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 7.30189930901507e-46 2.15406029615945e-43 5 549.727272727273 9 7.30189930901499e-47 1 2.28720419199492 -2.30763278766137 -1 28.1789358123183 2 994 4715 1 126 1 9 2 181 9 7 2 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 2.22749446878787e-107 1.05137738926788e-103 5 621.727272727273 24 2.22749446878789e-108 1 3.3629067818636 3.49360975213941 1 100 1 981 4714 234 503 2 24 1 364 1 14 3 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 5.46359317498895e-32 6.1400380442733e-30 5 216.181818181818 30 4.96690288635362e-33 3 3.05470281134605 3.15151499426625 1 25.7665716006507 3 1303 21 243 161 4 15 14 540 44 30 4 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 8.51283765035185e-11 1.26310212782858e-09 10 142.272727272727 52 7.73894331880116e-12 8 3.47997603709255 3.5899099283365 1 8.94123826137895 48 256 254 284 52 12 38 8 109 496 8 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 1.12474219293598e-22 6.89452357228289e-21 10 399.454545454545 68 1.02249290266907e-23 7 2.85120989761175 3.01772085533014 1 16.5986529119665 7 1361 50 68 1816 7 32 163 598 61 231 6 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 6.69507791758426e-23 4.21343570279969e-21 5 305.545454545455 92 6.08643447053114e-24 4 2.83621026081964 -2.9200554924167 -1 16.6864832156199 4 1296 48 9 1416 5 92 113 133 58 187 7 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 5.60239397472224e-18 2.18539665790818e-16 105 617.818181818182 101 5.60239397472224e-19 3 2.28862133025407 -2.28750674757035 -1 10.3487053431372 101 1006 4294 7 562 3 257 101 386 68 11 8 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 2.88212993036394e-26 2.23010709365865e-24 100 350.909090909091 105 2.62011811851266e-27 35 3.16130415973891 3.270328271575 1 21.5900817858837 96 1397 38 661 90 35 300 456 614 105 68 9 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 4.04950964101753e-09 4.68472683960851e-08 35 214.818181818182 119 3.68137240770127e-10 33 3.67135980413051 3.87196603682436 1 7.76936770455992 119 589 328 254 157 33 45 43 64 698 33 10 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 1.44611423986507e-17 5.4605273697305e-16 15 278.272727272727 120 1.31464930896824e-18 11 2.6930387274294 2.85080822822147 1 11.8682791228002 170 1219 87 49 285 11 535 31 539 120 15 11 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 7.7508687629027e-08 3.25786793959256e-07 125 569.909090909091 124 7.04624457815933e-09 23 2.18126531256783 -2.47063171718514 -1 4.08515677001975 367 650 1468 123 807 124 31 23 32 2537 107 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 5.51714734761153e-16 1.6481604734637e-14 55 300.181818181818 128 5.01558849782867e-17 22 2.42011164935198 -2.42950822977744 -1 9.63127487837539 107 1125 115 22 480 54 400 159 659 128 53 13 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 5.76998844509506e-21 2.99278521547788e-19 65 548.454545454545 130 5.2454440409955e-22 47 2.64150237064449 2.73482791663428 1 14.1286599175913 63 1120 62 69 2198 47 130 247 1482 100 515 14 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 1.49672797721666e-41 2.94356502185943e-39 15 692.363636363636 137 1.49672797721666e-42 14 2.8103857615847 3.04289878646013 1 31.2686491281449 132 998 4276 21 261 14 529 137 1197 14 37 15 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 2.95761919478438e-08 2.65398528505367e-07 55 329.090909090909 138 2.688744758678e-09 20 2.46332885467662 2.6009833600688 1 4.67685996633608 87 150 469 749 41 20 52 53 1586 275 138 16 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 2.4132016746313e-83 3.79677063475325e-80 10 270.363636363636 149 2.19381970421028e-84 1 3.23315388810819 3.48524793708441 1 74.1477295663095 179 1040 1 8 224 8 325 149 921 7 112 17 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 6.63984704377868e-08 3.14536172538656e-07 155 294.545454545455 152 6.03622476743337e-09 22 2.78600644167873 3.0820264322819 1 5.23025676136355 155 127 410 142 649 22 137 152 702 677 67 18 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 7.42588252477397e-21 3.80980059966664e-19 225 370.727272727273 163 6.75080229524903e-22 63 3.45291703346861 3.58635428596838 1 18.3644348644191 222 163 63 1130 117 107 632 97 1196 145 206 19 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 1.49546825192641e-15 4.10384310993759e-14 180 363.636363636364 177 1.35951659266037e-16 9 2.53560836808918 2.87635308303926 1 9.80086770861621 177 1198 126 497 347 9 315 71 1078 137 45 20 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 1.30631730669588e-18 5.40861200667066e-17 150 317.727272727273 181 1.18756118790534e-19 56 2.90613566865238 3.23093609102446 1 13.6501397518856 150 1294 78 292 100 56 288 191 793 181 72 21 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 1.33355767727337e-24 9.39461527870192e-23 65 471.363636363636 186 1.2123251611576e-25 23 2.47438468437618 2.55128421886014 1 15.7378220029748 61 1116 52 251 1841 23 162 186 1051 36 406 22 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 1.72036823050406e-23 1.12779695110822e-21 195 536.727272727273 192 1.56397111864006e-24 45 3.29987956081023 3.3693019675337 1 19.9600014008922 192 1312 45 918 1487 93 383 75 1223 119 57 23 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 4.08260104416215e-08 2.9351990282604e-07 420 334.636363636364 196 3.71145556356737e-09 19 2.72231401813219 3.09410301686436 1 5.1342744824622 416 524 851 147 196 179 274 99 185 791 19 24 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 3.40050413390341e-17 1.22521981007818e-15 405 367 199 3.09136739445764e-18 29 2.44898247460991 2.76366384694927 1 10.5444348119509 403 1110 92 77 134 29 543 199 1009 191 250 25 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 1.04101425176033e-21 5.78069090389264e-20 170 393.363636363636 212 9.46376592509384e-23 43 2.89890465493996 3.08600400988013 1 16.1032865605215 167 1291 56 43 951 212 533 172 541 92 269 26 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 1.97533450793476e-12 3.83686373557697e-11 165 430.909090909091 212 1.79575864357867e-13 149 3.00639628185955 3.36927939295181 1 9.04170333125468 165 149 191 161 1661 178 361 243 1084 335 212 27 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 1.97036663496017e-21 1.08141052523395e-19 60 438.545454545455 216 1.79124239541834e-22 29 2.73804857358859 -2.98162254243226 -1 14.9946248524217 430 1152 57 29 107 216 872 60 1520 126 255 28 M11266 KEGG_LYSOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSOSOME.html Lysosome 120/155 KEGG 2.72697641868869e-08 2.51885101687096e-07 220 1040.81818181818 219 2.47906950226409e-09 13 1.48049386549106 -1.59697981975408 -1 2.82021512558133 219 43 3438 2758 26 13 135 694 805 3207 111 29 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 3.77929999312303e-24 2.54832799536296e-22 55 695.727272727273 225 3.77929999312303e-25 33 2.49176197949883 2.65038569798714 1 15.5365247638386 51 999 4295 33 444 53 227 41 1247 38 225 30 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 3.26488937573322e-13 6.97297640428091e-12 135 560 228 2.96808125066701e-14 74 2.24038560907869 2.3013872709039 1 7.21681445317731 133 1173 210 90 926 74 228 481 2009 114 722 31 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 8.96100652357747e-16 2.53269166414884e-14 390 512.181818181818 228 8.14636956688857e-17 69 2.41864375254024 2.71247814476751 1 9.49511981233238 388 1139 123 95 498 69 495 210 2302 87 228 32 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 3.48700145705764e-48 1.17561763409372e-45 295 353 236 3.17000132459788e-49 8 3.12353141360667 3.50600711849347 1 40.5241519143163 291 1085 8 236 359 26 856 25 832 46 119 33 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 3.99175405358079e-08 2.9351990282604e-07 240 1420.27272727273 238 3.62886738728046e-09 5 1.22442859411148 -1.18159448718751 -1 2.30879401846591 238 1842 3206 3855 180 30 5 128 3501 2600 38 34 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 2.40583294305577e-19 1.04179187992874e-17 160 459.636363636364 242 2.18712085732342e-20 23 3.47837871427072 3.84406373325443 1 17.056613681685 158 23 74 242 2170 297 699 399 204 228 562 35 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 6.75927410855155e-14 1.55628164840797e-12 245 356.454545454545 243 6.14479464413794e-15 6 2.41594083387974 2.62916019280354 1 8.23677919066836 243 1114 155 279 168 6 453 240 891 270 102 36 M7169 REACTOME_NCAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NCAM1_INTERACTIONS.html Genes involved in NCAM1 interactions 43/60 Reactome 3.18365146060189e-18 1.27346058424075e-16 15 578.272727272727 245 2.89422860054717e-19 14 3.97659283403056 4.08912063160287 1 18.2513502613628 14 382 82 676 3240 139 368 868 216 245 131 37 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 4.52538230843895e-36 6.28229543995054e-34 55 351.545454545455 246 4.11398391676268e-37 16 3.09352158309346 3.40484253274416 1 29.6583288210989 52 1190 16 471 298 163 371 138 868 54 246 38 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 9.64660181346129e-13 1.97965045911032e-11 190 461.181818181818 246 8.76963801224136e-14 165 3.22176419021204 3.38333317996062 1 9.95684726922546 189 205 179 756 1277 165 246 676 838 349 193 39 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 3.04397442884243e-13 6.56052936261931e-12 155 377 248 2.76724948076624e-14 25 3.07093924498695 3.09953555503651 1 9.91602565500686 151 25 169 348 1728 59 248 382 448 370 219 40 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 4.35979211667642e-08 2.97164560412799e-07 205 1415.09090909091 249 3.96344745734132e-09 12 1.55583746321175 -1.59095416349193 -1 2.93152696797428 201 2344 2828 3848 249 37 12 24 3163 2776 84 41 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 1.88752037469916e-12 3.68144469776035e-11 110 545 252 1.71592761336436e-13 106 3.07467551904946 3.24619074001554 1 9.26301614780692 106 252 190 346 2153 114 171 417 1708 194 344 42 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 7.71630571131957e-11 1.15256211890596e-09 1225 505.818181818182 252 7.01482337417294e-12 31 2.39437396733755 2.50029372239006 1 6.17919000788322 58 1222 252 294 1224 31 131 109 1737 216 290 43 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 5.13047846722883e-19 2.16213021118929e-17 370 419.181818181818 260 4.66407133384437e-20 45 3.68934159485809 -4.01774425418622 -1 17.753322255894 370 301 77 45 1182 162 360 90 1547 217 260 44 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 4.7614979579918e-13 9.98856460520946e-12 630 639.363636363636 262 4.32863450726621e-14 143 2.93057944907595 3.22975195997807 1 9.30827187090799 629 143 173 1763 208 240 1209 262 1897 180 329 45 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 1.32032773255682e-10 1.89420878348578e-09 245 262.727272727273 263 1.20029793876006e-11 28 3.87862385244703 4.47079712022288 1 9.76848881833122 284 544 263 375 244 149 242 29 387 345 28 46 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 1.82169517227438e-07 4.50178073986129e-07 70 430.818181818182 270 1.65608665738058e-08 67 2.78214772489178 2.92534342177787 1 5.09791342163736 67 440 653 304 1705 88 98 146 270 757 211 47 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 1.89888909784409e-10 2.65170311888287e-09 355 399.181818181818 271 1.72626281637089e-11 26 2.47657176059848 -2.58935107740804 -1 6.13256550311231 354 1355 271 51 144 42 799 94 897 358 26 48 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 1.0455217472883e-14 2.63896398246031e-13 145 446 271 9.50474315716644e-16 95 2.73114517640887 2.97086011133978 1 9.91931469800246 271 1371 141 342 95 257 572 323 1257 143 134 49 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 1.17932927496662e-14 2.92970219886445e-13 440 529.363636363636 273 1.07211752269693e-15 111 2.81194340853289 3.06807864275992 1 10.1759371248543 437 1309 143 733 269 111 791 162 1436 273 159 50 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 1.94385711562857e-10 2.6985310546373e-09 675 505.454545454545 276 1.76714283254575e-11 103 2.47338242913084 2.69727502846446 1 6.11923696395349 675 1289 273 276 103 230 979 258 792 208 477 51 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 4.74747308227707e-08 3.0118377618747e-07 280 401.636363636364 277 4.3158847133862e-09 1 3.47515331589441 4.01449786377808 1 6.54313169502247 277 526 666 818 309 170 79 26 143 1403 1 52 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 2.45049427113117e-16 7.65982315214511e-15 280 626.454545454545 277 2.2277220646647e-17 34 3.38373032873884 3.67830217680829 1 13.7916739905608 34 235 109 1132 2853 277 614 678 434 276 249 53 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 2.97004436485733e-20 1.4756430949607e-18 70 527.090909090909 278 2.70004033168849e-21 66 2.81754289502017 3.02952459540808 1 14.5065569313832 181 1336 66 278 1860 66 673 564 463 112 199 54 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 9.61593936495699e-07 1.44453322096108e-06 125 598.636363636364 283 8.74176687997523e-08 103 2.50966750616404 2.59297302342859 1 4.23159745602095 103 737 672 731 3028 121 214 141 123 432 283 55 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 7.81303278755461e-07 1.22516660323115e-06 110 624.272727272727 285 7.10275960205426e-08 106 2.52159499776055 2.7394343583583 1 4.30379877311188 211 473 1049 433 2883 268 108 154 106 897 285 56 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 3.30982509617802e-10 4.51513712542203e-09 140 335.545454545455 287 3.00893190606907e-11 1 2.64874103368565 -2.74873573735674 -1 6.38216162609926 138 1 278 480 757 215 299 107 464 287 665 57 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 7.86565095790127e-10 1.0199415527828e-08 185 629.363636363636 291 7.15059178246682e-11 25 2.4485899017963 2.49540980304242 1 5.64959740679037 182 1332 291 701 1662 25 158 246 1650 196 480 58 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 2.39525664555739e-12 4.59577697846784e-11 175 711.818181818182 292 2.17750604141817e-13 174 3.26897303302843 3.44711461577604 1 9.75748500056492 200 268 194 1573 1599 174 574 2099 682 292 175 59 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 6.12227767768947e-11 9.26190725599176e-10 295 421.363636363636 294 5.5657069798726e-12 124 3.33769987451362 3.75735446404344 1 8.7055090075161 153 294 248 780 1341 203 292 328 401 471 124 60 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 1.69853192407213e-08 1.73906088538405e-07 40 575.454545454545 295 1.54411994289619e-09 23 2.27642977696612 2.30481548118197 1 4.44262830264442 23 240 646 947 2926 38 36 156 664 295 359 61 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 9.25623927184501e-15 2.34889512704884e-13 40 655.181818181818 301 8.41476297440455e-16 38 3.48669909831229 3.69733733090654 1 12.7145836602547 38 1498 140 492 3360 94 182 558 301 392 152 62 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 2.80676066455647e-07 5.72758769420948e-07 305 663.818181818182 304 2.55160092967558e-08 42 2.65044545972449 2.84604668991198 1 4.77649948694174 304 651 1122 713 2137 234 143 42 94 1787 75 63 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 5.0354571188461e-17 1.77368340305624e-15 120 508.272727272727 306 4.57768828986007e-18 67 3.29354669375833 3.48989191006074 1 14.0283215544097 117 123 95 67 2243 407 929 660 306 171 473 64 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 5.8198176306355e-15 1.50106771675407e-13 95 466.090909090909 307 5.29074330057774e-16 50 3.14468717036353 3.54731826367635 1 11.6439067400148 92 1420 137 307 1774 78 339 116 480 334 50 65 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 1.57667241214963e-09 1.93799317326725e-08 255 540.727272727273 308 1.43333855752689e-10 148 3.31848335501594 3.68183833045708 1 7.38985582524159 148 213 308 364 1619 251 593 1057 273 871 251 66 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 1.53682418665805e-09 1.89890318351466e-08 310 633.272727272727 310 1.39711289793782e-10 151 2.8787980292424 -2.71722166040624 -1 6.41797282636795 310 151 306 253 1679 243 636 316 2082 754 236 67 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 1.88971985832915e-09 2.30477460757457e-08 85 633.818181818182 311 1.71792714541123e-10 32 3.65768500034625 3.93000201378593 1 8.06579697245768 81 1606 311 535 2985 101 190 130 357 644 32 68 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 2.94042605796783e-09 3.45244054567367e-08 315 438.090909090909 315 2.67311460172535e-10 10 4.83083313326864 5.32990819587484 1 10.4082433629119 315 587 323 351 2257 157 90 30 72 627 10 69 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 2.13964439811754e-09 2.59617520799866e-08 170 442.727272727273 316 1.94513127290771e-10 91 3.02905145400847 3.15742352671923 1 6.6341826912542 169 195 313 316 1505 91 113 354 798 516 500 70 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 4.80573146970896e-08 3.02364809600699e-07 320 454.454545454545 320 4.36884688607862e-09 78 2.56745620427732 2.91766125378183 1 4.83260495687746 268 1359 406 320 319 89 493 628 279 760 78 71 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 2.83926021553533e-13 6.14738909051685e-12 45 545.363636363636 322 2.58114565048699e-14 13 3.12256570533624 3.3998445087715 1 10.1082123228148 42 13 168 510 2886 122 320 677 485 454 322 72 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 4.81881151430946e-12 8.7144790603604e-11 375 391.363636363636 325 4.38073774029091e-13 156 3.46017920658229 3.58916967455619 1 10.0506089059667 375 405 206 325 950 231 156 185 349 214 909 73 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 2.52699244960843e-17 9.24604989314093e-16 325 460.545454545455 325 2.2972658632804e-18 91 2.39758735269585 2.60081393205598 1 10.4077715358399 325 1065 91 261 320 242 707 780 691 115 469 74 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 8.8341151537176e-07 1.35379946511517e-06 260 641.363636363636 328 8.03101700096785e-08 49 3.68626949557393 3.63689924420863 1 6.24588127403287 257 758 794 413 2965 195 51 72 328 1173 49 75 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 2.62039565404666e-11 4.23570804352748e-10 330 323.909090909091 328 2.38217786734352e-12 56 3.27078470950941 -3.10608625937077 -1 8.85187327748484 328 376 231 56 330 430 661 189 578 213 171 76 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 8.68785081322965e-14 1.99061436108951e-12 330 586.363636363636 330 7.89804619384545e-15 99 2.19085661735286 2.36519212481643 1 7.40168022054994 99 1097 338 528 1798 159 329 176 1487 109 330 77 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 6.03524399542591e-07 1.00162980514804e-06 335 1197.63636363636 331 6.03524563451419e-08 35 3.18086492972367 -3.18086492972367 -1 5.50960971676209 331 880 4220 1769 2915 317 50 35 234 2139 284 78 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 7.29592657611084e-15 1.87156377387191e-13 185 622.090909090909 332 6.63266052373715e-16 32 2.89084323586097 -2.942643133265 -1 10.6239485336863 1517 1400 138 32 365 696 1772 223 332 183 185 79 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 2.08914075070591e-13 4.629457438184e-12 470 591.363636363636 333 1.89921886427828e-14 139 2.37826194746298 2.75580337274697 1 7.78316581832807 470 1127 163 712 333 211 1027 139 1943 182 198 80 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 5.19337740542399e-09 5.90668466351837e-08 315 922.818181818182 333 4.7212521978942e-10 37 3.49413694241473 3.62636063548572 1 7.29272174107816 312 369 333 3016 2867 52 134 37 2238 690 103 81 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 8.97229480348118e-08 3.31497675696653e-07 175 442.636363636364 336 8.15663197218155e-09 80 2.84254290626527 3.22176116223336 1 5.31768898465265 171 238 417 336 1757 184 355 80 591 499 241 82 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 2.06045069351089e-16 6.61586889344994e-15 1125 645.636363636364 336 1.8731369941008e-17 106 3.15099240796568 -2.87568204754795 -1 12.900901480256 1121 1389 106 238 1121 589 1626 173 268 336 135 83 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 3.47482585900623e-69 3.28023561090188e-66 485 376.272727272727 337 3.15893259909661e-70 3 3.43966452552109 3.65060374480497 1 65.0413589440333 482 1101 3 6 473 65 890 272 497 13 337 84 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 6.07892669904336e-13 1.26958115130463e-11 265 751.545454545455 338 5.52629699913185e-14 174 2.6553953580597 2.90617928461038 1 8.35426960880439 263 1297 174 976 1330 292 663 235 2522 338 177 85 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 2.13535971291489e-07 4.90234925824382e-07 300 652.272727272727 339 1.94123629106981e-08 61 2.48248737650496 2.77035003537393 1 4.52219530286964 298 670 1092 339 1865 371 327 61 307 1677 168 86 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 4.27198175518061e-11 6.68225816248049e-10 10 1031.81818181818 340 3.88361977751233e-12 9 1.66330942537152 1.67331003790458 1 4.40596763966481 9 71 1688 2708 3416 62 13 340 1980 237 826 87 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 4.17904215871869e-14 9.8625394945761e-13 115 461.454545454545 345 3.79912923519887e-15 113 2.91201830092354 3.0313650675169 1 10.0948351855711 113 140 151 1129 1134 158 345 493 724 192 497 88 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 5.74829339151911e-09 6.4754044887757e-08 350 661 347 5.22572127867145e-10 9 2.67529221215732 2.80167468973607 1 5.55264186539469 346 9 336 1174 710 17 347 1562 1936 705 129 89 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 1.63319178741262e-12 3.23893497335611e-11 290 791.090909090909 352 1.48471980673984e-13 41 2.44072500767461 2.53418004330978 1 7.39214583992345 286 1217 186 1574 1797 41 295 352 2199 167 588 90 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 7.45064787005775e-12 1.32705879044047e-10 185 549.909090909091 352 6.77331624552996e-13 103 2.8611708734006 3.20669398229786 1 8.15964525798933 184 1410 209 110 415 103 475 1254 1299 352 238 91 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 5.23142754753104e-08 3.05598242875576e-07 350 404.727272727273 352 4.75584333811844e-09 58 3.15846332086148 3.04592390725411 1 5.94101547298977 350 570 520 694 393 208 229 231 352 847 58 92 M5485 REACTOME_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MUSCLE_CONTRACTION.html Genes involved in Muscle contraction 51/77 Reactome 4.1599187278918e-08 2.95100601223086e-07 355 375.181818181818 353 3.78174436959141e-09 21 2.9679103584086 3.44634149891196 1 5.5955469574504 353 353 512 378 210 466 875 54 160 745 21 93 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 4.20768441998171e-08 2.95100601223086e-07 755 604.363636363636 359 3.82516772768838e-09 41 2.44074782799872 2.56284898461339 1 4.60150859555097 751 41 501 310 218 302 762 1134 1924 359 346 94 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 1.0669976523744e-08 1.13428579261422e-07 65 621.818181818182 359 9.69997870499384e-10 23 3.63032052645969 3.80732044240872 1 7.27992046815912 65 1608 359 531 2672 105 155 129 412 781 23 95 M695 REACTOME_GLYCOSAMINOGLYCAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSAMINOGLYCAN_METABOLISM.html Genes involved in Glycosaminoglycan metabolism 99/122 Reactome 1.08972239353597e-08 1.15584038145837e-07 175 355.363636363636 360 9.90656726303336e-10 83 2.71389800733287 2.93996120749197 1 5.43558434007524 172 83 360 266 676 199 577 281 444 430 421 96 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 4.52062594525478e-08 2.99073619127066e-07 360 473.181818181818 360 4.10966003467815e-09 148 2.43221556406621 2.16889840601382 1 4.58134064250004 360 504 775 1151 271 148 154 703 304 614 221 97 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 6.93274262617624e-08 3.15197676064735e-07 555 670.181818181818 366 6.30249349513099e-09 44 3.14658609961996 3.40178861712385 1 5.90646663870716 552 1821 1183 172 699 366 87 44 73 2328 47 98 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 2.32578384945871e-09 2.81479481267824e-08 20 712.363636363636 367 2.11434895628861e-10 16 2.21655225078831 2.22742388096096 1 4.83195388436754 16 356 530 1572 3280 70 39 367 600 281 725 99 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 1.41589513350174e-63 9.54717861446891e-61 5 762.272727272727 369 1.41589513350177e-64 4 2.97669007106207 3.19740447000204 1 51.5901397337328 369 975 4451 4 83 10 646 610 1060 4 173 100 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 1.61700748070341e-09 1.98240917114807e-08 350 383.454545454545 370 1.47000680171992e-10 48 2.95727099322639 3.46260347548474 1 6.57698258989234 348 48 309 748 832 142 458 513 370 373 77 101 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 5.4490870407438e-07 9.26125268814525e-07 95 624.727272727273 373 4.95371671855055e-08 85 2.35252121070519 2.57097123482508 1 4.09772501292781 95 392 1102 1171 2633 85 112 170 196 543 373 102 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 5.08801298107624e-08 3.0357704374324e-07 220 514.909090909091 373 4.62546645340764e-09 36 2.43018456080328 2.59744112911802 1 4.57295937258505 218 465 652 2052 373 36 225 311 779 468 85 103 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 5.3925696974126e-10 7.2104614650956e-09 285 502.909090909091 377 4.90233608975856e-11 49 2.83947428168424 3.14133916397057 1 6.67510978674698 285 49 283 377 1938 161 348 504 624 456 507 104 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 9.27698776940004e-10 1.18664992605876e-08 225 589.272727272727 378 8.43362524846544e-11 45 3.10075728156449 3.40061447343467 1 7.09569417181458 221 189 295 414 1415 45 378 864 1958 649 54 105 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 5.55666987631176e-17 1.942776430829e-15 235 672.909090909091 379 5.05151806937431e-18 76 3.20186758969793 3.31423638192101 1 13.6012411778345 232 85 96 76 1994 379 504 1677 1410 316 633 106 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 7.94893022999506e-32 8.72533736873876e-30 205 520.454545454545 380 7.22630020908644e-33 22 2.95114667711641 3.22313908511625 1 24.7629881576547 204 1211 22 44 1150 153 770 632 1095 64 380 107 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 4.05234811628329e-08 2.9351990282604e-07 385 1751.09090909091 383 3.68395290084236e-09 58 0.862858303658212 -0.825849574679723 -1 1.62675934768654 383 2324 3838 3934 191 123 58 98 4327 3830 156 108 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 8.90362888043168e-10 1.14198718249015e-08 260 551.272727272727 383 8.09420807639555e-11 193 3.12266072858781 3.38283646578973 1 7.16084733393763 1083 260 294 260 193 778 1150 561 277 383 825 109 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 4.03150673773531e-26 3.06914706485656e-24 40 537.363636363636 383 3.6650061252139e-27 39 2.48491637755181 2.8143772112712 1 16.87099763297 223 1073 39 664 600 194 750 123 1822 40 383 110 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 2.75306397393723e-07 5.67443753580075e-07 335 952.363636363636 388 2.50278574404882e-08 121 1.93673985842697 2.06862020230783 1 3.49232762558387 335 121 1433 2288 2113 176 385 388 2104 777 356 111 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 3.1284494180099e-09 3.65502011213038e-08 175 681.181818181818 389 2.84404492950784e-10 173 3.10211570695349 3.16221221136225 1 6.66115437730138 173 220 325 766 2329 173 343 842 1162 771 389 112 M17844 KEGG_OTHER_GLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OTHER_GLYCAN_DEGRADATION.html Other glycan degradation 16/17 KEGG 1.83674573805874e-08 1.86439567390048e-07 540 849.818181818182 392 1.66976886672131e-09 1 1.44307965454109 -1.52654223900996 -1 2.80337160061661 540 775 2779 1840 1 132 22 66 392 2759 42 113 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 6.97727971721679e-10 9.14798896257313e-09 170 593.909090909091 392 6.34298156311783e-11 111 2.35861087562371 2.51459716266216 1 5.47413931382528 687 1131 288 111 169 168 987 607 1637 356 392 114 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 3.64248205215268e-08 2.8614986551519e-07 590 399 395 3.3113473749639e-09 121 2.46932328828935 2.70891732455088 1 4.66492978386693 395 186 589 160 121 509 882 201 587 515 244 115 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 5.50088915999952e-15 1.42660422171416e-13 90 764.272727272727 396 5.00080832727228e-16 89 3.22927649064085 3.42086080881587 1 11.9777460028311 89 1483 136 782 2379 282 396 450 1966 220 224 116 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 1.15828963460724e-07 3.60088818242439e-07 195 761.909090909091 396 1.05299063235513e-08 172 3.49333977000378 3.79190769238979 1 6.49912125046467 191 476 425 396 3140 339 270 1833 286 853 172 117 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 8.95164070493561e-12 1.57655761669015e-10 85 698.818181818182 398 8.13785518633821e-13 82 2.95857273053209 3.27977089981037 1 8.37352987458332 82 2055 212 739 1837 217 398 261 1052 712 122 118 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 4.53137575571305e-15 1.18166262800915e-13 460 521 398 4.11943250519369e-16 33 2.89550363552688 3.11729907917307 1 10.8080591153569 456 33 135 312 1426 398 551 956 937 149 378 119 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 6.48731013110075e-13 1.34890325192932e-11 400 621.363636363636 399 5.89755466463878e-14 175 3.47798146378447 3.62878449534344 1 10.9160809783255 399 254 175 309 2022 343 387 1631 400 501 414 120 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 3.12979917769859e-42 6.71484187215335e-40 300 935.181818181818 399 3.12979917769857e-43 11 2.52301559735291 2.64851278752671 1 28.5388655066381 299 979 4553 239 975 24 437 363 2008 11 399 121 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 5.29003680819993e-08 3.06874196014832e-07 605 482.818181818182 400 4.80912448672925e-09 200 2.64992727114485 2.86189344941855 1 4.9829445321123 602 307 635 319 400 465 965 200 213 908 297 122 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 1.30039209948069e-08 1.35493393146774e-07 405 813.272727272727 403 1.18217464287923e-09 36 3.20361089418485 -3.03810679153907 -1 6.35272107809828 874 402 367 63 2529 991 1731 36 1362 403 188 123 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 5.83072836532352e-08 3.09921597796476e-07 385 983.636363636364 403 5.30066229077922e-09 64 4.28468237641396 4.28468237641396 1 8.0521728440759 64 1745 403 834 3947 385 382 1311 393 996 360 124 M835 KEGG_DILATED_CARDIOMYOPATHY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DILATED_CARDIOMYOPATHY.html Dilated cardiomyopathy 80/122 KEGG 1.31009857186177e-07 3.80936578171426e-07 315 496.909090909091 406 1.19099877261642e-08 125 2.75492260527505 3.12855701243792 1 5.10571922374695 314 183 461 362 1378 594 640 125 406 716 287 125 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 4.93137412326395e-08 3.0357704374324e-07 650 431.545454545455 408 4.48306748527489e-09 11 4.11762234169566 3.56376493178844 1 7.74886542152815 648 729 568 255 341 408 107 96 11 830 754 126 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 2.78701967119505e-07 5.7040140234568e-07 410 584.272727272727 408 2.53365456751121e-08 40 2.85447256624243 3.18825199519049 1 5.14572957999235 408 419 679 116 2128 133 101 40 1317 945 141 127 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 1.00703582958842e-09 1.27431879776336e-08 410 649.909090909091 409 9.15487118226712e-11 93 2.90992440720922 -2.80951328140801 -1 6.63293272994512 792 409 298 93 1398 426 409 2666 217 244 197 128 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 1.93233541411165e-32 2.28015578865175e-30 215 456.272727272727 410 1.75666855828333e-33 20 2.70146606870825 2.9547211403467 1 23.1225008047518 214 1095 20 659 326 187 784 410 853 37 434 129 M994 REACTOME_DSCAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DSCAM_INTERACTIONS.html Genes involved in DSCAM interactions 15/19 Reactome 4.40409577994282e-08 2.97677410474742e-07 865 702.818181818182 412 4.00372351646066e-09 42 2.13256631598341 -2.39706018275969 -1 4.01806427638047 864 795 1977 412 256 703 192 122 42 2199 169 130 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 3.9709790736792e-07 7.23389472318249e-07 645 673 417 3.6099816276703e-08 34 3.99624424056319 3.97373447267524 1 7.08525438644972 644 801 898 107 2429 417 259 174 34 1431 209 131 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 7.77989364161424e-08 3.26053563650771e-07 350 557 417 7.07263083339619e-09 185 2.17375381289795 2.0442590283599 1 4.07086284842678 349 285 1125 376 812 468 185 293 650 1167 417 132 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 4.79555490697255e-11 7.34903219510079e-10 85 763.363636363636 421 4.35959537007008e-12 83 2.24135404629787 2.38214734324632 1 5.91072408444661 83 86 421 1317 2963 97 308 711 1344 155 912 133 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 1.20471373040038e-27 1.01540157276604e-25 545 493 423 1.09519430036398e-28 33 2.87018646048431 2.91498577960096 1 20.7138189588078 543 1142 33 477 237 192 971 423 962 73 370 134 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 3.8160605111391e-14 9.09687152150331e-13 425 596.181818181818 423 3.46914591921741e-15 131 2.62835708559999 2.88971687443724 1 9.13804567867686 423 1384 149 700 131 382 1007 608 1145 226 403 135 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 2.81477092402909e-07 5.73154390052516e-07 425 1017.54545454545 424 2.55888298560235e-08 94 2.29736348349548 -2.630660730175 -1 4.13987923098698 424 2287 1763 734 2142 177 239 181 128 3024 94 136 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 3.57994574887676e-07 6.73469268023049e-07 105 579.909090909091 429 3.25449666492988e-08 76 2.18985560218197 2.34352944537959 1 3.90181447599152 102 501 947 755 2345 96 76 297 227 604 429 137 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 2.62154081705945e-14 6.28105210990893e-13 640 610.545454545455 431 2.38321892459952e-15 29 3.28336805625383 3.62879827336151 1 11.5680602515547 638 29 148 264 1586 871 1494 142 824 289 431 138 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 1.30521298008653e-07 3.80049677113412e-07 735 722.727272727273 434 1.18655732502003e-08 27 2.34952744726108 -2.35902205767585 -1 4.35495732763266 734 380 1624 153 1376 434 629 134 221 2238 27 139 M631 REACTOME_COLLAGEN_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COLLAGEN_FORMATION.html Genes involved in Collagen formation 57/64 Reactome 1.93840296154592e-15 5.19844430596406e-14 20 884.181818181818 435 1.76218451049629e-16 19 3.83507331494837 3.85390555785243 1 14.7104070257546 19 1581 130 1128 3770 362 705 793 405 435 398 140 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 3.78607346383661e-28 3.24913940896524e-26 35 572.272727272727 439 3.44188496712418e-29 32 2.78502178254887 3.09651708595245 1 20.4971506613779 568 1145 32 35 896 141 868 187 1909 75 439 141 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 2.50668222811392e-09 2.9953266118222e-08 685 539.909090909091 439 2.27880202815458e-10 45 2.59865931760679 -2.75427047292005 -1 5.64481447822245 684 1284 317 61 45 421 733 439 1007 414 534 142 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 2.90512236569058e-17 1.05478288969689e-15 455 851.545454545455 440 2.90512236569058e-18 40 2.62880971662763 2.86630727286972 1 11.3681498446356 454 1043 4443 40 440 43 757 335 1606 74 132 143 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 8.17750358515495e-13 1.69288670710225e-11 65 815.090909090909 440 7.43409416832545e-14 62 3.13922165711371 3.41637794782399 1 9.76333385033135 62 2092 177 763 2728 270 440 381 1347 557 149 144 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 2.00076506288072e-07 4.74685412934128e-07 125 702.363636363636 440 1.81887749530732e-08 101 3.41520933301108 3.75473788362258 1 6.23540646784992 125 403 440 794 3213 210 473 425 519 1023 101 145 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 2.09224752511418e-08 2.06598500387844e-07 205 671.727272727273 441 1.90204322273809e-09 137 2.46451121034696 2.61475657909297 1 4.75651370827647 202 1265 386 516 1236 137 277 441 1680 246 1003 146 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 2.40308040221381e-07 5.25604239965208e-07 340 943.636363636364 442 2.18461878609505e-08 200 3.51377657653885 4.13805371467453 1 6.37049159533199 1074 337 442 381 2193 1818 2665 203 200 729 338 147 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 2.48282673728223e-07 5.33113588540658e-07 190 784.818181818182 443 2.25711547043962e-08 160 2.68317696256858 2.88399246486558 1 4.85963393226897 188 1454 443 1003 2786 160 318 338 1185 579 179 148 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 1.69240904449144e-25 1.24815167031244e-23 1230 706.454545454545 448 1.5385536768104e-26 40 2.96754724113656 3.37855549554364 1 19.625841538066 1228 1208 40 256 325 581 1565 346 1698 76 448 149 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 2.25960060846545e-16 7.20629383240333e-15 835 534.818181818182 456 2.05418237133223e-17 12 3.76884216466699 4.28150736664981 1 15.3902886143216 833 131 107 271 1557 456 1009 104 940 463 12 150 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 4.32574419434218e-09 4.97988112129149e-08 435 597 457 3.93249472986151e-10 94 2.75506101664239 3.01936568586676 1 5.80896220255257 431 94 330 133 1405 446 1177 840 693 457 561 151 M8728 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM.html Hypertrophic cardiomyopathy (HCM) 79/137 KEGG 2.16456345714557e-07 4.93714606651884e-07 420 612.090909090909 462 1.96778515465033e-08 210 2.68745450233847 3.16379793284835 1 4.89325869955818 419 210 549 393 1878 634 867 217 462 686 418 152 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 5.96306768237363e-16 1.77016851954739e-14 165 660.272727272727 463 5.42097062033964e-17 116 3.07223444621074 3.57662976557579 1 12.1992332474469 162 1402 116 496 2549 138 480 463 869 408 180 153 M706 REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS.html Genes involved in Glycerophospholipid biosynthesis 69/85 Reactome 2.52234933452359e-07 5.3772241226543e-07 290 1143.54545454545 468 2.29304511246968e-08 228 1.83274871283095 -1.83455211948634 -1 3.31712997927624 468 287 2319 3257 2033 228 294 286 1165 1980 262 154 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 1.39119391878001e-08 1.43685673887126e-07 45 964.545454545455 468 1.26472175234307e-09 5 1.95505212667131 1.97939838662872 1 3.86211530131732 45 5 807 2064 3473 81 213 468 2147 241 1066 155 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 5.63012338500393e-08 3.08643233184884e-07 230 790.090909090909 470 5.11829411735189e-09 60 2.06365099533063 2.18440752016015 1 3.87882773179567 227 1220 1016 1591 470 64 302 387 2235 1119 60 156 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 7.11820158513885e-08 3.17725226229176e-07 155 520.636363636364 471 6.47109255950141e-09 90 2.75105440539458 2.93104775657992 1 5.16114903517375 152 116 427 715 729 90 165 539 1831 492 471 157 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 4.76650310109512e-07 8.32638587608029e-07 250 812.090909090909 472 4.33318557618394e-08 55 2.52174642175087 2.5388149227756 1 4.4262028948736 250 99 472 1583 2703 55 194 264 2220 493 600 158 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 2.70903531801952e-48 9.8358820777324e-46 20 818.636363636364 473 2.70903531801949e-49 8 2.87748635564281 3.14094300147363 1 37.396295079496 473 976 4452 16 240 18 739 506 1340 8 237 159 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 2.76583310100206e-07 5.68167826037923e-07 415 832 474 2.51439404429254e-08 92 2.73270336817887 3.1835200378404 1 4.92752529974206 413 474 1058 1154 2120 274 624 317 285 2341 92 160 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 2.54844659387351e-44 7.07568701357821e-42 475 759.545454545455 475 2.31676963079412e-45 10 2.84888584289616 3.05569810543202 1 33.8516404450556 53 1067 10 472 2133 475 665 360 2399 30 691 161 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 1.39508747073867e-25 1.04520839077564e-23 255 962.181818181818 475 1.39508747073868e-26 33 2.63643036044747 2.89949869249815 1 17.4945772414929 255 1046 4362 475 1192 244 740 284 1517 33 436 162 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 5.17909178103108e-07 8.91513975436421e-07 360 958.636363636364 476 4.70826636387125e-08 198 3.04123275918221 3.30016648594439 1 5.31213206768994 356 1595 476 365 3107 198 326 1636 1083 1104 299 163 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 8.01371856812217e-33 9.69865426706068e-31 270 535.545454545455 478 7.28519869829293e-34 19 2.83434883336495 3.11936989091359 1 24.5637741241425 269 1129 19 478 568 424 702 287 1228 43 744 164 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 3.27234921255301e-22 1.93068603540628e-20 55 578.454545454545 479 2.97486292050273e-23 52 2.75600054938337 2.86626704168287 1 15.6884487042164 308 1233 53 479 921 338 628 467 1014 52 870 165 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 9.42504143147286e-08 3.3764305071295e-07 190 787.636363636364 480 8.56821985022912e-09 151 3.15780319512517 3.77974368580941 1 5.9002836901586 186 480 420 788 3320 440 528 1257 299 795 151 166 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 5.7976729874036e-38 9.43621258639483e-36 425 932.818181818182 481 5.79767298740356e-39 19 2.57982458732572 2.88871573465602 1 26.0915532654517 422 987 4662 469 534 253 1212 299 923 19 481 167 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 3.24248206427171e-07 6.29297505894838e-07 485 1247.63636363636 483 2.94771140196982e-08 145 2.24826943554841 2.26073856795918 1 4.02504451396305 483 430 1408 3567 2267 145 435 283 3205 1195 306 168 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 6.85174932574518e-16 1.9719668791169e-14 80 811.272727272727 483 6.22886302340468e-17 80 3.40041644182087 3.73211127670954 1 13.456433563587 80 181 120 483 3694 726 859 1172 338 239 1032 169 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 2.73770059474249e-07 5.66073041584045e-07 635 885.545454545455 484 2.48881903220416e-08 95 2.69340876896238 3.30961938775456 1 4.85790577646523 634 484 1339 1588 2104 345 408 151 95 2245 348 170 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 2.16817112578274e-11 3.56577272254165e-10 695 704.454545454545 484 1.97106465982192e-12 48 2.58003796246021 -2.34270071463109 -1 7.03799917845158 691 1306 226 484 611 175 1216 267 2437 288 48 171 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 7.85954818807437e-08 3.26618753937265e-07 485 624.545454545455 484 7.14504406259861e-09 34 2.00848199006072 -1.91010346103998 -1 3.76085094641545 484 1253 1273 91 821 34 469 852 341 1155 97 172 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 4.11854786637982e-11 6.47984864310425e-10 95 712.636363636364 486 3.74413442405175e-12 72 2.06243510189943 2.0727162789412 1 5.4713805671131 94 1231 470 486 2332 72 362 671 998 154 969 173 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 3.16211947158384e-08 2.69553239732593e-07 35 795.363636363636 487 2.8746541063944e-09 31 2.07798303592441 1.95210466911851 1 3.94106224328892 31 239 977 1331 3664 82 133 529 487 447 829 174 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 4.10042915504269e-07 7.39546157616882e-07 490 660.636363636364 488 3.72766356299434e-08 57 1.97666700672797 2.06711371065085 1 3.49867680212384 57 147 1108 1161 2458 95 96 488 488 513 656 175 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 2.34676977886633e-07 5.19303954817115e-07 330 852.818181818182 490 2.13342729927225e-08 202 2.09616738178812 2.04618833192462 1 3.80318280055371 327 490 1505 1395 1953 271 202 402 215 1933 688 176 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 4.16729278017017e-96 9.83481096120161e-93 5 902.181818181818 490 4.16729278017017e-97 2 2.81599905862896 3.04927088376253 1 74.8157305383844 679 960 4613 2 449 32 1290 310 1097 2 490 177 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 2.05680500116388e-08 2.04371751765397e-07 140 773.090909090909 491 1.86982274581198e-09 140 3.399575639939 3.79083013995737 1 6.566137596076 140 491 382 812 3548 209 363 898 545 962 154 178 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 1.41195556613166e-07 3.97401924397223e-07 40 640.545454545455 492 1.28359605159154e-08 3 2.56717533052444 2.56717533052444 1 4.74408381778823 40 637 785 1374 2641 49 3 91 492 675 259 179 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 2.46835501621877e-16 7.6648918924688e-15 390 878.545454545455 493 2.24395910565342e-17 44 3.67961629620014 3.73288341739891 1 14.9974393282552 44 1529 110 1131 3657 390 779 776 493 386 369 180 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 4.68411688872633e-08 2.99073619127066e-07 575 805.818181818182 494 4.25828817132539e-09 238 2.48327194058308 2.46784906504877 1 4.67752892134432 572 253 560 1349 300 238 494 1801 2466 474 357 181 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 1.13295988093371e-15 3.1642429810693e-14 975 716.727272727273 495 1.02996352812155e-16 47 2.5361738771743 3.10904661840265 1 9.88575211705913 973 1992 122 495 47 332 1266 826 1423 179 229 182 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 7.4625188971417e-34 9.51975383635373e-32 100 582.727272727273 496 6.78410808831065e-35 17 2.85857135370435 3.07698146971991 1 25.6058326766177 100 1103 17 662 1901 295 496 368 887 49 532 183 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 1.08664426731285e-07 3.51706922314159e-07 725 658.454545454545 497 9.87858473623078e-09 174 2.70976708485642 2.98313325378395 1 5.04914812679038 724 319 817 174 1194 399 497 238 1428 1117 336 184 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 3.16845062694104e-08 2.69553239732593e-07 315 750.636363636364 497 2.88040970233929e-09 71 2.49194009676764 2.65470395027982 1 4.72633674545588 632 497 1175 1226 71 365 314 315 2386 1049 227 185 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 2.42621164559067e-10 3.33869357643964e-09 710 653.090909090909 498 2.20564695078022e-11 88 3.11037194486943 3.20051437860542 1 7.61235921357248 710 88 275 269 1889 774 1402 289 188 498 802 186 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 1.17129677659572e-06 1.70949931525411e-06 325 1098.54545454545 499 1.06481581836683e-07 299 3.03354390032746 3.62509149313522 1 5.05102473391691 324 425 499 1658 3130 299 305 2081 2067 944 352 187 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 8.30839037850198e-09 9.11990757826263e-08 305 683.545454545455 500 7.55308219079903e-10 183 3.14369339041581 3.40540575089768 1 6.38996288772049 301 1566 346 809 1042 183 251 1266 974 500 281 188 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 2.45453743782731e-12 4.69045210791292e-11 505 811.272727272727 502 2.23139767075458e-13 163 3.13772475863467 3.3922202666879 1 9.35766648451847 163 266 195 983 2490 394 502 1577 1596 255 503 189 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 6.24987417746818e-08 3.14536172538656e-07 195 581.818181818182 503 5.68170395910716e-09 9 2.20980079145551 -2.30583251376279 -1 4.14834978772307 1039 191 1235 503 578 481 1068 166 195 935 9 190 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 8.45007890609472e-13 1.74167565226057e-11 485 602.818181818182 506 7.6818899146345e-14 4 2.76684325415484 3.14961567729595 1 8.59523405202935 485 4 178 506 357 716 1134 724 1573 323 631 191 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 4.23638935018956e-08 2.95358312155018e-07 515 502.181818181818 507 3.85126311978799e-09 56 2.43786748384139 -2.49747553798826 -1 4.59581042860841 514 196 905 518 223 353 507 56 1333 831 88 192 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 8.55051930149711e-10 1.09968531615985e-08 40 718.363636363636 507 7.77319936801853e-11 19 2.98427257754068 3.14068013193558 1 6.85758566847383 36 1516 293 1008 3151 19 94 507 669 569 40 193 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 3.53412494697696e-11 5.61652180125631e-10 400 842.636363636364 507 3.21284086093975e-12 151 2.17012743270714 2.26917004368427 1 5.79603340143826 398 1243 430 507 2610 367 464 695 1025 151 1379 194 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 2.70136017671642e-07 5.60951167360383e-07 195 706.636363636364 508 2.45578228037642e-08 68 2.90286924028123 2.99924867082581 1 5.23907030069857 193 687 753 1622 2094 190 68 378 508 812 468 195 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 8.12464644218396e-68 6.39138853451805e-65 5 850.818181818182 512 8.12464644218394e-69 3 2.96797372493795 3.25305294172087 1 55.0166154861577 512 971 4453 5 336 16 1040 746 997 3 280 196 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 4.31386832490926e-08 2.97164560412799e-07 670 891.363636363636 513 3.92169855408882e-09 105 1.99293140595366 2.13846223533291 1 3.75534641606127 669 717 2001 2734 241 487 240 105 398 1700 513 197 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 5.31499864459608e-08 3.06874196014832e-07 520 635.363636363636 517 4.83181706636507e-09 74 2.23395837318042 2.47534734781072 1 4.2006180689397 517 1258 643 584 408 146 1060 190 1732 377 74 198 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 5.11700440493577e-08 3.0357704374324e-07 1075 649.272727272727 519 4.6518222945025e-09 95 2.63718777618256 3.32106608746795 1 4.96255759737177 1073 95 492 102 378 519 1327 952 1186 723 295 199 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 2.15341004925394e-07 4.92098932637662e-07 350 676.363636363636 520 1.95764569094058e-08 153 3.84485178335284 4.01614153992541 1 7.00257394446103 347 784 797 311 1874 489 264 520 153 1272 629 200 M96 BIOCARTA_FREE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FREE_PATHWAY.html Free Radical Induced Apoptosis 13/19 BioCarta 2.16526067289e-05 2.45614765105523e-05 510 1569 522 1.96843816716605e-06 35 2.08924134354035 -2.08924134354035 -1 2.7801900012297 506 3184 2473 1923 4491 375 35 313 293 3144 522 201 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 2.8709866333992e-07 5.80593697928201e-07 525 668.727272727273 523 2.60998818914662e-08 282 4.0621766717535 4.21987343870938 1 7.31418780424126 601 830 526 523 2159 522 282 470 486 664 293 202 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 1.18925018763085e-19 5.34996041685392e-18 525 594 524 1.08113653420986e-20 71 2.63523807580202 3.04012828050905 1 13.1422174859385 524 1168 71 485 809 470 1267 280 794 127 539 203 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 3.13304250169633e-08 2.69553239732593e-07 2980 1334.36363636364 525 2.84822049664938e-09 63 2.66075627914004 -2.67380052917291 -1 5.04658021056352 2976 320 449 71 63 3012 3079 525 1082 291 2810 204 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 1.93026083775009e-07 4.65075607666177e-07 125 711 527 1.75478273373592e-08 121 2.56411706107945 2.83068516084598 1 4.68786486556265 121 2078 550 804 1755 152 450 527 432 785 167 205 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 1.48956637823703e-11 2.51098332331385e-10 1020 613.272727272727 527 1.35415125295193e-12 67 2.75275298683752 3.28676293572511 1 7.63027094873833 1020 67 221 273 914 527 974 501 1063 227 959 206 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 3.61808154065269e-07 6.79560082446506e-07 760 826.909090909091 531 3.28916557788745e-08 50 3.78756613578201 3.71223646100911 1 6.74491577405278 757 681 510 145 2352 531 514 50 2532 866 158 207 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 1.35617118698632e-37 2.06488000083078e-35 535 949.454545454545 531 1.35617118698631e-38 21 2.42898295786256 2.62025734017279 1 24.3273917211074 531 968 4642 26 312 50 1204 961 1463 21 266 208 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 8.4747244223219e-07 1.31106847831397e-06 535 1069.54545454545 532 7.70429789719317e-08 20 2.3124575315048 2.54097115013762 1 3.9271242661091 532 739 1718 2092 2933 404 333 337 202 2455 20 209 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 5.42833523087444e-08 3.06874196014832e-07 190 758.363636363636 532 4.93485033164959e-09 190 2.23401098671812 2.2130218464115 1 4.20071702096007 190 1333 532 979 430 351 456 195 2190 671 1015 210 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 4.04323345937974e-07 7.31604867117337e-07 535 908.909090909091 535 3.67566745678079e-08 78 2.27120885450374 -1.99672306066766 -1 4.02321572646681 535 814 1842 1175 2448 335 78 383 87 2000 301 211 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 1.23132364973413e-07 3.71619986983812e-07 635 481.181818181818 535 1.1193851987731e-08 38 3.06952593534195 3.41686674644949 1 5.69840602512978 633 615 680 285 1317 535 342 38 93 608 147 212 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 2.80953927877524e-07 5.72979094207008e-07 210 650.181818181818 535 2.5541269432466e-08 16 3.09965846492798 3.33622189981213 1 5.58604504830131 210 535 687 1363 2138 57 16 27 894 1127 98 213 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 3.82632354210472e-08 2.89891607042284e-07 485 957.181818181818 537 3.47847600786689e-09 160 2.02962024452639 -2.4227237889183 -1 3.83080330647588 617 302 1431 1807 160 483 431 537 2267 2009 485 214 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 1.2034325880579e-31 1.26226707014073e-29 25 920.545454545455 538 1.09402962550719e-32 23 3.01446703582838 -3.10274523906539 -1 25.1547294944923 1767 1136 23 25 323 1165 3246 1440 538 72 391 215 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 5.96467407702084e-08 3.10399797613433e-07 540 733.272727272727 538 5.42243112612365e-09 127 2.34034213341293 2.28115269117028 1 4.39734480670804 538 248 828 2096 533 155 755 259 1712 815 127 216 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 1.82471642354622e-07 4.50217538899015e-07 250 696.909090909091 542 1.65883324990112e-08 108 2.65099471126458 2.73042891822053 1 4.8575233266918 249 805 1031 1167 1709 349 542 196 260 1250 108 217 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 1.03233440671371e-30 1.0367273190827e-28 765 719.181818181818 542 9.38485824285189e-32 24 2.75241430772761 2.94313061962119 1 22.2410572121602 761 1091 24 274 542 340 1241 418 2605 51 564 218 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 9.25303571269685e-12 1.61756772458997e-10 500 571.181818181818 545 8.41185064794162e-13 168 3.22440896514182 3.53988770450714 1 9.11560876832746 497 230 214 168 576 378 792 847 1490 545 546 219 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 1.81642671048258e-10 2.582389781168e-09 240 906.272727272727 548 1.65129700966595e-11 239 3.52200487499257 3.70092091511292 1 8.73336270500062 239 451 266 801 2877 548 602 1611 1542 530 502 220 M8821 REACTOME_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AXON_GUIDANCE.html Genes involved in Axon guidance 271/342 Reactome 5.99134441318433e-14 1.38623262893285e-12 415 628 549 5.44667673925861e-15 154 2.63808973070925 3.03080051283569 1 9.03252226477718 415 1181 154 287 337 549 1160 1085 785 320 635 221 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 2.25916290109853e-08 2.19408413440022e-07 150 651.454545454545 551 2.05378447663428e-09 104 2.86285018146294 3.05038187396509 1 5.50385011671874 149 1542 385 705 1786 213 466 551 556 709 104 222 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 1.40729047142906e-16 4.67775424305998e-15 1650 1254.45454545455 551 1.27935497402642e-17 102 3.3751378216538 3.59876224484993 1 13.9653950305002 1649 180 102 246 551 2344 2805 2305 264 218 3135 223 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 2.53680593059668e-09 3.01605138348018e-08 555 642.363636363636 551 2.30618721229259e-10 276 2.39501355001891 2.72084475654561 1 5.2003161032778 551 1216 318 324 535 276 1282 553 849 668 494 224 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 5.81952615331935e-08 3.09852566478612e-07 770 699.363636363636 553 5.29047846114521e-09 24 2.96940014823582 3.4784742213937 1 5.58019094183736 766 1482 553 1207 501 410 907 124 522 1197 24 225 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 1.86994250096794e-06 2.55607547192838e-06 395 981.727272727273 553 1.69994917306553e-07 335 3.09290003047787 3.39569202696386 1 4.99384082868001 359 697 1045 1584 3373 553 393 534 394 1532 335 226 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 9.9077818691036e-07 1.47989653234712e-06 260 908.272727272727 553 9.00707848282987e-08 48 2.08978587805681 2.22677622265999 1 3.51714447596326 258 820 1499 1836 3047 186 48 168 553 1251 325 227 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 7.14169799129911e-08 3.17725226229176e-07 760 609.909090909091 558 6.49245293012254e-09 55 3.77307564379659 4.0385753376725 1 7.07884437763516 758 558 413 937 1464 536 573 55 294 654 467 228 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 1.39197130213842e-27 1.15264992036725e-25 305 777 561 1.26542845648947e-28 34 2.73981260317496 2.94667976393225 1 19.7293251477966 305 1997 34 1312 561 249 582 591 2518 71 327 229 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 1.4847820371423e-07 4.06742380459178e-07 530 675.545454545455 565 1.3498019430458e-08 86 2.85942044797063 3.24866084569608 1 5.27591359884931 527 735 1154 695 1493 484 222 86 193 1277 565 230 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 1.29389480566119e-08 1.35414267909553e-07 395 1006.72727272727 565 1.17626801206457e-09 194 3.54791512562761 3.67227441232066 1 7.03582462344904 392 520 365 1155 3073 647 538 194 2223 565 1402 231 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 1.4541853750636e-14 3.57487238036469e-13 25 771.363636363636 568 1.32198670460328e-15 22 2.17968180772876 2.34264249431133 1 7.83329329943211 22 1407 479 939 2904 108 166 568 908 102 882 232 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 1.74475423993318e-08 1.77866954913275e-07 105 1012.81818181818 568 1.58614023070028e-09 104 3.62480476761618 3.68972802935476 1 7.06435891464817 104 1744 373 779 3935 355 564 1679 646 568 394 233 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 5.02945322215165e-08 3.0357704374324e-07 1080 971 569 4.57223030648251e-09 265 2.23157473406811 -2.40634907332861 -1 4.19915824210769 1078 512 1552 2521 362 547 460 1756 265 1059 569 234 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 2.68273598953663e-10 3.67029387553997e-09 645 827.272727272727 571 2.43885089987616e-11 89 3.07342347048334 3.33522363557639 1 7.48542328613507 643 1568 277 571 1747 171 212 1224 2153 445 89 235 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 7.40231092786062e-08 3.21721064267975e-07 85 980.454545454545 572 7.40231117443456e-09 2 3.24054813744551 3.24054813744551 1 6.07454386484178 727 914 4474 572 864 460 2 84 134 2471 83 236 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 2.87286680822073e-23 1.8324231533516e-21 50 684.272727272727 573 2.61169709838247e-24 47 2.82002225468557 2.9068144295944 1 16.8857055567534 573 1162 47 47 1446 83 771 435 2229 111 623 237 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 8.5880664216087e-08 3.28305665915602e-07 170 775 573 7.80733341532562e-09 166 3.17839220166097 3.30921474841153 1 5.94993775996135 166 1599 416 760 1980 232 268 1271 573 956 304 238 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 2.96721972733008e-12 5.55764964801508e-11 160 980 575 2.69747247939462e-13 159 4.08948812583605 4.18026861289486 1 12.1093763350918 159 1690 200 721 3914 458 447 1435 499 682 575 239 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 2.02154868673492e-10 2.7981553669762e-09 115 761.454545454545 576 1.83777153356425e-11 115 3.55641007991917 3.87176135671418 1 8.78289448205903 115 1666 274 737 2685 136 241 1101 644 576 201 240 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 3.27854659219204e-07 6.3369123321648e-07 580 1120 582 3.27854707589119e-08 33 2.34954842056804 2.58059071814734 1 4.20435151660522 580 890 4315 611 2349 582 196 73 33 2141 550 241 M15394 BIOCARTA_AMI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AMI_PATHWAY.html Acute Myocardial Infarction 24/34 BioCarta 1.89703613804954e-15 5.11657746948218e-14 275 1084.90909090909 585 1.72457830731775e-16 129 4.46947228479857 4.22832562963714 1 17.1528467733815 273 585 129 275 3751 1150 1575 2326 138 497 1235 242 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 8.75861849917297e-16 2.49040236843954e-14 455 745.909090909091 585 7.9623804537936e-17 103 3.06547543011373 3.44767001157841 1 12.0411574344958 452 103 121 744 2469 585 732 739 1722 199 339 243 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 1.96774451067648e-08 1.96774451067648e-07 540 838.636363636364 589 1.7888586620696e-09 267 2.77991914542412 3.33142235973852 1 5.38234692610787 537 267 379 397 2627 700 595 1317 1232 589 585 244 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 5.79745455507522e-09 6.51523464284644e-08 590 737.272727272727 589 5.2704132457752e-10 288 2.23302869240282 2.43394919442792 1 4.63285223782518 589 1096 337 288 1016 342 865 362 2120 410 685 245 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 6.33801864668817e-08 3.14536172538656e-07 820 981.363636363636 590 5.7618352993466e-09 194 2.50798053098497 3.00775873317541 1 4.70822409556828 820 194 569 2706 590 583 695 321 2830 559 928 246 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 2.2917672509233e-07 5.10724335427666e-07 660 834.454545454545 590 2.0834249905996e-08 15 2.34929221834916 2.54571126880136 1 4.2674522567467 657 15 579 550 1933 254 590 69 3214 666 652 247 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 3.86315316792526e-20 1.87980236624817e-18 625 590.909090909091 590 3.51195742538659e-21 68 2.98920300948201 3.14117266836348 1 15.2996818207712 622 1347 68 314 970 264 718 384 1057 166 590 248 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 4.50360675556509e-17 1.60336235348416e-15 40 955.090909090909 591 4.09418795960461e-18 37 3.65889413694417 3.82020759635427 1 15.6308787338931 37 1596 93 675 3968 591 848 1659 321 225 493 249 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 5.58379399671845e-08 3.07843567066819e-07 445 927.909090909091 592 5.07617648949097e-09 208 3.10645825984852 3.01266965516875 1 5.84032878326868 445 2729 1065 1846 462 652 208 592 529 1337 342 250 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 1.03934886660764e-11 1.79696946900661e-10 5 865.090909090909 592 9.44862606011408e-13 5 2.0308769241196 2.02044082571634 1 5.71431137000134 5 1325 592 2040 3257 48 53 511 718 157 810 251 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 1.40379100035042e-07 3.95812038330586e-07 525 733.363636363636 596 1.27617371811317e-08 323 2.82860522449614 3.03100937963419 1 5.22871027489678 522 323 511 596 1440 569 812 371 825 957 1141 252 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 4.52250678855922e-11 7.00550870485945e-10 185 844.454545454545 597 4.11136980786562e-12 185 3.59980413812223 4.08256852044902 1 9.51525634245507 185 362 241 736 3363 659 1096 1089 377 597 584 253 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 4.04500645986942e-08 2.9351990282604e-07 1575 1100.90909090909 599 3.67727866749317e-09 104 2.37576584618987 2.48514998669356 1 4.48057622627094 1571 104 599 343 190 1985 3609 222 1838 514 1135 254 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 6.27140578003261e-10 8.2916065214997e-09 365 895.090909090909 600 5.70127798347307e-11 285 3.23072423921614 3.67031022583716 1 7.53838365239578 365 1544 285 1183 3162 600 623 689 581 450 364 255 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 2.49250714674781e-08 2.35764203059111e-07 1710 1181 605 2.26591561362442e-09 127 3.10173059170813 -2.89212210990196 -1 5.93520440418473 1710 434 390 514 127 605 662 4062 2770 448 1269 256 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 2.6103364118004e-06 3.42910878477536e-06 90 877.818181818182 606 2.37303591728446e-07 4 2.29421759156949 2.29421759156949 1 3.61951576366998 86 761 951 1824 3521 110 4 478 606 532 783 257 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 8.26763341735319e-08 3.27411388472988e-07 295 717.181818181818 607 7.51603066186559e-09 177 2.05913739363217 -2.03858215380864 -1 3.85509819682155 292 177 1081 616 887 323 487 599 2189 631 607 258 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 2.10929426213201e-08 2.07846950256015e-07 410 943 608 1.91754025668663e-09 126 3.76995549640972 4.13383378502585 1 7.27363278027191 126 1707 384 824 3604 400 608 1226 407 679 408 259 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 1.11693924792682e-07 3.55972535463511e-07 500 746.090909090909 610 1.0153993678489e-08 67 3.12205729561391 3.53705604644435 1 5.81278540500606 498 1638 741 813 1225 412 610 67 482 1479 242 260 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 6.19742557082023e-07 1.02172017793474e-06 420 980.363636363636 610 5.63402483331174e-08 207 2.27060160965013 -2.10218884844763 -1 3.92703156364314 417 370 1365 996 2724 391 207 562 610 2283 859 261 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 8.38938010003281e-08 3.27411388472988e-07 50 1307.18181818182 611 7.62670947268147e-09 46 1.22657811301943 -1.16819494218316 -1 2.2960400714229 293 464 3277 1517 907 46 49 611 4162 2905 148 262 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 6.12247017385447e-08 3.12995510041999e-07 555 1349.36363636364 612 5.56588213112657e-09 121 2.29680043882995 -2.81579228349475 -1 4.31311817501137 2271 551 1191 590 555 3162 4380 121 612 984 426 263 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 1.41762776286809e-07 3.98285895281988e-07 610 830.818181818182 612 1.28875259474242e-08 188 2.41917820286252 2.38389006645561 1 4.46986461533046 607 308 1436 1422 1447 638 612 188 453 1660 368 264 M3005 NABA_COLLAGENS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_COLLAGENS.html Genes encoding collagen proteins 22159717 38/45 Alexandra Naba 1.40080999461148e-14 3.46168752595089e-13 75 960.454545454545 613 1.27346363146499e-15 71 4.24722370252139 4.3545211495425 1 15.2815343605107 71 1670 144 691 3894 572 918 1248 319 425 613 265 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 1.40465355680965e-09 1.74933107866532e-08 1285 777.545454545455 615 1.27695777973318e-10 12 3.3950134727038 3.66731084915063 1 7.60390545889169 1282 485 303 553 1707 896 990 12 1335 375 615 266 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 7.34296194711023e-07 1.16853608868376e-06 130 1062.18181818182 618 6.67542217998099e-08 81 1.81847416498242 2.05422238490518 1 3.11428117821475 129 424 2220 2321 2833 272 81 397 627 1762 618 267 M649 REACTOME_PHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHOLIPID_METABOLISM.html Genes involved in Phospholipid metabolism 180/208 Reactome 6.41725666150395e-08 3.14536172538656e-07 580 1135.63636363636 619 5.83386986244651e-09 28 1.66963619514643 -1.69488783419159 -1 3.13411495084826 577 1318 3006 1804 608 28 619 452 712 3161 207 268 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 1.65989510479359e-27 1.32791608383487e-25 230 836.818181818182 619 1.50899554981234e-28 34 2.67926719470043 2.72675490384017 1 19.2457596908648 229 1158 36 670 1665 427 544 619 2643 34 1180 269 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 1.0403209919916e-07 3.47369293280946e-07 620 908.545454545455 620 9.45746401077809e-09 46 2.79348664089298 3.10210540313498 1 5.20951807721415 620 1504 546 2261 1142 77 174 68 2365 1191 46 270 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 1.11409815028929e-06 1.63664589771722e-06 380 1064.81818181818 620 1.01281701316198e-07 230 3.5484181393411 3.59565302658614 1 5.92784664802809 377 1727 506 774 3105 524 620 2097 230 1161 592 271 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 3.56001344238514e-08 2.83360260506878e-07 2020 1247.90909090909 621 3.23637590908442e-09 114 2.44355260499745 -2.71979162903935 -1 4.61923812141321 2016 318 621 331 114 2348 3260 2369 222 434 1694 272 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 1.42233867314421e-07 3.98409119822705e-07 610 723.545454545455 621 1.29303524100084e-08 306 2.89580307126614 2.77309350837576 1 5.35057170468887 609 400 500 306 1451 708 621 1000 696 404 1264 273 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 3.12806315800462e-08 2.69553239732593e-07 905 818.272727272727 622 2.84369382043716e-09 62 2.6492693159364 2.90738736577314 1 5.02478949803703 904 622 941 388 62 1571 2956 270 100 891 296 274 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 1.17500922009915e-06 1.71385770051545e-06 385 947.636363636364 623 1.06819077060572e-07 114 2.83616999730386 3.3470193511151 1 4.72142415732899 426 623 881 790 3132 381 179 114 2424 1093 381 275 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 6.33367027013836e-08 3.14536172538656e-07 960 975.818181818182 623 5.75788222952819e-09 92 2.59794020331651 -2.79160541361519 -1 4.87713600541193 956 1382 447 92 589 907 1930 288 3303 623 217 276 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 5.49338876488677e-07 9.31350394046895e-07 2265 1031.63636363636 625 4.99399103325784e-08 77 2.59383676207463 -2.53780819274961 -1 4.51631731526011 411 804 1475 2262 2642 248 181 77 625 2265 358 277 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 2.19898450701232e-08 2.1533624218046e-07 30 974.363636363636 625 1.9990768445382e-09 11 2.03312925470471 2.03312925470471 1 3.91323271217155 28 625 1069 1808 3734 104 11 557 1678 398 706 278 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 4.48041245654664e-08 2.99073619127066e-07 1390 812.363636363636 628 4.07310231617504e-09 63 2.65232268455417 2.90166402920267 1 4.99601411769487 1390 63 521 303 268 1226 1997 927 628 600 1013 279 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 4.4238488300157e-09 5.08042979992071e-08 240 1010.45454545455 632 4.0216807626467e-10 196 3.22164983409108 3.40830503563163 1 6.78482002069914 237 1584 331 783 2674 196 505 1600 2194 632 379 280 M2699 BIOCARTA_SODD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SODD_PATHWAY.html SODD/TNFR1 Signaling Pathway 14/15 BioCarta 1.48272969071129e-07 4.06416036013781e-07 585 907 633 1.34793617331141e-08 80 2.33054048030151 -2.58882429891327 -1 4.30015302052667 581 791 1536 2309 1492 298 80 633 159 1597 501 281 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 3.49597778291179e-10 4.74167101590335e-09 120 671 633 3.17816162133394e-11 118 3.0642410303234 3.40980424469687 1 7.36463494709682 118 1478 280 746 1473 334 550 675 681 633 413 282 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 7.19464456100798e-07 1.14997366501719e-06 310 850.272727272727 633 6.54058810351692e-08 206 2.06471822905604 2.11988012945001 1 3.54025652622185 235 633 966 1052 2818 206 307 308 1391 607 830 283 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 3.23488782849298e-08 2.73142585876331e-07 3655 1565.18181818182 634 2.94080716005353e-09 34 2.63685338429824 -2.57006911713149 -1 4.9968622333519 3655 34 471 103 77 3055 3886 2358 340 634 2604 284 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 5.09218008874789e-08 3.0357704374324e-07 375 800.727272727273 635 4.62925473328443e-09 226 2.32131267603247 2.53000860834767 1 4.36805292725193 420 2098 833 864 375 226 635 489 931 1563 374 285 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 2.41329650917133e-08 2.30582176584791e-07 750 738.272727272727 636 2.1939059414946e-09 15 2.2483481492218 2.82047216910413 1 4.30827489010455 747 1403 657 401 15 595 1084 535 379 1669 636 286 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 3.05931086622295e-30 2.88798945771446e-28 130 786 639 2.78119169656631e-31 27 3.15577388959279 3.40978006070132 1 25.0951015247153 127 2013 27 663 1829 425 813 639 1556 101 453 287 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 4.59193883159195e-07 8.08729525563956e-07 245 825.454545454545 639 4.17449071822031e-08 216 2.1938181323201 2.04496170939622 1 3.85852256556214 245 428 983 1055 2533 237 216 526 1438 639 780 288 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 1.26694955850676e-07 3.75976782685104e-07 640 793.818181818182 640 1.15177239224422e-08 116 2.20491874211145 2.45439423851863 1 4.08984476442692 640 1107 473 1180 1346 116 585 347 1581 572 785 289 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 1.22074718668352e-07 3.70192774369017e-07 45 845.909090909091 641 1.10977023129179e-08 41 2.28832566284453 2.29985566917688 1 4.249035747133 41 1372 641 1330 2951 51 114 699 1226 286 594 290 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 1.41881320830533e-15 3.91625634105332e-14 270 722.909090909091 642 1.28983018936848e-16 125 2.59860674987825 3.0579580537446 1 10.0596438206136 642 1990 125 685 270 793 1594 376 757 266 454 291 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 1.03463065019023e-06 1.5395512827547e-06 60 1023.36363636364 642 9.40573760694131e-08 34 1.92195406718979 2.04800325462022 1 3.22508635191367 60 1538 1409 2071 3368 40 34 208 1468 419 642 292 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 1.86081234814205e-06 2.54506933736032e-06 125 999.636363636364 643 1.69164902005752e-07 124 1.89527856631071 2.04950070939773 1 3.06083613486268 124 332 1162 1649 3372 180 465 503 1697 643 869 293 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 7.54126258663217e-07 1.19125700833012e-06 60 886.181818181818 646 6.85569561060233e-08 56 1.8576073016823 1.99906820965132 1 3.17683212907851 56 1192 992 1210 2855 68 170 483 1670 406 646 294 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 9.79045927112286e-10 1.24894507458648e-08 60 892.727272727273 650 8.90041752316347e-11 59 2.05210382775466 2.17577948416 1 4.68252353301807 59 1353 650 1372 3155 125 163 573 1338 189 843 295 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 2.74980818810515e-07 5.67043309561771e-07 670 768 651 2.4998259380066e-08 228 2.32172430560844 2.59281132282023 1 4.18690800585655 670 310 1134 607 2111 363 1099 228 651 1001 274 296 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 9.95087141102259e-08 3.41586276800194e-07 110 612.454545454545 651 9.04624714646621e-09 58 2.30458597123649 2.4549898420898 1 4.30247816453519 110 1505 651 805 1101 58 141 461 783 936 186 297 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 4.57483214257772e-08 2.99073619127066e-07 345 760.272727272727 652 4.15893839791812e-09 92 2.5006193636009 2.98547618302069 1 4.71021080902032 341 1383 561 855 281 92 741 652 1817 1515 125 298 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 4.2301167069501e-08 2.95358312155018e-07 655 819.090909090909 653 3.84556071662359e-09 132 2.45250117263302 -2.43086999068965 -1 4.62340268469001 653 1756 1632 1012 219 419 421 755 132 1869 142 299 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 8.38763885328304e-08 3.27411388472988e-07 455 1249.09090909091 654 7.62512652097008e-09 150 1.32177210807213 -1.28207873065599 -1 2.47430121742424 455 344 3150 1097 904 150 199 654 3822 2658 307 300 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 1.54985054619925e-09 1.90999858434999e-08 1300 803.727272727273 654 1.4089550429919e-10 137 2.48270352927233 2.8678665464593 1 5.53298996404541 1296 1153 307 406 137 654 1743 710 1358 524 553 301 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 1.58797723820726e-11 2.64849913934215e-10 600 1047.09090909091 654 1.44361567110793e-12 223 3.34052920813374 3.66965408286394 1 9.23735673346129 599 316 223 333 2670 1311 1673 1908 654 374 1457 302 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 8.35328322367893e-09 9.12673537401957e-08 105 1096 655 7.59389386854171e-10 105 3.60795830304217 3.5538700332198 1 7.33342987008547 105 1784 348 832 4107 480 655 1680 571 968 526 303 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 6.71392588282796e-08 3.14536172538656e-07 660 977.454545454545 656 6.71392608567356e-09 109 2.17059858075109 2.32622635525373 1 4.07474213544337 656 1010 4509 352 764 109 1061 391 1017 302 581 304 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 1.05387176586105e-08 1.12286111396482e-07 445 1071.27272727273 657 9.58065246281307e-10 100 2.45754470873001 2.6356928903493 1 4.9309823083699 441 1230 358 2269 1907 377 657 100 2932 453 1060 305 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 6.68914930783411e-09 7.44641149362665e-08 920 602.454545454545 657 6.0810448437933e-10 62 2.79180086783182 3.26509730052976 1 5.74557762396202 916 62 341 299 523 809 1439 169 690 722 657 306 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 9.00761148773e-08 3.3189637956351e-07 190 836.909090909091 658 8.18873805139535e-09 9 3.28662878895174 3.6073721051939 1 6.14810206512526 187 658 760 803 2589 281 148 9 2195 1261 315 307 M977 REACTOME_KINESINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KINESINS.html Genes involved in Kinesins 28/32 Reactome 7.02272194769399e-07 1.12823149542591e-06 630 1269.36363636364 658 6.38429471768236e-08 362 1.82317747987868 2.03656410445558 1 3.1303636441482 627 618 2253 2747 2802 437 633 658 1353 1473 362 308 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 1.22413897574509e-11 2.08589746047538e-10 2790 1573.27272727273 660 1.11285361431991e-12 156 3.14159327021124 3.5256935556555 1 8.78128111157026 2787 156 218 308 660 3016 3452 2398 548 290 3473 309 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 8.51881568672571e-08 3.28305665915602e-07 960 605.636363636364 660 7.74437819690033e-09 33 2.9734791974822 3.07226410808781 1 5.56628588812724 957 673 855 98 928 660 592 33 56 1399 411 310 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 1.94335473094272e-11 3.21846818598233e-10 35 1399.45454545455 661 1.76668611905444e-12 32 3.00599270090448 -3.16022462620219 -1 8.2387199371542 32 2574 225 2257 4011 233 609 661 3480 152 1160 311 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 6.61030182844658e-08 3.14536172538656e-07 905 757.272727272727 663 6.00936547915019e-09 64 3.09008554068714 2.96754823085683 1 5.8012079445532 903 838 695 2519 644 518 64 241 1029 663 216 312 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 5.55304978751094e-08 3.07843567066819e-07 795 1048.18181818182 665 5.55304992627456e-09 113 2.13525035296985 2.4184159276895 1 4.0141300890084 794 991 4500 349 552 113 1350 665 1176 529 511 313 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 1.190139499512e-19 5.34996041685392e-18 1340 850.727272727273 667 1.08194499955636e-20 72 2.94874127940087 3.26973257161717 1 14.7057943596758 1339 1330 72 667 349 887 2721 565 944 118 366 314 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 8.80548235590906e-21 4.46901900213879e-19 460 835.454545454545 668 8.00498395991734e-22 64 2.50474513975198 2.91456457338117 1 13.2711893046293 1025 1104 64 668 154 1088 2455 458 1610 107 457 315 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 1.88970733517357e-14 4.59763846495836e-13 395 659 668 1.71791575924871e-15 146 2.65909806614184 3.06641209476355 1 9.47249199407175 393 1241 146 706 763 668 1181 431 1135 231 354 316 M676 REACTOME_PI_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI_METABOLISM.html Genes involved in PI Metabolism 47/51 Reactome 1.92507873594993e-07 4.64778897147911e-07 995 1353.27272727273 669 1.75007173127385e-08 13 1.49421735982558 -1.71856794273484 -1 2.73157348291898 993 449 3044 2579 1750 305 669 640 144 4300 13 317 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 9.59745576556022e-07 1.44359436626655e-06 475 1031.54545454545 671 8.72496359312143e-08 140 2.15011830967847 2.50905000907937 1 3.62540672173275 471 581 1582 1257 3025 409 950 140 671 1705 556 318 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 3.23157807285377e-08 2.73142585876331e-07 2300 1179.36363636364 671 2.93779829120219e-09 16 2.32033294074913 2.68001616971148 1 4.39694959255929 2298 16 671 554 76 2353 3088 1106 2085 504 222 319 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 8.16326544679045e-12 1.44851928228763e-10 675 1067.27272727273 671 8.16326544682043e-13 73 2.41527724334726 2.72744051914252 1 6.86136019046261 671 1001 4572 489 439 73 1359 1010 1711 138 277 320 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 2.43217694606493e-07 5.28053136404162e-07 520 1165.54545454545 674 2.21107019540968e-08 20 3.82148620428205 4.09882412682049 1 6.92621813628278 516 736 674 2306 3120 324 223 20 3338 950 614 321 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 2.46169013187787e-07 5.31315294702385e-07 385 796.545454545455 675 2.23790037029886e-08 140 2.69840715989217 2.93339426836767 1 4.88836641186742 382 1502 698 441 2006 289 503 893 675 1233 140 322 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 9.08616297531245e-09 9.83639661547586e-08 250 1213.36363636364 675 8.26014819349e-10 248 3.18367760898416 3.2873273429512 1 6.44105091550735 248 1649 352 1637 3611 637 675 2056 1488 512 482 323 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 2.78328244184091e-07 5.7012075759436e-07 230 1041.63636363636 676 2.53025708541993e-08 226 3.6177691987187 3.71610547047293 1 6.52217050357391 226 1693 450 823 3559 439 356 1930 505 801 676 324 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 1.14861155721405e-07 3.59285478750119e-07 680 677.454545454545 676 1.04419237925693e-08 39 2.73101603358763 2.8216894760394 1 5.08144672128492 678 447 849 280 1257 485 676 39 1325 1190 226 325 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 3.38197822766809e-07 6.47469491127629e-07 655 1616.63636363636 678 3.38197874236815e-08 22 3.21704879786949 3.21704879786949 1 5.74832233386936 652 1949 4417 3018 3201 661 77 22 678 2559 549 326 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 1.00009017650903e-07 3.41896906035439e-07 680 882.818181818182 679 9.0917292906525e-09 223 2.6373832334298 -2.33503362345848 -1 4.92360784650723 855 1683 1333 586 1104 388 446 679 679 1735 223 327 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 4.51794900452105e-17 1.60336235348416e-15 465 765.727272727273 681 4.10722636774641e-18 94 3.39904335225019 -3.55719786183073 -1 14.5207291181384 463 167 94 1761 221 681 692 786 2414 172 972 328 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 7.15195278629246e-08 3.17725226229176e-07 1365 790.363636363636 681 6.5017754716313e-09 11 2.38667689947701 2.91663743981743 1 4.47744010649395 1365 11 539 159 1286 656 1491 1345 890 271 681 329 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 5.53925903417218e-08 3.07843567066819e-07 490 885.272727272727 683 5.03569015785650e-09 102 3.24302713279794 3.0617905390666 1 6.09712436296939 584 488 487 2043 450 683 897 102 2029 852 1123 330 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 6.35991298228823e-08 3.14536172538656e-07 3475 1542.18181818182 683 5.78173924195001e-09 119 3.22338127241533 3.44562493068444 1 6.05148938774519 3472 505 535 119 594 3342 2286 331 1174 683 3923 331 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 6.52187670916249e-08 3.14536172538656e-07 485 982.090909090909 689 6.52187690056944e-09 31 2.05974853829547 -1.87597652534286 -1 3.86660562391381 941 1050 4292 482 740 102 1340 485 689 651 31 332 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 1.97381725596787e-11 3.25748861824068e-10 1415 841.909090909091 690 1.79437932362325e-12 51 2.42133204435238 2.52605398406609 1 6.63247551520307 1414 51 322 1565 151 602 1312 690 1735 147 1272 333 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 5.58947923729011e-14 1.29962275862115e-12 10 1070.18181818182 691 5.08134476117294e-15 10 1.89236854998738 1.97755421288174 1 6.49432424773902 10 1299 691 2047 3554 207 180 684 1802 108 1190 334 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 1.95466767833156e-07 4.68088860564431e-07 695 1014 692 1.7769707745463e-08 18 2.34475249030189 2.18174016736491 1 4.2848373363257 692 477 1179 1383 2426 420 358 18 2128 1992 81 335 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 2.07647092755126e-07 4.8447566871191e-07 215 1589.90909090909 693 1.88770102139917e-08 109 1.13792238960807 -1.09234957049101 -1 2.0741034773224 212 588 3217 2903 1834 120 109 693 4367 2886 560 336 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 9.18529434240881e-07 1.39499286304437e-06 405 1047.72727272727 693 8.35027107035848e-08 169 3.31311171794081 3.40785273913121 1 5.60107499400387 404 693 788 1417 2992 457 169 177 2872 1181 375 337 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 8.84855958058537e-07 1.35557290556193e-06 225 1098.72727272727 695 8.04414830867474e-08 98 3.10188897278718 3.2990122149889 1 5.25508232501443 224 2592 821 1711 2966 98 121 586 695 2108 164 338 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 3.88845907054805e-07 7.14145012178474e-07 530 1218.72727272727 696 3.53496341620556e-08 74 2.96562487858696 3.34069917298089 1 5.26254994403783 526 2643 604 1873 2410 370 696 74 2744 1065 401 339 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 6.77232530427669e-07 1.096819889561e-06 3215 1566.45454545455 697 6.15666126274782e-08 361 3.69179031702299 4.31492802446006 1 6.35269473990647 3212 609 523 389 2780 3561 3089 1323 361 697 687 340 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 4.25934816682381e-08 2.95390421094817e-07 3835 1991.63636363636 698 3.8721347720797e-09 229 3.41535518361621 2.90923923301788 1 6.43884604063384 3831 582 429 698 229 4225 4195 3380 473 480 3386 341 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 3.73094568223075e-08 2.87575261955407e-07 1185 619.727272727273 699 3.39176885954844e-09 128 2.35153954125119 2.60688851190713 1 4.44091181246071 1184 218 717 128 136 790 1135 377 469 964 699 342 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 3.35106426750025e-08 2.75614173569107e-07 1285 895.818181818182 699 3.0464221077673e-09 65 2.40968222685569 -2.45044314588406 -1 4.56357434653246 1284 1301 394 65 236 699 1861 1996 1114 429 475 343 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 1.76800687239029e-15 4.79597266533459e-14 1020 703.090909090909 700 1.60727897490027e-16 48 2.51763258644551 2.69900297449961 1 9.68217210853234 1019 1169 128 48 189 368 1042 1558 700 175 1338 344 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 2.5261395655428e-17 9.24604989314093e-16 410 787.272727272727 700 2.29649051412981e-18 90 2.60160040877219 2.80159862115287 1 11.2934523002784 410 1202 90 1564 634 246 700 788 2219 98 709 345 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 1.48047237759303e-06 2.07169570774951e-06 340 1069.90909090909 701 1.34588488533272e-07 204 3.01218590522356 3.6309469581695 1 4.94286448161481 339 1654 625 854 3283 479 701 1682 369 1579 204 346 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 7.06138096273637e-07 1.13327841360475e-06 2340 1583.27272727273 702 6.4194392993109e-08 106 3.08862290292455 3.13282397670153 1 5.30198017237508 2340 631 629 702 2806 2466 2611 106 441 696 3988 347 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 1.46781532744193e-10 2.09942071076543e-09 345 707.636363636364 702 1.33437757049078e-11 151 2.79278476387418 3.24171693437511 1 6.99748732504115 342 1404 264 151 1296 447 745 928 922 702 583 348 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 2.6469506356714e-12 5.01751285155381e-11 75 1107.36363636364 704 2.40631875970416e-13 74 4.23608530305575 4.52344630099605 1 12.5978105456841 74 2247 197 1166 4276 704 914 813 514 625 651 349 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 6.45371587323663e-07 1.05549337912948e-06 450 1075.81818181818 704 5.86701615130873e-08 315 3.5151529774288 3.41424209329287 1 6.06563344365815 448 2196 484 704 2754 491 596 2008 315 1037 801 350 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 6.95195635298679e-08 3.15431124190799e-07 1095 982.727272727273 704 6.3199605206066e-09 114 2.66825672620356 -2.68106787797346 -1 5.00821439348752 1091 114 588 1563 704 641 765 2903 350 678 1413 351 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 9.33445171941099e-08 3.36582216314896e-07 710 696.181818181818 706 8.48586555951412e-09 32 3.97983855797182 -4.63847365875708 -1 7.4380329528066 706 712 459 920 1022 1254 964 32 699 617 273 352 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 7.03953059620862e-07 1.13015593245254e-06 300 1138.18181818182 706 6.39957531700839e-08 95 2.99489791309342 3.26245106551099 1 5.14210046525568 297 2600 956 1719 2805 106 172 706 582 2482 95 353 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 6.53277911370536e-07 1.06694523933181e-06 425 1381.45454545455 707 6.53278103418029e-08 197 2.16971393568416 2.3868251384281 1 3.74072166311578 504 875 4627 2336 2816 707 428 421 197 1863 422 354 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 7.75512168062722e-06 9.30456897116433e-06 205 1296.90909090909 708 7.05013547090454e-07 203 1.59169971134376 1.71210701645913 1 2.31165663868205 203 708 2221 2767 3884 278 349 433 558 2029 836 355 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 6.97277247994193e-08 3.15546367261035e-07 535 1707 708 6.33888427358176e-09 34 2.27638759150025 2.50978267489998 1 4.27246044741437 534 3661 1794 4546 708 406 263 34 3178 3341 312 356 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 1.13089153546611e-42 2.66890402370003e-40 715 945.363636363636 712 1.1308915354661e-43 10 2.25846259274134 -2.23365179326901 -1 25.807631191329 712 952 4318 11 115 39 1466 1084 1484 10 208 357 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 2.74775923107151e-12 5.16710102416634e-11 1430 971.272727272727 712 2.49796293734085e-13 199 2.66645279100451 2.98200847547808 1 7.91969439960167 1427 1283 199 262 274 712 2111 1088 2629 234 465 358 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 1.46576544928796e-07 4.04349089458747e-07 135 709.272727272727 715 1.33251413358693e-08 86 2.67604957501734 3.00437940636202 1 4.93950148062863 134 1499 513 847 1479 86 389 715 1241 784 115 359 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 7.83314783942829e-11 1.16632358997166e-09 70 989.363636363636 716 7.12104349064287e-12 69 3.96226773220112 3.92722723360134 1 10.2201386957874 69 1734 253 727 3833 397 716 1779 212 773 390 360 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 1.61799747433581e-07 4.23099616557619e-07 720 841.272727272727 719 1.47090690302909e-08 17 2.93281581636369 -3.48964403052285 -1 5.39685591004154 719 644 831 267 1590 1044 1778 17 136 1995 233 361 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 3.72716179552292e-07 6.92061513566805e-07 450 977.181818181818 719 3.38832947905961e-08 81 2.4158323138722 2.57522923871737 1 4.29629088760648 446 719 1265 2111 2383 265 117 81 1645 1533 184 362 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 1.73091626211889e-08 1.76838198207818e-07 25 937.454545454545 720 1.57356025067037e-09 24 2.08263210332728 2.24445401125738 1 4.05997699978339 24 2035 906 1657 2764 71 118 484 932 720 601 363 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 6.30977544793826e-07 1.0366216538207e-06 725 1530 721 5.73616114330263e-08 274 1.2378609336496 -1.33274304700637 -1 2.13825519041014 721 541 3320 3118 2736 432 611 274 1595 2952 530 364 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 4.43461273982251e-11 6.90804360790834e-10 335 909.636363636364 723 4.03146612719263e-12 240 3.36652512434884 3.96294721401555 1 8.90449601535845 334 379 240 723 2686 917 1620 1307 626 422 752 365 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 1.16231486495321e-07 3.6092935280126e-07 165 1188.27272727273 723 1.05664993305564e-08 164 3.722424628129 3.90400857230353 1 6.9242861332573 164 1737 426 838 4240 565 723 2144 640 997 597 366 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 2.38681038740498e-07 5.22548577520102e-07 1320 1033 724 2.16982786032125e-08 571 2.64850117184273 2.9890070090154 1 4.80346817299414 1316 571 764 724 1977 868 704 2460 613 652 714 367 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 1.01239564034155e-07 3.43037144466053e-07 425 719.454545454545 724 9.20359715390871e-09 232 2.31044215158228 2.82831914452044 1 4.31218528661843 421 232 1255 846 1117 592 724 345 893 1187 302 368 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 2.92079940788044e-08 2.62593775337061e-07 965 745 724 2.65527222423458e-09 39 2.88572062854612 3.66270096428617 1 5.48280278715267 963 732 1294 184 39 724 455 825 408 2401 170 369 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 4.7891613471419e-08 3.01912311600589e-07 600 1018 725 4.35378313763341e-09 316 2.32950136260002 2.65146828983498 1 4.38507117635638 725 2042 517 598 316 833 1655 1283 2046 587 596 370 M9131 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROPHOSPHOLIPID_METABOLISM.html Glycerophospholipid metabolism 64/81 KEGG 1.30471231545146e-07 3.80049677113412e-07 730 1222.63636363636 726 1.18610217529779e-08 247 1.75927806473239 -1.55431023102418 -1 3.26068653176664 726 321 2489 3560 1375 263 247 392 975 2592 509 371 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 5.68326782809825e-08 3.09084324765911e-07 355 726.727272727273 726 5.16660724992212e-09 308 2.671128887898 2.92380591505992 1 5.0204151908567 351 2075 474 768 479 308 749 726 758 972 334 372 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 2.35663735073647e-08 2.27411413914072e-07 985 899.545454545455 726 2.14239761452794e-09 73 2.2686191172623 -2.32033481316361 -1 4.35106520085762 982 1278 414 73 252 604 1777 2185 1354 250 726 373 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 1.92249183892146e-07 4.64778897147911e-07 625 838.636363636364 729 1.74772000629122e-08 166 2.58424956101552 2.5287403864118 1 4.72488583990324 621 315 729 166 1748 279 604 890 1830 1201 842 374 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 1.58594456954851e-17 5.94099870497538e-16 730 978.272727272727 729 1.44176779049864e-18 46 3.27987538685779 3.46052202223328 1 14.4199806809754 729 46 88 296 2694 1203 1657 1945 623 264 1216 375 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 2.74875221184123e-08 2.52906636255178e-07 1005 944.181818181818 729 2.49886567835003e-09 28 2.19207287465116 2.25993531472217 1 4.17501407265103 1001 160 801 1143 28 702 1464 3468 729 596 294 376 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 4.27551263785828e-11 6.68225816248049e-10 920 701.090909090909 730 3.88682967085578e-12 160 2.65011300442742 3.03936854666305 1 7.02043884234635 917 1352 239 730 1252 284 1124 432 859 160 363 377 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 1.36593985660362e-24 9.48122959289569e-23 1055 868.727272727273 730 1.24176350600328e-25 43 3.40368210609577 3.64401400773241 1 21.6448359298559 1053 1346 43 474 730 671 1450 688 1647 88 1366 378 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 3.56895769264118e-07 6.71937786568264e-07 1040 876.181818181818 731 3.24450751965157e-08 95 3.64051990563105 3.90061911838511 1 6.48817157827943 1040 731 591 679 2343 1218 1035 95 878 616 412 379 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 5.72683752029477e-08 3.09093308316432e-07 720 1238.36363636364 732 5.20621606306414e-09 217 2.49237946506863 2.4243394744774 1 4.68438702344962 2412 217 716 732 487 2043 1568 1301 697 717 2732 380 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 9.98025976608563e-09 1.07060968399828e-07 660 986.090909090909 732 9.07296346487355e-10 164 2.36483462789788 -2.19803033861574 -1 4.75906220954507 659 1274 355 164 389 732 1478 2917 1495 327 1057 381 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 1.78502410686326e-26 1.40421896406576e-24 1310 671 733 1.6227491880575e-27 30 2.49816244904364 2.69129409311739 1 17.205902901258 1306 1049 37 30 93 262 1628 1399 733 55 789 382 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 1.7746951264899e-07 4.43266487055072e-07 1045 903.636363636364 733 1.61335933604632e-08 133 3.63355640272475 -4.3464597317261 -1 6.66531979692279 1045 728 733 725 1681 1341 1157 634 194 1569 133 383 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 2.45159731834261e-07 5.30318026699227e-07 805 912.363636363636 734 2.22872508321768e-08 391 2.38212331621341 2.56581445772532 1 4.31585486798936 801 1232 468 682 2003 523 734 1165 391 650 1387 384 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 1.95235629278419e-08 1.95650142291749e-07 1535 990.454545454545 736 1.77486937282734e-09 348 2.41170113569013 2.62261578986296 1 4.67103973419082 1535 1313 378 501 519 1101 2858 736 1024 348 582 385 M509 REACTOME_DEVELOPMENTAL_BIOLOGY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEVELOPMENTAL_BIOLOGY.html Genes involved in Developmental Biology 398/520 Reactome 1.00532178446082e-09 1.27431879776336e-08 740 754.818181818182 737 9.13928895382013e-11 297 2.38563161842378 2.83908729738088 1 5.43769536356039 737 1100 297 354 318 684 1419 993 1034 601 766 386 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 9.36761270164817e-09 1.01178791651669e-07 4715 1700.81818181818 737 8.51601158321407e-10 118 2.71163233000741 -2.47441480823179 -1 5.47631102277066 4714 118 353 295 328 3544 3377 2025 737 484 2734 387 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 4.5253836929555e-08 2.99073619127066e-07 4480 2212.81818181818 738 4.11398526003846e-09 273 2.85812878367255 -2.4868745700843 -1 5.38374501049158 4479 550 699 358 273 4284 4429 3869 312 738 4350 388 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 4.33297665807633e-07 7.73654416473282e-07 315 1035.09090909091 738 3.93907046497402e-08 91 2.5170105741856 2.70140884449575 1 4.44108142145784 311 1673 1185 2348 2492 117 126 175 738 2130 91 389 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 1.87724344918009e-06 2.56433384145237e-06 740 1194.90909090909 739 1.70658641001792e-07 123 2.46772801121006 -2.38236219559258 -1 3.98325673998898 739 1825 1862 1062 3375 438 191 457 292 2780 123 390 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 1.70141986718626e-16 5.57687623133275e-15 1410 860.181818181818 743 1.54674533380569e-17 103 2.76010077914452 3.29525153374084 1 11.3595281696132 1409 1290 103 272 743 1166 2218 296 713 212 1040 391 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 5.90894578943747e-18 2.28608394476597e-16 1210 882.818181818182 745 5.37176889948858e-19 85 3.40384334143274 3.93072799520758 1 15.3727168795044 1208 1412 85 674 585 1628 1947 373 745 235 819 392 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 1.09237850497717e-12 2.23022061728378e-11 2930 1572.63636363636 746 9.93071368161557e-14 106 3.28780812077145 3.58873661418529 1 10.1118330196415 2926 169 180 106 518 2621 2803 2908 746 272 4050 393 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 5.30945819870998e-08 3.06874196014832e-07 1185 736.454545454545 746 4.82678029713447e-09 110 2.51479995385632 2.91939626888566 1 4.72880611760667 1013 306 1184 1184 403 746 1406 438 435 876 110 394 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 4.31911858021052e-12 7.87113501876204e-11 80 982.545454545455 747 3.92647143656273e-13 78 1.88781758643333 1.86798122444292 1 5.5071547626709 78 1223 594 941 3171 224 346 747 2084 132 1268 395 M15181 BIOCARTA_PGC1A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PGC1A_PATHWAY.html Regulation of PGC-1a 29/30 BioCarta 3.73672892443893e-07 6.9302005985665e-07 750 1326.72727272727 748 3.397026871934e-08 316 1.81648464081422 2.20055679515004 1 3.2298882727213 748 612 2005 2162 2386 546 486 741 1541 3051 316 396 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 1.89405891142594e-06 2.58604514374615e-06 555 1029.18181818182 751 1.72187322008288e-07 220 2.27571044374644 2.47219531928562 1 3.67084046179577 554 751 1445 867 3378 492 220 349 807 1753 705 397 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 8.73899447476114e-07 1.34314731100204e-06 575 1100.72727272727 751 7.94454358738893e-08 202 4.40874169298575 4.64236970352876 1 7.47454832932398 769 2411 751 2051 2954 525 278 202 575 1020 572 398 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 1.07882168214149e-06 1.59525010642476e-06 275 879.727272727273 753 9.80747464697645e-08 119 2.13874491698951 2.10535666829548 1 3.57943158621551 272 119 889 1040 3085 429 587 753 938 407 1158 399 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 1.38048938885668e-07 3.92497786572715e-07 755 1058.90909090909 755 1.25499043225611e-08 73 3.04268191245776 3.20169406690622 1 5.62770728159567 755 1861 1447 1656 1423 482 341 614 320 2676 73 400 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 4.17912385898044e-07 7.49732596517966e-07 245 1298.63636363636 756 3.7992042298616e-08 218 1.72921749549197 -1.77904613222618 -1 3.05761971103924 244 539 1854 1900 2475 218 434 756 4313 982 570 401 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 3.6607648845748e-13 7.74834540591618e-12 1580 1055.18181818182 756 3.32796807688674e-14 171 2.58663277388195 2.83836305718259 1 8.29808959712982 1577 1254 171 395 638 756 2522 1051 2492 305 446 402 M902 REACTOME_CGMP_EFFECTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CGMP_EFFECTS.html Genes involved in cGMP effects 9/21 Reactome 1.44931854047606e-06 2.03452290235407e-06 1085 1207.09090909091 757 1.44931948571283e-07 111 5.18688755193839 5.43706028712541 1 8.52385368646711 1081 876 4250 361 3310 714 276 164 111 1378 757 403 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 1.28864028624907e-06 1.84841049164367e-06 855 1496.18181818182 757 1.28864103351689e-07 2 2.20306619354888 -2.20306619354888 -1 3.64641106168139 852 1945 4403 197 4224 757 243 63 2 3068 704 404 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 1.02190301618747e-10 1.48869822111261e-09 55 1158.63636363636 758 9.29002742031764e-12 55 3.3242071324869 3.41415662601197 1 8.47246937125928 55 1565 259 955 3974 758 752 1720 1621 415 671 405 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 3.13860928928858e-31 3.22048605335698e-29 1275 1221.09090909091 759 3.13860928928858e-32 13 2.61972138731218 -2.39563152614038 -1 21.5528806699567 1273 1000 4442 13 235 627 2330 2116 609 28 759 406 M1469 BIOCARTA_LYM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LYM_PATHWAY.html Adhesion and Diapedesis of Lymphocytes 10/14 BioCarta 2.44009300819689e-07 5.29284880454472e-07 140 757.909090909091 760 2.2182666171234e-08 139 3.34405034793964 2.79117734320254 1 6.05980912752081 926 837 981 140 1997 533 139 760 237 1216 571 407 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 1.96723430101961e-07 4.69668482590419e-07 620 895.636363636364 762 1.78839497902656e-08 161 3.07156648600199 -2.94882037791345 -1 5.61199785750737 616 762 1071 1414 1777 418 161 244 850 1940 599 408 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 4.28871567152941e-08 2.96379765294565e-07 2745 1539.90909090909 765 3.89883250466757e-09 239 3.12591175793481 2.94289136602539 1 5.89178500815335 2745 765 725 709 239 2138 901 4544 656 531 2986 409 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 1.14690616692309e-05 1.34561200792369e-05 445 1341.54545454545 767 1.04264740548114e-06 298 2.93751579853785 2.93751579853785 1 4.1310303499812 443 2437 1576 1370 3980 767 499 469 298 2316 602 410 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 5.74631559577044e-08 3.09093308316432e-07 770 1437 767 5.22392340532909e-09 179 2.46582277880347 2.75640935748194 1 4.63446498220932 767 1927 1907 4552 491 721 205 179 2286 2320 452 411 M7098 KEGG_ECM_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ECM_RECEPTOR_INTERACTION.html ECM-receptor interaction 85/94 KEGG 2.33734309967358e-13 5.13128345602758e-12 40 996.727272727273 768 2.12485736333985e-14 39 3.05218998671181 3.20275443556423 1 9.9495320911071 39 1485 165 1141 3409 504 768 1256 1387 314 496 412 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 3.94313401871008e-13 8.30874668228195e-12 200 1218.72727272727 768 3.58466728973708e-14 172 3.70286411114533 4.02700039876332 1 11.8469786934722 197 1517 172 1635 3746 463 474 1530 2367 537 768 413 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 6.89347448534121e-07 1.11260274499654e-06 970 1059.36363636364 769 6.26679695031065e-08 105 2.57475494148163 -2.36699080910101 -1 4.4256681600766 969 701 1580 1217 2792 444 132 769 105 2529 415 414 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 3.91894137110817e-54 1.84974032716306e-51 1560 846.636363636364 770 3.56267397373473e-55 6 3.49367069912908 3.9057000510281 1 51.1808737411532 1556 1189 6 15 434 499 1695 1209 770 26 1914 415 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 1.19510737211706e-11 2.05123883505183e-10 750 753 771 1.08646124738505e-12 6 2.95321783229981 3.36586477383463 1 8.26089393409147 750 6 217 367 1800 771 1041 1024 950 485 872 416 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 7.82438026124861e-08 3.26534702326202e-07 295 731 772 7.11307321775050e-09 75 1.92012915271039 -2.04050774845778 -1 3.59543573350074 294 1133 1508 929 817 75 650 428 772 1257 178 417 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 3.41455052217318e-08 2.77395498531109e-07 585 1264.81818181818 772 3.10413688651758e-09 98 3.30792467391425 -3.28679142134111 -1 6.26235845698165 2065 584 581 138 98 2020 1981 3557 151 772 1966 418 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 3.81036920081323e-22 2.22036328738746e-20 30 963.636363636364 772 3.46397200073929e-23 27 1.9741342645699 1.95132841653531 1 11.202844808598 27 1099 300 1758 3392 185 203 772 1467 45 1352 419 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 7.45643081589795e-08 3.2288397661503e-07 715 1202.63636363636 773 6.77857369874343e-09 183 2.1702057990669 2.47396594264526 1 4.06687561065666 715 591 1836 2834 773 454 972 183 2683 1912 276 420 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 2.21706341706811e-11 3.62094786455414e-10 195 723.818181818182 773 2.01551219735496e-12 35 2.70382633753477 3.0513551713686 1 7.37051202543223 195 35 228 773 1995 496 921 1072 1147 277 823 421 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 1.25981815258087e-07 3.75235906357741e-07 260 1069.18181818182 774 1.14528929520335e-08 10 3.11685182143147 3.23612983363036 1 5.78249226689007 256 774 859 1839 2893 301 167 10 3470 929 263 422 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 6.35799249479894e-17 2.18143974287033e-15 175 1015.36363636364 774 6.35799249479896e-18 78 2.56083788317873 2.71786305420988 1 10.8408222236523 174 1037 4496 913 1205 191 601 572 774 78 1128 423 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 9.3045755554082e-08 3.35829802760759e-07 610 1101 775 8.45870540811957e-09 106 2.49393504520537 2.4279828729364 1 4.66136417434317 608 106 418 408 2481 775 1022 1889 2248 704 1452 424 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 3.20727491651011e-08 2.72193698392339e-07 775 840.454545454545 775 2.91570451206131e-09 74 2.77023415897418 -2.85205473012042 -1 5.25087263446944 775 847 1563 1631 74 1309 553 126 83 1829 455 425 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 1.57594513610634e-07 4.1859656963545e-07 385 1356.72727272727 775 1.43267749908855e-08 297 2.60873023666019 2.69694094223914 1 4.80389139397838 384 3037 759 2771 1559 346 297 408 3808 780 775 426 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 3.33941505145667e-07 6.4099386103601e-07 50 1233.72727272727 776 3.03583232577446e-08 46 1.78355819650741 1.78628654721052 1 3.18878149606981 46 399 1852 2781 3583 188 59 666 2288 933 776 427 M5539 KEGG_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AXON_GUIDANCE.html Axon guidance 133/153 KEGG 5.03916682449644e-08 3.0357704374324e-07 675 750.727272727273 777 4.5810608544728e-09 226 2.36704313013921 2.97229257680388 1 4.45412165669671 672 1435 867 777 366 423 923 226 1422 826 321 428 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 9.56593191232997e-08 3.38845370705758e-07 780 1040.36363636364 777 8.69630211661011e-09 283 2.19689917152582 2.31473879610778 1 4.10361487908712 777 1432 626 1586 1048 320 1125 597 2996 283 654 429 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 5.8330679340073e-10 7.77742391200974e-09 415 1011.72727272727 778 5.30278903232172e-11 284 3.78642741355254 4.18425955838288 1 8.86557649164399 412 444 284 798 3434 933 1080 1706 567 693 778 430 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 2.76559119763431e-13 6.01547947135206e-12 1535 1059.18181818182 779 2.51417381603152e-14 141 2.70865705542863 -2.61408038078057 -1 8.7755822636097 1533 1396 167 681 675 1106 2122 779 2362 141 689 431 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 8.32405122274003e-07 1.29284375687177e-06 2025 1134.18181818182 779 7.56732215661761e-08 342 2.13857018800566 2.26495304228414 1 3.63551007107433 490 2021 682 991 2919 777 903 342 2022 550 779 432 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 6.77379232642015e-07 1.096819889561e-06 785 990.727272727273 782 6.15799492006303e-08 210 3.21373687568489 -3.22453672476749 -1 5.52996671899127 784 782 578 355 2781 610 210 1983 928 721 1166 433 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 1.57437138606138e-12 3.13545693764122e-11 615 757.636363636364 782 1.43124671460228e-13 24 2.8108141879886 3.0450378698954 1 8.52459928854292 611 24 185 678 1510 830 1067 1309 782 328 1010 434 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 9.01307434561336e-07 1.3754190401324e-06 150 1053.09090909091 783 8.19370730739873e-08 146 2.92277734532131 3.25222443571135 1 4.94626222111883 146 2142 490 2068 2977 330 392 815 1118 783 323 435 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 8.61212045170274e-09 9.3661770811145e-08 720 906.363636363636 783 7.82920044128705e-10 350 2.59422570524143 2.80548486356093 1 5.26427953860056 716 1339 350 1561 783 709 1178 396 1402 462 1074 436 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 2.01928232423846e-06 2.73251507179058e-06 360 1421 783 2.0192841591163e-07 7 2.22247908409391 2.22247908409391 1 3.56959998835407 357 884 4716 1868 3455 315 7 783 756 1865 625 437 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 2.81271581845287e-11 4.5003453095246e-10 1185 1000.90909090909 785 2.5570143804444e-12 234 2.36176013064677 2.78521952177946 1 6.37354946911839 1183 1081 234 699 974 776 1843 785 2409 378 648 438 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 4.09512916603496e-18 1.62428652636008e-16 470 750.090909090909 786 3.72284469639541e-19 83 3.40718218609811 3.79360401705796 1 15.5338326151463 467 112 83 487 1281 1082 1866 872 786 232 983 439 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 1.16296511420917e-06 1.69944128144498e-06 505 1184 787 1.05724157179712e-07 110 2.99680975972905 3.20055963803771 1 4.99206759724137 505 1688 787 1076 3126 229 197 110 3780 1390 136 440 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 3.39773303031924e-10 4.62170026026133e-09 785 948.454545454545 788 3.08884820985819e-11 279 2.5113530300026 3.00564678494055 1 6.04373274462866 781 2020 279 954 788 881 1816 662 1191 612 449 441 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 1.1757432713287e-06 1.71439859149567e-06 390 1065.36363636364 789 1.06885809061835e-07 337 3.13038465590875 3.24750004776098 1 5.21117416344956 386 528 502 753 3133 1052 1311 1886 337 789 1042 442 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 1.63206475599091e-07 4.24841431570192e-07 790 915.363636363636 789 1.48369534278659e-08 98 2.2538953041294 -2.23262371283969 -1 4.14617160763006 789 98 843 579 1598 607 1765 234 2311 807 438 443 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 2.47468216851877e-07 5.32828938285247e-07 790 855.636363636364 790 2.24971131534983e-08 342 2.52808364548875 2.69475814429406 1 4.5788563289405 790 342 904 405 2012 451 510 719 1153 907 1219 444 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 1.18337703974057e-07 3.64829498861888e-07 705 829.363636363636 792 1.07579736672206e-08 275 2.00400089997473 2.22956580709803 1 3.72465317322423 701 275 1570 1185 1284 414 429 792 1085 870 518 445 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 1.79516445392328e-12 3.51584075623149e-11 910 826.545454545455 792 1.63196768538614e-13 130 2.5143332726481 2.76506857223438 1 7.58923987117636 908 1239 189 792 911 130 1069 536 2725 153 440 446 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 6.8911275819223e-11 1.03257530751344e-09 385 825.818181818182 795 6.26466143830742e-12 67 2.61683059920201 2.85573066705955 1 6.78944313075389 385 1431 251 795 67 800 1264 486 2171 331 1103 447 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 9.44925979992944e-06 1.11949061886714e-05 535 1915.45454545455 796 8.59027307805474e-07 41 1.77012836094836 1.77012836094836 1 2.52983091323322 533 3759 2909 3655 4360 653 41 209 310 3845 796 448 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 2.5995453586125e-07 5.48089666740809e-07 720 999.818181818182 798 2.3632233325253e-08 56 2.57746378676585 2.95421363032068 1 4.65918259150605 718 56 519 781 2058 798 1557 1335 1211 764 1201 449 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 5.14636026765733e-08 3.0357704374324e-07 800 1175.54545454545 799 4.67850944367618e-09 160 2.1083468942283 2.59705517830863 1 3.96723262898169 799 704 1654 2783 385 685 351 2203 874 2333 160 450 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 4.84304551645141e-08 3.03172080074942e-07 1230 1195.27272727273 799 4.40276874824132e-09 206 2.58550863533103 2.51508554852799 1 4.86572574059664 1226 206 432 1146 324 727 1587 3795 2513 393 799 451 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 3.07062769192216e-07 6.079430665215e-07 50 1173.63636363636 800 2.79148010954726e-08 47 1.96058305964945 1.9349488243747 1 3.51838179725998 47 2028 714 1181 3198 376 416 800 2538 319 1293 452 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 3.35174863620058e-08 2.75614173569107e-07 45 949.181818181818 803 3.04704426115019e-09 43 1.9550571696175 2.04732432841377 1 3.70242062056871 43 1999 970 1196 3033 144 286 389 1321 257 803 453 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 2.66607001093313e-07 5.55333206160829e-07 500 1136.45454545455 803 2.42370030365534e-08 459 2.55909881358108 -2.64781172323327 -1 4.62176513172977 500 459 803 626 2086 768 1073 1494 3024 640 1028 454 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 3.17864249744275e-21 1.70490824862838e-19 60 744.272727272727 805 2.88967499767521e-22 58 3.01526005146867 3.43202818223706 1 16.3406841962651 805 1326 59 58 395 693 1085 1223 1515 117 911 455 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 5.31000539935321e-08 3.06874196014832e-07 810 991.636363636364 807 4.82727775228869e-09 117 2.62330190914314 2.97217254719352 1 4.93286933325146 807 1719 1084 1796 404 373 312 117 2666 1383 247 456 M15422 BIOCARTA_VITCB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VITCB_PATHWAY.html Vitamin C in the Brain 22/24 BioCarta 1.04495013308457e-07 3.47825432169194e-07 145 1282.18181818182 808 9.49954711561216e-09 141 3.75655834516947 3.843960166021 1 7.00521021514599 141 2341 423 808 4291 764 1195 1969 431 1086 655 457 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 6.76155614445482e-08 3.14536172538656e-07 590 958.545454545455 808 6.14686941115168e-09 367 2.87460773675068 3.63677361041457 1 5.39661812726613 588 510 846 1192 672 1539 2185 477 367 1360 808 458 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 5.05325096317373e-08 3.0357704374324e-07 965 886.090909090909 808 4.59386461749407e-09 125 2.1847830370544 -2.08132073555578 -1 4.11109216034224 961 1293 664 125 369 782 1804 1485 808 535 921 459 M6487 BIOCARTA_PLATELETAPP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLATELETAPP_PATHWAY.html Platelet Amyloid Precursor Protein Pathway 21/29 BioCarta 2.36253649247603e-09 2.84666323415439e-08 115 1208.81818181818 810 2.14776045001192e-10 112 3.83962421770936 3.84124439667743 1 8.36536521973199 112 1795 314 1197 4131 650 1039 1925 533 810 791 460 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 2.40153398280315e-09 2.88428508876104e-08 320 1081.72727272727 814 2.18321271402244e-10 250 3.26940538734336 3.50442758429054 1 7.11752183944202 316 250 316 1162 3315 760 814 1698 1726 389 1153 461 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 1.77162989326438e-07 4.43266487055072e-07 815 1217.36363636364 814 1.61057275993757e-08 139 3.07095531453936 3.57556990721975 1 5.63316277578896 814 3135 1453 1482 1677 735 272 444 139 3020 220 462 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 1.47237276182445e-07 4.04988312110223e-07 60 1129 815 1.33852078214958e-08 57 1.88651262697163 2.14163689400184 1 3.48153183521279 502 1747 2256 3027 1484 273 57 59 815 1814 385 463 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 4.92328245204918e-08 3.0357704374324e-07 1060 961 816 4.47571142020467e-09 338 2.20252650770754 2.41694262345498 1 4.1444869298648 1059 1117 483 369 338 796 1691 816 1916 658 1328 464 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 1.32543469315579e-07 3.83038247822062e-07 230 1170.90909090909 817 1.20494070273573e-08 230 3.22866680382949 3.44155968665445 1 5.98163334601411 230 1628 428 533 3500 803 817 2105 518 1141 1177 465 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 1.40951829049279e-12 2.8310324813302e-11 560 680.545454545455 818 1.28138026408518e-13 22 3.0349715297182 3.22869191203214 1 9.24336253739811 556 22 183 350 884 824 922 1077 1341 509 818 466 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 8.78503265470718e-11 1.29579231656931e-09 760 1227.09090909091 819 7.98639332277996e-12 253 3.6731578439935 4.01869949339798 1 9.42586537311174 253 1656 256 758 4166 812 819 1825 900 758 1295 467 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 5.38086762443797e-08 3.06874196014832e-07 775 978.636363636364 821 4.8916979600417e-09 418 2.47775011727532 2.58839486258821 1 4.65912526465017 774 1446 577 622 418 673 1008 1513 1974 939 821 468 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 3.1918655421018e-16 9.78286062254578e-15 210 1030.18181818182 821 2.90169594736526e-17 111 3.85087586955868 4.10299513945345 1 15.5776751045225 209 1539 111 697 3051 734 821 1658 880 387 1245 469 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 2.64096566893138e-06 3.46259943259892e-06 290 1235.72727272727 821 2.40088076295885e-07 288 3.23770992756126 3.55157425946985 1 5.10444215388978 288 1716 628 821 3527 807 1000 2241 362 1443 760 470 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 2.12820437928904e-07 4.90006081475329e-07 330 1233.63636363636 822 1.9347314410584e-08 326 4.19051089670591 4.12811751285952 1 7.63443519502893 326 1763 441 822 4006 679 509 2678 417 1096 833 471 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 1.75129504215627e-07 4.41094589059637e-07 440 1026.63636363636 824 1.59208652869722e-08 318 2.32639702282211 2.36027874290126 1 4.26861715734743 439 375 860 2266 1664 318 561 1189 2448 824 349 472 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 7.24620211663409e-36 9.77202114014655e-34 795 1357.63636363636 824 7.24620211663408e-37 22 2.85348671950387 2.93850394745682 1 27.1988957972966 824 1008 4551 470 720 792 1416 794 2790 22 1547 473 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 2.0104000860954e-05 2.28983793590016e-05 825 1326 827 1.8276531433934e-06 336 1.95107980696166 2.17435719759026 1 2.6134345077872 822 827 1824 2380 4108 791 414 336 615 1630 839 474 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 9.22917871013514e-07 1.3997983133624e-06 515 1039 827 8.39016598350258e-08 47 3.55980547771158 3.79119587747504 1 6.01665904644035 513 1875 1036 859 3562 564 463 47 827 1584 99 475 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 7.7162768374742e-07 1.21382269161171e-06 830 1215.45454545455 827 7.01479958534669e-08 560 2.33323030334587 -2.52580920244684 -1 3.98495991646397 827 560 1123 1264 2871 747 680 1524 2295 796 683 476 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 4.64324200509689e-08 2.99073619127066e-07 2490 1465.18181818182 827 4.22112918463229e-09 18 2.36714535142318 -2.49430304866558 -1 4.45875082737488 2488 18 572 158 294 2268 3299 2703 2949 827 541 477 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 4.04749215883754e-08 2.9351990282604e-07 210 995.727272727273 829 3.67953839391095e-09 207 2.7529629595671 3.09732577092379 1 5.19208797331923 207 1476 399 829 1546 561 730 1331 2269 844 761 478 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 6.97998125858878e-07 1.12384048690412e-06 700 926.363636363636 831 6.34543952103775e-08 64 2.44185194153103 2.6608242313679 1 4.19410323842931 699 64 708 872 2797 337 831 1042 1311 1050 479 479 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 3.21211631365535e-08 2.72193698392339e-07 1395 1227.90909090909 831 2.92010578232177e-09 75 1.68533203133584 -1.27934272384163 -1 3.1941449289639 1395 663 2427 2717 75 831 524 543 318 3014 1000 480 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 7.42022897832567e-07 1.1760739011987e-06 495 1466 832 6.74566498276814e-08 492 3.17658231164834 3.3399844339478 1 5.43823082420322 492 602 503 1582 2845 832 1775 2006 4133 653 703 481 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 1.41292576269143e-07 3.97437997610461e-07 830 1004.27272727273 833 1.28447804857731e-08 354 2.75887447796955 2.95289904114111 1 5.09837255925506 828 626 738 1577 1444 859 354 1573 833 605 1610 482 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 5.94223980938578e-08 3.10399797613433e-07 985 940.909090909091 833 5.4020363362607e-09 37 2.61841539671996 3.23537494681501 1 4.9199280282142 984 37 452 1241 527 1503 2069 833 1260 673 771 483 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 7.96283683369676e-08 3.27123182997709e-07 2515 1364 835 7.2389428380994e-09 198 2.88936323077569 3.4312821259739 1 5.41010579665352 2511 475 743 1233 835 3255 3733 198 356 898 767 484 M5882 NABA_PROTEOGLYCANS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_PROTEOGLYCANS.html Genes encoding proteoglycans 22159717 19/35 Alexandra Naba 3.349778186585e-06 4.28481112213583e-06 440 1305 835 3.04525753368794e-07 440 5.14842108309094 5.20433652674941 1 7.9797385173389 440 1860 623 1762 3626 1198 567 583 790 2071 835 485 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 8.61814701212596e-08 3.28305665915602e-07 755 806.545454545455 836 7.83467940884371e-09 93 2.25630237185877 2.54702018821144 1 4.22353932751157 836 108 931 752 941 783 1459 93 917 1299 753 486 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 4.26055609799119e-08 2.95390421094817e-07 1165 834.818181818182 836 3.87323289136529e-09 21 2.93475562582959 3.09246861863778 1 5.53266781160559 1164 812 1332 431 230 1401 836 848 21 1602 506 487 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 8.07948141030185e-24 5.37114820515841e-22 790 1184.72727272727 837 8.07948141030188e-25 39 2.75736257873767 2.98706734954179 1 16.9348498004394 788 1024 4571 476 766 596 1379 932 1624 39 837 488 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 7.6413014313098e-08 3.24764325922831e-07 170 1343.09090909091 839 6.946637906106e-09 168 3.04285593421081 3.13551454157665 1 5.70031624776189 168 2173 415 1225 3788 606 748 1486 2528 839 798 489 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 1.90174644595363e-07 4.61503507706999e-07 895 1039.90909090909 839 1.72886055486033e-08 8 2.29556309713389 2.28140353291833 1 4.19900867970739 893 8 544 839 1739 762 1429 390 3043 466 1326 490 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 3.90024972068903e-10 5.27483629846769e-09 1875 990.636363636364 839 3.54568156489135e-11 57 3.4706629822069 3.47826159870292 1 8.29516921755998 1874 387 281 165 57 1412 1584 839 1612 363 2323 491 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 4.02127282109447e-11 6.34796244667756e-10 135 1187 840 3.65570256469816e-12 131 3.70849376936582 3.90917557467401 1 9.84841784186201 131 2164 238 1206 3910 840 674 1267 761 1149 717 492 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 1.9217963948773e-07 4.64778897147911e-07 305 1186.81818181818 841 1.74708778432242e-08 302 3.33846234191042 3.49328903002956 1 6.10409432045279 302 1686 437 789 3232 841 719 1999 1172 802 1076 493 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 9.57748944739109e-07 1.44196970308408e-06 145 1366.54545454545 842 8.70681237896546e-08 145 1.74070135760085 1.88377713474187 1 2.9351530435583 145 1238 2404 2799 3022 450 432 721 2159 842 820 494 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 1.10219875569726e-06 1.62219461393547e-06 845 1567.81818181818 842 1.00199937081691e-07 437 2.97063412342182 3.48745436724028 1 4.96578743131462 842 695 1189 3294 3099 505 754 644 3510 2277 437 495 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 3.40317468004994e-08 2.77395498531109e-07 845 1087.36363636364 844 3.09379521153961e-09 97 2.18809163451412 2.46604097156932 1 4.14206820392711 844 2016 713 1856 97 786 1407 820 1570 599 1253 496 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 1.45128637982173e-06 2.03507775185934e-06 515 1610.27272727273 845 1.31935212472806e-07 64 2.68901971159245 2.6210927178493 1 4.41848447999462 511 3963 2018 1674 3309 713 606 64 552 3458 845 497 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 7.71754639306512e-07 1.21382269161171e-06 310 1129.54545454545 846 7.01595372760265e-08 309 2.31519023044717 2.45161860271437 1 3.95414233894545 309 2227 1130 1043 2872 694 744 754 570 846 1236 498 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 1.62376001270616e-13 3.66705610525028e-12 460 944.272727272727 847 1.47614546609662e-14 159 2.60183952419221 2.76112055880912 1 8.59097578170418 459 2039 159 540 847 808 982 1239 1594 344 1376 499 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 5.43057232185431e-06 6.68552461115085e-06 850 1707.18181818182 847 4.93689611541204e-07 330 2.87506780255558 3.023600924865 1 4.29539827195894 847 3429 1605 3689 3781 753 555 330 710 2402 678 500 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 9.49395551097056e-08 3.37690052839345e-07 500 1046.54545454545 850 8.63086901879635e-09 496 2.4251872592179 2.72466798848771 1 4.53116525657199 496 2532 656 1214 1041 850 742 692 1549 1017 723 501 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 2.26554452491789e-07 5.06973463057442e-07 685 1400.81818181818 853 2.05958614383828e-08 44 2.71836617796851 2.84038758272352 1 4.94051753092071 682 3863 705 2545 1922 61 617 853 1911 2206 44 502 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 1.77597378904298e-29 1.58162194043073e-27 30 865.818181818182 854 1.61452162640272e-30 28 3.40482954397911 3.86999946547869 1 26.3495955988066 1264 1271 30 28 854 1270 2361 1100 475 124 747 503 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 3.35949765113522e-08 2.75770937623621e-07 2215 1084.81818181818 854 3.05408882039659e-09 94 2.96620104268848 3.50082245121593 1 5.6175243703295 2212 436 854 183 94 1717 2345 778 416 1461 1437 504 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 1.2673285196017e-07 3.75976782685104e-07 50 756.090909090909 855 1.15211690237021e-08 15 1.92553291199826 2.05996760869963 1 3.57151032675393 50 1343 982 1611 1347 15 71 230 1545 855 268 505 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 1.61317998237438e-07 4.22307793500114e-07 265 895.363636363636 857 1.4665273642391e-08 265 2.07374641781653 1.92029884311024 1 3.81626400640256 265 1354 857 1033 1587 307 394 405 1568 603 1476 506 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 1.06644742712294e-07 3.48348225330125e-07 760 820.909090909091 857 9.69497708017146e-09 290 2.72614388849976 2.94870864048586 1 5.08294903027326 760 1615 890 857 1178 290 714 302 892 974 558 507 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 8.0783898576432e-08 3.27390259462129e-07 290 1122.54545454545 857 7.34399104934664e-09 84 1.67439352642188 -1.65645818887318 -1 3.13463686273776 287 1323 2406 1838 857 84 427 414 2592 1820 300 508 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 4.08644831124284e-08 2.9351990282604e-07 915 911 858 3.71495307922516e-09 198 2.05925468633232 2.41500070483633 1 3.88353717076441 913 1083 637 384 198 286 2532 1797 872 858 461 509 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 5.33605255090551e-07 9.1105962302715e-07 690 1183.45454545455 859 4.85095804104907e-08 165 2.71035330129044 -2.83620354687197 -1 4.72671850097444 689 1830 1131 1006 2619 648 369 859 2891 811 165 510 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 3.76345980592015e-08 2.87575261955407e-07 1220 807.818181818182 861 3.42132715481844e-09 148 2.12974138901627 2.2821548802461 1 4.02196198956151 1218 200 1262 380 148 688 1037 861 542 1466 1084 511 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 4.94053523016099e-07 8.56692561585236e-07 615 1233.36363636364 863 4.49139667241479e-08 282 3.36771745123589 3.49261776031798 1 5.8993234199697 612 2212 475 1659 3121 448 559 1284 2052 863 282 512 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 6.11895301811565e-07 1.01175656916164e-06 1050 1192.45454545455 863 6.11895470298766e-08 52 4.87985149798457 5.62164956740293 1 8.44674615620334 1046 863 4550 300 2778 1028 841 184 52 1042 433 513 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 4.34382683397534e-08 2.97164560412799e-07 1195 1089.45454545455 864 3.94893356340249e-09 76 2.05463852420759 -2.35258938486901 -1 3.87164984452813 1195 745 2292 1254 247 864 470 1574 76 2672 595 514 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 1.94950702155261e-30 1.87789247790374e-28 545 1035.63636363636 865 1.77227911050239e-31 14 3.44042864294249 3.58770249334324 1 27.5444935650445 544 14 26 1567 569 865 1364 1040 3574 77 1752 515 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 7.72486961316317e-09 8.51901508741359e-08 35 1175.27272727273 865 7.02260876389776e-10 33 1.88425093992973 1.87139216287915 1 3.84574441586758 33 1430 667 1359 3561 143 164 865 3136 229 1341 516 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 1.06367584867169e-07 3.48348225330125e-07 865 992 865 9.66978090999316e-09 486 2.93685971098787 2.70398080210566 1 5.47589941147855 865 1578 748 576 1173 855 1562 841 913 1315 486 517 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 5.80994527988588e-08 3.09852566478612e-07 1470 975.454545454545 867 5.28176857574529e-09 4 3.19609977931938 3.72567915592161 1 6.00627783703396 1467 713 899 520 2535 1638 1851 4 157 867 79 518 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 8.1601782753481e-08 3.27411388472988e-07 3400 1757.54545454545 868 7.41834416183925e-09 460 3.5208139591099 3.3631385035128 1 6.59224710522803 3399 682 596 1326 868 3525 3024 3943 460 656 854 519 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 9.9274894125254e-09 1.06737471587972e-07 870 828.909090909091 868 9.0249904157483e-10 225 2.64789064850073 2.74866959523225 1 5.3298004016923 868 1393 354 800 225 477 1017 1073 1420 595 896 520 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 2.19483097536798e-12 4.24573860808888e-11 600 1260 873 1.99530088670016e-13 192 3.5843556851478 3.91540062986221 1 10.7345578276175 597 373 192 710 3883 1146 1324 2289 873 646 1827 521 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 1.04824576030702e-06 1.55637621536619e-06 110 1259.18181818182 873 9.52951145246013e-08 109 1.90003387335635 2.06937633488874 1 3.18570398477525 109 2942 1155 1697 3067 220 283 512 2196 797 873 522 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 2.51997313212764e-08 2.37410642388073e-07 1420 850.363636363636 873 2.29088469181134e-09 20 2.56457811530874 2.7329833431657 1 4.9049683424295 1417 389 873 157 20 738 1111 1769 1641 975 264 523 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 1.17041449082888e-07 3.62490577212093e-07 505 898.818181818182 874 1.06401323008701e-08 118 2.78757450326802 3.05593704262299 1 5.18359495206147 503 2161 778 874 1275 118 357 1140 995 1452 234 524 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 2.10278564961716e-07 4.86526875793773e-07 690 902.636363636364 877 1.91162350054899e-08 42 2.46340766761245 3.0276873847466 1 4.4897779402085 686 42 806 877 1853 310 1236 1247 1096 1561 215 525 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 6.23857351331001e-18 2.39398918559539e-16 880 1279.63636363636 879 6.23857351331005e-19 70 2.53079077569474 2.6651046465991 1 11.4149062807509 735 1042 4602 494 588 625 1517 879 2644 70 880 526 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 1.07972913989423e-05 1.27109265058889e-05 325 1333.18181818182 880 9.81576762808912e-07 322 2.07801199882114 2.30149222731091 1 2.93690454954767 322 2348 1410 1626 3964 779 1499 361 707 880 769 527 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 3.07497780633319e-08 2.6944556055963e-07 945 774.818181818182 881 2.79543440846607e-09 55 2.50900814995477 3.25225400435712 1 4.75884047796327 943 580 1097 990 55 1258 825 290 363 1241 881 528 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 5.91665355074513e-08 3.10257041482984e-07 885 749.454545454545 883 5.378776099879e-09 165 2.3389046193712 2.54069436653149 1 4.39477821740096 884 445 1103 1019 517 571 883 165 1210 1015 432 529 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 7.50571704541738e-08 3.23844645192172e-07 905 1404.27272727273 885 7.50571729892844e-09 1 2.31458612585418 -2.31458612585418 -1 4.33663330553489 901 1953 4260 3581 885 312 1 197 736 2555 66 530 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 5.70562777946667e-11 8.65934505436742e-10 390 1175.63636363636 885 5.18693434510423e-12 247 3.93639434686405 4.23082827399505 1 10.300408821623 390 1709 247 791 3775 930 1463 1610 885 482 650 531 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 9.40188568132372e-07 1.42324889082258e-06 100 998.454545454545 886 8.54717245391029e-08 97 2.30888901109485 2.28136424182901 1 3.89729032215445 97 1453 752 886 3003 486 324 976 1054 708 1244 532 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 1.1310398471375e-05 1.3283175114429e-05 300 1255.36363636364 889 1.02822332905204e-06 254 2.01972725685597 2.12065838912739 1 2.84335115876792 300 779 1693 1475 3977 433 254 889 732 1969 1308 533 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 9.6968616307389e-07 1.45437517944352e-06 555 1361.72727272727 892 8.81533264072064e-08 462 2.56090813022812 2.5878761375101 1 4.31583209655217 553 2202 892 1877 3034 541 462 750 2265 734 1669 534 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 3.53703603549802e-08 2.82884790943581e-07 520 1144.63636363636 893 3.215487356695e-09 110 2.42356587303642 2.34313249674495 1 4.58195902151696 519 1524 893 3258 110 389 290 659 2763 1024 1162 535 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 4.53971092042801e-06 5.65516905368704e-06 280 1266.72727272727 893 4.1270184437919e-07 278 3.70412278552181 4.01435276231667 1 5.61201877912836 278 2264 536 1204 4024 665 893 1734 330 1528 478 536 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 9.13970627602577e-07 1.3902485859762e-06 320 1197.27272727273 893 8.30882733912587e-08 296 2.71598059381362 3.01397732932435 1 4.5925831532497 317 2221 571 1258 2988 514 296 1092 2187 833 893 537 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 2.2018450147964e-11 3.60857932980522e-10 900 936.818181818182 900 2.00167728619858e-12 141 2.45664444742739 2.64815004708747 1 6.69768045659002 900 1207 227 141 677 818 1331 1184 2431 297 1092 538 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 2.39058801933513e-35 3.13432651423939e-33 1025 1081.90909090909 900 2.39058801933513e-36 18 2.65817312569716 3.08135005211598 1 24.9486237002108 1024 1021 4625 18 204 411 1641 900 1244 23 790 539 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 5.00387287669385e-07 8.65395272138755e-07 1090 1216.72727272727 902 4.54897637710811e-08 6 1.7903163585992 -2.15865642910678 -1 3.1334737509419 1087 561 2286 1216 2582 672 902 273 98 3701 6 540 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 5.04695726316161e-11 7.70926805246692e-10 310 1262.81818181818 903 4.58814296661582e-12 245 3.32574292887821 3.60206741557016 1 8.7508475204764 306 1528 245 1176 3076 751 829 2218 2289 570 903 541 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 3.94139993179138e-08 2.9351990282604e-07 120 1236.09090909091 904 3.58309091127579e-09 120 3.76186431928397 3.85537693198414 1 7.09519153268727 120 2257 397 1242 4044 494 331 1928 1429 904 451 542 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 8.38837477399151e-08 3.27411388472988e-07 515 1698.63636363636 905 7.62579553984695e-09 218 1.52031181678792 -1.57136865876484 -1 2.84608849227129 515 2278 3032 3890 905 288 218 255 3946 2754 604 543 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 9.26080865568494e-07 1.40414445405824e-06 590 1215.81818181818 905 8.41892050362381e-08 145 2.66153480387932 3.07209030594677 1 4.49718121789877 586 578 937 2268 2997 718 625 145 2468 1147 905 544 M11184 REACTOME_ENDOGENOUS_STEROLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOGENOUS_STEROLS.html Genes involved in Endogenous sterols 6/15 Reactome 1.67992357455689e-07 4.30615063556468e-07 885 1302.72727272727 908 1.67992370155334e-08 255 2.97627725184635 3.3663791008966 1 5.4702729502647 885 908 4226 2277 1717 632 255 1280 584 1082 484 545 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 2.8685931812315e-07 5.80421217529276e-07 1120 1110.54545454545 908 2.60781232297196e-08 86 2.06906997032335 -2.14771640756873 -1 3.72513655476883 1117 786 1878 2264 2157 646 908 356 239 1779 86 546 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 8.9745014969373e-08 3.31497675696653e-07 645 1139.81818181818 908 8.15863805730531e-09 517 2.4403634979037 2.79344443212854 1 4.56518973061427 645 1534 908 856 982 517 891 1957 1284 2429 535 547 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 6.25647503584864e-09 6.99776354720511e-08 1765 933.636363636364 909 5.68770459421919e-10 184 2.66412518864122 -2.85865267568275 -1 5.5035411352585 1763 184 339 315 335 909 1656 2297 1235 223 1014 548 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 3.43179008847517e-55 2.02475615220035e-52 685 891.909090909091 909 3.1198091713411e-56 4 3.26723825567149 3.46884874634753 1 48.7700929703219 685 1090 4 909 748 962 1678 451 1997 24 1263 549 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 6.64040163371245e-08 3.14536172538656e-07 1305 1072.18181818182 910 6.03672894013088e-09 216 1.87510690459178 1.86648903268428 1 3.51991504382142 1303 216 1484 2115 650 717 916 722 2131 630 910 550 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 6.45353012696824e-08 3.14536172538656e-07 915 1726.63636363636 911 5.86684574207051e-09 464 1.65759063128979 1.62581979498784 1 3.11149771421951 911 2131 3334 3626 618 464 677 667 2773 3037 755 551 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 2.68878315103336e-09 3.16485198824874e-08 795 945.090909090909 915 2.44434832210865e-10 321 2.71949030310311 3.00874069886484 1 5.88854819718245 793 1327 321 1157 1107 601 1250 814 1254 857 915 552 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 5.36408037353209e-08 3.06874196014832e-07 860 1642.36363636364 915 5.3640805030122e-09 5 4.33944334092448 5.22685424916779 1 8.16047327960289 858 1946 4485 2730 3716 915 67 5 346 2473 525 553 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 3.49610975132529e-08 2.81118194655117e-07 915 827.272727272727 915 3.17828164262126e-09 106 2.13342049848947 -2.25316549745028 -1 4.03498727212905 915 439 1164 1362 106 1155 1254 369 466 759 1111 554 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 5.68400834527141e-08 3.09084324765911e-07 820 1192.81818181818 915 5.16728044738705e-09 166 1.91771996489541 2.09764026024264 1 3.60413215471736 819 1728 1689 2154 481 555 915 777 2698 1139 166 555 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 5.0417069491852e-37 7.21116872731943e-35 490 945.909090909091 916 4.58336995380475e-38 15 3.27902246109512 3.54596721238359 1 32.3269809420149 486 1182 15 914 1692 916 1279 351 2169 95 1306 556 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 7.20164054409922e-07 1.15045683784203e-06 400 1130.18181818182 916 6.54694809230716e-08 280 2.38137213098091 2.19913250456809 1 4.08321185310566 397 851 1204 2525 2819 488 280 309 1522 916 1121 557 M12868 KEGG_PATHWAYS_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PATHWAYS_IN_CANCER.html Pathways in cancer 338/425 KEGG 7.52689983184662e-08 3.2415116064157e-07 935 961.181818181818 917 6.842636444878e-09 204 2.20889016925346 2.50846645724132 1 4.1382988321332 933 2003 792 447 779 204 1342 1482 1269 917 405 558 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 2.54080912713862e-18 1.02501017778584e-16 355 1036.72727272727 919 2.30982647921693e-19 81 3.65873707138846 4.13491516638827 1 16.8920042961921 355 261 81 919 3397 1152 1301 1727 797 193 1221 559 M69 PID_REELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_REELIN_PATHWAY.html Reelin signaling pathway 18832364 42/47 Pathway Interaction Database 6.67546978225024e-08 3.14536172538656e-07 1085 1401.09090909091 920 6.06860907709485e-09 292 1.69727739392847 2.00836861584115 1 3.18601518075834 1082 2677 2616 1726 655 748 703 292 512 3481 920 560 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 3.84868232415047e-08 2.90188188019013e-07 950 888.454545454545 921 3.49880217407215e-09 164 4.0266196784439 -3.71977731792314 -1 7.60036763801785 948 1730 419 921 164 785 1280 1290 804 1071 361 561 M1084 REACTOME_TRYPTOPHAN_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRYPTOPHAN_CATABOLISM.html Genes involved in Tryptophan catabolism 5/11 Reactome 3.19591229610309e-06 4.11475887550643e-06 975 1365.09090909091 922 3.19591689234732e-07 44 3.95748590770674 -3.95748590770674 -1 6.15376083970982 975 922 4264 2057 3649 742 106 155 44 1845 257 562 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 6.6720824789818e-16 1.94396477165396e-14 130 1112.72727272727 922 6.0655295263471e-17 119 3.24064892782815 3.46049331906374 1 12.8299590919806 130 2100 119 922 3214 903 776 1201 1461 236 1178 563 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 5.91765868258717e-07 9.88527179765794e-07 925 1545.54545454545 925 5.91766025842855e-08 395 2.48729782869743 2.0882369374366 1 4.31219437505178 921 1929 4348 1790 2752 586 395 925 572 2142 641 564 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 2.52307251479256e-06 3.33116147407577e-06 550 1270.18181818182 926 2.29370491671437e-07 123 1.97365802898577 2.19281289291548 1 3.12083135631987 546 790 2020 1729 3503 471 123 375 1518 1971 926 565 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 1.1072462139438e-07 3.54078735082299e-07 215 1047.09090909091 926 1.00658751788255e-08 215 1.82623099269847 -1.99394909676554 -1 3.40102243389223 215 2195 1881 1595 1217 500 735 260 926 1465 529 566 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 3.95953374741799e-08 2.9351990282604e-07 375 1169.81818181818 927 3.59957619880111e-09 280 3.14413312066013 3.53935032986878 1 5.92995725927562 371 280 398 772 2907 908 1176 2800 1081 927 1248 567 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 1.49806724729219e-05 1.72966668474049e-05 885 1421.27272727273 929 1.36188858938493e-06 228 3.50026795481489 3.64153502342794 1 4.81237905193939 228 2314 883 1276 4047 737 881 1971 929 1706 662 568 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 2.73485387042484e-13 5.97616216129873e-12 160 1099.18181818182 930 2.48623079129562e-14 156 3.25707407973881 3.30311448236297 1 10.5552118450423 156 2150 166 1153 2774 628 930 1522 1464 364 784 569 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 3.37173271755564e-07 6.46203257714034e-07 1395 1081.81818181818 931 3.06521203119042e-08 258 2.58420539030207 2.73784492326694 1 4.61800313216634 1394 406 839 386 2294 1351 931 1439 258 699 1903 570 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 2.25147539305772e-07 5.05548030396173e-07 200 1031.09090909091 932 2.04679602133934e-08 65 1.95282772054973 -1.91924971213678 -1 3.54963019084371 198 65 932 1786 1916 506 578 1693 2263 376 1029 571 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 2.59172717392571e-11 4.2037636635496e-10 130 1333.36363636364 932 2.35611561268749e-12 128 4.24398295981473 4.58602900191681 1 11.4899693460393 128 2265 230 932 4432 1127 1210 1985 649 792 917 572 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 1.87567568657458e-07 4.5777497636445e-07 2010 1422.45454545455 933 1.87567584489176e-08 27 3.90909395927529 4.07664785619221 1 7.15503664900371 2010 933 4604 398 1826 1875 847 601 27 2217 309 573 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 5.11403258432481e-07 8.81923047059302e-07 300 1214.09090909091 934 4.64912161192081e-08 296 2.80337214500953 3.02589504747039 1 4.90039538287529 296 2569 486 1618 2593 537 667 1478 1263 914 934 574 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 1.03842092509851e-15 2.91746831337202e-14 10 1075.54545454545 934 9.44019022816829e-17 8 1.74426306350777 1.7750154276399 1 6.81645566183389 8 1146 934 2271 3382 134 103 581 2124 89 1059 575 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 8.58217002520817e-08 3.28305665915602e-07 1355 1195.63636363636 935 7.80197305454313e-09 40 2.34204866998428 -2.13337954008375 -1 4.38407929865951 1352 40 624 845 935 822 1399 2093 2972 648 1422 576 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 1.09398648775861e-11 1.88453146796374e-10 145 1061.18181818182 935 9.94533170694593e-13 144 3.71511611937972 4.12675264651958 1 10.4318300552928 144 1609 216 692 3940 980 992 1227 389 549 935 577 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 2.56527391545984e-23 1.65864286040691e-21 3805 1552.63636363636 936 2.33206719587258e-24 36 3.05860975305675 -2.82721105785981 -1 18.3526100039064 3803 1360 46 36 607 3692 4068 1852 936 142 537 578 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 3.14248817848179e-08 2.69553239732593e-07 2570 1125.45454545455 936 2.85680747579019e-09 66 2.56156291774953 -2.5191775463291 -1 4.85841089337509 2567 493 1275 368 66 2233 1625 860 183 1774 936 579 M5372 REACTOME_XENOBIOTICS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_XENOBIOTICS.html Genes involved in Xenobiotics 4/46 Reactome 5.9463095763485e-07 9.91751985878619e-07 860 1297.54545454545 937 5.94631116748599e-08 14 6.51328016735445 -6.51328016735445 -1 11.2907189585994 856 937 4224 973 2757 698 14 211 28 2214 1361 580 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 2.34515336381578e-08 2.26826308959231e-07 435 1161.18181818182 938 2.13195762619511e-09 387 3.59725622080838 4.06785500187409 1 6.90097214314338 433 506 387 830 3584 1074 1318 1958 769 976 938 581 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 9.043027734641e-11 1.32145792283299e-09 450 1271.63636363636 942 8.22093430455702e-12 258 3.88656945466913 4.41860149858821 1 9.96400141713816 450 1652 258 835 2520 942 1043 2393 2090 892 913 582 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 4.20627671197706e-20 2.02588021229916e-18 465 1073.09090909091 943 3.82388791997914e-21 69 3.03906267631674 3.54631359749114 1 15.5263711646373 462 2051 69 525 1770 943 1197 735 2068 396 1588 583 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 2.05208781871302e-08 2.04342922032183e-07 560 963.454545454545 944 1.86553439804929e-09 234 2.62890374777903 2.59995079828994 1 5.0774684493789 559 234 381 944 1159 1071 1593 650 2315 300 1392 584 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 1.83296400517884e-17 6.81227567279064e-16 1125 966.636363636364 944 1.66633091379894e-18 89 3.04059217710747 3.72681552712336 1 13.3157257749996 1122 1366 89 283 1231 1484 2275 751 925 163 944 585 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 6.07673134801036e-06 7.42292235057166e-06 880 1779.18181818182 944 6.07674796507306e-07 21 3.34079442951423 -3.34079442951423 -1 4.94750547996056 877 944 4680 3564 3836 770 21 282 1785 2219 593 586 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 2.49309220506515e-07 5.33829325923706e-07 445 1295 945 2.26644771598938e-08 113 1.80040993707426 1.91331573199423 1 3.26022479393372 604 113 2398 2567 2024 442 441 945 2401 1891 419 587 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 9.72472222244226e-08 3.39726302159777e-07 480 1458.63636363636 949 8.84065695664263e-09 294 1.29240480141586 -1.34451900900869 -1 2.4133233175474 479 492 3242 1111 1067 294 722 886 4160 2643 949 588 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 6.89978047975517e-08 3.15009389627869e-07 1405 1011.27272727273 949 6.27252790559134e-09 21 2.71959509969015 2.88931697896295 1 5.10504740874148 1401 21 411 402 949 2084 1987 314 1516 424 1615 589 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 2.03467239023355e-19 8.89227192768736e-18 65 1401 950 2.03467239023355e-20 11 1.81129332501342 1.84319224791441 1 8.91743210768172 11 2489 4692 1764 3225 63 56 472 1626 63 950 590 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 4.13918059167374e-07 7.44264091150478e-07 755 1073.90909090909 951 3.76289215494391e-08 115 3.37295827244891 3.65075127298955 1 5.96801401208415 753 2170 485 686 2468 967 951 115 1091 915 1212 591 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 1.16138872261666e-09 1.46180127220017e-08 245 1212.72727272727 953 1.05580793020887e-10 241 3.19288617827195 3.42693417371435 1 7.22304437394532 241 1631 301 825 3390 617 953 2101 1805 458 1018 592 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 1.81859586600693e-07 4.49883254064608e-07 605 1143.54545454545 954 1.65326910576214e-08 331 2.00035891647591 2.0400706862675 1 3.66531235176326 605 1206 1297 879 1703 331 751 850 3039 954 964 593 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 7.55773440592315e-08 3.24590595049657e-07 1750 1078.63636363636 958 6.8706678777787e-09 126 3.07217307996123 3.66090205374451 1 5.75545180587508 1749 822 946 1147 782 1763 1676 380 126 958 1516 594 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 1.93994953937041e-07 4.66108261912869e-07 590 1564.63636363636 958 1.76359064584933e-08 329 1.90234830430133 2.20897186864167 1 3.47723009554755 587 2609 2725 2156 1762 958 832 329 837 3933 483 595 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 2.32617958375165e-22 1.38981868801364e-20 1420 870.090909090909 959 2.1147087125015e-23 51 2.93954815102505 3.45086345442539 1 16.8545195484994 959 1245 51 673 767 1123 1420 598 1419 177 1139 596 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 8.66238764007501e-06 1.0324866076049e-05 855 1456.90909090909 959 7.87492886179268e-07 329 3.29849751819623 3.82106624585229 1 4.7483549052673 329 2312 852 1260 3913 959 952 2032 543 2023 851 597 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 8.2403358338044e-22 4.63028394470914e-20 960 1293.81818181818 960 7.49121439436761e-23 49 4.10828356588584 4.34504462421676 1 22.9360207144114 49 2113 55 923 4260 1264 960 1775 956 347 1530 598 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 8.31517446022663e-08 3.27411388472988e-07 4135 1867.09090909091 961 7.5592497950082e-09 337 3.06156637378517 -3.13281697704421 -1 5.73225587560258 4132 418 446 337 892 4512 4648 2541 1058 593 961 599 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 3.79415556384269e-07 7.01465501815021e-07 140 1002 963 3.4492329256264e-08 136 3.38787700043171 3.41175074433334 1 6.01957713577381 1099 819 963 136 2394 1027 425 1503 140 1598 918 600 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 3.85072389097046e-07 7.09091031152922e-07 670 1273.72727272727 963 3.50065869543092e-08 368 2.750406143489 -2.44284570049339 -1 4.88302796558632 667 368 790 1421 2403 396 963 2990 1773 1522 718 601 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 6.62717701991552e-08 3.14536172538656e-07 1675 1201.90909090909 963 6.02470656322681e-09 498 2.87643808873686 2.61222145374378 1 5.40005486999384 1674 498 709 958 647 1332 1411 2929 639 963 1461 602 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 2.96581747724819e-06 3.84789953067935e-06 1285 1278.72727272727 965 2.69620134133716e-07 103 3.89078907286301 5.10886888030667 1 6.08275260757103 1285 794 965 2573 3882 1324 484 103 165 1975 516 603 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 1.8730041541023e-07 4.5777497636445e-07 845 1383.18181818182 965 1.70273119414858e-08 267 2.52696340784559 2.94572073315457 1 4.62494008068092 845 2162 627 2553 1724 848 1560 871 2793 965 267 604 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 1.05482680334625e-06 1.56467080823203e-06 325 1246.54545454545 966 9.58933917364501e-08 102 2.19737217854524 2.36002813413726 1 3.682908222907 323 1820 1248 1859 3070 261 102 215 3413 966 435 605 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 8.05106302176411e-08 3.2731281190979e-07 4620 1842.72727272727 967 8.05106331345239e-09 55 3.05044636538624 2.22139883645966 1 5.71154764188642 4616 898 4297 120 967 3991 2289 412 55 1884 741 606 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 7.19190774724889e-09 7.96849872465135e-08 20 1125.27272727273 967 6.53809797341782e-10 18 1.90938392849488 1.96163579927212 1 3.91304877230124 18 2087 967 994 3593 128 110 664 2439 258 1120 607 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 1.23480136399526e-07 3.71755418903835e-07 970 1082.36363636364 967 1.1225467575467e-08 213 2.20682125198478 -2.45900717451278 -1 4.0964993229194 967 2088 816 750 1321 644 1649 983 1635 840 213 608 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 9.26009713032926e-08 3.3569630149888e-07 835 1040 968 8.41827047281751e-09 97 2.60616896157901 -2.15911565733806 -1 4.87130705935785 835 97 438 968 1013 810 1627 1960 2144 518 1030 609 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 3.14373624759811e-07 6.16726312912016e-07 2325 1499.27272727273 968 3.1437366923367e-08 129 1.78208970465024 1.9215676623038 1 3.19478078133052 336 1962 4455 1952 2324 129 500 968 2323 672 871 610 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 6.49952393827595e-08 3.14536172538656e-07 1630 1030.72727272727 969 5.90865830026661e-09 193 3.20960074657431 3.75659177197701 1 6.02561451650423 1626 411 692 193 627 1581 1687 969 814 1625 1113 611 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 4.01541229649152e-08 2.9351990282604e-07 360 1095.90909090909 970 3.65037488161847e-09 186 2.26377005255821 2.45367722048593 1 4.26931712602106 358 2085 1325 1229 186 690 830 970 1714 1931 737 612 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 9.96959507252712e-08 3.41896906035439e-07 4565 1934.45454545455 971 9.06326865846613e-09 298 2.8335658008291 -2.30936843974967 -1 5.2899160086026 4563 653 747 545 1102 4671 3676 298 484 971 3569 613 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 5.60336668521717e-07 9.45201709054455e-07 975 1317.63636363636 972 5.09397101126062e-08 324 2.62346628262689 2.90503617234906 1 4.56306022344783 972 324 805 2067 2655 1295 1652 837 2388 635 864 614 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 3.13486267181393e-08 2.69553239732593e-07 4240 2051.81818181818 976 2.84987519680343e-09 64 2.68318422736623 -2.3031506426555 -1 5.08912591770057 4240 291 533 536 64 3982 4706 3491 976 590 3161 615 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 8.03849747988503e-08 3.2731281190979e-07 980 1413.72727272727 976 7.30772524872791e-09 331 2.71222839897533 -2.6828256591053 -1 5.07818481153991 976 3002 611 2699 849 845 995 355 3826 1062 331 616 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 2.36603748177172e-16 7.49509859997485e-15 1065 1204.72727272727 978 2.36603748177172e-17 62 2.16922496172747 -2.02767449815099 -1 8.84710245840195 1062 978 4685 62 384 99 1782 1429 2059 82 630 617 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 7.34466454405327e-06 8.84132023665683e-06 405 1463.18181818182 980 7.34468881900996e-07 173 2.62354052418075 2.62354052418075 1 3.82758018491163 405 1939 4281 1082 3898 516 173 594 344 1883 980 618 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 2.98778455006973e-07 5.97810219428957e-07 980 936.454545454545 980 2.7161681416691e-08 286 2.72709109678056 3.03565611197851 1 4.90001068326089 1564 286 509 410 2189 1095 980 449 980 341 1498 619 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 6.06706202948537e-07 1.00584941268602e-06 985 1247.72727272727 981 5.51551245693943e-08 48 2.47936056658314 2.73082438584301 1 4.29302951908956 981 2351 1488 1037 2709 950 426 462 48 2462 811 620 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 1.34713520169548e-06 1.91809295686355e-06 435 1173.09090909091 981 1.22466911508466e-07 358 3.53453207172853 3.88939428953941 1 5.83430798433606 434 1653 559 1252 3220 763 981 1697 358 1271 716 621 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 1.52206293324848e-47 4.78942469662188e-45 985 1041.81818181818 981 1.38369357568044e-48 9 3.91289379401307 4.211022857638 1 50.076158599229 77 2033 9 910 3474 1076 1045 981 809 65 981 622 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 1.37463563534533e-08 1.4228684646557e-07 520 1111.81818181818 982 1.24966876721321e-09 3 2.13551224322011 -2.11360168283051 -1 4.22130545308766 518 3 525 982 1029 773 1149 2746 2784 238 1483 623 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 3.74348150455586e-08 2.87575261955407e-07 840 857.727272727273 983 3.40316506204936e-09 109 2.03547958330189 -2.22922355062864 -1 3.84391286511088 840 1286 1278 109 140 838 1169 1028 983 1002 762 624 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 4.67183943354953e-08 2.99073619127066e-07 1335 1169.36363636364 983 4.24712684796271e-09 295 2.71496917968244 2.72561594814059 1 5.11403774085629 1335 295 543 2515 297 983 894 1116 1899 523 2463 625 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 1.47994730617974e-07 4.06132387668711e-07 985 1272.81818181818 985 1.34540673248754e-08 118 3.23941251145246 3.74625321292997 1 5.97776072228107 985 856 1111 3595 1489 947 649 343 2493 1415 118 626 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 2.90160436966362e-08 2.61957344798642e-07 1720 1062.72727272727 985 2.63782218903018e-09 97 3.22350921896093 3.86014541725025 1 6.12567511533607 1717 363 392 97 174 2247 1592 985 1294 647 2182 627 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 3.0882956283426e-08 2.69553239732593e-07 990 1455.90909090909 986 2.8075415197229e-09 56 2.12473603631652 2.40006106945454 1 4.02975245437734 986 629 1857 3851 56 805 806 965 3422 1321 1317 628 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 7.71292725954022e-17 2.61609678054747e-15 1840 1285.54545454545 987 7.01175205412746e-18 94 2.95897108967966 2.89640265803361 1 12.4589529047237 1839 125 99 481 288 987 2768 3985 1567 94 1908 629 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 6.45183369699583e-11 9.69829778656698e-10 1280 1018.18181818182 987 5.86530336107731e-12 54 2.87106465903597 3.49443338474616 1 7.47171667067561 1280 54 250 931 987 1255 2149 1532 1609 438 715 630 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 1.07799140461717e-05 1.26988417950101e-05 600 1279.18181818182 988 9.7999698797197e-07 142 3.34966730898515 3.48181350447091 1 4.73509238040626 142 2290 600 1253 3962 428 599 2169 1003 988 637 631 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 3.1553298848006e-07 6.17717007725376e-07 335 1029.72727272727 989 2.86848212486453e-08 161 2.39004745623582 2.6769888599109 1 4.28448913066452 332 1785 1174 2308 2244 214 183 161 1513 989 424 632 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 3.03466486123131e-06 3.92535438339594e-06 625 1375.09090909091 990 2.75879004294111e-07 20 2.06847658828583 2.23853187277564 1 3.22822624540119 624 862 2057 2160 3585 615 20 358 2214 1641 990 633 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 4.17523812885996e-09 4.81836771839096e-08 55 1300.18181818182 991 3.7956710334399e-10 54 4.05151281054504 4.05151281054504 1 8.55964891788567 54 2285 329 1000 4476 895 991 1729 547 787 1209 634 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 2.91466782848031e-06 3.7846580881505e-06 235 1627.18181818182 991 2.64970153634751e-07 234 1.38653665220901 -1.40058441863281 -1 2.17000046170926 234 641 2665 1966 3568 275 262 908 4278 2111 991 635 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 1.06380876246546e-14 2.67083902065797e-13 1045 1076.36363636364 992 1.06380876246547e-15 99 2.19076487409334 2.19490850305217 1 7.95322488760003 510 1045 4334 291 979 140 1010 992 1395 99 1045 636 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 3.64726545858337e-08 2.8614986551519e-07 1220 996 993 3.31569592640863e-09 122 2.72134867535226 3.34940269937608 1 5.14113223800895 1219 398 744 617 122 1511 2304 1152 1064 832 993 637 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 6.54051870607877e-08 3.14536172538656e-07 1520 1308.27272727273 993 5.94592627320546e-09 408 2.64587575612941 3.02907177929318 1 4.96714173314733 1516 1358 408 993 2796 939 2182 2119 919 621 540 638 M18615 KEGG_ALLOGRAFT_REJECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALLOGRAFT_REJECTION.html Allograft rejection 29/70 KEGG 3.43354820999972e-07 6.52560643255266e-07 245 1309 994 3.12140795079544e-08 200 1.65294969144685 -1.65051776469811 -1 2.95149927441214 242 566 1937 1453 2316 200 513 1325 4095 994 758 639 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 2.41083610876035e-07 5.26812334877261e-07 1085 946.636363636364 994 2.19166942995287e-08 19 2.79245155492356 3.52221714210653 1 5.06174550277195 1085 269 994 1664 2527 814 1183 19 474 1314 70 640 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 2.0026989377938e-15 5.34053050078347e-14 1640 892 994 1.82063539799436e-16 83 2.58548674195972 2.96196529081626 1 9.90827328948017 1638 1193 131 83 331 597 1769 1263 1598 215 994 641 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 4.17835644061778e-07 7.49732596517966e-07 855 1428.36363636364 995 3.7985065765396e-08 319 1.64943820228411 -1.64460117975742 -1 2.91651342688852 319 579 1943 1464 2474 322 855 1665 4244 995 852 642 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 2.59332069816452e-07 5.47182552317235e-07 735 1056.27272727273 996 2.35756454896417e-08 393 2.6315911880344 2.87099123752813 1 4.75759136887816 732 1460 496 1224 2057 393 996 589 1713 1282 677 643 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 9.98043894774059e-07 1.48980619333762e-06 595 1445.09090909091 997 9.07313043221147e-08 403 2.17497011659655 2.51836526091191 1 3.6587257141766 593 2400 2028 885 3050 825 970 403 1207 2538 997 644 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 1.10508357304589e-07 3.53626743374685e-07 1000 1556.09090909091 997 1.00462148050493e-08 478 2.22275943526562 2.61796352630691 1 4.14002748256826 997 2768 1908 4131 1215 834 478 552 561 3149 524 645 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 6.87977383041655e-08 3.15009389627869e-07 3980 1758.81818181818 997 6.25434004141706e-09 96 2.74816782831623 -2.56652619154692 -1 5.1586913297175 3980 534 997 329 691 3582 3905 1453 96 986 2794 646 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 1.60897201594504e-07 4.22216547374584e-07 1100 1108.09090909091 998 1.46270193965215e-08 496 2.41370611687652 2.48622635420867 1 4.44209000486216 1098 1484 998 583 1581 1559 1762 496 841 817 970 647 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 6.45304408384503e-08 3.14536172538656e-07 1000 956.363636363636 998 5.86640388465987e-09 70 2.74515090555694 3.33390162054885 1 5.15354475858318 998 435 769 1776 616 1354 1003 70 1133 881 1485 648 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 8.68433936933422e-20 4.05842394289679e-18 550 974.909090909091 998 7.89485397212199e-21 70 2.92290913400509 3.04138163655234 1 14.6782362395706 547 1304 70 132 1356 867 1223 998 2516 139 1572 649 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 1.18614659372273e-08 1.24969016124359e-07 1000 1033.27272727273 999 1.0783150910163e-09 362 2.53660049898712 2.99984655281837 1 5.05558990216444 999 1385 362 372 1518 769 1873 1294 1442 487 865 650 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 1.96674189941202e-07 4.69668482590419e-07 640 1081.27272727273 999 1.78794734112143e-08 279 2.58332262744281 2.98877130075548 1 4.71980032999423 636 279 669 827 1776 804 999 2183 1561 1085 1075 651 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 9.66610662214582e-08 3.39696808054909e-07 1300 999.545454545455 999 8.78737004258553e-09 39 3.34749055187291 3.39615773550774 1 6.25221617532877 1300 723 865 399 1061 2047 1859 422 39 1281 999 652 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 1.1613484034283e-06 1.69761448690191e-06 650 1266.45454545455 1001 1.05577183317081e-07 402 2.22106854560671 -1.98161007830155 -1 3.69991918536853 646 1618 1190 1778 3124 402 511 817 2293 551 1001 653 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 1.5402135704102e-07 4.14706677258194e-07 1005 1244.81818181818 1003 1.40019425294556e-08 469 2.33667989827787 2.27484819950732 1 4.305565637165 1105 2096 659 1001 1528 469 933 1003 2573 912 1414 654 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 7.53059765660796e-07 1.18997057044491e-06 510 1121.18181818182 1005 6.84600021302907e-08 112 2.02931103795495 2.09594363280885 1 3.47083002359209 507 1287 1005 1403 2854 112 557 1422 1780 790 616 655 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 1.64614533463907e-06 2.27519940834448e-06 505 1504.09090909091 1006 1.64614655404785e-07 412 2.01858221374442 2.0213065912423 1 3.2884004291022 501 871 4404 2714 3365 566 412 505 1006 1040 1161 656 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 1.89603985415706e-05 2.16690269046521e-05 340 1643.09090909091 1007 1.72368745010355e-06 19 1.77915538594707 1.77915538594707 1 2.39538144656149 338 2842 2450 3132 4094 225 19 569 706 2692 1007 657 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 2.05838049158111e-07 4.82256251301052e-07 970 1236.18181818182 1007 1.87125516742625e-08 570 2.97939857862348 3.25543153146138 1 5.433691571862 968 1770 755 1368 1822 1007 1457 570 2347 837 697 658 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 1.31020432178297e-06 1.87487428343366e-06 295 1287.45454545455 1009 1.19109554733857e-07 89 3.01650923724754 3.08682354429571 1 4.98772389127956 295 2748 1009 2358 3200 269 159 89 1922 1873 240 659 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 5.09395145127764e-14 1.19619158457863e-12 25 1343.27272727273 1011 4.63086495570703e-15 21 4.43362712551872 4.43362712551872 1 15.262809177737 21 2225 153 984 4452 1011 937 1771 1227 588 1407 660 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 4.40094362338511e-51 1.88840490021616e-48 250 1260.90909090909 1012 4.40094362338507e-52 5 3.48423065259485 3.75129628389829 1 48.0151753077635 247 1012 4720 908 1589 954 1205 681 1486 5 1063 661 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 5.7318132897936e-08 3.09093308316432e-07 610 971.909090909091 1013 5.21073949011683e-09 380 2.21808050893774 2.52436497459963 1 4.16875176446389 610 2186 1450 1102 489 380 568 1013 1306 1200 387 662 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 4.57359787129263e-08 2.99073619127066e-07 360 1200.18181818182 1015 4.57359796542272e-09 359 2.16914018182595 2.32716519461824 1 4.08571659022073 1125 1015 4498 359 363 729 1616 497 1296 360 1344 663 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 4.98154492218391e-08 3.0357704374324e-07 1440 1467.54545454545 1018 4.98154503385496e-09 312 2.36516967568692 2.66176309477987 1 4.45059565094123 1439 1018 4494 509 441 888 2372 1675 2118 312 877 664 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 1.28458912377181e-06 1.84461839495069e-06 700 1538.72727272727 1018 1.16780897622667e-07 236 2.33284094285478 -2.59937450862945 -1 3.86185964555001 697 3144 1817 2307 3189 820 1018 236 269 2893 536 665 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 6.68596157697275e-08 3.14536172538656e-07 920 1443 1019 6.0781470728764e-09 244 1.71181907177057 -1.72860030989256 -1 3.21331922170225 918 244 2033 2400 657 603 1050 759 4085 2105 1019 666 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 2.98672383624098e-08 2.65971846975155e-07 1710 1530.90909090909 1020 2.98672387638332e-09 82 1.9226063749902 -1.76623556323492 -1 3.64953846185957 1709 1020 4670 547 82 787 2295 2284 1834 752 860 667 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 9.30646995786172e-08 3.35829802760759e-07 1135 1157 1021 8.46042759231391e-09 202 2.70501589843645 2.46252834245173 1 5.05596408105293 1133 202 431 286 1021 626 1161 3341 1119 732 2675 668 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 3.94854221417372e-07 7.20135983419627e-07 375 1248.27272727273 1021 3.58958447532278e-08 373 3.30341309537885 3.55380302895745 1 5.85859789895324 373 2189 462 1648 3014 960 808 1326 1234 1021 696 669 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 3.31760546833307e-12 6.16499913800477e-11 2510 1234.54545454545 1022 3.01600497121643e-13 31 2.35448773064808 -2.09439817431109 -1 6.94088059866212 2510 1079 202 31 853 1570 3357 2044 748 164 1022 670 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 4.5239480706098e-09 5.18277545953355e-08 1025 989.454545454545 1023 4.11268007264779e-10 309 2.60375972252014 3.07054861967522 1 5.4768606888795 1023 1292 332 1173 1737 392 1394 880 1888 309 464 671 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 1.39010107373657e-06 1.97153758053985e-06 770 1427.81818181818 1024 1.26372904735668e-07 171 2.25693667989406 -2.24433508111655 -1 3.71734344832072 770 746 2205 1024 3238 639 477 3001 171 2308 1127 672 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 4.64341743631646e-08 2.99073619127066e-07 1575 1224.90909090909 1025 4.22128866756588e-09 141 2.2885778249145 2.50530970569173 1 4.31073258433672 1572 141 707 1025 295 1999 2156 413 2564 573 2029 673 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 2.37558600598022e-07 5.22548577520102e-07 715 1237.45454545455 1025 2.15962387499894e-08 595 2.49193563429995 3.01436265593082 1 4.51946133990292 711 2524 595 1230 1967 1025 1723 1006 1372 856 603 674 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 4.61869571765268e-08 2.99073619127066e-07 1445 1075.45454545455 1026 4.19881437692537e-09 291 2.19907746731481 2.33874590033981 1 4.14211730176537 708 1445 1341 1442 291 449 1026 938 2138 1428 624 675 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 1.03870997767811e-08 1.10921065489608e-07 1620 1173.54545454545 1027 9.4428180234753e-10 232 2.54589706669687 2.90011880134394 1 5.11219456147688 1618 1302 357 297 232 921 2114 2862 1412 767 1027 676 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 1.88676574889778e-08 1.90289195187981e-07 25 1101.36363636364 1030 1.71524160461734e-09 25 1.89777031129558 1.9820672427456 1 3.68207511374654 25 1481 1030 1408 3791 154 122 669 1882 366 1187 677 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 2.85420875944137e-11 4.55130585964975e-10 1440 1180.18181818182 1032 2.59473523588945e-12 235 2.30006027902026 2.77322793567875 1 6.20377310292796 1438 1063 235 543 719 1760 2843 1032 2076 278 995 678 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 7.32402584047838e-08 3.2144561803028e-07 365 1221.09090909091 1033 6.6582055311843e-09 362 1.92957827169236 -1.90501108514139 -1 3.61693449648762 362 1461 1938 1476 749 695 942 1365 2426 1033 985 679 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 4.75683811232378e-10 6.41493596861949e-09 1215 875 1033 4.32439828486572e-11 174 2.26451715105296 2.3441787429728 1 5.35651081793169 1214 1159 344 327 453 473 1405 1218 1033 174 1825 680 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 8.40462157636776e-23 5.2197123474284e-21 680 1129.45454545455 1033 7.64056506942521e-24 49 3.25759760682796 3.52985015942187 1 19.0782975451307 676 2077 49 916 1033 1392 2020 476 2249 121 1415 681 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 6.273329923462e-08 3.14536172538656e-07 1035 1341.09090909091 1034 5.70302736576986e-09 88 2.38948011905585 2.32413691864027 1 4.48572294169082 1034 1706 1663 2564 580 578 1031 88 2845 2547 116 682 M13103 KEGG_AUTOIMMUNE_THYROID_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AUTOIMMUNE_THYROID_DISEASE.html Autoimmune thyroid disease 29/87 KEGG 3.28634900837345e-07 6.34679513892091e-07 370 1357.90909090909 1035 2.98759045389702e-08 293 1.72583644570229 -1.58321442426046 -1 3.08769691177487 366 567 1720 1450 2278 293 694 1705 3836 993 1035 683 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 1.53749047197837e-06 2.14132635814042e-06 705 1240.18181818182 1035 1.39771958769904e-07 93 1.95166083193136 2.01786931044218 1 3.19419514976283 703 93 1150 738 3299 1035 1271 1933 397 806 2217 684 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 2.16523143171483e-07 4.93714606651884e-07 1035 1138.63636363636 1036 1.96839240437826e-08 583 2.59357973350534 2.83925069980389 1 4.72230347577012 1033 676 767 1172 1879 1036 1132 1212 2095 583 940 685 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 2.47833747901538e-07 5.33004051263978e-07 2015 1201.09090909091 1036 2.25303432564033e-08 193 1.83027367318677 2.03449859834962 1 3.31467215938478 598 2032 2013 1073 2014 193 1036 1016 1656 854 727 686 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 3.1516789873833e-08 2.69553239732593e-07 30 1122.18181818182 1038 2.86516275684878e-09 30 1.85081636656821 1.90351177748113 1 3.5101281922445 30 2523 1305 1221 3722 131 152 638 1200 384 1038 687 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 6.29185543521067e-08 3.14536172538656e-07 1040 977.181818181818 1038 5.71986874104872e-09 264 2.46048861963741 2.60324829931917 1 4.61905136694521 1038 264 761 1335 586 682 1054 1623 1304 860 1242 688 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 8.37645623669517e-08 3.27411388472988e-07 1380 1183.09090909091 1038 7.61496050511556e-09 176 2.03536618637333 2.50235186432203 1 3.8105840166419 1380 1203 1038 1018 903 1010 2469 1242 1649 926 176 689 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 1.72711253930937e-06 2.37666798412252e-06 115 1351.54545454545 1039 1.57010354107505e-07 74 1.67623336717085 1.80099141652259 1 2.72137400256859 111 2133 2553 2149 3343 151 74 590 1704 1039 1020 690 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 1.48377717295457e-08 1.52913280706235e-07 140 1256.90909090909 1039 1.3488883481471e-09 137 3.74363206444857 3.90372632877909 1 7.36693841312041 137 2266 370 925 4049 1039 1065 1274 513 739 1449 691 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 1.26816758709335e-06 1.82659475467825e-06 270 1265.27272727273 1041 1.15288028919657e-07 169 2.090559719884 2.24990191085174 1 3.4632643771691 270 2310 1716 2605 3178 169 206 291 1041 1165 967 692 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 2.20663889114631e-07 4.98818753171004e-07 2680 1519.54545454545 1041 2.00603555679647e-08 192 3.01789635153558 -3.15856387201449 -1 5.49113329961486 2678 706 1041 318 1897 2922 4014 700 192 1279 968 693 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 1.05223140564213e-07 3.48348225330125e-07 140 947.909090909091 1042 9.56574050880909e-09 87 1.98255875505793 -2.07822790829035 -1 3.69628495258609 136 1514 1953 1042 1153 87 175 167 2246 1824 130 694 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 9.07292549787528e-07 1.38142607580553e-06 455 1470.81818181818 1045 8.2481174905488e-08 35 1.91815720056601 2.16341805101073 1 3.24478333080246 453 2987 2337 463 2984 44 517 1045 1853 3461 35 695 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 2.11153349209776e-05 2.39866139174523e-05 760 1544.18181818182 1050 2.11155355594767e-06 256 3.19426436405562 3.19355563254197 1 4.26060628778079 756 895 4271 1590 4143 1050 520 1074 256 922 1509 696 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 6.30359621333183e-07 1.0363279041075e-06 830 1164.90909090909 1050 5.73054365407609e-08 316 2.30429440511786 2.42447159294541 1 3.98121409590617 826 470 1257 593 2734 1222 1753 698 316 1895 1050 697 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 5.97199805312738e-30 5.52702564916887e-28 270 1156.81818181818 1050 5.42908913920677e-31 28 3.70486699931948 4.03745054789115 1 29.1601256719095 267 2067 28 911 3327 1437 1372 960 1050 113 1193 698 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 1.77099806151203e-07 4.43266487055072e-07 560 1074.09090909091 1051 1.60999836734294e-08 557 2.71882329100988 3.02449431681856 1 4.98713569179539 557 1470 706 814 1676 992 1208 1438 703 1051 1200 699 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 1.82212596241972e-75 2.15010863565527e-72 5 1917.63636363636 1051 1.65647814765429e-76 2 3.27007976128788 3.47644569928668 1 67.6735180486532 4054 1051 2 3 546 3719 4213 3622 596 6 3282 700 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 4.58691221837009e-08 2.99073619127066e-07 160 1306.90909090909 1052 4.16992028545942e-09 157 4.22612778752062 4.19881841772837 1 7.96100330059657 157 2317 401 1190 4219 799 1052 1949 348 1091 853 701 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 5.63394321334243e-07 9.48705385907109e-07 420 1061.90909090909 1053 5.12176786920913e-08 71 1.86114703860357 -1.91021623959976 -1 3.23602551786765 418 293 1633 1053 2661 115 253 1336 2330 1518 71 702 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 4.19069396197702e-08 2.95100601223086e-07 1055 1101.27272727273 1053 3.80972185618539e-09 91 2.51368052015234 2.91113960310928 1 4.73903334295843 1172 91 583 711 214 1053 1192 2878 1742 1052 1426 703 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 1.39998456502384e-06 1.98257640171392e-06 705 1463.45454545455 1055 1.27271405083098e-07 704 2.66934857729211 2.76318623918947 1 4.39490494504197 704 1650 1055 1246 3244 1005 833 2429 823 2243 866 704 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 1.67842169119714e-07 4.30551651220137e-07 4185 1951.45454545455 1056 1.52583801749739e-08 324 3.06729300803671 2.78363458028232 1 5.63763908823257 4182 601 451 508 1628 3655 4364 1056 324 399 4298 705 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 2.79970812399718e-07 5.71814034844946e-07 1160 1174 1056 2.54518952753326e-08 180 2.25917650273433 -2.80218325199922 -1 4.07171480953159 1156 843 2168 1056 2134 1180 498 245 180 2995 459 706 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 5.95393305061354e-07 9.92672695121721e-07 615 1194.54545454545 1056 5.41266787449711e-08 203 2.36424098920784 2.81947448540515 1 4.09756899897048 615 203 942 881 2693 1056 1471 1391 1297 1685 906 707 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 2.99738533157533e-07 5.98969465073478e-07 1060 1178.63636363636 1057 2.72489612723048e-08 441 2.20928157828221 -2.08581208543941 -1 3.96891529838564 1057 1684 1511 621 2191 761 598 550 1477 2074 441 708 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 4.20564419244723e-08 2.95100601223086e-07 710 1022.09090909091 1057 3.82331297531337e-09 28 2.4429196056235 2.65676250202434 1 4.60560378469666 709 2171 1388 1219 217 501 1057 28 1293 2595 65 709 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 2.47861633249199e-42 5.57098528064865e-40 555 1013.18181818182 1057 2.25328757499273e-43 13 2.94655951586767 3.10206199359476 1 33.3988973399005 555 1057 13 1311 1265 874 1171 307 3031 48 1513 710 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 7.22327136222992e-08 3.1923071937945e-07 3800 2145.09090909091 1061 7.22327159702034e-09 603 3.10880171346798 -3.99253514944968 -1 5.830574243345 3798 873 4427 603 831 4480 3868 2064 763 828 1061 711 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 9.6544457096999e-08 3.39696808054909e-07 1600 1443.72727272727 1061 8.77676921215827e-09 582 2.30098300592492 -2.42057932471697 -1 4.29735097490454 1597 661 1061 741 1059 1799 2309 3712 848 582 1512 712 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 3.43218440746974e-07 6.52560643255266e-07 1775 1046.45454545455 1062 3.12016812992672e-08 183 1.90836739778605 1.98646824374728 1 3.40770503570888 183 1311 1326 1772 2314 267 415 620 1772 469 1062 713 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 9.15853029270402e-08 3.34843245403276e-07 1170 1006.18181818182 1064 8.32593697633705e-09 4 3.98027182759029 4.56652501298368 1 7.44142842395769 1166 849 968 2050 997 1064 1185 11 1143 1631 4 714 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 1.86813506010254e-10 2.63744412329602e-09 265 966.818181818182 1066 1.69830460023743e-11 262 2.61804170921104 2.79203863069079 1 6.48469734271512 262 1317 268 1152 1066 629 642 1135 2684 304 1176 715 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 4.50226158623214e-08 2.99073619127066e-07 35 1484 1067 4.09296516215467e-09 35 1.83363251477397 1.92757309901952 1 3.45363285779754 35 3248 2382 3080 3357 252 186 482 1348 1067 887 716 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 9.72596582627711e-08 3.39726302159777e-07 1945 1240.09090909091 1068 8.84178750568337e-09 67 2.37398313931853 -2.12260853179969 -1 4.43368861586563 1943 339 875 687 1068 1357 1914 3236 67 746 1409 717 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 1.55545085634282e-07 4.16353338822743e-07 1070 1235.54545454545 1069 1.41404633301528e-08 554 1.8547020895181 -2.05227831968787 -1 3.41637408660659 1069 788 2259 1485 1540 849 837 1158 554 2121 931 718 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 2.29635753639824e-06 3.06181004853099e-06 145 1075 1069 2.08759993939743e-07 120 1.89689115451156 1.94501382235746 1 3.01946819671885 143 350 1673 2066 3468 241 120 1131 452 1112 1069 719 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 6.35077033117619e-17 2.18143974287033e-15 290 947.636363636364 1070 5.77342757379653e-18 97 3.00052164319271 3.23612038543946 1 12.702288042513 289 1320 97 317 1353 842 1070 1695 1947 207 1287 720 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 2.26054104722912e-07 5.06635980195699e-07 910 1364.54545454545 1071 2.05503752682178e-08 100 2.0939522438322 -2.22582469908095 -1 3.80564817966139 907 100 835 1027 1920 1542 2135 1368 3443 662 1071 721 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 1.09875217979038e-07 3.5351808374987e-07 715 1145.72727272727 1071 9.98865667877888e-09 321 1.92854951033021 1.89303093187372 1 3.59200354711657 714 1196 976 2042 1204 678 1063 1273 1071 321 2065 722 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 1.16008717671178e-12 2.34000490345282e-11 1515 1336.45454545455 1072 1.16008717671239e-13 39 2.13989101501831 -2.21219670191744 -1 6.56815526749577 1513 977 4510 39 165 1072 2301 1755 881 123 1365 723 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 1.69518724622002e-06 2.33750622324233e-06 430 1313.54545454545 1076 1.54108050220948e-07 429 2.85624722522054 3.267973138002 1 4.64369068664024 429 1641 639 1039 3337 924 1076 2154 847 1212 1151 724 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 2.2387788268292e-54 1.17411511807043e-51 2325 1240.18181818182 1077 2.03525347893565e-55 5 3.20156427678646 -3.1808149074677 -1 47.0840557133999 2325 1077 5 10 524 2260 3624 2041 409 32 1335 725 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 7.88585816065456e-08 3.2708309200767e-07 3925 2097.54545454545 1077 7.16896222120149e-09 313 2.29958209294111 2.24958254682052 1 4.30564645272904 3921 313 1077 360 823 3586 2913 4694 576 952 3858 726 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 2.99143794864427e-07 5.98034185413001e-07 3555 1780.90909090909 1078 2.71948941400317e-08 268 3.19571779398235 -3.25010411151718 -1 5.74203245464477 3551 395 453 268 2387 3987 4675 1078 877 1156 763 727 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 6.04228623296794e-10 8.01112107292378e-09 15 1216.63636363636 1080 5.49298748602497e-11 13 1.74151552604852 1.78931027420387 1 4.07066965198815 13 2174 1203 1841 4073 166 29 701 1667 436 1080 728 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 1.30082709683581e-07 3.79878839072891e-07 900 1016.27272727273 1081 1.18257015795616e-08 198 2.52839612553408 2.75473903037058 1 4.68670679823944 898 756 1137 2044 1370 1024 1081 306 198 1170 1195 729 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 8.57658460661397e-08 3.28305665915602e-07 2825 1512.54545454545 1082 7.79689540087969e-09 150 2.03116373293381 2.65967773700398 1 3.80201966558524 2824 192 1082 1223 934 3292 3856 630 1032 1423 150 730 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 5.55379443614498e-08 3.07843567066819e-07 1365 1197.72727272727 1083 5.04890416031625e-09 196 2.35960707093254 2.7913888369237 1 4.43599644994935 1363 665 1181 2700 454 1060 1083 1934 1028 1511 196 731 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 1.1097743058742e-06 1.63080159518251e-06 450 1156.27272727273 1084 1.00888624153848e-07 447 2.92783468359722 3.25576209147208 1 4.89228739224453 447 1559 557 1273 3104 613 634 1817 521 1084 1110 732 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 9.8455443773998e-08 3.40595929530574e-07 180 921.727272727273 1086 8.9504952891021e-09 16 2.44409061079798 2.70727995207488 1 4.56386428043597 178 1696 1270 1940 1086 27 65 46 2407 1408 16 733 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 2.84098693628442e-07 5.76750896312364e-07 275 1340.72727272727 1086 2.58271573014321e-08 33 2.58513771715665 2.72046182820364 1 4.65653210876525 274 3345 1086 2803 2149 76 33 144 2849 1736 253 734 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 7.34497912641607e-08 3.2144561803028e-07 2270 1534.09090909091 1087 6.67725397421593e-09 65 2.32642955476156 2.68770433675558 1 4.36099703821825 2269 679 1223 1023 756 3645 4592 65 439 1087 1097 735 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 8.87420689740609e-08 3.31003670356505e-07 790 1232.63636363636 1088 8.06746114124337e-09 616 2.44343374823882 2.76365311045118 1 4.57139132014054 786 2555 1220 1261 971 616 1088 1355 740 2221 746 736 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 1.29841194359358e-08 1.35493393146774e-07 1570 1208.54545454545 1089 1.1803745011424e-09 366 2.34170614707219 2.46323453216353 1 4.64334281258791 1569 1089 366 416 894 611 1923 1821 2205 645 1755 737 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 2.34756554913361e-06 3.12127025124243e-06 805 1774.81818181818 1090 2.13415277651495e-07 562 1.61087339686373 1.34219583216742 1 2.56017016770811 804 562 2816 1090 3479 900 600 2723 698 3452 2399 738 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 4.72661144701803e-19 2.02814600272046e-17 2535 1187 1090 4.29691949728913e-20 52 2.78648676173121 3.22854619043989 1 13.4308774553648 2535 1227 75 52 1090 1569 2992 460 2066 150 841 739 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 1.83290523783989e-16 5.96642256731331e-15 1180 981 1090 1.66627748894536e-17 104 2.54160783875775 2.8290738495626 1 10.4387049971167 1177 1218 104 328 664 1073 1847 1090 1876 133 1281 740 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 3.71592957258516e-07 6.91063340528052e-07 3525 1870.09090909091 1091 3.37811836384337e-08 242 2.45209368791798 -2.44844570954553 -1 4.36123451702461 3525 487 1023 708 2378 4651 4248 1091 242 1386 832 741 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 2.50945834042843e-05 2.82418773648598e-05 780 1733.18181818182 1093 2.28135178667762e-06 778 4.39971688427006 4.9818566963208 1 5.77869193630549 778 2874 1132 2763 4159 1031 1087 810 1093 2322 1016 742 M8395 REACTOME_HEMOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HEMOSTASIS.html Genes involved in Hemostasis 435/615 Reactome 8.46340959263086e-08 3.27455016694392e-07 1080 1320.54545454545 1094 7.6940090165624e-09 442 2.1811121165162 2.29687067851712 1 4.08347273270286 1076 1094 585 442 923 1142 1713 2034 2548 942 2027 743 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 1.29464860703447e-07 3.79650919404164e-07 395 1229.45454545455 1094 1.17695334838321e-08 394 2.15621036805208 2.19989248158749 1 3.99684821678759 394 2529 1094 1831 1363 476 442 763 2485 1135 1012 744 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 4.73526810400657e-12 8.59633286573501e-11 1645 1073.27272727273 1094 4.30478918546979e-13 205 2.74317530540013 3.16867432099612 1 7.97248109057391 1645 1425 205 945 1186 755 1524 256 2473 298 1094 745 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 4.15904491056761e-14 9.8625394945761e-13 1095 979.272727272727 1094 3.78094991869788e-15 150 2.57836561699401 2.80614837805366 1 8.93809237405129 1094 1163 150 347 1226 978 1730 1401 765 412 1506 746 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 2.67055397359237e-05 2.99691268553399e-05 340 1768.72727272727 1095 2.42780581062004e-06 66 1.73685820658036 1.73685820658036 1 2.26777920277299 337 2795 3104 1998 4172 300 66 1095 1019 3521 1049 747 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 6.18526357650907e-07 1.02007142142288e-06 400 1347 1095 5.62296846862397e-08 209 2.42315849273683 2.60092347956352 1 4.19142909336634 400 1771 1676 1095 2723 347 209 941 1476 3260 919 748 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 3.26370184164389e-07 6.3185696031826e-07 1100 1615.18181818182 1096 3.26370232097272e-08 25 1.91874367112316 1.91874367112316 1 3.43399633781911 1096 3535 4367 1669 2348 1055 25 76 399 3008 189 749 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 5.00540637602883e-08 3.0357704374324e-07 2135 1319.90909090909 1097 5.00540648877225e-09 1 5.6755403012864 -7.18013561472989 -1 10.6810037958419 2131 940 4233 258 448 2253 1097 92 1 1741 1325 750 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 6.69298724434885e-10 8.79969353574556e-09 1885 1643.09090909091 1097 6.69298724636467e-11 184 2.00955511764835 2.12754791335966 1 4.67366505414189 1881 1047 4697 680 1024 1097 2559 977 1810 184 2118 751 M17879 REACTOME_COMMON_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMMON_PATHWAY.html Genes involved in Common Pathway 10/15 Reactome 1.26964559390467e-06 1.82816571178464e-06 1100 1183 1100 1.15422393330228e-07 89 4.51956481108696 -4.60662767638821 -1 7.48771784825465 1100 842 701 270 3180 1191 405 1377 89 1638 2220 752 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 6.56341663322253e-08 3.14536172538656e-07 225 1197.27272727273 1100 5.96674257184872e-09 225 2.8348478304052 3.05396599609557 1 5.32196332315271 225 1519 409 970 3292 795 1100 1747 1310 446 1357 753 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 1.37864172606825e-07 3.92235620677646e-07 1110 1090.81818181818 1102 1.25331073860144e-08 455 2.63788852437417 2.61853856103707 1 4.87911282737461 1110 1500 455 797 1422 576 1102 1751 1720 591 975 754 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 1.53868576972193e-33 1.91120969291777e-31 995 984.545454545455 1103 1.39880524520176e-34 18 2.79788522633585 2.94513640299129 1 24.8176684432959 995 1989 18 1127 414 1103 1326 268 1824 69 1697 755 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 6.64256435856627e-06 8.05366138516126e-06 1425 1296.45454545455 1103 6.03871310441882e-07 91 1.9714671227855 2.07443147984224 1 2.89910187038756 91 2307 1200 1424 4210 358 235 1103 817 1095 1421 756 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 1.10317564157137e-08 1.16748632919661e-07 700 985.727272727273 1107 1.00288695191198e-09 118 2.73273261994248 2.89734381870718 1 5.46987783232991 698 1362 361 118 1655 1182 1418 1441 1107 613 888 757 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 2.0861870037152e-07 4.84679970737421e-07 1410 1173.72727272727 1108 1.8965338195831e-08 506 1.92971864007897 2.20406344355956 1 3.51781638924471 1410 1108 1213 599 1843 926 1829 921 1779 506 777 758 M203 PID_ALK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK2_PATHWAY.html ALK2 signaling events 18832364 9/13 Pathway Interaction Database 2.99029418320055e-05 3.34063634194239e-05 1110 1799.36363636364 1109 2.99033442232948e-06 88 3.11851564315202 3.11851564315202 1 4.03000148742786 1109 3198 4204 2345 4206 794 147 548 88 2922 232 759 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 2.97971034823515e-06 3.86380023177744e-06 1050 1718.09090909091 1110 2.70883125818509e-07 245 2.47181698764767 2.78172394046246 1 3.8627782341403 1049 3906 1609 884 3574 619 1110 894 1616 3393 245 760 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 3.63463836621604e-13 7.7276995894323e-12 1845 1400.72727272727 1111 3.63463836621662e-14 116 1.98926101079831 2.31248368829706 1 6.38214803132437 1844 955 4693 257 354 1111 2561 1286 1417 116 814 761 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 1.76303351596998e-19 7.77711980876478e-18 2350 1383.09090909091 1111 1.60275774179089e-20 37 2.42196776447304 -2.54324079594017 -1 11.9649189993553 2348 1111 73 37 567 2654 3573 1760 889 66 2136 762 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 1.01099562280848e-07 3.42922022949596e-07 660 1111.54545454545 1113 9.19086972061934e-09 144 2.33633736602369 2.58467161710974 1 4.36062384494846 660 2297 1428 1925 1113 348 338 494 1703 1777 144 763 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 3.63082012264301e-07 6.80990524068349e-07 1065 1191.81818181818 1113 3.30074611078529e-08 514 3.22120157244065 3.66573879283573 1 5.73535283497578 1063 1689 782 1013 2355 1201 1349 1113 621 1410 514 764 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 2.78940512656666e-11 4.48327355151198e-10 2055 1262.72727272727 1113 2.53582284236548e-12 53 2.25720230747701 2.45943192963528 1 6.09242286988642 2055 1113 232 53 307 1006 2245 2157 1633 156 2933 765 M872 REACTOME_L1CAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_L1CAM_INTERACTIONS.html Genes involved in L1CAM interactions 100/131 Reactome 1.01114418288351e-07 3.42922022949596e-07 2345 1733 1114 9.19222026688015e-09 96 2.47155123602598 2.9285985033738 1 4.61304170944357 2345 96 799 374 1114 3418 3934 2817 438 805 2923 766 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 1.28464376948863e-07 3.78024849874461e-07 1115 1433.90909090909 1114 1.16785804045701e-08 257 1.78394245012016 1.96798330639425 1 3.30760727929241 1114 257 2022 3845 1359 520 818 365 3392 1346 735 767 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 1.40660688627225e-30 1.38316343816772e-28 965 1089.54545454545 1114 1.27873353297479e-31 25 3.52177471315405 3.80751360915493 1 28.3308303600923 964 1345 25 244 1947 1114 1844 1964 630 96 1812 768 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 2.56027611958921e-09 3.03630735790479e-08 2125 1254.18181818182 1115 2.32752374778978e-10 117 2.65635613472394 3.21810028213534 1 5.7656359320076 2122 117 319 1581 2437 1911 2550 895 1115 293 456 769 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 1.01127096506952e-07 3.42922022949596e-07 685 1691.54545454545 1115 9.19337283231339e-09 333 1.78377957427037 2.08870690248023 1 3.32910645843969 683 2702 2508 3966 1115 495 603 987 1416 3799 333 770 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 5.23713756854992e-14 1.22372719423543e-12 1735 1155.90909090909 1115 4.76103415322729e-15 59 2.56384260475792 2.46829931364381 1 8.81837507910355 1735 1319 176 59 732 1115 3016 1015 1307 106 2135 771 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 2.04401049188802e-15 5.42007276500645e-14 780 1219.27272727273 1117 1.85819135626184e-16 132 3.40462094831242 3.36476033607609 1 13.0413740370766 779 1536 132 722 2219 981 1117 1874 2410 219 1423 772 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 5.81387470677407e-09 6.5181683173334e-08 80 1285.63636363636 1117 5.2853406564893e-10 76 1.80275797010136 1.8820698058975 1 3.73990421668929 76 2512 1117 2118 3603 126 269 704 2222 221 1174 773 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 1.016540243743e-07 3.43701285850069e-07 1000 1097.54545454545 1120 9.241275370124e-09 526 2.9628053058469 2.9904373499126 1 5.5292736441592 1000 1740 608 950 1120 1288 1684 1428 526 586 1143 774 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 1.18248831925159e-15 3.28314403933382e-14 1120 988.909090909091 1120 1.07498938113781e-16 124 2.60765386822504 2.88651910985632 1 10.1523351492275 1120 1151 124 293 945 1236 1689 803 1792 351 1374 775 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 1.80588770523147e-07 4.47913293152525e-07 1750 1224.90909090909 1120 1.64171623042657e-08 261 2.67171071713262 3.05943913250547 1 4.8972080643457 1746 821 1706 871 1697 1494 1120 668 261 2446 644 776 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 3.27301570727569e-08 2.73911952807469e-07 735 1389.90909090909 1121 2.97546886906316e-09 81 1.95527419385198 -2.01715927332034 -1 3.70435083719008 733 1436 1604 3275 81 135 1121 999 3718 1581 606 777 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 8.93694759670261e-07 1.3660101248846e-06 470 1339.63636363636 1123 8.12450111555929e-08 301 2.59075931134829 -2.35925164175638 -1 4.38651524644712 466 1726 933 2058 2972 588 301 1123 2570 669 1330 778 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 9.54734793960828e-07 1.43789030870935e-06 930 1407.81818181818 1124 8.67941098443347e-08 267 3.55825989645352 4.22011094843066 1 6.00206545620387 928 3394 1268 1287 3021 828 267 401 1124 2572 396 779 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 5.69054572972538e-06 6.97646125826072e-06 1545 1618 1124 6.32284457990559e-07 230 2.20800564052742 -2.20800564052742 -1 3.28680138368362 1545 948 4231 NA 3850 998 230 518 427 2183 1250 780 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 2.42199310203595e-08 2.3074467411864e-07 1930 1548 1124 2.20181193518165e-09 16 2.17501766148124 2.38501062725964 1 4.16753907983876 1926 251 1067 998 16 1905 2723 3391 933 1124 2694 781 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 1.06342917744261e-07 3.48348225330125e-07 1655 1230.36363636364 1124 9.66753844405745e-09 142 2.38969102581441 2.63514838670935 1 4.45551973194761 1654 142 658 2715 1172 1124 2233 269 2418 411 738 782 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 5.69054572972538e-06 6.97646125826072e-06 1550 1621.8 1125 6.32284457990559e-07 231 2.20800564052742 -2.20800564052742 -1 3.28680138368362 1546 949 4247 NA 3851 999 231 532 428 2184 1251 783 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 4.40931017627451e-16 1.33409897641126e-14 75 1240.27272727273 1126 4.00846379661318e-17 72 3.45464824458232 3.47462387410342 1 13.8403589489847 72 2139 113 1133 3872 901 1126 1642 1245 310 1090 784 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 5.69054572972538e-06 6.97646125826072e-06 1550 1622.8 1126 6.32284457990559e-07 232 2.20800564052742 -2.20800564052742 -1 3.28680138368362 1547 950 4248 NA 3852 1000 232 533 429 2185 1252 785 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 7.06050758199966e-10 9.23146697701895e-09 2695 1812.81818181818 1126 6.41864325842327e-11 57 2.2687055131857 2.26555023625879 1 5.26285911636034 2693 1072 289 57 1126 1958 3021 4408 1070 203 4044 786 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 1.14101240293017e-05 1.33969615468418e-05 1290 1559.2 1126 1.26779798803923e-06 61 5.33204906440321 5.33204906440321 1 7.50211242215123 1286 947 4385 NA 4028 996 176 271 61 2186 1256 787 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 1.9768982010799e-06 2.68208091667063e-06 1215 1346.09090909091 1128 1.79718179773024e-07 439 2.74042634857093 3.1211336673545 1 4.40809607368088 1212 1633 798 439 3400 1128 945 2345 632 1524 751 788 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 3.74492593355378e-08 2.87575261955407e-07 810 1010.18181818182 1128 3.40447817936488e-09 143 2.03609107920565 2.2513280018086 1 3.84506790674672 806 1270 1218 407 143 640 1334 1128 951 1772 1443 789 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 4.76515950028202e-08 3.0179250958721e-07 1820 1249.72727272727 1128 4.33196327590409e-09 310 2.94478342501372 3.21449340479217 1 5.54365690512614 1820 1773 1048 1015 310 1963 1764 655 1128 1089 1182 790 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 4.38194105691282e-08 2.9759369480041e-07 2560 1502.36363636364 1129 3.98358285835632e-09 254 2.27304511071248 2.63391533745086 1 4.28288361922936 2560 1427 739 987 254 2527 3444 1129 2510 567 382 791 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 1.98483393348113e-06 2.69130024878797e-06 1135 1397 1132 1.80439611290463e-07 111 2.69089785107072 2.85866411720608 1 4.32725374805808 1132 1800 1346 1028 3402 1740 845 111 930 1916 1117 792 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 9.83507170109941e-07 1.47164743569385e-06 1165 1319.81818181818 1132 8.94097827078028e-08 148 3.43739577374552 -3.0206073645846 -1 5.78815943215717 1163 808 783 344 3041 1534 2347 2675 148 1132 543 793 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 5.23067362190062e-06 6.45458287460678e-06 255 1420.81818181818 1133 4.75516914389214e-07 251 3.61080883901967 3.94973176755524 1 5.4107466232205 251 2303 542 1238 4231 922 1133 2217 916 1164 712 794 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 4.67968532277982e-08 2.99073619127066e-07 2175 1486.90909090909 1134 4.25425947483892e-09 299 2.88072130509799 2.9942533296504 1 5.42630846483203 2175 502 516 1134 299 2158 1724 3757 602 401 3088 795 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 5.37214626190442e-08 3.06874196014832e-07 1965 1105.09090909091 1134 4.88376944826005e-09 176 2.43623681721821 2.5926842269143 1 4.58104982832012 1963 176 891 930 416 1240 1750 1581 634 1134 1441 796 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 2.49251823650055e-06 3.29635362182197e-06 1135 1427.36363636364 1135 2.2659282367596e-07 594 2.50303503547213 2.45424326793117 1 3.96143291712038 1135 1597 856 594 3497 649 615 2396 1668 1116 1578 797 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 6.85970217832613e-08 3.15009389627869e-07 4495 2226.45454545455 1136 6.2360930838317e-09 152 2.64707986789663 2.63319680943161 1 4.9689035558111 4495 532 882 152 687 4237 4379 2630 1030 1136 4331 798 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 1.5628918690938e-07 4.16803047601943e-07 1250 1073.90909090909 1137 1.42081089102044e-08 413 1.94440518600641 2.14227186886461 1 3.58138623088454 1249 1137 1004 717 1548 413 1152 1363 1039 486 1705 799 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 2.22400161836606e-05 2.5179389874521e-05 1060 1896.72727272727 1138 2.02184009212287e-06 318 1.73265958097879 1.75401654808239 1 2.30013447718501 1058 846 2295 4125 4197 1138 797 318 3564 1629 897 800 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 2.06103715763409e-08 2.04371751765397e-07 2470 1555.90909090909 1138 1.87367016085692e-09 346 2.24797465627854 2.58322282668625 1 4.34157688108965 2468 1102 383 1138 917 2529 3680 2001 1072 346 1479 801 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 8.5188753625598e-09 9.28616436750168e-08 1140 1163.54545454545 1139 7.74443217776974e-10 20 2.86042937163607 3.16401190666373 1 5.80763391284447 1139 20 349 425 1189 1867 2210 1943 577 888 2192 802 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 7.10833334985059e-07 1.13887757675814e-06 340 1304 1142 6.46212331508839e-08 340 2.13505059042034 2.18310865178328 1 3.66347692241738 340 347 1142 1910 2810 474 1523 784 2834 816 1364 803 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 8.69947949996399e-08 3.29546895985795e-07 2085 1188.18181818182 1144 7.9086180399712e-09 35 2.39056319738499 2.10904160743554 1 4.47378013965487 2082 760 1460 345 952 2270 1911 1144 35 1972 139 804 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 3.3115530424176e-08 2.74345541741202e-07 365 1475.45454545455 1145 3.01050281114983e-09 363 4.0526918370259 4.39887063163045 1 7.67811858993382 363 2358 393 1218 4337 1102 1257 2564 544 949 1145 805 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 2.4100222446545e-18 9.80629740928382e-17 70 1306.81818181818 1145 2.19092931332227e-19 68 3.93174388867843 4.11885101731584 1 18.1743372422226 68 1535 80 1145 4134 1086 957 1691 1983 248 1448 806 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 2.16941338191432e-08 2.13325649221575e-07 1510 1029.27272727273 1146 1.97219400300621e-09 5 2.62831748009398 3.12067231162509 1 5.06215585000546 1507 1804 1146 2727 5 1388 1242 48 305 818 332 807 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 2.58310330182428e-07 5.45605448940105e-07 335 1301.09090909091 1147 2.34827600465115e-08 333 2.23169185429132 2.48241878944073 1 4.03529977250827 333 2947 690 1237 2054 674 905 1353 1954 1018 1147 808 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 4.61957339504421e-08 2.99073619127066e-07 1370 1117.36363636364 1147 4.19961226549664e-09 263 2.19987135741438 2.3692042183978 1 4.14361296063267 1367 1147 522 529 1327 826 1867 950 1786 263 1707 809 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 1.46789654050961e-12 2.93579308101922e-11 4245 2060.81818181818 1148 1.33445140046417e-13 113 2.39276883066701 -2.375303026929 -1 7.27637293544675 4245 1148 184 249 113 4338 4500 3692 1059 284 2857 810 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 5.26395164932149e-16 1.58253833024188e-14 305 1348.45454545455 1149 4.78541059029226e-17 114 3.55252330814052 3.64825125819485 1 14.1564174944092 303 305 114 2254 2935 1037 1720 1162 3517 337 1149 811 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 1.51732824538889e-07 4.1136067307499e-07 1150 1082.72727272727 1149 1.37938940912566e-08 530 2.3099242026456 2.33673843435772 1 4.25860249954762 1149 565 1231 530 1513 972 1314 1892 796 1336 612 812 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 7.9944986734285e-08 3.27123182997709e-07 1640 1416 1151 7.26772633085238e-09 425 2.09813473660471 2.30615481136083 1 3.9283566965741 1637 2499 1151 1284 840 823 2205 1061 2598 1053 425 813 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 1.05097264201832e-07 3.48348225330125e-07 255 1012.27272727273 1152 9.5542972020441e-09 3 2.39764225338591 2.4086510549313 1 4.47034746471289 254 2250 1299 2599 1152 79 54 13 1360 2072 3 814 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 3.78254621772978e-07 6.99593187605194e-07 3205 1799.27272727273 1154 3.43867897097994e-08 86 3.2562586969017 -1.9205833938568 -1 5.78677581602574 3205 750 763 322 2393 3613 4273 459 86 1154 2774 815 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 2.42542737652197e-16 7.63201147812248e-15 560 1113.09090909091 1154 2.20493397865634e-17 108 3.42378110962111 3.67111757056086 1 13.9564881284092 560 1553 108 671 2470 1278 1469 1765 1021 195 1154 816 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 2.85887871946753e-07 5.78889213036755e-07 480 1251.81818181818 1155 2.59898099179648e-08 181 1.86517701877849 1.90415581556634 1 3.35858269759432 480 2008 2069 614 2155 181 686 1542 1881 999 1155 817 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 2.58222977567073e-06 3.39786020104987e-06 75 1445.63636363636 1157 2.34748436958561e-07 73 2.07072306986045 2.04616274192636 1 3.26920880508581 75 2627 1776 2153 4092 147 73 1118 1861 823 1157 818 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 4.91662511521494e-09 5.60542766758805e-08 20 1358.27272727273 1157 4.46965920563887e-10 17 1.82026651596767 1.79082755178006 1 3.81067233306664 17 2552 1157 1830 4022 303 146 1115 1939 262 1598 819 M2890 KEGG_CALCIUM_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CALCIUM_SIGNALING_PATHWAY.html Calcium signaling pathway 114/193 KEGG 2.36417794022991e-09 2.84666323415439e-08 1660 1067.90909090909 1159 2.14925267524593e-10 30 2.71457842858596 2.75787554042467 1 5.91398263373885 1656 30 315 522 392 1159 2251 1932 1679 479 1332 820 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 3.11918802264319e-07 6.12957944182254e-07 915 1471.72727272727 1159 2.83562587716884e-08 174 2.64891508810118 -2.69878921245448 -1 4.75120754104685 914 2785 1159 1506 2234 890 1302 546 3589 1090 174 821 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 8.0474170132689e-08 3.2731281190979e-07 1845 1412.90909090909 1160 7.31583391603339e-09 157 2.34373362653063 2.79609989739364 1 4.38812421387218 2724 157 910 811 850 1841 1845 1417 1160 768 3059 822 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 7.0004680658764e-08 3.15651538021179e-07 1450 1360.90909090909 1162 6.36406208057589e-09 482 3.21447682607213 -3.24674124186346 -1 6.03334306702618 1450 482 668 770 712 1683 1162 3328 1199 755 2761 823 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 9.93490780435913e-08 3.41286498082788e-07 2290 1453 1163 9.03173477546033e-09 201 2.58415934936874 2.66086004230811 1 4.8248083843982 2289 201 1054 989 1100 2332 2349 1163 455 1664 2387 824 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 1.45701984376588e-27 1.18571270044396e-25 1550 1376.72727272727 1165 1.32456349433263e-28 35 2.8563227848314 2.82446337687014 1 20.5582185313431 1550 1165 35 241 721 1469 2708 3377 1106 84 2688 825 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 5.45633443029495e-18 2.14615820924935e-16 3900 1981.90909090909 1166 4.96030402754083e-19 66 2.60046729399799 -2.30043926297998 -1 11.764838818415 3899 1166 84 66 506 4064 4298 2704 831 90 4093 826 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 2.21747410912608e-08 2.16452651730241e-07 2165 1330.36363636364 1168 2.01588557406996e-09 6 2.71076078642791 2.92351432173947 1 5.21602220710832 2163 696 1345 1168 6 2530 3766 364 92 1836 668 827 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 7.13388479666947e-08 3.17725226229176e-07 1200 1149.81818181818 1168 6.48535002545291e-09 423 2.1126066508069 2.25976542389454 1 3.9631814789495 1197 423 1476 2134 731 1168 1016 766 1222 1014 1501 828 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 3.86377882277115e-08 2.90705627846226e-07 945 1133.72727272727 1169 3.51252626420842e-09 396 2.75571898980161 3.08140216827687 1 5.20061623156853 945 1521 396 966 1377 1541 1432 1169 953 546 1625 829 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 2.8118967620571e-07 5.72979094207008e-07 775 1641.81818181818 1171 2.55627011041409e-08 386 3.27659214589804 3.77448153073476 1 5.9049549930253 772 2389 825 3060 2140 663 386 782 4255 1171 1617 830 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 7.35987480774634e-07 1.17008537376044e-06 880 1323.27272727273 1171 6.69079751810751e-08 205 2.02323645826813 2.24079566008179 1 3.46471364226091 880 1750 1986 2624 2835 507 306 205 1171 1442 850 831 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 1.79373875811955e-07 4.45837121554727e-07 895 1631.09090909091 1172 1.63067173124501e-08 622 2.27049510993132 2.16243655269233 1 4.16297906541975 895 2395 1437 4117 1691 675 803 643 3492 1172 622 832 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 2.66933783294387e-08 2.48045842838732e-07 1235 1273.18181818182 1172 2.42667078666536e-09 253 2.16316594955731 -2.12945942248192 -1 4.12521136774772 1231 1172 527 1369 709 1134 1780 1159 3379 253 1292 833 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 7.92809356141665e-44 2.07892231166037e-41 155 1228 1172 7.20735778310604e-45 11 3.12525873417527 3.42882437902416 1 36.7132855094295 154 1988 11 915 3170 1335 1172 845 2140 41 1737 834 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 2.32107801203719e-12 4.47162784359817e-11 1220 977.090909090909 1173 2.11007092003603e-13 101 2.46987524331259 2.79920255068324 1 7.38054764257789 1220 1180 193 101 559 1454 2100 1063 1173 280 1425 835 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 1.75478320328104e-37 2.58830522483954e-35 2875 1765.09090909091 1174 1.59525745752822e-38 14 2.95052571453496 3.19083830975538 1 29.4674700033649 2874 1174 14 27 577 3116 3259 3083 896 35 4361 836 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 1.66113417547007e-07 4.2834032897358e-07 4300 1649.81818181818 1174 1.5101220917235e-08 59 3.25626093575966 -1.98537364501756 -1 5.98711517078647 4300 733 1074 728 1616 3471 2161 567 59 1174 2265 837 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 6.47091640540559e-08 3.14536172538656e-07 1840 1403.18181818182 1175 5.88265145066939e-09 114 2.25763144128186 2.43257440078984 1 4.23815854537901 1836 1175 552 114 623 1144 2002 3161 2402 765 1661 838 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 1.0544110737036e-07 3.48348225330125e-07 3025 1577.54545454545 1177 9.58555567490164e-09 192 2.98369320195387 -2.73180848514655 -1 5.5632361758039 3021 636 826 1774 1156 2962 2920 1995 694 1177 192 839 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 9.35128361335325e-51 3.67817155458561e-48 1955 1274.90909090909 1179 8.50116692123031e-52 7 3.39451323931107 3.81850142693143 1 46.4949752777205 1955 1179 7 14 825 1558 2543 2262 961 29 2691 840 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 1.04741340514907e-10 1.52116654532419e-09 3805 1732.36363636364 1180 9.52194004726309e-12 166 2.52451395151247 2.79107222579141 1 6.4272383821874 3801 1275 260 277 166 3810 4217 781 1180 190 3099 841 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 4.04326257264494e-07 7.31604867117337e-07 1425 1364.36363636364 1181 3.67569392339525e-08 354 2.35661952012059 2.24981813873366 1 4.17454443351433 1423 354 879 562 2449 1080 1206 3197 1940 737 1181 842 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 1.28606154835692e-05 1.49992846756725e-05 480 1381.90909090909 1182 1.16915369672051e-06 105 2.67901366710643 2.77623138212068 1 3.73094690310243 476 2280 1182 1959 4001 283 105 674 1777 1966 498 843 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 3.25928430656597e-08 2.73247281118852e-07 3560 1820.90909090909 1183 2.96298577713821e-09 80 3.31865037379747 -3.76082159572144 -1 6.28893722493496 3557 711 693 323 80 3903 2703 2605 303 1183 3969 844 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 7.94358294117826e-08 3.27123182997709e-07 1435 1418.09090909091 1183 7.22143929818069e-09 396 2.03427200712258 2.49930263527149 1 3.80875971209252 1432 396 2076 1810 830 986 656 1183 2689 2426 1115 845 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 1.38712767665887e-07 3.93386935835012e-07 1440 1173.63636363636 1183 1.2610252401082e-08 281 2.18315016285705 -2.34958311109029 -1 4.03706502195958 1437 281 1259 1004 1427 1183 1756 523 2501 1027 512 846 M19428 KEGG_WNT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_WNT_SIGNALING_PATHWAY.html Wnt signaling pathway 144/178 KEGG 1.07421571340809e-07 3.49675735674911e-07 1245 1185.36363636364 1184 9.7655978714535e-09 443 2.03893982990903 2.60037467664583 1 3.80045380082626 1241 1423 2030 443 1184 741 1461 1004 967 2057 488 847 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 6.69824344758444e-07 1.08719769850752e-06 595 1161 1185 6.08931407906372e-08 327 3.17732034548065 -3.47530007820035 -1 5.47080508851329 594 1672 704 1328 2773 327 512 1185 1743 1222 711 848 M16257 BIOCARTA_MITOCHONDRIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MITOCHONDRIA_PATHWAY.html Role of Mitochondria in Apoptotic Signaling 24/28 BioCarta 9.68416299306036e-07 1.45293227359329e-06 150 1538.90909090909 1186 8.80378841447927e-08 148 2.40899815552935 -2.68241346029834 -1 4.06007093649464 1072 2355 2250 2129 3032 1186 1131 148 150 2775 700 849 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 5.83903366301989e-25 4.17579377112938e-23 2650 1591.36363636364 1186 5.30821242092715e-26 3 2.78565206281546 2.78351709316412 1 18.0009436327809 2649 1186 42 240 3 2975 3359 2727 642 81 3601 850 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 1.24786245505294e-07 3.73725303797582e-07 1125 1192.81818181818 1187 1.13442047802998e-08 285 2.02597893035719 2.16003512708749 1 3.75939026132853 891 1341 1121 1256 1331 285 1187 1986 1472 1121 1130 851 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 2.07892014060482e-25 1.50961585594689e-23 635 961.818181818182 1187 1.88992740054984e-26 38 3.16094522320205 3.33739660550751 1 20.8295393273792 635 1187 41 38 1395 1251 1547 1828 905 197 1556 852 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 7.85213768540671e-08 3.26618753937265e-07 710 1066.81818181818 1188 7.13830724151051e-09 127 2.35793972517054 2.53383750797714 1 4.41535492340554 707 2083 722 1188 820 127 1239 1851 1374 1366 258 853 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 1.46363019048445e-11 2.47610555522817e-10 2985 1652.27272727273 1188 1.33057290044926e-12 188 2.95234931167901 3.42445025685409 1 8.18876714688061 2981 188 220 282 1188 3163 2889 2926 300 388 3650 854 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 9.20848664406989e-08 3.3523689347011e-07 1190 1949.45454545455 1189 8.37135184500665e-09 5 1.2430610211063 -1.22904469923142 -1 2.32322398109818 1189 2577 3819 2920 1006 235 658 978 3779 4278 5 855 M15955 KEGG_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPHINGOLIPID_METABOLISM.html Sphingolipid metabolism 39/46 KEGG 6.0074138007007e-08 3.10910012492405e-07 1805 1156.72727272727 1190 5.46128542249246e-09 157 1.87580316468575 -1.86402533587107 -1 3.52395013452325 1802 467 2117 1775 541 897 1412 1190 199 2167 157 856 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 4.94406316304895e-08 3.0357704374324e-07 2230 1313.27272727273 1190 4.49460297650633e-09 343 2.72045100228862 2.7038194904603 1 5.11926629883566 2227 351 1066 373 343 1190 1999 2364 527 1537 2469 857 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 5.04070082423068e-08 3.0357704374324e-07 1345 1265.45454545455 1191 4.58245539974965e-09 343 2.31135369517722 2.33244168624748 1 4.34930925095307 1343 1191 481 542 367 1697 1986 892 2494 343 2584 858 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 5.37757566845781e-08 3.06874196014832e-07 1685 1436.90909090909 1191 5.37757579859026e-09 371 2.15404401732575 2.45901546127552 1 4.05032049698554 1682 990 4537 371 516 966 2187 1207 1710 449 1191 859 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 1.4203239867224e-06 2.00296660213018e-06 490 1404.81818181818 1192 1.29120445789724e-07 488 2.5720992806339 2.92889142137673 1 4.23145853788969 488 2125 580 1266 3258 853 1055 1565 2027 1192 1044 860 M17787 REACTOME_GLUCURONIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCURONIDATION.html Genes involved in Glucuronidation 6/23 Reactome 3.82067676726829e-06 4.81537899639688e-06 1385 1366.27272727273 1192 3.82068333619111e-07 20 3.96756735519486 4.27921979601784 1 6.0912045583598 1384 913 4257 126 3951 1192 289 136 20 1554 1207 861 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 3.15450687574603e-08 2.69553239732593e-07 4300 2087.09090909091 1192 2.86773356452495e-09 31 2.17692125871053 2.123012314214 1 4.12874756380354 4296 31 1138 569 69 4226 3724 3915 1192 814 2984 862 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 1.08487749080015e-07 3.51706922314159e-07 1130 1261.90909090909 1193 9.8625231299845e-09 311 2.54137010711468 3.0427181624319 1 4.73531808071054 1126 472 1397 1704 1193 2045 1675 795 311 2524 639 863 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 7.43121577193208e-10 9.66669477319271e-09 1195 1163.63636363636 1193 6.75565070403838e-11 99 2.07729578534199 2.33003671617278 1 4.80675989575852 1193 1056 375 99 1536 846 1617 1907 1878 185 2108 864 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 2.63993171873443e-07 5.52984583090281e-07 385 1084.90909090909 1194 2.39993821410735e-08 319 2.75058037012139 3.07976986186673 1 4.96910966265985 381 2533 448 1235 2185 415 780 1196 1194 1248 319 865 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 2.79254750878077e-11 4.48327355151198e-10 4205 2008.81818181818 1195 2.53867955346928e-12 46 2.25022543845375 -2.34137297043115 -1 6.07358891530359 4204 1070 233 46 396 4438 4584 3085 1195 259 2587 866 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 1.51664369729622e-07 4.1136067307499e-07 1790 1230.90909090909 1195 1.37876709259195e-08 22 2.79747046063511 3.35866616159783 1 5.15763011521935 1790 553 995 1195 1512 1641 2189 1564 1094 985 22 867 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 2.03724856737795e-07 4.80499877897084e-07 1195 1252.27272727273 1198 1.85204432366518e-08 684 2.3372304161612 2.43831125903057 1 4.26341829742981 1192 2041 684 837 1806 944 1198 812 1203 1782 1276 868 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 8.55624368345103e-08 3.28305665915602e-07 1920 1474.81818181818 1199 7.77840365110964e-09 613 2.18996027714861 2.55782732975538 1 4.09932920761725 1919 1199 781 613 932 2230 3075 942 1874 1098 1560 869 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 3.69512570464853e-07 6.88550861663682e-07 110 1338.36363636364 1201 3.35920575025723e-08 108 1.76046069204298 1.90130824710321 1 3.13167399337489 108 2495 2894 1740 2372 309 332 832 1201 1457 982 870 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 2.18016259596279e-07 4.95921323033463e-07 520 1431 1202 2.18016280985272e-08 459 1.97732531926254 2.01754403780787 1 3.59893745575055 520 1059 4448 1202 1981 667 687 1211 1819 459 1688 871 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 1.22355367948751e-07 3.70192774369017e-07 1205 1172.63636363636 1205 1.1123215886698e-08 328 2.13017844654584 2.46441922760728 1 3.95532344809582 1205 1144 914 1262 1314 350 1733 1792 1827 1030 328 872 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 1.09188900026495e-06 1.60908410638946e-06 1210 1693.54545454545 1207 1.09188953676503e-07 8 4.4941166435911 5.21726525943179 1 7.517494733622 1207 916 4409 745 4252 1800 1062 58 8 2171 2001 873 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 7.02432279251059e-07 1.12823149542591e-06 1215 1229.63636363636 1208 6.38575003208124e-08 85 2.54423906572984 3.10693299764011 1 4.36875434731235 1215 2203 1095 196 2803 1208 1382 85 568 2091 680 874 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 4.1878092120952e-08 2.95100601223086e-07 2780 1773.90909090909 1209 3.80709935619295e-09 75 2.26147335598388 2.62247423298259 1 4.26346161343056 2780 1209 445 75 213 2449 2812 4574 629 326 4001 875 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 1.69036691938812e-07 4.31738736986575e-07 1025 1169 1210 1.53669731751567e-08 61 2.09456782539567 2.47889829865454 1 3.84878823154908 1021 61 1832 1884 1636 1210 1094 492 1331 1822 476 876 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 1.13035073903186e-07 3.58148551537347e-07 995 1462.81818181818 1211 1.02759163373528e-08 764 2.02181463100622 2.34355434078366 1 3.76245582053272 992 2968 1754 2112 1237 1014 1211 1025 854 2160 764 877 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 1.10308688130543e-07 3.53626743374685e-07 1295 1234.09090909091 1212 1.00280630601323e-08 247 2.36637991964297 2.52672755682069 1 4.40758520687188 1295 2012 482 435 1212 247 1543 1458 2656 1031 1204 878 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 1.21983894309226e-07 3.70192774369017e-07 1180 1594.72727272727 1213 1.10894455520814e-08 218 1.8772981990038 1.97118412097936 1 3.48567219134286 1176 2727 2494 3074 1307 1043 552 218 1055 2683 1213 879 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 2.63900624161287e-08 2.4665563287946e-07 1215 1365.90909090909 1213 2.63900627295246e-09 36 2.67482193913812 3.25119494999347 1 5.10304116483673 1213 901 4349 2087 36 1749 1355 827 226 1592 690 880 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 1.71483940131534e-13 3.854305702004e-12 2975 1460.27272727273 1214 1.55894491028679e-14 80 2.81194323960753 3.01008421142742 1 9.26722153179005 2971 1214 160 80 1289 2144 3003 986 1011 317 2888 881 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 1.13059606311578e-07 3.58148551537347e-07 975 1124.45454545455 1214 1.02781465565267e-08 44 2.29516325922999 2.70938756135476 1 4.27125497713932 971 44 909 870 1238 990 1417 1502 1663 1214 1551 882 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 7.59308658591026e-08 3.24764325922831e-07 1595 1295.09090909091 1215 6.90280622543483e-09 465 2.39266484569169 2.60638858733136 1 4.48210055452188 1592 1215 465 2046 787 1145 1573 1069 1889 566 1899 883 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 3.26562983201772e-09 3.80586982891941e-08 3530 1697.36363636364 1215 2.96875439715013e-10 96 2.38398876014011 -2.22622446576173 -1 5.10683395986691 3530 1200 326 96 155 2310 3600 3487 1215 385 2367 884 M6370 KEGG_P53_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_P53_SIGNALING_PATHWAY.html p53 signaling pathway 79/91 KEGG 3.16715056421758e-07 6.19260590849501e-07 935 1312.72727272727 1216 2.87922820015005e-08 333 2.28004848144122 2.60002001610733 1 4.0865475568362 934 2154 1568 1081 2247 333 545 1216 1534 1655 1173 885 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 3.30881842605206e-07 6.37974794565594e-07 1220 1519.18181818182 1217 3.30881891872474e-08 46 5.00378910756918 5.44633279857506 1 8.95067385360631 1217 1940 4620 980 2358 1110 317 680 46 1889 1554 886 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 1.86735790562999e-08 1.88735103095793e-07 1220 1409.45454545455 1218 1.69759811043646e-09 376 3.3887849399056 3.73255937047138 1 6.57912012024087 530 1640 376 1601 3752 1216 1218 1912 820 884 1555 887 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 1.11093193732411e-07 3.54776640336251e-07 1160 1784.72727272727 1219 1.00993817583885e-08 934 2.04111662242584 2.13503117018489 1 3.80080507039382 1159 1697 1549 4133 1219 1158 934 995 3461 1029 2298 888 M129 PID_PLK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PLK1_PATHWAY.html PLK1 signaling events 18832364 63/65 Pathway Interaction Database 3.04704019864574e-07 6.04540972577044e-07 380 1189.45454545455 1220 2.77003692787859e-08 329 1.85536131701657 2.14449923816969 1 3.33081469835026 380 1575 2032 1875 2211 329 787 685 1462 1220 528 889 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 3.31457918233031e-08 2.74345541741202e-07 1010 1174.18181818182 1220 3.01325384751696e-09 87 2.40853437046616 2.35214027832582 1 4.56279359878585 1007 1562 1006 1377 87 1220 1758 1989 617 862 1431 890 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 4.39284272873072e-07 7.81413808490477e-07 825 1265.81818181818 1221 3.99349418715489e-08 303 2.51879779507487 -2.88310490991367 -1 4.44108311493107 823 1624 1393 844 2504 1348 1221 370 835 2659 303 891 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 5.1645253046463e-10 6.92515893123027e-09 15 1436 1222 4.69502300532608e-11 12 1.63292017974364 1.63867811335492 1 3.84661258155972 12 2004 2696 2587 3410 167 82 697 2597 322 1222 892 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 1.42313088140059e-07 3.98409119822705e-07 550 1273.09090909091 1223 1.29375543041796e-08 170 1.63089704566165 -1.45286479380072 -1 3.01303019471273 548 170 2135 1060 1454 431 556 2957 1514 1956 1223 893 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 6.66894099870653e-08 3.14536172538656e-07 655 1132.45454545455 1224 6.06267381896783e-09 427 2.11725410957177 2.51909582532231 1 3.97458040438135 1278 1224 830 860 654 1440 1934 651 1393 427 1766 894 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 2.70190882789244e-16 8.33530043637407e-15 3400 1841.27272727273 1225 2.4562807526295e-17 83 2.41551124376498 2.6855946197179 1 9.81948360266918 3397 1225 156 491 733 4186 3865 2133 1205 83 2780 895 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 1.05968539156112e-07 3.48348225330125e-07 1225 1251.09090909091 1225 9.63350402366857e-09 144 2.53369633914236 3.15725807045369 1 4.7240659763617 1225 144 1034 1861 1164 1409 1890 379 1683 1948 1025 896 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 4.81656588643238e-07 8.39209707787407e-07 1895 1467.54545454545 1225 4.37869721904241e-08 619 2.66936589484321 -3.19670092271443 -1 4.68272543620768 1895 698 1120 619 2564 1613 1225 730 3176 879 1624 897 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 1.03727795430671e-07 3.47369293280946e-07 1870 1519.09090909091 1226 1.03727800272426e-08 71 3.42852065151513 3.71150937213231 1 6.3939762663736 1867 921 4240 357 1246 1608 565 3804 71 1226 805 898 M7923 REACTOME_SEMAPHORIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMAPHORIN_INTERACTIONS.html Genes involved in Semaphorin interactions 85/106 Reactome 7.51292132384381e-08 3.23844645192172e-07 1170 1342.54545454545 1227 6.82992870946129e-09 325 2.5246489544195 3.10226973905508 1 4.73028743688111 1170 2144 926 1203 778 1249 1546 325 2491 1709 1227 899 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 8.01092166496098e-08 3.27123182997709e-07 1555 1491.09090909091 1227 7.28265632424083e-09 844 2.20047375314233 2.58506869308022 1 4.12000897752049 1551 2073 1032 1227 844 1842 2590 1127 1969 937 1210 900 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 5.38229832535123e-07 9.17459302840658e-07 1710 1546.72727272727 1228 5.38229962896276e-08 326 5.01894013091192 -4.71716261228997 -1 8.74910447112545 1706 930 4549 326 2689 1550 864 653 595 1228 1924 901 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 1.19641045333796e-07 3.67886471645288e-07 1805 1364.90909090909 1229 1.08764592581955e-08 534 3.02770681318637 2.55624518151155 1 5.62459338312187 1805 659 811 534 1290 1515 1229 2981 875 890 2425 902 M666 REACTOME_HYALURONAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HYALURONAN_METABOLISM.html Genes involved in Hyaluronan metabolism 20/23 Reactome 1.29779488938406e-05 1.51249182170192e-05 700 1410 1231 1.17982049566107e-06 474 2.20166362225797 1.89876552667957 1 3.06370555258765 696 1844 1749 1428 4004 851 639 474 1231 1541 1053 903 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 2.79194954057306e-06 3.63765113357903e-06 90 1511.36363636364 1231 2.53813916704827e-07 88 1.76557118077267 1.8030442775672 1 2.77221625710364 88 2952 1799 2429 3551 202 224 768 2651 730 1231 904 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 1.35862890265379e-09 1.69648900013913e-08 15 1427.18181818182 1232 1.23511718499348e-10 15 1.82912460623065 1.90727327049365 1 4.10337958229466 15 2548 1295 1906 4008 172 70 645 3298 510 1232 905 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 1.65206589822529e-19 7.35636890530507e-18 1235 1461.45454545455 1232 1.6520658982253e-20 62 2.5626713961328 2.98570286911527 1 12.6779432192597 1232 1032 4542 247 583 1427 2079 1070 2040 62 1762 906 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 8.48326373300187e-06 1.01190307858905e-05 940 1834.54545454545 1232 8.48329611776946e-07 688 3.72397110000071 3.72397110000071 1 5.3703613458189 688 1938 4555 1788 3933 1232 1044 939 981 2145 937 907 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 1.10160943985786e-07 3.53626743374685e-07 2025 1266.90909090909 1237 1.00146317728993e-08 625 2.22073437077708 2.48512975399572 1 4.13625488948399 2024 1374 876 625 1209 765 2009 1408 1330 1237 1079 908 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 1.97555482860613e-13 4.39840509010422e-12 2345 1233.45454545455 1237 1.79595893509664e-14 60 2.2986692790964 -2.05233055222371 -1 7.53741874368471 2344 1080 162 60 526 1367 2684 2294 1614 200 1237 909 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 7.00345345026853e-08 3.15651538021179e-07 1970 1298.81818181818 1238 6.36677606655967e-09 55 2.24936541819606 2.62246720739679 1 4.22163938692872 1969 55 1238 2102 714 1794 1887 917 1101 1151 1359 910 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 2.8788849825546e-08 2.61314175339571e-07 4210 1816.45454545455 1239 2.61716820020658e-09 34 2.87129086382492 2.67228891914489 1 5.4571412155443 4210 463 827 1158 34 3420 2771 2111 372 1239 3376 911 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 2.60643769775931e-06 3.42589416135448e-06 550 1337.45454545455 1239 2.36949162338811e-07 100 2.55750195148589 2.40995355049949 1 4.03529097068926 550 1878 1239 1852 3519 664 100 1075 1491 1436 908 912 M2920 KEGG_LINOLEIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LINOLEIC_ACID_METABOLISM.html Linoleic acid metabolism 18/62 KEGG 1.95792546464472e-07 4.68156443420621e-07 1240 1092.81818181818 1240 1.77993239899406e-08 193 3.2217261185055 -3.30788045802211 -1 5.88769646512345 1240 759 1018 1366 1773 614 193 1455 345 1936 1322 913 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 9.21901457042802e-08 3.3523689347011e-07 1605 1251.36363636364 1240 8.38092268795205e-09 419 2.47649803141486 2.83897194098973 1 4.62931578346188 1601 1240 504 419 1008 889 1601 2002 1559 992 1950 914 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 7.75814314428398e-08 3.25786793959256e-07 3345 1939.90909090909 1240 7.05285765260853e-09 107 2.70735448182518 -2.94568091069178 -1 5.07064434567064 3345 598 1161 179 810 3475 2457 4649 107 1240 3318 915 M17906 KEGG_VIBRIO_CHOLERAE_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIBRIO_CHOLERAE_INFECTION.html Vibrio cholerae infection 55/73 KEGG 1.13506915920926e-07 3.5893637536524e-07 1010 1339.27272727273 1241 1.03188110706552e-08 336 1.90676709984663 -1.68674732416097 -1 3.54778595912396 1010 1611 2277 1429 1241 387 917 2016 336 3165 343 916 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 8.14497602270173e-07 1.2703836641158e-06 1160 1578.90909090909 1243 7.40452639835153e-08 603 2.8615319899484 2.97139791394376 1 4.87110543169698 1160 2589 603 1243 2901 697 781 2179 2655 1213 1347 917 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 1.5119339356645e-07 4.1084215177527e-07 595 1426.63636363636 1243 1.37448549051915e-08 138 3.19317383576682 3.34150125184424 1 5.88780599151635 592 1894 1243 2794 1509 534 138 888 3052 2202 847 918 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 1.58139334450583e-05 1.81964324379998e-05 1245 1516.27272727273 1243 1.4376406471957e-06 266 2.94372943099612 3.00823383742906 1 4.02835822369811 1243 2882 1699 1678 4331 1137 266 278 1204 1647 314 919 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 5.58019780775018e-08 3.07843567066819e-07 1885 1022 1245 5.07290722662666e-09 115 2.95231633479128 3.10508164519728 1 5.55048993385591 1884 499 916 115 461 1527 1836 1245 154 1291 1314 920 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 4.59117987495359e-07 8.08729525563956e-07 965 1481.36363636364 1245 4.17380075735198e-08 662 2.7064203359322 3.41610362184298 1 4.76029680897256 962 1636 662 2174 2532 1047 870 1785 2498 1245 884 921 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 4.55736994908501e-11 7.0296686796344e-10 1945 1265.63636363636 1246 4.14306359016312e-12 243 2.63241985250853 2.92519438805884 1 6.95682990413106 1944 1246 243 305 377 1475 1958 2522 863 367 2622 922 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 2.85381106280896e-08 2.59537345211143e-07 1400 1546.36363636364 1246 2.85381109945802e-09 65 2.12607200384434 2.54120800012057 1 4.04238273098244 1396 1026 4487 493 65 1972 2926 1246 1170 395 1834 923 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 9.91950175208148e-29 8.67037930922677e-27 2960 1666.18181818182 1247 9.01772886552869e-30 31 3.00561784029458 3.4286517333162 1 22.6187066763573 2959 1247 31 473 340 2934 4148 2677 857 50 2612 924 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 1.55897189364695e-05 1.79647151806972e-05 1250 1641.54545454545 1247 1.4172572190901e-06 401 2.35693683219626 2.66378337694601 1 3.22897602514961 401 1762 1474 2319 4058 750 737 687 3375 1247 1247 925 M5374 BIOCARTA_SARS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SARS_PATHWAY.html The SARS-coronavirus Life Cycle 11/14 BioCarta 4.80161894914998e-06 5.96568608580887e-06 1155 1619.63636363636 1248 4.36511766270451e-07 160 1.73676536723859 1.66267062156138 1 2.61922735817544 1248 1917 2285 2330 3744 1151 160 266 767 2796 1152 926 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 1.14170182232005e-07 3.59285478750119e-07 4385 2072.45454545455 1248 1.03791080142662e-08 112 3.35960085353673 -3.59442441548956 -1 6.2512171101723 4385 766 675 385 1248 4101 3515 4575 112 1046 1989 927 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 1.72969710849572e-07 4.37757123436987e-07 795 1297.45454545455 1248 1.57245204044456e-08 435 2.75253634552603 3.32782652664027 1 5.05330348624075 791 1452 435 620 1910 1248 1633 1020 2662 1235 1266 928 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 7.29389484377507e-08 3.2144561803028e-07 1925 1359.63636363636 1249 6.63081371417943e-09 457 2.64164561869471 2.69958786850151 1 4.95200045872006 1922 457 1249 831 747 1803 2209 891 776 2129 1942 929 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 7.95457287602659e-08 3.27123182997709e-07 1190 1271.45454545455 1250 7.2314301487648e-09 585 1.88801992006556 1.95116671934788 1 3.53487056378961 1186 1250 1896 585 833 948 1741 1709 1262 1759 817 930 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 1.10233139134507e-12 2.23304899877627e-11 1235 1235.63636363636 1251 1.00211944667783e-13 181 3.1994189928303 -3.35663009664105 -1 9.83945575807029 1233 229 181 1560 1251 1882 2126 1179 2099 329 1523 931 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 2.98148084994253e-08 2.65971846975155e-07 3110 1792.27272727273 1252 2.71043717304375e-09 44 3.00750404421489 3.23402476854333 1 5.70940379420226 3107 776 990 1211 44 2726 1252 3284 1259 1048 4018 932 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 2.53606479853958e-09 3.01605138348018e-08 1590 1520.72727272727 1253 2.53606480143381e-10 204 1.88896543950064 1.93404344609435 1 4.10134695147452 1253 974 4705 1587 946 498 1889 1193 1893 204 1586 933 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 3.71539798264737e-07 6.91063340528052e-07 2375 1174.27272727273 1254 3.37763510010031e-08 85 4.36776720147377 4.95345968220669 1 7.76907798879304 2375 619 555 735 2377 1854 1530 277 85 1256 1254 934 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 9.75122178662859e-08 3.39726302159777e-07 885 1240.18181818182 1255 8.864747471672e-09 571 1.87888471894643 1.81644818035867 1 3.50885531187061 882 1380 1400 1231 1074 710 1449 571 2325 1365 1255 935 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 1.14850243936191e-07 3.59285478750119e-07 935 1880.36363636364 1256 1.04409318119917e-08 593 2.1399733568045 2.50460800551689 1 3.98154071030995 935 3880 2320 3675 1256 902 857 593 1914 3236 1116 936 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 6.42987812954642e-08 3.14536172538656e-07 2335 1482.36363636364 1257 5.84534392497335e-09 612 1.90303086008706 -1.90687100033515 -1 3.57234618914301 2331 1257 1637 1860 612 1132 2464 909 1992 940 1172 937 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 2.42071212211647e-07 5.2719175985577e-07 1065 1403.27272727273 1258 2.20064762588472e-08 299 2.00955596664526 2.18757735464124 1 3.64220459246592 1065 299 1258 802 1986 1838 3247 1356 812 687 2086 938 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 7.33161365186587e-08 3.2144561803028e-07 2465 1708.72727272727 1258 6.66510354199606e-09 390 2.77976790333532 -3.03324092594025 -1 5.21096804321294 2463 390 772 2053 750 1936 3406 3866 789 1113 1258 939 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 9.86296384990877e-12 1.71151431513123e-10 625 1370.45454545455 1259 8.96633077268455e-13 140 1.79319656015053 1.77961802042436 1 5.05640243435346 625 1098 975 1387 2162 725 1259 1670 3037 140 1997 940 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 9.06037844097669e-08 3.33060640509423e-07 1265 1127.09090909091 1261 8.23670801283196e-09 303 2.23893851633677 2.55287453163499 1 4.18699204316954 1261 1433 593 963 990 1455 1809 303 1781 528 1282 941 M7253 KEGG_FOCAL_ADHESION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOCAL_ADHESION.html Focal adhesion 214/245 KEGG 8.73933853168092e-08 3.30738824521022e-07 650 1141.63636363636 1262 7.94485352622252e-09 433 2.44874563604832 2.69341454731132 1 4.5815769541405 647 2045 433 862 953 1262 1381 1370 1351 941 1313 942 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 1.52948654211642e-07 4.12818153481133e-07 985 1306.54545454545 1262 1.39044240768143e-08 457 2.95764127765364 3.33107578449631 1 5.45167072500981 983 1490 457 754 1522 1538 1262 2679 534 1169 1984 943 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 6.93532068096495e-07 1.1176071565092e-06 1265 1972.27272727273 1263 6.93532284540618e-08 653 2.59757907724631 1.97236148222473 1 4.46344555315731 1263 925 4244 4119 2863 1070 653 1046 2928 1553 1031 944 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 8.6034290330451e-08 3.28305665915602e-07 1210 1788.63636363636 1265 7.82129942681368e-09 733 1.40856105966852 -1.3153439610099 -1 2.63634117697766 1206 1594 3239 2928 939 733 1265 757 4054 2165 795 945 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 1.58901153964178e-07 4.20175600398276e-07 820 1415.18181818182 1265 1.444556049466e-08 717 1.86130998353899 2.04238532649954 1 3.42641580403807 818 2208 2138 1713 1570 1063 717 802 1265 2232 1041 946 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 1.15431877631374e-07 3.59296663856335e-07 1375 1335.18181818182 1267 1.04938076079976e-08 550 3.34709000324214 -4.15363122360675 -1 6.22792186709251 1372 683 945 2524 1267 1446 1082 1920 550 1678 1220 947 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 1.05666581267532e-13 2.39781857491707e-12 2715 1742.54545454545 1268 9.60605284250337e-15 129 2.82711444315754 -2.78389890446151 -1 9.48550351114215 2714 1268 158 684 129 2773 3265 3453 1255 285 3184 948 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 7.49186022095885e-07 1.18503955237687e-06 785 1525.54545454545 1269 6.81078433839219e-08 72 1.58515697885263 -1.06482528506609 -1 2.71180854388995 783 1903 2904 2395 2852 291 72 1269 247 3560 505 949 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 6.01616945979754e-10 7.99896333809701e-09 2640 1651.18181818182 1270 5.46924496494793e-11 178 2.18919133456251 2.26694053169907 1 5.11771864296436 2638 1157 478 502 1023 2648 3538 1588 1270 178 3143 950 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 1.95755666252939e-07 4.68156443420621e-07 525 1177.72727272727 1271 1.7795971242841e-08 216 2.51646864794739 2.7710854127671 1 4.59865164289415 523 366 1047 1271 1772 1445 1375 216 1915 1205 1820 951 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 8.46497371339057e-08 3.27455016694392e-07 2080 1452.90909090909 1271 7.69543094463515e-09 379 3.88863582652757 4.22111944799278 1 7.28096872058804 2080 852 962 1032 924 1271 379 3423 2125 1420 1514 952 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 8.44955150369033e-16 2.41708382408596e-14 135 1107.63636363636 1272 7.6814104579003e-17 86 1.88833955736511 1.83030526613862 1 7.42412512493518 135 1272 597 1345 2829 219 260 1354 2454 86 1633 953 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 5.15076512189637e-08 3.0357704374324e-07 4295 2195.63636363636 1273 4.6825138568082e-09 386 2.05589465843146 -1.76983766230423 -1 3.86851291627045 4293 1273 935 720 386 4606 4055 2072 1140 574 4098 954 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 1.06114470811279e-07 3.48348225330125e-07 1455 1488 1274 1.06114475878406e-08 177 2.13117897877414 2.33115418268199 1 3.97343724648846 1454 1027 4482 177 1274 872 1977 1052 2063 371 1619 955 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 1.20969458291346e-11 2.0687530548375e-10 10 1288.81818181818 1275 1.09972234810919e-12 6 1.84958548210905 1.85957555077708 1 5.17146235978778 6 2513 1311 2073 3686 325 256 878 1630 224 1275 956 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 3.15018545198692e-07 6.17221890136083e-07 430 1404.90909090909 1275 2.86380536642077e-08 430 2.39902058115831 2.52314349924371 1 4.30081916920159 2106 600 1037 430 2241 1872 2454 1275 430 991 2018 957 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 3.57333852932698e-06 4.53391340280197e-06 1160 1711.09090909091 1276 3.24849484846968e-07 230 3.15295816444022 3.27366374217113 1 4.86421479109343 1157 3101 1012 2346 3655 1219 1276 386 3118 1322 230 958 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 8.9637262294315e-11 1.31803077267653e-09 1525 1413.54545454545 1276 8.96372622979305e-12 159 2.42849085463391 2.70789035363412 1 6.22639181191228 1521 983 4547 665 242 1356 2192 1210 1276 159 1398 959 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 3.27058485796944e-07 6.32670513508843e-07 1280 1410.27272727273 1277 2.97325940380394e-08 109 2.28276983048727 2.63979038930325 1 4.08529294645749 1277 752 1696 2360 2274 1049 778 856 1905 2457 109 960 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 2.78795770171924e-07 5.7040140234568e-07 3690 1798 1277 2.53450732274929e-08 178 2.63218251255869 -2.53822595148496 -1 4.74494241465038 3687 178 791 561 2129 4264 3488 1555 590 1258 1277 961 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 6.49835207849709e-06 7.89097551080686e-06 530 1347.18181818182 1278 5.90761024853222e-07 63 2.72499408577601 2.90556538045573 1 4.01448907659362 529 1831 1687 1278 3829 319 63 348 2333 2330 272 962 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 2.65367607891794e-06 3.47636721967602e-06 875 1744.54545454545 1278 2.41243570893723e-07 521 2.36324911037136 2.48570766049441 1 3.72439398408027 872 3435 1665 2372 3530 971 527 1222 2797 1278 521 963 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 8.88520445639178e-08 3.31003670356505e-07 1165 1296.63636363636 1281 8.07745892294651e-09 480 2.12792547415527 2.4498273586425 1 3.98099940077101 1162 2500 1432 1867 973 542 1281 480 1519 1783 724 964 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 4.0637204021554e-08 2.9351990282604e-07 2355 1558.18181818182 1281 3.69429134292567e-09 194 2.29635495968545 2.60243185565514 1 4.33078245376423 2353 1260 514 767 194 2670 3705 1891 1281 465 2040 965 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 8.44085331854652e-15 2.15355825208322e-13 3495 1973.36363636364 1282 7.67350301686047e-16 50 2.81775056757311 2.98458735960903 1 10.3057141367468 3494 1282 139 50 264 3086 4083 3950 498 299 4562 966 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 9.46629450968446e-12 1.64874206958342e-10 1285 1349.54545454545 1283 8.60572228156835e-13 10 2.69345789274308 -2.50676483577855 -1 7.60798661955989 1283 10 215 537 493 1397 2254 3650 3300 173 1533 967 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 1.20584622848544e-10 1.74054868454168e-09 2050 1374.54545454545 1286 1.09622384413776e-11 240 2.55636638085129 3.00194101736652 1 6.46515243747297 2047 1195 261 819 633 2130 3072 1668 1286 240 1769 968 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 2.29972369981726e-07 5.1201395580837e-07 2015 1559.90909090909 1286 2.09065812746733e-08 191 2.48453081880439 2.34891485725399 1 4.51237484615122 2012 648 1286 1020 1936 1362 659 3831 191 1263 2951 969 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 8.53664361816351e-11 1.26310212782858e-09 495 1193.81818181818 1286 7.76058510772252e-12 255 2.901829642108 3.2158464815956 1 7.45564106649499 491 1464 255 601 2061 1286 1490 1320 2524 426 1214 970 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 1.10884676975214e-07 3.54350491078546e-07 2210 1393.09090909091 1287 1.00804256876399e-08 371 2.38597520889371 -2.22850744895531 -1 4.44347846818651 2206 597 1287 1365 1218 1307 743 3389 371 1870 971 971 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 8.07189587061918e-06 9.65762953341509e-06 195 1511.36363636364 1288 7.33811407900819e-07 194 2.57864004458306 2.90789612072919 1 3.73349978648401 194 2218 1104 1288 3897 677 548 1398 1569 3012 720 972 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 2.66760635428604e-07 5.55408116110725e-07 740 1521 1289 2.42509697976933e-08 664 2.52343140936968 2.7820549904338 1 4.55729465457798 736 3047 1289 1070 2088 925 664 918 2904 1670 1420 973 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 4.1374616758368e-06 5.19245389788612e-06 495 1349.45454545455 1289 3.76133587003105e-07 226 2.18782015646906 1.98294547887634 1 3.33777741368858 495 2299 1573 1459 3701 540 226 509 1289 1810 943 974 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 3.01916797394325e-06 3.90745073677328e-06 90 1609.18181818182 1290 2.74470192482145e-07 90 1.50651641540808 1.64658142687904 1 2.35181695845498 90 2056 3304 2151 3581 579 613 875 1931 1231 1290 975 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 1.14443114718445e-05 1.34337602952266e-05 2045 1613.63636363636 1290 1.04039736410235e-06 575 2.63259235584424 3.07036199291429 1 3.70267596943271 2043 2272 1149 1069 3978 1625 1277 575 1527 1290 945 976 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 8.39387352941041e-08 3.27411388472988e-07 3305 1896.09090909091 1291 7.63079440879093e-09 678 3.00189974715536 -3.03485096643703 -1 5.62052360472588 3304 1798 678 924 908 4530 3720 1062 1291 970 1672 977 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 1.6590232592358e-05 1.90478953626684e-05 1030 2090.36363636364 1292 1.5082143364426e-06 803 2.60931792790614 2.97867768053008 1 3.55566899596765 1030 2271 921 3819 4071 1092 1292 2368 4226 803 1101 978 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 5.29434767247288e-08 3.06874196014832e-07 3270 2124.54545454545 1292 4.81304345443864e-09 401 2.28941913180972 2.60763420618855 1 4.3049249518717 3269 486 1292 965 401 3559 4256 3890 468 901 3883 979 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 6.60406444003029e-08 3.14536172538656e-07 1755 1357.81818181818 1293 6.00369512570384e-09 125 2.70310567770678 2.79843261090205 1 5.07459894262014 1751 667 1293 194 642 1614 1231 3052 125 2109 2258 980 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 8.20422524458865e-08 3.27411388472988e-07 1295 1104.90909090909 1294 7.45838686412735e-09 55 2.70904806061696 -2.7238551791079 -1 5.07212685741155 1294 2138 711 1322 876 1066 1637 57 1440 1558 55 981 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 8.95403253142735e-08 3.31497675696653e-07 1100 1470.09090909091 1294 8.14002990532531e-09 772 2.3941224183199 2.65127362219976 1 4.47867018941127 1097 2530 838 1375 980 772 1294 2129 2693 1325 1138 982 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 2.84495366604298e-07 5.77024553420288e-07 1600 1390 1298 2.58632184903754e-08 751 2.52933992466326 2.83166352676833 1 4.55585613444516 1598 1458 762 2544 2151 1298 1954 903 979 751 892 983 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 1.78569424565077e-07 4.45009336825324e-07 665 1418.36363636364 1298 1.6233585369017e-08 664 2.26003748774373 2.43421618952363 1 4.14432765695362 664 2229 1579 2754 1686 728 689 899 1298 1817 1259 984 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 8.56799075466956e-08 3.28305665915602e-07 3500 2057.36363636364 1300 7.78908280759412e-09 536 2.42436008328438 2.47017120844568 1 4.53818824802781 3500 536 1178 1022 933 3708 4225 2691 964 1300 2574 985 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 1.06743957774996e-07 3.48431176139683e-07 4445 1955 1300 9.70399663220103e-09 171 2.63088795319919 -2.29305682214413 -1 4.90523380761168 4445 223 655 171 1179 3600 2734 3818 1300 825 2555 986 M3115 KEGG_LONG_TERM_POTENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_POTENTIATION.html Long-term potentiation 65/89 KEGG 1.02035452216185e-07 3.44497378011726e-07 1210 1729.09090909091 1301 9.27595063168768e-09 856 1.95605063050196 2.08918247819008 1 3.6495785121049 1210 3024 2778 1301 1124 856 1020 1393 1558 3637 1119 987 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 1.17681535814495e-09 1.47727885384154e-08 4455 2060.81818181818 1301 1.06983214434041e-10 302 3.35887512637458 3.49815212329584 1 7.59415783685445 4451 372 302 933 632 3896 3840 2409 1301 318 4215 988 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 1.21110639904779e-07 3.69968882213284e-07 1150 1491.72727272727 1302 1.10100587792687e-08 21 3.14683188993368 4.02738334824868 1 5.84369925917765 1147 3044 757 2292 1302 2567 2883 21 663 1306 427 989 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 3.98102191763328e-08 2.9351990282604e-07 2575 1478.90909090909 1302 3.61911089970188e-09 105 2.19191288831016 -2.34800467383174 -1 4.13377203657353 2572 1184 602 105 179 2521 3579 2303 1451 470 1302 990 M9488 KEGG_RETINOL_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RETINOL_METABOLISM.html Retinol metabolism 24/101 KEGG 1.21796791221401e-07 3.70192774369017e-07 4160 2208 1305 1.10724361785761e-08 314 3.1750300787869 2.98991189032621 1 5.895830415216 4160 657 952 580 1305 4144 3470 2863 314 1260 4583 991 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 2.14359334663911e-13 4.72792551221336e-12 1545 1170.27272727273 1306 1.94872122421756e-14 131 2.51773021327625 2.7233393184659 1 8.23299858837406 1541 1244 164 353 314 1828 2260 1306 2081 131 1651 992 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 1.5574642827765e-07 4.16500363439382e-07 875 1217.45454545455 1307 1.41587672094125e-08 236 1.85764693549227 -2.07473766247408 -1 3.42171762965788 875 236 2094 1793 1542 558 1307 905 1339 2011 732 993 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 6.18166450775047e-08 3.14073804914771e-07 1410 1147.18181818182 1308 5.61969516495073e-09 369 2.32225401846113 2.40974374894003 1 4.35992492714288 1408 1308 518 526 570 1315 1735 1202 2107 369 1561 994 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 3.99354677185192e-08 2.9351990282604e-07 1730 1421.45454545455 1308 3.63049713122248e-09 182 2.749333556256 -2.93020473968691 -1 5.18524178335902 1728 563 974 1599 182 740 641 3315 3167 1308 1419 995 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 5.89912521483797e-07 9.86322033795085e-07 380 1489.09090909091 1309 5.36284254240193e-08 88 1.83166305175236 1.87203774661782 1 3.17581523878374 379 2302 2002 2800 2687 197 88 394 3491 1309 731 996 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 1.2222646690658e-07 3.70192774369017e-07 4260 1989 1310 1.11114976088341e-08 378 2.67610503086466 2.75441358684821 1 4.9692227498891 4260 378 688 764 1310 3876 3718 1305 3074 1480 1026 997 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 2.93246524703941e-21 1.59094666276161e-19 3175 1960.72727272727 1310 2.66587749730855e-22 58 3.0167947152145 -2.73429654549925 -1 16.3751752990955 3171 1310 58 252 1132 3456 4414 3802 1273 146 2554 998 M1053 KEGG_HEDGEHOG_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEDGEHOG_SIGNALING_PATHWAY.html Hedgehog signaling pathway 40/61 KEGG 2.63288075262082e-07 5.52643162903538e-07 1630 1371.27272727273 1313 2.39352824337687e-08 177 2.92371344090345 3.43874970744228 1 5.28216694237111 1627 495 1313 977 2069 1089 1544 2527 177 2545 721 999 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 1.48306296830029e-09 1.83728535705443e-08 3100 1616.72727272727 1313 1.34823906300005e-10 120 2.79295353396554 -2.75620863273724 -1 6.23812016712925 3098 120 305 1313 398 3205 3811 870 2298 315 2051 1000 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 1.54261286692283e-16 5.09170121110192e-15 2160 1100.90909090909 1314 1.40237533356621e-17 80 2.57948221942513 2.80409826312846 1 10.6455572917446 2157 1314 152 313 512 1805 2285 407 1700 80 1385 1001 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 7.14570147357512e-06 8.61719748474057e-06 510 1783 1315 6.49611334840785e-07 384 1.90439241455426 -2.06261013391707 -1 2.78428454610578 509 3082 2633 3396 3861 384 482 454 1315 2854 643 1002 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 1.66879125156759e-07 4.29439298099957e-07 1320 1171.90909090909 1318 1.51708307104758e-08 271 2.20520684826044 2.59054052489088 1 4.053610833688 1318 1419 1099 1463 1620 321 1502 1153 1256 1469 271 1003 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 1.33755190638219e-08 1.38752637321406e-07 1335 1251.81818181818 1318 1.21595628592201e-09 369 2.39797776369577 2.36587167896658 1 4.74779561415125 1332 2025 369 404 1362 1042 1664 1262 1318 502 2490 1004 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 9.44716547518094e-08 3.3764305071295e-07 1070 1701.09090909091 1320 8.58833261896176e-09 260 1.76353898702687 1.94130387083111 1 3.2947523217206 1067 1398 2366 4537 1036 260 924 1628 2865 1311 1320 1005 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 1.12243655905288e-06 1.64670090125232e-06 605 1420.63636363636 1320 1.02039739247151e-07 531 3.15121846235548 3.33359526661023 1 5.2617837137109 603 2238 531 1228 3110 1376 1389 1880 754 1320 1198 1006 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 1.23423763770534e-07 3.71755418903835e-07 3785 2001.90909090909 1320 1.12203427904381e-08 41 2.64295763330951 -2.30533037021032 -1 4.90626497294172 3783 753 1080 321 1320 3705 3550 3648 41 911 2909 1007 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 1.2352434472212e-07 3.71755418903835e-07 315 1383.36363636364 1322 1.12294865143358e-08 60 2.10290355378055 2.3601379116442 1 3.90355742208651 313 2165 1556 3362 1322 60 261 333 4050 1547 248 1008 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 3.32760235896006e-07 6.40549883127711e-07 680 1534.36363636364 1323 3.02509351115955e-08 26 2.70015536997189 2.74254328383271 1 4.82822116593841 680 1871 1323 3589 2285 287 26 702 3871 1939 305 1009 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 2.00433372928003e-07 4.74922449909727e-07 1150 1457.45454545455 1323 1.82212173807913e-08 275 1.76399671290484 -1.9785367578246 -1 3.22013558606162 576 1526 1966 2410 1791 435 1323 1146 3436 1148 275 1010 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 2.63870668682378e-06 3.46129383620488e-06 745 1629.90909090909 1323 2.39882713793264e-07 359 2.38636701264603 -2.53737529155139 -1 3.76213582551584 742 835 1629 2363 3526 1323 1098 3206 359 1802 1046 1011 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 2.12077896385156e-09 2.5799166776751e-08 4715 2331.63636363636 1323 1.92798087808725e-10 262 2.86605627067671 -3.26864039445308 -1 6.27940475317605 4715 262 312 951 957 4134 4666 4114 1323 325 3889 1012 M17807 KEGG_BASAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_CELL_CARCINOMA.html Basal cell carcinoma 45/60 KEGG 1.93746929873702e-06 2.63616462670474e-06 1030 1428.81818181818 1324 1.76133727727825e-07 726 2.48798047206898 2.88040811219874 1 4.00733428597247 1027 1646 877 1585 3388 898 1454 1849 726 943 1324 1013 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 4.68888371100848e-08 2.99073619127066e-07 1325 1519.81818181818 1324 4.26262164631197e-09 302 2.64985362897848 2.98242465786018 1 4.99136251054217 1324 1509 558 757 302 1751 2351 3669 1243 713 2541 1014 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 1.92567149180417e-06 2.62313692390063e-06 1325 1780.18181818182 1325 1.75061197941505e-07 86 1.51974743518041 -1.75764072679357 -1 2.44843208843343 1325 4060 3019 1961 3386 1068 86 248 704 3582 143 1015 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 1.48297863815324e-09 1.83728535705443e-08 1870 1179.63636363636 1325 1.34816239922989e-10 78 2.34026833245245 2.55763930768213 1 5.22689869162997 1869 1123 304 78 529 1325 2389 1578 1471 308 2002 1016 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 2.42477454158571e-08 2.3074467411864e-07 3815 2193.63636363636 1328 2.20434051664623e-09 278 2.49367869659028 -1.77344750382114 -1 4.77824988509279 3812 1328 389 953 278 4206 4163 3290 1069 391 4251 1017 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 6.37762051812368e-20 3.01023688455438e-18 1330 1506.54545454545 1329 6.37762051812368e-21 57 2.33367278077258 2.56524077361323 1 11.8064819393315 1329 1004 4293 72 181 1658 2440 1066 2383 57 2089 1018 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 4.01503723622944e-12 7.34533943992363e-11 730 1355.63636363636 1331 3.65003385112434e-13 204 2.84637147466455 3.18588198368157 1 8.32857112571476 728 2090 204 515 3096 1331 1287 1838 1677 428 1718 1019 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 4.45150315546512e-08 2.98029714805608e-07 4005 2002.36363636364 1331 4.04682113230665e-09 265 2.38613263728974 -2.19801340302839 -1 4.49556847318405 4004 1331 586 500 265 3676 3760 3210 1132 715 2847 1020 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 6.50993547478611e-08 3.14536172538656e-07 1335 1110.72727272727 1331 5.91812333401739e-09 298 1.93989840118894 2.35438304589365 1 3.64157017159381 1331 595 1801 1623 628 789 1534 1337 410 1872 298 1021 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 1.25077484132953e-07 3.7431417048731e-07 1420 1217.81818181818 1332 1.13706810221849e-08 137 2.18093152484898 -2.44068271870996 -1 4.04655431179221 1420 137 683 934 1332 1784 3032 1523 1664 534 353 1022 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 2.66332715598886e-07 5.55287751817547e-07 1335 1166.72727272727 1333 2.42120679855651e-08 244 2.75618988530082 2.86235531942853 1 4.97780875211082 1333 311 814 1364 2083 1156 1549 1338 244 1000 1642 1023 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 1.05937724189134e-07 3.48348225330125e-07 905 1377.27272727273 1334 9.63070266276432e-09 171 2.24193004170502 -2.12874361559333 -1 4.17996977870984 902 171 928 2255 1163 1346 1472 3240 1898 441 1334 1024 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 2.23545146763061e-06 2.98989258351274e-06 1340 1896 1336 2.03223067191641e-07 39 1.21237029722523 -1.28931922046624 -1 1.9331520601577 1336 1884 3294 3950 3457 403 516 1166 343 4468 39 1025 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 5.31516433924803e-08 3.06874196014832e-07 1085 1311.72727272727 1336 4.83196769787411e-09 409 1.88399942514744 -2.08662950373023 -1 3.54243870166004 1084 2046 1610 551 409 1707 2303 982 1367 1034 1336 1026 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 4.38589084448017e-07 7.80649012507429e-07 3140 1758.90909090909 1336 3.98717428985982e-08 30 3.31452176961736 4.47744581152908 1 5.84476344027859 3137 767 1336 437 2502 4573 3948 83 30 2128 407 1027 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 1.58730339422728e-07 4.19959193988384e-07 795 1399.90909090909 1337 1.44300318977407e-08 199 2.37889862410718 2.22863415179313 1 4.37961854626434 795 199 1170 1687 1568 623 583 2780 2733 1924 1337 1028 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 1.38052498962845e-06 1.96031225964087e-06 1835 1481 1337 1.25502350538574e-07 633 2.18471428703685 2.10581777298218 1 3.59992463256719 876 1833 1463 633 3234 1301 1337 1111 971 1699 1833 1029 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 5.79498200438423e-06 7.10080868657673e-06 1340 1768.90909090909 1338 5.26817933536595e-07 54 1.9364374344898 -2.17984330922048 -1 2.878153088625 1338 3764 2921 1931 4324 965 588 158 54 3294 121 1030 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 1.18092236871643e-08 1.24696948106075e-07 20 1639.27272727273 1339 1.07356579550492e-09 10 1.43590301100575 1.46144556671698 1 2.86185555666853 20 2638 2845 3124 3698 100 10 475 3076 1339 707 1031 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 3.10550111447732e-07 6.11341009591772e-07 2590 1685.36363636364 1340 2.82318322986117e-08 450 3.23723748502877 3.56722884703197 1 5.80771143888921 2586 507 720 1340 2229 3343 2885 2748 537 1194 450 1032 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 9.16921195198953e-06 1.08822430006011e-05 1340 1598.63636363636 1340 9.16924978571076e-07 156 1.54384618277063 1.79536499002223 1 2.21180733150525 1340 874 4594 1439 3946 1345 518 440 156 2381 552 1033 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 1.90694304520776e-07 4.62051908284427e-07 1345 1442.63636363636 1342 1.73358473681831e-08 145 2.65984384501593 2.70064950733498 1 4.86508595859706 1342 2640 1553 2315 1742 1113 1170 595 1015 2239 145 1034 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 1.64057967488842e-15 4.47603240778805e-14 1465 1201 1342 1.49143606808038e-16 84 2.99274277339946 3.15521184972883 1 11.5353987577295 1464 1342 127 84 540 1728 1842 2709 717 324 2334 1035 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 6.45393367023976e-08 3.14536172538656e-07 3315 1822.90909090909 1342 5.86721259961162e-09 150 1.96605186899778 -2.02459594733162 -1 3.69067697781188 3312 1249 1193 150 619 2924 4330 2256 1342 761 1916 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 1.93488893032698e-08 1.94312250024327e-07 30 1477.18181818182 1343 1.75898995213112e-09 26 1.72681987019671 1.80840124203994 1 3.34578687070992 26 2081 2331 2830 2970 156 40 616 2804 1343 1052 1037 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 1.89283542743316e-10 2.65170311888287e-09 1395 1162.36363636364 1345 1.72075947963274e-11 269 2.65896926990158 3.00578548283944 1 6.58428743363922 1391 2082 269 541 390 1245 1670 1630 1756 467 1345 1038 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 9.75993359594613e-08 3.39726302159777e-07 1520 1297.27272727273 1345 8.87266729902669e-09 443 2.4389559028138 2.47367372025728 1 4.55505635419905 1519 2079 850 828 1077 443 1489 1648 1345 1852 1140 1039 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 2.61297563076909e-07 5.49854880839506e-07 1095 1568.45454545455 1346 2.37543267374226e-08 399 2.27002706706036 2.81623742424219 1 4.10242287797611 1092 743 1500 3826 2064 1094 399 2696 1346 1412 1081 1040 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 1.08154112467171e-06 1.59877046929234e-06 1350 1455.90909090909 1347 9.83219687607339e-08 87 3.50791389240451 3.99795564754485 1 5.87047242251986 1347 675 793 411 3086 1780 1308 87 2134 1389 3005 1041 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 6.76762724970789e-07 1.09657399995267e-06 930 1568.81818181818 1347 6.76762931074381e-08 228 3.9026753639578 3.9026753639578 1 6.71573677938906 930 929 4325 1347 2849 1521 1368 789 228 1847 1124 1042 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 7.72306202394555e-06 9.26845989143732e-06 365 1656.81818181818 1348 7.02099012341337e-07 364 3.61146475992877 3.88393925769591 1 5.24785497355398 364 2622 562 1232 4097 1212 1392 3035 991 1348 1370 1043 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 1.03939005916019e-07 3.47369293280946e-07 1390 1352 1348 9.44900098423794e-09 127 2.45714970307639 -2.23709776369363 -1 4.58218625931139 1388 2076 582 127 1138 1688 2174 2753 668 930 1348 1044 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 1.30022457087362e-07 3.79878839072891e-07 975 1290.09090909091 1349 1.18202240701668e-08 631 1.97583921263441 2.13965329050116 1 3.66228339220811 649 2034 1532 631 1369 975 973 725 1875 2079 1349 1045 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 3.61531097576489e-07 6.79310024108689e-07 945 1513 1350 3.28664688170677e-08 36 1.84903320148603 -1.7912344615218 -1 3.2924116162979 944 36 1350 1436 2350 1125 1129 1651 3514 1168 1940 1046 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 4.01962210811458e-08 2.9351990282604e-07 1610 1434.63636363636 1350 3.65420198323376e-09 187 2.022544051818 2.39900592157855 1 3.81428943059834 1607 1351 944 1209 187 2094 2608 1148 2557 726 1350 1047 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 3.81137856708373e-08 2.89689321040824e-07 2865 1484.72727272727 1350 3.46488966646706e-09 156 2.10515615985377 2.4790673377306 1 3.97358978476273 2864 1350 1096 564 156 2689 3429 1405 1142 1372 265 1048 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 1.17631480833278e-06 1.71470225303604e-06 450 1639.54545454545 1351 1.06937767026846e-07 449 1.92279096486147 -1.84051995877339 -1 3.20050916421705 449 2147 1168 2184 3134 829 910 1351 3791 636 1436 1049 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 1.03918767391088e-20 5.21804874559508e-19 2330 1401.72727272727 1352 9.44716067191708e-22 65 2.5783551602428 2.62163234194221 1 13.6111270523002 2328 1052 65 82 475 1352 2939 2150 1736 136 3104 1050 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 3.96224787717998e-08 2.9351990282604e-07 1360 1223.36363636364 1352 3.60204358958266e-09 177 2.18867244118673 2.518774571639 1 4.12765953965285 1489 1150 972 440 177 1360 2284 1352 1604 1356 1273 1051 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 3.00625250398001e-07 5.99979358088189e-07 1245 1715.90909090909 1353 2.73295719525273e-08 322 1.879972639484 1.98469428589562 1 3.37679502926986 1244 677 1954 4148 2195 1272 1410 322 3655 1353 645 1052 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 5.54281336957027e-09 6.25887059913198e-08 1355 1330.63636363636 1355 5.03892125775925e-10 335 2.35956890989827 2.75807512636217 1 4.90731221015729 1355 1143 335 560 986 1857 2491 1491 2376 578 1465 1053 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 3.07693129537375e-08 2.6944556055963e-07 1355 1398.27272727273 1355 2.79721030764352e-09 29 1.91883836876876 1.96344622123037 1 3.63926174279007 29 2626 1355 1670 4244 250 60 1041 2001 750 1355 1054 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 1.7342700159673e-07 4.38209554355764e-07 1745 1538.36363636364 1356 1.73427015131348e-08 45 3.04298480373917 3.80483856962043 1 5.58622626315425 1792 897 4679 2270 1743 1744 1356 1120 45 1186 90 1055 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 1.63836008323145e-05 1.88243904402445e-05 1350 1485.90909090909 1357 1.48942934943251e-06 510 3.80576067457883 4.41674187554296 1 5.19206759858972 1350 815 644 1576 4070 1802 1431 510 1357 808 1982 1056 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 1.28263987875399e-07 3.77906381255858e-07 2490 1690.81818181818 1357 1.16603632139475e-08 312 2.48786634077885 2.01518214108258 1 4.6131900617461 2487 312 1114 771 1357 2279 2687 3162 525 1284 2621 1057 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 1.13342246102226e-07 3.58803086252519e-07 1955 1656.54545454545 1357 1.03038410855935e-08 836 2.2047312041373 1.98611490676476 1 4.10242387012531 1951 1357 895 836 1240 2049 2644 1132 2186 1350 2582 1058 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 2.47869468755176e-07 5.33004051263978e-07 4580 1758.18181818182 1357 2.25335906074658e-08 58 2.52958693567172 -1.99478187415352 -1 4.581475354567 4576 58 736 424 2015 2988 4143 305 692 1357 2046 1059 M14857 REACTOME_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPHINGOLIPID_METABOLISM.html Genes involved in Sphingolipid metabolism 65/73 Reactome 2.96601253685641e-08 2.65646663642548e-07 2400 1691.18181818182 1358 2.69637506985802e-09 42 1.61588761463536 -1.46450458341212 -1 3.06742790871465 2398 322 3312 2777 42 882 2060 1358 1074 3081 1297 1060 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 6.00293450131842e-08 3.10910012492405e-07 1575 1335 1358 5.45721333192263e-09 401 2.04033529436789 2.58088507598412 1 3.83312155876549 1575 401 1358 1801 539 2166 1996 807 2529 1066 447 1061 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 1.18266583773404e-07 3.64829498861888e-07 2250 1763.90909090909 1359 1.07515081937387e-08 874 2.14550428058579 -2.04458663453916 -1 3.98771338237936 2248 1261 874 1163 1283 2254 3458 2042 1359 1106 2355 1062 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 1.40224882924844e-06 1.98417328584169e-06 150 1552.36363636364 1359 1.27477247547525e-07 147 2.2459914177919 2.26854975901045 1 3.69751214596332 147 3293 1359 1922 3246 490 198 587 3368 1500 966 1063 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 1.13654673647467e-07 3.5893637536524e-07 765 1743.90909090909 1360 1.03322435926369e-08 654 2.22628505579489 2.31678983090708 1 4.1424346324859 765 3040 1918 2885 1243 1059 654 1022 3667 1570 1360 1064 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 3.67240929037489e-09 4.26940193363781e-08 860 1495.81818181818 1360 3.33855390591379e-10 327 2.71125772254792 2.8074608986607 1 5.76892993378557 860 2118 327 1215 2161 936 1360 1970 3369 421 1717 1065 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 1.13840625830882e-07 3.5893637536524e-07 1420 1435.36363636364 1360 1.03491483383318e-08 726 2.07382730835988 2.14978823523649 1 3.85869847441327 1419 1413 1141 726 1245 1615 2367 1360 2180 1152 1171 1066 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 4.41672941339469e-08 2.97677410474742e-07 2045 1268.18181818182 1361 4.01520863824104e-09 257 2.30172939384269 -2.57991080642924 -1 4.33686037626175 2044 647 1361 1570 257 2105 1880 804 373 1262 1647 1067 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 7.94099868592637e-08 3.27123182997709e-07 2295 1466.81818181818 1361 7.21908997505481e-09 139 2.34613485077522 2.45192113987136 1 4.39279136835216 2295 139 732 2048 829 2465 2725 193 1361 580 2768 1068 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 5.02688227146913e-06 6.22589460019267e-06 2035 1733.45454545455 1362 5.02689364280075e-07 22 4.28517057780349 5.83500455679592 1 6.44081482358288 2033 893 4638 747 3787 2129 1362 251 22 2148 1058 1069 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 1.93783390509398e-13 4.33487015736664e-12 625 1282 1363 1.76166718644923e-14 161 3.12776558537727 3.44292938557534 1 10.2620731961257 623 2108 161 928 2442 1363 1390 980 1942 542 1623 1070 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 3.76996028024905e-08 2.87575261955407e-07 2925 1663.54545454545 1363 3.42723667713797e-09 149 3.12738960617785 3.19223888941299 1 5.90639853551095 2921 421 565 162 149 1955 2551 2619 918 1363 4675 1071 M875 REACTOME_NETRIN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NETRIN1_SIGNALING.html Genes involved in Netrin-1 signaling 43/54 Reactome 1.49999934875487e-07 4.08899989016697e-07 1500 1202 1364 1.36363586457047e-08 224 2.45830279718924 2.39935144138959 1 4.53405997699028 1501 453 1364 400 1498 1500 2186 1931 224 1110 1055 1072 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 5.92048769599741e-08 3.10257041482984e-07 1365 1610.81818181818 1364 5.9204878537322e-09 574 2.13424424532632 2.71289804153328 1 4.01014806818916 1364 1971 4342 574 630 1586 2596 1339 1443 887 987 1073 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 4.4422479264855e-07 7.88248504248555e-07 540 1396.09090909091 1364 4.03840802133279e-08 539 1.87434451067379 1.98191211526464 1 3.30253133152117 539 1364 2584 1883 2509 1032 769 1001 830 1450 1396 1074 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 4.40356359624905e-15 1.15471223190531e-13 3585 2040.81818181818 1365 4.00323963295368e-16 134 3.03137408638196 2.9073498800938 1 11.3240345595912 3582 1365 134 259 610 3125 3759 4719 1080 409 3407 1075 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 1.29567315472725e-07 3.79650919404164e-07 1855 1519.90909090909 1365 1.1778847554863e-08 613 3.03250758230986 3.23135578397064 1 5.6215420713593 1854 2560 613 1773 1365 1078 988 2672 1475 1108 1233 1076 M5493 WNT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/WNT_SIGNALING.html Genes related to Wnt-mediated signal transduction 98/137 SuperArray 1.30221178309309e-07 3.79878839072891e-07 1745 1042.27272727273 1367 1.18382896379354e-08 146 2.41490081143295 3.03664335072537 1 4.47629000039334 1744 146 1367 426 1373 1436 1599 691 231 2247 205 1077 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 5.22732480602149e-08 3.05598242875576e-07 3735 1880.27272727273 1367 4.75211357293244e-09 89 3.62185494220359 -3.6385705971743 -1 6.81277355378081 3732 620 610 89 391 4371 4579 1780 883 1367 2261 1078 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 1.29885726616558e-07 3.79878839072891e-07 2555 1386.72727272727 1367 1.1807794025898e-08 193 2.30175240485775 2.60197436856938 1 4.26651635835796 2555 193 809 1149 1367 1921 1591 1472 744 1078 2375 1079 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 1.00751522371703e-07 3.42613246105503e-07 1370 1432.54545454545 1368 9.15922972597587e-09 178 2.62125970502136 -2.75200678138845 -1 4.89281428717506 1368 2384 1506 3266 1112 1062 793 178 1845 1725 519 1080 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 5.06792724755844e-07 8.74931112233937e-07 670 1441 1369 4.60720765000746e-08 207 1.89890794971255 1.85293606810285 1 3.3209770394636 666 1540 2392 207 2588 528 594 1488 988 3491 1369 1081 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 5.43918164565403e-08 3.06874196014832e-07 1130 1292.18181818182 1369 4.94471070920902e-09 433 2.66706213448412 2.6622745376013 1 5.01517063627239 1127 1533 541 1144 433 1467 1369 1613 2780 611 1596 1082 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 7.37849606092999e-08 3.2144561803028e-07 1880 1442.27272727273 1369 6.70772391672235e-09 304 2.13510910917831 2.19978859084386 1 4.00228740793872 1877 1329 940 2738 761 1369 1701 304 1847 1199 1800 1083 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 4.56735076246905e-08 2.99073619127066e-07 2370 1304.36363636364 1369 4.15213714299126e-09 75 2.50956393313551 2.74479710164799 1 4.72706203911598 2367 678 1369 591 279 2554 2688 656 75 1680 1411 1084 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 2.86890402647416e-07 5.80421217529276e-07 1280 1355 1370 2.60809490962988e-08 367 2.47873702858722 2.82910137457022 1 4.46286829513948 1276 1494 1085 1049 2158 1425 2152 437 1370 2092 367 1085 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 2.19112283432765e-07 4.96977404037796e-07 1895 1592.90909090909 1370 1.99193004777803e-08 430 2.66176139766809 2.78178619644954 1 4.84427024844805 1370 1891 2111 3596 1891 1364 809 447 437 3176 430 1086 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 2.23150984101062e-07 5.03221535684115e-07 430 1433.72727272727 1371 2.02864551577977e-08 427 1.61827454357022 1.63801219975508 1 2.94230565951084 427 1138 3448 640 1905 577 944 1685 1867 1769 1371 1087 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 7.04028627603225e-09 7.81885911126405e-08 565 1568.36363636364 1371 6.40026027142008e-10 342 2.83845057192688 3.25533523121674 1 5.82422452057794 561 1598 342 2527 3087 1096 1371 1834 3538 437 861 1088 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 8.38346226810718e-06 1.00177068115104e-05 1665 1616.45454545455 1371 8.38349389537294e-07 281 3.54904548997051 -3.9793462212642 -1 5.12253875701439 1663 938 4629 1371 3928 1810 840 420 281 1456 445 1089 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 1.20413070152557e-07 3.68821352676486e-07 2510 1535.27272727273 1373 1.09466433402865e-08 422 2.30016606852736 2.62352166019052 1 4.27209646595841 2507 1269 723 422 1297 2148 2801 1528 867 1373 1953 1090 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 1.20792853679682e-06 1.75374429211966e-06 1375 1813.45454545455 1374 1.09811745456425e-07 289 1.5843904218177 1.68000390658885 1 2.63261233807618 1374 1880 2765 3414 3150 1157 1023 762 289 3177 957 1091 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 4.99573121575782e-08 3.0357704374324e-07 1430 1153.90909090909 1374 4.54157393563656e-09 353 2.21396599650175 -2.28573520632226 -1 4.16601705208308 1426 668 1378 1002 353 1770 2171 1374 494 1512 545 1092 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 1.22924201161797e-06 1.78085398859326e-06 565 1579.27272727273 1375 1.11749336223002e-07 187 2.05780794736202 2.18713331745173 1 3.41553831165753 562 187 2226 1724 3159 952 904 1836 788 3659 1375 1093 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 2.05878463214326e-07 4.82256251301052e-07 4360 1945.45454545455 1375 1.87162256800605e-08 357 2.67695814077005 -1.97229953469232 -1 4.88202702815137 4359 357 823 693 1823 3514 3745 1375 471 740 3500 1094 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 1.4302374378142e-07 3.99214707657188e-07 2265 1447 1376 1.43023752986527e-08 15 3.07659777775259 2.58969889687954 1 5.68390026309889 2265 858 4207 1148 1555 2338 1681 15 31 1376 443 1095 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 3.73438050050281e-08 2.87575261955407e-07 2240 1571.09090909091 1376 3.3948914217199e-09 139 2.59376582612304 2.51568945324672 1 4.89844790158513 2238 468 878 2554 139 1712 1376 990 3072 642 3213 1096 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 8.11639247326397e-08 3.27411388472988e-07 1700 1702.36363636364 1376 7.37853888427232e-09 696 2.32692248198386 3.2570207360602 1 4.35655500305406 1700 754 1376 1594 860 3051 4481 696 957 2125 1132 1097 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 3.8935299045382e-12 7.15076309315965e-11 1815 1323.45454545455 1378 3.53957264049553e-13 203 2.71532070735642 3.36599340496956 1 7.95421491707979 1814 1263 203 338 1514 2035 2886 1194 1378 267 1666 1098 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 2.93182324415827e-07 5.89612514376951e-07 2750 1623.90909090909 1379 2.93182363095978e-08 178 2.61367397386618 -3.45865793164468 -1 4.70071396093726 2749 865 4316 298 2262 2347 2322 374 178 1379 773 1099 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 8.16704157790912e-10 1.05323596305276e-08 1435 1335.81818181818 1380 7.42458325540087e-11 155 3.28667817906498 3.23457196469507 1 7.57036166193599 1434 513 292 155 1431 1211 1380 2384 3363 381 2150 1100 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 5.55407316382365e-08 3.07843567066819e-07 2235 1621.09090909091 1381 5.04915754912783e-09 456 2.13039790742489 2.3669138604218 1 4.00500585345038 2232 1262 796 1367 456 1978 2880 2281 2727 472 1381 1101 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 2.85300208925133e-08 2.59537345211143e-07 1170 1673.72727272727 1381 2.59363829659055e-09 33 2.11457232869228 -2.13671429268563 -1 4.02051329612299 1169 458 1756 3669 33 1381 1623 854 4169 2339 960 1102 M11480 REACTOME_MEMBRANE_TRAFFICKING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEMBRANE_TRAFFICKING.html Genes involved in Membrane Trafficking 151/177 Reactome 4.08891712307553e-08 2.9351990282604e-07 1140 1898.63636363636 1382 3.71719745370189e-09 199 1.25614627350468 -1.12161469372199 -1 2.36862348342474 1137 1414 3989 3444 199 354 977 1382 3383 4318 288 1103 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 1.92108652717913e-10 2.67478714108717e-09 1445 1080.63636363636 1383 1.74644229758808e-11 100 2.61309654391538 2.97040287100191 1 6.46783953707949 1442 1401 272 100 1637 1383 1895 1509 911 439 898 1104 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 5.95701246202547e-08 3.10399797613433e-07 4050 2105 1384 5.41546602120497e-09 105 2.23603130344489 2.16023850839417 1 4.20131341226761 4049 105 996 577 531 3362 2970 4675 1384 1076 3430 1105 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 1.47997395506395e-07 4.06132387668711e-07 830 1288.63636363636 1385 1.34543095874917e-08 391 2.19517128916697 2.47263236914955 1 4.05052127028795 1385 391 1724 892 1490 1734 2167 603 828 2133 828 1106 M17400 BIOCARTA_ALK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ALK_PATHWAY.html ALK in cardiac myocytes 38/51 BioCarta 1.42825645660301e-07 3.99040920610323e-07 1300 1764.09090909091 1386 1.29841504484227e-08 393 1.9783426629796 2.54108386323279 1 3.65471524022498 1299 3077 2412 4149 1455 1083 1386 393 987 2607 557 1107 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 1.0723553971551e-14 2.67805157384765e-13 890 1071.72727272727 1387 9.74868542868271e-16 28 2.9825321119172 3.1575745908559 1 10.8269130165643 888 28 142 517 2063 1417 1387 1941 1493 135 1778 1108 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 8.62862159432811e-08 3.28305665915602e-07 4095 2186.72727272727 1387 7.84420175704666e-09 515 2.35832875290064 -2.3132750198887 -1 4.41455996195126 4094 515 1302 850 942 4129 3230 4561 709 1387 2335 1109 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 3.96632764073611e-08 2.9351990282604e-07 2150 1403.90909090909 1388 3.60575246567645e-09 178 2.30075996386703 2.59015952328839 1 4.33909166958227 2148 1388 606 2054 178 1633 2350 637 2977 700 772 1110 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 2.26189093690785e-06 3.02319087211613e-06 1070 1731.81818181818 1390 2.05626660221291e-07 523 1.86503756760054 1.62716327111311 1 2.97171813205534 1068 523 1390 2787 3459 781 1226 1869 2588 903 2456 1111 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 1.25886418885076e-07 3.75235906357741e-07 1135 1623.45454545455 1390 1.14442205534941e-08 574 2.31727426681236 2.58445162317397 1 4.29886712628261 1131 2069 574 1021 1339 1390 1704 3047 2316 701 2566 1112 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 2.13640565740513e-07 4.90234925824382e-07 1820 1389.63636363636 1391 1.94218714988192e-08 250 2.50732551861747 2.73570647810728 1 4.56745004387989 1817 1571 1727 449 1867 1391 1215 765 250 3814 420 1113 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 4.15479318806287e-06 5.21281867295501e-06 810 1366 1391 3.77709184962413e-07 143 2.79989224913518 2.95454253015728 1 4.27043203130827 809 2393 1391 1431 3702 630 293 143 1745 1938 551 1114 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 1.39093992937031e-07 3.9383542091349e-07 2705 1833.90909090909 1391 1.26449092482897e-08 390 2.14771474587033 2.69336218714669 1 3.97121724076524 2702 1298 1089 390 1429 3773 4427 855 886 1391 1933 1115 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 4.27300513526333e-08 2.95727041619398e-07 1325 1466.90909090909 1391 3.88455019841532e-09 234 1.88893699274311 2.2403369743997 1 3.56049008639494 1322 1391 1865 888 234 2051 2473 1219 1643 1906 1144 1116 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 7.8419099655918e-08 3.26618753937265e-07 3935 2232.63636363636 1392 7.12900931374276e-09 156 2.32319739316521 -2.22670551990992 -1 4.35028555397162 3932 1392 780 156 819 4252 4226 3359 741 1057 3845 1117 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 1.76766769191926e-06 2.42469965296685e-06 375 1788.27272727273 1393 1.60697192019627e-07 372 1.54305922496088 -1.59215732118109 -1 2.50122478509474 372 2159 2856 1954 3355 573 597 1346 3860 1206 1393 1118 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 8.23876183349852e-07 1.28275572265141e-06 280 1656.18181818182 1394 7.48978628984296e-08 276 1.78067112160933 1.92864746194946 1 3.02869675797797 276 3234 2458 1941 2908 511 709 748 2960 1079 1394 1119 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 9.74029052857231e-08 3.39726302159777e-07 615 1888 1394 8.85480996346765e-09 612 2.31933550537027 2.56350521950701 1 4.33160799960776 3230 1356 612 1348 1071 2713 2847 1394 2578 615 3004 1120 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 1.56406729765333e-06 2.17769842033149e-06 70 1206.09090909091 1395 1.4218803723745e-07 66 1.76318897497507 1.79695631492863 1 2.88192425635788 66 1395 1420 1706 3302 306 303 926 1813 536 1494 1121 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 1.33008408512788e-07 3.83038247822062e-07 2530 1716.18181818182 1396 1.20916742322055e-08 537 2.42591320062802 2.98706701218153 1 4.49418684118615 2529 1248 537 597 1396 2553 2788 1319 2077 886 2948 1122 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 5.46619895072531e-07 9.28408026175727e-07 1400 1690.09090909091 1398 4.96927300807016e-08 785 2.97929038354353 3.17629856985166 1 5.18876882374832 1398 1787 1210 2353 2635 1023 785 1205 2668 2460 1067 1123 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 8.52595123994112e-08 3.28305665915602e-07 2950 1529.63636363636 1400 7.7508650639624e-09 508 2.09941677549697 -2.42578054105979 -1 3.92980759023488 2946 508 1917 1244 929 2113 1863 521 579 2806 1400 1124 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 1.33990229113102e-07 3.85177943176647e-07 1110 1573.09090909091 1400 1.21809306612482e-08 252 1.98458079514599 2.09846343263324 1 3.67504221395165 1107 738 2179 3290 1400 1320 1453 252 3742 1545 278 1125 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 1.58194899458423e-07 4.19012303840493e-07 765 1283.81818181818 1400 1.43813555303372e-08 80 2.00279729369316 2.15518374020771 1 3.6876363130112 763 80 1783 1199 1565 1400 1182 1634 666 2222 1628 1126 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 6.72122081918637e-07 1.09017739747628e-06 1220 1579.81818181818 1401 6.11020261144334e-08 871 1.98254204993668 2.10800922197036 1 3.41259575388561 871 2058 1516 2547 2776 970 1220 1220 1406 1393 1401 1127 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 1.25294686321724e-07 3.74535097807815e-07 1075 1616.09090909091 1401 1.13904266779567e-08 667 1.95365612117856 2.1963091360446 1 3.62462758153014 1075 2519 2212 2364 1335 893 1401 1014 1753 2544 667 1128 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 3.34959088519465e-06 4.28481112213583e-06 955 1922 1401 3.0450872591782e-07 695 2.06496879347432 -2.02886034359252 -1 3.20005976600636 953 2136 1382 1798 3625 1257 1304 4490 1401 695 2101 1129 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 1.05287808406713e-07 3.48348225330125e-07 2070 1244.72727272727 1403 9.57161940414431e-09 188 1.85555032452955 -1.75430994048873 -1 3.4594351014306 2068 1185 1567 188 1154 574 1968 1403 1674 1523 388 1130 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 3.29272924079976e-08 2.74345541741202e-07 4655 1887.72727272727 1403 2.99339026371079e-09 84 2.23266844445413 1.89136678309684 1 4.22956547098186 4653 607 1403 335 84 4654 4473 1467 90 1621 1378 1131 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 2.90280212198624e-07 5.85144864192606e-07 1310 1845.54545454545 1404 2.63891136818013e-08 377 1.94313969527231 2.16727091809002 1 3.49638512969772 1308 2365 2829 4145 2169 982 1174 1404 888 2660 377 1132 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 8.00871150958511e-09 8.81144949306334e-08 2070 1412.90909090909 1405 7.28064685339949e-10 345 2.73788685852102 -2.86493058102162 -1 5.57681156640198 2069 1405 345 488 1486 1577 3040 2812 1208 703 409 1133 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 4.93985812705992e-08 3.0357704374324e-07 895 1382.27272727273 1406 4.49078021634454e-09 342 2.22736943386115 2.58451339874741 1 4.19124349792208 892 2534 1093 1705 342 1172 1428 1963 1258 1406 1412 1134 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 1.40771300207113e-06 1.98815241465461e-06 2160 1436.36363636364 1409 1.27973991165874e-07 93 2.26715454452231 2.7135459072084 1 3.73179090287437 2158 483 1153 2530 3253 1308 1427 253 1733 1409 93 1135 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 1.35654172419961e-07 3.8811262131939e-07 1090 1922.63636363636 1409 1.23321982531393e-08 144 1.47134991742845 -1.49249427731735 -1 2.72301915890463 1088 3477 3107 4364 1409 512 144 733 3418 2697 200 1136 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 6.14672525924055e-08 3.12995510041999e-07 2010 1318.27272727273 1409 5.58793220997995e-09 332 2.35920493693011 2.63519495869642 1 4.43032980598654 2009 1409 466 332 564 2066 2196 1543 806 505 2605 1137 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 8.95203214218267e-08 3.31497675696653e-07 825 1396.81818181818 1409 8.13821136950029e-09 605 3.02995466864311 3.32552952298782 1 5.66834644859859 825 1710 605 1782 978 1120 1409 2107 2216 684 1929 1138 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 4.42702568937156e-07 7.86730468894344e-07 695 1420.63636363636 1410 4.02456961837753e-08 467 3.27087563885725 4.2012532792659 1 5.76460420512077 693 1721 467 815 3748 1543 1581 2380 481 788 1410 1139 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 2.82764621628448e-08 2.58315223218602e-07 2445 1623.81818181818 1411 2.57058750238914e-09 31 2.39876017253102 2.84548220217503 1 4.56238562699224 2441 660 1522 1411 31 3789 4570 157 420 1662 1199 1140 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 3.32718958453694e-08 2.74551308374377e-07 4615 2507.54545454545 1413 3.02471784986908e-09 91 2.324714928473 -2.35710542055245 -1 4.40375519237488 4613 207 1070 1356 91 4719 4484 4633 1413 1246 3751 1141 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 1.35951723588238e-07 3.88198508975488e-07 880 1275.36363636364 1413 1.23592483626858e-08 137 2.8308836251341 3.00433261527793 1 5.23981798866632 878 1824 1755 2575 1413 436 287 1559 388 2777 137 1142 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 4.62931084102606e-06 5.75766723837761e-06 405 1486.45454545455 1414 4.20847325654518e-07 176 3.30029352117852 3.33499499642522 1 4.99265942717268 1590 840 1188 176 3738 1596 403 3542 404 1414 1460 1143 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 1.3652138382068e-07 3.89589438714396e-07 160 1591.72727272727 1414 1.24110356629581e-08 8 1.69272700244253 -1.69272700244253 -1 3.13204387034416 160 2766 2818 3881 1414 21 8 62 3925 2413 41 1144 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 1.05766562304641e-07 3.48348225330125e-07 1315 1883.54545454545 1414 9.61514248994942e-09 728 2.16063457665061 2.31829028493396 1 4.0283670959773 1857 2624 1315 3298 1161 920 1414 2343 3744 728 1315 1145 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 6.59544349987547e-08 3.14536172538656e-07 1465 1607.90909090909 1415 6.59544369562492e-09 265 2.27916671863073 2.54130302426984 1 4.27859405088646 1461 1003 4668 265 746 2223 2108 1415 1292 379 2127 1146 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 4.61100006911569e-06 5.73640493574751e-06 175 1465.72727272727 1416 4.19182703034651e-07 111 1.62474773893892 1.67058586285765 1 2.4582228146257 175 2253 2346 1488 3737 182 111 997 2060 1358 1416 1147 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 7.12135002189597e-08 3.17725226229176e-07 1420 1550.27272727273 1416 6.4739547749204e-09 7 2.99136229119876 3.127495449909 1 5.61205680112583 1416 694 765 3264 1761 1741 1727 7 3420 969 1289 1148 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 4.36985540608011e-16 1.3306914526902e-14 575 1226.63636363636 1418 3.97259582370918e-17 112 2.83740912877529 3.3822667949283 1 11.3682697160316 574 1418 112 498 2323 1612 2033 1635 1181 169 1938 1149 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 2.81461156425949e-08 2.57960516180675e-07 1695 1219.09090909091 1419 2.55873781842614e-09 30 2.15522524145002 2.30442569411897 1 4.09947184687698 1692 1109 700 566 30 1419 2554 1492 1557 476 1815 1150 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 1.37443674162722e-07 3.91275115831152e-07 1205 1615 1421 1.24948802499485e-08 1198 2.09176766930024 2.4538107368626 1 3.86945718042159 1203 2040 1201 1382 1421 2127 2177 1321 1652 1198 2043 1151 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 1.27679958686364e-08 1.33922089999919e-07 2445 1664.63636363636 1421 1.1607269038852e-09 135 2.70576990644202 2.67440114770946 1 5.36933279907655 2444 1408 364 135 1381 1421 1948 3461 2034 440 3275 1152 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 2.36083883088761e-08 2.27411413914072e-07 1375 1515.54545454545 1422 2.14621714201999e-09 10 2.48626409149412 -2.44880915328177 -1 4.76857686210895 1373 1548 917 1391 10 1565 2000 3087 2101 1422 1257 1153 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 1.99396983142679e-08 1.98975425038783e-07 2195 1445.54545454545 1422 1.81269986318103e-09 121 2.50351599447011 2.56320877302078 1 4.84361042049365 2194 1422 380 121 451 1470 2204 4299 755 332 2273 1154 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 1.13807204779883e-07 3.5893637536524e-07 1335 1756.81818181818 1424 1.13807210608319e-08 575 1.8103806891057 1.93316991773584 1 3.36840307872492 1424 965 4458 2259 1334 1334 1744 1349 2007 575 1876 1155 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 2.46803972921147e-06 3.26764306364044e-06 635 1649.72727272727 1425 2.24367499813839e-07 631 2.92251275569911 3.53808955157482 1 4.62867063260464 631 1632 1007 1280 3493 1040 1425 1948 2691 2191 809 1156 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 5.84091288107104e-08 3.09924122670556e-07 2995 1897.09090909091 1426 5.30992094194996e-09 263 2.48453819099225 2.29477397589219 1 4.66881038319327 2992 1426 460 263 504 2673 3637 3483 684 776 3970 1157 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 9.18862883729863e-07 1.39499286304437e-06 980 1886.54545454545 1426 8.35330243188094e-08 979 1.93730191885866 -2.11987555571034 -1 3.27480303685276 979 2788 2197 3571 2994 1385 1056 1276 1426 1837 1243 1158 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 1.15884515870819e-07 3.60088818242439e-07 1650 1404.72727272727 1427 1.05349565431828e-08 731 2.06917351110008 2.29849961417368 1 3.84920556069411 1646 1204 1712 1427 1270 843 1882 731 1437 1993 1307 1159 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 8.96462112258255e-08 3.31497675696653e-07 2305 1801.90909090909 1427 8.14965589806859e-09 443 2.44821516036705 2.84566006265593 1 4.57988061240433 2305 443 1046 2276 981 2770 3527 1021 3227 798 1427 1160 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 1.3518958895517e-07 3.87428573083425e-07 2500 1440 1429 1.22899633875041e-08 382 2.57103585944531 2.68093439565245 1 4.75941439070953 2500 393 912 1164 1407 1599 1588 1673 382 1429 2793 1161 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 1.72186216216113e-07 4.36189144709654e-07 1430 1564.63636363636 1429 1.5653293608411e-08 617 2.34198344342301 2.7760304160994 1 4.30050647091348 1429 1376 617 769 1652 2106 2446 2206 977 934 2699 1162 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 1.12928473059036e-07 3.58148551537347e-07 2370 1806.72727272727 1429 1.02662253505256e-08 556 2.16640944787383 -2.14397880220875 -1 4.031598275536 2368 1429 871 556 1235 2510 4089 2848 1242 638 2088 1163 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 8.24400517361596e-07 1.28275572265141e-06 2090 1476.36363636364 1430 7.49455296624827e-08 38 4.32297277618614 3.67923998271566 1 7.35406062296682 2086 1908 1147 969 2910 1430 340 1282 38 1833 2297 1164 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 5.73738210275369e-06 7.03205492729095e-06 1430 1883.18181818182 1430 5.21581551393872e-07 763 1.8236333746863 -1.48778604483939 -1 2.71266589651029 1430 763 1996 2732 3798 1402 1358 1173 1100 2361 2602 1165 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 1.11918754334085e-07 3.56448394370366e-07 4575 2275.27272727273 1432 1.0174432729785e-08 469 2.7914392223873 2.78121073248454 1 5.19666707337194 4575 469 556 1333 1227 3857 3746 2717 1432 688 4428 1166 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 1.21422212583537e-05 1.4210583768765e-05 1435 1999.18181818182 1432 1.10384438855597e-06 95 3.76432528974411 4.79220869040904 1 5.26826216390224 1431 2863 870 3854 4043 802 95 242 4346 1432 2013 1167 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 1.68784848872566e-07 4.3132890453628e-07 1130 1559.81818181818 1433 1.53440783474369e-08 764 2.24299188579016 2.42251023536968 1 4.12184702891272 1130 3572 1011 2543 1635 931 1433 764 1498 1653 988 1168 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 3.04834588604082e-07 6.04545906811457e-07 1435 1741.81818181818 1433 3.04834630419947e-08 69 4.08853350987495 4.08853350987495 1 7.34092228024435 1433 2481 4416 2752 2292 1189 69 1208 317 2653 350 1169 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 1.32064599213522e-06 1.88606628831414e-06 855 1599.90909090909 1433 1.20058798628297e-07 851 2.51141266423346 2.6100894792814 1 4.15054038391619 851 2619 1156 1290 3208 1020 911 1829 1632 1650 1433 1170 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 1.86602882218599e-10 2.63744412329602e-09 770 1499.72727272727 1433 1.69638983849479e-11 267 3.54240169438573 3.48393265045833 1 8.77457335655543 768 1661 267 742 3001 1433 1611 2799 959 541 2715 1171 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 4.48169237481845e-07 7.93160405292204e-07 1315 1670.90909090909 1434 4.07426662527182e-08 568 2.48136771172085 2.67777790873186 1 4.37043142453759 1315 2999 1434 1742 2516 636 1243 2292 1202 2433 568 1172 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 7.21593517663132e-08 3.19205379884722e-07 1940 1615 1434 7.21593541094506e-09 85 2.0934282254344 2.26388808026651 1 3.92597535576076 1940 1009 4309 85 828 1468 2722 1434 1001 762 2207 1173 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 8.33056151424149e-09 9.12302792278883e-08 4355 2272.27272727273 1434 7.57323776889653e-10 146 2.32342128894238 -1.95176145300358 -1 4.72232946796403 4351 1112 347 146 862 4354 4599 2587 1434 527 4676 1174 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 6.87756518825987e-08 3.15009389627869e-07 1435 1746.90909090909 1435 6.87756540111393e-09 784 1.82862744511917 2.05718563783243 1 3.43229857612341 1435 1030 4556 1843 784 1067 2103 1348 2530 1514 1006 1175 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 1.27467166010305e-07 3.76660766944629e-07 1680 1670 1437 1.27467173321851e-08 573 1.98919080737336 2.31312730973041 1 3.68915910678008 1680 1965 4436 573 1437 904 2483 1182 1572 1004 1134 1176 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 1.81312916566016e-11 3.01336959926618e-10 2435 1648.54545454545 1437 1.64829924152282e-12 73 2.78809195057043 -2.73865630138245 -1 7.66446606095676 2435 1437 224 340 73 2947 3557 4130 551 350 2090 1177 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 5.37854320063412e-08 3.06874196014832e-07 1675 1590.09090909091 1437 4.88958484738938e-09 417 2.09367837169179 2.31574659318375 1 3.93678883085126 1671 1075 1019 1437 417 2087 2235 1278 2280 1208 2784 1178 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 9.73019752890451e-08 3.39726302159777e-07 4390 1965.72727272727 1438 8.84563450841214e-09 124 2.14850640829288 2.15548378707638 1 4.01250288481093 4390 278 1329 124 1069 4496 3891 1766 131 1438 2711 1179 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 9.8652080056945e-08 3.40830460958105e-07 2595 1824.18181818182 1439 8.96837131642614e-09 681 2.40490439332251 -1.91488384474962 -1 4.49047021937139 2594 1370 681 765 1089 1439 2416 4223 1759 987 2743 1180 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 1.60144890103442e-07 4.21105226344428e-07 1295 1589.63636363636 1439 1.45586274328083e-08 621 2.46252394248144 -2.82328495529712 -1 4.53276376116285 1291 621 953 1063 1579 1522 2035 2825 3320 838 1439 1181 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 1.40230107320336e-07 3.95628276480565e-07 2235 1575.36363636364 1439 1.2748192387158e-08 155 2.40679281111374 2.29587351069586 1 4.44899674965204 2233 155 913 2098 1439 1764 2564 1181 1418 1019 2545 1182 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 6.70424662307957e-06 8.12218790065081e-06 3650 2189.27272727273 1440 6.09478823053289e-07 414 2.69269926672594 2.14938377496945 1 3.95714945140237 3648 669 1022 995 3837 4079 4067 3092 414 819 1440 1183 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 1.29485713364213e-06 1.85541155761714e-06 850 1518 1441 1.17714354159879e-07 603 2.59266490287751 -2.00444604088903 -1 4.29017956633459 849 1736 1246 1695 3195 730 1137 2540 603 1441 1526 1184 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 2.76617614731729e-07 5.68167826037923e-07 1540 1375 1442 2.51470590465753e-08 232 2.10625387798163 2.53133370214869 1 3.79773370802185 1540 442 1352 1189 2121 1645 1964 1442 232 2488 710 1185 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 1.94145941296759e-07 4.66108261912869e-07 1175 1701.81818181818 1443 1.76496325845256e-08 896 2.13658991345577 2.34583071810266 1 3.90549747912542 1171 2496 1344 896 1764 1205 1330 1443 1699 3120 2252 1186 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 7.70425521316049e-08 3.24764325922831e-07 2165 1586.54545454545 1445 7.00386862087132e-09 331 2.62670002729826 -2.84643887748954 -1 4.92059523099115 2165 331 758 1628 801 1747 2914 3551 1337 775 1445 1187 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 1.41600375247855e-07 3.9806657008331e-07 1770 1404.09090909091 1445 1.28727622147087e-08 527 1.82985348291987 -1.48786051895095 -1 3.38089832181826 1768 527 1833 2099 1445 1382 1038 1788 1136 850 1579 1188 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 1.93827125583748e-07 4.66108261912869e-07 1145 1664.90909090909 1446 1.7620649332777e-08 783 2.31097679566249 2.50122170206143 1 4.22433158397367 1141 1537 1051 2845 1759 878 783 1446 3444 1209 2221 1189 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 3.04222464100811e-08 2.68216360173252e-07 3265 1457.27272727273 1446 2.76565880279718e-09 51 2.49994976943937 -2.066208613108 -1 4.7430898390733 3265 198 989 527 51 1473 1760 4301 162 1446 1858 1190 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 8.07040877262746e-08 3.27390259462129e-07 2990 1961 1447 7.33673551698159e-09 481 2.19725093970406 2.62589883191395 1 4.11374866977636 2986 481 1438 1044 856 3511 4586 2501 565 1447 2156 1191 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 4.62303667323764e-08 2.99073619127066e-07 1500 1739.63636363636 1447 4.62303676941374e-09 372 3.85965651529396 -4.19810281741624 -1 7.27058530922764 1498 882 4648 417 372 1447 900 2782 3384 829 1977 1192 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 9.7327774115835e-20 4.46006887210428e-18 2240 1701.54545454545 1448 9.73277741158351e-21 60 2.24366504742459 2.38111650095647 1 11.240461595172 2239 1028 4530 519 571 1329 2907 1448 2083 60 2003 1193 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 5.65856585368958e-06 6.94266462942937e-06 1270 1745.63636363636 1449 5.14416400727268e-07 36 2.13210252502776 2.27485580211407 1 3.17508208650003 1269 2424 2284 1449 3796 1105 647 799 2098 3295 36 1194 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 9.07731687813544e-12 1.59274853772488e-10 2255 1363.27272727273 1449 8.25210625288445e-13 173 2.57010670240393 -2.77970071549455 -1 7.2706637295673 2254 1235 213 666 173 2355 2787 1449 1993 260 1611 1195 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 3.04397483805287e-12 5.67887795873896e-11 820 1566.18181818182 1450 2.76724985277917e-13 201 2.99280416713481 3.76083365611084 1 8.85365746990308 816 1450 201 956 2941 2320 2897 1955 1238 355 2099 1196 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 1.86431934892996e-06 2.54912726736657e-06 1580 1501 1452 1.69483720799036e-07 79 2.34059537270783 2.29332672824176 1 3.77974840873016 1576 1749 1461 1384 3871 1452 1325 79 259 2094 1261 1197 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 7.50549716205285e-06 9.02571888022661e-06 280 1568.18181818182 1454 6.8232025162285e-07 280 2.77455580640556 2.83512430813051 1 4.04076910188862 280 2737 1059 1394 3876 877 541 1590 1865 1577 1454 1198 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 4.33356077822198e-08 2.97164560412799e-07 4085 1923 1454 3.93960078507679e-09 245 2.5481109162885 -2.85328361744634 -1 4.80172943140152 4083 1457 903 740 245 4297 4071 1454 722 1388 1793 1199 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 6.13801298972078e-07 1.01382117030735e-06 1010 1446.90909090909 1454 5.58001336566426e-08 620 2.16105189103893 2.38989884676266 1 3.7396258906667 1008 1520 1837 1454 2718 620 626 1055 1856 2477 745 1200 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 1.31037350354675e-07 3.80936578171426e-07 1560 1373 1455 1.31037358081529e-08 12 3.32538072703647 3.44123234591418 1 6.16313199548889 1560 926 4255 341 1460 1549 233 3129 12 1455 183 1201 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 9.47304638800595e-08 3.3764305071295e-07 2110 1528.81818181818 1455 8.61186072355337e-09 531 2.20197089855693 2.44427566220316 1 4.11407199713126 2109 1462 1380 1887 1038 1710 2741 1099 1455 1405 531 1202 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 1.89617743530985e-07 4.60823355474758e-07 2795 1607.54545454545 1455 1.72379781703744e-08 29 4.11528008916707 5.57755977055866 1 7.5290509342276 2792 836 957 113 1733 3490 2848 2009 29 1421 1455 1203 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 1.20956942481213e-06 1.75558661903852e-06 820 1557.36363636364 1456 1.099609172581e-07 497 3.08195446240531 3.66128184303482 1 5.12136286145064 817 1629 497 1245 3183 1179 1456 2410 2115 932 1668 1204 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 7.33939194278859e-07 1.16836188768844e-06 1460 1493.09090909091 1456 6.67217671934083e-08 626 3.32414762939357 -4.28556358749278 -1 5.69364167406134 1456 2399 869 1630 2832 1544 1566 626 1000 1434 1068 1205 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 1.43623026058688e-07 4.00413870642061e-07 2980 1779.90909090909 1457 1.30566395849872e-08 128 1.64913055247954 2.02140511762216 1 3.0456875831624 897 2620 2976 3652 1457 510 637 740 2978 2984 128 1206 M11358 BIOCARTA_ARF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARF_PATHWAY.html Tumor Suppressor Arf Inhibits Ribosomal Biogenesis 25/28 BioCarta 3.52357576740418e-07 6.65517311810633e-07 2310 1585.45454545455 1459 3.20325121068102e-08 554 2.16440092449342 2.16745129266003 1 3.85967416015135 2308 686 1899 639 2336 1242 554 2627 1459 2583 1107 1207 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 1.85194513108635e-07 4.54495434594235e-07 1460 1635.09090909091 1460 1.68358662452897e-08 150 1.33678030472208 -1.38504631564917 -1 2.44742345910028 1460 792 3143 3406 1719 964 337 150 2736 2938 341 1208 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 1.06375007786938e-07 3.48348225330125e-07 655 1514.36363636364 1463 9.6704557209466e-09 415 3.69395743763369 4.28919493418679 1 6.88776225491516 651 1781 424 1187 4091 1463 1635 2583 415 820 1608 1209 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 2.26554560126417e-07 5.06973463057442e-07 1465 1433.27272727273 1465 2.0595871223351e-08 627 2.18450101802754 2.14428768379337 1 3.97007063742518 1465 1387 818 627 1923 923 1483 2542 2188 691 1719 1210 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 3.48195016661989e-08 2.80457419563923e-07 3290 2015.72727272727 1466 3.16540929248079e-09 105 2.64523889064754 -2.35483111207006 -1 5.00398847999032 3287 616 1371 3024 105 3111 4657 2231 843 1462 1466 1211 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 2.93498697160379e-07 5.89997381003828e-07 995 1505.27272727273 1467 2.66817033014188e-08 351 2.21575702283717 2.61987342013753 1 3.98474462461734 994 2097 1591 894 2178 538 1467 1812 1277 3359 351 1212 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 3.09805121961761e-13 6.6467280711796e-12 315 1600.72727272727 1467 2.81641019965277e-14 170 3.35487039526031 -3.55281310890715 -1 10.8274235734729 1923 314 170 1320 2227 2273 3152 580 3869 313 1467 1213 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 9.06051530103391e-07 1.38042712139703e-06 955 1451.09090909091 1467 8.23683548412112e-08 80 2.17424908282075 2.43046860688599 1 3.67830442116737 955 2586 1559 1645 2981 618 1317 416 2338 1467 80 1214 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 3.50403113323953e-20 1.7228153071761e-18 1560 1390 1469 3.18548284839956e-21 67 3.20081340229451 3.25935784936665 1 16.4178370981719 1559 1368 67 677 422 1635 2258 3015 1469 168 2652 1215 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 1.41500265415101e-06 1.99605873508452e-06 1470 2243.63636363636 1470 1.41500355515645e-07 129 0.782033748744023 0.782033748744023 1 1.28629290046624 1470 935 4567 4564 3301 886 129 946 3001 3870 1011 1216 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 1.45047281144838e-07 4.01774159039693e-07 600 1597.18181818182 1470 1.3186117337081e-08 221 1.95072033485447 -1.99255973002674 -1 3.60200483665045 600 221 1242 3309 1470 1174 1578 1621 3824 960 1570 1217 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 4.48450815602052e-06 5.59230607567156e-06 1475 1580.27272727273 1471 4.07683390665948e-07 547 2.59057476129728 -3.05593349831549 -1 3.92828419237868 641 1778 1304 1074 3727 1471 1030 547 2789 1474 1548 1218 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 2.24952689588132e-08 2.18923029867213e-07 2870 1560.54545454545 1471 2.04502447171182e-09 8 2.72212370862602 2.66079041464597 1 5.23401616467582 2870 246 407 1321 8 2029 2807 1471 3140 418 2449 1219 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 1.32446972184489e-07 3.83038247822062e-07 2680 1810.36363636364 1472 1.3244698007848e-08 9 2.87119114733316 2.81787378579807 1 5.31925585721062 2679 939 4254 366 1472 2593 1165 4027 9 1744 666 1220 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 2.71649949031682e-07 5.62856786404538e-07 550 1345.81818181818 1472 2.46954529612978e-08 162 2.39172321780942 -2.14772076502588 -1 4.31539002770979 549 2366 1537 1472 2100 557 472 1965 2227 1397 162 1221 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 1.10487959805648e-07 3.53626743374685e-07 3565 1956.45454545455 1472 1.00443604867775e-08 179 2.0916262685761 -2.04626283299734 -1 3.8957330017894 3561 179 1469 1361 1214 3152 3625 2958 1692 1472 838 1222 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 1.46032423693145e-07 4.03555643929533e-07 815 2004.27272727273 1476 1.32756757624128e-08 323 1.46106712781699 1.41866249660829 1 2.69683339654109 811 2755 3124 3918 1476 556 323 1436 3446 3054 1148 1223 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 3.39984441709119e-07 6.49538261636117e-07 1655 1587.09090909091 1477 3.09076812954341e-08 707 1.61981456751906 -1.85054742034743 -1 2.89325912313542 1655 707 2756 1951 2302 1107 966 1477 945 2584 1008 1224 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 5.74751970485965e-07 9.65076236461669e-07 545 1346.63636363636 1477 5.22501927854988e-08 316 1.81494902458588 1.79118661969618 1 3.15178428982509 545 1607 2190 1892 2671 386 316 962 1533 1477 1234 1225 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 3.28876623811613e-07 6.34886570302991e-07 585 1695.45454545455 1477 2.98978793613803e-08 462 1.80360087726101 -1.73347200646306 -1 3.22679041974717 583 1477 2066 2820 2279 462 1322 1053 3897 2059 632 1226 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 6.99906203987279e-07 1.12595681077708e-06 650 1448.90909090909 1477 6.36278569686333e-08 72 2.18809396310075 2.44435543303945 1 3.75764502315485 650 72 960 1671 2799 1477 1424 1904 2119 928 1934 1227 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 3.61955480437046e-07 6.79566375363109e-07 1890 1420.81818181818 1478 3.29050490898058e-08 73 2.49570727257642 2.48680203059265 1 4.44407069343368 1886 73 464 2060 2353 1478 2146 582 2875 442 1270 1228 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 1.46714195836206e-07 4.04415675414145e-07 1530 1255.27272727273 1480 1.3337655056393e-08 173 2.04756315677943 2.15345202697689 1 3.77918513160616 1530 1255 1498 173 1480 515 1686 1481 1122 1287 1781 1229 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 9.47286051151772e-07 1.43020027673303e-06 1485 1668.36363636364 1481 8.61169508217068e-08 409 2.30181238641268 2.88444074292894 1 3.88393622240478 1481 2295 1542 1710 3012 1057 1270 409 3394 1439 743 1230 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 2.43354757277055e-09 2.91531587397893e-08 2880 1782.90909090909 1481 2.21231597769313e-10 202 2.4869837329842 2.61635060841319 1 5.41063990926124 2880 272 480 301 447 2576 3051 4444 1481 202 3478 1231 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 5.60686995941601e-08 3.08412808034375e-07 850 1573.90909090909 1483 5.09715463846494e-09 374 1.72981627536445 -1.63897584463281 -1 3.25137640205883 1483 374 2851 2795 465 928 850 2193 1662 2863 849 1232 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 3.65351003015168e-08 2.8614986551519e-07 4005 2061.90909090909 1483 3.32137280984094e-09 124 2.07938977781961 -1.9275231524323 -1 3.92814966499919 4005 1124 598 513 124 3156 3314 4071 1483 372 3921 1233 M1519 KEGG_ENDOCYTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOCYTOSIS.html Endocytosis 203/231 KEGG 4.36303051623028e-08 2.97164560412799e-07 1025 1629.90909090909 1484 3.96639145705248e-09 251 1.50593337641236 -1.35207026433336 -1 2.83746948233068 1022 1276 3186 1484 251 801 2077 1575 3091 2016 1150 1234 M638 KEGG_ADHERENS_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADHERENS_JUNCTION.html Adherens junction 96/111 KEGG 5.05644227169678e-08 3.0357704374324e-07 4610 2169.09090909091 1485 4.59676580719382e-09 134 2.4650060158978 -1.68493345421342 -1 4.63849640815455 4607 134 1029 423 371 3941 4284 2667 574 1485 4345 1235 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 1.2065705631378e-06 1.75231171015706e-06 1015 1572.45454545455 1485 1.09688293170116e-07 570 3.03885102381784 3.72090553155862 1 5.0504362976533 1012 1687 570 858 3149 1485 1910 2521 1885 1115 1105 1236 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 8.8585334255874e-05 9.60980872644737e-05 1045 2002.72727272727 1486 8.0535364944947e-06 602 3.44390435162403 3.3333820501617 1 3.99423442983615 1044 2844 1206 2802 4500 1486 998 602 3145 2004 1399 1237 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 7.16364791077505e-12 1.28077341435069e-10 4220 1963.81818181818 1488 6.51240719163491e-13 74 4.87732445700273 -4.1894885546607 -1 13.9317449047562 4220 781 208 74 2027 3373 1488 3450 1421 477 4083 1238 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 2.61410089800722e-09 3.09236998461004e-08 555 2164.18181818182 1488 2.37645536464852e-10 320 3.1276942984528 -2.2433308947196 -1 6.78165459482639 4180 1488 320 552 1388 4454 4340 2067 715 553 3749 1239 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 2.11498847473057e-07 4.87915229752116e-07 685 1429.36363636364 1489 1.92271698005163e-08 87 1.92179144287154 2.20338175078254 1 3.50175841733824 681 1814 1819 3866 1858 313 157 132 3507 1489 87 1240 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 1.74084313360098e-06 2.39346914960578e-06 1905 1706.63636363636 1489 1.58258591919848e-07 649 3.01097931515256 3.61162701961683 1 4.88636720781837 1902 2777 1143 3050 3346 1489 1064 836 1537 980 649 1241 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 5.41226957752417e-08 3.06874196014832e-07 1360 2274.45454545455 1490 4.92024519152059e-09 426 1.98808140155395 2.1064662059456 1 3.73818911684874 1359 4593 2957 4583 426 1490 1075 649 3691 3200 996 1242 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 1.10432336653413e-07 3.53626743374685e-07 1215 1604.09090909091 1491 1.00393038360665e-08 989 2.06101315899577 1.92921871928755 1 3.83870232146075 989 1338 1212 1643 1213 1491 2102 1008 2179 2633 1837 1243 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 1.6327660973168e-09 1.99654299982779e-08 1495 1427.90909090909 1491 1.48433281684417e-10 153 3.03391980139986 3.01997603591857 1 6.74476911785515 1491 153 310 3015 1647 1930 2269 609 2261 584 1438 1244 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 4.11253134475217e-08 2.9351990282604e-07 3510 2173.27272727273 1492 3.73866492875367e-09 206 2.04663231158312 2.303394399707 1 3.85972742357602 3509 1300 1439 445 206 4481 4286 2187 948 1492 3613 1245 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 1.27500634202071e-07 3.76660766944629e-07 1495 1452.36363636364 1492 1.15909674173954e-08 621 1.7724314571933 1.82039947993903 1 3.28706272276535 738 1161 2083 1492 1351 621 1493 1646 2300 1464 1627 1246 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 1.56738113673098e-24 1.07217956019858e-22 3280 1643.90909090909 1493 1.42489194248271e-25 44 2.54621227612195 2.70063827395793 1 16.1524966321631 3277 1053 44 94 591 3009 3548 1493 2047 110 2817 1247 M2164 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION.html Leukocyte transendothelial migration 100/141 KEGG 2.76620691575243e-07 5.68167826037923e-07 4280 1936 1496 2.51473387596924e-08 81 2.60664038668094 -2.73332522516211 -1 4.70017273780015 4279 81 576 112 2122 4132 3490 3744 333 931 1496 1248 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 8.48672896493941e-07 1.31235122400304e-06 2315 1550.81818181818 1496 7.71521112616838e-08 126 2.58742315324067 3.30830920725769 1 4.39386892856422 2311 126 731 644 2934 1758 2222 1470 2056 1496 1311 1249 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 1.59370490430525e-07 4.20318657884309e-07 695 1354.81818181818 1496 1.44882274523186e-08 375 2.14695801553492 2.37354926982727 1 3.95229509157079 694 617 2140 1917 1573 539 375 2029 1496 2885 638 1250 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 4.57643955661782e-08 2.99073619127066e-07 4615 2415.63636363636 1497 4.16039968346992e-09 282 2.07137818009602 -1.71156880462455 -1 3.90153668313966 4612 1064 746 544 282 4111 4432 4279 1497 380 4625 1251 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 1.75905087837196e-07 4.42620781379724e-07 2120 1713.45454545455 1498 1.59913729001832e-08 1042 2.2127510516551 2.32114452431174 1 4.05909193360906 2117 1369 1042 1397 1666 2237 3302 1122 1454 1498 1644 1252 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 2.45901664389186e-07 5.31315294702385e-07 1915 1558.18181818182 1499 2.23546992613161e-08 852 2.32525745642851 2.63575868097177 1 4.21225870396496 1913 1586 1136 852 2005 1499 1296 2138 1224 978 2513 1253 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 1.21820274355942e-05 1.42501039643135e-05 455 1603 1499 1.10746317195249e-06 334 2.38215223466892 2.38215223466892 1 3.3327324032831 451 2869 1868 1499 3991 643 334 621 1791 2089 1477 1254 M619 REACTOME_TRIGLYCERIDE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRIGLYCERIDE_BIOSYNTHESIS.html Genes involved in Triglyceride Biosynthesis 37/42 Reactome 1.50039932448906e-07 4.08899989016697e-07 1090 1779.09090909091 1500 1.36399947892387e-08 453 1.70221728723164 -1.52605528951275 -1 3.13928131566633 1090 2699 2711 3323 1500 1133 815 453 2523 2236 1087 1255 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 1.09675713113094e-07 3.53357928937751e-07 2130 1382.81818181818 1500 9.970519870974e-09 227 2.44905422192693 -2.54108374024547 -1 4.56183682561929 2129 227 986 1603 1202 1743 2238 1500 616 1003 1964 1256 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 6.11170758039919e-08 3.12995510041999e-07 1500 1644.90909090909 1500 5.55609795471401e-09 553 2.01535114613255 2.39658468845936 1 3.78448431626419 1500 1493 2006 2101 553 1442 1621 3241 984 1951 1202 1257 M12705 SIG_CD40PATHWAYMAP http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CD40PATHWAYMAP.html Genes related to CD40 signaling 33/36 Signaling Gateway 4.67349497992545e-07 8.1942408266152e-07 1155 1759.27272727273 1501 4.2486327024761e-08 619 1.40485011892885 -1.49188722172885 -1 2.46824866958259 1151 1741 3267 1501 2546 1018 1721 1047 1290 3451 619 1258 M1076 REACTOME_AMYLOIDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMYLOIDS.html Genes involved in Amyloids 35/136 Reactome 1.76186095835722e-06 2.42025137469327e-06 675 2031.45454545455 1501 1.60169306303446e-07 350 2.21709963696406 -2.47518150075086 -1 3.59469867571577 673 3089 1263 3182 3349 689 350 2532 4288 1501 1430 1259 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 7.36747487326603e-07 1.17046386407996e-06 1640 1721.90909090909 1501 6.69770667320512e-08 445 1.76288180967185 -1.74878755555237 -1 3.0186841066385 1639 1472 2465 1283 2838 445 984 3652 1501 1771 891 1260 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 6.71426995534737e-16 1.94425485823556e-14 1505 1471.63636363636 1502 6.10388177758852e-17 85 2.17424670282215 2.32269464951152 1 8.60767287903007 1502 1069 236 1315 1073 1859 2702 1748 2681 85 1918 1261 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 3.10507181895895e-07 6.11341009591772e-07 1775 1771.81818181818 1503 2.82279296109793e-08 538 2.04601834730457 -1.91285320931811 -1 3.67030784394167 1771 1503 1470 1106 2228 657 1321 4498 1964 2434 538 1262 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 7.85573019319036e-06 9.42048945931364e-06 285 1412.72727272727 1504 7.14159840405956e-07 61 2.13285918557243 2.30920270395255 1 3.09457418548946 282 2705 1534 2140 3886 296 61 327 2103 1504 702 1263 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 4.52686473513164e-11 7.00550870485945e-10 570 1404.72727272727 1504 4.11533157747707e-12 242 3.61544384547939 3.70736868965295 1 9.55660006277194 566 1691 242 729 3143 1746 1797 2222 1131 681 1504 1264 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 1.50295474221137e-07 4.08899989016697e-07 950 2018.36363636364 1504 1.36632258626129e-08 528 1.45598277536706 1.42320245516458 1 2.68504348369216 949 3026 3132 3682 1504 711 1127 528 3846 2641 1056 1265 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 1.28220114915287e-06 1.84343266037209e-06 1510 1694.36363636364 1506 1.16563808767663e-07 129 2.82686154293469 -2.33256829515642 -1 4.6800875339858 1506 859 1267 2061 3186 1184 715 3924 129 1644 2163 1266 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 3.54080352226816e-12 6.52835649418193e-11 3570 1955.27272727273 1506 3.5408035222738e-13 130 2.09052825398966 -2.08259754290716 -1 6.14763445221913 3570 988 4538 248 152 2444 3909 2577 1506 130 1446 1267 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 7.62630505136823e-08 3.24764325922831e-07 2080 1636.27272727273 1506 7.62630531309062e-09 5 3.84806230133988 -3.56106761757019 -1 7.20897277974785 2077 923 4557 108 906 1506 236 3593 5 2216 1872 1268 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 1.77319164849195e-07 4.43266487055072e-07 1005 1650.90909090909 1507 1.61199253764595e-08 452 2.59182727656086 2.63425247518324 1 4.75414675750031 2426 452 1115 1005 1678 1507 1518 4458 1079 1920 1002 1269 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 4.51041988831895e-07 7.96750818595264e-07 1245 1448 1508 4.10038255731034e-08 190 1.81760907799805 -1.7001754854963 -1 3.20009383956554 1245 1508 2296 1471 2522 304 644 1592 2446 1710 190 1270 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 2.46638933015839e-06 3.26637419706722e-06 320 1672 1509 2.24217463199765e-07 55 1.57649520466768 1.6188163461471 1 2.49653045817687 320 2352 2550 2848 3492 222 55 935 3073 1509 1036 1271 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 3.90259646221401e-11 6.18129372538594e-10 2850 1693.72727272727 1510 3.54781496571202e-12 69 2.78686343490214 3.20274996430072 1 7.40998585405595 2846 69 237 971 1469 3096 3477 1968 1510 242 2746 1272 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 2.08884812767253e-07 4.84679970737421e-07 2460 1328.27272727273 1510 1.89895302363978e-08 69 2.22484881759269 -2.70924869669647 -1 4.05596115118065 2457 489 2065 167 1847 1986 1510 822 69 2449 750 1273 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 2.61282626980837e-08 2.44693253839197e-07 1010 1230.18181818182 1511 2.37529663712687e-09 22 1.87671512212374 -1.53064968831667 -1 3.58203121627058 1647 87 1732 1784 22 1009 2088 1909 1511 1007 736 1274 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 7.83780989223894e-08 3.26618753937265e-07 1515 1514.90909090909 1512 7.12528197406543e-09 586 2.41390442538548 2.7004234356513 1 4.52017194469775 1512 2260 1479 799 818 1969 2568 1978 633 2062 586 1275 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 1.21660749986988e-07 3.70192774369017e-07 1120 1718.27272727273 1513 1.10600687922608e-08 767 2.01305766380555 1.98446979340201 1 3.73780577583585 1118 1406 1513 2568 1304 1405 1841 767 2752 2431 1796 1276 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 3.7742761068782e-07 6.98611106841768e-07 1515 1640.81818181818 1515 3.43116068580512e-08 18 2.9572191841569 4.03322572972673 1 5.25578736642388 1515 802 1360 952 2391 2457 2730 2625 18 2881 318 1277 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 5.39836414981107e-08 3.06874196014832e-07 4025 2150.54545454545 1516 4.90760389297838e-09 109 2.32284170298325 2.36914446523524 1 4.36778388681679 4021 109 993 418 423 4646 4158 2510 467 1516 4395 1278 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 9.76525829792225e-07 1.46323870368867e-06 140 1715.36363636364 1517 9.76526258913702e-08 139 1.79338573527867 1.85326434224803 1 3.02072184692308 139 2490 4603 2173 3080 441 575 1033 2292 526 1517 1279 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 7.15369872771143e-06 8.62243564729264e-06 495 1654.72727272727 1520 6.5033836266957e-07 240 1.69928327177717 1.65645628759972 1 2.48418594295445 240 2580 1991 1520 3863 493 491 712 3117 1303 1892 1280 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 1.63770278062753e-07 4.25105288852828e-07 2130 1463.90909090909 1520 1.48882082049075e-08 593 2.59494909908728 3.14606625700971 1 4.77348819668386 2130 593 1250 1909 1605 1595 1520 975 1404 1440 1682 1281 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 4.70122961761098e-08 2.99073619127066e-07 2420 1703 1521 4.27384519824785e-09 305 2.16665975859206 2.473315971229 1 4.08104356683071 2419 2558 1271 2756 305 1122 1351 1261 1521 2025 2144 1282 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 1.81542141843015e-06 2.48658998693857e-06 85 1546.72727272727 1522 1.65038446954755e-07 84 1.69523284080148 1.71794152778807 1 2.74261741156306 84 2509 1971 2620 3366 328 311 1186 2614 503 1522 1283 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 3.05615694941254e-08 2.68623106168104e-07 1525 1471.54545454545 1522 2.77832453806138e-09 54 1.89544210215471 2.35628185667062 1 3.59560464732456 1522 1415 1810 636 54 2189 2637 1191 1636 2355 742 1284 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 1.37428735643915e-07 3.91275115831152e-07 885 1721.72727272727 1523 1.24935222026145e-08 731 1.96805198540782 2.12928716706844 1 3.64055073555093 883 2001 1523 3651 1420 731 763 1533 3241 1176 2017 1285 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 8.95968539242043e-07 1.36904224837243e-06 1865 1734.90909090909 1524 8.14517185575443e-08 1043 2.01248466600366 1.99457085117469 1 3.40666413166245 1862 2062 1165 1434 2973 1231 1699 1221 1524 1043 2870 1286 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 7.6594042198588e-08 3.24764325922831e-07 4000 1946.72727272727 1524 6.96309498774964e-09 136 2.06907794181151 -2.24021095447615 -1 3.87581933751594 3999 136 1524 946 794 4014 4004 2525 743 1070 1659 1287 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 1.17747250770084e-07 3.63937846185494e-07 1965 1538.09090909091 1525 1.07042960974629e-08 629 2.08255912136323 2.36404444452874 1 3.8713350084918 1462 2037 1525 629 1279 1399 1956 869 1965 1963 1835 1288 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 2.09446770026857e-07 4.84839997315725e-07 1525 1469 1525 1.90406172697124e-08 163 1.94632698228167 2.04669707061465 1 3.54801971121894 1525 1167 911 163 1852 1646 1554 2658 1188 841 2654 1289 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 3.11594859156652e-08 2.69553239732593e-07 1525 1453.72727272727 1525 2.83268057790813e-09 59 2.33573960417089 2.79344149669403 1 4.43002518161328 802 2120 984 1916 59 1514 1521 1841 1525 1717 1992 1290 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 1.96890398305083e-14 4.7657573333333e-13 1225 1691.45454545455 1525 1.78991271186441e-15 147 2.57756754340833 -2.06668681776084 -1 9.17042073061478 2790 1221 147 169 1223 1525 3203 3486 2290 256 2296 1291 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 1.95258872920804e-06 2.6552056473241e-06 735 1762.27272727273 1526 1.77508223837404e-07 344 2.86624313187318 3.15028934929352 1 4.61413742180848 731 1928 1526 3100 3391 875 344 530 2952 3113 895 1292 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 4.73851970552371e-07 8.28670359765539e-07 765 1636.45454545455 1527 4.30774611467345e-08 163 2.95157065022699 3.15017062403408 1 5.18255122185018 764 3398 1527 3120 2555 359 249 415 3295 2156 163 1293 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 4.99877824058213e-20 2.38325588843915e-18 3040 1825.09090909091 1527 4.99877824058214e-21 24 2.51077204498179 -2.32294228086083 -1 12.7760641178939 3039 980 4554 24 557 2156 3673 2366 1144 56 1527 1294 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 2.81269610440177e-07 5.72979094207008e-07 1530 1831.90909090909 1529 2.55699678545867e-08 965 2.3313527044065 2.7519095472791 1 4.20123043145914 965 2561 1425 2409 2141 1526 1529 1300 2948 2024 1323 1295 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 5.951283183382e-06 7.28098927567731e-06 630 1739.09090909091 1530 5.4102720749364e-07 626 1.94548135491111 2.07717993572034 1 2.88548553708462 626 1832 1781 2574 3803 1061 862 646 2944 1530 1471 1296 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 6.22002419284035e-08 3.14330987047178e-07 1535 1772.81818181818 1531 5.65456760790736e-09 575 2.04455499466558 2.45842810431442 1 3.83824493209709 1531 1658 2139 3096 575 1225 713 1456 3755 2043 1310 1297 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 4.16760703152214e-07 7.48804917730662e-07 1520 1738.45454545455 1532 3.78873438274545e-08 446 1.96035091845386 -2.16575208472519 -1 3.46673165819483 1518 2184 2435 446 2471 1532 2119 1361 993 3080 984 1298 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 1.26441210253182e-07 3.75824578325571e-07 1175 1808.63636363636 1533 1.14946561381976e-08 311 1.67459544984262 -1.52992755413387 -1 3.10604015225405 1174 1322 2960 2772 1343 311 1533 2246 3063 2154 1017 1299 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 6.3195339076276e-10 8.33189945363192e-09 745 1746.54545454545 1537 5.74503082676625e-11 154 2.99620437362199 3.51288587146806 1 6.98928461214903 2508 154 286 743 1537 2796 3219 2425 1386 741 3417 1300 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 4.10029866175117e-08 2.9351990282604e-07 2170 1618.45454545455 1537 3.72754430742854e-09 202 2.2398662779064 2.36920148513257 1 4.22422712967596 2170 1256 412 1139 202 1537 2302 3331 1857 268 3329 1301 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 4.57372751883382e-07 8.06726229031974e-07 435 1690.90909090909 1538 4.57372846018834e-08 416 2.04323504956898 1.96881735575289 1 3.59425101605526 432 2940 4298 1629 2586 526 777 1139 2319 416 1538 1302 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 1.09621013391915e-12 2.23022061728378e-11 2605 1667.54545454545 1538 9.9655466719972e-14 122 2.53723088552636 2.75970529559407 1 7.80319520300912 2603 1344 182 927 511 2451 3083 2843 1538 122 2739 1303 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 1.03938312060002e-07 3.47369293280946e-07 1540 2322.81818181818 1539 9.44893790641227e-09 324 0.960012976950875 -0.891779822827817 -1 1.78974392411516 1539 3181 3514 4190 1137 1276 1033 324 4511 3682 1164 1304 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 1.54688940294901e-05 1.78385486975796e-05 1005 2098.27272727273 1539 1.40627298156679e-06 746 2.54274012278221 2.54702265184593 1 3.48583968390141 1003 3772 2229 3613 4055 1008 746 1048 1539 3298 770 1305 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 2.09699732710532e-06 2.82348880041385e-06 1545 1976.63636363636 1542 1.90636302356833e-07 617 2.63480952724642 2.56131790550483 1 4.22119608019881 1542 3057 1377 2892 3430 1387 1015 629 3557 2240 617 1306 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 3.7341617739413e-08 2.87575261955407e-07 3990 1965.54545454545 1543 3.39469257938451e-09 138 2.28226923853656 -1.76042996542667 -1 4.31006860767274 3989 1543 1317 1354 138 2264 2290 3300 528 1332 3566 1307 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 5.47016210427125e-12 9.85464318021385e-11 1545 1207.18181818182 1543 4.97287464025896e-13 134 2.52402929805302 2.88855849602788 1 7.292268035953 1543 1390 282 499 1925 1143 1572 1618 1564 134 1609 1308 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 3.14704647247769e-07 6.17119208562305e-07 870 1698.45454545455 1545 3.14704691815334e-08 240 3.22826645369576 4.00651234190299 1 5.78780615612998 866 1937 4630 1179 2325 1545 1495 1251 240 1594 1621 1309 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 2.66075919772714e-07 5.55287751817547e-07 1330 1794.45454545455 1546 2.66075951631096e-08 105 1.95827032787137 2.30058114539237 1 3.53647909444608 1327 1944 4543 2806 2176 1173 443 1546 1532 2144 105 1310 M7963 KEGG_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CELL_CYCLE.html Cell cycle 132/142 KEGG 3.25722312567327e-06 4.18570464284722e-06 205 1793.90909090909 1547 2.96111631653127e-07 205 1.58185740789708 1.69298644920428 1 2.4558281159411 205 2537 3407 1547 3610 256 304 1150 3009 2410 1298 1311 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 1.77494419604679e-07 4.43266487055072e-07 835 1499.90909090909 1547 1.61358576295275e-08 685 2.11953537803358 -2.33113876889814 -1 3.8876724307942 834 1729 2191 1876 1682 1547 1233 1155 685 2665 902 1312 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 2.70813525559733e-07 5.6211074786365e-07 1935 1516.90909090909 1547 2.46194144450988e-08 57 2.13275195524195 2.5053188517934 1 3.84838924943306 1935 57 1547 1064 2096 1630 2145 612 2809 1507 1284 1313 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 8.35426664383949e-07 1.2966832804644e-06 475 1637.27272727273 1549 7.59479074207755e-08 361 1.5979531406621 -1.46574889411979 -1 2.71566406751813 474 1573 2733 1103 2921 361 436 922 4072 1866 1549 1314 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 5.38773472568834e-08 3.06874196014832e-07 1040 1663.09090909091 1549 4.89794077966578e-09 421 2.11199478798308 -2.11884887304728 -1 3.9712371207241 1036 1549 1684 3277 421 633 975 3011 2258 1925 1525 1315 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 9.03270829885258e-06 1.07337319160584e-05 480 1818.45454545455 1550 8.21158671395201e-07 168 1.77961245299873 1.96994344114398 1 2.55277859231698 477 2673 2326 2907 3924 205 168 1030 3881 1550 862 1316 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 1.44825384026016e-07 4.01516692856374e-07 1340 1732.90909090909 1552 1.31659448690755e-08 1116 1.94250802375852 2.30678456079952 1 3.586993338574 1337 3116 2060 1519 1467 2062 1116 1424 1552 1731 1678 1317 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 7.3806153735513e-08 3.2144561803028e-07 1555 1735.72727272727 1553 6.70965056468912e-09 762 1.99897906010193 2.30757322909156 1 3.74705509638279 1553 3235 2216 1676 762 1263 1891 991 1441 2860 1205 1318 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 3.40355082727703e-08 2.77395498531109e-07 2255 1814.18181818182 1554 3.40355087940573e-09 141 1.93393336594887 2.31605297156637 1 3.66084530675237 2251 1019 4616 866 141 1554 3266 1432 2080 1949 782 1319 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 1.81387963135639e-07 4.4942319475077e-07 1555 1605.36363636364 1555 1.64898161900827e-08 517 2.92976459806569 3.35979968667536 1 5.36906391005745 1594 1809 1502 2293 1700 1306 1109 1553 1555 2721 517 1320 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 1.57346708795813e-07 4.1859656963545e-07 1080 1765.54545454545 1556 1.43042472772222e-08 670 1.97487967575541 2.23497915833059 1 3.63646704223884 1080 2522 2509 3572 1556 670 795 1633 1116 2728 1240 1321 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 1.15396296530335e-06 1.68890083604088e-06 125 1883.81818181818 1557 1.15396356453753e-07 122 1.67440478510977 1.72698656164878 1 2.79013974600777 122 3229 4341 2657 3179 550 336 835 2807 1109 1557 1322 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 1.56301142850729e-07 4.16803047601943e-07 1560 1631.54545454545 1558 1.42091958141179e-08 502 2.68801727770143 3.07205576924417 1 4.95136951242577 1558 1523 948 848 1549 1945 2160 2530 502 2104 2280 1323 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 3.33562619629337e-07 6.4099386103601e-07 1395 1538.45454545455 1558 3.03238791094457e-08 284 1.99368720826997 2.15674220440725 1 3.56456766049182 1968 284 1646 1698 2288 1393 1558 1315 2400 1394 979 1324 M17673 KEGG_CARDIAC_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CARDIAC_MUSCLE_CONTRACTION.html Cardiac muscle contraction 71/118 KEGG 9.47832716514107e-08 3.3764305071295e-07 2770 1991.27272727273 1560 8.61666143045342e-09 236 2.94114455978651 3.94154725609573 1 5.49540284523769 2770 1560 950 1208 1039 4341 4715 1541 236 1954 1590 1325 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 1.05618855725935e-07 3.48348225330125e-07 2345 1444.72727272727 1560 9.60171461786774e-09 161 2.14038385241584 2.1930257404451 1 3.99060282315821 2341 161 1343 997 1158 1910 2076 1605 952 1560 1789 1326 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 6.43070916190916e-08 3.14536172538656e-07 2970 1898.09090909091 1561 5.8460994089836e-09 349 1.9693247812715 1.88856272466786 1 3.69682232992995 2970 349 1561 759 613 2330 2306 3527 1212 1107 4145 1327 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 9.58707282191857e-08 3.38845370705758e-07 1580 2078.54545454545 1561 8.71552112700024e-09 17 1.2252638175015 -1.19967918114982 -1 2.28830435391187 1578 1561 3770 3960 1051 567 1029 1147 3862 4322 17 1328 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 5.58944781729372e-08 3.07843567066819e-07 2940 2067.27272727273 1562 5.08131632663863e-09 390 2.27931221001604 2.16766364116553 1 4.28501500805316 2936 1335 551 1562 463 2795 3328 3686 1478 390 4216 1329 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 1.20726625674564e-07 3.69299853003203e-07 800 1495.18181818182 1562 1.09751483908661e-08 798 2.37833936286471 2.74886990428878 1 4.41693022067981 798 2135 985 2172 1300 1680 1665 1279 1946 925 1562 1330 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 9.8475002248491e-08 3.40595929530574e-07 1815 1500.63636363636 1563 8.95227333239695e-09 219 2.71986654963809 2.78815695167523 1 5.07891944393583 1813 1527 719 2522 1087 1563 1933 219 1998 1285 1841 1331 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 3.12040314361787e-08 2.69553239732593e-07 1565 1472.27272727273 1565 2.8367301707969e-09 61 2.76905937913244 -3.06176531537576 -1 5.25203065693694 1565 1828 1351 1632 61 1965 3701 787 323 2182 800 1332 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 6.76855634633491e-08 3.14536172538656e-07 3345 2056.09090909091 1566 6.15323323143404e-09 674 2.1391336286655 -1.86305883503917 -1 4.01566227207604 3342 1197 1215 807 674 2026 3962 4532 1566 1564 1732 1333 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 6.37181435679662e-16 1.879685235255e-14 1805 1622.63636363636 1568 5.79255850617875e-17 104 2.45540718396942 2.70320254185341 1 9.73127679821204 1803 1183 117 1568 1547 2103 2527 541 3685 104 2671 1334 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 5.87994680132084e-08 3.10127287236487e-07 4200 2281.90909090909 1569 5.34540632588581e-09 404 1.89573608697179 1.37279195352668 1 3.56200525655117 4200 404 1569 1159 508 3844 3570 4687 1216 1268 2676 1335 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 8.77500313452962e-08 3.31003670356505e-07 2140 1597 1571 7.97727589502973e-09 361 2.64688640609897 2.48513108162279 1 4.95210021129019 2139 361 703 1571 956 2384 1992 2835 1405 733 2488 1336 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 1.55889499480918e-07 4.16646906879917e-07 4000 1756.18181818182 1571 1.41717736842793e-08 186 2.31050045138125 1.93207386808225 1 4.25596526320535 3998 709 1571 833 1543 3053 2043 663 186 1720 2999 1337 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 9.83072540185335e-08 3.40595929530574e-07 1665 1703.45454545455 1571 8.93702349194591e-09 464 2.04069057687117 2.26685674022762 1 3.81045094313071 1664 2121 1562 2148 1083 1498 2541 464 2603 1483 1571 1338 M12294 KEGG_VIRAL_MYOCARDITIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIRAL_MYOCARDITIS.html Viral myocarditis 70/116 KEGG 1.76267882001408e-07 4.42780416735842e-07 2450 1754.54545454545 1572 1.60243541931185e-08 233 2.18171779795704 -1.70090437810191 -1 4.00205349203473 2448 233 1118 429 1670 1572 2546 3702 1109 822 3651 1339 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 6.66116486751456e-08 3.14536172538656e-07 2185 1697.27272727273 1574 6.05560460836498e-09 652 1.98101729220267 -1.86114815825706 -1 3.71877666014331 2181 2006 1550 1418 652 1574 2028 1231 3380 1011 1639 1340 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 1.40991250154719e-11 2.39380827600818e-10 240 1484.72727272727 1575 1.28173863777838e-12 219 3.16856607733423 3.54171775694119 1 8.80197019634423 236 2114 219 978 3534 1686 1610 1495 1784 1101 1575 1341 M33 PID_GLYPICAN_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_GLYPICAN_1PATHWAY.html Glypican 1 network 18832364 30/37 Pathway Interaction Database 4.29714840763272e-07 7.69152085097703e-07 1155 1646.09090909091 1576 3.90649931543014e-08 966 2.72702918543317 3.35408751633895 1 4.81371186408078 1154 2322 1145 1908 2485 1715 1486 966 1364 1986 1576 1342 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 1.60037771688931e-07 4.21105226344428e-07 2850 1705.36363636364 1576 1.45488893937083e-08 133 2.59676426479539 -2.62660442124556 -1 4.77990665476255 2849 133 489 690 1576 2831 4026 2604 1251 464 1846 1343 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 8.40299932682247e-18 3.19856103408081e-16 2105 1374.27272727273 1577 7.63909029711132e-19 86 2.43652544299721 2.8828650710929 1 10.9011654298461 2103 1074 86 917 601 1844 2840 2225 1725 125 1577 1344 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 4.61978708281467e-07 8.1151451547768e-07 1560 1547.72727272727 1578 4.1998073208414e-08 106 2.62716400030489 2.97867125432659 1 4.61973574450365 1557 1913 1967 1897 2541 1578 424 574 1479 2989 106 1345 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 1.25888441180421e-18 5.25834904753616e-17 1625 1620.63636363636 1579 1.25888441180422e-19 67 2.4809580965139 2.68796649920407 1 11.6617179955365 1621 1035 4311 672 228 1299 1983 1579 2358 67 2674 1346 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 8.46294576376127e-08 3.27455016694392e-07 3220 1781.90909090909 1580 7.6935873539212e-09 197 2.61986102513521 3.18108680698208 1 4.90507062137226 3219 197 750 1580 922 3179 3132 2793 635 637 2557 1347 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 7.86099373882908e-08 3.26618753937265e-07 1515 2193.45454545455 1582 7.14635819974223e-09 542 1.12399772820654 -1.22033502783656 -1 2.1042887679112 1514 1923 3249 4548 822 1215 1582 1087 3928 3718 542 1348 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 7.58146205212225e-07 1.19560644457123e-06 1530 1939.72727272727 1582 6.89224060435057e-08 427 3.14397193679485 -3.31585266589977 -1 5.37589927481041 1526 2443 922 1407 2860 2326 3564 427 3615 665 1582 1349 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 7.4100353931513e-07 1.17531255663477e-06 325 1745.18181818182 1583 6.73639808090821e-08 234 1.68057469995925 1.65521111537815 1 2.87683341258033 321 2375 2298 3603 2842 266 234 1583 3747 1542 386 1350 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 5.46908120853506e-07 9.28563428211708e-07 1835 1663 1585 4.97189324374508e-08 310 2.46834984298614 3.05652718398014 1 4.29870896064217 1834 1703 1585 1057 2636 1268 1448 3253 751 2448 310 1351 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 2.26970378927721e-07 5.07021281482396e-07 1270 1603.81818181818 1585 2.06336729403531e-08 627 2.38151956903488 2.97262383666279 1 4.32817792121622 1268 2119 1310 1728 1927 1495 2194 1585 1239 2150 627 1352 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 1.39382604661793e-07 3.94416003599317e-07 1955 1706.90909090909 1585 1.26711466811345e-08 358 3.00059651492508 -3.12369103494527 -1 5.54802015048484 1953 358 498 3019 1430 1585 2699 3601 2137 909 587 1353 M6220 BIOCARTA_AGR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGR_PATHWAY.html Agrin in Postsynaptic Differentiation 50/59 BioCarta 1.08166619729925e-07 3.51132355656979e-07 3605 2008.18181818182 1586 9.83332954982869e-09 355 2.42575322626056 -1.48081523673859 -1 4.52034810833588 3605 407 1307 883 1191 4393 4064 1586 355 2042 2257 1354 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 4.55790148350767e-05 5.02177754485439e-05 410 1902.81818181818 1587 4.14363265057934e-06 406 2.02428936651885 -2.19086971658702 -1 2.51216986212263 406 2651 1353 1430 4254 1587 1140 1876 3333 834 2067 1355 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 5.99196389378621e-07 9.96900584373313e-07 890 1825.09090909091 1589 5.4472413870637e-08 478 1.62422727178198 -1.81242932372615 -1 2.81388370499471 889 478 3108 2629 2700 1153 1474 2057 912 3087 1589 1356 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 2.62477514911927e-07 5.51354637465196e-07 1590 1818.81818181818 1589 2.3861595111599e-08 533 2.66469157682526 -2.84294193674896 -1 4.81490529840786 1589 533 1015 3055 2068 1592 2441 3718 1356 1056 1584 1357 M15798 KEGG_MELANOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOMA.html Melanoma 67/89 KEGG 3.98673031108636e-07 7.25418930930131e-07 1950 1729.27272727273 1590 3.62430093958357e-08 209 2.54231918345427 2.80031447482281 1 4.5062701990144 1947 1590 1370 209 2432 1403 1343 2412 855 2813 2648 1358 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 3.57825042452944e-08 2.8385448745847e-07 4085 2143.45454545455 1591 3.57825048214688e-09 14 3.29495857767584 -4.51488228276085 -1 6.22829727434405 4081 889 4246 719 170 4635 4317 82 14 1591 2834 1359 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 7.25628986399417e-07 1.15747509827822e-06 1595 1889.27272727273 1591 6.59662932486111e-08 501 1.90152636803007 2.25563075656987 1 3.25882201152185 1591 2871 2683 2423 2825 1396 1328 1459 501 2804 901 1360 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 5.072756493577e-07 8.75444630701405e-07 345 1679.45454545455 1592 4.61159787568432e-08 343 1.89524340707113 -1.89142214397004 -1 3.31442704385177 343 1592 1383 1944 2590 976 1658 1160 4215 770 1843 1361 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 1.23771354337569e-07 3.71755418903835e-07 2925 1956.36363636364 1593 1.12519419364464e-08 278 2.18395088473139 2.87280923050284 1 4.05403637188345 2922 1589 1726 1593 1325 3617 3771 359 278 2790 1550 1362 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 7.42366461522874e-07 1.17622346370861e-06 640 1977.63636363636 1593 6.74878829115102e-08 298 2.35505161254174 2.38087849821302 1 4.03153015063408 637 2359 1593 3839 2846 503 298 3231 4319 1508 621 1363 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 2.39273629581567e-07 5.23584391110336e-07 1480 2055.81818181818 1596 2.17521505095589e-08 1033 2.11874837401188 2.21847121378835 1 3.84198074731453 1480 3631 2474 3353 1979 1560 1199 1596 1535 2774 1033 1364 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 3.82421569746149e-07 7.05917015722262e-07 3470 2010.81818181818 1596 3.47656032928852e-08 228 2.10504882646821 2.40981683651701 1 3.73825292126346 3468 228 1596 1193 2398 3279 3165 1569 1076 1288 2859 1365 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 8.40085491801117e-08 3.27411388472988e-07 1600 1656.54545454545 1596 8.40085523559579e-09 687 1.90289696414149 2.07222909732233 1 3.56252093921902 1596 985 4497 1609 1010 687 1748 910 2363 1111 1706 1366 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 7.65217878459455e-08 3.24764325922831e-07 2375 1681.18181818182 1596 6.95652640977952e-09 338 2.57645661829 -2.05064216137358 -1 4.82645781444313 2372 338 636 1596 792 2116 3772 1820 647 641 3763 1367 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 1.52326981950588e-07 4.1209216255052e-07 2280 1521.36363636364 1596 1.38479084088763e-08 102 2.50691548309435 2.97935711591031 1 4.62129275973939 2276 102 645 582 1517 2506 2400 2127 884 1596 2100 1368 M3896 KEGG_INOSITOL_PHOSPHATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INOSITOL_PHOSPHATE_METABOLISM.html Inositol phosphate metabolism 50/55 KEGG 1.63936535632394e-07 4.25154092409285e-07 1900 1657.54545454545 1597 1.49033225316718e-08 153 1.47198368767899 -1.77367965302957 -1 2.70736506289775 1899 429 2850 2789 1607 945 1400 1597 645 3919 153 1369 M16650 KEGG_PHENYLALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHENYLALANINE_METABOLISM.html Phenylalanine metabolism 20/27 KEGG 1.56496140536523e-07 4.17028099662921e-07 3545 2188.18181818182 1598 1.42269228789833e-08 692 2.70921701823101 -2.98291814171971 -1 4.99024315331109 3543 692 885 1598 1550 3193 2617 3808 866 1276 4042 1370 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 5.83276266444252e-07 9.77540122330492e-07 525 2116.18181818182 1598 5.30251291896151e-08 237 2.51197823951109 2.51336477016752 1 4.35851197427893 521 4237 1598 4369 2679 1085 1189 237 4056 2211 1096 1371 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 2.07815917559619e-07 4.84630005376185e-07 1600 1566 1599 1.88923579263893e-08 443 1.73353059231603 -1.43514328158354 -1 3.16010659331151 1599 857 2204 1405 1835 1431 839 2028 443 1830 2755 1372 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 3.47733155309454e-08 2.80457419563923e-07 2590 1898.45454545455 1600 3.4773316075078e-09 159 1.91870036481058 2.20278322168425 1 3.62936170749206 2587 1023 4323 988 159 1600 3620 3095 1585 1693 210 1373 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 9.15835389156975e-08 3.34843245403276e-07 3080 1909.81818181818 1600 8.3257766116562e-09 233 3.23083583479769 2.74274136642834 1 6.04013724395246 3078 1890 1119 1600 996 2463 1344 2854 233 1435 3996 1374 M45 PID_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD40_PATHWAY.html CD40/CD40L signaling 18832364 37/44 Pathway Interaction Database 7.48212447821817e-07 1.18389633044552e-06 565 1639.81818181818 1602 6.80193365714929e-08 563 1.77482140116574 -2.02610493069116 -1 3.03659498805591 563 2275 2607 1504 2851 1003 1602 1650 750 2235 998 1375 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 8.33445894335068e-08 3.27411388472988e-07 1915 1623.81818181818 1606 7.57678114462957e-09 180 1.97076521720553 2.20262139368786 1 3.6896116507876 1911 1375 2370 180 898 2161 2599 1081 871 2810 1606 1376 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 1.56183594933294e-07 4.16803047601943e-07 1555 2120.54545454545 1606 1.41985096382878e-08 549 1.52740048845177 -1.60416927730781 -1 2.81312348965909 1552 3684 3218 2634 1545 1606 1244 1430 549 3600 2264 1377 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 1.50900002143921e-11 2.53469042747084e-10 1610 1628.27272727273 1610 1.50900002144945e-12 144 2.27734686876641 2.47000480444444 1 6.30967487105105 1610 1048 4287 714 267 1259 2048 1759 2480 144 2295 1378 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 9.45798702715566e-07 1.42853436058159e-06 80 2024 1610 8.59817372111556e-08 79 1.59763404206308 1.67143789924429 1 2.69571914034784 79 3570 3528 2942 3011 956 521 1285 3181 1610 1581 1379 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 1.65091957649273e-07 4.26977556221681e-07 580 1417.36363636364 1611 1.5008360912552e-08 270 1.83441703155481 -1.93760217405116 -1 3.37320279026077 578 599 1708 1895 1611 739 1227 1885 3092 1987 270 1380 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 1.26826910512673e-07 3.76019483429534e-07 1620 1802.09090909091 1616 1.15297198021879e-08 559 2.1934831649684 2.3380067406815 1 4.06859751121179 1616 1439 1861 4138 1349 1167 2021 559 2184 1930 1559 1381 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 7.62263051106542e-09 8.42595222768824e-08 3900 2186.09090909091 1618 6.92966412497869e-10 117 2.57636722776033 -2.66966896048702 -1 5.26221481716438 3900 1334 343 117 547 4604 4172 3780 1618 670 2962 1382 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 7.20254227928641e-07 1.15045683784203e-06 545 1835.45454545455 1618 6.54776785210497e-08 275 1.92437614615358 1.71560778626275 1 3.29945990629027 542 3347 1873 2414 2820 455 275 1105 4221 1520 1618 1383 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 3.58734931243048e-08 2.84098804608588e-07 2760 1589.18181818182 1619 3.26122670084208e-09 119 2.70239273167157 2.49860876238974 1 5.10775288226148 2757 572 897 1619 119 2416 2677 2533 1073 727 2091 1384 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 8.53315854288225e-08 3.28305665915602e-07 1620 1513.72727272727 1620 7.75741715805325e-09 400 2.20212943496414 2.38476349100021 1 4.12211312117748 1620 1121 529 1654 930 1954 2402 1054 2788 400 2199 1385 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 6.61063761825396e-08 3.14536172538656e-07 3670 2170.81818181818 1622 6.00967074262976e-09 645 2.42553206850586 2.6092913789841 1 4.55341553635417 3666 1463 1126 1213 645 3624 3742 1622 1332 1878 3568 1386 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 2.21040494852932e-07 4.99430893109544e-07 1320 1643.45454545455 1622 2.00945924601387e-08 820 2.33408763433705 2.71664729541498 1 4.24637312035414 1319 1205 820 1268 1900 1673 1622 2003 2751 1317 2200 1387 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 7.68098942741928e-08 3.24764325922831e-07 2245 1590.63636363636 1622 6.98271790508201e-09 185 2.00631661255843 2.15780811473711 1 3.75822800540641 2242 1264 1622 185 797 1919 2131 2000 844 1590 2903 1388 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 4.79093901247545e-08 3.01912311600589e-07 1820 1547.36363636364 1623 4.35539919709791e-09 317 2.19929677119349 2.28373812751741 1 4.13992491530072 1819 1623 1652 2117 317 2048 1570 1188 1320 1294 2073 1389 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 6.67126520280519e-06 8.0843059710502e-06 1625 1794.90909090909 1625 6.06480493890074e-07 124 2.44915926676602 2.81338177854105 1 3.60060479043259 1625 3193 2192 2408 3835 1280 124 516 1121 3110 340 1390 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 1.51004299281932e-07 4.10564684683595e-07 2535 1758 1627 1.37276645133286e-08 861 2.17488022074133 2.31140942948158 1 4.01011180945253 2532 2036 1348 861 1508 2010 2163 1076 1130 1627 3047 1391 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 7.15554905681386e-08 3.17725226229176e-07 2780 2077.63636363636 1627 6.50504480868155e-09 705 1.88780001653906 1.75089422664337 1 3.54135987750808 2777 705 1441 2520 738 3021 3081 1068 1627 1280 4596 1392 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 6.63513513029967e-08 3.14536172538656e-07 4415 2294.36363636364 1631 6.03194120946671e-09 198 2.18432680023828 -1.97602939574079 -1 4.10051879416426 4412 518 1631 198 648 4650 4351 3589 252 1264 3725 1393 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 4.63966858104353e-08 2.99073619127066e-07 1635 1898.45454545455 1632 4.63966867791288e-09 376 1.847869433375 2.13210961301488 1 3.48045467300853 1632 989 4433 1445 376 2163 3100 1479 2026 951 2289 1394 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 1.08652175208994e-06 1.60462536604022e-06 1635 2283.90909090909 1633 1.08652228332859e-07 239 3.74453620548333 4.2880923885838 1 6.26479993105949 1633 2470 4512 4337 3144 1602 876 239 3797 1327 1186 1395 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 3.52606977259431e-12 6.52668601044908e-11 2915 1920.36363636364 1634 3.5260697725999e-13 41 2.44675176940009 2.81952619534713 1 7.19540930811314 2913 970 4672 41 848 1634 3321 2492 1328 129 2776 1396 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 2.50971084298627e-07 5.35608210768807e-07 1125 1732.09090909091 1636 2.5097111264255e-08 452 2.03994173897248 2.09975259242215 1 3.69323814958048 1123 1966 4661 1636 2116 624 1306 1407 2110 452 1652 1397 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 8.20631905320124e-08 3.27411388472988e-07 1690 1537.54545454545 1637 7.46029032664442e-09 421 2.23045505884411 -2.06698072440418 -1 4.17590922396718 1690 1777 2351 1390 878 1792 1354 1164 421 2459 1637 1398 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 5.34182575358584e-08 3.06874196014832e-07 2780 1705.09090909091 1639 4.85620534844623e-09 330 2.13768999106663 2.44678258174722 1 4.01956293894565 2776 330 1639 1613 412 3069 2756 828 1026 1707 2600 1399 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 1.5802207642474e-07 4.1878955683592e-07 1940 1646.72727272727 1639 1.43656443431986e-08 787 2.46261678124013 2.67475852847839 1 4.5346376532709 1938 1639 1264 1402 1564 1459 1980 2436 787 1702 1943 1400 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 5.13369727088214e-08 3.0357704374324e-07 1780 1450.81818181818 1641 4.6669976278881e-09 333 1.9057777489984 1.87924244918856 1 3.58597971349662 1776 333 1751 1641 383 2245 2343 1121 1512 1708 1146 1401 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 1.4355357164425e-06 2.01838801954382e-06 1240 1845.90909090909 1642 1.30503332104883e-07 566 1.99103051068385 2.22924814178916 1 3.27341048649088 1236 1723 2214 3327 3268 951 1642 566 3285 1359 734 1402 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 4.07647192121434e-06 5.12135945385459e-06 260 1618.45454545455 1642 3.70589043154462e-07 237 1.75246706556519 1.87194300529983 1 2.6764535046759 259 1642 2185 2138 3697 344 237 1199 3209 1964 929 1403 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 8.98976747651942e-08 3.31497675696653e-07 1705 1569.90909090909 1642 8.98976784019105e-09 192 3.42029439162562 4.21341907248826 1 6.39869301597385 1704 2889 4531 2069 1095 1642 281 192 274 2378 214 1404 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 2.51296064650594e-06 3.3215273737071e-06 75 1887.18181818182 1643 2.28451228813817e-07 44 1.37480399465015 1.39484322584016 1 2.17413610084962 73 2593 3365 2641 4217 459 44 929 3337 1458 1643 1405 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 3.09760484662449e-07 6.10722425900902e-07 1565 1691.90909090909 1643 2.81600480251638e-08 79 2.07450481120204 2.38495612148088 1 3.7216844609523 1561 79 1710 1524 2226 1990 2779 1643 1424 3022 653 1406 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 1.40371884140637e-06 1.98445382170338e-06 1620 1909.18181818182 1644 1.27610885186875e-07 635 2.39722371851297 -2.33922054488626 -1 3.9464970993993 1617 1765 1458 635 3249 1644 2995 1497 2950 1808 1383 1407 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 2.8294242502721e-06 3.67903098107006e-06 940 1792.18181818182 1644 2.57220717200604e-07 670 1.7195407515112 2.0076188998998 1 2.69747978920785 939 1676 2618 1515 3560 745 670 1644 1903 3170 1274 1408 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 1.70288026541744e-07 4.33060067498401e-07 3615 2463.54545454545 1644 1.54807308838782e-08 581 2.0979681494159 2.35108311315318 1 3.85423376241788 3611 1164 745 992 1644 3866 4271 4073 1458 581 4694 1409 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 3.16953491634723e-08 2.69553239732593e-07 2125 1619.81818181818 1644 2.88139542000967e-09 72 2.2759353570912 2.9496166942465 1 4.3165768199467 2124 110 927 1644 72 2199 3469 2790 1236 1203 2044 1410 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 7.22063487124093e-05 7.86010069009621e-05 920 1610.18181818182 1644 6.56442897370565e-06 217 2.73747742459088 2.91947651693123 1 3.24374383021361 920 2385 1644 2562 4310 817 217 1647 445 2070 695 1411 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 5.61285173943916e-08 3.08412808034375e-07 3220 1813.36363636364 1645 5.10259262058149e-09 201 2.81832443645103 2.52565789800195 1 5.29788698077876 3220 1645 1043 762 467 2852 2288 2447 201 1296 3726 1412 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 1.07227835203655e-07 3.4928597802709e-07 1500 1817.36363636364 1647 9.74798549363018e-09 247 2.30907277796859 2.20625971117366 1 4.30440145237395 1497 247 1217 2094 1183 1647 2387 3750 1592 2466 1911 1413 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 4.05872749420396e-07 7.33149398111086e-07 355 1632.45454545455 1648 3.68975294817191e-08 352 1.99240204604555 -1.8864775609645 -1 3.52870511225866 352 461 1648 2867 2454 472 584 2389 3777 1682 1271 1414 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 1.71458295143281e-07 4.35332519137324e-07 2150 1780.81818181818 1649 1.55871189550896e-08 673 2.17854078531848 2.15585942863869 1 4.00085910884586 2147 2015 673 1483 1649 1451 2141 1437 3135 769 2689 1415 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 2.49622653071318e-07 5.33952390873115e-07 1745 1691.81818181818 1649 2.26929710358834e-08 384 2.81724128018225 2.68921893024597 1 5.10193199914041 1742 1869 1254 2725 2026 1480 384 3132 781 1568 1649 1416 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 6.11648105589324e-08 3.12995510041999e-07 2640 1751.72727272727 1651 5.56043747813161e-09 554 2.05055452730792 2.46638751963443 1 3.85060528268527 2636 1078 1040 1026 554 2678 2878 2238 1625 1651 1865 1417 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 6.74439965061241e-08 3.14536172538656e-07 3480 2250.27272727273 1651 6.13127259761016e-09 667 1.96786377037425 -2.10146572713301 -1 3.69407907693046 3478 1525 2055 1651 667 3314 4144 4156 1049 1341 1373 1418 M4974 REACTOME_BASIGIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASIGIN_INTERACTIONS.html Genes involved in Basigin interactions 22/30 Reactome 9.21868610718376e-07 1.39865632998738e-06 885 1825.81818181818 1653 8.3806272455482e-08 690 1.82615323547537 1.84474552833324 1 3.086267939627 881 690 1653 3048 2996 1175 1163 2584 3268 747 1879 1419 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 1.19763411318047e-06 1.74085013275705e-06 890 1667.18181818182 1655 1.08875887740727e-07 670 2.94395146779512 3.11202782711595 1 4.89511331459778 890 2176 670 1072 3146 1655 1872 2314 1571 1232 1741 1420 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 3.15324499925247e-08 2.69553239732593e-07 1660 1404.18181818182 1659 2.86658640404338e-09 68 2.33214304396337 2.62080197814803 1 4.42320252464319 1659 1242 436 546 68 1981 3140 2282 1770 413 1909 1421 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 1.60925332357389e-07 4.22216547374584e-07 1750 1706.54545454545 1660 1.46295767389761e-08 203 2.10480585003642 2.05354756831698 1 3.87349184724289 1747 431 1952 1660 1582 1300 2458 4266 1809 1364 203 1422 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 8.88239766351104e-08 3.31003670356505e-07 1235 1790.90909090909 1660 8.8823980185475e-09 880 2.15852326921618 2.4476067027276 1 4.03825523980394 1234 1974 4624 880 1078 985 1640 1884 1815 1926 1660 1423 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 3.77137896505078e-08 2.87575261955407e-07 2485 1731.18181818182 1660 3.42852639063832e-09 150 2.13292457755626 -2.11011484911706 -1 4.02797464684313 2481 1188 841 816 150 1660 2502 3637 2206 878 2684 1424 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 3.89745122327557e-08 2.92463748392062e-07 1855 1647.36363636364 1662 3.89745129163113e-09 238 2.12102161395561 2.32534636131823 1 4.00100775561006 1851 982 4532 392 238 1398 2237 1662 2472 490 1867 1425 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 4.35909046579926e-07 7.76704680957814e-07 1380 1910.72727272727 1663 3.96281029955614e-08 756 2.43367711243148 2.86812515498243 1 4.29281614030665 1377 1663 1014 3267 2500 1771 1839 1406 3900 1525 756 1426 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 1.58745746897425e-06 2.20636020422805e-06 490 1631.45454545455 1663 1.44314419494509e-07 489 1.88827517628778 1.75378878937665 1 3.08334178812806 489 1456 1446 1692 3308 1131 1663 1857 1774 694 2436 1427 M15997 BIOCARTA_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTRINSIC_PATHWAY.html Intrinsic Prothrombin Activation Pathway 25/36 BioCarta 1.65266892638398e-12 3.2638482562897e-11 190 1408.63636363636 1664 1.50242629671383e-13 187 4.28757792554181 4.10394029899895 1 12.9821819461834 464 1746 187 689 3866 1713 1808 2616 187 555 1664 1428 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 4.94830658589446e-05 5.43795275562791e-05 330 1890.90909090909 1664 4.49856171655336e-06 330 1.73416370662973 1.64810594612701 1 2.13468122150266 330 2614 2148 1491 4266 894 993 1664 2963 1244 2193 1429 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 1.95555978863637e-06 2.65847989699414e-06 70 1499.18181818182 1665 1.77778320628878e-07 70 1.71323132983658 1.69004171966831 1 2.75738392691178 70 2104 2072 1725 3806 532 445 1083 1945 1044 1665 1430 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 1.40731625154433e-06 1.98815241465461e-06 1450 1741.09090909091 1665 1.27937922890014e-07 633 2.93880432934153 3.79352912584947 1 4.83759777040584 1449 1665 633 841 3252 2064 2401 2637 1996 947 1267 1431 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 2.38603458408557e-07 5.22548577520102e-07 810 1358.90909090909 1666 2.16912258442332e-08 52 2.3667330342859 2.74967266455965 1 4.29234626411515 810 2372 1946 1666 1975 891 711 108 1886 2531 52 1432 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 1.75968759726518e-07 4.42620781379724e-07 2020 1573.63636363636 1667 1.59971612546838e-08 352 1.89511543541823 1.8956340595217 1 3.47629444540652 1271 2017 1730 1285 1667 352 1179 2023 2019 2162 1605 1433 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 2.82244342179617e-07 5.73983092245837e-07 2295 1481.63636363636 1667 2.56585798535967e-08 130 3.08222617888347 2.8874689831283 1 5.55394791951736 2291 691 774 130 2144 1920 2533 1667 2460 813 875 1434 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 1.7610622496761e-07 4.42620781379724e-07 690 1769.27272727273 1668 1.60096580967829e-08 690 1.64963785022959 -1.76036484497608 -1 3.02589243522615 690 2199 3090 2413 1668 1026 1139 1381 1066 2895 1895 1435 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 1.22258923552949e-07 3.70192774369017e-07 1670 1812.27272727273 1669 1.11144482133774e-08 631 1.35013065420888 -1.35097443679601 -1 2.50661233064278 1669 702 3127 2819 1311 1666 631 974 2266 2783 1987 1436 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 3.86549151663924e-07 7.10756523511384e-07 1670 1655.27272727273 1670 3.51408381438395e-08 609 2.7571906269608 3.03679005978567 1 4.89426396011797 1670 1760 1105 1379 2407 1200 909 3570 1823 1776 609 1437 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 2.97869559579063e-07 5.96497378537623e-07 3350 1984.18181818182 1670 2.70790545371996e-08 25 2.69742821912636 3.66091752052875 1 4.84744705546514 3346 829 1670 1661 2187 3765 4000 1241 834 2268 25 1438 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 6.95686017547928e-08 3.15431124190799e-07 1840 1482.36363636364 1671 6.32441854133614e-09 557 1.70975864058356 1.41321178473371 1 3.20884125261465 1837 557 2403 1444 705 1772 1694 2048 819 1671 1356 1439 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 7.45630723272123e-08 3.2288397661503e-07 3185 1949.18181818182 1671 6.77846135039333e-09 283 1.90730927857932 -1.44312563253358 -1 3.57411410072056 3184 283 1671 1802 772 2402 3007 4624 731 1401 1564 1440 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 2.68103183322872e-07 5.57918631626685e-07 1675 1906.45454545455 1672 2.43730196359359e-08 495 2.86146599308606 -3.80925720634682 -1 5.16627907867006 1672 2891 1459 1489 2089 2013 2385 495 3855 1645 978 1441 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 1.4593841379213e-05 1.68872104216439e-05 1675 1981.27272727273 1673 1.45939372211916e-06 26 2.52311581316657 3.11927568149158 1 3.47627159876685 1673 1948 4372 3305 4065 1619 888 332 26 2833 733 1442 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 2.02200116193683e-05 2.30083063749803e-05 1935 1701.27272727273 1673 1.83819976928681e-06 291 2.44890658825983 2.66271743497677 1 3.27901301926594 1932 462 1546 1673 4112 2171 3087 1093 291 1683 664 1443 M233 PID_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPO_PATHWAY.html EPO signaling pathway 18832364 47/58 Pathway Interaction Database 1.30177964013205e-07 3.79878839072891e-07 2120 1845.36363636364 1675 1.18343610650973e-08 637 1.49727251394552 -1.86071190811939 -1 2.77503555214159 2116 1675 3111 637 1372 1917 2645 1426 1523 3184 693 1444 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 1.78357293235019e-07 4.44950541262839e-07 1160 1563.90909090909 1675 1.62143006995194e-08 531 2.07932006376896 2.451142770793 1 3.81290394878398 1158 1551 1797 1675 1684 1848 1921 531 1666 2010 1362 1445 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 6.33327476984354e-06 7.71035772856887e-06 1675 2165.54545454545 1675 5.75753909263915e-07 423 2.60255077814329 2.24174592880472 1 3.8416230926596 1675 3799 2440 3113 3820 955 423 737 1336 3954 1569 1446 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 3.24091184200224e-06 4.16587796684384e-06 1680 1869.90909090909 1676 2.94628783303147e-07 324 2.16483566728163 2.66078777933017 1 3.36250630049116 1676 2327 2133 1080 3609 1379 1320 2311 901 3509 324 1447 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 1.22249622085043e-10 1.75920187878476e-09 3660 2103.36363636364 1676 1.11136020083487e-11 211 2.60997320653965 -2.33071852258493 -1 6.59725519262495 3659 1386 262 718 211 3534 4293 2934 1676 307 4157 1448 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 4.93790044811037e-07 8.56556049800843e-07 1605 1722.54545454545 1677 4.48900141492961e-08 611 1.7382382597925 2.17376328864935 1 3.04453782277219 1605 1677 2668 1949 2576 1881 1438 743 1509 2291 611 1449 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 5.02588185431563e-08 3.0357704374324e-07 2480 1518.72727272727 1678 4.56898360830135e-09 270 2.30914893279993 -1.57503581482649 -1 4.34515969459621 2480 270 663 1835 361 1512 2727 1678 2370 875 1935 1450 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 5.26616310464249e-07 9.02880125459955e-07 1490 1831.27272727273 1679 4.78742215019082e-08 491 2.38793320719128 3.15624660772412 1 4.16703253430473 1486 3316 1999 646 2608 1679 2395 1138 530 3856 491 1451 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 5.82387273655475e-07 9.76507258136356e-07 2235 1642.81818181818 1679 5.29443116205415e-08 879 2.24472705903745 2.37685185567869 1 3.89501269587851 2231 1679 1366 1065 2678 1989 1752 1552 879 1028 1852 1452 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 1.77434406327032e-07 4.43266487055072e-07 1255 1492.54545454545 1680 1.6130401876134e-08 659 2.336548555263 -2.52572499881274 -1 4.28580830230197 1252 2057 661 806 1680 1750 2830 1119 1687 659 1917 1453 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 7.37526175355393e-07 1.17130671186994e-06 840 1634.54545454545 1680 6.70478566002884e-08 839 2.63639300247316 2.97754181007339 1 4.51463644712909 839 1555 1010 2180 2839 1054 1680 2212 1723 1784 1104 1454 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 1.23913127408842e-06 1.79078371515533e-06 1685 1757.36363636364 1681 1.2391319650398e-07 68 2.19505302640393 -2.56627642783422 -1 3.64186374222674 1681 2475 4234 2551 3228 1154 219 549 68 2827 345 1455 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 6.88694840834926e-08 3.15009389627869e-07 1465 1635.90909090909 1681 6.26086238540041e-09 348 1.94720666433525 2.21339138044127 1 3.65492534545544 1463 348 1603 2093 694 1887 2629 1897 1681 1255 2445 1456 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 2.7251078815045e-06 3.56203522589345e-06 725 1723.90909090909 1682 2.47737387005609e-07 291 2.52736518423326 -2.53253146711 -1 3.97537872451088 722 2723 1682 3304 3539 502 679 1149 2145 2227 291 1457 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 3.10626971765373e-09 3.63811242365399e-08 1685 1740.45454545455 1683 2.82388156549054e-10 324 3.50151149021484 3.92610648856609 1 7.52092146285251 1683 514 324 793 3114 2288 2574 3318 1179 382 2976 1458 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 6.12307522169981e-06 7.47179809886843e-06 3840 2074.63636363636 1684 6.12309209318781e-07 168 4.23576987054722 4.09333392599741 1 6.26965210319135 1684 2467 4382 1169 3838 1432 309 830 168 2705 3837 1459 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 2.22072184816899e-06 2.97187613364266e-06 1255 1954.63636363636 1684 2.0188400816464e-07 720 1.85161702195632 1.54583073999546 1 2.95430315100922 1255 1669 2160 2113 3454 1461 1441 2877 720 1684 2667 1460 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 1.68749386898552e-07 4.3132890453628e-07 2085 1850.36363636364 1685 1.53408545311228e-08 146 2.60044839749572 3.15040478584475 1 4.77886632354433 2085 2796 1685 1575 1634 2431 2425 1240 146 2890 1447 1461 M14091 KEGG_OLFACTORY_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OLFACTORY_TRANSDUCTION.html Olfactory transduction 29/833 KEGG 2.89967216553077e-07 5.84959799502929e-07 1685 1852.09090909091 1685 2.63606595247013e-08 308 2.18419490323953 2.35966888906675 1 3.93032090815758 1685 632 1746 3875 2167 1084 1299 829 4000 2748 308 1462 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 2.26352785273498e-07 5.06973463057442e-07 1105 1680 1686 2.05775280511275e-08 734 2.13138978694123 -1.94875909651186 -1 3.87352635417746 1102 1863 1941 1686 1921 1380 1154 734 3669 1937 1093 1463 M8719 BIOCARTA_MCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCALPAIN_PATHWAY.html mCalpain and friends in Cell motility 39/49 BioCarta 1.04137192795029e-07 3.47369293280946e-07 2850 1773.09090909091 1687 9.46701797494297e-09 170 2.65047768867943 2.94593832516061 1 4.94277941166377 2850 494 1163 1265 1144 3361 3333 1687 170 2168 1869 1464 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 1.61569791469931e-07 4.22732492094277e-07 2630 1897.90909090909 1689 1.46881639396136e-08 1121 1.63793618995084 1.72164197846072 1 3.01386578961665 1404 2060 2908 1689 1588 1121 1272 2626 2627 1451 2131 1465 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 7.03107643373749e-08 3.15977748626312e-07 3680 2039.54545454545 1689 6.39188787131525e-09 397 2.13955870973437 -1.93255536765505 -1 4.01523347500571 3680 397 1600 1633 717 3405 3456 2354 1689 835 2669 1466 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 3.60124874877451e-08 2.84721844124216e-07 3135 2041.90909090909 1690 3.60124880713498e-09 82 3.10533300630338 -3.38135278899614 -1 5.86861970299446 3131 888 4366 189 176 4247 4189 1690 82 1593 1910 1467 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 5.8917940262821e-08 3.10127287236487e-07 1975 1616.90909090909 1692 5.35617653097231e-09 513 3.29976565243053 -3.44967180233324 -1 6.20075336683496 1974 1692 564 761 513 1817 1837 4197 1225 804 2402 1468 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 2.40632805768124e-06 3.19489969964992e-06 395 1899.72727272727 1692 2.18757335426543e-07 391 1.85429527170269 -1.89156594618394 -1 2.94175014956041 391 2210 1997 2904 3484 854 1034 647 4393 1692 1291 1469 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 6.75711795416422e-08 3.14536172538656e-07 4495 2648.36363636364 1693 6.14283469245773e-09 671 2.27740896858559 -2.4722276872536 -1 4.2752936284921 4494 1497 1288 1693 671 4042 4243 4566 1098 1562 3978 1470 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 1.80354235777676e-07 4.47913293152525e-07 1030 1612.09090909091 1693 1.63958409602703e-08 811 1.92378011751437 -2.1413981150999 -1 3.52602070067657 1028 1733 2211 2106 1693 1141 811 1850 3306 849 1005 1471 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 9.03582409933412e-11 1.32145792283299e-09 1695 1553.54545454545 1693 8.21438554518658e-12 249 2.64845155791023 2.53868550659309 1 6.78956312582787 1693 2064 257 2513 407 552 1984 3654 2257 249 1459 1472 M15902 KEGG_GLYCEROLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROLIPID_METABOLISM.html Glycerolipid metabolism 53/70 KEGG 6.73623975648355e-08 3.14536172538656e-07 1720 1594.45454545455 1694 6.12385451158392e-09 383 1.98418446436382 -1.86144302252581 -1 3.72472347036035 1719 383 1774 3265 662 1694 1703 1264 2093 1305 1677 1473 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 1.6712429852202e-08 1.7148406283129e-07 830 1612.36363636364 1694 1.51931181628718e-09 372 2.7538305088975 3.13516609603214 1 5.37933691674853 830 1467 372 960 2373 1846 2365 2736 1694 622 2471 1474 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 2.13626457855244e-07 4.90234925824382e-07 930 1598.18181818182 1697 1.94205889635457e-08 221 2.16382180073645 2.30673471623102 1 3.94159116448609 927 2983 1697 901 1866 221 729 1899 2595 3258 504 1475 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 2.20964239073058e-06 2.96040649567084e-06 1700 1857.27272727273 1697 2.00876782732795e-07 235 1.37960456986015 -1.59285932695902 -1 2.20164445317542 1697 1807 3110 2425 3451 1204 1289 1343 1597 2272 235 1476 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 5.15336548004162e-06 6.37251377149501e-06 1680 1974.81818181818 1698 4.68488868320431e-07 726 2.06067778904407 2.42792298217776 1 3.09083405275764 1677 2713 1961 1495 3762 1564 726 775 3191 2161 1698 1477 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 1.12089765964474e-07 3.56647562954991e-07 870 1968 1700 1.01899792432215e-08 243 2.6303127262117 -2.4023097418914 -1 4.89647286116853 870 3721 1700 4126 1228 612 767 1710 3884 2787 243 1478 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 1.81574632162191e-07 4.49649666214869e-07 4225 2431.36363636364 1701 1.65067861043872e-08 531 3.26232465111441 -2.98315113673991 -1 5.97840254495588 4225 1620 587 716 1701 4690 4154 4051 531 924 3546 1479 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 3.41612121133077e-07 6.50806317028999e-07 2120 1754.18181818182 1701 3.10556521980015e-08 158 2.74236530996721 4.00365487949879 1 4.89824822844723 2119 158 463 786 2310 3013 3638 1701 1628 1150 2330 1480 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 7.16935339371359e-08 3.18038985134663e-07 3575 2420.72727272727 1701 6.51759420668023e-09 739 2.09725990157368 -1.65171378664722 -1 3.93412561554656 3574 1154 1448 1250 739 3130 3976 4620 1508 1701 3528 1481 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 2.76905154054798e-06 3.61147368648424e-06 1705 1815 1701 2.51732275077087e-07 573 3.17420112043739 3.59368571620004 1 4.98754245954305 1701 2219 573 842 3547 1727 1632 3017 1390 1122 2195 1482 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 2.40944497875517e-08 2.30582176584791e-07 2095 1534.63636363636 1701 2.19040455013042e-09 14 2.42449873915404 2.48432077598565 1 4.64588136199482 2093 2249 1588 1872 14 1701 1643 426 773 2075 2447 1483 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 5.56639584466788e-06 6.8384665244228e-06 375 1645.18181818182 1703 5.06037266245528e-07 374 2.35186579528486 2.35186579528486 1 3.50689788218859 374 1895 1703 2391 3790 676 581 1080 1923 2438 1246 1484 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 4.81733764448572e-08 3.02364809600699e-07 1055 1741.09090909091 1703 4.379397954519e-09 321 1.88535757705309 -1.71381080563938 -1 3.54849319304954 1054 2026 2348 3743 321 364 983 2657 3085 1703 868 1485 M7761 KEGG_MELANOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOGENESIS.html Melanogenesis 86/110 KEGG 4.4779028620112e-07 7.92787003326814e-07 1760 1767 1704 4.07082161222587e-08 623 2.12228356863475 2.31370642788379 1 3.73797742832042 1757 1518 1704 623 2515 1202 1515 3156 1843 2303 1301 1486 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 5.06984882694762e-06 6.27581601447489e-06 85 1935.45454545455 1704 4.60896410030364e-07 27 1.34139308382106 1.34139308382106 1 2.01424229981228 85 2725 2993 2420 4357 336 27 1151 3806 1704 1686 1487 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 5.77528188047083e-08 3.09765119043436e-07 3085 1944.18181818182 1709 5.25025639279946e-09 495 2.18015903973745 2.41531411350171 1 4.09687225874102 3082 1377 815 600 495 2512 3339 4018 2618 821 1709 1488 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 3.29680656023287e-08 2.74345541741202e-07 2620 1771.09090909091 1709 2.99709691785192e-09 86 2.11638377499561 2.35618690816495 1 4.00923101748849 2616 1135 710 1316 86 1883 2782 4268 1709 475 2502 1489 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 1.40227497913318e-05 1.62542679310133e-05 220 1739.45454545455 1709 1.27480356116514e-06 201 1.96877068581681 2.11723220467441 1 2.72175451777322 220 2625 1709 2838 4031 374 201 554 3284 1907 1391 1490 M144 PID_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CERAMIDE_PATHWAY.html Ceramide signaling pathway 18832364 64/69 Pathway Interaction Database 1.83071347848852e-07 4.51437058787818e-07 940 1770.54545454545 1710 1.66428511893635e-08 405 1.64191706583102 -1.58818932165369 -1 3.00766525773746 940 2190 3324 2447 1710 405 866 1846 1129 3730 889 1491 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 7.99146575632388e-07 1.2498249956875e-06 1115 1967.27272727273 1710 7.2649715083753e-08 214 1.64110353761266 -1.5789341166494 -1 2.79659490339545 1113 214 2279 1512 2892 1659 1710 2963 3927 894 2477 1492 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 3.92431172619777e-07 7.18771880002076e-07 745 1662.63636363636 1711 3.56755675109824e-08 594 1.75068604621608 -1.40433273125583 -1 3.10485035426621 741 594 1711 1068 2417 892 2007 2190 3598 1732 1339 1493 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 1.40036700620803e-05 1.62361392024119e-05 1715 2007.09090909091 1712 1.27306901822725e-06 18 2.68366221496359 3.20636143093504 1 3.7107546281316 1712 4038 1920 3719 4460 1235 204 883 342 3547 18 1494 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 3.03791873678994e-08 2.68216360173252e-07 1540 2070 1714 2.76174434430883e-09 50 1.3844308511839 -1.25166738045042 -1 2.62626039931789 1538 1714 3328 3424 50 994 1391 2270 3678 3527 856 1495 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 6.3692158922479e-08 3.14536172538656e-07 2765 1870.90909090909 1714 5.79019643331178e-09 596 2.16735103674445 2.46053586537434 1 4.06864441580694 2763 1348 919 1385 596 2618 3034 2573 2882 748 1714 1496 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 1.97102626272097e-06 2.67642231301582e-06 1715 2043.27272727273 1715 1.79184366237006e-07 842 2.40360004871816 2.40759705059614 1 3.86682694797714 1715 2454 1626 3600 3396 1030 842 1715 2697 1642 1759 1497 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 1.38205788407596e-07 3.92497786572715e-07 3340 2307.27272727273 1716 1.25641633717997e-08 768 2.62836127311239 -3.18348572432203 -1 4.86126760422257 3339 768 1342 2350 1425 3498 4301 4180 1400 1061 1716 1498 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 5.95711198646632e-07 9.92851997744386e-07 3080 1887.90909090909 1717 5.4155578177461e-08 580 3.67875652002705 3.7788385163732 1 6.37620867161235 3076 1918 1477 1608 2695 2515 1717 1452 1111 2618 580 1499 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 1.61205939780433e-07 4.22248632499246e-07 1900 1728.18181818182 1717 1.46550865084425e-08 1045 1.86058623543885 -1.80304654819065 -1 3.42393477369527 1152 1448 1875 1717 1585 1207 1899 1900 3459 1045 1723 1500 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 2.4618147699153e-07 5.31315294702385e-07 1240 1862.27272727273 1718 2.46181504263928e-08 18 5.7890701004329 5.7890701004329 1 10.4883200423589 1239 2930 4268 3306 2095 1038 18 1718 390 2652 831 1501 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 8.43837785155943e-07 1.30673042845671e-06 1720 1608 1718 7.67125553473416e-08 423 3.02468315113595 -3.28766194486134 -1 5.13818180998786 1718 703 654 957 2930 1931 1942 3958 423 618 1854 1502 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 2.01843684999481e-05 2.29843713678541e-05 270 1559.45454545455 1719 1.83495942619218e-06 266 1.68870208060159 1.68832856247374 1 2.26107485921233 266 1812 1719 1890 4109 545 376 1308 2176 1073 1880 1503 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 2.1366430400832e-07 4.90234925824382e-07 4145 1894.90909090909 1719 1.94240295235844e-08 62 2.48800355176423 -1.73961703088627 -1 4.53224569559204 4141 727 1613 363 1868 2776 1881 1465 62 1719 4229 1504 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 2.65040727072107e-08 2.47231666359752e-07 2000 1620.81818181818 1723 2.40946118422848e-09 23 2.51145818052878 2.34094118167551 1 4.79058752251085 1999 334 642 3025 23 1723 1991 1027 2547 724 3794 1505 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 1.87096139168852e-07 4.5777497636445e-07 1480 1520 1723 1.70087413709274e-08 114 2.03803954854321 2.64398516566015 1 3.7299272489969 1478 1743 1883 2822 1723 752 816 1142 2191 2056 114 1506 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 7.53033452859485e-07 1.18997057044491e-06 1820 1740.27272727273 1725 7.53033708036328e-08 142 3.64896035693823 -3.00029860685936 -1 6.24168299877822 1816 917 4445 1350 2914 1725 690 2132 142 2172 840 1507 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 1.87459544911124e-07 4.5777497636445e-07 2635 1856.18181818182 1725 1.70417782622131e-08 221 2.04940587118335 -2.78423464917442 -1 3.75073417919356 2635 860 1962 2150 1725 3494 4209 221 1373 1417 372 1508 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 5.38443146788464e-08 3.06874196014832e-07 2395 1586.72727272727 1726 4.89493781787903e-09 419 2.9239931169243 3.34604150608962 1 5.49838923207488 2391 720 795 1770 419 2613 2072 1726 1008 865 3075 1509 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 1.45045965390285e-06 2.03452290235407e-06 1260 1758.72727272727 1726 1.3186005547196e-07 852 2.64175333950583 2.32179547441168 1 4.34089355719682 1257 2386 1485 1896 3275 1782 852 971 1248 1726 2468 1510 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 3.03309131322851e-07 6.04058691917239e-07 2825 1842.54545454545 1728 2.75735611944925e-08 335 3.80361770275801 3.34745788831129 1 6.82968327176577 2822 853 861 961 2201 2421 1728 4283 335 1419 2384 1511 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 1.22306165710738e-07 3.70192774369017e-07 2790 1911.54545454545 1728 1.1118742955472e-08 53 2.32060183131717 2.91982170714563 1 4.30897931027676 2789 798 1728 2062 1313 3232 3683 1549 53 2204 1616 1512 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 3.94194188547107e-08 2.9351990282604e-07 2465 1635.09090909091 1729 3.58358359645678e-09 171 2.09822540182786 2.51539632171344 1 3.95704813063813 2465 552 1729 1277 171 2568 2530 2121 1267 1385 1921 1513 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 4.44537574226354e-08 2.98029714805608e-07 2320 1854.81818181818 1729 4.04125075644358e-09 262 2.29369454209686 2.60570220349685 1 4.32137807021196 2319 1563 1280 3035 262 2856 3167 1096 1917 1179 1729 1514 M12836 BIOCARTA_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPO_PATHWAY.html EPO Signaling Pathway 31/36 BioCarta 1.63588944010607e-07 4.24953118178353e-07 1730 2079.18181818182 1730 1.48717232886232e-08 227 1.1173413492113 -1.17366655146263 -1 2.05494328496687 1730 2743 3727 227 1604 1079 936 2252 3783 4129 661 1515 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 1.06873481289896e-07 3.48612876080379e-07 1735 1861.18181818182 1731 9.71577149833523e-09 1023 2.07475547231804 2.46714551344625 1 3.86801907817478 1731 2089 1466 2589 1180 1429 2104 2070 3169 1623 1023 1516 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 1.89497323375808e-07 4.60823355474758e-07 1665 1837 1732 1.72270308816537e-08 489 1.81964890602645 1.81022053606287 1 3.32863176175033 1662 2188 2420 1481 1732 1820 1697 1540 489 3045 2133 1517 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 8.1460985579428e-08 3.27411388472988e-07 2725 1544.45454545455 1733 7.4055444177948e-09 99 3.17640250386441 3.29841736422662 1 5.94729906334726 2721 1766 1128 1606 866 2295 2563 153 99 1733 2059 1518 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 4.07280089998939e-07 7.35410108949883e-07 540 1580.09090909091 1734 3.70254695816026e-08 407 1.94239816194836 1.94080860147597 1 3.43937259350195 536 1557 2271 2546 2457 570 407 2224 580 2499 1734 1519 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 6.10870789811819e-07 1.01062394949589e-06 1105 1653.45454545455 1735 5.55337235846804e-08 91 2.24788629374874 2.1425904458018 1 3.89081487265105 1101 2418 1735 3301 2715 551 91 2665 1287 1780 544 1520 M523 KEGG_THYROID_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_THYROID_CANCER.html Thyroid cancer 36/43 KEGG 6.26108837134441e-06 7.62640957748274e-06 1205 1798.09090909091 1737 5.69191471832293e-07 171 2.99686669761647 3.82552475624137 1 4.42791740482921 1201 3373 2012 898 3942 1737 1747 171 383 3852 463 1521 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 3.47228221932576e-07 6.57407624356902e-07 1225 1861.63636363636 1737 3.15662069759972e-08 263 1.95339544117898 -1.67971406152768 -1 3.48631751966352 1221 263 2540 1737 2328 1279 1647 3404 353 3358 2348 1522 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 1.48475487353136e-10 2.11723353567009e-09 4720 2201.45454545455 1737 1.34977715784688e-11 210 2.23873545734513 -1.78030049896807 -1 5.60674108728353 4720 1093 265 559 486 4020 4698 1737 2419 210 4009 1523 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 4.3347869044684e-08 2.97164560412799e-07 2170 1771.72727272727 1738 4.3347869890251e-09 311 1.90426775567966 -1.9161603227238 -1 3.58823625439693 2169 1022 4511 926 311 1738 3115 1990 1302 610 1795 1524 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 1.90063091239374e-07 4.61470056918643e-07 3040 2103.09090909091 1738 1.72784643326696e-08 586 2.72164705473136 3.55461959778137 1 4.97857950832645 3038 869 1543 3820 1738 3147 2982 791 586 1646 2974 1525 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 5.67959217087939e-08 3.09084324765911e-07 1740 2085.36363636364 1738 5.16326574318693e-09 370 2.78296398950576 3.05298363828663 1 5.23064651731983 1738 4305 2163 3896 478 1375 370 1110 4415 2696 393 1526 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 3.05479442141395e-07 6.05570334694407e-07 1005 1811.63636363636 1740 2.77708622325941e-08 436 1.87701834583815 2.21599797901648 1 3.36930379895541 1004 2442 2255 3045 2212 1605 1740 1655 436 2323 1211 1527 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 2.18134543508665e-10 3.01051182854064e-09 2300 1655.72727272727 1740 1.98304130482085e-11 170 2.12766176989533 -2.17228723846099 -1 5.23459965452873 754 2023 632 2296 2298 1194 1985 1681 3440 170 1740 1528 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 1.40566471881501e-06 1.98644834515175e-06 570 1838.45454545455 1741 1.27787783359012e-07 177 1.56417734918638 1.73693618544654 1 2.57457466699546 567 2284 2781 3604 3251 497 177 1741 2415 1503 1403 1529 M6034 REACTOME_SEROTONIN_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEROTONIN_RECEPTORS.html Genes involved in Serotonin receptors 3/12 Reactome 1.34159436140341e-07 3.85177943176647e-07 2860 2086.09090909091 1742 1.34159444239781e-08 6 5.12752597890555 4.33509176396581 1 9.49650503839708 2856 942 4236 88 1485 2706 2598 4578 6 1742 1710 1530 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 3.94045944606363e-05 4.36493043544246e-05 1235 2364.27272727273 1746 3.94052932030034e-06 127 2.0329547557582 2.0329547557582 1 2.55866677606331 1235 3221 4525 4147 4358 1177 127 448 4350 1746 673 1531 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 2.37101146912407e-05 2.67539424677638e-05 2100 1943 1747 2.37103676713319e-06 339 3.94593484018008 4.33417879762339 1 5.20937859540331 2099 945 4666 1325 4296 2331 1896 339 1382 1747 347 1532 M17770 BIOCARTA_CELLCYCLE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELLCYCLE_PATHWAY.html Cyclins and Cell Cycle Regulation 26/30 BioCarta 2.35001035170258e-05 2.65296552500267e-05 430 1847.90909090909 1748 2.1363958677926e-06 428 1.96552617514089 1.99656507834831 1 2.59650831685094 428 2758 2297 1521 4147 797 468 1232 2519 2412 1748 1533 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 2.13933107293557e-07 4.90414893844385e-07 1395 1838 1748 1.94484661906283e-08 787 2.07111363773535 2.71764570944572 1 3.77258287953932 1393 2180 2170 1748 1870 1261 1541 2124 1450 3694 787 1534 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 1.71526949043876e-06 2.3624371155153e-06 1065 1990.63636363636 1748 1.71527081440743e-07 30 2.49608344153501 -2.49608344153501 -1 4.05470632011413 1061 2482 4689 3827 3377 1065 30 577 2859 1748 182 1535 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 4.01040719843663e-08 2.9351990282604e-07 4625 2496.45454545455 1749 3.64582479231168e-09 185 2.12344617809905 -2.13645765743196 -1 4.0046224040093 4622 1105 740 548 185 4622 4703 4041 1749 1659 3487 1536 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 1.73697035086663e-07 4.38438423227236e-07 2930 2008.72727272727 1749 1.73697048663461e-08 7 4.92697687527457 4.85647797037032 1 9.04501677620043 2929 943 4696 131 1745 2735 2518 1396 7 1749 3247 1537 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 1.05863100807165e-06 1.56982040782224e-06 1750 2186.54545454545 1750 9.62392288619009e-08 438 1.71389685188206 -1.43542665703815 -1 2.87168308607482 1750 438 1745 1497 3072 1523 2001 4499 3853 1105 2569 1538 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 3.85822573006765e-07 7.0969701659857e-07 1965 1677.54545454545 1750 3.50747855154537e-08 364 2.35324155643096 2.39731553259823 1 4.17753170687264 1961 364 1291 863 2406 2304 3026 1639 503 1750 2346 1539 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 2.08787144908298e-08 2.06598500387844e-07 1105 2069.90909090909 1750 1.89806497172505e-09 4 2.44438274992404 -2.11331397744909 -1 4.7176586871854 3639 341 955 2267 4 3577 3997 4034 1102 1103 1750 1540 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 5.03251066984978e-08 3.0357704374324e-07 2305 1803.36363636364 1750 4.57500980451702e-09 364 2.34581871276673 2.5757772624307 1 4.41417543984543 2303 1156 534 1610 364 2915 3183 1937 1750 525 3560 1541 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 3.46374017684686e-05 3.84769443038766e-05 200 2029 1751 3.14890428374701e-06 199 1.47913681995065 1.44134941901689 1 1.88479597347665 199 2594 3048 1733 4216 899 570 1607 3544 1751 2158 1542 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 1.9260434967761e-07 4.64778897147911e-07 1665 1936.54545454545 1751 1.7509487867239e-08 1272 2.39772378057879 2.25451120216927 1 4.38379119826348 1320 1662 1272 2105 1751 1665 1577 3532 2013 2194 2211 1543 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 7.34884353034081e-07 1.16907790573672e-06 2020 1634 1752 6.68076907739769e-08 607 2.98906172785014 3.77362191843308 1 5.11938586733116 2020 1882 1416 1845 2834 1669 1071 1962 607 1752 916 1544 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 4.06692573447113e-08 2.9351990282604e-07 980 1831.18181818182 1752 3.6972052815022e-09 195 2.57986391306397 2.95237382840174 1 4.86556902441448 2671 642 980 2260 195 3133 2966 1752 1139 979 3426 1545 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 1.92774205327471e-07 4.64778897147911e-07 3460 2097.63636363636 1752 1.75249292926585e-08 206 2.82079730751627 2.55933857977071 1 5.15745429577269 3460 715 1106 578 1752 2900 2523 3891 206 1676 4267 1546 M19 PID_P73PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P73PATHWAY.html p73 transcription factor network 18832364 102/123 Pathway Interaction Database 1.45455311542838e-06 2.03844735891388e-06 900 1790 1754 1.32232188829304e-07 705 1.7845805432038 1.93803510659874 1 2.9316879890258 896 2128 2736 1537 3277 911 775 705 1833 3138 1754 1547 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 8.79795118508742e-07 1.34913351506214e-06 1180 1772.54545454545 1754 7.99814063950048e-08 273 1.78664344313855 -1.79043441905765 -1 3.02755353080607 1179 832 2429 3315 2962 857 273 1754 2824 2001 1072 1548 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 1.32017574970774e-07 3.82284020774267e-07 1755 2175.36363636364 1754 1.20015984448077e-08 739 2.01337551577427 2.5987095896696 1 3.73028091841116 1754 3896 2868 3471 1387 1108 1123 752 3025 3806 739 1549 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 5.12881678681513e-08 3.0357704374324e-07 1865 1512.63636363636 1756 4.66256082398384e-09 370 2.41102522732025 2.65680815056062 1 4.53689982491372 1864 1266 454 370 381 1756 2382 2864 1766 619 2917 1550 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 1.08675697619309e-07 3.51706922314159e-07 1360 2290.09090909091 1757 9.87960936251605e-09 1195 1.67216208247429 1.87551164030945 1 3.11543393502119 1360 3840 3779 2243 1195 1718 1606 1409 1757 4276 2008 1551 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 4.52650267979883e-08 2.99073619127066e-07 2085 1697.27272727273 1757 4.52650277200035e-09 350 2.10456073959017 2.35614504890691 1 3.96405136794765 2083 992 4535 379 350 1493 2552 1757 2185 397 1947 1552 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 2.3564327067128e-07 5.20709849048895e-07 2055 2001.81818181818 1757 2.14221178101064e-08 1064 2.65885883951306 2.30710016270463 1 4.82343216262634 2053 1757 1064 2076 1956 1428 1651 3882 1503 1324 3326 1553 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 1.46772044911956e-07 4.04415675414145e-07 2875 1756.36363636364 1757 1.33429140639809e-08 211 2.40953380219781 2.77570878922359 1 4.44742623116507 2872 748 1628 1797 1481 2578 1739 2158 211 1757 2351 1554 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 3.82874318570473e-05 4.24516510136864e-05 1405 2190.18181818182 1757 3.48073620035785e-06 1288 3.21637672159138 -3.4985739022457 -1 4.05983933190051 1403 3118 1384 1901 4227 1757 2155 1676 3561 1622 1288 1555 M17294 BIOCARTA_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAS_PATHWAY.html Ras Signaling Pathway 42/44 BioCarta 1.76470060713526e-06 2.42274196209378e-06 1600 2269.90909090909 1758 1.60427456606169e-07 1086 1.28373139814244 -1.27174624644027 -1 2.08085213215621 1600 3357 3737 1307 3351 1326 1388 1758 1086 4248 1811 1556 M576 REACTOME_GLYCOSPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSPHINGOLIPID_METABOLISM.html Genes involved in Glycosphingolipid metabolism 32/36 Reactome 2.43639869810782e-08 2.3138434316034e-07 1775 2023.72727272727 1759 2.21490793189983e-09 17 1.58837513961411 -1.19440639962855 -1 3.04269288946341 1773 1759 3227 3882 17 1293 2549 1570 1154 3352 1685 1557 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 5.51744667185663e-07 9.34087097961381e-07 1480 1933.27272727273 1759 5.01586186872207e-08 1023 2.08495223305795 2.39989038239825 1 3.62932538265394 1479 2962 1786 1525 2646 1289 1759 1023 2252 3046 1499 1558 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 4.89517450534438e-08 3.0357704374324e-07 2550 1828.18181818182 1760 4.45015874024173e-09 303 2.25487956834244 2.31787341101419 1 4.24301998621439 2550 1229 495 1760 334 1531 2437 4060 2902 303 2509 1559 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 5.48071420817917e-08 3.07843567066819e-07 2055 1516 1761 4.98246758610597e-09 442 2.4468192226274 -2.25285127515702 -1 4.59998473342683 2052 1394 567 1323 442 2078 2603 2047 1871 538 1761 1560 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 1.10134709907205e-07 3.53626743374685e-07 1890 2125.72727272727 1763 1.00122468564258e-08 547 1.70188769105811 -1.73619425487067 -1 3.1696696736637 1890 4403 3475 1116 1208 1017 1763 1445 2213 4306 547 1561 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 2.56492191665644e-08 2.40893977213289e-07 1765 1952.54545454545 1764 2.33174722414562e-09 21 1.44307778029379 -1.34893750107787 -1 2.75699327551798 1764 76 3241 2804 21 819 1336 4611 2221 2840 1745 1562 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 6.54403885749308e-08 3.14536172538656e-07 3655 2469 1765 5.94912641104515e-09 340 2.09073732007593 2.04823566552982 1 3.92479141070697 3654 1140 721 1765 635 3900 4569 4271 1492 340 4672 1563 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 3.51311683491463e-06 4.46710976853369e-06 935 1996.09090909091 1767 3.19374767720234e-07 118 1.97599710987943 1.97705218726107 1 3.05181927503862 931 3413 2416 3385 3723 1087 433 118 3880 1767 804 1564 M11520 BIOCARTA_TPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TPO_PATHWAY.html TPO Signaling Pathway 37/42 BioCarta 1.57989631981346e-07 4.1878955683592e-07 1870 2044.90909090909 1770 1.43626948479209e-08 226 1.35554236825966 -1.52539137371168 -1 2.49569480749182 1866 3079 3499 226 1563 1458 1615 1770 1952 4086 1380 1565 M6929 KEGG_O_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_O_GLYCAN_BIOSYNTHESIS.html O-Glycan biosynthesis 23/33 KEGG 5.05383177234942e-08 3.0357704374324e-07 2240 1795.63636363636 1771 4.59439262585985e-09 370 2.80059229055546 3.05912739368223 1 5.2700992392017 2240 634 689 1771 370 2979 2744 4501 839 674 2311 1566 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 1.95670830509718e-07 4.68156443420621e-07 1450 1957.72727272727 1771 1.7788258901176e-08 309 1.47671819140232 -1.19033845508175 -1 2.69823229482356 1448 309 3013 2851 1771 560 869 2935 3477 2668 1634 1567 M11355 KEGG_TIGHT_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TIGHT_JUNCTION.html Tight junction 114/153 KEGG 1.87571356840857e-07 4.5777497636445e-07 2845 1736.54545454545 1772 1.70519429848307e-08 68 2.73455484887676 -2.56884736375105 -1 5.00495222354458 2845 68 930 356 1726 2931 3906 2615 163 1790 1772 1568 M735 REACTOME_NEURONAL_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEURONAL_SYSTEM.html Genes involved in Neuronal System 192/338 Reactome 4.95013283467382e-08 3.0357704374324e-07 3160 1956.72727272727 1775 4.50012086004983e-09 402 2.45242719431294 2.64490824393157 1 4.61482196159878 3159 1288 402 524 881 2740 3744 4244 1775 592 2175 1569 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 3.20403941532087e-07 6.24404047907287e-07 1060 2120.63636363636 1775 2.91276352904669e-08 666 2.3214430488728 2.72339449036282 1 4.15834690457321 1060 3384 1775 3376 2255 1048 666 1572 3758 2734 1699 1570 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 2.47211015536455e-07 5.32558645975384e-07 2595 1786.09090909091 1776 2.24737312104751e-08 953 2.40383199658512 3.06022103706591 1 4.35392280417375 2593 2185 1133 1604 2011 2022 1776 953 1719 1589 2062 1571 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 5.42920891310656e-07 9.23454633148215e-07 2635 1691.90909090909 1777 4.93564568449024e-08 159 2.97735025783287 3.63076764770223 1 5.18738679733502 1777 159 620 853 2631 2662 2265 2347 1319 1344 2634 1572 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 5.22000027260886e-07 8.96593933286528e-07 2025 1673.27272727273 1778 4.7454559192482e-08 245 1.99313203464974 -2.01334393954215 -1 3.47969373052609 2021 1815 2507 448 2602 1778 1607 844 245 3230 1309 1573 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 1.52478191431457e-07 4.1209216255052e-07 3745 2215.09090909091 1781 1.38616547272234e-08 110 2.82678998316395 -3.85254486758291 -1 5.21106502641541 3741 1848 1623 1642 1519 4100 3913 1781 110 2396 1693 1574 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 9.58810730933022e-14 2.18627374396322e-12 3185 1630.90909090909 1781 8.71646119030059e-15 47 3.19540334717187 3.59159787957743 1 10.7583064993189 3183 47 157 134 233 1781 3067 2925 1808 431 4174 1575 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 1.04410211248392e-07 3.47825432169194e-07 3340 2171.27272727273 1782 9.4918378366924e-09 387 1.94353594831862 2.13775683488575 1 3.62387989958679 3336 1062 1167 387 1146 3973 3978 3184 1782 782 3087 1576 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 4.28230094417118e-07 7.66785298045825e-07 1190 2438.18181818182 1784 3.89300161611043e-08 1188 1.53505528392638 1.87015093147045 1 2.70987385019155 1188 4581 3272 3731 2483 1637 1650 1784 1295 3887 1312 1577 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 3.545464780794e-42 7.27591033275986e-40 1790 1652.72727272727 1786 3.54546478079396e-43 12 2.55532282562257 2.61259712917204 1 28.8786003956224 1786 959 4718 658 287 1130 2277 2017 1928 12 2408 1578 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 3.55306125900026e-08 2.83284613893264e-07 4210 2429.63636363636 1787 3.23005574216653e-09 112 2.40205179319335 2.524401437175 1 4.54085170074913 4208 290 1233 1787 112 4660 4134 4109 459 1611 4123 1579 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 2.05378644057289e-07 4.8204236695694e-07 1260 1900 1787 1.86707875663814e-08 1089 2.22973024112696 2.10960605232421 1 4.06638788654831 1256 1604 1160 2518 1818 1787 1089 2549 2769 1571 2779 1580 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 6.37793823127341e-17 2.18143974287033e-15 3430 2196.54545454545 1789 5.79812566479398e-18 91 2.55007534806763 2.8256065631321 1 10.795257449477 3426 1251 98 1135 1030 3910 3849 3312 1789 91 4271 1581 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 8.84371288473441e-08 3.31003670356505e-07 2575 1802.90909090909 1790 8.03973930930923e-09 841 1.61805190017767 1.9289085123759 1 3.02690322421013 2573 841 2463 3057 965 2261 2379 1790 1002 1418 1083 1582 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 4.10354107372588e-07 7.39546157616882e-07 3075 1794.36363636364 1791 3.73049258103401e-08 16 2.09863329401668 1.03162516553668 1 3.71460880839222 3072 813 1791 382 2462 2244 1579 1295 16 2269 3815 1583 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 2.00696901714545e-07 4.75069897739545e-07 4575 2607.63636363636 1792 1.82451745475723e-08 829 2.37261837825678 -1.91947360037438 -1 4.33136530605512 4572 1475 829 1415 1792 4542 4697 2407 1672 919 4364 1584 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 7.00272356511634e-08 3.15651538021179e-07 4640 2441.90909090909 1792 6.36611253456089e-09 427 1.87004711694344 2.12293462819484 1 3.50958442964658 4636 1434 1792 427 713 3698 3767 3268 1343 1734 4049 1585 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 3.44374981308135e-06 4.39073449966072e-06 2935 2047.63636363636 1793 3.1306865488503e-07 51 2.04152140456502 2.63421465710204 1 3.15746168708925 2931 855 1793 1353 3638 2259 1790 1619 51 2619 3616 1586 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 8.78409274427871e-07 1.34744614081883e-06 1795 1754.54545454545 1794 7.98554204687851e-08 670 2.79551772806478 3.36019934917737 1 4.73806481092029 1794 870 2039 3149 2961 1090 877 670 2372 2799 679 1587 M17406 BIOCARTA_CYTOKINE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CYTOKINE_PATHWAY.html Cytokine Network 5/34 BioCarta 1.32834035766546e-05 1.54580041621819e-05 2620 2210 1795 1.32834829792874e-06 365 3.15541890756283 -3.9793462212642 -1 4.38264837315811 2620 932 4188 1795 4038 3383 4457 514 795 1223 365 1588 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 4.25025733492798e-08 2.95390421094817e-07 3685 2063.27272727273 1795 3.86387037912745e-09 226 2.0795030784188 -1.74792445162317 -1 3.92007531910748 3683 1115 545 532 226 2666 4446 4645 1795 495 2548 1589 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 2.2391820502623e-07 5.03558912349762e-07 1190 1936.09090909091 1795 2.03562025288048e-08 1186 2.59751583688819 2.77132458625003 1 4.72304017769068 2222 1603 1186 2312 1912 1664 1485 2661 1189 1795 3268 1590 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 1.16380279047156e-06 1.70013901919708e-06 1610 2109.72727272727 1795 1.05800309647742e-07 1184 2.55743357728634 3.05395873792716 1 4.25989947112172 1609 2859 1795 3590 3127 1610 1224 1966 1184 2698 1545 1591 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 1.83240001323359e-07 4.51437058787818e-07 1770 1740.72727272727 1796 1.83240016432964e-08 167 2.78658119562131 2.85572024733105 1 5.10506258277694 1766 896 4425 1820 1796 1970 804 1505 167 1861 2138 1592 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 7.15111092156041e-08 3.17725226229176e-07 1800 1642.63636363636 1797 6.50101014000694e-09 494 2.67280293643052 2.7288853945151 1 5.01431991662453 1797 2103 494 2108 737 1347 2008 1168 2973 594 2740 1593 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 7.44120590670282e-06 8.95296759613492e-06 1075 1748.54545454545 1798 6.76475552336932e-07 115 2.1224684804661 2.37914973228764 1 3.09304296511567 1071 2371 1798 1513 3873 873 115 906 2334 2251 2129 1594 M4217 REACTOME_MITOTIC_PROMETAPHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_PROMETAPHASE.html Genes involved in Mitotic Prometaphase 102/108 Reactome 1.22576120717632e-06 1.77635643164637e-06 95 1761.09090909091 1798 1.11432899102463e-07 93 1.56228131825865 1.6024341686039 1 2.59335396116515 93 3282 3265 2847 3158 189 93 1291 1798 2489 867 1595 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 5.38275088926828e-08 3.06874196014832e-07 2550 1884.90909090909 1799 5.3827510196513e-09 520 1.93176772407982 -1.92066192698489 -1 3.63227812123785 2548 1025 4601 557 520 2235 2990 1468 1986 1005 1799 1596 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 2.2030608586643e-07 4.9824855068977e-07 3125 1961.18181818182 1800 2.00278279934266e-08 511 2.6652464115458 2.97056445900929 1 4.84976009814257 3124 1902 1473 1639 1896 2450 887 4502 511 1800 1389 1597 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 4.74732709954418e-22 2.73260779388397e-20 3060 1657.45454545455 1800 4.31575190867653e-23 54 2.47787313244961 2.45123756844019 1 13.9971824113612 3059 1141 54 81 1057 2423 2700 2209 1800 97 3611 1598 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 5.99452230417363e-08 3.10910012492405e-07 2190 1939.54545454545 1801 5.44956587955578e-09 77 2.08677740758857 2.22158056386889 1 3.92039067949588 2187 77 1541 1957 537 1513 1801 3343 3171 1739 3469 1599 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 1.75107153777008e-08 1.78126242635233e-07 3875 1939.81818181818 1802 1.59188322882508e-09 17 2.72080046217121 2.61301132013751 1 5.30183883106768 3871 17 374 154 1802 2857 3381 3074 1474 667 3667 1600 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 2.03112854290429e-07 4.79586129190007e-07 3855 2175.09090909091 1803 1.84648066402388e-08 295 1.72941090731609 -2.05151077651438 -1 3.15486372566825 3852 654 1748 2258 1803 3538 2749 1663 295 1531 3835 1601 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 1.64588898131716e-07 4.26143499276852e-07 2415 1963.09090909091 1803 1.49626282222845e-08 326 2.26125471832069 1.85629829935008 1 4.15884469155773 2411 326 1427 2100 1609 1692 2113 4340 1803 1118 2655 1602 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 8.14184462342675e-08 3.27411388472988e-07 2510 1620 1803 7.40167720431207e-09 50 2.60339783323622 -2.41566733934446 -1 4.87428527509571 2509 50 491 1566 863 2099 2267 3261 2256 655 1803 1603 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 2.7922055205417e-06 3.63765113357903e-06 1740 2193.18181818182 1803 2.53837187670134e-07 693 3.34815098573085 3.688484006899 1 5.25788017452126 1739 2850 1060 3033 3552 1416 693 3062 3941 1803 976 1604 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 1.23693657321927e-07 3.71755418903835e-07 3910 2179.45454545455 1804 1.12448785705935e-08 141 3.06579955203757 3.23108171036633 1 5.69134706156613 3910 811 978 521 1324 4287 3583 2516 141 1804 4099 1605 M1840 KEGG_GLUTATHIONE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLUTATHIONE_METABOLISM.html Glutathione metabolism 43/58 KEGG 5.71569637881832e-08 3.09093308316432e-07 2005 1617.18181818182 1805 5.19608775210421e-09 446 1.73621083957299 -1.79198529004812 -1 3.2629189634025 2004 460 2172 1805 485 2098 1722 2547 446 1407 2643 1606 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 3.47165899964791e-07 6.57407624356902e-07 4220 2406.09090909091 1806 3.15605413407739e-08 274 2.2770386244532 2.82191868519536 1 4.06408156982334 4216 274 1806 1088 2327 4021 4033 1483 1473 1370 4376 1607 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 2.97354250608889e-08 2.65816678574613e-07 3495 2142.27272727273 1806 2.70322049661781e-09 43 2.05559242878864 2.50695347090468 1 3.90218585902334 3491 415 1349 1806 43 4644 4552 2633 1182 946 2504 1608 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 1.15041968619923e-07 3.59285478750119e-07 1810 1932.45454545455 1807 1.0458361330516e-08 731 1.35870170746415 1.53392435393235 1 2.52762643800926 1807 1932 2969 3842 1262 1607 731 897 2829 2616 765 1609 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 1.02312396219054e-09 1.29121526779127e-08 2190 1664.90909090909 1807 9.30112693333044e-11 299 3.12493220072141 3.00689536634112 1 7.11792684941299 2189 346 299 302 2035 1109 2130 3366 1807 522 4209 1610 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 2.71354245271665e-07 5.62856786404538e-07 2655 1977.81818181818 1807 2.46685707946613e-08 378 3.65276576731833 3.2015895558556 1 6.59114525245506 2655 1896 1109 1781 2097 1807 1310 2722 378 1600 4401 1611 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 8.01174575307948e-08 3.27123182997709e-07 4665 2708.45454545455 1809 7.28340549531224e-09 775 1.875025021262 2.14280728238009 1 3.51053476224853 3838 1128 1809 775 845 4661 4661 4559 1746 1536 4235 1612 M278 PID_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAC1_PATHWAY.html RAC1 signaling pathway 18832364 73/83 Pathway Interaction Database 4.58430828803252e-08 2.99073619127066e-07 1745 1919.36363636364 1810 4.16755307596296e-09 273 1.43282879607503 -1.20416641686479 -1 2.69853383812275 1743 273 3371 2648 283 1415 1442 2884 2005 3239 1810 1613 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 1.55505609419551e-07 4.16353338822743e-07 1945 1895.09090909091 1811 1.41368745828516e-08 886 2.31157480233135 2.60334219566066 1 4.25814895776173 1942 2623 1811 3954 1539 1528 976 902 1961 2724 886 1614 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 6.99637623242941e-07 1.12590848336402e-06 1785 1989.27272727273 1811 6.996378435148e-08 451 2.6697435120387 -2.91795454904957 -1 4.58499264252962 1785 894 4210 3032 2869 1561 451 1811 2276 2138 855 1615 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 2.23934355301303e-07 5.03558912349762e-07 1165 1612.54545454545 1811 2.03576707359285e-08 563 2.01586569008878 2.20373209516039 1 3.66523796413228 1165 569 1747 3078 1913 1953 2109 563 2225 1811 605 1616 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 3.04114059248853e-07 6.04363454990223e-07 1345 1827.27272727273 1811 2.76467364806965e-08 90 2.27721446754645 2.07232361761225 1 4.08842111414513 2197 90 777 3017 2205 1342 1811 1425 3187 1342 2707 1617 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 9.71245800002843e-08 3.39726302159777e-07 2495 1941.27272727273 1812 8.8295076625541e-09 422 2.51385970100471 2.88305122269203 1 4.69497505381965 2495 1279 422 949 1269 2441 3095 3146 1812 680 3766 1618 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 1.52526484740627e-07 4.1209216255052e-07 1785 2143 1812 1.38660450286657e-08 1159 2.55391258704905 -2.30327221043621 -1 4.70794420748075 1784 2717 1404 2533 1520 1706 2078 4429 1159 1812 2431 1619 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 6.09189853144829e-07 1.0089038971381e-06 2090 1705.36363636364 1813 5.5380911075663e-08 462 2.54219467847641 2.62789927241177 1 4.4008823550048 2088 1813 1638 2097 2712 1944 1335 1571 636 2463 462 1620 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 3.11721660782827e-06 4.0233148452145e-06 1120 2004.18181818182 1813 2.83383729515737e-07 520 1.70690966306229 2.02251205083543 1 2.65850957297414 1116 2642 2772 2649 3595 1708 1095 920 520 3216 1813 1621 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 1.27676509140234e-07 3.76711668300292e-07 3445 1870.90909090909 1813 1.1606956049992e-08 182 2.0477456555294 -1.62614719736736 -1 3.79774575241712 3445 592 2019 1638 1354 3348 3531 265 182 1813 2393 1622 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 2.53505330618264e-06 3.34043875074877e-06 1830 1791.27272727273 1814 2.30459657029234e-07 78 2.2202454909837 -1.40608869786766 -1 3.51007909774702 1828 769 1814 2078 3508 1161 826 3578 78 2761 1303 1623 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 2.53505330618264e-06 3.34043875074877e-06 1830 1792.27272727273 1815 2.30459657029234e-07 79 2.2202454909837 -1.40608869786766 -1 3.51007909774702 1829 770 1815 2079 3509 1162 827 3579 79 2762 1304 1624 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 2.53505330618264e-06 3.34043875074877e-06 1830 1797.45454545455 1816 2.30459657029234e-07 80 2.2202454909837 -1.40608869786766 -1 3.51007909774702 1830 771 1816 2080 3510 1163 828 3626 80 2763 1305 1625 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 6.65888767877541e-07 1.0811816251744e-06 2130 1735.63636363636 1816 6.0535360856968e-08 500 2.30219359757567 2.41196280264607 1 3.96535053629578 2127 500 1205 1816 2772 2038 2154 1463 935 1340 2742 1626 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 1.93861947933205e-07 4.66108261912869e-07 2575 1966.36363636364 1816 1.76238150014674e-08 685 2.58872035048957 2.83151567857974 1 4.73213421545656 2574 1468 685 1251 1760 2974 3436 1816 1972 1234 2460 1627 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 4.68990194026177e-08 2.99073619127066e-07 1190 1487.72727272727 1817 4.26354730930896e-09 303 1.81748276838185 -1.67682901487256 -1 3.42320734750469 1187 2084 2538 1817 303 357 906 2090 1927 2579 577 1628 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 1.92804466232121e-07 4.64778897147911e-07 4370 2529.27272727273 1818 1.75276802844724e-08 1309 2.61566459662636 2.66173540217822 1 4.78233366448111 4367 1803 1309 1818 1754 3953 3552 2997 1397 1510 3362 1629 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 4.71460371586263e-07 8.25405398326098e-07 910 2036.27272727273 1819 4.28600429654846e-08 799 2.9237474332007 2.42809611055222 1 5.13513687602845 2286 799 907 1605 2552 1819 1143 4040 3567 910 2771 1630 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 3.16593611118575e-07 6.19260590849501e-07 925 1600.18181818182 1819 2.87812415162148e-08 261 2.28457761153346 2.60416430853194 1 4.09466686075138 923 2311 1965 2595 2246 1004 525 1819 1271 2682 261 1631 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 2.10598954989342e-07 4.87029430450609e-07 950 1509.81818181818 1819 1.91453613772098e-08 344 1.70618202949409 1.69825997683062 1 3.1091817010683 950 1819 2581 2167 1854 973 537 344 2062 2274 1047 1632 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 2.05536343255138e-07 4.82172733680045e-07 3480 2181.18181818182 1820 1.86851238597726e-08 365 2.367560604075 -1.92796789777448 -1 4.31772385695664 3479 365 1276 592 1820 3649 4294 1195 1622 2353 3348 1633 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 9.87830658031119e-08 3.40830460958105e-07 2580 1746.36363636364 1821 8.98027911260083e-09 289 2.10081061420599 2.29494028374522 1 3.9225532634509 2578 289 2035 2765 1093 2685 2394 867 955 1821 1728 1634 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 8.40123597918884e-06 1.00338648334442e-05 825 1756.36363636364 1821 7.63751641956974e-07 614 3.25786057688379 4.15280963544931 1 4.70152591852074 614 2328 822 1269 3907 1938 1821 2456 822 1915 1428 1635 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 9.44181704778376e-08 3.3764305071295e-07 2595 1501.45454545455 1821 8.5834704118196e-09 301 1.97366373024455 1.9076581275995 1 3.68742295513332 2591 635 1821 1834 1035 1892 2627 301 672 1097 2011 1636 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 5.22149773202979e-06 6.44494489936732e-06 290 2106.45454545455 1822 4.74682738619616e-07 290 1.21342603033885 -1.21342603033885 -1 1.81795748520434 290 1822 2980 2442 3768 575 753 1617 4531 2891 1502 1637 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 8.42944329062487e-08 3.27455016694392e-07 3360 1845 1822 7.66313055782227e-09 173 2.25691204463529 -2.2789006476189 -1 4.22541510493567 3356 173 1456 191 916 3959 3963 1830 334 2295 1822 1638 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 2.46993506671683e-07 5.32333037210203e-07 1975 1601.54545454545 1823 2.24539576728721e-08 61 2.43320927353471 -2.48405607216038 -1 4.40727200134811 1973 2300 1823 1400 2010 885 688 806 2568 3103 61 1639 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 3.99970809493864e-07 7.2680200999597e-07 1050 2098.54545454545 1823 3.63609892918673e-08 1048 2.06903744470263 1.90098808801336 1 3.66672197019139 1048 2146 1661 3579 2435 1314 1823 1653 3456 1624 2345 1640 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 4.70153867356532e-08 2.99073619127066e-07 1825 1859.36363636364 1824 4.27412615821832e-09 306 2.15348474952368 2.00989026747019 1 4.05622234894371 1824 2801 1660 2735 306 1319 1113 2588 1268 2256 2583 1641 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 1.79141048763971e-07 4.45678935751464e-07 1995 1771.90909090909 1826 1.62855512137296e-08 1077 2.30459248094964 2.37336374562158 1 4.2256124877647 1993 2231 1261 2121 1689 1826 1766 1872 1832 1077 1823 1642 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 7.43434364972236e-10 9.66669477319271e-09 3415 1787 1826 6.7584942293042e-11 186 2.22578349336182 2.60888522720619 1 5.15041469013563 3413 1149 391 558 432 3044 3354 1826 1858 186 3446 1643 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 4.23525289804041e-08 2.95358312155018e-07 1830 1632 1827 3.8502299814308e-09 222 1.81329850570655 -1.69376977344157 -1 3.4181670175237 1726 1084 2563 1827 222 827 1827 1881 2002 2894 1099 1644 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 4.33446194077828e-07 7.73654416473282e-07 285 1476.09090909091 1827 3.94042072250776e-08 153 1.56814797653418 1.63961245669874 1 2.76655793099419 281 1827 2441 2166 2493 227 153 742 3113 1997 797 1645 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 8.04833692960523e-08 3.2731281190979e-07 1460 1775.81818181818 1834 7.31667020367308e-09 851 2.12199902027476 -2.38644016697881 -1 3.97289358820705 1459 2245 1592 2377 851 1834 2484 1927 2371 1269 1125 1646 M10320 REACTOME_BIOLOGICAL_OXIDATIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BIOLOGICAL_OXIDATIONS.html Genes involved in Biological oxidations 79/219 Reactome 8.53566205402886e-08 3.28305665915602e-07 4650 2435.45454545455 1836 7.75969307745406e-09 226 2.60969830639621 -2.66582147697043 -1 4.88519090168676 4648 226 619 1780 931 3484 3958 4525 1836 491 4292 1647 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 2.26977959273793e-07 5.07021281482396e-07 2405 1647.09090909091 1837 2.06343620628655e-08 385 3.42839538384512 -4.05603868453281 -1 6.23115052167988 2402 1837 918 938 1928 2897 2981 1049 385 2034 749 1648 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 1.44326750202921e-07 4.00954832818002e-07 1880 1962.90909090909 1837 1.44326759576516e-08 1033 1.97115544531982 2.21233967048114 1 3.64025191091329 1879 1033 4712 1837 1569 1813 1945 1328 1272 2230 1974 1649 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 1.89135861149077e-07 4.60770843938523e-07 3075 1962.72727272727 1838 1.89135877246647e-08 686 3.73265758720096 4.35046679949177 1 6.82900275347714 3074 887 4388 1150 1838 2339 2249 686 989 1185 2805 1650 M2909 REACTOME_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_METABOLISM.html Genes involved in Pyrimidine metabolism 22/29 Reactome 2.05644503741482e-07 4.82186814535418e-07 2045 2119.18181818182 1839 1.86949566330962e-08 496 2.2118931028775 2.33161533839003 1 4.03376806671233 2045 699 1564 3556 1821 3235 4199 1067 496 1839 2790 1651 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 3.29770628093847e-06 4.23163104572409e-06 1550 1979.36363636364 1839 2.99791929460916e-07 127 2.17225698730416 2.54958954796233 1 3.36977011196208 1549 3902 2261 2010 3616 1839 1556 127 563 3259 1091 1652 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 2.41402713023801e-07 5.27025877124579e-07 1615 1898.81818181818 1839 2.19457035920513e-08 259 1.66208470746149 -1.56205213124123 -1 3.01234958859312 1615 259 1839 2390 1982 1622 2257 1535 3736 2078 1574 1653 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 1.90456351331178e-07 4.61712366863461e-07 2220 1888.27272727273 1840 1.731421525629e-08 138 1.70061967587412 -1.58757169153761 -1 3.11042760444582 2220 138 2775 213 1741 1704 2736 1469 3631 2304 1840 1654 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 1.14248545560967e-07 3.59285478750119e-07 1680 2232.27272727273 1840 1.03862319540024e-08 160 2.0127476040543 2.41708734019316 1 3.74477883896354 1679 3674 2586 4356 1249 2357 1840 160 1599 3604 1451 1655 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 2.86152103620294e-06 3.71871676510955e-06 1135 2324.90909090909 1840 2.60138614378678e-07 713 2.17612249438357 2.25521666375522 1 3.41102982307875 1134 3141 1830 2556 3564 1662 1810 4140 3184 1840 713 1656 M16597 REACTOME_EGFR_DOWNREGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EGFR_DOWNREGULATION.html Genes involved in EGFR downregulation 32/36 Reactome 6.45739351748106e-08 3.14536172538656e-07 1845 2213.63636363636 1842 5.87035791547008e-09 621 1.69112193108886 -1.54709354478854 -1 3.17445743541242 1842 3381 3131 3445 621 1265 1295 2435 1575 3614 1746 1657 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 1.06250621013417e-07 3.48348225330125e-07 1425 2027.45454545455 1842 9.65914783135173e-09 677 1.80034010762738 1.98807030599411 1 3.35647711981364 677 3255 2971 3637 1170 1424 1421 1842 2275 2258 1372 1658 M14863 BIOCARTA_P53_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P53_PATHWAY.html p53 Signaling Pathway 21/22 BioCarta 2.32351638682422e-06 3.09277984935429e-06 1055 1814.90909090909 1843 2.11228985526845e-07 238 2.15336337964751 2.39653088029359 1 3.42511891310451 1055 2374 1843 1985 3475 860 238 1814 2688 2393 1239 1659 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 5.86952282287341e-08 3.10127287236487e-07 4190 2622.09090909091 1843 5.33592998133658e-09 507 2.36458123378996 2.40008493858235 1 4.44315781602592 4186 1424 1219 1191 507 4521 4062 4534 665 1843 4691 1660 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 5.45079660331939e-07 9.26125268814525e-07 1845 1966.45454545455 1845 4.95527086711655e-08 1168 2.21952058761746 2.44203963198121 1 3.8660099771058 1845 3263 1406 1938 2634 1374 1677 1233 1168 1962 3131 1661 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 2.3611293144357e-07 5.20853420399124e-07 620 1589.81818181818 1845 2.14648142531066e-08 328 2.13822791509792 1.99498558424592 1 3.87871373770175 619 2326 1845 3104 1959 356 328 618 2863 2285 1185 1662 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 9.74024874848787e-07 1.45995471873175e-06 780 1900.18181818182 1847 8.85477550988584e-08 604 1.33317860790287 -1.21342603033885 -1 2.24571823863987 776 604 2582 1960 3037 919 1230 1882 4300 1765 1847 1663 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 1.57889348038547e-07 4.1878955683592e-07 1505 2155.36363636364 1847 1.43535781245394e-08 1438 1.9909917955435 2.28241164314968 1 3.66602721552449 1504 2997 1847 3690 1562 1438 2118 1567 3006 2427 1553 1664 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 1.10544744503246e-06 1.62596196340082e-06 745 1906.45454545455 1848 1.00495272772162e-07 745 1.97387054467001 1.87927220655961 1 3.29870889896857 745 2779 1848 1496 3101 1517 1551 2131 1975 1789 2039 1665 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 2.48388152227549e-08 2.35420096087155e-07 3525 2141.09090909091 1849 2.25807413665403e-09 18 2.07421475372884 -1.63338831728858 -1 3.96913323793319 3521 282 1849 876 18 3585 4174 3973 535 1689 3050 1666 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 2.09168761618914e-07 4.84679970737421e-07 2665 2097.54545454545 1849 1.90153437732722e-08 75 2.10979840722032 2.15526903609131 1 3.84617651911742 2665 75 1226 1592 1849 2846 4028 2439 588 1145 4620 1667 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 5.02879648605559e-19 2.13837111839481e-17 1885 1625.72727272727 1850 4.57163316914144e-20 76 3.11236950048284 3.29762820692021 1 14.9810777634578 1882 1363 76 281 785 1864 2839 3585 1850 243 3115 1668 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 1.67044608328712e-07 4.29439298099957e-07 3270 2496.54545454545 1851 1.51858746374823e-08 1192 2.35695473468401 -1.3372665938659 -1 4.33261304202999 3266 1558 1192 1851 1623 4030 4268 2944 1350 1661 3719 1669 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 5.02643373235958e-06 6.22589460019267e-06 940 1913.54545454545 1851 4.56949565136692e-07 449 1.66001247759854 1.58547419266051 1 2.49454990574759 936 3114 2627 1933 3757 946 449 1104 1851 2850 1482 1670 M853 REACTOME_MYOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MYOGENESIS.html Genes involved in Myogenesis 29/38 Reactome 3.54560172352395e-07 6.68874505796685e-07 2630 1771.63636363636 1852 3.22327481358766e-08 169 2.27482206441365 2.5720814202267 1 4.0551914302775 2629 590 1738 1652 2339 2362 1852 1519 169 1868 2770 1671 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 1.55043629283796e-07 4.16035207629061e-07 1855 1939.90909090909 1852 1.40948763827637e-08 716 2.33906013598203 2.50495614157349 1 4.30901411935286 1852 2632 1091 3823 1534 1947 2616 716 3429 736 963 1672 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 5.84390824527108e-08 3.09924122670556e-07 3880 2266.54545454545 1853 5.31264400045828e-09 202 2.15549317482987 -1.38783630944922 -1 4.05037263569254 3879 522 1853 202 505 3981 4230 4658 829 1687 2586 1673 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 6.19259511343889e-06 7.55077471853049e-06 1250 2198 1853 5.62964776774831e-07 473 1.48044302521868 -1.48044302521868 -1 2.18879236298087 1247 3482 3167 3101 3816 1556 1853 473 585 4170 728 1674 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 1.36218914513014e-06 1.93718974540954e-06 1300 1857.27272727273 1853 1.23835453506082e-07 491 1.62080011558705 -1.57189187849357 -1 2.67290861456588 1297 2256 2951 1853 3227 1002 1383 2045 491 2871 1054 1675 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 9.47479448407844e-06 1.12223412709787e-05 805 2237.81818181818 1854 9.47483488159957e-07 84 2.48488332807731 2.48488332807731 1 3.55092898927921 803 3798 4203 3625 4050 513 84 225 4397 1854 1064 1676 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 1.19918617012816e-07 3.68260164151263e-07 1250 2017.63636363636 1854 1.09016930499451e-08 1021 1.84193035733081 1.8431634763929 1 3.4211958229567 1246 3244 3136 2008 1293 1488 1021 1423 1854 3409 2072 1677 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 3.00490557863545e-07 5.99964227206402e-07 1275 1982.09090909091 1855 2.7317327173322e-08 117 1.94926896501947 -1.87843822619379 -1 3.50130256694613 1272 1839 2025 3821 2194 1187 1969 1855 4257 1267 117 1678 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 3.28141314319351e-05 3.65548030112659e-05 4225 2309.54545454545 1856 3.2814615987255e-06 62 2.21909806127479 2.21909806127479 1 2.84238705965663 771 3507 4221 3621 4223 593 62 798 4467 1856 1286 1679 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 3.50688256303472e-08 2.81504858801426e-07 2735 2102.81818181818 1856 3.18807510812341e-09 108 1.72043320055218 1.84948747145593 1 3.25343159934542 2735 645 2307 4357 108 1827 1484 1856 3986 1352 2474 1680 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 3.11383575302173e-08 2.69553239732593e-07 2140 1706.54545454545 1856 2.83075981554031e-09 58 2.32136120580485 2.66862524000869 1 4.40274943084857 2137 1444 888 3020 58 1856 2124 1177 1716 2257 2095 1681 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 3.25860801151754e-08 2.73247281118852e-07 1880 1586.90909090909 1856 2.96237096343961e-09 79 1.91348364162358 2.22218457688139 1 3.62574144419335 1876 345 2327 875 79 1912 1856 1550 3252 1910 1474 1682 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 9.88740495999906e-08 3.40895189270968e-07 2285 1970.18181818182 1856 8.98855036760571e-09 366 3.96729998853066 4.2942256855453 1 7.40826163994346 2282 1856 648 959 1094 3466 3463 366 2233 1566 3739 1683 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 5.94841668243021e-08 3.10399797613433e-07 1010 1989.90909090909 1857 5.40765167569548e-09 528 2.2316622886442 2.65673986496166 1 4.19310272058803 1009 3614 1922 3695 528 1224 1365 2250 1849 2576 1857 1684 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 1.14741124797169e-07 3.59285478750119e-07 1840 2113.72727272727 1858 1.04310118892272e-08 727 2.08144473467464 2.31901185782717 1 3.87262136180351 1838 1858 2523 4353 1254 1627 727 2937 2443 2740 951 1685 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 4.18622645113622e-08 2.95100601223086e-07 3705 2288.72727272727 1858 3.8056604825391e-09 212 2.8168048350671 2.81497528355441 1 5.31061645076292 3705 2618 1135 1858 212 4041 4169 1612 313 1729 3784 1686 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 4.60925315672528e-08 2.99073619127066e-07 2245 1960.90909090909 1858 4.19023023026767e-09 290 2.06910391068615 1.77417839928482 1 3.89725204574298 2243 2644 1587 3847 290 1620 854 1858 2840 1395 2392 1687 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 7.96339594094902e-07 1.2458478237083e-06 1365 2109.45454545455 1860 7.96339879465582e-08 818 3.79227168059839 4.66384739439762 1 6.46503274322689 1362 1935 4383 2739 2956 1752 2619 1302 818 1860 1478 1688 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 2.33909419563384e-05 2.64127382856261e-05 120 1932.81818181818 1861 2.12647187802704e-06 28 1.45638659112479 1.49495344991063 1 1.92450601225241 116 2668 3106 1534 4347 395 28 1332 3504 2370 1861 1689 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 5.52600431178006e-09 6.25485380134338e-08 1530 1700.36363636364 1861 5.0236402960549e-10 334 3.31174206318693 3.8943606576927 1 6.8882080345299 1528 1635 334 751 2351 1861 2263 3560 1868 511 2042 1690 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 1.96523905293245e-05 2.24056239851236e-05 1865 2207.18181818182 1862 1.96525643288918e-06 312 4.91792966030624 5.41162933330593 1 6.6022004250072 1196 899 4580 3292 4435 1321 1025 312 3493 1862 1864 1691 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 1.22270532240319e-07 3.70192774369017e-07 2055 1999.90909090909 1862 1.11155035487102e-08 885 2.37653665329769 2.29987011254727 1 4.41286191753748 2051 1862 1678 3030 1312 1516 1785 3443 2368 2069 885 1692 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 1.00038535546358e-07 3.41896906035439e-07 1865 2115.54545454545 1864 9.09441273593784e-09 542 1.15198655000584 1.37981542813195 1 2.1501048982043 1861 1864 3388 3914 1105 2169 1263 542 1921 3948 1296 1693 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 1.70934306068203e-07 4.34469534002111e-07 3110 2197.72727272727 1864 1.55394835772144e-08 124 2.26313586450986 2.61035960300434 1 4.156813397896 3110 124 1116 588 1645 3527 4218 2585 1864 1329 4069 1694 M177 PID_EPHA_FWDPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHA_FWDPATHWAY.html EPHA forward signaling 18832364 37/45 Pathway Interaction Database 6.29076682734649e-08 3.14536172538656e-07 3005 1648.90909090909 1865 5.71887909747924e-09 302 2.56380447817204 2.65760376781078 1 4.81304139080729 3001 554 1457 428 584 2645 1865 2058 302 1967 3277 1695 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 8.97839461173507e-08 3.31497675696653e-07 1860 2108.63636363636 1866 8.16217725286481e-09 983 1.7494082174134 -1.47234019245631 -1 3.27237532407612 1860 1705 2536 3611 983 1349 2179 1866 3570 2169 1367 1696 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 1.20695147119127e-07 3.69299853003203e-07 3940 2454 1869 1.09722867036942e-08 734 2.29824036936689 -2.04890483791747 -1 4.26814545861033 3937 1349 734 1222 1299 4124 3569 3592 1869 1063 4236 1697 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 1.05731693357795e-07 3.48348225330125e-07 1875 1923.27272727273 1871 9.61197258538592e-09 376 1.690755598146 -1.35162748914041 -1 3.15212001807138 1871 2686 2792 2817 1160 847 1462 2490 963 3692 376 1698 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 6.26564456586472e-07 1.03152571855185e-06 1055 1777.36363636364 1873 5.69604213666698e-08 771 2.06511726339334 2.45317100822796 1 3.56909243958011 1051 2550 2009 2211 2730 1252 1535 771 1873 2447 1122 1699 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 2.21974823127887e-07 5.01301992901256e-07 1780 2040.36363636364 1874 2.01795314113298e-08 1176 1.68395482486739 -1.34871433289548 -1 3.06256593468277 1778 1495 2516 1874 1902 1176 1818 3625 1870 2296 2094 1700 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 6.89094453084157e-07 1.11260274499654e-06 2435 1732.72727272727 1876 6.26449699023355e-08 573 2.19905993913164 2.63613596606433 1 3.77977173778526 2434 573 1876 615 2791 1980 1745 3203 730 2505 608 1701 M13247 BIOCARTA_TCYTOTOXIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCYTOTOXIC_PATHWAY.html T Cytotoxic Cell Surface Molecules 7/15 BioCarta 4.90568896127945e-06 6.08537500584469e-06 1130 2475.81818181818 1879 4.90569979091599e-07 188 1.9025163210948 1.9025163210948 1 2.86454020941921 1128 911 4197 3849 3777 815 188 4327 4674 1879 1489 1702 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 8.20446775813203e-08 3.27411388472988e-07 4400 2477.27272727273 1879 7.45860733100141e-09 618 1.97361864792854 -1.91935044297606 -1 3.69495501126361 4400 1130 1199 618 877 3680 4222 4331 1879 1411 3503 1703 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 5.96579863194175e-07 9.93598078432077e-07 965 2209.09090909091 1879 5.42345477245808e-08 964 3.19278375389594 3.45337234982453 1 5.53348130146148 2683 1879 964 964 2697 1762 1955 4523 1583 1275 4015 1704 M6427 BIOCARTA_THELPER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_THELPER_PATHWAY.html T Helper Cell Surface Molecules 7/15 BioCarta 4.90568896127945e-06 6.08537500584469e-06 1130 2476.81818181818 1880 4.90569979091599e-07 189 1.9025163210948 1.9025163210948 1 2.86454020941921 1129 912 4198 3850 3778 816 189 4328 4675 1880 1490 1705 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 1.71978726202032e-07 4.35984396870383e-07 1365 2100.90909090909 1882 1.56344308769073e-08 1361 1.79348834782785 1.94391217544467 1 3.2932270095247 1361 3258 2576 2412 1651 1696 1377 1783 2983 2131 1882 1706 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 1.90538883154458e-08 1.91757681980606e-07 2125 1524.63636363636 1883 1.73217168004263e-09 377 2.5608607943352 2.81170752397971 1 4.96644273602606 2121 1340 377 549 431 1991 2180 2628 1883 460 2811 1707 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 3.94550459993483e-07 7.20069166225622e-07 495 1703.27272727273 1885 3.9455053004503e-08 2 2.31798039347924 2.31798039347924 1 4.11070459472937 494 2464 4303 3040 2496 236 37 372 3407 1885 2 1708 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 1.66460690662151e-06 2.29735222200396e-06 1780 2044 1885 1.51328015102744e-07 1368 1.87200752753318 2.24635220298568 1 3.04728350437271 1780 1857 2085 1682 3334 1885 1580 2022 2638 2253 1368 1709 M3412 BIOCARTA_CACAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CACAM_PATHWAY.html Ca++/ Calmodulin-dependent Protein Kinase Activation 15/15 BioCarta 8.62318719133794e-06 1.02807384549419e-05 440 1516.45454545455 1887 7.83929181021027e-07 85 2.06759020224993 2.12440699546091 1 2.97719038580987 438 2414 1972 2828 3912 223 85 544 1887 2197 181 1710 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 6.94759470885812e-07 1.11920297016417e-06 1535 2262.36363636364 1887 6.94759688096733e-08 489 2.26617564846037 2.46471774702161 1 3.8934763959007 1534 909 4475 3064 2864 1441 761 3520 3942 1887 489 1711 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 2.18729044144041e-07 4.96585420086519e-07 3085 2340.63636363636 1888 1.98844605355079e-08 609 2.75051713000924 -2.8716956103899 -1 5.0061020569038 3081 1817 813 3269 1888 2406 1440 4679 3971 609 1774 1712 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 2.06114176087179e-07 4.82568904331093e-07 1890 2006.09090909091 1889 1.873765412706e-08 385 1.55697708241506 1.99441864377146 1 2.83900620386195 1889 734 2814 3680 1825 2023 2748 385 611 3729 1629 1713 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 2.32373318062813e-07 5.15868718890617e-07 1585 2074.81818181818 1890 2.11248493279155e-08 1241 1.96684994043326 2.37848282981474 1 3.57013956722131 1582 3054 2352 2862 1944 1890 1512 1773 1600 3013 1241 1714 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 2.14281309146319e-06 2.87904292391297e-06 1585 2071.81818181818 1890 1.94801379870794e-07 545 3.31859523142441 4.0985728484484 1 5.30879518283125 1584 2861 1890 3708 3441 1287 618 545 2729 3564 563 1715 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 8.58943139955299e-08 3.28305665915602e-07 4410 2354.90909090909 1890 7.80857430446279e-09 936 1.82376969656717 1.53662016715819 1 3.41372263886323 4407 1546 2029 1870 936 3479 3665 1640 1053 1890 3389 1716 M6031 BIOCARTA_SKP2E2F_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SKP2E2F_PATHWAY.html E2F1 Destruction Pathway 13/15 BioCarta 5.89784169005103e-05 6.45439665593343e-05 835 2167.36363636364 1894 5.36181800683226e-06 832 1.7480755001474 1.77786127771104 1 2.11424698495787 832 2848 2693 1732 4286 1290 1894 1796 2339 2261 1870 1717 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 2.70521674801962e-06 3.53799474941884e-06 2115 1886.90909090909 1895 2.7052200412142e-07 118 1.65613029516399 1.87775902608608 1 2.60609328676703 2111 941 4559 2569 3573 1895 1028 636 118 3009 317 1718 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 6.01677223669981e-08 3.10925873699031e-07 865 1829.90909090909 1896 5.46979309204754e-09 543 1.97924854433349 2.2061788026452 1 3.71832111868998 863 2018 1988 2139 543 1896 1668 3265 1776 1686 2287 1719 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 1.23679765779535e-05 1.44568720772513e-05 425 1955.90909090909 1897 1.12436782808042e-06 425 1.55968287879187 1.64649351248568 1 2.1789476529341 425 2603 2975 2214 3993 766 958 884 3307 1493 1897 1720 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 1.34242736813487e-05 1.56103896959758e-05 1350 2477.36363636364 1897 1.22039596329052e-06 1261 1.94660837020798 2.42758725795208 1 2.70097332868296 1346 3966 1897 3404 4014 1609 1261 1848 4242 1505 2159 1721 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 1.16135533436574e-06 1.69761448690191e-06 1900 1942.45454545455 1898 1.05577813402968e-07 179 2.93123023678904 -3.16673200307319 -1 4.88320213741201 1898 2349 1368 3052 3125 1266 1235 3864 179 2720 311 1722 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 8.14245798032429e-07 1.2703836641158e-06 1980 1942.72727272727 1899 7.40223726722276e-08 939 3.09635429430635 2.93772737953137 1 5.27090751826554 1977 3431 1429 3023 2899 1377 939 2210 1027 1899 1159 1723 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 2.24792420467423e-05 2.5431932516928e-05 2180 1866.72727272727 1899 2.04358833993325e-06 189 2.55361683595296 2.8904543353605 1 3.38718104491193 2177 1899 1903 2362 4137 1580 1155 556 189 3297 1279 1724 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 1.0798901544198e-05 1.27109265058889e-05 1425 2244.27272727273 1899 9.81723141087252e-07 1253 1.82055979291565 -1.94892254143464 -1 2.57293441605124 1422 2309 2381 2368 3965 1899 1253 1289 4161 1809 1831 1725 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 6.53554329851352e-09 7.29261569006709e-08 2970 1647.63636363636 1899 5.94140301629877e-10 45 2.85359944389271 -2.85830019183033 -1 5.88024794954023 2969 45 340 144 1899 3259 3440 1462 2035 517 2014 1726 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 2.9396997374261e-07 5.90693178401499e-07 3210 1838.27272727273 1900 2.67245466385167e-08 175 3.14710713570623 -2.90367703637477 -1 5.65955093144786 3206 638 1021 175 2179 3090 3099 2592 705 1616 1900 1727 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 1.57368098547314e-06 2.1887247433757e-06 2230 2028.81818181818 1901 1.43062010103935e-07 202 2.19988875143615 -2.61426880493135 -1 3.59452799544299 2226 1840 1901 3073 3305 1479 986 4510 263 2532 202 1728 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 9.9099120886651e-06 1.17200664140565e-05 925 2276 1902 9.00905157109097e-07 925 2.38710382203814 2.43138262081144 1 3.39817581790631 925 3642 1050 2876 3939 1902 1297 1414 4230 1588 2173 1729 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 5.82286496751121e-08 3.09852566478612e-07 1615 1951 1902 5.2935137469348e-09 187 2.78987959377665 2.36372795354804 1 5.24277814893659 1613 3436 1319 2723 502 584 187 2705 1925 1902 4565 1730 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 1.5939380110738e-07 4.20318657884309e-07 1825 2021.81818181818 1903 1.44903466050671e-08 296 2.65982878423934 -2.73660805860708 -1 4.89663510896788 1822 1582 508 1625 2206 1971 1903 4571 3724 296 2032 1731 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 2.03132377612732e-06 2.74802184675293e-06 750 1853.27272727273 1904 1.84665968337262e-07 547 1.65788425597157 1.59457146128657 1 2.66138948149105 746 1556 2609 3591 3411 559 547 1942 1904 1486 2035 1732 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 6.80032018440444e-07 1.10036034523102e-06 1905 2144.36363636364 1904 6.18211116947407e-08 842 2.42895470750074 2.59100915922616 1 4.17837812894871 1904 2209 842 1341 2783 1466 1347 4017 2850 864 3965 1733 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 2.52708817437314e-06 3.33459775874789e-06 1905 2399.63636363636 1905 2.29735552471314e-07 766 2.70469338993162 2.10489692906029 1 4.27674463126241 1905 2387 832 1826 3505 1779 1834 4337 3989 766 3236 1734 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 9.17093271692491e-07 1.39409991703335e-06 1305 1965.54545454545 1905 8.3372150362977e-08 1301 1.90534851700223 1.81824242063557 1 3.22092800094941 1301 2201 2017 1438 2990 1700 2838 1905 2089 1656 1486 1735 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 1.12066353784226e-06 1.64526653145116e-06 3750 2419.36363636364 1905 1.0187855533639e-07 878 2.53399570944306 -2.60859337436704 -1 4.23127706009521 3749 1847 1412 2722 3108 4527 4095 1431 939 1905 878 1736 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 1.01194670169135e-06 1.50912746666136e-06 235 1592.27272727273 1905 9.19951970147838e-08 231 1.71650393014188 1.70399350344111 1 2.88454042092527 231 1984 2162 2186 3054 666 643 1259 3057 368 1905 1737 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 4.47369341792919e-07 7.92610251039008e-07 2060 1618 1906 4.06699484332152e-08 58 1.75164198703586 2.11603667211761 1 3.08506507631667 2058 807 2258 2095 2513 1653 1906 1400 58 2002 1048 1738 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 7.0358604619969e-08 3.15977748626312e-07 1910 1811.72727272727 1906 6.39623698819279e-09 220 3.42793630680324 -3.7966764653341 -1 6.43360439579399 1906 2343 694 2263 718 3143 3447 220 3469 1092 634 1739 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 3.10342275636209e-32 3.57272083171441e-30 4125 2140.36363636364 1906 3.10342275636207e-33 12 2.79211819892923 -2.66396741390573 -1 23.7411938582012 4121 1036 4612 12 582 3678 4461 1924 1187 25 1906 1740 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 1.9022758563719e-06 2.59426236407841e-06 2435 2011.63636363636 1907 1.72934318292397e-07 842 2.74134481004232 2.27910093637114 1 4.42101872040365 1907 2434 1630 2762 3383 2318 2433 943 842 1632 1844 1741 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 2.23555596336122e-07 5.03558912349762e-07 905 2060.63636363636 1908 2.03232380957264e-08 660 1.48237883879828 1.59131895371674 1 2.69502661749264 905 3039 3228 3193 1908 780 660 1228 3438 3119 1169 1742 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 1.07209577721276e-06 1.58779167506879e-06 2260 2203.63636363636 1908 9.74632999693478e-08 328 1.61205748383615 -1.5197127518158 -1 2.69869589379754 2260 328 3350 1298 3078 1815 1897 3775 1908 3210 1321 1743 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 2.2368666723796e-07 5.03558912349762e-07 1850 1881.54545454545 1909 2.03351536346795e-08 738 2.21129770711249 2.43366179091507 1 4.02065508445007 1849 2378 1870 2565 1909 2306 1789 738 927 2035 2331 1744 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 2.26634323527797e-07 5.06973463057442e-07 1045 2101.36363636364 1910 2.0603122443152e-08 727 1.17629119894117 1.22988658834897 1 2.13737174575702 1041 1910 3248 4181 1924 806 1341 727 3944 2693 1300 1745 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 8.36817519442722e-07 1.29779509491601e-06 1910 1952 1910 7.60743488858645e-08 430 2.62129973545741 -2.69727474857324 -1 4.45507476905099 1910 2412 1667 3318 2923 1823 1754 430 2572 2203 460 1746 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 3.58878952804661e-07 6.74595243822381e-07 1185 1871.54545454545 1912 3.26253646679499e-08 802 2.27274572044622 2.06688347821888 1 4.04906190119852 1182 2049 802 1912 2347 1426 1273 2276 3498 1026 2796 1747 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 8.49135728412135e-07 1.31235122400304e-06 890 2049.63636363636 1912 7.71941869230816e-08 479 1.43151310516623 1.2576634863525 1 2.43055927380977 886 1612 3263 2837 2937 912 479 2570 1912 3365 1773 1748 M3618 BIOCARTA_TNFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR1_PATHWAY.html TNFR1 Signaling Pathway 33/35 BioCarta 2.92669980843394e-07 5.88833039037007e-07 1495 2260.45454545455 1913 2.66063654343471e-08 1021 1.27948420715483 -1.1233754312016 -1 2.30093537539418 1494 1751 3483 3674 2175 1021 1585 1341 2728 3700 1913 1749 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 9.61812425354034e-08 3.39286984245748e-07 4335 2305.63636363636 1913 8.74374970366607e-09 384 2.99336377595599 -2.45045920372023 -1 5.59116420846476 4333 555 961 820 1054 3452 4117 4285 384 1913 3488 1750 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 7.67220956870682e-08 3.24764325922831e-07 2325 1772.36363636364 1913 6.97473621478638e-09 714 2.32074075985764 2.96756775869144 1 4.34734163267238 2321 1550 1087 2273 796 2579 3332 714 1913 1983 948 1751 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 1.28035407995098e-06 1.84133798213548e-06 1475 2146.72727272727 1915 1.16395893190085e-07 499 1.43899369045845 1.78178445679618 1 2.38214745431903 1474 1915 2804 4141 3185 1116 549 1795 3142 2994 499 1752 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 1.32634659574474e-07 3.83038247822062e-07 1205 1870.36363636364 1915 1.20576970518925e-08 808 1.9349255182433 2.13528661638135 1 3.58442086920651 1202 3560 2433 1915 1389 1077 2046 808 1973 3325 846 1753 M2668 KEGG_BETA_ALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BETA_ALANINE_METABOLISM.html beta-Alanine metabolism 24/30 KEGG 2.20587350090456e-06 2.95619617384143e-06 1975 2177.27272727273 1916 2.00534155697305e-07 1378 2.70504205194474 2.99820116177011 1 4.31815657564319 1975 1823 1544 3578 3450 2292 1916 1378 2818 1786 1390 1754 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 3.99437920238429e-08 2.9351990282604e-07 2355 1688 1917 3.63125388627938e-09 183 1.85415264251242 -1.51709840368893 -1 3.49665055804654 2352 2124 2455 1842 183 1091 1917 2749 458 2902 495 1755 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 8.68294260437544e-06 1.03467531160445e-05 100 1912.72727272727 1918 7.89361534030364e-07 89 1.366487739519 1.43861254949344 1 1.96626119723875 98 2602 3368 2646 4079 239 89 1060 3703 1918 1238 1756 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 1.40866560069327e-07 3.96712508071135e-07 2295 1798.36363636364 1919 1.28060517353681e-08 826 1.89805209481173 1.97279290813283 1 3.50774752331597 2293 1305 1974 826 1443 2149 2208 1521 1919 1392 2752 1757 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 6.93243435233625e-07 1.11752357045858e-06 1415 2044.54545454545 1919 6.30221503347376e-08 953 2.09582926003918 -1.91720233492123 -1 3.60113721557961 1415 2252 1530 2778 2795 1237 1919 2716 3033 953 1862 1758 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 0.000271924052100926 0.000287840665152808 775 2069.45454545455 1920 2.71957332043043e-05 150 1.72631568971453 1.72631568971453 1 1.76424521587256 773 2910 4380 1920 4486 788 150 1098 1956 3266 1037 1759 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 4.78404363114572e-11 7.34903219510079e-10 3090 1826 1920 4.34913057386341e-12 87 2.40515986469838 2.66087148954172 1 6.34276296179383 3086 1176 244 87 399 2548 3018 3163 1920 311 4134 1760 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 4.10283947368545e-08 2.9351990282604e-07 4610 2333.72727272727 1921 3.72985413654582e-09 175 2.52857113356309 -1.85558283566082 -1 4.76881479735566 4609 549 1683 869 203 4551 4658 1921 175 2298 4155 1761 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 3.11557740375407e-06 4.02229905517484e-06 2070 2049.90909090909 1921 2.83234710541353e-07 286 1.3730215051686 -1.51693135794667 -1 2.13835419836127 2066 1921 2671 2842 3594 1814 1693 555 3468 1639 286 1762 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 3.38874994135193e-07 6.48091560906852e-07 1925 2042.81818181818 1921 3.0806822393955e-08 1277 1.90680930552622 2.03148810479256 1 3.40656542816666 1921 1277 1486 1681 2300 2286 3173 1917 2481 1338 2611 1763 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 6.4131506179817e-08 3.14536172538656e-07 2190 1974.09090909091 1923 5.83013709539041e-09 606 2.21183286015638 -1.42786661963238 -1 4.15216528189175 2190 2248 1879 2877 606 1372 1345 3298 1261 2716 1923 1764 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 1.62360245291284e-06 2.24997169047228e-06 725 1989.36363636364 1924 1.62360363915227e-07 78 3.27547219674163 3.27547219674163 1 5.34107161483476 723 2901 4650 1924 3359 635 418 78 4117 2384 694 1765 M72 PID_NECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NECTIN_PATHWAY.html Nectin adhesion pathway 18832364 51/55 Pathway Interaction Database 1.92787023023149e-07 4.64778897147911e-07 3590 2394 1928 1.75260945379244e-08 701 2.18401454798507 -1.8282350707651 -1 3.99298691407295 3590 1634 1702 1259 1753 3782 3597 2020 701 1928 4368 1766 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 8.11576145890619e-08 3.27411388472988e-07 1930 1824.90909090909 1928 7.37796523481386e-09 835 2.25638575291472 1.99122838237734 1 4.22446727890624 1928 1790 2031 2146 859 835 873 3378 2092 2344 1798 1767 M17 PID_NOTCH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NOTCH_PATHWAY.html Notch signaling pathway 18832364 77/87 Pathway Interaction Database 1.81755777614759e-07 4.4986222881052e-07 3385 2205.72727272727 1929 1.65232538755222e-08 860 2.01016365576144 2.54287766002584 1 3.6832938472595 3384 1545 1929 1058 1702 3486 2964 1599 860 2403 3333 1768 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 2.28559182966085e-07 5.09634715320873e-07 1080 2240.63636363636 1929 2.07781097010204e-08 1077 1.99857825357787 2.29236689007615 1 3.63079259401839 1077 4369 2570 2242 1931 1652 1473 1712 1929 3871 1821 1769 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 6.20591801920666e-07 1.02240604016249e-06 1615 2160.18181818182 1930 5.64174524528843e-08 900 2.11247436282789 2.25754073580906 1 3.65331091230679 1614 4153 2114 900 2726 1880 1819 1238 2576 2812 1930 1770 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 6.36182913688932e-07 1.04335766247803e-06 3730 2234.54545454545 1931 5.78348270596906e-08 49 2.66847318317777 -3.7745457160226 -1 4.60829289924754 3728 1931 1608 1413 2741 4478 3090 49 662 1643 3237 1771 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 6.52568378715109e-06 7.92212640826984e-06 1865 2249.72727272727 1931 5.93245740349509e-07 1066 2.52185614860006 2.99782494484767 1 3.71391394714369 1863 3675 1931 3119 3830 1483 1066 1557 2114 2190 1919 1772 M5410 KEGG_ARACHIDONIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARACHIDONIC_ACID_METABOLISM.html Arachidonic acid metabolism 39/108 KEGG 3.02368018076936e-07 6.02693009004703e-07 2065 1907.45454545455 1932 2.74880054213097e-08 537 2.72364993672473 -2.80085722522139 -1 4.89104801707519 2064 537 915 2285 2199 1239 1446 3109 3625 1932 1631 1773 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 1.44713488068046e-06 2.03287995143207e-06 3080 2356.72727272727 1932 1.31557802962739e-07 1085 2.38972158498735 2.42089297372555 1 3.92691830464529 3079 1897 1818 1932 3271 3195 1716 3971 2182 1778 1085 1774 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 4.17129408302575e-07 7.4918219451604e-07 865 2120.90909090909 1932 3.79208624901922e-08 862 1.69108054251012 -1.81631197212562 -1 2.99032232136209 862 1626 2411 2606 2472 1505 1932 1225 3996 3214 1481 1775 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 1.74052354373126e-07 4.3884995333395e-07 660 2235.18181818182 1932 1.58229425584753e-08 658 1.94926192140573 2.13879488917433 1 3.57773386735852 658 3575 2620 3665 1660 1906 1505 936 2740 3390 1932 1776 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 3.04584680196743e-08 2.68216360173252e-07 2230 1992.27272727273 1933 3.04584684371476e-09 92 2.0418423672679 -2.12659711820619 -1 3.87377671527349 2229 885 4690 3287 92 1582 1105 2024 1933 2386 1702 1777 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 1.33579345942761e-06 1.90481725936505e-06 785 1812 1935 1.21435842772166e-07 445 2.16767106223307 2.70543819376578 1 3.57964121766489 785 2718 1935 2206 3215 914 892 445 3642 2225 955 1778 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 4.32748360528247e-08 2.97164560412799e-07 3060 1974.09090909091 1935 3.93407608218701e-09 243 3.02609233548303 -3.12528651352543 -1 5.70261217181774 3056 1574 590 2275 243 2636 4361 2449 1935 1494 1102 1779 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 1.93339788857705e-05 2.20692576398638e-05 1790 2197.54545454545 1936 1.9334147099063e-06 313 1.68701134207137 1.52199555406835 1 2.2674058859543 1788 1936 4390 2550 4121 1420 313 1746 969 2706 2234 1780 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 4.02678088788011e-07 7.30173099915256e-07 2005 1956.45454545455 1936 3.66071056811285e-08 985 2.14688523711513 -2.46264129757224 -1 3.80346934315612 2005 1887 1936 3628 2443 1869 1032 2420 985 1973 1343 1781 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 5.92249140627476e-08 3.10257041482984e-07 4705 2380.09090909091 1938 5.38408324155519e-09 483 2.25349233483603 2.09102233444433 1 4.23425794131627 4703 1201 647 570 522 4586 4431 3640 1938 483 3460 1782 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 2.82942733906816e-08 2.58315223218602e-07 2920 1935.36363636364 1938 2.57220670496138e-09 32 2.15103565730638 2.22593372654237 1 4.0911304545212 2919 1492 1290 1011 32 2784 2739 1938 3047 1716 2321 1783 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 2.67957113618539e-12 5.05903030511802e-11 2375 1819.81818181818 1939 2.4359737601715e-13 198 2.77384716722313 2.85007144337462 1 8.24605646941269 2374 1379 198 1318 834 2175 1939 2860 2660 342 3939 1784 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 2.31718915821906e-07 5.15280358069739e-07 4265 1982.27272727273 1939 2.10653582025561e-08 174 2.48628424882198 2.05258082409675 1 4.51357718565959 4265 174 566 403 1939 3160 3556 2589 1906 1025 2222 1785 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 8.59705823529249e-08 3.28305665915602e-07 2260 1834.63636363636 1939 7.81550779204034e-09 608 2.01790789464945 2.07651350411971 1 3.77720119595758 2257 608 1812 3272 938 2590 2239 821 2382 1323 1939 1786 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 1.78968916793993e-07 4.45534434212895e-07 2690 2053.18181818182 1940 1.62699028502753e-08 789 2.13732226128431 -1.78786088041568 -1 3.91893662461892 2690 789 1940 3276 1688 1798 898 3361 1123 2123 2899 1787 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 7.76279080986862e-07 1.21931356481131e-06 1485 1977 1941 7.05708504454797e-08 906 2.15213990887687 -2.25003446745022 -1 3.67438783742406 1484 1738 1555 1865 2876 1941 2106 2014 3314 906 1948 1788 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 3.40422523415443e-08 2.77395498531109e-07 2000 1841.27272727273 1941 3.4042252863038e-09 142 2.0236253182211 2.32114215880328 1 3.83066791913226 2000 1017 4717 1355 142 2109 2232 1511 1941 261 2969 1789 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 2.32259912260711e-07 5.15868718890617e-07 2805 2022.27272727273 1942 2.11145397073652e-08 1035 2.73657594993437 -2.49007555037021 -1 4.96764946847843 2804 1695 1035 1844 1942 2577 2802 1204 2350 2342 1650 1790 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 9.11543312530367e-06 1.08265838830985e-05 1640 2272.18181818182 1942 8.28679172201286e-07 574 2.45891635255465 2.45997461434121 1 3.52488393353893 1640 3161 1723 3841 3925 1297 928 2634 3329 1942 574 1791 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 6.75504750629922e-08 3.14536172538656e-07 2635 1904.54545454545 1945 6.14095246701033e-09 623 1.97169550145957 -1.52040422091605 -1 3.70127368979258 2632 747 2062 3262 669 2693 3053 623 1593 1945 1671 1792 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 1.21472900570489e-05 1.42129918367057e-05 1950 2452.72727272727 1946 1.10430519352496e-06 191 1.0263372973095 -1.0263372973095 -1 1.43573499712683 1946 4318 3526 3939 3990 1675 1435 434 1253 4273 191 1793 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 2.32468806161089e-07 5.15868718890617e-07 4320 2490.45454545455 1946 2.11335300659567e-08 999 1.96271896856089 -1.76626095436346 -1 3.56263939960037 4317 1486 1802 999 1946 3609 3313 4048 1056 1207 3612 1794 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 5.66941003494552e-07 9.53317255608936e-07 2360 1861.18181818182 1947 5.15401045086872e-08 748 2.30426708064936 -2.13470098539502 -1 4.00529374254003 2360 1872 1947 2532 2666 2037 1742 849 1414 2306 748 1795 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 1.00318960372302e-09 1.27431879776336e-08 1990 1776.27272727273 1947 9.11990549254968e-11 26 2.53232941972816 -2.62830366806223 -1 5.77212432660536 1990 26 296 943 1507 2788 3740 1947 3275 354 2673 1796 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 1.99935019842098e-07 4.74685412934128e-07 2795 2245.18181818182 1950 1.81759125465551e-08 166 2.18163794421465 2.3395556119707 1 3.98287059933702 2791 166 1386 610 1787 3614 4485 4306 958 1950 2644 1797 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 1.41965751573645e-07 3.98409119822705e-07 1725 2090.54545454545 1951 1.29059782486073e-08 949 2.03046336794602 2.50072446935554 1 3.75142723403577 1725 2514 2481 1731 1448 2381 2451 1296 949 4069 1951 1798 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 2.34508088893938e-07 5.19173630196711e-07 1825 2175.81818181818 1952 2.13189194446577e-08 585 2.4083510342936 -2.59674682761534 -1 4.36979751974733 1823 2132 1216 1907 1952 2894 3696 585 3713 2301 1715 1799 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 2.33223358294854e-07 5.17056952161443e-07 1300 2198.45454545455 1952 2.12021257290009e-08 902 2.56185752761046 2.71351382226242 1 4.64969258241852 1298 3303 902 2604 1949 1649 1927 2681 3905 2013 1952 1800 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 1.97616057590114e-06 2.68208091667063e-06 1855 2474.72727272727 1954 1.796511228181e-07 1237 2.28916533553597 2.20074799685317 1 3.68208109327025 1855 3904 1237 3479 3398 1624 1893 2260 3923 1695 1954 1801 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 7.98873401550779e-08 3.27123182997709e-07 2305 1782.54545454545 1956 7.26248573236191e-09 135 1.95534845154769 2.15581160577371 1 3.66095802356676 2304 135 1767 2313 839 2525 2316 1916 2423 1114 1956 1802 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 2.17926771746773e-08 2.13849139842987e-07 3970 1990.81818181818 1956 2.17926773883916e-09 12 3.7595879442631 2.76244010342069 1 7.24020495957417 3968 1956 4583 981 12 3174 2884 709 77 2655 900 1803 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 3.93570603341109e-07 7.19184377766178e-07 3710 2212.72727272727 1957 3.57791521590206e-08 1034 2.98063057143004 -2.9299306250066 -1 5.28655371321635 3709 1906 1430 1034 2423 3957 3202 1293 1383 2046 1957 1804 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 1.29901755459427e-07 3.79878839072891e-07 1730 2078.36363636364 1957 1.18092511936036e-08 1368 1.86886154037919 2.11958287641105 1 3.46395010051892 1727 2508 1957 1755 1368 1720 1965 2219 2663 3102 1878 1805 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 1.66261072990883e-07 4.2835822298961e-07 1485 2090.45454545455 1957 1.51146441414335e-08 963 1.91525285834066 2.14889607738163 1 3.52110962698553 1485 1337 2071 3642 1618 963 1957 3499 2738 2554 1131 1806 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 7.61185771771347e-07 1.19959827805034e-06 1750 2231.90909090909 1957 7.61186032503174e-08 221 2.57093783371558 -2.57093783371558 -1 4.39483264454821 1748 1957 4581 1393 2925 1588 221 4565 2680 2654 239 1807 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 1.79215809333958e-07 4.45678935751464e-07 1765 2257.63636363636 1958 1.62923476302899e-08 1208 2.31039734236 -2.02752471671702 -1 4.23625822879506 1765 2688 1616 1958 1690 2526 3809 3766 1747 2061 1208 1808 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 1.64428620858249e-07 4.25962179171755e-07 1535 2132.72727272727 1960 1.49480575588811e-08 1532 2.03193982340644 2.49215467374316 1 3.73711541362992 1532 2972 2322 2207 1608 1845 1883 2733 1651 2747 1960 1809 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 1.25316906961847e-05 1.46373620603791e-05 1960 2379.72727272727 1960 1.25317613662179e-06 712 2.31167578851786 2.50858607210094 1 3.22633413780677 1960 1952 4524 2814 4023 1663 712 2063 3676 1227 1563 1810 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 5.65676297102408e-08 3.08669609517152e-07 2970 2059.45454545455 1960 5.14251192406723e-09 476 2.31228729721339 2.65350591439202 1 4.34624223326591 2968 1806 1927 3093 476 3392 2614 745 516 1960 3157 1811 M15926 BIOCARTA_TFF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TFF_PATHWAY.html Trefoil Factors Initiate Mucosal Healing 34/40 BioCarta 1.06129310194405e-07 3.48348225330125e-07 3235 1935.09090909091 1961 9.64811957401332e-09 266 1.43402109212551 -1.80706576752885 -1 2.67335235450402 3232 577 3182 464 1167 2257 3137 1961 266 4101 942 1812 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 5.62647087289259e-08 3.08643233184884e-07 2170 1840.36363636364 1962 5.11497365162621e-09 469 1.61661058267751 -1.52176956409006 -1 3.03838630034169 2168 2787 2825 1962 469 1711 1145 934 1127 3126 1990 1813 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 1.44073447514296e-07 4.00898570192211e-07 1260 2362.63636363636 1964 1.30975869953972e-08 1202 2.24175109778598 1.87176898123905 1 4.14013495165135 1258 3603 1531 1964 1459 1386 1202 4252 3370 3183 2781 1814 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 7.23951539986928e-08 3.19649323548952e-07 2235 1959.72727272727 1967 6.58137785281747e-09 224 1.7134702420484 -1.84915227659729 -1 3.21295442350247 1912 2235 3029 224 745 2108 2234 1967 1644 3920 1539 1815 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 1.82297503905034e-07 4.50217538899015e-07 1970 1956.63636363636 1967 1.6572501728242e-08 420 1.76511103451165 2.0091494367633 1 3.23399550927216 1967 420 2528 2874 1706 1793 2524 1215 2500 3049 947 1816 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 9.50877188164542e-07 1.43345267586606e-06 1950 2022.27272727273 1967 9.50877595040128e-08 56 2.14081000321357 2.36807710920309 1 3.61160064203295 1948 892 4228 2324 3065 1967 1051 1299 2490 2925 56 1817 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 1.76110556659136e-07 4.42620781379724e-07 3365 2373.09090909091 1967 1.60100518869847e-08 521 1.92200509700831 2.0680463303431 1 3.52563156766936 3363 521 2303 1701 1669 4166 4547 3183 749 1935 1967 1818 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 6.36824360164232e-08 3.14536172538656e-07 1970 2062.54545454545 1968 5.78931253271006e-09 595 1.88577320870868 -1.83035570708774 -1 3.53994252672197 2732 2011 1968 1905 595 1462 2718 3914 2351 1064 1968 1819 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 5.57423722199432e-08 3.07843567066819e-07 1695 1979.54545454545 1969 5.57423736181886e-09 556 1.88187349676648 -1.8386720516801 -1 3.53769607248408 1695 1969 4327 1099 556 906 1994 2792 2396 2522 1519 1820 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 1.70218857218391e-07 4.33060067498401e-07 2115 1849.09090909091 1969 1.54744427626001e-08 301 2.24005673531251 -2.4816703604884 -1 4.11532686314029 2115 2086 735 1358 1641 2445 3240 838 3612 301 1969 1821 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 2.38120312828483e-07 5.22548577520102e-07 2835 1684.27272727273 1970 2.16473035092543e-08 7 2.65471357886266 2.77260633877388 1 4.81473735822669 2834 7 444 1142 1970 2140 2013 2480 1654 556 3287 1822 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 9.6867155410426e-05 0.00010474524021471 720 2167 1970 8.80649279864398e-06 717 4.42258876734014 4.07364219062024 1 5.08176775439232 717 2830 887 1357 4342 1721 1059 2308 4106 2540 1970 1823 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 6.21456467713854e-08 3.14330987047178e-07 2360 1991.36363636364 1970 6.2145648509322e-09 684 1.98562153210635 2.44332403808777 1 3.72758426246291 2359 1970 4647 1380 684 1450 2810 2992 2079 794 740 1824 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 1.30148802182788e-07 3.79878839072891e-07 2315 1744 1973 1.18317099892911e-08 560 2.15539925828061 2.29336884400027 1 3.99518215657742 2315 574 1490 2065 1371 2686 1973 560 2341 1404 2405 1825 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 1.8680001256139e-07 4.57548551785034e-07 1035 2216.45454545455 1974 1.86800028263802e-08 1032 1.71740224494597 1.85781756018619 1 3.14308249248068 1032 1961 4289 1115 1819 1889 1974 2073 2440 3182 2607 1826 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 3.67267109795352e-07 6.86806956511118e-07 3455 2020.09090909091 1974 3.33879246460717e-08 210 2.24484189599342 -2.65399752612108 -1 3.99428800537372 3453 793 2014 785 2364 4414 4247 214 210 1974 1753 1827 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 1.30347504535533e-07 3.80012490060355e-07 1990 1640.36363636364 1975 1.18497738416796e-08 386 1.81059300793218 1.66202338534911 1 3.35584217283923 1988 386 2482 1903 1374 1982 2022 673 766 2493 1975 1828 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 1.0401238578181e-07 3.47369293280946e-07 2040 1869.72727272727 1976 9.45567188175866e-09 1130 1.91707309888107 2.20245542076638 1 3.57484154089882 2038 2000 1976 1493 1140 1937 2376 1130 1796 2312 2369 1829 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 1.3895205043257e-06 1.97130651650655e-06 2365 2197.09090909091 1976 1.26320125631631e-07 960 3.04266613551876 3.38902707100117 1 5.01184319024155 2363 1886 1491 3289 3237 2227 1564 3512 960 1976 1663 1830 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 1.55603239339686e-07 4.16353338822743e-07 2640 1989 1977 1.41457500313918e-08 235 3.05343846641578 -2.55256651564586 -1 5.62501148365874 2637 796 1266 1825 1541 3099 2410 3340 235 1977 2753 1831 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 2.88624768871605e-07 5.82930641452279e-07 1310 2009.63636363636 1978 2.62386187942894e-08 397 2.16104964977263 2.15075245583853 1 3.88960511011681 1307 2656 1615 1978 2164 1169 1291 2580 4232 2717 397 1832 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 1.12604441529764e-07 3.57907719879114e-07 1020 1952.90909090909 1983 1.02367679357538e-08 556 1.76086199183191 -1.90185569006276 -1 3.27687855674943 1018 556 2373 3312 1230 1983 2910 1902 2053 3106 1039 1833 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 2.41416749403438e-07 5.27025877124579e-07 3165 2334.72727272727 1983 2.19469796268437e-08 374 2.5763262162254 2.07836794793761 1 4.66978767145734 3161 433 1002 1634 1983 3545 3457 4372 374 1460 4261 1834 M6391 KEGG_PEROXISOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PEROXISOME.html Peroxisome 78/92 KEGG 2.41516307673827e-07 5.27025877124579e-07 530 2143.63636363636 1984 2.19560303806841e-08 417 1.33378257127408 -1.15225622203472 -1 2.41716718002102 528 3294 3680 3935 1984 609 417 624 3471 3912 1126 1835 M19096 KEGG_BLADDER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BLADDER_CANCER.html Bladder cancer 51/58 KEGG 3.88575613999326e-07 7.13926390843449e-07 3090 2183.54545454545 1984 3.532506205742e-08 647 2.46369958145919 2.717369484147 1 4.37182410153486 3090 2650 1606 647 2409 1795 1761 1984 1023 2597 4457 1836 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 4.20832320475604e-07 7.54397475368345e-07 1565 2341.36363636364 1984 3.82574909977777e-08 1086 1.3240432405972 -1.41873831959732 -1 2.33995476378945 1563 3403 3457 1984 2478 1915 1629 1086 3014 3429 1797 1837 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 6.39293545108042e-08 3.14536172538656e-07 2865 1984.54545454545 1984 5.81175966986494e-09 602 2.06017222459911 -2.03107607130007 -1 3.8674011544095 2863 2545 2144 1473 602 1984 1946 1738 2534 2521 1480 1838 M99 PID_TXA2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TXA2PATHWAY.html Thromboxane A2 receptor signaling 18832364 74/89 Pathway Interaction Database 6.93835562354364e-08 3.15197676064735e-07 2745 1987.81818181818 1985 6.30759622033217e-09 630 2.24942958580678 -2.09773247667896 -1 4.22216575091298 2743 1554 1423 630 702 2307 3634 3066 2509 1313 1985 1839 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 2.0641056175216e-07 4.82841727350294e-07 955 1998.72727272727 1985 1.87645982834743e-08 927 1.67020985749243 -1.57324395991213 -1 3.04542013345575 952 1985 3080 2389 1827 927 2266 2357 3270 1259 1674 1840 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 2.42124663431338e-07 5.2719175985577e-07 2155 1784.81818181818 1988 2.20113354617068e-08 676 2.65309335679208 3.08448085125173 1 4.80885492270161 2153 1570 1003 1338 1988 2337 2504 2167 676 1876 2021 1841 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 2.112174205371e-07 4.87504266471937e-07 1195 2220.90909090909 1988 2.11217440612861e-08 133 3.51118969642283 -3.83845404933082 -1 6.39893583319621 1191 2894 4563 2775 1943 1988 2436 133 3833 1380 1294 1842 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 1.63097336442194e-06 2.25819720741318e-06 1990 2149.27272727273 1988 1.48270415777072e-07 941 2.15280306858822 -1.30971322988415 -1 3.50913721312853 1066 1748 1647 1967 3323 941 1988 4056 2304 1988 2614 1843 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 2.17866250524382e-06 2.92149147537536e-06 1030 1979.27272727273 1990 1.98060423888979e-07 395 1.89274172215449 1.91955951023484 1 3.02399658094748 1026 2697 2522 1990 3447 759 616 1744 2778 3798 395 1844 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 2.15463405259747e-06 2.89327815882221e-06 870 1770.36363636364 1991 1.95876014800359e-07 736 2.15023774884146 -2.35109853886476 -1 3.43812693734409 869 2360 2171 1991 3443 736 844 862 3045 2331 822 1845 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 8.83082626126675e-06 1.05097075020623e-05 1785 2256.36363636364 1991 8.02805609864361e-07 204 2.57500096789081 2.94732555446654 1 3.70092582033076 1783 4304 2245 4136 4146 1562 530 204 1991 2996 923 1846 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 4.18598346672911e-06 5.24776678963118e-06 1145 2097.09090909091 1992 3.80544675591252e-07 416 1.7413577370728 1.71308264250253 1 2.65415660672824 1144 2707 2698 1992 3705 934 638 1944 3036 3854 416 1847 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 3.01141337727385e-07 6.00755331391908e-07 3020 1696.27272727273 1995 2.73764889953044e-08 149 2.88930702501021 -3.68787115790268 -1 5.18974920868754 3017 722 1214 581 2196 2150 2067 2668 149 1900 1995 1848 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 1.92455634163325e-05 2.19736476354836e-05 945 2056.54545454545 1996 1.74961197984211e-06 265 1.93868693111687 -2.42621430431798 -1 2.60685130458078 942 2794 1905 2466 4098 422 265 2988 3954 1996 792 1849 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 7.80554832597416e-08 3.26249199126138e-07 1860 2028.18181818182 1997 7.09595327537561e-09 52 1.73527032211205 -1.65507883571532 -1 3.24939559364221 1859 52 2312 1869 815 1997 2610 2496 3988 2422 1890 1850 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 1.5262697328041e-11 2.55460749604091e-10 2950 2151.18181818182 1998 1.38751793892245e-12 205 2.35829750097165 2.44757187560203 1 6.53167449074032 2949 1998 222 948 1122 1837 3424 4537 2925 205 3496 1851 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 4.68645180404167e-08 2.99073619127066e-07 915 2010.90909090909 1998 4.26041082170247e-09 301 1.84790840104996 1.94078738676841 1 3.48052808663169 912 2157 2500 3365 301 1874 1998 1782 2827 1892 2512 1852 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 1.83683007996899e-07 4.5191269540042e-07 3230 2019.63636363636 1998 1.66984566666376e-08 359 2.24346867037054 -1.65289873050332 -1 4.10960735269217 3228 359 844 1030 1713 2614 4150 1998 2868 998 2414 1853 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 5.56813813592064e-07 9.41318481430709e-07 1310 1919.18181818182 1999 5.06194504109205e-08 320 2.95415020870838 2.94623950445108 1 5.13986076222125 2598 2423 1372 3280 2650 2145 1706 1310 1308 1999 320 1854 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 1.22430279828397e-07 3.70192774369017e-07 1490 2029.36363636364 1999 1.11300260583326e-08 27 1.77046383693223 1.88987069701879 1 3.28725854338495 1487 27 3078 3145 1315 2496 1898 1589 1999 2486 2803 1855 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 2.44810306375187e-07 5.30157871195484e-07 1815 2127.90909090909 2000 2.22554848742772e-08 538 1.44620125703931 1.46726067325649 1 2.61989757411292 1811 538 2988 2637 2000 1949 1378 2708 1349 3965 2084 1856 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 6.20243667619986e-08 3.14150822411035e-07 4565 2189 2000 5.6385789555132e-09 128 2.90955597522745 -2.8701842723661 -1 5.46268565653172 4562 128 488 1170 573 4292 4082 2837 2000 743 3204 1857 M46 PID_ATR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATR_PATHWAY.html ATR signaling pathway 18832364 50/52 Pathway Interaction Database 9.29502879291925e-06 1.10232502267786e-05 280 1963.81818181818 2002 8.45006187706349e-07 279 1.45511251536498 1.4587378768446 1 2.08228325739002 279 2653 3271 2002 3930 467 330 1175 2642 2979 1874 1858 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 5.19864441557284e-08 3.0481492722365e-07 2005 1917.09090909091 2002 4.72604048947078e-09 282 1.5377404546692 -1.42545293550093 -1 2.89251645296879 2002 2323 3018 2812 388 1730 1492 2553 282 3445 1043 1859 M16817 KEGG_OOCYTE_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OOCYTE_MEIOSIS.html Oocyte meiosis 104/119 KEGG 2.68952542044537e-07 5.59231717378949e-07 585 1821.90909090909 2003 2.44502340840274e-08 544 1.64542639686898 1.758498388768 1 2.96991001520884 582 2130 3335 2003 2091 544 725 1624 2775 3243 989 1860 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 9.49785720260128e-07 1.43318049860224e-06 2010 2196.81818181818 2006 8.63441936638735e-08 772 2.05922365498807 2.61218671122475 1 3.47397862212009 2006 3406 2193 3594 3015 1636 772 1745 1088 2844 1866 1861 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 2.46183590998753e-07 5.31315294702385e-07 490 1553.27272727273 2007 2.23803289588276e-08 34 2.16894266882418 2.27052261537819 1 3.92903287857254 487 3405 2064 2886 2007 314 419 45 3078 2347 34 1862 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 2.46729963518155e-07 5.32037128177284e-07 4010 2254.09090909091 2008 2.24299991989928e-08 546 3.25821228936569 -4.16343519412423 -1 5.90211921618755 4010 714 702 1165 2008 4668 3860 3995 546 657 2470 1863 M8560 BIOCARTA_G2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G2_PATHWAY.html Cell Cycle: G2/M Checkpoint 38/43 BioCarta 3.2385320431949e-06 4.16395294031052e-06 410 1620.45454545455 2009 2.94412437319842e-07 97 2.11724710376794 2.2661876400948 1 3.28869369718706 409 2276 2049 2009 3608 316 97 1059 2417 2608 977 1864 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 4.34423430648884e-06 5.42885515663948e-06 1960 2285.27272727273 2009 3.94931171351212e-07 1059 2.392403672483 2.30990911979966 1 3.63661639086349 1956 3396 1838 1059 3717 2009 1830 2188 2913 2461 1771 1865 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 2.48372199406972e-07 5.33113588540658e-07 1180 2316.45454545455 2012 2.25792934043015e-08 1178 1.49425226999701 -1.34331562526661 -1 2.70593221631687 1178 1587 3410 4560 2018 1275 1978 2327 3673 2012 1463 1866 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 5.81683806485506e-07 9.75674330707743e-07 1890 2161.81818181818 2015 5.2880360025797e-08 458 1.82440670739754 -1.96578958307803 -1 3.16571383819431 1887 3698 2497 3322 2677 1256 1746 1369 2015 2855 458 1867 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 9.29339077467369e-08 3.35829802760759e-07 2015 2396.90909090909 2015 8.44853742477408e-09 1018 1.91484149074388 1.96060839976657 1 3.5787919795237 2015 3773 2200 4210 1018 1888 1884 1206 4118 1599 2455 1868 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 1.97496758345967e-07 4.70878541974394e-07 4575 2563.54545454545 2016 1.79542523705001e-08 756 2.71551579196304 -2.8007279306618 -1 4.96048862635396 4574 1522 756 1847 1780 3927 4130 3762 2398 1487 2016 1869 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 1.66480425398265e-08 1.7119555727229e-07 4285 2041.09090909091 2018 1.51345842416428e-09 269 2.25611113210765 -2.28056682025571 -1 4.40741183122863 4282 1155 371 490 659 3951 3979 2103 2018 269 3175 1870 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 1.59285356576639e-07 4.20318657884309e-07 2860 2171.09090909091 2018 1.44804880099353e-08 641 1.93062459999632 2.00054076846407 1 3.55396413987829 2857 1471 1855 641 1571 3165 3999 2192 1740 2018 2373 1871 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 3.76418358947612e-07 6.97289895695734e-07 1980 2321.36363636364 2019 3.42198566684116e-08 1243 2.02713073736114 -1.64851203002244 -1 3.60297612921512 1978 2616 1614 2323 2389 2019 3510 4455 1842 1243 1546 1872 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 4.60242325709477e-07 8.09669689656628e-07 2355 1943.27272727273 2023 4.18402201811533e-08 414 1.61726165778662 -1.79533213697455 -1 2.84400377010622 2355 414 2973 460 2537 2002 2023 2671 982 3733 1226 1873 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 5.74751906302802e-08 3.09093308316432e-07 4515 2377.72727272727 2023 5.22501746652951e-09 165 2.1760226107748 -2.39563905339495 -1 4.08969008840962 4514 165 1110 2081 492 4689 4135 1258 2023 1559 4129 1874 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 3.90809540931569e-07 7.16357682794954e-07 3015 2025.90909090909 2024 3.55281463959334e-08 742 1.97406276084285 -1.53041707178295 -1 3.5019528762654 3013 742 2121 3059 2414 2508 1967 851 2024 1897 1689 1875 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 7.97503225941135e-08 3.27123182997709e-07 1200 2339.27272727273 2024 7.9750325456165e-09 955 1.82103824562168 2.02933840192566 1 3.40943266998243 1199 3230 4396 1751 955 2215 2024 1750 1449 4148 2615 1876 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 1.44444100290859e-07 4.0104479610168e-07 2025 1984.81818181818 2025 1.31312827067765e-08 148 2.06880815476252 2.46383892618432 1 3.82057753678238 2025 148 1787 2580 1465 1850 2760 3386 954 2737 2141 1877 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 3.71657560391063e-08 2.87575261955407e-07 2030 2130 2026 3.37870515154246e-09 135 1.48900238543304 -1.0598012545661 -1 2.81168368304309 2026 1881 2575 3325 135 1684 1497 2686 3254 2624 1743 1878 M4470 BIOCARTA_EXTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EXTRINSIC_PATHWAY.html Extrinsic Prothrombin Activation Pathway 9/13 BioCarta 3.69279416167627e-07 6.88550861663682e-07 2535 2128.54545454545 2027 3.69279477532921e-08 13 4.23089443569286 -4.45158316237533 -1 7.52752389026483 2531 833 4190 250 2455 2027 1525 4153 13 753 4684 1879 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 2.49300226983927e-07 5.33829325923706e-07 1960 2378.45454545455 2028 2.2663659566746e-08 1148 1.99425912219105 2.17273349470172 1 3.6113442104451 1959 4143 2422 2964 2023 1148 1468 1450 3335 3223 2028 1880 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 4.6102410106422e-06 5.73640493574751e-06 2570 2210.36363636364 2030 4.19113697429643e-07 1268 2.12026883885138 -2.24114201588005 -1 3.20820267181924 2566 1836 1548 2786 3736 2164 2963 1268 1787 2030 1630 1881 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 1.91224118880946e-07 4.62860431342597e-07 2740 2173.81818181818 2030 1.73840123183781e-08 1006 2.05038535312099 2.15410521428894 1 3.7496864020691 2740 1177 1063 1016 1746 2030 2188 4660 2243 1006 4043 1882 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 2.03651437592056e-14 4.9042591093597e-13 3095 2012.63636363636 2031 2.03651437592058e-15 103 2.37508612215232 2.66408319235139 1 8.44143565739242 3093 1044 4306 683 515 2499 3036 2031 1574 103 3255 1883 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 3.82418408755351e-08 2.89891607042284e-07 2505 1665.81818181818 2031 3.47653104911635e-09 158 2.08090580452936 2.33856289482683 1 3.92762391459473 2503 1132 575 1140 158 2044 3065 3160 2031 455 2061 1884 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 1.7163973293243e-07 4.35558892172617e-07 2255 2155.54545454545 2032 1.560361330213e-08 1144 2.64648894481167 -2.42743463507235 -1 4.86025170765029 2252 2674 1144 1668 1650 1767 2086 4440 2032 2526 1472 1885 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 7.41044527234125e-07 1.17531255663477e-06 1790 2644.81818181818 2033 6.73677069860464e-08 1434 1.05100626706221 1.08980837683077 1 1.79880589865596 1787 3353 3791 1554 2843 1832 1434 2026 4191 4249 2033 1886 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 6.55431097488761e-08 3.14536172538656e-07 1605 1982.81818181818 2033 5.95846470014159e-09 637 1.99103556363096 -1.82401008498461 -1 3.73758737072535 1604 2115 2156 3838 637 645 846 2033 3188 3570 1179 1887 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 7.34332407234618e-08 3.2144561803028e-07 2655 1937.45454545455 2036 6.67574937950648e-09 604 2.10008516365514 2.41342005101947 1 3.93662047667454 2651 2014 724 604 755 3289 3112 2639 2036 861 2627 1888 M181 PID_BMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BMP_PATHWAY.html BMP receptor signaling 18832364 47/54 Pathway Interaction Database 5.6508529624216e-08 3.08669609517152e-07 2100 2098.36363636364 2037 5.1371391886979e-09 451 2.22348258711664 2.23496292258763 1 4.17928924622042 2098 4193 2548 3907 474 1496 2037 1376 451 3388 1114 1889 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 5.76101132910732e-08 3.09351234054455e-07 3455 2208.27272727273 2037 5.23728316360686e-09 448 1.84266363878064 -1.70541880742446 -1 3.46283932011221 3454 448 1985 1663 494 2711 3656 3186 1403 2037 3254 1890 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 1.10026510314872e-07 3.53626743374685e-07 2250 1615.81818181818 2039 1.00024105288658e-08 233 1.90921529814264 2.51476329533625 1 3.55591055690083 2247 1767 2238 2541 1206 2491 2039 233 296 2157 559 1891 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 4.02004006647193e-09 4.66206120730897e-08 3275 2141.81818181818 2039 3.65458188528882e-10 209 2.11943092516234 2.0817671055695 1 4.48608555435774 3275 1228 563 2039 736 2867 3414 3275 1695 209 4259 1892 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 7.46382285664516e-07 1.18139650849648e-06 990 2263.90909090909 2040 6.78529580805255e-08 987 1.65705975054672 -1.60411750198515 -1 2.83549516850599 987 2974 3330 2456 2850 1474 1729 1561 3864 2040 1638 1893 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 2.54530897325978e-07 5.41164790711089e-07 3280 2097.54545454545 2040 2.31391751612867e-08 395 2.39268079359972 2.70260854327614 1 4.32891102101224 3276 2333 1444 1894 2040 2806 1630 395 2133 2022 3100 1894 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 4.10123788313024e-06 5.14973205862589e-06 2040 2105.81818181818 2040 3.72840502606718e-07 566 2.23568939609592 2.71774726987715 1 3.41314280148924 2040 3306 2042 1738 3699 2211 1465 1389 566 3575 1133 1895 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 2.63325100290266e-07 5.52643162903538e-07 3030 2367.63636363636 2041 2.39386483462275e-08 1208 2.87278763705429 2.91381541115061 1 5.1901461384624 3026 2240 1208 1828 2070 2041 1669 4047 1579 1919 4417 1896 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 2.551946455112e-07 5.41950314819278e-07 3260 2178.81818181818 2041 2.31995159193785e-08 576 2.02497667797151 -2.16434654008456 -1 3.66314880839066 2354 3259 1551 2821 2041 1935 3258 576 3541 977 1654 1897 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 6.47441630306179e-08 3.14536172538656e-07 1645 2131.54545454545 2041 5.88583317599861e-09 624 1.81457107308862 1.75441046652994 1 3.40625052450784 1642 3597 2153 4008 624 863 1237 1798 3371 2041 2113 1898 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 6.34860074020578e-08 3.14536172538656e-07 2410 1871 2041 5.77145538491737e-09 361 2.64201302084613 2.81974221058924 1 4.95988890555236 2408 1474 405 2041 744 3127 3867 1357 2297 361 2500 1899 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 4.52094610237509e-07 7.98012924577801e-07 3540 2424.54545454545 2043 4.10995184674428e-08 1221 2.14059938910509 -1.58043730352758 -1 3.7684807407698 3539 1567 2043 1614 2525 4191 4168 1444 1221 1718 2640 1900 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 1.18230563847318e-06 1.72077786419779e-06 2235 2024.90909090909 2043 1.0748238853259e-07 770 1.97463824496527 2.34066385099364 1 3.28595693626239 951 2988 2232 2235 3139 1676 1920 770 2043 2912 1408 1901 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 2.55916647403557e-07 5.42888348649344e-07 2370 1520.27272727273 2044 2.32651524702961e-08 69 2.47617681549146 2.5321879363517 1 4.47901717600075 2171 455 1282 420 2044 2369 2529 2831 184 2369 69 1902 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 3.19512671461923e-07 6.2318173938028e-07 2225 2028.27272727273 2045 2.90466107150661e-08 1355 2.09372213057968 2.25622128300126 1 3.75086573470374 2225 1440 1501 2212 2253 1617 2045 3027 1355 2026 2610 1903 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 1.25141474794274e-07 3.7431417048731e-07 2930 1951.36363636364 2045 1.13764983556939e-08 12 2.02407555334011 1.9546990528584 1 3.75545791355919 2927 12 1033 2045 1333 2774 3228 2293 1981 540 3299 1904 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 2.60823726327026e-06 3.42730508982061e-06 1015 2195.09090909091 2046 2.37112759591218e-07 413 1.43889196234171 1.52669783083161 1 2.26986893520496 1015 3011 3587 1999 3520 622 413 2046 2108 4168 1657 1905 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 4.57173226798834e-06 5.69355575327308e-06 860 2204.09090909091 2047 4.15612888031863e-07 857 2.2219757479516 -2.51301171345879 -1 3.36422714000862 857 3041 2047 1969 3732 1804 2477 1009 3034 2791 1484 1906 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 5.41124265338833e-08 3.06874196014832e-07 3015 2058.09090909091 2047 4.91931162407845e-09 425 2.36674390355119 2.98918160179764 1 4.45035220734239 3014 2511 728 1009 425 3540 3726 2550 1987 1102 2047 1907 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 7.09558125693789e-06 8.55894289106743e-06 1225 2242.18181818182 2048 6.45054922015045e-07 707 1.85230274254215 -2.00915057294455 -1 2.70967987650875 1224 3678 2926 2865 3859 1129 954 707 2048 3480 1794 1908 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 3.92148356445834e-06 4.93715722172402e-06 825 1834.09090909091 2048 3.56499141317358e-07 357 1.95519229147894 -2.01668062970881 -1 2.99514669561669 821 2439 2266 2365 3688 1015 1002 357 3250 2048 924 1909 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 1.25483722996995e-07 3.74750186367376e-07 3375 2643.81818181818 2048 1.1407611832213e-08 1336 1.94789748136272 2.38605251785452 1 3.61380076344948 3373 2048 1504 1696 1336 3711 4493 4325 1859 2039 2698 1910 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 2.77771717774351e-07 5.69540620284507e-07 2050 2004.90909090909 2049 2.77771752495064e-08 515 2.40011972884341 -2.431166735689 -1 4.32698966669006 2049 931 4562 3284 2213 1681 515 613 1046 2561 2599 1911 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 2.90749235980846e-08 2.61957344798642e-07 4125 2529.09090909091 2049 2.64317490748502e-09 37 3.79995982811525 -3.81936583592685 -1 7.22126548677854 4122 1876 1112 2049 37 3641 3604 4450 1576 1943 3410 1912 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 2.07942627707191e-07 4.84679970737421e-07 2485 2208 2050 1.8903877032891e-08 1286 1.93120098476375 1.97399038634212 1 3.52051931862394 2485 2050 1866 1879 1836 2089 3013 3307 1718 1286 2759 1913 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 3.67792235587134e-07 6.87516575038127e-07 3700 2213.90909090909 2051 3.34356633703659e-08 1149 2.34637854188826 -1.73797228000365 -1 4.17468909157019 3696 1907 2203 1702 2365 2240 1638 1487 1149 2051 3915 1914 M3430 BIOCARTA_CALCINEURIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CALCINEURIN_PATHWAY.html Effects of calcineurin in Keratinocyte Differentiation 21/22 BioCarta 1.23415602194569e-07 3.71755418903835e-07 2605 2292 2053 1.12196008289034e-08 1193 1.79293611149816 1.57926359553117 1 3.32804710436627 2601 2806 3009 1465 1319 2053 1193 4122 1282 3727 1635 1915 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 1.05368831910992e-07 3.48348225330125e-07 3810 2397.18181818182 2054 9.57898517796586e-09 605 2.40352863161761 -2.1288006097514 -1 4.48132459278402 3810 2054 784 605 1155 2893 4568 4681 1504 1219 3096 1916 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 6.40620100350414e-08 3.14536172538656e-07 3240 1898 2054 5.82381926367902e-09 208 2.50187772270276 2.17758479309952 1 4.69676521654347 3238 208 737 568 604 2054 2450 2418 2975 1036 4590 1917 M13883 BIOCARTA_MPR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MPR_PATHWAY.html How Progesterone Initiates Oocyte Membrane 56/66 BioCarta 2.58353427623122e-07 5.45605448940105e-07 1775 2105.81818181818 2055 2.34866779965856e-08 214 2.21979451924391 2.60852864959112 1 4.01378266172079 1772 2207 1955 214 2055 2854 3586 2468 425 3623 2005 1918 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 1.23138487212433e-07 3.71619986983812e-07 2900 2147.18181818182 2055 1.11944085549769e-08 568 2.04545292723137 2.14602089094685 1 3.79698346628887 2899 568 1803 1398 1318 2824 2652 3906 1047 2055 3149 1919 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 6.05990919634102e-38 9.53425713557653e-36 20 2180.27272727273 2055 6.05990919634099e-39 19 2.83583112679212 3.02398020617343 1 28.6771341240517 2897 995 4656 19 629 1783 3770 3485 2055 20 3674 1920 M913 REACTOME_NEPHRIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEPHRIN_INTERACTIONS.html Genes involved in Nephrin interactions 27/33 Reactome 6.81223279577273e-07 1.10191017121478e-06 1850 1879.18181818182 2056 6.19294082287338e-08 166 2.16399216287585 2.01265190296834 1 3.72210379124 1846 646 2056 415 2784 2319 2932 3409 166 2849 1249 1921 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 1.87761393136852e-06 2.56433384145237e-06 1870 2211.54545454545 2057 1.70692321258224e-07 410 1.58654824430122 1.7431295809543 1 2.56060229381424 1870 2845 2718 1928 3376 2057 1537 1038 2867 3681 410 1922 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 3.8497716517599e-21 2.04167665127042e-19 3700 1997.54545454545 2057 3.49979241069081e-22 60 3.27826899850821 3.26651773411211 1 17.6919820079201 3698 1367 60 669 1222 3030 3038 2597 2057 162 4073 1923 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 2.60040923086499e-07 5.48089666740809e-07 3245 2372.72727272727 2059 2.36400867112227e-08 78 2.29658015403767 2.41061224352695 1 4.15134613986551 3243 78 1173 170 2059 3571 3975 4391 1543 1549 4348 1924 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 2.60110350317672e-07 5.48089666740809e-07 1445 2035.18181818182 2060 2.36463982791852e-08 885 2.12624056913922 2.24744424869845 1 3.84337287161722 1444 3852 1225 2829 2060 1170 1158 2923 2445 885 2396 1925 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 7.45471126532024e-08 3.2288397661503e-07 950 2007 2060 6.77701047083955e-09 771 1.77875641368919 1.82492108610494 1 3.33316034563704 946 2047 3015 3170 771 2060 1504 797 2471 3047 2249 1926 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 1.58853219604574e-05 1.82696685315202e-05 2120 2213.18181818182 2063 1.44413060574425e-06 1518 2.90668080341175 -2.41553489124754 -1 3.97618387190786 2120 2738 1578 1970 4063 2139 1548 1518 1608 3000 2063 1927 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 2.57054393671266e-06 3.38437025977232e-06 3720 2105.36363636364 2065 2.33686085474165e-07 208 3.34782151737703 3.20204675074364 1 5.28766312446586 3718 662 1079 1234 3514 3936 4242 275 208 2065 2226 1928 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 1.76766331827111e-07 4.43266487055072e-07 2820 2190.45454545455 2065 1.60696678209085e-08 641 2.30932086756337 2.73333625692696 1 4.23585594774989 2817 2065 864 967 1673 3209 3646 3107 641 1499 3607 1929 M6382 KEGG_REGULATION_OF_AUTOPHAGY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_REGULATION_OF_AUTOPHAGY.html Regulation of autophagy 23/60 KEGG 1.03755156957282e-06 1.54292482935844e-06 1495 2465.18181818182 2068 9.43229144452132e-08 1089 1.02099837133526 -1.00265179795003 -1 1.71257643259419 1495 1838 3693 3454 3062 1313 1552 2068 3696 3857 1089 1930 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 4.25291114731613e-21 2.23041562392579e-19 2895 1997.27272727273 2068 3.86628286119646e-22 61 2.94269062215319 3.05108997122907 1 15.8482337192992 2891 2068 61 1759 998 1366 3234 4144 3026 79 2344 1931 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 7.69115499179019e-08 3.24764325922831e-07 4430 2728.18181818182 2071 6.99195932788308e-09 799 1.99899635916876 -1.82903842917037 -1 3.74451257971809 4427 1982 1422 1926 799 3905 4365 4100 2071 1470 3543 1932 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 4.60761717824861e-08 2.99073619127066e-07 1270 1852.81818181818 2071 4.18874297704475e-09 289 1.88553877693871 2.33704082515565 1 3.55142228900043 1270 2991 2109 1746 289 1536 2071 2229 2142 2569 1429 1933 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 2.63529182847227e-07 5.52825663572849e-07 2075 2209.81818181818 2071 2.39572013103943e-08 1148 1.89186019647198 1.91551717325337 1 3.41757282218256 1148 3267 3097 1745 2071 2073 1316 1974 1642 3121 2854 1934 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 3.44879113529365e-07 6.54535350164295e-07 3470 2158.09090909091 2072 3.13526515994311e-08 548 2.29839232463688 -2.44265176221522 -1 4.10346404661625 3470 548 1234 2072 2320 3122 3735 1516 1967 983 2772 1935 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 1.60039758363428e-07 4.21105226344428e-07 2075 2180.18181818182 2072 1.4549070000507e-08 1233 1.85948507222651 2.0860783173709 1 3.42254018020821 2072 2965 2637 1536 1577 1233 1990 2322 1937 3596 2117 1936 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 2.02115608375283e-07 4.7747030607174e-07 1555 2538.81818181818 2072 1.83741479039813e-08 1395 1.40350997446532 1.60661675357536 1 2.56095754085844 1555 2970 3958 3771 1801 1395 1550 2574 2072 4212 2069 1937 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 4.56221761708482e-08 2.99073619127066e-07 4665 2288.36363636364 2072 4.14747064699375e-09 277 2.43378752700635 -2.30376453947906 -1 4.58430216111797 4664 2072 458 707 277 4238 4336 3805 631 1016 2968 1938 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 8.54380019925288e-08 3.28305665915602e-07 2075 2051.72727272727 2073 8.54380052773723e-09 172 4.50355853466408 4.55083181134823 1 8.43100305977333 2073 877 4592 1329 1027 2715 2585 2737 172 1381 3081 1939 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 6.41099520545223e-08 3.14536172538656e-07 2085 1606.36363636364 2074 5.82817762934029e-09 49 2.95089100857322 3.30511079094225 1 5.53985067579276 2081 2368 1321 391 605 2193 2089 2801 49 1698 2074 1940 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 1.89865387958315e-10 2.65170311888287e-09 840 1637.54545454545 2075 1.72604898158819e-11 270 3.50196710961932 3.77010946690913 1 8.67203859341261 838 2181 270 1160 2166 2075 2346 2201 1731 685 2360 1941 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 8.31632755530905e-08 3.27411388472988e-07 2610 1967.72727272727 2076 7.56029806334423e-09 843 2.05132096788821 2.44143247573377 1 3.84046108646621 2610 2951 1514 843 893 2727 2669 1504 1379 2076 2479 1942 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 5.42153349939381e-06 6.6761383034539e-06 870 2396 2077 4.92867896355094e-07 749 1.58286623436277 1.69834887970771 1 2.36471978547296 867 3590 3434 4020 3780 749 926 1660 3821 2077 1432 1943 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 3.60937091359226e-06 4.57409320811995e-06 475 2146 2078 3.28125166838483e-07 472 2.21487685902702 2.23094810845919 1 3.41428626392132 472 3005 1766 2654 3659 1139 1086 2078 3428 2490 1829 1944 M1473 BIOCARTA_BLYMPHOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BLYMPHOCYTE_PATHWAY.html B Lymphocyte Cell Surface Molecules 10/18 BioCarta 9.30173395268083e-07 1.40989673271206e-06 2080 2484.09090909091 2079 8.45612535046627e-08 879 1.65396509281296 1.8586933767276 1 2.7935219643873 1958 879 2079 3624 2998 1671 1275 4220 4673 2080 1868 1945 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 3.95982751552264e-07 7.21636520203353e-07 2080 1924.63636363636 2079 3.59984384387338e-08 1165 2.21249499434083 2.5818541253531 1 3.92299437838677 2079 2316 1705 1412 2428 2563 2244 1324 2359 1576 1165 1946 M4085 KEGG_PRIMARY_IMMUNODEFICIENCY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_IMMUNODEFICIENCY.html Primary immunodeficiency 21/48 KEGG 2.65387873817139e-07 5.54506757156662e-07 1400 2173.63636363636 2080 2.41261732573737e-08 350 1.99375345725873 -2.07508085685527 -1 3.60092629863766 1848 2373 1721 3297 2080 2350 2583 350 4515 1396 1397 1947 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 8.32109869378598e-08 3.27411388472988e-07 2080 1996.54545454545 2080 7.5646354622876e-09 895 1.91041407852008 2.17103329704848 1 3.57659755637337 2703 1986 2080 1007 895 2080 2476 2544 1146 2865 2180 1948 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 2.04237615860835e-07 4.80997306448512e-07 1890 2109.81818181818 2080 1.85670577110268e-08 638 2.01480532850348 2.43232144553857 1 3.67489190783886 2196 3046 2288 638 1810 2429 1886 2080 1275 3674 1886 1949 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 1.83571842022262e-07 4.5191269540042e-07 3855 2472.27272727273 2082 1.66883506672562e-08 147 2.30847323502214 2.1706465552974 1 4.22870829240273 3853 1904 1872 2082 1712 3411 2271 3583 147 2047 4313 1950 M4956 BIOCARTA_MONOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MONOCYTE_PATHWAY.html Monocyte and its Surface Molecules 10/16 BioCarta 0.000132530005183519 0.00014252486317298 745 2244.72727272727 2083 1.20489081441105e-05 310 2.46272854623993 2.46272854623993 1 2.73429161158115 744 2876 1449 3065 4373 969 310 2300 4550 2083 1973 1951 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 4.42056149891743e-05 4.87501174646969e-05 745 2286.45454545455 2083 4.01877302345262e-06 743 2.6228164311492 -2.66181627995456 -1 3.26496089561094 743 2747 1478 2388 4249 1705 2083 1724 3847 1871 2316 1952 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 1.55343881468801e-07 4.16353338822743e-07 2390 2040.81818181818 2083 1.41221720397969e-08 444 2.06694337511074 2.11363389035324 1 3.80742256865191 2390 2022 840 2083 1535 1754 2459 2648 3324 444 2950 1953 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 2.66349887736213e-07 5.55287751817547e-07 3065 2032.63636363636 2084 2.42136290893365e-08 531 2.81434040408821 2.14320924806301 1 5.08284950033721 3065 531 618 1597 2084 2266 1589 3536 2563 689 3821 1954 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 7.94281803875772e-07 1.24337120984687e-06 1225 2010 2085 7.22074627855621e-08 686 1.76327055866346 1.95914979606296 1 3.00598794160443 1223 1930 2251 3364 2890 988 738 2397 3558 2085 686 1955 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 9.21845920172731e-08 3.3523689347011e-07 1850 2129.09090909091 2085 8.38041780727275e-09 283 2.14460387561997 2.71441659123875 1 4.00879087174421 1847 3392 2371 2873 1007 2085 1696 3418 283 3168 1280 1956 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 3.53674796809168e-08 2.82884790943581e-07 3090 2093.72727272727 2086 3.21522547722625e-09 109 2.45659262456478 -2.45969160862308 -1 4.6444106637601 3087 164 665 2086 109 1891 2567 4596 3778 602 3486 1957 M18256 KEGG_SULFUR_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SULFUR_METABOLISM.html Sulfur metabolism 8/18 KEGG 2.42485870899762e-07 5.2719175985577e-07 2135 1957.72727272727 2087 2.42485897359494e-08 137 2.55987003767078 -1.85918021345519 -1 4.63985306250866 2132 2461 4183 778 2087 1524 569 3544 137 2137 1983 1958 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 7.88071674535324e-39 1.37766603844694e-36 2365 1884.54545454545 2088 7.88071674535315e-40 17 2.58453588760868 2.7636631918187 1 26.7628699313095 2365 1016 4330 237 280 2088 3298 2148 1578 17 3373 1959 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 6.41847320836132e-08 3.14536172538656e-07 4085 2439.54545454545 2088 6.41847339374691e-09 494 1.90776091483615 -1.82060280485645 -1 3.58122753075561 4082 956 4337 1346 723 1977 4025 4541 2088 494 2266 1960 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 1.2031954426951e-05 1.40885201923117e-05 1225 2636.09090909091 2091 1.09382002100529e-06 929 1.25155707951919 -1.3157842867824 -1 1.75236276286864 1222 4250 3687 1552 3988 929 1159 2091 4388 4047 1684 1961 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 6.24208735177151e-06 7.60522774918986e-06 1810 2147.45454545455 2093 5.67464096599446e-07 62 2.33024685134728 2.81869845681288 1 3.4435973537631 1810 2885 2093 2750 3818 1840 1604 2590 1553 2617 62 1962 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 5.55391796155503e-08 3.07843567066819e-07 4455 2705.18181818182 2094 5.04901645614924e-09 455 2.12819022395369 -2.03789901373253 -1 4.00085466332529 4454 2094 1180 1201 455 4609 4641 3825 1665 1236 4397 1963 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 6.6630318800916e-08 3.14536172538656e-07 3280 2359.54545454545 2095 6.05730189262871e-09 596 2.03446594120392 1.95793056580499 1 3.81913399968642 3278 596 1752 3070 653 2502 1935 4383 1368 2095 4323 1964 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 6.61765213615451e-07 1.07633763206924e-06 1445 2065.81818181818 2096 6.01604920614618e-08 672 2.08533539858575 2.74440091559737 1 3.59292222710092 1445 1648 2120 3076 2767 2096 1925 1580 2756 2639 672 1965 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 2.03907045641496e-07 4.80499877897084e-07 1045 2272.81818181818 2097 1.85370058673297e-08 880 1.58072901469325 1.54089071264489 1 2.88318060769571 1043 3853 3755 2247 1809 937 880 1982 2305 4093 2097 1966 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 9.42018561946515e-08 3.3764305071295e-07 2455 2206.63636363636 2099 8.5638054752985e-09 883 1.60407345037952 -1.50952698944062 -1 2.99675108529341 2454 1996 3405 1975 1031 938 2761 3751 2980 2099 883 1967 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 2.17319839389159e-07 4.94814106086266e-07 1755 2156.27272727273 2100 1.9756350986945e-08 1623 2.0409345577469 -2.34881265807396 -1 3.71531267173024 1752 1667 2100 2351 1882 2739 3011 2258 1623 2649 1687 1968 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 2.71543373238027e-07 5.62856786404538e-07 2100 2212.45454545455 2100 2.46857642503915e-08 509 1.54067245016287 1.28344844843999 1 2.77953127992261 2100 509 2865 3347 2099 1776 1396 3260 2422 2487 2076 1969 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 5.20652934610126e-06 6.42815027821029e-06 1345 2299.45454545455 2101 4.73321969812414e-07 1154 1.56657220354651 1.74185141896771 1 2.34780513376018 1341 2419 2768 3587 3767 1956 2101 1154 1640 3296 1265 1970 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 2.72368687218712e-07 5.63850966522947e-07 1570 1958.27272727273 2102 2.47607928126397e-08 726 2.49935783782382 2.93727384240043 1 4.50908096050875 1567 1473 726 2125 2102 1791 2378 2663 2929 1333 2454 1971 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 2.50017298677437e-07 5.34457268911911e-07 2845 2388.18181818182 2103 2.27288479173149e-08 1114 2.11717969588947 2.67004757644124 1 3.83367835236377 2842 1659 1980 2103 2028 3657 4567 1114 2106 2503 1711 1972 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 3.7985447267024e-07 7.02002001176012e-07 1480 2213.18181818182 2103 3.45322307505778e-08 1013 1.94497086056142 -1.62571236308693 -1 3.45526934163846 1476 2528 1451 1939 2395 1406 2539 4536 2959 1013 2103 1973 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 3.8678630145642e-08 2.90705627846226e-07 2325 1941 2104 3.86786308188583e-09 227 2.07493149272031 2.25252338485338 1 3.91561551147002 2323 1055 4401 421 227 2557 3407 2104 1411 620 2825 1974 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 3.73892941434961e-07 6.93155806587988e-07 2050 1993.63636363636 2104 3.73893004343145e-08 173 2.59274709937316 3.19818097792354 1 4.61046363684526 2046 2903 4610 1447 2463 2104 410 3073 173 2146 555 1975 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 2.64336601138914e-06 3.4647841082357e-06 1080 2251.27272727273 2105 2.40306289770733e-07 923 1.82287435756523 -1.89862519344981 -1 2.87334920231556 1079 2994 2782 2007 3528 1573 2105 923 3133 3041 1599 1976 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 4.30577692169174e-07 7.69851607702568e-07 880 2057 2105 3.91434342218753e-08 879 1.70630028445704 1.70459169728506 1 3.01141928115252 879 1993 3000 2615 2487 1456 1938 2171 2105 1038 2945 1977 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 1.42876939794798e-07 3.99040920610323e-07 1895 2294.90909090909 2106 1.29888135521644e-08 1074 2.13421643924949 2.25513570237557 1 3.94273840941406 1891 2166 1328 4345 1456 1281 1074 3855 3299 2106 2443 1978 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 2.74161646834985e-07 5.66073041584045e-07 3565 2032.45454545455 2108 2.49237891818838e-08 60 2.51603086833481 2.82328900906192 1 4.53792541630698 3565 60 477 563 2108 3777 3755 2932 1012 552 3556 1979 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 5.08313844608768e-07 8.76915696839687e-07 1930 2436 2109 4.62103601868734e-08 1462 2.41096446372283 -2.65152560878461 -1 4.21605366814046 1929 1912 1462 3568 2591 2786 4006 2109 3330 1628 1475 1980 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 7.79313504739144e-07 1.22245255645356e-06 3895 2506.81818181818 2109 7.08467073452874e-08 1068 2.39106063202698 2.48829190295163 1 4.08162621409568 3895 1541 1068 1410 2882 3918 3880 2084 2109 1128 3660 1981 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 4.62587629819731e-08 2.99073619127066e-07 1650 2088 2110 4.20534217769479e-09 292 1.84091284505064 1.96156093994632 1 3.46734872418886 1648 2262 2496 3636 292 1394 1500 2110 3318 2906 1406 1982 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 2.2678772025733e-05 2.56453770870771e-05 3180 2242.36363636364 2110 2.26790034760726e-06 40 6.46451939457559 8.48181005510024 1 8.56924315541237 3178 1951 4681 1275 4352 3891 2110 334 40 2562 292 1983 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 5.63702420317476e-08 3.08663042215602e-07 1795 2297 2112 5.12456758873755e-09 471 1.4763647168266 -1.30315930519581 -1 2.77471047831882 1795 3883 3708 654 471 1626 2004 2316 2357 4341 2112 1984 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 6.73747697744038e-08 3.14536172538656e-07 2830 2217.54545454545 2113 6.12497925797718e-09 663 1.85601627155151 -1.64503022687967 -1 3.4840697010875 2829 2027 2152 2283 663 1677 4009 3672 2113 1180 1788 1985 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 1.99557469230072e-06 2.70431023475722e-06 750 1733 2115 1.81416045677066e-07 295 2.08244977493815 -2.11143587276632 -1 3.34734949455675 749 2408 2115 3293 3404 554 365 295 2520 2873 487 1986 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 2.75813338480799e-07 5.67992564410721e-07 3145 2044 2115 2.50739430054037e-08 508 2.53544629558105 2.64338783644306 1 4.57187343604904 3141 1399 515 784 2115 3340 3722 2253 1099 508 3608 1987 M916 REACTOME_PLATELET_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_HOMEOSTASIS.html Genes involved in Platelet homeostasis 64/91 Reactome 8.88135937087089e-08 3.31003670356505e-07 2285 1899.90909090909 2116 8.0739633903725e-09 972 2.3345444099627 2.79419994302585 1 4.36763316004014 2284 1588 1229 2116 972 2535 2793 2264 1334 1437 2347 1988 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 1.57884426885853e-07 4.1878955683592e-07 2730 2088.36363636364 2116 1.43531307469574e-08 1561 1.88297341615566 2.24143316297688 1 3.46708548289738 2728 1664 1887 2137 1561 2405 2305 1954 2116 1921 2294 1989 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 2.54092013068696e-07 5.40718801480723e-07 2370 2045.54545454545 2117 2.30992765832187e-08 277 2.26932139879193 2.42055322665693 1 4.10591567424884 2370 277 1389 3082 2038 2454 2293 1652 2117 1758 3071 1990 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 2.61534638254218e-12 4.97759472806415e-11 3105 2060.09090909091 2117 2.37758762049572e-13 196 3.14917373260822 3.59554579914521 1 9.36834790568853 2250 2117 196 1319 1166 3101 3103 3670 1793 507 3439 1991 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 3.02213659521546e-08 2.67626355148536e-07 3980 2130.72727272727 2121 2.74739694248229e-09 49 2.53210595633072 -2.17473241466153 -1 4.80480930857192 3978 519 715 2114 49 3770 4011 2419 3114 628 2121 1992 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 5.56703637984401e-08 3.07843567066819e-07 3620 2480.27272727273 2122 5.06094229156023e-09 32 2.09715610171563 2.33815786388692 1 3.9425000380105 3616 32 1625 2122 458 3734 3577 4362 1877 1819 4061 1993 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 2.31766991563995e-07 5.15280358069739e-07 3120 2000.63636363636 2122 2.10697287254849e-08 145 2.06913725244132 -2.2961351951262 -1 3.75614791521082 3117 145 2122 444 1940 2665 4001 3449 594 2421 1109 1994 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 2.76762419234467e-07 5.68211665413957e-07 800 1739.54545454545 2123 2.516022309559e-08 341 1.6338676161929 1.83432331257364 1 2.94577686431816 796 2160 3101 2453 2123 341 483 1380 2127 3592 579 1995 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 2.77142418104993e-07 5.68744440632855e-07 850 2319.54545454545 2124 2.51947684561537e-08 519 1.72682678308021 1.84638994067107 1 3.11322337061403 848 3619 3296 3751 2124 1925 1395 519 2936 3225 1877 1996 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 3.74129413657471e-06 4.72289604831041e-06 2125 2169.45454545455 2125 3.40118227180972e-07 790 3.222030559631 2.57277281433719 1 4.95429392052043 2125 878 1020 2104 3676 2188 790 3945 2912 1217 3009 1997 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 2.77596279324917e-07 5.6942826528188e-07 2515 1987.72727272727 2125 2.52360285774597e-08 127 1.81411497240361 1.98109251761334 1 3.27036173872496 2513 700 2393 1443 2125 2792 3134 1822 127 2786 2030 1998 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 2.77977582175974e-07 5.69715235723229e-07 835 2167.18181818182 2126 2.52706924817642e-08 135 2.19424678151956 2.41732588947719 1 3.95567906599595 831 4448 3023 3188 2126 2143 1707 135 506 4092 1640 1999 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 4.08359991005958e-08 2.9351990282604e-07 4460 2473.81818181818 2127 3.71236362350784e-09 197 1.91089961312635 2.13111737030725 1 3.60369309567285 4456 1854 2092 2852 197 3357 2127 996 3509 1544 4228 2000 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 3.50699902432105e-06 4.46173460776155e-06 730 2070.27272727273 2127 3.18818601346112e-07 730 1.64050966866751 1.69500236444069 1 2.53377876991737 730 2610 2749 2127 3647 918 948 2233 3332 1730 1749 2001 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 1.42821630818508e-07 3.99040920610323e-07 2130 2465.36363636364 2128 1.42821639997616e-08 843 1.905809357609 -1.97728730634905 -1 3.52068838218297 2128 2491 4284 1881 1554 2081 3435 3242 3122 843 2058 2002 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 6.15381002794438e-08 3.12995510041999e-07 3125 2164.27272727273 2128 5.59437290916175e-09 566 2.82180430737336 2.9011456183119 1 5.29920990835849 3125 757 1211 2736 566 3091 2128 3540 1529 1567 3557 2003 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 1.13752859453566e-07 3.5893637536524e-07 2720 1954.63636363636 2129 1.03411695759322e-08 1210 1.92324619640291 2.1788136799938 1 3.57845488624674 2150 1321 1677 2719 1244 1535 2613 2184 2129 1210 2719 2004 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 1.00705117631838e-07 3.42613246105503e-07 2630 1952.27272727273 2133 9.1550111128746e-09 802 1.71100619743398 -1.65801980677586 -1 3.19344608582018 2630 2376 2685 1945 1111 2133 1455 1097 802 3095 2146 2005 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 8.98943623677196e-08 3.31497675696653e-07 2200 1815.81818181818 2133 8.17221509462728e-09 410 2.15426244562543 -2.14665894929274 -1 4.02987930958586 2199 410 1455 1388 985 2221 2133 1696 2202 2193 3092 2006 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 7.96738415226687e-08 3.27123182997709e-07 1690 2659.36363636364 2134 7.2430767643716e-09 836 2.27653572159041 2.78567105625051 1 4.26245171577942 3898 1619 1690 1862 836 3829 3608 4070 1688 2134 4019 2007 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 2.56715403682806e-08 2.40893977213289e-07 1920 2017.09090909091 2135 2.56715406648431e-09 254 2.06430860264712 2.38213421599513 1 3.94422261566881 1918 964 4492 1156 405 2583 2624 2135 2776 254 2881 2008 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 2.04570509545471e-06 2.76509967083225e-06 950 2126.36363636364 2135 1.85973363426246e-07 920 1.78012271241205 1.76150002817037 1 2.85629841954973 947 1622 2944 3632 3414 1353 920 1544 2714 2135 2165 2009 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 1.6835336022878e-07 4.31159989299968e-07 2140 2340.18181818182 2136 1.53048521010815e-08 951 1.64080034527882 1.63464268380587 1 3.01507561017129 2136 1660 2715 1921 1630 3188 3896 951 2006 2795 2844 2010 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 2.42469365654774e-07 5.2719175985577e-07 4340 2726.45454545455 2137 2.20426720343762e-08 864 2.15665869570776 2.77273564220396 1 3.90888287731302 4340 1754 2127 3311 1991 4109 4472 1972 864 2914 2137 2011 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 4.95899377010716e-07 8.59267642984794e-07 2140 2332 2138 4.5081771708258e-08 901 2.68230686480545 2.53357535663862 1 4.69748591458344 2138 1644 901 1036 2578 2477 3020 4345 1826 1204 4483 2012 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 8.24017690360558e-08 3.27411388472988e-07 2395 2072 2139 7.49107019294937e-09 322 2.10849343257168 -1.88997892491606 -1 3.94752276686478 2393 327 2040 2609 882 1829 2576 4349 322 3326 2139 2013 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 1.49119328117918e-18 6.12037590188325e-17 3515 1987.27272727273 2139 1.35563025561743e-19 79 3.0271452922238 3.27736224113637 1 14.1716245766806 3513 1280 79 1136 394 3652 3401 2139 2582 233 3451 2014 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 7.88602878611714e-08 3.2708309200767e-07 3520 2369.45454545455 2139 7.16911733526952e-09 438 2.32212544934613 2.48886884126069 1 4.34786418436527 3516 1210 925 438 824 2566 3120 4710 2139 2038 4578 2015 M868 REACTOME_CHROMOSOME_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHROMOSOME_MAINTENANCE.html Genes involved in Chromosome Maintenance 96/251 Reactome 3.90130792811014e-06 4.91306654767339e-06 275 1976.90909090909 2140 3.54664986036515e-07 201 1.39055848531049 1.28380644034114 1 2.13079200613824 275 2140 3119 2936 3687 201 245 1102 3804 2769 1468 2016 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 4.42820703942705e-08 2.97736997522731e-07 2800 1668.81818181818 2142 4.02564284414451e-09 260 2.14815720198777 -2.23076879228639 -1 4.0473921433471 2799 1694 2157 632 260 2202 2764 957 562 2188 2142 2017 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 5.70602693607141e-08 3.09093308316432e-07 3405 2026.72727272727 2143 5.18729734915064e-09 347 2.00773668582047 1.35353566957569 1 3.77334124872949 3403 576 2143 608 483 3065 4126 2272 347 1672 3599 2018 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 2.8224888921665e-07 5.73983092245837e-07 1670 1937.36363636364 2145 2.56589932207058e-08 232 2.06517348718562 -1.49882589244043 -1 3.7210085551552 1668 2872 2521 3874 2145 1318 728 232 2819 2514 620 2019 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 2.10174177622366e-06 2.82788517211394e-06 1145 2464.18181818182 2145 1.91067616736217e-07 1142 2.37556415267398 2.69728169184735 1 3.80531397603468 1142 3949 2045 3738 3433 1520 1255 1620 3450 2809 2145 2020 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 3.49051993831748e-07 6.60595593779411e-07 2150 2101 2146 3.17320044738498e-08 257 1.54691585096136 -1.44319160219502 -1 2.75973640281206 2146 1769 2750 2591 2330 2000 1119 2142 257 3345 2662 2021 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 1.90985561641425e-16 6.17432774621593e-15 4295 2348.90909090909 2147 1.7362323785584e-17 2 2.83278342030832 -2.60069754443232 -1 11.6225302342548 4294 2 105 245 2147 4587 4353 3879 2065 148 4013 2022 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 0.000607203136677175 0.000634491654885159 865 2452.63636363636 2147 6.07369113551261e-05 671 3.73695657560672 3.73695657560672 1 3.44963927896495 861 2911 4626 3893 4515 862 671 1230 4127 2147 1136 2023 M1386 KEGG_PENTOSE_PHOSPHATE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_PHOSPHATE_PATHWAY.html Pentose phosphate pathway 28/33 KEGG 2.44657439203678e-06 3.2428618731855e-06 1785 2234.09090909091 2148 2.2241610116597e-07 1385 1.49745062894241 -1.44785672451793 -1 2.3726693309859 1781 1783 3040 2155 3490 1873 2148 2088 1385 2645 2187 2024 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 4.64644896411623e-08 2.99073619127066e-07 2020 1912.45454545455 2149 4.22404460204571e-09 122 1.76035750857851 1.92754818962048 1 3.31558552249718 2017 122 2519 453 296 2587 2685 2149 2004 3212 2993 2025 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 2.52507434795045e-06 3.33287218185853e-06 200 1866.90909090909 2149 2.29552476921558e-07 196 1.66598101199285 1.7169546334574 1 2.63407793383276 196 2149 2914 2673 3504 372 279 1005 2903 2954 1587 2026 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 5.42458853971854e-07 9.23001366527452e-07 1760 2160.90909090909 2149 4.93144534297432e-08 579 2.19511750672951 -1.92571695756323 -1 3.82442481840518 1756 2741 2149 3377 2630 1699 1284 579 4151 2685 719 2027 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 7.60992382735844e-06 9.13999575402239e-06 1910 2294 2149 7.60994988740732e-07 777 2.59723575372848 2.62343948697542 1 3.7783730537058 1908 900 4665 1010 3905 2312 2090 2767 777 2149 2751 2028 M10 PID_BCR_5PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BCR_5PATHWAY.html BCR signaling pathway 18832364 85/107 Pathway Interaction Database 7.55274270543481e-07 1.19195346041176e-06 1895 2691.90909090909 2151 6.86613208940146e-08 1541 1.48036873031001 -1.63000032162249 -1 2.53140502492925 1892 2151 3517 1541 2857 2122 3565 2060 4264 3594 2048 2029 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 2.16871497102307e-07 4.9403159571568e-07 1715 2036.90909090909 2152 1.97155925891871e-08 499 2.28950074586066 2.53223905730715 1 4.16836132456184 1713 2666 1533 2152 1881 2289 2891 499 2487 2479 1816 2030 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 8.24336272016396e-07 1.28275572265141e-06 1735 2304.36363636364 2153 7.49396891721783e-08 1044 1.57917796546096 2.0285013007817 1 2.68588487525833 1734 1788 2740 3395 2909 2153 1090 1044 3151 3622 1722 2031 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 2.78619626549733e-06 3.63283048981973e-06 1570 2219.72727272727 2153 2.53290890371799e-07 949 1.84156924673067 2.02412513918679 1 2.89188815471749 1570 3265 2339 1739 3549 2742 2120 949 1684 2153 2307 2032 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 5.37720379050372e-06 6.63019903113311e-06 1490 2385.18181818182 2153 4.88837903038335e-07 640 1.27572717931083 -1.40398158314386 -1 1.90680758506445 1488 2153 3759 2478 3772 1185 2073 874 4159 3656 640 2033 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 6.19707303682028e-30 5.62503552572918e-28 4365 2301.27272727273 2154 5.63370276074575e-31 29 3.52870963941287 -3.2685670110601 -1 27.7658135317761 4362 1381 29 660 1014 4580 4327 2645 2154 53 4109 2034 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 1.44977385075722e-06 2.03452290235407e-06 1070 2188.09090909091 2155 1.31797709649258e-07 1070 2.31862375538453 -2.0255637534631 -1 3.80982601648931 1070 3108 1844 2339 3273 1093 1561 2155 3680 2750 1196 2035 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 9.67442013677286e-07 1.4519320523233e-06 760 2111.54545454545 2155 8.794931264606e-08 759 1.55946900270556 1.68521765567054 1 2.62812467698803 759 2155 3364 3677 3031 869 1329 1316 2428 2542 1757 2036 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 1.08790700546329e-07 3.51706922314159e-07 2285 2315.72727272727 2158 9.89006417509676e-09 1198 1.97313074046702 2.35018942052757 1 3.67632884580337 2281 3250 2099 3401 1198 1994 2405 2082 2158 3001 1604 2037 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 5.06658531220416e-07 8.74931112233937e-07 2285 1997.09090909091 2159 4.60598770821432e-08 805 2.11166716056423 -2.40148452312382 -1 3.69316554334915 2283 1764 1750 2793 2587 2159 2632 805 3004 1334 857 2038 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 4.99100199437371e-08 3.0357704374324e-07 2160 1913.18181818182 2159 4.53727464327405e-09 352 2.06045577534246 2.26939498057398 1 3.8770973387313 2159 1995 1607 2576 352 2170 2681 1178 2308 1521 2498 2039 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 1.01132935581745e-07 3.42922022949596e-07 2810 1875.81818181818 2161 9.19390365734343e-09 710 2.03498525636702 2.47439744687816 1 3.79805836272877 2810 710 2161 1282 1116 2736 2569 818 1038 3134 2260 2040 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 4.88641403019824e-06 6.06624782286578e-06 2165 1669.18181818182 2162 4.44220443948448e-07 119 1.70472522199802 1.83398248765898 1 2.56731780077213 318 2692 2467 2164 3749 119 128 2235 2162 1853 474 2041 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 8.8428602326191e-08 3.31003670356505e-07 2380 2126.36363636364 2162 8.03896417096025e-09 964 2.14502737068859 -2.38274398048815 -1 4.01300116537922 2376 2095 1076 2813 964 2162 3015 1594 3536 1580 2179 2042 M1835 KEGG_GLIOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLIOMA.html Glioma 66/75 KEGG 2.88512164612908e-07 5.82930641452279e-07 1765 1796.72727272727 2163 2.62283820408133e-08 221 1.85603424169236 1.77745999671708 1 3.34049592736561 1761 336 2390 221 2163 1269 925 2452 2641 3142 2464 2043 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 5.55526117961741e-07 9.39478064055685e-07 2225 2214.27272727273 2165 5.05023871126118e-08 1335 2.11670879604658 2.30953942702211 1 3.68309026887149 2221 2329 1618 2165 2649 1927 2091 2038 2710 1335 3274 2044 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 5.10519239759202e-05 5.60253618150066e-05 1735 2506.81818181818 2165 4.64119169961329e-06 759 2.25878851830916 2.7157622131859 1 2.77228621995895 1732 3765 2469 3160 4272 1871 759 2165 2011 3778 1593 2045 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 1.22197786794118e-07 3.70192774369017e-07 4160 2704 2165 1.11088903255934e-08 129 1.80621456168369 -1.44717656671961 -1 3.35365508076796 4159 129 2165 1247 1309 4665 4435 4546 1230 1535 4324 2046 M980 KEGG_TRYPTOPHAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TRYPTOPHAN_METABOLISM.html Tryptophan metabolism 31/53 KEGG 5.50370202626534e-07 9.32094494580997e-07 4330 2721.72727272727 2166 5.00336673010678e-08 619 2.83170521892082 -3.57755930239218 -1 4.93028271625878 4329 1753 1312 1665 2645 4623 4244 2166 619 2093 4490 2047 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 4.25137567223295e-07 7.61825860779784e-07 180 2116.18181818182 2167 4.25137648557195e-08 180 1.68780492749268 1.77454874665973 1 2.98098602273186 180 3826 4319 3234 2547 543 522 896 2167 3874 1170 2048 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 3.7250875264076e-07 6.91948568462963e-07 1540 1996.72727272727 2167 3.38644377922511e-08 657 1.81545415032405 2.01905271812897 1 3.22840775384182 1537 2277 2108 2639 2382 2167 2672 657 2810 1573 1142 2049 M243 PID_ARF_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF_3PATHWAY.html Arf1 pathway 18832364 30/33 Pathway Interaction Database 5.7069939587095e-08 3.09093308316432e-07 1980 2466.90909090909 2168 5.18817646068543e-09 484 0.886125112556109 -0.807420265154699 -1 1.66490276897973 1980 630 3903 4610 484 1358 913 2947 3922 4221 2168 2050 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 1.03326082950161e-07 3.47116805355702e-07 1595 1913.36363636364 2168 9.39328070936505e-09 914 1.98516716939365 2.07887619182485 1 3.70203084631046 1595 1442 2215 2168 1131 2671 3001 914 1394 2248 2268 2051 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 2.48000737453973e-07 5.33043479409269e-07 3165 2079.36363636364 2168 2.2545524128228e-08 63 1.62589898344084 -1.79062502736666 -1 2.94443313854156 1714 2168 3165 2454 2016 1045 1877 2341 3161 2869 63 2052 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 5.60454012217555e-07 9.45201709054455e-07 2660 2227.81818181818 2170 5.09503777267535e-08 1277 1.89457460851481 2.20753073799532 1 3.29504148069654 1527 1855 2502 2659 2656 1884 1757 1277 2898 3321 2170 2053 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 6.88253948047256e-08 3.15009389627869e-07 1695 2025.63636363636 2172 6.256854268898e-09 692 2.94332689526558 3.75019879607926 1 5.52509307251874 2741 2404 1694 1093 692 2315 1692 2865 1675 2939 2172 2054 M754 REACTOME_GLYCOPROTEIN_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOPROTEIN_HORMONES.html Genes involved in Glycoprotein hormones 3/9 Reactome 0.000314301908977252 0.000331657726441456 1450 2426.54545454545 2173 3.14346371388595e-05 815 4.49224518711489 -4.49224518711489 -1 4.5124989634844 1446 2931 4229 1615 4610 2173 1268 1017 3054 3534 815 2055 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 0.000314301908977252 0.000331657726441456 1450 2427.54545454545 2174 3.14346371388595e-05 816 4.49224518711489 -4.49224518711489 -1 4.5124989634844 1447 2932 4230 1616 4611 2174 1269 1018 3055 3535 816 2056 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 9.15201841541606e-08 3.34843245403276e-07 2025 2208.81818181818 2174 8.32001708740075e-09 995 1.82066114208831 1.83028723866079 1 3.40340058042917 2022 2520 2174 3616 995 1594 1875 2481 3068 1307 2645 2057 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 6.40261511499757e-08 3.14536172538656e-07 3280 2255.54545454545 2174 5.82055936484688e-09 603 1.85251190738767 -1.39937232561071 -1 3.47748976556349 3279 1285 1910 2376 603 1668 2580 4208 2174 1326 3402 2058 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 2.43212176346049e-07 5.28053136404162e-07 2460 2502.72727272727 2175 2.21102002939455e-08 902 2.29770715963578 2.30716922130903 1 4.16411513285334 2456 2175 959 2773 1993 2114 2164 3917 3874 902 4203 2059 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 9.42177648817275e-08 3.3764305071295e-07 1920 2354.72727272727 2176 9.42177688763719e-09 1069 1.86328575656282 1.96917586169665 1 3.48115410655931 1917 1972 4307 2176 1133 2591 2556 2043 2998 1069 3140 2060 M3126 KEGG_LEISHMANIA_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEISHMANIA_INFECTION.html Leishmania infection 68/98 KEGG 3.10091189822383e-06 4.00446078238481e-06 1170 2200.54545454545 2178 2.81901478998596e-07 1168 1.73784113448453 -1.77397425994834 -1 2.70772462098647 1168 2178 2407 2195 3592 1339 1831 2371 3820 1374 1931 2061 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 4.81691781241904e-08 3.02364809600699e-07 2180 1939.63636363636 2180 4.81691791683119e-09 279 2.1461576937483 2.36962973761492 1 4.03947277355222 2180 997 4326 555 402 2426 2709 2700 1844 279 2918 2062 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 1.50063009086367e-07 4.08899989016697e-07 4515 2861.18181818182 2180 1.36420926656577e-08 1501 2.00857534137032 -1.28980521178533 -1 3.704431250442 4169 1601 2180 1507 1501 4095 4513 4512 1962 2166 3267 2063 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 2.62313428759188e-06 3.44400384907752e-06 4405 2663.27272727273 2180 2.38467037749881e-07 924 1.69284959619739 -1.61464834750927 -1 2.66961023657537 4404 1818 1951 1249 3523 3587 2051 4082 924 2180 3527 2064 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 6.60684056779025e-07 1.07532025793e-06 3770 2183.18181818182 2180 6.00622050172505e-08 329 2.47841064956124 3.01365918699819 1 4.27062630642536 3768 516 1101 851 2765 4550 4254 2180 329 1060 2641 2065 M81 PID_CDC42_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CDC42_PATHWAY.html CDC42 signaling events 18832364 97/107 Pathway Interaction Database 2.15639598322845e-07 4.92413596557247e-07 2185 2490.18181818182 2182 1.96036017690373e-08 1863 1.45710217480827 -1.3382803148299 -1 2.65314778351905 2182 2137 3640 2232 1876 1863 2190 3656 1902 3618 2096 2066 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 5.92776204728266e-07 9.89008019200217e-07 2440 2193.54545454545 2182 5.92776362850958e-08 119 3.08011682126013 2.75823236984766 1 5.33997403105666 2436 3530 4393 1240 2753 2182 1783 1255 119 3476 962 2067 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 3.714204803857e-08 2.87575261955407e-07 2185 2122.63636363636 2183 3.37654987869364e-09 395 2.94724383462081 3.07675157305461 1 5.56612501055425 2183 2145 395 1334 1793 2481 2362 2392 3695 533 4036 2068 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 2.51009610639958e-07 5.35608210768807e-07 1800 2123.90909090909 2186 2.28190581162703e-08 376 1.97606696099712 2.27304369019243 1 3.57756828548796 1800 2283 2186 2107 2031 2435 3004 2197 376 2101 2843 2069 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 1.08733153653687e-07 3.51706922314159e-07 2190 2316.54545454545 2186 9.88483263888472e-09 834 2.03318799587133 2.1487228334879 1 3.78825348651674 2186 3016 1777 3639 1196 1648 2720 4111 3051 1304 834 2070 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 1.66331470256576e-06 2.29624024454823e-06 1255 2104.09090909091 2187 1.51210541829066e-07 713 2.20678211514919 -2.19484716676337 -1 3.59252289925131 1251 2273 1398 1490 3333 2187 3127 713 3834 961 2578 2071 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 1.48110201060478e-07 4.06205780944483e-07 3655 2449.09090909091 2187 1.34645646392432e-08 508 1.95715684891706 -1.53839542943137 -1 3.61120023729364 3651 2392 2187 1885 1491 3406 3012 508 4122 2122 2164 2072 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 3.65056051048743e-08 2.8614986551519e-07 3950 2384.63636363636 2189 3.31869142823896e-09 123 2.12981758732533 -2.644091383266 -1 4.02343310816135 3949 740 1939 2816 123 3964 4454 723 3936 1398 2189 2073 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 4.98006248384014e-07 8.62474236381943e-07 2580 2126.90909090909 2190 4.52733055559972e-08 661 2.05721307575943 -1.48577209103895 -1 3.60160633653695 2656 2578 1860 1809 2579 1959 2601 1939 661 2564 2190 2074 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 7.66963410256529e-08 3.24764325922831e-07 2500 1826.09090909091 2191 6.97239488176717e-09 182 2.6053714205377 2.53329338317174 1 4.88063337373187 2497 2719 979 3028 795 2191 1514 182 2879 905 2398 2075 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 5.70382460979465e-08 3.09093308316432e-07 895 2487 2191 5.70382475619591e-09 581 1.67284711741282 1.90362214774537 1 3.14380597169731 894 4089 4391 1757 581 2407 2191 2050 2074 4297 2626 2076 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 5.13436149401899e-06 6.35067773893334e-06 220 1917.27272727273 2191 4.66761225148589e-07 217 1.5286195802051 1.58688762759275 1 2.29322951796797 217 2744 2812 2191 3761 715 364 801 2694 3347 1444 2077 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 2.1404071908408e-07 4.90423395182941e-07 2610 2039.72727272727 2192 1.9458249082579e-08 601 2.85669150818389 3.04689261208101 1 5.20385219552158 2606 2192 601 1767 1871 2324 2224 2506 1617 899 3830 2078 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 3.63681967047084e-08 2.8614986551519e-07 2195 2008.90909090909 2192 3.30619975508282e-09 120 1.80001921072823 -1.44813345967814 -1 3.40027844053897 2192 2567 2635 1508 120 1333 2355 1601 1901 3667 2219 2079 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 7.07526934160611e-08 3.1722620893472e-07 4685 2600.09090909091 2193 6.43206324468093e-09 725 1.93474405377382 -2.23743700155321 -1 3.62982588516629 4681 1416 1657 1811 725 4597 4686 3096 2193 1126 2613 2080 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 6.89943069953998e-08 3.15009389627869e-07 1865 1963.90909090909 2195 6.2722099235576e-09 200 2.23614941077389 2.35099675578263 1 4.19740142673519 1865 2044 949 200 695 2197 2195 3851 2306 2278 3023 2081 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 3.51597070678405e-06 4.46833110824467e-06 2310 2155.18181818182 2198 3.19634211446387e-07 886 2.62921725315089 2.90345636014421 1 4.06087659464824 2307 2590 886 1503 3650 1593 1426 3333 2876 1345 2198 2082 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 1.45514845714392e-07 4.02832886669754e-07 1725 2774.36363636364 2198 1.32286232126543e-08 1471 1.64090654688369 1.88736321060397 1 3.02925536843107 1721 3836 3884 4642 1471 1886 2062 2198 2408 4361 2049 2083 M16120 BIOCARTA_SALMONELLA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SALMONELLA_PATHWAY.html How does salmonella hijack a cell 20/24 BioCarta 2.06774954512615e-07 4.82918251014122e-07 3005 2306.18181818182 2199 1.87977249042826e-08 97 2.28311164749219 -1.15396682335079 -1 4.16324108569683 3005 741 2233 2199 1832 2168 1971 3128 97 3320 4674 2084 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 2.30148012859385e-06 3.06749822982686e-06 1185 2310 2200 2.09225685112603e-07 1181 2.36865666788665 2.51891385325084 1 3.77008663137136 1181 3900 1507 2416 3469 2200 1559 2234 2132 1727 3085 2085 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 1.00930163507332e-06 1.50565857065299e-06 2200 2687.45454545455 2200 9.17547361922212e-08 1618 2.00197122865791 2.24785155764921 1 3.36498183511376 1858 4700 2737 4596 3053 1618 1770 2200 2979 2196 1855 2086 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 2.3363505270033e-07 5.17595283421683e-07 1290 2415 2200 2.33635077263736e-08 1288 1.61404974817863 1.73190481543616 1 2.92892132957715 1288 2934 4431 2929 2051 1443 1902 2114 2200 2727 2546 2087 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 3.47273005116794e-06 4.42171185365866e-06 2300 2277.90909090909 2200 3.15703230266534e-07 625 3.78916616008953 -3.87352902832129 -1 5.85780384921348 2299 1919 1252 3271 3642 2801 2200 625 3452 1831 1765 2088 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 8.85651650022174e-08 3.31003670356505e-07 3780 2146.18181818182 2200 8.05137896068874e-09 24 2.99836336666506 3.3033023991171 1 5.60979820024319 3778 809 1362 186 968 3591 3274 3836 24 2200 3580 2089 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 1.78369210917857e-12 3.50792781471786e-11 2570 1800.90909090909 2201 1.62153828107274e-13 130 2.29134917955053 2.57315246672597 1 6.91675786386444 2569 1171 188 289 130 3139 3195 2979 2201 201 3748 2090 M1073 REACTOME_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POTASSIUM_CHANNELS.html Genes involved in Potassium Channels 45/106 Reactome 3.03598874943752e-07 6.04334478806247e-07 4685 2512 2202 2.75999015309317e-08 548 3.18822745066621 -3.08666579141766 -1 5.72438167081026 4685 1655 548 935 2202 4335 3861 3213 811 756 4631 2091 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 6.42847285425265e-08 3.14536172538656e-07 2645 2476.90909090909 2203 6.42847304021633e-09 724 2.46674111725715 2.72882078087487 1 4.63079130870878 2641 902 4239 4114 724 2203 2121 4655 1657 1184 2806 2092 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 1.01864687134877e-05 1.20350769280756e-05 3055 2756.09090909091 2203 9.26046898119441e-07 1928 2.84816807270786 2.65349367166679 1 4.04521930673087 3052 3740 2041 3822 3949 2178 2203 2189 2017 3198 1928 2093 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 0.000104290001359425 0.000112565471396407 510 2350.36363636364 2204 9.48135868252072e-06 75 1.14496660609983 1.14496660609983 1 1.30464455212317 508 2875 3046 2204 4479 905 75 1914 4121 3805 1922 2094 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 1.31106823937851e-06 1.87487428343366e-06 1665 2722 2205 1.19188092790665e-07 1661 2.20595437410169 2.28105863474017 1 3.64725990175903 1661 4159 2007 3977 3203 2025 2068 1993 3801 2843 2205 2095 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 4.99378088198451e-08 3.0357704374324e-07 2600 2171.54545454545 2206 4.99378099420483e-09 6 1.91534615568017 -2.08160922802232 -1 3.60398829491129 2597 2459 4335 4122 443 2206 1597 6 3155 1859 1108 2096 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 1.65393380190488e-05 1.89987041737431e-05 850 2212.27272727273 2207 1.50358748737556e-06 83 2.44172532132488 2.44172532132488 1 3.32803016698366 850 4281 2207 3481 4506 720 83 285 3842 2675 1405 2097 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 3.04386965859639e-07 6.04363454990223e-07 3720 2513.18181818182 2208 2.76715461794482e-08 742 3.50054260350192 -3.60569945672136 -1 6.28519894685784 3719 1793 742 1337 2208 4510 4529 3534 1089 990 3194 2098 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 1.29580006601718e-07 3.79650919404164e-07 2565 2468.72727272727 2208 1.17800012939983e-08 1366 2.18755345344613 2.25754901922015 1 4.05495968558434 2561 2542 1664 3608 1366 2016 2096 3262 3664 2208 2169 2099 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 2.0031308774835e-06 2.71299217839946e-06 1230 2088.27272727273 2209 1.82102972851327e-07 774 1.88613286105108 -2.15564488423709 -1 3.03094846273298 1229 2763 2209 2923 3406 1228 1248 1656 3189 2346 774 2100 M11420 BIOCARTA_CTCF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTCF_PATHWAY.html CTCF: First Multivalent Nuclear Factor 30/34 BioCarta 7.21134728345276e-06 8.68748320007581e-06 2340 2438.36363636364 2210 6.55579174684478e-07 1198 2.17375495045833 2.34053648100176 1 3.17600879694532 2337 3985 2340 2210 3865 1995 1443 1723 1198 3884 1842 2101 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 1.05976917203674e-07 3.48348225330125e-07 3440 2215.54545454545 2210 9.63426566442934e-09 1165 2.15751997276778 -1.85738943949384 -1 4.02255887157055 3437 2354 2210 1662 1165 2885 1860 1749 1177 2917 2955 2102 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 5.79008710397348e-08 3.09852566478612e-07 2230 1772.81818181818 2213 5.26371568760031e-09 276 2.63226868334725 2.93050815034375 1 4.94654500928399 2228 2342 1443 606 496 2702 3757 2594 276 2213 844 2103 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 1.32555855121366e-06 1.89079370254714e-06 4480 2224.45454545455 2213 1.20505395445331e-07 112 3.34343375561661 -1.99186227798011 -1 5.52483371733806 4480 2853 1318 1700 3212 3295 3876 112 158 1252 2213 2104 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 4.10092257388096e-07 7.39546157616882e-07 2105 2316.27272727273 2213 3.72811212574179e-08 1095 1.95793960522012 2.09361464982566 1 3.4655213665549 2105 2995 2213 2627 2459 2003 1982 1694 3658 2648 1095 2105 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 7.78080845953865e-07 1.22173705685371e-06 3755 2389.81818181818 2213 7.07346473763886e-08 664 2.42118739968154 -2.32097777615819 -1 4.13324230984001 3752 664 1334 2577 2878 3448 4644 2213 2003 2067 708 2106 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 3.33430156826821e-07 6.4099386103601e-07 2215 2313.81818181818 2214 3.33430206855883e-08 579 1.61233284238473 1.68216658861873 1 2.88256904811774 579 3224 4312 2695 2362 1322 1246 1576 2211 3711 2214 2107 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 2.74620933580912e-05 3.0774235671935e-05 1290 2430.18181818182 2214 2.74624327389511e-06 461 4.86432685772979 -4.86432685772979 -1 6.33662821040887 1289 3205 4506 2769 4192 1566 461 2214 2712 2143 1675 2108 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 1.20196120553614e-07 3.68632676421739e-07 4050 2643.72727272727 2214 1.09269206473165e-08 1295 2.33063644514848 -1.79317923378629 -1 4.32885004000845 4046 2214 1454 1470 1295 3327 2808 4133 1872 2136 4326 2109 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 3.06040453369937e-07 6.06173285734831e-07 600 2287.90909090909 2215 2.7821863267547e-08 596 1.38788887276447 1.51068828318567 1 2.4909041706604 596 2992 3479 3726 2215 1171 1285 1340 2750 3834 1779 2110 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 1.90257948552334e-05 2.17385019890345e-05 615 2054.36363636364 2216 1.72963267218042e-06 436 1.68938367224513 -1.75764937608497 -1 2.27379486428134 613 2216 2906 3386 4095 811 978 436 2814 3421 922 2111 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 2.59324329404475e-07 5.47182552317235e-07 3035 2564.09090909091 2218 2.35749418156596e-08 542 2.39605041622485 3.13515083527104 1 4.33168569438281 3031 542 1440 3021 2056 4078 4430 4088 1693 1608 2218 2112 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 1.08985686660742e-07 3.51855294828115e-07 3560 2021.81818181818 2220 9.90779018725262e-09 330 2.67043649417874 -3.07008853876625 -1 4.97570911701408 3558 471 631 330 1199 3432 2220 3742 2639 851 3167 2113 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 1.4386547585799e-05 1.66636821116494e-05 920 2126.81818181818 2220 1.3078765150167e-06 400 1.67069499774604 1.76733110539723 1 2.30433317956264 919 3987 2979 2220 4035 961 562 683 2633 4016 400 2114 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 2.4261119911545e-07 5.27221390342967e-07 2810 2323.81818181818 2221 2.20555659881898e-08 938 1.93206955754992 2.2041076670834 1 3.50171810366435 2809 2493 1741 2157 1992 3242 3171 2221 2096 938 2702 2115 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 1.29214800833396e-06 1.85209189169034e-06 2225 2695.63636363636 2223 1.17468069751345e-07 1344 1.08718614741135 1.17829648820319 1 1.79875158922699 2223 1922 3464 4191 3194 2097 1563 1344 4047 3719 1888 2116 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 9.63655353922956e-07 1.44716935110288e-06 765 1952 2224 8.76050705480459e-08 280 1.65964354976187 -1.779023014483 -1 2.79768491147331 762 1583 2541 2901 3029 280 989 2948 3649 2224 566 2117 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 3.23711193941393e-06 4.16326113188931e-06 1165 2113.09090909091 2226 2.94283336596113e-07 930 1.86392241622103 2.34027980518941 1 2.8951433817732 1161 2226 2720 3358 3607 1277 1353 1721 2340 2551 930 2118 M258 PID_BARD1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BARD1_PATHWAY.html BARD1 signaling events 18832364 34/36 Pathway Interaction Database 2.57017643515444e-05 2.88701398713207e-05 365 1891.90909090909 2227 2.33655132912781e-06 23 1.85512765282543 1.90796039720623 1 2.43095153286849 361 2730 3070 2227 4182 164 23 858 2503 3761 932 2119 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 6.17208928973198e-11 9.30743177237539e-10 3160 2237.72727272727 2227 5.61099026355011e-12 249 3.23326948239427 3.51091682960594 1 8.4311147976648 3156 1512 249 1186 2479 3103 2227 3779 1892 560 4472 2120 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 8.86113759964949e-08 3.31003670356505e-07 810 2159.90909090909 2227 8.05557996050679e-09 808 2.38608852829179 -2.50950040210827 -1 4.46408461140356 3594 1579 808 1343 969 3838 3479 2227 2512 809 2601 2121 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 3.54205320863678e-08 2.82884790943581e-07 2925 2393.63636363636 2228 3.22004842333153e-09 111 1.94121363580947 -1.52687778934433 -1 3.66985934593703 2924 2074 2228 2110 111 2364 2006 4272 803 2868 4570 2122 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 8.97968499839923e-08 3.31497675696653e-07 4650 2652.36363636364 2228 8.1633503317462e-09 187 2.24029795442356 2.19572465405887 1 4.19085636322257 4646 1213 958 187 984 4662 4683 4280 1673 2228 3662 2123 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 1.39876235027511e-07 3.95338819957994e-07 1155 2099.54545454545 2229 1.27160221746234e-08 1155 1.73359453118096 1.93180444492503 1 3.2044966773055 1155 1991 3020 1532 1433 2229 2390 2437 1978 2571 2359 2124 M648 BIOCARTA_G1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G1_PATHWAY.html Cell Cycle: G1/S Check Point 34/39 BioCarta 6.33954753322325e-06 7.71600421784779e-06 1110 2263.81818181818 2230 5.76324163765133e-07 1108 1.7552741022208 2.01868558075485 1 2.59051712378097 1108 3088 2754 2230 3821 1181 1136 1860 3069 2730 1925 2125 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 3.78757153617122e-08 2.88344155656906e-07 3705 2298.72727272727 2230 3.4432469103445e-09 38 1.80691665513235 -1.60835774762311 -1 3.41158013734989 3701 38 1566 1589 153 3715 3155 3783 2230 896 4460 2126 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 3.10592318008701e-07 6.11341009591772e-07 2615 2060.09090909091 2230 2.8235669259783e-08 747 2.09732727202556 2.28208523466063 1 3.76237140863645 2613 2361 1828 2535 2230 2507 2223 866 747 2179 2572 2127 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 7.97939875838995e-08 3.27123182997709e-07 3230 2079.45454545455 2230 7.25399913436612e-09 306 1.90502966516892 2.05126206189133 1 3.5667250466415 3227 1082 1027 1137 838 3450 3903 2230 2303 306 3371 2128 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 5.75899694681868e-05 6.30683656356941e-05 165 2195 2231 5.23558882463417e-06 43 1.28008686036681 1.28900770571373 1 1.55171033459351 161 2694 3430 2231 4393 590 43 1538 4080 2807 2178 2129 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 8.85300819963312e-07 1.35581436412292e-06 210 2133.18181818182 2232 8.85301172654401e-08 208 1.64249336220298 1.55357761633532 1 2.78219726773886 208 3546 4686 3225 3036 608 439 881 2232 2904 1700 2130 M9052 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM.html Phosphatidylinositol signaling system 67/77 KEGG 3.11195898445767e-07 6.12018600276674e-07 3070 2106.18181818182 2233 2.82905402241154e-08 300 1.47621272060519 -1.61036890193434 -1 2.64770096186179 3066 300 2933 2375 2233 2091 2856 1649 1407 3731 527 2131 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 1.84810697506451e-08 1.87190234384217e-07 2235 2277.45454545455 2234 1.68009726417228e-09 2 1.96603380180929 2.18815386286088 1 3.81860006123793 2234 3677 2104 4339 2 1656 1436 2493 1602 2391 3118 2132 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 2.08703768379828e-07 4.84679970737421e-07 1985 2356.36363636364 2234 1.89730716525988e-08 1627 2.11844068161669 -1.80740739525787 -1 3.86193497098703 1982 1627 1805 3648 1844 1852 2794 3227 2385 2234 2522 2133 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 1.65700223776353e-06 2.28886466556742e-06 2740 2276.27272727273 2236 1.50636680526408e-07 1073 1.90928846447025 2.24681789034722 1 3.10887341057205 2736 1637 2166 2552 3330 3159 2773 2236 1448 1929 1073 2134 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 3.3737426801836e-06 4.30962529105998e-06 1635 2410.81818181818 2236 3.06704350354051e-07 756 2.43147573608257 2.34246858273764 1 3.76642367373697 1634 3145 1467 3121 3631 1238 756 4487 3729 1075 2236 2135 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 6.83945581376609e-08 3.15009389627869e-07 3615 2340 2237 6.21768729672191e-09 511 2.16121675548463 2.11468913287727 1 4.05671897769564 3613 511 1487 974 686 3807 3994 3098 1138 2237 4195 2136 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 4.59674160600827e-07 8.09273419632937e-07 4030 2450.63636363636 2237 4.1788568786042e-08 237 2.12300088555303 -1.82894783611239 -1 3.73376125486405 4028 237 1495 1389 2534 3532 4094 2237 1607 1587 4217 2137 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 1.14769628368798e-07 3.59285478750119e-07 2530 2350 2237 1.0433603123282e-08 426 2.09501447714438 2.4567242027741 1 3.89787409209887 2530 426 1733 2731 1255 2220 3585 3927 2237 2192 3014 2138 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 1.92503529963589e-07 4.64778897147911e-07 2240 2493.54545454545 2237 1.75003224370872e-08 1256 2.51412900425468 2.60900041954818 1 4.5966582773437 2237 3600 1256 2169 1749 2921 2604 3055 2197 2097 3544 2139 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 7.70958395830693e-07 1.2133790024411e-06 815 2201.09090909091 2238 7.00871514547382e-08 815 1.87966205063147 1.88403679141872 1 3.21022246619701 815 2985 2630 2437 2870 1785 1458 1587 1530 3877 2238 2140 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 3.13625365938636e-07 6.15514231696617e-07 1325 2801.63636363636 2239 2.8511400968012e-08 1323 1.64539998180134 1.89978852484896 1 2.95007480225697 1323 4235 3266 4398 2239 2179 1654 2036 4251 3446 1791 2141 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 6.38184967293408e-08 3.14536172538656e-07 2165 2465.27272727273 2240 5.80168168914673e-09 599 2.04926316466208 2.06754806906858 1 3.84691786338803 2164 2980 1650 4429 599 2082 2481 2240 3528 1978 2987 2142 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 1.45785244148504e-07 4.03108583702953e-07 3155 2254.18181818182 2240 1.32532048917375e-08 783 2.95862547379161 -3.02336556799095 -1 5.46231627662285 3152 783 845 1799 1475 3015 2814 3374 2240 1175 4124 2143 M3342 BIOCARTA_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTEGRIN_PATHWAY.html Integrin Signaling Pathway 62/74 BioCarta 2.55444089364745e-07 5.42129542176978e-07 1755 2353.90909090909 2241 2.32221926386005e-08 978 1.72771040800264 1.98456347922114 1 3.12520103259455 1755 3029 2837 2241 2043 2872 2366 1994 978 4022 1756 2144 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 5.30553353326707e-07 9.07323125979006e-07 2210 2412.72727272727 2241 4.8232134661393e-08 1313 2.17124457193863 -1.68765434536749 -1 3.78748797644038 2207 2646 1789 4150 2615 1903 1313 2983 2541 2241 2152 2145 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 1.07080308428214e-06 1.58637493967724e-06 1710 2099.63636363636 2242 9.73457823157325e-08 771 3.31228703627962 2.93517021734774 1 5.54627717694095 1707 1799 771 1777 3077 2242 2311 2290 2581 1368 3173 2146 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 3.15172797965786e-07 6.1726788647241e-07 2630 2417.18181818182 2242 2.86520766470512e-08 1923 2.01124035847891 2.58211009375311 1 3.60547219140844 2626 2979 1923 2483 2242 2228 2442 2010 3597 1927 2132 2147 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 5.04340032251199e-08 3.0357704374324e-07 3385 1873.54545454545 2242 4.58490948920876e-09 368 1.84210482898809 2.05512298670107 1 3.46614168799757 3381 413 2653 1871 368 3048 2494 500 1045 2242 2594 2148 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 9.92653592025834e-08 3.41247265430585e-07 2040 2613.27272727273 2242 9.02412397104525e-09 1099 1.71771908698542 1.8664803550793 1 3.20683906935128 2036 4355 3585 3995 1099 1865 1846 1704 2242 3670 2349 2149 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 1.19794093881248e-06 1.74085013275705e-06 2530 2312.27272727273 2243 1.08903781010374e-07 1547 1.86155200990686 -2.19396876908477 -1 3.09501560483917 2527 1547 2647 1950 3147 2040 2085 2243 3111 2543 1595 2150 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 3.58215713860645e-43 8.8988324706434e-41 35 1892.81818181818 2244 3.25650648964225e-44 12 2.99335141187007 3.24585013991458 1 34.6178501012219 3229 1118 12 34 1185 2972 3493 2244 2517 31 3986 2151 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 2.60480917584818e-06 3.42470732869176e-06 400 2132.18181818182 2244 2.36801114541656e-07 396 1.72645730398504 2.0057791714964 1 2.72384293970504 396 3279 2897 2244 3518 1051 697 1582 2496 3590 1704 2152 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 6.29663222285906e-07 1.0355436965817e-06 2715 2428.45454545455 2245 5.72421275002035e-08 1702 1.80594228035086 1.83134683499437 1 3.12017798963469 2711 1702 2219 3296 2733 2866 1878 2921 2151 1991 2245 2153 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 4.4320839591284e-07 7.87036730138677e-07 3700 2244.81818181818 2245 4.02916804728094e-08 665 1.62813421036845 1.86154630976311 1 2.86891813830321 665 2946 3696 2245 2507 1359 1430 1753 2274 3698 2120 2154 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 4.01966390813787e-07 7.29415512201235e-07 2820 2130.90909090909 2246 3.65424058416262e-08 603 2.84233176826761 3.1677605766162 1 5.03618683015136 2816 603 1356 2540 2440 2246 1813 3484 1169 1557 3416 2155 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 5.85757286420979e-08 3.10127287236487e-07 1015 2403.54545454545 2246 5.85757301861001e-09 614 1.69813117932923 1.98611320801203 1 3.19062448975499 1011 4095 4392 1310 614 2409 2246 2052 1771 4006 2533 2156 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 8.14690412868374e-07 1.2703836641158e-06 2250 2226.27272727273 2246 7.40627922326958e-08 1436 1.64762421642326 1.61312702558067 1 2.80433898000024 1436 2232 2520 2871 2902 1755 2247 1762 2967 1551 2246 2157 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 2.21955685248806e-08 2.16452651730241e-07 3290 2133.27272727273 2247 2.01777897716448e-09 7 2.55829750317501 -1.15448018124076 -1 4.92260524626605 3289 2391 1900 3066 7 4093 2716 773 1043 1941 2247 2158 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 4.39865337517049e-08 2.97677410474742e-07 1475 1953.90909090909 2247 3.99877587556058e-09 255 1.94274893606615 2.40986089292529 1 3.66034413334994 1473 1487 2247 899 255 2516 2950 2783 1120 3036 2727 2159 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 3.38668869852933e-06 4.32382219557978e-06 720 2008.09090909091 2248 3.07881264729321e-07 326 1.69638896127723 -1.85549931227838 -1 2.62679370855305 720 2604 2677 2435 3633 508 861 2248 3961 2116 326 2160 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 5.31833435852176e-08 3.06874196014832e-07 3365 2389.54545454545 2248 4.83484953371679e-09 410 1.8583471612528 -1.9851644847492 -1 3.49419364059114 3361 1569 1846 2770 410 3234 3616 2118 4403 710 2248 2161 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 6.40958325479226e-07 1.04973049835598e-06 2825 2164.36363636364 2248 5.82689556562827e-08 454 3.02681395597969 -3.26865294655851 -1 5.22493007436097 2825 3137 1645 1821 2745 3305 2248 758 454 3019 1851 2162 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 1.89950897768116e-06 2.59180037562929e-06 575 2080.72727272727 2249 1.72682783431292e-07 321 1.59017225949808 1.66775315143057 1 2.5643285824579 571 2981 3618 2249 3379 478 321 1616 2993 3153 1529 2163 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 1.06568491617408e-07 3.48348225330125e-07 1910 2091.81818181818 2249 9.68804516178272e-09 1175 1.6197860792216 1.68476989079193 1 3.01977352796917 1909 1585 3017 1712 1175 2256 2356 2249 1329 2757 2665 2164 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 3.17300416837395e-07 6.19797131312732e-07 2790 2257.45454545455 2249 2.88454966000762e-08 442 2.25320274298732 -2.40405706165788 -1 4.03817688247424 2786 2426 2058 1451 2249 2622 2181 2659 4355 1603 442 2165 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 3.46982267538244e-07 6.57407624356902e-07 800 2530.63636363636 2250 3.46982321716767e-08 800 1.70549640536248 1.92043509560093 1 3.04377104142456 800 3832 4328 2696 2397 1719 1596 1929 2250 4482 1808 2166 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 8.20079006468102e-08 3.27411388472988e-07 1860 2060.36363636364 2250 7.45526397306936e-09 502 2.24095371757789 2.3694791305613 1 4.1955691083572 1856 2566 1222 3853 874 2250 2636 502 3399 1230 2276 2167 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 3.29923776446285e-06 4.23163104572409e-06 560 2235.54545454545 2251 3.29924266270951e-07 558 1.50163916422633 1.56002830053366 1 2.32919087603547 558 2939 4420 2251 3663 1160 1053 1364 3107 2334 1742 2168 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 3.1804267196087e-07 6.20827713670515e-07 575 2209.72727272727 2251 2.8912974358061e-08 258 1.75887660581341 1.84114349740826 1 3.15169301574601 575 4106 3636 4629 2251 258 454 954 2669 4147 628 2169 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 3.60764852836704e-06 4.57375800534311e-06 1595 2135.63636363636 2251 3.27968585849804e-07 849 2.53307287009666 2.40973501921033 1 3.90494013433676 1593 2251 1515 2542 3658 1350 849 2885 1494 2292 3063 2170 M19829 BIOCARTA_AGPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGPCR_PATHWAY.html Attenuation of GPCR Signaling 18/21 BioCarta 8.16963128913079e-08 3.27411388472988e-07 1370 2171.63636363636 2254 7.42693781137046e-09 485 1.08083578704379 1.20503111619599 1 2.02312165850269 1369 3163 3462 2663 870 989 485 2254 3746 3993 894 2171 M1909 BIOCARTA_EGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EGF_PATHWAY.html EGF Signaling Pathway 49/53 BioCarta 3.20145629183431e-07 6.24158351815693e-07 1570 2296.54545454545 2254 2.91041523428426e-08 230 1.36495596957037 -1.48420641918097 -1 2.44472634515664 1568 2662 3559 230 2254 1716 2178 2561 2989 4021 1524 2172 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 4.13102324124476e-07 7.43080400101953e-07 445 1853.09090909091 2254 3.75547637903893e-08 80 1.18753753721715 -1.11153792778586 -1 2.10087326287807 444 2254 3568 2953 2467 80 178 600 4431 3157 252 2173 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 3.18487261835272e-06 4.1027835039915e-06 630 2257.63636363636 2255 2.89534293545874e-07 630 1.73839776496561 1.74457419578407 1 2.70330396936081 630 3283 3175 3155 3601 1260 889 2255 2987 2195 1404 2174 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 2.99218327847049e-08 2.65971846975155e-07 2075 2301.54545454545 2255 2.72016665378789e-09 46 2.27151438678553 2.23973472024497 1 4.31200049681576 2858 2255 2074 3824 46 2973 2270 2074 1605 2114 3224 2175 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 3.89803152644598e-07 7.14984191427816e-07 235 2158 2255 3.89803221020538e-08 233 1.66708799849822 1.82841959916758 1 2.95765230250843 233 3833 4561 3229 2484 651 534 728 2255 4002 1228 2176 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 1.36885291755059e-07 3.90391889476665e-07 4040 2324.72727272727 2256 1.24441182065585e-08 130 2.16461356252473 -1.88830848435893 -1 4.00485464127044 4040 130 1686 2256 1417 3329 3409 3667 714 1770 3154 2177 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 3.09648529459701e-07 6.10722425900902e-07 2230 2609.27272727273 2257 2.81498702765939e-08 896 0.99010823024775 -0.830417344382303 -1 1.77581482497157 2230 2776 3782 2479 2224 1591 896 2257 4026 4206 2235 2178 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 2.00519602167763e-06 2.71501010393528e-06 2095 2568.09090909091 2257 1.82290713574669e-07 680 1.99674704839092 1.07018807060921 1 3.20856585756791 2094 1865 2257 3583 3407 2090 1348 3426 680 3195 4304 2179 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 1.68049353193011e-07 4.30615063556468e-07 4275 2761 2258 1.52772150936039e-08 517 1.97172134399112 1.98642177778669 1 3.6236505448332 4271 2258 2244 1205 1629 4329 3774 4416 517 2019 3709 2180 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 2.61866330638498e-07 5.50603299046416e-07 2260 2469.09090909091 2258 2.38060328916811e-08 1055 2.64749857908398 2.80764474067005 1 4.78428599127748 2258 3645 1062 3407 2065 2058 2053 2569 3841 1055 3147 2181 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 5.74965942164888e-08 3.09093308316432e-07 2410 2114.63636363636 2258 5.74965957041251e-09 224 3.59859957295249 -2.50370840872397 -1 6.7638921731219 2410 906 4646 3818 587 2258 1803 224 3535 2476 598 2182 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 2.51131560620559e-08 2.37068193225807e-07 2380 1873.27272727273 2259 2.2830142135204e-09 19 2.33611754925198 -2.60237601336534 -1 4.46836472696991 2379 2428 2202 2832 19 3063 2259 1854 457 2443 670 2183 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 5.08923887981867e-08 3.0357704374324e-07 2765 1967.54545454545 2259 4.62658090686143e-09 297 2.12572234697052 2.09978554978887 1 3.99993475648649 2764 297 1557 3053 374 3094 3433 916 1528 2368 2259 2184 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 3.22088246340307e-07 6.26651493291941e-07 4120 2313 2260 2.92807539541131e-08 101 2.67588612400454 2.65151263177468 1 4.79217834708589 4119 101 786 849 2260 3861 3736 2914 495 1605 4717 2185 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 3.09747703491145e-07 6.10722425900902e-07 3940 2577 2261 2.81588861001726e-08 1297 2.12345062082068 1.95376517833708 1 3.80951410410886 3936 1507 1379 3039 2225 2884 2261 4385 1953 1297 3481 2186 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 2.79220104284832e-07 5.70774747606933e-07 4630 2769.63636363636 2262 2.53836490657236e-08 819 1.63993820300736 -1.78975949311147 -1 2.95579939729185 4627 1898 2378 878 2131 4596 4643 819 1728 2262 4506 2187 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 4.18451946449541e-08 2.95100601223086e-07 2840 1952.90909090909 2262 3.80410867644295e-09 357 2.25802998960367 2.6676164147476 1 4.2569686666095 2837 1316 400 383 2607 2262 3043 3155 2025 357 3097 2188 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 6.75689969500992e-08 3.14536172538656e-07 4265 2631 2263 6.14263627503254e-09 211 1.73359002058304 -1.82061887015939 -1 3.254197233457 4261 211 2263 840 670 4318 4223 4548 1820 1445 4342 2189 M15743 ST_GA12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA12_PATHWAY.html G alpha 12 Pathway 44/52 Signaling Transduction KE 2.84721747344615e-07 5.77024553420288e-07 4095 2566.09090909091 2264 2.58837985630017e-08 1104 2.05428247804715 -1.70023063800431 -1 3.70001918673996 4095 1699 2264 1104 2152 3733 2909 2653 2042 1955 3621 2190 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 1.33891570142837e-06 1.90869287548835e-06 1095 2250.18181818182 2265 1.21719683299141e-07 1095 1.74801282310864 -1.38411929562633 -1 2.88601510775859 1095 2172 2343 1509 3216 1217 2399 2265 4268 2726 1542 2191 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 1.19782919527795e-10 1.7342803072736e-09 3030 2256.18181818182 2267 1.08893563213016e-11 161 2.3232940704853 2.42939001983958 1 5.87667594482403 3030 2019 290 1332 1171 2267 3432 4234 3365 161 3517 2192 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 3.26234978011823e-07 6.31854368574397e-07 1150 2127.18181818182 2267 2.96577296717064e-08 984 1.8733780624947 2.00422814138523 1 3.35278561556321 1146 2958 2923 2572 2272 1629 1682 984 1031 3935 2267 2193 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 1.32743182031056e-07 3.83038247822062e-07 1220 2176.27272727273 2267 1.20675627309536e-08 587 1.61177895920571 -1.42505294362163 -1 2.98565280653983 1216 2267 3321 3889 1390 587 1553 2478 2700 3750 788 2194 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 1.50479232337026e-06 2.09950333027124e-06 2270 2254.54545454545 2267 1.36799395694904e-07 640 2.12034259001806 1.86940583709289 1 3.47558837386172 2267 640 1761 2741 3294 2625 2935 1136 3545 1619 2237 2195 M4741 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS.html Systemic lupus erythematosus 54/146 KEGG 1.72257746978558e-07 4.36189144709654e-07 1655 2477.27272727273 2268 1.5659796406015e-08 973 2.09868768758593 -2.58109576609486 -1 3.85366107080064 2268 1651 1435 4392 1653 2323 2795 3582 4153 973 2025 2196 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 3.24666022630685e-07 6.29849415050075e-07 2840 2328.09090909091 2268 2.95150973221304e-08 1064 2.08237624046074 -2.35404444466773 -1 3.72775581945468 2840 2340 2077 1425 2268 4049 4086 1064 2906 1351 1203 2197 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 1.10959873076408e-06 1.63080159518251e-06 655 2521.27272727273 2268 1.00872662764099e-07 654 1.6190534379675 1.65909352084089 1 2.70498449977726 654 3236 3783 2250 3103 1796 1941 2130 2268 4078 2495 2198 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 0.00196554850062631 0.00203095204092736 445 2339.36363636364 2269 0.000178846071137823 442 1.25464300997724 1.25464300997724 1 0.974548480919264 442 2883 2880 1968 4556 1230 766 2269 4347 1827 2565 2199 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 1.36603539818744e-06 1.94207442151949e-06 4430 2506.81818181818 2269 1.24185113308541e-07 575 3.02079227647922 3.10198861343014 1 4.98146635394062 4426 2269 834 575 3229 4260 4460 2596 1446 1361 2119 2200 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 3.24925178550311e-07 6.30093197517447e-07 4345 2084.81818181818 2269 2.95386569581436e-08 203 2.93230940672298 2.85928466499982 1 5.24946884188833 4345 583 800 511 2269 3214 3221 3325 203 1355 3107 2201 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 5.50244412361428e-08 3.07843567066819e-07 3295 2361.54545454545 2270 5.00222205566954e-09 446 2.03720201240554 -1.63875640483785 -1 3.82976611272201 3294 1600 2270 2132 446 3679 3386 2122 2212 2309 2527 2202 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 2.48775537397715e-07 5.3337783307865e-07 2730 2055.63636363636 2270 2.2615960502655e-08 605 2.66756117277151 2.63215841391816 1 4.83118061787238 2727 2270 1417 2531 2020 2908 2769 1039 605 1806 2520 2203 M1296 BIOCARTA_IL7_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL7_PATHWAY.html IL-7 Signal Transduction 25/27 BioCarta 3.30632736374575e-07 6.37755012541068e-07 2340 1832.36363636364 2271 3.00575260058716e-08 584 2.24285206316685 -2.31684475982982 -1 4.01158877186421 2339 689 2026 868 2281 2551 2887 584 1175 2271 2485 2204 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 1.78271048333836e-06 2.44391329693786e-06 1795 2457.90909090909 2271 1.62064720719201e-07 899 2.36850795798256 2.88154773046136 1 3.83735379677522 1791 2810 2113 4361 3358 2271 1153 1615 4062 2604 899 2205 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 9.80588772073794e-08 3.40572406489206e-07 3915 2478.09090909091 2272 8.91444377982556e-09 74 2.34534974485669 2.6248122634149 1 4.37947041765847 3915 74 923 2272 1081 3092 3900 4420 1778 1133 4671 2206 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 6.90500549042878e-08 3.15009389627869e-07 2275 2118.81818181818 2273 6.27727791559271e-09 335 2.33693134061096 -2.90710085027999 -1 4.38661464297157 2273 335 1057 3089 696 2398 3383 4172 3021 1125 1758 2207 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 2.143921347317e-05 2.43428163563537e-05 2090 2735.27272727273 2274 1.94903840029418e-06 1653 1.79159664998623 -2.41214844952163 -1 2.38599549389686 2089 3437 2240 3199 4122 2069 2274 2883 3870 2252 1653 2208 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 1.11633655392967e-05 1.3126827440329e-05 1935 2502.45454545455 2274 1.01485656231687e-06 836 3.22861084746014 3.22463002747603 1 4.55051455770343 1933 2734 836 2130 3970 2274 1532 4282 3496 1158 3182 2209 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 1.06642769520203e-07 3.48348225330125e-07 2445 2189 2275 9.69479769905486e-09 1177 1.92028964932421 2.00422979171428 1 3.58016330331241 2445 1307 1914 1792 1177 2691 2605 2275 2387 1894 3592 2210 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 5.92080160910482e-07 9.88527179765794e-07 2275 2130.09090909091 2275 5.38254836595913e-08 403 2.10886034862285 2.43859248947661 1 3.65597142040741 2275 1933 2132 3071 2691 2699 3017 1050 403 2620 1540 2211 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 5.29780667148582e-07 9.06330101102322e-07 2915 2035.72727272727 2276 4.8161890429526e-08 806 2.47882502275696 2.95884057272223 1 4.32448934720698 2911 3045 1503 2888 2614 2276 1567 1002 1499 2282 806 2212 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 7.78746765898736e-07 1.222049983644e-06 2280 2295.63636363636 2277 7.07951855960349e-08 145 2.63703301044377 -1.5359196167022 -1 4.50170741249045 2277 3124 2124 2428 2879 1126 1180 1862 145 3721 4386 2213 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 4.8372010023997e-07 8.41872740830627e-07 410 2114.90909090909 2277 4.39745642360803e-08 245 1.13735747398058 -1.14134522703792 -1 1.99425898885786 407 1698 3593 2924 2567 245 488 2277 4389 3749 927 2214 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 8.81275862957977e-06 1.0490850121467e-05 380 2257.90909090909 2280 8.0116308472007e-07 376 1.31705258967887 1.35778272237462 1 1.89281258982945 376 3245 4038 2506 3918 993 858 1298 3814 2280 1511 2215 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 6.11984111219596e-07 1.01175656916164e-06 2605 2268.09090909091 2281 5.56349346780087e-08 417 2.47685221787468 2.57699263022126 1 4.28686655693046 2605 2148 528 2281 2716 2209 2901 3332 3697 417 2115 2216 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 2.4166240257753e-06 3.20676564567315e-06 405 2066.45454545455 2282 2.19693334577947e-07 67 1.08010231684746 -1.09744602335435 -1 1.71266854697169 402 2282 3613 2945 3486 67 184 1367 4496 3518 371 2217 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 6.81540258656042e-08 3.15009389627869e-07 3435 2182.54545454545 2283 6.19582072517773e-09 679 1.77723025066591 -1.53912444502856 -1 3.33580282054751 3432 1119 2112 1462 679 2283 3449 3239 2391 918 2924 2218 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 1.69287907317814e-07 4.32146523818324e-07 4710 2857.36363636364 2284 1.53898109403962e-08 329 2.00608847856466 -2.03866908252988 -1 3.68593269713624 4708 329 1892 2284 1638 4229 3592 4642 2170 1796 4151 2219 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 7.32189808108086e-08 3.2144561803028e-07 3115 2166.27272727273 2286 7.32189832232673e-09 4 2.18156839191839 3.2036790351891 1 4.08939462789077 3112 919 4360 2286 852 4158 3955 52 4 3472 659 2220 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 5.06352428655531e-06 6.26963133067709e-06 2220 2597.36363636364 2287 4.60321449164566e-07 1339 2.69354435774947 2.66389275924322 1 4.04584043462701 2218 3502 1871 1722 3758 2287 1339 2750 4625 2081 2418 2221 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 7.15284483359308e-06 8.62243564729264e-06 125 2090.63636363636 2287 6.50260735426729e-07 123 1.32094283645827 1.36409157135148 1 1.93089745925026 123 2535 3948 2685 3862 686 536 1329 3405 2287 1601 2222 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 1.23338767596391e-06 1.78466886282944e-06 2290 2233.27272727273 2287 1.23338836052477e-07 180 2.5941340837742 3.29785640001625 1 4.30525781225148 2287 903 4644 3559 3224 2649 3741 180 1126 1595 658 2223 M5785 KEGG_TASTE_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TASTE_TRANSDUCTION.html Taste transduction 33/88 KEGG 1.66946332393942e-07 4.29439298099957e-07 3945 2637.81818181818 2288 1.51769404602377e-08 934 2.74547715790209 -2.74798576272289 -1 5.04694664247082 3944 2288 1240 1378 1621 4392 4684 3856 934 2054 2625 2224 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 8.4434062947542e-07 1.30708027914857e-06 1400 2292.90909090909 2288 7.67582685023722e-08 796 1.72642706798466 1.82924604718045 1 2.93234107158182 1397 2655 2476 4163 2931 1449 1749 796 3656 2288 1662 2225 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 5.12696630770037e-08 3.0357704374324e-07 2290 2048.36363636364 2288 4.66087857016473e-09 380 2.4047581744407 2.78460566793616 1 4.52510468119075 2288 3035 1666 2529 380 2519 2777 1176 2183 2484 1495 2226 M7747 BIOCARTA_IL2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL2_PATHWAY.html IL 2 signaling pathway 34/41 BioCarta 3.33681331796782e-07 6.4099386103601e-07 1770 2642.63636363636 2289 3.03346711279411e-08 1583 1.40713740031982 -1.33935817815438 -1 2.51560587875973 1770 3701 3535 2492 2289 1583 1598 1722 4332 3925 2122 2227 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 6.60833315811024e-08 3.14536172538656e-07 2585 2142.36363636364 2290 6.00757577873688e-09 452 1.96156190635905 2.41901000083563 1 3.68224644283127 2585 1236 2290 452 643 3488 3715 1888 1190 3726 2353 2228 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 2.85692741590162e-07 5.78742377813548e-07 3655 2539.36363636364 2290 2.59720707900296e-08 1127 2.57166012912112 2.63094309661804 1 4.6311391554841 3652 1761 1127 2290 2154 3766 3035 1952 2786 1463 3947 2229 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 7.20960832904361e-08 3.19205379884722e-07 4140 2762.45454545455 2291 6.55418960482665e-09 742 1.8239027381088 1.91733376771422 1 3.42040150472406 4138 1086 1984 2291 742 4413 4613 3204 2247 1229 4440 2230 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 2.76090185767084e-07 5.68167826037923e-07 1175 2643.63636363636 2291 2.50991109468343e-08 1041 1.27532817585898 -1.19545591414758 -1 2.29917255298476 1175 3272 3882 4631 2117 1041 1614 2291 3367 3964 1726 2231 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 2.36716723505147e-07 5.21517711362731e-07 1815 2142.81818181818 2294 2.15197044523198e-08 768 3.36341118824599 3.42424557322613 1 6.10113394346989 1815 2791 768 2294 1963 2708 2540 1988 2940 967 2797 2232 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 6.16439162865019e-07 1.01734015689612e-06 1380 2164.18181818182 2297 5.60399395991915e-08 563 2.39769688920673 -2.5897515601837 -1 4.14818433194281 1379 1532 697 2297 2721 2486 3723 2205 3654 563 2549 2233 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 1.64356146707055e-06 2.27229353385267e-06 3275 2237.72727272727 2299 1.49414790448444e-07 718 2.13554752982123 -2.22845029878654 -1 3.47933664312586 3271 718 1707 3038 3328 3531 2928 1366 2299 1266 1163 2234 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 6.44961156159857e-07 1.05518774941925e-06 4030 2570.18181818182 2300 5.8632849567221e-08 1274 1.95280353014925 -1.90203939716123 -1 3.36938224154988 4027 1758 1785 2300 2749 2887 3025 2216 1274 1989 4262 2235 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 5.44736923363091e-08 3.06874196014832e-07 2815 2195.27272727273 2301 4.95215397137451e-09 204 2.28800144840131 2.74139765576216 1 4.3022586678004 2811 204 1013 1617 436 4215 4536 2301 2758 1540 2717 2236 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 5.0053582477517e-07 8.65395272138755e-07 1855 2362.36363636364 2302 4.5503267150478e-08 872 2.52300473148938 2.58727647656723 1 4.41620283691235 1853 2274 872 2302 2583 1584 2664 3647 4193 1137 2877 2237 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 3.40107379239131e-07 6.49538261636117e-07 3090 2201.81818181818 2303 3.09188574379812e-08 195 2.57052968561845 2.75391606183541 1 4.59190050963186 3089 2606 1236 195 2303 3576 3398 1629 865 1612 3711 2238 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 1.65989737992868e-07 4.2834032897358e-07 1265 2665.45454545455 2303 1.50899773197069e-08 1265 1.42622080176165 -1.4698493161529 -1 2.62183286590892 1265 4243 3190 4040 1614 1413 1477 2102 4334 3339 2303 2239 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 2.23251249093758e-07 5.03221535684115e-07 4485 2853.81818181818 2304 2.02955701589832e-08 685 1.83169373971942 2.10479950856342 1 3.33045261163469 4481 685 1912 2304 1906 4446 3661 4221 1214 2177 4385 2240 M2587 BIOCARTA_HSP27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HSP27_PATHWAY.html Stress Induction of HSP Regulation 18/25 BioCarta 6.03056667839096e-06 7.3722545252539e-06 3505 2421.18181818182 2305 5.48234837203889e-07 155 3.13427553498728 3.65218989016852 1 4.64430300890693 3502 1870 1759 2171 3807 3712 3122 1506 155 2305 2724 2241 M13748 REACTOME_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCONEOGENESIS.html Genes involved in Gluconeogenesis 32/48 Reactome 6.50514276700178e-07 1.06279937210967e-06 1725 2397.72727272727 2305 5.91376790045204e-08 1236 1.27902298128988 -1.47271106643668 -1 2.20538601102797 1722 2305 3269 3423 2751 1378 1613 1236 3511 3353 1814 2242 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 5.4552321484934e-08 3.06897446256125e-07 3560 2410 2305 4.9593020761492e-09 438 2.12606692484323 2.27634520992343 1 3.99768285372156 3560 1071 939 2305 438 4227 4319 2670 1985 1054 3942 2243 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 5.58346032036493e-08 3.07843567066819e-07 3900 2589.45454545455 2307 5.58346046065256e-09 201 1.8673317001491 2.13701502279523 1 3.51035258628842 3896 951 4493 201 560 4656 4328 1865 2307 1375 3852 2244 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 2.71607035328027e-08 2.51369648382017e-07 3775 2278.72727272727 2307 2.46915489710205e-09 25 1.73858671818787 -1.26954091158112 -1 3.31245689060568 3772 1451 2983 1500 25 1579 2307 3313 1134 2789 4213 2245 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 3.41429731054449e-07 6.50806317028999e-07 4130 2470.63636363636 2309 3.10390712766146e-08 19 2.0349992858137 -2.90031071454505 -1 3.63457134575039 4126 1888 2495 1850 2309 3815 3632 1313 19 3549 2181 2246 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 4.2047230165917e-08 2.95100601223086e-07 4450 2489.36363636364 2310 3.82247554268541e-09 216 2.07508152815389 2.34878373743162 1 3.91199386578258 4447 744 1989 2310 216 3745 2772 3776 4049 1723 1612 2247 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 3.41793263915254e-07 6.50806317028999e-07 2135 2398.09090909091 2311 3.10721197287694e-08 1458 1.82772867993284 2.14959179643456 1 3.26429193711235 2134 3581 2852 2656 2311 1808 1915 2556 1536 3572 1458 2248 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 2.19247576208732e-07 4.97045417725848e-07 3715 2903.09090909091 2311 1.99315998235007e-08 1856 2.14371605727577 -2.19075022901297 -1 3.90124967489466 3712 2158 1856 2301 1892 3822 4394 4386 2236 2311 2866 2249 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 5.5110728118301e-08 3.07843567066819e-07 2550 2047.36363636364 2312 5.51107294850375e-09 139 1.97895344285284 2.16220709509801 1 3.72023914027227 2549 962 4688 139 548 1976 2844 2751 2312 562 3190 2250 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 1.19001172530963e-07 3.66635466283385e-07 3465 2300.18181818182 2313 1.08182889970826e-08 225 2.08494427104687 -1.99056643294111 -1 3.87383887456275 3463 225 1893 1494 1287 3022 3350 4348 683 3224 2313 2251 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 2.97479602187639e-07 5.9622238739943e-07 1800 2675.63636363636 2313 2.70436038556585e-08 1796 2.07129518849557 2.20728530302385 1 3.72216672256557 1796 4134 1934 3427 2186 2005 2159 2486 3520 2313 3472 2252 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 7.7879795567821e-07 1.222049983644e-06 2225 2452.27272727273 2313 7.07998392156454e-08 616 3.11267723613521 3.71443193113612 1 5.31384014343523 2224 2313 616 1392 2880 2500 4656 3173 4168 1166 1887 2253 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 6.53369299006049e-16 1.91546775857674e-14 2650 1775.18181818182 2314 5.93972090005497e-17 93 2.42256391521997 2.59388920245745 1 9.59537162531745 2648 1087 118 505 411 2594 2923 3165 2314 93 3669 2254 M12 PID_RHOA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHOA_PATHWAY.html RhoA signaling pathway 18832364 58/67 Pathway Interaction Database 9.16907731294093e-07 1.39409991703335e-06 4210 2738.36363636364 2315 8.33552830399702e-08 648 1.97496816317431 2.24145319317582 1 3.33864915844532 4209 2198 2300 2182 2989 4123 3445 2307 648 2315 3406 2255 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 2.52342191349137e-07 5.3772241226543e-07 3830 2465.18181818182 2315 2.2940201844822e-08 1152 2.72080168442022 2.53192901895662 1 4.92485285808068 3827 1752 1152 1934 2034 2722 3201 3848 3022 1310 2315 2256 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 1.89699105865986e-07 4.60823355474758e-07 3675 2666.63636363636 2316 1.72453747475589e-08 367 2.14597544154942 2.25361978170859 1 3.92572603646022 3672 367 1658 2316 1736 4013 4423 4059 858 1760 4471 2257 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 2.21427883535789e-06 2.96577641966209e-06 1320 2118 2317 2.01298278546488e-07 578 1.91767796931232 2.30008673398309 1 3.06022995700053 1317 3493 2449 3417 3452 1197 605 578 3743 2317 730 2258 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 1.58616233153092e-07 4.19892664320018e-07 2770 1775.90909090909 2317 1.44196585990047e-08 412 3.07521756337482 -2.85102758984648 -1 5.66187430039307 2769 412 456 817 1567 2317 2431 2821 2324 793 2828 2259 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 3.37025939900205e-07 6.46203257714034e-07 2320 2403.27272727273 2318 3.06387265027669e-08 284 2.6243490826507 2.76913089548361 1 4.6897537269257 2318 3486 1948 3599 2293 3423 3660 913 284 2992 1520 2260 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 9.0171852189301e-08 3.31989970618955e-07 1305 2686.72727272727 2318 8.19744144410849e-09 988 1.58164567538995 -1.47793592504088 -1 2.95818825884204 1304 3554 4018 4061 988 2061 2488 1926 2318 4524 2312 2261 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 8.63489160394527e-08 3.28305665915602e-07 4110 2357 2318 7.84990176623684e-09 185 1.94592907405769 1.97854763181877 1 3.64243761976039 4109 185 1784 2318 943 4484 4465 1213 728 2435 3263 2262 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 1.28879023513033e-05 1.50273960222707e-05 2920 2481.18181818182 2318 1.17163435009325e-06 1249 2.52278636910648 3.63581896791878 1 3.51273325149169 2918 3126 2125 2216 4002 2697 1961 1249 1959 2722 2318 2263 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 4.44610535070348e-08 2.98029714805608e-07 4150 2458.09090909091 2319 4.04191403687031e-09 246 2.94796182850763 -3.10670461947323 -1 5.55427974385141 4149 1905 1521 975 263 3954 4339 3456 246 2319 3912 2264 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 3.44458623626114e-07 6.54000282990852e-07 3175 2080.72727272727 2319 3.13144252326124e-08 507 2.37166382111436 -1.85005750479992 -1 4.23455094502835 3172 611 1320 567 2319 2470 4232 3215 507 1617 2858 2265 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 6.93754002322491e-08 3.15197676064735e-07 2580 2490.09090909091 2319 6.30685476545017e-09 701 1.95408840807165 2.23133126370661 1 3.66769905507728 2580 2066 2097 4374 701 1214 2036 3713 3721 2570 2319 2266 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 3.08170717274901e-07 6.09114650560107e-07 2020 2398.09090909091 2320 2.80155236766113e-08 904 2.27906726382391 2.61342125312239 1 4.08951010811638 2018 3340 2368 2320 2220 2763 4299 1713 904 3383 1051 2267 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 9.9187524536315e-08 3.41247265430585e-07 2980 2264.36363636364 2321 9.01704809165534e-09 1096 2.32393316844494 -2.39181859186535 -1 4.33889445744052 2977 1593 1669 1699 1096 2420 2321 3978 2014 2814 2327 2268 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 7.70977165577351e-08 3.24764325922831e-07 4590 2563.81818181818 2322 7.00888356905269e-09 19 2.15268406964642 -1.81326514641891 -1 4.03246605073296 4589 19 1001 873 804 4357 4621 3427 2322 1491 4698 2269 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 1.89644809482026e-07 4.60823355474758e-07 3930 2375 2324 1.72404387118023e-08 81 2.66723120222361 3.16178876035431 1 4.87949104321739 3928 826 1921 609 1735 4549 3937 2324 81 2439 3776 2270 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 3.19838277296203e-05 3.56888101380161e-05 1290 2444.90909090909 2324 2.90766297484389e-06 782 1.85872105107344 2.02840232505761 1 2.38623796617447 1287 2370 2324 3871 4198 1227 782 2892 3720 2178 2045 2271 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 1.06584731078781e-07 3.48348225330125e-07 4715 2457.63636363636 2325 9.68952147659601e-09 540 2.69579756756221 2.17452124128359 1 5.02635812865142 4711 540 896 1579 1176 4217 4468 2325 2667 1911 2544 2272 M3624 KEGG_GLYCOSAMINOGLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_DEGRADATION.html Glycosaminoglycan degradation 22/28 KEGG 3.41857561260752e-07 6.50806317028999e-07 2480 2345.90909090909 2326 3.10779649438129e-08 297 1.84796348133491 2.27078165836865 1 3.30044047957076 2479 1835 2512 2326 2312 3502 4179 1606 297 2528 2229 2273 M11773 REACTOME_PECAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PECAM1_INTERACTIONS.html Genes involved in PECAM1 interactions 16/17 Reactome 1.77315340585697e-06 2.43151774423152e-06 2330 2347.54545454545 2326 1.61195894089334e-07 1248 2.31091559776889 2.07037100823992 1 3.74549786489598 2326 2397 1651 1248 3356 2504 1674 2204 3901 1582 2980 2274 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 1.35184739700318e-06 1.9236417587745e-06 1725 2258.36363636364 2326 1.22895293425618e-07 798 1.52588004790794 -1.83435114856048 -1 2.51766572096227 1724 861 2477 3163 3222 1497 798 4475 3229 2326 1070 2275 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 2.17061749832333e-06 2.91308347798866e-06 2145 2854.09090909091 2328 1.9732905817761e-07 1065 0.892283460751963 1.05145333308193 1 1.42545113985445 2143 3690 3927 2033 3445 2328 1874 2125 4225 4540 1065 2276 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 1.86127032344311e-07 4.56373814371506e-07 1785 2349.63636363636 2329 1.69206407355686e-08 1146 1.26218906215831 1.37755452355584 1 2.31015833487822 1782 2345 3404 2671 1720 1616 1146 2329 2892 3631 2310 2277 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 6.00082187676869e-07 9.9767098479564e-07 1215 2404.54545454545 2329 5.45529410325571e-08 319 2.31182461801534 2.00424917158173 1 4.00524865523048 1211 3128 2067 3878 2702 723 319 3462 4422 2329 2209 2278 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 7.02659241945004e-08 3.15977748626312e-07 3310 2424.63636363636 2329 6.38781149442978e-09 716 1.97943042133954 2.07944755879621 1 3.71466196776228 3307 1126 1492 1703 716 3335 4140 3321 2329 1548 3654 2279 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 2.08884527004747e-07 4.84679970737421e-07 2980 2210.27272727273 2329 1.89895042579833e-08 656 2.3743343048439 -2.04640521994974 -1 4.32853521536946 2979 656 1796 2329 1846 2635 3267 3415 780 2414 2196 2280 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 5.00978081883755e-05 5.50166716261359e-05 460 2083.72727272727 2331 4.55444991259617e-06 99 1.33764212552449 1.33764212552449 1 1.64442913960004 458 3152 3550 2939 4270 416 99 831 2331 3889 986 2281 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 8.59376513471856e-08 3.28305665915602e-07 1410 2399.18181818182 2331 7.81251406401192e-09 322 1.3479239141606 1.30484643455287 1 2.52281224566352 1407 3390 3322 4439 937 1229 322 2331 4529 2509 1976 2282 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 1.01980261262046e-07 3.44497378011726e-07 1870 2290.72727272727 2332 9.27093327175522e-09 1123 1.91321711022634 1.60476816897905 1 3.56964132320855 1868 2783 2357 3577 1123 1957 2158 2559 2427 2332 2057 2283 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 3.0600504578937e-06 3.9538566003992e-06 2335 2493.36363636364 2332 2.78186792202198e-07 1327 2.13545537120849 2.26601235041007 1 3.33084894033282 2332 2197 1465 2536 3589 2865 2331 4001 1327 1444 3340 2284 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 2.22648947199402e-07 5.02343704962323e-07 3835 2575.36363636364 2333 2.02408154302168e-08 243 1.73628206307226 -1.65788963343147 -1 3.15730691328194 3832 243 2333 1620 1904 3061 4186 4599 1768 1957 2826 2285 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 2.59443029860272e-06 3.41201198367368e-06 2335 2272.72727272727 2334 2.35857578016763e-07 120 1.43351217946266 -1.43071971439001 -1 2.26218301982498 1798 2334 3021 2854 3517 1407 1832 2334 2272 3511 120 2286 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 9.3015556056147e-06 1.10282196580009e-05 755 2055.63636363636 2336 8.45599539330626e-07 420 1.91340229970491 1.972378862174 1 2.73826449465649 752 2682 2391 2451 3932 719 420 1392 3641 1896 2336 2287 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 2.43701932141997e-07 5.28861204464473e-07 1900 2477.27272727273 2337 2.21547235579767e-08 1353 1.59433266861004 -1.31972850959719 -1 2.8888261246707 1896 3968 2977 3964 1996 1811 1367 2390 2337 3191 1353 2288 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 3.541717657334e-07 6.68408930132605e-07 4070 2535 2338 3.21974384318655e-08 517 2.00810380807832 1.88530408153051 1 3.57980285348389 4066 517 1743 1071 2338 3799 3751 3821 1322 1688 3769 2289 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 2.24393615712089e-07 5.043513648386e-07 3720 2593.72727272727 2340 2.03994216908718e-08 1100 1.98051574685328 2.35139608154135 1 3.6005591919296 3716 2111 2015 1100 1914 3917 3717 1608 2901 2340 3192 2290 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 2.28579807697942e-07 5.09634715320873e-07 1705 2400.72727272727 2341 2.07799846770334e-08 1274 2.48176900934066 2.76137037571051 1 4.50880755202603 1702 2696 1274 2581 1932 2341 3636 3518 3060 1805 1863 2291 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 4.50756806489992e-07 7.96545161599686e-07 2140 2380.63636363636 2341 4.09778998950305e-08 1252 1.74382660937831 1.77096082640366 1 3.07021345861961 2140 1252 2341 1935 2521 2329 2968 3130 3106 1506 2959 2292 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 7.43214422069793e-08 3.22720521818714e-07 2205 2277.09090909091 2342 7.43214446926340e-09 871 1.88686222418406 -1.8082254281832 -1 3.53590887405653 2202 1058 4296 1399 871 2602 3658 2342 2621 920 3079 2293 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 2.79866086974983e-07 5.71814034844946e-07 2740 2011.72727272727 2342 2.54423747797522e-08 115 2.44240923732155 2.54326647870433 1 4.40202510661839 2737 115 609 2123 2132 2703 3133 2469 2992 774 2342 2294 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 6.74082876307445e-08 3.14536172538656e-07 540 2593.36363636364 2343 6.12802633601305e-09 479 3.23735486072285 -3.53874573337296 -1 6.07772676086159 4643 479 538 1794 665 4224 4704 4700 2343 539 3898 2295 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 1.62892076810987e-07 4.24544783295338e-07 2345 2270.90909090909 2343 1.48083717156199e-08 735 2.30291435899808 2.546813947779 1 4.23656547575431 2343 2205 1172 3569 1597 2609 2941 1728 3539 735 2542 2296 M14933 KEGG_STEROID_HORMONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_HORMONE_BIOSYNTHESIS.html Steroid hormone biosynthesis 21/88 KEGG 9.64707910338147e-08 3.39696808054909e-07 2875 1984.36363636364 2344 8.77007229673581e-09 773 3.8828498062416 -3.72293131871237 -1 7.25226168875352 2871 2362 773 962 1058 2359 2344 3523 898 2027 2651 2297 M2130 KEGG_ETHER_LIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ETHER_LIPID_METABOLISM.html Ether lipid metabolism 26/37 KEGG 3.57314488774827e-07 6.72457889560281e-07 2600 2359.45454545455 2344 3.24831406189377e-08 1104 2.32398019759192 -1.9165085411612 -1 4.14128414113488 2599 1782 1395 2279 2344 2612 3131 4162 1104 1764 2782 2298 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 3.45255446207951e-07 6.5498621627875e-07 2660 2345.54545454545 2346 3.13868636718529e-08 966 1.77358848441695 1.64212106181219 1 3.16614898733024 2660 2693 2525 2209 2321 1849 1794 2346 966 2970 3468 2299 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 1.61108369722136e-07 4.22248632499246e-07 4065 2591.81818181818 2347 1.46462165018433e-08 1381 2.24680220145447 2.70955323395541 1 4.13484561896712 4063 1564 1381 2347 1583 3730 3602 3756 1415 1665 3404 2300 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 8.80975149431984e-08 3.31003670356505e-07 2350 2568.27272727273 2347 8.00886531554583e-09 960 2.08361126456975 2.85481355934426 1 3.89807684880774 2347 2840 2217 4382 960 1974 1711 3078 3454 3178 2110 2301 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 5.81417304005148e-08 3.09852566478612e-07 3680 2520.36363636364 2349 5.28561199428071e-09 317 2.37462120814759 2.53479515283598 1 4.46229096688284 3676 317 1322 1857 499 4269 4125 3967 2094 2349 3249 2302 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 1.07800295738993e-07 3.50633492024923e-07 4620 2788.63636363636 2349 9.80002736556567e-09 456 1.87143099475656 1.67167431935384 1 3.48751530989452 4619 1718 1859 456 1187 4698 4705 4000 2349 1289 3795 2303 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 1.32257996379558e-06 1.8879860699608e-06 665 1975.09090909091 2350 1.20234614445021e-07 47 2.09663648816015 -2.09663648816015 -1 3.46464182376876 661 2887 2350 3861 3209 529 47 1322 2838 3578 444 2304 M6889 KEGG_RIBOFLAVIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOFLAVIN_METABOLISM.html Riboflavin metabolism 17/19 KEGG 7.64546301417594e-08 3.24764325922831e-07 3370 2471 2350 6.95042116351991e-09 785 1.8588174212025 -1.78898518900789 -1 3.4818695119991 3367 785 2364 3049 791 4320 4207 2168 1661 2119 2350 2305 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 6.22901963339981e-07 1.02585389635894e-06 1385 2221.09090909091 2350 5.66274672460731e-08 824 2.0522525204746 2.03893628975439 1 3.54827229891182 1383 3027 2483 2897 2727 1294 824 1915 3326 2350 2206 2306 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 3.84576873611993e-08 2.90188188019013e-07 1615 2119.36363636364 2351 3.49615345758811e-09 163 1.88841510775803 2.18116665215503 1 3.56398382040721 1612 2943 2577 2796 163 2547 2026 2086 1620 2351 2592 2307 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 1.25601901189196e-07 3.74750186367376e-07 3520 2328.18181818182 2352 1.14183553054574e-08 1061 1.93502673986665 -1.71437550318491 -1 3.58991686721249 3517 1834 2396 2352 1337 3476 2198 1777 1061 2661 3001 2308 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 2.18273271327852e-07 4.96027848178845e-07 3915 2484.09090909091 2353 1.98430266348967e-08 882 1.88019559149605 -1.49021427081382 -1 3.42205830960096 3912 1987 1375 1101 1886 4310 3734 2353 2497 882 3288 2309 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 4.30190654905951e-06 5.37738318632438e-06 2250 2404.09090909091 2353 3.91083178280229e-07 1125 2.03903776968005 -2.16816851381054 -1 3.10178498036682 2249 3692 2486 2801 3715 1685 2353 1125 1729 2969 1641 2310 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 9.20666734757214e-08 3.3523689347011e-07 4045 2621.27272727273 2354 8.36969793896113e-09 999 2.13071247728776 -1.4406403391237 -1 3.98281886056769 4041 3304 2318 2354 1005 4219 3851 2100 999 3043 1600 2311 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 1.63511750097643e-07 4.24953118178353e-07 2805 2723.63636363636 2354 1.48647056591285e-08 1354 2.03301645384835 -2.33165483847531 -1 3.73970067973968 2802 4239 2335 4415 1603 2354 1870 2120 4222 2646 1354 2312 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 2.74035306346827e-07 5.66073041584045e-07 4110 2822.09090909091 2355 2.49123036800984e-08 846 2.06816084275883 2.61122611095798 1 3.72999155543225 4107 1511 1851 2355 2106 4694 4522 3212 846 1792 4047 2313 M6778 BIOCARTA_IL10_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL10_PATHWAY.html IL-10 Anti-inflammatory Signaling Pathway 16/19 BioCarta 7.20863375401167e-06 8.68643127876821e-06 1005 2246.45454545455 2356 6.55332488572919e-07 843 1.33169117474592 -1.28412357022286 -1 1.94538098925156 1002 2825 3145 3679 3864 957 843 887 4220 2356 933 2314 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 8.49365776729684e-08 3.28069268916866e-07 3525 2341 2356 7.7215073592873e-09 394 2.50289487980392 2.75889633617984 1 4.6854524568086 3524 1613 630 942 927 2968 3528 4237 2356 394 4632 2315 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 3.5639975802214e-06 4.52327738065206e-06 2115 2454.27272727273 2356 3.24000304900605e-07 1034 1.76912003064009 2.22451217996603 1 2.72944656054605 2114 2356 2201 1694 3654 2929 3279 1034 2342 2587 2807 2316 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 1.09991748339818e-06 1.62035284695362e-06 2720 2510 2356 1.09991802781687e-07 915 2.39612223973461 -2.51237912108551 -1 4.00559356288063 2718 915 4513 2534 3152 2154 2143 4341 1701 1083 2356 2317 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 3.65553670148936e-07 6.84959636007534e-07 1580 2218.63636363636 2359 3.32321573536024e-08 1418 1.78016750159342 1.9290046056771 1 3.16790740052279 1579 2123 3049 2932 2359 1530 2525 1641 2617 2632 1418 2318 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 9.61354105300735e-07 1.44453322096108e-06 2180 2113.09090909091 2359 9.61354521191759e-08 147 2.59832136645804 -3.17372751706404 -1 4.38110881897084 2176 2921 4343 2359 3071 2379 2255 147 450 2830 313 2319 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 1.89989486792042e-06 2.59180037562929e-06 2555 2231 2359 1.72717864422718e-07 1238 2.02452496980926 1.98313557688749 1 3.26500562027204 2554 1674 1599 1419 3380 2531 2655 2359 2207 1238 2925 2320 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 1.05089696803073e-07 3.48348225330125e-07 2515 2296.54545454545 2360 9.55360925663659e-09 1151 1.97583959989242 -2.53829063273844 -1 3.68375483238682 2515 2553 2105 1741 1151 2077 2360 2721 2413 3396 2230 2321 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 3.41383887802856e-07 6.50806317028999e-07 2685 2608.45454545455 2361 3.10349037069946e-08 1777 1.86070788576985 1.88375391664986 1 3.3232077722004 2685 2611 2291 2090 2307 3031 3681 3695 2361 2164 1777 2322 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 7.93637985395293e-08 3.27123182997709e-07 3160 2176.36363636364 2361 7.21489103659411e-09 451 1.91181710559431 2.0490356919107 1 3.57943601928246 3160 1088 999 1914 827 3673 4053 2361 2696 451 2718 2323 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 3.66754727488673e-07 6.86319792543513e-07 2365 2494.81818181818 2363 3.33413444208323e-08 422 2.48000971348863 -2.99324169960953 -1 4.41303729737107 4177 422 1574 1404 2361 3629 2866 3388 990 2363 4269 2324 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 2.76483804597162e-07 5.68167826037923e-07 4425 2505.72727272727 2363 2.51348944858291e-08 450 2.47388080138289 1.5707395233202 1 4.46074295848503 4423 450 987 776 2118 4540 4554 2641 3349 1362 2363 2325 M13 PID_ERBB4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB4_PATHWAY.html ErbB4 signaling events 18832364 51/81 Pathway Interaction Database 2.07324256207902e-07 4.83961666321116e-07 4455 2341.36363636364 2364 1.88476614314354e-08 199 2.11526029295945 -2.06478998878027 -1 3.85652923254926 4455 408 1869 199 1833 4365 4118 2869 583 2364 2692 2326 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 3.08405542253431e-06 3.9837825928741e-06 380 1919.81818181818 2364 2.80369067809587e-07 378 1.53124021529126 -1.58685450185296 -1 2.38671217917549 378 2364 2484 3360 3590 383 471 1035 3921 2662 470 2327 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 7.41762422547665e-07 1.17605597394188e-06 2990 2340.18181818182 2365 6.74329702403559e-08 1430 2.28280485852076 2.80432976550042 1 3.90786781505548 2990 1647 1529 1891 2844 3395 3256 2922 1430 2365 1473 2328 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 1.7338460200687e-07 4.38209554355764e-07 4000 2816.72727272727 2366 1.57622377883198e-08 1083 2.29411811073986 2.40461966931448 1 4.21126579675196 3997 2107 1083 2366 1657 3971 4664 1807 2965 1850 4517 2329 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 3.68427790581027e-07 6.88244008420549e-07 4565 2589.09090909091 2366 3.34934411164185e-08 1056 3.23537595251386 -3.1999487762396 -1 5.75629524317692 4561 1873 1056 3833 2366 3902 2940 1126 2282 1283 3258 2330 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 2.35378611716682e-07 5.20368640422829e-07 4425 2804.81818181818 2366 2.13980578999917e-08 1044 3.12979939955801 -3.02657981432123 -1 5.678174626357 4421 1853 1044 1177 1955 4519 4469 3220 4286 1543 2366 2331 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 0.000179557969911811 0.000192005803802389 1045 2485 2366 1.79572480040982e-05 824 2.69453525393091 3.24119908182391 1 2.8910378084247 1042 3516 4609 3332 4546 1590 1144 824 2366 2711 1655 2332 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 1.51549783764711e-07 4.1135498326197e-07 2200 2548.81818181818 2368 1.37772540185828e-08 294 2.28246476079584 -2.35446045069694 -1 4.20797168078005 2200 1491 634 2341 2368 3666 4077 3957 3556 294 3453 2333 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 6.42586083626485e-07 1.05203132664482e-06 3970 2199.36363636364 2368 5.84169337560045e-08 806 2.62465109324427 2.60493200919087 1 4.5298756170405 3970 806 1497 891 2746 2368 1470 4595 1004 2445 2401 2334 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 3.69059490937255e-07 6.88550861663682e-07 1110 2309.45454545455 2369 3.3550868440781e-08 453 1.49060337360811 -1.22446018771231 -1 2.65149424013676 1106 3030 3421 2974 2369 453 1286 1901 4317 3633 914 2335 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 3.25408243924005e-07 6.30770805470762e-07 3680 2521.90909090909 2369 2.95825720050975e-08 446 1.73170564121941 -1.66391531110299 -1 3.09954202343265 3678 446 2119 2369 2270 3297 2875 1894 3156 1022 4615 2336 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 8.24056430611264e-08 3.27411388472988e-07 3180 2522.09090909091 2369 7.49142237707305e-09 883 1.84009412525898 1.98573265470661 1 3.44491576858682 3180 1212 2173 3602 883 2611 3275 2095 2369 2207 4136 2337 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 8.23003218450509e-08 3.27411388472988e-07 1295 2169.63636363636 2370 7.48184772034941e-09 880 1.75184513890243 1.68074825029216 1 3.2796599094051 1293 3243 2991 2640 880 1296 1217 2660 3164 2112 2370 2338 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 7.70741642453414e-08 3.24764325922831e-07 2375 2161.72727272727 2371 7.00674244959411e-09 803 2.21754420660041 -2.14204152871941 -1 4.15398976598874 2371 2781 2222 2840 803 1368 1487 2529 2301 2590 2487 2339 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 9.41600990372246e-07 1.42447329312724e-06 2445 2130.36363636364 2373 8.56001266707396e-08 803 1.76932546192822 1.94844257927427 1 2.98614168000077 2442 803 2626 1918 3005 2201 985 2373 2771 3173 1137 2340 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 7.67730187063844e-07 1.20870129517723e-06 4055 2844.27272727273 2373 6.97936777252224e-08 559 2.01234628774978 -1.1250403406293 -1 3.43786575730022 4052 1883 2141 2373 2868 4342 4523 2196 559 1970 4380 2341 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 8.21880655602401e-08 3.27411388472988e-07 2565 2273.81818181818 2373 7.47164260278541e-09 879 2.30598552531062 1.78388444574758 1 4.31734826644966 2564 2346 1260 3058 879 2373 2170 3390 3170 1178 2624 2342 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 2.30478719123409e-15 6.07742767744407e-14 4355 2353.72727272727 2373 2.09526108294008e-16 111 3.33235518272542 -3.24758336143521 -1 12.7167035995387 4352 111 133 2252 452 4185 3346 4625 2373 362 3700 2343 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 5.27237420205406e-07 9.03616784084791e-07 3225 2122.45454545455 2374 5.27237545296131e-08 43 5.28280499678733 -6.06748618525739 -1 9.21919566323894 3225 872 4205 290 2675 4004 3413 1517 43 2374 729 2344 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 1.73539406856887e-05 1.98957007618292e-05 665 2075.72727272727 2374 1.57764341616109e-06 401 1.98423884441519 2.19464855254507 1 2.69284273658427 663 4137 2784 3216 4080 401 708 491 2374 3456 523 2345 M7897 BIOCARTA_GLEEVEC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLEEVEC_PATHWAY.html Inhibition of Cellular Proliferation by Gleevec 41/42 BioCarta 3.71502710471144e-07 6.91063340528052e-07 2195 2546.81818181818 2376 3.3772979382265e-08 233 1.09668016903293 -1.34255092856289 -1 1.95005271637142 2195 3946 3801 233 2376 1765 2031 2656 2897 4385 1730 2346 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 7.4975888061482e-07 1.18554838073767e-06 1515 2522.27272727273 2376 7.49759133577209e-08 901 2.03010491821483 -2.53877043105884 -1 3.47313605772024 1511 3795 4514 3299 2912 1909 1862 901 3158 2376 1508 2347 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 3.39577331182516e-08 2.77395498531109e-07 4670 2908.18181818182 2378 3.08706669476369e-09 96 1.94658498792522 -1.74574386378115 -1 3.68479986945767 4669 2031 1882 2280 96 3783 4478 4232 2378 1626 4535 2348 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 5.38666564429762e-08 3.06874196014832e-07 2380 2171.90909090909 2378 4.89696888744481e-09 420 2.29900890420833 2.84509945888417 1 4.32296075397122 2378 2517 810 1047 420 3113 3640 2847 1984 1668 3467 2349 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 3.54220102745694e-05 3.93300137605193e-05 2380 2226.18181818182 2378 3.54225749107018e-06 424 2.20929139664483 2.59542289590301 1 2.80954785695176 1344 2897 4539 2378 4367 1546 788 424 2817 2379 1009 2350 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 6.89935362579703e-07 1.11295109753117e-06 2420 2292.54545454545 2379 6.27214162680313e-08 919 2.1084903386052 2.54251751527894 1 3.62398132394663 2420 2347 2075 2379 2794 2980 2775 919 2968 2064 1497 2351 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 1.8644587692733e-07 4.5691824459865e-07 3000 2489.27272727273 2379 1.6949626611661e-08 643 1.83597326865744 1.91202588972944 1 3.36046065380867 3000 643 2379 3565 1721 2117 1774 4050 2844 1618 3671 2352 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 2.39476604935733e-05 2.70090698995618e-05 1615 2423 2380 2.17708374318364e-06 591 1.69768766801526 1.26247494065449 1 2.23875667265316 1611 2407 2380 1955 4150 1482 591 3964 3861 3175 1077 2353 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 2.36309326515815e-07 5.20962177092315e-07 2665 1789.81818181818 2380 2.14826683544173e-08 385 2.69093763822339 2.72527594623657 1 4.88147316722507 2664 385 754 432 1962 2438 2515 2632 2380 779 2747 2354 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 5.88322771613898e-08 3.10127287236487e-07 2380 2257.63636363636 2380 5.34838897587994e-09 510 2.01679917158824 2.1808567171407 1 3.78953250641533 2380 1122 1098 1646 510 3252 3337 3918 2674 1402 3495 2355 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 4.32466814325329e-07 7.72905476567798e-07 1625 2220.63636363636 2381 3.93151726670793e-08 877 2.00058442586724 1.99278874461487 1 3.52995145277829 1623 2525 1489 2831 2489 1678 2381 3103 3283 877 2148 2356 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 1.34961324213931e-07 3.87181458914906e-07 2720 2320.09090909091 2382 1.22692120448433e-08 1404 1.68515395900916 -1.49054048770469 -1 3.1193379178756 2717 2330 2510 2382 1404 2484 2479 1786 3785 1613 2031 2357 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 4.40059662768394e-05 4.85412855402389e-05 2210 2760.90909090909 2382 4.40068377374081e-06 1413 2.1486587922649 1.41117133972574 1 2.67571624619515 2208 3504 4621 3109 4264 1922 1413 2287 1957 2382 2703 2358 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 1.03959837596164e-07 3.47369293280946e-07 2385 2466.81818181818 2383 9.45089477352108e-09 1139 2.09670637263005 2.50768250532301 1 3.90989147299466 2383 3130 2278 3629 1139 2367 2478 2350 2832 2781 1768 2359 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 1.83958538222114e-06 2.51680129373303e-06 2650 2308.45454545455 2385 1.67235174585324e-07 1043 3.14476540260834 2.76839580977193 1 5.08370455989651 2647 2390 1194 1220 3370 2385 3427 1043 2278 1724 3715 2360 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 1.83887647165173e-07 4.52057132614383e-07 3095 2285.54545454545 2386 1.6717060230498e-08 377 1.34116789634713 -1.3444909161614 -1 2.45636400648498 3091 377 3451 650 1715 2813 3501 2386 1907 3677 1573 2361 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 4.46543285496351e-06 5.57293576822522e-06 1800 2617.36363636364 2386 4.05949265333346e-07 1602 2.2812698449925 2.68185242719462 1 3.46015161140703 1799 2767 1602 2386 3724 1672 1993 3545 4339 2345 2619 2362 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 1.57584472836137e-07 4.1859656963545e-07 1760 2621.72727272727 2386 1.43258621930732e-08 1534 1.55790027184812 1.69444633488304 1 2.86847543614112 1760 2945 3831 3795 1558 2225 2315 1534 3042 3448 2386 2363 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 2.0482722741895e-05 2.32960123715047e-05 2390 2208.45454545455 2388 1.86208304047804e-06 419 3.63106130693257 3.76794078338426 1 4.85663998063025 2388 2864 1251 2528 4114 2322 1408 1108 419 2516 3375 2364 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 2.04726416844876e-07 4.81168919655711e-07 3720 2600.27272727273 2388 1.86114941723817e-08 674 2.28907925519332 1.7647136481919 1 4.17516701284425 3717 674 1635 2089 1814 4487 3520 2388 1068 2589 4622 2365 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 3.76353636852813e-07 6.97289895695734e-07 1360 1893.63636363636 2388 3.42139728395985e-08 100 1.89190477849261 2.14342171193253 1 3.36257112412284 1356 2870 2612 3334 2388 1365 373 682 3231 2519 100 2366 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 1.30485722050432e-08 1.35659164774899e-07 3660 2315.90909090909 2390 1.18623384385787e-09 70 2.74002288341837 -2.4664448012739 -1 5.43288694894759 3660 70 368 1342 360 4295 4651 3844 2390 423 4072 2367 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 3.3270921851322e-07 6.40549883127711e-07 2750 2301.81818181818 2391 3.0246297166303e-08 726 2.77054192093011 3.07178230918473 1 4.95410372238323 2750 726 1540 3281 2284 2391 2507 3576 1707 1534 3024 2368 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 6.13985932273769e-08 3.12995510041999e-07 3330 1832.63636363636 2392 5.58169044917425e-09 241 2.86833248992422 2.95216426714828 1 5.38660175236215 3326 241 507 589 558 2544 3391 2518 2392 692 3401 2369 M7416 ST_GAQ_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GAQ_PATHWAY.html G alpha q Pathway 31/35 Signaling Transduction KE 5.3237057856759e-07 9.09771589731725e-07 1570 2466 2395 4.83973370358358e-08 1253 1.20011028091369 -1.39097479746781 -1 2.09266436645267 1566 2304 3484 1980 2617 2395 2951 1253 3243 3514 1819 2370 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 7.0251533157982e-07 1.12823149542591e-06 495 2540.54545454545 2395 6.38650505373395e-08 493 1.52649182196397 1.66429788347892 1 2.6208194280463 493 3553 3911 2248 2804 1576 1609 1764 3259 4334 2395 2371 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 3.8036161308436e-07 7.02389207260634e-07 3070 2708.81818181818 2396 3.45783344405201e-08 1295 2.39247259049003 2.08883679386779 1 4.25029547474547 3067 2243 1306 3828 2396 2067 1879 3893 3760 1295 4063 2372 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 2.9633660662116e-07 5.94436371972747e-07 3055 2523.36363636364 2397 2.69396951397501e-08 834 2.07511281875052 1.72876234097359 1 3.72980940673078 3053 2331 2397 3041 2183 1979 834 4653 1155 2752 3379 2373 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 4.3837232230375e-05 4.83777732352981e-05 1140 2396.81818181818 2398 3.98528234146137e-06 1016 2.08783066909603 2.21223009468197 1 2.60082631833234 1140 4035 2888 2398 4248 1926 2565 1512 1016 2942 1695 2374 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 2.17873940536468e-06 2.92149147537536e-06 1350 2002.36363636364 2401 1.98067414822904e-07 113 1.98369904768 2.21778810949963 1 3.16935871986069 1349 2401 2741 3128 3448 658 258 955 3773 3202 113 2375 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 2.92078709529141e-05 3.26607796488402e-05 1115 2243 2402 2.65529624842948e-06 252 2.22361862195125 2.52712544770448 1 2.8795893484844 1112 3962 2402 2499 4186 669 252 1292 3571 3901 827 2376 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 9.42409036187204e-08 3.3764305071295e-07 2545 2426.90909090909 2402 8.567355241427e-09 1032 1.77542305795454 2.09439133428941 1 3.31696068037094 2545 3262 2919 2402 1032 2382 2374 3061 1900 2948 1871 2377 M4013 KEGG_GAP_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GAP_JUNCTION.html Gap junction 85/107 KEGG 1.20413920439505e-07 3.68821352676486e-07 2470 2015.27272727273 2403 1.09467206391085e-08 205 2.30254035099466 2.30340021139125 1 4.27650710782614 2466 1530 1597 205 1298 2403 2486 3222 1183 2424 3354 2378 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 6.5980258623601e-07 1.07425602174335e-06 2310 2148.36363636364 2403 5.9982071283424e-08 248 1.68916362268299 -2.16793239091047 -1 2.91058572898974 2310 2403 2789 2383 2763 2538 2983 979 248 2937 1299 2379 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 1.63827652632054e-07 4.25105288852828e-07 2665 2283 2403 1.48934240756207e-08 717 1.92255406439266 2.10561635894173 1 3.5363737913044 2663 2944 2000 1735 1606 3191 3310 717 2403 1714 2830 2380 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 2.38613825856144e-07 5.22548577520102e-07 1995 2560.27272727273 2403 2.16921683396729e-08 1518 2.91622709995063 3.65017373025212 1 5.28911778766467 1995 3382 1518 3116 1976 2333 2962 3438 1685 3355 2403 2381 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 3.38751283697115e-07 6.48091560906852e-07 4285 2644.81818181818 2404 3.07955759870293e-08 1065 2.58365627677593 -1.86135011179689 -1 4.61607624310697 4283 3023 1363 2404 2299 4670 3212 1065 1246 1681 3847 2382 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 4.30243056684614e-07 7.69805620754882e-07 2200 2472.63636363636 2405 3.91130128022847e-08 1222 2.2128118505029 1.80940769067041 1 3.90562487113377 2198 3372 2044 1466 2486 1753 1222 3905 3211 2405 3137 2383 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 0.0104648483690897 0.0106751857147403 2090 2637.36363636364 2405 0.00105144583613733 476 4.44314247125247 5.7890701004329 1 2.52877389833371 2090 3213 4215 2405 4712 1950 884 4705 476 2826 1535 2384 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 3.85342901463399e-07 7.09091031152922e-07 3860 2933.36363636364 2405 3.50311789962259e-08 1721 2.0409030920509 -2.17826802147353 -1 3.62316517690004 3857 2122 2048 2333 2405 4255 4480 4413 1721 1947 2686 2385 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 0.0104648483690897 0.0106751857147403 2095 2643.09090909091 2406 0.00105144583613733 477 4.44314247125247 5.7890701004329 1 2.52877389833371 2091 3214 4267 2406 4713 1951 885 4706 477 2828 1536 2386 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 0.000118680157329604 0.000127863579684029 2410 2646.63636363636 2406 1.07896872796989e-05 674 2.15662540401934 2.7663109257816 1 2.42368675228197 2406 4246 2177 4192 4361 1878 1184 2867 2855 2273 674 2387 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 4.88117397350783e-08 3.0357704374324e-07 4570 2567.63636363636 2406 4.43743098346108e-09 332 1.98892565034079 -1.91112517328716 -1 3.74247136363057 4566 1076 1148 1446 332 3983 4180 3707 2406 1120 4280 2388 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 8.86508750988709e-07 1.35722390680075e-06 2290 2527.27272727273 2406 8.05917371104699e-08 775 1.74414354891082 2.02881756058289 1 2.95420716753365 2290 3670 3274 2910 2967 2305 2406 1197 775 3832 2174 2389 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 0.0104648483690897 0.0106751857147403 2095 2644.27272727273 2407 0.00105144583613733 478 4.44314247125247 5.7890701004329 1 2.52877389833371 2092 3215 4270 2407 4714 1952 886 4707 478 2829 1537 2390 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 3.23141898228807e-07 6.27666567753073e-07 2805 2555.81818181818 2407 2.93765405175241e-08 1433 2.03397912047849 1.89846830085895 1 3.64198348232835 2803 3261 1590 1433 2265 2218 2407 3412 2835 1961 3929 2391 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 3.87737944785173e-07 7.12664758327888e-07 465 2115.54545454545 2408 3.52489102838071e-08 465 1.27466419450954 -1.30595198157885 -1 2.2617530684193 465 3308 3912 2489 2408 642 490 744 3999 4151 663 2392 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 2.31353770344423e-05 2.6142920661376e-05 1980 2395.54545454545 2408 2.10323821195553e-06 848 3.17656315011658 3.62738006005017 1 4.20269851950376 1979 2289 848 2726 4142 2448 2207 2408 2767 1215 3322 2393 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 3.12223189226853e-07 6.13017243407133e-07 2945 2458.18181818182 2408 2.83839303215874e-08 1447 1.87081168586141 1.60197473865279 1 3.35529225146884 2943 3187 2594 2823 2237 2408 1855 1460 1447 2325 3761 2394 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 2.38268141224242e-07 5.22548577520102e-07 4155 2597.63636363636 2409 2.16607424572334e-08 375 2.50079713468757 -2.12628624817862 -1 4.53553592886434 4152 2409 1863 1281 1972 4418 2456 4313 375 3174 2161 2395 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 3.41949081828796e-07 6.50806317028999e-07 2220 2555.36363636364 2410 3.10862849980393e-08 1171 3.0021396879433 3.52820265340526 1 5.36232321219863 2219 2410 1171 2538 2313 2631 4236 4194 3576 1433 1388 2396 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 0.000235856086347887 0.000250278940549017 1505 2576.18181818182 2412 2.35881122729851e-05 1174 1.44803816943441 1.44803816943441 1 1.50510755439053 1505 3529 4361 3141 4436 1344 1361 1174 2412 3473 1602 2397 M11792 BIOCARTA_SHH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SHH_PATHWAY.html Sonic Hedgehog (Shh) Pathway 16/19 BioCarta 3.34624054292702e-06 4.28268954228619e-06 1500 2780.72727272727 2413 3.04204148421035e-07 1496 1.44876480862046 1.63208057640416 1 2.24496808378407 1496 2413 3056 4383 3623 1908 2335 2337 3389 3842 1806 2398 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 6.29079531794745e-08 3.14536172538656e-07 3355 2506.54545454545 2413 6.29079549603092e-09 698 1.74862356696292 -1.66350280173064 -1 3.28242482660997 3354 1068 4302 1715 698 1824 3524 3457 2234 2983 2413 2399 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 2.79059198908524e-06 3.63755708049774e-06 2415 2234.54545454545 2413 2.53690502620042e-07 290 2.69007271231045 4.07958512835989 1 4.22428451657478 2413 3739 1983 643 3550 3067 3029 1260 290 2679 1927 2400 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 1.64815870453276e-07 4.26497208629091e-07 3745 2676.63636363636 2414 1.49832620727885e-08 959 2.44494878155224 2.0125800863245 1 4.49650592119604 3742 1914 1327 3902 1610 3187 1659 2414 4414 959 4315 2401 M9134 BIOCARTA_TRKA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TRKA_PATHWAY.html Trka Receptor Signaling Pathway 22/25 BioCarta 2.1460653798589e-06 2.88259208677689e-06 2125 2575.27272727273 2415 1.95097043028615e-07 1296 1.50938413750481 1.62283435253444 1 2.41387648976138 2123 3733 3112 1296 3442 2415 1679 2440 2157 4195 1736 2402 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 1.27768360694022e-07 3.76711668300292e-07 2490 2420.36363636364 2415 1.27768368040162e-08 778 2.19372021050159 2.54145542132573 1 4.06853132386701 2486 1978 4440 1800 1441 2120 3451 2415 2971 778 2744 2403 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 8.47081727508163e-08 3.27455016694392e-07 2415 2357.09090909091 2415 7.70074327385419e-09 925 2.09963663739212 2.36422547442639 1 3.93090236657393 2415 3870 2110 3187 925 2720 2241 2471 1163 2297 2529 2404 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 1.30786468555872e-05 1.5234751519835e-05 2420 2474.27272727273 2416 1.30787238291764e-06 907 3.45123433884373 -3.84893135309516 -1 4.79989185435722 2416 2925 4623 2282 4034 2717 3059 1318 1087 1849 907 2405 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 1.76674327364704e-06 2.42413611965524e-06 3010 2445.81818181818 2417 1.60613153859867e-07 1647 2.90945275456015 -2.46125512047865 -1 4.71693049681526 3010 2417 1762 1647 3354 2543 2296 2695 3258 2198 1724 2406 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 1.14198946751304e-06 1.67345243299023e-06 2365 2458.72727272727 2417 1.03817278209486e-07 1511 1.83118424453629 1.68530334325912 1 3.05357965555435 2361 2563 2199 1511 3115 2065 2706 2417 1816 2718 3575 2407 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 3.63932598660845e-07 6.82192956981409e-07 1415 2048.72727272727 2417 3.30847871694556e-08 718 1.88312104642075 -1.68228112283295 -1 3.35212461669615 1411 2637 2448 2782 2357 1682 2417 718 2580 2550 954 2408 M13950 KEGG_ASTHMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASTHMA.html Asthma 12/39 KEGG 5.29388390777846e-07 9.06191365830477e-07 2860 2202.72727272727 2420 4.81262289241084e-08 519 2.52027471784 -2.5895316790789 -1 4.39686412250365 2859 2420 1073 2074 2612 2829 2767 2145 3441 519 1491 2409 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 1.35859150142706e-07 3.8816900040773e-07 4060 2568.72727272727 2420 1.23508325938704e-08 948 2.03604493934709 -1.63853914660203 -1 3.76839059647192 4058 1134 971 1435 1412 4168 4115 3724 2420 948 3871 2410 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 5.58276953141865e-07 9.42778969169804e-07 2395 2508.45454545455 2421 5.07524631646846e-08 1093 1.92849289851209 -1.62912652214858 -1 3.3546682479104 2394 2421 2394 3307 2653 1835 1093 3752 2045 2442 3257 2411 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 3.93375367126592e-07 7.19184377766178e-07 2080 2663.18181818182 2421 3.57614034058976e-08 1395 1.83847366535725 2.06987917054923 1 3.26045304240859 2076 4201 2817 3920 2421 2251 2319 1395 2273 3160 2462 2412 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 1.87191479089866e-10 2.63744412329602e-09 3150 2082.54545454545 2421 1.70174071914358e-11 64 2.14707885846963 2.20358771133968 1 5.31800195063928 3147 1066 287 64 806 3089 3262 4029 2421 165 4572 2413 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 0.000335354227547697 0.000353477435021244 740 2474.81818181818 2422 3.04913961598771e-05 406 1.04144347533146 1.09288866678658 1 1.03715557568045 740 2847 3262 2422 4454 1327 406 1843 3957 3683 2282 2414 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 1.18203906963257e-07 3.64829498861888e-07 2835 2578.45454545455 2423 1.07458103012946e-08 1282 2.30828513624976 2.97808387685156 1 4.29032923333993 2832 2116 1419 2342 1282 3172 3108 4692 1801 2423 3176 2415 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 3.93846613449467e-07 7.19410222709553e-07 2720 2666.09090909091 2424 3.58042439960339e-08 1779 1.34921473522107 1.45038704119282 1 2.39249127637187 2719 2222 3495 4187 2424 2131 1779 2076 2889 3555 1850 2416 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 2.55244819882046e-07 5.41950314819278e-07 2685 2354.81818181818 2424 2.32040772268772e-08 973 1.97091057426793 2.63327490880353 1 3.56532113760707 2681 1708 2376 3091 2042 2424 2485 2910 2405 2808 973 2417 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 8.77116856951255e-07 1.34590102887189e-06 1960 2156.18181818182 2424 7.97379278771558e-08 893 2.31501925220012 -2.30416305379615 -1 3.92386300358066 1957 1685 1202 1456 2960 2628 2641 2424 3108 893 2764 2418 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 8.08071297189364e-08 3.27390259462129e-07 2430 2356.09090909091 2426 7.34610297154762e-09 858 1.64208997179845 -1.80826590822756 -1 3.07414466938322 4150 1742 3055 2322 858 3104 2426 2427 1013 2913 1907 2419 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 1.277786824044e-07 3.76711668300292e-07 975 2751.63636363636 2426 1.16162445296311e-08 974 1.44221302074631 -1.36987298286113 -1 2.674471216163 974 4379 3833 4491 1355 1731 1771 1625 4092 3591 2426 2420 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 9.28868693584561e-08 3.35829802760759e-07 2690 2289.36363636364 2427 8.44426120729644e-09 807 1.84370311296723 -1.30768228168171 -1 3.44580408979114 2686 3411 2676 3905 1017 2427 2333 994 2404 2523 807 2421 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 5.11755114097638e-06 6.33154426878336e-06 4195 2458.72727272727 2427 4.65233004114174e-07 218 3.65784664710824 -3.03031281958819 -1 5.49007208837241 4194 1920 1227 565 3760 3685 2427 2572 218 2090 4388 2422 M10628 BIOCARTA_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ATM_PATHWAY.html ATM Signaling Pathway 31/32 BioCarta 3.22575047422114e-06 4.15091118820168e-06 2520 2312.72727272727 2428 2.93250473089834e-07 271 1.83605565117499 2.18096233736263 1 2.85253041678479 2516 2318 2564 1538 3605 1370 271 2428 3005 2416 3409 2423 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 2.12438991317686e-07 4.89605487802479e-07 2430 2641.54545454545 2428 1.93126374392247e-08 1629 1.99770815676733 -1.79111986665285 -1 3.63925634729812 2428 2975 1829 2075 1861 2860 3929 4712 1629 1793 2966 2424 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 4.04249387490208e-06 5.08002425174064e-06 1055 2178.72727272727 2429 3.67500118453858e-07 291 1.59318619691231 1.5790846945438 1 2.4347328303066 1052 3494 2690 4555 3696 913 291 455 2429 3279 1112 2425 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 1.1517450387512e-07 3.59285478750119e-07 2910 2631.63636363636 2430 1.04704099913401e-08 1263 2.00882501071874 2.20601015525453 1 3.73747905477219 2907 2237 2317 1302 1263 3537 3497 3326 1963 2430 4169 2426 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 1.21153207031791e-06 1.75735444741872e-06 3120 2475.81818181818 2430 1.1013933977316e-07 223 1.76183529620399 1.50593201434029 1 2.92709563162628 3120 2350 2430 1448 3154 2198 2040 4079 223 3128 3064 2427 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 5.57550002141538e-08 3.07843567066819e-07 2660 2246.90909090909 2430 5.06863651156026e-09 459 1.80464819367692 -1.43423433514427 -1 3.39248643542579 2659 1106 2730 2430 459 1476 2804 4323 1738 3384 1607 2428 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 0.00043690664045054 0.000459184890431207 840 2407.09090909091 2430 3.97266755988943e-05 837 3.31462761233907 3.68516760023162 1 3.19410387347131 837 2789 1196 1455 4470 2430 2132 3110 3301 2275 2483 2429 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 1.29000011945924e-09 1.61506646255905e-08 3045 2154.36363636364 2430 1.29000012020808e-10 104 2.24042457852972 2.51808740639676 1 5.04008532300758 3042 1005 4673 504 104 1907 3475 3191 2430 198 3169 2430 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 0.000843690633321825 0.000878495431122659 860 2257.45454545455 2431 7.67285780824814e-05 380 1.45991652860138 -1.43500621917426 -1 1.28757165854659 859 2849 3311 2431 4521 1246 380 1330 2798 2879 2228 2431 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 5.03814733534187e-05 5.53153184992176e-05 1090 2063.72727272727 2432 4.58023883271742e-06 136 1.54735956388019 1.77051818206119 1 1.9013295973352 1086 2432 2916 2652 4271 722 136 538 2999 3145 1804 2432 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 2.92574350613069e-07 5.88833039037007e-07 3665 2615.54545454545 2432 2.65976717747322e-08 1517 2.94570491607207 -3.93242663961975 -1 5.29847243529383 3661 1850 1517 2748 2174 3742 3249 2989 2377 2032 2432 2433 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 0.00016731115926952 0.000179194161958733 285 2313.45454545455 2433 1.52112622478414e-05 200 1.04533467149037 1.09870123574747 1 1.13009270222157 283 2760 3419 2433 4392 813 200 1609 3998 3430 2111 2434 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 1.05767739250608e-07 3.48348225330125e-07 2595 2468 2433 9.61524948504766e-09 1162 2.05755472195036 -2.06339103093857 -1 3.83614010646712 2595 2109 2027 3356 1162 2913 3938 2433 3086 2014 1515 2435 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 2.07070654397457e-06 2.79329376609317e-06 980 2312.81818181818 2434 1.88246226635343e-07 863 3.3706742332711 3.56752870652542 1 5.40490139458847 980 3065 863 2720 3422 2434 1798 1913 3297 2189 2760 2436 M15285 BIOCARTA_NFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NFKB_PATHWAY.html NF-kB Signaling Pathway 28/37 BioCarta 7.87515660187143e-06 9.44138662962488e-06 595 2124.27272727273 2436 7.15925890186754e-07 540 1.57736195799325 -1.71159141508568 -1 2.28793831777065 595 2762 3077 2436 3887 784 1048 540 3487 2961 1790 2437 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 2.90817052276458e-08 2.61957344798642e-07 2425 2344.54545454545 2436 2.64379141927961e-09 38 2.02835768107819 -1.66924311810282 -1 3.8541942694056 2424 2617 2306 2203 38 2128 2609 2546 3717 2436 2766 2438 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 1.68556963708243e-07 4.3132890453628e-07 2675 2167.72727272727 2438 1.532336151114e-08 103 2.09542140176986 1.84706882790126 1 3.85060660624747 2673 854 1898 3022 1631 2669 3434 2438 103 2087 3036 2439 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 2.00232766345731e-07 4.74685412934128e-07 1700 2491.54545454545 2438 1.82029804154452e-08 1363 1.99482786933789 1.98101687338198 1 3.64175017608365 1698 3989 2438 3439 1790 1853 1363 2819 2709 3152 2157 2440 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 4.00990115203464e-07 7.27951286061673e-07 2885 2136.72727272727 2439 3.6453653481022e-08 660 3.00463239076413 3.43817690125154 1 5.32456560574878 2882 1643 660 1602 2439 2748 3269 3150 1324 749 3038 2441 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 2.09850879459593e-06 2.82434032235324e-06 2440 2181.63636363636 2439 1.90773708754384e-07 884 2.96581842527676 -3.19292656826179 -1 4.75149743546168 2439 2728 884 2751 3432 2643 3162 1214 2285 1242 1218 2442 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 5.2589922788061e-07 9.02134545035336e-07 4205 2694.18181818182 2444 4.78090321449351e-08 1008 2.06825796893308 -1.58723662618157 -1 3.6092862881959 4202 2052 1008 1612 2605 4165 4378 2444 1466 1012 4692 2443 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 1.75846104455837e-05 2.01552601513247e-05 970 2274.90909090909 2445 1.59861372736649e-06 211 1.24959710946469 1.30717358538029 1 1.6934983975009 966 2445 3314 4157 4081 662 211 1124 3584 2800 1680 2444 M7825 BIOCARTA_ACTINY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACTINY_PATHWAY.html Y branching of actin filaments 29/36 BioCarta 9.59104693353587e-08 3.38845370705758e-07 4105 2071.36363636364 2446 8.71913395605816e-09 70 2.45847173801062 -1.29059347542756 -1 4.59231203390996 4103 610 1867 1263 1052 2925 2505 2446 70 2749 3195 2445 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 7.43201341122142e-07 1.17715111748205e-06 1175 1991.72727272727 2447 6.7563781108149e-08 598 1.93897802020593 -1.90162543994022 -1 3.3189245055557 1173 2607 2447 3143 2847 598 967 2765 1217 3271 874 2446 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 5.88194368752602e-08 3.10127287236487e-07 4160 2257.72727272727 2448 5.34722167707845e-09 427 2.80711829993036 -2.66996856167567 -1 5.27486668864284 4158 427 524 986 509 4420 4564 2448 2543 544 3712 2447 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 1.42278892222534e-07 3.98409119822705e-07 2375 2500.54545454545 2449 1.29344455840024e-08 1226 1.76529444378972 2.03286313285851 1 3.26139607375661 2373 1226 2793 2449 1452 2939 2984 2320 2432 3497 3041 2448 M16697 BIOCARTA_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CD40_PATHWAY.html CD40L Signaling Pathway 18/19 BioCarta 0.000135093706229386 0.00014521573523177 830 2456.36363636364 2450 1.22820002307117e-05 829 1.44752902004206 -1.56703979122441 -1 1.60339641356783 829 3167 3331 2450 4374 1552 1527 1362 3391 3057 1980 2449 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 7.61273709924353e-08 3.24764325922831e-07 1845 2657.90909090909 2450 6.92067032969976e-09 789 2.1061638596778 2.27030039421939 1 3.94530452108839 1841 3691 2063 4344 789 2378 3111 2514 3926 2450 2130 2450 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 2.84071373016619e-07 5.76750896312364e-07 2525 2381 2451 2.58246736088066e-08 628 1.64956040193189 1.38761893951495 1 2.97099264407953 2521 628 2451 2311 2148 3056 3943 3403 652 2209 2869 2451 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 7.18028054859488e-08 3.18224640275754e-07 2965 2072.54545454545 2451 6.52752798449301e-09 716 1.96932737512947 -2.21813207949067 -1 3.69394789972288 2965 2629 2375 1087 741 2848 3039 1433 716 2451 2514 2452 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 4.78888358991775e-05 5.26643302525904e-05 3450 2501.27272727273 2451 4.35362530531758e-06 586 1.46187362247997 -1.75592748146113 -1 1.80524421911924 3450 2451 3276 3892 4263 2135 586 1229 2164 3282 786 2453 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 4.045526913509e-07 7.31604867117337e-07 3610 2464.90909090909 2451 3.6777524158467e-08 615 3.92307395382419 -4.12960188011914 -1 6.94995336387695 3609 2756 615 985 2451 3879 4449 2011 2970 1369 2020 2454 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 5.5780629516648e-08 3.07843567066819e-07 3065 2230.18181818182 2452 5.07096644826877e-09 460 2.72974879176903 2.61223732064122 1 5.13198782573547 3063 1614 1331 1198 460 2674 3410 4258 768 2452 3304 2455 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 1.27234645953151e-07 3.76660766944629e-07 1520 2510.45454545455 2452 1.27234653238046e-08 1408 1.66879994817013 1.8269410587092 1 3.09482254944135 1520 1959 4384 3177 1434 1408 2324 2901 2452 3503 2553 2456 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 7.39040294204484e-07 1.17292205401653e-06 2115 2635 2452 6.71855038607718e-08 1442 1.82799618537757 -1.63030992922529 -1 3.12973406303732 2113 2452 2565 4347 2841 1510 2184 4152 3291 2088 1442 2457 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 2.26989475232587e-06 3.03171823675388e-06 1145 2326.63636363636 2452 2.06354281303576e-07 1145 1.71880093461268 1.64066786314995 1 2.73803256850628 1145 2565 2753 2452 3461 1302 1315 2422 2801 3222 2155 2458 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 1.06134205497047e-07 3.48348225330125e-07 3135 1968 2452 9.64856460156916e-09 195 1.93447335896055 1.82842768139073 1 3.60661359092106 3134 525 2452 1061 1168 3115 2728 3245 708 3317 195 2459 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 2.97147293667793e-07 5.95809356886993e-07 2725 2534.90909090909 2453 2.70133939820527e-08 900 2.0642724568328 1.94048537553615 1 3.70972318501979 2722 2211 1560 3340 2184 2335 2453 3121 3975 900 3083 2460 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 1.00366364092082e-05 1.18639929505291e-05 3690 2467.72727272727 2455 9.12425654337677e-07 846 2.72323054007579 3.06121724726084 1 3.87262388091608 3686 1900 1509 3046 3944 3181 3366 846 2455 2006 1206 2461 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 3.69440392701236e-07 6.88550861663682e-07 4020 2740.18181818182 2456 3.69440454120041e-08 1350 2.89620638459573 -2.4904255281599 -1 5.1526015322471 4020 2899 4317 1607 2456 3979 3233 1350 2210 1886 2185 2462 M16517 BIOCARTA_WNT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_WNT_PATHWAY.html WNT Signaling Pathway 43/48 BioCarta 3.07394658643397e-07 6.08140323900428e-07 2615 2549.72727272727 2457 2.79449728721887e-08 912 1.46197466588187 1.78227046181349 1 2.62332113356618 2614 3942 3547 2670 2216 2412 2137 912 1240 3900 2457 2463 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 2.74721855117602e-07 5.66981703609568e-07 3170 2792.45454545455 2458 2.49747172202824e-08 1738 2.05796467789534 -1.58022529566219 -1 3.71118426339438 3169 2292 2231 2415 2110 2899 3198 4022 2458 1738 4185 2464 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 1.47407405532283e-05 1.70321408595441e-05 2300 2885.09090909091 2458 1.34007630200713e-06 1586 1.23206142168648 1.20095927947059 1 1.6957353177092 2300 3153 3441 3948 4042 2142 1586 2128 4504 2458 2034 2465 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 1.73422244408893e-06 2.38575632063531e-06 2005 2558.09090909091 2460 1.57656710104399e-07 1117 1.46581518217419 -1.29109174398725 -1 2.37894920385529 2001 2405 2770 3363 3344 2460 1972 1117 3551 2358 2798 2466 M9664 BIOCARTA_GPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GPCR_PATHWAY.html Signaling Pathway from G-Protein Families 51/55 BioCarta 2.12624079507785e-07 4.89792901550389e-07 2305 2548.90909090909 2461 1.93294636415758e-08 649 1.57918708640509 1.64948326823156 1 2.87657369381225 2302 3655 3445 649 1862 2461 2452 2964 2506 4308 1434 2467 M6705 BIOCARTA_TH1TH2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TH1TH2_PATHWAY.html Th1/Th2 Differentiation 7/21 BioCarta 4.42993700016967e-07 7.86951548392957e-07 3165 2258.90909090909 2463 4.4299378832653e-08 279 1.71037279885351 -1.99703155839171 -1 3.01389661124116 3164 904 4199 3067 2570 3129 2463 279 1151 1881 2041 2468 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 2.7397659018424e-07 5.66073041584045e-07 3430 2759 2464 2.49069658458063e-08 1517 1.77559980485586 2.05229249298459 1 3.20222690185785 3427 1605 2336 2434 2105 2464 2874 4414 3202 1517 3971 2469 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 4.11530201670041e-07 7.40997389212297e-07 1020 2118.90909090909 2464 3.74118435136877e-08 501 1.81767681191039 2.17296506910153 1 3.2167499131511 1016 3066 2632 4406 2464 858 501 642 4203 2947 573 2470 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 7.36919015527489e-08 3.2144561803028e-07 4645 2647.27272727273 2465 6.69926400192331e-09 271 2.13313299751282 -2.03084721678567 -1 3.99858236594617 4642 271 1426 890 758 4259 4582 4418 2465 1471 3938 2471 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 4.11630329346322e-07 7.40997389212297e-07 1895 2500.54545454545 2465 3.7420946033119e-08 1145 1.73527305178672 2.22267659262781 1 3.07088060193323 1893 3599 2791 2692 2465 2031 2074 1145 3648 3841 1327 2472 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 6.5789848007084e-07 1.07189534895905e-06 3145 2428.72727272727 2466 5.98089706192744e-08 797 1.6884157925826 -1.58499355128491 -1 2.90976258122924 3143 797 2466 1084 2761 3134 2404 4651 1092 2357 2827 2473 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 2.62003180012341e-07 5.50603299046416e-07 2015 2221.27272727273 2467 2.38184737468111e-08 1075 1.72606542031093 2.03262863482172 1 3.11886738033452 2013 1794 2524 1075 2067 2467 2980 2620 2704 2848 1342 2474 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 1.6224393074052e-06 2.24902012656462e-06 1105 2833.27272727273 2467 1.47494591264606e-07 1103 1.65653537248142 1.84670301564945 1 2.70085256073646 1103 4364 3887 4514 3319 1444 1624 1840 2467 4442 2162 2475 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 0.000124471446115108 0.000134011228481595 2750 2675 2469 1.24478418578171e-05 974 2.18866341696365 2.47856588208213 1 2.44681554850757 2746 2469 4243 1832 4376 3493 4676 1281 1453 1882 974 2476 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 8.00798745041842e-08 3.27123182997709e-07 2955 1793.81818181818 2469 7.27998885628065e-09 149 2.64912546142323 -2.71144804241066 -1 4.96020782006956 2954 564 640 149 843 2958 3064 2840 2469 585 2666 2477 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 2.6647907645553e-06 3.48802340784832e-06 2640 2683.90909090909 2470 2.42253999303452e-07 1476 1.9866151858722 1.68285999693208 1 3.12986149232254 2640 2431 2470 2638 3533 2442 1476 4092 3706 2259 1836 2478 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 1.60535160247539e-06 2.22840410143078e-06 2575 2010.81818181818 2470 1.60535276219576e-07 104 3.57098538442076 -4.12931817278376 -1 5.82733444938073 2575 905 4438 1822 3353 2505 2496 254 104 2470 1197 2479 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 9.04515905357001e-08 3.32760333069762e-07 3340 2195.63636363636 2471 8.22287220495994e-09 231 1.74139703932114 1.94597384415981 1 3.25655573780722 3337 231 2471 2399 989 3164 3092 443 1690 2690 3646 2480 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 3.94464840377452e-05 4.36854539319937e-05 1935 2531.36363636364 2472 3.58610830360344e-06 429 3.0256638626843 -3.76705912541431 -1 3.80819200877957 1934 3792 1858 3644 4282 2472 2482 429 4111 2321 520 2481 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 4.17789602114428e-07 7.49732596517966e-07 2420 2539.81818181818 2473 3.79808801322289e-08 1519 2.16865422447303 2.52781890694518 1 3.83485502427156 2418 3864 1519 2690 2473 2313 2273 3153 2802 2702 1731 2482 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 7.30044964854141e-06 8.79033733191721e-06 1120 2488.36363636364 2474 7.30047363210657e-07 285 5.13078948381241 -5.13078948381241 -1 7.49004258320855 1119 3522 4505 4113 3893 866 285 2622 1896 2474 2077 2483 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 2.11108879629285e-07 4.87492129085239e-07 2605 2343.63636363636 2474 1.91917181715451e-08 381 1.76673285402141 1.87890827694337 1 3.21934386082674 2604 381 2761 2759 1857 2443 2474 4368 1233 1658 3242 2484 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 2.56255996174272e-07 5.43188862500952e-07 1835 2622.18181818182 2475 2.3296002365725e-08 1831 1.58066118413658 -1.4303939497207 -1 2.85874804537053 1831 2167 3071 2665 2045 2152 2719 2374 4395 2950 2475 2485 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 1.53231418746484e-07 4.13050997420563e-07 2215 2289.81818181818 2475 1.39301299471957e-08 624 2.11016973483447 2.02844255834369 1 3.88917322946841 2211 2961 1053 2374 1526 2559 2475 2538 3482 624 3385 2486 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 1.26663839171708e-06 1.82494908696722e-06 2475 2559.90909090909 2475 1.15149010998004e-07 1150 1.90252229202495 -2.04900064950509 -1 3.15189527759158 3223 2798 2475 1911 3177 2471 2555 3690 1150 2400 2309 2487 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 9.44215414630895e-09 1.01751067512736e-07 4070 2435.36363636364 2475 9.44215418642836e-10 70 2.14863594318493 -1.85219730312426 -1 4.33760600869896 4069 986 4643 70 722 2475 4369 4356 1821 230 3048 2488 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 3.80217861258134e-07 7.02389207260634e-07 1020 2271.18181818182 2476 3.80217926312679e-08 522 1.69621110041429 1.93666674307032 1 3.01311650805126 1017 3550 4313 3781 2476 562 1234 522 2994 3569 965 2489 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 0.0027724798844431 0.00285162454882794 940 2744.18181818182 2476 0.000252361817333776 571 1.48781168248526 -1.55029853488607 -1 1.09249931035743 937 4259 3534 2476 4570 1601 571 2470 3644 3787 2337 2490 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 5.2066788626849e-08 3.04907248534401e-07 2405 2350.45454545455 2477 5.20667898467767e-09 488 1.72230581387941 1.9344071284053 1 3.23972506347747 2403 969 4277 1293 488 2986 3283 2477 2126 2686 2867 2491 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 2.03980146938336e-05 2.32052613533128e-05 2145 2631.90909090909 2478 1.85438216573712e-06 1655 1.78580754420453 -1.43988498132087 -1 2.38900097459559 2142 1851 2478 1655 4113 2196 1953 3171 2619 3197 3576 2492 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 9.14533361058881e-05 9.91181966520762e-05 2485 2510 2478 8.31428527406689e-06 1473 2.53011974116003 -3.65647679646691 -1 2.9243816628165 2483 2890 1932 1943 4330 2478 1725 1473 3689 3109 1558 2493 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 9.83752819059457e-08 3.40595929530574e-07 2395 2663.72727272727 2478 8.9432078458999e-09 1084 2.80905637163596 2.41003717178305 1 5.24549553663211 2395 3334 1374 4535 1084 2904 3798 2156 3663 2478 1580 2494 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 1.2389221905418e-07 3.71755418903835e-07 2480 2051.81818181818 2478 1.12629296391934e-08 488 2.0703434660835 2.51091167786596 1 3.84310376192934 2478 1324 853 1360 1328 2952 3078 2498 2566 488 3645 2495 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 1.63478529839686e-07 4.24953118178353e-07 2595 2351.18181818182 2479 1.48616856352289e-08 388 1.56129068701325 1.94540993589329 1 2.87176895378615 2592 388 2929 3623 1602 2479 2052 2360 2577 3363 1898 2496 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 4.22894586155573e-05 4.67133734297754e-05 2035 2815.27272727273 2479 4.22902634163521e-06 781 1.07565599174487 -1.28583356474301 -1 1.34425789574793 2035 2479 4632 3336 4256 2190 3672 1161 4208 2218 781 2497 M10082 BIOCARTA_TNFR2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR2_PATHWAY.html TNFR2 Signaling Pathway 21/22 BioCarta 0.000107884251637625 0.000116391695481049 925 2556 2480 9.80814022370455e-06 922 1.53680502313065 -1.66836676453895 -1 1.74498164839177 922 3149 3213 2917 4354 1868 2030 1347 3442 2394 2480 2498 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 9.61457555832763e-06 1.13821912804882e-05 2030 2453.45454545455 2480 9.61461715660935e-07 96 0.933149517462278 -0.933149517462278 -1 1.33128918888609 2027 2480 4412 3863 4193 1766 627 227 3555 3742 96 2499 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 6.3583154536938e-08 3.14536172538656e-07 3865 2413.09090909091 2480 5.78028694314387e-09 592 3.28234284237599 -3.71870703259578 -1 6.1621980100791 3863 2670 880 1833 592 4403 4161 3108 941 2480 1613 2500 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 3.52141579177977e-06 4.4728424481164e-06 1355 2610.18181818182 2481 3.20129220756713e-07 838 2.1152493200642 2.34145113125314 1 3.26660717752419 1351 3699 2150 2906 3651 1423 838 3478 4329 2406 2481 2501 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 4.27158047550886e-07 7.65155971324546e-07 3775 2794.81818181818 2482 3.88325573171899e-08 1046 2.1895022049593 2.4534909527727 1 3.86613766435101 3773 2279 1772 1046 2482 4199 4123 3886 1934 1606 3643 2502 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 8.06821759447527e-08 3.27390259462129e-07 4490 2538.36363636364 2483 7.33474353669708e-09 214 2.1482307421287 -2.20106567476458 -1 4.02195260260748 4489 352 1636 1066 855 4207 4108 4454 214 2483 4058 2503 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 1.38768908509596e-07 3.93386935835012e-07 2805 2372.18181818182 2483 1.26153561147902e-08 1295 1.80163566261718 2.21103962072198 1 3.33142072952736 2805 1295 2301 3063 1428 2483 2577 3255 1646 2352 2889 2504 M226 PID_VEGFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGFR1_PATHWAY.html VEGFR1 specific signals 18832364 38/43 Pathway Interaction Database 7.67629226894455e-06 9.21467434115419e-06 1425 2671.72727272727 2484 6.97847186670614e-07 576 1.39550841769004 1.34762691411281 1 2.02831705977183 1425 4215 3492 2484 3881 1267 576 1427 4353 3797 2472 2505 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 9.03541186088457e-07 1.37749173072917e-06 2485 2340.72727272727 2484 8.21401415612293e-08 1448 1.89789715875452 2.15966549272715 1 3.21118087964892 2484 2956 2147 2617 2980 2520 2308 1827 1761 1448 2700 2506 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 7.14755222455105e-08 3.17725226229176e-07 3580 2286.72727272727 2484 6.49777496069723e-09 734 1.6380481929546 -1.52255159845783 -1 3.07273174057424 3579 1160 2723 1474 734 1894 3204 4004 2484 1319 2579 2507 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 4.91764347484583e-08 3.0357704374324e-07 4025 2771.90909090909 2486 4.91764358367031e-09 424 1.71529523366731 -1.5261362582107 -1 3.22747489660317 4025 1060 4507 1927 424 3675 4400 4186 2486 1994 1807 2508 M1017 REACTOME_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPLICATION.html Genes involved in DNA Replication 206/224 Reactome 1.54475091113566e-05 1.78182412037153e-05 220 2432.18181818182 2488 1.40432887077967e-06 216 1.3972775499771 1.47108813282608 1 1.91533786676346 216 3254 3968 2488 4054 974 1046 2147 3120 3385 2102 2509 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 5.00885493590391e-08 3.0357704374324e-07 3085 2202.36363636364 2488 4.55350459085741e-09 355 2.38924045170969 2.53063194091842 1 4.49589896466283 3085 2223 1017 1029 355 2620 2816 3037 2488 1526 4030 2510 M10792 KEGG_MAPK_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MAPK_SIGNALING_PATHWAY.html MAPK signaling pathway 233/294 KEGG 8.93830310745923e-08 3.31497675696653e-07 2490 2502.90909090909 2490 8.12573042782766e-09 976 2.13575425906478 2.33625944660817 1 3.99524949937942 2490 3573 2010 1531 976 1900 2065 3998 2531 3460 2998 2511 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 1.3907097892973e-07 3.9383542091349e-07 2235 2731.72727272727 2490 1.39070987633062e-08 1518 1.61048562163787 -1.59271154412458 -1 2.97764195665608 2235 3831 4636 2490 1523 1518 2597 2818 2436 4182 1783 2512 M8809 BIOCARTA_PTDINS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTDINS_PATHWAY.html Phosphoinositides and their downstream targets. 39/42 BioCarta 4.70876168752113e-07 8.24688503343219e-07 2865 2349.18181818182 2492 4.28069335941769e-08 555 1.6468085733795 -1.61533515516193 -1 2.89218287130568 2861 1704 3120 1716 2551 2294 2492 4127 555 2968 1453 2513 M276 PID_FGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FGF_PATHWAY.html FGF signaling pathway 18832364 68/84 Pathway Interaction Database 2.15921634691026e-07 4.92819204904082e-07 4345 2626.63636363636 2492 1.96292414439015e-08 296 2.01883326695303 -1.77300930119173 -1 3.67609298970187 4344 296 1831 1105 1877 4302 3546 3615 1634 2492 3851 2514 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 1.49172344679599e-06 2.08373325506868e-06 2105 2631.36363636364 2492 1.35611314388104e-07 1909 1.96207194506045 1.73214101260075 1 3.21794782532703 2101 3427 2492 2185 3289 2433 1909 3336 2923 2530 2320 2515 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 2.73222642725671e-06 3.56738830889397e-06 2520 2338 2492 2.48384529133843e-07 848 2.32745150854922 -2.22069321149593 -1 3.66042125223834 2520 2732 1107 1889 3543 2492 2879 1507 4236 848 1965 2516 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 7.72522275658583e-07 1.21462529683828e-06 1250 2260.54545454545 2493 7.02293224479275e-08 508 1.67226938968501 1.92457379580001 1 2.85571198671657 1250 3383 2493 3664 2873 1149 874 2163 3873 2636 508 2517 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 6.90751521747552e-08 3.15009389627869e-07 2495 2317.45454545455 2493 6.27955948577844e-09 394 1.8036750276654 1.74584922815035 1 3.385451614898 2493 394 2651 3857 697 1870 1501 4366 2890 2494 2279 2518 M9726 KEGG_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PANCREATIC_CANCER.html Pancreatic cancer 83/90 KEGG 4.33541510926236e-07 7.73654416473282e-07 2425 2522.36363636364 2494 3.94128723965294e-08 905 1.70195075822572 -1.51084512532064 -1 3.00268895943438 2425 2583 3034 905 2494 2490 2357 3898 2156 2811 2593 2519 M18607 REACTOME_STEROID_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_STEROID_HORMONES.html Genes involved in Steroid hormones 19/44 Reactome 1.50305398505078e-07 4.08899989016697e-07 2495 2386.54545454545 2494 1.36641280703672e-08 961 2.13064862861536 2.46420858349189 1 3.92962431911567 2494 2818 2595 3860 1506 2293 961 3503 2050 2821 1351 2520 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 1.01256321518393e-06 1.50956992282633e-06 2150 2686.90909090909 2494 9.20512437475028e-08 1868 1.85683923264279 2.27546013975682 1 3.12037242027552 2149 2228 2514 4166 3055 2494 2044 1868 3532 3141 2365 2521 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 7.00853414928381e-08 3.15651538021179e-07 3695 2135.09090909091 2495 6.37139488414045e-09 172 1.80523260664384 -1.82498041076127 -1 3.38791486292586 3694 172 2315 436 715 3390 3516 3431 643 2495 2679 2522 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 5.15558418731776e-06 6.3730763672774e-06 3680 2463.81818181818 2495 4.68690569927049e-07 692 1.14654651990898 -1.19788465715617 -1 1.71932338224476 1237 2669 3678 2480 3763 692 946 2495 4523 3678 941 2523 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 6.62518109759307e-07 1.07719100174438e-06 3210 2559.63636363636 2495 6.02289372066489e-08 1300 1.79948236594389 2.00290527536 1 3.10011570193785 3208 2241 2282 1300 2768 3007 3342 2170 2495 1785 3558 2524 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 7.18310576121944e-07 1.14890746163862e-06 815 2582 2495 6.53009827867188e-08 812 1.52269861981257 -1.39411156449288 -1 2.61083692777617 812 3860 3959 2495 2815 1453 1511 2338 3246 4089 1824 2525 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 8.3164311119554e-07 1.29208541304903e-06 2735 2659.63636363636 2496 7.56039477793726e-08 1955 2.11849456412001 -2.27696219798699 -1 3.60152986544757 2733 3964 2323 3092 2918 2298 3534 1973 1970 2496 1955 2526 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 0.000117367096428001 0.000126477784278577 2455 2656 2497 1.06703052977623e-05 560 3.00046839879087 3.65158498332585 1 3.37646282330209 2453 3150 1820 2295 4359 2497 2412 3554 560 3096 3020 2527 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 1.22877233086598e-07 3.71306363744394e-07 3200 2315.81818181818 2497 1.11706581772451e-08 1199 1.69879520422877 1.85528474576906 1 3.15351507252612 2003 2497 3198 2935 1316 1199 2682 1953 3200 3035 1456 2528 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 3.31527783677587e-08 2.74345541741202e-07 3740 2329.54545454545 2498 3.01388898794115e-09 88 2.23390420538872 -1.86486440244199 -1 4.23190697232885 3736 2498 676 2059 88 4173 3992 1767 2741 481 3414 2529 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 8.98019858316446e-08 3.31497675696653e-07 2250 2728.27272727273 2501 8.98019894606234e-09 1092 1.61789522743582 -1.49656944747904 -1 3.02630746282571 2246 2488 4503 3441 1092 2115 3471 2707 3162 2501 2285 2530 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 1.67695932565219e-07 4.30410441385446e-07 2505 2783.36363636364 2501 1.52450859407195e-08 1627 1.9759915166085 2.28440246881138 1 3.63161796121038 2501 3624 2372 4135 1627 2428 2150 2977 3344 2404 3055 2531 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 4.11674100997539e-08 2.9351990282604e-07 2505 2267.54545454545 2502 3.74249189728159e-09 207 1.77869934214672 2.25631018437468 1 3.35432203097198 2502 1610 2764 4121 207 2386 2924 2215 2549 2817 848 2532 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 4.17971549899374e-08 2.95100601223086e-07 2240 2471.90909090909 2502 4.17971557760884e-09 286 2.00434636405945 2.50408901761459 1 3.77861286355078 2236 3233 4600 1750 286 3126 2949 2134 1755 2502 2620 2533 M13143 BIOCARTA_UCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_UCALPAIN_PATHWAY.html uCalpain and friends in Cell spread 32/44 BioCarta 2.8038816223149e-06 3.64883409355565e-06 2505 2429.18181818182 2504 2.54898654167726e-07 461 2.3494518507019 2.74574768638659 1 3.68837847179051 2505 3087 1731 2194 3557 3410 3947 1499 461 2504 1826 2534 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 1.47177060171864e-07 4.04988312110223e-07 3165 2371.81818181818 2504 1.3379733637983e-08 275 1.85763487060186 -1.65578403057979 -1 3.42822516776612 3162 559 2504 450 1483 3568 4638 4267 275 2731 2453 2535 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 4.10618367960312e-07 7.39739960600256e-07 4630 2415.63636363636 2505 4.10618443833681e-08 418 3.25018903266819 2.0930165996011 1 5.75324358528767 4626 928 4305 512 2523 4713 3648 2505 418 1846 548 2536 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 5.39607806976643e-07 9.19476118747204e-07 2625 2357.54545454545 2505 4.90552672117892e-08 666 2.740626686238 -2.58917847730307 -1 4.77636280921058 2782 666 1224 1783 2625 2623 2871 4718 2505 2110 2026 2537 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 1.9879805236461e-07 4.72935366845837e-07 1270 2914.72727272727 2505 1.80725518480501e-08 1267 1.45307806590852 1.53920578999352 1 2.65317295096431 1267 4690 4105 4302 1783 2208 1719 1661 3347 4475 2505 2538 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 1.55987378344291e-07 4.16672566941172e-07 2130 2338.36363636364 2506 1.41806717640291e-08 605 1.86093834799087 2.33557325183264 1 3.42768534610866 2126 605 2583 3885 1544 3084 2869 2049 1399 2506 3072 2539 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 7.99748823387645e-08 3.27123182997709e-07 3465 2762.27272727273 2506 7.27044411327539e-09 841 2.37271483675968 2.40140828905101 1 4.44256822876953 3461 2506 862 1236 841 4033 4250 4474 1944 2314 4464 2540 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 5.41169636308169e-07 9.2147210799948e-07 2730 2405 2506 4.91972517662251e-08 1082 2.02316226588093 2.45796903047848 1 3.5251905132677 2730 3442 2506 3061 2628 2514 1258 1082 2449 2456 2329 2541 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 1.0014113039825e-07 3.41896906035439e-07 2505 2802 2506 9.10373954150393e-09 1108 1.927240885891 -1.8631395246764 -1 3.59764427287546 3552 2503 2123 3837 1108 3108 4262 3311 2504 2008 2506 2542 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 4.44168262372448e-07 7.88248504248555e-07 2850 2140.54545454545 2508 4.03789410952433e-08 244 1.98331569205631 2.21669131362647 1 3.49458492583599 910 3720 2848 4249 2508 530 244 882 3087 2847 1721 2543 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 1.57067456315221e-06 2.18560847231086e-06 3470 2226.36363636364 2508 1.4278869859322e-07 789 3.88665127142866 -3.66369821901662 -1 6.35198366831127 3466 800 789 1768 3304 3169 2508 2890 1105 1153 3538 2544 M16811 BIOCARTA_ERK5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK5_PATHWAY.html Role of Erk5 in Neuronal Survival 31/34 BioCarta 4.600307311903e-07 8.09599198813653e-07 2910 2238.18181818182 2509 4.18209843077271e-08 253 1.83408564606167 1.8889057600462 1 3.22543084464365 2908 613 2634 451 2536 3724 2509 2442 253 4130 2420 2545 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 1.44053300797871e-07 4.00898570192211e-07 3960 2761.81818181818 2510 1.30957554754823e-08 1458 1.9146864622635 -1.8373952159336 -1 3.53597624777763 3957 2510 1959 2192 1458 1879 3547 3716 2218 2841 4103 2546 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 1.14956554152719e-07 3.59285478750119e-07 4020 2527.09090909091 2511 1.04505963781402e-08 255 2.20534113847688 -1.94349844110804 -1 4.10318745226243 4019 255 1581 4123 1258 3716 4056 2850 2511 1347 2082 2547 M8066 BIOCARTA_IL22BP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL22BP_PATHWAY.html IL22 Soluble Receptor Signaling Pathway 12/17 BioCarta 1.07427791942078e-06 1.59002564429792e-06 1060 2107 2512 9.76616767272537e-08 390 1.35472881928747 -1.38551581328374 -1 2.26753352514423 1056 2868 3062 2912 3081 1104 390 843 3704 2512 1645 2548 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 9.18395111939529e-06 1.08969957977742e-05 255 2498.36363636364 2512 8.34908132566973e-07 252 1.43625021722232 1.47734790983823 1 2.05735480417665 252 3558 4101 2512 3927 821 810 2141 3152 4123 2085 2549 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 9.39381197200207e-07 1.42248291651748e-06 1745 2505.63636363636 2513 8.53983271189262e-08 899 2.49668374233794 -2.55052771918732 -1 4.21451714073586 1741 3625 1232 3097 3002 2513 3379 4096 899 1728 2250 2550 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 9.78116383807446e-08 3.40214394367807e-07 3645 2411.18181818182 2514 8.89196752085763e-09 1041 2.12698935408603 2.09645550657269 1 3.97192652535484 3641 1447 1407 1041 1079 2552 2648 4602 2514 1301 4291 2551 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 9.79402816130512e-07 1.46615328009388e-06 2575 2409.63636363636 2515 8.90366592858511e-08 1671 2.19642741347732 -2.10963393182978 -1 3.69923787625805 2571 2448 1979 2827 3040 2345 2820 2563 1671 2515 1727 2552 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 3.21399124723282e-07 6.2582667850408e-07 2210 2657 2515 2.92181065160594e-08 1717 1.6762535634364 1.8122281362295 1 3.00191620161267 2210 1717 2515 3357 2258 2371 2905 3051 3166 3316 2361 2553 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 1.45415779305439e-06 2.03844735891388e-06 3250 2314.72727272727 2516 1.32196250384153e-07 1006 2.60152461940088 2.05566116705817 1 4.27414843368372 3250 1901 1471 1680 3276 2714 1006 3425 3093 1130 2516 2554 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 1.26006125334114e-07 3.75235906357741e-07 4705 2975.54545454545 2516 1.14551029591982e-08 1340 1.8545387722233 -1.81434739728704 -1 3.44025621448584 4705 2516 2252 1621 1340 4431 4663 3662 1500 2279 3762 2555 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 4.54475211586721e-09 5.19400241813395e-08 3535 2366.90909090909 2516 4.13159284114159e-10 211 2.31580266720572 2.42598591425085 1 4.8704356889449 3532 1170 388 2516 327 3394 3091 4426 2328 211 4653 2556 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 1.35757190211507e-07 3.8811262131939e-07 4475 2524.45454545455 2517 1.23415635080716e-08 224 2.33001405192573 2.27901810605159 1 4.31264678572135 4471 224 969 2517 1411 4317 3617 3827 1167 872 4377 2557 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 8.95236508470874e-06 1.0646299622027e-05 4400 2860.27272727273 2517 8.13854683126298e-07 889 3.59140955436096 3.49950529377921 1 5.15628533632156 4397 2433 1303 889 3921 4405 3819 3558 2112 2517 2109 2558 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 2.20221535629246e-07 4.9824855068977e-07 3265 2430 2518 2.0020141606689e-08 325 2.01258344573375 1.89323423215808 1 3.66194461144212 3261 325 1316 2760 1895 2518 1822 3597 3792 725 4719 2559 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 1.02108007022164e-05 1.20608056342496e-05 815 2117.54545454545 2518 9.28258917603495e-07 250 1.48915785308763 1.61690025671679 1 2.11422342289343 813 2866 2788 3868 3950 1022 1164 250 3230 2518 824 2560 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 1.62377898688151e-07 4.23438498236503e-07 3260 2612.18181818182 2518 1.47616282429965e-08 1228 2.28272921625503 2.65199727226332 1 4.20017119988033 3256 2518 1228 2158 1596 3417 3243 4202 1705 1468 3943 2561 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 2.44573311186299e-07 5.30021133516681e-07 4520 2953.36363636364 2519 2.22339398523129e-08 1373 1.84051673507572 -1.5615190140656 -1 3.33452280287907 4518 1373 2182 2586 1999 4288 4612 2519 2058 2220 4132 2562 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 9.67588877496772e-08 3.39696808054909e-07 1005 2538.81818181818 2520 8.7962629095691e-09 1001 1.26833838096087 -0.942341479283232 -1 2.36838156654856 1651 3958 3856 4462 1063 1001 1001 2520 2586 4159 1670 2563 M9152 BIOCARTA_CCR3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CCR3_PATHWAY.html CCR3 signaling in Eosinophils 38/52 BioCarta 4.09175178063758e-08 2.9351990282604e-07 2665 2690.63636363636 2521 3.71977441521778e-09 200 1.41804471414235 -1.51191251017228 -1 2.67401458600005 2662 4208 3452 2482 200 2374 2519 2803 2521 4133 2243 2564 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 5.55942661080944e-08 3.07843567066819e-07 3535 2487 2523 5.05402431936076e-09 457 1.92754449222648 2.10133009156166 1 3.62357296010403 2883 2948 1822 4180 457 2141 2327 2523 3533 1010 3533 2565 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 7.9686518979468e-08 3.27123182997709e-07 4135 2608.45454545455 2525 7.24422926052776e-09 192 2.00552717934167 1.83644070042536 1 3.75492871003675 4135 1682 2052 192 837 4210 4139 4276 207 2525 4438 2566 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 2.63770703871907e-06 3.46121134911148e-06 4510 2735.09090909091 2526 2.39791836474878e-07 626 2.19590573375497 -2.14070117879406 -1 3.46180918491014 4510 1780 1245 2063 3525 4491 2526 2096 2877 626 4347 2567 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 4.53087329579824e-07 7.99466241352062e-07 4070 2469.18181818182 2526 4.11897657175124e-08 595 2.96126803712366 3.13175704996571 1 5.21290534753415 4070 684 1166 595 2526 3888 3698 3022 1619 1675 4218 2568 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 1.0831660778195e-05 1.27463073729944e-05 3425 2329.72727272727 2526 9.8470128255012e-07 577 2.87711934542373 3.00560173111744 1 4.06563055345435 3422 772 770 1829 3966 3602 3119 2502 2542 577 2526 2569 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 7.98445771682499e-06 9.5627100795265e-06 1850 2421 2527 7.25862426814212e-07 626 2.12597848389393 2.42257940166521 1 3.08059315817345 1850 2672 2260 3142 3891 2938 4585 1304 836 2527 626 2570 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 2.03521138888916e-07 4.80309887777842e-07 2380 2400 2528 1.85019234287799e-08 353 2.14231947243623 -2.16169715812253 -1 3.90790930479207 2377 2105 779 2808 1804 2528 3659 3177 4065 353 2745 2571 M16853 KEGG_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DNA_REPLICATION.html DNA replication 35/36 KEGG 0.000581044408336026 0.000607964887463099 3605 2485 2530 5.28361750343231e-05 264 1.09632236094609 1.12447464749758 1 1.01729429086847 264 2716 3601 2001 4493 1282 546 2027 4270 3605 2530 2572 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 4.58651121176017e-07 8.086788539226e-07 1015 2130.90909090909 2530 4.16955651631466e-08 863 1.9923976838866 1.69625301129806 1 3.50419762129552 1014 3022 2866 1460 2530 1422 863 1539 3137 2971 2616 2573 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 1.83252839965564e-07 4.51437058787818e-07 4545 2851.27272727273 2531 1.66593504754482e-08 1038 2.08158797112969 2.31673358833931 1 3.81328548874799 4543 2531 1584 1038 1711 4716 3855 4269 1156 1807 4154 2574 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 6.14815422694616e-08 3.12995510041999e-07 4205 2601.63636363636 2531 5.58923127160313e-09 565 1.91023396451712 -2.11518669242143 -1 3.58704732573054 4203 724 2175 3125 565 4117 4474 2531 1551 2181 2972 2575 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 4.26188298232141e-08 2.95390421094817e-07 2895 2207.90909090909 2532 3.87443914989405e-09 231 2.2827415405776 2.1749134693374 1 4.30328472229061 2893 1449 936 2070 231 2532 2717 3060 2954 1088 4357 2576 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 0.000763350093476845 0.000796069916308155 2535 2851 2533 6.94195533979462e-05 1791 1.65953317337951 -2.12572878003377 -1 1.48424583732 2533 4044 3057 2462 4510 2185 1791 2729 2384 3542 2124 2577 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 2.48160109558645e-07 5.33113588540658e-07 3120 2431.27272727273 2534 2.25600125046474e-08 1113 1.76723305432083 -1.54753643159677 -1 3.20042878728853 3119 2126 2639 1239 2017 1923 2902 4580 1113 2552 2534 2578 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 4.33947908555939e-07 7.74086972178394e-07 4315 2874 2534 3.94498176501614e-08 327 2.50663975879656 2.161076144681 1 4.42260361712005 4311 2363 1565 2792 2495 4314 4267 1951 327 2534 4695 2579 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 5.01626816436897e-08 3.0357704374324e-07 3780 2553 2535 4.56024388976909e-09 358 2.12921395395338 2.15333767244209 1 4.00650626736704 3777 2494 900 1324 358 3751 3782 4049 2535 714 4399 2580 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 6.77052439193379e-08 3.14536172538656e-07 3010 2447.54545454545 2535 6.77052459821379e-09 770 2.04782323921731 2.29411663415834 1 3.84421420128474 3006 1061 4691 1406 770 3042 3324 2535 1863 2060 3165 2581 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 3.55678586314228e-07 6.70180809342577e-07 2540 2221.36363636364 2536 3.23344221652309e-08 343 1.8763378111871 1.89790112481694 1 3.34422701404977 2540 343 2359 1085 2341 2762 2536 2621 2842 1867 3139 2582 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 1.73515351734346e-06 2.38634166720895e-06 2215 2807.81818181818 2536 1.57741353261019e-07 1507 1.04961400821566 1.23312321724698 1 1.70319738924302 2215 3127 3531 3422 3345 2536 2166 2273 2474 4290 1507 2583 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 1.2600128176762e-16 4.21791524782386e-15 3670 2411.27272727273 2536 1.14546619788745e-17 101 2.86640276699302 -2.7089515924275 -1 11.8974561406732 3667 1281 101 688 1646 4121 4614 4520 2536 252 3098 2584 M4557 BIOCARTA_NEUROTRANSMITTERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NEUROTRANSMITTERS_PATHWAY.html Biosynthesis of neurotransmitters 3/9 BioCarta 5.18817473497319e-08 3.04579412301909e-07 1955 2532.27272727273 2537 5.18817485610039e-09 3 5.31176750922839 -5.31176750922839 -1 9.99415558087614 1954 3540 4187 2537 4558 1946 1366 3 3945 2651 1168 2585 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 0.000923932171227849 0.000960563843214856 980 2483 2537 8.40291293225429e-05 977 2.12153381886981 -2.12153381886981 -1 1.84771294130287 977 3495 2537 4355 4526 1418 1024 2949 1193 3114 1725 2586 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 7.2129300913144e-07 1.15172632039932e-06 1540 2389.45454545455 2538 6.55721132377277e-08 1078 1.82073957896158 1.70509481827778 1 3.12147050303693 1536 3012 3253 2025 2822 1338 1078 1529 3502 3651 2538 2587 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 7.65817316024063e-08 3.24764325922831e-07 3470 2762.90909090909 2538 6.96197584256429e-09 793 1.9659124818849 2.20724062157424 1 3.68252572814155 3469 2538 2038 1077 793 4071 4575 4663 1380 2468 3320 2588 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 5.82458553283676e-06 7.13523065533079e-06 1490 2721.54545454545 2539 5.29509177610052e-07 1490 1.50765287278318 1.4818702114376 1 2.23973974861043 1490 3618 3454 3697 3799 1621 1600 1871 2073 4175 2539 2589 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 0.000690373746754825 0.000720761797098601 1945 2574.72727272727 2539 6.2780953234177e-05 890 2.0577682339934 2.18398640555177 1 1.86626999028049 1945 3479 2539 2460 4505 2017 1092 3417 3100 2878 890 2590 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 9.3752230008799e-08 3.37597645620766e-07 4435 2619.54545454545 2539 8.52293036400163e-09 649 1.72956713141272 -1.61148640150107 -1 3.23129658370037 4431 649 2136 2539 1025 3628 2916 3963 1279 1959 4290 2591 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 2.08102970429738e-06 2.8064172012239e-06 2540 2586 2539 1.89184697526637e-07 1125 2.86719207174726 -2.41153930341331 -1 4.59574994036616 2539 3359 1338 2633 3423 2458 3575 4007 1125 2392 1597 2592 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 4.61157948563713e-07 8.10374354884857e-07 1740 2352.81818181818 2540 4.19234586573093e-08 1373 1.5736557006253 1.41823494772264 1 2.76712646410669 1740 1731 2678 2610 2540 1833 1373 1793 3263 3608 2712 2593 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 1.13002362278105e-05 1.32745433039487e-05 2455 3103.72727272727 2540 1.02729947923307e-06 2071 1.72186949652806 1.54994833035295 1 2.42404342726872 2455 4452 3286 4306 3975 2387 2098 2071 2226 4345 2540 2594 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 1.60519675002496e-07 4.21620960496262e-07 4370 2742.63636363636 2541 1.45926987922339e-08 107 1.83234773509867 -1.56749113095047 -1 3.37229777845138 4370 107 2311 2334 1580 3337 4047 3525 1465 2541 4552 2595 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 1.10269491956608e-07 3.53626743374685e-07 2350 2391.09090909091 2546 1.00244997712355e-08 1142 1.86232956592767 1.9384096080899 1 3.46856480070086 2350 3705 3102 2853 1211 2546 1142 1501 1250 3615 3027 2596 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 0.000210984690800752 0.000224948665141078 1125 2921 2546 1.91822661272306e-05 1124 2.04000587469044 2.208285959022 1 2.14805624818405 1124 4270 2546 3929 4409 2414 2338 1853 4374 2603 2271 2597 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 7.67416383070497e-08 3.24764325922831e-07 920 2288.72727272727 2547 7.67416409572252e-09 381 2.13301053454479 1.86832759950833 1 3.99560518071257 2890 918 4515 2712 918 3018 3572 1531 381 2174 2547 2598 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 3.62499067570634e-06 4.59081191020497e-06 3050 2700.45454545455 2548 3.29545149881886e-07 1253 1.90897085698802 2.196674741281 1 2.94173236164536 3050 2436 1834 2548 3662 2606 2140 4634 3653 1253 1889 2599 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 2.56847249926399e-07 5.43397140140119e-07 3255 2578.36363636364 2548 2.33497527193636e-08 584 2.51768394511744 -2.53616714934353 -1 4.55381575920689 3253 1465 584 2514 2050 4032 4544 2548 3134 874 3364 2600 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 4.89062477835986e-07 8.49850527373285e-07 1985 2641.72727272727 2549 4.44602351413781e-08 1103 2.02164010501851 1.52759849856298 1 3.54305135908096 1984 3648 2786 3722 2571 2447 2443 2453 1103 2549 3353 2601 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 3.94236990755123e-07 7.19844718129277e-07 2300 2706.54545454545 2550 3.58397328547155e-08 718 2.16219156414182 -2.44335608116527 -1 3.83445545347911 2297 3299 1039 3756 2425 2550 3498 4121 4277 718 1792 2602 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 9.74399588173488e-08 3.39726302159777e-07 3355 1936.54545454545 2550 8.85817846664106e-09 122 2.38157161477213 -2.67429914565862 -1 4.44786372638359 3352 212 696 122 1072 3643 3674 2846 2550 571 2564 2603 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 1.0061334857611e-07 3.42613246105503e-07 1110 2623.09090909091 2550 9.14666847068134e-09 1109 1.74133156233987 1.9828622064115 1 3.25006104021035 2145 4105 3231 4269 1109 2124 2201 1109 2720 3291 2550 2604 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 5.99390143193747e-08 3.10910012492405e-07 3120 2116.27272727273 2551 5.44900145021941e-09 59 2.70321177454966 2.96931773801103 1 5.07872912411104 3116 59 404 787 1386 3118 3139 4095 2551 420 4204 2605 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 2.38509789051097e-07 5.22548577520102e-07 3575 2606.63636363636 2551 2.16827104462537e-08 292 1.9820786625521 -1.55724709314048 -1 3.59459073205265 3575 292 1950 3263 1974 3909 4436 3351 1706 1666 2551 2606 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 4.76193714874911e-07 8.3214895750077e-07 2560 2475.90909090909 2556 4.32903470861704e-08 215 1.66785527352103 -1.70015272605774 -1 2.92727316271547 1994 2556 3291 215 2557 2356 3371 1554 3904 3492 1945 2607 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 9.40590459013538e-08 3.3764305071295e-07 3190 2251.45454545455 2556 8.55082272025136e-09 162 1.87928530134027 2.14441074425093 1 3.51105325734884 3189 162 1960 1083 1028 3019 2835 4257 2883 1794 2556 2608 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 1.68645518626801e-14 4.12438781304924e-13 3485 2099.54545454545 2556 1.53314107842548e-15 86 3.63853215001203 3.69139163092598 1 13.0114085554839 3484 340 145 86 617 3565 3712 3730 2556 187 4673 2609 M3462 REACTOME_LIPOPROTEIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIPOPROTEIN_METABOLISM.html Genes involved in Lipoprotein metabolism 26/44 Reactome 2.71430523882124e-07 5.62856786404538e-07 2075 2472.81818181818 2557 2.46755052155047e-08 1247 2.744377274279 3.09949791661966 1 4.95181130615975 2075 2775 1247 2557 2098 2994 4551 2698 2899 1766 1541 2610 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 5.33281570793446e-07 9.10998557417686e-07 1765 2471.54545454545 2557 4.84801545510294e-08 1481 1.59765873243435 -1.46207172031884 -1 2.78589551207254 1762 2557 3086 2193 2618 1481 2050 3054 3002 3488 1896 2611 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 4.92432006293246e-08 3.0357704374324e-07 3565 2183.18181818182 2558 4.47665470286804e-09 39 2.17609937499805 2.54526369382543 1 4.09474874598706 3563 39 1902 1813 339 2997 2558 3179 667 3033 3925 2612 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 6.02089509662954e-08 3.10925873699031e-07 2835 2237.36363636364 2558 6.02089525975984e-09 602 2.13565963992894 2.37153121830677 1 4.01223135157603 2835 993 4534 602 646 2410 3191 2558 2749 859 3234 2613 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 1.23820840301871e-07 3.71755418903835e-07 4700 2631.45454545455 2559 1.12564406609801e-08 606 1.78495844296347 1.44343576649199 1 3.31323512760103 4699 606 2208 1420 1326 4398 3859 3812 813 3246 2559 2614 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 3.8452065556048e-05 4.26241778827024e-05 1700 2737.72727272727 2559 3.49570342234842e-06 1583 1.81989710012646 2.07614788272369 1 2.29584726677952 2559 3755 2265 3429 4228 2014 1583 1700 3856 3030 1696 2615 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 1.02995551533921e-05 1.21595548584319e-05 3155 2583.36363636364 2559 9.36327579297285e-07 845 2.43427680793763 2.73101116427088 1 3.45410802266446 3151 845 1414 2278 3953 3037 2332 3013 2559 1218 4617 2616 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 9.61553231219531e-08 3.39286984245748e-07 4425 2597.90909090909 2559 8.74139339314643e-09 943 2.76463160344869 -2.46113585789155 -1 5.16386026396392 4424 2802 1575 2559 1053 3821 2762 2405 943 2535 3698 2617 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 4.77562522024125e-07 8.33306877616958e-07 3935 2295.18181818182 2560 4.34147841536821e-08 624 2.30567571413363 2.20503452099965 1 4.0466469260671 3931 624 1373 1426 2560 3071 1805 2984 2631 1615 3227 2618 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 4.77842857994098e-07 8.33487911948316e-07 3150 2583.27272727273 2561 4.34402692529291e-08 753 1.30795042602931 1.42538269450443 1 2.29515018964416 2460 1796 3212 1295 2561 3146 3514 3149 753 4145 2385 2619 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 3.95070662172771e-08 2.9351990282604e-07 4050 2748.90909090909 2561 3.59155153879413e-09 172 1.81985913911158 -1.59674683218626 -1 3.43196228326451 4048 1421 2362 2561 172 4416 3950 3439 1456 1834 4579 2620 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 6.79920626903139e-08 3.15009389627869e-07 3175 2794.63636363636 2562 6.18109679924012e-09 678 1.28690658190195 -1.42230293229854 -1 2.41524376285101 3175 3623 3766 2027 678 2562 2336 2543 3433 4293 2305 2621 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 1.78774670663518e-07 4.45285723235782e-07 4280 2728.90909090909 2563 1.62522441082697e-08 608 2.59133905222248 -2.21346436484098 -1 4.75177403146979 4277 2325 1826 2563 1687 3416 2933 4209 608 2286 3888 2622 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 8.00700211785378e-08 3.27123182997709e-07 3075 2313.54545454545 2565 7.2790930993385e-09 607 2.21285292870168 2.40053529653892 1 4.14319170208099 3075 1994 607 972 842 3725 3606 3347 2565 889 3827 2623 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 6.07867276381762e-07 1.00742048613831e-06 4480 2625.63636363636 2566 5.52606767579606e-08 637 2.37660536943525 -2.33660175722854 -1 4.11460733873305 4477 2427 1769 2131 2710 3341 2566 3402 637 1797 3625 2624 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 4.10258187561916e-07 7.39546157616882e-07 2480 2838.36363636364 2567 3.72962058242992e-08 1595 1.59275799234241 1.34432849294884 1 2.8189951823615 2476 2204 2748 4434 2460 2072 1595 2930 3968 2567 3768 2625 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 1.5192801931394e-07 4.1165341628117e-07 3970 2450.54545454545 2568 1.3811639073256e-08 454 1.74248577123011 -2.29853196663193 -1 3.21209951956533 3967 454 2758 1627 1515 3932 4302 1893 456 3484 2568 2626 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 1.23085648966102e-06 1.78214027384633e-06 3070 2580.18181818182 2568 1.11896107118311e-07 968 2.08326848048577 2.70837561588706 1 3.45761958508613 3069 2568 1916 1441 3160 4221 3725 1890 968 2485 2939 2627 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 7.69002866822949e-08 3.24764325922831e-07 2570 2667.36363636364 2568 6.99093539730178e-09 798 1.78775768268014 -1.74079319925936 -1 3.34873005476256 2568 3843 3197 3379 798 1643 2503 3049 2540 3371 2450 2628 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 9.85604156316312e-07 1.47312375810264e-06 2835 2269.90909090909 2569 8.96004179881011e-08 135 3.07391918964043 3.27360582113979 1 5.17563114771345 2831 1786 1176 1791 3044 2569 2945 3338 135 2343 3011 2629 M5576 BIOCARTA_PLCE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLCE_PATHWAY.html Phospholipase C-epsilon pathway 15/16 BioCarta 4.8549593148191e-07 8.44340750403322e-07 2030 2407.36363636364 2569 4.41360035110155e-08 684 1.3290917851132 1.37712657570923 1 2.33010597610134 2028 3172 3181 2644 2569 1961 1300 1474 3693 3775 684 2630 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 4.35253239045958e-08 2.97164560412799e-07 2065 2451.81818181818 2569 3.95684770597373e-09 248 1.6370886314692 1.85229566178764 1 3.08466634156154 2061 3667 2956 3897 248 2272 2579 1303 2569 3187 2231 2631 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 1.702493741663e-07 4.33060067498401e-07 3220 2520.54545454545 2570 1.54772170310212e-08 686 2.77174095727486 2.9655359216019 1 5.09231654349601 3218 4209 2036 2570 1642 2723 2294 2784 686 3601 1963 2632 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 6.4442291194356e-08 3.14536172538656e-07 2760 2329.27272727273 2571 5.85839028018151e-09 419 2.2481270406647 3.22505040071455 1 4.22031269936206 2760 3715 2571 3146 615 2601 1574 419 2037 3708 2476 2633 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 1.04542528414742e-06 1.55362868922787e-06 1805 2583.36363636364 2571 9.5038707356987e-08 932 1.97512084161065 2.52542262072866 1 3.31207072572834 1801 3117 2503 4165 3063 1866 932 2040 3112 3247 2571 2634 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 9.93603709104566e-07 1.48364742390811e-06 3825 2735.72727272727 2572 9.03276507140082e-08 1141 2.12149265988414 -1.85540625559973 -1 3.56984710985165 3822 2106 1994 2585 3048 2542 2572 3794 1141 2497 3992 2635 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 6.51475161048074e-08 3.14536172538656e-07 2575 2636.72727272727 2572 5.92250163945351e-09 631 1.56152211116459 -1.68292781682557 -1 2.93111558532071 2437 2293 2572 4175 631 2572 2930 3428 2908 2736 2322 2636 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 7.09783421862045e-05 7.72820703849793e-05 1315 2579.90909090909 2573 6.4527847505072e-06 655 2.51168356620869 2.51168356620869 1 2.98145120908246 1313 3784 2985 3200 4309 2033 2573 1910 655 3561 2056 2637 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 6.75908429135684e-06 8.18442223068351e-06 1545 2625.63636363636 2573 6.14464096132315e-07 1542 1.79206246950365 2.22741786183934 1 2.63158391320327 2097 3166 2573 2661 3840 2176 1542 1545 3059 3756 2467 2638 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 3.65568578189956e-08 2.8614986551519e-07 4445 2702 2575 3.32335076604109e-09 125 1.91840356560746 2.18249983910952 1 3.62396590703786 4443 1411 1691 1640 125 3826 3889 3981 2575 1985 4156 2639 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 2.08588632144171e-07 4.84679970737421e-07 2800 2630.90909090909 2577 1.89626047200991e-08 1842 1.89516305774003 2.10985633740859 1 3.45480722566813 2798 2582 2881 4151 1842 2394 2092 2517 2041 2577 3065 2640 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 1.55425119320061e-07 4.16353338822743e-07 2890 2321.09090909091 2578 1.41295573000456e-08 437 1.97480617763452 -1.6909712739998 -1 3.63766242461405 2887 437 2578 2419 1538 2549 2649 3229 2900 2743 1603 2641 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 1.39746512751489e-07 3.9520883174777e-07 3125 2328.72727272727 2578 1.27042292389407e-08 628 1.93914563216499 2.03858461665554 1 3.58463372514111 3121 1267 2276 628 1432 3066 3611 3445 906 2578 3286 2642 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 4.47187671872106e-08 2.98969661648207e-07 2035 2537.36363636364 2579 4.06534255419967e-09 266 1.77520892732087 1.93726817653291 1 3.34364243079997 2032 4178 3011 4416 266 1650 997 2579 3080 3494 2208 2643 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 3.70013763589546e-07 6.8921269303183e-07 2585 2329.27272727273 2581 3.36376205292239e-08 455 2.36424885465687 -2.14656894236423 -1 4.20576004168468 3383 2584 1572 455 2374 3487 3472 2747 762 2205 2581 2644 M17902 BIOCARTA_CASPASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CASPASE_PATHWAY.html Caspase Cascade in Apoptosis 25/39 BioCarta 8.28055615080326e-08 3.27411388472988e-07 3145 2307.90909090909 2581 7.5277786022493e-09 354 2.060511621236 -2.18039650175458 -1 3.85767158800437 3144 672 2239 1690 888 3120 3393 4025 354 2581 3281 2645 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 5.85068231598198e-07 9.78916006077099e-07 1835 2453.27272727273 2582 5.31880351992148e-08 1249 1.56349014716469 1.79079061279406 1 2.71219738648441 1832 2335 2982 3337 2684 2582 2989 1903 1249 3510 1583 2646 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 6.13633986297292e-06 7.48604914790183e-06 2000 2598 2582 5.57850634436131e-07 411 2.00870650482217 -2.29929266246459 -1 2.97229072955743 1996 4183 3171 2905 3814 2296 2582 411 2271 3997 952 2647 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 3.99762936894409e-06 5.02766070381458e-06 2155 2501.18181818182 2584 3.63421512097447e-07 131 2.35043728803542 -3.20104046975488 -1 3.59543967927562 2155 2813 2287 2584 3825 3198 3613 131 2394 3324 1189 2648 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 2.57772294913413e-07 5.44865755482002e-07 2585 2361.09090909091 2584 2.34338477378544e-08 1140 2.34358692676295 2.5513558540492 1 4.23806807809199 2584 1724 1330 1814 2053 2664 2607 4274 2878 1140 2904 2649 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 2.11058166178392e-07 4.87492129085239e-07 2280 2740 2585 1.91871078569429e-08 1500 1.31640658462809 1.51716463904618 1 2.39853895852804 2279 3912 3742 2028 1856 3006 3227 1614 2585 4391 1500 2650 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 5.0302559264493e-07 8.69063249371913e-07 2765 2146.54545454545 2585 4.57296097873419e-08 256 1.67249839442597 -1.79665547704681 -1 2.92632085446369 2762 2591 3170 1054 2585 1996 2325 3019 903 2951 256 2651 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 8.17880187477829e-08 3.27411388472988e-07 4120 2683.27272727273 2586 7.43527470803318e-09 742 2.26284071203192 2.2310833429451 1 4.23655489440117 4116 2773 2424 2357 872 4245 3821 3488 742 2586 2092 2652 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 4.53781184840111e-08 2.99073619127066e-07 3395 2604.18181818182 2588 4.12528358363628e-09 276 1.52897633423037 -1.76447292036249 -1 2.87967215700092 3394 1811 3149 4348 276 4336 4258 1137 2033 2588 1316 2653 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 1.6010534750616e-07 4.21105226344428e-07 2625 2156.18181818182 2589 1.45550326507139e-08 279 1.46729951687068 1.56206685338158 1 2.70050769914812 2622 810 2974 2614 1578 2589 2409 3133 1313 3397 279 2654 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 5.29162518671227e-07 9.06191365830477e-07 1040 2430.36363636364 2589 4.81056950863539e-08 1037 1.60495017181723 1.56545741225573 1 2.79967869684349 1037 2989 3256 3169 2611 1745 1702 2509 2224 2903 2589 2655 M1072 REACTOME_INFLAMMASOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLAMMASOMES.html Genes involved in Inflammasomes 14/20 Reactome 5.99931425870451e-07 9.9767098479564e-07 1925 2476 2591 5.45392354063158e-08 805 1.84004869520173 1.5790846945438 1 3.18771854603086 1925 3179 2330 4158 2701 1729 805 1397 3546 2875 2591 2656 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 1.17287688556769e-07 3.63015009828163e-07 2095 2509.72727272727 2591 1.06625177099708e-08 1276 1.9236479377516 2.54844298981909 1 3.57647675424354 2095 3586 2268 2239 1276 3003 2600 2809 2591 2746 2394 2657 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 7.08315113248588e-12 1.27119670514575e-10 3365 2015.27272727273 2592 6.43922830228064e-13 89 2.9057317013818 2.91352267763679 1 8.30241138225742 3364 89 207 940 2592 2667 3010 3639 1220 333 4107 2658 M19118 BIOCARTA_KERATINOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KERATINOCYTE_PATHWAY.html Keratinocyte Differentiation 58/63 BioCarta 1.83961111512266e-06 2.51680129373303e-06 1425 2405.36363636364 2593 1.6723751394392e-07 1304 1.61611572586453 -1.62867244495479 -1 2.61213069032004 1421 1621 3287 1304 3371 2095 2618 2603 2593 3172 2374 2659 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 1.21226572235469e-07 3.69968882213284e-07 4620 2991.27272727273 2593 1.10205980832196e-08 677 2.03682248164712 -1.48201633563015 -1 3.78209652293026 4620 2179 2091 1094 1303 4653 4557 4672 677 2593 4465 2660 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 3.00259311181756e-07 5.99756220388442e-07 2650 2329.90909090909 2594 2.72963047419643e-08 1107 1.79190812519549 -1.44249181197549 -1 3.21865734648665 2646 3378 2827 1107 2192 2650 2594 1235 1352 3189 2459 2661 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 2.54159770872804e-05 2.85627171076103e-05 810 2520.36363636364 2594 2.31057006505604e-06 808 1.68189937137252 1.70509969770411 1 2.20613155765459 808 4024 2907 3992 4165 1568 1346 1895 2594 3201 1224 2662 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 9.81465529612016e-05 0.000106080084721061 1470 2558.90909090909 2595 8.92281197777587e-06 942 1.87628615780281 -2.42297373981113 -1 2.15246767831734 1466 3377 2625 2201 4344 2595 2999 2245 942 3188 2166 2663 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 5.18848298810229e-07 8.92166881053583e-07 960 3080.90909090909 2598 4.71680382886838e-08 958 1.23436816387239 1.32582708214665 1 2.15545019863756 958 4354 4173 4324 2598 2100 2153 2263 3889 4620 2458 2664 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 2.1823144827859e-07 4.96027848178845e-07 1885 2833.63636363636 2598 1.98392245387549e-08 456 1.45529221565304 1.22217883189287 1 2.64851638970733 2292 456 3093 4565 1885 2071 1885 4507 3513 2598 4305 2665 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 1.51495479145982e-06 2.11180939624641e-06 1915 2550.90909090909 2598 1.37723257698423e-07 1352 1.9076517828321 2.15557283742193 1 3.12546877794975 1915 1515 2401 2598 3296 1714 1352 4397 2915 3078 2879 2666 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 6.0091389356389e-07 9.98701963951254e-07 3820 2615.36363636364 2599 5.46285506999259e-08 938 2.49577063393927 -2.45360446674073 -1 4.32368138223105 3818 1576 938 2588 2704 3752 3890 3291 2599 1459 2154 2667 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 3.03703682993309e-07 6.04334478806247e-07 3195 2594.81818181818 2600 2.76094295380672e-08 1071 2.12472058304317 2.39356300647377 1 3.81459470041019 3194 3700 2151 2631 2203 2600 1864 1071 3608 3105 2416 2668 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 4.768993354265e-07 8.32765395195367e-07 4015 2811.27272727273 2600 4.33544944368325e-08 862 1.97149710813008 2.14770549461526 1 3.46017237975243 4013 2745 2369 2600 2558 2754 2547 3649 862 2158 4669 2669 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 2.63723891224365e-07 5.5290113522262e-07 3475 2687 2601 2.39749020761944e-08 1867 1.73824878897541 -2.01150893782033 -1 3.13998001703705 3471 1867 2822 2178 2072 3364 2921 2283 2508 2601 3470 2670 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 2.08370530693061e-07 4.84679970737421e-07 3495 2692.63636363636 2602 1.8942777311695e-08 1453 1.90850615010941 1.98562949063409 1 3.47913721905309 3492 2043 1742 1505 1840 3081 3061 4359 2602 1453 4441 2671 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 5.22314012927213e-07 8.96806890147851e-07 2345 2757.27272727273 2603 4.74831033575159e-08 1021 1.25962534816316 -1.06737815851108 -1 2.19875241067728 2342 3890 3994 2510 2603 1519 2842 1708 3463 4438 1021 2672 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 5.40951867738363e-06 6.66308146066042e-06 1420 2515 2603 4.91775634431282e-07 1418 1.8347164858501 -1.87274365715694 -1 2.7415584385621 1418 2984 1808 2896 3779 1939 2854 1717 3759 1908 2603 2673 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 5.25788904664742e-07 9.02134545035336e-07 2570 2420.45454545455 2604 4.779900275688e-08 64 1.73453131287233 -2.253404128078 -1 3.02676587311615 2570 3972 3083 4129 2604 2615 2403 249 1010 3926 64 2674 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 3.51186205774745e-07 6.63570412832985e-07 3575 2722.72727272727 2606 3.19260238031494e-08 1128 1.65877938617869 1.51430555261118 1 2.95843133632673 3572 1774 2606 2161 2335 2327 1128 2968 3839 2751 4489 2675 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 3.66861194192221e-07 6.86319792543513e-07 2610 2444.27272727273 2606 3.33510232152914e-08 498 2.66681121032412 -2.66344436694836 -1 4.74550489412936 2628 3444 1886 2426 2363 2607 2813 498 3679 2606 1937 2676 M8601 BIOCARTA_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAC1_PATHWAY.html Rac 1 cell motility signaling pathway 35/38 BioCarta 3.98118030639131e-07 7.24688432169957e-07 4075 2893.18181818182 2608 3.61925547894255e-08 622 1.76923649680899 -1.6756671073477 -1 3.13593989214689 4075 1732 2354 2608 2431 4474 4219 2310 622 2853 4147 2677 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 9.75584616961539e-08 3.39726302159777e-07 3390 2475.72727272727 2608 8.86895145657822e-09 1067 1.83836505387683 2.07907610412464 1 3.43316544056194 3388 2521 2608 1067 1075 2995 2860 3908 1587 2372 2852 2678 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 3.0202238812805e-06 3.90774581130591e-06 1695 2372.54545454545 2608 2.74566184321774e-07 736 2.0825396985507 1.84743332218331 1 3.25135429087505 1691 3707 2544 3068 3582 1384 736 2924 2608 2915 939 2679 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 2.54404750090205e-10 3.4906698268191e-09 2965 2057.27272727273 2609 2.31277045563295e-11 53 2.66955369333925 2.6419128374661 1 6.51847095107347 2962 1378 276 1352 53 2803 4024 2609 3147 251 3775 2680 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 5.2768080649479e-07 9.04048423468388e-07 4580 2936 2609 4.79709939146968e-08 245 1.69832711375978 -1.58095652700297 -1 2.96312001618108 4577 245 2388 2325 2609 4482 4407 4198 1588 1958 3519 2681 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 1.02431732384275e-07 3.45516390326962e-07 4290 2617.09090909091 2610 9.31197610486216e-09 1125 1.79120508225387 1.22883963334413 1 3.34127537367642 4286 1866 2384 2421 1125 3481 3364 2610 2774 1721 2756 2682 M1441 REACTOME_P38MAPK_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P38MAPK_EVENTS.html Genes involved in p38MAPK events 15/15 Reactome 1.1177748308358e-05 1.31385011454392e-05 2615 2479.90909090909 2612 1.0161641000551e-06 262 1.88836816128022 -2.10477311054962 -1 2.66096261816938 2612 2415 2526 1255 3971 3265 2753 2508 262 3029 2683 2683 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 2.31102237972542e-07 5.1428692278661e-07 2280 2557.45454545455 2612 2.10092965680928e-08 1937 1.90303876820033 2.13125402737526 1 3.45501730232196 2278 2957 2485 2612 1937 2125 2757 2823 2425 2870 2863 2684 M9546 BIOCARTA_TID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TID_PATHWAY.html Chaperones modulate interferon Signaling Pathway 30/35 BioCarta 2.20368662931671e-05 2.49613652276815e-05 1670 2736.45454545455 2614 2.00337154856421e-06 1666 1.82668277669998 -1.41805268464985 -1 2.42699080163038 1666 2750 2614 2680 4130 2006 2017 2476 3879 3443 2440 2685 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 1.5028434496382e-07 4.08899989016697e-07 3145 2499.45454545455 2615 1.36622141118095e-08 1096 2.22805981179062 -2.1716033382867 -1 4.10932230020088 3142 2701 1987 1096 1503 2452 2615 3207 1910 3302 3579 2686 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 3.44415864275255e-05 3.82684293639173e-05 2455 2386 2615 3.13110233014179e-06 238 2.04860128696209 2.77658148243518 1 2.61216599336191 2452 2892 2188 3138 4372 2682 3362 406 238 2615 1901 2687 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 1.56218722000473e-05 1.79929811576924e-05 1970 2782.90909090909 2615 1.42018028452154e-06 276 1.81224161610506 1.81224161610506 1 2.48219355404938 1966 4068 2615 2955 4626 2123 1452 276 4601 3720 2210 2688 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 1.61122944010496e-07 4.22248632499246e-07 4600 3022.18181818182 2615 1.46475414373429e-08 1005 2.05244809619537 -1.8638967946832 -1 3.77709644904747 4599 2615 2596 2583 1584 3713 4688 2208 1005 3205 4448 2689 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 1.80038610254406e-06 2.46671187344209e-06 2620 2741.72727272727 2617 1.63671597809536e-07 1120 1.4918088667076 2.09286635567457 1 2.41490798078551 2617 3999 3316 1120 3362 3291 2264 1702 1762 4487 2239 2690 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 7.75231298251371e-08 3.25786793959256e-07 2730 2371.27272727273 2619 7.04755750517098e-09 441 1.59409670232694 2.10539543880274 1 2.98525317188743 2729 441 2619 3610 808 3254 3687 1864 2277 2901 1894 2691 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 8.80044907716952e-08 3.31003670356505e-07 1940 2818.54545454545 2620 8.80044942568509e-09 1065 1.53708856328887 -1.49157484558974 -1 2.8754013341149 1937 4353 4522 2985 1065 1732 2123 3244 2620 4135 2288 2692 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 1.51049567236438e-06 2.10621553133231e-06 1390 2649.72727272727 2621 1.37317882677728e-07 489 2.06900893516459 2.09625446146218 1 3.39059504408983 1387 4278 2621 4235 3295 1343 489 1847 3577 3915 2160 2693 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 1.70266321913411e-05 1.95346873950243e-05 1950 2921.36363636364 2622 1.54788763348328e-06 1785 2.12812782017916 1.94246418108085 1 2.89306645715242 1950 4595 2622 3710 4075 2232 1833 2328 3911 3094 1785 2694 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 9.43144679640544e-06 1.11766078029208e-05 700 2226.18181818182 2623 8.57407929951014e-07 17 2.05899207405063 -2.05899207405063 -1 2.94323193268812 700 3754 2623 4000 3934 326 17 1058 3965 2936 1175 2695 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 4.87338337332406e-07 8.4723276324455e-07 1200 3008.45454545455 2623 4.87338444206833e-08 1200 1.58320878702899 1.68825828336906 1 2.775098645784 1200 4688 4585 3811 2623 1898 1949 2504 2995 4534 2306 2696 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 2.60615995507785e-07 5.48665253700599e-07 4585 3008.27272727273 2623 2.36923660346213e-08 1984 1.94224075287936 -1.80268167050895 -1 3.51044630164475 4585 2169 2053 2623 2062 4456 4673 2226 2799 1984 3461 2697 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 8.4320357107649e-07 1.30617684787694e-06 3635 2724.36363636364 2625 7.66548994777239e-08 1663 2.02348342024824 -1.79154552116796 -1 3.4372157539768 3633 1775 1675 2317 2929 4459 3425 2239 2625 1663 3228 2698 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 4.35100221791892e-07 7.75556286577692e-07 4040 2826.81818181818 2626 3.95545734402651e-08 360 2.00687517104883 -0.988968650903232 -1 3.54019222912076 4038 2449 2517 2626 2499 3202 2595 4154 360 3272 3383 2699 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 2.05913527263428e-06 2.77847869835158e-06 1830 2369.18181818182 2626 1.8719429090244e-07 1086 2.63831674127401 -2.62454383651647 -1 4.23213305193168 1827 2774 1284 2790 3421 1651 2626 3984 3128 1490 1086 2700 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 1.08788725399402e-07 3.51706922314159e-07 2630 2601.81818181818 2627 9.88988461626738e-09 1133 0.968582040976383 -0.946198810345964 -1 1.80421944765212 2627 4013 3778 2967 1197 1411 1700 1133 4400 4008 1386 2701 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 5.42454229202758e-07 9.23001366527452e-07 2630 2477 2629 4.93140329959819e-08 1636 2.0399551781154 2.0120600311785 1 3.55403368732677 1636 3004 1850 2594 2629 2630 3110 2083 2038 2738 2935 2702 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 6.09970231351404e-07 1.0098419824548e-06 1705 2298.45454545455 2631 5.54518545883023e-08 82 1.64637273410345 -1.4914334095058 -1 2.84959817130217 1705 2541 3148 2965 2713 360 1734 3723 3681 2631 82 2703 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 8.34934863965115e-06 9.97946963260406e-06 2175 2701 2633 7.59034575174612e-07 1528 2.49292217428296 3.0197062500404 1 3.59911532532003 2173 3354 1528 3368 3903 2633 2134 1654 3659 2389 2916 2704 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 5.44831729365316e-08 3.06874196014832e-07 2565 2563.45454545455 2633 4.95301584416471e-09 437 2.1300803057124 3.02703236803994 1 4.00525115203524 2563 3751 2529 3210 437 2896 2633 907 3500 3757 2015 2705 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 6.86617781630538e-08 3.15009389627869e-07 2635 2064.81818181818 2634 6.24198002781647e-09 688 1.95495295871468 2.2872026621371 1 3.66946863983186 2634 1194 1413 1855 688 2725 2826 2754 2687 1100 2837 2706 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 2.72748738948484e-06 3.56317201172666e-06 1735 2789.63636363636 2635 2.4795370644905e-07 1545 2.08941820209217 2.5593698023521 1 3.28628414633338 1733 3363 2532 1545 3541 2599 2586 3475 3304 3373 2635 2707 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 6.87669221117406e-08 3.15009389627869e-07 3355 2610.72727272727 2636 6.25153856920328e-09 689 2.23977219788301 -1.69314679923814 -1 4.20420303493783 3353 3260 1340 2147 689 4172 4152 2740 2320 1909 2636 2708 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 1.48972669605968e-06 2.08182067281266e-06 3795 2573.45454545455 2636 1.35429791347893e-07 853 1.49337144192073 -1.19201007942962 -1 2.44920943202166 3795 1926 2666 3129 3287 2157 853 2636 1848 2621 3390 2709 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 5.36854390877431e-07 9.15445348606024e-07 1510 2543.36363636364 2637 4.88049565348381e-08 935 1.60198179097752 -1.21004506555083 -1 2.79245785163126 1510 3253 3424 3209 2624 935 1374 2913 2637 3574 2524 2710 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 9.45674313172489e-08 3.3764305071295e-07 2160 2670.18181818182 2637 9.45674353415986e-09 1013 1.67301339514381 1.89849264957227 1 3.12558261347753 2160 1013 4660 1303 1141 2637 3097 4262 1950 3998 3151 2711 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 1.01648559809002e-07 3.43701285850069e-07 2135 2534.36363636364 2637 9.24077859141473e-09 1119 1.67046437933439 1.94794224731645 1 3.11709362862324 2133 3856 3432 3741 1119 1285 1590 3508 3182 2637 1395 2712 M12095 BIOCARTA_IL1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL1R_PATHWAY.html Signal transduction through IL1R 34/52 BioCarta 1.80432427180194e-05 2.06558587506795e-05 3290 2741.72727272727 2638 1.64030824553672e-06 924 1.60500104640781 -1.65384103992987 -1 2.17046124338515 924 3385 3290 2445 4086 1914 2638 1835 4002 3286 2354 2713 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 5.47384467636892e-07 9.28703851408851e-07 3780 2888.72727272727 2638 4.97622367120257e-08 1091 1.78717344288427 1.46355662292384 1 3.11214722887685 3776 1722 2613 1091 2638 3757 2495 3501 2870 2610 4703 2714 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 2.13385943128949e-07 4.90234925824382e-07 3370 2774.18181818182 2638 1.9398723984184e-08 848 1.90223664100539 -1.93050800354185 -1 3.46498673078374 3370 848 2158 2798 1864 4209 4193 2638 4006 1826 2606 2715 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 5.44261592047483e-08 3.06874196014832e-07 2745 2561.36363636364 2638 5.44261605377414e-09 536 1.8539767002614 2.16697991566266 1 3.48597397006633 2744 2485 4674 1963 536 3110 3562 1593 1977 2638 2893 2716 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 4.04879214068733e-07 7.31847334860324e-07 2640 2516.27272727273 2639 3.68072080528278e-08 956 2.21317702102118 -2.41649003832467 -1 3.92030425117466 2639 2675 2198 3566 2452 3201 3170 2897 1852 2073 956 2717 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 3.27040824381614e-07 6.32670513508843e-07 2905 2477.36363636364 2639 2.97309884543502e-08 1237 2.15184551994326 2.71316270430698 1 3.85093864427979 2904 3679 2559 3369 2273 2647 2639 1237 1435 2700 1809 2718 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 1.10129034972405e-06 1.62181349791844e-06 2565 2914.72727272727 2641 1.00117354637776e-07 2212 1.97747781882967 -1.76875946355779 -1 3.30537244227315 2562 3122 2641 2385 3097 3114 3325 4412 2607 2212 2585 2719 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 5.50116102744389e-08 3.07843567066819e-07 4225 2715.27272727273 2642 5.00105560454722e-09 84 1.83155282341782 1.66288247825808 1 3.44307622094379 4222 84 2642 2571 445 4396 3439 4389 1365 2015 4300 2720 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 2.63799439940962e-07 5.5290113522262e-07 1310 2675.36363636364 2642 2.39817701429865e-08 1310 1.50256886729465 1.64042525321093 1 2.71413002019068 1310 3875 3699 3715 2073 2219 2016 1568 2654 3658 2642 2721 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 8.75196592853296e-08 3.30738824521022e-07 4285 2700.36363636364 2642 8.75196627321905e-09 102 2.28079527052068 1.09139969499011 1 4.2672845374364 4281 2460 4614 1182 1056 4655 2834 2642 102 3439 2439 2722 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 1.53314795642197e-05 1.76887273388211e-05 2605 2859.54545454545 2643 1.39378058255547e-06 1447 1.898552519107 -1.64636841087929 -1 2.60451352720668 2602 3744 2701 2643 4053 2076 1447 3230 2613 2539 3807 2723 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 7.57562605679683e-06 9.10541252561269e-06 1630 2698.45454545455 2643 6.88695649394208e-07 341 3.09683672047577 3.10814614884372 1 4.50681404626647 1630 4619 2643 4034 3878 2059 1826 341 3903 3533 1217 2724 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 5.43414974183933e-07 9.23962059851644e-07 2645 2441.54545454545 2644 4.94013734919252e-08 804 2.31347672436323 2.59026763916947 1 4.03037978035839 2644 2156 804 1708 2632 3002 2978 3509 3089 1302 3033 2725 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 6.93558877356769e-08 3.15197676064735e-07 3580 2819.54545454545 2644 6.30508090201355e-09 700 2.32338463525289 2.78099882062499 1 4.36100725016211 3580 2261 2183 1723 700 4061 4314 4203 3119 2644 2227 2726 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 6.98599882293061e-08 3.15651538021179e-07 2810 1891.45454545455 2645 6.3509082225162e-09 219 2.18893183070439 2.32281781097383 1 4.10819367282084 2807 219 929 587 711 2655 3163 3079 2645 799 3212 2727 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 7.93537781023867e-08 3.27123182997709e-07 2580 2506.72727272727 2646 7.21398008769722e-09 826 1.75883433007894 -1.0033490636593 -1 3.29294217885895 2577 3276 2965 3186 826 2646 2313 1203 2927 3164 2491 2728 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 1.24635932024238e-06 1.7995766263518e-06 1745 2573.27272727273 2646 1.13305456939918e-07 1024 1.69256485836061 1.92497558610383 1 2.80693703650757 1745 1776 2968 3856 3168 1998 3487 2646 2583 3055 1024 2729 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 6.55114519545075e-08 3.14536172538656e-07 3930 2427.72727272727 2646 5.95558671866394e-09 554 1.91335967258712 2.19965303296479 1 3.591739984169 3526 1981 1324 1457 636 3928 3869 2856 2646 554 3928 2730 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 8.36908982735717e-08 3.27411388472988e-07 3705 2982.36363636364 2647 7.60826376884399e-09 902 1.92178331203887 2.04492317420656 1 3.5978876870701 3702 2559 2574 1913 902 3700 3184 4669 2533 2647 4423 2731 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 1.13574009247005e-07 3.5893637536524e-07 2355 2399.36363636364 2647 1.03249104645648e-08 1188 2.0759556923287 -1.9108505016341 -1 3.86265956855495 2351 3025 1895 2766 1242 3014 3839 2647 1696 1188 2730 2732 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 3.58697620708332e-06 4.54877154686547e-06 1990 2885.54545454545 2649 3.26089277769049e-07 120 2.42781672975657 -2.42781672975657 -1 3.74431122550324 1989 4066 2649 3894 4241 2456 2430 120 4194 3586 2116 2733 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 4.09878390755282e-06 5.14802023513819e-06 2045 2504.09090909091 2649 4.09879146758573e-07 822 2.11324202284892 1.86256957903871 1 3.22624794376246 2041 2904 4640 1650 3730 1690 822 3360 2731 1328 2649 2734 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 1.72485775248674e-05 1.97845166263364e-05 2655 2807.90909090909 2652 1.56806479633887e-06 1416 1.75074565257618 2.07645584054761 1 2.37709439380316 2652 2585 2358 2824 4077 3723 4669 1416 3421 1481 1681 2735 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 5.57827176390298e-07 9.42356575720188e-07 3150 2490.81818181818 2652 5.07115743483439e-08 470 2.24102502066119 2.25563950582745 1 3.89859229444861 3148 3611 2107 1721 2652 2905 3334 1778 470 3482 2191 2736 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 3.40885262676098e-08 2.77395498531109e-07 3190 2704.27272727273 2652 3.40885267905223e-09 145 1.79183599944405 2.15402682500242 1 3.39179835905175 3188 1960 4618 1469 145 4561 4321 2652 1811 2302 2720 2737 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 2.84237439916565e-07 5.76784486847028e-07 3665 2651.81818181818 2653 2.58397706036108e-08 1540 2.36005379810924 -2.22687713233237 -1 4.25100287142711 3662 2641 1827 1679 2150 2729 2653 4493 1540 3048 2748 2738 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 3.9356746362927e-07 7.19184377766178e-07 2470 2714.72727272727 2654 3.57788667305694e-08 251 2.16322116861027 2.27945191319332 1 3.83653075177207 2467 2654 2225 3037 2422 3872 4347 1498 251 3676 3413 2739 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 1.88095419052633e-07 4.58816732779548e-07 2695 2420.36363636364 2654 1.70995850122183e-08 1211 1.98278641115347 2.04656750184691 1 3.62821689112358 2695 2061 1464 3044 1727 2110 2654 3131 3084 1211 3443 2740 M17636 KEGG_RENIN_ANGIOTENSIN_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENIN_ANGIOTENSIN_SYSTEM.html Renin-angiotensin system 10/30 KEGG 0.0011348847840451 0.00117651135090992 2170 2901.45454545455 2655 0.000103224604103601 1545 2.37371400281982 -2.46299543208687 -1 2.00708030993652 2167 4321 2655 4182 4539 2436 1545 1584 3197 3107 2183 2741 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 4.02105754819409e-07 7.29415512201235e-07 3850 2870.27272727273 2655 3.65550753013132e-08 1586 1.91967329951817 -1.64584173239213 -1 3.40109440746057 3849 1983 1619 2427 2441 4502 3706 2655 3292 1586 3513 2742 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 5.60512623653267e-07 9.45201709054455e-07 3710 2387.45454545455 2657 5.09557060418059e-08 178 2.50040059670322 2.27504371571907 1 4.34896860752856 3708 288 554 178 2657 4278 4598 3263 2611 443 3684 2743 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 1.16435050370923e-07 3.6108635857474e-07 2210 2751.45454545455 2657 1.05850051393864e-08 1272 1.30876477894974 1.53260627998448 1 2.43387524483626 2209 2657 3398 3999 1272 2343 2312 2123 4083 2980 2890 2744 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 9.15904186982658e-06 1.08729068474803e-05 1630 2546.45454545455 2657 9.15907961966715e-07 51 1.80173066965676 1.80173066965676 1 2.58160604024916 1629 3821 4645 4362 3945 1557 401 940 4003 2657 51 2745 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 6.91016016893621e-07 1.11431349495657e-06 3535 2446.27272727273 2657 6.91016231770125e-08 15 2.11979033011615 0.986997823697379 1 3.64308264898412 3534 2463 4675 1048 2862 2692 2643 1243 15 3077 2657 2746 M4052 REACTOME_TELOMERE_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TELOMERE_MAINTENANCE.html Genes involved in Telomere Maintenance 47/93 Reactome 3.33383147857076e-05 3.71124636293726e-05 1260 2611.45454545455 2658 3.03080181799048e-06 1259 1.33655885822046 1.02555318182171 1 1.70908442107368 1259 2658 2939 2458 4208 1464 1714 2005 3907 2714 3400 2747 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 2.05244329900323e-07 4.81966784641554e-07 2495 2589.54545454545 2659 1.86585771861963e-08 1209 1.7476373809273 -2.0216183882613 -1 3.18703704011716 2492 2659 2943 2196 1817 2932 3420 3175 1209 3386 2256 2748 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 5.47581105608227e-07 9.28703851408851e-07 3270 2908.63636363636 2659 4.97801129001352e-08 1554 2.28139857720185 2.25249209035679 1 3.97301894582111 3270 2663 1554 2335 2639 2659 1943 3987 4019 2338 4588 2749 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 5.62365974881478e-07 9.47649911260469e-07 2645 2589.09090909091 2659 5.11241926030931e-08 1196 2.24015821165917 -2.01420515637238 -1 3.89551038577146 2642 2230 1209 3279 2659 2698 4035 3099 3475 1196 1958 2750 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 5.63033974181941e-07 9.48436958650522e-07 2580 2916.36363636364 2660 5.11849198432908e-08 1983 1.87856760398119 -1.91606352516324 -1 3.26638984420633 2576 3006 2654 1983 2660 2580 2419 3463 3807 3593 3339 2751 M11521 KEGG_GLYCOLYSIS_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOLYSIS_GLUCONEOGENESIS.html Glycolysis / Gluconeogenesis 52/81 KEGG 3.43298078038157e-07 6.52560643255266e-07 2330 2751.54545454545 2661 3.12089210552703e-08 1934 1.69515158034453 -1.8167367240499 -1 3.02687676146527 2327 2648 2797 3687 2315 1934 2081 3955 2661 3140 2722 2752 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 2.61977558446022e-07 5.50603299046416e-07 2940 2631.09090909091 2662 2.38161445129546e-08 655 1.71472158710466 -2.01187797288189 -1 3.0983642860392 2938 655 2662 3107 2066 3460 4138 2274 2552 3231 1859 2753 M787 REACTOME_POL_SWITCHING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POL_SWITCHING.html Genes involved in Polymerase switching 13/14 Reactome 0.00041255293228441 0.000433782544081625 790 2562.36363636364 2663 3.75118469274488e-05 698 0.947257018863473 0.981577400051684 1 0.918959004626221 787 2852 3308 1976 4469 1328 698 2013 4200 3892 2663 2754 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 8.45893916447266e-08 3.27455016694392e-07 3425 2418.72727272727 2664 8.4589394864641e-09 394 2.14366356208207 2.45464142100711 1 4.01334685283766 3424 1011 4533 394 1020 3266 3807 2664 2326 706 3455 2755 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 5.65920484407874e-07 9.51940372917022e-07 1725 2521 2665 5.14473299984889e-08 1337 1.75344006876703 1.85095102000926 1 3.04795416904014 1723 3277 3270 3381 2665 1337 1576 2077 3506 2867 2052 2756 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 9.1813129912661e-08 3.35125431650715e-07 1590 2450.81818181818 2666 8.34664852221095e-09 1001 1.78208635730634 1.87801664601127 1 3.33108540179639 1588 3084 2672 3643 1001 2024 2115 2687 3719 2666 1760 2757 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 2.69122627294296e-07 5.59338969981981e-07 2670 2732.27272727273 2666 2.44656963832418e-08 1537 2.28315168986043 2.09167767382989 1 4.12125028729116 2666 2676 1577 3575 2092 3823 4580 1537 3102 2036 2391 2758 M11911 KEGG_ABC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ABC_TRANSPORTERS.html ABC transporters 35/50 KEGG 9.52400002632003e-07 1.43483179458125e-06 2950 2214.27272727273 2667 8.65818559031704e-08 479 2.91208368216694 -2.51826048165217 -1 4.91271797489301 2948 2711 1335 1848 3020 3132 2667 479 3218 1737 1262 2759 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 9.13426382182694e-08 3.34733891607323e-07 2620 2904.27272727273 2667 8.30387654643269e-09 994 2.29196462074196 2.72519739177168 1 4.28473504438672 2619 3861 2016 2667 994 3980 4282 2087 2502 3573 3366 2760 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 4.36800523710429e-06 5.4542287616752e-06 345 2274.54545454545 2668 3.97092173601332e-07 344 1.25540491836784 1.23028495541354 1 1.90715743236111 344 3593 3907 2668 3720 461 558 1489 3061 3506 1713 2761 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 2.32416837554254e-07 5.15868718890617e-07 1880 2662.36363636364 2668 2.11288056461551e-08 1274 2.10472548759946 2.23556255105834 1 3.82046557924069 1878 3633 2347 3627 1945 1548 1274 3612 3527 3227 2668 2762 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 5.7204396348471e-07 9.60870999162928e-07 3605 2612.90909090909 2669 5.20040102025115e-08 395 2.0165395643438 -1.00784031016647 -1 3.50306021130277 3603 3451 2328 1109 2669 4425 4445 1566 395 3199 1552 2763 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 1.06134393988833e-07 3.48348225330125e-07 4055 2746.90909090909 2670 9.6485817371877e-09 755 3.12441787357089 -2.25061883255538 -1 5.82566456254747 4051 755 924 2265 1169 3958 4344 4370 2670 1424 4286 2764 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 1.96378264769892e-07 4.69319194791844e-07 4495 2808.36363636364 2670 1.78525711181071e-08 465 2.18019744679678 1.91878071621389 1 3.98334872212967 4493 2177 2349 2558 1775 4282 3961 2870 465 3292 2670 2765 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 9.89233068226047e-07 1.47805637291135e-06 485 2343.27272727273 2671 8.99303193669413e-08 481 1.51712755389047 1.49639060431613 1 2.55335166708261 481 3571 3652 3712 3046 852 801 1520 2671 3589 1881 2766 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 4.04996872596433e-07 7.31847334860324e-07 2030 2747.90909090909 2672 3.68179042865563e-08 1592 1.88102166919221 -2.02329323435009 -1 3.33181263081089 2030 3246 2569 3449 2453 2672 3881 2061 3316 2958 1592 2767 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 3.68296190200441e-06 4.65673189859652e-06 2435 2699.45454545455 2673 3.3481527886983e-07 1423 1.62181902885952 -1.60818084462662 -1 2.49620085357476 2432 4016 3114 3432 3670 1893 1423 1735 2673 3520 1786 2768 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 8.36584694884037e-07 1.29779509491601e-06 3225 2469 2673 7.60531830007937e-08 727 2.17394615135658 2.19042546834271 1 3.69462034453199 3221 1802 1800 1902 2922 3223 2673 3697 727 2415 2777 2769 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 5.64272529589893e-07 9.49845342248321e-07 1810 2613.72727272727 2674 5.12975158471638e-08 940 1.21404052466023 1.20512511930125 1 2.11040201907802 1808 2321 3491 2674 2663 1695 940 3408 2969 3765 3017 2770 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 6.13877310325931e-07 1.01382117030735e-06 2915 2454.90909090909 2674 5.58070437835763e-08 850 2.75821353934558 -2.99382312642259 -1 4.77323157127712 2912 850 1698 1815 2719 3304 3121 2674 4181 1416 2314 2771 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 9.31875317526894e-07 1.41202295304236e-06 2675 2615 2675 8.47159738409623e-08 1110 1.81709876902578 1.60234846677278 1 3.06879382434218 2675 3033 2681 1110 2999 2079 2221 3322 1748 4366 2531 2772 M86 PID_ARF6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_PATHWAY.html Arf6 signaling events 18832364 55/66 Pathway Interaction Database 3.84389764734381e-08 2.90188188019013e-07 3190 2379.36363636364 2675 3.49445246773217e-09 162 2.56304176581076 2.58848138940003 1 4.83750655196666 3190 3043 1621 882 162 2675 2947 3806 856 2281 4710 2773 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 5.80013632445328e-07 9.73218750494827e-07 2425 2833 2676 5.27285259419695e-08 1701 1.19480618997005 -1.23027463858802 -1 2.07331022381282 2421 3724 3396 2630 2676 2205 3481 1991 2730 4208 1701 2774 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 1.9766229873827e-06 2.68208091667063e-06 2460 2744.45454545455 2677 1.79693160301045e-07 1701 3.14270376848488 4.3403705521623 1 5.05530339871483 2458 3473 1701 3047 3399 2677 2575 1976 3412 2876 2595 2775 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 1.79921498932876e-05 2.06073641097591e-05 1285 2449.45454545455 2677 1.63566336720648e-06 786 1.38776996216568 1.50872300118607 1 1.87698966829863 1281 3455 3099 3150 4085 1340 786 1287 3931 2677 1853 2776 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 0.000173409230764396 0.000185641090770685 180 2425.27272727273 2678 1.57657182546179e-05 176 1.08192856962223 1.10780326140574 1 1.16488810420393 176 2742 3353 1988 4532 1119 668 2220 4315 2887 2678 2777 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 4.8487056979303e-07 8.43563984306341e-07 3445 2902.09090909091 2679 4.40791524233144e-08 1140 2.28304675376586 1.71195332499035 1 4.00342011895937 3442 3288 1140 2632 2568 2679 2646 3798 3595 1648 4487 2778 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 2.23899179623272e-06 2.99377939892874e-06 1270 2482.09090909091 2681 2.03544915900967e-07 1013 1.55427722940356 1.63754618193443 1 2.47832013127329 1266 2986 3521 2681 3458 1013 1168 2451 2841 3724 2194 2779 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 1.0199215410638e-06 1.51958007380717e-06 1475 2345.18181818182 2681 9.27201830818586e-08 490 2.38402121504391 -2.54087046960072 -1 4.00455723814232 1472 3050 1028 3338 3057 2681 3218 490 4338 742 2383 2780 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 1.57674942089919e-05 1.81518469918151e-05 2295 2984.90909090909 2682 1.43341883785746e-06 1141 2.35391859481134 2.73605801063809 1 3.2217808677328 2294 4262 2682 4653 4060 2495 1802 1141 3183 3988 2274 2781 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 6.26623368832103e-05 6.83694475470996e-05 1330 2570.54545454545 2682 5.69673834165742e-06 215 1.32503168227285 1.10097192779515 1 1.59281122188292 1328 3422 3576 2682 4299 754 215 1684 4045 3632 2639 2782 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 8.35366434221446e-08 3.27411388472988e-07 2685 2158.54545454545 2682 7.59424059946651e-09 190 2.25295150114453 2.71767833527671 1 4.21803626762372 2682 190 1354 2718 900 3043 3271 2689 3028 1529 2340 2783 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 5.84876756547698e-07 9.78916006077099e-07 4605 3024.36363636364 2683 5.31706283671852e-08 1846 2.32078428716821 2.19259947647144 1 4.02629806487828 4601 2601 1933 2344 2683 4516 3972 3793 1846 1877 3102 2784 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 1.31052868346508e-06 1.87487428343366e-06 990 2467.36363636364 2687 1.19139042194629e-07 870 1.30195733725816 -1.12352743721897 -1 2.15226489325463 990 2687 3656 4417 3202 870 1122 1252 4112 3003 1830 2785 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 1.16129442743779e-06 1.69761448690191e-06 2690 2497.36363636364 2688 1.05572276403673e-07 272 1.83606609246422 2.10332742256381 1 3.05842184053151 2688 2726 2842 1953 3123 3158 2334 2108 272 3764 2503 2786 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 1.50037034352225e-07 4.08899989016697e-07 1460 2387.45454545455 2688 1.36397313258682e-08 1458 1.67693510271807 1.80391046927171 1 3.09264234294862 1458 1510 2875 3172 1499 2340 3164 2140 2721 2688 2695 2787 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 7.29711618178687e-07 1.16241607755768e-06 3915 2699.09090909091 2690 6.63374418377027e-08 811 1.95148546530402 1.33438406018594 1 3.3434216941214 3914 2690 2176 1714 2828 3833 4354 811 2478 2805 2087 2788 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 3.67849056267978e-06 4.65232461303552e-06 2695 2377.45454545455 2691 3.34408792116529e-07 669 2.13192202653861 2.92008425630047 1 3.28184306077627 2694 2691 2417 1098 3669 2584 2766 2808 1065 3691 669 2789 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 2.19984504230687e-07 4.98020421652984e-07 2695 2472.45454545455 2691 1.99985932934173e-08 479 1.83733349447414 1.34850541435 1 3.34310357757484 2691 2380 2457 3042 1894 2837 3394 2774 479 2255 2994 2790 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 5.9227857296137e-07 9.88527179765794e-07 715 2495.81818181818 2692 5.38435211284732e-08 713 1.71847807642011 1.87522875848512 1 2.97903580595616 713 4482 3146 4623 2692 1317 1148 958 3692 2916 1767 2791 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 9.82203803476685e-08 3.40595929530574e-07 4525 2462.45454545455 2693 8.92912588479808e-09 529 2.82686984718851 -2.47715641602302 -1 5.27876501837809 4525 529 847 810 1082 4432 3389 2693 3430 1123 4227 2792 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 2.26729196816882e-05 2.56449031626093e-05 370 2422.18181818182 2694 2.06119575902554e-06 368 1.61900756128095 1.66950407864546 1 2.14548357209723 368 3587 3518 2694 4138 1244 959 1421 2762 4190 1763 2793 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 1.24554746379626e-05 1.45519406661346e-05 2260 2805.81818181818 2695 1.13232228692545e-06 1531 1.89874306551966 1.8407541088589 1 2.65125659339486 2256 2695 1949 3601 3994 2236 2991 3168 4341 2102 1531 2794 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 1.4576072840505e-07 4.03108583702953e-07 2195 2674.18181818182 2696 1.32509761874918e-08 1474 1.46199649710007 1.52993369329163 1 2.69875259660932 2191 2960 3850 3714 1474 1773 2280 2719 2622 3137 2696 2795 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 5.96116560169191e-07 9.9317690222329e-07 1875 2627.81818181818 2696 5.41924292449301e-08 1450 2.36311073305742 2.76606943752853 1 4.09545920216825 1872 3610 1662 3704 2696 1809 2506 3396 2990 3211 1450 2796 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 3.36461126583797e-06 4.29912430285739e-06 310 2305.63636363636 2697 3.05874219234576e-07 307 1.45775672798893 1.42456501874202 1 2.25820686403883 307 3237 3845 2697 3630 631 381 1731 2815 4020 2068 2797 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 3.70259219736917e-07 6.89397837143294e-07 2700 2672.36363636364 2698 3.36599347319479e-08 1685 1.79780680034852 2.17052936100519 1 3.19784989007527 2698 2338 2900 1752 2375 2383 1685 2829 3233 3621 3582 2798 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 4.77367697855267e-07 8.33274975546176e-07 3110 2585.36363636364 2700 4.33970728579163e-08 723 1.71403618766781 2.11604875051863 1 3.00805902949437 3108 2700 2695 1677 2559 3467 3981 2789 723 2856 1884 2799 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 3.95460818731726e-07 7.20963717425162e-07 2700 2775.27272727273 2700 3.59509899834337e-08 2147 1.83427397532012 -1.39014097918325 -1 3.25243468140324 2700 3639 3082 2959 2427 2147 2423 2485 2630 3028 3008 2800 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 8.95574151237703e-41 1.69084399753678e-38 3045 2145.90909090909 2701 8.95574151237698e-42 15 2.25994286348391 2.49055523239061 1 24.6487281471859 3045 954 4607 17 598 2844 3677 2701 1658 15 3489 2801 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 3.27019454863052e-06 4.20122979573654e-06 435 2668.36363636364 2702 2.97290855420735e-07 435 1.43243255462039 1.54958711387654 1 2.22310012311212 435 3567 3947 3231 3612 1698 1815 1799 2702 4370 2176 2802 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 1.43343822892132e-06 2.01664036974921e-06 265 2110.27272727273 2703 1.30312651172476e-07 261 1.48078315451336 1.64592614431254 1 2.43446389978489 261 3241 3735 2980 3266 563 481 588 2703 4018 1377 2803 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 6.83907710199925e-08 3.15009389627869e-07 4060 2501 2704 6.21734301327610e-09 592 2.24458320170916 2.5081583339996 1 4.21323546276237 4056 2704 1634 2724 685 2853 1207 4106 592 2407 4543 2804 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 3.43423863950441e-07 6.52560643255266e-07 3570 2527.72727272727 2705 3.12203561417746e-08 371 2.46257796285178 -2.28244911148844 -1 4.39758963054878 3568 371 988 2705 2317 4381 4240 2970 1790 1349 3126 2805 M10401 BIOCARTA_TEL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TEL_PATHWAY.html Telomeres, Telomerase, Cellular Aging, and Immortality 34/37 BioCarta 7.1646886198323e-07 1.14732512658561e-06 2695 2947.09090909091 2706 6.51335541194616e-08 1644 2.01416525134874 1.98200405436688 1 3.45413750974984 2692 3706 2706 2240 2812 2265 1644 3292 2604 3760 4697 2806 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 2.68422305799937e-06 3.51151131756015e-06 115 2575.45454545455 2706 2.68422630027893e-07 114 1.59578227524819 1.60090405948012 1 2.51260167197614 114 4091 4684 3807 3571 876 492 1556 2706 4421 2012 2807 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 1.24049474789066e-07 3.71990801146373e-07 2450 2527.36363636364 2707 1.12772256167032e-08 1020 1.58671769567826 1.78881110056974 1 2.94503956567504 2446 1805 3069 3117 1329 2596 2707 3266 1020 3337 3109 2808 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 6.05790937357102e-07 1.00503804018472e-06 4450 2926.81818181818 2707 5.50719185606788e-08 973 3.02638859484514 -2.94614616506242 -1 5.24070854786137 4449 2306 973 1376 2707 4303 4080 4715 2148 1159 3979 2809 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 1.43426416945265e-07 4.00102061454877e-07 4545 2392.63636363636 2708 1.43426426202278e-08 3 2.4812537220771 1.52138439407402 1 4.58316664603393 4541 910 4484 148 1560 4467 4611 51 3 2836 2708 2810 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 7.24068691478064e-07 1.15576740743201e-06 2710 2462.81818181818 2708 6.58244481622915e-08 1219 2.39887651253043 1.67458482654166 1 4.11184651603303 2708 3732 2405 2791 2823 2936 1712 1288 1219 2784 2693 2811 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 2.74991977878579e-07 5.67043309561771e-07 2710 2565.63636363636 2709 2.49992738410527e-08 417 1.71218040904702 1.81106209326921 1 3.08745393667693 2709 417 3122 1947 2112 3039 3222 3874 2039 3290 2451 2812 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 1.77231950676325e-07 4.43266487055072e-07 3540 2587.36363636364 2709 1.77231964811351e-08 225 2.02899748413541 -1.18424025927274 -1 3.72157015188272 3538 1942 4483 3056 1769 4430 3984 605 225 2709 1720 2813 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 1.39347069030854e-05 1.61680965050548e-05 2895 2185.36363636364 2709 1.26679956051926e-06 674 3.73988578620676 3.23058326157983 1 5.1735252405119 2894 823 1025 2709 4027 2970 3101 1732 674 1265 2819 2814 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 6.83384388909198e-08 3.15009389627869e-07 2275 2465.90909090909 2709 6.21258554670107e-09 682 1.98770684803253 2.08429154876153 1 3.73096248850197 2272 2966 1734 2403 682 2802 3322 3296 3287 1652 2709 2815 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 6.40590183752988e-07 1.04949172763419e-06 1305 2551.36363636364 2710 5.82354882071291e-08 802 1.71164170367031 1.95244880790507 1 2.95433527002767 1305 2841 2710 4205 2744 1761 802 2296 4223 3403 1775 2816 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 8.50906693664427e-07 1.31465780494144e-06 2080 2499.90909090909 2710 7.73551838886087e-08 627 1.47156171241115 1.68326626532979 1 2.498257636342 2078 3093 2952 1744 2938 2297 2710 627 3868 3454 1738 2817 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 1.42004943412057e-07 3.98409119822705e-07 3715 2773.18181818182 2711 1.29095411434682e-08 660 2.03707441665815 -1.95396504797578 -1 3.76364442683607 3713 2053 1472 2711 1449 3945 4287 3986 2537 660 3692 2818 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 6.08971950411358e-07 1.00889701858252e-06 4030 3098.18181818182 2711 5.53611017252879e-08 1715 2.14136732069372 2.25640192479194 1 3.70686208623764 4026 2564 1715 2417 2711 3760 3128 4326 2658 2159 4616 2819 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 1.3106800909966e-07 3.80936578171426e-07 2110 2854.09090909091 2711 1.19152742643833e-08 1379 1.01302474986687 1.17815869578027 1 1.8769019466939 2107 4267 3577 4428 1379 1657 1646 3273 2711 4127 2223 2820 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 3.7720706540726e-07 6.98476794320231e-07 3930 2641.81818181818 2712 3.42915572802139e-08 749 1.85934807716901 -1.90769793059933 -1 3.30429517985086 3930 749 2712 2120 2390 3883 3864 1383 1229 2974 3826 2821 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 6.82729128663061e-06 8.25430708834439e-06 2475 2430.72727272727 2713 6.20664770359346e-07 326 2.50322459630507 2.80609674201363 1 3.67357440150365 2472 3048 1993 1730 3845 2843 2713 1740 326 2862 3166 2822 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 1.08825373036e-06 1.606178113602e-06 2620 2804.81818181818 2714 9.89322062433472e-08 1526 1.94877836966141 1.8623816016523 1 3.25975610058834 2618 3321 2714 4597 3091 2255 2337 1526 2822 3215 2357 2823 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 2.64882314242033e-07 5.54186402137587e-07 4645 3005.27272727273 2716 2.40802132849226e-08 1026 2.50483135323993 -2.68876490151833 -1 4.52438850810106 4644 2621 1026 2716 2077 4658 4173 2268 3484 1761 3630 2824 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 4.09826761216088e-08 2.9351990282604e-07 4650 2949.54545454545 2720 3.72569789864128e-09 201 1.95969673585433 -2.07410658545651 -1 3.69573973339033 4647 2720 2530 1479 201 4301 4413 2367 4363 1775 3649 2825 M4377 KEGG_GALACTOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GALACTOSE_METABOLISM.html Galactose metabolism 29/39 KEGG 1.11355312664781e-07 3.552969556871e-07 2435 2673.54545454545 2721 1.01232107546498e-08 1220 1.55168671398829 -1.47336477065665 -1 2.88893589607612 2431 3397 3225 3392 1220 1768 2117 2649 2869 3620 2721 2826 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 6.1794056796176e-07 1.01946154518683e-06 3910 2878.63636363636 2722 5.61764310482053e-08 1045 2.24367455274088 1.86944393805605 1 3.8810733991156 3907 2369 1765 1045 2722 4370 4692 3277 1158 1697 4663 2827 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 9.66531735030322e-06 1.14393926513117e-05 2660 2470.81818181818 2722 8.7866907395046e-07 213 1.96039297654207 2.23831410137247 1 2.79653439716985 2657 2722 2549 2833 4189 3473 2796 213 1108 3455 1184 2828 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 1.94616349347701e-07 4.6676278908595e-07 4005 2735.36363636364 2725 1.769239696035e-08 288 1.76797240483013 -1.58605710282051 -1 3.231237531464 4003 2244 2670 462 1766 3701 3816 4678 288 3736 2725 2829 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 1.2652229977952e-07 3.75824578325571e-07 2795 2547.36363636364 2725 1.15020279141668e-08 1192 1.81231653273901 2.23132650576462 1 3.36155609541714 2793 2191 2644 3375 1345 3533 3430 2838 1955 2725 1192 2830 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 1.23038760191099e-05 1.43855077558084e-05 1380 2599.27272727273 2728 1.11854043919802e-06 1107 2.01142886513591 2.06856931831581 1 2.81155502254929 1378 3423 2728 3482 3992 1312 1107 1875 3364 3924 2007 2831 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 6.32764739950068e-08 3.14536172538656e-07 2910 2449.90909090909 2729 6.32764757967673e-09 706 1.90231558470083 -1.76399266610116 -1 3.57100315922282 2906 1980 4564 1727 706 1234 3595 3164 2779 2729 1565 2832 M6856 KEGG_HEMATOPOIETIC_CELL_LINEAGE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEMATOPOIETIC_CELL_LINEAGE.html Hematopoietic cell lineage 52/107 KEGG 2.25247353373549e-07 5.05548030396173e-07 1880 2829.63636363636 2731 2.04770342214127e-08 1177 2.53714838684229 2.15297903812658 1 4.61200018174336 1880 3327 1177 4538 1917 2314 2731 3975 3708 1575 3984 2833 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 6.66874596393487e-08 3.14536172538656e-07 4075 2455.45454545455 2731 6.66874616405965e-09 174 3.05511436232396 -2.63842596747505 -1 5.735544649282 4071 868 4471 1351 751 4037 3623 2731 174 1041 3892 2834 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 2.56500740033994e-07 5.43294568670404e-07 3065 2600.09090909091 2731 2.33182518127036e-08 472 2.74528577414536 -2.35449479125198 -1 4.96562935012717 3064 2731 1978 2084 2047 3470 3870 3865 2021 2999 472 2835 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 3.63790734312839e-06 4.60490309750369e-06 2165 2593.90909090909 2732 3.30719396251361e-07 895 1.90562644091379 2.12170726642295 1 2.93584467678945 2162 3650 2769 895 3665 2732 2480 3459 1309 3827 1585 2836 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 5.49920900545066e-07 9.31667857348426e-07 4605 2879.18181818182 2732 4.99928216368698e-08 1469 2.42518888398228 -2.87310286213905 -1 4.22251260816248 4604 3371 1601 3633 2644 4200 3316 2332 1769 2732 1469 2837 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 6.29187047766238e-07 1.03512124972347e-06 3025 2867.09090909091 2732 5.71988388827364e-08 1700 1.95006098221912 2.14889384616448 1 3.36934450312094 3024 1700 2059 1882 2732 3371 4442 4644 2451 1990 3243 2838 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 4.9866267996653e-07 8.62788801115111e-07 2385 3110.72727272727 2732 4.53329811814428e-08 1835 1.13120183793511 1.03776953675563 1 1.97997948654681 2385 2671 3734 4243 2581 2172 1835 2732 4336 3611 3918 2839 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 1.93720203591243e-07 4.66108261912869e-07 2845 2600.18181818182 2734 1.76109291499279e-08 1326 1.81060259147979 2.01745949642935 1 3.30949005770201 2844 2543 2734 2187 1758 3478 3280 2279 1326 2884 3289 2840 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 2.91099696303606e-07 5.86173449894634e-07 1755 2830.09090909091 2735 2.64636122564869e-08 1753 1.35972684473443 1.29682932881735 1 2.44606411117344 1753 2544 3560 3747 2173 2042 2165 2735 3473 3487 3452 2841 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 5.9222903286355e-08 3.10257041482984e-07 4420 2518.18181818182 2735 5.38390044369144e-09 493 2.52280775210174 2.22272178588373 1 4.74039807523996 4418 1438 493 1779 521 3984 4292 4685 2735 520 2835 2842 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 1.61905146417572e-06 2.24498322882179e-06 3815 2690.54545454545 2736 1.47186605062683e-07 1170 3.21083446402245 -2.75254097928377 -1 5.23654837288263 3811 2736 1277 1849 3318 4026 3500 1170 3201 2284 2424 2843 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 2.38543197179103e-08 2.29312401361581e-07 3500 2482.81818181818 2736 2.1685745433236e-09 11 2.51368109291114 2.3788656423178 1 4.81854711800938 3496 2152 812 2721 11 3784 3707 3007 3850 1035 2736 2844 M8 PID_ENDOTHELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ENDOTHELIN_PATHWAY.html Endothelins 18832364 88/104 Pathway Interaction Database 3.04486503382786e-07 6.04363454990223e-07 3615 2573.36363636364 2737 2.76805950476933e-08 458 2.53289023439598 3.31589093117923 1 4.54754801597037 3612 2573 1405 458 2210 3878 3533 3476 1653 2772 2737 2845 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 1.1722169654618e-06 1.71031347047286e-06 970 2493.36363636364 2738 1.06565235459075e-07 970 1.75890200636122 1.53600227347984 1 2.9282058688545 970 2099 2738 3630 3131 1509 1186 3364 3228 2594 2978 2846 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 6.31668317784259e-07 1.03703459476233e-06 4345 2804 2738 5.74244090136527e-08 597 2.3698846879126 -2.1879291046746 -1 4.0943587542731 4342 688 1641 3553 2738 4616 4045 2715 597 1679 4230 2847 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 7.01148337828892e-07 1.12718670114182e-06 1905 2884.63636363636 2739 6.37407782988749e-08 1270 1.68937806821918 -1.44409862551166 -1 2.90076548393072 1903 4176 3477 3961 2801 2533 2705 1270 2739 4111 2055 2848 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 1.03910694662054e-07 3.47369293280946e-07 1355 2837.54545454545 2741 9.44642723363432e-09 1136 1.33477347640317 1.44580218999591 1 2.48874293066423 1354 3862 4029 4647 1136 1623 2010 2483 3293 4035 2741 2849 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 2.19008495085261e-07 4.96977404037796e-07 3900 2796.63636363636 2741 1.99098651715827e-08 920 1.43145055400802 -0.882023297778033 -1 2.60476902269838 3897 1843 2849 2757 1890 4700 4494 2673 920 2741 1999 2850 M2529 BIOCARTA_PDGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PDGF_PATHWAY.html PDGF Signaling Pathway 48/52 BioCarta 3.8470191042627e-07 7.08740443876656e-07 2665 2817.45454545455 2742 3.49729070633632e-08 229 1.37243826991564 -1.40888404193707 -1 2.43625898718228 2661 3664 3586 229 2402 2439 3210 3100 2742 4231 2728 2851 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 6.65704769768033e-07 1.0811816251744e-06 2555 2668 2742 6.05186337459794e-08 1221 2.56117929642601 2.06263032839018 1 4.41153028049651 2551 3064 1418 2742 2771 2052 1936 3516 3568 1221 4509 2852 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 6.39034509990108e-07 1.04767033246034e-06 1015 2354.90909090909 2742 5.80940632373351e-08 140 0.955224835043183 1.05152141893276 1 1.64856877322351 1353 3770 3648 3721 2742 1012 140 1011 3354 3970 1183 2853 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 2.73987335329839e-08 2.52582074757195e-07 4310 2768 2742 2.49079398856426e-09 27 1.57665339056682 -1.37243404291489 -1 3.00290044308811 4310 2110 3480 1514 27 2961 2742 3839 2360 2425 4680 2854 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 6.01262277273939e-06 7.35412787958796e-06 4560 2665.36363636364 2743 5.46603564123868e-07 182 2.31066094643303 -2.45261444159247 -1 3.42437541594133 4560 1768 1771 182 3804 3819 2743 4335 190 2573 3574 2855 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 4.96813720733862e-08 3.0357704374324e-07 3110 2148.36363636364 2743 4.51648847230116e-09 330 2.17387447902837 -2.10778608759793 -1 4.09056129644171 3109 1178 434 1569 346 2822 3690 4404 2743 330 3007 2856 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 6.04832167043142e-08 3.11320373876078e-07 3750 2594.81818181818 2744 5.49847439701285e-09 53 1.93606647604434 -1.89730664391076 -1 3.63687033991555 3746 53 1888 2744 545 3363 3704 4557 2136 2223 3584 2857 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 1.463272906999e-07 4.03897550937735e-07 2380 2812 2744 1.33024818574982e-08 1478 1.93105083584175 -1.87071205392871 -1 3.56439991363525 3327 2070 2377 2745 1478 3360 4417 4549 1489 2744 2376 2858 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 5.11172166354387e-08 3.0357704374324e-07 3425 2741.45454545455 2744 5.11172178112751e-09 468 1.93896911392427 -1.83821527681294 -1 3.64844877625816 3421 1038 4545 2340 468 2744 3700 4072 1979 2670 3179 2859 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 1.8043044830001e-05 2.06558587506795e-05 1690 2956.36363636364 2744 1.80431913298351e-06 1319 1.09171005477991 1.19400599420346 1 1.47605651615451 1689 3513 4695 4412 4105 1487 1319 2744 4478 2387 1691 2860 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 1.48723303545749e-07 4.07166653130138e-07 2535 2542.90909090909 2745 1.35203012363335e-08 645 1.66017739349531 1.56485287346356 1 3.0626132256475 2534 1455 3185 645 1494 2745 3571 3376 2560 2883 3524 2861 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 2.65743059038591e-06 3.48031975211474e-06 1245 2384.09090909091 2745 2.41584890942078e-07 1036 1.64859523390939 2.12050297178499 1 2.59763026654928 1242 3468 2854 3162 3531 1598 1671 1036 2745 3179 1739 2862 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 3.2940519589745e-08 2.74345541741202e-07 3985 2783 2746 2.99459273481475e-09 85 1.88822312652961 2.56612222279191 1 3.57691563126825 3983 2664 2746 2438 85 4708 4527 1180 711 3387 4184 2863 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 6.14623062113277e-08 3.12995510041999e-07 3380 2515.18181818182 2746 5.58748253894778e-09 563 2.44928856660712 2.76863062239299 1 4.59952993546531 3377 2746 1672 2566 563 3594 3336 3219 791 2155 3648 2864 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 6.44350877164491e-07 1.05455483363953e-06 3540 2771.18181818182 2747 5.85773696260374e-08 1713 2.36316150472243 2.92801914685358 1 4.07777586088876 3536 2751 1713 2331 2747 3956 4238 3065 1804 1914 2428 2865 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 1.94820915361034e-07 4.66779045941157e-07 2750 2738.09090909091 2747 1.77109938739449e-08 1331 1.7002676672196 -1.62901120385481 -1 3.10745645094096 2747 3238 3519 1997 1768 2241 3812 3274 1814 4378 1331 2866 M13036 KEGG_PRION_DISEASES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRION_DISEASES.html Prion diseases 41/49 KEGG 2.68043631056904e-05 3.00728770760301e-05 2750 2923.72727272727 2748 2.43678997184528e-06 492 2.06446797830602 2.15283502292236 1 2.69480010403146 2748 4509 2558 3191 4173 2300 2242 2059 4292 3597 492 2867 M1749 KEGG_VEGF_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VEGF_SIGNALING_PATHWAY.html VEGF signaling pathway 68/89 KEGG 2.42176010335445e-07 5.2719175985577e-07 3005 2703.81818181818 2750 2.20160033631078e-08 1294 1.61486315227632 -2.00089984994425 -1 2.926677399679 3004 2183 3188 1294 1989 2523 2750 3623 3458 3898 1832 2868 M10654 REACTOME_PYRIMIDINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_CATABOLISM.html Genes involved in Pyrimidine catabolism 10/16 Reactome 1.37824778322973e-06 1.95766763070849e-06 2755 2426.27272727273 2751 1.25295331515455e-07 271 3.04391793042723 2.7607772765767 1 5.0165557685745 2751 2880 1695 3034 3233 3912 3973 319 271 2612 2009 2869 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 3.06997885959513e-05 3.42884529514648e-05 2475 3314.45454545455 2751 2.79092881845147e-06 2271 1.36727573124333 -1.50204767448337 -1 1.7619532169724 2473 4396 4095 2511 4194 2641 2751 2271 4123 4522 2482 2870 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 1.98638670434118e-05 2.26303288546714e-05 1385 2716.81818181818 2751 1.80582239973998e-06 1215 1.91359240589824 -1.65000255461113 -1 2.56603010728947 1382 4010 2751 4551 4106 1722 1370 1551 4094 3133 1215 2871 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 3.31005340712662e-06 4.24434992709525e-06 2335 2552.54545454545 2752 3.00914398849388e-07 969 1.90026329044427 2.10986133510266 1 2.94700976620383 2333 3367 2752 2839 3618 1759 969 3044 2435 3457 1505 2872 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 0.000313811279192309 0.000331362245590089 2755 2802.63636363636 2752 2.85323682401772e-05 1314 2.33964524224094 -2.50989305372309 -1 2.35004258040693 2752 3787 2597 2911 4449 2397 1688 1314 3750 3280 1904 2873 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 1.411322186038e-06 1.99174945947362e-06 460 2445.09090909091 2753 1.41132308236244e-07 460 1.55780708047759 1.64597206072473 1 2.56356528840262 460 3545 4520 3000 3300 1099 1309 1595 3144 2753 2171 2874 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 3.28556272604779e-07 6.34679513892091e-07 3465 2728.72727272727 2753 2.98687565156926e-08 1427 1.92229318227896 2.03600655596483 1 3.4392760392573 3462 1877 1964 2788 2277 3459 3536 2528 2753 1427 3945 2875 M882 BIOCARTA_CXCR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CXCR4_PATHWAY.html CXCR4 Signaling Pathway 41/45 BioCarta 3.68473010440408e-07 6.88244008420549e-07 2755 2429 2754 3.34975520141029e-08 211 1.93655829747962 -1.96901660180566 -1 3.44512748332679 2754 3351 2809 211 2367 2731 2790 2873 500 3943 2390 2876 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 5.40798552233759e-09 6.1359835734215e-08 3870 2587.09090909091 2754 5.40798553549842e-10 222 2.18420655276904 -2.10463561747257 -1 4.54797005748752 3866 1977 4605 538 572 3397 4306 3952 2754 222 2269 2877 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 3.09741268182856e-05 3.45784954073576e-05 1345 2412.27272727273 2755 2.81586935601948e-06 589 1.73811796315506 -1.87072651480907 -1 2.23824021885151 1345 3368 3091 2622 4196 910 796 3124 3739 2755 589 2878 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 2.73751016272184e-07 5.66073041584045e-07 3465 2532.45454545455 2755 2.48864591214229e-08 716 1.40542178001088 1.87066487532896 1 2.5344453050891 3465 716 2877 2755 2103 4461 4002 2062 910 2892 1614 2879 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 6.53596450421601e-07 1.06708708584733e-06 1900 2819.27272727273 2755 5.94178767816537e-08 1187 1.51676163957608 1.73814816630849 1 2.61470683350288 1900 4398 3592 4489 2755 1457 1522 1187 3813 4117 1782 2880 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 3.39361904363546e-07 6.48759898175755e-07 3115 2661.72727272727 2756 3.08510869738152e-08 1117 1.87458613868308 1.93977878336904 1 3.34874102144131 3099 1713 2004 2337 2301 3808 3113 3115 1117 2756 3916 2881 M8232 KEGG_LONG_TERM_DEPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_DEPRESSION.html Long-term depression 61/94 KEGG 5.31156706966457e-08 3.06874196014832e-07 4655 2645.90909090909 2758 4.8286974526403e-09 406 2.52823527771556 -1.96352245545521 -1 4.75407437551685 4651 2628 1656 1734 406 3901 3532 2770 1316 2758 3753 2882 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 3.0142596805177e-06 3.90431001428198e-06 1010 2688.90909090909 2758 2.74023982765197e-07 1006 1.02630648641974 -1.12362113946348 -1 1.6019920352404 1006 3432 3661 3990 3578 1389 1118 2758 2507 4198 1941 2883 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 1.00983099318937e-08 1.08081684531833e-07 3415 2550.90909090909 2759 9.18028179840583e-10 274 2.65876075184929 2.69113735982445 1 5.34751090155675 3414 2091 356 2701 1718 2759 2952 4032 3127 274 4636 2884 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 1.03705996563548e-06 1.54267981021099e-06 3015 2610.90909090909 2759 9.42782231360386e-08 1114 1.74317199582462 -2.1274406300735 -1 2.9245617179164 3015 2667 2759 1114 3061 2777 2420 1217 3800 3486 2404 2885 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 0.00127446606534637 0.00132092222846616 1255 2771.18181818182 2760 0.00011592772421705 1254 1.55026151583374 1.55532054535817 1 1.28800711266449 1254 2843 3221 3183 4540 1801 2371 2472 3674 2760 2364 2886 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 1.19724838754342e-06 1.74085013275705e-06 3315 2546.36363636364 2760 1.08840821735551e-07 483 2.55583523458127 -2.26200988567586 -1 4.24965184708057 3313 1735 1510 2299 3145 3097 2895 2760 483 2103 4670 2887 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 1.94490598438834e-07 4.66698334840516e-07 4145 3067.63636363636 2761 1.76809650575219e-08 1765 1.88864500118805 -1.77664187373779 -1 3.45187648918654 4145 3251 2444 2761 1765 3365 4713 4124 2479 2117 2580 2888 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 5.10211496248355e-08 3.0357704374324e-07 3770 2688.18181818182 2761 5.10211507962564e-09 466 2.07530630324566 -1.79319654529509 -1 3.90504733601822 3766 1964 4336 1864 466 3671 3441 2463 2761 598 4240 2889 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 5.96427524051994e-08 3.10399797613433e-07 2775 2372.09090909091 2761 5.42206854746681e-09 532 2.6089469648637 2.8247883958995 1 4.90213399953554 2774 3376 1308 3573 532 2782 1848 2761 2610 1157 3372 2890 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 1.2106321265139e-07 3.69968882213284e-07 2895 2554.27272727273 2761 1.10057472103041e-08 1197 2.32904642252224 -2.3586252181158 -1 4.32483937862831 2895 1657 1197 3099 1301 2761 3935 3936 3282 1527 2507 2891 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 1.27522013893542e-07 3.76660766944629e-07 4155 2614.72727272727 2763 1.15929110259363e-08 161 1.69094166135267 -1.33164126652522 -1 3.13589622307617 4155 1808 2624 1683 1352 4177 3554 2763 161 3124 3361 2892 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 3.20316742929408e-05 3.57337515156418e-05 2680 2891 2764 2.91201278898936e-06 1249 1.58114929538092 -1.59357796484695 -1 2.02951140547379 2677 3170 2958 2621 4199 2183 1249 3902 2143 2764 3935 2893 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 4.12408777192277e-08 2.93600215437036e-07 2540 2365.63636363636 2764 4.12408784845921e-09 275 1.98389013695025 2.25127008679882 1 3.74130798950591 2538 1029 4517 1653 275 2966 2944 2776 2764 1009 3551 2894 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 7.10240951385808e-07 1.13831486945365e-06 2660 2808.63636363636 2764 6.45673800616204e-08 1452 2.37306025882803 -2.45075262995521 -1 4.07211452335319 2658 2764 1452 2381 2809 3386 3982 3586 3660 1917 2300 2895 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 1.44221561903893e-07 4.00898570192211e-07 2500 2531.27272727273 2765 1.31110519416705e-08 249 2.07155594123182 -1.33265241496977 -1 3.82574790388912 2499 3967 2855 904 1462 2269 2765 3270 249 4100 3504 2896 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 7.31944950659552e-07 1.16558035327702e-06 2765 2823.45454545455 2765 6.65404721981271e-08 1602 1.33829380748057 -1.30752855922917 -1 2.29213187050462 2765 3979 3615 2487 2830 1993 1796 1602 4120 3885 1986 2897 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 8.48715082655045e-06 1.01211096264068e-05 1985 2795.36363636364 2765 7.7156214258385e-07 1191 1.4354465750507 1.24479086794596 1 2.06949993014946 1983 2765 3058 2004 3911 1847 1191 4558 3951 3963 1518 2898 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 0.000770675329058351 0.000803354141597928 460 2561.63636363636 2765 7.00859485884557e-05 457 0.995571349444724 1.02520590283428 1 0.888932790059548 457 2816 3370 1982 4512 1247 760 2164 4282 3823 2765 2899 M12467 KEGG_ERBB_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ERBB_SIGNALING_PATHWAY.html ErbB signaling pathway 84/90 KEGG 7.33884592057625e-08 3.2144561803028e-07 3955 2371.90909090909 2766 6.67167833217124e-09 242 1.8265659738397 -1.93032778642851 -1 3.42379516334251 3955 242 2766 457 753 3781 4671 3248 882 3377 1959 2900 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 8.16721795111981e-08 3.27411388472988e-07 3515 2617.90909090909 2766 7.42474386756122e-09 547 1.84476726527819 1.8593797815674 1 3.45366673333819 3515 547 2089 1035 869 3767 4046 4139 2766 2565 3459 2901 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 5.12869543214693e-08 3.0357704374324e-07 3300 2204.90909090909 2766 5.12869555051275e-09 129 1.87570821075482 2.07022770850134 1 3.52938620262584 3299 973 4707 129 472 3141 3814 2766 1363 719 2871 2902 M3494 BIOCARTA_PAR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PAR1_PATHWAY.html Thrombin signaling and protease-activated receptors 53/59 BioCarta 3.07860471771335e-07 6.08756358089946e-07 3920 2667.63636363636 2767 2.79873195320259e-08 402 1.99265966358703 -1.98963453409087 -1 3.575625161905 3917 2636 2547 1688 2218 3465 3518 3028 402 2767 3158 2903 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 1.35021330799563e-07 3.87181458914906e-07 3115 2499.54545454545 2768 1.22746671896611e-08 1406 1.81891607829457 -2.00788200153182 -1 3.36700933150233 3115 2134 2807 1709 1406 2841 3242 2117 3296 2768 2060 2904 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 2.85494122992222e-06 3.71118771832357e-06 1655 2801 2768 2.59540448617071e-07 1460 1.8016754746069 1.9995490851565 1 2.82440109171975 1652 3484 2568 4200 3563 1670 1460 2768 4057 3147 2242 2905 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 3.69125290991905e-07 6.88550861663682e-07 2525 2663.81818181818 2769 3.35568502659381e-08 707 2.74602910886208 -3.22549920196167 -1 4.88537851372013 2523 2769 819 3324 2370 3627 3988 1669 4110 707 3396 2906 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 4.1937138017906e-05 4.63350401321434e-05 655 2403.72727272727 2770 3.81253976900311e-06 655 1.39753225112952 1.44003563635266 1 1.74819280866784 655 2770 3315 3176 4243 995 1288 1457 3196 3336 2010 2907 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 6.65462275816466e-07 1.0811816251744e-06 4695 2659.18181818182 2770 6.04965888279526e-08 839 2.98528047758652 -3.10618354463601 -1 5.14217045624908 4695 839 1158 3286 2770 4050 3695 2706 1797 1131 3124 2908 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 9.58423033184697e-08 3.38845370705758e-07 3710 2740.09090909091 2772 8.71293704489178e-09 1049 2.04656435048513 2.4866936609518 1 3.82274368414225 3707 2009 1421 3157 1049 4094 3285 2772 2160 2568 3919 2909 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 1.19808586492585e-07 3.68161802242839e-07 3085 2363.36363636364 2773 1.08916902742887e-08 618 1.55296271177695 1.81894077826227 1 2.8843850988888 3083 639 2773 1684 1291 3893 4707 3190 618 3127 992 2910 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 0.000161465709033636 0.000173129974247788 1690 2865.09090909091 2773 1.46797782532374e-05 1686 1.40642488156532 -1.41476296232744 -1 1.52683064582809 1686 3180 2785 3670 4386 2055 2066 2394 4516 2005 2773 2911 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 9.42169005971355e-07 1.42487590778109e-06 4165 2825.63636363636 2774 8.56517644966922e-08 509 2.0677192731624 -1.51445076914189 -1 3.48982151238036 4163 1911 2184 2774 3006 3668 4389 2021 509 2513 3944 2912 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 1.44149192881754e-07 4.00898570192211e-07 4560 2564.45454545455 2774 1.31044729387954e-08 671 2.72989124013502 -2.97967237189828 -1 5.04183474942748 4557 671 858 4128 1461 3271 2774 1887 3131 895 4576 2913 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 2.6696459356372e-08 2.48045842838732e-07 2775 2558.45454545455 2775 2.42695088002972e-09 24 1.70369830940238 1.86770817429732 1 3.2488121792142 4030 384 2771 1279 24 4584 4496 3990 914 2896 2775 2914 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 4.90842834637601e-07 8.52069944644898e-07 4215 3060.36363636364 2776 4.46220858317969e-08 778 1.58339182872324 1.7890633314648 1 2.77428909088202 4214 1772 2767 2776 2574 4072 4463 2551 778 3348 4349 2915 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 6.7282309751538e-07 1.09093954664122e-06 4420 2525 2777 6.11657548440061e-08 60 1.83436176976919 0.658271919946973 1 3.1573044431349 4416 3420 2534 1212 2777 3469 3190 2362 60 3522 813 2916 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 2.01224867929982e-06 2.72377796567111e-06 4230 2737.18181818182 2778 1.82931865438411e-07 1384 2.08228222784563 1.36086055771331 1 3.34520697967434 4229 1829 2555 1899 3408 3691 3030 3741 1565 2778 1384 2917 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 4.76435952433889e-05 5.24068444532266e-05 2560 2950.72727272727 2781 4.33132973208456e-06 1567 2.23571742130425 2.68993967907104 1 2.762681604986 2557 4036 2811 4408 4262 2661 2229 1739 2781 3407 1567 2918 M8492 KEGG_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_APOPTOSIS.html Apoptosis 90/107 KEGG 6.7913441126647e-07 1.09928478092515e-06 3010 2588.27272727273 2782 6.17395109921479e-08 1289 2.12308420712245 -2.09797164120219 -1 3.6523602473107 3007 2143 2281 1289 2782 3378 3894 2828 1866 3088 1915 2919 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 1.12132411742628e-07 3.56647562954991e-07 4390 2846.18181818182 2782 1.01938561325398e-08 902 2.08950196049593 -1.70023429055461 -1 3.8895465651671 4389 2782 2308 1458 1229 3886 3800 4513 902 2464 3577 2920 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 9.01616223687747e-07 1.37544556425539e-06 3865 3028.36363636364 2784 8.19651448357573e-08 2242 1.8751777928992 2.08439365509792 1 3.17307971211447 3864 2242 2385 2784 2978 3763 3308 2617 2463 2715 4193 2921 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 5.12239993298574e-07 8.82398820572726e-07 2180 2852.63636363636 2785 5.12240111374028e-08 1906 2.48149910363638 3.09695157877818 1 4.33748299095819 2178 2898 4218 4134 2662 3054 2785 1906 2231 2924 2389 2922 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 1.75665912384336e-06 2.41380817017195e-06 2625 2823.63636363636 2785 1.59696411500418e-07 972 1.54951415173316 1.57719103612339 1 2.51256635594441 2623 1841 2708 2785 3348 3519 4401 3829 972 1696 3338 2923 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 1.99816960291473e-07 4.74685412934128e-07 3940 2309.36363636364 2785 1.81651798581844e-08 439 3.50043784210637 -3.01054474097538 -1 6.39103610996114 3938 466 439 936 2785 4169 3526 2973 1505 800 3866 2924 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 2.03222214001394e-06 2.74844942718218e-06 1375 2520 2785 1.84747637932349e-07 956 1.3658098559851 1.36749566098036 1 2.19234619036668 1375 3133 3008 3367 3412 1492 956 1725 3732 2785 2735 2925 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 6.84570021631739e-07 1.10694433097013e-06 4565 2936.45454545455 2787 6.22336576952953e-08 540 3.27298436545738 2.94693367795077 1 5.62815993683951 4565 2597 540 1327 2787 4511 4310 4295 2476 1068 3825 2926 M13515 KEGG_MISMATCH_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MISMATCH_REPAIR.html Mismatch repair 22/23 KEGG 0.00135556561874375 0.00140436122047201 705 2723.54545454545 2788 0.000123309235788638 540 0.940090883337386 0.968028723492628 1 0.773497333556141 702 2820 3746 2470 4542 1465 540 2323 4369 4194 2788 2927 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 5.57504021069536e-07 9.42147862315865e-07 3230 2744.36363636364 2788 5.06821965770176e-08 1603 1.65429950210401 1.09764737782625 1 2.87771749791873 2867 2660 3226 2218 2651 1603 1888 2788 3322 3735 3230 2928 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 9.83696538053834e-07 1.47164743569385e-06 2205 2352.81818181818 2790 8.9426997990823e-08 660 1.85072898314971 2.2903518554778 1 3.11600656158486 2205 2790 2798 3372 3042 1858 1106 2916 660 3426 1708 2929 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 0.000272115511254267 0.000287978747336354 1885 2900.18181818182 2791 2.47408340675897e-05 1480 2.28462363276853 -1.19704613712827 -1 2.33496110028499 1883 3081 1480 2443 4439 2417 2791 3209 4124 2299 3736 2930 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 2.69613794190679e-05 3.02346663953435e-05 1370 2808.18181818182 2792 2.45106453100834e-06 1366 1.95397175823294 -1.82674114714614 -1 2.54920582188264 1366 3339 2601 2647 4175 1992 1907 4151 2792 3100 2820 2931 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 5.97339238269071e-07 9.94511888758383e-07 2795 2937.18181818182 2794 5.43035818597627e-08 161 1.85634032169486 -1.91341609908897 -1 3.21668827487202 2794 4113 2757 4259 2698 1860 3596 3867 3914 2290 161 2932 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 3.29420966097149e-07 6.35677416180926e-07 4670 3273.63636363636 2795 2.99473650385092e-08 2152 1.79617359075129 2.27367731828184 1 3.2132184307791 4666 2549 2731 2651 2280 4175 4037 2795 2152 3558 4416 2933 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 1.00085593423614e-05 1.18337675591047e-05 3150 2859.54545454545 2796 9.09873170458396e-07 1005 1.8319242299928 -2.00747116566084 -1 2.60542823883627 3146 2792 2796 2611 3943 2284 1005 3736 3153 3331 2658 2934 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 1.63909097343931e-06 2.26744120593011e-06 2195 2766.54545454545 2797 1.49008381330103e-07 1891 2.38542894721593 -1.77035369882879 -1 3.88719574362057 2193 2827 1891 2797 3326 2422 2809 4107 2640 2126 3294 2935 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 2.18481836285705e-07 4.96262881264931e-07 2800 2765.54545454545 2797 1.98619870893748e-08 1509 1.7342136260567 1.88240512563765 1 3.15619328546975 2797 3993 2694 3844 1887 2575 1509 2811 3105 2276 2930 2936 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 0.0022631492982765 0.00233487752740221 2000 2981.7 2798.5 0.000251714324749137 935 2.24145449982807 2.24145449982807 1 1.70253486826301 1998 3543 4526 NA 4568 2007 935 2834 4456 2187 2763 2937 M19877 KEGG_ENDOMETRIAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOMETRIAL_CANCER.html Endometrial cancer 56/61 KEGG 5.18855527222899e-07 8.92166881053583e-07 3140 2511.09090909091 2799 4.71686954174185e-08 465 2.01382470693412 2.16040501177918 1 3.51707890432756 3138 3042 2567 465 2599 2830 2799 1719 564 3783 4116 2938 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 7.00224732170375e-07 1.12608542958916e-06 1690 2673.09090909091 2800 6.36568140946165e-08 904 1.73669121539337 2.07517390270228 1 2.98224206717209 1688 4421 3343 4646 2800 1918 1792 904 2976 3499 1417 2939 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 2.28625128210955e-06 3.05005823955825e-06 4300 2755.54545454545 2800 2.07841241636097e-07 614 2.20359235438824 -1.49680969228148 -1 3.5088766462432 4299 614 1753 2779 3466 3756 3244 1591 2800 1578 4431 2940 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 4.49668379510665e-06 5.60452799390108e-06 1495 2826.90909090909 2800 4.08790271465192e-07 1493 2.30872208804102 2.52100795125291 1 3.50016390001185 2800 3933 1493 3588 3729 2509 1912 3788 3321 1495 2528 2941 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 8.91700836758974e-07 1.36340393569885e-06 1775 2343.45454545455 2800 8.10637452892799e-08 820 1.95855650323329 1.8460417392162 1 3.31636698967572 1775 2800 2830 4146 2971 1472 820 1244 2957 3219 1544 2942 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 0.0010021681200561 0.00104052651268473 1840 2911.54545454545 2800 9.11477209108775e-05 1840 1.74947747249477 -1.94688644967529 -1 1.50598232154354 1840 3098 2815 2898 4529 2489 2471 2318 4361 2408 2800 2943 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 1.37145519654289e-07 3.90897857951837e-07 2805 2784.09090909091 2801 1.24677752912533e-08 1156 0.888732564109521 -0.942304116328127 -1 1.64363439731685 2801 2857 3414 4168 1418 2585 2014 1736 4583 3893 1156 2944 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 5.38180606222923e-06 6.63240851533211e-06 2610 2996.27272727273 2801 4.8925629342314e-07 2113 1.91774665212963 2.19898931007085 1 2.86677644010339 2609 3074 2543 3676 3774 2639 2342 3123 4265 2113 2801 2945 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 6.27537549483333e-07 1.03276751518875e-06 3500 2980.72727272727 2802 5.70488844077218e-08 1089 1.59931568866492 -1.86585618690436 -1 2.76362320888252 3497 1680 2802 1089 2731 3976 4499 2779 4308 3099 2328 2946 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 1.66163377616658e-07 4.2834032897358e-07 4475 2292.45454545455 2805 1.51057627424346e-08 182 2.12312948622778 -1.6063645559695 -1 3.90338643425919 4473 182 1725 624 1617 3186 3635 2805 687 2966 3317 2947 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 9.15284553527833e-06 1.08682845098148e-05 2425 2810.90909090909 2805 8.32080328623209e-07 287 1.98576062082055 -1.60888040444256 -1 2.84548684094149 4588 2422 2423 2805 3926 3518 2438 1007 287 3405 4101 2948 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 1.43229848057163e-06 2.01662637075827e-06 4600 2709 2805 1.30209037551174e-07 986 3.37396727991731 3.7188993637086 1 5.54803484331402 4600 2805 1124 1468 3263 4104 3491 3737 986 1944 2277 2949 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 7.06770313275646e-07 1.13390750464346e-06 1410 2861.45454545455 2807 6.42518673029306e-08 645 1.22538803113261 1.13804039985001 1 2.10291608762413 1406 4252 3707 4039 2807 1702 645 2467 4351 4209 1891 2950 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 1.31228909204292e-06 1.87583419577304e-06 210 2401.72727272727 2808 1.19299079528865e-07 206 1.39981326065109 1.50027762826477 1 2.31400534337469 206 3849 4100 3238 3205 883 764 1527 2808 4305 1534 2951 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 2.66071949226726e-06 3.48366047253855e-06 4260 2951.63636363636 2809 2.41883882744966e-07 1632 2.03167109264995 -1.86597467192512 -1 3.20118435580858 4257 3421 2680 2809 3532 4636 3166 2019 1783 2533 1632 2952 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 1.2887963830507e-06 1.84841049164367e-06 3775 2639.09090909091 2810 1.17163376186323e-07 777 1.75912614388435 1.16888319908384 1 2.91144890355436 3774 777 2159 2810 3192 3998 4366 2181 784 3310 1679 2953 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 1.054799056115e-06 1.56467080823203e-06 2785 2641.90909090909 2811 9.58908692584626e-08 642 1.702511978073 -1.96876991024196 -1 2.85330322728967 2783 2587 3121 642 3069 2993 3892 2126 2811 2897 2140 2954 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 6.48937034713301e-07 1.06095698089601e-06 585 2223.27272727273 2811 6.48937224217052e-08 6 0.812220246145905 -0.812220246145905 -1 1.40035258743002 585 3199 4590 3908 2811 259 6 515 4337 4217 29 2955 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 6.83502470351684e-08 3.15009389627869e-07 3695 2699.54545454545 2811 6.21365901442671e-09 683 2.19537854408433 -2.17719174879503 -1 4.12085608941583 3693 2101 1269 4127 683 2811 2917 4314 2393 913 4474 2956 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 2.75746481546052e-07 5.67992564410721e-07 2815 2589.54545454545 2812 2.5067865100721e-08 1012 2.25361054547246 2.52194142847997 1 4.06357628401102 3263 2993 1357 3614 2114 3505 3312 1012 2812 1691 2812 2957 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 3.93831536749257e-05 4.36357946820774e-05 3985 2836.90909090909 2812 3.58035079159104e-06 1547 2.9532892664669 -2.33090167512051 -1 3.71749980485303 3984 2812 1681 2188 4230 3743 3482 1547 1563 2254 3722 2958 M7239 BIOCARTA_DNAFRAGMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DNAFRAGMENT_PATHWAY.html Apoptotic DNA fragmentation and tissue homeostasis 9/18 BioCarta 1.86632627385968e-05 2.13346088946905e-05 1940 2708.36363636364 2813 1.86634194832687e-06 721 1.36228892193484 1.28079832726387 1 1.83658499134015 1936 3509 4186 3673 4115 1964 721 1560 2813 3432 1883 2959 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 7.178501256736e-07 1.14877151628667e-06 3505 2706.27272727273 2813 6.52591236277256e-08 447 3.41029027687824 3.13403429357577 1 5.84844207732863 3501 3188 1512 2729 2813 3296 1660 4640 447 2324 3659 2960 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 7.19137716308784e-07 1.14984079301405e-06 2815 2760.72727272727 2813 6.53761773982899e-08 1923 1.77388388664755 -1.71426822621156 -1 3.0414835737697 2813 3601 3156 2625 2817 2400 3028 1923 2584 3167 2254 2961 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 1.63525943343478e-06 2.2628040239848e-06 2815 2527 2814 1.48660058993087e-07 212 1.61755656620728 2.01411912513445 1 2.63604089340379 2814 4295 2918 4178 3325 3447 2202 212 1148 2691 567 2962 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 6.87971129046451e-08 3.15009389627869e-07 4435 2902.09090909091 2814 6.25428318691164e-09 690 1.62687173623335 -2.20648375212725 -1 3.05351195600163 4432 2444 2645 4372 690 3520 3678 2365 1548 3415 2814 2963 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 1.24368927294063e-06 1.79627092052625e-06 2360 2588.63636363636 2815 1.13062725092299e-07 631 2.19590992185735 2.97321971750346 1 3.64244324283982 2357 2815 2102 2855 3167 3536 4265 631 2321 3196 1230 2964 M6682 BIOCARTA_MCM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCM_PATHWAY.html CDK Regulation of DNA Replication 19/19 BioCarta 0.000229670964905345 0.000243989861434443 390 2472.63636363636 2818 2.08813586468852e-05 125 1.32046676114284 1.32046676114284 1 1.3766468494299 389 3160 3162 3982 4465 655 125 2085 4233 2818 2125 2965 M18810 REACTOME_PD1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PD1_SIGNALING.html Genes involved in PD-1 signaling 11/21 Reactome 1.59611863882655e-07 4.20640981309956e-07 3420 2851.36363636364 2818 1.45101704966029e-08 1466 1.88175368428103 -1.89788853345167 -1 3.46379807415233 3419 2447 2129 3909 1575 3369 2818 1466 4413 1825 3995 2966 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 2.25954702476369e-07 5.06635980195699e-07 2870 2529.90909090909 2818 2.05413386984937e-08 677 2.5550421102525 -2.72745294947674 -1 4.643844448851 2866 3285 677 2367 1919 2946 4078 2739 3289 845 2818 2967 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 3.41098937100773e-05 3.79177339405475e-05 910 2306.27272727273 2819 3.10094750711878e-06 641 1.54046528441505 -1.64073406384952 -1 1.96580805204405 909 2819 3299 2914 4214 1213 1077 641 3065 3194 2024 2968 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 1.50417770172323e-06 2.09926633711816e-06 2275 2861.18181818182 2820 1.36743520923298e-07 2107 1.57504637941295 -1.85901082550523 -1 2.5815594672463 2274 3425 2580 2940 3293 2121 2548 2820 4148 3217 2107 2969 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 0.000179019921943772 0.000191560651003084 1730 2913.90909090909 2820 1.79034345238705e-05 1676 2.67947967298411 -3.16187403770565 -1 2.87565943488431 1729 3514 4219 4162 4401 2068 1709 2321 2820 3434 1676 2970 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 1.73061560619903e-05 1.98457377581618e-05 2155 3058.90909090909 2820 1.57329929102127e-06 1928 2.58887000918195 1.98031968392986 1 3.51447630642401 2152 3449 1928 2597 4078 2828 2726 4639 2411 2820 4020 2971 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 1.05586775287861e-07 3.48348225330125e-07 3245 2683.09090909091 2821 9.59879821412654e-09 1157 1.67766889913233 -1.59153653992411 -1 3.12771547499806 3244 1625 2821 4130 1157 2627 3074 3911 3097 1293 2535 2972 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 2.5269433968631e-05 2.8411559869447e-05 1210 2460.63636363636 2821 2.29724765642767e-06 448 1.23069756278582 1.22068741788801 1 1.6148822854211 1209 2821 3628 3468 4163 997 448 1950 2826 4064 1493 2973 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 2.14266432453359e-07 4.9070235865107e-07 2910 2429.27272727273 2822 1.9478768483781e-08 871 1.76138087125457 -1.76484173201413 -1 3.20813900745502 2910 3158 2839 3351 1872 2243 871 1387 2854 2822 2415 2974 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 6.9722540611386e-08 3.15546367261035e-07 2465 2706.36363636364 2822 6.33841298373068e-09 707 1.56618650723632 -1.42113066116642 -1 2.93924383399239 2462 3256 3626 3692 707 2437 2822 2349 3611 3135 1673 2975 M923 REACTOME_RAP1_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAP1_SIGNALLING.html Genes involved in Rap1 signalling 19/20 Reactome 2.78438965792289e-05 3.11650917367704e-05 1455 2835.09090909091 2823 2.53129536242222e-06 526 2.30372511349604 2.82961063078929 1 2.99690131591844 1453 4029 2823 4246 4181 1292 526 2489 3548 4063 2536 2976 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 5.19406454417028e-06 6.41611741650974e-06 3405 2692.81818181818 2823 4.721888006434e-07 852 2.44758062712935 2.80184135847735 1 3.66922261302121 3404 3441 2242 1936 3765 3813 2671 989 852 2823 3685 2977 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 4.18403708618823e-06 5.24672025685665e-06 3150 2832.18181818182 2823 3.80367731232522e-07 1674 2.43742430324261 -1.88969451036449 -1 3.71549818909083 3150 1779 1885 3557 3704 2823 2714 3784 2676 1674 3408 2978 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 7.75960909484418e-17 2.61609678054747e-15 2880 2310.63636363636 2824 7.05419008622198e-18 100 3.14969489313306 3.25390821339619 1 13.2620642187688 2876 1469 100 3255 1941 1932 3415 4128 3319 158 2824 2979 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 3.07420087463225e-07 6.08140323900428e-07 2110 2688.27272727273 2824 2.79472845837282e-08 860 1.86440805901403 1.76233481764464 1 3.34567198909267 2110 3447 2593 3387 2217 1661 860 3616 3796 2824 3060 2980 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 7.25473522533018e-07 1.15747509827822e-06 1260 2119.90909090909 2824 6.59521601605253e-08 126 1.69431080665181 -1.67593079610972 -1 2.90360363344752 1260 3257 3209 2890 2824 255 1944 1167 3221 3166 126 2981 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 1.7008324540196e-05 1.95184273838378e-05 2310 2666.63636363636 2825 1.54622327581264e-06 220 1.99571581182531 2.20130689966802 1 2.71321482434154 2309 3102 2410 2237 4074 2825 2623 3018 220 3515 3000 2982 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 9.51482977984451e-07 1.43390793617069e-06 3275 2701.90909090909 2825 8.64984899539751e-08 771 1.91476297297206 -2.29961753442285 -1 3.23008638399039 3272 2402 2700 2825 3018 3248 2329 2423 771 2941 3792 2983 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 2.95276272452548e-07 5.9281327349044e-07 2830 2698.18181818182 2826 2.68433010985e-08 2021 1.98399937197306 2.24506656725644 1 3.56668451029402 2826 2969 2021 2215 2181 3142 3489 2497 2858 2596 2886 2984 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 8.47124576081564e-07 1.31095999970655e-06 2175 2637.36363636364 2826 7.70113547520609e-08 1948 2.15134347562792 -1.39140196892466 -1 3.65347510382604 2174 2826 2272 1948 2932 2126 1951 3399 3323 2944 3116 2985 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 1.17817167154965e-07 3.63937846185494e-07 2935 2617.54545454545 2827 1.07106521331326e-08 232 1.43792468752314 1.60552208564463 1 2.67273705993598 2934 1417 3804 232 1280 2716 2827 3740 2254 4427 3162 2986 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 8.13805212846668e-05 8.83838151089801e-05 2820 2783.54545454545 2828 7.39850289084753e-06 1979 2.56176533526574 -3.45866305337857 -1 2.99779432858623 2820 2851 2003 3136 4319 2942 2828 2312 2988 2441 1979 2987 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 9.30232385938272e-08 3.35829802760759e-07 2830 2464.45454545455 2828 8.45665841155966e-09 614 2.29214912504285 -2.38179610854932 -1 4.28414045152493 2828 2977 614 4112 1019 2809 4419 3228 3050 629 1424 2988 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 0.000780086616539111 0.000812984948126431 2830 2833.18181818182 2830 7.09421237097145e-05 1662 2.80098241498078 3.25295950021044 1 2.4983369161433 2830 4054 2305 3094 4513 3228 1662 1940 2163 3414 1962 2989 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 3.31956304344836e-07 6.39523982248011e-07 3020 2500.81818181818 2831 3.01778504030434e-08 1037 1.52234194751198 -1.17627797639243 -1 2.72207129228744 3016 2831 2862 2844 2283 2459 1480 1037 3462 2359 2876 2990 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 1.27296970795966e-05 1.48502645120356e-05 1325 2634.18181818182 2833 1.15725188519062e-06 566 1.89163709898766 1.96838309067685 1 2.6365170149312 1321 3955 2833 3716 3999 1164 566 2012 3749 3690 1971 2991 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 1.28964862685651e-07 3.79261153816994e-07 3840 2749.54545454545 2833 1.17240791132385e-08 1360 1.46318892774963 -1.17634758251861 -1 2.71214424826226 3840 2833 2867 2394 1360 3317 2157 1977 3222 2625 3653 2992 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 3.18578657423166e-06 4.10284109969262e-06 2350 2666.09090909091 2834 3.18579114139712e-07 320 2.40916289462528 2.22258100927312 1 3.74670867635986 2349 2478 4394 3900 3645 1797 519 320 3374 2834 3717 2993 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 1.35704532815337e-07 3.8811262131939e-07 2245 2623.63636363636 2834 1.23367764714654e-08 635 1.58358824815766 1.76694991660243 1 2.93080372116472 2245 3346 2887 4211 1410 2834 2340 635 3445 2946 2561 2994 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 6.06866199441486e-08 3.11746643088069e-07 4470 2852.09090909091 2835 5.5169656016526e-09 549 2.33127067788418 -1.88596015063075 -1 4.37903098323306 4467 2286 1925 2835 549 4012 3529 4436 1767 2667 2900 2995 M19043 ST_ADRENERGIC http://www.broadinstitute.org/gsea/msigdb/cards/ST_ADRENERGIC.html Adrenergic Pathway 44/55 Signaling Transduction KE 5.17387121276379e-08 3.04252738648075e-07 4405 2825.90909090909 2836 4.7035193949462e-09 387 1.84088703794486 -1.86500854039618 -1 3.46333641905864 4403 1701 2836 1526 387 4262 4023 4104 2168 3382 2293 2996 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 3.35416255306915e-06 4.28821438010781e-06 2590 2667.36363636364 2836 3.04924333354652e-07 1419 2.12226710965589 -2.54499389064947 -1 3.28866693634553 2589 2836 1889 3418 3627 2948 2621 1419 3524 1583 2887 2997 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 2.50445064292574e-07 5.35129336107265e-07 3095 2503 2836 2.27677357093555e-08 617 2.24646249283999 2.43593171122835 1 4.06747543943479 3095 3192 2585 3095 2029 2836 1398 617 657 3585 4444 2998 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 0.000297241799997823 0.000314217535496019 3400 2609.36363636364 2837 2.7025633446229e-05 618 1.06468085143121 1.11571183961502 1 1.07603638648212 618 2837 3205 3399 4444 1206 773 2004 4185 3400 2632 2999 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 1.68648139001261e-07 4.3132890453628e-07 1635 2326.45454545455 2838 1.53316501754121e-08 219 1.65953617882909 -2.25632508751245 -1 3.049432219046 2991 3086 2935 219 1632 2838 3335 1632 1035 3976 1912 3000 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 1.59339837723565e-07 4.20318657884309e-07 2975 2636.09090909091 2838 1.44854408421914e-08 231 1.40152552774486 -1.49840278550016 -1 2.57974322969284 2973 2596 3572 231 1572 2132 3054 2344 3906 3779 2838 3001 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 1.96320287940329e-05 2.23878173249179e-05 570 2211.45454545455 2839 1.7847458168695e-06 402 1.55432748224947 1.71722439801135 1 2.08621255054074 569 3407 3394 2957 4102 568 402 959 2839 3904 1225 3002 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 3.8368417542037e-07 7.07417698431307e-07 2065 3216.36363636364 2839 3.83684241666481e-08 1816 1.43308088806273 -1.48757937231398 -1 2.54428142542057 2062 4685 4301 4101 2480 1816 2584 2839 3403 4616 2493 3003 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 3.20936796497292e-05 3.57860070745859e-05 1760 2604.45454545455 2839 2.91764980391381e-06 604 1.30977771215618 1.1144987844509 1 1.68079988034161 1759 2839 3273 3698 4201 1502 994 604 3827 3846 2106 3004 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 1.71873864008989e-06 2.36652461529296e-06 3520 2811.09090909091 2841 1.56249089349731e-07 152 1.74960772243114 -1.73246006306138 -1 2.84147381981074 3518 2367 2705 2183 3341 3385 2339 4009 152 4082 2841 3005 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 3.34621074903091e-06 4.28268954228619e-06 105 1986.81818181818 2843 3.04201439876786e-07 101 3.13167141690647 3.63343736505021 1 4.85375670786676 2843 764 1078 104 3622 3184 3047 2851 101 1047 3214 3006 M11675 KEGG_HOMOLOGOUS_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HOMOLOGOUS_RECOMBINATION.html Homologous recombination 27/27 KEGG 8.8743621463816e-05 9.62476776905357e-05 785 2453.54545454545 2845 8.06792740064154e-06 506 1.19522268585443 1.28958477593553 1 1.38542170162359 782 3408 3552 3434 4327 680 506 1638 4073 2845 1744 3007 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 2.88778815581659e-07 5.82992305194795e-07 2320 2531.36363636364 2845 2.62526230443335e-08 809 2.0121790301564 1.77163242182696 1 3.62157154971258 2320 3337 1864 3388 2165 2845 2846 809 3627 1476 3168 3008 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 9.98103162959728e-08 3.41896906035439e-07 4175 2709.18181818182 2846 9.07366552947272e-09 532 2.14444372880319 2.27519684302273 1 4.00320107256354 4173 2759 1981 2387 1103 3347 3180 4214 532 2846 3279 3009 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 9.84986109765326e-08 3.40595929530574e-07 4140 2902.18181818182 2846 8.95441958059292e-09 1088 1.80943345280734 -1.39304901140627 -1 3.37854170425305 4139 1572 2801 2846 1088 3398 3691 4113 1895 2335 4046 3010 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 4.12200521889821e-07 7.41740931498268e-07 3205 2563.45454545455 2846 3.74727817383026e-08 433 2.53043745514764 3.18517760875762 1 4.47814474951607 3203 3349 2128 2393 2466 3612 2868 1992 433 2908 2846 3011 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 2.48042651248829e-05 2.79284664574063e-05 1545 3095.18181818182 2847 2.25495861719101e-06 1544 1.671221732649 -1.84721570888193 -1 2.19682674746104 1544 3750 2704 3901 4157 2847 2424 3233 4365 2307 2815 3012 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 4.15763566511508e-07 7.4729780424003e-07 4310 3115.18181818182 2850 4.15763644298232e-08 1150 1.47154340448539 1.55874342737027 1 2.60246974444886 1150 4096 4310 4309 2528 2616 2850 2454 2450 4519 2985 3013 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 4.45300444182032e-07 7.8986023921052e-07 3495 2787 2850 4.04818667559097e-08 1347 2.4346076090266 -2.08223343564109 -1 4.28932967714547 3495 3009 1347 1819 2510 3787 3942 4178 1613 2107 2850 3014 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 1.63275923065324e-07 4.24841431570192e-07 2740 2931.72727272727 2851 1.48432668348241e-08 1601 1.62301472149946 1.76375282156065 1 2.98538896284815 2739 3561 3709 2475 1601 2851 2490 2909 2313 4232 3369 3015 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 4.97465379405977e-05 5.46436255712406e-05 1625 2647.90909090909 2853 4.52251480436763e-06 698 1.79921213349304 -1.81309828129507 -1 2.21369218702213 1624 3921 3054 3478 4268 953 2206 2445 2853 3627 698 3016 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 9.50146956211072e-07 1.43326738041427e-06 2855 2986.63636363636 2855 8.63770333241381e-08 1386 1.32179868666473 -1.34867676186164 -1 2.22959974004591 2855 3932 3676 1551 3016 2541 2422 1386 4463 4179 2832 3017 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 2.78417022511653e-07 5.7012075759436e-07 4315 2843.36363636364 2855 2.53106416132929e-08 265 1.89709988282115 2.41961264498041 1 3.41971147535067 4312 265 2579 2159 2127 4463 4456 2855 719 3192 4150 3018 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 6.41104432822986e-06 7.79498434550359e-06 2840 2987.90909090909 2856 5.82823910072841e-07 2487 1.5346224675127 1.51243536978268 1 2.26280072265999 2839 3059 3318 2664 3824 2791 2781 2487 3267 2981 2856 3019 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 3.93337443821519e-07 7.19184377766178e-07 2975 2702 2856 3.57579558314763e-08 1449 2.13001646499251 -2.03100014135212 -1 3.77762809845341 2974 3274 1594 3291 2420 2839 3156 3309 2856 1449 2560 3020 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 1.64207098668729e-06 2.27089805366658e-06 2370 3039.27272727273 2856 1.64207220006726e-07 1674 1.63205466442292 -1.91896867770414 -1 2.65894453766092 2366 2458 4706 2856 3364 3243 4566 1674 3573 1864 2762 3021 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 0.00230255009082573 0.00237448906023541 1945 2893.09090909091 2857 0.000230493935740015 1298 1.44672722701334 -1.59260913952879 -1 1.09552866279926 1941 3508 4196 2857 4578 2524 1298 1742 3832 2921 2427 3022 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 2.38689562104521e-07 5.22548577520102e-07 4225 2994 2857 2.16990534546555e-08 1026 2.07773747771018 1.37917719362479 1 3.76811395802364 4223 4526 2360 4539 1978 3523 2670 1026 3046 2857 2186 3023 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 9.30126884083111e-20 4.30411656163949e-18 3245 2251.45454545455 2859 9.30126884083116e-21 59 2.244657333133 2.61885516761437 1 11.2554524143693 3241 957 4357 912 693 2859 3388 3394 1546 59 3360 3024 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 3.49316149892927e-07 6.60830552102051e-07 2335 2666.81818181818 2859 3.17560186688529e-08 146 1.75625953359883 -1.94785243022157 -1 3.13324898501201 2967 2973 3173 2179 2331 2336 4360 2859 2332 3679 146 3025 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 1.08861469345482e-05 1.28072316877038e-05 2860 3171.18181818182 2860 9.89654618389343e-07 1931 2.08440368943301 2.13126027617184 1 2.94396766195558 2860 3499 2605 4411 3967 2642 1931 2578 4534 3281 2575 3026 M7739 BIOCARTA_PYK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PYK2_PATHWAY.html Links between Pyk2 and Map Kinases 43/47 BioCarta 1.44869264392882e-07 4.01516692856374e-07 3045 2746.63636363636 2861 1.31699339938614e-08 225 1.29265337697479 -1.5527119844758 -1 2.38669764041442 3043 3940 3634 225 1468 2971 2745 2861 2791 4284 2251 3027 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 9.38407014945857e-08 3.37597645620766e-07 3905 2949.36363636364 2861 8.53097322703167e-09 1026 1.83128721494072 -1.37176240873974 -1 3.42138771482286 3901 1234 2426 3320 1026 4277 4507 2702 2861 2500 3689 3028 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 1.98865797485805e-07 4.72935366845837e-07 2980 2754.36363636364 2863 1.80787104965447e-08 1375 1.67584142409742 -1.14232363411267 -1 3.06004826051894 2980 3097 2859 2863 1784 2281 2715 3745 1375 3453 3146 3029 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 5.44161564152239e-06 6.69562717100774e-06 4380 3060.09090909091 2865 4.9469355465424e-07 1683 1.92290564582909 -1.96865930398606 -1 2.87220307248094 4376 2865 2716 3649 3783 4422 3049 1683 2628 2266 2224 3030 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 6.07641761951321e-08 3.11746643088069e-07 4045 2629.45454545455 2868 5.52401617031305e-09 550 1.95479888565457 2.15614559164487 1 3.67173177410355 4045 2024 1090 1270 550 4462 4479 2868 2874 883 4379 3031 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 8.64067527378646e-08 3.28305665915602e-07 2645 2870.45454545455 2868 8.64067560976218e-09 1044 1.81593375810421 1.96803517110167 1 3.39905166924399 2645 2937 4441 1523 1044 2868 3709 3658 1930 4091 2729 3032 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 6.46538607068251e-08 3.14536172538656e-07 2870 2506.90909090909 2868 5.87762387335277e-09 622 1.73053151952367 -1.75197641840958 -1 3.24845446848458 2868 3877 2928 4464 622 1304 2500 1813 3017 3083 1100 3033 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 7.36699986535658e-07 1.17046386407996e-06 4365 3123.72727272727 2869 6.69727484754368e-08 638 1.78429828211869 -1.59440341839876 -1 3.0553672303543 4364 2680 2869 2596 2837 4263 4272 3581 638 2244 4017 3034 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 2.34546721912013e-06 3.11935905163342e-06 2870 3053.18181818182 2869 2.13224519970619e-07 1122 1.62339788441505 1.94839773256651 1 2.5802068013836 2869 4418 3571 1122 3478 2657 2740 3819 2352 4480 2079 3035 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 3.3356569907231e-05 3.71240297010446e-05 3055 3112.27272727273 2869 3.03246142480508e-06 1722 1.50422469480392 1.07306526242403 1 1.92353133263943 3055 2809 2453 3663 4209 2869 2498 2400 4284 1722 4273 3036 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 5.18199293058463e-07 8.91688174712339e-07 2820 2951 2869 4.71090377379841e-08 1817 1.9011166455916 2.12949044080953 1 3.32031772071269 2818 4138 2938 2869 2597 2640 1817 3185 3253 2432 3774 3037 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 0.000230521264014307 0.00024478298451013 2090 2713.36363636364 2870 2.30545180530039e-05 563 3.32146164185884 -3.61863660079864 -1 3.46272871295814 2087 3203 4273 2870 4433 1303 563 3999 3898 2140 1078 3038 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 6.48541427685184e-08 3.14536172538656e-07 3360 2783.54545454545 2870 5.89583133457855e-09 626 1.44478604081591 -1.31859079024155 -1 2.7119272303702 3360 2093 3880 3701 626 2710 2870 3324 1682 4176 2197 3039 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 7.97303754098442e-06 9.55145614046865e-06 3000 2960.72727272727 2870 7.24824221479995e-07 466 2.16235130657969 2.03237784178533 1 3.13363230083206 2996 4285 2355 4396 3890 2870 2449 466 4030 2627 2204 3040 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 3.27537886497118e-07 6.33338313914952e-07 4165 2859.54545454545 2872 2.97761759328409e-08 688 2.8775516624881 -3.14709907470506 -1 5.14957074792929 4162 2396 2073 1486 2276 4578 4371 3613 688 2940 2872 3041 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 3.44861583231605e-06 4.39575120943336e-06 2580 2827.27272727273 2873 3.13511021655891e-07 1571 1.66064047973523 1.37318546177684 1 2.5679844036999 2579 4002 2873 2213 3639 2766 1571 1802 3425 3328 2902 3042 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 1.08083038433498e-07 3.51102506129464e-07 2875 2894.81818181818 2873 9.82573124940658e-09 1190 1.69963170248414 1.66715269632989 1 3.16699382180496 2873 3589 3386 2635 1190 2411 2852 3320 3352 2745 3490 3043 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 2.28016297595564e-07 5.09099775142413e-07 4430 2808 2874 2.0728756475276e-08 524 2.09292246402408 -1.54948979980776 -1 3.80250287124938 4429 1671 2050 2356 1929 4579 3737 2874 524 2959 3780 3044 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 4.63094243158141e-07 8.13171438878878e-07 4430 3171.45454545455 2875 4.20994855125723e-08 1285 2.69710213411251 -2.43045388118894 -1 4.74205146084169 4430 1893 1285 2749 2542 4583 4608 2875 3753 1998 4170 3045 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 6.40035044584039e-07 1.04894632306829e-06 4525 2889.27272727273 2877 5.81850209805749e-08 1156 1.87712832915945 1.2185011523229 1 3.24017486149955 4523 2877 2130 3085 2743 4383 3276 1156 2111 1832 3666 3046 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 1.27583823002124e-08 1.33922089999919e-07 2880 2343.36363636364 2877 1.15985294310924e-09 363 3.73850556790843 4.40885470951352 1 7.41902333885688 2877 680 363 1344 1698 3647 4620 2899 3603 405 3641 3047 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 2.1683005690829e-05 2.45900497022376e-05 1575 2835.54545454545 2878 1.97120176359698e-06 1388 1.51444166317133 -1.57236119678908 -1 2.01483622463947 1574 3424 3130 2878 4125 2011 2534 1388 4532 3218 2377 3048 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 7.7058422304705e-08 3.24764325922831e-07 3290 3103.81818181818 2878 7.00531136398146e-09 802 1.93167288198014 -1.59256763039567 -1 3.61837348325423 3290 3286 2461 4574 802 2700 2864 4551 3966 2770 2878 3049 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 5.71643405984305e-07 9.60540005783524e-07 3160 2926.63636363636 2878 5.19675958653625e-08 1503 1.69885510981904 -1.28800926815396 -1 2.95112788051785 3157 2377 2878 3352 2668 2963 3426 4703 2768 2398 1503 3050 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 0.0170573784728771 0.0173701890813333 1985 2813.63636363636 2879 0.00171897400035948 799 4.44314247125247 5.7890701004329 1 2.25750596717157 1985 3807 4211 2879 4663 2092 1012 4157 799 3062 2283 3051 M4844 KEGG_CHEMOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHEMOKINE_SIGNALING_PATHWAY.html Chemokine signaling pathway 161/239 KEGG 1.65238609224027e-07 4.27122801499128e-07 3625 2928.27272727273 2880 1.50216928758951e-08 1108 1.89689044913502 -1.87691287889343 -1 3.48802994960394 3622 2526 2479 1108 1612 3812 4477 3440 2880 2773 3482 3052 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 0.0170573784728771 0.0173701890813333 1990 2821.09090909091 2880 0.00171897400035948 800 4.44314247125247 5.7890701004329 1 2.25750596717157 1986 3808 4265 2880 4664 2093 1013 4174 800 3065 2284 3053 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 1.54451549654947e-07 4.15043368091742e-07 2320 2884.45454545455 2881 1.40410509543871e-08 578 1.18214348822662 -1.38773439160532 -1 2.17767132852465 2316 4196 3776 4502 1531 1748 1619 2881 4219 4363 578 3054 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 7.08429683323969e-07 1.1357975901118e-06 800 2925 2881 7.08429909166746e-08 797 1.43506427285332 1.54254038034678 1 2.46259386728679 797 4090 4671 3813 2881 2028 1825 1815 3310 4564 2381 3055 M14314 KEGG_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PURINE_METABOLISM.html Purine metabolism 139/171 KEGG 3.32908701351448e-07 6.40574427386399e-07 1510 2934.27272727273 2882 3.02644319752651e-08 1508 1.63381750993703 1.82894673832064 1 2.92112546901802 1508 4122 3543 4598 2286 2498 2882 1689 3215 3318 2618 3056 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 1.07835397507601e-06 1.59505821446529e-06 2725 2696.81818181818 2882 9.80322276039383e-08 466 1.49665552931565 -1.36532612068846 -1 2.50458634701098 2723 3490 2882 3888 3084 2453 1966 944 4494 3275 466 3057 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 3.03977152486278e-07 6.04363454990223e-07 2280 2811.09090909091 2882 2.76342904079314e-08 2193 1.79027216525639 -2.06055070103319 -1 3.21399991508932 2280 2193 2650 2894 2204 3088 3395 3362 3762 2882 2212 3058 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 8.68089109388226e-07 1.33682890581156e-06 2670 2625.27272727273 2884 7.89172229021989e-08 175 1.79711776302737 1.96208226764305 1 3.04737275032445 2670 175 2299 2884 2947 2705 2993 3934 2964 1979 3328 3059 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 1.76535768616562e-07 4.43217461633071e-07 4150 2704.45454545455 2884 1.60487075256743e-08 23 2.80763213679622 -2.52512543160588 -1 5.150104775887 4147 2884 2283 1200 1672 4308 3175 4281 23 3116 2660 3060 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 1.47438560853762e-07 4.05305770081394e-07 2885 2809.90909090909 2884 1.4743857063592e-08 1593 1.95305039615337 2.31183764394587 1 3.60416478978037 2884 2941 4663 2135 1593 3922 3506 2146 1648 2465 3006 3061 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 1.71404630140477e-07 4.35332519137324e-07 4040 2622.45454545455 2885 1.55822403177107e-08 294 2.04450907415283 -1.36227037001354 -1 3.7546587894137 4037 2213 1825 4553 1648 4352 3006 294 1067 2967 2885 3062 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 7.8403596818504e-07 1.22863538175079e-06 1205 3163.09090909091 2885 7.12760225090822e-08 1204 0.975470399102875 1.07907667288863 1 1.66403584219843 1204 4711 4178 4699 2885 1836 1569 2280 4183 4619 2630 3063 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 7.7980031835272e-08 3.26249199126138e-07 2930 2537.81818181818 2885 7.08909405448283e-09 360 1.64340067697818 1.87018946425557 1 3.07731868676102 2930 360 2443 3830 814 3211 2493 3820 2885 1667 3463 3064 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 5.08708910367086e-08 3.0357704374324e-07 2890 2504 2886 5.087089220124e-09 464 2.23926849129793 2.65685055139284 1 4.21363856867259 2886 1976 4288 1409 464 3175 3365 2089 3020 1254 3618 3065 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 0.000360093543514695 0.000378961321157048 2985 3194.81818181818 2886 3.27411360666747e-05 2535 1.99589800086621 2.04415047020736 1 1.97104501980972 2982 3709 2535 4365 4459 2760 2853 2775 2886 2793 3026 3066 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 6.21174472816676e-05 6.78219641844716e-05 1975 2371.36363636364 2887 5.64720011361401e-06 289 1.35596074614653 1.54115000907075 1 1.63137812468407 1972 3491 3340 3140 4368 1739 532 524 2887 3803 289 3067 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 3.65833145731406e-07 6.85211288830252e-07 4195 2588.45454545455 2888 3.32575642331824e-08 215 1.75426103225279 1.45824849583542 1 3.12171204548639 4195 215 2338 1416 2360 3870 3182 4332 721 2888 2956 3068 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 7.16592049401353e-07 1.14732512658561e-06 2085 2648.63636363636 2888 7.1659228047833e-08 909 1.88661836740773 2.26839979734607 1 3.2353499326188 2084 3512 4413 3342 2888 2207 1612 3528 909 2928 1712 3069 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 1.6143006054222e-05 1.85569869887793e-05 2100 2531.72727272727 2888 1.46755677349628e-06 254 1.50242342500697 1.65260752549149 1 2.05187868224951 2096 2450 3003 4390 4068 1726 444 2888 3247 3283 254 3070 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 7.85933401925128e-07 1.23120001894677e-06 2890 2839.81818181818 2889 7.14485166085497e-08 1980 1.72871743574954 1.91163817284172 1 2.9491982428882 2104 3104 2889 3723 2887 2180 2112 1980 2933 3939 3387 3071 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 3.99095251695458e-07 7.25907355684995e-07 2435 2920 2889 3.62813930994657e-08 117 2.20613455579783 -0.763247326524183 -1 3.91008158149306 3581 3171 2432 2768 2433 2889 2049 4312 117 3777 4591 3072 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 1.07368916690635e-06 1.58965271888268e-06 2505 3019.27272727273 2889 9.76081537191398e-08 2504 1.63232002936234 1.94724788300439 1 2.73238782898309 2504 3412 3305 2889 3079 2707 2780 3870 2544 2851 3271 3073 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 1.48557317343521e-06 2.07821736177065e-06 2980 2918.72727272727 2891 1.35052197871372e-07 1951 1.91175604147994 1.46950861912003 1 3.13603930400904 2978 2786 2126 2143 3284 2891 2125 4013 1951 3642 4167 3074 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 2.75830317224642e-06 3.59944455985709e-06 2895 3212.81818181818 2892 2.50755148231069e-07 1559 1.51725413239539 1.84709793372753 1 2.38420851156482 2892 4406 3821 1559 3545 2741 2704 3875 2862 4558 2378 3075 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 7.69884202670448e-08 3.24764325922831e-07 2060 2591.81818181818 2892 6.99894754193042e-09 800 1.36752257121021 1.58327041810991 1 2.56136612947541 2056 3053 3435 3463 800 2892 2364 1312 3331 2599 3205 3076 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 3.69696371025703e-08 2.87575261955407e-07 4095 2937.09090909091 2892 3.3608761567111e-09 132 2.22451375088237 -2.16389169563411 -1 4.20097549269246 4092 2200 1680 2733 132 4440 4720 4388 3427 1604 2892 3077 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 1.12816385602911e-07 3.58148551537347e-07 4085 2538 2893 1.02560355807414e-08 108 1.82237006867132 -3.0199016248329 -1 3.39121845320012 4084 3741 2893 1502 1233 4402 3829 257 108 4202 1667 3078 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 7.29654482871831e-07 1.16241607755768e-06 1455 2685.90909090909 2894 7.29654722449991e-08 1452 1.50446482131227 1.63412171684649 1 2.57735729082502 1452 2938 4560 3213 2894 1831 1918 2152 2916 3193 2478 3079 M5500 KEGG_BASE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASE_EXCISION_REPAIR.html Base excision repair 33/35 KEGG 3.63806857004052e-06 4.60490309750369e-06 1920 2772.27272727273 2895 3.30734053291848e-07 1605 1.2515802721506 1.21799200489768 1 1.92791297125577 1920 3090 3342 3887 3666 1904 1605 1627 2895 3699 2860 3080 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 1.21813741267528e-07 3.70192774369017e-07 2455 2772.90909090909 2896 1.21813747944893e-08 868 1.85555782642065 1.93206686012637 1 3.44529579419362 2451 2492 4523 2607 1401 3121 2896 3090 3357 868 3696 3081 M2821 BIOCARTA_NTHI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NTHI_PATHWAY.html NFkB activation by Nontypeable Hemophilus influenzae 32/42 BioCarta 3.33641881683118e-06 4.27351338275255e-06 2400 2675.63636363636 2897 3.03311261518295e-07 1299 1.58321445418538 -1.89226772805764 -1 2.45381354459615 2399 3389 3092 1299 3621 2918 3519 1804 1702 2792 2897 3082 M14766 REACTOME_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTRINSIC_PATHWAY.html Genes involved in Intrinsic Pathway 10/23 Reactome 2.1375073672597e-07 4.90234925824382e-07 2900 3002.36363636364 2898 1.94318870448974e-08 1869 2.20117292172345 2.19018094909406 1 4.00964437470817 2898 3498 1926 4541 1869 2826 3138 4023 2816 2086 3405 3083 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 2.98085421392571e-06 3.86422188676994e-06 1825 2827.81818181818 2898 2.709871138903e-07 1691 1.65675322870368 1.71792053646856 1 2.58874838474316 1821 3992 2898 3947 3575 1691 1799 1877 4481 3034 1991 3084 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 2.44257646824229e-07 5.29580198902324e-07 4190 3107.09090909091 2898 2.22052430857484e-08 1998 1.75800383901299 -1.96207365823823 -1 3.18517643478134 4189 2438 2131 3592 1998 4008 4670 2898 2526 2052 3676 3085 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 4.04287680655072e-07 7.31604867117337e-07 4245 2995.63636363636 2899 3.67534322681706e-08 1392 1.65816475091788 1.83554842524958 1 2.93703789505962 4244 2163 3045 1942 2447 3696 2373 4166 1392 2899 4585 3086 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 3.97873415469712e-06 5.00523059972559e-06 1825 3123.90909090909 2899 3.61703759119802e-07 1825 2.16874542792061 -2.36993407191782 -1 3.31865704141807 1825 4415 2732 3203 3691 2787 2899 2759 3592 4041 2419 3087 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 1.00103426852917e-07 3.41896906035439e-07 3345 2808.36363636364 2900 1.0010343136223e-08 1207 1.73006852617308 2.00807971621541 1 3.22948799037928 3341 2936 4278 2224 1207 3474 2666 2054 2587 2900 3225 3088 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 8.14390346614649e-07 1.2703836641158e-06 4045 3091.54545454545 2900 7.40355134621573e-08 1952 1.93470362913438 1.87695608893516 1 3.2931126019379 4043 2315 2425 2780 2900 4044 3893 3034 2064 1952 4557 3089 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 1.23627319681585e-07 3.71755418903835e-07 2900 2439.18181818182 2900 1.12388478753389e-08 547 2.36348544560032 -2.41516941466585 -1 4.3873745812342 2900 1552 776 1396 1323 3257 4300 4222 3343 547 3215 3090 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 0.000413164527622777 0.000434328857545548 1440 2847.54545454545 2900 4.13241364946727e-05 195 3.62672715288655 4.17191991307124 1 3.52024755812074 1440 2900 4654 3869 4499 1404 195 3747 4125 2385 2105 3091 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 1.09636771386262e-07 3.53357928937751e-07 3100 2689.18181818182 2900 9.96697971363629e-09 1200 1.70017124080807 1.99002780627978 1 3.16663415441892 2335 2950 3098 2836 1200 2701 2900 2980 2527 3097 2957 3092 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 1.45895947290572e-05 1.68864362729647e-05 2405 2765.27272727273 2903 1.45896905152657e-06 400 1.6760759505333 2.33397551733495 1 2.30896652889481 2401 4334 4329 4224 4064 2903 1422 400 1166 4087 1088 3093 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 4.25782384518247e-06 5.33075027831864e-06 2905 2868 2903 3.8707564415349e-07 1539 2.15170441859873 1.98461937468031 1 3.2755714111047 2903 2685 1877 2578 3710 3058 2095 4087 3613 1539 3403 3094 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 8.19474002470227e-07 1.27738351772109e-06 475 2626.36363636364 2905 7.44976643377061e-08 475 1.08301169374005 -1.14755402125216 -1 1.84229869891415 475 4165 4084 3538 2905 1193 1104 1412 4482 4498 1034 3095 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 2.11294746236987e-06 2.84134245652017e-06 2905 2770 2905 1.92086317428376e-07 972 1.42347718693762 -1.47658587579602 -1 2.27901413158867 2905 2757 3134 3635 3436 2619 2392 972 3596 3151 1873 3096 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 0.00432056296856946 0.00443230976127969 2315 3150.81818181818 2906 0.000432898629591031 1860 1.04342659456766 -1.21481929552192 -1 0.70821916589846 2312 2906 4245 1995 4586 1924 2236 4379 4357 3859 1860 3097 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 5.46260483620913e-06 6.71970154467216e-06 2105 3043.54545454545 2906 4.96601672719645e-07 2102 1.72662560577513 1.55248885055694 1 2.5781586922204 2102 4028 2879 3873 3784 2906 2256 3276 2209 3313 2853 3098 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 3.89702086801035e-07 7.14984191427816e-07 3515 3057.72727272727 2906 3.54274687119847e-08 1496 2.32236772028901 -1.808247129511 -1 4.12055071455349 3511 2220 1496 3029 2412 4273 4092 4659 2173 2864 2906 3099 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 1.08934571086271e-06 1.60728720077273e-06 2430 2832.27272727273 2907 9.90314772963987e-08 1691 1.97866864941536 -1.85913211314874 -1 3.30959602556935 2429 3585 2518 1691 3092 2907 3845 3567 2049 2371 3101 3100 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 8.74664410995444e-08 3.30738824521022e-07 3735 2650.36363636364 2909 7.95149496154447e-09 954 2.04019660526907 -1.41352422617362 -1 3.81704237380584 3731 3568 1758 1747 954 3839 3347 1733 2909 1711 3857 3101 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 3.21612164698702e-07 6.25983264898092e-07 2655 3014.81818181818 2912 2.92374737922128e-08 2176 1.12492379103734 1.13305933797466 1 2.01424951021736 2653 3718 3643 3752 2259 2213 2176 2404 3121 4312 2912 3102 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 1.47361360029959e-05 1.70309896998385e-05 2855 3013.18181818182 2912 1.3396577009228e-06 1272 2.07559926064391 2.43380698482956 1 2.85733742288184 2853 3710 2912 2679 4041 2815 2292 1272 3195 3697 3679 3103 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 2.45679799462099e-07 5.31199566404539e-07 2465 3112.63636363636 2913 2.23345297179832e-08 2004 1.61857804342601 -1.62406973147609 -1 2.93187473501572 2464 4195 3387 4609 2004 2849 2215 2562 3709 3332 2913 3104 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 2.38030612360785e-07 5.22548577520102e-07 3010 2316.27272727273 2914 2.16391489195169e-08 505 2.56118790540546 -2.59721074512194 -1 4.64508360971869 3008 1513 505 796 1969 3461 3904 3250 2914 676 3483 3105 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 1.08943548345437e-07 3.51855294828115e-07 2885 3000.81818181818 2914 1.08943553686351e-08 1292 1.72193082702037 1.91466654526257 1 3.20809349434356 2914 3828 4450 2472 1292 2881 3098 2882 1764 4240 3188 3106 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 6.31893594018103e-07 1.03704372870843e-06 2920 2823.45454545455 2915 5.74448886830373e-08 1539 2.22069137040688 2.87800296585398 1 3.8365465131903 2917 3147 2365 3448 2739 2757 1539 2915 2287 3641 3303 3107 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 7.60013954849949e-07 1.19815159214822e-06 2635 3231.45454545455 2915 6.90922015822884e-08 2542 2.46036216205198 -1.99027924431496 -1 4.20614679957252 2633 4042 2542 4174 2861 2878 2915 3517 4289 3031 2664 3108 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 6.40097113992164e-06 7.78674839701808e-06 2050 2606.81818181818 2916 5.81908160348183e-07 879 1.23372547263134 -1.12758427463283 -1 1.81912280150422 2048 2394 3382 2916 3823 1806 879 1839 3416 3058 3114 3109 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 8.96447928161892e-07 1.36933146308224e-06 2920 2645.36363636364 2916 8.14952994039466e-08 1088 3.16716904254555 3.24375800380332 1 5.36168402699982 2334 3140 1088 2707 2974 2916 2918 3454 4132 1842 1594 3110 M7934 KEGG_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRUVATE_METABOLISM.html Pyruvate metabolism 41/49 KEGG 1.90386617985268e-07 4.61712366863461e-07 3675 2970.36363636364 2918 1.73078758601098e-08 1740 1.82901610181824 -2.0954051213356 -1 3.34532926069432 3671 2263 3202 2918 1740 4122 4606 1774 3032 2642 2704 3111 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 8.18140570304489e-08 3.27411388472988e-07 3670 2433 2918 7.43764182481522e-09 575 2.58896223068153 -1.68287857123097 -1 4.84725303369021 3669 575 1024 1373 873 3546 3932 4093 2918 1072 3688 3112 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 1.43782341117308e-06 2.02100253148807e-06 1810 2471.90909090909 2918 1.30711304624745e-07 560 1.84926968860437 1.76998489709442 1 3.03998302320071 1809 3729 2218 3185 3269 1188 560 911 4429 2918 2975 3113 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 9.18691802368603e-07 1.39499286304437e-06 3955 3061.36363636364 2919 8.35174714547954e-08 2199 1.95552398183926 -1.77239046709096 -1 3.30561359957844 3954 3360 2545 4194 2993 2919 2199 2822 2677 2390 3622 3114 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 3.15617475335061e-06 4.06914636323815e-06 4105 2600.27272727273 2919 2.86925389207869e-07 1244 3.60514639395489 -3.76052435363152 -1 5.61084750751219 4105 3168 1244 1785 3599 2954 2183 3032 2919 2127 1487 3115 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 2.90340947444721e-07 5.85144864192606e-07 1475 2513.45454545455 2920 2.63946350692673e-08 970 1.93242379554951 -1.91724721800722 -1 3.47709874365117 1471 3350 2920 3685 2171 2112 3023 3005 970 3154 1787 3116 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 2.13073221500944e-07 4.90234925824382e-07 3035 2762.27272727273 2920 2.13073241931036e-08 938 2.5084703652161 2.37559238039074 1 4.56953593806966 3032 2920 4575 3585 1951 2194 938 3329 3400 2175 2286 3117 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 2.20806427522269e-05 2.50049505255545e-05 2075 2862.72727272727 2921 2.00735130646836e-06 1898 1.66482803631682 1.66533369170608 1 2.21150471122976 2074 3478 2648 2921 4132 2432 3022 1898 3610 2263 3012 3118 M3397 KEGG_BUTANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BUTANOATE_METABOLISM.html Butanoate metabolism 36/48 KEGG 1.38173168692333e-07 3.92497786572715e-07 3215 2647.18181818182 2922 1.25611979427669e-08 545 1.87613731709855 1.75262909254571 1 3.46975042788666 3215 545 2273 2619 1424 3245 2922 3852 3125 2664 3235 3119 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 3.55006770380073e-07 6.69449443145803e-07 2680 3078.72727272727 2922 3.22733479696693e-08 1654 1.6988734850778 -1.62352631245787 -1 3.02808066308225 2676 4359 3899 3529 2340 1654 2857 3301 2922 4473 1856 3120 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 5.25990311003653e-07 9.02134545035336e-07 3310 3098.09090909091 2924 4.78173124328074e-08 1989 1.97272274329476 3.00650040101404 1 3.44252939813962 3308 3704 2924 4022 2606 2768 2544 3571 1989 3927 2716 3121 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 8.38064035307007e-07 1.2990680612969e-06 2925 2691.54545454545 2925 7.61876685961619e-08 1042 1.60559886853279 -1.89912707917767 -1 2.72829184731777 2925 1889 3118 2815 2927 3564 3694 1373 1042 3662 2598 3122 M18928 BIOCARTA_IL5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL5_PATHWAY.html IL 5 Signaling Pathway 5/16 BioCarta 8.50892083717134e-05 9.23266812676982e-05 3240 2903.09090909091 2926 8.5092466625323e-06 1225 3.36417079505181 2.14930034413098 1 3.91863078947666 2266 2926 4193 1937 4334 2107 2516 3237 3240 1225 3953 3123 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 0.000190377241665033 0.000203298773904741 855 2695.54545454545 2927 1.90393553204152e-05 116 1.19241591404711 1.19241591404711 1 1.27034792618453 853 3521 4398 3931 4502 1081 116 2106 4146 2927 2070 3124 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 2.02106037575097e-07 4.7747030607174e-07 2320 2925.72727272727 2927 1.83732778310772e-08 1250 1.46094897501019 -1.23472155931077 -1 2.66580062559627 2317 4383 3664 3514 1799 1250 2927 2079 4015 4237 1998 3125 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 0.000605577148736341 0.000633213146219657 2930 2691.54545454545 2928 5.50676277805207e-05 449 2.30470854925579 -1.36407377717907 -1 2.12776304658376 2928 4291 3065 1518 4496 1589 794 4607 449 4042 1828 3126 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 1.62033738323681e-07 4.23355458787827e-07 4365 2785.09090909091 2928 1.4730340932522e-08 164 1.97348290262452 1.99886778395484 1 3.63109668632453 4361 3379 2790 1904 1591 3914 3739 1810 164 4056 2928 3127 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 6.4750932424754e-08 3.14536172538656e-07 2450 2821.90909090909 2929 5.88644857550174e-09 625 1.51682201218562 -1.60968597133344 -1 2.84718487622573 2447 2547 3383 3924 625 2021 2929 3352 3526 3725 2562 3128 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 2.15978919815783e-05 2.450530051756e-05 1385 2579.09090909091 2930 2.15981018954718e-06 43 2.66832609790265 2.66832609790265 1 3.5517931821555 1381 4646 4466 4360 4149 1069 579 1761 2986 2930 43 3129 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 2.46405113816711e-06 3.26419348081637e-06 440 2806.90909090909 2930 2.46405387036797e-07 436 1.33392046331691 1.39525100202837 1 2.11236941805056 436 4352 4639 3250 3537 1435 1445 1787 2930 4653 2412 3130 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 8.45496192927269e-06 1.00878211087379e-05 3840 2682.81818181818 2931 8.45499409831649e-07 113 2.70987109608226 -2.86049095826456 -1 3.90873679431738 3836 2455 4521 1194 3976 4574 4358 207 113 2931 1346 3131 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 2.11635019329428e-07 4.87990860398095e-07 3055 2687.90909090909 2932 1.92395490625673e-08 1774 1.74318249642187 1.92740471525956 1 3.17619533841993 3051 2976 2932 2371 1859 1774 2129 3305 3082 2622 3466 3132 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 2.72275365321284e-06 3.55994383467163e-06 3540 2848.63636363636 2933 2.4752336572184e-07 599 2.21281058934929 -2.27468433372885 -1 3.48066087632166 3919 2896 2891 1685 3538 2933 1506 4243 599 3588 3537 3133 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 1.87467576093698e-06 2.5618035876151e-06 2410 2980.09090909091 2934 1.70425214399784e-07 1874 1.46214453996714 1.54297106740869 1 2.35993498361418 2407 1874 2934 3110 3374 3761 4333 2612 2204 2671 3501 3134 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 4.36050491106803e-08 2.97164560412799e-07 4640 2942.81818181818 2934 3.96409545226846e-09 222 1.8313207058793 -1.50014961480311 -1 3.45074819421213 4638 222 2454 2592 250 4566 4409 4472 1589 2934 4245 3135 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 6.69526857123054e-08 3.14536172538656e-07 4610 2645.18181818182 2935 6.08660797726172e-09 612 1.92126506337545 -1.77438227377442 -1 3.60658346482547 4606 1315 2095 612 658 4564 4127 4135 735 2935 3315 3136 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 1.31947666344626e-07 3.82284020774267e-07 3310 2609 2936 1.19952431143953e-08 744 1.85953510988203 -1.57507115494421 -1 3.44518733674166 3615 2515 1924 3031 1385 3921 3307 2936 2012 744 3309 3137 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 3.92312538354527e-06 4.93790714942231e-06 2940 2616.72727272727 2937 3.56648398130198e-07 219 2.92607502088092 3.02247974488725 1 4.4828077737206 2937 3391 1760 2170 3689 3485 3159 2174 219 2998 2802 3138 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 8.06902459432764e-07 1.26111907566975e-06 2755 3057.90909090909 2938 7.33547959439666e-08 1516 1.60891221991153 1.4670537684849 1 2.73990584617555 2755 3386 3339 4542 2896 2487 1516 3137 2938 2511 4130 3139 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 3.63146853618651e-07 6.80990524068349e-07 4185 3063.81818181818 2939 3.3013355778376e-08 2139 1.33892368609511 1.23760624468592 1 2.38345174457321 4183 2778 3141 3389 2356 3438 2139 2939 4032 2919 2388 3140 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 1.976293202651e-07 4.70878541974394e-07 3330 2927.18181818182 2940 1.79663034562221e-08 1582 1.55696346039579 -1.48702397223099 -1 2.84376974374136 3328 2206 2940 2753 1782 3017 4253 4352 1582 2132 3854 3141 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 8.53632320247153e-07 1.31800606855301e-06 980 2585.54545454545 2940 7.76029683153831e-08 978 1.68281810947507 1.82780733106459 1 2.85649264350431 978 4112 3512 3755 2940 1540 1608 1334 3044 3669 1949 3142 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 2.79043360883925e-07 5.70660599381337e-07 4020 3213.72727272727 2940 2.53675814797457e-08 2130 1.94200121892326 -1.34290829005822 -1 3.50044049144578 4018 2661 2374 4171 2130 4359 4573 2940 2344 2481 3300 3143 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 7.8951305962728e-06 9.46292951102276e-06 250 2466.63636363636 2941 7.17741720876052e-07 246 1.44286550536039 1.52633472930284 1 2.09236751232501 246 3583 3922 2963 3888 1033 1175 2151 2941 3209 2022 3144 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 1.22450799090489e-06 1.77508529394075e-06 2945 2568.09090909091 2941 1.11318970223626e-07 606 2.29657305437344 2.31721483029296 1 3.81287372327975 2862 1791 1129 2085 3157 2941 4106 3599 3030 606 2943 3145 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 5.85820421881648e-07 9.798272116518e-07 1035 2373.27272727273 2942 5.8582057631521e-08 46 2.32997751094002 2.32997751094002 1 4.04197881761788 1035 3810 4227 3148 2748 701 46 2942 3449 3467 533 3146 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 8.60169900295678e-07 1.32723175200902e-06 2975 3003 2942 7.81972942373202e-08 2061 2.22326286237837 1.75553557021569 1 3.77220013222507 2414 3443 2061 2384 2942 2911 2974 4656 2279 2972 3997 3147 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 1.46296029770762e-07 4.03897550937735e-07 2180 2789.63636363636 2942 1.32996399544713e-08 1251 1.47294535374827 1.31762616512891 1 2.71860875795381 2179 2398 3051 4144 1477 1975 1251 4553 2942 3061 3655 3148 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 9.23800758572551e-08 3.3560004976122e-07 2945 3007.54545454545 2942 8.39818906694381e-09 1009 1.49500385635691 -1.31389294968785 -1 2.79406515548773 2942 3578 3793 4414 1009 1966 2783 3407 2561 4304 2326 3149 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 9.60330407215321e-07 1.44401386494308e-06 3030 2883.63636363636 2943 8.73028024011886e-08 1535 1.26175883444988 -1.4007279348467 -1 2.12710385321754 3028 2639 3588 1535 3026 2290 2943 2539 4480 4004 1648 3150 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 1.97149312610032e-05 2.24660732863195e-05 2035 3156.45454545455 2943 1.79228253957017e-06 2034 1.55161241618653 1.70119307247248 1 2.08188791169443 2034 3928 3589 2943 4104 2361 2786 2631 3769 3959 2617 3151 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 8.69547531538411e-07 1.3386349937369e-06 4175 2669.18181818182 2945 7.90498068387534e-08 203 2.10591976079829 -1.89937023583061 -1 3.57079976266194 4172 1506 2034 203 2948 3843 4687 2945 1157 2294 3572 3152 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 8.84197349392761e-06 1.05203213741715e-05 2790 3142.63636363636 2945 8.03819002792393e-07 2355 1.75351707290645 2.36145527303274 1 2.51974952463498 2788 4194 2998 2843 3919 4180 3255 2355 2606 2945 2486 3153 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 2.66299245022384e-07 5.55287751817547e-07 2060 2775.18181818182 2946 2.42090252051464e-08 1850 1.82529910000809 2.12668203649366 1 3.29628523962583 2060 3336 2946 3192 2082 2396 1850 3170 3098 3789 2608 3154 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 4.50426570357497e-05 4.96616073834942e-05 1915 2821.45454545455 2946 4.09487084205611e-06 1049 3.27880667216576 3.04138695322762 1 4.07415560817544 1914 4058 2456 3684 4251 1929 1049 2946 3342 2997 2410 3155 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 1.19599535879904e-05 1.40111642927065e-05 950 2370.36363636364 2947 1.08727441880815e-06 461 1.69496588750592 1.7407492655269 1 2.37467536993604 461 3908 3117 2947 3986 949 947 1896 3540 3241 1082 3156 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 4.89204212473139e-07 8.49850527373285e-07 3570 2716 2948 4.44731201141216e-08 1387 2.40536793394493 2.74024699359774 1 4.21572198748131 3569 1711 1387 3079 2572 3422 2948 2827 3095 1934 3332 3157 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 2.76997323940473e-05 3.10331680275109e-05 4045 3187 2949 2.51818919651256e-06 1526 2.05106575469361 2.76366986718349 1 2.66921504678154 2552 4041 2588 2949 4177 3521 2620 4219 1526 4043 2821 3158 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 2.36066267184185e-07 5.20853420399124e-07 4125 3009.72727272727 2949 2.14605720467975e-08 1496 1.8066909325482 1.61082370102234 1 3.27717701633518 4125 1496 2178 2850 1958 4626 4391 3547 3272 1715 2949 3159 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 8.69829136820144e-07 1.3386349937369e-06 2670 2595 2949 7.90754073391514e-08 530 1.8814579394389 1.83935104159492 1 3.19011025694163 2667 530 1780 1452 2949 3070 3143 4343 3277 1484 3850 3160 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 8.70139313616131e-07 1.33867586710174e-06 4220 2741.72727272727 2950 7.91036052519972e-08 730 2.75951278218217 -2.51140571029718 -1 4.67928953150965 4218 2572 730 1078 2950 4092 3263 3746 2457 731 4322 3161 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 1.67024957676712e-07 4.29439298099957e-07 4005 2756.81818181818 2951 1.51840882143019e-08 749 2.43239094159143 2.67365343007474 1 4.47130932843076 4001 2127 749 3259 1622 3588 4518 2075 2951 1193 4242 3162 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 2.44973372262151e-07 5.30157871195484e-07 3310 2731.45454545455 2951 2.22703090491196e-08 834 2.0772882078814 -1.99217639546854 -1 3.76353282816109 3306 3393 2611 4132 2002 2951 3251 834 1982 3344 2240 3163 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 2.72300544507697e-07 5.63850966522947e-07 2520 3253.54545454545 2952 2.47545980191956e-08 1871 1.4809978982217 1.50330523894324 1 2.67151113232597 2518 4716 3918 4652 2101 2779 1871 3138 2692 4452 2952 3164 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 1.09104704760116e-06 1.60879164782177e-06 2935 2515.27272727273 2953 9.91861444259104e-08 780 2.11157125736294 2.3869092755675 1 3.5317040577365 2932 780 1617 3558 3094 3774 3418 2953 973 1273 3296 3165 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 5.99551362446916e-08 3.10910012492405e-07 3695 2585 2953 5.45046707987356e-09 538 2.00896875095195 -1.8013621577078 -1 3.77418085873203 3695 2038 1942 1079 538 3036 3618 4176 1976 2953 3384 3166 M8353 BIOCARTA_HCMV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HCMV_PATHWAY.html Human Cytomegalovirus and Map Kinase Pathways 25/25 BioCarta 0.000245138142079883 0.000259953275807021 2215 2721 2954 2.2287769200843e-05 426 1.3983296157541 -1.57372195354136 -1 1.44675956288675 2213 3726 3392 648 4427 2455 2954 2536 426 4173 2981 3167 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 4.59101279550667e-07 8.08729525563956e-07 2995 2802.45454545455 2954 4.17364886688229e-08 675 1.98529810485842 2.64082729112198 1 3.4916923243436 2993 3959 2954 4409 2531 3001 2752 1867 2317 3369 675 3168 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 1.90383957985416e-05 2.17476350844909e-05 4395 3021.36363636364 2955 1.90385589077399e-06 504 1.90982064899707 1.26116147200076 1 2.57049974069605 4391 2916 4347 2590 4119 4059 3417 2955 504 2831 1106 3169 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 2.23915682040382e-07 5.03558912349762e-07 4080 2803 2956 2.03559731664083e-08 673 2.39606212224959 -1.99293873429271 -1 4.35667186084787 4077 2613 1757 1050 1911 3889 4534 3524 673 2956 3849 3170 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 8.2384938394717e-07 1.28275572265141e-06 2960 2441.72727272727 2956 8.23849689374843e-08 120 3.15881680893572 -2.82733215540524 -1 5.37341519291288 2956 3525 4678 2119 2982 3046 1047 1384 120 3269 1733 3171 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 1.00686203139712e-07 3.42613246105503e-07 4550 2675.27272727273 2956 9.15329161343301e-09 433 2.07927766712648 -1.82244762923485 -1 3.88097853677487 4548 2029 954 3261 1110 3923 4514 2956 2482 433 3218 3172 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 2.54418699092255e-07 5.41164790711089e-07 4555 3072.81818181818 2958 2.31289753194978e-08 1546 1.93477010914924 -2.1256895151137 -1 3.50028021351262 4555 1852 2087 2593 2039 4139 3382 4245 2958 1546 4405 3173 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 1.32824674811474e-07 3.83038247822062e-07 4175 3185.90909090909 2959 1.20749711664313e-08 1391 1.85375004406277 1.90039524907949 1 3.4340083704447 4171 2959 2243 3707 1391 4285 4583 2688 2747 3557 2714 3174 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 7.08096006774885e-07 1.13564836968313e-06 3770 2911.54545454545 2960 6.43723849712779e-08 1792 2.20013629060489 -2.39731508204843 -1 3.77596546583273 3769 1792 2086 3088 2808 3199 2747 3460 2178 2960 3940 3175 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 9.38035391118843e-08 3.37597645620766e-07 2540 3100.63636363636 2960 9.38035430714813e-09 1129 1.55332829691556 1.73888789380727 1 2.90194727297107 2715 4345 4338 4106 1129 2537 2987 1823 2539 4628 2960 3176 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 1.16290041881021e-05 1.36336064997123e-05 3115 3072.09090909091 2961 1.05718778713073e-06 1229 1.64601451055802 1.52209813633854 1 2.31170763020995 3114 3945 2961 2444 3983 2718 1767 4704 4021 2907 1229 3177 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 1.43300102701763e-06 2.01662637075827e-06 3870 2538.18181818182 2962 1.30272905493083e-07 206 2.59594130584426 -2.36009912423464 -1 4.26847728168006 3869 2752 1770 206 3265 3558 3421 3279 241 2962 2597 3178 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 5.15180533979523e-08 3.0357704374324e-07 3800 2948.09090909091 2962 5.15180545923017e-09 477 2.14428275596153 2.62777507135345 1 4.03486707568241 3797 1979 4541 2740 477 4155 3884 2962 2456 1330 4108 3179 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 1.67178794183132e-07 4.29550304052466e-07 3130 2958.27272727273 2963 1.51980733533736e-08 1624 1.85671688010523 -1.68454533189024 -1 3.41282033978368 3127 2963 2363 3451 1624 1703 3376 4485 2701 2681 4067 3180 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 2.08828045082294e-07 4.84679970737421e-07 2965 2708.81818181818 2963 1.89843695367853e-08 1292 2.31052103286556 2.61821348190845 1 4.21217714468202 2963 2540 1612 1292 1845 3415 3214 3225 3431 2669 3591 3181 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 4.82638744024442e-07 8.40300579784348e-07 2710 2996 2966 4.38762590823967e-08 2100 1.81612960527768 -1.6867584582274 -1 3.18536759070064 2710 4118 2667 2966 2566 2377 3473 3350 3457 2100 3172 3182 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 9.0331954902972e-07 1.37749173072917e-06 3785 2957.81818181818 2966 8.21199927211597e-08 2294 1.44220170294332 -1.57827845750787 -1 2.4399520333468 3781 2294 2966 3656 2979 3251 3136 2421 2937 2735 2380 3183 M16743 KEGG_TYROSINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYROSINE_METABOLISM.html Tyrosine metabolism 33/53 KEGG 8.87148666006389e-07 1.35776319829772e-06 4385 3091.45454545455 2968 8.06499112498866e-08 1639 2.50705245308794 -2.70091815774319 -1 4.24666398127897 4383 2714 1768 2141 2968 4279 3537 3913 1639 2053 4611 3184 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 1.21769536301703e-06 1.76575180136417e-06 2410 2870.45454545455 2970 1.10699639728124e-07 790 1.72077747540096 -2.13362462564969 -1 2.85783377767352 2409 3058 2970 3734 3156 2804 3303 790 3981 2680 2690 3185 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 0.000943331191601048 0.000980300137463001 1935 2904.63636363636 2970 8.57941747859008e-05 388 1.87994009686157 1.55596319950083 1 1.63240802574064 1931 4271 3375 2970 4582 1735 388 1372 4435 4050 2842 3186 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 1.76921542880598e-07 4.43266487055072e-07 2975 2842.90909090909 2971 1.60837779189484e-08 1674 1.62114378482923 1.72589039971718 1 2.97331518370968 2449 2971 3443 2221 1674 3287 3545 2972 2866 3040 2804 3187 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 1.26482204519086e-07 3.75824578325571e-07 3715 3027.27272727273 2974 1.14983828900718e-08 1344 2.15430150535851 -1.54733550659991 -1 3.99604582631927 3711 3419 2468 4549 1344 3148 2447 2457 2974 2327 4456 3188 M6910 BIOCARTA_INFLAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INFLAM_PATHWAY.html Cytokines and Inflammatory Response 13/44 BioCarta 9.00143043958296e-07 1.37453095033425e-06 4360 2957.18181818182 2975 8.18312192961244e-08 1129 2.66792689389962 2.16238480254082 1 4.51511578244598 4356 2854 1241 2303 2975 3840 3792 2738 3029 1129 4272 3189 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 2.06676988924642e-07 4.82918251014122e-07 3025 2986.72727272727 2975 1.87888189400659e-08 1831 1.61575724724394 1.6434938046838 1 2.94607237239713 3023 2949 3674 2222 1831 3283 2975 3216 2782 2861 4038 3190 M9379 REACTOME_SIGNAL_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_AMPLIFICATION.html Genes involved in Signal amplification 28/36 Reactome 9.01150712848112e-07 1.3754190401324e-06 3975 2893.27272727273 2976 8.19228256338397e-08 845 2.17600410693003 2.58634064359237 1 3.68226601677633 3972 3112 2437 1929 2976 3599 2521 3489 845 2963 3983 3191 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 1.38504249345622e-05 1.60782109422365e-05 2495 3238.63636363636 2976 1.25913746661151e-06 1942 1.01263449805915 -0.962585584378652 -1 1.40089541631295 2491 3331 3990 2975 4025 1942 2513 2976 4503 4309 2570 3192 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 1.29152133462702e-07 3.79339184781551e-07 1965 3027.81818181818 2976 1.29152140968825e-08 1450 1.84088931847256 2.03835124921071 1 3.4124186643051 1962 4094 4344 2915 1450 3553 2845 3152 2215 2976 3800 3193 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 1.9332257482252e-06 2.63114923057179e-06 2510 3022.09090909091 2977 1.93322743004007e-07 1618 1.88609620915224 -2.32925483090509 -1 3.03813488932541 2506 2913 4463 4352 3440 2608 1618 1626 3668 3072 2977 3194 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 1.80885240806413e-07 4.48412991915058e-07 2770 2862 2978 1.64441141526274e-08 1699 1.59629459676611 1.56560705107331 1 2.92541557314782 2768 2579 2978 3393 1699 2248 1858 3036 3090 3334 4499 3195 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 3.8594760565871e-05 4.2772310371193e-05 2405 3232.18181818182 2981 3.50867615029108e-06 2136 1.27724705260076 1.63085845294138 1 1.61046766496219 2404 4517 3826 2981 4229 2840 2798 2136 2434 4386 3003 3196 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 6.78960855367989e-06 8.21716727522284e-06 2400 3001.54545454545 2981 6.17239046160299e-07 1904 2.0490513883863 1.75520298637324 1 3.00806102358468 2400 3433 2294 3835 3841 2981 2375 3548 2836 1904 3570 3197 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 4.53242105154241e-06 5.64757850139392e-06 545 2784.72727272727 2982 4.12039126293105e-07 541 1.36144360616573 1.42874475337911 1 2.06237189199513 541 2982 3896 4267 3731 1284 1451 2568 3415 4080 2417 3198 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 8.53027741724121e-07 1.31750358014982e-06 2315 3381.81818181818 2982 7.75480065888343e-08 2314 1.25441842984562 1.50588055772594 1 2.12914809616907 2314 4171 3954 4494 2939 2982 2789 2961 3774 4072 2750 3199 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 1.82092261844679e-07 4.50178073986129e-07 4135 2918.90909090909 2982 1.65538433560285e-08 826 1.96612458869123 -1.65102459039221 -1 3.60240758576307 4133 3329 2389 1272 1704 4678 4259 2395 826 2982 4141 3200 M87 PID_LKB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LKB1_PATHWAY.html LKB1 signaling events 18832364 68/103 Pathway Interaction Database 7.47259750529232e-08 3.22991394001646e-07 3135 2551.72727272727 2984 6.79327069009927e-09 212 1.87978412194551 2.34747439009519 1 3.52244376141473 3132 3021 2984 212 775 4034 4451 2162 1137 3270 2891 3201 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 7.38777885236828e-08 3.2144561803028e-07 2560 2562.27272727273 2985 6.71616281859628e-09 355 1.67442203561819 -1.51306477690822 -1 3.13853816604494 3029 355 2557 3178 765 2556 2985 3480 4138 1649 3493 3202 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 2.37609844262531e-07 5.22548577520102e-07 2985 2195.72727272727 2985 2.1600897265951e-08 91 2.28879939719878 -2.80337672179658 -1 4.15097616563901 2985 3191 2436 3026 1968 4031 2997 119 91 3115 194 3203 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 1.70275141853038e-07 4.33060067498401e-07 3425 2775.63636363636 2987 1.54795595483599e-08 554 1.57952818036924 -1.36532612068846 -1 2.90158089306417 3425 3186 2674 4367 1643 3303 2855 1094 4444 2987 554 3204 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 9.12365049882193e-07 1.38825371871178e-06 2050 2866.63636363636 2987 8.29423116591442e-08 1555 1.48732396764753 1.62875053176319 1 2.5148663339801 2050 3939 3338 3464 2987 2015 1555 2333 4105 3101 2646 3205 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 7.74302510157721e-07 1.2166137975847e-06 3060 2693.45454545455 2988 7.03911620616389e-08 465 1.5959388841928 -1.89522645999048 -1 2.72499669708471 3060 4300 3233 4384 2875 3038 2432 465 1949 2988 904 3206 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 2.40483438628753e-06 3.19381494183375e-06 2560 3104 2989 2.18621546821068e-07 1875 1.58973236382328 1.59833626327337 1 2.5219786488992 2558 3669 2989 4253 3483 2653 2557 2465 3818 1875 3824 3207 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 2.24766300218238e-05 2.5431932516928e-05 1095 2477.81818181818 2990 2.04335087827007e-06 404 1.25474393198194 1.29900660803612 1 1.66388553372691 1093 2441 3025 3952 4136 844 683 3387 4301 2990 404 3208 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 0.00221128614003316 0.00228186938805345 2625 3413.54545454545 2990 0.000201228354808712 2282 1.70260141808644 1.57394107476293 1 1.29793617341962 2621 4594 2990 4373 4559 2945 2282 2500 4109 3654 2922 3209 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 1.15278949998772e-05 1.35217853875299e-05 2185 2808.54545454545 2990 1.04799594599454e-06 930 1.58462663964297 2.23287351506054 1 2.22709735511262 2185 3154 2726 2658 3981 2990 3887 930 4038 3060 1285 3210 M1979 KEGG_GNRH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GNRH_SIGNALING_PATHWAY.html GnRH signaling pathway 90/116 KEGG 8.94039993696283e-08 3.31497675696653e-07 3875 2479.90909090909 2991 8.12763663662221e-09 204 2.18565940013433 -2.12989785423855 -1 4.08862469623624 3872 209 1945 204 977 3736 4510 4196 1550 3089 2991 3211 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 2.19994190497134e-07 4.98020421652984e-07 4080 2763.36363636364 2991 2.19994212275987e-08 84 3.66031645533307 -4.52246887169521 -1 6.66095036798829 4079 1925 4235 2253 1985 4027 3419 2991 84 1377 4022 3212 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 3.25405957615507e-08 2.73247281118852e-07 4065 2636.81818181818 2992 2.9582360220786e-09 78 1.61826629576152 -1.61478691499571 -1 3.06621952277322 4061 298 2992 1971 78 3802 3553 3630 2389 2689 3542 3213 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 4.08307268529188e-05 4.51443032901796e-05 3765 3010.36363636364 2992 3.71195315157007e-06 1956 2.3779249695527 2.83871852758717 1 2.9829479038648 3763 3731 1956 2181 4238 2992 2535 2662 2442 3018 3596 3214 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 2.7645743191746e-06 3.60663095259926e-06 3865 2927.27272727273 2993 2.5132525392846e-07 1591 1.71094031990192 -1.7368615704471 -1 2.68824838657826 3861 2440 2414 2124 3546 3554 1708 3992 1591 2993 3977 3215 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 3.7828798861897e-06 4.77066091342903e-06 630 2493.72727272727 2993 3.43898762802976e-07 452 1.28422907730979 1.28355518760314 1 1.97253173191877 628 3574 4085 2993 3679 452 580 1645 3636 4181 1978 3216 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 3.8312696227317e-06 4.82744063515579e-06 1340 2567.72727272727 2994 3.48297844986465e-07 1336 1.66395751022736 -1.43929519269314 -1 2.55356728361272 1562 3563 3095 3405 3682 1336 2994 2526 3190 1552 1340 3217 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 1.23467868367289e-06 1.78544221413482e-06 2660 2974.54545454545 2995 1.1224357969062e-07 2056 1.71124505520118 -1.22968383497621 -1 2.83961786941704 2995 3015 3115 2660 3164 2056 2587 4353 2086 4033 2656 3218 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 8.63624664477982e-08 3.28305665915602e-07 2730 2935.09090909091 2995 7.85113362163768e-09 944 1.76532359819187 -1.70581386186523 -1 3.30429593296455 2726 3555 3575 2922 944 2728 3278 3223 2102 4238 2995 3219 M13191 KEGG_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROSTATE_CANCER.html Prostate cancer 96/121 KEGG 1.45729811906018e-06 2.04108223203682e-06 2970 2757.54545454545 2996 1.32481734944305e-07 467 1.79474551199854 1.94555739065294 1 2.94810104296705 2966 2996 3052 467 3279 2316 2391 3059 1926 3907 3974 3220 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 6.86302012292899e-07 1.10936489658304e-06 2550 3087.81818181818 2996 6.23911114898774e-08 1603 1.65788707451477 1.76639561369778 1 2.84999102430787 2546 2595 3043 4170 2788 3797 4443 2996 1603 2553 3432 3221 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 8.21826378105998e-07 1.28062743633553e-06 4070 3329 2996 7.47115168277745e-08 1949 1.31228917372014 1.46926168750695 1 2.23208491812917 1949 4381 4070 4070 2906 2996 2724 2769 3947 4435 2372 3222 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 1.54498135113812e-07 4.15043368091742e-07 3875 2837.18181818182 2997 1.40452859966967e-08 825 3.132176168638 -2.45476063688211 -1 5.77132126220374 3875 825 1195 2289 1532 4007 3508 4688 2997 2264 4029 3223 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 1.06810351099478e-05 1.2587886571524e-05 935 3012 2997 9.71007906081471e-07 932 1.30180326766398 -1.28979786854083 -1 1.84113627463533 932 3844 4116 2997 3961 1611 2317 2699 3892 4329 2434 3224 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 2.40877513050724e-06 3.19724932958216e-06 3000 2857.81818181818 2997 2.1897979707944e-07 1476 1.95507120749831 2.14935890834127 1 3.10149288015675 2997 2761 2167 3115 3485 4096 3172 1476 2438 1614 4115 3225 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 0.00104330436392363 0.00108252288364905 995 3001 2998 9.48908598282598e-05 991 1.17241941350808 -1.21599329635277 -1 1.00313837785991 991 4474 4104 2998 4692 1851 2019 1402 4184 4495 1801 3226 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 1.89189384651029e-07 4.60770843938523e-07 3000 2684.36363636364 2998 1.71990364473096e-08 557 1.90427812909456 -2.20131936596269 -1 3.48350885550564 2998 3264 2931 1888 1730 3221 3080 2629 557 3960 3270 3227 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 1.82082069469294e-06 2.493261873789e-06 1030 2920.63636363636 2999 1.65529291062658e-07 1029 1.27451821624698 -1.1293090039145 -1 2.06132594114127 1029 4151 4001 2999 3367 1843 1812 2387 4439 4364 1735 3228 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 1.30112132787168e-05 1.51599424032445e-05 2400 2964.09090909091 2999 1.18284456637396e-06 1956 1.70316488606523 -1.84855008661875 -1 2.36933498800894 2397 3361 2999 3622 4005 2560 2501 1956 3212 3693 2299 3229 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 3.92980411980699e-07 7.19184377766178e-07 3715 2976.72727272727 2999 3.57254983798009e-08 1993 1.867212193567 -1.33650052772861 -1 3.31143303559009 3714 2536 2008 1993 2419 2999 4066 4188 3257 2017 3547 3230 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 4.2339653367942e-08 2.95358312155018e-07 4035 2897.18181818182 2999 3.84905947116193e-09 132 1.68996245965367 1.99907755409146 1 3.18561322912202 4033 132 2903 3883 220 4703 4668 2999 2634 1694 4000 3231 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 1.47587319458241e-06 2.06587232456375e-06 1585 2775.90909090909 3001 1.34170380425001e-07 1100 1.46058216694205 1.50908868121367 1 2.39682297065634 1581 3001 3544 4274 3282 1100 1922 2199 4107 3244 2281 3232 M699 KEGG_FATTY_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FATTY_ACID_METABOLISM.html Fatty acid metabolism 42/56 KEGG 2.65145084292359e-07 5.54437896191504e-07 2815 2898.81818181818 3002 2.41041014770709e-08 496 1.31534163745833 -1.32739953201083 -1 2.37537133217044 2888 496 3508 3949 2078 3150 3317 2814 3872 3002 2813 3233 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 2.88604899106399e-06 3.74852813368795e-06 1645 2599.54545454545 3002 2.62368434282432e-07 119 1.36719837926561 -1.31391919500694 -1 2.1413677464947 1641 3496 3002 3904 3566 1196 119 2764 4096 3108 1703 3234 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 9.86103472372398e-05 0.000106532579299559 610 3018.63636363636 3002 8.96497886498986e-06 606 1.41032704979883 1.54464141766671 1 1.61695458523957 606 4129 3976 3002 4346 1830 1950 2676 3448 4310 2932 3235 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 8.83242509795035e-08 3.31003670356505e-07 3430 2469.18181818182 3002 8.02947768413557e-09 303 1.48022358623054 1.89100157139008 1 2.76899327541061 3428 303 3211 1274 961 3446 3794 2286 2121 3335 3002 3236 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 2.18394973536345e-05 2.47615727862491e-05 3005 2889.27272727273 3003 1.98542855984585e-06 114 1.6402427584257 -0.928560028048485 -1 2.18084561911173 3003 3448 2846 3072 4126 2086 2514 2173 114 3754 4646 3237 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 4.29840509570444e-06 5.37516935233637e-06 4480 3021.09090909091 3006 4.29841341005593e-07 996 6.27506012816843 -6.60579085381157 -1 9.54773711408454 4478 1955 4252 1578 3741 4523 3813 2741 996 3006 2149 3238 M5298 BIOCARTA_STEM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STEM_PATHWAY.html Regulation of hematopoiesis by cytokines 6/15 BioCarta 8.56574474141898e-07 1.32211625832235e-06 3300 2755.09090909091 3007 8.56574804315999e-08 920 3.31970752366073 2.19427883734139 1 5.63456535849568 3296 920 4195 1803 3007 3052 3351 2586 2441 1080 4575 3239 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 0.00211456103188265 0.00218348896750954 1330 2759.09090909091 3007 0.000192417837379091 1326 1.21521979786573 1.28963650749148 1 0.932862642472116 1326 3497 3219 3152 4587 1742 2027 1672 3007 4038 2083 3240 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 2.83451482477585e-05 3.17110926118559e-05 1140 2462.18181818182 3007 2.576864859793e-06 774 1.50080937266458 -1.48641031526878 -1 1.94882425192282 1136 3742 3007 3410 4184 968 1138 774 4131 3406 1188 3241 M17681 BIOCARTA_IL3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL3_PATHWAY.html IL 3 signaling pathway 27/29 BioCarta 9.43996035402061e-07 1.42718170630933e-06 2990 3112.81818181818 3008 8.58178582237019e-08 1513 1.02487401584836 -0.912391443075692 -1 1.72910292473453 2988 4240 3675 2500 3008 2050 1513 3105 4627 4105 2430 3242 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 2.90940570259275e-05 3.25412201806583e-05 1645 2768.81818181818 3008 2.64494925358954e-06 1480 1.41282253554533 -1.33105117083901 -1 1.82994295769979 1644 3165 3346 1973 4185 2375 3281 3008 1480 3661 2339 3243 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 0.00230429694274522 0.00237577142196536 1660 3195.90909090909 3008 0.000209701275108448 1657 1.04335463940604 -1.12762628954438 -1 0.789765515345213 1657 4431 4138 3008 4677 2136 2231 1703 4513 4611 2050 3244 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 1.07903391946007e-05 1.2707185877873e-05 2115 2649.45454545455 3008 9.80944738030613e-07 404 1.98157700694108 1.91899183745695 1 2.80064381703129 2112 3356 2472 2934 3963 1118 404 3368 3008 3156 3253 3245 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 6.98114471949765e-07 1.12384048690412e-06 3825 3038.45454545455 3008 6.34649721344427e-08 2014 1.70198641788781 1.74451295444572 1 2.92305580104304 2217 3552 3824 2014 2798 2888 3008 3113 2264 3825 3920 3246 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 4.60025818773651e-06 5.72605976954544e-06 4015 2950.63636363636 3010 4.1820616427511e-07 1371 2.16510643143202 -1.85897111324093 -1 3.27655526632555 4011 3010 1401 2197 3735 3831 4260 2066 2354 1371 4221 3247 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 0.000267220035783176 0.000282988236234371 1530 2829.18181818182 3010 2.67252174168776e-05 149 2.12846892465597 2.12846892465597 1 2.17997321254863 1529 3818 4582 4550 4504 1361 149 3344 2945 3010 1329 3248 M543 REACTOME_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE.html Genes involved in Cell Cycle 434/635 Reactome 4.88779092598734e-06 6.06636160154096e-06 4080 2472.18181818182 3011 4.44345616849033e-07 260 1.47368470783394 1.48411188264581 1 2.21925036623257 260 3556 4077 3011 3750 705 589 1707 3388 4076 2075 3249 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 7.80562671149691e-05 8.48515847035132e-05 2955 3251 3012 7.09627606348871e-06 1447 1.70379500869918 -2.32205704370237 -1 2.00221805015777 2952 4641 3012 3437 4316 2818 1959 1447 4304 4352 2523 3250 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 9.54804390475491e-08 3.38845370705758e-07 4295 2624.18181818182 3012 8.68004029012906e-09 432 1.86924178451682 -1.61473774467659 -1 3.49145116887906 4291 432 1909 1667 1045 4098 3559 3012 3219 2289 3345 3251 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 2.90001256533232e-07 5.84959799502929e-07 3125 2780.09090909091 3014 2.63637540691675e-08 1092 1.80692085674791 -2.04150416110937 -1 3.25129129130423 3122 3049 3014 1092 2168 3462 3574 2683 1799 3826 2792 3252 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 9.58978629950201e-07 1.44301253896562e-06 2010 2857.72727272727 3014 8.7179913451695e-08 2007 1.34108246984215 1.42204315931302 1 2.26100038832014 2007 3014 3682 3181 3023 2102 2099 3045 2459 3929 2894 3253 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 4.38618894315615e-07 7.80649012507429e-07 2700 2920.63636363636 3015 3.98744528876421e-08 2098 1.94500394590208 2.16600371090632 1 3.42942636841959 2699 2570 2262 3114 2503 3319 3465 3416 3666 2098 3015 3254 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 1.56562244195486e-07 4.17028099662921e-07 3450 2989.81818181818 3015 1.42329323033805e-08 1551 1.69777288245498 -1.74420833919913 -1 3.1268917418864 3446 2990 3194 2887 1551 2488 3749 3591 3015 3625 2352 3255 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 1.15040449315856e-07 3.59285478750119e-07 3385 2637.90909090909 3016 1.045822321195e-08 1261 2.17080935807301 -1.68767314211673 -1 4.03892523512001 3382 2102 1679 3370 1261 3426 3114 1818 3016 2771 3078 3256 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 9.50520161944272e-07 1.43337225698944e-06 3275 2881 3017 8.64109611473769e-08 442 1.9498396188101 -2.06691765354657 -1 3.28936565615128 3273 3466 2531 3321 3017 3346 2953 442 4027 2628 2687 3257 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 1.44800276912521e-06 2.03349392153257e-06 3020 2901.18181818182 3019 1.31636702016091e-07 1481 2.49389748988287 2.63403375288958 1 4.09804882620082 3019 2703 1481 3345 3272 2949 3292 2879 3040 1574 4359 3258 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 9.18622997502336e-08 3.35125431650715e-07 3020 2871.27272727273 3020 8.35111850781805e-09 1002 1.68342671945741 -2.13032306022459 -1 3.14662259169386 3020 3091 2808 3433 1002 3603 3558 2938 2546 3360 2225 3259 M529 REACTOME_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOSIS.html Genes involved in Meiosis 75/238 Reactome 3.28546249491318e-06 4.21969604788849e-06 1770 2689.81818181818 3021 2.98678854673362e-07 962 1.45871346018589 1.12095206768062 1 2.26310092594727 1769 3307 3361 3782 3613 984 962 1873 4239 3021 2677 3260 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 2.52488933211863e-05 2.83952290864902e-05 1645 2783.36363636364 3022 2.29538028196145e-06 1232 1.62168066693647 1.75423956420521 1 2.12830847383072 1643 4210 3022 2016 4162 1775 1232 1461 3586 4250 3260 3261 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 6.49707239164133e-07 1.06184839641784e-06 3025 3163.90909090909 3022 5.90643119124283e-08 1591 1.60284342612165 1.45937717241943 1 2.76413917908151 3022 1591 3177 1986 2750 4203 4565 4647 1891 2957 4014 3262 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 9.29524406222266e-05 0.000100696699503537 930 2548.81818181818 3027 8.45057892711691e-06 615 1.70979144581751 -1.46093379260365 -1 1.97255662297459 929 3146 3027 3968 4336 1274 919 615 4366 3640 1817 3263 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 1.73858537690912e-07 4.38595562747785e-07 3630 2865.90909090909 3027 1.58053228573059e-08 1653 1.59282391969738 1.79328044350039 1 2.92347518124321 3626 2182 3072 3462 1659 2676 1653 3910 2447 3027 3811 3264 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 1.42846209370267e-06 2.01228324214565e-06 3735 2796.18181818182 3027 1.29860274655028e-07 801 2.68958960910781 2.37372796612288 1 4.42322042122678 4307 2784 1659 865 3261 3731 3027 3735 801 2779 3809 3265 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 2.28406758274397e-06 3.04800650001457e-06 2715 3024.90909090909 3030 2.07642723099547e-07 1987 1.84477709392465 1.98473988707082 1 2.93753481570789 2713 2187 3030 3941 3465 2753 3662 1987 3601 3500 2435 3266 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 1.54177930827738e-07 4.14709982727636e-07 4040 2778.09090909091 3031 1.40161765120604e-08 915 2.95308494560596 -2.34046271014271 -1 5.44157764263364 4036 3487 1911 3278 1529 3500 3031 2807 915 2318 3747 3267 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 0.000222784057524655 0.000237153980946408 2850 3271.81818181818 3031 2.22806395407848e-05 1718 1.45256481979555 1.57346536201628 1 1.51962783812891 2848 2919 4476 3672 4426 3023 1718 2714 4090 3073 3031 3268 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 3.62567833285612e-07 6.80445396862064e-07 3080 3024.72727272727 3031 3.29607175489178e-08 2296 1.74619802252319 1.83156878260456 1 3.10888840553097 3077 2576 3031 3638 2354 3288 2969 3596 2296 2723 3724 3269 M13494 BIOCARTA_BIOPEPTIDES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BIOPEPTIDES_PATHWAY.html Bioactive Peptide Induced Signaling Pathway 59/67 BioCarta 1.49349185722573e-07 4.08180750787808e-07 3875 2689.81818181818 3032 1.35771996237538e-08 216 1.84197097341444 -1.60663928454183 -1 3.39749674038971 3874 1617 2675 216 1497 3032 3086 4668 1544 3428 3951 3270 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 2.64672955569256e-07 5.53993946912146e-07 3405 3185.81818181818 3032 2.40611806737251e-08 1930 2.13847513837699 2.00152096853879 1 3.86261937400362 3401 3032 2137 1930 2075 3943 4384 4421 2262 2911 4548 3271 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 2.20005741932375e-06 2.94923914206422e-06 3330 2707.81818181818 3033 2.00005419949243e-07 946 1.77544379215504 -2.16715829397057 -1 2.83443382633987 3330 2215 2777 1880 3449 3033 3911 3653 1507 3085 946 3272 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 1.31668614385053e-07 3.81741928683936e-07 4050 3020.27272727273 3033 1.19698747513943e-08 1384 2.1535061436971 2.16677312807748 1 3.99035108605413 4050 3847 1411 2217 1384 3997 3756 3033 2907 1965 4656 3273 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 2.29921859507565e-05 2.59935611227715e-05 900 2987.72727272727 3034 2.09022056776918e-06 899 1.45616230109983 1.60578866331794 1 1.92713089635126 899 3598 3962 2990 4139 2074 2738 2513 3269 3649 3034 3274 M10680 KEGG_PROTEASOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEASOME.html Proteasome 41/48 KEGG 0.0556464390740233 0.0563145781366616 1275 3319.72727272727 3035 0.00519144563247134 1275 0.865628135528858 -0.956807690417655 -1 0.311436575866295 1275 4530 4082 2507 4671 2634 2281 2912 4046 4544 3035 3275 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 1.32078724113278e-05 1.53776906219702e-05 215 2724.27272727273 3035 1.20072288240831e-06 213 1.47815923075911 1.58261994207331 1 2.05356393884847 213 3839 4097 3247 4009 1553 1278 2007 3035 4372 2317 3276 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 4.36427936505446e-06 5.45101841837975e-06 2390 3141.18181818182 3036 3.96753456615995e-07 2128 1.61810198873739 -1.60348259053124 -1 2.45851962113571 2386 3659 3036 2486 3719 2574 3944 3983 3844 2794 2128 3277 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 3.14925463475301e-07 6.17221890136083e-07 4685 2874.54545454545 3036 2.8629591686931e-08 601 1.89237653002291 -1.66819375536755 -1 3.39235642029469 4683 1715 2081 3036 2240 3444 3102 4469 601 1572 4677 3278 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 3.69167382697754e-07 6.88550861663682e-07 3730 2978.09090909091 3039 3.35606767859359e-08 1678 1.42446613745692 -1.18400252353089 -1 2.53381071048814 3729 1678 3261 3724 2371 3274 2701 2640 3790 3039 2552 3279 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 3.73588548247052e-07 6.9302005985665e-07 2975 2669.09090909091 3042 3.39626010624773e-08 124 2.49776711527377 -1.94562050689786 -1 4.44159853454391 2972 3925 2098 1477 2385 3276 3340 3042 124 3672 3049 3280 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 2.98133909609084e-07 5.96773559522848e-07 1780 2978.72727272727 3042 2.7103086364621e-08 1779 1.49747480482649 1.66507312822644 1 2.69058570096035 1779 4116 3830 3788 2188 2522 2025 2055 3139 4282 3042 3281 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 9.85414535664465e-07 1.47312375810264e-06 2815 2825.09090909091 3043 8.958317973158e-08 263 3.26428213013859 -3.79763215483709 -1 5.49620311711723 2812 3747 1198 3344 3043 3965 4316 263 3793 1755 2840 3282 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 1.16667589988037e-05 1.36744729263356e-05 3635 3075.81818181818 3043 1.16668202502258e-06 1303 3.67913274667572 -2.66010598839839 -1 5.16675721443082 3635 2908 4552 2392 4000 3171 3655 3043 1303 2710 2465 3283 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 1.32956923870264e-07 3.83038247822062e-07 3045 2635.54545454545 3044 1.20869938095919e-08 384 2.45068336484844 -2.3690395655041 -1 4.5400842299325 3044 4377 1000 3958 1393 2493 4184 3086 3930 1142 384 3284 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 1.52338453313821e-06 2.12293327322478e-06 1390 3043.18181818182 3046 1.38489598909369e-07 1389 1.27867239337525 1.35503960306082 1 2.09383169978112 1389 3850 4112 3233 3297 2285 2511 2382 2896 4474 3046 3285 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 6.31562197978906e-07 1.03703459476233e-06 3050 2944.90909090909 3047 5.74147617530812e-08 2044 1.59735545097829 1.68147474619807 1 2.75940889008744 3047 3055 2884 3090 2737 3212 3513 3406 2833 2044 2573 3286 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 7.46866760108092e-08 3.22991394001646e-07 2910 3178.90909090909 3048 6.78969804966445e-09 774 1.36819331097011 1.39324659091915 1 2.56356210846523 2909 2953 4039 2496 774 2565 3048 4621 3396 4294 3873 3287 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 5.98228606097339e-07 9.95641403659887e-07 3540 3221.54545454545 3049 5.43844335244523e-08 1799 1.71403259103519 1.80064035775689 1 2.96978574543807 3537 2435 2587 4534 2699 3501 3702 4598 3049 1799 2996 3288 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 4.00354256015094e-07 7.27076601920448e-07 3995 3059.36363636364 3050 3.63958480792057e-08 2438 1.35135466239518 1.02591333220819 1 2.39449084614199 3992 2689 3087 2662 2438 3608 3286 2582 2612 3050 3647 3289 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 8.35286192143204e-07 1.2966832804644e-06 3675 2791.45454545455 3051 7.59351372073735e-08 1194 1.38007253403376 1.5148904561111 1 2.34526634733632 1554 3051 3558 3980 2920 1769 2138 3196 3671 3675 1194 3290 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 3.63348879536403e-05 4.03056806442261e-05 3895 3259.45454545455 3051 3.63354820681493e-06 858 2.4802229458478 -2.05724595234508 -1 3.14657423899889 3892 2453 4576 3051 4233 4149 4635 2608 3019 2380 858 3291 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 8.44423563798598e-06 1.00801194262251e-05 3450 2697.72727272727 3052 7.67660731779663e-07 442 2.34981960751482 -1.72519190304687 -1 3.38950666733066 3449 627 1913 1432 3909 3845 4662 3469 442 3052 2875 3292 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 3.57747121432885e-05 3.97029488164405e-05 1380 2457.45454545455 3052 3.25229944522316e-06 681 1.89382170935651 1.71358331983117 1 2.40600178017351 1376 3195 2383 3159 4221 1355 681 761 3737 3112 3052 3293 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 4.78242217060552e-08 3.01912311600589e-07 4675 3062.63636363636 3052 4.34765661324289e-09 315 1.69230971657427 -1.31198681763833 -1 3.18538115074584 4675 2630 3041 3415 315 3396 3052 2391 2616 3626 4532 3294 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 3.2069271322478e-07 6.2470887594757e-07 3740 3177.72727272727 3053 2.91538872701799e-08 2144 1.5802153188553 -1.90190689113151 -1 2.83023118311367 3740 2753 2922 2144 2256 4379 4206 2348 3646 3053 3508 3295 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 2.81253737201316e-06 3.65808112314745e-06 4255 2940 3054 2.81254093168441e-07 1081 3.2420380154061 -2.97629881031946 -1 5.08893777773536 4251 2471 4214 3054 3591 3256 1519 2432 2294 1081 4177 3296 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 2.5717116277957e-07 5.43838659641385e-07 2170 3172 3055 2.33791993492592e-08 1484 1.26658747031959 1.46381892820926 1 2.29036038900523 2166 4450 3938 4679 2052 2734 3055 1484 4213 4303 1818 3297 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 3.72216924360783e-07 6.91862886359655e-07 4690 3380.09090909091 3056 3.38379079396361e-08 1654 1.70800617414026 1.70403763911616 1 3.03730941547458 4688 2502 3016 3953 2380 4419 4111 3056 2981 1654 4421 3298 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 2.26993479845089e-06 3.03171823675388e-06 3525 2905.27272727273 3057 2.06357921867909e-07 1480 2.41149981862903 1.09463860110213 1 3.84184203513996 3523 2862 1782 1480 3462 3057 3378 2742 3565 2050 4057 3299 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 1.66035506182896e-06 2.29282501223893e-06 3330 3071.72727272727 3057 1.50941483173783e-07 1218 1.84480345345367 -2.1911361913887 -1 3.00344412656902 3329 2998 2953 1974 3332 4120 4625 3205 1218 2978 3057 3300 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 2.74942960781013e-06 3.58885723143357e-06 3060 2438.09090909091 3058 2.49948458535482e-07 228 1.56382345000311 -1.8071710173411 -1 2.45799153649089 3058 3136 3200 228 3544 2252 1475 3568 965 3923 1470 3301 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 0.000100301975609836 0.000108335314617488 1995 2875.36363636364 3058 9.1187771681877e-06 967 1.29576943766361 -1.35453472086053 -1 1.48281631404838 1991 3763 3504 3413 4348 2586 2213 967 3058 4265 1521 3302 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 1.03124492802518e-06 1.53548140702802e-06 2800 3030.81818181818 3059 9.37495828562887e-08 1118 1.67454804705123 1.64832901061416 1 2.8103779575835 2796 3654 3348 1118 3059 2629 2908 4116 2375 3958 3378 3303 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 2.47341697571714e-06 3.27384411816738e-06 3185 2709.72727272727 3059 2.24856341503259e-07 773 2.06309959325574 1.87803760075196 1 3.26678973845339 3181 773 2267 1878 3494 2765 3899 4046 1371 3059 3074 3304 M10462 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY.html Adipocytokine signaling pathway 70/102 KEGG 8.24551030195841e-07 1.28275572265141e-06 3300 2974.27272727273 3060 7.49592126576697e-08 2385 1.73476437916521 -1.40174629586108 -1 2.95059297962827 3297 2605 3060 2468 2911 3075 4157 2385 3168 2453 3138 3305 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 2.47562258826175e-07 5.32828938285247e-07 4415 3302.54545454545 3061 2.25056624258127e-08 2013 1.81019633815011 -1.42947728203967 -1 3.27837674227124 4413 3061 2967 3493 2013 4375 2817 4061 2794 3485 2849 3306 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 1.99253239173471e-06 2.70096292044452e-06 3065 2921.81818181818 3061 1.81139472396972e-07 1846 1.91887273287395 -1.94466585839307 -1 3.08464459604359 3061 1846 2155 4343 3403 3301 3375 2383 2609 2399 3265 3307 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 1.50914496522862e-06 2.10495397041344e-06 2425 2912.72727272727 3062 1.50914599011294e-07 1018 1.58974911016959 -1.75440890112836 -1 2.60512640181402 2423 3211 4529 3062 3331 2871 3810 2143 1018 3984 1658 3308 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 1.96105925512155e-06 2.6651885068165e-06 2515 2897.72727272727 3063 1.78278273017587e-07 1357 1.41487030074849 -1.414301460491 -1 2.27658543559097 2512 4019 3063 4256 3393 1555 1357 2317 4391 3524 1488 3309 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 8.73654961322333e-07 1.34314731100204e-06 960 3041.63636363636 3064 7.94232098422541e-08 823 1.23117535553493 1.08234789925367 1 2.08670487473125 960 4436 4022 4696 2953 1305 823 3064 4070 4432 2697 3310 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 4.53893849821406e-05 5.00205223244696e-05 2010 3059.45454545455 3064 4.53903120971131e-06 1091 2.86356507741601 3.0857157449942 1 3.55549258969965 2008 4653 4263 4385 4269 1693 1091 1410 4475 3064 2343 3311 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 3.03194862252726e-07 6.04058691917239e-07 4280 3257.18181818182 3066 2.75631730943446e-08 1946 1.69290248296784 -1.76882093280324 -1 3.03925648213146 4280 2507 3047 1946 2200 4236 4719 4342 3066 2007 3479 3312 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 1.23300288853328e-06 1.78465919468785e-06 1295 2328.63636363636 3066 1.23300357266707e-07 284 1.42443262588342 -1.58216700702121 -1 2.36361903853679 1292 3527 4352 3886 3223 1046 284 300 4048 3066 591 3313 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 6.0448395133722e-08 3.11320373876078e-07 4395 2989 3067 5.49530879951226e-09 544 2.48365648448834 -1.83782264923826 -1 4.66575314806903 4395 2678 1714 1707 544 4267 4295 3349 3067 2388 4475 3314 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 2.48680252367833e-07 5.3337783307865e-07 2360 3059.54545454545 3067 2.26072982252526e-08 2019 1.80217634630205 -1.59151204621506 -1 3.26361552501708 2358 4108 2562 3438 2019 3207 4073 2974 3579 2270 3067 3315 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 5.8171396935458e-08 3.09852566478612e-07 3485 2929.18181818182 3068 5.2883089521454e-09 500 1.4291725918049 -1.22032434245905 -1 2.6852996961874 3481 886 2747 4153 500 3068 3846 4627 2755 2613 3545 3316 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 1.27430343265882e-07 3.76660766944629e-07 4045 3069.09090909091 3068 1.27430350573204e-08 934 2.01176058875013 2.29317859922571 1 3.73102686229819 4042 934 4439 2807 1435 3930 4069 3068 1855 2835 4346 3317 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 2.08679617199918e-07 4.84679970737421e-07 3360 3218.81818181818 3069 2.08679636796153e-08 1935 1.7976401227911 -1.5790299420038 -1 3.27698245338117 3359 3834 4488 2950 1935 2712 3729 3069 2699 2366 4266 3318 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 1.52084380382024e-07 4.11840662881901e-07 3650 2629.27272727273 3069 1.38258537177733e-08 413 2.26524151354843 -1.22133254625607 -1 4.17587704276328 3647 2320 2224 1267 1516 3194 3069 4246 413 3261 3765 3319 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 2.80566714057704e-06 3.65015129645083e-06 1635 2934.27272727273 3070 2.55060974423622e-07 1635 1.00201544691271 1.082050002149 1 1.57251363269037 1635 3070 3981 4254 3558 1822 1904 2195 4175 3936 1747 3320 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 2.09330914239179e-07 4.84809575666794e-07 2785 3065.54545454545 3071 1.90300849233732e-08 1851 1.50929666556815 1.57896647498142 1 2.75116209129984 2785 2382 3166 4142 1851 3631 2961 3444 3071 2975 3313 3321 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 1.31122034102002e-06 1.87487428343366e-06 3010 3001.81818181818 3072 1.19201920229102e-07 1283 2.77768794219715 -2.66590252121487 -1 4.59277055683993 3009 3072 1283 2909 3204 3824 4403 3375 3684 1773 2484 3322 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 9.61311825980275e-07 1.44453322096108e-06 3030 3103.36363636364 3073 8.7392022366843e-08 1845 1.69965385602225 1.39820661105301 1 2.86554024836975 2547 4033 3073 4208 3027 3026 1905 1845 3302 3759 3412 3323 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 4.11198892470124e-08 2.9351990282604e-07 4560 2569.54545454545 3075 3.73817181959805e-09 205 1.62354154238264 -1.08374395063538 -1 3.06164588562751 4558 3075 2963 223 205 3477 3787 2191 308 3599 3879 3324 M6467 REACTOME_OPIOID_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OPIOID_SIGNALLING.html Genes involved in Opioid Signalling 74/93 Reactome 3.34698517962934e-07 6.42185774302865e-07 3760 3093.63636363636 3075 3.0427142625685e-08 1894 1.70661480642617 -1.14331708439617 -1 3.05078146791398 3758 2599 3075 2000 2291 3855 4382 3327 1894 3780 3069 3325 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 3.51145123517139e-07 6.63570412832985e-07 4165 3240.09090909091 3076 3.19222890512658e-08 2022 2.00605937581688 1.96475343294412 1 3.57798516791569 4164 3076 2246 2022 2334 3811 2836 4484 2843 3315 4510 3326 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 4.95115514941178e-08 3.0357704374324e-07 3380 2578.27272727273 3076 4.9511552597245e-09 435 2.12228571844045 2.30769955754967 1 3.99346671988079 3379 996 4536 1014 435 3076 3666 3246 2939 763 4311 3327 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 0.000258223051628099 0.000273644545057168 3150 2776.09090909091 3077 2.34775786646792e-05 915 2.50604880934264 -3.14050976418055 -1 2.57739457090197 3149 3196 1904 3077 4536 3495 3105 915 3003 2614 1543 3328 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 1.87369438885097e-07 4.5777497636445e-07 2740 2924.72727272727 3079 1.87369454683387e-08 1291 1.71096914115977 1.82881243789566 1 3.13119964365978 2738 1975 4399 1291 1824 3381 3956 3334 2130 3079 4065 3329 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 2.80242968431623e-06 3.64876303741972e-06 1795 2638.45454545455 3081 2.54766659467845e-07 604 2.27567128644907 -1.1422033082372 -1 3.57252968929138 3334 3387 1982 3081 3555 2224 1795 1794 604 3444 3823 3330 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 2.16631717106401e-07 4.93723662357418e-07 4200 3021.09090909091 3081 1.96937944034459e-08 1788 1.93440496851352 -1.2575854921592 -1 3.52187668838974 4199 1826 2206 3086 1880 4390 2967 3883 3081 1788 3926 3331 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 9.77846886728697e-07 1.46475319116453e-06 415 2630.45454545455 3082 9.77847317012001e-08 414 1.52192388503268 1.49203527010329 1 2.56315232491859 414 3830 4320 3239 3082 1291 1130 2159 3350 3973 2147 3332 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 2.00089874912262e-07 4.74685412934128e-07 2585 2973.81818181818 3082 1.81899902827661e-08 1788 1.34641164713993 1.48770262821558 1 2.45772401311337 2581 3342 3605 4203 1788 3082 2386 2426 2146 4030 3123 3333 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 1.07580591442701e-06 1.59178806147194e-06 3370 2940.63636363636 3083 9.78005854999415e-08 1816 1.83872397225569 2.02679087626748 1 3.07769274599317 3368 2234 2249 3555 3083 3887 3875 3663 1988 1816 2629 3334 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 8.04035096783719e-06 9.62476707283579e-06 4275 3053.90909090909 3083 7.30943668463482e-07 1585 2.08801855918568 1.71963602189807 1 3.02387913241266 4275 1892 2024 3083 3895 3786 2320 3342 3075 1585 4316 3335 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 4.62893912010917e-08 2.99073619127066e-07 4695 2834.63636363636 3084 4.20812656136818e-09 293 1.50110738596553 1.54881039034404 1 2.82716811441753 4694 416 3237 893 293 4268 4074 3006 2806 3084 4410 3336 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 9.45499987115781e-07 1.42853436058159e-06 3840 3089.45454545455 3084 8.59545812241934e-08 1752 1.88818511802387 -1.72030623916698 -1 3.18612829209815 3837 4181 2832 2219 3010 2902 3380 3365 1752 3422 3084 3337 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 6.1422346153496e-06 7.49130423370804e-06 4635 3324.72727272727 3084 5.58386524006721e-07 1765 2.04385985509817 2.67763325255681 1 3.02414248268261 4631 2834 2445 2397 3815 4251 3084 4443 1765 2360 4547 3338 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 5.16485327107757e-06 6.38170351819008e-06 3085 3035.72727272727 3084 4.69533217858167e-07 218 2.00637516158369 2.40948868709414 1 3.00899963352351 3084 3056 2460 1994 3764 3408 4717 2896 4372 3424 218 3339 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 3.75540113835558e-08 2.87575261955407e-07 4430 2845.90909090909 3084 3.41400109314574e-09 146 2.93311937262571 -2.56660251397516 -1 5.53944561403191 4428 2832 1385 3084 146 4629 4596 1418 3278 2201 3308 3340 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 2.3852488396268e-05 2.69081609059237e-05 3415 3219.90909090909 3085 2.38527444236769e-06 1598 2.44042295291244 -3.65942777028636 -1 3.21973107705047 3415 2914 4457 3609 4171 3085 2047 1598 4399 3071 2653 3341 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 1.57973105083895e-05 1.81817375273344e-05 3170 3113.09090909091 3088 1.43612944942087e-06 2165 1.77571971045036 -1.73122155934 -1 2.4298288416999 3168 2715 3088 3661 4061 2626 2460 3472 2165 3810 3018 3342 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 1.08313046580205e-06 1.60025868724311e-06 4120 3092.18181818182 3088 9.8466454460203e-08 205 2.1376587521962 2.81553777665841 1 3.57677295794653 4120 2780 2656 2826 3088 4348 3920 4205 205 3235 2631 3343 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 4.03614095138383e-06 5.07339155540125e-06 3555 2895.09090909091 3092 3.66922577831407e-07 1498 1.68350817691546 1.65005936249174 1 2.57308900304175 3553 3092 2949 1498 3695 2752 1928 3467 1584 3822 3506 3344 M11079 KEGG_N_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_N_GLYCAN_BIOSYNTHESIS.html N-Glycan biosynthesis 46/50 KEGG 3.96058045234473e-08 2.9351990282604e-07 1605 2687.90909090909 3093 3.60052774876876e-09 175 1.25657265037711 -1.08371921569313 -1 2.3694277635813 1603 3671 3658 3681 175 2046 2005 3093 2310 4028 3297 3345 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 9.73337942055157e-06 1.1517059630234e-05 3545 3164.54545454545 3094 8.84856589441124e-07 2319 1.99692817441865 1.57705650300015 1 2.84697399288194 3541 2319 2387 2396 3937 3817 3094 2797 2664 3354 4504 3346 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 6.08730542278115e-05 6.65402538108546e-05 2825 3049 3094 5.53406714766385e-06 1828 1.67197660205822 2.1921641416854 1 2.01578310369396 2823 3139 3094 4427 4290 2767 1828 1946 3409 3723 2093 3347 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 1.88503863075064e-07 4.59575533943339e-07 3580 3007 3096 1.7136716293341e-08 1522 1.73642095661053 -1.78061182139465 -1 3.17693631437556 3578 2527 3096 1522 1729 3653 3188 4199 2707 2739 4139 3348 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 4.82678419598456e-08 3.0255539714538e-07 3100 2929.63636363636 3097 4.38798572898533e-09 322 1.83538063691728 1.55856853369051 1 3.45426208911728 3097 3062 2763 3394 322 3220 2363 4407 3126 2766 3706 3349 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 1.10447055046278e-06 1.62503148322454e-06 4350 2674 3100 1.0040646408571e-07 766 2.41895128784989 -2.18112886801478 -1 4.04289039281383 4346 1459 766 1017 3100 3944 4588 3317 1659 786 4432 3350 M13266 KEGG_RENAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENAL_CELL_CARCINOMA.html Renal cell carcinoma 74/78 KEGG 6.44704328632818e-06 7.83471789687667e-06 2625 3271.63636363636 3102 5.86096561754531e-07 2246 1.61258760596387 1.84613132895176 1 2.37677584651497 2625 4442 3474 2246 3827 3011 3438 3102 2746 4344 2733 3351 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 2.04657987448538e-07 4.81168919655711e-07 4570 3243.54545454545 3102 1.86052733170116e-08 1813 1.92637110117614 -1.51596212246087 -1 3.51346885372665 4570 2608 2501 3102 1813 3924 4072 4063 2203 2163 4660 3352 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 1.10630654811866e-06 1.62671866265423e-06 4510 2914.27272727273 3102 1.00573373131244e-07 787 2.06867210566358 -2.35083025524463 -1 3.45706079760155 4509 787 1655 1672 3102 4493 3644 3543 2825 1274 4553 3353 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 0.00026820154335911 0.000283963949002916 2745 3254.81818181818 3103 2.43849313940996e-05 2418 1.76561207710414 -2.00083840674753 -1 1.80742705708227 2742 3103 2603 3134 4438 3100 3431 3574 4306 2418 2954 3354 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 9.44057906942353e-08 3.3764305071295e-07 4440 2959.90909090909 3105 8.58234497685006e-09 816 1.44313272224193 -1.3330472025067 -1 2.69599308463175 4437 2259 3067 2891 1034 3454 3580 3916 816 4000 3105 3355 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 6.61205608551407e-07 1.07579816351694e-06 2365 2711.90909090909 3105 6.01096188432288e-08 924 2.96283150910477 3.10613278779985 1 5.10535017618168 2364 3366 943 4338 2766 3105 3273 924 4173 1202 3377 3356 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 5.11991055587712e-08 3.0357704374324e-07 3245 2684.72727272727 3105 4.65446425002665e-09 379 1.76781071801814 -1.73575774960175 -1 3.3263136486458 3245 2030 3105 3123 379 2291 3226 4437 1948 2640 3108 3357 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 1.5689426086945e-06 2.18384226276557e-06 2475 3127.63636363636 3106 1.42631247963275e-07 2472 1.13111978162586 1.15313481267733 1 1.84810166578215 2477 3106 3537 2474 3303 3318 2472 2893 4077 3938 2809 3358 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 2.30854271407413e-06 3.07458284718677e-06 3145 2877.72727272727 3106 2.09867739683487e-07 1533 1.59456510003491 -1.54384044781771 -1 2.53725632702303 3145 2296 2834 1533 3472 2363 3650 3106 3378 3288 2590 3359 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 1.03881176802791e-06 1.54431229766668e-06 2765 3202 3106 1.03881225363668e-07 1941 1.08739869159013 -0.917221501544594 -1 1.82388676446565 2761 1941 4314 3919 3116 2912 2434 2690 4594 3435 3106 3360 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 1.26312432034375e-07 3.75824578325571e-07 2065 3035.54545454545 3107 1.1482949026052e-08 1342 1.69935108161724 -1.48205873699084 -1 3.15196963863666 2063 4109 3369 3526 1342 2160 3107 3982 3101 3931 2701 3361 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 7.36981948297301e-08 3.2144561803028e-07 3140 3002.45454545455 3109 6.69983611805086e-09 759 1.77512139947725 1.82131510846815 1 3.32734094386175 3139 1602 2566 4567 759 2772 3109 4476 3817 2118 4102 3362 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 4.39379713502908e-07 7.81413808490477e-07 3535 3194.63636363636 3110 3.99436182959084e-08 1763 1.81738251150257 -1.49261928449634 -1 3.2041248626868 3535 3592 3001 3135 2505 3073 4227 4637 1763 2563 3110 3363 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 3.28632346321169e-05 3.66008653760245e-05 2890 3043.27272727273 3111 2.98761141344769e-06 672 1.96184893231545 -2.25673393234915 -1 2.51247342350568 2889 4062 2275 3942 4205 3328 3044 672 4486 3111 1462 3364 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 3.08344508205758e-07 6.09203046769015e-07 4360 3205.81818181818 3111 2.80313228565711e-08 1312 1.72934420251008 1.71248552474332 1 3.10285944353825 4360 2505 2400 3634 2221 4228 3850 3111 2984 1312 4659 3365 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 1.3428005280593e-06 1.91249803634276e-06 3945 3030.90909090909 3111 1.22072849786994e-07 422 2.50268990744983 2.79938015463415 1 4.1317535844748 3941 3111 1788 2868 3219 4625 4187 3072 422 2965 3142 3366 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 2.6407356997574e-07 5.52984583090281e-07 3600 2854.81818181818 3112 2.40066910612186e-08 1213 2.86599306614135 -1.84856561116389 -1 5.17764665251111 3596 3178 1919 3859 2074 3312 1807 3112 1213 2874 4459 3367 M12524 KEGG_HISTIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HISTIDINE_METABOLISM.html Histidine metabolism 27/36 KEGG 3.86383432003613e-06 4.86717320271432e-06 3210 2872.54545454545 3113 3.51258282369085e-07 1281 3.23808724389152 -3.55292545699276 -1 4.96676792673971 3210 3113 1281 3075 3683 3425 3387 2697 2161 2210 3356 3368 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 1.72403650860778e-06 2.37312695264763e-06 3115 2871 3113 1.56730714514143e-07 817 2.10226953575906 2.10863540481632 1 3.41365805787103 3113 817 1906 3584 3342 3690 4630 2298 2718 1801 3682 3369 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 3.51541617555142e-06 4.46833110824467e-06 3770 2614.72727272727 3114 3.5154217367317e-07 10 4.18132787760256 -3.41518762795442 -1 6.45864976077003 3770 867 4291 696 3684 3966 4205 3114 10 1858 2301 3370 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 1.81041137284592e-05 2.07205181373248e-05 3615 3106.63636363636 3115 1.64584206468265e-06 1969 2.01832618626729 -1.6771714415857 -1 2.72883626612534 3614 3115 1969 3098 4087 3264 2872 3335 2259 2066 4494 3371 M7860 BIOCARTA_NGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NGF_PATHWAY.html Nerve growth factor pathway (NGF) 31/34 BioCarta 6.12910567816256e-07 1.01293343140502e-06 3325 2668.63636363636 3116 5.57191580518709e-08 220 1.6689462679891 -1.67938821187504 -1 2.88804126786574 3321 3388 3191 220 2717 2474 3116 3323 1601 4358 1646 3372 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 1.55337246781982e-05 1.7908935144381e-05 4140 3059.09090909091 3118 1.41216675995966e-06 255 2.32913263032482 -0.914474448819345 -1 3.19178278625134 4136 3501 2321 3106 4056 3720 2398 2880 255 3118 4159 3373 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 2.05503877317061e-06 2.77374406902067e-06 1510 2551.27272727273 3119 1.86821881163853e-07 446 1.28209588748761 1.22857805876538 1 2.05644592514977 1509 3119 3389 4199 3420 1597 1114 446 4312 3431 1528 3374 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 1.59400507968838e-07 4.20318657884309e-07 3445 2767.18181818182 3119 1.44909563198334e-08 1146 2.12939941037726 2.67215055585257 1 3.91996473758718 3441 2709 1627 3586 1574 3119 3522 2309 3225 1146 4181 3375 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 5.75994302119751e-07 9.66818316502569e-07 3510 2893.81818181818 3120 5.23631320840087e-08 752 2.13852946293629 1.2339898199494 1 3.71337394444841 3508 3120 2342 2746 2673 3161 3360 1805 752 3839 4526 3376 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 8.42785994493625e-07 1.30595859947797e-06 3205 3118.81818181818 3121 7.66169379410986e-08 1580 1.48302138848046 1.6015011058535 1 2.51895409809813 1580 3028 3203 4238 2928 2644 3082 3166 4113 3204 3121 3377 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 5.25012069732656e-05 5.75890534310513e-05 3125 3055.72727272727 3123 5.25024473840404e-06 876 1.49020544697601 1.73685468505443 1 1.82354102645355 3123 2907 4332 2603 4284 3871 3669 876 2847 3768 1333 3378 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 1.40153739013536e-06 1.98417328584169e-06 2770 3015.09090909091 3123 1.27412571182091e-07 1338 1.76297936658379 2.00044720185585 1 2.90215783526397 2766 3123 2744 4572 3245 2380 1338 2051 4281 3150 3516 3379 M19422 BIOCARTA_IL17_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL17_PATHWAY.html IL 17 Signaling Pathway 5/14 BioCarta 3.31515528369473e-06 4.24973735443756e-06 4405 2963.54545454545 3124 3.31516022931966e-07 1224 3.4179402453528 1.98285714472174 1 5.30083241985765 4402 2476 4192 1812 3667 3590 3124 2900 1381 1224 3831 3380 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 1.53383966888674e-07 4.13226212165833e-07 3105 3191.09090909091 3124 1.53383977475663e-08 1475 1.71348521445453 -1.58543395754238 -1 3.15780609106701 3103 4326 4397 4209 1633 3124 2971 1475 3983 3437 2444 3381 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 2.11387651863085e-05 2.40074522808894e-05 3165 3071.72727272727 3124 1.92172439104477e-06 749 1.50192682478635 2.07477079866207 1 2.00269546683502 3163 3460 2945 4380 4120 3087 2831 749 3124 3548 2382 3382 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 4.69387414566827e-08 2.99073619127066e-07 3955 2994.36363636364 3125 4.2671584052871e-09 304 1.68045965668428 1.55493644552303 1 3.16506099683835 3952 3125 2760 4156 304 3083 1784 3857 2477 3130 4310 3383 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 4.39613999105057e-07 7.81535998408991e-07 3095 3107.09090909091 3126 3.99649169955226e-08 1861 1.36252705298026 -1.47881230567491 -1 2.40195250327805 3092 3938 3756 3969 2506 2984 3126 1861 3262 3603 2081 3384 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 8.6458462443452e-08 3.28305665915602e-07 3130 2802.36363636364 3127 7.85986053101904e-09 947 1.6665952886823 -1.39106448716802 -1 3.11945016927979 3808 1259 3035 3397 947 2920 3372 3127 3130 2575 3256 3385 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 3.35425582444026e-06 4.28821438010781e-06 3130 3081.18181818182 3128 3.04932812596063e-07 2243 1.83188713021852 -1.84442744409884 -1 2.83857601975157 3128 3465 2304 4159 3628 2704 2243 3281 2462 2765 3754 3386 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 3.94665028183408e-07 7.20069166225622e-07 2500 3031.81818181818 3129 3.94665098275643e-08 1402 1.70425033819898 1.75396285838521 1 3.02208814836825 1402 3827 4322 3244 2497 2964 2497 2857 3129 3305 3306 3387 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 7.29577949184233e-07 1.16241607755768e-06 3430 3177.36363636364 3129 6.63252901028737e-08 2336 1.96954966000948 -1.68051045087892 -1 3.37437851171823 3430 3134 2910 3400 2827 2812 2965 4251 2336 3129 3757 3388 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 0.000464646585983707 0.000487904757695906 3130 3263.63636363636 3130 4.22495227054863e-05 130 2.51701368714178 3.12436452780217 1 2.4061349011234 3130 4223 2664 2678 4474 4377 4372 2537 130 4254 3061 3389 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 2.8911443376142e-08 2.61923249012265e-07 2670 2961.90909090909 3131 2.62831306873488e-09 35 1.68667265431637 1.53588860142251 1 3.20482214991744 2668 4009 2955 3974 35 2151 1672 4470 4368 3131 3148 3390 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 9.75603010772526e-08 3.39726302159777e-07 4690 2918.45454545455 3132 8.86911867305657e-09 759 3.05639871470125 -4.0477540130112 -1 5.7084263756923 4687 3132 1620 3598 1076 4060 3288 2985 759 3016 3882 3391 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 6.30835966466394e-07 1.0366216538207e-06 3880 2710.72727272727 3134 5.73487406686051e-08 1298 2.2784334140665 -1.81527265486831 -1 3.93644246407833 3878 1531 1298 1530 2735 3183 3399 4005 3362 1763 3134 3392 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 1.17676940622038e-06 1.71483531872806e-06 2205 2992.72727272727 3135 1.0697909415174e-07 1604 1.31971004450159 1.57811630272372 1 2.19639057293752 2201 4023 3455 4617 3135 1913 2032 1604 4352 3652 1936 3393 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 1.02804679559677e-07 3.46153508287541e-07 4350 2795.09090909091 3135 1.02804684315638e-08 1008 1.8552032172386 -1.63123266972499 -1 3.46025827241131 4348 1039 4655 1031 1239 3135 3530 4378 2051 1008 4332 3394 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 7.83546567334015e-07 1.22827625301114e-06 3295 3043.45454545455 3136 7.1231531490924e-08 670 2.13363204029428 2.5642931328947 1 3.64082195605071 3291 3693 2560 2858 2884 3919 3965 3539 670 3136 2963 3395 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 3.27796394814376e-05 3.65249996110448e-05 890 2620.18181818182 3137 2.98001162753478e-06 648 1.62314997677831 -1.62314997677831 -1 2.07898681960844 887 4031 3137 3957 4204 1195 1393 648 4182 3753 1435 3396 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 4.47192362837999e-06 5.57956106950926e-06 1820 2984 3138 4.06539338041067e-07 1245 1.3261917065555 1.59374978997394 1 2.01096374401151 1818 3898 3889 3798 3725 2063 1245 1883 3138 4499 2868 3397 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 7.78521962361056e-08 3.26053563650771e-07 2545 2889.27272727273 3138 7.07747263555358e-09 813 2.72087410325455 -2.49273653598417 -1 5.09569045233282 2543 3138 1482 3554 813 3640 4512 4329 3877 1841 2053 3398 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 3.20378448946876e-06 4.12376950921531e-06 2945 3124.18181818182 3139 2.9125355954906e-07 760 1.50415352540446 0.972282928359937 1 2.33796283912362 2944 3109 3159 3139 3602 2571 2735 4643 760 4014 3690 3399 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 8.72921622686156e-09 9.47170128523829e-08 3140 2772.27272727273 3140 7.93565114681596e-10 351 3.225138081935 3.5514825117978 1 6.5402236865217 3140 3018 351 4336 3347 2370 3264 4179 3740 548 2202 3400 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 3.58683036555468e-06 4.54877154686547e-06 3825 3145.27272727273 3140 3.2607601940503e-07 1237 1.51179647868302 -1.93540047727545 -1 2.3312499111124 3821 2873 2724 3303 3656 4184 3806 3140 1237 2801 3053 3401 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 3.76274377897e-08 2.87575261955407e-07 3765 2578.27272727273 3141 3.76274384268209e-09 209 2.05161788043556 2.30092345268804 1 3.87439615209014 3765 1031 4606 409 209 4289 4194 3141 2175 489 4053 3402 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 4.38458949929351e-07 7.80649012507429e-07 3050 3390.27272727273 3142 3.9859912483094e-08 2066 0.777905711106803 -0.73799186131903 -1 1.37108467750612 3046 4020 3861 4475 2501 2588 2859 3142 4411 4324 2066 3403 M15513 BIOCARTA_D4GDI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_D4GDI_PATHWAY.html D4-GDI Signaling Pathway 13/26 BioCarta 1.60204937739785e-06 2.22467580503615e-06 3830 3111.90909090909 3143 1.45640958547112e-07 1909 1.3845779175636 1.68738451830954 1 2.25919537603916 3829 1909 3061 3133 3313 4347 3682 2455 1932 3143 3427 3404 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 2.55037971911558e-07 5.41950314819278e-07 1650 3325 3143 2.55038001181528e-08 1650 1.48558466688929 1.56595437803701 1 2.6871682869764 1650 4671 4504 4706 2136 2390 2487 2906 3143 4623 3359 3405 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 5.32275123659626e-07 9.09771589731725e-07 3675 3045.27272727273 3144 4.83886593127306e-08 218 1.47330148808755 -1.55704043976711 -1 2.5692312451487 3675 2647 3418 218 2616 3144 4578 3587 2678 4256 2681 3406 M7946 KEGG_NOTCH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NOTCH_SIGNALING_PATHWAY.html Notch signaling pathway 47/52 KEGG 1.91070066052101e-06 2.60349512634502e-06 3740 3195.18181818182 3145 1.73700210906102e-07 1366 1.56834347572697 -1.24640783112608 -1 2.52822994820787 3739 2239 3085 3130 3384 3145 2958 4398 1366 3930 3773 3407 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 3.47730549931251e-05 3.86185457806001e-05 910 2965.45454545455 3145 3.16123678417298e-06 906 1.34343453179084 1.46848253400521 1 1.71117888161632 906 3280 3973 2030 4218 2165 3019 2943 3547 3394 3145 3408 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 1.73703358354858e-07 4.38438423227236e-07 3600 2920.09090909091 3145 1.57912156427086e-08 1187 2.12325429404406 2.02322022638905 1 3.89741139077712 3597 4100 1187 2728 1658 3737 3145 3704 1631 1946 4688 3409 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 3.67944935516136e-08 2.87533128416583e-07 4605 2702.81818181818 3146 3.34495401518118e-09 128 2.2298241609457 -1.69540189240871 -1 4.21104718740055 4602 152 1392 1898 128 3293 3495 4539 3146 2420 4666 3410 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 0.00898037111009994 0.0091727659899744 2705 3316.90909090909 3146 0.000819749066910889 1190 2.05874742550035 2.43323887775548 1 1.21041732008099 2704 4052 2755 4214 4602 2401 1190 4081 4510 3146 2831 3411 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 5.35267040405409e-08 3.06874196014832e-07 3200 2712.09090909091 3147 4.86606412207845e-09 413 1.59779168285493 -1.47283638371732 -1 3.00415833537301 3197 1466 3344 3147 413 3204 4016 1837 3865 3091 2253 3412 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 3.75994999128481e-08 2.87575261955407e-07 3860 3084.72727272727 3149 3.41813641413174e-09 147 1.80316094782412 2.0266750144595 1 3.40509112467317 3856 2954 2729 2432 147 4222 4714 3643 3149 2467 3619 3413 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 5.93692204956592e-06 7.26530258593496e-06 3745 3077.7 3149.5 6.59659746108568e-07 243 1.09160474461017 -0.594490776427999 -1 1.61895597205425 3744 2484 4462 NA 3868 4560 3050 2379 243 3249 2738 3414 M9043 BIOCARTA_GH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GH_PATHWAY.html Growth Hormone Signaling Pathway 44/53 BioCarta 1.15363631088418e-07 3.59296663856335e-07 3565 2634.45454545455 3151 1.04876033761689e-08 210 1.4080732151036 1.34441250496527 1 2.6194992773799 3562 503 3151 210 1266 4231 3995 4090 1062 3790 3119 3415 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 1.96220921194286e-06 2.66598373067654e-06 3395 3285.72727272727 3151 1.78382814733227e-07 2836 1.11595654923145 1.08126170666976 1 1.7953969991782 2933 3404 3391 2937 3394 3151 2996 3675 4462 2964 2836 3416 M79 PID_TRAIL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TRAIL_PATHWAY.html TRAIL signaling pathway 18832364 28/31 Pathway Interaction Database 3.04570877668018e-06 3.93640345726464e-06 3155 3054.18181818182 3153 2.76882999382493e-07 1358 1.21204746032955 -0.967293403780201 -1 1.89083213262989 3153 3400 3540 4018 3588 2358 2578 2474 2985 4144 1358 3417 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 1.21031965145625e-06 1.75613549181479e-06 595 2235.09090909091 3153 1.10029119755312e-07 510 1.24373298660279 1.29267358951368 1 2.06618054666204 591 3612 3913 3219 3153 521 682 937 3639 3809 510 3418 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 3.29417424596167e-06 4.22973406989638e-06 3155 2831.45454545455 3154 2.99470834410016e-07 861 1.73624227133929 2.31206782684201 1 2.69331569778641 3154 1934 2491 3371 3614 3622 2299 3159 861 3587 3054 3419 M18009 KEGG_CIRCADIAN_RHYTHM_MAMMAL http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CIRCADIAN_RHYTHM_MAMMAL.html Circadian rhythm - mammal 14/14 KEGG 4.03389558195388e-05 4.46424083161132e-05 1315 2857.09090909091 3155 3.66724504446754e-06 1311 1.63418838453528 -1.83717009715725 -1 2.05200189631057 1311 4049 3155 4376 4235 1790 1536 2137 3251 3968 1620 3420 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 4.19432657663748e-08 2.95100601223086e-07 4510 2709.81818181818 3155 3.8130242332753e-09 215 2.33063994638674 2.44156100745426 1 4.39388485153279 4507 3269 1253 2841 215 4306 3866 2053 3199 1144 3155 3421 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 0.000200406299899756 0.000213960130180241 1965 3075.90909090909 3156 1.82204143631094e-05 1964 1.47271606462253 1.13748974796599 1 1.55972982253953 1964 3156 3222 2020 4403 2480 2674 4303 2208 3653 3752 3422 M7298 BIOCARTA_ASBCELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ASBCELL_PATHWAY.html Antigen Dependent B Cell Activation 3/14 BioCarta 1.07805633628402e-05 1.26988417950101e-05 3160 3196.27272727273 3158 1.07806156624431e-06 1740 1.60992651392486 1.5245484541906 1 2.27534605239408 3158 1958 4185 3112 3985 3351 4324 2725 3559 1740 3062 3423 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 6.0235515921371e-07 1.00039280488695e-06 1315 3200.09090909091 3158 6.02355322488052e-08 1314 1.56439326039629 1.47892835246382 1 2.70950680460359 1314 4351 4435 3808 2769 2469 2369 3158 2553 4477 3498 3424 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 4.38955365241868e-06 5.47968612520925e-06 1670 2945.36363636364 3158 3.99051128246123e-07 1667 1.69385091708726 1.73376918317606 1 2.57253747564218 1667 3296 3158 2675 3721 2733 3758 2669 1837 3704 3181 3425 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 2.90991022468099e-07 5.86173449894634e-07 3240 2905.18181818182 3158 2.64537328142813e-08 1411 2.15082776159382 2.38020623418343 1 3.86970663383866 3237 3069 2068 3313 2172 3384 3468 1411 2623 3158 4054 3426 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 9.85581638369912e-05 0.000106500579970375 1115 2470 3159 8.96023449431057e-06 377 1.28916466128601 -0.940667082030481 -1 1.47801522255246 1111 3159 3236 3936 4345 744 377 1451 3955 4062 794 3427 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 3.44124967645669e-07 6.53629717218333e-07 3630 3102.72727272727 3159 3.128409286126e-08 1844 1.64382671893378 1.14511229190606 1 2.93486712888532 3630 3355 3116 2006 2318 3107 4132 1844 4234 3159 3229 3428 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 5.60076287058877e-06 6.87889689023653e-06 3295 2900 3164 5.09161557188092e-07 1590 1.7441459956008 1.19090670786527 1 2.59920699233642 3292 3352 3164 1718 3792 2810 1892 2844 1590 3539 3907 3429 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 2.17998978033103e-07 4.95921323033463e-07 3345 2639.09090909091 3164 1.98180908758838e-08 487 1.27411272202605 -1.6050154991979 -1 2.31871116982565 3343 3728 3428 3164 1883 3200 2253 487 1744 4049 1751 3430 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 4.03361198566131e-07 7.31130897554584e-07 3965 3232.54545454545 3167 3.66692065928011e-08 2289 1.86317226848958 -1.55834359761966 -1 3.30041705372187 3962 2631 2289 3923 2445 3575 4549 3167 3116 2574 3327 3431 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 2.36964753400048e-07 5.21676136216523e-07 4270 3034.63636363636 3168 2.15422526294383e-08 1384 2.19284274003168 2.35341275408232 1 3.97737218342212 4268 1725 1779 3168 1966 4067 4098 4053 2759 1384 4114 3432 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 8.65219329088614e-07 1.33355275483062e-06 3625 3201.81818181818 3169 7.86563335785062e-08 1110 1.55538266360659 1.17893764241241 1 2.63782527619965 3621 2733 3010 3103 2944 3992 4367 3938 1110 3169 3233 3433 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 4.80840783076741e-06 5.97254867400583e-06 3170 3195.45454545455 3170 4.37128940022517e-07 2023 1.75170525929309 -1.63878331661521 -1 2.64151315639006 3170 3761 2831 4185 3745 2651 2278 3977 3652 2877 2023 3434 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 2.78418303410947e-05 3.11650917367704e-05 3530 2952.54545454545 3171 2.53110751783717e-06 720 1.37247310553028 1.68778384796284 1 1.785093335176 2433 3362 3503 3171 4180 2978 2873 720 3529 3526 2203 3435 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 1.66086489039294e-07 4.2834032897358e-07 4660 3124.63636363636 3171 1.50987728707096e-08 1308 1.67625833528784 -1.41397966813275 -1 3.08162982418254 4657 2007 3362 1308 1615 4069 4605 2781 2335 3171 4461 3436 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 1.30648072980707e-06 1.87036367749147e-06 3860 3245.27272727273 3172 1.18771045969788e-07 1756 2.18135509481691 -1.46908702011264 -1 3.60723750478994 3859 2828 1840 3831 3199 3095 3169 3172 4470 1756 4479 3437 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 1.26099998644864e-06 1.81874292061228e-06 1500 2985.90909090909 3173 1.14636428111953e-07 1499 1.63069444922212 1.63910195120271 1 2.70213358814295 1499 3978 3295 3736 3173 2540 3068 1981 3549 3702 2324 3438 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 3.18278818107626e-06 4.10121763982526e-06 4375 3123.09090909091 3174 3.18279273964872e-07 933 3.18781717194341 -2.87609217140496 -1 4.9581014788028 4375 2905 4477 3043 3644 3522 3993 933 1580 2708 3174 3439 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 1.37080927401478e-05 1.59208163714315e-05 3630 3090.09090909091 3175 1.24619801412276e-06 1376 2.15427730168212 -1.57677369555217 -1 2.98389188554705 3627 3175 2590 2899 4020 3249 2461 2965 1376 3545 4084 3440 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 1.37080927401478e-05 1.59208163714315e-05 3630 3091.09090909091 3176 1.24619801412276e-06 1377 2.15427730168212 -1.57677369555217 -1 2.98389188554705 3628 3176 2591 2900 4021 3250 2462 2966 1377 3546 4085 3441 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 3.1220945256585e-07 6.13017243407133e-07 3180 3191.63636363636 3176 2.83826815338691e-08 834 1.13684140052834 1.26228675721001 1 2.03858196141817 2841 834 3176 4545 2236 3109 3803 3180 4362 3895 3127 3442 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 6.76271764284838e-08 3.14536172538656e-07 3180 3152.54545454545 3176 6.76271784865296e-09 769 1.53684707337099 -1.32791429439492 -1 2.88478473894078 3176 3544 4698 2984 769 1709 3450 4497 2848 4277 2726 3443 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 1.7967855541077e-06 2.46249355847513e-06 3365 3150 3177 1.63344274689213e-07 1543 1.51935712396572 -1.4696329107682 -1 2.45984453207551 3886 3096 3109 1543 3361 3177 3713 2858 3094 3450 3363 3444 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 5.21619917694828e-07 8.96267204775969e-07 3075 3059.54545454545 3177 4.74200037609939e-08 1737 2.75158770809777 3.00833181912964 1 4.80429107824146 3073 3395 1737 2859 2601 3290 3177 4264 3650 2021 3588 3445 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 0.000509108869839161 0.000533879996809784 2265 3138.27272727273 3179 4.62933384087255e-05 1143 2.15124223699462 2.5856267396029 1 2.0320568125508 2262 4627 3179 4463 4642 2325 1498 1143 3934 4116 2332 3446 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 2.42861864607885e-05 2.73647171389166e-05 3180 2907.54545454545 3179 2.2078595058555e-06 1115 2.87025125712952 2.45195620781381 1 3.78091335453246 3179 4051 2096 3331 4154 2737 1115 1157 3745 3972 2446 3447 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 1.17860739850453e-06 1.7169836175745e-06 4640 3343.36363636364 3180 1.07146184538281e-07 1720 1.83839621036781 -1.80539206688323 -1 3.05968871647216 4637 2291 2464 1720 3136 4162 3924 4256 3180 2733 4274 3448 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 8.00526103073529e-08 3.27123182997709e-07 2760 2857 3181 8.00526131911421e-09 959 1.44380172170227 -1.31387929626303 -1 2.70297444210941 2759 3231 4285 4087 959 1209 3181 2491 3516 4449 1260 3449 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 1.04790730517625e-07 3.48348225330125e-07 3715 3043.72727272727 3181 9.52643050082118e-09 1148 1.78938138714932 -1.8587148354865 -1 3.3360409070104 3715 2967 3214 3127 1148 3584 4107 4020 2155 3181 2263 3450 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 2.81086033625007e-07 5.72979094207008e-07 3395 2839.63636363636 3181 2.55532790489417e-08 837 2.88514153023377 3.16920579455235 1 5.19939405336007 3395 3085 837 3274 2139 3707 2698 3181 3809 1138 3973 3451 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 1.31637454260969e-07 3.81741928683936e-07 3285 3240 3182 1.19670420125022e-08 1383 1.60603282153257 -0.96858937565373 -1 2.97568840488383 3283 3182 2972 4400 1383 3155 3000 3941 2150 3686 4488 3452 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 8.78805504507301e-08 3.31003670356505e-07 3185 2960.45454545455 3182 8.78805539260762e-09 1062 1.7138142903415 2.01427783916389 1 3.20609770491418 3182 2486 4449 2969 1062 3281 3297 2644 2028 3739 3428 3453 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 5.64969291315229e-07 9.50679163995679e-07 2810 3217.72727272727 3183 5.13608578547073e-08 2097 1.36444671990328 -1.14251435343324 -1 2.37181405326963 2808 3984 3527 4472 2664 2234 2097 2223 4590 3613 3183 3454 M15381 REACTOME_TCR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TCR_SIGNALING.html Genes involved in TCR signaling 47/65 Reactome 1.10159620218782e-06 1.62181349791844e-06 4595 3480.63636363636 3185 1.00145159435051e-07 2200 1.75940188833044 -1.68204604098315 -1 2.94076152315391 4595 2665 2948 2200 3098 4460 3384 3040 4383 3185 4329 3455 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 3.26392252432217e-05 3.63771294328232e-05 1405 3216.54545454545 3185 2.96724631719999e-06 1405 1.59479908508029 1.56571295388334 1 2.04347031264259 1405 4238 2997 4026 4203 2781 2252 2266 4582 3447 3185 3456 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 1.90911354598301e-07 4.6234047906823e-07 3600 3244.81818181818 3186 1.73555791968352e-08 1744 1.9720975542162 1.98544503738859 1 3.60676099562426 3598 3841 2709 3156 1744 4080 3642 3003 3186 2788 3946 3457 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 8.80342762877039e-08 3.31003670356505e-07 3790 2907.72727272727 3187 8.00311634640424e-09 958 1.46495436235836 1.30452084732117 1 2.74042088245082 3790 2712 3187 3912 958 2610 1072 3705 3958 2300 3781 3458 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 3.89908751850678e-07 7.14984191427816e-07 3960 3196.81818181818 3187 3.54462564504283e-08 2413 1.96119706486032 -2.18963029284286 -1 3.47959576400584 3960 3439 2663 2860 2413 4010 3187 3789 2649 2605 3590 3459 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 1.28372562802803e-06 1.84450075016508e-06 3335 3150 3187 1.16702397917954e-07 1256 1.83309560961274 1.84233065243069 1 3.03439535568865 3331 3052 2699 3659 3187 2468 1256 4057 3157 3395 4389 3460 M5489 BIOCARTA_IL6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL6_PATHWAY.html IL 6 signaling pathway 34/36 BioCarta 2.06435297837477e-07 4.82841727350294e-07 2880 3136 3189 1.87668470189252e-08 1732 1.026430608888 -1.16790668917492 -1 1.8712366744015 2878 3975 3810 2505 1828 2352 1732 3502 4489 4236 3189 3461 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 6.58033129814853e-06 7.9864139180409e-06 2305 3060.18181818182 3189 5.98213725490416e-07 1240 0.871569175131058 1.01199839632543 1 1.28210472001235 2301 3183 3395 3189 3831 1897 1240 3337 4598 4172 2519 3462 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 1.83733148829111e-07 4.5191269540042e-07 3285 3028.27272727273 3189 1.67030149248727e-08 1714 1.85585802654483 -1.69986249287727 -1 3.39942965718897 3284 2546 2660 3355 1714 3189 4312 4435 2253 3379 2184 3463 M983 REACTOME_INTERFERON_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_SIGNALING.html Genes involved in Interferon Signaling 180/246 Reactome 1.28542860293577e-06 1.84526247136766e-06 3140 3278.63636363636 3190 1.16857213999452e-07 2363 1.50604240803408 -1.5651600419941 -1 2.49277965523311 3136 3584 3694 2497 3190 3604 3670 2363 4005 3162 3160 3464 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 3.22578497116717e-07 6.27088346948477e-07 3195 2969.54545454545 3191 2.93253222195737e-08 1382 2.31631193770627 -2.44032647061818 -1 4.14790764571867 3191 4266 2088 3933 2263 3779 4563 1716 3235 2249 1382 3465 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 9.05764834116069e-07 1.38042712139703e-06 1350 3242.90909090909 3191 9.0576520330075e-08 1348 1.51414976502703 1.56528496220722 1 2.5613142760524 1348 4346 4419 3817 3049 2503 2368 2643 3288 4700 3191 3466 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 0.000527995809212082 0.000553071508983806 1805 3082.18181818182 3194 4.8011142708525e-05 1793 1.8698523015439 -1.44824034946687 -1 1.75786257527237 1804 4596 3264 3194 4484 2146 1793 2832 3686 3890 2215 3467 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 8.35322089245924e-08 3.27411388472988e-07 2385 2804.09090909091 3194 7.5938374632948e-09 899 1.4748973841904 1.38397325620289 1 2.76104501032316 2384 2539 3722 1297 899 3339 3194 4003 1452 4054 3962 3468 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 9.47490633743922e-08 3.3764305071295e-07 3195 2947 3195 9.47490674142154e-09 1032 1.83667236381083 1.90274702694688 1 3.43142032638114 3195 1968 4308 2872 1145 3762 3511 3382 3148 1032 4094 3469 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 4.74538617627436e-08 3.0118377618747e-07 3995 2547.63636363636 3195 4.31398752602914e-09 308 2.31239585340955 -2.61778582976079 -1 4.35356593322047 3993 1580 824 2298 308 4119 3804 3195 3767 473 3663 3470 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 1.44685690279143e-07 4.01479399246064e-07 3880 3388 3195 1.31532454358705e-08 1466 1.64348372434651 -1.20298937745393 -1 3.03470808392533 3877 2575 2780 3195 1466 4541 4691 4146 3727 3180 3090 3471 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 5.33703359675862e-07 9.1105962302715e-07 2655 2994.27272727273 3195 4.85184990134822e-08 1433 1.57639298700675 1.72233397146272 1 2.74878894406009 2654 3402 3195 3877 2620 3753 3949 2399 1433 3709 1946 3472 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 2.52214283997646e-05 2.83711015364369e-05 3045 3160.63636363636 3196 2.29288341364226e-06 1389 1.52152443475171 1.03268548914164 1 1.99697152976759 3041 3453 3254 3196 4161 2418 2287 4550 1389 3888 3130 3473 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 0.00139085385723907 0.00144028745198956 1585 3003.81818181818 3196 0.000126521267532796 1303 1.89983497773476 -1.2585057191664 -1 1.55802608045519 1583 4623 3196 3740 4543 1640 1303 2680 3929 3844 1961 3474 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 9.54139430682833e-08 3.38845370705758e-07 2265 2904.54545454545 3196 9.54139471650027e-09 1126 1.76176135246024 2.0433174673222 1 3.29064501381832 2261 4088 4490 1126 1149 3323 3196 2430 2123 4556 3208 3475 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 1.56974500793198e-07 4.17890380002196e-07 3040 2881.72727272727 3196 1.4270410181241e-08 1286 1.95640200719392 2.08451516087095 1 3.60284918413699 3040 3842 2490 1286 1553 3196 3779 3357 2054 3507 3595 3476 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 5.0247529693813e-07 8.68430392364692e-07 2840 3260.36363636364 3197 4.56795828820409e-08 2584 1.84702426275564 1.80068878824634 1 3.23194220938721 2838 3607 2950 3197 2584 3682 3998 3174 3437 2687 3710 3477 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 6.47453626163689e-06 7.86407904141177e-06 3855 3347.63636363636 3198 5.88595937826185e-07 1944 1.96017485822899 2.31569788205327 1 2.8883471661495 3851 2724 1944 3870 3828 4556 2986 4478 3198 2226 3163 3478 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 4.51088475114697e-08 2.99073619127066e-07 3200 2372.63636363636 3199 4.51088484271333e-09 143 1.87924023105693 2.03667176006297 1 3.5395560672095 3199 963 4429 143 345 3689 4147 3414 1669 478 3623 3479 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 2.21949318551925e-06 2.97107425855101e-06 1305 2457.81818181818 3200 2.21949540228987e-07 366 1.06240339897064 -1.18193719522358 -1 1.69476110718376 1302 3200 4212 4366 3489 1604 366 517 3937 3433 610 3480 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 1.9346060469298e-07 4.65884721505545e-07 4520 3121.09090909091 3200 1.75873292459325e-08 1756 1.74838748651106 -1.50124481631447 -1 3.19584644645074 4517 3249 2810 3184 1756 3208 4182 3200 2705 3745 1776 3481 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 0.00552125191628932 0.00564809472147498 2255 3146.72727272727 3200 0.000503196114774989 1188 2.53881185182378 2.53881185182378 1 1.64726009149533 2253 4331 2687 3491 4705 2683 1188 2037 4086 3953 3200 3482 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 1.52909614180137e-05 1.76462928833801e-05 2545 3208.27272727273 3201 1.39009706344654e-06 1371 1.61880418785569 -1.78954322619829 -1 2.2211037866616 2544 4272 3201 3450 4052 3178 3033 1371 3837 4061 2292 3483 M85 BIOCARTA_BAD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BAD_PATHWAY.html Regulation of BAD phosphorylation 37/40 BioCarta 8.80474751938641e-06 1.04839576921049e-05 2070 3108.27272727273 3202 8.00434796143114e-07 1238 1.50131733760656 1.28516219611388 1 2.15787437944288 2070 3369 3037 2669 3917 1940 1238 4603 4061 4085 3202 3484 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 4.0212765476326e-05 4.45131925535316e-05 2500 3228.36363636364 3204 3.65577277503332e-06 1532 1.68695636597849 -2.04110652869255 -1 2.11890213565667 2498 4626 3204 3774 4234 2349 2517 3058 4167 3553 1532 3485 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 1.31626411312233e-06 1.88094659822507e-06 4195 3076.54545454545 3206 1.19660445513297e-07 778 1.90504762176093 -2.03245608571624 -1 3.14885953533103 4191 778 2070 2526 3206 4394 4285 3968 1660 2124 4640 3486 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 1.82413470650643e-07 4.50217538899015e-07 3765 3354.09090909091 3206 1.65830441614088e-08 1708 1.72175869584666 1.78366311039312 1 3.15454520488142 3764 4125 3123 3206 1708 4691 4388 2411 2719 3824 2936 3487 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 1.39241917187744e-06 1.97423204904221e-06 3830 3219 3206 1.26583641196828e-07 2224 1.97911755335646 -1.09649654146284 -1 3.25930957346877 3828 2224 2356 2883 3239 4433 3651 2787 3206 3086 3716 3488 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 4.94715317803679e-05 5.43795132751133e-05 3305 3236.18181818182 3206 4.9472633159482e-06 2018 1.60588595682323 1.90053716100293 1 1.97671314755084 3305 3206 4649 2864 4278 4154 3270 2018 2590 3076 2188 3489 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 0.00132190065485497 0.00136978509130965 2350 3262.90909090909 3207 0.000120245055098526 1971 1.2067725452576 -0.9398799133112 -1 0.996937366422522 2346 4175 4008 2693 4541 2883 2217 3398 1971 4453 3207 3490 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 1.31724433536007e-06 1.88177762194296e-06 4340 3310.45454545455 3207 1.1974955673249e-07 2376 1.85803868496936 -1.49587473057318 -1 3.07103412806617 4336 4003 2431 4179 3207 3366 2591 2376 4274 3015 2637 3491 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 2.56288473896106e-07 5.43188862500952e-07 4215 3064.54545454545 3207 2.32989548865796e-08 2046 1.93663887291532 -2.04381890877504 -1 3.50275521426237 4213 3278 2164 2175 2046 4212 4102 3448 3207 2096 2769 3492 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 0.00112688743545334 0.00116847730565461 2900 3097.27272727273 3207 0.000102496824160207 1516 2.82144316905845 -2.55897835882604 -1 2.38824212216295 2896 3083 1589 1516 4537 3344 3207 4132 2873 3370 3523 3493 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 1.0004609529631e-07 3.41896906035439e-07 4370 3066.54545454545 3208 9.09509998599599e-09 1106 2.08213974596348 -1.61215755773249 -1 3.88686832318738 4369 2005 1396 2343 1106 4417 4665 3897 1739 3208 4587 3494 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 1.04588897166081e-05 1.23322406850838e-05 2385 3268.63636363636 3210 9.50812676266119e-07 1922 1.21757514469474 1.38976969019143 1 1.72508995385829 2382 4535 3769 3217 3959 2926 2800 1922 3210 4337 2898 3495 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 3.55543522192733e-07 6.70180809342577e-07 2325 3371.72727272727 3213 3.55543579077784e-08 2322 1.72745088643588 1.85739174412352 1 3.07879511115534 2322 4087 4421 3552 2415 3213 2821 3067 3109 4521 3561 3496 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 0.000155296379571378 0.000166628531842897 2855 3320.90909090909 3213 1.41188493556267e-05 2106 2.01908896707925 -2.58395400224677 -1 2.202012691583 2852 3743 2106 2448 4383 2895 3213 4304 4377 2678 3531 3497 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 4.73394426123447e-07 8.28177053855696e-07 3215 3037.81818181818 3213 4.30358661807411e-08 2151 1.27144447809758 -1.35461325979035 -1 2.23208590567845 3213 3401 3302 4217 2554 2278 2310 2852 3626 3512 2151 3498 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 2.36782299883545e-07 5.21517711362731e-07 3215 3244.45454545455 3214 2.15256659425482e-08 1964 1.86012024349881 1.92623968763853 1 3.37382118945263 3214 3845 2994 3703 1964 3072 2865 3628 3010 3289 4105 3499 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 2.06545784204119e-07 4.82860872433601e-07 2940 3279.27272727273 3215 1.87768912359598e-08 1830 1.57636764367163 1.7382921352335 1 2.87425428477814 2940 3730 3005 3198 1830 3216 3215 3988 4606 3639 2705 3500 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 8.35905895176571e-08 3.27411388472988e-07 2775 3227.63636363636 3217 8.35905926619812e-09 1004 1.78904498072575 1.91948701429361 1 3.3493206735197 2772 4678 4481 3240 1004 3217 2693 2251 2881 4500 3787 3501 M9577 MOOTHA_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_MITOCHONDRIA.html Mitochondrial genes 12808457 501/573 Vamsi Mootha 2.40632236157922e-07 5.26069548247056e-07 3220 3457 3217 2.40632262214669e-08 1981 1.38076599881878 -1.32577175695285 -1 2.50265842953522 1981 4692 4589 4105 2076 3117 2960 3217 3217 4632 3441 3502 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 1.34257195167588e-06 1.91249803634276e-06 4420 3443.54545454545 3218 1.2205207009041e-07 2114 1.93176805588061 1.86253694586516 1 3.18900788176786 4420 3060 2874 2441 3218 4594 4234 4175 2828 3921 2114 3503 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 2.87648423927008e-07 5.81456343013053e-07 3740 3228.18181818182 3218 2.61498601397128e-08 1768 1.68022009745957 -1.53505691107058 -1 3.02451711570279 3738 3855 3038 3218 2160 3010 4263 4055 3464 1768 2941 3504 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 1.09015302990264e-06 1.60797571910639e-06 1920 3286.63636363636 3218 9.91048700091016e-08 1916 1.44209720413432 1.51039012757971 1 2.41179530302844 1916 4370 4054 3800 3093 2083 2560 3218 3803 4373 2883 3505 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 4.38665232997362e-05 4.83987821352863e-05 1845 2488.90909090909 3219 4.38673892461341e-06 76 3.08152476794895 3.08152476794895 1 3.83892066487858 1843 3219 4359 4186 4596 1371 142 471 3249 3866 76 3506 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 5.74417437324376e-08 3.09093308316432e-07 4000 2174.63636363636 3219 5.22197683929408e-09 92 2.4575552405941 -2.10068107221225 -1 4.6189234203095 3996 92 547 137 490 3772 3983 3677 3606 402 3219 3507 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 7.23023567575677e-06 8.70801540943403e-06 4515 3259 3220 6.57296312529477e-07 1182 2.26886207086057 -2.89899710181863 -1 3.3143329871452 4511 2357 1611 3105 3867 4171 4609 2895 3220 1182 4321 3508 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 9.45018773471271e-07 1.42827044853807e-06 2995 3283.81818181818 3220 8.59108344916454e-08 2274 2.01462719647885 2.49854839986935 1 3.39959133011009 2994 4212 2274 3419 3009 3336 2976 2718 4322 3220 3642 3509 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 1.62364513632598e-05 1.86598613183799e-05 1470 2986.18181818182 3220 1.47605192662183e-06 1468 1.51383498072168 1.51383498072168 1 2.06642057634565 1468 3748 3220 3457 4069 2034 1857 2202 4514 3758 2521 3510 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 3.01793203160506e-07 6.01801402162057e-07 3830 2984.81818181818 3224 2.74357495054657e-08 468 1.43932333328329 -1.34056306752505 -1 2.58455429936914 3830 3038 3520 468 2197 3224 4455 4250 1206 4343 2302 3511 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 1.92846682233997e-06 2.62618678633718e-06 4345 2798.09090909091 3224 1.92846849588495e-07 325 3.32774524223439 -3.51627795815938 -1 5.36179784611082 4341 864 4527 1339 3439 4294 2193 3224 325 2377 3856 3512 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 3.38234227852246e-07 6.47469491127629e-07 3990 2852.45454545455 3226 3.07485708957587e-08 1415 2.36650073249419 -2.21023187688956 -1 4.22830900952792 3988 1720 1415 1624 2296 3419 3261 4064 3226 1712 4652 3513 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 1.35932008422978e-06 1.93369222349746e-06 4300 2987.63636363636 3226 1.23574629465215e-07 586 1.48059849689225 -1.56108449139205 -1 2.44195908240522 4297 586 2795 2109 3226 4053 3854 3974 1090 2510 4370 3514 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 8.33250219648336e-08 3.27411388472988e-07 4290 3375.09090909091 3226 8.33250250892103e-09 1000 1.67483592523705 1.87921210041618 1 3.13545175138997 4290 2935 4699 2946 1000 3946 4636 3226 2461 2866 4121 3515 M18155 KEGG_INSULIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INSULIN_SIGNALING_PATHWAY.html Insulin signaling pathway 129/174 KEGG 3.23091402499081e-07 6.27666567753073e-07 2985 3157 3227 2.93719499952914e-08 1309 1.452309347378 1.65039890866024 1 2.60021629273802 2984 3873 3829 1309 2264 3227 3323 3668 3150 4420 2680 3516 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 2.52110373344264e-06 3.32973711114987e-06 2675 3345.72727272727 3227 2.29191511138349e-07 2006 1.09231414113457 -1.36592381263172 -1 1.72688717007465 2674 4534 3792 3227 3501 2877 3192 2228 4316 4456 2006 3517 M984 BIOCARTA_TOLL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TOLL_PATHWAY.html Toll-Like Receptor Pathway 56/78 BioCarta 3.29662222769319e-06 4.23163104572409e-06 2160 3115.09090909091 3228 2.99693378870493e-07 1879 1.85348201700984 -1.74835046768144 -1 2.87513575599017 2156 3924 2899 3488 3615 3098 3914 1879 3707 3228 2358 3518 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 5.02602864931416e-06 6.22589460019267e-06 1505 2998.09090909091 3228 4.56912739237022e-07 1503 1.06105861954326 0.893679088857956 1 1.59417343041793 1503 3643 3894 3228 3756 1821 2012 2065 3852 4252 2953 3519 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 4.34401147310096e-07 7.74602725841954e-07 3760 3479.36363636364 3229 3.94910211895297e-08 2498 1.98903146041521 -1.78850488798947 -1 3.50901457454262 3757 4120 3076 3201 2498 3229 3151 4567 3011 3577 4086 3520 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 1.36845211988066e-06 1.94492442211283e-06 1065 2473 3230 1.24404815553731e-07 59 1.17076147509505 -1.2858896300664 -1 1.92991258292496 1064 3644 3788 3517 3230 369 1112 1688 4434 4298 59 3521 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 8.4622842309433e-05 9.18628830957966e-05 470 2667.27272727273 3230 7.69328159057209e-06 469 1.1089224386393 1.10116099613693 1 1.29181052936026 469 3913 4012 3230 4323 1058 747 947 4410 4426 1805 3522 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 3.3340306039214e-07 6.4099386103601e-07 1765 2861.81818181818 3231 3.03093737198484e-08 1460 2.71460336625435 2.32828485976495 1 4.85382474882251 3231 3409 1764 3283 2287 4006 4428 1763 1460 2411 3438 3523 M1443 REACTOME_GLUTATHIONE_CONJUGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUTATHIONE_CONJUGATION.html Genes involved in Glutathione conjugation 20/32 Reactome 8.29208476715617e-07 1.28901576356507e-06 4020 3315.45454545455 3231 7.53826172050174e-08 2602 1.31825335838426 -1.37812481565684 -1 2.24115402408945 4016 3434 3113 3137 2916 3231 2692 3634 3266 2602 4429 3524 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 0.00467625904477628 0.00479199797901521 2360 3316.09090909091 3232 0.000468612861675878 2015 2.56561235469494 2.56561235469494 1 1.71754452743612 2356 4082 4406 4172 4613 2638 2147 2015 4258 2558 3232 3525 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 8.69623813293552e-08 3.29546895985795e-07 2960 3144.36363636364 3232 8.69623847324603e-09 1047 1.66476757219462 -1.59178062341595 -1 3.1152403602925 2958 3232 4548 3486 1047 3123 4453 3838 3472 1835 2596 3526 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 1.47983485482633e-07 4.06132387668711e-07 4075 3205.81818181818 3232 1.34530450397068e-08 1488 1.8040484550432 -1.78393187495666 -1 3.32866951763551 4072 3290 2697 3903 1488 3570 4543 3232 3013 2889 2567 3527 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 4.47115777831709e-07 7.92484593077607e-07 3815 3341.54545454545 3234 4.0646897154642e-08 1803 2.00118676253721 -1.75630702436769 -1 3.52473626217915 3814 4496 2589 4218 2512 4444 4183 1803 3234 3186 2278 3528 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 3.54843235492434e-06 4.50594584752297e-06 2340 3003.54545454545 3234 3.22585279844387e-07 353 1.5419621015457 1.8178339047096 1 2.37961289290952 2336 4241 3367 4606 3652 2755 3073 353 3854 3234 1568 3529 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 2.1633811670284e-06 2.90419769862743e-06 1680 3114.54545454545 3234 1.96671208582107e-07 1678 1.38212861034203 1.46657955041959 1 2.20899667734041 1678 4149 3832 2986 3444 2239 1806 3234 3620 4214 3058 3530 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 1.32977086474514e-07 3.83038247822062e-07 3335 3108 3235 1.20888267738363e-08 1394 1.88280238367195 -1.41355970584044 -1 3.48784033187897 3335 4115 2917 2440 1394 2863 3235 3531 2122 3911 4325 3531 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 6.89483692609087e-07 1.11260274499654e-06 3235 3088.72727272727 3235 6.26803553358663e-08 402 1.54497973516001 -1.80264684726135 -1 2.65527431036591 3235 3680 3059 3458 2793 3638 3852 2499 4356 3004 402 3532 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 1.38455246303699e-06 1.96542553863412e-06 4165 3358.36363636364 3235 1.25868484944983e-07 1640 2.03098008505148 2.26169838509324 1 3.34588065074903 4161 3063 1640 3131 3235 4307 3897 3946 3104 2293 4165 3533 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 2.51756453960585e-05 2.83263519116558e-05 3065 3241.45454545455 3236 2.28872122704976e-06 955 0.904582341458818 0.861231087378372 1 1.18707673622811 3062 2895 3446 3996 4160 3236 955 2370 4501 3955 3080 3534 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 1.27216619627e-07 3.76660766944629e-07 4655 2993 3236 1.15651479075813e-08 638 2.59964351883851 -2.60093499608566 -1 4.82157082368288 4654 2581 638 3256 1350 4667 4297 3002 3236 1482 3760 3535 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 4.04704445450463e-05 4.47669318614058e-05 3525 3120.72727272727 3237 3.67919900405644e-06 2145 1.9266246493482 -1.92225600986587 -1 2.41868656211269 3522 2430 2145 3285 4237 3686 2694 3522 3237 2437 3133 3536 M10066 BIOCARTA_GCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GCR_PATHWAY.html Corticosteroids and cardioprotection 29/35 BioCarta 8.65396628823348e-07 1.33355275483062e-06 3880 3304.27272727273 3237 7.86724517488885e-08 1539 1.36543132445363 0.912357561802296 1 2.31557528263232 3880 2771 3373 1539 2945 3237 2428 4519 3160 4011 4484 3537 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 0.000142859022786616 0.000153388213729033 2710 3357.54545454545 3237 1.29880273010951e-05 2299 1.58390021761157 -1.68992646603846 -1 1.7436573919813 2706 3685 3184 3983 4379 2956 3442 2299 4214 3237 2848 3538 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 1.76378271667388e-06 2.42218633188849e-06 4115 3229.63636363636 3238 1.60344011884938e-07 1674 2.19986919985088 -2.39828573455926 -1 3.56653490382645 4115 2835 1674 2560 3350 4066 4051 3238 4152 2630 2855 3539 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 1.03202628699614e-05 1.21779101865545e-05 3510 3077.90909090909 3238 9.38210116629767e-07 1583 3.11213936133058 3.70061283353298 1 4.41560970773225 3507 2416 1583 3574 3956 3238 2686 4255 1860 2362 4420 3540 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 2.72928816497217e-06 3.56453794650489e-06 345 2752.45454545455 3239 2.48117413717587e-07 345 1.31059601076955 1.350664100811 1 2.0609509607627 345 3239 4117 4313 3542 1223 1404 1997 3665 3782 2650 3541 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 5.52902100904318e-07 9.35710977507486e-07 3240 3012.81818181818 3239 5.0263839987204e-08 1079 1.83889974491957 1.74983139656332 1 3.20051381555716 3239 2281 1958 3619 2647 4293 4290 1079 4044 1609 4082 3542 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 2.58792970069832e-06 3.40441142343815e-06 2485 3189 3240 2.35266613178821e-07 2421 1.4845189073985 1.36163319660529 1 2.34312104694089 2482 3634 3573 3207 3516 2751 2421 3991 2635 3240 3629 3543 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 1.39625740464051e-06 1.9790795645355e-06 2945 3259.36363636364 3241 1.26932571890314e-07 1849 1.82099902922506 1.8169030742429 1 2.99828323261468 2941 3762 3147 4220 3241 2592 3070 3561 3920 3550 1849 3544 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 1.39731755923409e-06 1.97998765523414e-06 2385 3273.81818181818 3242 1.27028949703021e-07 2371 1.40058525966149 1.60272984427932 1 2.30579060825557 2381 4251 3356 4466 3242 2404 2448 3513 4455 3125 2371 3545 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 1.17036341609854e-06 1.70866542653422e-06 3895 3391.54545454545 3242 1.0639673079208e-07 2383 1.95907246969916 -1.56746778604193 -1 3.26178291746481 3891 2383 2826 2642 3129 4315 4052 4289 3242 3418 3120 3546 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 8.72895234429315e-07 1.34247817090465e-06 1720 3409.72727272727 3243 7.93541437062398e-08 1716 1.22751283480454 1.2668311086343 1 2.08057145901606 1716 4362 4143 3804 2952 3050 2931 3243 3185 4614 3507 3547 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 1.69773792369951e-07 4.32684827206353e-07 3945 3075.81818181818 3245 1.543398231558e-08 1540 1.87073879170006 -1.86315705173458 -1 3.43689467487527 3943 3716 2841 3383 1640 3222 1540 3641 2416 3245 4247 3548 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 0.000524150986484114 0.000549287889921185 3245 2998.63636363636 3245 4.76614461237361e-05 1477 1.01021829545974 1.08213925921157 1 0.950187712864334 1477 2893 3245 3420 4483 1987 1496 2802 4354 3583 3245 3549 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 3.37870282497139e-05 3.7576525291859e-05 1775 2736 3246 3.07159519575181e-06 352 1.37728025728663 1.12084563792959 1 1.75903555613616 1774 3452 3358 2672 4212 1243 352 2458 4007 3322 3246 3550 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 2.17267338979587e-06 2.91501375777047e-06 1955 3277.90909090909 3246 1.97515957771368e-07 1952 1.07335360957076 -1.21574129824548 -1 1.71480207045765 1952 4121 4131 3246 3446 2783 2328 2651 4254 4602 2543 3551 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 2.09508757815135e-06 2.82214993403949e-06 3380 2997.18181818182 3247 1.90462688484743e-07 1536 1.52022382194706 1.44206342518108 1 2.43525803495269 3380 3616 3579 2464 3428 3247 3062 1536 1828 4330 2499 3552 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 1.28280705244557e-06 1.84374217038462e-06 3250 3012.18181818182 3249 1.28280779296345e-07 672 1.72535859577644 -1.23941712038319 -1 2.85609241674418 3249 1943 4516 4137 3255 2155 672 2849 4010 3772 2576 3553 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 2.68695832634477e-09 3.16485198824874e-08 4185 2703.63636363636 3249 2.68695832959365e-10 206 2.01634905250714 -1.80591920976995 -1 4.36580447885465 4184 953 4719 1314 661 4360 3699 3249 2044 206 4351 3554 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 7.05403010471962e-05 7.68228474717965e-05 2330 3315 3250 6.41296026699509e-06 2329 1.77733895465016 -1.69142372502352 -1 2.11083653839238 2329 3736 3074 3984 4308 2785 3250 2462 4579 2663 3295 3555 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 0.134113889153098 0.135317989910778 3100 3134.45454545455 3251 0.0142970022535343 589 3.29660719612483 -1.75128721289162 -1 0.826038116865068 3100 3534 4217 2418 4698 3020 1773 4461 589 3251 3418 3556 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 9.59053037020156e-07 1.44301253896562e-06 1895 3400 3251 8.71866777366792e-08 1894 0.910926101101319 -0.870774517157543 -1 1.53550121678456 1894 3903 4109 3232 3024 2914 2712 3251 4293 4583 3485 3557 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 1.57855120949319e-06 2.19462789655607e-06 4195 2647.63636363636 3252 1.43504758376506e-07 208 2.46371576889083 -2.28817967925274 -1 4.0248816207699 4193 2739 1880 208 3307 3549 3671 3252 229 3342 2754 3558 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 2.3115460742573e-06 3.07771437813665e-06 500 2921.45454545455 3253 2.31154847872118e-07 499 1.3654453589241 1.37241780094283 1 2.17238516154368 499 4092 4422 3253 3511 1786 1603 2261 3481 4640 2588 3559 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 1.41084855349641e-06 1.99174945947362e-06 2000 2993.72727272727 3254 1.28259041660642e-07 1690 1.85832023024433 -2.15100980763938 -1 3.05826320597049 1997 3020 2418 3702 3254 2909 3769 3541 3341 1690 3290 3560 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 3.34630487965074e-06 4.28268954228619e-06 640 2263.09090909091 3255 3.04209997231893e-07 206 1.67120638307467 1.83208651820034 1 2.58978998067485 639 3922 3255 3750 3624 599 367 206 4052 3820 660 3561 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 4.98115417029063e-07 8.62474236381943e-07 4510 3182.90909090909 3256 4.98115528682634e-08 47 2.02149290073034 -1.89916813322977 -1 3.53905531695966 4508 2456 4381 2077 2640 4631 4555 3256 47 2926 3535 3562 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 7.33850146129529e-08 3.2144561803028e-07 3730 2888.63636363636 3256 6.67136518734946e-09 752 1.68340479913006 -1.69071323300148 -1 3.15538008677333 3726 1577 2604 2875 752 4086 3795 3970 3256 1292 3842 3563 M17157 REACTOME_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRUVATE_METABOLISM.html Genes involved in Pyruvate metabolism 18/19 Reactome 4.27349445857892e-06 5.34895090015713e-06 2265 3092.09090909091 3258 3.88500250895793e-07 1480 1.61273464912566 1.93811467800023 1 2.45418465975892 2264 3746 3258 3668 3711 3412 4422 1480 3123 2674 2255 3564 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 6.64469075260634e-06 8.0541706092198e-06 4550 2997.36363636364 3258 6.6447106210518e-07 515 1.5721363492054 -0.915290649346106 -1 2.31168699121519 4549 907 4374 3302 3870 3258 1781 4275 515 3067 3073 3565 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 3.16492418017095e-06 4.07931243320778e-06 3260 3199.90909090909 3259 2.8772079393146e-07 2345 2.52896881676583 2.84964519458829 1 3.93489664299108 3259 3696 2345 2938 3600 3168 2863 3709 2905 3367 3349 3566 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 1.42173616580129e-06 2.00435923016192e-06 3920 2962.27272727273 3259 1.29248825871835e-07 536 2.26257525298778 -1.65637074645608 -1 3.72194789886914 3918 2217 1538 1866 3259 3952 4315 4619 536 1657 4708 3567 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 1.42615617988822e-06 2.00999019679678e-06 1335 2988.81818181818 3260 1.29650645854437e-07 1219 1.74677519372966 1.91227323694366 1 2.87264324087972 1334 4706 3657 4672 3260 1567 1219 2416 3563 4419 2064 3568 M161 PID_IFNG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IFNG_PATHWAY.html IFN-gamma pathway 18832364 55/57 Pathway Interaction Database 3.78250963495039e-07 6.99593187605194e-07 3255 3420.81818181818 3261 3.43864571389633e-08 2392 1.20643791537129 1.41020489746545 1 2.14344769311469 3255 3647 3751 2973 2392 3261 2849 4562 3690 4001 3248 3569 M477 BIOCARTA_GABA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GABA_PATHWAY.html Gamma-aminobutyric Acid Receptor Life Cycle 8/14 BioCarta 2.0195847830244e-05 2.29863520035572e-05 2615 3069.63636363636 3263 2.0196031375113e-06 876 1.08204678922499 -1.04623263034012 -1 1.44847723397011 2611 3202 4191 3938 4133 2282 3296 1699 4275 3263 876 3570 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 2.63923655010622e-06 3.46129383620488e-06 1400 2577.72727272727 3264 2.63923968461777e-07 104 2.06722834466515 2.02662772837421 1 3.25889475170064 1400 2468 4225 3645 3567 1019 104 4350 3355 3264 958 3571 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 9.84210268286156e-06 1.16427881361169e-05 2405 2966.45454545455 3264 8.94740610325924e-07 1079 1.20506341063949 1.20512511930125 1 1.71604843565159 2405 2708 3548 2688 3938 1968 1079 3569 3609 3855 3264 3572 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 5.84084085937782e-07 9.78309753593447e-07 3265 3036.27272727273 3264 5.30985673643582e-08 1475 1.79757589239818 -1.94087847484823 -1 3.11853619269381 3264 2332 2037 3605 2681 3616 3926 4131 2934 1475 3398 3573 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 3.16552415078745e-07 6.19260590849501e-07 3290 3189.09090909091 3265 2.87774964206071e-08 2245 1.68616593322246 -1.83258466502017 -1 3.02190317685376 3288 3268 3216 2469 2245 4128 4308 2524 3265 3746 2623 3574 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 4.17156216708126e-06 5.23246702860046e-06 1190 2924.72727272727 3266 3.79233643370078e-07 1190 1.56396644409521 1.46320280845097 1 2.3842638429395 1190 3266 3646 2229 3703 2249 1929 4044 2682 3882 3352 3575 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 1.43431432110211e-06 2.0172716315858e-06 845 2907.63636363636 3267 1.30392296020004e-07 843 1.36154048662662 1.26271684976709 1 2.23830161231733 843 4428 3999 4314 3267 1140 851 2624 3757 4399 2362 3576 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 1.69685570208369e-07 4.32684827206353e-07 1455 2712.81818181818 3267 1.69685583165306e-08 16 3.43824044001177 3.43824044001177 1 6.31740809496276 1451 3804 4444 4379 4440 1733 622 16 4063 3267 1622 3577 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 1.26117491083983e-06 1.81874292061228e-06 4680 3053.72727272727 3268 1.14652330347564e-07 828 2.09089787645874 -1.86919641094317 -1 3.46495431340828 4676 828 1643 3268 3174 4475 4491 4149 876 1430 4581 3578 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 0.000151329330185325 0.000162408921890572 3265 3407.81818181818 3268 1.51339636427887e-05 1525 1.27319714725053 1.26395212037793 1 1.39232247560526 3262 2909 4591 3657 4391 3149 2691 1525 4449 3268 3594 3579 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 2.15397541277417e-07 4.92098932637662e-07 3925 3230.27272727273 3268 1.95815965787779e-08 1875 2.24203933697032 2.27550925924115 1 4.08303533842922 3925 4147 1998 2764 1875 3541 3268 4641 2061 3238 4075 3580 M9670 BIOCARTA_STRESS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STRESS_PATHWAY.html TNF/Stress Related Signaling 32/35 BioCarta 5.47318974310407e-07 9.28703851408851e-07 2300 3152.90909090909 3269 4.97562827702917e-08 2296 1.22596767231599 -1.37250851163794 -1 2.13460452268641 2296 2308 3485 2908 2637 3353 4320 2975 3519 3612 3269 3581 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 9.73357213360625e-08 3.39726302159777e-07 3720 2584.90909090909 3269 8.84870233113968e-09 658 2.48578417747601 2.76340355039619 1 4.64253057385762 3720 816 1744 3562 1070 3269 3560 4612 658 1601 3822 3582 M4629 KEGG_NITROGEN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NITROGEN_METABOLISM.html Nitrogen metabolism 16/23 KEGG 1.27086789543441e-06 1.82874153395809e-06 4090 2957.09090909091 3270 1.15533511779431e-07 1402 2.74393137024953 -2.52350839864683 -1 4.54551833572597 4089 1885 1402 3270 3182 4076 3593 3774 1760 1968 3529 3583 M15303 REACTOME_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOSIS.html Genes involved in Apoptosis 173/213 Reactome 4.66862098432501e-07 8.18873691787962e-07 3700 3164.63636363636 3270 4.24420179550325e-08 1754 1.8589315135711 -1.75068804784646 -1 3.26648112762468 3697 3588 3252 1754 2545 3270 3330 4142 2241 4034 2958 3584 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 1.28352406976251e-07 3.77930979992455e-07 3660 3130.36363636364 3270 1.16684013149626e-08 1358 1.85064997461127 -1.18006017008476 -1 3.43137953100324 3658 3270 2853 2686 1358 4208 3838 2554 2708 3644 3657 3585 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 1.21909067885315e-07 3.70192774369017e-07 4515 3070.81818181818 3271 1.10826431491535e-08 1306 1.93301642755216 -1.61464130704129 -1 3.58915253951609 4513 3271 2146 2849 1306 3703 3390 4415 2653 2231 3302 3586 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 1.23391570601059e-06 1.78488572858412e-06 3580 3390 3272 1.12174218007127e-07 2061 1.74130353863006 1.64850373568123 1 2.88957973018821 3577 3911 3024 2689 3163 3272 2061 4226 3829 3092 4446 3587 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 6.65804036386971e-07 1.0811816251744e-06 4535 3259.36363636364 3273 6.65804235869812e-08 1454 3.31450755359125 -2.79053966257744 -1 5.70936182321574 4532 1954 4184 3273 2831 4362 4439 1824 2852 1454 4148 3588 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 1.94164557461529e-05 2.21526882092922e-05 4035 3177.18181818182 3273 1.76514791921275e-06 209 1.9705820594593 -1.08310475823053 -1 2.64774775883321 4031 3489 2551 2628 4100 4613 3847 3192 209 3273 3016 3589 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 6.35948480646325e-08 3.14536172538656e-07 4540 3015.45454545455 3273 5.78134999117754e-09 593 2.36761441788147 1.95162140583942 1 4.44466701907891 4537 3273 1535 2202 593 4408 4215 3474 1283 3139 4511 3590 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 1.46249764059358e-05 1.69149445322267e-05 2760 3019.45454545455 3274 1.32955214813985e-06 1503 1.25642306413772 -1.37504266899882 -1 1.73037019459612 2756 4053 3360 4169 4039 2263 1503 1514 4229 3274 2054 3591 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 1.45042547606159e-06 2.03452290235407e-06 3965 3067.36363636364 3274 1.31856948391385e-07 1075 2.19149664349229 2.51422268721485 1 3.6008910071696 3963 3594 1075 2650 3274 4537 4008 2941 3077 1298 3324 3592 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 3.3188835664031e-08 2.74345541741202e-07 3865 2904.63636363636 3274 3.01716692406476e-09 89 2.0910157098637 -1.93245585334032 -1 3.96116398687257 3862 2504 1052 2710 89 4326 4208 4360 3274 873 4693 3593 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 2.60325181279176e-05 2.92208051281263e-05 1185 2726.45454545455 3276 2.366620561349e-06 438 1.2124178552048 1.17460625312897 1 1.58661319935752 1185 4056 3333 4575 4170 940 438 1379 4423 3276 2216 3594 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 1.52428339629205e-07 4.1209216255052e-07 3215 3584.54545454545 3276 1.52428350084686e-08 1625 1.35221338658391 1.47984695182683 1 2.49229756741763 3211 4676 4340 4530 1625 3268 2938 3194 3276 4649 3723 3595 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 6.99066840176044e-06 8.44102196375269e-06 2950 3220.18181818182 3277 6.35517328658474e-07 1979 1.99009401071715 1.93167048343394 1 2.91477722468762 2947 3682 2235 1979 3854 3277 2660 3711 3752 2609 4716 3596 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 9.85619666967825e-07 1.47312375810264e-06 4240 3158.81818181818 3277 8.9601828048593e-08 461 1.68731834556348 -1.47497157112485 -1 2.84058966222547 4239 3094 3133 461 3045 3775 3277 4406 907 4102 4308 3597 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 2.11713752710584e-06 2.84535567424247e-06 3195 3185.27272727273 3278 1.92467233136785e-07 1918 1.34819249604771 1.57697728166267 1 2.1581977122112 3192 3426 3281 3180 3438 3059 2439 1918 4031 3796 3278 3598 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 2.42097751276785e-07 5.2719175985577e-07 4235 3329.45454545455 3280 2.20088889016635e-08 1987 1.73853591100174 -1.97721674011514 -1 3.15088016865137 4235 2635 2911 3898 1987 4608 4646 2712 2348 3364 3280 3599 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 1.46933257687565e-06 2.05732713226137e-06 4685 3109.27272727273 3281 1.33575778019284e-07 229 2.25116985437929 1.79286614149291 1 3.69581790196788 4684 2797 1739 3597 3281 4508 4576 229 3849 2028 2914 3600 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 2.09416682655928e-06 2.82171493615752e-06 3260 3298.81818181818 3281 1.90378983635164e-07 2021 1.30534360964482 1.31206919097111 1 2.09094328631344 3260 2645 3703 2021 3427 2991 2059 4570 3281 4136 4194 3601 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 1.51556422858594e-07 4.1135498326197e-07 4625 3005 3281 1.37778575726553e-08 739 2.49880025107472 -2.02832705571118 -1 4.60689129052098 4624 3281 1139 3333 1511 4577 3763 2743 739 2859 4486 3602 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 5.02120865196744e-10 6.75216662030949e-09 3420 2426.90909090909 3282 5.02120865310199e-11 55 2.48722063825534 2.75799260861488 1 5.86739951489731 3418 1034 4495 55 703 3282 4015 3572 1691 176 4255 3603 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 7.07980814096983e-08 3.1722620893472e-07 4175 2980.54545454545 3282 6.43618942618613e-09 726 1.68398693975187 -1.10067501856178 -1 3.15926201665382 4175 1849 2679 3282 726 4223 3304 4605 1730 2397 3816 3604 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 9.62511169290374e-08 3.39286984245748e-07 3285 2596.90909090909 3282 8.75010192182479e-09 365 2.21205784099112 -2.06020736412276 -1 4.13157457482125 3282 1428 718 2332 1055 4198 4058 3976 3376 365 3778 3605 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 1.17495121031315e-07 3.63418722980214e-07 2500 3137.72727272727 3283 1.06813752096693e-08 1278 1.77214749789875 2.08560168921228 1 3.29448987716852 2496 3857 3283 4453 1278 2935 2622 3921 2917 3410 3343 3606 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 7.57846236574448e-07 1.19553283309873e-06 3035 3404 3284 6.88951361485528e-08 2481 1.40658531059448 -1.50290975940574 -1 2.40466479865752 3033 3284 3789 2481 2859 3911 4228 2786 4060 4075 2938 3607 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 4.06111566377753e-08 2.9351990282604e-07 3740 3034 3284 3.69192339885833e-09 192 1.92761786769893 -1.62622372321726 -1 3.63522895344235 3737 2878 2684 4370 192 3492 4488 4229 1112 3284 2908 3608 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 1.48613917404036e-06 2.07824998114193e-06 3940 3142.09090909091 3285 1.35103652541344e-07 1305 1.45995918148604 -1.83437707651251 -1 2.39470656223459 3939 3714 3279 1305 3285 4102 3603 2473 2379 4077 2407 3609 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 7.17982197679172e-07 1.14877151628667e-06 3705 3405.36363636364 3285 6.52711301815226e-08 2225 1.69015703849737 1.96447763288626 1 2.89808290395259 3704 2955 3285 2225 2814 4344 4120 4357 2884 2909 3862 3610 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 8.8407711055893e-08 3.31003670356505e-07 4145 2688.72727272727 3286 8.0370649644169e-09 963 1.76644444533916 -1.49458906753134 -1 3.30458139227878 4143 1443 2078 1051 963 4266 3486 3286 3294 1633 3933 3611 M5872 KEGG_STEROID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_BIOSYNTHESIS.html Steroid biosynthesis 19/21 KEGG 7.11719566430819e-08 3.17725226229176e-07 2155 3122.81818181818 3287 6.47017808595985e-09 728 1.41454962042239 -1.58542749283598 -1 2.65336455378081 2154 4026 3234 4418 728 2299 3287 2841 4441 3529 3394 3612 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 1.33667825197603e-07 3.84702521300418e-07 3750 3113.54545454545 3287 1.21516212108188e-08 1399 1.40160368990232 1.62355814341625 1 2.59545060583526 3303 3287 3749 3749 1399 3389 3231 2613 2888 3038 3603 3613 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 5.17616417657635e-08 3.04252738648075e-07 4025 2800.36363636364 3288 5.1761642971434e-09 282 1.91695975574224 -1.62101973212171 -1 3.60649074188329 4024 958 4430 1381 482 4410 4392 3288 2956 282 4201 3614 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 3.11813923012348e-08 2.69553239732593e-07 3205 2932.54545454545 3288 2.8346720675618e-09 60 1.43594670482382 1.67736068340737 1 2.72312249067034 3201 3668 3288 4221 60 2873 2093 3479 2270 3738 3367 3615 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 4.60762138446623e-07 8.09980370006727e-07 3410 3258.27272727273 3290 4.18874759043132e-08 2354 1.78767461395763 2.02945491935158 1 3.14368488284102 3408 4139 2739 3993 2539 3573 3290 2654 4066 2354 3086 3616 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 1.49973515905457e-06 2.09368528563666e-06 4245 2961.90909090909 3291 1.36339652856518e-07 894 2.76688284851449 -3.04223416764389 -1 4.53659916339418 4242 2339 894 2314 3291 3972 3245 3853 3788 1094 3549 3617 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 3.08230747859254e-05 3.44180063850409e-05 4465 2928.09090909091 3293 2.80213696733929e-06 37 2.10853166841596 -0.843407436398287 -1 2.71664965754635 4464 2425 2334 1423 4195 4555 3412 2259 37 3293 3812 3618 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 3.43258751200689e-08 2.78381667640421e-07 4360 2760 3293 3.1205341505131e-09 99 3.22408277025811 3.30114788650435 1 6.10217743982556 4357 3629 622 2287 99 4232 4279 3293 1884 1163 4515 3619 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 1.48845602899679e-07 4.07166653130138e-07 4535 3135.09090909091 3295 1.35314193609219e-08 1161 1.86019121317534 2.52551474369338 1 3.43169260752493 4531 2823 2600 3359 1495 4125 3295 4516 1161 3308 3273 3620 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 4.46440709981566e-07 7.91585330996616e-07 3650 3062.81818181818 3295 4.05855273251574e-08 1270 1.93927553533127 -1.94036229720289 -1 3.41594007428188 3646 2233 1642 3295 2511 4085 3144 4261 3764 1270 3840 3621 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 8.67463463270853e-07 1.33630141861567e-06 2395 3275.09090909091 3298 7.88603459375683e-08 2393 1.57588403789141 -1.23403754516606 -1 2.67219866614196 3298 3292 3458 3709 2946 2928 2393 4648 2395 3333 3626 3622 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 8.42926084185777e-08 3.27455016694392e-07 4070 3155.09090909091 3298 7.66296469529399e-09 915 1.98384669265907 -2.30616943724159 -1 3.7140749916153 4068 3298 2617 1989 915 4213 4149 2794 2685 3366 4612 3623 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 1.62295523404979e-07 4.23438498236503e-07 3300 3262.63636363636 3300 1.47541395797849e-08 1595 1.60966348386958 -1.41530842124522 -1 2.96149119682574 3300 4527 3317 4066 1595 3267 2520 2611 3886 3977 2823 3624 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 2.32374866560046e-05 2.6252019391178e-05 3395 2835.45454545455 3301 2.1125211004951e-06 326 2.61998897117041 2.50352236870687 1 3.46481316421198 3391 2856 2248 1854 4144 3755 3747 326 1408 3301 4160 3625 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 6.88888152300509e-07 1.11260274499654e-06 3305 3461.09090909091 3302 6.26262152738932e-08 2353 2.9295882596859 -2.5383329629807 -1 5.03569908756922 3302 4569 2353 3732 2789 3988 4502 2836 2911 3838 3252 3626 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 9.21268440811306e-07 1.39819518991298e-06 4255 3219.36363636364 3304 8.37517115091284e-08 546 1.47395512082109 -1.58555342105094 -1 2.49093466030575 4252 546 3138 3411 2995 3674 3590 3009 3018 3304 4476 3627 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 1.09841663182521e-07 3.5351808374987e-07 4170 2778.81818181818 3305 9.9856062424272e-09 1162 1.9307867711696 -1.7483498126824 -1 3.59617153753354 4170 2002 1790 3825 1203 3913 3780 3611 1806 1162 3305 3628 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 6.20316074968014e-07 1.02230861517075e-06 3620 3288.81818181818 3305 5.63923863521412e-08 2471 1.63323682929532 -1.92967718724325 -1 2.82434215019337 3617 3305 3068 2471 2725 4321 3786 2575 2962 3392 3955 3629 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 9.72195308997812e-07 1.4576753044694e-06 3235 3264.54545454545 3306 8.83814307834499e-08 1312 1.32141327576465 -1.08470479944802 -1 2.22615105616448 3233 3462 3549 3683 3035 3306 3224 4200 1312 3917 2989 3630 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 1.57384147860533e-06 2.1887247433757e-06 4575 3179.27272727273 3306 1.43076600409554e-07 351 2.28882961646176 2.46122810488885 1 3.73988854423436 4571 2446 2329 3111 3306 3985 3783 4201 351 3285 3604 3631 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 5.39996579386227e-05 5.91914504111238e-05 2315 3431.09090909091 3307 4.90918031108404e-06 1979 1.56060878960306 1.79172611514317 1 1.90436189194341 2313 4490 3238 4676 4277 2943 1979 2771 4398 3350 3307 3632 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 0.0179955901237365 0.0183137527779293 1990 3144.45454545455 3308 0.00181430015692881 1280 3.20891073880308 -3.20891073880308 -1 1.60888173515399 1987 4342 4249 3308 4636 2855 3630 2512 1280 3864 1926 3633 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 2.52211512009693e-07 5.3772241226543e-07 3885 3164.36363636364 3309 2.2928321902148e-08 2032 1.95269989445976 1.92482872480875 1 3.53428848807458 3884 3309 2181 3380 2032 3583 3282 3646 3141 2815 3555 3634 M11650 BIOCARTA_NOS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NOS1_PATHWAY.html Nitric Oxide Signaling Pathway 21/27 BioCarta 5.61717399329353e-06 6.89725838926781e-06 2705 3004.81818181818 3310 5.10653485041414e-07 878 1.42908336078502 1.48178946851272 1 2.12905275486218 2705 2811 3310 3466 3793 1901 878 4652 4495 3416 1626 3635 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 2.21742847373782e-06 2.96915245277802e-06 3310 3395.18181818182 3310 2.0158460988509e-07 2600 1.51024984744146 1.54386041743903 1 2.40965780462512 3310 3646 3606 2927 3453 3041 2919 3025 2600 4137 4683 3636 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 7.58565276947031e-08 3.24764325922831e-07 4440 2958.18181818182 3310 6.89604821002313e-09 786 1.85096667833234 -1.56328671571765 -1 3.46716014680338 4440 3557 2776 2198 786 3310 3799 3314 1444 3221 3695 3637 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 9.87583594364456e-08 3.40830460958105e-07 4600 3315.36363636364 3310 8.9780330790659e-09 1091 1.95883357790151 -1.77382201837349 -1 3.6574009591094 4598 2964 2189 3310 1091 4038 4464 4409 2260 2498 4648 3638 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 3.38275373966257e-07 6.47469491127629e-07 3970 3195.18181818182 3310 3.07523114527281e-08 1048 1.90640702611057 -1.04332516620953 -1 3.40607615448034 3969 4554 2962 4585 2297 4163 2656 1496 1048 4107 3310 3639 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 8.28226089914746e-08 3.27411388472988e-07 3315 3122 3311 7.529328373588e-09 889 0.914566444946286 -0.838410621601575 -1 1.71176416740486 3311 1816 3799 3742 889 2365 3147 4171 4271 3630 3201 3640 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 2.30719400578974e-06 3.07365388296008e-06 1610 2651.27272727273 3311 2.09745129582208e-07 1167 1.58322468381594 1.75534235602419 1 2.51926544209174 1608 3311 3329 3489 3471 1533 1167 1510 3317 3638 2791 3641 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 3.81787088694715e-05 4.23410493101282e-05 2490 3368.90909090909 3311 3.47085194884556e-06 2482 1.02680851384219 1.01150992656548 1 1.29582835160823 2489 3164 3545 3173 4226 2482 3647 3832 4144 3311 3045 3642 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 6.88919870480757e-07 1.11260274499654e-06 3755 3354.09090909091 3313 6.26290987466307e-08 1425 1.6477463201767 1.89006019191625 1 2.83195105394299 3754 4216 3280 3658 2790 3313 2696 3214 1425 3978 4571 3643 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 1.50027245642351e-05 1.73178918912178e-05 3750 3232.54545454545 3315 1.36389335228142e-06 973 1.58161749733145 -1.30078986289388 -1 2.17378754936244 3747 3897 3033 3221 4048 2790 3315 973 2695 3657 4182 3644 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 9.07453068881946e-08 3.33321282888933e-07 3360 3098.54545454545 3316 8.24957369374958e-09 991 1.96023607366286 2.092834200204 1 3.66549691902823 3358 3275 2051 3316 991 3440 3641 4432 3193 1874 4513 3645 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 6.74963208081174e-08 3.14536172538656e-07 3335 3371.18181818182 3316 6.74963228582063e-09 768 1.54253611734092 -1.50155668833723 -1 2.89546671740114 3332 3225 4518 4521 768 3316 3633 3294 2894 4479 3103 3646 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 1.61395886269427e-06 2.23857943929385e-06 1620 2811.27272727273 3317 1.46723640611293e-07 800 1.16524883886639 -1.14734398174154 -1 1.90027246407763 1619 4582 3688 4232 3317 837 800 1789 4484 4010 1566 3647 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 9.58556378162415e-05 0.000103746528432162 2855 3491.45454545455 3318 8.71452859750203e-06 2737 1.41768509564249 -1.08059101515779 -1 1.63010661856954 2851 3318 3539 3237 4338 3080 3197 3511 2737 4243 4355 3648 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 3.31807445831231e-07 6.39498221446881e-07 4530 3180.54545454545 3319 3.01643178068146e-08 466 1.86350462686923 1.71389286986935 1 3.33230036718398 4526 3319 2872 466 2282 4701 4255 4636 1531 3559 2839 3649 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 2.15788117975541e-05 2.449542849554e-05 2015 3125.18181818182 3319 1.96172940521206e-06 851 2.07949771451749 1.65397486008124 1 2.76792219134973 2014 4583 3319 4589 4123 2473 2070 3635 851 3858 2862 3650 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 1.28441880018172e-06 1.84461839495069e-06 3105 3291.18181818182 3319 1.16765413641851e-07 2068 1.89594389341111 2.00347542947723 1 3.13844496112569 3101 4133 2533 3739 3188 3226 3319 3573 3775 2068 3548 3651 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 2.82215757622881e-07 5.73983092245837e-07 3635 3117 3319 2.5655981256863e-08 2134 1.96280187870772 2.17428608050272 1 3.53651373742953 3634 3310 2134 3650 2143 3550 3581 3345 3248 2373 3319 3652 M504 REACTOME_ANDROGEN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANDROGEN_BIOSYNTHESIS.html Genes involved in Androgen biosynthesis 2/16 Reactome 0.000201726525462128 0.000215320940791778 3395 3453.3 3320 2.24160682000114e-05 734 1.4715934939278 1.4715934939278 1 1.5573702232899 3392 3223 4206 NA 4428 4290 4616 3193 734 3248 3203 3653 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 3.76225797547174e-06 4.74809027920498e-06 1590 3220.27272727273 3321 3.42024037217223e-07 1586 1.49128981724951 1.3735821091643 1 2.29159570730521 1586 4177 3081 3518 3677 2346 2593 3354 4451 3319 3321 3654 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 1.42280731536017e-07 3.98409119822705e-07 3175 3284.90909090909 3322 1.29346127943407e-08 1044 1.99410668658112 1.92468150567427 1 3.68424022556625 3550 4467 3282 3175 1453 3322 3174 3993 1044 4060 4614 3655 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 1.2652552883415e-06 1.82377156662599e-06 3570 3071.90909090909 3325 1.1502327418279e-07 1113 1.69160068152008 -1.44249181197549 -1 2.80250436664625 3566 3683 3229 1113 3175 3688 3657 2488 2075 3792 3325 3656 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 7.83083916625309e-05 8.51060577129049e-05 3280 3231.36363636364 3325 7.11919810608983e-06 647 2.3265138196818 2.52915803831273 1 2.73344838361037 3280 3488 2487 4154 4317 3325 4274 4204 2571 2798 647 3657 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 1.03151405962571e-05 1.21749096309911e-05 3325 3011.54545454545 3325 9.37744451016094e-07 1869 2.4322136353443 2.440033382487 1 3.45079483213925 3325 3440 2118 2189 3955 3074 1869 3507 3566 2742 3342 3658 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 4.51780599298726e-07 7.97756987912453e-07 3815 3524.18181818182 3326 4.10709720067341e-08 2524 1.31652890333197 -1.3719290239683 -1 2.31744315030672 3813 3326 3692 3223 2524 3180 3117 3189 4206 3862 4634 3659 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 7.88244240376943e-05 8.5647164239852e-05 2460 3082.54545454545 3326 7.88272201577049e-06 988 1.94439576175711 -2.34712278091451 -1 2.28280646600279 2459 2477 4703 3326 4326 3379 3374 988 4199 2838 1839 3660 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 0.0548443085337729 0.0555147193393541 3235 3415.90909090909 3327 0.00511465828999291 2338 1.32642406309467 -1.34122596873884 -1 0.480060317947094 3234 4007 3639 3998 4720 2850 2415 2918 4129 3327 2338 3661 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 1.35228698793442e-05 1.57134283186865e-05 3070 3275.45454545455 3327 1.22935936380746e-06 1655 1.89391559334266 2.26577106766987 1 2.62627472715033 3070 4006 3327 1996 4018 3842 3789 2694 1655 4319 3314 3662 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 1.62076973311357e-07 4.23355458787827e-07 4625 3111.18181818182 3327 1.47342713865261e-08 1316 1.72820638492781 -1.55395198474445 -1 3.17969474509368 4625 2112 2236 3343 1592 3904 3327 4601 2675 1316 4492 3663 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 7.9449312900385e-07 1.24337120984687e-06 3925 3211.27272727273 3328 7.22266741747157e-08 1634 1.97661722151205 -1.83903622205885 -1 3.36980122787874 3923 2888 2227 3328 2891 3356 3209 4052 4179 1634 3637 3664 M1 PID_FANCONI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FANCONI_PATHWAY.html Fanconi anemia pathway 18832364 55/62 Pathway Interaction Database 1.67356693774961e-05 1.92102041492659e-05 1375 2807.54545454545 3328 1.52143606264892e-06 652 1.30013580244786 1.13940178226691 1 1.76985525128564 1371 3328 3795 3501 4072 1098 652 2315 4155 3357 3239 3665 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 4.02197719989508e-08 2.9351990282604e-07 4380 2937.54545454545 3328 3.65634297583974e-09 188 2.06815181484014 -1.62567165908396 -1 3.9003199382454 4380 2571 1692 2327 188 4466 4220 3458 3328 1497 4186 3666 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 1.0660880996801e-06 1.57988566106439e-06 4705 3408.45454545455 3330 9.69171469355713e-08 1841 2.30834781461232 -2.18321872100324 -1 3.86615119659671 4704 2679 1841 3330 3075 4522 4096 3854 2141 3026 4225 3667 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 4.49213823409507e-06 5.6003413800657e-06 2135 3058.90909090909 3330 4.08377036957552e-07 1975 1.32656326514218 1.59608278295482 1 2.0109089524242 2135 3330 3536 3778 3728 2101 1975 2595 3543 4350 2577 3668 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 4.53285176811473e-05 4.9965110568663e-05 3155 3319.45454545455 3331 4.12085924100451e-06 1124 1.09581950472864 -1.0491060261805 -1 1.3602246164832 3155 3068 3890 1124 4253 2660 2893 3843 4098 4199 3331 3669 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 4.74640658066007e-07 8.29742187433908e-07 3750 3331.09090909091 3331 4.31491600425221e-08 2444 1.31906506463252 -0.729161527237062 -1 2.31540621560314 3748 3775 3168 3945 2556 3331 2465 4177 2444 3802 3231 3670 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 2.55736024248724e-05 2.87330167687211e-05 2725 3447.72727272727 3332 2.3248999733266e-06 2598 1.51831816221956 1.43356377803627 1 1.99034794105266 2725 4032 3193 4198 4167 3332 2625 2598 4165 3995 2895 3671 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 1.35277526838316e-07 3.87445343857314e-07 1965 3188.81818181818 3334 1.22979577415003e-08 1408 1.64757086227019 1.73602531234708 1 3.04960899131914 1965 4102 3820 3786 1408 3334 3005 2907 2961 4187 3602 3672 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 3.55832042638883e-07 6.70202410716491e-07 4270 3025.63636363636 3334 3.23483727447113e-08 1845 1.93012139456471 -1.35446981588438 -1 3.44010324574959 4270 1845 1973 3348 2342 4105 3507 2372 3334 2033 4153 3673 M12645 ST_GA13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA13_PATHWAY.html G alpha 13 Pathway 47/53 Signaling Transduction KE 1.61310659796197e-06 2.23805500951808e-06 2835 3504.63636363636 3335 1.46646161885616e-07 2330 1.15679056223453 -1.14534955027809 -1 1.88650655552427 2833 3335 3895 2968 3316 3738 4516 2330 4375 4081 3164 3674 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 1.67633383432335e-06 2.3121845990667e-06 2985 3408 3336 1.52394101058244e-07 2724 1.05324074790578 1.16548338737482 1 1.71325520944129 2983 3370 3883 2977 3336 3308 3411 2724 4069 4241 3186 3675 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 1.94091977004569e-07 4.66108261912869e-07 3340 2855.54545454545 3338 1.76447267389154e-08 521 2.18608040776659 -2.18662495886357 -1 3.99598167869602 3338 2554 1100 2655 1763 3512 4109 4430 3581 521 3848 3676 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 0.00363055963786524 0.00372851207369972 1720 3106.45454545455 3340 0.000330596805782788 1481 1.59750174396663 1.81897200557762 1 1.1193927482573 1720 4224 3574 4478 4605 2342 1481 1870 3340 4275 2262 3677 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 1.71245177259563e-06 2.359244707137e-06 2610 3347.54545454545 3340 1.55677555049779e-07 2397 1.30638084511517 1.30816137005195 1 2.12193183937559 2607 3252 3975 4505 3340 2930 2397 2752 3838 3706 3521 3678 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 5.80125362001622e-08 3.09852566478612e-07 3490 3066.45454545455 3343 5.27386706635583e-09 497 1.62030873605978 1.69200278328984 1 3.04454424315091 3486 3343 3142 1753 497 4261 4467 3420 1818 4328 3216 3679 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 3.0432742958785e-06 3.93433434033046e-06 855 2417.72727272727 3344 2.76661682333433e-07 630 1.17233480358293 1.32500569084395 1 1.82892821862381 854 3344 3798 3735 3587 884 630 1390 3643 4029 701 3680 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 9.67188757620194e-07 1.4519320523233e-06 1900 3203.09090909091 3344 8.79262893478965e-08 1705 1.43506399328478 1.37624974238189 1 2.41840006709093 1897 4221 3355 4611 3030 2372 1705 2905 4187 3607 3344 3681 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 3.40148764426854e-06 4.34036812136997e-06 4065 3517 3344 3.09226627584051e-07 2702 1.613925455645 -1.06488923943096 -1 2.49828719515753 4062 3129 2702 3158 3635 4220 3344 2810 4029 3330 4268 3682 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 1.26543472048732e-06 1.82377156662599e-06 3050 3411.09090909091 3345 1.15039586214811e-07 2149 1.82257440693562 2.2288616748799 1 3.01955751177513 3049 4438 3259 3467 3176 3345 3543 3878 2149 3883 3335 3683 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 1.2468223479786e-07 3.73650887775174e-07 1875 3337.54545454545 3345 1.24682241793407e-08 1419 1.53509424239223 1.6527376663762 1 2.84833821223526 1873 4674 4502 4702 1419 2555 2676 3038 3345 4549 3380 3684 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 3.84613970266746e-07 7.08740443876656e-07 4260 3403.63636363636 3346 3.49649125006109e-08 2353 1.50912608920349 1.992515770433 1 2.67898368234763 4258 2353 2858 3940 2401 4470 4458 2734 4037 2585 3346 3685 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 8.87517166232321e-07 1.35788687994054e-06 4660 3229.45454545455 3346 8.87517520691542e-08 891 3.03769537548295 -2.45130546232553 -1 5.14566082625437 4660 891 4701 3260 3038 4367 4044 3346 1314 1382 4521 3686 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 8.01831672037865e-06 9.60082570273648e-06 1655 2942.27272727273 3347 7.28940540436534e-07 1563 1.64474689110256 1.7665179739774 1 2.382261707451 1653 4180 3347 3801 3892 2119 1868 1563 3578 4074 2290 3687 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 4.64511594881923e-07 8.15356908829557e-07 4325 3293.45454545455 3348 4.22283357236081e-08 895 1.99311922263801 1.84088870851989 1 3.50341132036047 4321 3348 2835 2228 2543 4477 3731 4686 895 4200 2964 3688 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 6.42039730683608e-08 3.14536172538656e-07 3350 2886.09090909091 3348 5.83672499473321e-09 609 1.95871963149428 1.99826057024132 1 3.67690967288463 3348 3019 1545 3618 609 3778 3503 4554 3984 869 2920 3689 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 3.67357533943795e-06 4.64735341788987e-06 4530 2678.18181818182 3349 3.33961952146727e-07 181 2.10261708311433 1.72963630208654 1 3.2370016198588 4528 725 1804 181 3668 4003 3349 4291 620 2250 4041 3690 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 2.10806402232079e-07 4.87270430232818e-07 4330 3181.54545454545 3349 1.91642202210711e-08 304 1.69666737141132 1.62822216133569 1 3.09173303822844 4328 304 2408 3349 1855 4677 4426 4419 4012 1981 3238 3691 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 1.62633420010925e-06 2.25254382756131e-06 4135 3442.27272727273 3349 1.47848672942397e-07 2450 2.31060706821236 3.11311208220342 1 3.76715221632367 4131 2754 2556 4216 3321 4714 4239 2450 2615 3349 3520 3692 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 5.20171921977619e-07 8.94104687448785e-07 3680 3195.36363636364 3350 4.7288367724367e-08 1164 1.69417444138554 -1.50752360953707 -1 2.95822249019053 3679 4040 2658 3350 2600 3630 3158 3031 1164 3848 3991 3693 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 6.56937014512005e-08 3.14536172538656e-07 4090 3119.18181818182 3351 5.97215485571503e-09 639 1.44453369414785 -1.39438107383999 -1 2.71145341408629 4088 2129 3614 1117 639 4265 4452 3201 4205 3351 3250 3694 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 9.59506062805715e-06 1.13619383252458e-05 1625 2799.54545454545 3351 8.72282043284146e-07 880 1.56771088911518 -1.41001411987744 -1 2.23752980182717 1622 4536 3351 3497 3936 880 1196 2986 3867 3999 925 3695 M12718 BIOCARTA_P35ALZHEIMERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P35ALZHEIMERS_PATHWAY.html Deregulation of CDK5 in Alzheimers Disease 15/19 BioCarta 1.32296677591927e-05 1.53992680205646e-05 4010 3052.45454545455 3352 1.20270430147961e-06 65 1.82251945679797 -1.69067006053026 -1 2.53185383488908 3820 2829 2428 2601 4010 3352 3289 3401 65 3774 4008 3696 M5467 BIOCARTA_GRANULOCYTES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GRANULOCYTES_PATHWAY.html Adhesion and Diapedesis of Granulocytes 12/21 BioCarta 2.27223461879416e-06 3.03393137219474e-06 3795 2828.90909090909 3355 2.0656699687623e-07 844 3.00668857135219 -3.917433745098 -1 4.78999482636279 3792 844 1072 2743 3463 4669 4121 1809 4001 1249 3355 3697 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 2.49384250775799e-07 5.33829325923706e-07 3865 2880.81818181818 3355 2.26712980950113e-08 1314 2.51334435587509 -1.68468241480233 -1 4.55156433188125 3865 3874 1314 2549 2025 4176 3355 3410 1388 2152 3581 3698 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 8.28343413043169e-08 3.27411388472988e-07 4305 2464 3355 7.53039494756306e-09 66 2.2540986591786 -1.81019167230848 -1 4.22018444625291 4301 66 712 634 890 4040 4196 3355 3600 661 4649 3699 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 1.14317126374464e-07 3.59285478750119e-07 4300 3226.63636363636 3355 1.0392466574059e-08 1250 1.94969183479439 -1.69250092921855 -1 3.62743465662276 4298 2978 2280 3876 1250 3355 3627 4590 3175 1513 4551 3700 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 7.34143039602887e-08 3.2144561803028e-07 3465 2928.27272727273 3356 6.67402785546675e-09 754 1.83105896853368 -1.68835053825067 -1 3.43221914782892 3464 3605 2361 3921 754 2476 3356 3563 3815 1923 2973 3701 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 5.84616818431984e-07 9.7885469421744e-07 3005 3454.18181818182 3358 5.31469976168312e-08 2395 1.86602521841892 1.69220166784857 1 3.23718843205024 3002 3358 2395 4202 2682 3659 3123 4260 3640 3155 4520 3702 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 1.39731800602469e-05 1.62047690133576e-05 1525 3196.54545454545 3358 1.27029716462977e-06 1523 1.35613915327196 1.24051960234923 1 1.87506418866036 1523 3892 3917 2978 4030 2204 2759 3358 2489 4494 3518 3703 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 2.35582141362488e-11 3.8343024387274e-10 3405 2731.63636363636 3360 2.14165583059102e-12 229 2.8475776593582 2.89500773948522 1 7.74197240402864 3402 2059 229 2704 1527 3858 3719 4239 3360 561 4390 3704 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 3.3729751358397e-05 3.75216654281485e-05 3975 3336.54545454545 3361 3.0663880458273e-06 404 1.52362077092631 -1.13273263838371 -1 1.94630949664335 3973 3197 2787 4176 4320 3726 3361 404 4485 3117 3156 3705 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 9.5023708377637e-08 3.37734867125336e-07 3080 3207.90909090909 3362 8.63851931654165e-09 1043 1.69322613842745 2.14889334903148 1 3.16329744343551 3080 3375 2511 4161 1043 3875 4634 3895 2381 3362 2970 3706 M9494 BIOCARTA_BCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCR_PATHWAY.html BCR Signaling Pathway 47/57 BioCarta 3.25698833525785e-07 6.31074915534362e-07 3490 2912.36363636364 3363 2.96089892494413e-08 217 1.50717621318516 -1.59111077958794 -1 2.69745893132396 3490 2246 3363 217 2271 2827 3910 4483 3467 3609 2153 3707 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 1.00879008251294e-06 1.50537122651314e-06 3025 3388.90909090909 3363 9.17082313713451e-08 1815 1.56633523923732 1.62198452046364 1 2.63260000186998 3025 3909 2657 4239 3052 3894 3363 2887 4262 1815 4175 3708 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 0.00430208382268837 0.00441431209632372 2600 3682.36363636364 3363 0.000391865419965112 2596 0.921678506569757 -0.995229538204716 -1 0.625953226833182 2596 4513 4129 3006 4580 2917 2825 3363 4647 4639 3291 3709 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 3.89611203779873e-07 7.14984191427816e-07 3990 3297.45454545455 3364 3.54192066162251e-08 1031 1.51251401854787 1.45941948286125 1 2.68333611378752 3990 3364 3160 3617 2411 4526 4448 1031 2821 3606 3298 3710 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 0.000126950069604827 0.000136586352526734 2045 3257.63636363636 3366 1.15415814360699e-05 1661 1.82579017420814 1.42800912984603 1 2.0366406334345 2042 4550 3385 3205 4369 2389 1661 3876 3366 3940 3051 3711 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 4.97141988492407e-06 6.16367267056517e-06 3370 3107.18181818182 3366 4.51948283550695e-07 2049 2.47054062504136 2.7990651737109 1 3.716087117742 3366 3485 2082 3563 3754 2749 2467 2889 3993 2049 3782 3712 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 0.000761289509713192 0.000794096460960501 3220 3645.90909090909 3366 7.6155043830162e-05 2656 1.01835148774245 -1.30496559523845 -1 0.910772839473496 3217 3222 4635 3366 4516 3528 4280 3029 4384 2656 3272 3713 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 3.40849382572691e-07 6.50286615094221e-07 2475 3269.90909090909 3367 3.09863123073656e-08 2306 1.41933740765912 1.52718409936294 1 2.53486190067607 2475 3576 3971 4068 2306 3367 3211 2339 3887 4108 2661 3714 M5109 KEGG_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRIMIDINE_METABOLISM.html Pyrimidine metabolism 93/106 KEGG 4.80656825988207e-07 8.37777037911497e-07 1930 3090 3368 4.36960846365748e-08 1930 1.32800785296001 1.54106886229066 1 2.32950470268316 1930 2141 3689 4576 2563 3443 4245 2295 2172 3568 3368 3715 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 2.42565394006886e-05 2.73443673205756e-05 3230 3291.27272727273 3368 2.20516425910334e-06 1019 1.71592784315879 1.61663737058478 1 2.26016441128394 3226 4525 3423 4010 4152 2534 1019 3282 4259 3368 2406 3716 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 4.69869042317657e-07 8.23230096414009e-07 4315 3086.36363636364 3369 4.27153766064392e-08 824 1.73814433713987 -1.38778860439092 -1 3.0530235300001 4313 824 2602 4358 2550 4505 3790 3369 1485 2440 3714 3717 M18448 REACTOME_GLUCOSE_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_TRANSPORT.html Genes involved in Glucose transport 35/44 Reactome 1.82676161715359e-06 2.50067135526826e-06 1310 2954.09090909091 3369 1.66069375818173e-07 941 1.07202052633521 1.03893323290148 1 1.73328307223797 1309 4231 3768 4261 3369 1632 941 2285 3888 4486 2325 3718 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 7.40723086926477e-06 8.91436249437269e-06 4475 2911.54545454545 3370 7.40725555956171e-07 17 4.07196706034182 -6.62528644647984 -1 5.93701722088312 4475 1947 4253 703 3901 4702 4450 2039 17 2170 3370 3719 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 1.14374592794496e-06 1.6755061390131e-06 3475 3365.81818181818 3372 1.03976956596471e-07 2011 1.57865083172525 -1.65492390625927 -1 2.63210757106 3474 2598 3152 2011 3117 4178 4607 3319 3372 3815 3381 3720 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 5.15652089971025e-06 6.3730763672774e-06 3375 3311.90909090909 3372 5.15653286511783e-07 1764 2.58409940653747 3.23998285870527 1 3.87611026116929 3372 2927 4540 3865 3797 3275 4031 4465 1835 2560 1764 3721 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 9.27065745520688e-06 1.09971106279408e-05 4690 3234.18181818182 3373 8.42790592853381e-07 831 2.01917959789373 -1.48075754233811 -1 2.89040501051222 4689 831 2598 2133 3929 4503 3373 3815 2309 3299 4097 3722 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 1.18153942498399e-06 1.72019311718829e-06 2215 3308.90909090909 3374 1.07412732686002e-07 2214 1.7898053296616 1.69745144651429 1 2.97837575603221 2214 3374 2669 3706 3138 3093 2348 4393 3848 3525 4090 3723 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 0.000995992679410144 0.00103434223252275 1360 3011 3374 9.05858068313825e-05 1200 1.36095285976602 1.50953309164043 1 1.17235934087372 1358 4518 3384 4667 4693 1674 1200 1385 4447 3374 2421 3724 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 2.2938165444067e-06 3.05928626436835e-06 3515 3384.63636363636 3374 2.08528994185816e-07 2309 2.17039322520895 -1.10395612384436 -1 3.45517697895154 3514 3100 2309 3374 3467 2998 3396 4449 2953 3262 4409 3725 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 6.7660290589545e-07 1.09657399995267e-06 3645 3349.63636363636 3375 6.15093739984165e-08 2381 1.98538286320145 -1.42001996233611 -1 3.4160303027899 3642 4203 2890 3971 2779 4331 3077 2381 2632 3375 3565 3726 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 6.10773695763539e-07 1.01062394949589e-06 4150 3496.09090909091 3376 5.55248968481173e-08 2687 1.64254892223718 -1.52985877501442 -1 2.84281834084303 4146 3312 2905 2687 2714 4143 4535 3310 3621 3376 3708 3727 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 5.87680028867725e-06 7.19359371435597e-06 4540 3040.18181818182 3376 5.34255998843006e-07 1207 3.08651814947768 3.31465175943469 1 4.58302002964901 4540 2808 1207 2361 3802 3376 2657 4160 3432 1413 3686 3728 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 4.29695610104334e-06 5.37516935233637e-06 1975 2783.72727272727 3377 3.90633135792462e-07 964 1.43105149887249 -1.70173305500903 -1 2.17673312563273 1971 3656 3486 1544 3713 2376 3781 964 3377 3734 2019 3729 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 6.53816917853912e-07 1.06708708584733e-06 3760 3250.81818181818 3378 5.9437919287411e-08 1529 1.49447293994591 -1.37059042367435 -1 2.57627125370769 3760 3322 3378 1529 2756 3005 3777 3791 2327 3873 4241 3730 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 2.22492959062979e-07 5.02231834900651e-07 3380 3335 3378 2.02266346876726e-08 1903 1.55921396586316 1.58717396377641 1 2.83527673389438 3378 2735 2936 3930 1903 3453 2942 4147 4017 2684 4560 3731 M9642 GALLUZZI_PERMEABILIZE_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/GALLUZZI_PERMEABILIZE_MITOCHONDRIA.html Proteins that permeabilize mitochondria. 16892093 53/69 Arthur Liberzon 5.12102491270836e-07 8.82398820572726e-07 4580 3262.45454545455 3379 4.65547827704498e-08 2190 1.99588984184632 -2.05312647495201 -1 3.48850417119354 4578 2652 2237 2190 2595 4441 4350 3379 2397 3619 3449 3732 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 8.02206217487317e-08 3.27261309121878e-07 2430 3058.09090909091 3380 7.29278406126276e-09 846 1.86107860898836 2.23255484421098 1 3.48431851351562 2430 3835 3260 2683 846 3380 3446 3514 2624 4099 3522 3733 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 9.69088822029183e-05 0.00010476635913829 1495 2770.27272727273 3381 8.81028647756477e-06 836 1.76825654520136 1.78697154801235 1 2.03125038486829 1492 4169 3702 3513 4343 836 1173 3381 2181 4405 1278 3734 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 1.89992146179604e-06 2.59180037562929e-06 4285 3395.18181818182 3381 1.72720282051951e-07 2143 1.20309617832097 -1.20352094188309 -1 1.93991594376715 2964 3935 3844 3510 3381 2581 3348 3075 4285 4281 2143 3735 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 7.77208779159612e-08 3.26053563650771e-07 4470 2600.36363636364 3381 7.06553460560534e-09 82 2.31267926044503 -2.39887883669337 -1 4.3310883162822 4470 82 686 2091 811 4248 3688 4665 3381 461 4021 3736 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 2.45197949907231e-06 3.24911376631704e-06 670 2641.72727272727 3382 2.22907475626939e-07 668 1.44445380757327 1.65598114148671 1 2.28831794570807 668 3889 3600 3790 3491 1135 1004 1743 3382 4369 1988 3737 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 4.30594967020081e-07 7.69851607702568e-07 3810 3485.63636363636 3382 3.91450046634816e-08 2435 1.70433011985422 1.89625944175751 1 3.00794117786883 3809 3313 2913 4561 2488 3382 2435 4012 3657 3082 4690 3738 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 2.66586325319861e-07 5.55333206160829e-07 4250 3328 3383 2.42351234203296e-08 1480 1.55184734120987 -1.50354901671262 -1 2.80231709822674 4249 1480 3379 3122 2085 4697 3919 3383 1794 3785 4715 3739 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 2.91816362720246e-06 3.78785652887435e-06 3885 3162.90909090909 3384 2.65287954361164e-07 1828 1.60685109163519 -1.31549300862469 -1 2.51477040989464 3885 2881 2870 3384 3569 3000 1976 4270 3710 1828 3419 3740 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 2.33685497663476e-07 5.17595283421683e-07 2110 2875.45454545455 3384 2.12441384077921e-08 692 1.0980127824415 -0.978344684495666 -1 1.99222396160181 2108 3872 4094 3540 1950 979 2151 3384 4427 4433 692 3741 M13088 KEGG_PPAR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PPAR_SIGNALING_PATHWAY.html PPAR signaling pathway 52/91 KEGG 4.3427748401324e-08 2.97164560412799e-07 3385 2905.90909090909 3385 3.9479772053257e-09 246 1.90384475756104 -1.42721247015245 -1 3.58743900226747 3385 2634 1915 3570 246 3400 4012 4138 3245 1781 3639 3742 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 4.07909066486673e-05 4.5110843341544e-05 3370 3250.27272727273 3386 4.07916554221407e-06 1420 1.18421595316204 1.33820508553454 1 1.48519747784604 3369 3216 4331 2895 4250 3667 3652 1420 3386 3469 2098 3743 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 8.85370513532534e-32 9.497610963349e-30 4465 2569 3388 8.8537051353253e-33 23 2.35554640688362 -2.25188475137132 -1 19.7400961925606 4461 967 4324 23 167 4439 4546 4629 1288 27 3388 3744 M1061 REACTOME_MEIOTIC_SYNAPSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_SYNAPSIS.html Genes involved in Meiotic Synapsis 47/198 Reactome 2.05493706797316e-06 2.77374406902067e-06 3035 3208.72727272727 3389 1.86812635219538e-07 1634 1.426501523293 1.02664218103459 1 2.28816553698378 3035 3672 3153 3773 3419 2217 1634 3014 4296 3389 3694 3745 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 2.05298963734687e-06 2.77312613676111e-06 3955 3373.54545454545 3391 1.86635595741118e-07 1615 1.6661382571211 1.71195358380888 1 2.67274369673502 3951 3333 2861 2226 3417 4641 4716 2434 1615 3391 4524 3746 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 1.11406672545955e-07 3.552969556871e-07 2955 3301.72727272727 3392 1.01278798352293e-08 1221 0.729515554791671 -0.72188494189683 -1 1.35775830141065 2951 3459 3823 4601 1221 3029 3392 2785 3675 4340 3043 3747 M2842 BIOCARTA_FIBRINOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FIBRINOLYSIS_PATHWAY.html Fibrinolysis Pathway 10/15 BioCarta 3.40181903128068e-07 6.49538261636117e-07 4010 2926.81818181818 3393 3.09256323390703e-08 866 3.42170473423826 -3.98915927037879 -1 6.11269379167113 4006 1916 866 1336 2304 4504 4622 3494 4119 1635 3393 3748 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 2.56256875938456e-06 3.37575343128527e-06 3825 2876.36363636364 3393 2.32961067661793e-07 881 2.91716345346691 -3.52106073193286 -1 4.60828897211597 3823 881 1337 3832 3512 3607 2388 2757 3393 1637 4473 3749 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 3.04356756024512e-07 6.04363454990223e-07 3885 3141.54545454545 3393 2.76687998300404e-08 1749 1.50242955137594 -1.28564194799359 -1 2.69710975708704 3882 3445 3393 1749 2207 3722 3367 2113 3348 3891 3440 3750 M16024 KEGG_ALZHEIMERS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALZHEIMERS_DISEASE.html Alzheimer's disease 163/213 KEGG 5.87154456137553e-06 7.1890247288437e-06 2190 3296.18181818182 3395 5.33778202900434e-07 2188 1.66107401661233 -1.25394227033073 -1 2.46618223376313 2188 3596 3996 3236 3801 2719 2197 3395 2723 4455 3952 3751 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 3.19340435874978e-07 6.23103289512152e-07 3935 3372.54545454545 3395 2.90309529298879e-08 2252 1.4957263639988 -1.36227588786091 -1 2.67934462743064 3933 3641 3509 2948 2252 4571 3960 2804 3395 3093 2992 3752 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 1.4561946656609e-06 2.04014212582946e-06 3400 3547.72727272727 3396 1.32381420866069e-07 2692 1.67429028092028 2.00551488344792 1 2.75027671090473 3396 4117 3380 4299 3278 3747 3046 2692 4009 3056 4005 3753 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 2.4674349016527e-07 5.32037128177284e-07 4420 3090.72727272727 3397 2.24312288944609e-08 1113 3.70236881864713 -3.39813811784273 -1 6.70680814261842 4417 1924 1113 2274 2009 4593 4538 3813 3397 1636 4284 3754 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 0.000229099001365971 0.000243437029817061 2265 3111.18181818182 3397 2.08293511161504e-05 873 1.72123614712361 2.27173597011247 1 1.79521828325944 2263 4575 3397 4279 4598 2360 2383 873 3830 4347 1318 3755 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 1.01429829920127e-07 3.43435292125537e-07 3590 3226.09090909091 3398 9.22089405422688e-09 1118 1.71019347050582 1.53639686072969 1 3.19141481374717 3589 3324 2743 3582 1118 3167 3599 3661 3398 2825 4481 3756 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 0.0057012349038734 0.00582968560361405 1790 3129.72727272727 3400 0.000519642119248352 1011 1.28400666949951 1.61169172207114 1 0.827582129447904 1789 4307 3400 3975 4594 2036 1011 2960 4381 3894 2080 3757 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 5.89373255616798e-08 3.10127287236487e-07 3795 3205.90909090909 3400 5.35793883096299e-09 514 2.05629557760538 1.56451396178419 1 3.8637624722969 3791 2867 1930 3361 514 4023 3400 4670 3616 2699 4394 3758 M814 REACTOME_PURINE_SALVAGE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_SALVAGE.html Genes involved in Purine salvage 15/15 Reactome 4.72983655458028e-07 8.2776524054946e-07 2905 3368.63636363636 3401 4.29985233769118e-08 2553 1.35028742736863 1.208931840877 1 2.37063637732943 2901 4043 3352 4207 2553 2910 2778 3689 3662 3401 3559 3759 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 1.97861368429818e-06 2.68363695111708e-06 3870 3120.54545454545 3401 1.79874133073266e-07 1413 2.93232415456856 -1.70274149656121 -1 4.71661914671099 3867 3749 1539 4536 3401 4009 2038 1413 4498 2943 2333 3760 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 1.21242428890738e-05 1.41930621122094e-05 3960 2844.90909090909 3402 1.10220997332075e-06 411 2.64887023247343 -1.52628779805634 -1 3.70731107698762 3956 3753 2084 2142 3989 3606 2806 857 411 3402 4288 3761 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 2.56683662740466e-07 5.43294568670404e-07 2430 3116.90909090909 3402 2.33348811535347e-08 2049 1.49249712514315 1.62756551200639 1 2.6992120610016 2427 3017 3402 3426 2049 2901 2877 3605 3408 3502 3672 3762 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 0.000179363906918634 0.000191841749525482 4090 3313.18181818182 3402 1.79378385698407e-05 1538 1.46322886694321 1.94083254230714 1 1.56970003208275 4090 3515 4579 3402 4402 3354 1538 1935 2650 2932 4048 3763 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 1.77910298878507e-07 4.44070127290615e-07 4235 3179 3404 1.61736648423468e-08 1683 1.99272747314739 -1.41839360685868 -1 3.65457593811523 4233 3034 2310 2941 1683 3404 3664 3526 2069 3635 4470 3764 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 1.99966473171533e-06 2.70907506707703e-06 2025 3487.18181818182 3405 1.81787868117267e-07 2023 1.37978873536183 1.2615471581569 1 2.21729024164335 2023 4375 4046 4697 3405 2604 2250 3257 3361 4436 3905 3765 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 3.1721406127227e-07 6.19797131312732e-07 3285 3521.63636363636 3405 2.88376460918915e-08 2248 1.63766079943533 1.76359364363036 1 2.93477088160463 3281 4144 2996 4599 2248 3260 3405 4480 3731 3042 3552 3766 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 1.34888498999471e-05 1.56816186028941e-05 3820 3362.72727272727 3407 1.22626660043459e-06 1824 2.25711468659298 2.57604995194025 1 3.13065823167619 3819 3131 2721 3412 4015 3407 1824 3863 3062 3233 4503 3767 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 4.3784594633643e-08 2.9759369480041e-07 3410 3220.90909090909 3407 3.98041777318616e-09 253 2.06946274793895 2.4267158712481 1 3.89921551119978 3407 4373 2234 4349 253 3035 3663 4690 2281 3381 3764 3768 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 1.5606125763099e-05 1.79792320238778e-05 3200 3454.90909090909 3409 1.56062353622048e-06 1784 1.39663896998311 -1.55594374750078 -1 1.91288672070486 3200 2924 4411 3409 4076 2564 3178 4083 4394 3981 1784 3769 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 5.61148371658609e-07 9.45935826510226e-07 3350 3312.36363636364 3409 5.10135013444854e-08 1737 1.70731238543071 1.63521479765324 1 2.96910392119544 3347 3948 3409 3745 2658 2985 1737 2713 3490 4095 4309 3770 M4835 BIOCARTA_BCELLSURVIVAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCELLSURVIVAL_PATHWAY.html B Cell Survival Pathway 26/27 BioCarta 4.48995919725107e-07 7.94028003410456e-07 4035 3002.63636363636 3410 4.08178192145715e-08 396 2.71799665420894 -3.8899066988208 -1 4.78691532695209 4032 3410 2223 1510 2518 3746 4475 4129 396 3629 2961 3771 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 1.9035922854793e-06 2.59530779533861e-06 3410 3170.90909090909 3410 1.90359391612987e-07 921 2.52547873227483 2.36568317570918 1 4.07269197738722 3410 2912 4223 2618 3426 2927 1908 4248 4454 921 3833 3772 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 1.18018201350396e-06 1.71874702367747e-06 2955 3281.36363636364 3413 1.0728933150989e-07 2017 1.7530650763983 -1.91649061771984 -1 2.9174043223463 2955 3879 3337 2017 3137 3413 3730 3433 3560 3655 2979 3773 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 2.53289596638354e-06 3.34039367458237e-06 4130 3096 3415 2.30263534777525e-07 1831 2.57420987220176 1.82099919290087 1 4.06981788836298 4129 3415 2230 1919 3507 4343 4278 1831 2166 3786 2452 3774 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 0.000145689220801472 0.000156391431017272 2340 3175.63636363636 3416 1.32453517801791e-05 2018 1.58633649091196 -1.71181789040205 -1 1.74248326819554 2338 3416 3420 2018 4380 2658 3462 2340 4034 3707 3159 3775 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 1.16664917240838e-07 3.61561660785788e-07 3420 3328.54545454545 3416 1.06059021297747e-08 1273 1.37333086387802 1.76710539873165 1 2.55376302131153 3416 4132 3908 4651 1273 2832 2898 3118 2717 4192 3477 3776 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 3.97895742262027e-07 7.24563234366038e-07 4655 3679 3417 3.61723467478314e-08 2430 1.46281012500682 1.43867544950695 1 2.59268717237529 4655 3007 3349 2913 2430 4589 4652 4043 3417 2977 4437 3777 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 8.60766815286828e-07 1.32771874776269e-06 2960 3434.36363636364 3417 7.82515592789643e-08 2018 1.66942480908877 1.70278625076734 1 2.83221421938882 2960 4365 3417 4053 2943 2771 2018 3683 3238 4157 4173 3778 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 2.2950065302347e-07 5.11204852416602e-07 2520 3337.63636363636 3419 2.08636979058757e-08 1934 1.33234654176902 1.42678626221994 1 2.41965650106971 2517 4111 4063 4684 1934 2816 2512 3004 3419 4180 3474 3779 M287 BIOCARTA_ERK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK_PATHWAY.html Erk1/Erk2 Mapk Signaling pathway 49/54 BioCarta 1.03235586039469e-07 3.47059804919012e-07 3420 3160.90909090909 3420 9.38505371671148e-09 657 1.46375610009764 1.50753483141924 1 2.7294834707948 3420 3332 3440 657 1130 3906 3254 4169 2921 4247 4294 3780 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 1.92926163348486e-06 2.62651136719024e-06 2530 3449.81818181818 3420 1.75387575029823e-07 2063 1.18635032326929 1.17973884531113 1 1.91092301924911 2526 4590 3473 4450 3387 2864 2063 2762 4569 3420 3844 3781 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 6.37522733383108e-08 3.14536172538656e-07 2675 3019.09090909091 3421 5.79566138052215e-09 597 1.00848939367445 -0.975162803859741 -1 1.89271904500192 2672 3734 3683 4602 597 1724 2445 3421 3754 3950 2628 3782 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 4.9858768734904e-07 8.62788801115111e-07 3975 3470.09090909091 3422 4.53261636676715e-08 2167 1.65482225430958 -1.81730083176094 -1 2.89688808348075 3971 4532 3565 4035 2580 3218 3422 3120 3308 4253 2167 3783 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 2.8030539774754e-06 3.64876303741972e-06 3980 2612.63636363636 3422 2.54823413536012e-07 57 2.72906564783045 -2.91766560819435 -1 4.2844758065334 3977 866 1595 1178 3556 4073 4116 4259 57 1640 3422 3784 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 4.42101408353377e-08 2.97677410474742e-07 3675 2383.45454545455 3422 4.42101417148792e-09 74 3.54047200529974 2.87878168344249 1 6.67133145757988 3673 883 4395 334 329 3650 4039 3422 74 923 4496 3785 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 2.08436213821493e-06 2.80930590873057e-06 4660 3316.81818181818 3425 1.89487646638187e-07 254 1.76283823005451 -1.92298079478163 -1 2.82504979269935 4658 3757 2901 3398 3425 3955 3205 2987 254 4045 3900 3786 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 1.988933693197e-07 4.72935366845837e-07 4450 3095.27272727273 3425 1.8081217027352e-08 258 1.43206003596649 1.21296101584723 1 2.61478370459804 4450 258 3466 3378 1785 4565 4142 2278 2433 3425 3868 3787 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 2.35894216217915e-07 5.20853420399124e-07 3630 3306 3426 2.14449310465084e-08 1957 1.67051486648116 1.70344988776939 1 3.03010079672136 2795 4380 3426 4025 1957 2817 2732 3555 3423 3628 3628 3788 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 1.0638380011388e-06 1.5770462830952e-06 3445 3357 3426 9.67125923246865e-08 2241 2.18040379996126 -1.8939573187381 -1 3.65230747250787 3444 3418 2241 3341 3074 3850 3484 4358 3426 2782 3509 3789 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 3.35564688242349e-06 4.28883110886512e-06 2705 3445.90909090909 3427 3.05059272798419e-07 2553 1.24814892207595 1.37301208968104 1 1.93375536994762 2701 4261 3309 4046 3629 2656 2553 3134 4616 3427 3573 3790 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 1.54630721707464e-07 4.15163257371575e-07 2820 2887.27272727273 3429 1.40573393250861e-08 682 1.61066149402809 -1.57804978252435 -1 2.96731447470005 2819 4101 3800 4060 1533 839 3788 3429 3208 3501 682 3791 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 8.81757431954813e-07 1.35170350075567e-06 2035 3295 3429 8.01597986693054e-08 2031 1.58902023948492 1.79069524066638 1 2.69219695858784 2031 4141 3463 3796 2964 3429 3820 2232 3351 3671 3347 3792 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 3.25142981714064e-08 2.73247281118852e-07 4600 3391.90909090909 3430 3.25142986471371e-09 118 1.30603339286272 -0.843202142637049 -1 2.47444821865021 4596 3207 4232 3430 118 3634 3125 2777 4711 3063 4418 3793 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 2.94705597696255e-07 5.91919328138861e-07 2540 3384 3431 2.67914215612878e-08 2180 1.67074678403005 1.90907370795876 1 3.00372282571649 2537 4366 3431 4493 2180 2880 2352 2978 3910 3934 4163 3794 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 1.69719737279467e-07 4.32684827206353e-07 3700 3281.36363636364 3433 1.54290682156868e-08 1639 1.84321968159415 1.94160111937746 1 3.38632428724325 3699 3635 2552 4397 1639 3433 2754 4545 3825 2858 2758 3795 M13465 KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS.html Terpenoid backbone biosynthesis 15/17 KEGG 6.44670849393349e-06 7.83471789687667e-06 2525 3417.36363636364 3434 5.86066125903908e-07 2057 1.40843492851627 0.719083007601539 1 2.0757683275463 2525 4293 3401 4442 3826 2709 2057 3434 2690 4413 3801 3796 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 7.37844794599201e-07 1.1714185773657e-06 4285 3512.27272727273 3434 6.70768220055141e-08 2498 1.62850318932759 -1.82002907327318 -1 2.78834768039528 4284 3580 3053 2498 2840 4449 4185 4717 3434 2910 2685 3797 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 6.57267819832895e-08 3.14536172538656e-07 3435 3267.45454545455 3435 5.97516217699367e-09 640 1.80129240473198 2.31860784978419 1 3.38131796112507 3435 4520 3174 2026 640 4157 4197 3076 3499 3853 3365 3798 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 0.00193527310526226 0.0020001070849218 2440 3436 3435 0.00017608887324486 2438 1.84833573988934 1.90793666947607 1 1.43965644032155 2438 4244 2745 3910 4554 3435 2911 3188 3893 2719 3759 3799 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 1.1468985910298e-05 1.34561200792369e-05 2020 2910.63636363636 3436 1.04264051823361e-06 309 1.39982687518225 -0.794815477364843 -1 1.96812655794581 2019 3996 3436 3151 3979 1504 1507 3962 309 4244 3910 3800 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 2.43613945611048e-06 3.22993770585434e-06 3440 3283.63636363636 3436 2.43614212676355e-07 1560 2.73568922667386 3.36051373159482 1 4.33670660282501 3436 3520 4700 2328 3535 3008 2888 3787 1560 2713 4645 3801 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 0.000164081912027731 0.000175855273562872 4545 3522.90909090909 3437 1.4917650088693e-05 1970 2.2572084401232 -2.34707082408065 -1 2.4465506160527 4545 3142 1970 3319 4388 3437 2640 4161 4487 2536 4127 3802 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 3.14400240710702e-06 4.05677729949294e-06 4490 3316.90909090909 3438 2.85818809107701e-07 1773 2.5492106997663 1.60326903651274 1 3.96816943659393 4490 3438 1773 2411 3596 3938 4133 2796 4116 2973 2822 3803 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 0.0003140519187963 0.000331542173276344 3200 3466.27272727273 3439 2.85542508130211e-05 2234 1.35013315201853 1.24301601772185 1 1.35567692165178 3198 3778 2860 2234 4450 3439 3193 3447 4622 2880 4028 3804 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 2.30192345975566e-06 3.06749822982686e-06 2030 2728.54545454545 3439 2.09265988029828e-07 943 1.39798850034219 1.28809688873676 1 2.22476383659072 2029 4185 3439 3500 3470 1434 943 2534 3537 3624 1319 3805 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 1.02892663586318e-07 3.46153508287541e-07 3695 3224.45454545455 3440 9.35387894532228e-09 1128 1.64011826213064 -1.40259798270596 -1 3.05898969647687 3691 4367 3773 3440 1128 2793 2680 4118 2283 4019 3177 3806 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 0.000353374078990625 0.000372304833222266 3175 3176.36363636364 3440 3.53430284527899e-05 50 2.28045601440193 2.68934991064969 1 2.25725057329547 3174 3803 4676 2163 4463 4051 4541 2402 50 3440 2177 3807 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 0.00319183853318736 0.00327938134014896 3435 3366.27272727273 3441 0.000319643234724358 1859 2.95064319540827 3.75637713291306 1 2.11578407309971 3434 3511 4694 3126 4599 4349 3591 1859 1862 3441 2563 3808 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 7.02886763974446e-06 8.48497576971709e-06 2055 3168.81818181818 3444 6.38990008786739e-07 1689 1.19341285786872 1.40793148082175 1 1.74680165240748 2054 4274 3444 4468 3855 1689 1736 2115 4619 4066 2537 3809 M2064 BIOCARTA_41BB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_41BB_PATHWAY.html The 4-1BB-dependent immune response 19/25 BioCarta 0.000156898266535781 0.000168270806191522 3535 3280.18181818182 3446 1.42644961116907e-05 1699 1.15843883511432 -1.32207375780613 -1 1.26159811859048 1699 3446 3533 2933 4385 2684 3621 3392 3948 3531 2910 3810 M14631 KEGG_COLORECTAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_COLORECTAL_CANCER.html Colorectal cancer 72/82 KEGG 2.38120949989648e-07 5.22548577520102e-07 3845 3183.18181818182 3447 2.16473614330091e-08 906 1.55191540655827 1.87378048270236 1 2.81428297107019 3843 3907 3447 906 1971 4275 4318 2565 2464 4149 3170 3811 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 5.92285675538885e-05 6.47876799198966e-05 2060 2981.63636363636 3447 5.38456019727254e-06 678 1.07222917593737 1.29170267703948 1 1.29599052662329 2059 3756 3629 3447 4287 1948 678 2602 4079 4112 2201 3812 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 3.46677744657463e-06 4.41532367723482e-06 955 2941.27272727273 3447 3.15162082687461e-07 954 1.37629268827816 1.6137444849305 1 2.12735983223945 954 3923 3595 4664 3641 2039 1726 1657 3447 4183 2525 3813 M11932 REACTOME_TIE2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TIE2_SIGNALING.html Genes involved in Tie2 Signaling 21/24 Reactome 5.43833602539543e-06 6.69333664664053e-06 4550 3317.45454545455 3448 4.94395406259134e-07 1979 1.22701119630465 0.789944568388978 1 1.83250134241144 4550 2379 3161 2208 3782 4576 3448 1979 3811 4165 2433 3814 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 1.1158781231599e-05 1.31247065569766e-05 3345 3096.54545454545 3450 1.014439802843e-06 708 3.13130321927512 -2.06823837153165 -1 4.41340335065361 3344 3450 1722 3836 3969 3895 3601 708 3857 2819 2861 3815 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 1.39806631160607e-06 1.98045407886573e-06 4305 3234.63636363636 3452 1.27097018186963e-07 1611 2.07470185048691 1.87467676181316 1 3.4159454467843 4304 2268 2498 1987 3243 4557 4281 3452 1611 3748 3632 3816 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 1.30110362961095e-06 1.86323092589917e-06 4215 3404.63636363636 3453 1.18282218099841e-07 2142 1.62062589859938 1.55729400704201 1 2.68053262137971 2643 4110 3775 3453 3197 2937 2142 4002 2765 4213 4214 3817 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 6.80481724500239e-06 8.23346254714465e-06 2760 3485.09090909091 3454 6.18621663005931e-07 2351 1.32761440233737 -1.52509541966311 -1 1.94833955932684 2758 3454 3332 4215 3842 3241 4049 2351 4385 3665 3044 3818 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 3.72650022161811e-06 4.70673830506756e-06 2540 3240.27272727273 3455 3.38773321256061e-07 1922 1.36700157088368 -1.55895578431141 -1 2.10203554274863 2536 3632 3336 3455 3674 2440 4021 4344 4279 1922 2004 3819 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 2.2297991717877e-06 2.98317803028286e-06 3325 3570.72727272727 3456 2.0270922107208e-07 2168 0.880620952624114 -0.641093779605484 -1 1.40418277597213 3323 4631 3764 2979 3456 2835 2168 3959 4657 4415 3091 3820 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 1.49482337614575e-05 1.72676611243464e-05 4620 3547.27272727273 3456 1.35893957549688e-06 2097 2.04385985509817 2.67763325255681 1 2.81009335119981 4618 3456 2659 3390 4045 4099 2833 4524 2097 2673 4626 3821 M2623 BIOCARTA_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1_PATHWAY.html IGF-1 Signaling Pathway 36/41 BioCarta 2.0917226703223e-07 4.84679970737421e-07 3460 3044.63636363636 3457 1.90156624472707e-08 1167 1.11707363719118 -1.36751177260886 -1 2.03602738582383 3457 4217 3701 1555 1850 2413 3535 3801 3356 4439 1167 3822 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 1.63314840408376e-06 2.26054559157635e-06 3735 3436.63636363636 3458 1.48468146948792e-07 2011 1.0770094556638 1.12518919601504 1 1.75498873118423 3734 3458 3594 3179 3324 2886 2011 4333 4416 3755 3113 3823 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 0.00018512303949984 0.000197822220158308 3460 3200.63636363636 3458 1.85138463051088e-05 953 2.22826093011376 -1.8813474636059 -1 2.38227129416108 3458 3210 4491 3576 4405 3286 1528 3575 4552 2173 953 3824 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 0.124320813099116 0.125490641109459 2755 3477.90909090909 3459 0.0119961455839355 2753 1.84467947884789 1.72112877455883 1 0.47928813978357 2753 4230 3163 3459 4653 2987 2776 3810 2823 3875 3728 3825 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 6.40456144259049e-06 7.78910847952257e-06 3745 3455.54545454545 3459 6.40457990094862e-07 2832 1.41069883042391 -1.6212663493958 -1 2.08013918294021 3743 3212 4371 2866 3856 3656 3459 3348 2924 2832 3744 3826 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 0.000204233546280529 0.000217849116032564 3625 3299.18181818182 3459 1.85684098586977e-05 1981 0.997177080979006 -1.42524300640913 -1 1.05356342555086 3625 2886 3459 2005 4407 3848 3257 2635 4149 4039 1981 3827 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 2.26226910176148e-06 3.02319087211613e-06 590 2752.45454545455 3460 2.05661038915046e-07 590 1.40101724103782 1.34588549586895 1 2.23214198948035 590 4142 3952 4312 3460 861 651 2211 3638 4356 2104 3828 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 1.605678463764e-06 2.22840410143078e-06 2285 3025.72727272727 3460 1.45970875970527e-07 508 1.67266290680015 1.66754095630524 1 2.7290873691376 2285 4253 3460 4595 3314 1825 508 3693 947 4139 4264 3829 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 1.34107269655404e-07 3.85177943176647e-07 4665 3071.90909090909 3463 1.2191570711845e-08 267 2.08167610413189 -2.13306852306717 -1 3.85488522699883 4661 3073 2480 434 1403 4706 3968 4682 267 3463 4654 3830 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 5.55804411893948e-06 6.83176256286311e-06 4665 3254.45454545455 3464 5.55805802032292e-07 1427 1.49658703819841 0.921997921101746 1 2.23145138355538 4662 2472 4202 2145 3813 4298 2225 3084 1427 3464 4007 3831 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 2.42843423906085e-05 2.73647171389166e-05 4355 3480.27272727273 3464 2.20769185941065e-06 2015 1.90230582692538 2.68863099327609 1 2.50557151496258 4353 3464 3243 2015 4153 4386 3927 2969 2228 4204 3341 3832 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 2.43192236430897e-06 3.22525247528472e-06 2905 3279.90909090909 3464 2.2108409569154e-07 2359 1.46096834127305 -1.3640844676996 -1 2.31584078829317 2902 3662 3566 4231 3488 2769 2359 3464 3647 3206 2785 3833 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 2.70483753450417e-38 4.55958327244989e-36 20 2719.09090909091 3464 2.70483753450416e-39 18 2.36998320261593 -2.12277321084336 -1 24.1853844961655 4611 966 4683 20 780 4591 4650 4573 1554 18 3464 3834 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 6.61448526637907e-05 7.2085824191432e-05 3180 3568.72727272727 3468 6.0133492225637e-06 2461 1.6173745511881 2.25086243982897 1 1.93368833318857 3177 4269 3468 2971 4305 4068 4156 2461 2805 4444 3132 3835 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 0.000258969508169247 0.000274373979474488 2470 3132.81818181818 3468 2.58999692462784e-05 145 2.10722590455549 2.10722590455549 1 2.16637684025982 2469 4658 4299 4403 4673 1812 145 1333 4686 3468 2515 3836 M16227 REACTOME_CHOLESTEROL_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHOLESTEROL_BIOSYNTHESIS.html Genes involved in Cholesterol biosynthesis 22/24 Reactome 2.04321949031624e-07 4.80997306448512e-07 3095 3544.54545454545 3469 1.85747243643404e-08 1811 1.3897572978253 -1.60078548972232 -1 2.53457215266827 3094 4264 3469 4444 1811 3240 3848 3126 3385 4196 4113 3837 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 2.0018802140369e-07 4.74685412934128e-07 3075 3511.45454545455 3471 1.81989126927011e-08 1789 1.90862819939809 -2.27815924528071 -1 3.48434716709945 3071 4478 2794 4219 1789 3358 4020 4091 3912 3423 3471 3838 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 2.41893153805458e-05 2.72750999990865e-05 3850 3276.90909090909 3472 2.19905284996638e-06 280 2.12668619580096 -2.58856854186452 -1 2.80208461333346 3847 3430 2927 2613 4151 3472 4338 3373 280 3523 4092 3839 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 1.21258868810159e-07 3.69968882213284e-07 3475 3465.81818181818 3473 1.2125887542683e-08 1397 1.55706294063554 -1.48224816442529 -1 2.89104679388605 3473 3226 4501 4076 1397 3510 4408 3397 3204 3944 2988 3840 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 6.3211283387627e-05 6.89365197757855e-05 1715 2832.18181818182 3474 6.32130815094695e-06 523 2.01214747644007 -2.01214747644007 -1 2.41715057350657 1711 4079 4364 3973 4307 1855 523 606 4417 3474 1845 3841 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 4.35092131159969e-06 5.43577252269734e-06 4405 3203.63636363636 3474 3.95539083309421e-07 1426 2.03249733424028 1.96837273609481 1 3.08908011515022 4401 2406 1992 2882 3718 3780 3653 3419 3474 1426 4089 3842 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 9.05515409810797e-06 1.07576962856958e-05 4655 3527.54545454545 3475 9.05519099643666e-07 2318 1.94730001019439 1.18000872511093 1 2.79285582424026 4652 3217 4365 3087 3941 4110 2318 4077 2679 3475 2882 3843 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 1.15230920127906e-07 3.59285478750119e-07 4030 3443.63636363636 3477 1.04755387421305e-08 1264 1.68728767383807 -1.31292153175021 -1 3.13911135057729 4029 3865 3275 3477 1264 4718 3883 4319 3048 2701 3301 3844 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 9.4929588289653e-08 3.37690052839345e-07 4720 2952.09090909091 3478 8.62996294416794e-09 249 1.33680284957884 -1.2563734792469 -1 2.49726578931122 4718 249 3257 2602 1040 4189 3478 3845 1457 3505 4133 3845 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 4.74358818139907e-05 5.22026957710506e-05 2865 3419.18181818182 3478 4.74368944177097e-06 2000 3.4056168713857 4.74812787505352 1 4.21044696645689 2865 4333 4652 3916 4273 3239 2537 2178 4140 3478 2000 3846 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 0.000188836494202815 0.000201699084099861 2365 3355.09090909091 3480 1.71684277170846e-05 1526 0.896379659625101 1.01171905026544 1 0.955638015440943 2362 3169 3651 3480 4400 2308 1526 3393 4577 4379 3661 3847 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 6.55327769316234e-07 1.06881377718474e-06 3480 3596 3480 5.95752695020818e-08 2337 1.57556133696914 1.43240172506016 1 2.71578406015983 3480 3338 3232 3446 2758 3623 3898 4582 4343 2337 4519 3848 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 0.00030003636122066 0.000317100677331285 4580 3700.36363636364 3480 2.72797534584845e-05 2720 1.89392405430047 -1.35835942079901 -1 1.91262547282698 4580 3480 2895 3161 4445 4355 4216 2720 3213 3300 4339 3849 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 1.33740026996406e-05 1.55595989012334e-05 3485 3526.90909090909 3482 1.2158258183752e-06 2838 2.05733509254928 1.9984642880427 1 2.85549956996329 3482 3719 2838 3166 4012 3818 3385 4036 3358 3346 3636 3850 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 9.30222480259147e-05 0.0001007491993305 2220 3100.63636363636 3482 8.45692559123577e-06 1492 1.57606846661302 1.65672260896876 1 1.81811236322598 2216 4039 3482 4579 4333 2301 2279 1515 4207 3664 1492 3851 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 1.84237752087032e-07 4.52682035320557e-07 2770 3193.36363636364 3483 1.67488879559927e-08 1194 0.58124268545478 -0.537025712034132 -1 1.06396374811999 2767 3483 3891 4632 1716 2012 1194 3566 4401 4670 2795 3852 M832 REACTOME_ZINC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ZINC_TRANSPORTERS.html Genes involved in Zinc transporters 12/15 Reactome 6.92502658276159e-05 7.54353230340058e-05 2615 3353 3483 6.29567688559574e-06 1359 1.47531996454337 1.48020449764651 1 1.75537295361874 2615 3492 3284 4184 4306 3483 3930 1359 4408 3411 2411 3853 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 1.94794090896803e-07 4.66779045941157e-07 2175 3276.72727272727 3483 1.77085552858557e-08 1767 1.52360691114012 1.42884548041291 1 2.78449684942049 2172 3881 3453 4654 1767 2393 2851 3765 3950 3483 3675 3854 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 5.55392391939265e-07 9.39478064055685e-07 3415 3567.72727272727 3483 5.04902301953389e-08 2648 1.43311875254621 1.30648945208242 1 2.49335995054317 3412 3000 3621 3483 2648 3350 2973 4577 3672 3909 4600 3855 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 3.56312989651996e-06 4.52327738065206e-06 2690 3207 3485 3.23921424308569e-07 1898 2.13210529929921 1.89889330254792 1 3.28964684310745 2687 3737 2054 3640 3653 3140 2659 4505 3485 1898 3819 3856 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 0.000606909653139177 0.000634325412492674 2255 3277.90909090909 3488 5.51888313452208e-05 1198 1.32237091010346 -1.32237091010346 -1 1.22018685375335 2255 4071 3488 3699 4551 2807 2972 1198 4396 4316 2304 3857 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 7.55243259893634e-06 9.07984764823727e-06 4235 3345.63636363636 3489 6.86587138726126e-07 1743 1.73628781934499 1.69278369069165 1 2.5270464978098 4231 2721 3066 1743 3877 3827 2589 3505 3489 3090 4664 3858 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 1.40841113382849e-07 3.96712508071135e-07 3505 3302.81818181818 3489 1.28037383999376e-08 1442 1.67149040055654 1.69668191329052 1 3.08894112325234 3505 4187 3300 4394 1442 3535 3272 3872 2345 3489 2990 3859 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 7.51170325042692e-08 3.23844645192172e-07 4060 2835.27272727273 3489 6.82882136991573e-09 777 2.18514979755377 -1.98217870766558 -1 4.0940718503277 4060 2010 991 3561 777 3489 4100 4417 2760 1318 3705 3860 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 7.62924962109801e-08 3.24764325922831e-07 4095 3351.27272727273 3490 6.93568171424388e-09 790 1.86880435770152 -1.5745800154392 -1 3.50058130763168 4093 4356 2876 2465 790 4509 3824 3482 3083 3490 3896 3861 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 2.01499212444216e-07 4.76491123615581e-07 4120 3325.36363636364 3491 1.83181118999675e-08 1795 1.63900538709952 1.73751229890428 1 2.9912279532534 4118 2706 2871 4368 1795 3491 2832 4240 3738 2409 4011 3862 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 1.48891873581063e-07 4.07166653130138e-07 3685 3384.27272727273 3493 1.35356257870716e-08 1496 1.3789225050791 -1.37155138196072 -1 2.54362218526474 4023 3681 3493 4433 1496 4685 3236 1791 3683 3372 3334 3863 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 1.25604829413811e-07 3.74750186367376e-07 3905 3232.36363636364 3493 1.14186215077256e-08 1338 1.90699072914512 -1.53420707605508 -1 3.53789118002292 3904 3649 2629 3932 1338 3504 2414 3466 2659 3493 4568 3864 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 1.4396759625483e-07 4.00898570192211e-07 3725 2927.36363636364 3494 1.43967605581832e-08 121 1.4902952762695 -1.19801098026737 -1 2.7520344790322 3722 927 4608 3288 1566 3509 3765 3947 121 3254 3494 3865 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 1.1547733878603e-07 3.59296663856335e-07 3820 3238.18181818182 3494 1.04979404406728e-08 721 1.14004382622863 1.06891523659043 1 2.12070870091882 3816 721 3604 4197 1268 3197 2894 4616 3494 3132 4681 3866 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 5.19773831436497e-06 6.41897562632199e-06 4075 3299.54545454545 3495 4.72522781329582e-07 1494 2.22178559212689 -2.05488815802005 -1 3.33052469440041 4073 3297 1494 1956 3766 3814 4131 3385 3495 2310 4574 3867 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 2.32682357725922e-05 2.62804672999845e-05 1090 2825.81818181818 3495 2.11531653382296e-06 622 1.40549869948507 1.54449296535799 1 1.85811628167824 1089 3991 3500 3495 4145 2210 1648 622 3816 4131 2437 3868 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 8.39513692270775e-08 3.27411388472988e-07 4080 3101.36363636364 3495 7.63194294823983e-09 910 1.74680956028546 -1.53000707880813 -1 3.27023023881984 4080 2071 2799 1977 910 3557 4237 4563 2647 3495 3779 3869 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 6.2723931644682e-05 6.84208359978967e-05 1475 3227.90909090909 3496 5.70233818458458e-06 1475 0.910521318751671 0.979240523298608 1 1.09417600030692 1475 3712 3905 3496 4300 2238 2075 2591 4330 4466 2919 3870 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 7.49721571380456e-06 9.01805763739998e-06 780 2419.90909090909 3496 6.81567387557094e-07 151 1.64498177373574 1.76704803575166 1 2.39552026067991 780 3956 3496 4457 3875 580 151 596 4126 3598 1004 3871 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 2.03516918117483e-06 2.75164667291469e-06 3800 3671.18181818182 3497 1.85015551260478e-07 3023 1.41637496210393 -1.44086849246817 -1 2.27333675899259 3796 3970 3497 4461 3413 4535 3294 3198 4156 3023 3040 3872 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 2.06101128759589e-05 2.34352524149665e-05 4705 3718.90909090909 3497 1.87366417807577e-06 2879 1.20756968162402 1.2722191330936 1 1.61367886721735 4701 2879 3399 4195 4116 4257 3232 3790 3497 3413 3429 3873 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 9.65570554144078e-05 0.000104433845452797 1495 3389.45454545455 3497 8.77829941113881e-06 1493 1.48615190737069 1.56711685921655 1 1.70764321679025 1493 4374 4009 3543 4341 3192 3428 3080 1754 4573 3497 3874 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 8.07186406665628e-07 1.26114526297973e-06 3040 3299.54545454545 3498 7.33806093477112e-08 2502 1.64548178122076 -1.78412927803578 -1 2.8021974725526 3036 3562 3653 2502 2897 3632 3912 2933 3705 3498 2965 3875 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 4.95201505871632e-05 5.44076142391551e-05 3120 3586.81818181818 3499 4.50193320720468e-06 2413 1.22519309469324 -0.929769965079387 -1 1.50782807122089 3118 4030 3374 3499 4267 2687 2413 4168 4558 3949 3392 3876 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 0.000135143963027096 0.000145218247075588 3860 3529 3499 1.22865695917858e-05 2276 1.91002545307451 2.60637659371246 1 2.11596471002318 3858 4022 2813 3220 4375 3499 2276 3796 3479 3419 4062 3877 M8344 NAKAJIMA_EOSINOPHIL http://www.broadinstitute.org/gsea/msigdb/cards/NAKAJIMA_EOSINOPHIL.html Top 30 increased eosinophil specific transcripts. 11493461 20/52 Kevin Vogelsang 5.42184843058361e-08 3.06874196014832e-07 4120 2604 3499 4.92895324018528e-09 428 2.53932153080689 1.52236802503875 1 4.7749246583462 4632 730 1221 4116 428 4045 3499 3602 1178 1074 4119 3878 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 2.51916188419691e-06 3.32879173947632e-06 3220 3475.81818181818 3499 2.29014978984297e-07 2454 1.48659163219445 -1.53146626977926 -1 2.350581528303 3216 3971 3126 3494 3499 3768 3667 3176 4211 2454 3652 3879 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 3.68961472979122e-06 4.66389435581536e-06 4505 3341.81818181818 3502 3.35420083422706e-07 2023 2.03316429883997 1.58383567714675 1 3.12914395480842 4502 3078 2023 2136 3671 3836 3502 4117 2515 3303 4077 3880 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 9.4750768333563e-07 1.43020027673303e-06 3505 3499.81818181818 3504 8.61370992194106e-08 2313 1.47749813090461 -1.34813335943097 -1 2.49273074610571 3503 3565 4028 3504 3013 3882 4198 2313 2926 4422 3144 3881 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 8.76237339578324e-07 1.34542623383529e-06 3640 3586 3504 7.96579716886205e-08 2186 1.95660908457087 1.98548536842071 1 3.31632564684799 3638 4440 3157 3470 2958 4254 4679 2186 3716 3504 3444 3882 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 1.11570238719146e-06 1.63849261591279e-06 4245 3465.36363636364 3505 1.01427541182393e-07 1527 1.78252019323333 1.26491436679066 1 2.97712681841577 4241 3323 2646 1527 3106 4197 4269 4305 3787 3213 3505 3883 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 6.77501894742251e-06 8.20161308844172e-06 3295 3194.45454545455 3505 6.77503960290793e-07 115 2.70724092167508 1.69161763909914 1 3.97522040958769 3293 3505 4424 2555 3874 3636 2651 4253 115 2929 3904 3884 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 1.03783140974851e-07 3.47369293280946e-07 3090 3368.45454545455 3505 9.43483144279392e-09 1135 1.83743782561203 -1.72145812069461 -1 3.42630673805092 3610 4705 3089 3505 1135 3206 3685 4028 3027 3974 3089 3885 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 5.12024467395884e-07 8.82398820572726e-07 4160 3182.45454545455 3505 4.65476896876068e-08 963 1.59908418282255 2.03840262702842 1 2.79477852265025 4157 3414 3183 3667 2594 3978 4113 963 3505 3513 1920 3886 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 4.5817417544887e-06 5.70451624404819e-06 3440 3450.09090909091 3506 4.16522845136109e-07 2238 1.81368408591877 1.41015079751846 1 2.74544921525217 3438 3936 2844 2238 3733 3513 3206 3506 3387 3540 4610 3887 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 2.38348054266131e-07 5.22548577520102e-07 4385 3423.72727272727 3507 2.16680072807973e-08 1400 1.75669609929275 -1.76485907164531 -1 3.1857511557967 4384 4446 2599 4431 1973 3507 3037 3481 3694 1400 4709 3888 M19943 BIOCARTA_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CERAMIDE_PATHWAY.html Ceramide Signaling Pathway 29/33 BioCarta 4.29899667480292e-06 5.37516935233637e-06 1330 2724.27272727273 3508 3.90818643222703e-07 706 0.889091169302453 -0.866009597311649 -1 1.35204595916415 1330 3988 3936 3508 3714 743 706 1730 4555 4394 1363 3889 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 6.55189216807817e-07 1.06881377718474e-06 3195 3671.45454545455 3508 6.55189409980706e-08 2821 0.981582396229202 -1.00438699811576 -1 1.69162199812023 3193 3815 4200 4407 2821 3508 3301 3442 4468 3250 3981 3890 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 1.46106787369085e-05 1.69025499113255e-05 2690 3366.90909090909 3510 1.46107748001673e-06 2144 1.43537924734502 -1.47227983663804 -1 1.97708675156803 2689 3510 4194 3705 4066 2695 2144 2971 4578 2920 3564 3891 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 5.24897685875617e-06 6.47547589475408e-06 1315 2648.72727272727 3510 4.77180852938581e-07 423 1.24990176693477 1.30071057604309 1 1.87189060743998 1312 4617 3510 4424 3769 1551 1228 729 3726 3847 423 3892 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 1.70664778117799e-06 2.35262194134349e-06 4505 3567 3510 1.55149918646338e-07 1874 2.33601010172486 -2.68833674948346 -1 3.79584323989096 4504 3953 1874 4399 3338 4311 3466 2813 4197 2872 3510 3893 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 1.02819480378709e-07 3.46153508287541e-07 3750 3199.63636363636 3512 9.34722592582669e-09 1127 1.35889012809256 -1.74124045182739 -1 2.53432253506841 3750 3929 3659 3487 1127 4638 2602 2172 3512 3828 2492 3894 M7591 REACTOME_G1_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_PHASE.html Genes involved in G1 Phase 40/48 Reactome 7.6671461330453e-06 9.20603656778779e-06 3530 2830.81818181818 3512 6.97015713971748e-07 1305 1.6605657380639 1.97077103816892 1 2.41392643724773 1793 4218 3530 3512 3880 1631 1305 1800 3530 3902 2038 3895 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 8.33198659277987e-08 3.27411388472988e-07 3515 3048.72727272727 3512 8.33198690517889e-09 999 1.7233155165373 -1.62203865971894 -1 3.22623507756589 3512 3548 4280 2029 999 1877 3629 4586 2475 3705 2896 3896 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 2.86659844324563e-39 5.20397871235361e-37 4675 2759 3515 2.86659844324561e-40 16 2.70077083179353 -2.56655760287696 -1 28.2962639743553 4674 1007 4470 235 668 4620 4145 4529 2470 16 3515 3897 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 2.9555727510944e-07 5.93125143927107e-07 4630 3103.18181818182 3515 2.68688468014416e-08 836 2.01572182388751 -2.14829616976647 -1 3.62359356113577 4628 1789 1894 2582 2182 4384 4700 3960 3515 836 3665 3898 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 6.97302348483224e-06 8.42187073910137e-06 3205 3462.45454545455 3516 6.33913235119968e-07 2722 1.6054721884014 -1.4724197570268 -1 2.35173443094881 3202 4161 3956 3516 3853 2750 3093 3728 2722 4349 2757 3899 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 1.19754768132773e-05 1.40258686249799e-05 4680 3503 3516 1.08868563646066e-06 2226 1.21661197265988 -0.940765838176728 -1 1.70409046624204 4677 3099 3564 2925 3987 3300 2226 3235 4307 3516 3697 3900 M16763 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NEUROTROPHIN_SIGNALING_PATHWAY.html Neurotrophin signaling pathway 139/152 KEGG 3.09592159718335e-07 6.10722425900902e-07 3625 2980.18181818182 3517 2.81447457532091e-08 897 1.78295311817388 2.02997756643341 1 3.19851646434813 3624 1441 2805 897 2223 3873 3517 4552 1398 4163 4289 3901 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 7.61914025535731e-05 8.2843450829962e-05 2120 3192.54545454545 3517 7.61940149880561e-06 1014 0.772965914036517 -0.868800158412581 -1 0.9102035749779 2118 3517 4437 4430 4321 1789 1014 3405 4235 4216 1636 3902 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 1.41152583515662e-06 1.99174945947362e-06 3165 3526.27272727273 3518 1.2832061279965e-07 2466 1.40160508850645 -1.61490775988296 -1 2.30642911912665 3165 3901 3870 3503 3256 4063 4257 2466 3518 3808 2982 3903 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 0.00693550950303974 0.00708869745654993 2585 3538.63636363636 3519 0.000695725064313206 2232 2.75693713013218 -2.75693713013218 -1 1.71031328900118 2582 4084 4354 4558 4600 3263 3461 3519 3715 2557 2232 3904 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 1.02926146367626e-05 1.2154401072184e-05 3520 3125.90909090909 3519 9.35696617334203e-07 863 1.86925544253653 2.03560207539351 1 2.65227251489863 3519 3637 2561 2446 3952 3687 3154 3535 3805 3226 863 3905 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 0.10894461567982 0.109993280429679 2040 3628 3521 0.0104314558945505 2037 1.37125255428879 -1.03852692178035 -1 0.37872770190033 2037 4512 3963 3521 4652 3170 2612 3493 3990 4504 3454 3906 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 3.82738416420279e-07 7.06225694098404e-07 3280 3659.63636363636 3521 3.4794407546006e-08 2399 1.18763017968659 0.933073830121695 1 2.10861366836199 3209 4057 3084 4422 2399 3278 3521 4318 4612 3278 4078 3907 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 6.45192261270565e-06 7.83862927463853e-06 3500 3548 3523 6.45194134506963e-07 2749 1.88029270828107 -2.23232246416721 -1 2.77136886531331 3498 3523 4596 3317 3860 3589 3404 3636 3782 3074 2749 3908 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 7.08382254697447e-08 3.1722620893472e-07 3470 3025.36363636364 3524 6.4398388864253e-09 727 1.54769885509756 1.60221687091374 1 2.90350756439339 3467 3626 3524 2223 727 4270 3762 2441 1152 4184 3903 3909 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 6.77240384614481e-05 7.37898110660284e-05 3320 3482.36363636364 3524 6.77261024954024e-06 2268 2.13201942129789 -2.25162331724341 -1 2.54301087263218 3320 2915 4615 3862 4314 3524 2268 3264 4186 2475 3563 3910 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 2.63159306473038e-06 3.4541488502579e-06 1710 3331.90909090909 3524 2.39236019326467e-07 1708 1.48368581016218 1.62125455936471 1 2.3391069084175 1708 4389 3897 4698 3524 2446 2631 2377 3866 4242 2873 3911 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 7.08596939428564e-06 8.54953362500722e-06 3550 3471.09090909091 3525 6.44181110686656e-07 2663 1.34144727715655 1.20077631760984 1 1.962311751108 3547 4005 3525 2684 3858 3427 2663 3081 4130 4320 2942 3912 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 1.15218621909647e-06 1.68682349694025e-06 4675 3650.09090909091 3525 1.04744256592822e-07 1960 1.14242192373221 0.871299116627144 1 1.90357426207805 4671 3177 3442 3403 3119 4704 4276 3903 1960 3971 3525 3913 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 8.84821628333734e-08 3.31003670356505e-07 4100 3057.27272727273 3526 8.0438333083684e-09 966 1.68181294482815 -1.29543844080166 -1 3.14621548516921 4100 2063 3207 1119 966 3526 3877 4560 2291 3643 4278 3914 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 3.11933258882579e-07 6.12957944182254e-07 3530 3471 3527 2.83575730100848e-08 2235 1.94196099388653 1.69923102314016 1 3.48295452858386 3527 3660 2628 3373 2235 3884 3300 4080 4303 2650 4541 3915 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 1.11788602966279e-05 1.31385011454392e-05 4500 3308.27272727273 3528 1.01626519092512e-06 1342 1.67831965232403 1.29233656594761 1 2.36488044433647 4498 3954 3180 3884 3972 3697 3157 1342 3053 3528 2126 3916 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 2.572466119212e-05 2.88889842557237e-05 4170 3238.81818181818 3528 2.33863290874756e-06 1455 1.04551331553729 1.00746117835165 1 1.36957483014039 1455 4167 3993 3528 4168 1916 1645 2871 4433 4412 3039 3917 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 0.00186669571278812 0.00193050038658193 4550 3207.36363636364 3530 0.000169843771319693 996 1.04023781295459 -1.06029561743994 -1 0.814478661060398 996 3914 4021 3530 4550 1876 2384 2711 4548 3850 2901 3918 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 1.25795605852275e-05 1.46860069162192e-05 565 2794.72727272727 3531 1.14360295595504e-06 565 1.07281354378078 1.13663709406275 1 1.49638458275881 565 3905 4006 3531 3996 1112 968 1878 4412 4467 1902 3919 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 0.0753196854912598 0.0761750408225297 1470 3431.81818181818 3532 0.00709355811369726 1469 1.03254189851992 -0.995323413858235 -1 0.332538741793061 1469 4499 4093 3532 4646 2561 2211 3010 4291 4531 2907 3920 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 8.78113711954432e-06 1.04584827666538e-05 655 2790.27272727273 3533 7.98288378999897e-07 652 2.92418809531968 -2.45859505707345 -1 4.20470436238597 4488 652 1230 1386 3916 4610 4070 3533 653 1488 4667 3921 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 0.000480596415231512 0.000504316380589759 3590 3545.27272727273 3533 4.80700384690344e-05 1671 2.65554611141539 -0.950745688521899 -1 2.52759435541217 3588 3533 4628 4155 4485 3728 3423 1671 3174 3255 3358 3922 M95 PID_CIRCADIAN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CIRCADIAN_PATHWAY.html Circadian rhythm pathway 18832364 21/21 Pathway Interaction Database 1.04356238211288e-05 1.23078821678481e-05 3390 3592.54545454545 3534 9.4869757477071e-07 2341 1.65071813549296 -1.87415554632925 -1 2.33949314031219 3390 4018 3306 3955 3958 4160 4335 3104 3534 3417 2341 3923 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 1.98224964379702e-07 4.72059450995053e-07 2650 3633 3537 1.98224982061616e-08 1884 1.32377629244855 1.3443719917371 1 2.41731215705698 2650 4668 4290 4110 1884 3449 3223 3537 3503 4691 3958 3924 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 5.15215453518669e-05 5.65275904371947e-05 2070 3150.54545454545 3538 5.15227399021816e-06 42 3.24456347637029 3.24456347637029 1 3.97890519094237 2067 4665 4304 4577 4525 2137 42 2242 4587 3538 1972 3925 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 0.158856663772752 0.16018018650019 1660 3533.18181818182 3539 0.0156036362727089 1660 0.944138451581355 -0.954983938398336 -1 0.215988917603512 1660 4507 4090 3539 4667 2780 2230 3247 4378 4569 3198 3926 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 1.7684976439949e-05 2.02604584457668e-05 3455 3463.54545454545 3539 1.60773805495039e-06 2031 2.12577033340986 -1.64047978109888 -1 2.88013558757247 3451 2804 2419 3339 4084 3803 4690 3972 3967 2031 3539 3927 M100 PID_SHP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SHP2_PATHWAY.html SHP2 signaling 18832364 80/91 Pathway Interaction Database 1.12268718225211e-06 1.64670090125232e-06 4220 3567.72727272727 3540 1.02062523197606e-07 2488 1.88372750260372 1.92725697429556 1 3.14502948370141 4217 3008 2488 2962 3111 4447 3540 4307 3859 3163 4143 3928 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 1.44690565237417e-05 1.67510293824039e-05 4410 3461.72727272727 3542 1.31537742594033e-06 2169 2.11623058201535 -1.97153124353727 -1 2.91768755618099 4406 4001 2169 3435 4037 4018 3542 3063 3756 2582 3070 3929 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 0.076353346384609 0.0771873623763878 4605 3682.72727272727 3543 0.00719451196474131 2518 1.26686646536456 -0.763351335733939 -1 0.406102930222897 4605 4309 3139 4193 4709 3543 3085 3330 3279 3800 2518 3930 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 5.48012043693945e-06 6.73773598915192e-06 3545 3245 3544 4.98194007978989e-07 1754 2.00570659542143 1.63692285091239 1 2.99434123149859 3544 2824 2196 3641 3786 2778 2628 4290 3819 1754 4435 3931 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 3.10908661661045e-07 6.11708579841655e-07 4445 3580 3544 2.82644277817568e-08 2232 1.35059180405579 1.4443713207306 1 2.42240271794336 4442 3467 3372 4387 2232 4043 2354 4016 4099 3544 3424 3932 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 1.76927275279811e-07 4.43266487055072e-07 3115 3398.18181818182 3544 1.60842990462334e-08 1675 1.15076256219668 -0.989780478737097 -1 2.11034621378526 3111 4400 4091 3544 1675 2388 2642 3758 3766 4503 3502 3933 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 1.22885036517115e-05 1.43710944588896e-05 4240 2872.36363636364 3544 1.22885716055353e-06 116 2.4318708114838 -1.106945237389 -1 3.39973030310016 4236 924 4586 2056 4017 4363 3544 2335 116 1848 3571 3934 M15434 REACTOME_DNA_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPAIR.html Genes involved in DNA Repair 114/127 Reactome 1.55607907093053e-05 1.79357587662811e-05 1485 3132.36363636364 3545 1.41462734301971e-06 949 1.0415794989537 1.0089333693686 1 1.42668181714025 1482 3886 4113 3545 4057 1501 949 2726 4379 4559 3259 3935 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 0.000289659205593519 0.000306270486201033 2775 3477.72727272727 3546 2.63361227367772e-05 1768 0.924757260506004 1.07225007552694 1 0.937478075839954 2773 3174 3551 3469 4443 2758 1768 3546 4573 4339 3861 3936 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 0.106202750645812 0.107247963852852 1445 3495.27272727273 3546 0.0101550241626363 1443 0.85937270248867 -0.954983938398336 -1 0.239753568507108 1443 4504 4118 3546 4658 2775 2087 3117 4526 4608 3066 3937 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 1.31511978156429e-07 3.81741928683936e-07 4650 3488 3546 1.19556350925431e-08 1382 1.57808233038774 -1.61102725334092 -1 2.92388620898337 4649 2080 3546 3443 1382 4442 4505 4231 3203 3044 3843 3938 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 0.000220944897525374 0.00023540855898866 3550 3385.45454545455 3546 2.209668680913e-05 1166 1.89478420681595 1.22463643223119 1 1.98428147531192 3546 2928 4363 4543 4421 2819 1166 1297 4553 3007 4597 3939 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 0.00960101727975198 0.00980246626874958 1815 3542.72727272727 3547 0.000876652260469359 1812 0.917251651633575 -0.956979260725871 -1 0.531172665268576 1812 4491 4102 3547 4604 2756 2358 3071 4618 4574 3037 3940 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 5.45624161690884e-11 8.30756788122894e-10 250 2797.18181818182 3547 4.96021965185832e-12 246 2.32560923570002 -2.14145966687701 -1 6.09719168683884 3794 2501 246 1766 2729 3547 3858 3951 3851 247 4279 3941 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 2.01198165988427e-07 4.76017716022745e-07 3745 3449.90909090909 3550 1.82907440353408e-08 1794 1.9202197479983 -1.36115213688401 -1 3.50483871618362 3745 4283 2774 4578 1794 3560 2904 3550 3309 3543 3909 3942 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 0.0999225022764578 0.100927500694389 1940 3571.45454545455 3550 0.00952475044022923 1939 1.52120597321748 -0.954983938398336 -1 0.436647332722975 1939 4500 3949 3542 4649 3060 2630 3699 3550 4551 3217 3943 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 5.56143090658172e-06 6.83414576388069e-06 3210 3402.63636363636 3552 5.05585905954668e-07 2462 2.06352690242767 -1.53032079749263 -1 3.07700994501508 3207 4014 2462 3615 3789 2805 3225 3552 3572 3017 4171 3944 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 8.44000360106045e-06 1.00776162400722e-05 1670 3156.45454545455 3552 7.67275998197371e-07 1667 1.47460525190717 1.61751167873085 1 2.12677534825512 1806 4287 3140 4455 3908 1667 1667 3684 4670 3552 1885 3945 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 5.50879768283212e-05 6.03563720124597e-05 3585 3500.90909090909 3553 5.00812329809446e-06 2381 0.986856730008566 0.916560167071016 1 1.20150159231894 3585 2381 3610 3165 4280 3430 2489 3211 3553 4167 4639 3946 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 4.66751307408316e-07 8.18873691787962e-07 3555 3625.09090909091 3553 4.24319460394687e-08 2544 1.8074375042061 2.10039518815632 1 3.17597291816015 4608 3723 2762 3951 2544 4196 3416 3553 3552 3340 4231 3947 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 5.41538759541729e-08 3.06874196014832e-07 3555 3066.27272727273 3554 5.4153877273862e-09 380 2.85129263567919 4.11357093217089 1 5.36165903267353 3554 3503 4213 3314 530 3809 4061 3764 380 2923 3678 3948 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 1.46992068539027e-05 1.69924703282931e-05 1660 3449.72727272727 3554 1.33630046063178e-06 1658 1.50095323261572 1.59549654058517 1 2.06644876588759 1658 4205 3865 4056 4040 3428 2792 2894 4139 3554 3316 3949 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 1.14138655833791e-07 3.59285478750119e-07 2780 3134.90909090909 3556 1.03762419777675e-08 1247 1.71174156318671 -1.3823504234 -1 3.18461902869061 2778 4135 3561 3997 1247 2184 2219 3556 3115 4068 3624 3950 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 4.95008508972241e-08 3.0357704374324e-07 3845 3296.90909090909 3562 4.5000774555466e-09 344 1.52898092469328 -1.10515665560859 -1 2.87681501001325 3842 3291 3597 4013 344 3375 3953 3101 3562 4251 2937 3951 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 0.000639805859862032 0.000668411611011242 1925 3207.45454545455 3562 5.81810913214678e-05 1213 0.86662844988723 0.794146052620894 1 0.793675620311178 1924 4055 3562 3737 4498 2001 1213 2614 4642 4171 2865 3952 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 1.2000639914742e-07 3.68290119620171e-07 2680 3267.72727272727 3563 1.09096732448703e-08 1294 1.34154200328491 1.22672737886204 1 2.4915283451559 2680 4524 3563 4613 1294 2214 1415 4387 3096 4457 3702 3953 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 9.2782590240753e-08 3.35829802760759e-07 2935 3386.27272727273 3563 8.43478128670523e-09 1015 1.17557514976725 -1.15208159858422 -1 2.19678871055028 2935 4409 3979 4511 1015 2652 3563 3446 3952 4390 2397 3954 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 7.34959469641835e-05 7.99494975042512e-05 3715 3300 3565 6.68167294330883e-06 2247 2.15215000810878 1.35362680536678 1 2.54539121825428 3619 3769 2434 3108 4313 3062 2758 2247 3712 3565 3713 3955 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 2.86586411959746e-06 3.72333571277182e-06 3070 3474.45454545455 3565 2.60533441169692e-07 2058 1.97388212869035 2.3079632582593 1 3.09363464593056 3068 4604 2691 4404 3565 2965 2058 2650 4421 3918 3875 3956 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 9.79080706672745e-07 1.46613608359624e-06 4710 3703.45454545455 3566 8.90073765818044e-08 2806 1.26456030134939 -1.35270253121204 -1 2.12941742610473 4706 3185 3357 4183 3039 4358 4412 2806 2920 3566 4206 3957 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 0.00493756269300026 0.00505757289734401 3320 3542.8 3571 0.000549825760387943 684 0.872102914640049 0.872102914640049 1 0.577359867765419 3318 3824 4467 NA 4650 2875 684 3023 4662 4705 3220 3958 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 0.00493756269300026 0.00505757289734401 3320 3543.9 3572 0.000549825760387943 685 0.872102914640049 0.872102914640049 1 0.577359867765419 3319 3825 4469 NA 4651 2876 685 3024 4663 4706 3221 3959 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 9.24004244807949e-05 0.000100121672072854 3960 3368.27272727273 3579 8.40039141315099e-06 63 1.20280544782258 -0.672854849428859 -1 1.38826415693672 3958 3155 3476 3671 4332 3579 2988 4184 63 4401 3244 3960 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 3.0152691364784e-06 3.9045460422985e-06 1200 3098.18181818182 3579 2.74115751740408e-07 1198 1.42631656531001 1.33567524973964 1 2.22670444783835 1198 3871 3794 3787 3579 1928 2003 3097 3591 4079 3153 3961 M19553 BIOCARTA_AHSP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AHSP_PATHWAY.html Hemoglobin's Chaperone 10/21 BioCarta 1.81417152210302e-05 2.07534890555653e-05 1610 3000.54545454545 3580 1.64926043850815e-06 899 1.50939773353535 -1.63139060000017 -1 2.04023190333239 1606 4316 2896 4421 4089 1178 899 3956 4382 3580 1683 3962 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 3.01836660552798e-06 3.90745073677328e-06 4605 3081.90909090909 3580 2.743973406081e-07 981 2.04172386349108 -1.98355743915787 -1 3.18763323427953 4603 1797 1586 1863 3580 4709 4501 4720 1840 981 3721 3963 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 0.000235597868244534 0.000250061150913919 1390 3099.27272727273 3584 2.14202820172216e-05 359 0.778001515511143 0.768076061514083 1 0.808350125041513 1386 4059 3584 4588 4420 1575 359 2515 4440 4315 2851 3964 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 7.23003514601422e-05 7.86670490760422e-05 2885 3343.72727272727 3584 6.57297523940716e-06 1214 1.54246907848074 1.76633366337424 1 1.8271933432957 2885 3794 2824 3944 4312 2747 1214 4448 4533 3584 2496 3965 M84 PID_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATM_PATHWAY.html ATM pathway 18832364 41/48 Pathway Interaction Database 8.99008601199605e-06 1.06857733509497e-05 1445 2666 3585 8.17283886301662e-07 459 1.2017585305154 1.08271403692179 1 1.72426685721406 1441 3687 3811 3768 3923 932 459 1806 3585 3791 2123 3966 M7772 BIOCARTA_BARRESTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARRESTIN_PATHWAY.html fl-arrestins in GPCR Desensitization 19/23 BioCarta 1.04106158240276e-07 3.47369293280946e-07 4660 3558.63636363636 3586 9.46419665151656e-09 1143 1.08236060470346 1.11189784822689 1 2.01794532308244 4659 2814 3461 3988 1143 4531 4631 2607 4195 3530 3586 3967 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 3.81350569617186e-06 4.80762470243889e-06 4335 3720.36363636364 3587 3.81351224045923e-07 2918 1.45621170440891 1.02863322372079 1 2.23539695873074 4335 2918 4351 3335 3707 4130 3142 3287 3587 3470 4662 3968 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 1.31169980185621e-07 3.80998342446849e-07 3590 3242.90909090909 3587 1.31169987928125e-08 1463 2.06751279590929 2.33683729413271 1 3.83148038987695 3587 3829 4428 3654 1463 3804 3370 3057 2772 1791 3917 3969 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 1.15022956268947e-07 3.59285478750119e-07 4390 3367.54545454545 3590 1.04566329347919e-08 1259 1.55101409513348 -1.4111409209667 -1 2.88551184881195 4386 2551 3467 2019 1259 3482 3649 4509 3590 3695 4436 3970 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 0.000109441624297925 0.00011801792704734 2525 3530.81818181818 3590 9.94973354375196e-06 1970 1.05225817815162 1.24333408047073 1 1.19269517230006 2522 4635 3590 4482 4356 2351 1970 2919 4639 3843 3532 3971 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 5.41388711331657e-08 3.06874196014832e-07 4510 3025.54545454545 3590 4.92171567867695e-09 427 2.2216564364637 -2.09432075611644 -1 4.17748140971144 4506 2817 1778 2128 427 4712 3622 3590 3916 1425 4360 3972 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 0.000766957252190952 0.000799655010015749 2155 3490.18181818182 3591 6.9747705185848e-05 2015 0.786797692610472 0.733432144378676 1 0.702796260565562 2151 4073 3591 4608 4511 2425 2015 2993 4676 4272 3077 3973 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 8.14714269338674e-07 1.2703836641158e-06 3245 3482 3591 7.40649610043292e-08 1577 1.57430173020246 1.72571352858618 1 2.67950210360717 3591 4712 3980 3242 2903 4324 4224 1975 1577 4533 3241 3974 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 1.0967160457995e-07 3.53357928937751e-07 4155 2947.27272727273 3593 9.9701463679236e-09 276 2.00683978312236 2.46275735110026 1 3.73797143967913 4154 276 1649 3593 1201 4465 4177 3604 2777 1982 4542 3975 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 1.40261029568986e-06 1.98417328584169e-06 3595 3704.63636363636 3593 1.27510108175004e-07 2494 1.49516663913622 -1.57762400601961 -1 2.46116261226112 4501 3591 3450 2494 3247 4687 3977 4355 3593 3595 3261 3976 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 0.000247165337196219 0.000261985266464441 3530 3692.09090909091 3594 2.24721009151279e-05 2946 1.22394926913148 1.24143932900358 1 1.26503713101721 3529 3481 3359 4173 4430 3598 2946 4556 3594 3685 3262 3977 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 1.62641300091715e-06 2.25254382756131e-06 3985 3436.09090909091 3594 1.47855836662798e-07 821 2.23369983811062 2.67103224637792 1 3.64173604826524 3985 4168 2505 4458 3322 4242 3594 2756 821 3496 4450 3978 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 3.37203098252048e-07 6.46203257714034e-07 2715 3412.09090909091 3595 3.06548318124156e-08 2055 1.08190115999686 1.06545728837678 1 1.93286841416939 2712 3595 4126 4077 2295 2989 2055 3432 4022 4447 3783 3979 M15258 BIOCARTA_AKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKT_PATHWAY.html AKT Signaling Pathway 30/33 BioCarta 2.83008953671828e-05 3.16690910699627e-05 3395 3425.54545454545 3596 2.57284176706222e-06 1077 1.18984777255739 -1.69824846957671 -1 1.54505509773116 3393 4544 3596 2477 4183 4528 3928 2599 1077 4335 3021 3980 M125 PID_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IGF1_PATHWAY.html IGF1 pathway 18832364 50/54 Pathway Interaction Database 6.03391224995857e-07 1.00162980514804e-06 4015 3604.36363636364 3596 5.485376277157e-08 2706 1.1242136478396 -1.05070251095117 -1 1.94670541856933 4014 3666 3885 2983 2706 3596 4093 3299 3588 4407 3411 3981 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 3.15514719696077e-06 4.06914636323815e-06 4220 3150.27272727273 3597 2.86831974722624e-07 920 3.21167428200375 -3.08672859514768 -1 4.99837558976909 4219 2793 920 1401 3597 4705 4332 4042 3223 955 4466 3982 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 5.93291560349622e-08 3.10399797613433e-07 3795 3023.63636363636 3597 5.39355978499445e-09 525 2.51995341933033 2.15304851456767 1 4.73488838532222 3793 3627 727 3300 525 3597 3408 4491 4040 1143 4609 3983 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 9.25579021639763e-08 3.3569630149888e-07 3840 3370.90909090909 3598 8.41435509618651e-09 1012 1.28899205132508 1.54809800272751 1 2.4088774194386 2588 3628 3836 4047 1012 3542 3455 3598 3956 3840 3578 3984 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 5.40891830833718e-07 9.21331447685005e-07 4290 3495.45454545455 3599 4.91719967106715e-08 2116 2.04159455488336 -2.07549535985792 -1 3.55735416353975 4289 4227 2116 4240 2626 4603 4520 3538 3599 2417 2275 3985 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 1.20233101775429e-06 1.74669202948608e-06 3600 3499.81818181818 3599 1.09302879531422e-07 2058 1.7334206415024 1.87090362218042 1 2.88119688233982 3599 2612 2314 3391 3148 4602 4680 4277 3786 2058 4031 3986 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 5.92056529794127e-07 9.88527179765794e-07 3510 3402.81818181818 3600 5.38233353751299e-08 1112 1.36651894670459 -1.43923555072792 -1 2.36872717592707 3510 3295 3691 1112 2690 3867 4562 3600 4004 3913 3187 3987 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 2.72882987346919e-05 3.05867418731289e-05 3600 3431.54545454545 3600 2.72886338335448e-06 1098 1.03579835018314 -0.913436069740591 -1 1.34942266328222 3600 3532 4464 3686 4191 3898 2635 2566 4600 3477 1098 3988 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 6.35226666629566e-07 1.04215150034465e-06 3605 3432.54545454545 3602 5.77478954586003e-08 2421 1.87688098497526 1.68219099261688 1 3.24127747601352 3920 3604 2421 3472 2740 3776 3353 4211 3602 2580 4079 3989 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 2.05340589999578e-06 2.77312613676111e-06 3605 3826.54545454545 3602 1.86673437870744e-07 3002 1.24213802286908 -1.11412393338629 -1 1.99236249168866 3602 4714 4149 4526 3418 3377 3002 3510 3521 4617 3656 3990 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 1.18887312455747e-06 1.72926999935632e-06 3105 3498.09090909091 3602 1.08079433365571e-07 2409 1.41231320282692 -1.70068741818738 -1 2.34908560449215 3102 4202 3602 4012 3142 3273 3916 2545 4245 4031 2409 3991 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 0.000103727768451388 0.000112009852914791 3605 3517 3604 9.43024176666405e-06 2042 1.13299263350197 -0.901217479881299 -1 1.29169474511563 3604 3474 3366 2930 4349 2959 2042 3754 4345 4044 3820 3992 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 9.56104374202195e-08 3.38845370705758e-07 4040 2992.90909090909 3605 8.69185832503468e-09 902 1.84153792023774 -1.74815489513232 -1 3.43969191968589 4039 2562 2915 902 1046 4052 3605 4503 1036 3813 4449 3993 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 7.60813650437098e-06 9.13999575402239e-06 3535 3614.27272727273 3605 7.60816255217998e-07 2298 1.97774619514426 -1.89763707413255 -1 2.87695460019609 3531 3802 4633 3167 3904 2743 2298 4683 3605 2712 4679 3994 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 2.03891987198012e-07 4.80499877897084e-07 3725 3478.63636363636 3605 1.85356369176684e-08 1808 1.75935613187633 -1.48162794856027 -1 3.20908599143489 3725 3838 3223 3492 1808 3605 4589 4401 3273 2634 3677 3995 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 5.13020618252498e-08 3.0357704374324e-07 3610 2915 3606 4.66382391105172e-09 366 1.71124950964032 -2.00703396842102 -1 3.21986048879793 4097 1668 2703 3606 382 3800 3189 4638 366 3610 4006 3996 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 6.58783442765459e-07 1.07296682189543e-06 3610 3372.45454545455 3607 5.988942182148e-08 2332 1.92708732151477 -1.40726006846206 -1 3.32096187216293 3607 3920 2332 3911 2762 4054 2784 3666 2732 3242 4087 3997 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 5.84263494040179e-06 7.15548441066332e-06 3905 3428.18181818182 3607 5.31150041545203e-07 818 1.69627970484306 -1.26690894848911 -1 2.51946487404574 3902 818 2631 3607 3800 3321 4411 4677 3455 2444 4644 3998 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 1.50281443721591e-07 4.08899989016697e-07 3610 3375 3607 1.366195036248e-08 1502 1.56545957550781 -1.63123916830783 -1 2.88699935076717 3825 3608 3607 3431 1502 3516 4416 3500 2353 3668 3699 3999 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 1.29123955235731e-07 3.79339184781551e-07 4035 3324.90909090909 3608 1.17385420740333e-08 1361 1.71278605540341 -1.47779456286964 -1 3.17489634294527 4035 1489 3215 4381 1361 4710 3939 3608 2217 3508 4111 4000 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 7.43750457209217e-07 1.17762568199514e-06 3225 3469.63636363636 3609 6.76137007861686e-08 2485 1.37148587826182 -1.46609532162448 -1 2.34723386606549 3224 3609 3818 2485 2848 4151 3931 2853 4147 4160 2940 4001 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 2.6820283372054e-07 5.57918631626685e-07 3615 3038.54545454545 3609 2.4382078765205e-08 1673 2.07522208133822 2.6313977313138 1 3.74650589503547 3688 1755 1995 3612 2090 4611 3612 3609 3651 1673 3128 4002 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 7.71315274066723e-08 3.24764325922831e-07 4485 3206.81818181818 3609 7.01195728280793e-09 805 1.54417412546292 -1.47853014746674 -1 2.89234528225959 4483 3876 3609 3425 805 4518 4141 3940 1918 3442 1118 4003 M5193 SIG_CHEMOTAXIS http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CHEMOTAXIS.html Genes related to chemotaxis 50/63 Signaling Gateway 3.04431123668199e-07 6.04363454990223e-07 4250 3337.90909090909 3610 2.76755605267919e-08 1717 1.68281641685181 -1.57750203209144 -1 3.0210374554232 4250 2236 2930 3421 2209 4353 4124 3610 1717 3617 4250 4004 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 4.6658387045749e-05 5.13830113989583e-05 1930 2803.90909090909 3611 4.24176151117234e-06 155 1.46548613343387 -1.29956550874941 -1 1.81423414106688 1927 4528 3611 4490 4257 1283 1293 948 4217 4134 155 4005 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 2.1125526584606e-06 2.84134245652017e-06 3060 3425 3612 1.92050426094961e-07 576 1.16011065140402 1.42150847619929 1 1.85719992498481 3057 4236 3612 4064 3435 2820 2571 4296 4524 4484 576 4006 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 2.69642619727051e-07 5.60173048024507e-07 4380 3262.36363636364 3614 2.45129684341598e-08 1424 2.16614552107778 -2.11333681494977 -1 3.90959695191672 4377 3003 1424 2338 2093 4234 3619 4583 3614 2229 4372 4007 M321 KEGG_CHRONIC_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHRONIC_MYELOID_LEUKEMIA.html Chronic myeloid leukemia 83/90 KEGG 5.15846415940031e-07 8.88287151855872e-07 4240 3436.18181818182 3617 4.689513971759e-08 1550 1.38652994851421 1.28191584484689 1 2.42201865967226 4237 3617 3662 1550 2596 4524 4171 3308 3325 3881 2927 4008 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 3.29896292131268e-06 4.23163104572409e-06 4255 3417.72727272727 3617 2.99906169837484e-07 1738 2.16330403472749 2.26092992049343 1 3.35587806163041 3133 4254 2446 3725 3617 2690 1738 4254 3977 3232 4529 4009 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 0.000450553078224159 0.000473211065691596 3620 3460.27272727273 3618 4.09677615037703e-05 2494 1.40759098950855 -1.99655948178455 -1 1.35060241841034 3618 4315 3103 3962 4473 2976 2545 2494 4082 3712 2783 4010 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 1.42863583568434e-06 2.01228324214565e-06 3895 3410.54545454545 3618 1.29876069401147e-07 1739 1.35959792903388 1.32135439381442 1 2.23552907478604 3894 1739 3293 4189 3262 3975 4462 3618 4036 3104 1944 4011 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 4.82351298074932e-07 8.40110009931246e-07 4630 3687.09090909091 3618 4.38501276209792e-08 2565 1.51120893932354 -1.63897388282512 -1 2.65045589017861 4630 3289 3555 3475 2565 4258 3697 3671 3618 3556 4244 4012 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 4.76985618966225e-08 3.0179250958721e-07 3635 3077.63636363636 3619 4.33623299370754e-09 313 1.79899033378407 1.65213015444357 1 3.38632654685869 3632 1479 2439 3631 313 3619 4146 4394 3404 2367 4430 4013 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 7.55324745782114e-07 1.19195346041176e-06 3620 3595.63636363636 3620 6.86659095552231e-08 2858 1.37364413618433 -1.46113516962954 -1 2.34884571197528 3423 3620 3767 2976 2858 4361 3727 2876 4171 4156 3617 4014 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 5.07937369902655e-06 6.28595801242929e-06 3620 3320.09090909091 3620 4.61762311486735e-07 1296 2.64628671961297 -2.36292860139659 -1 3.97397886085218 3620 3162 1296 3829 3759 3916 3496 3030 4249 1565 4599 4015 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 1.46608300651765e-05 1.69522581841335e-05 3620 3575.27272727273 3620 1.46609267890468e-06 1768 1.24607477580539 -1.55050459565454 -1 1.71576689484954 3252 2466 4508 3620 4067 4351 4553 1768 3617 4155 2971 4016 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 3.77709232827536e-06 4.76553750052385e-06 1280 3141.72727272727 3622 3.43372619366386e-07 1279 1.02614670566085 1.1634366498725 1 1.57609126098148 1279 3622 4067 4071 3678 2216 1838 2304 4053 4502 2929 4017 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 3.46432872448841e-06 4.41339583794474e-06 3530 3579 3624 3.14939470887374e-07 2092 0.881612536279178 -0.625207312466338 -1 1.36246271380047 3528 4317 3603 4438 3640 4002 3057 2092 3624 3956 3112 4018 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 6.56022167103944e-07 1.06957672840436e-06 3835 3128.09090909091 3625 5.96383966113197e-08 1285 0.913479291056571 0.743712557293856 1 1.57411417552194 3835 1868 3625 1306 2759 4135 3096 3807 1285 4295 4398 4019 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 1.40203841564254e-07 3.95628276480565e-07 4355 3556.81818181818 3625 1.27458045908462e-08 1436 1.8406340414028 1.60910889264737 1 3.40224018597096 4354 4402 3004 4593 1436 3625 3460 3496 4091 3819 2845 4020 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 3.92815624551506e-07 7.19184377766178e-07 4400 3541.54545454545 3626 3.57105176990689e-08 1528 1.83944754211447 -1.48048805803351 -1 3.26218062671911 4396 3325 2707 1528 2418 4607 3626 4411 4058 3356 4525 4021 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 8.0444917636498e-07 1.2577012628164e-06 4675 3358.90909090909 3628 7.31317700471802e-08 793 1.84194469039453 1.76146608259809 1 3.13750139840713 4673 4148 3178 4003 2895 4497 3628 2952 2091 4090 793 4022 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 3.957864816453e-06 4.98030443445965e-06 3320 3552.09090909091 3630 3.5980653970785e-07 2508 1.13129736997878 -1.38212747455364 -1 1.73142983311169 3316 3630 4058 3524 3690 3644 3566 2904 3823 4410 2508 4023 M19888 KEGG_ACUTE_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ACUTE_MYELOID_LEUKEMIA.html Acute myeloid leukemia 64/71 KEGG 2.30649397202548e-05 2.60695678830467e-05 3375 3471.81818181818 3631 2.09683468528155e-06 1756 1.54200457336617 -1.63219719623884 -1 2.04022339765476 3631 4173 3730 1756 4141 3372 3403 3372 2554 4355 3703 4024 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 7.36013448028548e-07 1.17008537376044e-06 3705 3341.72727272727 3631 6.69103358421015e-08 655 1.48060557943547 1.62064190771125 1 2.53524838771752 3703 3602 3763 655 2836 3451 3797 4294 2596 4431 3631 4025 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 0.000877048171315999 0.00091222286659575 1700 3299.18181818182 3631 7.97634553710196e-05 1508 1.38959200055632 -1.62856262209891 -1 1.21894226581218 1696 4017 3631 4002 4522 2680 2661 1508 4575 4289 2710 4026 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 7.64982247868992e-07 1.20477684682738e-06 4255 3592.09090909091 3631 6.95438648971035e-08 2194 2.04159455488336 -2.07549535985792 -1 3.48867827925229 4254 4225 2194 4620 2865 4547 4601 3631 3628 2507 2441 4027 M10579 BIOCARTA_EDG1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EDG1_PATHWAY.html Phospholipids as signalling intermediaries 43/51 BioCarta 1.48991318490703e-06 2.08182067281266e-06 4375 3533 3632 1.35446744902433e-07 1546 1.48374581710551 -1.1699306694854 -1 2.43341733823465 4374 3673 3278 1546 3288 3578 4348 2950 3632 3899 4297 4028 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 7.64982247868992e-07 1.20477684682738e-06 4255 3593.09090909091 3632 6.95438648971035e-08 2195 2.04159455488336 -2.07549535985792 -1 3.48867827925229 4255 4226 2195 4621 2866 4548 4602 3632 3629 2508 2442 4029 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 2.79638935817308e-06 3.64209651505986e-06 3800 3207 3633 2.54217537511906e-07 472 1.42920697798923 1.26505714954113 1 2.24369012150391 3800 2301 3633 2861 3553 3732 3954 3437 472 3762 3772 4030 M776 REACTOME_PROTEIN_FOLDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROTEIN_FOLDING.html Genes involved in Protein folding 62/70 Reactome 1.18778423732746e-06 1.72821874235068e-06 4200 3400.45454545455 3634 1.07980443510449e-07 331 1.76307108188908 1.97564279666765 1 2.93284584335215 4198 3314 3039 2013 3141 4684 4560 4662 331 3634 3829 4031 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 1.19191235778946e-07 3.66742263935217e-07 4205 3618 3634 1.19191242171894e-08 1380 0.695882507787967 -0.89322012902301 -1 1.29235458344319 4205 2922 4702 2919 1380 3219 3148 4399 4554 4716 3634 4032 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 2.33152392722119e-07 5.17056952161443e-07 3325 3489.90909090909 3635 2.11956743119301e-08 1948 1.8355926181533 1.92315567015326 1 3.33129994134446 3322 3995 2902 4452 1948 3662 3369 3817 3635 3338 3949 4033 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 3.22696730547512e-06 4.1513452389868e-06 4330 3368.90909090909 3636 2.93361094437382e-07 523 1.86348606786707 -2.0210190137305 -1 2.89513525761368 4326 3031 2892 2177 3606 4666 4399 3942 523 3636 3860 4034 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 4.0071557721874e-08 2.9351990282604e-07 3810 3187.72727272727 3637 3.6428689501592e-09 184 1.78878355278896 1.87171401080242 1 3.37334400669024 3806 3577 2981 2457 184 3637 3908 4361 2239 4037 3878 4035 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 9.79329397453792e-08 3.40385475403674e-07 3835 3135.18181818182 3638 8.90299491862377e-09 1080 1.7051934584205 -1.31639156655833 -1 3.18398921162915 3834 3638 3028 1540 1080 4230 4331 3441 1266 3817 4282 4036 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 0.0113969435955372 0.011620992389487 4470 3422 3638 0.00104149240308458 1502 1.91043781657109 -1.5658508490269 -1 1.0664785272909 4468 3738 2783 4354 4608 3079 2323 3638 1502 3408 3741 4037 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 2.25056796234729e-07 5.05548030396173e-07 3795 3459.90909090909 3638 2.04597108416104e-08 1915 1.57012293484619 1.72474334807697 1 2.85382375585182 3411 3240 3523 4084 1915 3794 3689 3657 3313 3795 3638 4038 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 1.01533184692293e-06 1.51321955082924e-06 4645 3535.54545454545 3640 9.23029377739615e-08 1736 1.85926787482775 1.88682241709918 1 3.12389177820231 4645 3640 2843 1736 3056 4675 3863 2593 4172 2955 4713 4039 M19752 REACTOME_COMPLEMENT_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMPLEMENT_CASCADE.html Genes involved in Complement cascade 22/39 Reactome 9.09544004622507e-08 3.33570140001417e-07 3640 3343.81818181818 3640 8.26858220205186e-09 993 2.47349955364116 -2.54539965391687 -1 4.62525580073944 3640 3428 1483 4540 993 4676 4387 4396 4202 1838 3199 4040 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 0.000183369212808866 0.000195992455719622 2310 3470.45454545455 3642 1.6671318031894e-05 1751 1.0949197552697 1.27484418111772 1 1.17143505335578 2306 4325 3642 4616 4398 2789 1751 2684 4506 3713 3445 4041 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 0.000324434112153472 0.000342043558044313 3490 3525.81818181818 3643 3.2448148776017e-05 1029 1.84162385501803 -1.62103756428678 -1 1.84229737128162 3487 3528 4637 4160 4478 4017 3643 1029 3943 3075 2787 4042 M9503 BIOCARTA_FAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FAS_PATHWAY.html FAS signaling pathway ( CD95 ) 31/35 BioCarta 2.80352600065327e-07 5.72346138541671e-07 3805 3469.72727272727 3644 2.54866032537733e-08 2135 1.26569348895177 -0.967760686306813 -1 2.28063352627275 3802 2740 3644 3711 2135 3157 3252 4468 2947 3937 4374 4043 M3158 REACTOME_S_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_S_PHASE.html Genes involved in S Phase 111/124 Reactome 0.00066134890650522 0.000690764956562212 1180 3427.09090909091 3644 6.01407091261259e-05 1180 1.14895760061566 1.22584592674443 1 1.04777900668375 1180 4136 4081 2509 4501 2605 3237 3297 4134 4374 3644 4044 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 1.57294836199926e-05 1.81125061445145e-05 2775 3135.81818181818 3644 1.42996328029402e-06 1479 1.88077413048097 2.28490490598373 1 2.57453219151066 2775 3943 2499 3967 4059 2018 1479 3644 3789 3688 2633 4045 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 0.00012058920593697 0.000129861065941706 2475 3628.36363636364 3645 1.09632560303279e-05 2471 0.997853423852759 0.969216075587052 1 1.11901797130102 2471 4625 3645 3776 4362 2688 2841 3588 4660 4162 3094 4046 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 8.74807758620425e-06 1.04217380633226e-05 4720 3595.27272727273 3645 7.95282942931274e-07 2267 1.98319157136038 -1.73631303879766 -1 2.85223903843347 4719 3986 2640 3452 3915 4385 4695 2267 3645 3343 2501 4047 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 5.90914185502447e-05 6.46526415292431e-05 1665 2904.27272727273 3646 5.90929899171385e-06 476 0.957571247797254 -0.957571247797254 -1 1.15756332388379 1665 4074 4566 4410 4303 1330 476 2175 4490 3646 812 4048 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 3.52094724834006e-06 4.4728424481164e-06 4200 3392.36363636364 3647 3.52095282703379e-07 863 1.41637331971447 -1.57295941639464 -1 2.18703925327988 4197 3204 4346 3647 3685 4091 3179 863 4204 2704 3196 4049 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 0.000845984788175826 0.000880689942697375 4285 3343.63636363636 3647 8.46307021456529e-05 569 3.10155235386528 1.03692282481674 1 2.73540854334841 4285 3811 4569 2349 4527 4619 3610 1863 569 3647 2931 4050 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 4.94231746863686e-07 8.56692561585236e-07 3650 3688.09090909091 3649 4.49301688993886e-08 2577 1.20421276977944 -1.09858888220482 -1 2.10889934188 3649 4119 4033 3534 2577 3078 3291 4315 4227 4205 3541 4051 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 1.32956894791292e-07 3.83038247822062e-07 3655 3468.27272727273 3653 1.20869911660487e-08 1392 1.11301266683083 -1.00487724577459 -1 2.06147361212665 3653 4549 3599 4615 1392 2950 3135 2319 3908 4146 3885 4052 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 2.33963986767362e-06 3.11248595699534e-06 1630 3149.81818181818 3654 2.12694759620034e-07 1628 1.41114249164018 -1.42882365198423 -1 2.24312867307066 1628 3950 3681 4014 3477 2419 3654 1919 4088 3747 2071 4053 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 6.26099058427651e-08 3.14536172538656e-07 3925 3176.09090909091 3654 5.69180978405306e-09 579 1.85608447141601 -1.65532731153209 -1 3.48419775590434 3924 3846 2820 3965 579 3654 3775 3089 3110 1823 4352 4054 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 1.24726230606164e-06 1.80032968948347e-06 3660 3434.27272727273 3656 1.13387546652897e-07 1399 2.38394635954105 -2.48600254303697 -1 3.95374575512948 3656 3365 1399 4393 3169 4473 4421 3719 4180 1607 3395 4055 M136 PID_FOXO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FOXO_PATHWAY.html FoxO family signaling 18832364 57/65 Pathway Interaction Database 3.70914505441562e-06 4.68607191028955e-06 1705 2977.09090909091 3657 3.37195573450574e-07 1384 1.21649158061716 1.38432697082991 1 1.87117313329706 1703 3657 3934 3797 3673 1639 1384 3136 3735 4398 1692 4056 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 9.24322170952514e-08 3.3560004976122e-07 4665 3263.72727272727 3659 8.40292917988711e-09 1011 1.96055990536024 -1.65704057148111 -1 3.66442741146688 4663 4104 2717 1981 1011 3907 4229 3659 1686 3517 4427 4057 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 8.75892763088746e-07 1.34542623383529e-06 4470 3538.81818181818 3660 7.96266465282563e-08 1542 1.52544126000484 -1.56483780560968 -1 2.58533431023209 4466 3301 3325 1542 2955 4590 4325 3660 3973 3122 3668 4058 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 1.59566736006844e-06 2.21711802753107e-06 4635 3826.27272727273 3660 1.45060774310227e-07 2934 1.68306499912215 -2.20616796435862 -1 2.74713631234508 4633 4037 3128 3660 3311 4634 4699 3868 3634 3551 2934 4059 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 3.61142374726127e-06 4.57485777967612e-06 4110 3300.18181818182 3661 3.28311788693647e-07 440 2.22319717904651 -1.36150060554443 -1 3.42706887450551 4110 3189 2325 4139 3661 4458 4397 4228 440 2797 2558 4060 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 3.59179853227503e-05 3.98525836209171e-05 3410 3664.09090909091 3661 3.26532470418218e-06 2778 1.6329795186673 -1.17809671451585 -1 2.07372636511041 3406 3457 3169 4420 4222 3832 4211 2778 3661 3752 3397 4061 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 0.00214586168548 0.00221484083871979 1875 3117.54545454545 3662 0.000214793663104919 1156 1.44014479828735 1.44014479828735 1 1.10311076651094 1875 3816 4375 3662 4695 2334 1156 1714 4305 3867 2494 4062 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 2.26944364499895e-07 5.07021281482396e-07 3975 3275.81818181818 3663 2.06313079918811e-08 398 1.41570593527164 -1.29579241378212 -1 2.57255719122653 3301 3663 3542 4467 1926 4412 3974 398 3972 4071 2308 4063 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 2.52886918304879e-06 3.33601524426782e-06 3665 3055.54545454545 3663 2.29897462723015e-07 1354 2.2659049953422 2.69611702593559 1 3.58265838192622 3663 1801 1558 3843 3506 3890 2173 3688 4404 1354 3731 4064 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 2.35480258021622e-06 3.13001075151241e-06 3800 3475.27272727273 3666 2.14073190974347e-07 2012 1.7581586715587 1.25455992749791 1 2.7937136659548 3799 3463 3064 2012 3480 4019 4374 3749 2135 3666 4467 4065 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 4.50006987060383e-07 7.95517969634834e-07 3670 3329.63636363636 3668 4.09097344644293e-08 1037 1.74991396333264 1.78546736278359 1 3.0812171556849 3668 3461 2947 2645 2519 3908 4681 4110 1037 3916 3734 4066 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 4.04146665847083e-05 4.47157117392928e-05 695 2566.90909090909 3668 3.67412809395214e-06 422 1.26976279666277 1.39880700780702 1 1.59395015706676 695 3727 3668 4473 4236 706 422 1019 3959 4048 1283 4067 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 1.22177802647144e-07 3.70192774369017e-07 3310 3212.45454545455 3669 1.11070735847576e-08 1308 1.58320794060878 1.72053719763878 1 2.939485366565 3309 3893 3669 3696 1308 3681 2695 2511 2893 3781 3901 4068 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 2.48338298648365e-05 2.79550863253108e-05 1155 2630.72727272727 3670 2.25764638146663e-06 353 1.11996568756528 -1.03535609103543 -1 1.47178085137278 1153 4571 3670 4476 4158 691 353 931 4518 3989 428 4069 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 5.05853827240319e-05 5.55262805714955e-05 3275 3738.27272727273 3670 5.05865342573496e-06 2926 2.40621626710879 3.15457622566339 1 2.95598557994223 3274 3814 4667 2926 4281 3670 3153 4540 3312 3648 3836 4070 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 1.60136594463019e-06 2.22438118265288e-06 2840 3397.09090909091 3672 1.45578828205038e-07 1591 0.91653096382364 -0.886728595944971 -1 1.49521412020693 2836 3768 3672 3991 3312 3176 4151 2035 4572 4264 1591 4071 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 8.45443547828584e-06 1.00878211087379e-05 3775 3516 3673 8.45446764332371e-07 2356 1.57641761298029 2.01191960403973 1 2.27347539339108 3771 3518 4377 3917 3931 3368 2763 2356 3232 3770 3673 4072 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 5.14053304497715e-22 2.92329108099906e-20 4415 2724.36363636364 3673 5.14053304497715e-23 47 2.45975349840693 -2.27996018489421 -1 13.8740129194527 4411 1041 4499 54 620 4664 4540 3673 1751 47 4668 4073 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 2.06617799566465e-05 2.34883433033168e-05 3130 3651.18181818182 3676 1.87836127352837e-06 2236 1.5864860426626 -1.32223477089478 -1 2.11984595115956 3126 3676 3326 2236 4117 3853 4718 4587 2935 3602 3987 4074 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 4.4752252521588e-07 7.92610251039008e-07 4425 3357.81818181818 3678 4.06838742046035e-08 994 1.70128634325978 -1.34729022540514 -1 2.99635185084518 4422 2649 3050 3678 2514 4426 4065 2891 994 3872 4375 4075 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 3.0087481725131e-06 3.89931119556887e-06 1230 3447.81818181818 3680 2.73522935211227e-07 1227 1.2253966338593 1.14086078642643 1 1.91312168023203 1227 4363 4133 4317 3576 2212 2341 3680 4041 4588 3448 4076 M5113 REACTOME_GLYCOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOLYSIS.html Genes involved in Glycolysis 29/44 Reactome 3.33898686955804e-07 6.4099386103601e-07 4320 3642.27272727273 3681 3.03544306938481e-08 2290 1.07805253708221 -1.2154592035673 -1 1.92708391557103 4316 3399 3578 3746 2290 3648 4060 3681 3843 4013 3491 4077 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 3.45435288652634e-06 4.40187516857568e-06 1145 3366.09090909091 3681 3.45435825618732e-07 1143 1.25474621007878 1.18672874057414 1 1.93988725216606 1143 4689 4286 4329 3681 2321 2064 2682 3878 4661 3293 4078 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 4.79342675277151e-06 5.95707590128529e-06 4455 3553 3681 4.35767017897002e-07 2154 2.30271147425555 -1.30039271908707 -1 3.47343219811415 4452 3320 2154 3959 3743 4453 3985 2503 3604 3229 3681 4079 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 1.12591070255879e-06 1.65091597268639e-06 3365 3794 3682 1.02355570797734e-07 3041 1.27035758214281 -1.13207951125998 -1 2.12027298960349 3365 4703 4146 4527 3112 3244 3041 3682 4137 4599 3178 4080 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 1.04606609626402e-06 1.55362868922787e-06 4410 3679.09090909091 3682 9.50969630593323e-08 2941 1.74237150221866 -1.08982099098059 -1 2.92167296888443 4410 3695 2941 3416 3066 3399 4057 4241 3682 3459 4104 4081 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 2.81295202321195e-08 2.57960516180675e-07 4305 2872.18181818182 3686 2.55722914470797e-09 29 3.01849078978325 -3.09067940199014 -1 5.74184142160257 4302 1681 649 4111 29 4056 3686 4488 2955 1099 4538 4082 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 9.67654652365825e-08 3.39696808054909e-07 4670 3218.90909090909 3687 8.79686086297678e-09 168 1.4086065777495 -1.28913544639139 -1 2.63040109778851 4667 168 3341 2952 1064 4346 3778 3696 3687 3571 4138 4083 M4086 KEGG_PROPANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROPANOATE_METABOLISM.html Propanoate metabolism 33/36 KEGG 2.72625511721561e-06 3.56254821518763e-06 4185 3643.09090909091 3688 2.47841681419596e-07 1841 1.86162153622356 -1.80644280425527 -1 2.92794737507931 4185 3095 2819 3688 3540 4369 4497 4531 1841 3449 4060 4084 M18937 KEGG_NUCLEOTIDE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NUCLEOTIDE_EXCISION_REPAIR.html Nucleotide excision repair 45/47 KEGG 0.000278206170181551 0.000294292497368202 4445 3347 3688 2.52946688751238e-05 1602 0.85591520297332 0.899413976334333 1 0.871907162090288 1602 3688 4047 4504 4442 2192 1755 2552 4442 4568 3025 4085 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 0.000566685656302183 0.000593072349832884 1140 3207.72727272727 3689 5.15301525765234e-05 1138 0.875829558660694 0.930476786565789 1 0.815246446245204 1138 3689 4037 4065 4490 1973 1385 2571 4445 4545 2947 4086 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 3.74124879946195e-06 4.72289604831041e-06 4240 3813.54545454545 3689 3.40114105611248e-07 3071 1.31888557140399 -1.31926238666684 -1 2.02745052308628 4238 3071 3506 4405 3675 4148 3464 3932 3290 3689 4531 4087 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 0.00316934218128623 0.00325697694223187 3690 3439.27272727273 3689 0.000317387140365162 539 5.82519178475206 -6.03774189891158 -1 4.1828509980933 3689 4657 4687 2088 4647 3253 539 3826 4450 3479 2517 4088 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 0.00227321260446251 0.0023447472668407 2780 3533.72727272727 3691 0.000227554133082767 452 0.548899064439403 0.548899064439403 1 0.415984850783461 2779 3542 4376 3691 4648 2842 452 3714 4645 4698 3484 4089 M12975 BIOCARTA_VEGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VEGF_PATHWAY.html VEGF, Hypoxia, and Angiogenesis 40/64 BioCarta 4.00908328653965e-06 5.04072272575043e-06 2425 3551.90909090909 3692 3.64462781123018e-07 2422 1.66910685411472 1.41730021807174 1 2.55242274947577 2422 4213 3129 3748 3692 3324 2959 3629 3899 4067 3989 4090 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 9.67991963631043e-08 3.39696808054909e-07 3575 3664.27272727273 3693 9.67992005796425e-09 1174 1.44279582453721 -1.41575520693243 -1 2.69426625483663 3573 4679 4415 3009 1174 3693 4558 4288 3172 4624 3122 4091 M18053 BIOCARTA_LEPTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LEPTIN_PATHWAY.html Reversal of Insulin Resistance by Leptin 15/35 BioCarta 1.16053654017438e-05 1.36092732164548e-05 3885 3408.27272727273 3694 1.0550387838569e-06 1995 1.9540710715843 -1.2820308612692 -1 2.74494962794708 3883 2838 2638 3927 3982 3694 2683 4691 1995 2623 4537 4092 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 3.17383403894676e-07 6.19797131312732e-07 3580 3697.36363636364 3694 2.88530408801874e-08 2250 1.58954143215953 -1.68124195491287 -1 2.84851323634365 4597 3885 3583 3970 2250 3994 3576 3694 3580 3878 3664 4093 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 0.314439698776651 0.315912170759002 3555 3543.54545454545 3695 0.0337376448502598 1252 2.62216032959754 -1.67202963698445 -1 0.378060117958212 3555 4298 3230 4258 4697 3695 2172 3655 1252 4115 4052 4094 M185 PID_ALK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK1_PATHWAY.html ALK1 signaling events 18832364 29/33 Pathway Interaction Database 0.00995021325124545 0.0101567920730706 2060 3346 3697 0.000908682122926464 1464 1.16879342363591 1.36410261447684 1 0.671869834482503 2057 4560 3697 4480 4631 1960 2429 3269 4247 4012 1464 4095 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 2.47597249411367e-05 2.78849681990372e-05 3850 3353.72727272727 3698 2.25090941835286e-06 1911 1.51213140976429 1.98338488769387 1 1.98791555861093 3846 3776 3199 2455 4156 4409 3338 1911 3698 3969 2134 4096 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 4.1112315934987e-06 5.16090774503029e-06 3510 3655.90909090909 3700 3.73749025122586e-07 2262 1.44827893111642 -1.09466314040332 -1 2.21033581088847 3506 4219 3679 3730 3700 3246 2262 4606 4101 4025 3141 4097 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 1.62184585789604e-07 4.23402237238346e-07 3925 2903.27272727273 3701 1.4744054340536e-08 1169 2.66408669416878 -1.7619127642911 -1 4.90203301924192 3922 2336 1169 2126 1594 3771 4036 3954 3701 1620 3707 4098 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 8.88657442218683e-07 1.35919090319902e-06 3295 3579.63636363636 3703 8.07870728344462e-08 2601 1.1670489548484 -1.42619065350732 -1 1.97623506095927 3295 3703 3695 4234 2969 3996 4018 2601 4115 3876 2874 4099 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 1.5419830925572e-07 4.14709982727636e-07 4545 3218.45454545455 3703 1.40180290966821e-08 1439 1.71870753718944 -1.30815589948429 -1 3.16666045229571 4542 1630 2688 3846 1530 4672 3703 4618 1439 2233 4502 4100 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 4.10267555607893e-07 7.39546157616882e-07 3965 3669.36363636364 3703 3.72970574651602e-08 2461 1.5308469697488 -1.53486482254533 -1 2.70938644033986 3961 3380 3144 3442 2461 4693 4091 4119 2803 3703 4566 4101 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 8.76087768725827e-07 1.34542623383529e-06 4415 3286.09090909091 3704 7.96443743275631e-08 1189 1.97899247365403 2.2282372339287 1 3.35427389477295 4415 2683 1740 2893 2957 4411 4490 3725 3940 1189 3704 4102 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 2.52128822780713e-06 3.32973711114987e-06 2400 3684.36363636364 3704 2.29208283391744e-07 2396 1.39615747822844 1.34770242685617 1 2.20748597253981 2396 4163 3807 2988 3502 3704 4034 3455 4349 4450 3680 4103 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 0.00503347272410563 0.00515469543453647 3485 3440 3705 0.000458638731102723 835 1.13545986493288 1.15630601123628 1 0.749262074937968 3485 4067 3705 4248 4589 2800 835 2475 4535 4118 2983 4104 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 1.9404601245765e-06 2.63947313775247e-06 2735 3687.18181818182 3706 1.76405621465225e-07 2731 1.13181829334986 -1.10924243256623 -1 1.82234678849238 2731 4371 4145 3004 3389 3706 3476 3889 3177 4631 4040 4105 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 7.26946753680442e-07 1.15918536397692e-06 4020 3581.54545454545 3708 6.60860903532561e-08 2527 1.88992556302872 -1.34296162710975 -1 3.23858543365478 4017 3708 2527 4167 2826 4137 4160 2560 3264 3616 4415 4106 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 9.92164288194492e-08 3.41247265430585e-07 3875 2745.63636363636 3709 9.01967575399537e-09 1086 2.28214661649231 -1.97257017215616 -1 4.2608614774514 3873 1501 1301 1086 1097 3709 3773 4026 3763 1893 4180 4107 M15216 REACTOME_BOTULINUM_NEUROTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BOTULINUM_NEUROTOXICITY.html Genes involved in Botulinum neurotoxicity 15/20 Reactome 0.000228902615904587 0.000243283122510617 3315 3613.36363636364 3710 2.08114941748458e-05 1786 0.868427959359629 -0.743444097731811 -1 0.905396834409215 3314 3469 3710 3460 4417 3136 1786 3799 4464 4262 3930 4108 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 2.53525149788297e-07 5.39999416516589e-07 4685 3658.72727272727 3710 2.30477435458374e-08 2036 1.69841754527287 1.75204773982895 1 3.07303804077528 4682 3559 3619 2961 2036 3830 3901 4597 2724 3710 4627 4109 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 0.000228902615904587 0.000243283122510617 3315 3607.90909090909 3711 2.08114941748458e-05 1787 0.868427959359629 -0.743444097731811 -1 0.905396834409215 3315 3470 3711 3461 4418 3137 1787 3729 4465 4263 3931 4110 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 4.28081873589105e-06 5.35669788796547e-06 2165 3558.18181818182 3712 3.8916609687683e-07 2116 0.869400125921488 0.909828600679099 1 1.32245792418605 2161 4445 4134 4311 3712 2668 2116 3353 4517 4543 3180 4111 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 3.04075717693679e-06 3.9321572260662e-06 3790 3561.45454545455 3714 2.7643285270591e-07 2375 1.37684994857648 -1.4855976288593 -1 2.14823266856151 3788 4308 3411 3926 3586 4075 3320 2375 3895 3714 2778 4112 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 5.64935800400324e-08 3.08669609517152e-07 4275 3050.81818181818 3714 5.64935814762185e-09 574 1.88269324589313 -1.59317941495698 -1 3.53860477792423 4272 2487 4321 1440 574 3714 4702 4105 1758 2151 4035 4113 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 5.39334848126924e-06 6.64489815494409e-06 2855 3482 3715 4.90305609384298e-07 2555 1.65675382647356 2.04898967509872 1 2.47611873132226 2854 4146 3715 2995 3776 3791 3309 3048 2555 4381 3732 4114 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 8.26094663185129e-08 3.27411388472988e-07 2610 3048.90909090909 3717 7.50995176549805e-09 886 1.35612644819451 -0.951290883822956 -1 2.53863346902209 2608 3895 3835 3717 886 2696 2084 4238 1264 4189 4126 4115 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 4.41902233399917e-08 2.97677410474742e-07 4405 3355.27272727273 3717 4.01729311160157e-09 259 1.78891238729868 -1.62043610836162 -1 3.37043162769629 4405 3717 2863 3580 259 4218 3941 4310 2558 3905 3152 4116 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 1.27120783324502e-06 1.82874153395809e-06 3920 3291.27272727273 3717 1.15564415252467e-07 1331 2.10733333234743 -1.98678292772001 -1 3.49074837959045 3916 3899 1717 2467 3184 3717 3293 3929 4093 1331 4658 4117 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 1.96850300488979e-07 4.69733780742154e-07 4145 3494.18181818182 3717 1.7895483463876e-08 1778 1.01829045577537 -0.774440136261727 -1 1.85990464980516 4144 3080 3864 4237 1778 3457 2668 3717 3244 4027 4220 4118 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 2.99011374004858e-07 5.98022748009716e-07 2825 3578.36363636364 3719 2.71828558767978e-08 2190 1.27782442203206 1.38623496959083 1 2.29546776090942 2821 3910 3719 4614 2190 4081 4581 3039 3000 3818 3589 4119 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 0.00022790491601199 0.000242331877354493 2785 3440.18181818182 3720 2.07207753475762e-05 1875 1.82654157856371 -1.2189605564638 -1 1.90614491720009 2784 4629 3235 3720 4416 2890 2468 3773 3939 4113 1875 4120 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 6.01473167444394e-06 7.35480142574492e-06 2390 3118.81818181818 3720 5.4679528350877e-07 467 1.15056357784787 1.12169628428135 1 1.70467756515773 2389 4258 3720 4454 3805 1529 467 2600 4419 3722 2944 4121 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 1.33892524446607e-05 1.55735021041889e-05 4160 3152.81818181818 3720 1.21721217569678e-06 1487 1.98414530290326 -1.9265671398024 -1 2.75366216025498 4156 2799 2011 1487 4013 4202 4112 3720 1741 1901 4539 4122 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 0.000133093397210397 0.000143098140053092 3355 3691 3721 1.33101369115948e-05 2567 1.65314370365064 -1.81844459477455 -1 1.83431913841686 3355 4330 4426 4386 4381 3646 3721 2567 3359 3771 2659 4123 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 0.000103926507084833 0.000112198790814367 1835 3353.54545454545 3721 9.44831062065568e-06 1141 1.04870420273149 0.860788375277286 1 1.19531401584313 1833 4580 3721 4062 4351 1862 1141 3154 4652 4404 3129 4124 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 1.25817877375561e-06 1.81553158426367e-06 3780 3589.90909090909 3722 1.14379953937084e-07 1713 1.58108356827006 1.78605161255126 1 2.6202503502243 3779 2698 2986 3713 3172 4627 4678 4233 3722 1713 4168 4125 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 8.20166396415256e-08 3.27411388472988e-07 4545 3362.63636363636 3724 7.4560584271936e-09 875 1.68016796790295 -1.40300270171715 -1 3.14543658326538 4544 1092 3724 2902 875 4077 4709 4517 2648 3378 4523 4126 M13720 KEGG_LYSINE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSINE_DEGRADATION.html Lysine degradation 47/50 KEGG 6.09557231668999e-06 7.44208518747459e-06 3350 3693.90909090909 3725 5.54144473258842e-07 2733 1.59881100516132 1.71442048143443 1 2.36677201642995 3350 4199 3655 4273 3811 3027 2733 4593 3725 4185 3082 4127 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 8.83605366699858e-08 3.31003670356505e-07 3550 3425.81818181818 3725 8.03277638353529e-09 962 1.33740418304498 0.973820953102714 1 2.50174379735855 3548 3725 3608 3144 962 4090 3728 3837 2198 4207 4637 4128 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 3.58334088737425e-07 6.73839401928545e-07 1830 3278.18181818182 3726 3.25758315547803e-08 1826 1.15713390538908 -1.03243055463687 -1 2.06125815250443 1826 4182 3995 4067 2346 2366 2034 3726 3795 4514 3209 4129 M4732 BIOCARTA_LECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LECTIN_PATHWAY.html Lectin Induced Complement Pathway 10/15 BioCarta 1.82692811079036e-05 2.08943559072704e-05 3375 3566.27272727273 3727 1.66085752925209e-06 2082 2.03690056315495 -2.52389266406537 -1 2.75182314217439 3375 4314 2103 4177 4093 3727 4029 3504 4405 2082 3420 4130 M557 REACTOME_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEFENSINS.html Genes involved in Defensins 6/110 Reactome 0.279596155742415 0.280965266149499 3585 3960.09090909091 3727 0.0322624291368627 3185 1.07923973684482 -1.03495841513733 -1 0.170963802250552 3583 4338 4208 3727 4669 3562 3185 4697 4692 3465 3435 4131 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 4.80162018053893e-07 8.37223762546869e-07 3730 3379.90909090909 3727 4.36511020774462e-08 1913 0.790352252270541 -0.637947164034229 -1 1.38610110305935 2696 3779 3805 3729 2562 2879 1913 3727 4246 4228 3615 4132 M565 REACTOME_BETA_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BETA_DEFENSINS.html Genes involved in Beta defensins 6/55 Reactome 0.279596155742415 0.280965266149499 3585 3961.09090909091 3728 0.0322624291368627 3186 1.07923973684482 -1.03495841513733 -1 0.170963802250552 3584 4339 4209 3728 4670 3563 3186 4698 4693 3466 3436 4133 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 6.76689648784398e-08 3.14536172538656e-07 2775 3393.18181818182 3728 6.15172426907671e-09 673 1.32356364808483 -1.23956546738837 -1 2.48431517553122 2771 4372 4061 4079 673 2798 2936 3811 3728 4562 3534 4134 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 5.49653938316474e-07 9.31549942137795e-07 3135 3347.72727272727 3729 4.99685523312315e-08 1813 2.09884909476252 2.08043678947182 1 3.65423762891973 3135 2588 1813 3880 2643 4088 4594 4193 3734 2428 3729 4135 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 1.01612046572805e-05 1.20082338463605e-05 1430 3047.18181818182 3729 9.2375014449441e-07 1112 1.26687407555436 1.47504047185814 1 1.79920276338625 1428 4511 3729 4649 3948 2275 1854 1112 3919 4201 1893 4136 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 3.22360186303246e-07 6.26922158776812e-07 2565 3710.54545454545 3733 2.93054757761675e-08 2261 1.29726715025765 -1.24311346803198 -1 2.32272967931717 2565 4695 4180 4330 2261 3517 3305 3676 3733 4641 3913 4137 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 2.09727790979893e-06 2.82348880041385e-06 3680 3524.54545454545 3735 1.90661809923064e-07 2379 1.04128911520418 -1.14396682556596 -1 1.66771561602274 3677 3735 3762 2956 3431 3862 3971 3091 3960 3946 2379 4138 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 8.97975952502385e-05 9.73684010064612e-05 3735 3215.18181818182 3735 8.16375097601047e-06 36 4.20202394471385 -2.98023244463009 -1 4.86676951024143 3735 3786 2302 2737 4328 3825 3150 3271 36 3804 4393 4139 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 1.0874105011989e-06 1.60543558512944e-06 4550 3494.09090909091 3735 9.88555489710744e-08 1900 1.25922998954305 -1.41175579870064 -1 2.10610456428097 4547 2807 3250 4223 3090 3735 1900 4367 4324 2395 3797 4140 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 7.37039438847813e-08 3.2144561803028e-07 3890 3489.72727272727 3736 6.70035875945415e-09 760 1.5461969996513 -1.4609821341335 -1 2.89812708450035 3888 3868 3736 3222 760 3721 4241 4617 2284 3650 4400 4141 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 3.72316044778289e-07 6.91862886359655e-07 4320 3431.90909090909 3737 3.38469188897316e-08 1075 1.98607866626945 2.37718271748838 1 3.53193977564145 4320 3937 2806 3428 2381 4659 4017 3169 1075 3737 4222 4142 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 1.29028276258133e-06 1.84998014562086e-06 3450 3636.36363636364 3739 1.17298501756607e-07 2772 1.44384132389665 -1.4001935325514 -1 2.38932740399084 3448 2772 2942 4377 3193 4035 4542 3739 4013 3148 3791 4143 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 4.22273333849466e-06 5.28962350257293e-06 4445 3097.90909090909 3739 4.2227413626807e-07 365 3.49156704218216 -4.95417457118981 -1 5.31919170592361 4444 3208 4593 1823 3739 4720 3843 885 365 2176 4281 4144 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 4.68139888879222e-07 8.2050511530261e-07 3755 3553.45454545455 3739 4.25581807722855e-08 1616 1.31384325040156 1.31801679816522 1 2.30808130523783 3751 1616 3739 4605 2548 4048 4639 3020 3630 2985 4507 4145 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 1.00178690899791e-07 3.41896906035439e-07 3580 3714.27272727273 3740 1.00178695415887e-08 1210 1.28064525649473 -1.11063213860509 -1 2.39033385909659 3576 4683 4456 3012 1210 3740 3539 4347 3402 4702 4190 4146 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 0.000201812926480901 0.000215364461449209 2965 3816.90909090909 3741 1.83483128903576e-05 2288 0.966440287148665 -0.818831420877146 -1 1.02245231814288 2961 4647 3567 4630 4404 3741 3492 2288 4623 4040 3593 4147 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 1.05406931123138e-06 1.56453055000381e-06 3695 3750.09090909091 3742 9.58245287509045e-08 2112 1.42389997849601 1.45194435345375 1 2.38624205559583 3692 4027 3376 4204 3068 4423 4627 2112 4448 3532 3742 4148 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 1.2308850196481e-06 1.78214027384633e-06 4625 3804.45454545455 3744 1.11898700756403e-07 3130 1.19671358652345 -1.13431851513802 -1 1.98582984483803 4621 3665 3744 4028 3161 4498 3130 3202 3508 4333 3959 4149 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 8.78366517522635e-08 3.31003670356505e-07 3755 3420 3745 8.78366552241384e-09 1060 1.63535064283683 -1.39188432631203 -1 3.05927333529797 3753 3547 4272 4479 1060 1687 3208 4713 2726 4430 3745 4150 M7146 BIOCARTA_CLASSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CLASSIC_PATHWAY.html Classical Complement Pathway 13/17 BioCarta 0.00055970474628584 0.000585896296843905 3225 3560.45454545455 3748 5.08951992915813e-05 1975 2.25130896122668 -2.5500498945168 -1 2.10037054122517 3222 4299 1975 4391 4489 3280 2819 3748 4459 2260 4223 4151 M899 REACTOME_IL1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL1_SIGNALING.html Genes involved in Interleukin-1 signaling 43/45 Reactome 3.29124029598464e-05 3.66469785257078e-05 1695 3119.09090909091 3748 2.99208139506689e-06 1656 1.61077280194931 -1.61024015358023 -1 2.06245364466204 1694 4502 3748 4443 4207 1962 1849 2094 4103 4052 1656 4152 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 5.58672051696325e-07 9.43108756797802e-07 4215 3752.72727272727 3749 5.07883812333259e-08 2606 1.46388122219357 1.51603273422877 1 2.54619130548312 4215 4407 3717 3527 2654 3749 2606 3710 4097 4286 4312 4153 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 8.36967853585662e-07 1.29779509491601e-06 3790 3420.90909090909 3750 7.60880156365298e-08 1859 0.917515449210691 -1.03602058478928 -1 1.55881922321361 3786 1859 3750 3456 2924 3863 3827 2791 4154 4164 3056 4154 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 0.000467516745860735 0.0004908093951207 3940 3617.09090909091 3750 4.67615132352074e-05 1829 1.72218844952547 0.866547502083541 1 1.64476912990456 3940 3531 4355 3354 4481 3750 2861 4322 1829 3471 3894 4155 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 0.0178848655871598 0.0182049958100915 2635 3469.72727272727 3752 0.00163926699359336 1403 0.896587114659456 0.896587114659456 1 0.449579361665353 2631 4651 3752 4637 4627 2598 1403 2479 4624 4317 2448 4156 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 1.58210284624929e-05 1.82001594791534e-05 3840 3629.81818181818 3753 1.43828565805562e-06 2459 1.22380797472901 -1.35161638471495 -1 1.67419020566559 3839 3965 3501 3753 4062 3611 3879 2459 4525 3696 2638 4157 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 4.68303819230986e-06 5.82295581340952e-06 3440 3719.27272727273 3753 4.25731650991477e-07 2658 0.870927252816507 -0.662463370598532 -1 1.31566668445404 3439 3789 3753 3718 3740 3424 2658 4311 4084 4122 3874 4158 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 6.20314759506535e-08 3.14150822411035e-07 4100 2939.45454545455 3753 6.20314776822102e-09 681 1.85402242520459 1.97400668894923 1 3.48061100688076 4098 984 4339 1789 681 4436 4590 3753 2499 711 4454 4159 M19784 BIOCARTA_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCR_PATHWAY.html T Cell Receptor Signaling Pathway 61/73 BioCarta 1.16870715116869e-06 1.70677529502358e-06 3785 3384.09090909091 3754 1.06246161092915e-07 222 1.6455555251459 -1.67382503165184 -1 2.73987941600524 3784 3036 3345 222 3128 3754 4368 4514 2966 3851 4257 4160 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 3.70695359585463e-06 4.68455715460076e-06 4145 3658.18181818182 3754 3.36996349273453e-07 2742 1.82355331110927 -1.15341004133978 -1 2.80544217115231 4274 3157 2742 3899 3672 4240 3754 4145 3012 3203 4142 4161 M1045 REACTOME_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IMMUNE_SYSTEM.html Genes involved in Immune System 856/1251 Reactome 2.84722496804206e-07 5.77024553420288e-07 3755 3666 3755 2.84722533284317e-08 2238 1.64968046260377 -1.72521054267053 -1 2.97111080650305 3755 4093 4258 3010 2238 4015 4105 3687 3623 4331 3211 4162 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 4.97442518108502e-06 6.16577911100874e-06 2925 3671.81818181818 3755 4.52221493527738e-07 2054 0.872152004931141 0.80341075677126 1 1.31126108015259 2923 4636 3790 4643 3755 3112 2054 3070 4651 4230 3526 4163 M2482 BIOCARTA_ARAP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARAP_PATHWAY.html ADP-Ribosylation Factor 21/22 BioCarta 1.78547756149803e-07 4.45009336825324e-07 3335 3234.72727272727 3756 1.62316155127633e-08 1203 0.912376462491618 -0.718901777852581 -1 1.672550236253 3333 2803 3813 4225 1685 2134 1203 4369 3938 4323 3756 4164 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 2.33842774740321e-06 3.11175048428056e-06 3760 3418.27272727273 3756 2.12584566633865e-07 1279 2.94681920673096 -3.18364721465381 -1 4.68523955212302 3756 3976 1279 4346 3476 4001 3453 2998 4373 1953 3990 4165 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 0.349125305679307 0.350685559226714 2015 3609.72727272727 3757 0.0382875972460002 2011 1.07982950485903 1.27137519420923 1 0.141040638008883 2011 4312 3725 3757 4676 2969 2228 3562 4432 4268 3767 4166 M5415 BIOCARTA_IL4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL4_PATHWAY.html IL 4 signaling pathway 17/20 BioCarta 4.65096724680981e-05 5.12311911433893e-05 3520 3786.36363636364 3758 4.22824143154851e-06 3283 1.01977453142155 -1.07538640399174 -1 1.26257110814149 3520 3758 3529 3498 4255 3421 3946 3283 4469 4161 3810 4167 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 1.04478326104166e-07 3.47825432169194e-07 3760 3438.09090909091 3759 9.49803009689615e-09 1147 1.73189790815155 -1.48470719138484 -1 3.22916987152235 3759 3854 3649 2439 1147 3925 4122 4155 3451 3314 4004 4168 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 8.40725853451825e-08 3.27411388472988e-07 4540 3045.45454545455 3761 7.64296259618187e-09 913 2.43207775445892 -1.86438213141732 -1 4.55346972828551 4536 2337 1442 3840 913 4406 4048 1490 3761 2020 4707 4169 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 7.81712611832576e-06 9.37657821562836e-06 3765 3635.90909090909 3761 7.10650354052951e-07 2713 2.04371728399002 -1.29534520217242 -1 2.966399305273 3761 4634 2713 4423 3885 3539 2823 2931 4067 3896 3323 4170 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 4.60645863839834e-07 8.09980370006727e-07 3765 3645.54545454545 3763 4.18769054810871e-08 2538 1.68516025539656 1.57996147041217 1 2.96336060298678 3762 4397 3541 4497 2538 2955 2581 4021 3894 3763 4152 4171 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 7.61020832909067e-06 9.13999575402239e-06 2555 3472.81818181818 3764 6.91839514031023e-07 2418 1.36399410003592 1.26382143742321 1 1.98388472235134 2553 4190 3650 3764 3879 2517 2418 3953 4243 4005 3029 4172 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 1.40975893753505e-05 1.6337005119483e-05 3105 3696.18181818182 3765 1.28160724667687e-06 2953 0.994895195260543 1.02281014888411 1 1.37434720319279 3104 4510 4036 3235 4032 2953 3284 3830 3765 4579 3330 4173 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 1.19153260964113e-07 3.66742263935217e-07 4570 3525.72727272727 3765 1.08321152197748e-08 1288 1.52884216729865 -1.30631251576164 -1 2.84031227746437 4568 3867 3765 2951 1288 3441 3805 3094 3373 4098 4533 4174 M18933 BIOCARTA_TGFB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TGFB_PATHWAY.html TGF beta signaling pathway 24/26 BioCarta 2.23092583074253e-05 2.52517264295078e-05 4265 3539.90909090909 3766 2.02813495811603e-06 1431 1.36625560884969 -0.963668662163189 -1 1.81305342367044 4264 4015 3471 3766 4135 3299 2729 3278 1431 3922 4629 4175 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 1.95173575066629e-05 2.22624280887987e-05 4175 3678.63636363636 3766 1.77432096886916e-06 2443 1.79272950389193 -1.25174356921468 -1 2.40758969320619 4174 3766 2959 4569 4101 4107 3784 2443 3132 3684 3746 4176 M12851 BIOCARTA_CELL2CELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELL2CELL_PATHWAY.html Cell to Cell Adhesion Signaling 14/19 BioCarta 1.90516124348422e-05 2.17574668987309e-05 2245 3652 3767 1.73197976549544e-06 2244 0.847398205875383 1.08070457041005 1 1.14001806676737 2244 3767 3623 4236 4096 2898 3058 4137 4679 4224 3210 4177 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 1.395208851584e-05 1.61842855234123e-05 2810 3753.27272727273 3767 1.26837972716323e-06 2806 0.933192166608628 0.893459724682445 1 1.29015643884194 2806 4277 3686 3767 4029 2967 3161 3961 4649 4246 3737 4178 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 1.49678327943861e-06 2.09018256773675e-06 4015 3676.36363636364 3768 1.36071299798647e-07 2542 1.5943547425072 -1.66463519314984 -1 2.6140842166712 2542 4103 4014 3548 3290 3642 4188 4015 3768 3831 3499 4179 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 1.29521050305253e-07 3.79650919404164e-07 3770 3655.45454545455 3769 1.17746416300521e-08 1364 1.18139540139116 1.21412846737946 1 2.18949808499474 3727 4155 3915 3769 1364 4058 3582 3768 3353 4388 4131 4180 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 0.611701028915314 0.612869636272614 2465 3790.45454545455 3769 0.0824040747360702 2461 1.13019159257623 1.16241592584234 1 0.0685329954526909 2461 4257 3556 3507 4711 3434 3474 3769 4638 3837 4051 4181 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 0.000126442332751787 0.000136071092245426 4400 3678.36363636364 3770 1.14954182233051e-05 2463 1.38884447501966 -0.607394761081891 -1 1.54968664511207 4398 3774 3313 2463 4366 4216 2979 3703 3255 4225 3770 4182 M105 PID_TELOMERASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TELOMERASE_PATHWAY.html Regulation of Telomerase 18832364 83/89 Pathway Interaction Database 3.50574934931839e-06 4.46134724421213e-06 3270 3689 3770 3.18704994165553e-07 2291 1.30071737368334 1.12420691921081 1 2.00880293039298 3268 4441 4051 3241 3646 2724 2291 4035 3770 4408 4704 4183 M7968 BIOCARTA_CARM1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARM1_PATHWAY.html Transcription Regulation by Methyltransferase of CARM1 14/15 BioCarta 0.00024467571074306 0.00025957953578495 3390 3538.63636363636 3771 2.22457206264938e-05 1788 1.00218147282552 1.21737604966943 1 1.0368279807408 3389 3771 3620 3202 4424 3990 4645 3792 1788 4226 2078 4184 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 8.11597404024086e-07 1.26761738815145e-06 4190 3705.72727272727 3771 7.37816094026313e-08 2677 1.29984942428815 0.988060039485538 1 2.21258239988166 4190 3341 3538 2677 2898 4333 4487 4192 3079 4257 3771 4185 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 3.8296419812647e-07 7.06366164578718e-07 3255 3506.90909090909 3771 3.48149331628036e-08 1698 1.47904984691353 1.48723512713413 1 2.62619792914558 3251 4719 3953 4522 2400 2858 1698 3771 3917 3576 3911 4186 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 0.00137843691914773 0.00142774243106809 2075 3311.45454545455 3771 0.000137929270610584 1548 1.27980825416946 1.27980825416946 1 1.05067447730551 2071 4340 4402 4587 4555 2309 1937 1548 3771 3980 2926 4187 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 1.14395327901576e-07 3.59285478750119e-07 3950 2903.54545454545 3772 1.03995758045355e-08 459 1.61994599510525 1.82766199565044 1 3.01379126771879 3950 1237 3413 459 1253 4316 4170 3772 1396 3863 4110 4188 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 3.06036189804921e-07 6.06173285734831e-07 3405 3659.45454545455 3772 2.78214756706196e-08 2214 1.28708500785724 -0.919283456668623 -1 2.30992455676714 3405 4471 3772 4487 2214 2730 3200 4438 3962 4128 3447 4189 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 0.00159908151232541 0.00165446399346251 3505 3813.09090909091 3773 0.000160023335678628 2890 1.10139033046838 -1.28714480296863 -1 0.883722921354959 3504 3806 4584 3190 4548 3387 2890 4236 4564 3773 3462 4190 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 5.38020141130236e-06 6.63216261722307e-06 390 2856.18181818182 3773 4.89110415352542e-07 387 1.30947483469055 1.26596426468815 1 1.95722378552984 387 4376 4000 4319 3773 1136 710 1711 3909 4600 2497 4191 M14236 REACTOME_SIGNAL_ATTENUATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_ATTENUATION.html Genes involved in Signal attenuation 15/20 Reactome 6.832369375552e-06 8.25833122986054e-06 3620 3783.09090909091 3776 6.21126417673084e-07 2846 0.920126854565371 -0.782699946706028 -1 1.34971912504156 4408 2846 3502 2954 3846 3620 4101 4623 4318 3776 3620 4192 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 0.00435060864553892 0.00446216271337325 3110 3622.81818181818 3778 0.000435914969684865 2511 2.66740116077398 -4.03717758547244 -1 1.80957661969058 3106 3820 4711 3834 4588 3458 2892 3778 4142 3011 2511 4193 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 0.000118874583829717 0.000128043823750859 1585 2780.72727272727 3781 1.18880943333518e-05 250 2.02938770347919 2.02938770347919 1 2.28028350165091 1585 4324 4358 4437 4371 1508 250 1234 3781 3861 879 4194 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 6.92145708805464e-06 8.36172957655949e-06 2735 3387.45454545455 3781 6.29225351260308e-07 1192 1.33213990452313 1.66679685441348 1 1.95240134136064 2734 4614 3781 4666 3849 2721 2411 1192 4631 4197 2466 4195 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 0.00108332423795249 0.00112355315384218 4635 3847.45454545455 3781 9.85325506032235e-05 2995 1.79763676767929 -1.9042164052007 -1 1.53015562287567 4635 3781 2995 3693 4534 4082 3063 4364 3699 3687 3789 4196 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 2.47498998531725e-06 3.27500777423533e-06 3785 3689.45454545455 3782 2.24999342697646e-07 2024 1.37436204226627 1.62340863903746 1 2.17586792055923 3782 3653 3581 2024 3495 4024 3793 4479 3476 4058 4219 4197 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 9.58604452267081e-08 3.38845370705758e-07 4130 3388.45454545455 3783 8.7145863094208e-09 1050 2.08507702521925 -1.55109978854735 -1 3.89469708055577 4130 3783 2386 4557 1050 4103 4087 3302 2943 2991 3941 4198 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 1.60499371340364e-05 1.84544953161149e-05 3410 3612.18181818182 3784 1.60500530554316e-06 1107 1.75759838922868 2.01083506241825 1 2.40174140982211 3409 4327 4379 4226 4082 3758 3118 1107 3784 4153 3391 4199 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 5.47839844620909e-06 6.73737380565578e-06 1740 2873 3785 4.98037462587362e-07 355 0.906666378539801 -0.871646361360641 -1 1.35310625999868 1736 3973 4016 4485 3785 1016 1683 1637 4446 4471 355 4200 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 9.47018078903261e-08 3.3764305071295e-07 4180 3246.81818181818 3785 8.60925563335333e-09 907 1.61977731946753 -1.53658123079014 -1 3.02609769211083 4178 3866 3740 907 1037 3785 4370 4447 1880 3991 3514 4201 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 1.15035157672935e-07 3.59285478750119e-07 3785 3292.72727272727 3785 1.04577421534523e-08 1260 1.48410428149056 -1.11907792558821 -1 2.76099544904938 3477 4392 3785 4270 1260 2195 1940 4495 2244 4377 3785 4202 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 0.000125522136636015 0.000135111627120181 4365 3719.90909090909 3785 1.14117544489534e-05 2815 1.13430489532325 0.8498567065549 1 1.26651756042587 3324 4572 3777 3785 4365 3045 2815 2826 4364 3906 4140 4203 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 6.0392286143335e-08 3.11320373876078e-07 3785 2753.90909090909 3785 6.03922877845877e-09 190 2.08463463024176 2.27934510389561 1 3.91601936991187 3785 972 4478 190 651 3937 4104 4141 1890 2045 4100 4204 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 3.12480322170311e-05 3.48760255531773e-05 3560 3377 3786 3.12484716235099e-06 176 2.260097181267 1.65440507281645 1 2.90824287321406 3556 2902 4578 1467 4215 4115 4532 4382 176 3438 3786 4205 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 0.00410184899715307 0.00420976892075723 4295 3653.45454545455 3786 0.000410944004924326 2107 3.01446049575753 2.42659103806306 1 2.06714692165245 4295 3506 4622 3153 4584 4391 2107 3786 3466 2383 3895 4206 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 1.42435868925315e-07 3.98516479743619e-07 2670 3580.45454545455 3788 1.42435878054905e-08 1552 1.65699239938521 1.83699617196282 1 3.06119831985081 2669 4350 4378 4321 1552 3788 3341 3370 3154 4607 3855 4207 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 0.163841484654039 0.165100727490834 2260 3683.45454545455 3791 0.0161354133225115 2259 0.999411426022028 -1.03852692178035 -1 0.224891860433176 2259 4211 4073 3791 4660 3203 2588 3603 4020 4513 3597 4208 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 8.02320345281594e-10 1.03752110403538e-08 4560 2610 3791 8.02320345571266e-11 79 2.12757913875268 2.26985412514253 1 4.90426118772461 4556 1002 4664 79 397 4374 3791 4170 1278 188 4211 4209 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 0.000137474560525585 0.000147674084133082 1885 3480.54545454545 3792 1.24984683497778e-05 1885 0.877574902779193 0.91121156084216 1 0.969883963967485 1885 4232 3982 3792 4377 2821 3106 2728 4678 4441 2244 4210 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 7.81062701297745e-08 3.26249199126138e-07 2940 3511 3793 7.10057026388814e-09 816 1.56144012868857 -1.36853406472752 -1 2.92380206420947 2939 4107 3704 4625 816 3326 4390 4033 2991 3897 3793 4211 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 6.88681550923943e-06 8.32200952473377e-06 4250 3713.09090909091 3793 6.26076097056299e-07 2525 1.2540914662557 -1.25249028077148 -1 1.83871095074963 4246 3951 3677 3763 3848 4011 4329 3116 2525 3793 3585 4212 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 5.62237850599598e-06 6.90185345859585e-06 4700 3699.72727272727 3794 5.11126624977038e-07 2346 1.24680338290657 1.16284218941622 1 1.85727749007258 4698 2860 3244 3408 3794 4170 4363 3781 2346 4227 3806 4213 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 5.84009982664946e-05 6.3926881219354e-05 2990 3685.63636363636 3794 5.30932260287799e-06 2539 1.37069698218646 -1.44420940044332 -1 1.65928395416343 2989 4220 3472 3794 4285 2539 3060 4569 4559 4109 2946 4214 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 0.000185980899044088 0.000198693943750135 3795 3992.45454545455 3794 1.69087839209093e-05 3440 1.36107350960173 -1.02093567570097 -1 1.45406089574968 3440 4207 3673 4628 4399 3793 3743 4428 3700 3794 4112 4215 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 1.96450386592945e-06 2.66833330854303e-06 4075 3631.09090909091 3796 1.78591420013432e-07 2735 1.58665347820525 0.994540412284344 1 2.55286167270266 4074 3110 2735 4005 3395 3796 4088 3559 4043 3886 3251 4216 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 6.36131567867557e-06 7.74050270774651e-06 4635 3616.90909090909 3796 5.78303097503605e-07 2003 1.73127313009634 2.1063637762313 1 2.55439530989889 4634 2855 2610 3382 3822 4323 3796 3755 4076 2003 4530 4217 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 2.97686568150277e-07 5.96383956565921e-07 1525 3569 3796 2.97686608028066e-08 1524 1.21022488516178 1.22989213845268 1 2.17440371646846 1524 4682 4617 4335 2275 3185 2499 3529 4104 4713 3796 4218 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 3.15588779553432e-06 4.06914636323815e-06 3400 3957.09090909091 3798 2.86899302058813e-07 3400 1.3060662458571 1.09908163548736 1 2.0321389165323 3400 4591 3685 4636 3598 3580 3764 4227 4240 4009 3798 4219 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 1.33959044844039e-06 1.9090781753136e-06 4055 3490.18181818182 3798 1.21781024011279e-07 2142 2.23355946464546 -2.58053903525642 -1 3.68784808490435 4053 4233 2142 3879 3217 3798 2216 4506 3531 2348 4469 4220 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 2.25545522517739e-07 5.05976647473255e-07 3915 3450.09090909091 3799 2.05041405128023e-08 1918 1.79944610795763 -1.92381690135173 -1 3.27057148205355 3911 2858 2316 4342 1918 4569 4420 3151 3799 2695 3972 4221 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 5.83417484026482e-07 9.77540122330492e-07 1970 3546 3799 5.3037967158444e-08 1970 1.26150015617026 1.34959194403983 1 2.1883893669066 1970 3851 4110 3799 2680 3506 3923 3490 3286 4553 3838 4222 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 0.000596098179072842 0.000623439708669136 3460 3833.72727272727 3800 5.42054323077743e-05 2923 0.595081434296807 -0.511805998429584 -1 0.549915587607324 3459 4610 3974 3525 4495 2923 3056 3800 4701 4511 3117 4223 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 0.000234169309447007 0.000248600796353998 4610 3460.27272727273 3800 2.34193988976707e-05 1250 3.76773345789485 2.42659103806306 1 3.92078423555889 4610 3800 4423 2370 4434 4618 4415 1250 3159 2375 2609 4224 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 2.97248480198195e-06 3.85549004269162e-06 4390 3886.54545454545 3801 2.70226256200119e-07 2020 1.45202579361156 -1.5054720466628 -1 2.26915844430989 4387 3652 3774 3700 3572 4601 3801 4489 2020 4423 4333 4225 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 0.000606656560654952 0.000634201321437734 3050 3778.90909090909 3802 5.51658102382874e-05 2866 0.699046095441358 0.703696394055428 1 0.644639597982101 3048 4046 3802 4626 4497 3393 3071 2866 4519 4416 3284 4226 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 3.31699245714964e-06 4.25048523690687e-06 3725 3911.45454545455 3802 3.01545223478983e-07 3305 1.22016025952939 -0.935758987166697 -1 1.8917475331073 3724 3931 3760 4435 3619 3391 3802 4676 3305 4150 4233 4227 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 0.0234887511294062 0.0238834350130972 2145 3704.90909090909 3803 0.00215848612494267 2144 1.02453720469284 -0.961638291466092 -1 0.47897830004693 2144 4497 4083 3803 4618 3302 2876 3272 4376 4507 3276 4228 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 1.0046991838178e-07 3.42613246105503e-07 3650 3328.81818181818 3803 1.00469922924172e-08 1125 1.78844678564437 2.00766638329575 1 3.33802127504165 3650 2933 4434 1125 1216 4112 4393 3803 2626 4428 3897 4229 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 0.0328044432535106 0.0332982735820581 1275 3379.45454545455 3805 0.0030276413877452 1274 0.873716177808702 -0.935014748756834 -1 0.371928730216115 1274 4472 4132 3805 4655 2231 2326 2710 4502 4594 2473 4230 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 0.000553152641692104 0.000579294534898321 3700 3598.81818181818 3805 5.53290379978661e-05 1200 2.03308040493248 2.45033011001164 1 1.89957878396983 3700 3805 4369 3204 4577 3935 4084 1200 3542 4152 3019 4231 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 1.12159579000954e-06 1.64612317439211e-06 4205 3290.81818181818 3805 1.01963305619793e-07 868 3.21436977774026 -2.92377573258784 -1 5.36739007047799 4201 3105 868 2818 3109 4567 4508 3994 4064 1160 3805 4232 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 0.0257899811893713 0.0262116098361634 3555 3764.72727272727 3806 0.00237248787510192 1976 0.864779650327152 0.962172320652466 1 0.39406840732957 1976 4640 3806 4257 4620 3034 3555 3147 4557 4267 3553 4233 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 4.41891897093717e-08 2.97677410474742e-07 3810 3603.90909090909 3807 4.01719914517777e-09 258 1.01909309855176 -1.02524985838639 -1 1.91966949939045 3807 4559 4024 3522 258 3718 3568 3515 4228 4483 3961 4234 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 1.32379764393516e-06 1.8888527446717e-06 3035 3560.09090909091 3807 1.20345312772687e-07 2663 1.25414462662242 1.20753013023738 1 2.07202581445891 3034 3894 3841 4659 3211 2663 2934 3119 4100 3807 3899 4235 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 3.38511478132765e-06 4.32298208005046e-06 4720 3754.63636363636 3808 3.07738180906926e-07 2344 1.95764172445462 -1.99643287963613 -1 3.03151401847325 4717 3476 2344 4594 3632 4624 4710 2507 4263 2626 3808 4236 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 6.08484379773065e-06 7.43090885518466e-06 3910 3739.27272727273 3810 5.53169147953507e-07 3064 1.31724363357624 -1.42970799220569 -1 1.95005524560326 3906 3969 3632 3775 3810 3064 3199 3182 3812 4141 4642 4237 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 2.57606062673337e-06 3.39068771839975e-06 1690 3643 3810 2.3418760392201e-07 1687 1.22848900211289 1.19274850884892 1 1.93948472146264 1687 4694 4177 4331 3515 2746 2770 3948 3810 4662 3733 4238 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 2.3493803558374e-07 5.19638016848759e-07 3710 3436.63636363636 3811 2.13580055157072e-08 1129 1.48222530297362 1.97321042750975 1 2.68890473725205 3706 2298 3449 4395 1954 4421 3915 4477 4248 3811 1129 4239 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 1.90487182171841e-06 2.59630233858241e-06 4190 3279.36363636364 3812 1.90487345456187e-07 490 2.10875035234469 -0.750342687109584 -1 3.40041502125189 4187 3812 4473 4556 3429 2632 1332 2576 490 3983 4603 4240 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 2.42423794575662e-07 5.2719175985577e-07 3340 3697.81818181818 3814 2.20385292080893e-08 1990 1.52126913620359 -1.25368919699677 -1 2.75700351369948 3340 4696 4142 3814 1990 3436 3146 4182 2787 4650 4493 4241 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 2.36149643994518e-07 5.20853420399124e-07 3815 3434.72727272727 3814 2.14681517584546e-08 1798 2.25681388423207 -2.50021056926848 -1 4.09387469659218 4392 3777 1835 4378 1960 3374 3815 4316 4323 1798 3814 4242 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 0.000315808770592182 0.000333173311845128 3815 3758.36363636364 3814 3.15853660401765e-05 2029 0.674398804937638 0.528312148846687 1 0.676321781017788 2920 3813 4266 4446 4455 2597 2029 3814 4700 4688 3614 4243 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 6.10521046461517e-06 7.4519248494915e-06 3815 3935.27272727273 3815 5.55020673384008e-07 3567 1.18504486434134 -1.01870018240025 -1 1.7538412475997 3567 3980 3815 4465 3812 3621 4291 3797 3622 4336 3982 4244 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 9.09115469263428e-08 3.33570140001417e-07 4540 3685.18181818182 3816 8.26468642573816e-09 992 0.953056985071315 -0.808921326897249 -1 1.78161453404817 4539 3173 3635 3211 992 4647 4629 3816 3831 3399 4665 4245 M16929 REACTOME_PI3K_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_CASCADE.html Genes involved in PI3K Cascade 61/105 Reactome 1.17018366672542e-05 1.37121819934062e-05 3610 3820.36363636364 3816 1.06380899181655e-06 2829 1.36273307932188 1.68382339577012 1 1.91272910986012 3606 4470 3816 2992 3984 3665 2829 4699 3315 4400 4248 4246 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 1.49603277815427e-05 1.72774032612874e-05 480 2793.36363636364 3816 1.36003904681538e-06 478 1.28211881768692 1.30364503410175 1 1.76236746107468 478 3888 4015 4290 4046 1147 912 1666 3980 3816 2489 4247 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 1.85100089522927e-07 4.54495434594235e-07 3170 3759.18181818182 3816 1.85100104940848e-08 1805 1.36002722935121 1.35915723334079 1 2.48999970863499 3166 4086 4669 3816 1805 3669 3525 4190 3216 4714 4495 4248 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 0.000439337354927239 0.000461636757626128 4520 3943.09090909091 3817 3.99477376914076e-05 2955 1.25375867286122 1.5450087895662 1 1.20679768706708 3643 4516 3817 4519 4471 3359 2955 4317 3424 4563 3790 4249 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 0.00206579272943715 0.00213359774243837 2270 3268.36363636364 3817 0.000206771562052098 430 0.893354403695748 0.893354403695748 1 0.688144371358768 2270 3817 4386 4201 4607 2222 430 2555 4629 3868 2967 4250 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 6.81860243840645e-06 8.24591429907212e-06 3290 3724.09090909091 3818 6.19874870166742e-07 2098 0.978635704459318 -1.18946332843292 -1 1.4357842460015 3286 4551 3780 4058 3844 3530 3818 2098 4333 4375 3292 4251 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 6.32869159760395e-06 7.70676582577158e-06 3990 3455.54545454545 3819 5.75337254844105e-07 1839 1.81436542879003 1.77082607578777 1 2.67802850871487 3987 3121 2592 2616 3819 4337 4591 4230 1839 2852 4027 4252 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 0.00617479000074224 0.00631254251754459 4140 3738.72727272727 3822 0.000562926302892437 2686 1.77997851503869 1.84299613760009 1 1.12982085343465 4137 3785 2686 4351 4597 4243 3822 2824 4128 2986 3567 4253 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 8.39427617770787e-08 3.27411388472988e-07 3455 3504.90909090909 3822 7.63116045272564e-09 909 1.51082127477081 1.69670553899935 1 2.82831641646749 3455 3859 3822 4262 909 4055 4577 2886 3435 3879 3415 4254 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 0.000849420661132298 0.000884071779612888 875 2893.27272727273 3827 7.72498909173544e-05 372 0.762334816400858 -0.762334816400858 -1 0.671323795027566 873 4290 3827 4017 4518 1029 372 1936 4457 4266 2241 4255 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 0.000321946172459501 0.000339496410636472 3540 3839.54545454545 3828 3.21992824174114e-05 2713 1.56211276956294 -2.12041681218006 -1 1.56401765288439 3362 3539 4269 4359 4456 3828 3239 4661 4272 3537 2713 4256 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 2.49667992935798e-07 5.33952390873115e-07 3770 3946.54545454545 3828 2.4966802098615e-08 2109 1.3618736887366 -1.30587447625452 -1 2.46586384239166 3767 4673 4546 4708 2109 3480 3631 4225 3794 4651 3828 4257 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 6.58840696399182e-06 7.99415960669445e-06 3130 3523.63636363636 3832 5.9894788132522e-07 1933 1.45264448505187 -2.18458276688717 -1 2.13728179140781 3129 3934 3456 4295 3832 1933 2647 4265 4189 4070 3010 4258 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 1.64858468001245e-06 2.27790389041534e-06 3595 3656.36363636364 3832 1.49871446853789e-07 2182 1.43330933191769 1.73887134471994 1 2.33448993911873 3593 4140 3758 4051 3329 3967 3832 2182 3840 4097 3431 4259 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 0.00232656586273308 0.00239768359652841 3350 3754.54545454545 3832 0.000232900526686351 2302 4.63823010906618 -1.03777808050078 -1 3.50852776169928 3349 4080 4577 4115 4565 3837 3614 2302 3776 3253 3832 4260 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 8.60470429220653e-08 3.28305665915602e-07 3430 3484.63636363636 3833 7.82245875341478e-09 940 1.453908044082 1.59758734958401 1 2.72124284303828 3429 3564 3985 3779 940 3864 3833 4293 2100 4476 4068 4261 M7151 KEGG_SELENOAMINO_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SELENOAMINO_ACID_METABOLISM.html Selenoamino acid metabolism 26/28 KEGG 4.37906648934296e-05 4.83376843538324e-05 4500 3740.27272727273 3835 3.9810487785668e-06 1808 1.57293357083709 -1.76591489141867 -1 1.95936625380861 4496 3722 3268 3913 4247 4183 4424 1808 3637 3835 3610 4262 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 1.8359730895088e-05 2.0992715558337e-05 3855 3655.09090909091 3835 1.83598825827251e-06 2069 2.79330751618324 -0.810010130251772 -1 3.77239264505017 3855 3801 4373 3989 4111 4643 3835 2069 2652 3436 3442 4263 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 3.45669244431749e-07 6.55507767664867e-07 3575 3413.54545454545 3835 3.14244817040124e-08 2272 1.42442019413376 -1.41953956778927 -1 2.54251404292489 3571 4123 3846 2504 2322 2603 4136 4159 3835 4178 2272 4264 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 1.73089459445893e-07 4.37825427966033e-07 4030 3368.81818181818 3835 1.57354066421872e-08 1654 1.33091847018972 0.980280453384373 1 2.44292461495698 4009 4214 3513 4222 1654 3835 4027 2557 1968 4026 3032 4265 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 5.64635251266098e-06 6.92948098277687e-06 4115 3659.27272727273 3841 5.1330609129196e-07 1121 1.49373819545483 -1.09867591884843 -1 2.22454157356615 4112 4503 3733 1121 3795 3529 3841 3996 3311 4285 4026 4266 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 9.36807428832792e-06 1.11042969967122e-05 2475 3190.63636363636 3841 9.36811378092937e-07 823 1.49510345597132 -1.47041443931245 -1 2.13816092435982 3841 2473 4479 2811 3954 4138 4405 823 3863 2472 1838 4267 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 1.1524538449739e-07 3.59285478750119e-07 4080 3766.27272727273 3841 1.15245390474065e-08 1348 1.48428309229426 -1.38604902242551 -1 2.76132820857005 4078 4669 4519 4528 1348 3138 3761 3841 3488 4609 3450 4268 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 1.38495875879176e-06 1.96542553863412e-06 4280 3786.63636363636 3841 1.25905420969187e-07 2429 0.918145223512085 -0.821682660783146 -1 1.51210041348305 4276 2429 3532 4389 3236 3841 3679 4235 4269 3567 4200 4269 M10450 REACTOME_GAB1_SIGNALOSOME http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAB1_SIGNALOSOME.html Genes involved in GAB1 signalosome 46/46 Reactome 6.81080323446564e-06 8.23859335383849e-06 4505 3779 3843 6.19165847234138e-07 2829 1.15735120812963 -1.51726624776448 -1 1.69826904950593 3173 4501 3906 4301 3843 3388 3842 3303 3978 4505 2829 4270 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 6.5973525671569e-06 8.00295659649976e-06 3975 3258.81818181818 3846 6.59737215351615e-07 424 3.12811606764754 2.82140739972771 1 4.60297199939432 3975 2462 4565 2055 3869 3846 3828 4300 424 1888 4635 4271 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 6.23421309808656e-06 7.59759510017263e-06 4210 2931.72727272727 3847 6.23423058759145e-07 368 2.21197267211316 -1.20561366364813 -1 3.26904869841018 4206 2474 4410 1461 3847 4187 3969 1171 368 1555 4601 4272 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 6.06121277735395e-07 1.00523275857732e-06 3850 3552.27272727273 3850 5.51019495207031e-08 1123 1.378615112924 -1.57112983720197 -1 2.38680498237491 3850 3891 3869 1123 2708 4118 4231 3823 3483 4140 3839 4273 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 6.74155785850993e-08 3.14536172538656e-07 4325 3594.81818181818 3850 6.1286891500859e-09 666 1.50514383956257 -1.26624650319709 -1 2.82525746819813 4324 3579 3627 4592 666 3445 4309 3850 2672 4036 4443 4274 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 8.65098242024151e-07 1.33355275483062e-06 4270 3261.09090909091 3852 8.65098578802072e-08 732 2.24764734086368 -2.74753430155994 -1 3.81224336026142 4267 2923 4460 3852 3019 4136 4653 732 4472 1556 1802 4275 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 6.05680881129945e-06 7.4005015763224e-06 4090 3547.45454545455 3852 5.50620498757568e-07 1903 1.9448430414113 -1.66664395058747 -1 2.88056757575923 4086 3151 1963 4363 3809 3852 2711 4405 4059 1903 4720 4276 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 0.0257951117985125 0.0262116098361634 3665 3841.09090909091 3852 0.00237296550676684 2618 0.219414189439996 -0.215197796429512 -1 0.0993412961170471 3665 4655 3852 4048 4696 3047 2824 2618 4702 4720 3425 4277 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 0.472261293720185 0.473666235945446 1415 3705.90909090909 3853 0.0564490441627235 1413 0.757793491855832 -0.776605742099468 -1 0.0701529924604143 1413 4457 4175 3549 4686 3049 2444 3828 4653 4658 3853 4278 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 8.47771363283366e-12 1.49868196056086e-10 4440 3050.18181818182 3853 7.70701239351484e-13 211 2.50051968784645 -2.43787537115841 -1 7.09287294692532 4439 3247 211 2713 1779 4204 3853 4381 4157 265 4303 4279 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 2.09315318427616e-05 2.37835412368403e-05 3855 3824.09090909091 3854 2.09317290034367e-06 2464 1.23904462665196 -1.26436082515168 -1 1.65346904724612 3854 3524 4279 4188 4140 3702 4618 2464 4610 3265 3421 4280 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 4.2073037692999e-07 7.54397475368345e-07 4250 3670.63636363636 3854 3.82482233991766e-08 2477 1.3352994687061 -0.978763144078425 -1 2.35985498988401 4248 3613 3886 4241 2477 3854 3454 3624 2785 4325 3870 4281 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 1.09192720185709e-06 1.60908410638946e-06 4505 3482.90909090909 3858 9.92661585285716e-08 510 1.80160457983026 -0.841560485634506 -1 3.01310243795767 4503 3417 2840 3858 3095 4192 4005 3521 510 3987 4384 4282 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 1.8390352554951e-22 1.11285210332524e-20 45 2624.27272727273 3859 1.8390352554951e-23 42 2.3333648658547 2.50291984466539 1 13.443697072732 4124 961 4599 42 272 3950 4191 4576 2251 42 3859 4283 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 2.58556445220143e-05 2.90291727269047e-05 4170 3832 3860 2.35054076337954e-06 2686 1.74868786094984 -1.41531631569073 -1 2.2902191388103 3860 4170 3498 3793 4169 3581 3329 4143 2686 4418 4505 4284 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 0.000112582038115321 0.000121348988331655 4120 3518.72727272727 3861 1.12587742143922e-05 1745 2.27363183954232 2.64843043222069 1 2.57013973822828 4117 2483 4468 3346 4364 3660 2212 3861 4192 1745 4258 4285 M16 PID_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INSULIN_PATHWAY.html Insulin Pathway 18832364 60/68 Pathway Interaction Database 1.63218350548874e-07 4.24841431570192e-07 4520 3575.18181818182 3862 1.48380329689155e-08 1600 1.403946857002 -1.23971332114238 -1 2.58231715791474 4516 3917 3641 2233 1600 4673 3862 3715 3064 3942 4164 4286 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 4.22483364694603e-06 5.2908503087252e-06 3420 3847.72727272727 3862 3.84076523659033e-07 2694 1.28640410280495 -1.67121851875624 -1 1.95917763180248 3417 4432 3951 4694 3709 2694 3241 3862 4212 4526 3587 4287 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 1.57554942795557e-07 4.1859656963545e-07 4500 3224.90909090909 3863 1.5755495396616e-08 339 2.15673042435615 -2.01406820216751 -1 3.97139928872219 4497 1973 4708 2703 1656 4562 3874 4126 3173 339 3863 4288 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 2.1149691521659e-06 2.84325103908375e-06 3390 3698.27272727273 3864 1.92270107763038e-07 2650 0.951333211684878 1.05098345922618 1 1.52273682037492 3386 3960 3921 3519 3437 3338 2650 3980 4267 4359 3864 4289 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 2.04495733697127e-07 4.81166432228533e-07 4335 3280.90909090909 3864 1.85905229732309e-08 1538 1.70490637013049 -1.67918480910005 -1 3.10944594352698 4331 1712 2293 3864 1812 4332 3885 4555 3179 1538 4589 4290 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 0.0114343696065913 0.0116566359704344 3205 3891.36363636364 3865 0.00104493046608719 3001 1.49534328649608 -0.954983938398336 -1 0.833995636896906 3204 4481 3926 3001 4609 3865 3598 4351 3465 4506 3799 4291 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 8.39913749218217e-06 1.00338648334442e-05 3660 3911.09090909091 3866 7.63560868954068e-07 3125 0.799694857625176 -0.794294530186899 -1 1.15341609435009 3657 3760 3866 4268 3906 3593 3523 4533 4588 4203 3125 4292 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 8.44217723152604e-08 3.27455016694392e-07 3960 3418.81818181818 3867 7.67470686862018e-09 919 1.87451588155296 -1.82555121541055 -1 3.50934294144558 3959 3658 2442 3867 919 4249 4059 3997 3714 2336 4407 4293 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 1.0327073456202e-06 1.53717397392852e-06 4005 3330.54545454545 3869 9.38825300351075e-08 1818 2.0888191578056 -1.97086011089989 -1 3.5055696862839 4002 3869 1884 2401 3060 4153 4304 4112 2837 1818 4196 4294 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 0.0433208912561606 0.043906937240515 3725 3806.36363636364 3869 0.00441893298972064 2070 3.32090857415667 3.32090857415667 1 1.30089469668483 3723 4662 4407 4590 4668 3663 3483 2845 2070 3869 3890 4295 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 1.53057578091522e-07 4.12818153481133e-07 4585 3449 3869 1.39143262490898e-08 1525 2.05478851132888 -1.91478112423383 -1 3.78722491095678 4584 3918 2269 4021 1525 3869 4447 3371 3523 1851 4561 4296 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 0.00436629160203339 0.00447727489932601 3870 3964.18181818182 3870 0.000397725585424471 3399 0.935629686820897 -0.985264702435598 -1 0.633779355970203 3870 3791 3487 3484 4581 4429 4249 3619 4576 4121 3399 4297 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 0.000216020573329333 0.00023021384197662 2525 3786.36363636364 3871 1.96401625053121e-05 2524 1.22481258395343 -1.09701934904088 -1 1.2857876702743 2524 3930 3690 3772 4411 3077 3871 4187 4424 3784 3980 4298 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 4.73303046717371e-06 5.88356697525939e-06 4485 3846.54545454545 3872 4.30276422703597e-07 2267 2.09746354836773 -2.34467202098891 -1 3.1670235223516 4482 3780 2313 3872 3742 4598 4604 3849 4297 2267 4508 4299 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 0.000521272484111411 0.000546392654898037 2325 3547.45454545455 3875 4.73996396784417e-05 2041 1.08434773980757 0.978229099846794 1 1.02069400512805 2324 4618 3875 4272 4482 2874 2041 2378 4276 4124 3758 4300 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 1.02800698458709e-06 1.53114325252479e-06 3685 3885.81818181818 3876 9.34552240863904e-08 3058 1.53411901094688 -1.48845210738638 -1 2.57516934818876 3685 3858 3745 4097 3058 3497 4153 4631 3924 4220 3876 4301 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 0.0094495335867547 0.00964989150356602 4605 3605.27272727273 3876 0.000862760671352948 1457 1.27795120128273 -1.30496871120933 -1 0.742903578311109 1457 4707 4179 4104 4603 2764 2297 3465 3876 4601 3605 4302 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 3.08902231927033e-07 6.10049596106943e-07 3945 3522.63636363636 3877 2.8082025027276e-08 2222 1.60395914654949 1.96913555203402 1 2.87754672064896 3945 3107 2803 4388 2222 3877 4181 4284 3406 2419 4117 4303 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 1.27034675401389e-06 1.82861746841889e-06 4350 3706.90909090909 3880 1.15486135231931e-07 2862 1.40942153285749 -1.26035149633391 -1 2.33440054251285 4349 4154 3741 2991 3181 4133 2862 3143 3969 3880 4373 4304 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 2.0898841449482e-07 4.84679970737421e-07 4645 3660.09090909091 3882 1.89989485770566e-08 1848 1.46215847673478 -1.35684969759137 -1 2.66526022262942 4641 3242 3972 4030 1848 3615 3882 3734 2715 4032 4550 4305 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 8.44488526616396e-08 3.27455016694392e-07 4165 3017.09090909091 3884 7.67716871848003e-09 920 2.37512484013113 -2.33191574568372 -1 4.44677949191224 4165 3884 1736 1972 920 4195 3970 4019 1562 2115 4650 4306 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 0.00050591760841113 0.000530651358155674 3380 3612.27272727273 3884 5.06032824011514e-05 927 1.14457961664937 0.842496059533052 1 1.08163403480269 3376 4077 4709 3666 4488 2799 927 4384 4586 2839 3884 4307 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 1.13190658096322e-06 1.65919225532498e-06 4230 3490.36363636364 3885 1.02900651212088e-07 840 2.20522709082866 2.1684094315504 1 3.67985509955469 4226 3302 2413 4340 3113 4387 4079 3885 840 3123 4686 4308 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 1.04584992080079e-06 1.55362868922787e-06 3990 3559 3886 9.50773107258068e-08 1668 2.1772191891929 -1.92367205647046 -1 3.651056613998 3986 3686 1668 4371 3064 4464 4466 3471 4024 2063 3886 4309 M765 BIOCARTA_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INSULIN_PATHWAY.html Insulin Signaling Pathway 37/44 BioCarta 2.56611460961219e-07 5.43294568670404e-07 4410 3326.54545454545 3887 2.33283173538898e-08 652 1.28548583180426 1.21091679470918 1 2.32470836906507 4409 3961 3490 652 2048 3230 4007 4527 1994 4387 3887 4310 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 4.75615192915913e-05 5.23287578219839e-05 1395 2983.27272727273 3888 4.32386795901182e-06 1265 1.35451524588516 -1.31005782852962 -1 1.67369167938682 1392 4454 3888 4507 4261 1316 1333 1265 4436 4274 1690 4311 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 4.04423105372551e-07 7.31604867117337e-07 4185 3776.63636363636 3888 3.67657436106489e-08 2450 1.23249055156966 1.00568999324537 1 2.18283786927098 4181 4192 3868 3784 2450 4514 3888 3122 3103 4478 3963 4312 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 7.89921688423415e-06 9.46542363381193e-06 1760 3164.36363636364 3889 7.18113204266783e-07 1058 0.814279434379115 0.86813098792837 1 1.18042297236466 1758 4263 3920 4055 3889 1736 1058 2401 4637 4292 2799 4313 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 0.0594413811813298 0.0601421906057614 4150 3797.63636363636 3890 0.00555553831972941 2082 1.35665584783055 -0.812774534658181 -1 0.477399752146109 4148 4313 3624 4440 4637 4250 2082 3367 3890 3801 3222 4314 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 2.08325215671278e-07 4.84679970737421e-07 4380 3753.54545454545 3893 1.89386577634799e-08 1839 1.58027134413474 -1.22675473499111 -1 2.88062898445509 4379 3837 3893 3005 1839 4201 4440 3761 3401 4193 4340 4315 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 0.0147174071124548 0.0149970124289263 3690 3964.09090909091 3895 0.00134698133467312 2406 0.999050631264494 1.33475269890932 1 0.525343277976795 3690 4622 3857 4669 4638 3874 3895 2406 4630 4491 2833 4316 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 0.00035623136968364 0.000375147716400442 4375 3525.54545454545 3896 3.56288487925626e-05 946 1.86207768361348 1.64483364089701 1 1.84119518338551 4371 946 4241 4341 4466 3847 3443 4392 3896 1743 3095 4317 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 8.07016310723969e-06 9.65762953341509e-06 1170 3225.45454545455 3896 7.3365388280142e-07 1167 1.18324913553993 1.25306368096656 1 1.71270841786565 1167 4423 4052 4690 3896 2186 1715 1832 4216 4621 2682 4318 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 6.26221782581396e-05 6.83414292204437e-05 990 2816.54545454545 3898 5.69308734964459e-06 720 0.82777965402077 -0.821666005793681 -1 0.994787389831817 988 4012 3898 4001 4298 1034 720 1464 4188 4383 1996 4319 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 3.92123247010339e-07 7.18486694832609e-07 4200 3493.45454545455 3899 3.56475742637779e-08 2078 2.57588865392037 2.60343724233858 1 4.56888544698571 4196 3190 2090 4547 2416 3899 4492 4150 2078 2803 4567 4320 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 2.39945552686603e-08 2.3019166843105e-07 1480 2927.72727272727 3899 2.1813232300327e-09 13 2.2030810204567 -1.83349343943276 -1 4.22198518142744 4512 2194 1394 1478 13 4507 4459 3899 4176 1478 4095 4321 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 3.39482871934558e-06 4.33304260554655e-06 3450 3712.09090909091 3902 3.08621268902777e-07 2177 1.3055068062046 1.27228051883315 1 2.02098034969661 3447 3713 3663 4037 3634 3995 4342 2177 3982 3941 3902 4322 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 0.0274043435609927 0.0278288514646914 3595 4053.81818181818 3904 0.00252288914775994 3556 0.681279610798621 -0.640743483037545 -1 0.305151879098826 3592 4310 3853 4036 4622 3556 3668 3904 4633 4680 3738 4323 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 0.00277490152045345 0.00285349350251422 1360 3427.81818181818 3904 0.000252582522648843 531 0.622366585619273 0.622366585619273 1 0.456451284870981 1357 4637 3904 4657 4571 1788 531 3824 4690 4717 3030 4324 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 0.000110247237284092 0.000118859515756262 3725 3661.36363636364 3906 1.10252707170019e-05 1963 1.30647735891502 -0.737187094245198 -1 1.47988694105362 3721 3526 4387 3906 4363 3182 1963 3925 4008 4088 3206 4325 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 3.99454224216854e-07 7.26280407667008e-07 3910 3551.54545454545 3909 3.63140269768924e-08 1734 1.61940193629773 -1.11821416260641 -1 2.86984223520411 3909 3651 3354 4247 2434 4141 4672 2685 1734 4169 4071 4326 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 0.00015642184315936 0.000167797977207313 3535 3660.63636363636 3910 1.42211787264231e-05 2647 0.672387309057764 0.798671047691391 1 0.732139462139234 3533 3143 3910 2691 4384 4181 2746 4210 4359 4463 2647 4327 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 3.5729894522702e-08 2.8385448745847e-07 3685 3533.81818181818 3913 3.24817228208965e-09 116 1.3421696825728 1.43589171389514 1 2.53652651297657 3682 4387 4040 4506 116 3920 2690 3858 3913 4327 3433 4328 M2602 BIOCARTA_RANKL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RANKL_PATHWAY.html Bone Remodelling 17/19 BioCarta 0.0207802276453989 0.0211385074323886 2920 3917.54545454545 3914 0.00190719490374877 2916 1.34368022532431 -1.41689184287947 -1 0.649021274066356 2916 4284 3408 4627 4617 3309 3253 4564 4595 3914 3606 4329 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 6.0437381662436e-06 7.38644333109005e-06 4710 3710.18181818182 3915 5.4943225176229e-07 1990 2.17527595245826 -1.71118982198063 -1 3.22248969769874 4710 3500 1990 3915 3808 4246 4600 2830 4074 2611 4528 4330 M938 REACTOME_CIRCADIAN_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CIRCADIAN_CLOCK.html Genes involved in Circadian Clock 61/72 Reactome 4.00049072451172e-07 7.2680200999597e-07 3640 3872.54545454545 3915 3.63681041087553e-08 2436 1.48739462814775 -1.12912100193349 -1 2.63569979960004 3636 4172 3787 4483 2436 3915 4689 3620 3828 4110 3922 4331 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 3.7121143968087e-08 2.87575261955407e-07 3805 3580 3915 3.37464950858556e-09 133 1.48182853946621 1.40063931521879 1 2.79813315763508 3804 3915 3616 3485 133 4253 4040 4673 2871 4017 4573 4332 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 4.33105030008116e-07 7.73654416473282e-07 3890 3856.45454545455 3916 3.93731922974328e-08 2491 1.38427927668575 -0.833604787021875 -1 2.44207211205762 3887 3916 3855 4486 2491 3939 2998 4654 3963 4429 3803 4333 M1011 REACTOME_MEIOTIC_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_RECOMBINATION.html Genes involved in Meiotic Recombination 42/98 Reactome 8.96227642296592e-06 1.06554016917882e-05 4215 3484 3918 8.14755721214125e-07 1519 1.71916125163805 1.171457749792 1 2.46761375988675 4211 3067 2409 2666 3922 4039 4275 3691 3918 1519 4607 4334 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 1.80531319844948e-07 4.47913293152525e-07 4620 3453.27272727273 3919 1.64119395144813e-08 1305 2.05625677717929 -1.98878004591591 -1 3.76889125819401 4617 3919 2722 4120 1695 4680 4660 4098 1305 3306 2864 4335 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 8.84720216760967e-06 1.05238896751809e-05 3540 3986.72727272727 3920 8.04294340585461e-07 3141 0.776954387999362 0.84274666927392 1 1.11594657458155 3540 4599 3928 4488 3920 3851 3141 3492 4566 4512 3817 4336 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 0.00079799543941947 0.000831465446812339 4500 4011.72727272727 3922 7.98282142853761e-05 2929 1.81921380246747 -0.814279315135219 -1 1.61721821731433 4499 2929 4350 3922 4523 3820 3645 4363 4536 3740 3802 4337 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 0.68618940391 0.686334813828184 3270 3913.09090909091 3923 0.1 2912 0.918603259450358 -0.954983938398336 -1 0.0424990946845989 3267 4480 4120 3003 4701 3769 2912 3923 4360 4603 3906 4338 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 3.42218535615623e-06 4.36441904378746e-06 2600 3739.18181818182 3924 3.11108243591811e-07 2600 1.15085201657188 1.37759390031496 1 1.7804247536212 2600 4206 3924 4050 3637 3986 4525 3021 3582 4143 3457 4339 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 1.67691411934523e-07 4.30410441385446e-07 4260 3307.09090909091 3924 1.52446749742299e-08 1626 1.98505602299553 -1.66632186189627 -1 3.64828130789288 4259 4460 2886 2944 1626 4114 4013 2352 1727 4073 3924 4340 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 2.28041568409135e-06 3.04399378645678e-06 4170 3757.36363636364 3925 2.07310731624141e-07 2684 1.83369091439461 -1.30765795001902 -1 2.92017948139359 4166 2684 3208 3925 3464 4679 4326 3678 4201 2842 4158 4341 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 2.14809407425019e-07 4.9146893022108e-07 4615 3551 3926 1.95281298544681e-08 1548 1.27134279459339 1.06012307465043 1 2.31510630533583 4614 3926 3647 1548 1873 4380 4019 3254 3932 4003 3865 4342 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 4.48763574917288e-07 7.9391457031844e-07 4365 3623.45454545455 3926 4.07966969506957e-08 2517 1.07111307822348 -0.74859684498117 -1 1.88593362086551 4365 2822 3713 4004 2517 3926 2562 3050 4658 4065 4176 4343 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 0.000303894165635322 0.000321034123052534 2445 3409.81818181818 3928 3.03935731884406e-05 1639 2.30510505151226 -2.30510505151226 -1 2.32448983432562 2443 4652 4595 3928 4453 2573 1639 4482 2087 4218 2438 4344 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 0.00246586729703337 0.00253902566361202 2720 3900.54545454545 3928 0.000224421409652728 2720 0.694014678514103 -0.613028276983595 -1 0.519260611937938 2720 4483 4151 3810 4564 3128 2903 3928 4699 4643 3877 4345 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 1.24003251456745e-06 1.79153763965667e-06 4180 3790.36363636364 3929 1.12730292137613e-07 2579 1.49756370892225 1.57653207473015 1 2.48429018455009 4179 3582 3929 2958 3166 4533 3830 4308 2579 4177 4453 4346 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 8.76558467549887e-07 1.34548161523105e-06 3930 3652.81818181818 3929 7.968716516384e-08 992 1.91778285442505 2.10116895020317 1 3.25049071045666 3929 4191 3100 4242 2959 4592 4574 3627 992 3829 4146 4347 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 0.000311009429779087 0.000328477178016848 2205 3431.63636363636 3933 2.82775822945224e-05 1924 0.803010829156934 0.803010829156934 1 0.80689433495881 2203 4607 3933 4656 4448 2302 1924 2336 4547 4501 2291 4348 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 2.00612422693734e-07 4.75069897739545e-07 3545 3721.45454545455 3933 2.00612440804141e-08 1898 1.5288206276561 -1.44560187825848 -1 2.79065268275166 3542 4347 4544 4318 1898 3190 4264 3933 3261 4642 2997 4349 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 6.82427518267949e-08 3.15009389627869e-07 4595 3606.27272727273 3933 6.82427539224779e-09 776 1.61199326014584 -1.38436302818943 -1 3.02557833419298 4593 3227 4658 2508 776 3933 3872 4403 2562 4592 4545 4350 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 0.14744289486823 0.148703090550864 2370 3752.36363636364 3934 0.0143967330302421 2369 0.663833659769916 -0.559634329144145 -1 0.157797844469599 2369 4444 4156 3013 4657 3131 2977 3221 4703 4671 3934 4351 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 5.34553669321269e-07 9.12181243382642e-07 3935 3458.36363636364 3934 4.85957999278724e-08 1022 1.89311626457004 1.84088870851989 1 3.30094680202601 3934 4487 2937 2676 2621 4271 4221 4674 1022 4186 3013 4352 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 4.35008252315918e-05 4.80289813083306e-05 4105 3725.45454545455 3934 3.95469867287948e-06 2925 1.56965281500489 1.41378374565856 1 1.95653887667281 4104 4608 2925 4043 4246 3934 3549 2928 2931 3309 4403 4353 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 8.14394726642396e-08 3.27411388472988e-07 4410 3801.54545454545 3935 7.40358869808742e-09 865 1.51822760087273 1.72888517015531 1 2.84218557048141 3935 4488 3617 4477 865 4483 4406 3907 3882 4406 3351 4354 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 2.48834319584574e-07 5.3337783307865e-07 4230 3650.18181818182 3935 2.26213043390327e-08 2021 1.79091510890833 -1.55011997063384 -1 3.24321682827453 4227 3300 2800 3895 2021 3970 4617 4206 3935 2898 4283 4355 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 1.40383290480246e-06 1.98445382170338e-06 4415 3781.63636363636 3937 1.27621254599752e-07 2046 2.26398692990315 -2.18699596108407 -1 3.72710440952042 4414 3793 2046 3937 3250 4692 4539 3473 4671 2084 4699 4356 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 3.40848915090804e-07 6.50286615094221e-07 4635 3504.36363636364 3937 3.0986269808999e-08 2246 1.63055051862715 1.2961238577727 1 2.91220557384351 3974 3941 2885 3154 2305 4388 4632 3937 2453 2246 4633 4357 M6981 KEGG_PROTEIN_EXPORT http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEIN_EXPORT.html Protein export 33/39 KEGG 1.12199374573254e-05 1.31834963401981e-05 2990 3774.09090909091 3939 1.01999951628146e-06 2689 0.839378224384909 -0.627002911583216 -1 1.18195752741852 2987 4547 3939 4509 3973 2862 2689 3157 4597 4515 3740 4358 M10570 BIOCARTA_RNA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RNA_PATHWAY.html Double Stranded RNA Induced Gene Expression 17/17 BioCarta 0.000319781872619803 0.00033728948352301 3710 3816.63636363636 3939 2.90753058274469e-05 2692 2.39066722493426 -1.33600370640975 -1 2.39599462981159 3710 4279 2692 3214 4451 4501 4528 3939 2757 3660 4252 4359 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 1.32022228469486e-05 1.53749054620275e-05 3830 4033.63636363636 3942 1.20020927948097e-06 3223 0.984395360382171 1.15048563376573 1 1.36732669546148 3826 4508 3942 4686 4007 3710 3907 3770 4198 4593 3223 4360 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 2.66134806306635e-07 5.55287751817547e-07 4340 3828.90909090909 3942 2.6613483817912e-08 2177 1.54685363479379 -1.48339310738595 -1 2.79331259868875 4338 4097 4261 3007 2177 3942 3752 4592 3607 4454 3891 4361 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 3.35985583216768e-05 3.73845344833367e-05 1230 3132.72727272727 3943 3.05446104111351e-06 374 0.754537204097683 0.52808360196953 1 0.963775502128286 1230 4256 3943 4285 4211 1241 374 2920 4540 4576 2884 4362 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 0.000354390911855166 0.000373292814986919 3105 3761.18181818182 3943 3.5444744135677e-05 2233 1.55307893626222 2.08735463141096 1 1.53648422863694 3105 3209 4275 3943 4464 4304 3991 3833 4371 3645 2233 4363 M13486 KEGG_HUNTINGTONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HUNTINGTONS_DISEASE.html Huntington's disease 188/233 KEGG 0.211230088261169 0.212671931867048 1890 3576.45454545455 3944 0.0213399761170458 1888 1.3741455449821 -1.18171003209726 -1 0.26590604917967 1888 4385 4136 3551 4703 2624 1960 3944 4087 4626 3437 4364 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 8.49330942722775e-05 9.21784789526672e-05 675 3040.18181818182 3944 7.72148848840587e-06 397 0.722635738514204 0.605960748759824 1 0.841204977335539 674 3944 4066 4300 4325 1075 397 2606 4549 4595 2911 4365 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 0.000128474719928599 0.000138195232010708 850 3284.72727272727 3945 1.16802021052132e-05 846 1.17952558641183 -1.09936546592473 -1 1.31370539536147 846 4486 3991 4083 4370 2277 2396 2581 4426 3945 2731 4366 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 4.91703593089818e-07 8.53250352714684e-07 3285 3850.45454545455 3945 4.4700336635128e-08 2575 1.55899507333884 1.54775846418506 1 2.73125916609898 3285 4701 3945 4073 2575 3496 3512 4584 3439 4458 4287 4367 M3061 BIOCARTA_FEEDER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FEEDER_PATHWAY.html Feeder Pathways for Glycolysis 10/15 BioCarta 2.38241934412911e-06 3.16493647742454e-06 3950 3814.27272727273 3947 2.16583811281594e-07 2842 1.04612689375417 -0.749857791298901 -1 1.66049073934805 3947 4064 3425 4571 3482 4455 4486 2842 4078 3579 3028 4368 M18799 REACTOME_DIABETES_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DIABETES_PATHWAYS.html Genes involved in Diabetes pathways 158/214 Reactome 4.58877580700466e-08 2.99073619127066e-07 4700 3425 3947 4.17161445701608e-09 284 1.80788302112383 -1.52194022790748 -1 3.40512178740263 4697 4378 3192 2653 284 3947 3675 4456 2030 3961 4402 4369 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 0.000165552910953503 0.000177351280004661 2395 3626.54545454545 3947 1.5051397303795e-05 1989 1.2778975633858 1.20412801875568 1 1.38336061521077 2392 4603 3808 4266 4390 2797 1989 4078 4166 3947 3456 4370 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 3.78317453367899e-06 4.77066091342903e-06 3020 3900.18181818182 3947 3.43925549030487e-07 3018 0.74890902373961 -0.718807085220375 -1 1.14993948949399 3018 3947 4059 4069 3680 3409 3711 4609 4508 4518 3374 4371 M14449 BIOCARTA_ETS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETS_PATHWAY.html METS affect on Macrophage Differentiation 26/27 BioCarta 4.21175004768866e-06 5.27726578844982e-06 3950 4002.27272727273 3948 3.82887100983515e-07 3494 1.35203760329826 1.25244248397428 1 2.05961649824871 3948 4249 3494 4041 3708 3897 3936 4195 4287 3836 4434 4372 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 8.26802772783632e-07 1.28583495470799e-06 3225 3882.45454545455 3948 7.51639166829411e-08 2913 1.42543663589254 1.67037910768075 1 2.42388731732515 3730 4453 3714 3224 2913 3948 4438 4278 3224 4307 4478 4373 M1389 BIOCARTA_SPRY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SPRY_PATHWAY.html Sprouty regulation of tyrosine kinase signals 28/30 BioCarta 9.1080944206367e-07 1.38633362352161e-06 4100 3653.36363636364 3949 8.28008926493551e-08 2023 1.61744156866028 -1.8071710173411 -1 2.73523392864607 4096 4545 3298 2023 2986 3816 4626 4486 3949 3962 2400 4374 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 2.62181470455552e-06 3.44322910559323e-06 4555 3928.54545454545 3949 2.38347075369668e-07 2493 0.899539610636991 -0.836059941539229 -1 1.41818849446785 4551 3702 3851 2493 3522 3949 4489 3871 4114 4465 4207 4375 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 1.71073871179682e-06 2.35757276487036e-06 3790 3990.36363636364 3950 1.55521822007567e-07 3238 0.88121015481356 -1.07333997024282 -1 1.43113245258046 3789 4529 3950 4633 3339 3739 3238 4463 4081 4440 3693 4376 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 0.38661662934677 0.388179215170549 3000 3817.18181818182 3950 0.0434604997924032 2283 1.3573347228833 1.32093538241642 1 0.160217374950162 2999 4276 3422 4471 4716 3626 2283 4321 4602 3323 3950 4377 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 1.28609443430043e-06 1.84565695649074e-06 4110 3901.81818181818 3951 1.16917744194264e-07 3125 1.70608947869485 1.37349476376648 1 2.82396335271438 4106 4437 3125 4604 3191 3963 3951 4224 3741 3732 3846 4378 M842 REACTOME_PURINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_CATABOLISM.html Genes involved in Purine catabolism 10/15 Reactome 0.0343732442345348 0.0348756906248934 3955 3794.45454545455 3952 0.00317475890935318 2570 1.77514162735323 -0.893018122259391 -1 0.74623777701876 3881 4649 3289 4591 4674 3315 2570 2730 3953 3952 4135 4379 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 2.3124585971539e-08 2.24123297301158e-07 4525 2856.18181818182 3954 2.10223511041868e-09 9 2.13999696664916 -1.59691630418587 -1 4.10823609570215 4521 543 1300 2702 9 4400 4375 4120 3992 1502 3954 4380 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 0.00233372923323832 0.00240454092575526 3980 3908.45454545455 3956 0.000233618369323754 2837 0.84310074202519 -1.24772215511158 -1 0.636745674804799 3979 3823 4259 3956 4566 3515 2837 4181 4683 3536 3658 4381 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 2.54048137539816e-07 5.40718801480723e-07 4465 3739.54545454545 3956 2.30952878978538e-08 2037 1.87271486308544 -1.79142191678193 -1 3.38817926233189 4463 4717 3240 2931 2037 4276 4712 4334 2636 3833 3956 4382 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 1.2358916847318e-06 1.78664892861687e-06 4460 3367.54545454545 3957 1.12353852637992e-07 877 2.92622225846183 -2.49921133786547 -1 4.85609889267978 4458 3957 1520 3329 3165 4490 4545 877 4190 2546 3966 4383 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 1.03242408305471e-05 1.2179559290223e-05 3255 3396.09090909091 3957 9.38571752803831e-07 1201 1.92283144304776 1.6707176690026 1 2.72781717083934 3254 4615 2883 4260 3957 2794 1201 2160 4051 3994 4188 4384 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 3.85305089328257e-07 7.09091031152922e-07 4290 3490.63636363636 3959 3.50277415281907e-08 2207 2.03819097804164 -1.87126884212103 -1 3.618349282857 4287 4393 2554 4448 2404 4312 3959 2207 4068 2949 2816 4385 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 7.9206823725575e-05 8.60428556926845e-05 1050 3092 3960 7.20087959642275e-06 391 0.732824009977485 0.540493809183992 1 0.859407427703517 1047 4248 3960 4289 4318 1117 391 2745 4544 4586 2767 4386 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 1.53012489035417e-07 4.12818153481133e-07 4235 3634.81818181818 3960 1.3910227243419e-08 1524 0.856988891237328 -0.928530042833486 -1 1.57903256986075 4234 1810 3860 3963 1524 4538 4261 3738 3885 4210 3960 4387 M6917 BIOCARTA_EPONFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPONFKB_PATHWAY.html Erythropoietin mediated neuroprotection through NF-kB 15/18 BioCarta 0.00266091896088639 0.00273747547850562 3200 3813 3962 0.000242194802330401 2864 1.59194274979247 -1.09713117244685 -1 1.17717895883402 3196 4045 2864 4007 4567 3962 4200 3785 3554 3398 4365 4388 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 2.44883438254532e-07 5.30157871195484e-07 3965 3854 3964 2.22621332284247e-08 2001 1.42145520024271 -1.3049812635912 -1 2.5750535745444 3964 3697 3654 4459 2001 4450 4385 3840 3858 3966 4120 4389 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 2.08397773567559e-06 2.80930590873057e-06 4520 3980.63636363636 3965 1.89452700886581e-07 3023 1.18682187653356 -1.51430843761723 -1 1.90166896900728 4519 4443 3930 3770 3424 4495 4166 3965 3023 4425 3627 4390 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 6.15953508617516e-05 6.72986240896916e-05 1415 3397.54545454545 3965 5.59973413354633e-06 1412 0.994233077704807 1.00665367613243 1 1.19691384216993 1412 4542 3965 4495 4293 2118 1636 3088 4299 4188 3337 4391 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 0.0370938363098084 0.0376279620421869 3970 3757.54545454545 3966 0.00377279641043037 1283 0.523089016455474 0.577831926146169 1 0.214306948840631 3966 4075 4222 3215 4639 2882 1283 3777 4709 4672 3893 4392 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 1.12843802396805e-07 3.58148551537347e-07 4715 3790.18181818182 3966 1.02585280168056e-08 1234 1.33891714013949 -1.18881451097193 -1 2.49134036017887 4712 3606 3901 4016 1234 4552 3966 4031 3088 3908 4678 4393 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 4.92922239641484e-08 3.0357704374324e-07 4090 2767.45454545455 3966 4.92922250575239e-09 429 2.06113704742738 -1.7172889404813 -1 3.87837955260608 4087 1054 4704 539 429 4492 4530 3966 1445 558 4638 4394 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 0.000985814248115491 0.00102399719434532 4465 3829.36363636364 3967 9.86251844732517e-05 2538 1.86920798385889 -1.40774050182217 -1 1.61286119209639 4462 2917 4405 4143 4535 3849 2538 4515 3723 3069 3967 4395 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 0.050678893159388 0.0513314110970626 3670 3805.90909090909 3968 0.00518731658748992 2528 2.22500061373416 1.65055786139868 1 0.827718314778686 3670 4335 4447 4196 4682 3968 2528 2911 3933 3070 4125 4396 M7721 BIOCARTA_EIF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF_PATHWAY.html Eukaryotic protein translation 21/40 BioCarta 0.00290679130087279 0.00298846764106285 1905 3641.63636363636 3969 0.000264603552077244 1901 0.637558763644414 0.726196659020174 1 0.463919161333281 1901 4280 3969 4282 4572 2814 2272 3199 4650 4510 3609 4397 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 1.34958557083785e-05 1.56858997644784e-05 3185 3631.18181818182 3969 1.22690349992224e-06 2483 1.93707516966033 2.65894225928506 1 2.68656928775359 3185 4568 3251 2501 4016 3969 4434 4038 2483 4348 3150 4398 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 0.0105558942657136 0.0107657348604512 2560 3762.90909090909 3972 0.000964262338018399 2415 2.23956578927046 -1.70225650946157 -1 1.27182893575693 2556 3782 2415 3972 4606 3683 4597 4701 4320 2694 4066 4399 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 2.15949334388865e-05 2.450530051756e-05 3390 3929 3974 1.96319503773179e-06 3350 1.5682365060171 -1.79768924182014 -1 2.0871152895144 3387 4188 3553 4027 4124 3790 4649 4504 3974 3673 3350 4400 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 4.47336843805576e-06 5.57988874937188e-06 4070 3845.09090909091 3974 4.0667068490929e-07 2399 2.17108688834908 -2.55807482882448 -1 3.29264880720088 4067 3974 2399 3465 3726 4057 3922 4714 4574 3190 4208 4401 M1001 BIOCARTA_RHO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RHO_PATHWAY.html Rho cell motility signaling pathway 48/53 BioCarta 3.15696789723802e-08 2.69553239732593e-07 4490 3520.27272727273 3975 2.86997085685459e-09 70 1.42857529395286 -1.31917391768802 -1 2.70913896061491 4486 3927 3516 4607 70 4448 4076 4431 2016 3975 3171 4402 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 1.29575685478315e-06 1.85613728515219e-06 3980 3734.27272727273 3976 1.17796147087196e-07 2153 1.23185864057713 -1.50329537157073 -1 2.03789006214791 3976 4476 3834 3783 3196 4140 4483 2153 4163 4451 2422 4403 M7561 KEGG_MTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MTOR_SIGNALING_PATHWAY.html mTOR signaling pathway 56/78 KEGG 3.50940050457855e-07 6.63570412832985e-07 3230 3682.72727272727 3977 3.19036460399267e-08 2333 1.4288644790977 1.41438103798355 1 2.54825895130148 3982 4184 3726 3226 2333 3977 3229 4058 2857 4382 4556 4404 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 0.000171273531512474 0.000183396340458003 2530 3565.36363636364 3977 1.55715333532101e-05 2169 0.742687552817894 -0.79117823794649 -1 0.800497974315919 2528 3997 3977 4038 4394 2617 2169 3430 4335 4508 3226 4405 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 5.67921494481276e-05 6.22090845660623e-05 4640 3740.45454545455 3977 5.16305596077232e-06 2367 2.65556675607838 -2.9578672030407 -1 3.22454941110655 4640 3977 2367 2881 4283 4649 4119 3125 3194 3361 4549 4406 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 3.49178539909619e-06 4.44477537317531e-06 3950 3900.90909090909 3978 3.17435540107603e-07 2038 1.2688596634513 1.53925762402074 1 1.96017357999545 3946 4435 3978 2038 3643 4280 3494 4589 3460 4535 4512 4407 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 1.07864370851735e-07 3.50633492024923e-07 4115 3700.45454545455 3978 1.0786437608736e-08 1285 1.9086628668578 1.93618012961013 1 3.55691610161149 4111 3551 4710 3978 1285 4299 4075 3873 2851 3380 4592 4408 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 4.19010310276215e-06 5.2515365493992e-06 3055 3739.90909090909 3979 3.80919189383784e-07 2982 1.34526163894663 1.51468634202397 1 2.05011460938121 3054 4114 4005 4090 3706 3215 4176 2982 3979 4326 3492 4409 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 0.0285147600914412 0.0289502404025818 3595 3744.18181818182 3981 0.00288873987564954 1926 0.556539367450169 -0.620955358644267 -1 0.246364522516027 3595 4343 4598 3981 4625 3468 1926 2902 4607 4712 2429 4410 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 3.99132004930123e-05 4.41919555071588e-05 1050 3172 3982 3.62853860283738e-06 691 0.785161418423355 0.612302680285383 1 0.986455011671057 1050 3982 3998 4675 4232 1373 691 2959 4561 4582 2789 4411 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 0.00214049069174472 0.00220978041667434 2625 3386.54545454545 3982 0.00021425552562899 1147 1.06963743061076 1.06963743061076 1 0.819397693573782 2624 4659 4472 4228 4561 2511 1147 2413 4145 3982 2510 4412 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 9.3511846517929e-07 1.41648239911625e-06 3930 3928.27272727273 3983 8.50108056959298e-08 3000 1.32213299623538 -1.66396567545678 -1 2.23211709265215 3926 3983 3712 4019 3000 3618 3584 4604 4209 4222 4334 4413 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 4.87686313981177e-05 5.36193664568171e-05 665 2775.18181818182 3984 4.43361022847446e-06 457 0.854688732299672 -0.84762672159126 -1 1.05315728802009 662 3998 3984 4045 4265 977 457 1327 4380 4396 2036 4414 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 0.00856013913568574 0.00874542353256205 2955 3839.36363636364 3985 0.000781238997645572 2953 1.42488205001329 -1.52167866425827 -1 0.846003261026866 2953 4613 3247 3985 4601 3464 4190 3016 4141 4296 3727 4415 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 0.000135157576144715 0.000145218247075588 2585 3294.18181818182 3985 1.35165797255125e-05 1510 1.1786767667703 -1.1786767667703 -1 1.30543208767654 2583 4336 4573 4566 4382 2399 1531 1686 4685 3985 1510 4416 M13863 BIOCARTA_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MAPK_PATHWAY.html MAPKinase Signaling Pathway 102/109 BioCarta 2.74130620943672e-07 5.66073041584045e-07 3435 3773.27272727273 3987 2.4920968645607e-08 2107 1.18236416922582 -1.22652414888582 -1 2.13206116150348 3433 3887 4023 2989 2107 4000 4556 4380 3987 4461 3683 4417 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 0.188984724764689 0.190315319157101 3995 3701.45454545455 3987 0.0188624163753278 2567 2.03019181942995 1.80006754971907 1 0.421544913970954 3991 4303 3323 3987 4717 4211 2592 3316 2567 4229 3480 4418 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 2.01946351794747e-05 2.29863520035572e-05 1115 3120.27272727273 3988 1.83589277782543e-06 411 0.729814479070666 0.51945252713107 1 0.976682600311906 1115 4245 3988 4292 4110 1221 411 2927 4543 4591 2880 4419 M14663 REACTOME_ETHANOL_OXIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ETHANOL_OXIDATION.html Genes involved in Ethanol oxidation 9/13 Reactome 0.000221742720495087 0.000236151994751086 4190 3644.54545454545 3989 2.21764850028299e-05 1857 2.82550169907375 -3.22441236008444 -1 2.95826581003512 4188 3194 4256 2636 4422 3989 4398 3145 3688 1857 4317 4420 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 4.18643501070826e-05 4.62654489593608e-05 2590 3852.09090909091 3991 3.80592243413573e-06 2590 1.34741025255981 1.23153954836734 1 1.68571758190868 2590 4475 3854 4307 4242 3330 3176 3880 3991 4367 4161 4421 M194 BIOCARTA_PROTEASOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PROTEASOME_PATHWAY.html Proteasome Complex 31/35 BioCarta 0.68618940391 0.686334813828184 2850 3979.27272727273 3993 0.1 2847 0.642735238893053 -0.700759062448593 -1 0.0294774198840712 2847 4577 4079 3802 4691 3574 3042 3935 4643 4589 3993 4422 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 6.25845181113138e-05 6.83161252278911e-05 4255 3949.81818181818 3994 5.68966350507431e-06 3285 1.14548043626639 -1.13473102074943 -1 1.37696930324436 4253 3475 3489 3994 4297 4489 3836 4610 4158 3562 3285 4423 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 2.91873605837203e-06 3.78785652887435e-06 3485 3895.90909090909 3995 2.65339993696466e-07 3153 1.25644857420988 -0.944139791334051 -1 1.96619207733226 3483 4157 3964 4059 3570 3153 3980 4207 3995 4096 4191 4424 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 7.38916304158589e-08 3.2144561803028e-07 3995 3641.27272727273 3995 7.38916328728468e-09 861 1.56629860139045 -1.25255890479774 -1 2.9358158851191 3995 4349 4356 3806 861 3004 3837 4528 2574 4656 4088 4425 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 2.68155631260744e-06 3.50899523024872e-06 4680 3387.90909090909 3996 2.43778143739376e-07 651 1.59533026731585 -1.43891627918949 -1 2.51203313492405 4680 2633 3246 651 3536 4164 4043 4433 1369 3996 4516 4426 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 0.000933830986824918 0.000970641325217708 1635 3737 3996 8.49297822270345e-05 1631 1.11053881025607 1.17702597141674 1 0.965340472545316 1631 4152 4064 3533 4528 3210 3996 3470 4210 4365 3948 4427 M12469 REACTOME_HIV_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIV_INFECTION.html Genes involved in HIV Infection 235/285 Reactome 1.26554395391799e-05 1.47672866810703e-05 3360 4005.18181818182 3998 1.15050112180313e-06 3357 1.01542400808244 -1.13164835372886 -1 1.41558744761449 3357 4704 4168 4323 3998 3993 3358 3651 4314 4637 3554 4428 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 2.41925384380389e-06 3.20935304742955e-06 3320 3924.18181818182 3999 2.19932409469699e-07 2370 1.11623589177286 1.43174640116278 1 1.76987980584897 3317 4601 3684 4644 3487 3868 2370 4496 4298 4402 3999 4429 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 6.49874387145116e-08 3.14536172538656e-07 4095 3652 3999 6.49874406150268e-09 735 1.69362534841564 -1.59968721162676 -1 3.17915795277585 4091 3549 4489 3979 735 3999 4444 4024 2831 4301 3730 4430 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 1.15719937210094e-06 1.69311253450603e-06 4000 3823.09090909091 4000 1.05199998253448e-07 2796 1.79287144109428 1.81614455485329 1 2.98704726659507 4000 4404 3429 4432 3122 4256 3220 4085 2796 3680 4630 4431 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 0.06379707387151 0.0645354026304173 2145 3561.36363636364 4002 0.00597508001745038 1437 0.730459014191222 0.857190327428581 1 0.250188522619066 2141 4624 4002 4680 4645 2181 1437 2995 4665 4539 3266 4432 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 0.000359344132893064 0.000378256981992699 4115 3886.63636363636 4004 3.26729855415912e-05 1825 1.3968220545031 1.65403426209638 1 1.37949613683818 4113 4004 3569 3212 4458 4539 4659 4666 1825 3990 3718 4433 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 1.0248367509698e-07 3.45516390326962e-07 4495 3142.45454545455 4005 1.02483679823287e-08 1058 1.89524481600668 -1.70287262992166 -1 3.53539888061185 4491 1963 4274 1893 1232 4005 4511 4263 2355 1058 4522 4434 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 0.000214396028055801 0.000228534158180528 3790 4035.09090909091 4006 1.94924476715643e-05 3312 1.1987403141673 -0.855939211456283 -1 1.25949998010839 3787 4282 3406 4006 4410 3672 4506 4427 4603 3312 3975 4435 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 2.82427830231814e-07 5.74099637680519e-07 3030 3862.27272727273 4007 2.56752605898961e-08 2146 1.3074861940366 1.24558077968429 1 2.35546600779626 3027 4410 4007 4291 2146 3664 3505 4667 3902 4529 4337 4436 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 6.17568415796727e-05 6.74438436501747e-05 3455 3696.36363636364 4007 5.61441593110142e-06 1260 1.60770325307476 1.43363567050414 1 1.93554069876705 3452 4174 3622 4510 4295 2960 1260 3411 4326 4007 4643 4437 M13158 BIOCARTA_LONGEVITY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LONGEVITY_PATHWAY.html The IGF-1 Receptor and Longevity 22/25 BioCarta 6.20416974841064e-06 7.56293419744272e-06 4010 3861.90909090909 4008 5.6401702224701e-07 2542 1.22712987946496 0.877912900886765 1 1.81388117289355 4008 4265 3416 3761 3817 4350 2542 4464 2860 4443 4555 4438 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 2.8262388304009e-07 5.74250851463291e-07 3675 3908.18181818182 4008 2.82623918984413e-08 2231 1.58607115904105 -1.47158821050419 -1 2.85747427308838 3674 4348 4432 3550 2231 3881 4685 4008 3633 4489 4059 4439 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 1.86933578317857e-07 4.57638220778156e-07 3790 3870 4008 1.69939631092335e-08 1722 1.09807432887933 -0.983294908376577 -1 2.00928956657993 4347 4008 3786 4619 1722 4364 3306 4543 4310 3788 3777 4440 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 0.000405873050424367 0.000426854010250226 2185 3627 4010 3.69043589432612e-05 1814 0.718500160924824 0.714929038317126 1 0.698278768642983 2184 4573 4010 4499 4468 2177 1814 3701 4592 4567 3312 4441 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 0.000716453237312563 0.000747658474489343 2815 3737.90909090909 4011 6.51533331189871e-05 2032 1.42248859522173 1.67384113301286 1 1.28330841471291 2815 4430 4011 2032 4508 4147 4212 3842 2910 4302 3908 4442 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 4.12115090475555e-05 4.55546423195462e-05 4530 3785.63636363636 4011 3.74657100568771e-06 2673 1.60624847604886 -1.00333180273264 -1 2.0128291221083 4530 3471 2673 4011 4239 4339 4266 3721 4224 3032 3136 4443 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 3.41921251353549e-05 3.80001955824995e-05 4125 3572.27272727273 4011 3.41926512423875e-06 1848 2.19795296874718 -3.01528590398144 -1 2.80460557114888 4123 3220 4651 3069 4225 4559 4373 1959 4011 3257 1848 4444 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 6.56849011285397e-05 7.16010931470456e-05 4140 3730.45454545455 4011 5.97153294088332e-06 2254 2.43829317832531 -2.52852570003987 -1 2.91765628269067 4140 4011 2254 3891 4304 4614 3990 2623 4273 2591 4344 4445 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 0.00449429140244022 0.00460752724142438 3445 4032.54545454545 4012 0.00040940899579716 3318 0.623544254459609 0.578932524872766 1 0.419848324540272 3443 4296 3879 4648 4583 3333 3318 3497 4655 4694 4012 4446 M139 PID_MYC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_PATHWAY.html C-MYC pathway 18832364 34/39 Pathway Interaction Database 4.83539044700057e-06 6.00448379632798e-06 3895 4114.36363636364 4013 4.39581915887354e-07 3706 0.749291932288851 -0.732084186446036 -1 1.12891326587881 3893 4533 4013 4671 3747 4022 3785 3706 4491 4530 3867 4447 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 5.30839329869868e-06 6.54706463806056e-06 4400 3976.81818181818 4014 4.82582373399656e-07 3258 1.43184497560456 1.45175681045067 1 2.14252535448215 3258 4399 4004 4310 3771 4286 3567 3633 4014 4397 4106 4448 M4864 KEGG_BASAL_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_TRANSCRIPTION_FACTORS.html Basal transcription factors 31/38 KEGG 0.000357719848533368 0.000376631203452486 1035 3006.09090909091 4017 3.25252751818438e-05 1031 0.874883082916578 0.873250274770662 1 0.864181946959957 1031 4242 4017 4276 4457 1410 1108 1603 4452 4434 2037 4449 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 0.428930129128185 0.430572141532334 2950 3771.72727272727 4018 0.0496559921947979 2034 1.17296192053112 -0.954983938398336 -1 0.123090790146731 2950 4484 4056 2034 4675 3633 3217 4102 4018 4448 3872 4450 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 1.24027790000826e-05 1.44939630800669e-05 4335 3673.54545454545 4019 1.24028482236435e-06 1855 1.88160636883675 -1.14296032318469 -1 2.62826249900452 4332 2457 4216 4140 4019 4494 2881 3835 3772 1855 4408 4451 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 0.0190077984386275 0.0193396871373834 3090 3854.27272727273 4021 0.00174309440026004 2662 1.05752326365759 1.24193743635632 1 0.522414045162983 3088 4021 3872 3762 4616 3370 2662 4074 4340 4291 4301 4452 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 3.46911108707135e-07 6.57407624356902e-07 3805 3908.45454545455 4023 3.15373784918612e-08 2326 1.50729678170098 -1.46059684767211 -1 2.68994737627479 3805 4357 3931 4075 2326 3729 4362 4626 3702 4057 4023 4453 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 3.46740955073849e-08 2.80242689717221e-07 4675 3758.36363636364 4023 3.15219055035288e-09 102 1.41445222808715 -1.05778714133892 -1 2.67544907537918 4672 4160 3582 4023 102 4382 4509 3708 3798 3812 4594 4454 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 5.30373904833273e-05 5.81595513909171e-05 4155 3855.54545454545 4024 4.8216971951675e-06 2503 1.64455262619381 -0.688874743352732 -1 2.01046941257663 4151 4563 3478 2503 4274 4334 3748 3900 3041 4395 4024 4455 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 0.00465269939987423 0.0047688905900991 4115 3916.63636363636 4024 0.000423869859650399 2532 1.14782634757623 -1.22478096317084 -1 0.768630089457779 4114 4275 3660 4024 4585 4239 4674 3259 3970 3751 2532 4456 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 1.48647710515575e-06 2.07824998114193e-06 4375 3964.72727272727 4024 1.35134373593344e-07 3286 1.50431860195313 -1.1945278272154 -1 2.46749353085489 4372 3882 3665 3744 3286 4451 4252 4065 3569 4024 4302 4457 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 0.0374080522625639 0.0379385489212079 2420 3486 4025 0.00345997202360415 1247 0.688372914836179 0.779953642748963 1 0.281585452692296 2417 4602 4025 4298 4632 2032 1247 2951 4666 4561 2915 4458 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 0.00562426244289299 0.00575222507702165 3240 3938.09090909091 4025 0.000512608404216346 2994 1.29521477261501 1.52800429076326 1 0.836986350522469 3236 4449 4050 2994 4592 4437 3945 3892 3239 4460 4025 4459 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 2.77341064403115e-05 3.10643052677433e-05 4180 3700.81818181818 4025 2.52131418855045e-06 1553 0.880474753758172 1.18426836638922 1 1.14522953479486 4472 4025 3812 1553 4178 3569 2957 3295 4178 4424 4246 4460 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 1.38962873254673e-05 1.61274836922069e-05 4420 3802.09090909091 4026 1.26330682746021e-06 2473 1.99842025883827 -0.532662838211709 -1 2.7647194646721 4419 4048 3042 2473 4026 3805 3368 4054 3751 4260 4577 4461 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 2.18746744678908e-05 2.47955003574555e-05 3190 3890.81818181818 4027 1.98862654286792e-06 3160 1.1798448113012 1.07692101123304 1 1.56826208623566 3186 4158 4027 4303 4127 3225 3160 3846 4025 4555 4187 4462 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 8.32517392691752e-08 3.27411388472988e-07 4590 3687.90909090909 4029 7.56834021996026e-09 897 1.52638519208895 -1.48270000562373 -1 2.85746155042122 4590 3569 3871 4029 897 4642 4277 4212 3346 2548 4586 4463 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 8.29847819620931e-06 9.92117960641032e-06 3965 4120.18181818182 4030 7.54409954411758e-07 3711 1.25261122210802 -1.10300044595193 -1 1.80892852406967 3965 4000 3761 4622 3902 4345 4402 4030 3711 4346 4238 4464 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 1.4282893767189e-05 1.65476825186873e-05 2710 3998.81818181818 4030 1.29845331779853e-06 2707 1.51851024655864 -1.60649889762523 -1 2.0956817259835 2707 4358 4030 4098 4033 3856 4682 4242 3985 3986 4010 4465 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 1.75090058524012e-07 4.41094589059637e-07 4565 3857.72727272727 4031 1.59172793144363e-08 1663 1.33203900255677 -1.34830713554551 -1 2.44373940484745 4564 4390 3892 4031 1663 4452 3732 4696 3192 4311 3512 4466 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 1.44001184954535e-05 1.66753089544996e-05 1240 3395.81818181818 4031 1.30911025021944e-06 1238 1.31822568251612 1.31451840559664 1 1.81788713605498 1238 4416 4031 4093 4036 2280 1482 3280 4461 4497 3540 4467 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 4.69072358471187e-05 5.1645008910287e-05 4495 3780.09090909091 4034 4.26438509165773e-06 1556 0.81774967203499 1.04773400007283 1 1.01145078129233 4650 4034 3847 1556 4258 3572 2737 3664 4280 4492 4491 4468 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 0.000585604941463117 0.000612600913941913 4495 3897.18181818182 4038 5.32509889346054e-05 2519 1.31579473401712 0.99804618055898 1 1.21986496751125 2519 4492 3935 4288 4494 3285 4038 4693 2713 4409 4003 4469 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 6.56636719866755e-07 1.07020901856736e-06 3560 3680.09090909091 4039 5.96942650776373e-08 2161 1.03951764711197 1.32458623166848 1 1.79134618849352 3559 4541 3743 4484 2760 4113 4708 2161 4039 4103 2270 4470 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 0.000225131437698333 0.000239544721807063 4345 3955.09090909091 4039 2.25154248824793e-05 2954 1.09208834392108 0.721398699100601 1 1.14092113382144 3844 4341 4345 4570 4431 3442 3014 2954 4661 3865 4039 4471 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 0.000837437722085212 0.000872176974457679 2975 4116.90909090909 4041 7.6159696879664e-05 2975 0.682408652687071 0.872038178574757 1 0.602008536461161 2975 4587 3997 4668 4517 3764 4041 3621 4591 4488 4037 4472 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 7.05617146920858e-06 8.51575794800933e-06 4555 4058.09090909091 4042 6.41472190993316e-07 3708 1.17573409363676 -1.07159076206661 -1 1.72037848962677 4554 4228 3728 4042 3857 3885 3708 3731 4256 4055 4595 4473 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 7.22731395220139e-05 7.86555726409743e-05 2880 3758.18181818182 4042 6.57050126427167e-06 1631 0.552151991379415 0.552482406944111 1 0.653530794287957 2879 4592 4042 4515 4311 3025 1631 3477 4691 4719 3458 4474 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 0.000854968406046624 0.000889649664140226 2885 3801.09090909091 4043 7.77546224060054e-05 2240 0.697122958263028 0.73898992627961 1 0.613273686826241 2881 4562 4043 4513 4519 2944 2240 3267 4620 4590 3633 4475 M15371 BIOCARTA_ETC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETC_PATHWAY.html Electron Transport Reaction in Mitochondria 13/16 BioCarta 0.161102337996494 0.162409875126752 2700 4004.63636363636 4044 0.0158428475617116 2697 0.858887038251014 1.0724721933494 1 0.194919328409619 2697 4319 3840 4044 4659 3551 4346 3909 4565 4371 3750 4476 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 1.37014438792387e-06 1.94674338079491e-06 4045 4004.54545454545 4044 1.2455865829462e-07 3231 1.56879362764186 1.532871727424 1 2.58614768569896 4044 4189 3390 4655 3231 4300 3921 3356 4348 3910 4706 4477 M745 REACTOME_MRNA_CAPPING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_CAPPING.html Genes involved in mRNA Capping 29/31 Reactome 0.0411123603492352 0.0416774787045511 2440 3947.18181818182 4045 0.00380921510323355 2440 0.734171042888908 0.816195593943112 1 0.291722825553425 2440 4578 4045 4683 4630 3349 3216 3564 4589 4537 3788 4478 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 3.10351963482028e-07 6.11341009591772e-07 3460 4043.81818181818 4045 3.1035200682529e-08 2308 1.40945457770746 1.46750893918194 1 2.52812195516421 3456 4677 4657 4533 2308 3974 3817 4045 3994 4630 4391 4479 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 0.68618940391 0.686334813828184 3590 4114.90909090909 4046 0.1 3415 1.35492365480119 1.63668743903956 1 0.0630945311749115 3586 4302 3415 4650 4718 4686 3485 3912 4584 4046 3880 4480 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 0.000858149015087804 0.000892762475471553 4390 4002.36363636364 4047 7.80439940219598e-05 3326 1.09326163329434 1.15525576146949 1 0.961775752658995 4388 4047 3637 3476 4520 3860 3326 4136 4568 3541 4527 4481 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 8.10660951259794e-06 9.69424801101148e-06 3955 3804.18181818182 4047 7.36967216742656e-07 1807 2.4463322060213 -1.56844257953102 -1 3.5407318281543 3953 4288 1807 4559 3900 4047 4615 3763 4136 2629 4149 4482 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 2.19064435750556e-05 2.48255495016236e-05 4050 4058.54545454545 4047 1.99151470099514e-06 3522 1.28009766295655 -1.70104004095328 -1 1.70139798322692 4047 4555 3522 4645 4128 3859 4099 3969 4135 4015 3670 4483 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 3.20857200552012e-05 3.57855856948369e-05 1195 3206.63636363636 4049 2.91692618330145e-06 648 0.697305153397416 0.514305143960335 1 0.894429809576295 1194 4543 4049 4085 4200 1273 648 3178 4567 4615 2921 4484 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 9.39342540523089e-05 0.000101713622190158 4390 4103.72727272727 4050 8.53984227630765e-06 3758 0.65254523131231 0.783015240152444 1 0.751475179866318 4457 4050 3877 3758 4335 4389 3844 3901 4390 4259 3881 4485 M2220 KEGG_FOLATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOLATE_BIOSYNTHESIS.html Folate biosynthesis 8/12 KEGG 1.38498048309368e-05 1.60782109422365e-05 3645 4075 4051 1.38498911493862e-06 3403 1.27921852745149 -0.894929775847636 -1 1.76991894930289 3644 4648 4182 4573 4051 3403 3509 4614 4477 3767 3957 4486 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 5.68429494047388e-07 9.55479776318971e-07 4550 3241.81818181818 4051 5.16754219015067e-08 454 1.67670509262415 -1.54549899504671 -1 2.91374991863713 4546 2681 3224 454 2667 4241 4204 4650 764 4051 4178 4487 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 0.00231924303403882 0.0023906589038356 3935 4090.63636363636 4053 0.00021106287252706 3398 0.687098748905989 0.845328722060578 1 0.519265847696531 3398 4552 4053 4078 4560 3566 3933 3743 4611 4571 3932 4488 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 0.000441250237412696 0.000463543538969047 4475 3488.36363636364 4055 4.01217057342521e-05 1587 0.856472294339954 0.930476786565789 1 0.823676460234715 1587 4200 4055 4074 4472 2485 2380 2872 4473 4577 3197 4489 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 1.34814348805265e-06 1.91894971761414e-06 4690 3843.27272727273 4055 1.2255857401687e-07 2491 1.93934640717078 -2.08760688602006 -1 3.20070270552397 4686 3621 2689 4402 3221 4546 3857 4365 4055 2491 4343 4490 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 0.000479149608488583 0.000502909973774985 1995 3868 4056 4.35685451673529e-05 1992 1.17293880952543 1.26941570836223 1 1.1163531904969 1992 4162 4044 4080 4475 3548 4433 3498 4237 4023 4056 4491 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 3.73004116081397e-07 6.92323801771212e-07 4670 3513.72727272727 4059 3.39094708475693e-08 339 1.87853710604278 -1.72225573651207 -1 3.34048988449421 4668 4166 3189 2461 2384 4399 4032 4492 339 4059 4462 4492 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 2.60375108870298e-07 5.4840272818733e-07 4060 3871.72727272727 4059 2.60375139378141e-08 2156 1.46865044503119 -1.22662149476064 -1 2.65434746236643 4059 4686 4611 3014 2156 3592 3692 4302 3410 4648 4419 4493 M9174 ST_STAT3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_STAT3_PATHWAY.html STAT3 Pathway 17/19 Signaling Transduction KE 2.19378220952085e-05 2.48551416921229e-05 4680 3824.18181818182 4064 1.99436735058743e-06 2636 2.10844129532159 -1.36388413331777 -1 2.80260492201113 4678 3752 2636 3174 4129 4434 4504 4442 2946 3307 4064 4494 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 0.00100725732480873 0.00104558050870843 4315 3935.90909090909 4065 9.16107988716399e-05 2906 1.08729217225818 -0.923319409295834 -1 0.934974346658889 4315 4065 3515 3759 4530 4214 2906 3339 4474 3715 4463 4495 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 0.48573992226653 0.487081460186535 3245 3979.09090909091 4066 0.0586656820553672 2470 0.339226091460647 -0.339226091460647 -1 0.0297400896193165 3242 4650 3937 3523 4694 3552 2470 4066 4719 4685 4232 4496 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 1.43289248679399e-06 2.01662637075827e-06 2830 3667.81818181818 4068 1.3026303818717e-07 2303 1.01956486837426 -0.782050284903195 -1 1.67593608413265 2827 4494 4068 4089 3264 2303 2675 4148 4438 4565 3475 4497 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 0.00379298993974813 0.00389447737994587 1550 3611 4069 0.000345413200903281 1548 0.865389422490291 0.900531957680023 1 0.601269850441562 1548 4539 4069 4687 4576 2545 2408 3041 4527 4541 3240 4498 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 5.8099784102942e-05 6.36119185724626e-05 4505 3857.18181818182 4069 5.81013031720495e-06 2364 2.08954182957771 1.57579677510457 1 2.53122060613675 4505 4069 4713 3646 4302 4515 3825 3135 2364 2933 4422 4499 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 6.35932729877919e-05 6.9337086741136e-05 3375 3799.18181818182 4070 5.78137375376767e-06 1788 0.909259719352895 1.1094910244411 1 1.09114186414212 3371 4061 3580 4460 4301 2738 1788 4452 4617 4353 4070 4500 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 5.35467706817705e-07 9.13410761178015e-07 3490 3879.27272727273 4071 4.86788942861452e-08 2622 1.39145311534718 1.55492677815714 1 2.4257546821041 3489 4361 4071 4081 2622 3684 3768 4099 3670 4528 4299 4501 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 0.219577652265513 0.220982200147809 3815 3904.45454545455 4072 0.024487205765075 2214 1.25092533198502 -0.804499453964237 -1 0.235971592115731 3815 4072 4251 4425 4683 3401 2214 3413 4437 3860 4378 4502 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 1.32279024011872e-06 1.8879860699608e-06 4480 4001.09090909091 4072 1.20253730497384e-07 3210 1.39676919964446 -1.23877055002142 -1 2.30784029657272 4476 4368 4072 4082 3210 3834 3986 3733 3327 4542 4382 4503 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 0.00192272781222495 0.00198801210814934 3015 4119.27272727273 4074 0.000174946388380363 3012 0.677217758434934 0.816195593943112 1 0.527449815411738 3012 4556 4062 4685 4552 3748 3684 3759 4608 4572 4074 4504 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 2.19466624777275e-07 4.97303153599971e-07 4305 3782.54545454545 4075 1.9951513333703e-08 1893 1.64490542223477 1.66003514497359 1 2.99317992142114 4305 3878 3154 4054 1893 4376 4303 4457 4075 2520 4593 4505 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 1.40226788790329e-07 3.95628276480565e-07 4230 3812.09090909091 4075 1.27478907025735e-08 1438 1.36443086019448 1.51139615430357 1 2.52180022417346 4230 3566 4075 2996 1438 4682 4521 3920 3486 4411 4608 4506 M14691 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMINOACYL_TRNA_BIOSYNTHESIS.html Aminoacyl-tRNA biosynthesis 41/41 KEGG 2.77996158255057e-05 3.11302934036505e-05 2685 3823.18181818182 4076 2.52726973753821e-06 2684 0.716208669145921 -0.773351733179895 -1 0.931218092705845 2684 4506 4076 4670 4179 3024 3402 3424 4409 4605 3076 4507 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 0.615838063119859 0.616883628592048 2875 3945.18181818182 4081 0.0832971624345528 2875 0.583125542569814 -0.505974578305196 -1 0.0344654736936709 2875 4493 4159 3251 4684 3307 3345 3809 4718 4675 4081 4508 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 1.76833194447296e-05 2.02604584457668e-05 4215 3851.54545454545 4083 1.60758741659961e-06 2010 1.56244589666171 -1.33603517752716 -1 2.11667777791923 4212 4427 3698 2987 4083 3635 4030 4424 2010 4255 4606 4509 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 0.000798683553939723 0.000831998758462921 3685 3899.63636363636 4083 7.26339685325427e-05 2786 0.889186549850908 -0.814591354039103 -1 0.789944289494187 3681 4598 3873 4496 4514 3102 4137 2994 4632 4083 2786 4510 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 0.00102929890372568 0.00106822577519464 2330 3756.36363636364 4083 0.000102977597005442 2330 2.54368949720178 2.54368949720178 1 2.18166475013136 2330 4083 4631 4568 4538 2558 2678 4330 4605 3256 3743 4511 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 7.73305681455128e-07 1.21545215333607e-06 4315 3872.45454545455 4084 7.0300541206746e-08 2874 1.29280696347622 -1.25059014196984 -1 2.20740331665842 4314 3615 3859 2972 2874 4617 3480 4084 4218 4234 4330 4512 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 0.000203872120335669 0.000217512750448543 4085 4007.09090909091 4085 1.85355468583918e-05 3336 1.56664173841867 -1.48781344648132 -1 1.65602448707575 4085 4514 3437 3490 4406 4083 4114 3949 4570 4094 3336 4513 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 2.28536206690846e-07 5.09634715320873e-07 4135 3881 4086 2.0776020948292e-08 1930 1.47292550637463 -1.34654286717214 -1 2.67561915732123 4134 4391 4035 4086 1930 4025 3352 4473 3390 4462 4413 4514 M456 REACTOME_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRNA_AMINOACYLATION.html Genes involved in tRNA Aminoacylation 43/43 Reactome 8.45881456580419e-05 9.18463417312993e-05 3040 3919.45454545455 4087 7.69012710691138e-06 3037 0.669954501969437 -0.757713267577631 -1 0.780120353035643 3037 4204 4087 4293 4322 3414 3311 3894 4406 4610 3536 4515 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 1.81203324238651e-05 2.0734053100762e-05 4435 4075.81818181818 4088 1.64731651581556e-06 3377 0.97321698656565 -0.906088417229507 -1 1.31529224053181 4433 3796 3377 3474 4088 4553 4533 3594 4648 3717 4621 4516 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 0.00152280532933472 0.00157589150503395 3665 4023.54545454545 4089 0.000138532764887708 3248 1.124196849237 -1.12351071172137 -1 0.908899744120034 3664 4433 4124 3248 4547 4089 3710 3722 4387 4580 3755 4517 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 9.63839482961435e-05 0.000104270510189731 3500 4090.63636363636 4089 8.76256102011739e-06 3149 0.56191199415741 0.548895549300022 1 0.645232195002435 3499 4579 4026 4674 4340 3567 3149 4089 4684 4689 3701 4518 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 1.52525080369447e-06 2.12490666866525e-06 3965 4164.90909090909 4090 1.38659260104136e-07 3298 1.4653629830868 1.73599651506003 1 2.39949337709501 4474 4405 3961 4072 3298 4330 4090 4039 3964 4481 4700 4519 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 0.259939998849951 0.261379802848694 3550 3943.81818181818 4091 0.0269947677826571 2035 1.12278237427495 -0.975480201076276 -1 0.188070402724113 3549 4465 4080 2035 4666 4106 3776 4103 4042 4469 4091 4520 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 0.186798399993432 0.188153744765045 2720 3865.54545454545 4091 0.0186222615660635 2716 0.932379752029183 -0.954983938398336 -1 0.19446734414058 2716 4498 4106 4091 4680 3610 2867 3304 4492 4557 3600 4521 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 0.000209667550581642 0.000223594857375814 4640 3235 4095 1.90625032077559e-05 807 0.607765853538187 0.615250459129322 1 0.639811987534894 1290 4505 4121 4095 4408 1460 807 2815 4640 4636 2808 4522 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 3.46048179755701e-08 2.80162505737034e-07 3915 3591.63636363636 4096 3.14589259271684e-09 101 0.791283717808621 -0.725719735878986 -1 1.49636917071554 3913 4459 4096 4678 101 2861 1952 4630 4250 4552 4016 4523 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 0.000496439845189049 0.000520825976726452 1835 3515.81818181818 4096 4.51410822240612e-05 1444 0.538863452580054 0.541194685445877 1 0.510036097343069 1835 4538 4115 4096 4477 2004 1444 3606 4687 4679 3193 4524 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 3.50881365140234e-06 4.46284032191297e-06 4535 3689.27272727273 4096 3.18983567970491e-07 1724 1.46431311776757 -1.81602801113334 -1 2.2615039396048 4534 2710 3210 4152 3648 4711 4640 4591 1724 2566 4096 4525 M9271 REACTOME_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_METABOLISM.html Genes involved in Purine metabolism 34/39 Reactome 2.5307645101794e-05 2.84477458634122e-05 3880 4087.09090909091 4097 2.30072147566787e-06 3495 1.3392771613633 -1.1344112447482 -1 1.75721920003969 3876 4540 3784 4639 4164 4407 4097 3495 3915 4104 3937 4526 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 6.20089465314871e-08 3.14150822411035e-07 4460 3778.54545454545 4098 6.20089482617863e-09 680 1.5406675139122 -1.22778039991409 -1 2.89219501005828 4459 4098 4588 3245 680 3892 3917 4459 3280 4445 4501 4527 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 1.38705513976418e-07 3.93386935835012e-07 3645 3878.72727272727 4099 1.38705522634068e-08 1521 1.41873244052982 1.50787654144864 1 2.62320787510118 3645 4681 4486 4099 1521 4126 3987 3665 3525 4604 4327 4528 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 1.93597663975532e-05 2.20933504343451e-05 3495 4014.18181818182 4099 1.75999425123098e-06 3046 1.19400941178476 0.975828364691224 1 1.60437789767482 3493 4632 3732 4638 4099 3929 4246 3046 4488 4270 3583 4529 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 2.65237451186529e-07 5.54437896191504e-07 3640 3893.81818181818 4099 2.41124984694744e-08 2079 1.23468731166613 -1.19160952291558 -1 2.2296651237123 3637 4382 4099 4689 2079 3431 3551 4518 3575 4578 4293 4530 M19540 KEGG_OXIDATIVE_PHOSPHORYLATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OXIDATIVE_PHOSPHORYLATION.html Oxidative phosphorylation 126/155 KEGG 0.0439292625450024 0.0445139800799509 705 3317.45454545455 4100 0.00407561527325126 705 1.05215944731292 -1.03897583766156 -1 0.409760660780904 705 4417 4148 4100 4699 2008 1397 2816 4546 4634 3022 4531 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 4.52341944335535e-08 2.99073619127066e-07 4395 3129.81818181818 4101 4.5234195354313e-09 348 1.94651603550834 1.98227304756374 1 3.66630113373233 4394 1967 4480 887 348 4628 4503 4101 1990 2816 4314 4532 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 0.000222243195732439 0.000236631600238464 4105 3769.81818181818 4102 2.22265425278523e-05 1901 2.00523961151951 -3.3738861184051 -1 2.09870115632352 4102 3538 4408 4164 4423 3311 1901 3208 4260 3741 4412 4533 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 0.000177287359878969 0.000189749736650506 4105 4024.27272727273 4102 1.61183316565356e-05 3144 0.857888957766656 -0.530459473621968 -1 0.921136181501269 4101 3472 3716 4227 4395 4319 4537 3144 4102 4269 3985 4534 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 0.230031317298277 0.231453382572557 1265 3650.36363636364 4103 0.023483987173599 1262 0.748096447216314 -0.733766172193422 -1 0.136429499024559 1262 4479 4147 4103 4679 2501 1995 3922 4689 4657 3720 4535 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 1.29137117428932e-05 1.50537711599051e-05 3565 4028.72727272727 4106 1.17398068593745e-06 3357 1.48423118864612 1.71361154417743 1 2.06596576122819 3564 4566 3814 4033 4003 4131 4165 4339 4238 4106 3357 4536 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 0.00506511090270075 0.0051859703819409 3190 4117.09090909091 4107 0.000461528195615413 3187 0.665686680253776 0.763600420270661 1 0.438408950777173 3187 4523 4107 4691 4590 3555 3541 3884 4621 4613 3976 4537 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 3.66104704704469e-07 6.8544791995442e-07 3945 3912 4107 3.66104765019177e-08 2444 1.51192064040523 -1.4008080201676 -1 2.69028223656307 3942 4672 4570 4107 2444 3699 4167 4249 3038 4633 3511 4538 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 1.74403005555809e-06 2.39715255161158e-06 4495 3368.36363636364 4108 1.74403142429797e-07 66 4.08416827325177 -3.24176823815052 -1 6.62751107804113 4492 1950 4262 2523 3385 4397 4694 4108 66 2556 4619 4539 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 6.07281710767435e-08 3.11746643088069e-07 4110 3056.18181818182 4108 6.07281727363034e-09 564 1.84950302535401 1.84139376456844 1 3.47390638518364 4108 1014 4283 1886 656 4328 4619 4494 3260 564 4406 4540 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 3.01394194604605e-06 3.90431001428198e-06 4440 4078.63636363636 4108 2.73995097734082e-07 3093 1.62624077177668 -1.97941511112523 -1 2.5389506313555 4436 4386 3839 4692 3577 4575 4081 3614 4108 4464 3093 4541 M8229 REACTOME_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSLATION.html Genes involved in Translation 171/283 Reactome 0.00306564859745339 0.0031511022168946 2785 3967.09090909091 4109 0.000279084441790931 2781 0.671383777144035 -0.620379008966358 -1 0.484115854921973 2781 4413 4154 4109 4573 3463 3104 3674 4697 4668 4002 4542 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 0.00240647836256922 0.00247895632285612 940 3377.54545454545 4111 0.000219010430571664 938 0.644670451909369 0.663120347292926 1 0.48421581374869 938 4519 4111 4308 4562 1777 1508 3148 4596 4618 3068 4543 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 1.65880017149576e-07 4.2834032897358e-07 4270 3869.27272727273 4116 1.50800026960848e-08 1613 1.63194342285999 -1.38541895267591 -1 3.00013861103091 4269 4394 3731 4281 1613 4116 4042 4247 3730 3821 4318 4544 M10960 REACTOME_P2Y_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P2Y_RECEPTORS.html Genes involved in P2Y receptors 5/14 Reactome 2.68547775996822e-08 2.49026621356581e-07 3995 3149.54545454545 4118 2.68547779242128e-09 40 2.69369196616872 -2.02994167789428 -1 5.13581586077883 3994 936 4237 4118 40 4305 4711 4446 1409 1844 4605 4545 M963 KEGG_RNA_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_DEGRADATION.html RNA degradation 70/72 KEGG 0.00024495954257338 0.000259822256392439 2450 3792.09090909091 4119 2.22715292642317e-05 2450 0.886464692184159 1.00761908074957 1 0.916907390277048 2450 4477 4119 4316 4425 3298 3168 2755 4644 4596 3465 4546 M3075 BIOCARTA_SET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SET_PATHWAY.html Granzyme A mediated Apoptosis Pathway 12/25 BioCarta 0.000230270833944609 0.00024457208285746 4120 3901.36363636364 4119 2.09359035994391e-05 2945 0.926005923259616 0.735444578919843 1 0.964869341800427 2945 4306 3700 4612 4419 3040 3009 4125 4522 4119 4118 4547 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 0.000302150122789446 0.000319263169815578 4325 3875.18181818182 4120 2.74719662145143e-05 2665 1.59276540776139 1.87514881582314 1 1.60699853075119 4322 3788 3427 4212 4446 4500 4164 3549 2665 4120 3434 4548 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 1.80486630459687e-07 4.47913293152525e-07 4485 3802.54545454545 4122 1.64078768424272e-08 1694 1.3774955376082 -1.32106602670632 -1 2.52451265525502 4484 4693 4122 4294 1694 4065 4288 3082 2734 4554 3818 4549 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 7.90744371333834e-07 1.2383256246502e-06 4370 3445.63636363636 4123 7.18858777773309e-08 653 1.75889516136622 1.95062282663101 1 2.99942365089872 4368 4131 3303 653 2889 4233 3397 4123 1715 4376 4714 4550 M2531 REACTOME_MRNA_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_PROCESSING.html Genes involved in mRNA Processing 181/233 Reactome 5.9704265336068e-05 6.52928944361077e-05 570 3130.72727272727 4124 5.42780778818541e-06 570 0.745402850766107 0.716986672553503 1 0.899970802540224 570 4124 4160 4328 4288 1310 789 3000 4520 4677 2672 4551 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 0.0221073670161433 0.022483682895108 4720 3714.27272727273 4124 0.00223304276200229 122 4.23452397915232 -7.0371197661977 -1 2.01444085071269 4716 3537 4238 4124 4619 4424 4003 4646 122 3005 3423 4552 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 0.000163991352283814 0.000175798133722371 845 3080.81818181818 4125 1.49094161568128e-05 335 0.615745658828517 0.53223963555781 1 0.66679519125598 841 4489 4125 4315 4387 879 335 2798 4604 4655 2461 4553 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 2.13169146098902e-07 4.90234925824382e-07 4330 3808.45454545455 4127 1.93790151594494e-08 1470 1.60293930332405 1.86492409204313 1 2.91967124621692 4330 4127 3630 4032 1863 4695 4550 4680 1470 3932 4584 4554 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 2.15387116480855e-07 4.92098932637662e-07 4695 3805.54545454545 4127 2.15387137357082e-08 1965 1.48515662306347 -1.26769145031187 -1 2.70436604466594 4693 3809 4389 4206 1965 4127 3248 3979 4430 2469 4546 4555 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 8.29394252954901e-07 1.28901576356507e-06 4130 4122.81818181818 4127 7.53995059667756e-08 2917 1.12415414760006 -1.12437613466775 -1 1.91104038782053 4665 4130 4127 4088 2917 4558 3967 4702 3583 4581 4033 4556 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 9.00519870843337e-05 9.7621814202585e-05 525 3104.81818181818 4128 8.18687939713455e-06 525 0.692536868896795 0.643849247633828 1 0.801148677997887 525 4128 4157 4332 4329 1253 607 2833 4593 4673 2723 4557 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 0.00198237057258254 0.00204788555539277 2245 3817.09090909091 4128 0.000180378099892338 2241 0.74547020171111 0.827170148074264 1 0.577920865368266 2241 4485 4128 4695 4557 2940 2925 3285 4580 4622 3530 4558 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 0.00515933438482927 0.00528129652925486 3375 4153.27272727273 4132 0.000470133971162538 3374 1.14919935084371 -1.13040257504119 -1 0.754841987316083 3374 4546 3909 4057 4591 4108 4155 4094 4425 4132 4295 4559 M7272 KEGG_PARKINSONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PARKINSONS_DISEASE.html Parkinson's disease 123/151 KEGG 0.440315839591987 0.441907455427212 2515 3868 4135 0.0513943025797479 2377 1.32354100384441 -0.867800621569739 -1 0.134689970324376 2514 4425 4135 4102 4690 3106 2377 4069 4252 4629 4249 4560 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 0.000394424645149562 0.00041490624584487 3605 3931.81818181818 4137 3.58632160821828e-05 2466 0.670661797842247 -0.610513787953476 -1 0.654117164918177 3601 4286 3925 4049 4467 3233 2466 4320 4428 4338 4137 4561 M15347 BIOCARTA_AKAPCENTROSOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAPCENTROSOME_PATHWAY.html Protein Kinase A at the Centrosome 24/25 BioCarta 1.06961004255208e-07 3.48657417185485e-07 4635 3953.72727272727 4138 9.72372813231879e-09 1181 0.955774057802941 -0.914511521379508 -1 1.78139388566629 4573 4247 3771 4634 1181 4633 3989 4395 3875 4138 4055 4562 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 1.14700578350272e-06 1.67976025384202e-06 3610 4000.36363636364 4141 1.04273307410298e-07 3118 1.31901284073357 1.42439281376218 1 2.19864824023833 3608 4713 4141 4322 3118 3744 3343 4068 4150 4635 4162 4563 M1870 REACTOME_GLUCOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_METABOLISM.html Genes involved in Glucose metabolism 62/81 Reactome 3.24195511781338e-07 6.29297505894838e-07 4690 3930.45454545455 4142 2.94723235959378e-08 2266 1.14169801694314 -1.26739642102282 -1 2.04354164601669 4690 3315 3878 4263 2266 4468 4548 3584 3677 4142 4404 4564 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 0.000179261066745458 0.000191775211930771 4015 4123 4143 1.62977886378632e-05 3601 1.65099941324099 1.72810439282652 1 1.7713159696365 4012 4522 3797 4284 4396 3601 3693 4191 4143 4053 4661 4565 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 3.01852283208949e-08 2.67626355148536e-07 4340 3495 4144 2.74411170318664e-09 48 2.40379288787694 2.90981990122703 1 4.56128460798763 4337 4606 2857 4554 48 4479 4642 4075 1040 3663 4144 4566 M14033 REACTOME_MRNA_SPLICING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_SPLICING.html Genes involved in mRNA Splicing 129/178 Reactome 0.000226241534059941 0.000240671634158873 565 3161.18181818182 4145 2.05695275840517e-05 564 0.660194809624219 0.669775393970016 1 0.688986241439379 564 4145 4161 4327 4414 1414 774 2967 4636 4665 2706 4567 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 2.36345208247237e-05 2.66750211125528e-05 4535 4101.09090909091 4148 2.14861588484993e-06 3331 1.21442621606101 1.26727075893229 1 1.60312546462796 4533 4537 3940 3520 4148 4435 3331 4324 4023 4357 3964 4568 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 0.0493983544530244 0.0500451240648799 4570 3963.36363636364 4150 0.00459488232848112 2661 1.79878292724114 -1.87688623937965 -1 0.674721676078055 4569 4063 2661 4213 4633 4150 3588 4086 4418 2802 4414 4569 M189 KEGG_RIBOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOSOME.html Ribosome 98/184 KEGG 0.566203287940965 0.567405418063982 3250 4001.18181818182 4152 0.0731146385768703 2698 0.591931412250168 -0.508598422177359 -1 0.0412053280032264 3248 4495 4152 2698 4700 3595 3750 3732 4717 4666 4260 4570 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 9.92217792126614e-08 3.41247265430585e-07 4450 3776.72727272727 4152 9.0201621534222e-09 1098 1.71866892091458 -1.60917846102206 -1 3.20861280679848 4446 4702 3557 4481 1098 4152 4202 3685 3165 4321 3735 4571 M2044 KEGG_SPLICEOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPLICEOSOME.html Spliceosome 141/188 KEGG 0.000708144131421023 0.000739150884632293 1005 3405.90909090909 4153 6.43974703856916e-05 1005 0.649740091085026 0.634426725164517 1 0.586632347488604 1005 4408 4153 4333 4507 2111 1103 3187 4680 4667 3311 4572 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 0.00106902898075743 0.00110897072289562 4155 3866.72727272727 4153 9.72317090365856e-05 2431 1.53534112763387 -1.5750515055703 -1 1.30927821994055 4153 2749 3481 4582 4533 4545 4235 2431 3522 4223 4080 4573 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 9.4319078923345e-05 0.000102106892779401 2205 3278.18181818182 4154 9.43230824023885e-06 895 0.829033515075285 0.895623054453376 1 0.954551936923639 2204 4332 4446 4618 4350 2070 895 2030 4538 4154 2423 4574 M14025 REACTOME_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTION.html Genes involved in Transcription 182/275 Reactome 2.46321101478908e-05 2.77478663241156e-05 3015 3986.27272727273 4155 2.23930781304631e-06 3011 0.986327107504324 0.783609401029964 1 1.2969798768925 3011 4384 4163 4705 4155 3262 3045 4014 4370 4664 4076 4575 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 9.18754891008528e-08 3.35125431650715e-07 4225 3413.63636363636 4156 8.35231753979266e-09 810 1.73896913951647 1.70497874908739 1 3.2504696268885 4221 4156 3135 2205 1003 4568 4345 4522 810 3957 4628 4576 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 0.000556178075913519 0.000582333744079816 1400 3483.18181818182 4158 5.05744301896379e-05 1399 0.677632486732545 0.717667545245385 1 0.632117030064194 1399 4426 4158 4703 4487 1943 1666 3139 4609 4674 3111 4577 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 3.31753974846714e-06 4.25048523690687e-06 4375 3995 4158 3.01594977385162e-07 2960 1.36286997952583 1.538571722634 1 2.11310671766766 4373 3694 3598 2960 3620 4087 4322 4511 4164 4158 4458 4578 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 5.30459467665038e-05 5.81595513909171e-05 4145 4038.36363636364 4159 4.82247507660194e-06 3433 2.05710528941052 2.32705780771505 1 2.51503207529173 4142 4311 3433 4229 4275 4640 4159 3607 3891 3563 4172 4579 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 0.000261674317937345 0.00027717746424243 4055 4033.36363636364 4164 2.37914043105454e-05 2634 0.972891197882818 -0.642284645901957 -1 0.998496774884785 4055 4070 3465 4441 4437 3658 2634 4164 4613 4271 4559 4580 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 9.41403951536717e-07 1.42447329312724e-06 4530 4056.72727272727 4164 8.55822140339963e-08 3004 1.71737721616258 1.44962049528059 1 2.89844183647204 4527 4164 3297 4015 3004 4637 4624 3887 4266 3928 4275 4581 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 2.08458534901765e-05 2.36918922402199e-05 4060 4090.63636363636 4166 1.89509554684962e-06 2306 0.919831985060289 -0.987526091351146 -1 1.22771252693306 4057 4588 3849 4635 4118 4145 4203 2306 4479 4166 4451 4582 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 3.53106611069798e-07 6.6666528169978e-07 4540 3766.09090909091 4166 3.21006061585894e-08 2337 1.24857871800756 -1.37398916267126 -1 2.22589726910879 4538 3636 3932 4271 2337 4696 4356 2484 2657 4354 4166 4583 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 2.4202434730751e-07 5.2719175985577e-07 4385 3725.18181818182 4167 2.42024373666618e-08 2081 0.992154418670251 0.98508188138662 1 1.79778673873944 4382 3218 4528 4562 2081 4167 4270 2176 4309 3252 4032 4584 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 0.000109015133615495 0.000117584879036823 4170 4067.36363636364 4168 9.91095781313901e-06 3301 1.31944537466984 1.23135218227427 1 1.49636882475882 4168 4273 3301 3506 4355 4084 3589 4441 4585 3728 4711 4585 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 0.000221267185489587 0.000235698739677465 4415 3616.63636363636 4169 2.01172220718735e-05 1737 0.793868170083419 0.740453099438606 1 0.83074223650713 1737 4411 4169 4701 4412 2226 1800 3530 4581 4654 3562 4586 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 0.272344701709205 0.27379488648934 1575 3746.36363636364 4170 0.0284888473337437 1573 0.850036499217894 -0.713000904786434 -1 0.137228344266127 1573 4456 4170 4325 4678 2833 2094 3822 4672 4660 3927 4587 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 6.7123724322123e-07 1.08911646201588e-06 3845 3901.27272727273 4170 6.10215861837328e-08 2388 1.08628530356694 -0.720491935300856 -1 1.86959142257867 3845 2388 3511 4584 2775 4182 4628 4471 4170 4126 4234 4588 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 0.000227628427078002 0.000242092423571016 2040 3721.54545454545 4171 2.06956347842666e-05 2039 0.780225617620204 0.730060914951712 1 0.813832316777739 2039 4424 4171 4700 4415 2392 2136 3760 4562 4647 3691 4589 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 0.254107033648371 0.25556897481788 3480 4122.63636363636 4173 0.0263000730134141 3254 0.603164083124471 -0.57320157905671 -1 0.102334306190616 3476 4455 4162 3254 4665 3806 3714 4173 4712 4678 4254 4590 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 0.000664081873708343 0.000693466027412252 4435 3834.36363636364 4174 6.03893104690464e-05 1549 1.05017400522498 1.32289415563798 1 0.957106379297529 4435 4301 3718 1549 4503 3795 2679 4067 4174 4393 4564 4591 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 3.38683136002617e-05 3.76580542269105e-05 4715 3740.63636363636 4174 3.07898500032911e-06 1692 1.30608045605006 1.60879160376266 1 1.66770103298294 4713 4255 3671 3509 4213 4485 2175 1692 3997 4174 4263 4592 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 2.96731418235819e-05 3.31653396654764e-05 1105 3529.90909090909 4174 2.6975947323906e-06 1104 0.955012669061415 0.848267477084322 1 1.23441532425295 1104 4718 4174 4704 4188 2462 1962 3077 4231 4659 3550 4593 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 3.6098511017472e-06 4.57409320811995e-06 2545 3942.54545454545 4176 3.28168820450362e-07 2541 1.05949168369035 1.02081100590949 1 1.63278275560383 2541 4699 4176 4707 3660 3294 2937 4402 4295 4663 3994 4594 M15109 BIOCARTA_GLYCOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLYCOLYSIS_PATHWAY.html Glycolysis Pathway 19/35 BioCarta 1.40279369806223e-06 1.98417328584169e-06 4500 3871.36363636364 4177 1.27526781139207e-07 2314 0.958915896409211 -1.01013424134656 -1 1.57814253278926 4500 3745 3554 4250 3248 3320 2314 4585 4177 4245 4647 4595 M862 BIOCARTA_P38MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P38MAPK_PATHWAY.html p38 MAPK Signaling Pathway 57/62 BioCarta 2.76582901956939e-07 5.68167826037923e-07 4710 4051.18181818182 4179 2.51439033389827e-08 2119 1.25068356801319 -1.20826987676572 -1 2.25472639864812 4709 4179 3863 3780 2119 4717 3957 4538 3976 4280 4445 4596 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 0.0762488143362652 0.0770982012997369 4170 4188.36363636364 4179 0.00789988292471367 3565 0.339743846991582 0.26947666696748 1 0.108326180290416 4167 3822 4558 3694 4643 4356 3716 3565 4664 4708 4179 4597 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 2.56840010058057e-06 3.38249120388959e-06 4695 3851.90909090909 4186 2.33491190825087e-07 2531 1.90077267262277 2.07471196998784 1 3.0019050722054 4691 4186 3026 3473 3513 3639 2531 4375 4321 4233 4383 4598 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 0.00517828099662196 0.00529954169645612 4010 3974.90909090909 4188 0.000519038728637693 2403 3.43965659507072 -3.04287467407555 -1 2.25953872725944 4007 4078 4653 4544 4593 4188 4633 2403 4505 2837 3283 4599 M9367 BIOCARTA_ERYTH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERYTH_PATHWAY.html Erythrocyte Differentiation Pathway 8/15 BioCarta 0.000281207151696209 0.000297400348645778 4350 4087.81818181818 4189 2.81242742893063e-05 2703 1.93526644249722 1.74716128620926 1 1.9699616552025 4350 4076 4189 3976 4447 4281 4129 3896 4563 2703 4356 4600 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 6.16922559677141e-05 6.73889026076395e-05 4460 3867.18181818182 4189 5.60854418234877e-06 1557 0.91270859648645 1.12717156877805 1 1.09854600537146 4460 4609 3828 1557 4294 4156 3066 3580 4420 4380 4189 4601 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 2.97688632402445e-05 3.32644494540611e-05 4315 4026.63636363636 4190 2.70629691448531e-06 3173 1.27147121664064 -1.06516195813975 -1 1.64326797938315 3240 4451 3848 4681 4190 3173 4313 4167 4311 4279 3640 4602 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 1.89625815074365e-07 4.60823355474758e-07 4680 3482.27272727273 4191 1.72387119471717e-08 656 1.31047557143072 -1.31341155113307 -1 2.39697451103112 4679 3013 3706 656 1734 4621 4251 4371 2601 4191 4482 4603 M917 BIOCARTA_COMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_COMP_PATHWAY.html Complement Pathway 17/24 BioCarta 0.000107464166406575 0.000115964989812308 4195 3807.90909090909 4192 9.76994691865088e-06 2101 2.22399788395886 -2.40495112130706 -1 2.52667164702215 4192 4611 2101 4413 4353 3651 3578 4158 4471 2120 4239 4604 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 1.76561366635899e-06 2.42329063832929e-06 4065 4008.90909090909 4192 1.60510462123343e-07 3292 1.36181341286542 1.76022401112274 1 2.20743214378677 4064 4292 3292 4252 3352 4373 3561 4581 4290 3849 4192 4605 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 1.6580918991251e-05 1.90418339753539e-05 4525 3672 4192 1.65810427096438e-06 725 1.58248865269025 0.71902966839253 1 2.1561520572374 4522 3519 4634 2459 4090 4296 4192 3400 725 4219 4336 4606 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 4.28437663566108e-05 4.73145945725791e-05 3250 4141.81818181818 4198 3.89496370342591e-06 3246 0.715713215458483 0.711273392703191 1 0.892997802371871 3246 4420 4166 4334 4245 3801 3607 4165 4695 4683 4198 4607 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 2.65336316336949e-06 3.47636721967602e-06 4595 4101.09090909091 4198 2.4121512395706e-07 3529 1.11518193183549 -1.18165427022317 -1 1.75703097462508 4594 4198 3914 4009 3529 4291 4383 3877 3802 4239 4276 4608 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 1.47164135796954e-07 4.04988312110223e-07 4335 3773.27272727273 4199 1.33785586946522e-08 1482 1.62676407843939 -1.52012685894612 -1 3.00205104317807 4334 4691 3983 3511 1482 4327 3834 4689 2245 4211 4199 4609 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 0.00754053134728566 0.00770541415007324 2475 3454.45454545455 4201 0.000756624103934348 758 0.919262312487938 1.01859603670689 1 0.560088896532382 2474 4323 4201 4603 4719 2570 758 3700 4656 4215 1780 4610 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 7.54062756790788e-08 3.24446327443256e-07 4265 3826.90909090909 4201 6.85511620578843e-09 781 1.33395845667285 -1.2908346083242 -1 2.49864337743806 4263 3990 3507 4469 781 4028 4201 4453 3619 4288 4497 4611 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 3.24560689273604e-05 3.61815411755174e-05 4235 4038.63636363636 4202 2.95059525034547e-06 3172 1.80359397359494 -1.40547190480728 -1 2.31233848538011 4232 4521 3172 3515 4202 4585 4437 3989 4342 3462 3968 4612 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 2.37684026080645e-06 3.15841386008064e-06 4700 3742 4205 2.1607662079142e-07 2031 1.98753570875535 1.85793603016727 1 3.15605444610077 4700 4439 3470 2031 3481 4205 4357 2482 2783 4527 4687 4613 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 2.04802618556848e-07 4.81168919655711e-07 4360 3629.27272727273 4210 1.86184216020324e-08 1815 1.67827946601625 -1.77710265611475 -1 3.06086866688331 4358 4222 3079 4563 1815 4525 4210 3053 2795 3025 4277 4614 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 0.000525681494625278 0.000550769512681756 3490 3929.27272727273 4212 5.25805889507469e-05 2465 1.86376332004023 0.697342469338212 1 1.75311034314455 3488 2465 4181 4350 4492 4469 4381 3026 4392 3766 4212 4615 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 1.97560472662373e-07 4.70878541974394e-07 4345 4035.81818181818 4216 1.79600445821226e-08 1781 1.34498362870134 -1.22432271177137 -1 2.45647458213765 4343 4697 4150 4523 1781 4070 4214 4216 3414 4575 4411 4616 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 1.34043481639768e-07 3.85177943176647e-07 4445 3794 4217 1.21857718006258e-08 1402 1.49029083756661 1.43028080367267 1 2.75950266607349 4441 3848 3946 4451 1402 4506 4441 4217 2177 3967 4338 4617 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 3.57213186121214e-05 3.96530159570116e-05 3310 3919.27272727273 4220 3.2474453300941e-06 2811 1.3612968030552 -1.33316913807406 -1 1.72942928555773 4399 4320 3307 3946 4220 4657 2811 3306 4328 3581 4237 4618 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 1.2640909248024e-05 1.47539791421052e-05 4310 3959.81818181818 4224 1.14918017105475e-06 2957 0.927627338191352 -0.897350094885985 -1 1.29322182869271 4309 4260 3809 4278 3997 2957 3076 3767 4497 4384 4224 4619 M1724 KEGG_RNA_POLYMERASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_POLYMERASE.html RNA polymerase 27/29 KEGG 9.59329803435797e-05 0.00010380643448457 3475 4196.09090909091 4226 8.72156034935817e-06 3475 0.739845856710569 0.804429676058956 1 0.850236671664712 3475 4584 4020 4677 4339 4029 3738 3888 4615 4566 4226 4620 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 0.000722772422758823 0.000754086170517605 4230 4085.36363636364 4228 6.57281805969715e-05 3287 1.24603650234196 -1.3826697664147 -1 1.12267636091164 4228 3981 3667 3502 4509 3880 4526 4354 4407 3287 4598 4621 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 1.96901598390352e-05 2.24432635692457e-05 4230 3950 4229 1.79003055178223e-06 2635 1.84451739473403 1.55766235831106 1 2.47529299520656 4363 4229 2719 4230 4103 4520 4377 4134 4453 2635 3687 4622 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 0.234917116731457 0.236319009158669 3625 3995.90909090909 4233 0.0264217824785403 2056 0.139031439787791 -0.139031439787791 -1 0.0242910200358784 3623 4667 4368 4233 4702 3028 2056 3930 4716 4696 3936 4623 M16563 BIOCARTA_MTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MTOR_PATHWAY.html mTOR Signaling Pathway 32/32 BioCarta 0.000275883976055899 0.000291901449671339 4180 4228.90909090909 4234 2.50835071345584e-05 3642 0.641150370818118 0.723788937952263 1 0.653569476174035 4176 4234 4048 4297 4441 3961 4395 3642 4530 4597 4197 4624 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 1.16390870213351e-07 3.6108635857474e-07 4625 3950 4235 1.05809887610003e-08 1271 1.25779977968549 1.18230195296458 1 2.33906344256056 4623 4401 3923 4503 1271 4378 4561 4037 3883 4235 3635 4625 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 2.9221296301198e-05 3.26680527100082e-05 4625 4170.54545454545 4235 2.65651676705255e-06 2864 1.33154924494394 -1.08055691808857 -1 1.72397548141721 4308 4709 4130 3809 4187 4235 3878 4508 2864 4625 4623 4626 M121 PID_MTOR_4PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MTOR_4PATHWAY.html mTOR signaling pathway 18832364 93/104 Pathway Interaction Database 8.48870241232702e-07 1.31235122400304e-06 4555 4209.36363636364 4241 7.71700517063232e-08 2936 0.995965904974585 1.0869833254654 1 1.6907836964091 4552 4150 4108 4094 2936 4532 4341 4097 4241 4547 4705 4627 M6285 REACTOME_OPSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OPSINS.html Genes involved in Opsins 4/8 Reactome 3.66506398735092e-06 4.63782895986497e-06 4260 4011.45454545455 4242 3.66507003207727e-07 2215 1.86930199890867 -1.76210482683143 -1 2.87819589748999 4256 3819 4242 4375 3693 4146 4305 4547 4483 2215 4045 4628 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 0.000352078762454172 0.000371022942349562 3835 4005.72727272727 4243 3.52134556650479e-05 1876 0.704199443696932 0.577979880112176 1 0.696742905127699 3833 4081 4370 3733 4462 3455 1876 4608 4705 4697 4243 4629 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 0.0336117688710877 0.0341104169149719 3825 4255.36363636364 4244 0.00341312499416536 3503 0.688573282209701 0.691939856150273 1 0.290852603966025 3824 4656 4418 4244 4628 3503 4050 4185 4688 4699 3914 4630 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 8.40698255862827e-08 3.27411388472988e-07 4250 3663.18181818182 4247 7.64271170899001e-09 912 1.56445977332739 1.70719611929641 1 2.92876035956697 4247 4463 3570 2491 912 4366 4531 3617 3099 4342 4657 4631 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 8.08078704030407e-06 9.66581724030289e-06 4130 4226.63636363636 4253 7.34619701988592e-07 3899 1.0639735082267 1.10668440654687 1 1.5398615544454 4127 4197 3966 4283 3899 4471 4595 3931 4253 4332 4439 4632 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 4.04261323148533e-07 7.31604867117337e-07 3920 4092.72727272727 4253 3.67510361303319e-08 2446 1.48526064641295 -1.51351038413731 -1 2.63069026986587 4591 4715 3919 4516 2446 4340 4296 3919 4033 3992 4253 4633 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 0.00038596169287061 0.000406094335788961 4015 4065.18181818182 4255 3.50935837744594e-05 3129 0.959150515098743 -0.764329707160793 -1 0.938441811547031 4015 4297 3867 4255 4461 3661 3129 3782 4512 4261 4477 4634 M19358 BIOCARTA_MET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MET_PATHWAY.html Signaling of Hepatocyte Growth Factor Receptor 60/65 BioCarta 6.15252336734078e-07 1.01573663147424e-06 4695 3376.09090909091 4258 5.59320462541553e-08 593 2.05453003975255 -1.82256323804649 -1 3.55476469596017 4692 3317 2513 903 2720 4663 4647 4287 593 4258 4544 4635 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 4.71554285991974e-05 5.19061620774748e-05 4635 4294.45454545455 4259 4.28694903385991e-06 3803 0.683449344494039 -0.736608812561608 -1 0.844764836316511 3889 4620 3803 4474 4259 4244 4063 4632 4635 4437 4183 4636 M6924 BIOCARTA_EIF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF2_PATHWAY.html Regulation of eIF2 15/16 BioCarta 0.162580660707596 0.163865197211158 3870 4151.54545454545 4264 0.0160006378093676 3258 0.856310787264175 -0.97639474927016 -1 0.193374076059073 3868 4639 3837 4264 4689 4395 3918 3258 4551 4414 3834 4637 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 5.29507581983147e-07 9.06191365830477e-07 4270 3737.18181818182 4266 4.81370644934421e-08 1558 1.60267942091536 1.82956535435624 1 2.79571637521503 4266 4388 3754 1558 2613 4570 4085 4373 2545 4472 4485 4638 M6831 BIOCARTA_KREB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KREB_PATHWAY.html The Citric Acid Cycle 11/11 BioCarta 8.15211408514742e-08 3.27411388472988e-07 3685 3911.09090909091 4270 7.41101307929502e-09 867 0.816111147098806 1.00985795879983 1 1.52739587595457 3684 4642 3666 4245 867 4274 4337 4695 4028 4314 4270 4639 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 0.00141183839430447 0.00146137658357831 4545 4039.72727272727 4273 0.000128431386273426 2652 2.13095364267508 2.10081407235724 1 1.74378316026649 4273 4268 2652 4052 4545 4681 4289 3289 4541 3329 4518 4640 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 0.6513215599 0.652150564855324 3435 4057.27272727273 4273 0.1 2755 1.43417541992053 1.20445072162451 1 0.0760243879105199 3431 4654 4353 4426 4688 3402 2755 4273 4669 3769 4210 4641 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 2.51122967975178e-06 3.32016921244492e-06 4445 4167.09090909091 4275 2.28293867840434e-07 3476 0.843466801765456 0.948990870659797 1 1.33358169801982 4065 3952 4041 4275 3498 4445 4498 4628 4443 4517 3476 4642 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 0.00141007929443759 0.00145987590913477 3260 3807.72727272727 4277 0.000128271262701648 1994 1.61475423583214 1.75227104287384 1 1.32137083233088 3257 4558 3757 4277 4544 4372 4693 2773 3271 4389 1994 4643 M4891 BIOCARTA_PML_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PML_PATHWAY.html Regulation of transcriptional activity by PML 22/26 BioCarta 5.45053046295233e-05 5.97318406898885e-05 4585 3836.54545454545 4279 4.95515045934842e-06 2727 2.37605650904624 2.85727532303564 1 2.89716913252346 4582 3148 2727 3208 4279 4683 4517 4410 2748 3519 4381 4644 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 5.00994677100571e-08 3.0357704374324e-07 4465 3748.09090909091 4283 4.55449716826786e-09 356 1.42887482307233 1.26974776315549 1 2.68840653814297 4465 4458 3738 4580 356 4401 4054 3881 2589 4283 4424 4645 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 6.15818937511676e-05 6.72986240896916e-05 3775 3850.81818181818 4289 5.59851069135657e-06 2194 1.11602511880807 -1.38236385283811 -1 1.3436394798102 3775 4289 3381 4581 4292 4443 4637 2194 4458 3404 2905 4646 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 0.0857327692782985 0.0866135854010208 3910 4056.45454545455 4294 0.00811528954816319 2162 1.19605379968757 -1.07700092479691 -1 0.366072657960741 3908 4294 3505 4470 4644 3940 2162 4434 4614 4114 4536 4647 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 0.000137793856274271 0.000147983390583518 4020 4192.27272727273 4296 1.25274988684015e-05 3504 0.735859081879956 0.677965376226733 1 0.812929368845817 4262 3711 4019 4296 4378 4016 3504 4423 4507 4485 4514 4648 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 8.94830102743378e-08 3.31497675696653e-07 3820 3595.81818181818 4296 8.9483013877582e-09 1085 1.60824839443674 1.9305432876223 1 3.00825772063425 3817 3228 4659 2036 1085 4632 4495 4530 2192 4584 4296 4649 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 1.0832259546063e-06 1.60025868724311e-06 4455 3866.45454545455 4297 9.84751352691379e-08 2964 1.96852967827877 1.93292441594217 1 3.29371469510403 4453 4434 2964 2982 3089 4639 4696 4297 3453 3098 4426 4650 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 3.41133376616778e-06 4.35175550711133e-06 4705 4052.90909090909 4299 3.10121732346795e-07 1638 1.36900639736355 -1.24318665683058 -1 2.11858247344432 4702 4464 3902 4265 3636 4543 4022 4613 1638 4299 4498 4651 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 2.14778487196397e-07 4.9146893022108e-07 4560 3955.18181818182 4300 2.14778507954809e-08 1961 1.41404581639397 -1.36430765372604 -1 2.57506418650357 4559 4099 4300 3243 1961 4513 3873 4657 3411 4520 4371 4652 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 6.59492675991167e-08 3.14536172538656e-07 3850 3967 4304 5.99538814327946e-09 641 1.03055480184587 0.997059328135228 1 1.93414994552786 3848 4419 4089 4304 641 4605 4162 4664 3845 4560 4500 4653 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 0.00244593537360524 0.00251905192306715 3630 4228.63636363636 4305 0.000222605361583568 3629 0.919341733815443 -0.690711883945685 -1 0.689040147300392 3629 4515 4103 4305 4563 4062 4233 3698 4528 4538 4341 4654 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 1.66873579801764e-06 2.30237736528596e-06 4310 3951.81818181818 4306 1.51703369434749e-07 2037 1.48120943119918 1.80520133630044 1 2.41055049086917 4306 4395 3900 2037 3335 4715 4404 4588 3056 4532 4202 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 0.000881817239151201 0.000916981134345378 3890 4215.72727272727 4307 8.01973539013265e-05 3451 0.955046934708335 -0.762079536181796 -1 0.836869318747295 3890 4589 4003 4286 4524 4074 4386 3451 4460 4403 4307 4656 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 1.44276713458368e-06 2.02734768539297e-06 4310 4121.18181818182 4307 1.31160734614174e-07 3270 1.13009997892572 -1.05813813123719 -1 1.85697293009012 4381 4585 3796 4456 3270 4368 4307 3436 4344 4084 4306 4657 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 0.0161382053751671 0.016441253911243 3985 4175.81818181818 4313 0.00147798346971601 3070 1.41856433209257 1.37570420831223 1 0.729946461485467 3981 4557 3747 4641 4614 4415 4418 4309 3070 4313 3869 4658 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 0.68618940391 0.686334813828184 4320 4203.63636363636 4319 0.1 2847 1.83480459691867 -2.10516755242444 -1 0.0857461366730798 4319 4645 2847 4251 4707 4194 4476 3859 4668 3716 4558 4659 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 1.71992149782342e-07 4.35984396870383e-07 4320 4037.90909090909 4320 1.71992163093928e-08 1731 1.35985301599019 -1.21503556287139 -1 2.49677182797479 4303 4684 4619 4320 1731 4563 4655 3595 2982 4646 4319 4660 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 0.0177325937594794 0.0180538918345002 4630 3706.09090909091 4322 0.00162519611039265 25 2.84922984173926 -0.841430148681626 -1 1.43355504185837 4629 4322 2987 2424 4615 4699 4410 4671 25 3951 4034 4661 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 0.000181975857279137 0.00019454723586807 4335 3969.36363636364 4323 1.65446283083503e-05 2459 1.81044428329661 1.03845820106748 1 1.93920521679059 4448 3790 2459 3436 4397 4190 4323 4542 4331 3412 4335 4662 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 7.51063437386966e-05 8.16824752181216e-05 4325 4313.81818181818 4325 6.82808253957134e-06 3925 0.582654062616942 -0.646935727534456 -1 0.686921639102753 4325 3994 4057 4287 4315 4544 3925 4466 4509 4676 4354 4663 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 0.00193030756528739 0.00199541211304347 3250 4248.90909090909 4325 0.000175636665884548 3247 0.754695344233117 0.906805949692654 1 0.587539986400975 3247 4597 3986 4063 4553 4142 4610 4425 4325 4525 4265 4664 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 0.131102905913116 0.132308256555464 4320 4314.63636363636 4325 0.0126942468505207 3639 1.02714953958372 -0.986876218911593 -1 0.25967956889972 4318 4473 4086 4092 4654 4325 3639 4708 4493 4417 4256 4665 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 0.368275737615415 0.369842868413779 2915 4038.18181818182 4326 0.0408950298440622 2797 0.996278092814335 -0.753892845790237 -1 0.123415580456807 2915 4412 4155 4326 4672 3284 2797 4292 4556 4645 4366 4666 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 0.000943759755376619 0.000980529615975708 4555 4164.54545454545 4327 9.44160802223028e-05 3536 1.00603728750464 0.529601617686841 1 0.873142242928104 4327 3536 4568 3653 4531 4554 4571 3577 4196 3743 4554 4667 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 0.00253381023814449 0.00260784655997427 2470 3434.09090909091 4333 0.000253670397037645 1690 0.927785251018406 -0.927785251018406 -1 0.69134571287116 2470 4661 4333 4447 4708 2311 1690 1772 4698 4692 1993 4668 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 0.00256435206835823 0.00263870542024217 4590 3264.63636363636 4337 0.000256731603893394 1101 0.804379809382686 -0.858204703653505 -1 0.598088044062376 2387 4337 4587 4586 4575 1448 1101 1776 4634 4710 1770 4669 M15247 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS.html Ubiquitin mediated proteolysis 140/154 KEGG 6.7542003081933e-06 8.18060699375734e-06 4580 4126.18181818182 4338 6.14020094935667e-07 2846 1.1627285400322 1.01302363726358 1 1.70719355717917 4579 4126 4123 3535 3839 4652 4396 4338 2846 4585 4369 4670 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 0.00535875570776005 0.0054830537482392 3100 3828.90909090909 4344 0.00053717220538737 1151 0.524689641479601 0.524689641479601 1 0.341703030801787 3096 4344 4677 4600 4595 2808 1151 3645 4646 4715 3841 4671 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 1.85264664440531e-07 4.54495434594235e-07 4210 4063.72727272727 4349 1.85264679885881e-08 1807 1.30701175218055 -1.26479887742646 -1 2.39290298632741 4207 4675 4454 4531 1807 3792 4349 4439 3748 4701 3998 4672 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 0.00251985840828155 0.00259405271256029 4245 3618.54545454545 4352 0.000252272033559631 946 2.62900194074221 -1.65166835920546 -1 1.96234719022552 4243 3201 4461 1965 4569 4612 4352 4390 946 2707 4358 4673 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 7.55024556489343e-08 3.24564290221284e-07 4670 4034.45454545455 4353 7.55024582142137e-09 891 0.98633338743067 -0.996319016376494 -1 1.84723592762737 4670 4687 4459 4108 891 4499 3823 4115 4071 4703 4353 4674 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 2.05200707992573e-06 2.77282376674763e-06 4655 4295.72727272727 4355 1.86546272172527e-07 3415 0.657452816115353 -0.781968455941594 -1 1.05414363843637 4355 4328 3723 4624 3415 4159 3940 4709 4654 4695 4651 4675 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 2.69423932341117e-05 3.02205551485283e-05 4660 4307.63636363636 4358 2.44933847190267e-06 3789 0.823638837863153 -0.84106967607268 -1 1.07409206351573 4656 4565 3987 3789 4174 4457 3831 4711 4358 4536 4320 4676 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 2.47705599497523e-06 3.27682295299414e-06 3955 4304.09090909091 4360 2.25187162180231e-07 3496 0.695802606493408 -0.638127104562974 -1 1.10110990649686 4592 4570 3955 4500 3496 4322 3952 4298 4659 4360 4641 4677 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 4.99038455175348e-08 3.0357704374324e-07 4380 3802.36363636364 4360 4.53671333177563e-09 351 1.40957745239208 -1.18703638755756 -1 2.65208719234777 4378 4360 4060 4512 351 4517 4110 3435 3339 4368 4396 4678 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 6.06855704434699e-05 6.63506816060176e-05 4130 4420.63636363636 4362 5.51702222546779e-06 4128 0.971779444473257 1.05651866435422 1 1.17159225332551 4128 4720 4164 4709 4289 4309 4283 4445 4537 4681 4362 4679 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 6.02312815652668e-07 1.00039280488695e-06 4365 4117.45454545455 4362 5.47557255048238e-08 2705 1.15846046816041 1.57085274053835 1 2.00621350211608 4022 4616 3638 4640 2705 4534 3467 4684 4261 4362 4363 4680 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 0.000247127165432244 0.000261985266464441 3930 4289.63636363636 4367 2.24686299749125e-05 3753 0.629195009447825 0.593928684143245 1 0.649898483094565 3927 4605 3944 4658 4429 3960 3753 4183 4667 4693 4367 4681 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 0.169419455336551 0.170685128962331 4175 4283.72727272727 4374 0.016733894851611 3252 0.810820013243992 -0.650165704080764 -1 0.178909185331008 3905 4447 4172 3252 4661 4174 4343 4374 4626 4687 4480 4682 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 8.3629867944526e-08 3.27411388472988e-07 4590 3846.27272727273 4387 7.60271555669058e-09 901 1.37762257771239 -1.20551676374077 -1 2.57888731781085 4587 4698 4114 4508 901 3166 4175 4451 2716 4606 4387 4683 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 1.25772764312697e-05 1.46860069162192e-05 4395 4191.54545454545 4392 1.14339530322074e-06 3382 0.745873624187393 0.610485036147345 1 1.04009890361632 4393 4630 3842 3765 3995 4599 4623 4010 4476 4392 3382 4684 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 0.0262688702875071 0.0266872724401708 4625 3819.72727272727 4400 0.00265846610071427 2300 1.38449394871378 -1.76030424229577 -1 0.62829025561606 2957 4660 4400 4436 4624 2977 2300 4622 4694 3979 2368 4685 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 0.00395527745975195 0.00406022392562618 4640 4364.18181818182 4404 0.000360218765342032 3777 0.509249425534157 0.603983172152576 1 0.350808655472894 4639 4329 3874 3777 4579 4404 4311 4163 4704 4686 4540 4686 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 1.60431128665272e-07 4.21620960496262e-07 4710 4068.63636363636 4414 1.60431140247439e-08 1671 1.33687467201407 -1.20295239269765 -1 2.46018407818308 4707 4680 4414 4529 1671 3759 4103 4218 3478 4627 4569 4687 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 9.17670096202101e-07 1.39452764136314e-06 4225 4227.09090909091 4414 8.34245889984926e-08 2991 0.979548249952016 -1.02559638430213 -1 1.65543738749955 4224 4414 4098 4693 2991 4036 4587 4521 4571 4550 3813 4688 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 0.538571852419952 0.539829930648157 3545 4202.18181818182 4419 0.0744275731532845 3545 1.22443506918384 1.22443506918384 1 0.0938054090266504 3545 4663 4682 4419 4710 4046 4470 3847 4500 3744 3598 4689 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 9.0641730964361e-07 1.38053878719517e-06 4590 4263.18181818182 4429 8.24016075540809e-08 2983 1.07639620063998 -1.29975852186543 -1 1.82055661738609 4586 4429 4078 4688 2983 4615 4515 4213 4035 4548 4205 4690 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 0.000224606421653831 0.000239039979753344 4525 4179.90909090909 4433 2.04208505328455e-05 3277 1.07109151918363 -1.08310475823053 -1 1.11925220653856 4524 3797 3412 3754 4413 4472 4677 4579 4641 3277 4433 4691 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 4.90411124258383e-07 8.51633740433984e-07 4490 3850.27272727273 4445 4.45828394161813e-08 870 2.00032305815921 -1.88411853179724 -1 3.50515699689746 4487 4468 3403 4445 2573 4648 4519 4336 870 3903 4701 4692 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 0.0527216163499453 0.0533889785822231 4570 4300.27272727273 4446 0.00491174005686687 3541 1.11136998165593 -0.994612891344046 -1 0.407529906665143 4567 4466 4074 3541 4634 4476 3808 4572 4294 4446 4425 4693 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 0.00321859304527466 0.00330614998339421 4080 4350 4447 0.000293028318534889 3858 1.08185430320887 1.06848149731115 1 0.774104438684738 4076 4621 3858 4660 4574 4179 4128 4716 4466 4125 4447 4694 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 0.453385442843038 0.45483087996156 4440 4456.72727272727 4449 0.0586131675990452 3679 0.523249107839927 -0.523249107839927 -1 0.0508360583003207 4438 4664 4282 4449 4706 4529 4425 3679 4720 4690 4442 4695 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 0.00182143758479477 0.00188410813066652 3170 3964.54545454545 4459 0.000165722486445642 2080 0.92500591146608 0.663441247481369 1 0.726981475069571 3167 4628 3862 4661 4549 2983 2080 4600 4499 4459 4122 4696 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 0.217485014941637 0.218922855731398 4290 4368 4460 0.0220480549028261 3249 0.644553550304663 -0.546635902591709 -1 0.12192635360292 4288 4564 4140 3249 4662 4427 4376 4460 4710 4638 4534 4697 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 0.0268117466543856 0.0272329339807833 4090 4293.18181818182 4461 0.00246765380425164 3537 1.15300728970943 1.32462752751237 1 0.520169754864538 4434 4461 4088 3537 4621 4581 3587 4615 4089 4523 4689 4698 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 0.494979719761927 0.496241350313572 4685 4435.18181818182 4462 0.0602159402550221 3815 0.68461519034427 0.783890506921785 1 0.0592978666546384 4339 4462 4167 3815 4681 4313 4355 4568 4707 4684 4696 4699 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 2.72851846779955e-05 3.05867418731289e-05 4710 4359 4467 2.4805020985876e-06 3780 0.918659790067 0.91024502972013 1 1.19671888459008 3780 4710 4165 4710 4176 4097 4010 4467 4539 4682 4613 4700 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 7.5527202383093e-07 1.19195346041176e-06 4470 4187.09090909091 4469 6.86611166472789e-08 2856 1.08947177887651 1.41008022869592 1 1.86275053648527 4469 4586 3825 4663 2856 4674 3437 4215 4283 4470 4580 4701 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 0.0785400594161663 0.0793639649848651 4645 4426.63636363636 4471 0.00740841907710938 3812 0.679715552777531 -0.676257081911871 -1 0.215117917263239 4278 4531 4144 3812 4641 4536 4471 4462 4706 4644 4468 4702 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 0.000513042002036581 0.000537884995471493 4100 4358.81818181818 4480 4.66510620885219e-05 3536 0.982917787630617 0.949181843743037 1 0.927072090671677 4099 4469 4092 3536 4480 4582 4654 4377 4560 4496 4602 4703 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 0.4480172349803 0.449541103126492 4715 4275.3 4481.5 0.0638939382692898 2510 0.475242156542419 -0.287235194256882 -1 0.046790154416476 4366 4085 4597 NA 4704 4272 2510 4076 4714 4711 4718 4704 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 0.0135811046022319 0.0138421104993597 4555 4327.09090909091 4486 0.00124233415384811 3615 0.725093742027433 -0.748619895075893 -1 0.388335888622773 4553 4643 3843 3760 4612 4486 3615 4481 4599 4351 4655 4705 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 2.50819506747252e-07 5.35608210768807e-07 4515 4209.72727272727 4488 2.2801775940264e-08 2030 1.23299749160893 -1.11225482091554 -1 2.23195508322219 4515 4708 4137 4524 2030 4488 4482 4189 4016 4516 4702 4706 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 8.66649327918722e-08 3.28825146927361e-07 4700 4057.72727272727 4490 7.87863056417066e-09 948 0.624702953136513 0.559386239964626 1 1.1686255841332 4696 4600 3916 4492 948 4588 3902 4006 4545 4490 4452 4707 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 4.96739803902422e-06 6.16030445196909e-06 4535 4320.72727272727 4498 4.51582659544404e-07 3753 1.05273324636859 -0.653280510304012 -1 1.58305656258663 4535 4574 3876 4498 3753 4193 4593 3926 4386 4509 4685 4708 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 0.135558521151167 0.136746360297822 3355 3966.09090909091 4500 0.013155577946369 1820 0.756790283758527 0.65606935162299 1 0.187970446134996 3351 4567 4034 4518 4656 3154 1820 4500 4677 4546 3804 4709 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 0.633027668702641 0.633967875297361 4035 4345.27272727273 4517 0.0871041958287936 3677 0.700713973129407 -0.646972562048625 -1 0.039188616210017 4034 4638 3992 4517 4685 3677 4178 4535 4696 4718 4128 4710 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 0.0254424518270021 0.0258643921222162 4715 4258.63636363636 4520 0.0025738527190969 2697 0.612424221594043 -0.612424221594043 -1 0.279846290180473 4520 3541 4574 4401 4623 3931 2697 4422 4715 4709 4712 4711 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 0.0776538750835003 0.0784852870222958 4485 4410.54545454545 4520 0.00732167581798973 3834 0.689873717453531 -0.786984351613721 -1 0.219308874167427 4485 4576 4065 4520 4640 4283 4559 3834 4628 4598 4328 4712 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 0.0401164590633882 0.0406766244423614 4635 4427.09090909091 4524 0.00371520090038852 3903 0.599559798451016 0.56181811098896 1 0.239904797366509 3903 4633 3970 4501 4629 4161 4524 4635 4681 4669 4392 4713 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 5.90874841212133e-07 9.87581179363056e-07 4525 4346.81818181818 4525 5.37159090826405e-08 2688 0.933026792715948 0.925721541451315 1 1.61714964750264 4292 4422 4139 4525 2688 4707 4701 4526 4521 4612 4682 4714 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 0.9717524751 0.9717524751 4715 4460 4529 0.3 3964 0.239690686194416 -0.204826718161511 -1 0 4529 4666 4465 3986 4715 4428 3964 4286 4713 4704 4604 4715 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 1.64149775759942e-07 4.25473334204792e-07 4425 4170.45454545455 4532 1.6414978788526e-08 1696 1.46608368539081 1.56386517574453 1 2.69637194925561 4425 4670 4641 4532 1696 4600 4359 4346 3336 4652 4618 4716 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 6.63088375153676e-06 8.04156508408364e-06 4615 4331.09090909091 4548 6.02809430668832e-07 3826 0.995137267660396 1.25694353354596 1 1.46314039949114 4615 4548 3967 4673 3834 4572 3826 4011 4402 4570 4624 4717 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 1.04676290930035e-05 1.23394628668772e-05 3960 4427.27272727273 4553 9.51607172586626e-07 3957 0.849441139909071 -0.745707661872827 -1 1.20318599066189 4583 4553 3957 4662 3960 4645 4572 4376 4542 4287 4563 4718 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 0.000164532392799376 0.000176298046313974 4685 4470.36363636364 4561 1.49586090041998e-05 4032 0.64332209182814 0.593806282069017 1 0.696467377267442 4323 4561 4032 4682 4389 4630 4603 4400 4682 4587 4285 4719 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 0.683357934517389 0.684082598286761 4585 4450.18181818182 4582 0.0992647763656405 3860 0.573386531931066 -0.389535955987743 -1 0.026440337749041 4581 4644 3881 4280 4687 4688 4334 3860 4708 4707 4582 4720 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 0.0533064720763844 0.0539696585586732 4595 4426.54545454545 4594 0.0049676079054787 3733 0.761155831504397 1.00985795879983 1 0.277805332870101 3733 4612 3941 4665 4635 4595 4667 4594 4302 4493 4455