408 1.81761799079798 1.92861882178463 1 4.20951161517454 2082 3287 2870 3210 2373 1408 2358 2670 2543 2692 2472 2611 M9012 GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_DN.html Down-regulated genes from the set B (Fig. 5a): specific signature shared by cells expressing either AF4-MLL or MLL-AF4 [GeneID=4299;4297] fusion proteins. 17130830 10/11 Arthur Liberzon 5.58161747530445e-06 7.28372532027564e-06 3555 2575.45454545455 2543 5.07421057860913e-07 350 3.11370518015728 2.73467614164077 1 6.38338952993727 3552 2444 1646 2105 3548 2723 2095 3753 350 2543 3571 2612 M1509 BRACHAT_RESPONSE_TO_CISPLATIN http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_CISPLATIN.html Genes up-regulated in FL5.12 cells (pro-B lymphocyte) in response to cisplatin [PubChem=2767]. 12447701 23/27 John Newman 8.13126667317254e-06 1.02263732207233e-05 305 2072.81818181818 2543 7.39208793339645e-07 243 1.48422888172088 -1.55411386373449 -1 2.92865966353171 305 3175 2543 3858 3696 247 243 772 4351 3341 270 2613 M10165 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP.html Genes up-regulated in lobular carcinoma vs normal ductal breast cells. 17389037 113/129 Arthur Liberzon 1.767002715689e-07 7.40425773939871e-07 850 2532.72727272727 2544 1.60636623419243e-08 366 2.95074029430045 3.28438687470709 1 7.22489329592542 848 3875 366 2168 4154 2964 3838 2544 3582 1050 2471 2614 M1106 GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP.html Genes up-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) exposed to doxorubicin [PubChem=31703] in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 816/970 Arthur Liberzon 1.50377063857721e-07 7.26289540930751e-07 3795 2737.27272727273 2544 1.5037707403369e-08 731 1.85469111367834 1.93805078792277 1 4.52887287301376 3792 1999 4339 1380 731 2544 4239 3714 2461 937 3974 2615 M1590 LEE_AGING_NEOCORTEX_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_NEOCORTEX_UP.html Upregulated in the neocortex of aged adult mice (30-month) vs young adult (5-month) 10888876 152/194 John Newman 2.59780147635934e-07 8.27068974676848e-07 2550 2783.27272727273 2546 2.3616379846479e-08 1231 1.71745636463955 -1.6210751448495 -1 4.15108686341516 2546 4430 3330 4265 1231 1901 2406 1867 3392 3337 1911 2616 M10573 SWEET_KRAS_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_KRAS_ONCOGENIC_SIGNATURE.html Genes that contributed maximally to the GSEA score of the up-regulated gene set from the KrasLA mouse model in two human lung cancer expression data sets comparing mutant vs normal KRAS [GeneID=3845]. 15608639 108/149 Arthur Liberzon 1.34384513020202e-06 2.19430666644129e-06 1335 2121.54545454545 2546 1.22167813734121e-07 873 1.57604767759551 -1.56631989369998 -1 3.53659534146233 1333 3003 3201 2673 2778 1088 873 1122 2546 3238 1482 2617 M16476 KEGG_CELL_ADHESION_MOLECULES_CAMS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CELL_ADHESION_MOLECULES_CAMS.html Cell adhesion molecules (CAMs) 108/183 KEGG 4.08456893551909e-15 1.35768770251057e-13 3950 2182.72727272727 2547 3.71324448683553e-16 10 2.47993545733219 2.68754512556637 1 12.7828710264757 3947 10 100 919 2521 2950 3537 2547 2842 87 4550 2618 M10198 FUNG_IL2_SIGNALING_2 http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_SIGNALING_2.html Genes up-regulated by IL2 [GeneID=3558] in T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 10/15 Arthur Liberzon 6.3577751168422e-05 7.09593250212702e-05 2745 2319.54545454545 2547 5.77996259770737e-06 390 2.39124904772271 2.84942279524314 1 3.93991699747457 2742 3804 2593 3463 4556 1826 1377 390 1562 2547 655 2619 M1540 VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_UP.html Genes up-regulated after heat shock in peripheral lympocytes from old donors, compared to those from the young ones. 12618007 22/30 John Newman 0.000399955952315288 0.000424318295106352 2180 2768.63636363636 2547 3.63662438257476e-05 1238 2.08691350676325 2.21541160698414 1 2.78026215488529 2179 4032 2507 3704 4414 2770 2113 1753 1238 3198 2547 2620 M2325 LEE_BMP2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_BMP2_TARGETS_DN.html Genes down-regulated in uterus upon knockout of BMP2 [GeneID=650]. 17515606 1059/1243 Arthur Liberzon 5.52225030601936e-06 7.21469839074409e-06 155 2560.90909090909 2547 5.52226402892914e-07 155 1.55779760232887 1.57728489113351 1 3.17121948893834 155 3828 4684 3269 3592 986 710 1881 2547 4364 2154 2621 M1899 BASSO_CD40_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_CD40_SIGNALING_DN.html Gene down-regulated by CD40 [GeneID=958] signaling in Ramos cells (EBV negative Burkitt lymphoma). 15331443 76/105 Kevin Vogelsang 2.1661903481602e-06 3.23967631283782e-06 2550 2851 2548 1.96926589187584e-07 1597 2.22264936871132 2.4718397493571 1 4.85682966117235 2547 4190 1684 4566 3075 1597 2003 3655 3303 2193 2548 2622 M12008 GHO_ATF5_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GHO_ATF5_TARGETS_UP.html Genes up-regulated in HEP3B cells (liver cancer) overexpressing ATF5 [GeneID=22809] off a plasmid vector. 18701499 20/29 Jessica Robertson 6.02715948944088e-07 1.24278871853236e-06 3695 2753.54545454545 2549 5.47923740059359e-08 517 1.960675958537 1.40620070754554 1 4.60658180852544 3691 1885 2549 1901 2127 3837 4671 2852 517 2514 3745 2623 M2 PID_SMAD2_3NUCLEAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SMAD2_3NUCLEAR_PATHWAY.html Regulation of nuclear SMAD2/3 signaling 18832364 111/130 Pathway Interaction Database 1.80009758198114e-06 2.76397546745315e-06 1190 2141.54545454545 2550 1.63645368624526e-07 64 1.5906396248545 1.85075434004921 1 3.50568148399812 1190 3002 3006 1753 2980 449 2550 1952 3513 3098 64 2624 M4282 BHATTACHARYA_EMBRYONIC_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/BHATTACHARYA_EMBRYONIC_STEM_CELL.html The 'stemnes' signature: genes up-regulated and common to 6 human embryonic stem cell lines tested. 15070671 151/195 Kate Stafford 4.54226673781807e-06 6.07957070584449e-06 2365 2468.18181818182 2550 4.12934192373823e-07 658 1.81334282394458 2.11398515110091 1 3.75385971740505 2361 2981 2550 658 3454 3341 3297 1391 1932 2394 2791 2625 M2584 KAAB_HEART_ATRIUM_VS_VENTRICLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_HEART_ATRIUM_VS_VENTRICLE_DN.html Genes down-regulated in the ventricles of healthy hearts, compared to atria. 15103417 354/447 John Newman 3.64658759688021e-07 9.47297674322927e-07 2220 2460.18181818182 2550 3.31508018301524e-08 1080 1.8839228981579 1.89931257341916 1 4.51362690245018 2218 3846 2700 1080 1605 1364 2370 2781 2550 3824 2724 2626 M12701 MARTINEZ_RB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_TARGETS_DN.html Genes down-regulated in mice with skin specific knockout of RB1 [GeneID=5925] by Cre-lox. 18245467 675/937 Jessica Robertson 1.39859181281847e-07 7.20206492018647e-07 3395 2352.27272727273 2550 1.39859190084114e-08 355 2.06361694099743 2.33424941663581 1 5.04770588457003 3391 1120 4533 355 654 2550 4352 3289 1884 502 3245 2627 M2623 BIOCARTA_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1_PATHWAY.html IGF-1 Signaling Pathway 36/41 BioCarta 5.07125345997314e-07 1.12271652584771e-06 2470 2977.45454545455 2551 4.61023148086897e-08 1809 1.11291469992064 -1.06562782283062 -1 2.61289302435762 2468 3969 3735 2551 1959 2015 1900 3651 4256 4439 1809 2628 M16740 GRADE_COLON_AND_RECTAL_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_AND_RECTAL_CANCER_UP.html Up-regulated genes in both rectal and colon carcinoma compared to normal mucosa samples. 17210682 400/477 Jessica Robertson 9.78250222684123e-07 1.72546377095256e-06 365 2146.36363636364 2551 8.89318779702134e-08 364 1.66977060146962 1.74848393097585 1 3.81998256196136 364 3843 3755 2743 2551 593 544 1349 2730 3489 1649 2629 M108 PID_NETRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NETRIN_PATHWAY.html Netrin-mediated signaling events 18832364 54/58 Pathway Interaction Database 5.80647698535649e-08 5.56439156084225e-07 3435 1954.45454545455 2553 5.27861558055207e-09 78 1.5995244082681 -1.63832941942704 -1 3.97333157904123 3434 438 3139 487 78 2852 1912 2553 1042 2761 2803 2630 M18193 REACTOME_ACTIVATION_OF_KAINATE_RECEPTORS_UPON_GLUTAMATE_BINDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_KAINATE_RECEPTORS_UPON_GLUTAMATE_BINDING.html Genes involved in Activation of Kainate Receptors upon glutamate binding 27/38 Reactome 7.94953517239638e-07 1.49132774299328e-06 3995 2903 2553 7.22685276809346e-08 1827 1.77875015142603 -1.66875761106735 -1 4.11786874019208 3993 1827 2553 2416 2375 4267 2852 2389 2808 2435 4018 2631 M19661 WANG_ESOPHAGUS_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ESOPHAGUS_CANCER_PROGRESSION_UP.html Candidate progression biomarkers up-regulated in transition from non-tumor-risk associated to tumor-risk associated Barrett's esophagus and then to esophageal adenocarcinoma (EAC). 16449976 10/11 Arthur Liberzon 4.59711285413557e-06 6.1416282681913e-06 2555 2483.63636363636 2553 4.17920223661432e-07 1391 3.21520896657969 -4.44708579195034 -1 6.68888808891933 2553 2898 1513 1969 3463 3204 1391 2990 3754 1562 2023 2632 M1473 BIOCARTA_BLYMPHOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BLYMPHOCYTE_PATHWAY.html B Lymphocyte Cell Surface Molecules 10/18 BioCarta 6.87556985339314e-06 8.7709972183826e-06 1985 2872.72727272727 2554 6.25053758311263e-07 1504 1.32204152161894 1.46004145515402 1 2.63861423018566 1984 4091 2554 3968 3640 2021 1504 2923 4696 2005 2214 2633 M10401 BIOCARTA_TEL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TEL_PATHWAY.html Telomeres, Telomerase, Cellular Aging, and Immortality 34/37 BioCarta 3.57423142706092e-07 9.41752134134615e-07 3970 2465 2554 3.24930182522617e-08 158 1.99151908964684 1.84457687037775 1 4.7763129427103 3970 1798 2370 665 1579 2982 2554 4278 158 3243 3518 2634 M1320 INGRAM_SHH_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/INGRAM_SHH_TARGETS_UP.html Genes up-regulated in 10T1/2 cells (multipotent mesoderma) by expression of SHH [GeneID=6469]. 17873912 146/288 Jessica Robertson 2.5430229082984e-07 8.22189102913976e-07 4265 2438.27272727273 2554 2.31183927477402e-08 607 2.27200220521148 2.46183034610517 1 5.50992713928757 4263 1523 710 2554 1206 4679 3688 2060 2611 607 2920 2635 M1565 WESTON_VEGFA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS.html Genes up-regulated in MMEC cells (myometrial endothelium) by VEGFA [GeneID=7422] stimulation. 12200464 137/171 John Newman 2.78527929106687e-10 4.9054172588939e-09 1335 2178 2554 2.53207208310864e-11 208 2.73114653895579 2.78303884074972 1 9.07661191787891 1334 2554 208 2132 3479 2113 2882 2857 3207 305 2887 2636 M1073 REACTOME_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POTASSIUM_CHANNELS.html Genes involved in Potassium Channels 45/106 Reactome 3.70673937743728e-07 9.54490445253898e-07 2555 2255.09090909091 2555 3.36976363816281e-08 461 2.86712309836614 3.03984658567792 1 6.89156887723479 3413 478 461 2555 1623 3182 3252 3539 2553 539 3211 2637 M1832 MATZUK_SPERMATID_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATID_DIFFERENTIATION.html Genes important for spermatid differentiation, based on mouse models with male reproductive defects. 18989307 41/62 Jessica Robertson 1.38809942637105e-06 2.25226170246522e-06 2365 2748 2555 1.26190936563555e-07 1956 1.74909370975024 1.97166345515555 1 3.92243470969022 2362 3684 2895 4191 2796 2494 2354 1956 2652 2555 2289 2638 M4557 BIOCARTA_NEUROTRANSMITTERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NEUROTRANSMITTERS_PATHWAY.html Biosynthesis of neurotransmitters 3/9 BioCarta 1.62695046380897e-06 2.54784545095499e-06 2080 2694.81818181818 2556 1.62695165494572e-07 44 4.27337384396494 -4.27337384396494 -1 9.56344147943096 2077 1994 4187 4346 4472 2556 1525 44 4090 2603 1749 2639 M2279 MAEKAWA_ATF2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MAEKAWA_ATF2_TARGETS.html Genes down-regulated in MEF cells (embryonic fibroblast) upon knockout of ATF2 [GeneID=1386]. 17189429 23/46 Arthur Liberzon 7.84091121503641e-07 1.4791806928446e-06 4695 2743.09090909091 2556 7.1281036450711e-08 377 2.27684525714637 -1.93726910815793 -1 5.28824028881456 4695 758 1406 2556 2360 4292 4426 4011 377 1309 3984 2640 M800 REACTOME_G_ALPHA1213_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA1213_SIGNALLING_EVENTS.html Genes involved in G alpha (12/13) signalling events 83/97 Reactome 7.15575749170148e-08 6.06397110828564e-07 4135 2524.27272727273 2557 6.50523429495536e-09 145 1.85273394553977 -1.70534229610227 -1 4.5824214225648 4134 199 2029 1043 145 3779 3376 4276 2557 1611 4618 2641 M3134 HUMMEL_BURKITTS_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMEL_BURKITTS_LYMPHOMA_UP.html Up-regulated genes constituting the molecular signature of Burkitt 's lymphoma. 16760442 57/71 Arthur Liberzon 1.57393873162352e-06 2.48047396047511e-06 570 1925.63636363636 2559 1.43085441605676e-07 561 1.73632500996433 1.83752019890396 1 3.86416582944149 569 3369 2761 3460 2895 784 566 561 2775 2559 883 2642 M2208 CARD_MIR302A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CARD_MIR302A_TARGETS.html Potential targets of MIR302A [GeneID=407028]. 18710938 108/130 Arthur Liberzon 5.71324512934636e-06 7.42061557801729e-06 1300 2226.90909090909 2559 5.19387269663247e-07 714 1.74080845306034 1.93288783794719 1 3.54109806829666 1296 2583 2559 1992 3567 1357 2837 714 3621 3239 731 2643 M864 REACTOME_MITOTIC_G2_G2_M_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_G2_G2_M_PHASES.html Genes involved in Mitotic G2-G2/M phases 105/128 Reactome 9.90697670912356e-07 1.74091325640593e-06 645 2560.90909090909 2560 9.0063465185524e-08 642 1.45139582640936 1.545024013275 1 3.31159668444159 642 4174 3849 3803 2560 795 768 1880 3695 4142 1862 2644 M500 VANTVEER_BREAST_CANCER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_METASTASIS_UP.html Genes whose expression is significantly and positively correlated with poor breast cancer clinical outcome (defined as developing distant metastases in less than 5 years). 11823860 79/109 Jean Junior 1.85136699075724e-07 7.48271685670965e-07 3805 2461.54545454545 2560 1.68306104232312e-08 869 2.19896771754842 -1.67743462768317 -1 5.36738019181535 3803 3029 1623 2560 869 2787 2216 2350 1085 2813 3942 2645 M13585 CAFFAREL_RESPONSE_TO_THC_24HR_5_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_5_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 53/76 Jessica Robertson 1.83374167419536e-06 2.80701382030622e-06 1935 2697.90909090909 2561 1.66703927514142e-07 1842 1.64041666580855 1.38931319881574 1 3.61252625609124 1933 3072 3080 2506 2993 2229 1842 2561 2551 3389 3521 2646 M4939 MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP.html Genes correlated with the early tumor onset in the Emu-myc transgenic mouse lymphoma model. 18922927 132/151 Jessica Robertson 9.99133647048165e-07 1.74922507940183e-06 180 2074.09090909091 2561 9.0830372800605e-08 177 1.41921617537253 1.46541211320666 1 3.23588351213441 177 2561 3680 2979 2570 352 318 1601 3592 3335 1650 2647 M1912 ZHANG_TLX_TARGETS_36HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_36HR_UP.html Genes up-regulated in neural stem cells (NSC) at 36 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 305/403 Jessica Robertson 1.67738327081224e-07 7.33971845416521e-07 2815 2619.45454545455 2561 1.52489399882167e-08 754 1.86002400479 -1.67991399660078 -1 4.53862064682712 2811 2517 1883 2339 754 3275 3468 4424 2561 1453 3329 2648 M195 PID_CMYB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CMYB_PATHWAY.html C-MYB transcription factor network 18832364 121/152 Pathway Interaction Database 4.86498834271716e-07 1.09659718135745e-06 2820 2440.90909090909 2564 4.42271765321885e-08 1102 1.83022415702916 2.05532806346819 1 4.33676210509725 2817 2564 2041 1102 1919 2896 4370 2757 3448 1631 1305 2649 M2780 REACTOME_SIGNALING_BY_ROBO_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ROBO_RECEPTOR.html Genes involved in Signaling by Robo receptor 32/36 Reactome 8.90204580736847e-08 6.53462771551776e-07 2565 2108.90909090909 2564 8.09276924325411e-09 237 1.85364837376779 2.41495537997301 1 4.56050718691553 2564 642 2167 3119 237 2902 2987 1719 1435 2728 2698 2650 M1710 HILLION_HMGA1B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HILLION_HMGA1B_TARGETS.html Genes changed in Rat1a cells (fibroblasts) by overexpression of HMGA1 isoform b [GeneID=3159] off a plasmid vector. 19074878 127/192 Leona Saunders 1.7760346029409e-07 7.4119215967118e-07 4090 2944.18181818182 2564 1.6145770421074e-08 824 2.02654388755674 1.93943365616326 1 4.9459583853858 4089 3595 1719 2218 824 3845 4077 2408 2384 2564 4663 2651 M3495 AGARWAL_AKT_PATHWAY_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/AGARWAL_AKT_PATHWAY_TARGETS.html Angiogenic and metastatic genes changed in RKO cells (colorectal cancer) upon perturbation of key components of AKT pathway. 15592509 10/11 Leona Saunders 4.27425248261344e-06 5.77238103517466e-06 2735 2467.27272727273 2565 3.88569162439403e-07 353 3.5358397446497 2.86872454163183 1 7.39920678442887 2733 3235 1552 2342 3421 2565 2336 2587 353 2010 4006 2652 M1683 DURCHDEWALD_SKIN_CARCINOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DURCHDEWALD_SKIN_CARCINOGENESIS_UP.html Genes up-regulated upon skin specific knockout of FOS [GeneID=2353] by cre-lox in the K5-SOS-F mice (express a constitutively active form of SOS1 [GeneID=6654] in the skin). 18757399 108/170 Jessica Robertson 3.31672339137321e-06 4.6330081110629e-06 1865 2371.18181818182 2565 3.01520762880096e-07 1074 2.29537775429857 2.38431141032047 1 4.87397347512657 1861 2581 1074 2624 3303 1814 3144 2565 3061 1757 2299 2653 M1815 MATZUK_POST-IMPLANTATION_AND_POST-PARTUM http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_POST-IMPLANTATION_AND_POST-PARTUM.html Genes important for post-implantation and post-partum, based on mouse models with female fertility defects. 18989307 19/25 Jessica Robertson 1.12842593738391e-07 7.05613393308323e-07 4475 2608.63636363636 2566 1.02584181387567e-08 366 2.06464286474552 2.43906579530345 1 5.05762194506236 4471 879 2109 3313 366 4161 3905 3480 1058 2387 2566 2654 M1671 KYNG_RESPONSE_TO_H2O2 http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2.html Genes up-regulated in response to hydrogen peroxide [PubChem=784] in CS-B cells (Cockayne syndrome fibroblast, CS) expressing ERCC6 [GeneID=2074] off a plasmid vector. 12606941 92/120 John Newman 4.17442888449901e-07 1.00504816968881e-06 2110 2456 2567 3.79493606962146e-08 1098 1.61528817777176 1.882425640875 1 3.84618397116135 2109 3329 3183 2938 1766 2293 2585 1098 3516 2567 1632 2655 M9544 BOYLAN_MULTIPLE_MYELOMA_PCA3_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA3_DN.html Top down-regulated genes from principal component 3 (PCA3) which captures variation among different plasma cell tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 89/116 Arthur Liberzon 2.36050218980106e-07 8.00344136252823e-07 3030 2202.72727272727 2567 2.14591131188408e-08 198 2.10568467182698 2.5841074726656 1 5.11282427267758 3028 198 1616 2601 1133 3164 3490 2567 791 2556 3086 2656 M11205 IVANOVA_HEMATOPOIESIS_MATURE_CELL http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_MATURE_CELL.html Genes in the expression cluster 'MBC Shared': up-regulated in mature blood cell populations from adult bone marrow and fetal liver. 12228721 368/466 John Newman 2.72390398034611e-07 8.37744283366146e-07 3075 2424.90909090909 2568 2.47627665236647e-08 1243 1.7452871773168 -1.5496713029471 -1 4.21525535614599 3074 1243 2759 2458 1287 2625 2540 2248 2777 2568 3095 2657 M12467 KEGG_ERBB_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ERBB_SIGNALING_PATHWAY.html ErbB signaling pathway 84/90 KEGG 1.60682563534705e-07 7.33483268746427e-07 1635 2292.18181818182 2569 1.46075068427785e-08 700 1.57386281275438 -1.59106525314592 -1 3.83284732020874 2569 1631 3005 908 700 2872 2681 3973 1635 3171 2069 2658 M975 REACTOME_ADVANCED_GLYCOSYLATION_ENDPRODUCT_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADVANCED_GLYCOSYLATION_ENDPRODUCT_RECEPTOR_SIGNALING.html Genes involved in Advanced glycosylation endproduct receptor signaling 12/16 Reactome 6.97607854945097e-06 8.88480592374759e-06 2560 2642.36363636364 2569 6.34190970028103e-07 730 2.60030578885158 -3.52866108768882 -1 5.23238022685825 2557 4081 2569 3456 3646 2978 1472 730 2117 3435 2025 2659 M15638 RIZ_ERYTHROID_DIFFERENTIATION_APOBEC2 http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_APOBEC2.html Selected genes whose expression profile follows that of APOBEC2 [GeneID=10930] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 30/48 Leona Saunders 4.36047787367117e-07 1.02591716789194e-06 2845 2448 2569 3.9640715799396e-08 733 2.12349834812045 -1.93879340797228 -1 5.06441063933788 2845 1806 1887 2569 1813 3304 3379 3200 733 2187 3205 2660 M2307 WANG_NFKB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WANG_NFKB_TARGETS.html Representative genes up-regulated in C2C12 cells (myoblast) lacking NFkB activity due to expression of a super repressor form of NFKBIA [GeneID=4792]. 17438126 36/61 Arthur Liberzon 1.18927783029463e-06 1.99339181782339e-06 3815 2279.63636363636 2570 1.08116224835992e-07 590 2.35345719056461 2.89471129790909 1 5.34522864727305 3811 590 1176 1039 2693 3662 4582 3325 671 957 2570 2661 M10272 REACTOME_IONOTROPIC_ACTIVITY_OF_KAINATE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IONOTROPIC_ACTIVITY_OF_KAINATE_RECEPTORS.html Genes involved in Ionotropic activity of Kainate Receptors 11/15 Reactome 1.00421272744139e-06 1.75746535911137e-06 4605 2709.09090909091 2571 9.12921078022686e-08 367 1.94323813867492 1.58957956221357 1 4.44755996738869 4605 966 2063 1855 2571 3717 4622 2749 367 2242 4043 2662 M10189 REACTOME_SIGNALING_BY_NOTCH http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH.html Genes involved in Signaling by NOTCH 116/129 Reactome 5.57930208938297e-07 1.18659903470788e-06 4620 3022.18181818182 2571 5.0720940948367e-08 1766 1.77154952504238 -1.25886438927068 -1 4.17172068454472 4620 2568 2534 2954 2058 4275 4490 2571 1766 2557 2851 2663 M1877 REACTOME_GOLGI_ASSOCIATED_VESICLE_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GOLGI_ASSOCIATED_VESICLE_BIOGENESIS.html Genes involved in Golgi Associated Vesicle Biogenesis 76/88 Reactome 1.00766961529026e-06 1.76220844170806e-06 810 2201.81818181818 2573 9.16063706213754e-08 89 1.2489398442676 -1.16356676028958 -1 2.84002848655924 807 3349 3835 3223 2573 228 502 1379 4015 4220 89 2664 M3021 KOBAYASHI_RESPONSE_TO_ROMIDEPSIN http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_RESPONSE_TO_ROMIDEPSIN.html Genes up-regulated in MM-LH cells (malignant melanoma) after treatment with the HDAC inhibitor romidepsin (FK228) [PubChem=5352062]. 16186804 23/24 Arthur Liberzon 1.02903005423766e-06 1.78829965243068e-06 4000 2562.27272727273 2574 9.35482305052226e-08 796 2.77275766294827 -1.8248147271 -1 6.3590482487905 3997 796 1191 1409 2591 4314 3723 4468 1226 1896 2574 2665 M1252 CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN.html Genes down-regulated in K562 cells (chronic myelogenous leukemia, CML) expressing TP53 and MYC [GeneID=7157;4609]. 15856024 44/62 Arthur Liberzon 2.43060836464451e-07 8.07627467909088e-07 2910 2471.72727272727 2576 2.20964421198501e-08 328 2.15446377972473 2.79919498574982 1 5.22901536237679 2906 3395 2335 3875 1164 3675 3296 328 1670 2576 1969 2666 M6176 HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP.html Genes whose expression correlated with higher risk of late recurrence of hepatocellular carcinoma (HCC). 18923165 84/110 Yujin Hoshida 4.94533964509543e-07 1.10573202865232e-06 4715 2934.63636363636 2576 4.49576432431782e-08 745 2.5379616121623 2.7092965071428 1 6.02943563771944 4711 2148 745 2576 1936 3312 4222 4309 2574 1675 4073 2667 M11033 MENSE_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MENSE_HYPOXIA_UP.html Hypoxia response genes up-regulated in both astrocytes and HeLa cell line. 16507782 123/142 Kevin Vogelsang 4.65686302859193e-07 1.06391062415072e-06 2580 2771.81818181818 2577 4.23351274030586e-08 1355 1.80930201980244 -1.81286836408509 -1 4.29617710081414 2577 4434 3054 4618 1890 1355 1750 1832 3512 3679 1789 2668 M8108 FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by selective estrogen receptor modulators (SERM) 4-hydroxytamoxifen, raloxifene, or ICI 182780 but not by estradiol [PubChem=44959;5035;3478439;5757]. 14973112 25/33 Arthur Liberzon 2.38289444918802e-07 8.00711660757103e-07 3475 2276.09090909091 2577 2.16626791571584e-08 106 1.80237861588568 -1.04224149081158 -1 4.36901325216903 3472 765 2577 2348 1143 2938 1326 3034 106 3521 3807 2669 M16811 BIOCARTA_ERK5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK5_PATHWAY.html Role of Erk5 in Neuronal Survival 31/34 BioCarta 2.60274517916406e-07 8.27827307658648e-07 3845 2417.54545454545 2578 2.3661322609873e-08 322 1.79325885220607 2.04663442824097 1 4.33622266945329 3843 683 2464 491 1235 4438 3670 2578 322 3766 3103 2670 M8315 MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_DN.html The 'NPM1-mutated signature 2': genes down-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to the AML cases with the intact gene and without recurring cytogenetic anomalities or M7 phenotype. 17597811 98/115 Arthur Liberzon 6.88219172592577e-08 6.06043748999433e-07 4575 2429.09090909091 2579 6.25653812838112e-09 127 2.5167534906181 2.81452974085386 1 6.24295005112307 4573 1601 1221 1187 127 3702 2579 3965 596 2785 4384 2671 M17330 MARCHINI_TRABECTEDIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARCHINI_TRABECTEDIN_RESISTANCE_UP.html Genes up-regulated in chondrosarcoma and ovarian carcinoma cell lines which developed resistance to trabectedin [PubChem=3199]. 15661559 28/37 John Newman 7.2012830233465e-08 6.06397110828564e-07 3320 2597.54545454545 2580 6.54662114460626e-09 151 1.62576985405322 -1.78151806166181 -1 4.01493478547044 3320 1839 2433 4370 151 2790 1990 2580 3761 2562 2777 2672 M3501 ST_B_CELL_ANTIGEN_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/ST_B_CELL_ANTIGEN_RECEPTOR.html B Cell Antigen Receptor 58/69 Signaling Transduction KE 1.82394024060332e-07 7.47800341964416e-07 3370 2187.36363636364 2582 1.65812762892692e-08 387 1.78782827169361 -1.58465810694123 -1 4.35468623687127 3369 387 2582 502 848 2914 1980 4133 1010 2890 3446 2673 M66 PID_MYC_ACTIV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_ACTIV_PATHWAY.html Validated targets of C-MYC transcriptional activation 18832364 107/136 Pathway Interaction Database 8.19265362785484e-06 1.02953474769635e-05 1455 3025.36363636364 2582 7.44789466991902e-07 1451 1.51522486516845 1.84784830322885 1 2.98908649560474 1451 4447 3641 4548 3699 2007 2394 2133 1887 4490 2582 2674 M3158 REACTOME_S_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_S_PHASE.html Genes involved in S Phase 111/124 Reactome 5.23560987602701e-05 5.89660269281821e-05 310 2452.27272727273 2582 4.75975861673569e-06 310 1.21232023577257 1.28480397205644 1 2.01200041728273 310 2582 3979 1560 4140 982 911 2320 3506 3992 2693 2675 M1347 SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN.html Genes down-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 6 h. 18794802 710/839 Jessica Robertson 2.92174788246202e-07 8.65159975233422e-07 2025 2852.81818181818 2583 2.92174826660957e-08 1460 1.73179295506452 1.89273659817364 1 4.1725369750012 2583 4395 4441 2022 1460 2024 3197 3000 2232 4374 1653 2676 M704 REACTOME_SIGNALING_BY_FGFR_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR_MUTANTS.html Genes involved in Signaling by FGFR mutants 41/63 Reactome 1.17174941310628e-06 1.97312066709298e-06 2030 2538.63636363636 2585 1.06522730654195e-07 892 1.49544733036521 -1.22086201805887 -1 3.38092340790034 2029 3103 3302 1322 2681 2473 892 2463 2585 4204 2871 2677 M8009 KAAB_FAILED_HEART_ATRIUM_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_FAILED_HEART_ATRIUM_UP.html Genes up-regulated in atria of failing hearts (DCM and ICM) compared to healthy controls. 15103417 60/91 John Newman 4.66065862932565e-07 1.06426263814306e-06 3570 2641.27272727273 2586 4.23696328788882e-08 382 2.2150387751134 2.06819845736213 1 5.27068953667082 3570 2205 1834 1928 1891 3236 3215 3668 382 2586 4539 2678 M1441 REACTOME_P38MAPK_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P38MAPK_EVENTS.html Genes involved in p38MAPK events 15/15 Reactome 1.5756077310843e-05 1.88513876160422e-05 2070 2424.09090909091 2588 1.43238092315356e-06 417 1.95166774623477 -1.96949239026088 -1 3.65827933630601 2070 2850 2588 1692 3885 2972 2040 2469 417 3009 2673 2679 M9908 LANDIS_BREAST_CANCER_PROGRESSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_BREAST_CANCER_PROGRESSION_DN.html Genes down-regulated in preneoplastic mammary tissues and whose expression is maintained in tumors. 16434967 101/108 Lauren Kazmierski 1.18601165746412e-05 1.45025259669188e-05 920 2442.36363636364 2588 1.07819822841477e-06 827 2.30677656006732 2.68625899438141 1 4.43867736456154 920 2588 827 3129 3804 2086 3317 2709 3284 1642 2560 2680 M2712 TRAYNOR_RETT_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/TRAYNOR_RETT_SYNDROM_UP.html Genes up-regulated in primary fibroblasts from Rett syndrom patients who carry mutations inactivating MECP2 [GeneID=4204]. 12418965 48/68 John Newman 8.0325835631797e-07 1.50391885831845e-06 2020 2428.36363636364 2588 7.30235136001591e-08 313 2.62273989605589 2.82024621515645 1 6.09162508257016 2018 3666 901 4133 2382 2916 3841 313 2588 1187 2767 2681 M10320 REACTOME_BIOLOGICAL_OXIDATIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BIOLOGICAL_OXIDATIONS.html Genes involved in Biological oxidations 79/219 Reactome 3.37803811865163e-07 9.13746684768849e-07 3195 2238.72727272727 2589 3.07094421576363e-08 203 2.35764370717554 2.26658336097753 1 5.67602928581571 3194 203 559 2056 1524 2720 3582 4459 2589 504 3236 2682 M18988 LIU_NASOPHARYNGEAL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/LIU_NASOPHARYNGEAL_CARCINOMA.html Low abundance transcripts specific to nasopharyngeal carcinoma (NPC). 18332864 100/167 Jessica Robertson 6.63465674633557e-06 8.48890752038599e-06 1655 2679.27272727273 2589 6.03152432264225e-07 1655 1.4325273844751 -1.40165213213197 -1 2.87148972755281 1655 2589 3530 2990 3627 1817 2129 2415 2764 3929 2027 2683 M7995 HOSHIDA_LIVER_CANCER_SUBCLASS_S2 http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SUBCLASS_S2.html Genes from 'subtype S2' signature of hepatocellular carcinoma (HCC): proliferation, MYC and AKT1 [GeneID=4609;207] activation. 19723656 178/210 Jessica Robertson 6.08584371393095e-07 1.25055212580558e-06 1735 2808.45454545455 2590 5.53258672495821e-08 1731 1.82825960562751 2.11268402663869 1 4.29010355628458 1731 4422 2934 2545 2135 2597 3371 2384 2590 3991 2193 2684 M10080 REACTOME_M_G1_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_M_G1_TRANSITION.html Genes involved in M/G1 Transition 81/91 Reactome 5.58564459423953e-05 6.26377820974355e-05 305 2637.81818181818 2591 5.07798764986471e-06 303 1.08428956969216 1.18402943244162 1 1.78279302556311 303 3346 4029 2546 4159 1007 940 1980 4091 4024 2591 2685 M8244 BROCKE_APOPTOSIS_REVERSED_BY_IL6 http://www.broadinstitute.org/gsea/msigdb/cards/BROCKE_APOPTOSIS_REVERSED_BY_IL6.html Genes changed in INA-6 cells (multiple myeloma, MM) by re-addition of IL6 [GeneID=3569] after its initial withdrawal for 12h. 12969979 223/330 Kate Stafford 7.16192689084811e-07 1.39035364104918e-06 1815 2401.54545454545 2591 6.51084474759829e-08 842 1.71010078735753 -1.64507872074812 -1 3.97795201162349 1813 3573 2924 3475 2284 1214 1843 2739 3119 2591 842 2686 M2600 WARTERS_RESPONSE_TO_IR_SKIN http://www.broadinstitute.org/gsea/msigdb/cards/WARTERS_RESPONSE_TO_IR_SKIN.html Genes displaying an ionizing radiation response in the human skin cell samples. 19580510 100/132 Itai Pashtan 1.97221828138216e-07 7.64275064706388e-07 3395 2564.90909090909 2591 1.79292587107657e-08 927 2.00095670050732 2.19778616332404 1 4.87216103226284 3392 3010 1650 3877 927 1982 2591 1829 3195 1593 4168 2687 M18306 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_REGULATION_OF_ACTIN_CYTOSKELETON.html Regulation of actin cytoskeleton 193/251 KEGG 1.25792032477084e-07 7.16209778122308e-07 4465 2458.72727272727 2593 1.14356399699679e-08 461 2.01107148824528 2.29114493909538 1 4.91985774202451 4465 1415 1478 892 461 4474 3460 2890 1148 2593 3770 2688 M16679 SHAFFER_IRF4_MULTIPLE_MYELOMA_PROGRAM http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_MULTIPLE_MYELOMA_PROGRAM.html Direct targets of IRF4 [GeneID=3662] that constitute a multiple myeloma program. 18568025 55/62 Jessica Robertson 2.75934353672629e-07 8.39722855792913e-07 2595 2591.09090909091 2593 2.50849443892382e-08 1305 1.7892483824386 1.6643377497843 1 4.32195457514614 2593 3069 2733 3940 1305 2156 2144 3283 3697 1728 1854 2689 M1134 DARWICHE_PAPILLOMA_RISK_LOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_LOW_DN.html Genes down-regulated during skin tumor progression from low risk papilloma vs normal skin. 17525749 213/288 Arthur Liberzon 1.03264016408497e-06 1.79170077702221e-06 2295 2554.72727272727 2594 9.38764226170801e-08 1186 1.99147546937758 -1.73087621931585 -1 4.55249411958354 2292 3575 2663 1985 2594 1186 2096 3964 1683 3026 3038 2690 M860 REACTOME_SHC_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_MEDIATED_CASCADE.html Genes involved in SHC-mediated cascade 15/33 Reactome 6.0934550263204e-06 7.86252261460697e-06 2685 2775.81818181818 2596 5.53951991249711e-07 1314 1.67178966102603 2.4913753761739 1 3.38182810162291 2683 2413 2596 1747 3594 3854 4291 1314 2224 3787 2031 2691 M13096 SA_PROGRAMMED_CELL_DEATH http://www.broadinstitute.org/gsea/msigdb/cards/SA_PROGRAMMED_CELL_DEATH.html Programmed cell death, or apoptosis, eliminates damaged or unneeded cells. 11/19 SigmaAldrich 1.03398165636464e-06 1.79294394490855e-06 2045 2406.63636363636 2597 9.39983765752467e-08 286 1.39662615968328 -1.57123586715375 -1 3.17755903026159 2041 2889 3195 4577 2597 1972 286 296 3822 3294 1504 2692 M100 PID_SHP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SHP2_PATHWAY.html SHP2 signaling 18832364 80/91 Pathway Interaction Database 3.54785598246859e-07 9.40697096348413e-07 3395 2500.36363636364 2597 3.22532414056173e-08 646 2.01158014543981 -1.92594368087073 -1 4.82532375975441 3395 2158 1451 646 1567 3780 3238 2597 3367 2482 2823 2693 M3909 UDAYAKUMAR_MED1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/UDAYAKUMAR_MED1_TARGETS_UP.html Genes up-regulated in HeLa cells after knockdown of MED1 [GeneID=5469] by RNAi. 16574658 170/176 Leona Saunders 2.1374938740874e-07 7.7139268662581e-07 4085 2799.63636363636 2597 1.94317643796708e-08 1024 1.26381332115777 1.33212834905405 1 3.05679936769547 1367 4151 4082 4282 1024 1421 1730 2425 3633 4084 2597 2694 M13954 NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON.html Genes within amplicon 8q12-q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 125/161 Jessica Robertson 1.3328292298077e-07 7.20206492018647e-07 4550 2887 2597 1.21166300959518e-08 513 2.09915586413968 2.208196990245 1 5.13549751637663 4547 1568 2012 2568 513 4072 4451 4436 745 2597 4248 2695 M520 REACTOME_TRIF_MEDIATED_TLR3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRIF_MEDIATED_TLR3_SIGNALING.html Genes involved in TRIF mediated TLR3 signaling 85/102 Reactome 3.16528830508329e-07 8.94262307705344e-07 2240 2495.45454545455 2599 2.8775352368134e-08 1442 1.55868585240991 -1.59397721123461 -1 3.74144877838949 1742 3023 3476 2238 1442 2238 1493 2599 3428 3054 2717 2696 M13462 LUI_THYROID_CANCER_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_5.html Cluster 5: genes with similar expression profiles across follicular thyroid carcinoma (FTC) samples. 15608688 11/14 Leona Saunders 1.35565059481454e-07 7.20206492018647e-07 3550 2520.72727272727 2600 1.23240970759126e-08 528 2.12566245165232 -2.18678689205618 -1 5.20097661269153 3550 974 1854 3303 528 3467 2600 4511 1073 1761 4107 2697 M1955 MIKKELSEN_MCV6_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the bivalent trimethylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 42/64 Jessica Robertson 2.39272050170978e-05 2.78786491435945e-05 580 2035.36363636364 2600 2.17522411394514e-06 542 2.68084844364669 2.99624645119245 1 4.86057221618693 577 2691 542 2647 4163 1632 2960 2600 2716 681 1180 2698 M3494 BIOCARTA_PAR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PAR1_PATHWAY.html Thrombin signaling and protease-activated receptors 53/59 BioCarta 6.88568454418892e-07 1.35672236339074e-06 3810 2570.63636363636 2601 6.25971518119126e-08 700 1.9378817237311 -1.89554099389092 -1 4.52275734810986 3809 2660 2601 1929 2247 3508 2587 3067 700 2204 2965 2699 M2050 VISALA_AGING_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_AGING_LYMPHOCYTE_UP.html Genes up-regulated in peripheral lymphocytes from old individuals compared to those from young donors. 12618007 12/14 Arthur Liberzon 1.04103241189931e-06 1.80252127078677e-06 2720 2372.72727272727 2601 9.46393549556895e-08 249 2.45698215318389 2.56952335265995 1 5.62575036531958 2716 983 2114 2121 2601 2925 2972 3811 249 2452 3156 2700 M5248 ST_JAK_STAT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_JAK_STAT_PATHWAY.html Jak-STAT Pathway 11/13 Signaling Transduction KE 7.02190924050297e-07 1.37329085443823e-06 4685 2748.81818181818 2603 6.38355589249161e-08 698 2.33567595890101 2.8858369244731 1 5.45647561322895 4685 2434 2069 2603 2265 3565 1872 3638 698 3293 3115 2701 M18630 ROVERSI_GLIOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROVERSI_GLIOMA_COPY_NUMBER_DN.html Genes in the most frequently homozygous deleted loci in a panel of glioma cell lines. 16247447 57/83 Arthur Liberzon 2.76437204019957e-07 8.4037418352842e-07 3400 2620.09090909091 2603 2.51306580686548e-08 1307 2.26225559849373 2.365657477728 1 5.47743165915533 3400 2218 1659 2823 1307 1948 2603 4360 3133 2097 3273 2702 M19096 KEGG_BLADDER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BLADDER_CANCER.html Bladder cancer 51/58 KEGG 1.04750412793584e-06 1.81239717150189e-06 3920 2356.27272727273 2604 9.52276933357222e-08 484 2.3427436291483 2.62393745987283 1 5.35961626476004 3919 484 1710 670 2604 2878 3418 2589 1257 2737 3653 2703 M754 REACTOME_GLYCOPROTEIN_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOPROTEIN_HORMONES.html Genes involved in Glycoprotein hormones 3/9 Reactome 0.000364753662534748 0.00038775614575766 2345 2623.90909090909 2604 3.64813546724546e-05 827 2.92989862568339 -4.79225474339564 -1 3.96963978613381 2343 3540 4229 2077 4620 3116 1923 850 2734 2604 827 2704 M19586 VALK_AML_WITH_CEBPA http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_CEBPA.html Genes that best predicted acute myeloid leukemia (AML) with mutations in CEBPA [GeneID=1050]. 15084694 49/66 Jessica Robertson 1.23452656829312e-06 2.05102618878688e-06 3275 2227.18181818182 2604 1.12229751004211e-07 1006 2.31501742037271 -2.81040326893498 -1 5.24558148782472 3272 2670 1389 1453 2724 2727 3243 2604 1006 1629 1782 2705 M756 REACTOME_PEPTIDE_HORMONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEPTIDE_HORMONE_BIOSYNTHESIS.html Genes involved in Peptide hormone biosynthesis 3/11 Reactome 0.000364753662534748 0.00038775614575766 2345 2624.90909090909 2605 3.64813546724546e-05 828 2.92989862568339 -4.79225474339564 -1 3.96963978613381 2344 3541 4230 2078 4621 3117 1924 851 2735 2605 828 2706 M12153 HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_DN.html Genes down-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrom (MDS) compared to the low risk patients. 12411319 38/55 Arthur Liberzon 0.000435480311269559 0.000461280760590735 1945 2796.27272727273 2605 3.95969578704879e-05 1212 2.96250107615702 -2.75492265621704 -1 3.92452893619278 1945 3108 1212 1989 4423 3039 2318 4460 2605 2508 3152 2707 M2004 MIKKELSEN_ES_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density (ICP) promoters bearing histone H3 K4 trimethylation mark (H3K4me3) in embryonic stem cells (ES). 17603471 801/1213 Arthur Liberzon 1.0711756037229e-11 2.28775966043985e-10 4495 2631.72727272727 2606 1.07117560372806e-12 131 2.13982658227124 2.26400969786831 1 8.24623187758771 4495 1099 4643 285 547 2606 4040 4535 1993 131 4575 2708 M4223 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_DN.html Genes down-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing monocytes. 17898786 3/14 Arthur Liberzon 8.33570796066667e-06 1.04528537657669e-05 1370 2544.81818181818 2607 8.33573922864399e-07 15 2.04135032000366 2.04135032000366 1 4.03893596902802 1370 2932 4304 3879 4195 1035 15 1849 4517 2607 1290 2709 M5312 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transformed by activated KRAS [GeneID=3845] vs those reverted to normal cells upon over-expression of a dominant negative form of CDC25 [GeneID=5923]. 16607279 71/75 Lauren Kazmierski 4.86176565597714e-06 6.44231720836949e-06 1915 2547.54545454545 2607 4.41979672726782e-07 814 2.63555584286386 2.63928446275113 1 5.45196025538396 1911 3634 814 2607 3495 2624 4498 1186 3518 1456 2280 2710 M15473 SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN.html Selected genes down-regulated in peripheral blood monocytes (PBMC) of patients with hepatocellular carcinoma (HCC) compared to those with chronic hepatitis. 19074895 46/62 Arthur Liberzon 1.05787276895723e-06 1.82702950891153e-06 4045 2807.54545454545 2607 9.61702979670023e-08 501 1.8225582831199 1.8980378564807 1 4.15589128273085 4045 501 2327 2387 2607 4328 3573 4520 2267 1578 2750 2711 M17742 SMITH_TERT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMITH_TERT_TARGETS_UP.html Genes consistently up-regulated in HMEC cells (primary mammary epithelium) upon expression of TERT [GeneID=7015] off a retroviral vector. 12717449 206/229 Broad Institute 6.63059280737569e-07 1.32387470604117e-06 2135 2631.27272727273 2607 6.02781345979524e-08 1199 1.75495610772769 1.70454549405089 1 4.09862248050757 2132 4147 3085 2549 2217 1199 2607 2682 2923 2958 2445 2712 M5278 NIKOLSKY_BREAST_CANCER_7Q21_Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_7Q21_Q22_AMPLICON.html Genes within amplicon 7q21-q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 81/105 Jessica Robertson 7.3359614234438e-07 1.40984274913089e-06 2665 2657.45454545455 2608 6.66905806331069e-08 1438 2.26522255006515 2.40446528003746 1 5.27998431655093 2662 2608 1438 1945 2310 3337 4478 3304 2003 1839 3308 2713 M1816 KYNG_DNA_DAMAGE_BY_4NQO_OR_UV http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_4NQO_OR_UV.html 4NQO treatment and UV irradiation responding genes. 15897889 87/98 Jessica Robertson 1.05827127590541e-06 1.82702950891153e-06 2830 2451.54545454545 2608 9.62065259062295e-08 175 1.90663076743291 2.17517338715987 1 4.34990584856258 2829 175 2099 1861 2608 2684 2826 4285 2468 1704 3428 2714 M4835 BIOCARTA_BCELLSURVIVAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCELLSURVIVAL_PATHWAY.html B Cell Survival Pathway 26/27 BioCarta 7.91099128768773e-07 1.48705212576209e-06 2340 2618.90909090909 2609 7.19181284764233e-08 1683 1.7062740855073 -1.81407698106186 -1 3.94890094971598 2336 3160 2609 2718 2370 2082 1683 3627 2827 3001 2395 2715 M503 REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D.html Genes involved in Metabolism of steroid hormones and vitamins A and D 21/53 Reactome 1.78076206621097e-05 2.11185853078285e-05 2570 2874.54545454545 2609 1.61888770956977e-06 1026 2.83072310409274 2.26988479328047 1 5.27240308019974 2570 4038 2470 4192 3917 2609 2581 2931 1026 3076 2210 2716 M1762 TESAR_ALK_TARGETS_EPISC_4D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_EPISC_4D_UP.html Genes up-regulated in EpiSC cells (epiblast stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=4521392]. 17597760 3/8 Jessica Robertson 3.44630905536322e-05 3.94915725693479e-05 1510 2636 2609 3.44636250323728e-06 92 3.2886627788042 3.2886627788042 1 5.77391179961355 1507 2490 4525 3404 4086 948 92 4281 3444 2609 1610 2717 M1863 ZHOU_PANCREATIC_BETA_CELL http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_PANCREATIC_BETA_CELL.html Transcription factors expressed in adult pancreatic beta cells. 18754011 3/13 Jessica Robertson 2.37173905928932e-06 3.49285752257272e-06 3630 2578 2610 2.3717415906089e-07 114 3.96779080254809 -3.95237169723711 -1 8.65737253178438 3627 2489 4583 1824 3188 4471 3973 680 114 2610 799 2718 M279 PID_RB_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RB_1PATHWAY.html Regulation of retinoblastoma protein 18832364 77/92 Pathway Interaction Database 2.24460312534437e-07 7.84779759379662e-07 3370 2384 2611 2.04054850395951e-08 639 2.08681888116672 1.81773634101273 1 5.0737256826204 3370 2611 2476 639 1075 3246 3797 2117 667 2673 3553 2719 M2052 ZEMBUTSU_SENSITIVITY_TO_VINCRISTINE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_VINCRISTINE.html Top genes associated with chemosensitivity to vincristine [PubChem=5978] across 85 tumor xenografts. 11809704 17/33 Arthur Liberzon 1.11653389127932e-06 1.90460425256175e-06 3625 2180.45454545455 2611 1.01503132539806e-07 79 2.45142247266331 2.71643410870631 1 5.58932088911645 3622 857 1581 580 2643 3043 2611 3880 79 2465 2624 2720 M6121 REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT.html Genes involved in Initial triggering of complement 13/18 Reactome 0.000164497375494087 0.00017763157454406 2080 2939.90909090909 2612 1.49554251366303e-05 875 2.43981910382004 -2.72102207461593 -1 3.62993993018313 2079 4339 2163 4588 4330 2612 1737 2500 4472 2644 875 2721 M2107 KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_UP.html Genes whose expression significantly and positively correlated with oligodendrocyte density in layer VI of BA9 brain region in patients with bipolar disorder. 18762803 862/1054 Jessica Robertson 1.92902090322992e-07 7.56856081732769e-07 2140 2859.36363636364 2612 1.92902107068041e-08 1012 1.58906862016253 1.70749533675696 1 3.8616556330681 2140 3832 4659 1761 1012 2344 2612 3570 1592 4606 3325 2722 M14278 SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP.html Cluster 5: genes up-regulated in B493-6 cells (B lymphocytes) by MYC [GeneID=4609] alone or in combination with serum but not by serum alone. 15516975 66/88 Leona Saunders 1.06444117950461e-06 1.83564573155345e-06 1380 2945.90909090909 2613 9.67674267746256e-08 1377 1.27223295460174 1.38788213168404 1 2.8848568455764 1377 3903 3841 4639 2613 1793 1621 2156 3995 4044 2423 2723 M1561 LINDVALL_IMMORTALIZED_BY_TERT_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDVALL_IMMORTALIZED_BY_TERT_DN.html Genes down-regulated in BJ cells (foreskin fibroblasts) immortalized by expression of TERT [GeneID=7015]. 12702554 122/152 John Newman 1.30222002261302e-08 1.6657123324481e-07 1625 2395.81818181818 2614 1.183836391201e-09 292 2.70555285828661 2.79823905673401 1 7.32533381596905 1624 2113 292 2614 3511 3076 4143 2128 3190 642 3021 2724 M539 REACTOME_TRANS_GOLGI_NETWORK_VESICLE_BUDDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANS_GOLGI_NETWORK_VESICLE_BUDDING.html Genes involved in trans-Golgi Network Vesicle Budding 84/96 Reactome 1.0682399772761e-06 1.84074926531728e-06 660 2224.36363636364 2615 9.71127723613568e-08 55 1.20981994415327 -1.13127787151313 -1 2.74029060430097 660 3621 3902 3528 2615 146 456 1237 3988 4260 55 2725 M2382 LIU_TOPBP1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LIU_TOPBP1_TARGETS.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of TOPBP1 [GeneID=11073]. 19289498 18/22 Arthur Liberzon 3.55209587717405e-06 4.90804816752386e-06 4025 2608.54545454545 2615 3.22918328396552e-07 162 3.04939849625429 -2.49213987948244 -1 6.46077280578332 4022 870 1078 1468 3342 4421 4234 4646 162 2615 1836 2726 M11665 PRAMOONJAGO_SOX4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PRAMOONJAGO_SOX4_TARGETS_DN.html Genes down-regulated in ACC3 cells (adenoid cystic carcinoma) after knockdown of SOX4 [GeneID=6659] by RNAi. 16636670 64/70 Leona Saunders 1.088997001169e-06 1.8677657678519e-06 1255 2439.45454545455 2616 9.89997763837643e-08 1254 1.60378194957618 1.66268937342059 1 3.64484298028351 1254 2200 2978 3191 2630 1501 1518 2481 3771 2694 2616 2727 M18326 WILLIAMS_ESR2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR2_TARGETS_UP.html Genes uniquely up-regulated in T47D cells (breast cancer) by induction of ESR2 [GeneID=2100] expression in the Tet-Off system. 17700529 47/70 Jessica Robertson 1.30047277092386e-07 7.20206492018647e-07 3280 2409.27272727273 2617 1.18224804345267e-08 492 2.56004209484945 2.35311980227968 1 6.27402256704441 3277 4221 2044 2617 492 4330 3171 583 616 3382 1769 2728 M240 PID_SYNDECAN_2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_2_PATHWAY.html Syndecan-2-mediated signaling events 18832364 58/68 Pathway Interaction Database 3.66906865437532e-05 4.1983040117943e-05 1885 2500.09090909091 2618 3.33557258818879e-06 656 1.8471818180517 2.25946073629049 1 3.2014310584427 1881 3913 2618 909 4075 2630 4647 1484 983 3705 656 2729 M1618 LIU_SMARCA4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LIU_SMARCA4_TARGETS.html Genes up-regulated in SW-13 cells (kidney cancer) by transient expression of SMARCA4 [GeneID=6597] at 24 h off a plasmid vector. 11509180 82/109 John Newman 1.84610626361636e-07 7.47950348864313e-07 2620 2444 2619 1.67827856230036e-08 526 2.30248352976583 2.59280680154543 1 5.62257638630562 2619 1622 655 2114 868 3474 4480 4165 3016 526 3345 2730 M16591 MCCABE_HOXC6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_UP.html Genes with promoters bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and up-regulated upon loss of function (LOF) of HOXC6. 18339881 10/14 Jessica Robertson 0.000620157393032831 0.000651924920961016 2755 2582.45454545455 2619 5.63938434591593e-05 704 2.20301417948381 2.56018400594063 1 2.77248124276961 2753 2447 2264 3127 4455 2619 2089 1320 704 3110 3519 2731 M687 LIN_NPAS4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIN_NPAS4_TARGETS_UP.html Genes up-regulated in neurons after NPAS4 [GeneID=266743] knockdown by RNAi. 18815592 200/291 Jessica Robertson 4.42901962069318e-07 1.03461941815276e-06 2825 2451.27272727273 2619 4.02638228394506e-08 1414 1.7126372009076 1.94679942630703 1 4.07232458525398 2434 1414 2825 2857 1829 1763 2264 2825 2619 3495 2639 2732 M612 REACTOME_CIRCADIAN_REPRESSION_OF_EXPRESSION_BY_REV_ERBA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CIRCADIAN_REPRESSION_OF_EXPRESSION_BY_REV_ERBA.html Genes involved in Circadian Repression of Expression by REV-ERBA 26/30 Reactome 2.19604550614147e-06 3.27712877171311e-06 2120 2837.45454545455 2620 1.99640699840241e-07 1548 1.37222675260783 -1.49126583204687 -1 2.97662599143217 1707 4274 3537 3947 3083 2116 1548 2214 2119 4047 2620 2733 M1397 TOMIDA_LUNG_CANCER_POOR_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/TOMIDA_LUNG_CANCER_POOR_SURVIVAL.html Metastatic signature genes that best distinguished between favorable and unfavorable prognosis for the non-small cell lung cancer (NSCLC) patients. 17260014 2/5 Arthur Liberzon 0.00150166084968595 0.00156154201597658 2185 2912.1 2621 0.000166962668221348 1411 1.42630688736472 1.42630688736472 1 1.55975708675064 2183 4122 4462 NA 4566 2545 2697 1411 1507 3271 2357 2734 M1781 MCGOWAN_RSP6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCGOWAN_RSP6_TARGETS_DN.html Genes down-regulated by hemizygotic cre-lox knockout of RSP6 [GeneID=81492] in keratinocytes. 18641651 6/7 Jessica Robertson 1.04019096468186e-05 1.28694661947533e-05 2455 2681 2623 1.04019583370153e-06 173 3.54461275782479 -6.55862012806419 -1 6.92132006394958 2455 3533 4529 2583 3790 3185 2623 1036 173 4015 1569 2735 M18742 SENGUPTA_EBNA1_ANTICORRELATED http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_EBNA1_ANTICORRELATED.html Genes whose reduced expression in nasopharyngeal carinoma (NPC) correlated most with the increased expression of EBNA1 [GeneID=3783774], a latent gene of Epstein-Barr virus (EBV). 16912175 185/254 Arthur Liberzon 1.07975509553205e-06 1.85662806954873e-06 1135 2416.90909090909 2623 9.81596023158007e-08 698 1.65605222863185 -1.37850426679198 -1 3.76699603072371 1133 3301 3257 3422 2623 698 1736 1994 3530 3024 1868 2736 M562 REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING.html Genes involved in GRB2 events in ERBB2 signaling 28/28 Reactome 4.36420848098115e-06 5.87537479470366e-06 3700 2594.27272727273 2625 3.96747012583764e-07 664 2.04514191957517 -1.95044502799025 -1 4.25231414983418 3696 2323 2149 664 3430 3807 2573 2625 797 3512 2961 2737 M585 REACTOME_PRE_NOTCH_TRANSCRIPTION_AND_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRE_NOTCH_TRANSCRIPTION_AND_TRANSLATION.html Genes involved in Pre-NOTCH Transcription and Translation 31/31 Reactome 3.22204695475973e-07 9.00418095113436e-07 3160 2441.18181818182 2625 2.92913402422739e-08 297 1.70692829300664 2.00088895189621 1 4.10000169622427 3160 696 2625 1968 1464 3221 3951 2311 297 3234 3926 2738 M1625 BRACHAT_RESPONSE_TO_CAMPTOTHECIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_CAMPTOTHECIN_DN.html Genes specifically down-regulated in FL5.12 cells (pro-B lymphocyte) by camptothecin [PubChem=2538]. 12447701 66/92 John Newman 2.92392931898522e-06 4.14069798548161e-06 1535 2248.72727272727 2625 2.65812109551489e-07 349 1.47683288701079 1.39321152463757 1 3.14702038152815 1534 349 3370 1739 3261 1301 1124 3017 2625 3653 2763 2739 M15780 GRADE_COLON_AND_RECTAL_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_AND_RECTAL_CANCER_DN.html Down-regulated genes in both rectal and colon carcinoma compared to normal mucosa samples. 17210682 150/198 Jessica Robertson 1.15243525130865e-06 1.95093023489671e-06 1140 2514.18181818182 2626 1.04766895908554e-07 1137 2.08217269301101 2.43697080028194 1 4.73114313690226 2461 2980 1137 2626 2666 1779 4675 4072 2878 1245 1137 2740 M12039 KEGG_ONE_CARBON_POOL_BY_FOLATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ONE_CARBON_POOL_BY_FOLATE.html One carbon pool by folate 18/19 KEGG 4.72607726801747e-06 6.29323436734499e-06 970 2524.18181818182 2627 4.29644310971568e-07 967 1.20270007026252 1.21046416277131 1 2.46564269033048 967 1902 3185 3872 3474 1856 1891 1737 3215 3040 2627 2741 M9206 YAMASHITA_LIVER_CANCER_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_STEM_CELL_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) cells with hepatic stem cell properties. 19150350 73/175 Yujin Hoshida 6.55779879524734e-07 1.313786515856e-06 3080 2631.90909090909 2627 5.96163704546218e-08 718 2.65903870172652 2.52152680588855 1 6.23939709715135 3078 1653 718 2590 2206 2627 3090 4586 2687 1601 4115 2742 M2345 FARDIN_HYPOXIA_11 http://www.broadinstitute.org/gsea/msigdb/cards/FARDIN_HYPOXIA_11.html Genes in the hypoxia signature, based on analysis of 11 neuroblastoma cell lines in hypoxia and normal oxygen conditions. 20624283 47/53 Paolo Fardin 5.64546370672329e-07 1.19224110495454e-06 2855 2565.54545454545 2627 5.13224105037952e-08 1675 2.04418240020573 2.22173940056785 1 4.81973514038098 2854 2684 2186 2878 2074 3234 3056 2409 1675 2627 2544 2743 M740 SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_DN.html Genes down-regulated in CT60/4 cells (breast cancer reverted to normal by transfer of chromosome 8p region) vs parental MDA-MB-231 cells (deleted chromosome 8p). 15580292 36/43 Arthur Liberzon 1.14926875663298e-06 1.9484728919927e-06 2630 2113.09090909091 2628 1.0447903245505e-07 553 2.05798726889085 1.94241884589967 1 4.67606048655711 2628 553 1061 1166 2663 2778 3209 3373 3856 954 1003 2744 M8416 BROWNE_HCMV_INFECTION_10HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_10HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 10 h time point that were not down-regulated at the previous time point, 8 h. 11711622 72/92 John Newman 1.22579964412498e-07 7.12872631945934e-07 3910 2473.36363636364 2628 1.11436337493117e-08 440 2.34675529569461 2.44337003768695 1 5.75133637217222 3906 2628 1756 2777 440 3509 4058 2238 669 2271 2955 2745 M2074 WHITFIELD_CELL_CYCLE_G1_S http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_G1_S.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the G1/S phase of cell cycle. 12058064 168/193 Jessica Robertson 5.63895365359101e-06 7.34433257310971e-06 1170 2337.54545454545 2629 5.12633464289779e-07 732 1.60022488571136 1.75749148355514 1 3.25397448254098 1167 2975 3186 4197 3554 732 1272 1958 2629 2711 1332 2746 M736 REACTOME_NFKB_IS_ACTIVATED_AND_SIGNALS_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NFKB_IS_ACTIVATED_AND_SIGNALS_SURVIVAL.html Genes involved in NF-kB is activated and signals survival 16/19 Reactome 1.5309704969666e-05 1.83638646650123e-05 505 2070.27272727273 2630 1.39180104638905e-06 42 1.70586053881733 -1.34332907902803 -1 3.1990335475702 501 3488 2630 2949 3875 185 42 1023 4024 3555 501 2747 M7860 BIOCARTA_NGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NGF_PATHWAY.html Nerve growth factor pathway (NGF) 31/34 BioCarta 3.26506718273557e-07 9.05471040100582e-07 3290 2711.81818181818 2631 2.96824333391936e-08 906 1.61225383383293 -1.41011951270332 -1 3.86824475812243 3290 2315 2952 906 1479 3390 2548 4373 2631 4113 1833 2748 M106 PID_HNF3B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HNF3B_PATHWAY.html FOXA2 and FOXA3 transcription factor networks 18832364 40/64 Pathway Interaction Database 2.35478879162291e-06 3.47724806617102e-06 2260 2707.45454545455 2631 2.1407193746318e-07 1521 2.04222977475312 -2.1164307390735 -1 4.43328142925418 2257 3957 2631 2482 3120 3045 2309 1521 3457 3020 1983 2749 M1184 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP.html Genes up-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment wiht 4 nM docetaxel [PubChem=148124]. 17099726 27/109 Arthur Liberzon 1.09772878785393e-05 1.35105081582023e-05 4210 2798.63636363636 2631 9.97940241094111e-07 1098 2.93326324301358 3.6614154313179 1 5.6940464301002 4208 2778 1408 1876 3776 4170 4284 2631 1098 2109 2447 2750 M1977 ONO_AML1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONO_AML1_TARGETS_UP.html Genes up-regulated in CD4+ [GeneID=920] T lymphocytes by expression of AML1 [GeneID=861] off a viral vector. 17377532 16/29 Jessica Robertson 1.09303770782602e-06 1.87400580491784e-06 2000 2721 2633 9.93671137169219e-08 1600 1.84693624759457 2.12807012356715 1 4.20395917431942 1999 4068 3003 3543 2633 1872 1826 2293 4384 2710 1600 2751 M18342 ST_G_ALPHA_I_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_G_ALPHA_I_PATHWAY.html G alpha i Pathway 46/60 Signaling Transduction KE 1.46278434787088e-06 2.34363276373068e-06 3085 2166.90909090909 2634 1.32980483679999e-07 224 1.90303327738446 -1.80144712747215 -1 4.2588383770569 3083 518 2634 513 2843 2945 2428 3265 224 3328 2055 2752 M791 REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1.html Genes involved in Regulation of Insulin Secretion by Glucagon-like Peptide-1 42/55 Reactome 6.62785497312714e-07 1.32387470604117e-06 4330 3002.18181818182 2635 6.02532451806931e-08 1739 1.75106451104504 2.06798197557367 1 4.08942287142979 4330 1739 1931 2635 2216 4663 2539 4512 3141 1875 3443 2753 M1578 BOQUEST_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_DN.html Genes down-regulated in freshly isolated CD31- [GeneID=5175] (stromal stem cells from adipose tissue) versus the CD31+ (non-stem) counterparts. 15635089 285/359 Arthur Liberzon 5.63290014189536e-15 1.84633949095459e-13 3485 2589.45454545455 2635 5.12081831081395e-16 82 2.27737893817297 2.3716854820078 1 11.6124230006674 3485 2031 120 2045 2473 2635 3193 4541 3231 82 4648 2754 M19622 LEONARD_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/LEONARD_HYPOXIA.html Genes up-regulated in HK-2 cells kidney tubular epithelium) under hypoxia and down-regulated on re-oxygenation. 12885785 69/105 John Newman 1.47249567317051e-07 7.26289540930751e-07 3005 2501 2636 1.33863251975186e-08 614 2.08072697737117 1.97895163757611 1 5.08691613913186 3002 2636 1568 1246 614 2705 4508 4576 1847 1662 3147 2755 M9639 HAN_SATB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAN_SATB1_TARGETS_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of SATB1 [GeneID=6304] by RNAi. 18337816 507/684 Jessica Robertson 1.39874107840471e-07 7.20206492018647e-07 3480 2546.72727272727 2636 1.39874116644616e-08 388 2.17552191431108 -2.13122417909578 -1 5.32414420475088 3479 1173 4605 1158 655 4241 4095 3152 2636 388 2432 2756 M16393 BIOCARTA_NUCLEARRS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NUCLEARRS_PATHWAY.html Nuclear Receptors in Lipid Metabolism and Toxicity 12/24 BioCarta 1.10922362603705e-06 1.89693315757061e-06 4515 2491 2638 1.00838562299977e-07 836 2.72065950377962 2.81356643474359 1 6.21060310755046 4511 963 1382 836 2638 3586 2813 4384 1108 1180 4000 2757 M1926 REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_7ALPHA_HYDROXYCHOLESTEROL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_7ALPHA_HYDROXYCHOLESTEROL.html Genes involved in Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol 13/28 Reactome 4.781087406885e-06 6.35503592241543e-06 4225 2789.63636363636 2639 4.34645254298072e-07 1531 2.87255003046456 -2.00382385510651 -1 5.95355400421675 4224 2419 1603 2142 3483 3656 3529 1641 1531 2639 3819 2758 M2538 KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES http://www.broadinstitute.org/gsea/msigdb/cards/KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES.html Genes indentified by RNAi screen as regulating infection of THP-1 cells (macrophage) with Mycobacterium tuberculosis. 20211141 355/569 Arthur Liberzon 4.85213283836331e-07 1.09541410640518e-06 1960 2546.81818181818 2639 4.41103082591707e-08 1242 1.88509052549524 -1.44049497390238 -1 4.46862475434751 3971 1242 1364 2639 1915 2885 4102 3173 1959 1959 2806 2759 M2286 REACTOME_PEROXISOMAL_LIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEROXISOMAL_LIPID_METABOLISM.html Genes involved in Peroxisomal lipid metabolism 23/24 Reactome 1.26102804873582e-06 2.08551240015175e-06 2645 2778.72727272727 2643 1.14638979231894e-07 2116 1.98554697307895 -1.39518526061398 -1 4.48613304562047 2642 2370 2889 4189 2738 2932 2116 2147 2560 3340 2643 2760 M787 REACTOME_POL_SWITCHING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POL_SWITCHING.html Genes involved in Polymerase switching 13/14 Reactome 0.000208655161968265 0.000224186743567086 635 2412.81818181818 2643 1.89704503755595e-05 429 1.09556419799483 1.14531272830772 1 1.55786185296925 635 2870 3152 2893 4352 956 429 1970 4158 2643 2483 2761 M6220 BIOCARTA_AGR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGR_PATHWAY.html Agrin in Postsynaptic Differentiation 50/59 BioCarta 1.41985563257233e-06 2.28883831480239e-06 4195 2466.63636363636 2644 1.2907786808475e-07 875 2.07041739695528 -1.34383223362263 -1 4.6463868684379 4191 2249 1855 1740 2820 2775 1393 2644 875 2921 3670 2762 M3871 REACTOME_ASSOCIATION_OF_TRIC_CCT_WITH_TARGET_PROTEINS_DURING_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASSOCIATION_OF_TRIC_CCT_WITH_TARGET_PROTEINS_DURING_BIOSYNTHESIS.html Genes involved in Association of TriC/CCT with target proteins during biosynthesis 34/35 Reactome 1.119934431653e-06 1.90971478229847e-06 3880 2749.81818181818 2644 1.01812272888043e-07 628 1.33027773970845 -1.14651427224035 -1 3.00956856006881 3880 2290 3602 2411 2644 2704 2395 4593 628 3503 1598 2763 M7084 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP.html Genes up-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic B.D. chr3 (BD, large HSC size) vs parental B6 strain (tiny HSC size). 17220891 65/89 Leona Saunders 7.49380075835974e-07 1.43339075433049e-06 4580 2924.18181818182 2644 6.81254846450375e-08 1243 1.73124922198361 -1.5726899224951 -1 4.0185474831009 4577 1665 2171 1491 2321 4456 3808 3743 2644 1243 4047 2764 M2386 GILDEA_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/GILDEA_METASTASIS.html Top genes down-regulated in metastatic (T24T) vs non-metastatic (T24) bladder cancer cell lines. 12438227 60/78 Kevin Vogelsang 6.81202805644553e-07 1.34699507442073e-06 2530 2463.45454545455 2645 6.19275469609702e-08 398 2.77688255567415 3.1209542902548 1 6.50602662935581 2530 1679 398 1233 3373 3796 4494 3176 2645 560 3214 2765 M14728 BROWNE_HCMV_INFECTION_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_6HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 6 h time point that were not up-regulated at the previous time point, 4 h. 11711622 110/171 John Newman 5.90968559487938e-07 1.22717624319537e-06 4235 2758.90909090909 2645 5.37244289304725e-08 610 2.31881787688139 2.46320475335825 1 5.4622913260035 4233 1589 610 1712 2112 4630 4270 2645 3830 921 3796 2766 M1138 CROONQUIST_NRAS_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_SIGNALING_UP.html Genes up-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing a constantly active form of NRAS [GeneID=4893] off a plasmid vector compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 37/65 Arthur Liberzon 7.48240079948425e-07 1.43273556890733e-06 3510 2544.18181818182 2645 6.80218485847116e-08 601 2.0576934320218 -2.08214554839487 -1 4.78588377913504 3506 601 1586 2645 2319 3701 3112 2405 2894 1612 3605 2767 M9494 BIOCARTA_BCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCR_PATHWAY.html BCR Signaling Pathway 47/57 BioCarta 9.12854798239794e-08 6.55810448659335e-07 2905 2102.27272727273 2646 8.29868032833859e-09 180 1.59018274895792 -1.51338939553269 -1 3.90419812162657 2903 464 2646 180 255 2975 1670 3968 2719 2885 2460 2768 M1016 REACTOME_SYNTHESIS_OF_VERY_LONG_CHAIN_FATTY_ACYL_COAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_VERY_LONG_CHAIN_FATTY_ACYL_COAS.html Genes involved in Synthesis of very long-chain fatty acyl-CoAs 12/15 Reactome 2.97132768380289e-07 8.70294688256627e-07 3130 2567.27272727273 2646 2.70120735010138e-08 848 1.86877414287218 -1.47128379755354 -1 4.50460231050276 3128 2430 2345 2646 1376 3695 2677 2439 848 2968 3688 2769 M16490 GALI_TP53_TARGETS_APOPTOTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/GALI_TP53_TARGETS_APOPTOTIC_UP.html Apoptosis genes up-regulated by TP53 [GeneID=7157] in HCT116 cells (colon cancer) treated with thymoquinone [PubChem=10281]. 18632613 13/14 Jessica Robertson 0.00836280361065187 0.00856606619841077 855 2809.09090909091 2646 0.000763160284838537 854 2.05714046815033 -2.05714046815033 -1 1.66017896651163 854 4340 2638 4014 4576 1471 942 3739 3730 2646 1950 2770 M3283 BOWIE_RESPONSE_TO_TAMOXIFEN http://www.broadinstitute.org/gsea/msigdb/cards/BOWIE_RESPONSE_TO_TAMOXIFEN.html Genes up-regulated by tamoxifen [PubChem=5376] in HMEC-E6 cells (mammary epithelial cells damaged by expression of HPV-16 E6 [GeneID=1489078]). 17016442 31/52 Arthur Liberzon 9.07584112785762e-05 9.99719256090734e-05 1195 2782.18181818182 2648 8.25110505693606e-06 1192 1.86066609638283 -2.14490125799531 -1 2.94320826673802 1192 3722 2331 2948 4240 1764 1422 3356 4382 2599 2648 2771 M17936 NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON.html Genes within amplicon 8q23-q24 identified in a copy number alterations study of 191 breast tumor samples. 19010930 172/226 Jessica Robertson 7.4126182421258e-08 6.11670596203388e-07 2895 2628.63636363636 2649 6.73874408353138e-09 161 2.07334558604476 2.1679768679418 1 5.13088922949817 2893 4425 2103 4176 161 1024 2629 3752 2423 2649 2680 2772 M13240 WAGNER_APO2_SENSITIVITY http://www.broadinstitute.org/gsea/msigdb/cards/WAGNER_APO2_SENSITIVITY.html Genes whose expression most significantly correlated with cancer cell line sensitivity to the proapoptotic ligand APO2 [GeneID=8797]. 17767167 18/28 Jessica Robertson 1.74469485809903e-07 7.37919956089047e-07 4430 2472.72727272727 2649 1.58608636041897e-08 801 2.97895537777029 -2.51188057653158 -1 7.29622025368923 4429 873 1100 3292 801 4610 3239 895 2649 1855 3457 2773 M18567 ZHAN_MULTIPLE_MYELOMA_MS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MS_DN.html Top 50 down-regulated genes in cluster MS of multiple myeloma samples with characteristic expression spike of WHSC1 [GeneID=7468]. 16728703 64/96 Kevin Vogelsang 4.83758426026388e-07 1.09355353009797e-06 2650 2661.90909090909 2649 4.3978048400014e-08 699 1.84375467055034 -1.86010393453678 -1 4.37008794582649 3307 2646 2754 2337 1914 2649 2411 4170 699 2938 3456 2774 M2278 ISHIDA_TARGETS_OF_SYT_SSX_FUSIONS http://www.broadinstitute.org/gsea/msigdb/cards/ISHIDA_TARGETS_OF_SYT_SSX_FUSIONS.html Genes down-regulated in synovial sarcoma samples with SYT-SSX fusions resulting from translocation of SS18 [GeneID=SS18] to one of the SSX genes. 17101797 8/8 Arthur Liberzon 6.00514971782421e-07 1.2398754436915e-06 2650 2736.36363636364 2649 6.00515134060685e-08 883 3.96993627470404 -3.53135038534876 -1 9.38021625413895 2649 4105 4678 4148 2213 3228 1650 1303 883 3289 1954 2775 M2312 AZARE_STAT3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/AZARE_STAT3_TARGETS.html Genes up-regulated in RPWE-1 cells by activated STAT3 [GeneID=6774]. 17438134 40/48 Arthur Liberzon 9.88664027247858e-06 1.22737880289582e-05 1735 2586.09090909091 2649 8.98789518418335e-07 1553 2.89358019165887 3.05644322230014 1 5.6648544901705 1732 3690 1923 2701 3746 1926 2114 2649 1553 3511 2902 2776 M3835 BENPORATH_SOX2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_SOX2_TARGETS.html Set 'Sox2 targets': genes upregulated and identified by ChIP on chip as SOX2 [GeneID=6657] transcription factor targets in human embryonic stem cells. 18443585 958/1168 Jessica Robertson 2.97254239581052e-07 8.70294688256627e-07 2635 2962 2651 2.97254279343097e-08 1480 1.64783122363083 1.78495893166135 1 3.96611276262619 2632 4127 4450 3795 1480 1854 2925 2651 2391 4190 2087 2777 M2476 LIU_IL13_PRIMING_MODEL http://www.broadinstitute.org/gsea/msigdb/cards/LIU_IL13_PRIMING_MODEL.html Genes up-regulated in BEAS-2B cells (bronchial epithelium) stimulated with IL13 [GeneID=3596] on days 1 to 3, rested on days 4 and 5, and then restimulated on day 6 for 1 h before lysis (priming model). 20123980 26/30 Arthur Liberzon 3.60729586257016e-06 4.97122232739596e-06 3365 2291.36363636364 2651 3.27936525217672e-07 760 2.15965755863017 -2.07909458559366 -1 4.55625133299671 3363 760 1536 2819 3352 3124 3065 1634 1415 2651 1486 2778 M10277 MULLIGHAN_NPM1_SIGNATURE_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_SIGNATURE_3_UP.html The 'NPM1 signature 3': genes up-regulated in pediatric AML (acute myeloid leukemia) with mutated NPM1 [GeneID=4869] compared to the AML cases with intact NPM1 and MLL [GeneID=4297]. 17597811 400/533 Arthur Liberzon 2.48431111660543e-07 8.17709098352694e-07 1710 2173.81818181818 2652 2.25846490649265e-08 769 1.83124379189334 2.11069555280608 1 4.43306609659573 1706 3556 2968 2943 1182 1256 2652 1026 2838 3016 769 2779 M18513 ZHAN_MULTIPLE_MYELOMA_CD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD2_UP.html Top 50 up-regulated genes in cluster CD-2 of multiple myeloma samples with the characteristic expression spike of CCND3 [GeneID=896]. 16728703 49/60 Kevin Vogelsang 1.13241560550127e-06 1.92547610395431e-06 4150 3004.81818181818 2652 1.02946926217719e-07 1328 2.03716460117685 2.29124172068737 1 4.63246628532505 4147 2245 2147 1850 2652 3884 3902 4208 1328 2081 4609 2780 M15383 CONRAD_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/CONRAD_STEM_CELL.html Supplementary Table 2. Genelist comparing microarray expression profiles of spermatogonial cells, haGSCs and hES (H1) cells. Examples of expression rates of different hES cell enriched and germ cell specific genes, surface markers for germ cell selection and signal transduction in all three cell types (spermatogonial cells = SC). 18849962 40/84 Jessica Robertson 1.02463892700218e-06 1.78462030724401e-06 3165 2491.18181818182 2653 9.31490367475379e-08 52 1.84561315393094 2.11014010285041 1 4.21666573935451 3161 3408 2920 3482 2584 2528 2653 1565 2027 3023 52 2781 M4772 CAIRO_HEPATOBLASTOMA_CLASSES_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_CLASSES_UP.html Genes up-regulated in robust Cluster 2 (rC2) of hepatoblastoma samples compared to those in the robust Cluster 1 (rC1). 19061838 736/821 Arthur Liberzon 1.93290803746612e-06 2.93732322499681e-06 235 2423.45454545455 2653 1.93290971872825e-07 231 1.32415109189887 1.39896791958118 1 2.89590459177066 231 3836 4639 3039 3064 756 653 1207 2653 4641 1939 2782 M2404 BIOCARTA_PPARA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PPARA_PATHWAY.html Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha) 74/86 BioCarta 4.78887215032044e-07 1.08357989211469e-06 2430 2671.18181818182 2654 4.35352108431212e-08 1095 1.70360598820423 -1.75555756700977 -1 4.03682870043582 3023 3633 2764 1095 1912 2904 2654 2429 4009 2428 2532 2783 M13547 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_DN.html Genes down-regulated in lobular carcinoma vs normal lobular breast cells. 17389037 116/135 Arthur Liberzon 3.8033955776632e-08 4.22927035979769e-07 1670 2440.09090909091 2654 3.4576324031063e-09 317 2.62260721753197 3.08228772530397 1 6.67241743795749 1670 1574 317 2106 3675 3367 4639 3113 2654 667 3059 2784 M1554 MEDINA_SMARCA4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MEDINA_SMARCA4_TARGETS.html Genes up-regulated in H1299 cells (lung cancer) by expression of SMARCA4 [GeneID=6597] off a plasmid vector. 15731117 66/89 John Newman 3.87575927925158e-07 9.75657802563599e-07 4485 3002.09090909091 2654 3.52341814731606e-08 1641 2.38367034912076 -2.01772110771587 -1 5.71194725108423 4483 2641 1641 2582 1670 4574 3735 3185 2348 2654 3510 2785 M12490 ONKEN_UVEAL_MELANOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONKEN_UVEAL_MELANOMA_UP.html Genes up-regulated in uveal melanoma: class 2 vs class 1 tumors. 16651410 1064/1255 Arthur Liberzon 1.51520430430262e-07 7.27669247795767e-07 2690 2750.72727272727 2656 1.51520440761561e-08 744 1.65677147470518 1.81978663665372 1 4.03969450247699 2689 2493 4277 2233 744 2881 3803 2656 2525 3352 2605 2786 M260 ABE_INNER_EAR http://www.broadinstitute.org/gsea/msigdb/cards/ABE_INNER_EAR.html Genes prefentially expressed in human inner ear tissue (cochlea and vestibule), at least 10-fold higher from a mixture of 29 other tissues. 12471561 60/83 John Newman 8.53656325469324e-08 6.48443648357969e-07 2865 2511.81818181818 2656 7.76051235084888e-09 210 2.02459554222911 2.29100666141143 1 4.98842731626701 2864 2647 1820 2557 210 3657 4718 3052 629 2820 2656 2787 M13408 REACTOME_ERK_MAPK_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ERK_MAPK_TARGETS.html Genes involved in ERK/MAPK targets 26/26 Reactome 7.56666720545897e-07 1.43952717492005e-06 2390 2770.09090909091 2657 6.87879073448667e-08 1466 1.30182277604872 1.34742017706076 1 3.00838706734009 2388 3998 3566 3000 2337 1720 1466 2657 2489 3839 3011 2788 M938 REACTOME_CIRCADIAN_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CIRCADIAN_CLOCK.html Genes involved in Circadian Clock 61/72 Reactome 7.56629077418557e-07 1.43952717492005e-06 1475 2797.81818181818 2657 6.87844852400274e-08 1050 1.39503418321388 -1.20617171174421 -1 3.22737234880025 1475 4205 3737 4018 2336 1673 1050 2042 3483 4100 2657 2789 M1552 MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN.html Cluster 10: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate and TSA [PubChem=5222465;5562] with the same kinetics with which each alters the level of histone H4 acetylation. 10969808 85/101 John Newman 1.89181007451491e-07 7.49827400961101e-07 2130 2940.45454545455 2657 1.71982748835842e-08 895 1.80246271009358 2.1267440272845 1 4.38988931446721 2126 2601 2403 4446 895 3123 4706 3836 2937 2657 2615 2790 M15997 BIOCARTA_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTRINSIC_PATHWAY.html Intrinsic Prothrombin Activation Pathway 25/36 BioCarta 1.1800916957229e-05 1.44338761435918e-05 535 2365 2658 1.07281638713184e-06 505 3.22930061101366 3.13792966509459 1 6.2364763334405 531 3154 505 2658 4419 2262 3400 3337 2761 894 2094 2791 M1243 WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_UP.html Genes up-regulated by telomere shortening due to the knockout of TERC [GeneID=7012] in the presence of chronic liver damage. 15608677 16/28 Leona Saunders 1.88930208365732e-05 2.23384414700966e-05 2660 2641 2658 1.7175620988012e-06 1096 1.72499181311199 -1.61832235568052 -1 3.17644370254898 1897 2852 2184 3481 3930 2658 2659 1096 4363 1512 2419 2792 M18705 JAZAG_TGFB1_SIGNALING_VIA_SMAD4_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_VIA_SMAD4_DN.html Genes down-regulated in PANC-1-S4KD cells (pancreatic cancer; SMAD4 [GeneID=4089] knocked down by RNAi) after stimulation by TGF1B [GeneID=7040] for 2 h. 15592526 77/105 Leona Saunders 7.38185029825517e-07 1.41635501657579e-06 3910 2318.54545454545 2658 6.71077525013857e-08 250 2.44931733585048 2.49497615528863 1 5.71118404249656 3907 250 817 1428 2313 2999 2838 3992 2658 718 3584 2793 M9150 GRESHOCK_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRESHOCK_CANCER_COPY_NUMBER_UP.html Genes from common genomic gains observed in a meta analyis of copy number alterations across a panel of different cancer cell lines and tumor samples. 17440070 384/483 Jessica Robertson 3.00564738695211e-07 8.75179251475259e-07 3410 2571.18181818182 2658 2.7324070887134e-08 654 2.00845598446212 2.18540911154149 1 4.84307629573009 3406 2508 1490 654 1391 3570 4506 3600 955 2658 3545 2794 M2155 MCBRYAN_PUBERTAL_BREAST_6_7WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_6_7WK_UP.html Genes up-regulated during pubertal mammary gland development between week 6 and 7. 17486082 280/343 Arthur Liberzon 7.51141977881572e-08 6.16173757276429e-07 3265 2587.72727272727 2660 6.82856366843342e-09 164 1.8757225818655 -1.86147315735366 -1 4.63466102519975 3263 2952 2313 2660 164 2607 2290 4549 1177 3129 3361 2795 M17193 MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN.html Down-regulated genes distinguishing in multiple myeloma (MM) samples with lower expression of TACI [GeneID=23495]. 15827134 199/217 Kevin Vogelsang 1.14595995634243e-06 1.94425988279521e-06 880 2897.54545454545 2661 1.04178232114815e-07 773 1.03253954806755 1.06905215638709 1 2.32154508220157 878 4421 4178 4687 2661 1166 773 2017 4063 4628 2401 2796 M8537 HOFMANN_CELL_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_CELL_LYMPHOMA_DN.html Genes down-regulated in lymph nodes from patients with mantle cell lymphoma (MCL) compared to the non-malignant hyperplastic lymph nodes. 11468180 53/91 Kevin Vogelsang 1.85626254827057e-06 2.8354560607887e-06 2285 2272.54545454545 2662 1.68751283136776e-07 385 1.74743872143504 1.71025299591429 1 3.84839782237434 2281 2662 2760 3180 2999 1328 1666 1094 3469 3174 385 2797 M15315 BERNARD_PPAPDC1B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERNARD_PPAPDC1B_TARGETS_UP.html Genes up-regulated in ZR-75-1 cells (breast cancer, amplified 8p11-12 region) upon knockdown of PPAPDC1B [GeneID=84513] by RNAi. 18757432 54/63 Jessica Robertson 2.64419651311341e-07 8.31486178673903e-07 1775 2599.63636363636 2663 2.40381530083766e-08 1253 1.52091698685098 -1.3490031483074 -1 3.6689107660836 1771 2663 3335 3476 1253 1565 1332 3534 3865 3817 1985 2798 M3464 VANTVEER_BREAST_CANCER_BRCA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_BRCA1_DN.html Down-regulated genes from the optimal set of 100 markers discriminating ER(-) breast cancer tumors by BRCA1 [GeneID=672] mutation status. 11823860 56/71 Arthur Liberzon 6.32581238091451e-07 1.28310418727617e-06 3985 2951.09090909091 2663 5.75074018165443e-08 1584 2.20118810270038 -1.68108628071709 -1 5.16552639134779 3984 2659 1584 4145 2171 3524 2663 3644 2141 1838 4109 2799 M135 PID_IL5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL5_PATHWAY.html IL5-mediated signaling events 18832364 22/23 Pathway Interaction Database 4.78743412038637e-06 6.35988996572578e-06 1075 2408.90909090909 2665 4.35222230762203e-07 675 1.67779930226444 -1.46853315524717 -1 3.45631720792674 1074 3463 2665 3547 3485 928 675 1848 4322 3529 962 2800 M6905 JAATINEN_HEMATOPOIETIC_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAATINEN_HEMATOPOIETIC_STEM_CELL_DN.html Genes down-regulated in CD133+ [GeneID=8842] cells (hematopoietic stem cells, HSC) compared to the CD133- cells. 16210406 206/410 Arthur Liberzon 5.25727728166095e-21 3.22264269732983e-19 4260 2264 2665 4.77934298332815e-22 50 2.80329073298509 -2.59261993822063 -1 20.7971611347505 4259 1385 50 697 149 3920 3368 4101 2665 67 4243 2801 M18122 DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_UP.html Genes exclusively up-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071] after high dose UVC irradiation. 15608684 38/42 Arthur Liberzon 4.37617693357731e-07 1.02755171379273e-06 4510 2699.45454545455 2665 3.97834345824921e-08 582 2.34443455943378 2.75009620241309 1 5.59588384473406 4507 582 1592 2665 1819 4500 2669 3885 1358 2230 3887 2802 M6452 KAUFFMANN_MELANOMA_RELAPSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_MELANOMA_RELAPSE_DN.html DNA repair and replication genes down-regulated in melanoma patients who will relapse vs patients who will not. 17891185 8/9 Jessica Robertson 4.05556164895011e-06 5.51173365477815e-06 2430 2956.27272727273 2665 4.05556905038025e-07 1570 1.33965675352103 -1.62496029722638 -1 2.78313886810066 2430 2469 4426 4582 3447 2656 1570 2423 3080 2665 2771 2803 M19523 HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_DN.html Genes down-regulated during differentiation from large pre-BII to small pre-BII lymphocyte. 11779835 105/133 Arthur Liberzon 1.15262094945595e-06 1.95093023489671e-06 3635 2411.90909090909 2667 1.04783777575997e-07 523 2.42995774110924 2.67958343268155 1 5.5297430941284 3633 1585 523 1019 2667 3745 4704 3226 1244 686 3499 2804 M13013 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA.html Genes whose expression is coregulated with that of IL3RA [GeneID=3563] in hematopoietic stem cells (HSC). 15711547 18/24 Arthur Liberzon 1.20750972313553e-05 1.47348652874863e-05 2975 2591.90909090909 2668 1.09774213711055e-06 154 2.67828177991868 3.70408913623502 1 5.15414789489284 2972 3194 1884 1313 3812 3962 4446 1493 154 2613 2668 2805 M2548 HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_DN.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 10/32 Arthur Liberzon 0.00040721357543289 0.000431823876891315 3160 2935.09090909091 2669 3.70262699104038e-05 1141 2.45105352674961 -1.07785518849246 -1 3.26660744904955 3157 4348 2506 4386 4417 2669 2125 2457 1141 3116 1964 2806 M738 REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS.html Genes involved in Phase 1 - Functionalization of compounds 41/126 Reactome 1.52848722907059e-07 7.28175281873995e-07 4400 2522.63636363636 2670 1.38953394114985e-08 441 2.96273889675634 2.71806329185898 1 7.2631084900564 4399 525 441 2053 647 4454 4316 3572 2670 740 3932 2807 M4786 OKAWA_NEUROBLASTOMA_1P36_31_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/OKAWA_NEUROBLASTOMA_1P36_31_DELETION.html Genes in the smallest region of deletion (SRD) in 1p36.3 area in neuroblastoma samples. 17667943 22/25 Jessica Robertson 1.15552604052852e-06 1.95416800834634e-06 2300 2278.27272727273 2670 1.05047877041494e-07 819 1.57697344762679 1.98947171182358 1 3.57062476563564 2299 2799 2838 2816 2670 2860 2567 897 965 3531 819 2808 M9271 REACTOME_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_METABOLISM.html Genes involved in Purine metabolism 34/39 Reactome 1.15621001684405e-06 1.95462438377647e-06 2095 2913 2671 1.0511005677188e-07 1769 1.25073982866967 1.15334202725674 1 2.82155566039767 2092 3124 3501 4603 2671 2074 2275 1769 3425 3937 2572 2809 M2248 BRUINS_UVC_RESPONSE_EARLY_LATE http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_EARLY_LATE.html Early-late response genes: differentially expressed in the first 3 h and after 12 h following UV-C irradiation of MEF cells (embryonic fibroblast). 18195040 399/493 Arthur Liberzon 2.32925447575324e-07 7.97250262911913e-07 2455 2900.18181818182 2671 2.11750429305778e-08 1115 1.63810195633886 1.8168296484262 1 3.96748118095498 2452 4401 3788 4644 1115 2016 2731 1892 2671 4219 1973 2810 M13715 LANDIS_ERBB2_BREAST_TUMORS_65_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_65_DN.html Down-regulated genes from the 65 most significantly changed (p<0.01) genes identified by two analytical methods in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 49/55 Leona Saunders 6.66676987827158e-06 8.52537356419449e-06 2475 2615.45454545455 2672 6.0607182554573e-07 1106 2.37756230577598 3.12901374591792 1 4.79703409011609 2833 2672 1106 3665 3629 2475 3395 2471 2904 1423 2197 2811 M1569 BRACHAT_RESPONSE_TO_METHOTREXATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_METHOTREXATE_UP.html Genes up-regulated in FL5.12 cells (pro-B lymphocyte) in response to methotrexate [PubChem=4112]. 12447701 30/54 John Newman 6.7042229421742e-06 8.56862504388363e-06 655 2261.45454545455 2673 6.09476670230589e-07 318 1.51860772059056 -1.66279688371063 -1 3.04456465934679 653 2772 2673 3399 3631 806 973 1679 4283 3689 318 2812 M1917 ZHANG_TLX_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_UP.html Genes up-regulated in neural stem cells (NSC) at both 36 h and 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 141/204 Jessica Robertson 8.50796950820495e-08 6.48443648357969e-07 3965 2665.45454545455 2673 7.7345180338456e-09 207 2.15460950985723 -1.95143748881153 -1 5.3119836736549 3963 2553 1052 2291 207 4355 3308 4102 2673 849 3967 2813 M60 PID_NFAT_TFPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFAT_TFPATHWAY.html Calcineurin-regulated NFAT-dependent transcription in lymphocytes 18832364 49/61 Pathway Interaction Database 8.25162253705193e-07 1.53096141410712e-06 4640 2796.54545454545 2674 7.50147784729145e-08 1254 2.07605437789923 -1.64225629957779 -1 4.80499115683461 4638 2674 1622 2156 2410 3541 1905 3766 3120 1254 3676 2814 M16067 REACTOME_PREFOLDIN_MEDIATED_TRANSFER_OF_SUBSTRATE_TO_CCT_TRIC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PREFOLDIN_MEDIATED_TRANSFER_OF_SUBSTRATE_TO_CCT_TRIC.html Genes involved in Prefoldin mediated transfer of substrate to CCT/TriC 31/39 Reactome 4.57847834096576e-05 5.18608537781579e-05 2675 2762.09090909091 2674 4.16233966151721e-06 1556 1.85171744628143 2.31974850065976 1 3.14107778172217 2221 3142 2674 1556 4118 2672 2386 2752 1875 3961 3026 2815 M1957 MIKKELSEN_MCV6_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 19/57 Jessica Robertson 1.1626242005707e-06 1.96195431773104e-06 1465 2209.18181818182 2675 1.05693164997999e-07 540 2.23980895502708 1.94149265378534 1 5.09091043280551 1461 2823 1860 3302 2675 877 851 3488 3648 2776 540 2816 M1908 BIOCARTA_FCER1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FCER1_PATHWAY.html Fc Epsilon Receptor I Signaling in Mast Cells 53/61 BioCarta 1.23145313004074e-07 7.12872631945934e-07 2760 2196.09090909091 2676 1.11950290815592e-08 191 1.56674436494808 -1.46594817773752 -1 3.82308471942146 2756 1695 2822 191 445 2810 1970 3235 2676 3172 2385 2817 M1294 GALIE_TUMOR_ANGIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/GALIE_TUMOR_ANGIOGENESIS.html Angiogenic genes up-regulated in A17 carcinomas (high vascularization) compared to the syngeneic BB1 and spontaneous tumors (little vascularization). 17998939 9/9 Jessica Robertson 1.05828361808562e-06 1.82702950891153e-06 2680 2552.63636363636 2676 1.05828412206985e-07 592 3.40485417265768 2.7243912615817 1 7.80736480030966 2197 2907 4425 1161 2676 2680 2182 3629 592 2320 3310 2818 M1453 NADLER_HYPERGLYCEMIA_AT_OBESITY http://www.broadinstitute.org/gsea/msigdb/cards/NADLER_HYPERGLYCEMIA_AT_OBESITY.html Genes correlated with the development of hyperglycemia in obese mice. 11027337 69/86 Kevin Vogelsang 4.20566835532929e-07 1.00849031419935e-06 2220 2454.45454545455 2676 3.82333559937584e-08 1083 1.68752716615707 1.77444350901974 1 4.01942323373208 2220 2181 3035 1264 1773 3047 3185 3146 1083 2676 3389 2819 M1833 MATZUK_SPERMATOZOA http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATOZOA.html Spermatozoa genes, based on mouse models with male reproductive defects. 18989307 119/220 Jessica Robertson 1.19680093898544e-07 7.06112554001409e-07 4695 2851.54545454545 2677 1.08800091281042e-08 421 1.79332946393725 2.227461277519 1 4.38620622564492 4693 1581 2784 2677 421 4441 3901 2406 2555 1950 3958 2820 M92 PID_ANGIOPOIETIN_RECEPTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ANGIOPOIETIN_RECEPTOR_PATHWAY.html Angiopoietin receptor Tie2-mediated signaling 18832364 72/84 Pathway Interaction Database 6.60681018676449e-07 1.32080237532945e-06 1670 2554.45454545455 2678 6.00619288259414e-08 1538 1.64663441263502 -1.64903729367457 -1 3.84322168783535 1669 3040 2847 1538 2214 2863 2427 1887 4022 2914 2678 2821 M14577 HAHTOLA_SEZARY_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_SEZARY_SYNDROM_UP.html Genes up-regulated in monocytes isolated from peripheral blood samples of Sezary syndrom patients compared to those from healthy normal donors. 16914566 111/196 Arthur Liberzon 8.19782690254449e-07 1.52517709814781e-06 3780 2892.36363636364 2679 7.45257268844546e-08 1427 1.90805093162849 -1.99094704531465 -1 4.41336241430264 3779 2573 2199 2136 2401 4200 3558 3934 1427 2930 2679 2822 M10431 GRUETZMANN_PANCREATIC_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRUETZMANN_PANCREATIC_CANCER_DN.html Genes down-regulated in pancreatic ductal adenocarcinoma (PDAC) identified in a meta analysis across four independent studies. 15897887 241/350 Leona Saunders 2.46134695054966e-07 8.12416615845762e-07 2680 2640.27272727273 2680 2.2375883872034e-08 1176 1.81411849666843 -1.62479649117656 -1 4.39319873907719 2680 2055 2661 2704 1176 2102 1785 4003 2963 3921 2993 2823 M1611 WENG_POR_TARGETS_GLOBAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_GLOBAL_UP.html Genes up-regulated in liver from transgenic mice with reduced expression of POR [GeneID=5447] in all tissues. 16006652 20/49 John Newman 9.1180124119566e-07 1.63888113421307e-06 2680 2565.72727272727 2680 8.28910562815056e-08 826 1.8221730446225 1.24057769244325 1 4.18958942075935 1769 3188 2677 3439 2503 1841 826 2680 3520 2933 2847 2824 M7747 BIOCARTA_IL2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL2_PATHWAY.html IL 2 signaling pathway 34/41 BioCarta 2.36372823291618e-07 8.00344136252823e-07 2250 2448.81818181818 2681 2.14884407898214e-08 1101 1.58321792190772 -1.33680855403944 -1 3.83180462372858 2249 2748 3128 1101 1134 2681 1834 1754 3437 3935 2936 2825 M2073 BAE_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAE_BRCA1_TARGETS_DN.html Genes concordantly down-regulated in DU-145 and MCF-7 cells (lprostate, breast cancer) upon expression of BRCA1. 15520196 50/58 Arthur Liberzon 3.13913200933862e-07 8.9311049331394e-07 4220 3041.36363636364 2681 2.85375677932236e-08 1278 1.90229254863683 1.96744768106101 1 4.57769644712986 4218 2681 2617 1278 1431 4684 3887 2661 2511 3168 4319 2826 M2367 PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_DN http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_DN.html Genes down-regulated in HEK-293 cells (fibroblast) upon knockdown of CTBP1 but not of SATB1 [GeneID=1487, 6304] by RNAi. 19103759 519/815 Arthur Liberzon 2.45968593785892e-07 8.12416615845762e-07 3055 2524.81818181818 2682 2.45968621011144e-08 1018 2.01816289366066 2.13935352742498 1 4.89295517382136 3051 1172 4691 1018 1282 2682 3982 2762 1596 2634 2903 2827 M1447 BROWN_MYELOID_CELL_DEVELOPMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWN_MYELOID_CELL_DEVELOPMENT_DN.html Genes defining proliferation and self renewal potential of the bipotential myeloid cell line FDB. 16769770 141/182 Kevin Vogelsang 1.59369254065037e-06 2.50494287549628e-06 920 2261.18181818182 2684 1.44881245011955e-07 918 1.66060975095501 1.51670582113926 1 3.69063360249635 918 1549 2684 1671 2902 1181 1001 3548 3456 3055 2908 2828 M14279 DOUGLAS_BMI1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOUGLAS_BMI1_TARGETS_DN.html Genes down-regulated in A4573 cells (Ewing's sarcoma, ESFT) after knockdown of BMI1 [GeneID=648] by RNAi. 18701473 411/491 Jessica Robertson 2.75488798515804e-07 8.38907825157802e-07 3845 2800.09090909091 2684 2.50444393648289e-08 1304 1.70361114563658 -1.44191239938279 -1 4.11299068011918 2684 3842 3273 3238 1304 2098 2323 3929 2051 3844 2215 2829 M3485 MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN.html The postradiation tumor escape signature: genes down-regulated in tumors from irradiated stroma vs those from non-irradiated stroma. 18794119 516/596 Jessica Robertson 2.09751754595943e-07 7.70763712250053e-07 3670 3016.18181818182 2684 2.09751774394055e-08 1102 1.6356964533077 -1.54478400811932 -1 3.97123395819173 3668 2015 4507 2209 1102 4244 4686 3361 2684 2239 2463 2830 M13669 TSAI_DNAJB4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_DNAJB4_TARGETS_UP.html Genes up-regulated in CL1-5 cells (lung cancer) overexpressing DNAJB4 [GeneID=11080] off a plasmid vector. 16788156 21/34 Jessica Robertson 9.81833536657385e-07 1.72984482755612e-06 2695 2739.90909090909 2684 8.92576340761959e-08 1495 1.84268664641402 -1.84436470802837 -1 4.21993316458973 2694 2817 2286 1495 2553 2570 2165 3583 2989 2684 4303 2831 M7825 BIOCARTA_ACTINY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACTINY_PATHWAY.html Y branching of actin filaments 29/36 BioCarta 6.88709064128012e-07 1.35672236339074e-06 4505 2644.81818181818 2686 6.26099345207442e-08 736 2.03646598498345 -0.921770195380291 -1 4.75538535841037 4502 2769 2278 2686 2248 3669 1792 1976 736 3613 2824 2832 M5388 BROWNE_HCMV_INFECTION_18HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_18HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 18 h time point that were not up-regulated at the previous time point, 16 h. 11711622 249/313 John Newman 1.87804355474054e-07 7.48978540381421e-07 2385 2456.36363636364 2686 1.70731246823718e-08 890 1.77905320374613 1.77719144334328 1 4.33257767657535 2384 3567 3154 1545 890 2686 2726 1964 1799 3497 2808 2833 M7068 BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING.html Genes whose expression in optimally debulked ovarian tumors is associated with survival prognosis. 18593951 335/433 Jessica Robertson 2.33567922947077e-07 7.98113405922816e-07 2965 2484.54545454545 2686 2.12334497949402e-08 1119 1.93079670994331 -1.69084845742303 -1 4.68496326156154 2965 2511 1649 1950 1119 2966 2686 3977 2860 1349 3298 2834 M6241 VALK_AML_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_8.html Top 40 genes from cluster 8 of aculte myeloid leukemia (AML) expression profile; 69% of the samples are FAB M2 subtype. 15084694 31/38 Jessica Robertson 1.1767811568075e-06 1.97736100396276e-06 4575 2460.63636363636 2687 1.06980162388075e-07 189 1.81411902109647 -1.66282934649504 -1 4.11136225114386 4571 2307 2391 1037 2687 3723 2871 542 189 2949 3800 2835 M1392 SHIN_B_CELL_LYMPHOMA_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_8.html Cluster 8 of genes distinguishing among different B lymphocyte neoplasms. 19010892 45/65 Jessica Robertson 1.54480545435567e-06 2.4443452043442e-06 3790 2696.54545454545 2688 1.40436958099533e-07 1093 1.87585782832724 2.33389370950779 1 4.18352223112415 3790 1735 2174 1093 2884 3179 4417 2263 2385 2688 3054 2836 M6929 KEGG_O_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_O_GLYCAN_BIOSYNTHESIS.html O-Glycan biosynthesis 23/33 KEGG 5.887629242528e-07 1.22475977943572e-06 3425 2551.81818181818 2690 5.35239165288458e-08 788 2.68856214824082 3.28866854482136 1 6.34217849521781 3424 788 1000 1802 2108 3423 3948 4425 3156 1306 2690 2837 M1483 SCHURINGA_STAT5A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHURINGA_STAT5A_TARGETS_DN.html Genes down-regulated in hematopoietic stem cells (HSC) overexpressing a constitutively active form of STAT5 [GeneID=6776] off retroviral vector. 15353555 13/96 Kevin Vogelsang 0.00765628285606132 0.00784918659439822 2560 3117.72727272727 2690 0.000698459840953194 1871 2.01516737589091 -1.72057668030067 -1 1.65604542617748 2556 4079 2504 3911 4573 2690 1871 2612 4277 2170 3052 2838 M6541 WU_HBX_TARGETS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_3_UP.html Genes up-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] both in SK-Hep-1 cells (hepatocellular carcinoma) and normal primary hepatocytes. 11439330 29/36 John Newman 1.19302166925536e-06 1.99753894249212e-06 830 2163.36363636364 2690 1.08456574200974e-07 403 1.76262869287797 1.80968525399581 1 3.99012324356667 830 3723 2918 3749 2696 468 403 1245 4073 2690 1002 2839 M12362 DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_UP.html Genes up-regulated in RMS cells (rhabdomyosarcoma) expressing PAX3 or PAX7 fusions with FOXO1 [GeneID=5077;5081;2308] compared to the fusion negative cell lines. 16849537 78/95 Arthur Liberzon 2.04145911680098e-06 3.07947811802513e-06 3990 2416.09090909091 2691 1.85587364649707e-07 233 2.08386489532529 -1.75007794482455 -1 4.56889757854695 3986 233 1089 1795 3045 3714 4144 2691 1528 755 3597 2840 M1099 GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP.html Genes up-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) upon serum deprivation for 22 hr in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 313/538 Arthur Liberzon 1.80999099722412e-07 7.47800341964416e-07 3535 2316.36363636364 2691 1.64544649648754e-08 300 2.12232003004981 -1.92439577501994 -1 5.17878310418011 3535 2029 423 1417 840 2998 3104 4289 2691 300 3854 2841 M14736 BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP.html Genes up-regulated in ALL (acute lymphoblastic leukemia) patients who developed t-ML (treatment related myeloid leukemia). 16341039 33/63 Arthur Liberzon 4.94692279163305e-06 6.53290342868971e-06 1630 2462.63636363636 2693 4.49721265029539e-07 690 1.75030781859843 1.64501204833767 1 3.59964418450329 1630 2751 2693 3670 3507 1351 1096 3610 2651 3440 690 2842 M1806 BOCHKIS_FOXA2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BOCHKIS_FOXA2_TARGETS.html Direct targets of FOXA2 [GeneID=3170] in liver, according to a ChIP-chip analysis. 18660816 505/732 Jessica Robertson 4.93689057445732e-07 1.10488968759784e-06 2995 2863.09090909091 2693 4.93689167123764e-08 1923 1.93333174448086 -1.92420916620136 -1 4.5813531599188 2994 3554 4564 1970 2032 2328 3465 2693 2571 3400 1923 2843 M4000 TSUDA_ALVEOLAR_SOFT_PART_SARCOMA http://www.broadinstitute.org/gsea/msigdb/cards/TSUDA_ALVEOLAR_SOFT_PART_SARCOMA.html Protein kinase genes most significantly up-regulated in ASPS (alveolar soft part sarcoma) tumors compared to four other types of primitive sarcomas. 17283122 17/18 Jessica Robertson 0.000237070538546779 0.000253908087574495 1835 2729.90909090909 2694 2.15541899059296e-05 1526 2.19109716915454 -2.0752851524861 -1 3.11807289269563 1831 3485 2995 2486 4369 2838 2561 1919 1526 3325 2694 2844 M591 REACTOME_SIGNALING_BY_HIPPO http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_HIPPO.html Genes involved in Signaling by Hippo 26/26 Reactome 8.90991042055714e-07 1.61749143019345e-06 2800 2629.63636363636 2695 8.09992184457875e-08 987 1.48093712030268 -1.50500874102879 -1 3.39903822366005 2799 4281 3492 2695 2477 2431 987 1631 1290 4046 2797 2845 M1535 JIANG_AGING_HYPOTHALAMUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_HYPOTHALAMUS_DN.html Down-regulated in the hypothalamus of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 64/71 John Newman 3.1449612872428e-07 8.93484919997849e-07 3925 2598.63636363636 2695 2.85905612438533e-08 354 1.7868028562429 2.37074275400594 1 4.29661225407854 3925 354 2490 2909 1433 3663 4185 3982 1002 2695 1947 2846 M2545 ROESSLER_LIVER_CANCER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROESSLER_LIVER_CANCER_METASTASIS_DN.html Genes down-regulated in liver samples containing tumor thrombi in the major branches of the portal vein at surgery (PT) compared to those from metastasis-free HCC patients (PN) at the time of surgery and at follow-up. 21159642 61/68 Yujin Hoshida 1.19673823741516e-05 1.46261120678393e-05 1830 2999.09090909091 2696 1.0879497703498e-06 1583 1.85408947218313 -1.64968838206147 -1 3.55505391728983 1827 4503 3581 4202 3806 2567 1583 1738 2696 4186 2301 2847 M6897 NATSUME_RESPONSE_TO_INTERFERON_BETA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NATSUME_RESPONSE_TO_INTERFERON_BETA_UP.html Genes up-regulated in T98 cells (glioma) 48 h after treatment with interferon beta. 16140920 124/170 John Newman 7.18639185735718e-07 1.393009017114e-06 3355 2756.45454545455 2697 6.53308564074833e-08 1055 1.79231856999229 -1.09682250204758 -1 4.17101134030449 3352 3597 2508 2252 2288 3351 4514 1055 3462 2697 1245 2848 M70 PID_PS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PS1_PATHWAY.html Presenilin action in Notch and Wnt signaling 18832364 75/83 Pathway Interaction Database 1.09742440838453e-06 1.88016087389291e-06 4270 2816.27272727273 2698 9.97659050738482e-08 946 1.78875840620173 2.23869677177281 1 4.06893534775802 4270 1644 2579 1079 2635 4290 3538 3143 946 2698 4157 2849 M1076 REACTOME_AMYLOIDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMYLOIDS.html Genes involved in Amyloids 35/136 Reactome 5.16983325837147e-05 5.82655515270137e-05 1745 2690.54545454545 2698 4.69995886321063e-06 1588 2.66112381235788 -3.70393087498131 -1 4.48182728334691 1743 3116 1588 2860 4137 2663 1655 2698 3986 3086 2064 2850 M4308 SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1.html Genes up-regulated in the pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 12839967 527/867 John Newman 2.13333092229155e-15 7.24411651310511e-14 3430 2464.81818181818 2698 2.13333092229155e-16 80 2.3810436755353 -2.21124407540981 -1 12.5323737009123 3426 1155 4499 273 1161 3269 2698 4557 2076 80 3919 2851 M608 REACTOME_SIGNALING_BY_THE_B_CELL_RECEPTOR_BCR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_THE_B_CELL_RECEPTOR_BCR.html Genes involved in Signaling by the B Cell Receptor (BCR) 136/158 Reactome 1.20452308156571e-06 2.01465235470948e-06 2565 3066.90909090909 2700 1.09502158277749e-07 1757 1.28840200334442 -1.36529683659967 -1 2.90121804661717 2562 3870 4011 1757 2700 3418 2515 2468 3349 4415 2671 2852 M1063 REACTOME_THE_NLRP3_INFLAMMASOME http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THE_NLRP3_INFLAMMASOME.html Genes involved in The NLRP3 inflammasome 11/16 Reactome 3.76162440078183e-05 4.29483966417278e-05 1260 2507.72727272727 2701 3.41971701788784e-06 530 1.72972998143037 1.48776509980794 1 2.98782058212517 1257 4345 2904 4196 4082 1183 530 819 2701 3719 1849 2853 M18436 BOYAULT_LIVER_CANCER_SUBCLASS_G3_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G3_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G3, defined by unsupervised clustering. 17187432 258/323 Yujin Hoshida 2.04514099873914e-06 3.08306148644163e-06 1025 2645.72727272727 2702 1.85922081811292e-07 1024 1.28373186290675 1.42728127039838 1 2.7951234532581 1024 3566 4103 3259 3048 1564 1519 1525 2702 4466 2327 2854 M7455 REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS.html Genes involved in Intrinsic Pathway for Apoptosis 40/55 Reactome 1.46345024759121e-06 2.3439040273602e-06 3560 2668.54545454545 2703 1.33041020098731e-07 879 1.72792248161027 1.87308391416649 1 3.86231504442039 3560 2707 2539 2703 2845 2261 2643 2333 879 3021 3863 2855 M13897 REACTOME_CD28_DEPENDENT_PI3K_AKT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CD28_DEPENDENT_PI3K_AKT_SIGNALING.html Genes involved in CD28 dependent PI3K/Akt signaling 25/29 Reactome 9.29906780614239e-08 6.56798957981166e-07 4070 2594.45454545455 2704 8.45369836290906e-09 266 1.49562959476586 -1.60773838445775 -1 3.66868363780106 4069 786 2850 1077 266 3536 2704 4611 1439 2503 4698 2856 M8901 LANDIS_ERBB2_BREAST_TUMORS_324_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_324_DN.html Down-regulated genes from the 324 genes identified by two analytical methods as changed in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 203/229 Leona Saunders 8.7319122582711e-07 1.59191293391424e-06 3135 2612.18181818182 2705 7.93810520364869e-08 619 2.20925342020193 2.61997590223493 1 5.10142416940045 3131 2065 619 2108 2462 2733 4215 3500 2705 1171 4025 2857 M11984 FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN.html Genes down-regulated in genomically unstable Ewing's sarcoma tumors compared to the stable ones. 17952124 106/142 Jessica Robertson 2.82369041066675e-07 8.49446700978142e-07 3115 2458 2707 2.56699161189658e-08 640 1.8694268386448 -1.65963788548834 -1 4.51410981026432 3111 3319 2756 2388 1328 2765 2674 2754 640 2596 2707 2858 M14473 WEBER_METHYLATED_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_IN_COLON_CANCER.html Genes identified as hypermethylated in SW48 cells (colon cancer). 16007088 16/24 John Newman 3.15188590214505e-06 4.43556990403239e-06 2180 2872.45454545455 2708 2.86535492525776e-07 1633 2.50006397662099 2.80044189059184 1 5.33207968379768 2177 3213 2406 3965 3279 1874 1633 3922 3902 2708 2518 2859 M4303 WOTTON_RUNX_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WOTTON_RUNX_TARGETS_DN.html Common target genes down-regulated by all three Runx family members (RUNX1, RUNX2, and RUNX3 [GeneID=861;860;864]) in MEF cells (embryonic fibroblasts). 18560354 41/53 Jessica Robertson 7.49176305440241e-07 1.43339075433049e-06 3720 2793.63636363636 2709 6.81069600509891e-08 1420 1.98174906860741 2.04706323852021 1 4.60724367949441 3718 2709 2032 4151 2320 3049 3472 1618 1420 2275 3966 2860 M6423 REACTOME_LOSS_OF_NLP_FROM_MITOTIC_CENTROSOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LOSS_OF_NLP_FROM_MITOTIC_CENTROSOMES.html Genes involved in Loss of Nlp from mitotic centrosomes 85/107 Reactome 4.35032695606739e-07 1.02565151012178e-06 1190 2953 2710 3.95484346937325e-08 1162 1.25467968863876 1.26440518400557 1 2.97191681591703 1186 4464 3992 4673 1810 1373 1162 2710 4248 4379 2486 2861 M19654 TOOKER_GEMCITABINE_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOOKER_GEMCITABINE_RESISTANCE_UP.html Up-regulated genes in Calu3 cells (non-small cell lung cancer, NSCLC) resistant to gemcitabine [PubChem=3461] which became down-regulated in response to bexarotene [PubChem=82146]. 17483357 100/134 Jessica Robertson 2.22479216535618e-07 7.8190759646174e-07 2710 2650.45454545455 2710 2.02253853667508e-08 1065 1.66493341354425 -1.6445130459466 -1 4.03893721149016 2710 1600 3243 1961 1065 3002 3512 4712 1722 2940 2688 2862 M705 REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION.html Genes involved in MHC class II antigen presentation 110/131 Reactome 1.44059666688723e-07 7.26289540930751e-07 3910 2306.36363636364 2712 1.30963341929083e-08 72 1.70230403362055 -1.58561818260738 -1 4.15265565473547 3910 72 2712 1445 591 3080 3218 3355 976 2195 3816 2863 M13453 DER_IFN_BETA_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_BETA_RESPONSE_UP.html Genes up-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon beta for 6 h. 9861020 167/237 Yujin Hoshida 2.09537504462035e-06 3.14773081177851e-06 795 2416.45454545455 2712 1.90488821849884e-07 793 1.53558950215426 -1.58808850892879 -1 3.34775307401356 793 2976 3314 2712 3059 1488 1327 2300 3834 2811 1967 2864 M1012 REACTOME_IL_2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_2_SIGNALING.html Genes involved in Interleukin-2 signaling 48/57 Reactome 3.35358155762475e-07 9.11803280644519e-07 3130 2495.54545454545 2713 3.04871097166348e-08 661 1.92811082556362 -1.79480208014887 -1 4.63352935334509 3129 1713 2154 661 1514 4231 3525 1193 3455 2713 3163 2865 M972 MMS_MOUSE_LYMPH_HIGH_4HRS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MMS_MOUSE_LYMPH_HIGH_4HRS_UP.html Up-regulated at 4 hours following treatment of mouse lymphocytes (TK 3.7.2C) with a high dose of methyl methanesulfonate (MMS) 15515172 53/77 John Newman 6.33266743182088e-06 8.13458736096948e-06 2195 2642.18181818182 2713 5.75698696398527e-07 660 1.59622412763882 1.99856803660247 1 3.21722269648722 2194 2661 2716 3165 3608 2751 2713 1953 660 4045 2598 2866 M8213 LEE_INTRATHYMIC_T_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/LEE_INTRATHYMIC_T_PROGENITOR.html Genes enriched in the intrathymic T progenitor (ITTP) cells compared to all other T lymphocyte differentiation stages. 15210650 38/63 Arthur Liberzon 1.22550515579942e-06 2.03819039301383e-06 4395 2899.81818181818 2713 1.11409621678627e-07 1468 2.2918685396476 2.43950323388812 1 5.1951412385884 4393 2713 1468 2588 2718 4025 4350 1882 1637 1473 4651 2867 M751 REACTOME_DARPP_32_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DARPP_32_EVENTS.html Genes involved in DARPP-32 events 29/30 Reactome 2.7406212985602e-07 8.38703759494626e-07 2980 2721.54545454545 2714 2.49147421815416e-08 1260 1.24742936257973 1.00586799490459 1 2.99829547820772 2979 3435 3524 2714 1291 2579 2108 2209 1260 4294 3544 2868 M18536 FALVELLA_SMOKERS_WITH_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/FALVELLA_SMOKERS_WITH_LUNG_CANCER.html Genes that distinguish normal from cancer (lung adenocarcinoma) samples and smokers from non-smoking subjects. 17724461 107/126 Jessica Robertson 1.22325061118894e-06 2.03659361016288e-06 4525 3147.54545454545 2715 1.1120466284954e-07 1992 2.14901946940543 2.17628019191163 1 4.86851052220939 4521 2584 1992 2189 2715 4452 3201 4338 2604 1997 4030 2869 M1002 REACTOME_RIG_I_MDA5_MEDIATED_INDUCTION_OF_IFN_ALPHA_BETA_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RIG_I_MDA5_MEDIATED_INDUCTION_OF_IFN_ALPHA_BETA_PATHWAYS.html Genes involved in RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways 67/95 Reactome 1.69496675173676e-06 2.64034424692988e-06 815 2015 2716 1.54088005237036e-07 356 1.60591908257284 -1.76274732728935 -1 3.55267237792711 812 3050 3166 3497 2933 475 356 507 3772 2716 881 2870 M4078 ABE_VEGFA_TARGETS_30MIN http://www.broadinstitute.org/gsea/msigdb/cards/ABE_VEGFA_TARGETS_30MIN.html Genes up-regulated in HUVEC cells (endothelium) at 30 min after VEGFA [GeneID=7422] stimulation. 12197474 34/42 John Newman 1.04409070375359e-06 1.80715369333222e-06 2360 2965.54545454545 2718 9.49173817514061e-08 2042 1.94456171758985 2.26264154157135 1 4.4411543279834 2358 3973 2042 3407 2603 2973 3696 2613 4161 2077 2718 2871 M18073 THUM_MIR21_TARGETS_HEART_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/THUM_MIR21_TARGETS_HEART_DISEASE_DN.html Genes down-regulated in a mouse model of heart disease whose expression reverted to normal by silencing of MIR21 [GeneID=406991] microRNA. 19043405 13/16 Jessica Robertson 2.0754563534385e-05 2.43624819403873e-05 2230 2731.36363636364 2718 1.8867963030266e-06 1399 1.84392264326845 -1.93059053364639 -1 3.37096241851753 2229 3219 2718 3878 3966 2160 1399 1486 3363 2647 2980 2872 M85 BIOCARTA_BAD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BAD_PATHWAY.html Regulation of BAD phosphorylation 37/40 BioCarta 3.93760437191378e-06 5.37152966341995e-06 2255 2684.45454545455 2719 3.57964674503196e-07 1138 1.66000463954474 1.4292766040108 1 3.46809779896812 2255 2719 2640 1736 3390 1640 1138 3358 3477 3505 3671 2873 M16173 BIOCARTA_PS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PS1_PATHWAY.html Presenilin action in Notch and Wnt signaling 24/27 BioCarta 1.49223570074247e-07 7.26289540930751e-07 3145 2106.45454545455 2720 1.35657800178107e-08 375 1.41983222615271 -1.15824335810187 -1 3.4552818510817 3144 764 2776 1902 626 2839 1741 3516 375 2720 2768 2874 M1497 LEE_AGING_NEOCORTEX_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_NEOCORTEX_DN.html Downregulated in the neocortex of aged adult mice (30-month) vs young adult (5-month) 10888876 94/137 John Newman 2.86771020548624e-06 4.07698559334188e-06 1695 2179 2720 2.60701267596965e-07 590 1.89287820689757 2.05062250194692 1 4.05280452656485 1693 3618 2749 2720 3246 844 1340 590 3054 3404 711 2875 M12434 DONATO_CELL_CYCLE_TRETINOIN http://www.broadinstitute.org/gsea/msigdb/cards/DONATO_CELL_CYCLE_TRETINOIN.html Genes involved in cell cycle regulation which were up-regulated in MCF-7 cells (breast cancer) by tretinoin (retinoic acid) [PubChem=444795]. 17234770 6/6 Jessica Robertson 1.11545453791858e-06 1.90411881647541e-06 1900 2698.81818181818 2720 1.11545509782644e-07 529 1.02098039028953 -1.13116323008561 -1 2.2987156395618 1900 3254 4573 3900 2720 1642 529 1960 4653 3482 1074 2876 M14455 TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA.html Genes with hypermethylated DNA in all four esophageal squamous cell carcinoma (ESCC) lines analyzed. 17438526 97/177 Arthur Liberzon 3.76033236000266e-07 9.5981847370948e-07 3480 2523.90909090909 2721 3.41848454794055e-08 912 2.42072319667979 2.72183524276143 1 5.80843433814334 3478 3012 1236 3641 1641 3551 4443 1554 912 1574 2721 2877 M891 REACTOME_RECYCLING_PATHWAY_OF_L1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECYCLING_PATHWAY_OF_L1.html Genes involved in Recycling pathway of L1 35/41 Reactome 1.12568120307806e-06 1.91681653568774e-06 4240 2677.72727272727 2722 1.02334707187223e-07 214 1.65131503413015 -1.11145473580118 -1 3.74687580958725 4239 612 2722 1697 2649 4709 4165 3107 214 3085 2256 2878 M15501 MOREIRA_RESPONSE_TO_TSA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOREIRA_RESPONSE_TO_TSA_UP.html Up-regulated in CD4+ [GeneID=920] T lymphocytes after 4 h treatment with 100 nM TSA [PubChem=5562]. 14606959 42/46 John Newman 9.18396227370883e-05 0.000101139295221432 1305 2608.45454545455 2722 8.34940516656502e-06 880 1.71849779860114 1.74285166177376 1 2.71101824236096 1302 4525 3119 2722 4242 1098 928 880 2683 4337 2857 2879 M1942 MEISSNER_BRAIN_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) that have no histone H3 methylation marks in brain. 18600261 24/152 Jessica Robertson 1.31064325931546e-07 7.20206492018647e-07 3400 2371.54545454545 2722 1.19149394308785e-08 497 2.00857780017875 1.88310014758214 1 4.91174295833378 3396 2790 1930 2794 497 2722 1932 1720 3233 2034 3039 2880 M163 PID_LIS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LIS1_PATHWAY.html Lissencephaly gene (LIS1) in neuronal migration and development 18832364 47/57 Pathway Interaction Database 4.24286081969546e-07 1.01296424223382e-06 2630 2676.18181818182 2723 3.85714694360219e-08 514 1.71367757359374 1.95669783239592 1 4.08115990588234 2629 3939 3167 2723 1784 3223 2308 514 2641 3581 2929 2881 M19976 HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP.html Genes up-regulated during differentiation of immature to mature B lymphocyte. 11779835 50/72 Arthur Liberzon 5.11240084552488e-07 1.12704049506997e-06 1710 2828.09090909091 2724 4.64763821232224e-08 1036 1.83067241483471 1.86272104700211 1 4.32908102472496 4537 1710 2237 1036 1966 3726 2724 3952 3441 1710 4070 2882 M13494 BIOCARTA_BIOPEPTIDES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BIOPEPTIDES_PATHWAY.html Bioactive Peptide Induced Signaling Pathway 59/67 BioCarta 4.32937105395692e-07 1.02326646843649e-06 3450 2434.18181818182 2725 3.93579264175666e-08 471 1.78355433154634 -1.50230532906578 -1 4.24646104891732 3450 1683 2725 496 1805 2942 1481 4427 471 3396 3900 2883 M7591 REACTOME_G1_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_PHASE.html Genes involved in G1 Phase 40/48 Reactome 1.04043346341466e-06 1.80252127078677e-06 2700 2831.18181818182 2725 9.45849050419323e-08 2110 1.51491189508823 1.84881282699228 1 3.44950719525023 2696 3406 3366 2965 2599 2725 2780 2110 2451 3736 2309 2884 M7160 JAZAG_TGFB1_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_UP.html Genes up-regulated in PANC-1-puro cells (pancreatic cancer) stimulated by TGF1B [GeneID=7040] for 2 h. 15592526 160/228 Leona Saunders 5.23886443889624e-07 1.14003873451315e-06 4230 2932.45454545455 2726 4.76260516948046e-08 1261 1.76349951978775 -1.63746009923171 -1 4.16486602727772 4230 2085 2134 1261 1993 4704 4377 3588 1579 2726 3580 2885 M2236 JOHNSTONE_PARVB_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_1_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) upon overexpression of PARVB [GeneID=29780] under all three culture conditions. 17998334 13/13 Arthur Liberzon 1.50853319802805e-06 2.40063273590438e-06 2765 2547.27272727273 2726 1.37139475675054e-07 875 2.78556757152656 3.38115779416677 1 6.24539423064729 2763 1926 875 2091 2866 2726 4150 4510 3307 1361 1445 2886 M68 PID_RHOA_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHOA_REG_PATHWAY.html Regulation of RhoA activity 18832364 56/59 Pathway Interaction Database 2.65528341722829e-07 8.31648157220804e-07 3565 2732.45454545455 2727 2.41389430700634e-08 956 1.6688652826581 -1.66387578281882 -1 4.03061733023819 3562 1688 2727 2310 1259 3177 3984 4264 956 2018 4112 2887 M10501 RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP.html Genes up-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to normal thyroid tissue. 17406368 798/909 Arthur Liberzon 1.12572360951831e-06 1.91681653568774e-06 370 2520.90909090909 2727 1.12572417978285e-07 368 1.49899033970515 1.55529477076917 1 3.39663155111971 368 3834 4320 3248 2727 1019 950 1935 3131 4332 1866 2888 M18724 XU_AKT1_TARGETS_6HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_AKT1_TARGETS_6HR.html Genes up-regulated in DU-145 cells (prostate cancer) expressing a dominant negative form of AKT1 [GeneID=207] upon sham-treatment for 6 h (as a control for the HGF [GeneID=3082] experiments). 17099727 35/54 Arthur Liberzon 4.63102588096387e-07 1.06057458312225e-06 3165 2698.36363636364 2727 4.21002441436413e-08 610 1.83235143128224 -2.0351711478271 -1 4.35255031989895 3165 2727 2337 1867 1882 3317 3148 4357 610 2475 3797 2889 M7388 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 10 days after transduction. 16818636 151/278 Arthur Liberzon 1.92773530079677e-08 2.38191377480648e-07 4590 2629.90909090909 2728 1.75248665244401e-09 299 2.52501960704418 2.55297597061276 1 6.67546959599721 4587 1501 299 539 2210 3919 4634 4097 2728 363 4052 2890 M487 BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_DN.html Genes down-regulated in microdissected endothelial samples from ovarian cancer tumors with tumor-infiltrating lymphocytes (TIL) vs those without TILs. 18157142 32/39 Jessica Robertson 6.79780619799484e-07 1.3458743814822e-06 3925 2793.18181818182 2729 6.1798257258709e-08 662 2.3855958147323 2.19736864063588 1 5.58256740674378 3922 662 1916 1835 2237 4689 4493 1072 2798 2729 4372 2891 M9626 BOYERINAS_ONCOFETAL_TARGETS_OF_LET7A1 http://www.broadinstitute.org/gsea/msigdb/cards/BOYERINAS_ONCOFETAL_TARGETS_OF_LET7A1.html Embryonic genes targeted by LET7A1 [GeneID=406881] and which are up-regulated in many human cancers. 18413726 27/36 Jessica Robertson 0.000279304139272428 0.000298396454813458 615 2664.36363636364 2730 2.53945095483444e-05 613 2.68418700584306 3.01480694176052 1 3.75534225919181 613 3736 1330 2730 4385 2578 3673 3298 3234 1834 1897 2892 M6616 BENPORATH_NANOG_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_NANOG_TARGETS.html Set 'Nanog targets': genes upregulated and identified by ChIP on chip as Nanog [GeneID=79923] transcription factor targets in human embryonic stem cells. 18443585 1238/1499 Jessica Robertson 3.3505834525789e-07 9.11513192862964e-07 4450 2958.09090909091 2731 3.35058395776743e-08 1615 1.62659742676175 1.79000599832106 1 3.90121472498651 2731 3544 4449 3265 1615 1891 2989 2700 2506 4449 2400 2893 M207 PID_RETINOIC_ACID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RETINOIC_ACID_PATHWAY.html Retinoic acid receptors-mediated signaling 18832364 38/42 Pathway Interaction Database 1.48676908461189e-06 2.37319921520735e-06 2715 2955.09090909091 2732 1.35160917216139e-07 2112 0.929271451085719 1.04513865039113 1 2.05199797166019 2714 2732 3908 2540 2855 2259 2294 2112 3926 4408 2758 2894 M1440 WANG_TARGETS_OF_MLL_CBP_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TARGETS_OF_MLL_CBP_FUSION_UP.html Top 50 genes up-regulated in granulocyte/macrophage progenitors (GMP) upon expression of MLL-CBP fusion [GeneID=4297;1387]. 15635450 59/77 Kevin Vogelsang 3.48703186457128e-07 9.30654820258927e-07 4150 2550.54545454545 2734 3.17002947024636e-08 373 2.23948642222547 -2.08979327803682 -1 5.38188622595559 4146 382 1471 786 1549 4157 3763 4050 373 2734 4645 2895 M12889 LINDGREN_BLADDER_CANCER_CLUSTER_2A_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_2A_UP.html Genes whose expression profile is specific to Cluster IIa of urothelial cell carcinoma (UCC) tumors. 16532037 9/10 Leona Saunders 2.72441639408327e-07 8.37744283366146e-07 2480 2607.18181818182 2735 2.72441672809334e-08 13 1.85413102988406 -1.82885706226252 -1 4.48125792413905 2479 3239 4335 3854 2001 2735 2908 13 3495 1799 1821 2896 M19053 KYNG_DNA_DAMAGE_BY_4NQO_OR_GAMMA_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_4NQO_OR_GAMMA_RADIATION.html Genes responding to 4NQO treatment and gamma irradiation. 15897889 24/30 Jessica Robertson 1.56078912665886e-06 2.4628909470821e-06 2735 2500.54545454545 2735 1.41890021269199e-07 475 2.56778027229195 2.53919458847732 1 5.74170847704465 2735 2352 1630 1083 2893 2903 3082 4226 475 2377 3750 2897 M17034 REACTOME_INTEGRATION_OF_ENERGY_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRATION_OF_ENERGY_METABOLISM.html Genes involved in Integration of energy metabolism 128/186 Reactome 7.33442363027857e-08 6.11382278828356e-07 4410 2452.81818181818 2736 6.66765806799609e-09 41 1.87340223099657 -1.52240674193691 -1 4.63142017516527 4407 41 1716 1284 156 4320 3155 4090 2736 1366 3710 2898 M9740 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 8 days after transduction. 16818636 186/354 Arthur Liberzon 8.94367692680136e-13 2.13202803507588e-11 3220 2111.81818181818 2736 8.13061538800454e-14 144 2.662478403103 -2.57719479117491 -1 11.3761226873282 3216 1421 144 1125 1058 3694 2736 3163 2830 214 3629 2899 M13194 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_23 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_23.html Amplification hot spot 23: colocolized fragile sites and cancer genes in the 11q12-q25 region. 16751803 26/28 Arthur Liberzon 1.39955035702842e-06 2.26539015266602e-06 1600 2806.45454545455 2736 1.27231931578738e-07 1600 2.30688652049105 -1.7987386159145 -1 5.18692973322947 1600 4275 2645 4242 2805 2245 1707 1959 3031 3626 2736 2900 M9814 RODRIGUES_THYROID_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_DN.html Genes down-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to anaplastic thyroid carcinoma (ATC). 17406368 132/154 Arthur Liberzon 1.25826648212772e-06 2.08167465672726e-06 2165 2684.36363636364 2737 1.14387927434579e-07 1768 2.25913312750918 -2.17736019075979 -1 5.11189329942887 2162 3311 1768 2172 2737 3260 2931 3086 2521 2089 3491 2901 M2135 LUI_THYROID_CANCER_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_1.html Cluster 1: genes with similar expression profiles across follicular thyrorid carcinoma (FTC) samples. 15608688 72/82 Leona Saunders 4.89236465779988e-07 1.099106798882e-06 3335 2816.09090909091 2737 4.447605223423e-08 1815 1.75115535222571 1.88305313399295 1 4.14654574002802 3331 2178 2737 3694 1922 3951 4104 1997 2122 3126 1815 2902 M2138 SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN.html Cluster 6: genes down-regulated in B493-6 cells (B lymphocytes) by MYC [GeneID=4609] in combination with serum but not affected by serum alone; they are also up-regulated by MYC alone. 15516975 70/92 Leona Saunders 0.000255926472436697 0.000273854670120429 555 2588.18181818182 2738 2.32687499334392e-05 553 1.14300590904822 1.13988354425429 1 1.58753913508372 553 3908 4007 2738 4373 1096 730 848 4337 4159 1721 2903 M3256 HASLINGER_B_CLL_WITH_17P13_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_17P13_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 17p13 region. 15459216 34/36 Kevin Vogelsang 1.84414653086771e-07 7.47950348864313e-07 2785 2362.18181818182 2738 1.67649698677547e-08 109 1.91990327577888 2.56780080697134 1 4.68001592595215 2785 2738 2680 1516 863 2376 2956 3183 109 3939 2839 2904 M951 REACTOME_TRAF6_MEDIATED_INDUCTION_OF_NFKB_AND_MAP_KINASES_UPON_TLR7_8_OR_9_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_INDUCTION_OF_NFKB_AND_MAP_KINASES_UPON_TLR7_8_OR_9_ACTIVATION.html Genes involved in TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation 104/132 Reactome 3.24793343833335e-07 9.03906004064471e-07 2355 2765 2739 2.95266719803337e-08 1472 1.71513483578152 -1.75242828260589 -1 4.11879603847759 2353 3881 3351 3020 1472 3148 2378 1591 2637 3845 2739 2905 M18260 HEIDENBLAD_AMPLICON_8Q24_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_8Q24_UP.html Up-regulated genes whose expression is associated with amplification of the 8q24 chromosome region in pancreatic cancer cell lines. 15688027 51/65 Arthur Liberzon 5.5347459158343e-07 1.18261660130095e-06 2590 2887.81818181818 2739 5.03158846205693e-08 1568 1.50707087013725 1.42865433495351 1 3.5423297566598 2588 2247 3214 3379 2048 1818 1568 4480 3839 2739 3846 2906 M3848 LINDSTEDT_DENDRITIC_CELL_MATURATION_D http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_D.html Genes down-regulated during the course of maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli (cluster D). 12356685 85/129 Arthur Liberzon 3.17046945597644e-07 8.94262307705344e-07 3305 2669.54545454545 2740 2.88224537534546e-08 959 2.18542478643397 2.56602713200128 1 5.26598424460979 3302 3331 1130 2640 1446 3722 4532 1874 3689 959 2740 2907 M10986 CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN.html Marker genes down-regulated in the 'unannotated' subclass of hepatocellular carcinoma (HCC) samples. 18701503 246/288 Yujin Hoshida 6.19423755166263e-07 1.26483853347944e-06 785 2660.81818181818 2740 5.63112663244511e-08 782 1.36028167084386 1.45196703471697 1 3.17646294272433 782 3570 4084 2740 2155 1671 1546 2520 2874 4520 2807 2908 M2183 WANG_ADIPOGENIC_GENES_REPRESSED_BY_SIRT1 http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ADIPOGENIC_GENES_REPRESSED_BY_SIRT1.html Adipogenic genes (group 2) that are selectively repressed by SIRT1 [GeneID=23411] in mature 3T3-L1 adipocytes. 17954559 35/62 Arthur Liberzon 1.3571446535986e-07 7.20206492018647e-07 4180 2799.81818181818 2740 1.23376794301699e-08 529 1.97729775729463 -1.68347981365355 -1 4.83447201805271 4178 2740 2076 3101 529 3785 3398 2486 1634 2477 4394 2909 M965 REACTOME_INTERFERON_GAMMA_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_GAMMA_SIGNALING.html Genes involved in Interferon gamma signaling 83/110 Reactome 8.70501465437791e-06 1.08812683179724e-05 1155 2760.54545454545 2741 7.91368099889723e-07 1153 1.62815204900864 -1.48262583152624 -1 3.19984737384611 1153 3024 2741 2507 3719 2165 2117 3670 3816 2143 3311 2910 M5570 HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_DN.html Genes down-regulated in lesional skin biopsies from mycosis fundoides patients compared to the normal skin samples. 16914566 33/50 Arthur Liberzon 2.33381281941575e-08 2.76773781599054e-07 4265 2898.54545454545 2744 2.12164804015763e-09 6 2.16660273284441 2.19870271780735 1 5.66400022654522 4264 2744 2082 2398 6 4235 3965 2655 2607 2852 4076 2911 M17758 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM.html Alanine, aspartate and glutamate metabolism 28/35 KEGG 1.64496279577816e-05 1.9611579681922e-05 3720 2763.27272727273 2745 1.49543190496744e-06 757 1.92890738578043 1.5242149519433 1 3.60171417866787 3719 757 2314 4153 3899 2745 2441 1427 2821 2561 3559 2912 M690 REACTOME_KERATAN_SULFATE_KERATIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_KERATIN_METABOLISM.html Genes involved in Keratan sulfate/keratin metabolism 25/32 Reactome 6.77664375839247e-08 6.03504878105896e-07 3315 2242.36363636364 2745 6.16058542466631e-09 121 2.27537663518425 2.54422243116472 1 5.64107042459712 3315 732 912 3043 121 3097 3766 2523 2745 581 3831 2913 M1345 RHODES_CANCER_META_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/RHODES_CANCER_META_SIGNATURE.html Genes commonly up-regulated in cancer relative to normal tissue, according to the meta-analysis of the OncoMine gene expression database. 15184677 111/130 John Newman 8.604960153494e-06 1.07676065547433e-05 330 2354.81818181818 2745 7.82272164604608e-07 328 1.62638158655456 1.7143670472314 1 3.19929620435479 328 3606 3292 2745 3714 957 672 1971 3554 3395 1669 2914 M13965 GOUYER_TUMOR_INVASIVENESS http://www.broadinstitute.org/gsea/msigdb/cards/GOUYER_TUMOR_INVASIVENESS.html Genes up-regulated in constitutively invasive HT-29 5M21 cells (colon cancer) vs the parental non-invasive cells. 18317448 11/15 Jessica Robertson 1.21191537431846e-06 2.02414740508957e-06 3145 2681.09090909091 2747 1.10174185629777e-07 599 2.41342391155088 -2.39289291954805 -1 5.47624758763901 3142 2887 2057 2107 2705 3689 3708 1767 599 2747 4084 2915 M12458 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS.html Human environmental stress response genes not changed in primary fibroblasts from Werner syndrom (WS) patients in response to gamma radiation. 15897889 43/47 Jessica Robertson 2.39235394099375e-07 8.02552281555829e-07 4235 2686.09090909091 2748 2.17486745558764e-08 514 1.67437931369587 -1.27559599125265 -1 4.05451461494246 4232 514 2742 1688 1148 3777 3565 3527 1623 2748 3983 2916 M13448 MOOTHA_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_GLUCONEOGENESIS.html Genes involved in gluconeogenesis; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 34/51 Vamsi Mootha 2.16611835530948e-05 2.53699221763294e-05 2750 2482.72727272727 2749 1.96921789380782e-06 544 1.76679450689271 -2.44235413493833 -1 3.21536409647979 2749 3713 3131 3126 3974 2356 1800 544 872 3745 1300 2917 M8276 REACTOME_NUCLEAR_RECEPTOR_TRANSCRIPTION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEAR_RECEPTOR_TRANSCRIPTION_PATHWAY.html Genes involved in Nuclear Receptor transcription pathway 35/50 Reactome 5.30393881188844e-05 5.96914429950249e-05 1295 2507.63636363636 2750 4.82187880715672e-06 479 1.53080956412949 -1.74765712436547 -1 2.55045032675735 1294 4252 3222 3972 4145 1090 1275 1022 4083 2750 479 2918 M2231 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP.html Genes from the black module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 54/61 Arthur Liberzon 5.42235686664524e-05 6.09514751382842e-05 675 2484.63636363636 2750 4.92953683318398e-06 675 1.65335227876355 -1.77757785318377 -1 2.75258954169429 675 4505 3300 3981 4150 834 888 1319 2750 3816 1113 2919 M9378 ST_INTERLEUKIN_4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTERLEUKIN_4_PATHWAY.html Interleukin 4 (IL-4) Pathway 28/32 Signaling Transduction KE 3.99224539434251e-07 9.87599489585777e-07 1575 2636.90909090909 2751 3.62931465345299e-08 837 1.15540659381456 -1.09541528565496 -1 2.74044222215706 1571 3732 3679 3014 1708 1886 1430 837 4262 4136 2751 2920 M933 REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS.html Genes involved in Regulation of Water Balance by Renal Aquaporins 35/48 Reactome 1.10535637494477e-07 7.03739764799127e-07 3895 2512.09090909091 2751 1.00486948225611e-08 353 2.00126564570399 2.05002353507279 1 4.90176427047415 3895 628 1792 1642 353 4405 3319 3593 1613 2751 3642 2921 M1673 WESTON_VEGFA_TARGETS_3HR http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS_3HR.html Genes up-regulated in MMEC cells (myometrial endothelium) at 3 h after VEGFA [GeneID=7422] stimulation. 12200464 85/110 John Newman 3.46864395706142e-07 9.29699004959108e-07 3855 2811.54545454545 2751 3.15331318540681e-08 1066 2.36907339381734 2.09243411972809 1 5.6966274447068 3855 3028 1143 2655 1540 4472 4242 2751 3763 1066 2412 2922 M2502 PHONG_TNF_RESPONSE_VIA_P38_PARTIAL http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_RESPONSE_VIA_P38_PARTIAL.html Genes whose expression changes in Calu-6 cells (lung cancer) by TNF [GeneID=7124] were blocked partially by p38 inhibitor LY479754. 20516219 233/268 Arthur Liberzon 8.55052143307899e-13 2.06966467508374e-11 4705 2327.72727272727 2751 7.7732013028021e-14 141 2.49125644440519 -2.16752400434373 -1 10.654232310729 4702 1368 141 832 1023 3762 2951 3484 2751 178 4413 2923 M1391 SHIN_B_CELL_LYMPHOMA_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_7.html Cluster 7 of genes distinguishing among different B lymphocyte neoplasms. 19010892 35/37 Jessica Robertson 3.48776472072462e-07 9.30654820258927e-07 2915 2584.27272727273 2752 3.17069570332426e-08 1115 1.73732784130189 -1.72807279346644 -1 4.16388958263752 2914 2295 3024 3419 1550 3212 3137 1115 2515 2752 2494 2924 M15807 BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN.html Top highly correlated genes negatively associated with poor survival of patients with suboptimally debulked ovarian tumors. 18593951 32/41 Jessica Robertson 2.39911742279462e-05 2.79462838982987e-05 2720 2672.27272727273 2752 2.18103962341777e-06 1494 1.37628819052752 1.29395257863209 1 2.47037842186445 2720 2752 3416 2853 3998 1999 1695 1760 1494 3820 2888 2925 M9343 BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G5, defined by unsupervised clustering. 17187432 36/56 Yujin Hoshida 4.42654510835392e-06 5.9491152936875e-06 2595 2890.18181818182 2752 4.02414001352703e-07 1479 1.88557269780717 -1.69901948038407 -1 3.91252185551897 2591 2286 2077 3134 3439 2752 1479 3592 4224 1750 4468 2926 M1069 REACTOME_PIP3_ACTIVATES_AKT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PIP3_ACTIVATES_AKT_SIGNALING.html Genes involved in PIP3 activates AKT signaling 30/30 Reactome 1.29021601239008e-06 2.12262794649048e-06 1900 3057.90909090909 2753 1.17292433550285e-07 1075 0.849873924890165 -0.941683502909853 -1 1.88896188417527 1898 4546 3987 4654 2753 1489 1075 2033 4648 4483 2071 2927 M11404 CERVERA_SDHB_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/CERVERA_SDHB_TARGETS_1_DN.html Genes turned off in Hep3B cells (hepatocellular carcinoma, HCC) upon knockdown of SDHB [GeneID=6390] by RNAi. 18519664 43/73 Jessica Robertson 2.29882837142755e-06 3.40567166137415e-06 4380 2835.18181818182 2753 2.08984615775216e-07 1145 2.73905283311348 2.60310695034736 1 5.97297115655441 4378 2268 1145 1198 3110 4507 4438 2351 2818 2221 2753 2928 M17086 BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_UP.html Genes up-regulated in microdissected endothelial samples from ovarian cancer tumors with tumor-infiltrating lymphocytes (TIL) vs those without TILs. 18157142 31/41 Jessica Robertson 2.81867690003692e-06 4.02391801432108e-06 4600 2916.09090909091 2755 2.56243682852683e-07 1015 1.8720525218778 -1.37278415713602 -1 4.01194840166694 4598 2755 2591 1908 3233 4701 3687 1015 2504 2299 2786 2929 M7048 GENTILE_UV_HIGH_DOSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_HIGH_DOSE_UP.html Selected genes up-regulated in WS1 (fibroblast) in response to irradiation with high dose UV-C. 12907719 32/73 John Newman 4.32820004612057e-05 4.91202313481344e-05 1660 2725.54545454545 2758 3.93480472718245e-06 1600 1.93958628727983 -1.37001987382737 -1 3.31089700484616 1656 2758 2005 1984 4108 1964 1600 4407 3068 3057 3374 2930 M17309 GALI_TP53_TARGETS_APOPTOTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/GALI_TP53_TARGETS_APOPTOTIC_DN.html Apoptosis genes down-regulated by TP53 [GeneID=7157] in HCT116 cells (colon cancer) treated with thymoquinone [PubChem=10281]. 18632613 12/13 Jessica Robertson 2.25946690811057e-06 3.36282942339816e-06 2070 2793.09090909091 2758 2.05406293514103e-07 1946 2.20684743262949 -1.57419652313715 -1 4.8075637599876 3885 1946 2449 2923 3093 4412 3153 2068 2758 1967 2070 2931 M2594 GHANDHI_DIRECT_IRRADIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_DIRECT_IRRADIATION_DN.html Genes significantly (FDR < 10%) down-regulated in IMR-90 cells (fibroblast) in response to direct irradiation. 19108712 35/45 Itai Pashtan 9.67406797448979e-07 1.71338089454378e-06 3440 2933.63636363636 2758 8.79461111679437e-08 1363 2.16081846023183 2.44081134024263 1 4.96073407007319 3436 1778 1363 2758 2543 3288 4476 4582 2552 2191 3303 2932 M13984 MARZEC_IL2_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARZEC_IL2_SIGNALING_UP.html Genes up-regulated by IL2 [GeneID=3558] in cells derived from CD4+ [GeneID=920] cutaneous T-cell lymphoma (CTCL). 18281483 136/169 Jessica Robertson 1.47936651905858e-07 7.26289540930751e-07 2855 2422.72727272727 2759 1.34487874412456e-08 618 1.9359351568793 2.0144938363808 1 4.72945029678981 2855 2988 2009 2961 618 1785 2691 1589 3345 2759 3050 2933 M2491 BRIDEAU_IMPRINTED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BRIDEAU_IMPRINTED_GENES.html List of genomically imprinted genes. 20421412 56/85 Arthur Liberzon 8.56856125817467e-07 1.57123578626979e-06 2760 2428.54545454545 2759 7.78960417769112e-08 421 2.61163190681473 -2.7304560847103 -1 6.04564006158102 3012 421 913 2760 2445 3818 3265 2966 2759 1608 2747 2934 M6856 KEGG_HEMATOPOIETIC_CELL_LINEAGE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEMATOPOIETIC_CELL_LINEAGE.html Hematopoietic cell lineage 52/107 KEGG 2.29850120091063e-07 7.92470830408923e-07 4000 2660.54545454545 2763 2.08954676459266e-08 910 2.7307570556765 -3.2875494129853 -1 6.65013454690275 3998 2666 910 2763 1099 4465 2899 3159 2386 1022 3899 2935 M5040 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_WS http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_WS.html Human environmental stress response genes not changed in primary fibroblasts from Wilmor syndrom (WS) patients in response to 4NQO treatment. 15897889 54/61 Jessica Robertson 1.18229322189705e-06 1.98450355880301e-06 3980 2988 2763 1.07481259751728e-07 1406 1.84783856537732 -1.25622074459212 -1 4.18754768177015 3977 1696 2207 2653 2690 3939 4114 3538 1406 2763 3885 2936 M11507 IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_UP.html Genes up-regulated during transition from L1 (non-tumor, infected with HCV) to G1 (well differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 29/37 Yujin Hoshida 3.30508678906213e-06 4.6194876056776e-06 1505 2555 2764 3.00462886758609e-07 1109 1.51473776701934 1.77728861552081 1 3.20012923045608 1504 2764 2931 3745 3301 1790 1530 1109 3538 4029 1864 2937 M12 PID_RHOA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHOA_PATHWAY.html RhoA signaling pathway 18832364 58/67 Pathway Interaction Database 1.31590105167199e-06 2.15811430295058e-06 4675 2829 2766 1.19627439887413e-07 1072 1.92620833234142 -1.670716292188 -1 4.33905575046799 4672 2210 2117 1478 2766 4629 3576 3087 1072 1969 3543 2938 M2607 ELLWOOD_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELLWOOD_MYC_TARGETS_UP.html Genes up-regulated in transgenic mice expressing human MYC [GeneID=4609] in prostate. 14522256 16/17 Arthur Liberzon 4.22111956581574e-07 1.00930518493669e-06 3810 2783.72727272727 2767 3.83738215974386e-08 333 1.64093308308192 1.08053404478064 1 3.90683043383182 3810 2398 2767 2395 1780 3089 2024 4538 333 3165 4322 2939 M17668 BIOCARTA_AKAP13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAP13_PATHWAY.html Rho-Selective Guanine Exchange Factor AKAP13 Mediates Stress Fiber Formation 14/15 BioCarta 0.0257297220581467 0.0261226689856856 1750 3082.81818181818 2768 0.00236687825053254 1750 1.55607684654399 1.55607684654399 1 0.940584433565774 1750 4623 3411 4283 4711 1909 2436 2768 1823 4397 1800 2940 M7897 BIOCARTA_GLEEVEC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLEEVEC_PATHWAY.html Inhibition of Cellular Proliferation by Gleevec 41/42 BioCarta 1.32635626655097e-06 2.17236527112432e-06 2235 3030.90909090909 2769 1.20577915108866e-07 1565 0.958094693056679 -1.03239317174749 -1 2.13199324370114 2231 3689 3883 1565 2769 2549 1964 3485 4186 4452 2567 2941 M1056 REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS.html Genes involved in Voltage gated Potassium channels 15/43 Reactome 3.42721561171186e-06 4.76198342280835e-06 3035 2473.54545454545 2769 3.11565540975147e-07 781 3.2344696703871 3.23304361368804 1 6.87298809966063 3034 939 781 4344 3321 2389 2402 2769 3492 812 2926 2942 M598 REACTOME_RORA_ACTIVATES_CIRCADIAN_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RORA_ACTIVATES_CIRCADIAN_EXPRESSION.html Genes involved in RORA Activates Circadian Expression 30/34 Reactome 1.91966720600628e-06 2.92002230497894e-06 2025 2828.27272727273 2770 1.74515352823988e-07 1452 1.41765983614835 -1.4299995795043 -1 3.10540346124264 2021 3993 3567 3944 3015 2173 1452 2322 1769 4085 2770 2943 M1924 MIKKELSEN_DEDIFFERENTIATED_STATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_DEDIFFERENTIATED_STATE_UP.html Genes up-regulated in partially reprogrammed and pluripotent cell populations (induced, iPS; and embryonic stem cells, ES) compared to parental lineage-commited cell lines. 18509334 5/8 Jessica Robertson 7.2715187080305e-08 6.0961933040682e-07 2775 2511.90909090909 2772 7.27151894596793e-09 105 1.89504455673411 -2.00709540574285 -1 4.68645810775627 3750 1047 4608 2771 185 3449 2772 4227 105 1790 2927 2944 M13172 TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_DN.html Genes down-regulated in normal ductal and normal lobular breast cells. 17389037 19/23 Arthur Liberzon 5.15908964862546e-05 5.81583547683596e-05 2155 2769 2774 4.69019148668373e-06 1694 1.82890807707153 -1.57582840564197 -1 3.06516130866884 2153 1889 2468 2814 4136 2488 1694 3022 3422 2774 3599 2945 M1734 GAVIN_FOXP3_TARGETS_CLUSTER_P4 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P4.html Cluster P4 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 124/154 Jessica Robertson 1.30955438882782e-06 2.1509385589274e-06 4460 2971.36363636364 2774 1.19050469849394e-07 1287 1.88485699744883 2.01739098641649 1 4.24592828054078 4460 1562 1560 2774 2759 4123 4236 2515 3461 1287 3948 2946 M10922 WANG_RECURRENT_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RECURRENT_LIVER_CANCER_UP.html Genes up-regulated in samples from patients with recurrent hepatocellular carcinoma (HCC). 17975138 24/28 Yujin Hoshida 2.03254533440521e-07 7.65651554540509e-07 3740 2411.27272727273 2775 1.84776865653536e-08 498 1.26622881959153 1.38303302150547 1 3.06438951089209 2643 3740 3598 3737 964 1078 498 2775 3220 3104 1167 2947 M11363 NIELSEN_GIST http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST.html A cluster of genes specifically up-regulated in gastrointestinal stromal tumors (GIST). 11965276 139/182 Arthur Liberzon 1.47856622268065e-07 7.26289540930751e-07 3990 2779.72727272727 2776 1.34415120186498e-08 617 2.09795221880689 -1.82953346889718 -1 5.12944226677116 3989 2105 1227 2776 617 4570 3970 3827 1731 1518 4247 2948 M42 PID_DNA_PK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_DNA_PK_PATHWAY.html DNA-PK pathway in nonhomologous end joining 18832364 15/19 Pathway Interaction Database 0.000464005187205903 0.000490724733052176 2780 3029.63636363636 2777 4.21911891017095e-05 891 1.09992288456202 1.20228736256915 1 1.41376008022923 2777 4086 3879 2732 4431 1813 891 1457 4503 4421 2336 2949 M1981 ONO_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONO_FOXP3_TARGETS_UP.html Genes up-regulated in CD4+ [GeneID=920] T lymphocytes transduced with FOXP3 [GeneID=50943]. 17377532 22/32 Jessica Robertson 1.36105248415828e-07 7.20206492018647e-07 4165 2688.36363636364 2777 1.23732051669199e-08 536 2.9264231419756 -2.36187909140872 -1 7.17909191485423 4163 3177 1358 1842 536 4023 3685 2777 1626 1755 4630 2950 M1137 DARWICHE_PAPILLOMA_RISK_HIGH_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_DN.html Genes down-regulated during skin tumor progression from normal skin to high risk papilloma. 17525749 241/333 Arthur Liberzon 8.54998673244062e-07 1.56941388159522e-06 3375 2850.36363636364 2778 7.77271823206638e-08 1904 2.00672812847122 -1.73496214700522 -1 4.63417155130301 3374 3854 2455 1998 2442 2267 3198 3381 1904 2778 3703 2951 M7997 SA_CASPASE_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/SA_CASPASE_CASCADE.html Apoptosis is mediated by caspases, cysteine proteases arranged in a proteolytic cascade. 18/30 SigmaAldrich 1.54964743617621e-06 2.44954316769983e-06 965 2258.45454545455 2779 1.40877138884182e-07 339 1.50657542192674 -1.5949756404831 -1 3.34954242708416 965 3199 3025 3494 2888 785 339 2720 2779 3408 1241 2952 M2919 KIM_MYCN_AMPLIFICATION_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCN_AMPLIFICATION_TARGETS_DN.html Genes negatively correlated with amplifications of MYCN [GeneID=4613] in the SCLC (small cell lung cancer) cell lines. 16116477 192/256 Arthur Liberzon 1.68863477123886e-06 2.63134899975155e-06 3090 2573.09090909091 2779 1.5351236976099e-07 858 1.99118883952574 -1.67123718574286 -1 4.41817115093586 3090 2533 1329 1619 2932 3300 2779 3877 1782 858 4205 2953 M2082 WANG_METASTASIS_OF_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METASTASIS_OF_BREAST_CANCER_ESR1_UP.html Genes whose expression in primary ER(+) [GeneID=2099] breast cancer tumors positively correlates with developing distant metastases. 15721472 24/41 Arthur Liberzon 1.47080094050361e-05 1.77096439774925e-05 1855 2891.18181818182 2781 1.33710070324979e-06 1676 1.25674425017541 1.4279906528997 1 2.35158572708784 1853 2366 3384 4402 3861 2210 1700 1676 4154 3416 2781 2954 M3004 CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_DN.html Genes down-regulated in type 2B (EDL) vs type 1 (soleus) myofibers. 21364395 24/45 Emmanuelle Fouilloux-Meugnier 6.57125568138143e-07 1.31572979471297e-06 4315 2944.72727272727 2781 5.97387058561202e-08 821 1.66292814451181 -1.21877714720287 -1 3.88286375265624 4313 821 2781 2477 2207 4532 3341 2192 2425 3711 3592 2955 M120 PID_ARF6_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_DOWNSTREAM_PATHWAY.html Arf6 downstream pathway 18832364 26/29 Pathway Interaction Database 4.88545501592447e-07 1.099106798882e-06 2630 2882.18181818182 2782 4.44132372801721e-08 1825 0.932055173410473 -0.96223471595541 -1 2.18360064266747 2627 2782 3847 3001 1921 1825 1864 3598 3682 4202 2355 2956 M19909 AMIT_EGF_RESPONSE_40_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_40_MCF10A.html Genes whose expression peaked at 40 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 21/22 Leona Saunders 5.07983141688925e-06 6.69182369179941e-06 1855 2674.81818181818 2782 4.61803922393678e-07 1323 1.82060541785069 -1.70907257766731 -1 3.73858365333956 1855 2810 1949 2895 3516 2782 2235 3184 4394 1323 2480 2957 M2033 TRACEY_RESISTANCE_TO_IFNA2_UP http://www.broadinstitute.org/gsea/msigdb/cards/TRACEY_RESISTANCE_TO_IFNA2_UP.html Genes up-regulated in huT78R cells (cutaneous T-cell lymphoma, CTCL) resistant to IFNA2 [GeneID=3440] compared to the IFN2A sensitive parental cell line. 12414529 5/7 Arthur Liberzon 4.02446676948011e-06 5.47420263744845e-06 4410 2840.45454545455 2782 4.02447405784844e-07 1051 2.10093328828028 1.59608805503117 1 4.39563338731608 4406 1051 4651 2782 3440 3235 2590 1895 2535 1791 2869 2958 M200 PID_ERA_GENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERA_GENOMIC_PATHWAY.html Validated nuclear estrogen receptor alpha network 18832364 74/121 Pathway Interaction Database 1.35276749304814e-06 2.20554838244808e-06 2070 2603.81818181818 2783 1.22978938623445e-07 300 1.34615415971455 -1.2878805832726 -1 3.01222217895356 2068 2174 3479 2930 2783 1803 2082 3685 3475 3863 300 2959 M19146 LY_AGING_MIDDLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_MIDDLE_UP.html Genes up-regulated in fibroblasts from middle-age individuals, compared to those from the young donors. 10741968 17/21 John Newman 0.00603629154115941 0.00619645412663601 1480 3025.54545454545 2783 0.000550265239147165 1105 4.71195825828549 4.76166775369917 1 4.13378274429674 1476 4603 1105 4212 4565 2461 2120 2723 4355 2878 2783 2960 M4120 LOPEZ_MBD_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MBD_TARGETS.html Genes up-regulated in HeLa cells (cervical cancer) after simultaneus knockdown of all three MBD (methyl-CpG binding domain) proteins MeCP2, MBD1 and MBD2 [GeneID=4204;4152;8932] by RNAi. 18223687 1273/1612 Jessica Robertson 3.10479479829289e-07 8.87621529251511e-07 2785 2925.09090909091 2784 3.10479523208175e-08 1531 1.68553426599311 1.89232706893463 1 4.05220042022626 2784 3827 4434 2256 1531 1678 2765 2826 3098 4436 2541 2961 M2356 KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3 http://www.broadinstitute.org/gsea/msigdb/cards/KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3.html Genes with promoters occupied by SMAD2 or SMAD3 [GeneID=4087, 4088] in HaCaT cells (keratinocyte) according to a ChIP-chip analysis. 18955504 1120/1317 Arthur Liberzon 1.17219850641138e-07 7.06112554001409e-07 3535 2351.36363636364 2784 1.1721985682436e-08 370 1.89956480399718 2.08436095670232 1 4.64900558035217 3534 1077 4688 370 480 2784 4444 2788 1496 777 3427 2962 M19832 REACTOME_CELL_DEATH_SIGNALLING_VIA_NRAGE_NRIF_AND_NADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_DEATH_SIGNALLING_VIA_NRAGE_NRIF_AND_NADE.html Genes involved in Cell death signalling via NRAGE, NRIF and NADE 76/83 Reactome 3.03256032104867e-07 8.77601760597774e-07 3265 2707.27272727273 2785 2.75687339915267e-08 249 1.83867788106413 -1.64067331373772 -1 4.42856564379305 3261 249 2140 2785 1400 3302 3936 4626 2365 2192 3524 2963 M15896 MARTINEZ_RB1_AND_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_AND_TP53_TARGETS_UP.html Genes up-regulated in mice with skin specific double knockout of both RB1 and TP53 [GeneID=5925;7157] by Cre-lox. 18245467 754/970 Jessica Robertson 1.2543277314065e-07 7.16209778122308e-07 3705 2605.54545454545 2785 1.25432780220672e-08 441 2.07870243391691 2.20273215255101 1 5.08699187667117 3705 2001 4536 441 551 2785 4225 2957 2480 853 4127 2964 M8202 AMIT_SERUM_RESPONSE_480_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_480_MCF10A.html Genes whose expression peaked at 480 min after stimulation of MCF10A cells with serum. 17322878 47/67 Leona Saunders 2.40217703563968e-06 3.52667981593135e-06 3345 2670.81818181818 2786 2.18379968961596e-07 1192 2.41603722338411 3.1467321091944 1 5.24794655435534 3341 3091 1938 3705 3137 2786 3467 1786 2564 2372 1192 2965 M17811 PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN.html Genes down-regulated in post-GC, BCL6 [GeneID=604] dependent B cell non-Hodgkin's lymphoma (B-NHL) vs MYC [GeneID=4609] driven pre-GC lymphoma. 18066064 207/276 Jessica Robertson 1.3549516679944e-06 2.20758435379137e-06 2485 2709.72727272727 2787 1.23177500226582e-07 1624 1.85365715975641 1.8570098483349 1 4.16640178649189 2481 3297 2636 3713 2787 1624 3060 3255 2002 2868 2084 2966 M7846 BROWNE_HCMV_INFECTION_8HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_8HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 8 h time point that were not down-regulated at the previous time point, 6 h. 11711622 52/77 John Newman 8.22847385193999e-08 6.34342404134915e-07 3530 2373.09090909091 2787 7.48043105427514e-09 197 2.14467520473485 1.80804121684204 1 5.29549652394485 3530 477 1450 2787 197 3074 3024 4556 2456 1150 3403 2967 M18887 YAGI_AML_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_SURVIVAL.html Genes differentially expressed in pediatric AML (acute myeloid leukemia) samples from patients with good survival (>3 years without relapse) compared to those with poor survival (relapsed within one year after treatment). 12738660 188/221 Kevin Vogelsang 3.85220534807336e-07 9.71282545027043e-07 2790 2652.63636363636 2788 3.50200547508693e-08 1511 1.6610421548772 1.75351550638861 1 3.96646079542204 2788 2074 3041 1533 1667 2953 4149 3760 2213 3490 1511 2968 M12053 NIKOLSKY_BREAST_CANCER_22Q13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_22Q13_AMPLICON.html Genes within amplicon 22q13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 24/28 Jessica Robertson 6.4677940505317e-07 1.3066330228484e-06 2795 2506.27272727273 2791 5.87981450182125e-08 762 1.63026592689639 -1.13791413392338 -1 3.80759158449766 1860 2791 2795 3428 2182 1475 762 3888 2857 2376 3155 2969 M1145 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 1. 12554760 102/114 Arthur Liberzon 1.389480195008e-06 2.25372732661091e-06 2425 2713.27272727273 2791 1.26316461143575e-07 1673 2.19251648347986 -1.79195878432569 -1 4.92926972057354 2424 3612 1673 2924 2798 2217 2647 2791 3380 2348 3032 2970 M10100 CHOI_ATL_ACUTE_STAGE http://www.broadinstitute.org/gsea/msigdb/cards/CHOI_ATL_ACUTE_STAGE.html Acute stage-specific genes for adult T cell leukemia (ATL). 16909099 5/15 Leona Saunders 0.000259461508245546 0.000277385802699655 2135 2594.36363636364 2792 2.59491807348001e-05 442 2.35566270854454 -3.23966702651721 -1 3.31963260033554 2134 1987 4354 2792 4387 3030 3064 2827 442 1786 1735 2971 M1191 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment with 2 nM docetaxel [PubChem=148124]. 17099726 33/54 Arthur Liberzon 8.76712356776922e-06 1.09502046149433e-05 2795 2869.09090909091 2793 7.97014409585816e-07 1301 2.82924000579374 3.43383428936814 1 5.59416688933157 2793 3422 1301 3147 3722 2541 2283 4339 3720 2234 2058 2972 M1875 JU_AGING_TERC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JU_AGING_TERC_TARGETS_UP.html Cytokines, growth factors, and secreted proteins that show increased expression on a protein array of samples from aged TERC [GeneID=7012] knockout mice. 17486088 9/12 Jessica Robertson 3.06710431557894e-07 8.82385976514091e-07 2400 2676.81818181818 2793 3.06710473889981e-08 1321 3.65594022345103 3.85086009574879 1 8.8515335655072 2400 1970 4592 2793 1521 2869 3074 2224 3306 1321 3375 2973 M2372 IKEDA_MIR1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR1_TARGETS_UP.html Genes up-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-1 microRNA. 19188439 70/76 Arthur Liberzon 2.38260119064994e-07 8.00711660757103e-07 1775 2400.45454545455 2793 2.16600131698711e-08 201 1.83240825967316 2.24761108806485 1 4.44263957514946 1772 3635 2793 3760 1142 3316 3231 201 852 3547 2156 2974 M2550 HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_UP.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 54/60 Arthur Liberzon 2.26358781266024e-06 3.36720279727587e-06 2040 2295.09090909091 2793 2.05780921970649e-07 514 2.11659037738623 2.85246092496213 1 4.60841404235517 2038 3064 2230 3354 3095 2793 3225 1061 631 3241 514 2975 M5224 REACTOME_SYNTHESIS_OF_DNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_DNA.html Genes involved in Synthesis of DNA 93/105 Reactome 8.45006531680791e-05 9.33184564701295e-05 330 2597.18181818182 2794 7.68217263281582e-06 327 1.17642410788241 1.23965296733551 1 1.85662220377232 327 3021 3993 2035 4226 1068 1046 2244 3723 4092 2794 2976 M4385 XU_RESPONSE_TO_TRETINOIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_UP.html Genes up-regulated in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin [PubChem=444795] alone. 16140955 24/71 Kevin Vogelsang 1.82790566240271e-07 7.47800341964416e-07 2320 2641.81818181818 2794 1.66173255843385e-08 852 1.41840598213749 -1.38249049106563 -1 3.44453002544959 2319 2794 3026 2849 852 2644 2729 3144 3017 3103 2583 2977 M15927 RODRIGUES_DCC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_DCC_TARGETS_DN.html Genes down-regulated in HCT8/S1 cells (colon cancer) which normally lack DCC [GeneID=9423] compared to those stably expressing wild type DCC off a plasmid vector. 17334389 182/207 Arthur Liberzon 2.66635075702407e-07 8.32746245638274e-07 4645 2976.27272727273 2796 2.42395552743624e-08 1249 1.82772928170154 -1.49946599066261 -1 4.41864513682035 4644 1446 2796 2163 1264 4664 4263 4267 1249 2592 3391 2978 M9914 YAMASHITA_LIVER_CANCER_WITH_EPCAM_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_WITH_EPCAM_DN.html Down-regulated genes distinguishing hepatocellular carcinoma (HCC) samples positive for EPCAM [GeneID=4072] from the negative ones. 18316609 12/49 Yujin Hoshida 0.0256261411906026 0.0260231037908012 2625 2859.81818181818 2798 0.00235723646919515 1358 1.61303623211335 -1.77337356418787 -1 0.977921464325431 2622 3225 2768 3397 4671 2538 1358 2798 3309 2975 1797 2979 M1749 KEGG_VEGF_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VEGF_SIGNALING_PATHWAY.html VEGF signaling pathway 68/89 KEGG 9.00451568263808e-08 6.54873867828224e-07 2630 2340.18181818182 2799 8.18592368289955e-09 245 1.54867623689051 -1.61225423732485 -1 3.80137232653883 2630 313 2884 663 245 3165 2799 3735 3971 3033 2304 2980 M7362 HASLINGER_B_CLL_WITH_6Q21_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_6Q21_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 6q21 region. 15459216 23/53 Kevin Vogelsang 8.93188831558914e-05 9.84322037113723e-05 1830 2791.36363636364 2799 8.12022815121218e-06 1615 1.77180879046763 -2.13882804127236 -1 2.80506712198785 1828 3461 3118 2971 4238 2799 2196 1615 2012 4235 2232 2981 M4253 VALK_AML_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_4.html Top 40 genes from cluster 4 of acute myeloid leukemia (AML) expression profile; 87% of the samples are FAB M1 subtype, 53% bear mutations in CEBPA [GeneID=1050]. 15084694 39/59 Jessica Robertson 7.31078453542207e-06 9.28603417846936e-06 3085 2743.18181818182 2800 6.6461898453503e-07 1584 2.12207225456646 2.39627115805332 1 4.24449738371254 3081 2714 1780 3703 3658 3034 3115 2606 2100 1584 2800 2982 M2498 PHONG_TNF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_TARGETS_DN.html Genes down-regulated in Calu-6 cells (lung cancer) at 1 h time point after TNF [GeneID=7124] treatment. 20516219 6/8 Arthur Liberzon 0.00036471675749962 0.00038775614575766 1205 2495.18181818182 2800 3.6477662957071e-05 262 2.52062169873084 -2.52062169873084 -1 3.40813195162986 1201 3817 4709 3410 4544 1074 262 849 3236 2800 1545 2983 M1304 GROSS_HYPOXIA_VIA_ELK3_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_DN.html Genes down-regulated in SEND cells (skin endothelium) at hypoxia with ELK3 [GeneID=2004] knockdown by RNAi. 17704799 224/258 Jessica Robertson 2.72444380289626e-07 8.37744283366146e-07 2420 2600.27272727273 2801 2.47676740026086e-08 883 2.09962089773271 -2.01944408788536 -1 5.08120852974319 2801 2960 883 2418 1288 3188 2417 4177 3565 918 3988 2984 M5103 YAGI_AML_FAB_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_FAB_MARKERS.html Genes specifically expressed in FAB subtypes M2, M4, M5 and M7 of pediatric AML (acute myeloid leukemia). 12738660 293/403 Kevin Vogelsang 3.11439600582349e-07 8.89289119630179e-07 2985 2321 2801 2.83126949700748e-08 650 1.86212729904436 2.0511437621382 1 4.48138045129176 2983 1296 1340 650 1423 3309 4032 3511 3154 1032 2801 2985 M1534 VIETOR_IFRD1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/VIETOR_IFRD1_TARGETS.html Genes down-regulated in c-JunER cells (mammary gland epithelum) by overexpression of IFRD1 [GeneID=3475] off an adenovirus vector. 12198164 26/44 John Newman 1.69214925623533e-07 7.33971845416521e-07 4070 2658.27272727273 2801 1.53831762398953e-08 506 1.78572338717744 1.12523105653172 1 4.35532187807601 4070 1828 2135 3843 768 3069 2801 2614 506 3004 4603 2986 M1105 GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN.html Genes down-regulated in ME-A cells (breast cancer) undergoing apoptosis in response to doxorubicin [PubChem=31703]. 17160024 2335/2619 Arthur Liberzon 2.12279283492242e-07 7.70763712250053e-07 2755 2967.18181818182 2802 2.12279303770367e-08 1118 1.49762201574399 1.63333550906485 1 3.63178543250641 2751 4385 4338 4132 1118 1594 2822 1825 2802 4652 2220 2987 M453 MURAKAMI_UV_RESPONSE_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_6HR_UP.html Genes up-regulated in primary keratinocytes at 6 h after UVB irradiation. 11532376 60/71 John Newman 1.88467919319712e-07 7.49425930235081e-07 4715 3156.81818181818 2802 1.71334486786581e-08 894 2.16835168349268 -1.31441086343354 -1 5.29137022783902 4715 2654 2024 3708 894 4207 4596 2802 2800 2585 3740 2988 M12051 CHANG_IMMORTALIZED_BY_HPV31_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_IMMORTALIZED_BY_HPV31_DN.html Genes down-regulated in normal keratinocytes immortalized by infection with the high risk HPV31 (human papilloma virus) strain. 10756030 94/164 John Newman 9.32745250176783e-08 6.56798957981166e-07 2935 2408.72727272727 2804 8.47950263384423e-09 270 2.4158569846338 -2.25565953406008 -1 5.95672925825707 2933 2137 671 2092 270 2922 2804 3582 3248 1148 4689 2989 M226 PID_VEGFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGFR1_PATHWAY.html VEGFR1 specific signals 18832364 38/43 Pathway Interaction Database 2.2978261767654e-06 3.40567166137415e-06 1665 2534.27272727273 2805 2.08893506979204e-07 932 1.57398670303811 1.68062937641865 1 3.41106255825406 1663 3410 3075 2725 3108 1358 932 1683 4242 2805 2876 2990 M537 REACTOME_REGULATION_OF_KIT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_KIT_SIGNALING.html Genes involved in Regulation of KIT signaling 22/24 Reactome 6.80389730213431e-06 8.68660948500782e-06 4695 2776.63636363636 2806 6.18538031318777e-07 119 2.02922527335625 1.73046510715326 1 4.08024858977818 4694 2806 2257 169 3636 3858 2721 3769 119 2454 4060 2991 M14940 BILBAN_B_CLL_LPL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BILBAN_B_CLL_LPL_DN.html Genes down-regulated in B-CLL (B-cell chronic leukemia) samples expressing high levels of LPL [GeneID=4023] compared with those expressing low levels of the gene. 16617321 56/81 Arthur Liberzon 5.40096187027066e-07 1.16482288679751e-06 1340 2932.54545454545 2807 4.90996654199808e-08 1339 1.7995336603006 -1.76728183545404 -1 4.2442308721238 1339 4216 2807 3511 2022 1644 1351 4677 4309 3586 2796 2992 M581 ZIRN_TRETINOIN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_UP.html Genes up-regulated in MS427 cells (Wilms tumor with normal WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 22/25 Leona Saunders 1.08398928430372e-05 1.33553365228753e-05 2440 2997.72727272727 2807 9.8544965945327e-07 2273 1.85716293912925 1.88721281373992 1 3.59051234097464 2437 2807 2273 4143 3772 2497 2884 3989 2290 2458 3425 2993 M19548 STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_UP.html Genes up-regulated by estradiol [PubChem=5757] and up-regulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 38/42 Leona Saunders 1.71304051677656e-07 7.35006487528071e-07 3920 2852.45454545455 2808 1.55730968196663e-08 782 2.01505832602947 2.23472216816299 1 4.92059276673652 3917 2285 2479 3700 782 4137 4453 2308 1399 2808 3109 2994 M13569 ZHAN_MULTIPLE_MYELOMA_LB_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_LB_DN.html Top 50 down-regulated genes in cluster LB of multiple myeloma samples belonging to the low bone disease group. 16728703 49/56 Arthur Liberzon 8.20590355410526e-07 1.52607820233951e-06 3580 2944 2809 7.45991510442992e-08 1630 1.99357708427146 -1.82648824231894 -1 4.61322342590538 3576 2250 2027 2809 2402 3902 4218 3505 2537 1630 3528 2995 M2517 RAO_BOUND_BY_SALL4_ISOFORM_A http://www.broadinstitute.org/gsea/msigdb/cards/RAO_BOUND_BY_SALL4_ISOFORM_A.html Loci bound exclusively by SALL4 [GeneID=57167] isoform a in ES cells (embryonic stem). 20837710 178/360 Arthur Liberzon 2.27901424858622e-07 7.89211097089284e-07 3155 2727.81818181818 2810 2.07183134970262e-08 1091 1.87376265500269 2.17737349916317 1 4.54876635552229 3153 2539 2558 3716 1091 1224 3013 4189 3193 2810 2520 2996 M5611 PUJANA_BRCA1_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BRCA1_PCC_NETWORK.html Genes constituting the BRCA1-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC >= 0.4) with that of BRCA1 [GeneID=672] across a compendium of normal tissues. 17922014 1946/2578 Leona Saunders 1.2823995791252e-06 2.11197697608896e-06 1265 2994.81818181818 2811 1.28240031917271e-07 1263 1.45692312842013 1.5399175782433 1 3.27523305188291 1263 4386 4419 3041 2811 1958 1825 2285 3479 4707 2769 2997 M2589 SESTO_RESPONSE_TO_UV_C2 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C2.html Cluster 2: genes changed in primary keratinocytes by UVB irradiation. 11867738 91/103 John Newman 1.93705554914284e-06 2.94173172199299e-06 1945 2678.54545454545 2812 1.76096114062111e-07 990 1.78212147713699 -1.9391125489259 -1 3.9143200674343 1942 3330 2812 2469 3020 3070 2851 2638 990 3700 2642 2998 M1160 MARKS_ACETYLATED_NON_HISTONE_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/MARKS_ACETYLATED_NON_HISTONE_PROTEINS.html Non-histone proteins that are acetylated. 17322921 21/27 Leona Saunders 1.05057055712758e-05 1.29910742196547e-05 3745 2775.45454545455 2813 9.55068703611333e-07 387 2.20515722736268 -1.58859322763802 -1 4.28332735982337 3744 2813 2183 1528 3760 3708 2171 4091 387 2683 3462 2999 M1536 HASLINGER_B_CLL_WITH_CHROMOSOME_12_TRISOMY http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_CHROMOSOME_12_TRISOMY.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with trisomy of chromosome 12. 15459216 28/33 Kevin Vogelsang 4.98755156025002e-07 1.11141872398347e-06 2815 2405 2813 4.53413880996607e-08 733 1.54484745966896 2.0076809797156 1 3.64913041931993 2813 733 2907 3124 1944 3259 3940 2030 880 3230 1595 3000 M1654 SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_DN.html Genes down-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] which continued to respond normally to insulin in the insulin resistant cells. 14530283 23/28 John Newman 2.00901761335148e-05 2.36355013335469e-05 1725 2865.72727272727 2814 1.82639632702768e-06 1725 1.93837377374056 -1.48472513068314 -1 3.55645223723719 1725 3460 2814 3429 3953 2479 2186 2212 3299 2582 3384 3001 M8876 PODAR_RESPONSE_TO_ADAPHOSTIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/PODAR_RESPONSE_TO_ADAPHOSTIN_DN.html Down-regulated genes in MM1.S cells (multiple myeloma) treated with adaphostin [PubChem=387042], a tyrosine kinase inhibitor with anticancer properties. 17308109 28/33 Jessica Robertson 1.20131548563434e-06 2.00999967819713e-06 3315 2913 2814 1.09210558328742e-07 1677 2.55395713744143 2.93414884514107 1 5.80117083205885 3314 4266 1677 3748 2699 3876 2814 1763 2253 2910 2723 3002 M11420 BIOCARTA_CTCF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTCF_PATHWAY.html CTCF: First Multivalent Nuclear Factor 30/34 BioCarta 1.53206492738888e-06 2.42907170214159e-06 3505 2429.09090909091 2815 1.39278726755403e-07 174 2.13010428350345 2.50250834275101 1 4.75965433042584 3501 1811 2214 889 2878 3504 3502 2290 174 3142 2815 3003 M7912 DELLA_RESPONSE_TO_TSA_AND_BUTYRATE http://www.broadinstitute.org/gsea/msigdb/cards/DELLA_RESPONSE_TO_TSA_AND_BUTYRATE.html Genes up-regulated in HT-29 cells (colon cancer) by the combination of trichostatin A (TSA) and sodium butyrate [PubChem=5562;5222465]. 11423116 41/46 John Newman 0.000816194766184997 0.00085419940053064 1785 3074.90909090909 2816 7.42270663519572e-05 1782 1.98306980010645 2.37127224757351 1 2.39708918643115 1782 4238 2524 2543 4477 2816 2481 3517 3440 3372 2634 3004 M7928 MITSIADES_RESPONSE_TO_APLIDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/MITSIADES_RESPONSE_TO_APLIDIN_UP.html Genes up-regulated in the MM1S cells (multiple myeloma) after treatment with aplidin [PubChem=44152164], a marine-derived compound with potential anti-cancer properties. 18593922 569/742 Jessica Robertson 5.67711478159918e-07 1.19785345414162e-06 1480 3055.72727272727 2816 5.67711623193314e-08 1480 1.6090701948413 -1.52202163779397 -1 3.7818652526537 1480 4670 4548 4118 2164 1761 2032 2816 3813 4083 2128 3005 M2308 WANG_TNF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TNF_TARGETS.html Representative genes up-regulated in MEF cells (embryonic fibroblast) in response to TNF [GeneID=7124]. 17438126 22/31 Arthur Liberzon 8.72635125179872e-06 1.09050510745274e-05 2820 2758.27272727273 2816 7.93307805933315e-07 994 2.39012988507264 -2.60745473904165 -1 4.71988727238202 2816 2350 1004 2322 3720 3214 2727 3898 4454 994 2842 3006 M4866 FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_DN.html Down-regulated genes significantly associated with positive minimal residual disease (MRD) on day 46 after chemotherapy treatment of children with acute lymphoblastic leukemia (ALL). 16627760 33/38 Arthur Liberzon 2.28024840577406e-05 2.66405259288454e-05 2820 2463 2819 2.0729745821427e-06 229 1.90049526772692 2.10343547817835 1 3.44624934827865 2819 3122 2808 2407 4225 3463 2983 229 1275 2853 909 3007 M2509 ABDELMOHSEN_ELAVL4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ABDELMOHSEN_ELAVL4_TARGETS.html Major ELAVL4 [GeneID=1996] associated mRNAs encoding proteins with functions in neuronal physiology. 20584986 29/33 Arthur Liberzon 1.41944828449509e-06 2.28883831480239e-06 4325 2982.90909090909 2819 1.29040836393573e-07 2060 1.77412158876044 2.30155548138089 1 3.97428531122059 4321 3138 2496 3205 2819 4189 2431 2347 2060 2371 3435 3008 M1675 GERHOLD_ADIPOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_ADIPOGENESIS_UP.html Selected genes up-regulated during differentiation of 3T3-L1 cells (fibroblast) into adipocytes in response to adipogenic hormones. 12021175 62/71 John Newman 2.1951795215862e-06 3.27712877171311e-06 2800 2881.36363636364 2820 1.99561973814442e-07 2478 1.86480624562863 -1.92691414022804 -1 4.06308798000822 2796 3055 2509 2478 3081 2820 2883 2692 3706 2522 3153 3009 M2884 WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_UP.html Genes specifically up-regulated via JNK (MAPK8) [GeneID=5599] signaling pathway activated by paclitaxel [PubChem=4666] in BR cells (ovarian cancer). 16547493 20/35 Arthur Liberzon 0.00533297744077306 0.00548043838895033 2340 2881.54545454545 2821 0.000485995368322367 1819 1.51490048543067 1.72345910122968 1 1.32755541534235 2340 2821 3134 2003 4570 2507 2239 1819 3218 3902 3144 3010 M9780 CUI_GLUCOSE_DEPRIVATION http://www.broadinstitute.org/gsea/msigdb/cards/CUI_GLUCOSE_DEPRIVATION.html Representative genes up-regulated in MiaPaCa2 cells (pancreatic cancer) under glucose-deprived conditions. 17409444 79/162 Jessica Robertson 1.34780403255279e-06 2.19973548881367e-06 2825 2857 2822 1.22527714388157e-07 1639 1.77912513437586 -1.93883130209916 -1 3.99797356520007 2822 1639 2491 2896 2780 3908 3633 3196 2882 2815 2365 3011 M2460 KANG_GLIS3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KANG_GLIS3_TARGETS.html Genes downregulated in the postnatal day 3 pancreata with impaired function of GLIS3 [GeneID=169792]. 19805515 19/49 Arthur Liberzon 3.55994761441069e-06 4.91601894090651e-06 2600 2464.27272727273 2822 3.23632124998315e-07 733 2.12752573521839 2.25612781859074 1 4.49186743388869 2597 2822 1606 3135 3344 2899 1819 733 3297 1985 2870 3012 M18441 THUM_SYSTOLIC_HEART_FAILURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/THUM_SYSTOLIC_HEART_FAILURE_DN.html Genes down-regulated in samples with systolic heart failure compared to normal hearts. 17606841 290/337 Arthur Liberzon 3.19741977605315e-07 8.98528442785416e-07 1440 2862.09090909091 2823 2.9067456734159e-08 1439 1.70220161024983 -1.53733090315998 -1 4.08913433887825 1439 4692 3655 4612 1451 1936 1676 2823 2315 4020 2864 3013 M2024 NAKAMURA_ADIPOGENESIS_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_EARLY_UP.html Genes up-regulated in mesenchymal stem cells during early phase of adipogenesis, defined as days 1 to 5 of culturing with adipogenic hormones. 12646203 81/96 Arthur Liberzon 1.77518880929491e-06 2.7399905754977e-06 2825 2303.27272727273 2823 1.61380931063953e-07 181 2.24092937906293 2.72514595529596 1 4.96275156653675 2823 3027 1539 3071 2964 3926 3310 1204 1650 1641 181 3014 M1326 MANTOVANI_NFKB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_NFKB_TARGETS_DN.html NF-kB-controlled genes down-regulated in endothelial cells in response to viral GPCR protein. 17906691 19/22 Jessica Robertson 2.1654625233927e-05 2.53685358908254e-05 3270 2770.90909090909 2824 1.96862167123534e-06 790 2.00968658675534 2.78083731879343 1 3.6642980219675 3268 2824 2511 2171 3973 3122 2280 790 4288 3185 2068 3015 M11120 HASLINGER_B_CLL_WITH_MUTATED_VH_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_MUTATED_VH_GENES.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with mutations in the variable immunoglobulin veriable heavy chain (VH) genes. 15459216 22/44 Kevin Vogelsang 3.28047355012077e-06 4.58780300935408e-06 4705 2637.54545454545 2824 2.98225312884085e-07 397 2.09441218315005 -1.48973917037785 -1 4.4464518153831 4705 833 2071 2595 3298 3993 3054 1900 397 2824 3343 3016 M939 HADDAD_B_LYMPHOCYTE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/HADDAD_B_LYMPHOCYTE_PROGENITOR.html Genes up-regulated in hematopoietic progenitor cells (HPC) of B lymphocyte lineage CD34+CD45RA+CD10+ [GeneID=947;5788;4311]. 15331438 431/684 Kevin Vogelsang 1.42994206705925e-06 2.30273850444205e-06 3940 2794.18181818182 2824 1.29994817862253e-07 1398 1.80087441515233 -1.38991255726504 -1 4.03306558931244 3939 2506 2567 1539 2824 3415 2705 3150 2850 1398 3843 3017 M12085 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP.html Genes up-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing erythroid lineage. 17898786 57/83 Arthur Liberzon 1.1897750341255e-07 7.06112554001409e-07 4340 2412.72727272727 2825 1.08161372588123e-08 373 2.14867600612157 2.34433581669311 1 5.26524367147804 4336 373 740 2119 408 4469 2825 2840 3489 468 4473 3018 M1808 WEBER_METHYLATED_HCP_IN_SPERM_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_SPERM_DN.html Unmethylated germline-specific genes with high-CpG-density promoters (HCP) in sperm. 17334365 22/45 Jessica Robertson 7.07345942926771e-07 1.3784725468932e-06 3550 2972.36363636364 2825 6.43041973048514e-08 2084 2.19521933890664 2.16947377905662 1 5.12389575175449 3546 3746 2610 3892 2275 2897 2815 2084 2570 2825 3436 3019 M6181 DORN_ADENOVIRUS_INFECTION_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_48HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 48 h after infection with adenovirus Ad12. 15681441 20/33 Arthur Liberzon 6.92412596251844e-06 8.82101877006398e-06 3790 3102.54545454545 2825 6.29467977738519e-07 2332 1.99454110321574 1.78190736134065 1 4.0043034701607 3789 2825 2656 2438 3645 3924 2546 3186 2332 2517 4270 3020 M19580 KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS.html Pentose and glucuronate interconversions 14/32 KEGG 3.23257873409641e-06 4.53156270416842e-06 4120 2816.72727272727 2827 2.93871225809871e-07 1013 2.06656841950554 -1.21156912540854 -1 4.39112608031578 4120 1915 2125 2798 3291 2981 1559 4494 1013 2827 3861 3021 M267 PID_ANTHRAX_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ANTHRAX_PATHWAY.html Cellular roles of Anthrax toxin 18832364 14/18 Pathway Interaction Database 8.60158556779899e-07 1.57310167253419e-06 3690 2634.45454545455 2828 7.81962630078067e-08 598 2.0865982637786 -1.49059495314543 -1 4.81975320946416 3690 2866 2144 2166 2452 3515 3564 2029 598 2828 3127 3022 M18607 REACTOME_STEROID_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_STEROID_HORMONES.html Genes involved in Steroid hormones 19/44 Reactome 3.462754224124e-05 3.96511400724534e-05 2970 2871.18181818182 2829 3.14800793486912e-06 819 3.08135981067378 2.5105940169198 1 5.40462528117405 2969 3762 2341 3719 4071 3190 2829 2620 819 2771 2492 3023 M609 CHOI_ATL_CHRONIC_VS_ACUTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHOI_ATL_CHRONIC_VS_ACUTE_DN.html Genes down-regulated in adult T-cell leukemia (ATL), chronic vs acute clinical condition. 16909099 33/34 Arthur Liberzon 1.23148511126333e-07 7.12872631945934e-07 3515 2484.81818181818 2829 1.11953198199789e-08 215 1.99245671007633 2.13089593015799 1 4.8754809112342 3513 3711 2713 1915 446 2984 3117 1836 215 4054 2829 3024 M182 PID_IL3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL3_PATHWAY.html IL3-mediated signaling events 18832364 36/41 Pathway Interaction Database 1.23279880301897e-05 1.50279192929998e-05 2440 2862.27272727273 2830 1.12073246474787e-06 1636 1.33236469791075 -1.17424012609686 -1 2.53430575251707 2436 3115 3339 2019 3817 2830 2244 1636 4329 3443 2277 3025 M973 REACTOME_INTERFERON_ALPHA_BETA_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_ALPHA_BETA_SIGNALING.html Genes involved in Interferon alpha/beta signaling 74/120 Reactome 2.07541791834505e-05 2.43624819403873e-05 585 2670.27272727273 2830 1.88676136137329e-06 584 1.4477934070121 -1.44829399703105 -1 2.63603031069108 584 3629 3251 2996 3965 1299 1448 2830 4069 2633 2669 3026 M183 PID_IL6_7_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL6_7_PATHWAY.html IL6-mediated signaling events 18832364 68/74 Pathway Interaction Database 1.23385661629673e-07 7.12872631945934e-07 2305 2694.81818181818 2831 1.12168789590622e-08 449 1.73605183639748 -1.5604118517129 -1 4.24162681771347 2301 3047 2628 1537 449 2831 2203 3242 4317 3601 3487 3027 M5775 BROWNE_HCMV_INFECTION_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_12HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 12 h time point that were not down-regulated at the previous time point, 10 h. 11711622 169/225 John Newman 3.08421835331874e-07 8.84955053353463e-07 2675 2831.45454545455 2831 2.80383525972798e-08 1417 1.71235754665029 1.87323770284458 1 4.11838246332363 2674 3306 2831 3194 1417 2743 3228 3348 3542 2090 2773 3028 M17902 BIOCARTA_CASPASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CASPASE_PATHWAY.html Caspase Cascade in Apoptosis 25/39 BioCarta 1.4422259242299e-06 2.31698650863347e-06 2415 3035 2832 1.31111533608401e-07 2064 1.54424125633251 -1.47636767355838 -1 3.44954037151047 2411 2351 3028 3955 2832 2492 2064 4071 2721 3517 3943 3029 M6740 SABATES_COLORECTAL_ADENOMA_SIZE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_SIZE_UP.html A selection of genes whose expression displayed significant positive correlation with size of colorectal adenoma. 18171984 18/20 Leona Saunders 1.28347021472528e-05 1.55972693447563e-05 4380 3092.27272727273 2832 1.16679791135872e-06 639 1.87118290152402 -1.33328053193609 -1 3.56728031864829 4376 2832 2642 2830 3827 3961 4321 2592 639 3409 2586 3030 M15476 URS_ADIPOCYTE_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/URS_ADIPOCYTE_DIFFERENTIATION_UP.html Genes up-regulated in primary adipocytes compared to preadipocytes. 15051823 111/149 John Newman 2.3721041607894e-07 8.0069968374353e-07 4470 2448 2832 2.15645856050603e-08 61 2.45440192996338 2.54824865638917 1 5.96764266011415 4468 61 374 137 2024 4218 4487 3316 2832 787 4224 3031 M7284 SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP.html Genes up-regulated in CT60/4 cells (breast cancer reverted to normal by transfer of chromosome 8p region) vs parental MDA-MB-231 cells (deleted chromosome 8p). 15580292 106/147 Arthur Liberzon 1.34106147409835e-07 7.20206492018647e-07 4180 2531.27272727273 2833 1.21914686895081e-08 353 2.46264486793412 2.7996582172206 1 6.03342266338074 4177 1588 353 846 2833 4718 3495 2954 2300 448 4132 3032 M1576 GERHOLD_ADIPOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_ADIPOGENESIS_DN.html Selected genes down-regulated during differentiation of 3T3-L1 cells (fibroblast) into adipocytes in response to adipogenic hormones. 12021175 98/116 John Newman 1.44866198998349e-06 2.32653439697927e-06 3415 2990.72727272727 2834 1.31696631263933e-07 1921 2.19343004313405 2.25215328497335 1 4.91916413999012 3411 4179 2288 2528 2834 2671 3613 2240 3698 1921 3515 3033 M6656 HASINA_NOL7_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HASINA_NOL7_TARGETS_UP.html Genes up-regulated in SiHa cells (cervical carcinoma) by stable expression of NOL7 [GeneID=51406] off a plasmid vector. 16205646 14/17 Leona Saunders 0.00399886254499073 0.00411570676239778 2045 2977.18181818182 2835 0.000364195426111062 1032 2.21733308003678 2.31822590910511 1 2.07722554725146 2042 4078 2816 4591 4607 2588 2857 1701 3602 2835 1032 3034 M1884 YOSHIMURA_MAPK8_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIMURA_MAPK8_TARGETS_UP.html Genes up-regulated in vascular smooth muscle cells (VSMC) by MAPK8 (JNK1) [GeneID=5599]. 16311603 1201/2045 Jessica Robertson 2.87525055381128e-22 1.9114341709844e-20 4515 2617.18181818182 2835 2.87525055381128e-23 27 2.27765656995812 2.38005942163638 1 18.0119640604367 4513 1075 4599 27 409 2835 4458 4465 2269 39 4100 3035 M17749 DORN_ADENOVIRUS_INFECTION_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_12HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 12 h after infection with adenovirus Ad12. 15681441 62/84 Arthur Liberzon 2.41959983727674e-05 2.81570789742263e-05 2175 2894 2836 2.19966040807604e-06 2002 2.05890249342435 2.21758418900981 1 3.71775719069948 2173 3367 2002 2031 4003 2862 4178 2836 3547 2523 2312 3036 M1227 TRAYNOR_RETT_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/TRAYNOR_RETT_SYNDROM_DN.html Genes down-regulated in primary fibroblasts from Rett syndrom patients who carry mutations inactivating MECP2 [GeneID=4204]. 12418965 24/31 John Newman 5.66319816048716e-06 7.37184095904561e-06 3505 2749.90909090909 2837 5.14837521694245e-07 1256 2.31060861242747 2.33532280533777 1 4.71920716494477 3502 1840 1256 2766 3557 2837 2750 3682 3391 1430 3238 3037 M526 REACTOME_TETRAHYDROBIOPTERIN_BH4_SYNTHESIS_RECYCLING_SALVAGE_AND_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TETRAHYDROBIOPTERIN_BH4_SYNTHESIS_RECYCLING_SALVAGE_AND_REGULATION.html Genes involved in Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation 17/21 Reactome 2.22237980645765e-06 3.31530742303417e-06 1400 2636.09090909091 2838 2.02034731949827e-07 817 1.7712330691316 1.74032516342904 1 3.85311434495241 1396 2855 2792 3999 3085 1419 817 2838 4356 3320 2120 3038 M2742 LEE_LIVER_CANCER_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by overexpression of MYC [GeneID=4609]. 15565109 61/99 Yujin Hoshida 1.29434541498639e-07 7.20206492018647e-07 3815 2478.90909090909 2839 1.17667771921615e-08 485 2.28910161448542 2.44140263931772 1 5.60471959468319 3812 3054 1385 2839 485 3710 4521 1033 1343 1625 3461 3039 M12299 SEMENZA_HIF1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SEMENZA_HIF1_TARGETS.html Genes that are transcriptionally regulated by HIF1A [GeneID=3091]. 11516994 47/68 John Newman 1.50240378081154e-06 2.39168493943692e-06 2840 2707.72727272727 2839 1.36582255165482e-07 1198 2.78306717636621 2.68099186568622 1 6.24155843189521 2839 3674 1198 1693 2864 3296 4093 1549 2633 2373 3573 3040 M2199 THILLAINADESAN_ZNF217_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/THILLAINADESAN_ZNF217_TARGETS_DN.html Genes bound and repressed by ZNF217 [GeneID=7764] in MCF7 cells (breast cancer). 18625718 14/15 Arthur Liberzon 1.48255272618921e-06 2.36807068277938e-06 3440 2663.45454545455 2839 1.34777611387641e-07 496 2.02696110877358 -1.69844012804136 -1 4.5357651655781 3438 935 2265 1882 2853 4121 4461 4321 496 2839 1687 3041 M18941 KORKOLA_EMBRYONAL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONAL_CARCINOMA.html Genes predicting the embryonic carcinoma (EC) subtype of nonseminomatous male germ cell tumors (NSGCT). 15870693 10/19 Leona Saunders 0.0231110367616334 0.0234943126243613 2545 2920.18181818182 2841 0.00212340457336488 787 1.98160389706492 2.47141105760343 1 1.24818349561361 2543 4351 2841 3979 4619 2212 787 3963 1966 3108 1753 3042 M2245 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_C http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_C.html Category C genes: p53-independent genes whose expression in the absence of S389 phosphorylation is dissimilar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 141/201 Arthur Liberzon 1.06429895535887e-07 6.93852357637273e-07 1745 2506.36363636364 2841 9.67544551678820e-09 334 2.41028940530713 -2.0883700311144 -1 5.91978256653847 3404 3868 1172 2841 334 4188 3409 1741 1835 1743 3035 3043 M18912 XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_DN.html Genes down-regulated in DU-145 cells (prostate cancer) in the absence but not in the presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 44/54 Arthur Liberzon 6.07105835645207e-06 7.83790903787029e-06 3585 2933.36363636364 2842 5.51915919094485e-07 1727 1.88307478752487 2.54306676385141 1 3.81658737021066 3585 2264 2842 2410 3591 4308 3769 2460 1727 2856 2455 3044 M1256 INAMURA_LUNG_CANCER_SCC_SUBTYPES_UP http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_SUBTYPES_UP.html Up-regulated genes discriminating between two subtypes of squamous cell carcinoma (SCC) type of non-small cell lung cancer: SSC-A vs SSC-B. 16007138 17/17 Arthur Liberzon 5.04405025115347e-06 6.64839910233018e-06 2360 2986.18181818182 2842 4.58551074176125e-07 1064 1.18066808765503 1.38406210094633 1 2.40823733317984 2360 2842 3368 4590 3514 2756 2789 1983 3919 3663 1064 3045 M13930 JIANG_TIP30_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_TIP30_TARGETS_DN.html Down-regulated genes in HepG2 cells (liver cancer) overexpressing an oncogenic variant of tumor suppressor TIP30 [GeneID=10553] compared to its wild type form. 17440068 32/42 Jessica Robertson 6.30303714813686e-07 1.28013491132556e-06 2845 2715.09090909091 2842 5.73003541269851e-08 1338 2.4446603755103 3.22528988466364 1 5.74340639335368 2842 3125 1590 3111 2169 3152 4301 2832 1338 3058 2348 3046 M10500 XU_HGF_TARGETS_REPRESSED_BY_AKT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_REPRESSED_BY_AKT1_UP.html Genes up-regulated in DU-145 cells (prostate cancer) in the presence but not in the absence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 9/12 Arthur Liberzon 1.65596711009195e-06 2.58642116467042e-06 3240 2870.54545454545 2845 1.65596834409543e-07 1489 1.60223703686852 -1.78940969512504 -1 3.5501863912212 3239 2457 4381 3372 2985 2845 2616 1489 2055 2319 3818 3047 M10949 AMUNDSON_GENOTOXIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_GENOTOXIC_SIGNATURE.html Genes discriminating genotoxic (DNA damaging) agents from other kinds of stresses. 15824734 119/151 Arthur Liberzon 3.17325181992823e-07 8.94262307705344e-07 3065 2794.63636363636 2845 2.88477479784918e-08 1447 1.69730112942585 1.83209269360003 1 4.07862889358341 3064 2566 2845 2829 1447 2957 3997 2874 3209 2416 2537 3048 M1644 SAFFORD_T_LYMPHOCYTE_ANERGY http://www.broadinstitute.org/gsea/msigdb/cards/SAFFORD_T_LYMPHOCYTE_ANERGY.html Genes up-regulated in anergic mouse T helper cells (A.E7), versus non-anergic stimulated controls 15834410 113/156 John Newman 3.13271193514794e-07 8.91821491791211e-07 3140 2632.36363636364 2845 2.84792034657607e-08 1134 1.86001931990883 1.92641636429392 1 4.47532698066886 3139 2575 1862 2846 1429 4285 3501 1730 3610 1134 2845 3049 M6467 REACTOME_OPIOID_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OPIOID_SIGNALLING.html Genes involved in Opioid Signalling 74/93 Reactome 1.28150458175225e-07 7.20206492018647e-07 4285 2746.27272727273 2849 1.16500423309106e-08 474 1.69407090906864 2.0337598588235 1 4.13481808994475 4284 2168 2619 1304 474 4418 3713 3893 1122 2849 3365 3050 M10541 YANG_BREAST_CANCER_ESR1_LASER_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_LASER_UP.html Genes up-regulated in laser microdissected (LCM) samples of early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 38/49 Leona Saunders 0.000258890110413696 0.000276837635059503 2610 2995.63636363636 2850 2.35382346299001e-05 1912 1.83016817528422 -1.77323849205523 -1 2.56856857366782 2609 3409 3008 2850 4376 3218 3783 2663 1912 2807 2317 3051 M11756 WOTTON_RUNX_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WOTTON_RUNX_TARGETS_UP.html Common target genes up-regulated by all three Runx family members (RUNX1, RUNX2, and RUNX3 [GeneID=861;860;864]) in MEF cells (embryonic fibroblasts). 18560354 27/31 Jessica Robertson 4.4650150330555e-06 5.98888063541402e-06 2850 2833.18181818182 2850 4.05911281369338e-07 1874 1.79667498980955 -2.02770832783221 -1 3.72361145760335 2850 3158 2899 3893 3448 2363 1874 2541 3468 2768 1903 3052 M17006 RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_DN.html Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: moderately vs poorly differentiated tumors. 18679425 16/38 Jessica Robertson 5.62417486784488e-06 7.3291290381634e-06 1675 2396.45454545455 2851 5.112899314345e-07 335 1.25478117668027 1.25849151174183 1 2.54118510174575 1672 2851 3372 4405 3553 1104 849 335 3997 3561 662 3053 M7566 CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN.html Down-regulated genesin the left ventricle myocardium of patients with heart failure following implantation of LVAD (left ventricular assist device). 12824457 46/80 John Newman 1.98783206757774e-07 7.65527859584926e-07 4660 2664.45454545455 2851 1.80712022471848e-08 502 2.54038484856566 -2.99359771224449 -1 6.19838570897196 4658 502 852 2761 931 3621 3962 4392 2851 1221 3558 3054 M1828 MATZUK_MALE_REPRODUCTION_SERTOLI http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_MALE_REPRODUCTION_SERTOLI.html Genes important for Sertoli, peritubular, Leydig and interstitial cells, based on mouse models with male reproductive defects. 18989307 25/40 Jessica Robertson 4.50073043540874e-07 1.04185917010687e-06 3050 2772.27272727273 2851 4.09157396014762e-08 1850 1.54171014265878 1.70476882360076 1 3.65902110877967 3047 2348 3022 3360 1850 3381 2758 2851 3269 2165 2444 3055 M17377 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES.html Glycosphingolipid biosynthesis - lacto and neolacto series 14/26 KEGG 2.57654824651539e-07 8.26175796437001e-07 4655 2946.09090909091 2854 2.34231686206366e-08 1220 2.4140452030544 2.45138874481996 1 5.85549030839656 4651 2854 1487 2775 1220 4091 3891 4176 1693 1529 4040 3056 M15837 CHANG_IMMORTALIZED_BY_HPV31_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_IMMORTALIZED_BY_HPV31_UP.html Genes up-regulated in normal keratinocytes immortalized by infection with the high risk HPV31 (human papilloma virus) strain. 10756030 85/128 John Newman 3.12935950069215e-07 8.91404758193539e-07 4125 3100.81818181818 2854 2.84487267802149e-08 1210 1.91779057175937 1.82144378110036 1 4.61603903969717 4125 1626 2525 2820 1427 3855 4462 4499 1210 2854 4706 3057 M8924 WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP.html Genes up-regulated in esophageal adenocarcinoma (EAC) and Barret's esophagus (BE) relative to normal esophagi. 16449976 44/59 Leona Saunders 1.36073901614861e-07 7.20206492018647e-07 435 2371.63636363636 2855 1.23703554573886e-08 355 2.84770925480681 2.97362996294104 1 6.98464537597826 2677 460 355 431 2921 4053 3651 4650 2855 435 3600 3058 M2357 RAFFEL_VEGFA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAFFEL_VEGFA_TARGETS_UP.html Genes up-regulated in hearts of E18.5 embryos upon knockout of VEGFA [GeneID=7422]. 18981216 13/14 Arthur Liberzon 1.50269038497721e-05 1.80554019848169e-05 2515 2869.18181818182 2856 1.36609149915278e-06 1735 1.9385281824056 1.9083555303597 1 3.64791991313714 2513 2424 2000 2856 3869 3211 3403 3369 3453 1735 2728 3059 M17434 LIN_APC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LIN_APC_TARGETS.html Genes up-regulated by forced expression of APC [GeneID=324] in the APC-deficient SW480 cell line (colon cancer). 11522623 121/156 Yujin Hoshida 9.35103601193524e-08 6.56798957981166e-07 3790 2663.36363636364 2857 8.50094219036211e-09 69 1.94099334746569 -1.77088734969953 -1 4.77603231606734 3787 69 2238 2169 274 4698 4440 4012 1259 2857 3494 3060 M3993 PARK_APL_PATHOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARK_APL_PATHOGENESIS_UP.html Genes up-regulated in U937 cells (acute promyelocytic leukemia, APL) expressing RARA [GeneID=5914] fused with either PML or PLZF [GeneID=5371;7704]. 12893766 11/18 Arthur Liberzon 1.2767983846881e-07 7.20206492018647e-07 3185 2561 2857 1.16072587162614e-08 471 1.68543266202608 1.94114595342032 1 4.11347906960415 3182 2890 2857 4177 471 2099 2206 2488 1297 3306 3198 3061 M10122 REACTOME_RETROGRADE_NEUROTROPHIN_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RETROGRADE_NEUROTROPHIN_SIGNALLING.html Genes involved in Retrograde neurotrophin signalling 17/19 Reactome 1.49047080608787e-06 2.37669669078877e-06 4310 2912.27272727273 2858 1.3549743780573e-07 553 1.75671091648634 -0.920146971973212 -1 3.92323478838144 4309 910 2639 2656 2858 4298 4323 3317 553 3944 2228 3062 M1604 JACKSON_DNMT1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JACKSON_DNMT1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon Cre-lox knockout of DNMT1 [GeneID=1786]. 11137995 131/165 John Newman 4.10685047247808e-07 1.00046055710989e-06 4470 2765.81818181818 2859 3.73350112647698e-08 1102 1.7756281486942 -1.44781440463968 -1 4.23435730787955 4470 2109 1965 1751 1736 3343 3067 2859 3855 1102 4167 3063 M2031 RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_DN.html Genes down-regulated in the brain cortex of mice that were exposed to an enriched learning environment for one day. 11070096 14/16 Arthur Liberzon 2.32560533902922e-06 3.43886503766226e-06 3220 2303.90909090909 2859 2.1141889067407e-07 59 2.73989577904689 2.42481096685512 1 5.97018322744527 3217 2859 1858 1372 3116 3021 2890 138 59 2366 4447 3064 M1433 MA_MYELOID_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/MA_MYELOID_DIFFERENTIATION_DN.html Genes down-regulated during myeloid differentiation induced by tretinoin (ATRA) [PubChem=444795] and IL3 [GeneID=3652] in the EML cell line (myeloid progenitor). 12130493 55/71 Kevin Vogelsang 5.19973367002444e-07 1.1351884743169e-06 3015 2900.27272727273 2861 4.72703172635442e-08 1218 1.91150260223022 -1.46193359681259 -1 4.52002850159693 3011 3921 2493 3509 1984 2114 1218 4484 3905 2861 2403 3065 M140 PID_RANBP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RANBP2_PATHWAY.html Sumoylation by RanBP2 regulates transcriptional repression 18832364 15/19 Pathway Interaction Database 4.4670287886609e-05 5.06349084593647e-05 2180 2860.90909090909 2863 4.06101772073904e-06 906 0.876487837999934 0.910028593905867 1 1.46410035777064 2180 2863 3721 3213 4115 2357 1686 906 4364 4058 2007 3066 M4306 ONDER_CDH1_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_2_DN.html Genes down-regulated in HMLE cells (immortalized nontransformed mammary epithelium) after E-cadhedrin (CDH1) [GeneID=999] knockdown by RNAi. 18483246 600/793 Jessica Robertson 4.44779750523203e-42 1.2349178955703e-39 2950 2027.27272727273 2863 4.44779750523203e-43 5 2.63226423454732 -2.4142982618405 -1 41.1381885339693 2947 1117 4470 5 289 3032 2863 3707 987 10 2873 3067 M2377 IKEDA_MIR133_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR133_TARGETS_UP.html Genes up-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-133 microRNA. 19188439 66/94 Arthur Liberzon 2.67891426016845e-06 3.85502295975459e-06 1715 2378.63636363636 2864 2.43537956568778e-07 652 1.7670809446748 2.19592822414186 1 3.79741461129822 1711 2642 3084 2898 3205 2864 3664 652 911 3807 727 3068 M2609 ZWANG_EGF_PERSISTENTLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_PERSISTENTLY_UP.html Genes persistently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 32/40 Yaara Zwang 3.28560938635213e-07 9.05922275783096e-07 3135 2539.54545454545 2864 2.98691807004042e-08 671 1.56406583993769 1.45991054070732 1 3.75099673502578 3134 671 2864 2325 1490 3313 3223 3981 850 1862 4222 3069 M1225 OXFORD_RALA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_TARGETS_UP.html Genes up-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALA [GeneID=5898] by RNAi. 17496927 12/14 Arthur Liberzon 5.11988383441784e-07 1.12712781758131e-06 3880 2882.81818181818 2866 4.65444093266163e-08 1494 2.52388546864067 1.24175191976756 1 5.98726921337218 3876 2426 1494 2196 1969 2866 3260 4402 3747 1548 3927 3070 M3278 DE_YY1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DE_YY1_TARGETS_DN.html Genes down-regulated in SaOS-2 cells (osteosarcoma) upon knockdown of YY1 [GeneID=7528] by RNAi. 18339860 146/162 Jessica Robertson 1.89363191090176e-07 7.49827400961101e-07 2565 2518.18181818182 2866 1.72148370354054e-08 590 1.97429864948722 1.99904548674748 1 4.81316516606081 2565 2983 2547 1292 898 3354 3545 3371 590 2866 3689 3071 M11911 KEGG_ABC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ABC_TRANSPORTERS.html ABC transporters 35/50 KEGG 5.9251407453653e-06 7.67050584698963e-06 3205 2758.63636363636 2868 5.38650609389623e-07 1528 2.49675351026732 -1.75993058646451 -1 5.08610343053056 3204 1789 1528 3837 3581 4430 3473 1932 1803 1900 2868 3072 M1389 BIOCARTA_SPRY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SPRY_PATHWAY.html Sprouty regulation of tyrosine kinase signals 28/30 BioCarta 1.51458853111181e-06 2.40864483384359e-06 2595 2784.63636363636 2869 1.37689961257298e-07 1105 1.64942342830766 -1.59655577231814 -1 3.67672873427459 2592 3991 3096 1105 2869 2844 1887 3601 3030 3778 1838 3073 M15122 OZEN_MIR125B1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OZEN_MIR125B1_TARGETS.html Potential targets of MIR125B1 [GeneID=406911] microRNA which are up-regulated in prostate cancer. 17891175 39/45 Jessica Robertson 1.51606773194595e-06 2.41018514475745e-06 3510 2824.27272727273 2870 1.37824434245647e-07 1491 1.67911836336459 -1.87637007163268 -1 3.74363504223686 3510 1760 2676 2379 2870 4440 3179 3440 1491 2918 2404 3074 M9334 VALK_AML_CLUSTER_11 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_11.html Top 40 genes from cluster 11 of acute myeloid leukemia (AML) expression profile; 67% of the samples are FAB M4 or M5. 15084694 57/75 Jessica Robertson 1.53915636467535e-06 2.43622335387917e-06 3275 2296.63636363636 2870 1.39923403772331e-07 390 2.43509890333519 2.38204376462063 1 5.44706981625009 3273 390 828 1182 2883 2870 4001 4215 1561 914 3146 3075 M2503 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_OLD http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_OLD.html Human environmental stress response (H-ESR) genes not changed in primary fibroblasts from old donors in response to gamma radiation. 15897889 36/42 Jessica Robertson 4.5986564517677e-07 1.05469671780095e-06 4660 3076.09090909091 2871 4.180597648204e-08 1100 1.90549873617641 -1.42301104971382 -1 4.53015081998474 4656 1775 2653 1930 1878 4494 4380 4067 1100 2871 4033 3076 M18424 FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP.html Genes up-regulated early in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 29/33 Arthur Liberzon 1.29527790631807e-05 1.57286126005179e-05 2010 2573.36363636364 2872 1.17753230226719e-06 627 1.7267643204484 -1.53206072835807 -1 3.2855653948514 2009 3727 2872 4425 3830 1388 1456 627 3578 3353 1042 3077 M4976 DIRMEIER_LMP1_RESPONSE_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DIRMEIER_LMP1_RESPONSE_LATE_UP.html Cluster 3: genes up-regulated in B2264-19/3 cells (primary B lymphocytes) within 60-180 min after activation of LMP1 (an oncogene encoded by Epstein-Barr virus, EBV). 15674340 71/89 Arthur Liberzon 6.64577875048483e-07 1.32603226979258e-06 2105 2886.72727272727 2873 6.04161887095289e-08 1273 1.64513805018465 -1.63253692713483 -1 3.83854823626687 2101 3899 2873 3969 2218 2553 1273 3389 3570 2840 3069 3078 M12812 GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_DN.html Genes down-regulated in common hematopoietic progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 92/122 Arthur Liberzon 2.54308355299683e-07 8.22189102913976e-07 2765 2958.27272727273 2874 2.3118944063308e-08 1207 1.45648604263211 1.45360757447014 1 3.51422451693395 2761 3019 3648 3531 1207 2791 2874 2758 2854 3621 3477 3079 M9070 BIOCARTA_CREB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CREB_PATHWAY.html Transcription factor CREB and its extracellular signals 42/45 BioCarta 1.14655768226002e-07 7.06112554001409e-07 2880 2427.45454545455 2876 1.04232522001302e-08 385 1.18096187970034 1.22931344723032 1 2.87136374582312 2876 556 3535 514 385 2876 4033 3002 2427 3837 2661 3080 M4902 LUI_THYROID_CANCER_PAX8_PPARG_DN http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_PAX8_PPARG_DN.html Top down-regulated genes distinguishing between follicular thyroid carcinoma (FTC) samples by the presence or absence of the PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 61/83 Leona Saunders 2.00619738352103e-07 7.65527859584926e-07 2410 2795.90909090909 2877 1.82381596951616e-08 938 1.51529676615463 -1.82472211018706 -1 3.67704181400814 2407 4497 3631 2966 938 2715 2877 1669 3388 4101 1566 3081 M6822 ONDER_CDH1_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_1_DN.html Genes down-regulated in HMLE cells (mmortalized nontransformed mammary epithelial) by expression of a dominant-negative form of E-cadhedrin (CDH1) [GeneID=999]. 18483246 212/280 Jessica Robertson 1.3524221350864e-06 2.20554838244808e-06 2880 2712.18181818182 2877 1.22947542406499e-07 820 2.45091960692858 2.35031553710826 1 5.52536548913124 2877 3296 820 1683 2782 3181 3947 3109 1913 2223 4003 3082 M12827 BOQUEST_STEM_CELL_CULTURED_VS_FRESH_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_CULTURED_VS_FRESH_DN.html Genes down-regulated in cultured stromal stem cells from adipose tissue, compared to the freshly isolated cells. 15635089 35/44 Arthur Liberzon 1.27215371346254e-07 7.19819980220572e-07 2880 2363.09090909091 2877 1.15650344275004e-08 469 3.21534981969518 -3.03506564782084 -1 7.89312756850606 2880 1781 529 2262 469 3971 3275 3703 2877 880 3367 3083 M13077 WANG_RECURRENT_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RECURRENT_LIVER_CANCER_DN.html Genes down-regulated in samples from patients with recurrent hepatocellular carcinoma (HCC). 17975138 16/21 Yujin Hoshida 0.000532771201702631 0.000561688646869872 940 2592 2878 4.84454787260431e-05 199 1.98383066345208 -1.52187179034602 -1 2.54328220493597 940 4605 2878 4229 4446 887 199 1184 3742 3166 2236 3084 M6267 ZAIDI_OSTEOBLAST_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/ZAIDI_OSTEOBLAST_TRANSCRIPTION_FACTORS.html An assortment of osteoblast transcriptional regulators. 17618270 13/16 Jessica Robertson 3.05344405999839e-07 8.80936447462993e-07 2875 2900.45454545455 2879 2.77585862163169e-08 1408 1.97729257335763 -1.62346784008677 -1 4.76488988100458 2873 2879 2026 4171 1408 3068 1641 3401 4082 2172 4184 3085 M14079 BENPORATH_ES_CORE_NINE_CORRELATED http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_CORE_NINE_CORRELATED.html Breast cancer compendium: 100 transcription regulators showing most correlated expression with the 9 'embryonic stem cell' transcription factors that are preferentially and coordinately overexpressed in the high-grade, ER-negative breast cancer tumors. 18443585 117/141 Jessica Robertson 1.53441303437445e-06 2.43034905384331e-06 2405 2842.36363636364 2880 1.39492191324358e-07 2057 1.50597595769911 1.50661993188049 1 3.35025889441732 2405 2123 3420 2474 2880 2057 3312 3728 2892 2780 3195 3086 M2378 IKEDA_MIR133_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR133_TARGETS_DN.html Genes down-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-133 microRNA. 19188439 9/11 Arthur Liberzon 0.00130416385093459 0.00135856397625497 4665 3097.45454545455 2880 0.000130492986322132 519 2.20033558146758 3.12714340776377 1 2.4868732695032 4662 2456 4694 2636 4503 3557 2658 2044 519 3463 2880 3087 M1990 WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_DN.html Selected genes with immunologic function which were reciprocally changed in evasion and tolerogenic tumor models. 18381452 17/27 Arthur Liberzon 4.81394545246872e-06 6.39151126178688e-06 2370 3058.09090909091 2881 4.37632362379049e-07 1283 1.64324838425871 -1.58179427529011 -1 3.38268741308821 2370 2847 2824 3935 3488 2109 1283 3368 4439 2881 4095 3088 M2269 MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_DN.html Proteins significantly repressed by oxidative stress (hydrogen peroxide [PubChem=784] in 786-O cells (renal clear cell carcinoma, RCC) expressing VHL [GeneID=7428]. 18285459 12/14 Arthur Liberzon 5.24332282132207e-08 5.22119909633759e-07 3955 2654.63636363636 2881 4.76665722389788e-09 64 1.88793548405067 1.46456764519112 1 4.71977874121701 3955 2881 2555 4161 64 3140 2466 859 2639 2976 3505 3089 M15371 BIOCARTA_ETC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETC_PATHWAY.html Electron Transport Reaction in Mitochondria 13/16 BioCarta 0.000358968116279444 0.000382035965916342 1055 2858.63636363636 2883 3.26387910482056e-05 1052 0.765633142787549 0.812831551652167 1 1.00236125727813 1052 2883 3667 3975 4402 1065 1186 2390 4118 4375 2332 3090 M3447 AMIT_SERUM_RESPONSE_60_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_60_MCF10A.html Genes whose expression peaked at 60 min after stimulation of MCF10A cells with serum. 17322878 76/82 Leona Saunders 2.17894750675083e-07 7.76784911772201e-07 3515 2640.81818181818 2884 1.9808615659641e-08 763 2.13917019758232 -2.07460127749382 -1 5.20608951083567 3511 2620 1192 3117 1043 2884 2362 3643 3509 763 4405 3091 M2184 KAPOSI_LIVER_CANCER_MET_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAPOSI_LIVER_CANCER_MET_DN.html Selected down-regulated MET [GeneID=4233] target genes from a classifier of hepatocellular carcinoma (HCC) cases; associated with poor survival. 16710476 9/10 Yujin Hoshida 1.62112588437076e-05 1.93567269775613e-05 3600 2948.45454545455 2884 1.62113771071328e-06 1488 2.55874151944015 -2.66193926549785 -1 4.79994338714518 3596 1963 4622 1488 3918 3741 4573 1792 2884 2325 1531 3092 M1284 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6.html Cluster PAM6: genes changed exclusively in normal liver tissue adjacent to hepatocellular carcinoma (HCC) from mice deficient for TXNIP [GeneID=10628]. 16607285 50/57 Leona Saunders 8.86627054044224e-07 1.61204918917132e-06 4220 3038.36363636364 2886 8.06024919423665e-08 1708 1.88961626234326 2.10731582823203 1 4.35195676142242 4219 2664 2060 1801 2472 4716 4271 3383 3242 1708 2886 3093 M19681 FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP.html Genes upregulated in peripheral blood lymphocytes (PBL) from patients with well functioning kidneys more than 1-year post transplant compared to those from normal living kidney donors. 15307835 196/253 Jean Junior 1.41920037820757e-06 2.28883831480239e-06 2890 2969.54545454545 2886 1.29018299429264e-07 843 1.44525207913507 1.68774679455163 1 3.22829531262045 2886 4706 4019 2552 2818 2888 3832 843 1951 4566 1604 3094 M11695 STOSSI_RESPONSE_TO_ESTRADIOL http://www.broadinstitute.org/gsea/msigdb/cards/STOSSI_RESPONSE_TO_ESTRADIOL.html Genes up-regulated by estradiol (E2) [PubChem=5757] in U2OS cells (osteosarcoma) expressing ESR1 or ESR2 [GeneID=2099;2100]. 15033914 61/92 Kevin Vogelsang 1.00243357626329e-07 6.71132834037269e-07 4315 2435 2887 9.11303292672134e-09 312 2.53251550692935 2.44142208607674 1 6.23723871794413 4312 371 631 1836 312 4497 3693 4334 2887 529 3383 3095 M18631 ROME_INSULIN_TARGETS_IN_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROME_INSULIN_TARGETS_IN_MUSCLE_DN.html Genes down-regulated by 3 h of euglycemic hyperinsulinemic clamp in the vastus lateralis muscle of healthy lean subjects. 12621037 214/353 Jessica Robertson 2.0123158449218e-07 7.65527859584926e-07 3035 2722.18181818182 2887 1.82937820816922e-08 946 2.0108278423379 -1.7280054337569 -1 4.89586805454048 3031 3294 2432 2790 946 2887 2896 3800 1915 2330 3623 3096 M6520 BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_UP.html Genes up-regulated in patients at the incipient stage of Alzheimer's disease. 14769913 584/826 John Newman 4.78020700683511e-07 1.08317700778981e-06 1820 2997.72727272727 2888 4.78020803510247e-08 1817 1.71564455482651 -1.50208410689413 -1 4.06582005451171 1817 3552 4488 2707 1996 2034 1950 4651 2888 3205 3687 3097 M14532 ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY.html PI3K Pathway 46/55 Signaling Transduction KE 2.58563910013158e-07 8.26284126785448e-07 4020 2863.54545454545 2890 2.35058127638121e-08 1228 1.4910916385877 -1.8293890876594 -1 3.59761623851487 4017 2251 3284 1741 1228 4409 2976 2501 2166 4036 2890 3098 M321 KEGG_CHRONIC_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHRONIC_MYELOID_LEUKEMIA.html Chronic myeloid leukemia 83/90 KEGG 1.30706175301463e-07 7.20206492018647e-07 3205 2410.90909090909 2893 1.18823802788151e-08 495 1.45884690516304 -1.42475797366112 -1 3.5537453584976 3203 1623 3266 673 495 3630 2893 3491 1031 3467 2748 3099 M31 PID_BETA_CATENIN_DEG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BETA_CATENIN_DEG_PATHWAY.html Degradation of beta catenin 18832364 24/26 Pathway Interaction Database 6.97812265736203e-07 1.37020858278925e-06 3500 3045.81818181818 2893 6.34374988248686e-08 1404 1.6621408237705 2.07754962270893 1 3.8692236438667 3499 2792 2735 2678 2257 3825 4235 3772 1404 3414 2893 3100 M3471 AMIT_EGF_RESPONSE_120_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_120_MCF10A.html Genes whose expression peaked at 120 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 59/73 Leona Saunders 2.17697660224981e-06 3.25374590329927e-06 1870 2832.54545454545 2893 1.97907159676995e-07 1867 2.2570351940227 2.40371700423113 1 4.93103377844701 1867 3910 1941 3982 3078 2893 2993 1957 3442 2733 2362 3101 M700 REACTOME_ACYL_CHAIN_REMODELLING_OF_PG http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PG.html Genes involved in Acyl chain remodelling of PG 9/18 Reactome 0.000102772215108888 0.000112731781388322 1205 2599.45454545455 2894 1.02776968375966e-05 362 1.91510013291667 -2.18621198461764 -1 2.99059708205527 1203 3807 4219 4379 4277 791 362 972 4476 2894 1214 3102 M10839 BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN.html Down-regulated genes in MDA-MB-435 cells (breast cancer) undergoing G2/M arrest after treatment with 2-methoxyestradiol (2ME2) [PubChem=1573]. 17234781 183/294 Jessica Robertson 1.56122239696391e-06 2.4628909470821e-06 630 2046.27272727273 2894 1.41929409534644e-07 15 1.70058302011182 -1.64579212880112 -1 3.78570547862967 626 3304 3067 4388 2894 73 769 744 3230 3399 15 3103 M2534 PECE_MAMMARY_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PECE_MAMMARY_STEM_CELL_UP.html The '3/3 signature': genes consistently up-regulated in all three pools of normal mammary stem cells (defined by their ability to retain the dye PKH26). 20074520 188/297 Arthur Liberzon 7.94543172829982e-08 6.29674606547497e-07 2895 2450.54545454545 2894 7.22312001386715e-09 182 2.31746128200887 2.95882145389653 1 5.72914967313404 2894 3859 1852 2187 182 3363 3801 1104 1163 3599 2952 3104 M9183 STEGMEIER_PRE-MITOTIC_CELL_CYCLE_REGULATORS http://www.broadinstitute.org/gsea/msigdb/cards/STEGMEIER_PRE-MITOTIC_CELL_CYCLE_REGULATORS.html Pre-mitotic cell cycle regulators (CDC) identified in an shRNA screen of the ubiquitin pathway components. 17443180 10/12 Jessica Robertson 9.06230665683204e-08 6.55310251195451e-07 2515 2475.72727272727 2895 8.23846093648121e-09 249 1.50488213089966 1.55886200675437 1 3.69228549194604 2514 1010 2900 3853 249 3085 3732 2173 2895 3109 1713 3105 M3873 BIOCARTA_CHEMICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CHEMICAL_PATHWAY.html Apoptotic Signaling in Response to DNA Damage 29/34 BioCarta 3.44654717265001e-06 4.78602608264432e-06 3505 2812.90909090909 2896 3.13322961096838e-07 481 1.75407804690371 2.05989583902222 1 3.70283036412176 3504 2328 2896 1543 3325 2547 2582 3884 481 3610 4242 3106 M12363 REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE_FROM_THE_C_STRAND http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE_FROM_THE_C_STRAND.html Genes involved in Removal of the Flap Intermediate from the C-strand 10/11 Reactome 0.000137577241916511 0.000149347879909368 1370 2720.72727272727 2899 1.25078041888872e-05 921 1.31028580790807 1.4647738950673 1 1.96595601731372 1366 2899 2999 3412 4308 1447 921 2786 4124 2542 3124 3107 M1299 GROSS_ELK3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_ELK3_TARGETS_DN.html Genes down-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 47/58 Jessica Robertson 9.22334242264982e-08 6.56798957981166e-07 4075 2549.36363636364 2900 8.38485709939261e-09 262 2.56592380781021 2.53562421163681 1 6.32985414165552 4071 1730 887 3322 262 3895 3546 1708 2900 1270 4452 3108 M7813 PETRETTO_BLOOD_PRESSURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_BLOOD_PRESSURE_DN.html Genes that are most strongly negatively correlated with systolic blood pressure (SBP). 18443592 10/14 Jessica Robertson 1.55146610517609e-06 2.45159692548749e-06 2940 2883.45454545455 2901 1.4104247266268e-07 1614 0.969180514659503 -0.810634333585712 -1 2.13677175180349 2939 2901 3574 3472 2889 3539 2527 1614 1934 3988 2341 3109 M8910 LY_AGING_OLD_UP http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_OLD_UP.html Genes up-regulated in fibroblasts from old individuals, compared to those from young donors. 10741968 9/11 Arthur Liberzon 1.06347677971758e-05 1.31326183035636e-05 1130 2711.45454545455 2902 1.06348186917473e-06 158 3.39616230737316 3.39616230737316 1 6.61734904181872 1127 4633 4650 4213 4203 1037 1205 158 4429 2902 1269 3110 M1060 REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM.html Genes involved in Cytokine Signaling in Immune system 294/406 Reactome 1.59371683371087e-06 2.50494287549628e-06 1820 3116 2903 1.448834534752e-07 1818 1.64688252178674 -1.68523994172897 -1 3.65971180107357 1818 4137 3552 3601 2903 2840 2513 2694 3681 3728 2809 3111 M1334 HASEGAWA_TUMORIGENESIS_BY_RET_C634R http://www.broadinstitute.org/gsea/msigdb/cards/HASEGAWA_TUMORIGENESIS_BY_RET_C634R.html Genes up-regulated in salivary, thyroid and mammary gland carcinomas developed in transgenic mice carrying RET [GeneID=5979] allele with the MEN2A mutation (C634R). 18542059 32/35 Jessica Robertson 1.96806718849528e-06 2.98306908468135e-06 2695 2718.90909090909 2903 1.78915359007559e-07 430 2.9674172176129 2.73600720999269 1 6.54379688705512 2692 1784 430 884 3879 4097 4207 4355 2903 557 4120 3112 M1335 CAFFAREL_RESPONSE_TO_THC_8HR_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_3_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 9/10 Jessica Robertson 3.82206826354894e-06 5.23510220660214e-06 2575 2682.18181818182 2903 3.82207483725747e-07 757 1.10813018056038 -1.3314496097712 -1 2.30346042463945 2574 2458 4437 2925 3411 1567 757 2903 3752 3460 1260 3113 M1766 TESAR_JAK_TARGETS_MOUSE_ES_D3_DN http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_JAK_TARGETS_MOUSE_ES_D3_DN.html Genes down-regulated in mES cells (mouse embryonic stem cells) after tratment with JAK inhibitor I [PubChem=5494425]. 17597760 9/15 Jessica Robertson 0.000182161676404678 0.000196302080509151 4355 2935 2904 1.82176610421988e-05 514 2.81065101712853 -2.61263671796439 -1 4.1402034540083 4351 2904 4527 1832 4349 4100 2543 1117 514 2323 3725 3114 M62 PID_EPHB_FWD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHB_FWD_PATHWAY.html EPHB forward signaling 18832364 66/76 Pathway Interaction Database 1.68061511305263e-07 7.33971845416521e-07 4585 2906.54545454545 2905 1.52783203767047e-08 760 1.74885113312031 -1.51212342589353 -1 4.26435845156731 4583 2194 2802 1547 760 4286 2905 4245 787 3652 4211 3115 M747 REACTOME_METABOLISM_OF_POLYAMINES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_POLYAMINES.html Genes involved in Metabolism of polyamines 16/17 Reactome 4.16976741177715e-07 1.00504816968881e-06 2905 2854.63636363636 2905 3.79069836553976e-08 1764 1.673309217284 1.65827816769433 1 3.98613596485903 2905 3207 3153 3707 1764 2795 2469 2991 3957 2278 2175 3116 M10783 HOFMANN_CELL_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_CELL_LYMPHOMA_UP.html Genes up-regulated in lymph nodes from patients with mantle cell lymphoma (MCL) compared to the non-malignant hyperplastic lymph nodes. 11468180 73/116 Kevin Vogelsang 3.48611263740362e-07 9.30654820258927e-07 3065 2730.81818181818 2906 3.16919380891999e-08 1518 1.73078177867728 -1.8061041172457 -1 4.14801196427828 3061 2176 2913 1518 1548 3881 3532 2906 1839 2755 3910 3117 M14636 OUYANG_PROSTATE_CANCER_PROGRESSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUYANG_PROSTATE_CANCER_PROGRESSION_DN.html Genes down-regulated during prostate cancer progression in mice heterozygotic for both NKX3.1 and PTEN [GeneID=4824;5728]. 18381418 25/28 Jessica Robertson 1.1223196396748e-06 1.91309089897618e-06 4120 2760.63636363636 2906 1.02029110201935e-07 1166 1.63203874906396 -1.03977022961858 -1 3.7031079017474 4117 3453 2989 2906 2645 3176 1605 1166 2679 3213 2418 3118 M2364 PURBEY_TARGETS_OF_CTBP1_AND_SATB1_UP http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_AND_SATB1_UP.html Genes up-regulated in HEK-293 cells (fibroblast) upon knockdown of both CTBP1 and SATB1 [GeneID=1487, 6304] by RNAi. 19103759 154/216 Arthur Liberzon 1.57447033592869e-06 2.48047396047511e-06 4395 3211.18181818182 2906 1.43133769338944e-07 1106 1.98419117160443 -1.40541076289409 -1 4.42293130721374 4395 3309 1787 1106 2897 4645 4297 4221 2906 2855 2905 3119 M1423 ABBUD_LIF_SIGNALING_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_1_DN.html Genes down-regulated in AtT20 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 31/42 Kevin Vogelsang 4.6425330023361e-07 1.06166452379004e-06 4305 2720 2907 4.22048543820303e-08 679 1.92647933229715 1.77107917548489 1 4.57836564726586 4301 679 2192 3384 1886 3149 1733 3705 2907 1993 3991 3120 M1511 GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN.html Genes down-regulated in glioblastoma cell lines displaying spherical growth (cluster-1) compared to those displaying semiadherent or adherent growth phenotype (cluster-2). 18037961 31/34 Jessica Robertson 1.48861655617608e-06 2.37454212407945e-06 3215 2755.27272727273 2910 1.35328869403666e-07 1392 2.45541877778556 3.06255881256101 1 5.5039385911553 3214 3128 2119 3151 2857 2742 3367 2482 1392 2946 2910 3121 M19509 MORI_PLASMA_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PLASMA_CELL_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: plasma cell. 18922927 41/60 Jessica Robertson 6.50856870050341e-07 1.30791290081906e-06 2495 2900.81818181818 2910 5.91688238729583e-08 2195 1.93050193385612 1.88717834689891 1 4.51769713803014 2491 3403 2682 3391 2195 2677 3721 2910 2970 3122 2347 3122 M17541 REACTOME_REGULATION_OF_BETA_CELL_DEVELOPMENT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_BETA_CELL_DEVELOPMENT.html Genes involved in Regulation of beta-cell development 8/32 Reactome 1.05742870468781e-05 1.30656112202263e-05 1625 2552.90909090909 2911 1.0574337364211e-06 491 1.78037220653984 1.69772070550237 1 3.44680136141018 1621 2911 4225 2452 3798 1045 491 3765 2995 3278 1501 3123 M11585 NAGASHIMA_NRG1_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAGASHIMA_NRG1_SIGNALING_UP.html Genes up-regulated in MCF7 cells (breast cancer) after stimulation with NRG1 [GeneID=3084]. 17142811 231/284 Arthur Liberzon 3.67757860915915e-07 9.51132659464723e-07 4405 2850.54545454545 2912 3.34325383992103e-08 749 2.12880056038425 -1.88243849689906 -1 5.10532278090457 4405 2529 861 1502 1613 4191 3420 4716 2912 749 4458 3124 M14582 REACTOME_P75NTR_RECRUITS_SIGNALLING_COMPLEXES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P75NTR_RECRUITS_SIGNALLING_COMPLEXES.html Genes involved in p75NTR recruits signalling complexes 16/19 Reactome 4.87309167012227e-06 6.4518913556738e-06 1585 2517.45454545455 2914 4.4300931493244e-07 380 1.7002045928086 -1.2631675423661 -1 3.49887608155332 1581 3768 2914 3483 3498 1036 380 2679 4075 3554 724 3125 M14966 REACTOME_REGULATION_OF_GENE_EXPRESSION_IN_BETA_CELLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_GENE_EXPRESSION_IN_BETA_CELLS.html Genes involved in Regulation of gene expression in beta cells 6/22 Reactome 5.16303871053501e-06 6.78628312829998e-06 1170 2290.72727272727 2914 5.16305070621016e-07 135 1.94696773639916 1.94696773639916 1 3.9967730652024 1166 2923 4227 2914 3560 667 135 3561 1701 3475 869 3126 M1216 LI_WILMS_TUMOR_ANAPLASTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_ANAPLASTIC_DN.html Selected down-regulated genes distinguishing between Wilms tumors of different histological types: anaplastic vs favorable histology. 15531917 11/19 Leona Saunders 0.0660751206083314 0.0666256289834061 4650 3229.27272727273 2914 0.0061952094163564 1885 1.53166058527413 -1.98345520293377 -1 0.674570539461876 1957 3522 2662 2724 4650 2815 1885 2914 4649 3721 4023 3127 M2416 WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_36HR http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_36HR.html Genes with promoters bound by PPARG [GeneID=5468] at 36 h time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 35/37 Arthur Liberzon 8.23262582248736e-07 1.52924021574736e-06 3170 3081.18181818182 2915 7.48420809383823e-08 2300 1.43966305423617 1.5544683097502 1 3.31701920170349 3168 2300 3419 4211 2407 2821 2915 2331 2810 3603 3908 3128 M11268 WHITE_NEUROBLASTOMA_WITH_1P36.3_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/WHITE_NEUROBLASTOMA_WITH_1P36.3_DELETION.html Genes within the smallest region of consistend deletion (SRD) within 1p36.3 area across a large collection of neuroblastoma cell lines and biopsy samples. 15829979 21/23 Leona Saunders 1.6268242039095e-06 2.54784545095499e-06 2825 2758.72727272727 2916 1.4789321880829e-07 1371 1.45820640886882 1.84803755686647 1 3.23037701451542 2825 2805 3050 3362 2916 3605 3621 1586 1470 3735 1371 3129 M18562 MANALO_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANALO_HYPOXIA_DN.html Genes down-regulated in response to both hypoxia and overexpression of an active form of HIF1A [GeneID=3091]. 15374877 336/395 Kate Stafford 2.93146978989145e-06 4.15013119624705e-06 140 2433.54545454545 2916 2.66497608731089e-07 136 1.41521795222201 1.40033926942237 1 3.01307349430907 136 3847 4051 3026 3262 670 600 1696 2916 4263 2302 3130 M850 REACTOME_PI_3K_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI_3K_CASCADE.html Genes involved in PI-3K cascade 44/61 Reactome 7.08963438840848e-07 1.38048986440957e-06 2635 3038.09090909091 2917 6.44512424826137e-08 1503 1.11827642518543 -0.839591310586529 -1 2.58535333661404 2631 3099 3806 4304 2278 1784 1503 2917 4120 4434 2543 3131 M7429 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_DN.html Genes down-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 40/64 Arthur Liberzon 1.70814302657728e-06 2.65473661028803e-06 2985 2365.54545454545 2918 1.55285850257264e-07 546 2.19968269342233 2.39953249545372 1 4.88262971115686 2985 546 1356 1412 2939 3012 3971 2352 2918 1449 3081 3132 M1689 YANG_MUC2_TARGETS_DUODENUM_6MO_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_DUODENUM_6MO_UP.html Genes up-regulated in duodenum of 6 month old MUC2 [GeneID=4583] knockout mice. 18794118 7/16 Jessica Robertson 0.000330256487353317 0.000351955434704822 990 2780.27272727273 2918 3.30305578828068e-05 170 2.34180916002933 -2.34180916002933 -1 3.20243181950238 987 2918 4505 3364 4549 966 170 4683 4408 1812 2221 3133 M4399 MOHANKUMAR_TLX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOHANKUMAR_TLX1_TARGETS_UP.html Up-regulated in MCF7 cells (breast cancer) by TLX1 (HOX11) [GeneID=3195]. 17213808 551/650 Arthur Liberzon 3.78747762143535e-07 9.60855544952602e-07 2920 2771.09090909091 2919 3.7874782669599e-08 1157 1.60763904432477 1.7126189146725 1 3.84035952441326 2919 1157 4399 1299 1762 2776 3377 3058 2357 3619 3759 3134 M9372 KAUFFMANN_DNA_REPLICATION_GENES http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_DNA_REPLICATION_GENES.html Genes involved in DNA replication, compiled manually by the authors. 17891185 144/171 Jessica Robertson 5.9121847575787e-06 7.6600362491824e-06 210 2145.54545454545 2919 5.37472785980713e-07 177 1.29100631197926 1.32814390947197 1 2.60603554348105 208 2984 3939 3554 3578 177 250 1034 3705 2919 1253 3135 M4175 FERRANDO_LYL1_NEIGHBORS http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_LYL1_NEIGHBORS.html Nearest neighbors of LYL1 [GeneID=4066], based on the close agreement of their expression profiles with that of LYL1 in pediatric T cell acute lymphoblastic leukemia (T-ALL). 12086890 15/18 Jean Junior 1.63975413742893e-06 2.56449288557474e-06 4360 2716.90909090909 2919 1.49068669055375e-07 429 2.21049421426081 2.19158855262904 1 4.92022631576368 4359 901 1563 1829 2919 3704 4241 4718 429 1355 3868 3136 M14301 REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA.html Genes involved in G beta:gamma signalling through PI3Kgamma 21/30 Reactome 3.20631964612844e-07 8.98683416254527e-07 3555 2782.81818181818 2922 2.91483646674849e-08 1457 1.63649422329218 -1.65878518997889 -1 3.92930717765937 3555 1888 2922 2698 1457 3133 2443 2393 2927 3731 3464 3137 M14036 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN.html Genes down-regulated in monocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 50/74 Arthur Liberzon 8.18348911548486e-06 1.02865695406361e-05 1590 2661.81818181818 2922 7.43956323302047e-07 1182 1.63366433304552 1.71659697999893 1 3.22688682034534 1587 3385 3030 4415 3698 1417 1770 1182 4227 2922 1647 3138 M19107 GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP.html Genes up-regulated in myeloid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 36/46 Arthur Liberzon 1.19471018757322e-07 7.06112554001409e-07 2925 3104.18181818182 2923 1.0861002295018e-08 414 2.06317273991711 2.08975942101767 1 5.05373022245796 2923 3703 2443 4576 414 3513 3757 4507 2757 2869 2684 3139 M7615 RIZKI_TUMOR_INVASIVENESS_2D_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_2D_DN.html Genes down-regulated in monolayer (2D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 71/112 Jessica Robertson 3.16761640213658e-07 8.94262307705344e-07 4040 2948.27272727273 2923 2.87965168928927e-08 1444 2.09071553774612 -2.07720177639273 -1 5.03560505358579 4039 1661 2035 2611 1444 4392 3918 3190 3618 2600 2923 3140 M1132 DARWICHE_SKIN_TUMOR_PROMOTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SKIN_TUMOR_PROMOTER_DN.html Genes down-regulated during skin tumor progression: epidermis treated with the carcinogen DMBA [PubChem=6001] followed by 20 weekly applications of the tumor promoter TPA [PubChem=4792], compared to the untreated skin. 17525749 236/344 Arthur Liberzon 4.45466460269944e-07 1.03729733225167e-06 4670 3135.27272727273 2925 4.04969591336488e-08 1839 1.94410731866046 -1.62849898068079 -1 4.62860137975787 4666 3290 2774 2717 1839 4177 4496 2194 2925 3374 2036 3141 M2021 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_2.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 2. 12554760 108/141 Arthur Liberzon 6.29221762532312e-07 1.27848761048322e-06 2645 2824.81818181818 2925 5.72019947723666e-08 1594 2.25050860121213 -1.78382138086449 -1 5.28380470723435 2641 3321 1594 3741 2168 3050 2281 3181 2469 2925 3702 3142 M11798 PARK_TRETINOIN_RESPONSE_AND_RARA_PLZF_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/PARK_TRETINOIN_RESPONSE_AND_RARA_PLZF_FUSION.html Genes up-regulated by tretinoin (ATRA) [PubChem=444795] in U937 cells (acute promyelocytic leukemia, APL) made resistant to the drug by expression of the PLZF-RARA fusion [GeneID=7704, 5914]. 12893766 33/41 Arthur Liberzon 1.99677347201454e-05 2.35090316485623e-05 2675 3034.63636363636 2926 1.81526508676926e-06 1341 1.66197003973542 -1.16117687051058 -1 3.04373979226205 2673 2760 2926 3173 3950 3498 4140 2216 4176 2528 1341 3143 M5872 KEGG_STEROID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_BIOSYNTHESIS.html Steroid biosynthesis 19/21 KEGG 3.23781911588176e-08 3.70934617159269e-07 2950 2399.54545454545 2928 2.94347196684901e-09 15 2.22653336777124 -2.85083530136696 -1 5.70818330764415 2950 1896 2201 2577 15 2946 2928 3604 451 3536 3291 3144 M1812 MATZUK_MATERNAL_EFFECT http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_MATERNAL_EFFECT.html Maternal effect genes, based on mouse models wih female fertility defects. 18989307 5/12 Jessica Robertson 4.1063663328737e-05 4.67149893737379e-05 2540 2990.36363636364 2928 4.10644221494724e-06 504 0.625977287410741 0.625977287410741 1 1.04015148769229 2537 2928 4567 4417 4117 1320 504 2145 4344 3889 2126 3145 M237 PID_VEGFR1_2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGFR1_2_PATHWAY.html Signaling events mediated by VEGFR1 and VEGFR2 18832364 106/133 Pathway Interaction Database 8.96255462333098e-08 6.54205957136183e-07 2935 2529.27272727273 2931 8.14777726223225e-09 116 1.45299681262178 -1.39736224633293 -1 3.5636857202974 2931 116 3426 671 242 3822 3100 2845 4078 3706 2885 3146 M13148 CHEN_HOXA5_TARGETS_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_6HR_DN.html Genes down-regulated 6 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 9/14 Arthur Liberzon 0.000417754967462608 0.000442803378940829 3240 2871.63636363636 2932 4.17833521892968e-05 1271 2.13879025928166 2.36220045598763 1 2.83468901638375 3238 3238 4578 1504 4428 3052 2045 2403 1271 2899 2932 3147 M755 REACTOME_REGULATION_OF_INSULIN_LIKE_GROWTH_FACTOR_IGF_ACTIVITY_BY_INSULIN_LIKE_GROWTH_FACTOR_BINDING_PROTEINS_IGFBPS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_LIKE_GROWTH_FACTOR_IGF_ACTIVITY_BY_INSULIN_LIKE_GROWTH_FACTOR_BINDING_PROTEINS_IGFBPS.html Genes involved in Regulation of Insulin-like Growth Factor (IGF) Activity by Insulin-like Growth Factor Binding Proteins (IGFBPs) 14/52 Reactome 2.68270716048098e-05 3.10885779461582e-05 2775 2704.72727272727 2935 2.43885443118343e-06 665 3.9342511922089 4.8267330508031 1 7.08159206941824 2771 1927 665 4135 4019 3543 4101 930 2935 1210 3516 3148 M985 REACTOME_NEGATIVE_REGULATORS_OF_RIG_I_MDA5_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEGATIVE_REGULATORS_OF_RIG_I_MDA5_SIGNALING.html Genes involved in Negative regulators of RIG-I/MDA5 signaling 38/48 Reactome 2.61332652173387e-06 3.77329494725722e-06 2185 2306.45454545455 2935 2.37575420549644e-07 123 1.59204470377807 -1.66962535710446 -1 3.42226793784506 2181 3412 3103 2935 3190 1456 1156 574 3644 3597 123 3149 M15671 WALLACE_PROSTATE_CANCER_RACE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_RACE_DN.html Genes down-regulated in prostate cancer samples from African-American patients compared to those from the European-American patients. 18245496 121/165 Jessica Robertson 4.10446766104231e-07 1.00046055710989e-06 2935 2894.45454545455 2935 3.73133493345413e-08 1673 1.67243124191123 -1.5436343289477 -1 3.9853545771836 2935 2117 3071 3697 1735 3119 3250 4631 2753 2858 1673 3150 M8467 JISON_SICKLE_CELL_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/JISON_SICKLE_CELL_DISEASE_UP.html Genes up-regulated in peripheral blood mononuclear cells (PBMC) from sickle cell disease patients compared to those from healthy subjects. 15031206 265/378 Jessica Robertson 6.8720695175035e-07 1.3548942407108e-06 1445 2464 2935 6.24733787646435e-08 1108 1.74938389246143 -1.67257638239308 -1 4.07837342684524 1441 3563 2935 3018 2246 1108 1557 2962 3305 3570 1399 3151 M266 PID_NCADHERIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NCADHERIN_PATHWAY.html N-cadherin signaling events 18832364 64/76 Pathway Interaction Database 1.63651335892588e-07 7.3358205358541e-07 4615 2703.18181818182 2937 1.48773952787379e-08 716 1.9782248730606 -1.55920837124119 -1 4.83040436823529 4612 1671 2118 890 716 4125 3615 4166 824 2937 4061 3152 M1929 MEISSNER_ES_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_ES_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in ES cells (embryonic stem). 18600261 37/56 Jessica Robertson 5.43894763829911e-07 1.16813306373779e-06 2665 3110.81818181818 2937 4.94449907540256e-08 2034 2.24719531843647 -2.16348533226967 -1 5.31138227061499 2665 4248 2489 4362 2034 2792 2937 2581 3404 3740 2967 3153 M921 REACTOME_IL_RECEPTOR_SHC_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_RECEPTOR_SHC_SIGNALING.html Genes involved in Interleukin receptor SHC signaling 30/37 Reactome 5.54259270728557e-07 1.18363725097921e-06 3250 3101.18181818182 2940 5.03872191242262e-08 2049 1.84341945034635 -1.6762372018427 -1 4.34379765739917 3248 2762 2269 2498 2049 3996 3662 2940 4164 2816 3709 3154 M1527 MCDOWELL_ACUTE_LUNG_INJURY_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCDOWELL_ACUTE_LUNG_INJURY_UP.html Genes up-regulated in the mouse model of acute lung injury induced by inhaling nickel sulfate [PubChem=24586]. 12540486 72/112 John Newman 1.71145248070298e-06 2.65900451248125e-06 3520 2655.81818181818 2940 1.55586710190881e-07 510 2.89096989175134 2.53387469656199 1 6.43199195522017 3519 2173 510 1240 2940 3923 3681 4018 1845 1013 4352 3155 M10620 REACTOME_EICOSANOID_LIGAND_BINDING_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EICOSANOID_LIGAND_BINDING_RECEPTORS.html Genes involved in Eicosanoid ligand-binding receptors 5/14 Reactome 6.31855249179301e-07 1.28218262086255e-06 3680 2938.81818181818 2941 6.31855428837847e-08 259 4.94683064381036 6.22637873617819 1 11.6717580099585 3680 2924 4240 3299 2252 3566 4584 2088 259 2494 2941 3156 M12676 FOSTER_TOLERANT_MACROPHAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_TOLERANT_MACROPHAGE_DN.html Class NT (non-tolerizeable) genes: induced during the first LPS stimulation and induced at equal or greater degree in tolerant macrophages. 17538624 569/651 Jessica Robertson 1.95671235079419e-07 7.62019991398397e-07 2795 2834.90909090909 2941 1.95671252308676e-08 631 1.92955832256398 -1.76371542047371 -1 4.69752241648907 2791 2941 4523 1897 1031 3125 2075 4513 3358 631 4299 3157 M2420 WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK.html Genes with promoters bound by both PPARG and RXRA [GeneID=5468, 6256] at 8 (but not 0) day time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte) and that were newly modified by H4K20me1. 19414603 200/219 Arthur Liberzon 1.06128492735935e-07 6.93852357637273e-07 2655 2859.63636363636 2941 9.64804525959981e-09 331 1.44374304657015 -1.33321470418553 -1 3.52583455450436 2655 2965 3808 4433 331 2429 2816 3230 3225 2941 2623 3158 M10792 KEGG_MAPK_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MAPK_SIGNALING_PATHWAY.html MAPK signaling pathway 233/294 KEGG 9.73876136345799e-08 6.64473403617636e-07 4525 3016 2942 8.85341981324066e-09 297 1.94638783998735 -1.57115606018049 -1 4.78549598439488 4525 2528 1817 1092 297 4504 3815 4641 2942 2783 4232 3159 M10287 BIOCARTA_FMLP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FMLP_PATHWAY.html fMLP induced chemokine gene expression in HMC-1 cells 52/63 BioCarta 3.12328456339962e-07 8.90628469471876e-07 2945 2633.81818181818 2943 2.83935000618596e-08 667 1.45443548470589 -1.42167668430055 -1 3.48889526332436 2943 2233 3210 667 1425 2498 1556 4687 3130 3094 3529 3160 M2366 PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP.html Genes up-regulated in HEK-293 cells (fibroblast) upon knockdown of CTBP1 but not of SATB1 [GeneID=1487, 6304] by RNAi. 19103759 488/737 Arthur Liberzon 1.27615146125088e-06 2.10535997801613e-06 3805 3209.54545454545 2944 1.16013836500653e-07 1846 2.01218278695081 -1.73673326311295 -1 4.54365627874443 3804 2944 1846 2716 2746 3868 3590 3755 2929 2782 4325 3161 M15898 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM.html Fructose and mannose metabolism 36/41 KEGG 3.03346625707547e-05 3.50158002773202e-05 1130 2419.45454545455 2945 2.75773462252799e-06 307 1.38908306605207 -1.63399014374522 -1 2.43909705622724 1128 3968 3670 3508 4037 1003 979 307 2945 4163 906 3162 M547 REACTOME_SULFUR_AMINO_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SULFUR_AMINO_ACID_METABOLISM.html Genes involved in Sulfur amino acid metabolism 22/27 Reactome 4.23415471601435e-06 5.72713227875401e-06 2945 2945.27272727273 2945 3.84923896832481e-07 1854 1.51608882448037 1.44009400650679 1 3.14611551971579 2945 1854 2803 3093 3416 2452 2261 4522 3899 2085 3068 3163 M2661 REACTOME_REGULATED_PROTEOLYSIS_OF_P75NTR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATED_PROTEOLYSIS_OF_P75NTR.html Genes involved in Regulated proteolysis of p75NTR 13/13 Reactome 1.72580092884138e-06 2.67777132943173e-06 870 2175.45454545455 2945 1.56891116605089e-07 139 1.48209034746407 -1.00095474880828 -1 3.27123215990387 870 3499 3046 3976 2945 390 139 1276 3339 3908 542 3164 M1255 INAMURA_LUNG_CANCER_SCC_DN http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_DN.html Down-regulated genes characteristic to the squamous cell carcinoma (SCC) type of non-small cell lung cancer (NSCLC). 16007138 20/24 Arthur Liberzon 0.00113686758278738 0.00118664639335613 1285 3111.27272727273 2946 0.000103405044870132 1213 2.06860204872196 2.23345038223375 1 2.38387123635646 1284 4316 2946 4234 4675 2397 2359 1213 4422 3640 2738 3165 M7727 RICKMAN_HEAD_AND_NECK_CANCER_B http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_B.html Cluster b: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 84/167 Jessica Robertson 9.00247966798106e-09 1.19194676105687e-07 3875 2378.27272727273 2947 8.18407245892686e-10 278 3.01455681216332 2.8412843493543 1 8.34388764713702 3875 2146 278 359 2947 4261 3276 3490 1450 518 3561 3166 M12882 KEGG_TAURINE_AND_HYPOTAURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TAURINE_AND_HYPOTAURINE_METABOLISM.html Taurine and hypotaurine metabolism 8/12 KEGG 2.13172610037704e-07 7.70833597108584e-07 2950 2602.90909090909 2949 2.13172630486859e-08 747 2.2951232150633 1.52271441917218 1 5.592362588828 2949 1018 4181 3627 1126 1995 747 3788 4081 2062 3058 3167 M1247 CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP.html Genes up-regulated in K562 cells (chronic myelogenous leukemia, CML) expressing TP53 and MYC [GeneID=7157;4609]. 15856024 42/43 Arthur Liberzon 3.69938684508014e-06 5.08625281350954e-06 1805 2549.54545454545 2950 3.36308460523617e-07 417 1.78796170030884 -1.87529178866608 -1 3.75632541620782 1805 4236 3012 3521 3361 1675 1870 1051 4147 2950 417 3168 M1996 KYNG_WERNER_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_UP.html Genes distinctly up-regulated in primary fibroblast cultures from Werner syndrom patients compared to those from normal young donors. 14527998 27/29 Arthur Liberzon 7.91974760308251e-08 6.29674606547497e-07 3195 2580.36363636364 2950 7.19977080744034e-09 181 2.09579648780133 2.47042374932043 1 5.17637139261606 3192 4013 2950 4238 181 3036 2231 910 1831 3428 2374 3169 M17 PID_NOTCH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NOTCH_PATHWAY.html Notch signaling pathway 18832364 77/87 Pathway Interaction Database 1.73540004898106e-06 2.69001255539921e-06 4460 3040.09090909091 2951 1.57763765263429e-07 1218 1.76586323610948 -1.16773202800268 -1 3.90574228380876 4459 2613 2401 3168 2951 4049 3691 1218 1925 2867 4099 3170 M505 REACTOME_CTNNB1_PHOSPHORYLATION_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CTNNB1_PHOSPHORYLATION_CASCADE.html Genes involved in Beta-catenin phosphorylation cascade 18/18 Reactome 4.51199592070894e-07 1.04185917010687e-06 2825 3196.18181818182 2951 4.1018153146161e-08 1856 1.02976576147151 -1.02413531130103 -1 2.42738132538483 2951 4051 3610 4259 1856 2825 2325 2821 4298 4017 2145 3171 M1810 DAZARD_UV_RESPONSE_CLUSTER_G6 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G6.html Cluster G6: genes increasingly down-regulated in NHEK cells (normal keratinocyte) after UV-B irradiation. 12771951 222/252 John Newman 1.86076283263841e-07 7.48271685670965e-07 2495 2632.45454545455 2951 1.69160271820181e-08 875 1.82429554152436 2.04232352857422 1 4.44433091928537 2495 3291 2960 2467 875 3593 3743 1961 1346 3275 2951 3172 M9695 HOLLMANN_APOPTOSIS_VIA_CD40_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLMANN_APOPTOSIS_VIA_CD40_UP.html Genes up-regulated in DLBCL (diffuse large B-cell lymphoma) cell lines sensitive to stimulation of CD40 [GeneID=958] relative to the resistant ones. 16585179 281/339 Arthur Liberzon 5.7196966131188e-07 1.20368443390297e-06 3785 3032.90909090909 2952 5.19972554560145e-08 1057 1.77097140932767 1.92838075655165 1 4.16592107684349 3785 2041 2789 1057 2083 3743 3805 4588 2509 2952 4010 3173 M1020 REACTOME_PKB_MEDIATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PKB_MEDIATED_EVENTS.html Genes involved in PKB-mediated events 35/56 Reactome 1.20934666026911e-06 2.02200362609642e-06 2955 3158.72727272727 2953 1.0994066591374e-07 2351 1.23459357352383 -1.18475119027149 -1 2.77717733974109 2953 3972 3870 3572 2702 2595 2351 2455 3527 4256 2493 3174 M5792 LI_AMPLIFIED_IN_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LI_AMPLIFIED_IN_LUNG_CANCER.html Genes with increased copy number that correlates with increased expression across six different lung adenocarcinoma cell lines. 16369491 260/356 Arthur Liberzon 1.88009721024072e-07 7.48978540381421e-07 4235 2963.18181818182 2954 1.70917942810173e-08 891 2.14419799708787 2.05390644895912 1 5.23209489712945 4231 2954 1021 1709 891 4187 4425 4584 1812 2529 4252 3175 M4987 KIM_WT1_TARGETS_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_12HR_DN.html Genes down-regulated in UB27 cells (osteosarcoma) at 12 hr after inducing the expression of a mutated form of WT1 [GeneID=7490]. 17430890 258/315 Arthur Liberzon 2.37331446796192e-07 8.0069968374353e-07 2580 2989 2955 2.15755883999111e-08 1140 1.78536185348793 1.56992492036563 1 4.32729642109858 2579 2955 2945 3166 1140 2766 3507 4525 2336 3691 3269 3176 M15154 MARTIN_INTERACT_WITH_HDAC http://www.broadinstitute.org/gsea/msigdb/cards/MARTIN_INTERACT_WITH_HDAC.html Interaction partners of class IIa histone deacetylases (HDAC). 17694086 54/63 Leona Saunders 9.66163852234759e-07 1.71246465735939e-06 2010 2917.81818181818 2958 8.78331160491584e-08 1850 1.41380942036855 1.40795424417211 1 3.22860984197352 2007 3074 3428 4218 2541 2054 2777 3533 2958 3656 1850 3177 M936 REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION.html Genes involved in TRAF6 mediated IRF7 activation 18/36 Reactome 1.1162703205562e-05 1.37208226901699e-05 2400 2989.27272727273 2959 1.01479634954811e-06 1928 1.77224576910356 -1.48632028142533 -1 3.41569438509679 2396 3486 2959 3925 3781 2700 1928 1949 4049 3043 2666 3178 M8525 KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_DN.html Genes down-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 24 h. 18701491 1166/1371 Jessica Robertson 9.28968694432504e-07 1.66277293808169e-06 1365 3180.54545454545 2959 9.28969082775006e-08 1365 1.46383401098287 1.44838777611063 1 3.35214634311663 1365 4657 4504 4702 2582 1723 1756 2901 3176 4661 2959 3179 M1883 BOYAULT_LIVER_CANCER_SUBCLASS_G1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G1_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G1, defined by unsupervised clustering 17187432 56/75 Yujin Hoshida 7.51024583727775e-07 1.43364609476926e-06 3120 2710.45454545455 2959 6.82749854644339e-08 423 1.73528586039874 -1.28124537801131 -1 4.0279799458486 3116 423 2367 2917 2325 3067 3249 2745 3587 2959 3060 3180 M2047 KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP.html Genes up-regulated in response to hydorgen peroxyde [PubChem=784] in CS-B cells (Cockaine syndrome fibroblast, CS) with defficient ERCC6 [GeneID=2074]. 12606941 69/85 Arthur Liberzon 3.24208188919316e-06 4.54083872907765e-06 2230 2943.09090909091 2959 2.94735151543041e-07 1461 1.9222877936991 2.06583363771302 1 4.08037294335417 2226 4198 2679 2733 3294 2514 3425 3398 2959 3487 1461 3181 M229 PID_P38_ALPHA_BETA_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_ALPHA_BETA_DOWNSTREAM_PATHWAY.html Signaling mediated by p38-alpha and p38-beta 18832364 50/52 Pathway Interaction Database 0.000193203483225272 0.000208011049457866 1780 2773.54545454545 2960 1.75654956723766e-05 895 2.23301077090007 -1.91447184582928 -1 3.25643646653196 1776 4223 2982 2960 4345 2164 1465 3524 2106 4069 895 3182 M7014 BIOCARTA_MYOSIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MYOSIN_PATHWAY.html PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase 42/49 BioCarta 3.18587174970433e-06 4.47405970205427e-06 3900 2761.63636363636 2961 2.89625123931773e-07 637 2.08769129715687 -1.86578317090874 -1 4.44117679174693 3899 2706 2786 1920 3284 3932 3051 2961 637 2139 3063 3183 M11023 GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_DN.html Down-regulated genes from the set G (Fig. 5a): specific to cells expressing both MLL-AF4 [GeneID=4297;4299] and AF4-MLL fusion proteins. 17130830 54/64 Arthur Liberzon 3.36744938103106e-07 9.13746684768849e-07 2780 2947.63636363636 2962 3.06131808770253e-08 1519 1.78231691143629 1.94555852800051 1 4.27871914215952 2780 2220 2557 3655 1519 2962 4341 3980 3344 3028 2038 3184 M190 PID_TCR_JNK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_JNK_PATHWAY.html JNK signaling in the CD4+ TCR pathway 18832364 12/18 Pathway Interaction Database 0.00643844918243456 0.00660497286265836 1980 3017.72727272727 2963 0.00058703357322907 494 0.968465332678171 -0.997045461286716 -1 0.799078619918064 1979 4092 3423 4631 4626 2450 494 2191 4563 2963 1783 3185 M0 BROWNE_HCMV_INFECTION_30MIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_30MIN_DN.html Genes down-regulated in primary fibroblast cell culture at 30 min time point after infection with HCMV (AD169 strain). 11711622 204/317 Arthur Liberzon 1.17567428793287e-07 7.06112554001409e-07 2975 2743.45454545455 2963 1.06879486432782e-08 403 2.04937017825451 2.20407700136597 1 5.01958617683067 2975 2963 1562 2854 403 3394 4147 3798 3024 2355 2703 3186 M2105 KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP.html Genes whose expression was significantly and positively correlated with the number of perineuronal oligodendrocytes in the layer III of BA9 brain region. 18762803 941/1159 Jessica Robertson 1.33409463066277e-07 7.20206492018647e-07 2680 3105.81818181818 2963 1.33409471075416e-08 608 1.57478657406293 1.64395156363992 1 3.84015056788165 2679 3829 4658 2040 608 2660 2963 4094 2240 4612 3781 3187 M14387 DAIRKEE_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_TERT_TARGETS_DN.html Genes down-regulated in non-spontaneously immortalizing (NSI) primary breast cancer tumor cultures upon expression of TERT [GeneID=7015] off a retroviral vector. 17471242 199/295 Arthur Liberzon 9.22730400798215e-07 1.65474448775364e-06 3540 3039.27272727273 2964 8.38846170738828e-08 1792 1.86023711877058 -1.62865031441945 -1 4.27502287886006 3538 2964 2561 3097 2510 2985 2610 4653 2356 1792 4366 3188 M546 REACTOME_O_LINKED_GLYCOSYLATION_OF_MUCINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_O_LINKED_GLYCOSYLATION_OF_MUCINS.html Genes involved in O-linked glycosylation of mucins 38/61 Reactome 2.86292613325007e-06 4.07263753735392e-06 4330 2792.45454545455 2965 2.60266350806245e-07 586 2.64169805797653 -2.49747337593261 -1 5.67637503304144 4326 586 889 3288 3244 4344 2696 2902 2965 940 4537 3189 M2273 ZHU_SKIL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_SKIL_TARGETS_UP.html Genes up-regulated in A549 cells (lung adenocarcinoma) upon SKIL [GeneID=6498] knockdown by RNAi. 17074815 33/36 Arthur Liberzon 1.57560856240014e-05 1.88513876160422e-05 4140 2994.45454545455 2965 1.43238167890605e-06 1585 2.51782004002244 1.93104511559443 1 4.7340115664052 4136 3714 1585 1947 3886 4263 4132 2965 2677 1954 1680 3190 M90 PID_WNT_CANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_CANONICAL_PATHWAY.html Canonical Wnt signaling pathway 18832364 31/33 Pathway Interaction Database 1.22074540359246e-06 2.0345756726541e-06 3525 3006.09090909091 2966 1.10976916451401e-07 410 1.73060692847755 2.27902776141535 1 3.91117247474225 3521 3423 2723 2667 2712 4370 4160 2348 410 3767 2966 3191 M9267 TAGHAVI_NEOPLASTIC_TRANSFORMATION http://www.broadinstitute.org/gsea/msigdb/cards/TAGHAVI_NEOPLASTIC_TRANSFORMATION.html Genes that cooperate with MYC and TBX2 [GeneID=4609;6909] to transform MEF cells (embryo fibroblasts). 18762810 20/23 Jessica Robertson 1.77834464189069e-06 2.7411772276752e-06 3425 3094.72727272727 2968 1.616678253997e-07 2364 1.53923295418177 -1.20599955576643 -1 3.39299357981215 3423 2383 3002 2417 2968 3874 3290 2364 2917 2932 4472 3192 M16336 PODAR_RESPONSE_TO_ADAPHOSTIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/PODAR_RESPONSE_TO_ADAPHOSTIN_UP.html Up-regulated genes in MM1.S cells (multiple myeloma) treated with adaphostin [PubChem=387042], a tyrosine kinase inhibitor with anticancer properties. 17308109 193/252 Jessica Robertson 2.90517559447518e-06 4.11661026896513e-06 805 2455 2968 2.64107220987861e-07 14 1.77867562902525 -1.71511877002225 -1 3.80226400282614 801 4708 3069 4513 3259 75 583 2968 4285 2730 14 3193 M18448 REACTOME_GLUCOSE_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_TRANSPORT.html Genes involved in Glucose transport 35/44 Reactome 2.86392354618019e-06 4.07282890568559e-06 1565 2734.90909090909 2969 2.60357024945018e-07 770 1.28978574513527 1.42139565437095 1 2.74582242629929 1646 4264 3725 3783 3245 1562 770 1564 2969 4424 2132 3194 M14665 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP.html Genes up-regulated in lymphoblastoid cells from the European population compared to those from the Asian population. 17206142 668/882 Leona Saunders 3.22023514340394e-07 9.00418095113436e-07 2720 3387.45454545455 2969 3.22023561005018e-08 1565 1.31654284401896 1.41372620693225 1 3.15086118845429 2718 4667 4414 4701 1565 2318 2657 2839 3768 4646 2969 3195 M8139 HOEGERKORP_CD44_TARGETS_TEMPORAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_TEMPORAL_UP.html Genes temporally up-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 12/15 Kevin Vogelsang 6.53605329447124e-06 8.37637022804894e-06 2270 2805.27272727273 2969 5.94188428430045e-07 1448 1.47056588092876 1.55002028259828 1 2.95249399622713 2270 3223 2969 3907 3619 2305 2222 3191 3739 1965 1448 3196 M2375 EHRLICH_ICF_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/EHRLICH_ICF_SYNDROM_DN.html Down-regulated in B lymphocytes from patients with ICF syndrom caused by mutations in DNMT3B [GeneID=1789] compared to normals. 11741835 20/26 John Newman 1.44165588780646e-05 1.73897669063288e-05 3885 2987.18181818182 2969 1.31060485003383e-06 1422 2.94021209290165 2.24352288398078 1 5.57803247650705 3881 3179 1422 2361 3853 4627 2969 1603 2171 2156 4637 3197 M18308 REACTOME_THROMBOXANE_SIGNALLING_THROUGH_TP_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THROMBOXANE_SIGNALLING_THROUGH_TP_RECEPTOR.html Genes involved in Thromboxane signalling through TP receptor 19/26 Reactome 1.01675836957416e-06 1.7748149054697e-06 2730 2811.18181818182 2970 9.24326217711326e-08 642 1.83014077358105 -1.47639354803631 -1 4.18265767296699 2730 3756 2970 4198 2578 2509 642 1699 3683 3182 2976 3198 M8991 ZERBINI_RESPONSE_TO_SULINDAC_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZERBINI_RESPONSE_TO_SULINDAC_UP.html Selected genes up-regulated in DU145 and PC-3 cells (prostate cancer) after treatment with the NSAID (non-steroid anti-inflammatory drug) sulindac [PubChem=5352]. 17178890 12/12 Arthur Liberzon 1.85174480840513e-05 2.19108435589677e-05 2545 3134 2970 1.68341854069575e-06 2150 1.82064942804654 -1.66462806252814 -1 3.36151070201568 2476 4082 2542 3496 3927 2543 2150 3795 4129 2970 2364 3199 M6921 NUTT_GBM_VS_AO_GLIOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUTT_GBM_VS_AO_GLIOMA_UP.html Top 50 marker genes for glioblastoma multiforme (GBM), a class of high grade glioma. 12670911 86/110 Arthur Liberzon 8.61982173148744e-07 1.57573813216966e-06 4390 3057.81818181818 2970 7.83620464438393e-08 1618 1.52862125348585 -1.22465229892528 -1 3.51707602347635 4389 1618 2939 2210 2454 4144 3617 3975 3161 2159 2970 3200 M15491 HAN_SATB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAN_SATB1_TARGETS_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of SATB1 [GeneID=6304] by RNAi. 18337816 600/767 Jessica Robertson 1.59039341191676e-07 7.31918027928963e-07 4260 2576.18181818182 2970 1.59039352573758e-08 418 2.03128729506977 -1.83565235903854 -1 4.96211935237489 4257 1146 4606 418 806 3231 2970 3696 1872 851 4485 3201 M5755 KAPOSI_LIVER_CANCER_MET_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAPOSI_LIVER_CANCER_MET_UP.html Selected up-regulated MET [GeneID=4233] target genes from a classifier of hepatocellular carcinoma (HCC) cases; associated with poor survival. 16710476 37/40 Yujin Hoshida 8.39569243306803e-07 1.55037825837563e-06 3640 3036.18181818182 2970 7.63245057913989e-08 2410 1.68912489136799 -1.46793337572204 -1 3.89640580156793 3636 2718 2708 2970 2422 3406 2781 3084 3114 2410 4149 3202 M14030 WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_UP.html Up-regulated genes in pediatric adrenocortical carcinoma (ACC) compared to the adenoma (ACA) tumors. 17234769 18/26 Jessica Robertson 1.86417730957671e-06 2.846624684957e-06 2735 2741 2971 1.69470808108675e-07 641 1.58819887517218 1.74684328246698 1 3.49205244304441 2734 2834 2971 2693 3001 1432 641 3308 3842 3049 3646 3203 M2290 CHANGOLKAR_H2AFY_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANGOLKAR_H2AFY_TARGETS_DN.html Genes down-regulated in liver tissue upon knockout of H2AFY [GeneID=9555]. 17242180 41/47 Arthur Liberzon 1.7822476362543e-06 2.7446032114585e-06 3375 2810.18181818182 2971 1.62022643643376e-07 335 2.1018428972108 2.7362530023109 1 4.65100819955413 3372 2274 2297 3094 2971 4446 3778 2015 335 3373 2957 3204 M10202 TSUNODA_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSUNODA_CISPLATIN_RESISTANCE_UP.html Genes up-regulated in bladder cancer cells resistant to cisplatin [PubChem=2767] compared to the parental cells sensitive to the drug. 15608674 18/21 Leona Saunders 1.47122184169189e-05 1.7710194064743e-05 2290 2405.18181818182 2972 1.3374833458107e-06 215 2.35152715024033 2.71877790276818 1 4.44368970865502 2290 3196 1473 3374 3862 3129 3288 215 2972 1493 1165 3205 M10084 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_DN.html Genes down-rgulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 6h. 16818636 49/66 Arthur Liberzon 1.78703739119212e-06 2.74912181490967e-06 2365 2716.27272727273 2973 1.62458076616898e-07 1075 2.35458505311509 2.66114302487268 1 5.21562244851 2365 3078 1075 2802 2973 3582 4266 3013 3888 1628 1209 3206 M14663 REACTOME_ETHANOL_OXIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ETHANOL_OXIDATION.html Genes involved in Ethanol oxidation 9/13 Reactome 5.02287826627039e-06 6.62419262833088e-06 4365 2947.09090909091 2974 5.02288961949424e-07 1008 2.76880476557524 2.41823966243745 1 5.71666801992387 4365 1008 4256 1038 3544 4160 2958 1712 2974 2318 4085 3207 M15672 RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP.html Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: moderately vs poorly differentiated tumors. 18679425 163/186 Jessica Robertson 8.27893570365502e-07 1.53421972992743e-06 3835 2895.90909090909 2974 7.52630801740591e-08 1441 2.09361917590566 2.34049711770872 1 4.84529050949043 3832 2974 1441 1667 2414 4656 3452 3528 1963 1835 4093 3208 M1177 KOINUMA_COLON_CANCER_MSI_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOINUMA_COLON_CANCER_MSI_DN.html Genes down-regulated in colorectal carcinoma samples positive for MSI (microsatellite instability) compared to the MSI negative ones. 16247484 11/12 Arthur Liberzon 1.79132046892827e-06 2.75408228447603e-06 4550 3491.54545454545 2975 1.62847447953507e-07 2743 1.31179897328876 -1.12214559412812 -1 2.8831821411278 4546 2882 2853 2875 2975 4653 3874 2955 3332 2743 4719 3209 M16858 OSMAN_BLADDER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/OSMAN_BLADDER_CANCER_DN.html Genes down-regulated in blood samples from bladder cancer patients. 16740760 561/764 Leona Saunders 1.62938774933519e-06 2.55044698879158e-06 1160 3088.54545454545 2976 1.62938894404342e-07 1159 1.30966424708751 -1.19445266108872 -1 2.89597975807323 1159 4675 4301 4698 2976 1222 1202 2880 3835 4653 2373 3210 M1773 JEPSEN_SMRT_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/JEPSEN_SMRT_TARGETS.html Genes up-regulated in neural progenitor cells (NPC) isolated from E13 cortical tissue of SMRT [GeneID=9612] knockout mice. 17928865 39/47 Jessica Robertson 6.1411223431144e-07 1.25698601298786e-06 4200 3070.63636363636 2976 5.58284005214526e-08 2044 2.07844086589682 -1.25660826146033 -1 4.88215081686789 4197 2725 2442 3361 2147 4343 2044 3676 2976 2620 3246 3211 M13045 SAMOLS_TARGETS_OF_KHSV_MIRNAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAMOLS_TARGETS_OF_KHSV_MIRNAS_UP.html Genes up-regulated in 293 cells (embryonic kidney) upon expression of KHSV (Kaposi sarcoma-associated herpesvirus) microRNAs. 17500590 35/44 Arthur Liberzon 0.000495001855664338 0.000522569617252444 3415 2967.09090909091 2979 4.50102969632312e-05 1418 2.46327388107796 -1.32545760915815 -1 3.20108175772158 2227 3411 1418 2444 4437 2979 2420 3293 3413 2473 4123 3212 M6195 HWANG_PROSTATE_CANCER_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/HWANG_PROSTATE_CANCER_MARKERS.html Proteins implicated in prostate carcinogenesis. 16799640 37/47 Arthur Liberzon 6.23911559363876e-06 8.03290387397026e-06 3745 2706.36363636364 2980 5.67193935236496e-07 822 2.30512223046349 -2.74522609312377 -1 4.67330777611514 3743 2281 1815 822 3601 4102 2980 3130 1489 2997 2810 3213 M11844 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY.html Cytosolic DNA-sensing pathway 42/60 KEGG 4.93226176016327e-06 6.51743435273535e-06 725 2371.54545454545 2981 4.4838843800172e-07 495 1.72442789302114 -1.8040370486757 -1 3.54639426592518 721 3958 2981 4244 3505 677 495 936 4050 3201 1319 3214 M2978 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_DN.html Genes specifically down-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and low-dose methotrexate (LDMTX) [PubChem=4112]. 12704389 23/38 Jean Junior 7.44195863595114e-07 1.42672805693296e-06 3120 2844.72727272727 2982 6.76541923031817e-08 1398 2.41602213696539 -2.83431940606222 -1 5.62978875779897 3120 1867 1640 2821 2317 4699 4163 3108 1398 2982 3177 3215 M711 REACTOME_ENOS_ACTIVATION_AND_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENOS_ACTIVATION_AND_REGULATION.html Genes involved in eNOS activation and regulation 26/31 Reactome 1.14837691461656e-06 1.94766045166732e-06 2750 3014.54545454545 2985 1.04397955823427e-07 2043 1.74611526924014 1.93651043915294 1 3.95998425102173 2750 3163 3065 2985 2662 2695 2043 2919 4259 3623 2996 3216 M64 PID_S1P_S1P4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P4_PATHWAY.html S1P4 pathway 18832364 15/18 Pathway Interaction Database 1.4006904525514e-06 2.26645832569167e-06 4090 3003.63636363636 2986 1.27335576758205e-07 85 1.66799549293847 -1.39809420720801 -1 3.73641712678455 4090 2862 2858 1289 2806 4416 2986 3328 85 3785 4535 3217 M17043 CHANDRAN_METASTASIS_TOP50_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_TOP50_DN.html Top 50 genes down-regulated in metastatic vs primary prostate cancer tumors. 17430594 59/61 Arthur Liberzon 4.14331754927666e-07 1.00337562730974e-06 2190 2783.09090909091 2986 3.7666530269079e-08 1343 1.74987281162434 1.95472089621635 1 4.17132330739011 2188 4203 3014 4572 1751 2184 3139 1883 3351 2986 1343 3218 M1638 ZAMORA_NOS2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZAMORA_NOS2_TARGETS_DN.html Down-regulated in hepatocytes upon expression of NOS2 [GeneID=4843]. 12381414 135/193 John Newman 1.67184806545293e-07 7.3358205358541e-07 2610 2484.90909090909 2987 1.5198619931835e-08 661 1.56517484487776 1.59802391393098 1 3.81137637852281 2607 2987 3133 3499 748 2138 3433 661 3007 4112 1009 3219 M2203 PHESSE_TARGETS_OF_APC_AND_MBD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/PHESSE_TARGETS_OF_APC_AND_MBD2_DN.html Genes down-regulated in small intestine upon loss of both APC and MBD2 [GeneID=324, 8932]. 18644872 17/22 Arthur Liberzon 1.45582954247312e-05 1.75383242482724e-05 1985 2968.18181818182 2987 1.32349016034454e-06 1248 1.6886361046883 1.41133476100999 1 3.17979278163272 1982 3770 3064 3941 3858 2224 1248 2987 2885 3949 2742 3220 M1939 MEISSNER_BRAIN_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in brain. 18600261 39/57 Jessica Robertson 8.42383003966258e-07 1.55360068962103e-06 2910 2978.45454545455 2988 7.65803024105485e-08 2266 2.12165569820703 -2.09352255773212 -1 4.90619409560567 2908 3955 2266 3368 2427 2937 2988 2274 3034 3448 3158 3221 M10066 BIOCARTA_GCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GCR_PATHWAY.html Corticosteroids and cardioprotection 29/35 BioCarta 3.69127477162455e-07 9.53629826057355e-07 2990 2915.54545454545 2989 3.35570490087822e-08 1555 1.41407761307515 -1.7100942451861 -1 3.37381598668469 2989 2773 3262 1555 1617 3071 2793 3622 4258 3612 2519 3222 M4891 BIOCARTA_PML_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PML_PATHWAY.html Regulation of transcriptional activity by PML 22/26 BioCarta 9.94598821803372e-05 0.000109149184815436 2915 2621.72727272727 2989 9.04221626822555e-06 218 2.83199305046784 -2.19498810857344 -1 4.4623365550489 2912 3468 2385 1529 4253 2989 1119 3064 218 3809 3093 3223 M1609 LEE_CALORIE_RESTRICTION_NEOCORTEX_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_NEOCORTEX_DN.html Down-regulated in the neocortex of aged (30-month) mice subjected to caloric restriction since young adulthood. 10888876 141/204 John Newman 1.73802816374639e-06 2.69320188210209e-06 3565 3202.09090909091 2989 1.58002685164765e-07 2095 1.92499652645858 2.02504577080205 1 4.26182462103164 3565 2989 2095 2544 2952 3273 4701 4156 3079 2905 2964 3224 M6840 XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR.html Genes changed similarly in DU-145 cells (prostate cancer) in the absence and presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 6 h. 17099727 40/48 Arthur Liberzon 6.05288255462922e-07 1.24618809732525e-06 3020 2896.09090909091 2990 5.50262201815059e-08 1718 1.71985321601858 -1.71146080750319 -1 4.03380561449769 3017 2712 2502 3381 2130 3424 1718 3699 2990 2445 3839 3225 M55 PID_S1P_S1P3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P3_PATHWAY.html S1P3 pathway 18832364 39/42 Pathway Interaction Database 7.94738932778614e-07 1.49132774299328e-06 3975 3110.18181818182 2991 7.22490199885636e-08 2237 1.80280446099852 -1.72111014121119 -1 4.17423196747955 3975 3413 2744 2237 2374 4134 2991 3215 3722 2917 2490 3226 M14523 IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM.html Genes in the expression cluster 'ST-HSC Shared': up-regulated in short term hematopoietic stem cells (ST-HSC) from adult bone marrow and fetal liver. 12228721 34/52 John Newman 1.16574810216315e-07 7.06112554001409e-07 2645 2782.18181818182 2991 1.05977105812223e-08 392 1.67396754870619 -1.59816120883871 -1 4.09093504487167 2644 2745 3099 3376 392 2991 2628 3679 2063 3246 3741 3227 M14046 DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_UP.html Common up-regulated transcripts in fibroblasts expressing either XP/CS or TDD mutant forms of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 128/179 Arthur Liberzon 2.43313635230765e-06 3.56547767242847e-06 1410 2337.45454545455 2992 2.2119445848093e-07 85 1.40912485168528 -1.21876383151706 -1 3.0372557906994 1410 2992 3346 3019 3142 269 988 3719 3789 2953 85 3228 M3274 POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_UP.html Top up-regulated marker genes for medulloblastoma classification: desmoplastic vs classic morphology. 11807556 98/133 Jean Junior 1.17293764566998e-06 1.97427306706966e-06 2210 3169.18181818182 2993 1.06630751911475e-07 2207 1.76745603304034 1.94790609629362 1 4.00480468714698 2207 3890 2993 3257 2682 2781 4313 3549 3636 2989 2564 3229 M13611 WEBER_METHYLATED_LCP_IN_FIBROBLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_LCP_IN_FIBROBLAST_DN.html Unmethylated germline-specific genes with low-CpG-density promoters (LCP) in primary fibroblasts. 17334365 4/15 Arthur Liberzon 0.000344121642587251 0.000366483337773426 2405 3104.36363636364 2993 3.44174943071326e-05 1204 1.27090442551326 -1.27090442551326 -1 1.70610570435053 2404 3538 4632 3888 4407 2360 1942 2114 4666 2993 1204 3230 M15652 REACTOME_DOUBLE_STRAND_BREAK_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOUBLE_STRAND_BREAK_REPAIR.html Genes involved in Double-Strand Break Repair 26/32 Reactome 3.09190273155892e-05 3.56293478831985e-05 700 2312.81818181818 2994 2.8108601693949e-06 45 1.18270096228966 1.19093771938086 1 2.06568745562209 700 3744 3657 2994 4189 192 45 896 4265 3624 1135 3231 M1995 KYNG_NORMAL_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_NORMAL_AGING_DN.html Genes distinctly down-regulated in primary fibroblast cultures from normal old donors compared to those from normal young donors. 14527998 39/60 Arthur Liberzon 7.26308144950417e-06 9.2279258254804e-06 2755 3166.45454545455 2994 6.60282311632444e-07 1774 1.74499298298782 1.8239403374985 1 3.48329798857449 2754 4532 3235 4479 3657 1774 2081 2624 2994 3842 2859 3232 M2831 BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP.html Genes up-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes depend on ATM [GeneID=472] but not NFKB signaling. 18849970 60/75 Jessica Robertson 2.48949889031242e-07 8.17750684987324e-07 3445 2613.81818181818 2995 2.26318106547434e-08 395 1.61470908674264 1.87911961905394 1 3.90294896355293 3442 395 2834 3850 1187 3025 2995 3756 2747 1376 3145 3233 M17951 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP.html Top 100 probe sets contrubuting to the positive side of the 1st principal component; predominantly associated with spindle cell and pleomorphic sarcoma samples. 17464315 75/136 Nikolaos Papanikolaou 1.62559260969142e-06 2.54740940164127e-06 3330 2888.90909090909 2995 1.47781255532032e-07 900 2.61587725138798 -3.01667853642192 -1 5.83477777843321 2470 4191 900 3326 2915 3308 2864 3330 4210 1269 2995 3234 M719 REACTOME_SHC1_EVENTS_IN_EGFR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC1_EVENTS_IN_EGFR_SIGNALING.html Genes involved in SHC1 events in EGFR signaling 24/25 Reactome 1.84613345946266e-06 2.82272430471776e-06 3295 2570.36363636364 2996 1.67830455331843e-07 207 1.56753704115056 -1.631265671302 -1 3.44827964787862 3293 2786 3004 207 2996 3481 2521 3650 453 3950 1933 3235 M18077 ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_UP.html Genes up-regulated in immunoglobulin light chain amyloidosis plasma cells (ALPC) compared to multiple myeloma (MM) cells. 15388584 32/42 Kevin Vogelsang 2.02466624957302e-06 3.05805590335508e-06 3700 2737.63636363636 2996 1.84060737534683e-07 1048 2.32072312855083 3.00452490611229 1 5.0967288374358 3699 2299 1538 2852 3041 3110 4336 1048 2996 2133 3062 3236 M2525 BOUDOUKHA_BOUND_BY_IGF2BP2 http://www.broadinstitute.org/gsea/msigdb/cards/BOUDOUKHA_BOUND_BY_IGF2BP2.html Transcripts bound to IGF2BP2 [GeneID=10644] complexes and differentially regulated in myoblasts with IGF2BP2 [GeneID=10644] knockdown by RNAi. 20956565 145/205 Arthur Liberzon 1.77578532201215e-07 7.4119215967118e-07 3000 2846.09090909091 2996 1.61435042304468e-08 823 1.51201891046126 1.79534171074972 1 3.67751089933016 2996 2985 3778 2972 823 3154 3299 1326 3258 4131 2585 3237 M14631 KEGG_COLORECTAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_COLORECTAL_CANCER.html Colorectal cancer 72/82 KEGG 6.97569006191187e-08 6.06161982149702e-07 4220 2462.18181818182 2997 6.34153662099531e-09 133 1.5053885930264 -1.18103158788044 -1 3.71404307462384 4216 311 3121 507 133 4067 4275 2759 775 3923 2997 3238 M4052 REACTOME_TELOMERE_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TELOMERE_MAINTENANCE.html Genes involved in Telomere Maintenance 47/93 Reactome 0.000137093167826726 0.000148890877161101 460 2349.63636363636 2997 1.24637919584827e-05 355 1.16643946391648 1.19511804218265 1 1.74525976669966 456 3094 3719 2997 4306 355 404 1009 4369 3582 1555 3239 M1594 BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP.html Genes specifically up-regulated in FL5.12 cells (pro-B lymphocyte) by camptothecin [PubChem=2538]. 12447701 35/56 John Newman 2.62947702948787e-06 3.79081599852864e-06 1345 2823.09090909091 2998 2.39043652026212e-07 1341 1.48696564813129 -1.83426945367682 -1 3.19188369934356 1341 3706 2998 2905 3196 2654 3083 1992 3775 3996 1408 3240 M18750 CAMPS_COLON_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAMPS_COLON_CANCER_COPY_NUMBER_UP.html Genes from chromosomal copy number gains in a panel of 51 primary colon carcinoma samples. 18316590 87/166 Jessica Robertson 2.51942361104017e-07 8.19550616410033e-07 4520 2775.09090909091 2999 2.29038536323884e-08 204 1.77119531298 2.04656815875102 1 4.28536436743556 4520 204 2821 1463 1201 4450 3698 3736 886 2999 4548 3241 M17394 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_DN.html Genes from the lightyellow module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 13/14 Arthur Liberzon 2.98771410533593e-05 3.45045524276624e-05 2965 3286.63636363636 3001 2.71614061892232e-06 2477 1.56709310731341 1.48703747539442 1 2.7621035588926 2963 3786 3001 4162 4035 2615 2477 2872 3889 3574 2779 3242 M16381 SCHLOSSER_SERUM_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_SERUM_RESPONSE_UP.html Cluster 1: genes up-regulated in B493-6 cells (B lymphocytes) upon serum stimulation but not by affected by MYC [GeneID=4609]. 15516975 208/270 Leona Saunders 1.43849647745469e-06 2.31335719713327e-06 1260 2618.09090909091 3004 1.30772492548526e-07 827 1.50908273843901 -1.17890514749941 -1 3.37027690809575 1259 3576 3673 3004 2828 827 1003 3041 3177 3912 2499 3243 M17669 XU_CREBBP_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_CREBBP_TARGETS_UP.html Genes up-regulated in pro-B lymphocytes after knockout of CREBBP [GeneID=1387]. 16424387 32/34 Kevin Vogelsang 0.000135130468967675 0.000146826844734675 1350 2885.72727272727 3004 1.22853427083851e-05 1194 1.77095192962575 1.56772940825355 1 2.6799982832566 1349 3720 2866 4193 4304 1298 1194 3671 2782 3362 3004 3244 M17537 JI_RESPONSE_TO_FSH_DN http://www.broadinstitute.org/gsea/msigdb/cards/JI_RESPONSE_TO_FSH_DN.html Down-regulated in ovarian epithelial cells (MCV152) 72 hours following FSH treatment, compared to untreated 15386376 103/115 John Newman 4.77188636577987e-07 1.08181093402886e-06 2055 2873.63636363636 3004 4.33807945529187e-08 1909 1.71849373922878 2.11525260850046 1 4.07303406626132 2054 3009 3206 2254 1909 2909 3572 3140 3004 3704 2849 3245 M459 SESTO_RESPONSE_TO_UV_C0 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C0.html Cluster 0: genes changed in primary keratinocytes by UVB irradiation. 11867738 157/177 John Newman 1.79921745533445e-06 2.76352306839525e-06 1875 3173.72727272727 3004 1.63565356980287e-07 1875 1.85981377520116 -2.13192315800713 -1 4.10744703130667 1875 4431 3495 4320 2979 2848 2262 3004 3341 4314 2042 3246 M9488 KEGG_RETINOL_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RETINOL_METABOLISM.html Retinol metabolism 24/101 KEGG 5.98006478386953e-06 7.72888986305153e-06 3005 3061.27272727273 3005 5.43643730819169e-07 1291 2.90869088174693 2.75313125175302 1 5.92965900928073 3005 3743 1291 4389 3588 2378 1440 4569 2933 2719 3619 3247 M3782 NAKAYAMA_FRA2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_FRA2_TARGETS.html Genes down-regulated in ST1 cells (adult T-cell leukemia, ATL) after knockdown of FRA2 [GeneID=2355] by RNAi. 18071306 51/56 Jessica Robertson 1.79111200608614e-05 2.12359926368415e-05 3125 2742.45454545455 3006 1.62829689858568e-06 436 2.01969321403994 2.41364015975829 1 3.74551615300209 3124 3077 2836 2394 3919 3401 4017 1608 2349 3006 436 3248 M1885 YOSHIMURA_MAPK8_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIMURA_MAPK8_TARGETS_DN.html Genes down-regulated in vascular smooth muscle cells (VSMC) by MAPK8 (JNK1) [GeneID=5599]. 16311603 508/619 Jessica Robertson 8.79404617209623e-08 6.51622504172635e-07 2445 2970.45454545455 3006 8.79404652010484e-09 290 1.78076403978674 2.09429351010224 1 4.38010049807077 3006 3270 4600 2235 290 3538 4500 2445 2445 3403 2943 3249 M862 BIOCARTA_P38MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P38MAPK_PATHWAY.html p38 MAPK Signaling Pathway 57/62 BioCarta 2.54509930373498e-07 8.22189102913976e-07 1750 2824.18181818182 3008 2.31372690742567e-08 1210 1.32496349138085 -1.22035219974484 -1 3.19236713080858 1746 3918 3751 3008 1210 2536 1450 2516 3655 3958 3318 3250 M18053 BIOCARTA_LEPTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LEPTIN_PATHWAY.html Reversal of Insulin Resistance by Leptin 15/35 BioCarta 1.33510615255494e-07 7.20206492018647e-07 3345 2572.45454545455 3008 1.21373293961642e-08 516 2.16558825024893 -1.64014289314562 -1 5.29960512194457 3345 3211 2474 2450 516 3678 2373 871 3357 3008 3014 3251 M12012 ST_P38_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_P38_MAPK_PATHWAY.html p38 MAPK Pathway 51/52 Signaling Transduction KE 9.41388509934781e-08 6.5925130072584e-07 2355 2826.90909090909 3008 8.55807772924693e-09 276 1.29268567223852 -1.41038576485303 -1 3.16324415231515 2355 3377 3724 2989 276 3008 3880 2016 4028 3657 1786 3252 M11280 PENG_LEUCINE_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_LEUCINE_DEPRIVATION_UP.html Genes up-regulated in BJAB cells (B-lymphoma) after leucine [PubChem=857] deprivation. 12101249 172/216 Broad Institute 8.30005688171378e-07 1.53614043097655e-06 3010 2969.81818181818 3008 7.54550910283817e-08 1861 1.75259911846622 1.87014344023203 1 4.04752998758515 3008 3582 3264 2494 2417 3159 3586 2867 1861 3546 2884 3253 M12086 SCHURINGA_STAT5A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHURINGA_STAT5A_TARGETS_UP.html Genes up-regulated in hematopoietic stem cells (HSC) overexpressing a constitutively active form of STAT5 [GeneID=6776] off retroviral vector. 15353555 23/32 Kevin Vogelsang 1.90174092736769e-06 2.89766168744993e-06 3665 2971.09090909091 3008 1.72885688298837e-07 1822 1.77422065607849 -1.70258354320782 -1 3.90142198814424 3663 1877 2274 3714 3008 2741 1822 3331 3963 2581 3708 3254 M13639 CORRE_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CORRE_MULTIPLE_MYELOMA_UP.html Genes up-regulated in multiple myeloma (MM) bone marrow mesenchymal stem cells. 17344918 77/139 Leona Saunders 9.30489591167117e-07 1.6643723873972e-06 3010 2919.18181818182 3009 8.45899986107046e-08 765 2.68068589458238 2.85755024847161 1 6.17985388286888 3009 3339 765 2562 2516 3800 4681 3759 3389 1395 2896 3255 M15593 MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_DN.html Genes down-regulated in FSHD (facioscapulohumeral muscular dystrophy) mesoangioblasts. 17761758 16/20 Arthur Liberzon 1.90189743807625e-06 2.89766168744993e-06 3795 2782 3009 1.72899916569669e-07 923 2.64002037263204 -1.98794484757474 -1 5.82968959612273 3794 923 1283 2402 3009 4171 3399 4055 2221 2279 3066 3256 M611 REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION.html Genes involved in NOTCH1 Intracellular Domain Regulates Transcription 50/56 Reactome 5.08203723613955e-06 6.69286153866593e-06 2620 3043.81818181818 3010 4.62004452342686e-07 2022 1.2226564845737 -1.40087716263327 -1 2.4942382005718 2616 3669 3771 3010 3517 2320 2079 2022 3975 4070 2433 3257 M859 REACTOME_JNK_C_JUN_KINASES_PHOSPHORYLATION_AND_ACTIVATION_MEDIATED_BY_ACTIVATED_HUMAN_TAK1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_JNK_C_JUN_KINASES_PHOSPHORYLATION_AND_ACTIVATION_MEDIATED_BY_ACTIVATED_HUMAN_TAK1.html Genes involved in JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 15/16 Reactome 7.82559814611621e-05 8.65639166854195e-05 1155 2325.27272727273 3010 7.11443320323053e-06 427 1.38345271559154 -1.41987547467544 -1 2.21031330765908 1152 3500 3379 3467 4400 1395 744 427 3381 3010 723 3258 M771 REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER.html Genes involved in Transcription-coupled NER (TC-NER) 46/49 Reactome 0.000104941381187433 0.000115030961264441 655 2733.45454545455 3013 9.5405806628649e-06 639 0.981573554996329 1.05543229660084 1 1.50496109284812 655 3105 3980 3013 4262 1067 639 2165 4327 4407 2448 3259 M15657 SAGIV_CD24_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAGIV_CD24_TARGETS_DN.html Genes down-regulated in HT29 cells (colon cancer) after knockdown of CD24 [GeneID=100133941] by both RNAi and monoclonal antibodies. 18413748 49/67 Jessica Robertson 3.6002380232384e-07 9.41752134134615e-07 3015 3097.90909090909 3014 3.27294419309758e-08 1591 1.93549041339159 1.74684409644921 1 4.64053015787144 3014 3931 2303 3942 1591 2590 2470 4087 4441 2082 3626 3260 M1 PID_FANCONI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FANCONI_PATHWAY.html Fanconi anemia pathway 18832364 55/62 Pathway Interaction Database 2.20053247058824e-05 2.57474299979586e-05 1015 2585.45454545455 3015 2.00050407413379e-06 462 1.28750788632161 1.20612982974023 1 2.32622193095343 1014 3376 3797 3015 3977 588 462 1988 4166 3533 2524 3261 M1923 MIKKELSEN_PLURIPOTENT_STATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_PLURIPOTENT_STATE_DN.html Genes down-regulated in the induced pluripotent cells (iPS) and embryonic stem cells (ES) compared to the parental lineage-committed and partially reprogrammed cell lines. 18509334 15/17 Jessica Robertson 0.000108137851417554 0.00011845222991201 4145 3297.54545454545 3015 9.83119701315284e-06 2470 2.34202802257191 2.77157285121536 1 3.64818978873984 4145 3776 2660 2492 4267 4437 3705 2512 2794 3015 2470 3262 M1520 ZHOU_TNF_SIGNALING_4HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_TNF_SIGNALING_4HR.html Genes up-regulated in HeLa cells (cervical carcinoma) at 4 h after stimulation with TNF [GeneID=7124]. 12673210 78/93 John Newman 8.0977221647104e-08 6.29674606547497e-07 3590 2661.90909090909 3016 7.36156587524541e-09 192 1.87001556660416 -2.30056969225544 -1 4.61332848885078 3588 3033 2419 2197 192 3765 3142 3016 1864 1957 4108 3263 M2504 PHONG_TNF_RESPONSE_NOT_VIA_P38 http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_RESPONSE_NOT_VIA_P38.html Genes whose expression changes in Calu-6 cells (lung cancer) by TNF [GeneID=7124] were not affected by p38 inhibitor LY479754. 20516219 487/583 Arthur Liberzon 1.63992838192769e-07 7.3358205358541e-07 3765 2744.09090909091 3016 1.49084409470143e-08 720 1.85860956033962 -1.58922039784428 -1 4.53530367015005 3764 2503 1431 3144 720 3452 3016 3915 2837 750 4653 3264 M255 PID_HIF1_TFPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF1_TFPATHWAY.html HIF-1-alpha transcription factor network 18832364 93/113 Pathway Interaction Database 4.54385544362582e-07 1.04517532621413e-06 3560 2873.63636363636 3017 4.13077852918993e-08 1465 2.18976985859705 2.18332436860092 1 5.21691282593742 3559 3017 1465 1704 1866 4184 3929 3855 2217 2093 3721 3265 M18954 MANN_RESPONSE_TO_AMIFOSTINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANN_RESPONSE_TO_AMIFOSTINE_UP.html Genes up-regulated in HCT116 cells (colon cancer) after treatment with amifostine [PubChem=2141] depending on the presence of TP53 [GeneID=7157]: TP53-positive vs TP53-null cells. 15750621 26/28 Leona Saunders 6.00155900284477e-06 7.75454653529355e-06 2050 3024.09090909091 3017 5.45597761368038e-07 1140 1.10781717415038 1.23382659915861 1 2.22677574649588 2050 4026 3812 3017 3589 2137 1140 2815 4430 4335 1914 3266 M12771 SA_PTEN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/SA_PTEN_PATHWAY.html PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate. 20/22 SigmaAldrich 3.21450713050832e-07 8.99909469513599e-07 3655 2649.90909090909 3019 2.92227963653889e-08 545 1.14065010328796 -1.04109322778245 -1 2.72332737319559 3652 1883 3466 1315 1461 3019 2232 4249 545 4114 3213 3267 M6364 HEIDENBLAD_AMPLIFIED_IN_SOFT_TISSUE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLIFIED_IN_SOFT_TISSUE_CANCER.html Genes from selected recurrently amplified regions in soft tissue tumors with supernumerary ring chromosomes. 16732325 15/18 Arthur Liberzon 0.00505343393722333 0.00519429620725046 3025 3206.81818181818 3021 0.000460461747211946 1568 2.52940676165743 2.94256064442179 1 2.27379849803266 3021 4326 2704 3136 4561 3998 4347 2603 1568 3012 1999 3268 M2220 KEGG_FOLATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOLATE_BIOSYNTHESIS.html Folate biosynthesis 8/12 KEGG 1.56738087993886e-06 2.4717800712701e-06 3025 3153.45454545455 3022 1.56738198544722e-07 2284 1.40532578076301 -1.46513612576165 -1 3.11885500692351 3022 3242 4182 3869 2943 2577 2575 2284 3913 3276 2805 3269 M6376 MCCABE_BOUND_BY_HOXC6 http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_BOUND_BY_HOXC6.html Genes whose promoters where bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer), according to a ChIP-chip analysis. 18339881 503/926 Jessica Robertson 1.69440829032773e-07 7.33971845416521e-07 3545 2849.18181818182 3022 1.69440841952361e-08 879 2.09365490681388 2.42920577726811 1 5.11498539397493 3542 2502 4541 3069 879 3022 4010 2706 1775 1877 3418 3270 M8475 WANG_ESOPHAGUS_CANCER_VS_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ESOPHAGUS_CANCER_VS_NORMAL_UP.html Up-regulated genes specific to esophageal adenocarcinoma (EAC) relative to normal tissue. 16449976 174/224 Arthur Liberzon 1.05182728990905e-06 1.81921026323588e-06 4595 2865.63636363636 3023 9.56207084355909e-08 328 1.99602271628032 -1.61925681216815 -1 4.55769137894461 4593 2073 517 1848 3028 4599 2945 4016 3023 328 4552 3271 M17998 CAFFAREL_RESPONSE_TO_THC_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated THC (delta-9-tetrahydrocannabinol) [PubChem=6610319]. 18454173 60/72 Jessica Robertson 4.94812071134867e-06 6.53290342868971e-06 2330 3140.27272727273 3023 4.49830167311684e-07 2328 1.70722245973039 2.05409322609038 1 3.50980408362906 2328 4202 3113 3023 3508 2846 2542 2748 4334 2584 3315 3272 M12307 NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON.html Genes within amplicon 16q24 identified in a copy number alterations study of 191 breast tumor samples. 19010930 58/71 Jessica Robertson 1.65380061629251e-07 7.3358205358541e-07 2700 3045.36363636364 3024 1.50345521873933e-08 730 1.36312655932377 -1.08012875595867 -1 3.31290683680959 2698 3654 3758 4636 730 2143 2225 3024 3958 4189 2484 3273 M2221 ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP.html Genes up-regulated in K562 cells (lymphoblast) by MYC [GeneID=4609] in the presence of CKN1B [GeneID=1027]. 18838534 101/112 Arthur Liberzon 1.34874562223831e-07 7.20206492018647e-07 4495 2871.27272727273 3024 1.22613245902304e-08 143 1.6829762113834 -1.37518805698856 -1 4.10741091133414 4493 143 2778 4567 524 4071 4038 3166 1780 3000 3024 3274 M14447 MASSARWEH_RESPONSE_TO_ESTRADIOL http://www.broadinstitute.org/gsea/msigdb/cards/MASSARWEH_RESPONSE_TO_ESTRADIOL.html Genes rapidly up-regulated in breast cancer cell cultures by estradiol [PubChem=5757]. 18245484 84/105 Jessica Robertson 1.62461255828424e-06 2.54671912158805e-06 3150 2993.18181818182 3025 1.47692159817935e-07 2179 1.7366084390531 1.86355278449938 1 3.85681064565696 3150 3025 2441 3727 2914 3200 4115 2297 3486 2391 2179 3275 M1547 BIOCARTA_HDAC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HDAC_PATHWAY.html Control of skeletal myogenesis by HDAC and calcium/calmodulin-dependent kinase (CaMK) 38/43 BioCarta 4.9266842821958e-07 1.10365210308325e-06 3300 2857.81818181818 3026 4.4788048958898e-08 1674 1.41870178460368 1.61617136216141 1 3.34880973237611 3298 1762 3194 2951 1930 3615 3287 3026 1674 3974 2725 3276 M1508 JIANG_AGING_CEREBRAL_CORTEX_UP http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_CEREBRAL_CORTEX_UP.html Up-regulated in the cerebral cortex of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 79/99 John Newman 6.27505721428837e-06 8.06817489824057e-06 2830 2719.90909090909 3026 5.70461373881599e-07 189 1.87745053885876 2.44214014654666 1 3.79554410588988 2828 3894 2622 3241 3606 3026 3589 189 2463 3206 1255 3277 M7927 REACTOME_NUCLEOTIDE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEOTIDE_EXCISION_REPAIR.html Genes involved in Nucleotide Excision Repair 51/54 Reactome 9.8454262442786e-05 0.000108121014129816 805 2859.72727272727 3027 8.95078806707742e-06 803 0.981573554996329 1.05543229660084 1 1.51558173226142 803 3398 4034 3027 4251 1187 1006 2355 4373 4471 2552 3278 M7714 AMIT_EGF_RESPONSE_240_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_240_HELA.html Genes whose expression peaked at 240 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 80/85 Leona Saunders 2.38380842805121e-07 8.00711660757103e-07 1640 2777.72727272727 3027 2.16709880577149e-08 1145 1.70998257059789 1.73564925680342 1 4.14247772878372 1636 3627 2770 3454 1145 3027 3960 1715 3362 2687 3172 3279 M16561 JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_DN.html Down-regulated genes distinguishing between breast cancer tumors with mutated BRCA1 [GeneID=672] from those with mutated BRCA2 [GeneID=675]. 12096084 52/68 John Newman 7.95998617454734e-06 1.00189692650303e-05 3695 2976.18181818182 3027 7.23637725029133e-07 1706 2.09838618215691 2.15403483790542 1 4.16872051645626 2571 3075 2608 3691 3693 2827 3178 1706 3019 3343 3027 3280 M12459 CHIBA_RESPONSE_TO_TSA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIBA_RESPONSE_TO_TSA_DN.html Cancer related genes down-regulated in any of four hepatoma cell lines following 24 h treatment with TSA [PubChem=5562]. 15452378 48/53 John Newman 4.8434738365916e-06 6.4252941283621e-06 3175 2669.18181818182 3028 4.4031677271953e-07 420 2.71753712335979 -3.01680928983303 -1 5.62436055040146 3171 2252 1217 862 3491 4013 3028 3987 420 2216 4704 3281 M175 PID_ERBB2_ERBB3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB2_ERBB3_PATHWAY.html ErbB2/ErbB3 signaling events 18832364 60/65 Pathway Interaction Database 3.57791275936088e-07 9.41752134134615e-07 2215 2886.18181818182 3029 3.25264849204141e-08 212 1.2574220923668 -1.1734873691086 -1 2.99726440373692 3639 2211 3606 212 1581 3388 2802 4686 2212 4382 3029 3282 M185 PID_ALK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK1_PATHWAY.html ALK1 signaling events 18832364 29/33 Pathway Interaction Database 7.8215095988862e-06 9.86308450620969e-06 2250 2841.90909090909 3030 7.11048855118452e-07 1725 1.17517892722414 1.31413872719893 1 2.31585195438806 2250 3151 3481 3510 3686 1725 2048 2271 4225 3030 1884 3283 M729 REACTOME_FATTY_ACYL_COA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FATTY_ACYL_COA_BIOSYNTHESIS.html Genes involved in Fatty Acyl-CoA Biosynthesis 16/19 Reactome 1.98965976786998e-06 3.01224464033987e-06 2520 2812.18181818182 3031 1.80878324300205e-07 1325 1.5466511034753 -1.24420474067155 -1 3.38411385733527 2519 3206 2791 3155 3031 3135 2054 2602 1325 3553 3563 3284 M1560 RASHI_RESPONSE_TO_IONIZING_RADIATION_6 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_6.html Cluster 6: late responding genes activated in ATM [GeneID=472] deficient but not in the wild type tissues. 16314843 81/120 Arthur Liberzon 8.29723141844558e-07 1.53614043097655e-06 4355 3258.90909090909 3031 7.54294049792928e-08 1976 2.08554534229355 -2.33312794360205 -1 4.82595643900324 4353 3031 1976 2596 2416 4391 3373 4125 2698 2558 4331 3285 M926 REACTOME_PROSTACYCLIN_SIGNALLING_THROUGH_PROSTACYCLIN_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROSTACYCLIN_SIGNALLING_THROUGH_PROSTACYCLIN_RECEPTOR.html Genes involved in Prostacyclin signalling through prostacyclin receptor 15/22 Reactome 3.99631189101447e-07 9.88087591701849e-07 3145 2788.27272727273 3032 3.6330114699517e-08 1168 1.4400272861245 -1.01645038138742 -1 3.427719406547 3145 2412 3032 3182 1709 2768 1168 1838 4007 3421 3989 3286 M15589 PENG_GLUTAMINE_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUTAMINE_DEPRIVATION_UP.html Genes up-regulated in BJAB cells (B-lymphoma) after glutamine [PubChem=738] deprivation. 12101249 68/87 Broad Institute 1.13571636651968e-07 7.05613393308323e-07 4365 2632.54545454545 3034 1.03246947740846e-08 372 1.65196019943502 1.63510626819895 1 4.03669846537768 4363 2639 3092 648 372 3473 3765 3666 1008 3034 2898 3287 M2126 CHICAS_RB1_TARGETS_LOW_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_LOW_SERUM.html Genes up-regulated in IMR90 cells (fibroblast) grown under low serum conditions and after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 100/154 Arthur Liberzon 2.00467526664716e-06 3.03241209795026e-06 1390 2765.36363636364 3034 1.82243372121976e-07 1389 1.74251161169544 1.62605539156684 1 3.81696751899777 1389 3616 3322 3534 3034 1679 1662 2025 3138 4174 2846 3288 M15196 TIEN_INTESTINE_PROBIOTICS_2HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_2HR_UP.html Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 2h. 16394013 54/79 Arthur Liberzon 2.00511825375058e-06 3.03241209795026e-06 3535 3189.36363636364 3035 1.82283643750233e-07 2193 1.97845366569543 2.28602112984258 1 4.34057322894836 3533 3374 2430 2219 3035 4523 4344 3386 2193 3027 3019 3289 M8458 GRATIAS_RETINOBLASTOMA_16Q24 http://www.broadinstitute.org/gsea/msigdb/cards/GRATIAS_RETINOBLASTOMA_16Q24.html Genes from 16q24 region up-regulated in retinoblastoma tumors with 16q24 LOH (loss of heterozygocity) compared to those without the LOH. 17210724 21/22 Jessica Robertson 1.16692850660237e-07 7.06112554001409e-07 2865 2927 3035 1.06084415318076e-08 394 0.919214409128211 -0.941833842361152 -1 2.22386672342167 2865 2811 3767 3220 394 2168 3066 3035 3737 4309 2825 3290 M635 REACTOME_SIGNALING_BY_FGFR_IN_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR_IN_DISEASE.html Genes involved in Signaling by FGFR in disease 130/165 Reactome 2.63213914811847e-07 8.29691125636501e-07 3040 2820.54545454545 3036 2.3928540573043e-08 1248 1.47526964796571 -1.1158172470397 -1 3.5578507036957 3036 3594 3694 1332 1248 2213 1454 3499 2763 4349 3844 3291 M10161 BROWNE_HCMV_INFECTION_4HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_4HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 4 h time point that were not up-regulated at the previous time point, 2 h. 11711622 76/108 Arthur Liberzon 2.09246715600276e-06 3.14436325257339e-06 2055 2507.72727272727 3036 1.90224467835979e-07 957 2.24487773440227 2.34253274093327 1 4.91761084117528 2053 3036 957 3184 3058 3331 4677 2105 3197 969 1018 3292 M11749 HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP.html Genes up-regulated in SCLC (small cell lung cancer) cells with acquired resistance to ABT-737 [PubChem=11228183], an inhibitor of the BCL2 [GeneID=596] family proteins. 18381439 75/114 Jessica Robertson 2.36572226991085e-05 2.75776960088398e-05 3845 2962.81818181818 3037 2.15067973597728e-06 1666 2.20583713958869 -1.85791051884878 -1 3.99465799592231 3845 2171 1876 1718 3995 3658 3037 1666 3744 2699 4182 3293 M1904 SCHRAETS_MLL_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAETS_MLL_TARGETS_DN.html Genes down-regulated in fibroblasts from MLL [GeneID=4297] knockout mice. 12789274 34/47 Arthur Liberzon 2.35021688700351e-05 2.74104860554894e-05 2850 2961 3037 2.13658363116859e-06 696 3.02330762939282 3.18018087242553 1 5.49681001645879 2847 2283 696 2563 3994 3037 3751 4351 3393 963 4693 3294 M12391 DAUER_STAT3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAUER_STAT3_TARGETS_UP.html Top 50 genes up-regulated in A549 cells (lung cancer) expressing STAT3 [GeneID=6774] off an adenovirus vector. 15735721 67/84 Arthur Liberzon 8.11669147401342e-07 1.51485898605549e-06 3185 2876.18181818182 3038 7.37881315326486e-08 1527 2.01727212434763 -1.92955607468019 -1 4.67124927712037 3185 3358 1700 3706 2393 3038 1996 2941 3567 1527 4227 3295 M1729 GAVIN_FOXP3_TARGETS_CLUSTER_T4 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_T4.html Cluster T4 of genes with similar expression profiles in thymic T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 107/126 Jessica Robertson 1.82286766111814e-07 7.47800341964416e-07 3685 2816.63636363636 3038 1.65715255650603e-08 118 1.74523790481508 -1.52611449032459 -1 4.24975513753832 3683 118 3038 3861 846 3398 2245 4361 2610 2339 4484 3296 M15555 CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP.html Protein biosynthesis, transport or catabolism genes up-regulated in hyperploid multiple myeloma (MM) compared to the non-hyperploid MM samples. 17409404 63/115 Jessica Robertson 0.000325954740594662 0.000347527981840254 1000 3065.63636363636 3038 2.96366404068039e-05 813 0.778619830947049 -0.815298883344518 -1 1.03308628252637 997 4229 4134 3038 4395 1403 813 2946 4674 4637 2456 3297 M12461 FINAK_BREAST_CANCER_SDPP_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/FINAK_BREAST_CANCER_SDPP_SIGNATURE.html Genes in the stroma-derived prognostic predictor of breast cancer disease outcome. 18438415 18/33 Arthur Liberzon 2.01841441499798e-06 3.04958900089323e-06 4140 2957.72727272727 3039 1.8349238789246e-07 825 3.54180088299627 2.82772702838267 1 7.80647981221762 4138 2827 1375 1407 3039 4582 4027 4570 825 3754 1991 3298 M13950 KEGG_ASTHMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASTHMA.html Asthma 12/39 KEGG 1.98970477736566e-05 2.34316530667813e-05 3040 2734.72727272727 3040 1.80883888427965e-06 1544 2.42398777011375 -2.51527488489685 -1 4.46364062637803 3040 3224 1805 3359 3948 3101 2191 1924 3748 1544 2198 3299 M554 REACTOME_SPHINGOLIPID_DE_NOVO_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPHINGOLIPID_DE_NOVO_BIOSYNTHESIS.html Genes involved in Sphingolipid de novo biosynthesis 33/37 Reactome 1.10638040540237e-07 7.03739764799127e-07 3890 2834.72727272727 3040 1.00580041912934e-08 354 1.47102451808661 1.57935791760678 1 3.58977014013697 3888 2302 3123 4147 354 3040 2317 3812 2517 3153 2529 3300 M11961 PUJANA_CHEK2_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_CHEK2_PCC_NETWORK.html Genes constituting the CHEK2-PCC network of transcripts whose expression positively correlates (Pearson correlation coefficient, PCC >= 0.4) with that of CHEK2 [GeneID=11200]. 17922014 959/1174 Leona Saunders 2.45536450169946e-06 3.58802490650819e-06 365 2661.81818181818 3040 2.45536721467036e-07 363 1.35850489842652 1.39380500156161 1 2.92485532424925 363 3830 4422 3040 3206 1288 1032 1869 3322 4658 2250 3301 M2587 BIOCARTA_HSP27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HSP27_PATHWAY.html Stress Induction of HSP Regulation 18/25 BioCarta 2.73727292243223e-05 3.16897919889137e-05 3700 2884.45454545455 3041 2.48846089144074e-06 622 2.50736587306686 -1.66392380340629 -1 4.48668453351377 3697 3190 1824 2415 4024 3560 2092 2771 622 3041 4493 3302 M36 PID_IL27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL27_PATHWAY.html IL27-mediated signaling events 18832364 16/27 Pathway Interaction Database 1.16511666163208e-05 1.42655010192047e-05 3045 3070 3042 1.05920257465272e-06 1535 1.37953285512191 -1.35700248507393 -1 2.63834117033937 3042 2849 2925 2915 3800 3665 2462 1535 3840 3161 3576 3303 M616 REACTOME_SIGNALING_BY_NOTCH1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH1.html Genes involved in Signaling by NOTCH1 75/86 Reactome 7.22749750344518e-06 9.18518799576232e-06 3035 3169.09090909091 3042 6.57047386138009e-07 2143 1.62226418283343 -1.22162529046002 -1 3.23610684700316 3035 3042 3141 2984 3656 2634 2143 4164 2528 3655 3878 3304 M12383 OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP.html Genes up-regulated in hematopoietic stem cells (HSC, CD34+ [GeneID=947]) cultured in a three-dimentional collagen gel compared to the cells grown in suspension. 16166251 306/392 Leona Saunders 9.37997196565531e-07 1.67505576320974e-06 4250 2980.72727272727 3044 8.52725087720427e-08 1159 2.04045342568561 2.0936712939627 1 4.68967887519984 4247 2519 1159 2239 2522 3871 3044 3558 3680 1655 4294 3305 M6312 WU_APOPTOSIS_BY_CDKN1A_NOT_VIA_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/WU_APOPTOSIS_BY_CDKN1A_NOT_VIA_TP53.html Genes downstream of CDKN1A [GeneID=1026] in a TP53 [GeneID=7157] independent pathway in 2774qw1 cells (ovarian cancer). 12138103 18/19 Arthur Liberzon 4.45813861908017e-06 5.983057799846e-06 2270 3027.36363636364 3044 4.05286150290608e-07 1917 1.66446792226421 1.92596325103868 1 3.44621296065501 2266 3483 2809 2462 3446 3096 2961 1917 4404 3413 3044 3306 M1077 REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION.html Genes involved in Platelet activation, signaling and aggregation 227/310 Reactome 1.68721720973696e-07 7.33971845416521e-07 3050 2724.18181818182 3046 1.53383394466593e-08 765 2.11311587129805 2.32249919481063 1 5.16299536944052 3046 2959 1126 1318 765 3215 4431 4257 3385 1746 3718 3307 M1602 HEIDENBLAD_AMPLICON_12P11_12_DN http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_12P11_12_DN.html Down-regulated genes whose expression is associated with amplification of the 12p11-12 chromosome in pancreatic cancer cell lines. 15688027 34/38 Arthur Liberzon 6.99251136376683e-06 8.90333251604517e-06 2290 2609.36363636364 3046 6.35684871723957e-07 167 1.58337961874763 -2.04301475630706 -1 3.16595925418073 2287 4254 3287 3689 3647 3046 2374 260 1754 3938 167 3308 M5989 IVANOV_MUTATED_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/IVANOV_MUTATED_IN_COLON_CANCER.html Genes mutated in colon cancer cell lines, identified using the GINI method described in the paper. 17086209 17/17 Leona Saunders 7.02710465138977e-07 1.37341341426748e-06 2905 3291.18181818182 3047 6.38827899631392e-08 2268 1.32825285577782 -1.09693344807391 -1 3.08138735180215 2901 4050 3601 3970 2268 2858 2340 4665 3047 3662 2841 3309 M18795 REACTOME_METAL_ION_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METAL_ION_SLC_TRANSPORTERS.html Genes involved in Metal ion SLC transporters 19/24 Reactome 3.28170590372465e-07 9.05922275783096e-07 4180 3216.81818181818 3048 2.98336944841067e-08 1488 1.56846965045671 -1.38840119263263 -1 3.76169899107788 4179 2826 3048 3684 1488 3766 2975 2913 3438 2772 4296 3310 M16929 REACTOME_PI3K_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_CASCADE.html Genes involved in PI3K Cascade 61/105 Reactome 3.54123285393563e-07 9.39877005182141e-07 2655 3087.72727272727 3048 3.21930311268251e-08 1564 1.27429305118067 -0.987206656150725 -1 3.03859394556164 3048 2655 3763 3028 1564 2412 2655 3611 3896 3993 3340 3311 M14801 HOOI_ST7_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOOI_ST7_TARGETS_DN.html Genes down-regulated in PC-3 cells (prostate cancer) stably expressing ST7 [GeneID=7982] off a plasmid vector. 16474848 172/228 Leona Saunders 3.12327221464826e-07 8.90628469471876e-07 4255 2750.90909090909 3048 2.83933878004516e-08 429 2.39102233223114 2.49923434183572 1 5.76779838947255 4255 1464 433 1816 1424 4322 4041 4435 3048 429 4593 3312 M16004 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION.html Antigen processing and presentation 67/124 KEGG 1.45340502466507e-05 1.75135862047973e-05 905 2632 3049 1.32128602409925e-06 543 1.46863263069535 -1.43651641816855 -1 2.75935736708772 905 3049 3310 3556 3857 543 1406 3927 4219 2955 1225 3313 M19930 BILBAN_B_CLL_LPL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BILBAN_B_CLL_LPL_UP.html Genes up-regulated in B-CLL (B-cell chronic leukemia) samples expressing high levels of LPL [GeneID=4023] compared with those expressing low levels of the gene. 16617321 108/156 Arthur Liberzon 2.6872956047473e-07 8.34447350002084e-07 4180 3128.90909090909 3051 2.44299630272726e-08 1272 1.87333402042581 1.79089620113079 1 4.52947814338235 4180 2578 2564 3369 1272 4688 3667 3051 2058 2560 4431 3314 M7955 SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES.html Genes related to the insulin receptor pathway 64/82 Signaling Gateway 3.37237415218843e-07 9.13746684768849e-07 3615 3031.54545454545 3053 3.06579515376262e-08 1329 1.34996100414226 -0.743606773923778 -1 3.22864586310192 3614 3053 3777 1329 1520 4000 4176 2639 2834 4480 1925 3315 M1411 LAU_APOPTOSIS_CDKN2A_UP http://www.broadinstitute.org/gsea/msigdb/cards/LAU_APOPTOSIS_CDKN2A_UP.html Genes up-regulated by UV-irradiation in cervical cancer cells after knockdown of CDKN2A [GeneID=1029]. 17369842 67/74 Leona Saunders 1.19121297818996e-06 1.99521833110597e-06 3055 2907.36363636364 3053 1.08292147562287e-07 1132 1.88519642766831 1.8885906543021 1 4.27144621110884 3053 3901 3116 3769 2695 2126 1604 2785 1132 3544 4256 3316 M2560 HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_DN.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 11/16 Arthur Liberzon 2.06073234596444e-06 3.1016124594873e-06 1230 2493.27272727273 3053 1.8733947965889e-07 558 1.53151245952631 -1.7842156977772 -1 3.34267987599189 1226 3511 3331 4589 3053 1184 558 716 3825 3725 1708 3317 M3042 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_KERATAN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_KERATAN_SULFATE.html Glycosaminoglycan biosynthesis - keratan sulfate 13/15 KEGG 2.06627626290296e-06 3.10797449359528e-06 3055 2960.09090909091 3054 1.87843473053295e-07 944 2.13099363490435 -1.74121224517351 -1 4.6699312271955 4669 944 1506 3051 3054 4477 4305 3463 1426 1358 4308 3318 M4904 REACTOME_G_ALPHA_S_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_S_SIGNALLING_EVENTS.html Genes involved in G alpha (s) signalling events 59/145 Reactome 1.07358837293439e-07 6.9798031959371e-07 3870 2602.81818181818 3055 9.75989477568131e-09 338 2.18517834706564 2.35945226238381 1 5.35996223069015 3868 389 1099 3055 338 4229 3983 4009 2707 1160 3794 3319 M1375 LASTOWSKA_COAMPLIFIED_WITH_MYCN http://www.broadinstitute.org/gsea/msigdb/cards/LASTOWSKA_COAMPLIFIED_WITH_MYCN.html Genes co-amplified within MYCN [GeneID=4613] in primary neuroblastoma tumors. 17533364 43/50 Leona Saunders 2.38738737353204e-06 3.51152022532603e-06 3040 3136 3055 2.17035451297422e-07 1087 1.99281538558091 -2.16087309948924 -1 4.32138803288106 3055 3680 2351 3318 3132 4377 4389 3030 3038 3039 1087 3320 M2117 THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP http://www.broadinstitute.org/gsea/msigdb/cards/THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP.html Genes up-regulated in polymorphonuclear neutrophilic granulocytes (PMNs) attracted to skin wounds. 15187151 95/117 Kevin Vogelsang 3.87890248139382e-07 9.75928556086292e-07 2630 2954.36363636364 3055 3.5262756048162e-08 1619 1.59962639697379 -1.60769710165535 -1 3.81662064881365 2626 3328 3055 4457 1671 2013 1619 3007 3874 3150 3698 3321 M2425 YANG_BCL3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BCL3_TARGETS_DN.html Genes down-regulated in neonatal cardiac myocytes upon knockdown of BCL3 [GeneID=602] by RNAi. 19451226 9/24 Arthur Liberzon 4.49377060065464e-07 1.04185917010687e-06 4080 3064 3055 4.49377150938373e-08 1014 3.53815080455559 -3.60586096975688 -1 8.4620736174853 4079 1014 4701 1609 1934 4028 4226 4368 3055 1801 2889 3322 M1444 STONER_ESOPHAGEAL_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STONER_ESOPHAGEAL_CARCINOGENESIS_DN.html Genes down-regulated in esophagus by the carcinogen NMBA [PubChem=13643] and brought back to normal by a diet with PEITC [PubChem=16741] or black raspberries. 18676871 8/8 Jessica Robertson 3.65403668279006e-07 9.47640282569729e-07 1715 2571.09090909091 3056 3.65403728362947e-08 216 1.76334243715394 -1.04431605006621 -1 4.22141827528295 3836 1029 4483 3056 1713 4374 3740 840 216 3283 1712 3323 M7102 BILD_CTNNB1_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_CTNNB1_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing activated beta-catenin (CTNNB1) [GeneID=1499] oncogene from control cells expressing GFP. 16273092 113/126 Arthur Liberzon 1.32643150664837e-06 2.17236527112432e-06 1830 3059 3056 1.20584755125969e-07 1802 1.66726817091487 -1.50812299092875 -1 3.74711345014939 1830 3879 3329 4030 2770 3033 1802 3056 2000 4240 3680 3324 M614 REACTOME_PRE_NOTCH_PROCESSING_IN_GOLGI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRE_NOTCH_PROCESSING_IN_GOLGI.html Genes involved in Pre-NOTCH Processing in Golgi 22/24 Reactome 3.89672243226771e-07 9.76357383103197e-07 4450 3104.45454545455 3057 3.54247556588178e-08 1202 2.04151357981826 2.43367542347155 1 4.88460500264103 4545 2353 1772 4141 1677 4447 4447 3057 2282 1202 4226 3325 M13881 REACTOME_SIGNALLING_TO_ERKS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_ERKS.html Genes involved in Signalling to ERKs 43/46 Reactome 4.48956643510767e-07 1.04182662604269e-06 3210 2746 3058 4.08142486481741e-08 494 1.69052174132485 -1.39735484289347 -1 4.0170424360556 3209 2696 3058 494 1848 3720 2393 4490 568 3894 3836 3326 M1449 NADLER_OBESITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/NADLER_OBESITY_DN.html Genes down-regulated in adipose tissue from obese mouse strains compared to the lean ones. 11027337 62/80 Kevin Vogelsang 4.11263213395186e-07 1.00046055710989e-06 4285 3158.90909090909 3058 3.73875718432596e-08 1739 2.21595641504657 2.02480222630544 1 5.29682074929779 4282 3058 2262 2681 1739 4293 4298 2841 1923 3765 3606 3327 M268 PID_S1P_S1P2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P2_PATHWAY.html S1P2 pathway 18832364 32/36 Pathway Interaction Database 2.77811901752296e-06 3.97234830739423e-06 2600 2938.27272727273 3059 2.52556593244191e-07 1816 1.51291204345971 -1.47033979936725 -1 3.23609257179927 2596 3429 3059 2715 3227 2534 2424 3642 3519 3360 1816 3328 M16991 BIOCARTA_IGF1MTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1MTOR_PATHWAY.html Skeletal muscle hypertrophy is regulated via AKT/mTOR pathway 29/32 BioCarta 2.10152350365649e-06 3.15596275445709e-06 2525 3321.72727272727 3060 1.91047773737654e-07 2525 0.83430414881068 -0.859826547541166 -1 1.79564234029908 2525 3730 3971 3588 3060 2652 2715 2648 4555 4474 2621 3329 M10855 XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN.html Genes down-regulated in DU-145 cells (prostate cancer) in the presence but not in the absence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 98/188 Arthur Liberzon 5.73565639008852e-07 1.20643039934126e-06 3730 2649.72727272727 3060 5.21423444131047e-08 148 2.72594133991225 -2.27454911805102 -1 6.43822881204061 3727 148 669 3060 2085 4617 3791 4642 931 1622 3855 3330 M9752 RICKMAN_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_METASTASIS_UP.html Genes up-regulated in metastatic vs non-metastatic HNSCC (head and neck squamous cell carcinoma) samples. 18679425 433/504 Jessica Robertson 2.49121222776274e-07 8.17750684987324e-07 2675 3201.45454545455 3061 2.26473864532726e-08 1188 1.59789464300133 1.81523634278868 1 3.86178534867873 2671 4399 3926 4279 1188 2400 3061 3536 2921 4404 2431 3331 M1660 MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_DN.html Genes similarly down-regulated in 3T3-L1 cells (fibroblasts able to differentiate to adipocytes) upon stimulation of INSR or IGFR1 by NTF3 [GeneID=3643;3480;4908]. 12213819 14/16 John Newman 3.67503878111238e-05 4.20358226681095e-05 2580 3111.54545454545 3061 3.34100015731666e-06 1763 1.68404026550585 -1.0533603820357 -1 2.91389454833594 2580 2874 3061 3435 4076 2890 2565 3472 1763 3999 3512 3332 M8144 KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP.html Genes up-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 6 h. 18701491 1143/1374 Jessica Robertson 4.257051316578e-07 1.01481223304284e-06 2500 3370 3062 4.25705213209008e-08 1894 1.55036529857546 -1.47525061797904 -1 3.6869661644464 2498 4388 4501 4538 1894 2883 2916 3162 3062 4456 2772 3333 M2018 MIKKELSEN_NPC_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in neural progenitor cells (NPC). 17603471 72/107 Arthur Liberzon 8.41191913696795e-07 1.55216021604725e-06 4510 3027.36363636364 3062 7.64720213940976e-08 1506 1.99342518356525 -1.50358438293167 -1 4.60696794349401 4509 2627 1908 3062 2426 4211 3240 3914 1506 2273 3625 3334 M19230 EPPERT_LSC_R http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_LSC_R.html Genes up-regulated in functionally defined leukemic stem cells (LSC) from acute myeloid leukemia (AML) patients. 21873988 57/67 Kolja Eppert 2.12654439172182e-07 7.70763712250053e-07 3275 2942.45454545455 3062 1.93322236115999e-08 1015 1.99532457782435 -1.66239735193663 -1 4.8553602223732 3093 3062 2730 4565 1015 3274 2808 4275 1931 2340 3274 3335 M13863 BIOCARTA_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MAPK_PATHWAY.html MAPKinase Signaling Pathway 102/109 BioCarta 2.57916213330383e-07 8.26284126785448e-07 1485 2846.63636363636 3064 2.3446931233373e-08 1222 1.25652525931934 -1.25584305090741 -1 3.02379714443249 1481 3882 3950 2039 1222 2462 1660 3434 3910 4209 3064 3336 M11763 MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP.html Genes commonly up-regulated in SK-N-BE cells (neuroblastoma) after RNAi knockdown of CCND1 and CDK4 [GeneID=595;1019]. 18413728 77/136 Jessica Robertson 2.05323360437931e-06 3.09427286483727e-06 4085 3210.45454545455 3064 1.86657774603645e-07 2170 1.89668692687396 2.17209086219571 1 4.15242557593929 4085 2170 2456 3386 3049 3727 4637 2465 3064 3746 2530 3337 M4319 BIOCARTA_IL12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL12_PATHWAY.html IL12 and Stat4 Dependent Signaling Pathway in Th1 Development 16/29 BioCarta 1.56332069326899e-05 1.87186039376703e-05 2615 3040.90909090909 3065 1.42121072940116e-06 1926 1.3914461882241 -1.1909813463527 -1 2.5955338093934 2613 2858 2972 2468 3883 3065 1926 3691 3740 3160 3074 3338 M186 PID_PDGFRB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PDGFRB_PATHWAY.html PDGFR-beta signaling pathway 18832364 184/200 Pathway Interaction Database 2.43673956567572e-07 8.08620221515313e-07 3210 2769.36363636364 3066 2.21521803233746e-08 511 1.72460403298171 -1.29947528414265 -1 4.17536599272268 3208 2967 3066 511 1166 3270 2426 4453 1911 3220 4265 3339 M10694 SASAI_TARGETS_OF_CXCR6_AND_PTCH1_UP http://www.broadinstitute.org/gsea/msigdb/cards/SASAI_TARGETS_OF_CXCR6_AND_PTCH1_UP.html Up-regulated genes in medulloblastoma tumors from heterozygotic CXCR6 [GeneID=10663] knockout mice compared to those from PTCH1 [GeneID=5727] heterozygotic knockout mice. 17413002 12/19 Jessica Robertson 4.8112449306892e-06 6.38972314936776e-06 3070 2708.27272727273 3066 4.37386859324995e-07 953 1.81939013382196 1.68411378548074 1 3.75073415832709 3066 953 1653 3047 3487 3088 3111 3954 3330 1183 2919 3340 M17387 XU_GH1_EXOGENOUS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_EXOGENOUS_TARGETS_DN.html Genes down-regulated in MFCF-7 cells (breast cancer) by exogenous HG1 [GeneID=2688]. 15845533 172/268 John Newman 1.45450300098077e-06 2.33194774613765e-06 3910 3149.63636363636 3067 1.32227632964407e-07 1593 2.03225989072954 2.20802284440995 1 4.55320929363435 3909 2973 1593 2908 2840 3744 4290 3613 3067 1978 3731 3341 M19655 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_DN.html Genes down-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic D.B. Chr 3 (DB, small HSC population) vs parental D2 strain (huge HSC population). 17220891 40/56 Leona Saunders 3.96990486773912e-06 5.4087200606618e-06 1780 3023.09090909091 3068 3.6090109376903e-07 1679 1.70187377678924 2.1104456335614 1 3.55478235207341 1780 4522 3068 4605 3394 1686 1679 2582 4580 3510 1848 3342 M1690 YANG_MUC2_TARGETS_DUODENUM_6MO_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_DUODENUM_6MO_DN.html Genes down-regulated in duodenum of 6 month old MUC2 [GeneID=4583] knockout mice. 18794118 21/59 Jessica Robertson 2.24357689582863e-06 3.34270295085578e-06 4405 3016.90909090909 3068 2.03961743986258e-07 1618 2.4816363568118 -3.49790193994789 -1 5.41501712850885 4404 1873 1618 3068 3089 4138 4434 3481 2811 1946 2324 3343 M10759 LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_UP.html Top genes associated with favorable overall survival of mesothelioma patients after surgery. 16540645 7/12 Arthur Liberzon 0.000226875167725515 0.000243430505038516 2775 3181.90909090909 3070 2.26898333608014e-05 718 2.16528901371829 2.16528901371829 1 3.09669375589952 2775 4368 4637 4375 4717 2493 1362 718 4275 3070 2211 3344 M14105 DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_DN.html Genes down-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071], after low dose UVC irradiation. 15608684 16/28 Arthur Liberzon 0.0021887248596456 0.00226651630924248 4380 3003.63636363636 3071 0.000199173218624857 920 2.74736173941671 -0.952003334558384 -1 2.87198328055804 4377 4325 2104 2969 4604 4482 3071 1492 1136 3560 920 3345 M2767 KANG_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_CISPLATIN_RESISTANCE_UP.html Genes up-regulated in gastric cancer cell lines resistant to cisplatin [PubChem=2767]. 14734480 21/30 Arthur Liberzon 1.30520915779923e-06 2.14578113530944e-06 1655 2706.81818181818 3073 1.186554483773e-07 206 1.42546653710265 -1.19297632273457 -1 3.19948337252683 1652 4036 3073 4422 2757 1374 1625 3940 3609 3081 206 3346 M4655 HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_DN.html Genes down-regulated during differentiation of immature to mature B lymphocyte. 11779835 52/64 Arthur Liberzon 2.29470593127739e-06 3.40276845605696e-06 4190 3036.63636363636 3073 2.08609847706333e-07 1673 2.33147921277446 -2.17621235965233 -1 5.07708916825013 4186 3073 1735 2371 3107 4634 3533 3594 1673 2590 2907 3347 M12016 OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_UP.html Genes up-regulated in epithelial ovarian cancer (EOC) biopsies: invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 174/234 Leona Saunders 1.8297078988782e-06 2.80396794893023e-06 1550 2959.90909090909 3074 1.66337220056485e-07 1343 1.4499249381378 1.20088425238254 1 3.1874897160995 1549 4152 3917 3602 2988 1697 1343 3074 2044 4515 3678 3348 M1790 NADELLA_PRKAR1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NADELLA_PRKAR1A_TARGETS_UP.html Epithelial and mesenchymal markers up-regulated in MEF cells (embryonic fibroblasts) after knockout of PRKAR1A [GeneID=5573]. 18413734 12/14 Jessica Robertson 1.44520159801319e-05 1.7423631015638e-05 3315 2823 3074 1.31382826524698e-06 1135 3.03966900866134 3.75651139359996 1 5.7673772079534 3311 2429 1243 3074 3855 3677 3785 1150 1135 2973 4421 3349 M2434 GUO_TARGETS_OF_IRS1_AND_IRS2 http://www.broadinstitute.org/gsea/msigdb/cards/GUO_TARGETS_OF_IRS1_AND_IRS2.html Transcripts dependent upon IRS1 and IRS2 [GeneID=3667, 8660] for normal expression in liver. 19596788 130/168 Arthur Liberzon 1.51609911991181e-07 7.27669247795767e-07 4435 3066.36363636364 3074 1.37827202217424e-08 643 1.99501023809446 -1.52770921294368 -1 4.87463511146875 4433 2994 2329 2684 643 4451 4182 4146 1334 3074 3460 3350 M3430 BIOCARTA_CALCINEURIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CALCINEURIN_PATHWAY.html Effects of calcineurin in Keratinocyte Differentiation 21/22 BioCarta 8.80664631035875e-08 6.51622504172635e-07 3245 2365.36363636364 3075 8.00604242080972e-09 228 1.73913133772434 1.65624581542566 1 4.27652776323445 3242 858 2867 637 228 3178 4213 4015 416 3075 3290 3351 M12482 CADWELL_ATG16L1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CADWELL_ATG16L1_TARGETS_DN.html Genes down-regulated in Paneth cell (part of intestiinal epithelium) of mice with hypomorphic (reduced function) form of ATG16L1 [GeneID=55054]. 18849966 94/111 Jessica Robertson 1.2621467681723e-06 2.08590082134919e-06 3645 2852.36363636364 3075 1.14740681115488e-07 420 2.1404937240336 2.33801256810578 1 4.84005395912189 3644 3888 2354 3934 2740 3075 3324 2005 3084 2908 420 3352 M12530 NEBEN_AML_WITH_FLT3_OR_NRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NEBEN_AML_WITH_FLT3_OR_NRAS_DN.html Genes down-regulated in acute myeloid leukemia (AML) samples with constitutively activated FLT3 [GeneID=2322] or with activating point mutations within NRAS [GeneID=4893]. 15674343 20/29 Arthur Liberzon 2.79795294718215e-06 3.99828577375106e-06 3190 2917 3077 2.54359682328734e-07 1689 2.22375469572009 2.81953990168412 1 4.77755487593259 3190 2819 2017 1689 3230 3632 4259 3278 3077 2513 2383 3353 M19666 TIEN_INTESTINE_PROBIOTICS_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_24HR_DN.html Genes down-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 24h. 16394013 299/389 Arthur Liberzon 5.85324250470414e-07 1.22123997631427e-06 3270 2586 3079 5.32113096545255e-08 485 1.54678604546493 -1.34930613659881 -1 3.62831573184937 1309 4694 3941 3268 2101 485 904 3079 3268 4521 876 3354 M1219 SMID_BREAST_CANCER_ERBB2_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_ERBB2_DN.html Genes down-regulated in the erbb2 subype of breast cancer samples, characterized by higher expression of ERBB2 [GeneID=2064]. 18451135 8/9 Jessica Robertson 0.111805391462956 0.112496578065477 3715 2988.45454545455 3079 0.011786429997578 245 2.2553684813508 -1.99374252196385 -1 0.81060102073513 3715 2459 4552 2657 4663 3169 2387 3280 245 2667 3079 3355 M15887 IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_UP.html Genes up-regulated in adipose tissue mesenchymal stem cells (ASC) vs bone marrow mesenchymal stem cells (rBMSC) 18519682 172/244 Leona Saunders 1.31053911657684e-06 2.15156334964963e-06 4300 2974.54545454545 3080 1.19139990660465e-07 1139 1.81209080367997 -1.30171735174805 -1 4.07998767583671 4296 1448 1321 3080 2761 4360 4445 3459 2395 1139 4016 3356 M3721 ST_JNK_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_JNK_MAPK_PATHWAY.html JNK MAPK Pathway 48/52 Signaling Transduction KE 1.867054389599e-07 7.48955275608059e-07 3330 2791.09090909091 3082 1.69732231640787e-08 882 1.69817682599618 -1.14190416680863 -1 4.13335169349579 3328 3082 2755 2015 882 3257 4565 4049 1154 3224 2391 3357 M290 PID_IL12_STAT4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL12_STAT4_PATHWAY.html IL12 signaling mediated by STAT4 18832364 21/40 Pathway Interaction Database 7.02269543409128e-06 8.93935341124888e-06 3005 3148.36363636364 3082 6.38428895598032e-07 1134 1.56913636458607 -1.43187912772551 -1 3.13592328524545 3001 3186 3082 2502 3649 2930 1134 4630 4198 3730 2590 3358 M1146 CORRADETTI_MTOR_PATHWAY_REGULATORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CORRADETTI_MTOR_PATHWAY_REGULATORS_DN.html Major antagonists linked to the mTOR [GeneID=2475] signaling network. 17041621 11/29 Leona Saunders 1.83219440482867e-06 2.80686711807573e-06 3860 2927.72727272727 3083 1.66563266428237e-07 635 1.68554102400334 -1.91886016853297 -1 3.71329093804155 3859 3232 3083 1526 2990 3606 3031 3540 635 3720 2983 3359 M16708 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 5. 12554760 52/62 Arthur Liberzon 3.07845836429569e-05 3.549061839297e-05 2870 2863.45454545455 3086 2.79863767453145e-06 630 2.79967575456027 2.99254648687811 1 4.96018884496524 2868 3071 630 1257 4041 3559 4691 3686 3086 761 3848 3360 M14529 KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION.html List of genes in the 19q13 amplicon region based on a copy number alterations study of a panel of 16 pancreatic cancer cell lines and 31 primary tumors. 17332321 59/72 Jessica Robertson 6.11710838597121e-05 6.84188426108629e-05 2275 2978.09090909091 3087 5.56116225365847e-06 950 1.80000021892344 -2.20979229414189 -1 2.9648418810054 2271 3915 3087 3966 4170 2206 3235 2276 2909 3774 950 3361 M18168 CASTELLANO_NRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_NRAS_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) isolated from NRAS [GeneID=4893] knockout mice. 16909116 89/117 Leona Saunders 1.71605328232189e-07 7.35006487528071e-07 3550 2624.18181818182 3088 1.56004856016202e-08 785 2.02507053274549 -1.79439173327284 -1 4.94529030219198 3549 1620 1462 3088 785 3640 2547 3413 3430 1040 4292 3362 M1700 BAFNA_MUC4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAFNA_MUC4_TARGETS_DN.html Genes down-regulated in NIH3T3 cells (fibroblast) engineered to stably express MUC4 [GeneID=4585]. 19010895 6/7 Leona Saunders 2.52523690431872e-07 8.20875908290935e-07 3960 2570.27272727273 3088 2.52523719127573e-08 1 2.62055529351138 2.39035103211257 1 6.36362567811406 3960 1039 4515 78 1310 4018 3716 3088 1 2797 3751 3363 M12256 REACTOME_SIGNALLING_TO_RAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_RAS.html Genes involved in Signalling to RAS 34/36 Reactome 6.53195956752209e-07 1.30974736829448e-06 4415 3068.90909090909 3089 5.93814682446279e-08 504 1.81406820622302 -1.37149090987924 -1 4.24176079800827 4413 2739 2992 504 2201 4706 4020 3089 837 3936 4321 3364 M878 REACTOME_SIGNAL_TRANSDUCTION_BY_L1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_TRANSDUCTION_BY_L1.html Genes involved in Signal transduction by L1 49/53 Reactome 1.53529439055738e-07 7.28175281873995e-07 3390 2394.81818181818 3090 1.39572227063601e-08 317 1.81833648748465 1.96737064285806 1 4.4382961099395 3387 447 2362 896 650 3151 3656 4008 317 3090 4379 3365 M1657 LEE_CALORIE_RESTRICTION_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_MUSCLE_DN.html Down-regulated in the gastrocnemius muscle of aged (30-month) mice subjected to caloric restriction diet since young adulthood. 10464095 68/90 John Newman 2.28041956200141e-06 3.38841855517567e-06 1740 2499.72727272727 3090 2.07311084162149e-07 258 1.61212138501881 -1.68394810431111 -1 3.49634841779978 1740 3639 3090 3756 3099 1237 952 3118 3006 3602 258 3366 M6706 MILICIC_FAMILIAL_ADENOMATOUS_POLYPOSIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MILICIC_FAMILIAL_ADENOMATOUS_POLYPOSIS_DN.html Top genes down-regulated in colon epithelium biopsies from FAP (familial adenomatous polyposis) patients with mutated APC [GeneID=324]. 18829530 7/29 Jessica Robertson 1.63521306109556e-05 1.95101255014435e-05 3315 2884.45454545455 3090 1.63522509386807e-06 278 3.31389719707055 -2.41124324671569 -1 6.22673857512934 3313 1038 4512 2585 3920 3700 4405 278 3075 1813 3090 3367 M6177 REACTOME_NOTCH_HLH_TRANSCRIPTION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOTCH_HLH_TRANSCRIPTION_PATHWAY.html Genes involved in Notch-HLH transcription pathway 14/14 Reactome 3.51084319512293e-06 4.86671949514838e-06 3095 2882 3092 3.19168072533798e-07 737 1.35896499648344 -1.64633795560514 -1 2.85351359166595 3092 2864 3142 3396 3333 3608 2560 2665 737 3311 2994 3368 M9162 UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN http://www.broadinstitute.org/gsea/msigdb/cards/UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN.html Genes up-regulated in HUVEC cells (primary endothelium) after stimulation with leukotriene LTD4 [PubChem=3908] or thrombin (F2) [GeneID=2147] for 1 h. 16606835 53/80 Arthur Liberzon 5.11713556844998e-08 5.19978203455085e-07 3095 2281 3094 4.65194153406641e-09 53 2.28513017491167 -2.17882518545955 -1 5.7249204647106 3094 451 720 3357 53 3224 2297 4350 3824 467 3254 3369 M10575 DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN.html Genes exclusively down-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071] after high dose UVC irradiation. 15608684 131/142 Arthur Liberzon 2.22431485523762e-07 7.8190759646174e-07 3395 2949.63636363636 3095 2.02210461829772e-08 1064 1.69996337371933 1.98326980140114 1 4.12496864592055 2844 1561 3095 3754 1064 3931 4437 2093 2883 3391 3393 3370 M2094 MARTENS_BOUND_BY_PML_RARA_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/MARTENS_BOUND_BY_PML_RARA_FUSION.html Genes with promoters occupied by PML-RARA fusion [GeneID=5371,5914] protein in acute promyelocytic leukemia(APL) cells NB4 and two APL primary blasts, based on Chip-seq data. 20159609 581/739 Arthur Liberzon 3.10456095744571e-07 8.87621529251511e-07 4060 2905.36363636364 3095 3.10456139116924e-08 845 1.82796523163573 -1.53603386062937 -1 4.39884757732932 4057 1150 4655 845 1530 4014 3095 4600 1869 1666 4478 3371 M8023 MARKS_HDAC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARKS_HDAC_TARGETS_UP.html Genes whose transcription is up-regulated by histone deacetylase inhibitors. 17322921 36/53 Arthur Liberzon 1.83498986421902e-05 2.17234817133528e-05 3100 3194.27272727273 3096 1.66818651799713e-06 1971 2.52840785128956 3.12981230258538 1 4.69150668769733 3096 3417 2315 4262 3925 2342 3002 2926 1971 3859 4022 3372 M2085 VARELA_ZMPSTE24_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VARELA_ZMPSTE24_TARGETS_UP.html Top genes up-regulated in liver tissue from mice with knockout of ZMPSTE24 [GeneID=10269]. 16079796 52/57 John Newman 6.70506125892136e-05 7.46412479766717e-05 915 2625.45454545455 3096 6.0956960195354e-06 640 1.57696746357709 -1.70055533324753 -1 2.56730243519749 913 4224 3294 4045 4190 1241 894 640 4294 3096 2049 3373 M8155 MCBRYAN_PUBERTAL_BREAST_3_4WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_3_4WK_DN.html Genes down-regulated during pubertal mammary gland development between weeks 3 and 4. 17486082 38/47 Arthur Liberzon 1.07911853704572e-07 6.98688397397428e-07 4395 2790.81818181818 3097 9.81016899979446e-09 340 2.70500773403854 -2.14105862278735 -1 6.64646128943074 4391 2730 1801 2146 340 3740 3428 3921 606 3097 4499 3374 M3923 YU_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YU_MYC_TARGETS_DN.html Genes down-regulated in B cell lymphoma tumors expressing an activated form of MYC [GeneID=4609]. 16382050 69/100 Kevin Vogelsang 1.37635523574922e-07 7.20206492018647e-07 4080 2712.36363636364 3097 1.25123211077838e-08 548 1.85386811933626 -1.78788386133835 -1 4.52956437393838 4076 1646 1809 1828 548 4717 4175 3097 3545 751 3644 3375 M1538 YANAGIHARA_ESX1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/YANAGIHARA_ESX1_TARGETS.html Genes down-regulated in U2-OS Tet-On cells (osteosarcoma) after induction of ESX1 [GeneID=80712] expression. 15897875 45/70 Arthur Liberzon 7.29469955835183e-08 6.10478402755685e-07 3490 2571.81818181818 3098 6.63154527293409e-09 154 1.75898781958328 -2.01998865587396 -1 4.34596377098907 3489 526 2445 3098 154 4106 3191 2782 1402 3217 3880 3376 M1526 MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_7 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_7.html Cluster 7: genes up-regulated in SW260 cells (colon cancer) by curcumin and sulindac [PubChem=969516;5352]. 10969808 27/28 John Newman 2.35191501217292e-07 7.98635889025624e-07 3175 2643.45454545455 3099 2.13810478509542e-08 424 2.21207509648367 3.24143937366441 1 5.37450509031997 3175 3996 2627 3739 1130 3099 3283 424 748 3918 2939 3377 M2433 IM_SREBF1A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/IM_SREBF1A_TARGETS.html Genes differentially expressed in liver tissue upon knockout of the 1a isoform of SREBF1 [GeneID=6720]. 19564420 7/7 Arthur Liberzon 5.43137936327459e-06 7.1092930101653e-06 3025 3293.36363636364 3099 5.43139263826705e-07 1312 0.841066785815231 -0.918024371081301 -1 1.69130580618552 3024 2921 4702 3465 3587 2865 1312 3009 4146 4097 3099 3378 M10973 MATTIOLI_MGUS_VS_PCL http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MGUS_VS_PCL.html Genes changed in MGUS (monoclonal gammopathy of undetermined significance) compared to PCL (plasma cell leukemia) samples. 15735737 135/226 Leona Saunders 2.28072155715955e-06 3.38841855517567e-06 1370 2834.45454545455 3100 2.07338538324355e-07 1368 1.43633312114034 1.29953236779569 1 3.10964492784785 1368 2990 3643 3247 3100 1835 1813 2864 3292 3868 3159 3379 M1786 YAMASHITA_SILENCED_BY_METHYLATION http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_SILENCED_BY_METHYLATION.html Genes silenced by DNA methylation in prostate cancer cell lines. 18381416 10/12 Jessica Robertson 1.42667276304811e-05 1.72310528188001e-05 4140 3012 3100 1.29698364993486e-06 1133 2.45875457162713 -0.75503191871605 -1 4.66037771601872 4140 2448 2120 3100 3849 4628 2769 1133 1801 3595 3549 3380 M9054 TOMLINS_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_METASTASIS_UP.html Top genes up-regulated in hormone refractory metastatic prostate cancer compared to localized prostate cancer. 17173048 24/28 Leona Saunders 4.23589381040895e-06 5.72713227875401e-06 4140 3194.27272727273 3101 3.85081996931588e-07 2354 1.68389207986415 1.78820465388534 1 3.49987106335855 4137 2354 2769 2882 3418 3580 3689 3680 2548 3101 2979 3381 M12527 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN.html Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs poorly differentiated tumors. 18679425 505/587 Jessica Robertson 1.72835209832321e-07 7.37919956089047e-07 3770 2763.18181818182 3102 1.72835223274726e-08 717 2.09983960953089 2.49124143100553 1 5.1282754807148 3768 2500 4440 2058 902 3736 4051 3102 1594 717 3527 3382 M2152 IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_UP.html Genes up-regulated during transition from L0 (non-tumor, not infected with HCV) to L1 (non-tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 24/37 Yujin Hoshida 2.68472138331159e-07 8.34415403671576e-07 4670 2752.45454545455 3102 2.44065610085062e-08 583 2.22914071793357 2.39493758904277 1 5.3992910683832 4668 2783 2242 855 1269 4099 3669 3455 583 3102 3552 3383 M15187 GENTILE_UV_RESPONSE_CLUSTER_D6 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D6.html Cluster d6: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 51/54 John Newman 1.89323557681074e-07 7.49827400961101e-07 2020 2863.72727272727 3102 1.7211233997594e-08 896 1.46629399823496 1.65154706433983 1 3.5618198297413 2017 3381 3532 4465 896 2900 2847 929 3773 3659 3102 3384 M1361 DAZARD_RESPONSE_TO_UV_SCC_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_SCC_UP.html Genes up-regulated in SCC12B2 cells (squamous cell carcinoma) by UV-B irradiation. 12771951 152/186 John Newman 2.15744108008936e-07 7.72948789223918e-07 4150 3191.18181818182 3102 1.96131026514539e-08 1034 1.68407491073487 1.60597769560895 1 4.08933709748406 4150 1517 3077 2211 1034 3707 4083 4596 3102 3050 4576 3385 M2567 NATSUME_RESPONSE_TO_INTERFERON_BETA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NATSUME_RESPONSE_TO_INTERFERON_BETA_DN.html Genes down-regulated in T98 cells (glioma) 48 h after treatment with interferon beta. 16140920 63/112 John Newman 1.86116728596973e-07 7.48271685670965e-07 2705 3005.45454545455 3105 1.69197040311067e-08 876 1.59867688124943 1.78810362298245 1 3.88849263301084 2704 4483 3130 4621 876 3105 3464 1251 2784 3941 2701 3386 M2046 MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_2 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_2.html Cluster 2: genes up-regulated in SW260 cells (colon cancer) by sodium butyrate, curcumin, sulindac and TSA [PubChem=5222465;969516;5352;5562]. 10969808 13/17 Arthur Liberzon 2.29285504031313e-06 3.40132919978204e-06 1235 2259.63636363636 3105 2.08441584540528e-07 171 1.46645609216066 -1.50184213839939 -1 3.17493616039145 1231 3220 3179 3929 3105 849 171 2139 3710 3141 182 3387 M1633 SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_UP.html Genes up-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] but displayed blunted response to insulin the insulin resistant cells. 14530283 25/26 John Newman 3.48798384965687e-07 9.30654820258927e-07 3110 2768.36363636364 3107 3.17089491150765e-08 1293 2.61830281517941 1.99290812075425 1 6.30071368919072 3107 2340 1368 3115 1551 3314 4309 2672 3415 1293 3968 3388 M9880 ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_DN.html Genes down-regulated in immunoglobulin light chain amyloidosis plasma cells (ALPC) compared to multiple myeloma (MM) cells. 15388584 25/26 Kevin Vogelsang 1.74914452941796e-06 2.70509901010904e-06 3950 3125.72727272727 3108 1.59013265464029e-07 777 1.45795522989075 -1.02052490544495 -1 3.21456136785633 3946 1844 3108 2495 2956 3925 4238 4585 777 3520 2989 3389 M18215 BIOCARTA_TOB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TOB1_PATHWAY.html Role of Tob in T-cell activation 12/22 BioCarta 0.000236337062915526 0.000253294944814097 2515 2905.18181818182 3109 2.14874959513771e-05 430 1.30772805738928 -1.10399693374686 -1 1.84136063888426 2515 3508 3109 2663 4368 1389 430 3532 2845 3433 4165 3390 M17702 KERLEY_RESPONSE_TO_CISPLATIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/KERLEY_RESPONSE_TO_CISPLATIN_DN.html Genes genes down-regulated in NT2/D1 cells (embryonal carcinoma) in response to treatment with cisplatin [PubChem=2767]. 15940259 6/10 Leona Saunders 2.12499546082846e-05 2.49006419441667e-05 2585 2714.72727272727 3109 2.12501578132763e-06 217 1.86982184544466 -2.5318751657453 -1 3.41187732631878 2584 3255 4343 1884 3993 3733 3561 393 3109 2790 217 3391 M5813 WU_HBX_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_1_DN.html Genes down-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in SK-Hep-1 cells (hepatocellular carcinoma). 11439330 39/40 John Newman 1.51068058892182e-06 2.40323976397405e-06 2780 3064.18181818182 3111 1.37334693296944e-07 1335 1.6011064930046 -1.51083372854249 -1 3.56818796776647 2776 3111 3392 2511 2867 2231 1335 3828 3862 4026 3767 3392 M14648 CAFFAREL_RESPONSE_TO_THC_8HR_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_3_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 36/40 Jessica Robertson 0.000185777969082547 0.000200153392848579 505 2327.72727272727 3112 1.68903326246369e-05 330 1.53103921648594 1.57131861597177 1 2.22730707484069 502 3112 3452 3464 4340 330 413 2160 3562 3445 825 3393 M4856 MORI_LARGE_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_LARGE_PRE_BII_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Large Pre-BII stage. 18922927 76/100 Jessica Robertson 3.22721306459633e-07 9.01328145851757e-07 3235 2494.36363636364 3112 2.93383048909197e-08 238 2.19261938711037 -2.12616744655578 -1 5.28047107490721 3231 238 772 983 1466 4591 4625 4601 3112 482 3337 3394 M2112 KIM_ALL_DISORDERS_DURATION_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_DURATION_CORR_UP.html Genes whose expression in brain significantly and positively correlated with the duration of all psychiatric disorders studied. 18762803 10/16 Jessica Robertson 3.46995417736921e-06 4.81569647667824e-06 3645 2928.54545454545 3113 3.15450877306647e-07 394 2.17147201292675 2.97501683193439 1 4.59350500105679 3641 2894 2235 1946 3327 4311 4415 2562 394 3113 3376 3395 M5876 REACTOME_CTLA4_INHIBITORY_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CTLA4_INHIBITORY_SIGNALING.html Genes involved in CTLA4 inhibitory signaling 20/24 Reactome 1.27750258091248e-07 7.20206492018647e-07 4440 2785 3114 1.16136605008627e-08 112 1.5491586254343 -1.6629109981552 -1 3.77684196899817 4440 2815 3114 899 472 3973 2985 3581 112 3639 4605 3396 M18833 HU_ANGIOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HU_ANGIOGENESIS_DN.html Down-regulated genes that separate angiogenic from non-angiogenic non-small cell lung carcinoma (NSCLC) samples. 15592519 57/71 Leona Saunders 2.32080862032282e-06 3.43392372662185e-06 710 2661.09090909091 3114 2.10982824416149e-07 708 1.29669851033405 1.45364377852571 1 2.79945190568719 708 3650 3528 4273 3114 1404 1313 1296 3881 3959 2146 3397 M2376 IKEDA_MIR1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR1_TARGETS_DN.html Genes down-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-1 microRNA. 19188439 10/11 Arthur Liberzon 0.000103235908771896 0.000113214100697804 3255 2725.72727272727 3115 9.38552304343984e-06 788 1.39173294856837 -1.49584598638833 -1 2.15860109553467 3255 998 2930 3333 4258 3356 3722 2734 788 3115 1494 3398 M19251 TIEN_INTESTINE_PROBIOTICS_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_6HR_UP.html Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 6h. 16394013 85/131 Arthur Liberzon 2.21083862533602e-05 2.58616067201636e-05 1595 3036.63636363636 3117 2.00987349359554e-06 1015 1.73893079741315 -1.27857879919888 -1 3.15803632178465 1593 4479 3605 2744 3978 1545 1015 3050 3785 4492 3117 3399 M9096 IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_UP.html Genes up-regulated during transition from G2 (moderately differentiated tumor, infected with HCV) to G3 (poorly differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 37/49 Yujin Hoshida 0.00019534319286648 0.000210218848684402 1885 2781.63636363636 3117 1.77600490914646e-05 653 1.40794260399988 1.47126151208193 1 2.03214160004072 1884 3964 3640 3768 4622 1881 1727 653 3117 3739 1603 3400 M11782 SMID_BREAST_CANCER_RELAPSE_IN_LIVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LIVER_DN.html Genes down-regulated in liver relapse of breast cancer. 18451135 11/14 Jessica Robertson 1.58448315699622e-05 1.89479617456857e-05 3120 2671.54545454545 3117 1.44044960806346e-06 372 3.19893172998731 2.90617846849672 1 6.02532041210849 3117 1944 971 2070 3889 3763 3272 4605 372 1339 4045 3401 M2522 JIANG_HYPOXIA_VIA_VHL http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_HYPOXIA_VIA_VHL.html Genes up-regulated in 786-0 cells (renal carcinoma, RCC) by the loss of VHL [GeneID=7428] and in response to hypoxia. 12692265 44/50 Arthur Liberzon 2.3314849402925e-06 3.44566323250493e-06 3920 2657.54545454545 3117 2.11953401011305e-07 746 1.02661507134503 1.13747440050857 1 2.20533283491434 1136 4231 3918 4629 3117 823 746 1500 3918 4187 1028 3402 M7988 BORCZUK_MALIGNANT_MESOTHELIOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BORCZUK_MALIGNANT_MESOTHELIOMA_DN.html Genes down-regulated in biphasic (mixed) vs epithelial subtypes of malignant peritoneal mesothelioma. 16862182 112/198 Arthur Liberzon 3.42933834378849e-07 9.21518482625961e-07 4300 2593.81818181818 3118 3.11758079850044e-08 86 2.24281848514814 -1.93126703609339 -1 5.39383280497646 4298 86 911 1439 1536 4331 3392 4645 3118 1304 3472 3403 M6244 OHM_EMBRYONIC_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/OHM_EMBRYONIC_CARCINOMA_UP.html Genes with a high basal transcription state in undifferentiated embryonic carcinoma cells. 17211412 10/14 Leona Saunders 4.25461634853904e-06 5.74902181255242e-06 3320 2483.36363636364 3118 3.86784052421288e-07 270 2.00116857665883 2.25748239717478 1 4.16740627527376 3317 986 2092 3118 3419 3293 4495 818 270 2011 3498 3404 M2340 DALESSIO_TSA_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/DALESSIO_TSA_RESPONSE.html Top genes up-regulated in HEK293 cells (fibroblast) in response to trichostatin A (TSA) [PubChem=5562]. 17709385 27/59 Arthur Liberzon 6.62630208795058e-05 7.37993059347021e-05 2195 3191.36363636364 3118 6.02409243421512e-06 2126 2.58618525417887 -1.95057051242026 -1 4.24745509101458 2193 4017 2126 2483 4186 3422 3118 2981 4162 3429 2988 3405 M10547 BIOCARTA_MAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MAL_PATHWAY.html Role of MAL in Rho-Mediated Activation of SRF 34/42 BioCarta 2.58520581325041e-07 8.26284126785448e-07 4400 2942.09090909091 3119 2.35018737912393e-08 910 1.50152132454325 -0.973548547012057 -1 3.62313035083243 4398 3119 2991 910 1227 4242 3544 2169 1690 4214 3859 3406 M2317 KASLER_HDAC7_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/KASLER_HDAC7_TARGETS_1_UP.html Genes up-regulated in DO11.10 cells (hybridoma) by expression of transciptionally activating form of HDAC7 [GeneID=51564] and down-regulated by its transcriptionally repressing form. 17470548 232/263 Arthur Liberzon 2.48774169869076e-07 8.17750684987324e-07 4030 3003.27272727273 3120 2.26158361818415e-08 1185 1.81782558775432 2.0920463329354 1 4.40020058548425 4030 2056 2785 3855 1185 2718 3366 3615 2156 3120 4150 3407 M12113 WEI_MYCN_TARGETS_WITH_E_BOX http://www.broadinstitute.org/gsea/msigdb/cards/WEI_MYCN_TARGETS_WITH_E_BOX.html Genes whose promoters contain E-box motifs and whose expression changed in MYCN-3 cells (neuroblastoma) upon induction of MYCN [GeneID=4613]. 18504438 947/1100 Jessica Robertson 9.66054187526188e-07 1.71246465735939e-06 1310 3011.54545454545 3121 9.66054607493758e-08 1310 1.54229333081999 1.44716926137674 1 3.52656611757285 1310 3831 4435 3274 2611 2032 1841 3121 2835 4548 3289 3408 M19907 KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN.html Genes down-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 6 h. 18701491 1042/1244 Jessica Robertson 3.74501181182685e-07 9.58593045109694e-07 1510 3166.18181818182 3121 3.74501244295711e-08 1508 1.50826005653394 1.49238433682519 1 3.60048894152383 1508 4660 4502 4696 1743 1821 1911 3203 3121 4623 3040 3409 M19844 VALK_AML_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_1.html Top 40 genes from cluster 1 of acute myeloid leukemia (AML) expression profile; 57% of the samples are FAB M1 subtype, 43% have 11q23 abnormalities, and 36% have up-regulated EVI1 [GeneID=2122] expression. 15084694 30/45 Jessica Robertson 2.35524620075185e-06 3.47724806617102e-06 4545 2916.36363636364 3121 2.14113520200292e-07 1190 2.58449416114651 -2.25768740930304 -1 5.62371751053158 4541 3133 1190 1853 3121 4423 3677 1905 1841 1886 4510 3410 M1819 MATZUK_MEIOTIC_AND_DNA_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_MEIOTIC_AND_DNA_REPAIR.html Meitic and DNA repair genes important for female fertility, based on mouse models with female fertility defects. 18989307 41/156 Jessica Robertson 1.02399900360609e-05 1.26824332118099e-05 985 2299.72727272727 3123 9.30912518074927e-07 340 1.6171579898068 1.70376076987454 1 3.13463873466966 983 3697 3306 3527 3754 579 340 908 4304 3123 776 3411 M899 REACTOME_IL1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL1_SIGNALING.html Genes involved in Interleukin-1 signaling 43/45 Reactome 2.36916106853408e-06 3.49104621277383e-06 1100 2475.36363636364 3126 2.15378510897009e-07 552 1.51114451391066 -1.63932646742316 -1 3.26634170620181 1098 3947 3589 4245 3126 1136 552 1129 3983 3729 695 3412 M1739 GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_UP.html FOXP3 [GeneID=50943] target genes up-regulated in T lymphocytes after stimulation with IL2 [GeneID=3558]. 17220874 21/28 Jessica Robertson 1.62825744825657e-07 7.3358205358541e-07 3955 3031.27272727273 3126 1.48023415342426e-08 710 1.67829310202035 2.14560835310902 1 4.09044831245514 3954 1884 2714 3846 710 3752 3126 4514 2412 3080 3352 3413 M1507 ZAMORA_NOS2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZAMORA_NOS2_TARGETS_UP.html Up-regulated in hepatocytes upon expression of NOS2 [GeneID=4843]. 12381414 104/123 John Newman 2.74772169635322e-07 8.38703759494626e-07 3350 2921.36363636364 3129 2.49792912684904e-08 1298 1.73048041556649 1.72623583985402 1 4.17872327679853 1902 4175 3129 3007 1298 3003 3348 1865 3348 3629 3431 3414 M1632 BURTON_ADIPOGENESIS_11 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_11.html Strongly down-regulated at 2-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 110/129 John Newman 5.18846310882442e-07 1.13430041100747e-06 2330 3022.09090909091 3129 4.71678575678908e-08 1822 2.05445482411141 2.63043725382924 1 4.86208287746017 2326 3876 1822 3775 1982 3748 4216 3129 2642 2509 3218 3415 M7934 KEGG_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRUVATE_METABOLISM.html Pyruvate metabolism 41/49 KEGG 2.37901855072671e-06 3.50139306499223e-06 3130 3051.81818181818 3130 2.16274647575892e-07 1282 1.80468304552662 1.39313162498591 1 3.90961265619817 4590 2705 3149 1963 3130 3833 3754 1282 2071 3964 3129 3416 M567 REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE.html Genes involved in SRP-dependent cotranslational protein targeting to membrane 126/217 Reactome 0.000580895565032632 0.000611590909947591 4680 3087.36363636364 3130 5.28226366743886e-05 694 0.641765497584894 -0.521698566163872 -1 0.779356258877135 694 4463 4159 2749 4451 1711 801 2443 4680 4680 3130 3417 M7223 REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS.html Genes involved in Trafficking of AMPA receptors 25/32 Reactome 7.77518016666174e-07 1.46971767667775e-06 3745 3057.27272727273 3130 7.06834810413285e-08 1572 1.64549358201697 1.90962932184585 1 3.8098215298096 3742 1833 2611 2891 2355 3130 3289 3799 3917 1572 4491 3418 M19336 ST_TYPE_I_INTERFERON_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_TYPE_I_INTERFERON_PATHWAY.html Type I Interferon (alpha/beta IFN) Pathway 11/14 Signaling Transduction KE 0.000418196472994248 0.00044317183487491 2920 3080.45454545455 3131 3.80250898939538e-05 1162 1.72776344733337 2.33597572525868 1 2.28005930144285 2918 4085 2869 3131 4420 3564 4481 1162 1184 3717 2354 3419 M12001 SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5.html Cluster 5 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts good survival outcome. 18641660 128/191 Arthur Liberzon 2.38087729215042e-06 3.50303641488466e-06 1160 2860.45454545455 3131 2.16443624434554e-07 1160 1.29724590114459 -1.14762750663021 -1 2.79613997673925 1160 3600 3972 4082 3131 1348 1407 2690 3854 4108 2113 3420 M13526 AMIT_EGF_RESPONSE_20_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_20_HELA.html Genes whose expression peaked at 20 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 11/15 Leona Saunders 0.00393354265520212 0.00404936125028441 2875 3083.54545454545 3132 0.000358235762035088 1954 2.75775451929234 -2.78273253870707 -1 2.60352216763078 2875 3802 1954 3132 4553 2510 2002 2570 3950 3301 3270 3421 M2558 HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_UP.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 26/27 Arthur Liberzon 1.03279353227013e-06 1.79170077702221e-06 2875 3502.81818181818 3132 9.38903651924575e-08 1854 0.696155903745625 0.709519362434807 1 1.5588600404096 2871 4568 4028 4529 2595 2754 1854 3028 4613 4559 3132 3422 M18973 NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON.html Genes within amplicon 20q12-q13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 134/193 Jessica Robertson 2.39079619812501e-06 3.51543864646419e-06 4350 3091.90909090909 3133 2.17345345115297e-07 1175 1.8262906403664 1.95985866019525 1 3.95574483726449 4347 1555 2352 1479 3133 4491 4505 4002 1175 2985 3987 3423 M5451 HOSHIDA_LIVER_CANCER_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SURVIVAL_DN.html Survival signature genes defined in adjacent liver tissue: genes correlated with good survival of hepatocellular carcinoma (HCC) patients. 18923165 120/179 Yujin Hoshida 9.98710154920194e-08 6.71132834037269e-07 3705 3267.72727272727 3133 9.07918363870509e-09 310 1.7680579267818 1.44211761195475 1 4.33938036362094 3704 2997 3039 3398 310 4644 4421 4340 2846 3133 3113 3424 M14171 KEGG_STARCH_AND_SUCROSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STARCH_AND_SUCROSE_METABOLISM.html Starch and sucrose metabolism 27/58 KEGG 3.379208129365e-06 4.70636245813007e-06 3170 2995.72727272727 3134 3.07201210895667e-07 1638 2.1344399517569 2.10239314178965 1 4.52287586233502 3167 2779 2189 4357 3313 3134 2287 3553 1638 2764 3772 3425 M10628 BIOCARTA_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ATM_PATHWAY.html ATM Signaling Pathway 31/32 BioCarta 1.01088410841536e-05 1.25397450505138e-05 4550 2917.81818181818 3134 9.18989775804273e-07 507 2.02734378202688 -1.50411346949787 -1 3.94642569077531 4548 3134 2415 1546 3750 3981 3597 2804 507 1991 3823 3426 M1107 GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN.html Genes down-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) exposed to doxorubicin [PubChem=31703] in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 1007/1118 Arthur Liberzon 5.53273404407577e-07 1.18261660130095e-06 2955 3443.27272727273 3134 5.53273542157781e-08 2136 1.30858943269874 1.38163007675268 1 3.06921454630975 2955 4662 4340 4561 2136 2185 2430 3116 3684 4673 3134 3427 M1599 LEE_AGING_CEREBELLUM_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_CEREBELLUM_UP.html Upregulated in the cerebellum of aged adult mice (30-month) vs young adult (5-month) 10888876 114/161 John Newman 3.82613579719454e-07 9.66775212139092e-07 1660 2821.90909090909 3134 3.47830587510738e-08 1660 1.90443103672041 -1.96766355108027 -1 4.55653663211802 3453 3317 1978 3408 1660 3976 3134 2220 3951 1660 2284 3428 M17700 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP.html Genes up-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 16/24 John Newman 4.10199290796005e-05 4.66764863200854e-05 3295 2945.54545454545 3136 3.72915399395153e-06 485 1.37871573330636 -0.785594311410224 -1 2.35130322384062 3292 2848 3136 3717 4098 2856 2620 485 3743 3562 2044 3429 M19460 WOOD_EBV_EBNA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WOOD_EBV_EBNA1_TARGETS_DN.html Genes down-regulated in the Ad/AH cells (adenocarcinoma) engineered to stably express the Epstein-Barr virus (EBV) gene EBNA1. 17486072 60/74 Arthur Liberzon 2.90596936180489e-07 8.62110332351922e-07 4125 2916.72727272727 3137 2.6417906778664e-08 1358 2.00518331622828 -1.78060449909978 -1 4.84037243734377 4121 3056 2038 3137 1358 3491 3850 3156 2194 2150 3533 3430 M2177 FIGUEROA_AML_METHYLATION_CLUSTER_6_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_6_UP.html Cluster 6 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 152/199 Arthur Liberzon 5.43733736139899e-06 7.11511847679602e-06 3430 3156 3137 4.94304618174284e-07 1751 1.64513653359164 1.92834231101947 1 3.35581484151321 3429 3310 3472 4397 3537 1751 2994 3137 2980 3051 2658 3431 M18000 GOERING_BLOOD_HDL_CHOLESTEROL_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/GOERING_BLOOD_HDL_CHOLESTEROL_QTL_TRANS.html Top scoring trans-regulated expression quantitative trait loci (eQTL) influencing blood levels of high-density lipoprotein (HDL) cholesterol. 17873875 13/31 Leona Saunders 2.40136439063415e-07 8.03892842673661e-07 3155 2646.72727272727 3139 2.1830587752274e-08 951 1.48935792758215 1.60305977547452 1 3.60052143775333 3151 951 2648 2332 1151 3193 3773 4554 957 3139 3265 3432 M9257 KEGG_DRUG_METABOLISM_CYTOCHROME_P450 http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DRUG_METABOLISM_CYTOCHROME_P450.html Drug metabolism - cytochrome P450 41/122 KEGG 2.232481040655e-06 3.32932401639545e-06 4045 2706.27272727273 3140 2.02953027827259e-07 543 2.67199505543761 2.14211128778264 1 5.83609625738617 4041 543 757 1851 3086 3368 3277 3868 3140 1168 4670 3433 M16229 KANNAN_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANNAN_TP53_TARGETS_UP.html Primary up-regulated targets of TP53 [GeneID=7157] in the H1299 (lung cancer) cell line. 11402317 72/111 Broad Institute 1.32045907940691e-06 2.16408571347243e-06 3850 3226.09090909091 3140 1.20041806541688e-07 1999 1.83694127073895 2.36279155390176 1 4.13476371184187 3850 2635 1999 3140 2768 3569 2033 4404 3263 3127 4699 3434 M13327 VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_DN.html Genes down-regulated in uterine fibroids with deletions in the 7q region vs those without the deletion. 15940248 53/68 Leona Saunders 2.68897122744316e-07 8.34447350002084e-07 3545 3112.63636363636 3142 2.44451959645938e-08 1274 1.62579427296008 -1.70807617123331 -1 3.92434736999213 3545 3923 2909 4449 1274 2970 2243 2477 4134 3173 3142 3435 M2611 ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF.html Class I of genes transiently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 645/861 Yaara Zwang 1.25860775894996e-07 7.16209778122308e-07 4295 2789.63636363636 3142 1.25860783023417e-08 556 1.96518039821344 -1.62562466422067 -1 4.80644859855781 4293 1134 4717 2086 556 4280 3500 3142 1964 565 4449 3436 M14344 DASU_IL6_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_UP.html Genes up-regulated in normal fibroblasts in response to IL6 [GeneID=3569]. 15095275 113/166 Arthur Liberzon 2.43739964324839e-06 3.57061648545388e-06 3925 3062.63636363636 3143 2.21582031242673e-07 1550 1.95387110378627 -1.52589561862894 -1 4.23026484165603 3924 2572 1550 1553 3143 3861 3136 3359 4108 2051 4432 3437 M2411 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_5 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_5.html Genes regulated in MCF7 cells (breast cancer) by expression of the truncated (611-CTF) form of ERBB2 [GeneID=2064] at 15 h time point. 19364815 13/13 Arthur Liberzon 3.2622395640834e-07 9.05218738534606e-07 2870 3000 3143 2.96567277074562e-08 1477 1.54407486875609 -2.01069919955495 -1 3.7026236679825 2869 3222 2372 3902 1477 3272 3143 2810 4525 2175 3233 3438 M592 REACTOME_ACTIVATED_NOTCH1_TRANSMITS_SIGNAL_TO_THE_NUCLEUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_NOTCH1_TRANSMITS_SIGNAL_TO_THE_NUCLEUS.html Genes involved in Activated NOTCH1 Transmits Signal to the Nucleus 30/38 Reactome 1.43432881653651e-05 1.73190893170947e-05 3445 2710.54545454545 3144 1.30394378907423e-06 691 2.04411600014843 -0.838955449382942 -1 3.86420503400123 3443 3434 2146 3416 3850 2713 1532 691 1811 3144 3636 3439 M8845 CHIN_BREAST_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIN_BREAST_CANCER_COPY_NUMBER_DN.html Genes from common regions of losses observed in more than 15% of 148 primary breast cancer tumors. 17001317 19/23 Arthur Liberzon 2.43897557056086e-06 3.5718165352303e-06 4160 2868.63636363636 3144 2.21725297679544e-07 802 2.25330730429898 -1.39981883749435 -1 4.88610082503415 4156 1893 2007 2182 3144 4082 4292 802 1381 3183 4433 3440 M19341 KRIGE_AMINO_ACID_DEPRIVATION http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_AMINO_ACID_DEPRIVATION.html The 'amino acid deprivation response' (AADR): genes up-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after amino acid deprivation or treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703]. 18701491 35/39 Jessica Robertson 0.0526011140131356 0.0531415364173801 2050 3311.81818181818 3144 0.00490023306917451 1857 1.72096925429986 -1.75720546262575 -1 0.832099869479013 2049 4269 3144 4511 4720 2036 1857 2733 4416 3088 3607 3441 M901 REACTOME_GLOBAL_GENOMIC_NER_GG_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLOBAL_GENOMIC_NER_GG_NER.html Genes involved in Global Genomic NER (GG-NER) 33/34 Reactome 2.41859157260973e-05 2.81522866158272e-05 935 2812.81818181818 3146 2.19874378367508e-06 935 1.10499279515685 1.17208918928932 1 1.97213399647024 935 3146 3874 3549 4002 1165 1041 2346 4268 4181 2434 3442 M1141 SAENZ_DETOX_PATHWAY_AND_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAENZ_DETOX_PATHWAY_AND_CARCINOGENESIS_DN.html Detoxification pathway genes down-regulated in enterocytes of transgenic mice expressing SV40 T antigen. 17334401 20/56 Arthur Liberzon 2.44784507270025e-06 3.58157643084674e-06 3130 2965 3146 2.22531617846917e-07 852 2.06938140523403 -2.23613277220198 -1 4.48220298518405 3127 852 1453 3366 3146 4073 4592 4200 2711 1218 3877 3443 M1381 PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_UP.html Up-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that were identified as candidate genes for the regulation of left ventricle mass (LVM). 18443592 7/8 Jessica Robertson 2.1878763026454e-05 2.56056934006603e-05 3115 3030 3146 2.18789784355611e-06 1054 3.37984985973792 -4.42077842440997 -1 6.19116300243225 3114 3249 4457 2633 4000 3795 3146 1563 1054 3064 3255 3444 M2093 KAMIKUBO_MYELOID_MN1_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/KAMIKUBO_MYELOID_MN1_NETWORK.html Network of differentially expressed myeloid genes centered around MN1 [GeneID=4330]. 20478528 29/31 Arthur Liberzon 9.94155567654439e-06 1.23354739204231e-05 3380 2791.54545454545 3146 9.03781872874058e-07 1106 1.61104042625327 2.17059447358724 1 3.1303964613014 3377 3153 3193 3146 3748 2773 2858 1106 1397 3832 2124 3445 M1598 CHEN_PDGF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_PDGF_TARGETS.html Up-regulated PDGF targets identified by a gene-trap screen. 14981515 30/37 John Newman 3.54338575298161e-06 4.90031665809352e-06 3160 2826.81818181818 3147 3.22126496370679e-07 833 1.83047795355416 -0.929831009436455 -1 3.8587438860048 3156 3147 2485 4230 3340 3595 3351 2951 833 2817 1190 3446 M9043 BIOCARTA_GH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GH_PATHWAY.html Growth Hormone Signaling Pathway 44/53 BioCarta 2.62211405960084e-07 8.29211725993449e-07 3915 2967.54545454545 3148 2.38374033829346e-08 668 1.48287253152112 -1.19100390790698 -1 3.57659384394216 3914 2695 3148 668 1244 3758 2488 4710 1876 3955 4187 3447 M17693 GARY_CD5_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARY_CD5_TARGETS_UP.html Genes up-regulated in Daudi cells (B lymphocytes) stably expressing CD5 [GeneID=921] off a plasmid vector. 17878328 610/741 Arthur Liberzon 3.65892282551342e-07 9.48386366634999e-07 2815 3053.36363636364 3148 3.65892342796078e-08 1173 1.45048042600618 -1.39276471741115 -1 3.46335354578397 2814 4128 4285 3036 1715 2401 3280 3148 3165 4442 1173 3448 M2168 FIGUEROA_AML_METHYLATION_CLUSTER_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_3_UP.html Cluster 3 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 225/343 Arthur Liberzon 6.36773043489598e-07 1.29049753768609e-06 2170 2851.45454545455 3148 5.78884752544292e-08 992 1.65487873547725 1.79684855019501 1 3.86942331662327 2170 4414 3752 4071 2174 992 1830 3410 3148 3673 1732 3449 M4648 ZEMBUTSU_SENSITIVITY_TO_NIMUSTINE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_NIMUSTINE.html Top genes associated with chemosensitivity to nimustine [PubChem=39214] across 85 tumor xenografts. 11809704 17/30 Arthur Liberzon 2.45316015539831e-06 3.58632862080742e-06 4135 3006.90909090909 3149 2.23014808259522e-07 911 2.04692500033036 2.03829046647126 1 4.43254621465264 4131 911 2034 4345 3149 3922 3033 3387 1556 2049 4559 3450 M13143 BIOCARTA_UCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_UCALPAIN_PATHWAY.html uCalpain and friends in Cell spread 32/44 BioCarta 0.000152160322658473 0.000164535331717754 3590 2983.63636363636 3151 1.38337134237416e-05 1211 2.22663634285025 2.6705046467341 1 3.33818069876471 3586 3980 2282 2231 4321 4407 3151 2161 1211 3359 2131 3451 M18008 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_DN.html Genes from the red module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 38/50 Arthur Liberzon 6.11105883872111e-07 1.25409555298972e-06 3700 3095.09090909091 3154 5.55550957838507e-08 1170 2.01393149140543 2.44252923888336 1 4.72987836521533 3154 3699 2530 3484 2140 3698 4551 4095 1170 2806 2719 3452 M13976 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_UP.html Genes exclusively up-regulated in B lymphocytes from WM (Waldenstroem's macroblobulinemia) patients but with a similiar expression pattern in the normal cells and in the cells from CLL (chronic lymphocytic leukemia) patients. 17252022 13/16 Arthur Liberzon 2.46841950324091e-06 3.60375504339533e-06 4215 3159.81818181818 3154 2.24402024803076e-07 464 1.88033428361785 -1.0655187257306 -1 4.06613545251248 4214 2877 2356 3096 3154 3952 4646 4053 464 2173 3773 3453 M125 PID_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IGF1_PATHWAY.html IGF1 pathway 18832364 50/54 Pathway Interaction Database 4.43379711902865e-07 1.03485499371455e-06 3155 3143 3155 4.0307254659997e-08 1831 1.17665086215821 -0.961207668222355 -1 2.78214490536432 3155 3384 3816 2548 1831 2960 2324 2615 3804 4503 3633 3454 M14942 WANG_RESPONSE_TO_FORSKOLIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_FORSKOLIN_UP.html Genes up-regulated in LNCaP cells (prostate cancer) treated with forskolin [PubChem=47936], an activator of PKA pathway. 16751804 33/50 Arthur Liberzon 0.00034395340903792 0.000366386840591059 2725 3369.18181818182 3155 3.12733813938758e-05 2075 1.83448458525392 1.74661951061302 1 2.48494831121517 2723 3976 2861 4376 4398 2717 2601 4656 2075 3155 3523 3455 M1776 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_DN.html All common down-regulated stress response genes (Human Environmental Stress Response, H-ESR). 15897889 23/24 Jessica Robertson 4.54293344904947e-06 6.07957070584449e-06 3790 2852.27272727273 3155 4.12994802736067e-07 817 1.61135082861894 -1.22812942398074 -1 3.33013580128326 3786 817 2574 3856 3455 3846 2672 3155 902 2226 4086 3456 M10911 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYSTEINE_AND_METHIONINE_METABOLISM.html Cysteine and methionine metabolism 27/39 KEGG 6.28657295197763e-06 8.08078004720437e-06 2390 3064.18181818182 3156 5.71508265103652e-07 1614 1.47939775941819 1.3770513563953 1 2.9798093679765 2390 3156 3403 4383 3607 1852 1614 3903 3974 3130 2294 3457 M5304 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_8 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_8.html Amplification hot spot 8: colocolized fragile sites and cancer genes in the 9q11-34 region. 16751803 15/17 Arthur Liberzon 5.61486680328534e-06 7.32104179875878e-06 2520 3193.63636363636 3158 5.10443739424364e-07 2517 1.87609394208478 2.13553428936338 1 3.82460681939759 2517 3777 2911 3469 3551 3158 2872 4036 3025 2534 3280 3458 M17651 FRASOR_TAMOXIFEN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_TAMOXIFEN_RESPONSE_UP.html Genes preferentially up-regulated in MCF-7 cells (breast cancer) by tamoxifen [PubChem=5376] but not by estradiol or fulvestrant (ICI 182780) [PubChem=5757;3478439]. 16849584 64/76 Arthur Liberzon 3.38624452408102e-06 4.7119912009618e-06 3320 3039.81818181818 3159 3.07840885109708e-07 355 1.74747257414501 1.90933449388453 1 3.69345603277658 4438 355 2613 3317 3316 4389 3159 4638 2369 2693 2151 3459 M2565 HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP.html Genes distinguishing asparaginase resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 27/41 Arthur Liberzon 1.22540420199582e-06 2.03819039301383e-06 3830 3113.63636363636 3159 1.11400444049894e-07 1241 1.41717994871337 -0.714758628580653 -1 3.19332584931865 3828 3159 3245 4179 2717 2959 1241 3623 2559 3920 2820 3460 M12455 JAZAG_TGFB1_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_DN.html Genes down-regulated in PANC-1-puro cells (pancreatic cancer) stimulated by TGF1B [GeneID=7040] for 2 h. 15592526 41/68 Leona Saunders 1.22392410790916e-05 1.49313047023294e-05 4670 3216 3160 1.11266447000787e-06 1847 1.63751215581973 1.91721095777826 1 3.1280346443296 4667 2277 2923 3160 3814 3581 4395 1847 2036 3965 2711 3461 M14702 KIM_GASTRIC_CANCER_CHEMOSENSITIVITY http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GASTRIC_CANCER_CHEMOSENSITIVITY.html Genes up-regulated in gastric cancer patients refractory to chemotherapy treatment with 5-fluorouracil and cisplatin [PubChem=3385;2767] compared to the sensitive state. 15033468 122/169 John Newman 1.91195337233392e-06 2.91016443644505e-06 3450 3065.90909090909 3160 1.73814093996065e-07 1950 1.80707344607801 2.01030658614925 1 3.97323125952992 3449 3601 2849 2964 3012 3525 3423 2296 1950 3496 3160 3462 M13191 KEGG_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROSTATE_CANCER.html Prostate cancer 96/121 KEGG 3.37661116310889e-07 9.13746684768849e-07 4250 2500.09090909091 3161 3.06964698305376e-08 150 1.76757855902872 -1.59522398587252 -1 4.24292374818101 4248 150 2575 203 1523 4034 3189 4253 789 3376 3161 3463 M152 REACTOME_NUCLEAR_EVENTS_KINASE_AND_TRANSCRIPTION_FACTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEAR_EVENTS_KINASE_AND_TRANSCRIPTION_FACTOR_ACTIVATION.html Genes involved in Nuclear Events (kinase and transcription factor activation) 31/31 Reactome 2.49678815927559e-06 3.63617405485369e-06 2705 3066.09090909091 3161 2.26980999354022e-07 2071 1.40973207108161 1.34742017706076 1 3.03375189920199 2702 3427 3623 2517 3161 2207 2071 4106 2084 3960 3869 3464 M2332 BILANGES_SERUM_SENSITIVE_VIA_TSC1 http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_SENSITIVE_VIA_TSC1.html Genes translationally up-regulated by serum in MEF cells (embryonic fibroblast) lacking TSC1 [GeneID=7248]. 17562867 27/35 Arthur Liberzon 2.14626810190193e-06 3.21497475118283e-06 2580 3362.63636363636 3161 1.9511547234121e-07 2523 1.90696436735146 1.98740973712112 1 4.16245194675435 2578 4551 2523 4233 3071 2643 3200 3161 4575 3919 2535 3465 M4196 NUYTTEN_EZH2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_EZH2_TARGETS_UP.html Genes up-regulated in PC3 cells (prostate cancer) after knockdown of EZH2 [GeneID=2146] by RNAi. 17724462 1328/1657 Jessica Robertson 1.41474196067748e-07 7.20206492018647e-07 3870 2856.72727272727 3163 1.41474205074475e-08 361 1.90749990952731 -1.70064673789644 -1 4.6620507286525 3866 1072 4430 2125 671 3664 3163 4709 2790 361 4573 3466 M841 REACTOME_ADP_SIGNALLING_THROUGH_P2RY12 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADP_SIGNALLING_THROUGH_P2RY12.html Genes involved in ADP signalling through P2Y purinoceptor 12 16/23 Reactome 4.10015029042449e-06 5.5675228339481e-06 4370 3135.36363636364 3164 3.72741630173973e-07 1701 1.88770888101504 -1.01582819175635 -1 3.93886769875751 4367 1913 2417 2669 3403 3928 1701 4621 2210 3164 4096 3467 M1629 KYNG_RESPONSE_TO_H2O2_VIA_ERCC6 http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2_VIA_ERCC6.html Genes down-regulated in CS-B cells (Cockayne syndrome fibroblast, CS) with defficient ERCC6 [GeneID=2074] in response to hydrogen peroxide [PubChem=784]. 12606941 25/42 John Newman 2.57126038352487e-06 3.71938369912271e-06 2060 2539.63636363636 3164 2.33751217154772e-07 228 1.53327768485738 1.82447731673917 1 3.29794878469541 2058 3169 3164 3961 3182 1860 2453 228 3750 3211 900 3468 M2026 NAKAMURA_ADIPOGENESIS_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_LATE_UP.html Genes up-regulated in mesenchymal stem cells during late phase of adipogenesis, defined as days 7 to 14 of culturing with adipogenic hormones. 12646203 153/185 Arthur Liberzon 3.80521915161672e-07 9.64070552637194e-07 3275 2765.54545454545 3164 3.45929073616794e-08 1656 1.88582728554473 2.22453145096315 1 4.51245929612406 3271 2979 1733 3164 1656 3655 3598 3260 3327 1955 1823 3469 M8180 SAKAI_TUMOR_INFILTRATING_MONOCYTES_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_TUMOR_INFILTRATING_MONOCYTES_DN.html Selected genes down-regulated in inflammatory monocytes infiltrating hepatocellular carcinoma (HCC). 19074895 100/137 Jessica Robertson 2.50984888647538e-06 3.65068928941874e-06 945 2911.18181818182 3165 2.28168340892452e-07 941 1.21495464452357 1.3501728259878 1 2.60683086200562 941 4181 4024 4315 3165 1710 1176 1587 4130 4356 2438 3470 M745 REACTOME_MRNA_CAPPING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_CAPPING.html Genes involved in mRNA Capping 29/31 Reactome 0.000373332642905571 0.000396518918657583 1340 3102.90909090909 3166 3.3945091932897e-05 1338 0.793475950907134 0.848785317965048 1 1.03547585555187 1338 3166 3991 2533 4406 2063 1665 2779 4425 4538 3228 3471 M2106 KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_DN.html Genes whose expression was significantly and negatively correlated with the number of perineuronal oligodendrocytes in the layer III of BA9 brain region. 18762803 55/111 Jessica Robertson 3.94184548562724e-06 5.3757615406416e-06 2890 3080.18181818182 3167 3.58350231676229e-07 1563 2.01350483634066 -1.39436687683137 -1 4.2170123719844 2890 3371 1718 3167 3391 3417 2941 4654 1563 2158 4612 3472 M1854 RIZ_ERYTHROID_DIFFERENTIATION_6HR http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_6HR.html Selected genes down-regulated in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts) at 6 h time point. 17213805 32/53 Leona Saunders 1.82260137396578e-06 2.79398456808005e-06 4655 3234.36363636364 3169 1.65691171264642e-07 1613 2.13172328456477 2.27084840194983 1 4.71120029292402 4654 3707 1613 2779 2987 4089 4019 3608 3095 1858 3169 3473 M1336 RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_UP http://www.broadinstitute.org/gsea/msigdb/cards/RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_UP.html Angiogenic genes up-regulated in hepatocytes after knockout of VHL and HIF2A [GeneID=7428;2034]. 18490920 7/13 Jessica Robertson 2.98243412917218e-06 4.22101621879841e-06 3180 3069.63636363636 3169 2.98243813189074e-07 1030 2.49629252369708 -2.53133099799988 -1 5.3455771975081 3179 1030 4438 2825 3299 4609 1674 4367 3169 2401 2775 3474 M1652 MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6.html Cluster 6: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate and sulindac [PubChem=5222465;5352]. 10969808 73/95 John Newman 2.56174929902168e-06 3.70856209820526e-06 3170 3175 3169 2.32886571091648e-07 2688 1.60046942063895 1.64470229230503 1 3.44547967778511 3169 3043 3510 2967 3179 3062 3269 3713 2688 2757 3568 3475 M2036 BAUS_TFF2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAUS_TFF2_TARGETS_DN.html Genes down-regulated in pyloric atrium with knockout of TFF2 [GeneID=7032]. 16121031 10/14 Arthur Liberzon 2.5208232708159e-06 3.66213783879687e-06 4585 3096.36363636364 3169 2.29166014477485e-07 1955 1.66777055918947 -1.66539000518614 -1 3.59613860252284 4581 1955 2346 2372 3169 3987 3854 2764 3829 2017 3186 3476 M270 PID_MAPK_TRK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MAPK_TRK_PATHWAY.html Trk receptor signaling mediated by the MAPK pathway 18832364 47/49 Pathway Interaction Database 1.68737334136782e-07 7.33971845416521e-07 3305 3076.81818181818 3170 1.53397588253393e-08 766 1.89068286689991 2.4324180260042 1 4.61425570689299 3303 2689 2598 1997 766 3170 4562 4195 3608 3932 3025 3477 M6753 ODONNELL_TFRC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TFRC_TARGETS_UP.html Genes up-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) upon knockdown of TFRC [GeneID=7037] by RNAi. 16508012 545/822 Leona Saunders 2.72048642260994e-09 4.01271747334967e-08 3940 2553.54545454545 3170 2.72048642594041e-10 96 2.16806630900385 2.3886287657233 1 6.39912180215468 3936 1156 4306 96 1663 3342 3170 3878 2223 195 4124 3478 M1140 DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN.html Genes down-regulated in squamous cell carcinoma (SCC) compared to normal skin. 17525749 225/323 Arthur Liberzon 6.57307384731608e-07 1.31572979471297e-06 4365 3066.27272727273 3170 5.97552346472198e-08 759 1.91024383010153 -1.45588005387347 -1 4.46777663158085 4364 4145 3062 2721 2208 3769 3833 3321 2377 3170 759 3479 M615 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION.html Intestinal immune network for IgA production 26/53 KEGG 2.53313170331503e-06 3.67549389475774e-06 3935 2667.18181818182 3172 2.3028496545701e-07 648 2.29350087981791 -2.64793952126324 -1 4.96268789854341 3933 747 1047 2755 3172 3671 4611 3606 1852 648 3297 3480 M19520 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_DN.html Genes from the green module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 33/42 Arthur Liberzon 1.70813673904316e-05 2.0303211806305e-05 3545 3010 3173 1.55286363781955e-06 1094 2.0346390687396 2.38459863567018 1 3.78956583096517 3543 3724 2753 3158 3910 4625 3173 2414 1277 3439 1094 3481 M7946 KEGG_NOTCH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NOTCH_SIGNALING_PATHWAY.html Notch signaling pathway 47/52 KEGG 5.05290370466534e-06 6.65820923674495e-06 3370 3219.54545454545 3174 4.59355937280235e-07 2046 1.60639424581322 -1.20042979262826 -1 3.29423005313871 3367 3084 2976 3927 3515 3174 2823 3456 2046 3146 3901 3482 M776 REACTOME_PROTEIN_FOLDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROTEIN_FOLDING.html Genes involved in Protein folding 62/70 Reactome 1.07567825143525e-06 1.85102453776376e-06 3980 3087.09090909091 3174 9.77889797620675e-08 1666 1.58911229692426 -1.10656084056237 -1 3.61354518941563 3979 2650 3174 2011 2618 3706 3556 3937 1666 3596 3065 3483 M15164 FAELT_B_CLL_WITH_VH3_21_UP http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH3_21_UP.html Genes up-regulated in samples from B-CLL (B-cell chronic lymphocytic leukemia) with the immunoglobulin heavy chain VH3-21 gene. 15817677 63/70 Kevin Vogelsang 1.43639217296135e-06 2.31076041457995e-06 2335 3442.27272727273 3174 1.30581191890055e-07 2331 1.38775603258844 1.44401092061586 1 3.09556392305251 2331 4496 3898 4502 2827 3100 3121 3630 3174 4232 2554 3484 M4517 MUNSHI_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MUNSHI_MULTIPLE_MYELOMA_UP.html Genes up-regulated in multiple myeloma (MM) compared to normal plasma cells from the patient's identical twin. 12969976 146/189 Kevin Vogelsang 4.38713653178267e-07 1.02918908697884e-06 3045 3263.09090909091 3176 3.98830673331367e-08 1821 1.57925006761634 -1.52638488689991 -1 3.75270984995389 3043 4162 3636 2736 1821 2965 3176 4181 3850 3773 2551 3485 M11338 GENTILE_RESPONSE_CLUSTER_D3 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_RESPONSE_CLUSTER_D3.html Cluster d3: genes progressively down-regulated in WS1 cells (fibroblast) through 12 h irradiation with high dose UV-C. 12907719 72/80 John Newman 3.32565882597511e-06 4.64411528361021e-06 2605 3225.63636363636 3176 3.02333077569226e-07 2602 1.29694156952825 1.50009859185882 1 2.73160042778793 2602 3044 3796 3770 3304 2693 2738 3259 3175 3925 3176 3486 M3190 WU_HBX_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_1_UP.html Genes up-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in SK-Hep-1 cells (hepatocellular carcinoma). 11439330 21/24 John Newman 4.9957267900564e-08 5.11493068309462e-07 3640 2817.18181818182 3178 4.54156991227146e-09 52 2.52334107095395 -2.88310285596853 -1 6.33417568203148 3640 3178 1835 3924 52 4534 3326 689 4058 3079 2674 3487 M4361 KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION.html Proximal tubule bicarbonate reclamation 21/32 KEGG 8.313757528e-06 1.04280987329684e-05 4690 2939.72727272727 3180 7.5579899506322e-07 231 2.55038102619784 2.13914966082519 1 5.0596176599681 4686 3180 1829 3667 3705 3382 3093 231 2791 2300 3473 3488 M181 PID_BMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BMP_PATHWAY.html BMP receptor signaling 18832364 47/54 Pathway Interaction Database 1.65930411432914e-07 7.3358205358541e-07 3180 2967.36363636364 3180 1.5084583995261e-08 735 1.99845784461505 2.31641375649733 1 4.88032075347256 3180 3935 2783 4002 735 3517 4198 1401 2682 3781 2427 3489 M535 DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_UP.html Genes up-regulated in CD34+ [GeneID=947] cells isolated from bone marrow of CML (chronic myelogenous leukemia) patients, compared to those from normal donors. 17252012 1707/1965 Leona Saunders 3.89150059394355e-07 9.76357383103197e-07 1865 3228.54545454545 3180 3.89150127541367e-08 1791 1.29210437768513 1.27078642630171 1 3.07317142159335 1865 4652 4290 4343 1791 2284 2109 2790 3508 4702 3180 3490 M15615 DER_IFN_GAMMA_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_GAMMA_RESPONSE_UP.html Genes up-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon gamma for 6 h. 9861020 128/230 Yujin Hoshida 1.76038891456288e-06 2.71892528689031e-06 3585 3187 3180 1.60035483926072e-07 1556 1.49056371610382 -1.25041520809715 -1 3.286249822431 3584 1556 2719 2242 2959 3323 3180 4291 4037 2781 4385 3491 M15884 NIKOLSKY_BREAST_CANCER_7P22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_7P22_AMPLICON.html Genes within amplicon 7p22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 51/58 Jessica Robertson 1.11230263501139e-06 1.90082130240904e-06 2520 3237.63636363636 3181 1.01118472489384e-07 2330 1.58262075094172 1.89793974219775 1 3.59124147589723 2518 4509 3229 4493 2640 2441 2330 2689 3396 4188 3181 3492 M2360 TERAO_AOX4_TARGETS_HG_UP http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_HG_UP.html Genes up-regulated in Harderian gland tissue upon knockout of AOX4 [GeneID=71872]. 18981221 39/44 Arthur Liberzon 4.20878877766368e-06 5.69701262706411e-06 1585 2828 3181 3.82617893587211e-07 753 1.10491090693345 -0.92976112407777 -1 2.28030565309574 1582 4242 3945 3781 3414 1232 753 2607 3181 4352 2019 3493 M10445 DORSAM_HOXA9_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORSAM_HOXA9_TARGETS_UP.html HOXA9 [GeneID=3205] targets up-regulated in hematopoietic stem cells. 14604967 54/66 Broad Institute 5.2907824872673e-07 1.14710580339466e-06 3430 2833.09090909091 3182 4.80980341786237e-08 1507 1.59968234778022 1.95845670167752 1 3.77160342562982 3430 1705 3182 2466 2004 3334 3976 3213 3107 3240 1507 3494 M519 REACTOME_GROWTH_HORMONE_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GROWTH_HORMONE_RECEPTOR_SIGNALING.html Genes involved in Growth hormone receptor signaling 25/54 Reactome 0.000110250615437047 0.000120654510749562 1570 2814.27272727273 3184 1.00232855377098e-05 991 1.78493081568777 -1.54317456502892 -1 2.76275124197916 1566 4562 3184 4035 4272 1250 991 1170 3611 4002 2314 3495 M1403 PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN.html Genes down-regulated in long term hematopoietic stem cells (LT-HSC) compared to multipotent progenitor (MPP) cells. 11781229 24/32 Kate Stafford 4.66935705780205e-06 6.22580941040274e-06 2655 2790.18181818182 3184 4.24487906203497e-07 1229 1.1326774190196 1.62203585162485 1 2.32130772737595 2654 2360 3542 3446 3470 3184 3632 1229 1543 4389 1243 3496 M6509 PARK_HSC_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_MARKERS.html Genes in a cCDNA library from hematopoietic stem cells (HSC) after subtraction of lineage-specific markers. 11781229 50/59 Kevin Vogelsang 1.00497794111678e-07 6.71883269415184e-07 2805 2713.36363636364 3186 9.13616351840906e-09 313 1.62237152337679 -1.70593824091703 -1 3.97737959278054 2803 4507 3393 4427 313 3186 3295 575 1896 3780 1672 3497 M13123 LEE_LIVER_CANCER_HEPATOBLAST http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_HEPATOBLAST.html Fig.5, Supplementary Fig.2 Genes overexpressed in human hepatocellular carcinoma with hepatoblast property 16532004 19/21 Yujin Hoshida 0.000154846189900918 0.000167362953133119 3850 3366.54545454545 3187 1.40779172515497e-05 1754 3.35799210774614 -2.83973545853934 -1 5.04974341030929 3847 4580 1754 2170 4324 4297 2650 2846 3088 3187 4289 3498 M17776 REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR.html Genes involved in Downstream signaling of activated FGFR 94/117 Reactome 1.67330603977525e-07 7.3358205358541e-07 4470 2741.36363636364 3188 1.52118742458715e-08 177 1.55874661240239 -1.10308659759531 -1 3.79551740655857 4466 177 3188 510 752 4255 3048 4565 1879 4034 3281 3499 M2276 KIM_PTEN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_PTEN_TARGETS_UP.html Genes up-regulated in HCT116 cells (colorectal carcinoma) upon knockout of PTEN [GeneID=5728]. 17060456 19/23 Arthur Liberzon 2.63879658516453e-05 3.05872295726341e-05 3190 3165.90909090909 3188 2.39893476074606e-06 1984 1.46449943952778 1.33273548838499 1 2.60882398557752 3188 3757 3270 2937 4018 3187 3592 2265 4228 1984 2399 3500 M12977 KORKOLA_EMBRYONAL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONAL_CARCINOMA_DN.html Genes from the 12p region that were down-regulated in embryonic carcinoma tumors compared to normal tissue. 16424014 32/70 Arthur Liberzon 1.43357151722464e-06 2.30700905601783e-06 2825 3188.81818181818 3189 1.30324768306751e-07 1692 2.39391072349717 2.32217028878108 1 5.37687559740837 3556 4261 2197 3189 2825 4558 4411 1692 1749 3818 2821 3501 M632 KORKOLA_SEMINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_SEMINOMA_DN.html Genes from the 12p region that were down-regulated in seminoma tumors compared to normal testis. 16424014 32/69 Arthur Liberzon 1.43357151722464e-06 2.30700905601783e-06 3560 3189.81818181818 3190 1.30324768306751e-07 1693 2.39391072349717 2.32217028878108 1 5.37687559740837 3557 4262 2198 3190 2826 4559 4412 1693 1750 3819 2822 3502 M2172 FIGUEROA_AML_METHYLATION_CLUSTER_5_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_5_UP.html Cluster 5 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 14/20 Arthur Liberzon 0.0209107573199594 0.0212804602307478 3195 3112.09090909091 3191 0.0019192906769892 761 2.45019514425324 2.33381790502029 1 1.59752773560028 3191 4332 3088 4403 4667 1604 761 2760 2416 3315 3696 3503 M668 BIOCARTA_BARR_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARR_MAPK_PATHWAY.html Role of fl-arrestins in the activation and targeting of MAP kinases 22/26 BioCarta 1.2303015127863e-06 2.04544668557638e-06 3195 3380.45454545455 3193 1.11845654618713e-07 2721 0.866954661653874 -0.810838715280362 -1 1.93354019944288 3193 3181 3857 3579 2721 3276 3034 2986 4405 4031 2922 3504 M1062 REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC.html Genes involved in Antigen Presentation: Folding, assembly and peptide loading of class I MHC 45/62 Reactome 5.23573345033922e-05 5.89660269281821e-05 1250 2799.72727272727 3195 4.75987096236685e-06 1182 1.05866860866008 -1.05874356587961 -1 1.75065409858116 1249 3387 3815 2542 4141 1182 1562 3195 4542 3833 1349 3505 M1745 MARSON_FOXP3_CORE_DIRECT_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_CORE_DIRECT_TARGETS.html Direct FOXP3 [GeneID=50943] targets that exhibit consistent transcriptional behavior in hybridoma and in ex vivo T lymphocytes. 17237765 20/32 Jessica Robertson 2.29301472748018e-06 3.40132919978204e-06 4395 2948.81818181818 3195 2.08456101585976e-07 1295 2.16477401379294 2.08391908766739 1 4.71064983541348 4394 3195 2328 1980 3106 4402 3619 1295 3410 1464 3244 3506 M1695 TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_UP http://www.broadinstitute.org/gsea/msigdb/cards/TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_UP.html Genes up-regulated in small intestine tissue from transgenic mice expressing a mutant form of COL13A1 [GeneID=1305], compared to normal controls. 19074901 23/40 Leona Saunders 0.000232653083160189 0.000249573307390021 3200 3078.18181818182 3196 2.11525172902708e-05 1934 2.21783201449789 -2.20322151114479 -1 3.16339902487032 3196 2356 1971 2346 4365 3531 1934 4562 3600 2583 3416 3507 M1307 GROSS_HIF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HIF1A_TARGETS_DN.html Genes down-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 27/46 Jessica Robertson 0.000132954981330611 0.000144529597393017 1470 2791.72727272727 3198 1.20875470020728e-05 858 1.48006301613649 1.49184073503212 1 2.23565095174805 1469 4003 3198 3993 4302 1500 858 1876 3320 4105 2085 3508 M2388 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS.html Transcripts in hematopoietic stem cells (HSC) which are trans-regulated (i.e., modulated by a QTL (quantitative trait locus) not in a close proximity to the gene). 15711547 1053/1453 Jean Junior 2.0672028999147e-07 7.68728418959517e-07 3930 2894.90909090909 3199 2.06720309221447e-08 882 1.8848858596746 2.05419601727267 1 4.58472307788806 3927 1996 4478 882 1087 3199 4455 3649 2595 1989 3587 3509 M1001 BIOCARTA_RHO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RHO_PATHWAY.html Rho cell motility signaling pathway 48/53 BioCarta 1.06394181210528e-07 6.93852357637273e-07 3835 2671 3200 9.67219875962332e-09 332 1.56674991160439 -1.67130102913373 -1 3.83049872022536 3835 3383 3421 3200 332 3217 2266 2545 1089 3667 2426 3510 M1173 HESSON_TUMOR_SUPPRESSOR_CLUSTER_3P21_3 http://www.broadinstitute.org/gsea/msigdb/cards/HESSON_TUMOR_SUPPRESSOR_CLUSTER_3P21_3.html Genes in the tumor suppressor cluster of the 3p21.3 region. 17533367 6/8 Leona Saunders 9.77451710155789e-07 1.72546377095256e-06 2830 2703.90909090909 3201 9.77452140091384e-08 31 3.93440055065041 3.93440055065041 1 9.06870510201716 2827 4111 4360 4363 3201 3416 2999 31 611 3478 346 3511 M18899 BIOCARTA_DREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DREAM_PATHWAY.html Repression of Pain Sensation by the Transcriptional Regulator DREAM 14/17 BioCarta 4.13176782776306e-06 5.60426437478643e-06 3190 3196.27272727273 3202 3.75615962505331e-07 1422 1.70930169701099 2.01944609243065 1 3.55991300817536 3189 4330 2685 3202 3405 3937 4581 1422 3078 3684 1646 3512 M3644 BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_DN http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_DN.html Genes down-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes depend on ATM [GeneID=472] but not NFKB signaling. 18849970 65/85 Jessica Robertson 1.46571093715172e-06 2.34593273087695e-06 1905 2961.09090909091 3204 1.33246537605138e-07 1788 1.43639469369389 -1.03968131714244 -1 3.20202244677834 1905 3356 3237 3207 2847 1788 2564 3647 3798 3019 3204 3513 M10245 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP.html Genes up-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic D.B. Chr 3 (DB, small HSC population) vs parental D2 strain (huge HSC population). 17220891 45/53 Leona Saunders 5.45244469086056e-07 1.17032919239936e-06 4050 2824.18181818182 3205 4.95676912926014e-08 498 1.44712362792339 -1.82561136725246 -1 3.40207483474387 4048 498 3205 3328 2037 4455 4018 1948 1236 3218 3075 3514 M1338 FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_UP.html Genes commonly up-regulated in both non-tumorous and tumorous liver tissues of PARK2 [GeneID=5071] knockout mice. 18574468 20/31 Jessica Robertson 3.07176333923725e-06 4.33963572618972e-06 3210 3115.27272727273 3206 2.79251602564893e-07 1638 2.47922757905173 -3.17524996418118 -1 5.29669140201898 3206 3751 1638 3204 3269 3986 3039 3712 4236 1818 2409 3515 M13606 AIYAR_COBRA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/AIYAR_COBRA1_TARGETS_DN.html Genes down-regulated in T47D cells (breast cancer) after COBRA1 [GeneID=25920] knockdown by RNAi. 17043641 45/55 Arthur Liberzon 5.51108202246757e-07 1.17941666689155e-06 3390 2868.27272727273 3207 5.0100758209224e-08 388 2.00198170185156 1.76633874416145 1 4.72298365204293 3390 2692 2188 1925 2044 3287 3207 4659 388 3216 4555 3516 M1228 OXFORD_RALB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALB_TARGETS_DN.html Genes down-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALB [GeneID=5899] by RNAi. 17496927 11/13 Arthur Liberzon 3.96576770665894e-07 9.84661945051561e-07 3480 3048.54545454545 3207 3.60524401957909e-08 1623 1.43355854904083 1.30467560325594 1 3.41296656292692 3480 3792 3043 3724 1699 2424 1623 3207 4183 2245 4114 3517 M4072 REACTOME_OLFACTORY_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OLFACTORY_SIGNALING_PATHWAY.html Genes involved in Olfactory Signaling Pathway 7/764 Reactome 1.5511371824258e-07 7.28467912574107e-07 4040 3231.18181818182 3208 1.55113729069701e-08 778 1.319268290364 -0.804376840334956 -1 3.20631690531697 4037 2919 4232 3208 778 3057 2240 2921 4627 3643 3881 3518 M11121 REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PLC_BETA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PLC_BETA.html Genes involved in G beta:gamma signalling through PLC beta 16/23 Reactome 1.89955799328645e-06 2.89596696650906e-06 3655 3313.90909090909 3209 1.72687239403104e-07 2050 1.61426216417714 -1.09551461251993 -1 3.54533505005452 3653 3209 3078 3956 3007 3497 2050 2261 4155 3162 4425 3519 M17115 SCHEIDEREIT_IKK_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SCHEIDEREIT_IKK_TARGETS.html Genes encoding substrates of IkappaB kinase (IKK) complex. 17072322 25/32 Arthur Liberzon 2.02294593245578e-05 2.3787505732913e-05 235 2285.45454545455 3210 1.83905866736859e-06 68 1.29576587694005 -1.36115066561212 -1 2.35938136564833 232 3739 3336 3539 3954 349 68 1092 4402 3210 1219 3520 M288 PID_HES_HEY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HES_HEY_PATHWAY.html Notch-mediated HES/HEY network 18832364 61/75 Pathway Interaction Database 2.15623466685207e-06 3.22887932345868e-06 3725 2760.54545454545 3212 1.96021525472267e-07 1042 1.98700074498704 1.34778335759941 1 4.33775480504498 3723 3363 2161 1042 3072 4057 3212 3418 1087 2002 3229 3521 M18970 CHANDRAN_METASTASIS_TOP50_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_TOP50_UP.html Top 50 genes up-regulated in metastatic vs primary prostate cancer tumors. 17430594 56/90 Arthur Liberzon 9.73647044748792e-07 1.72120376449974e-06 3215 3366.18181818182 3212 8.85134068775413e-08 2547 1.35251240783132 -1.26415869595105 -1 3.08525862732331 3212 4508 3854 3006 2547 3660 3106 2741 2722 4312 3360 3522 M14718 TURJANSKI_MAPK14_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK14_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK14 [GeneID=1432] phosphorylation. 17496919 13/13 Arthur Liberzon 0.00023595064643438 0.000252938235559908 3310 2773.45454545455 3214 2.14523596373514e-05 521 3.47585310544261 4.09540547456993 1 4.97802636924899 3309 4083 2006 3214 4367 2993 3961 877 521 3909 1268 3523 M14414 BOYAULT_LIVER_CANCER_SUBCLASS_G6_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G6_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G6, defined by unsupervised clustering. 17187432 25/30 Yujin Hoshida 9.96138297697579e-07 1.74527571088811e-06 4185 3106.27272727273 3214 9.05580680672236e-08 908 2.12058419952549 -1.59361547786391 -1 4.86060274901461 4185 4012 2402 2892 2567 4442 3520 1807 908 3214 4220 3524 M11619 VETTER_TARGETS_OF_PRKCA_AND_ETS1_DN http://www.broadinstitute.org/gsea/msigdb/cards/VETTER_TARGETS_OF_PRKCA_AND_ETS1_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PRKCA and ETS1 [GeneID=5578;2113] by RNAi. 15531915 21/27 Leona Saunders 0.000367539080943173 0.000390453401317078 1955 3062.90909090909 3215 3.34182270518294e-05 1232 1.68629531633275 -1.3614785124847 -1 2.26143552395554 1951 4583 3215 4012 4405 1510 1232 2909 4513 3734 1628 3525 M18395 URS_ADIPOCYTE_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/URS_ADIPOCYTE_DIFFERENTIATION_DN.html Genes down-regulated in primary adipocytes compared to preadipocytes. 15051823 56/64 John Newman 0.00060210786503313 0.000633232870533952 800 2742.09090909091 3215 5.47520651207932e-05 797 2.83203966565702 2.97367494725796 1 3.59278293933741 797 3658 873 3215 4454 2315 3404 3984 3326 1837 2300 3526 M1358 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_UP.html Early prostate development genes (up-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in localized vs metastatic prostate cancers. 18794802 13/15 Jessica Robertson 7.55554427174695e-06 9.55834064932876e-06 3655 2799.09090909091 3216 6.86870020015166e-07 785 2.30264322418933 -2.66762490544069 -1 4.59830330471541 3654 3216 1960 1844 3673 4646 3261 3639 785 2169 1943 3527 M14027 NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_DN.html Down-regulated genes in lung tissue of smokers with chronic obstructive pulmonary disease (COPD) vs smokers without disease (GOLD-2 vs GOLD-0). 15469929 184/270 Kate Stafford 4.0259206437047e-07 9.93104581177629e-07 3410 2970.90909090909 3216 3.65992852766713e-08 1716 1.81974072334461 1.94508253991739 1 4.34314157991026 3410 3579 2131 2224 1716 3353 4497 3093 3279 2182 3216 3528 M16922 YAGI_AML_WITH_T_9_11_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_T_9_11_TRANSLOCATION.html Genes specifically expressed in samples from patients with pediatric acute myeloid leukemia (AML) bearing t(9;11) translocation. 12738660 164/231 Arthur Liberzon 4.46402064402771e-07 1.03872096525265e-06 2965 3216.81818181818 3216 4.05820140892956e-08 1841 1.7135724537762 1.8694779278228 1 4.07339164463593 2964 4153 3173 3905 1841 3315 4433 3216 2868 3358 2159 3529 M2081 KARLSSON_TGFB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KARLSSON_TGFB1_TARGETS_DN.html Genes down-regulated by TGFB1 [GeneID=7040] in MEF cells (embryonic fibroblast) via TGFB1R [GeneID=7046]. 15769904 307/385 Arthur Liberzon 2.54410888092586e-07 8.22189102913976e-07 3520 2921.90909090909 3216 2.31282652284546e-08 1209 1.54471158101566 -1.38354482850234 -1 3.73012696790894 3517 1272 3216 1931 1209 4029 3636 3947 2870 2353 4161 3530 M1072 REACTOME_INFLAMMASOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLAMMASOMES.html Genes involved in Inflammasomes 14/20 Reactome 2.56892842391919e-06 3.71714965079661e-06 3275 3366 3217 2.33539220331663e-07 2463 1.95179975541375 1.48776509980794 1 4.21201678056551 3274 3217 2463 4164 3181 2898 2728 3725 4029 2833 4514 3531 M15009 SCHRAMM_INHBA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAMM_INHBA_TARGETS_DN.html Genes down-regulated in Kelly cells (neuroblastoma) by overexpressing INHBA [GeneID=3624] off a plasmid vector. 15580313 32/37 Arthur Liberzon 1.15209628870996e-06 1.95093023489671e-06 3230 3020.90909090909 3217 1.04736081094576e-07 1630 1.92153333021243 1.98592018978031 1 4.36227567419424 3230 3984 3160 3462 2665 3511 2763 1630 2001 3607 3217 3532 M164 PID_ERBB1_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_DOWNSTREAM_PATHWAY.html ErbB1 downstream signaling 18832364 147/159 Pathway Interaction Database 9.26430810373116e-08 6.56798957981166e-07 3220 2919.54545454545 3218 8.42209863077797e-09 265 1.48817243538676 -1.39232925230832 -1 3.65014221961872 3218 2551 3706 916 265 3573 2788 4637 2920 4040 3501 3533 M3634 REACTOME_CASPASE_MEDIATED_CLEAVAGE_OF_CYTOSKELETAL_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CASPASE_MEDIATED_CLEAVAGE_OF_CYTOSKELETAL_PROTEINS.html Genes involved in Caspase-mediated cleavage of cytoskeletal proteins 17/20 Reactome 2.54669590775473e-07 8.22189102913976e-07 3360 3233.63636363636 3219 2.31517836596137e-08 1212 1.83543658597121 2.01342832889184 1 4.44157902906547 3360 4060 2983 3219 1212 2738 3896 4478 3049 3945 2630 3534 M14591 WEIGEL_OXIDATIVE_STRESS_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_RESPONSE.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to HNE, tBH and H2O2 [PubChem=5283344;6410;784]. 12419474 86/100 John Newman 1.06910096711403e-05 1.31856717135569e-05 3175 3140.90909090909 3219 9.7191469318075e-07 1103 1.65805042447139 -1.43505993687227 -1 3.20389959928878 3174 3334 3031 2538 3768 3651 3362 1103 3219 2927 4443 3535 M2561 HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 35/41 Arthur Liberzon 4.50908504649808e-07 1.04185917010687e-06 3365 2649.18181818182 3219 4.0991690642484e-08 82 1.50506523986963 2.28413151168086 1 3.57086051596472 3365 2292 3375 3434 1853 3219 4593 2229 567 4132 82 3536 M15468 GENTILE_UV_RESPONSE_CLUSTER_D4 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D4.html Cluster d4: genes progressively down-regulated in WS1 cells (fibroblast) through 12 h after irradiation with high dose UV-C. 12907719 84/89 John Newman 4.16059856667964e-07 1.0045025695513e-06 2150 2905.63636363636 3220 3.78236304865856e-08 1236 1.92580333877585 2.13915501555396 1 4.5953572597243 2149 4189 3220 3773 1761 3455 3957 1236 1998 3802 2422 3537 M16542 YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP.html Up-regulated genes distinguishing hepatocellular carcinoma (HCC) samples positive for EPCAM [GeneID=4072] from the negative ones. 18316609 66/108 Yujin Hoshida 7.25997503024573e-08 6.0961933040682e-07 3650 2830.18181818182 3222 6.59997751802189e-09 153 1.62950523538519 -1.48911552683391 -1 4.02276619740174 3647 3645 3367 2491 153 3015 2399 3526 1302 4365 3222 3538 M789 BROWNE_HCMV_INFECTION_4HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_4HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 4 h time point that were not down-regulated at the previous time point, 2 h. 11711622 398/570 Arthur Liberzon 4.69772537267365e-07 1.07065493766391e-06 3225 3232.27272727273 3222 4.27066034163018e-08 1898 1.79309815133077 -1.62360928033845 -1 4.25527396997162 3222 3844 3157 3009 1898 3527 3487 3874 2807 2951 3779 3539 M13266 KEGG_RENAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENAL_CELL_CARCINOMA.html Renal cell carcinoma 74/78 KEGG 7.09948315143347e-07 1.38126795032011e-06 3470 3136.36363636364 3223 6.45407767496777e-08 2016 1.52602254828211 1.76300825765496 1 3.54611964931019 3467 3348 3223 2248 2280 3458 4550 3172 2016 3757 2981 3540 M124 PID_CXCR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CXCR4_PATHWAY.html CXCR4-mediated signaling events 18832364 119/141 Pathway Interaction Database 7.432693349969e-08 6.12256764604776e-07 3585 2900.81818181818 3223 6.75699418280211e-09 162 1.59954785324854 -1.37178198138038 -1 3.94668433024772 3583 1575 3177 1320 162 3507 3455 4353 2880 3223 4674 3541 M1048 REACTOME_BINDING_AND_ENTRY_OF_HIV_VIRION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BINDING_AND_ENTRY_OF_HIV_VIRION.html Genes involved in Binding and entry of HIV virion 3/8 Reactome 0.000206815980515265 0.000222261254105658 2875 2982.45454545455 3223 2.06835230819193e-05 646 3.62441793104895 -3.62441793104895 -1 5.27478113606476 2872 4650 4259 4398 4684 2557 646 697 3223 3567 1254 3542 M1147 DARWICHE_PAPILLOMA_PROGRESSION_RISK http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_PROGRESSION_RISK.html Genes that classify progression risk of benign papilloma samples: low vs high risk. 17525749 69/112 Arthur Liberzon 1.20919085064103e-07 7.08111763650825e-07 4455 2727.18181818182 3223 1.09926447009278e-08 426 2.15650891197402 2.18518927304535 1 5.28355540449365 4454 2180 1391 3291 426 4633 4212 3590 1385 1214 3223 3543 M1151 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_DN.html Apoptotic genes dependent on SMAD4 [GeneID=4089] and down-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 14/15 Arthur Liberzon 6.25578020997136e-08 5.80103783714436e-07 3215 3187.36363636364 3224 5.68707307986979e-09 97 1.75420166528902 -1.2788874247143 -1 4.34963890439518 3224 3215 2928 4387 97 3453 3213 4256 3503 2834 3951 3544 M6327 BIOCARTA_CSK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CSK_PATHWAY.html Activation of Csk by cAMP-dependent Protein Kinase Inhibits Signaling through the T Cell Receptor 23/36 BioCarta 1.19518461186384e-07 7.06112554001409e-07 3225 2957.36363636364 3225 1.0865315243583e-08 416 1.80230488514128 1.75158690542936 1 4.40840914700155 3225 3168 2519 1716 416 3948 4107 4030 3657 3338 2407 3545 M11672 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP.html Genes from the blue module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 183/193 Arthur Liberzon 6.0076168214459e-07 1.2398754436915e-06 1430 2967.54545454545 3225 5.46147132906131e-08 922 1.4559026569727 -1.37109255103352 -1 3.40833849700137 1429 4716 3869 4545 2125 922 1297 3225 4098 4320 2097 3546 M5290 BIOCARTA_MEF2D_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MEF2D_PATHWAY.html Role of MEF2D in T-cell Apoptosis 20/26 BioCarta 1.52386085706691e-05 1.82878801051508e-05 3570 3313.36363636364 3226 1.38533764764112e-06 2820 1.21716000244891 1.05900934898348 1 2.26911052677258 3568 2820 3369 3226 3874 3195 3266 3011 3172 3901 3045 3547 M1393 SHIN_B_CELL_LYMPHOMA_CLUSTER_9 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_9.html Cluster 9 of genes distinguishing among different B lymphocyte neoplasms. 19010892 8/25 Jessica Robertson 1.73623540330283e-05 2.06320017713731e-05 3410 3183.81818181818 3226 1.7362489687622e-06 1939 2.05913955564794 -1.22339235508561 -1 3.83002374015133 3408 2916 4461 3897 3938 3226 1968 2952 1939 2666 3651 3548 M79 PID_TRAIL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TRAIL_PATHWAY.html TRAIL signaling pathway 18832364 28/31 Pathway Interaction Database 4.86332042270785e-06 6.44256873286024e-06 2835 3190.09090909091 3227 4.42121015781652e-07 1801 1.38390552777779 -1.00343820250299 -1 2.83900037339155 2835 3443 3470 4056 3496 2796 2783 3114 4070 3227 1801 3549 M12456 VERNELL_RETINOBLASTOMA_PATHWAY_DN http://www.broadinstitute.org/gsea/msigdb/cards/VERNELL_RETINOBLASTOMA_PATHWAY_DN.html Cluster 2: genes down-regulated by RB1, CDNK2A [GeneID=1029;5925], and one of the E2Fs (E2F1, E2F2, or E2F3 [GeneID=1869;1870;1871]). 12923195 28/44 Kevin Vogelsang 0.000125737335914784 0.000136999128697549 1780 3199.63636363636 3229 1.14313202543515e-05 1779 1.46415411032222 -1.22550315780884 -1 2.22476627529083 1779 3733 3221 4431 4293 2600 1823 2659 4152 3229 3276 3550 M1780 MCGOWAN_RSP6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCGOWAN_RSP6_TARGETS_UP.html Genes up-regulated by hemizygotic cre-lox knockout of RSP6 [GeneID=81492] in keratinocytes. 18641651 17/23 Jessica Robertson 6.43237525355185e-06 8.25022043390346e-06 3865 3378.27272727273 3229 5.84763096422927e-07 2798 1.58643509202918 1.96142607451908 1 3.1932748576938 3862 2839 2798 4384 3614 3183 3229 2881 4099 2880 3392 3551 M7517 SMID_BREAST_CANCER_LUMINAL_A_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_A_UP.html Genes up-regulated in the luminal A subtype of breast cancer. 18451135 109/160 Jessica Robertson 3.17204775440375e-10 5.50443580911238e-09 3340 2636.72727272727 3229 2.88367977714646e-11 212 2.83801980860562 3.18050659467279 1 9.37664020867748 3336 1584 212 2054 1684 3682 4319 4594 3229 497 3813 3552 M5355 CASTELLANO_HRAS_AND_NRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_AND_NRAS_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) isolated from HRAS and NRAS [GeneID=3265;4893] double knockout mice. 16909116 11/12 Leona Saunders 2.63767406210332e-05 3.05817282562704e-05 2340 2955.81818181818 3230 2.39791426076021e-06 568 2.20891749168887 2.5383267991524 1 3.96041608562748 2337 3230 2259 2872 4017 2501 3781 3645 4005 3299 568 3553 M7076 NAM_FXYD5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAM_FXYD5_TARGETS_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of FXYD5 [GeneID=53827] by RNAi. 16849564 21/29 Arthur Liberzon 2.80427131652441e-06 4.00610188074916e-06 1880 2896.45454545455 3231 2.54934081004353e-07 540 1.09274505390507 1.25615445879992 1 2.32185145372277 1877 4572 3689 4620 3231 2221 1486 540 3866 3972 1787 3554 M1948 YAMANAKA_GLIOBLASTOMA_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMANAKA_GLIOBLASTOMA_SURVIVAL_DN.html Genes whose expression most strongly and consistently associated with the short term survival of patients with high grade glioma tumors. 16652150 11/12 Arthur Liberzon 2.05770362311391e-06 3.09903034495776e-06 3785 3250.63636363636 3231 1.87064140702493e-07 1401 1.09196145120968 0.970831227656172 1 2.369113566533 3781 3229 3231 3468 3051 2655 1401 2249 4435 3724 4533 3555 M11835 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION.html Valine, leucine and isoleucine degradation 52/60 KEGG 1.37115104750711e-05 1.65944434467528e-05 2450 3147.09090909091 3232 1.2465087211701e-06 2134 1.68977010235265 1.73843575025839 1 3.19828848353875 2446 3665 3232 3776 3841 2134 2181 4092 2373 4126 2752 3556 M199 PID_P38_MK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_MK2_PATHWAY.html p38 signaling mediated by MAPKAP kinases 18832364 22/24 Pathway Interaction Database 1.47469847669166e-06 2.35791897357203e-06 2700 3076.72727272727 3232 1.34063587746252e-07 1639 1.35828664552471 1.18602841772866 1 3.02397342339709 2697 4031 3630 4011 2849 1853 1639 3232 3799 4193 1910 3557 M2101 STAMBOLSKY_TARGETS_OF_MUTATED_TP53_UP http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_TARGETS_OF_MUTATED_TP53_UP.html Genes induced in SKBR3 cells (breast cancer) by mutated TP53 [GeneID=7157]. 20227041 53/63 Arthur Liberzon 2.03434058037666e-06 3.0707027628327e-06 3235 3082.09090909091 3232 1.84940223775852e-07 1307 1.76011690177969 -1.75432577848323 -1 3.8521799316407 3232 2243 2707 3906 3043 4129 3806 3660 1307 3584 2286 3558 M870 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_DN.html Genes down-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic B.D. chr3 (BD, large HSC size) vs parental B6 strain (tiny HSC size). 17220891 54/65 Leona Saunders 1.6852281392311e-05 2.00511137312094e-05 4500 3223.09090909091 3233 1.53203731675694e-06 970 1.73663451907951 1.26122959916606 1 3.23098596059019 4500 3070 2954 2796 3907 3799 4653 3233 1603 3969 970 3559 M12243 SCHUHMACHER_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHUHMACHER_MYC_TARGETS_UP.html Genes up-regulated in P493-6 cells (Burkitt's lymphoma) induced to express MYC [GeneID=4609]. 11139609 105/115 Yujin Hoshida 1.67245005648429e-05 1.99091154264965e-05 645 2786.90909090909 3234 1.52042070060126e-06 644 1.22156949222303 1.17624541302839 1 2.25939006069418 644 3608 3988 3234 3905 1361 1122 2195 3664 4143 2792 3560 M4035 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_UP.html Genes from the red module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 20/21 Arthur Liberzon 2.82881859096352e-06 4.03506308532724e-06 3670 3342.27272727273 3236 2.5716565712185e-07 1817 1.86726068525252 1.45408052325124 1 4.00064902519889 3669 2818 2195 2862 3236 4265 4537 2549 4159 1817 4658 3561 M15669 GNATENKO_PLATELET_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/GNATENKO_PLATELET_SIGNATURE.html Top 50 most up-regulated genes in human platelet cells. 12433680 88/172 Kate Stafford 4.77591670333244e-06 6.3499512224589e-06 3285 3174.90909090909 3236 4.34175188296737e-07 1542 1.69638976104351 -1.39084191553635 -1 3.4956319136373 3283 2150 2481 1542 3482 4401 3949 3236 3100 3233 4067 3562 M1603 ZHOU_TNF_SIGNALING_30MIN http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_TNF_SIGNALING_30MIN.html Genes up-regulated in HeLa cells (cervical carcinoma) at 30 min after stimulation with TNF [GeneID=7124]. 12673210 82/102 John Newman 2.0134133855652e-07 7.65527859584926e-07 4190 3313.45454545455 3236 1.83037597257307e-08 949 2.0446290823878 1.98415107401157 1 4.97900681276463 4189 4460 2538 3236 949 4230 3829 2808 3008 3219 3982 3563 M1962 MIKKELSEN_MEF_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the bivalent tri-methylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MEF cells (embryonic fibroblasts). 18509334 27/63 Jessica Robertson 5.78984900844781e-06 7.51390907887646e-06 4505 3005.90909090909 3237 5.26351295085134e-07 1084 2.85233759028656 2.68215134337995 1 5.82786107101429 4503 2775 1084 3832 3570 3237 2631 4666 1168 1275 4324 3564 M5395 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_UP.html Genes up-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing granulocytes. 17898786 23/36 Arthur Liberzon 1.20251550431537e-05 1.46777170425874e-05 3185 3212.72727272727 3238 1.09320188844622e-06 1483 1.86217236885918 -1.93660591998093 -1 3.56962477999443 3184 4028 2023 4031 3811 3238 2786 1483 4444 2580 3732 3565 M4508 ENK_UV_RESPONSE_EPIDERMIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_EPIDERMIS_DN.html Genes down-regulated in epidermis after to UVB irradiation. 16434974 729/857 Lauren Kazmierski 2.02897320411174e-07 7.65527859584926e-07 4500 2627.90909090909 3238 2.02897338936472e-08 421 2.14774407065447 2.5206294293344 1 5.23263218467798 4499 1112 4326 421 1069 4543 3517 3238 1756 445 3981 3566 M5839 COLLIS_PRKDC_REGULATORS http://www.broadinstitute.org/gsea/msigdb/cards/COLLIS_PRKDC_REGULATORS.html Proteins that regulate activity of PRKDC [GeneID=5591]. 15592499 24/24 Jessica Robertson 1.02662729979084e-07 6.8232212069871e-07 3130 2756.18181818182 3239 9.33297588816619e-09 319 1.57836584197863 1.50528282733709 1 3.86388865578453 3130 3745 3239 3937 319 2291 1120 3547 505 4129 4356 3567 M10102 NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_UP.html Top 20 positive significant genes associated with malignant fibrous histiocytoma tumors. 11965276 31/44 John Newman 6.23991538232401e-05 6.97098239161405e-05 4030 3145.54545454545 3239 5.6728112487663e-06 975 2.9291301697602 -3.26281391609004 -1 4.84649526721912 4026 3716 975 2911 4173 4252 2955 2529 4101 1724 3239 3568 M12975 BIOCARTA_VEGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VEGF_PATHWAY.html VEGF, Hypoxia, and Angiogenesis 40/64 BioCarta 2.85540565530867e-06 4.06684209205098e-06 2860 3394.09090909091 3240 2.59582669216337e-07 2718 1.72007286276135 1.64861886076248 1 3.67899474866532 2857 3956 2957 2986 3240 3332 3158 3854 4020 2718 4257 3569 M846 REACTOME_FRS2_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FRS2_MEDIATED_CASCADE.html Genes involved in FRS2-mediated cascade 26/43 Reactome 1.49260245466104e-06 2.37848871910874e-06 2880 3111.18181818182 3240 1.35691224302417e-07 1754 1.39981036491572 2.08380100447023 1 3.11582438575035 2878 3447 3354 1754 2860 3240 4641 1893 3548 4334 2274 3570 M8321 WEST_ADRENOCORTICAL_TUMOR_MARKERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_MARKERS_DN.html Top down-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 23/40 Arthur Liberzon 1.9484143337096e-05 2.29797992381542e-05 3970 3067.72727272727 3240 1.77130144537851e-06 935 2.92148459183571 -2.27139845195433 -1 5.39995918758162 3968 2804 935 4137 3943 4208 2525 3240 2296 1093 4596 3571 M10765 BIOCARTA_TCRA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCRA_PATHWAY.html Lck and Fyn tyrosine kinases in initiation of TCR Activation 10/20 BioCarta 1.33115806134284e-06 2.17829989116007e-06 3535 2902.45454545455 3242 1.21014442435435e-07 1229 2.75749501708491 2.64184566183042 1 6.22875675779901 3531 2439 1446 1229 2771 4236 4029 3436 4011 1557 3242 3572 M3231 SEIDEN_ONCOGENESIS_BY_MET http://www.broadinstitute.org/gsea/msigdb/cards/SEIDEN_ONCOGENESIS_BY_MET.html Genes changed in xenograft tumors formed by DLD-1 or DKO-4 cells (colon cancer) overexpressing MET [GeneID=4233]. 16158056 131/151 Arthur Liberzon 2.83315080928227e-07 8.50666146298494e-07 2050 3126.27272727273 3242 2.57559197648575e-08 1332 1.46338848554367 1.42409810587927 1 3.52241325236268 2046 4164 3826 3242 1332 3171 3624 2970 2097 4316 3601 3573 M13962 REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS.html Genes involved in Activation of the AP-1 family of transcription factors 9/10 Reactome 0.0223834228341759 0.02276443778869 2555 3475.54545454545 3243 0.00226121296807377 2554 0.919005854675507 -0.968660635179806 -1 0.557102450878875 2554 3243 4245 2987 4617 2842 2707 4022 4526 3877 2611 3574 M17211 YEMELYANOV_GR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YEMELYANOV_GR_TARGETS_DN.html Transcription factors down-regulated in LNCaP cells (prostate cancer) by expression of GR [GeneID=2908] off a lentiviral vector. 17016446 19/26 Aravind Subramanian 4.42760594217061e-05 5.02121577295658e-05 4575 2985.18181818182 3243 4.02517732034826e-06 1478 1.81482059821314 -0.790545927718202 -1 3.08773282230562 4572 4044 2566 3243 4113 3696 1648 1478 1946 3539 1992 3575 M832 REACTOME_ZINC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ZINC_TRANSPORTERS.html Genes involved in Zinc transporters 12/15 Reactome 1.4351953759704e-05 1.73251206511004e-05 2895 3223.54545454545 3244 1.30473158065317e-06 1101 1.5772422565596 1.77217059976403 1 2.9701006987125 2895 3791 3135 4186 3851 3244 3842 1101 3980 2965 2469 3576 M17496 LEE_RECENT_THYMIC_EMIGRANT http://www.broadinstitute.org/gsea/msigdb/cards/LEE_RECENT_THYMIC_EMIGRANT.html Candidate genes specific for recent thymic emigrants (RTEs). 15210650 294/387 Arthur Liberzon 4.32895623212605e-07 1.02326646843649e-06 3685 3092.45454545455 3244 3.93541553085291e-08 1804 1.62524579304588 1.63006078497563 1 3.86510325008981 3681 2037 3101 2887 1804 3759 3481 3641 3244 2181 4201 3577 M1045 REACTOME_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IMMUNE_SYSTEM.html Genes involved in Immune System 856/1251 Reactome 3.30493503236385e-07 9.06126045087621e-07 2675 3203.45454545455 3245 3.30493552388076e-08 1600 1.64062777316031 -1.71602103676937 -1 3.93699511142297 2675 3833 4258 2553 1600 3737 3131 3245 3397 3971 2838 3578 M19965 NGO_MALIGNANT_GLIOMA_1P_LOH http://www.broadinstitute.org/gsea/msigdb/cards/NGO_MALIGNANT_GLIOMA_1P_LOH.html Proteins with reduced expression in mulignant glioma cell line (A172) which bears loss of heterozygosity (LOH) in the 1p region. 17440165 29/43 Jessica Robertson 0.000113076886867446 0.000123632825113353 1100 2420.27272727273 3245 1.02802453888795e-05 357 2.03295542308986 2.1096517245457 1 3.14494321470219 1099 4561 3248 3245 4344 1093 609 506 3386 4175 357 3579 M10355 JI_RESPONSE_TO_FSH_UP http://www.broadinstitute.org/gsea/msigdb/cards/JI_RESPONSE_TO_FSH_UP.html Genes up-regulated in MCV152 cells (ovarian cancer) treated with follicle stimulating hormone (FSH). 15386376 128/208 John Newman 6.20352099087415e-06 7.99143533758897e-06 2725 3127.72727272727 3247 5.63958043956518e-07 2381 1.82543587503926 2.11328576425342 1 3.69204946516422 2721 3871 2487 2728 3599 2381 3534 3112 3338 3387 3247 3580 M7300 BLUM_RESPONSE_TO_SALIRASIB_UP http://www.broadinstitute.org/gsea/msigdb/cards/BLUM_RESPONSE_TO_SALIRASIB_UP.html Selected genes up-regulated in response to the Ras inhibitor salirasib [PubChem=5469318] in a panel of cancer cell lines with constantly active HRAS [GeneID=3265]. 17409441 327/391 Jessica Robertson 8.99483409370124e-07 1.626651989359e-06 1505 2832.63636363636 3247 8.17712524663281e-08 920 1.59818308483753 -1.45531711369805 -1 3.67052553165777 1505 4691 3859 4325 2487 920 1402 3333 3247 4435 955 3581 M511 REACTOME_SIGNALING_BY_NODAL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NODAL.html Genes involved in Signaling by NODAL 13/22 Reactome 3.49028852962435e-06 4.84107019095707e-06 4700 3194.54545454545 3249 3.17299460632836e-07 601 1.16989116443395 -0.750831533399871 -1 2.4506201025287 4699 3784 3249 4207 3330 3225 2984 601 2913 3907 2241 3582 M689 REACTOME_SIGNALING_BY_FGFR3_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR3_MUTANTS.html Genes involved in Signaling by FGFR3 mutants 5/14 Reactome 7.54335723084807e-06 9.54804133269051e-06 1850 2602.54545454545 3249 7.54338283697765e-07 866 1.7680576518869 2.17993586744528 1 3.51946958479752 1850 3259 4217 3725 3704 1611 900 866 3985 3249 1262 3583 M16347 WANG_PROSTATE_CANCER_ANDROGEN_INDEPENDENT http://www.broadinstitute.org/gsea/msigdb/cards/WANG_PROSTATE_CANCER_ANDROGEN_INDEPENDENT.html Genes changed in prostate cancer: androgen independent vs androgen dependent samples. 19047173 100/131 Jessica Robertson 4.11398766209316e-07 1.00046055710989e-06 3250 3145.36363636364 3249 3.73998948309704e-08 1740 1.83548944764559 1.98742423520133 1 4.37879600634995 3249 3324 2451 3721 1740 2988 3424 4483 3536 2565 3118 3584 M6391 KEGG_PEROXISOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PEROXISOME.html Peroxisome 78/92 KEGG 2.87542362039565e-06 4.0830323370239e-06 885 2577.54545454545 3250 2.61402488964733e-07 882 1.47002402184558 -1.33547893808916 -1 3.13588127084093 882 3345 3715 4261 3250 1297 885 953 4031 3914 1820 3585 M1992 KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP.html Genes up-regulated similarly in primary fibroblast cultures from Werner syndrom patients and normal old donors compared to those from normal young donors. 14527998 118/142 Arthur Liberzon 2.70839178732558e-06 3.89506679956634e-06 3450 3171.63636363636 3250 2.46217738327065e-07 1576 1.67831457119609 2.05792692656484 1 3.60111511463046 3448 4170 3556 3788 3207 2583 2949 1576 3250 4090 2271 3586 M1750 CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_UP http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_UP.html Genes up-regulated in neuroblastoma xenografts: resistant vs those that reverted to be sensitive to the topoisomerase inhibitor irinotecan [PubChem=3750]. 16501609 6/7 Arthur Liberzon 9.48785678416206e-06 1.18004437473636e-05 3420 2964.54545454545 3252 9.48789729314734e-07 1089 2.0633496319906 -1.4740912498922 -1 4.03930204324942 3419 3252 4410 3152 3758 2674 1889 3263 3586 2118 1089 3587 M11829 MENSSEN_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MENSSEN_MYC_TARGETS.html Genes up-regulated by adenoviral expression of c-MYC [GeneID=4609] in HUVEC cells (umbilical vein endothelium). 11983916 81/88 Yujin Hoshida 7.70597633084662e-06 9.73039279871484e-06 465 2518.81818181818 3252 7.00545756620867e-07 464 1.18581251003517 1.27956534426435 1 2.34006489356757 464 3630 3927 3252 3681 724 466 1419 4165 4319 1660 3588 M4339 HANN_RESISTANCE_TO_BCL2_INHIBITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HANN_RESISTANCE_TO_BCL2_INHIBITOR_DN.html Genes down-regulated in SCLC (small cell lung cancer) cells with acquired resistance to ABT-737 [PubChem=11228183], an inhibitor of the BCL2 [GeneID=596] family proteins. 18381439 44/76 Jessica Robertson 9.07195107144913e-06 1.13099865444374e-05 3610 2956.09090909091 3252 8.24726225535515e-07 1232 2.4089357474826 2.85597671210443 1 4.7420776177304 3610 3092 1271 2580 3729 3252 3426 4301 2668 1232 3356 3589 M3645 DELYS_THYROID_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELYS_THYROID_CANCER_UP.html Genes up-regulated in papillary thyroid carcinoma (PTC) compared to normal tissue. 17621275 569/768 Aravind Subramanian 3.55459592708139e-35 6.08305554409805e-33 4075 2418.36363636364 3253 3.55459592708136e-36 17 2.54040698581138 2.68175364096354 1 32.8634522178424 4072 1130 4330 231 345 3519 4079 3253 1228 17 4398 3590 M6117 GARCIA_TARGETS_OF_FLI1_AND_DAX1_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARCIA_TARGETS_OF_FLI1_AND_DAX1_UP.html Genes up-regulated in the A673 cells (Ewing sarcoma) after double knockdown of both FLI1 and DAX1 [GeneID=2313;190] by RNAi. 18591936 91/113 Jessica Robertson 1.36378337028345e-06 2.21890986133675e-06 4115 3352.90909090909 3253 1.23980383245053e-07 1829 1.60158055608738 -1.26812368074433 -1 3.59158192819523 4114 2593 2964 2880 2789 4499 4073 3717 3253 1829 4171 3591 M2080 KARLSSON_TGFB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KARLSSON_TGFB1_TARGETS_UP.html Genes up-regulated by TGFB1 [GeneID=7040] in MEF cells (embryonic fibroblast) via TGFB1R [GeneID=7046]. 15769904 181/201 Arthur Liberzon 5.53755881349644e-05 6.21576161705189e-05 525 2614.18181818182 3253 5.03427109341926e-06 521 1.60566695786208 1.65035765052737 1 2.66626199893519 521 3860 3611 3253 4156 1519 1424 1469 3265 3827 1851 3592 M1198 TERAMOTO_OPN_TARGETS_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_3.html Cluster 3: genes whose up-regulation peaked 3 days after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 5/5 Arthur Liberzon 0.00468742215113191 0.00482018138417051 2175 3123 3254 0.000469733897077274 587 1.25974639243302 1.25974639243302 1 1.12377316881268 2172 4375 4386 3939 4602 1862 587 1803 4629 3254 2744 3593 M5415 BIOCARTA_IL4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL4_PATHWAY.html IL 4 signaling pathway 17/20 BioCarta 7.59834660517346e-07 1.44438968894155e-06 2445 3123.90909090909 3255 6.90759020862459e-08 1929 1.24877125466523 -1.20894383004537 -1 2.88301552005953 2443 4053 3255 4033 2340 2533 1933 1929 4367 3942 3535 3594 M7407 KONDO_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_HYPOXIA.html Genes up-regulated in HSC-2/8 cells (chondrosarcoma) under hypoxic conditions. 16247469 5/9 Arthur Liberzon 0.0135435623426652 0.0138277339946744 1480 3121.54545454545 3255 0.00136268200222729 688 2.59245439114162 2.59245439114162 1 1.88838929766001 1477 4379 4406 3983 4630 1906 688 2302 4552 3255 2759 3595 M8463 DAZARD_UV_RESPONSE_CLUSTER_G3 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G3.html Cluster G3: genes increasingly up-regulated in NHEK cells (normal keratinocyte) after 6 h time point upon UV-B irradiation. 12771951 13/27 John Newman 5.17264934190238e-06 6.79702252053988e-06 2525 3221.90909090909 3256 4.70241954899774e-07 1267 2.24208381449841 -1.76946568603459 -1 4.60955834814703 2523 4614 2620 4418 3524 1782 1267 4315 3982 3140 3256 3596 M1665 JIANG_AGING_CEREBRAL_CORTEX_DN http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_CEREBRAL_CORTEX_DN.html Down-regulated in the cerebral cortex of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 91/114 John Newman 8.59347795375981e-06 1.0756090146313e-05 2060 3211.90909090909 3256 7.81228320104908e-07 2059 1.51416716600241 1.50528530560802 1 2.97538700847523 2059 4185 3807 3256 3712 2576 2682 3605 2135 4261 3053 3597 M10595 BUDHU_LIVER_CANCER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUDHU_LIVER_CANCER_METASTASIS_UP.html Genes up-regulated in tumor-adjacent liver tissue, which is asociated with intrahepatic metastasis of hepatocellular carcinoma 16904609 5/9 Yujin Hoshida 4.79277958569001e-05 5.41712635164197e-05 2305 3061 3256 4.79288295714049e-06 1164 2.34505188447522 -2.82406994052835 -1 3.97340237886848 2303 3256 4623 2863 4143 3420 4548 2452 3581 1164 1318 3598 M2179 FIGUEROA_AML_METHYLATION_CLUSTER_7_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_7_UP.html Cluster 7 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 154/215 Arthur Liberzon 6.3976855665099e-07 1.29545585044731e-06 2705 3137.54545454545 3257 5.81607947907501e-08 2176 1.70466007333853 -1.3673909178457 -1 3.98618507353869 2701 3587 3554 2991 2176 3410 3257 3771 2919 3392 2755 3599 M3395 MARTORIATI_MDM4_TARGETS_FETAL_LIVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_FETAL_LIVER_DN.html Genes down-regulated in non-apoptotic tissues (fetal liver) after MDM4 [GeneID=4194] knockout. 15608685 684/902 Arthur Liberzon 2.50417474354858e-07 8.18539112849675e-07 2270 3040.63636363636 3258 2.50417502573873e-08 1303 1.69617280018937 1.94603431180774 1 4.10209564170109 2269 3549 4396 3258 1303 3264 3745 2370 1942 4418 2933 3600 M1244 WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_DN.html Genes down-regulated by telomere shortening due to the knockout of TERC [GeneID=7012] in the presence of chronic liver damage. 15608677 6/9 Leona Saunders 0.0001664561219192 0.000179664508451549 2410 3072.45454545455 3258 1.66468591672044e-05 1227 1.62966191686079 -1.80618209734922 -1 2.40474151751872 2406 3258 4400 3427 4339 2122 1227 4636 4522 2116 1344 3601 M967 REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION_IN_TLR7_8_OR_9_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION_IN_TLR7_8_OR_9_SIGNALING.html Genes involved in TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling 29/50 Reactome 4.85798398286864e-06 6.43911384418421e-06 3260 2744.18181818182 3259 4.41635882743485e-07 620 2.45381817880043 2.44886429376345 1 5.07277710293343 3259 4268 2258 3711 3494 3979 2496 620 672 3615 1814 3602 M4752 WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN.html Genes down-regulated in rectal cancer patients resistant to radiotherapy (non-responders) relative to the sensitive ones (responders). 16585155 174/204 Arthur Liberzon 3.32169491787439e-07 9.06790052768486e-07 3105 3312.36363636364 3260 3.01972310854942e-08 1508 1.86881870691611 2.26132941699253 1 4.49130265283785 3103 4424 2762 3260 1508 3938 4396 3853 3423 2736 3033 3603 M1343 FUJIWARA_PARK2_IN_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_IN_LIVER_CANCER_UP.html Genes up-regulated in tumorous liver tissues from PARK2 [GeneID=5071] knockout mice compared to the normal, non-tumorous tissue from wild type mice. 18574468 6/9 Jessica Robertson 4.85191009271127e-07 1.09541410640518e-06 4120 3205.18181818182 3260 4.85191115205801e-08 1532 3.88129696403937 3.56847495977389 1 9.25363741463343 4119 3260 4439 3149 2013 3429 3627 3254 1532 2794 3641 3604 M2303 VANDESLUIS_NORMAL_EMBRYOS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_NORMAL_EMBRYOS_UP.html Genes up-regulated in normal 9.5 days post coitus (dpc) embryos compared to normal 8.5 dpc and 9.5 dpc embryos. 17371845 5/13 Arthur Liberzon 6.29355586861811e-05 7.02924365827673e-05 3270 2706.45454545455 3260 6.29373411552755e-06 286 3.93818896798133 -0.612162396284091 -1 6.5275815363368 3270 2927 4681 1280 4336 4262 4534 410 525 3260 286 3605 M6778 BIOCARTA_IL10_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL10_PATHWAY.html IL-10 Anti-inflammatory Signaling Pathway 16/19 BioCarta 3.43560368495826e-05 3.94071674192053e-05 955 2342.27272727273 3261 3.12332485256843e-06 374 1.25270730317911 -1.3697038697172 -1 2.16887167125432 951 3765 3261 3461 4066 859 374 571 4217 3549 691 3606 M697 KONDO_COLON_CANCER_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_COLON_CANCER_HCP_WITH_H3K27ME3.html Genes with high histone H3 tri-methylation mark at K27 (H3K27me3) in SW48 cells (colon cancer), by ChIP-chip assay on a 12K CpG array (high-CpG-density promoters, HCP). 18488029 5/21 Jessica Robertson 0.00208206257717974 0.00215795682131936 3265 2950.18181818182 3262 0.000208401589645496 383 0.809312096536476 0.809312096536476 1 0.817663366343195 2097 3262 4528 3958 4647 1258 383 3262 4598 3887 572 3607 M261 PID_P53_REGULATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P53_REGULATION_PATHWAY.html p53 pathway 18832364 81/90 Pathway Interaction Database 3.00830181746922e-06 4.25507479126602e-06 3265 3047.09090909091 3263 2.73482357368984e-07 1000 1.36772708983755 1.7423282329627 1 2.90431836938671 3063 3626 3800 3263 3265 3194 2832 1620 1000 4549 3306 3608 M2163 FIGUEROA_AML_METHYLATION_CLUSTER_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_2_DN.html Cluster 2 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 8/12 Arthur Liberzon 0.000233836930981037 0.000250729285377214 2395 3330.63636363636 3264 2.33861540495334e-05 1369 2.34975744050606 2.62926814606012 1 3.35265041612465 2395 3525 4665 4195 4374 2974 3264 1369 4112 2670 3094 3609 M2394 JUBAN_TARGETS_OF_SPI1_AND_FLI1_DN http://www.broadinstitute.org/gsea/msigdb/cards/JUBAN_TARGETS_OF_SPI1_AND_FLI1_DN.html Genes down-regulated in 745A cells (erythroleukemia) upon knockdown of FLI1 [GeneID=2313] by RNAi and down-regulation of SPI1 [GeneID=6688] by HMBA [PubChem=3616]. 19289502 137/161 Arthur Liberzon 3.66494309203446e-06 5.04183369116953e-06 1950 3244.45454545455 3264 3.33177199765083e-07 1948 1.70309751420801 1.80578602618503 1 3.57826858519681 1948 4433 3837 3264 3358 2504 2626 2681 3555 4453 3030 3610 M281 PID_FAK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FAK_PATHWAY.html Signaling events mediated by focal adhesion kinase 18832364 102/118 Pathway Interaction Database 4.50880934719025e-07 1.04185917010687e-06 3265 2751 3265 4.09891842841128e-08 199 1.84875649380259 -1.75616342773528 -1 4.39771561410448 3265 3609 2943 199 1852 3711 2742 3296 1146 3674 3824 3611 M1930 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_UP.html Genes from the yellow module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 42/51 Arthur Liberzon 7.53190286084372e-06 9.54121886827224e-06 3270 3417.09090909091 3267 6.84720786102843e-07 2805 1.47405242389314 1.25029558356154 1 2.92609058644861 3267 3952 3218 4194 3669 2829 2805 4319 2953 3451 2931 3612 M12801 DORN_ADENOVIRUS_INFECTION_32HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_32HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 32 h after infection with adenovirus Ad12. 15681441 16/29 Arthur Liberzon 3.69753509356258e-05 4.22575439264295e-05 4200 3322 3269 3.36145203583156e-06 1889 2.05663862631497 1.78190736134065 1 3.56778259873001 4199 3200 2225 1903 4079 4515 4393 3269 1889 2285 4585 3613 M14215 HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_UP.html Genes up-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 14/15 Arthur Liberzon 3.0976921128648e-06 4.37495714324412e-06 4670 3198.54545454545 3270 2.81608770413963e-07 697 2.13594239936191 -1.82143554470582 -1 4.5533348191191 4670 2411 2113 2290 3270 4197 4504 3961 697 2363 4708 3614 M2239 JOHNSTONE_PARVB_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_2_DN.html Genes down-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D collagen I and 3D Matrigel only. 17998334 471/524 Arthur Liberzon 1.96978579632911e-07 7.64036221497417e-07 2605 3325.36363636364 3270 1.7907145206321e-08 924 1.48743653043996 1.57757756784551 1 3.60902246408135 2604 4398 4069 4292 924 3213 3421 3075 3270 4331 2982 3615 M13630 GENTILE_UV_HIGH_DOSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_HIGH_DOSE_DN.html Selected genes down-regulated in WS1 (fibroblast) in response to irradiation with high dose UV-C. 12907719 407/485 John Newman 5.8699410462018e-07 1.22354714668656e-06 3135 3429.63636363636 3271 5.33631146581241e-08 2104 1.60945654394585 1.8142257246346 1 3.77681949604848 3135 4402 3911 3271 2104 3617 4452 2404 3254 4275 2901 3616 M9565 AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_UP.html Up-regulated genes whose expression correlates with copy number gains in pancreatic adenocarcinoma cell lines and primary tumor specimens. 15199222 364/425 Arthur Liberzon 2.36782472299504e-07 8.0069968374353e-07 3735 3421 3272 2.15256816167296e-08 1137 1.29068675690088 1.38442898224921 1 3.11445661859235 3734 4689 4132 4674 1137 2521 3108 3272 2819 4603 2942 3617 M770 REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE.html Genes involved in p53-Dependent G1 DNA Damage Response 59/69 Reactome 0.138017800778524 0.138752719845502 1845 3160.09090909091 3273 0.0134111365953679 1227 1.22951388393137 1.53183819795196 1 0.374092952139015 1841 4506 3932 3273 4678 2162 1734 3100 1227 4601 3707 3618 M2602 BIOCARTA_RANKL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RANKL_PATHWAY.html Bone Remodelling 17/19 BioCarta 1.14843973678717e-05 1.40868907422959e-05 665 2735.90909090909 3276 1.04404157444895e-06 247 1.22220299580418 -1.25922353488325 -1 2.33443260289067 661 4057 3276 4467 3792 650 247 2676 4711 3660 1898 3619 M2328 BILANGES_SERUM_AND_RAPAMYCIN_SENSITIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_AND_RAPAMYCIN_SENSITIVE_GENES.html Genes translationally regulated in MEF cells (embryonic fibroblasts) in response to serum starvation and by rapamycin (sirolimus) [PubChem=6610346]. 17562867 79/117 Arthur Liberzon 1.56602554045465e-05 1.87462352293836e-05 425 2834.63636363636 3276 1.42366971636552e-06 378 0.670363424572542 -0.601750453751562 -1 1.22435901365541 422 3646 4145 3276 3884 790 378 3020 4663 4635 2322 3620 M713 REACTOME_NEGATIVE_REGULATION_OF_THE_PI3K_AKT_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEGATIVE_REGULATION_OF_THE_PI3K_AKT_NETWORK.html Genes involved in Negative regulation of the PI3K/AKT network 8/8 Reactome 6.36761792214277e-06 8.1738255622828e-06 3335 3349 3277 6.36763616816744e-07 2506 0.947146418722267 -1.10333985095434 -1 1.8878503622631 3335 2914 4222 2939 3648 3840 3041 2552 4565 3277 2506 3621 M6714 HAHTOLA_MYCOSIS_FUNGOIDES_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_UP.html Genes up-regulated in monocytes isolated from peripheral blood samples of patients with mucosis fungoides compared to those from normal healthy donors. 16914566 17/56 Arthur Liberzon 0.00066421981352074 0.000697157553884344 1665 2731.54545454545 3277 6.04018580281039e-05 291 1.94656993846381 -2.47020027905849 -1 2.42111631111116 1664 4328 3277 4036 4713 1454 291 1013 3577 3946 1748 3622 M136 PID_FOXO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FOXO_PATHWAY.html FoxO family signaling 18832364 57/65 Pathway Interaction Database 1.18794637388962e-06 1.99186745462132e-06 2750 3033.72727272727 3278 1.07995183213835e-07 1453 1.40664356618804 1.70029694845033 1 3.17486035491249 2747 3922 3828 3797 2692 2271 1453 3585 3278 4168 1630 3623 M17946 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS.html Valine, leucine and isoleucine biosynthesis 10/11 KEGG 0.295968019018743 0.296785436534623 3325 3417.36363636364 3280 0.0313993358204154 1954 2.125509315237 2.82877969195613 1 0.400918026622969 3322 4102 3181 2992 4693 3280 2900 3720 1954 4268 3179 3624 M3342 BIOCARTA_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTEGRIN_PATHWAY.html Integrin Signaling Pathway 62/74 BioCarta 5.18479373074754e-06 6.8110844445111e-06 2445 2999.90909090909 3281 4.71345995447079e-07 1609 1.61485263633971 2.04437575755202 1 3.30543649402761 2441 4206 3281 1760 3525 3548 4579 1609 2082 4287 1681 3625 M3574 REACTOME_SIGNALLING_BY_NGF http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_BY_NGF.html Genes involved in Signalling by NGF 254/279 Reactome 9.87826577877909e-08 6.69905380399961e-07 4010 2729.09090909091 3281 8.98024202029562e-09 303 1.66689244147971 -1.39202515045951 -1 4.08875776711621 4007 1341 3094 497 303 3643 3281 4173 1657 3327 4697 3626 M1356 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_UP.html Early prostate development genes (up-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 8/9 Jessica Robertson 9.35721338263806e-07 1.67168990030476e-06 1815 3057 3281 9.35721732272528e-08 30 2.53306496879855 2.53306496879855 1 5.83484326881972 1811 4636 4444 4394 4580 2433 1315 30 4612 3281 2091 3627 M2521 RAO_BOUND_BY_SALL4 http://www.broadinstitute.org/gsea/msigdb/cards/RAO_BOUND_BY_SALL4.html Loci bound by both isoforms (a and b) of SALL4 [GeneID=57167] in ES cells (embryonic stem). 20837710 315/435 Arthur Liberzon 4.71802876708721e-07 1.0737268939562e-06 4225 3252.63636363636 3281 4.2891179808149e-08 1901 1.97415415260828 2.27473755218489 1 4.68900986592423 4223 3281 1924 2202 1901 4594 4243 4042 2285 2740 4344 3628 M13642 REACTOME_PEPTIDE_CHAIN_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEPTIDE_CHAIN_ELONGATION.html Genes involved in Peptide chain elongation 99/185 Reactome 0.0022790070990529 0.00235793807705605 480 2988.27272727273 3282 0.000207397398195762 455 0.574623241389462 -0.517908585971778 -1 0.557148076719996 476 4491 4162 3282 4525 993 455 2478 4709 4683 2617 3629 M19990 TIEN_INTESTINE_PROBIOTICS_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_6HR_DN.html Genes down-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 6h. 16394013 224/273 Arthur Liberzon 1.65520075468251e-07 7.3358205358541e-07 3475 2956.90909090909 3282 1.5047280720126e-08 732 1.56480571066057 1.64850617567109 1 3.81046569440803 3475 2059 3626 3750 732 2520 3941 3895 2362 2884 3282 3630 M9435 GRADE_COLON_VS_RECTAL_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_VS_RECTAL_CANCER_DN.html Genes down-regulated in rectal but up-regulated in colon carcinoma compared to normal mucosa samples. 17210682 71/101 Jessica Robertson 3.66911907243425e-06 5.04610781523592e-06 2750 2865.54545454545 3282 3.33556835612461e-07 1702 1.56906010232839 1.962489457548 1 3.29248095298077 2746 3353 3282 3502 3359 1702 2556 1812 3333 3604 2272 3631 M189 KEGG_RIBOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOSOME.html Ribosome 98/184 KEGG 0.00466438008351086 0.00479753192289633 540 2994.18181818182 3283 0.000424936257170985 537 0.579250623781911 -0.509392676072704 -1 0.490175249396153 537 4494 4155 3283 4558 1134 560 2035 4708 4674 2798 3632 M8577 WANG_CLIM2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CLIM2_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) engineered to conditionally express a dominant negative form of CLIM2 [GeneID=8861] by a Tet Off system. 17452977 290/317 Arthur Liberzon 2.74717293836092e-06 3.93515256239949e-06 2345 3422.18181818182 3283 2.49743306254809e-07 2047 1.48005347275714 -1.40394703397513 -1 3.16715383648378 2345 4693 4066 4102 3219 3346 3226 2047 3283 4556 2761 3633 M1067 REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX.html Genes involved in Nonsense Mediated Decay Enhanced by the Exon Junction Complex 128/218 Reactome 0.000702043263452511 0.000736529051677229 720 3112.72727272727 3284 6.38424902744405e-05 554 0.681834059093802 -0.562590472597335 -1 0.809002890997965 717 4457 4173 3284 4463 1378 554 2980 4655 4698 2881 3634 M781 REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION.html Genes involved in 3' -UTR-mediated translational regulation 124/229 Reactome 0.000889169972651288 0.000929953970953707 505 3037.18181818182 3286 8.08663227572414e-05 443 0.595698780756036 -0.549787535325843 -1 0.676220043654492 504 4468 4166 3286 4480 1109 443 2984 4707 4687 2575 3635 M16737 VANTVEER_BREAST_CANCER_BRCA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_BRCA1_UP.html Up-regulated genes from the optimal set of 100 markers discriminating ER(-) breast cancer tumors by BRCA1 [GeneID=672] mutation status. 11823860 44/54 Arthur Liberzon 8.36844017654784e-07 1.5459505923016e-06 3290 3119.45454545455 3287 7.60767578160665e-08 1079 1.56488231955629 -1.63679841942438 -1 3.60690921972034 3287 3685 3441 4203 2420 3636 2644 1079 2755 3956 3208 3636 M1927 MIKKELSEN_DEDIFFERENTIATED_STATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_DEDIFFERENTIATED_STATE_DN.html Genes down-regulated in partially reprogrammed and pluripotent cell populations (induced, iPS; and embryonic stem cells, ES) compared to parental lineage-commited cell lines. 18509334 8/9 Jessica Robertson 0.00045046873144237 0.000476729240450221 1270 3054.72727272727 3287 4.50560072437849e-05 937 2.30870954358901 2.30870954358901 1 3.03410256606489 1266 3808 4609 4571 4659 2085 2031 937 4276 3287 2073 3637 M3019 ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_UP.html Genes up-regulated in 3 out of 4 NSCLC cell lines (non-small cell lung cancer) after treatment with azacitidine [PubChem=9444] and TSA [PubChem=5562]. 17043644 255/350 Leona Saunders 7.76296433397638e-07 1.46858483592659e-06 3970 3048.27272727273 3288 7.05724279384817e-08 1536 1.84228250109111 2.1131369533519 1 4.27168032567309 3969 3288 2018 2222 2353 3609 2744 3943 3559 1536 4290 3638 M2804 HAHTOLA_CTCL_CUTANEOUS http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_CTCL_CUTANEOUS.html Genes showing similar expression profiles in all subtypes of cutaneous T cell lymphoma (CTCL). 16914566 25/65 Arthur Liberzon 1.38076264177069e-05 1.66979238256665e-05 3015 3216.72727272727 3288 1.25524664343709e-06 1394 1.59206704601223 -1.39817517240523 -1 3.008740652526 3013 3167 3288 2921 3843 2329 1394 4010 3399 3801 4219 3639 M12403 WATANABE_COLON_CANCER_MSI_VS_MSS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_COLON_CANCER_MSI_VS_MSS_UP.html Up-regulated genes discriminating between MSI (microsatellite instability) and MSS (microsatellite stability) colon cancers. 17047040 29/42 Leona Saunders 2.632145160624e-06 3.79234589686975e-06 4635 3452.63636363636 3289 2.39286209982337e-07 1819 1.63380213057623 -1.59911576698824 -1 3.51190524675395 4635 1819 3047 2904 3198 3289 2558 4668 3832 3354 4675 3640 M1548 KEEN_RESPONSE_TO_ROSIGLITAZONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KEEN_RESPONSE_TO_ROSIGLITAZONE_UP.html Genes up-regulated in aorta biopsies from mice treated with rosiglitazone [PubChem=77999]. 15054141 41/55 John Newman 7.75344246796685e-06 9.78247753242543e-06 855 2768.54545454545 3289 7.04860890317925e-07 852 1.40028600034809 1.31064690472157 1 2.77104811276548 852 3953 3504 4236 3684 996 981 2225 3289 4103 2631 3641 M9869 SASSON_RESPONSE_TO_FORSKOLIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_FORSKOLIN_UP.html Genes up-regulated in primary granulosa cells in response to forskolin [PubChem=47936]. 15026540 127/158 Arthur Liberzon 5.14316209438141e-08 5.19978203455085e-07 4625 2814.36363636364 3289 4.67560201328937e-09 55 1.57770536707781 1.64589976755852 1 3.93712371640993 4624 1558 3289 1295 55 4156 3318 3920 1571 3200 3972 3642 M14309 REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING.html Genes involved in G-protein beta:gamma signalling 24/34 Reactome 4.11078801341815e-07 1.00046055710989e-06 3900 3196.54545454545 3290 3.73708071048685e-08 1738 1.5970398870169 -1.65878518997889 -1 3.80344357011209 3896 2802 3110 2227 1738 3712 3680 3047 3290 3710 3950 3643 M17842 REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_24_HYDROXYCHOLESTEROL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_24_HYDROXYCHOLESTEROL.html Genes involved in Synthesis of bile acids and bile salts via 24-hydroxycholesterol 10/20 Reactome 2.87405857259225e-06 4.08232213741662e-06 4280 3400.36363636364 3291 2.61278393385568e-07 1520 2.64307675891041 -2.08134068354411 -1 5.67826720493466 4277 2443 1520 2837 3249 4530 4683 4014 3291 2007 4553 3644 M1409 PEART_HDAC_PROLIFERATION_CLUSTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/PEART_HDAC_PROLIFERATION_CLUSTER_UP.html Cell proliferation genes up-regulated by histone deacetylase (HDAC) inhibitors SAHA and depsipeptide [PubChem=5311;5352062]. 15738394 79/88 Kate Stafford 3.23637909025037e-06 4.53554314310622e-06 2475 3514.36363636364 3292 2.94216713748843e-07 2475 1.4120894419354 1.72773919926664 1 2.98440010258448 2475 4472 3873 4525 3292 3064 2891 3025 3945 4055 3041 3645 M7257 REACTOME_NRIF_SIGNALS_CELL_DEATH_FROM_THE_NUCLEUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NRIF_SIGNALS_CELL_DEATH_FROM_THE_NUCLEUS.html Genes involved in NRIF signals cell death from the nucleus 19/23 Reactome 0.000172974206845163 0.000186614458584953 1335 2707.18181818182 3293 1.57261643979109e-05 375 1.25022445391484 -0.864158937345837 -1 1.82490293260937 1331 3477 3293 4240 4337 989 375 2289 4234 4076 1138 3646 M13522 DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN.html Common down-regulated transcripts in fibroblasts expressing either XP/CS or TDD mutant forms of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 707/799 Arthur Liberzon 2.01530898161739e-07 7.65527859584926e-07 2660 3296.36363636364 3293 2.01530916438357e-08 1062 1.60912997083255 1.91334909468008 1 3.90783737374494 2659 3837 4392 2746 1062 4081 4363 2969 2342 4516 3293 3647 M2588 SMIRNOV_RESPONSE_TO_IR_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_6HR_UP.html Genes up-regulated in B lymphocytes at 6 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 223/276 Itai Pashtan 4.10174505965142e-07 1.00046055710989e-06 3865 3144.18181818182 3293 3.72885984035736e-08 1734 1.91326605727079 2.36813570680163 1 4.56646236946757 3863 3293 2333 3470 1734 4152 4466 3979 2039 3093 2164 3648 M15676 BECKER_TAMOXIFEN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BECKER_TAMOXIFEN_RESISTANCE_DN.html Genes down-regulated in a breast cancer cell line resistant to tamoxifen [PubChem=5376] compared to the parental line sensitive to the drug. 15657362 113/132 Jean Junior 1.27777379296452e-05 1.55342122357558e-05 3355 2584.90909090909 3295 1.16161928583197e-06 68 2.10227619341479 -1.9029325902844 -1 4.01551072901415 3355 68 1397 2126 3825 3772 3364 3295 1705 1364 4163 3649 M3952 BIOCARTA_LAIR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LAIR_PATHWAY.html Cells and Molecules involved in local acute inflammatory response 15/23 BioCarta 3.259817701773e-06 4.56026661303158e-06 3625 3089.09090909091 3297 2.96347502906367e-07 886 2.69614669866098 2.28375108207702 1 5.74114924351479 3623 2407 886 3349 3297 3004 3133 3842 4375 1351 4713 3650 M6469 DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN.html Genes down-regulated in Kasumi-1 cells (acute myeloid leukaemia (AML) with the t(8;21) translocation) after knockdown of the AML1 MTG8 fusion [GeneID=861;862] by RNAi. 16652140 27/39 Leona Saunders 2.30889445652121e-06 3.41736652078397e-06 3300 2996.54545454545 3297 2.09899716336698e-07 1097 2.33404757291647 2.98778317107849 1 5.08099208700224 3297 4000 1492 3671 3113 3942 4485 1097 4181 1522 2162 3651 M2170 FIGUEROA_AML_METHYLATION_CLUSTER_4_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_4_UP.html Cluster 4 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 129/172 Arthur Liberzon 6.71365307260556e-07 1.33593771090633e-06 4510 3537.72727272727 3297 6.10332283762312e-08 2225 1.79904822058835 -1.41832626799394 -1 4.2000046798892 4506 2993 2961 4410 2225 3297 3524 4188 3132 3158 4521 3652 M1071 REACTOME_TANDEM_PORE_DOMAIN_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TANDEM_PORE_DOMAIN_POTASSIUM_CHANNELS.html Genes involved in Tandem pore domain potassium channels 5/12 Reactome 1.04068942891605e-06 1.80252127078677e-06 3465 2936.27272727273 3298 1.04068991628189e-07 175 2.81818435197124 -1.89591122806265 -1 6.46015078436474 3462 1052 4262 2574 2660 3298 3430 4488 175 2495 4403 3653 M12208 TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_DN.html Genes down-regulated in ductal vs lobular carcinoma breast tumor cells. 17389037 11/11 Arthur Liberzon 6.84557845231044e-05 7.61006316753291e-05 4610 3496 3298 6.22344679129827e-06 2276 2.46256546354364 -2.0802282982372 -1 4.02882745184722 4608 2891 2276 3092 4198 4468 4561 2312 2410 3298 4342 3654 M14495 VETTER_TARGETS_OF_PRKCA_AND_ETS1_UP http://www.broadinstitute.org/gsea/msigdb/cards/VETTER_TARGETS_OF_PRKCA_AND_ETS1_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PRKCA and ETS1 [GeneID=5578;2113] by RNAi. 15531915 19/21 Leona Saunders 1.5342482100255e-07 7.28175281873995e-07 3300 3261.36363636364 3300 1.39477119729251e-08 649 1.94068026513872 2.39592803296197 1 4.74028622718106 3300 4310 3091 3990 649 4076 4520 3145 3217 3540 2037 3655 M1357 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_DN.html Early prostate development genes (down-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 11/11 Jessica Robertson 0.0446163398531988 0.0451617250926653 2090 3270.09090909091 3300 0.00414070181066568 1768 1.64359947345094 -1.69900403156779 -1 0.839149660688719 2086 3514 3250 4600 4634 2097 1768 3453 4251 3300 3018 3656 M1476 ZHAN_EARLY_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_EARLY_DIFFERENTIATION_GENES_DN.html B lymphocyte early differentiation genes (EDG): top genes down-regulated in tonsil B lymphocytes (TBC) compared to the tonsil plasma cells (TPC). 12393520 50/58 Arthur Liberzon 3.29183757977694e-06 4.60233216129951e-06 3520 3305 3300 2.9925840957548e-07 2352 1.58012674299546 1.56899048386643 1 3.34146089510514 3520 2683 3189 2490 3300 3821 4674 3529 2352 3167 3630 3657 M842 REACTOME_PURINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_CATABOLISM.html Genes involved in Purine catabolism 10/15 Reactome 0.000101120654065713 0.000110945952391949 3220 3250.81818181818 3301 9.19320929707828e-06 922 2.39055335655775 -1.91023794211531 -1 3.75214869939971 3220 4090 2431 3692 4254 3301 2214 4618 922 3106 3911 3658 M588 GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_DN.html Down-regualted genes from the set F (Fig. 5a): specific signature shared by cells expressing AF4-MLL [GeneID=4299;4297] alone and those expressing both AF4-MLL and MLL-AF4 fusion proteins. 17130830 35/49 Arthur Liberzon 8.85129133274598e-08 6.51764353986912e-07 4275 2674.27272727273 3301 8.04662880805572e-09 232 1.82883084138284 -1.25057814689683 -1 4.49961029004886 4271 602 1737 2326 232 3725 3301 3818 3796 1903 3706 3659 M4709 NIKOLSKY_BREAST_CANCER_19Q13.4_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_19Q13.4_AMPLICON.html Genes within amplicon 19q13.4 identified in a copy number alterations study of 191 breast tumor samples. 19010930 3/6 Jessica Robertson 0.0138919774117848 0.0141803921677388 2170 3355.72727272727 3301 0.00139795934349458 1114 0.579502001472646 0.579502001472646 1 0.380718317822431 2168 3821 4465 2934 4593 1980 1114 3198 4628 4711 3301 3660 M1755 SANSOM_APC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS.html Genes up-regulated after Cre-lox knockout of APC [GeneID=324] in the small intestine. 17377531 275/346 Arthur Liberzon 2.36292624705803e-06 3.48531621441059e-06 3725 3214.54545454545 3305 2.14811707725475e-07 1753 1.91960125980213 2.13114336070259 1 4.16329733770294 3725 3285 2290 3720 3124 4114 4436 3338 1753 2270 3305 3661 M14775 ST_G_ALPHA_S_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_G_ALPHA_S_PATHWAY.html G alpha s Pathway 19/21 Signaling Transduction KE 3.15752108830967e-05 3.63499988702966e-05 1965 3036.45454545455 3307 2.87051491556977e-06 976 1.43509183397939 -1.67590115511811 -1 2.51216843422252 1964 3758 3307 4040 4045 2948 2326 976 4371 4244 1422 3662 M8699 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_CIS.html Transcripts in hematopoietic stem cells (HSC) which are cis-regulated (i.e., modulated by a QTL (quantitative trait locus) in close proximity to the gene). 15711547 154/211 Jean Junior 2.81846355878124e-07 8.49189526890862e-07 4225 3113.72727272727 3308 2.56223992714568e-08 1325 2.01973574163317 2.15145965534835 1 4.88119109766972 4221 3308 2732 1706 1325 3329 3449 4298 2522 3290 4071 3663 M6122 BROWNE_HCMV_INFECTION_20HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_20HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 20 h time point that were not up-regulated at the previous time point, 18 h. 11711622 406/539 John Newman 1.45399405482997e-06 2.33192386639398e-06 4310 3239.18181818182 3309 1.32181365071347e-07 1794 1.76831736249832 1.9600739406356 1 3.95535953621464 4308 4133 3324 2030 2838 3755 3309 1794 2731 3118 4291 3664 M11701 CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_UP.html Selected genes up-regulated during invasion of lymphatic vessels during metastasis. 18794116 28/35 Jessica Robertson 6.24329401742739e-07 1.27128333745717e-06 3860 3043.72727272727 3309 5.67572344471646e-08 987 2.23695668415288 -2.45708286062736 -1 5.25389365690945 3860 3439 1537 3841 2163 4408 3206 3125 3606 987 3309 3665 M1947 CHEN_LIVER_METABOLISM_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LIVER_METABOLISM_QTL_CIS.html Cis-regulated expression quantitative loci (cis-eQTL) in the liver that contribute to metabolic quantitative traits (weight, fat mass, and plasma glucose and cholesterol levels). 18344982 123/185 Arthur Liberzon 2.61295143626287e-07 8.29211725993449e-07 4240 3169.36363636364 3309 2.37541067873138e-08 1239 1.95492445853528 -1.90276783519917 -1 4.73108158519348 4236 3598 1942 3712 1239 4342 4233 1717 3276 3309 3259 3666 M9648 REACTOME_FORMATION_OF_TUBULIN_FOLDING_INTERMEDIATES_BY_CCT_TRIC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_TUBULIN_FOLDING_INTERMEDIATES_BY_CCT_TRIC.html Genes involved in Formation of tubulin folding intermediates by CCT/TriC 20/26 Reactome 0.000360375244107381 0.00038336063831121 2140 3184.45454545455 3311 3.27667536009807e-05 1554 1.57362691477775 1.42888035627473 1 2.11203499743423 2137 3189 3311 1554 4403 2537 1740 4704 3991 3638 3825 3667 M151 PID_AR_TF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_TF_PATHWAY.html Regulation of Androgen receptor activity 18832364 70/92 Pathway Interaction Database 4.93924788104427e-06 6.52483907039713e-06 2720 3458.90909090909 3313 4.4902354274974e-07 2717 1.23953655678246 -1.40969785758637 -1 2.53486901548045 2717 4480 3934 3583 3506 3242 2776 2822 3313 4465 3210 3668 M16713 DIRMEIER_LMP1_RESPONSE_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DIRMEIER_LMP1_RESPONSE_LATE_DN.html Cluster 4: genes down-regulated in B2264-19/3 cells (primary B lymphocytes) within 60-180 min after activation of LMP1 (an oncogene encoded by Epstein-Barr virus, EBV). 15674340 33/59 Arthur Liberzon 2.63076115196664e-06 3.79150920222367e-06 3375 3353.09090909091 3313 2.39160390712497e-07 1779 1.46327616424009 -0.869056656600388 -1 3.14018854493169 3375 3983 3271 4237 3197 2617 1779 3313 2446 4183 4483 3669 M1753 ZHENG_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_UP.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are up-regulated both in developing (located in the thymus) and mature (from peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 33/39 Jessica Robertson 1.33768282222808e-06 2.18573218506058e-06 4435 3228.18181818182 3315 1.21607603235481e-07 1438 2.37896698146477 2.88589136118473 1 5.36543620333675 4432 3712 1857 3315 2775 4195 4011 3015 2132 1438 4628 3670 M19895 KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM.html Nicotinate and nicotinamide metabolism 23/31 KEGG 1.8520449613218e-07 7.48271685670965e-07 4340 3031 3316 1.68367737930374e-08 870 2.6119010299034 2.64622592148323 1 6.38469030439806 4339 2361 2040 3316 870 4526 3604 4365 941 2578 4401 3671 M2658 BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_UP.html Genes from cluster 3: up-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 30/39 Jessica Robertson 1.30779420214711e-05 1.58683512445613e-05 3320 3090.72727272727 3318 1.18891088765402e-06 1476 1.35210821025313 1.33866464311248 1 2.55975078151965 3318 2325 3360 3948 3832 2428 2688 3153 4039 3431 1476 3672 M1090 REACTOME_SIGNALING_BY_FGFR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR.html Genes involved in Signaling by FGFR 110/136 Reactome 2.26064402110668e-07 7.86164283892477e-07 4355 3112.63636363636 3319 2.05513113945699e-08 1082 1.49666517945305 -1.0622915594028 -1 3.62426153604427 4355 3004 3512 1328 1082 3319 2501 4422 2500 4179 4037 3673 M14742 HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP.html Genes up-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrom (MDS) compared to the low risk patients. 12411319 29/43 Arthur Liberzon 1.54708243414652e-06 2.44712771084839e-06 2480 3072.54545454545 3321 1.40643956553255e-07 1091 1.32776116576023 -1.59924153666703 -1 2.94627777671336 2478 3989 3321 4223 2886 1844 1091 4083 3464 3617 2802 3674 M2216 WIERENGA_STAT5A_TARGETS_GROUP2 http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_GROUP2.html Genes up-regulated in a linear fashion in CD34+ [GeneID=947] cells upon increasing activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 59/93 Arthur Liberzon 1.39704416737126e-06 2.26302134298975e-06 4585 3172.81818181818 3322 1.2700409586574e-07 1459 2.3391790244915 -2.38075117672739 -1 5.26066582757187 4584 3366 1484 3113 2802 4382 3322 4243 2646 1459 3500 3675 M1717 ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_UP.html The vEDG up-regulated set: most variable early differentiation genes (EDG) with similar expression patterns in tonsil B lymphocytes (TBC) and multiple myeloma (MM) cells compared to the plasma cells from tonsil (TPC) and bone marrow (BPC). 12393520 22/35 Arthur Liberzon 3.44329861634096e-06 4.78292215100921e-06 3960 2977.45454545455 3323 3.13027636871134e-07 1304 2.04509837652398 -2.03049864318345 -1 4.32570299906854 3957 1875 1919 3863 3323 4221 3725 1304 3033 2087 3445 3676 M6752 TENEDINI_MEGAKARYOCYTE_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/TENEDINI_MEGAKARYOCYTE_MARKERS.html Genes essential to the development of megakaryocytes, as expressed in normal cells and essential thrombocythemic cells (ET). 15271793 79/96 Kate Stafford 1.45206466788981e-06 2.3304132038218e-06 4335 3173.81818181818 3325 1.32005966026915e-07 1306 2.2596446765649 -2.12571763270216 -1 5.06851552200119 4334 2609 1306 2009 2836 3642 4269 4262 3325 1674 4646 3677 M7034 MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_UP.html Up-regulated 'cooperation response genes': responded synergystically to the combination of mutant TP53 and HRAS [GeneID=7157;3265] in YAMC cells (colon). 18500333 32/35 Jessica Robertson 5.20440532409968e-07 1.13568160562878e-06 4210 3035.72727272727 3325 4.73127868661309e-08 894 2.55606812505101 2.44224873808984 1 6.06087712162278 4210 1802 894 3325 1986 4248 4133 3003 4321 1138 4333 3678 M569 REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING.html Genes involved in SHC1 events in ERBB4 signaling 29/30 Reactome 3.46895896292444e-06 4.81569647667824e-06 4290 2666.54545454545 3326 3.15360402980852e-07 198 2.03962102112234 -1.86891085010555 -1 4.31155080716796 4286 1812 2102 198 3326 4289 3511 2125 513 3614 3556 3679 M16517 BIOCARTA_WNT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_WNT_PATHWAY.html WNT Signaling Pathway 43/48 BioCarta 8.92314240639465e-07 1.61887766533698e-06 3515 3220.54545454545 3327 8.11195093236354e-08 1354 1.38203262416133 1.71845426303341 1 3.16848468416821 3671 3098 3515 3244 2478 4162 4289 1354 2773 3515 3327 3680 M15303 REACTOME_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOSIS.html Genes involved in Apoptosis 173/213 Reactome 5.324769097133e-07 1.15119470304061e-06 3620 3083.09090909091 3327 4.84070035083063e-08 2011 1.69584060260028 1.83150561935731 1 4.00027156278471 3617 3583 3327 2737 2011 2269 2903 3482 2182 3843 3960 3681 M10558 LU_IL4_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/LU_IL4_SIGNALING.html Genes up-regulated in peripheral B lymphocytes after incubation with IL4 [GeneID=3565] for 4 h. 15591113 120/180 Kate Stafford 2.94582996968863e-07 8.6793492240514e-07 3330 3135.81818181818 3327 2.67802760376304e-08 1369 1.94039332829929 -1.66952806237285 -1 4.68007517629977 3327 3872 2233 4373 1369 3784 2577 2737 3334 2984 3904 3682 M4389 RIZ_ERYTHROID_DIFFERENTIATION_12HR http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_12HR.html Selected genes down-regulated in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts) at 12 h time point. 17213805 47/63 Leona Saunders 1.4527496100418e-06 2.33071997260275e-06 4390 3100.36363636364 3329 1.32068233577493e-07 499 1.69184688007417 1.67756533440418 1 3.78229965802872 4390 499 2500 3329 2837 4105 4110 2886 3382 1658 4408 3683 M10885 DAZARD_UV_RESPONSE_CLUSTER_G4 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G4.html Cluster G4: genes increasingly up-regulated in NHEK cells (normal keratinocyte) after 12 h time point after UV-B irradiation. 12771951 37/83 John Newman 6.78478460112998e-07 1.34422242460247e-06 4125 2938.72727272727 3329 6.16798790323065e-08 618 1.61700808370299 1.63741680632369 1 3.76821005794772 4124 618 2466 1085 2234 3516 3329 3955 4127 2408 4464 3684 M4500 DACOSTA_UV_RESPONSE_VIA_ERCC3_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_DN.html Genes down-regulated in fibroblasts expressing mutant forms of ERCC3 [GeneID=2071] after UV irradiation. 15608684 1167/1296 Arthur Liberzon 1.69751099627471e-07 7.33971845416521e-07 2640 3312.45454545455 3330 1.69751112594419e-08 883 1.58329662195244 1.85557527174848 1 3.85593737737785 2638 4125 4391 2747 883 4107 4365 2967 2341 4543 3330 3685 M1751 ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_DN.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are down-regulated only in mature (peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 48/62 Jessica Robertson 1.06324102478404e-05 1.31326183035636e-05 3420 3266.09090909091 3331 9.66587421246338e-07 2224 2.08763753650591 -2.14166887112953 -1 4.04843765665872 3418 2253 2224 3331 3763 3647 3183 3521 2899 3226 4462 3686 M2417 WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D.html Genes with promoters bound by both PPARG and RXRA [GeneID=5468, 6256] at 8 day time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 1101/1344 Arthur Liberzon 3.37931006779854e-07 9.13746684768849e-07 2960 3537.81818181818 3331 3.37931058168679e-08 1628 1.51226043217005 -1.33931868645899 -1 3.62282642060824 2960 4658 4698 4689 1628 2192 2810 4568 3331 4487 2895 3687 M44 PID_HIF2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF2PATHWAY.html HIF-2-alpha transcription factor network 18832364 39/51 Pathway Interaction Database 2.51767788360161e-06 3.6598212536494e-06 3335 3250.63636363636 3332 2.28880069530398e-07 2209 1.79953479405216 1.93303768363762 1 3.88440802213798 3332 3695 2548 2890 3167 3470 3396 4655 2209 2916 3479 3688 M948 REACTOME_IRAK2_MEDIATED_ACTIVATION_OF_TAK1_COMPLEX_UPON_TLR7_8_OR_9_STIMULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IRAK2_MEDIATED_ACTIVATION_OF_TAK1_COMPLEX_UPON_TLR7_8_OR_9_STIMULATION.html Genes involved in IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation 11/14 Reactome 6.48846615360304e-05 7.23495399126065e-05 1100 2478.81818181818 3332 5.89877956910787e-06 116 1.4676468778415 -1.4676468778415 -1 2.39385339335958 1100 4349 3332 3493 4510 780 116 395 4045 4062 1085 3689 M1862 ZHOU_PANCREATIC_ENDOCRINE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_PANCREATIC_ENDOCRINE_PROGENITOR.html Transcription factors expressed in progenitors of endocrine pancreatic cells. 18754011 4/16 Jessica Robertson 0.00174982159075724 0.00181719645948827 3205 3564.72727272727 3333 0.000175120096367155 2084 1.90986687432687 -0.873195357560769 -1 2.05494831314141 3202 4116 4582 4358 4515 3333 2084 3135 3184 2992 3711 3690 M767 REACTOME_HOMOLOGOUS_RECOMBINATION_REPAIR_OF_REPLICATION_INDEPENDENT_DOUBLE_STRAND_BREAKS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HOMOLOGOUS_RECOMBINATION_REPAIR_OF_REPLICATION_INDEPENDENT_DOUBLE_STRAND_BREAKS.html Genes involved in Homologous recombination repair of replication-independent double-strand breaks 20/26 Reactome 9.61477959655075e-05 0.000105760334876997 4310 2670.09090909091 3334 8.74109074745632e-06 131 1.24038735225495 1.27059849169831 1 1.93317462317956 1222 4309 3506 4022 4245 566 131 1857 4308 3334 1871 3691 M17794 ASGHARZADEH_NEUROBLASTOMA_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ASGHARZADEH_NEUROBLASTOMA_POOR_SURVIVAL_DN.html Down-regulated genes associated with poor survival prognosis of patients with metastatic neuroblastoma that lack MYCN [GeneID=4613] amplification. 16954472 94/116 Jessica Robertson 4.6086590746135e-06 6.15531149750304e-06 3335 3236.54545454545 3334 4.18969884460763e-07 2329 1.95245843220529 2.39413996048815 1 4.04146404693291 3334 3327 2350 3466 3464 4111 4053 2329 2593 3576 2999 3692 M17523 ZHAN_MULTIPLE_MYELOMA_CD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD2_DN.html Top 50 down-regulated genes in cluster CD-2 of multiple myeloma samples with the charachteristic expression spike of CCND3 [GeneID=896]. 16728703 62/72 Kevin Vogelsang 1.24733695386332e-06 2.06794184131889e-06 4710 3380.90909090909 3334 1.13394332824381e-07 1682 1.72367759352893 1.56044596470222 1 3.8904147543076 4707 1682 2394 3334 2731 4257 4131 4416 3318 2314 3906 3693 M1383 SHIN_B_CELL_LYMPHOMA_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_1.html Cluster 1 of genes distinguishing among different B lymphocyte neoplasms. 19010892 11/18 Jessica Robertson 5.41685391192218e-06 7.09224700812003e-06 3490 3318.27272727273 3335 4.92442477216374e-07 1763 2.34794965005945 2.80276855852809 1 4.81213749463485 3487 4089 2088 4365 3536 3243 3220 3335 4427 1763 2948 3694 M10651 SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_DN.html Genes down-regulated in 293 cells (embryonic kidney) expressing polymorphic variants S427G (SNP ID=rs2070235) or I624M (SNP ID=rs11556379) of BMYB [GeneID=4605]. 18026132 24/28 Jessica Robertson 2.83677478565181e-06 4.04396767993855e-06 3240 3480.45454545455 3337 2.57888949410731e-07 1853 1.77914660190607 2.03252892881341 1 3.80881638414562 4456 1853 2726 3337 3238 3965 3237 4471 3783 2723 4496 3695 M8822 LU_TUMOR_ENDOTHELIAL_MARKERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_ENDOTHELIAL_MARKERS_DN.html Genes specifically down-regulated in tumor endothelium. 17308118 5/6 Jessica Robertson 0.00126726232943336 0.00132041461256633 3165 3649.45454545455 3338 0.000126798558920397 2283 3.00836462449735 4.2058839654713 1 3.43346822454372 3162 3261 4577 4570 4501 3338 3192 2283 4357 3258 3645 3696 M793 REACTOME_CLASS_C_3_METABOTROPIC_GLUTAMATE_PHEROMONE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_C_3_METABOTROPIC_GLUTAMATE_PHEROMONE_RECEPTORS.html Genes involved in Class C/3 (Metabotropic glutamate/pheromone receptors) 4/16 Reactome 0.000648744594001448 0.000681369489026888 3180 3211.27272727273 3339 6.48934063150278e-05 1063 3.55074819032967 -5.02476601528597 -1 4.47181240440314 3176 3536 4238 3339 4465 3556 2747 2458 1063 2990 3756 3697 M1390 SHIN_B_CELL_LYMPHOMA_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_6.html Cluster 6 of genes distinguishing among different B lymphocyte neoplasms. 19010892 6/16 Jessica Robertson 3.68953115588211e-05 4.21762825278846e-05 3795 3162.18181818182 3339 3.68959241419422e-06 412 4.63376637724132 -5.21293573886042 -1 8.10274925737491 3791 3813 4460 3311 4094 2912 2012 3845 412 2795 3339 3698 M8344 NAKAJIMA_EOSINOPHIL http://www.broadinstitute.org/gsea/msigdb/cards/NAKAJIMA_EOSINOPHIL.html Top 30 increased eosinophil specific transcripts. 11493461 20/52 Kevin Vogelsang 2.06756276548968e-07 7.68728418959517e-07 985 2684.36363636364 3339 1.87960269072683e-08 865 2.44209955082178 1.96157619371214 1 5.95486008272132 3892 865 1276 3834 982 3339 3823 4168 2568 983 3798 3699 M11303 SABATES_COLORECTAL_ADENOMA_SIZE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_SIZE_DN.html A selection of genes whose expression displayed significant negative correlation with size of colorectal adenoma. 18171984 12/21 Leona Saunders 0.00074716491639619 0.000782823175447285 3425 3446.72727272727 3340 6.79471626884769e-05 2416 1.95683742814508 1.4882956547637 1 2.39454069847675 3425 3226 2416 2797 4471 3340 3752 2896 4202 2971 4418 3700 M17866 KYNG_DNA_DAMAGE_BY_UV http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_UV.html UV only responding genes in primary fibroblasts from young donors. 15897889 77/99 Jessica Robertson 2.51230402806789e-07 8.19318755885969e-07 4485 3232.09090909091 3340 2.28391301360191e-08 1197 1.98913501630201 -1.56270810357425 -1 4.81891943618731 4482 3340 1944 2592 1197 4692 3795 3858 3226 2080 4347 3701 M3334 SHIPP_DLBCL_CURED_VS_FATAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_CURED_VS_FATAL_UP.html Top 50 up-regulated markers for the diffused large B-cell lymphoma (DLBCL) that distinguished between cured and fatal/refractory clinical outcomes. 11786909 81/144 Jean Junior 5.82425453396045e-05 6.51896642169631e-05 3110 3514.09090909091 3342 5.29491702755989e-06 2438 1.86235117006439 -1.6184730455377 -1 3.08500155007462 3109 3342 2438 3232 4166 3680 3195 3910 4041 2979 4563 3702 M19805 LI_CYTIDINE_ANALOGS_CYCTOTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/LI_CYTIDINE_ANALOGS_CYCTOTOXICITY.html Genes whose expression in a panel of lymphoblastoid cell lines was associated with cytotoxicity of the anti-cancer analogs of cytidine, gemcitabine and cytarabine [PubChem=596;3461;6253]. 18757419 17/18 Jessica Robertson 0.000487343468386041 0.000514599814492643 1635 2861.90909090909 3342 4.43137689168611e-05 842 1.30851079288785 1.04690528648409 1 1.6804955712497 1634 2853 3531 3459 4436 1332 842 3923 3342 3664 2465 3703 M2140 LU_EZH2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_EZH2_TARGETS_DN.html Genes down-regulated in SKOV3ip1 cells (ovarian cancer) upon knockdown of EZH2 [GeneID=2146] by RNAi. 20708159 536/670 Arthur Liberzon 3.39081179123092e-07 9.15271659547923e-07 4275 3234.63636363636 3342 3.39081230862324e-08 1633 1.86048584537717 2.05800032225159 1 4.46802806937263 4275 2499 4663 2670 1633 4649 3683 3342 2174 2489 3504 3704 M2601 WARTERS_IR_RESPONSE_5GY http://www.broadinstitute.org/gsea/msigdb/cards/WARTERS_IR_RESPONSE_5GY.html Genes up-regulated in the human skin cells at 4 h after exprosure to 5 Gy dose of ionizing radiation. 19580510 54/90 Itai Pashtan 1.13139715498198e-07 7.05613393308323e-07 3345 3067 3343 1.02854292106046e-08 367 1.62437371489742 -1.33596463767647 -1 3.96845307453915 3343 3068 2614 3926 367 3431 3259 4305 3797 2079 3548 3705 M17181 REACTOME_SIGNALLING_TO_P38_VIA_RIT_AND_RIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_P38_VIA_RIT_AND_RIN.html Genes involved in Signalling to p38 via RIT and RIN 18/20 Reactome 4.62598199740691e-06 6.17320752834623e-06 3350 2862.81818181818 3344 4.205447022342e-07 1099 1.62397887971469 2.28224630541888 1 3.35229072850821 3346 3479 3112 1099 3468 3344 3393 1596 2145 4198 2311 3706 M1028 REACTOME_RAF_MAP_KINASE_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAF_MAP_KINASE_CASCADE.html Genes involved in RAF/MAP kinase cascade 14/14 Reactome 0.000121382736833424 0.000132407330218109 3345 3210.09090909091 3344 1.10354031380381e-05 675 1.02851065378674 1.36357433069383 1 1.55404682209299 3344 3501 3629 675 4288 3192 3271 2492 3572 4400 2947 3707 M15936 NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON.html Genes within amplicon 17q21-q25 identified in a copy number alterations study of 191 breast tumor samples. 19010930 351/497 Jessica Robertson 5.77536340586945e-07 1.21154290114239e-06 3490 3072.36363636364 3344 5.25033174727118e-08 2091 1.92786392899066 2.35587225749914 1 4.53722681313443 3564 4135 2173 3489 2091 2153 3414 3344 2799 3486 3148 3708 M2500 PHONG_TNF_RESPONSE_VIA_P38_COMPLETE http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_RESPONSE_VIA_P38_COMPLETE.html Genes whose expression changes in Calu-6 cells (lung cancer) by TNF [GeneID=7124] were blocked completely by p38 inhibitor LY479754. 20516219 317/382 Arthur Liberzon 2.74302316597076e-07 8.38703759494626e-07 3965 3139.81818181818 3344 2.4936577345262e-08 1294 1.77191035035425 -1.26712278445629 -1 4.27996526025947 3964 2516 2859 3450 1294 3638 2868 4280 2131 3344 4194 3709 M7914 HENDRICKS_SMARCA4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HENDRICKS_SMARCA4_TARGETS_DN.html Genes down-regulated in ALAB cells (breast cancer) upon reintroduction of SMARCA4 [GeneID=6597] expressed off adenoviral vector. 14673169 45/89 John Newman 3.57113820307766e-06 4.93002992644824e-06 4420 2891.81818181818 3345 3.24649454538343e-07 1133 2.25882255683029 2.22410228847101 1 4.7710409516939 4416 2675 1331 1394 3345 3865 4397 3817 1723 1133 3714 3710 M10175 ELVIDGE_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_DN.html Genes down-regulated in MCF7 cells (breast cancer) under hypoxia conditions. 16565084 189/212 Arthur Liberzon 3.57826773279246e-06 4.93842798209954e-06 4280 3312.63636363636 3346 3.25297595709609e-07 2118 1.49060943780943 1.60270224524671 1 3.13097571038165 2118 4148 3973 4276 3346 2451 2734 3083 2681 4280 3349 3711 M816 BONOME_OVARIAN_CANCER_POOR_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_POOR_SURVIVAL_UP.html Top highly correlated genes positively associated with poor survival of patients with suboptimally debulked ovarian tumors. 18593951 40/45 Jessica Robertson 2.16300669738016e-06 3.23655703962543e-06 4505 3304.09090909091 3347 1.96637165819866e-07 2279 1.77501085949573 -1.29728350209172 -1 3.86889210590208 4501 2279 2829 3347 3073 3852 3485 3802 3514 3022 2641 3712 M2237 JOHNSTONE_PARVB_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_1_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) upon overexpression of PARVB [GeneID=29780] under all three culture conditions. 17998334 84/108 Arthur Liberzon 3.05712161193798e-06 4.32024371507402e-06 3270 3477.36363636364 3347 2.77920532738607e-07 1585 1.58330542143978 1.7173307655015 1 3.36577463195686 3631 4187 3268 4627 3268 3347 4091 1585 3183 3803 3261 3713 M5940 BIOCARTA_NDKDYNAMIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NDKDYNAMIN_PATHWAY.html Endocytotic role of NDK, Phosphins and Dynamin 21/24 BioCarta 2.49097043394518e-06 3.63218425956789e-06 3255 3351.63636363636 3348 2.26452114034005e-07 1862 0.765109661517902 -0.808344410569982 -1 1.62378701038998 3253 1862 3852 3224 3158 3348 2586 3379 4171 4426 3609 3714 M1704 HOWLIN_CITED1_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_2_UP.html Genes up-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs wild type (WT) animals. 16278680 22/27 Arthur Liberzon 3.58452268393111e-06 4.94416921921532e-06 3965 3183 3349 3.2586622948267e-07 1206 1.79121534666141 -1.86061250622464 -1 3.77211578148415 3965 2345 1927 2376 3349 4473 4575 4081 3039 1206 3677 3715 M627 REACTOME_TGF_BETA_RECEPTOR_SIGNALING_IN_EMT_EPITHELIAL_TO_MESENCHYMAL_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TGF_BETA_RECEPTOR_SIGNALING_IN_EMT_EPITHELIAL_TO_MESENCHYMAL_TRANSITION.html Genes involved in TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) 26/32 Reactome 3.18619260576065e-05 3.6662186979986e-05 4050 3157.90909090909 3350 2.89658068304341e-06 1844 1.2615032698062 -1.55407319917845 -1 2.2003601013649 3025 4018 3517 3503 4047 2719 2706 1844 3350 4048 1960 3716 M13658 HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_DN.html Genes whose expression correlated with lower risk of late recurrence of hepatocellular carcinoma (HCC). 18923165 64/119 Yujin Hoshida 1.65473174700478e-06 2.58534718499258e-06 3350 3274.72727272727 3350 1.50430271964899e-07 2267 1.85236753575241 1.98444822747555 1 4.11236351368025 3350 3362 2738 4371 2924 3486 3492 3214 3534 2267 3284 3717 M15031 STREICHER_LSM1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STREICHER_LSM1_TARGETS_UP.html Genes up-regulated in MCF10A cells (breast cancer) by expression of LSM1 [GeneID=27257] off a letiviral vector. 17001308 59/62 Arthur Liberzon 1.02546142337228e-06 1.7847263710609e-06 4050 3143.90909090909 3351 9.3223809214497e-08 431 1.81500020489016 1.95579067363901 1 4.14587564501621 3731 431 2256 3351 2587 4050 4048 4486 2233 2987 4423 3718 M18108 NIKOLSKY_MUTATED_AND_AMPLIFIED_IN_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_MUTATED_AND_AMPLIFIED_IN_BREAST_CANCER.html Genes both mutated and amplified in a panel of 191 breast tumor samples. 19010930 119/172 Jessica Robertson 2.78755087317769e-07 8.45238737886283e-07 3680 3072.27272727273 3351 2.53413747852688e-08 1313 2.14192372342067 2.8637066722685 1 5.1812602220266 3679 1582 1619 3393 1313 3788 4694 4592 2871 2913 3351 3719 M3185 HELLER_SILENCED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_SILENCED_BY_METHYLATION_DN.html Genes down-regulated in at least one of three multiple myeloma (MM) cell lines treated with the DNA hypomethylating agent decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 18172295 126/163 Jessica Robertson 4.30831934846394e-07 1.02188257382467e-06 4565 3318.81818181818 3352 3.91665472015815e-08 1678 2.07425996517588 -2.0851424147914 -1 4.94724749587475 4561 2995 1678 2629 1796 4273 3352 4698 3411 2498 4616 3720 M9134 BIOCARTA_TRKA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TRKA_PATHWAY.html Trka Receptor Signaling Pathway 22/25 BioCarta 1.97668587102728e-07 7.65377958264871e-07 3710 2616.09090909091 3353 1.79698731693751e-08 498 1.59133219741897 1.93854212621364 1 3.86411575286527 3707 829 2671 498 928 4048 4383 3407 1425 3528 3353 3721 M346 LIN_MELANOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIN_MELANOMA_COPY_NUMBER_UP.html Candidate genes in significant regions of chromosomal copy number gains in a panel of melanoma samples. 18245465 99/112 Jessica Robertson 3.16635161688161e-07 8.94262307705344e-07 1980 3009.90909090909 3354 2.87850188418099e-08 1443 1.41745102536609 -1.38172033718443 -1 3.39789663697182 1978 3889 3967 4517 1443 1913 1973 3354 3843 4341 1891 3722 M13709 NIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICON.html Genes within amplicon 12q13-q21 identified in a copy number alterations study of 191 breast tumor samples. 19010930 51/63 Jessica Robertson 1.4990346745202e-07 7.26289540930751e-07 4375 3172.18181818182 3355 1.36275888787395e-08 632 1.73809357091902 1.68869950143365 1 4.24101380268864 4372 1711 2644 3323 632 3555 4629 4238 3355 2025 4410 3723 M3682 FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN.html Genes down-regulated in peripheral blood lymphocytes (PBL) from patients with acute transplant rejection compared to those from patients with well functioning kidneys more than 1-year post transplant. 15307835 75/112 Jean Junior 1.12683493193877e-06 1.9180169054277e-06 2750 3108.63636363636 3355 1.02439591736495e-07 879 1.43519034875844 1.8649782682225 1 3.2497775941517 2748 4486 3921 3798 2650 2951 3355 879 4139 4197 1071 3724 M12861 GENTILE_UV_RESPONSE_CLUSTER_D2 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D2.html Cluster d2: genes down-regulated consistently in WS1 cells (fibroblast) between 6 h and 24 h after irradiation with high dose UV-C. 12907719 52/56 John Newman 3.79537581081117e-07 9.62093116381778e-07 2735 3199.90909090909 3358 3.45034224143499e-08 1655 2.03570392568861 2.46707726442047 1 4.87579497998889 2732 3930 2637 4445 1655 3425 4022 2793 3613 2589 3358 3725 M1882 MARSHALL_VIRAL_INFECTION_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARSHALL_VIRAL_INFECTION_RESPONSE_DN.html Genes down-regulated in the influenza-specific CD8+ [GeneID=925] T lymphocytes from bronchoalveolar lavage (BAL) compared to those from spleen. 15831586 40/60 Arthur Liberzon 3.97169996030879e-06 5.4087200606618e-06 3935 2985.36363636364 3359 3.61064284591726e-07 789 1.88661696448184 -1.68403980422773 -1 3.94609565565198 3931 2271 1804 3084 3395 3494 2132 4234 3359 789 4346 3726 M758 REACTOME_ABC_FAMILY_PROTEINS_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABC_FAMILY_PROTEINS_MEDIATED_TRANSPORT.html Genes involved in ABC-family proteins mediated transport 30/45 Reactome 1.49978593355669e-05 1.80264568535462e-05 4595 3269.54545454545 3362 1.36345105273466e-06 1434 2.7528678645992 3.34534253828979 1 5.2021344098248 4595 3130 1434 3079 3868 3810 4635 3362 1668 1884 4500 3727 M780 REACTOME_CDC6_ASSOCIATION_WITH_THE_ORC_ORIGIN_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CDC6_ASSOCIATION_WITH_THE_ORC_ORIGIN_COMPLEX.html Genes involved in CDC6 association with the ORC:origin complex 11/11 Reactome 1.89600223946549e-05 2.24120475088332e-05 960 2650.09090909091 3362 1.72365325433997e-06 178 1.17311606628345 1.17311606628345 1 2.1435233110393 957 4341 3362 4596 3932 529 178 1168 4415 3718 1955 3728 M1103 GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP.html Genes up-regulated in ME-A cells (breast cancer) undergoing apoptosis in response to doxorubicin [PubChem=31703]. 17160024 1500/1799 Arthur Liberzon 1.60537201426744e-07 7.33483268746427e-07 4120 2882.27272727273 3362 1.60537213024232e-08 697 1.8913070765724 1.95581553080729 1 4.61601558558713 4116 1069 4337 2060 816 4598 4003 4672 1975 697 3362 3729 M273 PID_EPHA2_FWD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHA2_FWD_PATHWAY.html EPHA2 forward signaling 18832364 38/46 Pathway Interaction Database 1.48776755561821e-07 7.26289540930751e-07 4585 2668.90909090909 3364 1.3525160511179e-08 392 1.68914750777398 -1.12014593984413 -1 4.12017447880949 4585 3404 2932 911 622 3603 3652 2397 392 3364 3496 3730 M5483 YANG_BREAST_CANCER_ESR1_BULK_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_BULK_DN.html Genes down-regulated in bulk samples from early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative samples. 16261164 27/44 Leona Saunders 8.76352679447573e-07 1.59521197338702e-06 3490 3190.09090909091 3364 7.96684571396325e-08 2321 1.6470333997774 1.48234645691904 1 3.78986327848583 3364 2774 2436 2321 2466 3826 3486 3951 3490 2767 4210 3731 M16284 INGA_TP53_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/INGA_TP53_TARGETS.html Genes whose promoters contain TP53 [GeneID=7157] response elements. 12446780 23/27 John Newman 5.79715174594167e-05 6.49016988634836e-05 3365 3520 3364 5.2702768277495e-06 2241 2.08330663433256 -1.03157647071804 -1 3.45856371928012 3362 4571 2703 4486 4165 3357 2241 2932 3908 3631 3364 3732 M1586 CHEN_ETV5_TARGETS_SERTOLI http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_ETV5_TARGETS_SERTOLI.html Genes down-regulated in Sertoli cells from both 4 and 10 week old ETV5 [GeneID=2119] knockout mice. 16107850 18/29 John Newman 5.1414595449223e-05 5.79734568849338e-05 3010 3484.09090909091 3364 4.67416336923177e-06 1837 2.3575877681983 -1.95692834547095 -1 3.96697820569561 3010 3763 1837 4586 4135 3364 3316 2527 4419 3048 4320 3733 M2579 ST_DIFFERENTIATION_PATHWAY_IN_PC12_CELLS http://www.broadinstitute.org/gsea/msigdb/cards/ST_DIFFERENTIATION_PATHWAY_IN_PC12_CELLS.html Differentiation Pathway in PC12 Cells; this is a specific case of PAC1 Receptor Pathway. 62/73 Signaling Transduction KE 3.86270779449893e-06 5.28004077325079e-06 4020 3173.45454545455 3365 3.51155870596935e-07 1565 1.69572407011678 1.87216233253875 1 3.54888772774909 4016 3365 2940 2541 3381 3267 3439 2504 3767 4123 1565 3734 M833 REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1.html Genes involved in Autodegradation of the E3 ubiquitin ligase COP1 52/62 Reactome 0.0975169887439756 0.0982035815813025 2455 3358.09090909091 3365 0.00928439617295039 1303 1.11358274108033 1.39908448933768 1 0.401328800900094 2451 4516 3955 3272 4657 2580 2149 3365 1303 4617 4074 3735 M12104 PENG_LEUCINE_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_LEUCINE_DEPRIVATION_DN.html Genes down-regulated in BJAB cells (B-lymphoma) after leucine [PubChem=857] deprivation. 12101249 256/307 Broad Institute 3.73875984279637e-06 5.13739343755425e-06 830 3027.09090909091 3365 3.3988783605415e-07 829 1.31622726779886 1.21377344027167 1 2.74975775037922 829 4410 4102 4329 3365 1339 1253 2590 3666 4537 2878 3736 M1752 VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP.html Genes up-regulated in uterine fibroids with deletions in the 7q region vs those without the deletion. 15940248 80/102 Leona Saunders 2.87254668967725e-06 4.08149821885962e-06 2965 3786.36363636364 3367 2.61140949125186e-07 2961 0.894949307280783 1.01626875050751 1 1.88960586234223 2961 4470 4123 4672 3247 3206 3365 3367 4399 4546 3294 3737 M27 BENPORATH_MYC_TARGETS_WITH_EBOX http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_MYC_TARGETS_WITH_EBOX.html Set 'Myc targets1': targets of c-Myc [GeneID=4609] identified by ChIP on chip in cultured cell lines, focusing on E-box-containing genes; high affinity bound subset 18443585 294/414 Jessica Robertson 3.83235954412435e-07 9.67829697606578e-07 4530 3436.81818181818 3369 3.48396382883137e-08 1662 1.64859443404004 1.83067336021263 1 3.93738689625677 4528 3283 3298 2025 1662 4487 3369 4261 2873 3651 4368 3738 M16 PID_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INSULIN_PATHWAY.html Insulin Pathway 18832364 60/68 Pathway Interaction Database 3.24152387197572e-07 9.03187289003859e-07 3530 3333.18181818182 3370 2.94684031780765e-08 1470 1.33436078554833 -1.0064437985442 -1 3.19346613424623 3528 3370 3618 2729 1470 3094 2773 4374 3081 4321 4307 3739 M17879 REACTOME_COMMON_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMMON_PATHWAY.html Genes involved in Common Pathway 10/15 Reactome 0.000623016511405143 0.000654784665738649 3460 3031.09090909091 3370 5.66539102736488e-05 1440 3.65018408118236 -3.84519909042788 -1 4.623815778645 2176 3803 1440 3370 4456 3460 2172 2554 3458 2540 3913 3740 M16311 NAGASHIMA_EGF_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAGASHIMA_EGF_SIGNALING_UP.html Genes up-regulated in MCF7 cells (breast cancer) after stimulation with EGF [GeneID=1950]. 17142811 78/109 Arthur Liberzon 1.92209845617174e-06 2.92277858026115e-06 4675 3275.63636363636 3371 1.74736375952265e-07 1176 2.10389744769032 2.41206325942154 1 4.63249091894729 4508 2618 1280 2955 3016 4675 4327 3435 3371 1176 4671 3741 M18773 CASTELLANO_HRAS_AND_NRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_AND_NRAS_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) isolated from HRAS and NRAS [GeneID=3265;4893] double knockout mice. 16909116 5/10 Leona Saunders 2.01797516816559e-05 2.37349683372579e-05 3075 3170.36363636364 3372 2.0179934934068e-06 978 0.977145286809497 -1.18919626966319 -1 1.76729801689345 3072 2483 4333 2451 3979 3372 3527 978 4633 3885 2161 3742 M2329 BILANGES_RAPAMYCIN_SENSITIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_RAPAMYCIN_SENSITIVE_GENES.html Genes translationally regulated in MEF cells (embryonic fibroblasts) by rapamycin (sirolimus) [PubChem=6610346] but not in response to serum deprivation. 17562867 46/63 Arthur Liberzon 3.80590553363017e-06 5.2190221146817e-06 1745 2790.63636363636 3372 3.45992010699933e-07 853 1.31786983860258 -1.39950878482162 -1 2.74962320048742 1745 3681 3591 4607 3372 1386 853 1782 3956 3727 1997 3743 M16516 TESAR_ALK_TARGETS_HUMAN_ES_4D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_HUMAN_ES_4D_DN.html Genes down-regulated in hES cells (human embryonic stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=16079008]. 17597760 2/7 Jessica Robertson 0.0126263349413545 0.0128968407104941 3385 3407.2 3372.5 0.00141086207576072 946 1.01453737084317 1.01453737084317 1 0.720900787097276 3382 3823 4467 NA 4594 2807 946 3363 4605 3272 2813 3744 M2555 MATTIOLI_MGUS_VS_MULTIPLE_MYELOMA http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MGUS_VS_MULTIPLE_MYELOMA.html Genes distinguishing between MGUS (monoclonal gammopathy of undetermined significance) and multiple myeloma (MM) samples. 15735737 22/24 Leona Saunders 0.0713434948675232 0.0719071739856309 3090 3476.45454545455 3373 0.00670617217271467 1575 1.59722796399634 1.28740573351491 1 0.684308142535564 3088 4293 3373 4206 4652 3180 3671 2995 1575 4195 3013 3745 M1563 MA_PITUITARY_FETAL_VS_ADULT_DN http://www.broadinstitute.org/gsea/msigdb/cards/MA_PITUITARY_FETAL_VS_ADULT_DN.html Down-regulated in human fetal pituitary tissue, compared to adult pituitary tissue 15894316 30/32 John Newman 2.85783747549151e-06 4.0686329389605e-06 3210 3388.36363636364 3373 2.59803744352529e-07 2299 1.31163217287674 -1.48997158749425 -1 2.79341490893007 3210 3431 3615 4455 3241 3373 2299 3414 3050 3899 3285 3746 M2169 FIGUEROA_AML_METHYLATION_CLUSTER_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_3_DN.html Cluster 3 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 56/108 Arthur Liberzon 3.3526054841048e-06 4.67482950811659e-06 3895 3236.90909090909 3373 3.04782781199094e-07 2098 2.1609997865711 2.84848668524511 1 4.58231609395831 3894 3373 2150 3218 3309 3441 4428 2750 3551 3394 2098 3747 M2811 TESAR_ALK_TARGETS_HUMAN_ES_5D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_HUMAN_ES_5D_DN.html Genes down-regulated in hES cells (human embryonic stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=4521392]. 17597760 2/10 Jessica Robertson 0.0126263349413545 0.0128968407104941 3385 3408.3 3373.5 0.00141086207576072 947 1.01453737084317 1.01453737084317 1 0.720900787097276 3383 3824 4469 NA 4595 2808 947 3364 4606 3273 2814 3748 M947 REACTOME_INHIBITION_OF_VOLTAGE_GATED_CA2_CHANNELS_VIA_GBETA_GAMMA_SUBUNITS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_VOLTAGE_GATED_CA2_CHANNELS_VIA_GBETA_GAMMA_SUBUNITS.html Genes involved in Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits 14/28 Reactome 3.37373154894475e-06 4.70012187456294e-06 3955 3294 3374 3.06703338420143e-07 1729 2.06007746055072 -1.55921632125173 -1 4.364035980027 3953 1936 2371 3695 3312 3374 1729 4395 3925 2832 4712 3749 M1149 MOTAMED_RESPONSE_TO_ANDROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOTAMED_RESPONSE_TO_ANDROGEN_DN.html Genes down-regulated in ovarian epithelial cells in response to dihydrotestosterone (DHT) [PubChem=10635]. 16832351 6/6 Arthur Liberzon 6.11332049182743e-06 7.88384500585395e-06 4630 3464.09090909091 3374 6.11333730960189e-07 1986 1.2125246812834 -0.539122924725273 -1 2.43847116804984 4630 1986 4351 3336 3632 4677 3300 2594 3374 3476 2749 3750 M82 PID_RET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RET_PATHWAY.html Signaling events regulated by Ret tyrosine kinase 18832364 53/63 Pathway Interaction Database 5.68132076780454e-06 7.3872821002858e-06 3905 3482.72727272727 3375 5.16485039945965e-07 2711 1.46920006128613 -1.10607967571541 -1 2.98194903612564 3901 3375 3343 2735 3562 3866 2711 3151 3347 3917 4402 3751 M1308 GROSS_HYPOXIA_VIA_HIF1A_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_HIF1A_UP.html Genes up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 120/154 Jessica Robertson 8.95654003862384e-07 1.62131916526563e-06 3100 3336.09090909091 3375 8.14231244088345e-08 2483 1.34438430299787 1.35780560133254 1 3.08045421383363 3100 2567 3774 3003 2483 2728 4128 3375 3756 3981 3802 3752 M3903 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_QTL http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_QTL.html Genes changed in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of reciprocal congenic strains D.B. Chr3 (DB), B.D. Chr3 (BD) and the parental strains B6 and D2. 17220891 23/33 Arthur Liberzon 0.000111094005955669 0.000121521137453246 4025 3376.90909090909 3375 1.00999651179018e-05 2438 1.64727660021955 -1.46253000344367 -1 2.54376931088718 4021 2801 2782 3445 4275 3375 2438 4138 2847 3342 3682 3753 M15069 ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_UP.html Genes up-regulated in A549 cells (lung carcinoma) upon infection with RSV (respiratory syncytial virus) and up-regulated by further treatment with ribavirin [PubChem=5064]. 12719586 52/82 John Newman 3.83740698198273e-06 5.25458687408137e-06 3825 2706.09090909091 3376 3.48855788681418e-07 1038 2.50053210107343 2.56607330918835 1 5.25908487729311 3823 3661 1167 1896 3376 3921 4256 1159 3793 1677 1038 3754 M8817 ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN.html Genes whose promoters display lower histone H3 trimethylation mark at K9 (H3K9me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 117/203 Jessica Robertson 1.26194570222914e-06 2.08590082134919e-06 3460 3259.45454545455 3377 1.14722402372411e-07 2460 1.66696298857439 1.93339280157326 1 3.75824352276462 3458 2570 2953 3718 2739 3577 4067 3377 3898 2460 3037 3755 M17830 TOMIDA_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOMIDA_METASTASIS_UP.html Up-regulated genes associated with the acquision of metastatic potential in LNM35 cells (large cell lung cancer). 17260014 46/61 Arthur Liberzon 1.60998565689952e-06 2.52714742286855e-06 3560 3425.36363636364 3380 1.46362439555182e-07 2667 1.69045764093607 1.34045699704782 1 3.75526297548485 3558 3088 2667 2726 2909 3380 3635 4061 3694 3329 4632 3756 M12921 BLALOCK_ALZHEIMERS_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_UP.html Genes up-regulated in brain from patients with Alzheimer's disease. 14769913 2149/2922 John Newman 1.67091427138825e-07 7.3358205358541e-07 4155 2956.09090909091 3380 1.67091439702622e-08 860 1.79226094010518 -1.49331874677514 -1 4.37161623162077 4153 1995 4493 1314 860 3817 3380 2434 2583 3493 3995 3757 M15842 NIELSEN_LIPOSARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LIPOSARCOMA_UP.html Top 20 positive significant genes associated with liposarcomas, versus other soft-tissue tumors. 11965276 17/21 John Newman 2.74085650946444e-05 3.17234985891912e-05 3380 3080.09090909091 3380 2.49171877895708e-06 1589 2.86206154853913 -2.23522526612661 -1 5.12792447019814 3380 3484 1631 3307 4026 2270 1589 3896 4233 2046 4019 3758 M18806 TOOKER_GEMCITABINE_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOOKER_GEMCITABINE_RESISTANCE_DN.html Down-regulated genes in Calu3 cells (non-small cell lung cancer, NSCLC) resistant to gemcitabine [PubChem=3461] which became up-regulated in response to bexarotene [PubChem=82146]. 17483357 163/171 Jessica Robertson 3.86060814988734e-07 9.72881498530072e-07 3810 3342.81818181818 3382 3.50964438850497e-08 1668 1.6558254910344 1.44826899972466 1 3.95337089501423 3807 3307 3382 2696 1668 3278 3744 4536 2142 3642 4569 3759 M12002 MAYBURD_RESPONSE_TO_L663536_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAYBURD_RESPONSE_TO_L663536_UP.html Genes up-regulated in H720 cells (lung cancer) after treatment with L663536 (MK886) [PubChem=105049], an inhibitor of leukotriene biosynthesis. 16551867 36/42 Arthur Liberzon 3.9318105352651e-07 9.79209711146668e-07 3575 3214 3383 3.57437385268472e-08 1689 1.6026736227457 1.35125553530983 1 3.82304695283073 3571 3418 3383 4187 1689 3059 2720 2928 2793 3444 4162 3760 M10579 BIOCARTA_EDG1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EDG1_PATHWAY.html Phospholipids as signalling intermediaries 43/51 BioCarta 3.88902660945794e-06 5.31140208236154e-06 4345 3407.54545454545 3385 3.53548498569127e-07 1325 1.59517889210969 1.75057810274414 1 3.33384545071775 4341 2699 3180 1325 3385 4488 4159 3757 2866 3038 4245 3761 M4138 REACTOME_ORC1_REMOVAL_FROM_CHROMATIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ORC1_REMOVAL_FROM_CHROMATIN.html Genes involved in Orc1 removal from chromatin 68/79 Reactome 0.000297801103825482 0.000318013848429022 1160 3160.90909090909 3385 2.70764930051203e-05 1156 1.06509216102597 1.10450258396895 1 1.44810237000521 1156 4487 4044 3034 4389 1757 1446 2740 3851 4481 3385 3762 M14787 CLAUS_PGR_POSITIVE_MENINGIOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CLAUS_PGR_POSITIVE_MENINGIOMA_DN.html Genes down-regulated in meningioma samples positive for PGR [GeneID=5241] compared to those without the receptor. 18172325 16/16 Jessica Robertson 0.000162299825144377 0.000175298666975162 3575 3226.63636363636 3385 1.47556181517256e-05 2282 1.74698104501409 -1.44033184886886 -1 2.58896670400227 3574 2402 2830 3406 4327 3385 2812 3473 3310 2282 3692 3763 M2218 BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G123, defined by unsupervised clustering. 17187432 50/80 Yujin Hoshida 6.68280616190458e-06 8.54356584078808e-06 3680 3303.09090909091 3385 6.07529678358603e-07 1917 1.64850781246816 -1.34941114763186 -1 3.31011688641824 3678 3378 3125 2888 3630 3572 1917 3726 2449 3385 4586 3764 M1456 PARK_HSC_AND_MULTIPOTENT_PROGENITORS http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_AND_MULTIPOTENT_PROGENITORS.html Genes commonly expressed in long term hematopoietic stem cells (HSC) and multipotent progenitors (MPP). 11781229 86/120 Kevin Vogelsang 1.19699942520683e-06 2.00348839963696e-06 3685 3194.27272727273 3386 1.08818188771229e-07 2027 1.39942355182656 1.4604848333968 1 3.15688577201888 3685 3620 3748 3591 2697 2341 2027 2608 3087 4347 3386 3765 M1636 YIH_RESPONSE_TO_ARSENITE_C3 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C3.html Genes in cluster 3: delayed up-regulation in HFW cells (fibroblast) by sodium arsenite [PubChem=26435]. 12016162 46/51 John Newman 2.31398100029222e-05 2.70145691847125e-05 3355 3367.81818181818 3386 2.10364121756697e-06 2296 1.35534766054317 1.69870179481332 1 2.44005643489293 3353 3386 3404 4048 3989 2774 2296 2765 4238 3875 2918 3766 M17507 MILI_PSEUDOPODIA http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA.html Transcripts significantly enriched in pseudopodia of NIH/3T3 cells (fibroblast) in response to both chemotactic (lysophosphatidic acid, LPA [PubChem=3988]) and haptotactic (fibronectin, FN1 [GeneID=2335) migratory stimuli. 18451862 52/56 Jessica Robertson 4.47178178261309e-07 1.03872096525265e-06 4525 2994 3387 4.06525699232753e-08 768 1.63687622860791 1.92806454277951 1 3.88883485845375 4522 1720 3051 3688 1845 4036 4689 768 1011 4217 3387 3767 M9642 GALLUZZI_PERMEABILIZE_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/GALLUZZI_PERMEABILIZE_MITOCHONDRIA.html Proteins that permeabilize mitochondria. 16892093 53/69 Arthur Liberzon 8.06846046077165e-07 1.50943850078645e-06 4400 3128.90909090909 3388 7.33496674533324e-08 1176 2.060177623796 -1.96477570426889 -1 4.77295647686196 4400 2235 2058 2666 2385 4614 4416 3431 1176 3388 3649 3768 M11584 HEIDENBLAD_AMPLICON_8Q24_DN http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_8Q24_DN.html Down-regulated genes whose expression is associated with amplification of the 8q24 chromosome region in pancreatic cancer cell lines. 15688027 67/76 Arthur Liberzon 3.90144496878153e-06 5.32374103863799e-06 3060 3201.90909090909 3388 3.54677444323553e-07 1818 2.11573658807424 2.55303800653557 1 4.4372567071748 3058 3051 1818 2694 3388 3848 4138 3822 3661 2292 3451 3769 M14951 ZUCCHI_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZUCCHI_METASTASIS_UP.html The 50 most up-regulated genes in primary invasive breast dutcal carcinoma (IDC) or lymph node metastases, compared to normal mammary epithelium. 15608061 60/78 Kate Stafford 3.65671920871164e-06 5.03198678283351e-06 750 2388.63636363636 3388 3.32429571520335e-07 75 1.61193097001724 1.81693896143694 1 3.38459632998786 746 4215 3388 4297 3666 548 543 75 4312 4073 412 3770 M6355 BIOCARTA_ECM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ECM_PATHWAY.html Erk and PI-3 Kinase Are Necessary for Collagen Binding in Corneal Epithelia 45/51 BioCarta 1.67265918956936e-07 7.3358205358541e-07 3485 3019.54545454545 3390 1.52059937885599e-08 750 1.69537019840092 1.80224348889787 1 4.1325788971482 3484 3390 3178 1326 750 4063 4464 3624 1669 4117 3150 3771 M8615 BIOCARTA_IL2RB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL2RB_PATHWAY.html IL-2 Receptor Beta Chain in T cell Activation 52/61 BioCarta 1.66650476539476e-07 7.3358205358541e-07 3165 3014.54545454545 3391 1.51500444693898e-08 743 1.42128885120627 -1.25350017697739 -1 3.45639793795983 3164 3662 3451 2036 743 3391 2819 2070 4017 4022 3785 3772 M1770 GAZIN_EPIGENETIC_SILENCING_BY_KRAS http://www.broadinstitute.org/gsea/msigdb/cards/GAZIN_EPIGENETIC_SILENCING_BY_KRAS.html Genes required for epigenetic silencing of FAS [GeneID=355] by activated KRAS [GeneID=3845] in NIH 3T3 cells, based on RNAi screen. 17960246 28/36 Jessica Robertson 1.50583906182884e-05 1.80853953481733e-05 2245 2953.72727272727 3391 1.36895397179898e-06 530 1.28393195727319 -1.31389009974243 -1 2.39883294907193 2245 1838 3431 3946 3870 2294 3103 3391 3864 3979 530 3773 M19693 DAZARD_RESPONSE_TO_UV_NHEK_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_NHEK_UP.html Genes up-regulated in NHEK cells (normal keratinocytes) by UV-B irradiation. 12771951 306/538 John Newman 4.90294701440652e-07 1.10042367608173e-06 3465 3037.18181818182 3392 4.45722555189422e-08 1906 1.95120130806171 1.86835785945245 1 4.62554084947695 3463 4136 1906 2024 1925 3392 2606 4450 3575 2329 3603 3774 M1906 VANASSE_BCL2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANASSE_BCL2_TARGETS_UP.html Genes up-regulated in primary B lymphocytes engineered to overexpress BCL2 [GeneID=12043]. 15561778 45/78 Arthur Liberzon 2.88077100392185e-06 4.08658460128947e-06 3845 3252.90909090909 3392 2.6188861601177e-07 1643 2.03523583343185 -1.56442899173036 -1 4.36053085981537 3842 3392 1643 1911 3254 4266 3141 4466 3847 2178 3842 3775 M1546 APPIERTO_RESPONSE_TO_FENRETINIDE_UP http://www.broadinstitute.org/gsea/msigdb/cards/APPIERTO_RESPONSE_TO_FENRETINIDE_UP.html Genes up-regulated in A2780 cells (ovarian carcinoma) exposed to fenretinide [PubChem=1744]. 17213814 56/71 Arthur Liberzon 6.91126348042236e-06 8.80714670218694e-06 4255 3269.45454545455 3393 6.28298653830668e-07 1893 1.79878341517164 -1.15773711561674 -1 3.60687764841617 4252 3655 2546 3764 3643 2969 1893 2767 4104 3393 2978 3776 M14242 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS.html Genes trans-regulated by the same QTL (quantitative trait loci) in brain and hematopoietic stem cells (HSC). 15711547 217/280 Jean Junior 5.12461079773198e-07 1.12712781758131e-06 3110 3455.45454545455 3394 4.65873817403918e-08 1862 1.60433837350765 -1.3656112109591 -1 3.7876497703533 3106 4701 3891 4497 1971 3266 2745 4347 1862 4230 3394 3777 M16479 FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_UP.html Up-regulated genes significantly associated with positive minimal residual disease (MRD) on day 46 after chemotherapy treatment of children with acute lymphoblastic leukemia (ALL). 16627760 59/75 Arthur Liberzon 7.05048519059484e-07 1.37627337053795e-06 1170 2846.90909090909 3394 6.4095340455558e-08 480 0.888345047038352 -0.706144169747543 -1 2.04395927883279 1170 4225 4075 3610 2272 755 480 3394 4471 4545 2319 3778 M727 REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES.html Genes involved in Metabolism of amino acids and derivatives 158/214 Reactome 3.97174231573173e-06 5.4087200606618e-06 2845 3291.63636363636 3396 3.61068135098624e-07 2347 1.50666519019714 1.20508633095429 1 3.14130179097495 2841 2545 3639 3736 3396 2351 2347 4713 2680 3777 4183 3779 M7577 ACEVEDO_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) compared to normal liver samples. 18413731 607/821 Jessica Robertson 1.59945224715807e-07 7.31918027928963e-07 3445 3193.45454545455 3397 1.59945236227921e-08 813 1.84034200737477 -1.83630316722638 -1 4.49096607347873 3445 2013 4545 2832 813 3522 3397 4649 2968 3215 3729 3780 M2443 PLASARI_TGFB1_TARGETS_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_1HR_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 1 h. 19752192 44/46 Arthur Liberzon 5.1336526729387e-07 1.12806520559919e-06 4080 3222.27272727273 3397 4.66695806442355e-08 1679 2.15528185323648 2.57146838933941 1 5.10523125972169 4078 3397 1679 2889 1973 3977 4590 2473 3726 2083 4580 3781 M6821 NIKOLSKY_BREAST_CANCER_20P13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_20P13_AMPLICON.html Genes within amplicon 20p13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 9/12 Jessica Robertson 0.000178049889243967 0.000191914929717179 1505 2704.27272727273 3401 1.78064156646233e-05 244 2.50238986132283 2.50238986132283 1 3.69051295590735 1502 4357 4466 3401 4347 987 697 2583 3702 3461 244 3782 M5467 BIOCARTA_GRANULOCYTES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GRANULOCYTES_PATHWAY.html Adhesion and Diapedesis of Granulocytes 12/21 BioCarta 4.08807638697488e-06 5.55272533712848e-06 3825 2879.63636363636 3402 3.71643998502346e-07 863 2.70108889999843 -4.01884776341066 -1 5.65887104844826 3822 962 863 4136 3402 4495 3836 2184 4379 895 2702 3783 M927 REACTOME_GABA_SYNTHESIS_RELEASE_REUPTAKE_AND_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_SYNTHESIS_RELEASE_REUPTAKE_AND_DEGRADATION.html Genes involved in GABA synthesis, release, reuptake and degradation 23/36 Reactome 4.42912432850744e-06 5.95088722759896e-06 3520 3039.81818181818 3402 4.0264847685595e-07 1160 1.86909650997709 -1.427776867275 -1 3.87779968399914 3516 4283 2437 3744 3441 1928 1160 2275 4271 2981 3402 3784 M12517 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN.html Genes from the blue module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 65/73 Arthur Liberzon 7.94818319874363e-06 1.00067817279461e-05 2560 3081.09090909091 3402 7.22564719469904e-07 1858 1.72609266605462 2.02363725748319 1 3.42059982020525 2559 3906 3455 3506 3692 2132 1858 2563 3821 3402 2998 3785 M5576 BIOCARTA_PLCE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLCE_PATHWAY.html Phospholipase C-epsilon pathway 15/16 BioCarta 5.58370393749608e-07 1.18659903470788e-06 3405 3206.09090909091 3403 5.07609577697002e-08 1703 1.22894501924454 1.25981175550084 1 2.87864656904479 3403 2865 3053 4188 2059 3672 4420 4695 1703 3417 1792 3786 M1154 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_DN.html Apoptotic genes dependent on MAPK1 [GeneID=5594] and down-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 8/8 Arthur Liberzon 0.0178910137590195 0.0182191121774697 4660 3335.36363636364 3405 0.001803670710798 2068 1.30848309635226 -1.46160340814059 -1 0.865311193784673 2243 4106 4353 3971 4660 2802 2077 2344 4660 2068 3405 3787 M14142 BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN.html Genes down-regulated in the invasive ductal carcinoma (IDC) compared to the invasive lobular carcinoma (ILC), the two major pathological types of breast cancer. 18490921 64/81 Jessica Robertson 7.15417975997848e-06 9.09936094505481e-06 1925 2861.63636363636 3405 6.5038209316007e-07 735 2.55409464396291 2.48945002904097 1 5.12785973760806 1923 3641 735 3690 3654 2801 2666 3405 4287 1060 3616 3788 M13115 REACTOME_G_PROTEIN_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_PROTEIN_ACTIVATION.html Genes involved in G-protein activation 18/30 Reactome 4.16222314551659e-06 5.64045169303426e-06 4290 3268.54545454545 3407 3.78384638193549e-07 1703 1.72630165811332 -1.03018823688827 -1 3.59387535869043 4290 1904 2527 4170 3407 3721 1703 4629 2459 3042 4102 3789 M3630 REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT.html Genes involved in Abortive elongation of HIV-1 transcript in the absence of Tat 25/27 Reactome 4.84803120367045e-05 5.47695243688955e-05 1630 3280.09090909091 3407 4.40739821875695e-06 1628 0.824424513139974 0.87359587232181 1 1.36285842591205 1628 3750 3919 3240 4127 2355 1958 2727 4484 4486 3407 3790 M10837 NIKOLSKY_BREAST_CANCER_20Q11_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_20Q11_AMPLICON.html Genes within amplicon 20q11 identified in a copy number alterations study of 191 breast tumor samples. 19010930 39/52 Jessica Robertson 5.28391388898724e-07 1.1469070160092e-06 3615 3129.45454545455 3408 4.80355923460638e-08 390 1.71323850488774 -1.42797894260312 -1 4.04294090642034 3612 3102 2826 3857 2000 3408 4364 3834 390 3841 3190 3791 M15841 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN.html Genes down-regulated in kidney biopsies from patients with well functioning kidneys more than 1-year post transplant compared to the biopsies from normal living kidney donors. 15307835 26/42 Jean Junior 9.01892211619405e-05 9.93681428301492e-05 2910 3116.09090909091 3408 8.19935624457663e-06 459 1.22663775667093 -1.73063270665857 -1 1.92454747322006 2909 4273 3577 4441 4260 3066 1468 459 3408 4336 2080 3792 M542 REACTOME_IL_7_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_7_SIGNALING.html Genes involved in Interleukin-7 signaling 12/13 Reactome 1.09894288166244e-06 1.88139659102166e-06 3975 3268.63636363636 3409 9.99039482369282e-08 2181 1.87007735234481 -1.33345400123543 -1 4.25597382043231 3973 2427 2181 3409 2636 4086 4595 3450 2291 2447 4460 3793 M1740 GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_DN.html FOXP3 [GeneID=50943] target genes down-regulated in T lymphocytes after stimulation with IL2 [GeneID=3558]. 17220874 8/8 Jessica Robertson 3.8114623611477e-06 5.22512411984233e-06 3685 3441.63636363636 3410 3.81146889842388e-07 2467 1.88559456649044 -0.996077383931308 -1 3.95530317549252 3682 2467 4516 4583 3410 3750 2749 2618 2936 3285 3862 3794 M8451 SENESE_HDAC3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC3_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC3 [GeneID=8841] by RNAi. 17470557 696/930 Leona Saunders 1.74357131017624e-07 7.37919956089047e-07 3975 3230.09090909091 3411 1.74357144697809e-08 911 1.84540532435065 -1.81580496872697 -1 4.50082742603292 3974 2006 4308 3193 911 4052 3411 4591 3232 1600 4253 3795 M2336 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 17. 12554760 225/259 Arthur Liberzon 5.65690445416634e-06 7.36567973066624e-06 845 3217 3412 5.1426536363013e-07 843 1.17327314539351 1.21940145706089 1 2.37184517221329 843 4415 4138 3815 3556 2404 1818 3412 2957 4619 3410 3796 M2511 ZHANG_ADIPOGENESIS_BY_BMP7 http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_ADIPOGENESIS_BY_BMP7.html Genes up-regulated in C3H10T1/2 cells (mesenchyme multipotent cells) upon their differentiation to brown adipocytes in response to BMP7 [GeneID=655]. 20584981 24/30 Arthur Liberzon 4.20781819288402e-06 5.69701262706411e-06 3415 3278 3413 3.82529658269677e-07 941 0.961043173912037 -0.986400473456469 -1 1.97687744249973 3240 4285 3711 3790 3413 2286 941 2089 4501 4390 3412 3797 M1498 BRACHAT_RESPONSE_TO_METHOTREXATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_METHOTREXATE_DN.html Genes down-regulated in FL5.12 cells (pro-B lymphocyte) in response to methotrexate [PubChem=4112]. 12447701 37/59 John Newman 3.43882299341378e-05 3.94335754565978e-05 3920 3402.90909090909 3414 3.12625158807191e-06 2217 1.48541568132578 1.36030428896 1 2.58089206655026 3920 3113 3414 2217 4067 3168 2939 4111 2615 3922 3946 3798 M10456 OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_UP.html Genes up-regulated in both the patients in the multicentric hepatocellular carcinoma (HCC) group and those with multicentric recurrence. 16788756 39/52 Yujin Hoshida 2.63321463178703e-07 8.29691125636501e-07 2975 3082.63636363636 3414 2.39383176996426e-08 1250 1.9230803158447 1.75307488516033 1 4.65300688840999 2971 3414 2051 3740 1250 3471 3784 2575 4278 2621 3754 3799 M1306 GROSS_HIF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HIF1A_TARGETS_UP.html Genes up-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 14/23 Jessica Robertson 5.56203467545709e-06 7.26218635357053e-06 2210 3113 3415 5.0564079431177e-07 1210 1.94499984478428 -2.03817255139371 -1 3.96965825524132 2209 3771 2347 3899 3546 2372 1210 4617 4021 2836 3415 3800 M8659 IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_DN.html Genes down-regulated during transition from L1 (non-tumor, infected with HCV) to G1 (well differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 12/15 Yujin Hoshida 0.00026976307562094 0.000288333722131077 3415 3283.81818181818 3415 2.45269235941359e-05 1766 0.863387733387294 0.925151942729737 1 1.17916301605336 3415 3227 3646 3738 4381 2333 1766 2573 3691 4121 3231 3801 M1606 IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR.html Genes in the expression cluster 'Early Progenitors Shared': up-regulated in hematopoietic progenitors from adult bone marrow and from fetal liver. 12228721 652/783 John Newman 6.64701769137552e-07 1.32603226979258e-06 2885 3552 3415 6.64701967960435e-08 2306 1.44744143071026 1.54220493389411 1 3.37125602963639 2885 4669 4486 4697 2306 2407 2818 3415 3569 4632 3188 3802 M269 PID_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAS_PATHWAY.html Regulation of Ras family activation 18832364 36/38 Pathway Interaction Database 2.90453443419676e-07 8.62110332351922e-07 4605 3133.81818181818 3416 2.64048619787813e-08 1357 2.12635473475151 1.96603993001581 1 5.13589547739976 4601 3416 1981 1471 1357 4282 4002 4075 2109 2571 4607 3803 M12524 KEGG_HISTIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HISTIDINE_METABOLISM.html Histidine metabolism 27/36 KEGG 0.000646516639079698 0.000679180622402888 4625 3401.18181818182 3417 5.87915190821317e-05 1706 2.47943783177951 2.10467557610457 1 3.10890057651024 4621 3440 1706 2429 4459 3361 2748 4145 3417 2432 4655 3804 M896 ZHAN_MULTIPLE_MYELOMA_SPIKED http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_SPIKED.html 'Spiked' genes: genes most highly up-regulated in multiple myeloma samples; were not differentially expressed as compared to the normal plasma cells. 11861292 20/30 Kevin Vogelsang 7.00008041549092e-07 1.37256413491944e-06 4335 2873.54545454545 3417 6.36371149346891e-08 853 3.0303208643767 -2.10900826765864 -1 7.09442773637716 4331 853 1058 2089 2261 4489 3956 3905 3431 1819 3417 3805 M15216 REACTOME_BOTULINUM_NEUROTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BOTULINUM_NEUROTOXICITY.html Genes involved in Botulinum neurotoxicity 15/20 Reactome 6.21120310352668e-05 6.94219243396778e-05 2160 3068 3418 5.64670769977191e-06 546 1.05536427486534 -0.888028324825543 -1 1.71494408937809 2157 3492 3594 3487 4171 1984 546 3267 4345 3418 3287 3806 M1593 MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_UP.html Genes similarly up-regulated in 3T3-L1 cells (fibroblasts able to differentiate to adipocytes) upon stimulation of INSR or IGFR1 by NTF3 [GeneID=3643;3480;4908]. 12213819 31/39 John Newman 2.18627558834781e-05 2.55933054985161e-05 3775 2734.36363636364 3418 1.98754301365276e-06 443 1.31869642832585 1.56814647928288 1 2.38516717699316 1142 3725 3498 3772 3976 2279 1505 443 3418 3771 2549 3807 M3828 REACTOME_PROTEOLYTIC_CLEAVAGE_OF_SNARE_COMPLEX_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROTEOLYTIC_CLEAVAGE_OF_SNARE_COMPLEX_PROTEINS.html Genes involved in Proteolytic cleavage of SNARE complex proteins 15/18 Reactome 6.21120310352668e-05 6.94219243396778e-05 2160 3058.63636363636 3419 5.64670769977191e-06 547 1.05536427486534 -0.888028324825543 -1 1.71494408937809 2158 3493 3595 3488 4172 1985 547 3154 4346 3419 3288 3808 M1559 MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_UP.html Cluster 9: genes up-regulated in SW260 cells (colon cancer) by sodium butyrate and TSA [PubChem=5222465;5562] with the same kinetics with which each alters the level of histone H4 acetylation. 10969808 108/120 John Newman 2.41158207129043e-07 8.0442878985801e-07 3915 3050.45454545455 3419 2.19234757785614e-08 1157 1.89110657326262 2.15715705940896 1 4.58502563057149 3912 1590 2435 3870 1157 3835 3419 3829 3122 1905 4481 3809 M9193 MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_DN.html Genes down-regulated in normal bone marrow plasma cells (BMPC) compared to polyclonal plasmablasts (PPC) that also distinguished multiple myeloma (MM) samples by expression of levels of TACI [GeneID=23495]. 15827134 82/89 Kevin Vogelsang 4.25573775700384e-06 5.74902181255242e-06 885 2822.90909090909 3420 3.86885999039725e-07 885 0.975736316212769 1.07414633888875 1 2.0063176905716 885 3622 4083 3597 3420 1452 959 1704 4089 4531 2710 3810 M805 REACTOME_FORMATION_OF_RNA_POL_II_ELONGATION_COMPLEX_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_RNA_POL_II_ELONGATION_COMPLEX_.html Genes involved in Formation of RNA Pol II elongation complex 45/48 Reactome 0.000115197306188038 0.000125863723427671 2110 3439.36363636364 3421 1.04730307853693e-05 2107 0.767883337549715 0.774525603256185 1 1.15436512931184 2107 3696 4072 3031 4281 2417 2372 3345 4499 4592 3421 3811 M16789 SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY.html Cluster 3: genes strongly up-regulated in B493-6 cells (B lymphocytes) by a combination of MYC [GeneID=4609] and serum but not by each of them alone. 15516975 45/50 Leona Saunders 8.93249532411787e-07 1.61940792708686e-06 2415 3153.36363636364 3422 8.12045359174012e-08 1429 1.12309320910256 1.10616491189671 1 2.56539403783846 2413 3675 3875 4462 2480 1781 1429 3422 4221 3669 3260 3812 M17138 BYSTRYKH_SCP2_QTL http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_SCP2_QTL.html Genes that physically map to the hematopoietic stem cell (HSC) proliferation QTL (quantitative trait locus) Scp2. 15711547 6/8 Jean Junior 7.106697737698e-07 1.38199725447916e-06 3425 3128.54545454545 3422 7.10670001043089e-08 699 2.08307328761747 -0.640129476948002 -1 4.85864858366687 3422 4372 4473 4404 2357 2618 699 3694 1093 4014 3268 3813 M17857 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT.html SNARE interactions in vesicular transport 34/39 KEGG 4.33842188064209e-06 5.85234389157779e-06 1170 2601.36363636364 3424 3.94402766916074e-07 162 0.957597640807707 -0.88495482500278 -1 1.96511144939048 1168 4251 3943 4496 3424 493 707 1300 4349 4322 162 3814 M9473 RAMALHO_STEMNESS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMALHO_STEMNESS_UP.html Genes enriched in embryonic, neural and hematopoietic stem cells. 12228720 260/297 John Newman 2.72613823310404e-06 3.91820111457097e-06 1990 3544.81818181818 3424 2.47831055564936e-07 1987 1.20487508095291 1.26647575917104 1 2.56990726138653 1987 4411 4152 3818 3209 3299 3470 3212 3424 4629 3382 3815 M15565 ZHU_CMV_24_HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_24_HR_UP.html Up-regulated at 24 h following infection of primary human foreskin fibroblasts with CMV 9826724 163/221 John Newman 2.85838703932056e-06 4.0686329389605e-06 3980 3600.81818181818 3425 2.59853704830436e-07 2900 1.52554109931307 -1.66353880443445 -1 3.25714231247182 3980 3863 3425 3021 3242 4690 4181 3115 3791 3401 2900 3816 M17405 ZHAN_MULTIPLE_MYELOMA_SUBGROUPS http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_SUBGROUPS.html Top genes up-regulated in MM4 vs MM1 subgroup of multiple myeloma samples. 11861292 33/37 Kevin Vogelsang 3.16415160691149e-05 3.64174483897153e-05 570 2727.27272727273 3426 2.87654283296495e-06 282 0.839754657302957 0.832813158209306 1 1.44898458993832 568 3426 3970 3570 4046 846 282 2083 4261 4393 2555 3817 M14024 GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP.html Genes up-regulated in erythroid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 36/39 Arthur Liberzon 7.78896941811702e-05 8.619914572922e-05 3655 3448.45454545455 3429 7.08113199602312e-06 2572 1.96513214395562 1.92227421135947 1 3.16213803067516 3651 3974 2848 3162 4217 3404 3541 4386 2749 2572 3429 3818 M3845 GALE_APL_WITH_FLT3_MUTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/GALE_APL_WITH_FLT3_MUTATED_UP.html Genes up-regulated in acute promyelocytic leukemia (APL) patients with mutated FLT3 [GeneID=2322]. 16105978 79/92 Kevin Vogelsang 3.92243800268906e-07 9.79032467188206e-07 4530 3584.54545454545 3429 3.56585336548277e-08 1686 1.57930195665684 1.49936995390583 1 3.76661599785432 4530 3035 3429 3413 1686 4387 4306 3711 2863 3386 4684 3819 M13276 MARZEC_IL2_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARZEC_IL2_SIGNALING_DN.html Genes down-regulated by IL2 [GeneID=3558] in cells derived from CD4+ [GeneID=920] cutaneous T-cell lymphoma (CTCL). 18281483 50/59 Jessica Robertson 1.58901683833352e-06 2.49994819571434e-06 4400 3500.72727272727 3429 1.44456180550033e-07 2638 1.8989073616351 2.21603573542984 1 4.22808206980378 4396 3382 2721 3898 2900 4415 4119 3429 3686 2924 2638 3820 M4864 KEGG_BASAL_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_TRANSCRIPTION_FACTORS.html Basal transcription factors 31/38 KEGG 1.10452743476087e-05 1.35870979725601e-05 4245 2443 3430 1.00412089106125e-06 221 0.933923862935213 0.966633936800922 1 1.7779037952946 527 3430 3922 4241 3778 410 221 931 4002 4243 1168 3821 M765 BIOCARTA_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INSULIN_PATHWAY.html Insulin Signaling Pathway 37/44 BioCarta 7.83639422602677e-07 1.47910399905015e-06 2885 3135.36363636364 3432 7.12399728849976e-08 1331 1.28497765641895 -1.02822467250545 -1 2.96272521699085 2884 3963 3509 1331 2358 2385 1909 4690 3432 4391 3637 3822 M222 PID_CXCR3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CXCR3_PATHWAY.html CXCR3-mediated signaling events 18832364 54/62 Pathway Interaction Database 4.02832892618923e-07 9.93104581177629e-07 3630 3301.27272727273 3432 3.66211787618187e-08 1717 1.3069090284404 1.49380860729866 1 3.10507437820541 3628 2665 3432 2739 1717 3156 3566 4115 4191 3968 3137 3823 M16093 GENTILE_UV_RESPONSE_CLUSTER_D7 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D7.html Cluster d7: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 52/70 John Newman 1.31874296448711e-05 1.59929773699362e-05 3435 3437.72727272727 3432 1.19886442679655e-06 2632 1.29822443284385 1.38916011925204 1 2.45397252862977 3432 3928 3858 3555 3835 3011 2881 3402 3065 4216 2632 3824 M917 BIOCARTA_COMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_COMP_PATHWAY.html Complement Pathway 17/24 BioCarta 0.000131543656837716 0.000143127261473956 2260 3292.54545454545 3433 1.19592293481511e-05 1772 2.56841187747454 -3.12062179483502 -1 3.92078162584222 2258 4321 1851 4592 4298 3568 2803 3433 4450 2872 1772 3825 M5190 MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP.html Genes up-regulated in at least 8 of 11 sarcoma cell lines by trabectedin [PubChem=3199]. 15897246 82/105 John Newman 4.75482020220593e-07 1.07949741964464e-06 4060 3463.63636363636 3433 4.32256475441538e-08 1906 1.86855224116866 1.75312598699351 1 4.43375843178184 4060 3030 2568 4399 1906 3433 4012 3663 3414 3390 4225 3826 M2219 WIERENGA_PML_INTERACTOME http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_PML_INTERACTOME.html Proteins identified in complex with PML [GeneID=5371] in K562 cells (lymphoblast). 18779318 74/96 Arthur Liberzon 9.71651934530452e-05 0.00010680477715379 3435 3323.72727272727 3435 8.83358955600511e-06 1154 1.80460638270883 1.99602644599749 1 2.8321872523241 3435 4484 3430 3611 4247 2923 3050 1154 3662 4176 2389 3827 M9044 HEIDENBLAD_AMPLIFIED_IN_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLIFIED_IN_PANCREATIC_CANCER.html Genes amplified and up-regulated more than twofold in at least two out of 10 pancreatic cancer cell lines studied. 15688027 49/53 Leona Saunders 1.13354424600271e-06 1.92665784700496e-06 2930 3191.27272727273 3436 1.03049530005349e-07 491 1.29171135391633 -1.15298036574174 -1 2.91887407399872 2929 491 3580 3954 2654 2873 2888 4545 3436 3864 3890 3828 M13626 MCCABE_HOXC6_TARGETS_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_CANCER_DN.html Genes whose promoters were bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and which were down-regulated in comparison of tumor vs normal prostate tissue samples. 18339881 30/32 Jessica Robertson 1.24322834853586e-07 7.16209778122308e-07 3690 2959.18181818182 3436 1.13020765344652e-08 453 1.63242842263167 -1.51245486562414 -1 3.9841295708032 3498 3428 3145 3436 453 4210 3643 3689 572 3690 2787 3829 M5500 KEGG_BASE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASE_EXCISION_REPAIR.html Base excision repair 33/35 KEGG 1.66332009829224e-05 1.98054259937925e-05 1380 2599.18181818182 3437 1.51212061275754e-06 704 1.484640661374 1.52866689015126 1 2.75809090799721 1378 3717 3493 3951 3904 1057 704 1164 3859 3437 1927 3830 M14151 DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP http://www.broadinstitute.org/gsea/msigdb/cards/DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP.html Genes up-regulated in HEK293 cells (embryonic kidney) at 6 h, 12 h or 24 h after infection with reovirus strain T3A (known as a strong inducer of apoptosis). 12885910 431/530 John Newman 3.11898128406801e-06 4.39879390978861e-06 1110 3295.63636363636 3438 2.83544155083189e-07 1109 1.52718727051406 -1.57948310300839 -1 3.23989957968746 1109 4685 4059 3618 3273 2524 1929 3438 4066 4494 3057 3831 M7968 BIOCARTA_CARM1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARM1_PATHWAY.html Transcription Regulation by Methyltransferase of CARM1 14/15 BioCarta 0.000204230814562813 0.000219533009505005 2980 3074.72727272727 3439 1.85681614746067e-05 561 1.19578916712991 1.31291212892134 1 1.70933755192202 2976 4076 3467 3217 4350 3439 4285 2036 561 4398 1017 3832 M32 PID_HDAC_CLASSIII_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HDAC_CLASSIII_PATHWAY.html Signaling events mediated by HDAC Class III 18832364 40/49 Pathway Interaction Database 4.74791850941303e-06 6.31806466434437e-06 2485 3152.45454545455 3440 4.31629886921774e-07 1750 1.96132559166517 -1.55755152027019 -1 4.05110580269192 2927 2724 2483 1750 3477 3440 3679 4442 2484 3509 3762 3833 M7870 HEIDENBLAD_AMPLIFIED_IN_BONE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLIFIED_IN_BONE_CANCER.html Genes from selected recurrently amplified regions in bone tissue tumors with supernumerary ring chromosomes. 16732325 8/11 Arthur Liberzon 2.94674927536694e-05 3.40481189222325e-05 3530 3126.36363636364 3440 2.94678835108702e-06 1032 2.39705628115064 -1.20457135373258 -1 4.25704341760554 3806 3526 4379 2947 4050 3526 3440 1050 1032 3279 3355 3834 M225 BIOCARTA_MTA3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MTA3_PATHWAY.html Downregulated of MTA-3 in ER-negative Breast Tumors 27/43 BioCarta 4.32779539620687e-07 1.02326646843649e-06 4680 3294.54545454545 3441 3.93436022505659e-08 1189 2.08233327680937 2.28761034544172 1 4.96620542897918 4676 3441 2248 3715 1802 4386 3919 2907 1189 3425 4532 3835 M12972 MATHEW_FANCONI_ANEMIA_GENES http://www.broadinstitute.org/gsea/msigdb/cards/MATHEW_FANCONI_ANEMIA_GENES.html Genes identified with the Fanconi anemia (FA) and the FA pathway. 16998502 11/11 Arthur Liberzon 0.000132390821603949 0.000144015828064218 1010 2699.81818181818 3442 1.20362535675674e-05 476 1.10818305948904 1.10818305948904 1 1.6620392555965 1009 3797 3442 4585 4299 786 476 1569 4010 4063 1662 3836 M14487 HOEGERKORP_CD44_TARGETS_DIRECT_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_DIRECT_UP.html Genes directly up-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 32/48 Kevin Vogelsang 5.73541282998007e-08 5.53602219989896e-07 3715 3188.90909090909 3442 5.21401179954785e-09 75 1.62914469646625 1.60381598043776 1 4.04929147109732 3712 3982 3352 4221 75 3442 2434 3506 4270 3056 3028 3837 M788 REACTOME_REGULATION_OF_THE_FANCONI_ANEMIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_THE_FANCONI_ANEMIA_PATHWAY.html Genes involved in Regulation of the Fanconi anemia pathway 10/13 Reactome 3.3113330421188e-05 3.80557388819107e-05 2745 3253.45454545455 3443 3.01034807613104e-06 791 1.22363554982967 -1.11049196476714 -1 2.12483493833573 2745 4098 3299 3443 4054 2158 791 4448 4257 3984 2511 3838 M262 AMUNDSON_RESPONSE_TO_ARSENITE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_RESPONSE_TO_ARSENITE.html Genes discriminating responses to sodium arsenite [PubChem=26435] from other stresses. 15824734 313/376 Arthur Liberzon 6.02963170643877e-07 1.24278871853236e-06 2075 3235.90909090909 3443 5.48148487182335e-08 1939 1.49108326270869 -1.40559207017437 -1 3.49129590377178 2072 4406 4022 4544 2128 2325 1939 3443 3978 3871 2867 3839 M13447 LANDIS_ERBB2_BREAST_PRENEOPLASTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_PRENEOPLASTIC_DN.html Down-regulated genes from top 82 genes out of the 324-gene signature identified in the pre-neoplastic tissue adjacent to the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 63/74 Leona Saunders 2.88574878419328e-06 4.09153927948102e-06 4170 3471.72727272727 3444 2.62341142677131e-07 2085 1.80867394813614 -1.42490186199084 -1 3.86916488750794 4169 3052 2827 4181 3256 4268 4507 2916 2085 3484 3444 3840 M1353 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_UP.html Early prostate development genes (up-regulated at 6 h dihydrotestosterone [PubChem=10635]) which are also up-regulated in normal epithelium vs high grade prostatic intraepithelial neoplasia (PIN). 18794802 27/30 Jessica Robertson 7.53699446372529e-06 9.54369061779154e-06 1930 3261.90909090909 3445 6.85183662262548e-07 1929 1.22901410453314 1.48952107587229 1 2.43129997270401 1929 3445 3592 4447 3670 2218 2449 3343 4353 3694 2741 3841 M1934 MEISSNER_NPC_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in neural precursor cells (NPC). 18600261 23/32 Jessica Robertson 4.45712120890679e-06 5.983057799846e-06 2945 3132.27272727273 3445 4.0519365808185e-07 1005 1.19956402984447 -1.09380986652465 -1 2.46967248568426 2942 4573 3772 4483 3445 2436 1551 1005 4410 4236 1602 3842 M213 PID_AR_NONGENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_NONGENOMIC_PATHWAY.html Nongenotropic Androgen signaling 18832364 43/48 Pathway Interaction Database 5.08242898670169e-07 1.12395348044995e-06 4295 3301.63636363636 3446 4.62039105531115e-08 914 1.4109655015939 -1.18276601600253 -1 3.3257836701668 4291 2704 3446 914 1961 4042 2894 4398 3419 4161 4088 3843 M1943 IRITANI_MAD1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IRITANI_MAD1_TARGETS_UP.html Genes up-regulated by overexpression of MAD1 [GeneID=4084] in primary thymocytes from RAG2 [GeneID=5897] knockout mice. 12234922 16/22 Jessica Robertson 3.77456430866e-07 9.60325320936429e-07 3450 3302.36363636364 3446 3.43142268751484e-08 1649 1.7780236026178 -1.79895565844421 -1 4.25285205197407 3446 4058 2883 4200 1649 2926 2592 3575 3211 3855 3931 3844 M942 REACTOME_REGULATION_OF_IFNG_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_IFNG_SIGNALING.html Genes involved in Regulation of IFNG signaling 18/20 Reactome 4.79020339300526e-05 5.41680882007303e-05 4020 3070.27272727273 3447 4.35482517855039e-06 759 1.37517127485786 -0.946599378088202 -1 2.30937822067564 2111 4047 3447 2962 4124 1896 759 2378 4018 4018 4013 3845 M2626 CHOW_RASSF1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHOW_RASSF1_TARGETS_UP.html Genes up-regulated in C666-1 cells (nasopharyngeal carcinoma) by stable expression of RASSF1 [GeneID=11186]. 16116475 35/36 Lauren Kazmierski 1.21942374993801e-06 2.03309081586274e-06 4370 3488.27272727273 3447 1.10856765985912e-07 2287 1.53137385443141 -1.35049902973862 -1 3.45534046213286 3942 2287 3122 4367 2711 4605 4294 4366 3447 2474 2756 3846 M1211 YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP http://www.broadinstitute.org/gsea/msigdb/cards/YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP.html Genes up-regulated in HUVEC cells (endothelium) by ETS1 [GeneID=2113] which were down-regulated by SP100 [GeneID=6672]. 15592518 31/37 Arthur Liberzon 1.65874976898446e-07 7.3358205358541e-07 4385 3324.81818181818 3448 1.50795444913675e-08 734 1.39791751719972 1.69848351229353 1 3.39873895748627 4381 2310 3057 3448 734 3500 2998 4609 3990 2945 4601 3847 M1789 WORSCHECH_TUMOR_REJECTION_DN http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_REJECTION_DN.html Down-regulated genes defining rejection of mammary carcinoma (MMC) tumors. 18381452 13/13 Jessica Robertson 4.69021570319118e-06 6.25185487688856e-06 3830 3064.09090909091 3448 4.26384154760728e-07 41 1.73703203144816 1.13687541329214 1 3.58530276339689 3830 3503 3100 2428 3471 3943 2661 3370 41 3910 3448 3848 M622 REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS.html Genes involved in Prolonged ERK activation events 25/26 Reactome 4.43792649109517e-06 5.96101680078805e-06 4010 3255.54545454545 3450 4.03448676680022e-07 1161 1.52193024752337 -1.07591280881938 -1 3.14779060031152 4010 3450 3191 1316 3443 4238 3886 2876 1161 4301 3939 3849 M2474 LIU_IL13_MEMORY_MODEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_IL13_MEMORY_MODEL_UP.html Genes up-regulated in BEAS-2B cells (bronchial epithelium) stimulated with IL13 [GeneID=3596] on days 1 to 3 and then rested for the next 3 days (repeated-stimulation or memory model) 20123980 25/35 Arthur Liberzon 1.24872049440154e-06 2.06950868454187e-06 4540 3503 3450 1.13520109379648e-07 2733 1.27708698164564 -1.47256128607402 -1 2.86930730444179 4538 4014 3407 3953 2733 3450 2743 2892 4289 3523 2991 3850 M17681 BIOCARTA_IL3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL3_PATHWAY.html IL 3 signaling pathway 27/29 BioCarta 3.02929905628823e-06 4.28349057689648e-06 3330 3445.27272727273 3452 2.75391202500189e-07 1997 1.16057206252319 -0.606051098255473 -1 2.4555045015065 3326 3452 3582 2038 3266 3350 1997 4046 4540 4360 3941 3851 M11563 KAUFFMANN_DNA_REPAIR_GENES http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_DNA_REPAIR_GENES.html Genes involved in DNA repair, compiled manually by the authors. 17891185 235/260 Jessica Robertson 6.58759036964388e-06 8.43325916591243e-06 355 2346.63636363636 3452 5.98873645030799e-07 142 1.28877275705222 1.32025054426572 1 2.57979390917007 351 3856 4099 3608 3624 142 238 1068 3452 4223 1152 3852 M19472 HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN.html Genes down-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with low risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 42/59 Arthur Liberzon 2.53482039516524e-07 8.22189102913976e-07 4100 3270.90909090909 3452 2.30438244293185e-08 562 1.32955620234578 1.08635903657288 1 3.20360625240665 4099 562 3045 3199 1204 4325 4612 3912 2947 3452 4623 3853 M1525 ZHENG_RESPONSE_TO_ARSENITE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_RESPONSE_TO_ARSENITE_DN.html Down-regulated in HEK293 cells (kidney epithelium) by treatment with sodium arsenite [PubChem=26435]. 12679051 25/29 John Newman 8.21932182377011e-06 1.03233632273004e-05 4340 3185.09090909091 3454 7.47213866524745e-07 1581 2.45339880411045 -1.88131282347639 -1 4.86964051131516 4338 3454 1608 3686 3700 4271 3230 4205 3093 1870 1581 3854 M11891 MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP.html The postradiation tumor escape signature: genes up-regulated in tumors from irradiated stroma vs those from non-irradiated stroma. 18794119 499/559 Jessica Robertson 1.41703764258391e-06 2.28820310400138e-06 2790 3526.36363636364 3454 1.28821686846367e-07 2692 1.68777302949649 1.72744583293659 1 3.77849868017746 2789 4397 3906 4288 2814 3095 3454 3187 2692 4455 3713 3855 M1455 WANG_TARGETS_OF_MLL_CBP_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TARGETS_OF_MLL_CBP_FUSION_DN.html Top 50 genes down-regulated in granulocyte/macrophage progenitors (GMP) upon expression of MLL-CBP fusion [GeneID=4297;1387]. 15635450 55/65 Kevin Vogelsang 2.88827635125147e-05 3.33888424636467e-05 1975 2887.27272727273 3455 2.62574024615263e-06 1142 1.39582581343836 1.50517088945327 1 2.46277851501667 1972 3659 3756 4044 4033 1464 1142 1979 1967 4289 3455 3856 M1881 MARSHALL_VIRAL_INFECTION_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARSHALL_VIRAL_INFECTION_RESPONSE_UP.html Genes up-regulated in the influenza-specific CD8+ [GeneID=925] T lymphocytes from bronchoalveolar lavage (BAL) compared to those from spleen. 15831586 7/8 Arthur Liberzon 1.2769658336959e-05 1.55302209096745e-05 3460 3308.63636363636 3456 1.27697317164308e-06 1683 1.61309630764168 1.42542270234753 1 3.06956839164473 3456 3248 4596 3090 3847 3659 4078 1732 3937 3069 1683 3857 M19358 BIOCARTA_MET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MET_PATHWAY.html Signaling of Hepatocyte Growth Factor Receptor 60/65 BioCarta 4.56320400181298e-06 6.09977991746171e-06 2695 3150.09090909091 3457 4.14837587887595e-07 1734 1.75128295395682 -1.33853222157792 -1 3.62266002528695 2695 3912 2860 1756 3461 3457 2106 4330 1734 4160 4180 3858 M1595 BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP.html Up-regulated genes in non-neoplastic mucosa samples from colon cancer patients who developed recurrence of the disease. 16091735 29/38 Leona Saunders 0.00205746831976101 0.00213293443208257 2615 3293.81818181818 3458 0.00018721772851887 1465 1.48760090479999 1.4821973887331 1 1.54791815418782 2614 4553 3458 4617 4590 2265 2110 1465 4332 3831 2397 3859 M7705 AKL_HTLV1_INFECTION_UP http://www.broadinstitute.org/gsea/msigdb/cards/AKL_HTLV1_INFECTION_UP.html Genes up-regulated in WE17/10 cells (CD4+ [GeneID=920] T lymphocytes) infected by HTLV1 (and thus displaying low CD7 [GeneID=924]) compared to the uninfected (i.e., CD7+) cells. 17287851 42/47 Arthur Liberzon 9.84066475290269e-08 6.68315649405766e-07 4205 2728.90909090909 3459 8.94605926643502e-09 302 1.53357307303909 1.54462913688436 1 3.75837007125124 4201 560 2994 1492 302 3746 3459 4542 384 3672 4666 3860 M1285 SCHMAHL_PDGF_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SCHMAHL_PDGF_SIGNALING.html These genes form a a network that controls specific processes downstream of PDGF signaling. 17143286 9/11 Leona Saunders 1.36475833850938e-06 2.21973099854041e-06 2710 3427.54545454545 3459 1.3647591766645e-07 2056 2.21223247334432 2.50250079490467 1 4.97991841645992 2708 4347 4413 4581 2863 3210 3798 3727 2541 3459 2056 3861 M2035 BAUS_TFF2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAUS_TFF2_TARGETS_UP.html Genes up-regulated in pyloric atrium with knockout of TFF2 [GeneID=7032]. 16121031 27/53 Arthur Liberzon 0.000110013163724443 0.000120450506327852 3310 3423.63636363636 3459 1.00016968569148e-05 2418 1.41954916751125 -1.5775936064601 -1 2.18738307435305 3308 2781 3297 4205 4270 3792 2418 2632 3803 3695 3459 3862 M7140 ZHOU_INFLAMMATORY_RESPONSE_FIMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_FIMA_UP.html Genes up-regulated in macrophages by P.gingivalis FimA pathogen. 18025224 563/856 Arthur Liberzon 4.13401917836265e-13 1.04906293128343e-11 4395 2713 3461 4.13401917836342e-14 110 2.46844602280003 2.63980792196499 1 10.8491704217806 4392 1152 4311 310 546 4595 3461 4470 2070 110 4426 3863 M6444 NUYTTEN_NIPP1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_NIPP1_TARGETS_UP.html Genes up-regulated in PC3 cells (prostate cancer) after knockdown of NIPP1 [GeneID=5511] by RNAi. 17724462 933/1265 Jessica Robertson 3.05901448599967e-07 8.80936447462993e-07 3840 3278.18181818182 3461 3.05901490709039e-08 1517 1.90852786254457 2.01888439671933 1 4.59744017183003 3840 3266 4428 2685 1517 3639 4276 3461 2955 2142 3851 3864 M16977 CHIBA_RESPONSE_TO_TSA http://www.broadinstitute.org/gsea/msigdb/cards/CHIBA_RESPONSE_TO_TSA.html Genes up-regulated in more than one of several human hepatoma cell lines by TSA [PubChem=5562]. 15336447 73/90 John Newman 2.73050625103713e-06 3.92328447637603e-06 2620 3228.81818181818 3461 2.48228149089216e-07 676 1.44699084202106 -1.62830541105608 -1 3.0960489767205 2618 3350 3496 3541 3210 3461 4135 3432 3632 3966 676 3865 M8629 NADERI_BREAST_CANCER_PROGNOSIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NADERI_BREAST_CANCER_PROGNOSIS_DN.html Down-regulated genes in the breast cancer prognostic signature of 70 genes that significantly correlated with survival. 16936776 20/23 Arthur Liberzon 5.19974042684985e-07 1.1351884743169e-06 3620 2775.54545454545 3462 4.72703786892588e-08 914 2.79516747416723 2.2786072745734 1 6.63271539680775 3619 3462 1193 1134 1985 4209 3653 4212 914 1462 4688 3866 M2161 FIGUEROA_AML_METHYLATION_CLUSTER_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_1_DN.html Cluster 1 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 57/122 Arthur Liberzon 4.57199564865204e-06 6.1098016595803e-06 3265 3511.63636363636 3462 4.15636831828079e-07 2771 1.88350369522521 -1.51318222455142 -1 3.89940627359633 2881 3653 2771 3964 3462 3263 3247 4258 3628 3263 4238 3867 M18160 STEIN_ESRRA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_DN.html Genes down-regulated by ESRRA [GeneID=2101] only. 18974123 171/207 Leona Saunders 1.73167653194852e-06 2.68600500519126e-06 3665 3201 3464 1.57425263181556e-07 177 1.68808303969801 1.41173178089951 1 3.73194338599937 3664 4150 3323 2480 2948 4662 3932 3464 2542 3869 177 3868 M10376 MOOTHA_GLYCOGEN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_GLYCOGEN_METABOLISM.html Genes involved in glycogen metabolism; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 20/25 Vamsi Mootha 7.09720906088671e-07 1.38126795032011e-06 2925 3330.90909090909 3465 6.4520103185912e-08 1037 1.37454995925105 1.37376499122718 1 3.18916608735549 2922 4307 3465 4428 2279 2907 2532 4719 1037 4412 3632 3869 M17856 MULLIGHAN_MLL_SIGNATURE_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_1_UP.html The 'MLL signature 1': genes up-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to all AML cases with the intact gene. 17597811 461/602 Arthur Liberzon 1.37942255852653e-07 7.20206492018647e-07 4160 3166.27272727273 3466 1.25402058637977e-08 550 1.62365823265482 1.82447880169495 1 3.96087799228064 4160 2505 3692 3222 550 2814 4142 4329 2029 3466 3920 3870 M18928 BIOCARTA_IL5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL5_PATHWAY.html IL 5 Signaling Pathway 5/16 BioCarta 0.00177740780350607 0.00184503295195704 2970 3577 3468 0.000177883103621345 2769 3.9738084300462 -5.82407740333957 -1 4.31919814617125 2966 3537 4193 3444 4516 2769 2797 3468 4293 3248 4116 3871 M16894 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_COMPLEMENT_AND_COAGULATION_CASCADES.html Complement and coagulation cascades 47/95 KEGG 8.67912588314434e-07 1.58465038824228e-06 3200 3316 3469 7.89011755191912e-08 937 2.91647525921227 -3.31022401066347 -1 6.75282898617498 3198 4230 937 4155 2458 4337 3434 3986 4141 2131 3469 3872 M621 REACTOME_ARMS_MEDIATED_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ARMS_MEDIATED_ACTIVATION.html Genes involved in ARMS-mediated activation 22/23 Reactome 1.7645751650173e-05 2.09424057804417e-05 3470 3430 3469 1.60417210770365e-06 1884 1.33876136430076 1.96280957880322 1 2.46911500761524 3469 3753 3415 2734 3914 3850 4541 1884 2752 4446 2972 3873 M13396 MORI_SMALL_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_SMALL_PRE_BII_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Small Pre-BII stage. 18922927 117/154 Jessica Robertson 6.12274365936514e-07 1.25560331082224e-06 2250 3067.09090909091 3469 5.56613214851395e-08 1918 1.62683624247258 1.5357484633688 1 3.81079538391973 2246 4171 3469 3251 2141 1918 2080 3597 3709 3678 3478 3874 M923 REACTOME_RAP1_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAP1_SIGNALLING.html Genes involved in Rap1 signalling 19/20 Reactome 0.000136289174780386 0.000148051761786748 2110 3200.36363636364 3471 1.2390692597816e-05 1385 1.50558861043472 1.6354906643288 1 2.2687391094666 2110 3755 3176 4007 4305 2199 1385 3733 3471 3828 3235 3875 M13936 PENG_GLUTAMINE_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUTAMINE_DEPRIVATION_DN.html Genes down-regulated in BJAB cells (B-lymphoma) after glutamine [PubChem=738] deprivation. 12101249 453/542 Broad Institute 4.71836443473089e-06 6.28760026310835e-06 1095 3262.09090909091 3472 4.28943141299079e-07 1093 1.27185203301546 1.20759392415626 1 2.61048635859415 1093 4683 4177 4338 3472 1857 1788 3008 3635 4640 3192 3876 M8516 BIOCARTA_PITX2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PITX2_PATHWAY.html Multi-step Regulation of Transcription by Pitx2 20/25 BioCarta 5.15317670807968e-07 1.13009793826767e-06 3145 3339.45454545455 3473 4.68470719557818e-08 1977 1.10390796268555 1.23371423798894 1 2.59007865951305 3143 3473 3422 4006 1977 3625 4060 2107 4581 3635 2705 3877 M557 REACTOME_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEFENSINS.html Genes involved in Defensins 6/110 Reactome 0.00023648259890702 0.000253335875361129 1795 3004.27272727273 3473 2.36507768485621e-05 298 1.86585570668206 -1.77626683879866 -1 2.64854111345163 1794 4640 4208 4439 4377 1278 298 2634 4668 3473 1238 3878 M565 REACTOME_BETA_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BETA_DEFENSINS.html Genes involved in Beta defensins 6/55 Reactome 0.00023648259890702 0.000253335875361129 1795 3005.27272727273 3474 2.36507768485621e-05 299 1.86585570668206 -1.77626683879866 -1 2.64854111345163 1795 4641 4209 4440 4378 1279 299 2635 4669 3474 1239 3879 M7090 TOMLINS_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_METASTASIS_DN.html Top genes down-regulated in hormone refractory metastatic prostate cancer compared to localized prostate cancer. 17173048 29/35 Leona Saunders 4.99406176734406e-05 5.63518325170069e-05 2420 2954.81818181818 3475 4.54015921595572e-06 1534 1.22756168205012 1.02670240774917 1 2.04764703132505 2417 3729 3475 4059 4132 1641 1534 1687 4230 4028 1571 3880 M15068 NOUZOVA_TRETINOIN_AND_H4_ACETYLATION http://www.broadinstitute.org/gsea/msigdb/cards/NOUZOVA_TRETINOIN_AND_H4_ACETYLATION.html Genes whose CpG islands showed greatly increased histone H4 acetylation in NB4 cells (acute promyelocytic leukemia, APL) upon treatment with tretinoin [PubChem=444795]. 15302897 184/239 Kevin Vogelsang 2.91834330583255e-06 4.13402773215176e-06 1505 3409.45454545455 3475 2.65304288825417e-07 1503 1.38789356338508 -1.27116770340088 -1 2.95487475325694 1503 4715 4065 4324 3260 2895 2506 3475 3523 4587 2651 3881 M3214 KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS.html Primary bile acid biosynthesis 14/26 KEGG 1.13597037875114e-05 1.39448119316135e-05 4015 3293.36363636364 3476 1.03270567670777e-06 1878 2.2546727196999 2.39333834862453 1 4.35273217915636 4014 2414 1878 2886 3788 3476 3005 4158 4196 2356 4056 3882 M19076 GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP.html Genes up-regulated in metastatic breast cancer tumors having type 2 amplification in the 20q13 region; involves MYBL2, STK6 and ZNF217 [GeneID=4605;6790;7764] 16899599 183/223 Leona Saunders 7.03286109607703e-07 1.3739695518826e-06 3225 3471.45454545455 3476 6.39351213119222e-08 2195 1.79490532500806 -1.31556924508621 -1 4.18141766751899 3223 4423 3385 2988 2270 3739 3476 3741 2195 4239 4507 3883 M12825 YAGUE_PRETUMOR_DRUG_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAGUE_PRETUMOR_DRUG_RESISTANCE_UP.html Up-regulated genes common to all pretumorigenic cells with acquired drug resistance. 17283147 9/15 Jessica Robertson 0.000151839515100056 0.000164226056661839 2900 3156.27272727273 3476 1.5184989095512e-05 67 2.42632161826456 2.71669045220883 1 3.64283419172675 4362 2900 4576 1624 4333 4302 4533 3476 67 2898 1648 3884 M2422 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_UP.html Genes from the magenta module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 73/117 Arthur Liberzon 0.000167739394107733 0.000181008216778349 590 2578.90909090909 3477 1.5250198617566e-05 343 1.56866293586183 -1.66880919405946 -1 2.31081659540867 590 4200 3477 4020 4334 343 825 2247 4038 3698 596 3885 M1907 CASTELLANO_HRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) isolated from HRAS [GeneID=3265] knockout mice. 16909116 6/9 Leona Saunders 0.000470541544220034 0.000497303199444371 2705 3019.90909090909 3477 4.70641208127298e-05 856 0.832944507701618 0.96672211591718 1 1.05652314945318 2703 3532 4331 3477 4464 2905 1574 952 4414 4011 856 3886 M1155 ABDULRAHMAN_KIDNEY_CANCER_VHL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABDULRAHMAN_KIDNEY_CANCER_VHL_UP.html Genes up-regulated in the RCC4 cells (renal cell carcinoma, RCC) expressing VHL [GeneID=7428] mutants Type 1 and 2B (associated with RCC) but not those of Type 2A and 2C (not associated with RCC). 17001320 6/9 Arthur Liberzon 5.5328039009854e-05 6.21190162051643e-05 4095 3138.54545454545 3477 5.53294165944816e-06 113 1.59318338176982 -2.40978466120774 -1 2.64531644602032 4091 1988 4355 3640 4168 4233 2409 2861 113 3477 3189 3887 M16626 BIOCARTA_CK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CK1_PATHWAY.html Regulation of ck1/cdk5 by type 1 glutamate receptors 23/32 BioCarta 4.75081629146328e-06 6.32013892212702e-06 4100 3265 3478 4.31893322791028e-07 589 1.74231401342303 -1.83304943264502 -1 3.59305145690763 4096 3458 2844 3163 3478 4334 4577 1460 589 3862 4054 3888 M4988 JAERVINEN_AMPLIFIED_IN_LARYNGEAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/JAERVINEN_AMPLIFIED_IN_LARYNGEAL_CANCER.html Genes whose expression was increased due to copy number gain in laryngeal cancer tumors (both in primary cultures and cell lines). 16715129 44/50 Arthur Liberzon 2.26782433127027e-07 7.86490142806441e-07 3595 3063.18181818182 3478 2.06165869549478e-08 1086 1.52286660809384 -1.64389533746917 -1 3.68847556964578 3594 3682 3568 3478 1086 4604 3981 2658 1246 3135 2663 3889 M13917 BIOCARTA_PARKIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PARKIN_PATHWAY.html Role of Parkin in the Ubiquitin-Proteasomal Pathway 12/15 BioCarta 8.31106571369587e-05 9.18263814809094e-05 4480 3627.63636363636 3479 7.55579972925548e-06 2174 1.11678451136968 1.104457284371 1 1.7631067778868 4479 2885 3435 3914 4223 3479 2174 4628 3073 2962 4652 3890 M1051 REACTOME_INTEGRATION_OF_PROVIRUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRATION_OF_PROVIRUS.html Genes involved in Integration of provirus 10/13 Reactome 3.37674225570231e-05 3.87602710284895e-05 2530 3315.18181818182 3479 3.06981280532146e-06 1916 1.14912134716845 0.940041884523095 1 1.98871282674938 2526 3518 3389 4216 4063 2289 1916 3479 4407 3591 3073 3891 M18256 KEGG_SULFUR_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SULFUR_METABOLISM.html Sulfur metabolism 8/18 KEGG 4.32218517029839e-06 5.83377580892434e-06 3835 2900.45454545455 3480 4.3221935768995e-07 676 2.05932269446119 -1.5956610510283 -1 4.28470178406105 3834 1034 4183 3658 3480 3730 2759 1332 676 2661 4558 3892 M9585 PUJANA_ATM_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_ATM_PCC_NETWORK.html Genes constituting the ATM-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC >= 0.4) with that of ATM [GeneID=472] across a compendium of normal tissues. 17922014 1698/2334 Leona Saunders 7.67796572257707e-07 1.45483734285684e-06 3055 3650.90909090909 3480 7.67796837538046e-08 2429 1.66338374744781 1.84869158828419 1 3.85474316197552 3052 4653 4421 3826 2429 3445 3770 3085 3405 4594 3480 3893 M7062 ELVIDGE_HIF1A_AND_HIF2A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_AND_HIF2A_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) after knockdown of both HIF1A and HIF2A [GeneID=3091;2034] by RNAi. 16565084 50/59 Arthur Liberzon 1.22270488960801e-06 2.03640334472471e-06 3695 3499.90909090909 3481 1.11155051741572e-07 2677 1.45869480403779 -1.1907760218722 -1 3.28856036966374 3694 2677 3500 4227 2714 3988 3325 4622 3481 2923 3348 3894 M10550 AMIT_DELAYED_EARLY_GENES http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_DELAYED_EARLY_GENES.html Delayed early genes (DEG) which are coordinately down-regulated in multiple epithelial tumor types. 17322878 20/21 Arthur Liberzon 0.0121145825464556 0.0123794824895585 1575 3375.27272727273 3481 0.00110743744687498 1542 1.36581523401826 -1.50729979526693 -1 0.9976003593803 1572 4312 3365 4477 4588 2586 1542 2929 4635 3641 3481 3895 M2365 PURBEY_TARGETS_OF_CTBP1_AND_SATB1_DN http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_AND_SATB1_DN.html Genes down-regulated in HEK-293 cells (fibroblast) upon knockdown of both CTBP1 and SATB1 [GeneID=1487, 6304] by RNAi. 19103759 198/356 Arthur Liberzon 4.20628556034833e-07 1.00849031419935e-06 4445 3145.63636363636 3482 3.82389669506224e-08 1179 1.92084154191623 1.72390086815884 1 4.5820592808426 4442 2535 2423 1179 1774 4319 4482 4343 2078 3545 3482 3896 M2444 PLASARI_TGFB1_TARGETS_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_1HR_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 1 h. 19752192 6/7 Arthur Liberzon 0.00155821494878827 0.00161928105642462 4705 3137.36363636364 3483 0.000155930864349847 1380 2.64250460688853 -2.64250460688853 -1 2.91565519473366 1435 4371 4703 4408 4701 2166 1587 1380 4436 3483 1841 3897 M17860 TAKAO_RESPONSE_TO_UVB_RADIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKAO_RESPONSE_TO_UVB_RADIATION_DN.html Genes down-regulated in primary tissue culture of epidermal kerationcytes after UVB irradiation. 11982916 127/173 John Newman 8.30231830385841e-07 1.53614043097655e-06 3435 3498.90909090909 3484 7.54756494270293e-08 2418 1.76729796980319 -1.98230577959268 -1 4.0818958216668 3433 4167 3410 3780 2418 3801 3097 4546 3484 3913 2439 3898 M1477 MARCINIAK_ER_STRESS_RESPONSE_VIA_CHOP http://www.broadinstitute.org/gsea/msigdb/cards/MARCINIAK_ER_STRESS_RESPONSE_VIA_CHOP.html Endoplasmic retuculum (ER) stress response (caused by tunicamycin [PubChem=5282055]) genes dependent on CHOP [GeneID=13198]. 15601821 35/36 Kevin Vogelsang 7.2833820869566e-07 1.40431223245242e-06 3825 3335.09090909091 3485 6.62125863474068e-08 1492 1.62289389604358 1.34655037944257 1 3.76971246766964 3824 3121 3076 3425 2302 4496 3504 4148 3485 3813 1492 3899 M1026 REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX.html Genes involved in Formation of the HIV-1 Early Elongation Complex 34/36 Reactome 6.35383778715784e-05 7.09321531584319e-05 1685 3350.81818181818 3489 5.77638300025527e-06 1685 0.786269119760783 0.835167665110616 1 1.26195645970065 1685 3726 4031 3254 4176 2425 1978 3012 4520 4563 3489 3900 M8432 NIKOLSKY_BREAST_CANCER_12Q24_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_12Q24_AMPLICON.html Genes within amplicon 12q24 identified in a copy number alterations study of 191 breast tumor samples. 19010930 15/18 Jessica Robertson 0.000366677882751058 0.000389626205894866 4415 3436.45454545455 3490 3.33399101695721e-05 1722 1.85192517618119 1.40210309267712 1 2.48915699712348 4412 3780 3334 3490 4404 4461 3342 1722 1956 3789 3111 3901 M1475 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN.html Genes down-regulated in kidney biopsies from patients with acute transplant rejection compared to the biopsies from patients with well functioning kidneys more than 1-year post transplant. 15307835 736/974 Jean Junior 1.4956357062489e-07 7.26289540930751e-07 4115 3020 3491 1.49563580691059e-08 197 1.80396314044328 1.79381366921033 1 4.40363432278922 4113 2002 4480 197 723 3421 4112 3792 2343 3491 4546 3902 M7636 REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION.html Genes involved in Influenza Viral RNA Transcription and Replication 118/206 Reactome 0.00167350439491797 0.00173870586484984 1255 3351.54545454545 3492 0.000152252614543459 869 0.625887056147001 -0.510287204785706 -1 0.644619361075604 1252 4469 4171 3285 4509 2000 869 3426 4699 4695 3492 3903 M14796 MAYBURD_RESPONSE_TO_L663536_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAYBURD_RESPONSE_TO_L663536_DN.html Genes down-regulated in H720 cells (lung cancer) after treatment with L663536 (MK886) [PubChem=105049], an inhibitor of leukotriene biosynthesis. 16551867 90/107 Arthur Liberzon 1.0292103415652e-05 1.27389444290337e-05 3495 3390.45454545455 3492 9.3565014225293e-07 2179 1.63869646704315 1.63911479204479 1 3.17578207031161 3492 4186 3616 2731 3755 3093 2670 3972 2179 4297 3304 3904 M1699 BAFNA_MUC4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAFNA_MUC4_TARGETS_UP.html Genes up-regulated in NIH3T3 cells (fibroblast) engineered to stably express MUC4 [GeneID=4585]. 19010895 9/10 Leona Saunders 0.000702967246908129 0.000737334534534749 1250 3066.36363636364 3492 7.0318971928962e-05 1071 1.36307851031254 -1.36307851031254 -1 1.66703989245706 1248 4107 4514 3492 4547 2296 1946 1071 4253 3880 2376 3905 M861 REACTOME_THROMBIN_SIGNALLING_THROUGH_PROTEINASE_ACTIVATED_RECEPTORS_PARS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THROMBIN_SIGNALLING_THROUGH_PROTEINASE_ACTIVATED_RECEPTORS_PARS.html Genes involved in Thrombin signalling through proteinase activated receptors (PARs) 28/35 Reactome 2.5916191306094e-06 3.74424312717366e-06 3420 3391.27272727273 3493 2.35602016687664e-07 832 1.66103987485664 -1.29360869257462 -1 3.57499112204892 3417 4271 3274 3762 3186 3167 832 3493 3973 3513 4416 3906 M17424 NAKAMURA_ALVEOLAR_EPITHELIUM http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ALVEOLAR_EPITHELIUM.html Differentiation markers for normal alveolar epithelium cells. 16491115 4/7 Arthur Liberzon 2.10310378595321e-05 2.46563583450054e-05 4335 3242.81818181818 3493 2.10312368992323e-06 266 2.73270669303149 1.67212355596369 1 5.01418607945588 4335 3263 4363 3293 3988 3583 3493 266 3624 2146 3317 3907 M17411 KEGG_JAK_STAT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_JAK_STAT_SIGNALING_PATHWAY.html Jak-STAT signaling pathway 101/186 KEGG 2.37012878233615e-07 8.0069968374353e-07 3605 3030.45454545455 3494 2.15466276152506e-08 1139 2.04603500137103 -1.92937333784008 -1 4.96641242143595 3604 3323 1652 2942 1139 4458 4014 3793 3494 1375 3541 3908 M9503 BIOCARTA_FAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FAS_PATHWAY.html FAS signaling pathway ( CD95 ) 31/35 BioCarta 4.10731561559244e-07 1.00046055710989e-06 3770 3238.27272727273 3494 3.73392398401156e-08 1737 1.38421013178384 -1.14853025018542 -1 3.28990889278077 3767 3141 3494 2932 1737 3596 2632 4179 2114 3506 4523 3909 M3621 MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_DN.html Genes correlated with the late tumor onset in the Emu-myc transgenic mouse lymphoma model. 18922927 28/33 Jessica Robertson 1.99055558130199e-06 3.01231880209855e-06 4190 3488.18181818182 3495 1.80959762032269e-07 2236 1.6172054398067 -1.54948946164967 -1 3.54076424264709 4187 4002 3169 2958 3033 3514 3349 4124 4303 2236 3495 3910 M1747 ZHENG_FOXP3_TARGETS_IN_THYMUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_THYMUS_DN.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are down-regulated only in developing (located in the thymus) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 15/34 Jessica Robertson 0.000401068921556179 0.000425403440392171 4645 3555.36363636364 3495 3.64674597012423e-05 2041 1.75787269310144 1.09598255881932 1 2.33322853387351 4645 3495 2602 3377 4415 4586 2660 4293 3981 3014 2041 3911 M16111 MOOTHA_GLYCOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_GLYCOLYSIS.html Genes involved in glycolysis; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 28/42 Vamsi Mootha 9.90258947717067e-06 1.22903555961729e-05 4035 3352.72727272727 3495 9.00239459159991e-07 1360 1.45059998325152 -2.0495313001649 -1 2.81459152123684 4031 4008 3450 3513 3747 3495 3372 1360 3384 4138 2382 3912 M19735 CHANG_POU5F1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_POU5F1_TARGETS_DN.html Genes down-regulated by POU5F1 [GeneID=5460] in bladder cancer cell lines. 18676852 7/9 Jessica Robertson 9.22946171479538e-05 0.000101616653356273 4350 3677.81818181818 3499 9.22984506053933e-06 3061 1.9738599023683 -1.91846426933195 -1 3.11967704680873 4346 3253 4476 3420 4255 3499 3124 3847 4109 3066 3061 3913 M7484 DAZARD_RESPONSE_TO_UV_SCC_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_SCC_DN.html Genes down-regulated in SCC12B2 cells (squamous cell carcinoma) by UV-B irradiation. 12771951 180/230 John Newman 2.43143777944664e-07 8.07627467909088e-07 4105 3215.63636363636 3500 2.21039822560813e-08 1124 1.6257421399366 1.86331597061145 1 3.93349610668767 4105 2969 3439 2508 1165 4517 3979 3731 1124 3500 4335 3914 M13133 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS.html Genes associated with the same cis-regulatory QTL (quantitative trait loci) in both brain and hematopoietic stem cells (HSC). 15711547 81/91 Jean Junior 9.61412540582607e-07 1.70596510960523e-06 3895 3436.81818181818 3501 8.74011782477839e-08 1434 1.54169492147029 1.4816373675238 1 3.52620232689043 4519 3895 3893 2999 2539 3501 3227 3261 1434 4262 4275 3915 M19652 CHEOK_RESPONSE_TO_MERCAPTOPURINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_UP.html Genes specifically up-regulated in pediadric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490]. 12704389 18/20 Jean Junior 4.91840388911154e-05 5.55246743760021e-05 4520 3312.18181818182 3501 4.47137622751457e-06 205 2.08758876227227 2.99227900587323 1 3.52267168016458 4518 3482 2632 3501 4130 3975 3059 2226 205 4201 4505 3916 M2426 LOPEZ_TRANSLATION_VIA_FN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_TRANSLATION_VIA_FN1_SIGNALING.html Genes translationally up-regulated in HUVEC cells (endothelium) grown on FN1 [GeneID=2335] compared to those grown on laminin 1. 19451229 46/54 Arthur Liberzon 4.5261284340915e-07 1.04262206973704e-06 3600 3426.63636363636 3502 4.11466305933295e-08 1862 1.46770667369721 1.46238796715825 1 3.48079534697954 3597 3679 3424 4228 1862 3220 3441 3502 3063 4145 3532 3917 M14236 REACTOME_SIGNAL_ATTENUATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_ATTENUATION.html Genes involved in Signal attenuation 15/20 Reactome 3.37181459053746e-05 3.87131230049545e-05 3610 3451.36363636364 3503 3.06533297229681e-06 2782 1.21780927398692 -1.03465768439971 -1 2.1108365695216 3607 3214 3341 2993 4062 2822 2782 3503 4229 3788 3624 3918 M10243 FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP.html Genes up-regulated in peripheral blood lymphocytes (PBL) from patients with acute transplant rejection compared to those from patients with well functioning kidneys more than 1-year post transplant. 15307835 84/112 Jean Junior 4.92363755664837e-06 6.50968326817376e-06 2745 3487.90909090909 3503 4.47604415987982e-07 2518 1.071032246442 1.11819223901182 1 2.18390831298322 2743 3625 3956 4309 3503 2518 3062 2900 4273 4313 3165 3919 M14970 SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL.html IRF4 [GeneID=3662] target genes up-regulated in plasmacytoid dendritic cells compared to monocytes. 18568025 90/97 Jessica Robertson 7.63875299331377e-06 9.65067294658484e-06 2930 3456 3503 6.94434501492612e-07 2614 1.51948051736498 -1.42099549077571 -1 3.01478328229429 2930 3892 3685 4260 3679 3468 2614 3194 3774 3017 3503 3920 M2015 CROONQUIST_STROMAL_STIMULATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_STROMAL_STIMULATION_DN.html Genes down-regulated in ANBL-6 cell line (multiple myeloma, MM) co-cultured with bone marrow stromal cells compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 14/20 Arthur Liberzon 0.000151524376542294 0.0001639227726976 4320 3514 3505 1.37758921588368e-05 2364 1.79236168277408 -1.60565261416591 -1 2.67852324803388 4318 3505 2997 3471 4320 3967 2535 2697 4284 2364 4196 3921 M1008 REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION.html Genes involved in Transcriptional Regulation of White Adipocyte Differentiation 83/93 Reactome 3.34006995825505e-07 9.10697066989583e-07 3390 3485.63636363636 3507 3.03642769577193e-08 1511 1.64294578104359 -1.27911816523262 -1 3.94118439523602 3388 4466 3674 4095 1511 3162 3036 3507 3802 4227 3474 3922 M6046 BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_UP.html Up-regulated genes in tumor samples from colon cancer patients who developed recurrence of the disease. 16091735 17/19 Leona Saunders 1.32368004510603e-05 1.6048728006423e-05 3510 3424.54545454545 3508 1.20335273581383e-06 2079 1.43841084474218 -1.79208820270959 -1 2.72348923293955 3508 4311 3247 3995 3836 4538 2722 2079 2278 3947 3209 3923 M4572 LOCKWOOD_AMPLIFIED_IN_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LOCKWOOD_AMPLIFIED_IN_LUNG_CANCER.html Overexpressed genes with amplified copy number across 27 non-small cell lung cancer (NSCLC) cell lines. 18391978 284/320 Jessica Robertson 2.45969660169147e-07 8.12416615845762e-07 3255 3316.09090909091 3509 2.23608806972399e-08 1175 1.54784301017314 1.67054788209335 1 3.74102259627565 3251 4138 3966 4101 1175 2812 3509 3838 2038 4406 3243 3924 M1516 HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_4HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_4HR.html Genes discriminating between direct (cisplatin, MMS, mitomycin C [PubChem=2767;4156;5746]) and indirect (paclitaxel, hydroxyurea, etoposide [PubChem=4666;3657;36462]) acting genotoxins at 4 h time point. 15120960 55/65 John Newman 4.95845251216474e-06 6.5447136066604e-06 4050 3277 3509 4.50769426160799e-07 679 2.00179537936212 2.51029453666022 1 4.1234058680748 4047 3925 2129 4604 3509 4347 4195 679 3251 3351 2010 3925 M9210 LINDSTEDT_DENDRITIC_CELL_MATURATION_C http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_C.html Maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli: genes up-regulated only at 48 hr after the stimulation (cluster C). 12356685 94/118 Arthur Liberzon 1.62969239792276e-06 2.55044698879158e-06 4630 3432.45454545455 3509 1.48153964104551e-07 2138 1.82265304395259 2.03460339308016 1 4.04991954354384 4626 2138 2220 3729 2917 4691 3831 3509 3275 2346 4475 3926 M1518 KUMAMOTO_RESPONSE_TO_NUTLIN_3A_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUMAMOTO_RESPONSE_TO_NUTLIN_3A_UP.html Genes up-regulated in response to nutlin-3a [PubChem=216345], an inhibitor of MDM2 [GeneID=4193], in skin fibroblast cultures after knockdown of TP53 [GeneID=7157] by RNAi. 18451145 12/13 Jessica Robertson 4.26390475907817e-05 4.84021896653414e-05 4585 3289.63636363636 3510 3.87635218336498e-06 1845 2.94138567897018 -1.66792282203441 -1 5.05439002637552 4582 3510 1845 2610 4107 3944 2015 4056 2772 2974 3771 3927 M779 REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION.html Genes involved in Downstream signal transduction 106/111 Reactome 2.65244397251569e-07 8.31648157220804e-07 4085 2995.27272727273 3511 2.41131299300849e-08 512 1.4759867624415 -1.24484071269166 -1 3.5589971161813 4082 2580 3511 512 1257 3843 2678 4040 2270 3926 4249 3928 M655 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_LATE_ENDOSOME_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_LATE_ENDOSOME_MEMBRANE.html Genes involved in Synthesis of PIPs at the late endosome membrane 13/13 Reactome 0.000240887954289085 0.000257938099873974 1235 2699.27272727273 3512 2.19013031131885e-05 816 1.08284991610152 -1.08284991610152 -1 1.51267860436457 1234 4087 3561 3512 4370 1382 1159 816 4314 4171 1086 3929 M935 REACTOME_IRAK1_RECRUITS_IKK_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IRAK1_RECRUITS_IKK_COMPLEX.html Genes involved in IRAK1 recruits IKK complex 11/11 Reactome 0.00109023917622537 0.0011387317795494 1895 2954.90909090909 3512 9.91618030770079e-05 1040 0.864788671758678 -0.987001842571966 -1 0.973694824104313 1895 3512 3675 4000 4487 1876 1040 1376 4510 4061 2072 3930 M732 REACTOME_SLBP_DEPENDENT_PROCESSING_OF_REPLICATION_DEPENDENT_HISTONE_PRE_MRNAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SLBP_DEPENDENT_PROCESSING_OF_REPLICATION_DEPENDENT_HISTONE_PRE_MRNAS.html Genes involved in SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs 11/14 Reactome 4.83848242420925e-05 5.46747355572604e-05 885 2703 3513 4.39871712793e-06 89 0.824858618989496 0.824858618989496 1 1.3638519455004 881 3513 3578 4421 4126 707 89 1839 4469 4060 2050 3931 M6693 POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN.html Top marker genes in medulloblastoma associated with poor response to treatment (poor outcome). 11807556 54/80 Jean Junior 5.03495217709857e-06 6.63826097092326e-06 2080 3097.09090909091 3513 4.57723972745517e-07 2076 1.38737324354083 1.58773907528684 1 2.83898888356468 2076 3657 3523 3761 3513 2591 2639 2102 3637 3970 2599 3932 M16075 WANG_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in LNCaP cells (prostate cancer) treated with synthetic androgen R1881 [PubChem=13766]. 16751804 39/55 Arthur Liberzon 0.00223440927472174 0.00231280960015057 2135 3286.72727272727 3514 0.000203334714863279 1883 1.52135348465709 1.81560260274774 1 1.56266119777227 2135 4533 3514 4630 4522 2416 1883 2646 3776 3840 2259 3933 M867 MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN.html Genes down-regulated in low grade (LMP and G1) serous ovarian carcinomas vs the higher grade invasive tumors (G2 and G3). 15558012 28/32 Arthur Liberzon 5.19131697427069e-06 6.81585983826361e-06 3530 3214.45454545455 3514 4.71939020382499e-07 2339 1.70284190956415 2.25975399230983 1 3.48805939593095 3065 3995 3320 3530 3527 3623 3605 2420 2421 3514 2339 3934 M2298 VANDESLUIS_COMMD1_TARGETS_GROUP_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_2_UP.html Genes up-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout compared to normal 8.5 dpc and 9.5 dpc embryos. 17371845 22/26 Arthur Liberzon 4.01268079440478e-06 5.45974440749223e-06 3530 3426.90909090909 3515 3.64789828485073e-07 2224 1.68450390472969 -1.57343241951599 -1 3.51522792076849 3527 4030 2800 3515 3399 4015 4547 2960 2869 3810 2224 3935 M109 REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS.html Genes involved in Viral Messenger RNA Synthesis 15/17 Reactome 0.000924288570350475 0.00096625516103084 960 3039.45454545455 3516 8.40615564859973e-05 960 0.851042129065172 0.91153049646667 1 0.981834768373207 960 3781 3676 3516 4482 1775 1475 2228 4365 4265 2911 3936 M1165 BAKER_HEMATOPOESIS_STAT5_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BAKER_HEMATOPOESIS_STAT5_TARGETS.html STAT5 [GeneID=6777] targets in hematopoietic signaling. 17934481 10/10 Arthur Liberzon 0.000144610302847147 0.000156730339710341 4475 3691.90909090909 3516 1.31472553854566e-05 2389 2.05291478230131 -1.13825741484135 -1 3.09125813297271 4474 3516 2389 3498 4315 4681 4679 3446 2432 2545 4636 3937 M15109 BIOCARTA_GLYCOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLYCOLYSIS_PATHWAY.html Glycolysis Pathway 19/35 BioCarta 3.54758726204937e-05 4.06126894903542e-05 3985 3473.36363636364 3520 3.22513133599327e-06 1881 1.2262752068335 0.799825831741906 1 2.11559897858222 3985 4315 3590 3520 4072 2797 1881 3439 2961 4383 3264 3938 M4242 RIZKI_TUMOR_INVASIVENESS_2D_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_2D_UP.html Genes up-regulated in monolayer (2D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 95/114 Jessica Robertson 7.67905244864992e-06 9.69899051582221e-06 1535 3029.81818181818 3522 6.98098113849772e-07 1158 1.85830389393127 2.22481369499321 1 3.69657540227758 1533 4180 2880 4658 3680 1158 2634 3522 3987 3743 1353 3939 M11068 KORKOLA_CHORIOCARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CHORIOCARCINOMA_DN.html Genes from the 12p region that were down-regulated in choriocarcinoma cells compared to normal testis. 16424014 31/69 Arthur Liberzon 9.2559400080202e-07 1.65861946992617e-06 3525 3134.18181818182 3524 8.41449445656696e-08 1443 2.39391072349717 2.32217028878108 1 5.51483855409415 3524 4263 2128 3731 2512 4562 4315 1443 1546 3769 2683 3940 M15964 CHESLER_BRAIN_D6MIT150_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_D6MIT150_QTL_TRANS.html Neurologically relevant genes modulated in brain tissue by a trans-regulatory QTL (quantitative trait locus) near D6Mit150 marker. 15711545 8/17 Jean Junior 0.000178029658865529 0.000191914929717179 3735 3190.36363636364 3524 1.78043923025616e-05 654 3.24576593692168 -3.22856104548177 -1 4.80170490780178 3733 3524 4477 4168 4408 2454 1196 654 2549 3282 4649 3941 M14136 FOURNIER_ACINAR_DEVELOPMENT_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_EARLY_DN.html Genes down-regulated early in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 11/12 Arthur Liberzon 1.90046272653135e-05 2.24591488964145e-05 3525 3553.36363636364 3525 1.72770831255848e-06 2626 1.64848034354926 1.56776343969087 1 3.03178256004594 3525 3793 2626 3949 3933 3484 3113 3179 4445 3297 3743 3942 M15262 YAGI_AML_RELAPSE_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_RELAPSE_PROGNOSIS.html Genes associated with clinical prognosis of pediatric AML (acute myeloid leukemia): good prognosis=no relapse > 3 years; poor prognosis=relapse < 1 year or no response to therapy. 12738660 49/57 Kate Stafford 2.86830471971025e-07 8.56860650445089e-07 3980 3135.90909090909 3525 2.60755008515698e-08 468 1.22218121802879 1.1027338435066 1 2.93202492441922 4152 468 3457 3431 1346 3978 4402 4299 1458 3525 3979 3943 M1239 JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_UP.html Genes up-regulated in early vs late brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 15/20 Leona Saunders 1.74798470812288e-05 2.07611671422747e-05 3530 3123.27272727273 3526 1.58908963335355e-06 195 2.26565698396573 2.34799460433606 1 4.21669735456562 3526 3769 2323 3891 3986 3161 3661 195 4042 3013 2789 3944 M2344 FARDIN_HYPOXIA_9 http://www.broadinstitute.org/gsea/msigdb/cards/FARDIN_HYPOXIA_9.html Genes in the hypoxia signature, based on analysis of nine neuroblastoma cell lines in hypoxia and normal oxygen conditions. 19832978 10/11 Paolo Fardin 5.19120835568082e-06 6.81585983826361e-06 3670 3040 3526 4.71929145918637e-07 352 2.14950295221126 1.81351530232544 1 4.41611378135899 3670 2446 2429 843 3526 4283 4183 4447 352 3114 4147 3945 M3988 ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_DN.html Genes down-regulated in 3 out of 4 NSCLC cell lines (non-small cell lung cancer) after treatment with azacitidine [PubChem=9444] and TSA [PubChem=5562]. 17043644 90/121 Leona Saunders 5.21099817142229e-06 6.83947982495514e-06 2405 3333.54545454545 3528 4.73728228583514e-07 1986 1.27034354400497 1.46307540684785 1 2.58866409001615 2403 4458 4012 4509 3528 2402 2964 1986 3779 4437 2191 3946 M19682 TRACEY_RESISTANCE_TO_IFNA2_DN http://www.broadinstitute.org/gsea/msigdb/cards/TRACEY_RESISTANCE_TO_IFNA2_DN.html Genes down-regulated in huT78R cells (cutaneous T-cell lymphoma, CTCL) resistant to IFNA2 [GeneID=3440] compared to the IFN2A sensitive parental cell line. 12414529 41/45 Arthur Liberzon 1.67431658763449e-06 2.61190491926172e-06 3765 3132.90909090909 3528 1.52210714716319e-07 1744 1.95275727551979 1.86653483248848 1 4.33446069570937 3761 3686 2607 2198 2928 3751 3788 3625 3528 2846 1744 3947 M8406 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_21 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_21.html Amplification hot spot 21: colocolized fragile sites and cancer genes in the 12q13-q21 region. 16751803 7/10 Arthur Liberzon 4.65782864560578e-06 6.21354855424385e-06 3345 3510.54545454545 3529 4.65783840855003e-07 2399 1.58423316894645 -1.71278646384275 -1 3.26721891805944 3342 3529 4370 3950 3521 3598 2638 2711 4447 2399 4111 3948 M7465 CAFFAREL_RESPONSE_TO_THC_24HR_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_3_UP.html Genes up-regulated in EVSA-T cells (breast cancer) after treatment with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 14/23 Jessica Robertson 9.03283555302831e-07 1.63102462931498e-06 3660 3337.09090909091 3529 8.21167205614826e-08 1661 1.57543279807924 1.75358033759835 1 3.61682430044085 3657 4077 3529 3546 2491 3396 2904 1661 4497 3688 3262 3949 M7700 KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) with early recurrence. 15288478 23/24 Yujin Hoshida 5.7366517825263e-05 6.42701077937909e-05 4600 3219.45454545455 3529 5.21527397740038e-06 1890 2.26084990929439 2.76180538589249 1 3.7614347487417 4600 3748 2073 1983 4161 4059 2757 1890 3529 2983 3631 3950 M8981 BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN.html Genes down-regulated in ALL (acute lymphoblastic leukemia) patients who developed t-ML (treatment related myeloid leukemia). 16341039 46/51 Arthur Liberzon 5.34499156818032e-06 7.00787783383642e-06 3540 3326.81818181818 3531 4.85909504918543e-07 2426 1.94445993787683 -1.10249411092263 -1 3.98064827947765 3539 3687 3212 3787 3531 3023 2921 2426 2612 3726 4131 3951 M2159 FIGUEROA_AML_METHYLATION_CLUSTER_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_1_UP.html Cluster 1 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 136/191 Arthur Liberzon 8.4733599463937e-07 1.56105616498744e-06 3765 3325.18181818182 3531 7.70305746357557e-08 2432 1.88743431883843 2.00940628194391 1 4.35746997866469 3762 3591 2810 4215 2432 2503 3799 3866 3467 2601 3531 3952 M2552 HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_DN.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 18/27 Arthur Liberzon 5.39540124372485e-06 7.06808045250661e-06 3770 3451.90909090909 3534 4.90492225068149e-07 2233 1.60089599467539 1.4333787449119 1 3.26608026621416 3770 4599 3132 4601 3534 3325 2233 2595 2452 3755 3975 3953 M2615 ZWANG_DOWN_BY_2ND_EGF_PULSE http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_DOWN_BY_2ND_EGF_PULSE.html Genes down-regulated by second pulse of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 284/454 Yaara Zwang 1.93585027521061e-05 2.28487454338436e-05 1175 2727.36363636364 3534 1.75987937235036e-06 985 1.6489838738966 -1.40699332205066 -1 3.02777073510659 1171 4139 3609 4480 3940 1075 1590 1759 3719 3534 985 3954 M7857 KEGG_NON_HOMOLOGOUS_END_JOINING http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NON_HOMOLOGOUS_END_JOINING.html Non-homologous end-joining 12/13 KEGG 0.000200054124997022 0.00021514136932922 2220 2828.18181818182 3535 1.81883926339736e-05 130 1.09992288456202 1.20228736256915 1 1.57217067133092 2217 4097 3722 3535 4599 1041 130 1247 4543 4344 1635 3955 M16082 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_25 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_25.html Amplification hot spot 25: colocalized fragile sites and cancer genes in the 2q13-q36 region. 16751803 6/11 Arthur Liberzon 0.104208231681581 0.104897174991909 2570 3495.72727272727 3535 0.0109443989194573 1509 1.47135105302109 -1.86918704238492 -1 0.52939742439615 2567 4645 4365 3915 4673 3688 1509 3437 3535 3479 2640 3956 M2327 BILANGES_SERUM_SENSITIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_SENSITIVE_GENES.html Genes translationally regulated in MEF cells (embryonic fibroblasts) in response to serum starvation but not by rapamycin (sirolimus) [PubChem=6610346]. 17562867 101/137 Arthur Liberzon 1.95353349102044e-06 2.96389523549227e-06 3650 3481.09090909091 3535 1.77594111427389e-07 2829 1.73703127430855 1.66070652458708 1 3.81173902312281 3649 3610 2958 3423 3022 3654 3692 3535 2829 3485 4435 3957 M13806 ZHAN_V1_LATE_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_V1_LATE_DIFFERENTIATION_GENES_DN.html The v1LDG down-regulated set: most variable late differentiation genes (LDG) with similar expression patterns in tonsil plasma cells (TPC) and multiple myeloma (MM) samples. 12393520 22/42 Arthur Liberzon 0.000126680112787344 0.000137899015764821 3310 3519.72727272727 3538 1.15170370775597e-05 1837 1.33699435489942 1.32864766860506 1 2.02567390751561 3310 4043 3538 3560 4295 3005 1837 3199 4519 4033 3378 3958 M18086 DAIRKEE_CANCER_PRONE_RESPONSE_BPA_E2 http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_CANCER_PRONE_RESPONSE_BPA_E2.html 'Cancer prone response profile' (CPRP): genes common to estradiol and bisphenol A [PubChem=5757;6623] response of epithelial cell cultures from patients at high risk of breast cancer. 18381411 155/217 Jessica Robertson 5.97647479856104e-07 1.23560933198459e-06 3490 3499.36363636364 3539 5.4331603837441e-08 2123 1.59630979164587 1.61513828677053 1 3.74282492549692 3486 4156 3713 4042 2123 3454 3581 3044 3421 3934 3539 3959 M1451 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN.html Top 100 probe sets contrubuting to the negative side of the 2nd principal component; associated with adipocytic differentiation. 17464315 85/131 Nikolaos Papanikolaou 9.54629250085352e-07 1.69775812373883e-06 4235 3156.81818181818 3539 8.67845149382369e-08 442 2.58916529508844 2.51070876008232 1 5.9581795722264 4234 3020 442 3287 2533 3808 4594 4610 3539 612 4046 3960 M376 PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_DN.html The XPRSS-Int network genes down-regulated in breast tumors from patients with germline mutations in BRCA1 [GeneID=672] compared to those with the wild type allele. 17922014 11/11 Arthur Liberzon 2.33143456574867e-05 2.7204873053977e-05 2915 3437.09090909091 3540 2.11950843029953e-06 2338 1.01372374673931 1.07324915109932 1 1.81116977953328 2913 4626 3716 3540 3991 2961 2605 2496 4556 4066 2338 3961 M3654 THUM_SYSTOLIC_HEART_FAILURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/THUM_SYSTOLIC_HEART_FAILURE_UP.html Genes up-regulated in samples with systolic heart failure compared to normal hearts. 17606841 522/717 Arthur Liberzon 2.21939827413923e-07 7.81758198055011e-07 4260 3231.63636363636 3541 2.21939849579705e-08 1169 2.20727288554035 2.53841195920327 1 5.37096336975959 4256 2501 4288 1260 1169 4270 4368 3541 3115 2255 4525 3962 M5931 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_1 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_1.html Amplification hot spot 1: colocolized fragile sites and cancer genes in the Xp22.3-p11.1 region. 16751803 3/18 Arthur Liberzon 0.000377909291257078 0.000401289506126751 1920 3189.09090909091 3542 3.77973573587696e-05 180 0.745719147515649 -0.745719147515649 -1 0.968584620158377 1919 3542 4376 4409 4579 1919 180 2470 4366 4706 2614 3963 M11521 KEGG_GLYCOLYSIS_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOLYSIS_GLUCONEOGENESIS.html Glycolysis / Gluconeogenesis 52/81 KEGG 8.74091088858798e-05 9.64176195235693e-05 3555 3506.72727272727 3543 7.94659836058949e-06 2012 1.82087113429069 1.36329575497693 1 2.89070300773444 3553 4218 3254 2012 4234 3724 3543 3158 3323 4125 3430 3964 M228 PID_SMAD2_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SMAD2_3PATHWAY.html Regulation of cytoplasmic and nuclear SMAD2/3 signaling 18832364 19/22 Pathway Interaction Database 3.0954687721425e-07 8.87104590437924e-07 2715 3369.36363636364 3544 2.81406291607702e-08 1419 0.620206118446323 -0.636667616753389 -1 1.45947780503354 2712 4588 3937 4520 1419 2640 1516 3544 4610 4489 3088 3965 M3590 ASTIER_INTEGRIN_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/ASTIER_INTEGRIN_SIGNALING.html Integrin signaling signature in precursor B leukemia (PBL) cells: fibronectin (FN1) [GeneID=2335] vs control treatment with poly-L-lysine. 12393420 72/81 Kevin Vogelsang 8.589404154793e-07 1.57310167253419e-06 4665 3437.90909090909 3544 7.80855228030373e-08 1185 1.7412304836536 2.02200151292176 1 4.01371942577181 4664 3636 2947 4458 2448 4112 4197 1185 3544 3488 3138 3966 M1697 TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_DN http://www.broadinstitute.org/gsea/msigdb/cards/TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_DN.html Genes down-regulated in small intestine tissue from transgenic mice expressing a mutant form of COL13A1 [GeneID=1305], compared to normal controls. 19074901 6/22 Leona Saunders 1.02399326945653e-05 1.26824332118099e-05 3545 3124.45454545455 3544 1.0239979880171e-06 1043 2.12808339618586 -2.10211168100655 -1 4.14080624698315 3544 1043 4513 2311 3783 3786 4179 1713 3040 2121 4336 3967 M16309 RAY_TARGETS_OF_P210_BCR_ABL_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TARGETS_OF_P210_BCR_ABL_FUSION_UP.html Genes up-regulated in HL-60 cells (acute myeloid leukemia, AML) by expression of p210 BCR-ABL [GeneID=613;25] fusion protein. 15155749 34/54 Arthur Liberzon 0.00214121573229376 0.00221829197902251 3385 3757.36363636364 3545 0.00019484568895954 2513 1.54137681979687 -1.50739774903776 -1 1.5951197714283 3381 4539 3545 4645 4518 3358 3203 2513 4252 3504 3873 3968 M216 SHARMA_ASTROCYTOMA_WITH_NF1_SYNDROM http://www.broadinstitute.org/gsea/msigdb/cards/SHARMA_ASTROCYTOMA_WITH_NF1_SYNDROM.html Genes up-regulated in pilocytic astrocytoma (PA) samples from patients with type 1 neurofibromatosis syndrom (NF1) compared to the PA tumors from non-NF1 patients. 17283119 3/5 Jessica Robertson 3.99611171180146e-05 4.55265442425848e-05 3110 3421.27272727273 3546 3.99618357370986e-06 2217 1.00539636958896 -1.4016083663307 -1 1.70546475638959 3108 2491 4574 3883 4112 3546 3070 2217 4464 3568 2601 3969 M14032 ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN.html Genes down-regulated in macrophage by live P.gingivalis. 18025224 483/706 Arthur Liberzon 4.08517940849783e-07 1.00010616224636e-06 4080 3521.36363636364 3547 3.71380015188626e-08 1731 1.70253829703648 -1.72239877321781 -1 4.05810492659157 4077 4680 3809 4505 1731 2927 3547 3897 3277 3432 2853 3970 M1500 BURTON_ADIPOGENESIS_10 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_10.html Strongly down-regulated at 8-48 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 41/42 John Newman 3.56095554584984e-07 9.41752134134615e-07 3435 3386.63636363636 3547 3.23723283839272e-08 1572 1.41387200690973 -1.45593033312466 -1 3.37641319868007 3431 3694 3547 3986 1572 3897 4258 2601 4150 3371 2746 3971 M13736 PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP.html Up-regulated genes in head and neck cancer compared to cervical carcinoma samples. 17510386 240/306 Arthur Liberzon 2.14058986055022e-06 3.20748702914192e-06 3300 3538.09090909091 3547 1.94599267576102e-07 2527 1.56393482341503 1.59845971126809 1 3.40533573095728 3296 3571 3831 3455 3070 3547 3304 4333 2527 3680 4305 3972 M2039 GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_DN.html Down-regulated genes from the set E (Fig. 5a): specific signature shared by cells expressing either MLL-AF4 [GeneID=4297;4299] or AF4-MLL fusion proteins alone, and those expressing both fusion proteins. 17130830 30/35 Arthur Liberzon 2.24203855507459e-06 3.34146573411811e-06 4715 3201.09090909091 3548 2.03821894541659e-07 1155 2.05967026622287 -1.84069962525675 -1 4.48589747384542 4714 2763 1496 4158 3088 3930 3548 2057 4034 1155 4269 3973 M12664 SESTO_RESPONSE_TO_UV_C3 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C3.html Cluster 3: genes changed in primary keratinocytes by UVB irradiation. 11867738 28/52 John Newman 0.00262016065316777 0.00270616154988006 1040 2928 3549 0.000238480584611884 797 1.333335804539 -1.40258452658513 -1 1.32677720023563 1036 4559 3549 4105 4532 1287 797 2251 4411 4137 1544 3974 M14339 BIOCARTA_ARENRF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARENRF2_PATHWAY.html Oxidative Stress Induced Gene Expression Via Nrf2 16/19 BioCarta 0.0011728747888153 0.00122314825523823 1560 3118.72727272727 3550 0.000106681867697525 910 1.0282892088988 -1.02566914941509 -1 1.1544023087632 1560 3775 3490 3568 4492 1568 910 4438 4592 3550 2363 3975 M12518 BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_DN.html Genes down-regulated in D-341 MED (OBR) cells (medulloblastoma) resistant to both carmustine and O6-BG [PubChem=2578;4578]. 12479369 109/140 John Newman 1.27795224812372e-05 1.55342122357558e-05 2245 3316.81818181818 3550 1.16178151967954e-06 2139 1.81619322523105 2.17534096594656 1 3.46226086852562 2244 3880 3074 3796 3826 3550 4672 2385 3212 3707 2139 3976 M633 REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION.html Genes involved in SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription 33/41 Reactome 1.42881544023981e-06 2.30170951465252e-06 3490 3352.72727272727 3551 1.29892397109215e-07 1333 1.01702909498816 -0.773798712781381 -1 2.2559411061706 3490 3129 3764 3551 2823 2530 1333 3999 4389 3681 4191 3977 M9025 OUILLETTE_CLL_13Q14_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUILLETTE_CLL_13Q14_DELETION_UP.html Genes up-regulated in chronic lymphocytic leukemia (CLL) samples bearing deletions in the 13q14 region. 18281475 95/129 Jessica Robertson 2.71749652626451e-07 8.37744283366146e-07 3415 3353.27272727273 3551 2.47045169266975e-08 1284 1.63240242998608 -1.69474759016245 -1 3.93937727971844 3412 4450 3551 4391 1284 3778 3536 2911 2144 3848 3581 3978 M1371 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX3 http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX3.html Early prostate development genes (up-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in lower grade vs higher grade locally invasive prostate cancers. 18794802 10/12 Jessica Robertson 1.75919975711485e-05 2.08891140970618e-05 3595 3161 3553 1.59928529497396e-06 687 0.864403440010494 0.761519802419769 1 1.57689862742901 3776 1966 3553 2953 3913 3155 687 3334 4246 3594 3594 3979 M2196 GABRIELY_MIR21_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GABRIELY_MIR21_TARGETS.html Genes significantly de-regulated (p < 0.05) by MIR21 [GeneID=406991] in A172 cells (glioma). 18591254 411/461 Arthur Liberzon 1.41752506585873e-07 7.20206492018647e-07 4155 3210 3554 1.28865923381279e-08 579 1.76524076310048 2.11694972644178 1 4.310628639856 4154 3276 3056 2671 579 4719 3554 3996 1664 3808 3833 3980 M928 REACTOME_INCRETIN_SYNTHESIS_SECRETION_AND_INACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INCRETIN_SYNTHESIS_SECRETION_AND_INACTIVATION.html Genes involved in Incretin Synthesis, Secretion, and Inactivation 16/29 Reactome 3.38259602671992e-06 4.70830234329638e-06 3935 3600 3556 3.07509202510922e-07 2413 1.97350957292131 -1.50598228789206 -1 4.1779498725226 3934 3490 2413 3485 3314 4163 3658 3091 4169 3556 4327 3981 M1418 KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_UP.html Up-regulated genes predicting response of patients with hepatocellular carcinoma (HCC) to combination chemotherapy with 5-fluorouracil (5-FU) [PubChem=3385] and IFN1@ [GeneID=3438]. 15447987 11/15 Yujin Hoshida 3.93197965265573e-05 4.48283670544325e-05 4345 3509.90909090909 3556 3.57459084477317e-06 2440 1.35802792142984 0.92373195272765 1 2.32485306775004 4344 2440 3228 3405 4091 3964 2849 3556 3001 3722 4009 3982 M932 REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GLP1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GLP1.html Genes involved in Synthesis, Secretion, and Inactivation of Glucagon-like Peptide-1 (GLP-1) 16/25 Reactome 3.38259602671992e-06 4.70830234329638e-06 3935 3601 3557 3.07509202510922e-07 2414 1.97350957292131 -1.50598228789206 -1 4.1779498725226 3935 3491 2414 3486 3315 4164 3659 3092 4170 3557 4328 3983 M9811 SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_UP.html Genes up-regulated in 293 cells (embryonic kidney) expressing polymorphic variants S427G (SNP ID=rs2070235) or I624M (SNP ID=rs11556379) of BMYB [GeneID=4605]. 18026132 14/18 Jessica Robertson 2.08747445223522e-05 2.44913731408159e-05 2110 2930.54545454545 3558 1.89772205412903e-06 958 1.0785678716402 1.50869821344752 1 1.95001819667399 2108 4616 3780 3558 3968 1749 958 1210 3999 4402 1888 3984 M5827 GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP.html Genes up-regulated in non-metastatic breast cancer tumors having type 1 amplification in the 20q13 region; involves ZNF217 [GeneID=7764] locus only. 16899599 96/109 Leona Saunders 5.04633241753809e-07 1.11935364902366e-06 3190 3565.09090909091 3560 4.58757597732715e-08 1953 1.13565655456336 -1.01599536528992 -1 2.66790367926669 3187 3886 4046 4500 1953 3328 2926 3519 3560 4491 3820 3985 M1822 MATZUK_EARLY_ANTRAL_FOLLICLE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_EARLY_ANTRAL_FOLLICLE.html Genes important for early anral follicle, based on mouse models with female fertility defects. 18989307 19/23 Jessica Robertson 1.13539816503756e-05 1.39414134728858e-05 2605 3337.18181818182 3560 1.03218547705195e-06 773 2.27613210704862 2.47407698977298 1 4.39473348616014 2601 4611 2833 4648 3787 3251 3560 773 4462 3830 2353 3986 M1142 SCIBETTA_KDM5B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCIBETTA_KDM5B_TARGETS_UP.html Genes up-regulated in HB2 cells (mammary epithelium) upon expression of KDM5B [GeneID=10765] off an adenoviral vector. 17709396 25/25 Leona Saunders 6.36447539613243e-06 8.17201411037679e-06 945 2324.09090909091 3564 5.78590346206714e-07 161 1.24922632584261 -1.15728185489196 -1 2.50596249103373 943 4035 3759 3564 3611 374 188 436 4491 4003 161 3987 M17042 CAFFAREL_RESPONSE_TO_THC_24HR_5_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_5_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 76/97 Jessica Robertson 5.70042088150503e-06 7.41007616653917e-06 2435 3503.27272727273 3564 5.18221422901949e-07 2431 1.49652965021533 1.72228984099168 1 3.03754380843092 2431 4192 3830 3580 3564 3290 3436 2653 3944 4221 3395 3988 M1731 GAVIN_FOXP3_TARGETS_CLUSTER_T7 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_T7.html Cluster T7 of genes with similar expression profiles in thymic T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 126/151 Jessica Robertson 1.81838657756849e-07 7.47800341964416e-07 2615 3233.63636363636 3564 1.65307884351392e-08 844 1.26309967673676 -1.08516509371774 -1 3.06189745960395 2612 4437 4081 4108 844 2335 2013 3564 3590 4523 3463 3989 M496 REACTOME_RNA_POL_I_TRANSCRIPTION_TERMINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_TRANSCRIPTION_TERMINATION.html Genes involved in RNA Polymerase I Transcription Termination 20/20 Reactome 0.000108335102271261 0.000118640761652054 2400 3340.54545454545 3565 9.84913067356784e-06 2135 0.897197642515387 1.02912079675173 1 1.36645179300311 2397 4594 3903 3565 4268 2348 2135 2456 4368 4506 2206 3990 M804 REACTOME_PROSTANOID_LIGAND_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROSTANOID_LIGAND_RECEPTORS.html Genes involved in Prostanoid ligand receptors 3/9 Reactome 0.00783435149147221 0.00802825424223813 2195 3137.63636363636 3566 0.000786210899523077 732 2.38773445907469 -2.38773445907469 -1 1.96206135905288 2195 4120 4241 4364 4695 2314 732 2013 4470 3566 1804 3991 M1533 CUI_TCF21_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_2_DN.html All significantly down-regulated genes in kidney glomeruli isolated from TCF21 [Gene ID=6943] knockout mice. 16207825 1137/1393 John Newman 1.53029700316904e-07 7.28175281873995e-07 4305 2871.18181818182 3566 1.53029710855045e-08 422 1.94676544337046 2.28339809630848 1 4.7553067188062 4304 1076 4492 2076 762 4651 3724 3566 2479 422 4031 3992 M1205 SCHRAMM_INHBA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAMM_INHBA_TARGETS_UP.html Genes up-regulated in Kelly cells (neuroblastoma) by overexpressing INHBA [GeneID=3624] off a plasmid vector. 15580313 7/8 Arthur Liberzon 4.13725792019576e-07 1.00297161701715e-06 3790 3268.27272727273 3568 4.1372586904566e-08 1181 1.59958982317102 -1.89194562344905 -1 3.80889594855516 3788 3810 4389 3974 1868 3352 3568 1181 4406 3062 2553 3993 M4086 KEGG_PROPANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROPANOATE_METABOLISM.html Propanoate metabolism 33/36 KEGG 5.96144553324101e-06 7.70693588520887e-06 3570 3290.45454545455 3569 5.41951062483384e-07 2049 1.63898733480968 1.5399382569094 1 3.32021260610127 3569 2749 2837 2214 3586 3482 3585 4230 2049 3865 4029 3994 M13036 KEGG_PRION_DISEASES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRION_DISEASES.html Prion diseases 41/49 KEGG 5.7780906052875e-06 7.50071167683086e-06 3605 3006.63636363636 3569 5.25282343722575e-07 1342 2.04959702258962 1.76844522237058 1 4.17425863187834 3603 3949 2020 2200 3569 3756 3933 1553 4305 2843 1342 3995 M13324 BIOCARTA_HIF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HIF_PATHWAY.html Hypoxia-Inducible Factor in the Cardiovascular System 21/24 BioCarta 0.000738042233041771 0.000773436798391909 2915 3621.27272727273 3569 6.71172675618012e-05 2292 2.45182872872273 2.17637370926674 1 3.01807391978091 2915 4593 2751 4248 4470 3480 4599 3569 4237 2680 2292 3996 M18919 LIU_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LIU_LIVER_CANCER.html Low abundance transcripts specific to hepatocellular carcinoma (HCC). 18332864 40/62 Jessica Robertson 0.000470228988795448 0.000497084171806163 4650 3591.90909090909 3569 4.2757229621501e-05 2159 1.42235705749674 -1.71041776109195 -1 1.83966259014253 4646 3961 3569 3533 4433 2891 2572 2159 4218 4071 3458 3997 M13597 GRADE_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_METASTASIS_DN.html Down-regulated genes in colon carcinoma tumors with lymph node metastases. 17210682 54/64 Jessica Robertson 1.5118832659373e-05 1.81533681384484e-05 735 2677.27272727273 3571 1.37444877817854e-06 497 1.10750641872597 0.963993879250194 1 2.06160720700033 731 3926 3900 3571 3871 509 497 2394 3809 4272 1970 3998 M4280 REACTOME_EARLY_PHASE_OF_HIV_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EARLY_PHASE_OF_HIV_LIFE_CYCLE.html Genes involved in Early Phase of HIV Life Cycle 13/19 Reactome 4.60128972013423e-05 5.21067357942264e-05 2805 3407.63636363636 3572 4.18307814428335e-06 1808 1.43583518810823 0.945540605779714 1 2.42319041803923 2805 3785 3150 3967 4119 2515 1808 4287 4088 3572 3388 3999 M10961 GOZGIT_ESR1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOZGIT_ESR1_TARGETS_DN.html Genes down-regulated in TMX2-28 cells (breast cancer) which do not express ESR1 [GeneID=2099]) compared to the parental MCF7 cells which do. 17726467 975/1368 Arthur Liberzon 9.04740259571715e-27 8.89661255245519e-25 3575 2453.18181818182 3572 9.04740259571718e-28 16 2.2331965335372 -2.1731196270243 -1 21.5501085181792 3572 1081 4324 16 592 4007 3817 4506 1376 31 3663 4000 M1128 LANG_MYB_FAMILY_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LANG_MYB_FAMILY_TARGETS.html Myb family target genes. 15608679 49/54 Arthur Liberzon 3.59726417963336e-07 9.41752134134615e-07 3340 3342.90909090909 3572 3.27024069802671e-08 1588 1.49535532858745 -1.66488698910598 -1 3.5738840845692 4457 3664 3337 2500 1588 3692 4103 2339 4184 3336 3572 4001 M12498 UEDA_PERIFERAL_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/UEDA_PERIFERAL_CLOCK.html Molecular timetable composed of 162 time-indicating genes (182 probes) in the peripheral (liver) clock. 15273285 232/267 Kate Stafford 6.6740976897258e-07 1.33031001247913e-06 4690 3349.27272727273 3572 6.06736337675895e-08 1741 1.8052050771577 1.96098312400756 1 4.21588051921385 4690 3572 2261 2700 2221 4390 4217 3966 3246 1741 3838 4002 M15659 RASHI_RESPONSE_TO_IONIZING_RADIATION_5 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_5.html Cluster 5: early responding genes activated in ATM [GeneID=472] deficient but not in the wild type tissues. 16314843 203/258 Arthur Liberzon 1.94268486608272e-07 7.601476063939e-07 3640 3435.90909090909 3573 1.76607730693574e-08 915 1.67906335684352 1.67596216061713 1 4.08191642281024 3637 3857 3394 3573 915 2748 4643 4288 3321 3849 3570 4003 M17037 PETRETTO_HEART_MASS_QTL_CIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_HEART_MASS_QTL_CIS_UP.html Up-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that colocalize with previously mapped cardiac mass QTLs. 18443592 40/45 Jessica Robertson 1.93560173066896e-06 2.94046996097763e-06 2795 3459.36363636364 3573 1.75963948513653e-07 2236 1.34087518505032 -1.21756423799289 -1 2.93286122568227 2794 4237 3573 4003 3019 2236 3333 4445 3766 3738 2909 4004 M10540 KANG_FLUOROURACIL_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_FLUOROURACIL_RESISTANCE_UP.html Genes up-regulated in gastric cancer cell lines resistant to 5-fluorouracil [PubChem=3385]. 14734480 31/37 John Newman 5.82479245747682e-06 7.5551031600139e-06 4690 3428.45454545455 3573 5.29527989040576e-07 2128 1.96182537331886 1.95515541048724 1 3.99088226039567 4688 3126 2400 4142 3573 3697 4556 3994 2128 2948 2461 4005 M12176 CAIRO_HEPATOBLASTOMA_CLASSES_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_CLASSES_DN.html Genes down-regulated in robust Cluster 2 (rC2) of hepatoblastoma samples compared to those in the robust Cluster 1 (rC1). 19061838 252/372 Arthur Liberzon 9.9870144490674e-08 6.71132834037269e-07 4500 3063.63636363636 3573 9.07910445675738e-09 309 2.04733175948705 2.1761741243259 1 5.03271141338464 4497 3565 1048 2804 309 3856 4588 3747 3573 1212 4501 4006 M13893 GARY_CD5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARY_CD5_TARGETS_DN.html Genes down-regulated in Daudi cells (B lymphocytes) stably expressing CD5 [GeneID=921] off a plasmid vector. 17878328 524/626 Arthur Liberzon 5.30294066545507e-06 6.95467628256402e-06 1515 3415.36363636364 3574 5.30295332002844e-07 1512 1.34356490640646 1.33639451569784 1 2.73683678297748 1512 4681 4286 4340 3574 2495 2312 2763 3652 4659 3295 4007 M538 REACTOME_VITAMIN_B5_PANTOTHENATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VITAMIN_B5_PANTOTHENATE_METABOLISM.html Genes involved in Vitamin B5 (pantothenate) metabolism 12/12 Reactome 2.40510899678617e-06 3.52878907828123e-06 3510 3488.45454545455 3575 2.18646511466434e-07 1950 0.85195139878078 -0.98310043455453 -1 1.81806719862444 3507 1950 3575 4395 3138 4448 4113 2234 4135 3822 3056 4008 M3053 MULLIGHAN_MLL_SIGNATURE_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_2_UP.html The 'MLL signature 2': genes up-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to the AML cases with intact MLL and NPM1 [GeneID=4869]. 17597811 506/649 Arthur Liberzon 1.51700538099795e-07 7.27669247795767e-07 3645 3064.36363636364 3575 1.5170054845567e-08 746 1.62803977495766 -1.53433358805641 -1 3.96877045271941 3643 2016 4302 1990 746 4006 4072 3744 2257 3575 3357 4009 M1831 MATZUK_SPERMATOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATOCYTE.html Genes important for spermatocyte, based on mouse models with male reproductive defects. 18989307 90/225 Jessica Robertson 5.84341190394111e-06 7.57717147983573e-06 3575 2469.72727272727 3575 5.31220674969426e-07 200 1.37975464155542 1.46644055846633 1 2.79124446703606 886 3619 3696 3575 3575 200 618 1613 4297 3900 1188 4010 M1005 REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER.html Genes involved in Formation of incision complex in GG-NER 21/21 Reactome 4.77094531671322e-05 5.39632444162147e-05 2345 3318.27272727273 3576 4.33731707556699e-06 1513 0.94500242698859 1.00002126804956 1 1.57195222647135 2342 4052 3931 3576 4123 1962 1513 3055 4528 4429 2990 4011 M89 BIOCARTA_CDK5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CDK5_PATHWAY.html Phosphorylation of MEK1 by cdk5/p35 down regulates the MAP kinase pathway 15/15 BioCarta 1.11407732826301e-05 1.37008137729121e-05 4265 3446.63636363636 3577 1.01280269997915e-06 1551 1.73043947998477 2.59194977654037 1 3.3343807749505 3577 4065 2942 1551 3779 3146 4262 2766 4207 4264 3354 4012 M810 REACTOME_ELONGATION_ARREST_AND_RECOVERY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ELONGATION_ARREST_AND_RECOVERY.html Genes involved in Elongation arrest and recovery 34/37 Reactome 9.75810744283005e-05 0.000107236943259972 2545 3565.18181818182 3577 8.87140026444966e-06 2545 0.790786084421599 0.796001163555138 1 1.2124079237472 2545 3721 4010 3577 4248 2598 2844 3221 4481 4534 3438 4013 M17450 LIU_SOX4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_SOX4_TARGETS_UP.html Genes up-regulated in LNCaP cells (prostate cancer) by overexpression of SOX4 [GeneID=6659] and down-regulated by its RNAi knockdown. 16618720 164/194 Arthur Liberzon 1.31754804039602e-06 2.16006486650545e-06 3395 3576.45454545455 3577 1.19777166314278e-07 2767 1.59813399223435 -1.63978704646502 -1 3.59124749661247 3393 4428 3649 4016 2767 3523 3254 3722 3329 3577 3683 4014 M2215 WIERENGA_STAT5A_TARGETS_GROUP1 http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_GROUP1.html Genes up-regulated to their maximal levels in CD34+ [GeneID=947] cells by intermediate activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 187/243 Arthur Liberzon 2.16701289297811e-07 7.74284697566742e-07 4625 3031.18181818182 3577 1.97001191493652e-08 916 2.118146689967 2.19925689196791 1 5.15562559125935 4623 3577 1149 2575 1040 3791 4684 4047 2490 916 4451 4015 M12393 LIU_VAV3_PROSTATE_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_VAV3_PROSTATE_CARCINOGENESIS_DN.html Selected genes down-regulated in prostate tumors developed by transgenic mice overexpressing VAV3 [GeneID=10451] in prostate epithelium. 18676865 25/44 Jessica Robertson 6.44743445920077e-05 7.19090043653772e-05 3555 3594.72727272727 3578 5.86147583529302e-06 2657 1.87847557952488 1.51997845224318 1 3.07995937747118 3554 4290 2657 4010 4180 3591 2833 2989 4338 3522 3578 4016 M9011 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION.html Vasopressin-regulated water reabsorption 50/62 KEGG 9.3193664550088e-08 6.56798957981166e-07 4445 3388.90909090909 3579 8.47215168162203e-09 269 1.5948838604361 1.71804005251856 1 3.91546860679764 4444 3934 3377 3518 269 4190 2504 4316 3596 3579 3551 4017 M15137 TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_UP.html Genes up-regulated in ductal vs lobular carcinoma breast tumor cells. 17389037 27/38 Arthur Liberzon 5.91737954324866e-06 7.66256006697769e-06 4610 3209.36363636364 3580 5.37945041762792e-07 1643 1.90246789184113 -1.60333257509181 -1 3.86392645322361 4609 2331 2368 3687 3580 4250 3694 1896 1643 2766 4479 4018 M13879 VANHARANTA_UTERINE_FIBROID_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_DN.html Genes down-regulated in uterine fibroids vs normal myometrium samples. 15940248 98/122 Leona Saunders 1.48773062651574e-06 2.37393122283783e-06 4190 3324.27272727273 3580 1.35248330234675e-07 1717 2.06199778805664 2.33016245216962 1 4.61414206129381 4188 4176 1717 4569 2856 4279 3580 2258 3500 1776 3668 4019 M1156 KONG_E2F1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KONG_E2F1_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblast) at 16 h after serum stimulation and knockdown of E2F1 [GeneID=1869] by RNAi. 16909124 15/22 Arthur Liberzon 5.93547471321456e-06 7.67967122981709e-06 3830 3362.09090909091 3583 5.39590066077074e-07 2104 2.02714739062723 -1.97510009470573 -1 4.11964090956099 3826 3783 2396 2982 3583 3985 2621 3224 4545 2104 3934 4020 M18937 KEGG_NUCLEOTIDE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NUCLEOTIDE_EXCISION_REPAIR.html Nucleotide excision repair 45/47 KEGG 6.56893245929528e-05 7.31949037013072e-05 650 2745.54545454545 3584 5.97193509802689e-06 446 1.03490485902539 1.07913719811387 1 1.67116195489361 647 3693 4026 3584 4184 741 446 1817 4370 4450 2243 4021 M15247 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS.html Ubiquitin mediated proteolysis 140/154 KEGG 2.56220783945918e-06 3.70856209820526e-06 4120 3543.81818181818 3584 2.32928256683055e-07 2841 1.0915682811608 1.02132792504323 1 2.33401045206741 3207 3593 4120 4116 3180 2841 3167 3010 3584 4542 3622 4022 M15537 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP.html Genes from the turquoise module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphocholine (oxPAPC). 16912112 108/122 Arthur Liberzon 9.93166570227438e-07 1.74265658419089e-06 4280 3423.18181818182 3584 9.02879107801991e-08 2021 1.46745132772969 -1.23430474134012 -1 3.34852692324575 2900 4173 3584 4277 2563 2794 2021 3825 4003 3237 4278 4023 M1674 JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP.html Genes up-regulated in H460 cells (non-small cell lung carcinoma, NSCLC) after treatment with sodium butyrate [PubChem=5222465]. 15318170 44/58 John Newman 5.4971552039182e-06 7.18940774798944e-06 4055 3726.81818181818 3585 4.99742630885995e-07 3179 1.54002202853334 1.56991415943973 1 3.13540719961125 4055 3676 3208 3179 3539 4260 3462 4375 4360 3585 3296 4024 M1208 YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_DN http://www.broadinstitute.org/gsea/msigdb/cards/YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_DN.html Genes down-regulated in HUVEC cells (endothelium) by ETS1 [GeneID=2113] which were up-regulated by SP100 [GeneID=6672]. 15592518 148/206 Arthur Liberzon 3.62334878273645e-06 4.99188740645535e-06 4620 3320.36363636364 3586 3.29395886392846e-07 1018 2.00239598265243 2.22194035731559 1 4.21938060130134 4617 3586 1372 2706 3354 4460 4081 3911 3501 1018 3918 4025 M101 PID_HDAC_CLASSI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HDAC_CLASSI_PATHWAY.html Signaling events mediated by HDAC Class I 18832364 80/88 Pathway Interaction Database 1.18506387743709e-06 1.98844703217315e-06 3440 3600.54545454545 3587 1.07733137799134e-07 2691 1.16405788613038 -1.45048326353855 -1 2.61905328040612 3440 3347 4000 3587 2691 4101 4237 3465 3784 4088 2866 4026 M16533 SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_DN.html Genes bound by EWSR1-FLT1 [GeneID=2130;2321] fusion and down-regulated in STA-ET-7.2 cells (Ewing's sarcoma) after knockdown of EWSR1-FLT1 by RNAi. 15735734 25/32 Arthur Liberzon 2.36976950545071e-06 3.49104621277383e-06 3130 3644.63636363636 3587 2.15433823463121e-07 2504 1.43328400906365 -1.63705155185376 -1 3.0954679536808 4543 3162 3126 3912 3127 3587 3574 3969 4051 2504 4536 4027 M16584 LIU_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LIU_BREAST_CANCER.html Low abundance transcripts specific for breast cancer. 18332864 41/57 Jessica Robertson 3.84139214878577e-06 5.25851825471834e-06 3895 3601.18181818182 3588 3.49218077837124e-07 3054 1.31341695064038 -1.28901988318555 -1 2.73843408307354 3891 4235 3614 4271 3377 3054 3224 3170 3629 3588 3560 4028 M14973 SENESE_HDAC1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC1 [GeneID=3065] by RNAi. 17470557 590/714 Leona Saunders 1.85370330285092e-07 7.48271685670965e-07 4345 3151.72727272727 3589 1.85370345748065e-08 967 1.8528042637694 1.8961756138567 1 4.51456553240316 4343 2495 4307 1296 967 4667 3800 3589 2998 1890 4317 4029 M3026 CHUNG_BLISTER_CYTOTOXICITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHUNG_BLISTER_CYTOTOXICITY_UP.html Genes up-regulated in blister cells from patients with adverse drug reactions (ADR). 19029983 141/182 Jessica Robertson 1.39527606598986e-07 7.20206492018647e-07 3680 3410.81818181818 3590 1.26843286770961e-08 565 1.53703955410926 1.45619541234992 1 3.74690428508616 3677 3590 3842 4043 565 3153 3182 4412 3116 3578 4361 4030 M843 STEIN_ESRRA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS.html Genes regulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 752/981 Arthur Liberzon 3.69652411017777e-07 9.53941705852328e-07 3595 3652.27272727273 3592 3.69652472507098e-08 1728 1.56635488617859 -1.6550237510361 -1 3.74242978787214 3518 4394 4636 3592 1728 4508 4362 3591 2536 4438 2872 4031 M9809 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION.html Cytokine-cytokine receptor interaction 144/310 KEGG 3.08181880897067e-11 6.13763070816099e-10 4300 2772.72727272727 3593 2.80165346273985e-12 182 2.66731094619575 2.49726167818126 1 9.83158387782997 4300 1534 182 3831 1170 4666 3761 3860 3593 203 3400 4032 M1011 REACTOME_MEIOTIC_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_RECOMBINATION.html Genes involved in Meiotic Recombination 42/98 Reactome 0.000158059715890289 0.000170758035935491 1305 2690.18181818182 3593 1.43700975349411e-05 455 1.2396783583262 1.19837092934322 1 1.82831332781375 1304 3691 3593 4070 4326 455 503 1223 4511 3671 2245 4033 M1061 REACTOME_MEIOTIC_SYNAPSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_SYNAPSIS.html Genes involved in Meiotic Synapsis 47/198 Reactome 9.5340330866408e-05 0.000104896587806398 2100 2818.36363636364 3593 8.66767843951704e-06 344 1.33721989923094 1.42095998202782 1 2.08991205804408 2099 4523 3762 3593 4244 1052 986 1681 4541 4177 344 4034 M1355 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_DN.html Early prostate development genes (down-regulated at 6 h dihydrotestosterone [PubChem=10635]) which are also down-regulated in normal epithelium vs high grade prostatic intraepithelial neoplasia (PIN). 18794802 10/12 Jessica Robertson 1.27019127472976e-06 2.09699294044228e-06 3675 3075 3593 1.15472000735234e-07 577 2.30490513543287 2.57209027338994 1 5.2135270174792 3852 4096 2729 3673 2743 3802 3172 577 1914 3593 3674 4035 M1874 LUDWICZEK_TREATING_IRON_OVERLOAD http://www.broadinstitute.org/gsea/msigdb/cards/LUDWICZEK_TREATING_IRON_OVERLOAD.html Genes changed in liver in response to nifedipine [PubChem=4485] treatment of iron overload. 17293870 8/10 Jessica Robertson 0.0584024863221842 0.0589394345607675 3915 3465 3593 0.00599966604705697 1080 2.21733678084379 -2.22504453585171 -1 1.04642603474844 3913 2913 4591 3375 4696 3729 3593 2800 1080 3286 4139 4036 M2284 LINSLEY_MIR16_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LINSLEY_MIR16_TARGETS.html Transcripts down-regulated by overexpression of MIR16 family of microRNA molecules in DLD-1 and HCT116 (colon cancer) cells hypomorphic for DICER1 [GeneID=23405]. 17242205 289/325 Arthur Liberzon 9.7638464393844e-07 1.7253970495655e-06 3595 3620.36363636364 3593 8.87622797517412e-08 2388 1.34058219666918 1.58041734146849 1 3.05703314649287 3593 4695 4100 4685 2548 2388 3120 3554 3692 4505 2944 4037 M824 REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX.html Genes involved in Formation of transcription-coupled NER (TC-NER) repair complex 31/33 Reactome 0.000148096404482884 0.000160361328093418 2005 3301.81818181818 3595 1.34642158873793e-05 1339 0.701407303977642 0.752896258488774 1 1.02042497633183 2001 4016 4042 3595 4318 1884 1339 2835 4597 4589 3104 4038 M10237 RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP.html Genes up-regulated in anaplastic thyroid carcinoma (ATC) compared to normal thyroid tissue. 17406368 980/1173 Arthur Liberzon 5.58413958463313e-07 1.18659903470788e-06 2930 3540.18181818182 3596 5.5841409878513e-08 2148 1.66254905244061 1.79902473405549 1 3.91196300064683 2928 3545 4322 3267 2148 4001 4273 3596 3126 3967 3769 4039 M1380 DEN_INTERACT_WITH_LCA5 http://www.broadinstitute.org/gsea/msigdb/cards/DEN_INTERACT_WITH_LCA5.html Proteins shown to interact with LCA5 [GeneID=167691] in vivo. 17546029 36/41 Jessica Robertson 7.50706954267648e-05 8.31378888818231e-05 1740 3043.45454545455 3596 6.82484156270392e-06 1484 1.37284786282804 1.46616588708273 1 2.20266939417834 1738 4259 3899 3596 4214 2026 1851 1643 4604 4164 1484 4040 M1777 ZHANG_GATA6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_GATA6_TARGETS_UP.html Genes up-regulated after cre-lox knockout of GATA6 [GeneID=2627] in airway epithelium. 18536717 17/29 Jessica Robertson 9.56547530397988e-06 1.18875838427554e-05 3805 3073.36363636364 3596 8.69592444943408e-07 1390 2.74470110324602 3.251010322897 1 5.38614112772596 3802 2836 1790 3639 3741 3991 3900 2243 1390 2879 3596 4041 M1798 JONES_TCOF1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/JONES_TCOF1_TARGETS.html Genes up-regulated in E8.5 embryos with heterozygous knockout of TCOF1 [GeneID=6949] compared to wild type. 18246078 5/5 Jessica Robertson 5.63397995940063e-06 7.3398800464728e-06 4170 3210.45454545455 3598 5.63399424323018e-07 280 2.62886505822848 -2.38491683864428 -1 5.37810386125113 4170 2926 4562 3833 3598 4459 1459 2904 280 3257 3867 4042 M16169 ALCALA_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/ALCALA_APOPTOSIS.html Genes able to induce cell death in an expression cDNA library screen. 17621274 130/200 Jessica Robertson 1.60759837004451e-06 2.52507963614313e-06 3075 3556.36363636364 3599 1.46145413160045e-07 2473 1.11335559142629 -1.0552086626573 -1 2.45633812575087 3073 3599 4091 3275 2907 2750 4203 3863 4339 4547 2473 4043 M13720 KEGG_LYSINE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSINE_DEGRADATION.html Lysine degradation 47/50 KEGG 9.79162768452513e-06 1.21622322818312e-05 2475 3285.54545454545 3600 8.90151933162206e-07 2149 1.44686526994518 1.39268734776176 1 2.80986444844492 2474 3396 3600 4286 3743 2228 2510 3894 3781 4080 2149 4044 M514 REACTOME_SPRY_REGULATION_OF_FGF_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPRY_REGULATION_OF_FGF_SIGNALING.html Genes involved in Spry regulation of FGF signaling 21/24 Reactome 0.00182969276017222 0.00189888958399579 1660 2908.45454545455 3600 0.000166474204593067 307 0.705250080360917 -0.69258818985868 -1 0.721847084739836 1659 4598 3977 3600 4534 940 307 2368 4690 4427 893 4045 M2637 UEDA_CENTRAL_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/UEDA_CENTRAL_CLOCK.html Molecular timetable composed of 96 time-indicating genes (103 probes) in the central (suprachiasmatic nucleus (SCN)) clock. 15273285 121/147 Kate Stafford 1.58134175079857e-06 2.48963744622057e-06 4105 3689.72727272727 3600 1.43758444314095e-07 2899 1.63398911338415 1.77942296677802 1 3.63241734422998 4101 3874 3402 3585 2899 3060 3550 4598 4125 3600 3793 4046 M3977 WEBER_METHYLATED_ICP_IN_SPERM_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_ICP_IN_SPERM_UP.html Methylated germline-specific genes with intermediate-CpG-density promoters (ICP) in sperm. 17334365 8/27 Arthur Liberzon 8.19644469588543e-06 1.02973699666168e-05 4665 3562.72727272727 3600 8.1964749278099e-07 2594 1.85102250814476 -1.78178078062632 -1 3.66254055855448 4663 3245 4633 2702 3728 3600 2594 4247 3365 2669 3744 4047 M1785 POS_HISTAMINE_RESPONSE_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/POS_HISTAMINE_RESPONSE_NETWORK.html Genes corresponding to the histamine [PubChem=774] response network. 18339882 44/55 Jessica Robertson 4.73453675718647e-06 6.30203426224482e-06 3605 3436.72727272727 3602 4.30413358748597e-07 998 1.54059046745917 1.81804559602091 1 3.17202983519026 3602 3944 3203 4602 3476 3875 4346 998 3170 3795 2793 4048 M16161 LOPEZ_MESOTHELIOMA_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_UP.html Top genes associated with favorable survival after surgery of patients with epithelioid mesothelioma. 16540645 16/17 Arthur Liberzon 7.52204205524851e-07 1.43450660609184e-06 4435 3385.27272727273 3602 6.83822238828971e-08 2284 1.37087978316484 1.28247561431642 1 3.17146197114687 4431 2406 3060 3885 2329 4181 4005 2949 4106 2284 3602 4049 M2065 HOFFMAN_CLOCK_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMAN_CLOCK_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) upon knockdown of CLOCK [GeneID=9575] by RNAi that also belong to the highest confidence network (according to Ingenuity Pathway Analysis). 20124474 6/13 Jessica Robertson 0.000209453090585745 0.000224992851061611 4360 3596.45454545455 3602 2.09472834973681e-05 2123 3.74252918695655 -3.71327781669312 -1 5.44031993884317 4360 3251 4653 3295 4364 3602 3993 2177 4397 2123 3346 4050 M4791 BIOCARTA_EIF4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF4_PATHWAY.html Regulation of eIF4e and p70 S6 Kinase 35/39 BioCarta 0.000195855530710084 0.000210722157499795 2285 3203.72727272727 3603 1.78066335426741e-05 1578 0.929031457464639 -0.983131371606884 -1 1.32350125070581 2283 4256 3981 3603 4348 1916 1995 2372 4558 4351 1578 4051 M19849 HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN.html Genes down-regulated in T helper cells (defines as CD4+) isolated from patients with mucosis fungoides compared to those from normal control donors. 16914566 152/191 Arthur Liberzon 6.95434648485525e-07 1.36825824962554e-06 3020 3626.63636363636 3603 6.32213516651949e-08 2253 0.98183771099943 1.02949385041653 1 2.26534068975976 3019 3588 4137 4317 2253 3345 3375 3603 4110 4528 3618 4052 M6318 GRANDVAUX_IFN_RESPONSE_NOT_VIA_IRF3 http://www.broadinstitute.org/gsea/msigdb/cards/GRANDVAUX_IFN_RESPONSE_NOT_VIA_IRF3.html Genes up-regulated in Jurkat cells (T lymphocyte) by IFN1@, and IFNB1 [GeneID=3438;3456] but not by overexpression of a constitutively active form of IRF3 [GeneID=3661]. 11991981 21/27 Yujin Hoshida 6.25202023219091e-06 8.04512963357173e-06 4015 3531.90909090909 3603 5.68367090856715e-07 1358 1.28564068145566 1.39718061485689 1 2.58398247456191 4011 4039 3328 4256 3603 3227 3952 1358 4413 3407 3257 4053 M162 PID_RXR_VDR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RXR_VDR_PATHWAY.html RXR and RAR heterodimerization with other nuclear receptor 18832364 32/36 Pathway Interaction Database 4.18275945580992e-05 4.75496739677813e-05 1605 2831.72727272727 3604 3.80258089347334e-06 836 1.5598910777699 -1.36686845899363 -1 2.66181081254802 1603 3992 3604 4039 4101 1506 836 1179 3836 4146 2307 4054 M1030 REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1.html Genes involved in APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 69/82 Reactome 0.000165270762133551 0.000178425891415911 825 3025 3607 1.50257435533758e-05 824 0.952534919014857 1.06516672698328 1 1.38592816109087 824 3904 4077 3607 4331 1455 1112 2586 3965 4551 2863 4055 M2486 GUILLAUMOND_KLF10_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUILLAUMOND_KLF10_TARGETS_DN.html Genes down-regulated in the liver tissue from 10 week old male mice with KLF10 [GeneID=7071] compared to wild-type littermates. 20385766 32/42 Arthur Liberzon 5.14671860715198e-07 1.12935898771536e-06 4420 3409.27272727273 3608 4.67883619198613e-08 1880 2.17470479074513 -1.61327481406946 -1 5.15125405763433 4418 3977 2239 3327 1976 4310 4513 2787 1880 3608 4467 4056 M1182 LA_MEN1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LA_MEN1_TARGETS.html Genes up-regulated in cells expressing MEN1 [GeneID=4221]. 16449969 29/35 Arthur Liberzon 4.83904700412817e-06 6.42122627480601e-06 4580 3407.09090909091 3609 4.39914331633471e-07 2072 2.17955472868846 -1.54255803863038 -1 4.5012587157754 4579 3988 2072 4174 3490 4010 3609 3090 2465 2367 3634 4057 M11298 CAFFAREL_RESPONSE_TO_THC_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated THC (delta-9-tetrahydrocannabinol) [PubChem=6610319]. 18454173 47/71 Jessica Robertson 6.3334631238455e-06 8.13458736096948e-06 1515 2773.09090909091 3609 5.75771032453591e-07 268 1.18680844741831 -1.33861214181949 -1 2.3792028982593 1513 4517 3895 4526 3609 1009 716 2120 4398 3933 268 4058 M2835 PIEPOLI_LGI1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PIEPOLI_LGI1_TARGETS_DN.html Down-regulated genes in U87 cells (glioblastoma multiforme, GBM) engineered to stably express LGI1 [GeneID=9211]. 16533756 20/35 Arthur Liberzon 0.0274820230983431 0.0278897331808599 2300 3655.27272727273 3611 0.00253013184490034 2300 1.89196087398161 -2.15693109297137 -1 1.13278396303711 2300 4318 3474 3567 4704 3611 3306 2484 4483 4282 3679 4059 M2569 KLEIN_TARGETS_OF_BCR_ABL1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/KLEIN_TARGETS_OF_BCR_ABL1_FUSION.html Genes changed in pre-B lymphoblastic leukemia cells with BCR-ABL1 fusion [GeneID=613, 25] vs normal pre-B lymphocytes. 16205638 40/75 Arthur Liberzon 1.34570662783203e-07 7.20206492018647e-07 3970 2709.72727272727 3611 1.22336973649716e-08 501 2.63847525428296 -2.75439839898253 -1 6.46777562553902 3966 2716 987 3624 523 4710 3958 501 4103 1108 3611 4060 M12967 REACTOME_MRNA_3_END_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_3_END_PROCESSING.html Genes involved in mRNA 3'-end processing 44/71 Reactome 4.04550804165699e-05 4.60781803972515e-05 2205 3404.63636363636 3613 3.67780221372396e-06 1417 0.644117969122673 0.623719177412355 1 1.07328902863921 2201 4253 4107 3613 4093 1753 1417 3423 4664 4611 3316 4061 M1488 HANSON_HRAS_SIGNALING_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/HANSON_HRAS_SIGNALING_VIA_NFKB.html Genes changed by expression of activated form of HRas[GeneID=3265] in MEF cells (embryonic fibroblast) with or without p65/c-Rel complex [GeneID=5970;5966]. 15492243 27/36 Kevin Vogelsang 1.46241791672808e-06 2.34363276373068e-06 3760 3087 3613 1.32947171713633e-07 1288 2.57317639959264 -1.95460895106545 -1 5.77618615427779 3756 2768 1288 2363 2842 3613 3711 3995 3782 1524 4315 4062 M2585 SMIRNOV_RESPONSE_TO_IR_2HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_2HR_UP.html Genes up-regulated in B lymphocytes at 2 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 68/87 Itai Pashtan 0.000531064826241609 0.000560014740808846 2035 3548 3613 4.82902786334761e-05 2031 1.58130644720354 -1.54023481905737 -1 2.01791549869032 2031 4498 3613 4531 4445 2330 2708 3467 4424 3874 3107 4063 M1019 REACTOME_CLEAVAGE_OF_GROWING_TRANSCRIPT_IN_THE_TERMINATION_REGION_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLEAVAGE_OF_GROWING_TRANSCRIPT_IN_THE_TERMINATION_REGION_.html Genes involved in Cleavage of Growing Transcript in the Termination Region 53/83 Reactome 3.27145044424957e-05 3.76065418822649e-05 1430 3035.81818181818 3614 2.97409008407325e-06 681 0.698925647713985 0.698622353922912 1 1.19367262269848 1430 3951 4114 3614 4053 1054 681 2533 4630 4599 2735 4064 M235 PID_TCR_CALCIUM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_CALCIUM_PATHWAY.html Calcium signaling in the CD4+ TCR pathway 18832364 24/34 Pathway Interaction Database 2.74793704357388e-06 3.93515256239949e-06 3615 3757.81818181818 3615 2.49812770538585e-07 3005 1.149986893378 1.30453479193587 1 2.449688386208 3615 4022 3464 4466 3222 3503 3528 4359 4443 3709 3005 4065 M725 REACTOME_TRANSPORT_OF_MATURE_TRANSCRIPT_TO_CYTOPLASM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_MATURE_TRANSCRIPT_TO_CYTOPLASM.html Genes involved in Transport of Mature Transcript to Cytoplasm 63/92 Reactome 3.44022180585702e-05 3.94335754565978e-05 1245 2992.09090909091 3616 3.12752327551125e-06 580 0.725475589492971 0.694666316978523 1 1.23490613680783 1241 4222 4128 3616 4068 974 580 2365 4607 4625 2487 4066 M134 PID_TCR_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_RAS_PATHWAY.html Ras signaling in the CD4+ TCR pathway 18832364 15/17 Pathway Interaction Database 2.08223139181492e-07 7.70063333918279e-07 3455 3217.09090909091 3617 1.89293780808332e-08 991 0.852643993867096 -0.818396257968612 -1 2.04627728437623 3452 3774 3617 2251 991 3768 2037 3809 4615 4057 3017 4067 M7775 EHLERS_ANEUPLOIDY_UP http://www.broadinstitute.org/gsea/msigdb/cards/EHLERS_ANEUPLOIDY_UP.html Up-regulated genes in the expression signature of aneuploidy in uveal melanoma tumors: low vs high aneuploidy. 18172260 44/54 Jessica Robertson 0.000105230746216457 0.000115321365716666 2020 3251 3617 9.56688908792356e-06 1312 1.483036919764 1.76764916661683 1 2.2987208625757 2019 4246 3773 4294 4263 2880 2982 1312 3617 4286 2089 4068 M2044 KEGG_SPLICEOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPLICEOSOME.html Spliceosome 141/188 KEGG 0.000226782661304836 0.0002433865760252 950 3202.09090909091 3619 2.06187311020484e-05 898 0.691341830346039 0.703540934980225 1 0.954685011327618 948 4438 4156 3619 4362 1794 898 2642 4645 4675 3046 4069 M911 REACTOME_PASSIVE_TRANSPORT_BY_AQUAPORINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PASSIVE_TRANSPORT_BY_AQUAPORINS.html Genes involved in Passive Transport by Aquaporins 4/10 Reactome 3.98639661484209e-05 4.54268276727539e-05 4615 3516.63636363636 3620 3.98646812775846e-06 903 5.38448362032062 -5.49119407338666 -1 9.35376105286278 4614 2929 4252 3620 4111 4600 4330 3266 903 2991 3067 4070 M12570 DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN.html Genes down-regulated in T-PLL cells (T-cell prolymphocytic leukemia) bearing the inv(14)/t(14:14) chromosomal aberration. 17713554 379/534 Leona Saunders 9.9274230956458e-07 1.74255994836178e-06 3305 3615.72727272727 3620 9.02493415942144e-08 2562 1.79821786214356 -1.57417843777032 -1 4.11458764673116 3305 4688 3400 4250 2562 3742 3164 3779 2848 3620 4415 4071 M603 REACTOME_YAP1_AND_WWTR1_TAZ_STIMULATED_GENE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_YAP1_AND_WWTR1_TAZ_STIMULATED_GENE_EXPRESSION.html Genes involved in YAP1- and WWTR1 (TAZ)-stimulated gene expression 26/30 Reactome 6.48743256258662e-07 1.30791290081906e-06 3370 3578.18181818182 3622 5.89766770511174e-08 2187 1.58332390477844 1.52654876255101 1 3.6962439360551 3368 4001 3316 3430 2187 3997 4652 4019 3026 3622 3742 4072 M982 REACTOME_REGULATION_OF_IFNA_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_IFNA_SIGNALING.html Genes involved in Regulation of IFNA signaling 16/31 Reactome 0.0235033320685471 0.0238879688551986 3615 3675 3624 0.00215984062827396 2817 1.42592976878823 -0.92090961199252 -1 0.880002875293361 3611 4319 3340 3504 4614 3624 2817 3046 4044 3850 3656 4073 M206 PID_PDGFRA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PDGFRA_PATHWAY.html PDGFR-alpha signaling pathway 18832364 31/35 Pathway Interaction Database 1.94217873386594e-06 2.94761531313416e-06 4060 3375.72727272727 3625 1.76561858949089e-07 2236 1.50313854928885 -1.24926601635117 -1 3.29319360600011 4058 3144 3252 2236 3021 3634 2486 3820 3625 3768 4089 4074 M8941 HEDENFALK_BREAST_CANCER_BRACX_DN http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_BRACX_DN.html Down-regulated genes distinguishing between two groups of non-BRCA1/BRCA2 [GeneID=672;675] breast tumors (BRACx): group A vs group B. 12610208 25/27 John Newman 8.71949059702368e-08 6.50173706444736e-07 3925 3297.72727272727 3625 7.92680994782947e-09 223 1.16174080831642 0.818799515602058 1 2.84056251511405 3923 3457 3625 4406 223 4501 3911 3239 2200 4165 2625 4075 M1179 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_6 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_6.html Amplification hot spot 6: colocolized fragile sites and cancer genes in the 17p13-p11.1 region. 16751803 9/9 Arthur Liberzon 6.02470073352782e-06 7.78231731315033e-06 4720 3308.45454545455 3626 6.02471706724866e-07 96 3.19291961112265 -1.29981448259462 -1 6.51013565557663 4719 3240 4373 2910 3626 4245 4122 1652 96 2895 4515 4076 M18201 GOTTWEIN_TARGETS_OF_KSHV_MIR_K12_11 http://www.broadinstitute.org/gsea/msigdb/cards/GOTTWEIN_TARGETS_OF_KSHV_MIR_K12_11.html Genes down-regulated in BJAB cell line (B lymphocyte) after expression of the viral microRNA miR-K12-11 which functions as an ortholog of cellular MIR155 [GeneID=406947]. 18075594 80/94 Jessica Robertson 1.77584602213406e-06 2.74010893248538e-06 4385 3743 3628 1.61440677782132e-07 2965 1.59033801193815 1.56729663891797 1 3.5074161171078 4385 3628 3526 3517 2965 3914 4700 4231 3841 3291 3175 4077 M6786 REACTOME_NUCLEOTIDE_LIKE_PURINERGIC_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEOTIDE_LIKE_PURINERGIC_RECEPTORS.html Genes involved in Nucleotide-like (purinergic) receptors 8/18 Reactome 1.784945169955e-06 2.74786079653869e-06 2990 3351.45454545455 3630 1.78494660366979e-07 1658 2.97504337853455 2.93906324514906 1 6.60341843307438 2990 3244 4239 3630 3026 3690 4265 4284 1658 2065 3775 4078 M2037 KAMMINGA_SENESCENCE http://www.broadinstitute.org/gsea/msigdb/cards/KAMMINGA_SENESCENCE.html Genes down-regulated on serial passage of MEF cells (embryonic fibroblast). 16293602 42/47 Arthur Liberzon 1.40318846442056e-06 2.26972225910385e-06 3890 3656.81818181818 3630 1.27562669035738e-07 2808 1.36207161006684 -1.28895413756861 -1 3.04160839458458 3890 3100 3398 4412 2808 3261 3630 4477 4231 3204 3814 4079 M1470 SESTO_RESPONSE_TO_UV_C5 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C5.html Cluster 5: genes changed in primary keratinocytes by UVB irradiation. 11867738 77/82 John Newman 1.49936445077297e-07 7.26289540930751e-07 4260 3202.54545454545 3631 1.36305868450823e-08 633 1.42224244574323 1.52509832669678 1 3.4612322643939 4258 3631 3662 2522 633 3957 3356 2150 2898 3861 4300 4080 M4697 ZHAN_MULTIPLE_MYELOMA_HP_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_HP_DN.html Top 50 down-regulated genes in cluster HP of multiple myeloma samples characterized by a hyperploid signature. 16728703 47/60 Arthur Liberzon 1.22664569170338e-05 1.49606399608267e-05 3305 3531.72727272727 3631 1.11513866465348e-06 2694 1.56415814755031 1.74032373112064 1 2.98513350679441 3304 2694 3204 3920 3815 3749 4268 3460 3631 2889 3915 4081 M4170 ST_INTERFERON_GAMMA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTERFERON_GAMMA_PATHWAY.html Interferon gamma pathway. 11/15 Signaling Transduction KE 1.6169918457876e-05 1.93220291446012e-05 3635 3120.45454545455 3632 1.47000339158184e-06 1161 1.96438974064005 -0.808095383098739 -1 3.6739916317685 3632 3795 2855 2664 3893 2611 1161 4307 1795 3716 3896 4082 M1658 LEE_AGING_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_MUSCLE_UP.html Upregulated in the gastrocnemius muscle of aged adult mice (30-month) vs young adult (5-month) 10464095 70/85 John Newman 6.46084596820434e-06 8.28448600106615e-06 3180 3608 3635 5.87351358378174e-07 2148 2.04726730730708 2.10468778549035 1 4.13391942600085 4006 4194 2148 3177 3615 3635 3920 4658 3954 3180 3201 4083 M5126 PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN.html Down-regulated genes in head and neck cancer compared to cervical carcinoma samples. 17510386 38/83 Arthur Liberzon 2.44791643345585e-06 3.58157643084674e-06 3635 3123.45454545455 3635 2.22538105202771e-07 1018 2.90926621867289 3.10510123236861 1 6.32167040716558 3635 2722 1018 4563 3147 4659 4130 1060 3770 1714 3940 4084 M1262 REACTOME_GRB2_SOS_PROVIDES_LINKAGE_TO_MAPK_SIGNALING_FOR_INTERGRINS_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GRB2_SOS_PROVIDES_LINKAGE_TO_MAPK_SIGNALING_FOR_INTERGRINS_.html Genes involved in GRB2:SOS provides linkage to MAPK signaling for Intergrins 20/22 Reactome 0.208961335310296 0.209850532481829 2785 3560.63636363636 3637 0.0210844066908012 1609 2.02350878361373 -1.85796484937963 -1 0.501777240898388 2781 4585 2901 4049 4709 3597 1609 3421 3867 3637 4011 4085 M1866 WANG_TUMOR_INVASIVENESS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TUMOR_INVASIVENESS_DN.html Down-regulated genes in the subpopulation of invasive PyMT cells (breast cancer) compared to the general population of PyMT cells. 17440055 292/318 Jessica Robertson 2.93878720397475e-07 8.6694222517255e-07 4325 3227.90909090909 3637 2.67162508776514e-08 1311 1.60591408032768 1.72242156921494 1 3.86503342172494 4323 1311 3627 2228 1366 4183 4680 3637 1772 4134 4246 4086 M11234 THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN http://www.broadinstitute.org/gsea/msigdb/cards/THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN.html Genes down-regulated in polymorphonuclear neutrophilic granulocytes (PMNs) attracted to skin wounds. 15187151 309/390 Kevin Vogelsang 3.0678516792773e-07 8.82385976514091e-07 3640 3417.90909090909 3638 2.78895646098414e-08 1412 1.35798768437866 1.4135195394752 1 3.25642373685881 3638 2518 4080 3261 1412 3073 4016 4419 3158 4119 3903 4087 M5490 WELCSH_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WELCSH_BRCA1_TARGETS_UP.html Up-regulated by induction of exogenous BRCA1 in EcR-293 cells 12032322 322/395 John Newman 7.07635377356405e-07 1.3784725468932e-06 4600 3333.54545454545 3638 6.43305095426505e-08 915 1.65204616795248 1.9322447464935 1 3.84368584174648 4599 2515 3638 915 2277 4467 4609 2958 2492 4093 4106 4088 M1585 FERRARI_RESPONSE_TO_FENRETINIDE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FERRARI_RESPONSE_TO_FENRETINIDE_DN.html Genes down-regulated in HUVEC cells (umbilical vein endothelium) by fenretinide [PubChem=1744]. 15958647 11/12 Arthur Liberzon 0.00012630093878688 0.000137549707215984 2995 3390.18181818182 3640 1.14825627496075e-05 534 1.42050792264339 1.42050792264339 1 2.1559596853069 2993 4634 3227 2537 4685 3709 2557 534 4712 4064 3640 4089 M28 PID_IL4_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL4_2PATHWAY.html IL4-mediated signaling events 18832364 76/106 Pathway Interaction Database 2.87998844656771e-06 4.08658460128947e-06 4435 3316.54545454545 3642 2.61817474247835e-07 1222 2.04020346310191 -1.63740998438703 -1 4.37129623071492 4435 2167 1222 2952 3253 4643 3642 4607 4043 1632 3886 4090 M8455 HOOI_ST7_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOOI_ST7_TARGETS_UP.html Genes up-regulated in PC-3 cells (prostate cancer) stably expressing ST7 [GeneID=7982] off a plasmid vector. 16474848 125/167 Leona Saunders 1.99982491245135e-07 7.65527859584926e-07 4440 3022.09090909091 3642 1.81802281294339e-08 936 2.37409062613932 -1.71611054275091 -1 5.78936239704715 4436 2115 1135 3642 936 4397 4696 4004 1800 2144 3938 4091 M7248 RASHI_RESPONSE_TO_IONIZING_RADIATION_3 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_3.html Cluster 3: genes activated by ionizing radiation regardless of ATM [GeneID=472] status. 16314843 66/83 Arthur Liberzon 6.84384546307642e-07 1.35102260918949e-06 3740 3534.18181818182 3643 6.22167962917034e-08 2243 1.68318340228982 -1.29019553559584 -1 3.92298664571118 3736 3643 3301 3566 2243 3561 3649 3906 2441 4140 4690 4092 M2563 HOLLEMAN_DAUNORUBICIN_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_ALL_UP.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 9/11 Arthur Liberzon 0.000153030171300966 0.000165438023028071 4145 3367.09090909091 3643 1.53040710527431e-05 285 1.87516167401004 -2.37539933287657 -1 2.80155841638606 4144 2908 4713 2844 4335 4214 4699 1788 285 3465 3643 4093 M541 REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY.html Genes involved in Resolution of AP sites via the multiple-nucleotide patch replacement pathway 17/19 Reactome 0.000466020997712928 0.000492746216219763 1960 3261 3644 4.23745221060297e-05 726 1.05766327452278 1.22383216838915 1 1.35676082575525 1958 4071 3644 4047 4432 1631 726 3487 4632 3943 3300 4094 M1078 REACTOME_CREATION_OF_C4_AND_C2_ACTIVATORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CREATION_OF_C4_AND_C2_ACTIVATORS.html Genes involved in Creation of C4 and C2 activators 7/11 Reactome 0.00636720904252067 0.00653331014797773 2375 3510.18181818182 3644 0.000638552656031937 2124 1.7368116768303 1.7368116768303 1 1.47604646205576 2374 4647 4263 4608 4569 2233 2500 2124 4705 3644 2945 4095 M2577 NUTT_GBM_VS_AO_GLIOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUTT_GBM_VS_AO_GLIOMA_DN.html Top 50 marker genes for anaplastic oligodendroglioma (AO), a class of high grade glioma. 12670911 65/82 Arthur Liberzon 7.15780747017578e-08 6.06397110828564e-07 2740 3155.18181818182 3644 6.50709791187141e-09 146 1.40992776896359 -1.21808518417329 -1 3.47525690863674 2739 3644 3634 4037 146 2734 2404 3810 3653 4116 3790 4096 M1966 MIKKELSEN_MEF_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing tri-methylation mark at H3K4 (H3K4me3) in MEF cells (embryonic fibroblasts). 18509334 170/230 Jessica Robertson 7.01300385222756e-07 1.37329085443823e-06 4565 3146.45454545455 3644 6.37546007980377e-08 588 2.36205856674025 2.81902831434139 1 5.51867438134641 4563 2972 588 3644 2263 4712 3712 3891 2828 854 4584 4097 M14766 REACTOME_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTRINSIC_PATHWAY.html Genes involved in Intrinsic Pathway 10/23 Reactome 6.91276108256721e-05 7.6808456472969e-05 1725 3217.54545454545 3646 6.28452572947441e-06 1094 1.70743927796155 1.70743927796155 1 2.77531500410486 1723 4356 2820 4430 4202 1498 1094 3646 4587 3986 3051 4098 M14050 KORKOLA_CHORIOCARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CHORIOCARCINOMA_UP.html Genes from the 12p region that were up-regulated in choriocarcinoma cells compared to normal testis. 16424014 7/17 Arthur Liberzon 0.0160737776549758 0.0163791516691464 2950 3216.81818181818 3646 0.00161912400537529 719 3.11212171399934 4.3971907118599 1 2.18491285610421 2946 4642 4275 3728 4714 2596 1972 4577 719 3646 1570 4099 M1081 REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21.html Genes involved in SCF(Skp2)-mediated degradation of p27/p21 57/69 Reactome 0.015650916196913 0.0159620407194099 1740 3415.36363636364 3647 0.00143303448587461 1737 0.90454018661415 1.02887852836988 1 0.603627824796769 1737 4219 4076 3270 4596 2211 1878 3292 4048 4595 3647 4100 M1379 HE_PTEN_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HE_PTEN_TARGETS_DN.html Genes down-regulated in the intestine after the tissue specific knockout of PTEN [GeneID=5728] by Cre-lox. 17237784 7/8 Jessica Robertson 0.0129610460790526 0.0132358583931476 3200 3389.90909090909 3648 0.00130372674247941 961 1.31641188922838 1.57731857601679 1 0.944326751763018 3197 3814 4447 4214 4608 3020 961 2215 4536 3648 2629 4101 M2536 ABRAMSON_INTERACT_WITH_AIRE http://www.broadinstitute.org/gsea/msigdb/cards/ABRAMSON_INTERACT_WITH_AIRE.html Proteins interacting with AIRE [GeneID=326], based on massspectroscopy analysis of co-immunoprecipitates in 293T cells (embryonic kidney). 20085707 63/101 Arthur Liberzon 2.0853785261154e-05 2.44728658460087e-05 860 2657.45454545455 3648 1.89581663060619e-06 555 0.976460933600276 1.04098952393663 1 1.76080388606248 859 3648 4035 4104 3967 725 555 1067 4272 4311 1689 4102 M7641 ZIRN_TRETINOIN_RESPONSE_WT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_WT1_DN.html Genes down-regulated in MZ128 cells (Wilms tumor with mutated WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 25/46 Leona Saunders 3.92928956527219e-07 9.79209711146668e-07 4215 3096.90909090909 3649 3.57208206096316e-08 751 2.6876629778407 2.51418826730244 1 6.44507491086834 4215 4555 1939 3676 1688 3649 4240 2071 751 3518 3764 4103 M9174 ST_STAT3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_STAT3_PATHWAY.html STAT3 Pathway 17/19 Signaling Transduction KE 0.0218164383090232 0.0221925837971098 2765 3385.72727272727 3650 0.0020032576745464 1002 1.93334502085872 -1.29611881855517 -1 1.2358146951081 2765 3773 3027 3186 4611 2626 1002 3745 3650 4156 4702 4104 M530 REACTOME_NEGATIVE_REGULATION_OF_FGFR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEGATIVE_REGULATION_OF_FGFR_SIGNALING.html Genes involved in Negative regulation of FGFR signaling 29/49 Reactome 0.000420391155817817 0.000445397588206531 3145 3454.81818181818 3650 3.82246825957151e-05 1284 1.23027551208098 -0.643147676384934 -1 1.60806060905718 3141 4554 3650 3032 4421 2155 1284 4213 3949 4292 3312 4105 M15132 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_UP.html Genes up-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 13/14 Arthur Liberzon 7.03403549328736e-06 8.95137436730017e-06 3705 3380.81818181818 3650 6.39459816657396e-07 1349 0.967816014575029 -0.748957758186492 -1 1.91478066524677 3703 3502 3666 4420 3650 2653 1349 2387 4494 3911 3454 4106 M13844 GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN.html Genes down-regulated in the A673 cells (Ewing sarcoma) after double knockdown of both FLI1 and DAX1 [GeneID=2313;190] by RNAi. 18591936 215/270 Jessica Robertson 7.05742910774515e-06 8.97872382440892e-06 2500 3394.54545454545 3651 6.41586522502836e-07 2076 1.35404816976091 1.45706532483765 1 2.69817086606222 2500 4416 4060 4549 3651 2347 2076 2345 4068 4285 3043 4107 M13059 ZHAN_V2_LATE_DIFFERENTIATION_GENES http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_V2_LATE_DIFFERENTIATION_GENES.html The v2LDG set: 50 most variable late differentiation genes (LDG) with similar expression patterns in bone marrow plasma cells (BPC) and multiple myeloma (MM) samples. 12393520 58/77 Kevin Vogelsang 4.0118972556418e-07 9.90902932842976e-07 4650 3443.72727272727 3651 3.64717998840675e-08 1711 1.7834158026622 1.4982668897448 1 4.25613805022651 4649 3651 2973 3917 1711 3594 4070 2269 2943 4000 4104 4108 M12618 KESHELAVA_MULTIPLE_DRUG_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/KESHELAVA_MULTIPLE_DRUG_RESISTANCE.html Genes up-regulated in multiple drug resistant neuroblastoma cell lines. 17623797 105/144 Jessica Robertson 3.90166305346934e-07 9.76357383103197e-07 4240 3392.09090909091 3651 3.54696704129355e-08 1679 1.52772123010789 -1.30766881969272 -1 3.6426924223023 4240 2132 3651 3452 1679 4312 4231 3105 2264 3676 4571 4109 M287 BIOCARTA_ERK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK_PATHWAY.html Erk1/Erk2 Mapk Signaling pathway 49/54 BioCarta 6.50093939405504e-07 1.30791290081906e-06 4310 3482 3652 5.90994665005957e-08 917 1.38464930092912 -1.28393997250843 -1 3.2261626641592 4307 3380 3516 917 2191 4561 3998 4263 3286 4231 3652 4110 M4090 BOYAULT_LIVER_CANCER_SUBCLASS_G3_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G3_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G3, defined by unsupervised clustering. 17187432 57/77 Yujin Hoshida 5.8714709475531e-07 1.22354714668656e-06 3950 3341.36363636364 3652 5.33770228596497e-08 2105 2.08847942246868 -2.22442567089466 -1 4.91580762440187 3950 3652 2142 4144 2105 4202 3700 4324 3085 2804 2647 4111 M3293 REACTOME_SHC_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_MEDIATED_SIGNALLING.html Genes involved in SHC-mediated signalling 19/20 Reactome 9.27734388284079e-06 1.15538425137226e-05 3730 3236 3656 8.43398455035843e-07 678 1.06501106300758 -0.488045335896415 -1 2.06462971032365 3729 3475 3656 678 3733 3940 4469 2157 2596 4385 2778 4112 M3996 JIANG_HYPOXIA_NORMAL http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_HYPOXIA_NORMAL.html Genes up-regulated in RPTEC cells (normal kidney) by hypoxia. 12692265 410/525 John Newman 2.02876163442319e-07 7.65527859584926e-07 3820 3166.18181818182 3656 1.84432892864399e-08 961 1.72930914102579 -1.4645816441886 -1 4.20343442756672 3818 4132 3052 3742 961 2892 2774 3656 2140 3884 3777 4113 M2592 ZEMBUTSU_SENSITIVITY_TO_MITOMYCIN http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_MITOMYCIN.html Top genes associated with chemosensitivity to mitomycin [PubChem=5746] across 85 tumor xenografts. 11809704 21/30 Arthur Liberzon 8.60206656103973e-07 1.57310167253419e-06 3865 3186 3656 7.8200635677051e-08 1882 2.29757067815741 -1.49032790155649 -1 5.31212946226607 3865 1882 1912 4352 2453 3990 2880 3803 3656 2304 3949 4114 M623 REACTOME_NGF_SIGNALLING_VIA_TRKA_FROM_THE_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NGF_SIGNALLING_VIA_TRKA_FROM_THE_PLASMA_MEMBRANE.html Genes involved in NGF signalling via TRKA from the plasma membrane 156/169 Reactome 1.10789970862026e-07 7.03739764799127e-07 4535 3209.27272727273 3657 1.00718160401188e-08 355 1.50467700393381 -1.2130863135244 -1 3.67303766052185 4534 2978 3624 912 355 4478 3657 4616 1909 4149 4090 4115 M1742 MARSON_BOUND_BY_FOXP3_STIMULATED http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_BOUND_BY_FOXP3_STIMULATED.html Genes with promoters bound by FOXP3 [GeneID=50943] in hybridoma cells stimulated by PMA [PubChem=4792] and ionomycin [PubChem=3733]. 17237765 1186/1510 Jessica Robertson 2.11382978544391e-07 7.70763712250053e-07 2940 3638 3657 2.11382998651637e-08 1112 1.44803298993448 -1.32869359887303 -1 3.5098734986378 2940 4387 4518 4692 1112 3633 3038 4037 3433 4571 3657 4116 M12242 PENG_GLUCOSE_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUCOSE_DEPRIVATION_UP.html Genes up-regulated in BJAB cells (B-lymphoma) after glucose [PubChem=206] deprivation. 12101249 51/80 Broad Institute 1.39429895312524e-06 2.25999006138431e-06 4700 3383.81818181818 3658 1.26754530617637e-07 1059 2.00337778610411 -1.64495390039806 -1 4.49875596901389 4696 2678 2378 3203 2801 3927 4366 4001 1059 3658 4455 4117 M5370 FONTAINE_FOLLICULAR_THYROID_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_FOLLICULAR_THYROID_ADENOMA_DN.html Genes down-regulated in follicular thyroid adenoma (FTA) compared to other thyroid tumors. 17968324 87/119 Arthur Liberzon 4.86195293780836e-07 1.09643659180389e-06 3740 3266.45454545455 3658 4.41995819299081e-08 1918 2.07914753593998 1.93061681014768 1 4.93345089376612 3738 4184 2130 4150 1918 4264 3860 3658 2483 2784 2762 4118 M17905 ELVIDGE_HIF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) after knockdown of HIF1A [GeneID=3091] by RNAi. 16565084 83/93 Arthur Liberzon 1.60099124022286e-06 2.51553883284018e-06 4150 3691.72727272727 3659 1.45544764118424e-07 2906 1.53522636661641 -1.10089543816219 -1 3.40706457243993 4149 3623 3659 4613 2906 3959 3006 2997 3240 3860 4597 4119 M1070 REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION.html Genes involved in Antigen processing: Ubiquitination & Proteasome degradation 198/234 Reactome 7.16385604879575e-07 1.39035364104918e-06 3125 3708.63636363636 3660 6.51259852869269e-08 2285 1.05372127000884 1.11749939769484 1 2.43190886869978 3123 4709 4150 4558 2285 2788 3181 4311 3394 4636 3660 4120 M10695 BROWNE_HCMV_INFECTION_8HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_8HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 8 h time point that were not up-regulated at the previous time point, 6 h. 11711622 165/217 John Newman 2.45783877028704e-06 3.59052893709527e-06 4465 3485.54545454545 3660 2.23440137835221e-07 2027 1.81430770759963 1.82777159328663 1 3.92276415354713 4461 2977 2280 2913 3152 4075 4606 3816 3660 2027 4374 4121 M1201 TERAMOTO_OPN_TARGETS_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_5.html Cluster 5: genes whose up-regulation peaked 5 days after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 7/8 Arthur Liberzon 0.000366106261373208 0.000389106407043805 3005 3244.18181818182 3662 3.66166590569622e-05 607 0.905046009881859 -0.575812454433725 -1 1.191091995819 3004 2477 4387 4180 4416 1769 607 3662 4409 4094 2681 4122 M2068 ONGUSAHA_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONGUSAHA_BRCA1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) lacking TP53 and BRCA1 [GeneID=7157;672] by expression of BRCA1. 12802282 26/28 Arthur Liberzon 7.37023766178459e-06 9.35148434506001e-06 2250 3597.27272727273 3662 6.70023850272068e-07 2248 1.87651132564626 -1.34598635909333 -1 3.74524259291379 2248 4019 3219 4622 3662 3365 3291 3082 4315 4050 3697 4123 M10960 REACTOME_P2Y_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P2Y_RECEPTORS.html Genes involved in P2Y receptors 5/14 Reactome 1.56855759533261e-07 7.31580222329043e-07 4240 3097.54545454545 3663 1.5685577060494e-08 222 3.86170375276026 -3.02901357861279 -1 9.47894288705558 4551 2486 4237 3054 790 3885 3663 4236 222 2493 4456 4124 M2480 ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP.html Genes up-regulated in normal tissue adjacent to liver tumor, compared to the normal liver samples. 18413731 260/382 Jessica Robertson 7.5144924543626e-07 1.43364609476926e-06 1785 3288.90909090909 3663 6.83135911006616e-08 1785 1.72664608024734 -1.60866265838844 -1 4.00767598777869 1785 4697 3663 4114 2328 2406 2423 3962 3693 3953 3154 4125 M6438 WONG_IFNA2_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WONG_IFNA2_RESISTANCE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) cell lines resistant to IFNA2 [GeneID=3440]. 15709204 37/93 Yujin Hoshida 3.19591699004172e-07 8.98528442785416e-07 2890 3167.18181818182 3664 2.90537950391758e-08 1178 1.12891573717114 1.0309116822365 1 2.69509937912566 2887 3962 3664 3980 1450 2129 1178 4372 3673 4304 3240 4126 M5489 BIOCARTA_IL6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL6_PATHWAY.html IL 6 signaling pathway 34/36 BioCarta 2.591203643477e-06 3.74424312717366e-06 2640 3383.63636363636 3665 2.35564245041189e-07 1434 0.954592893861476 -0.879125415088155 -1 2.03325191827067 2636 4544 3888 2255 3185 2809 1434 3768 4504 4532 3665 4127 M3254 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FLI1 http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FLI1.html Genes whose expression is coregulated with that of FLI1 [GeneID=2313] in hematopoietic stem cells (HSC). 15711547 7/9 Jean Junior 0.000203528422959854 0.000218827826052508 3670 3362.90909090909 3666 2.03547066081551e-05 695 1.22258969261257 1.14231093367783 1 1.74945640725966 3666 2474 4479 3380 4357 1965 695 4089 4282 3067 4538 4128 M2111 KIM_ALL_DISORDERS_CALB1_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_CALB1_CORR_DN.html Genes whose expression significantly and negatively correlated with the density of CALB1-positive [GeneID=793] GABAergic interneurons in the BA9 brain region across all subjects with psychiatric disorders. 18762803 24/82 Jessica Robertson 7.3949499722193e-06 9.38031815879471e-06 4065 3408 3666 6.72270439025823e-07 1384 2.8291660355793 -2.28154704107321 -1 5.67048358638761 4063 3174 1384 3666 3663 4655 4427 4413 2260 1721 4062 4129 M1442 STONER_ESOPHAGEAL_CARCINOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STONER_ESOPHAGEAL_CARCINOGENESIS_UP.html Genes up-regulated in esophagus by the carcinogen NMBA [PubChem=13643] and brought back to normal by a diet with PEITC [PubChem=16741] or black raspberries. 18676871 48/57 Jessica Robertson 2.2599353667413e-06 3.36282942339816e-06 3670 3161 3667 2.05448880749838e-07 618 2.10463349248277 -1.39006518668495 -1 4.58257560559967 4139 3667 2409 3373 3094 4528 4034 1415 618 3825 3669 4130 M23 PID_WNT_NONCANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_NONCANONICAL_PATHWAY.html Noncanonical Wnt signaling pathway 18832364 48/51 Pathway Interaction Database 4.12442640290049e-05 4.69091388474466e-05 3440 3623.18181818182 3668 3.74954884288326e-06 2522 1.57287353871783 -1.34000987445056 -1 2.68810640104495 3437 3942 3557 3562 4099 2522 2596 4065 3727 3668 4680 4131 M30 PID_HDAC_CLASSII_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HDAC_CLASSII_PATHWAY.html Signaling events mediated by HDAC Class II 18832364 50/63 Pathway Interaction Database 1.13127426080632e-05 1.38943911293413e-05 3690 3512.36363636364 3668 1.02843643457875e-06 1561 1.83338672162851 2.2416256232234 1 3.53123384922699 3688 3940 3312 1561 3785 3883 3612 4175 3668 3384 3628 4132 M806 REACTOME_POST_TRANSLATIONAL_MODIFICATION_SYNTHESIS_OF_GPI_ANCHORED_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_TRANSLATIONAL_MODIFICATION_SYNTHESIS_OF_GPI_ANCHORED_PROTEINS.html Genes involved in Post-translational modification: synthesis of GPI-anchored proteins 27/27 Reactome 0.0187679339782189 0.0191079914532341 3675 3690 3673 0.00172090723976384 2391 1.03486440097864 1.21823616341634 1 0.665291523456283 3672 4007 3850 4423 4606 3673 3575 2391 2460 4445 3488 4133 M13748 REACTOME_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCONEOGENESIS.html Genes involved in Gluconeogenesis 32/48 Reactome 3.22195643847089e-05 3.7046612398496e-05 4405 3640.90909090909 3674 2.92909420528817e-06 2081 1.47600526926728 0.712459157073722 1 2.58032143430382 4403 3985 3473 3500 4049 4537 3674 2081 2902 4009 3437 4134 M983 REACTOME_INTERFERON_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_SIGNALING.html Genes involved in Interferon Signaling 180/246 Reactome 6.56712547122748e-06 8.4124299247111e-06 2610 3638 3674 5.9701318859577e-07 2610 1.48970777870761 -1.5356284049586 -1 2.99045932448632 2610 4149 3817 3604 3621 3674 3361 3451 3907 4091 3733 4135 M19162 WANG_RESPONSE_TO_FORSKOLIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_FORSKOLIN_DN.html Genes down-regulated in LNCaP cells (prostate cancer) treated with forskolin [PubChem=47936], an activator of PKA pathway. 16751804 14/14 Arthur Liberzon 0.00072301156371791 0.00075785356001522 4050 3284.90909090909 3674 6.57499349810583e-05 581 2.05389798684694 -2.11664993487032 -1 2.52742226495127 4046 4073 2748 3674 4469 4205 3584 1311 581 3313 4130 4136 M1600 MCCLUNG_COCAIN_REWARD_4WK http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_COCAIN_REWARD_4WK.html Genes up-regulated in the nucleus accumbens (a major reward center in the brain) after 4 weeks of cocaine [PubChem=5760] treatment. 14566342 96/125 John Newman 1.63116685867289e-07 7.3358205358541e-07 4110 3191.45454545455 3674 1.48287907237641e-08 712 1.8866779114773 -1.63884065747232 -1 4.60455057363098 4109 2595 2570 4204 712 3894 3338 3851 3674 1650 4509 4137 M14385 WANG_CISPLATIN_RESPONSE_AND_XPC_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CISPLATIN_RESPONSE_AND_XPC_DN.html Genes down-regulated in fibroblasts with defective XPC [GeneID=7508] in response to cisplatin [PubChem=2767]. 15107491 312/382 John Newman 2.63308463732874e-07 8.29691125636501e-07 4535 3548.63636363636 3675 2.39371359315571e-08 1249 1.65239187383493 1.94936041859006 1 3.99101702827164 4532 4405 3533 4069 1249 4708 3978 2202 3237 3675 3447 4138 M19360 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_11 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_11.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 11. 12554760 146/171 Arthur Liberzon 2.87832067951497e-05 3.32819049664641e-05 1115 3291 3675 2.61668939824371e-06 1113 1.51059488977858 1.43048673476283 1 2.67023628777407 1113 3869 3860 3255 4032 2174 2207 4295 3675 4196 3525 4139 M10024 WENDT_COHESIN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WENDT_COHESIN_TARGETS_UP.html Cohesin targets identified by ChIP-chip which were up-regulated after knockdown of CTCF and RAD21 [GeneID=10664;5885] by RNAi. 18235444 46/49 Jessica Robertson 1.70510172182056e-06 2.65088278227702e-06 4635 3666.81818181818 3677 1.55009367577697e-07 2825 1.39099592185888 1.68757384782601 1 3.06954725191197 4633 3677 3750 3227 2938 4592 4293 2862 2825 4259 3279 4140 M6506 DANG_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DANG_MYC_TARGETS_UP.html Genes up-regulated by MYC [GeneID=4609] and whose promoters are bound by MYC, according to MYC Target Gene Database. 14519204 185/250 Chi Dang 7.63852599911256e-06 9.65067294658484e-06 625 3064.90909090909 3678 6.94413865512838e-07 621 1.36136245385169 1.4128790698876 1 2.6958562084323 621 4712 3998 4686 3678 1523 1405 1901 3861 4539 2790 4141 M17040 CASTELLANO_HRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) isolated from HRAS [GeneID=3265] knockout mice. 16909116 8/10 Leona Saunders 5.54856100437662e-05 6.22663051370843e-05 4480 3174.18181818182 3679 5.5486995486267e-06 1160 1.11581689258277 -0.583309224048541 -1 1.83724449038852 4480 2463 4332 3679 4169 3781 2060 1160 2886 3791 2115 4142 M14865 PALOMERO_GSI_SENSITIVITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/PALOMERO_GSI_SENSITIVITY_DN.html Down-regulated genes associated with sensitivity and resistance to gamma-secretase (GSI) in T-cell acute lymphoblastic leukemia (T-ALL) cell lines. 17873882 9/9 Jessica Robertson 4.02973735802666e-06 5.47821438072748e-06 4105 3205.90909090909 3679 4.02974466549773e-07 1212 1.58021340864246 -1.58021340864246 -1 3.29356421009308 2010 4104 4595 3887 3442 2152 1212 4105 3679 4207 1872 4143 M639 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_EARLY_ENDOSOME_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_EARLY_ENDOSOME_MEMBRANE.html Genes involved in Synthesis of PIPs at the early endosome membrane 15/15 Reactome 1.28460937398158e-05 1.56070945822215e-05 2165 2938.90909090909 3681 1.16783352277141e-06 870 0.784909750314527 -0.818307058118194 -1 1.46724167176701 2164 4080 3681 4021 3828 2005 1445 1228 4584 4422 870 4144 M1176 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_2 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_2.html Amplification hot spot 2: colocolized fragile sites and cancer genes in the 12p13-p11.1 region. 16751803 8/9 Arthur Liberzon 0.00058950266175726 0.000620114233005185 4175 3229 3681 5.89659101192042e-05 1006 1.76530506539772 2.43307259275993 1 2.22710904839296 4171 3527 4369 2230 4513 4697 2127 1006 1047 4151 3681 4145 M3061 BIOCARTA_FEEDER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FEEDER_PATHWAY.html Feeder Pathways for Glycolysis 10/15 BioCarta 0.000455951842762858 0.00048242382825391 3540 3695.09090909091 3684 4.14587605992292e-05 2220 0.992314719563997 1.23902756314278 1 1.27350998463075 3537 4635 3684 4481 4427 3254 2220 2380 4638 4269 3121 4146 M10914 STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN.html Genes down-regulated in prefrontal cortex (PFC) of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 609/707 Jessica Robertson 3.62277979251714e-07 9.43951209799063e-07 1680 3330.36363636364 3684 3.62278038312128e-08 1680 1.2548378259469 1.25234766042067 1 2.99049038421222 1680 4672 4456 4341 1705 2487 1827 3684 3256 4709 3817 4147 M953 REACTOME_TRAF3_DEPENDENT_IRF_ACTIVATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF3_DEPENDENT_IRF_ACTIVATION_PATHWAY.html Genes involved in TRAF3-dependent IRF activation pathway 14/18 Reactome 1.16404381948932e-05 1.42560633834706e-05 4280 3677.09090909091 3685 1.05822725328802e-06 2761 1.77083967906195 -1.55966877717634 -1 3.40110891093732 4276 3507 2912 3169 3799 4668 3844 2761 3566 3685 4261 4148 M11458 WONG_PROTEASOME_GENE_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_PROTEASOME_GENE_MODULE.html Genes that comprise the proteasome gene module 18199530 61/72 Jessica Robertson 6.22582651002796e-06 8.01798120800326e-06 2225 3571.36363636364 3686 5.65985829881438e-07 2222 1.08893587491746 1.1453035733462 1 2.18161670124896 2222 4211 3985 4311 3600 2736 2570 3311 4128 4525 3686 4149 M11865 BRUNEAU_SEPTATION_VENTRICULAR http://www.broadinstitute.org/gsea/msigdb/cards/BRUNEAU_SEPTATION_VENTRICULAR.html Genes for which mutations result in developmental defects in ventricular septation and atrioventricular cushion formation, a major class of congenital heart disease. 18288184 11/18 Jessica Robertson 0.0018375579240807 0.00190663297464517 2640 3343.63636363636 3686 0.000167190413464993 929 0.727994450257611 -0.665854333762401 -1 0.746222971396146 2637 3798 3686 3782 4514 2817 929 3119 4609 4717 2172 4150 M16304 NEBEN_AML_WITH_FLT3_OR_NRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NEBEN_AML_WITH_FLT3_OR_NRAS_UP.html Genes up-regulated in acute myeloid leukemia (AML) samples with constitutively activated FLT3 [GeneID=2322] or with activating point mutations within NRAS [GeneID=4893]. 15674343 10/14 Arthur Liberzon 0.000114256965423171 0.000124894135432461 3690 3283.27272727273 3687 1.03875363443964e-05 898 2.43001486551276 -2.22613480844431 -1 3.76465141740341 3687 3796 1872 2873 4279 4375 4709 898 4453 2546 2628 4151 M19938 SU_PANCREAS http://www.broadinstitute.org/gsea/msigdb/cards/SU_PANCREAS.html Genes up-regulated specifically in human pancreas. 11904358 41/94 John Newman 1.67387260955823e-07 7.3358205358541e-07 4165 3326.45454545455 3688 1.52170248810459e-08 753 1.87735715549295 2.18095363976076 1 4.58155551108343 4164 3688 2599 3868 753 4457 4211 3193 3403 2554 3701 4152 M18491 STEIN_ESRRA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_UP.html Genes up-regulated by ESRRA [GeneID=2101] only. 18974123 540/727 Leona Saunders 2.24915241603267e-07 7.85207056484778e-07 3050 3625.27272727273 3688 2.24915264367359e-08 1178 1.47198008755762 -1.52689346337907 -1 3.56397309413925 3050 4673 4522 3599 1178 4166 4488 3688 2742 4458 3314 4153 M2553 HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_UP.html Genes distinguishing asparaginase resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 33/47 Arthur Liberzon 4.43534305799961e-05 5.02878194421286e-05 3235 3313.36363636364 3688 4.03221134538522e-06 650 1.24094233334887 -0.706063755083387 -1 2.095188292605 3235 3999 3775 3024 4114 2203 650 3846 3688 4296 3617 4154 M4781 PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN.html Down-regulated genes in angioimmunoblastic lymphoma (AILT) compared to normal T lymphocytes. 18006812 174/221 Arthur Liberzon 2.10241174345612e-07 7.70763712250053e-07 1680 2901.36363636364 3690 1.91128358579216e-08 1002 1.43239646453668 -1.32957746381301 -1 3.47143194792952 1678 4427 3889 4540 1002 1748 1528 3690 4055 3713 1645 4155 M14520 REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_.html Genes involved in Cyclin E associated events during G1/S transition 67/79 Reactome 0.000437642032953604 0.000463466546004266 1795 3358.72727272727 3694 3.97935560497966e-05 1774 1.0038826430344 1.00872258331201 1 1.29596821936927 1792 4201 4064 3035 4424 2031 1774 3632 3741 4558 3694 4156 M13262 SYED_ESTRADIOL_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/SYED_ESTRADIOL_RESPONSE.html Genes responsive to estradiol [PubChem=5757] both in normal and cancer ovarian cell lines. 16116479 35/47 Arthur Liberzon 8.02220781660217e-06 1.00945936801819e-05 4340 3362.63636363636 3694 7.29294279036015e-07 1912 1.60327322355739 -1.45806214318272 -1 3.17120147013345 4340 2289 2916 1912 3694 4122 3977 2982 2762 3814 4181 4157 M18155 KEGG_INSULIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INSULIN_SIGNALING_PATHWAY.html Insulin signaling pathway 129/174 KEGG 7.51132652353197e-07 1.43364609476926e-06 3845 3475.72727272727 3695 6.82848098916348e-08 1755 1.37692958288811 -1.06757074664303 -1 3.18582300375522 4415 3314 3843 1755 2326 3842 3413 4516 2573 4541 3695 4158 M663 REACTOME_THE_ACTIVATION_OF_ARYLSULFATASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THE_ACTIVATION_OF_ARYLSULFATASES.html Genes involved in The activation of arylsulfatases 9/10 Reactome 7.3081309698638e-07 1.40678540692321e-06 3295 3582.18181818182 3697 7.30813337325992e-08 1975 1.38386949708839 1.91462377334151 1 3.20670365322414 3294 1975 4213 4579 2384 4065 4124 3697 3642 3455 3976 4159 M9729 WIKMAN_ASBESTOS_LUNG_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WIKMAN_ASBESTOS_LUNG_CANCER_DN.html Genes negatively correlated with the asbestos exposure of lung cancer patients. 17297452 27/41 Arthur Liberzon 7.07352393704856e-07 1.3784725468932e-06 4650 3564 3700 6.43047837395999e-08 2276 1.98089568340052 1.79947856999096 1 4.61875433019626 4647 3997 2775 2858 2276 4453 4329 2938 3700 3426 3805 4160 M15195 REACTOME_MAPK_TARGETS_NUCLEAR_EVENTS_MEDIATED_BY_MAP_KINASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MAPK_TARGETS_NUCLEAR_EVENTS_MEDIATED_BY_MAP_KINASES.html Genes involved in MAPK targets/ Nuclear events mediated by MAP kinases 36/37 Reactome 5.39355185162369e-05 6.06421265832868e-05 3705 3597.72727272727 3702 4.90334916841853e-06 2032 1.35679121334025 1.34742017706076 1 2.25108940537479 3702 3708 3687 2032 4149 2913 3248 4265 3553 4037 4281 4161 M3844 TONG_INTERACT_WITH_PTTG1 http://www.broadinstitute.org/gsea/msigdb/cards/TONG_INTERACT_WITH_PTTG1.html Proteins that interact with PTTG1 [GeneID=9232], based on protein array. 18663361 64/83 Jessica Robertson 2.75360820213174e-08 3.20914338618811e-07 4005 3401.54545454545 3702 2.50328021508819e-09 11 1.43517281465176 1.3397624938311 1 3.69788974657849 4003 3902 3697 3923 11 3610 4000 3474 2554 3702 4541 4162 M1667 VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_DN.html Genes down-regulated after heat shock in peripheral lympocytes from old donors, compared to those from the young ones. 12618007 25/28 John Newman 0.000449077783471591 0.000475363789635773 2400 3392.72727272727 3702 4.08335889316027e-05 1531 1.29568276478014 1.27783718350308 1 1.68147786165868 2399 4578 3702 4094 4426 2243 1531 2354 4661 4004 3328 4163 M4552 TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_UP.html Genes up-regulated in plasma cells compared with B lymphocytes. 12663452 101/118 Kate Stafford 4.16524602447194e-06 5.64292802396888e-06 4230 3915.72727272727 3703 3.78659446411517e-07 3408 1.4583205808934 1.55954306003673 1 3.02810367030846 4226 3615 3693 4289 3408 3521 3703 4219 4190 3628 4581 4164 M620 REACTOME_INSULIN_RECEPTOR_SIGNALLING_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INSULIN_RECEPTOR_SIGNALLING_CASCADE.html Genes involved in Insulin receptor signalling cascade 82/127 Reactome 1.65706901734739e-07 7.3358205358541e-07 3885 3108.63636363636 3704 1.50642649287275e-08 733 1.27960098337782 -0.997518647295497 -1 3.10684245250187 3737 3034 3884 1108 733 3103 2944 3881 3704 4281 3786 4165 M113 PID_NFAT_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFAT_3PATHWAY.html Role of Calcineurin-dependent NFAT signaling in lymphocytes 18832364 65/74 Pathway Interaction Database 5.94657967622173e-07 1.23104631893713e-06 4445 3702.09090909091 3707 5.40598298507029e-08 2119 1.33717360403127 -1.12205004187187 -1 3.12797653350753 4443 3364 3707 3012 2119 4624 3602 4069 3317 3763 4703 4166 M19304 TESAR_ALK_TARGETS_HUMAN_ES_5D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_HUMAN_ES_5D_UP.html Genes up-regulated in hES cells (human embryonic stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=4521392]. 17597760 3/9 Jessica Robertson 0.000173175003393572 0.000186788394885205 3875 3252.90909090909 3707 1.731885001857e-05 1047 2.2073602437501 2.66720679851042 1 3.25994383912293 3872 2488 4468 2401 4342 2859 1047 4302 3707 1692 4604 4167 M16649 ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_DN.html Genes commonly down-regulated in CD-1 and CD-2 clusters of multiple myeloma samples and which were higher expressed in the CD-1 group. 16728703 69/92 Kevin Vogelsang 2.19383013953853e-06 3.27686020842464e-06 3990 3496.90909090909 3708 1.9943930247447e-07 1502 1.79396568754634 -1.64992820032658 -1 3.90686360204972 3988 2638 2629 3367 3080 4556 4659 4130 3708 1502 4209 4168 M1993 KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_DN.html Genes down-regulated similarly in primary fibroblast cultures from Werner syndrom patients and normal old donors compared to those from normal young donors. 14527998 324/433 Arthur Liberzon 8.9543637412664e-07 1.62131916526563e-06 3710 3643.63636363636 3708 8.14033398712961e-08 2482 1.62295972649896 -1.48470376247094 -1 3.72913626221286 3708 3849 3787 3022 2482 3576 3196 4717 2991 4353 4399 4169 M3075 BIOCARTA_SET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SET_PATHWAY.html Granzyme A mediated Apoptosis Pathway 12/25 BioCarta 2.70515546740122e-05 3.13256472181888e-05 2855 3592.90909090909 3709 2.45926248272871e-06 2293 0.885914261144971 0.916308678056652 1 1.55468689542852 2853 4084 3709 4452 4023 3035 2293 3323 4374 3821 3555 4170 M772 REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING.html Genes involved in RNA Polymerase II Transcription Pre-Initiation And Promoter Opening 40/47 Reactome 0.000141345414829911 0.000153297416819205 675 2934.18181818182 3709 1.28504087995575e-05 673 0.776201449106232 0.8252755909526 1 1.14068038246509 673 3709 4050 3791 4312 1207 720 2349 4428 4540 2497 4171 M8293 NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON.html Genes within amplicon 8p12-p11 identified in a copy number alterations study of 191 breast tumor samples. 19010930 59/85 Jessica Robertson 1.6481286634424e-06 2.57588320908879e-06 2340 3533 3710 1.49829990739844e-07 2337 1.34597411824567 -1.21969840786597 -1 2.97532386759775 3587 3919 3710 4258 2922 2676 2337 4699 2338 4299 4118 4172 M15935 PARK_TRETINOIN_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/PARK_TRETINOIN_RESPONSE.html Genes up-regulated in U937 cells (acute promyelocytic leukemia, APL) by tretinoin (ATRA) [PubChem=444795]. 12893766 14/18 Arthur Liberzon 0.000585362670083465 0.000615896523137306 4100 3176.27272727273 3710 5.32289525343653e-05 656 2.31020835261207 -2.13819499600759 -1 2.9327579861827 2647 4075 2204 3710 4453 2340 656 4297 4097 2362 4098 4173 M1162 BAKER_HEMATOPOESIS_STAT1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BAKER_HEMATOPOESIS_STAT1_TARGETS.html STAT1 [GeneID=6772] targets in hematopoetic signaling. 17934481 10/11 Arthur Liberzon 0.0142793088048306 0.0145726135262272 3930 3619.54545454545 3711 0.00130662191248469 2544 1.89321693908521 2.23671396000113 1 1.34820730593801 3928 3519 2603 2944 4591 3999 4367 4501 3711 2544 3108 4174 M247 PID_INSULIN_GLUCOSE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INSULIN_GLUCOSE_PATHWAY.html Insulin-mediated glucose transport 18832364 34/41 Pathway Interaction Database 5.55470156550354e-07 1.18473526385796e-06 4040 3382.63636363636 3712 5.04972997090075e-08 1792 1.09361861919726 1.20579619015985 1 2.55645214004346 4040 2753 3712 3209 2053 4687 3897 2978 1792 4325 3763 4175 M855 REACTOME_MAP_KINASE_ACTIVATION_IN_TLR_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MAP_KINASE_ACTIVATION_IN_TLR_CASCADE.html Genes involved in MAP kinase activation in TLR cascade 55/56 Reactome 4.92946948547623e-06 6.51556874025422e-06 4700 3738.36363636364 3712 4.48134593710468e-07 1552 1.42611790737426 -1.40997985039397 -1 2.92431638908921 4698 3656 3701 1552 3504 4104 4564 4084 3045 3712 4502 4176 M2392 JUBAN_TARGETS_OF_SPI1_AND_FLI1_UP http://www.broadinstitute.org/gsea/msigdb/cards/JUBAN_TARGETS_OF_SPI1_AND_FLI1_UP.html Genes up-regulated in 745A cells (erythroleukemia) upon knockdown of FLI1 [GeneID=2313] by RNAi and down-regulation of SPI1 [GeneID=6688] by HMBA [PubChem=3616]. 19289502 169/224 Arthur Liberzon 6.04278068935138e-07 1.24495525332774e-06 3515 3615 3712 5.4934384992125e-08 2129 1.53116345045706 -1.38165165952062 -1 3.58602083033149 3514 3862 3468 4076 2129 3405 2876 4614 3712 4052 4057 4177 M1494 REACTOME_BASE_FREE_SUGAR_PHOSPHATE_REMOVAL_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASE_FREE_SUGAR_PHOSPHATE_REMOVAL_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY.html Genes involved in Base-free sugar-phosphate removal via the single-nucleotide replacement pathway 10/11 Reactome 0.0003902777500173 0.000414236784367361 2275 3253.72727272727 3715 3.54860910991786e-05 452 1.08429498237478 1.28494885399658 1 1.42505166631273 2273 4365 3555 4264 4411 1366 452 3715 4677 3983 2730 4178 M3009 HORTON_SREBF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HORTON_SREBF_TARGETS.html Genes up-regulated in liver from mice transgenic for SREBF1 or SREBF2 [GeneID = 6720, 6721] and down-regulated in mice lacking SCAP [GeneID=22937]. 14512514 33/35 Arthur Liberzon 1.01540900909346e-05 1.2592565745983e-05 4200 3616.36363636364 3715 9.2310335976314e-07 2966 1.4217933933182 1.08110510571866 1 2.75167232217872 4200 3715 3508 3185 3751 3819 2966 3567 3168 4184 3717 4179 M1029 REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS.html Genes involved in Interactions of Vpr with host cellular proteins 36/39 Reactome 8.65611016867824e-06 1.08230039724931e-05 1270 2994.90909090909 3717 7.8692220246893e-07 579 0.955013852572963 0.822624105883338 1 1.85712059766298 1267 3978 3962 4296 3717 1377 579 2367 4460 4372 2569 4180 M5298 BIOCARTA_STEM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STEM_PATHWAY.html Regulation of hematopoiesis by cytokines 6/15 BioCarta 7.89795295337885e-06 9.94619475452193e-06 3755 3466.27272727273 3718 7.89798102346663e-07 1484 2.88002747162237 1.79334509863746 1 5.74385962538031 3755 1985 4195 3350 3718 3811 4388 3285 3476 1484 4682 4181 M18292 MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_UP.html Top genes up-regulated in mesenchyme stem cells (MSC) grown in a tumor conditioned medium, which leads to carcinoma-associated fibroblast phenotype. 18519693 31/39 Leona Saunders 8.57441645966676e-05 9.46253114089949e-05 2820 2853.45454545455 3718 7.79522787502552e-06 653 2.27324412351033 2.93104828201468 1 3.62874364406304 2820 3718 1460 4140 4230 3933 4281 842 4061 1250 653 4182 M8731 BIOCARTA_SPPA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SPPA_PATHWAY.html Aspirin Blocks Signaling Pathway Involved in Platelet Activation 36/42 BioCarta 4.36041641383558e-07 1.02591716789194e-06 3930 3537.36363636364 3719 3.96401570733965e-08 1812 1.54186419972531 2.05050690501021 1 3.66354423429069 3926 4249 3444 2250 1812 4251 4126 3675 3601 3858 3719 4183 M1097 GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP.html Genes up-regulated in ME-A cells (breast cancer) undergoing apoptosis upon serum starvation (5% to 0% FCS) for 22 hr. 17160024 759/1097 Arthur Liberzon 2.34868542548049e-07 7.98113405922816e-07 3590 3293.72727272727 3722 2.34868567371507e-08 814 2.0630634424761 -1.85005278794916 -1 5.0093283449579 3590 3835 4336 3722 1226 3767 3204 4531 3162 814 4044 4184 M19582 REACTOME_MRNA_DECAY_BY_3_TO_5_EXORIBONUCLEASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_DECAY_BY_3_TO_5_EXORIBONUCLEASE.html Genes involved in mRNA Decay by 3' to 5' Exoribonuclease 11/11 Reactome 0.00222321981835621 0.00230173229713562 1115 3168 3723 0.00020231542607001 354 0.710348696266175 0.710348696266175 1 0.70355783007665 1112 4352 3723 4619 4521 1580 354 2332 4589 4691 2975 4185 M580 REACTOME_ASSOCIATION_OF_LICENSING_FACTORS_WITH_THE_PRE_REPLICATIVE_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASSOCIATION_OF_LICENSING_FACTORS_WITH_THE_PRE_REPLICATIVE_COMPLEX.html Genes involved in Association of licensing factors with the pre-replicative complex 16/19 Reactome 7.28252497101442e-05 8.08218148675947e-05 3115 3849.90909090909 3724 6.62069641012844e-06 2995 0.990386978302995 1.23712921242012 1 1.5799764319753 3113 4613 3632 4489 4207 2995 3253 3573 4640 4110 3724 4186 M19630 ZHU_CMV_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_ALL_UP.html Up-regulated at any timepoint following infection of primary human foreskin fibroblasts with CMV 9826724 199/272 John Newman 3.3685046475249e-06 4.69422554954754e-06 3765 3648.36363636364 3724 3.06228164107548e-07 2571 1.58436605601526 -1.76212142637308 -1 3.34508917765166 3765 3858 3395 3262 3311 4636 4519 3724 3849 3242 2571 4187 M5113 REACTOME_GLYCOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOLYSIS.html Genes involved in Glycolysis 29/44 Reactome 8.92440734882518e-06 1.11348672182011e-05 4595 3820.90909090909 3725 8.11313050120424e-07 2941 1.28119035306418 0.694509754404734 1 2.50213669650629 4594 4549 3661 2995 3725 4593 4004 3340 2941 4293 3335 4188 M5457 YAMANAKA_GLIOBLASTOMA_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMANAKA_GLIOBLASTOMA_SURVIVAL_UP.html Genes whose expression most strongly and consistently associated with the long term survival of patients with high grade glioma tumors. 16652150 15/17 Arthur Liberzon 1.63793338757855e-05 1.95327074011389e-05 2715 3408.36363636364 3725 1.48904143851665e-06 1369 1.52058722323512 -1.06554974180427 -1 2.82976456931822 2715 4072 2890 4231 3898 3048 1369 4229 3725 3424 3891 4189 M13354 KONDO_COLON_CANCER_HCP_WITH_H3K27ME1 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_COLON_CANCER_HCP_WITH_H3K27ME1.html Genes with high levels of histone H3 monomethylation mark at K27 (H3K27me1) in SW48 cells (colon cancer) by ChIP-chip assay on a 12K CpG array (CpG promoters only, HCP=high-CpG-density promoters). 18488029 28/37 Jessica Robertson 9.43440070411028e-07 1.68146476145018e-06 3165 3326.18181818182 3726 8.57673159084282e-08 1932 1.89889727981897 2.06000969966605 1 4.35959525901482 3163 2776 2292 3867 2527 3731 3726 4715 3903 1932 3956 4190 M1997 KYNG_WERNER_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_DN.html Genes distinctly down-regulated in primary fibroblast cultures from Werner syndrom patients compared to those from normal young donors. 14527998 40/63 Arthur Liberzon 8.99591993941915e-06 1.12211263514953e-05 3690 3763.63636363636 3726 8.17814247676073e-07 2568 1.28019810841914 1.2265352248995 1 2.49843465006607 3689 4527 3637 4499 3726 2871 2568 3723 4085 4178 3897 4191 M825 REACTOME_SHC_RELATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_RELATED_EVENTS.html Genes involved in SHC-related events 21/25 Reactome 1.52299064515233e-05 1.82820850587971e-05 3945 3407.45454545455 3727 1.38454653494421e-06 679 1.00427014640595 -0.472847943311948 -1 1.86353085232302 3943 3465 3727 679 3873 4353 4503 2869 2710 4430 2930 4192 M7919 BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transfrormed by expression of constitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression did NOT reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 27/31 Leona Saunders 3.67546271506966e-05 4.20358226681095e-05 4295 3181 3728 3.34138556470029e-06 1436 2.19107207107176 2.15600566433101 1 3.80627680447337 4294 3152 2015 1955 4077 3873 3987 1436 3728 1832 4642 4193 M1317 GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP.html Genes up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] and HIF1A [GeneID=3091] by RNAi. 17704799 193/210 Jessica Robertson 1.76166831055234e-07 7.40077165608328e-07 4475 3367.63636363636 3728 1.60151677419947e-08 814 1.87850374984568 1.9518019261811 1 4.58149211182028 4475 3578 2110 4172 814 4490 3728 4313 3302 1874 4188 4194 M1346 SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP.html Genes up-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 6 h. 18794802 228/305 Jessica Robertson 4.54240191116899e-07 1.04517532621413e-06 3480 3710.72727272727 3728 4.1294571355016e-08 1864 1.69518383205105 -1.42803179398447 -1 4.02730842020685 3477 4413 3378 4643 1864 4021 3408 4544 3595 3747 3728 4195 M15040 CONRAD_GERMLINE_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/CONRAD_GERMLINE_STEM_CELL.html Genes enriched in pluripotent adult germline stem cells. 18849962 9/17 Jessica Robertson 3.028974791543e-05 3.49725073778938e-05 3730 3504.81818181818 3728 3.02901607843233e-06 1800 1.44745230877041 -1.2032138451271 -1 2.54400318627945 3728 2450 4579 3120 4055 3960 3908 4505 3028 1800 3420 4196 M19724 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_UP.html Genes from the lightyellow module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 18/18 Arthur Liberzon 8.5723585290437e-05 9.46247246423907e-05 3120 3400.90909090909 3729 7.79335688317909e-06 1778 0.991903008437805 -1.06442080652236 -1 1.55515611262142 3118 3766 3729 4453 4229 2931 1778 2204 4496 4019 2687 4197 M2468 KRIEG_KDM3A_TARGETS_NOT_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/KRIEG_KDM3A_TARGETS_NOT_HYPOXIA.html Genes not induced under hypoxia, but dependent on KDM3A [GeneID=55818] for hypoxic expression in RCC4 cells (renal carcinoma) expressing VHL [GeneID=7428]. 19858293 255/310 Arthur Liberzon 1.69867202847159e-07 7.33971845416521e-07 3915 3485 3732 1.54424741784553e-08 772 1.6736499820519 -1.69471205883163 -1 4.07883807714212 3911 2525 3486 3732 772 4481 4345 4500 2508 3355 4720 4198 M2642 KEGG_TGF_BETA_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TGF_BETA_SIGNALING_PATHWAY.html TGF-beta signaling pathway 74/94 KEGG 2.12939805248743e-07 7.70763712250053e-07 3445 3577.45454545455 3733 1.9358165987215e-08 1020 1.72689707733938 1.90182500501224 1 4.19544575231802 3444 3896 3120 3733 1020 3917 4632 4688 3238 3605 4059 4199 M599 ST_PAC1_RECEPTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_PAC1_RECEPTOR_PATHWAY.html PAC1 Receptor Pathway 6/9 Signaling Transduction KE 0.00356907459585564 0.00367817294594729 4650 3548.72727272727 3733 0.000357481981875601 92 2.50018043772161 -3.71006243000218 -1 2.39766296139491 4648 2922 4202 3133 4552 4674 3733 3380 92 3472 4228 4200 M19979 CASORELLI_APL_SECONDARY_VS_DE_NOVO_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_APL_SECONDARY_VS_DE_NOVO_DN.html Genes down-regulated in secondary APL (acute promyelocytic leukemia) compared to the de novo tumors. 16990782 13/15 Leona Saunders 2.50483309661818e-06 3.64451671271203e-06 3905 3515.54545454545 3733 2.27712358956977e-07 1777 1.73447148868606 2.46258857041716 1 3.74342516606033 3902 3787 3089 4226 3164 3041 1777 4701 3733 3138 4113 4201 M7218 FAELT_B_CLL_WITH_VH3_21_DN http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH3_21_DN.html Genes down-regulated in samples from B-CLL (B-cell chronic lymphocytic leukemia) with the immunoglobulin heavy chain VH3-21 gene. 15817677 63/74 Kevin Vogelsang 7.87264298679896e-06 9.91961422789404e-06 4110 3631.18181818182 3734 7.15697378089909e-07 2375 1.20392650764206 1.59202647020722 1 2.37252531440362 3104 4501 3974 4109 3689 3198 2375 4107 3734 4470 2682 4202 M1596 HAN_JNK_SINGALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAN_JNK_SINGALING_UP.html Genes up-regulated in 3T3 cells (fibroblast) upon activation of JNK pathway. 12354774 46/58 John Newman 5.34833094133286e-07 1.15480887662814e-06 4450 3197 3734 4.8621202195858e-08 888 1.94400592925788 1.93034717400088 1 4.59191992543376 4449 3672 2004 4175 2016 4151 4666 888 4032 1380 3734 4203 M8382 MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5.html Cluster 5: genes up-regulated in SW260 cells (colon cancer) by curcumin and sulindac [PubChem=969516;5352]. 10969808 36/40 John Newman 9.44904730884197e-06 1.17583715522631e-05 4130 3484.72727272727 3737 8.59007990267945e-07 1522 1.28068456776309 0.958615448055917 1 2.48894215587972 4127 4247 3688 4606 3737 4498 3217 1522 2769 4038 1883 4204 M15801 SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC.html Cluster 2: genes up-regulated in B493-6 cells (B lymphocytes) by serum alone or in combination with MYC [GeneID=4609] but not by MYC alone. 15516975 128/146 Leona Saunders 1.00224743406871e-07 6.71132834037269e-07 4695 3306.36363636364 3739 9.11134072479818e-09 311 1.51660164494568 -1.09521681429083 -1 3.71510974662004 4692 3596 3739 2526 311 4565 3985 3616 901 4405 4034 4205 M4671 BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_DN.html Down-regulated genes in non-neoplastic mucosa samples from colon cancer patients who developed recurrence of the disease. 16091735 51/54 Leona Saunders 9.54287560312959e-06 1.18626212396028e-05 1875 3283.18181818182 3740 8.67537908839376e-07 1426 0.977982794642145 -0.924068159564055 -1 1.88732291306402 1873 4226 4023 4532 3740 1439 1426 3227 4625 4417 2587 4206 M2048 KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_DN.html Genes down-regulated in response to hydorgen peroxyde [PubChem=784] in CS-B cells (Cockaine syndrome fibroblast, CS) with defficient ERCC6 [GeneID=2074]. 12606941 61/81 Arthur Liberzon 1.25216545330852e-06 2.07376173319867e-06 4425 3754.72727272727 3742 1.13833287818112e-07 2735 1.33402762535704 1.35661800133584 1 2.9989918708354 4421 3907 3742 3491 2735 3628 4056 3372 3451 3995 4504 4207 M19367 GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_DN.html Genes down-regulated in dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the dividing cells from normal donors. 17717066 7/23 Arthur Liberzon 5.78954963273464e-07 1.21344024274012e-06 3750 3137.09090909091 3746 5.78955114108501e-08 1033 2.17284455106704 -1.35438726095029 -1 5.11955313599262 3746 1033 4317 3845 2175 4518 4414 3787 2154 1268 3251 4208 M2258 IVANOVSKA_MIR106B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVSKA_MIR106B_TARGETS.html A consensus set of genes that were significantly down-regulated by MIR106B [GeneID=406900]. 18212054 122/153 Arthur Liberzon 3.25420118549388e-07 9.04287770895433e-07 4555 3456.27272727273 3746 2.95836515168153e-08 1474 1.4629690401024 1.50355066600952 1 3.50577006706212 4553 3602 3746 3757 1474 3493 3927 4077 2662 3954 2774 4209 M2554 HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_DN.html Genes distinguishing asparaginase resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 23/36 Arthur Liberzon 0.237695191340622 0.238605126143712 3190 3708.18181818182 3747 0.0243716231855494 1962 1.02678167986924 -0.909944412434522 -1 0.206938899241595 3186 3747 3560 3458 4676 3114 1962 4268 3871 4237 4711 4210 M8214 CHNG_MULTIPLE_MYELOMA_HYPERPLOID_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHNG_MULTIPLE_MYELOMA_HYPERPLOID_DN.html Protein biosynthesis, transport or catabolism genes down-regulated in hyperploid multiple myeloma (MM) compared to the non-hyperploid MM samples. 17409404 36/41 Jessica Robertson 2.64793589568983e-07 8.3155405373626e-07 3825 3343 3750 2.40721474036123e-08 1255 1.00181925232279 -0.844050313798995 -1 2.3995981153129 3821 2733 3862 4243 1255 3253 2545 3750 3208 4039 4064 4211 M7559 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_15 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_15.html Amplification hot spot 15: colocalized fragile sites and cancer genes in the 6p25-p11.1 region. 16751803 18/23 Arthur Liberzon 0.0113483327507141 0.0116065288371334 2890 3591.27272727273 3751 0.00103702704513526 1345 1.79827701527937 -1.25247262366337 -1 1.34956631488452 2889 4327 3263 4504 4585 3413 1345 3677 3962 3751 3788 4212 M2162 FIGUEROA_AML_METHYLATION_CLUSTER_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_2_UP.html Cluster 2 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 68/98 Arthur Liberzon 2.51848865997794e-06 3.65987268321917e-06 4560 3750.90909090909 3751 2.28953776642428e-07 2604 1.65649779203291 -1.54098087472454 -1 3.57167244003282 4559 4478 3635 4451 3168 2707 2604 3353 3751 3873 4681 4213 M5714 WILLIAMS_ESR2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR2_TARGETS_DN.html Genes uniquely down-regulated in T47D cells (breast cancer) by induction of ESR2 [GeneID=2100] expression in the Tet-Off system. 17700529 18/19 Jessica Robertson 0.00864552551069729 0.0088518178764623 3880 3576.09090909091 3752 0.000789062605915963 1957 1.79859321581592 1.69454044408004 1 1.43492600940118 3879 4592 2832 4454 4578 3078 1957 3211 3994 3752 3010 4214 M4447 SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_UP.html Genes up-regulated in pilocytic astrocytoma (PA) from supratentorial regions compared to the infratentorial PA tumors. 17283119 22/32 Jessica Robertson 4.79142241139571e-05 5.41688952857192e-05 4195 3530.63636363636 3752 4.35593342535457e-06 2053 1.6860106121767 1.78975915042485 1 2.84268857760761 4193 3752 3155 3161 4125 4380 4501 2115 4203 3199 2053 4215 M12037 SHAFFER_IRF4_TARGETS_IN_PLASMA_CELL_VS_MATURE_B_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_PLASMA_CELL_VS_MATURE_B_LYMPHOCYTE.html IRF4 [GeneID=3662] target genes up-regulated in plasma cells compared to mature B lymphocytes. 18568025 83/93 Jessica Robertson 1.35174747370985e-06 2.20540894431749e-06 4205 3557.36363636364 3752 1.22886209478697e-07 2781 1.63039173834309 1.74949787936599 1 3.6588297105496 4205 3624 3192 3752 2781 3827 3839 2819 3878 2912 4302 4216 M1564 BURTON_ADIPOGENESIS_5 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_5.html Up-regulated at 48-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 160/197 John Newman 2.52854530376746e-06 3.66996735356163e-06 2000 3566.36363636364 3753 2.298680190843e-07 2000 1.57270758983243 -1.71479659772996 -1 3.38771984283007 2000 4720 3838 4625 3171 3699 3753 2362 3806 4173 3083 4217 M2537 MIZUSHIMA_AUTOPHAGOSOME_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/MIZUSHIMA_AUTOPHAGOSOME_FORMATION.html Key proteins in mammalian autophagosome formation. 20144757 22/22 Arthur Liberzon 4.89896372443472e-05 5.53184420558179e-05 1085 3108 3754 4.45370256185718e-06 1082 0.718477388202061 -0.767830764898488 -1 1.18003523749804 1082 3754 3905 4057 4129 1511 1146 3037 4426 4529 2612 4218 M9728 BARRIER_COLON_CANCER_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_COLON_CANCER_RECURRENCE_UP.html Up-regulated genes from the 70-gene prognosis predictor for stage 2 colon cancer, based on non-neoplastic mucosa gene expression profiles. 17043639 47/59 Arthur Liberzon 5.56181451966445e-07 1.18518124301653e-06 4055 3653.09090909091 3755 5.05619629613263e-08 2055 1.56743922477598 1.29865643974131 1 3.68563523989337 4053 3389 3309 3755 2055 4640 4121 3919 3420 3148 4375 4219 M2158 REACTOME_BASE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASE_EXCISION_REPAIR.html Genes involved in Base Excision Repair 19/21 Reactome 0.00068093792149687 0.000714545795790402 2065 3383.09090909091 3761 6.19226158994958e-05 1021 1.05766327452278 1.22383216838915 1 1.28810619653629 2061 4323 3761 4065 4462 1819 1021 3557 4636 4075 3434 4220 M1093 REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI.html Genes involved in Synthesis of glycosylphosphatidylinositol (GPI) 18/18 Reactome 0.00134051963367843 0.00139582013478099 4565 3532.45454545455 3761 0.000121939740554379 1237 1.07856819181282 -0.790368717728378 -1 1.18841807252313 4564 2841 3491 3886 4496 4544 3707 2130 1237 4200 3761 4221 M10292 HONMA_DOCETAXEL_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/HONMA_DOCETAXEL_RESISTANCE.html Genes up-regulated in MCF7-ADR cell line (breast cancer) resistant to docetaxel [PubChem=148124]. 18724378 62/83 Jessica Robertson 1.05236662141727e-05 1.30098754664472e-05 1995 3396.81818181818 3761 9.5670150493687e-07 1975 1.33259760719517 1.2749319567043 1 2.56831987003069 1992 4212 3882 4318 3761 2506 1975 2551 4324 4205 3639 4222 M6659 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP.html Genes up-regulated in monocyte-derived dendritic cells (MDDC) after stimulation with galecin-1 (lectin, LGALS1) [GeneID=3956] compared to that with bacterial lipopolysaccharide (LPS). 16785517 680/844 Arthur Liberzon 2.61038802862783e-07 8.29211725993449e-07 4635 3334.90909090909 3764 2.61038833526354e-08 1347 1.7694705212279 1.73931362874936 1 4.27752068450525 4632 2007 4283 2644 1347 3764 4554 4527 3052 1392 4482 4223 M11 PID_PRL_SIGNALING_EVENTS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PRL_SIGNALING_EVENTS_PATHWAY.html Signaling events mediated by PRL 18832364 35/41 Pathway Interaction Database 9.72138435791516e-08 6.64473403617636e-07 4455 3328.27272727273 3765 8.83762253407708e-09 294 1.90000858864271 -1.71039663093073 -1 4.67027310690765 4451 3971 3020 2525 294 3899 4288 3841 3473 3084 3765 4224 M9239 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_9 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_9.html Amplification hot spot 9: colocolized fragile sites and cancer genes in the 8p23-q12; 8q23 region. 16751803 16/17 Arthur Liberzon 0.000460057734554617 0.000486659011003539 3760 3659.09090909091 3766 4.18321789720842e-05 954 1.45123696616341 -1.26317887448124 -1 1.88340397465606 3757 4061 3199 3766 4429 3620 3406 4633 954 4111 4314 4225 M18933 BIOCARTA_TGFB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TGFB_PATHWAY.html TGF beta signaling pathway 24/26 BioCarta 0.263618803755468 0.264459246275411 3160 3361 3770 0.0274354703860225 1001 1.41009186538942 -1.05840545205319 -1 0.277534438963457 3159 4282 3438 3786 4718 2605 1752 3770 1001 4128 4332 4226 M1414 MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_DN.html Down-regulated genes discriminating multiple myeloma samples by type of immunoglobulin they produce: IgG vs IgA. 12623842 31/46 Kate Stafford 0.00861431461832232 0.00882177587296189 3630 3466.36363636364 3770 0.000786202807020284 1577 2.22907797552967 2.69494651092134 1 1.7916684702446 3629 4265 2318 4252 4577 3829 4608 2256 1577 3770 3049 4227 M238 PID_THROMBIN_PAR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_THROMBIN_PAR1_PATHWAY.html PAR1-mediated thrombin signaling events 18832364 56/67 Pathway Interaction Database 3.51274934839557e-06 4.86793215632035e-06 4015 3663.09090909091 3771 3.19341359748175e-07 2975 1.75715299177289 -1.42051734162731 -1 3.70420154313481 4015 3066 2975 3771 3334 3936 3972 4270 3580 3189 4186 4228 M2844 REACTOME_FORMATION_OF_FIBRIN_CLOT_CLOTTING_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_FIBRIN_CLOT_CLOTTING_CASCADE.html Genes involved in Formation of Fibrin Clot (Clotting Cascade) 21/39 Reactome 4.76120770212106e-06 6.33217817808155e-06 2685 3410.90909090909 3773 4.32838000571645e-07 1456 2.68725922534566 2.16477791539161 1 5.5679898864894 3871 4298 1456 3910 3481 3016 2684 3773 4116 2682 4233 4229 M5672 SU_KIDNEY http://www.broadinstitute.org/gsea/msigdb/cards/SU_KIDNEY.html Genes up-regulated specifically in human kidney tissue. 11904358 11/32 John Newman 5.33917053521853e-05 6.00593063065573e-05 3775 3657.54545454545 3773 4.85390919611024e-06 2307 2.07623819177357 -2.56640387892087 -1 3.47477809587569 3773 3231 2307 2386 4147 4291 4543 4251 4350 3304 3650 4230 M1487 MORI_PLASMA_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PLASMA_CELL_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: plasma cell. 18922927 60/65 Jessica Robertson 2.73232347392516e-06 3.92470079030029e-06 1685 3476.63636363636 3774 2.48393351580161e-07 1683 1.20077430748418 -0.945070310510708 -1 2.56064271226525 1683 4217 4004 4310 3211 2760 2184 3774 3998 4517 3585 4231 M2324 LEE_BMP2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_BMP2_TARGETS_UP.html Genes up-regulated in uterus upon knockout of BMP2 [GeneID=650]. 17515606 962/1167 Arthur Liberzon 6.16964479592404e-30 7.46685216327217e-28 4105 2651.72727272727 3774 6.16964479592403e-31 9 2.27299111042295 2.44018487552857 1 24.7468951409785 4104 1080 4683 9 947 4700 3883 4380 1583 26 3774 4232 M11079 KEGG_N_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_N_GLYCAN_BIOSYNTHESIS.html N-Glycan biosynthesis 46/50 KEGG 8.78252426529777e-07 1.5980537599154e-06 3625 3641.36363636364 3775 7.98411615575729e-08 2112 1.42655664256081 -1.23697884308482 -1 3.27539939270535 3621 3399 3714 4001 2468 4068 3775 4248 2112 4258 4391 4233 M5275 OSMAN_BLADDER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/OSMAN_BLADDER_CANCER_UP.html Genes up-regulated in blood samples from bladder cancer patients. 16740760 514/594 Leona Saunders 5.57322216750113e-07 1.18600579939609e-06 2965 3653.18181818182 3775 5.57322356523786e-08 2144 1.40299818941732 -1.34278852480419 -1 3.29355307420065 2962 4129 4300 3612 2144 3982 3519 3775 3288 4576 3898 4234 M1267 HOWLIN_PUBERTAL_MAMMARY_GLAND http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_PUBERTAL_MAMMARY_GLAND.html Genes up-regulated in pubertal mammary glands compared to mammary glands from other developmental stages. 16278680 71/115 Arthur Liberzon 1.06589569279454e-05 1.31500174729555e-05 3775 3377.72727272727 3775 9.69000779157576e-07 746 2.52113715068092 -2.58007315104026 -1 4.89890624899069 3775 3351 746 3077 3766 4483 4531 4441 3969 1179 3837 4235 M4397 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_DN.html Genes from the black module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 16/17 Arthur Liberzon 0.00140754425205792 0.00146464040337596 3245 3768.45454545455 3776 0.000128040508749211 2523 0.88115948662378 -0.903098829626997 -1 0.954338629316134 3245 4609 3776 4485 4502 3451 2523 2647 4689 3851 3675 4236 M1858 MALONEY_RESPONSE_TO_17AAG_DN http://www.broadinstitute.org/gsea/msigdb/cards/MALONEY_RESPONSE_TO_17AAG_DN.html Down-regulated genes in A2780 cells (ovarian cancer) treated with 17AAG [PubChem=6440175], a chemical with anticancer properties. 17409432 130/188 Jessica Robertson 9.15288620729585e-06 1.14048634895556e-05 3170 3761.18181818182 3776 8.32084026110114e-07 2853 1.36597120023549 1.31678119585812 1 2.66530704631903 3170 4435 4020 4117 3731 3540 2853 3309 3920 4502 3776 4237 M1537 MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_8 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_8.html Cluster 8: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate, curcumin, sulindac and TSA [PubChem=5222465;969516;5352;5562]. 10969808 15/19 John Newman 3.11922949492849e-06 4.39879390978861e-06 3860 3785 3777 2.83566719770853e-07 2356 1.1495406775234 -1.11410626594328 -1 2.42635599581579 3857 4331 3668 4253 3274 3732 2356 3777 4396 3423 4568 4238 M18669 MOOTHA_TCA http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_TCA.html Tricarboxylic acid related genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 19/21 Vamsi Mootha 0.000554226440449959 0.000583786833055971 3135 3293.36363636364 3777 5.03969191865893e-05 1337 0.764058145202788 0.802339597047185 1 0.943611665916371 1337 4049 3923 3777 4449 1970 1804 3133 4264 4386 3135 4239 M1309 GROSS_HYPOXIA_VIA_HIF1A_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_HIF1A_DN.html Genes down-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 142/182 Jessica Robertson 1.19028429033032e-06 1.9943705539081e-06 3780 3285.72727272727 3778 1.08207721301838e-07 1685 2.08718526971106 -1.68732951428144 -1 4.7346252629282 3778 3867 1685 3123 2694 4179 3828 3924 2985 2059 4021 4240 M2478 FU_INTERACT_WITH_ALKBH8 http://www.broadinstitute.org/gsea/msigdb/cards/FU_INTERACT_WITH_ALKBH8.html Proteins identified by mass spectrometry in complexes containing ALKBH8 [GeneID=91801]. 20308323 15/18 Arthur Liberzon 0.000443283827238345 0.000469335949879988 4425 3192.81818181818 3778 4.0306651897707e-05 598 0.754931030424053 0.6391360876173 1 0.96051468236544 1511 3778 3886 3002 4425 1815 598 4112 4448 4423 3123 4241 M1678 BURTON_ADIPOGENESIS_6 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_6.html Strongly up-regulated at 96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 223/254 John Newman 8.14983849680825e-08 6.31301093970522e-07 4505 3289.54545454545 3779 7.40894436246979e-09 195 1.62620125788074 -1.61694602508382 -1 4.00458197433538 4504 2958 3418 1937 195 4542 4657 4225 1688 3779 4282 4242 M5060 SA_FAS_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SA_FAS_SIGNALING.html The TNF-type receptor Fas induces apoptosis on ligand binding. 9/11 SigmaAldrich 6.1312177768335e-05 6.85604072652313e-05 3780 3374.81818181818 3780 6.13138694664401e-06 1845 1.50199157252454 1.69917068937199 1 2.4651552541813 3780 3806 4201 4401 4192 2954 1845 2163 4076 2893 2812 4243 M796 REACTOME_ACTIVATION_OF_GENES_BY_ATF4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_GENES_BY_ATF4.html Genes involved in Activation of Genes by ATF4 23/26 Reactome 0.00113120212661237 0.00118099403618898 2865 3739.63636363636 3780 0.000102889471847012 2625 1.06241463777497 0.865037291459492 1 1.20088137032451 2862 4305 3658 4280 4490 3013 2625 3780 4226 4367 3530 4244 M5868 REACTOME_AMINE_LIGAND_BINDING_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINE_LIGAND_BINDING_RECEPTORS.html Genes involved in Amine ligand-binding receptors 9/45 Reactome 9.94226086035672e-05 0.000109133654095078 1800 3375.27272727273 3782 9.94270570684749e-06 1796 3.03919284331197 -3.08548342523808 -1 4.79255516712019 3795 3236 4235 1796 4269 4362 3233 3782 1947 1796 4677 4245 M9905 FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN.html Genes downregulated in peripheral blood lymphocytes (PBL) from patients with well functioning kidneys more than 1-year post transplant compared to those from normal living kidney donors. 15307835 47/52 Jean Junior 1.44134235884171e-06 2.3163554421971e-06 3960 3843.90909090909 3782 1.3103120937692e-07 2831 1.39031514873628 1.50888249105191 1 3.10077737829414 3958 4512 3700 4623 2831 3087 3294 4455 3324 3782 4717 4246 M10334 WANG_CLIM2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CLIM2_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) engineered to conditionally express a dominant negative form of CLIM2 [GeneID=8861] by a Tet Off system. 17452977 340/426 Arthur Liberzon 3.07969359394281e-07 8.84194267847327e-07 4635 3457.63636363636 3783 2.79972184096101e-08 1416 1.78771491729932 2.07946898210486 1 4.30209466915925 4634 4403 3269 4274 1416 4694 3895 2453 2094 3783 3119 4247 M8341 PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN.html Antigen processing and presentation genes down-regulated in JY cells (B lymphocytes) treated with trichostatin A (TSA) [PubChem=5562]. 18829567 69/89 Jessica Robertson 5.56201758352003e-06 7.26218635357053e-06 1805 3610.45454545455 3783 5.05639240491453e-07 1804 0.954268105460495 -0.978948849708623 -1 1.92213118087426 1804 3637 4048 3800 3545 3783 4715 3126 4378 4413 2466 4248 M15130 MILI_PSEUDOPODIA_CHEMOTAXIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_CHEMOTAXIS_UP.html Transcripts enriched in pseudopodia of NIH/3T3 cells (fibroblast) in response to the chemotactic migration stimulus by lysophosphatidic acid (LPA) [PubChem=3988]. 18451862 89/95 Jessica Robertson 3.65005952518265e-07 9.47640282569729e-07 3595 3673.27272727273 3783 3.31823648251884e-08 1607 1.34433232178294 -1.13550544537582 -1 3.20642368211133 3595 4182 3760 4609 1607 3950 3298 3783 2813 4432 4377 4249 M12718 BIOCARTA_P35ALZHEIMERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P35ALZHEIMERS_PATHWAY.html Deregulation of CDK5 in Alzheimers Disease 15/19 BioCarta 0.000119020824421602 0.000129890934397678 3915 3432.81818181818 3784 1.08206603618677e-05 682 1.7780144799961 1.71856744398767 1 2.72894531313905 3915 3489 2794 3171 4286 3864 4385 3497 682 3784 3894 4250 M16036 CHANDRAN_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_UP.html Genes up-regulated in metastatic tumors from the whole panel of patients with prostate cancer. 17430594 267/361 Arthur Liberzon 3.8129002513736e-07 9.64463514816902e-07 3745 3530.72727272727 3784 3.46627355654674e-08 1659 1.58219543704705 -1.5529051591395 -1 3.77775171157718 3741 4409 3792 3239 1659 3966 3268 3907 2831 4242 3784 4251 M6831 BIOCARTA_KREB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KREB_PATHWAY.html The Citric Acid Cycle 11/11 BioCarta 1.15357480724089e-05 1.41425275069532e-05 4305 3552 3786 1.04870986916363e-06 1989 0.855259701237109 0.855259701237109 1 1.61795191973801 2103 4629 3786 4468 3794 2585 1989 3702 4302 4305 3409 4252 M1313 GROSS_HYPOXIA_VIA_ELK3_ONLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_ONLY_UP.html Genes specifically up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 45/48 Jessica Robertson 7.78749648760769e-06 9.82281758992739e-06 4045 3590.45454545455 3786 7.07956732154504e-07 1895 2.17113203760139 -2.36051631965442 -1 4.32247207868141 4043 3937 1895 4356 3685 4350 3665 3849 3786 2177 3752 4253 M8292 ZIRN_TRETINOIN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_DN.html Genes down-regulated in MS427 cells (Wilms tumor with normal WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 5/7 Leona Saunders 1.30609207593385e-05 1.58517732023856e-05 4345 3505.09090909091 3789 1.30609975244165e-06 1743 1.28656413908058 -1.76181544500418 -1 2.43347498215543 3990 2484 4345 3693 3852 3789 2887 1743 4343 3252 4178 4254 M1407 WELCH_GATA1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WELCH_GATA1_TARGETS.html Genes up-regulated after GATA1 [GeneID=2623] activation in G1E-ER4 cells (erythroid precursors engineered to express GATA1 upon addition of estradiol [PubChem=5757]). 15297311 22/30 Jean-Pierre Bourquin 0.00154702654697596 0.00160800821442997 1240 2858.54545454545 3789 0.000140737770796076 582 1.07434649182413 -1.12552629982815 -1 1.15701659749511 1237 4581 3789 4476 4719 874 582 1337 4595 4032 1222 4255 M11063 REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE.html Genes involved in mRNA Decay by 5' to 3' Exoribonuclease 13/14 Reactome 0.00135720334287647 0.00141256885962005 3645 3918.36363636364 3792 0.000123458303624131 3228 0.665175716733278 -0.562811486301962 -1 0.71235851969029 3645 3228 3784 3525 4500 3753 3792 3983 4492 4376 4024 4256 M17954 STARK_HYPPOCAMPUS_22Q11_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/STARK_HYPPOCAMPUS_22Q11_DELETION_DN.html Genes down-regulated in hyppocampus of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 20/21 Jessica Robertson 1.15287586468054e-05 1.41376307645937e-05 3215 3799.72727272727 3793 1.0480744601745e-06 2407 1.04141156090869 1.23947743218773 1 1.98106167755521 3211 4304 3745 4461 3793 3321 2407 3659 4354 4283 4259 4257 M2423 PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_DN.html Genes down-regulated in M2-10B4 cells (osteoblast) in response to phenylamil [PubChem=4755]. 19433444 8/13 Arthur Liberzon 9.40376908558061e-07 1.6781017044968e-06 4065 3407.18181818182 3793 9.40377306497227e-08 1022 1.96897676997016 -1.97025278443323 -1 4.52302284133545 4062 1022 4700 2605 2598 3793 4338 3909 3206 2672 4574 4258 M2618 ZWANG_TRANSIENTLY_UP_BY_1ST_EGF_PULSE_ONLY http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_TRANSIENTLY_UP_BY_1ST_EGF_PULSE_ONLY.html Genes transiently induced only by the first pulse of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 1886/2790 Yaara Zwang 6.88621799975563e-10 1.14045434943321e-08 3890 2771.18181818182 3793 6.88621800188953e-11 175 1.93979683022389 -1.73632257481039 -1 6.14633082724818 3887 1066 4719 1339 759 3889 3793 4096 2265 175 4495 4259 M16574 PACHER_TARGETS_OF_IGF1_AND_IGF2_UP http://www.broadinstitute.org/gsea/msigdb/cards/PACHER_TARGETS_OF_IGF1_AND_IGF2_UP.html Genes up-regulated in MCF7 cells (breast cancer) by IGF1 and IGF2 [GeneID=3479;3481]. 16774935 41/51 Arthur Liberzon 0.041751283130728 0.0422797803855474 3970 3535.90909090909 3795 0.00386957688616324 2021 1.72664955732872 -1.43756777394168 -1 0.903965597633698 3967 3104 2560 4369 4632 3157 2538 4684 3795 2021 4068 4260 M11954 XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_UP.html Genes up-regulated in DU-145 cells (prostate cancer) in the absence and presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 48/61 Arthur Liberzon 3.54990783012895e-06 4.90744910653488e-06 3800 3797.18181818182 3796 3.22719414386684e-07 2714 1.47781404636994 -1.60907874598577 -1 3.10529412536241 3796 3394 3349 4637 3341 4545 3174 3978 4380 2714 4461 4261 M19193 REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS.html Genes involved in Glycogen breakdown (glycogenolysis) 16/17 Reactome 0.0119140012220703 0.0121824275927582 1655 3062.18181818182 3798 0.00108900130948732 637 0.856748966368691 0.876174619733774 1 0.609526254902702 1654 4063 3798 4469 4586 1518 637 2189 4487 4290 1993 4262 M5583 REACTOME_MRNA_SPLICING_MINOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_SPLICING_MINOR_PATHWAY.html Genes involved in mRNA Splicing - Minor Pathway 47/59 Reactome 0.000110726159505241 0.000121146841183296 560 2908.90909090909 3799 1.00665211594167e-05 556 0.72287108254715 0.758590486503835 1 1.08858719304965 556 3948 4085 3799 4274 896 693 2222 4437 4573 2515 4263 M1825 REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_ACETYLCHOLINE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_ACETYLCHOLINE.html Genes involved in Regulation of Insulin Secretion by Acetylcholine 11/13 Reactome 5.09576518221883e-05 5.74719513980236e-05 3330 3425.18181818182 3799 4.63262110641738e-06 1760 1.63699086699741 -1.91222395879801 -1 2.74166118019689 3329 3799 2974 3960 4134 4182 2924 4172 4093 1760 2350 4264 M4324 LOPEZ_MBD_TARGETS_IMPRINTED_AND_X_LINKED http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MBD_TARGETS_IMPRINTED_AND_X_LINKED.html X chromosome and imprinted genes up-regulated in HeLa cells (cervical cancer) after knockdown of the MBD (methyl-CpG binding domain) proteins by RNAi. 18223687 25/54 Jessica Robertson 2.55050350468075e-05 2.96074189426787e-05 3965 3545.72727272727 3799 2.31866643059287e-06 2288 1.69830743266111 1.60592158975279 1 3.04296962262091 3961 3448 2962 2931 4011 3286 2288 4058 4286 3799 3973 4265 M1641 BURTON_ADIPOGENESIS_PEAK_AT_8HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_8HR.html Cluster 3: genes maximally expressed at 8 hr time point during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 67/78 John Newman 4.19733451715884e-05 4.77038741174806e-05 2295 3454.81818181818 3799 3.8158314539776e-06 1386 1.66987983440116 -1.65157245122034 -1 2.85208038117105 2294 4485 2963 4647 4102 2977 1386 4619 4438 2293 3799 4266 M5321 VERRECCHIA_RESPONSE_TO_TGFB1_C3 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C3.html Cluster 3: ECM related genes up-regulated in dermal fibroblasts within 30 min after TGFB1 [GeneID=7040] addition; returned rapidly to basal level after that. 11279127 25/28 John Newman 0.00754763273880574 0.00773948001893615 2975 3641.72727272727 3800 0.00068851379792302 2502 1.45415901316719 1.62756091209263 1 1.18465893150345 2973 4011 3097 4004 4572 3877 4668 2502 3144 3800 3411 4267 M699 KEGG_FATTY_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FATTY_ACID_METABOLISM.html Fatty acid metabolism 42/56 KEGG 3.64566383534358e-06 5.01823660041461e-06 3805 3696.45454545455 3801 3.31424534241798e-07 2875 1.45240825132182 -1.31347309057403 -1 3.04538627380646 3801 3401 3503 3237 3357 4589 4299 2875 3935 3835 3829 4268 M161 PID_IFNG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IFNG_PATHWAY.html IFN-gamma pathway 18832364 55/57 Pathway Interaction Database 8.72492332363483e-07 1.59125340369229e-06 3875 3633 3801 7.9317516216651e-08 2461 1.26531345935039 -1.08541843329107 -1 2.90046892615865 3874 4213 3801 3016 2461 3532 2929 3832 3525 4288 4492 4269 M314 NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_UP.html Up-regulated genes in lung tissue of smokers with chronic obstructive pulmonary disease (COPD) vs smokers without disease (GOLD-2 vs GOLD-0). 15469929 212/280 Kate Stafford 7.92647628670183e-07 1.4886566923604e-06 3450 3690.63636363636 3801 7.20589012960736e-08 2371 1.59352232102473 -1.50707609992139 -1 3.68434821827388 3447 4417 3558 4113 2371 3863 3099 3801 3777 4329 3822 4270 M865 REACTOME_RNA_POL_II_PRE_TRANSCRIPTION_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_II_PRE_TRANSCRIPTION_EVENTS.html Genes involved in RNA Polymerase II Pre-transcription Events 61/69 Reactome 7.22896190010599e-05 8.02462374611953e-05 1305 3170 3802 6.57199949718012e-06 1303 0.762365872806645 0.777878044141796 1 1.20564294818652 1303 3920 4108 3802 4206 1618 1306 2683 4479 4609 2836 4271 M6924 BIOCARTA_EIF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF2_PATHWAY.html Regulation of eIF2 15/16 BioCarta 0.0293603891545584 0.0297767590910003 1880 3429.63636363636 3804 0.00270542754993898 1254 1.20316207753847 -1.39886951041729 -1 0.68840111346606 1878 4619 3804 4634 4698 2687 1254 2524 4377 4420 2831 4272 M17864 GENTILE_UV_LOW_DOSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_LOW_DOSE_UP.html Selected genes up-regulated in WS1 (fibroblast) in response to irradiation with low dose UV-C. 12907719 41/54 John Newman 0.000781671531345087 0.000818431594487314 2885 3746.45454545455 3804 7.10863092333993e-05 2211 1.34937609620563 -1.23474909174214 -1 1.62518639547772 2882 4537 3654 4314 4475 2703 2211 4434 4622 3804 3575 4273 M16374 IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_DN.html Genes down-regulated during transition from G1 (well differentiated tumor, infected with HCV) to G2 (moderately differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 66/76 Yujin Hoshida 0.000389648374220947 0.000413661791795518 3805 3753.09090909091 3805 3.54288548263939e-05 2386 1.40151670741384 -0.95983990990182 -1 1.85694419575982 2386 4209 3803 3805 4410 3141 2494 4328 3790 4536 4382 4274 M73 TAKAO_RESPONSE_TO_UVB_RADIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKAO_RESPONSE_TO_UVB_RADIATION_UP.html Genes up-regulated in primary tissue culture of epidermal kerationcytes after UVB irradiation. 11982916 112/160 John Newman 4.14955344175553e-07 1.00337562730974e-06 3150 3562.18181818182 3805 3.77232202220744e-08 1756 1.27174598602959 1.45978263552153 1 3.01789908585434 3146 3877 3925 4661 1756 3446 3570 2795 3805 4333 3870 4275 M15114 DAZARD_UV_RESPONSE_CLUSTER_G5 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G5.html Cluster G5: genes up-regulated in NHEK cells (normal keratinocyte) at 3 h and 24 h time points after UV-B irradiation. 12771951 16/33 Arthur Liberzon 0.127818618478825 0.128553990884308 2955 3909.72727272727 3810 0.0123555690088638 2952 0.970432294410471 -1.13484505302435 -1 0.297660587018838 2952 4622 3810 3029 4664 3271 3760 4702 4682 4291 3224 4276 M963 KEGG_RNA_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_DEGRADATION.html RNA degradation 70/72 KEGG 5.26225782755708e-05 5.92506129438678e-05 1520 3210.63636363636 3811 4.78398518325347e-06 1485 0.782867575025 0.84657073932 1 1.28088531971267 1518 4204 4111 3811 4142 1942 1485 2031 4642 4605 2826 4277 M13038 CHASSOT_SKIN_WOUND http://www.broadinstitute.org/gsea/msigdb/cards/CHASSOT_SKIN_WOUND.html List of the transcription factors up-regulated 1 hr after wounding HDF cells (dermal fibroblasts). 17404577 13/13 Leona Saunders 0.0230292163990751 0.0234161786737687 2005 3541.18181818182 3811 0.00211580684408894 2002 1.44903390741295 -1.23925128705344 -1 0.900120627319608 2002 4093 2736 4051 4613 3084 2848 4423 4647 2645 3811 4278 M1370 COURTOIS_SENESCENCE_TRIGGERS http://www.broadinstitute.org/gsea/msigdb/cards/COURTOIS_SENESCENCE_TRIGGERS.html Genes that trigger senescence in vitro and in vivo. 18193093 8/8 Jessica Robertson 9.35196600394064e-05 0.000102941416834421 1530 2844.45454545455 3811 9.35235959395945e-06 297 0.879737492169207 0.879737492169207 1 1.36069520398349 1528 3811 4446 4266 4256 1176 297 1152 4546 4153 1658 4279 M3958 ZHAN_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_UP.html Genes most significantly up-regulated in multiple myeloma samples, compared to normal bone marrow plasma cells. 11861292 106/151 Kevin Vogelsang 6.56953743696718e-06 8.4124299247111e-06 3155 3885.54545454545 3812 5.97232459517784e-07 3152 1.41808574232985 -1.33033854500049 -1 2.84427860786174 3152 3607 3585 4246 3623 3812 4502 3916 3493 4226 4579 4280 M1811 MATZUK_FERTILIZATION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_FERTILIZATION.html Genes important for fertilization, based on mouse models with female fertility defects. 18989307 7/11 Jessica Robertson 0.149243621886507 0.149974429487825 3285 3876.36363636364 3812 0.0160330273351146 2843 1.25940131292327 -1.34703521166578 -1 0.36729602537235 3281 3812 4566 2941 4712 4027 3771 4572 4465 3650 2843 4281 M8410 REACTOME_ERKS_ARE_INACTIVATED http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ERKS_ARE_INACTIVATED.html Genes involved in ERKs are inactivated 15/15 Reactome 5.30310404896416e-07 1.14819500509683e-06 4665 3899.90909090909 3813 4.82100484298072e-08 2007 1.04770008679982 -1.13110939990642 -1 2.4527443192201 4665 4602 3718 3553 2007 4393 4618 3813 3808 3786 3936 4282 M14781 REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE.html Genes involved in Late Phase of HIV Life Cycle 110/125 Reactome 2.00599145755384e-05 2.36057832950739e-05 1710 3281 3813 1.8236452260948e-06 1410 0.806210106231355 0.782614805744489 1 1.4501541990813 1710 3887 4148 3813 3952 1738 1410 3101 4502 4631 3199 4283 M2319 KASLER_HDAC7_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/KASLER_HDAC7_TARGETS_2_UP.html Genes up-regulated in DO11.10 cells (hybridoma) by expression of transciptionally activating and by transcriptionally repressive forms of HDAC7 [GeneID=51564]. 17470548 4/9 Arthur Liberzon 0.163167154113597 0.163931240403613 2110 3524.27272727273 3814 0.0176553781713517 2106 1.07423215925319 1.07423215925319 1 0.28924072570582 2106 4380 4682 3936 4694 2582 2192 3814 4493 2994 2894 4284 M17002 REACTOME_BILE_SALT_AND_ORGANIC_ANION_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BILE_SALT_AND_ORGANIC_ANION_SLC_TRANSPORTERS.html Genes involved in Bile salt and organic anion SLC transporters 6/12 Reactome 2.35284873463445e-05 2.74344022417851e-05 2505 3309.27272727273 3815 2.35287364654293e-06 337 3.73686628791078 1.92711865046057 1 6.80540325393843 2503 3815 4244 3838 4015 3294 4688 4393 337 2787 2488 4285 M4322 AUNG_GASTRIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/AUNG_GASTRIC_CANCER.html Selected genes specifically expressed in gastric cancer. 16331256 51/111 Arthur Liberzon 5.3318515267451e-08 5.26942742450868e-07 4370 3343.72727272727 3815 4.84713786906017e-09 67 1.50789824652343 1.4927376487989 1 3.75720381152846 4368 2244 3156 3378 67 4005 4250 3815 3927 3005 4566 4286 M2294 BAKKER_FOXO3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAKKER_FOXO3_TARGETS_UP.html Genes up-regulated in I/11 erythroblast cells upon expression of an activated form of FOXO3 [GeneID=2309]. 17353275 84/100 Arthur Liberzon 1.50634055012129e-07 7.26289540930751e-07 4135 3229.90909090909 3815 1.36940059387316e-08 638 1.63866519127723 -1.57596574319034 -1 3.99554241238069 4135 2153 2668 3901 638 4217 4333 3993 3478 2198 3815 4287 M166 PID_ATF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATF2_PATHWAY.html ATF-2 transcription factor network 18832364 77/92 Pathway Interaction Database 5.60943120075238e-06 7.31597548150076e-06 4660 3193.27272727273 3816 5.09949591218428e-07 562 2.15205294443429 2.39372881516006 1 4.39479737668509 4657 2612 921 1541 3550 4426 3816 4604 4047 562 4390 4288 M4076 REACTOME_HIV_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIV_LIFE_CYCLE.html Genes involved in HIV Life Cycle 123/144 Reactome 1.91606443657829e-05 2.26208707870173e-05 1615 3283.09090909091 3817 1.74189193138394e-06 1314 0.883702424000817 0.801129101203037 1 1.60092945216897 1612 3878 4143 3817 3939 1740 1314 3388 4442 4621 3220 4289 M14539 BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP.html Genes up-regulated in medullary breast cancer (MBC) relative to ductal breast cancer (DBD). 16651414 255/307 Arthur Liberzon 5.47124990047791e-07 1.1732984793392e-06 3755 3441.63636363636 3820 4.97386478285537e-08 2039 1.47875140967875 -1.42898408236255 -1 3.47686843119993 3753 2047 3437 3992 2039 4249 3820 4134 3852 2678 3857 4290 M10179 REACTOME_FORMATION_OF_THE_TERNARY_COMPLEX_AND_SUBSEQUENTLY_THE_43S_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_THE_TERNARY_COMPLEX_AND_SUBSEQUENTLY_THE_43S_COMPLEX.html Genes involved in Formation of the ternary complex, and subsequently, the 43S complex 55/99 Reactome 0.00319912935913309 0.0032990803091781 1000 3274.63636363636 3821 0.000291253714987405 694 0.61752289754859 -0.485426113684062 -1 0.566255133116872 999 4540 4136 3821 4543 1528 694 3424 4702 4647 2987 4291 M5520 TCGA_GLIOBLASTOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/TCGA_GLIOBLASTOMA_COPY_NUMBER_DN.html Genes down-regulated and displaying decreased copy number in glioblastoma samples. 18772890 33/43 Jessica Robertson 1.25179998391829e-05 1.52398656798925e-05 3730 4066.54545454545 3821 1.13800646065168e-06 3724 1.22702076409488 -1.32739140490812 -1 2.32697230387929 4115 4542 3728 4463 3821 4707 3821 3786 3724 4295 3730 4292 M721 REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S.html Genes involved in Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 66/112 Reactome 0.00114033678962603 0.00119000434380607 820 3203.63636363636 3822 0.000103720754115326 630 0.669717118420827 -0.574842427332922 -1 0.737618619421863 820 4524 4142 3822 4491 1416 630 3360 4694 4650 2691 4293 M14033 REACTOME_MRNA_SPLICING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_SPLICING.html Genes involved in mRNA Splicing 129/178 Reactome 6.84583224774253e-05 7.61006316753291e-05 420 2940.36363636364 3823 6.22367752877804e-06 419 0.700121131870124 0.70996067295792 1 1.10960684968666 419 4172 4165 3823 4199 868 548 2440 4603 4672 2435 4294 M14990 REACTOME_FANCONI_ANEMIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FANCONI_ANEMIA_PATHWAY.html Genes involved in Fanconi Anemia pathway 24/27 Reactome 4.47533473986665e-05 5.07168786846833e-05 2935 3547.81818181818 3823 4.06856889240545e-06 1237 1.02910045743029 0.992926454169476 1 1.72744875658497 2932 4574 3823 4482 4116 2226 1237 3776 4475 4273 3112 4295 M13087 REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA.html Genes involved in Processing of Capped Intron-Containing Pre-mRNA 163/214 Reactome 4.07651172705927e-05 4.64089130528696e-05 435 2902.27272727273 3824 3.70598842285953e-06 432 0.726941704769848 0.713759532380496 1 1.21682357027875 432 4163 4160 3824 4095 843 435 2241 4599 4681 2452 4296 M733 REACTOME_REGULATION_OF_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_APOPTOSIS.html Genes involved in Regulation of Apoptosis 65/77 Reactome 0.55062716704513 0.551562017922966 3090 3786.72727272727 3824 0.0701373552257991 2633 0.950515115878537 1.05159035570841 1 0.0487411593887044 3089 4495 4063 3804 4691 2828 2633 3824 3778 4524 3925 4297 M813 REACTOME_SYNTHESIS_SECRETION_AND_DEACYLATION_OF_GHRELIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_SECRETION_AND_DEACYLATION_OF_GHRELIN.html Genes involved in Synthesis, Secretion, and Deacylation of Ghrelin 14/20 Reactome 3.56532241098112e-07 9.41752134134615e-07 3795 3524.54545454545 3824 3.24120271707072e-08 1575 2.27871754032799 -1.09981502701786 -1 5.47232448610692 3793 4070 2043 4190 1575 3824 4244 4348 3794 2831 4058 4298 M2531 REACTOME_MRNA_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_PROCESSING.html Genes involved in mRNA Processing 181/233 Reactome 2.2358883254591e-05 2.61327912983447e-05 480 2914.27272727273 3825 2.03264640854851e-06 479 0.794853912879584 0.796344730956142 1 1.41490412091525 479 4159 4163 3825 3982 860 557 2491 4478 4685 2378 4299 M12591 ROME_INSULIN_TARGETS_IN_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROME_INSULIN_TARGETS_IN_MUSCLE_UP.html Genes up-regulated by 3 h of euglycemic hyperinsulinemic clamp in the vastus lateralis muscle of healthy lean subjects. 12621037 576/722 Jessica Robertson 5.04657746847955e-07 1.11935364902366e-06 4675 3844.90909090909 3827 5.0465786145374e-08 2051 1.32036589360649 1.41561214059065 1 3.10996431468837 3937 4671 4619 4693 2051 3667 3827 3537 2928 4671 3693 4300 M504 REACTOME_ANDROGEN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANDROGEN_BIOSYNTHESIS.html Genes involved in Androgen biosynthesis 2/16 Reactome 0.00275378899398627 0.00284293176981959 3370 3710.8 3827.5 0.000306351692100103 1863 1.06888381288717 1.06888381288717 1 1.044497171147 3366 3822 4206 NA 4546 4444 4123 3833 1863 3267 3638 4301 M2419 WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D.html Genes with promoters bound by PPARG [GeneID=5468] at 8 day time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 872/1046 Arthur Liberzon 2.41651218889488e-07 8.05504062964961e-07 4710 3654.81818181818 3828 2.41651245167382e-08 1260 1.68798931659793 -1.46292027818182 -1 4.08679564909338 4706 4393 4699 3759 1260 3828 4633 3409 2196 3982 3338 4302 M8229 REACTOME_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSLATION.html Genes involved in Translation 171/283 Reactome 3.88673205801656e-05 4.43339181098071e-05 4680 3177.09090909091 3830 3.53345520588178e-06 646 0.657486013168539 -0.562885551321383 -1 1.101033971483 646 4440 4157 3830 4089 1716 796 2884 4676 4678 3036 4303 M4911 JISON_SICKLE_CELL_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/JISON_SICKLE_CELL_DISEASE_DN.html Genes down-regulated in peripheral blood mononuclear cells (PBMC) from sickle cell disease patients compared to those from healthy subjects. 15031206 227/300 Jessica Robertson 5.49875372405054e-07 1.1775915416297e-06 2655 3465.54545454545 3830 4.99886827129814e-08 2043 1.29107548840892 -1.04937200682592 -1 3.02842719000157 2652 4703 4119 4129 2043 2646 2087 3341 3941 4630 3830 4304 M7089 OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_DN.html Genes down-regulated in hematopoietic stem cells (HSC, CD34+ [GeneID=947]) cultured in a three-dimentional collagen gel compared to the cells grown in suspension. 16166251 358/496 Leona Saunders 4.7475515528888e-07 1.07836589651757e-06 3785 3731.27272727273 3831 4.3159568885457e-08 1905 1.9171964030588 2.10956739502326 1 4.5508365950138 3784 4690 3242 4291 1905 3831 3109 4662 2823 4007 4700 4305 M5488 REACTOME_TRAFFICKING_OF_GLUR2_CONTAINING_AMPA_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAFFICKING_OF_GLUR2_CONTAINING_AMPA_RECEPTORS.html Genes involved in Trafficking of GluR2-containing AMPA receptors 12/16 Reactome 1.31415991652324e-05 1.59414926907985e-05 4195 3756.09090909091 3833 1.19469796969356e-06 1942 1.18659456431868 1.55395813323232 1 2.23932956393808 4195 1942 3272 4597 3833 3797 3390 4020 4168 3434 4669 4306 M17456 CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_UP http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_UP.html Genes up-regulated in neuroblastoma xenografts: sensitive vs resistant to the topoisomerase inhibitor irinotecan [GeneID=3750]. 16501609 4/6 Arthur Liberzon 0.0035530320479076 0.00366243967375494 3575 3581.36363636364 3834 0.000355872568073627 799 1.2116327192141 1.35872320742183 1 1.13706977950112 3575 4119 4408 4416 4550 2569 799 2742 4623 3760 3834 4307 M16720 GOERING_BLOOD_HDL_CHOLESTEROL_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/GOERING_BLOOD_HDL_CHOLESTEROL_QTL_CIS.html Top scoring cis-regulated QTL (quantitative trait loci) influencing blood levels of high-density lipoprotein (HDL) cholesterol. 17873875 15/25 Leona Saunders 1.49853479790549e-05 1.80205968053857e-05 3870 3539.63636363636 3835 1.36231364118662e-06 2052 1.46824862154154 -1.37428824268999 -1 2.75130440724784 4352 3494 2885 2683 3866 3867 2052 3835 3870 3422 4610 4308 M8104 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM.html Amino sugar and nucleotide sugar metabolism 42/54 KEGG 0.000337647644175889 0.000359750988828487 3840 2868.36363636364 3836 3.06999523810193e-05 804 1.36304624931632 -1.25702288234337 -1 1.83784174857022 1230 4239 3839 4027 4542 1537 1368 804 4053 3836 2077 4309 M3990 GENTILE_UV_RESPONSE_CLUSTER_D1 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D1.html Cluster d1: genes down-regulated in WS1 cells (fibroblast) at 6 h after irradiation with high dose UV-C. 12907719 31/39 John Newman 1.32795918548178e-05 1.60964749755368e-05 4590 3768.90909090909 3837 1.20724291031609e-06 2392 1.35104499792995 -1.10965187258657 -1 2.55433046842389 4589 3981 3488 4239 3837 3622 2392 3953 4254 3772 3331 4310 M7202 FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP.html Genes up-regulated in B-CLL (B-cell chronic lymphocytic leukemia) patients with mutated immunoglobulin variable heavy chain (VH) genes. 15817677 96/138 Kevin Vogelsang 5.22429068874799e-07 1.13896776216584e-06 4665 3720.72727272727 3838 4.74935629940818e-08 1988 1.54364417888098 -1.44677591595179 -1 3.63964778333656 4661 3326 3290 3228 1988 4303 4255 4396 3838 3377 4266 4311 M11156 ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN.html Genes down-regulated in normal tissue adjacent to liver tumor, compared to the normal liver samples. 18413731 436/547 Jessica Robertson 2.06983368652507e-07 7.68728418959517e-07 3840 3650.81818181818 3838 1.88166716478362e-08 984 1.62345734651281 -1.6022567872 -1 3.94189450836015 3838 3555 3678 3526 984 4583 4439 4467 2876 4342 3871 4312 M15147 BOYAULT_LIVER_CANCER_SUBCLASS_G12_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G12_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G12, defined by unsupervised clustering 17187432 53/64 Yujin Hoshida 1.34408467247053e-05 1.62835720073432e-05 4520 3490.81818181818 3838 1.22190262199412e-06 1345 1.52195648071544 1.96534375904089 1 2.88071931468222 4516 3924 3579 3559 3838 4146 3955 2023 1345 4251 3263 4313 M18685 ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP.html Genes up-regulated in macrophage by live P.gingivalis. 18025224 524/771 Arthur Liberzon 5.45572914397425e-10 9.19680055698517e-09 3840 2630.36363636364 3839 5.45572914531367e-11 170 2.24442080560605 2.35953627413131 1 7.20374480434015 3839 1160 4287 347 212 4092 3861 4210 2393 170 4363 4314 M1292 GROSS_HYPOXIA_VIA_HIF1A_ONLY http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_HIF1A_ONLY.html Genes uniquely up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 9/9 Jessica Robertson 0.00588200645030689 0.00603938882868143 3880 3707.09090909091 3839 0.000589763379784104 2237 1.78347290496441 -2.42607423418733 -1 1.54153319285422 3797 3809 4424 3473 4568 3839 3877 2809 2237 3879 4066 4315 M19489 REACTOME_SOS_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SOS_MEDIATED_SIGNALLING.html Genes involved in SOS-mediated signalling 19/20 Reactome 1.36783850785386e-05 1.65585990178769e-05 4575 3756.45454545455 3840 1.24349728399305e-06 1563 1.00804225981413 -0.723616603110362 -1 1.88815124742255 4575 3764 3753 1563 3840 4621 2973 3883 4456 4384 3509 4316 M11171 DACOSTA_UV_RESPONSE_VIA_ERCC3_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_UP.html Genes up-regulated in fibroblasts expressing mutant forms of ERCC3 [GeneID=2071] after UV irradiation. 15608684 427/511 Arthur Liberzon 3.76743553440685e-07 9.5981847370948e-07 4320 3724.36363636364 3841 3.42494198142663e-08 1643 1.5767714037879 1.86918364404883 1 3.76595895678736 4320 3841 3824 3806 1643 4155 4161 3729 3316 4135 4038 4317 M2249 BRUINS_UVC_RESPONSE_MIDDLE http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_MIDDLE.html Middle response genes: differentially expressed in the period between 3 h and 12 h after UV-C irradiation of MEF cells (embryonic fibroblast). 18195040 119/136 Arthur Liberzon 3.02391081262571e-07 8.77601760597774e-07 4170 3505.09090909091 3841 2.74901020751255e-08 1396 1.45205489152133 1.54301365436433 1 3.48683962026622 3389 4169 3863 4514 1396 2882 3263 4266 2806 4167 3841 4318 M4495 COLLIS_PRKDC_SUBSTRATES http://www.broadinstitute.org/gsea/msigdb/cards/COLLIS_PRKDC_SUBSTRATES.html Substrates of PRKDC [GeneID=5591]. 15592499 27/40 Jessica Robertson 6.03471619215835e-05 6.75132980018664e-05 3420 3252 3844 5.4862561217891e-06 1278 1.07038148423123 1.10343718919829 1 1.74527052480545 3420 4289 3844 4093 4167 2285 1278 1859 4515 4106 1916 4319 M7623 HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN.html Genes down-regulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562]. 18172295 350/450 Jessica Robertson 1.72933769477867e-07 7.37919956089047e-07 4475 3420.18181818182 3845 1.57212530065042e-08 791 1.82024439485429 -1.62767850854041 -1 4.43877927770535 4473 3845 2284 4217 791 4607 4166 3560 3649 1707 4323 4320 M654 REACTOME_OXYGEN_DEPENDENT_PROLINE_HYDROXYLATION_OF_HYPOXIA_INDUCIBLE_FACTOR_ALPHA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OXYGEN_DEPENDENT_PROLINE_HYDROXYLATION_OF_HYPOXIA_INDUCIBLE_FACTOR_ALPHA.html Genes involved in Oxygen-dependent Proline Hydroxylation of Hypoxia-inducible Factor Alpha 19/27 Reactome 9.90020534935413e-05 0.000108697299951039 3230 3716.36363636364 3846 9.00059172355094e-06 2667 0.790809025623801 0.899072575654605 1 1.21057631685258 3229 4055 3846 4072 4252 3172 3383 3301 4658 4245 2667 4321 M14025 REACTOME_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTION.html Genes involved in Transcription 182/275 Reactome 1.39606906288299e-05 1.68700613845564e-05 1965 3327.18181818182 3846 1.26916174735703e-06 1530 0.796524967398295 0.827765543847185 1 1.47886911602073 1965 4157 4167 4131 3846 1530 1533 3326 4551 4689 2704 4322 M2071 REACTOME_PURINE_RIBONUCLEOSIDE_MONOPHOSPHATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_RIBONUCLEOSIDE_MONOPHOSPHATE_BIOSYNTHESIS.html Genes involved in Purine ribonucleoside monophosphate biosynthesis 12/12 Reactome 0.00149789825696772 0.00155797262514051 2660 3584.18181818182 3848 0.000136265372130652 2366 0.55296693992403 0.573812547866829 1 0.574287262188336 2658 4094 3848 4267 4505 2561 2366 2842 4588 4688 3009 4323 M2139 LU_EZH2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_EZH2_TARGETS_UP.html Genes up-regulated in SKOV3ip1 cells (ovarian cancer) upon knockdown of EZH2 [GeneID=2146] by RNAi. 20708159 346/459 Arthur Liberzon 4.14750225129133e-07 1.00337562730974e-06 4605 3707.90909090909 3848 3.77045730290037e-08 1754 1.71197504814377 1.77489768679151 1 4.07989945078858 4602 3848 3570 3977 1754 3447 3513 4673 2984 4005 4414 4324 M1115 GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_DN.html Down-regulated genes from the set C (Fig. 5a): specific to cells expressing AF4-MLL [GeneID=4299;4297] fusion protein alone. 17130830 17/26 Arthur Liberzon 0.00010382703590543 0.000113835913931157 4370 3635.45454545455 3849 9.43926693213394e-06 2463 1.69445288873866 -1.83101716583419 -1 2.63738751839379 4370 3203 2879 3417 4259 3849 2957 3890 4092 2463 4611 4325 M13486 KEGG_HUNTINGTONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HUNTINGTONS_DISEASE.html Huntington's disease 188/233 KEGG 0.000632902548579376 0.000665026720680021 1915 3591 3850 5.75531542940166e-05 1861 1.301912464547 1.31738573404687 1 1.61345839939965 1915 4717 4104 4688 4457 2310 1861 3339 3646 4614 3850 4326 M6231 BIOCARTA_NO2IL12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NO2IL12_PATHWAY.html NO2-dependent IL 12 Pathway in NK cells 9/23 BioCarta 0.000475200405727647 0.000502002219121418 2610 3641.81818181818 3853 4.7530205326237e-05 2606 1.54572070817521 -1.30042744344048 -1 2.00090183226753 2606 4108 4194 4046 4442 3126 2651 2908 4673 3453 3853 4327 M3492 REACTOME_MTORC1_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MTORC1_MEDIATED_SIGNALLING.html Genes involved in mTORC1-mediated signalling 12/12 Reactome 0.00111079015200508 0.00115994015873097 2835 3493.54545454545 3853 0.000101031944712757 914 0.758098447734616 -0.690554903365273 -1 0.844952196233496 2834 4625 3853 4495 4488 1822 914 3299 4657 4697 2745 4328 M9172 MURAKAMI_UV_RESPONSE_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_1HR_DN.html Genes down-regulated in primary keratinocytes at 1 h after UVB irradiation. 11532376 16/18 Arthur Liberzon 0.000320654721931169 0.000342186363896703 2430 3387 3856 2.91546788712719e-05 1573 1.20544716524023 1.56992180517335 1 1.63009897242743 2427 4612 3313 4278 4391 2147 1573 4116 4704 3856 1840 4329 M16909 PARENT_MTOR_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARENT_MTOR_SIGNALING_UP.html Genes up-regulated in HepaRG cells (liver cancer) expressing constituvely active form of MTOR [GeneID=2475]. 17483347 716/856 Arthur Liberzon 1.8730747538599e-07 7.48978540381421e-07 4170 3525.36363636364 3857 1.87307491173832e-08 977 1.52877914483202 -1.37922595583978 -1 3.71603916923175 4168 2004 4272 3552 977 3857 3702 4446 2766 4440 4595 4330 M2999 MOOTHA_ROS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_ROS.html Reactive oxidative species (ROS) genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 9/9 Vamsi Mootha 1.330264530829e-05 1.61202787818045e-05 735 2391.72727272727 3859 1.33027249411284e-06 19 1.06392479803806 -1.06392479803806 -1 2.0005831491056 734 4099 4590 3973 3859 379 57 300 4418 3881 19 4331 M8077 SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_DN.html Down-regulated genes whose expression correlated with histologic grade of invasive breast cancer tumors: comparison of grade 1 vs grade 3. 16478745 69/78 Arthur Liberzon 5.56894978437592e-06 7.26920436456149e-06 3315 3849.09090909091 3860 5.06269443757795e-07 3312 1.25034483086692 1.3487987083071 1 2.5338165704261 3312 3640 3795 4019 3547 3377 3991 4679 4192 3928 3860 4332 M1268 KREPPEL_CD99_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KREPPEL_CD99_TARGETS_UP.html Genes up-regulated in ESFT cells (Ewing's sarcoma family of tumors) after knockdown of CD99 [GeneID=4267] by RNAi. 16314831 5/5 Arthur Liberzon 0.131356203100298 0.132083783262337 3995 3670.18181818182 3863 0.0139835232062002 1654 1.85734275755948 -1.167949557413 -1 0.606646077416178 3995 4377 4407 3479 4666 3318 1654 3149 3863 3256 4208 4333 M1405 KIM_GERMINAL_CENTER_T_HELPER_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GERMINAL_CENTER_T_HELPER_UP.html Genes up-regulated in germinal center T helper cells compared to other CD4+ [GeneID=920] T lymphocyte types. 15213097 82/100 Kate Stafford 5.41356939137492e-07 1.1656955988727e-06 4305 3475.45454545455 3863 4.92142793045421e-08 2028 1.45238484500459 1.64668053959218 1 3.41563178672841 4302 2155 3267 2903 2028 4287 3863 4183 2881 3957 4404 4334 M14735 REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY.html Genes involved in Resolution of AP sites via the single-nucleotide replacement pathway 12/13 Reactome 0.00134444503342225 0.00139959871145854 2420 3388.54545454545 3864 0.000122297031154365 709 1.08429498237478 1.28494885399658 1 1.1944818336443 2419 4361 3690 4281 4497 1625 709 3864 4686 4120 3022 4335 M14298 PETRETTO_BLOOD_PRESSURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_BLOOD_PRESSURE_UP.html Genes that are most strongly positively correlated with systolic blood pressure (SBP). 18443592 12/17 Jessica Robertson 0.000132862186960899 0.000144461995497684 3865 3439.81818181818 3864 1.20791101308814e-05 101 2.96740785650279 -2.44461752957098 -1 4.53282700258514 3864 4088 2202 3652 4301 4061 3974 3721 101 3823 4051 4336 M529 REACTOME_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOSIS.html Genes involved in Meiosis 75/238 Reactome 3.20079686338226e-05 3.68212556547996e-05 895 2553.90909090909 3866 2.90985766633612e-06 191 1.32202506703378 1.33502783828163 1 2.30732535590322 891 4199 3866 4537 4048 191 296 862 4507 4030 666 4337 M18694 LIU_COMMON_CANCER_GENES http://www.broadinstitute.org/gsea/msigdb/cards/LIU_COMMON_CANCER_GENES.html Low abundance transcripts common to nasopharyngeal carcinoma (NPC), breast and liver tumors. 18332864 138/184 Jessica Robertson 5.72005123992448e-07 1.20368443390297e-06 4370 3786.90909090909 3867 5.20004793377423e-08 2084 1.61958607921361 2.05451336356024 1 3.80553455234419 4369 3592 3376 4299 2084 4671 4712 3247 3398 3867 4041 4338 M1659 CARDOSO_RESPONSE_TO_GAMMA_RADIATION_AND_3AB http://www.broadinstitute.org/gsea/msigdb/cards/CARDOSO_RESPONSE_TO_GAMMA_RADIATION_AND_3AB.html Down-regulated synergystically by gamma-irradiation and 3-aminobenzamine [PubChem=1645], an inhibitor of PARP1 [GeneID=142]. 12379459 21/42 John Newman 0.0383877292845198 0.0389070393435546 2415 3513 3868 0.00355221721877839 1171 0.911165185937891 0.742818749950262 1 0.466626830132696 2414 4037 3868 4610 4669 2739 1171 2626 4222 4431 3856 4339 M19422 BIOCARTA_IL17_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL17_PATHWAY.html IL 17 Signaling Pathway 5/14 BioCarta 7.50598392021971e-05 8.31378888818231e-05 4100 3654.63636363636 3871 7.50623746134836e-06 2492 2.7955351494337 -4.51005103109972 -1 4.53715748891488 4100 2925 4192 3871 4222 4573 3914 3319 3267 2492 3326 4340 M2415 WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR.html Genes with promoters bound by both PPARG and RXRA [GeneID=5468, 6256] at 36 h time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 197/236 Arthur Liberzon 3.6708432945679e-07 9.50432273744403e-07 2785 3366.90909090909 3871 3.33713082461105e-08 1606 1.56904699937285 -1.29485806352653 -1 3.74995798100537 2782 4705 3871 4649 1611 2272 1606 4303 3401 3931 3905 4341 M17340 DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS http://www.broadinstitute.org/gsea/msigdb/cards/DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS.html NF-kB-driven pro-inflammatory genes that are negatively regulated by glucocorticoids. 17072333 17/29 Arthur Liberzon 2.62052973039865e-05 3.03904184950409e-05 3750 3531.54545454545 3874 2.3823281321417e-06 1068 2.76952411145875 1.83367024168545 1 4.98127439049387 3749 3201 1068 3874 4016 3847 4661 3902 4333 1668 4528 4342 M1018 REACTOME_APOPTOSIS_INDUCED_DNA_FRAGMENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOSIS_INDUCED_DNA_FRAGMENTATION.html Genes involved in Apoptosis induced DNA fragmentation 14/16 Reactome 0.00147938109736344 0.00153905196816298 3235 3800.72727272727 3875 0.000134579712612468 2830 1.49733640333365 -1.83623854458664 -1 1.64371811448205 3233 3498 3016 2956 4504 4606 4525 4232 4533 2830 3875 4343 M7096 NIELSEN_SYNOVIAL_SARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SYNOVIAL_SARCOMA_DN.html Top 20 negative significant genes associated with synovial sarcoma tumors. 11965276 20/30 Arthur Liberzon 6.64622552141592e-06 8.50140500300357e-06 4320 3539.72727272727 3876 6.04204145438659e-07 2211 1.85043537979605 1.90528005908836 1 3.72330475008771 4316 2376 2211 3082 3628 4040 4295 3876 4027 2519 4567 4344 M731 WEBER_METHYLATED_ICP_IN_FIBROBLAST http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_ICP_IN_FIBROBLAST.html Germline-specific genes with intermediate-CpG-density promoters (ICP) that are methylated in primary fibroblasts. 17334365 17/105 Arthur Liberzon 7.84841328057585e-06 9.89436716995673e-06 4070 3819.09090909091 3877 7.134946617837e-07 2243 1.66670920634631 -1.75111398308448 -1 3.30448679762357 4068 3487 3361 2243 3687 4601 4558 4661 3877 3326 4141 4345 M524 REACTOME_ABCA_TRANSPORTERS_IN_LIPID_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABCA_TRANSPORTERS_IN_LIPID_HOMEOSTASIS.html Genes involved in ABCA transporters in lipid homeostasis 19/26 Reactome 0.00105090439324414 0.00109789037983894 3880 3402.54545454545 3878 9.55824299306377e-05 1602 2.98191299497665 3.81731728007779 1 3.49895720293352 3878 4303 2098 4353 4485 4394 3199 1602 2424 2770 3922 4346 M16091 DISTECHE_ESCAPED_FROM_X_INACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/DISTECHE_ESCAPED_FROM_X_INACTIVATION.html Genes that escape X inactivation. 12900543 24/53 Broad Institute 0.68618940391 0.68618940391 2975 3776.63636363636 3878 0.1 2492 0.9920641147296 -0.802752572188063 -1 0.0152167858247626 2974 4033 3878 3545 4699 3490 2492 3831 4249 4274 4078 4347 M720 REACTOME_METABOLISM_OF_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_PROTEINS.html Genes involved in Metabolism of proteins 467/627 Reactome 7.50291819957634e-07 1.43364609476926e-06 4690 3940.90909090909 3879 6.82083705307802e-08 2324 1.33713195779391 -1.04492039922558 -1 3.09229639809691 3497 4686 4164 3827 2324 3872 3080 4671 3879 4686 4664 4348 M646 REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS.html Genes involved in TGF-beta receptor signaling activates SMADs 34/38 Reactome 1.77757859869024e-06 2.7411772276752e-06 4695 3617.72727272727 3880 1.61598184996189e-07 2189 0.910378016117842 1.12171989594661 1 1.9863404256678 4691 4258 3880 4079 2966 3137 2189 2323 4348 4326 3598 4349 M17600 NAGASHIMA_NRG1_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAGASHIMA_NRG1_SIGNALING_DN.html Genes down-regulated in MCF7 cells (breast cancer) after stimulation with NRG1 [GeneID=3084]. 17142811 76/84 Arthur Liberzon 5.04041638862162e-07 1.11903882193293e-06 4055 3746.45454545455 3880 4.58219776675542e-08 1952 1.92440255867625 2.17781845066253 1 4.55568599305947 4054 3632 2594 3880 1952 4492 4692 4088 3713 3697 4417 4350 M14666 TIAN_TNF_SIGNALING_NOT_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/TIAN_TNF_SIGNALING_NOT_VIA_NFKB.html Genes modulated in HeLa cells (cervical carcinoma) by TNF [GeneID=7124] not via NFKB pathway. 15722553 30/31 Arthur Liberzon 1.5562489689658e-05 1.86442040423365e-05 3000 3620.18181818182 3880 1.41478179796411e-06 2466 1.89918585748233 2.03630409067481 1 3.56222551600872 2997 4552 2583 3536 3880 4169 4325 2466 4560 2819 3935 4351 M1543 HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_24HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_24HR.html Genes discriminating between direct (cisplatin, MMS, mitomycin C [PubChem=2767;4156;5746]) and indirect (paclitaxel, hydroxyurea, etoposide [PubChem=4666;3657;36462]) acting genotoxins at 24 h time point. 15120960 83/114 John Newman 7.87449427126808e-05 8.70843790074633e-05 2520 3275.45454545455 3881 7.1588873985389e-06 1415 1.25628364869706 -1.42173791097661 -1 2.0012231778097 2520 3338 3892 3005 4219 4226 3881 1458 3922 4154 1415 4352 M7151 KEGG_SELENOAMINO_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SELENOAMINO_ACID_METABOLISM.html Selenoamino acid metabolism 26/28 KEGG 0.00335501421833933 0.00345907975329 4680 3829 3882 0.000305467417002606 2379 1.89510934138523 -1.81667781620466 -1 1.8256201532202 4677 4277 3387 4390 4545 3542 3021 2379 3882 3346 4673 4353 M118 PID_INTEGRIN_A9B1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_A9B1_PATHWAY.html Alpha9 beta1 integrin signaling events 18832364 28/34 Pathway Interaction Database 3.27319683232476e-07 9.05922275783096e-07 4105 3243.72727272727 3882 2.97563392665142e-08 1386 2.77223320190409 2.72871767527651 1 6.68711680779447 4103 4267 1386 3882 1482 4295 2859 3892 3801 1637 4077 4354 M2188 LI_DCP2_BOUND_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/LI_DCP2_BOUND_MRNA.html Genes encoding mRNA transcripts specifically bound by DCP2 [GeneID=167227]. 18039849 104/114 Arthur Liberzon 3.10158145270427e-06 4.37783028013282e-06 2395 3763.09090909091 3882 2.81962347759334e-07 2391 0.958713486303992 0.902627287269136 1 2.01606723665926 2391 4456 4141 4682 3271 2924 2836 3789 4432 4590 3882 4355 M2492 TURJANSKI_MAPK11_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK11_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK11 [GeneID=5600] phosphorylation. 17496919 5/5 Arthur Liberzon 0.000543651321752447 0.000572775499703471 3225 3448.18181818182 3886 5.43784368106093e-05 848 2.60947657694878 2.60947657694878 1 3.35223578312213 3221 4378 4359 4595 4636 3132 4627 984 3264 3886 848 4356 M4925 STEARMAN_LUNG_CANCER_EARLY_VS_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEARMAN_LUNG_CANCER_EARLY_VS_LATE_UP.html Up-regulated genes classifying non-tumor lung tissues by age after incution of lung cancer by urethane injection [PubChem=5641]: early (24-26 weeks) vs late (46 weeks). 18172294 164/192 Jessica Robertson 3.98036365990569e-07 9.85176532498944e-07 4070 3666 3886 3.61851307277785e-08 1704 1.22055522457418 1.35308349141929 1 2.89830953963545 3384 3864 4068 4068 1704 3886 4658 3111 4361 4394 2828 4357 M1024 REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION.html Genes involved in RNA Polymerase III Transcription Termination 20/22 Reactome 7.39814193711904e-06 9.38184576657761e-06 3865 4020.27272727273 3888 6.72560619604284e-07 3435 1.17557649085247 1.649551966553 1 2.32692304993825 3861 4590 3672 4472 3664 3888 3435 4322 3765 4410 4144 4358 M13686 GENTILE_UV_RESPONSE_CLUSTER_D9 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D9.html Cluster d9: genes progressively down-regulated in WS1 cells (fibroblast) through 24 h after irradiation with high dose UV-C. 12907719 35/42 John Newman 2.28155734130041e-07 7.89313577332338e-07 3875 3599.18181818182 3888 2.07414325264933e-08 1092 1.33110152889778 -1.36320904246702 -1 3.21687490345162 3873 3419 3355 3997 1092 4124 3888 4336 4310 2753 4444 4359 M7982 ISHIKAWA_STING_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/ISHIKAWA_STING_SIGNALING.html Prmary innate immune response genes induced in 293T cells (embryonic kidney) by overexpression of STING (TMEM173) [GeneID=340061]. 18724357 8/9 Jessica Robertson 0.00379854854472774 0.00391209887216123 3400 3922.45454545455 3888 0.00038050572454518 2595 1.8728172999387 -2.36471687786175 -1 1.7633002720669 3399 4370 4584 4013 4555 3805 2595 3595 4549 3794 3888 4360 M12820 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_18 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_18.html Amplification hot spot 18: colocolized fragile sites and cancer genes in the 18q11.2-q23 region. 16751803 5/5 Arthur Liberzon 0.00425875188655225 0.00438223433715427 4265 3459 3889 0.000426693560382293 1330 1.07252699702185 -1.16521955925321 -1 0.967168442978774 4262 2480 4375 3889 4559 3284 1846 4149 1330 3253 4622 4361 M17961 NIKOLSKY_BREAST_CANCER_14Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_14Q22_AMPLICON.html Genes within amplicon 14q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 18/21 Jessica Robertson 0.00292325874318806 0.00301656783293565 3410 3830.09090909091 3889 0.000266104570548459 3127 1.59382346586454 1.71906662339708 1 1.56553110253113 3279 4048 3127 4598 4539 3407 3943 3889 4102 3410 3789 4362 M1920 CHEN_METABOLIC_SYNDROM_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_METABOLIC_SYNDROM_NETWORK.html Genes forming the macrophage-enriched metabolic network (MEMN) claimed to have a causal relationship with the metabolic syndrom traits. 18344982 1395/1952 Jessica Robertson 2.78642898645684e-41 6.57597240803814e-39 4435 2625.27272727273 3889 2.78642898645682e-42 12 2.19053263276856 2.3583671758709 1 33.5863629452318 4434 1068 4607 222 441 4130 3889 4118 1672 12 4285 4363 M14897 REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN.html Genes involved in Regulation of Glucokinase by Glucokinase Regulatory Protein 28/32 Reactome 1.6088354148e-05 1.92343038446201e-05 1550 3071.09090909091 3891 1.4625883455946e-06 427 0.823157182685815 0.733893487320154 1 1.51113276776397 1550 4280 3976 4521 3891 1349 427 2054 4547 4461 2726 4364 M2204 TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_UP.html Genes up-regulated in normal ductal and normal lobular breast cells. 17389037 91/102 Arthur Liberzon 1.4826128997538e-05 1.78336719848062e-05 4570 3848.09090909091 3891 1.34783899218011e-06 2746 1.76520417327805 2.09885530400204 1 3.32109476511411 4568 3891 2917 4220 3865 4535 3848 4461 2746 3089 4189 4365 M11025 HOEGERKORP_CD44_TARGETS_TEMPORAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_TEMPORAL_DN.html Genes temporally down-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 27/40 Kevin Vogelsang 9.11488079870396e-07 1.63888113421307e-06 4610 3687.90909090909 3891 8.28625870465237e-08 2439 1.69625557304119 1.77177973923166 1 3.89661885874798 4606 3161 2641 3918 2502 4661 4682 4202 3891 2439 3864 4366 M493 REACTOME_EXTRINSIC_PATHWAY_FOR_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTRINSIC_PATHWAY_FOR_APOPTOSIS.html Genes involved in Extrinsic Pathway for Apoptosis 14/17 Reactome 8.59601025673386e-07 1.57310167253419e-06 4175 3527.81818181818 3892 7.81455783221395e-08 2358 2.34629293596171 -2.08169394330479 -1 5.42583950723268 4173 4064 2552 4573 2449 4443 4628 2674 3000 2358 3892 4367 M11218 TURJANSKI_MAPK7_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK7_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK7 [GeneID=5598] phosphorylation. 17496919 9/9 Arthur Liberzon 0.234363650668882 0.235310876655418 4470 3917.72727272727 3892 0.0263513760972519 2608 2.84800619201555 2.84800619201555 1 0.669658234826536 4469 4637 4358 3548 4687 4525 2608 3396 3892 3878 3097 4368 M1668 JIANG_AGING_HYPOTHALAMUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_HYPOTHALAMUS_UP.html Up-regulated in the hypothalamus of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 66/78 John Newman 2.74146685809166e-06 3.93065722059315e-06 3845 3983.09090909091 3893 2.49224570390715e-07 3217 1.29886815837668 1.31678885709972 1 2.77357076676449 3844 4489 3612 4659 3217 3676 3499 4193 3893 4416 4316 4369 M1289 HUI_MAPK14_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUI_MAPK14_TARGETS_UP.html Genes up-regulated in fetal liver (days E13.5 and E15.5) samples from embryo-specific Cre-lox knockout of MAPK14 [GeneID=1432]. 17468757 25/34 Leona Saunders 4.09453511413195e-05 4.66028592686347e-05 4425 3356.54545454545 3895 3.72237392877554e-06 1292 1.86823993517869 -1.78560345405881 -1 3.20443371461788 4424 2795 2001 3895 4097 4296 4516 2667 4056 1292 2883 4370 M18799 REACTOME_DIABETES_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DIABETES_PATHWAYS.html Genes involved in Diabetes pathways 158/214 Reactome 3.74072783620337e-07 9.58016027502979e-07 3775 3750.54545454545 3896 3.40066224750092e-08 1637 1.67538981387939 -1.25199954296942 -1 4.00517862637147 3774 4432 3484 4662 1637 3896 2927 4408 3378 4370 4288 4371 M14118 ZHANG_RESPONSE_TO_CANTHARIDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_CANTHARIDIN_UP.html Genes up-regulated in HL-60 cells (promyeloid leukemia) by cantharidin [PubChem=6708701]. 14639605 19/31 John Newman 1.05542839627042e-06 1.82476997450418e-06 3390 3544.09090909091 3898 9.59480820547431e-08 1506 1.10772918138718 1.07005547461148 1 2.50651538638204 3386 4042 3409 3988 2605 3412 3898 1506 4567 4078 4094 4372 M13319 ABE_VEGFA_TARGETS_2HR http://www.broadinstitute.org/gsea/msigdb/cards/ABE_VEGFA_TARGETS_2HR.html Genes up-regulated in HUVEC cells (endothelium) at 2 h after VEGFA [GeneID=7422] stimulation. 12197474 36/49 John Newman 3.44041236716673e-05 3.94335754565978e-05 3860 3674.72727272727 3900 3.12769651848382e-06 2573 1.88525347305102 2.18460404337099 1 3.28907426094335 3858 3704 2633 3415 4069 4172 3959 3900 4036 2573 4103 4373 M1944 IRITANI_MAD1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IRITANI_MAD1_TARGETS_DN.html Genes down-regulated by overexpression of MAD1 [GeneID=4084] in primary thymocytes from RAG2 [GeneID=5897] knockout mice. 12234922 73/109 Jessica Robertson 2.03129944515486e-05 2.38738381004256e-05 1350 2958.54545454545 3900 1.84665290977208e-06 896 1.07716883206296 1.17666610281781 1 1.95222840015922 1350 3900 4005 4306 3956 1426 896 1424 4452 4298 2531 4374 M1792 WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_UP.html Protease genes up-regulated at tumor-bone interface compared to the tumor alone area. 18632634 20/35 Jessica Robertson 1.44936680229349e-05 1.74693853596151e-05 3360 3849.36363636364 3903 1.31761486441351e-06 2830 1.5472643845685 -1.04817539414045 -1 2.91045746957144 3358 4306 3405 4201 3856 3599 2830 4198 4145 3903 4542 4375 M2178 FIGUEROA_AML_METHYLATION_CLUSTER_6_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_6_DN.html Cluster 6 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 25/107 Arthur Liberzon 1.66221229084381e-05 1.97972294039434e-05 4185 3791.81818181818 3903 1.51111349985357e-06 2138 2.06749835944662 -2.32003230115383 -1 3.86068834311467 4182 3451 2138 4396 3903 4678 3727 3633 4291 2865 4446 4376 M10209 SHEPARD_BMYB_MORPHOLINO_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_BMYB_MORPHOLINO_UP.html Human orthologs of genes up-regulated in zebra fish after knockdown of BMYB [GeneID=4605] by morpholino. 16150706 254/302 Jennifer Shepard 1.4105935702439e-07 7.20206492018647e-07 4465 3604.90909090909 3904 1.2823578733529e-08 572 1.79607731363307 -1.68027491720396 -1 4.38680402310291 4464 4698 3265 3985 572 3687 4418 3904 2647 3742 4272 4377 M7399 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM.html Porphyrin and chlorophyll metabolism 25/48 KEGG 1.06487534127977e-05 1.31438588149595e-05 4010 3732.81818181818 3905 9.680731778873e-07 2699 1.68899359447294 2.10035638951003 1 3.26556274674925 4008 4556 2937 4400 3765 3905 4317 2956 2699 3208 4310 4378 M7561 KEGG_MTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MTOR_SIGNALING_PATHWAY.html mTOR signaling pathway 56/78 KEGG 7.44661332003388e-08 6.12334753842507e-07 4690 3444.63636363636 3905 6.76964870189879e-09 163 1.35592974222948 1.34108942329373 1 3.33793605798838 4689 2221 3565 2026 163 4676 4607 4559 3510 3905 3970 4379 M8692 NIKOLSKY_BREAST_CANCER_19Q13.1_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_19Q13.1_AMPLICON.html Genes within amplicon 19q13.1 identified in a copy number alterations study of 191 breast tumor samples. 19010930 73/126 Jessica Robertson 0.0043431722439611 0.00446812837652494 520 2975.81818181818 3905 0.000395615470320198 520 1.18864939851028 -1.18984508062924 -1 1.07327139560869 520 3905 4052 4115 4557 1450 909 2123 4508 4074 2521 4380 M15513 BIOCARTA_D4GDI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_D4GDI_PATHWAY.html D4-GDI Signaling Pathway 13/26 BioCarta 5.42972450908566e-05 6.10052360935118e-05 4315 3750.72727272727 3906 4.9362350203546e-06 2816 1.27660610433368 -0.776353644050385 -1 2.1137638555049 4311 4336 3371 4224 4151 3816 3305 2973 2816 3906 4049 4381 M9367 BIOCARTA_ERYTH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERYTH_PATHWAY.html Erythrocyte Differentiation Pathway 8/15 BioCarta 1.52536775657742e-05 1.83013111617829e-05 4175 3571.72727272727 3906 1.52537822703913e-06 2371 1.96274288123521 -2.76608829127845 -1 3.68947472551596 4174 2912 4189 4163 3906 3558 2371 2935 4240 2662 4179 4382 M2331 BILANGES_RAPAMYCIN_SENSITIVE_VIA_TSC1_AND_TSC2 http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_RAPAMYCIN_SENSITIVE_VIA_TSC1_AND_TSC2.html Genes translationally repressed by rapamycin (sirolimus) [PubChem=6610346] in MEF cells (embryonic fibroblast) lacking either TSC1 or TSC2 [GeneID=7248, 7249] but not in the wild type cells. 17562867 105/145 Arthur Liberzon 8.49073767192942e-06 1.06387793500151e-05 3505 3839.54545454545 3907 7.71888221952911e-07 3037 1.34341849583178 1.67716604598879 1 2.63679095205205 3503 4451 3907 3037 3708 4193 4052 3117 3914 4561 3792 4383 M3548 REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY.html Genes involved in NEP/NS2 Interacts with the Cellular Export Machinery 30/34 Reactome 1.6959292515006e-05 2.01733519835756e-05 1175 2896.18181818182 3908 1.54176575015371e-06 328 0.850038313675507 0.780132089369071 1 1.55503764395347 1172 4006 3978 4516 3908 1030 328 1671 4527 4328 2394 4384 M2458 SANDERSON_PPARA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANDERSON_PPARA_TARGETS.html Hepatic genes regulated by fasting or in response to WY14643 [PubChem=5694] and which require intact PPARA [GeneID=5465]. 19805517 16/18 Arthur Liberzon 0.000529250031683749 0.000558225731742412 4430 3915.81818181818 3909 4.81252177551615e-05 2670 1.6117626701018 -1.30974345331252 -1 2.0586453362832 4426 3204 2670 3909 4444 4555 3884 4121 3659 3563 4639 4385 M959 REACTOME_DESTABILIZATION_OF_MRNA_BY_KSRP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_KSRP.html Genes involved in Destabilization of mRNA by KSRP 20/20 Reactome 0.00014391701653707 0.000156014772176153 4510 3105.27272727273 3910 1.30842210903426e-05 510 0.771913544139567 0.696234671503779 1 1.13173371453508 1183 4584 3910 4507 4313 1487 510 1731 4433 4508 2992 4386 M41 PID_ER_NONGENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ER_NONGENOMIC_PATHWAY.html Plasma membrane estrogen receptor signaling 18832364 60/69 Pathway Interaction Database 1.58926791695339e-07 7.31918027928963e-07 4685 3469.54545454545 3911 1.44478911978295e-08 688 1.43860071509366 -1.12565747123006 -1 3.49967831031294 4681 3911 3543 1759 688 4339 3540 3251 4117 4253 4083 4387 M174 PID_UPA_UPAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_UPA_UPAR_PATHWAY.html Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling 18832364 49/84 Pathway Interaction Database 7.29207016751709e-05 8.09087240025403e-05 4210 3404.36363636364 3911 6.62937443639968e-06 1338 2.3644203852123 -2.45788981933428 -1 3.84096494889589 4610 3379 1338 2213 4208 4227 4523 3411 3911 1422 4206 4388 M11716 REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING.html Genes involved in Formation of ATP by chemiosmotic coupling 16/21 Reactome 0.034360831350972 0.034833145183975 1500 3466.36363636364 3914 0.00317359401324457 1004 0.569188552373289 0.569188552373289 1 0.283709168883062 1496 4624 3914 4523 4628 2012 1004 3139 4715 4696 3379 4389 M1065 MIDORIKAWA_AMPLIFIED_IN_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/MIDORIKAWA_AMPLIFIED_IN_LIVER_CANCER.html Candidate genes in genomic amplification regions in hepatocellular carcinoma (HCC) samples. 16785998 57/76 Arthur Liberzon 7.88673435151077e-08 6.28807198296129e-07 3910 3451 3917 7.16975875840061e-09 180 1.75370428848466 1.9799213262172 1 4.32369857598587 3908 3917 3117 4593 180 4185 4454 4242 2183 3261 3921 4390 M1612 BURTON_ADIPOGENESIS_1 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_1.html Strongly up-regulated at 2 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 41/47 John Newman 1.73717308081357e-05 2.06379485060157e-05 3725 3733.63636363636 3917 1.57926072554818e-06 1781 1.46551423626938 1.5786787515863 1 2.71137479582257 3724 4531 3202 4506 3912 4354 4489 2181 4473 1781 3917 4391 M5244 KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM.html Glyoxylate and dicarboxylate metabolism 16/18 KEGG 0.000411183063267705 0.000435935323140963 3665 3920.09090909091 3918 3.73872667336068e-05 3548 1.07153751003276 1.28852026703973 1 1.39814102543388 3665 4329 3576 3998 4418 3918 3596 3704 4342 3548 4027 4392 M12101 REACTOME_P130CAS_LINKAGE_TO_MAPK_SIGNALING_FOR_INTEGRINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P130CAS_LINKAGE_TO_MAPK_SIGNALING_FOR_INTEGRINS.html Genes involved in p130Cas linkage to MAPK signaling for integrins 19/21 Reactome 0.471956054430835 0.472958084270391 3280 3819.54545454545 3921 0.0563994443532475 2799 2.24008630977216 -2.17138010438628 -1 0.242907558061654 3280 4595 2799 4032 4710 4427 2842 3578 3921 3538 4293 4393 M2586 SMIRNOV_RESPONSE_TO_IR_2HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_2HR_DN.html Genes down-regulated in B lymphocytes at 2 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 70/81 Itai Pashtan 1.13591820779242e-06 1.92999781885537e-06 3925 3730.45454545455 3921 1.03265344936133e-07 2656 1.86808284585923 -1.5479510346841 -1 4.24305987050024 3921 4197 2691 3932 2656 3989 4435 3667 3641 3375 4531 4394 M8411 LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q.html Genes down-regulated in urothelial cell carcinoma (UCC) tumors with LOH on 9q as compared to the tumors showing retention. 16532037 152/181 Arthur Liberzon 6.16472476506731e-07 1.26017760463914e-06 3810 3672.90909090909 3923 5.60429681137716e-08 2151 1.46994302891443 -1.30136045816078 -1 3.4375204056021 3808 4161 3984 3793 2151 4615 3923 4100 2405 4139 3323 4395 M4741 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS.html Systemic lupus erythematosus 54/146 KEGG 1.16569924740532e-05 1.42689326964552e-05 4330 3769.27272727273 3927 1.05973220369416e-06 2392 1.87933812054183 -2.34092923043465 -1 3.61226269052897 3769 3927 2392 3514 3801 4216 4227 4201 4326 2760 4329 4396 M1767 JI_CARCINOGENESIS_BY_KRAS_AND_STK11_DN http://www.broadinstitute.org/gsea/msigdb/cards/JI_CARCINOGENESIS_BY_KRAS_AND_STK11_DN.html Cluster B: genes down-regulated in primary lung tumors driven by KRAS [GeneID=3845] activation and loss of STK11 [GeneID=6794]; also up-regulated in human squamous cell carcinoma (SCC) vs adenocarcinoma subtype of NSCLC (non-small cell lung cancer). 17676035 25/30 Jessica Robertson 0.470844637678165 0.471944508354415 2370 3670.27272727273 3928 0.0562190648303887 2025 2.51820245606431 2.86274310823651 1 0.280221451504993 2369 4286 2025 4210 4682 3738 4024 3928 4385 3212 3514 4397 M6515 SPIRA_SMOKERS_LUNG_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SPIRA_SMOKERS_LUNG_CANCER_DN.html Down-regulated genes that distinguished smokers with and without lung cancer. 17334370 53/87 Jessica Robertson 0.000916531359832372 0.000958358001419759 2285 3853.63636363636 3929 8.33557649436613e-05 2284 1.4500264846885 -1.35916040414164 -1 1.71016994699654 2284 3929 3791 4508 4481 3670 3563 3636 4325 4148 4055 4398 M1746 ZHENG_FOXP3_TARGETS_IN_THYMUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_THYMUS_UP.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are up-regulated only in developing (located in the thymus) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 258/299 Jessica Robertson 3.23963369003809e-07 9.03187289003859e-07 2820 3550 3930 2.94512197008539e-08 1469 1.38603829511639 -1.29972976123035 -1 3.31908146627623 2818 3852 4001 4522 1469 3371 2834 3930 3932 4122 4199 4399 M16409 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD.html Human environmental stress response genes not changed in primary fibroblasts from old donors in response to UV radiation. 15897889 31/34 Jessica Robertson 6.67089414141009e-05 7.42784155401171e-05 4600 3678 3930 6.06463311499202e-06 1941 2.28920148321047 -1.27448402033493 -1 3.75136662427908 4596 3145 2600 3930 4188 4272 4471 3857 1941 3235 4223 4400 M16335 MELLMAN_TUT1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MELLMAN_TUT1_TARGETS_DN.html Genes down-regulated in HEK293 cells (embryo kidney) after knockdown of TUT1 [GeneID=64852] by RNAi. 18288197 66/77 Jessica Robertson 1.95746920961858e-06 2.96891216883023e-06 4170 3529.72727272727 3930 1.77951904663279e-07 2371 1.75007055550001 -1.54089292643929 -1 3.84021106492133 4166 2649 2851 3991 3023 4278 4249 2371 4001 3318 3930 4401 M17517 WU_HBX_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_2_DN.html Genes down-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in primary hepatocytes. 11439330 19/22 John Newman 2.13675775211587e-06 3.20402407747356e-06 4515 3766 3931 1.94250893404744e-07 2428 2.27961585629911 -1.44120378758429 -1 4.98699850157474 4514 3198 2428 3931 3067 4552 4527 4064 3249 3541 4355 4402 M10597 WHITEHURST_PACLITAXEL_SENSITIVITY http://www.broadinstitute.org/gsea/msigdb/cards/WHITEHURST_PACLITAXEL_SENSITIVITY.html Genes that reduced viability of NCI-H1155 cells (non-small-cell lung cancer, NSCLC) in the presence of otherwise sublethal concentrations of paclitaxel [PubChem=4666], based on RNAi synthetic lethal screen. 17429401 47/65 Jessica Robertson 3.32945010220906e-06 4.64803445206352e-06 4700 3585 3933 3.02677740087661e-07 1622 2.16929834792685 -1.5823507494027 -1 4.60228293531233 4700 3933 2390 3421 3305 4016 4687 4358 1622 2625 4378 4403 M84 PID_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATM_PATHWAY.html ATM pathway 18832364 41/48 Pathway Interaction Database 4.13024129958513e-05 4.69639579234927e-05 1435 2885.72727272727 3935 3.75483531095165e-06 348 1.15909133958782 1.14137290844111 1 1.96753546299921 1434 4243 3935 4512 4100 814 348 2395 4060 4203 1699 4404 M8702 DAZARD_RESPONSE_TO_UV_NHEK_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_NHEK_DN.html Genes down-regulated in NHEK cells (normal keratinocytes) by UV-B irradiation. 12771951 438/494 John Newman 6.26497155130922e-07 1.27514729289261e-06 4640 3782.54545454545 3935 5.69543030490442e-08 2165 1.64425543026414 -1.36858955334131 -1 3.84769922275701 4639 4400 3915 3266 2165 4585 3813 3935 2318 4357 4215 4405 M1692 YANG_MUC2_TARGETS_COLON_3MO_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_COLON_3MO_DN.html Genes down-regulated in colon of 3 month old MUC2 [GeneID=4583] knockout mice. 18794118 8/18 Jessica Robertson 0.00255736512862403 0.00264419789859921 2940 3879.81818181818 3938 0.000256031295661789 2936 3.77947389389877 -4.80119855759473 -1 3.86797150900046 2936 4366 4506 3938 4536 4141 3177 4417 3860 3284 3517 4406 M1190 ZHAN_MULTIPLE_MYELOMA_CD1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_UP.html Top 50 up-regulated genes in cluster CD-1 of multiple myeloma samples with the characteristic expression spike of CCND1 [GeneID=595]. 16728703 45/75 Kevin Vogelsang 0.00225852308748512 0.00233725695525757 4545 3623.09090909091 3941 0.000205531366212108 1766 2.23351216573099 -2.30622245718897 -1 2.31347735474948 4544 3941 1766 2783 4524 4326 3678 3840 3970 1925 4557 4407 M11189 SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE.html IRF4 [GeneID=3662] target genes induced after activation of primary B lymphocytes by anti-IgM crosslinking. 18568025 114/132 Jessica Robertson 3.53117157349904e-06 4.88772135686671e-06 3945 3852.18181818182 3942 3.21016112847049e-07 3337 1.48356641607119 -1.70889358873957 -1 3.118619936406 4155 4445 3942 3794 3337 4307 3944 3652 3369 3990 3439 4408 M1558 BURTON_ADIPOGENESIS_12 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_12.html Strongly down-regulated at 2 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 49/54 John Newman 7.42227712669737e-06 9.40739743233393e-06 3060 3896.09090909091 3943 6.74754742528602e-07 3057 1.33872090433961 1.65148360800248 1 2.65615742111456 3057 3943 3897 4053 3667 4364 4423 3392 4014 4392 3655 4409 M712 REACTOME_MICRORNA_MIRNA_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MICRORNA_MIRNA_BIOGENESIS.html Genes involved in MicroRNA (miRNA) Biogenesis 23/27 Reactome 0.00310907929073869 0.00320691745023746 1435 3117 3944 0.000283043800908281 487 0.788988973346582 0.841720696283256 1 0.741283937244436 1433 4582 3944 4300 4541 1219 487 2186 4593 4463 2539 4410 M502 REACTOME_METABOLISM_OF_NON_CODING_RNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_NON_CODING_RNA.html Genes involved in Metabolism of non-coding RNA 50/58 Reactome 3.06700641956373e-05 3.53683613494767e-05 490 2798.45454545455 3945 2.78822652485947e-06 215 0.85832041829601 0.819162776275237 1 1.48650775149271 490 3945 4073 4110 4040 640 215 1797 4518 4544 2411 4411 M10828 SHEPARD_CRUSH_AND_BURN_MUTANT_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_CRUSH_AND_BURN_MUTANT_UP.html Human orthologs of genes up-regulated in the crb ('crash and burn') zebrafish mutant that represents a loss-of-function mutation in BMYB [GeneID=4605]. 16150706 236/269 Jennifer Shepard 2.28261200409917e-06 3.38909363301293e-06 3945 3771.45454545455 3945 2.07510397493525e-07 3102 1.73229149653582 1.8972090593539 1 3.76064141029929 3945 4143 3390 4064 3102 3277 3489 4371 3149 4067 4489 4412 M2556 HOLLEMAN_DAUNORUBICIN_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_B_ALL_UP.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 16/26 Arthur Liberzon 1.97494397595104e-05 2.32694347640762e-05 4580 3364.81818181818 3946 1.7954197320742e-06 1545 2.73197498887391 3.1640921891438 1 5.04045470478793 4576 3202 1545 2143 3946 4647 4526 4290 1590 2286 4262 4413 M19742 REACTOME_COPI_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COPI_MEDIATED_TRANSPORT.html Genes involved in COPI Mediated Transport 14/14 Reactome 0.00176342770067171 0.00183092361354387 1975 3283.09090909091 3949 0.000160440252596545 628 0.455189592723365 -0.471035814736997 -1 0.451057863041472 1975 4610 3949 4078 4511 1532 628 3180 4529 4679 2443 4414 M3694 LIN_MELANOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIN_MELANOMA_COPY_NUMBER_DN.html Candidate genes in significant regions of chromosomal copy number losses in a panel of melanoma samples. 18245465 55/59 Jessica Robertson 3.35452068367932e-05 3.8533311333576e-05 3955 4023.90909090909 3953 3.04961075809375e-06 3499 1.19525737205806 -1.23103068005938 -1 2.07179249388753 3567 4220 3953 4524 4059 3790 3639 4548 3499 4511 3953 4415 M1415 BYSTROEM_CORRELATED_WITH_IL5_UP http://www.broadinstitute.org/gsea/msigdb/cards/BYSTROEM_CORRELATED_WITH_IL5_UP.html Genes whose expression in bone marrow samples correlated directly with increased levels of serum IL5 [GeneID=3567]. 14525773 72/96 Kate Stafford 6.41719150475905e-07 1.29884836631487e-06 4685 3783.54545454545 3955 5.83381216053977e-08 2177 1.82110905764255 1.80859776110157 1 4.26107620488502 4684 3638 3240 3480 2177 4228 4049 4689 3955 3128 4351 4416 M15382 BROWNE_HCMV_INFECTION_10HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_10HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 10 h time point that were not up-regulated at the previous time point, 8 h. 11711622 178/261 John Newman 2.02469684575337e-05 2.38021646624058e-05 2810 3778.18181818182 3955 1.84065043601602e-06 2808 1.64212800863826 -1.41232949302211 -1 3.00324952650379 2808 4718 3691 4321 3955 3082 2934 4120 4013 3826 4092 4417 M1531 HU_GENOTOXIC_DAMAGE_24HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIC_DAMAGE_24HR.html Genes most consistently regulated at 24 h by all six genotoxins tested: cisplatin, methyl methanesulfonate, mitomycin C, taxol, hydroxyurea and etoposide [PubChem=2767;4156;5746;4666;3657;36462]. 15120960 48/88 John Newman 4.35094052758661e-06 5.86539343563559e-06 3960 3857.27272727273 3956 3.95540830224233e-07 3225 1.34211885640076 1.45361475038354 1 2.77376781822904 3956 3671 3412 4255 3426 3958 4028 3988 3928 3225 4583 4418 M739 REACTOME_RNA_POL_III_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION.html Genes involved in RNA Polymerase III Transcription 34/37 Reactome 9.33662761781623e-06 1.16246062664449e-05 3955 4016.63636363636 3957 8.48787931087971e-07 2978 0.958779403154485 -0.655666466915932 -1 1.85267553445326 3951 4545 3957 4515 3735 3934 2978 3634 4071 4533 4330 4419 M11383 BROWNE_HCMV_INFECTION_16HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_16HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 16 h time point that were not up-regulated at the previous time point, 14 h. 11711622 329/382 John Newman 9.17312320460896e-07 1.64593206000409e-06 4100 3590.63636363636 3958 8.33920639039817e-08 2507 1.52215282587414 1.49790450226547 1 3.49039491056266 4098 3559 3958 2532 2507 4203 3595 3998 2685 4210 4152 4420 M715 REACTOME_REGULATORY_RNA_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATORY_RNA_PATHWAYS.html Genes involved in Regulatory RNA pathways 26/30 Reactome 0.00132906060694735 0.00138419374774746 1770 3025.63636363636 3959 0.000120896745156579 402 0.777861450683316 0.825764338976704 1 0.844270899430832 1766 4034 3959 4295 4495 1084 402 2127 4568 4501 2051 4421 M497 REACTOME_PROCESSING_OF_INTRONLESS_PRE_MRNAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSING_OF_INTRONLESS_PRE_MRNAS.html Genes involved in Processing of Intronless Pre-mRNAs 18/18 Reactome 0.00307828751344515 0.00317585072425379 2870 3675.45454545455 3961 0.000280236652380123 1685 0.721645712252867 0.586509023306128 1 0.674968574945737 2870 4334 3961 4301 4540 2072 1685 3767 4688 4477 3735 4422 M13247 BIOCARTA_TCYTOTOXIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCYTOTOXIC_PATHWAY.html T Cytotoxic Cell Surface Molecules 7/15 BioCarta 0.000147962460157113 0.0001602530545988 1020 2909.27272727273 3962 1.47972312880747e-05 193 1.29416695475431 1.29416695475431 1 1.9252257204587 1018 4363 4197 3962 4328 879 193 4517 4700 2395 1450 4423 M14772 NOJIMA_SFRP2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NOJIMA_SFRP2_TARGETS_UP.html Cellular proliferation, growth, apoptosis and Wnt signaling genes up-regulated in SNU638 cells (gastric cancer) by overexpression of SFRP2 [GeneID=6423] off a plasmid vector. 17297461 42/48 Arthur Liberzon 1.06368643590092e-05 1.31326183035636e-05 3965 3636.27272727273 3962 9.66992344358243e-07 1635 1.90331519522915 -1.6376292307618 -1 3.68657384514571 3962 3954 2348 3994 3764 4400 4224 4558 4204 1635 2956 4424 M6427 BIOCARTA_THELPER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_THELPER_PATHWAY.html T Helper Cell Surface Molecules 7/15 BioCarta 0.000147962460157113 0.0001602530545988 1020 2910.27272727273 3963 1.47972312880747e-05 194 1.29416695475431 1.29416695475431 1 1.9252257204587 1019 4364 4198 3963 4329 880 194 4518 4701 2396 1451 4425 M2605 ONKEN_UVEAL_MELANOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONKEN_UVEAL_MELANOMA_DN.html Genes down-regulated in uveal melanoma: class 2 vs class 1 tumors. 16651410 769/1035 Arthur Liberzon 3.34179516954652e-07 9.10697066989583e-07 4555 3418.54545454545 3963 3.34179567208839e-08 1612 1.65985748491781 1.83403325334419 1 3.98226813519528 4554 3267 4278 2234 1612 4365 3996 2812 2309 3963 4214 4426 M669 REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY.html Genes involved in Downregulation of SMAD2/3:SMAD4 transcriptional activity 28/39 Reactome 1.48361190626065e-06 2.36896082461106e-06 2205 3355.18181818182 3965 1.34873900614868e-07 971 0.745640579615991 -0.612487199082522 -1 1.63685316423882 2204 4005 3965 4088 2854 1787 971 4703 4620 4460 3250 4427 M17694 REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM.html Genes involved in Branched-chain amino acid catabolism 20/20 Reactome 0.0810907905609094 0.0817140331869113 4135 3816.54545454545 3968 0.00765851879200642 1860 1.05782606210105 -0.384055070475647 -1 0.412690406974484 4133 4589 3785 4652 4715 3760 3968 2885 1860 4507 3128 4428 M8887 LEE_METASTASIS_AND_RNA_PROCESSING_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_METASTASIS_AND_RNA_PROCESSING_UP.html Components of RNA post-transcriptional modification machinery up-regulated in MDA-MB-435 cells (breast cancer) whose metastatic potential has been reduced by expression of NME1 [GeneID=4830]. 18245461 24/29 Jessica Robertson 2.23623610283929e-05 2.61327912983447e-05 2240 3512.18181818182 3968 2.03296257623023e-06 1797 0.830924200134889 0.821147027152301 1 1.48138281892347 2238 4296 3968 4089 3983 2061 1797 3562 4678 4476 3486 4429 M784 REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE.html Genes involved in Citric acid cycle (TCA cycle) 22/23 Reactome 6.77090288091699e-05 7.53386647758798e-05 1245 3305.18181818182 3969 6.15555570621079e-06 1244 0.757021475063128 0.794756985091462 1 1.20518413085392 1244 4297 3969 4641 4194 1752 1646 3033 4274 4447 2860 4430 M2228 PILON_KLF1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PILON_KLF1_TARGETS_DN.html Genes down-regulated in erythroid progenitor cells from fetal livers of E13.5 embryos with KLF1 [GeneID=10661] knockout compared to those from the wild type embryos. 18852285 2428/2834 Arthur Liberzon 2.19272694177767e-07 7.78436449348851e-07 4085 3816.18181818182 3969 2.19272715814001e-08 1158 1.36663213664482 1.39723831902932 1 3.30738955374987 4081 3825 4669 3829 1158 3757 3969 4469 3106 4719 4396 4431 M2123 HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_UP.html Up-regulated genes in the cancer gene signature, representing a gene signature of cellular transformation. 20385360 326/397 Arthur Liberzon 1.18039316271738e-07 7.06112554001409e-07 4440 3338.09090909091 3971 1.07308475095497e-08 404 1.8054303909983 -1.75459961774644 -1 4.41614085776648 4437 2513 2699 4594 404 4715 4173 4108 2849 2256 3971 4432 M14137 NIKOLSKY_BREAST_CANCER_19P13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_19P13_AMPLICON.html Genes within amplicon 19p13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 6/7 Jessica Robertson 2.96439138218739e-05 3.42435813116116e-05 4390 3602.72727272727 3972 2.96443092720303e-06 1477 1.3860616817994 -0.960490802618859 -1 2.43908151187861 4387 2479 4464 3903 4052 4612 4540 2948 3972 2796 1477 4433 M12964 XU_RESPONSE_TO_TRETINOIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_DN.html Genes down-regulated in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin [PubChem=444795] alone. 16140955 21/22 Kevin Vogelsang 3.03270650386731e-06 4.28702446788071e-06 3975 3940.72727272727 3973 2.75700971315478e-07 3267 0.952262734621465 0.924957176901862 1 2.00565145108841 3992 4301 3832 4475 3267 3972 3562 3406 4383 3973 4185 4434 M139 PID_MYC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_PATHWAY.html C-MYC pathway 18832364 34/39 Pathway Interaction Database 9.88661402184579e-07 1.73927760652673e-06 4330 3837.45454545455 3975 8.9878349680085e-08 2557 0.791899493629869 0.905033567546228 1 1.78424179899228 4329 3420 3975 4503 2557 3604 4300 3294 4423 4324 3483 4435 M2837 BARIS_THYROID_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARIS_THYROID_CANCER_UP.html Genes up-regulated in oncocytic follicular carcinoma (FTC) vs mitochondrial-rich papillary carcinoma (PTC) types of thyroid cancer. 15806164 29/39 Arthur Liberzon 0.0056166665122278 0.00576820407696153 3310 3921.54545454545 3976 0.00051191431771295 2937 1.1710140215131 1.23870475755256 1 1.00437148902949 3306 4548 3827 4474 4564 3549 3853 4076 3976 4027 2937 4436 M892 REACTOME_SYNTHESIS_OF_SUBSTRATES_IN_N_GLYCAN_BIOSYTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_SUBSTRATES_IN_N_GLYCAN_BIOSYTHESIS.html Genes involved in Synthesis of substrates in N-glycan biosythesis 15/18 Reactome 0.239479112432059 0.24029366723625 4710 3856.09090909091 3978 0.02457940193434 1681 0.563726872152276 -0.581993019295214 -1 0.0903543202807666 2812 4632 3951 4663 4707 3031 1681 3559 4710 4693 3978 4437 M1724 KEGG_RNA_POLYMERASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_POLYMERASE.html RNA polymerase 27/29 KEGG 2.23336440349251e-05 2.61186322707747e-05 2360 3605.72727272727 3980 2.03035188742067e-06 1638 0.745894043552105 0.827287492214753 1 1.32474011281972 2356 4569 3997 4528 3980 2620 1638 3160 4591 4562 3662 4438 M795 REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT.html Genes involved in Transport of Mature mRNA Derived from an Intronless Transcript 38/59 Reactome 2.2349832794139e-05 2.61310901135339e-05 1180 3043.45454545455 3981 2.03182362269572e-06 393 0.790673695035712 0.710873367622644 1 1.4072088352078 1179 4543 4057 4316 3981 938 393 2427 4585 4557 2502 4439 M19016 GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN.html Genes down-regulated in erythroid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 678/930 Arthur Liberzon 5.11701610602368e-07 1.12704049506997e-06 3325 3688.72727272727 3985 5.11701728429748e-08 2071 1.5989641866604 -1.37623972545269 -1 3.77481598526432 3321 4666 4280 4556 2071 2697 3241 3985 3370 4238 4151 4440 M8916 TIEN_INTESTINE_PROBIOTICS_2HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_2HR_DN.html Genes down-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 2h. 16394013 124/139 Arthur Liberzon 1.15368017058476e-06 1.95174566493192e-06 3455 3600.27272727273 3986 1.04880070506834e-07 1488 1.72726997259776 1.90757205846574 1 3.91607318807532 3454 4166 3619 4225 2669 4093 4580 3182 1488 4141 3986 4441 M4023 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP.html Genes up-regulated in kidney biopsies from patients with well functioning kidneys more than 1-year post transplant compared to the biopsies from normal living kidney donors. 15307835 775/962 Jean Junior 2.92622921489353e-07 8.65943692432442e-07 4480 3707.54545454545 3990 2.92622960022038e-08 1463 1.63367682819624 1.74210887853411 1 3.93304527512634 3662 4665 4481 3277 1463 4022 4479 2858 3407 4479 3990 4442 M2475 LIU_IL13_MEMORY_MODEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_IL13_MEMORY_MODEL_DN.html Genes down-regulated in BEAS-2B cells (bronchial epithelium) stimulated with IL13 [GeneID=3596] on days 1 to 3 and then rested for the next 3 days (repeated-stimulation or memory model) 20123980 9/9 Arthur Liberzon 6.23217219924586e-05 6.96398029839973e-05 4105 3759.18181818182 3992 6.23234698601124e-06 2069 1.87289844237219 -2.16563267634932 -1 3.08115549160444 2846 4101 4706 3978 4200 3992 4591 2069 4105 3464 3299 4443 M249 PID_PI3KCI_AKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PI3KCI_AKT_PATHWAY.html Class I PI3K signaling events mediated by Akt 18832364 46/49 Pathway Interaction Database 6.60968819556611e-07 1.32081830156952e-06 4515 3903.36363636364 3994 6.00880925580376e-08 2215 1.04039443106017 -0.961300352466082 -1 2.40984171653335 4515 4232 3994 3792 2215 4639 3508 3734 3108 4567 4633 4444 M1055 REACTOME_RNA_POL_III_CHAIN_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_CHAIN_ELONGATION.html Genes involved in RNA Polymerase III Chain Elongation 18/20 Reactome 8.42630882506323e-07 1.55360068962103e-06 3755 3829.54545454545 3994 7.66028368405413e-08 2428 1.17557649085247 1.649551966553 1 2.6961336448203 3754 4322 3586 4025 2428 3994 3542 4437 3549 4363 4125 4445 M12851 BIOCARTA_CELL2CELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELL2CELL_PATHWAY.html Cell to Cell Adhesion Signaling 14/19 BioCarta 0.000126743681668667 0.000137936402461634 3630 3831.09090909091 3995 1.15228167325483e-05 2807 1.02663124023243 1.06982413561371 1 1.54378021794536 2807 4337 3628 4034 4296 3530 3995 3628 4485 4211 3191 4446 M6051 DORSAM_HOXA9_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORSAM_HOXA9_TARGETS_DN.html HOXA9 [GeneID=3205] targets down-regulated in hematopoietic stem cells. 14604967 38/53 Broad Institute 6.09979653577596e-07 1.252328823352e-06 4125 3733.63636363636 3995 5.54527111547947e-08 2138 1.59569433274902 -1.46432551092405 -1 3.73761669649005 4123 3701 3102 4208 2138 3995 4252 4113 4182 3598 3658 4447 M665 REACTOME_TRANSCRIPTIONAL_ACTIVITY_OF_SMAD2_SMAD3_SMAD4_HETEROTRIMER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTIONAL_ACTIVITY_OF_SMAD2_SMAD3_SMAD4_HETEROTRIMER.html Genes involved in Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer 49/61 Reactome 1.9076121917567e-06 2.90543063733193e-06 3090 3624.09090909091 3996 1.73419440531134e-07 1473 0.941101048535213 -0.71280184131436 -1 2.04549784874116 3086 3936 3996 4091 3010 2645 1473 4180 4421 4317 4710 4448 M714 REACTOME_PI3K_AKT_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_AKT_ACTIVATION.html Genes involved in PI3K/AKT activation 44/47 Reactome 2.14883712443653e-07 7.72658093558287e-07 3235 3544 3997 1.95348848574816e-08 1030 1.14280952518752 -0.983860787787957 -1 2.75900817096296 3234 4234 3836 4665 1030 2554 2480 4240 4341 4373 3997 4449 M13713 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 13. 12554760 193/223 Arthur Liberzon 1.36349136524663e-06 2.21890986133675e-06 1420 3492.81818181818 3997 1.23953837299707e-07 1419 1.08031383518796 1.01672458616672 1 2.40634348375618 1419 4711 4180 4128 2788 2622 1867 3997 4119 4597 3993 4450 M1870 REACTOME_GLUCOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_METABOLISM.html Genes involved in Glucose metabolism 62/81 Reactome 1.9656309258741e-05 2.31654880652329e-05 2640 3660.09090909091 3999 1.78695317126268e-06 2213 1.08649341364328 0.708017083564208 1 1.97527673998194 2639 4493 3999 4092 3945 2434 2213 4182 3651 4459 4154 4451 M5754 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_DN http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_DN.html Genes down-regulated more than two-fold in lymphoblastoid cell lines from European population compared to those from Asian population. 17206142 20/30 Leona Saunders 3.8655947907566e-06 5.28245727051857e-06 4320 3676.09090909091 4000 3.51418325724147e-07 2078 1.78903601965938 1.96282753306154 1 3.74678564165483 4000 4299 2854 4385 3382 4318 4578 2078 4320 2931 3292 4452 M8655 DAIRKEE_CANCER_PRONE_RESPONSE_BPA http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_CANCER_PRONE_RESPONSE_BPA.html 'Cancer prone response profile' (CPRP): genes changed in response to bisphenol A [PubChem=6623] in epithelial cell cultures from patients at high risk of breast cancer. 18381411 62/87 Jessica Robertson 1.09072251006591e-05 1.34277784233466e-05 4005 3402.09090909091 4002 9.91570834290706e-07 696 1.73112103173067 -1.8394679663374 -1 3.34179999793942 4002 2652 3241 1520 3775 4626 4286 4152 696 4124 4349 4453 M1994 KYNG_NORMAL_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_NORMAL_AGING_UP.html Genes distinctly up-regulated in primary fibroblast cultures from normal old donors compared to those from normal young donors. 14527998 28/32 Arthur Liberzon 1.66348564522433e-07 7.3358205358541e-07 4445 3823.81818181818 4004 1.51225979182314e-08 740 1.39830986276338 1.57431608042193 1 3.39970690587928 4445 4004 3499 4254 740 4673 4705 4345 3758 3980 3659 4454 M17421 DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_UP.html Genes up-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071], after low dose UVC irradiation. 15608684 16/35 Arthur Liberzon 0.000225652451372262 0.000242228694672976 4345 3930.81818181818 4005 2.05159636099507e-05 3205 1.15453007787114 -1.29720449081965 -1 1.62879480540723 3205 4059 3338 4005 4361 4341 3640 4344 4459 3559 3928 4455 M7507 CHOI_ATL_STAGE_PREDICTOR http://www.broadinstitute.org/gsea/msigdb/cards/CHOI_ATL_STAGE_PREDICTOR.html Genes used to predict the clinical stages of acute T-cell leukemia (ATL): chronic vs acute. 16909099 86/133 Leona Saunders 6.1903777365597e-06 7.97885934368154e-06 2275 3662.90909090909 4007 5.62763195923919e-07 2272 1.1435592795524 -0.945203321884091 -1 2.29453826129421 2272 4462 4043 4656 3597 2641 2448 4007 4239 4222 3705 4456 M13814 GENTILE_UV_RESPONSE_CLUSTER_D5 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D5.html Cluster d5: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 52/57 John Newman 3.35657527241286e-05 3.85475311089749e-05 4675 3860.36363636364 4007 3.05147862301259e-06 2501 1.52992402176758 1.22219265017675 1 2.66579659883472 4671 3932 3502 2501 4061 4340 4007 3095 3426 4215 4714 4457 M783 REACTOME_PROCESSING_OF_CAPPED_INTRONLESS_PRE_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSING_OF_CAPPED_INTRONLESS_PRE_MRNA.html Genes involved in Processing of Capped Intronless Pre-mRNA 27/30 Reactome 7.50569911472335e-05 8.31378888818231e-05 1465 3118.45454545455 4008 6.82359563408789e-06 460 0.790225191416506 0.752799570563553 1 1.24664363719073 1463 4294 4008 4303 4213 854 460 3059 4626 4444 2579 4458 M3475 CHEN_HOXA5_TARGETS_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_6HR_UP.html Genes up-regulated 6 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 11/11 Arthur Liberzon 2.50831377465923e-05 2.91463343584234e-05 4460 3676 4008 2.28031124860931e-06 1932 2.84477652182441 -2.22843718735318 -1 5.13875101384103 4458 4342 1932 4184 4008 4417 3123 2588 3884 3305 4195 4459 M490 REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE.html Genes involved in Pyruvate metabolism and Citric Acid (TCA) cycle 42/44 Reactome 2.51319709169193e-05 2.91958904080382e-05 1760 3323 4009 2.28475072906142e-06 1760 0.949914520122134 0.999446682057921 1 1.68229695370028 1760 4530 4040 4308 4009 1883 1833 2459 4318 4467 2946 4460 M8397 ELVIDGE_HIF2A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF2A_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) after knockdown of HIF2A [GeneID=2034] by RNAi. 16565084 9/9 Arthur Liberzon 0.00209062631603112 0.00216635701683137 2615 3782.81818181818 4009 0.000209259574746032 2615 1.13978975582928 -0.607458601241949 -1 1.1712101749004 2615 4358 4314 4009 4526 3320 2701 3070 4634 4206 3858 4461 M15531 MOOTHA_FFA_OXYDATION http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_FFA_OXYDATION.html Genes involved in free fatty acid oxidation; based on literature and sequence annotation resources and coverted to Affymetrix HG-U133A probe sets. 12808457 26/29 Vamsi Mootha 6.90614514958363e-06 8.80524178985271e-06 4710 4051.63636363636 4009 6.27833348104729e-07 3470 0.872369814027263 -0.797815422977012 -1 1.72351786585936 4708 4009 3938 4268 3642 3681 3697 4110 3470 4425 4620 4462 M14449 BIOCARTA_ETS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETS_PATHWAY.html METS affect on Macrophage Differentiation 26/27 BioCarta 1.57424282371403e-06 2.48047396047511e-06 4455 3899.63636363636 4010 1.43113086380736e-07 2896 1.2801167847807 1.06519648026175 1 2.83573417414162 4455 4010 3283 3758 2896 4553 4111 4203 3665 3347 4615 4463 M15967 SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_DN.html Genes down-regulated in circulating endothelial cells (CEC) from cancer patients compared to those from healthy donors. 16540638 6/8 Arthur Liberzon 0.0157974166650456 0.0161079729226648 3080 3575.81818181818 4010 0.00159108545397589 1381 0.936399771778018 1.09487593139099 1 0.62516268014538 3080 4114 4299 4429 4603 2928 1381 2444 4687 4010 3359 4464 M1756 SANSOM_APC_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_MYC_TARGETS.html Genes down-regulated after double Cre-lox knockout of both APC and MYC [GeneID=324;4609] in small intestine. 17377531 278/308 Arthur Liberzon 5.74826078812739e-07 1.20768674427058e-06 4100 3848.63636363636 4012 5.2256929909635e-08 2087 1.43245710238117 1.72840554106862 1 3.35922652348234 4097 4140 4045 3605 2087 3823 4484 3805 3876 4361 4012 4465 M1271 CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_DN http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_DN.html Genes down-regulated in neuroblastoma xenografts: resistant vs those that reverted to be sensitive to the topoisomerase inhibitor irinotecan [PubChem=3750]. 16501609 6/9 Arthur Liberzon 0.00714344952822152 0.00732661490074002 3510 3588.54545454545 4013 0.000716651695011751 1076 1.20272078051147 1.34535529936789 1 0.982683820348925 3509 4373 4411 4251 4656 3229 1076 1969 4617 4013 3370 4466 M18854 PENG_RAPAMYCIN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_RAPAMYCIN_RESPONSE_DN.html Genes down-regulated in BJUB cells (B-lymphoma) in response to rapamycin (sirolimus) [PubChem=6610346] treatment. 12101249 314/354 Broad Institute 4.51725591413796e-06 6.05035411882269e-06 2285 3672.81818181818 4013 4.10660471767073e-07 2282 1.11602350730887 1.04331104532622 1 2.29201365321016 2282 4408 4176 4336 3452 2758 2472 4013 4087 4649 3768 4467 M18184 REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS.html Genes involved in Transport of Ribonucleoproteins into the Host Nucleus 31/33 Reactome 2.69139680907452e-05 3.11816223339021e-05 1355 3081.45454545455 4015 2.44675430469935e-06 350 0.791826789665879 0.704981540602562 1 1.3848963958058 1355 4550 4015 4530 4020 1252 350 2075 4553 4496 2700 4468 M4519 CHESLER_BRAIN_HIGHEST_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_HIGHEST_EXPRESSION.html Neurologically relevant transcripts with highest abundance fold range in brain tissue among mouse strains. 15711545 63/83 Jean Junior 2.51313325952772e-06 3.65434041434715e-06 4160 3603.36363636364 4015 2.28466920942556e-07 2010 1.86651130782276 -1.46717480327437 -1 4.03133189662656 4158 4490 2702 4015 3166 4436 3336 2564 2010 4147 4613 4469 M6979 GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_DN.html Genes down-regulated in myeloid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 74/110 Arthur Liberzon 0.000500228530224813 0.000527969289503828 2360 3654.36363636364 4016 4.5485664246306e-05 2357 1.23601532671537 -1.08879266198928 -1 1.57908183974864 2357 4488 4016 4546 4439 3029 2841 2407 4358 4468 3249 4470 M16563 BIOCARTA_MTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MTOR_PATHWAY.html mTOR Signaling Pathway 32/32 BioCarta 9.83874053540158e-05 0.00010807273755433 2770 3251.72727272727 4017 8.94470960605297e-06 1383 0.842812083227981 -0.889714771685767 -1 1.29432164207629 2766 4260 4017 4099 4250 2159 1383 1761 4362 4451 2261 4471 M1041 REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEX.html Genes involved in Signaling by TGF-beta Receptor Complex 85/100 Reactome 2.97753963868603e-07 8.70294688256627e-07 4430 3711.81818181818 4017 2.70685458334036e-08 1378 1.10578327883285 1.18082078214187 1 2.64501519713762 4430 4188 4009 4096 1378 3330 2553 4017 3947 4338 4544 4472 M3985 KEGG_CITRATE_CYCLE_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CITRATE_CYCLE_TCA_CYCLE.html Citrate cycle (TCA cycle) 30/33 KEGG 5.0863657505108e-07 1.12395348044995e-06 3080 3867.45454545455 4018 4.62396993315547e-08 1963 0.97013361379943 0.802339597047185 1 2.27106654712393 3077 4557 4018 4657 1963 3362 3607 4696 3846 4482 4277 4473 M105 PID_TELOMERASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TELOMERASE_PATHWAY.html Regulation of Telomerase 18832364 83/89 Pathway Interaction Database 1.55686122631643e-06 2.4584760750129e-06 3060 3629.81818181818 4021 1.41532938913861e-07 2088 1.20693784457206 1.05285528677709 1 2.67264445484876 3059 4193 4021 4122 2891 2584 2088 4526 3912 4359 4173 4474 M3141 RASHI_RESPONSE_TO_IONIZING_RADIATION_4 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_4.html Cluster 4: genes repressed by ionizing radiation regardless of ATM [GeneID=472] status. 16314843 76/108 Arthur Liberzon 1.13151320254641e-06 1.92528562221307e-06 4250 3831.18181818182 4021 1.02864889501039e-07 2651 1.61637248098224 1.32044774382247 1 3.66528687362802 4246 3898 3285 4599 2651 3544 4021 4431 4209 3194 4065 4475 M119 PID_ERB_GENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERB_GENOMIC_PATHWAY.html Validated nuclear estrogen receptor beta network 18832364 34/50 Pathway Interaction Database 0.000763762673438652 0.000800035467960594 4475 3786.90909090909 4023 6.94570867215684e-05 2165 1.13370200361198 -1.36637976705325 -1 1.36193277971869 2165 4250 3747 4471 4473 3128 3085 4023 4387 4323 3604 4476 M1788 NIKOLSKY_BREAST_CANCER_16P13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_16P13_AMPLICON.html Genes within amplicon 16p13 identified in a study of 191 breast tumor samples. 19010930 110/165 Jessica Robertson 1.18153275272085e-07 7.06112554001409e-07 4155 3679.81818181818 4023 1.07412074197844e-08 405 1.66074639846399 1.93483450154852 1 4.05822926400648 4151 3611 3559 4023 405 4090 3623 4352 3890 4180 4594 4477 M17580 ST_IL_13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_IL_13_PATHWAY.html Interleukin 13 (IL-13) Pathway 5/7 Signaling Transduction KE 0.0119932615591495 0.0122608175350196 2695 3839.81818181818 4024 0.00120584847705974 2298 0.644586523159516 -0.644586523159516 -1 0.445472075032362 2691 4382 4200 4024 4589 3092 2298 3586 4714 4677 3985 4478 M15891 GESERICK_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GESERICK_TERT_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) with TERT [GeneID=7015] knockout, after expression of the gene off a retroviral vector. 16501597 26/26 Lauren Kazmierski 0.000471640087531669 0.00049835263334441 3470 3945.72727272727 4024 4.28855662697522e-05 2728 1.6802801171447 -1.43443421537166 -1 2.18158329101482 3470 4024 2728 4222 4434 3980 3750 4439 4330 3348 4678 4479 M6416 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_UP.html Genes up-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 19/24 John Newman 6.05981236498077e-06 7.8255306053924e-06 4025 3977.54545454545 4024 5.50893550596082e-07 3426 1.06194428740193 -0.518824142190432 -1 2.13080657454723 4024 4579 3822 4488 3590 3426 3505 4057 4583 4247 3432 4480 M4910 ST_ERK1_ERK2_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_ERK1_ERK2_MAPK_PATHWAY.html ERK1/ERK2 MAPK Pathway 39/41 Signaling Transduction KE 5.5134012295686e-07 1.17941666689155e-06 4615 3801.45454545455 4025 5.01218419207078e-08 2045 1.24748097464451 -1.07648211977728 -1 2.9241421945412 4615 3107 3708 2531 2045 4475 4351 4533 3788 4025 4638 4481 M1479 MA_MYELOID_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/MA_MYELOID_DIFFERENTIATION_UP.html Genes up-regulated during myeloid differentiation induced by tretinoin (ATRA) [PubChem=444795] and IL3 [GeneID=3652] in the EML cell line (myeloid progenitor). 12130493 53/86 Kevin Vogelsang 0.00256889354013266 0.00265437336020713 2860 3916.54545454545 4025 0.000233808917792403 2859 1.41653566785399 1.60047125460354 1 1.41747067463752 2859 4513 3909 4313 4531 3384 4328 3457 4025 4250 3513 4482 M13055 DAVIES_MULTIPLE_MYELOMA_VS_MGUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVIES_MULTIPLE_MYELOMA_VS_MGUS_UP.html Genes up-regulated in multiple myeloma (MM) compared to monoclonal gammopathy of uncertain significance (MGUS). 12947006 24/40 Arthur Liberzon 0.000186458061464686 0.000200840267027229 4475 3938.81818181818 4027 1.6952169667636e-05 2852 2.06228459053056 2.88244814480666 1 3.01627402660194 4472 4027 2852 4614 4341 3728 4092 3351 4213 3952 3685 4483 M15347 BIOCARTA_AKAPCENTROSOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAPCENTROSOME_PATHWAY.html Protein Kinase A at the Centrosome 24/25 BioCarta 1.0805985807206e-07 6.98688397397428e-07 4540 3744.09090909091 4028 9.82362394361427e-09 342 1.08508403165088 0.960364116426979 1 2.63618936170099 4539 4020 3769 4028 342 4480 4196 4405 3271 4127 4008 4484 M15434 REACTOME_DNA_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPAIR.html Genes involved in DNA Repair 114/127 Reactome 2.82731037946307e-05 3.27081004682983e-05 895 2964 4029 2.57031519549456e-06 463 1.01635896709451 1.06669117040679 1 1.78330529946157 895 4177 4125 4554 4029 646 463 2277 4480 4577 2381 4485 M121 PID_MTOR_4PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MTOR_4PATHWAY.html mTOR signaling pathway 18832364 93/104 Pathway Interaction Database 9.72920346301006e-08 6.64473403617636e-07 4185 3549.63636363636 4032 8.84473081206453e-09 296 1.13969258830371 -1.09906906757409 -1 2.78137247098182 4184 2145 4032 3598 296 4074 3444 4552 3936 4527 4258 4486 M19806 REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION.html Genes involved in Post-translational protein modification 168/203 Reactome 2.04299884764237e-06 3.08081615363323e-06 4045 3799.27272727273 4035 1.85727340440618e-07 2783 1.76920352061508 1.97087495046189 1 3.87130912898654 4044 3585 3347 4199 3047 4541 4118 4228 2783 4035 3865 4487 M4203 LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_UP.html Genes with copy number gains in primary neuroblastoma tumors. 17533364 208/279 Arthur Liberzon 1.26017350153078e-05 1.53378517978991e-05 3175 3928.09090909091 4035 1.14561883630893e-06 2952 1.35080061215905 1.48442117387678 1 2.56524907891556 3173 4707 4092 4675 3822 2952 3094 4479 4035 4570 3610 4488 M8754 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_7 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_7.html Amplification hot spot 7: colocalized fragile sites and cancer genes in the 3q26.3-q29 region. 16751803 13/13 Arthur Liberzon 7.18710997212981e-05 7.98004212384208e-05 4095 3882.09090909091 4035 6.53394979661535e-06 2833 0.882850917528786 -0.836277371189936 -1 1.40495089543193 4094 3788 3596 3550 4205 4274 3374 2833 4577 4377 4035 4489 M16024 KEGG_ALZHEIMERS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALZHEIMERS_DISEASE.html Alzheimer's disease 163/213 KEGG 0.00377336142908475 0.00388700697190747 1340 3347.63636363636 4036 0.000343622631565773 1259 1.4388736182224 1.51541340701659 1 1.34475551777768 1340 4158 4036 4112 4548 2006 1259 4085 3561 4535 3184 4490 M8897 AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN.html Down-regulated genes whose expression correlates with copy number losses in pancreatic adenocarcinoma cell lines and primary tumor specimens. 15199222 294/354 Arthur Liberzon 3.27863326243648e-07 9.05922275783096e-07 4450 3628.27272727273 4036 2.98057613731574e-08 1485 1.47130373606137 1.54342356591719 1 3.52556383246812 4447 3560 3954 4435 1485 3574 4188 4119 1774 4339 4036 4491 M4204 AMIT_EGF_RESPONSE_40_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_40_HELA.html Genes whose expression peaked at 40 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 52/55 Leona Saunders 5.60940119404383e-05 6.2889248541299e-05 3610 3967 4037 5.09958565782909e-06 3196 1.55188556994949 -1.16464770259021 -1 2.57210852468924 3608 4227 3196 3582 4160 4037 4522 3826 4440 3526 4513 4492 M2078 WHITFIELD_CELL_CYCLE_M_G1 http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_M_G1.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the M/G1 phase of cell cycle. 12058064 212/254 Jessica Robertson 1.08540841302851e-06 1.86363321553094e-06 4330 3668.36363636364 4037 9.86735407758246e-08 2305 1.41144274634945 1.62350755854781 1 3.20226749532726 3600 4418 4037 4326 2627 3946 4248 2358 4157 4330 2305 4493 M1260 WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP.html Genes up-regulated in rectal cancer patients resistant to radiotherapy (non-responders) relative to the sensitive ones (responders). 16585155 140/172 Arthur Liberzon 1.19542341711682e-07 7.06112554001409e-07 4030 3807.72727272727 4038 1.08674862006642e-08 417 1.28757204535152 -1.11343900385015 -1 3.13509032421557 4029 4165 4038 4671 417 4511 3934 3797 3159 4499 4665 4494 M1807 MATZUK_OVULATION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_OVULATION.html Genes important for ovulation, based on mouse models with female fertility defects. 18989307 24/27 Jessica Robertson 1.63408737789202e-07 7.3358205358541e-07 4685 3596.90909090909 4038 1.48553409024241e-08 714 1.67956349004027 1.77263150550211 1 4.09358246294968 4682 4029 3023 4038 714 4366 4312 2860 4514 2724 4304 4495 M728 REACTOME_RNA_POL_I_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_TRANSCRIPTION.html Genes involved in RNA Polymerase I Transcription 50/103 Reactome 0.000137222454528087 0.000148997006066844 3395 3583.63636363636 4039 1.24755467606728e-05 2046 0.819008455714451 0.844972821559689 1 1.21041785255816 3394 4521 4039 4121 4307 2140 2046 2730 4651 4610 2861 4496 M792 REACTOME_PERK_REGULATED_GENE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PERK_REGULATED_GENE_EXPRESSION.html Genes involved in PERK regulated gene expression 31/34 Reactome 0.00256413090683679 0.0026506127639662 3255 3868.36363636364 4039 0.00023337493845338 2464 1.21646350649703 0.972996438689283 1 1.21050040083987 3252 4276 3677 4293 4529 3241 2464 4039 4457 4355 3969 4497 M934 REACTOME_DESTABILIZATION_OF_MRNA_BY_BRF1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_BRF1.html Genes involved in Destabilization of mRNA by Butyrate Response Factor 1 (BRF1) 21/22 Reactome 3.38095283818084e-05 3.8799167022158e-05 1750 3489.72727272727 4040 3.07364072515629e-06 1484 0.899731537039021 0.754850366442423 1 1.54609238873243 1747 4040 3818 4478 4064 2274 1484 4410 4142 4428 3502 4498 M884 REACTOME_RNA_POL_I_PROMOTER_OPENING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_PROMOTER_OPENING.html Genes involved in RNA Polymerase I Promoter Opening 23/75 Reactome 0.0216770486863629 0.0220555442551483 4020 4029.63636363636 4041 0.00199033006007128 2760 0.853374591969884 0.818486972441009 1 0.518458472253839 4018 4041 3717 3589 4610 4058 2760 3695 4679 4464 4695 4499 M8801 NICK_RESPONSE_TO_PROC_TREATMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/NICK_RESPONSE_TO_PROC_TREATMENT_DN.html Genes down-regulated in neutrophils upon treatment with activated protein C (PROC) [GeneID=5624] of pulmonary inflammation induced by bacterial lipopolysaccharide (LPS). 15339848 57/68 Arthur Liberzon 0.000322226195804829 0.000343785633860486 340 3018 4041 2.92975818920444e-05 338 1.03431189880815 -0.999509189351762 -1 1.3907305951069 338 4504 4041 4536 4392 1505 824 2072 4474 4170 2342 4500 M17621 CHEN_HOXA5_TARGETS_9HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_9HR_UP.html Genes up-regulated 9 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 330/394 Arthur Liberzon 3.120181944368e-05 3.59376739322034e-05 470 3302.54545454545 4043 2.83656927061833e-06 467 1.52160751500188 -1.4530212134293 -1 2.66966486768337 467 4407 4061 4332 4043 2130 1835 3277 4216 4454 3106 4501 M18979 HAMAI_APOPTOSIS_VIA_TRAIL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAMAI_APOPTOSIS_VIA_TRAIL_UP.html Genes up-regulated in T1 cells (primary melanoma, sensitive to TRAIL [GeneID=8743]) compared to G1 cells (metastatic melanoma, resistant to TRAIL). 16983347 759/869 Leona Saunders 2.00666909900636e-07 7.65527859584926e-07 4315 3539.54545454545 4044 2.00666928020882e-08 1057 1.86675357809642 2.08897708231005 1 4.54149775914864 4314 3548 4344 2432 1057 4590 4597 4044 1788 3857 4364 4502 M2189 WAGSCHAL_EHMT2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WAGSCHAL_EHMT2_TARGETS_UP.html Genes up-regulated in placenta of mice with EHMT2 [GeneID=10919] knocked out. 18039842 7/18 Arthur Liberzon 0.0020390097761616 0.00211426321254015 4395 3911.72727272727 4047 0.000204088309816171 3072 1.48296452780335 1.41771605228673 1 1.54521512977973 3337 4112 4667 3474 4523 3900 4047 3110 4395 3072 4392 4503 M1410 SCHLOSSER_SERUM_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_SERUM_RESPONSE_DN.html Cluster 4: genes down-regulated in B493-6 cells (B lymphocytes) upon serum stimulation but not affected by MYC [GeneID=4609]. 15516975 937/1138 Leona Saunders 2.87398204882074e-07 8.57471256032483e-07 3890 3779.27272727273 4048 2.87398242051058e-08 1440 1.58879150936759 1.75151501102799 1 3.82633834149288 3886 4392 4378 3278 1440 4204 4535 3730 3096 4585 4048 4504 M510 REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES.html Genes involved in Cross-presentation of soluble exogenous antigens (endosomes) 46/55 Reactome 0.100475759015598 0.101161600374066 1565 3516.81818181818 4049 0.00958011337739734 1562 0.886121649275892 0.958588324096656 1 0.304539560449977 1562 4526 4049 4323 4658 2202 1566 3177 4331 4568 3723 4505 M641 REACTOME_REGULATION_OF_HYPOXIA_INDUCIBLE_FACTOR_HIF_BY_OXYGEN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_HYPOXIA_INDUCIBLE_FACTOR_HIF_BY_OXYGEN.html Genes involved in Regulation of Hypoxia-inducible Factor (HIF) by Oxygen 26/35 Reactome 5.2885162781042e-05 5.95320697177482e-05 2765 3496.45454545455 4049 4.80785764681256e-06 1329 1.20165962833362 1.57878812520342 1 1.9918626643021 2764 4279 3548 4484 4144 3537 4459 1329 4180 4049 1688 4506 M1528 INGRAM_SHH_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/INGRAM_SHH_TARGETS.html Genes up-regulated by in C3H/10T1/2 cells (embryonic pluripotent cell) in response to SSH [GeneID=6469]. 12444557 6/8 John Newman 0.00115226829675084 0.00120218973489477 4495 3684.90909090909 4049 0.000115286620813716 2116 1.97070178875533 -1.62941141918923 -1 2.26420300953663 4049 3818 4491 4377 4494 4153 3384 2870 4662 2120 2116 4507 M2562 HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_DN.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 26/48 Arthur Liberzon 4.73107447856145e-05 5.3550771076283e-05 4720 3932.81818181818 4051 4.30106929348408e-06 2712 1.51690833423104 -1.4785668402245 -1 2.55559665773796 4720 4577 3386 3784 4121 3715 2712 3568 4080 4051 4547 4508 M1741 ZHENG_BOUND_BY_FOXP3 http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_BOUND_BY_FOXP3.html Genes whose promoters are bound by FOXP3 [GeneID=50943] based an a ChIP-chip analysis. 17237761 635/805 Jessica Robertson 1.77151706343899e-07 7.4119215967118e-07 4210 3124.27272727273 4052 1.77151720466127e-08 919 1.87394114548834 2.08576660919697 1 4.56975009004791 4209 1140 4517 1923 919 4368 4105 4052 3032 1828 4274 4509 M897 REACTOME_BIOSYNTHESIS_OF_THE_N_GLYCAN_PRECURSOR_DOLICHOL_LIPID_LINKED_OLIGOSACCHARIDE_LLO_AND_TRANSFER_TO_A_NASCENT_PROTEIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BIOSYNTHESIS_OF_THE_N_GLYCAN_PRECURSOR_DOLICHOL_LIPID_LINKED_OLIGOSACCHARIDE_LLO_AND_TRANSFER_TO_A_NASCENT_PROTEIN.html Genes involved in Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein 29/32 Reactome 0.0400591636291329 0.0405836557908365 2240 3689.90909090909 4053 0.00370979484480731 2039 0.697498132878079 -0.765172794527485 -1 0.340330067907079 2239 4570 4053 4666 4665 2868 2039 2641 4654 4574 3620 4510 M7772 BIOCARTA_BARRESTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARRESTIN_PATHWAY.html fl-arrestins in GPCR Desensitization 19/23 BioCarta 3.47194394625397e-06 4.81704157152226e-06 4375 3891.09090909091 4054 3.15631765957856e-07 2389 0.973476384011491 1.05306980019763 1 2.03162702070297 4373 2389 3621 4456 3328 4054 4314 4660 4290 3537 3780 4511 M13616 SUH_COEXPRESSED_WITH_ID1_AND_ID2_UP http://www.broadinstitute.org/gsea/msigdb/cards/SUH_COEXPRESSED_WITH_ID1_AND_ID2_UP.html Genes whose expression positively correlates with that of both ID1 and ID2 [GeneID=3397;3398] genes in a cohort of 285 patients with primaly AML (acule myelogenous leukemia) [PMID=15084694]. 18542061 21/22 Jessica Robertson 0.000111562708232899 0.00012200555673292 3820 4027.09090909091 4054 1.01425787286748e-05 3078 1.28961586118177 1.09793038748033 1 1.97969959216312 3819 4313 3487 4054 4276 4003 3780 4163 4618 3078 4707 4512 M13465 KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS.html Terpenoid backbone biosynthesis 15/17 KEGG 0.00273230654817722 0.00282137101452559 2675 3743.63636363636 4056 0.000248700533532158 1894 1.21555882109063 0.907660900547053 1 1.19630826905179 2672 4338 3740 4492 4533 2746 1894 4504 4539 4056 3666 4513 M17723 CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_DN.html Genes down-regulated by 2-methoxyestradiol (2ME2) [PubChem=1573] in the MM.1S cell line (multiple myeloma) sensitive to dexamethasone [PubChem=5743]. 12480690 157/223 Arthur Liberzon 4.07388531545125e-06 5.53504280049795e-06 3690 4050.81818181818 4056 3.70353896304849e-07 3401 1.21977563269678 -1.04762929656368 -1 2.52870896014654 3686 3866 4056 4124 3401 3941 3931 4663 4296 4315 4280 4514 M17157 REACTOME_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRUVATE_METABOLISM.html Genes involved in Pyruvate metabolism 18/19 Reactome 0.00786378248040878 0.00805666449045571 3830 4039.63636363636 4060 0.000717457511125035 3106 1.36630046644801 1.80383532140148 1 1.10047533019677 3829 4606 3704 4060 4575 3887 4664 3106 4313 4199 3493 4515 M14194 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_30 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_30.html Amplification hot spot 30: colocolized fragile sites and cancer genes in the 12q21-q24.3 region. 16751803 6/10 Arthur Liberzon 3.05042095403259e-05 3.52029019634079e-05 3835 3946.27272727273 4060 3.05046282764756e-06 3105 1.65886025463913 -1.16246294018996 -1 2.92097383475843 3833 3816 4371 3904 4060 4084 4394 4150 3105 3480 4212 4516 M16227 REACTOME_CHOLESTEROL_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHOLESTEROL_BIOSYNTHESIS.html Genes involved in Cholesterol biosynthesis 22/24 Reactome 0.000140434221420961 0.000152344179523543 3240 3927.09090909091 4063 1.27675624239388e-05 2946 0.987897153685552 0.917957144713124 1 1.46650454243942 3237 4300 3840 4063 4311 3685 2946 4151 4538 4194 3933 4517 M13596 YANAGISAWA_LUNG_CANCER_RECURRENCE http://www.broadinstitute.org/gsea/msigdb/cards/YANAGISAWA_LUNG_CANCER_RECURRENCE.html Genes defining a 25-signal proteomic signature associated with a high risk of cancer recurrence and poor survival of NSCLC (non-small cell lung cancer) patients. 17551146 11/31 Jessica Robertson 0.000218556520988928 0.000234718265999486 4130 3846.54545454545 4065 1.98707487509529e-05 2676 0.912751465807573 -0.964169546863117 -1 1.2822393772951 4130 3517 3445 3774 4355 4223 2676 3288 4608 4065 4231 4518 M6591 REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION.html Genes involved in Cytosolic tRNA aminoacylation 29/29 Reactome 0.000114900789946322 0.000125568818834601 3450 4065.81818181818 4067 1.0446071943754e-05 3336 0.554941977367598 0.480469175911874 1 0.820600269239322 3851 3449 4067 4533 4280 3336 3446 4029 4578 4684 4471 4519 M1359 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_DN.html Early prostate development genes (down-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in localized vs metastatic prostate cancers. 18794802 43/46 Jessica Robertson 1.34900812149747e-05 1.63390257466463e-05 4085 4069.72727272727 4070 1.2263785395371e-06 2584 0.75405056075101 -0.585951615019453 -1 1.40155303846227 4083 4528 4070 4535 3839 4051 4037 3873 4586 4581 2584 4520 M4470 BIOCARTA_EXTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EXTRINSIC_PATHWAY.html Extrinsic Prothrombin Activation Pathway 9/13 BioCarta 3.43084175283449e-05 3.93621124778288e-05 4205 3411.63636363636 4071 3.43089472202353e-06 1315 3.12150469755875 -3.1699910026508 -1 5.47967887009094 4204 2896 4190 1826 4085 4404 4071 4317 2481 1315 3739 4521 M13404 BIOCARTA_VDR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VDR_PATHWAY.html Control of Gene Expression by Vitamin D Receptor 15/17 BioCarta 1.58067936933634e-05 1.89072646306831e-05 4685 4050.63636363636 4072 1.43699156953057e-06 3105 0.685494224821356 0.784817009686611 1 1.25209941185061 4683 4324 3876 4050 3888 4198 3105 3508 4434 4419 4072 4522 M734 REACTOME_RNA_POL_II_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_II_TRANSCRIPTION.html Genes involved in RNA Polymerase II Transcription 114/152 Reactome 3.59695062790697e-05 4.11678151399634e-05 1075 3145.63636363636 4074 3.27000858053516e-06 993 0.736322341004447 0.744682795207993 1 1.24858263180618 1075 4178 4161 4331 4074 1131 993 2746 4570 4654 2689 4523 M17072 RUNNE_GENDER_EFFECT_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUNNE_GENDER_EFFECT_UP.html Up-regulated genes detecting gender effects in global expression profiling studies. 17724341 15/40 Arthur Liberzon 0.68618940391 0.68618940391 3775 4079.36363636364 4074 0.1 3262 1.04889341844752 -0.604489042744723 -1 0.0189547871424694 3771 4074 3743 3763 4702 3984 3262 4456 4263 4266 4589 4524 M2547 HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_UP.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 32/35 Arthur Liberzon 0.000841646604939616 0.000880445916514847 3085 3936.72727272727 4074 7.65426148555717e-05 2667 0.798205215580136 0.844543751561802 1 0.930736262873924 3085 4566 4074 4547 4479 3208 2667 3742 4652 4593 3691 4525 M194 BIOCARTA_PROTEASOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PROTEASOME_PATHWAY.html Proteasome Complex 31/35 BioCarta 0.0612703753331932 0.0617940537548444 1660 3636.27272727273 4078 0.00573149204934577 1658 0.574431165309841 0.454680707954039 1 0.229271294575184 1658 4560 4078 4322 4649 2403 1731 3620 4582 4588 3808 4526 M8256 REACTOME_GENERIC_TRANSCRIPTION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GENERIC_TRANSCRIPTION_PATHWAY.html Genes involved in Generic Transcription Pathway 356/490 Reactome 3.68439456407604e-05 4.21277673024199e-05 725 3152.90909090909 4078 3.34950569908396e-06 722 1.26596955798252 -1.26424579246164 -1 2.17760182242791 722 4404 4146 4555 4078 1584 1535 2396 4255 4457 2550 4527 M14691 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMINOACYL_TRNA_BIOSYNTHESIS.html Aminoacyl-tRNA biosynthesis 41/41 KEGG 2.05982638127527e-05 2.41970645087588e-05 4070 4134.09090909091 4079 1.87258697033429e-06 3715 0.724389791573771 0.580920399951373 1 1.29477336463992 4067 4241 4079 4097 3961 4493 3873 3925 4524 4500 3715 4528 M691 REACTOME_KERATAN_SULFATE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_DEGRADATION.html Genes involved in Keratan sulfate degradation 9/12 Reactome 3.50409093533424e-08 3.96709707574802e-07 4675 3417.81818181818 4079 3.50409099058818e-09 26 2.12318533304845 2.75490336944113 1 5.41599461345686 4673 1968 4218 3663 26 4087 4685 4079 3685 1794 4718 4529 M1589 ZHENG_RESPONSE_TO_ARSENITE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_RESPONSE_TO_ARSENITE_UP.html Up-regulated in HEK293 cells (kidney epithelium) by treatment with sodium arsenite [PubChem=26435]. 12679051 19/33 John Newman 0.0689384532190936 0.0694979707804618 4035 4062.18181818182 4079 0.00647258884369779 3122 1.17465900041592 1.02421777966763 1 0.49701844154234 4033 3767 3603 4628 4651 3466 3122 4571 4590 4079 4174 4530 M1620 SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_DN.html Genes down-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] but displayed blunted response to insulin the insulin resistant cells. 14530283 27/28 John Newman 0.000536828541954697 0.000565839820908033 4495 3931.27272727273 4080 4.88145072591502e-05 2756 1.76955601169102 -1.47992812916736 -1 2.2609005881797 4491 4015 3105 3457 4447 4253 4538 4675 2756 3427 4080 4531 M19134 KENNY_CTNNB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KENNY_CTNNB1_TARGETS_DN.html Genes down-regulated in HC11 cells (mammary epithelium) by expression of constantly active CTNNB1 [GeneID=1499]. 15642117 75/91 Yujin Hoshida 3.62440925878531e-06 4.99189136313588e-06 3960 4124.54545454545 4082 3.29492293623986e-07 3355 1.57435781359577 -1.22205919789082 -1 3.30673683916647 3959 4481 3802 4541 3355 4358 3917 4082 4000 4276 4599 4532 M17287 LIU_SOX4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_SOX4_TARGETS_DN.html Genes down-regulated in LNCaP cells (prostate cancer) by overexpression of SOX4 [GeneID=6659] and up-regulated by its RNAi knockdown. 16618720 412/471 Arthur Liberzon 2.13930726015505e-07 7.7139268662581e-07 4285 3760.45454545455 4086 1.94482497107633e-08 1026 1.35438328572615 1.37680303213204 1 3.27944781630532 4285 4131 4116 3594 1026 4019 4086 3869 3243 4493 4503 4533 M10311 BROWNE_HCMV_INFECTION_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_6HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 6 h time point that were not down-regulated at the previous time point, 4 h. 11711622 218/254 John Newman 1.69687774862398e-07 7.33971845416521e-07 4150 3704.36363636364 4088 1.54261625409595e-08 770 1.68044950588873 1.98591425565511 1 4.09561242421261 4088 4146 3399 4632 770 4150 4621 4508 3210 3442 3782 4534 M16005 IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR.html Genes in the expression cluster 'Intermediate Progenitors Shared': up-regulated in hematopoietic intemediate progenitor cells from adult bone marrow and fetal liver. 12228721 166/189 John Newman 1.24962981552785e-06 2.07028877827008e-06 3320 3817.72727272727 4089 1.13602775030462e-07 2734 1.39129105861491 1.28696851895568 1 3.13027941551015 3316 4429 4089 4542 2734 3305 3073 4222 3663 4381 4241 4535 M2260 CAFFAREL_RESPONSE_TO_THC_8HR_5_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_5_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 24/27 Jessica Robertson 4.70080673639481e-05 5.3220934986288e-05 3905 3967.27272727273 4090 4.27355198451192e-06 2579 1.38343735348273 -0.910062198941847 -1 2.32782285649721 3904 4575 3522 4090 4120 4180 3755 2579 4624 3951 4340 4536 M590 REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT.html Genes involved in Mitochondrial Protein Import 69/74 Reactome 7.44654428858538e-05 8.25644562887549e-05 4210 3400 4093 6.76981486420839e-06 1218 0.949310020143422 0.844132108626842 1 1.50883355961254 1218 4208 4093 4119 4210 2308 1463 3347 4550 4564 3320 4537 M895 REACTOME_ASSEMBLY_OF_THE_PRE_REPLICATIVE_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASSEMBLY_OF_THE_PRE_REPLICATIVE_COMPLEX.html Genes involved in Assembly of the pre-replicative complex 66/76 Reactome 0.000713844866535038 0.000748577598321568 1065 3354 4094 6.49160542344058e-05 1062 0.889430253621671 0.971070307592614 1 1.0680318690431 1062 4499 4094 4327 4466 1780 1392 2897 4458 4495 3424 4538 M2289 MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_UP.html Up-regulated target genes shared by acute myeloid leukemia (AML) translocation products PML RARA [GeneID=5371;5914], AML1 ETO [GeneID=861;862], and PLZF RARA [GeneID=5914;7704]. 15024077 21/22 Arthur Liberzon 0.000326511614757235 0.000348043094321171 4310 3973.36363636364 4094 2.96872803494691e-05 2816 0.778776308198736 -1.02726992678798 -1 1.03310249533043 3491 4308 3913 4077 4396 4094 4429 3385 4488 4310 2816 4539 M10970 CHUANG_OXIDATIVE_STRESS_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHUANG_OXIDATIVE_STRESS_RESPONSE_UP.html Genes up-regulated in MCF7 cells (breast cancer) after treatment with the oxydants: hydrogen peroxyde, menadione, and t-butyl hydroperoxyde [PubChem=784;4055;6410]. 12414654 42/43 John Newman 0.000122937544128815 0.000134072367903884 3985 3937.54545454545 4095 1.11767649547786e-05 2589 2.16767249947234 2.38773608734475 1 3.32597320320185 3981 3700 2589 3229 4289 4578 4568 4521 4095 3203 4560 4540 M2113 KIM_ALL_DISORDERS_DURATION_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_DURATION_CORR_DN.html Genes whose expression in brain significantly and negatively correlated with the duration of all psychiatric disorders studied. 18762803 180/208 Jessica Robertson 3.38825547950052e-07 9.15271659547923e-07 3800 3803.63636363636 4096 3.08023272848302e-08 1526 1.24770375578689 1.25785340238806 1 2.97992781524918 3799 4713 4096 4534 1526 3230 2974 4341 3746 4555 4326 4541 M790 REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_XBP1S http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_XBP1S.html Genes involved in Activation of Chaperone Genes by XBP1(S) 61/65 Reactome 3.31262067941939e-07 9.06126045087621e-07 3900 3892.63636363636 4097 3.01147379837541e-08 1504 0.871318891388358 -0.70524851555028 -1 2.06743066941011 3898 4502 4097 4670 1504 3645 2764 4613 3943 4554 4629 4542 M18213 WANG_BARRETTS_ESOPHAGUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_DN.html Genes down-regulated in Barrett's esophagus compared to the normal tissue. 16449976 33/44 Arthur Liberzon 9.36271858183597e-06 1.16540168001756e-05 4160 3804.90909090909 4098 8.51159857068623e-07 1777 1.69335703451124 1.15134933675645 1 3.30970899664422 4157 3975 2654 4041 3736 4098 4324 1777 4386 4182 4524 4543 M5784 SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE.html IRF4 [GeneID=3662] target genes up-regulated in primary myeloma vs. mature B lymphocytes. 18568025 125/146 Jessica Robertson 4.30041092839568e-06 5.80604679119782e-06 4025 4081.09090909091 4098 3.90947212233688e-07 3422 1.51531552998762 -1.57552673896898 -1 3.14086342550089 4023 4439 3946 4098 3422 4410 4360 4563 3738 4279 3614 4544 M628 REACTOME_DOWNREGULATION_OF_TGF_BETA_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNREGULATION_OF_TGF_BETA_RECEPTOR_SIGNALING.html Genes involved in Downregulation of TGF-beta receptor signaling 27/31 Reactome 4.78572972019938e-06 6.35941561918386e-06 3675 3786 4100 4.35067284616419e-07 1961 0.698710326315495 -0.653143069456948 -1 1.41017399962844 3673 4288 3986 4100 3484 2572 1961 4171 4681 4512 4218 4545 M730 REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC.html Genes involved in Regulation of ornithine decarboxylase (ODC) 47/55 Reactome 0.0516751057532373 0.0522283724101242 1725 3634.45454545455 4101 0.00481185122530093 1724 0.728973651385773 0.65583801690545 1 0.325828087600062 1724 4519 4101 4667 4640 2234 1772 3701 4311 4572 3738 4546 M1095 REACTOME_RNA_POL_I_TRANSCRIPTION_INITIATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_TRANSCRIPTION_INITIATION.html Genes involved in RNA Polymerase I Transcription Initiation 25/25 Reactome 6.34034210131042e-05 7.07982368539985e-05 3565 4004.63636363636 4103 5.76411348697645e-06 2968 0.594203739343012 0.588640985864627 1 0.941666183997612 3561 4576 4025 4103 4175 3201 2968 4323 4693 4699 3727 4547 M1619 RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_UP.html Genes up-regulated in the brain cortex of mice that were exposed to an enriched learning environment for one day. 11070096 30/36 John Newman 7.45716744662348e-05 8.26628237389921e-05 3280 3804.54545454545 4103 6.77947293488662e-06 1236 1.06655518108575 1.22888647246085 1 1.70114111542299 3278 4547 3813 4664 4211 4103 3606 3314 4594 4484 1236 4548 M597 REACTOME_ACTIVATION_OF_NF_KAPPAB_IN_B_CELLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_NF_KAPPAB_IN_B_CELLS.html Genes involved in Activation of NF-kappaB in B Cells 65/77 Reactome 0.00391579429729013 0.00403196969529001 3265 4026.90909090909 4105 0.000356616496574472 3262 0.836835876340442 -1.00443088141209 -1 0.755809944186736 3262 3914 4105 3810 4551 4524 4375 3349 4376 4565 3465 4549 M19135 REACTOME_POST_CHAPERONIN_TUBULIN_FOLDING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_CHAPERONIN_TUBULIN_FOLDING_PATHWAY.html Genes involved in Post-chaperonin tubulin folding pathway 17/22 Reactome 4.24850107166991e-05 4.82505415261838e-05 4350 3770.27272727273 4105 3.86234828932538e-06 2529 1.61860676036647 -1.49598787526552 -1 2.75975066921827 4348 4056 3033 2529 4105 4176 4146 3501 4113 2874 4592 4550 M709 REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6.html Genes involved in CDK-mediated phosphorylation and removal of Cdc6 50/60 Reactome 0.0418643417099183 0.0423851765059662 2460 3780.54545454545 4106 0.00388026182617108 2124 0.688112749909538 0.689967837386355 1 0.329857412086231 2458 4520 4106 4123 4633 2623 2124 3807 4505 4624 4063 4551 M7910 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_DN.html Genes specifically down-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and high dose methotrexate (HDMTX) [PubChem=4112]. 12704389 27/33 Arthur Liberzon 1.14801022594542e-05 1.40852827306015e-05 3465 4025.36363636364 4107 1.04365110597149e-06 3333 1.5501657352745 1.531070225158 1 2.97430586224123 3465 4564 3765 4257 3791 3588 4517 4691 4201 4107 3333 4552 M10680 KEGG_PROTEASOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEASOME.html Proteasome 41/48 KEGG 0.0605412293136137 0.061071725231942 2260 3747.18181818182 4109 0.00566130908622177 2038 0.577165645949802 0.477051077146326 1 0.231786183455419 2256 4535 4109 3807 4648 2614 2038 3875 4564 4620 4153 4553 M3905 XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_DN.html Genes down-regulated synergistically in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin and NSC682994 [PubChem=444795;388304]. 16140955 17/18 Kevin Vogelsang 4.35225273354614e-05 4.93813290921581e-05 3460 4033.63636363636 4109 3.95667166945722e-06 3460 1.15433252905741 0.880485595525157 1 1.94913275110608 3460 4320 3754 4626 4109 3563 3629 4575 4244 3948 4142 4554 M858 REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION.html Genes involved in RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription 85/143 Reactome 2.28183913440243e-05 2.66525135223446e-05 4310 4118.81818181818 4110 2.07442072906602e-06 3449 0.881189140190446 1.00660881537457 1 1.57099192420956 4306 4471 4110 4553 3985 3579 3772 3908 4532 4642 3449 4555 M2564 HOLLEMAN_DAUNORUBICIN_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_ALL_DN.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 10/10 Arthur Liberzon 4.38376550408327e-05 4.97269242472315e-05 4310 3800.63636363636 4110 3.98532078030757e-06 1457 0.896039731155034 -0.575729953573016 -1 1.5007081679465 4310 4354 3734 4008 4110 3044 1457 3669 4223 4271 4627 4556 M640 REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT.html Genes involved in p53-Independent G1/S DNA damage checkpoint 55/65 Reactome 0.180208160443216 0.181013517193441 2885 3870.63636363636 4112 0.0179018976070387 2562 0.731386545798293 0.697350403404793 1 0.168296461577875 2883 4510 4112 3615 4672 2910 2562 3837 4495 4608 4373 4557 M12809 BOYAULT_LIVER_CANCER_SUBCLASS_G23_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G23_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G23, defined by unsupervised clustering. 17187432 9/12 Yujin Hoshida 0.0177210486043042 0.018049924344479 4115 3882.90909090909 4112 0.00178639713070053 2336 1.26997433585057 1.10605532408546 1 0.840441827549946 4112 4362 4621 3987 4674 3891 2367 2336 4455 3462 4445 4558 M595 REACTOME_DOWNSTREAM_SIGNALING_EVENTS_OF_B_CELL_RECEPTOR_BCR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_SIGNALING_EVENTS_OF_B_CELL_RECEPTOR_BCR.html Genes involved in Downstream Signaling Events Of B Cell Receptor (BCR) 98/111 Reactome 0.000120991649527959 0.000132011231107713 2740 3798.72727272727 4113 1.09998458292557e-05 2673 0.870587804222865 -0.974377384669661 -1 1.3082030165532 2737 4183 4135 3820 4287 4113 3762 2673 4490 4618 2968 4559 M5032 DER_IFN_ALPHA_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_ALPHA_RESPONSE_DN.html Genes down-regulated in HT1080 cells (fibrosarcoma) by treatment with interferon alpha for 6 h. 9861020 5/5 Yujin Hoshida 0.0514396903549853 0.0520015717445985 4630 3940.81818181818 4117 0.00526707082237995 1943 1.4318387813624 1.86247045832425 1 0.689319894867097 4627 4117 4540 3989 4642 3444 1943 3231 4566 3888 4362 4560 M4953 REACTOME_CDT1_ASSOCIATION_WITH_THE_CDC6_ORC_ORIGIN_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CDT1_ASSOCIATION_WITH_THE_CDC6_ORC_ORIGIN_COMPLEX.html Genes involved in CDT1 association with the CDC6:ORC:origin complex 57/67 Reactome 0.0279970211330633 0.0284001589830343 1960 3727.63636363636 4118 0.00257816261980919 1899 0.700459083388168 0.708864063773643 1 0.385658934664764 1960 4511 4118 4676 4625 2288 1899 3821 4601 4616 3889 4561 M7298 BIOCARTA_ASBCELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ASBCELL_PATHWAY.html Antigen Dependent B Cell Activation 3/14 BioCarta 0.00123356797282884 0.00128615878766338 4065 4026.09090909091 4121 0.000123425326875814 2602 1.58820786538176 -1.05287627401069 -1 1.79630348039082 4061 4121 4185 3945 4499 3869 4413 4421 4523 2602 3648 4562 M998 REACTOME_DESTABILIZATION_OF_MRNA_BY_AUF1_HNRNP_D0 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_AUF1_HNRNP_D0.html Genes involved in Destabilization of mRNA by AUF1 (hnRNP D0) 60/72 Reactome 0.116115740426159 0.116808673233477 3405 3989 4122 0.0111581133591643 2694 0.670052215777969 0.625233901873903 1 0.201249667202008 3401 4515 4122 3819 4662 3007 2694 3941 4697 4634 4387 4563 M944 REACTOME_REGULATION_OF_MRNA_STABILITY_BY_PROTEINS_THAT_BIND_AU_RICH_ELEMENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_MRNA_STABILITY_BY_PROTEINS_THAT_BIND_AU_RICH_ELEMENTS.html Genes involved in Regulation of mRNA Stability by Proteins that Bind AU-rich Elements 99/115 Reactome 0.238871290605961 0.239734742007258 3620 3673.36363636364 4124 0.0245085573490198 1931 0.947118045189918 0.877415094463677 1 0.186219922788144 2496 4461 4124 3617 4677 2313 1931 3617 4412 4626 4133 4564 M1034 REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C.html Genes involved in Autodegradation of Cdh1 by Cdh1:APC/C 62/74 Reactome 0.00126416251446025 0.00131747561674815 1390 3372.09090909091 4125 0.000114989955598471 1357 0.677277250305242 0.68509813411958 1 0.734472758611134 1390 4214 4126 4125 4493 1828 1357 3071 4498 4622 3369 4565 M17095 REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1.html Genes involved in SCF-beta-TrCP mediated degradation of Emi1 53/63 Reactome 0.0474223179914847 0.0479608615641328 2790 3870 4126 0.00440695342864139 2385 0.68277530003139 0.703254100909977 1 0.312172851576286 2787 4514 4113 4328 4637 2694 2385 3867 4486 4633 4126 4566 M528 REACTOME_ER_PHAGOSOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ER_PHAGOSOME_PATHWAY.html Genes involved in ER-Phagosome pathway 77/109 Reactome 0.000151132030827166 0.000163535805938612 2560 4019.27272727273 4127 1.37402194589864e-05 2558 0.792626309209601 -0.918950428051071 -1 1.1569263780355 2558 4475 4121 4127 4319 4693 3684 3843 4572 4579 3241 4567 M3592 GOLDRATH_HOMEOSTATIC_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/GOLDRATH_HOMEOSTATIC_PROLIFERATION.html Up-regulated in CD8+ [GeneID=925] T lymphocytes undergoing homeostatic proliferation (HP) versus the naive cells; these genes are not up-regulated versus effector or memory cell population. 15548615 217/249 Kate Stafford 5.96518237003933e-07 1.23381510896519e-06 3680 4038.09090909091 4127 5.42289453406114e-08 2121 1.26370974809032 1.20902478292473 1 2.95288169719677 3676 4704 4127 4681 2121 4035 4280 3936 3904 4602 4353 4568 M17225 BROWNE_HCMV_INFECTION_14HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_14HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 14 h time point that were not up-regulated at the previous time point, 12 h. 11711622 228/312 John Newman 1.90108879788098e-05 2.2460923969958e-05 4560 4037.36363636364 4128 1.72827747816594e-06 3158 1.36415258971124 -1.22514268208654 -1 2.50021545546373 3158 4702 4054 4559 3934 3285 3394 4377 4260 4560 4128 4569 M13104 REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G.html Genes involved in Vif-mediated degradation of APOBEC3G 53/64 Reactome 0.0526803225152589 0.0532101695424828 4645 3824.72727272727 4129 0.00490779668349177 1954 0.587389522221466 0.51743195331229 1 0.250915431179435 2322 4518 4129 4679 4641 2559 1954 3852 4665 4643 4110 4570 M7272 KEGG_PARKINSONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PARKINSONS_DISEASE.html Parkinson's disease 123/151 KEGG 0.0119987933878718 0.0122638165419565 710 3347.27272727273 4130 0.00109679444151328 706 1.09585636642108 1.11459807251111 1 0.79232730488415 706 4448 4130 4557 4587 1902 1182 3320 4200 4639 3149 4571 M4391 PEREZ_TP53_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/PEREZ_TP53_TARGETS.html Genes up-regulated in the HMEC cells (primary mammary epithelium) upon expression of TP53 [GeneID=7157] off adenoviral vector. 17563751 1337/1775 Leona Saunders 3.8177180050146e-18 1.82016454380494e-16 4305 2623.18181818182 4134 3.8177180050146e-19 15 2.21332368936427 2.4857664905244 1 13.9602572336129 4303 1071 4357 15 541 4149 4134 4472 1120 52 4641 4572 M2362 TERAO_AOX4_TARGETS_SKIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_SKIN_UP.html Genes up-regulated in skin upon knockout of AOX4 [GeneID=71872]. 18981221 46/80 Arthur Liberzon 1.44980286050707e-06 2.32757466040591e-06 4075 4064.09090909091 4138 1.3180034690272e-07 2835 1.26970482844272 1.38898624729869 1 2.82637161750011 4074 4228 3669 4633 2835 4564 4552 3939 4197 3876 4138 4573 M5283 REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS.html Genes involved in Host Interactions of HIV factors 160/201 Reactome 3.51904110809068e-06 4.8736835183673e-06 4595 4033 4140 3.19913339730477e-07 3336 0.993587076932584 -1.12438783750629 -1 2.07260270776873 4238 3865 4140 3814 3336 3841 3443 4595 4188 4591 4312 4574 M2499 BIOCARTA_CARM_ER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARM_ER_PATHWAY.html CARM1 and Regulation of the Estrogen Receptor 35/48 BioCarta 6.53208751051949e-07 1.30974736829448e-06 4540 3768.09090909091 4143 5.93826313634768e-08 1697 1.08954278978253 1.2302834906744 1 2.52764845064565 4540 4255 3867 4084 2202 4143 3840 4155 4316 4350 1697 4575 M12469 REACTOME_HIV_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIV_INFECTION.html Genes involved in HIV Infection 235/285 Reactome 5.52260705206746e-06 7.21469839074409e-06 3815 3835 4144 5.02056446853068e-07 2571 0.974229859099605 0.842402067419476 1 1.96450208420535 3814 4144 4172 3279 3543 2939 2571 4464 4208 4645 4406 4576 M893 REACTOME_RESPIRATORY_ELECTRON_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESPIRATORY_ELECTRON_TRANSPORT.html Genes involved in Respiratory electron transport 79/93 Reactome 0.0568100855823833 0.0573569206307699 855 3507.18181818182 4147 0.00530294608870603 853 0.707564178948635 0.740647237668098 1 0.303213658994292 853 4500 4147 4690 4643 2101 1328 3449 4670 4656 3542 4577 M6907 BIOCARTA_RARRXR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RARRXR_PATHWAY.html Nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells 17/21 BioCarta 0.00032238694238993 0.000343879405215925 4625 4169.90909090909 4148 2.93121995010722e-05 2855 0.540003407156788 0.555038774989931 1 0.702146864227138 4020 4067 3952 4085 4393 4148 2855 4624 4621 4676 4428 4578 M10064 REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS.html Genes involved in Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis 11/13 Reactome 2.5834219624947e-07 8.26284126785448e-07 4525 3727.09090909091 4148 2.34856569623774e-08 1225 1.45256019509238 1.39311387141291 1 3.50335687334441 4523 2893 2846 4587 1225 4597 4148 4543 4096 3296 4244 4579 M1148 MOTAMED_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOTAMED_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in ovarian epithelial cells in response to dihydrotestosterone (DHT) [PubChem=10635]. 16832351 4/6 Arthur Liberzon 0.554051557836552 0.554874464881927 4150 3999.09090909091 4148 0.0775805218334498 2978 1.45031166668702 -0.462061526845237 -1 0.0991637364557456 4148 3264 4350 3916 4686 4388 4151 4540 2978 3759 3810 4580 M15112 WONG_MITOCHONDRIA_GENE_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_MITOCHONDRIA_GENE_MODULE.html Genes that comprise the mitochondria gene module 18199530 242/284 Jessica Robertson 5.31010196735092e-05 5.97465584884299e-05 4150 3831.54545454545 4149 4.82748194608665e-06 2123 1.23465652394732 0.975742326725391 1 2.04715654332841 2594 4700 4149 4684 4146 3010 2123 4403 3280 4638 4420 4581 M477 BIOCARTA_GABA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GABA_PATHWAY.html Gamma-aminobutyric Acid Receptor Life Cycle 8/14 BioCarta 0.00170092353596902 0.00176680437715092 1370 2887.63636363636 4150 0.000170222685358292 521 0.862262827374957 -0.862262827374957 -1 0.904552645076137 1369 4630 4191 4438 4517 983 999 1418 4548 4150 521 4582 M1066 REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION.html Genes involved in Class I MHC mediated antigen processing & presentation 262/328 Reactome 2.13934323474821e-06 3.20663704922564e-06 4415 4093.27272727273 4151 1.94485937737263e-07 3069 1.12843519067176 1.20698446225734 1 2.4431908159845 4414 4142 4151 4334 3069 3512 3843 4432 4077 4615 4437 4583 M1033 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 10. 12554760 93/111 Arthur Liberzon 8.13735771410307e-06 1.02313075148019e-05 3200 4086.54545454545 4151 7.39762528428108e-07 3199 1.07616860280715 0.873332754573864 1 2.10963339914521 3199 4465 4087 4668 3697 3652 3410 4388 4151 4604 4631 4584 M1025 REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_.html Genes involved in Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 98/117 Reactome 0.0464687392510632 0.0470166022004326 740 3473 4153 0.00431639105552119 739 0.773278322117837 0.790790357569125 1 0.362869969494118 739 4477 4153 4695 4635 2070 1222 3350 4659 4665 3538 4585 M18264 MOOTHA_VOXPHOS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_VOXPHOS.html Genes involved in oxidative phosphorylation; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 93/111 Vamsi Mootha 0.0576668369104941 0.0582094675401053 4645 3634.63636363636 4154 0.00538511985008298 1077 0.715209567279432 0.669147604494063 1 0.305187538253796 1077 4476 4154 4691 4645 2531 1515 3654 4643 4666 3929 4586 M6222 GRABARCZYK_BCL11B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRABARCZYK_BCL11B_TARGETS_UP.html Genes up-regulated in Jurkat cells (transformed T lymphocytes) after knockdown of BCL11B [GeneID=64919] by RNAi. 17173069 112/127 Arthur Liberzon 6.89660914713152e-06 8.7954593824536e-06 3470 4088.18181818182 4155 6.26966433351893e-07 3466 1.54152534823498 -1.18089892221162 -1 3.08423121767492 3466 4441 3782 4287 3641 4159 3994 4581 3814 4155 4650 4587 M8880 MCBRYAN_PUBERTAL_BREAST_5_6WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_5_6WK_DN.html Genes down-regulated during pubertal mammary gland development between week 5 and 6. 17486082 193/226 Arthur Liberzon 1.45271523673635e-07 7.26289540930751e-07 4335 3594.18181818182 4155 1.32065030242072e-08 599 1.46736410770528 1.5619690232905 1 3.57262980637068 4333 4419 3856 4290 599 4332 3087 3275 2938 4252 4155 4588 M17481 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_7.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 7. 12554760 104/120 Arthur Liberzon 3.85222885054479e-06 5.27029570277432e-06 4110 4225.36363636364 4156 3.50203235987687e-07 3378 1.25687867027962 1.24496336868466 1 2.61790845419593 4108 4453 4055 4550 3378 4115 4156 4573 3916 4598 4577 4589 M919 REACTOME_PLATELET_SENSITIZATION_BY_LDL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_SENSITIZATION_BY_LDL.html Genes involved in Platelet sensitization by LDL 22/23 Reactome 5.55004306817343e-05 6.22681323550715e-05 3530 3970.72727272727 4157 5.04562098786847e-06 2623 1.14829951766312 -1.07255912757373 -1 1.89217939601907 4279 4284 3534 3529 4157 4521 4636 2623 4065 3530 4520 4590 M516 REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT.html Genes involved in The citric acid (TCA) cycle and respiratory electron transport 136/157 Reactome 0.0408786930275604 0.0414050281309195 760 3436 4158 0.00378714867740955 759 0.84138824042517 0.872621109892139 1 0.417916223023876 759 4446 4158 4700 4631 1893 1432 3175 4600 4668 3334 4591 M1257 INAMURA_LUNG_CANCER_SCC_SUBTYPES_DN http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_SUBTYPES_DN.html Down-regulated genes discriminating between two subtypes of squamous cell carcinoma (SCC) type of non-small cell lung cancer: SSC-A vs SSC-B. 16007138 6/7 Arthur Liberzon 0.0260502453006185 0.0264423995309504 4300 4038.72727272727 4160 0.00263607575638546 2508 1.23286213936714 -0.469796042208967 -1 0.732201635976467 4299 4115 4402 4235 4700 4531 3555 2508 3909 4012 4160 4592 M3910 RODRIGUES_THYROID_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_UP.html Genes up-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to anaplastic thyroid carcinoma (ATC). 17406368 17/18 Arthur Liberzon 2.7347666985169e-08 3.1950739646039e-07 4315 3396.54545454545 4166 2.48615157501101e-09 10 1.54875928322902 1.76994782628413 1 3.99570721022775 4315 3761 3000 4166 10 4333 4430 4555 834 3661 4297 4593 M19283 REACTOME_METABOLISM_OF_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_MRNA.html Genes involved in Metabolism of mRNA 247/349 Reactome 2.78811680340043e-06 3.98543649668383e-06 3030 4017.18181818182 4168 2.5346548516901e-07 2754 0.811495091307231 -0.706625401400646 -1 1.7121094260802 3027 4710 4168 4342 3228 3901 2754 4697 4537 4690 4135 4594 M14670 DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER.html The lung adenocarcinoma TSP (tumor sequencing project) genes showing strong correlation between DNA copy number variation and gene expression. 18948947 130/141 Jessica Robertson 1.27910904547055e-06 2.1095019897348e-06 4260 4070.63636363636 4168 1.1628270810564e-07 2747 1.14140331244814 1.20618211192502 1 2.55532678891321 4260 4168 4115 3809 2747 4378 4108 4414 3671 4578 4529 4595 M2505 RATTENBACHER_BOUND_BY_CELF1 http://www.broadinstitute.org/gsea/msigdb/cards/RATTENBACHER_BOUND_BY_CELF1.html Transcripts bound by CELF1 [GeneID=10658] in HeLa cells (cervical carcinoma). 20547756 545/748 Arthur Liberzon 1.58239557617262e-07 7.31918027928963e-07 4500 3653.81818181818 4169 1.58239568885154e-08 798 1.95797135328429 -1.78119304601211 -1 4.78121388576414 4496 3553 4710 4169 798 4439 4509 3489 2326 2998 4705 4596 M4669 REACTOME_INFLUENZA_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLUENZA_LIFE_CYCLE.html Genes involved in Influenza Life Cycle 163/257 Reactome 1.51801444778025e-06 2.41165540004133e-06 4695 3826.81818181818 4170 1.38001408656473e-07 2188 0.705887326456207 -0.577201923505977 -1 1.54471573600429 2772 4442 4170 3828 2872 3438 2188 4682 4691 4694 4318 4597 M4950 ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_UP.html Genes up-regulated in liver tumor compared to the normal adjacent tissue. 18413731 1080/1311 Jessica Robertson 9.07492704559838e-07 1.63524808786642e-06 3785 3985.09090909091 4172 9.07493075154405e-08 2569 1.30721160809812 1.36492423648531 1 2.99194195085322 3783 4659 4546 4705 2569 3203 3320 4204 4006 4669 4172 4598 M19152 PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN http://www.broadinstitute.org/gsea/msigdb/cards/PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN.html Genes down-regulated in OV-90 cells (ovarian cancer) exposed to ascites which inhibited invasion. 17971902 179/201 Arthur Liberzon 7.02356805638536e-07 1.37329085443823e-06 3840 3996.81818181818 4173 6.38506390789291e-08 2267 1.45958766545051 -1.42491793964944 -1 3.39103868042877 3837 4714 4013 4307 2267 4173 4082 4382 3274 4504 4412 4599 M1272 WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_DN.html Genes specifically down-regulated via JNK (MAPK8) [GeneID=5599] signaling pathway activated by paclitaxel [PubChem=4666] in BR cells (ovarian cancer). 16547493 4/5 Arthur Liberzon 0.00036005177366131 0.000383102879098598 4690 3893.54545454545 4174 3.60110123743353e-05 845 0.995743516496212 0.466727795728194 1 1.31817367681216 4687 3820 4412 3957 4629 4363 4673 845 4174 3761 3508 4600 M5075 SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM.html Cluster 7: genes up-regulated in B493-6 cells (B lymphocytes) by MYC [GeneID=4609] and down-regulated by the combination of MYC and serum. 15516975 194/226 Leona Saunders 9.77507292842638e-05 0.000107398380405429 635 3223.63636363636 4175 8.88682480268099e-06 634 0.964523142946274 0.875495234125424 1 1.48951586199861 634 4719 4175 4699 4249 1760 1103 2361 4194 4662 2904 4601 M1152 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_UP.html Apoptotic genes dependent on MAPK1 [GeneID=5594] and up-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 12/12 Arthur Liberzon 0.00233444372174719 0.00241476536634818 4350 3924.36363636364 4177 0.000212447682844032 2683 2.43247555567359 -2.96794092725679 -1 2.51016118849006 3805 4346 2683 2959 4527 4120 4177 4349 4506 3436 4260 4602 M9433 MOOTHA_HUMAN_MITODB_6_2002 http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_HUMAN_MITODB_6_2002.html Mitochondrial genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 463/545 Vamsi Mootha 1.11007485943537e-06 1.89770131710791e-06 2265 3711.36363636364 4179 1.00915947232433e-07 2265 1.24819308005947 1.11503574634161 1 2.82215162267485 2265 4684 4179 4703 2639 2894 2289 4397 3875 4670 4230 4603 M518 REACTOME_ANTIGEN_PROCESSING_CROSS_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_PROCESSING_CROSS_PRESENTATION.html Genes involved in Antigen processing-Cross presentation 93/132 Reactome 0.000124116555115893 0.000135264405483033 4470 4087.45454545455 4186 1.12839598095479e-05 2838 1.02782504173663 -1.00418723079871 -1 1.5491451379856 2838 3893 4071 4126 4291 4548 4186 4485 4466 4469 3589 4604 M1222 DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_UP.html Genes that classify skin lesions into high risk papilloma. 17525749 9/9 Arthur Liberzon 3.7808738585581e-07 9.60480334359217e-07 4080 3767.90909090909 4190 3.78087450183357e-08 1759 1.17754128826827 -1.07816221867506 -1 2.79962730418859 4080 4355 4397 4424 1759 4683 4190 2288 4267 3458 3546 4605 M2482 BIOCARTA_ARAP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARAP_PATHWAY.html ADP-Ribosylation Factor 21/22 BioCarta 9.09591667153988e-06 1.13368699999124e-05 4310 3838.63636363636 4192 8.26904934444906e-07 2042 0.912944283803641 -0.738079905025851 -1 1.76571149587235 3482 4295 3901 4640 3730 2847 2042 4482 4306 4308 4192 4606 M19757 SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_DN.html Genes down-regulated in pilocytic astrocytoma (PA) from supratentorial regions compared to the infratentorial PA tumors. 17283119 6/8 Jessica Robertson 3.07911191354263e-05 3.549061839297e-05 4340 4054.18181818182 4198 3.07915457856044e-06 2798 1.36150726753298 1.67310627872166 1 2.38648038667575 4337 3530 4575 4372 4065 4462 3818 3974 4467 2798 4198 4607 M2250 LINDGREN_BLADDER_CANCER_CLUSTER_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_1_UP.html Up-regulated genes whose expression profile is specific to Custer I of urothelial cell carcinoma (UCC) tumors. 16532037 152/189 Leona Saunders 7.05251997224343e-08 6.06397110828564e-07 4320 3815.36363636364 4199 6.41138199847767e-09 139 1.3533468166049 -1.18291796592844 -1 3.3337854795339 4317 4160 4006 4302 139 4199 4408 4503 3961 4254 3720 4608 M5039 NAGY_PCAF_COMPONENTS_HUMAN http://www.broadinstitute.org/gsea/msigdb/cards/NAGY_PCAF_COMPONENTS_HUMAN.html Composition of the 2 MDa human PCAF complex. 17694077 10/12 Arthur Liberzon 5.12686378365011e-06 6.74436930290651e-06 3900 3981.45454545455 4200 4.66079611935879e-07 2137 0.558717184517257 0.517886837672915 1 1.11187191330606 3900 4627 3781 4624 3522 3248 2137 4381 4672 4704 4200 4609 M9693 FINETTI_BREAST_CANCERS_KINOME_GRAY http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCERS_KINOME_GRAY.html Genes in the gray cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 31/32 Jessica Robertson 0.000194372111807581 0.000209221520577373 2670 3879.54545454545 4202 1.76717533540624e-05 2649 0.882357777481363 -0.751497031395963 -1 1.25559735512159 2669 3728 3933 4298 4346 3402 2649 4534 4417 4497 4202 4610 M17261 KAYO_AGING_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_AGING_MUSCLE_DN.html Downregulated in the vastus lateralis muscle of aged vs young adult rhesus monkeys 11309484 174/237 John Newman 3.01524798407961e-07 8.77129148999025e-07 4655 3713.54545454545 4203 2.74113490667246e-08 1392 1.74199716082023 1.70206744385999 1 4.19323720112301 4655 4426 3279 2711 1392 4420 4407 4578 2634 4144 4203 4611 M9224 SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_UP.html Selected genes up-regulated in peripheral blood monocytes (PBMC) of patients with hepatocellular carcinoma (HCC) compared to those with chronic hepatitis. 19074895 110/146 Arthur Liberzon 5.18483452622741e-05 5.84206707180554e-05 3185 4112.72727272727 4205 4.71359702134752e-06 3181 1.28263512356677 1.27907700681027 1 2.13368066133103 3181 4449 4027 4677 4138 3683 3438 4670 4205 4485 4287 4612 M16256 ZHAN_EARLY_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_EARLY_DIFFERENTIATION_GENES_UP.html B lymphocyte early differentiation genes (EDG): top genes up-regulated in tonsil B lymphocytes (TBC) compared to the tonsil plasma cells (TPC). 12393520 7/7 Arthur Liberzon 0.000253692450306834 0.000271525706450852 4210 4053.90909090909 4206 2.53721416897763e-05 2403 1.49266303899879 -1.28090324324275 -1 2.09071698055996 4206 3250 4615 4159 4384 4620 3903 4664 3989 2403 4400 4613 M2381 KUWANO_RNA_STABILIZED_BY_NO http://www.broadinstitute.org/gsea/msigdb/cards/KUWANO_RNA_STABILIZED_BY_NO.html Transcripts stabilized by NO [PubChem=145068] identified as up-regulated by NO [PubChem=145068] in the presence of actinomycin D [PubChemiD=2019] in IMR-90 and NIH 3T3 cells (fibroblast). 19289500 9/9 Arthur Liberzon 0.0471798887339343 0.0477259054488149 3085 3936.72727272727 4208 0.00482125561780847 2724 1.07206076786298 1.37732905111928 1 0.519607034960827 3082 4367 4695 4459 4703 3307 3986 2724 4637 4208 3136 4614 M9788 MOOTHA_PGC http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_PGC.html Genes up-regulated in differentiating C2C12 cells (myoblasts) upon expression of PPARGC1A [GeneID=10891] off an adenoviral vector. 12808457 536/643 Vamsi Mootha 3.70365276567467e-07 9.54490445253898e-07 3830 3969.36363636364 4209 3.70365338294178e-08 1729 1.4937187505315 1.57686811768135 1 3.56641275333974 3827 4676 4588 4335 1729 3719 4054 4209 3491 4569 4466 4615 M1088 REACTOME_METABOLISM_OF_PORPHYRINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_PORPHYRINS.html Genes involved in Metabolism of porphyrins 15/22 Reactome 2.09849822055032e-05 2.46145914537711e-05 4385 4022.27272727273 4210 1.90774385237463e-06 2815 1.74200587368894 2.47051947784119 1 3.17874558846924 4383 4608 2815 4434 3969 4540 4210 3991 2843 4059 4393 4616 M10145 BIOCARTA_PTEN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTEN_PATHWAY.html PTEN dependent cell cycle arrest and apoptosis 23/25 BioCarta 7.50293478546019e-05 8.31378888818231e-05 4325 3868.18181818182 4212 6.82108243603138e-06 2249 0.947661976360291 -0.703875926405754 -1 1.50498171582904 4322 3165 3790 2249 4212 4713 4566 4310 3645 4366 3212 4617 M12707 MILI_PSEUDOPODIA_HAPTOTAXIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_HAPTOTAXIS_UP.html Transcripts enriched in pseudopodia of NIH/3T3 cells (fibroblast) in response to haptotactic migratory stimulus by fibronectin, FN1 [GeneID=2335]. 18451862 697/805 Jessica Robertson 1.03136443289789e-06 1.79165615366177e-06 3630 4172.36363636364 4212 1.03136491156887e-07 2655 1.19256605264098 1.28080497538749 1 2.70612678296363 3630 4668 4617 4709 2655 4212 4116 4192 4140 4718 4239 4618 M964 REACTOME_DESTABILIZATION_OF_MRNA_BY_TRISTETRAPROLIN_TTP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_TRISTETRAPROLIN_TTP.html Genes involved in Destabilization of mRNA by Tristetraprolin (TTP) 20/20 Reactome 0.000504080584377211 0.000531916020178948 2960 3935.27272727273 4213 4.58360109257953e-05 2932 0.912044719094626 0.710348696266175 1 1.15088891399035 2958 4314 3825 4055 4440 3249 2932 4457 4336 4509 4213 4619 M19131 MAHADEVAN_RESPONSE_TO_MP470_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_RESPONSE_TO_MP470_DN.html Bottom genes down-regulated in the GIST (gastrointestinal stromal tumor) cell line sensitive to imatinib [PubChem=5291] after treatment with MP470, a protein kinase inhibitor. 17325667 26/26 Arthur Liberzon 0.0107193974892579 0.0109680373182955 3350 4091.54545454545 4214 0.000979271485182706 3348 1.59688600357853 1.51698660105867 1 1.20860440335981 3916 4291 3348 3581 4583 4304 4090 4214 4639 3349 4692 4620 M682 FARMER_BREAST_CANCER_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_5.html Cluster 5: selected 17q21_23 amplicon genes clustered together across breast cancer samples. 15897907 23/23 Leona Saunders 1.56414226698837e-07 7.30242482708713e-07 4035 3744.09090909091 4214 1.42194761654071e-08 675 0.963452478122789 -0.804915355469805 -1 2.32764619461677 4035 3749 3794 4448 675 4300 4214 2480 4461 4368 4661 4621 M2202 JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_UP.html Up-regulated genes distinguishing between breast cancer tumors with mutated BRCA1 [GeneID=672] from those with mutated BRCA2 [GeneID=675]. 12096084 71/77 John Newman 1.80762309047426e-07 7.47800341964416e-07 4350 3761.45454545455 4216 1.6432938536337e-08 839 1.10110408131135 1.07219118005592 1 2.66278429949511 4349 2633 3940 3789 839 4269 4619 4216 3895 4473 4354 4622 M2099 MARTENS_TRETINOIN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTENS_TRETINOIN_RESPONSE_DN.html Genes down-regulated in NB4 cells (acute promyelocytic leukemia, APL) in response to tretinoin [PubChem=444795]; based on Chip-seq data. 20159609 922/1412 Arthur Liberzon 9.73394604679235e-07 1.72120376449974e-06 4660 4086.09090909091 4217 9.73395031053172e-08 2617 1.38485947928878 1.50003708965681 1 3.16024325346237 3772 4663 4657 4704 2617 3376 3928 4401 3952 4660 4217 4623 M11850 TANG_SENESCENCE_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TANG_SENESCENCE_TP53_TARGETS_UP.html Genes up-regulated in WI-38 cells (senescent primary fibroblasts) after inactivation of TP53 [GeneID=7157] by GSE56 polypeptide. 17533371 41/61 Leona Saunders 8.53426303449406e-05 9.42262491761683e-05 4245 3740.09090909091 4219 7.75872192227272e-06 1731 2.53794569322096 2.79837767881028 1 4.05898235844745 4243 4244 1731 4219 4228 4281 4398 2505 4156 3121 4015 4624 M1265 STANHILL_HRAS_TRANSFROMATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/STANHILL_HRAS_TRANSFROMATION_UP.html Selected genes up-regulated in Rat1Ras cells (fibroblasts) which were transformed by expression of an oncogenic activated form of HRAS [GeneID=3265] compared to the parental Rat1 cells. 16278678 14/14 Leona Saunders 0.00634030668437126 0.00650712058061151 4165 3952.09090909091 4222 0.000578059385975458 2539 1.40597734111857 1.3383749855079 1 1.18633873447267 4161 4344 3158 2539 4567 4222 4232 3419 4685 3687 4459 4625 M6669 HEDENFALK_BREAST_CANCER_BRACX_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_BRACX_UP.html Up-regulated genes distinguishing between two groups of non-BRCA1/BRCA2 [GeneID=672;675] breast tumors (BRACx): group A vs group B. 12610208 22/33 John Newman 3.97085388085255e-07 9.84888613642883e-07 4115 3780.90909090909 4223 3.60986781596862e-08 1701 0.945039215680237 -0.611408930640943 -1 2.23282729318188 4111 4302 3622 4460 1701 4383 4223 2538 4571 4343 3336 4626 M9152 BIOCARTA_CCR3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CCR3_PATHWAY.html CCR3 signaling in Eosinophils 38/52 BioCarta 3.82085555822849e-06 5.23496030038852e-06 4565 3954.18181818182 4225 3.47351108556833e-07 2037 1.27812358210351 0.933561771021023 1 2.66450624256646 4565 3965 3749 2037 3375 4338 4322 4597 3858 4225 4465 4627 M1058 REACTOME_ADAPTIVE_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADAPTIVE_IMMUNE_SYSTEM.html Genes involved in Adaptive Immune System 520/690 Reactome 2.51208103291162e-07 8.19318755885969e-07 4210 3697.45454545455 4228 2.51208131688647e-08 1306 1.4441361938069 -1.36321108729798 -1 3.48488449320785 4207 3269 4261 2550 1306 4560 4296 4496 3216 4228 4283 4628 M16399 WEBER_METHYLATED_ICP_IN_SPERM_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_ICP_IN_SPERM_DN.html Unmethylated germline-specific genes with intermediate-CpG-density promoters (ICP) in sperm. 17334365 9/78 Arthur Liberzon 0.000257758801699506 0.000275752843159943 3755 4191.36363636364 4230 2.57788704401088e-05 3542 1.48239590454787 -1.72044718554263 -1 2.07199233184648 3752 4353 4634 3542 4386 4140 4230 4528 4160 3882 4498 4629 M839 REACTOME_DEADENYLATION_DEPENDENT_MRNA_DECAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEADENYLATION_DEPENDENT_MRNA_DECAY.html Genes involved in Deadenylation-dependent mRNA decay 49/52 Reactome 0.00013276837945149 0.00014439326060162 3610 4089.54545454545 4233 1.20705811456747e-05 3606 0.758199694355305 0.821909681618643 1 1.12098932610773 3606 4233 4088 4312 4300 3661 3676 3700 4477 4584 4348 4630 M7435 HOEBEKE_LYMPHOID_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOEBEKE_LYMPHOID_STEM_CELL_DN.html Genes down-regulated in the common lymphoid progenitor (CLP, defined as CD34+CD38-CD7+ [GeneID=947;952;924]) compared to a multipotent cord blood cell (defined as CD34+CD38+CD7-). 17170726 114/150 Arthur Liberzon 1.42218569929075e-06 2.2918117107041e-06 4485 3999.72727272727 4235 1.29289692605522e-07 2821 1.67667600307203 -1.7678249132369 -1 3.75286477826414 4484 4443 3333 4080 2821 4294 4486 4235 4279 3796 3746 4631 M14690 REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION.html Genes involved in Mitochondrial Fatty Acid Beta-Oxidation 17/17 Reactome 8.82642191867615e-05 9.72926470251085e-05 4450 4208.09090909091 4237 8.02434186863116e-06 3758 0.580031601487743 -0.600695271608278 -1 0.885809223871119 4446 4062 3928 4061 4237 4309 3758 4237 4446 4462 4343 4632 M2353 VANLOO_SP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANLOO_SP3_TARGETS_UP.html Genes up-regulated in E12.5 hearts from mice with SP3 [GeneID=6670] knockout compared to the wild type organ. 17923686 6/10 Arthur Liberzon 0.00259519643152304 0.00268096457797959 4480 3862.18181818182 4237 0.000259823219239552 2124 4.14587038186989 -3.0419805526119 -1 4.23779902403745 4476 4113 4687 3095 4537 4237 4571 4458 3883 2124 2303 4633 M19443 GUTIERREZ_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_MULTIPLE_MYELOMA_UP.html Genes exclusively up-regulated in plasma cells from MM (multiple myeloma) patients but with a similiar expression pattern in the normal cells and in the cells from WM (Waldenstroem's macroblobulinemia) patients. 17252022 43/48 Arthur Liberzon 0.000123195479093843 0.000134322629088228 2715 4011.09090909091 4240 1.12002162116725e-05 2713 0.826102704400905 -0.910580257036856 -1 1.23629553859724 2713 4240 4086 4669 4290 3160 3856 4625 4468 4475 3540 4634 M16807 FIRESTEIN_CTNNB1_PATHWAY_AND_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/FIRESTEIN_CTNNB1_PATHWAY_AND_PROLIFERATION.html Genes required for both proliferation and CTNNB1 [GeneID=1499] activity in DLD-1 cell (colon cancer with APC [GeneID=324] deletions). 18794900 14/14 Jessica Robertson 4.88491728798449e-06 6.46573460439899e-06 4625 4208.81818181818 4243 4.44084375870122e-07 3499 1.06726644338049 0.979778633755166 1 2.17731638828295 4622 3779 3653 3996 3499 4372 4690 4551 4243 4213 4679 4635 M3889 ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP.html Genes commonly up-regulated in CD-1 and CD-2 clusters of multiple myeloma samples and which were higher expressed in the CD-1 group. 16728703 126/158 Kevin Vogelsang 1.85298385253854e-07 7.48271685670965e-07 4490 3812 4244 1.68453091691725e-08 871 1.51333363123918 1.62857999386349 1 3.6782394306694 4487 3313 3652 4473 871 4654 4419 4244 3356 3976 4487 4636 M19988 GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN.html Genes down-regulated in metastatic breast cancer tumors having type 2 amplification in the 20q13 region; involves MYBL2, STK6 and ZNF217 [GeneID=4605;6790;7764] 16899599 235/259 Leona Saunders 1.43941703281581e-06 2.31404918082106e-06 4680 4072.36363636364 4245 1.30856179509012e-07 2829 1.39926136405808 1.51934398784793 1 3.12129526785162 4679 4412 4090 4120 2829 4529 4245 4028 2962 4514 4388 4637 M910 REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GIP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GIP.html Genes involved in Synthesis, Secretion, and Inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) 9/17 Reactome 0.00060624028337438 0.000637436876259094 4250 4100.72727272727 4247 6.06405734179642e-05 3302 1.84695357020168 -1.45481488669143 -1 2.3235434689661 4588 3523 4251 3734 4461 4613 4246 3302 4247 3457 4686 4638 M3427 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_11 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_11.html Amplification hot spot 11: colocolized fragile sites and cancer genes in the 11q3 region. 16751803 3/3 Arthur Liberzon 0.0591313255425955 0.0596622181618322 3005 3742.81818181818 4249 0.00607663299824291 1129 0.371453980265895 -0.371453980265895 -1 0.132854417813087 3003 4384 4368 4249 4680 2525 1129 3859 4683 4705 3586 4639 M4535 CHEOK_RESPONSE_TO_HD_MTX_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_HD_MTX_DN.html Genes specifically down-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by high-dose methotrexate (HDMTX) [PubChem=4112]. 12704389 35/42 Jean Junior 0.00243971368174848 0.00252310442108958 4260 4021.18181818182 4257 0.000222038494222598 1531 1.04242877314731 -0.841367307972215 -1 1.03913621030104 4498 4257 3855 4642 4609 4306 3879 1531 4403 4257 3996 4640 M16066 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN.html Genes down-regulated in lymphoblastoid cells from the European population compared to those from the Asian population. 17206142 795/989 Leona Saunders 3.59985505756201e-07 9.41752134134615e-07 3340 3867.72727272727 4258 3.59985564071518e-08 1697 1.39256989754164 -1.43244442650855 -1 3.32478856775423 3338 4664 4415 4337 1697 4258 4193 4587 2948 4667 3441 4641 M11166 IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR.html Genes in the expression cluster 'Late Progenitors Shared': up-regulated in hematopoietic late progenitor cells from adult bone marrow and fetal liver. 12228721 660/849 John Newman 1.31673536039527e-07 7.20206492018647e-07 4485 3882.09090909091 4263 1.31673543841592e-08 595 1.7389144035011 1.80069459684518 1 4.24559475969295 4481 4396 4489 4263 595 4313 4651 4068 3189 4021 4237 4642 M1085 REACTOME_APOBEC3G_MEDIATED_RESISTANCE_TO_HIV1_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOBEC3G_MEDIATED_RESISTANCE_TO_HIV1_INFECTION.html Genes involved in APOBEC3G mediated resistance to HIV-1 infection 7/10 Reactome 5.92541693646168e-05 6.63062302989548e-05 4295 4218.72727272727 4266 5.92557493993762e-06 3645 1.1225383394681 -1.56728027245917 -1 1.83628815538485 4295 4110 4266 4442 4181 4004 4282 4128 4573 3645 4480 4643 M11031 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_UP.html Genes specifically up-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and low-dose methotrexate (LDMTX) [PubChem=4112]. 12704389 15/18 Jean Junior 0.091802444818858 0.092468531699746 4060 4185.27272727273 4267 0.00871573693242455 3010 1.25177248304242 -0.588371873005135 -1 0.470496861635192 4059 4615 3799 4635 4655 4033 3010 4274 4126 4267 4565 4644 M907 REACTOME_CALNEXIN_CALRETICULIN_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CALNEXIN_CALRETICULIN_CYCLE.html Genes involved in Calnexin/calreticulin cycle 12/14 Reactome 0.0237813991915043 0.024165383032056 4350 4227.81818181818 4269 0.00218567532640377 3783 0.991489756957889 -0.640650347916136 -1 0.594646815577389 4056 4621 3783 4269 4615 4349 3859 3949 4012 4346 4647 4645 M19553 BIOCARTA_AHSP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AHSP_PATHWAY.html Hemoglobin's Chaperone 10/21 BioCarta 0.147799949418353 0.148555315429009 3890 4192.63636363636 4270 0.0144342651619651 3518 0.798427342299443 -0.920993180967904 -1 0.215866926271099 3889 4643 3518 4066 4668 4403 3830 4294 4717 4270 3821 4646 M2355 YUAN_ZNF143_PARTNERS http://www.broadinstitute.org/gsea/msigdb/cards/YUAN_ZNF143_PARTNERS.html Proteins associated with ZNF143 [GeneID=7702] in HeLa cells, based on MudPIT analysis. 17938208 31/39 Arthur Liberzon 7.35828632248058e-05 8.16242337064826e-05 4650 4007.90909090909 4270 6.68957494982976e-06 2287 0.999134293677508 1.23942429527935 1 1.59264908188935 4650 4270 3885 4285 4209 4510 3559 2287 4299 4433 3700 4647 M2487 FORTSCHEGGER_PHF8_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FORTSCHEGGER_PHF8_TARGETS_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) upon knockdown of PHF8 [GeneID=23133] by RNAi. 20421419 334/415 Arthur Liberzon 7.30373838534812e-07 1.40651347118903e-06 4410 3800 4270 6.63976437282141e-08 2305 1.73489642284547 -1.58736052262902 -1 4.03285437572633 4409 3558 3079 4270 2305 4635 4693 4415 3221 2530 4685 4648 M918 REACTOME_N_GLYCAN_TRIMMING_IN_THE_ER_AND_CALNEXIN_CALRETICULIN_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_N_GLYCAN_TRIMMING_IN_THE_ER_AND_CALNEXIN_CALRETICULIN_CYCLE.html Genes involved in N-glycan trimming in the ER and Calnexin/Calreticulin cycle 14/16 Reactome 0.00556227627808769 0.00571358956095189 3855 4195 4272 0.000506944491176142 3315 0.968719546436541 -0.719646466727807 -1 0.823830357285169 3853 4335 3820 4272 4563 4132 3315 4657 4137 4399 4662 4649 M17423 LAIHO_COLORECTAL_CANCER_SERRATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/LAIHO_COLORECTAL_CANCER_SERRATED_DN.html Genes down-regulated in serrated vs conventional colorectal carcinoma (CRC) samples. 16819509 124/154 Arthur Liberzon 2.28210661930877e-06 3.38909363301293e-06 4570 3967.18181818182 4276 2.07464453326342e-07 1729 1.47945815419726 1.78894007238138 1 3.20446099587203 4570 4436 3877 4111 3101 4324 4201 4652 1729 4362 4276 4650 M6794 BUSA_SAM68_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUSA_SAM68_TARGETS_UP.html Genes up-regulated in LNCaP cells (prostate cancer) after knockdown of SAM68 [GeneID=10657] by RNAi. 17237817 8/10 Arthur Liberzon 0.00124553768597977 0.0012983520048199 4360 3945 4276 0.000124623635103529 1288 1.11941673691078 -0.950078125381668 -1 1.2494745249488 4261 4360 4346 3984 4653 4276 3475 1288 4602 3792 4358 4651 M905 CHOW_RASSF1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHOW_RASSF1_TARGETS_DN.html Genes down-regulated in C666-1 cells (nasopharyngeal carcinoma) by stable expression of RASSF1 [GeneID=11186]. 16116475 36/39 Lauren Kazmierski 1.14052578158566e-06 1.93643226226054e-06 4305 4102.36363636364 4278 1.03684215714399e-07 2658 1.10927435519171 0.951341157207474 1 2.49857454563535 4305 4538 3887 4490 2658 4381 4100 3938 4301 4278 4250 4652 M456 REACTOME_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRNA_AMINOACYLATION.html Genes involved in tRNA Aminoacylation 43/43 Reactome 0.000133195775584032 0.000144758015371087 4555 4295.36363636364 4279 1.21094400373307e-05 3960 0.669255277166072 0.539716454048734 1 0.983321285104831 4555 3960 4095 4107 4303 4219 4025 4567 4559 4580 4279 4653 M10762 IGARASHI_ATF4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IGARASHI_ATF4_TARGETS_UP.html Genes up-regulated in A549 cells (lung cancer) after knockdown of ATF4 [GeneID=468] by RNAi. 17297441 4/5 Leona Saunders 0.0392008842329527 0.0397226650020474 3465 4047.27272727273 4282 0.00399100752863209 2660 0.781797032784469 -0.781797032784469 -1 0.390437469445072 3461 4649 4282 4443 4670 3956 3216 2660 4716 4701 3766 4654 M1783 POS_RESPONSE_TO_HISTAMINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/POS_RESPONSE_TO_HISTAMINE_DN.html Genes gradually down-regulated by histamine [PubChem=774] in B16-F10 melanoma tumors. 18339882 14/14 Jessica Robertson 0.049030214848238 0.0495763954763675 4640 4140.36363636364 4284 0.0045598438913458 3026 0.826840428749338 -0.385609128706147 -1 0.383814583881443 3831 4343 3896 4083 4638 3703 3026 4639 4698 4403 4284 4655 M13492 REACTOME_DEADENYLATION_OF_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEADENYLATION_OF_MRNA.html Genes involved in Deadenylation of mRNA 25/27 Reactome 2.74293233314777e-05 3.17397416338746e-05 4240 4245.81818181818 4287 2.49360593843645e-06 3657 0.866114575115319 -0.814277579681973 -1 1.51683563961392 4237 4287 3964 4284 4027 4632 4369 3657 4393 4414 4440 4656 M10735 REACTOME_PLATELET_AGGREGATION_PLUG_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_AGGREGATION_PLUG_FORMATION.html Genes involved in Platelet Aggregation (Plug Formation) 41/51 Reactome 0.0015267465451102 0.00158727834645819 4530 4231.18181818182 4299 0.000138891554605358 3317 1.72715142365122 1.85503724711956 1 1.89437258075807 4703 4529 3317 4655 4507 4299 4031 3751 4123 4102 4526 4657 M7146 BIOCARTA_CLASSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CLASSIC_PATHWAY.html Classical Complement Pathway 13/17 BioCarta 0.000656058153868311 0.000688897549779406 2970 3714.63636363636 4301 5.9659443412844e-05 1660 2.43546001634268 -3.01834080049613 -1 3.04682789903355 2970 4333 1660 4578 4460 4301 3719 4497 4449 2636 3258 4658 M14524 GRADE_COLON_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_CANCER_UP.html Up-regulated genes in colon carcinoma tumors compared to the matched normal mucosa samples. 17210682 1119/1490 Jessica Robertson 4.48896439039831e-07 1.04182662604269e-06 4375 3879 4304 4.48896529718462e-08 1932 1.45524530813558 1.51401780228301 1 3.45101127525682 4375 4389 4570 3280 1932 3601 3834 4304 3053 4663 4668 4659 M1940 BIOCARTA_CHREBP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CHREBP2_PATHWAY.html Regulation And Function Of ChREBP in Liver 41/64 BioCarta 0.00479124904228291 0.00492587573068511 4675 3887.90909090909 4307 0.000436519594947544 841 1.27663350110734 1.45981502012354 1 1.13467190366493 4675 3959 3730 3235 4560 4514 4382 4153 841 4307 4411 4660 M1597 BURTON_ADIPOGENESIS_PEAK_AT_2HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_2HR.html Cluster 2: genes maximally expressed at 2 h time point during differentiation of 3T3-L1 fibroblasts into adipocytes (cluster 2) in response to adipogenic hormones. 12137940 75/83 John Newman 5.7970289829226e-05 6.49016988634836e-05 4470 3698.27272727273 4311 5.27016521912301e-06 1909 1.94643101333803 1.94373398728265 1 3.22804464068955 4467 4474 1968 3030 4164 4703 4311 2963 4323 1909 4369 4661 M15228 KRISHNAN_FURIN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRISHNAN_FURIN_TARGETS_UP.html Genes up-regulated in naive T lymphocytes lacking FURIN [GeneID=5045]: Cre-Lox knockout of FURIN in CD4+ [GeneID=920] cells. 18690214 18/25 Jessica Robertson 0.011201736642023 0.0114590803966945 4075 4107 4317 0.00102356203837259 3134 1.46814467428345 1.51316235164167 1 1.0959019133926 4073 4317 3163 3778 4584 4631 4448 3134 4671 3753 4625 4662 M6981 KEGG_PROTEIN_EXPORT http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEIN_EXPORT.html Protein export 33/39 KEGG 1.96225606060321e-05 2.31372685636952e-05 4200 4283.45454545455 4319 1.78388505714726e-06 3789 0.953175485026764 -0.490067216427825 -1 1.72696397704626 4198 4278 3929 4319 3944 4445 3789 4363 4616 4522 4715 4663 M15662 WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_DN.html Genes down-regulated in non-neoplastic rectal mucosa samples from patients having cancer associated with ulcerative collitis, compared to those who did not have the cancer. 17255260 18/27 Arthur Liberzon 0.0278863045330233 0.0282939289329041 3615 4221.81818181818 4323 0.00256783479535789 3456 1.13874483016136 -1.07457388998206 -1 0.659024609429922 3613 4607 3456 4638 4624 4323 3988 4566 4646 3750 4229 4664 M550 REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES.html Genes involved in Antiviral mechanism by IFN-stimulated genes 86/100 Reactome 5.46472939223729e-05 6.13693141359981e-05 4495 4302.90909090909 4327 4.96805921734746e-06 3609 1.20736943513568 1.06766714190637 1 1.99515545586503 4492 4467 4047 3609 4153 4118 4644 4327 4206 4553 4716 4665 M14594 LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN.html Genes with copy number losses in primary neuroblastoma tumors. 17533364 1015/1145 Arthur Liberzon 1.66856808595587e-07 7.3358205358541e-07 3620 3702.36363636364 4330 1.66856821124126e-08 858 1.5036024655968 -1.23478828009598 -1 3.65947231460948 3620 4391 4356 4330 858 3397 3150 4676 2630 4651 4667 4666 M9577 MOOTHA_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_MITOCHONDRIA.html Mitochondrial genes 12808457 501/573 Vamsi Mootha 7.0208920229764e-07 1.37329085443823e-06 2970 3788.09090909091 4339 7.020894241159e-08 2350 1.3372117262114 1.22493169590723 1 3.10252919288035 2967 4682 4589 4339 2350 3109 2415 4634 3314 4664 4606 4667 M486 REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER.html Genes involved in RNA Polymerase III Transcription Initiation From Type 2 Promoter 24/27 Reactome 8.26539201135552e-07 1.53231148050267e-06 4600 4124.45454545455 4342 7.51399556060176e-08 2413 1.04872831455712 -0.658152122540475 -1 2.4023410242419 4597 4567 3793 4275 2413 4670 4342 4142 3591 4388 4591 4668 M794 REACTOME_ACTIVATION_OF_CHAPERONES_BY_ATF6_ALPHA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_CHAPERONES_BY_ATF6_ALPHA.html Genes involved in Activation of Chaperones by ATF6-alpha 19/20 Reactome 9.69632977134025e-05 0.00010662234217796 4250 4331.54545454545 4342 8.8152337781307e-06 3720 1.1299964103599 -0.879444857414713 -1 1.75507233374368 4342 4604 3720 4491 4246 4608 3963 4099 4656 4246 4672 4669 M2566 HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_DN.html Genes distinguishing asparaginase resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 31/38 Arthur Liberzon 0.0158115563220777 0.0161189083888136 4245 4064.72727272727 4342 0.00144785016691544 2511 0.812539883621473 -0.788720435168818 -1 0.535756032655153 4241 4565 4033 3606 4597 3291 2511 4342 4631 4498 4397 4670 M716 REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX.html Genes involved in Regulation of pyruvate dehydrogenase (PDH) complex 12/13 Reactome 0.604724025000074 0.605365301802831 4640 4313.54545454545 4345 0.0809173167130324 3805 1.05091563037924 -0.544562597475181 -1 0.0420904979640956 4640 4628 3805 4062 4689 4008 4559 4241 4579 4345 3893 4671 M4967 KORKOLA_CORRELATED_WITH_POU5F1 http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CORRELATED_WITH_POU5F1.html Genes whose expression pattern in adult male germ cell tumors (GCT) correlates with POU5F1 [GeneID=5460]. 16424014 36/57 Arthur Liberzon 3.5638883466625e-07 9.41752134134615e-07 4480 3444.81818181818 4351 3.23989902181314e-08 1298 1.8368814574535 -1.64004983979536 -1 4.40155612631793 4477 1792 2434 4351 1573 4580 4586 4529 3823 1298 4450 4672 M801 REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_ATF6_ALPHA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_ATF6_ALPHA.html Genes involved in Activation of Chaperone Genes by ATF6-alpha 17/18 Reactome 0.00765929538202504 0.00785056985953489 4355 4195.27272727273 4354 0.00069873562754328 3032 1.30935906462598 -0.954796411680193 -1 1.05845313712676 4354 4617 3671 4074 4574 4376 3032 3917 4667 4157 4709 4673 M4735 WANG_LMO4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LMO4_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) engineered to conditionally express LMO4 [GeneID=8543] by a Tet Off system. 17452977 475/584 Arthur Liberzon 1.62156659738233e-07 7.3358205358541e-07 4675 3887.54545454545 4355 1.47415156082189e-08 705 1.56115809774192 1.63383458578845 1 3.80146673688201 4674 4678 3947 4081 705 4066 4355 4693 2467 4519 4578 4674 M1014 REACTOME_IL_6_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_6_SIGNALING.html Genes involved in Interleukin-6 signaling 11/11 Reactome 0.293359655734377 0.294232378892108 3870 4285.09090909091 4359 0.0310736510100915 3562 0.959422023013552 -0.511338891482759 -1 0.154964757918745 3870 4359 3562 4073 4679 4277 4381 4433 4684 4306 4512 4675 M5871 MOOTHA_PYR http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_PYR.html Genes involved in pyruvate metabolism; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 7/8 Vamsi Mootha 0.6513215599 0.651735798755141 4420 4257.09090909091 4359 0.1 3538 1.05091563037924 -0.544562597475181 -1 0.0285432386125361 4419 4374 4649 3538 4697 4550 3942 3931 4359 4096 4273 4676 M7331 KOBAYASHI_EGFR_SIGNALING_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_6HR_UP.html Genes up-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 6h. 17145885 8/12 Leona Saunders 0.0517834026190465 0.0523266239267608 4110 4219.72727272727 4369 0.00530312099931097 3120 0.817706071099083 -0.817706071099083 -1 0.371310892655293 4110 4369 4279 4464 4644 3803 4648 3120 4718 4700 3562 4677 M15709 ACEVEDO_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) compared to normal liver samples. 18413731 1238/1528 Jessica Robertson 4.95365127431113e-07 1.10654207358015e-06 4375 4084.27272727273 4370 4.95365237855122e-08 2036 1.49159864430889 1.51683101652321 1 3.52277069117123 4371 4656 4544 4694 2036 4062 4229 4370 3319 4644 4002 4678 M168 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_DN.html Genes from the magenta module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 14/15 Arthur Liberzon 0.0889933036181315 0.0896581415320342 3695 4187.45454545455 4372 0.00843738839643601 3166 1.13156673796047 1.20334444453776 1 0.426610695524669 3695 4620 3665 4450 4654 4367 4372 4519 4153 4401 3166 4679 M1976 OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_DN.html Genes down-regulated in both the patients in the multicentric hepatocellular carcinoma (HCC) group and those with multicentric recurrence. 16788756 5/13 Yujin Hoshida 0.0010194574734078 0.00106527325093753 4420 4058.45454545455 4372 0.000101992545768614 3186 2.15882191534348 2.81349462579816 1 2.53070744677344 4420 3535 4628 3928 4489 3892 3186 4385 4372 3259 4549 4680 M11197 HSIAO_HOUSEKEEPING_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HSIAO_HOUSEKEEPING_GENES.html Housekeeping genes identified as expressed across 19 normal tissues. 11773596 560/786 Arthur Liberzon 3.62381269524556e-07 9.43951209799063e-07 4375 3855.90909090909 4374 3.62381328618652e-08 1706 1.3664327435215 1.58338799427081 1 3.26088980552682 4374 4674 4611 2748 1706 4406 3862 3523 3400 4657 4454 4681 M138 PID_THROMBIN_PAR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_THROMBIN_PAR4_PATHWAY.html PAR4-mediated thrombin signaling events 18832364 22/29 Pathway Interaction Database 0.0246569895936845 0.0250443277129742 4445 4309.09090909091 4376 0.00226706851946221 3520 1.86535981545332 -1.80752368830834 -1 1.15121291234047 4441 4586 3520 4087 4618 4484 4376 4109 4328 4192 4659 4682 M1868 MIKI_COEXPRESSED_WITH_CYP19A1 http://www.broadinstitute.org/gsea/msigdb/cards/MIKI_COEXPRESSED_WITH_CYP19A1.html Nuclear receptors whose expression correlated with that of aromatase (CYP19A1) [GeneID=1588] in a panel of breast cancer biopsies. 17440110 6/9 Jessica Robertson 0.000578089987812777 0.000608787314251742 1315 2865 4376 5.78240427510534e-05 292 0.744557163789311 -0.744557163789311 -1 0.912797811970612 1311 4376 4587 4444 4623 681 292 999 4695 4715 792 4683 M2750 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_13 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_13.html Amplification hot spot 13: colocolized fragile sites and cancer genes in the Xq12-q28 region. 16751803 8/9 Arthur Liberzon 0.0529588150060029 0.0534800185768792 4660 4324.45454545455 4377 0.00542649278395652 3698 1.5746724085773 -1.03953655204128 -1 0.755364595740619 4660 4638 4377 4616 4646 4206 4152 3698 4482 3793 4301 4684 M2383 SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP.html Genes up-regulated in E12.5 forelimb buds with POR [GeneID=5447] knockout. 19273610 28/31 Arthur Liberzon 2.33674757157717e-05 2.72601298513204e-05 4505 4329.18181818182 4378 2.12433853808838e-06 3864 1.09007478857797 -1.30127858767958 -1 1.95096474375191 4505 4558 3864 4086 3992 4657 4155 4354 4521 4378 4551 4685 M1986 KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS_AND_CYCLIC_RGD http://www.broadinstitute.org/gsea/msigdb/cards/KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS_AND_CYCLIC_RGD.html Inflammatory cytokines and their receptors moduated in brain tumors in response to treatment with cyclic RGD peptide prior to the oncocytic virus therapy. 18042934 5/25 Jessica Robertson 0.0152031904786353 0.0155107703321109 2510 3873.36363636364 4381 0.00153082147959691 2473 2.93595615053201 2.93595615053201 1 2.08633442891817 2509 4381 4631 4426 4600 2616 2473 4476 4650 3890 3955 4686 M4762 WEBER_METHYLATED_LCP_IN_SPERM_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_LCP_IN_SPERM_DN.html Unmethylated germline-specific genes with low-CpG-density promoters (LCP) in sperm. 17334365 3/9 Arthur Liberzon 0.0306508465420407 0.0310788390286643 4015 4289.09090909091 4383 0.00310820036313859 3569 1.18270340802297 -1.18270340802297 -1 0.667003792761518 4012 4383 4635 4392 4627 4041 4141 4599 4706 3569 4075 4687 M2557 HOLLEMAN_DAUNORUBICIN_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_B_ALL_DN.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 19/21 Arthur Liberzon 8.75995137877691e-05 9.66050712799697e-05 4120 4249.81818181818 4384 7.96390927420269e-06 3748 0.838602142738925 0.943751018405289 1 1.30403614372754 4118 4600 3930 4510 4235 4384 4475 3748 4574 4387 3787 4688 M10514 NAGY_STAGA_COMPONENTS_HUMAN http://www.broadinstitute.org/gsea/msigdb/cards/NAGY_STAGA_COMPONENTS_HUMAN.html Composition of the 2 MDa human STAGA complex containing KAT2A [GeneID=2648]. 17694077 16/18 Arthur Liberzon 0.598078114403253 0.598839350866218 4705 4163.18181818182 4389 0.0795231345756548 3107 0.558717184517257 0.517886837672915 1 0 3740 4618 3936 4653 4688 3139 3107 4389 4703 4703 4119 4689 M2524 VANOEVELEN_MYOGENESIS_SIN3A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/VANOEVELEN_MYOGENESIS_SIN3A_TARGETS.html Loci bound exclusively by SIN3A [GeneID=25942] in myotubules. 20956564 279/323 Arthur Liberzon 1.3837275522793e-07 7.20206492018647e-07 4615 3970.81818181818 4392 1.25793421755565e-08 552 1.39797906676464 1.63650108370471 1 3.40338382851687 4611 4696 4058 4539 552 4024 4392 4312 3546 4472 4477 4690 M894 REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION.html Genes involved in Asparagine N-linked glycosylation 87/94 Reactome 6.2719482740016e-06 8.06637489190396e-06 4630 4162.81818181818 4409 5.70178741334532e-07 3037 1.4223432080531 1.69283120312582 1 2.86340334941824 4628 4459 3920 4650 3605 4539 3814 4308 3037 4409 4422 4691 M17695 REACTOME_PACKAGING_OF_TELOMERE_ENDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PACKAGING_OF_TELOMERE_ENDS.html Genes involved in Packaging Of Telomere Ends 20/64 Reactome 0.0240475370246655 0.0244305584925573 4660 4205.27272727273 4411 0.00221040796267718 3265 0.957631317049509 0.872659399036488 1 0.570806095413072 4659 4597 3766 4527 4616 3265 3871 3648 4644 4411 4254 4692 M9416 JIANG_CORE_DUPLICON_GENES http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_CORE_DUPLICON_GENES.html Genes mapped to core duplicons - elements shared by a majority of segmental duplication blocks. 17922013 8/15 Leona Saunders 0.000984396171093184 0.00102886402293176 4390 4380.27272727273 4418 9.84832509272927e-05 4103 0.795195069605036 -0.847224345563194 -1 0.905401667446788 4388 4103 4418 4432 4486 4658 4320 4167 4611 4152 4448 4693 M8478 DER_IFN_GAMMA_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_GAMMA_RESPONSE_DN.html Genes down-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon gamma for 6 h. 9861020 11/12 Yujin Hoshida 2.54540368034479e-06 3.69054148156428e-06 4560 3935 4419 2.31400602307807e-07 2412 1.31567013536088 -0.888055927915915 -1 2.8245810502908 4557 3794 3259 4419 3174 4682 4570 2412 4489 3303 4626 4694 M7721 BIOCARTA_EIF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF_PATHWAY.html Eukaryotic protein translation 21/40 BioCarta 0.0159235462796466 0.01622956995032 4600 4282.72727272727 4422 0.00145818019134254 3384 0.803330593536189 0.804302486682335 1 0.528156717434959 4038 4596 3960 4518 4598 4167 4422 3384 4596 4518 4313 4695 M15096 REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION.html Genes involved in Mitochondrial tRNA aminoacylation 27/27 Reactome 0.000776984771714797 0.000813704930662046 4425 4303.45454545455 4425 7.06599380899094e-05 3935 0.779700126140333 0.630085251778828 1 0.918733771559376 4425 4021 4002 4646 4474 4516 3935 4126 4557 4443 4193 4696 M15774 DANG_BOUND_BY_MYC http://www.broadinstitute.org/gsea/msigdb/cards/DANG_BOUND_BY_MYC.html Genes whose promoters are bound by MYC [GeneID=4609], according to MYC Target Gene Database. 14519204 1400/1799 Chi Dang 3.97613602032293e-07 9.84907668441108e-07 4655 4129.72727272727 4428 3.9761367317577e-08 1818 1.46332683421484 1.54068833749924 1 3.48481313075826 4428 4655 4641 4707 1818 3970 4511 4217 3480 4655 4345 4697 M1117 CAIRO_PML_TARGETS_BOUND_BY_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_PML_TARGETS_BOUND_BY_MYC_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) after knockout of PML [GeneID=5371] and whose promoters were bound by MYC [GeneID=4609]. 15735755 21/27 Lauren Kazmierski 0.473740803826086 0.47464584887691 3580 4164.45454545455 4431 0.0566898271092797 3374 1.58154311682839 -1.01347552326511 -1 0.155803354707936 4604 4587 3374 3578 4683 4431 4139 3580 4614 3733 4486 4698 M19540 KEGG_OXIDATIVE_PHOSPHORYLATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OXIDATIVE_PHOSPHORYLATION.html Oxidative phosphorylation 126/155 KEGG 0.0152051555776859 0.0155107703321109 2290 3867.63636363636 4434 0.00139193393076887 1658 1.0332413540623 0.824529902299235 1 0.701809031826848 2288 4444 4139 4678 4592 2818 1658 4564 4281 4648 4434 4699 M760 REACTOME_INTEGRIN_ALPHAIIB_BETA3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRIN_ALPHAIIB_BETA3_SIGNALING.html Genes involved in Integrin alphaIIb beta3 signaling 37/42 Reactome 0.00256846267460414 0.00265437336020713 4705 4247.72727272727 4435 0.000233769656506727 3296 1.72397252716428 1.86324220080738 1 1.73597024617266 4704 4536 3296 4651 4530 4435 4125 3764 4033 4087 4564 4700 M16154 NICK_RESPONSE_TO_PROC_TREATMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/NICK_RESPONSE_TO_PROC_TREATMENT_UP.html Genes up-regulated in neutrophils upon treatment with activated protein C (PROC) [GeneID=5624] of pulmonary inflammation induced by bacterial lipopolysaccharide (LPS). 15339848 5/6 Arthur Liberzon 4.06114340601694e-05 4.62451070600723e-05 2310 3089.72727272727 4437 4.06121762591186e-06 59 0.618367428588565 -0.618367428588565 -1 1.02799015725628 2307 4646 4598 4437 4582 1493 59 1250 4544 4716 1355 4701 M17753 BENPORATH_MYC_MAX_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_MYC_MAX_TARGETS.html Set 'Myc targets2': targets of c-Myc [GeneID=4609] and Max [GeneID=4149] identified by ChIP on chip in a Burkitt's lymphoma cell line; overlap set. 18443585 1015/1222 Jessica Robertson 5.89792818250858e-07 1.22635334896214e-06 4710 4213.36363636364 4438 5.89792974785922e-08 2188 1.29541262315107 1.37185943962005 1 3.02958883468993 4652 4661 4454 4708 2188 4095 4308 4325 3810 4708 4438 4702 M1269 KREPPEL_CD99_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KREPPEL_CD99_TARGETS_DN.html Genes down-regulated in ESFT cells (Ewing's sarcoma family of tumors) after knockdown of CD99 [GeneID=4267] by RNAi. 16314831 13/14 Arthur Liberzon 0.68618940391 0.68618940391 4275 4319.63636363636 4451 0.1 3448 1.65338716743585 -1.18332750016625 -1 0.0587159364516295 4273 4631 3448 4494 4708 4315 4583 4451 4562 4172 3879 4703 M10294 REACTOME_UNFOLDED_PROTEIN_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNFOLDED_PROTEIN_RESPONSE.html Genes involved in Unfolded Protein Response 99/108 Reactome 9.59598531962707e-07 1.7033866381587e-06 4625 4305.36363636364 4463 8.72362682292506e-08 2538 0.970443734379045 -0.915788069310636 -1 2.20133851748295 4625 4455 4117 4680 2538 4563 4463 4530 4335 4596 4457 4704 M1400 ZEILSTRA_CD44_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZEILSTRA_CD44_TARGETS_DN.html Genes implicated in apoptosis that were down-regulated in duodenum of CD44 [GeneID=960] knockout mice. 18483247 6/8 Jessica Robertson 0.0100062550935395 0.0102427941968134 3030 3588.54545454545 4470 0.00100515990298584 886 0.777161870041049 0.777161870041049 1 0.571795998069436 3030 4648 4472 4470 4690 2489 886 2108 4692 4712 3277 4705 M29 SHEN_SMARCA2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHEN_SMARCA2_TARGETS_UP.html Genes whose expression positively correlated with that of SMARCA2 [GeneID=6595] in prostate cancer samples. 19074882 532/578 Jessica Robertson 2.26269184974477e-07 7.86164283892477e-07 4710 4140.72727272727 4478 2.26269208013465e-08 1186 0.985463339198048 1.0098298418409 1 2.36926590522047 4478 4679 4459 4706 1186 4234 3921 4579 4040 4710 4556 4706 M7488 PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_UP.html Antigen processing and presentation genes up-regulated in JY cells (B lymphocytes) treated with TSA [PubChem=5562]. 18829567 80/89 Jessica Robertson 0.00288184101873702 0.0029744783749046 4035 4336.09090909091 4482 0.000262329359975872 3822 0.851747579220485 0.89943923247082 1 0.815421222847012 4034 4482 4133 4683 4538 3953 3822 4491 4512 4607 4442 4707 M224 WEBER_METHYLATED_HCP_IN_FIBROBLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_FIBROBLAST_UP.html Methylated germline-specific genes with high-CpG-density promoters (HCP) in primary fibroblasts. 17334365 3/7 Jessica Robertson 0.0461716546193533 0.0467260312614382 4715 4229.90909090909 4489 0.00471600010409408 3132 0.772051441640809 0.772051441640809 1 0.363050797409418 4489 4123 4558 3507 4639 3798 3132 4623 4713 4713 4234 4708 M7847 REACTOME_SIGNALING_BY_WNT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_WNT.html Genes involved in Signaling by Wnt 69/79 Reactome 0.0168335981843555 0.0171497050356482 4425 4224.09090909091 4492 0.00154216360471753 3088 0.726495215634593 -0.803960203880306 -1 0.465857438805904 4423 4492 4131 3816 4601 3465 3088 4694 4530 4627 4598 4709 M13265 KEGG_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI_ANCHOR_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI_ANCHOR_BIOSYNTHESIS.html Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 24/25 KEGG 0.415722739089479 0.416782355246886 4705 4340.09090909091 4498 0.0476785991009146 3616 0.69071731056946 -0.790368717728378 -1 0.0555444212503822 4701 4292 3995 4498 4681 3903 3616 4444 4516 4550 4545 4710 M1022 REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER.html Genes involved in RNA Polymerase III Transcription Initiation From Type 3 Promoter 27/30 Reactome 5.68092903154506e-06 7.3872821002858e-06 4560 4228 4501 5.16449427374812e-07 3561 1.03142830752534 -0.604807930831974 -1 2.07852005151588 4556 4563 3872 4501 3561 4554 3837 3957 4004 4513 4590 4711 M2974 NAGY_TFTC_COMPONENTS_HUMAN http://www.broadinstitute.org/gsea/msigdb/cards/NAGY_TFTC_COMPONENTS_HUMAN.html Composition of the 2 MDa human TFTC complex containing KAT2A [GeneID=2648]. 17694077 20/22 Arthur Liberzon 0.0101627202221949 0.0104007023956547 4510 4337.90909090909 4509 0.0009281792679379 3730 0.601960033780781 0.497211643616359 1 0.430002688757706 4165 4591 3983 4660 4581 3844 3730 4509 4675 4510 4469 4712 M17646 JAIN_NFKB_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/JAIN_NFKB_SIGNALING.html Genes abnormally regulated in response to CD40L and IL4 [GeneID=959;3565] stimulation of B lymphocytes from patients with a hypomorphic mutation of IKBKG [GeneID=8517]. 15578091 105/119 Kevin Vogelsang 5.62084733326882e-06 7.32681563463928e-06 4610 4368.54545454545 4509 5.10987426745006e-07 3552 1.03676179977883 0.964174265265115 1 2.09101502733542 4607 4452 4098 4551 3552 4232 4204 4705 4509 4530 4614 4713 M1818 MATZUK_STEROIDOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_STEROIDOGENESIS.html Genes important for steroidogenesis, based on mouse models with female fertility defects. 18989307 4/8 Jessica Robertson 0.00194688504212024 0.00201962580193572 2580 3835.90909090909 4519 0.000194859281083694 1526 0.48710836341595 -0.48710836341595 -1 0.477850295088627 2576 4651 4568 4615 4519 2647 1526 4033 4719 4714 3627 4714 M3862 REACTOME_AKT_PHOSPHORYLATES_TARGETS_IN_THE_CYTOSOL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AKT_PHOSPHORYLATES_TARGETS_IN_THE_CYTOSOL.html Genes involved in AKT phosphorylates targets in the cytosol 14/14 Reactome 4.71168936863931e-07 1.07280143849385e-06 4680 4120.54545454545 4531 4.28335488884662e-08 1900 0.716772565667296 -0.805025502195165 -1 1.67071599535504 4678 3506 3851 3785 1900 4616 4713 4640 4531 4682 4424 4715 M17094 GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN.html Genes down-regulated in non-metastatic breast cancer tumors having type 1 amplification in the 20q13 region; involves ZNF217 [GeneID=7764] locus only. 16899599 407/460 Leona Saunders 5.62496605895721e-07 1.18897625608052e-06 4555 4083.63636363636 4533 5.11360681559144e-08 2070 1.33675091960097 -1.21518405619811 -1 3.1350902141228 4533 4687 4144 4552 2070 4577 4334 4553 2598 4586 4286 4716 M16843 REACTOME_METABOLISM_OF_RNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_RNA.html Genes involved in Metabolism of RNA 292/402 Reactome 2.75488144137274e-06 3.94390063793732e-06 4545 4373.63636363636 4542 2.50444081008475e-07 3223 0.820188447801664 -0.723943870881061 -1 1.73248767551318 4542 4699 4169 4710 3223 4246 4605 4066 4534 4692 4624 4717 M2253 NIKOLSKY_BREAST_CANCER_17P11_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_17P11_AMPLICON.html Genes within amplicon 17p11 identified in a copy number alterations study of 191 breast tumor samples. 19010930 7/10 Jessica Robertson 0.02019072071526 0.0205521246012567 4615 4408.09090909091 4546 0.00203765507961446 3629 0.805456750113317 0.805456750113317 1 0.496468715817301 4225 4644 4463 4611 4612 3629 4546 4561 4720 4095 4383 4718 M1743 MARSON_BOUND_BY_FOXP3_UNSTIMULATED http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_BOUND_BY_FOXP3_UNSTIMULATED.html Genes with promoters bound by FOXP3 [GeneID=50943] in unstimulated hybridoma cells. 17237765 1434/1812 Jessica Robertson 2.73053695956157e-07 8.38703759494626e-07 4620 4152 4560 2.73053729507408e-08 1390 1.48697630853184 1.64047058189629 1 3.58367433686254 4616 4654 4519 4560 1390 4083 4630 4706 3564 4583 4367 4719 M1809 MATZUK_CUMULUS_EXPANSION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_CUMULUS_EXPANSION.html Genes important for cumulus expansion, based on mouse models with female fertility defects. 18989307 7/10 Jessica Robertson 0.635896688565434 0.636436041142674 4570 4374.81818181818 4565 0.0960956781920561 3649 2.69757593533295 2.36315621978857 1 0.162861745224037 4567 4639 4565 4413 4692 4680 3855 4174 4307 3649 4582 4720 M2277 KIM_PTEN_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_PTEN_TARGETS_DN.html Genes down-regulated in HCT116 cells (colorectal carcinoma) upon knockout of PTEN [GeneID=5728]. 17060456 5/7 Arthur Liberzon 0.104968542448326 0.105639983018358 4720 4499.45454545455 4661 0.0110283779220978 3524 0.621438479024454 -0.621438479024454 -1 0.193926408470376 4713 4118 4677 3524 4661 4587 4442 4720 4641 4720 4691