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 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 390/782 Daniel Hollern 1.3837343761806e-163 6.48417928678231e-160 5 58 4 1.25794034198232e-164 1 2.44225265135298 2.50290368106107 1 100 1 4 1 1 424 2 4 26 135 1 39 2 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 102/176 Daniel Hollern 4.65424248279337e-58 5.45244506859244e-55 5 64.8181818181818 17 4.23112952981216e-59 2 2.60370206530123 2.69162704496596 1 36.341014411621 2 55 4 103 326 4 17 13 134 6 49 3 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 351/695 Daniel Hollern 9.5660589517066e-41 2.24132761238486e-38 5 329.181818181818 25 8.69641722882418e-42 3 1.56501475680789 -1.55494694059693 -1 15.1557094702593 3 9 19 790 1248 16 25 127 1130 4 250 4 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 330/762 Arthur Liberzon 2.91185958207979e-31 3.59078263200681e-29 15 185 38 2.64714507461802e-32 1 2.15984704512173 2.26305149609476 1 15.8024611268054 14 267 37 7 752 1 57 38 798 52 12 5 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 124/324 Arthur Liberzon 2.47133030230648e-33 3.30875822760233e-31 35 114.181818181818 46 2.24666391118771e-34 4 2.37041660978081 2.52568787942817 1 18.5841670782041 12 54 34 4 427 31 72 46 441 44 91 6 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 318/808 Arthur Liberzon 6.68212315099469e-62 1.04374763618537e-58 5 109.363636363636 49 6.07465740999522e-63 3 2.32167542319212 2.53374243989646 1 34.6249314082699 17 15 3 104 228 21 102 49 600 5 59 7 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 184/460 John Newman 7.13529835605578e-36 1.11453360321591e-33 30 146.818181818182 57 6.48663486914166e-37 29 2.11744065495648 2.27840248887396 1 17.9474875955516 44 31 29 215 111 36 114 103 845 30 57 8 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 335/782 Arthur Liberzon 8.45614044520918e-27 8.25530710963546e-25 10 220.090909090909 71 7.68740040473559e-28 8 1.98714942864039 2.18478285110933 1 12.3096188032438 71 17 47 123 569 10 191 11 1297 77 8 9 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 36/74 Jessica Robertson 8.45431380292963e-21 4.8051130638796e-19 25 186.909090909091 78 7.68573982084512e-22 3 3.04787041633362 3.10564682701775 1 14.3608538658614 22 350 78 21 1123 3 27 176 124 111 21 10 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 137/354 Arthur Liberzon 7.33252703303618e-15 2.03314921164542e-13 85 138.181818181818 83 6.66593366639653e-16 39 2.18084373125069 2.32067732187353 1 7.11946722990463 132 51 163 39 83 80 83 65 458 157 209 11 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 112/259 Jessica Robertson 8.61351893653193e-21 4.8051130638796e-19 80 292.818181818182 83 7.83047176048353e-22 33 2.17594216570839 2.32724070876112 1 10.2525314424807 97 902 80 415 142 43 74 83 1273 79 33 12 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 40/124 Leona Saunders 5.67369027818017e-18 2.39521735527498e-16 35 111.545454545455 84 5.15790025289104e-19 29 2.52766578755467 2.5839370653618 1 10.1558802849609 35 126 106 31 337 29 59 59 262 84 99 13 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 29/65 John Newman 1.8868146100951e-10 2.53341354237984e-09 10 249.181818181818 88 1.71528600932447e-11 4 2.27669179635137 2.34697595357613 1 5.03401110537434 88 166 687 535 33 12 10 4 350 849 7 14 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 39/104 Arthur Liberzon 1.21941506011233e-19 6.01492523335409e-18 40 116.545454545455 90 1.10855914555666e-20 15 2.66896971643018 2.71157358609213 1 11.8221070589042 15 131 90 38 432 20 60 40 266 94 96 15 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 90/200 Yujin Hoshida 5.5625690135696e-19 2.60661983975871e-17 60 169.909090909091 95 5.05688092142691e-20 21 2.46389037031734 2.63811631757032 1 10.5101112961176 60 497 95 40 156 88 124 21 574 141 73 16 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 44/93 John Newman 1.86561599498717e-26 1.7841380719408e-24 50 201.909090909091 98 1.69601454089743e-27 17 2.79261810404042 2.94075156981507 1 17.0587704486664 37 123 48 17 932 50 98 311 388 63 154 17 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 31/72 Arthur Liberzon 4.79306890853867e-17 1.87169340878435e-15 25 78.0909090909091 103 4.35733537139878e-18 15 2.66157111780934 2.68887507610307 1 10.0826248744434 21 147 115 122 114 25 15 25 116 103 56 18 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 94/214 Jessica Robertson 1.91097346473816e-18 8.52840157691714e-17 95 211.454545454545 106 1.73724860430741e-19 71 2.40762961217652 2.56423975525947 1 9.95132211270251 95 71 100 146 506 92 437 78 589 106 106 19 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 60/143 John Newman 8.02594859114435e-12 1.35348439699083e-10 150 165.454545454545 108 7.29631690106695e-13 16 2.32183803430282 2.49901405987328 1 5.8936426177728 146 108 270 249 57 40 76 16 626 181 51 20 M631 REACTOME_COLLAGEN_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COLLAGEN_FORMATION.html Genes involved in Collagen formation 25/64 Reactome 1.85426484778298e-17 7.55572615366179e-16 110 175.545454545455 110 1.68569531616635e-18 10 3.4228055878756 3.4228055878756 1 13.3131926229925 10 171 110 109 891 49 11 201 33 148 198 21 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 42/80 Arthur Liberzon 8.244968697497e-20 4.15440035660978e-18 100 220 110 7.49542608863363e-21 16 2.82431552477558 2.80808290003823 1 12.6269639151064 16 346 88 110 992 97 33 205 145 98 290 22 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 20/34 Yujin Hoshida 2.73876684078136e-15 8.17443402286717e-14 25 174.181818181818 110 2.48978803707396e-16 22 3.03149479692423 3.03149479692423 1 10.2050140248636 24 187 151 147 969 22 48 110 84 129 45 23 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 20/32 Arthur Liberzon 7.71143900742381e-17 2.98643001560231e-15 20 277.181818181818 116 7.01039909765799e-18 3 3.14204754162654 3.14204754162654 1 11.7387815105167 19 182 116 32 1743 42 3 298 109 174 331 24 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 85/182 John Newman 6.40969197544415e-09 5.39242667808461e-08 85 213.818181818182 116 5.82699272192614e-10 41 2.11129385295826 2.28888719286049 1 3.94707300797257 116 78 416 89 362 41 85 213 474 397 81 25 M18 PID_INTEGRIN1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN1_PATHWAY.html Beta1 integrin cell surface interactions 18832364 44/86 Pathway Interaction Database 1.87661238697323e-22 1.29320671255243e-20 10 312.727272727273 118 1.70601126088475e-23 9 2.72807416726806 2.81321363815867 1 13.9557511877029 9 340 66 14 1740 118 92 272 345 62 382 26 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 124/327 Arthur Liberzon 8.02135337690379e-25 7.22847344695599e-23 60 253 118 7.29213943354887e-26 27 2.33351203222337 2.42346286509869 1 13.2893899434513 48 59 51 27 771 124 118 369 910 58 248 27 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 90/216 Leona Saunders 3.2259193671037e-12 5.74999998450024e-11 50 301.454545454545 119 2.93265397009858e-13 17 2.04343777951272 2.09276669315499 1 5.38237724998594 50 498 256 460 983 17 84 60 724 119 65 28 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 58/138 Jessica Robertson 2.14033218664009e-11 3.39903650064567e-10 125 182.272727272727 121 1.9457565333281e-12 55 2.29752281087121 2.48580889507328 1 5.59559535296604 121 109 287 66 396 55 221 74 317 273 86 29 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 27/69 Arthur Liberzon 2.73806758727413e-11 4.20674908654642e-10 65 224.909090909091 122 2.48915235209837e-12 28 2.74893368156217 2.78176122137238 1 6.6295341106051 64 370 297 76 1000 39 28 122 97 238 143 30 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 110/272 Jessica Robertson 1.33529030358176e-24 1.18059818161965e-22 55 356.363636363636 123 1.21390027598342e-25 25 2.36410502135166 2.48744440084409 1 13.334061316466 25 642 52 417 893 60 51 264 1304 89 123 31 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 37/61 Arthur Liberzon 4.52926609586285e-15 1.30209453528916e-13 190 194.727272727273 123 4.1175146326026e-16 12 2.80553674791229 2.7853433705015 1 9.29846183195431 31 138 157 23 1147 19 12 190 188 123 114 32 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 134/273 Arthur Liberzon 2.0944047035511e-14 5.48289410102818e-13 55 304.272727272727 124 1.90400427595555e-15 34 1.94916264042695 2.10056666290338 1 6.14712856126723 54 486 174 328 1302 34 58 50 624 124 113 33 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 103/276 John Newman 4.11698064337505e-14 1.00480058827372e-12 60 167.727272727273 125 3.74270967579555e-15 56 2.06034910808458 2.35117986316503 1 6.35836499892256 125 65 187 56 100 113 329 164 520 126 60 34 M7098 KEGG_ECM_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ECM_RECEPTOR_INTERACTION.html ECM-receptor interaction 42/94 KEGG 7.00876973844371e-14 1.63398482558941e-12 130 205.636363636364 127 6.37160885313083e-15 6 2.423825461934 2.5267643977043 1 7.34842329234418 28 130 196 233 1121 6 21 32 318 127 50 35 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 42/87 Arthur Liberzon 1.19714296067128e-15 3.69066573270106e-14 25 212.272727272727 127 1.08831178242844e-16 15 2.52833411203025 2.66533321226751 1 8.73580180022379 23 127 146 117 1042 15 20 295 219 228 103 36 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 18/110 John Newman 6.42868270335483e-11 9.2376612378475e-10 145 246.454545454545 129 5.84425700322061e-12 36 3.4282913059767 3.63473656568946 1 7.96668297430701 144 395 317 45 993 53 61 129 36 430 108 37 M236 PID_DELTA_NP63_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_DELTA_NP63_PATHWAY.html Validated transcriptional targets of deltaNp63 isoforms 18832364 46/93 Pathway Interaction Database 6.73663673600982e-14 1.5783939872471e-12 85 211.818181818182 130 6.12421521455455e-15 83 2.67013166455286 2.78047483548339 1 8.10548558935466 83 129 195 294 608 100 130 97 351 260 83 38 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 87/210 Leona Saunders 1.09130547940314e-21 6.72875983747779e-20 75 228.909090909091 131 9.92095890366493e-23 37 2.39331998830609 2.41974753111787 1 11.8023459738633 131 74 73 37 151 103 136 566 954 56 237 39 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 82/168 Arthur Liberzon 3.86248537448337e-09 3.72419886107594e-08 240 322.090909090909 132 3.51135034660421e-10 10 2.27451407500165 2.50526766667423 1 4.34626030820292 237 651 530 96 84 64 132 37 1118 584 10 40 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 25/84 Jessica Robertson 2.64289924362351e-18 1.16836092977545e-16 150 230.272727272727 132 2.40263567602136e-19 24 3.12245203238761 3.12245203238761 1 12.796060504489 27 172 101 148 1480 24 55 132 150 149 95 41 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 257/529 Arthur Liberzon 8.58093763765611e-21 4.8051130638796e-19 80 213.727272727273 132 7.80085239786915e-22 30 1.9994823292179 2.09459886162504 1 9.42109387573123 66 465 79 132 301 30 167 238 709 80 84 42 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 71/210 Jessica Robertson 7.06685379056614e-16 2.34860119592858e-14 140 175.636363636364 136 6.42441253687828e-17 66 2.2867678852433 2.58992341273612 1 8.01661138345829 293 85 136 118 139 132 284 66 355 198 126 43 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 14/21 Leona Saunders 3.38207389348781e-09 3.35061274099025e-08 175 242.181818181818 137 3.07461263517009e-10 52 2.11749571116853 2.17833490859042 1 4.07122574978401 171 409 658 137 52 82 67 120 263 628 77 44 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 69/144 Jessica Robertson 2.64176749250227e-14 6.76465708735826e-13 90 146 137 2.40160681136572e-15 14 2.38387061202008 2.74615778396457 1 7.46213606355937 90 318 178 42 207 14 81 137 366 154 19 45 M274 PID_LYMPH_ANGIOGENESIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LYMPH_ANGIOGENESIS_PATHWAY.html VEGFR3 signaling in lymphatic endothelium 18832364 31/57 Pathway Interaction Database 9.18996607157847e-09 6.87504636685147e-08 140 299.818181818182 139 8.35451464542483e-10 55 2.9885459433181 2.9885459433181 1 5.50600812965336 139 546 670 100 496 58 134 55 196 788 116 46 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 54/115 Jessica Robertson 2.22376167323716e-13 4.75824073095402e-12 305 195.090909090909 139 2.02160152112489e-14 97 2.30173810515644 2.45634476183065 1 6.7034591588268 102 118 213 302 97 99 302 139 497 146 131 47 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 176/437 Kate Stafford 6.43644380147092e-20 3.35124173929919e-18 140 325.272727272727 140 5.85131254679173e-21 59 2.11409205211674 2.32001690976153 1 9.50242922939806 59 627 85 140 1092 67 160 138 966 170 74 48 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 75/181 Arthur Liberzon 3.30423781175431e-11 5.01089268151479e-10 305 262.727272727273 140 3.00385255618541e-12 25 2.43975202086576 2.71619995697468 1 5.83621487124982 62 81 301 25 1374 150 140 123 88 301 245 49 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 354/968 Arthur Liberzon 1.37984207679473e-41 3.59218887325561e-39 80 213.545454545455 140 1.25440188799521e-42 17 2.14926220884694 2.37568306196492 1 21.2531787663434 80 264 17 217 275 119 196 90 924 27 140 50 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 39/71 Arthur Liberzon 1.39694171753659e-14 3.71935732294118e-13 45 136.272727272727 142 1.26994701594236e-15 18 2.7652853121143 2.88372375991685 1 8.84083745359026 45 142 171 113 325 18 41 180 159 183 122 51 M5887 NABA_BASEMENT_MEMBRANES http://www.broadinstitute.org/gsea/msigdb/cards/NABA_BASEMENT_MEMBRANES.html Genes encoding structural components of basement membranes 22159717 23/56 Alexandra Naba 2.35919901493919e-16 8.4390889954237e-15 30 326.818181818182 142 2.14472637721744e-17 26 3.10780468327856 3.10780468327856 1 11.2502150410682 26 177 126 34 2001 142 88 305 146 110 440 52 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 117/268 Arthur Liberzon 9.44172280511872e-16 2.98945358545853e-14 85 246.363636363636 143 8.58338436828976e-17 14 1.92078798533719 2.06946038566422 1 6.68184467289051 82 292 143 240 107 61 235 48 1269 219 14 53 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 20/45 Jessica Robertson 1.63294959423972e-09 1.81327056839036e-08 145 177.181818181818 144 1.48449963222888e-10 28 2.98493000326048 3.02623269691309 1 5.94374324240036 214 190 382 28 141 144 286 45 48 413 58 54 M3005 NABA_COLLAGENS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_COLLAGENS.html Genes encoding collagen proteins 22159717 17/45 Alexandra Naba 1.07679518420636e-15 3.34163061800728e-14 35 260.090909090909 145 9.78904712914869e-17 34 3.64550890388517 3.64550890388517 1 12.6362784343656 34 204 145 115 1339 86 70 354 50 200 264 55 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 40/82 Leona Saunders 1.3407684429687e-13 2.94969057453113e-12 130 167.090909090909 146 1.21888040269889e-14 54 2.64892537548929 2.80237696625534 1 7.85608417794024 126 137 207 167 328 62 112 146 252 247 54 56 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 44/104 Leona Saunders 4.26858751357911e-16 1.48167415471346e-14 45 234.363636363636 152 3.88053410325374e-17 43 2.34075180562451 2.50458892517723 1 8.32631022361537 43 124 130 119 669 152 169 414 399 73 286 57 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 175/696 Arthur Liberzon 1.12242119225791e-28 1.25230135879061e-26 155 211.272727272727 152 1.02038290205265e-29 8 2.38393666880625 2.63821786920173 1 15.8829649629885 154 37 41 8 133 359 454 152 502 75 409 58 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 27/82 Leona Saunders 2.66800567351254e-18 1.16843687720372e-16 145 222 157 2.42545970319322e-19 102 2.68853239785862 3.03754680410926 1 11.0178032603296 143 163 102 127 493 157 209 485 140 145 278 59 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 72/150 Aravind Subramanian 5.99101567913291e-15 1.6911987633986e-13 85 229.818181818182 160 5.44637789012085e-16 81 2.1547818814114 2.32644240555444 1 7.07871263391293 81 84 160 166 814 101 198 115 450 138 221 60 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 93/248 John Newman 7.27188128502248e-18 3.01557838067392e-16 95 316.727272727273 160 6.61080116820225e-19 18 2.60586026471757 2.71227372756664 1 10.403012787695 18 778 108 135 1196 93 94 338 309 160 255 61 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 58/125 Arthur Liberzon 2.04216809519157e-23 1.59493328234462e-21 165 237.181818181818 161 1.85651645017415e-24 12 2.71154418663269 2.84375036991168 1 14.5051237197568 55 102 58 12 884 161 163 198 544 66 366 62 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 151/355 John Newman 3.76246187319201e-24 3.2056175159596e-22 165 251.727272727273 162 3.42041988472001e-25 45 2.37040297031737 2.67376229112092 1 13.1050865482855 162 45 54 108 954 252 273 47 555 83 236 63 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 131/329 Arthur Liberzon 5.34147395171827e-15 1.52622847181413e-13 165 300.363636363636 164 4.85588541065298e-16 36 2.11813841306378 2.31828009323947 1 6.98261992051636 327 58 158 316 89 245 413 36 1334 164 164 64 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 12/28 Arthur Liberzon 4.89367917459761e-13 9.97033939659321e-12 125 259.727272727273 164 4.44879924963518e-14 18 3.34323131343403 3.4977008899197 1 9.46038303523718 123 223 224 164 1104 32 153 462 18 229 125 65 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 34/72 Jessica Robertson 6.8766328734652e-16 2.31826630539985e-14 40 411.909090909091 164 6.2514844304229e-17 38 2.67324408314033 2.70127013281541 1 9.3753444733432 38 357 134 129 1874 164 144 581 651 113 346 66 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 20/48 Jessica Robertson 8.16184544505244e-10 9.83198142815315e-09 180 323 164 7.41985949825494e-11 19 3.10413236334699 3.28318927035539 1 6.3933459295184 179 390 366 72 1548 76 19 130 164 527 82 67 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 137/290 John Newman 8.98052543626087e-16 2.88237960235058e-14 195 276.545454545455 173 8.16411403296443e-17 41 2.11730446799652 2.26212236301512 1 7.37409343147247 173 52 141 41 977 133 312 85 742 195 191 68 M6487 BIOCARTA_PLATELETAPP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLATELETAPP_PATHWAY.html Platelet Amyloid Precursor Protein Pathway 11/29 BioCarta 1.00757054543094e-10 1.40520106425279e-09 30 207.272727272727 174 9.15973223160985e-12 7 3.22541355871553 3.22541355871553 1 7.3440955743916 79 227 326 174 735 7 26 241 21 416 28 69 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 15/34 Reactome 1.64190607441605e-10 2.22369129037965e-09 75 194.818181818182 174 1.49264188594417e-11 26 3.03778024088816 3.03778024088816 1 6.76110986716307 73 212 335 178 514 26 35 174 79 398 119 70 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 24/52 John Newman 3.28337194448354e-14 8.16612819490704e-13 100 194.090909090909 174 2.98488358589417e-15 76 2.74866290400756 2.997894407069 1 8.54621922765645 98 174 183 333 135 110 141 435 234 216 76 71 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 36/62 Arthur Liberzon 2.17917603406426e-14 5.67312160868062e-13 45 257.636363636364 174 1.98106912187662e-15 38 2.84738624455945 2.82725381472473 1 8.96903308264037 41 144 175 124 1326 38 42 363 229 178 174 72 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 26/64 Arthur Liberzon 2.25635079368879e-12 4.17915407874532e-11 110 338.272727272727 174 2.05122799426464e-13 109 2.38680353830427 2.4574188569927 1 6.37187373625093 109 170 247 383 1077 163 174 685 149 128 436 73 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 25/76 Kevin Vogelsang 1.08477054693148e-11 1.80256552585847e-10 150 348.454545454545 176 9.8615504266984e-13 82 2.76895500469499 2.78255781237426 1 6.93995581049716 150 176 274 304 1867 158 82 88 131 250 353 74 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 21/38 Arthur Liberzon 3.90555848475263e-09 3.75029652859648e-08 195 205.636363636364 176 3.55050771971454e-10 5 2.70212178070927 2.84622504633033 1 5.16124764035499 76 192 486 194 176 8 5 128 203 741 53 75 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 45/91 Leona Saunders 2.65992408127315e-12 4.86890790814297e-11 20 303.181818181818 177 2.41811280116034e-13 6 2.4356461605316 2.4865766916351 1 6.46070207770347 20 345 250 177 1648 27 6 63 435 236 128 76 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 42/105 John Newman 2.36277540894392e-08 1.17368000814054e-07 220 311 179 2.14797766756351e-09 79 2.33618137913497 2.60024100559955 1 4.16453654930462 220 135 448 79 1209 116 179 101 284 506 144 77 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 6/11 Jessica Robertson 5.98874999576856e-09 5.16819198529862e-08 240 648.090909090909 181 5.98875001190787e-10 5 3.2632118993537 3.2632118993537 1 6.1160712585091 238 246 4471 15 883 140 181 44 5 776 130 78 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 125/318 Arthur Liberzon 7.68357535070696e-19 3.56487466271414e-17 135 367.727272727273 181 6.98506850064267e-20 29 2.00244044948394 2.15776838860587 1 8.47169313670129 135 637 96 495 437 65 170 181 1614 186 29 79 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 29/62 John Newman 8.81948016515886e-17 3.38754787327331e-15 55 380.636363636364 182 8.01770924105347e-18 53 3.06253145495155 3.06253145495155 1 11.3985919903708 53 368 117 145 1892 114 110 358 529 182 319 80 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 21/48 Arthur Liberzon 5.46753348225612e-11 8.00651934307881e-10 50 285.454545454545 184 4.97048498399273e-12 46 3.11954607315844 3.296565275305 1 7.29906262321747 70 184 311 49 1080 166 172 395 46 277 390 81 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 35/87 John Newman 4.08379465413114e-14 1.00191946331197e-12 95 280.363636363636 186 3.71254059466473e-15 39 2.86797306712257 2.99089571552223 1 8.85166260636206 91 672 186 297 873 91 39 261 125 133 316 82 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 22/51 John Newman 1.95279521537283e-11 3.1231393785792e-10 115 250.090909090909 186 1.77526837762742e-12 105 3.26897663778745 3.26487077626709 1 7.99247499475338 105 183 285 186 327 111 111 722 107 395 219 83 M15422 BIOCARTA_VITCB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VITCB_PATHWAY.html Vitamin C in the Brain 11/24 BioCarta 5.32577226651508e-12 9.24317364477395e-11 60 223.363636363636 187 4.84161115138906e-13 1 3.0227175880626 3.0227175880626 1 7.80149958386084 56 229 263 187 890 13 1 257 56 417 88 84 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 23/100 Arthur Liberzon 7.98165718306781e-08 2.74007659779163e-07 150 348.090909090909 189 7.25605224785859e-09 72 2.73032960157844 3.00406327214209 1 4.6085645788174 149 382 508 189 1146 159 99 179 72 690 256 85 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 108/301 Alexandra Naba 3.46469551697168e-43 1.05716996798728e-40 5 247.181818181818 191 3.14972319724699e-44 5 2.577599542603 2.74016159113616 1 26.5040288059764 5 60 14 105 815 191 230 469 409 20 401 86 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 288/749 Jessica Robertson 3.65599580209314e-31 4.39281957143806e-29 40 294.454545454545 193 3.3236325473574e-32 38 2.06801403439603 2.20633477595272 1 15.0839949524907 108 273 38 414 700 69 245 193 999 38 162 87 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 46/110 Arthur Liberzon 6.39500546144197e-14 1.5134846258746e-12 265 285.727272727273 193 5.81364132858376e-15 26 2.61758629199514 2.78101592436578 1 7.95825717700119 190 342 193 52 1272 89 262 39 417 261 26 88 M610 REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION.html Genes involved in Extracellular matrix organization 40/134 Reactome 3.43431679940166e-14 8.47010974841904e-13 95 293.272727272727 194 3.12210618127427e-15 94 2.92458839613597 3.15618313240932 1 9.08127129814996 94 141 185 121 695 375 444 291 168 194 518 89 M7169 REACTOME_NCAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NCAM1_INTERACTIONS.html Genes involved in NCAM1 interactions 20/60 Reactome 1.90415117683081e-11 3.055771374873e-10 45 273.727272727273 195 1.73104652440663e-12 2 3.0163104025928 3.0163104025928 1 7.38206703791113 42 195 284 159 1233 45 2 467 152 232 200 90 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 41/119 Arthur Liberzon 2.42785919630539e-13 5.17134008813048e-12 90 315.181818181818 195 2.20714472391423e-14 46 2.61084182533506 2.70393002100418 1 7.57939528300016 89 348 214 246 1676 46 71 262 195 144 176 91 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 21/40 Leona Saunders 7.54855694521563e-14 1.75111573491487e-12 200 274.818181818182 196 6.86232449565078e-15 28 3.13293720943033 3.37614420691626 1 9.47404095839357 101 196 197 46 1365 28 69 287 421 276 37 92 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 19/76 Jessica Robertson 2.29509290970716e-09 2.43321388572122e-08 60 272.181818181818 198 2.08644810191042e-10 57 2.89615278462935 2.89615278462935 1 5.67182380367144 57 198 390 183 746 73 103 527 207 377 133 93 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 51/190 Nikolaos Papanikolaou 2.0501873345121e-17 8.28204987027907e-16 105 239.272727272727 199 1.86380666773827e-18 11 2.80237730155197 3.02544977898445 1 10.8712693119742 103 110 111 11 805 289 336 216 67 199 385 94 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 18/41 Arthur Liberzon 1.33082833394313e-09 1.52849548354351e-08 220 232.636363636364 200 1.20984394068017e-10 55 2.96151656308948 3.38064885902238 1 5.9536419395865 216 200 376 149 433 104 176 350 55 330 170 95 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 84/201 Daniel Hollern 1.3201237722689e-22 9.37287878310918e-21 10 283.727272727273 200 1.20011252024445e-23 6 2.10163625369183 -2.1491843777409 -1 10.8267116130462 6 299 64 530 1202 48 200 160 289 41 282 96 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 193/443 Jessica Robertson 1.25602885594866e-34 1.89862942547594e-32 35 242.545454545455 203 1.14184441449878e-35 30 2.41572110140868 2.49604717959605 1 19.7106075717929 32 623 30 219 622 71 116 203 505 34 213 97 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 18/109 Arthur Liberzon 1.09306915316987e-13 2.45077610131771e-12 55 355 203 9.93699230154479e-15 51 2.9609739128112 2.9609739128112 1 8.84283512455202 51 561 203 150 1591 154 106 324 176 241 348 98 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 16/33 Arthur Liberzon 1.20839098260623e-08 7.9085476878391e-08 575 260.636363636364 204 1.09853726294868e-09 43 2.81674797792058 2.81674797792058 1 5.14542692465467 111 571 573 204 323 94 43 228 74 457 189 99 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 74/159 Jessica Robertson 1.11513641206121e-13 2.48834725091373e-12 15 268.545454545455 204 1.01376037460115e-14 7 2.24145224551877 2.37949810225555 1 6.69020179539577 40 788 204 425 517 11 32 7 634 283 13 100 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 53/129 John Newman 5.82760922061739e-09 5.04772214562165e-08 520 330.272727272727 208 5.29782657823112e-10 42 1.96424358953185 2.19267077640763 1 3.68665649828638 208 520 617 199 581 126 205 42 519 537 79 101 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 136/274 Kevin Vogelsang 2.89189956955202e-21 1.715372326952e-19 170 332 212 2.62899960868365e-22 49 2.18476779840306 2.32896752950078 1 10.5455050520918 170 49 75 138 916 177 321 509 776 212 309 102 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 64/180 John Newman 3.96299505045802e-18 1.71949951911539e-16 140 371.545454545455 212 3.60272277314363e-19 13 2.77227145119121 2.75795624325784 1 11.2413205650781 13 791 103 288 1625 66 137 430 282 140 212 103 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 35/134 Leona Saunders 7.55882576989929e-12 1.28802391119084e-10 400 229.727272727273 214 6.87165979084116e-13 139 2.77948588410972 3.17163399789209 1 7.07070602333558 398 149 268 244 289 214 152 169 187 318 139 104 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 16/34 Jessica Robertson 4.25209757456027e-15 1.23473751943219e-13 210 391.636363636364 216 3.86554324960026e-16 78 3.24226753034554 3.43165118896649 1 10.7651675946801 85 206 155 231 1681 216 208 622 78 243 583 105 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 162/415 Arthur Liberzon 2.29415623585961e-24 1.99081780022928e-22 100 275.909090909091 216 2.08559657805419e-25 53 2.28400064374457 2.57323290012463 1 12.748938325708 96 763 53 329 239 120 216 368 687 86 78 106 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 27/56 Leona Saunders 1.10699490174392e-08 7.53979376391282e-08 170 441.636363636364 220 1.00635900664917e-09 13 2.24168252182653 2.41669861370096 1 4.10689688814102 168 1273 828 932 402 23 13 64 220 908 27 107 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 31/77 Leona Saunders 3.32304957989987e-09 3.32021542247565e-08 225 251.909090909091 221 3.02095416810843e-10 6 2.39882555991778 2.988280303378 1 4.61456975517799 590 160 395 134 223 345 195 148 221 354 6 108 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 258/674 Arthur Liberzon 1.19192277134582e-39 2.65969052691739e-37 30 389.090909090909 222 1.08356615576893e-40 20 2.26055637450108 2.38142933263975 1 21.2667128533186 30 463 20 277 1336 130 222 489 1051 51 211 109 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 61/132 Arthur Liberzon 3.48882177583491e-17 1.39731784970619e-15 220 422.727272727273 223 3.1716561598499e-18 75 2.40495632119571 2.58996220260263 1 9.18903483198676 75 328 112 537 1448 223 220 80 1091 218 318 110 M53 PID_INTEGRIN3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN3_PATHWAY.html Beta3 integrin cell surface interactions 18832364 34/73 Pathway Interaction Database 8.97166243807042e-13 1.77389072509696e-11 70 360.909090909091 224 8.15605676188555e-14 69 2.50556682257633 2.57144254806818 1 6.92877537048236 69 151 231 469 1496 106 125 208 507 224 384 111 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 72/199 Jessica Robertson 6.14848449422257e-15 1.7248989899571e-13 285 258.363636363636 225 5.58953135838415e-16 43 2.35661743671124 2.58645624362438 1 7.73657205887957 284 87 161 43 471 217 341 225 622 256 135 112 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 28/47 John Newman 1.514125602962e-09 1.70148503009111e-08 225 353.181818181818 225 1.3764778218219e-10 19 2.08650423414628 2.27641043053535 1 4.16958341174671 225 818 612 462 150 122 183 19 429 793 72 113 M198 PID_SYNDECAN_1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_1_PATHWAY.html Syndecan-1-mediated signaling events 18832364 30/61 Pathway Interaction Database 4.38266420500893e-09 4.07483421918092e-08 135 391.818181818182 226 3.98424019430883e-10 118 3.23225091723198 3.38246789158177 1 6.14386576843735 134 369 406 158 1637 194 219 252 118 597 226 114 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 37/163 Arthur Liberzon 1.05648203681103e-13 2.38013212716176e-12 115 277.545454545455 226 9.60438215282799e-15 38 2.95705816859048 3.06120063787547 1 8.84080252880809 113 534 202 293 818 70 38 150 226 370 239 115 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 34/100 Jessica Robertson 5.73786361140975e-13 1.15894952082181e-11 120 326.636363636364 226 5.21623964673749e-14 20 2.57430512519732 2.58453676776195 1 7.24126826658439 118 681 226 20 306 35 53 504 1244 365 41 116 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 238/587 Yujin Hoshida 5.69541216527108e-51 2.96541126738447e-48 180 265.545454545455 227 5.17764742297376e-52 9 2.47001784637067 2.6810271968743 1 30.1958695546855 177 24 9 106 609 260 406 227 557 13 533 117 M15394 BIOCARTA_AMI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AMI_PATHWAY.html Acute Myocardial Infarction 13/34 BioCarta 6.11318359063014e-13 1.22420420109798e-11 285 350.545454545455 228 5.55743962784713e-14 37 3.04775946416375 3.17995835788288 1 8.55439973407067 282 218 228 234 1652 136 77 475 37 192 325 118 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 36/78 Arthur Liberzon 2.22609080308077e-21 1.33736685938929e-19 55 355.909090909091 228 2.02371891189161e-22 52 2.71627979830548 2.86469521427668 1 13.1865556272714 52 349 74 327 1422 193 228 558 198 57 457 119 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 26/106 Arthur Liberzon 3.26959671563341e-14 8.16612819490704e-13 185 346.363636363636 228 2.97236065057587e-15 139 2.64045133525766 2.86209814654079 1 8.20976479693302 325 169 182 287 1167 185 139 487 228 206 435 120 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 4/11 Arthur Liberzon 3.45041196185334e-09 3.39886048012754e-08 415 769.181818181818 231 3.45041196721075e-10 28 2.76467178585224 2.76467178585224 1 5.31111039841949 415 435 4603 142 1590 168 45 35 28 769 231 121 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 23/53 John Newman 8.49973868180835e-11 1.19608935324186e-09 375 256.636363636364 233 7.72703516557886e-12 54 2.59286587980439 2.56182322954011 1 5.9504861836866 74 373 323 338 691 54 65 373 106 193 233 122 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 553/1553 Jessica Robertson 3.60115402510106e-43 1.05716996798728e-40 5 643.090909090909 236 3.60115402510106e-44 2 2.16054379343219 2.32910873786434 1 22.2156754383938 236 3 4554 2 134 288 400 192 950 2 313 123 M3228 KEGG_SMALL_CELL_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SMALL_CELL_LUNG_CANCER.html Small cell lung cancer 55/124 KEGG 3.35637806426084e-09 3.33927550087607e-08 195 392.454545454545 237 3.05125279034675e-10 29 2.44536481285642 2.65426240507023 1 4.7025326742571 195 797 527 93 1249 123 237 29 473 437 157 124 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 32/76 Jessica Robertson 5.13949778823268e-10 6.42231643617556e-09 360 274.272727272727 238 4.67227071766668e-11 80 2.58205880420092 2.72045633147939 1 5.44090431773925 136 360 356 80 548 200 149 204 276 470 238 125 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 69/173 John Newman 1.22405725654675e-09 1.41627958127853e-08 230 327.454545454545 240 1.11277932475254e-10 64 2.38602083546961 2.50165617812457 1 4.81702595865597 228 1020 373 405 117 74 202 240 408 471 64 126 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 297/758 Arthur Liberzon 1.67681746705261e-37 3.27398610442021e-35 90 363.454545454545 241 1.52437951550238e-38 23 2.2832299260858 2.3925545004014 1 20.2524512493998 86 998 23 112 826 147 278 345 896 46 241 127 M15997 BIOCARTA_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTRINSIC_PATHWAY.html Intrinsic Prothrombin Activation Pathway 14/36 BioCarta 2.78050348808012e-14 7.08121703540406e-13 280 369.090909090909 242 2.52773044370923e-15 63 3.20225458927934 3.36535250802158 1 10.0075313112065 277 403 179 235 1733 165 95 290 63 242 378 128 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 131/342 Arthur Liberzon 1.2051214027542e-16 4.44661330181589e-15 185 443 242 1.09556491159473e-17 115 2.04097859511626 2.15525986567761 1 7.53439984453617 184 767 122 690 115 242 347 234 1753 165 254 129 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 44/93 John Newman 3.00313040556288e-15 8.79541817529228e-14 95 445.545454545455 242 2.73011855051171e-16 90 2.77436503430224 2.93124037189764 1 9.31673817821479 92 526 154 594 1903 174 90 458 242 215 453 130 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 81/220 Jessica Robertson 9.76903496600818e-19 4.44443668453537e-17 160 364.636363636364 245 8.88094087818923e-20 98 2.49820023263153 2.66071468428461 1 10.5075549762834 188 502 98 245 908 137 288 356 975 158 156 131 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 70/176 Jessica Robertson 2.10538178459036e-12 3.9150075565835e-11 170 320.818181818182 246 1.91398344053852e-13 12 2.3664458491953 2.59643737308747 1 6.33478615295465 167 90 246 397 1008 210 511 12 579 274 35 132 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 209/649 Jessica Robertson 5.36268827108515e-22 3.44240510113767e-20 70 363.090909090909 247 4.87517115553194e-23 67 2.27728966340387 2.48826393544229 1 11.4006553922325 247 280 70 67 941 151 306 474 1241 107 110 133 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 182/452 Leona Saunders 4.56647696681225e-13 9.38531187126412e-12 225 346.090909090909 248 4.15134269710291e-14 128 1.97936627162174 2.1525618025598 1 5.61440741910365 128 628 222 248 212 202 339 344 919 222 343 134 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 64/152 John Newman 2.32201495184107e-12 4.2838433324123e-11 85 371.636363636364 248 2.1109226834941e-13 43 2.57537315030175 2.66544488562442 1 6.86816624570665 84 1108 248 467 657 84 96 43 739 428 134 135 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 13/29 Yujin Hoshida 3.1976253198441e-10 4.17383628099985e-09 165 344.454545454545 251 2.9069321093717e-11 54 3.18202116155607 3.3603234600226 1 6.85832417611398 161 578 345 175 1280 162 54 251 115 411 257 136 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 427/1212 Jessica Robertson 1.17874103011615e-36 2.12445402581703e-34 245 393.181818181818 251 1.07158275465104e-37 25 2.12939771923151 2.32493484788518 1 18.4431071360353 242 752 25 139 408 251 282 404 1631 49 142 137 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 71/194 John Newman 6.02436504646184e-09 5.18937033230151e-08 255 377.545454545455 254 5.47669551178059e-10 119 2.04304847409877 2.35953603676134 1 3.82824792950693 221 317 415 254 119 172 251 554 948 668 234 138 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 145/339 Arthur Liberzon 3.84756708264718e-23 2.90801602407817e-21 155 304.545454545455 256 3.49778825695198e-24 48 2.17942117008239 2.41245222860571 1 11.5123564746401 155 48 60 458 67 393 602 256 752 53 506 139 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 28/61 Leona Saunders 9.07961470490271e-09 6.84036567639455e-08 260 596.727272727273 256 8.25419522034108e-10 30 1.93333622071109 2.08922171665276 1 3.56301325129585 256 1400 1039 823 211 112 44 197 1284 1168 30 140 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 24/59 Leona Saunders 1.1537198721675e-07 3.645536966269e-07 175 432.545454545455 258 1.04883630242788e-08 87 2.79938017284971 2.97619326348539 1 4.63583117681087 172 698 499 258 1356 167 87 243 410 744 124 141 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 42/104 Arthur Liberzon 4.99402678356982e-09 4.50905770863356e-08 260 410.636363636364 259 4.54002435900574e-10 54 1.86294049534614 2.03663829194965 1 3.52000676350884 259 352 616 696 87 156 122 54 1504 505 166 142 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 14/25 Arthur Liberzon 8.93814300980729e-09 6.76641973246477e-08 165 304.090909090909 261 8.12558458738282e-10 110 2.8193589002605 2.91216102314078 1 5.19931883097977 164 220 421 198 661 134 303 526 110 347 261 143 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 49/113 Jean Junior 3.27268480767533e-08 1.46656420133261e-07 120 410.272727272727 262 2.97516805123571e-09 82 2.49166297600328 2.70619823099135 1 4.37969439752875 119 343 465 82 1901 239 217 224 278 383 262 144 M8821 REACTOME_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AXON_GUIDANCE.html Genes involved in Axon guidance 124/342 Reactome 5.61467159371921e-09 4.9362760015325e-08 90 396.636363636364 263 5.10424691640777e-10 87 2.23387850366317 2.58920960555559 1 4.19830109542174 263 1306 482 87 105 90 194 366 720 641 109 145 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 74/171 John Newman 1.92045749080727e-23 1.55159720722808e-21 265 343.909090909091 263 1.74587044618843e-24 35 2.47078627008696 2.58602448165025 1 13.2248174016344 110 80 56 35 766 264 263 759 885 105 460 146 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 58/146 Arthur Liberzon 7.13317787292017e-12 1.2288996879597e-10 165 387 265 6.48470715722117e-13 15 2.08286361327967 2.12172861780924 1 5.30950886873333 163 114 265 501 469 83 242 326 1754 325 15 147 M4680 DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_UP.html Genes up-regulated in RD cells (embryonal rhabdomyosarcoma, ERMS) by expression of PAX3- or PAX7-FOXO1 [GeneID=5077;5081;2308] fusions off retroviral vectors. 16849537 186/462 Arthur Liberzon 5.39328806798594e-15 1.53169381130801e-13 210 381 266 4.9029891527145e-16 57 2.02235995058794 2.22540289254701 1 6.66607068453024 210 475 159 242 723 266 468 57 1135 169 287 148 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 34/71 Leona Saunders 3.16788360657112e-09 3.23658762261479e-08 115 338.363636363636 268 2.87989419193882e-10 5 2.72806701709447 2.72806701709447 1 5.25569867922727 112 1267 446 268 568 5 7 94 383 529 43 149 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. 197/546 Charles Durand 2.88297821864614e-27 2.8743906239523e-25 50 309.818181818182 268 2.6208892896783e-28 32 2.1132807635964 2.26670626068356 1 13.3400106263724 46 32 46 374 385 247 268 463 981 39 527 150 M5883 NABA_SECRETED_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_SECRETED_FACTORS.html Genes encoding secreted soluble factors 22159717 89/379 Alexandra Naba 3.97783971187688e-23 2.95875506188176e-21 270 358.454545454545 268 3.61621791988808e-24 61 2.37193643820657 2.40778378985953 1 12.5246966846869 268 645 61 218 759 148 310 443 813 95 183 151 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 90/256 Arthur Liberzon 2.80881118205772e-13 5.90228215207285e-12 255 403.272727272727 269 2.55346471096189e-14 74 2.37613895621837 2.56689915676189 1 6.86294976264886 255 1096 217 74 976 153 269 321 667 287 121 152 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 53/124 Leona Saunders 1.84437887548419e-08 1.00849001289602e-07 210 453.363636363636 270 1.67670808267873e-09 108 1.8456058680312 2.10247753356659 1 3.32129774113774 234 117 439 837 828 206 210 108 1266 472 270 153 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 42/98 John Newman 2.26783092851889e-08 1.14630899676912e-07 100 383.545454545455 270 2.06166450172402e-09 23 2.42872121739676 2.49243967593573 1 4.33590243613193 99 929 614 270 984 85 23 209 257 419 330 154 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 63/154 John Newman 4.05148036001742e-09 3.85878800143122e-08 190 368.818181818182 271 3.68316397043506e-10 83 2.3187180299774 2.5322325643971 1 4.42153201928468 186 106 400 83 1398 269 180 271 384 481 299 155 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 128/271 Kevin Vogelsang 2.89255321843578e-15 8.52484552301261e-14 140 510.545454545455 272 2.62959383494161e-16 138 2.4162175998788 2.57829578511358 1 8.12245841159351 138 899 153 301 1750 248 173 544 870 272 268 156 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 240/771 Arthur Liberzon 3.82653979823891e-16 1.33814667869758e-14 335 389.727272727273 274 3.47867254385355e-17 113 1.90243078478251 2.20360362507586 1 6.78880700582577 334 467 129 226 113 274 745 161 1379 175 284 157 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 21/64 Yaara Zwang 1.16044892055857e-09 1.34878851814819e-08 455 352.909090909091 275 1.05495356470061e-10 15 2.43025562727995 2.83851326761748 1 4.91958488063954 453 194 601 380 464 240 252 15 275 937 71 158 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 51/114 Reactome 3.49303721894345e-12 6.17674430489397e-11 75 357 276 3.17548838086273e-13 68 2.46611056343579 2.6085556644355 1 6.47596730936921 72 119 259 68 1424 146 276 385 431 359 388 159 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 493/1207 Arthur Liberzon 2.62659080731651e-32 3.418945700857e-30 280 332.181818181818 276 2.38780982483319e-33 35 1.85156402223852 2.00814989390676 1 14.0333122723423 58 449 35 276 237 186 427 300 1363 47 276 160 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 14/37 Arthur Liberzon 5.09104053383467e-09 4.57900497918412e-08 90 337.454545454545 279 4.62821867783262e-10 86 3.04607448761852 3.04607448761852 1 5.75028836635132 87 410 409 201 1180 95 86 481 136 348 279 161 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 224/604 Arthur Liberzon 6.14088298574232e-54 4.79602961186475e-51 280 478.454545454545 281 5.58262089612938e-55 4 2.28618955731248 2.4209582812842 1 29.5899304349716 4 278 6 590 1783 280 281 479 1104 7 451 162 M12868 KEGG_PATHWAYS_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PATHWAYS_IN_CANCER.html Pathways in cancer 189/425 KEGG 9.76194928334612e-12 1.63373194077714e-10 440 415.181818181818 282 8.87449934853585e-13 90 2.1190236618684 2.42063317284317 1 5.33428288675843 436 282 272 90 258 770 758 113 862 184 542 163 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 105/245 Leona Saunders 5.39361895832648e-19 2.55297964027454e-17 285 354.909090909091 283 4.90328996211497e-20 81 2.13260571915321 2.28185742715759 1 9.10191808038532 148 296 94 593 531 176 283 171 1246 81 285 164 M14072 WINTER_HYPOXIA_METAGENE http://www.broadinstitute.org/gsea/msigdb/cards/WINTER_HYPOXIA_METAGENE.html Genes regulated by hypoxia, based on literature searches. 17409455 178/364 Jessica Robertson 3.23581551435693e-10 4.21195319452128e-09 215 492.272727272727 284 2.94165046802988e-11 20 2.05976766245641 2.31519574883118 1 4.43739919836347 212 1650 346 522 284 68 247 175 1388 503 20 165 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 79/190 Arthur Liberzon 7.34979023049036e-22 4.65420500271322e-20 95 411.454545454545 284 6.68162748226397e-23 59 2.43510653855596 2.68344331377546 1 12.1086828826312 93 79 71 284 1489 326 267 608 681 59 569 166 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 20/55 Leona Saunders 1.45360350926189e-17 5.97507547754494e-16 30 549 284 1.32145773569262e-18 29 3.18002010525084 3.18002010525084 1 12.4522412656565 29 946 109 494 2508 284 186 586 141 130 626 167 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 62/139 Arthur Liberzon 1.64572966312689e-14 4.35699954882069e-13 240 378.454545454545 286 1.49611787556991e-15 105 2.63921786261065 2.80971344658218 1 8.39113944406828 240 105 172 143 257 298 348 1197 496 286 621 168 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 164/615 Jessica Robertson 2.28702982123255e-08 1.15236792927911e-07 265 373.636363636364 286 2.07911804091598e-09 55 1.90859922382917 2.12745913739557 1 3.40622468032402 265 286 447 171 761 127 332 270 927 469 55 169 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 66/161 Kevin Vogelsang 1.43568779369837e-09 1.62802597505962e-08 290 314.454545454545 288 1.30517072239571e-10 64 2.4636717609203 2.73563307864033 1 4.93544531471634 303 322 379 64 265 283 632 162 286 475 288 170 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 70/149 Arthur Liberzon 9.1673795858911e-17 3.49254802760046e-15 40 349.636363636364 288 8.33398144171914e-18 39 2.79604070753547 2.94668853373519 1 10.397192239153 39 657 118 144 680 249 439 508 288 221 503 171 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 47/126 Leona Saunders 2.18713994010102e-11 3.4508207943816e-10 195 402.090909090909 289 1.98830903647524e-12 85 2.37188221412859 2.35780930097227 1 5.77269080791093 193 125 289 381 181 346 565 601 1378 279 85 172 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 46/136 Arthur Liberzon 1.50678377804506e-09 1.70139488769137e-08 205 488.636363636364 290 1.3698034355246e-10 18 2.55135967838348 2.71765984453469 1 5.09854637392308 204 666 515 445 1758 255 150 18 290 873 201 173 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 52/122 Jessica Robertson 2.1470653098402e-11 3.39903650064567e-10 340 291.545454545455 290 1.95187755441924e-12 105 2.44566354913488 2.61491833530164 1 5.95639075152861 244 339 288 290 616 205 338 105 328 322 132 174 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 38/88 Leona Saunders 6.99795314884824e-12 1.21005197252778e-10 265 466.727272727273 291 6.36177558988228e-13 127 2.80139000281621 3.18913909034397 1 7.1459693023571 158 669 264 291 1622 458 270 403 127 264 608 175 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 12/26 Arthur Liberzon 2.47119600420624e-11 3.87291788485298e-10 315 376.909090909091 291 2.2465418220309e-12 88 3.4905446198919 3.54011489919135 1 8.45029798757834 314 414 291 88 1183 225 290 446 217 493 185 176 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 240/952 Jessica Robertson 3.60962857187291e-43 1.05716996798728e-40 80 306 292 3.28148051988446e-44 15 2.30868313437063 2.4163905434043 1 23.7389102645481 77 276 15 107 292 338 440 353 1036 21 411 177 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 13/54 Jessica Robertson 1.56717182595677e-08 9.08698406718676e-08 80 525.909090909091 292 1.42470167010957e-09 18 2.45551704995143 2.45551704995143 1 4.44745696580282 166 1216 825 917 1141 78 18 77 292 1009 46 178 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 16/37 Arthur Liberzon 5.56645303408205e-08 2.11724017189192e-07 225 522.545454545455 293 5.06041197720434e-09 40 2.50251624985164 2.50251624985164 1 4.29612327209778 222 1409 918 622 974 105 40 172 293 783 210 179 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 315/1178 Alexandra Naba 4.59543559347057e-77 1.07671055955015e-73 5 291.909090909091 296 4.17766872133687e-78 2 2.36742115260626 2.4937532387108 1 44.4330437672545 47 266 2 273 309 299 372 296 879 3 465 180 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 185/494 Arthur Liberzon 5.35729668374392e-51 2.96541126738447e-48 10 281.181818181818 297 4.87026971249452e-52 7 2.38970100125284 2.52458754648426 1 29.2139993228812 7 30 8 370 804 170 314 297 695 11 387 181 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 69/177 Kevin Vogelsang 3.24901781434355e-11 4.94314853182269e-10 200 329.454545454545 300 2.95365255853775e-12 160 2.32031664517879 2.69203269170665 1 5.55403747070709 197 653 300 160 508 160 197 565 301 207 376 182 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 33/75 Lauren Kazmierski 2.53214206113922e-08 1.22074256157391e-07 235 393.909090909091 303 2.3019473548032e-09 95 1.99543153723432 2.03818345285496 1 3.54834359579181 232 154 479 497 867 149 133 95 1089 335 303 183 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 67/135 Jessica Robertson 8.70953829853013e-14 2.0006321797506e-12 305 325.545454545455 303 7.91776208957314e-15 101 2.59754869652812 2.85475098729512 1 7.8163663723491 301 101 199 172 303 312 142 480 702 497 372 184 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 188/435 Chi Dang 3.27577106526403e-13 6.85279607670859e-12 165 382.363636363636 303 2.97797369569501e-14 165 1.87738362172161 2.08681438437019 1 5.39109105395792 165 474 218 303 384 236 391 317 1300 246 172 185 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 42/92 Leona Saunders 5.16420807166546e-10 6.43603165527244e-09 40 333.636363636364 306 4.69473461170698e-11 31 2.27805957273304 2.34753797288432 1 4.79977541878578 36 132 357 574 1093 56 31 306 637 351 97 186 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 12/24 Jessica Robertson 4.66919841338873e-11 6.96810947934381e-10 355 376.818181818182 306 4.24472583044348e-12 77 3.26043421609961 3.54011489919135 1 7.67930436379567 352 225 306 77 1268 237 128 589 93 350 520 187 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 85/230 Arthur Liberzon 8.7878298576374e-09 6.69372030380271e-08 205 433.090909090909 307 7.98893626612737e-10 32 1.97661575335091 2.06613167842633 1 3.64755973472148 203 1098 575 714 307 37 154 52 1016 576 32 188 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 57/169 Yujin Hoshida 1.62829642942812e-15 4.98705690738574e-14 215 346.818181818182 308 1.48026948129829e-16 53 2.66402237729282 2.83911988954065 1 9.11503989142931 213 112 147 53 477 462 215 645 578 308 605 189 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 21/46 Jessica Robertson 2.2160991992925e-08 1.13263174329229e-07 365 478.181818181818 308 2.01463565601424e-09 143 1.84484454858672 1.84455120437155 1 3.29600354053183 362 193 1026 961 575 263 254 143 239 936 308 190 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 51/110 Arthur Liberzon 3.09520047001505e-12 5.5785036163425e-11 35 484.272727272727 309 2.81381860910855e-13 33 2.43216439727366 2.46622339828357 1 6.41450262025825 33 663 254 510 1877 117 36 309 875 360 293 191 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 33/77 Arthur Liberzon 5.08718967734611e-11 7.49640592076852e-10 120 509.272727272727 309 4.6247178886034e-12 91 2.95691150325202 3.05069730125196 1 6.94027800983026 117 811 309 584 1965 125 91 743 381 270 206 192 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 50/150 Arthur Liberzon 7.83677695507785e-16 2.55021783413158e-14 300 417.636363636364 310 7.12434268643439e-17 113 2.58424032370378 3.00146059426518 1 9.03567081283473 297 113 139 454 1267 483 615 310 281 225 410 193 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 71/170 Arthur Liberzon 2.56961634608235e-11 3.98715966812645e-10 160 614.090909090909 310 2.33601486010215e-12 159 2.33993135463636 2.4467649881571 1 5.65716676963058 159 1707 294 1187 708 233 225 250 1294 388 310 194 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 29/87 Jessica Robertson 3.06955543685687e-10 4.01785943494728e-09 125 424 311 2.7905049429865e-11 122 2.40663239735817 2.54468219242017 1 5.19734004438646 122 547 344 125 1296 131 311 279 797 466 246 195 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 42/118 Arthur Liberzon 3.61840550184274e-13 7.50258769098898e-12 155 389.181818181818 314 3.2894595471303e-14 131 2.92052235956659 3.11856458937177 1 8.35701137242852 152 351 220 131 1224 212 547 465 373 292 314 196 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 70/163 Kevin Vogelsang 4.51845725062381e-09 4.17541107967623e-08 225 312.090909090909 314 4.10768841809455e-10 75 2.17972977477258 2.33529738599036 1 4.13729544292525 224 93 553 195 75 441 475 155 314 487 421 197 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 46/228 Jessica Robertson 7.3080122737863e-11 1.04089196094111e-09 180 360.909090909091 315 6.64364752184461e-12 119 2.59700109009906 2.65040522024417 1 6.00029486714558 178 804 320 331 988 169 315 154 119 446 146 198 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 30/76 John Newman 7.41847546112259e-09 6.00396822293963e-08 80 355.454545454545 315 6.74406862376175e-10 63 2.72782362069412 2.74463671393035 1 5.06694368691752 346 1044 584 366 164 77 80 315 273 598 63 199 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 57/129 Jessica Robertson 7.27167392515072e-12 1.24361547493636e-10 270 350.454545454545 317 6.6106126592498e-13 176 2.26232667114471 2.40437806572746 1 5.76397688903083 267 332 267 390 244 317 461 537 597 176 267 200 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 35/80 Arthur Liberzon 3.60259699331803e-09 3.52437776841092e-08 295 398.181818181818 319 3.27508818110676e-10 24 2.72998660659458 3.01548718473805 1 5.23341897194434 294 1125 523 736 319 115 162 33 365 684 24 201 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 87/284 Arthur Liberzon 4.56762498684914e-20 2.43226030549717e-18 160 440.818181818182 319 4.15238635168101e-21 18 2.4226351268654 2.83019591044881 1 10.9760085051635 160 306 83 18 1711 513 497 319 369 162 711 202 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 35/96 Arthur Liberzon 5.71976636618197e-08 2.15110956596538e-07 180 408.727272727273 319 5.19978774080894e-09 100 2.60107521737927 2.85077014869962 1 4.46071028188522 176 362 480 162 1816 189 100 379 130 319 383 203 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 21/48 Leona Saunders 2.63529759095222e-09 2.74876066106578e-08 200 379 320 2.39572508555359e-10 31 2.8736135745754 3.0457241897009 1 5.58854062424684 196 702 688 320 31 173 138 756 92 739 334 204 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 24/105 Jessica Robertson 7.5562473666171e-11 1.07298712605963e-09 320 401.181818181818 321 6.86931578806967e-12 79 2.88756998264616 2.98136119110552 1 6.66185003186365 316 553 321 475 1324 102 79 351 439 300 153 205 M9143 FRIDMAN_SENESCENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_SENESCENCE_UP.html Genes up-regulated in senescent cells. 18711403 68/146 Jessica Robertson 7.96571543465642e-11 1.12431754598795e-09 325 327.181818181818 322 7.2415594863135e-12 20 2.36549639159547 2.71538612551563 1 5.44503727980813 324 92 322 58 722 509 686 20 259 444 163 206 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 411/1473 Jessica Robertson 1.67698544079181e-53 1.12262196793577e-50 10 407 322 1.52453221890166e-54 7 2.1455726185652 2.28832114733899 1 27.5661024614656 130 996 7 274 411 258 421 407 1243 8 322 207 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 106/239 Arthur Liberzon 2.80490111796009e-10 3.68172734979299e-09 200 308.272727272727 323 2.54991010756155e-11 64 2.03132237347365 2.21660929449015 1 4.40664899220031 200 64 343 151 421 285 249 505 483 367 323 208 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 208/507 John Newman 3.31768760658351e-21 1.94333551555629e-19 515 329 326 3.01607964234864e-22 29 2.26343242418811 2.56732235010359 1 10.8936572908275 326 281 76 29 304 512 641 382 512 87 469 209 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 23/60 Jessica Robertson 2.2695444828699e-09 2.41158400152571e-08 105 384.636363636364 327 2.0632222592829e-10 59 2.9360774832765 3.12277248790342 1 5.75294092408351 104 383 389 256 1582 59 109 334 327 539 149 210 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 28/82 John Newman 1.02732187151262e-08 7.26051267693284e-08 425 345 328 9.33928978463502e-10 22 3.01294273658341 3.08380699366607 1 5.53259553668184 423 826 531 98 253 175 159 328 337 643 22 211 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 364/905 Jessica Robertson 2.31148673961082e-34 3.38488339431759e-32 245 338.909090909091 328 2.10135158146439e-35 12 2.01071149902279 2.2013066819023 1 16.2761425519966 245 12 31 221 447 328 582 521 838 28 475 212 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 76/179 Jessica Robertson 1.1641363652176e-10 1.6139476353283e-09 535 361.636363636364 328 1.05830578661745e-11 83 2.16464317478643 2.82605064216616 1 4.89528664738791 494 83 328 299 165 421 533 156 534 271 694 213 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 187/480 Arthur Liberzon 5.73915119734399e-14 1.36516053354081e-12 485 356.727272727273 328 5.21741017940377e-15 34 2.02431480868733 2.47007001106972 1 6.17785547253599 484 34 192 111 131 565 795 307 560 328 417 214 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 3/11 Leona Saunders 7.85504535239335e-11 1.11204660185242e-09 5 910.727272727273 329 7.85504535267101e-12 2 2.42858206718182 2.42858206718182 1 5.59322874897278 574 881 4293 116 1938 329 126 2 3 1752 4 215 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 25/59 Arthur Liberzon 1.68965542759764e-11 2.73025011507673e-10 475 438 330 1.53605038873692e-12 71 3.01913305782204 3.28318927035539 1 7.42696376662664 473 375 282 71 1466 330 177 629 294 410 311 216 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 121/262 Arthur Liberzon 1.21808278495277e-08 7.94977149065274e-08 320 332.545454545455 330 1.1073479924518e-09 107 2.06731885555631 2.45006210525495 1 3.77522452412455 317 491 452 168 330 139 356 185 532 581 107 217 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 35/86 Jessica Robertson 6.04852027894233e-09 5.20061761965574e-08 330 309.181818181818 330 5.4986548141561e-10 98 2.16478489069605 2.47989240045919 1 4.05583311532228 330 152 521 359 120 98 123 377 771 390 160 218 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 52/147 Yujin Hoshida 4.58704672266319e-17 1.80629419684031e-15 115 362.545454545455 330 4.17004247514836e-18 22 2.90160336416408 3.12242909856904 1 11.003448701078 566 111 114 22 931 361 926 330 167 125 335 219 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 138/361 Arthur Liberzon 3.9191014135067e-43 1.08028877786426e-40 15 378.090909090909 331 3.56281946682431e-44 11 2.54337345989532 2.7119633930562 1 26.1459547308882 11 632 16 216 907 268 331 528 761 45 444 220 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 165/530 John Newman 1.35294394583228e-09 1.54631593418782e-08 465 388.090909090909 331 1.22994904242209e-10 43 1.809028344825 2.02199217644835 1 3.6344114422352 465 43 377 230 331 276 768 145 866 326 442 221 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 18/42 Jessica Robertson 2.51416598425503e-11 3.92712726740636e-10 210 375.090909090909 331 2.28560544025796e-12 128 2.85600797367862 2.86365270017479 1 6.90970655654027 206 391 292 343 953 309 279 400 128 331 494 222 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 159/697 Jessica Robertson 1.39436037208933e-36 2.41998989022615e-34 425 401.090909090909 332 1.26760033826304e-37 5 2.44482291958367 2.51149314831919 1 21.1394915303915 312 42 26 5 422 332 424 978 1139 31 701 223 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 69/175 John Newman 2.56629845879313e-08 1.2308776435931e-07 425 474.363636363636 333 2.33299862611726e-09 165 2.28297090599436 2.84701600521571 1 4.05754724154655 422 1106 666 206 645 315 333 167 271 922 165 224 M7253 KEGG_FOCAL_ADHESION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOCAL_ADHESION.html Focal adhesion 101/245 KEGG 1.51239787685106e-10 2.05423085534031e-09 275 401.272727272727 334 1.37490716086821e-11 68 2.18797366520042 2.50444934845498 1 4.88909095957537 271 68 334 92 171 450 978 512 716 306 516 225 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 73/178 Jessica Robertson 1.43829187764244e-19 7.02066222774217e-18 280 397 334 1.30753807058403e-20 91 2.64148840981157 2.81210343518424 1 11.6547570376625 276 507 91 155 887 253 334 923 405 99 437 226 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 35/139 Leona Saunders 6.87366059244789e-09 5.72113206682253e-08 215 549.545454545455 336 6.24878237629444e-10 145 2.16491039683692 2.19819754905088 1 4.03299958374301 278 936 513 954 145 213 213 336 1771 317 369 227 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 60/144 Jessica Robertson 2.9805911408898e-12 5.39268343096896e-11 180 416.727272727273 336 2.70962830990349e-13 165 2.69052130392587 2.84983377872965 1 7.10606575910192 180 330 253 165 1350 336 425 283 562 358 342 228 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 91/298 Arthur Liberzon 8.57081534029309e-15 2.32155148465973e-13 530 403.545454545455 340 7.79165030935738e-16 61 2.04337380442258 2.30156697739127 1 6.64041144706426 529 72 168 282 340 689 786 61 708 147 657 229 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 13/32 Arthur Liberzon 1.19039753346168e-07 3.73123935906451e-07 100 398.090909090909 341 1.08217963442989e-08 86 3.009288532502 3.25900535745741 1 4.97563246739352 249 579 507 360 1315 96 97 341 86 550 199 230 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 324/768 Aravind Subramanian 3.68232604293518e-36 5.95013097834284e-34 345 388.545454545455 342 3.34756912994111e-37 16 2.01741668379222 2.23768611067399 1 17.2411198339178 341 16 28 16 812 474 531 342 1236 33 445 231 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 23/55 John Newman 3.62942382575081e-08 1.5764214383481e-07 175 421.272727272727 343 3.29947625966073e-09 148 2.70432141473622 2.816148500416 1 4.73167083657863 175 557 468 209 1006 271 161 593 148 343 703 232 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 91/239 Arthur Liberzon 3.22716601776262e-12 5.74999998450024e-11 125 462 344 2.93378728887942e-13 63 2.2974130541799 2.56606008049768 1 6.05134344429827 124 1557 257 63 621 344 558 92 774 391 301 233 M12950 BIOCARTA_ACE2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACE2_PATHWAY.html Angiotensin-converting enzyme 2 regulates heart function 10/27 BioCarta 3.71759105385522e-12 6.52458115294591e-11 235 372.272727272727 345 3.37962823078318e-13 26 3.57261085066806 3.54011489919135 1 9.35975543385784 235 420 261 180 756 238 378 748 26 345 508 234 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 23/59 Arthur Liberzon 2.62722567195845e-10 3.46793788698516e-09 345 448.909090909091 345 2.3883869747929e-11 179 2.91581782753549 3.06745244724483 1 6.34491434881027 513 179 341 342 762 529 345 445 185 342 955 235 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 61/168 Arthur Liberzon 5.62318617440872e-14 1.34440053128976e-12 335 514.090909090909 347 5.11198743128077e-15 36 2.77446281554581 3.27704607021606 1 8.47192562973471 335 107 191 36 1642 809 865 347 452 324 547 236 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 442/1581 Jessica Robertson 2.72659970016594e-38 5.55515051955548e-36 25 430.545454545455 347 2.47872700015086e-39 22 2.12403898777772 2.31326398878541 1 19.2613017289738 427 751 22 114 705 347 611 136 1418 23 182 237 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 269/856 Arthur Liberzon 4.26861882518172e-15 1.23473751943219e-13 350 449.727272727273 349 3.88056256834703e-16 118 1.93156885655645 2.15742141986243 1 6.41330858324448 349 620 156 339 391 215 681 361 1527 190 118 238 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 68/206 Arthur Liberzon 3.77045281711783e-10 4.8406416167162e-09 445 338.272727272727 350 3.42768437978549e-11 118 2.10806673738076 2.4134865379014 1 4.50868970842645 443 315 350 464 118 180 294 412 454 518 173 239 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 342/636 Jessica Robertson 5.09535631949569e-10 6.38418174148578e-09 355 391.727272727273 352 4.63214210970528e-11 44 1.75810655011779 2.05819991395671 1 3.70584488138106 275 455 355 44 153 533 708 153 977 352 304 240 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 36/74 Arthur Liberzon 1.35343788055383e-14 3.62411994758585e-13 360 337.363636363636 353 1.23039807323076e-15 33 2.78954526760635 3.21312460176222 1 8.92648153751758 356 353 170 33 1074 403 459 109 180 213 361 241 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 17/40 Leona Saunders 2.96066179693327e-08 1.36339724791565e-07 455 373.363636363636 354 2.69151076070594e-09 85 2.76502089711691 3.12703002323693 1 4.88271657835238 452 207 562 310 701 422 117 237 85 660 354 242 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 47/123 John Newman 2.43602551452678e-07 6.72458288635038e-07 355 719 354 2.21456889478555e-08 223 2.26495967340252 2.4688165065168 1 3.59590824765184 354 1118 941 807 1887 340 257 269 223 1439 274 243 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 35/64 Arthur Liberzon 1.09025390776132e-11 1.80527555186204e-10 390 360.181818181818 355 9.91139916151571e-13 48 2.77144675956195 3.06053088941481 1 6.9457359081023 388 355 275 48 874 478 616 87 231 252 358 244 M10508 HARRIS_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/HARRIS_HYPOXIA.html Genes known to be induced by hypoxia 11902584 72/148 John Newman 1.11235531392909e-08 7.5434715428961e-08 195 539 355 1.01123210868485e-09 16 2.27255118543057 2.52405539649475 1 4.16332633608131 192 2087 537 744 355 52 155 72 1020 699 16 245 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 39/88 Leona Saunders 1.94541245345489e-07 5.56205171256229e-07 235 569.636363636364 356 1.76855693225775e-08 147 2.00989246219257 2.07955875414754 1 3.2335715693617 231 356 686 207 1482 192 248 683 1313 721 147 246 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 148/368 Arthur Liberzon 2.32578809114177e-22 1.53502014015357e-20 270 408.363636363636 357 2.11435281012888e-23 69 2.28098092889756 2.46696857924129 1 11.624920556743 270 633 69 295 715 357 675 473 701 90 214 247 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 15/52 John Newman 3.10271994106945e-09 3.18147607086465e-08 170 431.545454545455 357 2.82065449585937e-10 47 3.12797639044659 3.12797639044659 1 6.03213651885391 169 574 393 357 1696 138 47 440 184 400 349 248 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 326/967 Jessica Robertson 3.50825906339743e-55 3.28794039421607e-52 80 482.363636363636 360 3.18932642127039e-56 5 2.31692017384323 2.45442473054418 1 30.6813344574055 78 456 5 453 1270 305 355 483 1532 9 360 249 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 67/163 Arthur Liberzon 2.61771798489276e-14 6.73990465780631e-13 380 400.090909090909 363 2.3797436226298e-15 78 2.28961202518378 2.4998135990063 1 7.16801971145504 380 91 177 300 1343 407 612 276 374 78 363 250 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 266/753 Arthur Liberzon 7.85813105524211e-41 1.93806326972971e-38 365 338.636363636364 363 7.14375550476558e-42 3 2.07652559098619 2.31501091098516 1 20.1429380089183 363 22 18 3 187 593 701 515 650 14 659 251 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 29/78 Kevin Vogelsang 7.3340025901013e-10 8.90340314435614e-09 190 396.454545454545 364 6.6672750841329e-11 122 2.48983479598296 2.52205891115155 1 5.15571657040455 187 157 364 388 1126 229 187 591 122 372 638 252 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 39/114 Arthur Liberzon 5.82483287378271e-09 5.04772214562165e-08 540 351 365 5.29530262654984e-10 82 2.41531351495768 2.69351464994427 1 4.53326227414842 537 533 489 313 110 365 304 82 446 593 89 253 M695 REACTOME_GLYCOSAMINOGLYCAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSAMINOGLYCAN_METABOLISM.html Genes involved in Glycosaminoglycan metabolism 51/122 Reactome 6.5788767989875e-09 5.52013569317386e-08 230 421.090909090909 366 5.98079710787361e-10 58 1.88931171895766 2.09070944836668 1 3.52713637495272 229 122 504 751 136 366 365 58 1217 421 463 254 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 4/10 Leona Saunders 1.27425905894952e-08 8.0434968418917e-08 370 846.090909090909 368 1.27425906625634e-09 16 2.6955779250803 2.6955779250803 1 4.91898760019239 368 439 4252 498 1528 232 16 134 343 1272 225 255 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 16/34 Arthur Liberzon 9.09740576374505e-10 1.08751131145177e-08 635 525.090909090909 368 8.27036887955184e-11 147 2.47160839282541 2.60708435622759 1 5.06274353503297 147 707 368 634 1646 325 350 633 246 171 549 256 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 120/315 Arthur Liberzon 2.1106663193965e-22 1.412940338956e-20 370 408.272727272727 369 1.91878756308772e-23 57 2.43732494357052 2.80575357967546 1 12.444284083507 369 57 68 279 1139 571 797 188 526 102 395 257 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 39/124 Arthur Liberzon 9.61657051513791e-10 1.14373729527757e-08 520 391.545454545455 369 8.74233683576497e-11 125 2.34020538511798 2.87700488732551 1 4.7804049160683 519 143 369 296 125 611 532 303 166 507 736 258 M17787 REACTOME_GLUCURONIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCURONIDATION.html Genes involved in Glucuronidation 3/23 Reactome 1.58019287828789e-08 9.10797518777006e-08 475 914.090909090909 370 1.58019288952443e-09 1 4.39353459956901 4.39353459956901 1 7.95648141391815 472 745 4085 13 2116 370 224 76 1 1745 208 259 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 41/108 Arthur Liberzon 5.49422958855899e-09 4.85772827395989e-08 370 451.909090909091 370 4.99475418389103e-10 41 2.59886005168114 2.90548974454525 1 4.88889595854482 370 1189 491 434 1122 87 189 41 342 556 150 260 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 439/1630 Jessica Robertson 2.31445479320764e-48 1.0845535160971e-45 195 465.272727272727 372 2.10404981200697e-49 10 2.11357038802879 2.3101845327898 1 24.4448611462069 194 994 10 372 589 313 520 333 1401 12 380 261 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 26/58 Jessica Robertson 2.72329013054315e-08 1.27349290946147e-07 365 544.363636363636 374 2.47571833113968e-09 145 2.40396960666271 2.52267436145948 1 4.26345937454698 399 1526 771 364 675 259 145 255 361 859 374 262 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 15/45 Arthur Liberzon 1.75879341075806e-09 1.94379856670101e-08 450 393 375 1.59890310196739e-10 15 3.27366429836227 3.79329039083413 1 6.49326550796369 450 213 383 176 1382 301 108 375 15 401 519 263 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 46/130 Arthur Liberzon 3.44494327402035e-09 3.39886048012754e-08 380 310.363636363636 377 3.13176661764976e-10 9 2.38060408013639 2.42298466567256 1 4.57329187037689 63 1028 396 377 658 9 46 34 414 380 9 264 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 38/93 John Newman 2.26327621273676e-09 2.41038916656465e-08 340 760.272727272727 377 2.05752383187738e-10 25 2.16298088422856 2.47743017068603 1 4.23825758219963 340 2230 1160 1632 25 377 190 67 432 1616 294 265 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 19/53 Jessica Robertson 8.23891148618388e-08 2.80782103449147e-07 335 721.181818181818 378 7.48991981338892e-09 64 1.75817585684705 1.75817585684705 1 2.96285481683891 331 1579 1574 516 1313 128 64 378 371 1609 70 266 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 141/275 Leona Saunders 2.19548574964837e-09 2.3488690006512e-08 615 406.636363636364 381 1.99589613803577e-10 43 1.94381709367179 2.37428564209669 1 3.81443057552396 611 53 388 188 43 748 743 149 903 266 381 267 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 24/63 Arthur Liberzon 6.29776959403893e-09 5.35424341998513e-08 530 394 382 5.72524510187915e-10 81 2.93726930442106 3.53011598666303 1 5.49356939701323 526 380 414 356 741 497 495 81 171 382 291 268 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 22/61 Arthur Liberzon 4.17958896336079e-10 5.32216138106213e-09 360 636.545454545455 382 3.79962633104985e-11 188 2.48864231602089 2.49032188016825 1 5.29629355584961 358 188 352 223 1722 466 382 1545 800 630 336 269 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 21/41 John Newman 1.06366966747295e-09 1.25867577317633e-08 175 422.181818181818 383 9.66972425442928e-11 85 3.11369171087971 3.3048327073343 1 6.32712057881066 174 833 370 85 914 287 135 383 438 573 452 270 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 52/110 John Newman 3.56669353036996e-12 6.28328040726076e-11 205 522.272727272727 384 3.24244866397795e-13 200 2.78229565930649 3.05904213246328 1 7.30094937613836 202 801 260 306 1993 457 287 200 422 384 433 271 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 32/94 John Newman 1.25251448494971e-08 8.0181460061125e-08 255 578 387 1.13864953825508e-09 238 1.91063986077657 1.7748620968069 1 3.48727805501202 251 684 756 603 348 277 238 885 1561 387 368 272 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 48/125 Dimitris Anastassiou 2.02809388509709e-23 1.59493328234462e-21 60 451.636363636364 387 1.84372171372462e-24 8 2.71458006568228 2.74971477191021 1 14.5213638393456 8 516 57 592 1834 187 184 639 387 60 504 273 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 37/112 John Newman 4.13578957931121e-09 3.92313966976768e-08 310 420.272727272727 389 3.75980871553281e-10 268 2.67020464198322 2.76565722013352 1 5.08684378466046 306 361 402 315 793 322 455 268 389 439 573 274 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 23/49 Jessica Robertson 5.12779941767413e-07 1.23860144697015e-06 330 626.727272727273 392 4.661636920792e-08 212 2.14271375179192 2.44225625237632 1 3.25562832710389 329 377 711 753 2218 392 313 364 212 689 536 275 M5882 NABA_PROTEOGLYCANS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_PROTEOGLYCANS.html Genes encoding proteoglycans 22159717 10/35 Alexandra Naba 2.63965492419889e-09 2.74876066106578e-08 210 431.545454545455 392 2.39968629760551e-10 63 2.87479108293623 2.87479108293623 1 5.59083061675647 209 235 392 866 704 63 73 1055 573 509 68 276 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 56/135 Kate Stafford 2.19590414389071e-10 2.93162587415153e-09 340 525.363636363636 393 1.99627649464536e-11 244 2.45733387222686 2.89562655993408 1 5.3933556569148 433 336 337 393 1491 350 250 244 788 623 534 277 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 20/34 Leona Saunders 1.5050906900044e-08 8.88515592336429e-08 295 571.545454545455 394 1.3682642730011e-09 163 2.90516062333939 3.05161844006112 1 5.26914518684917 241 394 435 163 1888 291 293 1026 501 676 379 278 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 38/123 Yujin Hoshida 7.18939860044779e-11 1.02711956834446e-09 395 474.181818181818 395 6.53581690971158e-12 148 2.69184374616335 2.81227967514545 1 6.22343126450853 395 148 319 181 1261 485 603 301 528 394 601 279 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 15/35 Jessica Robertson 3.88632772680774e-09 3.73949316793041e-08 400 414.363636363636 396 3.53302521243e-10 95 2.51788039327019 2.97973483192271 1 4.81014468217148 595 208 399 396 999 380 483 302 95 297 404 280 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 149/377 Jessica Robertson 3.69651210770065e-09 3.60121740887427e-08 430 480.909090909091 398 3.36046555810151e-10 168 1.85924909436665 2.02044850538035 1 3.55972452095896 430 766 398 579 484 244 380 278 1358 205 168 281 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 2/19 Jessica Robertson 1.84933839325112e-10 2.49022980194676e-09 920 977.5 398.5 2.05482043711458e-11 6 2.61300357472779 2.61300357472779 1 5.78265114912387 918 446 4506 NA 1294 334 351 6 243 1396 281 282 M9487 FRIDMAN_SENESCENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_SENESCENCE_DN.html Genes down-regulated in senescent cells. 18711403 16/38 Jessica Robertson 3.52505423486839e-09 3.45573308464294e-08 400 561.181818181818 402 3.20459476410597e-10 117 3.15462136706432 3.56098624602859 1 6.05438059608321 318 402 397 253 1677 714 649 396 117 458 792 283 M7923 REACTOME_SEMAPHORIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMAPHORIN_INTERACTIONS.html Genes involved in Semaphorin interactions 39/106 Reactome 3.55132504158709e-08 1.56258301829832e-07 205 803 403 3.22847736264904e-09 115 2.70693541239798 2.75635197822777 1 4.73891064355204 403 2423 856 205 1674 203 207 116 930 1701 115 284 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 85/202 John Newman 4.40704376137265e-18 1.89462450144883e-16 260 454.545454545455 404 4.00640341942966e-19 75 2.69052106700014 2.73342998172768 1 10.8806800925709 258 75 104 152 1515 413 548 761 404 311 459 285 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 191/464 Arthur Liberzon 1.09830705905571e-19 5.47517753056922e-18 305 451.454545454545 404 9.98460962777919e-21 33 1.97611075047134 2.12349807726534 1 8.77386712897918 305 33 89 281 855 404 489 738 1176 85 511 286 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 10/36 Jessica Robertson 1.43833280767111e-09 1.62802597505962e-08 20 439.181818181818 405 1.30757528055589e-10 17 2.53030574718532 2.86855503928522 1 5.06893241911138 702 237 826 60 860 527 405 17 201 978 18 287 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 7/11 Jessica Robertson 1.59754579914692e-07 4.75609886582113e-07 410 867.181818181818 408 1.5975459139938e-08 244 3.0676891739964 3.0676891739964 1 4.9890283815848 408 244 4304 538 1447 319 389 401 563 619 307 288 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 70/168 John Newman 1.40075148932163e-07 4.25675841696573e-07 210 470.909090909091 408 1.27341052591656e-08 190 2.17098244750332 2.43670654123127 1 3.5576006428496 207 324 510 202 1366 190 218 408 605 734 416 289 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 12/35 Arthur Liberzon 3.50260454025237e-08 1.54549951747859e-07 120 397.545454545455 408 3.18418599637918e-09 49 3.26136916227944 3.26136916227944 1 5.71353802462834 120 413 466 203 1512 135 49 495 76 496 408 290 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 146/457 Jessica Robertson 4.37200245512225e-09 4.07300268483159e-08 325 562.636363636364 410 3.9745476943733e-10 323 1.9110678993361 2.12582229478681 1 3.63265565833785 323 765 405 724 948 410 504 348 973 389 400 291 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) 45/95 KEGG 5.73420678297479e-09 5.01315167630967e-08 200 569.636363636364 411 5.21291527083706e-10 199 2.48638779697178 2.60468469674164 1 4.66856920122244 199 1030 411 243 1505 306 301 880 475 357 559 292 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 82/206 Kolja Eppert 5.80226978115222e-09 5.04442229953233e-08 615 460.545454545455 413 5.27479072405008e-10 47 2.03444765962384 2.2133406620261 1 3.81856998825735 612 311 413 81 591 653 1236 214 640 268 47 293 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 31/73 Jessica Robertson 1.4748685589719e-08 8.76448747936216e-08 130 424.454545454545 416 1.34078960805395e-09 129 2.52664064905655 2.73675270151053 1 4.58647567902492 129 366 438 735 416 207 320 580 494 647 337 294 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 127/356 John Newman 4.16839249421365e-13 8.60488424135910e-12 410 453.363636363636 419 3.78944772201312e-14 56 1.99716332130743 2.20849160335458 1 5.68425666713034 407 56 221 157 419 654 1014 612 576 155 716 295 M507 REACTOME_GPCR_LIGAND_BINDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPCR_LIGAND_BINDING.html Genes involved in GPCR ligand binding 100/454 Reactome 9.59983289926059e-19 4.41027617313089e-17 290 585.272727272727 420 8.72712081750962e-20 97 2.30205541719994 2.37230906977707 1 9.68454424618028 286 496 97 950 109 394 420 1273 1770 187 456 296 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 71/189 Arthur Liberzon 1.39775402863342e-12 2.67341852170457e-11 240 502.181818181818 420 1.27068548057664e-13 198 2.45540377713027 2.53627411642874 1 6.67754889871213 198 506 239 420 1725 333 432 708 244 239 480 297 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 186/458 John Newman 1.45871480345045e-12 2.77867380852391e-11 560 487.090909090909 422 1.32610436677402e-13 70 2.00190024042201 2.22467362094402 1 5.43559597244468 560 626 240 70 981 353 625 121 1222 422 138 298 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 178/461 Arthur Liberzon 3.67142394104411e-28 3.82317613060727e-26 145 466 422 3.33765812822193e-29 44 2.33556552679114 2.45904524665716 1 15.2695017156749 141 891 44 911 221 179 422 577 1218 50 472 299 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 9/22 Jessica Robertson 2.03298379581138e-09 2.200129807661e-08 505 752.545454545455 424 2.03298379767123e-10 24 2.61469894938459 2.75342193086517 1 5.15003642770874 503 236 4318 222 1316 424 496 24 42 267 430 300 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 225/525 Jessica Robertson 1.48889901641664e-20 8.11276836154464e-19 425 469.454545454545 425 1.35354456037876e-21 70 1.99853874243292 2.23338846163986 1 9.2997177049246 425 468 82 283 683 609 656 374 1197 70 317 301 M651 REACTOME_CS_DS_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CS_DS_DEGRADATION.html Genes involved in CS/DS degradation 8/13 Reactome 8.00923532773066e-08 2.74753124053776e-07 75 885.636363636364 426 8.00923561639600e-09 75 1.955850813086 1.955850813086 1 3.30071647342375 413 242 3946 1617 1256 141 75 490 426 1061 75 302 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 23/112 Jessica Robertson 7.96439920036256e-08 2.73881039085399e-07 520 587.636363636364 429 7.24036317153478e-09 202 2.33356637859825 2.58682302915695 1 3.93898239868741 516 384 541 1279 1144 297 316 219 1137 429 202 303 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 35/76 Jessica Robertson 1.22492293944116e-08 7.95012312219011e-08 360 481.636363636364 431 1.11356631478302e-09 155 2.07073190544248 2.04373257412647 1 3.78144701804976 357 155 634 431 335 511 508 327 952 685 403 304 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 127/317 Arthur Liberzon 1.5320051162847e-08 8.97371996863761e-08 110 558 434 1.39273193359369e-09 106 1.69697959039976 1.78130674932985 1 3.07596396667416 106 295 812 539 434 279 260 588 1557 862 406 305 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 52/156 Arthur Liberzon 1.73985414740693e-19 8.405109829638e-18 65 535.272727272727 434 1.58168558855175e-20 61 2.60296681770859 2.68441351004752 1 11.4324586355714 61 334 92 711 1441 472 434 881 416 101 945 306 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 4/22 Reactome 1.03125791062656e-07 3.33734431574315e-07 650 967.909090909091 436 1.03125795848375e-08 56 1.76954962055726 -1.76954962055726 -1 2.94787056436031 650 436 3960 962 1672 196 56 187 68 2041 419 307 M872 REACTOME_L1CAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_L1CAM_INTERACTIONS.html Genes involved in L1CAM interactions 46/131 Reactome 1.07232423906113e-08 7.39899659922656e-08 715 621.181818181818 437 9.74840222079867e-10 139 1.93924194721028 2.30985786315046 1 3.55689111466154 712 139 1196 309 273 732 770 199 437 1634 432 308 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 94/214 Lauren Kazmierski 1.55216645568314e-08 9.05784808384955e-08 185 516.909090909091 439 1.41106042421286e-09 168 2.03743219976904 2.08593149997842 1 3.69094840564275 183 1013 682 582 439 222 182 168 1366 544 305 309 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 27/64 Jessica Robertson 3.48459640074186e-11 5.2673608818956e-10 180 422.818181818182 440 3.16781490981551e-12 177 3.03670932109262 3.35360934218246 1 7.2472845695399 457 822 302 179 440 597 594 235 177 313 535 310 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 165/366 Arthur Liberzon 2.1990221911987e-14 5.69315910936857e-13 445 470.363636363636 441 1.99911108290792e-15 44 2.18548522374958 2.55033270529653 1 6.88323834829113 441 44 176 170 1105 460 832 712 706 201 327 311 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 50/129 Arthur Liberzon 2.93556474269463e-12 5.3318048001035e-11 140 674.454545454545 442 2.66869522063505e-13 137 2.86297895147095 2.91654518276903 1 7.56518297702739 137 1564 252 573 2258 321 241 442 829 338 464 312 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 60/108 Lauren Kazmierski 4.9633252640074e-16 1.68537262225643e-14 100 477.090909090909 442 4.51211387637036e-17 100 2.39957623356753 2.62789211292036 1 8.50102641042991 100 512 133 456 1427 376 344 688 442 151 619 313 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 18/45 Kevin Vogelsang 1.92562079213444e-08 1.03629956114056e-07 215 479.272727272727 442 1.75056437180823e-09 121 3.26952702962851 3.26697356837549 1 5.87380927046793 211 709 442 197 1034 231 121 927 143 727 530 314 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 311/767 Jessica Robertson 1.59321347259291e-09 1.77334877258204e-08 825 592.363636363636 447 1.44837588522427e-10 62 1.79015607814701 1.98503965647512 1 3.56910094122009 823 272 381 62 288 772 971 809 1464 227 447 315 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 5/9 Jessica Robertson 8.17097823328223e-08 2.78669606995346e-07 415 1104 447 8.17097853372423e-09 73 2.50387976280417 2.50387976280417 1 4.22161764719717 412 988 4579 765 2579 447 326 170 73 1536 269 316 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 12/32 Arthur Liberzon 1.60437124969088e-08 9.22009258052164e-08 460 481.818181818182 448 1.4585193285372e-09 207 2.2277340859126 2.36686197014286 1 4.03127531812246 458 852 870 239 448 343 416 607 368 492 207 317 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 27/62 Arthur Liberzon 2.03837763848329e-08 1.07324018134075e-07 745 364.636363636364 448 1.8530705976087e-09 75 2.80178544714688 3.11214912882391 1 5.02253413600612 744 175 456 75 544 448 465 246 267 486 105 318 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 45/94 Arthur Liberzon 8.60991719025421e-08 2.88805096303015e-07 130 631.272727272727 449 7.82719775201074e-09 127 2.55959880999438 2.6322855870862 1 4.30534687836316 127 2145 528 555 1179 181 393 233 449 964 190 319 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 65/178 John Newman 9.33449274282142e-08 3.07821484819572e-07 515 504.090909090909 452 8.48590285352675e-09 290 2.01570038884164 2.30229629326623 1 3.37612950032815 381 326 509 513 1211 290 452 449 515 337 562 320 M160 PID_AVB3_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AVB3_INTEGRIN_PATHWAY.html Integrins in angiogenesis 18832364 54/117 Pathway Interaction Database 3.62305940852974e-08 1.57638406577255e-07 205 568.545454545455 453 3.29369042563266e-09 117 2.79418906155406 2.90933183769797 1 4.88891699531169 243 1382 579 266 1504 204 453 117 522 779 205 321 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 15/36 Jessica Robertson 1.56834434147501e-07 4.68404179996934e-07 460 446.909090909091 454 1.42576768479977e-08 29 2.93764701180329 3.19583941520051 1 4.78254866200411 460 210 557 473 1401 201 146 454 29 710 275 322 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 98/227 Arthur Liberzon 5.35382273710703e-13 1.08606118381314e-11 265 462.818181818182 454 4.86711157918939e-14 69 1.9064454334393 2.20422687848415 1 5.37647771179841 261 69 225 532 687 454 469 346 1333 137 578 323 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 18/36 Jessica Robertson 2.60995985062483e-08 1.24039603791437e-07 300 549.727272727273 457 2.37269080144361e-09 66 3.25812147473551 3.14516225675335 1 5.78788862486595 239 1141 457 354 1531 300 299 499 66 554 607 324 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 30/85 Arthur Liberzon 3.2757137110294e-10 4.24032995853142e-09 455 498.272727272727 459 2.97792155592466e-11 158 2.19917886322333 2.16641288228351 1 4.73608604217102 451 158 348 459 241 574 609 1090 554 259 738 325 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 328/758 John Newman 1.00007275480407e-11 1.66773698541348e-10 300 507.272727272727 459 9.0915704982602e-13 184 1.88539881351353 2.08071661589226 1 4.74183312681362 298 459 273 184 216 484 839 539 1372 454 462 326 M509 REACTOME_DEVELOPMENTAL_BIOLOGY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEVELOPMENTAL_BIOLOGY.html Genes involved in Developmental Biology 192/520 Reactome 6.38757324189848e-09 5.3834834912835e-08 525 422.818181818182 464 5.80688478222219e-10 66 1.94921402829305 2.33444040468161 1 3.64442547593362 525 283 641 97 132 209 499 464 980 755 66 327 M1469 BIOCARTA_LYM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LYM_PATHWAY.html Adhesion and Diapedesis of Lymphocytes 6/14 BioCarta 4.22171795188626e-07 1.05396751851566e-06 380 932.454545454545 466 4.22171875391708e-08 107 2.69538356529929 2.69538356529929 1 4.14395520676381 379 429 3812 466 1800 211 107 910 726 1152 265 328 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 7/27 Reactome 6.70028802305907e-08 2.40042428716015e-07 395 1052.36363636364 466 6.70028822508145e-09 158 2.48101539888016 2.48101539888016 1 4.22442127865899 393 1361 4052 1276 1498 331 466 158 444 1348 249 329 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 87/177 John Newman 4.16684134349189e-09 3.94460980517233e-08 820 562.727272727273 466 3.78803759216724e-10 66 2.18205487399948 2.64486352845683 1 4.15556909150294 466 310 454 437 66 1095 817 280 967 816 482 330 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 72/165 Arthur Liberzon 4.78150904111109e-09 4.34227739663693e-08 440 573.727272727273 467 4.34682641045754e-10 85 2.10300882778218 2.18662070363966 1 3.98246745807489 438 909 550 885 85 261 478 436 1610 467 192 331 M9809 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION.html Cytokine-cytokine receptor interaction 86/310 KEGG 3.91879428015031e-08 1.65139118676118e-07 445 808.363636363636 470 3.56254031814057e-09 93 2.00188995091887 2.09015334397703 1 3.4922574729714 444 1313 470 1916 820 281 354 406 2018 777 93 332 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 315/712 Arthur Liberzon 1.04920858680367e-15 3.27772762517465e-14 360 506 470 9.5382598800333e-17 18 1.69589251492248 -1.54338960693825 -1 5.88206064419077 359 18 166 791 612 81 954 1001 1071 43 470 333 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 51/131 Reactome 8.12192696070322e-10 9.80911075717919e-09 265 581.727272727273 471 7.38356996700151e-11 221 2.31961522013035 2.38491544621756 1 4.77813888568423 262 522 365 547 1303 221 253 991 1044 420 471 334 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 218/538 John Newman 7.2803251448641e-09 5.95385752684697e-08 420 590 471 6.61847742632402e-10 159 1.85586146112776 2.14135291353263 1 3.44900784946381 418 471 419 190 159 1000 809 671 1065 405 883 335 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 32/96 Reactome 2.47314345277779e-08 1.20328077343124e-07 195 422.272727272727 477 2.24831225507253e-09 94 2.37765205425885 2.74829497343949 1 4.2318477065343 191 685 542 94 629 295 166 699 306 561 477 336 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 14/41 Arthur Liberzon 6.57822407293117e-10 8.0484485654714e-09 235 517.909090909091 479 5.98020370445285e-11 144 3.23026368724609 3.40241304071826 1 6.7253562489854 233 226 361 441 144 598 715 959 719 479 822 337 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 179/538 Arthur Liberzon 7.91040666417916e-15 2.15512590862463e-13 270 477.909090909091 480 7.19127878561745e-16 167 2.15146799495511 2.50626857157126 1 7.00956603093661 269 480 167 578 461 557 593 320 1055 262 515 338 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 24/57 John Newman 3.53125016550488e-08 1.55667340315671e-07 390 811.454545454545 480 3.21022747471406e-09 34 2.20330118234658 2.37195717432692 1 3.85815330394452 480 1337 861 352 1946 220 387 390 1181 1738 34 339 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 33/100 Arthur Liberzon 9.72749830047515e-11 1.36476218670738e-09 495 592.636363636364 480 8.84318027355022e-12 161 2.85198111670572 2.85889131899984 1 6.50311252940428 491 161 324 517 382 521 470 1808 480 336 1029 340 M5539 KEGG_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AXON_GUIDANCE.html Axon guidance 61/153 KEGG 2.47972625380724e-08 1.20328077343124e-07 390 669.545454545455 482 2.25429661977949e-09 215 2.1601517066118 2.40607406007553 1 3.84473118451492 482 1711 963 402 631 389 463 215 690 1033 386 341 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 154/566 Leona Saunders 2.27846004507065e-23 1.75030553626247e-21 115 590.818181818182 483 2.07132731370058e-24 59 2.13382924881593 2.19560903536466 1 11.3925396246551 114 483 59 632 1488 372 423 831 1299 72 726 342 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 36/94 Arthur Liberzon 4.07503775319771e-07 1.02389420436914e-06 485 1028.81818181818 483 3.70458046183002e-08 107 1.77917072562425 1.94406716902928 1 2.74109827931556 483 937 2106 1158 2040 107 192 397 479 3214 204 343 M1429 REACTOME_SMOOTH_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SMOOTH_MUSCLE_CONTRACTION.html Genes involved in Smooth Muscle Contraction 21/38 Reactome 5.21338102064573e-09 4.63565530602389e-08 230 505.636363636364 486 4.73943730272727e-10 55 3.49077228159441 3.7570192922463 1 6.58498088227843 227 559 410 55 798 435 486 1302 174 572 544 344 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 31/84 Pathway Interaction Database 2.0868486246277e-09 2.24288363646912e-08 445 703.363636363636 487 1.89713511509746e-10 22 1.82473060890993 1.97855772171073 1 3.59015380186202 445 1269 934 1234 22 250 487 166 1911 787 232 345 M3008 NABA_ECM_GLYCOPROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_ECM_GLYCOPROTEINS.html Genes encoding structural ECM glycoproteins 22159717 81/221 Alexandra Naba 6.54839913775688e-23 4.79465599367637e-21 50 432.818181818182 488 5.95309012523353e-24 49 2.27883638086824 2.45951060515889 1 11.9102078360475 49 77 62 558 1053 401 488 644 704 67 658 346 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 248/532 Kevin Vogelsang 4.91161111452293e-14 1.18638194240487e-12 735 501.909090909091 491 4.46510101320276e-15 27 2.05077397684953 2.38470779464094 1 6.29075977207409 731 27 189 173 127 903 890 790 969 231 491 347 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 54/109 John Newman 3.18594282162016e-08 1.44244715575962e-07 290 506.727272727273 491 2.89631169796143e-09 197 2.03652977851707 2.0827738853531 1 3.5834609460375 287 798 569 523 730 197 384 491 989 362 244 348 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. 120/268 Charles Durand 1.21221318285885e-08 7.92249787291016e-08 760 648.545454545455 492 1.10201199048929e-09 294 1.84593153050922 1.85301650450838 1 3.37164773905359 758 492 483 987 324 580 428 602 1797 294 389 349 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 54/127 Kevin Vogelsang 1.15495056550695e-13 2.56299535122659e-12 145 577.545454545455 494 1.04995505955183e-14 145 2.60951012811335 2.58939981510283 1 7.78015086751714 145 338 205 505 494 467 696 1072 1360 173 898 350 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 15/34 Jessica Robertson 8.6227826023218e-09 6.65673134670181e-08 735 769.727272727273 495 7.83889330556214e-10 197 1.52695397155732 1.71766159987011 1 2.8187188039696 735 221 1403 468 197 495 545 304 1242 2559 298 351 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 84/179 Arthur Liberzon 2.32502744070961e-09 2.45938568559035e-08 320 977.454545454545 496 2.11366131196979e-10 26 2.03826184489743 2.03855718082838 1 3.98929469518147 320 2726 661 1859 26 349 246 496 2790 938 341 352 M169 PID_INTEGRIN2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN2_PATHWAY.html Beta2 integrin cell surface interactions 18832364 14/38 Pathway Interaction Database 1.30003070369291e-08 8.13343641856472e-08 480 501 498 1.18184610125008e-09 222 2.40209745313394 2.56217458907273 1 4.38045009849278 643 222 498 533 365 480 396 557 676 478 663 353 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 15/28 Leona Saunders 5.78949313881126e-10 7.17713355779618e-09 850 539 499 5.26317558212255e-11 3 1.94152623125344 2.07744412755127 1 4.06707616347822 554 847 1109 848 3 246 129 419 499 1188 87 354 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 43/90 Arthur Liberzon 9.14570855114239e-08 3.03518344693012e-07 160 715.454545454545 501 8.31428084667483e-09 156 2.63794796608783 2.7212882055738 1 4.42249067733565 156 2340 561 745 1201 307 501 293 453 1036 277 355 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 179/478 Leona Saunders 5.18635934650382e-34 7.14802349932851e-32 35 447.909090909091 502 4.71487213318534e-35 9 2.23398103735691 2.58254034924164 1 17.8969016924264 635 35 33 9 481 813 1006 502 851 40 522 356 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 31/55 Leona Saunders 2.12798624278775e-09 2.28186350885661e-08 1235 677.545454545455 502 1.93453294986007e-10 292 2.78681487953194 2.97474056110172 1 5.47768891482592 626 363 387 292 502 1064 1233 1232 402 353 999 357 M9387 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION.html Vascular smooth muscle contraction 43/140 KEGG 3.75079473080669e-08 1.60367008289783e-07 450 669.272727272727 503 3.40981344977657e-09 182 2.4243698850805 2.59246874737464 1 4.23720676676179 446 1031 476 182 797 449 724 1632 503 625 497 358 M67 PID_ARF6_TRAFFICKING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_TRAFFICKING_PATHWAY.html Arf6 trafficking events 18832364 29/75 Pathway Interaction Database 3.24937810381242e-09 3.26970149506125e-08 660 585.636363636364 504 2.95398009873792e-10 47 2.11247802909 2.19984545386241 1 4.0673468723173 656 819 1148 695 47 310 375 163 504 1548 177 359 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 32/66 Pathway Interaction Database 2.45725631259135e-08 1.2003053648855e-07 220 554.272727272727 506 2.23386940003391e-09 93 2.73514673916303 2.73514673916303 1 4.86888865336905 217 545 506 666 1780 235 266 93 759 691 339 360 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 19/42 Kevin Vogelsang 3.84238373521023e-09 3.71245570787529e-08 510 732.727272727273 506 3.49307612901919e-10 61 2.15409204258453 2.30042617064118 1 4.11691153636737 506 838 998 1625 61 465 289 392 1177 1261 448 361 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 75/142 John Newman 1.82884046539357e-08 1.00233291471746e-07 655 610.545454545455 507 1.66258225508778e-09 104 1.61161260392243 1.73772240872542 1 2.90131285230727 115 654 917 654 507 184 203 104 1516 1466 396 362 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 23/67 Kolja Eppert 3.25155974540876e-09 3.26970149506125e-08 350 600.090909090909 509 2.95596340928592e-10 28 2.07124144431789 2.16732477656808 1 3.98795030553835 348 563 855 509 1956 275 227 28 906 865 69 363 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 122/274 Arthur Liberzon 2.08553445198996e-09 2.24288363646912e-08 390 574.454545454545 510 1.89594041269726e-10 23 2.05814243013142 2.47421865588869 1 4.04939111783678 390 1379 441 317 510 602 714 23 1008 834 101 364 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 192/465 Arthur Liberzon 3.83432594789343e-09 3.71232466773318e-08 425 635.909090909091 510 3.48575086779652e-10 60 1.78696361493876 1.96494257664887 1 3.41526085029222 424 1236 604 850 60 230 510 173 1917 891 100 365 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 114/229 Leona Saunders 4.54551366177965e-18 1.93638881991813e-16 315 634.363636363636 511 4.13228514707238e-19 63 2.24329811243477 2.51582876073541 1 9.06661106276296 311 63 105 378 511 1045 1023 1228 1078 139 1097 366 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 75/164 John Newman 1.00656294243708e-07 3.27152088668496e-07 340 645.818181818182 511 9.15057262263836e-09 184 2.54027582399561 2.87264340964689 1 4.23746656977161 338 1561 495 527 1295 224 402 511 888 679 184 367 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 100/269 Jessica Robertson 6.75328740123231e-20 3.47757195188732e-18 515 466.363636363636 511 6.13935218293843e-21 24 2.45269875718785 2.69095695385592 1 11.0142616230694 511 67 86 24 246 881 1022 945 543 92 713 368 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 69/149 John Newman 6.28989246731487e-13 1.24891678397617e-11 135 699.363636363636 513 5.71808406119696e-14 133 2.40400794902798 2.55826921655028 1 6.74216176448645 133 1179 230 897 2111 396 513 533 959 258 484 369 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 117/258 Arthur Liberzon 9.58108615777206e-09 7.02612984903285e-08 435 687.727272727273 517 8.71007836318005e-10 227 1.85623684317394 1.84664775280189 1 3.4153680222051 435 494 547 969 227 479 734 979 1806 378 517 370 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 62/150 Arthur Liberzon 9.15828163715894e-09 6.8744865580254e-08 520 522.727272727273 517 8.32571061389412e-10 213 2.17035031144901 2.29164766254639 1 3.99860852443622 517 795 571 541 213 386 529 275 1232 463 228 371 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 56/151 Arthur Liberzon 6.4367246251378e-08 2.33817764289889e-07 230 460.272727272727 519 5.85156801223859e-09 109 2.1526468251421 2.47515873219295 1 3.67162651604544 230 519 668 619 1048 109 168 277 566 730 129 372 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 310/965 John Newman 2.29054184950735e-15 6.92482523018801e-14 525 508.454545454545 522 2.0823107722794e-16 21 1.87862597552525 2.17908139226325 1 6.35889121401354 522 21 149 59 489 806 812 538 1288 191 718 373 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 62/153 Leona Saunders 1.80535870473944e-13 3.91519004345132e-12 495 575.818181818182 523 1.6412351861269e-14 192 2.9326773622554 3.24081773096523 1 8.60486015139815 495 916 210 192 892 720 851 523 707 464 364 374 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 2/8 Yujin Hoshida 1.07738279821242e-06 2.35257026673971e-06 1050 1109.6 523 1.19709257122589e-07 65 2.10404486189252 2.10404486189252 1 3.04609214964231 1046 445 4367 NA 2102 423 212 551 65 1390 495 375 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 23/51 Kate Stafford 1.49338366663731e-08 8.83585336093744e-08 430 552 524 1.35762152434051e-09 181 2.48604092631765 2.80631773528523 1 4.51052504092924 428 181 433 251 1292 672 524 915 307 540 529 376 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 156/399 Arthur Liberzon 5.93922731407034e-13 1.19447292676968e-11 350 536.727272727273 524 5.39929755824721e-14 46 1.98026148626138 2.16848945719714 1 5.56360305773562 347 46 227 571 417 625 651 524 1489 208 799 377 M17162 NAKAMURA_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_METASTASIS.html Genes up-regulated in highly metastatic pancreatic cancer cells. 17210693 28/70 Jessica Robertson 1.06666857987681e-09 1.25904507942134e-08 475 631.909090909091 526 9.69698709449079e-11 1 2.0035532978395 2.33151041695654 1 4.07121828369105 859 828 1203 472 386 526 678 91 472 1435 1 378 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 16/40 Arthur Liberzon 1.30955968746901e-07 4.02928213754418e-07 255 592.363636363636 526 1.19050887765557e-08 38 3.20001912290636 3.43836920046323 1 5.26352065774212 252 708 503 347 1906 553 526 399 38 589 695 379 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 80/276 Arthur Liberzon 1.80041646239324e-07 5.23047212819263e-07 315 698.636363636364 529 1.63674237248558e-08 180 1.86253637088959 1.94559356241705 1 3.00928941483869 575 312 529 1216 1458 490 569 312 1763 281 180 380 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 65/157 Kevin Vogelsang 3.49940578871312e-08 1.54549951747859e-07 300 477.909090909091 530 3.18127804034184e-09 99 1.84613718250684 2.11691781133373 1 3.23421672426636 296 99 635 260 769 538 346 294 530 804 686 381 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 93/236 Jessica Robertson 3.48223620163382e-09 3.42091380311448e-08 385 590.181818181818 534 3.16566927922329e-10 53 1.92869481347218 2.14297931871099 1 3.70375196213664 384 499 628 520 53 846 414 972 854 534 788 382 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 65/111 Kevin Vogelsang 1.21538708674568e-10 1.67508937896772e-09 280 647.909090909091 534 1.10489735164802e-11 95 2.12832873953412 2.18889376161099 1 4.80432207533374 280 95 330 534 2009 369 360 917 908 591 734 383 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 39/107 Leona Saunders 5.60830588989932e-11 8.16165260871684e-10 310 579.454545454545 536 5.09845990003845e-12 186 3.19523018104242 3.53689578601539 1 7.46929734513671 308 536 313 191 1601 534 643 702 186 594 766 384 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 114/201 Arthur Liberzon 6.34330897176825e-09 5.35581006156865e-08 475 641.818181818182 536 5.76664453641639e-10 130 1.76238032368941 1.93601440265345 1 3.29611900832174 474 772 730 871 130 292 536 1214 1515 302 224 385 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 34/65 Jessica Robertson 8.72369573453295e-09 6.66871748972617e-08 540 603.818181818182 538 7.93063251738651e-10 183 2.21237831430784 2.41614282103463 1 4.08355047618931 538 1126 1021 394 203 725 280 183 753 1117 302 386 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 10/17 Jessica Robertson 2.79933523719335e-09 2.89573618575895e-08 560 645.727272727273 539 2.54485021886845e-10 27 2.46155682175171 2.78656613357557 1 4.77285843702871 556 1157 989 255 1446 337 539 27 299 1361 137 387 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 60/138 Yujin Hoshida 1.00721202441965e-07 3.27152088668496e-07 305 682.727272727273 539 9.15647336847454e-09 115 1.96277011481258 2.02347389491064 1 3.27412186651146 302 115 496 153 1417 539 464 995 1558 872 599 388 M6856 KEGG_HEMATOPOIETIC_CELL_LINEAGE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEMATOPOIETIC_CELL_LINEAGE.html Hematopoietic cell lineage 35/107 KEGG 1.43448570876973e-08 8.64010286798835e-08 255 643.181818181818 542 1.30407792556648e-09 31 1.97896084281329 2.03886561956167 1 3.59546156924278 253 542 695 1383 688 57 78 69 2452 827 31 389 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 36/96 Arthur Liberzon 2.82145379652492e-08 1.30904282084315e-07 535 743.636363636364 542 2.56495802973589e-09 156 1.49476205260416 1.73805426293808 1 2.64637508642194 533 156 1621 1288 690 542 243 349 949 1477 332 390 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 146/470 Kevin Vogelsang 5.24657274413154e-20 2.76240897516858e-18 145 540.909090909091 544 4.76961158557412e-21 65 2.06341469980465 2.30366076310668 1 9.31918333296517 142 287 84 280 1523 633 544 546 962 65 884 391 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 113/315 Yujin Hoshida 1.189061047517e-20 6.55522361019372e-19 220 648.363636363636 544 1.08096458865182e-21 81 2.32981757972774 2.78781078744042 1 10.896724965946 218 1245 81 712 1698 544 447 226 1184 150 627 392 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 81/174 Arthur Liberzon 1.99846393012972e-08 1.06176893158592e-07 555 620.272727272727 545 1.81678540753057e-09 222 2.23183729699467 2.59457229766365 1 4.0035132576209 555 908 545 476 535 1057 885 222 638 510 492 393 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 19/41 Arthur Liberzon 5.49489473520425e-08 2.09947262849324e-07 340 579.636363636364 545 4.99535897495375e-09 151 2.71987449073982 3.12946817661677 1 4.6718272993186 337 396 675 483 966 545 431 661 151 1014 717 394 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 26/52 Yujin Hoshida 2.19975085628486e-08 1.12779349152635e-07 600 528.545454545455 546 1.99977352570898e-09 86 1.94489117650491 2.2772563135008 1 3.47567714122856 599 379 1182 267 787 416 113 86 546 860 579 395 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 37/116 Arthur Liberzon 8.31169572670078e-09 6.52405463573197e-08 640 567.909090909091 550 7.55608705282068e-10 34 2.2583502534021 2.37890120780867 1 4.17393706340493 189 677 637 1443 1843 72 34 51 550 640 111 396 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 17/39 Arthur Liberzon 5.48806999240193e-07 1.31075922448499e-06 405 726.545454545455 550 4.98915578313079e-08 393 2.66888583710333 2.66888583710333 1 4.03821006382076 401 406 976 799 1859 488 607 550 425 1088 393 397 M159 PID_AMB2_NEUTROPHILS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AMB2_NEUTROPHILS_PATHWAY.html amb2 Integrin signaling 18832364 26/76 Pathway Interaction Database 5.49787539249513e-08 2.09947262849324e-07 255 695.363636363636 551 4.99806866353539e-09 188 2.45370919740624 2.57246149770992 1 4.21464504895692 479 1976 778 551 967 254 401 254 945 856 188 398 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 296/758 Arthur Liberzon 5.14648503277561e-45 1.85510991258358e-42 70 583.727272727273 551 4.67862275706876e-46 10 2.03942703246837 2.13117634626756 1 21.8913330565733 67 20 13 710 1031 492 551 1139 1595 10 793 399 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 8/21 John Newman 1.14987580152147e-05 1.97881674841337e-05 285 1198.18181818182 552 1.14988175152942e-06 283 2.98476894774795 2.98476894774795 1 3.61109777862349 283 1541 4413 330 2963 552 500 794 440 511 853 400 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 58/171 John Newman 5.35352975313187e-08 2.07156403164128e-07 1160 749.272727272727 552 4.8668453485508e-09 283 2.31025291073604 2.74221332906027 1 3.97168911483467 1158 517 478 552 1160 1412 1122 456 669 435 283 401 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 18/43 Arthur Liberzon 1.19274227676649e-06 2.58519440745965e-06 315 624.181818181818 553 1.0843117485626e-07 158 2.69753391145753 2.78743374774555 1 3.8768914601436 315 569 663 641 2079 342 158 804 445 553 297 402 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 24/53 John Newman 1.05807803921908e-10 1.4712622230803e-09 295 602 554 9.61889126609064e-12 291 2.94861447430001 3.15473170528823 1 6.69870678062875 291 554 327 620 830 531 390 1177 953 299 650 403 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 68/181 Kevin Vogelsang 1.27707248193927e-08 8.0434968418917e-08 480 523 555 1.16097499032047e-09 316 1.85862730736042 2.13859612764894 1 3.39168992832826 478 316 587 660 358 432 560 710 652 445 555 404 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 30/89 John Newman 1.13051601639984e-09 1.32109677128421e-08 665 611.272727272727 557 1.02774183361889e-10 9 2.39635273797446 2.35942287874114 1 4.8565081220527 665 165 576 225 9 811 472 2182 462 600 557 405 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 378/940 Jessica Robertson 1.0434600886071e-08 7.29799100778042e-08 1150 777.181818181818 558 9.48600085051123e-10 14 1.74030411042703 2.12789880846955 1 3.1946782884445 1149 14 475 65 263 2151 1307 447 1287 558 833 406 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 35/125 Jessica Robertson 5.90296639522326e-08 2.19435778250278e-07 355 772.181818181818 558 5.36633323055425e-09 351 2.61486713487195 3.09217896992439 1 4.47854826204532 351 1037 481 1552 1390 409 359 448 1081 828 558 407 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 27/57 Jessica Robertson 6.07382459478084e-11 8.78455001578488e-10 275 599.727272727273 558 5.52165872268047e-12 86 3.0330366872016 3.49876443558075 1 7.06522836915468 273 816 315 86 1195 558 572 1184 304 393 901 408 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 92/329 Arthur Liberzon 3.65070856062773e-16 1.28625716654899e-14 1845 1036.27272727273 560 3.31882596420701e-17 10 2.24957754086708 2.5181923552963 1 8.03753556526737 1841 70 128 10 560 2688 2171 1786 396 96 1653 409 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 66/198 Jessica Robertson 1.80707183712594e-09 1.98312380064921e-08 385 721.272727272727 561 1.64279258055478e-10 325 2.34547809486867 2.56627295529925 1 4.6469738092634 524 325 385 385 1334 868 779 1142 561 355 1276 410 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 31/105 Jessica Robertson 1.00304011842802e-08 7.17594808389879e-08 1145 750.181818181818 563 9.11854657273776e-10 247 2.54060922179874 3.00798376032183 1 4.66858557238618 1144 364 563 879 247 1588 1579 450 305 646 487 411 M8728 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM.html Hypertrophic cardiomyopathy (HCM) 48/137 KEGG 3.00017159758116e-11 4.57941501832747e-10 310 661.272727272727 564 2.72742872511098e-12 244 2.47532239266976 2.65996986461588 1 5.94620195021007 310 921 299 336 1766 395 564 1181 593 244 665 412 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 32/90 John Newman 2.73304782211356e-10 3.59748935236633e-09 230 503.636363636364 565 2.48458892950280e-11 61 3.30868390097117 3.33778954884339 1 7.18624805463093 226 813 342 61 888 560 680 597 144 565 664 413 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 180/523 Arthur Liberzon 3.71053010559902e-08 1.59372539641036e-07 220 632 566 3.3732092438009e-09 36 1.91409458792925 2.09949842803631 1 3.3467001253353 219 1430 647 733 1516 47 240 194 1324 566 36 414 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 71/228 Leona Saunders 1.39117392087232e-08 8.47729648011404e-08 570 571 567 1.26470357242676e-09 321 2.10476911071674 2.46811290979136 1 3.82850812283267 567 321 464 481 389 675 642 598 713 513 918 415 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 28/68 John Newman 1.05220781272397e-09 1.24826476213279e-08 370 575 567 9.56552557479287e-11 14 2.9481375161578 3.29086978469793 1 5.99344452375415 367 1671 624 681 859 282 277 14 567 966 17 416 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 60/131 John Newman 1.95694952694461e-08 1.04803034094428e-07 470 743.545454545455 567 1.7790450403201e-09 145 2.20273646530581 2.54819294995916 1 3.95451628119281 467 1112 741 1557 527 400 567 274 1074 1315 145 417 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 49/103 Arthur Liberzon 1.38707283750958e-10 1.90053313349996e-09 5 674.909090909091 567 1.26097530690639e-11 3 2.35151212974182 2.39403575607388 1 5.27495044484229 279 2298 567 819 1090 188 199 3 1361 615 5 418 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 5/18 Reactome 4.5704688671038e-10 5.78843705709417e-09 840 1273.81818181818 568 4.57046886804382e-11 10 3.33843045665778 3.33843045665778 1 7.07348122087268 837 2786 4025 169 2583 568 456 10 245 2235 98 419 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 64/159 Kate Stafford 9.46121150832601e-10 1.1281230821378e-08 605 598.818181818182 568 8.60110137490439e-11 7 2.01065705022087 2.24619478876069 1 4.11031443858921 602 103 556 568 7 453 479 1454 755 883 727 420 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 13/32 John Newman 9.58224285048129e-07 2.12505395160224e-06 540 787.363636363636 568 8.7111336582654e-08 104 4.59794013764086 4.80916940048219 1 6.70882477031683 540 963 568 427 2317 516 408 1207 104 1008 603 421 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 11/31 Arthur Liberzon 1.49267541068973e-08 8.83585336093744e-08 575 497.636363636364 571 1.35697765528852e-09 70 1.89552815358378 1.92647559487356 1 3.43913367872879 571 418 811 955 829 182 104 70 860 580 94 422 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 83/185 Kevin Vogelsang 6.41057840035742e-08 2.33229583727289e-07 355 706.272727272727 574 5.82779871559566e-09 323 2.15656584806922 2.30090542168216 1 3.67891770543004 355 1755 574 674 1046 323 419 518 1014 617 474 423 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 11/30 Arthur Liberzon 2.16196691542967e-10 2.89456484734384e-09 795 516.636363636364 575 1.96542446876558e-11 5 1.83629860454085 2.07853300950489 1 4.03291730683631 791 856 1096 337 13 575 417 5 679 822 92 424 M666 REACTOME_HYALURONAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HYALURONAN_METABOLISM.html Genes involved in Hyaluronan metabolism 11/23 Reactome 4.92515372266089e-11 7.28052692252016e-10 365 634.909090909091 578 4.47741247524651e-12 1 1.97025498635765 2.06114963004305 1 4.63089058870843 365 588 888 769 1757 468 377 1 801 578 392 425 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 32/67 John Newman 2.22803095704711e-08 1.13458881725381e-07 440 673.909090909091 578 2.02548270873756e-09 438 2.22048143033887 2.24570856565509 1 3.96668907972425 439 940 559 796 578 438 484 754 1282 693 450 426 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 36/98 Arthur Liberzon 2.31636269377345e-08 1.15842855741968e-07 685 546.818181818182 578 2.10578428923841e-09 102 2.28709718484801 2.58645279791854 1 4.08037949768434 468 682 787 102 598 683 578 543 297 725 552 427 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 37/105 Jessica Robertson 7.06817245324175e-08 2.49973253704836e-07 580 612.727272727273 579 6.42561152757126e-09 273 2.05033659776739 2.51286375156292 1 3.48182026988793 579 535 813 525 1094 668 782 273 398 767 306 428 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 121/236 John Newman 6.18401686540319e-15 1.7248989899571e-13 375 501.181818181818 579 5.62183351400291e-16 54 2.14193065547568 2.42970249790776 1 7.03177382854351 371 291 162 717 54 579 628 992 832 122 765 429 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 53/141 Jessica Robertson 6.90339443957402e-09 5.73224814976679e-08 540 629.454545454545 580 6.27581314657841e-10 146 2.159076582535 2.2929764983148 1 4.02166363746253 539 1257 453 496 146 646 580 974 712 284 837 430 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 36/80 Jean Junior 2.24651297647789e-08 1.14053735728878e-07 835 675.545454545455 582 2.04228454492544e-09 153 2.41841963926086 2.93703871750948 1 4.31887508988762 832 153 877 504 582 856 726 453 467 1795 186 431 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 20/36 Arthur Liberzon 2.47830879827398e-09 2.60974270308132e-08 735 522.181818181818 583 2.25300800096891e-10 28 2.068647904075 2.14553352635847 1 4.03505389790083 734 201 680 542 28 613 588 583 988 528 259 432 M902 REACTOME_CGMP_EFFECTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CGMP_EFFECTS.html Genes involved in cGMP effects 5/21 Reactome 5.79726071990457e-07 1.37479573549964e-06 590 1257 586 5.79726223227556e-08 94 2.35317359950727 2.35317359950727 1 3.54797702222251 586 2044 4048 1917 1907 477 415 420 94 1525 394 433 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 40/90 Kevin Vogelsang 1.15952841327366e-13 2.56299535122659e-12 140 674.272727272727 586 1.05411673933975e-14 140 3.13099261914487 3.22741810569591 1 9.33493025797373 140 932 206 511 1657 586 410 664 814 530 967 434 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 13/30 Jessica Robertson 3.28015462642678e-07 8.55359186390421e-07 590 888.181818181818 587 2.98195919590106e-08 157 2.34478692907016 2.34478692907016 1 3.65962840906899 587 2165 1348 1269 1671 228 157 410 331 1333 271 435 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 41/82 Arthur Liberzon 2.74119943520027e-09 2.84187180383815e-08 595 585 594 2.49199948965073e-10 36 2.01449431287799 2.12624854508986 1 3.91024774818545 594 931 747 200 36 341 381 770 1256 812 367 436 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 163/336 Arthur Liberzon 8.46266834472074e-09 6.58738602381418e-08 530 750.636363636364 595 7.69333488843075e-10 190 1.96252571378902 2.18088487979524 1 3.62506915639888 530 1493 440 1006 190 451 614 810 1635 595 493 437 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 16/44 John Newman 3.22736953907118e-08 1.45557783061478e-07 775 986.272727272727 595 2.9339723512875e-09 100 2.22556939191541 2.10989328569746 1 3.91384060470573 775 572 1279 298 737 515 595 4508 100 1303 167 438 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 51/97 Jessica Robertson 3.20768195387038e-08 1.44809225778773e-07 565 621 595 2.91607454603598e-09 178 2.44129888082692 2.60100635199502 1 4.29462416067389 563 1263 514 305 734 795 637 178 595 801 446 439 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 23/61 John Newman 4.4796405937497e-07 1.10715167839194e-06 465 827.727272727273 596 4.07240136899501e-08 463 2.27267716270887 2.37996411195767 1 3.48157693467385 463 1051 613 761 1792 572 596 1619 558 541 539 440 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 47/86 Arthur Liberzon 7.62520995107006e-16 2.4987226455045e-14 1385 947.181818181818 597 6.93200904642729e-17 120 2.48183541197222 3.02611884736504 1 8.68327245631033 1382 120 138 561 597 2455 1806 1028 531 153 1648 441 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 130/309 Arthur Liberzon 1.96647399167857e-13 4.22701702981916e-12 700 576.181818181818 600 1.78770362879886e-14 212 2.23049377731651 2.43809947353465 1 6.52546728594002 698 488 212 334 474 939 600 796 675 255 867 442 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 8/28 Kate Stafford 5.04519301873972e-07 1.22306127707265e-06 340 1094.54545454545 600 5.04519416416885e-08 339 2.24728020121253 2.24728020121253 1 3.41767565738408 339 600 4364 656 2073 518 397 371 1407 751 564 443 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 3/7 Arthur Liberzon 5.7792474087477e-07 1.37191253076959e-06 1220 1111.36363636364 603 5.77924891173477e-08 6 3.47303948269677 3.47303948269677 1 5.23725965662503 1218 443 4288 136 2466 603 664 387 6 1751 263 444 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 86/219 Jessica Robertson 2.52162783263643e-09 2.64940538648751e-08 585 634.909090909091 604 2.29238894138791e-10 309 2.12791580361127 2.59775536179126 1 4.14707497695568 583 309 391 344 1298 662 730 793 850 604 420 445 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 25/62 Arthur Liberzon 1.11697229688001e-07 3.54136142299033e-07 595 637.545454545455 605 1.01542941235485e-08 242 2.78810726215729 3.1105549186851 1 4.62619278370846 592 696 605 818 1287 426 652 359 352 984 242 446 M10959 REACTOME_OTHER_SEMAPHORIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OTHER_SEMAPHORIN_INTERACTIONS.html Genes involved in Other semaphorin interactions 12/29 Reactome 1.82420348142129e-06 3.73447685187425e-06 275 792.454545454545 606 1.6583681763839e-07 229 2.59074230289071 2.59074230289071 1 3.61696523639012 272 965 1011 606 2553 311 229 555 680 1209 326 447 M158 PID_INTEGRIN4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN4_PATHWAY.html Alpha6 beta4 integrin-ligand interactions 18832364 4/12 Pathway Interaction Database 1.92841062167001e-08 1.03629956114056e-07 640 878.727272727273 607 1.92841063840446e-09 14 2.64162155607579 2.64162155607579 1 4.74575708058706 638 607 3900 692 1872 384 22 125 14 1271 141 448 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 2/18 Reactome 3.81423458330521e-08 1.61751160700165e-07 1355 1271.1 607 4.23803849773857e-09 16 1.76335539037613 -1.76335539037613 -1 3.08022185407484 1355 255 4087 NA 2621 588 626 131 16 2522 510 449 M3952 BIOCARTA_LAIR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LAIR_PATHWAY.html Cells and Molecules involved in local acute inflammatory response 9/23 BioCarta 1.23672794336101e-07 3.84559199906415e-07 625 920.272727272727 608 1.23672801218833e-08 238 2.33861044593562 2.72465217361639 1 3.85883049631485 623 238 3822 424 1358 596 445 935 459 608 615 450 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 3/16 Reactome 2.49127546716004e-07 6.83096362733292e-07 610 1091.63636363636 609 2.49127574645049e-08 49 2.08722671163046 -2.08722671163046 -1 3.31007517544568 726 609 3961 1024 2383 354 265 285 49 1743 609 451 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 40/98 Kevin Vogelsang 4.75697245256268e-10 5.99225078298622e-09 435 572.181818181818 609 4.32452041235568e-11 9 2.48276667531822 2.81553938093459 1 5.25089952928678 378 675 609 433 1073 434 623 9 619 1247 194 452 M835 KEGG_DILATED_CARDIOMYOPATHY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DILATED_CARDIOMYOPATHY.html Dilated cardiomyopathy 51/122 KEGG 1.20624564140876e-10 1.66739441759335e-09 250 686.818181818182 610 1.09658694679537e-11 248 2.35447599902114 2.47841878402019 1 5.31602015621281 250 920 329 423 1685 379 610 1318 663 248 730 453 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 20/64 Jessica Robertson 5.21805107754497e-11 7.66513710011778e-10 350 658.272727272727 613 4.74368279788065e-12 169 3.17155455648396 3.66812446672581 1 7.43618882582516 350 701 310 311 1777 695 613 971 169 323 1021 454 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 128/454 Leona Saunders 7.14107841946773e-09 5.87682771599029e-08 615 1319.18181818182 615 6.49188949331573e-10 127 1.6669008846714 1.80763399963307 1 3.10026067592534 615 4328 1484 1605 154 286 446 416 2969 2081 127 455 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 131/252 Lauren Kazmierski 1.51701996899772e-08 8.92928140317971e-08 915 659.545454545455 616 1.37910907223491e-09 143 1.74552121142214 1.93257551625749 1 3.16491904690752 616 288 436 540 452 955 911 986 1015 143 913 456 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 307/655 Leona Saunders 1.73356852775605e-08 9.65933664811514e-08 435 825.454545454545 617 1.57597140128757e-09 253 1.74207540857246 2.01946378516787 1 3.14337755473385 432 617 490 613 485 1369 1318 867 1329 253 1307 457 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 13/36 Arthur Liberzon 1.45319710134647e-08 8.70803275819636e-08 620 722.909090909091 618 1.32108828267771e-09 226 2.31135739980304 2.59453661465807 1 4.19735198939114 475 1637 1038 361 407 618 226 619 815 1331 425 458 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 26/82 John Newman 8.69439980271043e-09 6.66871748972617e-08 620 659.909090909091 618 7.90399985188246e-10 135 2.06966374632711 2.35726934493129 1 3.82013161660703 618 1045 1080 697 199 564 319 135 1018 1289 295 459 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 153/369 Arthur Liberzon 1.25226984926785e-08 8.0181460061125e-08 465 767.181818181818 619 1.13842714217813e-09 347 1.79822105796948 1.98761584931291 1 3.2820925273468 464 1240 585 999 347 439 619 455 1780 831 680 460 M6220 BIOCARTA_AGR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGR_PATHWAY.html Agrin in Postsynaptic Differentiation 22/59 BioCarta 4.30051592813903e-09 4.03852056898987e-08 625 507.545454545455 622 3.90955994231417e-10 70 2.77342597475175 3.109114100522 1 5.27450416198133 622 191 719 78 70 652 996 847 173 995 240 461 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 209/882 Alexandra Naba 2.12281821992858e-37 3.97901047143414e-35 25 534.181818181818 622 1.92983474538962e-38 24 2.21366397371758 2.26707653124583 1 19.5871686988685 328 622 24 371 282 656 677 734 1376 25 781 462 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 191/406 Leona Saunders 1.22235076535894e-08 7.95012312219011e-08 945 772.545454545455 625 1.11122797468226e-09 333 1.82228310239665 2.03223093448181 1 3.32774461649159 601 625 488 449 333 1318 1206 942 1226 366 944 463 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 43/118 Leona Saunders 5.90036091407277e-08 2.19435778250278e-07 290 668.181818181818 626 5.36396461119945e-09 63 1.84452832599253 1.84690455440584 1 3.15916967786336 288 1033 799 442 1012 218 63 1588 843 626 438 464 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 14/26 Pathway Interaction Database 3.28771538313328e-08 1.47146459268028e-07 335 713.818181818182 628 2.98883221115039e-09 333 1.95657255475977 2.11086126342659 1 3.43841569499527 333 962 1138 806 747 528 426 438 628 1441 405 465 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 127/276 Arthur Liberzon 1.02770328323237e-08 7.26051267693284e-08 630 676.272727272727 630 9.34275716393783e-10 254 1.89502977454015 1.95584109032516 1 3.47979830695745 630 768 758 471 254 699 517 1083 1317 622 320 466 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 35/115 Arthur Liberzon 9.24659576570444e-14 2.11363647600444e-12 310 803.272727272727 630 8.40599615064076e-15 97 2.33741918767567 2.27490169750694 1 7.01925537309169 309 532 200 630 1684 877 866 1452 611 97 1578 467 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 168/404 Leona Saunders 6.92439080607535e-09 5.73280835994154e-08 760 785.090909090909 631 6.29490075260866e-10 148 1.99693268974846 2.23780459916368 1 3.71962002082495 757 631 484 554 148 1278 1119 603 1733 748 581 468 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 32/91 Kate Stafford 3.64272694708442e-07 9.31758650329562e-07 415 753.272727272727 631 3.31157050021983e-08 162 1.96650827676427 2.21113029007693 1 3.05043598147752 414 162 631 567 1710 952 923 765 617 564 981 469 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 32/167 Jessica Robertson 1.07754344396777e-08 7.39899659922656e-08 1335 800 633 9.79584953859537e-10 386 2.4764854840481 2.96954653066164 1 4.54228485580236 1333 541 426 615 633 1194 1079 854 451 386 1288 470 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 117/271 Kevin Vogelsang 1.07856952226805e-16 4.01125141376832e-15 635 675.272727272727 634 9.80517747516404e-18 121 2.24255492556257 2.63476513924685 1 8.30434395028307 634 490 121 419 1429 1001 983 494 891 152 814 471 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 102/194 Arthur Liberzon 7.58650010386673e-12 1.28805577850433e-10 405 637.727272727273 635 6.89681827626627e-13 269 2.24033785491793 2.51688147301859 1 5.69916657271985 319 301 269 401 1062 755 635 907 1022 403 941 472 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 63/156 Jessica Robertson 1.70381316997681e-08 9.53891100897413e-08 1385 908 635 1.54892107561106e-09 333 2.39152251544989 2.74075792573571 1 4.31858289039767 1383 333 437 341 599 2032 1506 621 904 635 1197 473 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 10/21 John Newman 1.6527631681206e-06 3.43909778233265e-06 365 876.363636363636 636 1.50251309979103e-07 364 2.78360960037695 2.78360960037695 1 3.91185139569937 364 1153 586 1215 2399 387 374 636 1234 715 577 474 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 165/408 Arthur Liberzon 1.43140083392616e-07 4.33193130337659e-07 640 822.181818181818 637 1.30127357005306e-08 363 1.7317446749134 1.85164630788124 1 2.83443286205759 637 894 679 581 1371 502 566 1098 1892 363 461 475 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 12/38 Jessica Robertson 5.81144592241805e-08 2.18350347473569e-07 410 710.818181818182 638 5.28313279630114e-09 144 2.32350249251388 2.53977484888072 1 3.98080779208352 409 1150 981 638 1822 471 388 144 240 904 672 476 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 45/125 Yujin Hoshida 7.2377529502251e-16 2.38845847357428e-14 1260 756.636363636364 639 6.57977540929556e-17 133 2.90861776188936 3.21983265381097 1 10.1911326757283 1258 344 137 133 639 1573 1224 1068 320 163 1464 477 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 45/129 Arthur Liberzon 1.61460916082605e-07 4.79861624934624e-07 370 897.727272727273 640 1.4678266175676e-08 152 2.48238849495704 2.68155820345429 1 4.03467723065456 366 1922 640 1858 1669 318 239 218 1152 1341 152 478 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 38/94 Arthur Liberzon 1.00742736651438e-07 3.27152088668496e-07 425 626.181818181818 640 9.15843102406051e-09 323 2.37175370599423 2.45922524159113 1 3.95635265664949 421 678 830 323 1241 459 412 701 360 823 640 479 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 86/232 Arthur Liberzon 1.35458463570784e-11 2.21170160380729e-10 250 827.818181818182 640 1.2314405779238e-12 94 2.29317703509714 2.51182232563977 1 5.69509320004034 248 2058 279 1631 94 792 640 610 1521 368 865 480 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 36/69 Jessica Robertson 4.9129915869798e-08 1.94773930427981e-07 490 782.272727272727 642 4.46635608790513e-09 133 2.47834676335029 2.90151771539589 1 4.27773251325471 489 1663 642 659 1638 324 441 133 1200 1229 187 481 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 10/36 Kevin Vogelsang 2.01133783205564e-08 1.06410983827008e-07 690 616.818181818182 643 1.82848895494926e-09 188 2.15955218543332 2.25895845089041 1 3.87331552944247 687 860 898 418 537 411 188 643 664 979 500 482 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 81/177 Jessica Robertson 2.33441062007955e-12 4.28982281007559e-11 755 547.545454545455 644 2.12219147280185e-13 84 2.66372516035929 3.31755853766617 1 7.10337387241131 754 652 249 84 192 937 894 477 644 438 702 483 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 66/179 Arthur Liberzon 1.32202893380728e-12 2.53894573107414e-11 155 685.454545454545 645 1.20184448528007e-13 153 2.33339133866969 2.45420379775468 1 6.35918447182316 153 910 238 797 2178 419 343 773 777 307 645 484 M4956 BIOCARTA_MONOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MONOCYTE_PATHWAY.html Monocyte and its Surface Molecules 6/16 BioCarta 7.34641354003559e-09 5.98130460392027e-08 430 935 646 7.346413564322e-10 11 2.74699615216864 2.74699615216864 1 5.10371726586237 426 431 3848 693 646 183 24 988 1316 1719 11 485 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 273/587 Jessica Robertson 5.28617436643559e-09 4.69147975021159e-08 700 642.909090909091 646 4.80561307194297e-10 23 1.77196051810364 2.11858943379474 1 3.34025069589398 700 23 445 646 96 834 1080 665 1517 521 545 486 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 92/157 Arthur Liberzon 5.16438701720242e-08 2.01333756760487e-07 420 708.636363636364 646 4.69489739857616e-09 420 1.90092119008247 2.20218370647694 1 3.27403733225463 420 906 793 489 940 463 449 646 1368 746 575 487 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 138/385 Leona Saunders 2.02119533913311e-12 3.77343480445329e-11 555 700.909090909091 647 1.83745030830451e-13 245 2.05229767806823 2.08664266893204 1 5.50228052466687 552 1241 245 499 567 647 979 909 998 304 769 488 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 31/77 Arthur Liberzon 3.27028559331759e-10 4.24032995853142e-09 650 828.909090909091 648 2.97298690345793e-11 282 2.36442998547454 2.45928904213343 1 5.09196594895416 648 815 347 1753 370 487 823 848 2433 282 312 489 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 29/83 Arthur Liberzon 2.59304375777364e-08 1.23737301923903e-07 375 1162.36363636364 650 2.35731253485155e-09 115 1.80928525391754 1.89589187923473 1 3.21459716378497 375 2306 1364 2894 650 296 115 398 2372 1838 178 490 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 204/673 Arthur Liberzon 6.93881164616328e-09 5.73461576259632e-08 655 827.818181818182 650 6.30801060731666e-10 149 1.73039884046585 1.91083656729333 1 3.22309533477407 651 1554 460 1249 149 615 927 650 2133 316 402 491 M16334 BIOCARTA_EPHA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPHA4_PATHWAY.html Eph Kinases and ephrins support platelet aggregation 19/36 BioCarta 6.98477303533668e-08 2.47771736893169e-07 285 665.181818181818 652 6.34979387008729e-09 211 2.87580326803087 2.83032713877467 1 4.88644493737497 285 1205 729 211 1086 339 300 1182 316 1012 652 492 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 47/109 John Newman 1.26287144907587e-08 8.0434968418917e-08 315 762.363636363636 652 1.1480649602956e-09 313 2.24466740122615 2.47516596834019 1 4.0961498141619 313 925 540 1634 352 606 317 1121 1057 652 869 493 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 66/152 Jessica Robertson 6.48777524253939e-08 2.3512540438159e-07 500 650 652 5.89797766714831e-09 97 1.9804433722534 2.31657222560263 1 3.3766767232752 499 97 652 435 1054 592 586 668 1006 829 732 494 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 153/395 Leona Saunders 1.99249962755869e-08 1.05980173152554e-07 960 810.909090909091 653 1.81136331418581e-09 484 1.8316171321111 2.08056872005653 1 3.2859699207057 957 484 597 653 534 1163 1291 1261 789 621 570 495 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 330/861 Yaara Zwang 8.68868382382297e-09 6.66871748972617e-08 440 736 654 7.89880350739827e-10 198 1.66416157530438 1.89322247854539 1 3.07166619390838 437 887 463 1218 198 476 801 724 1868 654 370 496 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 116/304 Jean Junior 3.37884304976583e-09 3.35061274099025e-08 805 738.363636363636 655 3.07167550450471e-10 51 1.94233970318019 2.2212311305289 1 3.73446016220701 589 1307 655 626 51 1199 804 542 802 557 990 497 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 47/135 Arthur Liberzon 1.49053900467335e-10 2.03042609764515e-09 155 681.272727272727 656 1.35503545888576e-11 151 2.32759056818094 2.47571810775733 1 5.20409964268751 151 665 333 874 2254 412 353 656 772 278 746 498 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 70/210 Arthur Liberzon 3.66437175909955e-08 1.58260332379175e-07 375 776.090909090909 656 3.3312471092129e-09 372 1.81208626054491 -1.78760110531325 -1 3.16976117774599 372 656 630 794 788 399 822 641 2263 424 748 499 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 14/55 Arthur Liberzon 1.28729818168592e-07 3.9692324753772e-07 545 776.727272727273 656 1.17027114273665e-08 196 2.18753563098862 2.37970207270432 1 3.60181611430352 544 720 925 599 1483 627 556 196 1141 1097 656 500 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 189/406 Jessica Robertson 6.17987598824005e-11 8.91043042489011e-10 660 768.272727272727 657 5.61806908037605e-12 281 1.97180943515762 2.33242255639234 1 4.59004613397849 281 1171 316 657 1404 607 512 658 1584 705 556 501 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 505/1187 Arthur Liberzon 1.88184340993019e-08 1.02042166516299e-07 645 1162.81818181818 657 1.88184342586619e-09 252 1.72973921675272 1.9435786730913 1 3.11051486010293 644 1492 4670 972 550 836 657 357 1946 415 252 502 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 11/24 Leona Saunders 1.81470741966141e-09 1.98685022629284e-08 660 765.545454545455 658 1.64973401923482e-10 22 2.63092442402632 3.05480911866987 1 5.21196207741372 658 1155 1297 161 1606 928 399 22 91 1488 616 503 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 35/106 Jessica Robertson 1.73481923802054e-12 3.26480439733504e-11 65 676.818181818182 659 1.57710839820173e-13 65 3.00227626420622 3.0849822665144 1 8.09776370045851 65 674 243 882 2051 436 363 844 659 474 754 504 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 19/47 Arthur Liberzon 6.50106201821517e-08 2.35175333250705e-07 605 685.818181818182 660 5.91005655483945e-09 263 2.2683654342719 2.57347494524492 1 3.86753308773302 605 1139 968 698 1056 541 482 263 332 800 660 505 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 22/57 Leona Saunders 4.84629155272227e-08 1.92782022207611e-07 635 733.272727272727 661 4.40571969043572e-09 545 2.18529419513298 2.21029899458139 1 3.77442057363643 655 562 717 1040 910 634 687 545 1023 632 661 506 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 125/342 Kevin Vogelsang 2.44876353840937e-15 7.35570893652969e-14 460 648.545454545455 662 2.22614867128125e-16 131 2.03175553986653 2.2769215322518 1 6.86351344221153 459 290 150 382 1111 1103 968 662 905 131 973 507 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 24/61 Arthur Liberzon 2.54614744088158e-08 1.22429308722186e-07 400 682.454545454545 663 2.31467951849923e-09 400 2.85916194408609 3.26479610402892 1 5.08333060381623 400 556 555 663 642 885 711 827 470 920 878 508 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 19/33 Arthur Liberzon 1.94759341704794e-07 5.56489192212599e-07 665 786.727272727273 664 1.7705396267841e-08 302 2.73476937962029 2.95317351840536 1 4.39961807741387 664 567 517 461 2017 1141 757 728 302 376 1124 509 M33 PID_GLYPICAN_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_GLYPICAN_1PATHWAY.html Glypican 1 network 18832364 13/37 Pathway Interaction Database 2.30885214135756e-08 1.15651168041571e-07 775 781.181818181818 668 2.09895651417133e-09 25 2.15514257799408 2.34462304233104 1 3.84535973370808 771 584 1275 805 1849 622 668 100 123 1771 25 510 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 49/125 Kevin Vogelsang 5.01937838112638e-08 1.97820076484089e-07 925 723.090909090909 669 4.56307135967754e-09 439 2.41984272983263 2.64498948939365 1 4.1725571992017 548 922 512 439 925 669 535 888 951 614 951 511 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 28/59 Reactome 7.40741446040779e-08 2.59619627236132e-07 670 622.818181818182 670 6.73401337255992e-09 181 2.72582666553488 2.92499877759523 1 4.61738804074478 714 690 803 213 1108 667 443 571 181 791 670 512 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) 32/92 Reactome 2.58089114076707e-11 3.99143758601799e-10 1165 890 670 2.34626467345213e-12 24 2.45315750936036 2.5485018260831 1 5.93061566567332 1165 159 295 416 24 1728 1323 2661 670 189 1160 513 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 39/196 Jessica Robertson 3.38114357088992e-07 8.78759776660576e-07 345 1042.36363636364 671 3.07376735502945e-08 343 2.06204163551979 2.14663146527827 1 3.21211634490153 343 1719 627 1989 1680 415 395 1250 1869 508 671 514 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 2/9 Jessica Robertson 2.40236109020913e-06 4.77618331299109e-06 940 1233.2 672 2.66929295028053e-07 54 2.22892950160197 2.22892950160197 1 3.05057453133998 938 748 4515 NA 2622 594 322 596 54 1397 546 515 M14171 KEGG_STARCH_AND_SUCROSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STARCH_AND_SUCROSE_METABOLISM.html Starch and sucrose metabolism 15/58 KEGG 9.40161302388563e-09 6.97087953005191e-08 495 941.363636363636 673 8.54692096733006e-10 34 2.88281266412421 3.28267490037187 1 5.30675037585585 492 2703 1232 956 1337 673 653 56 34 1997 222 516 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 19/56 Kevin Vogelsang 7.6594490330419e-07 1.74014393434556e-06 675 860.454545454545 673 6.96313790884752e-08 205 1.79130641091844 1.92480467996231 1 2.65366987732711 673 205 1036 604 1971 911 522 498 1310 484 1251 517 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 70/261 Jessica Robertson 1.29249866726843e-09 1.48812008717932e-08 1070 695.363636363636 673 1.17499878911616e-10 26 2.18057790811409 2.27118907994628 1 4.39021406373366 934 508 375 26 673 1056 1066 1066 333 275 1337 518 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 20/39 Leona Saunders 1.84168936532004e-06 3.76533872857317e-06 590 1188.45454545455 677 1.67426446096189e-07 182 2.57998476025566 2.57998476025566 1 3.59957456256879 182 2386 589 1673 2781 590 362 965 2222 677 646 519 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 8/24 Arthur Liberzon 1.10095787120864e-06 2.40292901000638e-06 505 1105.27272727273 678 1.10095841665773e-07 41 2.56229285785372 2.56229285785372 1 3.70344999136151 502 1160 4276 958 2084 367 528 678 41 1065 499 520 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 26/50 John Newman 4.19342739383904e-07 1.04858061726413e-06 305 1048.27272727273 678 3.81220744831805e-08 89 2.00147128467175 2.00147128467175 1 3.07826140498182 304 2344 1768 1374 2070 320 89 534 678 1596 454 521 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 14/20 Arthur Liberzon 3.45359431971188e-08 1.53253247937215e-07 680 691.545454545455 679 3.13963124902448e-09 186 2.55409232722959 2.63021455434057 1 4.47687545306431 679 1281 838 798 763 671 624 186 498 845 424 522 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 15/29 Arthur Liberzon 2.53998101760287e-08 1.22326321156085e-07 685 891.909090909091 682 2.30907367902535e-09 229 1.62811465042914 1.87171280582882 1 2.89479313855079 682 1582 1656 1262 640 519 349 529 783 1580 229 523 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 52/160 Jessica Robertson 6.6470823558304e-14 1.56523758389051e-12 660 815.545454545455 685 6.04280214166417e-15 194 2.45715358899147 2.79963836996764 1 7.46126411014557 659 515 194 679 685 1411 1258 1096 803 321 1350 524 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 153/365 Yaara Zwang 7.96517698442409e-09 6.32624056762903e-08 635 886.545454545455 686 7.24107001205664e-10 50 1.85284004137914 1.95681208663821 1 3.43083611798494 631 50 534 617 177 1039 1139 1871 1693 686 1315 525 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 31/75 Jessica Robertson 1.16842983680135e-07 3.67220805851852e-07 185 737.181818181818 687 1.06220899896107e-08 151 2.05441854635207 2.04999405392606 1 3.40048644539911 181 687 665 1025 1308 171 151 789 1597 1138 397 526 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 83/232 John Newman 2.4379004662581e-08 1.19623053244874e-07 410 696.545454545455 688 2.21627317570307e-09 406 2.31626935548212 2.71960725881483 1 4.12411661862167 406 907 450 822 998 643 543 667 834 704 688 527 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 17/47 Jessica Robertson 2.780856552873e-07 7.47624429533153e-07 630 805.090909090909 690 2.52805173125498e-08 47 2.07618138184677 2.71275961402685 1 3.27162398863273 627 713 1401 577 1603 690 503 717 47 1807 171 528 M17807 KEGG_BASAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_CELL_CARCINOMA.html Basal cell carcinoma 26/60 KEGG 1.0931882693251e-07 3.48956418941242e-07 745 676.636363636364 692 9.93807566950948e-09 232 2.71215569649997 2.7777985268334 1 4.504633494464 742 692 511 232 1275 890 383 1089 256 450 923 529 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 64/196 Jessica Robertson 1.14761276286581e-08 7.71377224059447e-08 515 1916.36363636364 692 1.04328433532022e-09 294 2.14874942174208 2.34030409299749 1 3.93116213723494 3630 511 434 514 294 3862 3727 2453 692 375 4588 530 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 12/24 Arthur Liberzon 4.31742157712664e-08 1.76693777383541e-07 695 803 694 3.92492878350411e-09 121 3.60325405373543 3.60325405373543 1 6.25858389976015 694 1850 1040 345 862 680 1047 372 121 1626 196 531 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 29/64 John Newman 1.17451295704954e-08 7.80259491772358e-08 500 849.909090909091 694 1.06773905756355e-09 428 2.58400556329136 2.99262661949157 1 4.72416357115828 496 820 428 664 1863 1155 694 1111 487 465 1166 532 M7761 KEGG_MELANOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOGENESIS.html Melanogenesis 48/110 KEGG 1.08475551531524e-07 3.47210679287378e-07 825 773.727272727273 695 9.86141426183051e-09 133 1.93726529055233 2.05839914477601 1 3.21869927815739 824 133 760 609 1269 555 620 1460 1168 695 418 533 M7404 FRIDMAN_IMMORTALIZATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_IMMORTALIZATION_DN.html Genes down-regulated in immortalized cell lines. 18711403 24/63 Jessica Robertson 2.93153407145255e-08 1.35592118795245e-07 455 683.454545454545 696 2.66503100955971e-09 69 2.66673131390355 2.7718487527997 1 4.7107861685576 454 1136 795 69 696 986 1244 107 232 1132 667 534 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 38/105 Jessica Robertson 2.25329808426186e-08 1.14274402844709e-07 700 892.636363636364 696 2.04845282485521e-09 52 1.6889644044492 1.81254176618651 1 3.01583069822683 696 1392 1169 1233 583 278 236 182 2381 1617 52 535 M18928 BIOCARTA_IL5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL5_PATHWAY.html IL 5 Signaling Pathway 4/16 BioCarta 2.30096292595336e-06 4.59604103623932e-06 595 1138.36363636364 697 2.30096530845051e-07 298 2.83247449556628 2.83247449556628 1 3.88876776583293 593 742 3843 1032 2377 417 298 579 697 1268 676 536 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 385/1587 Jessica Robertson 9.05988980090664e-16 2.88807099367677e-14 700 677.727272727273 697 8.23626345536968e-17 142 1.90137446977672 2.10971082492016 1 6.62163900073555 697 997 142 565 942 429 939 902 1326 263 253 537 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 74/249 Leona Saunders 6.20668662026955e-18 2.59683334844492e-16 1085 670.909090909091 700 5.6424423820632e-19 82 2.25689228958035 2.44647950494988 1 9.04756703401441 1084 82 107 678 1227 1166 747 530 968 91 700 538 M16519 BIOCARTA_TCAPOPTOSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCAPOPTOSIS_PATHWAY.html HIV Induced T Cell Apoptosis 2/10 BioCarta 1.03422248109168e-07 3.3446283964083e-07 820 1118.8 700.5 1.14913614292242e-08 52 2.28633626261234 2.28633626261234 1 3.80822219449778 818 1083 3841 NA 2108 402 52 418 583 1387 496 539 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 22/40 Leona Saunders 2.10123892807087e-08 1.0940450685489e-07 625 776.363636363636 703 1.9102172255818e-09 556 2.59555997259629 2.48347213587712 1 4.64728357973642 625 703 618 650 556 927 1158 749 817 633 1104 540 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 36/94 Jessica Robertson 1.15723044923984e-08 7.71377224059447e-08 705 795.454545454545 704 1.05202768666094e-09 57 2.52758693559626 2.67141699229717 1 4.62424982650913 704 680 427 57 1814 983 1013 1010 656 596 810 541 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 52/104 Arthur Liberzon 3.71050575853221e-08 1.59372539641036e-07 775 751.090909090909 707 3.37318711010306e-09 292 2.2127407510184 2.43229015297885 1 3.8688682676689 773 1182 469 410 1713 759 935 707 582 440 292 542 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 171/413 Arthur Liberzon 1.05921528482362e-12 2.06811784361812e-11 185 806.181818181818 711 9.62922986203755e-14 135 1.8618513672471 2.00166396291802 1 5.11675735526535 185 1651 234 1576 755 388 471 711 2029 135 733 543 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 15/36 Arthur Liberzon 7.56023537726283e-08 2.63595706680458e-07 160 717.818181818182 712 6.87294148824375e-09 37 1.99348010157358 1.99348010157358 1 3.37345191340705 157 712 755 1246 2133 108 37 766 882 709 391 544 M691 REACTOME_KERATAN_SULFATE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_DEGRADATION.html Genes involved in Keratan sulfate degradation 6/12 Reactome 1.3495197438375e-07 4.13323498014543e-07 520 983.272727272727 713 1.34951982579166e-08 322 2.29806673120282 2.66251274894983 1 3.7734138857155 518 602 3958 795 1384 507 713 739 322 773 505 545 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 6/19 Arthur Liberzon 2.89145518275273e-07 7.70725767143305e-07 715 1152.63636363636 713 2.89145555897589e-08 270 2.11450455977111 2.01571935316162 1 3.32482503589985 713 601 4278 833 1655 520 457 2069 270 774 509 546 M5485 REACTOME_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MUSCLE_CONTRACTION.html Genes involved in Muscle contraction 36/77 Reactome 7.17095379945671e-12 1.23088239942323e-10 715 853.909090909091 715 6.51904890861826e-13 266 3.09398319561625 3.4444134494365 1 7.88643615567954 396 1328 266 715 711 966 1076 1768 654 414 1099 547 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 5/17 Leona Saunders 1.92454202876787e-06 3.91899024495642e-06 2240 1241.54545454545 715 1.92454369550781e-07 44 1.42697361874437 1.69994036744151 1 1.98452678767592 1229 247 4170 1026 2237 715 361 680 44 2239 709 548 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 127/297 Arthur Liberzon 4.38167045103197e-16 1.50974321570116e-14 720 653.818181818182 717 3.98333677366543e-17 131 2.23703799792954 2.6069299033554 1 7.95269910202658 336 1305 131 918 637 717 816 525 907 180 720 549 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 18/44 John Newman 1.63379806020076e-07 4.83920641129577e-07 335 885.090909090909 718 1.48527107412038e-08 332 2.54129996129025 2.54129996129025 1 4.12803607132171 332 1682 718 1261 1414 442 462 457 1466 939 563 550 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 18/35 Joao Pedro de Magalhaes 3.23582914673632e-06 6.24252588785772e-06 945 983.090909090909 718 2.94166718736848e-07 348 3.06202243661985 3.3249923212099 1 4.09918671893485 429 1895 611 1202 2864 348 394 718 943 942 468 551 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 12/24 Jessica Robertson 4.69249270022714e-07 1.15097176542038e-06 500 754.727272727273 719 4.26590336464841e-08 214 2.50234679015131 2.89248067536219 1 3.82256393312839 500 419 767 719 1805 884 915 616 214 494 969 552 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 15/73 Leona Saunders 1.23433977476228e-11 2.03666062835776e-10 775 659.818181818182 721 1.12212706797201e-12 185 3.18639344555449 3.34803813656035 1 7.94273944271451 772 216 276 185 758 963 721 1508 241 399 1219 553 M4013 KEGG_GAP_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GAP_JUNCTION.html Gap junction 39/107 KEGG 1.94455310233833e-09 2.11911065989707e-08 720 983.636363636364 723 1.76777554914281e-10 18 1.5106607618861 1.76931204402329 1 2.98180135041716 720 1330 1438 628 18 549 485 814 2415 1700 723 554 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 13/41 Jessica Robertson 2.3070804556136e-07 6.44661837507773e-07 470 1018.36363636364 724 2.09734608868265e-08 68 1.84888140480612 1.90617795188609 1 2.94405032012209 469 724 1199 2232 1973 198 68 625 2210 1335 169 555 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 12/33 Arthur Liberzon 9.00818255121532e-06 1.5803947373641e-05 710 1002.36363636364 725 8.18929039689743e-07 514 2.28465100246337 2.37017759483555 1 2.82144400407564 598 725 708 1063 2570 707 514 941 1452 672 1076 556 M7528 KEGG_PANTOTHENATE_AND_COA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PANTOTHENATE_AND_COA_BIOSYNTHESIS.html Pantothenate and CoA biosynthesis 11/20 KEGG 2.00696107592617e-08 1.06410983827008e-07 830 825 726 1.82451008566797e-09 151 2.68110098159039 2.68110098159039 1 4.80875167057491 829 423 1205 726 536 1289 1701 151 161 1482 572 557 M47 PID_INTEGRIN_CS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_CS_PATHWAY.html Integrin family cell surface interactions 18832364 14/27 Pathway Interaction Database 4.35105071276013e-08 1.77450162227972e-07 460 727.727272727273 728 3.95550072619368e-09 193 1.76227155446642 2.05804134056866 1 3.06009340666622 456 1145 1357 728 866 371 335 735 379 1440 193 558 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 18/34 John Newman 6.71621627245421e-08 2.4042925479542e-07 710 680.181818181818 728 6.10565134317143e-09 158 1.9852331735002 1.91834237640724 1 3.37989648262249 710 215 920 813 1071 517 509 1046 795 728 158 559 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 33/145 Reactome 3.21950804467725e-09 3.25764717911044e-08 560 943 729 2.92682549944428e-10 45 1.98294049117399 1.96944552201752 1 3.81875454985614 557 942 863 1991 45 658 574 1690 1823 501 729 560 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 85/177 Kevin Vogelsang 5.78663266503882e-09 5.04017856289441e-08 395 873.272727272727 729 5.26057516387212e-10 166 2.01421371882809 2.1328486154119 1 3.7807811258887 391 1100 412 1446 166 736 563 729 2389 959 715 561 M1878 HUNSBERGER_EXERCISE_REGULATED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HUNSBERGER_EXERCISE_REGULATED_GENES.html Exercise regulated genes in hyppocampus. 18059283 22/53 Jessica Robertson 3.31027764487767e-08 1.47873794508072e-07 260 660.272727272727 729 3.00934335880589e-09 30 1.94136002261481 2.04859175105498 1 3.41061238619316 257 699 1012 801 1052 33 30 1616 729 996 38 562 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 14/29 Arthur Liberzon 9.5219791250548e-07 2.1146106422627e-06 805 1018.90909090909 729 8.65634840575813e-08 279 2.37578400719923 2.49032816901309 1 3.46779846067518 804 2705 1326 408 2020 729 491 618 279 1455 373 563 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 102/331 Arthur Liberzon 4.19465717738168e-10 5.32687358623592e-09 790 746.909090909091 730 3.81332470743769e-11 233 1.85456206458026 2.08239837384955 1 3.94666948863777 786 298 353 730 467 1291 1044 600 1340 233 1074 564 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 112/224 Arthur Liberzon 1.92671478707534e-09 2.10456538280537e-08 420 771.636363636364 731 1.7515588988752e-10 386 2.03373762636029 2.48288544563975 1 4.01583575248981 416 493 386 610 1116 1079 762 731 1429 546 920 565 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 30/75 Arthur Liberzon 4.23746868970589e-08 1.74029608062768e-07 375 765.545454545455 731 3.85224433756791e-09 373 2.40136524603843 2.69277468241568 1 4.17506795361929 373 1042 472 774 1278 731 458 1287 565 402 1039 566 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 4/15 Arthur Liberzon 1.27260517241753e-08 8.0434968418917e-08 1900 1152.45454545455 733 1.27260517970538e-09 82 1.8149808491113 1.70600935332009 1 3.31204229720446 1900 249 4591 585 393 831 707 733 82 1279 1327 567 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 12/33 Jessica Robertson 3.08269147713557e-06 5.97414899166969e-06 205 1004.45454545455 735 2.80245072425771e-07 205 2.6090782108196 2.6090782108196 1 3.50562921143936 205 2161 735 835 3105 494 323 605 890 1215 481 568 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 8/13 Arthur Liberzon 3.58521104128048e-07 9.21069020802649e-07 740 1350.18181818182 736 3.58521161969883e-08 195 1.4639576977375 1.6451596627764 1 2.27276945680731 736 1854 4264 586 1744 535 258 657 1142 2881 195 569 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 313/819 John Newman 4.44880125463459e-14 1.0801597243118e-12 470 786.909090909091 736 4.04436477694063e-15 188 1.97928186285771 2.35460865455753 1 6.0921964666689 470 618 188 386 1230 1299 938 736 1419 295 1077 570 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 20/68 Jessica Robertson 3.77676251568626e-06 7.17385859282766e-06 570 1267.45454545455 737 3.43342636300792e-07 415 2.81570500532284 2.81570500532284 1 3.72569797754236 568 2236 1161 1108 3183 710 541 681 737 2602 415 571 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 21/55 Reactome 2.60120547784776e-08 1.23874480377994e-07 990 756 738 2.36473228054868e-09 345 1.97285441699011 2.32869036853875 1 3.50496994906947 990 392 950 951 652 1225 821 634 618 738 345 572 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 30/67 John Newman 5.05698837102918e-08 1.98484686911924e-07 525 753.090909090909 738 4.59726226115519e-09 367 2.0503771460336 2.18209095763641 1 3.53471602445939 523 367 738 883 928 692 669 1120 873 599 892 573 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 61/159 John Newman 4.22396742999399e-09 3.98259786256577e-08 730 860.181818181818 739 3.83997039827632e-10 69 1.94318542833003 2.14441529761635 1 3.69857866212196 729 1111 1186 444 69 807 739 594 2186 1374 223 574 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 60/121 Arthur Liberzon 3.17677177539312e-12 5.70358334846442e-11 690 856 741 2.88797434127063e-13 255 3.05677912799397 3.2384651948899 1 8.0542673458917 689 1110 255 426 1253 1050 671 1621 741 648 952 575 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 14/25 John Newman 2.1188268467107e-07 5.99204743734843e-07 715 1040.09090909091 745 1.926206409796e-08 253 2.1700270921029 2.38893692620829 1 3.47314945565084 711 1635 1181 1387 2166 499 561 253 745 1881 422 576 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 46/141 Arthur Liberzon 3.68271572581043e-08 1.58759943800807e-07 750 777.727272727273 746 3.34792344314334e-09 381 1.85044652212668 2.20154245041837 1 3.2362106884694 746 527 558 734 790 1186 1098 654 830 381 1051 577 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 53/123 Yujin Hoshida 9.47184673227331e-09 7.01185999801465e-08 1570 894.545454545455 747 8.61076979368477e-10 116 1.93400415460144 2.69084140705075 1 3.55889459216185 1568 116 716 767 222 2156 1440 497 407 747 1204 578 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 75/152 Jessica Robertson 3.31519286560431e-09 3.31944311286791e-08 1030 785.181818181818 748 3.01381170054546e-10 49 1.40435160208229 1.63620726667773 1 2.70155774136035 1030 86 1485 648 49 1251 748 365 1257 1127 591 579 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 159/576 Arthur Liberzon 2.1625179169591e-27 2.20294759975443e-25 900 710.909090909091 750 1.96592537905372e-28 40 2.17558434589583 2.44152956781589 1 13.7979564392136 896 40 45 220 99 1585 1112 1664 750 48 1361 580 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 188/404 Arthur Liberzon 1.65258035581356e-08 9.3526467963072e-08 560 727.909090909091 753 1.50234578929755e-09 38 1.49573978384912 -1.42504845710249 -1 2.70428393597643 559 38 1520 1031 463 51 886 753 1571 892 243 581 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 20/34 Leona Saunders 1.45805877827314e-07 4.39386716076395e-07 760 768.272727272727 757 1.32550806809689e-08 526 2.14291695924974 2.4276175783075 1 3.50402078647422 613 564 788 757 1381 871 759 767 685 526 740 582 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 87/175 Arthur Liberzon 3.89988442186935e-07 9.88899264116872e-07 670 880.727272727273 760 3.54535010290199e-08 181 1.93020270291369 2.06541883441351 1 2.98128566799253 666 1014 1033 252 2475 760 605 381 1186 1135 181 583 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 108/290 Leona Saunders 1.22259903556762e-08 7.95012312219011e-08 1010 755.545454545455 760 1.11145367487448e-09 184 2.02700066009253 2.35319252719627 1 3.70158762329653 1010 495 554 355 334 1693 1127 184 928 871 760 584 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 147/388 Aravind Subramanian 8.42536812140431e-21 4.8051130638796e-19 80 643.818181818182 762 7.65942556491297e-22 76 2.01244384361856 2.02855744078207 1 9.48216550658503 107 893 77 864 1153 420 450 826 1454 76 762 585 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 11/26 Leona Saunders 1.58313572438863e-07 4.72219860247302e-07 1450 978.181818181818 763 1.43921439846565e-08 25 2.5379699560084 2.93936755482804 1 4.12956615603959 1447 233 763 120 1405 2174 1897 716 25 1491 489 586 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 12/39 Kevin Vogelsang 3.47201842329334e-08 1.53779568351159e-07 925 826.272727272727 765 3.1563804346258e-09 182 2.07020111077599 2.40396878397044 1 3.62790621148573 923 1412 1288 406 765 976 646 587 182 1213 691 587 M8719 BIOCARTA_MCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCALPAIN_PATHWAY.html mCalpain and friends in Cell motility 21/49 BioCarta 9.30406717792084e-09 6.92045377710112e-08 1465 1066.81818181818 766 8.45824292478988e-10 95 2.30841380633638 2.61280982435545 1 4.25125533720446 1462 197 766 95 219 1837 2202 2301 490 737 1429 588 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 152/375 Leona Saunders 2.10718601530981e-08 1.09592382549853e-07 770 856.272727272727 766 1.91562366862972e-09 340 1.92014269105643 2.27852147362005 1 3.43759817288504 766 487 644 340 557 1702 1377 846 842 736 1122 589 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 22/67 Leona Saunders 1.57913512403192e-06 3.3134926769811e-06 730 865.363636363636 768 1.43557841592582e-07 203 2.50542063301895 2.72089696061168 1 3.53132105286765 768 203 728 845 2295 730 1131 507 821 810 681 590 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 71/140 John Newman 5.55138608762897e-08 2.11494269972596e-07 390 869.454545454545 771 5.0467147524639e-09 387 2.13880620570706 2.12009986884393 1 3.67199381459439 387 911 535 1424 971 505 771 1176 1708 514 662 591 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 113/253 Arthur Liberzon 2.12542069705042e-08 1.09930699628899e-07 565 893.909090909091 773 1.9322006523492e-09 561 1.58521788166404 1.74454488519603 1 2.83744223979908 639 773 907 890 564 657 952 1062 2110 718 561 592 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 20/57 Arthur Liberzon 3.56798643345016e-08 1.56664062128372e-07 415 1012.36363636364 773 3.24362408301472e-09 131 2.27674293223219 2.27674293223219 1 3.98513232433089 411 2843 1101 1777 773 226 131 432 1830 1074 538 593 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 78/177 Jessica Robertson 8.48600636087981e-08 2.85955903690318e-07 670 730.272727272727 774 7.71455153473499e-09 230 1.868650946922 2.21335188643058 1 3.14521463302862 667 1016 857 572 1172 651 774 230 974 869 251 594 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 34/58 Leona Saunders 1.04434101993382e-06 2.28895323639377e-06 385 1087 775 9.49401377893924e-08 383 2.16409554536892 2.3747057284782 1 3.13965661601509 383 1570 1061 775 2053 693 986 730 586 2634 486 595 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 215/575 Jessica Robertson 1.81305215413772e-13 3.91519004345132e-12 420 770.454545454545 775 1.64822923103443e-14 211 2.12950055748854 2.49235630302882 1 6.24823397002282 419 1091 211 607 1187 886 841 726 1283 449 775 596 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 16/32 Itai Pashtan 1.17392397778951e-06 2.55030494201281e-06 515 1019.36363636364 776 1.06720418563448e-07 296 2.22331617114533 2.32902515992742 1 3.19872111773774 512 1898 1215 1682 2147 551 358 468 296 1310 776 597 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 486/1078 Jessica Robertson 1.48710894259318e-16 5.44421289452472e-15 860 787.909090909091 779 1.35191722053925e-17 123 1.9017976185713 2.2396603343902 1 6.97760340628688 779 750 123 335 857 1429 1093 691 1524 230 856 598 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 73/300 Arthur Liberzon 3.84250283132858e-17 1.52592951420387e-15 550 787.636363636364 780 3.49318439211689e-18 89 2.35058393366338 2.57899168918361 1 8.95816499462005 550 89 113 1096 733 780 1259 1342 1586 142 974 599 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 16/39 Leona Saunders 1.3510717925337e-08 8.33042423659596e-08 205 857.636363636364 781 1.2282470916645e-09 14 1.7109086337577 1.7109086337577 1 3.11542866370989 201 1143 1091 1994 2241 44 14 207 1606 781 112 600 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 41/116 Arthur Liberzon 2.5710705460082e-06 5.06858922111671e-06 1390 1011.63636363636 782 2.33733959158372e-07 256 2.21258269937405 2.45861937061018 1 3.01351526270496 290 1388 709 1334 2281 431 256 782 1386 1573 698 601 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 264/820 Jessica Robertson 4.34194406828871e-46 1.69552915866674e-43 70 749 783 3.94722188026249e-47 12 2.26388965367706 2.45025373180597 1 24.9057855824966 68 757 12 325 1996 818 783 1020 1374 26 1060 602 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 11/33 Arthur Liberzon 5.44871925312357e-08 2.09505684742377e-07 755 1150.18181818182 785 4.95338126188316e-09 127 3.07590849971201 3.07590849971201 1 5.28409716253375 755 1812 1265 2403 2095 491 127 141 785 2617 161 603 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 267/623 Leona Saunders 1.21742189437817e-12 2.34767036915889e-11 385 760.181818181818 787 1.10674717670804e-13 211 1.84633679993054 2.08708951238816 1 5.04797075972553 385 889 237 694 682 1033 1026 787 1459 211 959 604 M17761 ST_WNT_BETA_CATENIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_WNT_BETA_CATENIN_PATHWAY.html Wnt/beta-catenin Pathway 20/54 Signaling Transduction KE 2.14533225843968e-08 1.10838224509905e-07 525 1113.54545454545 789 1.95030207214538e-09 84 2.22317079522895 2.38856148834916 1 3.97729691561713 676 2876 1343 1028 1957 789 521 84 747 1705 523 605 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 39/85 John Newman 9.25316986741124e-08 3.05835106730055e-07 790 810.272727272727 789 8.41197296054395e-09 272 3.21621647956903 3.80843078577753 1 5.3892195620868 789 1331 492 272 1206 857 670 1106 694 1023 473 606 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 46/229 Reactome 2.77376810880067e-07 7.4614680584615e-07 530 1165 790 2.52160768956221e-08 523 1.82347749417152 2.01757468727762 1 2.87381892031188 527 528 621 2068 1602 790 631 1440 2817 523 1268 607 M28 PID_IL4_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL4_2PATHWAY.html IL4-mediated signaling events 18832364 49/106 Pathway Interaction Database 3.50083853695873e-08 1.54549951747859e-07 685 781 791 3.1825805387884e-09 347 2.53904044140022 2.675317234546 1 4.4481023864181 684 347 594 670 770 905 791 989 837 852 1152 608 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 96/201 Arthur Liberzon 4.37171694608656e-09 4.07300268483159e-08 500 929.090909090909 792 3.97428814070345e-10 73 1.86926553553448 1.90311526881519 1 3.55319558139488 498 1438 804 1637 73 525 792 1131 2097 671 554 609 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 140/271 Lauren Kazmierski 3.78436630497889e-11 5.70210305631224e-10 1555 1263.54545454545 792 3.44033300458544e-12 47 1.86205153081788 2.21676225790425 1 4.42739890565665 1554 47 303 500 617 3510 2408 1809 792 177 2182 610 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 29/86 Jessica Robertson 7.16597442525538e-09 5.88086797841448e-08 645 825.181818181818 793 6.51452222599711e-10 157 2.41507141715373 2.37101084038375 1 4.49159402020153 641 1399 1032 817 157 793 732 434 674 1552 846 611 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 84/379 Jessica Robertson 3.29363685197915e-14 8.16612819490704e-13 2690 1741.72727272727 793 2.99421531998109e-15 117 2.05013608981633 -1.71941932266953 -1 6.37434015475502 2686 307 184 793 377 3982 2789 3475 775 117 3674 612 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 158/386 Arthur Liberzon 1.33860710957766e-14 3.60500742269017e-13 655 791 794 1.21691555416151e-15 116 1.81129474690996 -1.76655716740439 -1 5.79717188194661 654 284 169 910 1155 327 1872 1301 1119 116 794 613 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 14/29 Jessica Robertson 1.62655267934994e-08 9.24201006892422e-08 745 998 795 1.47868426488703e-09 404 1.64191409168653 1.68243457530621 1 2.97074840490081 741 412 1330 1712 459 728 404 1295 1654 1448 795 614 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 384/857 Lauren Kazmierski 6.24045211992346e-09 5.31686520617479e-08 800 789.909090909091 796 5.67313830693178e-10 126 1.64560969559066 1.84694769316529 1 3.0790685103773 796 263 423 649 126 1277 1248 1063 1576 257 1011 615 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 48/110 Pathway Interaction Database 1.58947351001096e-08 9.15021236844149e-08 955 857.090909090909 798 1.44497592863156e-09 446 2.30339829905927 2.47641176974437 1 4.17015378007914 952 667 798 1140 446 1270 1253 604 672 953 673 616 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 191/488 Jessica Robertson 1.42357906604301e-08 8.60760193997102e-08 920 830 798 1.29416279568612e-09 399 1.7949121923842 2.16504250778909 1 3.26182965945724 919 1001 786 618 399 1242 749 798 1173 813 632 617 M17400 BIOCARTA_ALK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ALK_PATHWAY.html ALK in cardiac myocytes 24/51 BioCarta 6.19116418254147e-08 2.26654651245229e-07 800 857.727272727273 799 5.62833123342824e-09 430 2.12126787289539 2.1936148801513 1 3.62547847863869 799 1455 1128 430 1037 845 573 501 791 1131 745 618 M523 KEGG_THYROID_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_THYROID_CANCER.html Thyroid cancer 19/43 KEGG 5.4341913856302e-08 2.09467654152284e-07 555 818.818181818182 800 4.94017410896313e-09 140 2.65388311829906 3.34911343899451 1 4.55915438018335 551 1206 800 446 2074 929 1081 140 157 1011 612 619 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 12/29 Reactome 1.40551428856101e-06 2.98831213983524e-06 800 921.272727272727 800 1.27774107863901e-07 315 2.4784579396195 2.54744758678763 1 3.52191616953233 800 1357 1045 518 2124 741 704 492 315 1208 830 620 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 54/131 Arthur Liberzon 1.65649137059003e-08 9.36347233122422e-08 685 874.545454545455 800 1.50590125732963e-09 460 2.07182263994195 2.506517584761 1 3.74556885531669 683 800 677 780 465 1561 1544 460 816 897 937 621 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 303/758 Kevin Vogelsang 1.70959930147127e-15 5.20206644590542e-14 1095 774.181818181818 800 1.55418118315569e-16 72 1.9047302168319 1.98061655560724 1 6.50811566576863 966 755 148 312 72 1091 800 1624 1522 132 1094 622 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 19/42 Leona Saunders 3.45253433320681e-09 3.39886048012754e-08 805 923.727272727273 801 3.13866758056817e-10 30 2.2384021285814 2.1842741606541 1 4.30011286308304 801 1464 1282 1809 1585 645 352 30 237 1260 696 623 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 65/182 Arthur Liberzon 7.72028072287913e-08 2.68377117710769e-07 380 765 802 7.01843726709149e-09 104 1.86806264626877 1.98510575408042 1 3.15746383331306 377 1441 1106 802 1125 199 214 592 1538 917 104 624 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 94/168 Arthur Liberzon 3.11332228171695e-08 1.41778699826294e-07 480 879.545454545455 802 2.83029302343184e-09 476 1.89331344565578 2.18866016216283 1 3.33510569689145 476 2056 835 825 719 496 476 883 1531 802 576 625 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 308/830 Jessica Robertson 7.71774659797461e-31 8.82081964831927e-29 580 674.454545454545 803 7.01613327088607e-32 40 2.02164847339323 2.27151346500329 1 14.5883683165819 578 458 40 376 808 1176 999 891 1248 42 803 626 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 94/199 Arthur Liberzon 3.90709312696873e-10 5.00236021665997e-09 805 1035.54545454545 803 3.55190284332964e-11 58 2.14755662366379 2.56541711348277 1 4.58526618546281 803 304 351 515 58 2493 1870 1435 921 706 1935 627 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 58/167 Jessica Robertson 7.3470594959923e-09 5.98130460392027e-08 570 1034.90909090909 805 6.67914501866212e-10 160 1.9526517723256 1.93672711917398 1 3.62788363831586 570 661 707 1411 160 768 810 2916 1270 805 1306 628 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 575/1393 John Newman 4.71538070261769e-09 4.2972296893054e-08 510 1152.72727272727 806 4.71538071262336e-10 108 1.79276087353825 2.04284585201834 1 3.39703937350453 507 885 4403 564 721 763 1162 894 1867 108 806 629 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 10/26 John Newman 1.62275293430935e-07 4.81279762669215e-07 810 802 807 1.4752300490964e-08 248 1.90811549466036 1.84125714820323 1 3.10067042927434 807 859 1224 844 1412 617 530 248 339 1362 580 630 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 25/58 Arthur Liberzon 3.46608787347977e-08 1.53662135999302e-07 1970 927 809 3.15098902553436e-09 378 2.16486639967424 -1.96777292570158 -1 3.79398633972698 1966 378 853 536 764 616 1831 918 392 809 1134 631 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 74/157 Arthur Liberzon 1.29512681313056e-08 8.11358856461202e-08 755 929.818181818182 809 1.17738801886808e-09 364 2.04641315373546 2.25009455545889 1 3.73238490213418 751 509 664 1116 364 1660 1190 1061 809 750 1354 632 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 39/91 Arthur Liberzon 1.2821446419844e-08 8.06460374810588e-08 3825 1722.27272727273 811 1.16558604496059e-09 50 1.96314930126591 -1.66169151557449 -1 3.58185072495245 3823 146 690 50 359 1562 4535 3804 811 722 2443 633 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 78/203 John Newman 8.26383237940181e-07 1.85995766233799e-06 1135 964.454545454545 812 7.51257771230583e-08 453 2.13618527405869 2.49095335831768 1 3.14868968724196 1133 1018 625 812 1988 1343 1474 471 564 453 728 634 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 51/147 Arthur Liberzon 2.79370832186904e-08 1.29745462797605e-07 555 889.818181818182 815 2.53973487031404e-09 437 2.3080080811874 2.53896505734824 1 4.08846478817236 553 1714 462 1366 880 1022 815 437 1059 678 802 635 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 102/290 Jessica Robertson 2.6783124968125e-08 1.26009762651238e-07 1100 925.454545454545 815 2.4348295721988e-09 227 1.63891576791513 -1.69564467192705 -1 2.90856611640971 1100 300 815 1350 667 227 1577 858 2074 515 697 636 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 48/148 Yujin Hoshida 4.56106853451373e-16 1.56008519363003e-14 1920 941.363636363636 817 4.14642594046703e-17 121 2.76549974896061 3.07983136467003 1 9.82125444671736 1918 121 132 126 817 2429 1555 834 556 196 1671 637 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 332/853 Arthur Liberzon 1.77598302092788e-16 6.40173572005235e-15 905 726.545454545455 818 1.61453001902534e-17 125 2.0054976167699 2.36526542228567 1 7.32177734000575 905 886 125 141 681 1357 1095 675 1121 188 818 638 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 13/40 Arthur Liberzon 1.02815896028294e-06 2.25876834875099e-06 550 964.636363636364 819 9.34690400716534e-08 547 2.42483844532509 2.36445717996959 1 3.52153666990055 547 850 659 1097 2047 819 550 1498 606 549 1389 639 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 50/146 Arthur Liberzon 3.30089668343638e-08 1.47595437581897e-07 1405 1110.36363636364 819 3.00081521178481e-09 142 2.37075136362875 2.54192219772026 1 4.16547300633047 677 2903 819 1901 748 923 689 142 1403 1403 606 640 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 11/21 Arthur Liberzon 2.39938256359044e-06 4.77228637223463e-06 785 1092.54545454545 820 2.18125925493572e-07 567 2.83391756175442 3.08024954810536 1 3.87883637109909 782 1943 727 1409 2359 631 1176 567 957 820 647 641 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 49/126 Jean-Pierre Bourquin 3.63353142907903e-07 9.30751827426188e-07 1120 1001.27272727273 824 3.30321093563191e-08 323 2.05149939138539 2.48367596298445 1 3.1825214682187 749 1117 824 1119 2417 758 793 323 1314 986 614 642 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 13/34 Arthur Liberzon 4.16674306429515e-08 1.71726983283088e-07 745 1080.45454545455 824 3.78794831201109e-09 193 1.83258508342144 2.06581006323082 1 3.18890053540602 743 2630 1848 1141 851 405 193 824 338 2276 636 643 M605 KEGG_ASCORBATE_AND_ALDARATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASCORBATE_AND_ALDARATE_METABOLISM.html Ascorbate and aldarate metabolism 4/30 KEGG 6.29843884936241e-08 2.29863586044488e-07 2205 1099.81818181818 825 6.29843902787891e-09 19 3.37166073222863 4.39353459956901 1 5.75724155852857 2202 251 3786 19 1082 2336 825 206 35 1266 90 644 M257 PID_EPHRINB_REV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHRINB_REV_PATHWAY.html Ephrin B reverse signaling 18832364 27/52 Pathway Interaction Database 3.73126511199751e-08 1.59823659184829e-07 610 987.727272727273 826 3.39205925025534e-09 610 1.76273131969909 1.88299734482174 1 3.08149230063421 610 1525 1495 826 795 670 781 1133 1169 1112 749 645 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 344/792 Kevin Vogelsang 8.38498381163848e-09 6.55960503194289e-08 830 1027.45454545455 826 7.62271258508787e-10 186 1.86213643200869 2.20804213282398 1 3.44051472288219 690 2723 522 673 186 1539 977 582 1756 826 828 646 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 40/94 Kevin Vogelsang 2.22215511906843e-08 1.1343157830016e-07 830 863.818181818182 828 2.02014103773979e-09 114 1.9462417606137 2.04425764282546 1 3.4768370324329 828 933 1041 1836 577 705 430 114 1174 1246 618 647 M670 REACTOME_KERATAN_SULFATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_BIOSYNTHESIS.html Genes involved in Keratan sulfate biosynthesis 13/27 Reactome 7.35464617056148e-09 5.98130460392027e-08 1045 773.454545454545 829 6.68604199558929e-10 161 2.14119929799769 2.36215032452963 1 3.97819111935141 1045 228 570 867 161 829 887 784 1443 548 1146 648 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 40/102 John Newman 2.70680786244151e-07 7.30651016324937e-07 995 884.363636363636 830 2.46073472316212e-08 208 3.03530570128767 3.44063318195749 1 4.79078834278618 995 1448 713 208 1953 1160 830 281 280 1249 611 649 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 30/64 Jean Junior 8.75740673365863e-08 2.92913689892394e-07 675 933.363636363636 832 7.96127916569042e-09 482 2.72010327493765 3.44189412059292 1 4.57102952093837 675 1521 710 1335 1185 794 590 832 482 1078 1065 650 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 15/65 Arthur Liberzon 9.93931050479247e-09 7.14401938687495e-08 2630 1549.90909090909 832 9.03573686336087e-10 243 2.43674596782295 2.692704589786 1 4.47894184364835 2627 407 832 682 243 2994 2314 2690 354 711 3195 651 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 17/74 Reactome 3.31309826235508e-07 8.63469324660505e-07 400 1031.72727272727 834 3.01190796481132e-08 201 1.99676227969096 2.12519327337579 1 3.11434364482258 397 1344 834 1586 1675 464 201 781 2419 861 787 652 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 80/223 Arthur Liberzon 2.46025673742357e-10 3.25671273208103e-09 870 868.727272727273 834 2.23659703427154e-11 235 1.97056007392304 -1.87387796617237 -1 4.30183585186093 868 500 340 834 1402 302 1966 1408 1109 235 592 653 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 15/32 Reactome 7.70158408002464e-09 6.14945597655651e-08 970 804 836 7.00144009725978e-10 173 1.97088409458931 2.27662965616174 1 3.6556539599262 968 219 595 836 173 1044 1212 802 1377 533 1085 654 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 31/92 Kevin Vogelsang 1.07613335656289e-09 1.26702535398334e-08 435 872.181818181818 836 9.7830305189935e-11 2 1.97042249562056 1.95046675405796 1 4.00250578267517 434 1522 836 1799 1335 129 119 53 2228 1137 2 655 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 118/257 Jessica Robertson 1.02781435539046e-08 7.26051267693284e-08 840 806.454545454545 839 9.34376691083893e-10 255 2.28849699450111 2.84579540475751 1 4.20231289131911 839 1175 443 265 255 1462 997 576 1070 1025 764 656 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 6/18 Arthur Liberzon 6.58969770213655e-07 1.52943652462664e-06 845 1358.81818181818 845 6.58969965622257e-08 483 2.25711068517737 2.25711068517737 1 3.37626268838362 845 738 4599 1287 1951 791 1304 709 511 1729 483 657 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 333/779 Jessica Robertson 3.34292231308557e-09 3.33296467215297e-08 880 731 846 3.03902028924107e-10 19 1.67084486027769 1.91474883846738 1 3.21345336023411 876 19 882 507 50 1209 846 843 1384 491 934 658 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 9/30 Jessica Robertson 8.41418092497127e-08 2.84321062687225e-07 620 1078.36363636364 847 8.41418124356425e-09 218 2.49918483860996 2.64668946373748 1 4.20809673913278 619 978 4474 847 1208 356 639 411 916 1196 218 659 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 24/60 Leona Saunders 8.23389833930685e-07 1.85589454631996e-06 585 1050.90909090909 848 7.48536492817636e-08 427 1.83384562457347 2.06899676740474 1 2.70349572194161 848 1335 1017 1668 2640 676 617 427 1165 583 584 660 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 45/104 Jessica Robertson 7.75008238313822e-15 2.12379450569507e-13 215 655.909090909091 848 7.04552943921659e-16 165 2.8436978085602 2.728214516935 1 9.26952974354086 215 926 165 1106 1075 430 328 984 901 237 848 661 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 13/29 Arthur Liberzon 8.59226480655716e-07 1.9283214982532e-06 825 1134.63636363636 851 7.81115287484761e-08 325 2.32086708758984 2.44186710673612 1 3.41154834555625 822 1848 851 1257 2322 666 325 431 2328 1007 624 662 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 51/108 John Newman 7.73023356947268e-07 1.75418278482077e-06 925 996.636363636364 852 7.0274875324355e-08 543 2.4292121414377 2.84547116510329 1 3.59649320973747 543 1759 671 704 1974 1177 852 839 598 925 921 663 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 14/26 Leona Saunders 4.22437808561359e-07 1.05407005906205e-06 855 1064 852 3.84034445160636e-08 343 1.9357199897517 -2.07006959250544 -1 2.97600689194348 852 1809 1530 1225 2502 385 738 343 818 1103 399 664 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 366/1518 Arthur Liberzon 1.9925450325484e-28 2.12206045966404e-26 855 1010.63636363636 854 1.81140457504399e-29 43 2.02655709782425 2.16000919038009 1 13.3825306101545 854 454 43 636 613 1913 1309 1842 1600 54 1799 665 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 85/175 Arthur Liberzon 4.72273429362416e-09 4.2972296893054e-08 590 848.545454545455 855 4.29339482160223e-10 82 1.76098157955188 2.05261908328126 1 3.3368219059576 588 1314 1010 777 82 1004 864 459 1783 855 598 666 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 59/137 Arthur Liberzon 5.50283828889726e-14 1.32237437034731e-12 300 683.454545454545 856 5.00258026263398e-15 91 2.66589294859971 2.87749556194657 1 8.14532295226748 299 1021 190 91 1212 1088 856 998 545 168 1050 667 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 36/77 Jessica Robertson 4.0193007973403e-08 1.6726859268505e-07 770 954.363636363636 857 3.65390988251919e-09 676 1.86399127518322 1.97912576143482 1 3.24902807623136 767 676 750 1312 838 1066 916 857 1457 724 1135 668 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 11/16 Jessica Robertson 3.42773137141654e-06 6.57753857758309e-06 725 1102.72727272727 857 3.11612428367123e-07 606 1.82772197631042 1.98685120613836 1 2.4361323547517 724 857 1402 1581 2436 767 606 620 647 1496 994 669 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 14/35 Arthur Liberzon 2.31520915550066e-07 6.45777982302147e-07 770 1053.09090909091 858 2.10473581740532e-08 612 2.66845703111603 2.49852473208349 1 4.24857892629605 770 1845 837 1579 1538 628 644 1172 612 1101 858 670 M2286 REACTOME_PEROXISOMAL_LIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEROXISOMAL_LIPID_METABOLISM.html Genes involved in Peroxisomal lipid metabolism 11/24 Reactome 8.29729500908257e-09 6.52405463573197e-08 885 1205.81818181818 861 7.54299549125071e-10 121 1.01792169826329 -1.01792169826329 -1 1.8813471615747 885 861 2788 2239 183 121 255 260 2844 2611 217 671 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 9/38 John Newman 1.19460252717531e-05 2.04527126136043e-05 525 1331.36363636364 862 1.19460894906229e-06 364 2.03601323141238 2.02327077516153 1 2.45574093572375 521 862 4396 1795 2656 440 364 1025 1255 610 721 672 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 334/808 Arthur Liberzon 2.67409124795842e-08 1.25937603898826e-07 3675 1753.90909090909 862 2.43099207314717e-09 651 1.58824964801389 -1.42394974266386 -1 2.81875112134342 3673 753 862 816 666 738 4006 2827 2417 651 1884 673 M256 PID_TAP63_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TAP63_PATHWAY.html Validated transcriptional targets of TAp63 isoforms 18832364 37/73 Pathway Interaction Database 1.13139111603507e-08 7.66141440713923e-08 1115 853.272727272727 863 1.02853738350315e-09 203 1.6114027382832 1.76195798417057 1 2.94930602759935 1114 683 1519 1128 286 810 972 863 1170 638 203 674 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 9/30 Kevin Vogelsang 1.21195716610294e-06 2.61836389135932e-06 535 1220.27272727273 863 1.21195782708152e-07 385 2.12403499494499 2.05075303841428 1 3.04963472687773 532 727 4386 913 2106 614 385 1450 569 878 863 675 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 288/651 Jessica Robertson 1.80090272103725e-08 9.92827076562417e-08 455 1045.36363636364 868 1.63718430525391e-09 273 1.5835867402745 1.68463289760502 1 2.85254482455746 455 2446 983 1427 500 314 868 630 2558 1045 273 676 M11980 REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS.html Genes involved in Adherens junctions interactions 8/34 Reactome 9.97052641702138e-09 7.14401938687495e-08 990 1122.63636363636 870 9.97052646175651e-10 62 2.24463510694339 2.4398668018708 1 4.12582607950702 987 870 4015 1159 1435 576 490 62 620 1541 594 677 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 53/119 John Newman 4.44120077279929e-08 1.80655093935221e-07 395 937.818181818182 870 4.03745532950456e-09 318 1.75575250566651 1.86635652698541 1 3.04526269659341 394 1611 904 1959 870 664 318 425 1729 876 566 678 M277 PID_INTEGRIN_A4B1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_A4B1_PATHWAY.html Alpha4 beta1 integrin signaling events 18832364 31/61 Pathway Interaction Database 2.35939680332455e-07 6.55761175585935e-07 595 1137.54545454545 871 2.14490641487166e-08 265 2.14555162233654 2.29974517069372 1 3.41235918207217 591 1968 1338 741 2207 769 871 265 756 1991 1016 679 M658 REACTOME_CHONDROITIN_SULFATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHONDROITIN_SULFATE_BIOSYNTHESIS.html Genes involved in Chondroitin sulfate biosynthesis 7/21 Reactome 8.18650372739729e-07 1.84698875621491e-06 385 1146.18181818182 871 8.1865067432468e-08 275 2.29113383453902 2.29113383453902 1 3.37887126358469 382 871 3950 1310 2005 364 275 1326 568 927 630 680 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 35/82 John Newman 9.66723333363435e-09 7.04076564672179e-08 1170 883.909090909091 872 8.78839397828555e-10 179 2.17105824219807 2.32998708395277 1 3.99411649025304 872 2190 1147 1053 231 587 692 439 1167 1166 179 681 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 78/277 Arthur Liberzon 3.45265173843767e-13 7.19072268725286e-12 875 1063.72727272727 874 3.13877430767111e-14 219 2.15610602398342 2.44427881558311 1 6.17987630964256 874 783 219 766 738 1763 1367 1819 1249 251 1872 682 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 55/204 Leona Saunders 3.65192525319893e-08 1.58014051121793e-07 665 1112.81818181818 876 3.31993210347241e-09 645 2.22485078504994 2.38266063690383 1 3.89216963753441 662 2371 808 2085 785 746 645 1027 1156 1080 876 683 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 357/874 Arthur Liberzon 4.6851024727212e-10 5.91762538737777e-09 880 896.272727272727 877 4.25918406701723e-11 32 1.68206656627714 1.93633382101317 1 3.55982247748775 877 268 354 691 32 1415 1289 1364 1889 489 1191 684 M13247 BIOCARTA_TCYTOTOXIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCYTOTOXIC_PATHWAY.html T Cytotoxic Cell Surface Molecules 4/15 BioCarta 6.33002743207803e-09 5.35424341998513e-08 655 1213.81818181818 879 6.33002745010919e-10 8 2.21319164912197 2.21319164912197 1 4.13932823264937 652 879 3875 2114 1747 256 8 111 2091 1269 350 685 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 293/717 Arthur Liberzon 7.74031060604269e-08 2.68420713822601e-07 485 1088 879 7.03664625306531e-09 481 1.87801334377925 2.13036457466228 1 3.17424877014649 481 2757 636 905 1127 659 893 879 2278 757 596 686 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 98/211 Jessica Robertson 2.88496153176683e-09 2.97773782772233e-08 880 921.363636363636 879 2.62269230504547e-10 37 1.74095723222419 2.01186945992819 1 3.3702144023632 1441 305 1236 849 37 1831 877 631 929 1120 879 687 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 9/17 John Newman 1.35332519219888e-07 4.13947901478063e-07 1775 1197.45454545455 879 1.35332527461589e-08 40 2.53514994187299 3.09923359804367 1 4.1622758360378 1775 239 4395 389 1388 1887 1742 211 40 879 227 688 M6427 BIOCARTA_THELPER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_THELPER_PATHWAY.html T Helper Cell Surface Molecules 4/15 BioCarta 6.33002743207803e-09 5.35424341998513e-08 655 1214.81818181818 880 6.33002745010919e-10 9 2.21319164912197 2.21319164912197 1 4.13932823264937 653 880 3876 2115 1748 257 9 112 2092 1270 351 689 M2049 REACTOME_SIGNALING_BY_PDGF http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_PDGF.html Genes involved in Signaling by PDGF 71/154 Reactome 1.81797882067987e-08 9.98716149320736e-08 565 783.818181818182 881 1.6527080324571e-09 450 1.8395514546658 2.13095758233804 1 3.31240365324828 562 510 933 450 504 944 1018 982 881 667 1171 690 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 157/392 Leona Saunders 2.62319582307316e-08 1.24415947640899e-07 880 1280.63636363636 882 2.38472350395559e-09 96 1.83177818264183 2.10303291105883 1 3.2534416446444 880 3051 817 1867 882 993 847 96 2576 1430 648 691 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 57/123 Leona Saunders 3.76828750824386e-08 1.60851553036647e-07 1150 975.454545454545 882 3.42571597526298e-09 512 2.08045877044729 2.28918329200488 1 3.63543291577072 1147 518 639 512 799 1879 1548 882 1129 657 1020 692 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 8/22 Jean Junior 1.85269855711694e-07 5.34261257763075e-07 885 1422.27272727273 882 1.85269871157909e-08 249 2.35618469176083 2.35618469176083 1 3.80129084836046 882 2754 4371 1092 1494 709 296 820 249 2107 871 693 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 76/250 Jessica Robertson 4.13046848839407e-11 6.20364594122263e-10 620 846.454545454545 882 3.75497135315602e-12 304 2.05524747049193 2.28725075044448 1 4.86740614685001 617 786 304 842 1129 1008 882 1024 1225 314 1180 694 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 68/168 Jessica Robertson 1.42298597050633e-10 1.94405605183459e-09 3525 1570.63636363636 883 1.29362360963488e-11 96 2.04598064460212 -2.04962861880001 -1 4.5844023055277 3523 96 332 718 350 2384 4574 2009 883 240 2168 695 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 213/744 Arthur Liberzon 1.40120347067762e-13 3.05397184353271e-12 635 855.909090909091 885 1.27382133697974e-14 209 2.00278401372283 2.32541915988801 1 5.93200929090603 632 1375 209 868 885 1152 834 943 1293 245 979 696 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 2/17 Arthur Liberzon 1.55974783070332e-06 3.27756875994429e-06 890 1216.5 888.5 1.73305434661637e-07 83 3.2684149265131 3.2684149265131 1 4.6107204587771 888 256 4107 NA 2767 589 165 889 83 1388 1033 697 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 163/368 Arthur Liberzon 9.7181704444168e-09 7.0453174588373e-08 695 947.727272727273 889 8.83470044304125e-10 235 1.60356127216572 1.82794389548512 1 2.94997109388261 693 485 1207 1251 235 889 1028 865 1990 1368 414 698 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 31/67 Jessica Robertson 4.61862759733217e-08 1.86255498460401e-07 360 969.909090909091 889 4.19875244935867e-09 356 1.8443656900057 1.95788835351836 1 3.19266769926202 360 1799 916 889 889 600 477 520 1870 1993 356 699 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 112/243 Arthur Liberzon 8.41556367791679e-08 2.84321062687225e-07 465 923.636363636364 889 7.65051272712153e-09 219 1.81216056751407 2.07600722074269 1 3.05129364998846 462 1752 889 1546 1169 219 540 267 1734 1175 407 700 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 7/22 Jessica Robertson 2.26066875777541e-07 6.33203454807864e-07 665 1120.18181818182 890 2.26066898775349e-08 101 3.66568914246573 3.7327140588403 1 5.84437238427098 663 730 4468 262 1561 681 924 1113 101 929 890 701 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 96/244 Leona Saunders 1.27557474709685e-07 3.94283856523472e-07 830 920.818181818182 892 1.15961347368685e-08 117 1.72001685110172 2.07225780871829 1 2.8333200469106 827 1250 892 1035 1340 762 546 422 1766 1172 117 702 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) 68/346 Reactome 1.22339785135399e-08 7.95012312219011e-08 295 1118.90909090909 893 1.11217987105198e-09 272 2.18621047987695 2.27065940267743 1 3.99232711047574 295 2186 429 2634 1218 293 272 1099 2566 893 423 703 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 122/536 Arthur Liberzon 2.89640987519875e-25 2.66128954415321e-23 65 925.272727272727 895 2.63309988654431e-26 50 2.41730699979847 2.86242464907125 1 14.0364240117908 1444 61 50 275 193 2574 1661 1202 895 61 1762 704 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 252/670 Arthur Liberzon 4.69389815194743e-08 1.88965693642832e-07 610 1135.90909090909 895 4.26718022917815e-09 466 1.72971609691118 2.15530713061612 1 2.99141353280325 1359 466 805 608 895 3083 1827 682 1212 948 610 705 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 235/644 Leona Saunders 8.49254937438694e-22 5.30614484911696e-20 650 647 897 7.72049943126087e-23 30 2.07324945709971 2.19122323787634 1 10.27897013876 649 1000 72 30 351 924 1137 897 986 93 978 706 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 124/267 Kate Stafford 2.59583066690325e-09 2.71519252346174e-08 1135 828.818181818182 897 2.35984606360558e-10 30 1.95702445584129 2.26624142558033 1 3.8086643299334 1132 769 897 322 30 1023 934 852 1364 1456 338 707 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 29/71 Jessica Robertson 3.82436726899784e-08 1.61887850248635e-07 565 910.636363636364 897 3.47669757770789e-09 40 1.86087999472388 2.01622627444182 1 3.25040184626539 564 1524 1175 1681 897 208 156 421 1798 1553 40 708 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 119/302 Yujin Hoshida 1.24528074729369e-09 1.43728708911779e-08 3315 1675.09090909091 897 1.13207340727143e-10 40 1.89864288384192 -1.54261174068074 -1 3.82995849864539 3312 293 374 493 40 3834 2697 1628 897 280 4578 709 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 19/48 Reactome 4.73708559966316e-08 1.89769579972418e-07 2160 1275.90909090909 898 4.30644154696642e-09 340 1.25272223301573 1.31970402729409 1 2.16589450570663 685 839 2156 2160 898 391 340 1591 2587 1605 783 710 M17967 REACTOME_TIGHT_JUNCTION_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TIGHT_JUNCTION_INTERACTIONS.html Genes involved in Tight junction interactions 17/35 Reactome 5.05206974078061e-07 1.22346247055803e-06 1225 1018.27272727273 900 4.59279172812356e-08 463 2.54025713613622 -2.69931921529144 -1 3.86314349595739 1222 1056 843 1699 1829 554 900 780 463 1084 771 711 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 68/149 Kevin Vogelsang 4.79224926378062e-07 1.16960833594146e-06 735 1088.63636363636 900 4.35659118879478e-08 470 2.21719508937014 2.43729548595556 1 3.38299028337705 733 2223 1135 900 1813 1162 857 470 794 1144 744 712 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 125/372 Arthur Liberzon 3.2871267618513e-09 3.29838886638869e-08 510 971.818181818182 900 2.9882970606934e-10 48 1.74245895101189 1.85349960574962 1 3.35321499453341 510 900 564 838 48 1189 1315 1245 1947 532 1602 713 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 27/58 Arthur Liberzon 3.87046441576139e-08 1.63396362632954e-07 1395 976.090909090909 904 3.5186040762314e-09 321 2.29277307779869 2.96543047801481 1 4.00241464050522 1393 552 854 1086 810 1501 1382 904 321 1113 821 714 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 19/44 Arthur Liberzon 6.9973494474642e-07 1.60969953415892e-06 420 963 906 6.36122879368321e-08 409 2.51314003628954 2.79370823719948 1 3.74488091606411 417 1201 705 1319 1942 821 906 409 1158 799 916 715 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 316/793 Jessica Robertson 1.94893132096774e-36 3.26167577501958e-34 910 825.727272727273 907 1.77175574633433e-37 27 2.01879266362737 2.21295509370461 1 17.3884522555435 907 457 27 557 546 1347 1142 1375 1554 32 1139 716 M8395 REACTOME_HEMOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HEMOSTASIS.html Genes involved in Hemostasis 244/615 Reactome 5.82151630573797e-08 2.18411732655629e-07 910 1057.81818181818 909 5.29228769071244e-09 519 1.7966819907481 2.03617264435337 1 3.07816087837378 546 1602 519 906 1002 909 833 1404 2141 701 1073 717 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 52/149 John Newman 8.96979967907361e-10 1.07499952164038e-08 910 864.818181818182 909 8.15436334793707e-11 279 2.2468877337315 2.8533442908347 1 4.60533915381099 909 341 367 616 279 1508 1229 968 1309 716 1271 718 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 29/80 Leona Saunders 1.61489923713594e-07 4.79861624934624e-07 910 859.636363636364 910 1.46809032334259e-08 308 2.16707332117967 2.32689024229447 1 3.52218894686952 910 372 802 308 1408 954 875 1039 406 1237 1145 719 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 47/208 Jessica Robertson 9.16891613052897e-09 6.8744865580254e-08 1075 903 910 8.33537833522014e-10 214 1.83530014319727 2.09789281101886 1 3.38131899132172 1074 530 1230 1217 214 910 974 1398 864 899 623 720 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 504/1186 Arthur Liberzon 9.38869953438584e-09 6.97087953005191e-08 1110 1230.81818181818 910 9.38869957405228e-10 6 1.66905203892983 1.96157770777218 1 3.07243074997209 1110 6 4676 392 259 1785 1243 845 1700 613 910 721 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 44/99 Kevin Vogelsang 1.23375499491317e-08 7.96332769443956e-08 915 1017.36363636364 911 1.12159545621095e-09 339 1.93942483394718 2.05261641373094 1 3.54130232834133 911 670 777 621 339 1534 1375 1586 983 786 1609 722 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 34/73 Arthur Liberzon 2.38748030403651e-06 4.75264770803529e-06 395 977.363636363636 911 2.17043899543437e-07 267 1.76663886416195 -1.6569591606699 -1 2.41884561285893 392 679 1076 1450 2265 267 672 1123 1138 778 911 723 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 81/168 Arthur Liberzon 3.19580230881928e-08 1.44412050329095e-07 1050 974.272727272727 913 2.90527486840246e-09 458 1.62977160224516 1.83542014665804 1 2.8675215037278 1048 505 874 1182 732 913 760 1097 1927 1221 458 724 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 70/262 Jessica Robertson 1.27174291701047e-08 8.0434968418917e-08 1215 923.636363636364 917 1.15612993123816e-09 318 2.24163688562616 2.76024565827166 1 4.0906196199994 1212 1381 431 358 917 1623 1199 318 915 735 1071 725 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 62/133 Arthur Liberzon 2.27534395427245e-08 1.14771386111095e-07 685 913.909090909091 917 2.06849452527739e-09 250 2.105246777156 2.09952750679322 1 3.75812790967844 681 917 632 250 588 1272 1234 1428 1106 824 1121 726 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 270/619 Jessica Robertson 2.12193453466049e-08 1.09930699628899e-07 1625 1164.18181818182 920 1.92903141375171e-09 99 1.82902001237839 2.28171818422416 1 3.27383305012097 1621 275 809 99 562 3399 1875 920 1259 1106 881 727 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 77/185 Arthur Liberzon 9.67086585064861e-09 7.04076564672179e-08 710 883.181818181818 920 8.79169626650936e-10 88 1.99185576340922 2.33153470910411 1 3.66443596856591 706 88 908 1130 232 1421 858 1084 920 1199 1169 728 M19096 KEGG_BLADDER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BLADDER_CANCER.html Bladder cancer 27/58 KEGG 1.16500156975218e-07 3.66951431633228e-07 925 970.818181818182 921 1.05909239222218e-08 288 1.84751513630506 2.25260069162233 1 3.05817005012385 921 947 1513 1238 1304 786 700 288 486 2017 479 729 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 181/435 Arthur Liberzon 1.29182746402966e-08 8.10375300728646e-08 840 1479 924 1.17438861055927e-09 363 1.84056110665694 2.23915000447502 1 3.35718756918577 2145 764 924 526 363 4519 2577 1347 1430 838 836 730 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 9/31 Arthur Liberzon 1.21118971457634e-06 2.61791282403354e-06 720 1230.09090909091 926 1.21119037471808e-07 465 2.56817217531206 2.64199913366935 1 3.68736491940986 719 976 4181 465 2105 967 1360 541 682 609 926 731 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 65/167 John Newman 2.72218024632022e-07 7.33954927172415e-07 950 947.272727272727 926 2.47470962104593e-08 73 2.36306175413205 2.5726898615747 1 3.72855809414408 949 513 590 73 1598 1637 1268 926 717 697 1452 732 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 46/109 Arthur Liberzon 4.12956761804182e-10 5.27279396679672e-09 835 996.727272727273 928 3.75415238074269e-11 1 2.21067935234117 2.52061114164605 1 4.70703801678379 834 928 1240 746 1 1868 1280 705 319 1885 1158 733 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 28/48 Jessica Robertson 5.05800270710366e-08 1.98484686911924e-07 505 1208.09090909091 929 4.59818438490166e-09 505 1.57983674940109 1.64554443515721 1 2.7235351234951 505 1398 1523 1999 929 663 919 575 2474 1764 540 734 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 15/36 Reactome 1.24594540088384e-07 3.8631207342317e-07 810 914.181818181818 931 1.13267770131506e-08 466 2.14472894566057 2.16511304148603 1 3.53782621494835 806 718 1053 1245 1332 1011 761 510 1223 931 466 735 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 83/182 Jessica Robertson 5.5431035707557e-09 4.88251566401526e-08 935 905.545454545455 931 5.03918507702006e-10 104 1.76191893921973 2.03720259554164 1 3.31346614066773 931 1102 910 814 104 619 985 961 1779 1134 622 736 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 55/133 Jean Junior 6.06443120842065e-09 5.20474810305113e-08 1230 942.363636363636 932 5.51311929557965e-10 121 2.42479845935517 3.05465786710763 1 4.54276656217315 1227 1258 1162 787 121 1707 932 693 335 1695 449 737 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 12/23 Arthur Liberzon 2.47111994162542e-08 1.20328077343124e-07 730 920.454545454545 932 2.24647269943813e-09 175 1.52480375506011 1.6072785492021 1 2.713911432098 728 1067 1898 1766 628 425 175 932 1073 1217 216 738 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 23/61 Leona Saunders 1.36955619881462e-07 4.17821637216491e-07 585 1016.54545454545 933 1.24505116733909e-08 102 1.76081720753542 1.82366311757515 1 2.88912379192297 584 1338 1286 933 1908 427 337 245 2374 1648 102 739 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 15/36 Kevin Vogelsang 4.72099359282276e-08 1.8973049722099e-07 840 908.818181818182 933 4.29181244920987e-09 156 3.8141492989758 3.8832328330305 1 6.59456284535356 836 1280 473 156 1597 1012 1061 1029 878 933 742 740 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 80/208 Jessica Robertson 1.05415318297384e-18 4.74977097636096e-17 895 1066.27272727273 933 9.58321075430759e-20 99 2.6218500525292 2.77170744200345 1 11.0081723503477 892 785 99 238 933 1871 1489 2058 1042 134 2188 741 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 29/52 Leona Saunders 5.99812359701375e-08 2.21665671731912e-07 310 746.272727272727 935 5.45283978231618e-09 297 2.31086147250376 2.30234461660649 1 3.95526017076738 307 1130 810 937 1020 351 297 951 935 1030 441 742 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 78/186 Jessica Robertson 7.36494399586427e-09 5.98130460392027e-08 1390 1102.27272727273 935 6.69540365501809e-10 162 1.98000731736953 2.48966081673451 1 3.67870823568215 1388 789 891 935 162 2191 1163 964 918 761 1963 743 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 15/43 John Newman 2.93885616144984e-08 1.35679605640925e-07 935 994.363636363636 935 2.67168745518941e-09 106 1.5233082001783 1.84345383656628 1 2.69081711427205 935 577 1449 1248 2461 623 553 106 1086 1585 315 744 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 16/54 Arthur Liberzon 4.74015418582857e-05 7.35752319138546e-05 345 1142.36363636364 936 4.30932392818919e-06 345 1.89425564233003 -1.89425564233003 -1 2.01386723576848 345 1343 732 936 2925 408 685 1388 2311 456 1037 745 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 16/54 Jessica Robertson 1.24878995412152e-07 3.86769975215695e-07 440 841.454545454545 936 1.13526365909711e-08 50 2.38137387449178 2.52741916651936 1 3.92786749281532 440 957 1114 1418 1600 178 50 725 936 1687 151 746 M1987 GYORFFY_DOXORUBICIN_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/GYORFFY_DOXORUBICIN_RESISTANCE.html Genes associated with resistance to doxorubicin [PubChem=31703]. 16044152 29/77 Arthur Liberzon 5.12051611915041e-08 2.00289971071276e-07 1030 934.454545454545 936 4.65501476211892e-09 173 2.11462211785463 1.98749813913415 1 3.64333137527494 1026 173 860 384 936 1436 1407 1585 428 851 1193 747 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 33/89 Arthur Liberzon 1.0681393534473e-07 3.43534729598769e-07 480 888.636363636364 936 9.71035823006712e-09 266 1.88877351045029 2.06137604883442 1 3.14037754071602 477 1618 936 1003 1260 524 411 574 1653 1053 266 748 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 11/35 Jessica Robertson 1.85061703298856e-07 5.33989619247807e-07 725 846.727272727273 937 1.68237926241868e-08 142 2.79008168686155 3.03083609150802 1 4.50146611324888 937 589 1035 721 1470 1051 722 486 142 1091 1070 749 M4383 BIOCARTA_NO1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NO1_PATHWAY.html Actions of Nitric Oxide in the Heart 19/50 BioCarta 1.66189739601463e-07 4.90406246708094e-07 580 959.090909090909 938 1.51081592868698e-08 473 2.50436124834717 2.46642396797774 1 4.06430912201605 577 1406 1031 856 1423 570 473 1238 784 1254 938 750 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 111/291 Arthur Liberzon 5.67941111018365e-08 2.14453831283808e-07 995 966.363636363636 938 5.16310114254591e-09 587 2.14562685923557 2.78294099227727 1 3.68037303299721 994 2138 698 781 991 982 662 938 819 1040 587 751 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 30/64 Pathway Interaction Database 7.39204009663896e-08 2.59487271084123e-07 940 1166.45454545455 939 6.72003667728443e-09 159 2.3754408915267 2.76146091102785 1 4.0239906931523 939 2484 1451 589 1542 869 1073 159 683 2283 759 752 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 126/258 Jessica Robertson 2.45967555688395e-09 2.59595487827888e-08 630 1086.45454545455 940 2.23606869057633e-10 27 1.7226380750741 1.96119326382061 1 3.36115492426558 629 1789 901 1133 27 940 1107 760 2500 1658 507 753 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 56/143 Jessica Robertson 7.99675802654194e-09 6.34057666876066e-08 720 927.636363636364 941 7.26978005055391e-10 178 1.98680100464513 1.96583058267557 1 3.67838436954193 718 1443 871 1348 178 941 767 1077 594 1311 956 754 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 9/30 Jessica Robertson 7.59835149547248e-07 1.72844053921282e-06 945 1569.54545454545 942 7.59835409354626e-08 357 2.56452702745612 3.27401273542861 1 3.80106453997918 942 2997 4573 920 2187 1246 764 429 357 2318 532 755 M2890 KEGG_CALCIUM_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CALCIUM_SIGNALING_PATHWAY.html Calcium signaling pathway 59/193 KEGG 5.29364667110804e-07 1.27080063016456e-06 720 1334.81818181818 943 4.81240722260667e-08 624 1.95165982805737 1.83393796780789 1 2.95974675319363 668 1506 720 2158 1848 624 752 2511 2234 719 943 756 M100 PID_SHP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SHP2_PATHWAY.html SHP2 signaling 18832364 38/91 Pathway Interaction Database 5.29828910408941e-08 2.05446354986844e-07 720 1153.18181818182 944 4.81662657426255e-09 329 1.67046480728337 2.04547957242855 1 2.87333918346527 717 812 1527 1504 951 779 944 329 2473 1893 756 757 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 10/17 Leona Saunders 2.53215964315709e-07 6.91323101041381e-07 270 780.181818181818 944 2.30196357691279e-08 171 2.00872653916444 2.00872653916444 1 3.18289765680146 266 1156 1197 993 1571 294 171 944 401 1359 230 758 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 15/27 Reactome 5.03473385042698e-08 1.98092047213273e-07 1280 1159.54545454545 948 4.5770308778615e-09 549 1.73030033384709 -2.0232398673656 -1 2.98330725053793 1277 717 1637 1410 927 948 2064 549 823 1577 826 759 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 28/67 Leona Saunders 2.11749152154121e-08 1.09884443742438e-07 3705 2082.72727272727 949 1.92499231083817e-09 167 2.03697876246392 -1.86990945883534 -1 3.64616218039076 3701 167 638 949 561 3991 3722 4207 300 341 4333 760 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 5/23 Reactome 1.55462460941265e-08 9.06090910411403e-08 945 1207.18181818182 950 1.55462462028851e-09 286 2.34357010932215 2.34357010932215 1 4.24544983689657 941 1296 4026 1482 478 812 291 286 1193 1524 950 761 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 6/16 Arthur Liberzon 2.42686274511609e-08 1.1945671033208e-07 955 1196.18181818182 951 2.42686277161957e-09 98 2.44401949345063 2.83802541059028 1 4.35195560630142 951 877 4630 237 1959 1015 1067 98 269 1731 324 762 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 108/210 Jessica Robertson 7.05369381434478e-09 5.81929739683444e-08 540 992.636363636364 953 6.41244894269137e-10 152 1.72007340126742 2.0187532996163 1 3.20104622794 536 1436 953 1074 152 797 933 1289 1851 1472 426 763 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 23/77 John Newman 3.62987352107896e-08 1.5764214383481e-07 955 1355.27272727273 955 3.29988507360888e-09 118 1.90043381867948 2.09509353497641 1 3.32513252899214 955 3019 1639 2599 853 925 798 118 2386 1320 296 764 M18256 KEGG_SULFUR_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SULFUR_METABOLISM.html Sulfur metabolism 4/18 KEGG 1.10691997408374e-08 7.53979376391282e-08 2015 1169.27272727273 957 1.10691997959746e-09 60 1.72563699660894 -1.73896616076338 -1 3.16147047238273 2014 250 3805 1022 329 957 1842 386 60 1267 930 765 M167 PID_AP1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AP1_PATHWAY.html AP-1 transcription factor network 18832364 70/143 Pathway Interaction Database 7.53785963683893e-07 1.71718085844566e-06 640 998.181818181818 957 6.8526020177608e-08 324 2.54087781836238 2.88563591767056 1 3.76786744946993 636 1608 560 324 1982 1231 980 687 757 957 1258 766 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 48/121 Jessica Robertson 7.14851002585246e-09 5.87682771599029e-08 960 908.545454545455 957 6.49864549916389e-10 155 1.9007491134722 1.88763893234245 1 3.53519386511549 1139 924 944 957 155 1075 959 1067 646 1293 835 767 M13380 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION.html Neuroactive ligand-receptor interaction 55/344 KEGG 2.52709412321152e-07 6.90493472966133e-07 645 1351.81818181818 958 2.29735855772145e-08 645 2.16722183643786 2.21388481368259 1 3.43432973432412 645 2642 678 2740 1570 764 838 1219 1866 950 958 768 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 27/56 Leona Saunders 1.53128803027971e-07 4.58505796159152e-07 900 963.545454545455 958 1.39208012442136e-08 551 1.8256441366204 2.202536055308 1 2.97654128756984 898 551 1375 1033 1396 1274 621 958 570 909 1014 769 M6889 KEGG_RIBOFLAVIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOFLAVIN_METABOLISM.html Riboflavin metabolism 4/19 KEGG 3.21281187747857e-09 3.25764717911044e-08 1440 1215.36363636364 960 3.21281188212353e-10 31 3.23659426785705 3.23659426785705 1 6.233046028966 1438 878 3801 1358 2454 960 285 31 81 2035 48 770 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 21/53 Reactome 5.43560963399865e-08 2.09467654152284e-07 960 1420.09090909091 960 4.94146342572546e-09 709 1.65542322707139 1.86753942046557 1 2.84388177891345 960 2023 2094 2482 959 873 709 1065 856 2712 888 771 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 52/123 Jessica Robertson 3.59665221305506e-08 1.57130266202042e-07 960 1230.27272727273 960 3.26968388350422e-09 254 1.93032248739945 1.95562364504272 1 3.37812916142656 254 2482 974 2277 779 684 592 957 2588 960 986 772 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 15/31 Arthur Liberzon 2.37089027178214e-06 4.72363597515778e-06 965 1289.45454545455 961 2.15535711530986e-07 639 1.70977206230634 1.81989615414021 1 2.34215421757378 961 958 1430 1769 2263 785 753 1281 2413 932 639 773 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 19/50 Reactome 5.45490657706562e-08 2.0952206737811e-07 405 871.272727272727 962 4.95900610210927e-09 105 2.01953305793122 2.13321471164182 1 3.46933415496637 404 1580 1260 2146 962 265 105 157 1235 1255 215 774 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 45/226 Reactome 6.17085451825064e-07 1.4488529178945e-06 390 1271.72727272727 963 5.60986931739564e-08 305 2.12138805477224 2.16557800321234 1 3.18607098128217 389 1880 566 2481 1894 383 305 1547 2820 963 761 775 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 22/52 John Newman 7.90320898201171e-06 1.40016776142559e-05 475 1095.81818181818 963 7.18476124853392e-07 382 1.65760212994153 -1.73993045854974 -1 2.06948651452955 471 950 1533 978 2541 382 849 1203 1553 631 963 776 M7054 SU_LIVER http://www.broadinstitute.org/gsea/msigdb/cards/SU_LIVER.html Genes up-regulated specifically in human liver tissue. 11904358 27/140 John Newman 8.34581047570006e-08 2.83582175257329e-07 1410 1058.27272727273 964 7.5871007202751e-09 360 2.37402305863199 -2.62565460141668 -1 3.9980409446397 1410 1672 977 964 1162 723 1809 360 941 911 712 777 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 417/992 Jessica Robertson 1.65937638340862e-16 6.02778118810295e-15 1395 839.727272727273 965 1.50852398491693e-17 10 1.87576534931573 2.29884045155582 1 6.8607559581742 1391 10 124 130 230 2422 1602 1117 1090 156 965 778 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 66/188 Arthur Liberzon 5.48735901958193e-08 2.09947262849324e-07 980 1164.18181818182 965 4.988508324046e-09 536 2.11883780832856 2.26109899497445 1 3.63944888674204 978 2140 546 773 965 981 937 2697 1616 536 637 779 M2 PID_SMAD2_3NUCLEAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SMAD2_3NUCLEAR_PATHWAY.html Regulation of nuclear SMAD2/3 signaling 18832364 55/130 Pathway Interaction Database 3.37102442595702e-08 1.50157989163827e-07 1610 1126 966 3.0645677069188e-09 220 2.35160957952365 2.73909846360056 1 4.12731865071169 1607 1713 966 368 753 2536 1670 220 356 1462 735 780 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 31/83 Arthur Liberzon 1.07648057221514e-07 3.45033376292761e-07 705 982.181818181818 968 9.78618749898495e-09 244 1.79314899065594 1.87334195562744 1 2.98051507210363 703 1396 1227 1200 1266 536 244 928 1547 789 968 781 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 9/20 Jessica Robertson 3.10576574105282e-07 8.19922155637944e-07 960 1426.27272727273 968 3.10576617511304e-08 577 2.79446335836209 3.09436245477458 1 4.37466962586015 956 2282 4528 1190 1686 968 577 719 782 1197 804 782 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 83/214 Yujin Hoshida 5.5018190093677e-08 2.09947262849324e-07 400 876.727272727273 968 5.00165376996244e-09 371 1.94604633879334 2.22882774177225 1 3.34265138960777 520 1316 1268 1209 968 397 398 478 1077 1642 371 783 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 84/301 Leona Saunders 4.76142300662815e-08 1.90213369216193e-07 1430 1105.09090909091 970 4.32856646334438e-09 196 2.09623454185043 2.27405614144528 1 3.62373855305444 1428 504 606 196 903 2400 1982 970 1210 499 1458 784 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 17/47 Arthur Liberzon 2.26516343440676e-06 4.53890946731742e-06 505 1062.45454545455 972 2.05924160606101e-07 288 2.32594085617875 2.36779443247654 1 3.19658636215941 504 1277 596 1354 2782 747 627 1165 972 288 1375 785 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 8/20 Arthur Liberzon 5.05935093945753e-08 1.98484686911924e-07 2230 1497.63636363636 973 5.05935105464417e-09 47 2.96819438686165 3.41439612096743 1 5.11697298191445 2228 243 4145 47 973 3018 2267 723 376 1542 912 786 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 57/173 Arthur Liberzon 3.19354756352466e-08 1.44412050329095e-07 1080 1153.09090909091 973 2.90322509989327e-09 731 1.94344677048998 2.05036533686404 1 3.41942114161993 1080 1563 906 973 731 837 970 2337 1198 887 1202 787 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 9/19 Arthur Liberzon 3.15814643579772e-06 6.10522862959906e-06 925 1639.72727272727 975 3.15815092405671e-07 272 2.35618469176083 2.35618469176083 1 3.16012195566203 922 3305 4605 1243 2348 773 367 908 272 2319 975 788 M166 PID_ATF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATF2_PATHWAY.html ATF-2 transcription factor network 18832364 49/92 Pathway Interaction Database 1.11696358445092e-07 3.54136142299033e-07 980 900.454545454545 979 1.01542149196396e-08 486 2.40478656132151 2.56175404539305 1 3.99016433315497 979 525 602 486 1286 1297 1175 859 657 985 1054 789 M746 REACTOME_SIGNALING_BY_GPCR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_GPCR.html Genes involved in Signaling by GPCR 212/1438 Reactome 2.2525409823141e-11 3.54208290037713e-10 535 979.636363636364 980 2.04776452939742e-12 202 1.96430910454204 2.05867032149859 1 4.77501096909136 534 1426 290 1285 202 980 953 1548 2025 234 1299 790 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 19/51 Jessica Robertson 7.66094096575947e-07 1.74014393434556e-06 780 1139.36363636364 983 6.96449421226253e-08 599 1.85464938035839 2.09028932964904 1 2.74750716973462 776 1530 1245 923 1972 782 599 983 1720 1264 739 791 M4281 REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Neurotransmitter Release Cycle 17/61 Reactome 8.0581439549226e-09 6.37823464217116e-08 990 1070.72727272727 986 7.32558544039809e-10 179 2.78223730854771 2.78223730854771 1 5.14922320338185 986 1631 1389 545 179 1475 1134 838 591 2219 791 792 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 145/340 Jessica Robertson 2.89510157385443e-39 6.16656635230993e-37 1000 833.363636363636 986 2.63191052168586e-40 6 2.23691403465564 2.46635826297064 1 20.8341594340223 998 41 21 6 986 1757 1664 1459 749 16 1470 793 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 26/80 Leona Saunders 5.65859609217774e-08 2.14185632374353e-07 1950 1395.09090909091 987 5.14417839792897e-09 376 2.27250487647353 2.28516307694405 1 3.89832335820891 1950 376 765 865 987 2838 1925 2127 596 451 2466 794 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 30/77 Arthur Liberzon 9.54514013669333e-08 3.13005785028306e-07 1135 1034.27272727273 987 8.67740050075303e-09 737 1.9368399377174 2.17358663271403 1 3.24043126691453 813 1131 848 737 1222 1353 1135 864 1544 743 987 795 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 14/30 Kate Stafford 8.52132149593865e-06 1.50116212518679e-05 800 1186.09090909091 988 7.74668591090034e-07 601 2.89871669618232 3.12407633279919 1 3.59644345967112 798 1214 988 1081 2558 830 854 1813 601 842 1468 796 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 297/770 Arthur Liberzon 1.79701669961717e-08 9.91851620071385e-08 1085 1053 988 1.63365155845061e-09 321 1.75613855787722 2.15905010905755 1 3.16355854556847 1083 1601 762 321 499 1962 1524 830 1393 988 620 797 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 8/19 Reactome 2.48671581633257e-08 1.20328077343124e-07 990 1537.18181818182 989 2.48671584415946e-09 99 1.32590590216134 1.46046878374407 1 2.3599044344805 989 731 4067 2525 2052 398 101 99 3508 2099 340 798 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 12/34 Jessica Robertson 1.09560795993074e-07 3.49490735210038e-07 865 1176.45454545455 989 9.96007285902201e-09 488 2.71840048958941 3.16026356463089 1 4.51454089124978 863 1987 1472 1623 1277 989 742 488 506 2152 842 799 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 170/474 Jessica Robertson 4.58077013477343e-09 4.20891938265653e-08 1145 955.909090909091 991 4.1643364948285e-10 78 1.65244093453221 1.88018278361914 1 3.13498499968423 1143 892 722 991 78 1382 1335 1200 1588 582 602 800 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 15/23 Arthur Liberzon 1.83799458522155e-07 5.31001394965978e-07 1210 963.090909090909 992 1.67090430797928e-08 412 2.34571579435204 2.31784846292373 1 3.78600485124281 849 1210 895 992 1468 547 429 1209 1396 1187 412 801 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 29/75 Jessica Robertson 1.20724312901955e-06 2.61299829218734e-06 995 1064.45454545455 992 1.09749435590087e-07 178 2.15511993238449 2.46448622073799 1 3.09475952438475 1123 178 796 878 2082 1094 992 1397 992 698 1479 802 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 12/36 Arthur Liberzon 1.79054692286109e-08 9.90614271608865e-08 1185 1084.81818181818 992 1.6277699431219e-09 497 2.83533174704043 2.68792759824043 1 5.10804372005546 1185 968 992 1702 497 1123 746 1771 743 1218 988 803 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 16/34 Yujin Hoshida 4.05801747756358e-06 7.63689554211364e-06 495 1065.90909090909 994 3.68911360255713e-07 339 1.83595243001076 -1.75373405824394 -1 2.41647635093897 493 568 619 1253 2673 561 1235 1725 994 339 1265 804 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 73/201 Jessica Robertson 5.69771234506808e-08 2.14798713185753e-07 2245 1592.36363636364 995 5.17973862966492e-09 542 1.89672614869118 2.2224106031264 1 3.253095555688 2242 655 744 811 995 4219 2580 1551 799 542 2378 805 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 131/551 Arthur Liberzon 1.09998542434762e-22 7.93004876691222e-21 65 812.636363636364 995 9.99986749406921e-24 63 2.31256395799531 2.61448090649692 1 11.9565019128201 1136 636 63 278 451 1544 1083 1057 995 64 1632 806 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 42/99 Yujin Hoshida 8.68500194879114e-16 2.80675304358864e-14 1035 755 996 7.89545631708282e-17 128 2.81063072777623 3.07157770419322 1 9.79714010309568 1034 128 140 285 1025 1215 1362 996 208 293 1619 807 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 16/47 Jessica Robertson 3.15413342346797e-08 1.43358576356653e-07 2860 1689.27272727273 999 2.86739406244425e-09 214 1.83622903303171 2.17999435291646 1 3.23227739731249 2860 214 999 1111 724 4566 4076 876 377 588 2191 808 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 3/18 Leona Saunders 5.27038639414835e-06 9.69271218327283e-06 890 1339.90909090909 1000 5.27039889382781e-07 231 1.79678495572281 1.79678495572281 1 2.31707722248156 889 442 4175 1296 2809 550 231 1399 1151 1000 797 809 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 270/583 Arthur Liberzon 5.88557551929788e-08 2.19435778250278e-07 610 1087 1000 5.35052334250219e-09 609 1.81112749822231 2.08588996072685 1 3.1019632430505 609 1864 703 820 1010 1126 1293 1000 1964 723 845 810 M5493 WNT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/WNT_SIGNALING.html Genes related to Wnt-mediated signal transduction 53/137 SuperArray 1.68930757525461e-08 9.50311560341307e-08 1120 937.181818181818 1003 1.53573417111477e-09 247 2.35099217619337 2.74321044002308 1 4.24638105007175 1120 1181 684 247 470 1959 1310 1171 533 1003 631 811 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 42/101 John Newman 1.18506947887905e-06 2.57094239723484e-06 1905 1315.72727272727 1003 1.0773364702168e-07 382 2.16125261208766 2.81486281085119 1 3.10748344668866 1904 531 1003 891 2078 2836 1855 563 382 989 1441 812 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 4/12 Jessica Robertson 1.00627722913636e-06 2.22425240364764e-06 1030 1323.90909090909 1003 1.00627768480389e-07 51 1.93890632442892 2.32983688248087 1 2.81916391369344 1028 743 4551 575 2061 970 1003 1668 51 1278 635 813 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 14/34 Jessica Robertson 9.46491193258341e-07 2.10401220664544e-06 845 1030.63636363636 1004 8.60446909510112e-08 197 2.45396218766072 2.58180725874108 1 3.58328814327762 1103 845 926 1098 2018 965 1250 1004 197 843 1088 814 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 32/65 Leona Saunders 1.04020012154834e-08 7.29697270894538e-08 1130 907.909090909091 1005 9.45636478605996e-10 164 2.01710719866067 2.1822575610081 1 3.70283751712737 1126 164 879 470 262 1781 1183 692 1005 1017 1408 815 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 3.63018317046797e-06 6.92631854104759e-06 905 1472.09090909091 1005 3.63018910068503e-07 235 3.14390465648115 3.14390465648115 1 4.17229919041867 901 1744 4283 1005 2389 1027 988 677 235 2245 699 816 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 192/448 Arthur Liberzon 7.68674359061021e-09 6.14945597655651e-08 1615 1120.18181818182 1006 6.98794874315227e-10 172 1.94497547927875 2.4017941712864 1 3.60759789313356 1614 1238 643 349 172 3024 1452 559 1375 890 1006 817 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 35/85 Arthur Liberzon 3.21332018249924e-09 3.25764717911044e-08 1010 995.545454545455 1006 2.9212001701751e-10 44 2.01525503509889 2.82889953345586 1 3.88098602835545 1006 686 1221 528 44 1667 1021 768 324 2347 1339 818 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 28/77 Jean Junior 2.46796718696273e-05 4.00585183169635e-05 860 1250.27272727273 1007 2.24363170284917e-06 674 1.97563540859833 2.11657681732779 1 2.23456015398088 858 1275 1525 1392 2984 708 998 1007 1367 965 674 819 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 33/68 John Newman 5.60598719562197e-11 8.16165260871684e-10 550 973.181818181818 1007 5.09635199614985e-12 312 2.6879615811595 2.93422764050705 1 6.28348602637622 549 810 312 872 1425 1355 1007 1348 1149 502 1376 820 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 55/104 Arthur Liberzon 5.88375945522975e-08 2.19435778250278e-07 600 1512.36363636364 1009 5.34887237507921e-09 596 1.92888076465848 2.01193974313104 1 3.30364221360549 596 3492 1411 1659 1009 984 909 962 2515 2185 914 821 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 132/465 Jessica Robertson 9.10868537364934e-12 1.52986737135917e-10 1005 962.363636363636 1012 8.28062306698823e-13 41 2.22118855992666 2.62444700109117 1 5.60776394237472 1003 1242 271 1039 41 1428 1002 1949 1075 524 1012 822 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 79/232 Leona Saunders 6.21627327760034e-10 7.66564646811453e-09 1015 1016.90909090909 1013 5.65115752668799e-11 4 2.03498518048047 2.51344131699149 1 4.24788342238538 1013 1560 669 1326 4 1855 1279 613 1140 785 942 823 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 4/9 Jessica Robertson 3.78740110577817e-08 1.61293330677829e-07 1230 1327.36363636364 1014 3.787401170328e-09 44 2.22022367570307 2.91594584973691 1 3.8789805225542 1226 608 4303 877 2142 1014 703 1108 525 2051 44 824 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 10/29 Arthur Liberzon 5.90500461744772e-08 2.19435778250278e-07 1815 1180.63636363636 1014 5.36818615994866e-09 126 3.12637079225899 3.07031739619692 1 5.35461339534541 1811 1688 770 596 1014 1685 803 2212 126 982 1300 825 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 4/7 Jessica Robertson 1.38586294998472e-07 4.21698297638209e-07 915 1155.09090909091 1015 1.38586303641246e-08 58 2.86771529795757 -2.86771529795757 -1 4.70234799593648 915 1082 4331 1112 1827 428 1015 210 58 1273 455 826 M15798 KEGG_MELANOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOMA.html Melanoma 32/89 KEGG 1.56336705908362e-08 9.08698406718676e-08 1255 1000.63636363636 1016 1.42124279108477e-09 441 1.94068803813975 2.31041975230582 1 3.51499348126383 1252 941 1157 1501 441 1210 794 670 997 1016 1028 827 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 148/388 Leona Saunders 1.42611807616188e-09 1.62203623905208e-08 1010 1039.54545454545 1017 1.29647097916939e-10 378 2.21857087524477 2.69175884286411 1 4.4453509949356 1007 2547 378 1087 476 1096 1017 1132 1475 498 722 828 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 676/1657 Jessica Robertson 2.05212564454039e-08 1.07805614016999e-07 585 1307.27272727273 1017 2.05212566349088e-09 541 1.56387059065255 1.78036717113519 1 2.80264205010706 541 1085 4308 1050 585 854 1202 1017 2363 585 790 829 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 39/71 John Newman 5.15834834772475e-09 4.60671733520751e-08 1020 1103.18181818182 1017 4.68940759983595e-10 92 1.9201476668042 2.1300347018454 1 3.6235030676757 1017 1190 1937 625 92 958 1490 1312 758 2327 429 830 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 41/111 Arthur Liberzon 1.39794185966059e-08 8.50747474593446e-08 3720 2109.63636363636 1021 1.27085624413046e-09 354 2.33315954070219 2.51694167909837 1 4.24301690615531 3716 354 516 688 390 3699 4114 3685 1021 477 4546 831 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 13/27 Jessica Robertson 3.58707859103988e-08 1.56947248156983e-07 4425 1947.09090909091 1021 3.26098059047894e-09 193 1.98022884118954 -1.3530668058686 -1 3.46572476316484 4424 232 1309 727 778 3273 4299 1021 193 758 4404 832 M19422 BIOCARTA_IL17_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL17_PATHWAY.html IL 17 Signaling Pathway 5/14 BioCarta 5.39198343280964e-06 9.88143698324051e-06 1025 1695 1022 5.39199651592273e-07 233 1.90414543435509 1.90414543435509 1 2.45142414047819 1022 1694 3842 2690 3135 456 233 816 3100 972 685 833 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 33/101 Reactome 4.50626320429295e-08 1.82355453091211e-07 880 1015.54545454545 1025 4.09660299690437e-09 543 1.80713311944722 2.04044275505942 1 3.13248858528511 1049 543 1122 1244 878 1610 1025 1100 991 732 877 834 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 53/124 Arthur Liberzon 7.80629989055863e-08 2.69835827198101e-07 1270 1019.09090909091 1025 7.09663651595545e-09 524 1.87895338088618 2.19112927722569 1 3.17473398488934 1269 524 759 700 1135 1651 1232 886 1025 636 1393 835 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 107/252 Arthur Liberzon 7.82367974935235e-08 2.70167747276825e-07 2475 1587.36363636364 1028 7.1124363887086e-09 754 1.63145114621296 -1.47689451492101 -1 2.75632298234472 2471 771 1028 959 1137 994 3270 3089 1000 754 1988 836 M165 PID_SYNDECAN_4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_4_PATHWAY.html Syndecan-4-mediated signaling events 18832364 29/62 Pathway Interaction Database 1.7864115782831e-07 5.1994563079718e-07 1030 1034 1029 1.62401065758243e-08 229 2.22830416754441 2.25402816023639 1 3.60173884386362 926 1619 1131 363 1886 1082 1120 229 1029 1029 960 837 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 129/372 Arthur Liberzon 5.11639736611744e-09 4.58593242377669e-08 1095 1062.81818181818 1030 4.65127034365118e-10 90 1.90342190021163 2.17051759420607 1 3.59290145327036 1092 489 683 930 90 2256 1654 1481 1030 535 1451 838 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 11/30 Jessica Robertson 2.1349009491361e-05 3.5053068842508e-05 260 1261.09090909091 1032 1.94083787881788e-06 260 2.19057623416162 2.19057623416162 1 2.51033359309228 260 1773 956 1884 2981 381 366 1478 2182 579 1032 839 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 32/95 Arthur Liberzon 1.9488277990895e-08 1.04532024081787e-07 665 1036.72727272727 1034 1.77166165122982e-09 79 2.11362669418819 2.31390885387851 1 3.79515112884773 661 1967 1034 1322 1573 682 755 79 1412 1205 714 840 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 285/822 Leona Saunders 4.35616183321732e-09 4.07300268483159e-08 1235 1000.27272727273 1034 3.96014712894805e-10 194 1.8376836060191 2.16816246448453 1 3.49316303009684 1231 888 404 809 194 1950 1400 1034 1552 418 1123 841 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 174/346 Jessica Robertson 3.070088177454e-07 8.11417552146049e-07 895 996.818181818182 1034 2.79098964171204e-08 210 1.78277808112588 2.20034963135993 1 2.79297543023322 893 1172 996 210 1641 1205 1034 825 1285 1432 272 842 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 404/997 Jessica Robertson 7.69597038689168e-15 2.12137160193967e-13 1480 935 1036 6.99633671535609e-16 11 1.842643635284 2.25659207233615 1 6.00665368767088 1480 11 164 332 361 2640 1673 1129 1280 179 1036 843 M16393 BIOCARTA_NUCLEARRS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NUCLEARRS_PATHWAY.html Nuclear Receptors in Lipid Metabolism and Toxicity 3/24 BioCarta 0.00055052322501868 0.000751238157378431 930 1543.27272727273 1037 5.50659656709575e-05 577 2.52682540278778 2.52682540278778 1 2.0305599418553 928 1697 3852 597 3446 1037 787 1480 577 999 1576 844 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 177/422 Leona Saunders 1.36574708099818e-23 1.12278786343114e-21 1040 873.272727272727 1038 1.24158825545289e-24 35 2.03793752954164 2.20806460300624 1 10.981645083687 1038 36 55 228 725 1961 1512 1522 1094 35 1400 845 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 5/11 Leona Saunders 1.3176207536476e-05 2.24033775456918e-05 1190 1617.45454545455 1038 1.31762856627282e-06 378 2.41978779529708 2.41978779529708 1 2.89400722737032 1189 2216 4291 996 3076 751 1038 815 378 2246 796 846 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 65/199 Arthur Liberzon 6.20363298841056e-08 2.26933834376986e-07 670 1207.90909090909 1038 5.63966651212968e-09 514 1.71724857685602 1.72853515626952 1 2.9347291921606 669 514 790 1871 1038 1060 862 2217 2162 916 1188 847 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 70/169 Broad Institute 3.73182279197055e-07 9.51426643855708e-07 1030 1238 1040 3.39256674999408e-08 792 1.75562827585803 2.04858488187722 1 2.71922350601887 1029 792 1206 1456 1719 1040 1027 890 2218 1232 1009 848 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 140/403 Kevin Vogelsang 1.7760958982421e-07 5.17264473534025e-07 550 1147.72727272727 1040 1.61463276511748e-08 314 2.03181117724055 2.50263081110928 1 3.28530908751816 1400 1376 548 546 1455 2330 1630 314 1017 969 1040 849 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 312/761 Arthur Liberzon 6.63665888199315e-08 2.38845215233596e-07 1045 991.909090909091 1041 6.03332643836256e-09 229 1.64446795370692 1.87371262858118 1 2.80095159544765 1041 270 681 229 1064 1976 1560 1161 1468 448 1013 850 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 61/147 Kevin Vogelsang 2.37888975659055e-08 1.17662724439535e-07 1045 1554.90909090909 1042 2.16262707483074e-09 500 1.468529581158 1.63160127891451 1 2.61742681033649 1042 2763 2120 2665 610 801 806 500 2753 2060 984 851 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 31/84 Arthur Liberzon 1.60686212741063e-08 9.22009258052164e-08 1045 1272.36363636364 1043 1.46078376286092e-09 449 1.76199302012753 1.80354890417399 1 3.188476990222 1043 1669 1488 2573 449 959 920 906 1962 1402 625 852 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 14/23 Arthur Liberzon 7.16972778291959e-07 1.64531559210388e-06 890 1074.90909090909 1043 6.5179364722831e-08 247 2.55283120286941 2.61341944482984 1 3.79778465952608 887 1284 1341 1157 1948 1043 967 1013 247 1098 839 853 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 63/145 Leona Saunders 1.11659926789538e-07 3.54136142299033e-07 2445 1269.54545454545 1043 1.01509029506167e-08 506 2.13530849174653 -2.15902554244562 -1 3.54303033106165 2443 659 544 506 1284 1338 2734 1043 677 847 1890 854 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 6/16 Arthur Liberzon 1.56918047202512e-05 2.63460397417044e-05 830 1563.18181818182 1043 1.56919155260833e-06 162 1.91395237776315 1.91395237776315 1 2.2543815250146 830 2328 4590 1247 3463 566 342 896 162 1728 1043 855 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 26/63 Jessica Robertson 4.35076308096962e-08 1.77450162227972e-07 1875 1201.90909090909 1044 3.95523924273743e-09 260 1.90548766113963 2.24555151857761 1 3.30878078588321 1872 694 1014 1284 865 2687 1902 452 1147 1044 260 856 M2130 KEGG_ETHER_LIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ETHER_LIPID_METABOLISM.html Ether lipid metabolism 15/37 KEGG 8.81759101895138e-09 6.69679603157312e-08 3685 1923 1047 8.01599186753842e-10 206 2.01498465055353 -1.33193019146473 -1 3.71826060991027 3684 411 1047 716 206 4546 3667 1833 394 708 3941 857 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 105/214 Arthur Liberzon 8.22786107390873e-09 6.490868180528e-08 1390 1056.54545454545 1047 7.47987373152766e-10 182 2.15533297307951 2.69870846833238 1 3.98476590359466 1386 2007 896 662 182 1836 1308 355 1047 1369 574 858 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 69/256 Arthur Liberzon 6.38714569152994e-07 1.49054605132018e-06 1550 1254.45454545455 1049 5.80649776897956e-08 389 2.04131819565851 2.36422841477126 1 3.05934630427696 1546 1655 823 974 2026 2170 1553 389 939 1049 675 859 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 64/151 Kevin Vogelsang 6.83980442197208e-07 1.57974002493747e-06 1055 1131 1051 6.21800595315416e-08 503 1.47543760729446 -1.38644305881241 -1 2.20167587188466 1051 793 1740 941 1931 503 766 1259 1740 664 1053 860 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 23/61 Arthur Liberzon 3.67057668990588e-09 3.58340049352061e-08 1055 1033.18181818182 1052 3.33688790548185e-10 55 1.76851901802951 1.72229249952747 1 3.38699223748776 1358 1052 1505 1391 55 804 555 1052 1343 1319 931 861 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 728/1952 Jessica Robertson 9.75757831256128e-14 2.21961223168263e-12 575 1225.54545454545 1052 9.75757831256169e-15 1 1.78885653342936 2.06030090470035 1 5.36214890917702 573 1 4547 326 840 1681 1052 1104 1792 55 1510 862 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 24/125 Jessica Robertson 3.78967044550342e-08 1.61293330677829e-07 1055 1084.63636363636 1053 3.44515500980311e-09 322 2.60254524990184 2.61204227098852 1 4.54693935821544 1098 1053 994 1516 801 1053 876 322 1415 1421 1382 863 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 488/1481 Arthur Liberzon 1.70395950013437e-22 1.19175436084025e-20 1055 873.636363636364 1054 1.54905409103124e-23 5 1.84382380822836 2.12577738774091 1 9.44910250360367 1054 5 65 224 103 2188 1451 1584 1417 136 1383 864 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 51/114 Jessica Robertson 4.01723537299039e-08 1.6726859268505e-07 1055 986.181818181818 1055 3.65203222395068e-09 175 2.07364415939727 2.62106645613042 1 3.61446334458452 1055 1716 1234 409 837 1684 1473 313 254 1698 175 865 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 98/480 Arthur Liberzon 2.88693246000041e-08 1.33809747849277e-07 970 1277.54545454545 1055 2.62448408898541e-09 442 1.95067847442256 1.96651673816469 1 3.44876073068325 967 1437 588 1575 693 1055 995 3239 1444 442 1618 866 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 357/939 Arthur Liberzon 3.72770696843995e-08 1.59817336268157e-07 1945 1450.18181818182 1055 3.38882457418424e-09 443 1.7631773485909 2.16872060117024 1 3.08227981167101 1941 615 883 443 794 4626 2160 1303 1323 1055 809 867 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 247/589 Arthur Liberzon 1.15242122016495e-08 7.71377224059447e-08 1645 1057.18181818182 1058 1.04765566018332e-09 277 1.45851532213827 -1.29909622295055 -1 2.66837073021289 1645 277 1172 912 295 355 2269 1689 1383 574 1058 868 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 67/174 Arthur Liberzon 4.28331961140378e-12 7.48941630561124e-11 1910 1071.90909090909 1058 3.89392691946557e-13 94 2.00364929452079 -2.01072474072331 -1 5.21842070682877 1907 94 262 633 1058 1150 3049 1159 892 167 1420 869 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 23/50 Jessica Robertson 2.22995369332214e-08 1.13458881725381e-07 845 995.727272727273 1058 2.02723065084117e-09 579 2.20647178835618 2.41523697893354 1 3.9416621211122 844 1339 1267 1219 579 1234 1276 660 607 1058 870 870 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 7/19 Arthur Liberzon 3.57446938177448e-07 9.18813138946527e-07 1020 1235.81818181818 1059 3.57446995673202e-08 225 2.94505428720718 3.41116111340962 1 4.57295370662034 1016 241 4154 379 1739 1208 1848 1059 225 618 1107 871 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 28/53 John Newman 1.40588289135778e-07 4.26958342767502e-07 815 1153.09090909091 1060 1.27807543745364e-08 763 2.23808032945832 2.33065875999477 1 3.66680219585955 815 1972 1153 1163 1367 1026 778 1620 1060 967 763 872 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 427/970 Jessica Robertson 1.711075434138e-12 3.23310463079463e-11 1060 1168.18181818182 1060 1.55552312194485e-13 242 1.86353515779703 2.22659971829163 1 5.02837306743182 1060 613 242 652 1306 2480 1653 981 1643 674 1546 873 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 87/313 Yujin Hoshida 1.36189890009696e-08 8.37514205492698e-08 4360 2158.63636363636 1062 1.23808991684339e-09 380 1.83979836322221 -1.46275822107501 -1 3.34902635372213 4359 784 875 914 380 2376 4432 4105 1062 1027 3431 874 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 694/1785 Arthur Liberzon 4.97072497470826e-10 6.24472311836002e-09 875 1272 1064 4.97072497582011e-11 88 1.65237174876965 1.99231595600608 1 3.48704735297764 875 884 4657 286 344 1767 1393 1064 1305 88 1329 875 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 101/276 Itai Pashtan 4.87567876118496e-08 1.93786519719362e-07 915 1157.18181818182 1064 4.43243533567328e-09 352 2.02596472242088 2.34030417954729 1 3.49805195404282 1064 1499 1078 1008 911 1461 1574 912 796 2074 352 876 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 5/27 Reactome 1.60202154200266e-06 3.35286866718378e-06 1065 1503 1065 1.6020226969167e-07 191 2.80713573457053 2.80713573457053 1 3.95287571216993 1062 2405 3912 1065 3050 781 799 522 191 1521 1225 877 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 138/331 Arthur Liberzon 1.42847332811587e-08 8.62606445302961e-08 790 1027.63636363636 1065 1.29861212490094e-09 400 1.60693416778275 1.97661899095064 1 2.919839290257 790 638 1077 482 400 1920 1065 934 1790 1122 1086 878 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 170/565 Jessica Robertson 2.23988415298448e-10 2.97339862348025e-09 1070 1200.72727272727 1066 2.0362583211023e-11 98 1.98534992243265 2.18592201336738 1 4.35430755771981 1066 2288 339 1048 98 2063 1238 922 2470 210 1466 879 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 90/349 Yujin Hoshida 6.65490060871928e-08 2.38964477030334e-07 3470 1971.45454545455 1067 6.04990982729731e-09 76 1.69578781368379 -1.46301992786692 -1 2.88826794906456 3468 76 726 635 1067 3660 3781 3444 849 425 3555 880 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 10/26 Jessica Robertson 3.22335329123171e-07 8.4525089662629e-07 1460 1212.18181818182 1068 2.93032160318621e-08 860 2.30788181624504 2.26433723731036 1 3.60509353352307 1457 974 1058 1113 1659 1142 888 2134 1068 981 860 881 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 4/11 Jessica Robertson 6.69099968849797e-06 1.20314752648893e-05 675 1387.09090909091 1068 6.69101983484791e-07 264 2.41102055748118 2.41102055748118 1 3.0509600850177 672 1231 4475 387 3136 703 264 1465 581 1276 1068 882 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 23/60 Arthur Liberzon 2.04172138860178e-08 1.07379421178316e-07 765 1032 1070 1.85611037050008e-09 23 1.62927341688257 1.46364883959992 1 2.92057264449471 762 953 1671 2028 1070 270 66 1699 1486 1324 23 883 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 47/145 Jessica Robertson 7.18460831088689e-09 5.88585219314965e-08 1365 1002.36363636364 1072 6.53146212213627e-10 158 1.98775814316855 1.96792581886585 1 3.69668082252979 1364 1921 1084 725 158 1617 1099 202 886 898 1072 884 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 20/68 Yujin Hoshida 1.069994942273e-08 7.39899659922656e-08 2850 1691.18181818182 1073 9.72722679524579e-10 269 1.77760705274826 2.31170792670977 1 3.2604259132553 2850 389 872 680 269 4191 3040 2519 603 1073 2117 885 M203 PID_ALK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK2_PATHWAY.html ALK2 signaling events 18832364 5/13 Pathway Interaction Database 1.56348839226751e-08 9.08698406718676e-08 1025 1386.45454545455 1074 1.56348840326774e-09 7 2.17446877958187 2.17446877958187 1 3.93841951161925 1024 1363 3903 307 3023 1368 1074 75 7 2232 875 886 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 44/119 Arthur Liberzon 2.84326664577731e-07 7.61345571549284e-07 250 1096.09090909091 1075 2.58478819385403e-08 246 1.56912636640511 1.61385097836276 1 2.46942435983093 246 808 1478 2036 1612 406 292 1384 2127 1075 593 887 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 11/25 John Newman 1.63375071975333e-06 3.40710096696222e-06 780 1250.63636363636 1075 1.48522903000063e-07 777 2.73376287181617 3.15119546375575 1 3.84465550918389 777 1990 1007 1075 2163 1127 789 948 1425 1494 962 888 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 8.28849052584436e-07 1.86461193490671e-06 690 1490.81818181818 1075 8.28849361730437e-08 502 2.25675566831264 2.47767774582412 1 3.32577773692453 686 1075 4432 1380 2008 843 502 1419 2539 620 895 889 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 17/79 Arthur Liberzon 8.62340300122058e-07 1.93438326777021e-06 815 1143.81818181818 1078 7.83946034669309e-08 353 2.45933741380121 2.85063537804583 1 3.6142299417182 927 1630 1378 1448 1995 1078 813 737 353 1408 815 890 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 56/231 Jessica Robertson 1.98073062016344e-22 1.34517444725883e-20 1080 1016.90909090909 1078 1.80066420014858e-23 67 2.55355656077307 2.93157580663518 1 13.0517493821238 1078 329 67 128 1729 2045 1949 2082 469 82 1228 891 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 393/1015 John Newman 8.45887761996117e-09 6.58738602381418e-08 1085 1062.27272727273 1079 7.68988877498643e-10 189 1.58026822051906 1.84082579954806 1 2.91898417592386 1081 453 947 1250 189 1680 1191 960 1982 1079 873 892 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 5/41 Jessica Robertson 1.16751286409157e-07 3.67220805851852e-07 195 1317.63636363636 1079 1.16751292543045e-08 185 1.85981042620095 1.85981042620095 1 3.07836984579954 582 1079 4507 1962 1797 195 185 195 2178 1534 280 893 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 40/76 Arthur Liberzon 2.34680771719788e-08 1.16990861306269e-07 325 975.909090909091 1082 2.13346158384727e-09 42 1.93816039112725 2.13745078168428 1 3.45571096661553 321 1884 1440 1082 2025 145 164 89 1752 1791 42 894 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 117/292 Jessica Robertson 8.73857268368474e-09 6.66921035761347e-08 730 1392.90909090909 1083 7.94415701672274e-10 204 1.46281108872386 1.62416687037527 1 2.70000659528771 730 1790 2001 2214 204 1083 1069 679 2536 2182 834 895 M920 REACTOME_AQUAPORIN_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AQUAPORIN_MEDIATED_TRANSPORT.html Genes involved in Aquaporin-mediated transport 23/54 Reactome 1.33435203932372e-06 2.85254272640098e-06 900 1370.54545454545 1084 1.21304804421862e-07 387 1.92910144036442 1.90896778420836 1 2.75129454988796 900 387 784 1324 2107 1084 863 3127 2118 1056 1326 896 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 54/154 Jessica Robertson 1.42354410467525e-08 8.60760193997102e-08 1060 1092.54545454545 1084 1.29413101262411e-09 398 1.56838019896511 1.78027318316653 1 2.85016115195533 1058 664 1263 1447 398 1302 878 611 1908 1405 1084 897 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 17/33 Arthur Liberzon 2.38059437582426e-07 6.60868794141734e-07 410 1031.27272727273 1085 2.16417693947786e-08 410 2.72045664608031 2.72045664608031 1 4.32435016014251 410 1209 749 966 1546 1178 633 1275 1268 1085 1025 898 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 367/764 Jessica Robertson 3.57391981253157e-08 1.56664062128372e-07 1065 1155.27272727273 1086 3.24901806417294e-09 655 1.63290441687267 1.96683362206442 1 2.85817952680462 1061 1086 980 665 776 2094 1247 1328 1581 655 1235 899 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 318/686 Leona Saunders 2.72153266186263e-08 1.27349290946147e-07 1210 1191.27272727273 1087 2.47412063229966e-09 346 1.76751974371466 2.01093317355342 1 3.13471038244861 1206 1087 459 412 938 2553 1281 1051 2150 346 1621 900 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 19/43 Kevin Vogelsang 2.8689569023705e-07 7.67211254594611e-07 785 1089.27272727273 1087 2.6081429786391e-08 349 1.89379590443305 2.21639155126308 1 2.97875189536885 784 1678 1559 904 1613 1105 729 564 349 1610 1087 901 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 6/17 BioCarta 2.92684980290371e-06 5.70753981540024e-06 535 1565.72727272727 1088 2.92685365781325e-07 531 1.37445203799412 1.37445203799412 1 1.85376094979031 727 1995 3825 2161 2329 629 534 939 1088 2465 531 902 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 85/248 Antony Bosco 7.09622944100411e-08 2.50776253096118e-07 1530 1153.72727272727 1088 6.4511178817247e-09 650 1.83438620542921 2.16376798626274 1 3.11444254983554 1527 650 927 655 1095 1731 1088 797 1777 1385 1059 903 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 91/288 Jessica Robertson 9.57115347400508e-09 7.02612984903285e-08 3510 1632.90909090909 1089 8.70104865058599e-10 303 2.16644984354464 2.29443856082935 1 3.98614196826353 2303 781 422 915 1089 3506 2103 3510 876 303 2154 904 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 54/115 John Newman 6.74863292754873e-08 2.41372228240618e-07 1110 1088.36363636364 1090 6.13512103142465e-09 62 1.67363105972836 2.01233590768064 1 2.84865622157567 1109 1383 1536 832 1217 1090 910 239 867 2727 62 905 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 18/54 Leona Saunders 1.00611091953068e-08 7.18694476969627e-08 2110 1281.09090909091 1092 9.14646294665322e-10 249 1.64228171205386 1.96191951585098 1 3.01755135910756 2107 714 1578 1089 249 2634 1681 755 1092 1169 1024 906 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 17/31 John Newman 3.92112893361266e-06 7.40903636407617e-06 610 1271 1092 3.56466902034642e-07 607 2.55876023268349 2.80590036197608 1 3.37649250920808 607 2239 1244 1636 2382 839 805 841 884 1412 1092 907 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 41/175 Yujin Hoshida 1.26536057740594e-08 8.0434968418917e-08 4410 1876.18181818182 1092 1.15032780425803e-09 51 1.96759840267954 -1.73510821579638 -1 3.59054431311238 4410 671 1092 51 353 2167 4381 3670 334 952 2557 908 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 26/46 Arthur Liberzon 4.79169012400423e-08 1.90966641526074e-07 710 1486.36363636364 1092 4.35608202579018e-09 617 1.36705595225106 1.50788135308376 1 2.36261157645392 709 1336 1714 2454 905 739 784 1092 2775 3225 617 909 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 9/26 Reactome 2.63028197939121e-06 5.17878208211227e-06 1095 1640.27272727273 1093 2.63028509266888e-07 643 2.37048671180718 2.71400884612502 1 3.22288375573927 1093 2572 3962 2441 2306 938 855 732 643 1669 832 910 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 11/29 John Newman 4.10832490060465e-05 6.44297539632979e-05 580 1297.81818181818 1093 3.73491056573467e-06 576 2.5897642567167 2.5897642567167 1 2.79169255575067 576 1478 773 1835 3017 826 601 969 1785 1093 1323 911 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 148/374 Jessica Robertson 3.92050468713855e-09 3.75694989037449e-08 1865 1276.18181818182 1093 3.56409517647734e-10 62 1.74226560457768 2.19779282435784 1 3.32750801038237 1865 289 911 318 62 3968 1770 1093 1494 970 1298 912 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 166/419 Jessica Robertson 3.17022312029623e-08 1.43671813749595e-07 1025 1235.09090909091 1093 2.88202105998134e-09 490 1.65144086696672 1.69492938869271 1 2.90659580261979 1023 1093 660 1626 729 1279 930 1615 2593 490 1548 913 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 5/9 Arthur Liberzon 1.46182511712747e-07 4.40238592471679e-07 1095 1524.81818181818 1094 1.46182521328945e-08 103 2.86001986016596 2.86001986016596 1 4.67598293057833 1094 2172 4202 1633 2342 848 956 217 103 2240 966 914 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 80/230 Yujin Hoshida 5.19973495429766e-08 2.02327199005734e-07 810 1165.81818181818 1094 4.72703188835839e-09 231 2.02300165112289 2.42152884012179 1 3.48318937499922 809 2059 1432 1094 943 1595 1208 231 1079 1339 1035 915 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 19/49 John Newman 2.02363549245641e-07 5.74712479857621e-07 1340 1030.36363636364 1095 1.83966879872488e-08 399 2.35348897741499 2.64795964796812 1 3.77775384916079 1337 399 1095 687 1492 1373 1151 791 466 797 1746 916 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 442/969 Jessica Robertson 2.8581196720339e-12 5.2113419389692e-11 1095 1180.18181818182 1095 2.59829061094327e-13 251 1.84687642734605 2.20208551794545 1 4.88493145496642 1095 995 251 580 1133 2512 1566 990 1619 702 1539 917 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 170/346 Arthur Liberzon 2.35128115780941e-08 1.17089303990382e-07 1195 993 1098 2.13752834812642e-09 452 1.78096405368815 1.87508841063829 1 3.17526489749931 1191 482 458 639 602 1536 1270 1387 1808 452 1098 918 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 87/217 Arthur Liberzon 1.15155255952461e-09 1.34233216266973e-08 485 890.363636363636 1099 1.04686596375215e-10 3 1.67642368550187 2.01377885319335 1 3.39449567269366 485 1099 1599 1125 1392 79 386 393 1592 1641 3 919 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 38/86 Leona Saunders 6.4462552812124e-11 9.2376612378475e-10 705 984.090909090909 1100 5.86023207400116e-12 318 2.77530020114887 3.16344257268273 1 6.44925846384891 705 1122 318 1100 694 1467 1404 1687 781 327 1220 920 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 17/40 John Newman 2.29331327726693e-06 4.58662655453387e-06 570 1239.63636363636 1101 2.08483242532261e-07 569 2.55876023268349 2.80590036197608 1 3.51356539249086 569 2202 1254 1524 2255 847 776 822 871 1415 1101 921 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 7/42 Jessica Robertson 4.97986096988554e-07 1.210982278406e-06 765 1384 1101 4.97986208584156e-08 105 2.24686822921251 2.59621526369676 1 3.41954026021014 765 1162 4577 1101 1858 742 1058 1402 105 1940 514 922 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 179/424 Arthur Liberzon 9.68730739682107e-09 7.04076564672179e-08 1105 1165.27272727273 1102 8.80664312679762e-10 233 1.80623452174266 2.12958151464556 1 3.32294678715258 1102 481 455 1069 233 2492 1615 1445 1739 426 1761 923 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 14/51 Andrew Gentles 1.57267265866164e-08 9.08698406718676e-08 155 866.545454545455 1102 1.42970242718537e-09 29 2.06387056774245 2.06387056774245 1 3.73810291789688 342 1215 1335 1488 2456 155 29 73 1182 1102 155 924 M638 KEGG_ADHERENS_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADHERENS_JUNCTION.html Adherens junction 53/111 KEGG 3.85965133538441e-08 1.63086800339147e-07 940 1168.27272727273 1103 3.50877400281602e-09 809 2.08089320635427 2.17686539618618 1 3.63298406816907 940 2062 1089 1135 809 1058 1114 1263 912 1366 1103 925 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 16/38 Leona Saunders 4.41719953415297e-07 1.09518502735666e-06 1130 1038.45454545455 1103 4.01563674640589e-08 413 2.05070303676496 2.42740883589424 1 3.14401809940951 1128 1058 1140 1416 1786 1433 1103 428 413 586 932 926 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 14/31 John Newman 7.28905050620174e-08 2.56237739475329e-07 1105 1416.09090909091 1105 6.62640977063903e-09 224 1.8342521323611 1.93246100238086 1 3.10980043711916 1813 224 961 1105 1103 2356 1979 2324 699 629 2384 927 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 2/5 Arthur Liberzon 5.71680830185325e-05 8.74884510205236e-05 1360 1700.4 1105.5 6.35217062217563e-06 535 1.6702004615836 -1.6702004615836 -1 1.74334986034192 1357 992 4655 NA 3042 740 936 1047 535 2536 1164 928 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 13/41 Arthur Liberzon 2.80066852541879e-07 7.50868047674773e-07 2040 1184.18181818182 1106 2.54606261995698e-08 583 2.09868653884942 2.25798496096293 1 3.30607244128262 2039 583 1176 994 1608 1925 1299 628 662 1006 1106 929 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 3/14 Reactome 4.69780825147675e-05 7.29662892489892e-05 1070 1763.90909090909 1108 4.69790756674231e-06 907 1.98178019662617 1.98178019662617 1 2.10875835152897 1067 1644 4008 1064 3271 907 1070 997 1474 2793 1108 930 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 6/13 Arthur Liberzon 1.51216000056538e-06 3.19128826853215e-06 1220 1418.81818181818 1108 1.5121610295489e-07 248 2.62363967420539 2.95809912409353 1 3.70896095736053 1219 2252 4665 927 2524 1108 663 513 248 1159 329 931 M19829 BIOCARTA_AGPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGPCR_PATHWAY.html Attenuation of GPCR Signaling 9/21 BioCarta 6.75285939443983e-08 2.41372228240618e-07 840 1399 1109 6.75285959964484e-09 582 1.59908050939098 1.59908050939098 1 2.72176511034213 838 1419 3816 1598 1109 582 818 1138 1031 2293 747 932 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 63/116 John Newman 2.44185292988808e-07 6.73089578203268e-07 700 1288.27272727273 1111 2.21986654628861e-08 586 1.80694160292802 1.89653682974505 1 2.86855752954412 699 2261 1308 1687 1557 777 765 963 2457 1111 586 933 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 174/415 Kevin Vogelsang 9.96736346248258e-16 3.13470236142237e-14 1115 977.272727272727 1113 9.06123951134779e-17 114 1.93638296595262 2.12330694498022 1 6.72583245872609 1113 479 144 395 519 1986 1453 1688 1551 114 1308 934 M115 PID_REG_GR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_REG_GR_PATHWAY.html Glucocorticoid receptor regulatory network 18832364 57/143 Pathway Interaction Database 7.67041081121742e-08 2.67039710708505e-07 1305 1011.27272727273 1114 6.97310098059105e-09 476 1.90282290554068 2.11775543953236 1 3.21727872543483 1301 1114 1159 784 1120 1226 969 872 1447 656 476 935 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 32/78 Kevin Vogelsang 7.49477758511554e-08 2.61898044473165e-07 1300 1277.72727272727 1114 6.8134344004013e-09 692 1.98102660275263 1.88884571502094 1 3.35380741468989 1300 1041 699 925 1114 2189 1730 1932 1032 692 1401 936 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 3/9 Arthur Liberzon 1.76255035991764e-05 2.93403587444904e-05 1025 1742.27272727273 1114 1.76256433970066e-06 403 1.62251695719854 1.62251695719854 1 1.8915987168177 1025 1645 4555 1770 3175 850 403 862 1114 2817 949 937 M13283 HSIAO_LIVER_SPECIFIC_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HSIAO_LIVER_SPECIFIC_GENES.html Liver selective genes 11773596 122/467 Kevin Vogelsang 4.83916234198316e-11 7.17604896662439e-10 3235 2038.45454545455 1115 4.39923849280874e-12 62 2.07652305349516 -2.06363606178362 -1 4.88401611019177 3232 62 308 637 487 4063 3573 4091 1115 349 4506 938 M181 PID_BMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BMP_PATHWAY.html BMP receptor signaling 18832364 26/54 Pathway Interaction Database 2.49847983463814e-07 6.84270982180849e-07 865 1405.36363636364 1116 2.27134556216701e-08 535 1.87980316441961 2.01536137597352 1 2.98076710560493 862 3066 2172 1490 1566 1112 579 535 630 2331 1116 939 M812 REACTOME_GPCR_DOWNSTREAM_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPCR_DOWNSTREAM_SIGNALING.html Genes involved in GPCR downstream signaling 161/1312 Reactome 3.09781938919976e-08 1.41209938305351e-07 610 1349.63636363636 1116 2.81619948438196e-09 392 1.91769710938108 1.96838436081645 1 3.37891906438318 606 2546 526 2074 717 1116 1012 1723 2495 392 1639 940 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 296/805 Jessica Robertson 1.33281346416208e-08 8.26322183149997e-08 1120 1307.18181818182 1116 1.21164861112417e-09 372 1.43214861528422 1.81284074086656 1 2.60912461238802 1116 1088 1563 852 372 2291 1832 801 2146 1378 940 941 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 16/35 Arthur Liberzon 3.78667048493728e-07 9.63319103822807e-07 375 917.545454545455 1117 3.44242830609492e-08 197 1.96252060030786 1.96252060030786 1 3.03694761898634 374 1213 1549 1199 1726 234 460 340 1117 1684 197 942 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 70/169 John Newman 1.06259458780814e-08 7.39899659922656e-08 1120 1158.36363636364 1119 9.65995084491313e-10 268 1.9233451533093 2.26551766043129 1 3.52773375837872 1119 658 865 1860 268 1846 1392 1194 1604 1082 854 943 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 17/45 Jessica Robertson 5.81522052170325e-08 2.18350347473569e-07 1200 1109.09090909091 1120 5.28656425037813e-09 211 1.40826327981567 -1.33183242784567 -1 2.41274767734039 1200 211 1791 1126 1001 591 850 1502 1722 1086 1120 944 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 147/664 Jessica Robertson 1.97019947814892e-11 3.14025671925368e-10 1240 1011.63636363636 1122 1.79109043469687e-12 254 1.93291472316833 2.1616291510251 1 4.72469399239333 1240 635 286 348 1039 1966 1286 1122 1322 254 1630 945 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 60/133 Arthur Liberzon 3.78097497413458e-08 1.61216093983573e-07 800 1399.72727272727 1123 3.43725003555941e-09 723 1.94760198987861 2.39622353549803 1 3.40278394940019 1655 796 723 895 800 2828 2041 1515 1123 993 2028 946 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 29/60 Arthur Liberzon 1.88362087145963e-08 1.02042166516299e-07 915 1136.90909090909 1123 1.71238262507913e-09 348 2.11267260866949 2.50059666613737 1 3.79912738402684 913 1929 1672 1419 521 1653 1123 936 348 1240 752 947 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 109/333 Arthur Liberzon 7.71290050160967e-08 2.68319612104996e-07 1125 1230.27272727273 1124 7.0117279745577e-09 889 1.74875197693434 2.00453896246753 1 2.95584267874231 1115 1497 990 1197 1124 1706 1094 1124 1371 889 1426 948 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 38/77 Leona Saunders 1.35365437081147e-08 8.33538026494423e-08 1720 1346.36363636364 1125 1.2305948901277e-09 378 2.06173683265891 2.51802350441007 1 3.75412200001734 1716 1449 1125 851 378 2967 2386 898 585 1372 1083 949 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 36/94 Arthur Liberzon 1.07418040041155e-07 3.44531783458488e-07 1125 1169.54545454545 1125 9.76527684418086e-09 802 2.02884235753101 2.13616463853706 1 3.37260681277855 1125 1764 937 1360 1265 802 913 1537 1171 1038 953 950 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 9/23 Jessica Robertson 1.86287705775801e-05 3.09116214329109e-05 1130 1758.45454545455 1127 1.86289267434146e-06 688 1.75123427455986 2.04340632798937 1 2.03145733806383 1127 2530 4461 1421 3602 1101 688 875 971 1678 889 951 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 419/1097 Arthur Liberzon 4.27036970820156e-09 4.01826354470533e-08 1315 1114.27272727273 1129 3.88215428771879e-10 403 1.82713702481318 2.23639667375258 1 3.47587722044401 1313 1649 403 1129 436 2206 1592 444 1705 637 743 952 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 28/71 Arthur Liberzon 1.62348832001285e-08 9.24201006892422e-08 885 1041.45454545455 1132 1.47589848363033e-09 458 1.85563558497119 2.20489846219583 1 3.35743905706854 881 1195 1132 480 458 1639 1622 868 1208 792 1181 953 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 20/32 Jessica Robertson 4.04324272684378e-09 3.85878521751323e-08 900 1027.90909090909 1134 3.67567521297693e-10 64 1.52877669308986 1.56180115756629 1 2.91520362907352 897 199 1480 1004 64 1134 1260 1071 1192 1710 1296 954 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 37/97 John Newman 3.27326280739354e-08 1.46656420133261e-07 1090 1298 1136 2.97569350554061e-09 584 1.56700198745323 1.64656842144435 1 2.75438118797011 1089 1834 1792 1136 744 824 584 1146 1879 2540 710 955 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 173/476 John Newman 3.64203935119248e-08 1.57780713967333e-07 1140 1240.81818181818 1138 3.31094491953223e-09 493 1.9320468236222 2.08748113749883 1 3.38025523700314 1138 1092 493 508 783 2088 1606 1744 1640 914 1643 956 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 32/67 Jessica Robertson 3.55244962540878e-07 9.13958571908345e-07 765 1226.09090909091 1140 3.22950018094605e-08 584 1.71052432559782 1.87282121994 1 2.65704080230916 761 817 1444 2157 1702 1325 982 584 1881 694 1140 957 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 26/79 Leona Saunders 4.28849092022786e-08 1.75816871847662e-07 1180 1166.45454545455 1141 3.89862818529457e-09 126 2.59657651256357 3.33347609774086 1 4.51150303155085 1178 3065 1055 400 1216 1593 1141 126 627 1917 513 958 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 31/62 Arthur Liberzon 3.00448185609587e-08 1.37759314849954e-07 1145 1271 1141 2.73134717920663e-09 553 1.69496572124018 1.92771299859531 1 2.99115789909821 1141 1397 1644 1526 709 1135 604 714 1793 2765 553 959 M19428 KEGG_WNT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_WNT_SIGNALING_PATHWAY.html Wnt signaling pathway 77/178 KEGG 2.3069869074518e-08 1.15651168041571e-07 1145 1092.36363636364 1142 2.09726084694869e-09 221 2.08953256155504 2.3509255619562 1 3.72829363704583 1142 2689 1194 362 596 1267 1325 221 902 1959 359 960 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 12/30 Leona Saunders 5.92964605144005e-08 2.19843018787655e-07 745 1106.27272727273 1144 5.39058746478313e-09 325 1.68612967009213 1.57954573041523 1 2.88752709745935 745 1151 1601 2148 1016 679 435 325 1713 1212 1144 961 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 15/43 Kevin Vogelsang 3.15385929280418e-06 6.09945713829154e-06 1325 1238.09090909091 1144 2.8671489219081e-07 385 2.54166990128727 2.78041570834862 1 3.40916382075659 1322 1144 814 1102 2326 1760 1569 842 385 934 1421 962 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 14/26 Lauren Kazmierski 4.17971142427934e-07 1.04626750716736e-06 880 1550.90909090909 1145 3.79973838033627e-08 878 1.60671895030408 1.60671895030408 1 2.47152892122099 878 1810 2136 2286 1765 945 1145 1035 1040 3012 1008 963 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 225/469 Arthur Liberzon 1.04507414529205e-47 4.45201585894415e-45 4450 1905 1149 9.50067404810968e-49 11 2.40612099106394 -2.16638884498108 -1 27.4488342736237 4447 25 11 531 1149 2692 3636 4070 653 18 3723 964 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 343/817 Jessica Robertson 2.51002090338182e-13 5.32215292002137e-12 1150 1322.36363636364 1150 2.28183718489283e-14 215 1.82786215682496 1.98761790498732 1 5.30049926807343 1150 616 215 869 659 3011 2079 1834 1723 217 2173 965 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 77/152 Arthur Liberzon 1.43593498888221e-07 4.33835677492071e-07 1045 1168.81818181818 1151 1.30539552964124e-08 520 2.11756437702328 2.34624294878768 1 3.46557264732571 1044 1019 520 1036 1375 1810 1331 1151 1347 551 1673 966 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 45/110 Yaara Zwang 1.98867871065697e-08 1.05897141342484e-07 1920 1373.63636363636 1151 1.80788975330322e-09 532 1.97464068472226 2.44642277353631 1 3.54273088677095 1919 1119 1151 543 532 3121 2122 1103 629 1342 1529 967 M12899 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GLOBO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GLOBO_SERIES.html Glycosphingolipid biosynthesis - globo series 5/15 KEGG 1.92188531543949e-08 1.03629956114056e-07 1260 1169.81818181818 1155 1.92188533206088e-09 177 1.78296098368774 2.06293636325362 1 3.20314600321224 1259 1424 3797 1313 559 1032 1155 177 194 1519 439 968 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 48/122 Leona Saunders 8.16741598125824e-08 2.78669606995346e-07 300 1322.18181818182 1156 7.42492389497312e-09 300 1.70211495061977 1.73382230510488 1 2.86981765202514 300 2144 1481 2275 1156 500 525 472 2702 2336 653 969 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 6/21 Jessica Robertson 0.000197507243812804 0.00028320653136683 845 1570.90909090909 1156 1.97524800109036e-05 415 2.93176403384336 2.93176403384336 1 2.67546108245572 842 1950 4358 643 3223 1038 1035 1255 415 1156 1365 970 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 37/73 Leona Saunders 6.25092904525394e-08 2.28307509790023e-07 820 1508.36363636364 1158 5.68266292987597e-09 731 1.63370921547689 1.92893600229264 1 2.79086141309363 816 2377 1802 2170 1041 1049 808 1158 1742 2898 731 971 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 327/800 Jessica Robertson 3.76122539831955e-34 5.34094006561376e-32 4380 1860.54545454545 1160 3.41929581665416e-35 32 2.0061226912072 -1.73597156775602 -1 16.1367897418483 4377 265 32 452 955 1998 4000 3868 1160 36 3323 972 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 79/243 Jessica Robertson 1.03627268394361e-07 3.34894744617914e-07 890 1253.27272727273 1161 9.42066120686797e-09 567 1.90897669198061 2.12638902588706 1 3.17940027132404 886 2415 1468 1161 1250 1052 733 1130 1260 1864 567 973 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 3/11 Arthur Liberzon 1.7597238807798e-06 3.62221394827095e-06 1470 1540.63636363636 1161 1.75972527426402e-07 31 2.42506436721195 2.42506436721195 1 3.3939287873779 1469 991 4659 1481 3031 1161 836 532 31 1760 996 974 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 41/113 Jessica Robertson 6.85718149658078e-08 2.44727741759159e-07 1595 1611.90909090909 1162 6.2338015548294e-09 811 1.62768811101907 1.50082134706761 1 2.76794728592947 1591 1035 1273 1834 1076 1158 1126 4584 2081 811 1162 975 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 137/323 Jessica Robertson 5.20282276572577e-08 2.02327199005734e-07 1165 1238.27272727273 1163 4.7298389897894e-09 191 1.7817372981115 2.13020893601709 1 3.06778215966598 1163 2291 1024 478 945 2392 1181 191 1482 1325 1149 976 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 82/188 Arthur Liberzon 4.40916022950301e-11 6.60106224774796e-10 1225 1244.90909090909 1164 4.0083274814467e-12 220 2.13518407938091 2.403923912139 1 5.04190830990637 1224 1015 305 768 949 2426 1692 1875 1164 220 2056 977 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 2/7 Jessica Robertson 9.80078743646126e-06 1.70793937996495e-05 1220 1565.5 1165 1.08898112533654e-06 433 2.56762160188233 -2.56762160188233 -1 3.14863915453895 1220 1747 4477 NA 3037 756 702 779 433 1394 1110 978 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 67/143 Jessica Robertson 1.42553320741627e-09 1.62203623905208e-08 2590 1618.18181818182 1166 1.29593928030907e-10 11 2.26637886202655 -1.65948119258219 -1 4.54114387412149 2590 794 743 263 11 4342 2530 993 1166 1286 3082 979 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 286/714 Leona Saunders 1.45967904596283e-08 8.7357037156856e-08 735 1279.54545454545 1167 1.32698095967969e-09 410 1.67005272980296 1.94736419766792 1 3.03217104477176 732 2655 1356 1270 410 1167 901 967 2215 1431 971 980 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 4/14 Jessica Robertson 2.47766673758961e-07 6.81358352837143e-07 1110 1453.09090909091 1167 2.47766701383711e-08 22 4.61284990662952 4.61284990662952 1 7.31670421096428 1107 1167 4464 457 2242 1458 1977 282 22 2053 755 981 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 11/24 Arthur Liberzon 1.90673895159094e-07 5.46816323571307e-07 1470 1228.36363636364 1168 1.73339919713449e-08 236 2.20317388453914 2.84622901229812 1 3.54871805311262 1470 1475 1168 1704 2798 694 859 236 1124 1486 498 982 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 11/36 Reactome 3.94805042747761e-06 7.45689814718262e-06 1170 1530.09090909091 1169 3.58914319321987e-07 824 2.09369693678286 2.09369693678286 1 2.76129757727656 1169 2034 2012 824 2385 1537 1133 954 1128 2613 1042 983 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 5/12 Leona Saunders 9.102251543797e-07 2.03303864319508e-06 1070 1600.45454545455 1170 9.10225527209338e-08 695 1.88477137354679 2.22808897923135 1 2.75937745807288 1069 989 4160 2237 2033 1170 1435 695 2015 973 829 984 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 18/31 Arthur Liberzon 4.55307984027085e-06 8.48676695764089e-06 575 1527.72727272727 1170 4.13917205751734e-07 572 1.66776900408867 1.66776900408867 1 2.17545561413037 572 2701 1433 2132 2414 605 589 937 3610 1170 642 985 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 29/115 Jessica Robertson 8.49348401115265e-08 2.85955903690318e-07 535 1248.09090909091 1173 7.72134939914406e-09 531 1.52760338709732 1.52377369377273 1 2.57118134429097 531 824 1583 1639 1173 635 773 1240 2255 2180 896 986 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 6/12 Jean Junior 0.000131091646150632 0.000191608064211435 860 1721.09090909091 1175 1.31099380051605e-05 238 2.09385778332322 2.09385778332322 1 2.0021973068039 857 2403 4366 2397 3097 891 654 1175 238 1723 1131 987 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 81/357 Jessica Robertson 7.05624955128529e-16 2.34860119592858e-14 3350 1947.54545454545 1175 6.41477231935025e-17 135 2.31075226022502 -2.18274507271134 -1 8.1006922470506 4081 501 135 562 638 3088 4388 3350 1175 159 3346 988 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 19/52 Arthur Liberzon 4.25875647756994e-07 1.05967115049171e-06 2640 1588.63636363636 1176 3.87159754725414e-08 599 2.37320924475392 -2.30062713536866 -1 3.64720494010948 2640 837 734 1176 1774 2266 4181 1015 599 796 1457 989 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 5/9 Jessica Robertson 3.21038733892536e-05 5.11001191243351e-05 780 1508.45454545455 1177 3.2104337195093e-06 604 2.50930674880936 2.50930674880936 1 2.76993405353504 778 604 4326 1177 3013 1273 1528 950 711 974 1259 990 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 38/77 Jessica Robertson 7.07497786575243e-06 1.26394762786565e-05 835 1276.72727272727 1177 6.4318187438812e-07 475 1.9108184806168 2.06483832738731 1 2.40747000941111 831 2018 1177 1591 2708 475 552 745 1844 1615 488 991 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 48/126 Jessica Robertson 4.85447919962838e-07 1.18417956946687e-06 870 1227.27272727273 1178 4.41316388255372e-08 754 1.46185665592939 1.5726065391173 1 2.22847500165512 867 807 1879 1589 1815 815 754 1042 1460 1294 1178 992 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 12/30 Yujin Hoshida 3.70670834833157e-08 1.59372539641036e-07 1405 1182.18181818182 1180 3.36973491889517e-09 119 2.18993128203055 2.83606471885094 1 3.82898703187534 1404 964 1180 1323 2566 1771 1124 119 155 1631 767 993 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 50/114 Jessica Robertson 9.00329269578018e-09 6.79378898106698e-08 2960 1787.09090909091 1183 8.18481157511392e-10 210 2.27885429613023 3.14760479159474 1 4.2015199796578 2959 1183 1059 743 210 4261 2857 1957 538 1179 2712 994 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 14/36 Reactome 1.39457155803519e-06 2.96773947363892e-06 515 1202 1185 1.26779312913594e-07 231 1.5614715521561 1.67076070322922 1 2.22007326560352 515 231 1317 1231 2122 822 891 1922 1890 1096 1185 995 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 16/47 Reactome 8.4537439488613e-07 1.89814298727188e-06 1140 1322 1187 7.68522472482536e-08 843 1.88064480281356 2.11359220957313 1 2.767759317821 1137 843 1187 1260 1992 1024 1037 1815 1765 1019 1463 996 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 108/296 Jessica Robertson 1.25207237782814e-08 8.0181460061125e-08 1310 1099.81818181818 1187 1.13824762268543e-09 66 1.4205243656981 1.63274299780706 1 2.59272479556177 1308 66 1350 884 346 1144 1187 1731 1702 1473 907 997 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 45/96 Arthur Liberzon 3.11964388811266e-08 1.41928653006757e-07 770 1155 1187 2.83603993849986e-09 423 2.00219195901441 2.09450260778128 1 3.52666073859117 769 1187 518 1629 720 1323 1194 1495 2523 423 924 998 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 11/27 Yujin Hoshida 5.8020066759589e-07 1.37522525460513e-06 1675 1240.72727272727 1189 5.27455291464421e-08 376 2.14798583268998 2.44955345847434 1 3.23853197997484 1673 1414 1352 1189 2357 1332 1167 376 852 1095 841 999 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 18/39 Jessica Robertson 9.21367716257516e-09 6.87504636685147e-08 1190 1245.90909090909 1190 8.37607018287487e-10 217 1.41344910520148 1.71096951853017 1 2.60409646539406 1190 1057 1770 1708 217 1223 1153 744 1760 2371 512 1000 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 60/211 Kevin Vogelsang 4.73599888804381e-08 1.89769579972418e-07 450 1105.72727272727 1191 4.30545362726995e-09 448 2.3064474560309 2.53752401532338 1 3.98773324694637 448 1831 474 1191 2012 1213 772 1070 1357 547 1248 1001 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 73/319 Alexandra Naba 1.62680896847635e-11 2.64695375912506e-10 1260 1084.81818181818 1191 1.47891724408034e-12 35 2.09716419994255 2.23087403204168 1 5.16621048100252 1256 790 280 1149 35 1930 1676 1191 1692 120 1814 1002 M16173 BIOCARTA_PS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PS1_PATHWAY.html Presenilin action in Notch and Wnt signaling 9/27 BioCarta 1.21618975718929e-06 2.62629732819771e-06 1065 1474 1192 1.21619042279269e-07 398 2.23650102526676 2.64122375424248 1 3.21035473331713 1065 1815 3856 1037 2426 1287 1192 482 993 1663 398 1003 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 185/483 Jessica Robertson 1.02002971737331e-08 7.25320069136774e-08 940 1386.36363636364 1193 9.27299747366073e-10 252 2.07187758991328 2.49983940297797 1 3.80477298596909 936 3880 1079 1376 252 1579 1193 973 1405 1800 777 1004 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 24/37 John Newman 1.04259292061301e-07 3.36705060371645e-07 845 1168.72727272727 1195 9.47811790929184e-09 468 1.83666762678074 1.99319272380636 1 3.05786344593259 841 1931 1512 623 1251 776 892 1247 468 2120 1195 1005 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 195/447 Jessica Robertson 2.97788866532303e-16 1.05715047618968e-14 365 1296.09090909091 1196 2.70717151393002e-17 127 2.19898389485478 2.29259242297772 1 7.90495435967422 361 2789 127 1196 875 1735 1106 2132 2070 482 1384 1006 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 10/26 Jessica Robertson 2.73284210761546e-07 7.36405872126858e-07 1200 1348.09090909091 1198 2.48440222462675e-08 215 2.36582140817013 2.36582140817013 1 3.73203135679647 1198 2502 1884 1438 3065 849 537 284 215 1857 1000 1007 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 218/510 John Newman 6.91148144391429e-09 5.73224814976679e-08 1550 1246.54545454545 1199 6.28316496875206e-10 147 1.76933367523827 2.02402457750959 1 3.29569820661159 1547 760 742 701 147 3085 1706 1199 1872 374 1579 1008 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 116/279 Leona Saunders 2.08664215113352e-08 1.08888122883347e-07 965 1153.63636363636 1201 1.89694742811343e-09 209 1.89970379302196 2.10958765795995 1 3.40237487419988 964 1308 494 576 553 2348 1201 1795 1508 209 1734 1009 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 126/287 Arthur Liberzon 6.55630266863453e-10 8.04262678147157e-09 445 1082.90909090909 1201 5.96027515508037e-11 360 2.1068245640273 2.40563097790204 1 4.38654456422665 431 2054 360 1071 2141 1328 1228 441 1201 441 1216 1010 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 142/518 Jessica Robertson 9.97219175867293e-17 3.76852343396301e-15 265 1336 1201 9.0656288715208e-18 119 2.22283293729443 2.34167570176122 1 8.24681134629217 264 2862 119 2013 2058 1157 665 1269 2776 312 1201 1011 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 25/96 John Newman 1.85795226938817e-07 5.35446761030318e-07 650 1290.54545454545 1202 1.6890476602697e-08 648 2.78774000833948 2.51452709178909 1 4.49683947402154 1525 1048 1002 1640 1471 1188 648 2317 648 1202 1507 1012 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 5/14 Jessica Robertson 5.32829875097136e-08 2.06350478901254e-07 1135 2194.54545454545 1206 5.32829887872981e-09 147 2.15852169662126 2.15852169662126 1 3.71177911304662 1135 3738 4467 4015 3529 1206 716 147 846 3295 1046 1013 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 12/29 Reactome 5.71938626851993e-08 2.15110956596538e-07 890 2091.81818181818 1207 5.19944219746184e-09 887 2.01389330496853 2.32941562561721 1 3.45372343969615 2819 967 1156 887 997 3380 2759 4581 887 1207 3370 1014 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 24/53 Reactome 1.10548879612958e-07 3.52163188216398e-07 870 1333.27272727273 1207 1.00498986516348e-08 428 1.64059050644658 1.80604179926071 1 2.72318876108616 866 1804 2421 1271 1281 584 562 746 1207 3496 428 1015 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 19/42 Kevin Vogelsang 2.21427511825563e-08 1.13263174329229e-07 2215 1314.36363636364 1207 2.01297740049278e-09 249 1.8799848641494 2.30686216012792 1 3.3587853137194 2212 1207 1379 2000 574 2287 1172 249 1144 1013 1221 1016 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 19/37 Arthur Liberzon 4.76193658808869e-07 1.16463647451898e-06 760 1348.54545454545 1210 4.32903419892554e-08 93 2.48914522842926 2.24751144209931 1 3.79911560170624 756 3232 1210 2374 1835 414 93 640 1261 2028 991 1017 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 233/562 Arthur Liberzon 3.57968874922832e-08 1.56770294195176e-07 3350 1602.09090909091 1214 3.25426255224958e-09 340 1.6747645605603 -1.67412221023624 -1 2.93132326635229 3347 469 543 1214 777 853 4401 2563 1655 340 1461 1018 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 12/24 Arthur Liberzon 3.76932977811555e-05 5.93517450949243e-05 1220 1494.36363636364 1216 3.42672214617027e-06 769 2.06813587755308 2.06813587755308 1 2.24835779265744 795 2355 1780 2585 2860 876 769 1160 824 1216 1218 1019 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 5/11 Arthur Liberzon 2.31756299166731e-05 3.78400703099408e-05 2245 1793.18181818182 1220 2.31758716196407e-06 261 2.80628337921234 2.80628337921234 1 3.19193209086815 1201 2537 4244 2242 2776 1220 1115 1073 261 2244 812 1020 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 78/204 Arthur Liberzon 8.06780144576677e-08 2.76357584611572e-07 915 1207.27272727273 1220 7.33436521966163e-09 575 2.07596105552692 2.38735158015449 1 3.50206564276696 912 1559 577 1332 1150 2008 1297 808 1220 575 1842 1021 M2442 STEINER_ERYTHROCYTE_MEMBRANE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/STEINER_ERYTHROCYTE_MEMBRANE_GENES.html Major erythrocyte membrane genes. 19687298 12/27 Arthur Liberzon 4.02389267821444e-06 7.58180984725084e-06 1225 1191.54545454545 1221 3.65809094372955e-07 138 2.91628121543454 3.08243050675952 1 3.84076106512259 1221 592 995 269 2393 1456 1635 1765 138 1219 1424 1022 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 10/37 Leona Saunders 1.41896427770397e-07 4.30140091681152e-07 1245 1035.45454545455 1222 1.28996760838625e-08 139 3.17460304173371 3.17460304173371 1 5.19853945288379 1244 1222 1325 928 1369 1264 1147 337 139 1855 560 1023 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 5/9 Jessica Robertson 5.00204616485998e-06 9.2488716680006e-06 1820 1500.72727272727 1222 5.00205742410527e-07 71 3.18049906441445 3.52285566791765 1 4.11812469799166 1817 740 4560 1222 2552 1227 1970 684 71 975 690 1024 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 75/157 Arthur Liberzon 9.69119471219709e-09 7.04076564672179e-08 2340 1531.81818181818 1224 8.81017704989786e-10 234 1.73755219475537 2.28573129883923 1 3.19659125041621 2336 319 1191 257 234 4370 2383 1224 880 1291 2365 1025 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 29/50 Arthur Liberzon 9.6897034435344e-08 3.17302238549282e-07 1245 1357.54545454545 1225 8.80882170028067e-09 507 2.3008275624015 2.43837944711028 1 3.84589705413529 1242 2616 1145 1093 1225 1036 507 2051 865 1836 1317 1026 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 138/343 Arthur Liberzon 1.72591355828617e-08 9.62813206443925e-08 930 1301.81818181818 1225 1.56901233802369e-09 482 1.75339069903123 1.89809328743296 1 3.16442848999 929 2368 1225 1165 482 1425 1241 1472 2019 846 1148 1027 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 93/241 Arthur Liberzon 2.82903778422923e-15 8.3904247195558e-14 2565 1833.27272727273 1226 2.57185253111748e-16 100 2.11502814069135 2.09429994539045 1 7.11372240553666 2561 303 152 569 1226 4603 3210 2921 1131 100 3390 1028 M916 REACTOME_PLATELET_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_HOMEOSTASIS.html Genes involved in Platelet homeostasis 31/91 Reactome 1.41132121176478e-08 8.5666466299608e-08 695 1155.18181818182 1227 1.28301929165322e-09 371 1.84695714828169 1.99807657625764 1 3.35739311866357 691 371 858 1227 395 1310 1372 2289 1747 1136 1311 1029 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 37/98 Jessica Robertson 9.85889065380765e-08 3.22391916285713e-07 1290 1184.72727272727 1229 8.9626282687414e-09 145 1.47025409803681 1.68619272399827 1 2.45495684625091 1290 145 1259 760 1229 1132 895 2033 2041 1565 683 1030 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 11/27 Yujin Hoshida 3.69618168545165e-06 7.03791441610176e-06 1070 1418.90909090909 1231 3.36017081396067e-07 204 3.03553284287715 3.03553284287715 1 4.02305828327031 1070 2499 1392 1879 2771 719 204 1178 1231 1973 692 1031 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 8/17 Arthur Liberzon 1.23036404711306e-06 2.65201744469723e-06 875 1551.81818181818 1231 1.23036472832165e-07 636 2.81843584766147 3.59710397796607 1 4.04261681994232 871 1739 4600 995 2117 1249 1231 817 636 2111 704 1032 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 66/209 Nikolaos Papanikolaou 3.57917964343511e-10 4.62039553970715e-09 325 1259.09090909091 1233 3.25379967637948e-11 322 2.63516378972502 2.90846107980651 1 5.64974190217471 322 2641 349 1131 1524 1596 1084 1297 1843 830 1233 1033 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 216/499 Jessica Robertson 7.75017553994835e-08 2.68420713822601e-07 1785 1486.09090909091 1234 7.04561437542916e-09 438 1.71763240567663 2.09495257250767 1 2.90317027569937 1783 1234 845 438 1132 3913 1964 696 1534 1034 1774 1034 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 99/221 Arthur Liberzon 1.15709444664171e-08 7.71377224059447e-08 2015 1326.90909090909 1235 1.05190404793407e-09 302 1.66397428127057 -1.64125546960532 -1 3.04426031352513 2013 780 1235 1359 302 374 3333 1367 2315 923 595 1035 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 163/354 Arthur Liberzon 2.2357566332028e-07 6.2697519947267e-07 490 1098.27272727273 1235 2.03250623673843e-08 159 1.7101079810417 1.93215035250088 1 2.72838994975524 486 2221 1365 1258 1529 636 438 757 1997 1235 159 1036 M5576 BIOCARTA_PLCE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLCE_PATHWAY.html Phospholipase C-epsilon pathway 6/16 BioCarta 5.27184825420733e-07 1.2668656881649e-06 605 1360.81818181818 1237 5.27184950486502e-08 289 1.37445203799412 1.37445203799412 1 2.08487107448853 604 1594 3854 1722 1879 373 527 424 1237 2466 289 1037 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 101/230 Jessica Robertson 1.34260500226175e-10 1.84499913214034e-09 560 1117.90909090909 1237 1.22055000213062e-11 331 2.12960930524367 2.52417910212699 1 4.78422927074078 558 1249 331 1710 1572 1543 1237 884 1125 433 1655 1038 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 40/110 Jessica Robertson 4.58708968821668e-08 1.85142999818978e-07 975 1420.36363636364 1240 4.17008162169033e-09 850 1.52709667407103 1.77490500942315 1 2.644484810585 971 1964 2273 1454 886 1713 1240 853 1043 2377 850 1039 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 9/23 John Newman 9.19874810687673e-08 3.05062516835275e-07 425 1294.81818181818 1242 9.19874848765309e-09 175 1.95025321718556 2.59757712968258 1 3.26847239801649 1610 425 4408 1295 1242 1290 666 423 175 1675 1034 1040 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 123/310 Reactome 5.57533702677539e-08 2.11889937611269e-07 865 1282.09090909091 1244 5.06848833460731e-09 492 1.96423393260312 2.21701333567208 1 3.37187055323488 861 1244 833 492 975 1648 1305 1820 1959 1143 1823 1041 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 44/119 Arthur Liberzon 1.0188919929213e-07 3.30417154244237e-07 3915 2309.54545454545 1244 9.26265491008665e-09 740 2.33559975654403 -2.21575213007698 -1 3.89345280043004 3914 1034 740 778 1244 4311 3436 3418 1180 1077 4273 1042 M6391 KEGG_PEROXISOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PEROXISOME.html Peroxisome 45/92 KEGG 1.02042770692486e-07 3.30686323281459e-07 545 1857.81818181818 1245 9.2766159477767e-09 75 0.876289716250561 -0.876289716250561 -1 1.46069811673607 545 2263 3538 3935 1245 75 369 391 3662 4166 247 1043 M735 REACTOME_NEURONAL_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEURONAL_SYSTEM.html Genes involved in Neuronal System 98/338 Reactome 1.09140245705806e-07 3.48623852336338e-07 895 1403.45454545455 1246 9.92184101092426e-09 894 1.63023424502428 1.7862183370461 1 2.70783808561555 894 2181 1246 1595 1274 1149 1016 1602 2202 1118 1161 1044 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 289/952 Kate Stafford 7.66315294601881e-20 3.90321029402654e-18 585 932.545454545455 1246 6.96650267819888e-21 87 2.15055062578477 2.34466155664364 1 9.62967542590117 581 756 87 404 1416 1350 1324 1246 1696 118 1280 1045 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 85/194 Kevin Vogelsang 9.44539754389178e-07 2.1016682284272e-06 1205 1328 1246 8.58672872649617e-08 503 1.58964122476269 1.8762430077192 1 2.32140011344613 1204 503 1386 902 2016 1672 1542 1011 2168 958 1246 1046 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 14/35 Arthur Liberzon 6.96870699557729e-07 1.60389788709603e-06 955 1245.45454545455 1247 6.33519018452888e-08 581 2.80635746273662 2.66354675382281 1 4.18294209388131 954 581 884 1588 1941 1283 1108 1643 1627 844 1247 1047 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 40/90 Kevin Vogelsang 1.53944322249806e-08 9.00603113686131e-08 1540 1291.90909090909 1248 1.39949384842751e-09 435 1.53992220297779 1.85138571524874 1 2.79066171575253 1708 935 1539 886 435 2230 1173 1747 1540 1248 770 1048 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 114/353 Arthur Liberzon 3.37332079431845e-12 5.98764440991526e-11 1515 1186.27272727273 1250 3.06665526756693e-13 223 2.07463399481018 2.43249414880713 1 5.45516193918172 1513 903 258 421 1240 2276 1768 1457 1250 223 1740 1049 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 51/136 Nikolaos Papanikolaou 2.61854798496095e-05 4.23705658063777e-05 405 1790.09090909091 1250 2.38052650247611e-06 405 1.98087049890475 2.03152674070834 1 2.22806484769765 405 3494 701 3299 2857 1185 717 1251 3606 926 1250 1050 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 105/242 Leona Saunders 5.84551045527905e-08 2.18786437647265e-07 2955 1748 1251 5.31410055508837e-09 740 1.74763804111349 -1.15715185336638 -1 2.99380181145314 2955 774 938 740 1005 3892 2194 1572 1251 976 2931 1051 M145 PID_P53_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P53_DOWNSTREAM_PATHWAY.html Direct p53 effectors 18832364 85/185 Pathway Interaction Database 3.9640165359534e-08 1.66446070676323e-07 975 1153.36363636364 1252 3.6036514612528e-09 703 1.59237462477525 1.75985225985375 1 2.77646378403105 974 1252 1413 703 821 1333 1430 919 1424 1561 857 1052 M5785 KEGG_TASTE_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TASTE_TRANSDUCTION.html Taste transduction 19/88 KEGG 9.78351346826635e-06 1.70607312545916e-05 785 1690.72727272727 1253 8.8941427057511e-07 783 1.69353085627509 1.46504374978349 1 2.07696041818546 783 955 1152 1630 2587 1253 940 4391 2083 794 2030 1053 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 59/156 John Newman 3.27363669354227e-08 1.46656420133261e-07 960 1285 1253 2.97603340204957e-09 715 1.66775461570578 1.8577274651355 1 2.93147806955632 959 1507 1272 2202 745 1498 1160 715 1593 1253 1231 1054 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 447/1156 Jessica Robertson 1.29112901548517e-28 1.4070303643171e-26 2530 1755.63636363636 1253 1.17375365044107e-29 8 1.94827078087147 2.18062207548106 1 12.9549889972943 2530 8 42 375 296 4390 2832 3417 1253 37 4132 1055 M240 PID_SYNDECAN_2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_2_PATHWAY.html Syndecan-2-mediated signaling events 18832364 34/68 Pathway Interaction Database 8.20050964092954e-07 1.84925833384965e-06 1090 1401.90909090909 1254 7.45501154334063e-08 615 1.76361278752091 2.26041792479211 1 2.60066263166008 1088 2148 1744 709 1984 1789 1254 615 768 2629 693 1056 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 87/191 Arthur Liberzon 1.63074033814655e-07 4.83342771951597e-07 860 1156.36363636364 1255 1.48249132638589e-08 493 1.92613993089891 2.21625587795449 1 3.12903964364955 856 1704 1192 588 1413 1555 1255 493 1348 1457 859 1057 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 283/867 John Newman 1.03643455091441e-16 3.88538584446793e-15 1370 1079.27272727273 1256 9.42213228104003e-18 120 1.97207600811898 2.16177422080146 1 7.30976407704116 1370 1089 120 350 618 2243 1504 1256 1591 121 1610 1058 M15902 KEGG_GLYCEROLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROLIPID_METABOLISM.html Glycerolipid metabolism 22/70 KEGG 2.19427820565025e-06 4.40925714908966e-06 755 1224.90909090909 1257 1.994800358386e-07 189 1.82083808320732 -1.77303507314553 -1 2.50830830910332 1475 189 1071 755 2247 754 1257 2139 1306 994 1287 1059 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 19/48 Reactome 3.54441603537529e-06 6.77647227326341e-06 780 1422.63636363636 1257 3.22220158708224e-07 209 1.56068218976119 1.67076070322922 1 2.07500593391977 780 209 1238 1522 2355 921 820 2459 2795 1257 1293 1060 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 19/30 Leona Saunders 1.80317890806723e-07 5.23201013201427e-07 1285 1224.63636363636 1258 1.63925368714602e-08 784 1.91538290730645 2.06379612336321 1 3.09461036315411 1282 1341 1277 1167 1460 1211 802 1966 923 1258 784 1061 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 3/7 Arthur Liberzon 3.79756093804743e-08 1.61336088446875e-07 920 1426.09090909091 1258 3.79756100294405e-09 4 5.63352245341962 5.63352245341962 1 9.84223098699464 920 1367 4287 474 2737 1258 1789 124 4 1750 977 1062 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 55/147 Arthur Liberzon 8.68702292375226e-05 0.000129723994329838 450 1574 1260 7.89760542051565e-06 447 2.21007664517442 2.27642942446498 1 2.20962336496863 447 3198 1178 2116 3090 1118 775 1094 1574 1464 1260 1063 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 57/149 John Newman 5.36083936792121e-06 9.83975451550285e-06 710 1295.54545454545 1262 4.87350220996836e-07 707 2.20422647703985 2.5669949654071 1 2.83879366685563 707 1322 818 1527 2449 1313 1262 1169 1035 1165 1484 1064 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 310/881 Jessica Robertson 2.89326501613704e-14 7.32856208952333e-13 1395 1056.27272727273 1262 2.63024092376098e-15 54 1.82318126408247 2.04063685049098 1 5.6907254165241 1392 271 180 54 595 2598 1684 1920 1548 115 1262 1065 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 29/84 Arthur Liberzon 4.01371417421162e-08 1.6726859268505e-07 1245 1418.09090909091 1264 3.64883113403494e-09 836 1.77402715354296 2.04675903622427 1 3.0922161961706 1241 944 1264 1854 836 1905 1788 1630 1931 1031 1175 1066 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 6/13 Reactome 1.52447936934034e-09 1.70902160878681e-08 1270 1328.72727272727 1265 1.52447937038616e-10 16 1.89977672455706 2.11866968711794 1 3.79549695947281 1266 1362 3951 1920 16 1265 961 68 1834 1153 820 1067 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 25/59 Jessica Robertson 2.55716161331082e-09 2.68072915435671e-08 1890 1176.27272727273 1265 2.3246923784392e-10 29 1.66370820399551 2.06225369404469 1 3.2402007374215 1890 388 1305 314 29 2358 1803 1265 990 1502 1095 1068 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 68/170 Jessica Robertson 3.37966922141057e-08 1.5040009469639e-07 3620 1933.54545454545 1267 3.07242661211772e-09 519 2.07820187707904 -1.55462239250127 -1 3.64708575365971 3617 913 649 1267 754 3016 3425 2364 955 519 3790 1069 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 33/75 Kevin Vogelsang 1.89839319151051e-08 1.02605196025585e-07 855 1289.36363636364 1268 1.72581200717441e-09 522 1.52953750476141 1.75755367968373 1 2.74956064285096 855 814 1340 1838 522 1308 1424 1268 2624 1052 1138 1070 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 35/90 John Newman 1.47571075996943e-08 8.76448747936216e-08 1050 1673 1268 1.3415552453347e-09 316 1.04502098101713 -0.891001630114858 -1 1.89697058773804 1047 1268 2903 2804 418 316 796 1927 3258 3123 543 1071 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 26/60 Jessica Robertson 1.35463903768801e-07 4.14079486667058e-07 945 1365.90909090909 1268 1.23149011009021e-08 549 1.95409832966088 2.12416191235247 1 3.20822059347794 944 549 816 1577 1354 1268 1203 2906 1101 1597 1710 1072 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 16/50 Jessica Robertson 6.51195160880519e-07 1.51439231954646e-06 695 1418 1270 5.9199577602994e-08 394 2.19402045960509 2.19402045960509 1 3.28431292070448 692 2430 1270 2844 2284 867 630 394 2099 1306 782 1073 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 352/837 Jessica Robertson 6.71542635263651e-09 5.60935612984932e-08 1385 1194.81818181818 1271 6.10493306648647e-10 140 1.76324142990788 2.10257797569153 1 3.28861897108936 1381 614 461 391 140 3584 1761 1271 1414 298 1828 1074 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 10/13 Arthur Liberzon 5.13741133084404e-05 7.92426250702277e-05 715 1484.90909090909 1275 4.67048300266017e-06 715 2.33064130725468 2.33064130725468 1 2.45848870601815 715 1903 1410 2107 2989 844 1275 994 1027 1860 1210 1075 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 22/63 Reactome 5.11704633682833e-06 9.43513672947462e-06 815 1335.18181818182 1277 4.65187112614496e-07 777 1.86739707434983 2.16170600405406 1 2.41375481331647 812 1137 1346 1518 2442 1399 1277 777 1211 1906 862 1076 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 134/337 Leona Saunders 1.11236424160077e-08 7.5434715428961e-08 1280 1208.54545454545 1278 1.01124022475009e-09 285 1.85054831949363 2.18204554008143 1 3.39021471287241 1278 1094 580 614 285 2766 1498 1707 1676 408 1388 1077 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 376/946 Arthur Liberzon 7.62228294401553e-09 6.13711647348054e-08 750 1447.63636363636 1278 6.92934815493115e-10 417 1.8320099174607 2.10733645664221 1 3.39847708686188 748 2826 417 1818 1450 2059 1042 900 2303 1083 1278 1078 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 49/110 Arthur Liberzon 7.96028767138415e-08 2.73881039085399e-07 605 1355.18181818182 1280 7.2366254176475e-09 603 1.83516311016843 1.89077982981 1 3.09769422010661 603 1029 846 2147 1143 1565 1619 1280 2184 853 1638 1079 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 18/33 John Newman 1.83618652187163e-05 3.04903261569471e-05 1275 1459.72727272727 1281 1.66927440674421e-06 431 1.48583113493658 -1.63627756689683 -1 1.72586347234024 1274 954 1266 1294 2714 1028 2007 1869 1281 431 1939 1080 M241 PID_RAC1_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAC1_REG_PATHWAY.html Regulation of RAC1 activity 18832364 26/51 Pathway Interaction Database 2.72580748653405e-08 1.27349290946147e-07 1730 1353.72727272727 1282 2.47800683664263e-09 676 1.7422363602916 1.67121564080209 1 3.08987009695711 1727 827 1465 1282 676 1827 1824 1014 746 857 2646 1081 M16864 REACTOME_METABOLISM_OF_CARBOHYDRATES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_CARBOHYDRATES.html Genes involved in Metabolism of carbohydrates 114/287 Reactome 1.51870193733125e-08 8.92928140317971e-08 1160 1344.45454545455 1282 1.3806381343774e-09 426 1.6198168026576 1.92667659855352 1 2.93699611946027 1159 1753 1276 1425 426 1934 1282 519 1957 1872 1186 1082 M19248 REACTOME_CELL_JUNCTION_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_JUNCTION_ORGANIZATION.html Genes involved in Cell junction organization 42/101 Reactome 2.48710534629051e-07 6.83096362733292e-07 1670 1225.45454545455 1283 2.26100511587129e-08 509 2.28759384896347 2.17382828275582 1 3.62783190324256 1668 1032 572 759 1563 1577 1283 1977 509 713 1827 1083 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 44/113 Arthur Liberzon 1.44284095268793e-07 4.35641282493275e-07 645 1215.18181818182 1283 1.31167367937705e-08 407 1.70496751442658 1.90400434002322 1 2.78953201896432 642 2339 1526 1998 1377 583 407 877 1901 1283 434 1084 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 74/162 Jessica Robertson 6.65026504982529e-08 2.38964477030334e-07 725 1677.81818181818 1284 6.04569568259335e-09 725 1.8074240094981 2.00390030918436 1 3.07840687303179 725 3953 1664 2333 1066 816 827 1284 2464 2551 773 1085 M9131 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROPHOSPHOLIPID_METABOLISM.html Glycerophospholipid metabolism 36/81 KEGG 1.11676242228773e-07 3.54136142299033e-07 1790 1149.18181818182 1285 1.01523861725159e-08 150 1.52245463984852 -1.34446288524977 -1 2.52614685727968 1786 150 1659 754 1285 638 1756 1037 521 1474 1581 1086 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 96/350 Arthur Liberzon 3.17028109001321e-09 3.23658762261479e-08 1460 1362.63636363636 1286 2.88207372234701e-10 204 1.90335131688461 2.09100582682892 1 3.6668603679529 1458 776 394 1281 728 2977 2119 1286 1634 204 2132 1087 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 49/108 Arthur Liberzon 1.33572166911104e-08 8.26322183149997e-08 1290 1069.27272727273 1288 1.21429243383711e-09 134 1.62282630026382 1.95628988469149 1 2.95650607568815 1015 134 1439 1458 373 1286 1288 578 1342 1354 1495 1088 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 61/134 Arthur Liberzon 1.11810870384233e-07 3.5425675363118e-07 4110 2023.81818181818 1288 1.01646250969828e-08 327 1.67245172348771 -1.36854639227923 -1 2.77496730022059 4107 327 1065 873 1288 1804 3424 3213 1278 895 3988 1089 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 13/33 Arthur Liberzon 1.12796545113097e-07 3.57138250270251e-07 1490 1407.18181818182 1289 1.02542318996642e-08 787 2.26469139595854 2.37578006286409 1 3.75557455281337 1487 2597 1426 1170 1289 1261 861 2066 787 1329 1206 1090 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 380/937 Jessica Robertson 7.91942181385548e-14 1.82809904530674e-12 2155 1429.63636363636 1289 7.19947437623251e-15 13 1.83752633437802 2.31517204754165 1 5.54787107155744 2155 13 198 241 488 4581 2283 1638 1289 483 2357 1091 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 25/73 Jessica Robertson 6.14182125850439e-08 2.25376463722409e-07 1290 1821.36363636364 1289 5.58347402724356e-09 1033 1.85378678412784 1.96709571582505 1 3.16949517355989 1289 2234 1211 3863 1033 1179 1075 2310 2822 1830 1189 1092 M749 REACTOME_CA_DEPENDENT_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CA_DEPENDENT_EVENTS.html Genes involved in Ca-dependent events 15/33 Reactome 1.1319681024085e-07 3.57921897968033e-07 1025 1268.18181818182 1291 1.02906196422888e-08 230 1.2569858542357 1.34432348151358 1 2.08417221156435 1021 230 2066 1968 1291 578 309 1376 2572 1578 961 1093 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 32/102 Reactome 1.33275826068746e-07 4.09259843353962e-07 1350 1262.27272727273 1291 1.21159849220533e-08 725 1.96229199936064 1.94987774369061 1 3.22423924591788 1157 1193 725 1539 1349 1120 1420 1908 1291 836 1347 1094 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 142/397 Kevin Vogelsang 1.16284797552682e-09 1.34878851814819e-08 465 1337.72727272727 1291 1.05713452376497e-10 366 2.05707308207119 2.2295562748505 1 4.16414859392627 461 3139 372 1965 366 1505 1004 1433 2414 765 1291 1095 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 20/32 Arthur Liberzon 7.26606810374421e-07 1.66497775717092e-06 1040 1619.18181818182 1292 6.60551863959269e-08 807 1.56532449242383 1.65660088997449 1 2.32661770810297 1037 2562 2162 2800 1954 835 807 1292 2179 1070 1113 1096 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 77/178 Arthur Liberzon 1.65838681879098e-11 2.6889967587732e-10 3215 1815.09090909091 1293 1.50762438073043e-12 109 1.96265301154348 2.12031611314918 1 4.83139700685413 3214 313 281 524 1293 3865 3353 2121 1254 109 3639 1097 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 46/122 Arthur Liberzon 1.97254546868946e-07 5.62589657107656e-07 510 1494.90909090909 1294 1.79322331413653e-08 508 1.83861292153764 1.95561327799112 1 2.95566806509161 508 2767 1710 2004 1485 1143 1294 1189 1252 2177 915 1098 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 4/9 Jessica Robertson 1.46017674500164e-06 3.09610327017091e-06 1400 1732.18181818182 1294 1.46017770445479e-07 606 1.53806463920936 1.77449307640069 1 2.17951848203298 1398 606 4550 2687 2157 1212 1087 1294 1633 1277 1153 1099 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 322/789 Leona Saunders 4.07414619591433e-09 3.87250488317537e-08 405 1130.27272727273 1295 3.70376927587199e-10 269 1.784389740964 2.07579744083926 1 3.40192128524707 1295 269 401 563 674 2999 1677 1382 1350 404 1419 1100 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 57/176 Kate Stafford 3.63049872389278e-07 9.30662856682799e-07 1185 1304.54545454545 1296 3.30045393000683e-08 763 1.91288807467187 2.22162414025739 1 2.96751208705028 1184 1113 1001 1220 1707 1747 1456 1394 1296 763 1469 1101 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 18/45 Jessica Robertson 1.61729491900532e-05 2.71053075481364e-05 1525 1394.63636363636 1296 1.47027891673945e-06 725 2.03282110997 2.23733786800963 1 2.38794135391304 1522 1680 1296 2035 2863 1198 725 833 869 940 1380 1102 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 174/374 Arthur Liberzon 7.9517739376051e-26 7.4524025343235e-24 2285 1821.36363636364 1297 7.2288853978228e-27 39 2.30088089201084 2.36294295172743 1 13.6875378946557 2285 39 49 591 1297 3943 2356 4541 961 71 3902 1103 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 199/539 John Newman 1.9049710589898e-07 5.46643869101422e-07 1105 1335.18181818182 1297 1.73179202176409e-08 827 1.8001654711053 2.07786571257189 1 2.89964374245645 1101 1867 1295 1297 1477 1908 1350 1148 1307 1110 827 1104 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 20/44 Kevin Vogelsang 8.36573574484402e-06 1.4748622159646e-05 1155 1490.54545454545 1298 7.60524323329089e-07 412 1.76409428449144 -1.6917888716045 -1 2.19219821983608 1516 700 693 1153 2554 1154 2560 1925 1298 412 2431 1105 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 21/70 Reactome 1.15767191953301e-07 3.65063971395134e-07 2555 1575.90909090909 1301 1.05242907313763e-08 623 1.9976251335195 -1.65378888592696 -1 3.30779614036437 2553 1199 1088 965 1301 1125 2313 2273 623 1819 2076 1106 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 19/44 Arthur Liberzon 1.77708225968394e-05 2.95612618703547e-05 1035 1691.36363636364 1301 1.61554237680801e-06 780 2.8568419073882 3.23802065098113 1 3.32823324410895 1033 3211 1358 1221 3369 1701 1278 849 780 2504 1301 1107 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 16/42 John Newman 8.95245305883111e-08 2.98585018033328e-07 2335 1665.09090909091 1304 8.13859402103003e-09 716 2.55693911442442 3.09975365779203 1 4.29136093624327 2333 716 1158 1029 1191 3268 2006 1941 922 1304 2448 1108 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 146/354 Arthur Liberzon 2.27776809326904e-06 4.55942814398066e-06 680 1634.72727272727 1306 2.07070041050698e-07 680 1.82962609758283 2.14160017312419 1 2.51356930502754 680 3083 1016 2426 2253 1306 991 911 2610 1479 1227 1109 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 204/531 Leona Saunders 2.45846542657182e-08 1.2003053648855e-07 625 1588.54545454545 1308 2.23496859458618e-09 451 1.7909583729271 2.17711495578757 1 3.18812024747098 1971 624 451 624 718 4537 2526 1308 1626 700 2389 1110 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 14/40 Arthur Liberzon 4.88910248332641e-07 1.190765812727e-06 1820 1364.81818181818 1310 4.44463960894676e-08 580 1.37292475393653 1.35316054201041 1 2.09205529864327 1293 580 1820 1929 1820 842 699 1310 2649 1442 629 1111 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 92/259 Arthur Liberzon 2.45775605836892e-08 1.2003053648855e-07 1435 1386.09090909091 1311 2.2343237143873e-09 625 1.81100462617085 2.06750010453737 1 3.22380497979091 1434 1097 844 1122 625 2607 1822 1864 1311 745 1776 1112 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 100/221 Kevin Vogelsang 8.33865984918347e-08 2.83582175257329e-07 1775 1446.72727272727 1311 7.58060015022152e-09 585 1.87527352576132 2.43481243857542 1 3.1581075864461 1771 1311 1416 944 1161 3123 2033 632 727 2211 585 1113 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 15/31 Arthur Liberzon 1.17739850045842e-07 3.69296477453023e-07 670 1283.27272727273 1311 1.07036233042779e-08 371 1.47296841005399 1.47185563596782 1 2.43713904297042 670 1211 1381 1452 1311 599 371 1334 2965 2014 808 1114 M195 PID_CMYB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CMYB_PATHWAY.html C-MYB transcription factor network 18832364 65/152 Pathway Interaction Database 4.67419681972099e-09 4.28635739671479e-08 1085 1340.72727272727 1312 4.24926984513816e-10 79 2.02322445680275 2.45436793900024 1 3.83430926461843 1082 2451 1312 1017 79 1840 1168 1003 1697 1575 1524 1115 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 91/268 John Newman 6.13841011772149e-08 2.25376463722409e-07 4095 2171.27272727273 1312 5.58037298999506e-09 559 1.96031294481075 -1.68161760813769 -1 3.3516273247794 4093 1312 629 821 1032 2098 3892 4059 1083 559 4306 1116 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 165/395 Arthur Liberzon 1.39578143837963e-13 3.05397184353271e-12 2520 1714.18181818182 1312 1.26889221670883e-14 202 2.04989930476204 -1.72048109836523 -1 6.07155921358207 2520 629 208 792 1312 4483 2372 2366 1028 202 2944 1117 M10792 KEGG_MAPK_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MAPK_SIGNALING_PATHWAY.html MAPK signaling pathway 120/294 KEGG 1.46505209929018e-08 8.75503631708099e-08 1240 1244.72727272727 1313 1.33186555367859e-09 367 1.67712450448001 1.8642279765011 1 3.04459650569099 1238 1496 1368 367 412 1295 1195 1831 1505 1313 1672 1118 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 97/204 Arthur Liberzon 1.45083900310612e-07 4.3749237892891e-07 1280 1405.36363636364 1315 1.31894463525903e-08 517 1.87260687476254 2.48578484606775 1 3.06292323690104 1279 1830 1315 1171 1380 2316 1434 517 1019 2083 1115 1119 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 7/15 Arthur Liberzon 6.53624359199973e-06 1.17622263717783e-05 1320 1690.09090909091 1316 6.53626281719545e-07 259 1.90681546089041 2.31812299180655 1 2.41774842222643 1316 1484 4451 2583 2821 1054 259 786 492 2690 655 1120 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 172/528 Leona Saunders 1.87825881450852e-14 4.94467460943084e-13 1320 1246 1317 1.70750801318957e-15 104 1.80264277366066 -1.72304830603748 -1 5.70585059123613 1317 1002 173 1213 1345 713 2775 1698 2003 104 1363 1121 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 63/136 Jessica Robertson 2.40919311727266e-06 4.78367752014393e-06 2940 1767.36363636364 1319 2.19017795959513e-07 309 2.00640196437779 -1.68818114589488 -1 2.74566576837967 2938 1319 689 929 2269 1192 2584 3242 1277 309 2693 1122 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 95/209 Arthur Liberzon 5.01867202734224e-07 1.21852316684589e-06 880 1283.27272727273 1320 4.56243015655398e-08 362 2.08336950701745 2.43823654201868 1 3.16926452154498 879 2448 1027 748 1935 1612 1320 362 1428 1438 919 1123 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 30/109 Kevin Vogelsang 2.03470129842588e-07 5.7750516562227e-07 1320 1496.63636363636 1320 1.84972862418922e-08 673 2.1635756932392 2.45428627825389 1 3.47173882288549 930 2425 673 1320 1493 1556 946 2062 2546 1316 1196 1124 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 52/140 John Newman 2.44105866778773e-06 4.8387482729498e-06 725 1699.18181818182 1320 2.21914670574781e-07 570 2.14550869265665 2.51763664913333 1 2.93328336170709 721 3493 1320 2515 3060 1738 1267 570 1102 1763 1142 1125 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 12/22 Jessica Robertson 8.35951006921651e-08 2.83582175257329e-07 1090 1348.72727272727 1321 7.59955489714483e-09 165 2.05762964528519 2.31525417548584 1 3.46520960412069 1086 2120 1321 1997 2126 604 780 165 2529 1630 478 1126 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 23/72 Jessica Robertson 7.55612810698029e-08 2.63595706680458e-07 3425 2185.09090909091 1321 6.86920760591215e-09 385 1.81544794127453 1.91202042812883 1 3.07217829178375 3421 385 1166 429 1117 4389 3805 3198 1196 1321 3609 1127 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 27/48 Arthur Liberzon 0.00011922110242 0.000175351564952956 1125 1476.72727272727 1321 1.08388694245338e-05 912 1.859857044985 2.05398160868569 1 1.79685996520619 1121 1620 1052 1321 3187 1416 1554 1144 1898 912 1019 1128 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 37/104 Jessica Robertson 5.069221906531e-06 9.35766889865965e-06 1340 1346.90909090909 1322 4.60839417002555e-07 531 2.09571376430049 2.53413148091906 1 2.71080186726293 1340 1329 864 875 2671 2350 2100 674 760 531 1322 1129 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 198/552 Arthur Liberzon 2.21407611262838e-07 6.21267105615364e-07 1525 1185.27272727273 1323 2.01279666859331e-08 473 1.64282707334105 1.88720564419322 1 2.62272510692728 1323 473 692 1066 1525 1521 1358 1471 2164 517 928 1130 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 7/16 Arthur Liberzon 2.90295937165503e-05 4.64433855089636e-05 975 1733.63636363636 1323 2.90299729463127e-06 549 3.05815383539335 3.05815383539335 1 3.40842945322566 973 2653 4247 2113 2830 765 549 1323 666 1934 1017 1131 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 20/63 Signaling Gateway 5.2782621781003e-07 1.26775687168519e-06 1165 1340.72727272727 1324 4.79842131315156e-08 218 2.38771011059459 2.66348470935236 1 3.62166887279379 1161 2109 1324 1344 1847 1217 1179 1186 218 1704 1459 1132 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 96/224 Kevin Vogelsang 2.63348074074421e-13 5.55877961762493e-12 610 1228.72727272727 1324 2.39407340067684e-14 216 2.37651417431142 2.54403775027989 1 6.87995150001126 608 2182 216 686 2006 1625 1111 1324 1862 369 1527 1133 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 188/460 Jessica Robertson 1.56420569196162e-07 4.67684172964278e-07 1075 1306.63636363636 1324 1.42200527561551e-08 752 1.67682897248112 1.93527027521932 1 2.73019949173551 1071 1429 752 1226 1399 1324 1461 1241 2281 1364 825 1134 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 52/121 Jessica Robertson 7.66333388571563e-09 6.14903811446292e-08 1330 1483.09090909091 1326 6.96666719309961e-10 170 1.58905965982923 1.94762109820531 1 2.94744675550789 1326 2143 2054 3039 170 766 710 1050 1828 2326 902 1135 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 34/54 John Newman 1.78555086693224e-09 1.96410595362547e-08 1030 1238.81818181818 1327 1.62322806216492e-10 17 1.6630889854 1.91458117441191 1 3.29678187840724 1027 1192 1327 1455 17 1396 1572 1211 2181 1343 906 1136 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 212/986 Arthur Liberzon 6.16427374705967e-32 7.80696939965449e-30 30 1843.36363636364 1327 5.60388522459971e-33 29 2.14329341619174 -2.04276665408255 -1 16.0466906720779 3912 29 36 559 678 3041 3560 3020 1327 29 4086 1137 M77 PID_WNT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_SIGNALING_PATHWAY.html Wnt signaling network 18832364 19/34 Pathway Interaction Database 1.23216283755186e-07 3.83648840981263e-07 1400 1228.09090909091 1328 1.12014809687464e-08 565 2.12716187112079 2.26250485529605 1 3.51049236421111 1396 1462 1082 689 1328 1644 1381 2141 1026 795 565 1138 M9379 REACTOME_SIGNAL_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_AMPLIFICATION.html Genes involved in Signal amplification 13/36 Reactome 6.39980029446622e-08 2.3301836969595e-07 2515 2009.54545454545 1328 5.81800043694219e-09 855 2.01389330496853 2.32941562561721 1 3.43573430531883 2511 855 1269 1079 1045 2991 2448 4507 900 1328 3172 1139 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 7/18 Reactome 1.110978663269e-08 7.5434715428961e-08 1175 1599.18181818182 1330 1.11097866882323e-09 332 2.98376420288166 2.98376420288166 1 5.46627258301763 1171 2717 4007 2235 332 1330 756 1587 464 1930 1062 1140 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 227/507 Arthur Liberzon 1.24229330265397e-07 3.85858309108113e-07 650 1285.90909090909 1330 1.12935761163967e-08 548 1.58980746461364 1.81776658168905 1 2.62266710986999 646 1866 1374 1554 1330 973 943 747 2330 1834 548 1141 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 492/998 Jessica Robertson 8.616876737281e-09 6.65673134670181e-08 1330 1347.18181818182 1330 7.83352433730114e-10 7 1.5471397762259 1.89667454817977 1 2.85598129685672 1330 7 1369 583 195 3601 1626 1107 1832 1130 2039 1142 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 325/930 Leona Saunders 1.2433761134299e-07 3.85858309108113e-07 875 1889 1331 1.13034198518356e-08 873 1.58617188965938 1.78043299103276 1 2.61666958888285 873 3878 2331 1956 1331 1239 1086 1195 2625 3115 1150 1143 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 49/102 John Newman 1.54361326981818e-05 2.59539712320343e-05 450 1690.63636363636 1331 1.40329463688153e-06 449 1.6502988656114 1.77995314224394 1 1.94659673684116 449 3376 2312 2222 2688 1071 1121 836 1331 2079 1112 1144 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 47/101 John Newman 1.53831767335339e-06 3.23543833812118e-06 855 1621.09090909091 1331 1.39847159000043e-07 503 2.28315100665409 2.90492274653058 1 3.22411802369106 853 2905 1293 2507 3033 1331 889 503 1365 2582 571 1145 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 190/551 Leona Saunders 3.82780980755991e-09 3.71232466773318e-08 1745 1438.63636363636 1333 3.47982710383634e-10 59 1.65458422547942 1.94375238168664 1 3.16225616082811 1744 476 650 432 59 4198 2442 1333 1648 512 2331 1146 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 17/38 John Newman 1.49364430285626e-06 3.15991747322096e-06 2540 1700.63636363636 1334 1.35785937903272e-07 570 1.83214320483744 -1.18796371962924 -1 2.59206783395123 2537 570 1074 963 2136 1334 2695 2545 1330 1087 2436 1147 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 15/43 Arthur Liberzon 2.67470881711618e-07 7.23236325274462e-07 1335 1494.63636363636 1335 2.43155376572829e-08 981 1.68292271505006 1.42787370383391 1 2.65816604135977 1335 1146 1507 2103 1593 1171 981 2175 1116 1186 2128 1148 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 17/29 Arthur Liberzon 6.0212070410444e-07 1.42071380636123e-06 1375 1278.36363636364 1336 5.47382608090599e-08 289 1.9700074097063 -1.79849927757808 -1 2.9630314271035 1375 710 551 967 2593 882 1336 1844 1665 289 1850 1149 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 102/308 John Newman 1.61742907614441e-08 9.23183294908041e-08 1420 1242.18181818182 1337 1.47039008003243e-09 454 1.72246256709468 1.81066249839761 1 3.11669839992336 1420 904 960 1337 454 1654 1475 1442 1820 896 1302 1150 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 17/33 Arthur Liberzon 6.0212070410444e-07 1.42071380636123e-06 1380 1279.36363636364 1337 5.47382608090599e-08 290 1.9700074097063 -1.79849927757808 -1 2.9630314271035 1376 711 552 968 2594 883 1337 1845 1666 290 1851 1151 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 133/284 Arthur Liberzon 4.19071272533691e-09 3.95920964333241e-08 660 1441.27272727273 1339 3.80973884847242e-10 68 1.72319896785843 1.77291327983412 1 3.28099929696894 660 2477 957 1686 68 1164 1339 2136 2342 1802 1223 1152 M50 PID_PTP1B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PTP1B_PATHWAY.html Signaling events mediated by PTP1B 18832364 43/115 Pathway Interaction Database 5.1566909224788e-08 2.0120111292869e-07 1405 1393.63636363636 1340 4.68790094849915e-09 741 1.89722792517363 2.00306745968294 1 3.26781593892859 1402 2374 1220 1145 939 1574 1883 741 1826 886 1340 1153 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 534/1255 Arthur Liberzon 3.60401486322521e-08 1.57247799339603e-07 1345 1767.09090909091 1341 3.60401492167537e-09 822 1.62828971030843 1.99615236465444 1 2.84942562332882 1341 2256 4109 857 822 3117 1423 1116 2195 1297 905 1154 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 112/410 Arthur Liberzon 4.7845391840624e-13 9.79054612074951e-12 615 1144.81818181818 1341 4.34958107642132e-14 223 2.18769013370361 2.32459895283018 1 6.19498088966899 614 1555 223 803 767 1932 1341 1627 1762 443 1526 1155 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 47/95 Yujin Hoshida 1.15377143595156e-08 7.71377224059447e-08 4640 2120.90909090909 1341 1.04888312909311e-09 298 1.82303036022585 -1.68110568010634 -1 3.33525528154341 4638 923 1044 1038 298 3776 3350 2886 1341 653 3383 1156 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 235/582 Leona Saunders 6.2903315486275e-10 7.73661250311508e-09 2710 1672.90909090909 1346 5.71848322766005e-11 28 1.80681222943505 1.96933531999995 1 3.76972904950097 2708 28 359 236 65 4310 2377 2956 1346 185 3832 1157 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 16/56 Yujin Hoshida 5.30236148810967e-06 9.74004936624143e-06 1200 1607.90909090909 1346 4.82034024337747e-07 899 1.62158103645682 1.93845030255155 1 2.09025724036393 1196 1346 1304 1928 2447 1241 899 1429 2876 1689 1332 1158 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 39/132 Jean Junior 2.43662104179275e-08 1.19623053244874e-07 4405 2154 1347 2.21511006252698e-09 620 1.60973111644673 -1.68388265523764 -1 2.86612551438673 4405 1266 1347 1041 620 3332 3731 2388 985 1184 3395 1159 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 8/27 Jessica Robertson 0.000156608530154266 0.000227273946207152 1015 2016.81818181818 1349 1.56619568053353e-05 683 2.10140759489409 2.4047544146882 1 1.96934495592366 1014 1780 4501 2989 4414 1021 683 1210 1349 2110 1114 1160 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 7/15 Jessica Robertson 1.01019948490105e-05 1.75781462541638e-05 835 1621.54545454545 1350 1.01020407719393e-06 835 3.04372930091596 3.04372930091596 1 3.72269683456141 835 986 4330 841 2618 1437 1771 1105 1159 1350 1405 1161 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 60/198 Arthur Liberzon 6.0537671280581e-08 2.23193963509679e-07 980 1679.63636363636 1351 5.5034248133094e-09 976 1.66731647128115 1.79898359590988 1 2.85249163959692 976 1321 1137 2444 1026 1822 1351 2469 2608 1314 2008 1162 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 58/115 Arthur Liberzon 2.01341806416104e-08 1.06410983827008e-07 1645 1457.18181818182 1353 1.83038007507967e-09 335 1.83569747337076 2.02213764235423 1 3.29245827433699 1642 335 885 1353 538 2649 1782 2780 1303 688 2074 1163 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 13/42 Arthur Liberzon 1.86267366983415e-07 5.35818834674208e-07 275 1050.09090909091 1353 1.69333984321922e-08 62 2.03310772344424 2.03310772344424 1 3.27940162101399 274 1353 1434 1960 2279 143 62 617 1528 1781 120 1164 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 6/31 Leona Saunders 1.57826235110137e-06 3.3134926769811e-06 2425 1706.63636363636 1356 1.57826347201292e-07 336 2.6138777530157 2.91994518331879 1 3.68418837155098 2424 1076 4463 1175 2189 2284 1356 689 336 775 2006 1165 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 22/46 Kate Stafford 6.86300432563076e-08 2.44749149694869e-07 1505 1296.27272727273 1357 6.23909503611403e-09 393 2.1310897621248 2.34474227162176 1 3.62398072228333 1503 393 1521 1683 1078 1621 1357 1306 686 1908 1203 1166 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 76/163 Jessica Robertson 2.262365012114e-08 1.14486419511514e-07 1490 1626.90909090909 1358 2.05669548670817e-09 586 1.74121205288858 1.67625012162277 1 3.10876405670148 1489 2608 1129 2324 586 1262 1082 2462 2681 915 1358 1167 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 10/23 Jessica Robertson 3.34353788687837e-06 6.43442239749981e-06 1010 1524.18181818182 1360 3.03958451669496e-07 788 1.88143611493075 2.06375882347462 1 2.51235025968965 1008 1991 1697 2166 2339 1074 853 788 2266 1360 1224 1168 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 59/148 Arthur Liberzon 3.65792950233606e-19 1.74908751509661e-17 4115 1953.90909090909 1362 3.32539045666913e-20 74 2.3763300674906 -2.01812845973276 -1 10.2425147323296 4111 323 93 631 1362 2259 4596 4418 457 74 3169 1169 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 4/14 Leona Saunders 4.03016162696933e-05 6.32674619228754e-05 1365 1738.54545454545 1362 4.03023471874728e-06 10 3.08207207991546 3.08207207991546 1 3.32865409810896 1362 2407 4301 1775 3504 1087 622 980 10 2050 1026 1170 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 51/108 Arthur Liberzon 2.1335497178932e-07 6.01915350875829e-07 1440 1384.45454545455 1363 1.9395908407308e-08 265 2.07056688341213 2.52931518666827 1 3.31291845672481 1436 1259 1363 943 1509 3044 1640 783 265 1242 1745 1171 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 199/439 Arthur Liberzon 1.38712338576277e-07 4.21807928986653e-07 1100 1612.72727272727 1364 1.26102133929307e-08 791 1.80285382443037 2.34197113253927 1 2.95618456993791 1097 2178 791 942 1364 3242 2071 1208 1741 1109 1997 1172 M3270 ST_INTEGRIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTEGRIN_SIGNALING_PATHWAY.html Integrin Signaling Pathway 61/127 Signaling Transduction KE 1.41422560637541e-07 4.29213807738028e-07 870 1385.81818181818 1368 1.2856597248055e-08 702 1.72020918288191 1.78294509682458 1 2.81732549474711 869 2830 1903 1142 1368 702 824 1816 1478 1587 725 1173 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 24/79 Arthur Liberzon 7.96627947659834e-08 2.73881039085399e-07 760 1271.90909090909 1368 7.24207251369111e-09 67 1.98148512984697 1.97240634573887 1 3.34468093391656 760 2526 1427 1368 2715 473 523 648 2066 1418 67 1174 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 160/496 Arthur Liberzon 2.01393850204144e-09 2.18456384735328e-08 2065 1449.54545454545 1369 1.83085318535005e-10 20 1.66982928428751 2.08068049761418 1 3.2903001642283 2065 630 733 916 20 4078 2284 1605 1572 673 1369 1175 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 105/260 Arthur Liberzon 4.74626435611767e-08 1.89769579972418e-07 1525 1353.36363636364 1370 4.31478587137568e-09 852 2.04294497886801 2.45963601347823 1 3.53215050979377 1523 1556 852 1042 902 2120 1239 1095 1721 1370 1467 1176 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 70/278 Leona Saunders 3.90423836286732e-08 1.64673816097176e-07 2120 1647.81818181818 1370 3.54930766559459e-09 778 1.9058738766662 -2.03322658865534 -1 3.32536004226996 2118 2417 1370 2702 811 778 2621 1153 2134 1233 789 1177 M86 PID_ARF6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_PATHWAY.html Arf6 signaling events 18832364 33/66 Pathway Interaction Database 7.43098041021687e-07 1.69861337572079e-06 690 1301.09090909091 1371 6.75543901835813e-08 376 2.0173459321695 1.91976776707316 1 2.99397198642824 688 2149 1371 2016 1962 508 376 977 1622 1842 801 1178 M9488 KEGG_RETINOL_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RETINOL_METABOLISM.html Retinol metabolism 12/101 KEGG 6.24841099326487e-07 1.46327106019186e-06 1935 1375.18181818182 1373 5.68037524357366e-08 375 2.62100601965068 3.59122646807815 1 3.93353818413573 1935 1736 1373 839 2571 2346 1009 384 420 2139 375 1179 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 125/356 Kevin Vogelsang 1.20601134331233e-12 2.33527651023206e-11 1375 1444.09090909091 1373 1.09637394846636e-13 203 1.8947861810387 2.16739239795253 1 5.18155399881118 1373 640 236 1264 946 2948 2177 1913 2156 203 2029 1180 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 67/156 Yujin Hoshida 2.59773692948464e-08 1.23835150066785e-07 1655 1456.27272727273 1374 2.3615790546895e-09 98 1.57481868906461 1.46805524822299 1 2.79787614249723 1651 98 932 998 651 1755 1374 3921 1943 649 2047 1181 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 149/431 Arthur Liberzon 1.68366435508083e-12 3.19419075623837e-11 635 1313.45454545455 1376 1.53060395916557e-13 241 2.23182802446022 2.59037302246333 1 6.0251559364087 633 2289 241 1000 1376 2225 1558 1283 1555 516 1772 1182 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 143/315 Arthur Liberzon 3.97004983359359e-08 1.66486954776987e-07 1035 1418.09090909091 1377 3.60913627748713e-09 823 1.62430316795603 1.72357040376062 1 2.83208982060551 1035 1377 1757 1559 823 1646 1039 2004 2242 1251 866 1183 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 29/53 Kevin Vogelsang 0.000339068509154858 0.000471196629270363 390 1608.36363636364 1377 3.08291616697245e-05 386 1.68011991781336 -1.68011991781336 -1 1.43769020528956 386 2100 1377 1827 3382 875 1156 1330 2949 848 1462 1184 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 4/20 BioCarta 5.1566027422944e-05 7.95124726896727e-05 850 1880.36363636364 1379 5.15672240368566e-06 674 1.53427618371744 1.53427618371744 1 1.61785622661837 850 1232 3845 2805 2945 674 735 1379 3235 2036 948 1185 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 123/341 Arthur Liberzon 6.15807461758515e-08 2.25796069311455e-07 2810 1669.27272727273 1380 5.59824980905214e-09 406 1.64220224194429 -1.58551288532599 -1 2.80739917039987 2810 1380 1023 1453 1035 899 3581 2271 2320 406 1184 1186 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 5/10 Jessica Robertson 1.08000718605868e-08 7.39899659922656e-08 3395 2014 1382 1.08000719130755e-09 313 1.67142486183275 -2.3721272000967 -1 3.06567016623484 3391 1080 4485 1382 313 3036 4168 778 1338 1532 651 1187 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 83/232 Arthur Liberzon 5.15387049471813e-08 2.0120111292869e-07 2165 1615.90909090909 1385 4.68533692314202e-09 477 2.04827488971657 2.33774548879327 1 3.52798168073183 2161 1017 477 642 1159 3622 1763 1385 1814 803 2932 1188 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 45/129 Arthur Liberzon 5.7618721279503e-07 1.3684811348999e-06 1075 1591.45454545455 1386 5.23806694273095e-08 1045 1.83708272242853 2.15329576620656 1 2.77079019937402 1075 1325 1085 2546 1878 1526 1045 1386 2767 1340 1533 1189 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 510/1167 Arthur Liberzon 1.87887510219611e-20 1.0120010033208e-18 805 1518.81818181818 1387 1.87887510219612e-21 22 1.91183865783586 2.1545869859053 1 8.84906533641125 805 261 4648 373 644 2560 1909 1954 1387 22 2144 1190 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 43/131 Nikolaos Papanikolaou 1.76643952010537e-09 1.94765543322676e-08 515 1358.45454545455 1388 1.60585411047608e-10 384 2.36379397219376 2.62050421437282 1 4.68802747999096 514 1264 384 1510 2690 1388 1113 1926 1905 627 1622 1191 M8731 BIOCARTA_SPPA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SPPA_PATHWAY.html Aspirin Blocks Signaling Pathway Involved in Platelet Activation 17/42 BioCarta 9.20282048336401e-09 6.87504636685147e-08 1815 1273.45454545455 1389 8.36620047441849e-10 215 1.64591952538035 2.18478320996416 1 3.03239306760104 1389 405 1713 742 215 1814 1815 1168 1127 2217 1403 1192 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 7/32 Jessica Robertson 7.09484565469094e-07 1.63132712158399e-06 1055 1612.63636363636 1389 7.09484791984952e-08 805 1.93467052534534 1.93467052534534 1 2.88000734515138 1053 1855 4493 1444 1975 906 1062 819 1389 1938 805 1193 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 90/197 John Newman 5.68841605138336e-07 1.35240576442326e-06 755 1688.72727272727 1390 5.17128865655053e-08 469 1.20841415417299 -1.11788457719014 -1 1.82419236030994 752 1251 3060 2217 1873 469 1109 1390 2823 2410 1222 1194 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 16/40 Arthur Liberzon 1.25717585542883e-05 2.14612971167194e-05 1090 1271.45454545455 1390 1.14289367230627e-06 404 1.68498282573278 -1.84767412579245 -1 2.02328459953873 1090 404 1173 1459 2644 648 1644 1513 1434 587 1390 1195 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 273/602 Arthur Liberzon 1.69772523316572e-08 9.53065333500722e-08 1930 1396.54545454545 1390 1.54338658751541e-09 351 1.66035969270427 1.97982725746729 1 2.99841833537209 1930 464 485 351 472 3708 2130 1479 1390 555 2398 1196 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 20/65 Arthur Liberzon 3.75638906649073e-05 5.91678627414304e-05 820 1581 1391 3.41495746043012e-06 639 1.80372991583937 -1.80372991583937 -1 1.96153610846854 817 1841 1448 1824 2859 639 1313 1341 3050 868 1391 1197 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 101/237 John Newman 4.21061278426601e-08 1.7307834655325e-07 3980 2117 1393 3.8278298771396e-09 855 1.88301859890214 -1.58496220204933 -1 3.2750116308718 3977 1177 1393 976 856 1592 3488 4573 855 1225 3175 1198 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 25/69 Reactome 1.52773021557524e-07 4.58025834304899e-07 3695 1806 1394 1.38884574696757e-08 381 2.44171645973861 -2.56202911661836 -1 3.98127508860156 3693 381 667 1277 1394 2539 4170 2410 514 806 2015 1199 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 115/305 Arthur Liberzon 5.47140045343795e-08 2.09709884827199e-07 3615 1971.09090909091 1394 4.97400053591972e-09 683 1.93177346039443 -1.83962696384423 -1 3.31837952247617 3612 1176 694 1118 964 1854 4361 3005 1394 683 2821 1200 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 8/13 Arthur Liberzon 2.74652036091574e-07 7.39666345474205e-07 1265 1624.63636363636 1394 2.74652070036764e-08 59 2.72185600402016 3.15973066327299 1 4.29232491653801 1262 1690 4204 1369 2777 1394 1468 292 59 2103 1253 1201 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 76/208 Jean Junior 1.11363470499151e-07 3.54036107706256e-07 1310 1701.81818181818 1394 1.01239523760312e-08 1064 1.91244480665632 2.3281065622476 1 3.17330203649042 1306 2829 1064 1341 1283 2307 1394 1304 2259 1702 1931 1202 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 29/123 Leona Saunders 1.08964365145674e-07 3.48299464578872e-07 2295 1687.90909090909 1397 9.90585186750893e-09 1049 2.299057942142 2.61960685448748 1 3.81900121057696 2293 1890 1397 1355 1273 3598 1691 1049 1084 1837 1100 1203 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 51/124 Yujin Hoshida 1.54757885606318e-07 4.63087772638063e-07 3215 1802.90909090909 1397 1.40688996811531e-08 570 2.19208102829458 -2.02726574439514 -1 3.57154733335653 3215 1027 704 612 1397 1995 4509 2585 1351 570 1867 1204 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 108/270 Kate Stafford 1.24699755242408e-08 8.0181460061125e-08 1670 1476.54545454545 1397 1.13363414499298e-09 342 1.91276474653154 2.1962640257405 1 3.49115637246406 1667 1247 867 411 342 3517 1860 1520 1397 772 2642 1205 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 44/118 Jessica Robertson 2.12336460604825e-08 1.09930699628899e-07 2370 1580.63636363636 1398 1.93033147867476e-09 332 2.17532044670412 -1.84497447798638 -1 3.89368951613064 2369 668 539 986 563 4018 1934 2995 1398 332 1585 1206 M8 PID_ENDOTHELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ENDOTHELIN_PATHWAY.html Endothelins 18832364 46/104 Pathway Interaction Database 1.77589848988848e-07 5.17264473534025e-07 1345 1402.54545454545 1399 1.61445330294886e-08 413 2.02141743821444 2.53368777247379 1 3.26850307331847 1345 1446 993 413 1454 2530 1867 1235 960 1399 1786 1207 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 20/47 Jessica Robertson 1.34443975772516e-06 2.86761834953383e-06 1070 1570.27272727273 1399 1.22221870847734e-07 484 2.4680372245581 2.4680372245581 1 3.51847441528809 1068 2198 1494 2885 2334 1131 1060 484 1399 2130 1090 1208 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 164/525 Jessica Robertson 1.78085638430969e-10 2.40492594146259e-09 405 1394.90909090909 1400 1.6189603495035e-11 336 1.98479060266876 2.20851097758355 1 4.40012606191761 402 2136 336 1883 2224 1400 950 1506 2580 675 1252 1209 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 2/17 Jean Junior 0.0012375088806174 0.00163535437523213 1395 1862.7 1400.5 0.000137576671799143 32 1.85771088732993 1.85771088732993 1 1.33143005460327 1394 883 4376 NA 3589 1405 1287 1735 32 2530 1396 1210 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 15/44 Kevin Vogelsang 1.6903242101412e-06 3.49706810098087e-06 1230 1552 1401 1.53665955351638e-07 758 1.85836618709333 2.33242619717541 1 2.60812176782971 1230 2350 1329 2445 2181 1401 1117 1058 1621 1582 758 1211 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 102/261 Arthur Liberzon 1.43462568846005e-07 4.33719740395083e-07 1105 1450.90909090909 1402 1.30420525637488e-08 783 1.65236479158573 2.04213425444108 1 2.70428358886618 1104 1010 1797 783 1373 2096 1734 1544 1195 1922 1402 1212 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 53/157 Arthur Liberzon 5.93356806617075e-08 2.19843018787655e-07 1405 1418.72727272727 1405 5.39415293291238e-09 476 1.69747697275344 2.09131721286857 1 2.90695955684991 1405 2515 1687 1776 1017 1363 966 476 1694 1813 894 1213 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) 38/91 BioCarta 4.0921583126406e-07 1.02654463881338e-06 1410 1410.27272727273 1406 3.72014461255608e-08 707 2.140551932913 2.6781881976124 1 3.29724594692347 1406 938 1112 707 1761 2030 1758 1118 734 2198 1751 1214 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 184/414 Jessica Robertson 1.07223324614052e-08 7.39899659922656e-08 1265 1491.36363636364 1409 9.74757501242145e-10 272 1.42725228144298 1.65497670828536 1 2.6178171610773 1263 478 1911 1030 272 2166 1409 2761 1893 1870 1352 1215 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 235/533 Arthur Liberzon 5.16117499142967e-09 4.60671733520751e-08 2505 1570.09090909091 1410 4.69197727594339e-10 93 1.82421540233398 2.31463526790711 1 3.44246966014313 2504 1302 973 398 93 3967 2067 1410 1456 1243 1858 1216 M19877 KEGG_ENDOMETRIAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOMETRIAL_CANCER.html Endometrial cancer 26/61 KEGG 2.14612141337127e-06 4.32175545468749e-06 1110 1417.18181818182 1414 1.95102136994224e-07 403 2.08573661483532 2.6548157868188 1 2.87789141193216 1106 1622 1753 1303 2663 1697 1166 547 403 1915 1414 1217 M7825 BIOCARTA_ACTINY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACTINY_PATHWAY.html Y branching of actin filaments 18/36 BioCarta 6.92647812871509e-07 1.59574614115826e-06 1420 1300.27272727273 1414 6.29680028131622e-08 258 2.46942514842322 2.82645203202564 1 3.68214208464337 1418 573 1284 901 1939 1753 1414 1542 258 1896 1325 1218 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 211/480 Arthur Liberzon 6.9814714573552e-08 2.47771736893169e-07 1425 1473.63636363636 1414 6.34679243536812e-09 945 1.55077792225742 1.74350583295216 1 2.63501705016888 1424 2447 1655 945 1085 2083 1143 1414 2076 949 989 1219 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 17/69 John Newman 6.44352058418604e-08 2.33883326549154e-07 1980 1375.54545454545 1414 5.85774615718963e-09 476 2.08669228580017 2.62234191909249 1 3.55906688670732 1977 715 1258 1428 1050 2178 1583 851 476 1414 2201 1220 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 24/55 Jessica Robertson 0.000214144394700533 0.000305939217550823 915 1900.09090909091 1414 1.94695674550886e-05 914 2.14413133082799 2.59905970674639 1 1.93819233018931 914 3097 1414 2281 3493 1391 1188 1253 2507 2121 1242 1221 M9257 KEGG_DRUG_METABOLISM_CYTOCHROME_P450 http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DRUG_METABOLISM_CYTOCHROME_P450.html Drug metabolism - cytochrome P450 24/122 KEGG 4.09129170406784e-08 1.69531955947187e-07 3325 1855.27272727273 1416 3.71935616377518e-09 185 2.13693620455413 -1.71751861814037 -1 3.72157605612994 3325 185 783 227 843 2366 3448 3829 478 1416 3508 1222 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 19/41 Jessica Robertson 2.64276890545727e-08 1.25091061524977e-07 4130 2147.45454545455 1419 2.40251721563977e-09 397 1.70398372246175 -1.14469807765224 -1 3.02543437808053 4128 397 1419 1107 660 3631 3899 2083 642 1262 4394 1223 M72 PID_NECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NECTIN_PATHWAY.html Nectin adhesion pathway 18832364 29/55 Pathway Interaction Database 1.82532150243699e-08 1.00157570965102e-07 1695 1430.18181818182 1421 1.65938319780139e-09 505 1.95905739770496 1.98823361922489 1 3.52696733885419 1695 1132 1421 672 505 1948 1774 1983 964 1236 2402 1224 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 5/9 Jessica Robertson 5.37695103971632e-06 9.8616017894758e-06 1425 1806.09090909091 1421 5.37696404998174e-07 682 1.70993342082461 2.17997599363941 1 2.20177659586326 1421 1295 4302 2118 2478 1309 682 1030 1978 2247 1007 1225 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 8/15 Jessica Robertson 2.73186756185605e-08 1.27505292777464e-07 2075 1563.54545454545 1423 2.73186759543999e-09 423 2.71636523318003 -2.62006962796862 -1 4.81712406840611 2071 599 4445 990 710 1099 1795 2100 423 1544 1423 1226 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 35/93 Jessica Robertson 1.13271020695255e-05 1.95214418160339e-05 585 1682.18181818182 1425 1.02974185360009e-06 585 2.14745517359225 2.17337652211296 1 2.60133608459255 585 2868 1256 2316 2623 1450 975 1110 2619 1425 1277 1227 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 12/55 Arthur Liberzon 3.97920165066635e-08 1.66486954776987e-07 3875 1962 1425 3.61745611149025e-09 209 1.65607899765883 1.8306976450118 1 2.88749327754939 3872 854 1425 764 827 3923 2382 3462 209 905 2959 1228 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 143/351 Jessica Robertson 2.21636974018913e-10 2.95054221662678e-09 1785 1555.18181818182 1426 2.01488158219311e-11 249 2.15371035959254 2.63533050442374 1 4.7254154384724 1784 1003 338 487 1426 3922 2682 1217 1513 249 2486 1229 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 83/263 Jean Junior 1.80826351186303e-06 3.70978866386931e-06 1055 1833.45454545455 1427 1.64387727104106e-07 488 2.23222290407158 2.34676836490483 1 3.11808607450323 488 4378 1070 3027 2202 1427 1053 740 2663 2068 1052 1230 M255 PID_HIF1_TFPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF1_TFPATHWAY.html HIF-1-alpha transcription factor network 18832364 61/113 Pathway Interaction Database 7.27512368663959e-07 1.66623800564971e-06 625 1423.36363636364 1428 6.61375099312066e-08 481 2.06697659766652 2.19432919668999 1 3.07207292601368 624 3252 1428 1816 1955 481 826 694 2136 1804 641 1231 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 24/75 Kevin Vogelsang 2.1228441857548e-06 4.28039924890146e-06 1430 1713 1429 1.92986021286532e-07 1165 1.59457809998542 1.75039721167766 1 2.20190547578203 1411 1801 1429 2394 2238 1426 1165 1307 1929 1420 2323 1232 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 14/23 Jessica Robertson 2.72759735083711e-05 4.39832112388943e-05 1430 1790 1430 2.47966469876285e-06 687 3.00512718635363 3.00512718635363 1 3.36759981688553 1430 3104 1628 1232 3163 2236 1091 1006 1098 3015 687 1233 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 41/83 John Newman 8.20906148729337e-10 9.86350311011712e-09 800 1503.27272727273 1430 7.46278317305137e-11 6 1.44316519541135 1.38022387248278 1 2.97186172434374 797 2189 1817 1015 6 1146 1385 2156 2460 2135 1430 1234 M653 REACTOME_SYNTHESIS_OF_PA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PA.html Genes involved in Synthesis of PA 9/29 Reactome 1.10865862440021e-07 3.52693436112653e-07 2010 1723.63636363636 1431 1.10865867971079e-08 724 1.55258647692568 -1.25889591003437 -1 2.57685138807412 2010 1292 3947 2395 1325 724 848 1933 1431 1668 1387 1235 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 46/188 Arthur Liberzon 1.68851159426427e-07 4.96816479437781e-07 2020 1801.81818181818 1431 1.53501065805313e-08 821 2.13658592029463 2.10044283478977 1 3.46434971775404 2019 1511 821 1072 1431 2653 1411 3750 1272 1400 2480 1236 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 16/36 Arthur Liberzon 0.000104701140995851 0.000154821567278812 1215 1500.09090909091 1431 9.51873856405995e-06 460 1.81104985687587 -1.84767412579245 -1 1.77489730548978 1211 1342 1063 1431 3045 685 1879 1756 2082 460 1547 1237 M6929 KEGG_O_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_O_GLYCAN_BIOSYNTHESIS.html O-Glycan biosynthesis 13/33 KEGG 7.04419127885312e-08 2.49313295564243e-07 2300 1549.45454545455 1432 6.40381045854679e-09 946 1.55374548770819 -1.16272772649895 -1 2.63898288998668 2300 1352 1787 1542 1091 2333 1534 1401 946 1326 1432 1238 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 21/55 Reactome 2.05534963893864e-06 4.15682710749524e-06 1000 1641.45454545455 1433 1.8685014174102e-07 565 1.56035823580172 1.60622919126034 1 2.15975837756829 997 565 1185 1198 2232 1473 1433 3379 2297 1145 2152 1239 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 22/43 Arthur Liberzon 3.14475372458206e-07 8.28708607154117e-07 1255 1589.72727272727 1433 2.85886743100344e-08 299 1.47797533090989 -1.46663097192672 -1 2.31197724067311 1251 2773 2703 1433 2396 577 1170 299 1699 2831 355 1240 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 7/18 Arthur Liberzon 2.01367112719491e-07 5.72924280633598e-07 965 1684.09090909091 1436 2.01367130966415e-08 697 2.54645641504563 2.54645641504563 1 4.08838619606448 965 1993 4534 1925 1526 851 697 1128 1436 2692 778 1241 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 89/215 Arthur Liberzon 1.70915405968727e-11 2.75226664044487e-10 3365 1590.54545454545 1438 1.55377641790959e-12 73 2.01739066067346 -1.65998251611157 -1 4.96090177676596 3365 73 283 752 1438 1523 4140 3064 1178 197 1483 1242 M18306 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_REGULATION_OF_ACTIN_CYTOSKELETON.html Regulation of actin cytoskeleton 94/251 KEGG 2.62785474448929e-08 1.24510893151434e-07 1585 1354.63636363636 1439 2.38895888716225e-09 646 1.71856426978506 2.12763248591897 1 3.05221469174852 1585 646 1360 747 656 2387 1439 1580 1215 1592 1694 1243 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 6/16 Yujin Hoshida 3.12088099873748e-07 8.23448668923638e-07 1440 1539.09090909091 1440 3.12088143703298e-08 331 1.68480905513244 -1.68480905513244 -1 2.63672290633857 1440 1691 4382 2111 1688 704 585 331 840 2489 669 1244 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 33/84 Leona Saunders 2.66781233073856e-06 5.24826556752346e-06 740 1412.45454545455 1442 2.42528687804113e-07 505 1.68117198762284 1.79366028551955 1 2.28319716395157 738 2837 1935 1937 2286 608 505 1167 1442 1556 526 1245 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 596/1317 Arthur Liberzon 9.51138195104977e-09 7.02612984903285e-08 1445 1594.18181818182 1442 9.51138199175964e-10 264 1.6565539154885 1.95448165265575 1 3.04796300546074 1442 611 4653 353 264 3134 1863 1405 1716 567 1528 1246 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 58/130 Reactome 1.54908033029046e-08 9.05111025902878e-08 2400 1869.54545454545 1445 1.4082548556345e-09 438 1.79001622065031 -1.47140956259738 -1 3.24288613325101 2399 919 1404 804 438 3990 2931 2179 1445 1051 3005 1247 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 63/192 Jessica Robertson 2.71495327106129e-09 2.82090266700514e-08 1835 1307.09090909091 1445 2.4681393403743e-10 34 1.95146433236931 2.36328713786046 1 3.78951743200509 1834 915 532 644 34 2716 1636 2311 1768 543 1445 1248 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 50/100 Jessica Robertson 5.37079734833472e-07 1.28734303704841e-06 1245 1430 1446 4.8825442359024e-08 304 1.8421160767594 -1.61477700944754 -1 2.7909591784989 1245 2483 1784 1880 1852 304 1397 1446 1087 1639 613 1249 M10122 REACTOME_RETROGRADE_NEUROTROPHIN_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RETROGRADE_NEUROTROPHIN_SIGNALLING.html Genes involved in Retrograde neurotrophin signalling 10/19 Reactome 4.1782835079599e-07 1.04626750716736e-06 790 1446.63636363636 1447 3.79844027409815e-08 224 2.08687810123024 2.08687810123024 1 3.21013185525404 788 1945 1630 2065 1764 1422 1185 1447 224 2438 1005 1250 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 18/40 Jessica Robertson 1.46164818026683e-05 2.46643261531522e-05 1200 1766.27272727273 1447 1.32877990121478e-06 588 2.01855626380717 2.1136048845204 1 2.39246422736958 1197 2493 1447 1561 3625 1379 1046 887 2834 2372 588 1251 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 2/9 Arthur Liberzon 0.000301690447891027 0.000421251918598734 1535 1908.7 1447 3.35256564036506e-05 763 1.16082797236574 1.16082797236574 1 1.00785762153947 1535 1954 4635 NA 3251 1007 763 1359 894 2535 1154 1252 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 34/96 Kevin Vogelsang 0.000299032130886628 0.000417664550025258 1380 2038.18181818182 1448 2.71884349250265e-05 1176 1.81817390231081 2.08172308585273 1 1.58031767545753 1379 3496 2486 2620 3346 1448 1326 1314 1194 2635 1176 1253 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 61/199 Reactome 1.76259059460256e-07 5.14610562386765e-07 1100 1580.45454545455 1449 1.60235521437943e-08 769 2.00233758275892 2.14237336593109 1 3.23880272525035 1096 1320 769 1919 1449 1575 1043 2732 2079 1173 2230 1254 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 5/12 Arthur Liberzon 1.01273732136657e-05 1.76092285266187e-05 720 1680.45454545455 1449 1.01274193676214e-06 647 1.75972261060524 1.75972261060524 1 2.1519182015564 716 1642 4110 2084 2944 722 647 763 1449 2238 1170 1255 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 14/41 Jessica Robertson 5.11804308926269e-08 2.00289971071276e-07 2960 2148.45454545455 1449 4.65276655302545e-09 584 2.15941521130017 1.95748135287102 1 3.72050643692556 2956 1063 1068 922 935 4096 2669 4370 584 1449 3521 1256 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 22/68 Kevin Vogelsang 2.64944660160855e-07 7.17582797930372e-07 445 1349.36363636364 1450 2.40858810970894e-08 148 1.69708305554515 1.77682025596624 1 2.68201995807759 442 2491 1450 2580 1627 272 307 415 2756 2355 148 1257 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 97/214 Jessica Robertson 4.12113677529425e-08 1.70597587712269e-07 1035 1557.09090909091 1451 3.74648804772108e-09 845 1.87474410872738 2.4069345528255 1 3.26364376437595 1032 2055 909 1371 845 2723 1775 1617 1451 1381 1969 1258 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 14/39 Jessica Robertson 6.4208338646127e-07 1.49766189594699e-06 1420 1461.63636363636 1451 5.83712339870263e-08 885 1.73897881234768 2.0189707069981 1 2.60530169845926 1417 1285 1704 2267 1910 1484 1480 1185 1010 1451 885 1259 M16650 KEGG_PHENYLALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHENYLALANINE_METABOLISM.html Phenylalanine metabolism 12/27 KEGG 1.77339154941573e-07 5.17119651559559e-07 2755 1688.45454545455 1452 1.61217426578777e-08 283 2.47958314858963 -1.89176079670615 -1 4.00940541514957 2754 1068 1022 683 1452 1895 2972 3509 283 1206 1729 1260 M706 REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS.html Genes involved in Glycerophospholipid biosynthesis 34/85 Reactome 2.51842155496818e-07 6.88927227471157e-07 1320 1449 1452 2.2894744029648e-08 687 1.69573343555819 -1.52688180256533 -1 2.68760669580447 1318 1452 1783 2102 1568 687 1645 1088 1136 1903 1257 1261 M267 PID_ANTHRAX_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ANTHRAX_PATHWAY.html Cellular roles of Anthrax toxin 18832364 9/18 Pathway Interaction Database 3.69739834620141e-10 4.75989248634611e-09 1780 1346.72727272727 1453 3.69739834681659e-11 8 2.19123725342032 2.95962927921392 1 4.69069080688217 1776 1543 3907 800 2394 1453 788 8 153 1664 328 1262 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 49/185 Leona Saunders 1.07097022625136e-07 3.43973028116097e-07 1995 1679.09090909091 1454 9.73609343987902e-09 645 2.1591915493284 2.37763423002613 1 3.58968177027173 1991 2014 1030 645 1263 3173 1759 2787 1001 1353 1454 1263 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 27/58 John Newman 4.16455193364772e-08 1.71726983283088e-07 905 1488.09090909091 1454 3.78595637498345e-09 850 1.46742273957135 1.40428756465356 1 2.55347766617947 903 1454 1690 2404 850 1307 1019 1603 2584 910 1645 1264 M18053 BIOCARTA_LEPTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LEPTIN_PATHWAY.html Reversal of Insulin Resistance by Leptin 6/35 BioCarta 6.3764640865282e-05 9.68561125104414e-05 1145 1745.54545454545 1455 6.37664706074164e-06 603 1.46401867999791 1.46401867999791 1 1.51150249870352 1145 603 3861 1932 3285 841 867 1455 1907 2467 838 1265 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 18/37 Reactome 6.02023951386891e-08 2.22132617023541e-07 1460 1406.36363636364 1456 5.47294516237374e-09 401 1.32304500310639 1.26485507637387 1 2.26420681872315 1456 401 1912 1592 1022 977 667 2441 2067 1508 1427 1266 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 26/47 John Newman 1.78839172221546e-07 5.20198858491723e-07 530 1446.36363636364 1456 1.62581078872254e-08 445 1.69785348893101 1.73003122335202 1 2.74424787112321 528 2839 1881 2218 1456 445 829 560 2101 2334 719 1267 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 34/81 Jessica Robertson 7.11984901521349e-06 1.2709947613444e-05 640 1562.54545454545 1457 6.4726109611361e-07 640 2.14964006349322 2.43661290082466 1 2.70702994141524 640 2457 859 1716 2522 1457 1161 1647 2327 1116 1286 1268 M226 PID_VEGFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGFR1_PATHWAY.html VEGFR1 specific signals 18832364 23/43 Pathway Interaction Database 1.21947913881625e-06 2.63218758382908e-06 1080 1557.90909090909 1458 1.10861801344061e-07 455 1.93272176895617 1.81285690161677 1 2.77381525812191 1076 2309 2091 980 2085 455 554 1458 2579 2953 597 1269 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 120/288 Arthur Liberzon 2.29716452395425e-08 1.15560048483612e-07 4415 2180.90909090909 1458 2.0883314072186e-09 592 1.72384451650929 -1.27422667797084 -1 3.07595858089131 4415 770 1222 1393 592 1886 4679 2427 1437 1458 3711 1270 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 41/105 Leona Saunders 1.80300643239905e-07 5.23201013201427e-07 2050 1523.90909090909 1459 1.63909689105833e-08 651 2.26145875994785 2.62134131721777 1 3.65375182247025 2048 1389 779 651 1459 2802 1835 2424 763 1572 1041 1271 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 31/66 Jessica Robertson 1.19306650390401e-07 3.73710537252286e-07 1250 1694.36363636364 1460 1.08460597145852e-08 1215 2.11032986997622 2.21881965969004 1 3.48890147956707 1247 2305 1460 2771 1317 1833 1380 1311 1807 1992 1215 1272 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 93/198 Leona Saunders 2.48567331116263e-08 1.20328077343124e-07 1410 1782.90909090909 1461 2.25970303567914e-09 632 1.75237575626933 2.2563013561948 1 3.11895391855906 1409 2295 1933 2055 632 2820 1261 1031 1461 3510 1205 1273 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 21/54 Arthur Liberzon 3.64422660970225e-06 6.95028322876059e-06 660 1273.54545454545 1461 3.31293876932369e-07 467 2.07343426114647 2.27204307518969 1 2.75086991117885 657 1578 1518 2079 2360 562 467 704 2086 1461 537 1274 M10320 REACTOME_BIOLOGICAL_OXIDATIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BIOLOGICAL_OXIDATIONS.html Genes involved in Biological oxidations 43/219 Reactome 1.25497800410831e-08 8.02295624454506e-08 3950 2286.27272727273 1463 1.14088910115206e-09 140 1.78176209833885 -1.32540227485389 -1 3.25193245036457 3950 140 894 953 349 3564 4304 3630 1463 1433 4469 1275 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 31/56 Arthur Liberzon 4.42071152937909e-07 1.09547616217189e-06 1095 1648 1463 4.01882947062131e-08 943 1.42565341856474 1.48429843785247 1 2.18568614363299 1091 943 1762 2353 1787 1463 1387 2647 2592 1139 964 1276 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 37/77 Arthur Liberzon 7.77434980634494e-09 6.19568081505653e-08 2010 1438.27272727273 1463 7.06759075801626e-10 193 2.10062051951472 2.22660149049401 1 3.8945356374858 2008 537 418 193 1463 3130 2420 2807 587 305 1953 1277 M11420 BIOCARTA_CTCF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTCF_PATHWAY.html CTCF: First Multivalent Nuclear Factor 17/34 BioCarta 3.51236045968231e-07 9.05829450416692e-07 1380 1504.72727272727 1464 3.19305547312767e-08 264 2.16399783428637 2.43104153561657 1 3.36360307172088 1380 1939 2116 1464 2647 1518 918 316 264 2776 1214 1278 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 21/37 Pathway Interaction Database 1.49437592711888e-07 4.48887538107633e-07 2090 1785.27272727273 1465 1.3585236623874e-08 834 1.51843270310812 1.45196065906341 1 2.47925791413704 2090 834 2232 1367 1389 2162 1344 2640 1465 1459 2656 1279 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 18/44 Jessica Robertson 1.57114887501645e-07 4.68942906262871e-07 1035 1566 1467 1.42831726111037e-08 905 1.39256591382449 1.50043011318952 1 2.26694650676904 1031 1467 1662 2046 1403 1608 905 1223 3312 1512 1057 1280 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 18/43 Jessica Robertson 1.8475596571725e-07 5.33435893623558e-07 740 1383.36363636364 1469 1.67959982939141e-08 120 1.76855996638975 1.93011735396469 1 2.85356678255237 737 3071 1597 2601 1469 352 120 332 2903 1899 136 1281 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 58/143 Arthur Liberzon 1.26607813401784e-07 3.91865398679499e-07 4670 2123 1469 1.15098018807217e-08 379 2.15034737564094 -2.19774450227042 -1 3.54366557233875 4670 918 502 1178 1379 2978 3656 2466 1469 379 3758 1282 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 67/233 Antony Bosco 5.34457529375757e-07 1.28171339951627e-06 885 1618.63636363636 1470 4.8587059928579e-08 727 2.1285904614708 2.21514397890281 1 3.22603385593333 884 3118 831 2351 1851 1878 1301 727 2138 1470 1256 1283 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 75/232 Reactome 1.80359738040123e-08 9.9314422145243e-08 1170 1576.63636363636 1471 1.63963399562494e-09 503 1.8734281330257 2.14375082759237 1 3.37457482088379 1167 1961 965 1677 503 1471 1110 2478 2405 1465 2141 1284 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 177/408 Leona Saunders 3.18858638465437e-09 3.24819908662834e-08 3885 1868.72727272727 1471 2.8987148993416e-10 42 1.64613571119874 -1.31237864422936 -1 3.17066864756319 3881 477 598 428 42 2235 3362 3590 1471 488 3984 1285 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 38/102 Arthur Liberzon 5.73118011821158e-05 8.76797585175954e-05 725 1488.81818181818 1471 5.21029947781029e-06 680 1.77661935127191 -1.93903426363832 -1 1.85399607295854 723 1720 1060 1567 2946 1006 1471 1336 2392 680 1476 1286 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 80/222 Jessica Robertson 6.51788692603137e-07 1.51502074084241e-06 1365 1488.27272727273 1472 5.925353506428e-08 1241 1.63887991508599 1.83839860096276 1 2.45322585443967 1363 1792 1241 1675 1916 1553 1296 1309 1472 1505 1249 1287 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 64/184 Jessica Robertson 5.41392218443482e-08 2.08975612489799e-07 2605 1672.45454545455 1473 4.92174756151329e-09 367 1.89891296193115 2.90056525172469 1 3.26267613595451 2603 1609 1473 903 958 3580 3527 367 448 1718 1211 1288 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 13/132 Yujin Hoshida 2.07537163080045e-08 1.08661286779844e-07 4105 2025.72727272727 1473 1.88670150034408e-09 367 2.51665606386296 2.50985250363396 1 4.50792446954143 4104 1473 1242 502 552 2478 3655 3930 367 1336 2644 1289 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 20/48 Arthur Liberzon 6.6372746200536e-07 1.53895442204706e-06 820 1649.27272727273 1474 6.03388783862034e-08 819 1.58673947327185 1.75487795834929 1 2.37239899826255 819 2346 1955 2532 1920 1298 1138 1474 2111 1376 1173 1290 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 13/26 Jessica Robertson 1.9632753343119e-07 5.60628166763288e-07 1475 1530.63636363636 1474 1.78479591774018e-08 242 1.635218308264 -1.77809300861946 -1 2.62933836861922 1474 2318 2430 1647 2171 964 1033 242 778 2916 864 1291 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 36/57 Lauren Kazmierski 8.3694867345473e-08 2.83582175257329e-07 1240 1502.45454545455 1475 7.60862459358972e-09 358 1.36280008178958 -1.58874895933892 -1 2.29506208482386 1236 358 1731 1843 1166 1109 2070 1589 2595 1475 1355 1292 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 8/13 Arthur Liberzon 1.70835600518802e-07 5.00960966227225e-07 1850 1719.09090909091 1475 1.70835613651964e-08 911 1.76923436766589 1.75762219492443 1 2.86706865190456 1847 1227 4246 1027 1475 2242 2059 1258 911 1064 1554 1293 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 46/132 Itai Pashtan 7.19808607795065e-08 2.53801590378305e-07 1285 1524.27272727273 1476 6.54371483041981e-09 362 1.56039314563419 1.84858005262127 1 2.6471636190252 1281 2906 1722 1892 1098 1156 1476 976 2262 1636 362 1294 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 451/1090 Jessica Robertson 2.77185048791383e-11 4.24473574717785e-10 4000 1895.72727272727 1477 2.51986407995342e-12 214 1.6641598526225 -1.51878893081308 -1 4.01174118444681 3997 262 298 1019 603 1477 4602 3900 1712 214 2769 1295 M11520 BIOCARTA_TPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TPO_PATHWAY.html TPO Signaling Pathway 18/42 BioCarta 2.04555191938835e-05 3.37516066699078e-05 1175 1902.90909090909 1479 1.85960994463868e-06 418 1.09594684225726 -1.09594684225726 -1 1.26055356171819 1175 2348 3116 1479 2912 418 1458 874 2992 3471 689 1296 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 45/99 John Newman 2.62218391200339e-08 1.24415947640899e-07 950 1543 1480 2.38380358477932e-09 655 2.18443513447835 2.58487282013622 1 3.8797996281467 1521 3524 1461 947 655 2107 1510 947 733 2088 1480 1297 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 10/24 John Newman 9.38020230407935e-07 2.08815334902213e-06 2160 1694.27272727273 1480 8.52746027595014e-08 660 2.37181109437461 1.81795271633575 1 3.46533529355971 2160 1480 923 1104 2015 2144 1322 2982 660 980 2867 1298 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 8/33 Arthur Liberzon 2.43669264639841e-07 6.72458288635038e-07 1115 1666.63636363636 1482 2.43669291358465e-08 828 1.68325684108649 1.95477983960535 1 2.67238181085995 1111 1482 4543 1875 1594 1005 828 1143 2354 1547 851 1299 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 20/54 Arthur Liberzon 1.50550870745865e-08 8.88515592336429e-08 1820 1664.63636363636 1483 1.3686442888738e-09 423 2.53392561748135 2.61182942684576 1 4.59582915472176 1820 2913 1019 1365 423 2656 1483 2709 853 1072 1998 1300 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 31/69 Jessica Robertson 1.92675471647888e-08 1.03629956114056e-07 1520 1724.72727272727 1484 1.75159521213942e-09 352 2.0626000770976 2.45522745004305 1 3.705526544526 1517 3322 1800 3546 524 1479 1251 352 1484 2367 1330 1301 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 273/630 Jessica Robertson 4.44567682571971e-08 1.80680326151974e-07 1110 1694.81818181818 1484 4.04152446868751e-09 871 1.66279259833997 1.99151934711095 1 2.8840025509029 1108 3007 939 2251 871 2382 1184 1484 2475 882 2060 1302 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 6/17 Jessica Robertson 0.000137123485483718 0.000200112317962224 1080 1955.36363636364 1485 1.37131947501232e-05 650 1.68878267819398 1.68878267819398 1 1.60666220782837 1077 2130 4340 2365 3104 1115 650 1485 1337 2488 1418 1303 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 119/300 Jessica Robertson 4.02639475227003e-06 7.58347500367257e-06 1235 1585.45454545455 1488 3.6603655648307e-07 638 2.27237092560376 2.58078937205031 1 2.99267129253887 1234 3554 912 1736 2408 2036 1488 638 1069 1591 774 1304 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 12/49 Arthur Liberzon 6.95417013818386e-05 0.000105120133121063 1305 1853.81818181818 1488 6.32217269844216e-06 598 1.8056806654061 1.82097424567562 1 1.8477306188611 1302 2207 1798 3873 3036 1111 598 1044 2715 1220 1488 1305 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 11/35 Arthur Liberzon 5.77135413586535e-09 5.03623193308474e-08 4505 2200.36363636364 1489 5.24668559182327e-10 23 2.24535412214744 -1.91525065633751 -1 4.21483986963472 4501 422 1362 763 108 3345 3551 4063 23 1489 4577 1306 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 247/528 Jessica Robertson 1.44540854562659e-08 8.68356980103357e-08 970 1282.81818181818 1489 1.31400777738453e-09 333 1.80137669177153 1.97337007229979 1 3.27180918622639 970 1824 578 898 404 2601 1772 1489 1520 333 1722 1307 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 131/274 John Newman 4.90072537477638e-08 1.94574076294416e-07 915 1564.36363636364 1491 4.45520498540459e-09 484 1.82308809202508 2.33702674507146 1 3.14693703644194 1595 1174 1491 484 912 3632 2298 913 1013 2196 1500 1308 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 6/12 Jessica Robertson 1.16219038933031e-05 1.99707523447079e-05 985 1663.63636363636 1491 1.1621964674643e-06 436 2.6025466118347 2.6025466118347 1 3.14599904509151 983 1819 4459 1706 2650 1519 1285 795 436 1157 1491 1309 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 40/171 Yaara Zwang 2.87008392937335e-07 7.67211254594611e-07 1235 1893.54545454545 1491 2.60916754890897e-08 623 2.01004951399987 2.13580377128605 1 3.16160723044528 1233 4210 1931 3897 1614 1230 814 623 1491 2730 1056 1310 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 40/79 John Newman 1.66711956144214e-05 2.7900436660421e-05 810 1379.18181818182 1492 1.51557472245615e-06 634 1.76780097716301 -1.74535289236635 -1 2.07091434245952 810 1512 959 786 2698 888 1492 1525 2143 634 1724 1311 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 11/25 John Newman 6.0146081353956e-06 1.08988606815405e-05 565 1396.81818181818 1493 5.46784052624785e-07 234 1.38860079897342 1.38860079897342 1 1.77250297511137 565 1154 2104 1897 2486 368 234 1782 2648 1493 634 1312 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 28/80 Yujin Hoshida 4.93000290637736e-08 1.95283124423367e-07 1840 1475.81818181818 1493 4.48182092441300e-09 374 1.55740887512814 1.84097403972823 1 2.68770002500473 1838 374 1608 1618 915 2192 1493 2508 1163 1436 1089 1313 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 47/174 Jessica Robertson 2.5708406845967e-08 1.23179544458283e-07 1495 1526.63636363636 1493 2.33712792239873e-09 545 2.13773803958436 2.12366443792806 1 3.79924539252835 1958 2518 757 1851 647 1493 1032 2710 1492 545 1790 1314 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 23/56 Arthur Liberzon 9.02537351769208e-05 0.000134562202685031 695 1729.72727272727 1494 8.20522163610801e-06 695 1.69369764442738 -1.69369764442738 -1 1.6864222283644 695 2153 1351 2548 3021 784 1589 1162 3366 864 1494 1315 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 124/304 Arthur Liberzon 6.31912168643262e-09 5.35424341998513e-08 1455 1550.18181818182 1495 5.74465609507566e-10 129 1.55053632089928 1.77860861624939 1 2.89996513851613 1452 1495 1424 1849 129 2280 1391 1327 2322 1797 1586 1316 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 8/20 Jessica Robertson 1.24286200127676e-07 3.85858309108113e-07 1495 1725.72727272727 1495 1.24286207078853e-08 735 2.81256937559136 2.43172099448799 1 4.63982816847316 1495 735 4535 1621 1359 1193 1132 2489 1219 1546 1659 1317 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 37/102 Arthur Liberzon 1.83256368022559e-07 5.30222290231014e-07 1895 1448.63636363636 1497 1.66596712079558e-08 339 1.87634667723433 -2.16005696354273 -1 3.02874690181002 1893 1391 1497 1719 1467 796 2619 339 1755 1562 897 1318 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 21/51 Arthur Liberzon 2.30381806849838e-06 4.59978332721917e-06 1325 1589.54545454545 1497 2.09438225548839e-07 718 2.20743713054676 2.51819676540262 1 3.03043920060996 1321 2154 1712 1430 2257 2132 1497 785 718 2205 1274 1319 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 138/455 John Newman 2.54887175023675e-11 3.96811063840844e-10 505 1522.81818181818 1497 2.3171561366057e-12 293 1.98900206673639 2.32036000581707 1 4.80980184812204 501 2827 293 1847 1534 1619 1104 1282 3126 1121 1497 1320 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 18/59 Arthur Liberzon 2.10440414008593e-07 5.95485374422865e-07 900 1682.27272727273 1502 1.91309485580198e-08 518 1.40105259478453 1.59756776556174 1 2.24337272413949 899 3029 2032 3472 1502 757 518 548 3252 1511 985 1321 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 43/123 Pathway Interaction Database 6.63039872843816e-08 2.3881666749778e-07 535 1095.09090909091 1504 6.02763538933298e-09 61 1.6322550164699 1.71962037530517 1 2.78017161746982 535 1718 1504 1649 1610 308 576 189 1939 1957 61 1322 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 5/7 Arthur Liberzon 1.25624865190257e-06 2.70283800863886e-06 1505 1561 1505 1.25624936207544e-07 300 2.13409108220699 2.65127275599538 1 3.05650333916305 1505 1785 4230 1921 2392 1034 951 1008 516 1529 300 1323 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 102/237 John Newman 1.07285781305219e-08 7.39899659922656e-08 2420 1768.45454545455 1506 9.75325289349201e-10 274 1.65313250100249 2.11598945121221 1 3.0321189429313 2416 777 1482 1049 274 4054 3062 1792 1796 1245 1506 1324 M16743 KEGG_TYROSINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYROSINE_METABOLISM.html Tyrosine metabolism 18/53 KEGG 1.36698414414621e-08 8.39539672276425e-08 3255 1902.18181818182 1507 1.24271286603641e-09 381 2.12100871637645 -1.69645378186879 -1 3.86034760588442 3254 842 1301 1151 381 2223 3116 4087 641 1507 2421 1325 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 5/12 Jessica Robertson 2.74567740535263e-05 4.42443064700221e-05 1330 1829.27272727273 1507 2.74571133029242e-06 255 3.23333654985361 3.23333654985361 1 3.62119760331347 1328 1425 4497 1110 2820 2060 2027 1507 255 2253 840 1326 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 21/61 Reactome 4.52722229867013e-08 1.83041964551926e-07 1510 1481.63636363636 1508 4.11565671984782e-09 202 1.35969210394073 1.23965531122119 1 2.35632253932081 1508 202 1699 1802 881 1183 811 2720 2240 1146 2106 1327 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 48/133 Reactome 6.19598347247422e-06 1.11928984394812e-05 710 1490.45454545455 1509 5.63272811149002e-07 444 1.60890420018295 1.60222870543632 1 2.04892845554822 708 1509 1598 2012 2491 444 480 2412 2324 1292 1125 1328 M1076 REACTOME_AMYLOIDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMYLOIDS.html Genes involved in Amyloids 52/136 Reactome 0.000348809563558581 0.00048344324603239 490 1665.45454545455 1509 3.17149890476858e-05 490 1.76420536585241 -1.8673467724699 -1 1.50458606838932 490 2418 1193 1951 3243 962 1450 1526 2972 606 1509 1329 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 398/936 Lauren Kazmierski 5.300568569763e-08 2.05446354986844e-07 2850 1651.54545454545 1509 4.81869881588382e-09 546 1.63575756659353 -1.4843355836505 -1 2.81363982218422 2848 1372 1509 750 952 546 3258 2483 2151 766 1532 1330 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 32/64 Reactome 0.000365735186170283 0.000506153302538082 295 1579.81818181818 1510 3.32541819397193e-05 292 1.80619988830192 -1.80619988830192 -1 1.53113848938519 292 2097 1198 1783 3378 997 1496 1510 2471 562 1594 1331 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 47/185 Alexandra Naba 5.93472938041792e-08 2.19843018787655e-07 985 1603 1510 5.39520867319403e-09 739 2.04378815711388 1.93584720574799 1 3.50002367327026 985 1510 739 2391 1018 2134 1389 2682 2301 771 1713 1332 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 129/360 Jennifer Shepard 1.80703732617205e-12 3.38711076417689e-11 920 1478.54545454545 1511 1.6427612056123e-13 244 2.34753948144765 2.80958239719792 1 6.3221578900884 916 2687 244 1556 1236 2404 1511 1266 2123 590 1731 1333 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 25/72 Arthur Liberzon 6.96827418959849e-08 2.47561280155106e-07 1515 1489.18181818182 1512 6.33479491846496e-09 516 2.11633000229137 2.45206141570916 1 3.59618048398318 1512 2105 1471 1774 1084 2067 1089 516 1673 1501 1589 1334 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 134/403 Leona Saunders 8.07147490996051e-09 6.37823464217116e-08 1515 1508.27272727273 1514 7.3377044905214e-10 180 1.54083887561932 1.70157187536714 1 2.85170607175865 1514 1173 1204 1381 180 1807 1662 1970 2271 1379 2050 1335 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 18/42 Leona Saunders 6.09888616535539e-06 1.10345098729171e-05 1610 1471 1515 5.54445733898293e-07 447 2.13064778602312 2.66722315131515 1 2.71675748739998 1609 2626 1493 731 2493 2125 1516 697 447 1515 929 1336 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 25/60 Reactome 1.8265899745013e-07 5.29011163196113e-07 2820 1967.90909090909 1516 1.6605364783248e-08 551 1.84386270495395 1.96349309937849 1 2.97678318911129 2816 697 1516 732 1464 4298 2690 2692 551 1200 2991 1337 M2587 BIOCARTA_HSP27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HSP27_PATHWAY.html Stress Induction of HSP Regulation 13/25 BioCarta 3.84015757548103e-07 9.75337582585589e-07 1935 1261.45454545455 1517 3.49105295071887e-08 285 2.37558209455708 2.71718391179482 1 3.67285885614625 1931 415 1025 448 1731 2074 1697 1517 285 1004 1749 1338 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 3/23 Arthur Liberzon 2.9013149736431e-05 4.64329302134274e-05 985 1883.45454545455 1519 2.90135285366774e-06 733 1.94694407355007 1.94694407355007 1 2.16999254798096 984 1298 4148 2484 2829 733 737 1519 2163 2796 1027 1339 M2164 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION.html Leukocyte transendothelial migration 64/141 KEGG 1.30526852677281e-08 8.15531775527654e-08 3785 2258.18181818182 1521 1.18660775865184e-09 432 2.68336736148415 -2.59289508542876 -1 4.89256685320595 3781 1504 432 436 1521 4448 2801 4561 1113 662 3581 1340 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 207/551 Arthur Liberzon 2.69765188504765e-08 1.26665297929191e-07 1425 1533.72727272727 1521 2.45241083466037e-09 670 1.67691557268156 2.02365881581997 1 2.9750319811382 1422 3314 1686 1083 670 1859 1521 772 1605 2067 872 1341 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 5/11 Reactome 2.98980781027114e-07 7.9288281827564e-07 1080 1716.81818181818 1522 2.98980821252399e-08 437 1.43583088799954 1.43583088799954 1 2.25313952743177 1079 437 3992 2747 1673 855 705 1827 3187 1522 861 1342 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 5/11 Reactome 2.54743036522474e-05 4.12911058161298e-05 835 1679.09090909091 1523 2.54745956800248e-06 515 1.66288389538822 1.66288389538822 1 1.87519020811974 833 1692 4022 2236 2800 691 515 1215 1711 1523 1232 1343 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 290/664 John Newman 6.14965465742376e-13 1.22626730743352e-11 1320 1662.90909090909 1523 5.59059514311407e-14 229 1.94598987275467 2.29478166198968 1 5.46160535829978 1320 1955 229 1223 979 3717 2215 2076 1523 269 2786 1344 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 268/649 Arthur Liberzon 8.10225627762246e-08 2.76930509970378e-07 1205 1640.81818181818 1525 7.36568779637811e-09 1004 1.59784185943083 1.8787254264302 1 2.69512743374604 1202 1699 1004 1525 1154 2741 1922 1451 2492 1318 1541 1345 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 134/311 John Newman 1.0248628393083e-06 2.25469824647826e-06 1530 1562.45454545455 1526 9.31693924306937e-08 757 2.02477445086593 2.36831596359631 1 2.94094089767042 1526 2006 1116 785 2044 2888 2162 873 1216 1814 757 1346 M1084 REACTOME_TRYPTOPHAN_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRYPTOPHAN_CATABOLISM.html Genes involved in Tryptophan catabolism 5/11 Reactome 0.000164352346685224 0.000237849010675404 975 1759.81818181818 1527 1.64364503212851e-05 660 2.16784701917423 -2.16784701917423 -1 2.02059534996118 972 1229 4097 2199 3125 660 728 1573 2105 1527 1143 1347 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 72/192 Jessica Robertson 1.19495335895507e-08 7.85207853988603e-08 1155 1692.81818181818 1530 1.08632124131416e-09 318 1.49347389819633 1.67305754527339 1 2.72936308541632 1155 2934 2227 1765 318 1530 1340 1157 2420 2697 1078 1348 M16894 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_COMPLEMENT_AND_COAGULATION_CASCADES.html Complement and coagulation cascades 27/95 KEGG 2.48679390772626e-07 6.83096362733292e-07 950 1503.54545454545 1531 2.26072198983977e-08 822 1.94457875674453 2.01987495097465 1 3.08385371031522 947 1971 822 2266 1562 1374 1531 1048 2527 907 1584 1349 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 16/28 Arthur Liberzon 2.24527687818078e-08 1.14053735728878e-07 3570 2220.27272727273 1531 2.04116081917786e-09 580 2.44476434607872 -2.21375849380597 -1 4.36592213739169 3568 1531 820 722 580 4475 3562 3212 1054 1020 3879 1350 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 17/31 Arthur Liberzon 6.05243829164347e-07 1.42653866748888e-06 995 1379.09090909091 1531 5.50221814248675e-08 303 2.55283120286941 2.61341944482984 1 3.83847318071762 993 1938 1602 1594 1889 1531 1647 1135 303 1411 1127 1351 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 16/33 Daniel Hollern 0.000276639906321883 0.000389056002708386 545 1665.63636363636 1531 2.51522453314535e-05 542 1.60629104993096 1.74041480946574 1 1.40888549607236 542 1936 1736 2363 3201 971 896 1531 2427 1309 1410 1352 M4844 KEGG_CHEMOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHEMOKINE_SIGNALING_PATHWAY.html Chemokine signaling pathway 87/239 KEGG 1.52578819838893e-08 8.94848998454387e-08 1455 1645.81818181818 1532 1.38708018997353e-09 430 1.47949659876295 1.71945192326417 1 2.68221718527488 1455 1501 1660 908 430 2338 1892 1532 2827 1026 2535 1353 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 19/46 Arthur Liberzon 9.25467736541225e-08 3.05835106730055e-07 1555 1383.09090909091 1532 8.41334341338739e-09 840 1.50573935912769 1.86486930255345 1 2.52307632145396 1552 1679 1870 1034 1207 1532 1317 840 1703 1606 874 1354 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 16/38 Leona Saunders 2.91752041569086e-06 5.6940860757715e-06 1485 1676.18181818182 1533 2.65229480432276e-07 595 1.43185891860147 1.65524425846436 1 1.93156466054729 1485 1533 1859 2636 2482 1113 880 595 2645 2161 1049 1355 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 1.02163759732318e-06 2.24993612111978e-06 1535 1704.63636363636 1533 1.021638067008e-07 357 2.89770876664814 2.89770876664814 1 4.20954351590347 1533 2132 4580 2208 3155 936 740 461 391 2258 357 1356 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 13/24 Arthur Liberzon 2.28745503361282e-07 6.39941151493114e-07 1495 1563.09090909091 1533 2.07950479222864e-08 493 1.97843095092202 2.14193890215521 1 3.15196175646422 1491 2074 1851 1301 1533 1522 1219 2174 493 1783 1753 1357 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 79/192 Jessica Robertson 4.3121553069033e-08 1.76632515455847e-07 1455 1672.45454545455 1534 3.92014126493146e-09 751 1.91371007126052 2.17100118533894 1 3.32404588091363 1454 3279 751 1534 861 2268 1011 1675 2459 1295 1810 1358 M4974 REACTOME_BASIGIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASIGIN_INTERACTIONS.html Genes involved in Basigin interactions 13/30 Reactome 3.95860100028457e-07 9.98923224950647e-07 965 1588 1535 3.59872882961928e-08 828 1.66210902320185 1.42883007763659 1 2.56533021431378 962 1535 1596 2272 1749 828 947 2935 2601 1005 1038 1359 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 5/15 Arthur Liberzon 5.85558151259339e-08 2.18988467422288e-07 3480 2193.63636363636 1535 5.85558166688865e-09 210 1.40147982257233 -1.34575916684001 -1 2.40066886117513 3480 876 4541 1186 1049 2676 4479 1500 210 1535 2598 1360 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 8/15 Jessica Robertson 1.51323997709741e-06 3.19128826853215e-06 1540 1955.36363636364 1536 1.51324100755124e-07 321 1.8648541473302 -1.8648541473302 -1 2.63628848486743 1536 1360 4322 1311 2784 752 1736 3578 925 2884 321 1361 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 231/491 Jessica Robertson 3.10119980339907e-09 3.18147607086465e-08 3395 1899.18181818182 1536 2.81927255251875e-10 39 1.60089890959157 -1.07533503356134 -1 3.08724850956766 3393 759 1314 1460 39 2158 3770 1847 1536 1161 3454 1362 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 13/90 Arthur Liberzon 8.67429843372891e-07 1.94486901724659e-06 1305 1673.27272727273 1536 7.88572895807978e-08 433 1.7382101642458 2.31689174551214 1 2.55341517981315 1304 1536 1658 2743 2363 1362 1371 433 1701 2925 1010 1363 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 24/49 Pathway Interaction Database 1.52988242106509e-06 3.22348427388085e-06 1150 1502.54545454545 1537 1.39080316813459e-07 559 1.44336968449403 1.73172180756599 1 2.03882995997064 1148 1803 2291 1857 2144 859 559 811 1537 2573 946 1364 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 254/627 Arthur Liberzon 1.3900713777247e-08 8.47729648011404e-08 2000 1709.27272727273 1538 1.26370126046171e-09 388 1.69514907348584 2.15037885675921 1 3.08342225126594 2000 1301 724 1123 388 4269 2449 1538 1913 670 2427 1365 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 490/1230 Arthur Liberzon 1.76539715908038e-08 9.80171929792733e-08 2190 1822.09090909091 1539 1.60490652113352e-09 479 1.71396930482346 2.058733409246 1 3.0898616200854 2189 993 886 479 491 4347 2877 1930 1539 1162 3150 1366 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 26/64 Arthur Liberzon 2.33788517024546e-07 6.50940576813442e-07 1520 1895.72727272727 1541 2.1253503806243e-08 537 1.08727786146795 -0.903775700157293 -1 1.73014019444361 1520 1574 2577 3411 1541 537 638 1053 2937 3929 1136 1367 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 85/174 Arthur Liberzon 1.10302877874387e-12 2.14472732663641e-11 3460 1675.36363636364 1542 1.0027534352222e-13 235 2.20266176708719 -2.27267192045832 -1 6.04442587607248 3458 649 235 952 1479 1542 4156 1874 1647 310 2127 1368 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 8/16 Arthur Liberzon 3.35611896948772e-06 6.45598254967958e-06 1125 1590 1543 3.35612403808904e-07 451 1.54569239251644 1.64046566125531 1 2.06344179181118 1124 1781 4243 1674 2364 1020 451 869 1737 1543 684 1369 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 10/23 Arthur Liberzon 9.47538149135824e-08 3.1159043977898e-07 4070 2238.90909090909 1544 8.61398354496555e-09 216 2.20792904713521 -1.38227001396331 -1 3.69509489485092 4067 864 1544 1230 1219 4030 3950 1579 216 1357 4572 1370 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 35/95 Arthur Liberzon 1.00953642659283e-06 2.22935329642507e-06 1405 1525.72727272727 1545 9.17760808953995e-08 686 2.18976465969926 2.56001332167999 1 3.18335086825937 1401 1722 1093 1547 2036 2186 1545 686 1772 1424 1371 1371 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 52/111 Broad Institute 1.18300072100521e-08 7.84080321527547e-08 2410 1779.27272727273 1546 1.07545520669685e-09 311 1.81349062742312 2.2504501054811 1 3.31449328399101 2410 1025 887 1329 311 4685 2688 1546 1575 832 2284 1372 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 37/75 Reactome 9.45762569906311e-05 0.000140515009593563 225 1659.72727272727 1547 8.59821118124568e-06 223 1.70908375791521 -1.70908375791521 -1 1.69347785141489 223 2301 1299 1820 3440 1065 1547 1535 2728 639 1660 1373 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 14/39 Jessica Robertson 5.39282606626177e-07 1.29130214340841e-06 1550 1510.72727272727 1548 4.90257035290669e-08 956 1.62941543045941 1.87288619781375 1 2.46814104987683 1548 1634 1989 2151 1854 1734 1338 966 956 1450 998 1374 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 16/31 Arthur Liberzon 7.69626186299683e-07 1.74731991715131e-06 1750 1556.27272727273 1548 6.99660414125644e-08 417 1.44459446231207 1.71841068454438 1 2.13938113086351 1750 846 2205 1548 2865 1776 1102 417 1441 2165 1004 1375 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 29/58 Arthur Liberzon 1.73833746738169e-06 3.58374367450533e-06 820 1449.90909090909 1549 1.58030803721496e-07 243 1.48333545014884 -1.56190231173113 -1 2.07772845384038 820 1928 2190 2458 2191 243 744 1150 1999 1549 677 1376 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 7/31 John Newman 1.83729981837873e-07 5.31001394965978e-07 1390 1899.90909090909 1549 1.83729997028393e-08 247 2.25812843286796 2.25812843286796 1 3.64463811150704 1390 2360 4404 2592 3055 1549 1328 247 488 2688 798 1377 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 338/799 Arthur Liberzon 8.70380142096293e-09 6.66871748972617e-08 960 1681 1550 7.91254677763413e-10 200 1.6534165363401 1.94086780416755 1 3.05183327880948 958 3815 1981 1828 200 1550 1448 1488 1998 2382 843 1378 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 127/347 Jessica Robertson 1.38965876575755e-08 8.47729648011404e-08 755 1404.27272727273 1551 1.26332615866865e-09 387 1.59959877037984 1.83460061048717 1 2.90961927680825 753 1494 1684 1551 387 1559 1507 1497 1672 1703 1640 1379 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 20/50 Jessica Robertson 7.93782333908756e-08 2.73504707110032e-07 1355 1498.63636363636 1551 7.21620329590209e-09 828 1.77449164662274 1.86851490494769 1 2.99555536449778 1351 2112 1826 1090 1142 1551 1211 1904 828 1711 1759 1380 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 29/59 Jessica Robertson 3.34245884124634e-07 8.70153451671131e-07 1000 1626.18181818182 1551 3.03859940824187e-08 308 1.92425375179729 2.3548559096993 1 2.99959476792596 999 2661 1492 2245 2816 1586 1332 308 1973 1551 925 1381 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 169/404 Arthur Liberzon 2.41026665895906e-07 6.67524205903201e-07 765 1561.36363636364 1551 2.19115174820189e-08 551 1.45984211145538 1.6823867236284 1 2.31888377619425 763 2179 1569 2375 1551 956 741 1060 2974 2456 551 1382 M12524 KEGG_HISTIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HISTIDINE_METABOLISM.html Histidine metabolism 11/36 KEGG 3.28761389891828e-06 6.3320011222076e-06 1480 1747.72727272727 1552 2.9887443744e-07 858 2.00795046994061 -1.70204166260363 -1 2.68488862552826 1476 858 970 1798 2336 1104 1607 3195 2849 1480 1552 1383 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 93/210 Jessica Robertson 3.95578342057538e-06 7.46849359742797e-06 1350 1849.54545454545 1552 3.59617321220153e-07 637 2.06071102499106 2.58538238142462 1 2.71743602655119 1347 2899 1552 1474 2590 2724 2142 637 1080 2791 1109 1384 M728 REACTOME_RNA_POL_I_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_TRANSCRIPTION.html Genes involved in RNA Polymerase I Transcription 50/103 Reactome 0.0003458806938968 0.000480093877843721 290 1797.63636363636 1556 3.14486440647117e-05 289 1.63948936532561 -1.63948936532561 -1 1.39949643913309 289 2516 2153 1984 3394 917 1413 1339 3036 1177 1556 1385 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 15/48 Kevin Vogelsang 4.12790392621898e-08 1.70726900249445e-07 2505 1694.81818181818 1556 3.75264000333787e-09 408 1.79455941264283 2.29182960652812 1 3.12390252507345 2503 408 1556 738 846 3771 2880 1033 461 1583 2864 1386 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 19/41 Reactome 1.74608173158038e-07 5.10558804956058e-07 1350 1676.54545454545 1557 1.58734715469298e-08 253 1.8570897046923 2.10926117000807 1 3.00550251312187 1350 2462 1894 1292 1443 2106 1968 1119 253 2998 1557 1387 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 37/109 Jean Junior 1.23112824616258e-08 7.95992601494109e-08 3780 2272.90909090909 1564 1.11920750277456e-09 338 1.93274140249842 -1.54885619156735 -1 3.52919092919885 3778 1123 1294 1068 338 3889 3607 3041 635 1564 4665 1388 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 38/82 John Newman 9.22366166228884e-08 3.05672408412203e-07 1565 1605.18181818182 1564 8.38514731727057e-09 1124 1.53005113943503 1.87579857698612 1 2.56390505337007 1564 1124 2031 1565 1203 1678 1464 1371 2319 1894 1444 1389 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 51/106 Arthur Liberzon 5.45974827840399e-09 4.83636681145579e-08 1770 1449.45454545455 1565 4.96340753813951e-10 101 2.14064408800165 2.0881716650721 1 4.02796793690989 1770 1565 651 1528 101 2018 1446 1997 2257 569 2042 1390 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 68/146 John Newman 1.98944812834584e-09 2.1630055520716e-08 2140 1754.09090909091 1567 1.80858920922262e-10 19 2.16765198638403 2.2139718922947 1 4.27363196707167 2137 912 646 970 19 3348 2418 3440 1567 780 3058 1391 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 47/110 John Newman 6.90690964440561e-07 1.59280406464984e-06 1040 1483.27272727273 1567 6.27901073893989e-08 691 2.03680961264891 2.04204289496832 1 3.03749201126297 1039 1567 691 1254 1936 1614 921 2225 2012 1050 2007 1392 M1053 KEGG_HEDGEHOG_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEDGEHOG_SIGNALING_PATHWAY.html Hedgehog signaling pathway 22/61 KEGG 6.1093880972208e-09 5.22419573422932e-08 2075 1483.72727272727 1568 5.55398919471503e-10 52 2.53209985537192 2.83519472122071 1 4.74273668323201 2074 1405 1054 154 123 2895 2264 2494 52 1568 2238 1393 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 26/61 Jessica Robertson 2.52180137984386e-07 6.89449315399552e-07 1725 1577.09090909091 1569 2.29254697173752e-08 443 1.69483699246504 2.32362526523392 1 2.68604248022018 1724 2618 1930 894 1569 2033 1487 1149 764 2737 443 1394 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 22/89 John Newman 7.57832073892265e-06 1.34719313287525e-05 675 1672.81818181818 1570 6.88940622183967e-07 674 2.12758724380277 2.18106599894862 1 2.66542111672983 674 2384 1646 2642 2533 974 831 1529 2335 1570 1283 1395 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 16/35 KEGG 2.21643898548663e-08 1.13263174329229e-07 580 2389.54545454545 1571 2.01494455256057e-09 576 1.66996892759362 -1.46529984562858 -1 2.9835703310565 4365 576 1571 1352 576 2880 4257 4135 1100 1300 4173 1396 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 106/309 Jessica Robertson 4.77374940474355e-08 1.90543353582864e-07 1775 1585.36363636364 1571 4.33977228029862e-09 881 1.82954852992668 2.19237816808704 1 3.16236698432995 1773 1829 1130 881 904 2587 1345 2250 1290 1571 1879 1397 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 11/42 Jessica Robertson 1.04542127482228e-06 2.29024969322916e-06 1415 1643.63636363636 1572 9.50383428725361e-08 137 2.20182468897985 2.09707885879041 1 3.19425455910443 1415 2528 1572 1002 2054 1870 1836 3124 137 1495 1047 1398 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 17/34 Leona Saunders 4.51209378695681e-07 1.11341082073089e-06 740 1351.72727272727 1573 4.10190428396884e-08 271 1.68664213303978 1.62973548260914 1 2.58275146927988 739 2156 1573 1212 1794 504 271 1670 1882 2221 847 1399 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 148/379 Arthur Liberzon 2.77804754313828e-08 1.29274387161331e-07 1575 1363.36363636364 1575 2.52549779838004e-09 501 2.06626452854901 2.31351570391391 1 3.66107359846843 1575 897 501 1622 686 2122 1593 1956 1514 817 1714 1400 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 11/20 Arthur Liberzon 2.82209588495652e-06 5.51934111723966e-06 600 1340.45454545455 1575 2.56554500460488e-07 303 2.23012813490621 2.23012813490621 1 3.01618774339615 597 2169 1575 1815 2397 303 409 776 2356 1971 377 1401 M69 PID_REELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_REELIN_PATHWAY.html Reelin signaling pathway 18832364 20/47 Pathway Interaction Database 7.9322210339719e-08 2.73504707110032e-07 1555 1782.54545454545 1576 7.21111029088409e-09 1140 1.42844563091846 1.62921801328242 1 2.41138802023803 1553 2563 2461 1981 1140 1576 1197 1204 2292 2126 1515 1402 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 19/37 John Newman 1.61555430104108e-05 2.70858227358802e-05 1580 1629.54545454545 1576 1.46869651351889e-06 783 1.67892942580814 -1.58424271928091 -1 1.97236199305912 1576 1278 1506 2071 2694 783 2178 1851 1743 798 1447 1403 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 4/11 Reactome 8.38254892288047e-08 2.83756616053022e-07 1580 1527 1577 8.38254923908255e-09 80 1.22719158510806 -1.22719158510806 -1 2.06660243239137 1577 2049 4058 2207 2569 446 819 606 341 2045 80 1404 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 21/35 Arthur Liberzon 3.67706463326063e-05 5.79768669968348e-05 1775 1633.09090909091 1577 3.34284190263654e-06 671 1.72074421682872 -1.73065067579744 -1 1.87519877373392 1772 1577 1515 1203 2853 1296 2206 1775 671 740 2356 1405 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 3/24 Arthur Liberzon 2.43591676873177e-05 3.95519957667258e-05 1115 1838.45454545455 1578 2.43594347075098e-06 395 3.1248909058783 3.1248909058783 1 3.53887805535806 1112 2409 4666 1578 2788 1016 1447 2314 395 1761 737 1406 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 196/518 Leona Saunders 5.71076269445819e-11 8.28502600192913e-10 750 1637.90909090909 1579 5.19160244964219e-12 314 2.03599660880157 2.45283001575671 1 4.75601443889164 750 3171 314 1399 1579 2715 1773 1345 2064 1129 1778 1407 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 15/40 Leona Saunders 8.53736966746909e-08 2.87193928655852e-07 3325 2440.45454545455 1579 7.76124545342927e-09 766 1.90384567175218 2.33095101676553 1 3.20353377039464 3323 1062 1457 1545 1175 4559 2872 4456 766 1579 4051 1408 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 84/169 Reactome 1.7290347992931e-07 5.06391066842967e-07 1290 1621.09090909091 1580 1.57184994107479e-08 556 1.3955206491381 1.41494458297259 1 2.25977971972981 1287 1253 2690 556 1440 1580 1116 2091 1758 2343 1718 1409 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 82/244 Arthur Liberzon 6.932700051022e-10 8.43808634781535e-09 1845 1509 1582 6.30245459382424e-11 314 1.98319286797784 2.29450499329738 1 4.11850161675318 1845 314 363 1020 513 3405 2025 2092 1582 468 2972 1410 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 7/25 John Newman 2.01783003186987e-07 5.73759194741638e-07 2150 1848.27272727273 1582 2.0178302150936e-08 751 2.09635204900924 2.0549576837343 1 3.36539366962947 2146 1545 4418 1582 1527 2029 1950 762 751 1351 2270 1411 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 502/1368 Arthur Liberzon 2.03462559203047e-21 1.23821500314997e-19 1585 1736.72727272727 1583 2.03462559203048e-22 19 1.79488644493193 1.8540803982838 1 8.72896927846754 1583 448 4152 455 428 3090 1904 2954 1501 19 2570 1412 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 67/154 Jessica Robertson 1.62313029890918e-06 3.38947797713387e-06 910 1679.72727272727 1583 1.4755740876673e-07 906 1.69591279979403 2.00548413057418 1 2.38604675503154 906 1918 1538 1856 2160 1583 1373 1299 1985 2386 1473 1413 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 223/565 Jessica Robertson 4.81925358689171e-09 4.35965681624992e-08 3955 2221.90909090909 1583 4.38113963404421e-10 408 1.97653601641625 -1.64521458050266 -1 3.74208396650209 3955 1303 408 667 1276 2123 4300 3745 1583 875 4206 1414 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 42/126 Arthur Liberzon 2.60824154047673e-07 7.08123977906949e-07 2490 1659.27272727273 1586 2.37112895427326e-08 615 2.10704532708513 -1.9106139852492 -1 3.33303548175062 2488 1188 840 1278 1586 1721 3482 2257 615 714 2083 1415 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 118/254 John Newman 2.70751169353974e-08 1.26899172948679e-07 1590 2027.63636363636 1586 2.46137429714612e-09 671 1.47784017785388 1.83789827948366 1 2.621545856652 1586 3610 2639 1570 671 2720 1556 1201 2296 3318 1137 1416 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 29/41 Jessica Robertson 1.7930083908048e-06 3.68348852227588e-06 1920 1612.72727272727 1590 1.63000895646831e-07 949 1.80448440057232 -1.68440067340937 -1 2.52203258072714 1920 1927 1463 1590 2199 949 2026 1262 1495 1032 1877 1417 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 177/382 Arthur Liberzon 1.20527676246474e-07 3.76528460593984e-07 1155 1705.45454545455 1590 1.09570620772382e-08 1151 1.42536706736445 1.61075541422931 1 2.35529099359204 1151 1603 2359 1299 1321 2044 1590 1562 2502 1944 1385 1418 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 50/109 Arthur Liberzon 1.34292135493701e-09 1.53861356216011e-08 795 1707.54545454545 1591 1.22083759614251e-10 10 1.70444942760493 1.73181167216141 1 3.42525891027833 792 3282 1591 2424 10 953 1005 1906 2868 2769 1183 1419 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 26/53 Arthur Liberzon 2.10823824027614e-06 4.25460998877432e-06 790 1639.63636363636 1594 1.91658205507518e-07 347 1.99896918316567 2.31428982235715 1 2.76166659554891 787 3795 1918 2648 2631 644 357 1141 2174 1594 347 1420 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 36/93 Jessica Robertson 2.1651037287913e-08 1.11490945858418e-07 825 1464.09090909091 1594 1.96827613645356e-09 444 2.61043648100432 2.91734959003131 1 4.66841077572866 821 1885 444 1961 1545 1793 1594 2402 1319 504 1837 1421 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 606/2731 Yaara Zwang 5.35680759528982e-22 3.44240510113767e-20 1595 1609.36363636364 1594 5.35680759528983e-23 2 1.9263569206321 2.15258635038157 1 9.64380232016074 1594 2 4685 560 321 3251 1727 1719 1590 17 2237 1422 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 6/16 Reactome 0.000434525026634334 0.000596819642874746 1310 2283.90909090909 1595 4.34610015423559e-05 750 0.600225059223041 -0.600225059223041 -1 0.49777008517914 1310 1595 4053 2761 3286 787 750 1441 3151 4499 1490 1423 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 17/40 Arthur Liberzon 4.00275125318403e-07 1.00789319572382e-06 660 1437.63636363636 1595 3.63886543768886e-08 657 2.39848227424693 2.70476365143926 1 3.69946741731901 1745 841 657 1117 1754 2762 1598 1412 1674 659 1595 1424 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 100/254 Yujin Hoshida 8.3867459076704e-08 2.83756616053022e-07 3190 1821 1598 7.62431475216941e-09 291 1.76385593335173 -1.60548817888865 -1 2.97035044985164 3189 1009 645 658 1168 1598 3758 2685 2288 291 2742 1425 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 75/203 Jessica Robertson 2.59711134293831e-06 5.11777281455379e-06 1610 1366.63636363636 1600 2.36101309895155e-07 462 1.75919879767406 -1.59188971292875 -1 2.39411320815201 969 1607 792 1084 2282 866 1785 1600 1979 462 1607 1426 M1835 KEGG_GLIOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLIOMA.html Glioma 32/75 KEGG 4.81232317501766e-05 7.45965808737438e-05 1590 1701.45454545455 1601 4.37493494903906e-06 903 1.75772438579123 2.12239573969817 1 1.86600783901263 1589 1523 1985 1830 3012 1499 903 987 1710 2077 1601 1427 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 12/28 Jessica Robertson 7.10827393655334e-07 1.6336131273511e-06 1605 1646.63636363636 1601 6.46206930296507e-08 723 1.60041507919882 1.67205347982294 1 2.38217448740462 1601 723 2039 1283 1944 2282 1530 2126 744 1214 2627 1428 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 16/28 Arthur Liberzon 6.75513909820683e-06 1.21374930269161e-05 1635 1519.63636363636 1601 6.14105440006421e-07 849 1.78379297380744 2.28164586751414 1 2.25550386396796 1633 849 1487 1922 2510 1615 1031 1601 874 2164 1030 1429 M71 PID_ILK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ILK_PATHWAY.html Integrin-linked kinase signaling 18832364 34/68 Pathway Interaction Database 1.14816825970786e-06 2.4978256569132e-06 1605 1733.45454545455 1602 1.04378987175562e-07 708 1.78017048521413 1.92765344543941 1 2.56529490693996 1519 3791 2099 1602 2069 1366 908 1331 2071 1604 708 1430 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 9/21 Yujin Hoshida 2.93014160629977e-08 1.35592118795245e-07 1655 1610.36363636364 1602 2.93014164493555e-09 326 3.08203064635011 2.89031533146982 1 5.44441329837196 1652 2125 4567 772 736 1602 1425 1213 326 1680 1616 1431 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 184/461 Arthur Liberzon 3.95160672078672e-07 9.98233374318413e-07 1000 1616.63636363636 1602 3.59237039142593e-08 1000 1.78514809111686 1.99762549596192 1 2.75536879554047 1000 1825 1388 1596 1745 2205 1817 1534 1286 1602 1785 1432 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 44/85 Leona Saunders 5.29155916833087e-08 2.05437003005787e-07 1260 1616.45454545455 1603 4.8105084505512e-09 950 1.95580346732369 2.01976413881584 1 3.3641555259002 1257 2064 1218 2041 950 1811 1090 2950 1603 1076 1721 1433 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 55/215 Jessica Robertson 7.32364792918778e-06 1.30489027361878e-05 765 1620 1603 6.65788391747193e-07 703 1.60649331181002 -1.52764000421025 -1 2.01832500156009 764 2013 1280 1603 2527 914 1679 2106 2744 703 1487 1434 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 44/96 Leona Saunders 2.33281848343981e-08 1.16417331346101e-07 2270 1534.18181818182 1604 2.12074409834215e-09 136 1.67933853829949 -1.50542715504779 -1 2.99515736626589 2269 136 1604 1070 601 1813 2808 2108 1483 1281 1703 1435 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 42/121 Jessica Robertson 2.79292388537008e-07 7.50008098959553e-07 2025 1756.09090909091 1605 2.53902203630442e-08 876 1.87524261724569 2.34033728582166 1 2.95432002861418 2025 1121 876 1150 1605 3282 2045 2296 1559 990 2368 1436 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 56/156 Reactome 1.61669491824587e-08 9.23183294908041e-08 3415 1576.72727272727 1607 1.46972266375122e-09 337 1.76737015074106 -1.53143163214022 -1 3.1979561331019 3415 337 1607 647 453 712 2864 2147 859 1981 2322 1437 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 36/119 Yujin Hoshida 4.35796634514356e-09 4.07300268483159e-08 3700 2074.54545454545 1607 3.96178759434203e-10 71 2.00396334339056 2.20390736180503 1 3.80923608252749 3698 1797 1099 1080 71 4284 2677 1005 1607 1228 4274 1438 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 45/90 Kate Stafford 7.22606688200212e-08 2.54405329895281e-07 1925 1724.63636363636 1607 6.56915192667982e-09 1087 1.83360893426803 2.27850478357297 1 3.11017998737177 1924 1186 1087 1314 1100 3136 2318 1607 1458 1821 2020 1439 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 21/46 Arthur Liberzon 3.16318074195001e-08 1.43491432301817e-07 3725 2087.81818181818 1608 2.8756188976641e-09 727 1.46095682813213 -1.29881988717982 -1 2.57154199133051 3721 952 1522 1420 727 1820 4213 3312 1608 1150 2521 1440 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 52/171 Arthur Liberzon 1.68530989771659e-07 4.9637725837209e-07 4220 2474.27272727273 1613 1.5321000243816e-08 714 2.25935104104875 -2.10804611873513 -1 3.66362945483511 4218 1613 714 1573 1430 3197 4352 3553 1247 961 4359 1441 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 50/134 Leona Saunders 1.281188986152e-11 2.09917887731059e-10 3085 1923.81818181818 1615 1.16471726014497e-12 278 2.64092438600692 3.20060835634155 1 6.57412626088451 3081 1261 278 521 1615 4684 2431 2671 808 473 3339 1442 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 49/162 Jessica Robertson 3.79281386592116e-06 7.20142859631546e-06 1415 1791.09090909091 1615 3.44801854979269e-07 1010 1.50719857956254 -1.65837145619922 -1 1.99365629604253 1413 1615 1592 1487 2371 1010 2426 1883 2615 1816 1474 1443 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 12/44 Leona Saunders 2.87990221253816e-07 7.69396908093147e-07 3595 1910.36363636364 1616 2.61809326320982e-08 289 2.1166943771248 -1.9662574634603 -1 3.3286763148137 3592 587 869 289 1616 2708 4305 3274 518 902 2354 1444 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 86/287 Arthur Liberzon 2.30136368840039e-08 1.15586176246991e-07 4575 2235.54545454545 1617 2.09214882952215e-09 538 1.73783952300362 -1.69285990989318 -1 3.10088682015271 4572 782 538 570 594 3137 3974 4200 1617 687 3920 1445 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 30/120 Jessica Robertson 5.40620818029452e-08 2.08849888976588e-07 1620 1896.18181818182 1617 4.91473483013174e-09 601 1.74668352641239 1.63550182854123 1 3.00123581977731 1617 1129 900 2352 957 1972 1527 3990 2706 601 3107 1446 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 334/902 Arthur Liberzon 1.9595657490508e-08 1.04823345891005e-07 1530 1678.90909090909 1619 1.78142342409534e-09 528 1.64647458596621 2.02593921864962 1 2.95583789938795 1529 2258 1860 1655 528 2784 1595 1692 1570 1619 1378 1447 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 25/80 John Newman 7.47561834952959e-06 1.32944013608712e-05 500 1580.63636363636 1619 6.79603977442176e-07 497 2.16444239408679 2.11004734537001 1 2.71480026672005 497 2151 656 1619 3239 1130 873 2190 2380 808 1844 1448 M3462 REACTOME_LIPOPROTEIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIPOPROTEIN_METABOLISM.html Genes involved in Lipoprotein metabolism 14/44 Reactome 5.82031910790006e-07 1.37747552220302e-06 1355 1596.45454545455 1620 5.29120058884002e-08 609 1.96220819647103 2.23636967356168 1 2.95807545961263 1352 1534 1620 2483 1881 1779 1403 609 1657 2399 844 1449 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 29/90 Arthur Liberzon 6.67899654940594e-10 8.15046297669693e-09 3035 2041.54545454545 1620 6.07181504675785e-11 362 2.63896521558845 -2.04935075895835 -1 5.49056942045939 3034 548 362 758 1620 2218 4154 4595 1479 373 3316 1450 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 62/137 John Newman 1.46741106858706e-08 8.75503631708099e-08 3035 1994.18181818182 1622 1.33401007124979e-09 413 2.01347735473911 2.80154202260536 1 3.65520041833126 3035 1562 1334 1173 413 4593 2727 1646 1359 1622 2472 1451 M11773 REACTOME_PECAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PECAM1_INTERACTIONS.html Genes involved in PECAM1 interactions 8/17 Reactome 2.65073799235483e-07 7.17582797930372e-07 1575 1729.09090909091 1623 2.65073830854342e-08 143 1.62126419201532 1.3176702208027 1 2.56219805500947 1571 1163 3966 2015 1623 697 143 2054 2623 2096 1069 1452 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 144/405 John Newman 3.48442454899171e-07 8.99119682630791e-07 1820 1686 1623 3.16765918260475e-08 890 1.76056226700813 2.10412250983846 1 2.7379864630036 1816 1653 890 1395 1697 3674 1810 1231 1623 1164 1593 1453 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 152/392 Jessica Robertson 2.91685978237445e-07 7.76613917057196e-07 1995 1931.90909090909 1624 2.65169106282275e-08 1167 1.83115238515991 2.1749408952788 1 2.87772818732264 1993 2686 1167 1495 1624 3396 1608 1523 1886 1559 2314 1454 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 157/433 Jessica Robertson 4.0367638412438e-08 1.67697476596351e-07 4515 2266.27272727273 1624 3.66978537755825e-09 634 1.48503912852399 -1.08298116863501 -1 2.58807107765565 4514 634 1624 1228 841 1952 4244 3451 1308 1176 3957 1455 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 19/61 Leona Saunders 1.05888212190777e-05 1.83455847329625e-05 1220 1783.81818181818 1625 9.62624744043857e-07 1066 2.26381474117964 2.41979836511827 1 2.75799952564469 1217 2312 1824 2841 2605 1726 1559 1625 1066 1608 1239 1456 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 12/33 Kevin Vogelsang 4.24395454792497e-06 7.95013905814568e-06 830 1866.36363636364 1627 3.85814794075776e-07 360 1.88945651422146 1.88945651422146 1 2.47841379544677 826 2993 1899 3889 3427 360 373 893 3812 1627 431 1457 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 25/48 Arthur Liberzon 2.94666426675083e-07 7.8303515934669e-07 2000 1659.81818181818 1629 2.67878605584092e-08 456 2.33030440677 2.07313754769242 1 3.66002184813585 1998 1528 1049 1099 1629 2509 1633 3229 456 1831 1297 1458 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 42/105 John Newman 0.000596075560299663 0.00081080118303751 975 2040.54545454545 1632 5.42033749407556e-05 785 1.57221220584831 1.55578520023162 1 1.25003108885874 975 3284 1400 2969 3452 935 785 2292 3437 1632 1285 1459 M7747 BIOCARTA_IL2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL2_PATHWAY.html IL 2 signaling pathway 16/41 BioCarta 1.17605278546849e-05 2.01867522077118e-05 1540 2156.63636363636 1633 1.06914461121311e-06 1009 0.880305826418611 -0.735963477502598 -1 1.06306942584606 1538 1633 3073 1953 2634 1009 1612 1487 3541 3761 1482 1460 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 161/402 Arthur Liberzon 5.65506754493507e-08 2.14185632374353e-07 3040 1924.90909090909 1633 5.1409706275434e-09 686 1.73785628362794 -1.52453591436324 -1 2.98117099752641 3038 1434 1098 2865 985 686 3487 3105 2008 835 1633 1461 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 93/193 Arthur Liberzon 2.39485889843391e-06 4.76531159153345e-06 1865 1660.81818181818 1634 2.17714682310433e-07 371 1.81702295515913 -1.89635611605865 -1 2.48729035246064 1862 1914 764 1564 2266 999 2586 1634 2704 371 1605 1462 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 468/970 Arthur Liberzon 1.15355426166855e-08 7.71377224059447e-08 1825 1633.27272727273 1636 1.04868569792466e-09 297 1.58898146599851 1.82049222328359 1 2.90706007556483 1821 1300 807 1073 297 4147 1884 1636 2213 669 2119 1463 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 14/36 John Newman 3.02717654307779e-07 8.00979631895118e-07 805 1496.27272727273 1636 2.75197905419468e-08 661 1.29234169109233 1.3411900568429 1 2.02650613633712 802 960 2211 1810 1636 1048 661 1763 1924 2403 1241 1464 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 102/254 John Newman 1.03809939608556e-08 7.29315407804641e-08 1275 1932.63636363636 1636 9.43726728167247e-10 261 1.61951167027327 1.87538508271845 1 2.97305939384072 1273 3522 2299 3014 261 1636 1588 1022 2709 2772 1163 1465 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 40/179 Arthur Liberzon 2.20651379201005e-05 3.61276157559717e-05 990 1833.90909090909 1637 2.00594174799046e-06 835 1.74504716679998 1.90560232724808 1 1.99388487123766 988 2342 1581 2664 2753 988 835 1637 3004 2378 1003 1466 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 58/143 Itai Pashtan 5.18559703861779e-09 4.61971629714124e-08 1410 1749.54545454545 1637 4.71417913712791e-10 95 1.80614231650516 1.94767588859494 1 3.40779549678916 1407 2764 1081 2129 95 2490 1637 1570 3042 1865 1165 1467 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 140/404 John Newman 9.78375979174308e-11 1.36855816071964e-09 2410 1917.09090909091 1638 8.89432708379838e-12 325 2.17779899809907 2.57035085792478 1 4.96516074274957 2409 1435 325 975 607 4438 2817 2383 1638 729 3332 1468 M522 REACTOME_CELL_CELL_COMMUNICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CELL_COMMUNICATION.html Genes involved in Cell-Cell communication 67/162 Reactome 3.04565551207862e-07 8.05414318826208e-07 3340 2204.45454545455 1639 2.76877812155987e-08 422 2.09624830277341 -2.05183693275509 -1 3.28581006904887 3339 1255 610 422 1639 4584 2497 4037 762 753 4351 1469 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 111/263 Jessica Robertson 4.84536840451487e-08 1.92782022207611e-07 1640 1874.09090909091 1639 4.40488046475566e-09 909 1.82549860539795 2.08574918584437 1 3.15298481634865 1639 1498 955 1678 909 3393 2644 3215 1565 947 2172 1470 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 31/74 Leona Saunders 3.22585636456912e-07 8.45434168029693e-07 1645 1663.18181818182 1643 2.9325971250691e-08 365 1.74942212231763 1.81932840641254 1 2.73269299848401 1643 365 985 919 1660 2446 2183 3786 893 525 2890 1471 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 3/11 Jessica Robertson 6.02689714860935e-05 9.18440326451493e-05 2055 2009.72727272727 1643 6.02706061055037e-06 987 1.71814688704653 2.04695942020124 1 1.78407125408198 2052 1643 4444 2104 2974 1624 1140 2635 987 1002 1502 1472 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 62/163 Arthur Liberzon 2.19924941019958e-08 1.12779349152635e-07 2205 1744.90909090909 1644 1.99931766562234e-09 573 1.78513592719606 2.0198294355081 1 3.19018162916895 2205 1109 1693 1077 573 3847 2351 1644 731 1621 2343 1473 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 46/189 Jessica Robertson 2.38037265831582e-08 1.17662724439535e-07 450 1767 1645 2.16397516733743e-09 447 2.30274330353629 -2.52150249555574 -1 4.10428384658578 2493 927 449 1870 1190 2623 4195 1482 1645 447 2116 1474 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 104/250 Arthur Liberzon 5.56056754937085e-08 2.11671970238439e-07 1925 1767 1646 5.05506153628718e-09 302 1.69520306804711 2.07058000219645 1 2.91023792103487 1922 302 1405 1134 972 3626 1991 1626 1646 2022 2791 1475 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 3/12 Leona Saunders 7.40172369745264e-05 0.000111382393212149 1190 1885.18181818182 1647 7.40197024382183e-06 516 1.98857680559365 1.98857680559365 1 2.02203180294651 1188 1647 4254 2802 3154 892 516 2074 1082 1749 1379 1476 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 544/1296 Arthur Liberzon 2.77286725193431e-07 7.4614680584615e-07 815 2145.54545454545 1647 2.77286759793004e-08 814 1.57856390497534 1.85941133893355 1 2.48783260513399 814 3487 4260 2262 1640 1647 1533 1577 2249 3084 1048 1477 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 24/71 Yujin Hoshida 2.26558029109165e-06 4.53890946731742e-06 600 1531.90909090909 1648 2.05962056746408e-07 481 1.86931224696568 2.11227969793763 1 2.569032622589 600 3231 1648 2459 2498 640 481 556 2451 1737 550 1478 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 44/107 Jessica Robertson 6.38481421157683e-06 1.15029755461165e-05 1670 1537.18181818182 1650 5.80439340144098e-07 708 1.97468913750066 2.34334658096703 1 2.50872527339156 1666 1120 1650 708 2501 2409 1078 1911 848 2064 954 1479 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 52/144 Yujin Hoshida 2.29837740475302e-08 1.15560048483612e-07 4535 2100.45454545455 1650 2.08943402614959e-09 593 1.86572503130283 -1.71776668161808 -1 3.3291244627707 4532 1614 1037 1363 593 2602 2748 2622 1650 833 3511 1480 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 9/34 Arthur Liberzon 1.03574732052434e-05 1.79826303963581e-05 1650 2187.09090909091 1650 1.03575214803231e-06 1198 1.84535203880686 1.92721292747573 1 2.25230669643501 1650 1542 4668 2742 2624 1590 1334 3178 2014 1198 1518 1481 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 13/37 Yujin Hoshida 3.15945773186902e-07 8.3082036652852e-07 2800 1817.54545454545 1651 2.87223471418568e-08 920 1.66033703394967 -1.24794901230865 -1 2.59677123506041 2800 1639 1632 1330 1651 920 2020 1835 1503 2273 2390 1482 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 3/7 Jessica Robertson 7.55289649889892e-05 0.000113547876143216 1545 2046.18181818182 1651 7.55315321928409e-06 519 1.09261403439648 -1.09261403439648 -1 1.1086454525974 1543 2000 4450 2452 3293 900 519 1403 1651 2812 1485 1483 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 150/356 Arthur Liberzon 4.50165673230533e-08 1.82355453091211e-07 2575 1866.81818181818 1652 4.09241529492597e-09 101 2.27361575761228 -1.80262625672438 -1 3.94109068725407 2575 1652 603 101 877 4366 2831 2653 730 854 3293 1484 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 22/51 Leona Saunders 9.3417236541319e-06 1.63584891790964e-05 1840 1722 1652 8.49251211049992e-07 844 2.04120088623602 1.9256681573352 1 2.51293003836456 1837 1458 1603 1628 2576 1917 929 2144 844 2354 1652 1485 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 207/516 Arthur Liberzon 8.35932499755712e-08 2.83582175257329e-07 1385 1734.63636363636 1654 7.59938665016896e-09 814 1.4674596271097 1.63796329550192 1 2.47131697344856 1385 2220 1585 2569 1163 1888 1245 1654 2758 814 1800 1486 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 47/97 John Newman 3.59743448965535e-07 9.23445667423136e-07 920 1644.36363636364 1655 3.27039552537006e-08 651 2.09920189297419 2.31429520034193 1 3.25837107509949 917 2904 1805 1016 1704 1914 1655 651 1063 3568 891 1487 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 66/178 Kevin Vogelsang 1.49021856043257e-08 8.83585336093744e-08 1660 1530.90909090909 1657 1.35474415502444e-09 420 1.99345615471074 1.87477762950864 1 3.61680843763238 891 1656 776 2048 420 1968 1657 1783 2313 1068 2260 1488 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 7/10 Leona Saunders 3.76899285604436e-08 1.60851553036647e-07 3480 1922.18181818182 1659 3.76899291996824e-09 340 1.98243695553973 -2.0562660850499 -1 3.46414773657028 3478 428 4162 1316 847 2399 3596 1659 340 928 1991 1489 M16973 BIOCARTA_CBL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CBL_PATHWAY.html CBL mediated ligand-induced downregulation of EGF receptors 9/21 BioCarta 9.04870578448694e-07 2.02204269461639e-06 1275 1762.36363636364 1661 9.04870946904747e-08 751 1.71751999808328 1.8773052927211 1 2.51555553800014 1275 1689 3821 2542 2030 858 1349 751 2329 1661 1081 1490 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 35/85 Leona Saunders 3.24590870821566e-07 8.49739005960816e-07 570 1725.09090909091 1662 2.9508265337467e-08 522 1.61309361268763 1.70942894963862 1 2.51882519604834 722 3058 2381 3881 1662 522 570 1102 2526 1984 568 1491 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 181/450 Arthur Liberzon 3.5399941722671e-07 9.11952319474635e-07 1020 1748.36363636364 1662 3.21817703807594e-08 847 1.96654937977334 2.15903810002543 1 3.05521978098858 1019 3881 847 2179 1700 1748 1071 1662 2590 1163 1372 1492 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 8/35 Arthur Liberzon 1.37462567484417e-08 8.42025609453569e-08 1660 1952 1663 1.37462568334736e-09 71 1.5643684373236 1.85433278652072 1 2.84671622774133 1658 2601 4169 3105 1663 1092 597 71 3384 2101 1031 1493 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 5/28 Jessica Robertson 0.000476626741162538 0.000652871356061868 1355 2305.63636363636 1663 4.76728999904755e-05 1055 2.03880554252119 2.03880554252119 1 1.67034961402514 1353 2681 4429 3284 4532 1514 1055 1427 1663 2252 1172 1494 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 276/913 Jessica Robertson 7.42068717270046e-31 8.69333502281859e-29 2140 1720.81818181818 1664 6.74607924790952e-32 24 1.90920851644079 1.99889113183502 1 13.7800979341033 2139 274 39 677 921 3803 2053 4673 1664 24 2662 1495 M685 REACTOME_HS_GAG_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HS_GAG_BIOSYNTHESIS.html Genes involved in HS-GAG biosynthesis 10/30 Reactome 2.18550727374081e-07 6.13986036255961e-07 1665 1894.27272727273 1665 1.98682499168349e-08 259 1.74018510783368 1.74018510783368 1 2.78044603148655 1665 2248 2230 2889 3058 1464 1302 259 1550 3177 995 1496 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 7/19 Reactome 4.29059432371784e-05 6.7153390116706e-05 1470 1903.81818181818 1666 4.29067716736745e-06 205 2.72022637551111 2.72022637551111 1 2.91974563908858 1466 2129 3927 1394 2901 2329 1364 1633 205 1928 1666 1497 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 10/16 Reactome 2.44965103751716e-06 4.85357192827462e-06 580 1425.54545454545 1666 2.2269579683212e-07 261 1.31074956405595 1.31074956405595 1 1.79157455496475 580 868 1992 2244 2273 573 261 1666 2563 1850 811 1498 M17906 KEGG_VIBRIO_CHOLERAE_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIBRIO_CHOLERAE_INFECTION.html Vibrio cholerae infection 30/73 KEGG 2.13305693284394e-07 6.01915350875829e-07 3640 2038.18181818182 1667 1.9391428542355e-08 793 1.75768899911149 -1.39558364633341 -1 2.81231208040689 3639 1043 1667 1009 1508 1533 3552 3372 793 2281 2023 1499 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 26/55 Leona Saunders 6.10705289431599e-09 5.22419573422932e-08 1215 1797.36363636364 1667 5.55186628297159e-10 122 1.3988786066952 1.44060237313786 1 2.62016232386705 1214 2695 2067 2782 122 1492 1217 856 2436 3223 1667 1500 M287 BIOCARTA_ERK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK_PATHWAY.html Erk1/Erk2 Mapk Signaling pathway 21/54 BioCarta 9.09052945974439e-08 3.023294609536e-07 1655 1557.63636363636 1669 8.26411803215496e-09 566 1.57192269110537 1.96878297479559 1 2.63600013306211 1654 566 1811 629 1198 2742 1845 949 1669 2202 1869 1501 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 27/77 Yujin Hoshida 1.13019568284847e-07 3.57602766362455e-07 1650 1829.27272727273 1669 1.02745067355408e-08 1046 1.91801647545831 2.22279843421421 1 3.18039936947547 1648 1046 1108 1669 1290 2575 2470 2344 2125 1114 2733 1502 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 15/35 Jessica Robertson 2.75104009675193e-06 5.39613808848035e-06 1490 1796.54545454545 1672 2.50094866987154e-07 1229 1.94432810262597 2.50076159773269 1 2.63455413283295 1490 2241 1249 1672 2296 2682 2211 1229 1421 1584 1687 1503 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 32/135 Arthur Liberzon 4.59032284057285e-07 1.13152303161096e-06 1210 1699 1675 4.1730216348625e-08 840 1.75136722466523 1.97890140904017 1 2.67870792209911 1207 1836 1618 2357 1796 1790 840 1369 2733 1468 1675 1504 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 8/12 Jessica Robertson 1.91527346941335e-07 5.48927919123605e-07 2295 1826 1675 1.91527363448563e-08 489 1.93348461103904 -1.39831902281595 -1 3.11348900466816 2292 1159 4361 1109 1503 721 1675 2446 489 2106 2225 1505 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 661/1775 Leona Saunders 4.46106499376882e-12 7.77120838691475e-11 1595 1737.36363636364 1677 4.46106499377777e-13 68 1.73643573377379 2.05693711679196 1 4.51530978351915 1593 259 4199 863 368 3679 2011 1770 1677 68 2624 1506 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 42/84 Arthur Liberzon 4.87299509800264e-06 9.02920325395033e-06 1680 1817.63636363636 1677 4.43000535609946e-07 775 2.49906835167276 3.08490605938944 1 3.2425154689614 1677 3227 775 1470 2429 3114 1856 1114 1658 991 1683 1507 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 29/62 Arthur Liberzon 3.34923682077849e-07 8.71433855756136e-07 470 1594.54545454545 1678 3.04476120969076e-08 467 1.45038283346295 1.31808962940968 1 2.26066974657645 811 2192 2157 2643 1678 470 618 1492 1970 3042 467 1508 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 61/177 Itai Pashtan 6.55421616266778e-07 1.52270981349832e-06 1175 2230.27272727273 1679 5.95838010481234e-08 1173 1.56309484960875 1.59692795283082 1 2.3388998614654 1173 4014 1567 4545 1917 2142 1436 1679 3544 1174 1342 1509 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 34/92 John Newman 1.34446383139689e-06 2.86761834953383e-06 2115 1508.27272727273 1680 1.2222405936602e-07 525 1.87482407329845 1.88319560542535 1 2.67277994947675 1315 1966 2112 1680 2113 1201 1029 861 1885 1904 525 1510 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 105/229 Broad Institute 4.8780545345922e-07 1.18869285226724e-06 1685 1821.81818181818 1681 4.43459601472941e-08 769 1.77710433321604 2.18953827563333 1 2.70828790443116 1681 2550 2233 948 1818 3168 1378 769 1052 2962 1481 1511 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 24/54 Arthur Liberzon 3.52625019667491e-05 5.57678313250713e-05 1620 1921.45454545455 1681 3.20573338011555e-06 919 1.63028934158045 -1.63651374515004 -1 1.78369926055306 1620 1674 1681 1469 2848 1546 3285 1797 2098 919 2199 1512 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 67/209 Jessica Robertson 1.0289789370708e-08 7.26051267693284e-08 3830 2461.72727272727 1682 9.35435401712285e-10 424 2.18678826299346 -1.98041384885857 -1 4.01554754431386 3828 1503 424 1514 1560 4265 3438 3691 1682 560 4614 1513 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 244/708 Arthur Liberzon 1.61937806497154e-08 9.23183294908041e-08 1760 1680.09090909091 1682 1.47216188808315e-09 456 1.50640729584441 1.7268883951799 1 2.72575860406805 1757 890 1372 1361 456 3279 1857 1682 2351 1252 2224 1514 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 16/26 Arthur Liberzon 1.33642279882662e-08 8.26322183149997e-08 1685 1683.90909090909 1683 1.21492982449538e-09 374 1.38849432260492 1.29431919586991 1 2.52959411005426 864 1685 2023 2330 374 1292 1376 1684 3547 1683 1665 1515 M4741 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS.html Systemic lupus erythematosus 64/146 KEGG 9.33055422315247e-05 0.000138759051379538 775 1832.27272727273 1684 8.48268179134403e-06 663 1.63721581096601 -1.63811151162245 -1 1.62456602890414 774 2514 1261 2257 3026 1114 1957 1553 3352 663 1684 1516 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 125/284 Arthur Liberzon 2.68997583580273e-07 7.26945026907244e-07 910 1818.36363636364 1685 2.44543287700956e-08 908 1.64840679503403 1.93464391034758 1 2.60270651263989 908 3277 1541 1685 1595 1741 1503 2050 2463 1811 1428 1517 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 144/538 John Newman 1.43097408995451e-08 8.63004451161753e-08 1690 1703.18181818182 1686 1.30088554478379e-09 401 2.01839292965858 2.42946717907075 1 3.66736612598947 1686 3882 842 2135 401 2519 1502 1305 1778 1866 819 1518 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 16/35 Jessica Robertson 2.65917553575711e-06 5.23347188599657e-06 1295 1852.18181818182 1686 2.41743522722816e-07 474 1.80149399154334 1.62288817697031 1 2.44717436625103 1292 2317 1332 3470 2285 744 474 2304 3490 1686 980 1519 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 2/6 Arthur Liberzon 0.000310512912611125 0.000433054615623729 1630 2379.6 1687 3.45061970616648e-05 720 1.00048107493175 1.00048107493175 1 0.865552434457092 1626 1748 4187 NA 4400 1181 720 1595 4246 2528 1565 1520 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 83/199 Arthur Liberzon 5.11831553059157e-09 4.58593242377669e-08 1690 1804.45454545455 1687 4.65301412954486e-10 91 1.29692632340234 1.53925392574431 1 2.44807960971559 1687 1606 2529 3096 91 1963 1470 655 1981 3516 1255 1521 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 31/107 Yujin Hoshida 3.65631184661331e-08 1.58057908793634e-07 790 2282.45454545455 1689 3.32391991579978e-09 168 1.72371233428198 -1.88800172741305 -1 3.01542101668393 4387 168 881 1512 786 4213 2986 4083 1689 790 3612 1522 M4835 BIOCARTA_BCELLSURVIVAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCELLSURVIVAL_PATHWAY.html B Cell Survival Pathway 17/27 BioCarta 8.5392180072213e-06 1.50374955211721e-05 1545 1908.09090909091 1690 7.76295559277987e-07 1172 1.84561729856389 2.11572145902124 1 2.2895058537724 1690 2496 2583 1172 2559 1504 1346 1776 1543 2775 1545 1523 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 137/396 Leona Saunders 1.44672752912602e-07 4.36533496554059e-07 1965 1790 1691 1.31520693114848e-08 712 1.86779457283461 2.20955495776809 1 3.05550981857623 1963 1827 712 1138 1378 4204 2570 1407 1691 900 1900 1524 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 3/10 Jessica Robertson 3.3362234055576e-07 8.69012944882875e-07 1695 1744.54545454545 1691 3.3362239064251e-08 444 2.04706321850362 2.28839098572284 1 3.19133443637769 1691 444 4306 1805 1712 1774 1319 3253 1099 1001 786 1525 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 22/39 Jessica Robertson 1.27429581725302e-08 8.0434968418917e-08 1625 2182.54545454545 1691 1.15845074966733e-09 354 1.16356506055425 1.19947093255826 1 2.12331527291579 1622 1676 2739 4343 354 1691 1587 1989 3695 2837 1475 1526 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 46/120 Jessica Robertson 0.000270897449191034 0.000381208842915672 1195 1927.54545454545 1691 2.4630073814116e-05 1022 1.50525538605903 -1.58255647849215 -1 1.32369280638581 1192 2731 1691 2017 3199 1124 2086 1671 3022 1022 1448 1527 M12836 BIOCARTA_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPO_PATHWAY.html EPO Signaling Pathway 15/36 BioCarta 1.20453715419482e-05 2.06002230093318e-05 905 1741.54545454545 1692 1.09503977208156e-06 443 0.992546710095538 -0.992546710095538 -1 1.19636505786706 904 1808 3199 1692 2639 443 917 837 2173 3714 831 1528 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 36/76 Arthur Liberzon 1.59944015971324e-05 2.68444720215482e-05 1285 1536.45454545455 1693 1.45404708004866e-06 600 2.70123993006333 3.26862481016189 1 3.17604634626328 1285 1925 948 2009 2826 2020 1693 975 826 1794 600 1529 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 79/198 Arthur Liberzon 3.45124465000084e-07 8.9203157362956e-07 1875 1694.18181818182 1693 3.13749562855829e-08 808 1.94044308457428 2.20688435222266 1 3.01944864112816 1874 1318 1528 808 1693 3388 1821 1243 1188 2073 1702 1530 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 81/205 Yujin Hoshida 1.83303480617636e-07 5.30222290231014e-07 1695 1733.72727272727 1694 1.66639541718582e-08 232 1.98702438906407 2.45023350070172 1 3.20739981521392 1694 2479 1537 1306 1781 3277 2374 232 1202 1386 1803 1531 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 28/61 Arthur Liberzon 1.34166910117819e-08 8.28334836379576e-08 1265 1649.63636363636 1694 1.21969919032759e-09 376 1.51929761554268 1.82063090910304 1 2.76748200733039 1261 1334 1593 1850 376 2311 1525 1694 2562 1767 1873 1532 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 83/209 Jessica Robertson 2.45511377455021e-08 1.2003053648855e-07 1885 1794.63636363636 1695 2.23192163813484e-09 624 1.69091439200697 2.01164271966336 1 3.01002997613968 1885 1916 1262 1413 624 2944 1550 3007 1695 2290 1155 1533 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 4/19 Arthur Liberzon 1.37900451170014e-05 2.33454304256751e-05 1700 1785.27272727273 1698 1.37901306921538e-06 227 2.82713397048955 2.82713397048955 1 3.36817518863242 1698 1169 4531 1762 2682 1717 1650 1467 227 2056 679 1534 M8492 KEGG_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_APOPTOSIS.html Apoptosis 59/107 KEGG 3.52378769132036e-07 9.08276629346932e-07 1560 1888.54545454545 1699 3.20344386884837e-08 1461 1.59638622814901 1.82071657619054 1 2.48085662085268 1557 2586 2100 1502 1699 2301 1784 1461 1681 2452 1651 1535 M19387 TCGA_GLIOBLASTOMA_MUTATED http://www.broadinstitute.org/gsea/msigdb/cards/TCGA_GLIOBLASTOMA_MUTATED.html Genes significantly mutated in 91 glioblastoma samples. 18772890 7/14 Arthur Liberzon 1.84029676268797e-06 3.76413384109813e-06 1640 1999.36363636364 1700 1.84029828670122e-07 147 3.52687399402316 3.52687399402316 1 4.92079318666616 1638 3000 4562 1825 3533 1359 1000 536 147 2693 1700 1536 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 10/49 Yujin Hoshida 2.46505993319804e-08 1.20200529104745e-07 3030 1991.54545454545 1700 2.24096360074417e-09 419 2.05328960365486 -1.87884802223163 -1 3.65477665381383 3027 866 1500 1700 627 3373 2395 4648 419 1363 1989 1537 M19895 KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM.html Nicotinate and nicotinamide metabolism 13/31 KEGG 1.0808781550592e-09 1.26942231443794e-08 2110 1508.72727272727 1701 9.82616505082035e-11 8 1.85298300189931 2.69851414672342 1 3.7635605083263 2106 853 1367 1701 8 3641 2436 223 513 1769 1979 1538 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 55/142 Arthur Liberzon 3.80515823760426e-07 9.67497097200953e-07 1270 1742.36363636364 1701 3.45923535977382e-08 878 1.63081852375994 1.97655081459689 1 2.52285917998522 1268 2090 1701 2897 1728 1554 1716 878 2060 1694 1580 1539 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 33/105 Kevin Vogelsang 0.000143967101344341 0.000209577457874987 1225 2041.36363636364 1703 1.30887748505326e-05 1174 1.90732159680417 2.32113393252617 1 1.80472766148972 1223 3256 1703 2993 3101 1527 1271 1174 2809 1845 1553 1540 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 86/278 Arthur Liberzon 1.55170181701108e-09 1.73538776002718e-08 2040 1557.45454545455 1705 1.41063801645956e-10 112 2.14757532961328 2.16880460872491 1 4.28689224784162 982 2335 380 1705 112 2040 1429 1838 2847 1427 2037 1541 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 7/21 Jessica Robertson 5.64394801422723e-06 1.030289847864e-05 1505 2236.90909090909 1705 5.64396234864559e-07 700 1.91510761012706 1.91510761012706 1 2.4566016295819 1504 2677 4354 3615 3827 1293 1001 700 1245 2685 1705 1542 M285 PID_HNF3A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HNF3A_PATHWAY.html FOXA1 transcription factor network 18832364 20/84 Pathway Interaction Database 7.48582550615477e-08 2.618966793322e-07 3165 2222.63636363636 1706 6.80529614624642e-09 1112 1.97787687215813 -1.76047566066714 -1 3.34847618441349 3165 1624 1409 1259 1112 2209 3301 4617 1426 1706 2621 1543 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 117/239 Kevin Vogelsang 3.60390855079903e-07 9.24352242421688e-07 3780 2167.72727272727 1706 3.2762810374272e-08 378 1.22218652887059 -1.21094059372796 -1 1.89693799105476 509 3779 3482 3778 1706 378 844 1183 3745 3469 972 1544 M222 PID_CXCR3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CXCR3_PATHWAY.html CXCR3-mediated signaling events 18832364 26/62 Pathway Interaction Database 2.40529056292823e-06 4.77997946475051e-06 1375 1729.90909090909 1708 2.1866301751544e-07 860 1.60603613771396 2.05082641550021 1 2.19792285762561 1371 1050 2365 860 2267 1788 1613 866 2408 2733 1708 1545 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 52/126 Jessica Robertson 6.07120895450057e-08 2.23485350831027e-07 1395 1771.81818181818 1709 5.51928102004011e-09 958 1.83057013109854 1.75415057158612 1 3.13152379364676 1395 3375 1709 1782 1028 1247 958 2606 1433 1762 2195 1546 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 70/288 Jessica Robertson 5.68717883299016e-09 4.99065917816327e-08 1575 1668.90909090909 1709 5.17016258881087e-10 100 1.71642078085284 1.79775342959785 1 3.22370179384587 1574 100 893 1709 106 3143 2478 2612 1833 1428 2482 1547 M6467 REACTOME_OPIOID_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OPIOID_SIGNALLING.html Genes involved in Opioid Signalling 35/93 Reactome 5.46878041677442e-08 2.09709884827199e-07 1710 1805.27272727273 1710 4.97161868428897e-09 963 1.47675505077536 1.58747376586451 1 2.5367537775456 1710 1039 1960 1201 963 2100 1812 3543 1476 1423 2631 1548 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 23/49 Leona Saunders 2.14781273313739e-07 6.05574637032601e-07 2020 1934.81818181818 1711 1.95255722074888e-08 532 0.94013598984399 -0.86357007561093 -1 1.50358613444901 2017 555 2972 1711 1513 532 1421 2896 2689 3798 1179 1549 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 35/68 John Newman 4.33014124748066e-07 1.07473738801347e-06 1435 1968.27272727273 1711 3.93649281796292e-08 999 1.83961566854739 2.23668499147233 1 2.82426429508755 1431 3015 1663 3700 1782 1711 1388 999 2387 1985 1590 1550 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 21/109 Arthur Liberzon 3.39634611812303e-06 6.52800570530129e-06 1715 1537.18181818182 1712 3.08759214672007e-07 361 1.84750023036927 -1.84469401575414 -1 2.46405442599125 1712 949 737 888 2343 1317 2517 2172 1829 361 2084 1551 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 12/31 Arthur Liberzon 6.0338747785598e-05 9.19204720817009e-05 1540 1775.72727272727 1712 5.48549115837197e-06 608 4.19466485939291 4.48269829232625 1 4.35522236800296 1537 2570 1285 1465 2960 2143 1216 1712 608 2154 1883 1552 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 20/45 Itai Pashtan 9.11422210559309e-07 2.03377356127663e-06 795 1605.36363636364 1713 8.28565989223722e-08 688 1.43707645619101 1.2763105843343 1 2.10387688626036 794 1055 1742 3158 2007 688 695 1978 2766 1713 1063 1553 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 25/57 Arthur Liberzon 5.93605545014341e-05 9.0577518200495e-05 1195 1790 1714 5.39655965750818e-06 807 2.18343541367147 -1.78721649690065 -1 2.27059954498235 1194 2742 1118 2180 2957 901 1948 2504 1714 807 1625 1554 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 75/218 Jernej Godec 1.8836043394943e-07 5.41175348551215e-07 1090 1810.09090909091 1716 1.71236772796861e-08 998 1.62242463567071 1.70673245658541 1 2.61516717682668 1087 2609 1307 2862 1476 1732 1223 1716 3135 998 1766 1555 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 131/344 Arthur Liberzon 2.90970748711931e-14 7.3305856369038e-13 4355 2071.27272727273 1717 2.64518862465395e-15 166 2.10957013067423 -1.93362567961906 -1 6.5845706308704 4352 639 181 1021 445 3098 4136 3469 1717 166 3560 1556 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 11/31 Arthur Liberzon 1.28871240880646e-05 2.19642396229151e-05 2010 1694 1718 1.1715635980608e-06 714 1.69060062940512 1.32378103309471 1 2.02565563327902 2006 863 2020 1718 2648 1233 1225 2947 714 1492 1768 1557 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 63/196 Arthur Liberzon 8.2631609301847e-08 2.81403867142772e-07 3845 2302.81818181818 1720 7.51196476413417e-09 722 1.64479996476348 -1.2417175493497 -1 2.77138882495547 3845 1710 1720 1155 1158 3210 3767 1504 722 2414 4126 1558 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 6/14 Reactome 1.91652188441512e-06 3.90470502189967e-06 995 1745.90909090909 1721 1.91652353729238e-07 433 1.43583088799954 1.43583088799954 1 1.99743053041973 992 433 3993 2646 2235 735 719 1751 3200 1721 780 1559 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 33/73 John Newman 7.33182850004911e-05 0.000110472502737074 1430 1833.54545454545 1721 6.66552077780238e-06 733 2.35420616659723 -1.82264527307118 -1 2.39596954945091 1426 2588 940 1609 2988 1276 1721 3165 1878 733 1845 1560 M5672 SU_KIDNEY http://www.broadinstitute.org/gsea/msigdb/cards/SU_KIDNEY.html Genes up-regulated specifically in human kidney tissue. 11904358 6/32 John Newman 2.44551967199185e-07 6.73308177611858e-07 1605 2113 1725 2.44551994111738e-08 907 1.74022602308435 1.74022602308435 1 2.76258202145108 1604 1078 4409 2200 1596 1791 907 3293 3450 1725 1190 1561 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 18/46 Jessica Robertson 3.79899483702953e-06 7.20732380822687e-06 1735 1598.36363636364 1725 3.45363763382712e-07 547 1.78817900150571 2.42451962207399 1 2.36516148214853 1732 956 1775 1725 2373 2140 1441 1218 547 1513 2162 1562 M389 NAKAJIMA_MAST_CELL http://www.broadinstitute.org/gsea/msigdb/cards/NAKAJIMA_MAST_CELL.html Top 50 most-increased mast cell specific genes. 11493461 39/75 Kevin Vogelsang 3.22566856830397e-09 3.25764717911044e-08 1560 2079.09090909091 1726 2.93242597548499e-10 46 1.74062353135776 -0.997705093200161 -1 3.35209957524586 1559 3464 1619 3755 46 2303 1030 1126 3160 3082 1726 1563 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 108/229 Kevin Vogelsang 1.75310203788839e-08 9.74500136363585e-08 4490 2030.54545454545 1727 1.59372913805295e-09 297 1.7713733351825 -1.77943626126341 -1 3.19449519956626 4487 297 593 779 490 3159 4058 2870 1727 436 3440 1564 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 16/42 Chi Dang 4.12178352059763e-06 7.74445772955914e-06 1730 1792.18181818182 1728 3.74708294812345e-07 705 1.58780843993415 2.0293836845947 1 2.08738902356823 1728 1471 1980 1642 2401 2659 2196 1206 705 2163 1563 1565 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 267/547 Jessica Robertson 1.71638482046217e-08 9.59782728960112e-08 2985 1642.72727272727 1729 1.56034984895725e-09 26 1.54714505778024 -1.39623599104784 -1 2.79275187875356 2983 26 2013 1729 479 585 3418 2426 1956 1046 1409 1566 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 32/93 Arthur Liberzon 3.85687521196235e-06 7.30235040131538e-06 1300 1958.45454545455 1729 3.50625633960334e-07 742 1.51647815186296 1.65807371637545 1 2.00357336429467 1297 3287 1678 2500 2376 1729 1097 742 2976 2455 1406 1567 M13883 BIOCARTA_MPR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MPR_PATHWAY.html How Progesterone Initiates Oocyte Membrane 26/66 BioCarta 7.97362860210532e-07 1.80504461978094e-06 1475 1678.45454545455 1731 7.24875590186373e-08 673 1.90248316414955 2.22487971475274 1 2.81058688640741 1473 1134 1640 858 1979 2175 1731 2444 673 2329 2027 1568 M15181 BIOCARTA_PGC1A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PGC1A_PATHWAY.html Regulation of PGC-1a 15/30 BioCarta 9.69739731485366e-06 1.69243962075993e-05 1005 1779.54545454545 1731 8.81585460031944e-07 442 1.26767118347569 1.38595840196447 1 1.55581865977485 1005 1731 2673 2858 3453 655 442 750 1936 3155 917 1569 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 46/119 Arthur Liberzon 1.56630953823323e-09 1.74755392765736e-08 1735 1864.27272727273 1731 1.42391776304398e-10 14 2.2506696354283 1.92581774224425 1 4.49092798168367 1731 2338 1226 1714 14 2130 1209 3591 1321 2509 2724 1570 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 29/56 Jessica Robertson 7.79175394471826e-08 2.69661440066099e-07 1240 1890.18181818182 1732 7.08341292789027e-09 1134 1.44269542572317 1.4648715092766 1 2.43772406144279 1239 3182 2450 2455 1134 1216 1204 1732 1963 3040 1177 1571 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 18/42 John Newman 0.000440976959628666 0.000604923311715436 1350 1958 1732 4.00968523326191e-05 1219 2.07891490018231 2.20184380666289 1 1.72092454646185 1348 3234 1219 2577 3461 1244 1249 1370 2204 1900 1732 1572 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 12/36 Reactome 1.01474878092204e-06 2.23875366638451e-06 1315 1589.54545454545 1733 9.22499317249689e-08 234 1.72192730757837 1.94079345038615 1 2.50242706424552 1314 234 1251 1389 2038 1733 1865 2592 2095 901 2073 1573 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 122/305 Jessica Robertson 1.76008987627251e-06 3.62221394827095e-06 1735 1977.81818181818 1733 1.60008298583445e-07 1313 1.6468851484027 2.07843187940346 1 2.30485047078654 2328 1378 1733 1328 2194 3792 1995 1313 1732 1696 2267 1574 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 24/110 KEGG 2.08667380173379e-08 1.08888122883347e-07 4515 2445 1734 1.89697620138696e-09 386 1.87262491079759 -1.39993230258042 -1 3.3538765163907 4511 386 1143 1023 554 3582 4492 4003 1048 1734 4419 1575 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 23/58 Jessica Robertson 1.78195812277584e-05 2.96318515377132e-05 1445 2194.81818181818 1734 1.61997505132828e-06 850 2.49338187493585 2.68199032696653 1 2.90413638696825 1443 4028 1734 3126 3250 1656 1540 850 2707 2954 855 1576 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 340/853 Jessica Robertson 1.0365365469318e-08 7.29310849688053e-08 2390 1847 1734 9.42305956195887e-10 260 1.78884282582704 2.26669056690603 1 3.28391460451973 2387 1750 789 1451 260 4132 2340 1734 1679 885 2910 1577 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 72/165 John Newman 1.50075791684263e-06 3.17210266049822e-06 905 2036.36363636364 1735 1.3643263096406e-07 902 1.53282465977701 1.71069020507531 1 2.16794080815495 902 3557 1735 3079 2137 1397 1057 1606 3393 2171 1366 1578 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 146/318 Jessica Robertson 8.97267223883623e-08 2.98833987997062e-07 1715 2073.54545454545 1735 8.15697509525957e-09 1193 1.71641796448453 2.06562371509541 1 2.88053796725026 1715 3396 2102 1735 1193 2841 1614 1839 1448 3598 1328 1579 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 9/17 Reactome 2.56004822555736e-05 4.14526122493496e-05 2280 2012.09090909091 1737 2.56007771834667e-06 549 1.93663493340807 2.44217969715538 1 2.18304751987052 2279 1737 3909 1486 2805 2845 1942 1724 549 1665 1192 1580 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 24/66 Arthur Liberzon 1.07211746728674e-08 7.39899659922656e-08 4325 2249.81818181818 1740 9.74652247737676e-10 180 1.77445729415245 -1.66946982103294 -1 3.25464873364569 4324 180 949 723 271 3107 4074 4337 839 1740 4204 1581 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 83/233 John Newman 2.31418350937402e-07 6.45777982302147e-07 3665 2122.27272727273 1742 2.10380341163944e-08 787 1.46621615755755 -1.54646606188231 -1 2.33443324699119 3662 787 1889 1620 1537 1395 3357 3809 1258 2289 1742 1582 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 14/62 Arthur Liberzon 3.93809157452871e-07 9.95355831620363e-07 2530 1857.63636363636 1742 3.58008389042152e-08 1041 2.02740628516142 1.91256908378366 1 3.12994715154638 1486 1847 1257 2526 1742 1584 1041 2527 3238 1883 1303 1583 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 78/193 John Newman 6.49732340708159e-08 2.35175333250705e-07 1625 1868.09090909091 1743 5.90665781724447e-09 1055 1.76339415910883 2.0069324069388 1 3.00656368950523 1623 1104 1580 1861 1055 2920 1743 2125 1568 2544 2426 1584 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 64/206 Arthur Liberzon 8.58116339533591e-08 2.88253273623972e-07 1745 1734.72727272727 1744 7.80105793640608e-09 752 2.08664868047389 2.57017431723181 1 3.51027173537812 1910 2610 951 1744 1177 2985 2291 752 1745 1717 1200 1585 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 166/568 John Newman 3.25151966452203e-07 8.50732615742616e-07 4215 2273.27272727273 1744 2.9559274046226e-08 447 1.82525290442796 -1.53219444958652 -1 2.84987098733439 4215 1432 748 447 1664 2273 4433 3949 1744 944 3157 1586 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 125/288 Leona Saunders 1.25265256645708e-11 2.05962453558523e-10 3420 1943.63636363636 1745 1.13877506042201e-12 112 1.99411615357855 -1.78192415507032 -1 4.96824597868652 3418 901 277 854 1486 1745 4020 3565 2038 112 2964 1587 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 3/16 Jean Junior 5.08115725035652e-07 1.22987101627948e-06 1235 1661.09090909091 1746 5.08115841217404e-08 235 1.2831435638629 1.2831435638629 1 1.95061559492883 1235 1746 4365 2278 1864 706 634 626 1773 2810 235 1588 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 27/62 John Newman 1.16135175949025e-05 1.99636623073049e-05 1250 1990.27272727273 1746 1.05577990014765e-06 741 2.45312787794547 2.45312787794547 1 2.96547663540225 1248 3858 1878 3243 3059 1746 1646 774 1680 2020 741 1589 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 5/8 Jessica Robertson 8.68452161475009e-05 0.000129723994329838 1660 1985 1746 8.68486102753915e-06 993 1.30524505433932 1.30524505433932 1 1.30497726497872 1656 1857 4498 1924 3030 1221 1125 1746 2252 1533 993 1590 M137 PID_VEGF_VEGFR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGF_VEGFR_PATHWAY.html VEGF and VEGFR signaling network 18832364 5/10 Pathway Interaction Database 2.27663607774872e-05 3.72237147952913e-05 980 1901.72727272727 1749 2.27665940190826e-06 632 3.57761803961429 3.57761803961429 1 4.07582939033124 977 2507 3898 2033 2773 632 1144 1233 1749 3268 705 1591 M18647 REACTOME_STRIATED_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_STRIATED_MUSCLE_CONTRACTION.html Genes involved in Striated Muscle Contraction 21/48 Reactome 3.98649694700765e-07 1.0050484731708e-06 1420 1816.27272727273 1751 3.62408879034422e-08 623 2.91530831607786 3.25911050806868 1 4.49755083371781 1419 2195 623 1544 1751 2868 2471 2429 1480 935 2264 1592 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 3/5 Arthur Liberzon 8.08764395676271e-05 0.000121198271766518 1755 2181.27272727273 1752 8.08793831677191e-06 45 3.57761803961429 3.57761803961429 1 3.60405294493173 1752 3136 4284 1417 3266 1541 1495 3366 45 2806 886 1593 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. 20/54 Signaling Transduction KE 3.73101374426286e-07 9.51426643855708e-07 1755 1778.36363636364 1753 3.3918312518285e-08 909 1.64996166998348 1.77101740707317 1 2.555560648103 1753 1463 1917 909 1718 2025 1330 3191 1038 2125 2093 1594 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 130/338 Arthur Liberzon 4.20242328836646e-08 1.72893376025331e-07 2290 1842.63636363636 1753 3.82038488058257e-09 261 1.93642155791191 2.48900839258653 1 3.36812322564538 2288 641 1331 261 854 4249 2793 1753 1183 2987 1929 1595 M1073 REACTOME_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POTASSIUM_CHANNELS.html Genes involved in Potassium Channels 25/106 Reactome 1.05501489871665e-06 2.30819078314557e-06 1410 1855.45454545455 1754 9.59104913319758e-08 983 1.74154459264047 1.9089312340065 1 2.52499401485456 1408 2910 1113 2985 2056 1754 1171 1945 2424 983 1661 1596 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 59/154 Jessica Robertson 2.70804893189669e-08 1.26899172948679e-07 3305 2089.27272727273 1755 2.46186269566447e-09 536 2.19235536258167 2.51872622151876 1 3.88902694339104 3302 1323 536 1755 672 4240 2675 2769 1190 720 3800 1597 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 107/250 Jessica Robertson 2.56396103987123e-07 6.97719014682729e-07 1755 1637.09090909091 1755 2.33087394425886e-08 839 1.59911518895539 1.87019028485218 1 2.53220899711177 1755 1246 935 1291 1580 2672 1962 2023 1875 839 1830 1598 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 97/214 Reactome 5.60057990028649e-08 2.12676802372306e-07 1760 1926.54545454545 1756 5.09143640260134e-09 978 1.37499257572842 -1.47204547696572 -1 2.35978946644873 1756 1310 2542 2276 978 1069 2573 1533 2469 2994 1692 1599 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 11/48 Leona Saunders 4.01685299662717e-07 1.00981615569715e-06 4430 2099.18181818182 1756 3.65168520912851e-08 202 2.41891326660665 -2.90549256862525 -1 3.73046554881282 4426 1070 978 1103 1756 3686 4580 1828 202 819 2643 1600 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 18/51 Arthur Liberzon 3.90778440238647e-06 7.39022486750358e-06 4230 2584.81818181818 1757 3.55253758515172e-07 941 2.08334098112356 2.58189394785726 1 2.7497296886913 4226 1683 1171 1757 2379 3977 4675 1695 1404 941 4525 1601 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 54/143 Jessica Robertson 3.02699121169535e-08 1.38520320488324e-07 1840 1729.45454545455 1758 2.75181023031261e-09 712 1.87405615832944 2.28451790134147 1 3.30605101630993 1840 1758 1216 2027 712 3158 1823 1423 1453 1204 2410 1602 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 5/11 Arthur Liberzon 1.57139116389299e-08 9.08698406718676e-08 2360 1860.72727272727 1758 1.5713911750047e-09 483 2.49362986735913 2.0770235132924 1 4.51648728404483 2359 605 4598 1758 483 1891 1549 2200 1179 1537 2309 1603 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 222/454 Arthur Liberzon 2.41170075550264e-07 6.67526860028668e-07 945 2167.18181818182 1759 2.19245547261816e-08 943 1.87511872899704 2.24083282827308 1 2.97852845719644 943 3741 1398 1751 1552 3209 1971 1714 1759 3484 2317 1604 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 63/141 Kevin Vogelsang 1.67872043108486e-07 4.94747417614066e-07 1765 1886.63636363636 1763 1.52610959925494e-08 1339 1.79990721771187 1.93008835079548 1 2.91928386836776 1763 2370 1339 1593 1428 2860 1739 2166 2051 1657 1787 1605 M142 PID_AJDISS_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AJDISS_2PATHWAY.html Posttranslational regulation of adherens junction stability and dissassembly 18832364 33/87 Pathway Interaction Database 8.55302344974657e-08 2.8751411682577e-07 2255 1985.09090909091 1764 7.77547616569613e-09 1176 1.89440707135723 2.34160276811013 1 3.18741597000713 2255 1837 1764 1740 1176 3672 2656 1315 1275 1555 2591 1606 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 2/6 Jessica Robertson 0.000726450565296512 0.000979892731427593 1585 2083.6 1764.5 8.07428021653747e-05 1002 1.84988755080588 -1.84988755080588 -1 1.43166158747384 1584 1953 4469 NA 3364 1002 1010 1888 2532 1393 1641 1607 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 51/120 Jessica Robertson 5.11824958735051e-06 9.43513672947462e-06 1390 1864.81818181818 1765 4.65296499534516e-07 1387 1.55132451839174 1.69080990324074 1 2.00520660935332 1387 1659 1765 2448 2443 2139 1641 1599 2085 1949 1398 1608 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 56/141 Arthur Liberzon 6.91593555515063e-07 1.59410103351873e-06 2085 1806.27272727273 1765 6.28721611749997e-08 1123 1.91671986750764 1.99916774700502 1 2.85822801554025 2081 1445 1123 1562 1937 2537 1765 2413 1615 1126 2265 1609 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 189/494 John Newman 1.69104200747602e-07 4.96816479437781e-07 1225 2541 1766 1.53731103405354e-08 1154 1.55553799642795 1.66198984190501 1 2.52221426884181 1225 4323 3175 4489 1434 1766 1154 1736 3072 3861 1716 1610 M714 REACTOME_PI3K_AKT_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_AKT_ACTIVATION.html Genes involved in PI3K/AKT activation 26/47 Reactome 0.00311096017635495 0.0039808736718731 1370 2396.81818181818 1767 0.000283215275386563 1367 1.7654626433235 1.7654626433235 1 1.08986395049191 1367 3797 3016 2923 3619 1676 1665 1757 1767 3220 1558 1611 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 44/108 Arthur Liberzon 3.79609497715915e-08 1.61336088446875e-07 2365 1777.18181818182 1767 3.45099549332791e-09 802 1.6617502899149 -1.11415388253386 -1 2.90321543633518 2364 1447 1477 1236 802 2923 1767 2040 1980 1504 2009 1612 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 49/442 Jessica Robertson 1.44512462646029e-08 8.68356980103357e-08 1770 1722.90909090909 1767 1.31374966904813e-09 403 2.07050922770685 2.3883671332274 1 3.76062996696171 1767 2226 954 1698 403 2367 1732 2375 2144 987 2299 1613 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 9/25 Leona Saunders 1.2860229556897e-05 2.19297800959314e-05 1185 1823.45454545455 1768 1.28603039809801e-06 582 2.11318050073528 2.11318050073528 1 2.53235602034598 1182 1853 4282 1768 3292 1175 698 1081 1840 2305 582 1614 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 28/71 Arthur Liberzon 7.11765718557763e-07 1.63496772409886e-06 810 1406.27272727273 1769 6.47059953486671e-08 258 2.00332202666683 2.13016281339537 1 2.98170512957171 808 3148 1769 2250 1947 501 494 405 1805 2084 258 1615 M70 PID_PS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PS1_PATHWAY.html Presenilin action in Notch and Wnt signaling 18832364 34/83 Pathway Interaction Database 4.24545884073794e-07 1.05820319828181e-06 2900 2078.72727272727 1771 3.8595087818248e-08 810 1.45550324344666 -0.735273456827019 -1 2.23707763539771 2900 1451 2019 810 1771 3261 3957 1380 1122 2628 1567 1616 M99 PID_TXA2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TXA2PATHWAY.html Thromboxane A2 receptor signaling 18832364 32/89 Pathway Interaction Database 6.11280139553188e-08 2.2466343011343e-07 2400 1821.63636363636 1773 5.55709233216262e-09 491 1.7910058422192 1.91988869284651 1 3.06278999013284 2400 1571 1613 491 1030 2983 2094 1773 1813 1467 2803 1617 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 23/66 Jessica Robertson 3.39645598281884e-07 8.81761370387206e-07 3825 2347.27272727273 1774 3.08768773379877e-08 1197 1.84731549600153 -1.66438617904774 -1 2.87692603630268 3824 1197 1610 1396 1682 2783 4243 2201 1774 1649 3461 1618 M18342 ST_G_ALPHA_I_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_G_ALPHA_I_PATHWAY.html G alpha i Pathway 26/60 Signaling Transduction KE 2.68327679126889e-08 1.26116700540481e-07 1180 1673.72727272727 1775 2.43934256726913e-09 668 1.57936493783261 1.69490424764613 1 2.8027322325109 1179 2740 2237 1572 668 1876 1384 870 1775 2330 1780 1619 M12898 REACTOME_GAP_JUNCTION_TRAFFICKING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_TRAFFICKING.html Genes involved in Gap junction trafficking 13/27 Reactome 0.00073695555641855 0.000993490718462982 1200 2194 1775 6.70184124979221e-05 1146 1.99791493939064 2.00297935901609 1 1.5431468766568 1199 2885 1337 3611 3339 1237 1146 2224 3737 1775 1644 1620 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 13/42 Arthur Liberzon 6.61898677315429e-09 5.53867357482161e-08 4540 2105.09090909091 1776 6.01726072097124e-10 114 2.211983270223 -1.06714720985841 -1 4.12870015741116 4539 1354 1696 1188 138 2406 3695 2333 114 1776 3917 1621 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 916/2621 Arthur Liberzon 8.58762673893955e-24 7.18600337476263e-22 2415 1707.54545454545 1777 8.58762673893959e-25 15 1.69281385986805 -1.58188501900896 -1 9.2062979005354 2412 257 4149 1062 699 803 3422 2338 1849 15 1777 1622 M201 PID_ERBB_NETWORK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB_NETWORK_PATHWAY.html ErbB receptor signaling network 18832364 7/18 Pathway Interaction Database 1.88618656377952e-08 1.02063166719063e-07 3130 2116 1778 1.88618657978916e-09 204 3.33060489418125 -3.1904076198608 -1 5.989205672295 3129 1165 3902 611 551 2969 1778 4606 204 1345 3016 1623 M16517 BIOCARTA_WNT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_WNT_PATHWAY.html WNT Signaling Pathway 19/48 BioCarta 4.29412703173729e-07 1.06636350136306e-06 2025 1748.72727272727 1779 3.90375260899802e-08 506 1.53251755339448 2.08923711772552 1 2.35413191562178 2024 1140 2087 544 1779 3993 2812 506 1264 2498 589 1624 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 244/737 Arthur Liberzon 2.66590125721833e-08 1.25904337637219e-07 2405 1824.90909090909 1780 2.42354662683911e-09 663 1.7331614893984 2.1305597977636 1 3.0759850407879 2402 2003 945 1780 663 3467 2747 1298 1848 1471 1450 1625 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 12/22 Reactome 6.24841380742655e-06 1.12789164489988e-05 935 1786.90909090909 1782 5.68039232197056e-07 721 1.74602219576791 1.8131477615262 1 2.22205410637046 932 3036 1782 2849 2494 1089 960 721 2345 2143 1305 1626 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 13/38 Jessica Robertson 0.000128413327985647 0.000187927812286303 1965 1735.63636363636 1782 1.16746203677221e-05 364 1.95935089186277 2.23338606649361 1 1.87782342142909 1965 1733 1907 1930 3079 2038 1688 1173 364 1782 1433 1627 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 7/14 Leona Saunders 5.03434499874291e-07 1.22106318137211e-06 1495 1792.63636363636 1783 5.03434613925159e-08 192 3.08979976541247 3.08979976541247 1 4.6995482965813 1493 1783 4300 1887 3407 1867 1538 370 192 1935 947 1628 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 35/107 Arthur Liberzon 6.50420896058287e-08 2.35175333250705e-07 1190 1757.54545454545 1783 5.91291741170648e-09 1057 1.61111603216075 1.95554908970448 1 2.74693148115951 1186 1514 1568 2572 1057 2082 1783 1335 2236 1987 2013 1629 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 78/206 Jessica Robertson 1.1542622304438e-08 7.71377224059447e-08 2450 1824 1784 1.04932930590892e-09 300 2.00011043603416 2.18339406755742 1 3.65922536388779 2449 1502 591 550 300 4234 2572 2268 1784 1104 2710 1630 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 61/146 Jessica Robertson 1.32326066371443e-07 4.06876605653925e-07 3100 2173.36363636364 1784 1.20296431209654e-08 925 2.06741508979513 2.67962260153309 1 3.3983156572741 3100 2453 1013 1784 1348 3945 3471 925 1400 1375 3093 1631 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 92/194 Arthur Liberzon 9.12339511574074e-13 1.79631216438492e-11 1435 1745.36363636364 1784 8.29399555976773e-14 226 2.35097055932076 2.75264943837653 1 6.49796354888097 1433 2084 232 627 1784 3780 2813 2380 1206 226 2634 1632 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 13/32 Arthur Liberzon 3.93640973471819e-07 9.95355831620363e-07 1455 1764.45454545455 1784 3.57855494459197e-08 1009 2.53080448655914 2.87025927183863 1 3.90710261644364 1453 1636 1009 2067 1741 2451 1947 1357 2109 1784 1855 1633 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 15/29 Arthur Liberzon 3.82164860918457e-08 1.61887850248635e-07 2665 1895.27272727273 1785 3.47422606870085e-09 199 1.87555757543395 2.70740360152869 1 3.27603919994161 2661 719 2079 1194 806 4432 3303 1785 199 2565 1105 1634 M10462 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY.html Adipocytokine signaling pathway 32/102 KEGG 3.79729007863292e-06 7.20700741533975e-06 1635 1856.45454545455 1786 3.45208784811537e-07 1226 1.42873105680325 1.62779517257447 1 1.88973928952262 1632 1332 2231 1823 2372 1629 1226 2518 2310 1786 1562 1635 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 243/619 Reactome 3.4264810969004e-08 1.52194221991235e-07 4040 2154.63636363636 1786 3.1149828638796e-09 621 1.57148752401631 -1.29986043825405 -1 2.75575895173517 4040 621 1786 870 760 1503 3783 3247 1656 1902 3533 1636 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) 21/43 BioCarta 1.3837282442892e-05 2.34084857499609e-05 705 1614 1787 1.2579426796047e-06 324 1.33384292213677 1.43082980333599 1 1.58870436595825 701 2429 2526 1787 2923 493 324 807 2695 2201 868 1637 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 67/122 Leona Saunders 1.37387782143265e-08 8.42025609453569e-08 785 1702.81818181818 1788 1.2489798454658e-09 383 1.71580178706293 1.74993356504433 1 3.12228290128448 785 3249 1808 1788 383 1465 1501 2249 2521 1886 1096 1638 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 11/21 Arthur Liberzon 1.74735025547916e-06 3.59915749326389e-06 2250 1661.63636363636 1790 1.58850149392168e-07 912 1.47525490448876 1.69704979776946 1 2.0657026412298 2249 972 1790 2081 2193 2068 912 1041 2344 1487 1141 1639 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 103/272 Arthur Liberzon 1.97108832217701e-08 1.0519954302644e-07 2080 1712.54545454545 1791 1.79189849076087e-09 530 1.83295333888994 -1.47790167658192 -1 3.28988088000236 2076 1791 991 896 530 3430 1666 1337 2027 1803 2291 1640 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 101/413 Jessica Robertson 9.2421859078672e-13 1.81208716168476e-11 4585 2263.27272727273 1791 8.40198718897369e-14 172 2.03481439050486 -1.61988846122991 -1 5.62213643725374 4585 1008 233 566 1791 2565 4323 3991 1076 172 4586 1641 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 82/216 Arthur Liberzon 4.3784012882298e-06 8.17743660288754e-06 1450 1987.36363636364 1793 3.98037272915571e-07 647 2.49630248403171 2.90962407526564 1 3.26655735667515 1450 3784 1005 1793 3498 2849 1880 647 1439 1994 1522 1642 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 219/571 Leona Saunders 1.10010417725607e-09 1.28877204365548e-08 4210 1956.09090909091 1794 1.00009470709652e-10 371 1.75858830155036 -1.61185041366321 -1 3.56886526673755 4207 470 371 595 831 1938 4677 3655 1794 385 2594 1643 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 25/74 Jessica Robertson 1.27619458407041e-08 8.0434968418917e-08 1875 1684 1794 1.16017690133951e-09 356 1.49285225529596 1.57775412133252 1 2.72421042163292 1883 1401 1874 3297 356 1794 984 1873 2248 1500 1314 1644 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 38/135 Arthur Liberzon 2.15274882966799e-05 3.52966445620162e-05 845 1798.81818181818 1794 1.95706354098335e-06 368 1.5325970877117 1.62532521042706 1 1.75512394803262 843 2644 1835 3218 2953 523 368 1794 3091 1618 900 1645 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 48/132 Arthur Liberzon 1.71653510910347e-07 5.03044622968033e-07 1240 1713.54545454545 1795 1.56048658457725e-08 696 1.80230722734818 1.95049415689936 1 2.9198280148343 1237 1920 1006 2197 1439 2318 1720 2018 2503 696 1795 1646 M10401 BIOCARTA_TEL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TEL_PATHWAY.html Telomeres, Telomerase, Cellular Aging, and Immortality 13/37 BioCarta 3.48414856491232e-06 6.67665386074957e-06 1785 1679.45454545455 1796 3.16741280253109e-07 527 1.78364416060074 2.42650573246184 1 2.37440194917673 1785 1537 2103 1057 2349 2362 2002 690 527 2266 1796 1647 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 13/35 Arthur Liberzon 2.49064101945607e-07 6.83096362733292e-07 1800 1828.18181818182 1798 2.26421936493088e-08 837 1.5996859566563 1.59350720886634 1 2.53689771216368 1798 2568 2150 1400 1565 1190 837 3110 1204 2277 2011 1648 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 5/11 Arthur Liberzon 5.98438906718211e-06 1.08482967771046e-05 1570 2040.45454545455 1799 5.98440518305383e-07 233 1.55066545428591 1.55066545428591 1 1.98017867854747 1566 2080 4658 2198 3071 1704 1799 706 233 3304 1126 1649 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 26/63 Arthur Liberzon 8.00238726941468e-07 1.81068019046244e-06 1800 1663.90909090909 1800 7.27490016385776e-08 877 1.99806197414046 1.59287083333816 1 2.95109214151573 1800 948 1839 1807 1980 1528 925 3189 877 1918 1492 1650 M118 PID_INTEGRIN_A9B1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_A9B1_PATHWAY.html Alpha9 beta1 integrin signaling events 18832364 15/34 Pathway Interaction Database 0.000225817418648843 0.000321342369811259 1485 2315.36363636364 1801 2.05309637133509e-05 1267 1.88728023980531 2.14616243986289 1 1.69565538149732 1483 3236 1542 2589 3310 1752 1652 1267 3120 3717 1801 1651 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 69/143 Reactome 0.000107991352249635 0.000159435247839253 345 1935.27272727273 1801 9.81787759846538e-06 344 1.47265539595374 -1.50798810898553 -1 1.43842722610544 344 2901 2943 2306 3188 750 1366 1125 3142 1801 1422 1652 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 20/65 Arthur Liberzon 5.67991662064416e-06 1.03550584080995e-05 1805 2012.27272727273 1801 5.163573895449e-07 1203 1.48398722853503 1.53071104843662 1 1.90274537866103 1801 1203 1795 1268 2465 2057 1298 3049 3299 2131 1769 1653 M177 PID_EPHA_FWDPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHA_FWDPATHWAY.html EPHA forward signaling 18832364 23/45 Pathway Interaction Database 6.77590733067265e-07 1.5672212118229e-06 1930 1769.81818181818 1802 6.15991765238587e-08 872 1.99568412986392 1.98226015759595 1 2.97977133142373 1788 3474 1842 1018 1928 1802 1207 1928 872 1644 1965 1654 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 98/231 Arthur Liberzon 9.87398883044012e-09 7.11838640914499e-08 2545 2037.18181818182 1802 8.97635352250575e-10 242 1.69172891155144 1.56335891963869 1 3.11021772076543 2543 643 850 1046 242 4134 2796 3995 1802 552 3806 1655 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 24/45 Jessica Robertson 3.30259046621884e-06 6.35823291894062e-06 1120 1909.36363636364 1802 3.00235947636701e-07 723 1.45467052032903 1.54684056673058 1 1.94441015525226 1117 1802 2242 3347 2337 1153 723 2012 2851 1739 1680 1656 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 53/117 Leona Saunders 4.35800573570181e-06 8.1458376057035e-06 1375 1868.72727272727 1803 3.96183124413663e-07 1227 1.57464543202551 1.75437264836683 1 2.06119630845819 1372 1612 1803 2122 2410 2246 1680 1227 2402 1588 2094 1657 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 30/104 Leona Saunders 1.68722178316094e-06 3.49373454524621e-06 1535 1968.72727272727 1803 1.53383916102251e-07 742 1.7909491765379 1.61996201527513 1 2.51369623789628 1534 1572 905 2003 2179 1803 1643 4512 2557 742 2206 1658 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 25/53 Paolo Fardin 9.41253645828058e-06 1.64640335362086e-05 1205 1812.27272727273 1803 8.55688793578121e-07 528 1.84217365320593 2.10774081302961 1 2.26658339547724 1205 3624 1904 2855 2596 951 928 1346 1803 2195 528 1659 M10654 REACTOME_PYRIMIDINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_CATABOLISM.html Genes involved in Pyrimidine catabolism 10/16 Reactome 3.22476945021826e-06 6.22375191257116e-06 1870 1750.36363636364 1805 2.9316128882808e-07 523 1.86317888720244 2.42200766707687 1 2.49489923243607 1868 975 1547 771 2330 2843 2603 1554 523 2435 1805 1660 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) 11/52 Reactome 9.66787230282568e-08 3.16808738538749e-07 2780 1935.54545454545 1806 8.78897520698106e-09 268 2.43274280503024 2.75960259013418 1 4.06682004243927 2778 1777 1459 1806 1223 3516 3434 672 268 1966 2392 1661 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 60/191 Arthur Liberzon 1.1538888092604e-08 7.71377224059447e-08 1810 1925.09090909091 1806 1.04898983210226e-09 299 1.20139584423227 1.31978958354832 1 2.19796761992893 1806 1875 2928 2411 299 1740 1478 1078 2701 3859 1001 1662 M17 PID_NOTCH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NOTCH_PATHWAY.html Notch signaling pathway 18832364 31/87 Pathway Interaction Database 2.44511325582166e-07 6.73308177611858e-07 4240 2404.72727272727 1807 2.2228304796139e-08 1272 1.46110051897231 -0.843905245944522 -1 2.31947454645729 4236 1272 1807 1423 1558 1540 3997 1965 1526 2763 4365 1663 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 12/30 Arthur Liberzon 1.03347288828984e-06 2.26725372402912e-06 1810 1732.72727272727 1807 9.39521248886184e-08 553 1.78465062379883 2.17032392763389 1 2.59105916188905 1807 2599 2065 2371 2050 1642 1869 553 861 1629 1614 1664 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 17/32 Kate Stafford 1.59312729343155e-06 3.33574374308321e-06 2200 1727.27272727273 1808 1.44829858826717e-07 604 1.83532203067257 2.05132337159758 1 2.58546339477718 2200 2026 1654 1492 2155 2370 1600 1193 604 1808 1898 1665 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 273/678 Arthur Liberzon 4.73114889344986e-07 1.15831576356876e-06 1170 1861.45454545455 1808 4.30104537354023e-08 1127 1.53391833985702 1.81257055567785 1 2.34211082472068 1166 2287 1127 2253 1808 2420 1584 1473 2920 1869 1569 1666 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 5/13 Arthur Liberzon 2.95864340942645e-06 5.76032661475326e-06 1880 1834.45454545455 1808 2.9586473485407e-07 20 2.52174964628496 3.52687399402316 1 3.39855935560247 1878 1548 4561 1055 2734 2138 1808 614 20 2257 1566 1667 M19358 BIOCARTA_MET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MET_PATHWAY.html Signaling of Hepatocyte Growth Factor Receptor 29/65 BioCarta 4.74283592176346e-07 1.16057071171716e-06 2135 1636.18181818182 1809 4.31166994930973e-08 271 2.05417265193495 2.74533379223048 1 3.13603106073494 2131 823 1399 271 1809 2968 2334 1748 540 1835 2140 1668 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 91/262 Arthur Liberzon 1.78483558899131e-06 3.66991644142749e-06 1445 1844.36363636364 1809 1.62257912455478e-07 1045 1.80961037126615 2.31969845227159 1 2.52994308214352 1445 2296 1418 1045 2197 2549 1405 1568 1809 2703 1853 1669 M187 PID_TRKR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TRKR_PATHWAY.html Neurotrophic factor-mediated Trk receptor signaling 18832364 48/98 Pathway Interaction Database 4.7772710172702e-07 1.16777735977716e-06 2655 2097.63636363636 1810 4.34297459513511e-08 440 1.86807831503562 -1.65612414838442 -1 2.85063575198585 2655 806 1385 440 1810 3966 2601 4682 658 1105 2966 1670 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 192/538 John Newman 1.47038275321014e-08 8.75503631708099e-08 3075 1773.36363636364 1810 1.33671160276139e-09 214 1.85753345349135 2.16228570595886 1 3.37210498393574 3071 762 721 214 415 3435 2693 2071 1810 568 3747 1671 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 18/50 Reactome 2.18934446863976e-07 6.14695517078843e-07 2775 1967.36363636364 1811 1.99031335137622e-08 847 1.9401402162386 -2.54311462774164 -1 3.09968153862806 2775 1142 1634 2440 1522 2419 3542 1811 847 1509 2000 1672 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 243/721 Arthur Liberzon 1.26953562548733e-08 8.0434968418917e-08 1815 1952.72727272727 1812 1.15412330255757e-09 430 1.70443006334789 1.82118747434817 1 3.11030523632602 1812 1233 430 1615 1110 3650 1986 3300 2567 500 3277 1673 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 85/188 Kevin Vogelsang 6.20867028904754e-08 2.26940943638664e-07 2045 1925.18181818182 1813 5.64424587660349e-09 1040 1.42639247881183 1.67084446199945 1 2.43765932871219 1414 1605 2044 1813 1040 2856 1791 1764 2425 2381 2044 1674 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 170/490 Jessica Robertson 4.52648064121964e-09 4.17541107967623e-08 2255 1791.09090909091 1815 4.11498240957531e-10 76 1.87935696878029 2.12623585990283 1 3.56716463132157 2254 285 525 346 76 4679 2686 3014 1815 943 3079 1675 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 74/158 Arthur Liberzon 1.01782876683411e-08 7.25320069136774e-08 3065 1920.54545454545 1815 9.25298883220992e-10 250 1.4818203781136 -1.10446771551482 -1 2.72119841737831 3065 1105 1909 485 250 3842 2642 1604 1804 1815 2605 1676 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 14/22 Jessica Robertson 4.01096486888916e-07 1.00924926617886e-06 565 1662.54545454545 1816 3.64633236377705e-08 223 1.24003596262673 1.24003596262673 1 1.91247011824308 561 2648 2685 3181 2065 489 223 335 1816 3631 654 1677 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 101/224 Arthur Liberzon 1.10304178491116e-08 7.53477230917447e-08 1780 1989.27272727273 1817 1.00276526403783e-09 283 1.46900540541339 1.77872690320775 1 2.69141529955604 1780 3341 1978 1817 283 2852 1668 1285 2764 2546 1568 1678 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 110/297 Arthur Liberzon 3.44993751794217e-07 8.9203157362956e-07 1820 2052.81818181818 1818 3.13630732631401e-08 831 2.12516970010259 2.6946234205082 1 3.30689462299043 1818 4046 1872 831 1692 3874 2487 1417 979 2322 1243 1679 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 9/30 Reactome 4.44008568537283e-07 1.09911471324126e-06 3380 2451.36363636364 1819 4.44008657251933e-08 178 1.95030904924115 -1.53206034366877 -1 2.9893195611701 3376 869 3936 1384 1819 1716 3167 4428 178 1667 4425 1680 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 15/37 Broad Institute 6.35309052773755e-07 1.48481706797896e-06 1315 1794.36363636364 1819 5.77553851123974e-08 1023 2.48057613455103 2.48057613455103 1 3.71873420963822 1312 3568 1788 1229 1905 1819 2024 1127 1932 2011 1023 1681 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 19/111 Jessica Robertson 5.55009396720453e-06 1.01473821031293e-05 1430 1738.09090909091 1819 5.04555269896768e-07 330 1.95066277728686 2.13948609462469 1 2.50552418791325 1429 3154 1819 2329 2460 918 330 1409 1884 2030 1357 1682 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 0.00024540432290526 0.000347421346566177 980 2041.90909090909 1822 2.45431427594805e-05 674 2.38400076161736 2.38400076161736 1 2.12116090554267 980 1822 4215 3088 3411 718 674 1559 2719 2049 1226 1683 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 41/105 John Newman 2.10324629763696e-06 4.24636456300163e-06 1690 2061.18181818182 1824 1.91204391671579e-07 913 2.57155489364323 3.21138282602901 1 3.55327704116739 1689 3344 913 2769 2234 2586 1819 2173 1564 1824 1758 1684 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 301/708 Jessica Robertson 2.06519182470368e-08 1.08249316449233e-07 3630 2207.45454545455 1824 1.87744713099103e-09 460 1.67687057884438 -1.52945494719777 -1 3.00438210081714 3626 460 674 960 549 3059 3737 4624 1824 461 4308 1685 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 20/41 Pathway Interaction Database 0.00537057773904999 0.00674344246655634 925 2307.63636363636 1825 0.000489430293106162 924 1.4568477735697 1.59921079889618 1 0.81357247396245 924 3996 2372 1405 4566 1581 1222 1825 3177 2597 1719 1686 M13 PID_ERBB4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB4_PATHWAY.html ErbB4 signaling events 18832364 25/81 Pathway Interaction Database 3.54904758425878e-08 1.56258301829832e-07 3690 2280.09090909091 1825 3.22640694682921e-09 386 2.02649331555295 -1.74844499673784 -1 3.54769107265718 3690 829 1255 782 772 4373 3166 3899 386 1825 4104 1687 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 137/334 Yujin Hoshida 8.79925673739323e-09 6.69372030380271e-08 1825 1724 1825 7.99932433871571e-10 205 1.77447271367577 2.08077812801306 1 3.27453384230947 1825 2292 1287 985 205 3696 2112 1220 1493 1923 1926 1688 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 68/143 Reactome 9.94488900501151e-08 3.24524720595292e-07 1275 2127.45454545455 1826 9.04080859505522e-09 1234 1.36308578902285 1.47637933581838 1 2.2750085263178 1272 3174 3126 2309 1234 1826 1457 1661 2667 3317 1359 1689 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 58/120 John Newman 4.99075281336583e-07 1.21237261189385e-06 570 1507.54545454545 1826 4.53704904139132e-08 392 1.52723974916138 1.71197778930136 1 2.3241317592537 487 2728 2005 2504 1826 567 392 569 2617 2387 501 1690 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 138/350 Leona Saunders 1.17124356613923e-08 7.79608998711424e-08 3540 2078.36363636364 1828 1.06476688397704e-09 305 1.90734857670868 2.35033530820025 1 3.48725476283759 3537 1828 866 934 305 2899 3756 2248 1502 1028 3959 1691 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 91/235 Kevin Vogelsang 2.63856349096717e-07 7.15527113349084e-07 1610 1863.54545454545 1829 2.39869437038414e-08 700 1.85042940398071 2.06721988357633 1 2.92495703026857 1608 2009 700 1426 1588 3271 2285 1829 2483 1140 2160 1692 M7146 BIOCARTA_CLASSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CLASSIC_PATHWAY.html Classical Complement Pathway 8/17 BioCarta 0.000257368096235236 0.000363151731092537 1730 2416 1830 2.5739790834635e-05 1539 1.85713849718638 2.09213623599676 1 1.64319930689081 1730 2821 3823 3612 3206 1830 1616 1708 3005 1539 1686 1693 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 37/83 Reactome 1.43195936596891e-07 4.33193130337659e-07 3785 2303.63636363636 1832 1.30178132652165e-08 540 1.48618819198652 -1.2077603293412 -1 2.43251829160687 3785 540 1892 1325 1372 1659 3895 4461 1609 1832 2970 1694 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 16/30 Jessica Robertson 1.16522349609527e-07 3.66951431633228e-07 4005 2266.72727272727 1832 1.05929414346454e-08 459 2.11990372189221 -2.30836218123675 -1 3.50905169988627 4001 1059 745 1832 1305 4179 4142 2591 1556 459 3065 1695 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 10/33 Arthur Liberzon 5.19975360184983e-06 9.57408462800326e-06 2245 1898.18181818182 1832 4.7270599014862e-07 17 3.03611476952321 3.69456489753489 1 3.91945452136751 2241 1288 1554 846 3731 3591 3245 676 17 1859 1832 1696 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 42/82 Pathway Interaction Database 3.02960118507531e-09 3.12015629742042e-08 1505 1892.18181818182 1833 2.75418289931576e-10 38 2.04368185789499 2.17556198737151 1 3.94557507857984 1501 3089 1489 2555 38 1909 1833 2904 1787 1889 1820 1697 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 14/53 Leona Saunders 1.90170273454721e-06 3.8761979182637e-06 845 1595.27272727273 1833 1.72882216218245e-07 427 2.16460829162487 2.88258243903255 1 3.01302813627841 1833 844 928 640 2215 2706 2491 2397 427 841 2226 1698 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 97/260 John Newman 8.17473092546503e-06 1.44390460296755e-05 1835 1915.18181818182 1834 7.43160118289107e-07 982 1.62850257233881 2.01104289393562 1 2.02756068943405 1255 3431 2184 2136 2548 1834 1164 1374 1831 2328 982 1699 M2668 KEGG_BETA_ALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BETA_ALANINE_METABOLISM.html beta-Alanine metabolism 11/30 KEGG 3.02339160401117e-06 5.87136885884638e-06 1835 1557.18181818182 1835 2.74854159906568e-07 250 3.07597731056386 3.51299338881786 1 4.138930679249 1835 2122 1165 1067 2619 2118 1943 599 250 1481 1930 1700 M8601 BIOCARTA_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAC1_PATHWAY.html Rac 1 cell motility signaling pathway 17/38 BioCarta 8.09367959861755e-08 2.76930509970378e-07 3085 2188.72727272727 1836 7.35789081489057e-09 1151 1.86572957235501 2.21904818012714 1 3.1469816502461 3083 1208 1609 1461 1151 3856 2523 2850 1836 1407 3092 1701 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 3/15 Jessica Robertson 0.000260045205756943 0.000366708346126101 1755 2615.36363636364 1836 2.60075641348728e-05 1480 1.51066073663357 -1.51066073663357 -1 1.33499047707486 1814 2788 4313 4009 3208 1480 1755 1564 4249 1753 1836 1702 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 20/49 Arthur Liberzon 5.14322811680547e-07 1.24104876186151e-06 2790 1972.54545454545 1837 4.67566301745969e-08 748 1.68775112458595 1.99914832316656 1 2.56398823790212 2789 831 1126 1309 1837 4297 2596 3079 748 866 2220 1703 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 4/8 Leona Saunders 3.51699281356272e-06 6.72953381966309e-06 2290 1815.36363636364 1838 3.51699837973242e-07 2 3.20508990983385 3.20508990983385 1 4.2638180312757 2290 1168 4213 684 2424 2355 1838 635 2 3097 1263 1704 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 118/381 John Newman 6.53263902520474e-08 2.36021175575246e-07 2325 1789.36363636364 1839 5.93876292653065e-09 918 1.77973955571475 1.93282377987678 1 3.03371860793039 2322 1868 1046 1051 1059 4077 1839 1988 1919 918 1596 1705 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 29/67 Arthur Liberzon 7.18159159803322e-07 1.64723143555476e-06 1675 1926.27272727273 1841 6.52872176578562e-08 1363 1.59977376555306 1.53595300472272 1 2.37973632730075 1675 1888 1446 1638 1949 1705 1363 2526 2979 1841 2179 1706 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 8/18 Arthur Liberzon 2.69965364672468e-07 7.2913988406639e-07 1195 2176.36363636364 1841 2.69965397469058e-08 148 2.09714656072664 2.09714656072664 1 3.3105256105196 1195 3837 4611 3814 4342 486 148 289 1841 2892 485 1707 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 162/475 Reactome 1.34371795860247e-07 4.11815719686799e-07 1845 1955.36363636364 1843 1.22156185515836e-08 626 1.76022471030784 1.88886738722135 1 2.89099858032622 1843 895 626 1616 1353 3532 2031 4365 2159 712 2377 1708 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 80/290 Arthur Liberzon 8.17090561292313e-08 2.78669606995346e-07 1810 2105.09090909091 1843 7.42809628763137e-09 825 1.59363861888288 1.7540109528218 1 2.68692323898812 1809 1654 1213 3343 1157 3274 1843 2581 2680 825 2777 1709 M853 REACTOME_MYOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MYOGENESIS.html Genes involved in Myogenesis 17/38 Reactome 4.1327794712496e-06 7.75889607462966e-06 1950 1886.54545454545 1844 3.75707930440504e-07 642 1.94452001138885 2.40841986688611 1 2.55593010302888 1946 3131 1844 2659 2799 1823 1438 642 909 2220 1341 1710 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 18/53 Leona Saunders 5.2578307398922e-07 1.26479439667017e-06 2980 1910.09090909091 1845 4.77984726952156e-08 400 1.92608309880047 -1.73608743779126 -1 2.92197824603976 2980 400 1050 1385 1845 2207 3144 3652 820 726 2802 1711 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 2/6 Arthur Liberzon 3.21647600480066e-05 5.11622761659738e-05 1725 1989.8 1846 3.57391331855586e-06 436 1.51395346754403 1.51395346754403 1 1.67099346010614 1721 1491 4186 NA 2934 820 436 1971 2710 2527 1102 1712 M15955 KEGG_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPHINGOLIPID_METABOLISM.html Sphingolipid metabolism 23/46 KEGG 4.68043480607748e-07 1.14950301369387e-06 1645 2382.36363636364 1847 4.25494163802402e-08 560 1.39900473929111 -1.43808897414682 -1 2.13730734705121 3535 560 1847 1540 1804 2657 3823 3830 1642 1643 3325 1713 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 139/333 Arthur Liberzon 1.07186378516341e-08 7.39899659922656e-08 4215 2177.54545454545 1847 9.74421627623314e-10 270 1.66191231519165 -1.32868750973697 -1 3.04822257816775 4214 898 1510 1298 270 1872 4317 2643 1685 1847 3399 1714 M1988 GYORFFY_MITOXANTRONE_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/GYORFFY_MITOXANTRONE_RESISTANCE.html Genes associated with resistance to mitoxantrone [PubChem=4212]. 16044152 35/111 Arthur Liberzon 4.23455247456194e-07 1.0560464553378e-06 1635 1958.09090909091 1847 3.84959389966125e-08 1040 1.50461087896329 1.68574162572865 1 2.31289794700049 1635 1665 1883 2346 1770 2026 1040 3657 1684 1986 1847 1715 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 66/186 Reactome 3.66770873830954e-06 6.9893790759327e-06 1105 1949.27272727273 1848 3.33428622991726e-07 1105 1.45488631897531 1.5359870909169 1 1.92931732832445 1105 1709 2041 2611 2362 1218 1290 2721 2740 1848 1797 1716 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 131/344 Arthur Liberzon 6.6979338590762e-08 2.40042428716015e-07 3955 2351.45454545455 1848 6.08903096635984e-09 1069 1.62783717759152 -1.20882204304196 -1 2.77171589990194 3953 1702 1755 1340 1069 1848 3968 2064 1344 2792 4031 1717 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 21/84 Jessica Robertson 6.06941728174412e-08 2.23485350831027e-07 1535 1858.63636363636 1848 5.51765222653524e-09 823 1.65990335061444 1.90825788889174 1 2.83956714514436 1532 2310 2127 2641 1027 2526 1792 823 1103 2716 1848 1718 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 132/340 Arthur Liberzon 2.40772892936952e-08 1.18764397505532e-07 1540 1747.54545454545 1850 2.18884450520021e-09 577 1.66873121211951 1.8088626683401 1 2.97251804470785 1540 1095 672 2392 614 2758 1850 2627 2752 577 2346 1719 M1088 REACTOME_METABOLISM_OF_PORPHYRINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_PORPHYRINS.html Genes involved in Metabolism of porphyrins 10/22 Reactome 1.74562619856315e-06 3.59718749624755e-06 3230 2046.09090909091 1851 1.58693416696411e-07 90 2.05813434107982 -0.772526732212725 -1 2.88199642923044 3230 1585 1652 720 2192 4108 3465 1924 90 1851 1690 1720 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 12/30 Arthur Liberzon 5.11874643606902e-07 1.23705238779884e-06 2245 2044.63636363636 1851 4.65340693368148e-08 966 1.7510890413692 1.43489774349704 1 2.66084049711734 2243 966 1387 2315 1833 1851 1149 4472 2000 1211 3064 1721 M7739 BIOCARTA_PYK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PYK2_PATHWAY.html Links between Pyk2 and Map Kinases 20/47 BioCarta 0.000399603885146226 0.000550262652305382 1855 2273.09090909091 1852 3.6334226082848e-05 1235 1.11956278877163 -1.19643571501781 -1 0.938617612561793 1852 1727 2799 1537 3265 1235 2786 1702 2865 3613 1623 1722 M13143 BIOCARTA_UCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_UCALPAIN_PATHWAY.html uCalpain and friends in Cell spread 24/44 BioCarta 1.92201882017641e-07 5.50524461573756e-07 2050 1706.18181818182 1852 1.74728998917511e-08 675 2.43251256090555 2.83019502732567 1 3.91628426770265 2050 2525 1134 675 1478 2529 2308 1996 804 1417 1852 1723 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 44/108 John Newman 5.78449801137645e-07 1.37246368006633e-06 1475 1799.72727272727 1852 5.25863593845914e-08 476 2.11798610139357 2.28735414580507 1 3.19377677226549 1472 1761 549 1007 2216 3171 2425 1852 2637 476 2231 1724 M3397 KEGG_BUTANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BUTANOATE_METABOLISM.html Butanoate metabolism 16/48 KEGG 9.99496932015215e-08 3.25705328471717e-07 3025 2077.63636363636 1853 9.08633615840035e-09 982 2.45154786326326 -1.91522746551738 -1 4.09067207548901 3023 1730 1853 1772 1237 1800 3094 2465 982 2651 2247 1725 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 26/59 Arthur Liberzon 5.41663595999324e-07 1.29634096570625e-06 1190 1998 1855 4.92421572147961e-08 919 1.21938272919744 -1.3708440573422 -1 1.84651749022512 2683 1047 2744 2752 1855 919 2262 1188 1187 3643 1698 1726 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 75/170 John Newman 3.81130732518363e-06 7.22483257516605e-06 1130 1814.63636363636 1855 3.46483084359617e-07 1130 1.56016350997824 1.8579880042873 1 2.06315051190267 1130 2336 1855 1568 2375 2043 1256 1192 2247 2342 1617 1727 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 39/82 Arthur Liberzon 2.99623094769958e-07 7.9368785872924e-07 4640 2364.18181818182 1856 2.72384668705754e-08 285 1.88874746366228 -1.7679494538366 -1 2.96365280091275 4636 529 533 685 1856 3536 4607 4295 899 285 4145 1728 M13036 KEGG_PRION_DISEASES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRION_DISEASES.html Prion diseases 24/49 KEGG 6.28886267221741e-06 1.13431911016208e-05 1545 2018 1857 5.71716422678938e-07 703 1.70645108409803 1.96049757419704 1 2.17061118808304 1545 3502 2248 1653 3295 2078 1182 703 1857 3024 1111 1729 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 209/534 Leona Saunders 2.10001734144493e-07 5.94962591415414e-07 1160 2081.63636363636 1857 1.90910685627529e-08 1160 1.49869582080792 1.73461986745457 1 2.39986662264565 1160 3169 2706 2220 1500 1857 1526 1316 2336 3652 1456 1730 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 264/702 Leona Saunders 1.70371269941567e-08 9.53891100897413e-08 4345 2254.63636363636 1860 1.54882973873588e-09 407 1.62580463545244 -1.25669401262993 -1 2.93585858919752 4342 1090 1097 407 475 2265 4173 4029 1860 1067 3996 1731 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 135/325 Arthur Liberzon 1.10213475805278e-07 3.51333569811927e-07 1135 2005.09090909091 1860 1.00194073933315e-08 1131 1.63887821598994 1.70370729684781 1 2.7207783521102 1131 2548 1174 3802 1279 1860 1564 2090 3001 1558 2049 1732 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 24/64 Arthur Liberzon 4.09177640154221e-08 1.69531955947187e-07 1780 1760.54545454545 1861 3.71979679785917e-09 818 1.55671728539788 1.7852188540844 1 2.71109714891045 1778 2490 2025 2697 844 1861 1432 818 2403 2119 899 1733 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 44/93 Jessica Robertson 7.00939557934459e-08 2.48457092925936e-07 1155 1853.18181818182 1861 6.37217800242743e-09 1087 1.27965806632604 1.38168564804379 1 2.17394662321516 1152 1265 1861 2652 1087 2041 1395 1986 3289 2065 1592 1734 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 55/140 Jessica Robertson 5.96552791598344e-09 5.15765015023956e-08 1180 1762.90909090909 1862 5.42320721105418e-10 116 1.76342377488769 1.86404188721036 1 3.30549715993493 1176 2730 1862 2366 116 2164 1663 1846 1876 1943 1650 1735 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 273/662 Arthur Liberzon 1.31706534802375e-08 8.21806687195643e-08 1870 1547.72727272727 1863 1.19733214173506e-09 329 1.80883320788042 2.02724287715419 1 3.29648539990503 1870 1863 497 661 367 3860 1766 1902 1972 329 1938 1736 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 183/489 Arthur Liberzon 4.6611147598578e-07 1.14593965779876e-06 1685 1937.63636363636 1863 4.23737795218467e-08 1277 1.51315182453795 1.80034115869775 1 2.31221856093313 1683 1957 1540 1900 1802 3084 1486 1277 2813 1863 1909 1737 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 5/25 Arthur Liberzon 5.33878111056391e-05 8.20785048691027e-05 1865 2020.90909090909 1864 5.33890937652775e-06 53 3.66213862770863 3.66213862770863 1 3.84864116233244 1864 1952 4236 2451 2952 1762 1798 1087 53 2242 1833 1738 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 23/64 Arthur Liberzon 7.0176122484409e-06 1.2551347708471e-05 1500 1907.63636363636 1865 6.37966784862461e-07 538 1.94663219606231 1.94924457092094 1 2.454113775868 1496 3656 1865 2534 2519 908 538 3057 1369 2024 1018 1739 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 38/128 Yujin Hoshida 4.45379344118569e-09 4.12667279105694e-08 2220 1936.36363636364 1865 4.04890313654745e-10 74 2.16327552208011 -2.0926932648123 -1 4.10890134946979 2219 1662 697 1624 74 3519 2140 3597 1865 962 2941 1740 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 247/926 Jessica Robertson 8.71389626313692e-09 6.66871748972617e-08 2950 1911.81818181818 1865 7.9217239069559e-10 201 1.7477725141231 2.18108218569989 1 3.2259931029539 2948 1865 1290 1192 201 2470 3240 2457 1594 921 2852 1741 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 70/200 Jessica Robertson 6.80741740530796e-09 5.67607792905216e-08 2300 1908.18181818182 1866 6.18856129670185e-10 143 1.99388824715681 2.14590868312802 1 3.71616432276748 2298 2481 1283 1532 143 3179 1866 2313 1698 1234 2963 1742 M1011 REACTOME_MEIOTIC_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_RECOMBINATION.html Genes involved in Meiotic Recombination 54/98 Reactome 0.00129229923440073 0.00170583498940897 355 2033.72727272727 1868 0.000117550815193275 353 1.54791936381861 -1.57766471087786 -1 1.10210482968413 353 2797 2036 1957 3613 1271 1868 1812 3395 1404 1865 1743 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 16/31 Leona Saunders 2.95767644698953e-07 7.85250528645491e-07 1635 2335 1871 2.68879713147195e-08 1631 1.93011697764004 1.56242210908646 1 3.03087043801864 2585 1686 1631 1853 1631 2751 1846 3823 1871 2160 3848 1744 M281 PID_FAK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FAK_PATHWAY.html Signaling events mediated by focal adhesion kinase 18832364 60/118 Pathway Interaction Database 1.28229457828882e-07 3.96099696365288e-07 3340 2487.54545454545 1873 1.16572241184436e-08 982 1.77304118228044 -1.49014960007093 -1 2.91975500553051 3336 1873 1545 982 1341 4478 3283 2909 1587 1733 4296 1745 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 20/61 Reactome 1.07349612358254e-07 3.44531783458488e-07 4250 2603.27272727273 1873 9.75905614512803e-09 1069 1.56503346456066 -1.5015348720686 -1 2.60160303048934 4250 1276 1717 1796 1264 3520 3717 3562 1873 1069 4592 1746 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 74/243 Reactome 7.89343854279329e-08 2.72375942647491e-07 1345 1780.45454545455 1873 7.17585347818551e-09 1138 1.55600386401206 1.73844720408484 1 2.62744051401121 1344 2513 1873 1898 1138 1939 1509 1677 2049 2063 1582 1747 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 50/116 Arthur Liberzon 6.19692951767447e-07 1.45412176864409e-06 2625 1958.09090909091 1874 5.63357387565244e-08 762 1.80320622606643 -1.85775109212622 -1 2.70746872877294 2623 1508 1202 1398 1896 1663 3158 2650 1874 762 2805 1748 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 55/160 John Newman 1.15713197811137e-07 3.65063971395134e-07 1210 1750.09090909091 1875 1.05193821724813e-08 706 2.29233402126572 2.42341624957276 1 3.79579409754263 1209 2262 706 1970 1300 2281 1794 3000 1903 951 1875 1749 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 15/18 Arthur Liberzon 4.02522769528761e-09 3.84943203675872e-08 2360 1624.54545454545 1875 3.65929791150214e-10 63 1.41895382865452 -1.45655805849416 -1 2.70616854546076 2358 1469 1875 2314 63 1204 2242 720 2594 2016 1015 1750 M200 PID_ERA_GENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERA_GENOMIC_PATHWAY.html Validated nuclear estrogen receptor alpha network 18832364 37/121 Pathway Interaction Database 2.25672078949688e-08 1.14324255346836e-07 3180 1905 1876 2.05156437513265e-09 359 1.35884001792721 -1.11685910778371 -1 2.4262912467922 3180 359 1876 1414 584 932 2710 4661 1992 1298 1949 1751 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 14/31 Leona Saunders 1.50554992931884e-06 3.17936321261293e-06 2035 1674.27272727273 1877 1.36868269057199e-07 372 1.83729088648948 -1.43106969672038 -1 2.59809149070514 2035 851 1767 2039 2139 1248 2082 2331 372 1877 1676 1752 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 49/114 Arthur Liberzon 2.10145548584718e-05 3.46130770006324e-05 1550 1906.72727272727 1877 1.91043232669668e-06 1154 1.79885121157748 2.20286170701494 1 2.06396688360812 1549 2299 1384 2121 2741 2462 1877 1154 2054 1817 1516 1753 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 52/125 Arthur Liberzon 8.36154140998193e-08 2.83582175257329e-07 2020 1905.27272727273 1877 7.60140157070828e-09 802 1.83183722498709 1.87337463897431 1 3.08495744680222 2020 802 1029 1877 1164 3476 2355 3382 1039 1115 2699 1754 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 298/658 Arthur Liberzon 1.60751507432484e-08 9.22009258052164e-08 2385 1796.18181818182 1877 1.46137735097342e-09 450 1.66717834446239 1.97621431075869 1 3.01690171807736 2382 461 599 1255 450 4447 2400 1892 1877 764 3231 1755 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 15/48 Jessica Robertson 1.11879089044869e-05 1.92886464777137e-05 1795 1811.63636363636 1880 1.01708780000281e-06 764 1.75807448061669 2.22535282474424 1 2.13201284848936 1793 2647 1908 2360 2802 1787 1177 764 1880 2010 800 1756 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 33/83 John Newman 3.92439631932677e-08 1.65226605142545e-07 1560 1678.45454545455 1880 3.56763308120983e-09 430 2.39646533714631 2.11462404761468 1 4.18044469676787 1556 2380 1661 1923 813 2258 2051 1338 430 2173 1880 1757 M36 PID_IL27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL27_PATHWAY.html IL27-mediated signaling events 18832364 11/27 Pathway Interaction Database 1.46431599015801e-05 2.47004489916502e-05 1885 1835.81818181818 1882 1.33120521519034e-06 1089 1.43605515024025 -1.22245216462543 -1 1.70182848470893 1882 1221 1758 2320 2675 1385 2019 2049 2090 1089 1706 1758 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 33/96 Arthur Liberzon 2.4916586055538e-08 1.20328077343124e-07 3550 1993.63636363636 1882 2.26514421252147e-09 634 1.84731945553573 -2.36919058009045 -1 3.28793881925129 3547 939 1306 1926 634 1882 4056 2403 1535 1557 2145 1759 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 667/1499 Jessica Robertson 2.55942992790524e-08 1.22884104940204e-07 4655 2362.45454545455 1883 2.55942995738331e-09 548 1.52342260413548 -1.10612743092284 -1 2.70787611221039 4655 749 4336 548 689 1195 4287 2818 1883 1365 3462 1760 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 8/24 Jessica Robertson 2.76275214092946e-05 4.44888540632146e-05 1900 2067.63636363636 1883 2.76278648912773e-06 362 2.51465891532339 3.24172746261654 1 2.81476121947556 1897 2435 4447 1842 3174 1883 1625 924 362 2888 1267 1761 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 41/112 Jessica Robertson 6.99025357140599e-06 1.25071890933977e-05 1315 1967.81818181818 1883 6.35479616568411e-07 548 1.09488493380623 -0.888520934480801 -1 1.38074935030642 1311 1883 3420 2506 2642 548 1214 713 2499 3974 936 1762 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 3/11 Leona Saunders 5.4778570817921e-07 1.30898716396113e-06 3360 2107.81818181818 1885 5.47785843210389e-08 27 4.00007467298419 -1.79853554857737 -1 6.0529960544412 3356 2443 4251 1195 3216 3395 1885 380 27 1748 1290 1763 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 22/48 Arthur Liberzon 3.91977550292137e-05 6.15964721887644e-05 1465 2187.63636363636 1885 3.56349576721472e-06 1462 2.04615792690837 2.82101203993729 1 2.21597935432785 1680 3475 2131 3069 2866 1715 1477 1463 1462 2841 1885 1764 M1061 REACTOME_MEIOTIC_SYNAPSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_SYNAPSIS.html Genes involved in Meiotic Synapsis 50/198 Reactome 0.000410005358546599 0.000564088405798404 850 2085.45454545455 1886 3.72801626888502e-05 847 1.70523900702195 -1.74011034267225 -1 1.42490918104874 847 3461 1886 2263 3268 1119 2127 1464 3548 1178 1779 1765 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 15/31 Jessica Robertson 5.88495008616523e-06 1.06928561860296e-05 1740 1813.09090909091 1886 5.34996893484741e-07 1155 1.34433945901874 1.71546145202445 1 1.71887049219968 1739 1349 2063 1886 2476 1892 1481 1155 1661 2007 2235 1766 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 84/216 Kevin Vogelsang 2.27011256722524e-08 1.14630899676912e-07 2170 1791.36363636364 1887 2.06373871877257e-09 587 1.907702377549 2.24329555410384 1 3.40574752495054 2169 2139 899 1339 587 3681 1887 2045 1541 1042 2376 1767 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 13/17 Arthur Liberzon 2.24460427337847e-06 4.50073411427107e-06 2255 2015.36363636364 1887 2.04055142135875e-07 989 1.49368538775042 1.64413147187352 1 2.05421050177482 1887 1811 2253 3229 2251 1700 989 1212 2528 2923 1386 1768 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 24/43 Yujin Hoshida 5.31666293567861e-05 8.17921290761326e-05 1005 1964.27272727273 1888 4.8334467508697e-06 1001 1.43391534225068 1.62259279443276 1 1.5075003830177 1001 1933 2202 3113 3684 1320 1200 1002 1888 3035 1229 1769 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 30/52 John Newman 6.48156773380734e-07 1.50882396426335e-06 680 1653.27272727273 1888 5.89233603944211e-08 147 1.53845945232267 1.7182797914903 1 2.30361165562697 678 3469 1888 3017 1914 262 147 1170 3011 2286 344 1770 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 19/51 Arthur Liberzon 4.92496468120338e-06 9.11828703916201e-06 1890 2022.45454545455 1889 4.47725064214899e-07 993 2.00651378396926 1.92020336530297 1 2.60123034599476 1889 3658 1550 2077 2431 1720 993 1018 3018 2029 1864 1771 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 85/220 John Newman 1.10835753595053e-07 3.52693436112653e-07 2440 2042.81818181818 1890 1.0075978107177e-08 1282 1.73629599891617 2.12713709111953 1 2.88175690091866 2438 1960 1606 1890 1282 4130 2537 1432 1380 1945 1871 1772 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 2/10 Jessica Robertson 0.00193704760036066 0.00252480934928453 1930 2226.8 1890.5 0.000215413028979762 172 2.47685408470999 2.47685408470999 1 1.65500758468288 1927 2970 4454 NA 3704 1821 1152 1681 172 2533 1854 1773 M636 REACTOME_HS_GAG_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HS_GAG_DEGRADATION.html Genes involved in HS-GAG degradation 8/21 Reactome 1.34012570767404e-05 2.27612506928618e-05 1725 2284.18181818182 1891 1.34013378945874e-06 821 1.53508400613621 1.99386664297753 1 1.83320538364599 1725 2651 3941 3865 2774 1516 914 821 1891 3675 1353 1774 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 80/295 Arthur Liberzon 9.95900842318852e-08 3.24759314342807e-07 1500 1938.36363636364 1891 9.05364443092286e-09 1103 1.45248622867366 1.73079163582484 1 2.4241018289049 1500 1103 1965 3398 1235 2508 1604 2095 2629 1891 1394 1775 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 29/94 Jessica Robertson 2.70376212983295e-06 5.30784639312829e-06 1645 1656 1891 2.45796859337799e-07 691 2.11499732441564 2.52229100000877 1 2.86970771799217 1641 691 731 2043 2291 1954 1591 1891 2198 1238 1947 1776 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 26/74 Arthur Liberzon 9.51897792011323e-06 1.66419479865774e-05 2395 2212.45454545455 1892 8.6536537337763e-07 1288 1.86367112535634 1.93775847182245 1 2.29079592672673 2394 1892 1423 1808 2582 2604 1873 3755 1887 1288 2831 1777 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 46/118 John Newman 2.33407251508812e-07 6.50265386783765e-07 4185 2396.72727272727 1893 2.1218843297452e-08 874 1.99985481850634 -1.51840048428961 -1 3.18251810176862 4182 1617 1110 1893 1540 3069 4044 2781 1585 874 3669 1778 M994 REACTOME_DSCAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DSCAM_INTERACTIONS.html Genes involved in DSCAM interactions 7/19 Reactome 2.26527389635008e-05 3.70638040443312e-05 1235 2065.81818181818 1894 2.26529698827759e-06 833 1.6717753836901 -1.6717753836901 -1 1.90538708931475 1232 2822 4068 1894 3260 833 1064 899 3037 2676 939 1779 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 21/56 Jessica Robertson 6.20170019098589e-06 1.11989083217572e-05 1565 1915.09090909091 1894 5.63792515760578e-07 884 1.47792099592165 1.60618227129506 1 1.88203360469125 1561 1894 2369 3344 2492 1314 884 2561 1105 2209 1333 1780 M3342 BIOCARTA_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTEGRIN_PATHWAY.html Integrin Signaling Pathway 35/74 BioCarta 5.61811057612874e-07 1.338407023881e-06 2695 2216.72727272727 1895 5.10737455528967e-08 676 1.81071398491622 2.26357726040536 1 2.73551412764887 2695 1569 1469 676 1868 4594 3659 1895 970 1982 3007 1781 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 18/63 Arthur Liberzon 2.84954582445478e-05 4.56980552135356e-05 1950 1952.90909090909 1896 2.59052975801117e-06 1439 1.65852624116399 -1.88384903464055 -1 1.85148821036081 1949 1896 1829 2080 2808 1439 2716 1468 1690 1510 2097 1782 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 189/397 Arthur Liberzon 1.0778262274679e-08 7.39899659922656e-08 945 1878.18181818182 1896 9.79842029771272e-10 276 1.53674980356277 1.7100812533243 1 2.81865377532929 945 2544 2078 2868 276 1896 1642 2152 2668 1887 1704 1783 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 26/95 Antony Bosco 2.37843506220471e-07 6.60660741048682e-07 2180 1687 1896 2.16221392667181e-08 364 2.37790887478241 -2.38918179881123 -1 3.77993088022691 2178 1969 524 1918 2500 1315 2810 1350 1896 364 1733 1784 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 15/41 Arthur Liberzon 6.22906720756266e-07 1.46020054700543e-06 740 1909.72727272727 1898 5.66278997387076e-08 727 1.1207799339561 1.1207799339561 1 1.68230046829082 740 2029 3064 2423 1898 860 727 1894 3522 2556 1294 1785 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 71/169 Jessica Robertson 4.03006705058362e-08 1.67567827853015e-07 1425 1906 1898 3.66369738582577e-09 839 1.44502087423819 1.59971028621621 1 2.51845358732195 1425 2585 2042 2503 839 1898 1455 2202 2953 1651 1413 1786 M1386 KEGG_PENTOSE_PHOSPHATE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_PHOSPHATE_PATHWAY.html Pentose phosphate pathway 14/33 KEGG 5.38234707543289e-06 9.86763630496031e-06 2425 1783.45454545455 1899 4.89305476682299e-07 749 1.303038053708 -1.11083814752228 -1 1.67775324458619 2425 1899 2089 1721 2451 749 1437 2339 825 2394 1289 1787 M19580 KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS.html Pentose and glucuronate interconversions 8/32 KEGG 4.24487067258982e-06 7.95013905814568e-06 1900 1758.54545454545 1899 4.24487878112878e-07 111 3.31279315049711 4.39353459956901 1 4.34541493168481 1899 2965 3785 988 2434 2019 1687 659 111 2090 707 1788 M56 PID_LPA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LPA4_PATHWAY.html LPA4-mediated signaling events 18832364 11/19 Pathway Interaction Database 8.78100363612836e-06 1.54284900783268e-05 865 1667.90909090909 1899 7.9827624404703e-07 557 1.37916864756669 1.37916864756669 1 1.70691713644473 865 973 2083 2594 2565 827 557 1899 2929 1964 1091 1789 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 27/75 Arthur Liberzon 1.20613866839525e-07 3.76546688880755e-07 2105 1719.45454545455 1899 1.09648975865562e-08 633 2.54316536087416 -1.82907563551443 -1 4.20233864147116 2101 1274 633 1181 1322 2839 2047 2683 1899 913 2022 1790 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 8/25 Arthur Liberzon 0.00170037433428359 0.00222506398504689 1745 2212.18181818182 1901 0.000170167680993783 1317 2.81936460680907 2.81936460680907 1 1.9236721747015 1742 1590 4137 1317 3437 2396 2111 1884 1719 2100 1901 1791 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 15/38 Jessica Robertson 0.000271282378256695 0.000381635912492007 840 1769.54545454545 1902 2.46650759917709e-05 621 1.59008827445835 -1.59008827445835 -1 1.39809435591734 840 2242 2319 2247 3290 621 1314 1448 1902 2008 1234 1792 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 56/129 Kevin Vogelsang 8.43959780387797e-09 6.58738602381418e-08 870 1869 1902 7.67236166932162e-10 188 1.48207907326006 1.37414311809644 1 2.7376145929965 870 2937 1902 2916 188 950 870 2788 3478 2581 1079 1793 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 31/70 Jessica Robertson 6.31439622822696e-07 1.47724716552529e-06 3605 2244.90909090909 1902 5.74036185506648e-08 645 2.40532383020241 -1.84829889887621 -1 3.60729371996804 3605 1520 662 1120 1902 4467 3387 2814 841 645 3731 1794 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 9/96 Kevin Vogelsang 1.48713920878056e-06 3.15042239256134e-06 1570 2024.09090909091 1904 1.48714020399386e-07 898 1.56532499674071 1.59774872697781 1 2.21510666220644 1567 1904 4393 2749 2165 1254 898 930 3029 2310 1066 1795 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 93/250 Reactome 2.01564202553553e-08 1.06410983827008e-07 2340 1614.54545454545 1905 1.83240185818441e-09 308 1.68164044098932 -1.38399669209412 -1 3.01614565134359 2829 308 1905 876 539 620 2259 2651 1096 2340 2337 1796 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 9/15 Arthur Liberzon 3.11746304185215e-05 4.97223683257971e-05 1705 2114.09090909091 1906 3.11750677630682e-06 308 2.1438456476786 2.56245409166559 1 2.37306013212004 1704 1906 4614 2755 3584 2022 1898 946 308 2320 1198 1797 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 65/231 Arthur Liberzon 1.90142768223975e-05 3.15178285071647e-05 650 1867.27272727273 1907 1.72858556018067e-06 647 1.98693316901855 2.21244449182533 1 2.30056089068126 647 3009 929 2491 2720 1491 1213 1907 2687 2031 1415 1798 M103 PID_S1P_S1P1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P1_PATHWAY.html S1P1 pathway 18832364 15/45 Pathway Interaction Database 3.34070266663952e-05 5.29764219826491e-05 1465 1896.45454545455 1908 3.0370485421168e-06 1049 1.97673429601348 1.86567193408554 1 2.17408364335622 1464 2954 1928 1908 2841 1182 1049 1754 2290 1576 1915 1799 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 4/16 Reactome 5.1370390322391e-05 7.92426250702277e-05 1660 2230.72727272727 1908 5.13715778736785e-06 872 1.8570979502901 1.8570979502901 1 1.95896907061625 1657 1908 3971 3404 2940 1202 872 1609 3360 2042 1573 1800 M8516 BIOCARTA_PITX2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PITX2_PATHWAY.html Multi-step Regulation of Transcription by Pitx2 9/25 BioCarta 5.81971072248013e-07 1.37747552220302e-06 1405 2006.90909090909 1909 5.81971224658717e-08 652 1.99193474370681 1.99193474370681 1 3.00288893882685 1403 2396 3849 2596 1909 1769 2090 652 2933 1662 817 1801 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 22/49 John Newman 1.05769477194601e-07 3.40643140985497e-07 2120 1809.63636363636 1909 9.61540747997128e-09 1054 1.65192314039846 1.86088219680127 1 2.74813702423718 2120 1054 1680 2274 1258 2638 2099 1392 1470 1909 2012 1802 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 77/143 John Newman 8.06761209607642e-10 9.76868999540416e-09 1500 1729.72727272727 1910 7.33419281730442e-11 5 1.50577328784668 1.74074926606996 1 3.1024131891677 1498 2183 1719 1938 5 2431 1708 1910 2488 1960 1187 1803 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 5/23 Reactome 5.85789424856327e-07 1.38496934655739e-06 1845 2175 1911 5.85789579273547e-08 659 1.04484269752161 -1.04484269752161 -1 1.5744918326845 1842 2538 3944 3466 1911 711 659 955 3627 3270 1002 1804 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 3/11 Yujin Hoshida 1.18822858632192e-05 2.03659076646106e-05 1905 2236.54545454545 1911 1.18823493986202e-06 799 1.15208329021912 -1.15208329021912 -1 1.39013456503358 1905 1911 4369 2843 3283 1222 1956 799 2989 1755 1570 1805 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 48/106 Kevin Vogelsang 7.56087674346172e-09 6.10866696894166e-08 4435 2466.81818181818 1912 6.87352433586058e-10 167 1.77499305277995 -1.68576804593479 -1 3.29362901943436 4435 805 1117 1723 167 3687 4249 3828 1912 1768 3444 1806 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 92/252 John Newman 5.11489859263304e-07 1.23676030985957e-06 1480 2418.09090909091 1912 4.64990889256707e-08 860 1.77100746106839 1.79689692262608 1 2.69115394468629 1478 4329 2582 4051 1832 1758 860 1368 2942 3487 1912 1807 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 22/80 Jessica Robertson 1.80897718671391e-06 3.70978866386931e-06 1155 2148.90909090909 1912 1.64452606742679e-07 1153 1.51021788622566 1.54907326975041 1 2.10955151374093 1153 3351 2144 3634 2203 1631 1306 1383 3333 1912 1588 1808 M2551 KEGG_ARGININE_AND_PROLINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARGININE_AND_PROLINE_METABOLISM.html Arginine and proline metabolism 26/66 KEGG 8.53932003023421e-09 6.62504199696647e-08 4135 2079 1914 7.76301823943604e-10 186 1.72661852761385 -1.94879577097695 -1 3.18821498439782 4132 186 1111 1513 191 3576 3987 1762 2033 1914 2464 1809 M1662 REACTOME_SIGNALING_BY_BMP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_BMP.html Genes involved in Signaling by BMP 13/27 Reactome 2.03889080840255e-07 5.78343966596509e-07 1765 1896.27272727273 1915 1.85353727032778e-08 932 1.93339595277544 1.87161302445326 1 3.10207197823475 1761 3074 2272 1967 1495 1915 1561 1536 932 2269 2077 1810 M2842 BIOCARTA_FIBRINOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FIBRINOLYSIS_PATHWAY.html Fibrinolysis Pathway 5/15 BioCarta 8.06583893336067e-07 1.82239735977474e-06 2750 2303.45454545455 1916 8.06584186096125e-08 1520 2.62991507207101 2.89579292955739 1 3.88242990113567 2747 1598 3836 1872 2004 3579 2923 1916 1706 1520 1637 1811 M44 PID_HIF2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF2PATHWAY.html HIF-2-alpha transcription factor network 18832364 26/51 Pathway Interaction Database 3.68808898695207e-07 9.42332878563653e-07 1925 2035.45454545455 1916 3.35280873202269e-08 1135 1.53162982841843 1.67549241610225 1 2.3739242986332 1925 1135 1893 2539 1715 2668 2569 1781 1827 1916 2422 1812 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 3/5 Arthur Liberzon 3.35317581902019e-05 5.31562310146434e-05 1875 2129.54545454545 1917 3.35322641714106e-06 8 3.56149969168527 3.56149969168527 1 3.91571787151069 1873 2825 4203 1397 3585 1947 1917 956 8 2800 1914 1813 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 15/52 Arthur Liberzon 1.05845261954072e-08 7.39181665449752e-08 1525 1851.54545454545 1917 9.62229658757363e-10 266 1.35039269958285 1.30742832593645 1 2.47699039613353 1524 1770 2170 2322 266 2104 1557 2515 2641 1581 1917 1814 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 147/390 Arthur Liberzon 7.51125047545515e-08 2.6227809037245e-07 1920 1859.63636363636 1917 6.82840975627693e-09 1041 1.773577019127 1.75565985221682 1 3.00231535189936 1917 2861 1274 1888 1115 2491 1218 1938 2129 1041 2584 1815 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 7/12 Arthur Liberzon 5.85851353351818e-06 1.06489505112747e-05 1915 2118.54545454545 1918 5.85852897855685e-07 1349 1.60326437247111 1.58899247498516 1 2.05066845344442 1915 1782 4185 2112 2503 2308 1937 1887 1408 1349 1918 1816 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 6/11 Arthur Liberzon 6.04379433281694e-07 1.42532562876599e-06 2565 1869.90909090909 1921 6.04379597655282e-08 156 2.49264357946951 -1.34568895273388 -1 3.74821108691634 2563 1166 4118 1412 1921 2655 2380 1075 156 1155 1968 1817 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 17/39 Arthur Liberzon 3.35252061860537e-07 8.71804196380953e-07 2315 1908.45454545455 1922 3.04774648135186e-08 1228 1.91482372446562 -2.08207133397645 -1 2.9844895064663 2313 1345 1406 2349 1679 1607 2799 2119 1228 2226 1922 1818 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 44/110 Yujin Hoshida 6.24209054864499e-07 1.46252181554752e-06 1615 1864.18181818182 1923 5.6746293815661e-08 972 1.87332690689291 1.78770199554485 1 2.81154778719057 1612 1923 972 2087 1899 1979 1399 2312 2583 1282 2458 1819 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 210/480 Arthur Liberzon 2.11208650928283e-08 1.09725469872498e-07 1975 1632.09090909091 1923 1.92007866323608e-09 279 1.53046798359729 -1.29264369292549 -1 2.73976276468436 1975 279 676 713 558 3807 1923 2882 1950 432 2758 1820 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 14/81 Arthur Liberzon 6.74069204129217e-07 1.56216038108284e-06 1040 2093.09090909091 1924 6.12790373328002e-08 658 1.16106373001491 1.22161352373863 1 1.73401260126958 1036 3265 2470 4149 1924 716 658 1649 3543 2407 1207 1821 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 40/85 Arthur Liberzon 8.37139231229147e-09 6.55960503194289e-08 1250 1866.27272727273 1924 7.61035667649647e-10 185 1.78395890254821 1.76900520920404 1 3.29607259008137 1740 1924 1248 2273 185 2238 1563 4066 1928 1250 2114 1822 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 107/303 Arthur Liberzon 1.07258092997312e-06 2.34426970049162e-06 965 1863.72727272727 1925 9.75074048087394e-08 919 1.62854121663687 1.74001569772314 1 2.35833347208866 963 2760 919 2280 2060 1796 1215 2048 2935 1600 1925 1823 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 10/25 Yujin Hoshida 5.91518974823493e-06 1.0739472747086e-05 1335 1930.18181818182 1925 5.37745968418113e-07 591 2.22785969173685 2.22785969173685 1 2.84745571619538 1332 3452 1814 3287 2479 814 591 2196 1925 2449 893 1824 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 12/36 BioCarta 5.64131801942519e-06 1.03021107712496e-05 1055 1872.81818181818 1927 5.1284840774044e-07 1052 1.63462049027174 1.63462049027174 1 2.09682109567204 1052 1413 1995 2409 2462 1708 1927 1582 2239 2140 1674 1825 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. 16/28 SigmaAldrich 1.1656351166869e-06 2.53464786858228e-06 1760 1740.27272727273 1927 1.05966884934604e-07 451 1.82365870984962 2.26588954520678 1 2.62498192450198 1759 2349 1927 451 2071 2904 2180 1205 580 2157 1560 1826 M16476 KEGG_CELL_ADHESION_MOLECULES_CAMS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CELL_ADHESION_MOLECULES_CAMS.html Cell adhesion molecules (CAMs) 63/183 KEGG 2.68449565738377e-11 4.13800876661196e-10 2395 1858.18181818182 1929 2.44045059765139e-12 104 2.16628561177248 2.12364183655112 1 5.22836330228761 2395 104 296 463 1929 3058 2467 3552 1497 356 4323 1827 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 68/139 Arthur Liberzon 7.44284320316595e-07 1.70049552657414e-06 4555 2101.18181818182 1929 6.76622338287572e-08 320 2.01027238697856 -1.66251430776149 -1 2.98322534655457 4552 320 581 403 1963 1929 4664 3036 833 334 4498 1828 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 7/17 Arthur Liberzon 6.85583656310144e-05 0.000103734097948639 2035 2023.45454545455 1932 6.85604808351318e-06 108 5.39435483696199 6.01015406068369 1 5.52797494826486 2031 2505 4179 1388 2993 2398 1748 1239 108 1932 1737 1829 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 26/87 Arthur Liberzon 6.86808164577132e-07 1.5854103739943e-06 2200 1875.54545454545 1933 6.24371253626177e-08 1043 1.75103019208504 1.7197463928158 1 2.61221952745716 2199 1133 1184 1289 1933 3163 2066 1878 2654 1043 2089 1830 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 34/89 Arthur Liberzon 8.66295648647927e-08 2.90168792677926e-07 1850 2019.63636363636 1933 7.87541529781925e-09 1127 1.38744317496335 1.69743528879212 1 2.33300432957815 1848 1127 2173 1933 1182 2900 1908 2072 2578 2633 1862 1831 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 12/31 Arthur Liberzon 0.00134472434904586 0.00177253960608408 1265 2014.45454545455 1933 0.000122322454561979 1174 1.92177306085073 2.0524667818407 1 1.36005068890231 1264 2631 1887 2008 4167 1424 1174 2148 1933 2153 1370 1832 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 45/102 John Newman 1.33924610165318e-07 4.10713824106467e-07 1915 2185.90909090909 1934 1.21749653016323e-08 1352 1.46007305151004 1.77823198329555 1 2.39846551420328 1912 2941 2130 1911 1352 2628 1485 1934 2642 3464 1646 1833 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 33/72 Jessica Robertson 1.34884896259556e-06 2.87435481524457e-06 1935 1920.72727272727 1934 1.22622708144848e-07 1036 1.53749005109806 1.82671671696909 1 2.19146800406702 1934 2836 2565 1403 2115 1630 1036 1657 1271 2571 2110 1834 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 19/43 Aravind Subramanian 0.000348292185649122 0.000482868988743131 3765 2567 1935 3.1667939783806e-05 1157 2.31444219242735 3.17858869115962 1 1.97415776327378 3764 1935 1303 1429 3242 4405 4214 1509 1157 1607 3672 1835 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 9/15 Kevin Vogelsang 2.79964462933824e-05 4.49901739817524e-05 1515 2424.27272727273 1935 2.79967990100887e-06 823 2.59785209396232 2.59785209396232 1 2.90463096160751 1515 4572 4392 4532 2823 1345 1242 1179 1935 2309 823 1836 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 50/103 Arthur Liberzon 3.57270846035358e-08 1.56664062128372e-07 1480 2015.90909090909 1940 3.24791683488444e-09 774 2.0368110125499 1.96361650729459 1 3.56516374268925 1477 2940 1675 3132 774 2778 1764 1940 2056 1638 2001 1837 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 13/23 Arthur Liberzon 2.49238150109564e-08 1.20328077343124e-07 4560 2394.90909090909 1940 2.26580139030168e-09 582 1.91007735358211 -1.97087281513942 -1 3.39963803943086 4557 582 1100 1881 635 3446 3393 3496 1940 1010 4304 1838 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 18/43 Arthur Liberzon 7.27060738191634e-06 1.29604171050801e-05 1020 2005.36363636364 1941 6.60966491826124e-07 568 1.27647278897041 1.30118291947147 1 1.60467242873397 1020 2627 2555 1941 2526 1419 568 2379 3628 1898 1498 1839 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 99/229 Jessica Robertson 4.27318812773173e-08 1.75342903384859e-07 1945 1877.09090909091 1942 3.88471655521123e-09 407 1.88819976931852 2.15292470797695 1 3.28128104146794 1942 775 505 924 858 3781 2668 3957 1989 407 2842 1840 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 7/19 Reactome 3.39373670008915e-07 8.8154380136462e-07 1945 1922.72727272727 1945 3.39373721837445e-08 230 2.01946010398694 2.49547986831 1 3.145071992865 1945 430 4086 2579 1720 2831 2273 771 230 2679 1606 1841 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 110/307 Arthur Liberzon 4.76893144094086e-05 7.3997393153142e-05 1585 2205.45454545455 1945 4.33548620001774e-06 1432 1.70549754796182 2.0288848629027 1 1.81210007929079 1582 3430 1759 1432 2902 2531 1621 1767 2117 3174 1945 1842 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 51/116 Reactome 2.16984246133672e-07 6.10683590019451e-07 4125 2407.63636363636 1947 1.97258425031507e-08 893 1.56880352419111 -1.22981203924149 -1 2.50755980367242 4121 1324 2062 893 1517 1670 3850 4275 1510 1947 3315 1843 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 8/45 Jessica Robertson 2.15350336589358e-07 6.06449325275079e-07 2155 1983.63636363636 1948 2.15350357458456e-08 266 1.55937916192377 -1.8108383327388 -1 2.49370800711443 2154 1948 4478 1726 2999 1305 2468 266 1370 2109 997 1844 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 19/44 Arthur Liberzon 1.29259995738928e-07 3.98232965175947e-07 1880 1884.54545454545 1950 1.17509093939582e-08 1259 1.6778079292754 1.9303127048444 1 2.76192296626774 1880 2110 1950 2751 1346 2161 1599 1340 2205 1259 2129 1845 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 36/102 Jessica Robertson 2.06212580453763e-07 5.84580854208309e-07 1955 1912.09090909091 1951 1.87465999802444e-08 1121 1.96243548630992 2.22849052978739 1 3.14631357182169 1951 1450 1121 1445 1497 2963 2083 2362 2504 1476 2181 1846 M62 PID_EPHB_FWD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHB_FWD_PATHWAY.html EPHB forward signaling 18832364 33/76 Pathway Interaction Database 1.79853911415125e-06 3.69323150259103e-06 1580 2163 1952 1.63503689499148e-07 1508 1.48830329797322 1.7746152309451 1 2.07968373810655 1578 3181 2405 1508 2200 2817 1858 1915 1811 2568 1952 1847 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 20/42 Jessica Robertson 7.25762501228625e-07 1.66385669312981e-06 3060 2310.09090909091 1952 6.59784309683646e-08 706 1.74138699730026 -1.70516903813818 -1 2.58843899449084 3058 706 1119 1362 1952 3920 2366 4671 1485 867 3905 1848 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 94/225 John Newman 2.18866601605596e-08 1.12580559289113e-07 1435 2019.72727272727 1952 1.98969639802715e-09 571 1.49370261605667 1.71386273865974 1 2.66966117388928 1432 3398 2154 3186 571 2000 1669 1362 2982 1952 1511 1849 M13191 KEGG_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROSTATE_CANCER.html Prostate cancer 46/121 KEGG 1.7408766416762e-08 9.68853674928108e-08 1880 1877.18181818182 1954 1.58261514131990e-09 486 1.69712325670985 2.16845245904953 1 3.06169424845563 1876 2612 2179 1954 486 2678 1535 914 2396 1884 2135 1850 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 51/125 John Newman 1.64114542800563e-09 1.81806323301049e-08 1955 1934.45454545455 1954 1.49195039020898e-10 15 1.27746870330212 1.39135878629339 1 2.54338333947016 1954 803 2508 1600 15 2542 1972 3917 1499 1697 2772 1851 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 437/1213 Arthur Liberzon 1.52472853564757e-08 8.94848998454387e-08 455 1954.81818181818 1955 1.3861168601953e-09 429 1.61981928475861 -1.30664249833768 -1 2.93661178824187 3540 451 653 1349 429 2181 3530 2605 1955 455 4355 1852 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 169/385 Arthur Liberzon 5.45412047132679e-07 1.30398002697129e-06 1470 2141.27272727273 1955 4.95829256680288e-08 1304 1.35101383255213 1.60312516128657 1 2.04496044374208 1467 1304 2586 1943 1857 3293 2535 1641 2541 1955 2432 1853 M19043 ST_ADRENERGIC http://www.broadinstitute.org/gsea/msigdb/cards/ST_ADRENERGIC.html Adrenergic Pathway 22/55 Signaling Transduction KE 1.64624717344455e-06 3.42858411322719e-06 1695 1844.36363636364 1957 1.49658945938455e-07 1109 1.5636703929962 1.66068814215258 1 2.19798590324984 1693 1461 2080 1982 2168 1957 1460 1109 2126 2350 1902 1854 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 195/447 John Newman 1.20309606072048e-08 7.88490649026037e-08 3180 2230.54545454545 1958 1.09372369754523e-09 322 1.76840681533183 -1.44466082587045 -1 3.23098613669621 3177 1237 1102 1139 322 2941 4059 3952 1958 815 3834 1855 M907 REACTOME_CALNEXIN_CALRETICULIN_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CALNEXIN_CALRETICULIN_CYCLE.html Genes involved in Calnexin/calreticulin cycle 4/14 Reactome 0.00123495284881281 0.00163243696742929 1960 2540.72727272727 1959 0.000123563968491592 922 0.478204203341293 -0.478204203341293 -1 0.342826406208081 1959 1909 4049 3114 3431 1018 922 1821 3485 4497 1743 1856 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 120/264 Arthur Liberzon 1.94677492055539e-06 3.95773851528094e-06 1220 1939.18181818182 1959 1.76979694841287e-07 1216 1.51070081917722 1.63852815567977 1 2.09930788990766 1216 1959 2467 2326 2221 1951 1431 1242 2870 2338 1310 1857 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 25/123 Arthur Liberzon 5.0312907423455e-06 9.29677776759898e-06 1400 1982.90909090909 1960 4.57391113517672e-07 668 1.95594036055882 2.15134673741631 1 2.53143161610966 1399 3443 2152 2133 3278 1960 1443 673 668 3142 1521 1858 M15 PID_LYSOPHOSPHOLIPID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LYSOPHOSPHOLIPID_PATHWAY.html LPA receptor mediated events 18832364 50/103 Pathway Interaction Database 1.56493551687577e-07 4.67684172964278e-07 1365 2012.36363636364 1961 1.42266875290456e-08 1365 1.66640407316742 1.6998145599339 1 2.71322575290977 1365 2832 2217 1792 1400 2353 1627 1961 2632 1637 2320 1859 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 39/90 Arthur Liberzon 1.62711444875426e-08 9.24201006892422e-08 1985 1989.36363636364 1961 1.47919496435305e-09 460 1.62815034733605 2.0276032738715 1 2.94584538182456 1981 1721 1815 3159 460 2911 1757 1511 2378 1961 2229 1860 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 27/179 Arthur Liberzon 7.41665302281142e-07 1.69616574255219e-06 2740 2085.72727272727 1961 6.74241411192641e-08 693 2.35597623814192 2.67571711295402 1 3.4969176146995 2736 693 880 1185 1961 4027 2480 3015 1034 1654 3278 1861 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 2/13 Arthur Liberzon 9.45489053754941e-07 2.10278201513795e-06 2190 2088.3 1962 1.05054383451788e-07 132 3.657176590991 -3.657176590991 -1 5.34046701190563 2188 2860 4632 NA 3617 1736 1567 466 132 2534 1151 1862 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 172/382 John Newman 7.4910011887923e-07 1.70899861590461e-06 895 1715.45454545455 1964 6.8100033995271e-08 895 1.5573494148425 1.78055492736312 1 2.31022412628446 895 2135 2140 2054 1964 1509 1361 1023 2376 2200 1213 1863 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) 18/31 Reactome 2.51235019642901e-07 6.87667816616024e-07 2335 1948.27272727273 1965 2.28395498484887e-08 715 1.32414674743608 1.25907553083066 1 2.09894106199803 2334 1629 2692 1169 1567 1965 1063 3234 715 2937 2126 1864 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 290/653 Leona Saunders 1.03035444519e-08 7.26051267693284e-08 1785 1966.36363636364 1965 9.36685863650538e-10 256 1.81496945161086 2.11670318517868 1 3.33278542250201 1782 2542 471 1463 256 3873 1965 2776 2697 665 3140 1865 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 29/71 Arthur Liberzon 7.51977739016509e-07 1.71472880050188e-06 2405 2108.90909090909 1966 6.83616360044262e-08 1239 1.75844794855666 2.39365300287576 1 2.60788290890304 2401 1724 1524 2799 1966 3912 2104 1973 1675 1239 1881 1866 M8535 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIO_SERIES.html Glycosphingolipid biosynthesis - ganglio series 5/16 KEGG 5.97954661142093e-05 9.1181761865013e-05 1970 1929 1967 5.979707514914e-06 236 2.27774383553145 2.27774383553145 1 2.36698108295339 1967 1997 3798 1670 2971 2425 1888 1112 236 2228 927 1867 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 622/2045 Jessica Robertson 8.02963428005657e-12 1.35348439699083e-10 1855 1853.72727272727 1967 8.02963428008556e-13 69 1.75103968981789 2.01025066607706 1 4.44475534767575 1854 260 4537 756 406 4114 1967 1999 2046 69 2383 1868 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 63/144 Aravind Subramanian 1.18465400691742e-08 7.84080321527547e-08 2910 2012.90909090909 1969 1.07695819390594e-09 312 1.77426195872033 1.87241129441237 1 3.24279555069805 2910 331 1043 1085 312 4217 2358 3059 1969 1656 3202 1869 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 14/57 Jessica Robertson 3.40295238871366e-06 6.53802168655688e-06 1970 2018 1969 3.09359786581822e-07 1452 1.88577019348641 1.77855066767703 1 2.51477301631647 1969 2162 1595 2640 2344 1937 1586 2195 2385 1452 1933 1870 M9152 BIOCARTA_CCR3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CCR3_PATHWAY.html CCR3 signaling in Eosinophils 17/52 BioCarta 3.09936479189435e-05 4.94505393762919e-05 3045 2302.63636363636 1970 2.81764405152206e-06 1279 1.87471791479813 -1.42342022986228 -1 2.07630595320112 3043 1937 1668 1342 2824 1970 3128 3613 1279 1805 2720 1871 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 29/66 Arthur Liberzon 3.64042402625507e-07 9.31678153305912e-07 2640 2294.27272727273 1970 3.30947693513643e-08 810 1.74697220941471 2.11158956232478 1 2.70990977162267 2639 1970 1711 1873 1709 3830 2667 3203 810 1554 3271 1872 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 285/596 Jessica Robertson 1.57099422300588e-08 9.08698406718676e-08 3045 2108.81818181818 1971 1.42817657656743e-09 443 1.52002768027305 -1.19645390258659 -1 2.75308920993404 3041 462 1349 1044 443 3559 3320 2852 1971 880 4276 1873 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 380/965 Jessica Robertson 9.72752965400711e-09 7.0453174588373e-08 4545 2076.36363636364 1973 8.84320881547127e-10 236 1.64399829815776 -1.50813156739853 -1 3.02436055969642 4543 452 467 1183 236 1973 4379 4108 2028 344 3127 1874 M4052 REACTOME_TELOMERE_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TELOMERE_MAINTENANCE.html Genes involved in Telomere Maintenance 45/93 Reactome 0.00180914663041907 0.00236278180327306 380 2042.18181818182 1974 0.000164603279816281 376 1.67549749225329 -1.67549749225329 -1 1.13196350259039 376 2975 1940 1985 3683 1488 2028 1890 2997 1128 1974 1875 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 575/1453 Jean Junior 9.14323182229528e-09 6.8744865580254e-08 3380 2107 1974 9.14323185991469e-10 248 1.68070994624516 -1.30090550614888 -1 3.09650519463397 3379 447 4378 264 248 1974 3022 2528 1789 605 4543 1876 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 32/78 Kate Stafford 6.56288076756324e-07 1.52396725851345e-06 1690 2271.27272727273 1975 5.96625702305014e-08 1085 1.40521875656688 1.64419990128002 1 2.10253612244481 1688 3060 1975 4274 1918 1594 1085 2002 3652 2454 1282 1877 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 25/121 John Newman 1.19176810528109e-08 7.85207853988603e-08 3450 2410.45454545455 1975 1.08342555612459e-09 316 1.56375149316415 -1.07225487480527 -1 2.85779726071687 3450 695 1577 1833 316 4337 2928 4049 1975 1201 4154 1878 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 164/394 Jessica Robertson 4.97109599327131e-08 1.96578530164298e-07 1060 1940.27272727273 1975 4.51917827781607e-09 919 1.65151084619114 1.83598235432796 1 2.84887686966565 1056 3082 1289 2726 919 2049 1482 1975 2895 1538 2332 1879 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 11/26 Arthur Liberzon 1.96658241184123e-07 5.61230522648479e-07 3210 1935.27272727273 1976 1.78780235239479e-08 313 1.97498372459331 -2.27828416911092 -1 3.17542503282019 3209 971 1708 1992 1484 2352 3720 1366 313 1976 2197 1880 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 9/23 Arthur Liberzon 3.1980670043079e-06 6.17730502151146e-06 2065 2131.45454545455 1977 3.19807160675187e-07 979 2.21154470774823 2.4611529022508 1 2.96323089231965 2063 979 4644 1845 2352 2461 2326 1361 1757 1681 1977 1881 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 36/85 Arthur Liberzon 7.90124974927545e-07 1.78952423030956e-06 4625 2479 1978 7.18295689726607e-08 399 2.09982325905874 -1.70940016492815 -1 3.10414806499389 4621 1038 878 399 1978 3042 4605 3799 1154 1227 4528 1882 M2491 BRIDEAU_IMPRINTED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BRIDEAU_IMPRINTED_GENES.html List of genomically imprinted genes. 20421412 23/85 Arthur Liberzon 2.76391564068856e-05 4.44923005574256e-05 2715 2147.27272727273 1978 2.51268215006412e-06 1059 2.03826947897675 -2.09064730223852 -1 2.28150123800463 2713 1457 1139 3155 2794 1978 3728 1705 2103 1059 1789 1883 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 38/98 John Newman 8.68430441191343e-09 6.66871748972617e-08 1980 1873.36363636364 1979 7.89482222381268e-10 265 2.05259089880721 -1.89717062785292 -1 3.7886189960866 1979 1326 420 776 2909 1933 2890 3092 2309 265 2708 1884 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 11/31 Arthur Liberzon 0.000464479684171678 0.000636791047404472 1290 2146.81818181818 1979 4.22343434026715e-05 1286 2.47205648640263 2.47205648640263 1 2.03218957413181 1286 2960 1436 2586 3281 1946 1370 1758 2877 1979 2136 1885 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 86/261 John Newman 1.64491419895776e-08 9.32051745624677e-08 1295 1968.63636363636 1980 1.49537655568781e-09 462 1.35949576042997 1.58442673690808 1 2.45847856729612 1294 2086 2463 3567 462 1980 1419 1581 2950 2971 882 1886 M19708 KEGG_TYPE_II_DIABETES_MELLITUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYPE_II_DIABETES_MELLITUS.html Type II diabetes mellitus 21/67 KEGG 9.75442794615187e-06 1.70175909738152e-05 2035 2118.27272727273 1982 8.86770108718565e-07 1533 1.5988459925462 1.68400662338571 1 1.96129029060779 2034 1980 2402 1533 2586 2150 1800 3356 1660 1818 1982 1887 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 13/39 Jessica Robertson 2.95883614206383e-06 5.76032661475326e-06 1920 2290.09090909091 1988 2.68985465589596e-07 1518 2.03160364579871 2.26688395661712 1 2.73799006288579 1518 3805 1916 3415 2313 2128 1988 1651 2759 1778 1920 1888 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 11/30 Arthur Liberzon 3.6024441762915e-06 6.87899486964221e-06 1990 2161.90909090909 1989 3.27495461383269e-07 1565 1.68268666299404 1.92585710285048 1 2.23439454788992 1565 1989 1882 3099 2358 2331 1987 1882 2605 1978 2105 1889 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 22/60 Kevin Vogelsang 0.00578442610067218 0.00724754564378338 1685 2497.54545454545 1990 0.000527244656692736 1189 1.64919123726782 1.85434723213342 1 0.907704782636671 1685 3895 1990 2773 3599 1969 1189 1964 3324 3350 1735 1890 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 10/24 Arthur Liberzon 1.63510406911072e-06 3.40840643587759e-06 2285 1833.18181818182 1991 1.48645934942631e-07 728 1.76544380406335 1.69609978508859 1 2.48277441121295 2282 728 1605 2075 2164 1991 904 3604 1420 1358 2034 1891 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 312/901 Arthur Liberzon 7.79666572861198e-09 6.20291606184648e-08 1895 1882.09090909091 1991 7.08787796022079e-10 175 1.45406689729407 1.84387824558338 1 2.69564013944902 1891 619 2160 2047 175 4176 2036 1571 1991 2071 1966 1892 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 16/47 Jessica Robertson 7.6078691904527e-08 2.65059293877036e-07 4390 2433.72727272727 1992 6.91624495776558e-09 1072 1.79610312661147 -1.16797800702723 -1 3.03833122797674 4389 1212 1511 2393 1119 1992 3553 3244 1072 1688 4598 1893 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 16/27 Jessica Robertson 1.42040209699623e-08 8.60760193997102e-08 3415 2124.18181818182 1993 1.29127464196989e-09 397 1.2172628599629 -1.25900097693664 -1 2.21208814194268 3412 1279 2576 1993 397 2340 3993 2353 1641 1685 1697 1894 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 6/24 Arthur Liberzon 7.76852069327937e-07 1.76201781068282e-06 1710 2380.45454545455 1994 7.76852340902682e-08 957 1.35437813255703 1.28937680918195 1 2.00450736688618 1709 2440 4147 4076 1994 1890 957 1415 3810 2477 1270 1895 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 103/330 Kate Stafford 4.50780723777208e-07 1.11293913151739e-06 1345 2456.36363636364 1994 4.09800741947594e-08 1343 1.43931825204407 1.55208752986862 1 2.20409304019485 1343 3915 2314 4133 1793 1994 1359 1592 3444 3307 1826 1896 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 6/13 Jessica Robertson 1.49724278697839e-06 3.16610094755447e-06 1450 2192.90909090909 1994 1.49724379576052e-07 1303 2.20072815744988 2.20072815744988 1 3.1130515388434 1449 2854 4527 2285 2169 1737 1303 1496 1994 2493 1815 1897 M2220 KEGG_FOLATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOLATE_BIOSYNTHESIS.html Folate biosynthesis 5/12 KEGG 5.18598407457326e-07 1.25072163527794e-06 3910 2339.54545454545 1995 5.18598528482304e-08 113 1.49777745285093 -0.674760948574577 -1 2.27408607992016 3909 741 3802 1995 1875 1662 2155 1718 113 3262 4503 1898 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 143/350 Leona Saunders 3.32023202045769e-08 1.48036225003471e-07 3865 2242.45454545455 1995 3.0183927914241e-09 717 1.8277200130243 -1.62128112345458 -1 3.21074363865317 3861 1751 839 983 750 2928 3897 2367 1995 717 4579 1899 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 52/114 Arthur Liberzon 9.56601523406695e-09 7.02612984903285e-08 1615 2146.18181818182 1996 8.69637752332889e-10 224 1.74945479877418 1.52034071312085 1 3.21889524776495 1611 1794 1532 2953 224 2226 1713 3406 3156 1996 2997 1900 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 125/375 Kate Stafford 2.31252826411789e-07 6.45777982302147e-07 2000 2167.81818181818 1999 2.10229864290832e-08 1237 1.64192880806003 1.89850858124617 1 2.6141938325409 1999 3173 1376 2819 1536 3508 1685 1237 2545 2357 1611 1901 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 56/177 Kate Stafford 8.71739380979483e-07 1.95172992798369e-06 4650 2460.36363636364 1999 7.92490660365632e-08 731 1.75533682518864 -1.57218712291147 -1 2.57788358361831 4649 1024 1200 1364 1999 2506 3985 3807 1863 731 3936 1902 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 73/161 John Newman 1.39235156182645e-05 2.35458658199883e-05 1800 2341.63636363636 1999 1.2657821581069e-06 1390 1.82642812761086 2.23930449074616 1 2.17421551995111 1797 3318 1390 3070 2667 3315 1890 1483 3030 1799 1999 1903 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 16/42 Jean Junior 1.01462562241636e-07 3.29261472759216e-07 3120 2073.90909090909 2000 9.22386972009305e-09 649 1.21116300894805 -1.22456001643267 -1 2.01948683228015 3117 2240 3056 2408 1243 1564 2000 1469 649 3250 1817 1904 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 426/1057 Arthur Liberzon 1.24692124776286e-08 8.0181460061125e-08 1870 1846.90909090909 2002 1.13356477711836e-09 341 1.71515382502191 1.98492127724101 1 3.13047915308517 1866 2002 607 977 341 4323 2411 2641 2189 707 2252 1905 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 8/28 Leona Saunders 5.28823068617588e-06 9.72081077206735e-06 2005 2122.09090909091 2003 5.28824327064074e-07 1047 1.18394711794591 -1.0877513467386 -1 1.52639795065253 2003 2210 4272 1903 2471 1047 1760 1444 2798 2104 1331 1906 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 69/156 Yujin Hoshida 8.99270965109317e-09 6.79378898106698e-08 3980 2263.09090909091 2003 8.17519062531973e-10 209 1.58677623622506 -1.6461332876217 -1 2.9255367152014 3979 1256 2003 2165 209 2698 4015 1951 1945 1383 3290 1907 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 194/499 Yujin Hoshida 4.456031652315e-09 4.12667279105694e-08 3770 2265 2004 4.05093787394596e-10 407 1.8071936658232 -1.72734019176864 -1 3.43256341617448 3768 761 407 1703 1511 3051 2956 4501 2004 427 3826 1908 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 155/467 Arthur Liberzon 1.33664578495027e-08 8.26322183149997e-08 2520 2137.36363636364 2005 1.21513253915571e-09 375 1.72110154763095 -1.48292954812316 -1 3.13554642453773 2516 896 654 1114 375 4433 2666 4497 2005 955 3400 1909 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 6/23 Arthur Liberzon 0.000223976793185453 0.000319013754670831 1515 2512.63636363636 2005 2.23999370909962e-05 978 1.83142050110627 -1.83142050110627 -1 1.64695526933432 1511 2853 4642 3165 3179 978 1933 2005 4285 1732 1356 1910 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 13/26 Reactome 5.35947997569351e-06 9.83975451550285e-06 2715 2259 2007 4.87226639283029e-07 898 1.57069946608124 -1.05915564357283 -1 2.02288267924113 2712 1411 2007 1052 2448 3153 1829 4504 898 2908 1927 1911 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 10/18 Reactome 6.89351120540759e-06 1.23435206375774e-05 2280 2170.36363636364 2007 6.2668480052074e-07 1356 1.70564636030621 2.09213623599676 1 2.1534848770177 1748 2280 1396 3400 2517 2007 2277 1759 3230 1356 1904 1912 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 127/323 Arthur Liberzon 1.29028865714024e-08 8.10375300728646e-08 3490 2315.54545454545 2009 1.17298969518884e-09 360 1.61285929458705 -1.12389710721712 -1 2.94185892900501 3486 1243 2009 1530 360 2466 3665 1990 1416 2637 4669 1913 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 13/35 Leona Saunders 2.41755845976389e-06 4.79622309163997e-06 2275 2045.81818181818 2009 2.19778283309028e-07 1505 1.31647513317738 1.63512056761109 1 1.80114843081586 2009 1902 2413 1855 2271 2496 2016 1985 1781 2271 1505 1914 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 157/350 Jessica Robertson 3.72067797950533e-07 9.49624020259367e-07 1895 2101 2009 3.38243509886633e-08 1207 1.76251556171267 1.98668927227089 1 2.73026433821859 1892 2476 1271 1207 1717 3544 1816 2028 2009 2176 2975 1915 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 65/126 Jessica Robertson 9.19319564161112e-07 2.05041955147976e-06 1550 2201.63636363636 2010 8.3574540756339e-08 1549 1.21938382911245 1.46243156612265 1 1.78406496100486 1628 1708 2650 3168 2010 2141 1804 1549 2861 3149 1550 1916 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 22/47 Arthur Liberzon 3.39375532533509e-08 1.50883657063759e-07 1745 2217.45454545455 2011 3.08523216153427e-09 633 1.04704572570695 -1.09070389010419 -1 1.83710981304946 1743 2623 3165 4008 757 701 1466 2011 3537 3748 633 1917 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 89/188 Arthur Liberzon 3.97269013791088e-08 1.66486954776987e-07 3780 2326.90909090909 2014 3.61153655422587e-09 648 1.47636258221454 -1.34022747928975 -1 2.57414471109799 3776 648 1323 1717 824 2014 4295 4631 2669 863 2836 1918 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 16/39 Arthur Liberzon 3.45830086728876e-07 8.93362616544384e-07 2610 1976.09090909091 2015 3.14391037356199e-08 370 1.66904450797432 -0.691189230485078 -1 2.59685775778587 2607 2114 2015 1800 1694 4103 2368 901 370 3244 521 1919 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 43/122 Arthur Liberzon 0.000123925182343839 0.000181813839844468 2420 2137.09090909091 2015 1.12665603230779e-05 1037 1.49288181221459 -1.47776356457037 -1 1.43627953407061 2418 2015 1558 1950 3072 1524 2553 1959 3248 1037 2174 1920 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 51/117 John Newman 7.8083094682165e-08 2.69835827198101e-07 3610 2687.36363636364 2016 7.09846340486502e-09 1136 1.61162585434126 -1.55271389347822 -1 2.72304963265845 3610 1876 1863 1646 1136 3816 3316 3707 2016 1948 4627 1921 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 130/310 Arthur Liberzon 2.09070443083124e-08 1.08977096361237e-07 2315 1933.27272727273 2017 1.90064040972694e-09 555 1.77631513270946 2.11656800556007 1 3.18122334906486 2315 2137 746 2066 555 4210 2017 1931 1951 759 2579 1922 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 16/29 Jessica Robertson 2.14189054565747e-05 3.51555134744341e-05 1285 1980.09090909091 2018 1.94719218100118e-06 677 0.98585807965501 -0.98585807965501 -1 1.12944180592516 1284 2116 2934 2018 2747 677 1180 1036 3471 3254 1064 1923 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 74/204 John Newman 1.52597583192341e-07 4.57792749577024e-07 1880 2300.54545454545 2020 1.38725085251726e-08 1393 2.06617664922308 2.46551059591807 1 3.3690662057928 1877 4149 1543 2340 1393 3662 2342 2020 1715 2280 1985 1924 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 21/56 BioCarta 3.24853453491567e-05 5.15846588634864e-05 2140 1901.09090909091 2022 2.95325682180262e-06 926 1.48737350170852 -1.26999621661268 -1 1.64029032352693 2136 1198 2022 1054 2837 1316 2609 2211 926 2709 1894 1925 M7897 BIOCARTA_GLEEVEC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLEEVEC_PATHWAY.html Inhibition of Cellular Proliferation by Gleevec 20/42 BioCarta 2.88347484833943e-07 7.6951287134201e-07 2025 2246.18181818182 2023 2.62134111478909e-08 753 0.848665987513177 -0.802364887261081 -1 1.33458277642107 2023 1625 3370 1664 1617 753 2513 2826 3587 3612 1118 1926 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 52/129 Jessica Robertson 1.57862810917665e-06 3.3134926769811e-06 1215 1997.09090909091 2023 1.43511749266853e-07 482 1.28520435116961 -1.22092571276678 -1 1.81145986509465 1213 1715 2672 2367 2150 482 2023 1832 3183 2950 1381 1927 M552 REACTOME_PROLACTIN_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROLACTIN_RECEPTOR_SIGNALING.html Genes involved in Prolactin receptor signaling 8/41 Reactome 8.77397426071703e-07 1.96345956951863e-06 2215 2061.90909090909 2024 8.77397772493703e-08 887 1.40213001530921 -1.59259836604244 -1 2.05822633963422 2211 2400 3928 2996 2024 887 1830 1140 1373 2870 1022 1928 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 23/92 Jessica Robertson 9.23245725736388e-08 3.05747665780969e-07 2795 2277.27272727273 2025 8.39314331346414e-09 400 2.06140074430351 2.35728418935636 1 3.45423040338227 2793 832 1490 1331 1204 4111 3330 4318 400 2025 3216 1929 M882 BIOCARTA_CXCR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CXCR4_PATHWAY.html CXCR4 Signaling Pathway 19/45 BioCarta 2.95163144560072e-06 5.75107898298751e-06 3010 2185.72727272727 2027 2.68330491424221e-07 705 1.69388538677035 -1.45195088813676 -1 2.28315150849377 3007 1202 1877 705 2312 1901 4303 3936 721 2027 2052 1930 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 17/28 John Newman 4.81596420923842e-05 7.46283342741113e-05 2520 2383.27272727273 2027 4.37824512501882e-06 1321 1.46157097234805 1.66274947443705 1 1.55154057006149 2517 2027 1850 3286 2906 3133 2003 1321 3409 1809 1955 1931 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 10/27 Arthur Liberzon 9.85560851416295e-07 2.18361141831525e-06 3855 2443 2027 8.95964811754813e-08 330 2.58278779873771 -2.2636803320791 -1 3.76068616604603 3855 1072 1150 1756 2027 3638 4270 3268 330 1861 3646 1932 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 8/21 Jessica Robertson 5.03328839225884e-06 9.29680307691167e-06 2140 1954.18181818182 2029 5.03329979259159e-07 980 1.00548583254634 -1.00443338707811 -1 1.30132690970077 2138 980 4339 2029 2459 1243 2186 1426 1148 2105 1443 1933 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 91/257 Arthur Liberzon 1.61941243793088e-08 9.23183294908041e-08 3600 2122.54545454545 2030 1.47219313622847e-09 457 1.5765505010407 -1.14515754801655 -1 2.85267876741973 3599 1558 2030 2073 457 805 2895 4000 1546 1640 2745 1934 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 96/210 Lauren Kazmierski 4.29187858779942e-07 1.06636350136306e-06 1160 2195.27272727273 2031 3.90170856825679e-08 1156 1.71775716411504 1.83814302481237 1 2.63868233935718 1156 3555 1415 2513 1778 2679 1754 2031 3266 1650 2351 1935 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 23/48 Arthur Liberzon 1.83238657120178e-08 1.00310320942191e-07 2605 2181.90909090909 2032 1.66580598769436e-09 509 2.14629631089253 2.33116066090754 1 3.86369549246177 2605 2840 1683 587 509 4517 3287 1979 2316 1646 2032 1936 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 65/168 Arthur Liberzon 1.69702582112469e-07 4.98260019035934e-07 3190 2470.54545454545 2032 1.542750865481e-08 1229 1.95212400425103 -1.66174362657478 -1 3.16462274550353 3188 1962 1229 1333 1436 4397 2990 4269 1490 2032 2850 1937 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 41/85 John Newman 1.34159832328342e-06 2.86541920825254e-06 2125 1967.63636363636 2033 1.21963558310377e-07 979 1.87236801522934 2.48845726799442 1 2.66943901466803 2121 1513 1635 979 2110 3464 2207 1279 1093 3210 2033 1938 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 30/90 Itai Pashtan 1.82356378190951e-06 3.73447685187425e-06 2345 2166.18181818182 2034 1.65778663040895e-07 1189 1.66659324207515 2.00914074336239 1 2.32674998809093 2345 2020 2034 1889 2205 3666 3019 1443 1189 2288 1730 1939 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 45/125 Arthur Liberzon 1.00840025091001e-06 2.22789418942211e-06 2675 2148.81818181818 2035 9.16727921022204e-08 1431 1.653284355468 -1.37445435743918 -1 2.40356826768019 2671 1796 1763 1498 2035 1431 2889 3211 2272 1574 2497 1940 M10183 BIOCARTA_RELA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RELA_PATHWAY.html Acetylation and Deacetylation of RelA in The Nucleus 10/19 BioCarta 4.27535665079594e-05 6.69372578203467e-05 1600 2240.54545454545 2036 3.88676339812776e-06 1597 1.18215083023456 -1.20275468644759 -1 1.26928311715683 2576 2036 2872 1597 2881 1862 3109 1992 2274 1849 1598 1941 M5298 BIOCARTA_STEM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STEM_PATHWAY.html Regulation of hematopoiesis by cytokines 4/15 BioCarta 1.98263590463063e-05 3.27711881802439e-05 1310 1984.36363636364 2037 1.98265359365583e-06 370 2.77074292823337 2.77074292823337 1 3.19602139967585 1309 2578 3858 2398 3139 861 370 1490 2901 2037 887 1942 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+ 55/153 Reactome 2.00908002652156e-07 5.71965310102068e-07 1175 2221.90909090909 2038 1.82643655454039e-08 1130 1.53526637505614 1.64644400321415 1 2.46518778163386 1174 3491 1923 2973 1487 1622 1130 2236 3577 2790 2038 1943 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 16/44 Arthur Liberzon 1.83286922129657e-06 3.75057867729071e-06 3575 1931.18181818182 2041 1.66624613482064e-07 217 2.10841266487972 -2.30788568955934 -1 2.94256589459456 3572 217 902 1256 2206 2559 3790 2041 1213 782 2705 1944 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 325/767 Arthur Liberzon 1.79341988174502e-08 9.91033675219008e-08 3100 2088.45454545455 2042 1.63038172396802e-09 498 1.6400856837971 -1.35227613975927 -1 2.95464869295212 3096 754 774 699 498 3648 3145 3536 2042 522 4259 1945 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 18/49 Arthur Liberzon 7.67633715628419e-06 1.36358286256057e-05 1380 1944.81818181818 2043 6.97851267366331e-07 1164 1.8366987605701 2.19421659467971 1 2.2985177115916 1377 2314 1745 2327 2536 1817 1520 1164 2177 2373 2043 1946 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 4/13 Reactome 1.05900142344566e-05 1.83455847329625e-05 2890 2125 2044 1.05900647015757e-06 613 2.17386458214244 -2.17386458214244 -1 2.64841347575456 2057 1998 4043 2890 2886 1722 2930 775 613 2044 1417 1947 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 24/74 Jessica Robertson 6.88999730754624e-06 1.2341944718334e-05 3175 2491.63636363636 2044 6.26365353259205e-07 1612 1.52449418515409 -0.90590408379543 -1 1.92479068195437 3171 1979 1843 2044 2516 4681 2731 1612 1825 3034 1972 1948 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 69/167 Arthur Liberzon 3.59796789660247e-08 1.57130266202042e-07 4290 2431.81818181818 2045 3.27087995949553e-09 685 2.01659743163118 -1.98059547447146 -1 3.52911321996589 4287 914 685 931 780 3721 3586 4643 2045 1182 3976 1949 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 4/17 Arthur Liberzon 7.48006222748671e-05 0.000112488997426196 1340 2158.81818181818 2046 7.48031402040432e-06 1051 2.22233885349446 2.22233885349446 1 2.25727233258679 1336 3045 4106 2891 3004 1342 1051 1477 2219 2046 1230 1950 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 27/74 Arthur Liberzon 4.79250470411146e-08 1.90966641526074e-07 1735 2025.72727272727 2046 4.35682255319266e-09 906 1.78185903479923 2.20314958972276 1 3.07949419692163 1734 2662 1443 2447 906 2196 1878 1722 2858 2391 2046 1951 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 23/55 Leona Saunders 4.06171241078273e-06 7.64078055276109e-06 2750 2223.63636363636 2047 3.69247264515387e-07 538 2.2382196797814 -2.07760306209093 -1 2.94581246340702 2750 1575 620 1760 2717 2047 3946 4104 2508 538 1895 1952 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 22/62 Kate Stafford 8.29965901269247e-09 6.52405463573197e-08 4055 2202.09090909091 2048 7.54514458545774e-10 184 2.55656613896127 -1.8760300415618 -1 4.72510683853303 4052 1893 1408 1168 184 2048 3005 3767 773 2834 3091 1953 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 4/12 Jessica Robertson 9.19348573583558e-05 0.000136807475891158 1050 2186.18181818182 2048 9.19386609879245e-06 629 2.2943115573049 2.2943115573049 1 2.28021508553561 1050 2048 4522 4265 3212 727 629 1425 3206 2055 909 1954 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 4/13 Arthur Liberzon 9.94635618096109e-06 1.73266264178378e-05 1960 1922.18181818182 2048 9.9464006997421e-07 154 4.69221782805636 5.3730444617881 1 5.74646950919857 1956 1081 4645 212 2613 2386 2423 2346 154 1280 2048 1955 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 69/158 Broad Institute 7.40260530005309e-09 6.00148934879737e-08 3305 2317 2050 6.72964120451051e-10 163 1.59001639237194 1.4830161911617 1 2.95353530141969 3301 1107 1442 1121 163 4259 3112 3530 2050 1181 4221 1956 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 344/821 Jessica Robertson 1.44791149366229e-08 8.68746896197371e-08 4235 2309.27272727273 2050 1.31628318471963e-09 405 1.55660004994516 -1.45622241772686 -1 2.82714753442926 4232 2050 1486 1931 405 1281 4523 3316 2600 1125 2453 1957 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 86/171 Jessica Robertson 8.7973354477547e-08 2.94039328874312e-07 2115 2090.18181818182 2050 7.99757799958328e-09 1186 1.55920101160523 1.86226400042335 1 2.61950952214294 2113 1754 2061 1370 1186 3952 2050 2143 1954 1599 2810 1958 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 210/541 Arthur Liberzon 1.75251250942199e-07 5.11987133363557e-07 1570 2084.36363636364 2050 1.59319331729687e-08 1103 1.50176882302382 1.77829025153929 1 2.42998468696126 1570 2177 1103 2050 1445 3507 2032 2253 3006 1715 2070 1959 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 9/21 Reactome 1.0302327207604e-08 7.26051267693284e-08 2265 2135.18181818182 2051 1.0302327255366e-09 287 1.65420141882913 2.08872479068143 1 3.03757087223919 2264 1816 3920 2051 287 2160 1412 1728 3027 3047 1775 1960 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 48/89 John Newman 2.02891422516809e-05 3.34888765732218e-05 935 2181.72727272727 2052 1.84448448794654e-06 643 1.63546498116211 1.68555027258039 1 1.8825329118558 933 3433 2052 2706 4598 880 897 1565 3304 2988 643 1961 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 5/14 Reactome 4.45282594019356e-06 8.30981376174713e-06 2055 2230.18181818182 2053 4.4528348626652e-07 669 1.58660779584012 1.98608450584498 1 2.07332259304061 2053 1745 4064 2798 2549 1723 1292 669 3646 2236 1757 1962 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 13/34 Arthur Liberzon 6.45080386338829e-07 1.50315598726194e-06 2120 1922.90909090909 2053 5.86436886807562e-08 777 1.46399140657962 1.35738497856602 1 2.19272244626836 2119 1220 2053 3161 1912 2111 777 1566 2412 1330 2491 1963 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 27/53 John Newman 0.000169818795243908 0.000245381089889903 1600 2249.09090909091 2053 1.54392640940772e-05 992 1.93038849393597 2.19326234185242 1 1.79254338827063 1597 3018 1810 1604 3486 2837 1629 2053 2400 3314 992 1964 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 144/346 Arthur Liberzon 1.22713572464638e-08 7.95346888754213e-08 3175 2133.90909090909 2053 1.11557793771928e-09 336 1.77831170706215 -1.46063617128399 -1 3.24736309053099 3173 2053 982 1078 336 3551 2484 2952 1683 1296 3885 1965 M1909 BIOCARTA_EGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EGF_PATHWAY.html EGF Signaling Pathway 25/53 BioCarta 2.80562403382759e-05 4.50553605980675e-05 1805 2177.18181818182 2056 2.55059983102823e-06 862 1.06794991550983 -0.994551689304647 -1 1.19389065731871 1802 1726 3182 1477 2803 862 2371 2056 2777 3559 1334 1966 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 30/62 Arthur Liberzon 5.85079766683448e-06 1.06390523348026e-05 1700 2022.81818181818 2056 5.31892111528787e-07 1393 1.63398043432461 1.58318894410858 1 2.0901258269528 1696 2946 2428 2056 2474 1393 1465 1593 2382 2287 1531 1967 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 4/16 Arthur Liberzon 2.0776891368916e-08 1.08661286779844e-07 3195 2320.27272727273 2057 2.07768915631716e-09 252 2.02777265469949 -1.75037552992211 -1 3.63221895737874 3195 252 4597 1351 590 3259 3975 3161 1046 2057 2040 1968 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 14/65 Arthur Liberzon 3.28291502057445e-05 5.20952921991598e-05 1750 1991 2057 2.98451273670485e-06 1322 1.44090840475548 1.76454685863099 1 1.58746264107114 1746 2204 2364 1583 2839 2115 2057 1322 1920 2408 1343 1969 M19 PID_P73PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P73PATHWAY.html p73 transcription factor network 18832364 63/123 Pathway Interaction Database 1.30333263429702e-05 2.21926479807989e-05 1000 2059.54545454545 2060 1.18485486874128e-06 996 1.59033373989288 1.78243951785798 1 1.90367925434269 996 4013 2060 2301 2653 1666 1008 1349 2484 2993 1132 1970 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 7/13 Reactome 4.49907632779626e-07 1.11136909183201e-06 2925 1969.36363636364 2060 4.49907723867245e-08 89 1.33250870045528 -0.760144090187977 -1 2.04074086957485 2921 427 3976 926 1823 987 2060 2824 89 2673 2957 1971 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 34/102 Arthur Liberzon 4.78464094072182e-07 1.16896910574674e-06 1650 2423.81818181818 2061 4.34967452845769e-08 1476 1.71162751018472 2.12915194577015 1 2.61170111366038 1647 3467 2056 4268 1811 2811 2061 1476 2317 3078 1670 1972 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 52/123 Arthur Liberzon 1.8791038630588e-07 5.40213540018007e-07 4650 2474.09090909091 2061 1.70827638505476e-08 607 1.80278344157297 -1.52564651401056 -1 2.90624366845125 4646 1260 962 892 1474 3390 4364 3176 2061 607 4383 1973 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 59/143 Arthur Liberzon 6.67474335589125e-08 2.39493471406634e-07 2905 2320.90909090909 2062 6.06794868945567e-09 660 1.6699289463363 -1.52084597239259 -1 2.84381259546477 2904 660 964 1265 1068 4639 2699 4287 2062 956 4026 1974 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 6/21 Reactome 0.000284602428615272 0.000398937176335975 1995 2526.09090909091 2063 2.84638884530625e-05 1418 2.00466713422145 2.00466713422145 1 1.75268662292488 1994 2535 3995 3281 3229 2016 2063 1418 1953 3440 1863 1975 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 9/21 Arthur Liberzon 5.47322213281401e-08 2.09709884827199e-07 1625 2313.90909090909 2065 5.47322226761673e-09 1023 1.01798550893964 1.05548292995155 1 1.74868437791623 1625 2359 4335 3735 1023 1990 1196 2065 3007 2306 1812 1976 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 11/22 Arthur Liberzon 2.4667379090734e-06 4.87933045247697e-06 2710 2229.90909090909 2065 2.24249152263097e-07 1381 1.95685602251154 2.29711829399704 1 2.67353664742066 2707 1416 1582 2496 2275 3698 3105 1824 1381 1980 2065 1977 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 98/207 Arthur Liberzon 1.77926907143041e-08 9.85538400558262e-08 2385 2197.36363636364 2068 1.61751735074582e-09 495 1.47383102458847 1.58715745065306 1 2.65605288063875 2383 1011 1732 1521 495 3890 2750 3147 2068 1119 4055 1978 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 68/129 Arthur Liberzon 1.14196692506804e-06 2.48664359241118e-06 2070 2212.18181818182 2068 1.03815228894178e-07 1062 2.33799718541893 2.35171408865051 1 3.37031676457507 2068 2297 1062 1489 2067 3685 2807 3196 1265 1714 2684 1979 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 14/25 Leona Saunders 9.92626590150173e-08 3.24142731807924e-07 2875 2210.63636363636 2069 9.02387849942619e-09 1232 1.78854030411302 2.17431477027495 1 2.98533321439393 2874 1355 1730 2313 1232 4023 2820 2722 1735 1444 2069 1980 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. 13/28 Signaling Transduction KE 8.06018259536806e-06 1.42582165503566e-05 955 1766.09090909091 2072 7.32746556887869e-07 274 1.27199974878556 1.1488113466221 1 1.58548895986655 953 2072 2611 2762 2681 698 274 1086 3254 2268 768 1981 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 255/682 John Newman 2.53848737803872e-07 6.91992545287344e-07 1660 2080.09090909091 2072 2.30771606449467e-08 1183 1.82314399415901 2.19777540421435 1 2.88863846687179 1659 2606 1183 1373 1576 3879 2072 2226 1906 2124 2277 1982 M2339 DUAN_PRDM5_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/DUAN_PRDM5_TARGETS.html Direct targets of PRDM5 [GeneID=11107]. 17636019 57/174 Arthur Liberzon 1.17669217986529e-07 3.69296477453023e-07 2395 1883.54545454545 2072 1.06972022072896e-08 658 1.92503416573025 1.98999712969825 1 3.18511652312955 2391 799 873 2072 1309 3289 2176 2486 1589 658 3077 1983 M13265 KEGG_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI_ANCHOR_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI_ANCHOR_BIOSYNTHESIS.html Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 13/25 KEGG 7.37066562293618e-05 0.000111021983635741 2065 2673.09090909091 2073 6.70082961283461e-06 1560 0.757827521217807 -0.757827521217807 -1 0.770851137269266 2064 2073 3486 3621 2990 1560 1931 1854 3459 4395 1971 1984 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 62/180 Kate Stafford 4.79361569609253e-09 4.34485167347961e-08 2075 1966.27272727273 2073 4.35783246048857e-10 86 1.53834573637037 -1.06164786662234 -1 2.91306315447691 2073 2088 1963 2765 86 2521 1570 1683 2941 2082 1857 1985 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 436/943 Jessica Robertson 2.4590122712123e-08 1.2003053648855e-07 2150 2110.63636363636 2075 2.23546572608862e-09 626 1.50760144925932 1.99397446042649 1 2.6837109771133 2149 1912 1636 855 626 4212 2452 2044 2250 2075 3006 1986 M17844 KEGG_OTHER_GLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OTHER_GLYCAN_DEGRADATION.html Other glycan degradation 7/17 KEGG 0.000232050557880516 0.000329811620936639 2300 2244.81818181818 2076 2.32074792799921e-05 1003 1.86839800914387 -1.96037590911895 -1 1.67326075018657 2296 1591 3791 1874 3185 2076 2463 1893 1003 1924 2597 1987 M1496 KIM_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/KIM_HYPOXIA.html Genes up-regulated in normal fibroblasts under hypoxia conditions. 14499499 23/42 John Newman 2.41352995655511e-06 4.79025894808016e-06 935 1750.09090909091 2076 2.19412054940374e-07 178 1.58563868447151 1.65878795523328 1 2.16962763773037 1040 2806 2076 2911 2270 799 178 933 2880 2425 933 1988 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 13/26 John Newman 4.15711993759552e-06 7.80146737187528e-06 760 1663.18181818182 2078 3.77920708446365e-07 390 1.21499763494209 1.2482209066028 1 1.59628327311752 759 2391 2204 2078 3106 390 493 931 2598 2918 427 1989 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 9/27 Jessica Robertson 0.000457072630151108 0.000626819533183521 1990 2512.81818181818 2079 4.57166669299794e-05 1236 1.26347545392425 1.20851636822969 1 1.04088565409427 1988 2079 4453 3046 3312 1611 1573 1393 3881 3069 1236 1990 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 42/109 Arthur Liberzon 0.000515147725443796 0.000704195519670254 1365 2195.90909090909 2079 4.68425809993502e-05 1168 1.56962175019742 1.80494491597096 1 1.27268842808532 1361 3057 1953 1826 3488 2079 1562 2188 2919 2554 1168 1991 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 83/199 Leona Saunders 9.56836695371947e-09 7.02612984903285e-08 2720 2189.72727272727 2080 8.69851545030431e-10 225 2.01199247004507 2.11669293548784 1 3.70194935072391 2719 1706 942 2370 225 4521 2080 2796 1845 1133 3750 1992 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 11/18 Jessica Robertson 0.00026169281002197 0.000368698889886636 1665 2243.18181818182 2080 2.37930858091711e-05 893 0.856702704882265 -0.912461086249316 -1 0.756561124581164 1664 1776 3138 2593 3194 893 1352 2080 2622 3903 1460 1993 M619 REACTOME_TRIGLYCERIDE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRIGLYCERIDE_BIOSYNTHESIS.html Genes involved in Triglyceride Biosynthesis 22/42 Reactome 1.15669156112785e-07 3.65063971395134e-07 2400 2077.54545454545 2084 1.05153783813009e-08 807 1.70144061912972 -1.14956969229561 -1 2.81735474555133 2398 1623 2084 2529 1299 1117 1874 4291 807 2352 2479 1994 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 7/12 Arthur Liberzon 2.09061334222667e-06 4.22267850072163e-06 1850 2349.45454545455 2084 2.09061530902814e-07 561 1.97085189894847 1.97085189894847 1 2.72447984924155 1846 3110 4518 2822 3506 2084 965 561 3253 1939 1240 1995 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 28/75 Leona Saunders 1.06699428480725e-05 1.8470392384953e-05 1210 2041.45454545455 2085 9.69999508851776e-07 758 1.74569950839887 1.84182112995195 1 2.12545888054215 1210 3063 2163 2591 3402 1964 1129 758 2779 2085 1312 1996 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 238/616 Jessica Robertson 5.50488836503020e-09 4.85798622947862e-08 2060 2172.09090909091 2085 5.00444398073152e-10 102 1.44659347256317 1.73328127688248 1 2.72127867392897 2029 2412 2169 2299 102 4398 2085 2057 2915 2059 1368 1997 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 15/41 Arthur Liberzon 5.82845052474217e-06 1.06025307294029e-05 3175 1917.90909090909 2085 5.29860542371665e-07 232 1.31766420305164 1.42436829925319 1 1.68601220641914 781 2351 2085 3172 3465 437 232 1576 3337 3171 490 1998 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 94/205 Arthur Liberzon 5.89268586441995e-08 2.19435778250278e-07 3350 2175.18181818182 2085 5.35698729295925e-09 1011 1.50058160835179 -1.48457886571519 -1 2.57008351457506 3346 2085 2507 1822 1011 1326 3409 1909 2640 1593 2279 1999 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 9/14 Arthur Liberzon 0.000378268750173599 0.000522418910496164 1400 2343.90909090909 2088 3.7833315486489e-05 955 1.56559453852349 1.73395211111896 1 1.32164249414673 1397 1481 4654 2748 3270 2017 955 3331 2160 1682 2088 2000 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 10/23 Arthur Liberzon 1.23981549669966e-06 2.66993355585229e-06 4255 2655.63636363636 2089 1.12710563218303e-07 1417 1.52714423019597 -1.11586031684344 -1 2.18930703518696 4253 1417 1633 2038 2089 2618 3885 3337 1533 1852 4557 2001 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 93/268 Reactome 8.82420604707616e-08 2.94727224066991e-07 1615 1981.90909090909 2090 8.02200581910484e-09 1042 1.74955495198594 1.85931686016059 1 2.93885380644709 1613 2260 1042 2984 1188 2781 1639 2869 2112 1223 2090 2002 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 95/317 Arthur Liberzon 1.64751468802705e-07 4.87082260447619e-07 3570 2313.18181818182 2092 1.4977407376405e-08 1142 1.62694730024769 -1.4102763384172 -1 2.64159656831138 3569 2057 1422 2092 1419 1481 3930 2930 2754 1142 2649 2003 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 103/258 Arthur Liberzon 4.74436763626753e-08 1.89769579972418e-07 4280 2253.90909090909 2093 4.31306158052843e-09 901 1.45407944373282 1.49017193504906 1 2.51403115395225 4277 1178 2072 1650 901 2199 3205 2670 2093 1956 2592 2004 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 13/26 Arthur Liberzon 8.80538354491691e-05 0.000131449593155402 2095 2112.18181818182 2093 8.00521454134701e-06 1115 2.50866091737281 2.45082245081606 1 2.50444327251344 2093 1986 1115 2795 3016 2643 1690 2140 1506 1338 2912 2005 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 27/85 Jessica Robertson 0.00087618722966308 0.00117275445821228 2100 2490.09090909091 2096 7.96851255225099e-05 865 1.16738450191114 -1.44827616862051 -1 0.880030327557755 2096 1975 3203 3808 4222 865 1745 2078 2815 3312 1272 2006 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 42/100 Arthur Liberzon 3.90459321143973e-07 9.89555727375806e-07 3245 2454.72727272727 2096 3.54963082221181e-08 1327 1.53452207884586 0.935518875510633 1 2.37002518921941 3245 1327 2096 2645 1735 4033 2620 1717 1636 1890 4058 2007 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 33/71 Leona Saunders 1.80232076622945e-06 3.69937586971143e-06 1120 2056.54545454545 2098 1.63847476614407e-07 990 1.31758628939789 1.32145386915264 1 1.84088727834898 1118 2098 2289 3228 2201 1280 990 2759 3162 1843 1654 2008 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 174/380 Broad Institute 1.76439686417205e-07 5.14817167217323e-07 2560 2190.18181818182 2098 1.60399727788767e-08 1451 1.63656415644782 -1.47256109878459 -1 2.64708682569478 2559 3339 1677 2062 1451 1511 2618 2098 2751 1846 2180 2009 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 84/208 John Newman 1.22670491505269e-07 3.82457700062334e-07 4285 2080.18181818182 2098 1.11518634859356e-08 259 2.03834831908264 -1.64771695918343 -1 3.36462985310084 4281 647 500 259 2098 2328 4494 2949 693 296 4337 2010 M273 PID_EPHA2_FWD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHA2_FWD_PATHWAY.html EPHA2 forward signaling 18832364 26/46 Pathway Interaction Database 8.86085493260663e-06 1.55571248460827e-05 1735 2071.90909090909 2099 8.05535511030061e-07 1378 1.73646096547888 1.80381307935168 1 2.1475066279526 1733 2590 2356 1378 2568 2271 1928 2025 1511 2332 2099 2011 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 14/26 Arthur Liberzon 1.0522721573657e-05 1.82492499238181e-05 2100 2061.54545454545 2100 9.56615627704799e-07 585 1.25928707499497 1.34797086638846 1 1.53492665733516 2100 585 2473 2487 2604 1853 1571 3100 2568 1443 1893 2012 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 28/66 Jessica Robertson 1.80614424627242e-07 5.23737124878252e-07 2460 2413.72727272727 2101 1.641949449593e-08 1461 1.24741356528326 1.50793337628663 1 2.0152552486882 2459 1621 2101 3107 1461 3462 1826 1841 3889 2086 2698 2013 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 13/34 Arthur Liberzon 1.65150911644666e-07 4.87955341719359e-07 4435 2332 2101 1.50137203674831e-08 500 2.36280595169076 -1.90907566063895 -1 3.83590249758469 4432 1066 1201 2101 1420 2854 4248 3044 500 1334 3452 2014 M13494 BIOCARTA_BIOPEPTIDES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BIOPEPTIDES_PATHWAY.html Bioactive Peptide Induced Signaling Pathway 28/67 BioCarta 7.29492195542401e-05 0.000109987143768072 1720 2041.63636363636 2102 6.63196714276922e-06 678 1.31972831717716 -1.24115848348406 -1 1.34378920294275 1720 2102 2749 2141 2987 678 1712 1667 2662 2965 1075 2015 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 27/141 Arthur Liberzon 6.88333214291431e-06 1.23347206201516e-05 2160 1747.72727272727 2102 6.25759425408281e-07 485 2.01689241586024 -1.86523899343272 -1 2.54661314853996 2157 1395 648 1263 2518 1159 2200 3021 2277 485 2102 2016 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 10/31 Jessica Robertson 0.0021584967506474 0.00279798499959439 1510 2508.36363636364 2103 0.00019641976733096 602 2.17992991712062 2.17992991712062 1 1.43158873521185 1510 3669 2357 4166 4410 2103 1491 1665 602 3846 1773 2017 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 46/112 Kevin Vogelsang 3.25316724376258e-08 1.46439401578016e-07 2105 2070.18181818182 2103 2.95742481078869e-09 740 1.7221503028387 2.0154360933015 1 3.02737640750604 2103 2093 1679 2373 740 3427 2556 3106 1274 1171 2250 2018 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 69/172 Arthur Liberzon 1.66607685108932e-06 3.4652623720393e-06 1590 2034.72727272727 2104 1.5146164662031e-07 514 1.43491238832938 1.66327085873133 1 2.01529050893488 1587 2866 2626 3040 2600 1679 1221 514 2104 3604 541 2019 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 28/80 Jessica Robertson 4.03780027250761e-06 7.60190119605088e-06 2040 2173.45454545455 2105 3.67073425759903e-07 1041 1.84428175652397 2.30411666420289 1 2.42838560377045 2036 1767 2105 1814 2395 3147 2239 2980 1041 1765 2619 2020 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 14/41 Arthur Liberzon 2.5243651640929e-06 4.98070533007973e-06 2410 1931.36363636364 2106 2.29488005513806e-07 631 1.96096365019204 2.42385517093192 1 2.67464412443821 2407 1638 1983 2106 2278 3113 2252 829 631 2409 1599 2021 M124 PID_CXCR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CXCR4_PATHWAY.html CXCR4-mediated signaling events 18832364 65/141 Pathway Interaction Database 4.71472261308926e-07 1.15550157766403e-06 1780 1905.54545454545 2108 4.28611238498263e-08 828 1.6763478579024 1.95336753417187 1 2.56003928800396 1777 2187 2108 828 1807 2876 2147 1372 2334 1382 2143 2022 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 241/653 Kevin Vogelsang 1.02535203843844e-13 2.32115925223311e-12 3430 2155.72727272727 2108 9.32138216762261e-15 201 1.77382478037008 -1.42650002235354 -1 5.30822671521867 3430 999 201 843 525 3935 3624 3249 2108 315 4484 2023 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 151/534 Arthur Liberzon 4.00042715584818e-08 1.67128287193363e-07 2110 2030.09090909091 2108 3.6367520259918e-09 832 1.79980942810729 2.03193229749791 1 3.13732468064311 2108 2052 1214 2204 832 3777 2174 2291 1812 1506 2361 2024 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 64/150 Jessica Robertson 9.95397697406317e-07 2.20228215771766e-06 1860 2269.72727272727 2109 9.04907407070704e-08 1015 1.6606809951724 1.69551434387393 1 2.41646660731499 1857 1963 1455 2952 2031 3172 2109 3549 2300 1015 2564 2025 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 74/135 Kevin Vogelsang 6.60530500673859e-05 0.000100104978206911 860 2203.09090909091 2110 6.00500303045762e-06 860 1.86735445705975 1.99995570314272 1 1.92103783185425 860 3712 1479 2874 2973 1446 1246 2110 2708 3117 1709 2026 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 142/254 John Newman 2.96479256428947e-08 1.36339724791565e-07 3710 2437.18181818182 2110 2.69526600385818e-09 703 1.71686939616305 -1.22615640912134 -1 3.03179858364732 3710 1826 1056 2110 703 2469 4179 1923 2561 1950 4322 2027 M184 PID_ECADHERIN_KERATINOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ECADHERIN_KERATINOCYTE_PATHWAY.html E-cadherin signaling in keratinocytes 18832364 16/40 Pathway Interaction Database 2.86801268430753e-06 5.6068032701982e-06 2105 2130.27272727273 2111 2.60728765743319e-07 633 2.33471367678686 2.28538056957028 1 3.15353641331129 2105 4060 2196 1666 2305 2149 1961 1594 633 2653 2111 2028 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 9/33 Reactome 2.99348871269567e-05 4.78264170054275e-05 1860 2235.90909090909 2111 2.99352903784621e-06 869 1.9834111369067 1.80053281399121 1 2.20408597939939 1859 2209 3973 3214 2840 1365 869 2111 2553 1670 1932 2029 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 2/11 Arthur Liberzon 0.000386406011725739 0.000533342730764894 2380 2287.8 2113 4.29413764111054e-05 1333 1.9683837287308 1.9683837287308 1 1.65711847153904 2376 2285 4222 NA 3716 1941 1333 1381 1339 2529 1756 2030 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 26/73 Kevin Vogelsang 7.14899505455174e-05 0.000107856377416708 2325 2029.63636363636 2113 6.49929761345821e-06 1083 2.21685204020947 2.89794189314072 1 2.26211372278614 2323 2308 1083 1164 2982 3222 2354 1431 1751 1595 2113 2031 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 58/126 John Newman 5.62155338861154e-08 2.13127825073088e-07 3800 2261.18181818182 2115 5.11050321114214e-09 662 1.64909288050708 -1.05250999879521 -1 2.82981562286747 3799 662 1170 1515 982 2221 4280 2804 1987 2115 3338 2032 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 6/17 Arthur Liberzon 1.61435714582522e-07 4.79861624934624e-07 2710 2336 2115 1.61435726310193e-08 432 1.41730132155574 -1.43440734759665 -1 2.30356898413774 2706 432 4610 2988 1453 1695 3068 2933 1966 1730 2115 2033 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 15/35 Lauren Kazmierski 4.30394275897247e-05 6.73173423516188e-05 2255 2220.90909090909 2116 3.91275178266355e-06 639 2.34593717003553 2.34593717003553 1 2.51736454935825 1271 4100 1987 2254 2883 2255 1852 2116 639 3163 1910 2034 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 10/25 Arthur Liberzon 5.97802247247636e-06 1.0840949421836e-05 1765 2197 2117 5.43458065137877e-07 985 1.77446984503799 2.21332253961193 1 2.26610816768555 1762 2750 2301 4011 2481 2117 1660 985 1161 3187 1752 2035 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 88/354 Arthur Liberzon 4.15532385109479e-08 1.7155812833683e-07 1665 2028 2117 3.77756720870898e-09 565 1.90239457060225 1.98830438812306 1 3.3105858255121 1661 3008 565 2070 849 3033 2282 2117 2819 1047 2857 2036 M13408 REACTOME_ERK_MAPK_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ERK_MAPK_TARGETS.html Genes involved in ERK/MAPK targets 15/26 Reactome 1.38390977429414e-07 4.21377595993653e-07 2170 1919.27272727273 2118 1.25809987395361e-08 571 1.37269982761163 1.4016233072206 1 2.25100675691569 2170 2118 2705 1272 1363 2173 1269 2408 571 3158 1905 2037 M10960 REACTOME_P2Y_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P2Y_RECEPTORS.html Genes involved in P2Y receptors 5/14 Reactome 0.0070569878276397 0.00878794710611736 1765 2367.18181818182 2118 0.00070794989896718 684 3.06480831208956 3.06480831208956 1 1.62087243302456 1509 3422 4006 3156 4028 1765 1353 2118 684 2234 1764 2038 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 89/269 Jessica Robertson 4.4822531293505e-08 1.81851412676506e-07 2260 2216.18181818182 2118 4.07477565515579e-09 876 1.58800429926766 1.85796743417155 1 2.75314117386235 2260 1915 1345 3038 876 3783 2118 1929 3109 1222 2783 2039 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 46/164 John Newman 1.57961755717487e-08 9.10797518777006e-08 2410 2011.36363636364 2120 1.43601597137877e-09 444 1.79395598086574 1.41932314464923 1 3.24876851209875 2408 1760 1313 2120 444 2824 1709 2354 2905 1021 3267 2040 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 253/635 Jessica Robertson 2.60996690862903e-08 1.24039603791437e-07 2690 1990.18181818182 2121 2.37269721781122e-09 409 1.69055315511551 1.91750251466135 1 3.00318239122697 2688 1374 780 549 653 3871 2701 3570 2121 409 3176 2041 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 24/59 Jessica Robertson 1.02221809685532e-06 2.24993612111978e-06 4175 2699.36363636364 2122 9.29289610748848e-08 830 1.67760120707209 -1.62712691562188 -1 2.43707549363754 4175 830 1645 1895 2043 4362 3461 2877 2031 2122 4252 2042 M1394 BIOCARTA_GATA3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GATA3_PATHWAY.html GATA3 participate in activating the Th2 cytokine genes expression 11/17 BioCarta 2.34702004029249e-06 4.68005783353642e-06 1645 2058.36363636364 2125 2.13365685832842e-07 1159 1.16310512243232 1.10051387373967 1 1.59449931981962 1644 2033 2670 2125 2261 1414 1159 2978 2230 2605 1523 2043 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 12/42 Reactome 1.02202379038041e-06 2.24993612111978e-06 2125 2466.45454545455 2125 9.29112968334799e-08 1609 1.48437683544197 1.71100374617795 1 2.15637563472033 1705 3300 2125 4453 2041 1893 1609 2335 3402 2144 2124 2044 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 43/159 Yujin Hoshida 1.40882335269864e-06 2.99398922029289e-06 2520 2130.09090909091 2125 1.28074932261241e-07 1035 1.55009969613402 -1.40809283052764 -1 2.20238010142254 2518 1386 1209 2269 2125 1545 3534 3263 2537 1035 2010 2045 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 49/114 Jessica Robertson 8.09730360656673e-08 2.76930509970378e-07 2985 2123.27272727273 2125 7.36118536781412e-09 1094 1.85079831182349 -1.48189153929951 -1 3.1217966465922 2981 1116 1094 2156 1152 4378 2125 3017 1263 1141 2933 2046 M976 REACTOME_GABA_RECEPTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_RECEPTOR_ACTIVATION.html Genes involved in GABA receptor activation 12/59 Reactome 1.02202379038041e-06 2.24993612111978e-06 1710 2465.54545454545 2126 9.29112968334799e-08 1610 1.48437683544197 1.71100374617795 1 2.15637563472033 1706 3301 2126 4454 2042 1894 1610 2315 3403 2145 2125 2047 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 8/11 Jessica Robertson 0.000161047788124966 0.000233210733978242 2095 2647.09090909091 2126 1.61059460691076e-05 1292 0.929382061829259 0.96964962085562 1 0.868297950094588 2092 2126 4327 3555 3124 1858 1568 1948 4342 2886 1292 2048 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 12/45 Jessica Robertson 1.14216164918727e-08 7.70096329221808e-08 2040 2047.81818181818 2126 1.03832877737906e-09 291 1.66242963465474 1.84914690463844 1 3.04174299125813 2040 1851 1674 2291 291 2126 1698 2485 2774 2754 2542 2049 M18899 BIOCARTA_DREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DREAM_PATHWAY.html Repression of Pain Sensation by the Transcriptional Regulator DREAM 9/17 BioCarta 7.00429573547811e-05 0.000105775474754916 950 1969.54545454545 2128 7.00451651598649e-06 942 1.32470237114888 1.32470237114888 1 1.35463176981001 948 2600 3860 2128 2997 1019 942 1674 2148 2294 1055 2050 M553 REACTOME_SIGNALING_BY_ERBB2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ERBB2.html Genes involved in Signaling by ERBB2 58/128 Reactome 2.16009267803445e-08 1.11389821060527e-07 2070 2125.36363636364 2128 1.96372063567595e-09 565 1.45887604482231 1.50405443004954 1 2.60914927036647 2069 2089 2693 1407 565 2689 1938 2748 2128 2701 2352 2051 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 20/49 Leona Saunders 6.641385306218e-08 2.38845215233596e-07 2545 2121.18181818182 2129 6.03762318791721e-09 1065 1.60840361261494 1.58531173490579 1 2.73952474842658 2545 1340 1789 1606 1065 2850 2459 2614 1435 2129 3501 2052 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 4/16 Kevin Vogelsang 0.00141278864223133 0.00186016509623377 2045 2436.09090909091 2129 0.000141368763400941 1362 3.19382918844313 3.19382918844313 1 2.24307773449363 2045 1999 4391 2940 3421 2208 2129 1741 1362 3108 1453 2053 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 86/239 Jessica Robertson 2.65707969886493e-08 1.25641528444814e-07 1930 2074.18181818182 2129 2.41552702814196e-09 662 1.61930927830204 1.88468444402241 1 2.87430006911452 1929 2794 2008 3485 662 2129 1273 1760 2193 2189 2394 2054 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 17/42 Arthur Liberzon 4.05719622707907e-08 1.68397001949447e-07 2660 2153.36363636364 2132 3.68836027445553e-09 842 1.74242659698874 -1.4614394463569 -1 3.03582620857137 2659 1768 1871 2442 842 3224 2132 3547 1580 1409 2213 2055 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 138/360 Arthur Liberzon 4.64889013162559e-05 7.22543918965092e-05 2445 2100.63636363636 2134 4.22635306519206e-06 1239 1.71528121353311 2.14411077095446 1 1.82706263823445 1606 2790 1239 2656 2898 2444 1649 1293 2444 1954 2134 2056 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 41/91 Yujin Hoshida 0.000185950769828541 0.000267865142150797 2335 2347.45454545455 2134 1.69060444381736e-05 1225 1.86432951361267 2.53786449028114 1 1.71294314529098 2332 3435 1796 2694 3412 3166 1974 1225 1652 2134 2002 2057 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 23/50 Arthur Liberzon 0.000135009241767196 0.000197149674952034 1415 2311 2135 1.22743207003868e-05 1396 2.03411891929173 2.27401915108038 1 1.93859503951099 1412 4093 2117 3192 3087 1688 1444 1396 2135 2422 2435 2058 M11355 KEGG_TIGHT_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TIGHT_JUNCTION.html Tight junction 69/153 KEGG 1.42314124520378e-07 4.31082086297668e-07 4210 2147.09090909091 2136 1.29376485205845e-08 735 2.5620103450828 -2.4484227805261 -1 4.19476829322413 4208 2185 768 853 1370 2136 4332 3514 735 1048 2469 2059 M220 PID_CASPASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CASPASE_PATHWAY.html Caspase cascade in apoptosis 18832364 42/81 Pathway Interaction Database 2.75502365072753e-06 5.4005317614638e-06 2570 2122.63636363636 2136 2.50457009164016e-07 863 1.95095006542007 2.22784519466085 1 2.64334948065991 2567 1881 1534 1402 2297 3569 2136 2133 863 2186 2781 2060 M2349 BIOCARTA_CCR5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CCR5_PATHWAY.html Pertussis toxin-insensitive CCR5 Signaling in Macrophage 12/27 BioCarta 0.000184543788104128 0.000266001904354336 2505 2229.90909090909 2142 1.67781154644144e-05 1091 2.15503377154485 -1.81800076117323 -1 1.9817221788239 2501 2747 1748 1091 3130 1943 3417 2274 1500 2142 2036 2061 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 540/1168 Jessica Robertson 2.37740125827347e-08 1.17662724439535e-07 3530 2527.09090909091 2145 2.37740128370763e-09 654 1.55138381767183 -1.15549443981957 -1 2.76510168218161 3529 1787 4337 940 654 2145 4123 2278 2035 1560 4410 2062 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 35/78 John Newman 2.4758510556584e-07 6.81258840094847e-07 2040 2366.09090909091 2147 2.25077394026133e-08 1559 1.42136939822339 1.6759806188316 1 2.25453807690687 2038 2147 1896 3625 1559 3220 2143 2228 2883 2346 1942 2063 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 31/53 Arthur Liberzon 1.66805086587879e-06 3.46652816773757e-06 3450 2045.27272727273 2148 1.51641102782231e-07 644 2.03068439446047 -1.76540647574814 -1 2.85195128985967 3449 1519 967 1132 2172 2148 3052 3117 688 644 3610 2064 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 113/279 Kevin Vogelsang 9.00261269161123e-08 2.99618203642686e-07 1640 2308 2148 8.18419369091535e-09 1090 1.75306006923851 1.81737280310483 1 2.94151848512628 1637 2863 1090 1648 1194 3415 2148 3996 2886 1367 3144 2065 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 16/65 Arthur Liberzon 4.08643280195317e-05 6.41078811849767e-05 2150 2364.45454545455 2148 3.71500791651654e-06 1307 1.8769597965944 1.97401783366934 1 2.02435954859491 2148 2070 1417 1934 2873 2886 2208 3825 3320 1307 2021 2066 M13266 KEGG_RENAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENAL_CELL_CARCINOMA.html Renal cell carcinoma 41/78 KEGG 2.27758840654489e-06 4.55942814398066e-06 1830 2277.63636363636 2149 2.07053705860134e-07 1691 1.39561247383184 1.78351695206339 1 1.91731446543634 1829 2341 2765 1691 2252 3002 2098 1826 1894 3207 2149 2067 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 16/28 Arthur Liberzon 0.000377040789164244 0.000520876514747538 3580 2398.72727272727 2149 3.42823111585328e-05 1308 1.66031697925686 1.59956359442651 1 1.4021536245119 3579 1684 1517 2149 3255 1988 3138 3158 2551 1308 2059 2068 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 25/48 Arthur Liberzon 0.00183686349361272 0.0023976441033619 950 1906.54545454545 2150 0.000167127177797947 642 1.79630055510117 -1.73895186445305 -1 1.21063880914545 946 2193 1155 1468 3434 1640 2226 2394 2724 642 2150 2069 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 14/52 Arthur Liberzon 2.01649495600476e-08 1.06410983827008e-07 2150 2106 2150 1.83317724953429e-09 541 1.33311636557432 1.4411098577929 1 2.39104207790963 2150 961 2124 2119 541 3290 2610 3205 2306 1446 2414 2070 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 128/339 Arthur Liberzon 2.53455631154309e-07 6.91323101041381e-07 2155 2268.72727272727 2151 2.3041423668564e-08 1466 1.68697345060654 2.13469614175386 1 2.67306856837339 2151 3053 2287 1466 1575 4092 2249 1655 1644 2663 2121 2071 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 54/127 Leona Saunders 3.70230657954791e-08 1.59372539641036e-07 1580 2282.36363636364 2151 3.36573331077525e-09 791 1.48811625803076 1.74404592367251 1 2.60189794573702 1580 3403 2151 3501 791 2501 1726 1056 3192 3381 1824 2072 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 75/230 Jessica Robertson 7.70322376918197e-09 6.14945597655651e-08 1815 1914.63636363636 2151 7.00293072377687e-10 174 1.36526207398925 -1.12041444897938 -1 2.53232830457226 1815 2369 2434 2994 174 559 1454 2151 2725 2861 1525 2073 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 13/31 Jessica Robertson 1.46913878258134e-08 8.75503631708099e-08 2955 2268.36363636364 2154 1.33558072035646e-09 414 1.53211764761225 1.68769796559655 1 2.78135582229878 2953 416 1698 2154 414 3400 2593 4311 1686 1777 3550 2074 M16811 BIOCARTA_ERK5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK5_PATHWAY.html Role of Erk5 in Neuronal Survival 16/34 BioCarta 8.08941740185561e-06 1.42991361543174e-05 2160 2003.81818181818 2156 7.35404286078228e-07 375 2.13401883479705 2.83415922864365 1 2.65927293267245 2588 2157 1816 706 2546 3376 2009 1876 375 2156 2437 2075 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 24/57 Arthur Liberzon 1.60995787369389e-06 3.36647148421667e-06 3170 2662.45454545455 2158 1.46359913805519e-07 1917 1.3714050535635 1.54281752104503 1 1.93052732332691 3170 1932 2011 2744 2158 3700 1959 1917 3674 2123 3899 2076 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 75/144 Yujin Hoshida 6.40432301269228e-05 9.72477564402982e-05 1380 2313.36363636364 2159 5.82228132155869e-06 1032 1.91921669267225 2.09496359018063 1 1.98059926264088 1378 3587 2159 1372 3063 3442 2139 1032 1921 3150 2204 2077 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 37/91 Jessica Robertson 1.17670326294634e-07 3.69296477453023e-07 2290 2217.81818181818 2159 1.06973029625827e-08 539 1.23553077077794 1.13900866175186 1 2.04428024999469 2289 539 2088 2159 1310 2901 2040 3824 2253 1566 3427 2078 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 29/83 Jean Junior 6.62964600025324e-07 1.53794659193993e-06 2190 2293.36363636364 2161 6.02695272552876e-08 1464 2.27006969387868 2.76742162148834 1 3.39424013586298 2187 3439 1464 3225 1919 2671 2161 1921 1488 3041 1711 2079 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 14/34 Jessica Robertson 2.08527839947834e-06 4.21371909441807e-06 2165 2292.54545454545 2164 1.89570943274551e-07 1453 1.33880533410485 1.28261313953796 1 1.85106454144934 1901 2163 2333 3756 2233 2397 1828 2164 3535 1453 1455 2080 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 34/84 Arthur Liberzon 1.27115742293105e-06 2.72865033616807e-06 1960 2081.27272727273 2165 1.15559832491356e-07 1040 1.38986783888311 1.57362957010808 1 1.98913077735849 1960 1040 2166 3093 2093 2389 1227 3364 2165 2215 1182 2081 M621 REACTOME_ARMS_MEDIATED_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ARMS_MEDIATED_ACTIVATION.html Genes involved in ARMS-mediated activation 11/23 Reactome 2.18854722350149e-06 4.40329924193489e-06 2170 2031.72727272727 2166 1.98959036423508e-07 1080 1.43336423185668 2.08224328858965 1 1.97475743604115 2166 1852 2191 1300 2244 2551 1737 2767 1134 3327 1080 2082 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 429/962 Jean Junior 1.72766727688126e-05 2.88211066552709e-05 1625 2393.18181818182 2166 1.57061894950791e-06 1373 1.66601453656206 2.07220552508032 1 1.94563315717593 1624 3517 1694 1613 2707 3749 2087 1373 2166 3488 2307 2083 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) 12/35 Reactome 1.08006319140843e-05 1.86707074748186e-05 2465 2059.90909090909 2169 9.81880448984998e-07 726 1.87059789361328 2.10014296744881 1 2.27527365496721 2465 726 1144 1627 2610 2674 2169 3534 1318 1210 3182 2084 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 9/15 Reactome 2.30036359850477e-06 4.59604103623932e-06 1720 1999.90909090909 2170 2.30036597976095e-07 365 1.05492035165557 -1.04371658822384 -1 1.44832367803816 1717 2170 4063 2489 2903 506 994 1074 3417 2301 365 2085 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 6/30 Arthur Liberzon 0.000322828160880077 0.000449560999074009 1755 2599.72727272727 2170 3.22875068580663e-05 712 1.18796300646413 1.18796300646413 1 1.02278571499739 1754 2131 4136 3796 3642 1228 712 2170 3886 3446 1696 2086 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 26/51 Arthur Liberzon 1.19083357033105e-08 7.85207853988603e-08 1285 2027.18181818182 2171 1.08257597888808e-09 315 1.34185533922738 1.3356551430069 1 2.45227613344605 1283 2617 2171 3746 315 1191 1092 2514 3702 2333 1335 2087 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 62/159 Arthur Liberzon 2.59376069982637e-07 7.05009433839116e-07 2250 2008.45454545455 2171 2.35796455056925e-08 582 1.98295773988763 2.28906707475806 1 3.13772360002222 2247 1022 582 1327 1583 3886 2587 3694 2383 611 2171 2088 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 45/96 Reactome 1.66984296790205e-06 3.46847701577527e-06 2090 2228.54545454545 2174 1.51804021395166e-07 362 1.17867203037766 -1.06349442588624 -1 1.65528664720716 2089 2519 3339 2298 2174 362 1801 2075 3281 3932 644 2089 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 9/17 Arthur Liberzon 2.1248155202792e-05 3.49487031520826e-05 1930 2186.63636363636 2174 2.12483583733709e-06 75 3.21809100137513 3.21809100137513 1 3.68890621170539 1926 3240 4200 2174 3034 2300 1541 895 75 3060 1608 2090 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 13/33 Jessica Robertson 6.50385913593969e-07 1.51326136598875e-06 2175 2044 2174 5.91260096243283e-08 541 3.11734876878434 3.59674840008371 1 4.66673853644431 2174 2916 1250 2176 1915 3316 2364 1861 541 1779 2192 2091 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 275/629 Jessica Robertson 4.00979765916453e-08 1.6726859268505e-07 1810 2190.36363636364 2175 3.64527066568047e-09 835 1.70733227515081 1.92269483514335 1 2.97596374930165 1808 2511 1000 1137 835 4094 2210 3129 2094 2175 3101 2092 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 30/89 John Newman 1.8777818211146e-08 1.02042166516299e-07 1760 1902.54545454545 2176 1.70707439740197e-09 518 1.3515088275217 1.47614160778302 1 2.43035954209998 1760 821 2176 2356 518 2639 2246 2284 2001 1601 2526 2093 M3574 REACTOME_SIGNALLING_BY_NGF http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_BY_NGF.html Genes involved in Signalling by NGF 130/279 Reactome 1.06416538418859e-07 3.42491688894763e-07 2195 2041.54545454545 2177 9.67423123330462e-09 488 1.46153003541495 1.60937677413321 1 2.4305157162348 2191 1005 2177 488 1259 4051 2227 2993 1579 1655 2832 2094 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 16/47 Leona Saunders 1.53229926493375e-06 3.22712555302452e-06 4630 2803.45454545455 2177 1.39300030198247e-07 1302 1.67626985809969 -1.55217955571762 -1 2.36760142751076 4630 2028 1986 3346 2145 3499 4047 2177 2119 1302 3559 2095 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 377/974 Jean Junior 1.68229799970148e-06 3.48507888001818e-06 2550 2318.81818181818 2177 1.52936298738547e-07 921 1.73321538528878 2.0170404118435 1 2.4331439304439 2547 2219 921 1563 2177 3877 2862 2003 2155 1873 3310 2096 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 26/61 Arthur Liberzon 9.96605949714277e-07 2.20391480904252e-06 2040 2121.27272727273 2177 9.06005819254322e-08 794 2.5695701293079 -1.90043699833957 -1 3.73878388989421 2037 3017 794 2177 2032 2834 2232 2812 1573 1290 2536 2097 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 97/204 Arthur Liberzon 3.8058956306006e-08 1.61543722146689e-07 2900 2412 2180 3.45990517858253e-09 803 1.80791226162476 1.90523219775839 1 3.15831278445904 2897 2180 1496 1977 803 3866 3396 2846 2106 1380 3585 2098 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 62/163 Arthur Liberzon 1.72134355741593e-08 9.61408332544819e-08 2110 2190.90909090909 2182 1.56485779171293e-09 480 1.57063442214373 1.92097949159196 1 2.83485562358256 2110 3086 1942 2603 480 2622 2182 3357 2370 1620 1728 2099 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 36/119 Reactome 1.06376730723616e-05 1.84213362960407e-05 2610 2058.81818181818 2183 9.6706586446487e-07 1082 1.78419631300607 2.13634840649588 1 2.17286033617157 2183 1393 1579 1652 2607 3275 2607 1082 2203 1792 2274 2100 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 181/425 Arthur Liberzon 9.62821298883117e-09 7.04076564672179e-08 3520 2277.90909090909 2183 8.75292093724427e-10 229 1.67554781842945 -1.44716287611149 -1 3.08252120366144 3518 1431 1051 1878 229 3138 3221 3310 2183 837 4261 2101 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 11/26 Reactome 0.000565338372140006 0.00077055718785575 1865 2475.09090909091 2185 5.14076091410148e-05 1365 1.23032662181026 1.15768064923775 1 0.985202166090239 1861 3076 2963 2185 3742 1850 1365 1411 3355 3331 2087 2102 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 40/114 Jessica Robertson 5.97645788216905e-10 7.38936190919371e-09 2190 2001.18181818182 2186 5.43314353072053e-11 358 2.29937363855667 2.33761607924413 1 4.80920370317059 2186 1390 358 1580 1950 3556 2302 3341 2280 760 2310 2103 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 42/87 Jessica Robertson 1.98495774458953e-05 3.27979971479074e-05 1440 2064.72727272727 2187 1.80452332196989e-06 1046 2.05403943113334 -1.71554620914541 -1 2.3691241375834 1437 2521 1813 2711 2732 1046 1939 2396 2229 2187 1701 2104 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 45/116 Kevin Vogelsang 4.9859218035819e-07 1.21182725993697e-06 2345 2090.72727272727 2188 4.53265721232338e-08 1070 1.28894223016455 -1.41455997847718 -1 1.96155872808279 2343 1387 2719 2188 1825 1070 2337 2303 2799 2087 1940 2105 M8809 BIOCARTA_PTDINS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTDINS_PATHWAY.html Phosphoinositides and their downstream targets. 25/42 BioCarta 4.61325606304658e-07 1.13657822878214e-06 4220 2818.45454545455 2191 4.19387002765134e-08 1798 1.41163735921276 -1.44340625867957 -1 2.15838972069616 4216 1839 2316 1976 1798 1997 4683 4224 2152 2191 3611 2106 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 23/33 Arthur Liberzon 2.32511275173536e-08 1.16156485657056e-07 2755 2013.81818181818 2191 2.11373888755341e-09 323 1.63506902449711 -0.845078128728825 -1 2.91661088378266 2751 1675 2040 668 600 3731 3398 2191 323 2428 2347 2107 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 24/48 Arthur Liberzon 5.8254571141536e-06 1.06012007910384e-05 2390 2359.63636363636 2193 5.29588412694806e-07 1355 2.45422924493703 -1.66299816200599 -1 3.14033424718309 2389 2805 1355 2155 2473 3867 3229 1772 1601 2117 2193 2108 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 56/141 Arthur Liberzon 2.03783754177119e-09 2.20030108772807e-08 3810 2369.18181818182 2193 1.85257958514439e-10 21 2.31853411788593 2.97971951850672 1 4.56667578783554 3808 2729 1104 1689 21 2884 4434 2193 1413 1312 4474 2109 M14691 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMINOACYL_TRNA_BIOSYNTHESIS.html Aminoacyl-tRNA biosynthesis 26/41 KEGG 0.00129655791600272 0.00171073628296925 825 2494.36363636364 2194 0.000117938424213207 817 0.698381445747426 -0.698381445747426 -1 0.497017431099245 825 2194 3628 3306 3555 817 1354 2122 3849 4227 1561 2110 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 25/101 Kevin Vogelsang 6.20951594553328e-07 1.45634593197042e-06 2495 2343.18181818182 2194 5.64501608924941e-08 1049 1.37166466787222 1.42312614063231 1 2.05928570966336 2494 1049 1915 2319 1897 3701 2151 3309 1968 2194 2778 2111 M17673 KEGG_CARDIAC_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CARDIAC_MUSCLE_CONTRACTION.html Cardiac muscle contraction 33/118 KEGG 1.76120259902708e-06 3.62291280906098e-06 2365 1845.45454545455 2195 1.60109455359407e-07 477 2.76986567664288 3.34240554442626 1 3.87642583877185 2362 1191 615 477 2195 4000 3070 2558 524 602 2706 2112 M13115 REACTOME_G_PROTEIN_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_PROTEIN_ACTIVATION.html Genes involved in G-protein activation 9/30 Reactome 4.48889675676689e-06 8.37379387030638e-06 2195 2322.27272727273 2195 4.48890582438e-07 1120 1.84358372294887 2.23271114484578 1 2.4075500736338 2195 1225 3997 1763 2432 2320 1921 4565 1120 1193 2814 2113 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 22/63 Arthur Liberzon 3.10804481745566e-06 6.0183049647096e-06 1730 2274.90909090909 2197 2.82549928031576e-07 1250 1.05161887347325 -1.07171931534909 -1 1.41211882451063 1729 2197 3331 2861 2323 1250 1903 2016 2893 2842 1679 2114 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 50/138 Jessica Robertson 3.43303054208925e-06 6.58501069186666e-06 1840 2323 2198 3.12094172657884e-07 1793 1.72875146259887 1.76476834012941 1 2.30399736283542 1839 3011 1793 2820 2346 2933 2146 2099 2497 1871 2198 2115 M9577 MOOTHA_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_MITOCHONDRIA.html Mitochondrial genes 12808457 286/573 Vamsi Mootha 1.79188466497474e-06 3.68279453511914e-06 885 2419.90909090909 2198 1.62898738586725e-07 737 1.03935850983927 -0.857447688802333 -1 1.4526783034208 883 3243 3764 2838 2198 737 1597 2183 3196 4377 1603 2116 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 38/107 Jessica Robertson 2.29953982961756e-07 6.42938164772547e-07 1890 2176.36363636364 2199 2.09049097270539e-08 1437 1.83740641618745 2.28483487642373 1 2.92632775104392 1886 2768 1437 2105 1535 3043 1787 2234 2607 2199 2339 2117 M10547 BIOCARTA_MAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MAL_PATHWAY.html Role of MAL in Rho-Mediated Activation of SRF 17/42 BioCarta 1.71920245620859e-06 3.5489791673099e-06 3260 2256.36363636364 2201 1.56291254517323e-07 393 1.89972237117071 -1.0604335214279 -1 2.66303607683559 3256 2201 1741 859 2186 2101 2865 3355 393 2778 3085 2118 M5202 BIOCARTA_P53HYPOXIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P53HYPOXIA_PATHWAY.html Hypoxia and p53 in the Cardiovascular system 24/44 BioCarta 1.81316983524216e-06 3.71676021344915e-06 2310 2292.81818181818 2204 1.64833757236421e-07 369 1.90926990217184 2.26247906427846 1 2.66656791916333 2306 1978 2004 369 2204 4229 3969 1853 1049 2572 2688 2119 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 21/46 Pathway Interaction Database 3.17426589506006e-07 8.33778586561179e-07 3525 2314.54545454545 2204 2.88569668459864e-08 671 1.69892947885635 -1.45785998321064 -1 2.65645537644857 3525 1204 2016 671 1654 2332 4385 2996 1332 2204 3141 2120 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 14/40 Arthur Liberzon 2.96409249548292e-06 5.76816338614325e-06 3460 2201.27272727273 2204 2.69463317186914e-07 325 3.77045716265505 -2.61023117486024 -1 5.0808686455787 3460 1410 997 1127 2314 4631 3769 2204 325 1445 2532 2121 M11266 KEGG_LYSOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSOSOME.html Lysosome 75/155 KEGG 2.19375719694632e-06 4.40925714908966e-06 1340 1958 2205 1.99432671316498e-07 1106 1.43682244712371 -1.40930604650144 -1 1.97930482344461 1338 1254 2286 2205 2246 1106 2499 2269 2626 1868 1841 2122 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 9/36 Reactome 5.04927643424457e-07 1.2234182715031e-06 3245 2196.72727272727 2205 5.0492775815286e-08 240 1.99237445605407 2.58751601644093 1 3.02994866932609 3242 240 4009 1415 1861 3565 2335 2205 1004 877 3411 2123 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 25/63 Leona Saunders 1.38502186450772e-06 2.9487562276616e-06 1060 2228.90909090909 2205 1.25911157859679e-07 1056 1.62116705875942 1.41037929291318 1 2.30610942584427 1059 2619 2517 3350 2120 1380 1056 3816 2569 1827 2205 2124 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 475/1265 Jessica Robertson 3.03637142322805e-08 1.38814014529235e-07 2915 2204.18181818182 2206 2.76033769557735e-09 713 1.55226575892414 1.93577572707099 1 2.73800837667869 2912 1861 1570 1657 713 2368 3280 2555 2206 1789 3335 2125 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 20/46 Jessica Robertson 5.9441259660679e-06 1.07836524494751e-05 2275 2251.18181818182 2207 5.40376547856055e-07 1038 1.88803309816283 2.44202887914702 1 2.41225316012366 2271 3129 1934 2698 2480 3204 1699 1038 2207 2128 1975 2126 M594 REACTOME_SIGNALING_BY_NOTCH4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH4.html Genes involved in Signaling by NOTCH4 8/16 Reactome 1.68025932724612e-06 3.48418396387941e-06 3095 2179.27272727273 2208 1.68026059771961e-07 310 1.99772592227113 -0.657021387884483 -1 2.80452973934668 3092 981 3934 600 2208 3437 4415 805 310 2871 1319 2127 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 83/235 Jessica Robertson 3.90669674700222e-07 9.89555727375806e-07 2420 2378.81818181818 2208 3.5515431279476e-08 1024 1.74285865805225 1.72669623750462 1 2.69179506914539 2419 1870 1431 2701 1736 3512 1973 3800 2208 1024 3493 2128 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 14/44 Jessica Robertson 6.34877187981741e-08 2.31520194776843e-07 2055 2067.45454545455 2208 5.77161096639149e-09 1014 2.08813548494754 2.01037219749569 1 3.56389723926119 2055 2352 2180 1014 1043 3049 2360 2799 1276 2406 2208 2129 M604 REACTOME_SIGNALING_BY_NOTCH2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH2.html Genes involved in Signaling by NOTCH2 8/16 Reactome 1.68025932724612e-06 3.48418396387941e-06 3095 2180.45454545455 2209 1.68026059771961e-07 311 1.99772592227113 -0.657021387884483 -1 2.80452973934668 3093 982 3937 601 2209 3438 4416 806 311 2872 1320 2130 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 232/605 Kevin Vogelsang 6.95221721545835e-08 2.47178223608785e-07 1465 1901.81818181818 2209 6.32019766832299e-09 1018 1.67287110905069 1.82680336644988 1 2.84292088074829 1463 2543 1018 2209 1083 2608 1638 2372 2453 1287 2246 2131 M618 REACTOME_SIGNALING_BY_NOTCH3 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH3.html Genes involved in Signaling by NOTCH3 8/16 Reactome 1.68025932724612e-06 3.48418396387941e-06 3095 2182.18181818182 2210 1.68026059771961e-07 312 1.99772592227113 -0.657021387884483 -1 2.80452973934668 3094 983 3940 602 2210 3439 4417 812 312 2874 1321 2132 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 22/73 Jessica Robertson 4.68352673624707e-08 1.88710286208545e-07 4370 2422.36363636364 2210 4.25775166904866e-09 894 2.18094839927489 -2.42033952010263 -1 3.7721153361519 4368 2107 1008 2210 894 2874 4132 1802 2912 1230 3109 2133 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 6/11 Arthur Liberzon 2.41231009095306e-05 3.91958567482872e-05 2200 2138.72727272727 2211 2.41233627793303e-06 61 3.49041964004825 3.49041964004825 1 3.95635899672124 2197 2402 4201 1731 2833 2414 2091 905 61 2480 2211 2134 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 24/58 Arthur Liberzon 1.86175774012114e-07 5.35818834674208e-07 2725 2394.63636363636 2212 1.69250717970278e-08 781 2.10008230997966 1.70366334212644 1 3.38743159867997 2723 1529 781 1837 1473 3754 2784 3699 2212 1419 4130 2135 M153 PID_P75_NTR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P75_NTR_PATHWAY.html p75(NTR)-mediated signaling 18832364 56/106 Pathway Interaction Database 4.42513687241222e-08 1.80314707688032e-07 3595 2189.90909090909 2214 4.02285178310961e-09 365 1.62298214980224 -1.00491464157274 -1 2.81532122861802 3594 523 1600 365 868 3086 4395 2214 1427 2580 3437 2136 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 10/23 Reactome 3.44622151059595e-07 8.9203157362956e-07 2670 1904.54545454545 2214 3.13292913675852e-08 424 1.18311942102554 -0.745001492376296 -1 1.84100641484845 2668 424 2214 1290 1691 1184 2266 2559 738 3180 2736 2137 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 6/8 Arthur Liberzon 0.00145389326566711 0.00191267373467604 1805 2724.36363636364 2214 0.000145484535499958 948 0.884261970846165 0.939686610424021 1 0.618281590206339 1804 2214 4190 4387 3919 1795 948 1761 3944 3447 1559 2138 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 38/119 Yujin Hoshida 1.02546562909325e-06 2.25496571465555e-06 1795 2218 2214 9.32241915531238e-08 1338 1.67092442032411 2.01161766830377 1 2.4269592380439 1791 2555 2225 2292 2045 2857 1907 2194 2214 2980 1338 2139 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 197/497 Jessica Robertson 4.71136830302103e-09 4.2972296893054e-08 4095 2580.54545454545 2215 4.28306210282779e-10 80 1.76103946452652 -1.21636711766709 -1 3.33693159016216 4092 2931 1394 2215 80 1936 4686 3895 1687 2168 3302 2140 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 236/593 Arthur Liberzon 7.64448693783896e-09 6.14443667079131e-08 1795 2071.36363636364 2216 6.94953360400162e-10 169 1.74971344405563 2.01938383426684 1 3.24557968926762 1794 2685 425 2216 169 3787 2199 2652 2830 756 3272 2141 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 38/89 Arthur Liberzon 1.92520604863203e-06 3.91899024495642e-06 4125 2499.54545454545 2217 1.7501888485179e-07 319 1.92738457839278 2.03208550804971 1 2.68046050930038 4122 809 1247 319 2217 3636 4231 3909 1352 1613 4040 2142 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 20/43 Arthur Liberzon 1.44297927255658e-06 3.06379740425924e-06 1265 2437.45454545455 2218 1.31180019909734e-07 1054 1.35602864136865 1.44484544752986 1 1.92315276321787 1265 3100 2218 4161 2129 1443 1054 2986 3670 2603 2183 2143 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 400/1035 Arthur Liberzon 6.78169147770025e-08 2.42218035552617e-07 2220 2519.90909090909 2220 6.16517426068346e-09 1072 1.48471940173931 1.89798233440525 1 2.52653302145296 2220 3911 2760 1571 1072 4224 2152 1703 2688 3490 1928 2144 M779 REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION.html Genes involved in Downstream signal transduction 55/111 Reactome 1.32321582015847e-08 8.23976483019129e-08 2060 2058.45454545455 2221 1.20292348010647e-09 369 1.23079438377008 1.30630545824764 1 2.24268319342552 2056 1026 2880 1060 369 2882 2221 2450 2765 1942 2992 2145 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 225/554 Lauren Kazmierski 1.07960774962274e-08 7.39899659922656e-08 4450 2421.90909090909 2221 9.81461595382464e-10 278 1.79546405669577 -1.54782956661185 -1 3.29317861983782 4449 1170 922 1237 278 2360 4671 4570 2221 650 4113 2146 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 28/91 John Newman 2.41317859407772e-07 6.6754161108903e-07 2250 2227.90909090909 2221 2.19379896252651e-08 1053 1.90009451696386 2.43890544107485 1 3.01819650827376 2248 3348 2050 2221 1553 3581 1790 1905 1053 2517 2241 2147 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 185/395 John Newman 2.49335388604724e-08 1.20328077343124e-07 2225 2188.63636363636 2221 2.26668537664135e-09 636 1.64390019265321 2.08921930633937 1 2.92588442066884 2221 2758 1723 1147 636 4371 2257 1645 2020 2362 2935 2148 M917 BIOCARTA_COMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_COMP_PATHWAY.html Complement Pathway 12/24 BioCarta 4.8934791090374e-05 7.58044400163612e-05 1625 2446.54545454545 2223 4.44871632591627e-06 1624 1.70564636030621 2.09213623599676 1 1.80766118432997 1968 3075 1625 3797 2907 2339 2223 1822 3375 1624 2157 2149 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 44/81 Reactome 0.0112444984784623 0.0138334785691978 2980 2101.63636363636 2223 0.00102748957053497 621 1.96838906393311 -1.80619988830192 -1 0.941249913744543 621 2977 1164 2021 3626 1778 2446 2223 2978 924 2360 2150 M17681 BIOCARTA_IL3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL3_PATHWAY.html IL 3 signaling pathway 11/29 BioCarta 0.00032980326541172 0.000459001515212153 1965 2484.36363636364 2224 2.99866106170769e-05 1147 0.746269952777204 -0.746269952777204 -1 0.640774198778366 1961 2468 3328 2186 3234 1147 2224 1608 3840 3894 1438 2151 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 57/121 Leona Saunders 3.03399460231863e-06 5.8870802097164e-06 1500 2112.18181818182 2224 2.75818071497604e-07 556 1.14819330756214 -1.11612787057571 -1 1.54462705312964 1497 2224 3187 2612 2319 556 1230 1969 3273 2963 1404 2152 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 128/267 Jessica Robertson 8.47729084832438e-08 2.85955903690318e-07 2230 2429.90909090909 2227 7.70662834089185e-09 884 1.83164169972258 1.88248059795617 1 3.08292261752641 2227 3084 958 2117 1171 3775 2505 4173 1952 884 3883 2153 M96 BIOCARTA_FREE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FREE_PATHWAY.html Free Radical Induced Apoptosis 5/19 BioCarta 0.00172895804772318 0.00226183623998627 4275 2757.90909090909 2229 0.000173030470572557 1572 1.42292978493861 -1.42292978493861 -1 0.968269397008015 1990 3081 3837 4272 4272 1572 1601 1639 4175 2229 1669 2154 M12705 SIG_CD40PATHWAYMAP http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CD40PATHWAYMAP.html Genes related to CD40 signaling 21/36 Signaling Gateway 0.000117323746843152 0.000172669308325067 2230 2267.63636363636 2230 1.06663640059623e-05 1156 1.58633927367078 -1.60193410962856 -1 1.53533832905825 2230 2666 2442 1734 3062 1605 3427 1156 2881 2203 1538 2155 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 22/217 Arthur Liberzon 0.000397998502251736 0.000548213104512533 2145 2314.63636363636 2230 3.61882292517434e-05 934 1.58109539971746 -1.56525921565106 -1 1.32621589959451 2142 2022 1941 2895 3849 934 2707 2230 2781 2832 1128 2156 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 232/485 John Newman 1.56824464709585e-08 9.08698406718676e-08 1860 2396.45454545455 2230 1.4256769620681e-09 442 1.58327474823864 1.71923797115257 1 2.86764293559635 1858 3879 1959 2230 442 3719 2055 2094 2963 2854 2308 2157 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 34/75 John Newman 0.000827394010644073 0.00110998234579964 1360 2182.63636363636 2230 7.52459406996168e-05 979 1.8023513386651 2.08612218529385 1 1.36977458776698 1356 1664 979 1759 3355 2902 2230 2533 2914 1344 2973 2158 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 206/551 Leona Saunders 1.51432263875246e-08 8.92593193106169e-08 4165 2255.27272727273 2231 1.37665695379634e-09 425 1.63739542724509 -1.44985852348406 -1 2.96893770362913 4165 472 841 1587 425 2231 3589 4679 2355 784 3680 2159 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 272/684 Jessica Robertson 4.57642659035872e-09 4.20891938265653e-08 3235 2007.27272727273 2231 4.16038781807142e-10 77 1.69927726831137 2.03493665311374 1 3.22384216291065 3235 758 487 815 77 3244 3394 3072 2231 480 4287 2160 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 78/196 Arthur Liberzon 4.64349446960607e-07 1.14282642250914e-06 2235 2028.72727272727 2232 4.22135949972648e-08 666 1.65690250511228 1.64257243781385 1 2.5323847903541 2232 1101 754 1166 1799 3661 2544 2938 2481 666 2974 2161 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 243/811 Arthur Liberzon 8.15775450618418e-07 1.84227651161345e-06 1820 2109.09090909091 2233 7.41614321012583e-08 682 1.74582094330551 1.86758166948231 1 2.57516407233329 1819 1700 702 2233 1983 3260 2280 2583 2442 682 3516 2162 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 9/26 John Newman 0.000586181260172204 0.000798501565455508 1650 2709 2234 5.86335941411811e-05 1649 2.18400542076756 2.18400542076756 1 1.74018371604573 1649 4311 4411 3687 3318 2234 1695 1991 2017 2311 2175 2163 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 41/103 Jessica Robertson 4.20065187362198e-07 1.04982691625561e-06 4645 2695.18181818182 2236 3.81877515971755e-08 673 1.55374646301158 -1.32768937514988 -1 2.38945473150032 4643 673 2236 1088 1768 2863 4219 4500 1761 2137 3759 2164 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 235/684 Kevin Vogelsang 1.58389509879591e-06 3.31937944228875e-06 2995 2194.81818181818 2237 1.43990567193274e-07 571 1.77201460675803 -1.30194094393911 -1 2.49725412837829 2993 3050 753 1346 2153 3577 3135 1069 2237 571 3259 2165 M16697 BIOCARTA_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CD40_PATHWAY.html CD40L Signaling Pathway 11/19 BioCarta 4.34991604334377e-06 8.13396112494371e-06 2790 2377 2239 3.95447694924722e-07 1538 1.1721693800311 -1.29779617837812 -1 1.53454987169928 2787 1538 2676 1778 2409 2239 4079 2102 1965 2604 1970 2166 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 19/38 Reactome 5.1829312188475e-06 9.54686151396202e-06 1375 2325.45454545455 2239 4.711766753855e-07 660 1.24505143319866 1.32128427609337 1 1.60768773654639 1374 2069 2807 3800 2445 1809 660 2239 3858 2999 1520 2167 M14863 BIOCARTA_P53_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P53_PATHWAY.html p53 Signaling Pathway 15/22 BioCarta 0.0118115586996311 0.0144968475815797 2205 2524.27272727273 2240 0.0010795867682458 1410 1.87596304913304 1.87596304913304 1 0.887237690208866 2201 3157 2247 2139 3857 3281 2240 2013 1410 3154 2068 2168 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 5/10 Arthur Liberzon 0.000287971060529286 0.000403417754750444 1885 2528.63636363636 2240 2.88008384635964e-05 691 1.18796300646413 1.18796300646413 1 1.03715747676633 1884 2045 4135 3613 3875 1062 691 2240 3837 3277 1156 2169 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 12/32 Arthur Liberzon 1.60487636092854e-06 3.35734403004961e-06 2145 2331.81818181818 2242 1.45897957424527e-07 1214 1.13255881069593 -0.917451794743083 -1 1.59464684034946 2141 1584 3090 2654 2156 1214 1348 3297 2505 3419 2242 2170 M8256 REACTOME_GENERIC_TRANSCRIPTION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GENERIC_TRANSCRIPTION_PATHWAY.html Genes involved in Generic Transcription Pathway 127/490 Reactome 2.10342206689262e-07 5.95485374422865e-07 1495 2553.09090909091 2243 1.91220206181912e-08 630 1.21983808719685 -1.22159120613536 -1 1.95321108155741 1492 4012 3614 4555 1501 630 2243 1738 2791 4157 1351 2171 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 278/649 Arthur Liberzon 3.5730829640931e-08 1.56664062128372e-07 4080 2362.90909090909 2243 3.24825729284052e-09 775 1.41171367308096 -1.27827665953867 -1 2.47101485498657 4080 1862 2439 1645 775 1187 4617 2656 2921 1567 2243 2172 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 22/95 Leona Saunders 6.11672450353647e-06 1.10625129384685e-05 2460 2071.36363636364 2243 5.56067410010104e-07 698 1.99847897543861 -2.33560577386633 -1 2.5476651498233 2460 2561 1725 2243 3123 1128 2891 698 2780 1910 1266 2173 M6778 BIOCARTA_IL10_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL10_PATHWAY.html IL-10 Anti-inflammatory Signaling Pathway 11/19 BioCarta 1.72616812401427e-05 2.88063526678449e-05 2760 2361.81818181818 2245 1.56925606186885e-06 1196 1.49600581638783 -1.25746807355542 -1 1.74717625921226 2756 2245 2206 3176 2706 1196 2167 4095 2375 1484 1574 2174 M1441 REACTOME_P38MAPK_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P38MAPK_EVENTS.html Genes involved in p38MAPK events 10/15 Reactome 0.00127641939147256 0.00168534834275582 1730 2496.54545454545 2247 0.000116105505467572 1729 1.33990843082745 -1.6511203213779 -1 0.955811342491125 2700 2247 2212 1730 3405 2153 4032 1729 2958 2437 1859 2175 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 25/68 John Newman 2.23057470485858e-06 4.477031124236e-06 4405 2624.27272727273 2248 2.02779724221465e-07 1353 2.06421092570876 -1.35881357855931 -1 2.84005093873341 4404 1673 1353 2052 2248 3361 4374 2679 1382 1828 3513 2176 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 24/49 Leona Saunders 2.01568399485444e-08 1.06410983827008e-07 2545 2306.81818181818 2249 1.8324400121114e-09 540 2.09969606274353 2.5784376138159 1 3.76595916922335 2541 3068 1726 1971 540 3344 2110 3168 2542 2116 2249 2177 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 5/10 Jessica Robertson 8.32816308163099e-06 1.46879082425754e-05 2085 2529.27272727273 2249 8.32819429303077e-07 1240 1.52369239932906 -1.99658319997009 -1 1.8941585791208 2084 1858 4355 3092 2574 2012 2828 3866 1240 2249 1664 2178 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 28/80 John Newman 2.23087231649404e-06 4.477031124236e-06 2315 2511.63636363636 2249 2.02806779879555e-07 1737 1.6017863743181 -1.71096636652854 -1 2.20382265232915 2314 2589 1737 3679 2249 2168 3664 1784 3574 1766 2104 2179 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 39/109 Arthur Liberzon 0.000139116335517585 0.000202894226030316 1735 2402.90909090909 2250 1.26477393887188e-05 1024 1.70731284743157 2.04012209912601 1 1.62165823476365 1735 3562 2250 3421 3678 2077 1024 1166 2936 2647 1936 2180 M19752 REACTOME_COMPLEMENT_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMPLEMENT_CASCADE.html Genes involved in Complement cascade 13/39 Reactome 0.000355145458625074 0.000491788303521601 1945 2508.63636363636 2251 3.22911638753931e-05 1774 1.70564636030621 2.09213623599676 1 1.45138368516121 1943 3159 1785 3870 3246 2373 1941 1872 3381 1774 2251 2181 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 28/58 Arthur Liberzon 9.7767786829026e-05 0.000144980964898992 1870 2264.63636363636 2251 8.88837562639396e-06 903 1.44326897999448 1.88411482033893 1 1.42504582928095 1867 2739 2525 2331 3566 2251 1896 1222 2224 3387 903 2182 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 13/34 Leona Saunders 1.88367739536745e-06 3.84782575182732e-06 1940 2320.45454545455 2252 1.71243546200544e-07 1286 1.35949349758296 1.44171199613348 1 1.89346359838979 1939 1286 2252 2695 2212 2801 2303 1848 3229 2915 2045 2183 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 44/91 Arthur Liberzon 6.85948496057752e-06 1.23013955320575e-05 3295 2480.72727272727 2252 6.23591486198755e-07 1833 1.49544141203585 -1.72636748717335 -1 1.88865907659385 3291 1833 1954 2240 2514 2252 3904 1870 2983 2066 2381 2184 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 5/11 Arthur Liberzon 3.83689866683012e-06 7.27040321583742e-06 1185 2224.18181818182 2254 3.83690529165233e-07 211 1.44829159652347 1.44829159652347 1 1.91419451869237 1181 2856 4502 4145 3603 563 211 1377 3170 2254 604 2185 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 33/71 John Newman 2.36689630322836e-08 1.17368000814054e-07 2155 2178.72727272727 2255 2.15172393517537e-09 606 1.38642467617587 -1.3562660542794 -1 2.47147592455755 2153 2908 2279 3632 606 1003 2255 1950 3250 2570 1360 2186 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 5/7 Jessica Robertson 1.3736675263324e-05 2.32718945350456e-05 1270 2339 2255 1.3736760177374e-06 448 1.93394114672946 1.93394114672946 1 2.30472957610917 1267 3336 4523 3283 4504 895 448 929 3699 2255 590 2187 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 56/114 John Newman 0.00111427525928148 0.00147624932569776 3590 2360.54545454545 2256 0.000101349093425307 788 1.49634148052205 -1.39179474916408 -1 1.08954378350795 1193 3588 2256 2926 3620 788 1769 2259 3590 2227 1750 2188 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 5/7 Arthur Liberzon 0.000142634038203905 0.000207830566860541 2035 2677.90909090909 2256 1.42643194041992e-05 1169 1.34258000364425 -1.34258000364425 -1 1.27161852899919 2032 1996 4556 3407 3109 1169 1266 4647 3675 2256 1344 2189 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 6/14 Jessica Robertson 0.000666551518878253 0.000902734224700432 2260 2472.45454545455 2257 6.6675153423705e-05 1395 2.0266934581226 2.64115770334761 1 1.58706286155328 2257 3365 4546 1720 3473 2464 1659 1453 1395 3458 1407 2190 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 73/173 Yujin Hoshida 1.20892558437955e-07 3.77165465273142e-07 1965 2349.45454545455 2258 1.09902331891948e-08 1191 1.87970556840384 2.1111241119831 1 3.10568967083352 1962 3224 1333 2258 1323 3578 2658 2186 2913 1191 3218 2191 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 38/82 Leona Saunders 1.67214001417348e-08 9.42917943010463e-08 2260 2127.54545454545 2259 1.52012729716619e-09 468 1.55249356564962 1.63625980233085 1 2.80548090171859 2259 2264 2244 1852 468 3680 2392 2370 1667 1614 2593 2192 M923 REACTOME_RAP1_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAP1_SIGNALLING.html Genes involved in Rap1 signalling 12/20 Reactome 0.000290097422362046 0.000406032413736125 1480 2456.18181818182 2260 2.63759711260397e-05 1479 1.270105221168 1.65623712167841 1 1.10795559430833 1479 2571 2260 2955 3211 1944 1918 2146 3256 3418 1860 2193 M10066 BIOCARTA_GCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GCR_PATHWAY.html Corticosteroids and cardioprotection 13/35 BioCarta 6.11021062167541e-07 1.43665062584902e-06 1330 2008 2261 5.55473847155155e-08 220 1.89880018062751 1.89880018062751 1 2.85356457793214 1329 2956 2455 2261 4030 637 506 1391 3400 2903 220 2194 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 155/426 Arthur Liberzon 3.83069084293743e-08 1.62009181317733e-07 2265 2359.72727272727 2262 3.48244628148937e-09 807 1.6920750536873 2.01223287904486 1 2.95540837483185 2262 3052 1821 1531 807 4506 2751 1711 1598 2995 2923 2195 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 5/7 Arthur Liberzon 3.48138928482603e-05 5.5095542683873e-05 1230 2466.45454545455 2262 3.4814438263497e-06 433 1.08284142632641 1.08284142632641 1 1.18620359829223 1228 2891 4669 4390 3393 996 433 1541 3672 2262 1656 2196 M16120 BIOCARTA_SALMONELLA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SALMONELLA_PATHWAY.html How does salmonella hijack a cell 13/24 BioCarta 2.21925766637587e-05 3.63235816438607e-05 2755 2079.63636363636 2264 2.01752732139189e-06 251 2.50473522269398 3.15601482470129 1 2.86038831661443 2752 1149 1557 1206 2754 3292 2113 2613 251 2264 2925 2197 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 140/319 Arthur Liberzon 3.08737206060216e-08 1.41008045574871e-07 1940 2251.18181818182 2264 2.80670191266257e-09 714 1.45431662960353 1.72450670748811 1 2.56269032737935 1936 1958 2264 3116 714 3392 1951 2285 3131 2389 1627 2198 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 35/71 John Newman 1.52979887770534e-07 4.58352783946755e-07 1895 2331.09090909091 2265 1.39072634916539e-08 1395 1.50168508678248 1.73214034734278 1 2.44841243805646 1894 2265 2329 2410 1395 2750 1752 4488 1530 3122 1707 2199 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 235/685 Jessica Robertson 5.84015412886537e-08 2.1876068943136e-07 3625 2437.36363636364 2265 5.30923116718091e-09 1004 1.47787947275822 -1.32026792749676 -1 2.53170967767532 3621 1956 2265 2958 1004 1129 3555 4314 2267 1589 2153 2200 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 78/229 Arthur Liberzon 6.17138374758306e-07 1.4488529178945e-06 4150 2516.45454545455 2265 5.61035043524049e-08 782 1.93036846318896 -1.87872067698204 -1 2.89918239574921 4150 2010 782 2265 1895 2510 4640 3714 1858 870 2987 2201 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 14/30 Yujin Hoshida 2.20075186849431e-09 2.34913969379598e-08 3295 2336.27272727273 2268 2.00068351881438e-10 23 2.09318745803402 1.76702661223971 1 4.10751912883445 3293 1472 1253 2268 23 3861 2756 3498 1625 1100 4550 2202 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 26/57 Jessica Robertson 3.59840330498217e-07 9.23445667423136e-07 3140 2627.54545454545 2268 3.27127626686434e-08 1165 1.4959664822874 -1.25408159369557 -1 2.32203191254326 3140 2268 2168 3222 1705 1165 3317 4667 3127 1921 2203 2203 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 12/38 Reactome 6.85239534116016e-06 1.22933861288961e-05 3995 2130.27272727273 2269 6.22946971325579e-07 434 1.74072102341054 -0.782095363462204 -1 2.19856022557954 3991 1476 1588 921 2513 2562 3529 1406 434 2744 2269 2204 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 12/19 Reactome 6.32449660555363e-07 1.4788718110591e-06 3650 2401.90909090909 2270 5.74954402154765e-08 189 1.59808877285737 -0.767415063461318 -1 2.39647708504712 3649 970 2396 2270 1904 1971 2204 3324 189 3416 4128 2205 M684 REACTOME_SYNTHESIS_OF_PC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PC.html Genes involved in Synthesis of PC 9/19 Reactome 2.71192790021906e-05 4.37606547535349e-05 2320 2123.27272727273 2272 2.71196099627572e-06 537 2.29589634554542 -2.20026217263632 -1 2.57412391014832 2319 1293 3956 1990 2818 1643 2887 1343 537 2298 2272 2206 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 12/45 Arthur Liberzon 1.97444094307689e-06 4.00702912917206e-06 2425 1952 2273 1.79494792280623e-07 417 2.38903337438026 -2.37050672811627 -1 3.31655786742889 2422 417 592 1574 2412 3365 2989 3132 1801 495 2273 2207 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 34/115 Arthur Liberzon 3.12230036398914e-06 6.04341160910909e-06 2325 2366.27272727273 2274 2.83845890477481e-07 1516 1.59181471288888 1.69953223139395 1 2.13675621402041 2239 1516 1832 2323 2324 2912 2274 2007 3225 2213 3164 2208 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 14/47 Arthur Liberzon 0.000131196219015791 0.00019170111702775 2485 2091.18181818182 2274 1.19276403190001e-05 347 3.10041016159577 -2.42083912100062 -1 2.9645189110472 2485 2274 1470 3094 3084 1668 3035 2340 347 1882 1324 2209 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 18/41 Arthur Liberzon 0.00010746800934989 0.000158712603786191 1005 2190.54545454545 2275 9.77029631126857e-06 864 1.52081352248017 -1.52081352248017 -1 1.48623781023925 1004 3477 2275 3304 3051 864 1415 1221 3520 2374 1591 2210 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 60/162 John Newman 2.12705820341298e-05 3.49733148813798e-05 1370 2096.18181818182 2276 1.93370797185412e-06 797 1.65182851536873 1.87213726234551 1 1.89336538548467 1366 1757 797 1519 2744 3080 2276 2684 3141 992 2702 2211 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 55/145 Michael Hecker 5.00927624881727e-08 1.97588118703348e-07 2280 2367.72727272727 2276 4.55388760261424e-09 924 1.80114006070122 2.11161588624959 1 3.10595847084073 2276 2936 969 3463 924 4037 2673 1944 2273 1081 3469 2212 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. 25/47 Signaling Transduction KE 1.34031199197221e-06 2.8639771976205e-06 2120 2440.90909090909 2277 1.21846618957712e-07 1186 1.6732533410951 1.87937295977329 1 2.38565487055321 2117 3654 2438 2517 2109 2277 1186 3466 1736 3136 2214 2213 M55 PID_S1P_S1P3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P3_PATHWAY.html S1P3 pathway 18832364 19/42 Pathway Interaction Database 7.57531275782363e-07 1.72487442095051e-06 2215 2346.09090909091 2278 6.88665033295499e-08 1702 1.58638375418684 1.72757925721349 1 2.35165602778189 2213 3324 2278 2623 1968 2184 1702 1858 2703 2500 2454 2214 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 13/32 Arthur Liberzon 0.00103822707629446 0.00138057096467533 1590 2431.09090909091 2278 9.44288510750359e-05 1313 1.47459447717938 1.60539544691 1 1.08474665783018 1590 2917 3004 3689 3880 1873 1417 2096 2685 2278 1313 2215 M529 REACTOME_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOSIS.html Genes involved in Meiosis 74/238 Reactome 0.00625701458892606 0.00782293766374266 850 2484.09090909091 2279 0.000570443757271369 846 1.49136567625022 -1.53504627762641 -1 0.808110983362716 846 3785 2680 2930 3568 1348 2228 1897 3808 2279 1956 2216 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 11/25 Jessica Robertson 0.000677853860920262 0.000917510299286428 2415 2227.54545454545 2279 6.16420734786626e-05 390 2.16899296853635 2.39200659246758 1 1.69456097991854 2415 2279 1777 1945 3324 2635 1985 1528 390 2620 3605 2217 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) 11/25 Reactome 6.72139790221071e-06 1.20815000267585e-05 2140 2523.81818181818 2280 6.11038039762255e-07 1542 2.67576643661336 2.67576643661336 1 3.38473533487878 2280 2246 2138 3475 2509 3545 2137 3298 1542 2614 1978 2218 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 76/166 Arthur Liberzon 1.48409487445242e-06 3.14539510704841e-06 4205 2473.27272727273 2280 1.34917806873347e-07 583 2.05213693363983 -1.4769907658925 -1 2.90436514708801 4201 1917 583 981 2280 3231 4576 2534 1855 616 4432 2219 M506 REACTOME_INSULIN_RECEPTOR_RECYCLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INSULIN_RECEPTOR_RECYCLING.html Genes involved in Insulin receptor recycling 9/27 Reactome 4.61631988538085e-05 7.17958014699457e-05 1180 2285.36363636364 2281 4.61641578502643e-06 601 0.855551505448501 -0.855551505448501 -1 0.911914483878162 1180 2281 3916 2756 2919 601 874 1356 4201 3774 1281 2220 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 18/54 Jessica Robertson 2.60427436853738e-06 5.12973084950237e-06 3965 2442.36363636364 2283 2.36752495580102e-07 1354 1.3793794557226 -1.25327425855214 -1 1.87685317979651 3963 1626 2158 1422 2283 3965 3053 2881 1354 1514 2647 2221 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 20/44 Jessica Robertson 7.53767330397276e-07 1.71718085844566e-06 3390 2628 2283 6.85243262413004e-08 1316 2.17185540328859 2.10066351162893 1 3.22064411796881 3388 1806 1316 2283 1967 4313 4063 2544 2047 1377 3804 2222 M7968 BIOCARTA_CARM1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARM1_PATHWAY.html Transcription Regulation by Methyltransferase of CARM1 6/15 BioCarta 0.000628622400965688 0.000852844403857908 1590 2354.27272727273 2284 6.28800296550246e-05 940 1.18566824011235 1.18566824011235 1 0.936002673035219 1481 2284 3882 2544 3329 1587 1955 2873 940 3435 1587 2223 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 56/137 Arthur Liberzon 2.67302196027781e-08 1.25937603898826e-07 4280 2592.27272727273 2285 2.43001999341391e-09 665 1.44782371729056 -1.20102125358467 -1 2.56952973465465 4276 1444 2285 2152 665 2782 3793 3605 1856 1518 4139 2224 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 354/839 Jessica Robertson 4.33305009738648e-08 1.77178645343395e-07 3895 2638.27272727273 2285 3.93913652975352e-09 863 1.56648536641461 -1.23098539783703 -1 2.72038874901655 3892 2134 1969 1144 863 1489 4148 3853 2285 2977 4267 2225 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 97/186 John Newman 2.67247693630188e-06 5.25523580508208e-06 3465 2552.45454545455 2287 2.4295274388468e-07 1500 1.61060469241812 -1.35256840377597 -1 2.18712102717587 3463 1500 1958 2057 2287 1829 3374 4118 2348 1888 3255 2226 M9526 ST_T_CELL_SIGNAL_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/ST_T_CELL_SIGNAL_TRANSDUCTION.html T Cell Signal Transduction 30/72 Signaling Transduction KE 4.08090833256821e-05 6.40426538727884e-05 2275 2368.36363636364 2288 3.70998548516664e-06 1300 1.58979405750819 1.82874040651025 1 1.71482311541298 2274 3530 2288 2190 2872 2955 1300 1491 1922 2664 2566 2227 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 11/25 Arthur Liberzon 2.67492885495274e-06 5.25746765168577e-06 3885 2839.09090909091 2288 2.43175646122008e-07 1239 1.31891317606751 -1.18769699031216 -1 1.7909558666547 3883 2077 2165 2153 2288 4008 3878 3074 1239 1968 4497 2228 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 30/77 Kate Stafford 4.08150674407464e-07 1.02442102853421e-06 2630 2473.27272727273 2288 3.71046136480759e-08 1577 1.84088143264729 2.19334682799547 1 2.83606776206637 2630 3412 1845 2852 1760 4156 2288 2675 1726 2285 1577 2229 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 1155/2922 John Newman 9.96932337335240e-09 7.14401938687495e-08 2680 2323.63636363636 2289 9.96932341807672e-10 281 1.58852023907909 1.94292008616143 1 2.9198323013851 2676 2176 4407 1143 281 2799 2805 1968 2289 1107 3909 2230 M15898 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM.html Fructose and mannose metabolism 15/41 KEGG 1.96366798065908e-06 3.99035045852925e-06 1510 2235.09090909091 2290 1.78515430307716e-07 333 0.953354991182611 -0.953354991182611 -1 1.32393207259339 1506 3385 3029 3752 2290 433 1576 1190 3940 3152 333 2231 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 6/58 Jessica Robertson 6.37053187420528e-07 1.4881511646324e-06 2165 2163 2293 6.37053370047144e-08 213 2.65481611184715 3.58156002581457 1 3.97927940181317 2165 2171 4431 2457 3100 2428 2293 402 213 2491 1642 2232 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 256/560 Arthur Liberzon 2.43833500924667e-06 4.83539477500207e-06 1630 2411.81818181818 2294 2.21667064703699e-07 273 1.44442277344838 -1.19169058178517 -1 1.9748888270501 1629 4143 3469 3522 2272 273 1715 2368 2294 4032 813 2233 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 18/60 Arthur Liberzon 1.25481845680064e-05 2.14366725795398e-05 1325 2365.36363636364 2294 1.14075055817385e-06 792 1.43712606539059 1.64310736240046 1 1.72584876868367 1325 3862 2294 4105 3200 1255 945 792 3550 3479 1212 2234 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 3/7 Arthur Liberzon 5.11751934191767e-05 7.89877985382944e-05 2080 2328.72727272727 2294 5.11763719625643e-06 112 3.47251860897681 3.47251860897681 1 3.66425325794537 2080 2001 4606 1761 2938 2570 2294 2777 112 2819 1658 2235 M90 PID_WNT_CANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_CANONICAL_PATHWAY.html Canonical Wnt signaling pathway 18832364 10/33 Pathway Interaction Database 1.28143059519682e-06 2.7481847913466e-06 1715 2201 2296 1.16493758326393e-07 1068 1.29451540603613 1.41629745251962 1 1.85163410081796 1713 3187 2923 2296 2096 1538 1068 2926 2514 2433 1517 2236 M211 PID_HEDGEHOG_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HEDGEHOG_2PATHWAY.html Signaling events mediated by the Hedgehog family 18832364 14/34 Pathway Interaction Database 3.7592617674971e-07 9.57385904483228e-07 2220 2289.72727272727 2297 3.41751128169375e-08 1226 1.41578789346721 1.64802976081926 1 2.19187056765621 2216 2671 2484 2297 1723 2867 2131 1226 2158 2396 3018 2237 M616 REACTOME_SIGNALING_BY_NOTCH1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH1.html Genes involved in Signaling by NOTCH1 33/86 Reactome 2.79058476739695e-06 5.46227450816096e-06 2300 2467.27272727273 2297 2.53689846101259e-07 1271 1.33045855319543 -0.734914480517631 -1 1.8009536426773 2871 1271 2269 2040 2300 4109 3232 2297 1302 3363 2086 2238 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 3/8 Arthur Liberzon 0.000111174705077435 0.000163980065468322 2915 2482.63636363636 2297 1.11180267385857e-05 344 3.18770858038524 -2.93378408188904 -1 3.10360989936706 2915 1297 4140 1543 3068 3151 2154 4653 344 1747 2297 2239 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 43/100 John Newman 1.20274284651451e-06 2.60566480756681e-06 2110 2314 2297 1.09340318550553e-07 585 1.87611406116274 2.58663631397611 1 2.69469513171966 2109 3056 2297 2425 2080 3629 2493 585 1058 3650 2072 2240 M12467 KEGG_ERBB_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ERBB_SIGNALING_PATHWAY.html ErbB signaling pathway 41/90 KEGG 2.76298073966609e-06 5.4127624356502e-06 3410 2315.63636363636 2299 2.51180382700057e-07 907 1.7035309646663 -1.54034655404557 -1 2.3076899135736 3407 1036 2307 907 2299 2272 4609 3008 914 2458 2255 2241 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 910/2790 Yaara Zwang 1.85685868171728e-08 1.01177206773572e-07 2300 2297.45454545455 2299 1.85685869723294e-09 396 1.5923882088861 -1.33828580253875 -1 2.86503673713277 2299 1551 4686 1550 545 4091 2336 2492 2153 396 3173 2242 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 9/27 Reactome 2.97060900472033e-06 5.7784449132916e-06 1545 2322.54545454545 2300 2.97061297576084e-07 1514 2.57752562897562 2.57752562897562 1 3.47282437359434 1542 2531 3981 2842 2333 2385 2042 2067 2011 2300 1514 2243 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 14/23 Jessica Robertson 2.13559774511506e-06 4.30241231023609e-06 1945 2434 2300 1.9414543801806e-07 1801 1.10303237741821 1.02039453042051 1 1.52251248774895 1944 1900 1801 3089 2240 2525 2300 2626 3683 2405 2261 2244 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 26/75 Yujin Hoshida 1.20827782637352e-06 2.61403042215434e-06 2305 2303.54545454545 2301 1.09843499089181e-07 995 1.32961384054763 -1.09237410629454 -1 1.90927124114769 2301 2488 2630 2604 2083 995 1851 2231 2832 3647 1677 2245 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 56/111 Arthur Liberzon 4.16229185781884e-07 1.04357943529904e-06 2350 1975.45454545455 2302 3.78390240482201e-08 521 1.7598982364755 1.93625544709407 1 2.70766209832346 2346 521 715 1280 1762 3740 2568 3153 2302 624 2719 2246 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 38/85 Emmanuelle Fouilloux-Meugnier 2.47215324314536e-06 4.88797894404184e-06 2160 2229.18181818182 2302 2.24741456465746e-07 600 2.56003158241154 2.9810370333413 1 3.49711337141656 2159 2658 600 1599 2302 4174 3429 2509 1353 681 3057 2247 M2499 BIOCARTA_CARM_ER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARM_ER_PATHWAY.html CARM1 and Regulation of the Estrogen Receptor 23/48 BioCarta 1.14858737085801e-05 1.97732565019862e-05 2305 2080.54545454545 2304 1.04417578864196e-06 514 1.27529891943112 -0.996964187709063 -1 1.54301701121662 2304 2196 2547 2949 2628 514 1603 1673 2871 2952 649 2248 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 861/1799 Arthur Liberzon 1.07166589642521e-08 7.39899659922656e-08 3100 2144.81818181818 2305 1.07166590159332e-09 258 1.57610399406503 -1.31524713836819 -1 2.89083588707109 3098 258 4164 938 310 2050 3050 2586 2305 520 4314 2249 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 4/22 Reactome 3.35785014285991e-05 5.32123292845504e-05 2365 2604.90909090909 2306 3.35790088214808e-06 1696 1.8150419096665 1.72681391821115 1 1.9953476377883 2365 1696 3929 1840 2855 3108 2306 4635 1937 2039 1944 2250 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 9/15 Leona Saunders 4.59168971508848e-06 8.55193084455669e-06 1100 2172.81818181818 2307 4.59169920274257e-07 571 1.43845163114042 1.43845163114042 1 1.87510248400174 1099 3419 4346 2905 2438 897 571 1860 3179 2307 880 2251 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 77/187 John Newman 0.00241897951077089 0.00312440407592954 1830 2513.63636363636 2307 0.000220149397061871 1685 1.96458076948989 2.23807552505791 1 1.26595012034905 1828 3851 1846 2790 3879 2810 1882 1685 2307 2706 2066 2252 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 9/18 Jean Junior 1.31127246872092e-05 2.23116295876043e-05 1185 2491.54545454545 2308 1.31128020624487e-06 327 1.72297609585397 1.72297609585397 1 2.061427190484 1183 3161 4380 3804 4320 832 327 1530 4253 2308 1309 2253 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 63/145 Leona Saunders 3.18131641770268e-07 8.35162394025478e-07 3720 2478.36363636364 2309 2.89210625248905e-08 1180 1.55346127258514 -1.69227582093524 -1 2.42871270760145 3719 1180 1456 1493 1656 4238 2309 3026 2549 1469 4167 2254 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 48/108 Arthur Liberzon 1.71413440298693e-05 2.86259223535166e-05 3940 2342.81818181818 2310 1.55831614440466e-06 788 1.77592957244046 -1.56751112242451 -1 2.07534408616568 3939 1616 1107 788 2705 2310 3693 3011 2192 954 3456 2255 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 21/51 Arthur Liberzon 9.47378515270292e-07 2.10498611785519e-06 2315 2448.18181818182 2311 8.61253566579023e-08 871 1.78538862973133 2.69463606231085 1 2.60694125798067 2077 3415 2315 3352 2019 3677 2311 871 1325 3700 1868 2256 M206 PID_PDGFRA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PDGFRA_PATHWAY.html PDGFR-alpha signaling pathway 18832364 21/35 Pathway Interaction Database 2.94360307123962e-07 7.82844721443183e-07 2225 2360.45454545455 2312 2.67600315008563e-08 1506 1.58982141816265 1.57453114664552 1 2.49704785899614 2223 2270 2497 1506 1628 2859 2312 2660 2299 2711 3000 2257 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 68/165 Jessica Robertson 0.000220374363718989 0.000314264841262076 1245 2319.27272727273 2314 2.00360401592438e-05 912 1.53893947047866 -1.26555347816666 -1 1.38651197352585 1243 3490 2948 3425 3161 912 1148 1400 2314 3756 1715 2258 M2529 BIOCARTA_PDGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PDGF_PATHWAY.html PDGF Signaling Pathway 26/52 BioCarta 2.97854746534636e-06 5.79148274797222e-06 1275 2264 2315 2.70777408905943e-07 1274 1.24926967466012 -0.994551689304647 -1 1.68288655100359 2182 1527 2780 1274 2315 1275 3160 2922 2362 3219 1888 2259 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 9/33 Yujin Hoshida 1.13752353340663e-08 7.68351012715883e-08 4015 2465.18181818182 2317 1.13752353922945e-09 345 1.38316162168773 -1.09141806298864 -1 2.53111760225056 4011 1226 4563 1160 345 4230 4048 1709 769 2317 2739 2260 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 112/254 Jessica Robertson 4.66348042557028e-07 1.14593965779876e-06 4320 2889.90909090909 2317 4.23952855828935e-08 1239 1.61088065130954 -1.28096355324122 -1 2.46155613857018 4316 1703 2317 1239 1803 2624 4489 4549 2157 2174 4418 2261 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 153/408 Jessica Robertson 1.27643281780611e-08 8.0434968418917e-08 4115 2364 2318 1.16039347746539e-09 357 1.57003058525896 -1.34080790630679 -1 2.86504822158816 4112 1701 1141 2318 357 1682 4291 4346 2456 997 2603 2262 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 12/31 Jessica Robertson 6.27029271334527e-06 1.13140514650504e-05 4595 2458.27272727273 2318 5.7002823496228e-07 64 2.06112702381911 1.75362399347195 1 2.62235238841798 4592 1941 2075 880 2496 3021 3925 2318 64 2151 3578 2263 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 33/81 Arthur Liberzon 2.78615396075674e-07 7.48619120418926e-07 4610 2413.09090909091 2319 2.53286755782246e-08 1270 1.81331457695596 -1.94391639113251 -1 2.85713199386574 4606 1270 1445 2456 1604 3185 3284 2892 2199 1284 2319 2264 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 39/102 Arthur Liberzon 5.59696731100692e-07 1.33404826141294e-06 1605 2323.81818181818 2319 5.08815339538044e-08 1183 1.50336829707471 1.61194235572766 1 2.27174314394059 1602 2422 1977 2991 1866 2898 2254 2319 3155 1183 2895 2265 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 101/241 Yujin Hoshida 1.17555100552984e-08 7.80259491772358e-08 4660 2385.09090909091 2319 1.06868273801027e-09 308 1.39492907732226 -1.31646075193687 -1 2.55025491085403 4658 1012 2704 1500 308 2319 3814 2700 1838 3217 2166 2266 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 55/92 Kevin Vogelsang 1.70269790986961e-06 3.51955994955845e-06 2980 2478.90909090909 2320 1.54790838880019e-07 1463 1.42179359071242 -1.35169759309485 -1 1.99439620326564 2978 2643 1657 2854 2183 2072 3794 2320 3056 1463 2248 2267 M11521 KEGG_GLYCOLYSIS_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOLYSIS_GLUCONEOGENESIS.html Glycolysis / Gluconeogenesis 32/81 KEGG 2.93406761541568e-08 1.35592118795245e-07 2100 2292.72727272727 2321 2.66733423140579e-09 697 1.65786036814353 -1.37002838930229 -1 2.92861355602097 2099 2802 2086 2957 697 1266 2321 2943 3240 2855 1954 2268 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 13/28 John Newman 1.37687624483062e-05 2.33178246594734e-05 2230 2257.90909090909 2323 1.25171351102289e-06 102 1.9117716641752 2.20914885886271 1 2.27788853390615 2229 2467 2323 1651 2666 3094 2639 1575 102 3988 2103 2269 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 300/764 Leona Saunders 2.50661013337888e-06 4.94775698610507e-06 2325 2280.27272727273 2324 2.27873908121402e-07 241 1.2583869865214 -1.19646363826057 -1 1.71730199244435 2324 3138 3639 2521 2276 241 2075 1900 2863 3428 678 2270 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 22/54 Jessica Robertson 3.67334517211735e-05 5.79377161781956e-05 1770 2459.90909090909 2324 3.33946046134711e-06 1396 1.21542612900322 1.12342654645971 1 1.32461482418468 1766 2807 2324 4094 2852 1880 1396 1424 3943 2356 2217 2271 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 20/35 Arthur Liberzon 1.36605488098185e-05 2.31512953789546e-05 2365 2022.36363636364 2325 1.24187578486846e-06 705 1.77868025992701 2.04014354412847 1 2.12073332876936 2363 705 1252 1517 2665 3671 2885 2325 1221 1071 2571 2272 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 12/30 John Newman 9.78643739059797e-06 1.70607312545916e-05 1740 2244.18181818182 2325 8.89680084060695e-07 1311 1.13218089961107 1.24854023140677 1 1.38851606163823 1737 2393 2638 2325 2588 2091 1311 3160 2388 2149 1906 2273 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 15/53 Leona Saunders 1.47376984576349e-05 2.48509733618126e-05 1470 2383 2326 1.3397997441566e-06 879 1.16815256504302 -1.07171236080545 -1 1.38355183998727 1468 3073 2930 4283 2676 879 1746 2326 3287 2005 1540 2274 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 5/8 Arthur Liberzon 2.88564608863655e-06 5.6389230906384e-06 3080 2473.18181818182 2327 2.88564983577241e-07 434 1.3483041198815 1.08377371434701 1 1.82031623030667 3077 434 4258 1812 2327 2756 2166 3696 1033 1530 4116 2275 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 58/138 Kate Stafford 1.0185428063779e-08 7.25320069136774e-08 2115 2314 2328 9.25948010084992e-10 251 1.56708769215727 1.7288414417004 1 2.8777823742932 2114 2225 1724 3034 251 3474 2350 3347 2493 2114 2328 2276 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 85/217 John Newman 2.36539816926619e-08 1.17368000814054e-07 2525 2335.09090909091 2330 2.15036199518045e-09 605 1.9761450604102 2.26256084008319 1 3.52272658596074 2524 3621 1354 2380 605 4441 2330 1987 1818 1384 3242 2277 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 20/65 Leona Saunders 7.42715920298837e-06 1.32132376709201e-05 2235 2381.36363636364 2331 6.75198570641693e-07 1288 1.47974269538648 -1.37105723202281 -1 1.85701255129612 2235 3022 2569 3616 2531 1288 2331 1803 3194 1709 1897 2278 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 102/326 Kevin Vogelsang 2.33081057120339e-07 6.49742911163539e-07 2320 2485.54545454545 2334 2.11891892558485e-08 1244 1.53566112048891 -1.65344338547049 -1 2.44394989421851 2316 2334 1382 2378 1539 3500 2096 3217 3387 1244 3948 2279 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 16/42 John Newman 3.2809228834123e-06 6.32171243078537e-06 3765 2385.81818181818 2335 2.98266161486963e-07 879 1.0168315733456 1.13959203951096 1 1.35981950495938 1460 3761 3081 3761 2335 922 879 2180 3519 3253 1093 2280 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 774/1740 Arthur Liberzon 3.02698836101892e-08 1.38520320488324e-07 3205 2633.45454545455 2336 3.02698840225088e-09 751 1.53306710662002 -1.03625131020186 -1 2.70450699705709 3202 1698 4634 1535 751 2296 3524 2336 2063 2702 4227 2281 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 264/667 Arthur Liberzon 3.26117225092649e-08 1.46518247055048e-07 3525 2451.18181818182 2338 2.96470209024411e-09 743 1.6071892841694 -1.5078405666155 -1 2.8251892195502 3524 1373 987 1293 743 3211 3600 4530 2338 752 4612 2282 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 8/28 Reactome 3.05916525903428e-06 5.93346374330903e-06 2410 2453.90909090909 2340 3.05916947036387e-07 120 2.62649067967334 2.62649067967334 1 3.53103003135598 2406 2327 3970 2203 2340 3219 2724 2168 120 3677 1839 2283 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 15/35 Jessica Robertson 3.84066978918984e-06 7.27460736950024e-06 1015 2227.36363636364 2340 3.49152408553642e-07 206 2.03059087211066 2.03059087211066 1 2.68368340825808 1011 3663 2340 4414 3586 498 206 1244 3599 3168 772 2284 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 126/338 Arthur Liberzon 5.83655954083015e-08 2.1876068943136e-07 4655 2260.72727272727 2340 5.30596335970272e-09 294 1.72601023411105 -1.73454580395163 -1 2.95677485682167 4651 294 622 1154 1003 2728 3994 4216 2340 320 3546 2285 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 24/52 Jessica Robertson 1.16802786323739e-07 3.67220805851852e-07 3125 2208 2341 1.06184356840958e-08 740 1.82676557264883 -1.22741982009886 -1 3.02367379379405 3121 2621 2092 2888 1307 1371 2341 3071 740 2578 2158 2286 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 14/29 Arthur Liberzon 1.19011074485844e-08 7.85207853988603e-08 2565 2118.45454545455 2341 1.08191886481496e-09 314 1.77338587323989 -1.85897357153587 -1 3.24090966989932 2564 722 1223 2987 314 2842 4189 2646 2021 1454 2341 2287 M183 PID_IL6_7_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL6_7_PATHWAY.html IL6-mediated signaling events 18832364 38/74 Pathway Interaction Database 1.3535856610898e-05 2.29648892391992e-05 1335 2164.54545454545 2342 1.23053999028794e-06 736 1.36887294644968 1.34156013434169 1 1.63335324828405 1334 3379 3084 2342 2662 933 736 1935 3483 2586 1336 2288 M9070 BIOCARTA_CREB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CREB_PATHWAY.html Transcription factor CREB and its extracellular signals 22/45 BioCarta 0.000150148393341294 0.000218304489977444 1660 2541.90909090909 2343 1.3650785621703e-05 587 0.979217719947125 1.07276107377484 1 0.922083280146708 1660 3861 3394 2343 3532 1093 587 2322 3762 4012 1395 2289 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 29/69 Arthur Liberzon 0.000252408437518213 0.000356798171405835 1940 2366.27272727273 2344 2.29488546609342e-05 1290 1.59521263345144 2.1267367538244 1 1.41459209444022 1938 2522 2344 2712 3210 2815 1634 1290 2279 3467 1818 2290 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 10/37 Arthur Liberzon 0.000939021209433467 0.0012529195294434 1580 2427.72727272727 2344 8.54020226797343e-05 1579 1.86229975020562 1.86229975020562 1 1.39013542940238 1579 2650 2213 2169 3372 2344 1711 2728 3688 2440 1811 2291 M14857 REACTOME_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPHINGOLIPID_METABOLISM.html Genes involved in Sphingolipid metabolism 41/73 Reactome 4.78820970112589e-07 1.16923140487108e-06 4335 3011 2346 4.35291885750945e-08 1585 1.45155173190842 -1.3034361158756 -1 2.21482590572073 4335 1762 2346 1585 1812 3429 4552 4636 1930 2132 4602 2292 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 32/80 Leona Saunders 1.68995645577353e-07 4.96816479437781e-07 2395 2290.27272727273 2346 1.5363241687178e-08 563 1.72338224245928 -1.71702335445176 -1 2.79436396181334 2393 1453 903 2001 1432 3595 2346 4378 2786 563 3343 2293 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 48/134 Arthur Liberzon 8.26051306720742e-07 1.85995766233799e-06 3870 2626.27272727273 2348 7.50956015349896e-08 818 1.7998557285546 -1.7173501280303 -1 2.65294736744367 3869 1185 1086 2348 1987 3555 3300 4611 2149 818 3981 2294 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 2/14 Kevin Vogelsang 1.32485749229271e-07 4.07100472713681e-07 3195 2379.6 2348.5 1.47206396700412e-08 609 1.62368849208258 -1.50510212232629 -1 2.66883979641787 3192 747 4388 NA 1409 3000 2363 4363 609 1391 2334 2295 M9664 BIOCARTA_GPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GPCR_PATHWAY.html Signaling Pathway from G-Protein Families 22/55 BioCarta 8.25616174605929e-07 1.85995766233799e-06 2660 2326.36363636364 2349 7.50560440403086e-08 767 1.59304818890994 1.82558282506098 1 2.34811762285027 2657 1200 2209 827 1986 3126 2529 4560 767 2349 3380 2296 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 16/26 Aravind Subramanian 2.19868138142824e-05 3.60119571945919e-05 2225 2260.45454545455 2349 1.99882123215566e-06 805 1.94351182190676 2.05056778103578 1 2.22134607874245 2222 2565 2148 1608 2752 3111 2428 2221 805 2656 2349 2297 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 14/36 Jessica Robertson 3.52582014453394e-06 6.74367069276981e-06 1915 2219.90909090909 2349 3.20529617744225e-07 700 1.6238712494565 1.9181537220441 1 2.15989918954024 1914 3478 2475 2644 2353 2349 1954 1054 700 3632 1866 2298 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 643/1490 Jessica Robertson 2.28135009817654e-06 4.56464840309789e-06 1895 2769.54545454545 2349 2.28135244023115e-07 972 1.27591541094535 -1.0378625730768 -1 1.75270963703273 1895 4108 4494 2935 2277 972 2268 2349 2991 4351 1825 2299 M7399 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM.html Porphyrin and chlorophyll metabolism 18/48 KEGG 4.69129148394091e-05 7.28892304169334e-05 2350 2275.27272727273 2350 4.26490138570181e-06 287 1.83875804791781 2.63843153469663 1 1.95678940027555 2350 2915 2322 1801 2899 3614 2389 1982 287 2933 1536 2300 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 341/741 Lauren Kazmierski 3.49698783271519e-06 6.69672455419018e-06 1345 2412.72727272727 2350 3.17908490120849e-07 1342 1.6873823909593 1.96491311553 1 2.24569168822579 1342 4109 2182 2435 2350 2975 1631 2154 2445 3126 1791 2301 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 133/454 Arthur Liberzon 9.24290612594376e-08 3.05835106730055e-07 2970 2264 2350 8.4026422856981e-09 986 1.69742070518098 -1.28732405862442 -1 2.84426518027032 2969 1006 986 2350 1205 3921 2732 2476 2287 1612 3360 2302 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 83/168 Arthur Liberzon 3.50156790287735e-06 6.70275620624316e-06 1635 2489.72727272727 2351 3.18324861460135e-07 1142 1.78399140229724 1.84685679606162 1 2.37408661346553 1631 3223 1142 2014 2351 3563 2214 3531 2987 1862 2869 2303 M204 PID_RHODOPSIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHODOPSIN_PATHWAY.html Visual signal transduction: Rods 18832364 9/35 Pathway Interaction Database 1.61428618758922e-06 3.37251229382216e-06 3770 2703.36363636364 2353 1.61428736025437e-07 1158 1.7990615842067 2.09387605348848 1 2.53217932566677 3770 1158 3904 2312 2196 4286 2353 2752 1267 1192 4547 2304 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 203/416 Jessica Robertson 1.37718220225643e-07 4.19601807527543e-07 2970 2664.81818181818 2353 1.25198389860629e-08 1361 1.41964134464177 -1.29471055920648 -1 2.32865302361062 2968 1428 2133 1773 1361 3683 2567 4582 2353 2070 4395 2305 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 15/79 Jessica Robertson 2.07413273010955e-06 4.19300516535519e-06 2355 2193.36363636364 2353 1.88557698688978e-07 540 1.98989005885004 -2.28611216119288 -1 2.7523655021478 2353 3354 2197 2663 3148 1398 2790 540 2002 2563 1119 2306 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 13/37 Jessica Robertson 1.99748993403583e-05 3.29934361328583e-05 2040 2506.27272727273 2354 1.81591642770511e-06 1301 2.17226130254383 -2.5341923348107 -1 2.50403929417426 3562 2354 2038 3036 2733 2302 3179 2038 1301 2917 2109 2307 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 101/224 Arthur Liberzon 5.22219410440412e-07 1.25751292771006e-06 2910 2635.72727272727 2355 4.74745031273599e-08 1309 1.5412605607866 1.88306350111328 1 2.33917445566832 2908 1309 2082 2181 1842 3956 3188 2355 1984 3787 3401 2308 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 2/10 Arthur Liberzon 0.0010219197787698 0.00135965817243477 2165 2609.8 2356 0.000113598246652368 1180 0.76611972013633 -0.76611972013633 -1 0.564882027916394 2162 2175 4656 NA 3401 1180 1402 2712 4174 2537 1699 2309 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 10/14 Jessica Robertson 9.93152449994089e-07 2.19835256526797e-06 2030 2370.81818181818 2357 9.02866271214631e-08 1658 1.43286198209415 1.41846218749369 1 2.08525166014532 2027 2357 2371 2986 2029 2051 1658 2142 3279 2448 2731 2310 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 10/26 Arthur Liberzon 4.80690834824736e-06 8.91043757303463e-06 4110 2583 2358 4.36992622833998e-07 298 1.56862426164133 -2.52900095904798 -1 2.03759390453439 4110 2124 2235 2211 2427 3947 4321 1943 298 2439 2358 2311 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 295/732 Jessica Robertson 1.69827049396736e-08 9.53065333500722e-08 4585 2356.63636363636 2358 1.54388227916091e-09 473 1.46218301068061 -1.13168921692058 -1 2.64053405164553 4582 1788 1706 1864 473 947 4091 2756 2437 2358 2921 2312 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 5/11 Arthur Liberzon 8.49594355895139e-05 0.000126991998460116 2270 2440.18181818182 2359 8.4962683911863e-06 412 1.50286816058275 2.06090709151773 1 1.5061332234871 2268 2217 4218 2531 3027 2988 2038 2543 412 2241 2359 2313 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 11/44 Jessica Robertson 7.46069797889486e-07 1.70374418757804e-06 2750 2240.81818181818 2359 6.78245500817055e-08 413 2.6836990224028 3.76395680468555 1 3.98201204379105 2748 2816 1972 2359 3181 3440 1894 413 710 3334 1782 2314 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 12/27 Leona Saunders 9.25957421790171e-09 6.89830918681835e-08 4130 2787.45454545455 2360 8.41779477897665e-10 218 1.80807206494361 1.48460459504461 1 3.33045583077463 4130 2276 2035 2127 218 3973 3768 4492 2360 2146 3137 2315 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 17/52 Yujin Hoshida 2.17289082737124e-05 3.56019804792364e-05 2360 2342.72727272727 2361 1.97537480802275e-06 477 1.91097126212411 2.48609487699773 1 2.18659786958455 2357 2071 2471 2651 2751 3603 2361 2235 477 2225 2568 2316 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 17/30 Arthur Liberzon 1.30356001676022e-07 4.01345744976241e-07 3880 2505.09090909091 2361 1.18505463090883e-08 661 1.7075682201501 -1.85717689135822 -1 2.80942767842929 3877 1408 1179 2030 1347 3957 2543 3661 2361 661 4532 2317 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 34/73 Arthur Liberzon 5.26966308001512e-07 1.2668656881649e-06 2920 2488.81818181818 2361 4.79060394750788e-08 1518 1.58925911251756 -1.05145037397901 -1 2.41070645453139 2919 1518 2097 2361 1846 1566 2874 4554 1602 3410 2630 2318 M18215 BIOCARTA_TOB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TOB1_PATHWAY.html Role of Tob in T-cell activation 8/22 BioCarta 4.47085707883736e-05 6.97650225488907e-05 2655 2327 2362 4.47094702991796e-06 836 1.97260072852261 2.35387452881836 1 2.10887688820134 2654 1589 3867 2362 2908 3971 2524 1378 836 2092 1416 2319 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 4/9 Arthur Liberzon 2.19715241669884e-06 4.41314025917307e-06 2400 2259.72727272727 2363 2.1971545890673e-07 12 4.14245896602343 4.14245896602343 1 5.70606641178142 2397 2363 4588 2201 3554 2495 1905 568 12 3112 1662 2320 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 4/9 Reactome 4.72855122144327e-07 1.1582849463504e-06 2390 2442.45454545455 2364 4.7285522276074e-08 253 1.36073930184096 1.20909138291071 1 2.07769105571129 2386 253 3999 2938 1839 2364 1725 3979 2194 2043 3147 2321 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 13/38 Reactome 1.47734866343605e-07 4.44627863639135e-07 3485 2485.63636363636 2364 1.34304432967572e-08 1383 1.57861289472418 -1.09131084261322 -1 2.5791999752814 3481 1942 1749 2364 1383 3079 4232 2399 1923 1773 3017 2322 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 3/7 Leona Saunders 0.00131365764091617 0.00173207645057209 1935 2860.27272727273 2365 0.00013144348509987 1210 0.592517296127967 0.592517296127967 1 0.420856464687236 1933 2365 4176 4012 3632 1548 1210 1598 4314 4552 2123 2323 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 6/19 Arthur Liberzon 3.02907200671564e-06 5.87996330715389e-06 3585 2607.81818181818 2365 3.02907613559831e-07 691 1.7879435921632 -1.52668607765083 -1 2.40550398594941 3582 1164 4664 1484 2338 3162 3864 2365 691 1158 4214 2324 M9134 BIOCARTA_TRKA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TRKA_PATHWAY.html Trka Receptor Signaling Pathway 13/25 BioCarta 4.00003238210092e-06 7.54291820624744e-06 2605 2173.81818181818 2367 3.63639968633132e-07 942 1.95892427052064 2.17749964166553 1 2.58104114112701 2601 1734 1828 946 2390 3479 2367 2686 942 2267 2672 2325 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 23/50 Leona Saunders 3.72377756382958e-06 7.08179852237621e-06 4195 2503.09090909091 2367 3.38525806073441e-07 1576 1.73040346781588 -1.89293954881562 -1 2.29214003947675 4193 1576 1961 2396 2367 2664 4407 1806 1612 1647 2905 2326 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 143/259 Arthur Liberzon 3.8105960050039e-07 9.68354277627348e-07 2030 2635.63636363636 2367 3.46417878639386e-08 1664 1.29724621559125 -0.978154412363189 -1 2.00669793617979 2030 2367 3608 2061 1730 1664 2839 3956 1983 4267 2487 2327 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 18/53 KEGG 1.42941223599951e-05 2.41473152380221e-05 2935 2509.18181818182 2368 1.29947411222239e-06 1474 1.86026738290253 -1.04211279529794 -1 2.20925694735968 2935 2155 1474 2108 2668 3898 3002 1653 2131 2368 3209 2328 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 11/15 Arthur Liberzon 5.49428584470269e-05 8.42756905671908e-05 2170 2335.81818181818 2368 4.99493005812823e-06 806 1.90742719707121 2.28816937718346 1 1.9989382124554 2168 3238 2327 2368 3775 3161 2723 1009 806 2615 1504 2329 M85 BIOCARTA_BAD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BAD_PATHWAY.html Regulation of BAD phosphorylation 18/40 BioCarta 3.75652421957111e-06 7.13831001334559e-06 950 1861 2369 3.41502784899355e-07 295 1.11137604992466 1.11137604992466 1 1.47117245805436 950 2593 2976 2475 2369 696 295 1136 3364 2935 682 2330 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 18/50 Jessica Robertson 0.0114757051574828 0.0141068085960032 1670 2723.63636363636 2370 0.00104872780838868 1379 1.95764537148624 2.18862136948886 1 0.93183370866287 1670 4497 2257 3580 3805 2314 1379 2332 3359 2370 2397 2331 M91 PID_TCPTP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCPTP_PATHWAY.html Signaling events mediated by TCPTP 18832364 31/71 Pathway Interaction Database 2.49023225712849e-07 6.83096362733292e-07 2500 2217.54545454545 2371 2.26384776273076e-08 689 1.65446232022273 2.19488581497702 1 2.62376603937122 2497 689 1685 1240 1564 3930 3090 2371 2449 1990 2888 2332 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 15/53 Reactome 1.54038405885215e-05 2.59089723610236e-05 2375 2042 2372 1.40035894939579e-06 931 1.80332951060521 2.4156689276524 1 2.12745239036149 2372 1347 1466 1180 2687 3154 2512 2382 931 1185 3246 2333 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 8/21 Leona Saunders 0.00430483305364714 0.00545496151687141 3075 2576 2372 0.000431319507526066 655 1.30398094144571 1.36912248431984 1 0.759091869557921 3073 1161 4174 2372 3999 3960 2932 1801 655 2102 2107 2334 M17726 KEGG_DRUG_METABOLISM_OTHER_ENZYMES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DRUG_METABOLISM_OTHER_ENZYMES.html Drug metabolism - other enzymes 15/80 KEGG 3.90953059485261e-06 7.39022486750358e-06 2915 2201 2373 3.55412503848894e-07 503 2.0257751542023 -0.850253766919107 -1 2.67375053930132 2914 1350 1124 503 2380 4218 4591 2373 725 2555 1478 2335 M13324 BIOCARTA_HIF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HIF_PATHWAY.html Hypoxia-Inducible Factor in the Cardiovascular System 13/24 BioCarta 0.00103235482845626 0.00137315206532672 1980 2540.72727272727 2373 9.38945074286656e-05 881 2.0534100996319 2.0534100996319 1 1.5117732093359 1978 3355 2373 3577 3494 1552 881 1823 3960 3519 1436 2336 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 18/119 Arthur Liberzon 3.57716554412199e-05 5.64946656688609e-05 1585 2238.27272727273 2375 3.25202155417961e-06 953 1.60880224116417 1.90468168550364 1 1.757863085456 1581 3155 2404 4019 3789 1294 1220 953 2684 2375 1147 2337 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 39/88 Reactome 1.28898119852788e-05 2.19642396229151e-05 2080 2275.27272727273 2376 1.17180795521608e-06 363 1.19630921958215 -1.06338725095379 -1 1.43340204780723 2078 2692 3202 2376 2649 363 1632 2027 3297 3933 779 2338 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 37/99 Yujin Hoshida 1.77225780307315e-08 9.82816575763406e-08 4085 2344.45454545455 2376 1.61114347031814e-09 492 2.47278575781064 -2.52468917045642 -1 4.45707530264521 4085 2376 1020 702 492 3110 3597 3831 917 1563 4096 2339 M4085 KEGG_PRIMARY_IMMUNODEFICIENCY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_IMMUNODEFICIENCY.html Primary immunodeficiency 11/48 KEGG 3.72113737192559e-06 7.07967914122749e-06 2370 2447.54545454545 2377 3.38285787815389e-07 1287 1.3951668667453 -1.1642013249729 -1 1.84812302216565 3141 1287 1665 2745 2366 2377 3211 2842 3436 1483 2370 2340 M544 REACTOME_SIGNALING_BY_ERBB4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ERBB4.html Genes involved in Signaling by ERBB4 50/137 Reactome 8.70673652778257e-07 1.95120838685744e-06 3615 2480.09090909091 2377 7.91521815779005e-08 1304 1.55764171514801 -1.34529502013669 -1 2.28759548284783 3615 2372 2377 1304 1997 1466 4306 2843 1477 3133 2391 2341 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 200/466 John Newman 9.80074363043926e-08 3.20714278297754e-07 3785 2592.63636363636 2377 8.90976733368274e-09 1228 1.59328327475216 -1.25570179355563 -1 2.66131342433916 3783 1913 1322 2377 1228 2707 3250 3984 2254 1437 4264 2342 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 96/360 Arthur Liberzon 7.14480117775258e-08 2.5211248734148e-07 1300 2067.54545454545 2377 6.49527400889983e-09 753 1.27231974860262 1.48953174403037 1 2.15940411763916 1296 2828 2776 3348 1097 1017 1205 2377 2634 3412 753 2343 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 11/32 Reactome 3.88397617866222e-06 7.35069158853439e-06 3705 2562.09090909091 2378 3.53089366874592e-07 591 1.68041516463587 -1.03790523929621 -1 2.21892866100088 3703 591 1626 840 2378 4524 4003 3826 689 1485 4518 2344 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 23/42 John Newman 3.68427812172337e-07 9.4187273750113e-07 1260 2444.72727272727 2378 3.34934430792655e-08 1059 1.37108402513002 1.20131393490538 1 2.12516377261716 1260 3098 2378 3745 1714 1632 1059 3698 3251 2956 2101 2345 M649 REACTOME_PHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHOLIPID_METABOLISM.html Genes involved in Phospholipid metabolism 101/208 Reactome 2.17829300260408e-07 6.12326395333097e-07 2380 2265.54545454545 2379 1.98026656207648e-08 1519 1.47822768350437 -1.36368036010667 -1 2.36234065733 2379 2008 2520 1964 1519 1725 3238 2443 2013 2545 2567 2346 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 32/65 John Newman 4.4323180207505e-07 1.0977717888603e-06 2505 2314.72727272727 2379 4.02938083065948e-08 1224 1.812981996204 -0.98798434752787 -1 2.77908027674933 2505 1798 1553 2379 1788 3764 2946 2512 1224 2078 2915 2347 M2881 REACTOME_LYSOSOME_VESICLE_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LYSOSOME_VESICLE_BIOGENESIS.html Genes involved in Lysosome Vesicle Biogenesis 21/42 Reactome 4.10388117622876e-06 7.71391383546249e-06 3370 2373.45454545455 2380 3.73080802875536e-07 1042 1.0964194476421 -0.863721018770136 -1 1.44187564877492 3368 1460 2890 1496 2400 1042 2292 3024 2057 3699 2380 2348 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 17/44 Jessica Robertson 0.000370331088463624 0.000512211180797091 1955 2600.09090909091 2383 3.36721310770289e-05 1344 1.87770723964183 1.90409780332998 1 1.58926065108551 1955 4097 2355 2383 4629 2681 1442 1344 3500 2784 1431 2349 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 25/48 Arthur Liberzon 9.65491397181923e-06 1.6856530131127e-05 1140 2298.09090909091 2383 8.77723303964416e-07 1140 1.48765789659662 1.68727630216451 1 1.82647712450357 1140 3184 2383 3885 2585 1319 1529 1437 3445 2645 1727 2350 M13968 BIOCARTA_HIVNEF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HIVNEF_PATHWAY.html HIV-I Nef: negative effector of Fas and TNF 42/87 BioCarta 4.58391844116706e-06 8.54085161642499e-06 2385 2409.72727272727 2384 4.16720726567649e-07 1064 1.91534616551873 -1.30936619966477 -1 2.49703873102247 2384 2976 2033 2184 2415 3371 2065 2135 1064 2927 2953 2351 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 49/166 Jessica Robertson 6.00965961375507e-08 2.21916981481925e-07 4495 2506.81818181818 2385 5.46332707083524e-09 1021 1.3576439281287 -1.04485764664405 -1 2.323565349213 4495 1566 2731 2123 1021 1806 3858 2266 2416 2385 2908 2352 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 15/27 Lauren Kazmierski 0.00162318430143676 0.00212821534318205 2195 2624.81818181818 2387 0.000147671194841213 2004 1.84264423902949 1.84264423902949 1 1.26640912986829 2192 3599 2310 2387 3424 3004 2477 2035 3293 2004 2148 2353 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 58/137 Arthur Liberzon 0.000957232959506622 0.001276129060668 2070 2659.18181818182 2388 8.70590646446965e-05 1628 1.79265804403455 1.96831867402558 1 1.3344749249053 2070 4206 2290 3499 3379 2757 1628 1862 2836 2388 2336 2354 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 58/142 Arthur Liberzon 4.0037915723368e-06 7.54696995493574e-06 2700 2127.27272727273 2391 3.63981714443337e-07 434 1.82142037956663 -1.7478978107033 -1 2.39975936545801 2697 1657 736 1462 2391 1899 3571 3410 2574 434 2569 2355 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 27/66 Jessica Robertson 2.33373372316355e-05 3.80908262861178e-05 1680 2205.54545454545 2392 2.1215986177271e-06 666 1.3619510033171 1.58951213840214 1 1.54810982178414 1679 3258 2580 2998 3219 1910 1484 1354 2721 2392 666 2356 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 48/146 Yujin Hoshida 5.20224299544021e-08 2.02327199005734e-07 2395 2305.72727272727 2392 4.7293119258685e-09 915 1.22868033863828 -0.980894114501977 -1 2.11553269310436 2392 1660 2353 3545 944 915 2401 3482 2848 2639 2184 2357 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 146/280 Kate Stafford 1.53632976443228e-06 3.23270825151759e-06 3065 2739.09090909091 2393 1.39666439754648e-07 1780 1.5748480883271 1.89717231378134 1 2.22404694433809 3063 2005 2051 1909 2148 4129 3196 1780 2393 3404 4052 2358 M16966 BIOCARTA_STATHMIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STATHMIN_PATHWAY.html Stathmin and breast cancer resistance to antimicrotubule agents 10/22 BioCarta 8.13874901100089e-06 1.43809117140084e-05 2550 2221.72727272727 2394 7.39889010900021e-07 690 1.49643378552958 1.38121017525064 1 1.8638033399738 1700 2394 2188 1641 2547 1392 690 4353 2550 2430 2554 2359 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 28/76 Arthur Liberzon 1.63175490601135e-06 3.40445391343241e-06 2115 2383.63636363636 2394 1.48341465117843e-07 1459 1.635168047466 1.35116111761502 1 2.29977727051758 2112 2770 2488 2284 2162 2394 1459 3615 1578 2515 2843 2360 M10911 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYSTEINE_AND_METHIONINE_METABOLISM.html Cysteine and methionine metabolism 14/39 KEGG 2.39612449880136e-05 3.89598868889075e-05 3860 2650.27272727273 2395 2.1783187241176e-06 1150 1.7174004915982 -2.32267623555092 -1 1.94781622968671 3857 1772 2093 1876 2768 4457 2323 2551 1150 2395 3911 2361 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 9/24 Arthur Liberzon 1.72552024746355e-05 2.88057993573716e-05 2045 2324 2396 1.72553364600054e-06 542 2.85854913428665 2.85854913428665 1 3.33848879155033 2041 2433 4139 1966 2985 3164 2396 860 542 2303 2735 2362 M275 PID_ALPHA_SYNUCLEIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALPHA_SYNUCLEIN_PATHWAY.html Alpha-synuclein signaling 18832364 14/48 Pathway Interaction Database 1.88460709289567e-06 3.84804742366409e-06 3730 2509.18181818182 2397 1.71328064302422e-07 531 1.56200324204272 2.01859064575425 1 2.17550334916211 3727 1356 2216 2537 2384 3449 4199 531 1108 2397 3697 2363 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 31/67 Leona Saunders 2.94365365135337e-06 5.73792055334522e-06 1760 2418.45454545455 2397 2.67605235458284e-07 1758 1.79291991030633 1.91469312797207 1 2.41709678611853 1758 2736 1833 3103 2310 2832 2397 2570 2102 2766 2196 2364 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 19/126 Reactome 6.13251700598268e-07 1.44117225125551e-06 3435 2687.36363636364 2399 5.57501701402473e-08 840 1.93593107650573 2.15325858767331 1 2.90868625522796 3435 840 975 1754 1893 4669 3641 4050 2399 1256 4649 2365 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 13/34 BioCarta 2.12374148578852e-05 3.49433026769838e-05 2400 2368.45454545455 2400 1.93069271575342e-06 934 1.47916826550593 1.22345374818121 1 1.6955999077804 2807 2392 2400 2088 2743 2743 2076 2400 934 2265 3205 2366 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 11/33 Arthur Liberzon 0.000234565938298125 0.000333184597412856 2125 2111.54545454545 2400 2.13264501508122e-05 539 2.48931046542116 2.5944528890203 1 2.22649516777087 2124 2708 1302 2400 3170 2547 2637 1701 539 1498 2601 2367 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 9/18 Jessica Robertson 1.26328975723442e-06 2.71549348733968e-06 2540 2495.72727272727 2401 1.26329047539045e-07 596 1.3456954134616 1.20689878969471 1 1.92663930228387 2539 596 4499 2401 2121 3112 1913 2907 2233 2314 2818 2368 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 16/32 John Newman 4.18379351946753e-06 7.84776168253046e-06 1385 2428.45454545455 2402 3.80345588719148e-07 1249 0.972495757296835 1.02841336127409 1 1.2770376535482 1384 2882 3026 3236 2402 1897 1747 1249 3609 3256 2025 2369 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 23/62 Arthur Liberzon 1.10723070145469e-06 2.41549491015675e-06 4550 2673.45454545455 2403 1.00657387155414e-07 951 1.50487565893113 -1.58780172721564 -1 2.17421863820991 4550 951 1228 1679 2062 2403 3977 4514 3340 1057 3647 2370 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 35/69 Arthur Liberzon 1.74653385476859e-07 5.10558804956058e-07 2405 2446 2403 1.58775817583842e-08 1167 1.59069349142077 1.72383041323808 1 2.5743684955508 2403 1517 1564 2006 1444 3984 2482 4124 2773 1167 3442 2371 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 4/8 Arthur Liberzon 1.18203876926333e-05 2.02746474113029e-05 2775 2206.63636363636 2404 1.18204505678083e-06 62 2.76585966975675 2.40577724967815 1 3.33874828584664 2773 1549 4182 1184 2652 2747 2427 2245 62 2048 2404 2372 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 5/15 Jessica Robertson 0.00653624617373742 0.00815030589945012 2405 2635.81818181818 2404 0.000655555126891247 1710 3.02142695095799 3.02142695095799 1 1.62335317347509 2404 2892 4328 2083 4228 1884 1710 1903 1854 3288 2420 2373 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 166/378 Jessica Robertson 4.87320258761303e-07 1.18812837281762e-06 3660 2511.63636363636 2404 4.4301851518842e-08 945 1.66356768004771 -1.40418889808187 -1 2.53534751995729 3659 1433 1233 1347 1817 3285 3884 3066 2404 945 4555 2374 M10189 REACTOME_SIGNALING_BY_NOTCH http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH.html Genes involved in Signaling by NOTCH 50/129 Reactome 3.80284950407011e-06 7.21171702795328e-06 3080 2645.45454545455 2405 3.45714188869983e-07 1691 1.46515262459261 -0.918238262921003 -1 1.93780608055938 3080 2454 2029 2405 2374 3900 3236 1691 1817 3721 2393 2375 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 33/82 Leona Saunders 1.68994491843999e-06 3.49706810098087e-06 1320 2530 2406 1.53631474234912e-07 1319 1.73610637956889 2.08633061443463 1 2.4365363754224 1319 3382 2406 2816 2180 2755 2310 2783 2200 3935 1744 2376 M10287 BIOCARTA_FMLP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FMLP_PATHWAY.html fMLP induced chemokine gene expression in HMC-1 cells 22/63 BioCarta 8.43937218050274e-05 0.000126226932773175 2925 2608.09090909091 2407 7.6724508534656e-06 1769 1.38783499712848 1.84919908136799 1 1.3917869447492 2923 2108 2407 1902 3008 3832 2744 1769 1853 2348 3795 2377 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 145/336 Arthur Liberzon 2.36323416958572e-08 1.17368000814054e-07 2670 2273.27272727273 2409 2.14839472270138e-09 604 1.7581703400403 2.04260014131268 1 3.13415926645804 2667 2290 1342 1819 604 4016 3110 2815 2409 1317 2617 2378 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 15/60 Arthur Liberzon 1.24768900325358e-08 8.0181460061125e-08 2445 2121 2410 1.13426273666329e-09 343 1.58434588257515 -1.37593905658376 -1 2.89172997569178 2444 1061 1998 2688 343 1815 2410 3838 2490 2566 1678 2379 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 47/112 Leona Saunders 2.23851204878729e-07 6.27372455778542e-07 2375 2486.18181818182 2411 2.0350111605065e-08 1530 1.40404633552294 1.5346160119097 1 2.23998484115266 2374 2300 2354 3163 1530 2703 1914 2411 2859 2944 2796 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 13/42 Jessica Robertson 4.37588407125918e-06 8.17599392261583e-06 4185 2700.90909090909 2411 3.9780843409855e-07 211 3.15808349792527 -2.67206149204757 -1 4.13259870166188 4185 2205 1361 2206 2411 3360 3710 4563 211 2274 3224 2381 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 358/844 Jessica Robertson 3.09233362875607e-06 5.99035774466761e-06 1940 2781.54545454545 2411 2.81121634124357e-07 1441 1.50986032218124 1.76021902142291 1 2.02823275912134 1940 2411 3360 1441 2321 4236 2233 3288 2260 3860 3247 2382 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 36/79 KEGG 6.32234898762331e-05 9.61276033614628e-05 1535 2308.09090909091 2412 5.74775516934763e-06 626 1.2278706916426 -1.15378169927326 -1 1.26873085450552 1531 3527 2941 3361 2966 626 2108 1360 3496 2412 1061 2383 M16763 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NEUROTROPHIN_SIGNALING_PATHWAY.html Neurotrophin signaling pathway 81/152 KEGG 6.50141851001968e-06 1.17070738863379e-05 2265 2309.81818181818 2412 5.91039793002513e-07 830 1.60405777201459 1.93590177415392 1 2.03470866550605 2261 2222 2412 830 2504 3607 2081 2475 1467 2961 2588 2384 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 15/38 John Newman 1.24648709990575e-07 3.8631207342317e-07 3185 2357.63636363636 2412 1.13317015502713e-08 380 1.78102063114208 -0.741963460389991 -1 2.93787306469742 3185 1282 1945 2412 1333 4540 3521 1788 380 2562 2986 2385 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 36/76 Arthur Liberzon 1.01521723925724e-05 1.76458011244786e-05 1675 2353.72727272727 2413 9.22929021939232e-07 1012 1.31052467269936 1.51259611651229 1 1.6023021450374 1672 3648 2812 3482 2597 2002 1178 1012 3102 2413 1973 2386 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 72/146 Leona Saunders 6.55564607942464e-08 2.36669934731771e-07 2415 2219.81818181818 2413 5.95967843161122e-09 745 1.65488267744644 -1.06702562399471 -1 2.8203819007368 2413 2584 2860 2713 1061 745 1426 3791 1577 3509 1739 2387 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 139/341 Jessica Robertson 2.97053570022046e-07 7.88218023286132e-07 1550 2272.81818181818 2413 2.70048736483199e-08 1146 1.55915757599527 1.65981236294173 1 2.44769440477131 1550 2413 1146 2906 1632 2913 2044 3174 3058 1660 2505 2388 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 28/91 Kevin Vogelsang 1.23653445678384e-07 3.84559199906415e-07 2535 2589.36363636364 2414 1.1241222966224e-08 1329 1.48550940305215 1.67237135623673 1 2.45116873347033 2531 2150 2226 2414 1329 4377 1975 3764 2052 2968 2697 2389 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 54/119 Jessica Robertson 3.15636313201588e-07 8.30472635408557e-07 3520 2800.27272727273 2416 2.86942144078428e-08 1491 1.36503035100088 -1.12323125463408 -1 2.13497464731628 3516 1832 2137 1491 1650 4686 2270 3697 2589 2416 4519 2390 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 11/31 Arthur Liberzon 4.62660688259315e-06 8.6135398696192e-06 3205 2360.63636363636 2416 4.20601510217322e-07 915 2.04791333442185 -2.41358604898228 -1 2.66792797339803 3203 969 915 1885 2416 3284 4392 2279 2674 1094 2856 2391 M18719 BIOCARTA_HER2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HER2_PATHWAY.html Role of ERBB2 in Signal Transduction and Oncology 14/37 BioCarta 5.51454068157982e-06 1.00902528832031e-05 3625 2531.54545454545 2418 5.01323136766168e-07 721 1.45411138595709 -1.16767246696538 -1 1.868646960697 3625 721 2077 1241 2457 2418 4585 4090 1725 1875 3033 2392 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 51/134 Jessica Robertson 4.90379820963947e-08 1.94574076294416e-07 4645 2777.36363636364 2419 4.45799847176826e-09 913 1.4966732816435 -1.04740003607146 -1 2.58349365142615 4644 2419 2512 2086 913 2295 4422 3151 2167 1699 4243 2393 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 23/55 BioCarta 3.26057677362314e-05 5.17583426869852e-05 1985 2346.90909090909 2420 2.96420463544869e-06 1242 1.61730088422195 1.90556958558635 1 1.78296828372931 1983 2982 2827 1242 2838 2809 1893 2010 2831 2420 1981 2394 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 16/47 Reactome 0.0110101438419103 0.0135522810725484 2175 2522.36363636364 2421 0.0010059667737651 1505 1.33515663287116 1.07315715698343 1 0.641511950576724 2172 1985 2604 2384 3624 2421 1505 2256 3269 2654 2872 2395 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 36/82 Signaling Gateway 0.00123803927897392 0.00163559404039239 1600 2653.09090909091 2423 0.00011261241172095 1569 1.47838462577235 1.69246250642462 1 1.05954090980002 1598 4086 3032 2625 3518 2179 2164 1569 2423 3821 2169 2396 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 177/372 Jessica Robertson 1.05063372342296e-07 3.39068156195592e-07 1350 2327 2423 9.55121612361014e-09 1254 1.68535497430936 2.14201244437213 1 2.8046266637871 1346 3742 1818 2520 1254 3248 2039 1796 2650 2761 2423 2397 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. 7/11 SigmaAldrich 6.77083259155373e-06 1.21610277976316e-05 2430 2431.45454545455 2427 6.77085322152049e-07 1546 1.60107911785492 2.01901834841514 1 2.02412619272884 2427 1546 3887 2492 2532 3326 2128 1830 1769 2670 2139 2398 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 62/144 Jessica Robertson 3.49837274900703e-08 1.54549951747859e-07 2380 2745.63636363636 2427 3.18033891330644e-09 768 1.55542518744507 1.73561096640287 1 2.72492322897438 2380 2935 2122 2427 768 4123 2349 4408 3115 2360 3215 2399 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 42/112 Kevin Vogelsang 1.32324492588863e-06 2.83008933031224e-06 4565 2562.45454545455 2427 1.20295065617091e-07 840 1.81728620247494 -1.7988559461218 -1 2.59342730766942 4562 2455 1189 1944 2103 2427 4373 2516 2037 840 3741 2400 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 19/48 Kevin Vogelsang 4.80699662497472e-06 8.91043757303463e-06 925 1979.54545454545 2428 4.370006480261e-07 575 2.08511903557437 2.08511903557437 1 2.70850454843061 925 2985 2528 3423 2428 650 575 1236 3089 3001 935 2401 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 42/161 Yujin Hoshida 6.65231327407955e-05 0.000100784804404581 855 2103.36363636364 2428 6.04774039439197e-06 851 1.60625050308147 1.56283715716949 1 1.65121312062475 851 3146 2870 2605 2975 1145 976 1737 2428 2932 1472 2402 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 12/28 Arthur Liberzon 0.000189128020018144 0.000271857025093565 2565 2443.18181818182 2429 1.71949346179117e-05 590 4.69221782805636 5.3730444617881 1 4.30344932983994 2562 4308 1615 2429 3137 2909 2258 2131 590 2747 2189 2403 M19540 KEGG_OXIDATIVE_PHOSPHORYLATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OXIDATIVE_PHOSPHORYLATION.html Oxidative phosphorylation 62/155 KEGG 0.000402839735822618 0.000554555523520796 630 2350.45454545455 2430 3.66285016642795e-05 628 0.760619333364537 -0.774626335977406 -1 0.63702669366142 628 2551 3736 2430 3500 661 931 1946 3982 4281 1209 2404 M233 PID_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPO_PATHWAY.html EPO signaling pathway 18832364 24/58 Pathway Interaction Database 1.50540345296851e-06 3.17936321261293e-06 3265 2424.72727272727 2431 1.36854953007126e-07 1012 1.2950419804209 -1.32364128418976 -1 1.83130361030976 3264 1196 2431 1012 2138 2290 4106 3338 2547 1735 2615 2405 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 101/284 Jessica Robertson 5.40613844465523e-08 2.08849888976588e-07 4135 2500.09090909091 2431 4.91467143409291e-09 696 1.73124184463707 -1.58628995277029 -1 2.9747031760218 4135 779 696 2347 956 2780 4389 4659 2431 881 3448 2406 M31 PID_BETA_CATENIN_DEG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BETA_CATENIN_DEG_PATHWAY.html Degradation of beta catenin 18832364 10/26 Pathway Interaction Database 0.0140564753915891 0.0171532926262986 1620 2459.45454545455 2432 0.00128609983594936 1517 1.30270333668636 1.51638959275924 1 0.59162878033368 1619 3302 2732 2768 3765 1750 1517 2042 3064 2432 2063 2407 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 34/79 Arthur Liberzon 0.0285369957296635 0.0339488098474748 1765 2592.72727272727 2432 0.00262854766004851 1714 1.86396837859815 1.93731181309263 1 0.704386071327354 1765 3751 2432 2192 3841 3187 1714 2963 1977 2631 2067 2408 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 17/55 Arthur Liberzon 0.000194086110958946 0.000278727402989158 2435 2214.90909090909 2433 1.7645748685179e-05 754 2.98178790452239 2.70080284092179 1 2.7264218860679 2433 3448 1531 2124 3142 2599 1312 1438 754 2783 2800 2409 M8873 ST_FAS_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_FAS_SIGNALING_PATHWAY.html Fas Signaling Pathway 48/100 Signaling Transduction KE 7.12669895794708e-07 1.63624259269672e-06 2210 2441.81818181818 2434 6.47881933325195e-08 940 1.56320878478537 2.13609281072299 1 2.32651307473711 2209 3749 2640 3025 1945 3206 1536 940 1569 3607 2434 2410 M155 PID_S1P_META_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_META_PATHWAY.html Sphingosine 1-phosphate (S1P) pathway 18832364 10/30 Pathway Interaction Database 9.37676930085984e-07 2.08815334902213e-06 2820 2555.90909090909 2434 8.52433936127154e-08 865 1.28888645927933 1.1048708420059 1 1.8831278410077 2817 865 2255 2590 2014 2925 2141 4122 2326 2434 3626 2411 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 17/38 John Newman 4.70028095507495e-05 7.29805054853586e-05 3510 2466.36363636364 2434 4.27307398106768e-06 1212 2.03111908001946 -1.95414554076943 -1 2.16121431772353 3506 2238 1212 1336 2900 2654 3532 2434 2044 1413 3861 2412 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 5/29 Arthur Liberzon 0.000558284179939425 0.000761163708814706 2435 2553.54545454545 2434 5.58424486102921e-05 723 1.51866537460901 -1.51866537460901 -1 1.21817450565879 2434 2406 4572 2485 4001 1650 2073 3245 723 3301 1199 2413 M14933 KEGG_STEROID_HORMONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_HORMONE_BIOSYNTHESIS.html Steroid hormone biosynthesis 14/88 KEGG 0.000223467250467398 0.000318384778257898 2725 2313.90909090909 2435 2.03172684191286e-05 179 3.94958267029417 4.39353459956901 1 3.5526418574934 2724 3329 1778 1483 3665 3843 2435 1264 179 3006 1747 2414 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 16/42 Leona Saunders 6.58505303560433e-09 5.52013569317386e-08 4565 2761.36363636364 2435 5.98641186846797e-10 137 1.51618745783271 -1.50665812770159 -1 2.83055453497259 4564 3629 2435 1401 137 4048 4119 1912 2358 2159 3613 2415 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 27/55 Jessica Robertson 4.96829290489816e-06 9.19124380274488e-06 1630 2292 2435 4.51664011354892e-07 684 1.42683983301841 1.57839229072931 1 1.84847483475488 1627 2523 2468 4346 2435 1440 684 1663 3463 2851 1712 2416 M276 PID_FGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FGF_PATHWAY.html FGF signaling pathway 18832364 32/84 Pathway Interaction Database 5.00339088313733e-06 9.2488716680006e-06 2475 2326.18181818182 2437 4.54854751111659e-07 1656 2.19121198428671 2.55421590132691 1 2.83719120709248 2472 3091 2073 2023 2437 2725 2201 1656 1974 2453 2483 2417 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 7/17 Arthur Liberzon 3.86761851551044e-05 6.07972504652194e-05 1310 2237.81818181818 2438 3.86768583028773e-06 852 1.86449845514149 1.86449845514149 1 2.02196311483251 1307 2438 4589 2581 2879 1072 1611 3704 889 2694 852 2418 M4891 BIOCARTA_PML_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PML_PATHWAY.html Regulation of transcriptional activity by PML 11/26 BioCarta 6.84872568619184e-05 0.000103659975986741 2440 2067.27272727273 2439 6.22630809111605e-06 160 1.83201588737834 -0.870972051916455 -1 1.87754172203796 2439 1069 1920 1975 2978 3026 2500 1563 160 2606 2504 2419 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 22/44 Reactome 2.3349941534549e-05 3.80981288408415e-05 2090 2258.45454545455 2440 2.1227444877636e-06 471 2.31106287745379 2.00985775182609 1 2.62690209261281 2086 3208 2440 1658 2759 2660 1895 2893 471 2830 1943 2420 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 15/39 Jessica Robertson 0.000920585989469712 0.00122972233371011 2440 2560.90909090909 2440 8.37246757110007e-05 2013 1.46178518319599 1.71405243446613 1 1.09421822169353 2021 2431 2135 2893 3367 3067 2602 2438 2440 2013 2763 2421 M924 REACTOME_PLATELET_CALCIUM_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_CALCIUM_HOMEOSTASIS.html Genes involved in Platelet calcium homeostasis 8/19 Reactome 3.41732118202383e-06 6.56024869273399e-06 2265 2793.27272727273 2441 3.41732643717303e-07 1905 1.51227280568183 1.13601694083737 1 2.01612136784329 2263 1905 4054 2851 2370 2441 2074 4366 3243 2098 3061 2422 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 5/8 Jessica Robertson 4.40831710836309e-06 8.23002947003564e-06 4265 2673.81818181818 2442 4.40832585335439e-07 43 1.99138478868163 -0.964096919135752 -1 2.60441695148906 4264 2329 4385 2037 3439 3907 3650 666 43 2250 2442 2423 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 45/91 KEGG 1.02513325600947e-05 1.78115477851701e-05 1925 2455.72727272727 2443 9.31943666227817e-07 1739 1.55016234574802 -1.53365212198061 -1 1.89367425762103 1923 2553 2443 1739 2598 1945 3174 2295 3116 3132 2095 2424 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 235/525 John Newman 6.36509941126157e-08 2.3193511540569e-07 2140 2536 2443 5.78645417765304e-09 1044 1.71403220569641 2.01163444927043 1 2.92505860722109 2140 3978 1739 2678 1044 4301 2443 2015 2398 2510 2650 2425 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 14/27 Arthur Liberzon 2.78731892166435e-08 1.29577147489277e-07 1715 2424.09090909091 2443 2.53392632452604e-09 102 2.98447002050345 2.98447002050345 1 5.28719967899109 1714 3602 2655 2470 4612 2443 1735 102 2390 3638 1304 2426 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 22/66 Arthur Liberzon 3.74227229717738e-08 1.60148748717563e-07 2785 2208.27272727273 2444 3.40206578257697e-09 729 2.38268833825796 2.8351282516545 1 4.16472009060597 2781 2774 1195 729 796 4038 3209 2972 1446 1907 2444 2427 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 34/60 Pathway Interaction Database 9.39054509125967e-08 3.09452139927165e-07 2525 2500.18181818182 2445 8.53685953826226e-09 1213 1.67986489383796 1.84428369549905 1 2.81264165509696 2521 2191 2295 1654 1213 3608 2445 3600 2185 2630 3160 2428 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 20/37 Arthur Liberzon 1.28429134326299e-07 3.9645515378988e-07 2870 2441.45454545455 2445 1.16753765294174e-08 835 1.19568117173006 -1.25996092592516 -1 1.96886771317389 2870 835 2445 1846 1342 4095 2297 3087 1822 3147 3070 2429 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 305/742 Jessica Robertson 1.07006545701322e-07 3.43918157171738e-07 3815 2596.54545454545 2445 9.72786826418636e-09 1180 1.43663264283702 -1.28436913898659 -1 2.38844447887005 3814 1553 1746 1955 1262 2445 3672 4111 2785 1180 4039 2430 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 19/54 KEGG 4.96557814927087e-07 1.20813599208117e-06 3890 2659 2446 4.51416297276585e-08 1009 1.27202136135848 -0.874547617487036 -1 1.9362414229018 3887 2311 2649 2446 1824 2275 3857 3994 1009 2026 2971 2431 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 33/94 KEGG 0.000470390985660037 0.000644518175088577 3245 2411.18181818182 2446 4.27719629086092e-05 1370 1.32395418487708 -1.37809207180491 -1 1.08659163452056 2446 2231 2925 1611 3284 1370 3242 2030 3245 2567 1572 2432 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 26/66 Jessica Robertson 0.000404679660610069 0.000556924784029011 1595 2489.54545454545 2446 3.67958289733787e-05 1284 2.64291238532371 2.22984147751082 1 2.21220879840396 1592 4218 1822 3194 3267 2204 1284 3103 1519 2736 2446 2433 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 2/21 Jessica Robertson 0.00151522741307221 0.0019894524117838 2360 2732.1 2446 0.000168472088212411 1427 1.07877990051541 1.07877990051541 1 0.749546939972322 2360 2722 4448 NA 3920 2005 1427 4323 2145 2532 1439 2434 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 94/223 Leona Saunders 3.2570057757515e-07 8.50742980221378e-07 2450 2312.63636363636 2447 2.96091477994305e-08 1207 1.47305797036101 -1.25151514307281 -1 2.29996699517921 2447 2582 2837 2011 1667 1207 3060 2891 1718 3554 1465 2435 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 10/39 John Newman 1.30548155267933e-06 2.7946489519668e-06 4405 2738.63636363636 2447 1.18680211577604e-07 867 1.26848195531195 -0.758119425383173 -1 1.81202095629442 4401 867 2347 1011 2100 4431 3310 2880 1764 2447 4567 2436 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 29/56 Reactome 1.196411454861e-08 7.85207853988603e-08 3690 2483.45454545455 2449 1.08764678306124e-09 320 1.3104759890356 -0.882982315220882 -1 2.39492953578296 3686 550 2352 2449 320 2885 4297 2101 1545 3038 4095 2437 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 90/185 Jessica Robertson 3.69512682912479e-07 9.43616584265872e-07 3190 2445.09090909091 2449 3.35920677250871e-08 952 2.05775134696038 -1.73295307670069 -1 3.18906478467933 3187 2449 952 1010 1716 4133 2753 3557 1799 1422 3918 2438 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 9/54 Reactome 7.74013014451372e-06 1.37335289122269e-05 3530 2336.90909090909 2450 7.74015710397246e-07 1007 1.59348371624151 -1.79025384526688 -1 1.99287787746322 3526 1289 3919 1939 2557 2450 3265 2602 1007 1666 1486 2439 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 19/52 Jessica Robertson 5.59592286434373e-07 1.33404826141294e-06 2645 2411.90909090909 2453 5.08720389793082e-08 1336 1.58095580181944 -0.899461273545443 -1 2.38898580422174 2645 1681 2128 2453 1865 3926 3133 1994 1336 2508 2862 2440 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 21/51 Arthur Liberzon 3.61196270173768e-08 1.57447974142723e-07 3000 2150.63636363636 2454 3.28360251003538e-09 398 1.49647191569195 1.34165671678679 1 2.61853838571354 2996 398 1721 2162 781 3491 2506 2458 2454 1147 3543 2441 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 14/42 John Newman 0.0093105466923318 0.0115086314429614 2180 2701.36363636364 2454 0.000850016781533149 1804 2.37496474116576 3.29372184307697 1 1.18448150019153 2180 3630 2261 1980 3856 3355 2001 2454 2559 3635 1804 2442 M7151 KEGG_SELENOAMINO_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SELENOAMINO_ACID_METABOLISM.html Selenoamino acid metabolism 12/28 KEGG 8.84600788835429e-06 1.55368789223494e-05 2460 2048.81818181818 2457 8.04185768870889e-07 590 0.840336604453076 -0.896188795567255 -1 1.03937868115386 2457 590 3245 2533 2567 916 1368 1270 2804 3413 1374 2443 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 31/81 Arthur Liberzon 9.51505038266409e-08 3.12401329271895e-07 2810 2678 2459 8.65004617653838e-09 1220 1.50041838944415 1.31272766631114 1 2.51059986172281 2808 2459 2391 1742 1220 4087 2791 3455 2256 2363 3886 2444 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 3/10 Arthur Liberzon 0.00242775664196548 0.00313401311962816 1655 2511.90909090909 2460 0.00024304130283207 1048 1.4332001522711 1.4332001522711 1 0.923043724498401 1653 1910 4209 2647 3823 1926 1048 2460 2853 2801 2301 2445 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 107/246 Leona Saunders 6.90711035679362e-08 2.45826582747679e-07 3325 2650.81818181818 2461 6.27919143058998e-09 1007 1.56660571162248 -1.44413232582598 -1 2.66329025980212 3322 1007 1501 1643 1081 3492 3683 4185 2461 2166 4618 2446 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 27/68 John Newman 1.15734485088275e-05 1.99067371602542e-05 2260 2259.18181818182 2461 1.05213721756683e-06 1101 1.58102376952611 2.18488608564566 1 1.91173320528649 2256 1573 1508 2584 2629 3294 2461 1101 2899 1652 2894 2447 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 142/338 Arthur Liberzon 6.5876475533944e-08 2.37642158854551e-07 2585 2648.45454545455 2461 5.98877068241269e-09 1063 1.81526303060433 -1.04803831780725 -1 3.09288350424846 2581 4080 1682 2095 1063 4216 3549 1855 2139 2461 3412 2448 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 32/58 Jessica Robertson 4.26695115339372e-07 1.06073915675347e-06 2835 2402.54545454545 2462 3.87904725543549e-08 933 1.69869358179801 -1.01683101560001 -1 2.61040186234381 2835 2066 2026 3049 1776 1352 2515 4555 933 2859 2462 2449 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 12/32 Arthur Liberzon 0.00105220849863487 0.00139836898031849 3430 2512.54545454545 2462 9.57010984139549e-05 291 2.15519594587319 2.3964442806457 1 1.5823294482201 2462 3937 2208 2007 3428 3342 2709 1540 291 3426 2288 2450 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 136/464 Leona Saunders 5.67699256866752e-08 2.14453831283808e-07 1865 2381.81818181818 2463 5.16090246832688e-09 829 1.6929624604888 2.12164240984207 1 2.90392211579318 1863 3818 829 2463 990 3852 1980 2708 3111 1716 2870 2451 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 43/87 Itai Pashtan 6.27413459809644e-07 1.46856117515884e-06 1450 2423.81818181818 2463 5.70376035218604e-08 1446 1.61533005012769 1.8635623293451 1 2.42359438485911 1446 3921 2511 3433 1900 2463 2097 1550 2699 2985 1657 2452 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 175/446 Arthur Liberzon 2.47941747391432e-08 1.20328077343124e-07 4380 2428.81818181818 2465 2.2540159107796e-09 612 1.71084994388457 -1.58731406101913 -1 3.04504448237505 4379 1239 801 1732 630 3354 3561 4432 2465 612 3512 2453 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 16/27 John Newman 0.000865288876910205 0.00115916057095518 2220 2770.09090909091 2466 7.86935812636035e-05 1410 1.02659060936514 -1.05950492659177 -1 0.775230170282218 2217 3185 2466 4403 3360 1410 1906 2153 4049 3251 2071 2454 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 13/30 Arthur Liberzon 1.40372380539014e-06 2.98586007810178e-06 2490 2395 2466 1.27611336458702e-07 1337 2.05309811192293 -1.80960031418655 -1 2.91766337679375 2489 2466 1529 3798 2123 2471 1704 2442 2646 1337 3340 2455 M7934 KEGG_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRUVATE_METABOLISM.html Pyruvate metabolism 21/49 KEGG 7.17254836268329e-06 1.27942754577594e-05 1465 2085.72727272727 2468 6.52051977007772e-07 798 1.4533306297655 -1.35872669374424 -1 1.82909763288098 1465 2984 2596 2468 2525 798 1347 1421 3815 2708 816 2456 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 9/15 Reactome 5.21662247017146e-06 9.60137191485603e-06 3890 2547.90909090909 2468 5.21663471612942e-07 57 1.59808877285737 -0.767415063461318 -1 2.06253513353337 3886 729 4074 1549 2468 2270 2295 3003 57 3056 4640 2457 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 19/67 Jessica Robertson 5.76444582652621e-06 1.04983261341243e-05 4020 2339.90909090909 2469 5.24041902781622e-07 329 2.43987123185564 -1.77112180494585 -1 3.12462008274919 4018 1465 1812 1356 2469 3369 2705 2830 329 3004 2382 2458 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 150/303 Jessica Robertson 5.92948957979563e-08 2.19843018787655e-07 1950 2395.54545454545 2469 5.39044521782596e-09 943 1.82995787589367 2.02368661402338 1 3.13383548033049 1948 3518 943 2582 1015 4166 2469 2983 2430 1226 3071 2459 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 35/108 Arthur Liberzon 5.77868120136734e-06 1.05201632127457e-05 3285 2417.09090909091 2470 5.2533603455733e-07 669 2.83975842042663 -1.63510635906709 -1 3.636076325155 3281 3179 931 669 2470 4318 3651 2149 1230 1983 2727 2460 M3430 BIOCARTA_CALCINEURIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CALCINEURIN_PATHWAY.html Effects of calcineurin in Keratinocyte Differentiation 8/22 BioCarta 5.28981380042077e-06 9.72081077206735e-06 2745 2302 2472 5.28982639242147e-07 424 2.19775962627501 2.04111382412325 1 2.83345088244778 2742 1588 3829 1162 2472 2505 1920 3907 424 1060 3713 2461 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 14/17 Reactome 7.74420836677466e-05 0.000116312052585596 3335 2722.36363636364 2472 7.04043725788991e-06 1846 1.06992009124331 -1.12406554891427 -1 1.08274385882978 3333 1846 2866 2289 2998 2472 4472 2060 3226 2398 1986 2462 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 47/105 John Newman 3.15971764239068e-08 1.43473225506228e-07 2810 2550.63636363636 2472 2.87247062524696e-09 726 1.34762240253378 1.71710330069286 1 2.3720724755945 2809 2337 2472 2053 726 4487 2911 1750 2124 2947 3441 2463 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 4/9 Arthur Liberzon 1.41911349069369e-07 4.30140091681152e-07 2270 2227.72727272727 2473 1.41911358131843e-08 212 2.16005859237514 -0.888020315717632 -1 3.53718227088062 2270 2637 4238 2848 3693 2473 1408 212 559 3100 1067 2464 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 46/102 Lauren Kazmierski 4.25675873857077e-07 1.05967115049171e-06 2475 2556.36363636364 2475 3.86978142018829e-08 1154 1.6464494328261 1.53019252868958 1 2.53030294867081 2475 2517 1154 3413 1773 3645 2138 2262 3382 1635 3726 2465 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 123/285 Jessica Robertson 1.55800724126273e-06 3.27537996077036e-06 3845 2559.09090909091 2476 1.41637122238304e-07 770 1.96425096407891 -1.55246006203083 -1 2.7710958126381 3842 2607 806 1471 2149 2476 3795 4316 2075 770 3843 2466 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 12/29 Reactome 7.93636162134753e-06 1.40513609760861e-05 2480 2581.18181818182 2477 7.21490022856134e-07 1659 2.67576643661336 2.67576643661336 1 3.33958776396207 2477 2356 2220 3683 2542 3859 2181 2849 1659 2745 1822 2467 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 21/37 Kevin Vogelsang 0.0463681234708167 0.0541173167084052 2480 2661.63636363636 2477 0.00430684027187473 1018 2.26831850043926 2.26831850043926 1 0.73903318285827 1018 4129 1476 3248 4308 2479 1733 2477 3773 2207 2430 2468 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 14/27 John Newman 0.00237480309716912 0.00306819060196705 1765 2540.72727272727 2477 0.000216124588478731 1489 1.7134851246103 1.7134851246103 1 1.10762249358729 1764 3700 2477 2550 3720 2250 1847 2473 2659 3019 1489 2469 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 22/76 Jessica Robertson 2.03526098569351e-08 1.07280460955678e-07 3465 2627.36363636364 2477 1.85023727683826e-09 543 1.83273514511949 -1.5160286686923 -1 3.28547907795178 3465 2461 1586 2238 543 3883 3938 3344 2477 1911 3055 2470 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 3/7 Arthur Liberzon 9.10815041943556e-07 2.03338698739757e-06 2480 2407.81818181818 2478 9.10815415256589e-08 69 1.18930956548402 1.36036572466762 1 1.74117190163379 2478 441 4233 1520 2034 3003 3525 4165 69 2803 2215 2471 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 41/126 Arthur Liberzon 8.33164466546942e-05 0.000124695263182337 2255 2448.90909090909 2478 7.57450928258987e-06 1085 2.22554235745678 2.26224361781249 1 2.23491500924804 2253 3122 1957 2707 3315 3425 1969 1085 2489 2138 2478 2472 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 14/38 Jean Junior 0.000479996852567626 0.000657103491420361 2480 2470.90909090909 2479 4.3645600951536e-05 1590 2.10265226300322 -2.15483653315686 -1 1.72114019399805 2479 2989 1590 3631 3287 1694 2692 1676 3092 1880 2170 2473 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 3/13 Jessica Robertson 0.00797811085383995 0.0099060486118426 2085 2882.90909090909 2479 0.000800689903545304 1578 2.6665523899803 2.6665523899803 1 1.37457370545129 2085 3608 4617 4448 3601 2092 1578 2017 2479 2820 2367 2474 M12718 BIOCARTA_P35ALZHEIMERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P35ALZHEIMERS_PATHWAY.html Deregulation of CDK5 in Alzheimers Disease 10/19 BioCarta 1.96184854281795e-05 3.24504845451638e-05 3430 2689.72727272727 2480 1.78351457982523e-06 1071 1.37908046411491 -1.32486779512132 -1 1.5922690123658 3426 1071 2389 2290 2729 2245 3115 4672 2480 2429 2741 2475 M10579 BIOCARTA_EDG1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EDG1_PATHWAY.html Phospholipids as signalling intermediaries 24/51 BioCarta 0.00217891081504073 0.00282210505231644 1910 2687.45454545455 2480 0.000198279257804838 1669 1.69891244075819 1.8624031011301 1 1.11406916347473 1906 3827 2789 2480 4307 2315 2134 1669 2825 3027 2283 2476 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 12/45 Emmanuelle Fouilloux-Meugnier 3.9701774816276e-06 7.4926506962976e-06 2730 2325.72727272727 2482 3.60925876939247e-07 906 2.36625302956551 -2.17750261611461 -1 3.11949719993755 2729 2167 1208 2493 2387 3450 2859 2482 1776 906 3126 2477 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 14/24 John Newman 6.05333030175416e-06 1.09624196475995e-05 2845 2615.36363636364 2483 5.50304268876365e-07 1219 1.35306995954205 1.75466215560122 1 1.72627013633792 2842 1219 2246 2703 2483 4194 3582 2115 1918 3020 2447 2478 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 2/13 Arthur Liberzon 0.00776078192760731 0.00964386743907925 1985 2769.5 2485.5 0.000865298026693532 1690 2.93378408188904 -2.93378408188904 -1 1.52111895815479 1985 2445 4132 NA 3682 1690 2909 1963 4173 2526 2190 2479 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 256/706 Arthur Liberzon 6.08702371812476e-08 2.23891625927258e-07 2370 2305.18181818182 2486 5.53365807867481e-09 726 1.33731077439777 -1.18278401892746 -1 2.28744239352308 2366 2971 3115 3437 1029 726 2628 1837 2486 3320 1442 2480 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 6/18 Leona Saunders 0.00382800107681874 0.00487181234274107 2230 2822.18181818182 2486 0.000383461122461018 1929 2.07294616869843 2.07294616869843 1 1.23291345479137 2226 2042 4274 3353 3526 2171 1929 2137 4247 2486 2653 2481 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 3/10 Leona Saunders 5.55271263182358e-06 1.01474223836211e-05 4145 2578.09090909091 2487 5.55272650655028e-07 418 1.11605897534891 -0.659473720973975 -1 1.433518723381 4144 440 4158 1676 2487 2294 3698 2029 418 2798 4217 2482 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 7/15 BioCarta 5.55444695134192e-06 1.01474223836211e-05 2835 2289.72727272727 2488 5.55446083473717e-07 491 1.44250879694753 -0.568192156212718 -1 1.85282631515661 2831 1483 3855 1047 2488 4568 2528 1596 491 2669 1631 2483 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 100/228 Leona Saunders 7.39810060111799e-08 2.59487271084123e-07 2720 2222.36363636364 2489 6.7255462271812e-09 823 1.52673973424716 -1.19061654234522 -1 2.58629306336983 2716 2791 2109 1863 1107 823 2489 3025 2533 2949 2041 2484 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 29/67 John Newman 2.55526262640463e-05 4.14037367473448e-05 2210 2706.09090909091 2489 2.32299300529869e-06 2055 1.43427787690001 1.50891007863694 1 1.61696077395966 2208 3651 2489 3428 2778 3181 2084 2055 3568 2179 2146 2485 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 5/17 Pathway Interaction Database 0.00282308695824872 0.00362437958530233 2485 2815.18181818182 2490 0.000282667980274635 1483 0.568192156212718 -0.568192156212718 -1 0.356713762982014 2482 2361 3897 2059 3496 1483 2508 2490 3911 4431 1849 2486 M2208 CARD_MIR302A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CARD_MIR302A_TARGETS.html Potential targets of MIR302A [GeneID=407028]. 18710938 59/130 Arthur Liberzon 0.000152502953302841 0.000221453002533968 750 2250.63636363636 2490 1.38648659782774e-05 747 1.64745772960731 1.69605547150236 1 1.54869833900198 747 4286 2490 3323 3384 1063 1118 1629 2653 3088 976 2487 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) 13/20 Reactome 2.05641026300261e-08 1.07909725559129e-07 4455 2632.81818181818 2491 1.86946389293139e-09 421 1.2238029601217 -1.51275390521405 -1 2.19306841406743 4455 421 2491 2150 547 4528 3825 2987 2116 2270 3171 2488 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 8/16 Reactome 7.05238017119108e-06 1.26039105576664e-05 2495 2305.09090909091 2492 7.05240255252078e-07 170 1.80171978954876 2.31851602198228 1 2.2705819870646 2492 732 4042 1357 2538 3610 3579 2723 170 2097 2016 2489 M17411 KEGG_JAK_STAT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_JAK_STAT_SIGNALING_PATHWAY.html Jak-STAT signaling pathway 59/186 KEGG 8.05249972124391e-08 2.76035213560709e-07 2025 2630.36363636364 2493 7.32045455998516e-09 1148 1.4948383793737 1.41715842151046 1 2.52192910838949 2022 3226 2386 4347 1148 1843 1428 3311 3363 3367 2493 2490 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 2/12 Reactome 1.89966329015011e-06 3.87372592586746e-06 2515 2384.4 2494 2.11073877114207e-07 562 2.7422831645027 2.7422831645027 1 3.81731858888197 2514 2474 4030 NA 3248 1956 1750 562 1786 2521 3003 2491 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 15/41 Jessica Robertson 1.34652062156349e-06 2.87069864997566e-06 3150 2505.54545454545 2494 1.22411040518967e-07 1417 1.14918565254888 -1.0861850606226 -1 1.63816001252379 3149 1771 2494 3043 2114 1417 3008 2957 3653 2009 1946 2492 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 16/28 Arthur Liberzon 2.34128123025144e-05 3.81874133134641e-05 2495 2522.27272727273 2495 2.12846013361482e-06 1180 1.58321085254195 2.24230551884624 1 1.79916480811364 2495 2497 2277 3117 2760 3763 2464 1180 2040 2660 2492 2493 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 33/117 Yujin Hoshida 8.61717506457923e-09 6.65673134670181e-08 2745 2165.72727272727 2496 7.83379554393804e-10 196 1.73488079970847 -1.75758301749169 -1 3.20254655234186 2745 1394 1069 2443 196 3782 2496 2657 2731 888 3422 2494 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 21/49 Jessica Robertson 0.000533515691541733 0.000728878871884712 1505 2666.72727272727 2496 4.85131924405052e-05 1174 2.11033647295688 2.11033647295688 1 1.7029918454666 1502 3931 2496 3118 4126 1953 1264 2342 3727 3701 1174 2495 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 46/112 Jessica Robertson 1.1825219197558e-06 2.56660385177198e-06 3725 2542.63636363636 2498 1.07502050488509e-07 971 1.78800862672556 -1.71946235533964 -1 2.57116460229692 3722 1568 971 1891 2077 2625 4117 3855 2498 1401 3244 2496 M11190 KEGG_DORSO_VENTRAL_AXIS_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DORSO_VENTRAL_AXIS_FORMATION.html Dorso-ventral axis formation 12/28 KEGG 4.97671018349456e-08 1.96634603034195e-07 2965 2353 2499 4.52428208734068e-09 920 1.5087677148647 -0.608044959261689 -1 2.60259509553201 2964 2121 2111 2770 920 4119 2833 1019 1788 2739 2499 2497 M1840 KEGG_GLUTATHIONE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLUTATHIONE_METABOLISM.html Glutathione metabolism 27/58 KEGG 2.36638664424939e-05 3.85639053044594e-05 1620 2497.36363636364 2501 2.15128372564027e-06 1168 1.27275223548644 -1.33089241194273 -1 1.44496395156174 1616 3206 2501 4223 2761 1168 1718 1791 3671 3308 1508 2498 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 109/287 Kevin Vogelsang 0.0178676537480892 0.0215848995781248 795 2723.72727272727 2501 0.00163767641102083 793 2.17636481414065 2.58433819365504 1 0.932537210837479 793 4248 1188 2835 4299 3192 2412 2455 2501 3538 2500 2499 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 115/295 John Newman 3.59290955895638e-06 6.86358507675076e-06 2445 2919.45454545455 2501 3.26628675154242e-07 1478 1.70808084165044 1.96728597749548 1 2.26854270847847 2441 3884 2441 1478 2356 4283 2501 2763 2426 3571 3970 2500 M4319 BIOCARTA_IL12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL12_PATHWAY.html IL12 and Stat4 Dependent Signaling Pathway in Th1 Development 13/29 BioCarta 3.42651163940947e-05 5.42453835887593e-05 4525 2855.63636363636 2502 3.11505909879387e-06 1474 1.52434076599818 -1.32610164636033 -1 1.6724941784907 4522 1474 1974 1529 2845 2502 4621 3150 2349 1770 4676 2501 M252 PID_IL8_CXCR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL8_CXCR1_PATHWAY.html IL8- and CXCR1-mediated signaling events 18832364 18/52 Pathway Interaction Database 5.20210998890445e-07 1.25396540164641e-06 4570 2875.63636363636 2502 4.72919201726675e-08 1840 1.46106106909143 -1.32447471800037 -1 2.21791658578292 4568 2113 2437 2502 1840 3527 4511 2778 2391 1897 3068 2502 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 19/63 Reactome 4.01244426566628e-07 1.00924926617886e-06 3115 2576.18181818182 2502 3.64767727042856e-08 1332 1.47695272254259 -1.56473182905116 -1 2.27785974250352 3111 2272 2674 2784 1755 2285 4599 1332 3138 2502 1886 2503 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 19/61 Arthur Liberzon 3.15624878681277e-05 5.02896355491487e-05 1165 2381 2503 2.86935824465002e-06 1162 1.41170039299567 1.29899180983253 1 1.56084676960642 1162 4398 2724 3692 2827 1474 1274 1642 3216 2503 1279 2504 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 6/17 Leona Saunders 0.00379059758601452 0.00482552031732248 2195 2756.18181818182 2506 0.000379707903504983 1284 1.02724578491863 -1.02724578491863 -1 0.612064136618365 2194 2506 4196 3301 4258 1284 1989 2420 3101 3449 1620 2505 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 26/56 Leona Saunders 5.17087284026505e-05 7.96538794526036e-05 1440 2529.27272727273 2506 4.70090398208306e-06 785 1.41453864815725 1.44153917332078 1 1.4913151774901 1439 4126 2506 4295 3366 1364 962 1859 3476 3644 785 2506 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 3/12 Reactome 5.94081737994468e-08 2.19894709655772e-07 3495 2764.63636363636 2507 5.94081753876459e-09 1060 1.8887703405796 -0.965824862979414 -1 3.23450327777352 3493 1823 4092 1318 1060 4525 2507 4477 1948 2794 2374 2507 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 10/25 Jessica Robertson 0.000532839355312758 0.000728167167977715 3755 2703.18181818182 2508 4.84516775113506e-05 732 1.91072283244553 -1.96949452951349 -1 1.54211683206402 3754 2322 1973 1728 3297 3218 3953 3805 732 2445 2508 2508 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 3/7 Arthur Liberzon 2.63943770821236e-05 4.2664384617741e-05 1640 2243.72727272727 2509 2.6394690585778e-06 790 1.97554943233383 1.97554943233383 1 2.22055470819498 1640 2509 4125 2902 3015 1029 790 916 3416 2795 1544 2509 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 12/35 Jessica Robertson 0.0016750910075345 0.00219320381707367 1805 2507.18181818182 2509 0.000152397071947797 1252 1.48676392249431 1.49252782130945 1 1.01682460634051 1803 2957 2027 3358 3426 1449 1252 2853 3795 2150 2509 2510 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 22/37 Reactome 6.81262451187499e-06 1.22314017098261e-05 3540 2745.72727272727 2511 6.19331418933013e-07 704 1.38843786853864 -1.40932216006651 -1 1.75440457569194 3538 704 2238 1286 2511 4369 4164 3528 1914 1569 4382 2511 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 375/844 Arthur Liberzon 9.95390862522348e-09 7.14401938687495e-08 2540 2427 2511 9.04900788205453e-10 245 1.40937241732772 1.64528836612518 1 2.59054368291573 2536 1552 1991 2511 245 3723 2444 3232 3154 1946 3363 2512 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 31/76 John Newman 4.09166367633723e-06 7.69403530791183e-06 2515 2364.36363636364 2513 3.71970116929634e-07 688 1.20900294507388 1.28530205123639 1 1.59028008460123 2513 688 2898 2999 2398 2582 1853 2229 2729 2366 2753 2513 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 99/207 Leona Saunders 1.2673545531316e-06 2.72173393032754e-06 2395 2540.27272727273 2513 1.15214116656132e-07 1102 1.48129043803516 -1.37290887379105 -1 2.12039161203594 3441 2792 2395 2337 2092 1102 3591 2771 2513 2393 2516 2514 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 61/142 John Newman 6.86950104689083e-06 1.231464495246e-05 4460 2767.36363636364 2515 6.24502045182262e-07 894 1.85538509902834 -1.521283913393 -1 2.34302481088132 4458 2142 914 2093 2515 3463 4043 3358 2443 894 4118 2515 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 28/60 Jessica Robertson 0.000119654703890814 0.00017587890289597 1930 2497.90909090909 2516 1.08782920205876e-05 1582 1.41726944615046 1.71621813829235 1 1.36878823942451 1928 3126 2186 2649 3066 2514 1582 2629 3425 2516 1856 2516 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 24/52 Pathway Interaction Database 9.95564903919863e-05 0.000147446812255641 2735 2467.81818181818 2517 9.05099962748465e-06 978 1.77838662201026 1.92606318633196 1 1.75258182125409 2732 1403 1952 2461 3039 3170 2348 2517 978 3031 3515 2517 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 25/89 Leona Saunders 1.69891791810728e-05 2.84123103649205e-05 3290 1994.09090909091 2517 1.54448276172273e-06 628 1.46219245859952 1.48031002287692 1 1.70993556131651 1072 3289 2558 3288 2700 874 1150 1216 2517 2643 628 2518 M60 PID_NFAT_TFPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFAT_TFPATHWAY.html Calcineurin-regulated NFAT-dependent transcription in lymphocytes 18832364 27/61 Pathway Interaction Database 5.84073570382242e-05 8.92683871758377e-05 2520 2853.45454545455 2519 5.3099007037294e-06 2018 1.10782004062598 1.19562995970243 1 1.15384647484886 2519 2307 2453 4023 2950 3451 2305 2238 3791 2018 3333 2519 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 32/72 Yujin Hoshida 1.28750178458671e-07 3.9692324753772e-07 2805 2385.45454545455 2519 1.17045623630449e-08 1344 1.69425745645303 -1.70714557964159 -1 2.78962482559117 2801 3468 1747 3690 1344 1520 2519 1798 2896 2860 1597 2520 M19553 BIOCARTA_AHSP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AHSP_PATHWAY.html Hemoglobin's Chaperone 6/21 BioCarta 0.00104423337434917 0.00138816385594333 2440 2942.63636363636 2520 0.000104472438961519 1881 0.826275926271427 -0.826275926271427 -1 0.607321817256028 2440 2043 3840 3738 3395 1881 2520 2389 4393 3432 2298 2521 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 54/136 Yujin Hoshida 7.84176725842782e-07 1.77691109153737e-06 4075 2778.72727272727 2520 7.12888186689076e-08 1633 1.47063846277708 1.89352208686894 1 2.175192315966 4074 2091 1999 1656 1977 3383 4350 2520 2658 1633 4225 2522 M286 PID_TGFBR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TGFBR_PATHWAY.html TGF-beta receptor signaling 18832364 43/85 Pathway Interaction Database 1.62861839328044e-05 2.72755746637317e-05 2700 2631.63636363636 2521 1.48057313614486e-06 1738 1.64000989506809 2.07114279438467 1 1.92536139067361 2696 3120 2521 1738 2696 4401 2509 2107 1976 2984 2200 2523 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 14/30 Broad Institute 7.11754475094894e-06 1.2709947613444e-05 4600 2517.18181818182 2521 6.47051616188447e-07 1148 1.53437799761388 -1.80812016599714 -1 1.93223373536531 4597 1148 1939 2535 2521 4083 3098 1567 1596 1879 2726 2524 M842 REACTOME_PURINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_CATABOLISM.html Genes involved in Purine catabolism 5/15 Reactome 2.50167430900464e-06 4.94009515886882e-06 2450 2500.72727272727 2522 2.50167712527755e-07 590 3.64426847717458 3.64426847717458 1 4.97391024988618 2448 3546 4036 2578 3607 2522 2393 590 790 3275 1723 2525 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 7/12 Leona Saunders 0.000152098590696595 0.000220934282704354 1775 2418.27272727273 2522 1.52109001991101e-05 731 1.22857810394719 1.22857810394719 1 1.15525088781416 1774 2716 4275 3122 3119 1148 731 2097 2522 3585 1512 2526 M11650 BIOCARTA_NOS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NOS1_PATHWAY.html Nitric Oxide Signaling Pathway 10/27 BioCarta 0.000334038120306679 0.000464619362349984 2030 2554.18181818182 2523 3.03717136307899e-05 1486 1.06521780346151 1.18566824011235 1 0.913186828197643 2026 2323 2523 2658 3236 1486 1910 3083 3217 3832 1802 2527 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 6/15 BioCarta 0.0178197018929281 0.0215325227102271 2100 2783.81818181818 2525 0.00179642294928028 1904 1.47006084395481 1.47006084395481 1 0.630296250752982 2098 3945 3862 2614 4154 2034 2077 2525 1904 3433 1976 2528 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 64/138 John Newman 5.04664741766056e-05 7.79709521897704e-05 2310 2523 2525 4.58796653451833e-06 1467 1.56087762052963 -1.10705172245753 -1 1.64932036713589 2310 3055 2906 1467 2917 1628 2525 2418 2032 3804 2691 2529 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 633/1344 Arthur Liberzon 5.72879435498683e-09 5.01315167630967e-08 4555 2660.18181818182 2525 5.72879436975541e-10 128 1.38645787705913 -1.06126524371585 -1 2.60328429723534 4554 1299 4663 1375 128 452 4419 4143 2525 3215 2489 2530 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 95/226 Arthur Liberzon 2.7733983837166e-05 4.46296182214835e-05 2235 2687.45454545455 2527 2.52130304252893e-06 1812 1.65184300405282 1.82099527897609 1 1.8483928692027 2233 3343 2527 2382 2795 3822 2287 2773 2472 1812 3116 2531 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 11/23 Arthur Liberzon 2.37373214776539e-05 3.86360154374041e-05 2530 2383.27272727273 2527 2.15796159999095e-06 1490 1.83959558065016 2.10522533168856 1 2.08812111302661 2527 1813 1688 1935 2764 3165 2236 2911 2794 1490 2893 2532 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 8/14 Arthur Liberzon 1.36492636972696e-05 2.31451413955894e-05 1795 2568.18181818182 2527 1.36493475340741e-06 1445 1.49262063186945 1.49262063186945 1 1.77970665976896 1792 2249 4285 3474 2680 2337 1445 1818 2761 2882 2527 2533 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 15/45 Reactome 7.38347969836063e-06 1.31505077409798e-05 3390 2605.09090909091 2528 6.71227679852149e-07 495 2.61321391168701 2.74169463437263 1 3.28085883424782 3386 2117 1718 1252 2528 4275 4071 4032 495 2000 2782 2534 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 27/49 Pathway Interaction Database 7.38826195186261e-06 1.3154025648339e-05 1615 2981.36363636364 2529 6.71662433089631e-07 1615 0.886817132063869 0.916179310560859 1 1.11336167213279 1615 4158 3549 4063 2529 1999 1981 2233 4379 4128 2161 2535 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 23/64 John Newman 2.08710373836031e-05 3.44008727328752e-05 4065 2803.90909090909 2529 1.89738503512041e-06 665 2.62901787915872 -1.94441608609398 -1 3.01829009644268 4061 2269 1743 2183 2739 3766 3818 2529 665 2426 4644 2536 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 33/65 Kate Stafford 7.99280689763452e-05 0.000119815397064348 3000 2604.36363636364 2530 7.26645208963342e-06 1947 1.6800731818802 -1.96862208605357 -1 1.69464078510085 2999 2945 1947 2421 3002 2213 3282 2321 2530 2172 2816 2537 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 55/109 Leona Saunders 3.23237729901192e-07 8.46669649143089e-07 2535 2600.45454545455 2532 2.93852524903005e-08 1584 1.81482513249653 1.93437789840131 1 2.83456003956792 2532 3645 1584 1684 1661 4257 2721 2840 2339 1693 3649 2538 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 27/46 John Newman 5.36057169800767e-05 8.23594720552916e-05 1770 2559.72727272727 2532 4.87336574492111e-06 1538 1.78162732859859 1.94514692790792 1 1.87168042623159 1769 4026 2423 1538 2929 2981 2144 2532 2673 2850 2292 2539 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 9/44 Arthur Liberzon 3.21548468201592e-06 6.20838946020873e-06 2625 2569.81818181818 2533 3.21548933472917e-07 1641 1.12121785844936 -0.88107349234914 -1 1.50168197212461 2621 2503 4119 2813 2354 1641 2566 1914 2902 2302 2533 2540 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 74/198 Arthur Liberzon 6.81006406056074e-07 1.57434436052233e-06 2315 2512.90909090909 2535 6.19096924418715e-08 608 2.03089320477902 2.44185549863055 1 3.03131348594835 2311 3432 608 1607 1930 4244 3078 2535 3088 1603 3206 2541 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 32/73 Kevin Vogelsang 2.59710698132031e-07 7.05509757360403e-07 3795 2452.27272727273 2535 2.36100662537242e-08 1018 1.78514864266326 -1.47646516977874 -1 2.82457984098004 3793 1128 1057 2686 1584 2535 3917 3640 2429 1018 3188 2542 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 37/71 John Newman 4.26039361401276e-07 1.05967115049171e-06 2885 2472.63636363636 2535 3.87308585368758e-08 538 1.50242394228434 1.95791939690549 1 2.30896110427614 2884 538 1670 2246 1775 4627 3834 1556 2535 2541 2993 2543 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 10/20 John Newman 1.70070701490756e-06 3.51699605995448e-06 2535 2534.18181818182 2535 1.54609848148931e-07 1540 0.986002844469198 0.832086359504498 1 1.38317852220981 2535 1540 2589 2602 2182 2927 2490 2352 3538 2450 2671 2544 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 10/22 Jessica Robertson 0.00175987675519258 0.0023016417736066 1565 2564.72727272727 2537 0.000160116921514297 1224 1.27592040226089 1.27592040226089 1 0.865746498068839 1563 3704 2537 2830 4257 1224 1416 1631 4090 3193 1767 2545 M1473 BIOCARTA_BLYMPHOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BLYMPHOCYTE_PATHWAY.html B Lymphocyte Cell Surface Molecules 4/18 BioCarta 2.13487292791145e-05 3.5053068842508e-05 2045 2354.27272727273 2539 2.13489343775965e-06 583 1.90268925636182 1.90268925636182 1 2.18042386358606 2042 2539 3817 3478 3590 1137 583 1198 3755 3090 668 2546 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 3/10 Leona Saunders 9.45489257775066e-05 0.000140515009593563 2785 2454.36363636364 2540 9.45529487931254e-06 958 3.57235249104043 -3.57235249104043 -1 3.53973302419234 2783 1488 4172 2163 3043 2540 3408 1466 958 2799 2178 2547 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 6/20 Jessica Robertson 0.00279679469355069 0.0035925931836564 2540 2609.63636363636 2540 0.000280032086833043 1668 2.67285680157156 2.67285680157156 1 1.68066325438684 2540 2890 4329 2850 3570 2572 1854 1727 1668 2487 2219 2548 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 16/57 Jessica Robertson 2.41946653633503e-05 3.92985101880968e-05 1835 2351.81818181818 2540 2.19953922273618e-06 1300 2.00008802305657 2.25072078158571 1 2.26649715530613 1831 3101 1300 3412 2769 2648 1674 1886 3019 1690 2540 2549 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 33/66 Broad Institute 1.48674554194658e-07 4.47168781101521e-07 2415 2409.18181818182 2541 1.35158694765444e-08 1194 1.30935433676948 1.53730017022467 1 2.13844121113485 2411 1194 2644 1972 1385 3630 2678 2468 2604 2974 2541 2550 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 9/20 Reactome 7.27121992515058e-06 1.29604171050801e-05 2840 2549.63636363636 2544 7.27124371704778e-07 1162 1.53258337429506 -0.568192156212718 -1 1.926632797362 2836 1946 3943 1499 2544 3801 2319 3384 1162 3048 1564 2551 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 11/29 Arthur Liberzon 1.20659652425484e-06 2.61280559734666e-06 2680 2573.72727272727 2544 1.09690653274254e-07 1827 2.04328885748407 2.20760527171793 1 2.93418654379495 2678 3216 1827 2498 2081 3456 2145 2128 2544 2616 3122 2552 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 27/60 KEGG 8.08809803456855e-06 1.42991361543174e-05 3470 2592.45454545455 2545 7.35284342715592e-07 1372 1.92839996685767 -1.19158558255153 -1 2.40304429731061 3466 2871 2147 2704 2545 1372 2988 2463 2100 3702 2159 2553 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 9/22 John Newman 0.000618396734473932 0.000839214334707457 2885 2648.63636363636 2545 6.18568888436617e-05 1409 1.32987883186227 -0.986847051477201 -1 1.05224034865867 2883 1587 4399 2495 3326 1571 2545 3446 1409 3065 2409 2554 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) 10/18 Reactome 1.87016576627965e-08 1.01783934736195e-07 3640 2449.63636363636 2546 1.70015071107043e-09 11 1.47911064032304 -0.709797655750482 -1 2.66023901455133 3638 1418 2546 1386 516 2227 2944 3769 11 3840 4651 2555 M7561 KEGG_MTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MTOR_SIGNALING_PATHWAY.html mTOR signaling pathway 34/78 KEGG 0.000709372739296786 0.000957959843327014 2000 2702.36363636364 2548 6.45092340252836e-05 1911 1.42572318983866 1.53610033428403 1 1.10699833621967 1996 2735 3211 2385 3332 2548 1911 2461 2882 3969 2296 2556 M1979 KEGG_GNRH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GNRH_SIGNALING_PATHWAY.html GnRH signaling pathway 44/116 KEGG 1.05059310465452e-06 2.30050434037901e-06 3100 2838.63636363636 2549 9.55085096688657e-08 1717 1.31922843321661 -1.43930888284466 -1 1.91318666434416 3097 1717 2259 2019 2055 3994 2549 4170 3026 1787 4552 2557 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 41/93 Reactome 2.92396023895036e-07 7.78062332749653e-07 3960 2623.54545454545 2549 2.65814602506004e-08 934 1.24045936443606 -1.07589588425704 -1 1.94917254590284 3959 934 3075 2545 1626 1923 3750 2549 2771 3208 2519 2558 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 119/280 Jessica Robertson 3.76916182402505e-07 9.59385785300455e-07 2820 2421.63636363636 2549 3.42651133616261e-08 1048 1.88157852549864 -1.32758784815956 -1 2.91255190403804 2820 2549 1048 1560 1724 3891 2752 2808 2201 2291 2994 2559 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 52/89 Jessica Robertson 4.69378370405111e-07 1.15097176542038e-06 2550 2614.18181818182 2549 4.26707700498911e-08 1219 0.931672049914953 -0.901752825009502 -1 1.42321426192478 2549 1793 3618 2476 1806 1219 2597 2829 3928 3951 1990 2560 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 24/47 Reactome 0.00025849924857884 0.00036463801289598 2135 2537.54545454545 2550 2.35026933772395e-05 645 2.31106287745379 2.00985775182609 1 2.04377798736021 2134 3893 2550 2140 3189 2915 2115 2937 645 3032 2363 2561 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 34/99 John Newman 5.31537243342562e-07 1.27536278663761e-06 2555 2458 2551 4.832157925147e-08 625 1.69037274998763 1.93506861359913 1 2.5628208831275 2551 3059 2234 3187 1850 3074 2551 2275 625 2214 3418 2562 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 92/231 Arthur Liberzon 3.40485075173709e-05 5.39389135315754e-05 2245 2666.36363636364 2551 3.09536677124792e-06 724 1.75485979935439 2.15747728882258 1 1.92652846050778 2244 4476 2200 2551 3572 4470 2763 1187 2596 2547 724 2563 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 69/198 Jessica Robertson 1.08630312249712e-07 3.47468698431501e-07 3300 2455.72727272727 2553 9.87548341941784e-09 1271 1.39697458487237 -0.854066577865156 -1 2.32090897470117 3296 1756 2553 1558 1271 1351 3015 3945 1450 3361 3457 2564 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 19/44 BioCarta 2.3227189256045e-06 4.6355455218836e-06 2425 2567.18181818182 2554 2.11156488899218e-07 1628 0.975804064383353 1.17961001846867 1 1.33877021829477 2421 1628 3236 1748 2259 3188 2594 2351 2554 3539 2721 2565 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 45/97 Arthur Liberzon 1.35139515117929e-05 2.29360292590589e-05 2135 2517.81818181818 2554 1.22854859315705e-06 1281 1.89941208305576 2.21180150243926 1 2.26666488667338 2135 2554 1281 3758 2661 3001 1935 2594 2321 2089 3367 2566 M7946 KEGG_NOTCH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NOTCH_SIGNALING_PATHWAY.html Notch signaling pathway 16/52 KEGG 8.42707862169109e-06 1.48511810534955e-05 4545 2537.54545454545 2555 7.6610099106427e-07 614 1.64375155690849 -0.796412107033839 -1 2.04137871118194 4544 1470 1857 1193 2555 2485 3621 2587 614 3239 3748 2567 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 42/124 Arthur Liberzon 6.06255808543224e-07 1.42687831181996e-06 3445 3079.81818181818 2555 5.51141796008818e-08 1891 1.53428139540574 1.36335607885209 1 2.30692636637279 3445 2375 2370 2406 1891 4683 2555 4511 3065 2188 4389 2568 M18009 KEGG_CIRCADIAN_RHYTHM_MAMMAL http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CIRCADIAN_RHYTHM_MAMMAL.html Circadian rhythm - mammal 7/14 KEGG 1.25886079675447e-06 2.70721509572807e-06 2560 2571.45454545455 2556 1.25886150988377e-07 985 1.20828553710034 -1.20828553710034 -1 1.73032093693841 2757 985 3808 2271 2119 2483 4238 2584 2560 1925 2556 2569 M7772 BIOCARTA_BARRESTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARRESTIN_PATHWAY.html fl-arrestins in GPCR Desensitization 6/23 BioCarta 7.71870019703411e-06 1.37006928497355e-05 2075 2886.72727272727 2556 7.7187270074149e-07 2075 1.23915040845225 1.23915040845225 1 1.55006502192658 2075 3366 3874 4155 2556 2424 2373 2381 2643 3434 2473 2570 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 15/40 Yujin Hoshida 1.87425913440484e-06 3.83025656512041e-06 2630 2315.09090909091 2556 1.70387339195957e-07 1060 1.05494086230994 -0.883108095905552 -1 1.46983067741373 2629 1060 2556 1338 2211 2986 1793 2750 3061 2015 3067 2571 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 5/9 Itai Pashtan 0.000759906000166295 0.00102325273470668 1250 2467.54545454545 2556 7.60165981005071e-05 1246 1.33444436673615 1.33444436673615 1 1.02629624887136 1246 2680 4684 2815 3357 1496 1342 2556 2875 2263 1829 2572 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 37/97 Reactome 3.7252738706055e-06 7.08179852237621e-06 3895 2967.36363636364 2557 3.38661834422744e-07 1299 1.74892959945376 -1.66742716084749 -1 2.31668026541288 3893 2557 2215 2049 2368 4609 3399 4515 1986 1299 3751 2573 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 20/56 John Newman 0.0259550771363795 0.0310031841603554 1340 2972.27272727273 2557 0.0023878585525337 1339 1.54728600425496 1.54728600425496 1 0.600401020388821 1339 4345 2557 4597 4567 2004 1585 2244 3492 3621 2344 2574 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 15/39 Leona Saunders 9.79644346340089e-09 7.07336426340471e-08 2965 2249.72727272727 2558 8.90585773365793e-10 240 1.3257996604592 -1.58537912017378 -1 2.43840203068122 2963 1843 2581 3091 240 1709 3410 3908 1315 2558 1129 2575 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 36/95 Jessica Robertson 6.95787803528984e-05 0.000105142265312377 1800 2424.54545454545 2558 6.32554372716607e-06 1020 1.34773344190492 1.47903539084654 1 1.37908715918568 1796 2558 3037 3927 2980 1665 1020 3028 2130 3213 1316 2576 M456 REACTOME_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRNA_AMINOACYLATION.html Genes involved in tRNA Aminoacylation 27/43 Reactome 0.00447031258943717 0.0056554764562912 890 2703.27272727273 2559 0.000407220182867048 890 0.672356225414246 -0.672356225414246 -1 0.38869014831485 890 2559 3640 3578 3695 1059 1722 2309 4029 4471 1784 2577 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 162/382 John Newman 2.01914562658722e-07 5.73785106500165e-07 2420 2678.45454545455 2560 1.8355871017301e-08 1490 1.43380709886366 1.72146186120148 1 2.30176512165238 2420 2051 2560 1904 1490 4586 2414 3399 2582 2726 3331 2578 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 58/130 John Newman 2.15300053504417e-07 6.06449325275079e-07 2560 2676.09090909091 2560 1.95727340522247e-08 1514 2.03912263242184 2.99789342532213 1 3.2608980949539 2560 3821 1555 2193 1514 4629 3311 1733 2270 2992 2859 2579 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 2/8 Arthur Liberzon 0.000608175863899024 0.000826061477748065 2600 2778.4 2561 6.75933685606006e-05 1077 1.91833741295756 1.91833741295756 1 1.52123184173443 2597 3846 4126 NA 4267 1866 1077 1456 4243 2525 1781 2580 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 14/27 Leona Saunders 8.59974560201756e-06 1.51251971172968e-05 3870 2259.45454545455 2561 7.81798110763132e-07 946 2.71572501497416 -2.71669962815009 -1 3.36711871402476 3868 1217 946 1076 2561 4367 2781 2716 984 1447 2891 2581 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 18/39 Yujin Hoshida 0.00791499815795064 0.00983289537862055 1860 2656.18181818182 2561 0.000722147128656334 1532 2.55922283494825 2.55922283494825 1 1.32136569031654 1856 4267 2585 3048 4022 2561 1532 2199 1897 3481 1770 2582 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 76/215 Arthur Liberzon 1.5115876462989e-09 1.70148503009111e-08 3345 2356.81818181818 2562 1.37417058848862e-10 12 1.35267270257595 1.75400307798388 1 2.70312487899186 3342 2184 2562 1974 12 3116 3726 800 1630 3659 2920 2583 M8232 KEGG_LONG_TERM_DEPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_DEPRESSION.html Long-term depression 17/94 KEGG 1.74320550617755e-07 5.10222423606997e-07 2635 2498.36363636364 2563 1.58473240391206e-08 1348 1.46653620721732 -1.00949675549757 -1 2.37354106949563 2632 1348 2014 1862 1442 3585 2563 3540 2223 2774 3499 2584 M1833 MATZUK_SPERMATOZOA http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATOZOA.html Spermatozoa genes, based on mouse models with male reproductive defects. 18989307 64/220 Jessica Robertson 1.93226987295458e-06 3.93166158257279e-06 1790 2580.72727272727 2563 1.75661051825269e-07 1437 1.26646855127146 1.48055012018724 1 1.76085178403801 1790 1919 2959 3573 2219 2563 2485 2598 3040 3805 1437 2585 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 36/112 Jessica Robertson 7.41229083890401e-07 1.69599584331563e-06 4330 2627.45454545455 2568 6.7384484875194e-08 765 1.69325481113688 -1.66941126449493 -1 2.51327537922943 4328 2734 2146 1848 1960 2568 4508 3821 765 2789 1435 2586 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 36/75 Jessica Robertson 7.74876536925914e-08 2.68420713822601e-07 3715 2537.09090909091 2568 7.04433240198502e-09 1039 1.42869561049981 -1.30597257935414 -1 2.41480456121034 3712 1835 1695 2568 1131 2401 4498 3519 2672 1039 2838 2587 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 92/356 Arthur Liberzon 3.98716413065413e-07 1.0050484731708e-06 2570 2388.36363636364 2568 3.62469532115176e-08 641 1.25130587511275 -1.12860188883862 -1 1.93043438849825 2568 3247 3024 3748 1752 641 2416 1614 3343 2760 1159 2588 M1519 KEGG_ENDOCYTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOCYTOSIS.html Endocytosis 112/231 KEGG 2.00386540434967e-06 4.06322513404697e-06 1870 2922.54545454545 2569 1.82169748142601e-07 1869 1.36700048278748 -0.895940912802677 -1 1.89560148930801 4583 1869 2345 2547 2227 1869 4587 2569 2971 2588 3993 2589 M185 PID_ALK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK1_PATHWAY.html ALK1 signaling events 18832364 11/33 Pathway Interaction Database 0.000122210583601176 0.000179579427643496 2680 2720.63636363636 2570 1.11106702690483e-05 1965 1.05486848635849 1.25145465504292 1 1.01633045827134 2679 2278 2570 2699 3067 3911 2541 2405 3700 1965 2112 2590 M14981 REACTOME_GAP_JUNCTION_ASSEMBLY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_ASSEMBLY.html Genes involved in Gap junction assembly 9/18 Reactome 0.000339397255588147 0.000471513649477041 1250 2457.45454545455 2570 3.39449102456757e-05 1195 2.31070184369061 2.39522909429741 1 1.97710998363109 1249 2634 4103 2570 3253 1865 1723 2609 3624 1195 2207 2591 M34 PID_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_PATHWAY.html TCR signaling in naïve CD4+ T cells 18832364 35/94 Pathway Interaction Database 3.2561215437838e-07 8.50742980221378e-07 2740 2627.90909090909 2573 2.9601109324617e-08 1515 1.35283942499909 1.31346458791675 1 2.11226310450962 2739 1515 2679 2094 1666 3613 2441 2573 3128 2345 4114 2592 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 15/39 Jessica Robertson 9.15778892664703e-06 1.60543954022701e-05 1960 2488.63636363636 2573 8.32529731578935e-07 1398 1.14264120066139 1.22560392532967 1 1.40910486781874 1957 2813 3104 3419 2573 1919 1398 2089 3298 3170 1635 2593 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 16/42 Arthur Liberzon 0.000340159587461905 0.000472432669486214 2235 2544.45454545455 2574 3.09283812402563e-05 1622 1.50721144035008 1.86384357966948 1 1.28929012493422 2231 2566 2574 2778 3240 2945 1744 1622 2318 3243 2728 2594 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 27/83 Arthur Liberzon 5.65343641388019e-06 1.0316200558973e-05 4285 2833.54545454545 2574 5.13950085619615e-07 1910 1.76927079361269 -1.99065819686173 -1 2.26927462926816 4283 2267 1910 2847 2463 3028 3851 2574 2024 2019 3903 2595 M913 REACTOME_NEPHRIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEPHRIN_INTERACTIONS.html Genes involved in Nephrin interactions 15/33 Reactome 9.25094568557302e-06 1.62055818626524e-05 4235 2708.09090909091 2575 8.40998598709112e-07 739 1.77812061426023 -1.54747027708297 -1 2.1909162835061 3586 1901 1806 739 2575 4233 2818 4149 1750 2001 4231 2596 M18788 REACTOME_PHASE_II_CONJUGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHASE_II_CONJUGATION.html Genes involved in Phase II conjugation 24/95 Reactome 1.19887799395541e-07 3.75280045402475e-07 4635 2556.27272727273 2575 1.08988914480692e-08 465 1.66062932977916 -1.13110461471459 -1 2.74465685766515 4632 558 1629 1152 1318 3409 3995 3972 465 2575 4414 2597 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 120/313 John Newman 3.21449177291034e-05 5.1148076223626e-05 1530 2482 2575 2.92230794714466e-06 1530 1.66108167804851 1.88427249989382 1 1.83343457490831 1530 4045 2575 2917 2832 2632 1717 1590 2365 3569 1530 2598 M11079 KEGG_N_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_N_GLYCAN_BIOSYNTHESIS.html N-Glycan biosynthesis 30/50 KEGG 9.35875403086286e-06 1.63821895362807e-05 2490 2576.90909090909 2577 8.50799440276734e-07 825 0.761578748528553 -0.60979951964965 -1 0.937459141981765 2490 825 3505 3219 2577 894 2248 2749 3718 4170 1951 2599 M6322 REACTOME_ACTIVATION_OF_RAC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_RAC.html Genes involved in Activation of Rac 4/20 Reactome 1.78266114692886e-05 2.96330263728579e-05 2060 2367 2577 1.78267544755376e-06 744 1.06553911467527 -1.06553911467527 -1 1.24106895706749 2059 744 4016 2587 2728 1568 2217 2833 2577 3093 1615 2600 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 41/80 Broad Institute 1.02853672693778e-07 3.33083835689734e-07 3905 2768.63636363636 2577 9.35033431839633e-09 835 2.17221401289905 -1.66561090196163 -1 3.61913768377369 3901 4017 1772 2255 1247 2864 4584 3944 835 2459 2577 2601 M7857 KEGG_NON_HOMOLOGOUS_END_JOINING http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NON_HOMOLOGOUS_END_JOINING.html Non-homologous end-joining 7/13 KEGG 6.20655338784273e-05 9.44896334484438e-05 1785 2476 2578 6.20672674052924e-06 492 0.645514332841861 -0.645514332841861 -1 0.668234465976968 1781 2401 3806 3418 3086 642 492 2578 3582 4405 1045 2602 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 37/116 Jessica Robertson 5.69192454243344e-08 2.14753288291813e-07 4685 2845.54545454545 2579 5.17447699063374e-09 994 1.41248655198562 -0.842294806505618 -1 2.4226042969024 4683 2019 2579 2167 994 2452 3815 3846 1335 2900 4511 2603 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 22/45 Jessica Robertson 4.00166321448896e-08 1.67128287193363e-07 2580 2430.63636363636 2580 3.63787571570611e-09 833 1.61230913808198 1.93658591371007 1 2.81048489506019 3057 836 2095 2576 833 4258 3184 2580 1632 2833 2853 2604 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 838/1930 John Newman 1.20907932334629e-06 2.61455731850517e-06 1860 2763.09090909091 2580 1.20907998118955e-07 984 1.53305491307174 1.92076845023619 1 2.20136984048806 1860 2580 4400 984 2104 4339 2777 2467 2022 4110 2751 2605 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 22/66 Yujin Hoshida 1.43648933260024e-05 2.42572577029359e-05 2050 2300.54545454545 2581 1.30590792021702e-06 902 1.00646767320346 -1.03176802313027 -1 1.19477202052609 2047 1459 2728 3171 2672 902 2581 1721 3906 2835 1284 2606 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 144/284 Jessica Robertson 0.000553432360169042 0.000754988075619253 675 2431.72727272727 2581 5.03246937050494e-05 671 0.966390462867399 -0.881423565072854 -1 0.776054885516242 671 2581 3748 2627 3302 942 1499 1896 3517 4271 1695 2607 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 42/73 Arthur Liberzon 1.01147452135579e-05 1.75937995808213e-05 2585 2594.45454545455 2583 9.19526519775073e-07 1398 1.70129033145238 1.77993766604239 1 2.08062949648495 2583 2229 1738 2486 2595 3838 2694 2872 2088 1398 4018 2608 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 84/251 John Newman 1.24689184351956e-06 2.68393898885284e-06 4245 2745.18181818182 2584 1.13353868201799e-07 1487 1.53014113038835 -1.68007333105706 -1 2.19270909714801 4241 1705 2185 1811 2090 2584 4096 3890 1487 3118 2990 2609 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 6/9 Arthur Liberzon 7.47743474008446e-05 0.000112485583281014 2660 2387.63636363636 2585 7.47768635613666e-06 70 3.23072020201824 -1.37607614472097 -1 3.28151572074403 2656 2718 4231 2465 3614 2677 1686 1080 70 2482 2585 2610 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 41/95 Jessica Robertson 5.12671786862194e-08 2.00365303856234e-07 2780 2623.09090909091 2586 4.66065271644655e-09 937 1.49872941551533 -0.924028346338687 -1 2.58213256781539 2780 2420 1754 3157 937 4653 3281 2219 2931 2136 2586 2611 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 139/310 Yaara Zwang 4.71970406035727e-09 4.2972296893054e-08 4045 2548.36363636364 2586 4.29064006407505e-10 81 1.36354269568632 -1.18093225710577 -1 2.58372892971579 4041 1004 1993 1713 81 2673 4112 3404 2586 1988 4437 2612 M16 PID_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INSULIN_PATHWAY.html Insulin Pathway 18832364 29/68 Pathway Interaction Database 2.65305237098197e-05 4.28696669324879e-05 3730 2850.18181818182 2587 2.41189487777584e-06 1688 1.37877984722294 -1.03898230368447 -1 1.54903510802751 3729 1889 2587 1688 2787 4043 2825 2577 2394 2178 4655 2613 M4322 AUNG_GASTRIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/AUNG_GASTRIC_CANCER.html Selected genes specifically expressed in gastric cancer. 16331256 29/111 Arthur Liberzon 0.000414614254791646 0.000570261930717245 2895 2747.45454545455 2590 3.76993103674349e-05 1516 1.62627337322828 1.93143854947711 1 1.35694754605635 2893 3924 2540 2541 3269 3697 1876 1516 2039 2590 3337 2614 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 210/675 Arthur Liberzon 5.90377752648522e-08 2.19435778250278e-07 3415 2452.90909090909 2590 5.36707062265018e-09 1013 1.37450908405714 -1.15104428364123 -1 2.35415594258881 3411 1427 2499 2899 1013 1304 3835 3712 2814 1478 2590 2615 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 29/55 Arthur Liberzon 1.14834400220914e-05 1.97732565019862e-05 2620 2564.54545454545 2591 1.04395454210577e-06 1751 1.84601998572887 1.81826051647926 1 2.23354722530276 2620 1891 1956 2469 2627 3312 1751 4536 1821 2591 2636 2616 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 29/118 Yujin Hoshida 1.07901629379346e-08 7.39899659922656e-08 3730 2736.18181818182 2592 9.80923908259657e-10 277 1.19212209309505 -1.5290084008131 -1 2.18654940248301 3728 945 2017 2279 277 4173 2465 4139 3501 2592 3982 2617 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 21/53 Jessica Robertson 0.000987206179899283 0.00131496536640365 1600 2678 2596 8.97863134095119e-05 1518 1.80253190000959 1.80253190000959 1 1.33578866469667 1600 4163 2028 3946 3621 2596 1696 1518 3567 2718 2005 2618 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 20/36 Lauren Kazmierski 2.97270134885886e-05 4.75267093850312e-05 2435 2883.81818181818 2597 2.70249228871667e-06 1360 0.835178504833416 -0.817215360504498 -1 0.928687044898831 2435 2592 3230 4218 2817 1360 2538 2597 4019 3958 1958 2619 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 66/142 Kevin Vogelsang 1.94965832367652e-08 1.04532024081787e-07 2900 2611.90909090909 2597 1.77241667359505e-09 526 1.50932605478552 1.62125235505745 1 2.7100908439959 2899 1442 1913 2597 526 4237 3486 4169 2458 1611 3393 2620 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 12/17 Jessica Robertson 3.48508223290513e-06 6.67665386074957e-06 1500 2200.27272727273 2597 3.1682615943043e-07 624 1.65584178814976 1.65584178814976 1 2.20427035215885 1499 3160 2908 3576 2854 1354 964 624 2597 3423 1244 2621 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 10/99 Reactome 1.45310980106706e-05 2.45290797110959e-05 980 2274.81818181818 2599 1.32101763546435e-06 977 1.58097334409282 1.87641140388286 1 1.87479652454765 1964 977 1566 3278 2674 2789 2773 2851 2575 977 2599 2622 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 20/53 Leona Saunders 0.000124679428248289 0.000182863161430824 2650 2498 2600 1.1335135881799e-05 1002 1.50085221216026 1.6556146882117 1 1.44298290577438 2649 3293 2766 2501 3073 3655 1834 2369 1002 2600 1736 2623 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 40/171 John Newman 0.000216480079208767 0.000309181850403011 1255 2460.36363636364 2601 1.96819439810303e-05 845 1.66238347783868 1.84279811233627 1 1.5007573519182 1253 4209 2601 3314 4423 1321 845 1254 2959 3486 1399 2624 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 37/98 Jessica Robertson 4.46842038212635e-07 1.10496136731631e-06 2645 2504.90909090909 2602 4.0622011724614e-08 1790 1.26796029526118 1.41915627453889 1 1.94270380279648 2643 2146 2320 2689 1790 3825 2121 2967 2618 1833 2602 2625 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 16/64 Kate Stafford 7.83172743827302e-07 1.77549466742851e-06 2355 2709.90909090909 2602 7.11975475115668e-08 1652 1.80665016116751 1.85381084759884 1 2.67234157180325 2355 3697 2602 3743 1976 3012 2296 1652 2906 3249 2321 2626 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 40/71 Leona Saunders 5.38698682168347e-07 1.29056340728061e-06 1995 2591.63636363636 2603 4.89726194614352e-08 1853 1.4676798427047 1.70976795061852 1 2.22324745364235 1992 2421 2503 2963 1853 3250 2638 2680 2603 3124 2481 2627 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 39/116 KEGG 1.03877003047301e-05 1.80217562487839e-05 2605 2740.27272727273 2604 9.44340850224676e-07 1345 1.34225242291786 -1.31748460809479 -1 1.6379328110833 3501 2017 3140 1345 2601 2691 4399 2604 2217 3080 2548 2628 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 2/8 Reactome 0.000322631649279772 0.000449420900274973 2690 2656.1 2604 3.5853102380763e-05 1353 1.21907478952994 1.21907478952994 1 1.04961409002386 2689 2475 3965 NA 3538 2946 1912 1353 2450 2519 2714 2629 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 4/6 Aravind Subramanian 0.00455953912896829 0.00576213601897126 1425 2701.18181818182 2604 0.000456892146244085 1157 1.90728617305932 1.90728617305932 1 1.0986246465718 1423 2604 4155 3101 3813 1907 1157 2862 4194 2047 2450 2630 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 15/26 Reactome 0.000140912182123785 0.000205449435417566 2755 2629.81818181818 2605 1.2811018954385e-05 661 1.82801167087174 2.57921306703885 1 1.73374607139461 2755 3934 2605 2303 3093 3805 2453 1578 661 3160 2581 2631 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 38/65 Leona Saunders 9.23115305675201e-06 1.61769570770157e-05 2615 2154 2607 8.39199253700073e-07 510 1.30670218054906 -1.29820698753883 -1 1.61031474671016 2203 2614 2607 3417 2871 510 1729 1248 2612 3359 524 2632 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 11/34 Pathway Interaction Database 0.000160011131909154 0.000231781194474899 1015 2167.63636363636 2608 1.45475246433829e-05 771 1.42484561477406 1.42484561477406 1 1.33217568371923 1012 3571 2687 3011 3348 771 973 2654 2226 2608 983 2633 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 13/35 Arthur Liberzon 3.00864527878779e-07 7.96526089062123e-07 3510 2514.36363636364 2608 2.73513244567271e-08 1172 2.06676906763434 -2.13450505951093 -1 3.2421641919822 3509 1583 1729 2691 1635 4473 3276 2608 1172 1785 3197 2634 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 11/44 Reactome 4.60756654038296e-05 7.16834555386272e-05 3765 2446.63636363636 2609 4.18878458337259e-06 1152 1.100585021613 -1.22855262584011 -1 1.17328318598029 3763 1152 2616 1936 2897 2023 2649 2026 2947 2609 2295 2635 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 6/12 Arthur Liberzon 1.30786057934212e-05 2.22616588259977e-05 2415 2928.54545454545 2609 1.3078682766527e-06 813 1.74579347364676 1.74579347364676 1 2.08916394764181 2414 3769 4163 4330 3926 2609 2225 813 3175 2478 2312 2636 M9642 GALLUZZI_PERMEABILIZE_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/GALLUZZI_PERMEABILIZE_MITOCHONDRIA.html Proteins that permeabilize mitochondria. 16892093 29/69 Arthur Liberzon 7.02203261609482e-06 1.25544619759711e-05 3660 2736.45454545455 2609 6.3836863903186e-07 1470 1.52486315571842 -1.09659666899316 -1 1.92234841811171 3658 2101 2609 2959 2520 1470 2407 4548 1670 3039 3120 2637 M6349 SU_PLACENTA http://www.broadinstitute.org/gsea/msigdb/cards/SU_PLACENTA.html Genes up-regulated specifically in human placenta. 11904358 9/52 John Newman 3.13932853865046e-05 5.00370528303267e-05 2610 2897.18181818182 2609 3.13937288875878e-06 1676 1.9322467425252 1.65165619920102 1 2.13747583966205 2609 2532 4421 3875 2846 2567 2495 3719 2120 1676 3009 2638 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 11/28 Reactome 1.18221158433174e-06 2.56660385177198e-06 4525 2612.54545454545 2610 1.07473838146906e-07 358 2.07721155187231 -1.38041624355762 -1 2.98703976904668 4525 1944 1653 553 2076 3216 3327 4339 358 2610 4137 2639 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 189/493 Jessica Robertson 6.87939019510597e-08 2.45146938815715e-07 2615 2701.63636363636 2611 6.25399128202201e-09 1079 1.54996102760197 1.70047376994371 1 2.63547300655292 2611 3245 1614 2474 1079 4326 1940 4263 3093 1503 3570 2640 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 16/38 Reactome 0.000266918494316483 0.00037572245850617 2615 2730.81818181818 2612 2.42682621935033e-05 1468 1.34512829520329 -1.06202955627937 -1 1.1850583634359 1997 3031 2422 3805 3198 1468 2612 2611 3597 3241 2057 2641 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 11/24 Reactome 0.0719516087877331 0.0825980496764619 2375 2959.45454545455 2612 0.0067653207351772 2271 1.34020889861358 1.69988554785486 1 0.373346004423745 2371 2529 2304 4388 3859 3157 2271 2431 3335 2612 3297 2642 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 6/24 Leona Saunders 7.89866249561483e-06 1.39989154517591e-05 2615 2663.90909090909 2612 7.89869057074642e-07 1640 1.68076187492899 1.68076187492899 1 2.09843808611854 2612 1742 4212 2657 2562 3444 3159 1640 1961 2481 2833 2643 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 7/15 Arthur Liberzon 0.000777217371776426 0.00104596226425742 2615 2833.36363636364 2613 7.77489335736219e-05 1941 1.96587418912276 1.90169685550916 1 1.50709677565497 2613 3109 4625 2358 3359 3618 2660 2241 2325 1941 2318 2644 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 56/137 KEGG 3.37811090441219e-06 6.49562072140974e-06 3675 2720.45454545455 2614 3.07101462866307e-07 1059 1.4123076867111 -1.32023625010504 -1 1.88441247640907 3674 2765 2891 1059 2341 2416 4447 3145 2614 2579 1994 2645 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 8/21 Kevin Vogelsang 9.68906847044265e-05 0.000143725783008845 2455 2577.90909090909 2614 9.68949094758303e-06 1043 1.84986047392981 1.93300121074444 1 1.82830045562718 2451 2713 4384 1043 3049 2748 2614 2944 2087 2108 2216 2646 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 61/175 Leona Saunders 2.12873997967538e-07 6.01282431872141e-07 4455 3030.18181818182 2614 1.93521835059474e-08 1507 1.58310428875491 1.50762868153135 1 2.53316161267471 4451 1712 2474 2229 1507 2614 4600 4491 3188 2061 4005 2647 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 51/110 Arthur Liberzon 1.1100149822246e-05 1.9151436696261e-05 1730 2478.72727272727 2617 1.00910962079081e-06 1422 1.34171019292056 1.54969497034349 1 1.62815876777925 1726 2798 2958 2787 2617 2176 1422 1574 3318 3503 2387 2648 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 74/161 John Newman 1.16604915091886e-05 2.00297152536869e-05 2620 2216.81818181818 2618 1.06005030116885e-06 749 1.65259442719603 -1.58875845940266 -1 1.99713766650311 2618 2011 1066 1435 2632 2108 3260 2835 2928 749 2743 2649 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 17/28 Leona Saunders 2.13010035776066e-06 4.29318291460923e-06 2620 2952.72727272727 2619 1.93645674562279e-07 2222 1.09559382192682 1.22242084437598 1 1.51250789007685 2619 2463 2543 3125 2239 3755 2473 3947 3781 2222 3313 2650 M161 PID_IFNG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IFNG_PATHWAY.html IFN-gamma pathway 18832364 25/57 Pathway Interaction Database 1.0291254351075e-05 1.78742838729198e-05 2355 2736.18181818182 2620 9.35572953841933e-07 2068 1.05724724185233 1.25806342541507 1 1.29111513913674 2352 2620 3392 2478 2599 2636 2068 2445 3264 3561 2683 2651 M210 PID_IL8_CXCR2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL8_CXCR2_PATHWAY.html IL8- and CXCR2-mediated signaling events 18832364 25/67 Pathway Interaction Database 2.80949671630773e-05 4.51020952813225e-05 2445 2552.36363636364 2620 2.55412054132489e-06 1826 1.48044062185481 1.47062923600033 1 1.6548540224634 2442 2741 2715 2556 2804 2612 2117 2717 2620 1826 2926 2652 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 12/30 Reactome 1.11698429387908e-05 1.92645874167e-05 4405 2680.72727272727 2620 1.01544542279413e-06 363 2.07721155187231 -1.38041624355762 -1 2.51931928273207 4402 1774 1761 490 2620 2468 4177 4161 363 2743 4529 2653 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 36/144 Jean Junior 2.80093330630709e-07 7.50868047674773e-07 4640 2858.81818181818 2621 2.54630332991673e-08 1412 2.14353516757645 -1.81590187888444 -1 3.37672273721692 4637 2458 1412 1899 1609 2621 4012 4654 1432 2787 3926 2654 M117 PID_CONE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CONE_PATHWAY.html Visual signal transduction: Cones 18832364 8/34 Pathway Interaction Database 2.71708936507065e-07 7.33004073962065e-07 4370 2740.54545454545 2624 2.71708969728656e-08 1355 1.80920307159442 -1.35683988028404 -1 2.85491385948946 4367 1544 3896 2354 1633 3710 3738 2624 1355 1540 3385 2655 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 6/32 Reactome 0.0152771152483139 0.018546259599378 2330 2860.09090909091 2626 0.00153831684278173 1597 0.998503722835491 0.998503722835491 1 0.444766201225202 2329 1597 4041 2817 4650 2626 1996 2086 3758 3443 2118 2656 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 13/24 Yujin Hoshida 6.38250733146739e-07 1.49020574764605e-06 2630 2557.09090909091 2626 5.80228107556608e-08 388 2.55100861112958 3.24335547657847 1 3.82329012501399 2626 2886 1971 2509 3409 4242 3130 388 1509 2924 2534 2657 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 49/95 Leona Saunders 1.1379334247222e-08 7.68351012715883e-08 3875 2601.09090909091 2627 1.03448493691643e-09 290 1.54010752492194 -1.5615326871795 -1 2.81832089474426 3871 2063 2268 2947 290 1977 4453 3275 2627 2721 2120 2658 M9494 BIOCARTA_BCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCR_PATHWAY.html BCR Signaling Pathway 21/57 BioCarta 0.00194975447848839 0.00254004711876469 2630 2808.09090909091 2628 0.000177407690854305 1273 1.31379937011953 -0.994889203108584 -1 0.876983605637041 2628 2235 2667 1273 3442 2086 4158 3983 2581 3227 2609 2659 M16597 REACTOME_EGFR_DOWNREGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EGFR_DOWNREGULATION.html Genes involved in EGFR downregulation 17/36 Reactome 0.0182643051894543 0.022052701395976 1680 2763.45454545455 2628 0.00167433825116401 1678 1.66321357784771 1.66321357784771 1 0.708676507321784 1678 4032 2654 3365 4206 2545 1786 2171 2628 3374 1959 2660 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 16/29 Arthur Liberzon 6.60340515153291e-06 1.18785245835252e-05 1255 2564.63636363636 2628 6.00311361095671e-07 1136 1.09095326112749 0.94730493654221 1 1.38207606015793 1254 2628 2847 3308 2507 1638 1136 3329 3872 3247 2445 2661 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 15/71 Kevin Vogelsang 5.16157740581983e-05 7.95629990910254e-05 2215 2553.18181818182 2629 4.69245319023472e-06 1196 1.53716737932763 1.64953001605056 1 1.62079584011523 2214 2629 2762 4096 2922 2861 1781 1196 2073 3165 2386 2662 M868 REACTOME_CHROMOSOME_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHROMOSOME_MAINTENANCE.html Genes involved in Chromosome Maintenance 78/251 Reactome 0.0766432543837599 0.0871512472803443 1325 2810.09090909091 2630 0.00722284465345405 1324 1.73892736419789 -1.62324381437667 -1 0.473994918726525 1324 4082 2351 2630 3950 2185 2991 2452 3709 2543 2694 2663 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 10/33 Arthur Liberzon 0.000736902818729699 0.000993490718462982 2635 2740.18181818182 2631 6.70136149484149e-05 1224 0.740105711021322 -0.740105711021322 -1 0.571641727674685 2631 1224 3382 3061 3338 1633 2561 2393 3891 3841 2187 2664 M186 PID_PDGFRB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PDGFRB_PATHWAY.html PDGFR-beta signaling pathway 18832364 101/200 Pathway Interaction Database 3.55363320106062e-07 9.13958571908345e-07 3150 2790.54545454545 2632 3.2305761591589e-08 1308 1.51822752921583 -1.13767621883075 -1 2.35833679233561 3150 2972 2481 1308 1703 4374 2422 2632 2308 2982 4364 2665 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 34/74 Leona Saunders 1.19377273567315e-08 7.85207853988603e-08 4140 2587.90909090909 2632 1.08524794740986e-09 317 1.95548692752733 -1.31019828563704 -1 3.57370419338121 4137 1668 1649 1584 317 3169 4625 3488 1402 2632 3796 2666 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 5/13 Jessica Robertson 0.000241885528037839 0.00034275040350327 3840 2653.36363636364 2633 2.4191186094588e-05 1112 2.41560526053631 -2.47082448533988 -1 2.15293348452372 3838 1821 4321 1771 3340 2633 3286 1300 1112 2248 3517 2667 M1072 REACTOME_INFLAMMASOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLAMMASOMES.html Genes involved in Inflammasomes 10/20 Reactome 9.78920130488486e-05 0.000145119257559919 1125 2301.27272727273 2634 8.89966992358226e-06 530 1.40147939168687 1.40147939168687 1 1.38363462023559 1122 3453 2634 4018 3476 530 679 1449 3863 3186 904 2668 M8066 BIOCARTA_IL22BP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL22BP_PATHWAY.html IL22 Soluble Receptor Signaling Pathway 9/17 BioCarta 0.000125861106194169 0.000184423121834232 1750 2348.27272727273 2635 1.25868235220568e-05 610 1.14500177383651 -1.14500177383651 -1 1.09976666458725 1749 2635 3844 3749 3279 610 842 1558 3562 3046 957 2669 M17879 REACTOME_COMMON_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMMON_PATHWAY.html Genes involved in Common Pathway 6/15 Reactome 0.00617119557326511 0.00771770014847086 1720 2811.09090909091 2636 0.000618840050023749 1720 2.41933142177562 -2.38676499556811 -1 1.3145986731271 2925 2212 3988 2034 3783 2089 2636 4471 3344 1720 1720 2670 M7860 BIOCARTA_NGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NGF_PATHWAY.html Nerve growth factor pathway (NGF) 16/34 BioCarta 4.02968429031904e-05 6.32674619228754e-05 2640 2263.36363636364 2637 3.66341645719871e-06 829 1.35398316581689 -0.98421073508418 -1 1.46230883889141 2637 1984 2642 829 2870 1413 3085 1901 1126 3762 2648 2671 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 11/39 Jessica Robertson 0.000234668989642605 0.000333229965292499 4490 2944.72727272727 2637 2.13358204534559e-05 1423 1.93016891306558 -1.05921867653794 -1 1.72635700503959 4489 1775 1594 2637 3171 3448 4469 2334 1423 2622 4430 2672 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 19/52 Jessica Robertson 0.00536497629254552 0.00673821466278968 2075 2585.72727272727 2637 0.000488918572995799 1169 1.9538782856834 2.10203129503923 1 1.09130708783762 2072 2700 2637 3551 4286 2693 1169 2510 1835 3003 1987 2673 M19118 BIOCARTA_KERATINOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KERATINOCYTE_PATHWAY.html Keratinocyte Differentiation 30/63 BioCarta 1.20100140739287e-05 2.05472529939503e-05 3030 2677.36363636364 2638 1.09182542166048e-06 1210 1.31719854467521 -0.933729853705236 -1 1.58806268659724 3030 1333 2822 1210 2638 4296 2960 2575 2114 2282 4191 2674 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 48/117 Reactome 1.52340723066768e-07 4.57314944452834e-07 2130 2373.90909090909 2638 1.38491576014292e-08 1385 1.18359253905235 1.18871518525981 1 1.93008023353206 2127 1385 3168 1507 1391 2713 2029 2897 3095 2638 3163 2675 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 11/26 Reactome 0.0159883507699573 0.0193895993033177 3390 2720.45454545455 2639 0.00146415828661444 1111 3.15677548662844 -2.09929102094452 -1 1.39045020757401 3387 2848 2210 2639 3662 1517 2635 2439 1111 3325 4152 2676 M733 REACTOME_REGULATION_OF_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_APOPTOSIS.html Genes involved in Regulation of Apoptosis 37/77 Reactome 0.0239435024716789 0.0286734609205948 2095 2710.27272727273 2639 0.00220073912691719 1447 1.18637206170694 -0.761818076603688 -1 0.470706476669109 2095 2693 3539 2428 3748 1447 2237 3102 1846 4039 2639 2677 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 13/37 John Newman 0.00038783051959081 0.000535151300000747 2445 2656.72727272727 2641 3.52635368902552e-05 1130 2.55434881739393 -2.55434881739393 -1 2.14945759935536 2445 3936 2641 3763 4072 1133 1494 1351 3272 3987 1130 2678 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 25/78 Arthur Liberzon 3.99087258062644e-06 7.52867508567451e-06 1900 2705.27272727273 2642 3.62807256383577e-07 1896 0.987103020116836 1.09037223143739 1 1.30079635976129 1896 2663 3114 3866 2388 2606 2150 2270 3487 2642 2676 2679 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 49/172 Jessica Robertson 4.65903375845971e-06 8.66014763670853e-06 2645 2585.18181818182 2642 4.23549420465756e-07 595 1.47508045312106 -0.82900161410081 -1 1.92077818725733 2642 3177 2783 3303 2420 595 2018 4326 1624 4015 1534 2680 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 25/44 Jessica Robertson 0.00229400825085664 0.00296789692532143 4120 2601.81818181818 2644 0.000208763980200916 484 2.53423858095146 -1.3233678633787 -1 1.64757840346422 4119 2427 1535 1434 3462 2663 2938 2493 484 2644 4421 2681 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 88/189 Kate Stafford 0.000109471722607986 0.000161569918784574 1065 2475.18181818182 2644 9.95247002605544e-06 772 1.96157087808213 2.45184663531193 1 1.91306481464141 1063 3643 772 1343 3913 3587 2627 2747 2644 2076 2812 2682 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 701/1612 Jessica Robertson 1.23152931302439e-08 7.95992601494109e-08 2725 2651 2645 1.23152931984938e-09 379 1.5649087815034 -1.13433964771407 -1 2.85752754662367 2721 4141 4312 1275 379 3047 2645 2163 2180 2379 3919 2683 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 23/80 Arthur Liberzon 1.26910198413959e-05 2.16491150261308e-05 1430 2519.45454545455 2646 1.1537357319982e-06 1427 1.24923719643395 1.19621863085803 1 1.49883630582717 1427 2772 2018 3068 2646 2085 2030 2755 3783 2427 2703 2684 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 49/111 Arthur Liberzon 6.06644907321332e-06 1.09800619378438e-05 1680 2921.45454545455 2647 5.51496891033708e-07 1451 0.904821328611837 -0.846631040641199 -1 1.15422414873064 1676 3590 3440 4052 2485 1451 2647 2430 4095 4016 2254 2685 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 53/120 John Newman 1.35739702464052e-07 4.14652050682235e-07 2650 2470.72727272727 2648 1.23399737126522e-08 1355 1.55861949863448 2.02849980073202 1 2.55868647520223 3628 1384 1948 1767 1355 3217 3649 2648 1392 2650 3540 2686 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 44/122 Arthur Liberzon 3.6348182761202e-07 9.30751827426188e-07 2595 2792.54545454545 2648 3.30438079696492e-08 1708 1.40927117581602 1.68039927125742 1 2.18622323420367 2595 3525 2648 3560 1708 3796 2193 2589 2524 2700 2880 2687 M6034 REACTOME_SEROTONIN_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEROTONIN_RECEPTORS.html Genes involved in Serotonin receptors 2/12 Reactome 0.0042346018457181 0.00537032320677538 2320 2968 2650 0.000471399208040427 1814 3.09723556134655 3.09723556134655 1 1.80841729179592 2318 3394 4001 NA 3866 2297 2778 1814 4170 2520 2522 2688 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 9/37 Jessica Robertson 0.000100058758331854 0.00014814386778612 3070 2689.36363636364 2650 1.00063263907181e-05 1512 1.45377614032516 1.83062230273119 1 1.43191554561058 3068 1738 4489 2650 3052 3745 3149 1512 2084 1679 2417 2689 M7014 BIOCARTA_MYOSIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MYOSIN_PATHWAY.html PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase 16/49 BioCarta 0.0142038965320666 0.0173151558660937 2625 2856.36363636364 2652 0.00129967626816291 2228 1.8989423936588 -1.73954741189521 -1 0.860421320635253 2622 3567 2375 3637 3653 2228 2919 2276 3210 2652 2281 2690 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 7/17 Jessica Robertson 7.800381502619e-05 0.000117080678159105 2655 2608.81818181818 2652 7.80065532292862e-06 96 1.85336565683789 2.45625244795674 1 1.87421609280259 2651 2652 4504 2801 3080 3307 2440 1091 96 3590 2485 2691 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 50/191 Arthur Liberzon 2.54012740026532e-07 6.92037034746702e-07 3545 2666.45454545455 2653 2.30920699413575e-08 1115 1.10458764335449 -0.991566545476792 -1 1.75013040702505 3545 1115 3263 2653 1577 1712 4166 2039 2491 3912 2858 2692 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 64/146 Jessica Robertson 2.66801125210751e-08 1.25904337637219e-07 2655 2584.54545454545 2653 2.42546480405759e-09 664 1.20245778779883 1.36937507616704 1 2.13410122294943 2525 1505 2653 2960 664 4635 2655 2267 3122 2464 2980 2693 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 5/22 Jessica Robertson 0.0132731220538997 0.0162269371105072 2165 3000.90909090909 2654 0.00133530740750145 1312 0.896783387209909 -0.896783387209909 -1 0.412839889395351 2164 2654 4548 3924 3936 1312 1648 2481 3722 4654 1967 2694 M11792 BIOCARTA_SHH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SHH_PATHWAY.html Sonic Hedgehog (Shh) Pathway 7/19 BioCarta 0.0172315927427023 0.0208541434897477 1600 2764.54545454545 2655 0.00173666869267133 1599 1.18566824011235 1.18566824011235 1 0.512601306992863 1599 2755 3871 2655 3677 2183 2190 3847 1839 3573 2221 2695 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 16/50 Reactome 2.17642271285067e-06 4.38089211014529e-06 3225 2491.90909090909 2655 1.97856805995614e-07 1352 1.33750029103319 -1.37915299522038 -1 1.84344714009584 3221 2115 2779 2863 2243 1764 3699 1352 3178 2655 1542 2696 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 49/101 Jessica Robertson 2.29870205649289e-06 4.59544276310822e-06 3670 2783.09090909091 2656 2.0897313257534e-07 1586 1.35466123708746 -1.10809859892629 -1 1.8598643848839 3668 2656 2293 1779 2256 2278 3833 3634 3136 1586 3495 2697 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 6/21 Leona Saunders 1.19659841139327e-05 2.0479401591632e-05 4385 2863.36363636364 2657 1.19660485475701e-06 937 2.30016030758065 -1.68149320805822 -1 2.77400735077028 4384 1486 4143 1715 2657 4208 2949 2655 937 2476 3887 2698 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 51/100 Arthur Liberzon 0.00146008123092961 0.00192027523102334 1635 2322.27272727273 2658 0.000132822831741015 1105 1.78304099636605 -1.6440022972723 -1 1.24592378919914 1634 2766 1105 1536 3415 2274 2915 2658 3166 1241 2835 2699 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 21/36 Kevin Vogelsang 1.31997406347978e-05 2.24352501322679e-05 2825 2598.90909090909 2658 1.1999836211228e-06 1363 1.31004870590688 1.59099837989072 1 1.56657817646238 2825 1934 2456 2693 2658 4124 2847 1363 2377 1820 3491 2700 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 41/72 Kate Stafford 1.02784535742227e-06 2.25876834875099e-06 4510 2908.36363636364 2659 9.34405306940398e-08 1823 1.48526255193337 -1.26315267067927 -1 2.15701229517426 4508 2659 1924 2171 2046 2081 3546 4071 3028 1823 4135 2701 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 21/62 Jessica Robertson 0.000183180313250639 0.000264199122158354 3905 2707.54545454545 2659 1.66541424830816e-05 1149 1.81068633126813 -1.37962479473969 -1 1.66644322903484 3903 2387 1781 1927 3129 3528 4185 2659 1512 1149 3623 2702 M6370 KEGG_P53_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_P53_SIGNALING_PATHWAY.html p53 signaling pathway 47/91 KEGG 1.34687951823902e-05 2.28676718205363e-05 1530 2391.90909090909 2660 1.22444342195276e-06 1167 1.47907443802603 1.79998626310023 1 1.76554774458362 1528 3683 2207 2673 2660 2893 2043 1539 2682 3236 1167 2703 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 165/387 Arthur Liberzon 1.14576207488469e-06 2.49374876122138e-06 4660 2857.81818181818 2660 1.04160242872644e-07 1692 1.380509914531 -1.25108253423192 -1 1.98962034185381 4659 2545 2266 2660 2068 2326 4279 3068 2966 1692 2907 2704 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 21/53 Broad Institute 4.99667426622979e-05 7.72752990480291e-05 2125 2566.27272727273 2661 4.54253432280237e-06 1386 1.63130847925844 1.59418141819566 1 1.72537514309323 2122 3020 2387 3005 2915 2661 1386 2726 2485 3229 2293 2705 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 67/144 Jessica Robertson 3.71189080932168e-06 7.06495545592259e-06 2335 2609.18181818182 2661 3.37445188374943e-07 1282 1.2180832721921 -1.03501484472299 -1 1.61383055752544 2335 3117 2879 2473 2365 1282 2661 3369 2993 3232 1995 2706 M1296 BIOCARTA_IL7_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL7_PATHWAY.html IL-7 Signal Transduction 14/27 BioCarta 1.3651978407471e-05 2.31451413955894e-05 3065 2526.63636363636 2664 1.24109664770949e-06 1147 1.52236588651829 1.72691815645553 1 1.81517302879678 3062 1147 1838 1205 2664 4248 2952 3123 2282 1874 3398 2707 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 362/930 Arthur Liberzon 1.20476827921514e-07 3.76528460593984e-07 4165 2923.72727272727 2664 1.09524395017354e-08 825 1.53608641636945 -1.28970172202859 -1 2.53824478503806 4162 3776 2664 2522 1320 825 4536 4603 2447 3173 2133 2708 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 24/50 Arthur Liberzon 6.53442547615751e-05 9.91269594732085e-05 1450 2330.90909090909 2664 5.94056324482053e-06 581 1.04665756219706 -1.08295704753513 -1 1.07789506872277 1448 2664 3124 3629 3895 581 1101 1147 3730 3497 824 2709 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 16/33 Arthur Liberzon 2.9476611632257e-07 7.8303515934669e-07 4080 3091.18181818182 2664 2.67969232560633e-08 1630 1.197381575693 -1.58585143001652 -1 1.88063090507681 4078 2564 2533 3233 1630 4480 2664 2637 2630 4076 3478 2710 M699 KEGG_FATTY_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FATTY_ACID_METABOLISM.html Fatty acid metabolism 22/56 KEGG 3.04798845236067e-05 4.8680551764697e-05 1540 2458.63636363636 2665 2.77093698319485e-06 569 0.89230372176514 -0.888736086174946 -1 0.98981711868377 1539 2665 3254 3821 3373 569 1700 1434 3973 4011 706 2711 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 6/24 John Newman 4.12688014356066e-06 7.75092599307625e-06 3615 2769 2665 4.12688780759356e-07 1262 1.34028349715856 -0.798766154439785 -1 1.76185896735955 3613 1741 4398 1803 2413 2665 3689 3503 1262 2490 2882 2712 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 175/569 Arthur Liberzon 1.27477196086283e-07 3.94283856523472e-07 3220 2616.45454545455 2666 1.15888366793495e-08 1338 1.77071317567226 -1.1402671791938 -1 2.916830230806 3218 3220 1622 2552 1338 3413 2868 2088 2251 2666 3545 2713 M9367 BIOCARTA_ERYTH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERYTH_PATHWAY.html Erythrocyte Differentiation Pathway 7/15 BioCarta 0.00473035416188615 0.00597478156404272 2345 2931 2667 0.000474045374501243 1802 1.51972922381089 1.86520417189864 1 0.869233970175251 2341 3871 3832 3886 3549 2224 1802 1817 4008 2667 2244 2714 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 5/18 Jessica Robertson 0.0017913928353709 0.00234040317586258 2550 3056.09090909091 2667 0.00017928385656228 1783 0.611072505945245 -0.611072505945245 -1 0.413489106478577 2546 2215 4545 2667 3443 1783 2650 3167 3691 4653 2257 2715 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 29/62 Arthur Liberzon 1.00292138918038e-07 3.26594136879726e-07 3135 2702.09090909091 2668 9.11746759000818e-09 1238 1.48905280442711 -1.09796992555821 -1 2.48419185615855 3133 1800 1864 2538 1238 4641 2967 2668 3171 1839 3864 2716 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 9/40 Yujin Hoshida 0.000909047024945546 0.00121465479295547 2305 2953.90909090909 2668 9.09419104102559e-05 2105 1.72320752647883 1.76413061414314 1 1.29227893993051 2302 3218 4608 3617 3383 2630 2105 2547 2341 3074 2668 2717 M542 REACTOME_IL_7_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_7_SIGNALING.html Genes involved in Interleukin-7 signaling 9/13 Reactome 1.08724998580271e-05 1.87863327192902e-05 2795 2782 2671 1.08725530534573e-06 1291 1.77808538455654 -1.01338664762393 -1 2.16152117312242 2792 1291 3926 2042 2637 3505 2671 4357 2006 2297 3078 2718 M6924 BIOCARTA_EIF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF2_PATHWAY.html Regulation of eIF2 4/16 BioCarta 0.0482512987845321 0.0562311828162938 2675 3025 2672 0.0049332163550944 1842 0.506019761523048 -0.506019761523048 -1 0.16269849086216 2672 2254 3857 3052 3874 1842 2165 2356 4191 4423 2589 2719 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 7/18 Reactome 0.00262463330524014 0.00337671845704244 2390 2973 2672 0.000262773838294837 1713 1.8570979502901 1.8570979502901 1 1.1805786928208 2390 3421 3969 4216 3909 2381 2220 1713 3579 2672 2233 2720 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 116/286 Kate Stafford 1.33122816844027e-08 8.26322183149997e-08 1740 2331.18181818182 2672 1.2102074331778e-09 371 1.26651754114169 -1.15286264465786 -1 2.30737370268004 1736 3140 2769 2672 371 1356 2779 2070 3583 3226 1941 2721 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 11/40 Arthur Liberzon 1.53963012328521e-05 2.5905589794307e-05 2675 2592.36363636364 2673 1.39967354383012e-06 1366 2.6031709627587 2.48162213267109 1 3.07109205119986 2317 2673 1366 3102 2686 3441 2672 3687 1611 1497 3464 2722 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 7/19 Reactome 3.81954497277658e-05 6.00818655335046e-05 3485 2586.27272727273 2674 3.81961062452182e-06 485 1.87544689413192 2.27841424264865 1 2.03631596605604 2641 3482 3983 1494 2875 3483 2114 3425 485 2674 1793 2723 M19888 KEGG_ACUTE_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ACUTE_MYELOID_LEUKEMIA.html Acute myeloid leukemia 28/71 KEGG 1.358968515063e-07 4.14861658735193e-07 3655 2959 2675 1.23542599909841e-08 1357 1.43856948068896 -0.964185733915071 -1 2.36152676808618 3653 2486 2675 2336 1357 4308 2451 3118 3114 2512 4539 2724 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 5/17 Arthur Liberzon 1.19166602718234e-06 2.58405691965593e-06 2675 2740.18181818182 2675 1.19166666621339e-07 1292 1.56418461060084 1.97554943233383 1 2.24812045123051 2675 2577 4108 3000 2101 3325 2548 2145 1292 3276 3095 2725 M14766 REACTOME_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTRINSIC_PATHWAY.html Genes involved in Intrinsic Pathway 7/23 Reactome 2.03137705566345e-06 4.1118932539261e-06 2310 2885 2677 2.03137891258757e-07 552 2.47637693953587 2.47637693953587 1 3.430665612135 2307 4006 4071 3934 3961 2412 2439 552 3096 2677 2280 2726 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 24/61 John Newman 1.47781559232455e-05 2.49102297324922e-05 2355 2970.45454545455 2677 1.34347774492093e-06 1753 1.16830136454558 1.53745960730706 1 1.38341725475294 2354 4091 3067 4363 2677 2321 1753 2037 3951 3852 2209 2727 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 7/13 Reactome 0.00546138427359199 0.00685378861972471 2215 2774.09090909091 2678 0.000547485290650506 1993 1.13846467167739 1.35308190545524 1 0.633708108398381 2215 2128 4075 2499 3562 2701 2534 1993 3354 2678 2776 2728 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 33/113 Yujin Hoshida 5.45000916988812e-08 2.09505684742377e-07 4030 2510.09090909091 2678 4.95455391354539e-09 544 1.68843162253045 -1.72787817655924 -1 2.90055326750671 4030 544 827 1485 961 4046 3654 4209 2678 603 4574 2729 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 5/10 Leona Saunders 0.000492708340784427 0.000674111324063014 2655 2802.81818181818 2679 4.9281761756472e-05 1387 1.32493911280626 -1.62909679526683 -1 1.08075566634374 2653 2362 4434 3672 3299 1387 2888 2084 2679 3294 2079 2730 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 19/40 John Newman 8.78094051634584e-07 1.96408053745091e-06 2685 2644.09090909091 2682 7.98267638283337e-08 930 1.00160533447844 -1.08746747902108 -1 1.47024938192971 2682 3628 3297 4402 2000 930 2135 1137 3516 3924 1434 2731 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 216/543 Arthur Liberzon 1.62502915243955e-06 3.39193167408986e-06 4050 2733.09090909091 2683 1.47730032069814e-07 1235 1.29937146489991 -1.05465491874512 -1 1.82803198811285 4048 1235 2805 1690 2161 2015 4411 3286 2683 2460 3270 2732 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 7/22 Jessica Robertson 3.44787810315548e-07 8.9203157362956e-07 4305 2607.45454545455 2683 3.44787863810946e-08 295 1.85337711239604 -1.05824099979461 -1 2.88396863036743 4304 1592 4310 1555 1727 3175 4038 1793 295 2683 3210 2733 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 9/32 John Newman 1.38316809215747e-05 2.34074600211264e-05 1705 2870.36363636364 2683 1.38317670142575e-06 1702 1.11885217990095 1.11885217990095 1 1.33264012785933 1702 2078 4412 4077 2683 2195 1924 3136 4044 3067 2256 2734 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 4/18 Jessica Robertson 0.000595088593645292 0.000809693713653263 1990 2803.72727272727 2683 5.95248012427255e-05 992 0.863395555614495 -0.863395555614495 -1 0.686598407218905 1987 2683 4452 3298 3629 992 1728 1939 4298 4627 1208 2735 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 37/147 Arthur Liberzon 5.90554536296164e-07 1.39553129454555e-06 2710 2704 2684 5.3686790438279e-08 1830 1.61039915273855 -1.6051842621009 -1 2.42537222619212 2709 2556 1830 3008 1883 2684 3894 2488 3497 2167 3028 2736 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 96/216 Broad Institute 1.94407095926186e-07 5.56160959407879e-07 1845 2558 2685 1.76733739186666e-08 1365 1.42203705585755 1.59710036230884 1 2.28782580914315 1844 3746 3326 4049 1481 2685 1390 1365 3464 3411 1377 2737 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 4/10 Arthur Liberzon 8.30212241036935e-06 1.46474945839574e-05 4375 2703.54545454545 2685 8.30215342688886e-07 222 3.06850435983569 -2.39918863475494 -1 3.81551632904266 4372 1600 4652 1707 2572 3364 3440 3067 222 2058 2685 2738 M557 REACTOME_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEFENSINS.html Genes involved in Defensins 10/110 Reactome 0.0818798001122937 0.0902966141827776 2920 3019.90909090909 2688 0.00773600915179959 1927 1.79543842036098 -1.93713366690156 -1 0.482287666115846 2918 4068 2571 4098 4060 1927 2685 2688 3365 2436 2403 2739 M3042 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_KERATAN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_KERATAN_SULFATE.html Glycosaminoglycan biosynthesis - keratan sulfate 8/15 KEGG 9.64165396510551e-09 7.04076564672179e-08 2750 2287 2689 9.64165400693816e-10 267 1.48185451127454 1.50748431949828 1 2.72618176582712 2749 984 3793 1511 267 2699 2048 2689 3043 2091 3283 2740 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 16/30 Reactome 7.96356011102825e-06 1.40926143052411e-05 2695 2882.81818181818 2691 7.23962630697238e-07 1649 0.868075858056633 -0.81857348619386 -1 1.08314927050084 2691 2702 3497 4494 2543 1649 1859 2242 3956 3767 2311 2741 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 7/23 Jessica Robertson 0.000102386046661693 0.000151541697617402 1005 2306.18181818182 2691 1.02390764273755e-05 636 1.60493174638815 1.60493174638815 1 1.57673263640307 1002 2966 4490 2997 3733 863 636 1700 3368 2691 922 2742 M16473 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION.html Aldosterone-regulated sodium reabsorption 20/55 KEGG 0.000312767242322594 0.000435939112886281 4570 2921.27272727273 2692 2.84374287575269e-05 1865 1.92274584135992 -2.12142825934423 -1 1.66201139990453 4566 2068 1996 1865 3228 4482 3380 2263 2692 2595 2999 2743 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 74/166 Leona Saunders 8.36758003381553e-08 2.83582175257329e-07 1830 2702.81818181818 2693 7.60689122915628e-09 1165 1.58823918714233 1.73812005661212 1 2.67471923204409 1830 4428 2919 3504 1165 3346 1926 2019 2693 3599 2302 2744 M12012 ST_P38_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_P38_MAPK_PATHWAY.html p38 MAPK Pathway 28/52 Signaling Transduction KE 1.62527594074809e-05 2.72293280598697e-05 2915 2783.81818181818 2695 1.47753449799084e-06 1930 1.38903378767268 -1.86087757365729 -1 1.63098028456221 4673 1930 2913 2091 2695 3800 2783 2222 2911 2513 2091 2745 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 7/31 Arthur Liberzon 2.49379039296798e-07 6.83386069090522e-07 3130 2119.63636363636 2695 2.49379067282259e-08 13 1.72752791801742 -1.1094331860282 -1 2.73955693357521 3126 426 4628 605 1599 3678 2762 835 13 2695 2949 2746 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 205/459 Arthur Liberzon 1.58415501285164e-07 4.7222330726608e-07 2380 2535.81818181818 2696 1.44014102447452e-08 1041 1.3185899777636 -1.15417955911103 -1 2.14549488408678 2377 3552 2892 3429 1406 1041 2696 2207 2723 3660 1911 2747 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 464/1046 Arthur Liberzon 7.58111808729658e-09 6.11447837471115e-08 3440 2655.72727272727 2697 6.89192555765532e-10 168 1.41062630424953 -1.02312523039793 -1 2.61737007024833 3440 2218 2697 2716 168 1404 3329 2638 2538 3597 4468 2748 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 287/727 Leona Saunders 3.31774557934822e-08 1.48036225003471e-07 2700 2278.81818181818 2698 3.0161323903473e-09 358 1.36025388017704 -1.25318761693463 -1 2.38954892530719 2698 3006 3338 3133 749 358 2632 1958 2980 3366 849 2749 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 53/111 Pathway Interaction Database 6.05807073901593e-07 1.42653866748888e-06 4440 2773.09090909091 2700 5.50733855200767e-08 1211 1.43048025267942 -1.04038010941268 -1 2.1508902897924 4440 1262 2700 1211 1890 2819 4614 3273 1238 2649 4408 2750 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 14/76 Jessica Robertson 1.70361438367551e-05 2.8480688554775e-05 2080 2702.27272727273 2702 1.54875234190927e-06 1892 1.71739393163804 1.71199284886271 1 2.00791537678165 2079 3326 2132 2903 2702 2879 2238 4278 2275 3021 1892 2751 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 3/23 Jessica Robertson 1.1945937310972e-05 2.04527126136043e-05 4685 2835.54545454545 2702 1.19460015288961e-06 610 1.246479369252 -0.855409952406405 -1 1.50344319808062 4682 610 4508 2746 2655 2702 2304 2960 1861 1757 4406 2752 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 70/165 Jessica Robertson 5.09954109562293e-07 1.23368350924569e-06 2330 2789.54545454545 2704 4.63594752516662e-08 1830 1.23428283298646 1.53052743652885 1 1.87591148541894 2326 1871 3218 3486 1830 3588 2398 3478 3203 2583 2704 2753 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 249/602 Arthur Liberzon 8.47599413959115e-08 2.85955903690318e-07 2905 2759.81818181818 2705 7.7054495146799e-09 1170 1.48414567929145 1.76639742116662 1 2.49803561955503 2905 3678 2666 1947 1170 3561 2133 3340 2705 2359 3894 2754 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 138/454 Yaara Zwang 4.43035830981344e-08 1.80370625888669e-07 3105 2578.45454545455 2705 4.02759854457452e-09 869 1.46320157216891 -1.22274816386183 -1 2.53810564738337 3105 3744 2632 3310 869 1236 2999 2499 2846 2705 2418 2755 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 12/29 Reactome 0.000151934180676671 0.000220763897876242 1780 2426.81818181818 2707 1.38131522196721e-05 1273 0.943146655066262 -1.01550323078863 -1 0.886936539201757 1779 2707 2971 2901 3107 1407 2574 1395 3835 2746 1273 2756 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 9/17 Arthur Liberzon 1.89423534385587e-07 5.43896251305673e-07 1675 2766.09090909091 2708 1.89423550532162e-08 1358 1.43304115919997 1.39447174655389 1 2.30909931826184 3409 1358 4184 1671 1499 3757 2708 4309 1967 1673 3892 2757 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 9/23 Jessica Robertson 4.63762844867367e-06 8.63063022656267e-06 4160 2803.72727272727 2710 4.63763812712103e-07 939 2.24281267436179 -1.54594220400586 -1 2.92133734420676 4157 2710 4616 939 2440 2798 3324 2129 1132 2321 4275 2758 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 25/65 Kevin Vogelsang 8.77986873900297e-06 1.54284900783268e-05 3670 2767.18181818182 2712 7.98173070757533e-07 1402 1.83003489630944 -1.60763536528366 -1 2.2649282425432 3670 1402 1462 2945 2564 2488 3510 4422 2712 1499 3765 2759 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 73/172 Kate Stafford 4.79153167627291e-05 7.4298866429566e-05 2500 2622.54545454545 2713 4.35603276138809e-06 1458 2.06100360411715 -1.62357954974553 -1 2.1888910951703 2496 3714 1458 1794 2905 2343 2993 3710 2713 1798 2924 2760 M5372 REACTOME_XENOBIOTICS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_XENOBIOTICS.html Genes involved in Xenobiotics 2/46 Reactome 0.0506562115530118 0.0589166064376802 2150 3098.2 2714.5 0.00575938214268728 1811 0.92507730984588 0.92507730984588 1 0.292615661989956 2147 2605 3978 NA 3939 2374 1811 2506 4338 4460 2824 2761 M63 PID_AVB3_OPN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AVB3_OPN_PATHWAY.html Osteopontin-mediated events 18832364 31/54 Pathway Interaction Database 3.66515886451268e-05 5.78280620845334e-05 2530 2803.54545454545 2715 3.33201811527115e-06 1695 1.59522061119651 -1.29498411527797 -1 1.73886606960272 2529 3720 2691 1695 2851 3572 2715 2596 2564 2764 3142 2762 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 8/24 Reactome 0.00211531080040352 0.00274428195201852 1190 2469.09090909091 2715 0.00021173270449864 1187 1.13882232878564 1.13882232878564 1 0.750344982995052 1187 2715 3921 2961 3756 1327 1383 1678 3622 2869 1741 2763 M1012 REACTOME_IL_2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_2_SIGNALING.html Genes involved in Interleukin-2 signaling 23/57 Reactome 0.000118870288544802 0.000174890477902965 2715 2723.72727272727 2715 1.08069738021912e-05 1829 1.08570818110079 -0.991329361270237 -1 1.0492523144899 2715 2428 2991 1829 3064 1832 3842 2189 3752 3398 1921 2764 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 21/69 Jessica Robertson 0.000253881470759926 0.00035877218696653 1175 2458.81818181818 2717 2.30827975986981e-05 1172 1.25184052289501 1.38117450296621 1 1.10932725719514 1172 3383 2899 3636 4331 1173 1449 1291 3632 2717 1364 2765 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 17/47 Arthur Liberzon 0.00649713574251727 0.00810369392851635 2130 2963.36363636364 2718 0.000592400279575727 1847 2.13439854431028 2.35384427044852 1 1.14813772254241 2130 4672 2718 4111 4443 2910 1932 1880 1847 3380 2574 2766 M81 PID_CDC42_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CDC42_PATHWAY.html CDC42 signaling events 18832364 49/107 Pathway Interaction Database 2.01332851354813e-06 4.08064767062567e-06 4545 2809.63636363636 2720 1.83030032367884e-07 1184 1.52378052889666 -1.29260855954297 -1 2.11227801979596 4542 1184 2384 1437 2228 3831 3093 4628 1560 2720 3299 2767 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 72/201 Arthur Liberzon 9.29445758644499e-08 3.06933250529114e-07 4360 2779.45454545455 2720 8.44950725373904e-09 1160 1.61948040852142 -1.59900025890459 -1 2.71301691731346 4358 2480 1705 3280 1210 2732 3749 4604 2720 1160 2576 2768 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 93/230 John Newman 2.01730974301648e-06 4.08518299730996e-06 2795 2946.54545454545 2721 1.83391962982648e-07 1658 1.46943219243561 -0.934556674168475 -1 2.03675753311762 2795 3584 2698 2721 2230 4388 2663 1658 2171 3712 3792 2769 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 7/22 Arthur Liberzon 2.3468467226468e-05 3.82648703629885e-05 2370 2859.45454545455 2722 2.34687150761811e-06 1818 1.67862869638619 1.98150301181115 1 1.9072179391745 2367 3573 4220 4328 2783 2869 1818 1857 2235 2682 2722 2770 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 30/57 John Newman 1.69808205377803e-07 4.98260019035934e-07 2005 2487.18181818182 2722 1.54371107713222e-08 1437 1.31435338046374 1.30927836692592 1 2.1307214388863 2004 1670 2774 3300 1437 2722 2263 2155 2894 3130 3010 2771 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 17/53 Leona Saunders 1.9238060471284e-05 3.18662252981395e-05 2920 2696 2723 1.74892988199696e-06 1410 2.03612553348133 2.25540668461542 1 2.35501759773484 2920 2315 1565 3543 2723 3262 2394 4024 2496 1410 3004 2772 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 10/23 Reactome 0.0362181421149715 0.042707149962445 2620 2966.36363636364 2724 0.00334804624993357 2260 1.43682176194096 1.92578918256472 1 0.50613136637734 2617 2995 2620 2724 4038 3434 2450 2260 3081 3838 2573 2773 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 287/748 Arthur Liberzon 4.3611148048313e-07 1.08185198387715e-06 3845 2748.63636363636 2724 3.96465060849653e-08 1383 1.60447258982285 -1.32456576841557 -1 2.46207900205097 3841 2724 1715 3066 1785 1383 3615 4625 2161 2380 2940 2774 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 4/20 Reactome 1.77011514443333e-05 2.94558223253359e-05 2465 2897.36363636364 2725 1.77012924447572e-06 2040 1.60510167359752 -1.15214528075526 -1 1.87059101629599 2461 2255 3935 4266 2725 3010 2728 2176 3621 2040 2654 2775 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 25/64 Jessica Robertson 0.0204366566406169 0.0245995820749886 2185 3021.54545454545 2726 0.00187536426761267 2138 1.8579348954421 2.53323307024907 1 0.768961526075307 2181 4297 2258 4085 3758 3593 2726 2138 2371 3141 2689 2776 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 25/55 Reactome 4.24652114010641e-06 7.95013905814568e-06 2730 2923.54545454545 2728 3.86048121538208e-07 1649 1.4792671092175 1.93330341275268 1 1.94036533544292 2728 4214 2957 3196 2405 4168 2475 1752 1649 3890 2725 2777 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 50/114 John Newman 1.97493915020996e-05 3.26554864427801e-05 1975 2919.54545454545 2730 1.79541534495809e-06 1469 1.22313486117135 1.33861172130137 1 1.41135569997522 1972 3985 3438 3718 2730 2690 1469 2553 3328 4038 2194 2778 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 26/63 Arthur Liberzon 0.0489898345591208 0.0570634761978722 1475 2859.27272727273 2730 0.00455600136552498 1471 1.14890275678844 -1.03582286375409 -1 0.367516642627763 1471 3260 2730 2389 4169 1906 2124 3441 4087 3648 2227 2779 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 13/29 Reactome 0.000154319240308184 0.000224021053309836 1700 2492.72727272727 2731 1.40300060101177e-05 1467 1.28468912000559 1.28468912000559 1 1.20602178998636 1699 2845 3279 2731 3108 1839 1467 1660 3389 3525 1878 2780 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 6/15 Reactome 1.79558235695178e-05 2.98266534019002e-05 1955 2559.36363636364 2731 1.79559686563878e-06 1172 1.10863215158535 -1.10863215158535 -1 1.29045428730754 1952 2785 4038 3623 2731 1172 2261 1317 3407 3442 1425 2781 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 11/56 Arthur Liberzon 5.029022779968e-07 1.22040397446556e-06 2735 2343.18181818182 2731 4.57183993596588e-08 593 1.23434306149738 1.51104138237922 1 1.87749528802343 2731 593 1869 3104 1828 2770 1958 2928 3423 1090 3481 2782 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 9/27 John Newman 9.98239707377037e-06 1.73829478586726e-05 2015 2813.45454545455 2731 9.98244191576696e-07 1605 1.13771453223551 1.39066550476377 1 1.39292463508819 2015 2780 4397 3119 2614 2544 1605 2731 3893 3064 2186 2783 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 55/151 Arthur Liberzon 5.25138743605749e-07 1.26389324732231e-06 3270 2818.72727272727 2734 4.7739897177828e-08 1776 1.95793706156808 -1.2610803783286 -1 2.97045842158648 3268 4117 1776 2168 1844 4600 2794 2865 2734 2183 2657 2784 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 78/147 Kate Stafford 4.28748713332679e-06 8.02042503264244e-06 2735 2855.09090909091 2734 3.8977231718657e-07 1618 1.541425402798 1.85311418267922 1 2.0203832189517 2734 3400 1964 3010 2407 4604 2712 1618 3207 2033 3717 2785 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 26/61 Jessica Robertson 1.27504776098306e-06 2.73574808057079e-06 2760 2533.18181818182 2734 1.15913499996315e-07 1209 1.52860876378565 -1.13248641470478 -1 2.18724841557678 2759 1977 2328 2995 2094 3656 2849 2734 1209 1920 3344 2786 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 22/43 Jessica Robertson 0.0019680650860761 0.00256176472037572 2240 2959.90909090909 2735 0.000179075261463638 1648 2.67580213436899 3.34151687714849 1 1.78359920493895 2240 4057 2366 1983 4465 3881 2735 1648 2283 3747 3154 2787 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 373/882 Leona Saunders 5.92109130472156e-07 1.398499690218e-06 2535 2806.72727272727 2736 5.38281172575246e-08 1080 1.27485574281727 -1.0180583497972 -1 1.91971805994442 2533 3947 3664 2933 1884 1080 2554 2736 3106 4295 2142 2788 M9011 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION.html Vasopressin-regulated water reabsorption 29/62 KEGG 0.000128407617758 0.000187927812286303 1495 2415 2737 1.16741011955109e-05 1329 1.13247972871221 1.20596568196816 1 1.08535780450971 1494 2737 3010 3894 3078 1381 1329 1514 3540 3037 1551 2789 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 547/1300 Jessica Robertson 1.27595212462965e-08 8.0434968418917e-08 3120 2279.36363636364 2737 1.27595213195589e-09 394 1.57923843981265 -1.27001781779565 -1 2.88185104665929 3119 612 4307 519 394 2737 3007 3166 2176 1108 3928 2790 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 18/32 John Newman 1.04271830053808e-06 2.28646605349622e-06 3260 2015.27272727273 2737 9.47926177043779e-08 308 1.20977813366181 1.24109191471061 1 1.75528556731995 1203 3212 3258 3635 3257 665 308 451 2737 2940 502 2791 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 28/64 KEGG 2.07839407593663e-05 3.42693688945779e-05 3410 2903 2738 1.88946701026912e-06 1455 1.54609356410605 1.85596301791098 1 1.77568123477463 3406 2487 2524 2096 2738 4365 3202 2672 1455 2964 4024 2792 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 5/11 Reactome 0.000187976569089879 0.000270367772484707 2610 2864.72727272727 2738 1.87992471818898e-05 1526 1.77267615144533 2.10917532077524 1 1.62689066277737 2606 2636 4095 3544 3153 3072 2978 2487 2677 1526 2738 2793 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 47/94 Reactome 2.82153629338959e-06 5.51934111723966e-06 2740 2919.27272727273 2740 2.56503628369358e-07 1121 0.812780894501433 -0.594850873819174 -1 1.09926395302427 2740 1661 3599 4021 2304 1121 2588 3505 3878 4185 2510 2794 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 20/47 Arthur Liberzon 9.52828351463544e-07 2.1146106422627e-06 3565 2745.72727272727 2740 8.6620796739761e-08 1587 2.01456076675595 1.56590705308182 1 2.94054115507505 3564 1840 1587 2369 2021 3694 2766 2740 3408 1707 4507 2795 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 17/24 Jessica Robertson 0.0395459566070322 0.0464791453876481 1170 2712.45454545455 2740 0.00366138476670861 1168 2.70029679748918 2.70029679748918 1 0.925669876445319 1168 3451 1292 1906 4674 3234 2608 3085 3456 2223 2740 2796 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 13/35 Arthur Liberzon 2.09139546449387e-05 3.44594906702471e-05 2895 2623.09090909091 2740 1.90128667843741e-06 1430 1.44991651830206 -0.711128515279308 -1 1.66432624746113 2891 2569 2332 3170 2740 3423 1837 1430 2055 3536 2871 2797 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 15/27 Reactome 6.94714630223366e-07 1.59972125662245e-06 3565 2726.54545454545 2742 6.31558954181832e-08 592 1.39091669745038 -0.757827521217807 -1 2.07359922277292 3563 1844 2742 1764 1940 2267 2987 4137 592 4050 4106 2798 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 55/243 Arthur Liberzon 2.10437747439775e-05 3.46490261596199e-05 4325 2662.54545454545 2742 1.91308873070811e-06 592 1.83204845360371 -1.69419621196314 -1 2.10184431389446 4323 2012 761 2571 2742 2749 3707 3675 2520 592 3636 2799 M13881 REACTOME_SIGNALLING_TO_ERKS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_ERKS.html Genes involved in Signalling to ERKs 24/46 Reactome 6.9138115402061e-05 0.000104577536725003 4395 2698.27272727273 2744 6.28548075098576e-06 1013 1.54565733560047 -1.47565755842777 -1 1.58254547402067 4394 2021 1970 1013 2979 3692 2963 2744 1852 2574 3479 2800 M15096 REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION.html Genes involved in Mitochondrial tRNA aminoacylation 16/27 Reactome 0.00259657694867797 0.00334181806687859 1350 2670.27272727273 2745 0.000236331514902159 946 0.742947126330904 -0.742947126330904 -1 0.473162216099198 1349 2745 3499 3888 3563 946 1551 1810 3971 4468 1583 2801 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 23/37 Reactome 0.000298941310666336 0.000417662188963164 3610 2890.54545454545 2745 2.71801762965874e-05 1913 1.3524016773324 -1.36485625162497 -1 1.17547926827469 3606 2948 2745 2248 3215 2440 4330 2572 3358 2421 1913 2802 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 11/25 Reactome 2.14966836955254e-05 3.52624722332713e-05 4420 3045.72727272727 2748 1.95426306792923e-06 1477 1.56307668120776 -1.81372494641113 -1 1.79019818642154 4419 1477 1891 1996 2748 4024 4650 4279 2401 1967 3651 2803 M8179 BIOCARTA_RAB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAB_PATHWAY.html Rab GTPases Mark Targets In The Endocytotic Machinery 15/29 BioCarta 0.00575802076437554 0.00721639082692265 3550 2565.72727272727 2749 0.000524831507498129 536 2.78846020197939 -1.51084966270157 -1 1.53609349864027 3548 3032 1383 1733 3559 4325 3517 1843 536 1998 2749 2804 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 17/55 Reactome 0.030593558961128 0.0363124157274179 2270 2905 2752 0.0028206790462282 1941 2.49538482091688 2.49538482091688 1 0.924234081421985 2267 4221 2141 3381 4481 2752 2347 2220 1941 3375 2829 2805 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 44/97 Arthur Liberzon 0.0839184282471183 0.0902966141827776 1555 2914.36363636364 2752 0.00793650793650794 1551 1.95813581565122 2.15634318236045 1 0.525991187728551 1551 4387 1938 2518 4487 3249 2173 2973 3331 2699 2752 2806 M251 PID_SYNDECAN_3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_3_PATHWAY.html Syndecan-3-mediated signaling events 18832364 8/26 Pathway Interaction Database 6.90002394493545e-06 1.23504630274895e-05 3635 2873.36363636364 2755 6.90004536967777e-07 734 0.965616108591276 -0.657021387884483 -1 1.2190897999997 3634 734 3906 2328 2534 2073 2123 4572 2755 3672 3276 2807 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 2/5 Yujin Hoshida 7.43089997268397e-08 2.6024811115095e-07 4060 2560.9 2755.5 8.25655579788723e-09 9 1.35590630502035 -1.00777405046467 -1 2.29645820351623 4060 254 4455 NA 1197 4664 3959 1552 9 1392 4067 2808 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 5/9 Jessica Robertson 0.0025451890391312 0.00328289453271918 1685 2750.45454545455 2756 0.000254810884107464 1495 0.776755014341631 0.776755014341631 1 0.496237106763718 1684 2756 4370 3812 3480 1495 1552 1849 4431 3291 1535 2809 M3873 BIOCARTA_CHEMICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CHEMICAL_PATHWAY.html Apoptotic Signaling in Response to DNA Damage 18/34 BioCarta 2.28340395265273e-05 3.73083365485728e-05 3995 2646.45454545455 2757 2.07584332063212e-06 481 1.65738587681525 2.17757010064951 1 1.88776932223675 3992 2271 2539 1440 2757 3594 3492 1422 481 2934 4189 2810 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 11/28 Jessica Robertson 0.00513147857029416 0.00645839696278438 1750 2873.54545454545 2757 0.000467589720503416 786 2.39038530062981 2.39038530062981 1 1.346436598394 1747 4228 2757 3697 4281 2434 2290 3822 786 3904 1663 2811 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 68/174 Jessica Robertson 1.11539378530877e-06 2.43217090644806e-06 3010 2683.72727272727 2757 1.01399486437333e-07 1067 2.0391920199014 -1.59474943676517 -1 2.94462263535414 3008 3142 1067 2796 2063 4578 2591 2757 2518 1517 3484 2812 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 13/53 Reactome 7.02658874939081e-05 0.000106077947421538 1305 2444.18181818182 2758 6.3880119835671e-06 498 1.47390972333993 1.47390972333993 1 1.50674008434158 1305 4065 2758 4389 3833 838 498 1743 3506 2907 1044 2813 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 11/16 Reactome 2.28877958345294e-05 3.73831339423509e-05 2095 2600.45454545455 2758 2.08073035928896e-06 1384 0.908534712187729 -0.908534712187729 -1 1.03462140441877 2094 2674 3167 3224 2758 1384 2829 2059 3594 3329 1493 2814 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 11/40 Jean Junior 7.17827761458487e-05 0.000108263305123736 2760 2596.54545454545 2758 6.52591985633093e-06 1092 2.0676586538502 -2.01974360224949 -1 2.10900443448079 2758 2032 1344 2212 2983 3599 2848 4061 2686 1092 2947 2815 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 148/359 Arthur Liberzon 4.7869455497421e-11 7.12115137971159e-10 1085 2233.63636363636 2759 4.35176868167840e-12 307 1.82276461739191 2.06961217564962 1 4.28873578142373 1085 2759 307 1635 3280 3045 2092 2918 3268 1066 3115 2816 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 10/28 Arthur Liberzon 3.09074301963379e-07 8.16416109921304e-07 4500 2966.36363636364 2760 2.8097667762247e-08 858 2.98508673354221 -2.44904265550146 -1 4.67451519666144 4496 2633 1231 2760 1643 3970 4623 3876 858 1854 4686 2817 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 12/29 Arthur Liberzon 4.52824201398765e-06 8.44382892063118e-06 2765 2927.27272727273 2761 4.11659212223457e-07 653 2.33211249054191 2.33211249054191 1 3.04335380079129 2761 4631 2683 3241 4300 3724 2376 653 1938 3943 1950 2818 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 61/248 Jessica Robertson 1.7969118728128e-07 5.22352917866053e-07 4495 2866.72727272727 2762 1.63355638143695e-08 1457 1.59972942067188 -1.61356640233272 -1 2.58491105824361 4491 1872 2055 3016 1457 2486 4685 3339 2762 2062 3309 2819 M12294 KEGG_VIRAL_MYOCARDITIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIRAL_MYOCARDITIS.html Viral myocarditis 41/116 KEGG 2.36847886184878e-05 3.85639053044594e-05 1135 2604.81818181818 2763 2.15318578257604e-06 1133 2.27807601570636 3.15269794122516 1 2.58631479447701 3383 3283 1133 2020 2763 4468 3543 1787 1133 1822 3318 2820 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 7/23 Reactome 1.31847443313461e-06 2.82117406103597e-06 2885 2474 2764 1.31847521540394e-07 736 1.86060134060747 2.39078298157576 1 2.65589760215119 2882 736 4033 1390 2131 3039 2764 4197 1107 1347 3588 2821 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 34/78 Kate Stafford 0.0604376877867229 0.0698424179947185 1675 2849.63636363636 2764 0.00565134685225019 1671 1.73521147878008 1.79069168486228 1 0.515898121164841 1671 4052 2764 2558 3886 3035 1813 2664 3193 3407 2303 2822 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) 31/55 Reactome 0.0455240431314548 0.0531984204773061 1990 3014.81818181818 2766 0.00422675342451453 1683 0.655453019594912 -0.673582288505426 -1 0.214804696162878 1986 2694 3703 3023 3776 1683 2720 2766 3998 4263 2551 2823 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 53/197 Jessica Robertson 2.37955494752955e-05 3.87039031035178e-05 2705 2741.81818181818 2766 2.16325516869419e-06 1151 1.70325661399549 -1.42913841719884 -1 1.93302899397695 2703 3176 1617 2869 2766 2222 3470 4632 2948 1151 2606 2824 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 116/236 Arthur Liberzon 3.62092820095605e-08 1.57638406577255e-07 3210 2402.90909090909 2767 3.29175296413824e-09 782 1.55617001245056 -1.1287944801278 -1 2.72278846900988 3210 2414 2850 899 782 3020 3271 2024 1628 2767 3567 2825 M106 PID_HNF3B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HNF3B_PATHWAY.html FOXA2 and FOXA3 transcription factor networks 18832364 18/64 Pathway Interaction Database 9.36917227554904e-06 1.63943021968718e-05 3090 2890 2768 8.51746561492577e-07 2025 1.51795158443523 1.17624300815271 1 1.86838499248803 3086 2025 2530 3496 2578 3845 2959 2768 2058 2369 4076 2826 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 83/179 Arthur Liberzon 2.27996494825404e-07 6.38226747163587e-07 4685 2935.45454545455 2768 2.07269562230702e-08 1442 1.42202365869175 -0.897016045620169 -1 2.26594066539 4685 2795 2628 1442 1532 2803 4282 2302 2760 2768 4293 2827 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 192/450 Jessica Robertson 1.96997447605389e-08 1.0519954302644e-07 3190 2757.63636363636 2769 1.79088590335807e-09 529 1.38552452458459 -1.23632550014152 -1 2.48681210259202 3186 2004 2262 1785 529 3202 2769 4575 3062 2451 4509 2828 M15743 ST_GA12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA12_PATHWAY.html G alpha 12 Pathway 25/52 Signaling Transduction KE 1.29902220716493e-06 2.78209235044556e-06 3250 2961.27272727273 2770 1.18092997653841e-07 2099 1.46262594006346 -0.962585653847108 -1 2.09009059097047 3249 2911 2110 2725 2099 4481 2604 2770 2652 3135 3838 2829 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 19/54 Pathway Interaction Database 1.09924600781177e-05 1.89796123530064e-05 1410 2718.90909090909 2771 9.99319545738954e-07 1406 1.50238230441565 -1.53193195032133 -1 1.82464614033201 4198 1407 2771 1406 2615 3566 3538 2915 2089 2501 2902 2830 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 22/49 Reactome 9.11069269258851e-08 3.02570559585186e-07 2310 2600.63636363636 2772 8.28244824534795e-09 1199 1.28145180859854 1.07128345539471 1 2.14878741926656 2308 2874 2937 2608 1199 2772 1945 3305 2438 3345 2876 2831 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 2.48661798920528e-05 4.03333052870057e-05 4580 2882.27272727273 2772 2.2605873594712e-06 849 3.11597386147268 -2.65224144210048 -1 3.52197077675568 4576 2746 849 1896 2772 3996 3779 4164 1356 903 4668 2832 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 67/192 Leona Saunders 3.78010378271543e-09 3.67501376054035e-08 2775 2586.18181818182 2772 3.43645799019138e-10 56 1.62895101787588 1.81145880479492 1 3.11510385639089 2772 2141 2465 1509 56 4067 3677 2936 2803 2661 3361 2833 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 22/45 Reactome 9.11069269258851e-08 3.02570559585186e-07 2310 2601.63636363636 2773 8.28244824534795e-09 1200 1.28145180859854 1.07128345539471 1 2.14878741926656 2309 2875 2938 2609 1200 2773 1946 3306 2439 3346 2877 2834 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 149/389 Arthur Liberzon 1.0564461546945e-07 3.40475012441432e-07 2560 2886 2773 9.60405641295764e-09 1257 1.6054560203588 1.76753352594208 1 2.67092292051339 2556 3428 2773 1377 1257 4444 2605 4262 1942 3511 3591 2835 M175 PID_ERBB2_ERBB3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB2_ERBB3_PATHWAY.html ErbB2/ErbB3 signaling events 18832364 33/65 Pathway Interaction Database 6.75672184115151e-07 1.56510126285892e-06 3515 2666.81818181818 2775 6.14247628754723e-08 861 1.49544355340329 -0.756096325967382 -1 2.23308434532395 3511 2232 2775 861 1925 4045 3723 2104 1145 3710 3304 2836 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 26/59 John Newman 1.14362206544041e-05 1.97022536715211e-05 3825 2851.09090909091 2775 1.03966182759436e-06 1919 1.5901197612569 -1.75935821975121 -1 1.92456589529178 3825 2152 2436 2775 2626 3743 2841 2103 2944 1919 3998 2837 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 31/63 Pathway Interaction Database 3.25574654876621e-07 8.50742980221378e-07 2780 2702.54545454545 2776 2.95977002779935e-08 1472 1.33529977110867 -0.998796184122537 -1 2.08487746890475 2776 3125 2274 1472 1665 2721 2056 3185 3475 3216 3763 2838 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 34/77 Jessica Robertson 5.10917138671324e-08 2.00180410686775e-07 4635 2992.81818181818 2776 4.64470136851467e-09 934 1.44373570972755 -0.961735527420606 -1 2.48753383561347 4631 2379 2399 2776 934 2546 4528 3721 2956 2636 3415 2839 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 40/99 Jessica Robertson 6.18066415612926e-08 2.26447163687426e-07 2780 2731.09090909091 2777 5.61878575433492e-09 1036 1.36723081230942 -1.1916172402973 -1 2.33688658915605 2777 3090 2832 2700 1036 3793 2413 3033 2957 2729 2682 2840 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 8/46 Arthur Liberzon 0.000199266408515961 0.000285466949038763 2035 2665.81818181818 2779 1.99284278966993e-05 1257 2.39504967565061 2.86844224371202 1 2.18354080303905 2033 3542 4593 3289 4033 2779 1779 1257 1320 2891 1808 2841 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 50/154 Arthur Liberzon 1.78546056868563e-05 2.96690362583718e-05 2535 2810.81818181818 2781 1.62315914469629e-06 1875 1.42398900631751 -1.13668002279836 -1 1.65837439267913 2534 2831 2621 2781 2713 1875 2982 3837 3075 2771 2899 2842 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 66/193 Jessica Robertson 1.86101042477103e-07 5.35818834674208e-07 2605 2954 2782 1.69182780199681e-08 1472 1.7501250660607 1.95569781637256 1 2.82295072316725 2602 3820 2342 3928 1472 4395 2782 2437 2078 3206 3432 2843 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 525/1412 Arthur Liberzon 8.02016224804832e-07 1.81382626903255e-06 1710 2888.45454545455 2782 8.02016514258491e-08 926 1.25124960742994 -0.992958006571301 -1 1.84782451442461 1707 4414 4620 3536 2003 926 2320 2782 3353 4374 1738 2844 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 5/9 Arthur Liberzon 0.000113871519134381 0.000167746601277494 3055 2811.72727272727 2783 1.13877354580521e-05 1230 1.59635447583147 -1.93666133038175 -1 1.55018936968192 3052 1230 4123 2317 3074 3077 4655 2343 2783 1528 2747 2845 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 18/48 Arthur Liberzon 8.16245944360144e-07 1.84245110562217e-06 1565 2636.45454545455 2783 7.42042042913265e-08 426 2.98447002050345 2.98447002050345 1 4.40219548767733 1562 4302 2862 2783 4357 2477 1814 426 3025 3880 1513 2846 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 136/253 Jean Junior 2.88362057634778e-07 7.6951287134201e-07 4000 2658.72727272727 2784 2.62147359483141e-08 1569 1.52592312752603 -1.37532139871973 -1 2.39961409878459 3998 2294 2784 1569 1618 1635 3983 3359 2034 2843 3129 2847 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 12/18 Arthur Liberzon 4.6866925539096e-06 8.70120495547559e-06 3045 2531.09090909091 2785 4.26063867097261e-07 1512 1.14045091578763 -1.17493768070834 -1 1.48443723728087 3042 2031 2882 3235 2423 1512 2785 2844 2923 2147 2018 2848 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 37/95 Arthur Liberzon 6.16587141886204e-06 1.11427973269524e-05 2785 2838 2785 5.60535336347769e-07 2006 1.83170313962831 2.39251132958029 1 2.33357935031694 2785 3123 2006 2510 2490 4355 3000 2308 2293 2899 3449 2849 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 22/69 Yujin Hoshida 0.000125645798716155 0.000184222845051283 2355 2868.54545454545 2785 1.14229977398616e-05 1152 2.44664401057313 -2.44664401057313 -1 2.35028266999244 2351 3726 2785 3704 4652 1634 2626 1152 3531 3746 1647 2850 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 17/32 Arthur Liberzon 2.45060844692654e-06 4.85357192827462e-06 4145 2771.90909090909 2785 2.22782834245021e-07 575 1.56433501028479 -0.832601756923598 -1 2.1381833195948 4145 575 2476 1882 2274 2851 4649 4081 1037 2785 3736 2851 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 12/31 John Newman 2.6315143823433e-05 4.25509882527975e-05 4565 3154.81818181818 2786 2.39231441776627e-06 1276 1.90468778078023 -1.25418849542798 -1 2.14147113483717 4561 2632 2480 3937 2786 3611 4643 1276 1738 2751 4288 2852 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 33/70 Kevin Vogelsang 7.13369887555161e-06 1.27298221366469e-05 2245 3007.18181818182 2787 6.48520182483644e-07 2093 1.73547418173187 2.03795325641878 1 2.18517016619755 2245 4054 2599 4108 2523 4105 2676 2093 2787 2976 2913 2853 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 92/203 Reactome 2.94810552300207e-08 1.35972662212477e-07 2895 2484.45454545455 2788 2.68009596591645e-09 698 1.21212497545869 -0.938539012804175 -1 2.14084158060512 2895 905 3139 2069 698 1081 2788 4596 2298 3808 3052 2854 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 319/683 Arthur Liberzon 6.76484525358325e-07 1.56606891526335e-06 2210 2862.54545454545 2788 6.14986121247862e-08 1926 1.46971016376561 1.87251852906302 1 2.19455625479365 2206 3488 2415 2560 1926 4160 2908 2523 2788 3406 3108 2855 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 10/20 Reactome 2.69644046068842e-05 4.3540730526485e-05 2690 2936.27272727273 2789 2.45133955482386e-06 1960 1.83893678450795 1.83893678450795 1 2.06282277004832 2690 2395 2606 3740 2789 4122 2809 3481 1960 3183 2524 2856 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 143/312 John Newman 4.46532056604516e-07 1.10477783381666e-06 3640 2787.18181818182 2792 4.0593831566978e-08 1789 1.59012492648569 -1.38553104104205 -1 2.43633750607797 3637 3519 2618 2345 1789 2080 3613 2792 2907 2170 3189 2857 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 9/21 Yujin Hoshida 1.93962651313447e-07 5.55228456966897e-07 4120 2742.90909090909 2792 1.93962668243128e-08 553 1.28947235045098 0.76679597687415 1 2.07479250622414 4120 1290 4568 2321 1510 3885 2792 1980 553 3072 4081 2858 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 23/69 Arthur Liberzon 0.0234704980128542 0.0281429768905412 3410 2921 2792 0.00215679051884547 1217 2.04102632759331 2.68013394603415 1 0.814058011118211 3408 2697 1217 1436 3818 4440 4400 2361 2792 1323 4239 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 5/9 Arthur Liberzon 0.0396096956183406 0.0465423855736068 1935 3119.36363636364 2792 0.00403339493235794 1932 1.49136553795257 1.49136553795257 1 0.511017983173948 1932 2508 4660 4449 3769 2792 2466 2480 4189 2260 2808 2860 M19166 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_CHONDROITIN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_CHONDROITIN_SULFATE.html Glycosaminoglycan biosynthesis - chondroitin sulfate 9/24 KEGG 0.0231314199811981 0.0277434947611708 2030 3026 2793 0.00233757857656883 1580 1.67604294392116 2.01586532861384 1 0.67116198363171 2028 3865 3792 4267 3837 2733 1580 2793 2716 3043 2632 2861 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 52/150 John Newman 1.08835791402244e-05 1.87985447294845e-05 4345 3056.18181818182 2793 9.89421180231775e-07 1643 1.76192715040447 2.28053555585036 1 2.14175058817785 4344 3281 1643 1986 2612 3711 4476 2160 2793 1995 4617 2862 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 97/208 Jessica Robertson 5.65287246709709e-05 8.65948361582771e-05 1665 2563.63636363636 2793 5.13910702015722e-06 700 1.04580008070575 -0.833077007566914 -1 1.09280206025436 1662 2793 3678 3646 2941 700 1762 2272 3239 4158 1349 2863 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 44/91 Daniel Hollern 0.0457755285651115 0.0534523117009999 1180 2743.54545454545 2794 0.00425060777683161 1177 1.5123163008758 -1.57645533747889 -1 0.494811388441121 1177 3345 1319 3587 3784 2010 3472 2538 4365 1788 2794 2864 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 14/32 Jessica Robertson 2.77940326145009e-05 4.47108948958295e-05 3815 2916.90909090909 2796 2.52676216007499e-06 2169 1.333186018981 -1.40310130666929 -1 1.4915484441662 3815 3158 2519 3622 2796 2169 3244 2451 2639 3022 2651 2865 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 14/33 Arthur Liberzon 2.78610662039111e-05 4.47986122764764e-05 4355 2639.54545454545 2797 2.53285627691641e-06 206 1.62832179620455 -1.09224847125169 -1 1.82138544665293 4353 1351 1823 2109 2797 3664 4042 3058 206 2400 3232 2866 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 20/37 John Newman 0.000683049620700163 0.000924009966108823 3880 2883.63636363636 2797 6.21147076538334e-05 1576 1.82909286823776 -0.929653765640686 -1 1.42756614159906 3879 2237 1576 3464 3327 2797 3674 2265 1800 2601 4100 2867 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 15/27 Yujin Hoshida 1.53482995230119e-06 3.23100321495209e-06 2250 2591.81818181818 2800 1.39530093006938e-07 959 1.11204800463508 1.02630850378887 1 1.57053248333978 2246 959 2800 2213 2146 3264 2951 3243 2927 2561 3200 2868 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 5/11 Arthur Liberzon 1.98216513711832e-07 5.64645947266653e-07 1630 2705.09090909091 2800 1.98216531392238e-08 258 3.89176473827446 3.89176473827446 1 6.2546329567646 1630 4411 4638 3688 4586 2065 1295 258 2800 3303 1082 2869 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 30/67 Kolja Eppert 1.39986164077769e-08 8.5081084937539e-08 2005 2612.27272727273 2803 1.27260149971366e-09 392 1.46055239244773 1.33772852165837 1 2.65610638408533 2001 2803 2727 3682 392 2979 2010 3735 2347 3131 2928 2870 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 193/496 Leona Saunders 2.19360361890625e-08 1.12710817524065e-07 2670 2755.27272727273 2804 1.99418512798047e-09 572 1.47398757121591 -1.12743597995266 -1 2.63423451350319 2666 3170 2183 2386 572 4345 2804 2695 2934 3175 3378 2871 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 52/139 Arthur Liberzon 0.00147682887068182 0.00194121180589482 1810 2590.90909090909 2804 0.000134347379791061 1392 1.51485399857111 1.87493153690861 1 1.05668948588601 1810 3199 2449 3050 3659 2804 1841 1866 2879 3551 1392 2872 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 3/5 Arthur Liberzon 0.00941699879436113 0.0116371456620191 2575 2714.36363636364 2804 0.000945714437412979 770 1.4332001522711 1.4332001522711 1 0.713011196005562 2572 1646 4234 2536 3611 3149 2433 3187 770 2804 2916 2873 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 27/70 Jessica Robertson 4.91176321157461e-06 9.09743968752514e-06 4020 2996.72727272727 2804 4.46524925246173e-07 2072 1.73303902826718 -1.37847151695662 -1 2.2471426931974 4016 2804 2509 2462 2430 2415 3598 3953 2072 2849 3856 2874 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 23/51 BioCarta 2.83993059939487e-05 4.55750506464532e-05 3450 2784.90909090909 2806 2.58178841825802e-06 529 1.4722112519552 -1.24489379637535 -1 1.64393956064415 3448 1404 2321 529 2806 4660 3376 4007 1629 2419 4035 2875 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 477/1166 Jessica Robertson 2.38320660860246e-08 1.17678674055965e-07 2810 2650.36363636364 2806 2.1665514858356e-09 611 1.32561835581019 -1.01345982694078 -1 2.36268956576003 2806 1749 2994 2294 611 3253 3308 2742 2828 2704 3865 2876 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 23/56 Jessica Robertson 8.65829243940924e-08 2.90168792677926e-07 3415 2500.72727272727 2806 7.8711752546945e-09 1181 1.59378266626388 -1.37094040657514 -1 2.67996698673509 3414 1456 1841 2806 1181 1985 3593 4112 2821 1322 2977 2877 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 10/14 Arthur Liberzon 2.84702188137941e-05 4.56732096410268e-05 1575 2643.18181818182 2807 2.58823520489223e-06 1096 1.27906814079255 1.27906814079255 1 1.42795954505596 1573 2996 2743 3702 2807 1500 1096 4442 3613 3192 1411 2878 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 17/61 Jessica Robertson 7.74363145543953e-08 2.68420713822601e-07 2830 2877.45454545455 2807 7.03966520727492e-09 1128 1.35122390556507 1.21955523303005 1 2.28386061372872 2828 2199 2318 2807 1128 4175 3541 4438 2746 1810 3662 2879 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 3/12 Jessica Robertson 0.0143057042087239 0.0174211356346362 2595 2977.45454545455 2809 0.00143986412850094 1786 1.0605218207371 -1.0605218207371 -1 0.479805326955121 2593 3168 4333 3696 4020 1786 1889 2068 4180 2809 2210 2880 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 10/23 Jessica Robertson 5.38225378588066e-05 8.2665490791992e-05 3060 2693.27272727273 2809 4.89307769645371e-06 2037 1.45567299953437 -1.58638310677387 -1 1.52864747928627 3060 2037 2229 3045 2930 2305 3100 2406 3261 2444 2809 2881 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 16/63 Kevin Vogelsang 7.38644235877113e-05 0.000111223871764786 4010 3077.54545454545 2809 6.71517306208701e-06 1773 1.92864323609918 -1.48305452742611 -1 1.96139677189178 4007 1842 1773 2809 2991 2774 4612 4610 2065 2162 4208 2882 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 24/49 Pathway Interaction Database 2.85722033785687e-05 4.58054550229124e-05 3450 2929.18181818182 2810 2.59750676935954e-06 1789 1.38493831859155 -0.830867535631743 -1 1.54570637516557 3447 2622 2419 1789 2810 4646 3533 2169 2026 3030 3730 2883 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 39/156 John Newman 5.95021480554485e-08 2.20068718064587e-07 3625 2639.90909090909 2810 5.40928633316084e-09 1019 1.60980283601723 1.66537449990228 1 2.75663150178923 2470 1965 1190 2810 1019 3621 2892 4387 3634 1429 3622 2884 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 55/141 Jessica Robertson 1.31235856407087e-05 2.23220044690966e-05 2460 2878.18181818182 2811 1.19306035700404e-06 1862 1.28938007653511 1.39574325478884 1 1.54259115497771 2458 2061 2835 3422 2654 4020 1862 4138 3215 2184 2811 2885 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 22/78 Arthur Liberzon 0.00100673598825328 0.00134059813610539 2280 2583.27272727273 2812 9.1563361210459e-05 1472 1.91053181761825 2.42902660776803 1 1.41170314617139 2278 3350 1926 2812 4409 2970 1472 1524 3146 2838 1691 2886 M17902 BIOCARTA_CASPASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CASPASE_PATHWAY.html Caspase Cascade in Apoptosis 19/39 BioCarta 2.88511586109446e-05 4.62052389784301e-05 1855 2701.54545454545 2813 2.62286699788075e-06 1100 1.34044143575674 1.45548959156119 1 1.49474292571479 1855 4266 2920 4182 2813 1849 1100 1557 3570 3920 1685 2887 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 49/117 Kevin Vogelsang 4.40525546392646e-05 6.87871612927671e-05 1755 2786.54545454545 2813 4.00485788794862e-06 1751 1.62243511779572 1.9214387196088 1 1.7370785186857 1751 3589 2504 3369 2889 2998 2327 2813 2749 3388 2275 2888 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 60/154 Arthur Liberzon 5.63512036553346e-07 1.34177713581757e-06 2815 2939.81818181818 2814 5.12283800811276e-08 1869 1.63498652956943 1.83283232878669 1 2.46957667999714 2814 3225 2090 2613 1869 4620 3237 3409 2369 2548 3544 2889 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 43/78 John Newman 2.89438053373844e-05 4.63377764984569e-05 3820 2611.63636363636 2814 2.63128964882412e-06 1481 1.68473177185751 -0.962393017969741 -1 1.87812635611124 3816 2456 2282 1746 2814 1687 3051 3125 1481 3356 2914 2890 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 3/13 Jessica Robertson 0.00608942189427235 0.00761746689710631 1985 2875.81818181818 2814 0.000610617300992243 1418 1.57792514413848 1.57792514413848 1 0.859705635050991 1982 3550 4536 3624 4616 1856 1418 1889 3330 2814 2019 2891 M1886 CHAN_INTERFERON_PRODUCING_DENDRITIC_CELL http://www.broadinstitute.org/gsea/msigdb/cards/CHAN_INTERFERON_PRODUCING_DENDRITIC_CELL.html Genes up-regulated in spleen interferon-producing dendritic cells (IKDC) compared to plasmacytoid dendritic cells (PDC) and conventional dendritic cells (cDC). 16444266 3/24 Jessica Robertson 0.000437930394977549 0.000600920009038007 1420 2691 2815 4.38016721285503e-05 751 1.13280397110321 1.13280397110321 1 0.938574599397546 1416 2926 4538 3806 3308 1409 751 2513 4313 2815 1806 2892 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 3/18 Jessica Robertson 2.36736859217935e-05 3.85639053044594e-05 2680 2641.09090909091 2816 2.36739381251072e-06 30 5.81869432397637 5.81869432397637 1 6.60600255089437 3033 3002 4544 2082 3904 3381 2679 903 30 2816 2678 2893 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 3/10 Jessica Robertson 0.0591808712934334 0.068440662112791 2435 3174.63636363636 2818 0.00608186708115067 2037 1.59486697271216 -1.59486697271216 -1 0.477784150987669 2431 3192 4578 4394 4120 2037 2316 2409 4284 2818 2342 2894 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 16/32 Leona Saunders 2.62557375599476e-07 7.12416828059726e-07 4400 2946.90909090909 2820 2.38688551758361e-08 848 1.15330824571124 -1.30695892231851 -1 1.82358507656729 4399 848 2532 2600 1587 3929 3576 2820 2908 2657 4560 2895 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 15/38 Arthur Liberzon 0.000570318812677947 0.000777119498752212 2825 2643.27272727273 2821 5.18606103114261e-05 1011 1.6368691710854 2.10597055970773 1 1.30919654902059 2821 1064 2203 3864 3609 4177 3092 1413 1011 3161 2661 2896 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 8/22 Arthur Liberzon 0.0122839080368247 0.015056864520157 2825 3061.54545454545 2822 0.00123523435337982 1418 0.682023106312868 -0.682023106312868 -1 0.319675335952178 2822 2573 4540 3424 4209 1418 2078 2345 3728 4651 1889 2897 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 12/83 Arthur Liberzon 0.00378427088098341 0.00482008517213597 2640 3063.90909090909 2823 0.000344617819264008 2070 2.81362918808129 2.6646762767208 1 1.67680002971243 2823 4355 2070 3678 3515 3421 2324 3486 2636 2755 2640 2898 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 3/9 Arthur Liberzon 4.54292296524144e-08 1.8351842254415e-07 4180 2672.81818181818 2823 4.54292305811311e-09 922 1.40577876156398 -2.14189533648495 -1 2.43578168079496 4179 1368 4673 1566 922 4354 4210 1076 1391 2823 2839 2899 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 97/204 Jessica Robertson 3.13136859682451e-07 8.25750886028117e-07 2825 2724.72727272727 2824 2.84669912957067e-08 1224 1.57101681506058 1.60822155409749 1 2.45814828932178 2824 3246 1751 2618 1644 4097 3026 3490 2397 1224 3655 2900 M11911 KEGG_ABC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ABC_TRANSPORTERS.html ABC transporters 17/50 KEGG 3.13698712080279e-05 5.00167459955151e-05 3960 2793.63636363636 2825 2.85184713826968e-06 610 2.21038840456919 2.74169463437263 1 2.44525993094692 3957 2388 1638 1115 2825 4080 4226 4542 610 1406 3943 2901 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 13/51 Reactome 2.46242831276956e-06 4.87286278447558e-06 2455 2459.72727272727 2825 2.2385736990313e-07 572 1.74257102246259 -1.74257102246259 -1 2.38102989779737 2452 3266 2737 2825 3116 1434 3189 572 3212 2909 1345 2902 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 7/26 Arthur Liberzon 0.00122820063275937 0.0016244279325742 2585 2906.45454545455 2825 0.000122887997581039 1919 2.71105788006271 2.71105788006271 1 1.94505814352716 2582 2574 4681 3166 3408 2825 1919 2208 2964 2696 2948 2903 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 13/36 Reactome 2.46242831276956e-06 4.87286278447558e-06 2455 2460.72727272727 2826 2.2385736990313e-07 573 1.74257102246259 -1.74257102246259 -1 2.38102989779737 2453 3267 2738 2826 3117 1435 3190 573 3213 2910 1346 2904 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 9/35 Reactome 3.5628978641446e-05 5.62904227625813e-05 1370 2313.09090909091 2828 3.56295498951899e-06 673 1.54430428091604 1.54430428091604 1 1.68801396837562 1369 3304 4018 2828 3670 872 673 1470 3439 3051 750 2905 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 81/195 Kate Stafford 4.74348319120653e-08 1.89769579972418e-07 2440 2569.45454545455 2828 4.31225753952922e-09 900 1.94025869318869 2.17768047636333 1 3.35461100579549 2437 3248 2000 1058 900 4488 3257 2948 1671 3429 2828 2906 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 14/23 Arthur Liberzon 0.0106843392155639 0.0131652833115252 1980 2962.90909090909 2828 0.000976053041959174 1343 1.46278546136487 1.65344437304571 1 0.707568757808356 1976 3900 2828 4235 4594 2062 1343 2384 4013 3023 2234 2907 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 8/26 Reactome 1.08062165292566e-07 3.46123927929571e-07 4680 2708.54545454545 2832 1.0806217054741e-08 976 1.93940287606491 -1.48802277055406 -1 3.22292995747615 4676 1074 4032 1449 1314 4680 3765 2832 976 1062 3934 2908 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 18/51 John Newman 2.1124689984417e-06 4.26131283973217e-06 2020 3018.27272727273 2835 1.92042820624092e-07 2018 0.837679262205542 0.940342922046133 1 1.1571444665984 2018 2744 3094 4291 2236 2835 2203 3283 4053 3879 2565 2909 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 29/64 Arthur Liberzon 3.24046844237865e-05 5.14740173592758e-05 4355 2975.09090909091 2836 2.94592379411392e-06 1475 1.61809893282476 -1.22411430044654 -1 1.78484375802131 4351 2485 1475 2288 2836 3372 4619 2703 2909 1550 4138 2910 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 40/115 Jessica Robertson 1.17403079507792e-05 2.01594294823566e-05 3480 2833.36363636364 2836 1.06730641849482e-06 1054 1.78601175804473 2.23467691969302 1 2.15708280882092 3479 2587 1291 2252 2633 4630 3278 2836 2922 1054 4205 2911 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 28/87 Jessica Robertson 1.13846666279166e-06 2.48017423609564e-06 3575 2879.54545454545 2837 1.03497022902848e-07 1434 1.97937594684715 1.87867524663711 1 2.85392582775577 3571 1973 1766 3111 2066 4254 2837 4213 2187 1434 4263 2912 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 59/133 Pathway Interaction Database 5.55049657596101e-08 2.11494269972596e-07 2905 2805.81818181818 2838 5.0459061054522e-09 970 1.21286972847948 1.20116332766305 1 2.08230644329948 2901 2727 2838 1408 970 3359 2175 3618 3515 2757 4596 2913 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 30/55 John Newman 5.40053374392743e-10 6.71270586844667e-09 3585 2823.09090909091 2838 4.90957613204833e-11 2 1.68055384526001 1.8902000014368 1 3.53295441697412 3583 2838 2145 1940 2 4649 3172 3396 2750 1913 4666 2914 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 19/45 Reactome 0.0219251594233002 0.0263371692021493 1850 2695.45454545455 2839 0.00201334211753293 1420 1.28905274832982 -1.04759854789961 -1 0.523684636705354 1850 2950 3035 2334 3717 1420 2054 2839 3802 3541 2108 2915 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 22/47 Arthur Liberzon 1.01059807378069e-06 2.23064652554702e-06 4035 2959.90909090909 2842 9.18725943647375e-08 868 1.83499667625774 -1.09467330062666 -1 2.66749116333484 4032 2842 2325 2355 2037 2989 4669 4591 868 2840 3011 2916 M64 PID_S1P_S1P4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P4_PATHWAY.html S1P4 pathway 18832364 7/18 Pathway Interaction Database 0.0151035126165389 0.0183497692821108 3015 2916 2843 0.00152071576649097 1529 2.53204610565318 -2.53204610565318 -1 1.13086910195021 3011 3838 3895 2670 3666 2393 2843 2243 1529 3575 2413 2917 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 44/89 Arthur Liberzon 5.57108141298268e-07 1.32923052450289e-06 2970 2936.63636363636 2843 5.06462074886686e-08 1862 1.2795604582219 -1.18973833237757 -1 1.93406372524364 2967 3611 2740 2772 1862 2215 3388 3628 2843 3695 2582 2918 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 411/981 Arthur Liberzon 9.41852602886401e-08 3.09938293337477e-07 2995 2334.81818181818 2844 8.56229675644098e-09 335 1.42259317920909 -1.28255093114704 -1 2.38163541190506 2995 3194 3027 2872 1215 335 2866 2357 2784 2844 1194 2919 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 134/307 Arthur Liberzon 7.97919867295344e-08 2.74007659779163e-07 4635 2963.36363636364 2845 7.25381723850154e-09 1145 1.32720070022518 -0.999057895085049 -1 2.24020200081565 4633 1604 3059 2661 1145 2257 4464 3783 2845 2552 3594 2920 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 12/44 Kevin Vogelsang 0.000198694898263028 0.000284735257877844 4425 3015.72727272727 2845 1.80648041666891e-05 1012 1.91480949937582 -1.4431392246559 -1 1.74625995833532 4421 2277 2074 2845 3146 2383 3928 4600 1012 2750 3737 2921 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 45/128 John Newman 0.00309264178465452 0.00395851390409481 1915 2769.18181818182 2846 0.00028154525723639 1836 1.66117375301107 1.68546164142525 1 1.02652903923623 1911 2657 1836 3356 3495 3693 2846 2130 3237 2415 2885 2922 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 46/116 Arthur Liberzon 0.000126304227442391 0.000185014570114113 4415 3104.72727272727 2847 1.14828617526222e-05 2161 1.51803116591494 -1.53320586050901 -1 1.45751604684162 4413 3013 2161 3803 3077 2577 4682 2306 2573 2847 2700 2923 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 13/37 Arthur Liberzon 0.00398819766632758 0.00506880777445376 2705 3062.63636363636 2848 0.000363222358339982 2518 1.09399817185665 1.02435157902394 1 0.645826190515594 2702 2598 2518 4089 3521 2848 2630 2831 3733 2914 3305 2924 M242 PID_AURORA_A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AURORA_A_PATHWAY.html Aurora A signaling 18832364 26/47 Pathway Interaction Database 2.3441867020515e-06 4.67639799310911e-06 2160 2734.36363636364 2849 2.13108109079867e-07 649 1.16817974039757 1.4956485913496 1 1.60155819571941 2158 3653 2931 4050 2260 3178 2049 649 2197 4104 2849 2925 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 10/14 Leona Saunders 8.44767858963144e-07 1.89769040608883e-06 3475 3074.81818181818 2849 7.67971075765305e-08 1610 1.40674449787342 1.16169421833624 1 2.07035403920757 3473 2849 2513 1610 1991 4516 2758 3336 3741 2443 4593 2926 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 9/23 Reactome 3.33121821779786e-05 5.28439017217358e-05 3510 2809.18181818182 2850 3.3312681554181e-06 508 1.90815420028888 -1.53789415792912 -1 2.09919064961256 3510 3241 3977 1457 2850 4502 2486 3411 508 2299 2660 2927 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 4/25 Jessica Robertson 0.000493333654484545 0.000674769849653993 2485 2865.54545454545 2850 4.93443208858363e-05 1522 2.28835566352079 2.28835566352079 1 1.8663671665624 2481 3046 4350 4209 3300 2200 1522 2618 2850 3107 1838 2928 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 16/41 Arthur Liberzon 2.56696967648753e-05 4.1550327820451e-05 3620 2859.72727272727 2851 2.33363602590172e-06 411 1.3191125413905 -0.778355195575413 -1 1.48660610590734 3616 1581 2682 1804 2780 3839 4575 4073 411 3245 2851 2929 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 51/156 Reactome 4.70990783019825e-08 1.89447451436129e-07 2270 2787.27272727273 2853 4.28173448275558e-09 896 1.27387535179532 1.32272881292511 1 2.20270895910128 2266 2902 2712 3184 896 3328 2417 3857 2835 2853 3410 2930 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 9/34 Reactome 0.00168504880271585 0.00220562533226996 1210 2402.45454545455 2854 0.000168632789322957 1105 1.39838784027699 1.39838784027699 1 0.955500375548775 1208 3077 4020 3188 3556 1122 1105 1805 2854 3052 1440 2931 M2333 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION.html Pathogenic Escherichia coli infection 52/116 KEGG 1.05508848858254e-06 2.30819078314557e-06 4525 2622.36363636364 2855 9.5917181326201e-08 862 2.17342439935261 -1.70981591133418 -1 3.15115887100529 4521 2939 1589 862 2057 3230 3563 3942 965 2323 2855 2932 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 6/14 Reactome 0.00257978295436678 0.00332202883324066 2730 3082.90909090909 2855 0.000258278273279424 1759 0.568192156212718 -0.568192156212718 -1 0.362242595774375 2726 2855 4080 2431 3482 1759 2539 3163 4519 4512 1846 2933 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 4/16 Leona Saunders 0.000599170675906158 0.000814774749650684 2350 2996 2855 5.99332289712378e-05 2348 1.09985950447488 1.09985950447488 1 0.873873203983334 2348 2540 4281 2896 3321 2855 2437 2765 3935 3104 2474 2934 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 11/40 Leona Saunders 2.91494295331869e-06 5.69142611635474e-06 2855 2845.27272727273 2855 2.64995165049971e-07 1975 1.23073565958685 1.15719086328063 1 1.66031542226946 2855 2500 2280 3002 2308 3468 3274 2593 3316 1975 3727 2935 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 4/12 Yujin Hoshida 1.67590239173452e-08 9.43903678806246e-08 3995 2326.45454545455 2856 1.67590240437344e-09 19 1.1948175887567 -1.03864312378156 -1 2.15899209888314 3994 248 4377 762 512 4484 2917 2856 19 1274 4148 2936 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 17/40 Jessica Robertson 0.000894499720756118 0.00119555781273907 2055 2577.27272727273 2856 8.13512384779308e-05 1275 1.3927182555177 1.53566831136157 1 1.04690168761316 2051 2952 2865 3001 4337 2926 1678 2185 2856 2224 1275 2937 M3061 BIOCARTA_FEEDER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FEEDER_PATHWAY.html Feeder Pathways for Glycolysis 6/15 BioCarta 5.01829290131938e-05 7.75584450382013e-05 2860 2566.72727272727 2857 5.01840622960765e-06 397 2.36065660156068 -0.741454967134874 -1 2.49581552022595 2857 3310 3835 2490 2933 3407 2179 1555 397 3431 1840 2938 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. 32/73 Signaling Transduction KE 5.42072283362643e-06 9.9263412264062e-06 2865 2777.36363636364 2857 4.92794199103949e-07 1505 1.88526050678703 -1.82882062837316 -1 2.42615655830981 2863 3321 2448 1505 2453 3804 2654 3060 1507 2857 4079 2939 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 11/19 Leona Saunders 1.70744922426001e-05 2.85256180963288e-05 2720 2896.54545454545 2857 1.55223861467658e-06 1922 0.861639017579721 -0.873840597478686 -1 1.00724560170006 2718 2208 3393 2857 2703 1922 3089 3138 3374 3900 2560 2940 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 73/172 John Newman 0.0010658781004605 0.00141493053222603 2400 2962.27272727273 2857 9.69449871212462e-05 930 2.09739867034412 2.76705814713432 1 1.53713652587013 2396 3401 930 1914 3835 4632 4017 2822 2857 2197 3584 2941 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 33/57 Leona Saunders 1.37488918201764e-07 4.19175712877986e-07 2860 2587.27272727273 2858 1.24989933449208e-08 1360 1.91233545428905 -1.23945167581943 -1 3.13704160307636 2858 3718 1560 4144 1360 3184 2170 1416 3118 1844 3088 2942 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 3/7 Leona Saunders 0.00578602110922541 0.00724760623304739 2580 2971 2858 0.00058011416658055 1550 1.90010720726427 -0.702978853181996 -1 1.04580565780725 2580 1550 4435 1969 3573 2858 2955 3236 4169 2811 2545 2943 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 4/14 Reactome 1.4067704774049e-05 2.37811199751781e-05 2860 2863 2859 1.40677938299854e-06 828 3.73296295246194 -3.73296295246194 -1 4.43964612325566 2859 4136 4045 4393 4198 1825 1891 828 2407 3095 1816 2944 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 9/39 Reactome 0.000238560948586953 0.000338244055999534 4095 2881.72727272727 2860 2.38586562553802e-05 1671 1.4745098586229 1.69867002515411 1 1.31635222721146 2133 3634 4093 4095 3195 2299 2275 2305 3139 1671 2860 2945 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 10/24 Arthur Liberzon 4.77599965141078e-06 8.8599898521421e-06 2505 2675.63636363636 2861 4.34182729063873e-07 129 5.81869432397637 5.81869432397637 1 7.56199318614022 2502 4571 2505 3195 3994 3142 2022 663 129 3848 2861 2946 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 57/156 Arthur Liberzon 8.81090056149072e-07 1.96984160453939e-06 4680 3091.18181818182 2862 8.00991280928959e-08 2002 1.34214413562951 -1.27111012763242 -1 1.9696848242107 4677 2611 2531 3945 2002 2433 3989 3270 2862 2627 3056 2947 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 19/37 Yujin Hoshida 2.84052259604588e-07 7.61045676676443e-07 2620 2841.36363636364 2863 2.5822936025446e-08 1466 1.26547471478951 1.14416004311913 1 1.99160595385528 2616 1466 2900 2471 1611 3633 2863 4478 3326 2505 3386 2948 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 42/126 Arthur Liberzon 0.0043208212035778 0.0054737410543297 1770 2612.90909090909 2863 0.000393575522293451 1406 1.37817686283292 1.38570555275999 1 0.801754766970925 1768 2834 2863 3183 3799 1406 1463 3583 3283 2931 1629 2949 M9503 BIOCARTA_FAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FAS_PATHWAY.html FAS signaling pathway ( CD95 ) 17/35 BioCarta 4.6455602649311e-06 8.64195927013384e-06 3810 2994.90909090909 2864 4.22324552237289e-07 2286 1.23325618295572 -0.667817596392549 -1 1.60617596399093 3810 2495 2841 2864 2418 2286 3491 3209 2331 3812 3387 2950 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 81/163 Arthur Liberzon 2.01548960188672e-06 4.08326168371861e-06 3845 3037 2864 1.83226495303898e-07 1475 1.52490677716203 -1.27159811394158 -1 2.1137301500263 3844 2864 1676 1475 2229 3722 4344 3940 2736 1951 4626 2951 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 73/169 John Newman 7.60679136602379e-07 1.72952083169275e-06 3685 2981.81818181818 2865 6.91526726924903e-08 1962 1.63006199502891 1.65622919059367 1 2.41591482873522 3685 2865 2388 2138 1970 4076 3224 3803 2735 1962 3954 2952 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 13/152 Jessica Robertson 5.91735817235873e-05 9.03510602661226e-05 2870 2907.54545454545 2866 5.3795612163853e-06 1780 1.37708976950319 1.5844644952853 1 1.43244907496802 2866 3035 2485 4493 2955 3182 2107 2607 3725 1780 2748 2953 M1467 BIOCARTA_CTLA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTLA4_PATHWAY.html The Co-Stimulatory Signal During T-cell Activation 8/29 BioCarta 0.000248015857840864 0.0003509064945176 2870 2357.63636363636 2867 2.48043542529166e-05 676 1.8570979502901 1.8570979502901 1 1.65027923428852 1541 3162 3880 2867 3296 990 676 1462 3580 2867 1613 2954 M5374 BIOCARTA_SARS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SARS_PATHWAY.html The SARS-coronavirus Life Cycle 8/14 BioCarta 0.00856107421327021 0.010610207289972 3950 2994.90909090909 2868 0.000859423555250457 1316 1.56335386190999 1.56335386190999 1 0.793896263950951 2060 3705 3881 3948 4057 2288 1316 2546 3948 2868 2327 2955 M264 PID_TOLL_ENDOGENOUS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TOLL_ENDOGENOUS_PATHWAY.html Endogenous TLR signaling 18832364 20/47 Pathway Interaction Database 0.000254717769207091 0.000359737030290666 3835 2997 2868 2.31588423105904e-05 1916 1.77187360516393 -1.13929534009419 -1 1.56962672599597 3835 3534 2425 2134 3184 2459 3616 4398 1916 2598 2868 2956 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 3/9 Leona Saunders 0.000281893016377912 0.000395731178773786 2870 2800 2868 2.81928781415997e-05 1319 0.82547704454513 -0.82547704454513 -1 0.722461028090422 2868 1371 4279 3477 4448 1361 2093 1319 3499 4586 1499 2957 M12 PID_RHOA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHOA_PATHWAY.html RhoA signaling pathway 18832364 31/67 Pathway Interaction Database 1.26621852438e-06 2.72054103862662e-06 3055 2514.27272727273 2869 1.15110841196142e-07 996 2.21009009781891 -1.68007825355965 -1 3.16373943902374 3055 2869 1483 1737 2091 3998 2997 3550 996 1989 2892 2958 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 102/353 Jessica Robertson 7.58250162564947e-07 1.7256727837685e-06 3945 3163.54545454545 2872 6.89318567184491e-08 1761 1.46492749117023 -1.3909464137389 -1 2.17153346428756 3943 4375 2759 4498 1969 1761 3900 3377 2872 2773 2572 2959 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 27/127 Jessica Robertson 1.65097838374133e-06 3.43691013159123e-06 4285 3037.72727272727 2872 1.50089056610058e-07 984 2.77869914320112 -2.6969178861815 -1 3.90514816399558 4282 2872 984 2635 2170 4577 3712 3977 2243 1653 4310 2960 M980 KEGG_TRYPTOPHAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TRYPTOPHAN_METABOLISM.html Tryptophan metabolism 16/53 KEGG 0.000181991226514468 0.000262564928401108 2925 2529.18181818182 2873 1.65460257427551e-05 1467 2.1416141040277 -1.83123569468545 -1 1.97249300756802 2922 2316 1467 2992 3128 1597 3063 3019 2873 2155 2289 2961 M18607 REACTOME_STEROID_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_STEROID_HORMONES.html Genes involved in Steroid hormones 10/44 Reactome 0.000369702366582619 0.000511492556777724 1725 2705 2873 3.36149553093499e-05 718 1.30300956275443 1.30300956275443 1 1.10305024178975 1722 4132 2873 4153 4406 1339 718 1960 3874 3181 1397 2962 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 71/169 Arthur Liberzon 3.27229354145426e-07 8.54260029819202e-07 3850 2852.27272727273 2873 2.97481275288847e-08 1124 1.4562322088095 -1.18259328356327 -1 2.27302488333427 3847 2690 2064 3018 1668 2432 3721 4678 3260 1124 2873 2963 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 356/869 Leona Saunders 6.33902399679583e-06 1.14248717111482e-05 2550 3144.90909090909 2873 5.76276569270171e-07 2334 1.66492655673209 2.11576183481475 1 2.11645740084436 2548 4518 2334 3322 2499 4169 2873 2360 2802 3665 3504 2964 M3812 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS.html Amyotrophic lateral sclerosis (ALS) 28/69 KEGG 4.13138772198911e-05 6.47697653571127e-05 3885 3119.72727272727 2874 3.7558775522763e-06 1842 1.61706223062378 -1.41180512210385 -1 1.74219646211668 3885 2769 2300 2219 2874 4400 3752 3593 1842 2511 4172 2965 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 8/35 BioCarta 7.93724978738792e-06 1.40513609760861e-05 4185 3039.09090909091 2875 7.93727813750082e-07 733 1.14601522663969 -0.568192156212718 -1 1.43032592422431 4184 733 3868 1741 2563 3841 4157 2875 1934 2864 4670 2966 M599 ST_PAC1_RECEPTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_PAC1_RECEPTOR_PATHWAY.html PAC1 Receptor Pathway 4/9 Signaling Transduction KE 8.91633889113037e-06 1.5648675671849e-05 3960 2815.72727272727 2875 8.91637466682706e-07 963 1.68907130294759 -2.33341055335211 -1 2.08779202869681 3958 1365 3889 2943 2589 2875 4586 2264 963 2038 3503 2967 M18933 BIOCARTA_TGFB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TGFB_PATHWAY.html TGF beta signaling pathway 13/26 BioCarta 4.2263662143341e-05 6.62144837190558e-05 3865 2859.09090909091 2877 3.84222491655082e-06 460 1.63077505929214 2.28088817069255 1 1.75295171217328 3865 2166 2510 2668 2877 3932 3862 1974 460 3520 3616 2968 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 8/45 Reactome 1.25543809292944e-05 2.14394420680298e-05 1880 2963.36363636364 2877 1.25544518554746e-06 803 2.51901949649299 2.51901949649299 1 3.0250614679132 1879 4231 4000 4455 4428 2541 2494 803 2885 2877 2004 2969 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 43/136 Kate Stafford 3.95509693074558e-07 9.98576735855269e-07 4070 2896 2878 3.59554331071068e-08 1746 1.41828130242846 -1.22726887226869 -1 2.18905687338956 4070 1882 2815 2419 1746 2211 4021 3093 2878 3355 3366 2970 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 7/17 Jessica Robertson 0.000669463323422794 0.00090641581437712 2880 2703.90909090909 2879 6.69665090489591e-05 616 3.02067525646586 3.27803121667969 1 2.3640567683983 2879 3543 4342 2402 3337 3237 2332 3116 616 1936 2003 2971 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 6/14 Kevin Vogelsang 0.000279909924159138 0.000393182825122818 2170 2944.54545454545 2879 2.7994518771523e-05 1462 0.86801925374003 0.86801925374003 1 0.760320593873829 2167 2041 4387 3681 3221 2746 1462 2879 4255 3453 2098 2972 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 16/41 Leona Saunders 2.73291175242767e-05 4.40537477532716e-05 4040 3149.54545454545 2881 2.48449609285384e-06 1136 2.25707798727393 -2.28477929531366 -1 2.52891829131424 4039 2881 1136 2859 2792 4588 3948 3959 2478 1301 4664 2973 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 13/29 Reactome 0.000167410100151518 0.000242124607811733 1155 2373.63636363636 2884 1.52202582421928e-05 870 1.06202955627937 -1.06202955627937 -1 0.987777080038038 1154 2884 3028 3003 3120 870 1539 1521 3828 3527 1636 2974 M3721 ST_JNK_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_JNK_MAPK_PATHWAY.html JNK MAPK Pathway 29/52 Signaling Transduction KE 2.36077508782955e-06 4.70548365017833e-06 3660 3041.72727272727 2885 2.14616147375718e-07 1731 1.61787868635759 -1.1226862103811 -1 2.21696868910821 3657 3498 2885 2676 2262 4430 2565 1766 1731 3465 4524 2975 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 13/18 Reactome 5.15140665286494e-06 9.492525196746e-06 2790 2893.27272727273 2887 4.68310792288444e-07 1455 0.914447900242698 -0.863380363541572 -1 1.18137492155127 2790 2887 3479 4401 2444 1455 1656 2961 3996 3521 2236 2976 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 8/17 Reactome 9.31745689078165e-08 3.07476077395795e-07 3300 2514.54545454545 2887 9.31745728144917e-09 597 0.788859417927847 -0.840305854871636 -1 1.3213723292947 3297 597 3954 2076 1246 1902 3322 2894 2887 3676 1809 2977 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 139/298 Arthur Liberzon 5.13373058622289e-07 1.23939523580837e-06 3025 2937.81818181818 2887 4.66702889471496e-08 1836 1.41483996683956 1.8168519099487 1 2.14959928758768 3024 2293 2887 2130 1836 3640 3760 2711 2747 3799 3489 2978 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 21/66 John Newman 1.36449696236363e-06 2.90637852983453e-06 3640 2799 2887 1.24045255332792e-07 1298 2.04724065861547 2.54731837337323 1 2.91550946197902 3640 2667 1298 2126 2118 4189 3383 2887 3008 1460 4013 2979 M6267 ZAIDI_OSTEOBLAST_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/ZAIDI_OSTEOBLAST_TRANSCRIPTION_FACTORS.html An assortment of osteoblast transcriptional regulators. 17618270 8/16 Jessica Robertson 0.00579102223342764 0.00725193217152377 3575 3078.36363636364 2890 0.00058061689882928 1915 1.2866703384641 1.2866703384641 1 0.708088481638083 2491 3511 4524 3574 3574 2745 1915 2216 4200 2890 2222 2980 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 7/18 Arthur Liberzon 2.49958235194045e-06 4.93804506795656e-06 4010 2636.27272727273 2891 2.49958516350527e-07 200 2.64487765199816 -2.02731965225982 -1 3.61000591721478 4009 1422 4111 1797 2294 2891 3888 2998 200 1931 3458 2981 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 93/241 Arthur Liberzon 0.011642856711136 0.0143010292394189 3620 2676 2891 0.00106408486805452 1073 1.73927667019692 2.03786836865115 1 0.825234076079626 1073 3620 1149 1743 3753 3616 2914 3529 2891 2341 2807 2982 M1462 BIOCARTA_CTL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTL_PATHWAY.html CTL mediated immune response against target cells 20/57 BioCarta 0.00368513570354485 0.00469636820963045 2895 2974.27272727273 2892 0.000335574822535213 2305 1.58894115192199 1.98558443864654 1 0.951554685076166 2892 2878 2349 2305 3513 4011 2921 2568 3390 2596 3294 2983 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 26/64 Leona Saunders 4.53101715736609e-05 7.06332215549485e-05 4540 2695.72727272727 2892 4.11919134433471e-06 785 2.42751844253716 -1.79050720817204 -1 2.59186860825206 4536 2460 785 1204 2892 3236 3949 3432 1662 858 4639 2984 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 16/29 Arthur Liberzon 2.99079797724836e-05 4.77997248341945e-05 4075 3350.18181818182 2892 2.71894421503068e-06 2563 1.3162221327239 1.49683721255523 1 1.46274736233396 4075 2844 2563 2892 2819 4279 4351 2706 3202 2658 4463 2985 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 95/237 Yujin Hoshida 2.97646441278828e-08 1.36608347094279e-07 2895 3021.72727272727 2893 2.70587677550729e-09 707 1.5626192187073 1.95735524330089 1 2.75906648990633 2727 4147 2893 2624 707 4648 3097 3501 2892 2417 3586 2986 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 56/188 KEGG 7.65067134616564e-06 1.35953909473387e-05 3140 2889.81818181818 2894 6.95517995645514e-07 1749 1.47126666078539 -1.10572209183997 -1 1.84168955548336 3136 3087 2284 1749 2535 4495 2918 2327 2806 2894 3557 2987 M18155 KEGG_INSULIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INSULIN_SIGNALING_PATHWAY.html Insulin signaling pathway 60/174 KEGG 3.43931846536436e-07 8.91407429684591e-07 2345 2606 2895 3.12665363912934e-08 1023 1.18018260521469 1.30540286349836 1 1.83652882470713 2342 1023 3101 1302 1689 4226 3194 2895 2115 3403 3376 2988 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 14/22 Reactome 0.00204549115790509 0.00265738052840124 1740 2941.18181818182 2895 0.000186126860985158 1738 1.34183922335154 -1.34183922335154 -1 0.888931755362673 1738 3998 2895 4294 3449 1782 2362 2550 4213 3011 2061 2989 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 99/226 Jessica Robertson 1.89636509786744e-05 3.14450348499888e-05 4425 3372.81818181818 2895 1.72398313130091e-06 2702 1.6933461737353 1.94050594116716 1 1.96106997595411 2928 4425 2825 4425 2719 4668 2702 2817 2757 2895 3940 2990 M278 PID_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAC1_PATHWAY.html RAC1 signaling pathway 18832364 37/83 Pathway Interaction Database 1.68037894971564e-06 3.48418396387941e-06 4515 2938.18181818182 2897 1.52761839382266e-07 1704 1.34190485389791 -1.01943101880598 -1 1.88384797338652 4515 2065 2802 2422 2175 3418 3131 3980 1704 2897 3211 2991 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 4/9 Arthur Liberzon 0.0115056291737423 0.0141398841615936 2500 2912.90909090909 2897 0.00115656376899179 1874 1.90268925636182 1.90268925636182 1 0.90517698508617 2500 2787 4268 3355 3702 2897 2191 3457 1909 3102 1874 2992 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 40/100 Kate Stafford 2.63062336701109e-05 4.25509882527975e-05 4535 2979.72727272727 2897 2.39150438445284e-06 1763 1.40292067889578 -0.984904765978064 -1 1.57732624814621 4531 1763 1997 2946 2785 2695 4349 3013 2676 3125 2897 2993 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 17/30 Pathway Interaction Database 0.000212448077655327 0.000303700943225401 2430 2703 2898 1.93153269062084e-05 1153 1.79874424232927 2.2325160850876 1 1.6274543104034 2426 3384 2343 3227 3698 3627 2898 1252 1153 2779 2946 2994 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 17/37 Arthur Liberzon 8.3126411275935e-07 1.86914761631013e-06 3605 2825.63636363636 2899 7.55694933500397e-08 163 1.6688147239926 -1.10402136693391 -1 2.45887700117993 3601 3295 2614 1553 1989 4564 2899 3290 163 2786 4328 2995 M290 PID_IL12_STAT4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL12_STAT4_PATHWAY.html IL12 signaling mediated by STAT4 18832364 16/40 Pathway Interaction Database 7.69811438473947e-06 1.36693308097344e-05 4495 3343.09090909091 2900 6.99831029243066e-07 2158 1.50747727999201 -1.34846188832545 -1 1.88610361804672 4494 2527 2362 2293 2537 3715 4570 4586 2900 2158 4632 2996 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 9/21 Reactome 0.00114519341801767 0.00151678246377355 2390 2889.81818181818 2900 0.000114578400699455 2153 1.26007990414833 0.980720086498354 1 0.913699874832655 2388 2675 3994 3006 3403 2805 2153 2471 2943 3050 2900 2997 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 6/46 Arthur Liberzon 0.0001811051674373 0.000261447570736657 2830 2822.09090909091 2900 1.81119928717199e-05 1199 1.35354029514855 1.59994109373172 1 1.24729732591648 2827 1487 4640 2530 3147 3327 2905 2900 1199 3461 2620 2998 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 61/165 Reactome 4.96752708908896e-08 1.96578530164298e-07 2815 2862.63636363636 2901 4.51593381932189e-09 918 1.18511626610461 1.16563191336076 1 2.0443403242179 2811 1874 3365 1696 918 4228 2687 3422 3288 2901 4299 2999 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 7/23 Reactome 4.63606466162307e-07 1.14159742534765e-06 3360 2739.18181818182 2901 4.63606562881265e-08 1346 1.86060134060747 2.39078298157576 1 2.84393867889067 3359 1485 4014 1523 1831 3623 2901 4655 1411 1346 3983 3000 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 22/37 Reactome 3.15555102635877e-07 8.30472635408557e-07 2905 2496.63636363636 2902 2.86868316270236e-08 1024 1.26017518280542 1.25907553083066 1 1.97097598752862 2902 1805 2953 1439 1649 3046 1844 4089 1024 3347 3365 3001 M16626 BIOCARTA_CK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CK1_PATHWAY.html Regulation of ck1/cdk5 by type 1 glutamate receptors 13/32 BioCarta 5.6953466200382e-06 1.0376514098561e-05 3340 2796.09090909091 2905 5.17760124015485e-07 443 1.58982927062609 1.4876631370217 1 2.03808681794193 3338 2030 2254 1724 2467 4614 3704 3663 443 2905 3615 3002 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 19/36 Kevin Vogelsang 3.61252116382586e-06 6.89542736199104e-06 1150 2474.54545454545 2905 3.28411554163474e-07 542 1.15900580980451 1.26449906301035 1 1.53870379582024 1146 4096 2905 4575 4186 1136 542 627 3770 3000 1237 3003 M7416 ST_GAQ_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GAQ_PATHWAY.html G alpha q Pathway 19/35 Signaling Transduction KE 2.80373100585306e-05 4.50403959322161e-05 2980 2813.72727272727 2907 2.54887885262596e-06 1686 1.19513815586559 -1.31774443289117 -1 1.33612227365186 2976 2914 2861 2907 2801 1686 3841 3266 3284 2499 1916 3004 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 107/271 Jessica Robertson 8.49446474470599e-08 2.85955903690318e-07 4165 2699.45454545455 2908 7.72224097517046e-09 868 1.64401217089843 -1.50782203889239 -1 2.76711447759839 4161 1248 868 2741 1174 2908 4624 4613 3047 946 3364 3005 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 119/276 Jessica Robertson 3.90959612602248e-06 7.39022486750358e-06 2485 2773.72727272727 2909 3.55418461249147e-07 1590 1.6197591532435 -1.40199144713681 -1 2.13786402396006 2483 3583 1868 2909 2381 4220 2390 3010 3031 1590 3046 3006 M12617 KEGG_TYPE_I_DIABETES_MELLITUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYPE_I_DIABETES_MELLITUS.html Type I diabetes mellitus 23/78 KEGG 0.00255119618779901 0.00328973729665001 2430 2776.63636363636 2912 0.000232196314108741 2023 1.49441505808388 -1.26953623209048 -1 0.954373446232726 2429 2912 2071 2968 3472 2035 3207 3214 3549 2023 2663 3007 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 47/137 John Newman 5.55116014259779e-05 8.51202108253052e-05 4335 2986.54545454545 2912 5.04663656131842e-06 1623 2.24429120334059 -1.75411636763076 -1 2.34946390807822 4332 2800 1623 2912 2935 2555 3791 4547 1910 1953 3494 3008 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 13/33 Leona Saunders 0.0148504664119607 0.0180563792440187 2240 2984.45454545455 2913 0.00135924253582097 1750 2.06552091748536 2.83764541876496 1 0.926227323625911 2237 3999 1750 3871 3657 3115 2798 2530 3611 2913 2348 3009 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 23/53 Nick Houstis 0.00087849226174031 0.00117550392304829 2915 3093.54545454545 2913 7.98948411651749e-05 1816 1.51441350880475 -1.55302163139075 -1 1.14124132063189 2913 4616 2864 4246 3361 1816 2746 2433 3329 3399 2306 3010 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 7/15 Arthur Liberzon 1.81743553594157e-06 3.72387534823884e-06 2975 2231.63636363636 2913 1.81743702232565e-07 158 2.73867587991721 2.70522400268406 1 3.82436674129842 2975 245 4671 598 2226 3928 2936 2913 158 930 2968 3011 M5876 REACTOME_CTLA4_INHIBITORY_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CTLA4_INHIBITORY_SIGNALING.html Genes involved in CTLA4 inhibitory signaling 9/24 Reactome 1.98122288804132e-07 5.64645947266653e-07 2935 2816 2915 1.98122306467733e-08 855 1.07823857017755 1.28468912000559 1 1.7328863250687 2931 2250 4023 2915 1520 4361 3661 855 2635 3054 2771 3012 M1443 REACTOME_GLUTATHIONE_CONJUGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUTATHIONE_CONJUGATION.html Genes involved in Glutathione conjugation 13/32 Reactome 0.00493202018846133 0.00621609645054593 3540 3022.63636363636 2916 0.000449373795765842 2319 1.03981233217151 -1.0058151416288 -1 0.590138481849698 2373 2319 2916 4014 3540 2363 2387 3601 3539 3528 2669 3013 M6195 HWANG_PROSTATE_CANCER_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/HWANG_PROSTATE_CANCER_MARKERS.html Proteins implicated in prostate carcinogenesis. 16799640 20/47 Arthur Liberzon 5.00106602541147e-05 7.73177017323594e-05 2940 2792.45454545455 2916 4.54652701259465e-06 1739 1.5220049048506 -1.53043468994994 -1 1.60967547933778 2936 3694 2561 3191 2916 1739 3036 2290 3789 2127 2438 3014 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 232/477 Jessica Robertson 2.16076285411905e-08 1.11389821060527e-07 2920 2912 2916 1.96432988667391e-09 566 1.59130227795527 -0.868578250386159 -1 2.84598902043825 2916 3619 2457 2195 566 3772 3846 2531 2418 3882 3830 3015 M13720 KEGG_LYSINE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSINE_DEGRADATION.html Lysine degradation 20/50 KEGG 0.000335563743193335 0.000466602878517498 2255 2527.18181818182 2917 3.05104488472011e-05 761 1.52996218366452 -1.01365629855792 -1 1.31087355928921 2251 3627 3134 3487 3237 761 1515 2022 2917 3610 1238 3016 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 9/21 Reactome 0.0291678857716508 0.0346729357498619 1795 2976.90909090909 2917 0.00295579555993624 1582 0.400708102253764 -0.400708102253764 -1 0.150481060840449 1795 2397 4083 3239 3740 1582 1992 2917 4220 4515 2266 3017 M1090 REACTOME_SIGNALING_BY_FGFR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR.html Genes involved in Signaling by FGFR 53/136 Reactome 3.40172888173819e-07 8.82641281274925e-07 2160 2561 2918 3.09248127975215e-08 1614 1.16884454462834 1.16563191336076 1 1.82017559504209 2156 2092 3322 1614 1683 2918 1960 3001 3208 2991 3226 3018 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 38/162 Jessica Robertson 5.82920566413885e-07 1.37888226866e-06 2200 2903.81818181818 2918 5.29927928060768e-08 1858 1.67517446874527 1.62926436458203 1 2.52517425785142 2198 3202 1858 4334 1882 3095 2157 4532 2918 2587 3179 3019 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 13/34 BioCarta 0.000431330165138819 0.000593078977065877 3820 2925 2919 3.92195231445926e-05 1849 2.21112731191857 -2.29204183964783 -1 1.83525412304433 3819 3331 1849 1866 3273 3167 4025 2919 2142 2906 2878 3020 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 13/32 John Newman 1.52367883828933e-05 2.56556199648717e-05 4295 2968.54545454545 2919 1.38517217373292e-06 1739 1.54389669305363 -2.11859462158408 -1 1.82308493579954 4294 1849 2068 3035 2684 4515 3623 1739 3233 2919 2695 3021 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 11/35 Arthur Liberzon 0.00204819882058137 0.00266016066331604 2050 3126.54545454545 2919 0.000186373471064458 2008 1.00294703572289 1.00294703572289 1 0.664307752583833 2046 2919 2883 3502 3450 2581 2008 4134 4349 3908 2612 3022 M16024 KEGG_ALZHEIMERS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALZHEIMERS_DISEASE.html Alzheimer's disease 89/213 KEGG 5.10315395407952e-05 7.87920244771553e-05 3730 2904.45454545455 2920 4.63933848315502e-06 1487 1.27153035201675 -0.986626655601575 -1 1.34209008180893 3370 2583 3340 2675 2920 1487 2424 3730 3024 3729 2667 3023 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 2/9 Jessica Robertson 4.95294995392961e-05 7.66243759792477e-05 3420 2715.9 2920 5.50339887462944e-06 517 1.45108638874357 -1.0605218207371 -1 1.53613202482928 3417 1490 4360 NA 2961 3875 2698 3573 517 1389 2879 3024 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 13/23 Jessica Robertson 0.000188126220049161 0.000270499989920334 2225 2995.81818181818 2920 1.71038462735683e-05 1907 1.72934352464987 1.72934352464987 1 1.58702727288961 2224 4130 2010 4459 3134 2197 2582 3584 3807 2920 1907 3025 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 4/14 Jessica Robertson 0.00107173343432208 0.00142189775572856 2625 2777.09090909091 2926 0.000107225066108117 1537 1.58792511380941 -1.58792511380941 -1 1.16288340549035 2624 2330 4510 3097 3397 2058 2926 2945 3070 2054 1537 3026 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 63/144 KEGG 3.24332772637611e-06 6.25441717111048e-06 4260 2873.54545454545 2927 2.9484840980264e-07 1868 1.41229016869985 -1.34153383635175 -1 1.890358918825 4259 2060 2808 1868 2331 3057 3713 3408 3009 2169 2927 3027 M13486 KEGG_HUNTINGTONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HUNTINGTONS_DISEASE.html Huntington's disease 92/233 KEGG 0.000810518421057379 0.00108858965923614 1510 2672.63636363636 2927 7.37106531188621e-05 896 1.2286484614289 -1.05198749608363 -1 0.936435320833486 1507 3783 3651 2927 3696 896 1500 3251 2694 4240 1254 3028 M58 PID_AR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_PATHWAY.html Coregulation of Androgen receptor activity 18832364 53/113 Pathway Interaction Database 1.48079693736436e-05 2.49515082649745e-05 2545 2752.63636363636 2927 1.34618809504295e-06 1344 1.39446145896354 -1.22956990620223 -1 1.65096166786924 2544 3374 2927 3244 2678 1344 3203 3394 2621 2990 1960 3029 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 16/30 Leona Saunders 5.33824774895058e-05 8.20785048691027e-05 4170 3054.72727272727 2927 4.85307025878617e-06 1940 1.60739954743527 -1.70095090566385 -1 1.68925981580568 4170 1940 2376 4022 2927 2515 3587 2687 3150 2659 3569 3030 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 15/37 Jessica Robertson 5.3451823451901e-05 8.21499654626462e-05 3005 2967.36363636364 2928 4.85937474333884e-06 2162 2.26760054038307 2.83613770123925 1 2.3828626038529 3004 3661 2763 3426 2928 4136 2419 2162 2337 3167 2638 3031 M1940 BIOCARTA_CHREBP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CHREBP2_PATHWAY.html Regulation And Function Of ChREBP in Liver 24/64 BioCarta 3.75106528993877e-05 5.91038733982955e-05 1335 2566 2929 3.41011749840173e-06 1117 1.28686393723648 1.4051463681712 1 1.3996056275965 1331 3725 2929 2966 2858 1599 1797 2985 3069 3850 1117 3032 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 513/1300 Jessica Robertson 8.51551190504967e-09 6.61752716203362e-08 2530 2889 2929 8.51551193768093e-10 220 1.37560155866796 1.6581013892415 1 2.54023369001713 2526 2929 4347 2956 220 3833 2643 2867 2824 2989 3645 3033 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 160/354 Arthur Liberzon 2.77217614723829e-08 1.29129397872352e-07 4530 3011.72727272727 2929 2.52016016560903e-09 684 1.24422656607078 -0.955411810862725 -1 2.20471632485065 4528 2332 3409 2818 684 1569 4645 4334 2080 3801 2929 3034 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 15/48 Reactome 0.0618040278413097 0.0713509914915933 2525 2940.45454545455 2930 0.00578288946453714 1850 3.00696692176923 3.00696692176923 1 0.886827532960542 2522 4564 2129 3140 4457 2940 2256 2398 1850 3159 2930 3035 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 289/739 Arthur Liberzon 3.71599379135307e-08 1.59461052255316e-07 2510 2949 2930 3.3781762310177e-09 792 1.54257227765611 -1.23869962966765 -1 2.6970159451286 3350 2930 2270 2508 792 3411 3421 3928 2510 2725 4594 3036 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 222/643 Arthur Liberzon 2.39346141772759e-07 6.64047377351775e-07 2635 2976.90909090909 2932 2.17587425283741e-08 1547 1.67469944803674 1.80186811284109 1 2.66115053078685 2634 3709 1921 3769 1547 4126 2012 3450 2932 2549 4097 3037 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 5/8 Jessica Robertson 3.06272696093861e-05 4.8882624451493e-05 2935 3005.18181818182 2932 3.06276917309139e-06 1355 2.99933534640068 2.99933534640068 1 3.32572353306135 2932 3547 4344 4391 2843 2907 1741 1355 2602 3289 3106 3038 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 275/545 Vamsi Mootha 0.000111061752431839 0.00016386504152884 995 2601.81818181818 2932 1.00970326832534e-05 943 1.03438359912849 -0.90300737993931 -1 1.00717524728856 991 3244 3768 2932 3053 943 1871 2246 3438 4371 1763 3039 M5489 BIOCARTA_IL6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL6_PATHWAY.html IL 6 signaling pathway 17/36 BioCarta 1.10531540811643e-05 1.90773775411918e-05 2620 2696.09090909091 2934 1.0048372376709e-06 1728 1.04067219581218 -0.770429370934945 -1 1.26330099794587 3075 1728 2956 1910 2616 1805 2934 3252 2952 3813 2616 3040 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 50/190 Arthur Liberzon 8.83762157838552e-08 2.94965062082013e-07 2935 3107.45454545455 2934 8.03420175763792e-09 1189 1.51284865158844 1.21694627396857 1 2.54110478825175 2934 2373 2195 3691 1189 4324 2657 4220 3589 2457 4553 3041 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 22/48 BioCarta 0.00324203123354028 0.00414520009832736 2540 3040.63636363636 2936 0.000295165339522441 2407 1.3389287446241 1.78188597516488 1 0.820503913315977 2538 3758 2936 2417 3505 3797 2958 2407 2763 3739 2629 3042 M720 REACTOME_METABOLISM_OF_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_PROTEINS.html Genes involved in Metabolism of proteins 260/627 Reactome 0.00329763756937351 0.00421284886861621 2290 3120.54545454545 2936 0.00030023553475004 998 1.24275362462944 -0.910617846416443 -1 0.759319875040924 2287 4466 3763 2936 3846 998 2409 4299 2726 4373 2223 3043 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 11/29 Jessica Robertson 0.000434560098482423 0.000596819642874746 4590 3202 2936 3.95132690652562e-05 1974 1.4911114939689 -1.81745981606683 -1 1.23658763366453 4587 2469 2336 4530 3276 4381 3642 2805 2286 1974 2936 3044 M247 PID_INSULIN_GLUCOSE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INSULIN_GLUCOSE_PATHWAY.html Insulin-mediated glucose transport 18832364 18/41 Pathway Interaction Database 5.62260445780095e-05 8.61875187741421e-05 1545 2713.36363636364 2937 5.1115892377202e-06 1050 0.863743724117616 0.709063395943937 1 0.903018322646364 1544 3233 3270 3968 2937 1460 1050 2421 4076 3874 2014 3045 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 14/31 Reactome 1.00462320474734e-07 3.26921134544863e-07 3635 2792.45454545455 2938 9.13293864202861e-09 1065 1.31863644536094 -0.827840190752322 -1 2.1997382304718 3633 1065 2410 1978 1239 4415 2706 3625 2938 3010 3698 3046 M7494 REACTOME_TOLL_RECEPTOR_CASCADES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TOLL_RECEPTOR_CASCADES.html Genes involved in Toll Receptor Cascades 81/182 Reactome 7.8529840853532e-06 1.39284948614554e-05 4670 3033.90909090909 2938 7.13910192456375e-07 2390 1.37733089202817 -1.44009187421081 -1 1.72037914999706 4669 2761 2947 2390 2539 3007 3467 2863 3130 2662 2938 3047 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 20/42 Reactome 0.011047233949712 0.0135943640463105 2165 2956.45454545455 2939 0.00100937276770588 2001 1.25187888122465 1.04030876225625 1 0.601065322718219 2163 3099 2886 3316 3848 2775 2149 2001 3729 3616 2939 3048 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 10/14 Leona Saunders 9.52004050790155e-08 3.12401329271895e-07 4605 2910.18181818182 2939 8.65458265441948e-09 1221 2.09218329331422 -2.63622401184884 -1 3.50078034916359 4601 1778 1561 2939 1221 4496 4445 3742 1728 1853 3648 3049 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 60/120 Arthur Liberzon 2.42543201144802e-07 6.7053536316492e-07 4270 2627.72727272727 2939 2.20493843531312e-08 1085 1.1890825476437 -1.09656970623394 -1 1.8881983190645 4269 1658 3374 3020 1554 1085 3863 1937 2939 3663 1543 3050 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 85/181 Arthur Liberzon 5.03328839587699e-08 1.98092047213273e-07 2945 2401.54545454545 2941 4.57571682821046e-09 774 1.12560735875939 -1.01903309081812 -1 1.94072231265306 2941 1315 3063 3399 926 774 3153 2694 2970 3390 1792 3051 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 7/16 Jessica Robertson 4.59203016158052e-05 7.14654710633222e-05 3840 3173.54545454545 2942 4.59212505467482e-06 1593 1.80244596278445 -1.58107091505956 -1 1.92211827875922 3836 1593 4341 2942 2918 2881 4273 4133 2312 2684 2996 3052 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 18/41 Arthur Liberzon 0.00196449438810645 0.00255782736945453 1835 2762.81818181818 2942 0.000178750071218963 987 1.47909546948591 1.72991017624044 1 0.98616906314909 1832 4304 3021 4351 4470 1852 987 1672 3489 2942 1471 3053 M321 KEGG_CHRONIC_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHRONIC_MYELOID_LEUKEMIA.html Chronic myeloid leukemia 39/90 KEGG 1.44628381520152e-06 3.06942298824019e-06 4120 2955.45454545455 2943 1.3148043327199e-07 1746 1.41990706090511 -1.1329650303511 -1 2.01345572717105 4117 2943 3062 1958 2130 2201 4480 4184 1746 3081 2608 3054 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 36/73 Pathway Interaction Database 7.74566210849021e-08 2.68420713822601e-07 4270 2840.45454545455 2943 7.04151125563275e-09 1130 1.49399185822501 -1.14701178999315 -1 2.52516935104007 4267 2801 2736 1174 1130 2943 4029 3070 2107 3211 3777 3055 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 5/15 Jessica Robertson 0.00354208329822211 0.00451774696120544 2945 2860 2943 0.000354774185564438 1581 3.95434776071584 3.95434776071584 1 2.38523306477788 2943 3273 4500 1839 4562 2520 1581 3120 2220 3298 1604 3056 M12882 KEGG_TAURINE_AND_HYPOTAURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TAURINE_AND_HYPOTAURINE_METABOLISM.html Taurine and hypotaurine metabolism 5/12 KEGG 2.11549673441141e-05 3.48198724884154e-05 2950 2744 2946 2.11551687365019e-06 812 3.59799874776149 -3.59799874776149 -1 4.12587983137444 2946 3972 3790 3926 3915 2460 2391 892 812 3261 1819 3057 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 43/85 John Newman 8.94816709177296e-05 0.00013353857003837 3470 2877.36363636364 2947 8.13502824150434e-06 1807 1.85582139590529 2.370227576525 1 1.84943264441461 3467 3988 2460 1949 3018 2947 3644 1807 2556 3651 2164 3058 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 7/12 Reactome 5.27681207527651e-05 8.12057188333193e-05 4215 3272 2948 5.27693738081976e-06 1940 0.739977775625943 -0.840311139849728 -1 0.778546304012178 3549 2251 3922 4215 2948 1940 2806 2908 4211 4444 2798 3059 M6591 REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION.html Genes involved in Cytosolic tRNA aminoacylation 20/29 Reactome 0.0236527832881935 0.0283470441146994 1165 2888.36363636364 2949 0.00217372503112508 1164 0.675451826308051 -0.675451826308051 -1 0.268856907494407 1164 2949 3603 3372 3807 1441 2034 2496 4219 4469 2218 3060 M15303 REACTOME_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOSIS.html Genes involved in Apoptosis 95/213 Reactome 4.54741192222577e-05 7.08553063742751e-05 3960 3126.36363636364 2949 4.13409629108797e-06 1438 1.63493918010211 2.11788283208409 1 1.74505597948117 3960 2898 2949 1693 2893 2812 4403 3206 1438 3757 4381 3061 M3624 KEGG_GLYCOSAMINOGLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_DEGRADATION.html Glycosaminoglycan degradation 12/28 KEGG 1.87608091583023e-05 3.11196997224087e-05 2765 2995.27272727273 2950 1.70554264960444e-06 1877 1.08090434759399 1.43705545434952 1 1.25305468896674 2765 2243 2950 3737 2718 3855 3464 1877 3103 3414 2822 3062 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 8/22 Reactome 0.000257042880814811 0.000362802090210302 3235 3037.63636363636 2950 2.57072617625054e-05 2411 1.15513881390647 -1.18284051816847 -1 1.0221930071078 3231 2820 4069 2708 3205 2453 2950 3184 3504 2879 2411 3063 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 20/54 Arthur Liberzon 2.87306839832147e-05 4.60280291095193e-05 2950 3195.18181818182 2950 2.6119144723292e-06 1772 1.17915335407203 -0.791817944245487 -1 1.31539470872473 2950 3995 2801 3961 2812 1772 2421 4505 3600 3959 2371 3064 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 29/75 Arthur Liberzon 6.46821302339661e-07 1.50646353020062e-06 3020 2711.81818181818 2950 5.88019538646787e-08 1707 1.87837666692459 1.40264029771886 1 2.81291512817082 3019 1766 1966 2950 1913 4005 2966 3401 1707 1840 4297 3065 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 80/194 John Newman 9.53063951442343e-07 2.1146106422627e-06 4520 3118.36363636364 2951 8.66422149382066e-08 2022 1.19955327286358 -0.982490579367142 -1 1.75092042428746 4516 2416 2951 2187 2022 2327 4050 4567 3249 3151 2866 3066 M1749 KEGG_VEGF_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VEGF_SIGNALING_PATHWAY.html VEGF signaling pathway 32/89 KEGG 6.26422269089828e-05 9.53056737972382e-05 4240 2941.81818181818 2952 5.69491005804904e-06 1056 1.41761300102798 -1.47565755842777 -1 1.46614714808905 4237 1723 2444 1056 2964 3306 4110 4160 2552 2856 2952 3067 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 14/26 Jessica Robertson 0.000129534210301397 0.000189491942713496 4360 3006.54545454545 2955 1.17765307090066e-05 1563 1.89332052430149 -1.73451429804849 -1 1.81278750811188 4357 2955 2535 3223 3081 2726 4057 2283 1563 3633 2659 3068 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 23/67 Kevin Vogelsang 8.96210085360211e-05 0.000133703930595286 2615 2903.27272727273 2955 8.14769632902976e-06 2043 1.86733664951632 1.59440136127059 1 1.86065011353283 2614 3069 2043 3686 3019 3311 2212 4375 2175 2955 2477 3069 M15285 BIOCARTA_NFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NFKB_PATHWAY.html NF-kB Signaling Pathway 17/37 BioCarta 0.00118940152460813 0.00157444506901517 2465 3110.36363636364 2956 0.000108185913297871 2461 1.0842767263307 -1.08118499052035 -1 0.7817034829007 3788 2464 3283 2610 3398 2956 4568 2479 3430 2777 2461 3070 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 33/79 Arthur Liberzon 0.000590183694383005 0.000803486575211726 2960 2878.45454545455 2956 5.36674617896588e-05 1420 1.42126301957182 1.7644230963703 1 1.13145351526548 2771 2424 2624 3373 3674 4290 2198 1420 2960 2973 2956 3071 M22 PID_GMCSF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_GMCSF_PATHWAY.html GMCSF-mediated signaling events 18832364 25/57 Pathway Interaction Database 1.00392558327904e-05 1.74754653909569e-05 2960 2915.90909090909 2957 9.12663785927292e-07 1861 0.93271194269963 -0.946488895799319 -1 1.14138312304675 2957 3228 3442 2264 2592 1889 3971 2063 3921 3887 1861 3072 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 7/18 Reactome 0.000650523693654151 0.000881536734662624 2670 3069.36363636364 2958 6.50714203632831e-05 1984 0.969269995251331 -1.01411338845782 -1 0.761588491239166 2669 2473 4062 4270 3334 1984 2088 2958 4207 3581 2137 3073 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 254/584 Arthur Liberzon 3.95340939296081e-08 1.66149564263806e-07 4310 3052.09090909091 2958 3.59400860363977e-09 819 1.50654011742953 -1.30004505973714 -1 2.62710282073101 4308 4011 2751 2561 819 2135 3682 4368 2468 3512 2958 3074 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 12/26 Jessica Robertson 0.000971767444321727 0.00129513715702264 2210 2564.72727272727 2958 8.83815410685606e-05 1295 1.08177417999098 -1.08177417999098 -1 0.803498161374806 2210 2958 2989 3676 3468 1408 1916 1527 3341 3424 1295 3075 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 14/29 Vamsi Mootha 0.000229728826375015 0.000326610825362051 2960 2835.72727272727 2958 2.08866198791435e-05 1274 0.924887702486975 -0.925898426487045 -1 0.829299027336179 2958 2353 3354 3892 4017 1337 2571 1274 3719 4029 1689 3076 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 18/52 John Newman 6.00673789282323e-05 9.15666030116125e-05 3735 3037.18181818182 2959 5.4608199119854e-06 1876 1.90674828033481 -1.78591755888852 -1 1.98055357386807 3733 3964 2714 3891 2959 1993 3214 3897 2227 2941 1876 3077 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 23/66 Arthur Liberzon 6.76758334060665e-07 1.56606891526335e-06 4615 2666.18181818182 2959 6.15235038403101e-08 455 1.8365460302336 -1.92869191045366 -1 2.74231188950366 4615 1138 1551 1001 1927 3602 4336 4151 455 2959 3593 3078 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 7/19 Reactome 3.59125375080143e-06 6.86321985165396e-06 3810 2700.18181818182 2961 3.59125955451121e-07 274 1.90815420028888 -1.53789415792912 -1 2.53427625273874 3809 2533 3975 1124 2386 4560 3038 3113 274 1929 2961 3079 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 113/343 Arthur Liberzon 2.1771198688513e-07 6.12326395333097e-07 2965 2907.63636363636 2961 1.97920007663555e-08 1518 1.27150144293436 1.60937424743418 1 2.0319735206296 2961 3278 3011 2720 1518 3963 2815 1898 3119 3928 2773 3080 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 42/74 Leona Saunders 6.08247484653942e-05 9.26307349069994e-05 2725 3058 2962 5.52967547178101e-06 1879 1.59711210445775 2.21663140925814 1 1.65687073334313 2722 4255 2452 3247 2962 4453 3033 1879 2304 3601 2730 3081 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 134/310 Arthur Liberzon 1.64146206007471e-07 4.85599192772103e-07 3390 2811.63636363636 2962 1.49223834777032e-08 1418 1.48103545080595 -1.28982510872566 -1 2.40519096259263 3390 2512 3009 2962 1418 1627 3337 3982 2852 3514 2325 3082 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 275/574 Arthur Liberzon 2.43630934025425e-08 1.19623053244874e-07 3685 2757.90909090909 2965 2.2148266974857e-09 619 1.57962942087301 -0.88339220029377 -1 2.81252945523241 3683 2286 2965 1208 619 2696 4488 3487 1227 3553 4125 3083 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 35/76 Yujin Hoshida 6.27999414867857e-05 9.55146140237189e-05 3360 2872.72727272727 2965 5.70924856451225e-06 1245 2.01748465204917 -1.31618107929341 -1 2.08606287363802 3360 4440 2335 3654 2965 1245 2550 3474 1498 3997 2082 3084 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 38/110 KEGG 0.000792002174354816 0.00106524747101799 2805 2897.81818181818 2966 7.20261308822582e-05 1095 1.32506841874973 -1.22222836676919 -1 1.01313191072189 2805 2302 2966 1095 3349 3465 2095 3648 2962 2979 4210 3085 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 160/333 Jessica Robertson 9.41539685147622e-08 3.09938293337477e-07 2985 2966.27272727273 2966 8.55945204948127e-09 1214 1.50921496771756 1.88644348380579 1 2.52665335552458 2982 3582 2573 2304 1214 3644 3929 2966 2540 2845 4050 3086 M5872 KEGG_STEROID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_BIOSYNTHESIS.html Steroid biosynthesis 5/21 KEGG 0.044869454746711 0.052498942557575 2135 3078.63636363636 2967 0.00458020385198689 2064 1.57996202995876 -1.57996202995876 -1 0.520120588231947 2132 2967 3787 4269 3858 2064 2583 2341 3924 3260 2680 3087 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 50/111 Vamsi Mootha 0.0262400426537028 0.0313276025159876 1170 2951.45454545455 2971 0.00241439483764412 1170 0.551045920544606 -0.553640977962683 -1 0.213184151226378 1170 3462 3750 2880 3825 1478 1944 2971 4382 4346 2258 3088 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 6/9 Jean Junior 0.00308731602716139 0.00395277674952958 2975 2909.90909090909 2971 0.000309161361673411 1724 1.14555164133745 -1.02423981565032 -1 0.708083803177638 2971 2575 4379 3465 3508 1903 2622 3523 3015 1724 2324 3089 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 26/63 Arthur Liberzon 1.05888279439391e-05 1.83455847329625e-05 4510 2941.54545454545 2971 9.62625355400774e-07 1525 2.20611774155623 -1.42285557472576 -1 2.68770741780498 4506 3723 1982 3178 2606 2971 3956 1998 1525 2738 3174 3090 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 20/53 Leona Saunders 2.4294670790318e-07 6.71254878086261e-07 3170 2897.54545454545 2974 2.20860667938061e-08 1295 1.28257900256117 0.893138593905819 1 2.03651195673463 3167 1981 2974 2898 1555 4184 2209 3653 1295 3960 3997 3091 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 13/30 Reactome 6.65997413757199e-05 0.000100868257300137 3035 2788.18181818182 2976 6.05470523719541e-06 1772 1.75368024876122 2.09785593356431 1 1.80260763729263 3031 2672 2121 1946 2976 3398 3796 3706 1895 1772 3357 3092 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. 48/117 Reactome 0.0139629607294305 0.0170436139562676 985 2832 2976 0.00127748876125088 981 0.561305261497117 -0.561305261497117 -1 0.255321480432401 981 2732 3749 2976 3791 1303 1738 3048 4397 4341 2096 3093 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 12/21 BioCarta 1.5518323277882e-05 2.60734538831678e-05 4115 3394.27272727273 2980 1.4107666128957e-06 2076 1.17793630114626 0.883219245680619 1 1.3888208395778 4114 2076 2797 2553 2689 4260 2980 4609 4177 2740 4342 3094 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 13/19 Reactome 1.0333613265896e-06 2.26725372402912e-06 3020 2767.81818181818 2981 9.39419829063409e-08 1259 0.948986310760025 -1.06635119514437 -1 1.37779320149329 3018 2119 3213 3869 2049 1259 2265 2981 3801 3981 1891 3095 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 25/69 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2930 3147.54545454545 2981 0.00793650793650794 2568 1.38478412088406 -1.38930063212691 -1 0.371978346040226 2930 3150 2568 2734 4233 2669 3241 3499 3977 2641 2981 3096 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 10/19 Jessica Robertson 0.000256028350095394 0.000361479014325705 2845 2946.18181818182 2981 2.32780136945399e-05 2416 1.59935836685152 1.99622412991439 1 1.41593981010525 2843 3388 2594 3059 3186 3455 2981 2416 2511 3196 2779 3097 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 36/69 Reactome 0.0839184282471183 0.0902966141827776 2335 3124.27272727273 2982 0.00793650793650794 1988 1.22394084699391 -0.673582288505426 -1 0.328772875638091 2331 3124 3531 2877 3957 2039 2922 4473 1988 4143 2982 3098 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 101/270 Leona Saunders 4.29692403285515e-05 6.72300033988621e-05 4265 3077.81818181818 2983 3.9063708730957e-06 2247 1.4825433184032 -1.28879187687224 -1 1.59109384923801 4265 2933 2999 2714 2882 2247 3565 3858 2323 2983 3087 3099 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 16/33 Leona Saunders 5.75426791455002e-05 8.80042410169105e-05 3535 3043.90909090909 2983 5.23128947939161e-06 2154 1.21406319918973 0.855696056328309 1 1.26643799330608 3532 2158 2983 3100 2947 2369 3548 4684 2154 3769 2239 3100 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 4/10 Yujin Hoshida 0.0703546774022884 0.0808440456859057 2255 3350 2983 0.00726866843057195 1864 0.980980613361588 0.980980613361588 1 0.275626753743424 2252 2968 4565 4025 3891 2448 1864 2825 4371 4658 2983 3101 M9052 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM.html Phosphatidylinositol signaling system 37/77 KEGG 6.33756264138112e-05 9.6327663112267e-05 3850 3291.54545454545 2984 5.76158655960328e-06 2733 1.31433708211933 -1.44528215314706 -1 1.35776937802075 3846 2733 2819 3483 2967 2914 4604 2838 3414 3605 2984 3102 M4388 BIOCARTA_CDMAC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CDMAC_PATHWAY.html Cadmium induces DNA synthesis and proliferation in macrophages 10/29 BioCarta 0.00606116688455303 0.00758414633404953 2525 3048 2984 0.000552539141281439 2009 0.82486086033758 -0.82486086033758 -1 0.449815226597077 2523 3670 3237 2436 3565 2009 2984 2590 4210 3829 2475 3103 M19943 BIOCARTA_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CERAMIDE_PATHWAY.html Ceramide Signaling Pathway 17/33 BioCarta 0.000244667815426703 0.000346588084368056 2985 2805.45454545455 2984 2.22450027107743e-05 1375 0.823873855183742 -0.646836285726526 -1 0.733261318252083 2984 1632 3371 2715 3176 1375 2757 3190 3912 3811 1937 3104 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 26/77 Kevin Vogelsang 1.93465083943591e-05 3.20345365144759e-05 2050 2802.36363636364 2985 1.75878895700765e-06 1976 1.95998490898957 2.10975938968945 1 2.26579865836186 2049 4260 2427 3054 2724 3025 2116 1976 2986 3224 2985 3105 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 18/32 Reactome 0.000254322392921452 0.000359286925905916 1130 2508.63636363636 2986 2.31228906932464e-05 612 0.576424022797191 -0.576424022797191 -1 0.510709757351149 1129 2986 3596 4030 3291 612 706 1436 4050 4495 1264 3106 M14091 KEGG_OLFACTORY_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OLFACTORY_TRANSDUCTION.html Olfactory transduction 35/833 KEGG 0.0400029871205297 0.0469691800668509 1890 3098.54545454545 2987 0.00370449464916986 1888 1.31310217616138 1.41041406685048 1 0.448596866417068 1888 4024 2987 4232 4108 2765 2260 2287 3557 2722 3254 3107 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 456/1138 Leona Saunders 0.000388468261105547 0.00053587349765693 2185 3130 2988 3.53215338569444e-05 2185 1.49759951828191 1.87342341104983 1 1.25998850347485 2185 4043 3189 2523 3261 4434 2700 2293 2841 3973 2988 3108 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. 14/30 SigmaAldrich 0.00544912131403009 0.00684023104139968 2990 2784.18181818182 2989 0.000496605916843208 1549 1.44923091001082 1.62232226651495 1 0.807011765795336 2349 2990 2228 2512 3553 3737 3096 2616 1549 3007 2989 3109 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 2/8 Arthur Liberzon 0.0341496658052175 0.0403594789314626 2610 3153.5 2989 0.00385326707588758 1707 1.26337156305408 1.26337156305408 1 0.453011595537936 2608 3370 4115 NA 4073 2516 1707 3743 4480 2524 2399 3110 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 49/123 Arthur Liberzon 5.53516212936215e-07 1.32133315018803e-06 4130 2969.18181818182 2990 5.03196683818174e-08 1860 1.4454400446492 1.8264068171536 1 2.18575398251331 3577 1879 2684 2990 1860 3298 4128 3542 2191 2383 4129 3111 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 67/185 Jessica Robertson 3.25690105647183e-08 1.46466778796804e-07 4665 3003.90909090909 2991 2.96081918607936e-09 742 1.70610281380798 -1.224412659621 -1 2.99913081938865 4664 2640 1962 3402 742 2980 4065 2991 2665 3231 3701 3112 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 15/38 Jessica Robertson 7.39929021694703e-05 0.000111381541781605 2600 2769.81818181818 2992 6.72685371819072e-06 1728 2.35285893824088 2.26906769282247 1 2.3924445164765 2596 2811 1728 3279 2992 3048 2005 3398 3311 3169 2131 3113 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 43/106 Jessica Robertson 7.59709996878776e-05 0.000114175787215329 4615 2914.63636363636 2994 6.90669302418052e-06 930 1.43876116105266 -1.34179209656029 -1 1.45898517836649 4612 930 2536 1942 2994 3718 3744 3544 1637 2626 3778 3114 M13917 BIOCARTA_PARKIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PARKIN_PATHWAY.html Role of Parkin in the Ubiquitin-Proteasomal Pathway 4/15 BioCarta 6.93006816849253e-05 0.000104789607736547 2060 2916.72727272727 2996 6.93028429428014e-06 1537 1.01548258100456 1.01548258100456 1 1.03948786924599 2058 2408 3864 3680 2996 1613 1537 4084 4415 3091 2338 3115 M269 PID_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAS_PATHWAY.html Regulation of Ras family activation 18832364 17/38 Pathway Interaction Database 3.44412485732759e-07 8.9203157362956e-07 4375 3010.72727272727 2996 3.13102308773577e-08 1468 1.43086995393162 -1.79564251465388 -1 2.22652149065069 4375 1468 1897 2758 1690 4569 3506 3795 2996 2780 3284 3116 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 23/71 Kevin Vogelsang 3.73383183536203e-07 9.51426643855708e-07 3005 2874.54545454545 2996 3.39439315369703e-08 1721 1.38895625548731 1.6160537023006 1 2.15129960730949 3002 3151 2451 2332 1721 4628 2996 1919 3477 2424 3519 3117 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 11/33 Arthur Liberzon 0.0571810499776742 0.0661932806806772 2575 3061.81818181818 2996 0.00533851813763542 2249 1.42069573054689 -1.42069573054689 -1 0.430905361880603 2571 3665 2996 2622 4069 2249 2575 3281 4032 3342 2278 3118 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 18/75 Arthur Liberzon 0.0550284127022038 0.0637801488801699 2120 3200.36363636364 2997 0.00513227720133621 1780 2.48728141965849 2.48728141965849 1 0.764725674086665 2116 4619 2462 4552 4111 2105 1780 2997 4055 3877 2530 3119 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 41/87 Broad Institute 0.00297885556783838 0.00381704052252957 3000 2945.45454545455 2998 0.000271172425096627 2001 1.35094194359541 -1.2850680330853 -1 0.840312130178898 2998 3684 2313 3321 3490 2001 2852 3143 3916 2133 2549 3120 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 183/570 Arthur Liberzon 9.88824028782472e-08 3.23126178443142e-07 3960 3006.63636363636 2998 8.98930975660637e-09 961 1.36117874877599 -1.0206797788643 -1 2.27248234474279 3956 2725 2915 3906 1231 961 4274 4379 2998 3353 2375 3121 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 362/707 Jessica Robertson 7.36569541417384e-07 1.68615772891151e-06 1560 2804.09090909091 2999 6.69608898203796e-08 1240 0.887814266886663 -0.765290827639797 -1 1.31834766541034 1558 3372 3782 3147 1958 1240 2381 2999 3847 4385 2176 3122 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 235/511 Arthur Liberzon 5.61870365253155e-08 2.13127825073088e-07 3110 2938 3001 5.10791254184617e-09 980 1.47501442375602 1.94409920618922 1 2.53109989889375 3110 4322 3001 2097 980 3063 3832 2576 2565 2981 3791 3123 M13095 SU_THYMUS http://www.broadinstitute.org/gsea/msigdb/cards/SU_THYMUS.html Genes up-regulated specifically in human thymus. 11904358 5/22 John Newman 7.299922341909e-05 0.000110027134429674 4020 3066 3003 7.30016215289411e-06 2114 1.67060862658343 -1.18267722452022 -1 1.70099887084616 4020 2133 4406 2282 3003 3258 4267 2114 2172 2251 3820 3124 M2642 KEGG_TGF_BETA_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TGF_BETA_SIGNALING_PATHWAY.html TGF-beta signaling pathway 37/94 KEGG 0.00520432974963849 0.00654521986226676 2790 3287.63636363636 3006 0.000474243823957279 2660 1.43152451804728 1.48303206796617 1 0.804201841970757 2788 4156 2660 2908 3546 4512 3187 3006 2867 2896 3638 3125 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. 13/30 SigmaAldrich 8.29134418554202e-05 0.000124131753525399 2385 3136.27272727273 3006 7.53786971419478e-06 2385 1.32472876598512 1.51123813573534 1 1.33097790577183 2385 3330 2694 4169 3006 3352 2514 2620 3664 3978 2787 3126 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 23/63 Arthur Liberzon 1.49240370095061e-06 3.15871894428843e-06 4090 3263.36363636364 3007 1.35673155758772e-07 2135 1.71202399573413 -1.3486449949623 -1 2.422198886065 4089 2983 2267 3007 2135 3659 3585 4175 2869 2958 4170 3127 M9378 ST_INTERLEUKIN_4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTERLEUKIN_4_PATHWAY.html Interleukin 4 (IL-4) Pathway 16/32 Signaling Transduction KE 0.0839184282471183 0.0902966141827776 2995 3196.27272727273 3008 0.00793650793650794 1967 0.950186236719624 -0.881074581165348 -1 0.255237337436282 2994 2883 3008 2919 4088 1967 3453 3592 3946 3763 2546 3128 M12256 REACTOME_SIGNALLING_TO_RAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_RAS.html Genes involved in Signalling to RAS 20/36 Reactome 9.54951577765702e-05 0.000141835280298259 4580 2840.27272727273 3008 8.68175483420784e-06 1497 1.52031362544786 -1.29959280055686 -1 1.50484311530988 4578 2345 1968 1497 3029 3008 3652 3267 2113 2599 3187 3129 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 2/18 Arthur Liberzon 0.00643667586377308 0.00803291189310319 2595 3163.9 3009.5 0.000717240502796978 1263 0.396651489930449 0.396651489930449 1 0.213755696905485 2594 3425 4237 NA 3801 2114 1263 2579 4523 4572 2531 3130 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 35/122 John Newman 5.06165601493275e-08 1.98484686911924e-07 3010 2803.18181818182 3010 4.60150557398996e-09 930 1.6858783669912 1.81296914694157 1 2.90634394397484 3010 1926 1163 2764 930 4241 3076 4680 3607 1426 4012 3131 M79 PID_TRAIL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TRAIL_PATHWAY.html TRAIL signaling pathway 18832364 17/31 Pathway Interaction Database 8.58324969105474e-05 0.000128256084350391 4085 2955.27272727273 3011 7.80325871170074e-06 1185 1.23737708486398 -0.787987409428176 -1 1.23869622397307 4082 1982 2830 1601 3011 2497 4514 3726 1185 3370 3710 3132 M862 BIOCARTA_P38MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P38MAPK_PATHWAY.html p38 MAPK Signaling Pathway 30/62 BioCarta 2.27399716964613e-05 3.71935453297095e-05 3195 2964.90909090909 3012 2.06729152256243e-06 1838 1.13968280195095 1.30748925093429 1 1.298495644997 3191 1838 3012 2137 2755 4384 2511 3385 2441 3127 3833 3133 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 47/87 Kevin Vogelsang 2.88922965197516e-07 7.70570867908685e-07 3895 3106 3012 2.62657275583071e-08 1619 1.52822432783645 -1.10552614420422 -1 2.40299833485665 3891 3012 2418 2260 1619 3829 3119 4415 2406 2946 4251 3134 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 19/42 Jessica Robertson 0.000587239721764929 0.000799710937573513 2275 2999.45454545455 3012 5.33996845991184e-05 1765 1.27997078860305 1.38627474186823 1 1.01964560647978 2275 3535 3177 3827 3306 2710 2897 2565 3012 3925 1765 3135 M4170 ST_INTERFERON_GAMMA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTERFERON_GAMMA_PATHWAY.html Interferon gamma pathway. 5/15 Signaling Transduction KE 0.0064369577803249 0.00803291189310319 3850 3075.36363636364 3013 0.000645567964113064 2140 1.33785616567943 -1.07378519301828 -1 0.720971899382271 3850 2253 3883 3004 3583 2754 3013 3586 2140 2231 3532 3136 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 37/87 Arthur Liberzon 4.52470550600269e-07 1.11593526321729e-06 3505 3007.63636363636 3014 4.11336948781095e-08 1660 1.63340226533357 1.81896192299812 1 2.50081213531314 3502 3014 2271 1660 1795 4380 3678 3162 2743 2539 4340 3137 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 33/56 Reactome 4.31334268752551e-05 6.74348989725088e-05 3085 3133.90909090909 3016 3.92129750698945e-06 1703 1.36467110592102 -1.36485625162497 -1 1.46412722423642 3082 3016 2767 2814 2884 3813 1703 4292 3527 2569 4006 3138 M16227 REACTOME_CHOLESTEROL_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHOLESTEROL_BIOSYNTHESIS.html Genes involved in Cholesterol biosynthesis 9/24 Reactome 0.000805255201405569 0.00108183081243879 2420 3089.18181818182 3018 8.05547146479806e-05 1493 2.27944347140938 -2.27944347140938 -1 1.73890267746854 2417 3509 4099 4091 3929 2513 3018 1493 2455 3780 2677 3139 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 14/28 John Newman 0.000888490753216344 0.00118820424359926 3655 2820.90909090909 3018 8.0804525600056e-05 98 2.23083455124014 -0.775702197033469 -1 1.67844855904285 3652 3033 2193 2497 3517 4625 2819 1494 98 3018 4084 3140 M19784 BIOCARTA_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCR_PATHWAY.html T Cell Receptor Signaling Pathway 27/73 BioCarta 0.000191682294365632 0.000275396527889456 3935 2973.72727272727 3020 1.74271815780487e-05 1061 1.36891857351901 -0.994889203108584 -1 1.25352008424576 3933 2067 2688 1061 3140 4376 3020 3173 1944 2848 4461 3141 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 5/13 Arthur Liberzon 0.000477938765691581 0.000654477222685783 3355 2830 3021 4.78041588275469e-05 346 2.32005800818955 -3.57235249104043 -1 1.90013705789398 3351 2047 4662 2010 3294 3305 3021 2542 346 2261 4291 3142 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 2/18 Reactome 0.0387608672964907 0.0455907189134928 2525 3119.2 3021.5 0.00438281880554584 1648 2.08444512705948 -2.08444512705948 -1 0.719047894356083 3396 1648 4102 NA 4288 3529 4208 2328 2647 2523 2523 3143 M266 PID_NCADHERIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NCADHERIN_PATHWAY.html N-cadherin signaling events 18832364 30/76 Pathway Interaction Database 0.000287872439506026 0.000403400194834103 3185 2861 3022 2.61736468032664e-05 1143 2.17407803873997 -1.96175299816459 -1 1.89810124542105 3182 3888 2298 1662 3209 3794 2653 3022 1143 2665 3955 3144 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 18/39 Lauren Kazmierski 9.03664821855585e-05 0.000134687447684964 1950 2828.72727272727 3022 8.21547220574221e-06 1497 0.669502378785339 -0.714760665131282 -1 0.666556769919425 1947 3213 3556 3583 3022 1497 2615 1865 3959 3876 1983 3145 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 3/15 Arthur Liberzon 0.0765897756730953 0.0871115749524574 3160 3157 3022 0.00793650793650794 1613 2.50378433986248 2.50378433986248 1 0.682606238641597 3160 3580 4224 4148 4212 2957 2472 2537 1613 2802 3022 3146 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 19/51 Reactome 0.000158102729037985 0.000229300336822036 2145 2954 3024 1.43740083831281e-05 1710 1.03133325374213 -0.995862687582032 -1 0.965496515371559 2143 3024 3193 4093 3111 1710 2503 2691 3922 3543 2561 3147 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 64/154 Arthur Liberzon 7.01601284447106e-08 2.48503674899406e-07 4270 3115.90909090909 3025 6.37819369838044e-09 1088 1.32876461475967 -0.95157374729545 -1 2.25734344630468 4268 2796 3025 2710 1088 3208 4496 3851 2432 2462 3939 3148 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 19/49 Kevin Vogelsang 1.74108501042746e-05 2.90242773349807e-05 4250 3234.09090909091 3025 1.58281708142414e-06 2393 1.62007787426108 -1.48057384181982 -1 1.89071533937548 4249 3025 2393 2860 2709 4414 3378 3111 3020 2506 3910 3149 M8615 BIOCARTA_IL2RB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL2RB_PATHWAY.html IL-2 Receptor Beta Chain in T cell Activation 24/61 BioCarta 1.71308927099816e-06 3.53791816831088e-06 4030 2927.72727272727 3026 1.55735509540248e-07 1148 1.28320751218798 -0.812229576784589 -1 1.7992512262323 4026 2106 2874 1148 2185 3269 3079 2673 3246 3026 4573 3150 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 23/66 Arthur Liberzon 0.0135281211723001 0.0165343703217001 3030 2916 3026 0.00123745734734982 1781 1.36430664444467 -0.951600223726383 -1 0.625206877985811 3026 3657 2615 1781 4100 2532 3037 2032 2209 4044 3043 3151 M860 REACTOME_SHC_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_MEDIATED_CASCADE.html Genes involved in SHC-mediated cascade 6/33 Reactome 2.78676813456954e-05 4.47986122764764e-05 3455 3080.90909090909 3027 2.78680308253122e-06 1743 1.21133442262259 -1.29797303893402 -1 1.35495748105319 3451 1743 4040 3112 2822 2680 4533 3027 3255 2473 2754 3152 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 3/9 Leona Saunders 4.64212935542387e-05 7.21732520222835e-05 4050 2987 3027 4.64222633041724e-06 1097 1.58675622707323 -0.636990133433295 -1 1.69036108341456 4049 1366 4157 2287 2921 3027 3397 4180 1097 2797 3579 3153 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 17/28 Yujin Hoshida 8.4715122742881e-05 0.000126667219263925 2430 2872.45454545455 3027 7.70167136666421e-06 1613 1.19252529396294 -1.19252529396294 -1 1.19545720478589 2428 3800 3494 3747 3009 1626 3027 1613 3242 3817 1794 3154 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 32/62 Reactome 0.0499378877776708 0.0581099930782631 1745 2912.72727272727 3028 0.00464625580603754 1155 1.30383685576401 -0.673582288505426 -1 0.414430822911129 1741 3061 3537 3028 4053 1652 2557 4452 1155 4194 2610 3155 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 18/52 Jessica Robertson 0.00820145168927003 0.0101779667944702 4605 2942.36363636364 3028 0.000748380607049464 1146 2.73730811210396 -1.52854289568402 -1 1.40276698985485 4602 3028 1311 1661 3595 3735 4630 2150 1146 1901 4607 3156 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 10/43 Reactome 6.58505223060846e-05 9.98303291900072e-05 2845 3088.36363636364 3029 5.98659031183449e-06 1355 1.67742104923276 1.62082375883462 1 1.72615893503216 2841 3359 1866 4003 2972 3453 3029 4171 2796 1355 4127 3157 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 4/10 Leona Saunders 0.00165788572361098 0.00217189055097597 3425 3241.09090909091 3030 0.000165912388715603 2330 0.627446108612559 -0.627446108612559 -1 0.429806025264257 3425 2858 4161 2607 3433 2714 3030 2330 4176 4549 2369 3158 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 36/61 Arthur Liberzon 1.3392238086903e-07 4.10713824106467e-07 2220 2891.45454545455 3034 1.21747626383087e-08 1351 1.05994153045913 1.28281538767284 1 1.7411684434446 2218 1666 3034 4078 1351 3387 2328 4380 3041 3555 2768 3159 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 12/41 Leona Saunders 1.75145372685217e-05 2.91763674512238e-05 3615 3267.27272727273 3034 1.59224333690837e-06 2275 1.08424641264961 -1.25313903882334 -1 1.26473900162281 3614 2275 2843 2948 2711 4657 2780 3637 3034 3420 4021 3160 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 503/1201 Arthur Liberzon 2.22461579523201e-08 1.13433619330328e-07 3095 2576.54545454545 3034 2.22461581750212e-09 161 1.71734062260224 -1.57508558521373 -1 3.06791624133601 3095 450 4650 1224 623 3846 3034 4333 2269 161 4657 3161 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 13/32 Jessica Robertson 0.000264868986900649 0.00037306163889884 3040 2912.54545454545 3036 2.40818982887959e-05 1278 2.45740648028068 -1.98366457983327 -1 2.16692686864889 3036 3332 1278 2965 3196 4357 2800 3077 2422 2272 3303 3162 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 24/86 Kevin Vogelsang 0.000434712537103751 0.000596854072331725 2085 2855.81818181818 3036 3.95271325996629e-05 963 1.24948344325695 1.48045000038779 1 1.03619596726641 2082 4056 3055 3835 3277 2216 963 2633 3777 3036 2484 3163 M13950 KEGG_ASTHMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASTHMA.html Asthma 12/39 KEGG 8.2420591693369e-06 1.45470016073494e-05 2555 2979.90909090909 3037 7.4928091340648e-07 1562 2.0291870020814 -1.45017249237024 -1 2.52474283787256 4411 2168 1562 3037 2551 3937 3896 3086 2555 1623 3953 3164 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 15/39 Reactome 5.66276099016309e-05 8.66896373730945e-05 4200 3147.18181818182 3038 5.14809704898145e-06 2002 1.62870425166879 -1.98340402959854 -1 1.70170506763922 4199 2159 2045 3547 2942 4320 3414 2704 3038 2002 4249 3165 M997 REACTOME_ION_CHANNEL_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ION_CHANNEL_TRANSPORT.html Genes involved in Ion channel transport 15/63 Reactome 5.66276099016309e-05 8.66896373730945e-05 4200 3148.18181818182 3039 5.14809704898145e-06 2003 1.62870425166879 -1.98340402959854 -1 1.70170506763922 4200 2160 2046 3548 2943 4321 3415 2705 3039 2003 4250 3166 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 9/27 Arthur Liberzon 1.84932608373534e-08 1.01001655342469e-07 4135 3027 3039 1.84932609912537e-09 542 2.21267924797738 -2.39164300650953 -1 3.98149832232076 4131 2324 4436 1844 542 4542 3039 4102 2748 1677 3912 3167 M3501 ST_B_CELL_ANTIGEN_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/ST_B_CELL_ANTIGEN_RECEPTOR.html B Cell Antigen Receptor 35/69 Signaling Transduction KE 9.10596591595616e-05 0.000135591217928728 3040 3067.54545454545 3040 8.27849349144968e-06 1915 1.50702283430257 1.75341395931243 1 1.49926680433544 3040 3612 2809 1915 3024 4498 2648 3219 2059 3120 3799 3168 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. 10/22 SigmaAldrich 0.0455557452759694 0.0532221945557698 4520 3384.72727272727 3040 0.00422976017904399 2302 1.47087208944752 1.34525049189224 1 0.481960230572157 4520 3040 2896 2302 3777 2995 4347 2841 3412 2431 4671 3169 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 6/8 Arthur Liberzon 9.05473954660038e-05 0.000134914179699108 3495 2993.81818181818 3040 9.05510851514683e-06 1596 1.43973714488956 -1.24266757955908 -1 1.43313246864677 3492 1596 4529 3671 3040 3552 2836 1800 1859 2494 4063 3170 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 30/67 John Newman 2.44171048795595e-07 6.73089578203268e-07 3045 2875.36363636364 3041 2.21973705359429e-08 1556 1.41736608849552 -1.1369094188598 -1 2.25009821871153 3812 2233 1979 3041 1556 2439 4465 3391 3045 3129 2539 3171 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 12/30 Jessica Robertson 1.11897205076623e-06 2.43883861855374e-06 3255 2979.45454545455 3042 1.01724783627481e-07 1988 0.852267297992833 -0.66737909651217 -1 1.23042548069296 3253 1988 3042 3173 2064 4199 3255 2905 3317 2748 2830 3172 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 14/34 Reactome 0.000104280953576943 0.000154248910499228 3015 2942.09090909091 3044 9.48053607885322e-06 1876 1.75368024876122 2.09785593356431 1 1.71939885467819 3015 3237 2194 2472 3044 3466 3762 3680 2132 1876 3485 3173 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 26/70 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3045 3255.09090909091 3044 0.00793650793650794 2677 1.38478412088406 -1.38930063212691 -1 0.371978346040226 3044 3444 2677 2833 4236 2760 3502 3555 3987 2734 3034 3174 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 308/650 Arthur Liberzon 6.13289786691175e-09 5.23474670388861e-08 4525 2992.27272727273 3044 5.57536171273483e-10 124 1.36939683274278 -1.18296749920368 -1 2.56463299912568 4524 3489 3044 2098 124 2109 4337 3636 2925 3609 3020 3175 M3412 BIOCARTA_CACAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CACAM_PATHWAY.html Ca++/ Calmodulin-dependent Protein Kinase Activation 9/15 BioCarta 0.0002897467353405 0.000405662743294169 1215 2559.36363636364 3045 2.89784521201415e-05 693 1.18521587936807 1.18521587936807 1 1.0340243417406 1215 3188 3820 3491 4146 1197 693 1505 4185 3045 1668 3176 M7 PID_FCER1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FCER1_PATHWAY.html Fc-epsilon receptor I signaling in mast cells 18832364 34/97 Pathway Interaction Database 0.000138216014960296 0.000201643912236597 3200 2703.54545454545 3045 1.25658817462764e-05 749 1.2412218123654 -1.19768312118103 -1 1.17980766500643 3196 1887 3045 749 3091 2163 4393 3445 2482 3076 2212 3177 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 26/69 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3045 3256.09090909091 3045 0.00793650793650794 2678 1.38478412088406 -1.38930063212691 -1 0.371978346040226 3045 3445 2678 2834 4237 2761 3503 3556 3988 2735 3035 3178 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 25/58 Jessica Robertson 0.000135195625139967 0.000197360342494046 2575 2756.18181818182 3045 1.22912667246962e-05 1395 2.71271872689019 2.6231652361469 1 2.5850036827426 2573 3414 1395 2621 3088 3864 3045 3299 1926 1829 3264 3179 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 48/97 Jessica Robertson 3.64614082093206e-06 6.95110491736681e-06 3015 3040.45454545455 3046 3.31467896711746e-07 1301 1.45371500104753 -1.33889226843783 -1 1.92865575433391 3013 4208 3201 2925 2361 1301 3356 3046 3529 4002 2503 3180 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 4/8 Jessica Robertson 3.23871378263626e-05 5.14740173592758e-05 3305 2566.81818181818 3047 3.23876098530582e-06 418 1.00288032434752 1.00288032434752 1 1.10622689332315 1711 3047 4334 3305 3305 1444 418 2448 4367 3105 751 3181 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 11/49 John Newman 0.000105355650414248 0.000155691131454168 3735 3028.18181818182 3047 9.57824510201069e-06 2035 1.66422529626314 -1.8157009667225 -1 1.6299624353334 3734 2035 2326 3550 3047 3233 4354 2522 2147 3338 3024 3182 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 49/138 Jessica Robertson 5.65886825638756e-06 1.03220928958475e-05 3355 2870.09090909091 3047 5.14443892023053e-07 1310 1.53326906830177 -1.38877136409504 -1 1.96647993144552 3355 1878 1310 3401 2464 2786 4386 3491 3373 2080 3047 3183 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 36/72 KEGG 1.93391845186497e-06 3.93330810131912e-06 3860 3095 3048 1.75810922898683e-07 2164 1.74215296167564 -1.36468099549591 -1 2.42214467390237 3860 3286 2164 2505 2220 4419 2540 3768 3048 2411 3824 3184 M13404 BIOCARTA_VDR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VDR_PATHWAY.html Control of Gene Expression by Vitamin D Receptor 3/17 BioCarta 0.0659569350025166 0.0759769413524564 2860 3246.09090909091 3049 0.00680004769352603 2061 0.355296461720089 -0.355296461720089 -1 0.102292131440779 2856 3049 3824 3494 3830 2061 2357 2801 4341 4413 2681 3185 M8410 REACTOME_ERKS_ARE_INACTIVATED http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ERKS_ARE_INACTIVATED.html Genes involved in ERKs are inactivated 9/15 Reactome 2.31006174321192e-08 1.15651168041571e-07 3465 2743.27272727273 3049 2.31006176722565e-09 572 1.09193464851778 0.95296366180351 1 1.94830789620719 3461 1420 3964 1786 641 4264 2562 4470 572 3049 3987 3186 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 7/14 Arthur Liberzon 0.00963814523842209 0.0118978789745116 3620 3130.45454545455 3049 0.000968020443203319 2123 1.10223360761761 -1.11396046116871 -1 0.545628385233847 3556 2823 4129 3619 3618 2298 2976 2123 3563 2681 3049 3187 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 18/70 Arthur Liberzon 2.40638751519583e-06 4.7801322154335e-06 3055 3012.45454545455 3051 2.18762740666965e-07 1627 1.17122032903091 -1.28910127798797 -1 1.60285628975708 3051 1627 2636 2173 2268 3985 3580 3607 2543 3878 3789 3188 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 26/58 Arthur Liberzon 1.64535486258695e-06 3.42824939354489e-06 2430 3051.54545454545 3051 1.49577826648213e-07 2167 1.53980931372004 1.76150566025985 1 2.16446217475974 2430 3892 2867 3710 2167 3925 2399 3051 3638 2335 3153 3189 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 168/326 Arthur Liberzon 3.46368941518486e-07 8.94261630829546e-07 3925 3063.27272727273 3051 3.14880905500884e-08 1695 1.21637564226736 -1.03930060947532 -1 1.89241587268156 3925 2639 3221 2606 1695 2202 4380 3483 2855 3639 3051 3190 M18810 REACTOME_PD1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PD1_SIGNALING.html Genes involved in PD-1 signaling 9/21 Reactome 0.000282687247863681 0.000396608516014733 2045 2744.81818181818 3053 2.82723214739234e-05 1320 1.8570979502901 1.8570979502901 1 1.62488089630365 2044 3303 4021 4457 3712 1476 1321 1320 3726 3053 1760 3191 M10680 KEGG_PROTEASOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEASOME.html Proteasome 28/48 KEGG 0.0236686396545985 0.0283587945337379 1605 3008.81818181818 3054 0.00217519824173116 1442 0.470679763611151 -0.491152635212271 -1 0.187327561597251 1603 2981 3726 3078 3790 1442 2359 3054 4309 4400 2355 3192 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 18/43 Jessica Robertson 1.74690530561861e-05 2.91109468781252e-05 2945 3043.54545454545 3054 1.58810834276102e-06 1389 1.05847622614541 -1.14926151299477 -1 1.23494431309817 2942 3294 3054 4164 2710 1389 4539 2298 4116 3477 1496 3193 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 101/218 Leona Saunders 2.74446801166297e-08 1.27965941319927e-07 4615 2555 3055 2.49497095081802e-09 644 1.30293176303965 -1.41929657638834 -1 2.31005676323553 4613 644 1967 1727 679 3245 4024 3182 3055 1373 3596 3194 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 44/122 Arthur Liberzon 7.23502663010494e-08 2.54529540455494e-07 3245 2750.18181818182 3056 6.57729715276324e-09 1101 1.07084069131898 -0.863083182078301 -1 1.81630881005952 3243 2188 3143 3056 1101 1513 3204 4493 2007 4045 2259 3195 M15513 BIOCARTA_D4GDI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_D4GDI_PATHWAY.html D4-GDI Signaling Pathway 10/26 BioCarta 3.20411488510766e-05 5.1017609077861e-05 2780 3192.09090909091 3059 2.91287413754222e-06 2657 1.34573681838736 1.53924887227166 1 1.48575361554911 2779 3702 2657 4024 2831 3521 2893 2737 3080 3830 3059 3196 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 33/83 Jean Junior 0.000395341888362702 0.000544874143784595 3175 3045.09090909091 3060 3.59466317743341e-05 1566 2.42145010502433 2.92634344208807 1 2.03275437963545 3172 3650 1901 2829 3263 4682 3419 2979 1566 2975 3060 3197 M138 PID_THROMBIN_PAR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_THROMBIN_PAR4_PATHWAY.html PAR4-mediated thrombin signaling events 18832364 12/29 Pathway Interaction Database 0.015298444803417 0.0185673432656855 3855 3281.36363636364 3061 0.00140053409624801 2061 2.50031980883096 -2.48221855288985 -1 1.11340716687628 3851 4501 2201 3831 4412 3061 3729 2061 2797 2742 2909 3198 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 27/54 John Newman 0.0839184282471183 0.0902966141827776 2775 3204.81818181818 3061 0.00793650793650794 2423 1.26107627908333 -1.06512879720308 -1 0.338748137725244 2774 3692 2635 3517 4063 2423 3061 2860 4040 3313 2875 3199 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 31/83 Arthur Liberzon 1.07831118181466e-05 1.86525145735825e-05 4375 3071.90909090909 3062 9.802876973645e-07 938 1.86916903677859 -1.3105030183318 -1 2.27373924250225 4371 3062 2119 2717 2609 3304 4490 4114 938 2365 3702 3200 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 10/19 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2510 3277.54545454545 3064 0.00793650793650794 2442 1.35617365902733 1.50796351817516 1 0.364293048215545 2509 4356 2857 3833 4585 3064 2646 3233 3694 2442 2834 3201 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 27/74 Jessica Robertson 4.14900600901247e-08 1.71448343547023e-07 2645 2925.27272727273 3064 3.77182371569007e-09 848 1.41070320416718 1.62996575297017 1 2.45503530399147 2644 3064 2149 3943 848 4100 3201 3043 3507 2021 3658 3202 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 25/47 Arthur Liberzon 9.64286533632605e-06 1.68417692754468e-05 3765 3073 3068 8.76627963857017e-07 2269 1.10849199330292 0.834243956411063 1 1.36106330160687 3762 2383 3068 3956 2584 2269 3291 2857 3692 3137 2804 3203 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 43/131 Jessica Robertson 5.81929770986723e-07 1.37747552220302e-06 4105 3192.09090909091 3068 5.29027204468253e-08 1880 1.43711456709728 -0.73294718323429 -1 2.16648428493568 4102 3406 2567 2249 1880 3068 4565 2495 2732 3867 4182 3204 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 9/66 Jessica Robertson 0.00198279241433295 0.00257878580448632 3620 3083.81818181818 3068 0.000198456379877777 1639 1.6858127191998 -1.92381993635717 -1 1.12245856339937 3618 1779 4425 2754 3458 2976 4661 3276 1639 3068 2268 3205 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 29/63 Jessica Robertson 0.00474564298197828 0.00599086288080555 2305 2904.90909090909 3068 0.000432355534547903 1073 1.2890528523293 -1.18553020205028 -1 0.736907764423595 2305 3471 3260 4460 3715 1073 2432 3053 3068 3468 1649 3206 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 40/80 John Newman 3.51446222452042e-05 5.56001687511907e-05 2640 3309.90909090909 3069 3.19501669882423e-06 2636 1.37385579731591 1.54176573839647 1 1.50359742847829 2636 4487 3069 4027 2847 4112 2860 2665 2738 3755 3213 3207 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 16/51 Arthur Liberzon 0.00129674248337746 0.00171073628296925 1940 2830.36363636364 3069 0.000117955222868424 1691 1.78171274293555 1.89350653426702 1 1.26799262385022 1937 3325 1771 4165 3406 2883 1807 3623 3457 1691 3069 3208 M13748 REACTOME_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCONEOGENESIS.html Genes involved in Gluconeogenesis 20/48 Reactome 0.00281503081865056 0.00361502724477843 2300 2947.27272727273 3070 0.000256239934888541 1403 1.18810955682658 -1.25847681399154 -1 0.746244031167669 2297 4094 3070 3185 4661 1403 2345 1706 3895 3957 1807 3209 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 113/279 Arthur Liberzon 0.000123194732955 0.000180855425635066 2370 3083 3070 1.12001483732709e-05 1285 1.08099096049684 -0.947901141944973 -1 1.04064360440462 2368 3679 3623 4199 3070 1285 2957 2775 3923 4135 1899 3210 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 33/83 John Newman 9.37279383255986e-05 0.000139342994604618 4505 2939.36363636364 3071 8.52108470110548e-06 1285 1.61859313336072 1.74805240455012 1 1.60532792746333 4502 2615 1627 1305 3028 3821 3802 3388 3071 1285 3889 3211 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 56/129 John Newman 2.53423784230728e-07 6.91323101041381e-07 3070 3293.54545454545 3072 2.30385284930258e-08 1574 1.70928592644419 -1.52728512982318 -1 2.70842347131423 3070 3253 3006 2823 1574 4608 3072 4253 2395 3915 4260 3212 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 11/79 Jean Junior 0.0647549894340987 0.0746474490745846 2125 3113.54545454545 3073 0.00606758473710858 2123 1.53528109214719 1.53528109214719 1 0.445045617702111 2123 3806 2424 3824 4029 2794 2403 3073 4108 3336 2329 3213 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 54/196 Arthur Liberzon 5.67396644532294e-08 2.14453831283808e-07 2970 2892.72727272727 3074 5.15815144696259e-09 989 1.58380169164146 -1.39003518279491 -1 2.71667969220328 2970 4288 2305 3074 989 2124 3761 3155 3743 3085 2326 3214 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 9/32 Jessica Robertson 0.000114416121327913 0.000168495897090697 3075 3317.27272727273 3075 1.14422012726798e-05 1779 1.54851339472048 -2.24746547769135 -1 1.50296084669373 4047 2714 4487 3620 3075 3649 4040 1779 2994 3071 3014 3215 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 9/22 Arthur Liberzon 0.00167035247225435 0.00218761086779873 2295 3019.36363636364 3075 0.000167160933690423 1446 1.12653220100534 1.21592254526036 1 0.770776920337272 2294 3635 4629 4396 3845 2264 2037 1635 3957 3075 1446 3216 M984 BIOCARTA_TOLL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TOLL_PATHWAY.html Toll-Like Receptor Pathway 37/78 BioCarta 1.90811905755397e-05 3.16175597726234e-05 3080 2782.81818181818 3076 1.73466873398521e-06 1482 1.15043704451088 -1.10823094706245 -1 1.33162182978017 3076 3203 3432 2674 2721 1482 3951 1836 3428 3259 1549 3217 M164 PID_ERBB1_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_DOWNSTREAM_PATHWAY.html ErbB1 downstream signaling 18832364 83/159 Pathway Interaction Database 2.96447837137345e-08 1.36339724791565e-07 3805 2759.90909090909 3076 2.69498037392683e-09 702 1.36824210516035 -1.22672525673722 -1 2.41616188821261 3805 1317 3076 789 702 3590 2920 4503 2434 3083 4140 3218 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 18/42 Arthur Liberzon 0.35943518917414 0.375209021267548 2470 3201 3077 0.0396825396825397 2458 0.958293861551194 -0.863504854417499 -1 0.104936706313007 2468 3235 3077 2831 4156 2458 2717 3500 4320 3480 2969 3219 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) 13/39 Reactome 0.00887366861034252 0.0109801983385437 3080 2880.18181818182 3078 0.000809969441056644 1120 2.20827988129199 2.11903732415393 1 1.11294465455859 3078 3034 1120 2638 3608 3760 3497 2203 3204 1327 4213 3220 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 14/32 John Newman 8.25381720461917e-05 0.000123609419689503 2595 2890.63636363636 3080 7.50375171112861e-06 1243 1.91482700449267 -1.64473217177056 -1 1.924761880611 2592 3327 1243 3123 3005 3321 2185 3775 3744 2402 3080 3221 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 5/13 Jessica Robertson 0.000236659576277181 0.00033564975013162 2185 2804.72727272727 3080 2.36684783545209e-05 1355 0.905952316297927 1.12311789004697 1 0.809557943798612 2184 3080 4472 4329 3191 2237 1355 1697 3176 3296 1835 3222 M2602 BIOCARTA_RANKL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RANKL_PATHWAY.html Bone Remodelling 8/19 BioCarta 1.35160024137629e-07 4.13690315551226e-07 4615 2928.45454545455 3082 1.35160032358334e-08 1386 0.883200082297997 -0.757123283643423 -1 1.45012239164484 4611 1817 3819 2407 1386 3522 3157 3082 2333 2862 3217 3223 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 16/35 Reactome 0.0241571102031586 0.0289144874615584 4590 3369.36363636364 3082 0.00222059256425866 2557 1.348304959562 -1.12854764670495 -1 0.533694433696438 4586 2953 2846 2588 3703 2557 3082 4310 3060 3242 4136 3224 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 20/38 Arthur Liberzon 0.000129562992841238 0.000189491942713496 2715 2734 3082 1.17791476117358e-05 1157 1.29441754663162 -1.72412316387061 -1 1.23935899958588 2714 3210 2707 3929 3082 1402 3736 1777 3214 3146 1157 3225 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 19/34 Kevin Vogelsang 1.01549159181174e-06 2.23933816434344e-06 4100 3052.90909090909 3082 9.23174600499863e-08 1742 1.2550481592238 -1.12504292513991 -1 1.82388846907603 4096 2492 2123 3732 2039 3082 4335 1742 4026 2507 3408 3226 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 14/35 Leona Saunders 0.0357302674320502 0.0421424699689372 2635 3121.63636363636 3084 0.00330219190810569 1694 1.43819866273146 1.16213420133918 1 0.508754799403932 2633 3902 2590 4571 3750 2936 1694 3773 3084 1878 3527 3227 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 12/24 Arthur Liberzon 0.00875559061080981 0.010839814425959 3085 3195.45454545455 3084 0.00079914832979 2052 1.9051202221208 1.9051202221208 1 0.96289449970055 3084 2847 2617 3744 3600 4592 4018 2052 2448 3425 2723 3228 M196 PID_IL23_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL23_PATHWAY.html IL23-mediated signaling events 18832364 23/54 Pathway Interaction Database 0.000132089945088969 0.000192946846224099 1645 3165.63636363636 3085 1.20088978684329e-05 1642 1.61687716527099 -1.50045547849937 -1 1.54483928635601 3706 2743 1642 2549 3085 4531 2816 4041 3480 1645 4584 3229 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 17/49 Leona Saunders 4.68372208808902e-06 8.69913662496438e-06 3085 2868.27272727273 3085 4.25793823599745e-07 1318 2.15472549534648 1.87580546970531 1 2.80469785526732 3085 2951 1318 3230 2422 3758 3141 3423 2343 1806 4074 3230 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 9/15 Arthur Liberzon 1.03868641569548e-05 1.80217562487839e-05 3580 3051.81818181818 3085 1.03869127064004e-06 1294 1.56634649174956 -1.30894417006215 -1 1.91139186372216 3580 1294 4180 2692 2625 3384 2802 4496 3085 1672 3760 3231 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 54/131 Kate Stafford 3.64316543987739e-08 1.57780713967333e-07 2685 3053.18181818182 3086 3.3119686365524e-09 784 1.6984473157449 -1.09961202757929 -1 2.97155602738554 2681 4433 2748 3711 784 4672 3218 2124 2467 3086 3661 3232 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 473/1154 Arthur Liberzon 2.54734477174843e-08 1.22429308722186e-07 4475 3225.09090909091 3087 2.31576800113065e-09 643 1.52681348162681 -1.13909538956911 -1 2.71453578519651 4475 3641 2459 2437 643 2613 4654 4676 3051 3087 3740 3233 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 47/98 Jessica Robertson 4.19320415191581e-07 1.04858061726413e-06 3745 2949.27272727273 3088 3.81200450103776e-08 1767 1.6419874757901 -1.31263216345157 -1 2.52537552555207 3741 3088 2283 2295 1767 3296 3304 3948 2225 2212 4283 3234 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 12/32 Jessica Robertson 0.00285740369357276 0.00366642763090962 2890 3161.36363636364 3088 0.000260101973513038 1743 1.29965259510191 -1.29965259510191 -1 0.814253796275105 2888 4001 2990 4339 3484 1743 3088 3352 4038 2752 2100 3235 M7298 BIOCARTA_ASBCELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ASBCELL_PATHWAY.html Antigen Dependent B Cell Activation 4/14 BioCarta 0.000291293820700473 0.000407585202688091 2770 2964.81818181818 3089 2.91332011186764e-05 1325 2.60483654455918 2.60483654455918 1 2.27117626764072 2768 2579 3814 3795 3966 3509 2585 1325 3121 3089 2062 3236 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 7/19 Arthur Liberzon 5.4309658820277e-07 1.29910699965196e-06 3495 2888.09090909091 3090 5.43096720932072e-08 1352 1.75784938746856 -2.2513590317629 -1 2.6615018504322 3494 1641 4646 3090 1885 3104 4258 2213 3221 1352 2865 3237 M4361 KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION.html Proximal tubule bicarbonate reclamation 11/32 KEGG 0.000546172471388387 0.000745735489780298 3900 2997.18181818182 3091 4.96643737662853e-05 1514 2.04770299478202 -2.44774995282229 -1 1.64721822732991 3899 1640 1514 2757 3301 4014 3091 2923 3336 1963 4531 3238 M1014 REACTOME_IL_6_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_6_SIGNALING.html Genes involved in Interleukin-6 signaling 5/11 Reactome 0.000125744371978238 0.00018430970506413 4380 3066 3092 1.25751487786122e-05 1328 1.61652544647971 -1.07378519301828 -1 1.55277322184092 4378 2441 4070 2467 3092 3658 3801 1623 1328 2237 4631 3239 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 32/64 Reactome 0.0235838094051917 0.0282716118886488 1330 3005.54545454545 3092 0.0021673169398565 1327 0.706354207113552 -0.722052427229176 -1 0.281367552405707 1327 3092 3706 3448 4119 1438 2344 3088 4042 4195 2262 3240 M7272 KEGG_PARKINSONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PARKINSONS_DISEASE.html Parkinson's disease 56/151 KEGG 0.0428771499461111 0.0502180266552054 1575 3011.63636363636 3094 0.00397603146351268 1572 0.754090720104267 -0.606091518622159 -1 0.251986916132925 1572 2973 3744 3447 3899 1618 1990 3094 4079 4293 2419 3241 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 36/56 Reactome 9.28846911473137e-07 2.06969882413843e-06 3955 2947.72727272727 3095 8.44406639668593e-08 1473 1.14157512436636 -1.04310806218078 -1 1.66903057893561 3951 2378 3195 1473 2013 4424 2624 3095 2367 3212 3693 3242 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 4/14 Jessica Robertson 6.23921997469913e-05 9.49561052336477e-05 3590 2950.63636363636 3095 6.23939515701801e-06 944 4.19475304697008 -4.19475304697008 -1 4.34008911647785 3587 2893 4470 3095 3945 3056 4637 1040 944 3109 1681 3243 M9043 BIOCARTA_GH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GH_PATHWAY.html Growth Hormone Signaling Pathway 20/53 BioCarta 3.9454666527246e-05 6.1979405748131e-05 4285 3048.09090909091 3096 3.58685219296435e-06 1307 1.02391562163237 -1.04389931158987 -1 1.10818679455815 4284 1677 3096 1307 2868 3673 4162 3047 2671 3611 3133 3244 M776 REACTOME_PROTEIN_FOLDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROTEIN_FOLDING.html Genes involved in Protein folding 32/70 Reactome 0.000143126366249945 0.000208483106076233 3750 2937.81818181818 3096 1.30123344120903e-05 1050 2.07082207954634 -1.2799152368075 -1 1.96064463288943 3748 3497 1936 1503 3096 3600 4673 2206 1050 2858 4149 3245 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 6/11 Arthur Liberzon 0.000801057403242342 0.00107680866081286 3100 3235.09090909091 3097 8.01346311660333e-05 1722 1.82390502655396 -2.07292754694891 -1 1.39233732946914 3880 2922 4167 3213 3363 3097 4265 3097 3059 1722 2801 3246 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 24/60 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2020 3037.36363636364 3097 0.00793650793650794 1907 1.40077785715242 -1.03660694008453 -1 0.376274558634319 2016 3476 2397 1907 4220 2395 2590 4092 3721 3500 3097 3247 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 8/20 Arthur Liberzon 0.0120011583743011 0.0147179869515768 2835 3074.81818181818 3097 0.0012066467834731 1410 1.11755754078413 -1.11755754078413 -1 0.526659362846537 2834 2472 4624 3810 3889 1601 1410 4315 3097 3690 2081 3248 M7330 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE.html Glycosaminoglycan biosynthesis - heparan sulfate 14/28 KEGG 2.37819740348256e-05 3.86952535858308e-05 2970 3102.45454545455 3098 2.16202101105227e-06 2195 1.22680867950906 1.01090525868976 1 1.39233794653838 3014 3105 2970 3878 2765 3333 2195 2970 3098 3622 3177 3249 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 29/69 Jessica Robertson 6.82641344509838e-05 0.000103355649123525 4465 3034.72727272727 3098 6.20602297465539e-06 850 2.106346793294 -2.32004384040047 -1 2.1593816185328 4463 2909 1075 3098 2977 3420 4104 3403 3076 850 4007 3250 M846 REACTOME_FRS2_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FRS2_MEDIATED_CASCADE.html Genes involved in FRS2-mediated cascade 11/43 Reactome 7.91656423467771e-05 0.000118786487363752 3915 3144.90909090909 3099 7.19713556518949e-06 2429 0.965415757139475 -0.947255398924408 -1 0.97471671558863 3913 2649 2853 2913 3001 3099 3455 3115 3839 3328 2429 3251 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 4/10 Arthur Liberzon 0.00106115242297389 0.00140945585432416 2105 2597.81818181818 3099 0.000106165948379313 902 2.30449734757622 2.30449734757622 1 1.68991251614096 2102 3675 4229 3360 3850 1515 902 3137 1345 3099 1362 3252 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 11/30 Arthur Liberzon 0.00256892401401224 0.00331077500815768 3100 3141.09090909091 3099 0.000233811694630799 2501 1.14309940308281 -0.796846259398028 -1 0.729199827165067 3099 2501 2663 3249 3475 3523 2592 2883 4190 2624 3753 3253 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 47/103 Jessica Robertson 3.43232225253714e-07 8.90086445787992e-07 4125 3227.09090909091 3100 3.12029344366345e-08 1687 1.40178370798179 -0.957800766929357 -1 2.18160332858939 4125 3434 2411 4088 1687 2102 4367 4362 2874 2948 3100 3254 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 47/113 Jessica Robertson 0.00018086915709894 0.000261187325166605 4245 3251.36363636364 3102 1.64440026047706e-05 2045 1.34611457439969 1.51157753778911 1 1.24060422306167 4244 2227 2219 2045 3126 3102 4556 4642 2211 2945 4448 3255 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 15/21 Reactome 0.000150504593329997 0.000218754505069592 2695 2979.90909090909 3103 1.36831718648066e-05 1140 0.554904359272267 -0.472701998249631 -1 0.522399599494114 2693 3264 3594 4040 3103 1140 1546 2789 4077 4502 2031 3256 M3126 KEGG_LEISHMANIA_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEISHMANIA_INFECTION.html Leishmania infection 38/98 KEGG 0.000219829857356405 0.000313583778256351 3235 2802.09090909091 3104 1.9986529674035e-05 1892 1.62979583055486 -1.38794197185771 -1 1.4687642701993 3234 3465 2251 2058 3159 2229 3817 3261 3104 1892 2353 3257 M938 REACTOME_CIRCADIAN_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CIRCADIAN_CLOCK.html Genes involved in Circadian Clock 29/72 Reactome 6.41353808614114e-05 9.73561369344262e-05 3555 3354.18181818182 3106 5.83065914917649e-06 2381 1.3923338735933 -1.08709638443122 -1 1.43669177652711 3552 2381 2514 3106 2969 4171 3872 4550 2807 2589 4385 3258 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 4/18 Jessica Robertson 0.147859119791321 0.157148522418265 3020 3273.18181818182 3106 0.0158730158730159 2325 1.11529087534716 1.11529087534716 1 0.230555155166984 3016 2684 4348 3220 3964 2942 2325 3075 4193 3106 3132 3259 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 10/36 Kevin Vogelsang 0.00358130819655938 0.0045665333902251 3110 2862.63636363636 3106 0.000326104673854762 1688 2.09082388470198 -2.36108544931495 -1 1.25866059874732 3106 4178 1922 4279 3510 1818 3428 2281 3421 1858 1688 3260 M238 PID_THROMBIN_PAR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_THROMBIN_PAR1_PATHWAY.html PAR1-mediated thrombin signaling events 18832364 28/67 Pathway Interaction Database 4.92740421346573e-05 7.62795379725814e-05 4520 3295.18181818182 3110 4.47955870676065e-06 2107 1.90311234084921 -1.57714779180282 -1 2.0156093971861 4519 3472 2107 2617 2911 3670 4613 3925 2789 2514 3110 3261 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 7/27 Arthur Liberzon 0.000789981230515076 0.00106283435147679 2755 2982.27272727273 3110 7.90262202756753e-05 1486 1.94717444446043 2.38400076161736 1 1.48928034415417 2753 3307 4217 3110 3477 3330 2985 1486 2810 1933 3397 3262 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 0.00146502891101159 0.00192624171633006 1555 2882.18181818182 3110 0.000146599564748972 949 2.40944734495185 2.40944734495185 1 1.68279870340346 1555 3578 4480 4331 3832 1677 949 3050 3641 3110 1501 3263 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 0.0276048446219415 0.0328816222415907 2480 3313.36363636364 3111 0.00279538747602644 1620 1.03140326698423 1.03140326698423 1 0.393442980924476 2476 3774 4511 4616 4247 2341 1620 2567 4344 3111 2840 3264 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 11/22 Leona Saunders 1.97582750214892e-06 4.00810721864495e-06 3115 3185.45454545455 3112 1.79620843331688e-07 1972 1.06733086822602 1.17848259371103 1 1.48168197123711 3112 3106 2750 2964 2225 4271 3540 3614 3667 1972 3819 3265 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 6/14 Signaling Transduction KE 0.0193912804128818 0.0233712808679949 4110 3150 3113 0.00195625979571453 2359 1.33785616567943 -1.07378519301828 -1 0.561366432123181 4109 3113 3888 3363 3692 2359 2369 3748 2599 2468 2942 3266 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 103/212 John Newman 0.000147035312933227 0.000213911045142845 2980 3245.72727272727 3113 1.33677400768366e-05 2278 1.31602104008172 1.59299450840142 1 1.24222399366017 2977 3951 3318 2970 3099 3933 2278 2666 3113 3694 3704 3267 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 98/189 John Newman 0.000159618056460208 0.000231283306299485 1295 2724.27272727273 3114 1.45117853191996e-05 840 1.07302947944549 -1.01407500118673 -1 1.00349887618879 1291 3782 3632 4622 3114 840 1963 1611 3630 4213 1269 3268 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 4/11 Paolo Fardin 0.00567325606269545 0.00711586667820955 2815 3122.18181818182 3114 0.000568779194372123 1406 1.35057753767812 -1.84462823571403 -1 0.746115914513452 2813 2082 4651 3480 3567 2220 1406 4465 4182 3114 2364 3269 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 78/182 Jessica Robertson 4.21329912002767e-07 1.05242642198559e-06 2990 3370.45454545455 3116 3.83027266084724e-08 1769 1.39200336508642 -1.23615713939635 -1 2.14033085162998 2987 3116 2710 4589 1769 4485 2739 3859 3458 2762 4601 3270 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 4/16 Jessica Robertson 0.000277715369868309 0.000390334200120844 3120 3081 3116 2.77750082595958e-05 2052 2.43606906156709 -2.43606906156709 -1 2.1357952572027 3116 2081 4426 3733 3220 2982 3671 2282 4172 2052 2156 3271 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 34/77 Kevin Vogelsang 3.27832682725389e-07 8.55358547467245e-07 4025 3221.36363636364 3117 2.98029755979399e-08 1670 1.13020040841655 -0.941727955806409 -1 1.76396133610481 4024 2660 2772 3127 1670 2580 4100 4675 3631 3079 3117 3272 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 15/25 Leona Saunders 0.0530236311286824 0.0615936379447213 3120 3358.27272727273 3118 0.0049405858464696 1671 0.900760186822357 -0.934976260824443 -1 0.280452599789536 3118 3802 3085 4358 4338 1671 2811 2779 4471 4053 2455 3273 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 43/84 Jessica Robertson 4.71595680258559e-06 8.75206874333311e-06 3810 3097.36363636364 3118 4.28724264710893e-07 1958 1.57901296458696 -1.44403546237377 -1 2.05425171417559 3806 3200 2302 3190 2425 2905 4230 4159 2778 1958 3118 3274 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 64/149 Arthur Liberzon 0.0755750203764945 0.0865879084313577 4555 3402.27272727273 3119 0.00711848618638459 2167 1.74038430203952 -1.66137637405259 -1 0.475652807249538 4555 3119 2167 3064 3834 2645 4460 4469 2769 2463 3880 3275 M777 REACTOME_METABOLISM_OF_NUCLEOTIDES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_NUCLEOTIDES.html Genes involved in Metabolism of nucleotides 46/85 Reactome 5.07023502639711e-06 9.35766889865965e-06 2865 2986.45454545455 3120 4.6093151923305e-07 2254 1.35820819768518 -1.12678613558014 -1 1.7568397095108 2865 3405 2330 3484 2439 2254 3120 3452 3380 3203 2919 3276 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 13/36 Reactome 5.63473196761842e-05 8.63451733167428e-05 4055 3265.63636363636 3120 5.12261481082201e-06 2244 1.12913049004234 -1.12191087089677 -1 1.18024183174032 4054 2320 3120 3174 2939 4522 2244 3484 2973 2911 4181 3277 M9726 KEGG_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PANCREATIC_CANCER.html Pancreatic cancer 43/90 KEGG 1.43788972703689e-06 3.05437500493874e-06 4325 3075.27272727273 3121 1.30717333347517e-07 2097 1.53123717604802 -0.931650753329631 -1 2.17216465175047 4322 3121 2668 2479 2128 2097 4387 3327 2169 3354 3776 3278 M12975 BIOCARTA_VEGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VEGF_PATHWAY.html VEGF, Hypoxia, and Angiogenesis 18/64 BioCarta 0.000168320982738112 0.000243366900682133 4500 3184.72727272727 3121 1.5303078388933e-05 1747 1.38710434887839 -1.22334608594422 -1 1.28933113996825 4499 1807 2770 1747 3121 2958 3826 4395 3079 3472 3358 3279 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 7/29 Leona Saunders 0.0266663774620906 0.0318122822778403 2805 3230.90909090909 3122 0.00269918814928266 1949 0.830764244560445 0.830764244560445 1 0.319974614793053 2802 1949 4183 3630 3723 3122 2454 2286 3936 4554 2901 3280 M5467 BIOCARTA_GRANULOCYTES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GRANULOCYTES_PATHWAY.html Adhesion and Diapedesis of Granulocytes 7/21 BioCarta 7.0452794550207e-05 0.000106325859987849 3135 2997.27272727273 3128 7.04550282681933e-06 1818 1.54990050327641 -1.37350612673371 -1 1.58401935955338 3134 1818 3811 3736 3000 3071 2035 3128 3856 1926 3455 3281 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 62/185 Arthur Liberzon 4.07758503668159e-07 1.0239851812374e-06 3920 2899 3128 3.70689617494624e-08 1217 1.32338694769547 -1.45266914749509 -1 2.03887697025799 3920 3143 3128 3759 1759 1885 4553 2085 3468 2972 1217 3282 M3896 KEGG_INOSITOL_PHOSPHATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INOSITOL_PHOSPHATE_METABOLISM.html Inositol phosphate metabolism 30/55 KEGG 0.0122903780077079 0.015059517491591 3130 3085.36363636364 3129 0.00112359822653728 1485 1.14522948991433 -1.23974577310138 -1 0.536765316801567 2225 3721 3129 4500 3772 1485 3126 2178 3900 4033 1870 3283 M110 PID_IL1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL1_PATHWAY.html IL1-mediated signaling events 18832364 22/47 Pathway Interaction Database 6.48931523514881e-05 9.84745181085081e-05 3825 3185.36363636364 3129 5.89955150695888e-06 2470 1.2463326098237 -1.28627259752637 -1 1.28444885122328 3821 3262 3314 3129 2970 3050 4092 2470 3429 2829 2673 3284 M591 REACTOME_SIGNALING_BY_HIPPO http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_HIPPO.html Genes involved in Signaling by Hippo 9/26 Reactome 0.0088458490687038 0.0109486658045288 3010 3280.27272727273 3130 0.000888125968431512 1813 1.32302679193761 -1.32302679193761 -1 0.667213434090615 3006 4070 3933 3130 4552 2027 2948 2378 4451 3775 1813 3285 M10145 BIOCARTA_PTEN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTEN_PATHWAY.html PTEN dependent cell cycle arrest and apoptosis 14/25 BioCarta 0.000184994535192078 0.00026656961620851 2855 3121.81818181818 3131 1.68190993566125e-05 2225 1.14200350026204 1.14200350026204 1 1.04988950092001 2853 2596 3291 2225 3131 4040 3122 2348 3657 3626 3451 3286 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 25/97 Arthur Liberzon 4.2498711233292e-07 1.05873982370657e-06 3140 3106.18181818182 3131 3.86351994936578e-08 1772 0.967055201932302 -0.82887870993599 -1 1.48628850876547 3137 2489 3131 4013 1772 4099 3017 2733 3616 3565 2596 3287 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 52/117 John Newman 9.74696651930311e-09 7.04850078849604e-08 3260 2763.54545454545 3131 8.86087869316951e-10 238 1.43939711801021 -1.50192937768388 -1 2.64789593920818 3259 1877 2487 3131 238 3953 3251 2395 3323 2325 4160 3288 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 15/37 Reactome 0.0242979610646906 0.0290756500380848 3370 3397.63636363636 3132 0.00223368588937729 2795 0.912226597010345 -0.912226597010345 -1 0.360516717032778 3366 2812 3132 2873 3705 2795 4610 3081 4062 4052 2886 3289 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 16/49 Yujin Hoshida 0.00566528973271165 0.007107777158631 2910 3049.36363636364 3133 0.000516357401190754 1840 1.40497433309857 -0.714895043095391 -1 0.776345526591132 2907 3133 2839 4214 3648 3836 2213 1840 2261 3248 3404 3290 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 29/54 Arthur Liberzon 0.000186276660920399 0.000268087356594899 4570 3152.45454545455 3133 1.69356759145887e-05 1725 1.71389554079335 -1.18267460795288 -1 1.57456585988917 4570 1725 2024 3552 3133 1900 3784 4284 2657 2594 4454 3291 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 50/109 Leona Saunders 1.20346811623131e-07 3.76465393368485e-07 4365 3048.27272727273 3134 1.09406198369522e-08 1319 1.11272158211391 1.10730427667598 1 1.83869319856096 4364 1795 3356 3115 1319 2768 3941 3569 2910 3134 3260 3292 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 3/11 Jessica Robertson 0.00732610594564487 0.0091109693368609 2570 3367.36363636364 3134 0.000735037093059881 1272 1.26337156305408 1.26337156305408 1 0.663059496255043 2569 3845 4519 3134 4383 2865 1272 4189 4530 2813 2922 3293 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 104/291 Jessica Robertson 3.86951832724706e-07 9.81730529587423e-07 3135 3050.54545454545 3135 3.51774455258724e-08 1734 1.34264481503691 1.69463273404523 1 2.07486700452881 3135 3340 2981 2543 1734 2853 3520 4099 2359 3857 3135 3294 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 27/80 Arthur Liberzon 0.000332475508107329 0.000462583203975934 3650 2905.90909090909 3137 3.02296149253223e-05 1371 1.58595046812523 -1.53373221336214 -1 1.36037722930349 3648 1974 1837 2418 3235 2717 4438 3927 3137 1371 3263 3295 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 19/46 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2285 3215.63636363636 3137 0.00793650793650794 1906 2.24791556170663 2.40978488626181 1 0.603831373012804 2283 4346 1906 3137 4332 3808 2745 3265 3470 3005 3075 3296 M16004 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION.html Antigen processing and presentation 37/124 KEGG 0.0602356178333645 0.0696260742888865 2680 3055.18181818182 3139 0.00563190759326863 1916 1.71563433116437 -1.54273944451248 -1 0.510672184394779 2680 4023 2222 3523 3882 1916 3139 3612 3772 2538 2300 3297 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 24/59 Arthur Liberzon 5.90168447261807e-06 1.07191059839877e-05 3140 3217.45454545455 3139 5.36518209494636e-07 1110 1.89660377915803 2.44354422956331 1 2.4244754740411 3139 4216 2629 3053 2477 4634 3469 4410 1110 3033 3222 3298 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 25/57 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3140 3320.36363636364 3139 0.00793650793650794 1867 2.18874896282492 2.71175764880545 1 0.587938133121874 2586 4029 1867 3136 4217 4302 3724 2864 2940 3139 3720 3299 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 13/70 Jessica Robertson 0.0354336647325688 0.0418031603567013 2605 3108.90909090909 3140 0.00327432513579128 1332 1.99215858981355 -2.01992374486849 -1 0.706514158700366 2604 3506 1380 3893 3749 2997 4525 3140 3947 1332 3125 3300 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 3/15 Leona Saunders 0.0380734407788366 0.0448046568281337 2840 3555.27272727273 3141 0.0038741931737165 2839 0.406574583152766 0.406574583152766 1 0.141041253195656 2839 3004 4294 4156 3766 3141 2845 2951 4638 4590 2884 3301 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 118/223 Arthur Liberzon 3.54424856337993e-05 5.60335653441241e-05 1855 3099.63636363636 3141 3.22209605754047e-06 1780 0.963272989046071 -0.729418501777003 -1 1.05340518730559 1853 3141 3747 3520 2849 1780 2787 4058 3291 4320 2750 3302 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 20/82 Jessica Robertson 1.89655418442519e-06 3.86906961611512e-06 3145 3026.90909090909 3143 1.72414165399072e-07 1712 1.47203036226379 1.40898679135154 1 2.0492963764157 3143 2699 1919 4005 2214 4181 3151 2753 3285 1712 4234 3303 M45 PID_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD40_PATHWAY.html CD40/CD40L signaling 18832364 19/44 Pathway Interaction Database 0.000196306471416403 0.000281657111162665 3330 3345.72727272727 3144 1.78476354612202e-05 2465 0.971071846008465 -0.909071110128096 -1 0.886773007862258 3330 2879 3117 3135 3144 2465 4240 4281 4059 3540 2613 3304 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 60/132 Reactome 4.21636630200767e-06 7.90315699648318e-06 4225 3158.72727272727 3144 3.83306762074767e-07 2307 1.14769397922732 -1.10999835001704 -1 1.50619831544463 4223 3144 3436 2307 2404 3605 2774 3154 2990 3661 3048 3305 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 14/33 KEGG 2.23503023336603e-06 4.483455339706e-06 3930 3123.09090909091 3145 2.03184773089774e-07 1218 0.94259587479026 -0.992158660100881 -1 1.29672232912412 3929 1218 2803 3731 2250 2739 3725 4345 3145 3623 2846 3306 M3578 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION.html Progesterone-mediated oocyte maturation 41/92 KEGG 3.41187624358744e-06 6.55248035961097e-06 3145 3391.45454545455 3145 3.10171048628808e-07 1988 1.0535435932745 -0.983601040288021 -1 1.40469531819552 3145 2833 3123 1988 2345 4289 2743 4564 3894 3795 4587 3307 M10 PID_BCR_5PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BCR_5PATHWAY.html BCR signaling pathway 18832364 44/107 Pathway Interaction Database 0.00148533339744043 0.00195129585096884 2835 2973.63636363636 3145 0.000135121561044105 1589 1.20145178176832 -1.09044480724238 -1 0.837379702848927 2832 3145 3488 1752 3418 1589 4430 3107 3466 3391 2092 3308 M213 PID_AR_NONGENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_NONGENOMIC_PATHWAY.html Nongenotropic Androgen signaling 18832364 20/48 Pathway Interaction Database 7.87055409554986e-06 1.39543762738353e-05 4025 3134.45454545455 3145 7.15507477526517e-07 1750 1.26869319072951 -1.05915564357283 -1 1.58442021977061 4021 2591 3051 1750 2540 3145 4345 3467 2585 3615 3369 3309 M12851 BIOCARTA_CELL2CELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELL2CELL_PATHWAY.html Cell to Cell Adhesion Signaling 12/19 BioCarta 0.0721378223378617 0.0827915345273622 2285 3261.54545454545 3146 0.00678343995359921 2284 0.991842276281657 0.852324912716711 1 0.276041180595446 2284 3603 2926 4045 3998 3146 2479 2432 4106 3940 2918 3310 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 9/33 Reactome 9.48410886776248e-08 3.11658724784958e-07 3800 2555.45454545455 3146 9.48410927252995e-09 552 2.27191614097923 -2.20026217263632 -1 3.80212533149564 3797 1073 4034 989 1252 4663 3547 3146 552 1194 3863 3311 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 41/101 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2055 3269.90909090909 3146 0.00793650793650794 2054 1.72048670288955 -1.72048670288955 -1 0.462154252187622 2054 4123 2878 3146 4256 2719 3228 2859 4159 3518 3029 3312 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 9/15 Leona Saunders 0.000306310698135448 0.000427448460828681 2885 3275.54545454545 3147 3.06352928137869e-05 1329 2.36973920306049 2.36973920306049 1 2.0535968650933 2885 4507 4122 4188 4208 3019 2317 1329 3147 3781 2528 3313 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 5/17 Arthur Liberzon 3.62778726619553e-05 5.7257699997953e-05 3355 3210.72727272727 3148 3.62784649133831e-06 2046 1.40577876156398 -2.14189533648495 -1 1.53392199801493 3352 2046 4168 3051 2869 3148 4341 2187 3831 3280 3045 3314 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 40/83 Jessica Robertson 8.04153827056801e-07 1.81778332541639e-06 3150 3124.18181818182 3148 7.31049200904409e-08 1661 1.19372653320641 -0.995449885902186 -1 1.76258479270359 3148 3647 3416 3896 1981 1661 3111 4113 3017 3754 2622 3315 M3115 KEGG_LONG_TERM_POTENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_POTENTIATION.html Long-term potentiation 27/89 KEGG 0.00797645275407024 0.0099060486118426 2205 3123.18181818182 3149 0.000727774574061887 2204 0.9711721650105 1.02504897046356 1 0.500626713499423 2204 3149 3327 2972 3592 2686 2241 4178 3278 3703 3025 3316 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 4/22 Leona Saunders 0.000184152074869336 0.000265518960873141 3915 3019.45454545455 3149 1.84167337043393e-05 1275 2.30885704463788 -2.09768976779706 -1 2.12364342045647 3566 1364 4433 1841 3149 3119 3915 4585 2053 1275 3914 3317 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 173/414 Jessica Robertson 5.73145617198581e-07 1.36194744533091e-06 4115 3272 3151 5.21041605922684e-08 1876 1.50345442876063 -1.37277701139468 -1 2.26839720725577 4113 4243 3036 3596 1876 2099 4382 2940 2700 3856 3151 3318 M18615 KEGG_ALLOGRAFT_REJECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALLOGRAFT_REJECTION.html Allograft rejection 23/70 KEGG 0.00255713584416037 0.00329648928906066 2685 3020.45454545455 3152 0.000232737539724061 2090 1.46572460616215 -1.18902074987566 -1 0.935715244470939 2684 3152 2187 3584 3474 2090 3275 3841 3679 2418 2841 3319 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 15/34 KEGG 4.65514065337189e-07 1.14509129142786e-06 3630 2847.90909090909 3153 4.23194694398853e-08 1499 1.79926544623094 -0.961614057493543 -1 2.74957224601464 3629 3102 1752 3542 1801 3617 4159 1499 1782 3153 3291 3320 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 21/42 John Newman 0.0209910952686448 0.0252410244877777 2910 3325.09090909091 3153 0.00192673607012477 2360 1.57387070609035 -1.40425182612122 -1 0.646867449712014 2909 3153 2360 3872 3691 4469 2850 4127 2509 2715 3921 3321 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 7/23 Arthur Liberzon 0.00195226810957139 0.00254261488645123 3155 3173.63636363636 3154 0.000195398534104661 2439 1.05957410129607 -1.30164419585379 -1 0.707164244626893 3154 2439 4117 3296 3455 2650 3912 2501 2916 3583 2887 3322 M207 PID_RETINOIC_ACID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RETINOIC_ACID_PATHWAY.html Retinoic acid receptors-mediated signaling 18832364 15/42 Pathway Interaction Database 0.0073400851003581 0.00912593228449935 2675 3163.54545454545 3156 0.000669517234628604 1748 0.96999246583219 1.04138280700785 1 0.508906513545847 2673 4269 3030 3978 3636 2573 2189 3224 4323 3156 1748 3323 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 5/14 Reactome 0.0008151022306216 0.00109443239332172 3160 3315.09090909091 3157 8.15401361294657e-05 1501 0.728959731498437 -0.728959731498437 -1 0.55515308144977 3157 3044 3982 3940 3815 2738 2770 1501 4162 4461 2896 3324 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 29/60 Kevin Vogelsang 0.00178848844844726 0.00233775644893273 2890 3037.27272727273 3157 0.000162722186891697 1905 1.68228425485592 1.76321341392251 1 1.13854963910311 2887 3531 2057 1905 3429 4555 3457 2503 3157 2593 3336 3325 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 6/28 Jessica Robertson 6.05764709860744e-07 1.42653866748888e-06 4330 3025 3159 6.05764874988704e-08 874 1.2269195893251 -0.942131393986518 -1 1.84481357405211 4326 874 4437 2234 1922 4471 3369 3159 1496 2492 4495 3326 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 44/127 Arthur Liberzon 2.97457905487111e-08 1.36608347094279e-07 3310 3231.45454545455 3161 2.70416281371805e-09 706 1.2998202411423 -1.04477180248239 -1 2.29505075271807 3306 2942 3161 2821 706 4636 3263 3134 3046 3910 4621 3327 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 11/47 Arthur Liberzon 4.78539187007702e-05 7.42282234464777e-05 4110 3016.45454545455 3162 4.35045087640364e-06 821 1.83990847420842 -2.33215913706765 -1 1.95427226329771 4106 1479 1237 3162 2904 4494 3522 3739 3074 821 4643 3328 M3293 REACTOME_SHC_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_MEDIATED_SIGNALLING.html Genes involved in SHC-mediated signalling 8/20 Reactome 0.00326925366617415 0.00417772639206219 2465 3009 3163 0.000327407325705466 1377 0.568192156212718 -0.568192156212718 -1 0.347695486252776 2463 3163 4082 2227 3511 1377 2101 3363 4544 4514 1754 3329 M825 REACTOME_SHC_RELATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_RELATED_EVENTS.html Genes involved in SHC-related events 8/25 Reactome 0.00326925366617415 0.00417772639206219 2465 3013.72727272727 3164 0.000327407325705466 1378 0.568192156212718 -0.568192156212718 -1 0.347695486252776 2464 3164 4104 2228 3512 1378 2102 3365 4545 4534 1755 3330 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 15/50 Jessica Robertson 0.00092382262387608 0.0012336941622922 2570 2944.90909090909 3164 8.40191621006751e-05 1214 1.93194653505631 2.27511705657153 1 1.44546130096607 3244 2567 2426 2774 3368 2569 4233 3301 1214 3164 3534 3331 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 119/299 Jessica Robertson 4.17637237852712e-08 1.71972591966415e-07 3060 3113.81818181818 3164 3.79670223437212e-09 852 1.26801734865389 -0.933364295853969 -1 2.20628778647398 3059 3520 3164 3067 852 3815 3610 2404 3134 3820 3807 3332 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 6/20 Jessica Robertson 2.55784458025384e-06 5.04463792216729e-06 3550 2866.72727272727 3165 2.55784752441461e-07 875 1.47693126402706 -0.95763839813972 -1 2.01234684768583 3550 875 4446 2488 2303 4621 3990 3456 913 1727 3165 3333 M144 PID_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CERAMIDE_PATHWAY.html Ceramide signaling pathway 18832364 34/69 Pathway Interaction Database 0.000228936381694661 0.000325582969536018 2950 2960.18181818182 3167 2.08145644310787e-05 1445 0.939529005920763 -0.869894079126447 -1 0.842757941552612 2947 2303 3329 2723 3167 1445 3235 3317 3905 3750 2441 3334 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 6/14 Arthur Liberzon 1.54520004167261e-05 2.59713321207957e-05 3570 3134.09090909091 3167 1.54521078617202e-06 1820 1.31640756399544 -0.990419481627758 -1 1.552659565358 3570 1820 4232 3167 2701 2615 3289 4482 2866 2483 3250 3335 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 8/12 Pathway Interaction Database 0.000209480056566963 0.000299549449213545 4170 3112.90909090909 3168 2.09499806039534e-05 2094 1.60845739101771 -1.70368443960667 -1 1.45776104807169 4169 2325 3905 2241 3168 4328 3860 2415 3451 2094 2286 3336 M874 REACTOME_SIGNALING_BY_ILS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ILS.html Genes involved in Signaling by Interleukins 61/135 Reactome 1.68170091401583e-06 3.48507888001818e-06 4075 3161.54545454545 3168 1.52882018138671e-07 1663 1.23324144868274 -1.01120000563021 -1 1.73126425273674 4072 2452 3136 1663 2176 3419 3509 4466 3168 2902 3814 3337 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 505/1159 Jessica Robertson 2.48435562924177e-08 1.20328077343124e-07 4580 2975 3168 2.48435565701587e-09 677 1.41034385144754 -1.04780170512137 -1 2.5101907471588 4580 2257 4621 1146 677 1494 4505 4283 2188 3806 3168 3338 M15243 REACTOME_GAP_JUNCTION_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_DEGRADATION.html Genes involved in Gap junction degradation 6/11 Reactome 5.40278290699221e-05 8.29536064946444e-05 1875 2598.09090909091 3169 5.40291426677118e-06 807 1.45541725130039 1.45541725130039 1 1.52781324747264 1875 3545 3910 4079 3658 1238 1072 1789 3169 3437 807 3339 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 36/100 Kevin Vogelsang 4.65114296384963e-06 8.64891108277753e-06 4160 3176.81818181818 3169 4.22832072465458e-07 2072 1.1022113581348 -1.07137178419643 -1 1.43540595057596 4158 2343 2595 3169 2419 3139 4414 3289 3739 2072 3608 3340 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 11/22 John Newman 0.0352414509196509 0.0415868645201421 2260 2888.27272727273 3169 0.0032562701929093 1915 2.34404715641229 3.13106785956278 1 0.832668972065078 2258 3217 2047 2811 3944 3276 3169 2254 1915 3339 3541 3341 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 9/17 Arthur Liberzon 0.000122449900821364 0.000179874681896211 3545 2971.90909090909 3169 1.22456648634869e-05 1163 1.93274757540048 -1.93274757540048 -1 1.86178305402792 3169 3541 4552 3941 3544 2193 2821 1163 1678 3784 2305 3342 M4123 WEBER_METHYLATED_LCP_IN_FIBROBLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_LCP_IN_FIBROBLAST_UP.html Methylated germline-specific genes with low-CpG-density promoters (LCP) in primary fibroblasts. 17334365 3/12 Arthur Liberzon 0.0274392664210276 0.0326927033940847 3935 3285 3171 0.00277840850465841 1617 0.511007778343266 0.511007778343266 1 0.195259761611459 2272 2895 4581 3931 3934 2054 1617 3171 4391 4664 2625 3343 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 140/302 Jennifer Shepard 6.42640590079967e-08 2.33624034531786e-07 4025 3132.90909090909 3172 5.8421873532009e-09 1047 1.46907374536569 -1.07477503422561 -1 2.50583733791731 4022 3172 3105 3015 1047 2021 4502 3864 2366 3713 3635 3344 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 18/36 Jessica Robertson 0.000236298402671356 0.000335330348459625 4440 3267.18181818182 3172 2.14839806285052e-05 1516 1.27957372565468 -1.25795030733277 -1 1.1435617755211 4439 3027 2623 3880 3172 2564 4620 3052 3608 1516 3438 3345 M14547 WEBER_METHYLATED_LCP_IN_SPERM_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_LCP_IN_SPERM_UP.html Methylated germline-specific genes with low-CpG-density promoters (LCP) in sperm. 17334365 3/18 Arthur Liberzon 0.0274392664210276 0.0326927033940847 3935 3286.27272727273 3172 0.00277840850465841 1618 0.511007778343266 0.511007778343266 1 0.195259761611459 2273 2896 4584 3932 3935 2055 1618 3172 4392 4666 2626 3346 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 15/31 Arthur Liberzon 1.34388361737583e-06 2.86761834953383e-06 4455 3304.72727272727 3172 1.22171312572378e-07 2069 1.85143351738976 -1.74889285492399 -1 2.63943398666015 4454 2704 2069 4151 2112 3022 4081 4021 2241 3172 4325 3347 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 63/146 Arthur Liberzon 2.89379461128078e-06 5.65248918235171e-06 4395 2946.54545454545 3173 2.63072583424809e-07 968 1.692531005973 -1.55451686367121 -1 2.28459524438834 4391 2552 1015 2022 2307 3619 3702 4544 3173 968 4119 3348 M119 PID_ERB_GENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERB_GENOMIC_PATHWAY.html Validated nuclear estrogen receptor beta network 18832364 12/50 Pathway Interaction Database 0.0387074129505982 0.0455392761954565 3175 3211 3174 0.00358233673183236 2232 1.32905179650919 -1.04866057361562 -1 0.458635782734986 3174 2959 3107 3562 4324 4315 3227 2277 2232 2741 3403 3349 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 6/8 Arthur Liberzon 1.18013484131659e-05 2.02494026598664e-05 4660 3358.27272727273 3174 1.18014110859553e-06 1784 1.61750479470802 1.22666287468456 1 1.95276131642119 4657 1784 4639 2766 2651 3174 4227 3892 2196 2497 4458 3350 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 22/68 Kevin Vogelsang 4.4824338327034e-05 6.99223866180031e-05 4665 3039.54545454545 3175 4.07502287595435e-06 1231 2.05497341708117 -2.18022971298104 -1 2.19642305177082 4663 2624 1328 3175 2891 4280 3484 3360 2782 1231 3617 3351 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 7/19 Jean Junior 0.00107679132228234 0.00142820383136571 3600 3091.90909090909 3176 0.000107731344418614 133 3.76259966423702 -1.70650500449768 -1 2.75360070891926 3598 2678 4373 2856 4659 4316 3176 1561 133 2686 3975 3352 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 45/88 Kate Stafford 3.14612166480404e-07 8.28708607154117e-07 1985 3066.63636363636 3176 2.86011101337902e-08 1647 1.00644584633981 1.1027478190855 1 1.57436984320987 1984 4439 3285 4240 1647 3176 1840 2557 3975 3727 2863 3353 M14025 REACTOME_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTION.html Genes involved in Transcription 123/275 Reactome 0.000245226661561473 0.000347274746472367 620 2563.90909090909 3177 2.22958182205329e-05 620 1.30372526582025 -1.36021227138194 -1 1.16004886214541 620 3981 3670 3267 3177 1067 1901 1583 3564 3656 1717 3354 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 157/376 Arthur Liberzon 3.67422603373284e-08 1.5853980841687e-07 4155 3001.63636363636 3178 3.34020554099655e-09 540 1.4557004795295 -1.17693477794449 -1 2.54607243965614 4155 4145 3178 2732 789 540 3666 4226 3014 3728 2845 3355 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 13/43 Arthur Liberzon 0.000246194552528078 0.000348434815205851 3695 2986.45454545455 3178 2.23838279676515e-05 831 2.85144342739516 2.43334851688529 1 2.53613948863727 3691 3186 1673 2175 3178 4349 3315 2858 831 2921 4674 3356 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 6/14 Arthur Liberzon 0.00201468396386822 0.00261880972390748 3460 3230.90909090909 3178 0.000201651282602993 1423 0.719746787318546 -0.822587501215724 -1 0.477987989512978 3050 1423 4615 3406 3460 3070 4055 2821 3003 3459 3178 3357 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 10/20 Reactome 9.67667741312814e-05 0.000143587429885746 3800 2912.63636363636 3179 8.79736642454743e-06 510 1.45025388763829 1.48695511236464 1 1.43350723881519 3798 1223 2350 2005 3035 4580 3867 3345 510 3179 4147 3358 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 0.0839184282471183 0.0902966141827776 2690 3148.63636363636 3179 0.00793650793650794 1825 1.69703972065934 1.82485058701179 1 0.45585596024003 2687 3693 1825 2142 3927 4205 3163 3179 3556 2577 3681 3359 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 14/42 John Newman 3.90972917135324e-07 9.89788811289102e-07 4550 3219.72727272727 3179 3.55429987833708e-08 1737 1.24096496380498 -0.663591887590555 -1 1.91660198385753 4548 2465 2223 3179 1737 3537 4520 2252 2714 4024 4218 3360 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 131/277 Jessica Robertson 2.55743977832783e-05 4.14246899455382e-05 3180 3169.81818181818 3179 2.32497228031731e-06 1700 1.52661943569996 -1.29435925877114 -1 1.72097754066576 3179 3778 1700 2433 2779 2932 4124 3741 3524 2996 3682 3361 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 34/65 Reactome 0.0662933545316329 0.0763457014832223 1590 3118.18181818182 3180 0.00621632314079795 1588 0.692356482930176 -0.673582288505426 -1 0.198959602020636 1588 3180 3687 3262 3951 1742 2680 3062 4264 4284 2600 3362 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 301/774 Arthur Liberzon 2.5828289390976e-08 1.23375498558729e-07 2905 2693.54545454545 3180 2.34802633583668e-09 649 1.47869962027272 1.61166770804742 1 2.62772200502307 2903 2083 1611 3189 649 3853 3246 3434 3180 1123 4358 3363 M17115 SCHEIDEREIT_IKK_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SCHEIDEREIT_IKK_TARGETS.html Genes encoding substrates of IkappaB kinase (IKK) complex. 17072322 14/32 Arthur Liberzon 0.000600744316583613 0.00081667765230949 3990 3282.72727272727 3180 5.46280383572269e-05 2401 1.58737339339384 -1.52995442319004 -1 1.2608048694509 3986 3804 2829 4036 3307 3180 4051 2502 3000 3014 2401 3364 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 262/576 Jessica Robertson 0.00179151220482694 0.00234040317586258 1455 3062.09090909091 3181 0.000162997521917043 1451 1.66494894482801 2.15309293080241 1 1.12660685913878 1451 4199 2048 2196 3430 4148 3074 2764 3181 3934 3258 3365 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 10/35 Reactome 5.4342097598483e-06 9.94715114634731e-06 3595 3056.72727272727 3182 4.94020289355541e-07 1415 1.12307037547568 -0.966373877341117 -1 1.44502526955283 3591 1415 2417 2002 2455 4557 4146 4177 1618 3182 4064 3366 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 36/112 Arthur Liberzon 8.89463303272328e-09 6.74437708597756e-08 3645 2728.54545454545 3183 8.0860300624404e-10 208 1.51404592190257 -1.14452088996612 -1 2.79267854373025 3641 1765 1641 3670 208 3654 3183 3609 3032 1793 3818 3367 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 27/52 Jean Junior 0.0345714892470221 0.0408374082711232 1825 3155 3183 0.00319336520219025 1667 1.20542520312401 1.22604172012697 1 0.430648360538374 1824 3754 3183 3965 4591 2866 1667 3055 3633 3707 2460 3368 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 70/136 Arthur Liberzon 5.21714877210459e-08 2.0271607915491e-07 4475 2930.09090909091 3183 4.7428626325688e-09 947 1.1471455963977 -0.804556002500267 -1 1.97490070170808 4471 2450 3433 2554 947 1454 4573 3282 2077 3807 3183 3369 M8560 BIOCARTA_G2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G2_PATHWAY.html Cell Cycle: G2/M Checkpoint 20/43 BioCarta 0.0144085169087187 0.017541779743896 2345 3093.18181818182 3184 0.00131852339993326 2046 1.4582750031687 1.66418516766621 1 0.658634195451681 2344 3566 2593 2832 4002 3643 3348 2046 2512 3955 3184 3370 M15381 REACTOME_TCR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TCR_SIGNALING.html Genes involved in TCR signaling 25/65 Reactome 0.000169373358010217 0.000244812941281887 3640 3365.09090909091 3184 1.5398763555755e-05 1997 1.73133795297382 -1.66214309195643 -1 1.60815493936799 3184 3756 2968 3639 3122 3637 1997 4329 3110 2640 4634 3371 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 10/23 Reactome 0.000804132849416051 0.00108063278817425 4545 3129.18181818182 3184 7.3129720224891e-05 2190 1.59970937747694 -1.8220016464438 -1 1.22055674780226 4545 2779 2398 2413 3352 4314 3668 2197 2190 3184 3381 3372 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 198/437 Arthur Liberzon 0.053963031942606 0.0625917741789732 1485 3028.81818181818 3186 0.00503036262657392 1484 1.76944080870328 2.0643872495025 1 0.547739958451506 1484 4079 1616 2064 3798 4222 3129 3023 3186 3491 3225 3373 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 8/27 Jessica Robertson 0.0291764090881776 0.0346742716173472 2510 3338.54545454545 3189 0.00295667090767094 1651 0.71288373905307 0.816051492465286 1 0.267711927911111 2507 3189 4484 4533 3741 2240 1651 2447 4270 4635 3027 3374 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 105/254 Arthur Liberzon 8.71396881743172e-07 1.95172992798369e-06 4395 3157.45454545455 3189 7.92179297176829e-08 1867 1.28266582777137 -1.11762685481303 -1 1.88371999736626 4392 2333 2980 3231 1998 2437 3972 4528 3189 1867 3805 3375 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 6/16 Reactome 0.00023575786195956 0.000334674747392457 4650 3289.18181818182 3190 2.35782877491057e-05 1541 2.55405768686388 -1.15376761301191 -1 2.28313336303991 4647 2602 3955 1541 3190 3802 4292 3018 2264 2472 4398 3376 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 205/493 Arthur Liberzon 7.48914960104883e-08 2.618966793322e-07 3185 3162.27272727273 3190 6.80831805090128e-09 1113 1.46479911308798 -1.15318579775124 -1 2.4798534755017 3183 4417 3111 3575 1113 3190 2289 4369 2096 3395 4047 3377 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 29/54 Leona Saunders 0.0728482692268782 0.0835659705256184 2900 3251.09090909091 3193 0.0068525992569048 1777 1.0740089985374 -1.06681208721384 -1 0.297792111675607 2896 4125 3545 2786 4529 1777 2578 3193 3961 4006 2366 3378 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 3/13 Leona Saunders 0.0109193484390424 0.0134475865401715 2125 3117.54545454545 3193 0.00109733769306008 2087 3.72601005955801 -3.72601005955801 -1 1.7934901417393 2125 3193 4299 3799 3633 2087 3338 2436 4203 2807 2373 3379 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 342/849 John Newman 7.20522289405232e-08 2.53862214146836e-07 4625 3212.27272727273 3193 6.55020284548245e-09 1099 1.43086929856904 -1.07579103269021 -1 2.42739181826529 4623 3581 2787 3193 1099 1506 4315 4598 2670 4080 2883 3380 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 10/30 Jean-Pierre Bourquin 0.000220765083697627 0.0003147262495306 2715 2994.18181818182 3194 2.00715672811983e-05 1260 1.04749419538691 -1.04749419538691 -1 0.943571186817291 2711 3633 3286 3898 4341 1718 3102 1260 3767 3194 2026 3381 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 88/197 Jessica Robertson 2.99305778434912e-07 7.93295745331447e-07 2145 3030.90909090909 3194 2.72096199231724e-08 1634 1.89586495638527 1.99589692483873 1 2.97492558665388 2144 4203 2276 3944 1634 3713 2339 3676 2494 3723 3194 3382 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 14/38 Arthur Liberzon 3.97617673455122e-08 1.66486954776987e-07 4600 2673.81818181818 3195 3.6147061876498e-09 586 1.67713680680051 -1.55526269479208 -1 2.92420909057538 4596 586 1407 3349 825 4047 3195 3414 2890 1099 4004 3383 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 274/815 Arthur Liberzon 2.79871183917402e-07 7.50868047674773e-07 3395 3163 3195 2.54428381382718e-08 1607 1.30057852707203 -1.09494572363134 -1 2.04880842184492 3394 3313 2973 3019 1607 3160 2912 3779 3195 3258 4183 3384 M13863 BIOCARTA_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MAPK_PATHWAY.html MAPKinase Signaling Pathway 46/109 BioCarta 3.1860084699566e-05 5.07465523120892e-05 3945 3175.45454545455 3196 2.89641328200921e-06 1745 1.17750465335445 -1.07925939433838 -1 1.30071847299617 3942 2228 3196 1745 2828 4202 2964 4250 2690 3202 3683 3385 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 179/403 Jessica Robertson 3.94278273749233e-08 1.65851704738681e-07 3300 2972.90909090909 3196 3.58434800741261e-09 816 1.45659870840179 -1.40499480023489 -1 2.54030700641179 3298 3196 2292 3252 816 3428 3108 4453 2611 1598 4650 3386 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 11/32 Jessica Robertson 0.000266768359490544 0.000375623958104775 2725 3076 3197 2.42546102611701e-05 1992 1.09678743762576 1.30926774132331 1 0.966302090829382 2725 3038 2671 4158 3197 3414 2015 3647 3639 3340 1992 3387 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 10/27 Arthur Liberzon 0.0450886994135845 0.05274229791614 2240 3041.36363636364 3197 0.00418547291626558 1724 1.24586410007536 1.24586410007536 1 0.409492485703032 2238 3703 2995 3901 3778 2146 1724 3493 3908 3197 2372 3388 M565 REACTOME_BETA_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BETA_DEFENSINS.html Genes involved in Beta defensins 8/55 Reactome 0.0765897756730953 0.0871115749524574 3200 3228.81818181818 3198 0.00793650793650794 2095 1.79543842036098 -1.93713366690156 -1 0.489489967656505 3198 3870 3931 3882 4065 2507 3047 2823 3307 2095 2792 3389 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 52/145 Arthur Liberzon 0.00425676698885844 0.00539697243230267 4185 3216.81818181818 3198 0.00038772961478185 1233 2.78519357067073 3.59860936131655 1 1.62468175702452 4181 4290 2139 1987 4490 3198 4503 1778 1233 2951 4635 3390 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 10/16 Arthur Liberzon 0.000119598419506442 0.000175851331599368 2555 3030.36363636364 3198 1.08731747018532e-05 1145 2.46769972725504 2.46769972725504 1 2.38332932986979 2552 3108 2263 3884 3819 3205 3647 1145 3447 3198 3066 3391 M8626 SIG_BCR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/SIG_BCR_SIGNALING_PATHWAY.html Members of the BCR signaling pathway 27/63 Signaling Gateway 0.0839184282471183 0.0902966141827776 3125 3284.54545454545 3199 0.00793650793650794 2104 1.235729733515 1.03008369140658 1 0.331939588024267 3125 2104 3155 2224 3955 4575 3199 3938 3219 2390 4246 3392 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 7/12 Reactome 0.00712269700061208 0.00886741714794586 2180 3013.36363636364 3200 0.00071456302870711 1798 2.21470533971337 -1.60043826348591 -1 1.16905475121949 2176 3943 3953 3868 3591 2313 1936 3200 3698 2671 1798 3393 M18988 LIU_NASOPHARYNGEAL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/LIU_NASOPHARYNGEAL_CARCINOMA.html Low abundance transcripts specific to nasopharyngeal carcinoma (NPC). 18332864 51/167 Jessica Robertson 0.000605659799821335 0.000822882523039366 3555 3171.63636363636 3200 5.50751456546918e-05 1730 1.52194770505639 -1.40913272359347 -1 1.20755229776974 3554 3495 2824 2788 3311 1730 4518 4305 2638 3200 2525 3394 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 42/105 Jessica Robertson 1.56664674287951e-05 2.63129270148149e-05 3310 3156.18181818182 3201 1.4242344538842e-06 2367 1.63201529402676 1.85672116706895 1 1.92252635675821 3307 3201 2367 2914 2691 4049 3459 3758 3010 2553 3409 3395 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 568/1329 Jessica Robertson 1.66420205591514e-07 4.90777270863333e-07 1975 3207.63636363636 3201 1.66420218054574e-08 1465 1.37942091316661 1.59642146067685 1 2.23853524109142 1974 3976 4311 4139 1465 4330 2640 2698 3190 3360 3201 3396 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 30/60 Reactome 0.0284046064299229 0.033799894802087 1305 3041.27272727273 3202 0.00261619205645884 1303 0.673582288505426 -0.673582288505426 -1 0.254874653668406 1303 3413 3695 3202 4070 1502 2370 2988 4326 4252 2333 3397 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 14/40 Kevin Vogelsang 0.000277880466202436 0.000390449134819975 2960 3211.09090909091 3203 2.52650519362079e-05 2098 1.38112323960458 -0.830653400739644 -1 1.21083824547013 2960 2815 2098 2767 3203 3903 3332 3626 3750 3017 3851 3398 M11725 REACTOME_CD28_CO_STIMULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CD28_CO_STIMULATION.html Genes involved in CD28 co-stimulation 18/41 Reactome 0.00230854199887046 0.00298587574018962 2545 3045.36363636364 3204 0.000210088000250732 2378 1.32558297488614 1.28468912000559 1 0.860903639669542 2542 3030 3345 2679 3464 3247 2378 2552 3584 3474 3204 3399 M2909 REACTOME_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_METABOLISM.html Genes involved in Pyrimidine metabolism 17/29 Reactome 1.18469965215542e-05 2.03128524332246e-05 3895 2984 3204 1.07700548346297e-06 1692 1.53402079047502 -0.823631289193537 -1 1.85143765406431 3894 1729 1692 1963 2635 3714 4455 3204 2170 3376 3992 3400 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 11/15 Leona Saunders 0.00307419855454165 0.003938134069596 4230 3048.72727272727 3204 0.000279863886225431 1726 1.69542543850919 -1.69542543850919 -1 1.0486725872227 2647 4227 3204 4227 3579 2028 3601 1726 2968 3333 1996 3401 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 121/273 Arthur Liberzon 3.25275626818818e-08 1.46439401578016e-07 2845 3071.27272727273 3205 2.95705119661911e-09 739 1.31772117031882 1.54825118713635 1 2.31642841495074 2844 2932 3223 2131 739 4612 2616 3744 3205 3749 3989 3402 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 28/93 Yujin Hoshida 0.0309913691582142 0.0367473572559189 3205 3256.72727272727 3205 0.00285788664224036 2138 1.78945688873753 1.85353478433602 1 0.660394203992464 3205 3690 2341 2951 3732 4674 3069 4348 2291 3385 2138 3403 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 49/90 John Newman 3.85509082383821e-07 9.78599978358931e-07 3990 3179.72727272727 3206 3.50462863579214e-08 1732 1.1181892467602 -0.965843827112912 -1 1.72840169586539 3990 2799 3206 2143 1732 2253 4242 4271 3108 3658 3575 3404 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 125/263 Arthur Liberzon 5.70357788330117e-08 2.14846993256827e-07 3935 3007.27272727273 3208 5.18507093742585e-09 996 1.35173682260711 -1.2109745936316 -1 2.31834446376423 3932 3642 3208 4420 996 1335 4036 3197 2985 3558 1771 3405 M23 PID_WNT_NONCANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_NONCANONICAL_PATHWAY.html Noncanonical Wnt signaling pathway 18832364 25/51 Pathway Interaction Database 2.18943389537096e-06 4.40329924193489e-06 3335 3176.81818181818 3209 1.99039643117503e-07 2192 1.46488936865048 1.67367042804883 1 2.01818987537211 3334 3067 2500 2420 2245 4245 3476 4533 3209 2192 3724 3406 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 41/108 Arthur Liberzon 1.15761542385174e-05 1.99067371602542e-05 3050 3293.27272727273 3209 1.05238319558151e-06 2613 1.17620516343729 1.46283335416905 1 1.42223692271271 3047 2613 2686 3250 2630 4591 3407 3090 3790 3209 3913 3407 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 27/60 Reactome 0.00185369852336031 0.00241759846380919 3140 3093.54545454545 3210 0.000168660206963249 2103 1.03391853786232 -0.912359745957386 -1 0.69586475820293 3138 2103 3210 2182 3436 2219 3385 4088 3602 3704 2962 3408 M893 REACTOME_RESPIRATORY_ELECTRON_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESPIRATORY_ELECTRON_TRANSPORT.html Genes involved in Respiratory electron transport 38/93 Reactome 0.0116092854024536 0.0142635320912159 1135 2933.36363636364 3210 0.00106100031245187 1134 0.621529196213374 -0.621529196213374 -1 0.295078915332405 1134 3178 3724 3446 3916 1257 1671 3210 4400 4307 2024 3409 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 28/56 John Newman 0.0839184282471183 0.0902966141827776 3215 3283.81818181818 3212 0.00793650793650794 2518 1.29821510746195 -1.13666824965392 -1 0.348724312118327 3212 3755 2786 3388 3982 2675 3837 2876 3903 2518 3190 3410 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 525/1118 Arthur Liberzon 1.07428968709615e-06 2.3469097779639e-06 2965 3149 3213 1.07429020644075e-07 878 1.26498270902083 -0.986913839073938 -1 1.83169571487447 2962 4645 4166 3783 2075 878 3213 3683 3013 4339 1882 3411 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 24/50 Kevin Vogelsang 0.0678892863239047 0.0781068489353836 3215 3303.81818181818 3213 0.00637086306768945 1918 1.04344012002425 -0.795495884058718 -1 0.297190878994806 3213 3127 3351 3141 3824 1918 2625 4199 4012 3851 3081 3412 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 16/29 BioCarta 0.014211401268636 0.0173197987892922 3010 3128.09090909091 3214 0.00130036745007353 2516 1.6269006557983 2.18532685984389 1 0.737108946329449 3009 3214 2876 2827 3654 3391 2527 3608 2516 3240 3547 3413 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 44/85 Jessica Robertson 0.0839184282471183 0.0902966141827776 1280 3128 3214 0.00793650793650794 1280 1.32799069485386 1.68416079049457 1 0.356722584154533 1280 4338 2755 4470 4133 3214 1993 2474 3377 3911 2463 3414 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 26/65 Jessica Robertson 0.000297717206788136 0.000416076000897466 1800 2833.54545454545 3214 2.70688639365836e-05 1311 0.86434182658501 -0.870893084702041 -1 0.751635158196021 1799 3259 3643 4178 3214 1311 1953 2385 3479 4105 1843 3415 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 21/69 Jessica Robertson 3.91673488083599e-07 9.91026979027941e-07 1805 2967.45454545455 3215 3.56066870740528e-08 1738 1.9614482599719 2.18689958394822 1 3.02907492433573 3001 3896 1804 3215 1738 3669 1805 3539 3404 2208 4363 3416 M14990 REACTOME_FANCONI_ANEMIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FANCONI_ANEMIA_PATHWAY.html Genes involved in Fanconi Anemia pathway 12/27 Reactome 0.40805247398117 0.425013090259116 2175 3380.81818181818 3216 0.0465487913533096 2173 1.10683428238631 -1.10683428238631 -1 0.10579214540015 2173 4066 3031 3975 4074 2503 3124 3216 4467 3417 3143 3417 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 132/317 Arthur Liberzon 0.00633830471449512 0.00791612363862583 2975 3307.18181818182 3216 0.000577876333476811 1459 1.26140112101932 -1.05320749600898 -1 0.681833857057257 2972 4424 3562 4440 3571 1459 3216 2974 3117 4193 2451 3418 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 2/14 Arthur Liberzon 0.0692024938784801 0.0795590987032772 2500 3348.6 3216 0.00793650793650794 2062 1.41251446300786 1.41251446300786 1 0.399403251767693 2499 2927 4138 NA 4115 2791 2062 3098 3979 4543 3334 3419 M10570 BIOCARTA_RNA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RNA_PATHWAY.html Double Stranded RNA Induced Gene Expression 8/17 BioCarta 5.24955468195242e-05 8.08393468275683e-05 3445 2992.72727272727 3217 5.24967869628518e-06 87 2.15679126947704 -0.692504774557804 -1 2.27029567645965 3443 2999 3827 2779 3217 4565 4121 1016 87 3670 3196 3420 M8344 NAKAJIMA_EOSINOPHIL http://www.broadinstitute.org/gsea/msigdb/cards/NAKAJIMA_EOSINOPHIL.html Top 30 increased eosinophil specific transcripts. 11493461 15/52 Kevin Vogelsang 0.000933365304085903 0.00124572766019554 2875 2886.81818181818 3218 8.48874114699063e-05 1420 1.69299717743045 -2.0690443803027 -1 1.26484622205121 2875 2273 1420 3469 3371 3447 2052 4065 3218 2012 3553 3421 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 30/64 Jessica Robertson 0.000302649928344318 0.000422465762353731 2155 2919.09090909091 3218 2.75174155777549e-05 1329 0.758490896513073 -0.70311977113051 -1 0.658295420319526 2152 2266 3585 3505 3218 1329 2184 3477 4007 4037 2350 3422 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 190/390 Kevin Vogelsang 1.09624090481392e-08 7.49924799993871e-08 3280 3031.81818181818 3219 9.96582645705811e-10 280 1.29453183575976 -1.1928491074312 -1 2.37243965305153 3280 3219 3154 2619 280 4012 2797 3383 3125 3394 4087 3423 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 9/24 John Newman 0.000201153039312992 0.000287993627320709 3985 3337.36363636364 3219 2.01171249778343e-05 1422 1.4433043350964 -0.822587501215724 -1 1.31442405962356 3983 2751 4401 3734 3162 4675 3219 1918 1422 3066 4380 3424 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 395/796 Leona Saunders 0.00535054601231619 0.00672189238973557 1485 3193.90909090909 3220 0.000487600306903758 1482 1.66411310836611 2.07192984953338 1 0.92991425293106 1482 4415 1779 2632 3551 4329 3220 3078 3063 4018 3566 3425 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 48/118 John Newman 0.000718235582684127 0.000969090682538963 3220 2794 3220 6.53154702545486e-05 1229 2.23611128887399 2.94884787007545 1 1.73333611061064 3220 4118 1707 1665 3335 4530 3231 1560 1229 2337 3802 3426 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 6/14 Arthur Liberzon 0.00262513558237423 0.00337671845704244 3830 3370.36363636364 3221 0.000262824184962637 2696 1.01132039207933 -1.07718898369982 -1 0.642907998291714 3830 3079 4211 3221 3485 3091 4259 2696 3023 3450 2729 3427 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 26/50 Leona Saunders 3.20566477704994e-07 8.41083154829563e-07 3430 3173.09090909091 3221 2.91424113104906e-08 1658 1.38619980510551 -1.27101831496113 -1 2.16611882316648 3428 3891 3302 3566 1658 2964 4014 2806 3148 3221 2906 3428 M258 PID_BARD1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BARD1_PATHWAY.html BARD1 signaling events 18832364 17/36 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 3105 3304.72727272727 3222 0.00793650793650794 2379 1.48661521269198 -0.586927951036094 -1 0.399332055752257 3101 3730 2713 3022 3932 2822 3222 3682 2379 4093 3656 3429 M18799 REACTOME_DIABETES_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DIABETES_PATHWAYS.html Genes involved in Diabetes pathways 87/214 Reactome 1.70944713823126e-06 3.53195294962597e-06 3225 3248.63636363636 3222 1.55404406046342e-07 2184 1.37992963286063 1.51699992297259 1 1.93513042717862 3222 2478 3190 3642 2184 3060 3679 3861 2284 4118 4017 3430 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 91/201 Arthur Liberzon 0.00016703327869672 0.000241654196965986 3005 3391.54545454545 3222 1.51859965378078e-05 2352 1.32848956536813 -0.797196743362818 -1 1.23589602423465 3003 3556 3222 4039 3118 4276 3197 2649 2352 4086 3809 3431 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 107/252 Jessica Robertson 2.39821421577485e-07 6.64972296752719e-07 2800 3115.81818181818 3222 2.18019497927599e-08 1549 1.39724493629163 1.33469308103657 1 2.22004922848293 2799 3222 2564 2099 1549 4225 3344 4523 3349 2585 4015 3432 M128 PID_TNF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TNF_PATHWAY.html TNF receptor signaling pathway 18832364 30/60 Pathway Interaction Database 1.42946334763708e-05 2.41473152380221e-05 4215 3259.63636363636 3224 1.29952057795127e-06 2642 1.11028124550738 -1.14500685402627 -1 1.3185719523513 4213 2738 3224 3435 2669 2642 4105 3257 3780 3128 2665 3433 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 118/247 Arthur Liberzon 1.58234167447601e-06 3.31760764500877e-06 3375 3154.63636363636 3225 1.43849346597311e-07 2152 1.43141444607437 -1.39573834200169 -1 2.01734050668626 4146 2688 2492 3371 2152 3032 4310 3225 3267 2646 3372 3434 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 25/70 Leona Saunders 0.00411648314220109 0.00522759891716919 3230 3311.27272727273 3226 0.000374927804526778 1692 1.04011371166637 -0.786042240301996 -1 0.610432251877234 3226 4554 3181 4376 4152 1692 2803 1774 4060 3891 2715 3435 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 31/93 Leona Saunders 7.39514758187555e-08 2.59487271084123e-07 4065 3064.45454545455 3226 6.72286166405303e-09 1106 1.85566855028618 -2.26029218036849 -1 3.14349765197001 4063 3093 1441 3226 1106 4032 3075 3307 3626 2364 4376 3436 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 8/23 Jessica Robertson 0.000507812509202622 0.000694371000327834 2760 3106 3227 5.07928589632546e-05 1543 0.847342801684535 1.10143836428552 1 0.688376424782191 2760 3041 4320 3699 3304 3736 3296 1543 2357 2883 3227 3437 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 32/85 Jessica Robertson 0.0839184282471183 0.0902966141827776 3050 3230.90909090909 3227 0.00793650793650794 1912 1.26024930177562 -1.01638907274593 -1 0.338525996365353 3049 2870 2554 3581 3971 1912 3420 4513 3227 3653 2790 3438 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 340/783 John Newman 8.74197590982936e-08 2.92606422239003e-07 2995 3082.81818181818 3228 7.94725114291159e-09 1184 1.14522247578124 -0.928979886005026 -1 1.92463671657772 2991 3816 3690 4556 1184 1203 3073 3778 3228 4107 2285 3439 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 51/102 Reactome 2.67670030439533e-06 5.25746765168577e-06 3230 3265.54545454545 3229 2.43336687372167e-07 2014 1.09033472218782 -1.03687826228463 -1 1.48056851196177 3229 2974 3446 2191 2289 3878 2014 4527 2961 3735 4677 3440 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 151/287 Jessica Robertson 1.45557759276159e-06 3.0877485738709e-06 4200 3352.90909090909 3229 1.3232532325552e-07 1993 1.65734571933896 -1.22536990328776 -1 2.34904632476195 4197 4110 2541 2824 2132 3229 4463 4558 1993 2648 4187 3441 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 24/62 Jessica Robertson 1.52557148318753e-05 2.56782613872728e-05 3230 3421.54545454545 3230 1.38689278385207e-06 2637 1.15801243356846 -0.895575190528817 -1 1.3673057111017 4672 3230 3228 4159 2685 2637 4333 3342 2812 3499 3040 3442 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 0.0765897756730953 0.0871115749524574 3945 3444.36363636364 3230 0.00793650793650794 2631 2.76690955811237 -2.76690955811237 -1 0.754342038272259 3944 3005 4661 3476 3910 3927 3150 2631 3132 2822 3230 3443 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 12/34 John Newman 1.22734011738529e-06 2.64793544662406e-06 3740 3026.54545454545 3232 1.11576436554239e-07 1391 2.19489243554435 -1.83318638993428 -1 3.14861643084017 3736 2321 1391 2750 2086 4624 3302 3898 3232 1628 4324 3444 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. 7/19 SigmaAldrich 0.000297219354954967 0.000415628140053409 3020 3196.45454545455 3233 2.97259115144818e-05 2040 1.04127646862172 1.20292067687629 1 0.905623556088315 3020 2040 3892 2696 3233 4117 3545 2746 2945 3574 3353 3445 M5290 BIOCARTA_MEF2D_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MEF2D_PATHWAY.html Role of MEF2D in T-cell Apoptosis 9/26 BioCarta 0.0398723412781862 0.0468275165988924 3155 3429.27272727273 3234 0.00406063578461409 2295 1.49365922110134 -1.54594220400586 -1 0.510784847813308 3803 2962 3863 2910 3771 3152 4011 4568 3153 2295 3234 3446 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 35/110 Arthur Liberzon 5.48766609906312e-05 8.42017136221669e-05 3825 3122.54545454545 3234 4.98891180712721e-06 1358 1.31689183635637 -0.804427089742084 -1 1.38020035864449 3822 2304 2781 3234 2932 3358 4255 1358 2276 3995 4033 3447 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 11/25 Jessica Robertson 0.000260925249566828 0.000367728035930874 2620 3243.81818181818 3235 2.37232910057681e-05 2617 0.954267593519216 -1.0232585880304 -1 0.843002560950067 3534 3667 3041 3754 3193 2617 3273 3235 3798 2619 2951 3448 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 299/637 Jessica Robertson 0.00400318403629428 0.00508647516108324 2180 3213 3235 0.000364589723393145 2179 1.59490887608452 1.91036995366326 1 0.940911854551408 2179 4197 3324 2737 3522 4338 2907 2636 2384 3884 3235 3449 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 16/38 Jessica Robertson 9.20960173493916e-07 2.05310150951117e-06 3545 3074.90909090909 3236 8.37236871840806e-08 1305 1.36436656870063 1.43080025319096 1 1.99598816448168 3543 2389 2189 3414 2011 4185 3168 3842 3236 1305 4542 3450 M4086 KEGG_PROPANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROPANOATE_METABOLISM.html Propanoate metabolism 16/36 KEGG 9.63547057622733e-07 2.13584745128672e-06 4145 3054 3238 8.75952254212196e-08 1996 1.7558588282196 -0.785130726671005 -1 2.56096842766366 4143 2595 2380 2763 2023 3340 4116 3427 1996 3238 3573 3451 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 61/150 Arthur Liberzon 0.000191707954326804 0.000275396527889456 2550 3202.18181818182 3238 1.74295147083857e-05 1610 1.15055726449581 1.26564845466765 1 1.0535663847212 2550 1610 3332 2918 3141 4459 2458 3998 3635 3885 3238 3452 M15926 BIOCARTA_TFF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TFF_PATHWAY.html Trefoil Factors Initiate Mucosal Healing 19/40 BioCarta 3.22526329982107e-05 5.12846414080812e-05 2705 3044.09090909091 3240 2.93210053098139e-06 1697 1.06237145658541 1.20008908302962 1 1.17228600229897 2704 3503 3410 1697 2834 3690 2854 2034 3598 3921 3240 3453 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 12/31 Reactome 0.000197149203955969 0.000282779666280279 3155 2837.63636363636 3240 1.79242612144112e-05 703 5.08536425931551 5.08536425931551 1 4.6416446338767 3151 3299 2544 3240 3342 3784 2502 1234 703 3942 3473 3454 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 12/27 Arthur Liberzon 0.0199045595351449 0.0239775748024907 2735 3117.54545454545 3240 0.00182608738171748 2126 1.21266842978357 1.27722277878667 1 0.505368067051176 2735 3387 2390 4624 3681 3357 2126 3240 4068 2148 2537 3455 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 28/65 Kevin Vogelsang 0.000346504276609888 0.000480817009237174 3010 3365.54545454545 3241 3.15053512494563e-05 1947 0.997923696519533 -0.579213561940665 -1 0.85167703800839 3219 3440 3122 3009 3241 4549 3009 1947 3532 4140 3813 3456 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 65/142 Jessica Robertson 3.16729248438994e-07 8.32413493093172e-07 2455 3204.90909090909 3244 2.87935721852572e-08 1653 1.38115736811265 1.76495896902422 1 2.15983794485808 2454 4431 3244 4619 1653 4064 3077 2359 2633 3396 3324 3457 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 86/220 Arthur Liberzon 6.84014620272756e-07 1.57974002493747e-06 4460 3422 3245 6.21831666312507e-08 1932 1.44919513343381 -1.40179118225197 -1 2.16251635281243 4457 4330 2795 3075 1932 2283 4622 4480 3453 2970 3245 3458 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 11/27 Leona Saunders 0.00366479644244522 0.00467171820709965 3250 3097.72727272727 3246 0.000333719599688436 1203 2.78485267113203 -0.484341082948553 -1 1.66937658877003 3246 4180 2478 3512 3759 3954 2974 1755 1203 3902 3112 3459 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 30/114 Jessica Robertson 2.3775328747317e-06 4.7348572252413e-06 3665 3079.72727272727 3246 2.16139585829788e-07 2264 1.79264433040805 -0.743532349470392 -1 2.45520277165941 3663 3257 2339 2777 2264 3246 4107 3381 2350 4036 2457 3460 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 42/67 Leona Saunders 0.00588185584537011 0.00736371266134232 1830 3073.90909090909 3247 0.000536149137940076 1826 1.2474481394286 -0.967855150971501 -1 0.684371936169216 1826 3646 3147 3444 3561 2147 2714 3314 3247 4126 2641 3461 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 66/157 Reactome 0.0297316988312618 0.0353162840870197 4350 3031.36363636364 3251 0.00274011597285215 1276 0.630465093550842 -0.537901863813632 -1 0.235468834916224 1276 3251 3752 3207 3725 1547 1976 3465 4347 4350 2449 3462 M13166 REACTOME_DOWNSTREAM_TCR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_TCR_SIGNALING.html Genes involved in Downstream TCR signaling 17/42 Reactome 8.37123099709174e-05 0.000125247728136564 3255 3330.63636363636 3252 7.61049958926425e-06 2299 1.54214476769908 -1.22719158510806 -1 1.54787773510363 3252 3504 2960 3065 3007 3809 2299 3819 3511 2781 4630 3463 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 6/12 John Newman 2.85016778320291e-07 7.62757637469379e-07 4250 2691.90909090909 3252 2.85016814875851e-08 987 1.33851712623877 -1.72393795688582 -1 2.10622424880175 4246 987 4420 1235 1645 3869 3269 3771 1191 1726 3252 3464 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 11/24 Arthur Liberzon 0.000372081658333963 0.000514458864297121 3375 3016.36363636364 3252 3.38313275159051e-05 1439 1.9489974178807 -2.16299605170649 -1 1.64864619915238 3372 4002 1852 4405 3252 2454 3810 1439 3427 2623 2544 3465 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 13/36 Reactome 0.000693124570943782 0.000936557594994972 3375 3151.90909090909 3253 6.30311855271935e-05 2390 1.01852261163992 -1.0325796580047 -1 0.79339942113621 3374 2992 3253 3879 3330 2666 3592 2390 3720 2912 2563 3466 M1870 REACTOME_GLUCOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_METABOLISM.html Genes involved in Glucose metabolism 36/81 Reactome 0.00726014835622445 0.00903613683858374 3135 3158.90909090909 3253 0.000662201692358016 1151 1.31395447360187 -1.0404266536288 -1 0.690817640455632 2906 4087 3308 3315 4323 1151 3253 3135 3133 4144 1993 3467 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 67/157 Arthur Liberzon 0.07148155469249 0.0820986679629922 3255 3394.54545454545 3255 0.00671959755355752 2870 1.46067260007457 -1.019681444924 -1 0.407893455467575 3255 4115 2881 2870 3829 4068 3381 3231 3090 2978 3642 3468 M14631 KEGG_COLORECTAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_COLORECTAL_CANCER.html Colorectal cancer 42/82 KEGG 0.000218429388454035 0.000311775849617913 3815 3076.09090909091 3257 1.98591889516356e-05 1900 1.47423900436451 -0.752976825600008 -1 1.32952938783766 3813 3407 2910 2145 3157 3394 3466 1952 1900 3257 4436 3469 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 97/221 Arthur Liberzon 1.65629985733573e-07 4.89062453149038e-07 1905 2881.72727272727 3257 1.5057272563932e-08 1421 1.24781049291723 1.30334291773179 1 2.02544467627989 1902 3342 3273 3384 1421 3347 2245 2693 3257 3235 3600 3470 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 34/69 Reactome 0.0847636317045532 0.0911851189548981 1875 3251 3258 0.00801975254261943 1828 0.757837899155235 -0.673582288505426 -1 0.20274009237634 1871 3622 3669 3206 4121 1828 2853 3258 4403 4217 2713 3471 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 2/12 Yujin Hoshida 0.00233208038133736 0.00301465618398534 3125 3141.4 3258.5 0.000259389010179685 1596 0.69731936708822 -0.69731936708822 -1 0.45212871584538 3122 3395 4574 NA 3483 1620 1596 1856 4639 4662 2467 3472 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 7/22 Reactome 0.00729018967501458 0.00907111758287795 3590 3217.54545454545 3259 0.0007314216774916 2215 1.3610857033382 1.31749628524341 1 0.715009653949633 3590 2784 4019 2669 3593 4274 2546 2215 3259 2675 3769 3473 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 8/22 Reactome 0.0765897756730953 0.0871115749524574 3260 3408.81818181818 3260 0.00793650793650794 2876 1.43493669986389 1.10332537124671 1 0.391206422810078 3260 2964 3996 3057 3862 3854 3083 2955 3275 2876 4315 3474 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 232/471 Arthur Liberzon 0.000468049613813683 0.000641497657306499 2850 2863.09090909091 3261 4.25590200869169e-05 775 1.16567681122325 -1.13149282497399 -1 0.957302370224861 2849 3551 3668 3261 3282 775 3225 1962 3401 4172 1348 3475 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 60/141 Leona Saunders 6.96697150508758e-05 0.000105245739757706 3270 3064.45454545455 3261 6.33381104117069e-06 1045 2.233741485595 3.23772297561748 1 2.28546201778784 3270 4532 2118 2791 4625 3612 3905 1045 1406 3144 3261 3476 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 23/48 Jessica Robertson 5.641309045944e-07 1.3420813982999e-06 4630 3321.45454545455 3261 5.12846408409698e-08 1870 1.73733898183319 -1.33937367944584 -1 2.62413165739782 4629 3261 1949 4037 1870 2959 4275 4190 2332 2423 4611 3477 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 93/280 Jean Junior 0.0186642966340279 0.0225298542058358 3835 3264.72727272727 3262 0.00171132244132544 1386 1.40669905213426 -0.843950441736596 -1 0.596014787368133 3832 4111 3171 3705 3884 1386 2939 3029 2476 4117 3262 3478 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 21/36 Kevin Vogelsang 0.00143732599834438 0.00189140961197465 2720 3130.09090909091 3262 0.000130751446031668 588 1.8936589780008 2.31254859285663 1 1.32642355849012 2720 4396 3262 3200 3612 4188 3435 1597 588 4176 3257 3479 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 83/188 Jessica Robertson 0.0045095506522784 0.00570203841245995 1840 2953.18181818182 3263 0.000410801902182338 1061 1.55413217790619 -1.35882950458419 -1 0.897022957206765 1836 4653 3481 3263 4556 1061 2120 2181 3294 3976 2064 3480 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) 36/72 Reactome 0.0117579178964069 0.0144347925759924 1465 3090.54545454545 3264 0.00107465749389753 1260 0.673582288505426 -0.673582288505426 -1 0.318893734435092 1461 3923 3714 3264 4195 1260 2216 3104 4388 4294 2177 3481 M4047 BIOCARTA_NKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NKT_PATHWAY.html Selective expression of chemokine receptors during T-cell polarization 5/30 BioCarta 0.00871743222336705 0.0107954247882394 2930 3292.81818181818 3265 0.000875181935960319 1967 1.65059221295528 -1.65059221295528 -1 0.835006382970685 2929 4276 3869 4608 4495 2375 3366 1967 2606 3265 2465 3482 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 43/109 Pathway Interaction Database 7.60870323176499e-05 0.000114313508637546 4275 3211.72727272727 3265 6.91724217420006e-06 2024 1.36619073623246 -1.21622522354361 -1 1.38521067749857 4275 2520 2821 2024 2995 3265 4113 3727 3455 2625 3509 3483 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 24/52 Pathway Interaction Database 1.6088375271008e-05 2.6992526501949e-05 3320 3379.09090909091 3267 1.46259026589614e-06 2692 1.18162985436057 -0.904851077110175 -1 1.3886029584745 3316 3229 3102 3238 2692 4638 3267 2920 3339 3494 3935 3484 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 2/11 Jessica Robertson 0.0451470329877922 0.0527973537760904 3310 3298 3267.5 0.00511994943717761 2363 1.50510212232629 -1.50510212232629 -1 0.494523858024007 3310 3424 4443 NA 4191 3225 4301 2363 2609 2531 2583 3485 M1908 BIOCARTA_FCER1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FCER1_PATHWAY.html Fc Epsilon Receptor I Signaling in Mast Cells 24/61 BioCarta 0.00450398080613381 0.00569653280905344 3800 3265.54545454545 3268 0.000410293469024373 1612 1.31379937011953 -0.994889203108584 -1 0.758448024638367 3800 3096 2901 1612 3531 3081 3908 4660 2571 3493 3268 3486 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 21/109 Kevin Vogelsang 2.65640480383448e-07 7.18701669212953e-07 3470 3119.36363636364 3268 2.41491374962174e-08 1592 1.28472449067858 1.41433287165309 1 2.03011700896556 3469 2625 2549 3883 1592 4618 3268 2645 3302 2206 4156 3487 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 19/47 Jessica Robertson 8.1888160085295e-06 1.44584746857457e-05 2765 3109.36363636364 3269 7.44440589909998e-07 1978 1.08770863105931 1.16502578122324 1 1.35408387657744 2762 3536 3269 4293 2550 3789 1978 2536 3346 3549 2595 3488 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 5/22 Reactome 0.00242075479345835 0.00312583548144002 2580 3275.63636363636 3271 0.000242339586770353 1696 1.21907478952994 1.21907478952994 1 0.785493373883919 2577 4235 3986 4183 3831 2872 2229 1696 4254 3271 2898 3489 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 7/14 Reactome 0.000751365257385199 0.00101233398392957 2665 2928.18181818182 3271 7.51619425730768e-05 1261 0.82445716223047 -0.82445716223047 -1 0.635062556049173 2665 3271 4061 3492 3497 1430 3200 1503 4250 3580 1261 3490 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 10/18 Arthur Liberzon 0.000879452260841638 0.00117645255332684 2405 2991.45454545455 3271 7.99821836058873e-05 1984 0.894839344941697 1.01393111903747 1 0.674257976536325 2405 3507 3142 3434 3362 2482 1984 3271 3313 3843 2163 3491 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 5/12 Reactome 0.0150586799694454 0.0183000452118313 2450 3260 3272 0.00151617076577045 1877 1.26822912868535 -1.26822912868535 -1 0.56680414769085 2450 4135 4003 4570 4429 1877 2253 2081 4394 3272 2396 3492 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 5/8 Leona Saunders 0.000103216662554338 0.000152722854666759 2840 3042.27272727273 3272 1.03221457023501e-05 1134 1.21907478952994 1.21907478952994 1 1.19659793660245 2838 3272 4156 3960 4039 2705 2021 1134 3406 3279 2655 3493 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 11/23 Leona Saunders 0.000260925249566828 0.000367728035930874 2620 3247 3272 2.37232910057681e-05 2616 0.954267593519216 -1.0232585880304 -1 0.843002560950067 3533 3666 3040 3753 3192 2616 3272 3280 3797 2618 2950 3494 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 598/1311 Jessica Robertson 8.59144958360958e-06 1.51181121850524e-05 2070 3022.45454545455 3272 8.59148279964301e-07 1098 1.24870649402088 -0.982624729442736 -1 1.54828642605897 2066 4142 4466 3272 2580 1098 2521 3368 3290 4359 2085 3495 M10082 BIOCARTA_TNFR2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR2_PATHWAY.html TNFR2 Signaling Pathway 11/22 BioCarta 0.000432393047452721 0.000594366037067601 4330 3111.72727272727 3274 3.93161867605146e-05 1385 1.1782140216879 -1.37389083880467 -1 0.977642057933054 4327 1539 2856 1979 3274 4582 3865 4172 1385 2607 3643 3496 M832 REACTOME_ZINC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ZINC_TRANSPORTERS.html Genes involved in Zinc transporters 5/15 Reactome 0.00948089837371187 0.011713021296919 2565 3095.54545454545 3274 0.000952159228180397 1624 0.941251668605736 1.16951732687086 1 0.467585436927153 2565 3311 4027 4086 4107 2870 1624 1981 3974 3274 2232 3497 M17580 ST_IL_13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_IL_13_PATHWAY.html Interleukin 13 (IL-13) Pathway 3/7 Signaling Transduction KE 0.0175549302154944 0.0212290072231759 3190 3374.45454545455 3275 0.00176951709706301 2120 0.739338359774914 -0.739338359774914 -1 0.318167511408801 3190 3275 3884 4219 4525 2187 2315 2120 4289 4429 2686 3498 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 25/56 Arthur Liberzon 0.000433467064608261 0.000595667643622965 3940 3354.36363636364 3275 3.94138631272612e-05 2143 1.68589458332652 -1.03444951629638 -1 1.39848630290454 3936 3095 2143 2753 3275 3888 4646 4443 2368 2193 4158 3499 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 330/741 Arthur Liberzon 5.44569218028224e-08 2.09505684742377e-07 4455 3189.45454545455 3275 4.95062937734568e-09 960 1.32239449970002 -1.03789291642125 -1 2.27173878863194 4452 2366 3109 3443 960 1812 4540 4463 2727 3937 3275 3500 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 57/177 Arthur Liberzon 0.0027815239233225 0.00357395697962415 3275 3118.36363636364 3275 0.000253186083849098 1809 1.6192844615486 1.84528233279381 1 1.01912912634429 3275 3175 1809 3633 3479 3863 3391 2662 2897 2339 3779 3501 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 73/154 Jessica Robertson 1.91676683416711e-08 1.03478909964367e-07 2095 3063.18181818182 3278 1.74251531897008e-09 523 1.16002882530053 1.45925867190613 1 2.08421754598779 2091 3917 3278 3205 523 4013 2617 3177 3855 3737 3282 3502 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 33/88 Leona Saunders 1.06745291388256e-05 1.8471507955885e-05 3645 3269.18181818182 3281 9.70416448419941e-07 2099 1.07783289179173 -1.04118168384211 -1 1.31229724447718 3643 2099 3281 3693 2608 2816 3812 3254 3277 3711 3767 3503 M13158 BIOCARTA_LONGEVITY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LONGEVITY_PATHWAY.html The IGF-1 Receptor and Longevity 11/25 BioCarta 0.108437719587605 0.1160665038802 3145 3368.63636363636 3282 0.0103802929927882 2516 0.790277450904924 0.929665700953106 1 0.190118999728427 3144 3037 3282 2516 4046 3934 2674 2539 4216 3895 3772 3504 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 68/189 Kevin Vogelsang 1.19108954286489e-05 2.0407479334058e-05 3285 3189.72727272727 3282 1.08281453774929e-06 2434 1.23773520250041 -0.897231888563311 -1 1.49320252992871 3282 2762 3367 2434 2636 3454 3323 2571 3280 3919 4059 3505 M6705 BIOCARTA_TH1TH2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TH1TH2_PATHWAY.html Th1/Th2 Differentiation 5/21 BioCarta 0.00474523267444353 0.00599086288080555 2865 3367.72727272727 3284 0.000475539598661804 2824 2.47240509827518 -2.47240509827518 -1 1.41339027579971 2862 2824 3878 4006 3547 2972 3866 3284 3629 3266 2911 3506 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 12/28 Jessica Robertson 0.0295260394735699 0.0350808876706766 3285 3221 3285 0.00272090141226062 2210 1.12512186860379 -1.09794665760462 -1 0.42105609900413 3285 2706 2753 4168 3816 2593 3559 2210 3796 3421 3124 3507 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 96/201 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2100 3242.36363636364 3285 0.00793650793650794 2097 1.98830975400982 2.41897494490158 1 0.534096464182691 2097 4477 2306 3029 4067 4404 3370 2719 2122 3790 3285 3508 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 34/79 Reactome 0.000112597142245459 0.000165921449233402 4545 3305.27272727273 3286 1.02366277671466e-05 1667 1.07730476989782 1.2014390949434 1 1.0474665943885 4541 1667 3053 1821 3057 3286 4450 4264 3413 3077 3729 3509 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 5/9 Jessica Robertson 0.0022035084303747 0.00285238687976128 3440 3222.18181818182 3286 0.000220569643670733 1686 1.27365440468027 -1.27365440468027 -1 0.833685786408161 3436 2857 4305 4531 3838 2351 3046 1686 3696 3286 2412 3510 M6917 BIOCARTA_EPONFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPONFKB_PATHWAY.html Erythropoietin mediated neuroprotection through NF-kB 7/18 BioCarta 0.0765897756730953 0.0871115749524574 2600 3178.90909090909 3287 0.00793650793650794 2600 1.39439327074034 1.72192072622306 1 0.380153072138138 2600 3390 3833 3364 3948 3351 3152 3287 2631 2668 2744 3511 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 10/107 Arthur Liberzon 0.0987694848195973 0.106057242407111 2995 3567.45454545455 3287 0.00940947038617951 1930 0.442156343526102 -0.137725615479201 -1 0.110824959593545 2992 4637 3058 4480 4193 2949 1930 2560 4481 4675 3287 3512 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 5/9 Arthur Liberzon 0.000437294396677598 0.000600223064684014 3290 3210.45454545455 3288 4.37380472392706e-05 1547 1.29820460281742 -0.690869608346921 -1 1.07578413526599 3290 1547 4144 2598 3288 2248 3363 4409 4171 3278 2979 3513 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 13/27 Reactome 0.00386414466658638 0.00491514166873609 3090 3127.09090909091 3289 0.00035190440912595 2058 0.887921247252696 -0.96456061495227 -1 0.527225078809657 3087 3215 3289 3362 3519 2324 3926 2159 3933 3526 2058 3514 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 21/71 Leona Saunders 8.16840411407902e-05 0.000122369378767821 4265 2989.27272727273 3291 7.42609765037878e-06 696 2.03009661761262 -1.03873407510365 -1 2.04291607343922 4263 3291 1756 3044 3638 3570 4288 1079 696 2713 4544 3515 M122 PID_IL2_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_1PATHWAY.html IL2-mediated signaling events 18832364 38/87 Pathway Interaction Database 0.000613991057303687 0.000833476852411667 3295 2913.27272727273 3292 5.58329528284524e-05 1379 1.07608400379568 -0.976710038129106 -1 0.852254808842866 3292 2867 3071 1379 3313 1673 3368 3792 3766 3358 2167 3516 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 11/21 Arthur Liberzon 9.93554453037889e-05 0.000147242130516621 2920 3140.72727272727 3292 9.0327211486376e-06 1969 1.56365031840394 1.88409116518677 1 1.54120400834261 2917 3334 2221 3685 3038 4026 2235 4097 3292 1969 3734 3517 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 5/18 Kevin Vogelsang 0.269244478572805 0.283143307010075 2880 3491.63636363636 3292 0.030880771582827 2475 0.771249082135919 -0.771249082135919 -1 0.108709641025375 2878 3810 4394 4176 4098 2475 2954 2845 4413 3292 3073 3518 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 22/58 Leona Saunders 0.106294554105423 0.11382456136609 2340 3382.63636363636 3292 0.0101642672021328 1952 1.0352953840372 1.14430277970311 1 0.251319398503885 2337 3292 3039 3766 3965 3254 1952 4420 4232 3745 3207 3519 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 23/59 Arthur Liberzon 2.12818085702599e-05 3.49795001614303e-05 4015 3275.90909090909 3292 1.9347285857885e-06 2557 1.26871254609305 -1.05974214091542 -1 1.45420357815444 4013 2841 2597 2557 2745 2620 4412 4131 3426 3401 3292 3520 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 15/44 Leona Saunders 0.000252196818996483 0.00035660660646274 4625 3169.27272727273 3296 2.29296121998868e-05 2002 1.71222665280141 -1.75649499280725 -1 1.51845974706299 4622 3296 2002 3801 3182 3567 3631 2678 3322 2006 2755 3521 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 313/643 Vamsi Mootha 3.5506011041496e-07 9.13958571908345e-07 4190 3134.27272727273 3296 3.2278197065315e-08 1701 1.34953625928509 -0.958906072795439 -1 2.09630040003013 4186 2897 3305 2439 1701 1942 3947 3878 2718 4168 3296 3522 M1389 BIOCARTA_SPRY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SPRY_PATHWAY.html Sprouty regulation of tyrosine kinase signals 9/30 BioCarta 0.000187734051643822 0.000270101862451013 4170 3333.27272727273 3297 1.87749913363151e-05 1586 0.912318569588217 -0.568192156212718 -1 0.837389358947097 4166 1586 3873 2477 3151 3969 3297 2456 3265 3772 4654 3523 M11358 BIOCARTA_ARF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARF_PATHWAY.html Tumor Suppressor Arf Inhibits Ribosomal Biogenesis 14/28 BioCarta 0.00053660518899757 0.000732886014468847 3525 3056 3298 4.87941925325727e-05 827 2.42414097555029 2.85530116442926 1 1.95474005465582 3521 3803 2515 3021 3298 4382 2651 2198 827 3627 3773 3524 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) 13/32 Reactome 0.0627624969870759 0.0724218322781181 3210 3315 3298 0.00587526880928403 2388 1.14078115111992 -1.12036724565486 -1 0.334545590015613 3207 4402 3298 3972 4183 2388 2869 2401 3460 3524 2761 3525 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 13/31 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3695 3177 3298 0.00793650793650794 1647 2.07833577998118 -1.37651439359345 -1 0.558279115445955 3695 3298 1647 2803 4223 2456 4652 3881 3510 2275 2507 3526 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 70/192 John Newman 6.84669971576011e-06 1.22878724121225e-05 4410 3361.72727272727 3299 6.22429183974112e-07 2059 1.51602211587014 -1.37807758642751 -1 1.91483763331817 4407 3054 2059 3199 2512 3299 4224 4364 3315 2584 3962 3527 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 17/34 Arthur Liberzon 0.000374752881204828 0.000517868475766979 3610 3361.72727272727 3302 3.40742484245315e-05 1983 0.968130475502912 -0.751211522531373 -1 0.81822174750557 3609 1983 3151 3302 3254 2325 4360 4587 3892 3377 3139 3528 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 20/37 Arthur Liberzon 0.000391973992318862 0.000540391329216295 4635 3155.18181818182 3303 3.56403497953568e-05 1453 2.24175392354812 -2.0392989938727 -1 1.8839721498528 4634 2111 1453 3557 3262 3303 4517 3723 2245 1708 4194 3529 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 35/72 Jessica Robertson 0.0839184282471183 0.0902966141827776 3305 3606.27272727273 3303 0.00793650793650794 2682 1.34634623909296 -1.48666270955596 -1 0.361653221937242 3303 4543 3192 2682 4604 2827 4391 3004 3976 4132 3015 3530 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 11/39 Arthur Liberzon 0.0307704553787369 0.0365038870644965 1705 2972.09090909091 3303 0.00283722263555688 1525 0.865179412920101 -0.865179412920101 -1 0.319934469974026 1701 3604 3303 3513 3958 1525 1796 2855 4380 3907 2151 3531 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) 18/32 Reactome 0.000829954407363699 0.00111309855549694 2195 2973 3304 7.54788795265567e-05 808 0.863115394565618 -0.670671107040231 -1 0.655691331559614 2193 4305 3304 4483 4640 808 1369 1475 4558 3875 1693 3532 M13088 KEGG_PPAR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PPAR_SIGNALING_PATHWAY.html PPAR signaling pathway 26/91 KEGG 0.0067089999099859 0.00835904641802551 3265 3339.27272727273 3305 0.000611777007904892 1794 1.81966741128327 1.96602171824185 1 0.972530870288536 3261 2524 1794 3290 3578 4658 3449 4219 3305 2732 3922 3533 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 84/194 Arthur Liberzon 1.62154414809401e-07 4.81225831410294e-07 3420 3160.54545454545 3305 1.47413115237496e-08 1411 1.14678101798836 -0.985710299660121 -1 1.86352305790888 3416 1439 3153 3294 1411 4352 3305 4022 3472 2344 4558 3534 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 40/76 Kevin Vogelsang 1.65912892959432e-05 2.77766279531225e-05 3305 3405.18181818182 3305 1.5083104018538e-06 2416 1.15195711171558 1.35465646517558 1 1.35004795165573 3305 2979 3231 2416 2697 3955 3609 4545 3123 3485 4112 3535 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 55/113 Reactome 4.34119383826668e-05 6.78320584398721e-05 4375 3383.36363636364 3306 3.94661773100521e-06 2519 1.11146758046636 -1.02351913412346 -1 1.19174129731254 4373 3787 3474 2519 2887 3609 3143 3194 3306 3692 3233 3536 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 5/34 Jessica Robertson 0.00433540803125192 0.00549073568498554 3635 3150.63636363636 3306 0.000434388942163589 822 2.3345673399213 -3.72601005955801 -1 1.35732690473567 3631 2719 4491 3291 3974 3470 3852 1804 822 3297 3306 3537 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 164/510 Arthur Liberzon 1.03225681919525e-06 2.26670827307822e-06 4500 3162.81818181818 3308 9.38415730489414e-08 1699 1.49642797363396 -1.30210266446988 -1 2.17264100733648 4498 3710 2591 4100 2048 1699 3637 3308 2664 3655 2881 3538 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 7/22 Arthur Liberzon 0.00177593118636468 0.00232199038485069 1900 2681.18181818182 3308 0.000177735205396546 931 0.861640273348152 -0.861640273348152 -1 0.583798943413982 1898 3308 4205 3490 3454 931 1128 1850 4196 3584 1449 3539 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 8/19 Reactome 0.000548613984756372 0.000748850897922621 4560 3208.54545454545 3309 5.48749471621321e-05 632 2.93456791321727 -1.86913631510178 -1 2.35926572380615 4559 3389 3980 2705 3309 3100 4212 2288 632 2875 4245 3540 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 86/220 Arthur Liberzon 1.50012924112503e-05 2.52681726236948e-05 3030 3300.09090909091 3309 1.36376315477988e-06 1498 1.76958605859363 -1.56330462193359 -1 2.09259458017063 3028 3850 1498 3309 2679 4656 2965 4355 3442 2190 4329 3541 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 19/45 Jessica Robertson 0.00518454671439795 0.00652209017548155 3310 2870 3309 0.000472436831178285 1073 2.5673249061908 3.08575110529799 1 1.44328721339878 3309 2809 1073 1266 3893 4442 4191 4344 1312 1263 3668 3542 M214 PID_ERBB1_INTERNALIZATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_INTERNALIZATION_PATHWAY.html Internalization of ErbB1 18832364 27/64 Pathway Interaction Database 0.00217392087063519 0.0028164205694765 3775 3049.09090909091 3310 0.000197824727089978 1440 1.56517464937248 -0.6968744773511 -1 1.02672254718647 3774 3094 2631 2866 3456 3539 3570 2161 1440 3310 3699 3543 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 28/71 Jessica Robertson 5.92338805671019e-05 9.04136691652897e-05 4440 3550.90909090909 3310 5.38504322448318e-06 2956 1.24542045781518 1.62129940632717 1 1.29539023604304 4438 3288 2977 4408 2956 2974 3774 4246 3310 2967 3722 3544 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 65/156 Jessica Robertson 5.80886379265591e-05 8.88102307745044e-05 3055 3272.27272727273 3311 5.2809247046704e-06 2281 1.27687244865903 1.59873683997216 1 1.33065645558603 3054 3250 2281 3311 2949 4558 3566 2417 3415 3397 3797 3545 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 5/12 Arthur Liberzon 0.0013667383853415 0.00180105063940109 3490 2862.09090909091 3312 0.000136757970189351 941 0.751165001316394 -0.751165001316394 -1 0.530265035925464 2265 3312 4207 3489 3487 1097 941 2280 4217 4562 1626 3546 M5193 SIG_CHEMOTAXIS http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CHEMOTAXIS.html Genes related to chemotaxis 22/63 Signaling Gateway 0.0839184282471183 0.0902966141827776 3305 3548.90909090909 3313 0.00793650793650794 2405 1.0228908018278 0.971830674306845 1 0.274767124787084 3304 3290 3248 3313 4099 4262 2405 4214 3838 2828 4237 3547 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 50/111 Jessica Robertson 3.55948927107113e-05 5.62555370126116e-05 4175 3055.54545454545 3314 3.23595169374595e-06 952 1.67509124135809 -0.988436276929965 -1 1.83108770771081 4174 3404 2178 3357 3314 3200 3675 952 2238 2770 4349 3548 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 10/14 Reactome 0.00292569198193899 0.00375096925509332 2665 3201.18181818182 3315 0.000266326363812408 1715 1.03589480737568 1.03589480737568 1 0.646367196861049 2662 3668 3315 3977 3745 3426 2576 1715 4184 3178 2767 3549 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 6/13 Arthur Liberzon 0.000685318630618073 0.000926811862359679 3315 3433.72727272727 3315 6.85530070127477e-05 2485 1.15372135695802 1.09461439938376 1 0.900063465672971 3315 2534 4269 3232 3344 4272 3920 4462 2888 2485 3050 3550 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 87/294 Jessica Robertson 6.1312728129585e-06 1.10845464512051e-05 3805 3236.81818181818 3315 5.57389990957094e-07 2489 1.48872928780815 -1.21671731284512 -1 1.89750423469351 3804 3315 2495 3436 2489 3363 2722 3692 3211 2731 4347 3551 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 113/275 Arthur Liberzon 2.64844378621792e-07 7.17582797930372e-07 3315 3337.54545454545 3316 2.40767645913429e-08 1589 1.32431926517175 -1.14968869617103 -1 2.09291502194449 3311 3221 2469 4028 1589 3730 3405 4116 3184 3316 4344 3552 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 84/205 Jessica Robertson 5.87996697347456e-08 2.19435778250278e-07 4235 3137 3316 5.34542466420835e-09 1007 1.43616656733538 -1.14473564845592 -1 2.45975825945791 4234 3316 2483 1476 1007 3101 4615 3869 3591 3119 3696 3553 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 17/44 Arthur Liberzon 4.67863764582328e-06 8.69313878204913e-06 3330 2854.27272727273 3316 4.25331599608538e-07 975 0.759773060614497 -0.605020782697527 -1 0.989016797221798 3326 1532 3316 3554 2421 975 2205 4191 3814 4101 1962 3554 M9174 ST_STAT3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_STAT3_PATHWAY.html STAT3 Pathway 8/19 Signaling Transduction KE 0.000610416517972495 0.000828864619883834 3320 3095 3317 6.10584256569821e-05 1947 1.5208414202026 1.81887890499214 1 1.20544396612991 3317 1947 3886 2464 3323 4491 4439 2000 2246 2093 3839 3555 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 24/64 Reactome 1.7075193930901e-05 2.85256180963288e-05 4610 3146.81818181818 3317 1.55230240551232e-06 1736 1.88459201429803 -2.0218161924639 -1 2.20306554968626 4610 2771 1760 3900 2704 3475 3512 3521 3309 1736 3317 3556 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 222/516 Jessica Robertson 1.57967192496282e-06 3.3134926769811e-06 3460 3269.63636363636 3317 1.43606641747277e-07 1831 1.55910315475253 2.04405728876699 1 2.19751267283605 3456 3195 2711 1831 2151 3317 4201 3961 2696 4063 4384 3557 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 78/189 Kolja Eppert 0.00123427943672621 0.00163200717847038 3620 3390.72727272727 3317 0.000112270223313721 2466 1.45148660764138 -1.11134313651618 -1 1.04061938071617 3619 3317 2645 2466 3400 3733 4235 3131 2995 3306 4451 3558 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 16/35 Reactome 0.000280629628315427 0.000394075648272728 3920 3422.72727272727 3318 2.55150392292977e-05 2462 1.34502001489159 -1.54416225010333 -1 1.17779726604196 3916 3132 2877 2780 3204 4534 3318 3681 2462 3768 3978 3559 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 134/317 Jessica Robertson 0.0839184282471183 0.0902966141827776 1605 3125.09090909091 3318 0.00793650793650794 1499 1.85800769312939 2.28939432449317 1 0.499094926981007 1605 3950 1499 2344 4229 4039 3171 3318 3159 3666 3396 3560 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 51/167 Leona Saunders 1.97214173527406e-06 4.00409712803044e-06 3860 3020 3319 1.79285773014498e-07 1336 1.21757570153488 -1.08392867951588 -1 1.69038989343833 3859 3319 3049 4411 2223 1336 4109 2077 3411 3502 1924 3561 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 48/107 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3000 3305.81818181818 3319 0.00793650793650794 2137 1.96248016386525 -1.33691469339505 -1 0.527158159797933 3000 4438 2633 3914 4096 2217 3319 4130 2137 3828 2652 3562 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 213/435 John Newman 7.12868350044818e-08 2.51733314868878e-07 3320 3299.81818181818 3319 6.48062157403609e-09 1096 1.42624727728792 -1.00245132504074 -1 2.42089253145431 3319 3817 3173 2922 1096 2729 3747 4431 3152 3809 4103 3563 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 143/308 Arthur Liberzon 2.35022156570248e-07 6.53986832356403e-07 4035 3321 3319 2.13656528797507e-08 1543 1.41378847472746 -1.12929929505813 -1 2.24896570627955 4031 4421 3163 3652 1543 2533 3778 4110 2829 3319 3152 3564 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 6/12 Arthur Liberzon 0.000593832588192081 0.000808219433130436 3320 3511.36363636364 3320 5.93991334613163e-05 2484 1.87450393082045 -2.56372673412928 -1 1.49104440569009 4094 3367 4245 2904 3320 3320 4522 4479 2741 2484 3149 3565 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 51/112 Arthur Liberzon 2.70811158417382e-05 4.37141263638943e-05 4595 3376.18181818182 3320 2.4619499277396e-06 2552 1.38036218317621 -1.18349081794302 -1 1.54780494475553 4593 3320 2600 3742 2790 2552 3874 3157 2691 3931 3888 3566 M17395 KEGG_LIMONENE_AND_PINENE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LIMONENE_AND_PINENE_DEGRADATION.html Limonene and pinene degradation 6/14 KEGG 9.05812700632135e-05 0.000134921751912339 2710 3009.09090909091 3321 9.0584962509963e-06 908 1.32791299754787 -1.32791299754787 -1 1.32181296342254 2710 2603 3804 3809 3331 2190 3321 2738 4256 3430 908 3567 M4629 KEGG_NITROGEN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NITROGEN_METABOLISM.html Nitrogen metabolism 11/23 KEGG 2.75631482222764e-05 4.4400451209896e-05 2950 3223.63636363636 3321 2.50577214171381e-06 2037 1.68563999418775 -1.11397378331121 -1 1.88718068779576 2949 4035 2037 3813 2793 3457 3032 3669 3902 3321 2452 3568 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 15/84 Jessica Robertson 0.0010569293654045 0.00140424468564941 3250 2952.45454545455 3321 9.6130679979464e-05 1072 2.25655075784723 -2.00018433978233 -1 1.65568648366626 3248 2669 1072 3553 3386 4101 2858 3321 3465 1190 3614 3569 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 3/12 Jessica Robertson 0.000601392131837184 0.000817321209335569 4530 2786.90909090909 3322 6.01554946477024e-05 39 2.26270804656831 -1.50398914217864 -1 1.79700468036259 4530 746 4325 971 3322 3887 4590 2540 39 1754 3952 3570 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 48/113 John Newman 3.08205009086098e-06 5.97414899166969e-06 2325 3151.36363636364 3322 2.80186764419238e-07 2320 1.47367045004796 1.40459867950395 1 1.98006403709383 2321 3788 2433 3771 2320 3322 2498 3256 3866 3344 3746 3571 M95 PID_CIRCADIAN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CIRCADIAN_PATHWAY.html Circadian rhythm pathway 18832364 11/21 Pathway Interaction Database 6.89809683075482e-07 1.59155498517563e-06 4225 3305.09090909091 3323 6.27099908513912e-08 1934 1.02909419183691 -1.10379170595632 -1 1.53477715460366 4222 2994 2734 3060 1934 3482 3986 3665 4039 3323 2917 3572 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 59/110 Yujin Hoshida 0.0839184282471183 0.0902966141827776 1460 3084.72727272727 3323 0.00793650793650794 1459 1.73719500385344 -1.56462529663292 -1 0.46664241004033 1459 3955 1834 2566 4271 2984 3578 3323 3822 2758 3382 3573 M965 REACTOME_INTERFERON_GAMMA_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_GAMMA_SIGNALING.html Genes involved in Interferon gamma signaling 47/110 Reactome 0.00533224623166151 0.0067006988043888 3115 3381.27272727273 3324 0.000485928570865482 2073 1.51692868961164 1.89122227742701 1 0.848202001059705 3114 3986 2946 3324 3550 4402 3087 2073 3503 3237 3972 3574 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 138/382 Jessica Robertson 0.000632580418071973 0.000857965800024679 4260 3397.09090909091 3326 5.75238528471851e-05 2631 1.60749216952367 -1.00537339863448 -1 1.26792832295897 4260 3913 2689 3326 3316 2631 4030 2667 2675 3788 4073 3575 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 39/77 Reactome 0.0259982449973805 0.031046833857728 4245 3088.36363636364 3328 0.00239187793498831 1472 0.755496851689263 -0.755496851689263 -1 0.293040323909894 1663 3685 3720 3328 4243 1472 2388 2868 4135 4242 2228 3576 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 487/1173 Arthur Liberzon 3.42043874360547e-05 5.41675429284732e-05 3230 3597.63636363636 3328 3.10953811259943e-06 2844 1.52172491325104 1.982547280777 1 1.66986818982784 3228 4585 3290 3271 2844 3558 3572 3328 3144 4278 4476 3577 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 20/38 Arthur Liberzon 0.000691066055445783 0.000934045438655592 4650 3455.36363636364 3328 6.2843929933924e-05 2700 1.60221264168278 1.74261607170194 1 1.24855778735023 4648 2877 3019 3497 3328 2700 3454 3238 3078 3619 4551 3578 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 91/223 Arthur Liberzon 2.12671063701936e-07 6.01071534684723e-07 3330 3028.27272727273 3328 1.93337349327788e-08 1506 1.21157338965622 -1.03868860100126 -1 1.93871389787865 3328 2900 3467 2563 1506 1669 4023 4034 3385 3930 2506 3579 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 40/76 Reactome 0.122768338121077 0.131105841484815 1300 3220.36363636364 3329 0.0118370361940064 1298 0.810874607777414 -0.810874607777414 -1 0.184037589665987 1298 3824 3683 3329 4021 2006 2795 3133 4354 4249 2732 3580 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 83/201 Kevin Vogelsang 1.33922670784079e-05 2.27542289809353e-05 3335 3254.90909090909 3331 1.21748623664642e-06 1914 1.49935522454234 -1.37485270780226 -1 1.79058955750958 3331 3399 1914 2871 2659 4489 2947 4009 3488 2069 4628 3581 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 40/100 Jessica Robertson 1.97200960182193e-06 4.00409712803044e-06 4425 3104.09090909091 3332 1.79273760860951e-07 1790 1.43306031781462 -1.22982790957364 -1 1.98955245320141 4423 2016 1994 2089 2222 3769 4424 4128 3332 1790 3958 3582 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 21/87 Leona Saunders 4.3143368996923e-05 6.74348989725088e-05 4315 3298.27272727273 3333 3.92220137167867e-06 1454 2.36666501622561 -2.39210940399602 -1 2.53914579116351 4313 3565 1454 4146 2885 3651 4674 3333 2258 2714 3288 3583 M5839 COLLIS_PRKDC_REGULATORS http://www.broadinstitute.org/gsea/msigdb/cards/COLLIS_PRKDC_REGULATORS.html Proteins that regulate activity of PRKDC [GeneID=5591]. 15592499 10/24 Jessica Robertson 0.00602119966074854 0.00753614893436637 2590 3083.54545454545 3333 0.000548885687061874 1958 0.885672564651066 -0.885672564651066 -1 0.483605359485668 2589 3361 3333 4109 3564 1958 2158 2912 3684 3845 2406 3584 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 6/22 Reactome 4.68981922682668e-07 1.15097176542038e-06 3380 2620 3334 4.68982021657517e-08 872 1.86060134060747 2.39078298157576 1 2.84223892126266 3378 872 4056 1156 1838 3571 3334 4447 1067 1154 3947 3585 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 155/403 Jessica Robertson 1.81208015493629e-07 5.25133432655007e-07 2650 3376 3334 1.64734573108402e-08 1462 1.43031613717829 1.65163339525243 1 2.31031757521203 2646 4468 3229 4303 1462 4344 2943 3535 3334 3552 3320 3586 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 5/13 Reactome 0.000862015052642401 0.00115523816047737 3425 3007.27272727273 3335 8.62349616787691e-05 728 1.41803206962777 -1.82564920723962 -1 1.07136429987351 3424 990 3925 2528 3375 3335 4160 4270 728 3269 3076 3587 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 40/100 Reactome 0.0019968629383975 0.00259636507473104 1825 3144.81818181818 3335 0.000181697975224391 1650 1.30252163713435 -1.38399438905113 -1 0.86626470325111 1823 4441 3335 4322 4370 1698 2742 1650 4052 4085 2075 3588 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 7/18 Jessica Robertson 2.67697776716224e-06 5.25746765168577e-06 3815 3019 3335 2.67698099196219e-07 1937 1.66572334674153 -1.29474146677724 -1 2.26189041726097 3811 2437 4481 3610 2311 2354 3335 3362 2216 1937 3355 3589 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 11/23 John Newman 2.92479762569175e-06 5.70591243713221e-06 4300 3428.72727272727 3337 2.65891046734667e-07 2115 3.05761040436108 -3.12283821235046 -1 4.12398020745283 4300 3239 2115 4004 2309 4277 4547 2819 2842 3337 3927 3590 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 41/92 John Newman 0.00851670167925883 0.0105580063674621 4680 3288 3339 0.00077725923422195 1936 1.5684284914731 -1.73635481807689 -1 0.797337360283032 4679 3346 2932 2729 3699 3339 3766 1936 3296 2826 3620 3591 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 31/70 John Newman 0.000743364695196273 0.00100184266945348 2175 3049.81818181818 3341 6.76014538035792e-05 1543 1.11287474810111 1.21374689406118 1 0.858519898368182 2171 3613 3390 4180 3341 3005 1543 2087 4034 3871 2313 3592 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 13/23 Leona Saunders 3.69363457672774e-06 7.03592342542528e-06 2455 2626 3341 3.35785525279731e-07 413 0.84869227752131 -0.84869227752131 -1 1.12481716757122 2455 3631 3341 4398 3351 743 1825 1389 3803 3537 413 3593 M8353 BIOCARTA_HCMV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HCMV_PATHWAY.html Human Cytomegalovirus and Map Kinase Pathways 14/25 BioCarta 0.017256860698596 0.0208793310698737 3070 3286.90909090909 3342 0.0015812481284064 1479 0.90479717458496 -0.538668831779534 -1 0.391049945453436 3066 3662 3337 3319 3960 3023 1479 3412 3932 3624 3342 3594 M1036 REACTOME_INNATE_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INNATE_IMMUNE_SYSTEM.html Genes involved in Innate Immune System 150/416 Reactome 3.12740907584889e-06 6.05080054889675e-06 4645 3253.54545454545 3342 2.84310320147709e-07 2216 1.41323692696383 -1.39023074762517 -1 1.89685122375149 4645 3949 3048 3776 2325 2588 3639 3495 3342 2216 2766 3595 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 27/63 Jessica Robertson 0.0175144895029816 0.0211855699047423 1570 2942.90909090909 3342 0.00160504534687478 1565 1.41527190170248 1.41649128538397 1 0.609373351685512 1569 3825 3342 4298 4144 1838 1565 2167 3970 3706 1948 3596 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 9/15 Jessica Robertson 0.000686183283509877 0.000927713464087502 2795 3443.45454545455 3345 6.86395257010055e-05 2623 1.17087502807703 1.02307246390571 1 0.913318547112306 2794 2889 4351 4016 3345 3417 2623 3264 4261 3063 3855 3597 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 21/60 Kevin Vogelsang 2.72012119230075e-05 4.38777552740838e-05 3975 3105.09090909091 3345 2.4728680227006e-06 1148 1.45502579031658 -1.40604138147204 -1 1.63091825221288 3972 2385 1932 3345 2791 4089 3799 3407 2651 1148 4637 3598 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 11/32 Jessica Robertson 0.0013708006658027 0.00180589595725371 3405 3024 3345 0.000124695958679892 1977 1.56286998548503 -1.67929552325288 -1 1.10279785048758 3401 2918 2408 3359 3410 2306 3626 3695 3345 1977 2819 3599 M2821 BIOCARTA_NTHI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NTHI_PATHWAY.html NFkB activation by Nontypeable Hemophilus influenzae 21/42 BioCarta 0.000130939763764983 0.000191445782528146 3350 3453.54545454545 3346 1.19043234270026e-05 2677 1.40721192264765 1.1766273066722 1 1.34574309923217 3353 3021 3078 2677 3083 4306 3346 4619 3347 2710 4449 3600 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 11/31 Reactome 0.0104974857909117 0.0129416517801137 2665 3150.54545454545 3346 0.000958901146940303 1921 0.846170978263511 -0.846170978263511 -1 0.410923469562139 2663 3835 3346 3829 3728 1921 3292 1984 4105 3899 2054 3601 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) 30/55 Reactome 0.0102504511382298 0.0126470811041983 1290 2948.72727272727 3347 0.000936229536690744 1229 0.673582288505426 -0.673582288505426 -1 0.328842160607702 1288 3347 3680 3777 4047 1229 2046 2449 4242 4251 2080 3602 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 7/32 Reactome 0.000697362438902323 0.000942012219284026 2985 3413.90909090909 3347 6.97581377072406e-05 2286 1.04353530721098 -0.867995824892017 -1 0.812206633483019 2985 4071 3984 4507 3347 3310 2286 2300 4005 3577 3181 3603 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 10/13 Reactome 0.0181613202590888 0.0219340068902295 2015 3149.18181818182 3347 0.00166481822942179 1657 0.771417317390613 -0.771417317390613 -1 0.32915714945196 2011 4067 3347 4282 4636 1657 2307 2419 4119 3839 1957 3604 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 42/94 Jessica Robertson 0.0839184282471183 0.0902966141827776 3225 3484.72727272727 3347 0.00793650793650794 2666 1.43466451033661 1.50868547743597 1 0.385377138778123 3225 3561 2782 3242 4362 4273 3347 4266 2666 2930 3678 3605 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 22/54 Arthur Liberzon 5.53273168858304e-06 1.01195865311086e-05 2180 3210.18181818182 3348 5.02976872979769e-07 2177 1.19189241952835 1.21510174480512 1 1.5312885198508 2177 3894 2909 4352 2458 3362 2231 4067 3717 3348 2797 3606 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 51/109 Jessica Robertson 0.0839184282471183 0.0902966141827776 2580 3379.54545454545 3348 0.00793650793650794 2154 0.960268869092699 -1.00792951491886 -1 0.257945718483462 2579 4084 3348 3838 4273 2154 3212 3056 4061 4057 2513 3607 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 22/42 Arthur Liberzon 2.52894481572108e-05 4.10056588459135e-05 4100 3122.09090909091 3349 2.2990671699316e-06 1837 1.96673133771488 -1.01341586027078 -1 2.2193550365747 4099 3349 1900 3488 2775 3458 4548 2036 1837 2353 4500 3608 M2623 BIOCARTA_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1_PATHWAY.html IGF-1 Signaling Pathway 17/41 BioCarta 9.00397068516813e-05 0.000134285826323036 3790 3338.72727272727 3350 8.185762920953e-06 1769 0.829456335318086 -0.597251892441931 -1 0.8260837316564 3790 1769 3350 1791 3020 3009 4668 4136 3816 4091 3286 3609 M68 PID_RHOA_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHOA_REG_PATHWAY.html Regulation of RhoA activity 18832364 31/59 Pathway Interaction Database 0.000798539079990178 0.00107373145734117 4000 3261.36363636364 3350 7.26208249944391e-05 1659 1.59075848327727 -1.5152472163566 -1 1.21486583312308 4000 3410 2368 2900 3350 3177 4031 4107 3270 1659 3603 3610 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 19/36 John Newman 0.000815769082465697 0.00109501401330113 4400 3316.18181818182 3353 7.4188339103014e-05 2023 1.34320963678133 -0.733362418531409 -1 1.0228671844778 4397 2347 2603 3677 3353 3034 3780 3736 2023 3002 4526 3611 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 25/50 Arthur Liberzon 0.000213530767300624 0.000305155588768137 3355 3454 3354 1.94137722994449e-05 2174 1.51322325167783 1.5280443890969 1 1.36831502164351 3354 3724 2174 4017 3156 4499 2559 3906 3300 3140 4165 3612 M12985 BIOCARTA_TALL1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TALL1_PATHWAY.html TACI and BCMA stimulation of B cell immune responses. 8/23 BioCarta 0.00028285417404071 0.000396723932820942 4530 3508.27272727273 3356 2.82890183409329e-05 2752 1.38779688105996 -0.876971649114014 -1 1.21421746740868 4529 2752 3877 3121 3226 3201 3868 3891 3356 2866 3904 3613 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 12/41 Arthur Liberzon 9.9449463885784e-05 0.000147334868090036 3315 3079.54545454545 3356 9.0412690648987e-06 1115 0.973364839368405 -1.10629716339206 -1 0.959323576788292 3314 3356 3002 4399 3809 2402 3507 1115 3469 3947 1555 3614 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 15/70 Reactome 8.5834713577934e-06 1.5109747100909e-05 4025 3377.36363636364 3357 7.80318622459853e-07 1999 1.57228458998555 -1.6508173466325 -1 1.94959212194971 4023 3103 2142 4567 2560 3215 4510 4210 3357 1999 3465 3615 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 124/285 Broad Institute 0.0049566353734682 0.00624208367645041 3360 3366.45454545455 3357 0.000451621645866576 2647 1.36248246926096 -1.07133622821776 -1 0.772632844854459 3357 3429 3066 3907 3543 2647 3528 2994 3282 2960 4318 3616 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 43/97 Jessica Robertson 4.9112023264313e-07 1.19552696631985e-06 3435 3288.90909090909 3357 4.46473038435555e-08 1821 1.16525865850078 -1.00093459410662 -1 1.7750953688572 3431 2094 2701 3890 1821 4659 3134 2885 3603 3357 4603 3617 M120 PID_ARF6_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_DOWNSTREAM_PATHWAY.html Arf6 downstream pathway 18832364 11/29 Pathway Interaction Database 4.94534934608419e-06 9.15241194144965e-06 3225 3509 3358 4.49578223881915e-07 2433 1.09422296797373 1.32617178593443 1 1.41808625684277 3223 3358 3005 3641 2433 4393 4642 2874 4186 3324 3520 3618 M19938 SU_PANCREAS http://www.broadinstitute.org/gsea/msigdb/cards/SU_PANCREAS.html Genes up-regulated specifically in human pancreas. 11904358 22/94 John Newman 0.000181657595090861 0.0002621643026165 4205 3435.81818181818 3358 1.65156905990497e-05 2307 1.65502929638105 -1.80391216259892 -1 1.52461556826216 4203 4298 2482 4082 3127 4504 3358 2307 2739 2836 3858 3619 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 27/56 Arthur Liberzon 0.0670017562171727 0.0771236132728252 3020 3379.54545454545 3360 0.00628489061132381 2116 1.24237197240071 -0.94448093173218 -1 0.355608489496275 3017 3826 3083 4125 3821 2116 3360 4035 3926 3311 2555 3620 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 42/105 Leona Saunders 0.0168623831222826 0.0204231396513352 3130 3440.18181818182 3361 0.00154482115256767 2484 1.99885025832729 -2.03706788980585 -1 0.868828512591481 3130 4388 3000 4445 3669 2484 3361 2902 3647 4124 2692 3621 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 14/46 Leona Saunders 2.79058582427173e-06 5.46227450816096e-06 4565 3294.72727272727 3362 2.53689942181028e-07 2164 1.39109790982014 -1.48236659459435 -1 1.88303713403647 4563 2164 2447 3568 2301 3624 4657 3471 3362 3013 3072 3622 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 8/16 Jessica Robertson 3.059445751663e-05 4.88468919669262e-05 3365 3330.09090909091 3364 3.05948787341656e-06 2127 1.59440086086604 1.43381882203572 1 1.76803397695485 3364 2127 4324 3292 2842 3401 2476 4235 3461 2885 4224 3623 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 19/42 Jean Junior 0.0010703296773473 0.00142043751573193 1360 2830.72727272727 3364 9.73500692844543e-05 985 0.991879197949882 -0.991879197949882 -1 0.726495539597576 1360 4168 3364 4290 4114 985 1518 2440 3658 3923 1318 3624 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 6/14 Arthur Liberzon 1.3008425703479e-05 2.21582998351518e-05 3840 3523.72727272727 3364 1.3008501852719e-06 2495 1.8277394024481 -1.55384441263553 -1 2.18817754161835 3840 3364 4607 4385 2670 2727 4470 3112 4093 2495 2998 3625 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 62/186 Leona Saunders 1.89428541426765e-06 3.86612432546089e-06 4490 3369 3367 1.72207913211173e-07 2213 1.40309091626643 -1.1295181311618 -1 1.95344123993381 4490 3402 2416 3367 2213 3416 4028 3002 3351 3233 4141 3626 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 17/27 Leona Saunders 0.000832666531528376 0.0011164164139462 3930 3509 3367 7.57256227487793e-05 2656 0.90348945303553 -1.06906080942659 -1 0.68606230938319 3928 2880 2656 3694 3356 3195 4286 3367 4141 3816 3280 3627 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 54/166 Yujin Hoshida 2.03250680304478e-06 4.11240366108284e-06 4385 3191.45454545455 3368 1.84773516437511e-07 1203 1.71784132900364 -1.49194746598497 -1 2.37979926839134 4382 2938 1452 3368 2231 3727 4427 4068 3094 1203 4216 3628 M13519 KEGG_GRAFT_VERSUS_HOST_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GRAFT_VERSUS_HOST_DISEASE.html Graft-versus-host disease 22/73 KEGG 0.001531991407466 0.00201089964576629 3655 3174.72727272727 3369 0.000139369024163086 1854 1.58935274088619 -1.18902074987566 -1 1.1023943455224 3651 3070 1854 2671 3420 2992 4229 4072 3369 1905 3689 3629 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 157/406 Reactome 2.54248423798282e-07 6.92276649575101e-07 3690 3384.18181818182 3370 2.31134957437393e-08 1578 1.37288587435124 -1.22880696215077 -1 2.17517436611316 3687 3980 3249 2979 1578 3319 3192 4360 3370 3463 4049 3630 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 43/96 Kate Stafford 0.000930168607135817 0.00124181484132149 2285 3077.27272727273 3370 8.45965562737687e-05 1881 1.52189257812761 1.89053223309313 1 1.13754797370458 2281 3560 2363 2875 3370 3748 2927 1881 3706 3649 3490 3631 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 461/1054 Jessica Robertson 1.23164414793778e-07 3.83648840981263e-07 4470 3066.09090909091 3371 1.11967656080903e-08 1256 1.35202476633598 -0.96751746244559 -1 2.23126999281106 4466 3371 3705 1667 1327 1256 4133 4147 2656 4200 2799 3632 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 16/26 Reactome 0.212929009659434 0.225132071133598 1650 3213.18181818182 3373 0.0215317933760754 1646 0.575115470224843 -0.575115470224843 -1 0.0957931713375773 1646 3699 3373 3391 4245 2210 2492 2878 4576 4071 2764 3633 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 125/352 Jennifer Shepard 5.05523676802116e-09 4.55554605672061e-08 3560 2865.54545454545 3375 4.59566979967024e-10 88 1.75784627305116 -1.31705360517739 -1 3.3194181518937 3558 3397 1503 2256 88 3375 3806 3454 2924 2759 4401 3634 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 290/826 John Newman 8.97194592035101e-08 2.98833987997062e-07 4200 3141.54545454545 3376 8.1563148056737e-09 1192 1.49352955716252 -1.20091547261089 -1 2.5064807267395 4196 3458 2240 3376 1192 1983 4466 3849 2904 2926 3967 3635 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 588/1374 Jessica Robertson 1.04261343861976e-08 7.29799100778042e-08 3380 3045.18181818182 3377 1.04261344351145e-09 293 1.27168441041469 -0.984854917723848 -1 2.33443250019953 3320 2928 4422 3377 293 1013 3539 3378 3083 3858 4286 3636 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 46/124 Yujin Hoshida 1.58792671203256e-07 4.73046698829279e-07 2880 3304.09090909091 3377 1.4435698424061e-08 1407 0.965765064405728 1.11591698849899 1 1.57122087958425 2877 3377 3294 4574 1407 4178 1998 3781 3995 3759 3105 3637 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 19/63 Jessica Robertson 1.16709691124822e-06 2.53664940914154e-06 3980 3089.18181818182 3377 1.06099775490178e-07 1265 1.67523178471789 -1.76485842956498 -1 2.41118785640748 3976 2024 1435 3793 2072 4479 3377 4183 3057 1265 4320 3638 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 15/38 Reactome 5.36627240834226e-06 9.84587020575248e-06 4575 3626.90909090909 3378 4.87844136170697e-07 2450 1.12271760066476 -0.766440026140171 -1 1.44585488428311 4575 2498 3089 4456 2450 3105 4579 4194 3378 3157 4415 3639 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 36/77 John Newman 0.00205474381013199 0.00266792172188376 3125 3087.09090909091 3378 0.000186969581949517 1510 1.46748327731354 -1.2814499027947 -1 0.971518540467504 3123 3466 3378 4238 3451 1510 2867 3188 3392 3557 1788 3640 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 17/38 Arthur Liberzon 0.0141815231641464 0.0172968811939588 2990 3230.36363636364 3378 0.0012976157222659 2069 1.33189544294786 -0.957626199699611 -1 0.603646252113351 2990 3417 2935 4087 3651 2069 2599 3199 3614 3378 3595 3641 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 9/31 Leona Saunders 0.00215016734511402 0.0027887307443134 3310 3394.09090909091 3379 0.000215225063146159 1680 1.16236650595704 1.16091047932182 1 0.763771490483664 3308 3270 4298 4210 3575 3746 3215 1680 3379 3062 3592 3642 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 8/22 Jessica Robertson 0.0319675869977362 0.0378474261423425 4685 3443.18181818182 3379 0.00324369858169732 2251 1.23962180934793 -1.23962180934793 -1 0.453394437406523 4684 2676 4558 3012 3782 4351 3028 2251 2466 3688 3379 3643 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 177/391 Jessica Robertson 2.57079643620631e-07 6.99173076033823e-07 4525 3273.45454545455 3380 2.33708794237745e-08 1581 1.49030970700413 1.68862863952195 1 2.35956823017225 4523 3553 3380 2785 1581 1603 4320 4402 2772 3990 3099 3644 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 22/51 John Newman 0.00285586872890922 0.00366546175394922 3040 3221.09090909091 3382 0.0002599620678969 1710 1.98320790284352 2.74654553835786 1 1.24257095785312 3039 4265 2296 3382 3780 4652 3173 1710 1819 3744 3572 3645 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 11/41 Reactome 0.0290822761074793 0.0345799405835189 3050 3338.45454545455 3383 0.00267945362579788 1600 0.677466195648696 -0.711822105486279 -1 0.254617595534228 3046 4103 3383 3969 4041 1600 3175 2209 4279 4448 2470 3646 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 5/20 Jessica Robertson 0.000942447450798806 0.00125691872713371 3565 3118.27272727273 3385 9.42847382771071e-05 80 2.87716939633553 -0.668974533355545 -1 2.14667261283547 3565 2404 4315 2595 3385 4643 4611 1953 80 3287 3463 3647 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 13/19 Reactome 0.0196394617365218 0.0236643141417693 1700 3093.27272727273 3388 0.00180154606310463 1507 0.771417317390613 -0.771417317390613 -1 0.322614022583703 1697 4174 3388 4504 3972 1507 2163 2392 4269 3980 1980 3648 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 16/37 Reactome 0.00108917026485118 0.00144421388259554 4070 3438.63636363636 3388 9.90645329512024e-05 2053 0.734826292378402 -0.759767391097041 -1 0.536856095966921 3233 4223 3591 4581 3388 2053 3099 2784 4066 4070 2737 3649 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 5/12 Yujin Hoshida 0.0289091861467241 0.0343828543866876 4620 3404.81818181818 3388 0.00292923030384749 736 2.27156065788458 -3.59799874776149 -1 0.855189876749082 4619 2682 4564 3282 3738 4285 4468 2391 736 3300 3388 3650 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 4/18 Arthur Liberzon 0.104760652828003 0.11220763866332 3070 3438.36363636364 3389 0.0110054094055075 2548 1.07352181014657 -1.07352181014657 -1 0.262314659696238 3069 3707 4216 3432 4124 2759 3389 2548 4366 3098 3114 3651 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 52/138 Jessica Robertson 0.000481344995363376 0.000658756614565648 3485 3314.90909090909 3389 4.37682129668938e-05 2324 1.39988639202398 -1.18146964069079 -1 1.14549346056819 3484 3919 2818 3389 3289 2407 3640 4460 3575 2324 3159 3652 M83 PID_CDC42_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CDC42_REG_PATHWAY.html Regulation of CDC42 activity 18832364 22/42 Pathway Interaction Database 1.23893233266965e-06 2.66925834983446e-06 4035 3260.90909090909 3392 1.1263027548875e-07 2030 1.64956879094365 1.42896751969689 1 2.36486095304572 4034 3128 2458 4007 2088 4041 4070 3392 2030 2351 4271 3653 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 5/20 Reactome 3.57823661342678e-05 5.64946656688609e-05 3395 3202.90909090909 3392 3.57829423173021e-06 1693 1.24410517080608 -1.20035457134061 -1 1.35937557788706 3392 1693 3913 2941 2867 4154 3460 3429 3199 2233 3951 3654 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 4/65 Arthur Liberzon 0.00165724644745171 0.00217166019372448 1980 3136.18181818182 3392 0.000165848365581438 1265 0.956236661165351 0.956236661165351 1 0.655041846920054 1980 3392 4530 4220 3432 1655 1265 3222 4428 4649 1725 3655 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 3/8 Arthur Liberzon 0.00102088843468012 0.00135867174237746 4470 3367.27272727273 3392 0.000102135773407823 1489 1.04750228804751 -1.0929432195086 -1 0.772438462906138 4467 1489 4641 2887 3392 4590 3746 3076 2816 1759 4177 3656 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 108/234 Reactome 0.00799450352638987 0.009923773119116 2470 3211.63636363636 3394 0.000729427557608425 1174 1.00298157949189 -0.863507686813377 -1 0.516823772012086 2466 3781 3733 4319 4663 1174 2733 2718 3394 4330 2017 3657 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 8/19 Pathway Interaction Database 0.00308035209234133 0.00394493848174679 2435 3021.81818181818 3395 0.000308463029706298 1107 0.750984811849884 -0.750984811849884 -1 0.464362176230786 2432 2283 3894 4395 4433 1107 1623 3395 3677 4430 1571 3658 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 142/288 Yujin Hoshida 0.00923910880526289 0.0114233413882485 1975 3180 3396 0.000843467180783321 1931 1.21545988771884 -1.14777099920001 -1 0.607204033189534 1973 4244 3655 3396 3605 1931 2749 2800 3760 4260 2607 3659 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 6/18 Arthur Liberzon 9.2195141608645e-05 0.000137151248754956 3645 3369.81818181818 3396 9.21989668068626e-06 1994 0.890125240534269 -0.469890165769339 -1 0.884406548267047 3645 1994 4626 3180 3041 4006 4163 2931 3396 2496 3590 3660 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 2/18 Jessica Robertson 0.383137645605797 0.399595594771593 3340 3641.7 3396.5 0.0522635471675761 2659 0.599131121627424 -0.599131121627424 -1 0.0613925723592059 3337 3456 4428 NA 4084 2763 2659 3272 4571 4624 3223 3661 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 210/460 Leona Saunders 0.00119601102298265 0.00158274714874236 3030 3308 3399 0.000108787429032377 1863 1.19430560836604 -1.0190287764163 -1 0.860326594561057 3029 4044 3679 4437 3399 1863 3447 2562 3165 4088 2675 3662 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 48/99 Reactome 1.26752364152533e-05 2.16300647639756e-05 3645 3298 3400 1.15230085853188e-06 1790 1.10142690710094 -1.03687826228463 -1 1.32160163136445 3644 3254 3400 1790 2645 4650 2438 3888 2988 3608 3973 3663 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 10/29 Arthur Liberzon 9.56952359654416e-09 7.02612984903285e-08 3400 2990.18181818182 3400 8.69956694379045e-10 226 1.70867386402713 2.24418166935811 1 3.14386069079374 3400 3540 2338 2616 226 4466 3496 2387 3680 3191 3552 3664 M311 KEGG_ALPHA_LINOLENIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALPHA_LINOLENIC_ACID_METABOLISM.html alpha-Linolenic acid metabolism 2/21 KEGG 0.122343341493153 0.130681763901735 3290 3518.5 3402 0.0143953606097224 2619 0.767427193702663 -0.767427193702663 -1 0.174454418707473 3288 3338 3795 NA 4117 2887 2940 2619 4339 4396 3466 3665 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 5/15 Leona Saunders 0.0765897756730953 0.0871115749524574 3200 3488.18181818182 3402 0.00793650793650794 2515 2.39918863475494 -2.39918863475494 -1 0.654090322935269 3197 3673 4235 4397 4291 2646 3155 3402 3576 3283 2515 3666 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 36/96 Arthur Liberzon 0.0474049650955014 0.0553136619615337 2930 3376.72727272727 3402 0.00440530466980981 1791 2.26233607276368 -1.50933799312144 -1 0.731558159543663 2926 4490 2625 2929 4219 4462 3402 2329 1791 4010 3961 3667 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 15/34 Jessica Robertson 0.0839184282471183 0.0902966141827776 3405 3579.72727272727 3403 0.00793650793650794 2730 1.43283825192011 -0.95763839813972 -1 0.384886572078925 3403 3660 2992 3062 3997 4640 4632 3718 2730 3166 3377 3668 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 12/28 Jessica Robertson 0.000186273538890294 0.000268087356594899 4125 3456.72727272727 3403 1.6935392045599e-05 2432 1.27442402801794 -1.3539102598645 -1 1.17082075535536 4124 2432 2852 3403 3132 4493 3739 4013 2534 2753 4549 3669 M3618 BIOCARTA_TNFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR1_PATHWAY.html TNFR1 Signaling Pathway 18/35 BioCarta 0.000357577278808182 0.000495009491431357 4245 3532.81818181818 3405 3.25123100822591e-05 3046 1.16996824282861 -0.880234708049936 -1 0.994706406568269 4242 3156 3046 3246 3247 3459 4245 4182 3163 3470 3405 3670 M16929 REACTOME_PI3K_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_CASCADE.html Genes involved in PI3K Cascade 33/105 Reactome 0.0839184282471183 0.0902966141827776 2790 3470.18181818182 3405 0.00793650793650794 2281 1.36810775831266 1.20275394584118 1 0.3674987674289 2786 3147 3405 4512 4246 3518 2281 3332 3581 3364 4000 3671 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 12/42 John Newman 1.22404282720748e-05 2.0926175440694e-05 2815 3204.09090909091 3405 1.11277239784363e-06 2075 1.17182230924798 -1.10619844114132 -1 1.4103997291808 4217 2075 2811 3405 2641 2813 4094 3606 2655 3422 3506 3672 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 21/62 Arthur Liberzon 0.00021864334155392 0.000311986205396367 3220 3362.09090909091 3405 1.98786430984258e-05 2192 1.58226266729158 1.67382672128754 1 1.42683037311384 3217 3446 2192 4335 3158 4375 2219 4252 3405 2210 4174 3673 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 2/5 Jessica Robertson 0.000116112206131906 0.000170939930233776 3995 2940.7 3406.5 1.29020220655271e-05 1045 1.59295389029515 -1.56440768406518 -1 1.54353148982359 3993 1084 4482 NA 3095 4403 3960 2232 1045 1395 3718 3674 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 2/13 Reactome 0.0817779004076875 0.0902966141827776 4105 3476.6 3407 0.00943476390464625 2521 0.455933431392626 0.455933431392626 1 0.122471916568814 2730 3847 4101 NA 4105 2862 2558 2521 4543 4532 2967 3675 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 9/32 Kevin Vogelsang 0.000224162604457701 0.000319181393038222 3075 3405.45454545455 3408 2.24185219661396e-05 2358 2.21264872175401 -0.887802936882498 -1 1.98965542804867 3074 2358 4383 3408 3180 3295 2760 4222 3443 3783 3554 3676 M17636 KEGG_RENIN_ANGIOTENSIN_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENIN_ANGIOTENSIN_SYSTEM.html Renin-angiotensin system 9/30 KEGG 7.76106060060447e-05 0.000116527811516926 3670 3386.54545454545 3409 7.76133166720582e-06 2036 2.15351587062948 -2.27319791499829 -1 2.17888170171417 3669 2781 3807 3409 3010 4159 3776 2953 2036 3044 4608 3677 M94 PID_FAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FAS_PATHWAY.html FAS (CD95) signaling pathway 18832364 33/54 Pathway Interaction Database 5.41151381490833e-05 8.30604446009185e-05 4535 3441.90909090909 3409 4.91967902797565e-06 2730 1.12579480765286 -0.910640293791403 -1 1.1816326676384 4533 3409 3194 2730 2931 2906 3907 3571 3736 3362 3582 3678 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 14/27 Reactome 0.0839184282471183 0.0902966141827776 2720 3532.45454545455 3411 0.00793650793650794 2717 1.21439333515164 1.28156669367829 1 0.326208237836719 2717 4173 3280 4038 4382 4158 3411 2730 3185 3009 3774 3679 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 30/63 Jessica Robertson 5.26966517867348e-06 9.69271218327283e-06 3775 3141.81818181818 3411 4.79061618287019e-07 1887 1.06760752919181 -1.24178582937626 -1 1.3767529190484 3772 3411 3087 3816 2446 2177 3913 2347 3669 4035 1887 3680 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 15/28 Jessica Robertson 1.63475538819488e-07 4.83920641129577e-07 4275 3296.45454545455 3412 1.48614137242615e-08 1415 1.33867812554095 -0.831478790642593 -1 2.17452147224928 4271 2988 2311 3684 1415 4598 3412 3937 3161 2560 3924 3681 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 7/24 John Newman 0.00020236566455621 0.000289641265763715 4310 3211.81818181818 3413 2.02384095256409e-05 737 1.26148316101982 -0.822587501215724 -1 1.14803472875551 4310 737 4416 3160 3164 3432 4359 3413 1562 2689 4088 3682 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 644/1528 Jessica Robertson 0.00290951399214122 0.00373124865002019 3290 3464.27272727273 3413 0.000291333039873405 1086 1.38675253274957 -1.01873704640736 -1 0.866108522681805 3287 4516 4465 3336 3503 1086 3413 4592 3172 4309 2428 3683 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 24/87 Jessica Robertson 3.7992939874543e-05 5.97833835635018e-05 3395 3389.09090909091 3413 3.45396327365186e-06 1808 0.882721232978556 -0.759188748951093 -1 0.958928855629637 3395 3594 3413 4580 2862 1808 3349 3502 4206 3854 2717 3684 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 5/26 BioCarta 0.00130552211017621 0.00172183411435005 3435 3115 3414 0.000130628971952624 1907 1.24319927951425 -0.596537758914796 -1 0.883850350428912 3433 1907 3866 2666 3414 2962 3612 3673 2043 3264 3425 3685 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 211/524 Arthur Liberzon 3.09610963610864e-08 1.41209938305351e-07 2235 3187.63636363636 3414 2.81464516334627e-09 716 1.32829554990799 1.62889259327126 1 2.34041288839221 2234 3948 3444 4117 716 4556 2814 2866 2808 4147 3414 3686 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 12/27 Reactome 0.0839184282471183 0.0902966141827776 4570 3290.54545454545 3415 0.00793650793650794 575 2.05079292901753 -1.82564920723962 -1 0.550880597601105 4567 2846 2198 2797 3912 3291 4316 4039 575 3415 4240 3687 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 47/131 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3015 3389.27272727273 3415 0.00793650793650794 2048 2.51639122664591 -2.1131715856076 -1 0.675948889118259 3012 4608 2717 2793 4182 4372 2741 3415 2048 3567 3827 3688 M10628 BIOCARTA_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ATM_PATHWAY.html ATM Signaling Pathway 20/32 BioCarta 0.000678049117889223 0.000917510299286428 3680 3366.45454545455 3416 6.16598350593511e-05 2113 1.46541825638977 1.94474388534782 1 1.14488174110408 3679 3416 2548 3076 3325 3983 4366 2113 2373 3954 4198 3689 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 134/297 John Newman 0.00148015333530847 0.00194503604297687 4440 3602.36363636364 3417 0.0001346500106363 2514 1.15340330090991 -0.776682821697149 -1 0.804305189774196 4437 3197 3584 2514 3417 2697 4478 3334 3367 4167 4434 3690 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 10/17 Reactome 0.0144687744860642 0.0176059925322505 2515 3154.36363636364 3418 0.00132407427054159 1567 0.748237640175529 -0.748237640175529 -1 0.337638222083849 2515 3418 3429 3703 4519 1567 2761 2047 4089 4465 2185 3691 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 161/415 Arthur Liberzon 4.34326439011501e-08 1.7744147281673e-07 3050 3255.63636363636 3419 3.94842225078201e-09 864 1.27606295305365 1.44815296305916 1 2.21582423930413 3048 3743 2942 4364 864 3705 2886 3806 3419 3405 3630 3692 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 18/35 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3200 3409.36363636364 3420 0.00793650793650794 2382 1.43066153989093 -1.13711778872387 -1 0.384301867074629 3199 3596 2382 2971 4202 2987 3690 3987 4130 2939 3420 3693 M765 BIOCARTA_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INSULIN_PATHWAY.html Insulin Signaling Pathway 17/44 BioCarta 4.55000639977052e-05 7.08585243912419e-05 4010 3306.09090909091 3421 4.13645500457524e-06 1480 0.817787329167989 -0.597251892441931 -1 0.872862873674473 4006 1897 3421 1480 2895 2973 4530 4125 3596 4092 3352 3694 M40 PID_E2F_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_E2F_PATHWAY.html E2F transcription factor network 18832364 48/115 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 2610 3446.18181818182 3421 0.00793650793650794 2610 1.57760897252447 1.82083545577165 1 0.423774658182164 2610 4050 2669 3077 4283 4252 2730 3421 3105 3827 3884 3695 M4470 BIOCARTA_EXTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EXTRINSIC_PATHWAY.html Extrinsic Prothrombin Activation Pathway 5/13 BioCarta 9.11994516622702e-06 1.5994035572208e-05 4315 2637.54545454545 3422 9.11998259447313e-07 277 2.06304859410856 -2.38676499556811 -1 2.54501931626268 4314 739 3834 1315 2591 3422 4484 3435 277 971 3631 3696 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 36/98 Arthur Liberzon 2.86856169016642e-05 4.5971546101641e-05 3935 3421.90909090909 3422 2.60781735798758e-06 2096 0.945577150486866 -0.849140105730222 -1 1.05496037742944 3905 2096 3422 3933 2811 3207 3932 2554 3295 4145 4341 3697 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. 6/15 SigmaAldrich 0.00438775035578172 0.00555402435634606 3990 3384.72727272727 3423 0.000439643806680213 2010 1.6747084718584 -1.21182315017377 -1 0.971538217243616 3987 3112 3891 3164 3537 4595 3669 3375 2010 2469 3423 3698 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 26/60 Reactome 0.000824683232061709 0.00110666255024088 3585 3264.09090909091 3426 7.4999321078508e-05 1730 1.96262464584197 1.98750421843384 1 1.49223791305249 3581 3442 2113 3124 3354 4503 3426 2699 1730 3641 4292 3699 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 9/24 Leona Saunders 0.000348022195093467 0.000482780345236231 3600 3471.63636363636 3426 3.48076710861617e-05 2767 0.810778622778136 -0.802280406703579 -1 0.691589135952208 3597 2782 4267 3495 3258 2767 2994 3426 4230 4584 2788 3700 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 151/323 John Newman 0.00109243254900381 0.00144812982309247 3165 3642.36363636364 3427 9.93613986355947e-05 2629 1.41115819464071 2.04690140792493 1 1.03055017352684 3161 4326 3427 2629 3389 4138 4188 3376 2951 4164 4317 3701 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 163/433 Arthur Liberzon 1.95486403191248e-05 3.23463730704162e-05 4040 3321.90909090909 3427 1.77716491141186e-06 1563 1.39308829075292 -1.12769294165441 -1 1.60894235228758 4037 3427 3284 3514 2727 1563 3831 4320 2981 3862 2995 3702 M5113 REACTOME_GLYCOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOLYSIS.html Genes involved in Glycolysis 18/44 Reactome 0.0177483147183026 0.0214517933376235 2850 3330.72727272727 3428 0.0016266487349544 1367 1.01499004118078 -1.01499004118078 -1 0.435608094924681 2847 4498 3428 4522 4239 1367 3023 2227 4401 4122 1964 3703 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 378/786 Arthur Liberzon 5.94758011740743e-05 9.0723829525297e-05 3105 3484.72727272727 3428 5.40703719370983e-06 2438 1.30822124130393 -0.997883354371271 -1 1.36021031104726 3104 4369 3709 3151 2958 2438 3648 3923 3271 4333 3428 3704 M6910 BIOCARTA_INFLAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INFLAM_PATHWAY.html Cytokines and Inflammatory Response 13/44 BioCarta 0.016793469685597 0.0203449325094901 3365 3326.81818181818 3429 0.00153845888913953 1984 1.99128303920357 -1.21182315017377 -1 0.86639275259665 3362 4063 1984 4162 3668 4102 2633 2754 3534 2904 3429 3705 M1001 BIOCARTA_RHO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RHO_PATHWAY.html Rho cell motility signaling pathway 24/53 BioCarta 0.0107941479666061 0.0132968920535005 4560 3488.63636363636 3431 0.000986134125028905 1995 1.26699146273347 -1.42966056540226 -1 0.611452743802319 4560 2947 3052 3431 4681 4165 3501 1995 3325 3028 3690 3706 M19193 REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS.html Genes involved in Glycogen breakdown (glycogenolysis) 8/17 Reactome 0.027714121494405 0.0329950135474547 3725 3227.54545454545 3431 0.00280659453642775 698 1.85066682478859 -0.786071119189638 -1 0.705250829203345 3725 3420 3908 3109 3729 4492 3431 2505 698 3673 2813 3707 M163 PID_LIS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LIS1_PATHWAY.html Lissencephaly gene (LIS1) in neuronal migration and development 18832364 25/57 Pathway Interaction Database 8.6017105622667e-08 2.88736502111617e-07 4310 3336.72727272727 3432 7.81973718052937e-09 1178 1.7996741175326 -1.15893054893402 -1 3.02717104838315 4307 4553 2888 3910 1178 2244 3164 4223 3432 3562 3243 3708 M5410 KEGG_ARACHIDONIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARACHIDONIC_ACID_METABOLISM.html Arachidonic acid metabolism 18/108 KEGG 5.11263884366381e-06 9.4322148115782e-06 4390 3306.90909090909 3433 4.64786429554603e-07 1774 1.9466703785947 -1.80403976059102 -1 2.51628903897799 4386 2646 1774 3614 2441 3778 4660 3433 3077 1895 4672 3709 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 8/19 Jessica Robertson 2.49020822199559e-06 4.92160089762604e-06 3700 3135.45454545455 3433 2.49021101251164e-07 1473 1.84683923035486 -1.89303783033208 -1 2.52144763247882 3696 2399 4492 3468 2292 4062 3433 3031 1473 1545 4599 3710 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 37/82 Arthur Liberzon 0.00184106701381164 0.00240246171727133 4335 3318.09090909091 3435 0.0001675099559748 2046 1.27929927466456 1.35282299269016 1 0.86191253072505 4334 3205 3525 3507 3435 2046 4641 3912 3301 2542 2051 3711 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. 6/13 SigmaAldrich 0.598881260040338 0.61556428702545 2600 3462.36363636364 3436 0.0873015873015873 2598 1.03418660626638 1.03418660626638 1 0.0560551180140436 2598 3191 3890 2920 4165 3487 2870 3688 4450 3436 3391 3712 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 12/22 Yujin Hoshida 1.28336032814488e-06 2.75106427158595e-06 2750 3307.72727272727 3436 1.16669188798918e-07 2097 1.21992268910664 -1.22561562483547 -1 1.74479630296485 4248 2748 2619 4090 2097 2966 4294 3436 3685 2749 3453 3713 M1 PID_FANCONI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FANCONI_PATHWAY.html Fanconi anemia pathway 18832364 34/62 Pathway Interaction Database 0.414188582710937 0.431212552451333 1560 3388.72727272727 3437 0.0474515479418923 1560 0.873486817494249 -0.883270412925045 -1 0.0820755528922468 1560 3925 3437 3779 4077 2504 3024 3302 4437 4112 3119 3714 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 36/137 Arthur Liberzon 7.40845746287479e-06 1.31849721500309e-05 4015 3258.36363636364 3437 6.73498400984516e-07 1796 1.67926495112603 -1.59340795321112 -1 2.10780602199588 4014 4051 2049 4273 2530 4602 2542 3437 2805 1796 3743 3715 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 4/18 Reactome 0.0648282557713868 0.0747135284172943 3440 3498.81818181818 3438 0.0066800965802515 2428 1.47157038893948 -1.47157038893948 -1 0.426431766315514 3438 4236 3959 4281 4641 2694 2953 2428 4086 3092 2679 3716 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 28/77 John Newman 4.16469565083839e-07 1.04362373368068e-06 3640 3018.63636363636 3438 3.78608767203053e-08 1518 2.1562196933522 -1.40405645311606 -1 3.31740569394984 3636 3926 1951 3438 1763 3817 3680 2795 1518 2969 3712 3717 M576 REACTOME_GLYCOSPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSPHINGOLIPID_METABOLISM.html Genes involved in Glycosphingolipid metabolism 19/36 Reactome 0.00734894189371359 0.0091345203485257 3985 3317.63636363636 3439 0.000670327811557269 1949 1.55974692625662 -1.14460704958925 -1 0.818157411196524 3985 3263 2559 3285 3588 2740 3628 3439 1949 3542 4516 3718 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 6/16 Reactome 0.00891107642729828 0.0110235755380992 2425 3041.09090909091 3439 0.000894701268393483 1327 1.35515758353814 -1.35515758353814 -1 0.682385054450074 2423 4008 3957 4174 4215 1696 1327 2701 3604 3439 1908 3719 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 15/50 Arthur Liberzon 0.0342414973129827 0.0404578054484712 4370 3375.54545454545 3439 0.00316239571790124 2122 1.38967434032336 -1.63276622845616 -1 0.49792270931527 4366 4351 2699 3826 4095 2662 3439 2255 4154 3162 2122 3720 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 71/193 Kate Stafford 6.50309716733625e-06 1.17070738863379e-05 3285 3275.18181818182 3440 5.91192399115187e-07 1359 1.83027655883532 2.25882088778278 1 2.32166178040842 3283 3852 1359 3440 2505 4527 3406 3559 3592 2361 4143 3721 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 46/108 Arthur Liberzon 0.00193751908237883 0.00252480934928453 4035 3618.90909090909 3441 0.000176293413078203 3180 1.28685129882685 1.38039933198535 1 0.859860263424301 4035 3378 3180 3312 3441 3620 4281 3430 3533 3205 4393 3722 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 66/153 Arthur Liberzon 4.45016767851568e-05 6.94653089324599e-05 2770 3389.27272727273 3441 4.04568881746557e-06 2462 1.28826022919909 -1.00280260870147 -1 1.37787855429158 2769 3644 3110 3947 2890 4511 2462 3713 3441 3483 3312 3723 M15258 BIOCARTA_AKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKT_PATHWAY.html AKT Signaling Pathway 16/33 BioCarta 0.000240716310640271 0.000341196803285031 3445 3530.90909090909 3442 2.18856957284485e-05 1913 0.946538167990916 0.800427232948665 1 0.84409228632929 3442 3353 3441 1913 3173 4235 2718 4148 3999 3760 4658 3724 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 6/16 Reactome 7.97255088314342e-05 0.000119549995002912 3675 3138.63636363636 3442 7.9728369246407e-06 1228 1.05672436420312 -1.29440465807749 -1 1.06614871485936 3671 1228 4066 3674 3014 3155 3442 2079 4192 3445 2559 3725 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 77/193 Arthur Liberzon 0.00150145314887886 0.00197191969048384 1725 3463.72727272727 3443 0.000136588985348011 1723 0.970384787807554 1.04053308912667 1 0.675192463504176 1723 4112 3501 4442 3419 3443 2579 3431 4137 4066 3248 3726 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 2/12 Arthur Liberzon 0.363601881567944 0.379474034972692 2805 3643.2 3443 0.0489746387291015 2522 0.548923785362734 0.548923785362734 1 0.0594160010052625 2803 3426 4586 NA 4172 3014 2522 3207 4575 4667 3460 3727 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 547/1222 Jessica Robertson 0.00181102063098992 0.00236457026381131 2090 3046.09090909091 3445 0.000181249823412904 1030 1.13226820708633 -1.00420029871652 -1 0.764862869680002 2088 4320 4338 3460 3445 1030 2564 2491 3585 4365 1821 3728 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 2/5 Arthur Liberzon 0.292170754851511 0.306838224391345 3300 3655.8 3445.5 0.0376669769292759 2610 0.427400492082032 -0.427400492082032 -1 0.0564060995161249 3299 3369 4255 NA 4044 2610 3252 3522 4499 4577 3131 3729 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 41/112 John Newman 0.000195473048899057 0.000280547230364772 3825 3090.72727272727 3446 1.77718562828276e-05 1230 1.83584356607401 -1.09238750542367 -1 1.67728371739841 3446 3822 2522 2259 3942 3823 4577 1230 1620 2825 3932 3730 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 21/41 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3930 3264.18181818182 3446 0.00793650793650794 1404 1.7846394744398 2.05210836744682 1 0.479386870035989 3926 3130 1976 1404 4110 3941 4425 3169 3446 2719 3660 3731 M194 BIOCARTA_PROTEASOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PROTEASOME_PATHWAY.html Proteasome Complex 22/35 BioCarta 0.0240983261756575 0.0288514962849083 1685 3094.63636363636 3447 0.00221512858055031 1452 0.425723047596813 -0.425723047596813 -1 0.168615908151694 1682 3447 3667 3521 3968 1452 1861 3121 4476 4421 2425 3732 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 68/179 Yujin Hoshida 0.00140267259417189 0.0018473647488166 4295 3457.54545454545 3447 0.00012759706428014 2212 1.05817039284384 -1.05154507202834 -1 0.743986205764964 4295 3085 3447 3976 3413 2212 4348 2816 3909 4031 2501 3733 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 10/34 Reactome 0.00685617658718087 0.00854014978403231 4175 3501.09090909091 3448 0.000625239742586793 2038 1.04799433512538 1.03607847827701 1 0.557596744118924 4173 2038 2979 3410 3580 3075 4339 4437 3448 3176 3857 3734 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 18/32 Reactome 0.177854170618208 0.188259463184306 1675 3194.36363636364 3448 0.0176458639856056 1674 0.556960592769585 -0.556960592769585 -1 0.103897696855406 1674 3598 3448 3519 4151 2137 2430 2790 4559 4123 2709 3735 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 6/28 Arthur Liberzon 0.0765897756730953 0.0871115749524574 3760 3526.54545454545 3448 0.00793650793650794 2540 4.37872827285431 4.37872827285431 1 1.1937719991507 3760 3391 4192 2540 3996 4455 4228 2582 3054 3448 3146 3736 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 26/55 Leona Saunders 0.0201181786850461 0.0242286777995698 2470 3227.63636363636 3449 0.00184586747675493 1432 1.1986579267562 -1.1986579267562 -1 0.498134363678639 2469 4341 3578 3449 4627 1432 2740 2625 4031 4228 1984 3737 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 88/211 Jean Junior 5.27311410722709e-05 8.11754688123067e-05 3725 3369.63636363636 3449 4.79385500105553e-06 2499 1.37374318528012 -1.18747568576853 -1 1.44540168450622 3724 4148 3135 2978 2926 2499 3844 3811 3449 3513 3039 3738 M9271 REACTOME_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_METABOLISM.html Genes involved in Purine metabolism 17/39 Reactome 0.00161307817476302 0.00211555676656577 4640 3549.27272727273 3450 0.00014675110247107 2401 1.48641200463775 -1.34530676252928 -1 1.02256902895605 4639 3450 2401 4147 3423 3252 4126 4098 2967 2782 3757 3739 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 33/63 Reactome 0.0189587403686375 0.0228617234604826 4280 3059.81818181818 3451 0.00173855618941079 1368 0.665586262913776 -0.665586262913776 -1 0.280919864743611 1368 3623 3708 3451 4199 1390 2251 2810 4277 4277 2304 3740 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 6/20 Leona Saunders 0.0156343648966162 0.0189701278885405 2970 3352.09090909091 3451 0.00157454615537733 2168 1.21588374898368 -0.94493713846385 -1 0.538525159619055 2966 3190 4271 3561 3671 3212 2168 3080 3704 3451 3599 3741 M7847 REACTOME_SIGNALING_BY_WNT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_WNT.html Genes involved in Signaling by Wnt 38/79 Reactome 0.0056905171044856 0.00713560694450616 1435 3001.81818181818 3452 0.000518662701038535 1110 0.639748845136235 -0.639748845136235 -1 0.353226116557341 1435 3649 3732 3452 4405 1110 2013 2601 4357 4305 1961 3742 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 10/20 Jessica Robertson 2.47548685653346e-05 4.01666600059412e-05 4370 3167.81818181818 3452 2.25046791970693e-06 1814 1.07553993967883 -0.993940288290496 -1 1.21617509259872 4370 1814 2358 2381 2770 3880 3653 4524 3452 1856 3788 3743 M5244 KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM.html Glyoxylate and dicarboxylate metabolism 8/18 KEGG 0.0709536511723695 0.0815123337567354 2865 3363.81818181818 3453 0.00733264901395975 2378 1.04907507975788 -1.04907507975788 -1 0.293794561063235 2861 2998 3799 4565 3869 2378 2924 3453 4102 3668 2385 3744 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 5/21 BioCarta 0.1342861003216 0.143209983183208 3055 3488.72727272727 3454 0.0143166080951129 2159 0.386790298712793 -0.386790298712793 -1 0.0839710040044223 3053 3454 3851 4226 4061 2159 2827 2617 4625 4419 3084 3745 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 38/79 Reactome 0.101827953446509 0.109191256258659 1920 3307.36363636364 3454 0.00971555428923957 1916 0.757837899155235 -0.673582288505426 -1 0.1874842406226 1916 3854 3681 3454 4135 1928 2896 3180 4330 4237 2770 3746 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 36/96 Kate Stafford 0.0839184282471183 0.0902966141827776 3365 3570.45454545455 3454 0.00793650793650794 2691 1.5323379289168 -1.38316872314315 -1 0.411614020765641 3361 3717 2967 3370 4008 4490 2691 3963 3454 2788 4466 3747 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 51/149 Reactome 0.0062591882023048 0.00782356786236338 3455 3172.27272727273 3455 0.000570642489433626 2056 1.05238189110722 -0.977195863740235 -1 0.570233820958162 3455 2691 3553 2310 3569 2056 4559 2739 3787 3736 2440 3748 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 130/337 Arthur Liberzon 1.61214539780846e-06 3.36954207588333e-06 3580 3255.81818181818 3455 1.46558779925374e-07 1727 1.19298986713564 -1.12983020445687 -1 1.67925068380333 3576 3745 3455 4353 2159 1727 4601 2603 3086 4179 2330 3749 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 35/65 John Newman 0.161385165508919 0.171020100763183 2115 3429.72727272727 3455 0.0158730158730159 2115 1.33733882599708 -1.39865863599391 -1 0.26382044713753 2115 4089 2894 3455 4303 2667 3400 3468 4236 3998 3102 3750 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 6/9 Jessica Robertson 0.00101993058582688 0.00135778259238204 2530 3241.09090909091 3456 0.000102039900471315 1820 0.960100788946416 0.960100788946416 1 0.708057932827165 2528 3484 4513 3751 3391 2435 1820 3790 3880 3456 2604 3751 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 387/856 Arthur Liberzon 6.45698386417493e-08 2.3419060671458e-07 3540 3064.72727272727 3457 5.86998550335176e-09 1051 1.35922922258179 -1.10838510139728 -1 2.31810488004198 3794 3457 3540 4362 1051 1263 3711 3538 2898 3402 2696 3752 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 6/21 Arthur Liberzon 0.000127174476705002 0.000186231124324888 1640 2887.81818181818 3457 1.27181755297641e-05 581 1.25580756342175 1.25580756342175 1 1.20482633848105 1636 3944 4539 4617 4079 1200 581 1730 4355 3457 1628 3753 M3075 BIOCARTA_SET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SET_PATHWAY.html Granzyme A mediated Apoptosis Pathway 9/25 BioCarta 0.0605276844533131 0.0699291739024224 3460 3362.90909090909 3459 0.00622424143233414 1744 0.749665637071345 -0.54309461297734 -1 0.222780045876518 3459 3242 3839 3967 3876 1744 2188 2959 4452 4418 2848 3754 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 102/216 John Newman 2.75558502809645e-06 5.4005317614638e-06 4480 3522.63636363636 3459 2.50508043598113e-07 2298 1.54305517918208 -1.31931788978699 -1 2.09069114155885 4478 3459 3226 3378 2298 3089 4526 3725 2833 3654 4083 3755 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 25/64 Yujin Hoshida 2.97181896709356e-05 4.75267093850312e-05 3545 3106.54545454545 3459 2.70169010179992e-06 921 1.43681472385224 -0.744429732077701 -1 1.59768401694239 3541 2873 2696 4412 3459 4031 2971 921 1205 3892 4171 3756 M288 PID_HES_HEY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HES_HEY_PATHWAY.html Notch-mediated HES/HEY network 18832364 28/75 Pathway Interaction Database 5.86840432786672e-05 8.96620237378006e-05 3465 3515.09090909091 3462 5.3350553371329e-06 2426 1.1199076434188 -0.954764838035492 -1 1.16588584536642 3462 2426 2912 4026 2951 4665 2906 4163 3462 3382 4311 3757 M108 PID_NETRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NETRIN_PATHWAY.html Netrin-mediated signaling events 18832364 29/58 Pathway Interaction Database 1.24538641284245e-05 2.12832995280077e-05 3470 3430.63636363636 3466 1.1321758753097e-06 2335 1.32861772545431 1.37821238985655 1 1.59660647449896 3490 3470 3275 2335 2643 4350 3044 4085 2955 3466 4624 3758 M199 PID_P38_MK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_MK2_PATHWAY.html p38 signaling mediated by MAPKAP kinases 18832364 17/24 Pathway Interaction Database 0.00235146353877386 0.00303887428094162 2665 3082.81818181818 3466 0.000213998241914879 1401 1.03441785868897 0.933444451572392 1 0.669772542407112 2664 3729 3020 3970 3466 1797 1401 3643 4113 3814 2294 3759 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 15/40 Kate Stafford 3.46889512593038e-06 6.65108124390743e-06 4285 3260.27272727273 3467 3.15354599599454e-07 1189 1.31318416089548 -1.21606086261912 -1 1.74868456095472 4285 2390 2058 3467 2347 4281 4093 4077 3087 1189 4589 3760 M1063 REACTOME_THE_NLRP3_INFLAMMASOME http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THE_NLRP3_INFLAMMASOME.html Genes involved in The NLRP3 inflammasome 9/16 Reactome 0.000711162428496441 0.000960100011505135 1490 2740.63636363636 3470 7.11390119455657e-05 734 1.38561901139476 1.38561901139476 1 1.07551414935438 1488 3941 4091 4230 3470 734 883 1942 4222 3779 1367 3761 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 5/23 Jessica Robertson 0.000199867305917214 0.000286240279806865 3520 3262.90909090909 3472 1.99885284315997e-05 1531 2.15800710620792 -2.06574327196403 -1 1.96677947787153 3517 1599 4314 2494 3160 3639 4236 4569 3361 1531 3472 3762 M14775 ST_G_ALPHA_S_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_G_ALPHA_S_PATHWAY.html G alpha s Pathway 12/21 Signaling Transduction KE 0.000311070882672385 0.000433703706100207 3635 3268.81818181818 3473 2.82831705013506e-05 2244 1.43502534020888 -1.61715623675446 -1 1.24125242540941 3635 2244 2337 3473 3225 4056 3043 3579 2570 3941 3854 3763 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 22/56 Reactome 0.0255781674154978 0.0305607579064311 2765 3336.18181818182 3473 0.00235277116630418 2560 0.965780801893113 -0.687733597573058 -1 0.376307257130644 2764 2560 3252 3695 3714 3901 2768 3810 3473 3742 3019 3764 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 7/18 Arthur Liberzon 0.0761871494376025 0.0871115749524574 4495 3136 3473 0.00789326037131955 99 1.95486879423142 -0.348237896777569 -1 0.532955453143151 4492 1740 4533 1973 3852 3076 3473 3220 99 3591 4447 3765 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 12/15 Yujin Hoshida 0.00257903205718505 0.00332197477184418 3475 3333.36363636364 3474 0.000234732763180933 1693 1.81683481937656 -1.81683481937656 -1 1.1583002285559 3474 4309 2778 4175 4051 2600 3354 1693 3792 3945 2496 3766 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 24/68 Yujin Hoshida 0.000308767225220456 0.00043074820404378 3985 3436.90909090909 3474 2.8073688075257e-05 2198 1.06113193774888 -0.985384641780342 -1 0.918656709525845 3982 3207 2845 4535 3222 2198 3474 3733 3724 3855 3031 3767 M747 REACTOME_METABOLISM_OF_POLYAMINES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_POLYAMINES.html Genes involved in Metabolism of polyamines 10/17 Reactome 0.00276928185449642 0.00355920317338733 4330 3524.54545454545 3475 0.000252070353052603 2746 1.16237243063368 -1.58050850648907 -1 0.732099454887613 4329 3360 2746 2846 3478 4410 3217 3873 3201 3835 3475 3768 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 13/31 Jessica Robertson 0.719133524926691 0.735295591928099 2570 3394.90909090909 3475 0.10902887875614 2194 1.24970168842576 -1.24970168842576 -1 0.0429247598968448 2570 3480 3080 2194 4305 3065 3475 3818 4514 3535 3308 3769 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 758/1799 Chi Dang 4.50552142964437e-05 7.02591461541216e-05 2980 3323.54545454545 3476 4.50561278100619e-06 1340 1.30464159670392 -1.05573032984186 -1 1.39374347178131 2979 4413 4594 3539 2914 1340 3485 3476 3174 4363 2282 3770 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 24/42 Arthur Liberzon 3.02261635459648e-06 5.87136885884638e-06 3480 3143.36363636364 3477 2.74783682493365e-07 2244 1.57922715748867 -0.811567750904211 -1 2.12495436474493 3477 2645 2610 2460 2318 4346 3816 3554 2244 3501 3606 3771 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 118/227 Arthur Liberzon 0.00115572178183612 0.00153029450965924 4110 3485.81818181818 3478 0.000105120851076473 1724 1.78010126863436 -1.10320690644554 -1 1.28901043864009 4108 3914 2954 2308 3396 3478 4355 3464 1724 4005 4638 3772 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 149/323 Arthur Liberzon 1.61758529380252e-08 9.23183294908041e-08 3745 2921.90909090909 3479 1.47053209608734e-09 455 1.14920079448819 -0.797799600160059 -1 2.07941363914177 3745 2259 3528 4280 455 979 3479 3973 2742 4148 2553 3773 M2158 REACTOME_BASE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASE_EXCISION_REPAIR.html Genes involved in Base Excision Repair 15/21 Reactome 0.0557735175558829 0.0645798624331276 1910 3271.09090909091 3480 0.00520361619879462 1874 0.771417317390613 -0.771417317390613 -1 0.236101745409236 1909 4500 3480 4579 4056 1874 2365 2621 4278 4049 2271 3774 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 11/35 John Newman 0.00159918055525205 0.00209791715619012 3150 3270.36363636364 3480 0.000145485834941162 1412 1.06706914890029 -1.06706914890029 -1 0.735082399249637 3147 2920 2741 3887 3719 1935 4603 3480 4225 3905 1412 3775 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 19/69 Jessica Robertson 0.0839184282471183 0.0902966141827776 3405 3373.81818181818 3481 0.00793650793650794 2058 1.36146557264901 0.832413085100215 1 0.365714553832922 3402 2808 2756 3481 4012 3948 2058 3537 3433 3546 4131 3776 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 33/83 John Newman 0.000157497609772454 0.000228493436344805 3120 3575.90909090909 3482 1.43189896480545e-05 2995 1.07148282650049 -0.770633820735009 -1 1.00350502506292 3120 3593 3403 4184 3110 4610 2995 3757 3482 3936 3145 3777 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 18/53 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3215 3513.27272727273 3482 0.00793650793650794 2447 1.46157276687401 -0.879939109766205 -1 0.392605192853881 3211 4560 2842 4477 3949 2447 3703 3255 3742 3482 2978 3778 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 61/131 Reactome 1.69000688662296e-07 4.96816479437781e-07 3780 3359 3484 1.5363700149516e-08 1433 1.34271701921104 -1.41567018737428 -1 2.17713741945925 3780 3010 2612 3698 1433 3944 3104 4259 3484 3201 4424 3779 M15343 REACTOME_ACTIVATED_TLR4_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_TLR4_SIGNALLING.html Genes involved in Activated TLR4 signalling 60/124 Reactome 2.15467526006472e-05 3.53158736224669e-05 3990 3419.09090909091 3484 1.95881487563378e-06 2338 1.09519479507684 -1.01996004488145 -1 1.25414592985444 3988 3460 3484 2338 2750 4002 2977 4006 3286 3662 3657 3780 M92 PID_ANGIOPOIETIN_RECEPTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ANGIOPOIETIN_RECEPTOR_PATHWAY.html Angiopoietin receptor Tie2-mediated signaling 18832364 35/84 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 3485 3404 3485 0.00793650793650794 2144 1.47504414400974 -1.56297474339718 -1 0.396223853255628 3485 2835 2245 2144 4437 4451 2942 4154 3593 2723 4435 3781 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 14/32 Jessica Robertson 0.000349957457111096 0.000484890787706267 4390 3484.36363636364 3488 3.1819376163111e-05 1895 1.70884792480714 1.08669591115868 1 1.45680426576391 4388 2991 1895 4010 3244 3488 4408 3449 4178 2401 3876 3782 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 35/85 Pathway Interaction Database 0.0131831239222548 0.0161211165708993 4075 3317.81818181818 3489 0.0012057082446063 1886 0.95334114580918 -0.92827433319917 -1 0.439573386203925 4073 1886 3489 2026 3643 2410 4639 4607 3572 3121 3030 3783 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 70/154 Jessica Robertson 0.000892546750970954 0.00119328789587729 3250 3492.45454545455 3490 8.11735514302284e-05 2538 1.07659017879939 -0.824870144484516 -1 0.809497765879186 3247 3819 3490 2928 3365 2538 3943 3893 3853 3967 3374 3784 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 46/124 Jean Junior 0.0207090238749418 0.0249146305206616 3280 3362.36363636364 3491 0.00190059729278687 1840 1.93270429587737 2.45937718134914 1 0.797159609000517 3278 4085 1840 3258 3689 4541 3611 2498 3491 2846 3849 3785 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 4/8 Leona Saunders 1.29572854428078e-06 2.77630725125731e-06 4145 2789.72727272727 3492 1.29572929979201e-07 438 2.57660643374357 -3.08026669878871 -1 3.68256658092703 4142 438 4265 2032 2127 4299 3785 4254 1085 768 3492 3786 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 34/86 Kevin Vogelsang 1.08015979437118e-05 1.86707074748186e-05 3885 3654 3493 9.81968270722563e-07 2611 1.29364603392878 1.50881864646693 1 1.5735068593139 3884 3855 3425 4306 2611 3412 4084 3485 3493 3409 4230 3787 M477 BIOCARTA_GABA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GABA_PATHWAY.html Gamma-aminobutyric Acid Receptor Life Cycle 4/14 BioCarta 0.000106195063936279 0.000156882115260215 2705 3286.18181818182 3494 1.06200139103844e-05 2158 0.758905538301572 0.925706133078978 1 0.742635134180046 2701 2442 3838 3877 3061 3597 3748 2158 3494 4417 2815 3788 M850 REACTOME_PI_3K_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI_3K_CASCADE.html Genes involved in PI-3K cascade 24/61 Reactome 0.0839184282471183 0.0902966141827776 2510 3473.72727272727 3495 0.00793650793650794 2415 1.24603734783725 1.0364354030317 1 0.334708403373183 2508 4264 3464 4559 3954 3040 2415 3241 3715 3495 3556 3789 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 7/12 Arthur Liberzon 5.92501194940761e-06 1.0753139424835e-05 3495 3161.63636363636 3495 5.92502774706186e-07 873 1.78735274690659 1.78735274690659 1 2.28418424305116 3495 873 4114 3549 2506 4611 3922 2109 3231 2680 3688 3790 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 17/69 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4275 3666.09090909091 3495 0.00793650793650794 2952 1.3333982556433 -1.15625889773216 -1 0.358175154734483 4272 3072 2952 4163 3979 3495 4467 3250 3896 3379 3402 3791 M18837 BIOCARTA_EGFR_SMRTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EGFR_SMRTE_PATHWAY.html Map Kinase Inactivation of SMRT Corepressor 5/18 BioCarta 0.0164575227026241 0.0199482543674332 4275 3443.45454545455 3496 0.00165806909753516 2576 1.01524046409662 -0.538668831779534 -1 0.443956701007125 4273 2576 3847 2718 3675 3496 2968 3871 3241 3263 3950 3792 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) 23/51 Reactome 0.00628435379575369 0.00785292850317382 2515 3326.09090909091 3497 0.000572943393261115 1867 1.25187888122465 1.04030876225625 1 0.677807604582022 2512 3625 2986 4057 4018 3473 2876 1867 3879 3797 3497 3793 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. 14/37 SigmaAldrich 0.00164875553963296 0.00216113803041121 2945 3304.27272727273 3498 0.000149999315603645 2155 0.759275788473854 -0.759275788473854 -1 0.520531495602486 2945 3538 3498 2735 3425 2155 4007 3672 4036 4020 2316 3794 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 9/29 Jessica Robertson 0.000868238041580869 0.00116277892622119 3500 3006 3498 8.68577455017362e-05 595 2.30499743123529 -1.91307529901426 -1 1.7398171877883 3498 595 4449 2031 3377 4196 3733 3611 1061 2312 4203 3795 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 43/108 Itai Pashtan 3.19098998329518e-06 6.16617693266854e-06 2555 3272 3498 2.9009041924327e-07 1689 1.74231626875589 1.77542848559034 1 2.33486638335575 2554 3887 1689 4190 2328 3849 2531 4663 3817 2986 3498 3796 M225 BIOCARTA_MTA3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MTA3_PATHWAY.html Downregulated of MTA-3 in ER-negative Breast Tumors 12/43 BioCarta 0.00311855103642983 0.0039894977222796 4445 3013.63636363636 3499 0.000283907313425088 1095 1.81440913734134 -1.55632471788141 -1 1.11964123057257 4442 2888 1727 2090 3499 3530 4143 3717 1095 2141 3878 3797 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 28/55 John Newman 0.00334090020122289 0.00426695512208516 3700 3434.81818181818 3499 0.00030418040679963 1740 1.85797635127603 2.47193850332673 1 1.13257115827458 3700 3499 2429 3493 3680 3568 4519 1740 3149 3386 4620 3798 M16355 BIOCARTA_NKCELLS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NKCELLS_PATHWAY.html Ras-Independent pathway in NK cell-mediated cytotoxicity 25/65 BioCarta 0.0839184282471183 0.0902966141827776 2500 3224.90909090909 3500 0.00793650793650794 2066 1.2761060076368 -1.07273638382946 -1 0.342785400064313 2498 3500 3141 2564 4036 2066 3772 3875 3904 3560 2558 3799 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 487/1174 Leona Saunders 0.0839184282471183 0.0902966141827776 2240 3525.45454545455 3500 0.00793650793650794 2236 1.13349229132564 -0.999118176846951 -1 0.30447672510394 2236 4586 3781 3277 4129 2345 3500 3387 3992 4392 3155 3800 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 4/10 Reactome 0.00286192922476303 0.00367122922180114 1830 2914.36363636364 3501 0.000286562170684842 1138 0.906250129012054 0.906250129012054 1 0.567648103351127 1827 3549 3963 4338 3501 1138 1719 1745 4212 4454 1612 3801 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 24/50 Arthur Liberzon 4.27339909205226e-05 6.69289710740538e-05 4445 3602.36363636364 3501 3.88498373011543e-06 2576 1.44930210061273 -1.95196731803822 -1 1.55614528454431 4444 3992 2844 4499 2880 3501 4261 3774 3388 2576 3467 3802 M139 PID_MYC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_PATHWAY.html C-MYC pathway 18832364 14/39 Pathway Interaction Database 0.0936436407328969 0.100622357366282 2955 3548.63636363636 3502 0.0088985998887549 1955 0.646917822627977 -0.646917822627977 -1 0.16594931568359 2952 4452 3502 4515 4682 1955 3041 2497 4384 4432 2623 3803 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 12/36 Pathway Interaction Database 0.000284053505138893 0.000398286871657944 3985 3390.45454545455 3502 2.58263806730305e-05 1625 1.31139696487879 1.3611838722313 1 1.14679730624798 3984 2206 2181 2853 3207 4417 4398 4531 3502 1625 4391 3804 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 3/8 Jessica Robertson 0.102835261441851 0.110246175958937 3035 3432.09090909091 3502 0.0107929119026905 2488 1.21907478952994 1.21907478952994 1 0.300282073172363 3032 3843 4332 3760 3883 3502 2488 2713 4296 2808 3096 3805 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 19/39 Reactome 0.00455462814587472 0.00575748246333124 3965 2995.72727272727 3503 0.00041491681341326 1056 2.83879045447583 -1.57264120016787 -1 1.63544100790061 3503 3963 1702 1869 3697 4544 3961 1790 1056 2997 3871 3806 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 3/20 Reactome 9.52490492957758e-06 1.66419479865774e-05 3965 3018 3504 9.52494575554013e-07 1369 1.56125115852961 -2.08444512705948 -1 1.9190659131335 3961 1369 3945 4142 2602 3540 1513 3504 2837 1742 4043 3807 M2537 MIZUSHIMA_AUTOPHAGOSOME_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/MIZUSHIMA_AUTOPHAGOSOME_FORMATION.html Key proteins in mammalian autophagosome formation. 20144757 16/22 Arthur Liberzon 0.000149576382476098 0.000217540325351644 3850 3585.54545454545 3505 1.3598777548406e-05 3099 1.0113609322928 -1.23556915703596 -1 0.952747202404345 3849 3505 3099 4340 3102 3144 4313 3479 3654 3770 3186 3808 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 45/89 Jessica Robertson 0.00197827986193251 0.00257363115852741 1270 2764.54545454545 3506 0.000180005546339012 898 1.16070157170931 -1.03928137363917 -1 0.773085078475841 1270 4049 3506 4134 3686 898 1519 1972 3678 4064 1634 3809 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 35/117 Pathway Interaction Database 0.00494691984097344 0.00623152321903267 3975 3519 3507 0.000450734420792595 2681 1.09665165250514 -0.908412621209418 -1 0.622093618641795 3974 3380 3166 2681 3542 2711 4404 4075 3765 3504 3507 3810 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 113/308 Arthur Liberzon 1.85260362314119e-05 3.07520388878484e-05 4540 3370.54545454545 3508 1.68419929451119e-06 1376 1.24167370454723 -1.02173324258546 -1 1.44107749420666 4540 3982 2840 3139 2716 1376 4477 4683 3660 3508 2155 3811 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 20/35 Arthur Liberzon 7.92863934416438e-05 0.000118929590162466 1805 2888.27272727273 3508 7.20811372814035e-06 461 0.746529143602322 -0.746529143602322 -1 0.753620863933437 1805 4448 3508 4584 4515 461 843 2043 4433 4161 970 3812 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 248/594 Leona Saunders 1.88154124637406e-08 1.02042166516299e-07 3955 3057.36363636364 3509 1.71049205678715e-09 520 1.25538836073193 -1.13983956661711 -1 2.25751027213807 3954 3777 3412 3509 520 1100 4684 2837 3645 3953 2240 3813 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 311/723 Leona Saunders 4.50635114553186e-08 1.82355453091211e-07 2870 3190.54545454545 3509 4.09668294348847e-09 879 1.25674825723903 -1.07497264162581 -1 2.17845017085658 2869 4416 3634 4380 879 1724 3764 3313 3509 4203 2405 3814 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 8/11 Reactome 0.00206072711187649 0.00267494937569341 1705 2873.54545454545 3510 0.000206264057796866 1035 0.771417317390613 -0.771417317390613 -1 0.510474920472344 1703 3510 3979 4084 4475 1035 1740 1885 4043 3678 1477 3815 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 6/10 Reactome 0.00923286204116394 0.0114186306479003 3405 3546.81818181818 3511 0.000927144844995016 2645 0.684431101129569 -0.684431101129569 -1 0.341950849907075 3404 3908 4039 3317 3610 2734 3511 2925 4430 4492 2645 3816 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 6/11 Reactome 0.159516339402303 0.169384447414274 2590 3395.54545454545 3513 0.0172276539389735 2127 0.460683679265589 -0.460683679265589 -1 0.0913747308961107 2587 3513 4094 4106 4353 2127 2222 2727 4407 4525 2690 3817 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 3/24 Reactome 9.52490492957758e-06 1.66419479865774e-05 3965 3033.81818181818 3513 9.52494575554013e-07 1370 1.56125115852961 -2.08444512705948 -1 1.9190659131335 3962 1370 4098 4143 2603 3541 1514 3513 2838 1746 4044 3818 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 646/1509 Jessica Robertson 6.43131150552066e-07 1.49935948830198e-06 3515 3545.81818181818 3513 6.43131336680096e-08 1943 1.33764638121248 -1.08177608613534 -1 2.00386451482068 3513 4366 4309 3335 1943 2380 4172 3975 3397 4303 3311 3819 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 17/44 Reactome 2.36809493138579e-05 3.85639053044594e-05 4395 3431.63636363636 3514 2.15283674736772e-06 2218 1.22893392402178 -1.31083090718894 -1 1.39521672812057 4393 2494 2720 3293 2762 3514 4542 4043 3813 2218 3956 3820 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 30/97 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4350 3616.27272727273 3515 0.00793650793650794 2342 1.49674162701175 1.65759476609987 1 0.402052197437954 4347 4294 3118 3380 4622 2342 3495 3886 3686 3515 3094 3821 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 3/6 Jessica Robertson 0.000218384541391776 0.000311775849617913 2700 3112.90909090909 3515 2.18406005674128e-05 1278 0.947480196066163 -0.947480196066163 -1 0.854476546084646 2699 3515 4496 4327 3931 1714 2301 1278 3661 4638 1682 3822 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 9/38 Reactome 0.00228538703007257 0.00295755968597627 4100 3751.63636363636 3516 0.000228774078488435 2711 1.1585156325314 0.998503722835491 1 0.753634394064448 4097 2711 4037 3351 3471 4651 3516 4340 3398 3055 4641 3823 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 444/989 Leona Saunders 9.88221771107008e-07 2.18847222089198e-06 3740 3221 3516 8.98383831825744e-08 991 1.1149847288891 -0.923180322362171 -1 1.62320420993861 3740 3516 3780 3268 2028 991 3828 4126 3386 4344 2424 3824 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 153/356 Jessica Robertson 2.282784245633e-05 3.73083365485728e-05 4385 3482.09090909091 3518 2.07527993892097e-06 2680 1.37375200859648 1.39956202010002 1 1.56470914461442 4383 4202 3306 2680 2756 2683 3933 3397 3518 3758 3687 3825 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 15/37 Arthur Liberzon 0.000122767838789613 0.000180285206069611 4010 3403.27272727273 3519 1.11613354734294e-05 1988 1.7548713651823 -1.16766828442922 -1 1.68999099792919 4008 3832 1988 3047 3069 3981 3519 3642 3198 2557 4595 3826 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 102/212 Arthur Liberzon 0.0374903460079213 0.0441406435661104 3520 3413 3520 0.00346771741812141 1770 1.40635587283508 -1.27726057224293 -1 0.490212898745177 3520 4247 3399 3386 4197 1770 4060 3752 3263 3802 2147 3827 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 28/57 Leona Saunders 0.0364706119888949 0.0429832212726262 2555 3596.63636363636 3520 0.00337178366212385 1682 1.05368018902714 1.12171468555489 1 0.370408358713141 2555 4550 3520 4587 4483 2826 1682 4650 3877 3383 3450 3828 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 108/219 Arthur Liberzon 4.2713810040719e-06 7.99348697487257e-06 4210 3268 3521 3.8830811792163e-07 800 1.19333012120232 -0.824469172932125 -1 1.56457482205622 4209 3521 3552 3366 2406 800 4319 4351 2698 4231 2495 3829 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 13/35 Reactome 0.013068646690807 0.0159852984581367 4230 3508.27272727273 3522 0.00119517546451422 2533 1.67064359506418 -1.52177352823087 -1 0.771891453451516 4228 3614 2869 3024 3641 4472 2533 3259 3314 3522 4115 3830 M9670 BIOCARTA_STRESS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STRESS_PATHWAY.html TNF/Stress Related Signaling 18/35 BioCarta 0.000158485617358882 0.000229713455905884 4520 3532.90909090909 3523 1.4408821422065e-05 2719 1.11359781740068 -1.0647688134427 -1 1.04228569257655 4518 3026 3287 2719 3113 4164 4008 3812 3523 2936 3756 3831 M528 REACTOME_ER_PHAGOSOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ER_PHAGOSOME_PATHWAY.html Genes involved in ER-Phagosome pathway 47/109 Reactome 0.00489964749585144 0.00618028214416146 1060 2863.54545454545 3523 0.000446417609735344 1057 0.926729949463158 -0.784039603916093 -1 0.526557490556387 1057 3523 3675 3600 3990 1077 1672 2785 4017 4184 1919 3832 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 114/270 Jessica Robertson 0.000234208253336205 0.000332777403011964 2350 3353.27272727273 3523 2.12939264058855e-05 2152 1.03284814049097 -1.05759629212626 -1 0.923943532185658 2347 3780 3613 4605 3169 2152 3523 2984 3884 4282 2547 3833 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 21/65 Jessica Robertson 0.00415618541210046 0.00527515840766597 3755 3450.90909090909 3524 0.000378550727647919 2388 1.33405154599498 1.5072877995712 1 0.781591810013161 3755 3209 2446 2388 3524 3946 3477 3966 3842 3228 4179 3834 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 17/36 Jean Junior 0.415320710913563 0.431528348412628 3240 3727.36363636364 3525 0.0476190476190476 3026 1.05628050981928 1.17003110091122 1 0.0991650834963562 3237 4170 3414 3026 4268 4535 3340 3035 4352 4099 3525 3835 M279 PID_RB_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RB_1PATHWAY.html Regulation of retinoblastoma protein 18832364 39/92 Pathway Interaction Database 1.75762245823028e-05 2.92687236647729e-05 3945 3527.90909090909 3526 1.59785136397487e-06 2708 1.43599626667226 1.4491989215333 1 1.67453713015994 3945 3526 2708 3511 2712 3851 3325 3836 3197 3725 4471 3836 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 5/15 Arthur Liberzon 0.00391115788261888 0.00497224249537495 3665 3442.18181818182 3527 0.000391805870274374 2517 0.603691000490928 -0.603691000490928 -1 0.357677389653886 3661 2536 4127 3874 3527 2517 3206 2707 4226 4538 2945 3837 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 31/72 Kevin Vogelsang 1.95064750508209e-05 3.22880049763853e-05 4085 3483.27272727273 3528 1.77333163715282e-06 2454 1.33724558897073 -1.08269413134691 -1 1.54471681093909 4083 3528 2454 4591 2726 2527 4165 3292 3955 3872 3123 3838 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 31/72 Reactome 0.00402648986467084 0.00511470086902889 3850 3402.54545454545 3529 0.00036671619779866 2294 1.28817580015058 1.45547583517057 1 0.759159214027025 2881 3529 3478 3848 3523 3917 2631 2294 3850 3870 3607 3839 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 94/201 Reactome 0.00493846899338997 0.00622255060581484 2130 3221.54545454545 3529 0.000449962693493427 1989 0.986092745485595 -0.922243380103839 -1 0.559535968027352 2128 3585 3702 3529 3541 1989 3031 3285 3788 4226 2633 3840 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 13/28 Leona Saunders 0.0802433012195792 0.0902966141827776 3965 3411.45454545455 3529 0.00757535235299144 2464 1.37310737299932 -1.29865073551797 -1 0.368841756160367 3964 3966 2982 2615 3917 3738 2875 2464 3244 3529 4232 3841 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 10/36 Arthur Liberzon 0.00443535460274003 0.00561276577597617 4065 3572.09090909091 3530 0.000404029264522549 2752 1.02864762011777 -1.00848632386612 -1 0.59553394229611 4062 2817 2752 4099 3530 2950 4253 4296 3985 3190 3359 3842 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 80/182 Jessica Robertson 1.6669429083393e-08 9.41119815479273e-08 4610 3452.54545454545 3530 1.51540265542704e-09 466 1.23304732438529 -1.0963624885513 -1 2.22847869358937 4609 3115 3396 4123 466 2390 4618 4588 3530 3793 3350 3843 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) 56/111 Reactome 0.0170621874010878 0.0206597959073637 2745 3241.90909090909 3531 0.00156326988287961 1358 0.805263348870809 -0.728386196035852 -1 0.34898260320178 2743 3748 3735 3531 4081 1358 2598 3349 4075 4241 2202 3844 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 49/99 Reactome 0.0989758960346248 0.106254535811742 1870 3375.45454545455 3532 0.00943009776789101 1869 0.662095261720201 -0.662095261720201 -1 0.165814537013752 1869 4119 3715 3532 4430 1911 2975 2964 4556 4343 2716 3845 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 13/39 John Newman 5.64212623698421e-07 1.3420813982999e-06 4240 3217.54545454545 3532 5.12920698542366e-08 1735 1.13190587677723 1.0217212549122 1 1.70966630357647 4239 1735 2598 2178 1871 4098 3181 4356 3578 3532 4027 3846 M10080 REACTOME_M_G1_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_M_G1_TRANSITION.html Genes involved in M/G1 Transition 49/91 Reactome 0.313169047472843 0.328228619203252 1355 3407.09090909091 3533 0.0335749710942013 1354 0.767100741713436 -0.767100741713436 -1 0.095463450490012 1354 3957 3692 3533 4139 2371 3066 3512 4508 4304 3042 3847 M12469 REACTOME_HIV_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIV_INFECTION.html Genes involved in HIV Infection 131/285 Reactome 0.0839184282471183 0.0902966141827776 1905 3268.18181818182 3534 0.00793650793650794 1835 0.950470521483396 -0.863180515569398 -1 0.25531370156796 1903 4246 3757 3534 3946 1835 2855 3040 3938 4316 2580 3848 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 6/18 Reactome 0.00417358386538967 0.00529580665941403 2695 3219.18181818182 3535 0.000418144310848133 1845 0.508863584380225 -0.508863584380225 -1 0.297909916892647 2694 3737 4047 3638 3535 1845 2771 2008 4307 4494 2335 3849 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 79/226 Leona Saunders 0.0839184282471183 0.0902966141827776 4090 3591.27272727273 3535 0.00793650793650794 2584 1.33244650509835 1.51228539798117 1 0.357919496981407 2584 4249 3535 2881 3865 4523 2662 4086 3525 4089 3505 3850 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 44/139 Antony Bosco 1.06359396336012e-06 2.32571223159379e-06 3095 3468.09090909091 3535 9.66904070506257e-08 2059 1.31372211776427 1.49760379450667 1 1.90360192594233 3091 3987 2777 4345 2059 4533 3456 2969 3701 3696 3535 3851 M899 REACTOME_IL1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL1_SIGNALING.html Genes involved in Interleukin-1 signaling 25/45 Reactome 3.24013193621558e-05 5.14740173592758e-05 3565 3373.09090909091 3539 2.94561787040853e-06 2365 0.909726079484054 -0.836375635217107 -1 1.00347310676419 3539 3564 3472 3958 2835 2365 4665 2848 3887 3563 2408 3852 M16843 REACTOME_METABOLISM_OF_RNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_RNA.html Genes involved in Metabolism of RNA 184/402 Reactome 0.0839184282471183 0.0902966141827776 2815 3538.18181818182 3540 0.00793650793650794 2024 0.929183497504208 -0.81476950559515 -1 0.249595614250797 2812 4524 3775 3540 4244 2024 3336 3443 4074 4391 2757 3853 M6231 BIOCARTA_NO2IL12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NO2IL12_PATHWAY.html NO2-dependent IL 12 Pathway in NK cells 5/23 BioCarta 0.00415568768736256 0.00527515840766597 4300 3515.81818181818 3541 0.000416347958603661 1695 1.37180212223403 -1.07378519301828 -1 0.803709058303544 4297 1695 3850 3177 3534 4069 4200 3541 3418 2230 4663 3854 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 19/41 Jessica Robertson 0.0677806561953461 0.0780010203662553 3335 3362.63636363636 3541 0.00636033638767474 1749 0.870506321157789 -0.857792761024161 -1 0.248067971549919 3332 3537 3541 3905 3947 1749 2547 3664 4453 3926 2388 3855 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 3/7 Arthur Liberzon 0.00858890410999784 0.0106418838338048 3545 3552 3542 0.000862228199044006 2331 0.828779327635385 -0.828779327635385 -1 0.4205914002603 3542 2331 4188 3416 3606 2554 3463 3756 4312 4555 3349 3856 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 37/85 Kevin Vogelsang 0.000647943123321731 0.000878293744832408 3745 3546.54545454545 3542 5.89212758176874e-05 2394 1.42244571967261 -1.25349096262074 -1 1.11824984372304 3742 4022 2394 3741 3319 3309 4512 3524 3542 3606 3301 3857 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 24/58 John Newman 0.0726053966580226 0.0833077592408163 3285 3554.81818181818 3543 0.00682895111776956 1775 0.94624265339988 -0.94624265339988 -1 0.262693234046462 3284 4617 3543 3990 4665 1775 3067 3192 4303 4211 2456 3858 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 35/87 Arthur Liberzon 0.000554453449874307 0.000756160903990397 3830 3577.72727272727 3544 5.04175668125231e-05 2745 1.23114095253838 -0.883724016233107 -1 0.988447986130049 3829 3688 3074 3774 3303 3872 3544 2745 3498 3505 4523 3859 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 48/91 Jean Junior 0.00270164222612376 0.00347417548617342 2365 3034.54545454545 3545 0.00024590596451705 1232 1.22372505333682 -1.01978407855412 -1 0.774046643172302 2361 4384 3586 3981 4467 1232 2089 2105 3545 4111 1519 3860 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 26/66 Reactome 3.72203686712863e-05 5.86662117704836e-05 3655 3378.09090909091 3546 3.38372712667306e-06 1694 1.08685494274965 -1.09447585320635 -1 1.18297626452224 3654 2382 3232 1694 2856 4661 2933 4026 3546 3642 4533 3861 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 37/81 Arthur Liberzon 0.0329120125327236 0.038926221789082 2005 3206.90909090909 3546 0.00303772198709779 1705 0.978200829646444 1.06578053353229 1 0.35470796804522 2002 4293 3546 4560 3744 2594 1705 2261 4001 4041 2529 3862 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 13/31 Jessica Robertson 0.0839184282471183 0.0902966141827776 4500 3649.09090909091 3547 0.00793650793650794 2716 1.34925133009917 -1.26468383816262 -1 0.36243358297099 4497 3479 2716 3500 3975 3547 4033 3303 3907 3530 3653 3863 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 42/93 Leona Saunders 0.071840887519233 0.0824911538630546 2440 3349.18181818182 3548 0.0067545487420028 1773 1.2037761218022 -1.06326346706864 -1 0.335513636579067 2436 4386 3548 3603 4200 1773 2935 3246 4037 4206 2471 3864 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 28/59 Arthur Liberzon 0.0138701419231166 0.0169347277362492 2855 3362.90909090909 3551 0.00126894249690382 1658 0.737071049411995 -0.652958344218841 -1 0.335800014505731 2854 3927 3551 4187 3646 1658 3441 2939 4275 4238 2276 3865 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 72/151 Arthur Liberzon 0.0114639563201416 0.014096063845758 2625 3532.45454545455 3551 0.00104764847200585 2625 1.24076295994517 1.3149483867401 1 0.590705222243731 2625 3373 3169 4110 3628 4613 2973 3761 3824 3230 3551 3866 M5500 KEGG_BASE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASE_EXCISION_REPAIR.html Base excision repair 21/35 KEGG 0.133098071940946 0.142007642330436 2045 3441.90909090909 3554 0.0129005583290909 2043 0.696112722184918 -0.696112722184918 -1 0.151779748637675 2043 4495 3554 4585 4204 2180 2736 2942 4410 4174 2538 3867 M4910 ST_ERK1_ERK2_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_ERK1_ERK2_MAPK_PATHWAY.html ERK1/ERK2 MAPK Pathway 15/41 Signaling Transduction KE 5.20883378488269e-07 1.25494062292855e-06 4595 3193.90909090909 3554 4.73530456195775e-08 1283 1.03231030662085 -1.11165695143818 -1 1.56697562199386 4594 1283 3209 2223 1841 3554 4217 3856 2745 3716 3895 3868 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 16/36 Reactome 0.0836444304251769 0.0902966141827776 2580 3223.36363636364 3554 0.00790953670915768 2312 1.22521224419743 -1.22521224419743 -1 0.329114396380101 2578 3659 3133 3571 3987 2312 3554 2890 3601 3765 2407 3869 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 13/30 Reactome 0.0316041743624749 0.0374360872251156 3335 3467.90909090909 3555 0.00291523012234449 2133 0.951892164018103 -0.951892164018103 -1 0.349318626235335 3335 4403 3555 4601 3737 2133 2925 2634 4129 3984 2711 3870 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 7/19 Arthur Liberzon 6.90895453432977e-08 2.45826582747679e-07 3865 3167.27272727273 3555 6.90895474913122e-09 1118 0.739035145113627 -0.82435336198083 -1 1.25638819791586 3862 1992 4112 3673 1118 3053 4342 2791 3555 3582 2760 3871 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 9/13 Jessica Robertson 0.00636180130341877 0.00794335222697052 3750 3326.90909090909 3557 0.000638008765694436 2039 1.31381163179374 -0.831224969347787 -1 0.709659736550188 3746 2039 4462 3217 3582 4647 3557 2524 2411 2313 4098 3872 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 11/41 Reactome 0.0839184282471183 0.0902966141827776 3890 3742.81818181818 3558 0.00793650793650794 2749 1.1585156325314 0.998503722835491 1 0.311198456151059 3889 2749 3095 3558 4422 4476 3011 4593 3435 3330 4613 3873 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 46/118 Arthur Liberzon 4.39608004263227e-05 6.8666770265916e-05 4165 3476.63636363636 3558 3.99651626214665e-06 1885 1.53281947661444 -1.18616549907526 -1 1.64143045116291 4164 4048 1885 3708 2888 3840 3403 3114 3558 3204 4431 3874 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 11/27 Reactome 0.487868448914791 0.504892127123391 3330 3728.45454545455 3559 0.0590205493222717 2606 0.224510463834676 -0.220034839489532 -1 0.0171394077644587 3329 4457 3559 4603 4421 2785 2606 3130 4552 4508 3063 3875 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 16/39 Arthur Liberzon 3.2500931438916e-06 6.26488542668698e-06 3930 3433.27272727273 3559 2.95463449573918e-07 2332 1.03248981749687 -1.05619808205233 -1 1.38180091529877 3930 2594 3072 3559 2332 4004 3963 2702 3851 3246 4513 3876 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 265/559 Jessica Robertson 1.73816953824745e-06 3.58374367450533e-06 3560 3596.54545454545 3559 1.58015537412441e-07 2190 1.46470192517969 -1.10304993619697 -1 2.05162821535431 3559 4371 3312 4317 2190 3378 3326 3589 2884 4017 4619 3877 M10450 REACTOME_GAB1_SIGNALOSOME http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAB1_SIGNALOSOME.html Genes involved in GAB1 signalosome 25/46 Reactome 0.0518561552922324 0.0602822981144632 2200 3326.45454545455 3560 0.00482912512817247 2196 1.19294016028599 1.19294016028599 1 0.374290979968362 2196 4444 3560 3659 4092 3054 2725 2350 3829 3889 2793 3878 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 10/27 Arthur Liberzon 0.00646217889076578 0.00806223915924612 3560 3498.18181818182 3560 0.000589203547741621 2175 1.59788359919978 -1.84873803126738 -1 0.860450478543009 3560 3268 2175 3626 3576 3728 3193 4526 3399 3188 4241 3879 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 62/161 Jessica Robertson 1.66816496334789e-06 3.46652816773757e-06 4370 3480.90909090909 3560 1.51651475295151e-07 2173 1.44117404344233 -1.23875015652895 -1 2.02402601674836 4369 4251 3057 4476 2173 2322 4658 2758 3560 3732 2934 3880 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 40/90 Arthur Liberzon 0.00159314730693368 0.00209058758899222 3705 3391.72727272727 3561 0.000144936560734651 1831 1.84909653914961 2.52853947292451 1 1.27452836420744 3705 3823 1831 2728 3422 3691 4446 3561 3383 2376 4343 3881 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 35/106 Arthur Liberzon 2.14991214618984e-05 3.52624722332713e-05 4130 3583.45454545455 3561 1.95448468738529e-06 2597 0.964552473253642 -1.01261537576657 -1 1.10470585432368 4126 3437 2871 4195 2749 2597 4204 4057 4115 3506 3561 3882 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 15/39 John Newman 0.000250812893512221 0.000354756782070108 3720 3447 3561 2.28037720197008e-05 1288 1.03546394664322 -0.972249767163523 -1 0.918885478038036 4289 2668 2921 4450 3227 4615 3462 1288 3561 3720 3716 3883 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 42/88 Arthur Liberzon 2.07089163829991e-05 3.41576846781887e-05 4270 3510.27272727273 3562 1.88264648377965e-06 2552 1.36902077950108 -1.34850188980038 -1 1.5728131592271 4270 3990 3259 4192 2736 3241 2552 4217 3665 2929 3562 3884 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 30/64 Leona Saunders 0.000942554931102827 0.00125691872713371 3740 3420.63636363636 3563 8.57235451018571e-05 2284 1.44242969257965 1.69329273875038 1 1.07620497232319 3738 3563 2933 3182 3374 3914 3903 3840 2548 2284 4348 3885 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 26/126 Jessica Robertson 0.0532674694134433 0.0618615518392553 4230 3355.72727272727 3563 0.00496388123277145 1674 0.77581904405034 -0.72555798491732 -1 0.241175869281598 2658 4090 3563 4614 3828 1674 2998 2741 4228 4229 2290 3886 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 9/25 Reactome 0.000872400768309995 0.0011680200000859 3650 3284.45454545455 3564 8.72743445056313e-05 1912 0.918240049342238 -0.568192156212718 -1 0.692628200958042 3650 2712 3968 1912 3380 2131 3564 4670 3848 3776 2518 3887 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 3/10 Leona Saunders 0.0763578316439441 0.0871115749524574 3400 3600.09090909091 3564 0.00791159190324385 2543 0.636990133433295 -0.636990133433295 -1 0.173662337198798 3397 3048 4159 3564 3853 2543 2882 4237 4496 4548 2874 3888 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 22/42 John Newman 0.00106541280414486 0.00141471362998662 3565 3626.72727272727 3564 9.69026464358742e-05 2962 1.16036481756198 1.51782620615088 1 0.850425171341127 3061 3994 2962 3516 3387 4474 3279 3564 4078 4014 3565 3889 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 63/145 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2475 3244.63636363636 3564 0.00793650793650794 1548 1.56100781239792 -1.62040319173622 -1 0.419315280334767 2474 4015 1548 2231 4415 3228 3944 3575 3990 2707 3564 3890 M17157 REACTOME_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRUVATE_METABOLISM.html Genes involved in Pyruvate metabolism 8/19 Reactome 0.000391785487502122 0.000540290404483504 3200 3467.27272727273 3565 3.91854577786864e-05 2595 1.1275696721646 -0.328789034457426 -1 0.947634055444665 3200 2851 4035 3565 3272 4151 2595 2884 4006 3680 3901 3891 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 37/89 Leona Saunders 0.0839184282471183 0.0902966141827776 3130 3513.90909090909 3565 0.00793650793650794 2352 1.28637775545141 1.37210007603112 1 0.345544581007653 3127 3592 2978 3073 4227 4340 2352 4052 3565 3864 3483 3892 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 18/36 Signaling Gateway 0.0418790047830774 0.0490857970018761 4600 3462.63636363636 3566 0.00388164768782998 2189 1.17237753333263 1.47063508193543 1 0.394748271253766 4599 2200 3145 2189 3767 2921 4452 3620 3566 3473 4157 3893 M17294 BIOCARTA_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAS_PATHWAY.html Ras Signaling Pathway 19/44 BioCarta 0.0839184282471183 0.0902966141827776 3515 3559.09090909091 3567 0.00793650793650794 2095 0.730912814542024 -0.568192156212718 -1 0.196336451357955 3515 4058 3567 2628 4130 2095 3451 4522 4139 4141 2904 3894 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 17/40 John Newman 0.0276643396628195 0.0329441157966892 3570 3522.72727272727 3567 0.00254713277184104 1975 0.986847051477201 -0.986847051477201 -1 0.376237073633166 3567 4348 3216 4128 4668 1975 3437 2786 4470 4100 2055 3895 M6981 KEGG_PROTEIN_EXPORT http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEIN_EXPORT.html Protein export 16/39 KEGG 0.116711452472972 0.124808276195424 2655 3563.81818181818 3568 0.011218718328399 2110 0.641791828249097 -0.641791828249097 -1 0.149191382927386 2652 4499 3529 4252 3890 2110 2652 3568 4566 4401 3083 3896 M4377 KEGG_GALACTOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GALACTOSE_METABOLISM.html Galactose metabolism 12/39 KEGG 0.0151970615080242 0.0184586392500262 3455 3506.45454545455 3569 0.00139118778800156 2472 1.46561643975186 -0.713337045814159 -1 0.653608894155049 3452 4177 2498 3569 3660 4536 3991 2472 3224 3938 3054 3897 M11675 KEGG_HOMOLOGOUS_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HOMOLOGOUS_RECOMBINATION.html Homologous recombination 22/27 KEGG 0.430504430287037 0.447007259101497 2210 3611.36363636364 3569 0.0498944609802047 2207 0.386033993562977 -0.394893287541691 -1 0.0347215494556043 2207 4167 3569 4443 4317 2528 3048 3304 4610 4404 3128 3898 M1020 REACTOME_PKB_MEDIATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PKB_MEDIATED_EVENTS.html Genes involved in PKB-mediated events 18/56 Reactome 0.0759129290706722 0.0869537975128745 3720 3595.18181818182 3569 0.00715148547691599 2634 1.17365542178104 1.07202741173364 1 0.320211012887309 3720 2810 3379 3955 3836 4585 2634 3181 3569 3475 4403 3899 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 63/118 Kate Stafford 5.39988633557514e-06 9.89205135594414e-06 4430 3496.90909090909 3570 4.9089996269165e-07 2452 1.34180121121564 -1.17807497511525 -1 1.72729313884513 4429 3280 2969 3503 2452 2534 4153 4239 3623 3570 3714 3900 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 5/24 Arthur Liberzon 0.0325601399072797 0.038529498890281 2260 3442.54545454545 3570 0.00330472893497419 2258 1.8329977797877 -2.63102655242759 -1 0.666765869249869 4043 3638 4595 3570 4619 3504 2404 2258 3308 2259 3670 3901 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 7/11 KEGG 0.0368108611748676 0.0433624171607414 4235 3272.54545454545 3572 0.00374352354207808 190 2.09908974580625 -0.41804490327357 -1 0.735849950973612 4235 2852 3789 2164 3761 3096 3452 4434 190 3572 4453 3902 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 47/107 Reactome 0.0839184282471183 0.0902966141827776 3575 3656.18181818182 3573 0.00793650793650794 2683 1.0086258302757 -0.95875473720787 -1 0.270935290285864 3573 3559 3526 2683 4344 4152 2824 3577 3937 3566 4477 3903 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 6/12 Arthur Liberzon 0.252686742429382 0.265908393223464 4295 3549 3574 0.0287069779726256 2391 1.32259722491213 -1.56440768406518 -1 0.19570233360622 4292 3574 4189 3307 4005 2391 3384 3867 4315 2479 3236 3904 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 41/90 Arthur Liberzon 1.52937701964134e-06 3.22348427388085e-06 3750 3124.45454545455 3574 1.3903437116559e-07 1599 1.57570872902107 -1.18742750282795 -1 2.22576532380764 3749 2095 1669 3867 2143 4015 3574 4202 1599 2827 4629 3905 M13515 KEGG_MISMATCH_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MISMATCH_REPAIR.html Mismatch repair 14/23 KEGG 0.718667593472423 0.734979559801784 3265 3847.54545454545 3575 0.10889461283015 2922 0.460683679265589 -0.460683679265589 -1 0.0158455537097245 3265 4354 3575 4313 4543 2922 3432 3507 4562 4403 3447 3906 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 6/10 Reactome 0.00232503392909571 0.00300637665335058 3700 3063.72727272727 3575 0.000232747011945101 359 3.9490755071868 3.9490755071868 1 2.56172024762046 3697 3575 3952 2399 4179 3682 4353 2564 359 3438 1503 3907 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 11/27 Reactome 0.0265664862590401 0.0317011852838966 2770 3264 3576 0.00244480228267952 1606 0.62027449444304 -0.62027449444304 -1 0.239145373180148 2767 4003 3576 4048 4034 1606 2518 2192 4227 4435 2498 3908 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 62/152 Kevin Vogelsang 0.00864500744545466 0.0107085659237115 3795 3463.36363636364 3576 0.000789015135845553 2308 1.73002501763775 -1.5264048192315 -1 0.87675130659731 3792 4252 2308 2921 3598 3191 4263 3576 3182 3234 3780 3909 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 2/8 Jessica Robertson 0.00120127982921378 0.00158927082995364 3555 3517.8 3576.5 0.000133546853402063 1786 0.767758433342683 0.767758433342683 1 0.552707434296929 3551 1786 4438 NA 3416 3791 3113 3715 3140 4626 3602 3910 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 8/30 Reactome 0.00257861055617874 0.00332197477184418 3715 3524.81818181818 3577 0.000258160760646026 2398 1.11156909944472 -1.07182604882211 -1 0.708666840580006 3715 2398 3938 3925 3481 2931 3827 4580 3528 2873 3577 3911 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 420/909 Arthur Liberzon 0.0066954053740779 0.00834432701673645 3250 3602.36363636364 3577 0.000610533562487572 2731 1.36229872574686 -1.1722037076319 -1 0.728355911876694 3250 4321 3621 3083 3577 2731 4073 3633 3553 4288 3496 3912 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 457/969 Jessica Robertson 0.0839184282471183 0.0902966141827776 1600 3529.36363636364 3577 0.00793650793650794 1596 1.22807741631134 -1.09109914850055 -1 0.329884034463003 1596 4587 3742 3541 4083 2644 3577 3472 4073 4372 3136 3913 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 145/323 Yujin Hoshida 0.0319325001387185 0.0378154398913407 1915 3171.27272727273 3577 0.00294596690503413 1535 1.24330892661874 -1.17259560054013 -1 0.454860437655131 1913 4327 3577 3920 3967 1535 2767 2566 3710 4114 2488 3914 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 7/19 Reactome 0.0602216865529404 0.0696260742888865 3580 3396.81818181818 3579 0.00619187765443714 1899 1.17161346877642 -1.41039436697649 -1 0.348739986312699 2486 3616 4028 3579 3817 2769 1899 4317 4373 3578 2903 3915 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 4/9 Jessica Robertson 0.0334762684347583 0.0395835967411752 2325 3390.18181818182 3579 0.00339915240711798 1683 0.687723363725024 0.687723363725024 1 0.248090560637291 2325 3579 4525 3950 3988 2361 1683 3141 4482 4647 2611 3916 M3985 KEGG_CITRATE_CYCLE_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CITRATE_CYCLE_TCA_CYCLE.html Citrate cycle (TCA cycle) 17/33 KEGG 0.0222909090195883 0.0267696565007153 2490 3376.90909090909 3580 0.00204727475750007 1423 0.452089405640855 -0.452089405640855 -1 0.182841058064454 2487 4222 3580 4312 4024 1423 2250 3218 4601 4394 2635 3917 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 56/132 Jessica Robertson 2.02824726703356e-05 3.34888765732218e-05 2600 3384.36363636364 3581 1.84387815118784e-06 2402 1.2450047514181 1.39499760994884 1 1.43308622536009 2599 3681 2793 4239 2735 4532 2402 3581 3823 3199 3644 3918 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 3/8 Jessica Robertson 7.48838538967342e-07 1.70899861590461e-06 4675 2833.27272727273 3583 7.48838791309081e-08 548 1.79446738664432 -1.51356822265907 -1 2.66197287621681 4671 882 4549 997 1985 3583 4250 4324 548 1758 3619 3919 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 2/9 Yujin Hoshida 0.440502120100776 0.45688201301289 3430 3769.1 3583.5 0.062486338470953 2871 0.344018838022555 -0.344018838022555 -1 0.030102804479508 3427 3740 4566 NA 4605 2871 2883 3108 4553 4659 3279 3920 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 24/43 John Newman 0.0783763175232263 0.089078686372505 3375 3320.81818181818 3585 0.00739238565696713 2118 1.64410544280664 1.5760488177539 1 0.44413090447156 3373 3757 2348 3585 3840 3725 3081 3671 3782 2118 3249 3921 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 23/45 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3585 3657.81818181818 3585 0.00793650793650794 2831 1.15927297941479 -1.180602488811 -1 0.311401893494525 3585 3473 2831 3063 4032 4282 3379 4538 3870 2957 4226 3922 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 34/57 Arthur Liberzon 0.0839184282471183 0.0902966141827776 1990 3415.63636363636 3586 0.00793650793650794 1989 1.68200779129104 1.89744714945107 1 0.451818106721501 1989 4664 2681 4302 4168 3744 2629 3037 3586 3751 3021 3923 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 27/69 Arthur Liberzon 0.00354005128735936 0.00451638451744241 3965 3405.18181818182 3586 0.000322341863623881 1749 1.92209932997966 1.92209932997966 1 1.15946062686868 2340 4219 3227 4519 3763 3586 3117 1749 3964 3965 3008 3924 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 7/16 John Newman 0.0765897756730953 0.0871115749524574 3490 3697.36363636364 3587 0.00793650793650794 3055 3.50316581303129 3.50316581303129 1 0.955067500966325 3488 3736 4415 3055 4348 4292 3226 3419 3223 3587 3882 3925 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 16/41 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2895 3490.54545454545 3587 0.00793650793650794 2338 0.831204546108061 0.828269092307074 1 0.223276660512828 2894 2987 3456 3823 4019 3615 2338 4590 3832 3255 3587 3926 M54 PID_IL12_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL12_2PATHWAY.html IL12-mediated signaling events 18832364 42/119 Pathway Interaction Database 0.000194798289650533 0.000279664456281372 4350 3453.36363636364 3588 1.77105036491496e-05 2063 1.45531726343135 -1.24157392027542 -1 1.33013537296844 4348 2978 2725 2063 3143 3741 3942 4494 3588 2928 4037 3927 M151 PID_AR_TF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_TF_PATHWAY.html Regulation of Androgen receptor activity 18832364 43/92 Pathway Interaction Database 1.61530992777485e-05 2.70858227358802e-05 3930 3555.36363636364 3588 1.46847435274153e-06 2693 1.1635078507326 -1.4121002257206 -1 1.36685825982012 3927 2907 2998 3430 2693 4025 3588 4358 3486 3866 3831 3928 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 7/21 Arthur Liberzon 5.07936732446599e-05 7.84506106870389e-05 3735 3544.54545454545 3588 5.07948342807685e-06 2460 0.964473724294166 0.565667944060102 1 1.01846208279368 3295 3734 4441 4534 2936 3127 2460 2989 3731 3588 4155 3929 M84 PID_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATM_PATHWAY.html ATM pathway 18832364 29/48 Pathway Interaction Database 0.170680284275562 0.180706690491478 2990 3591.63636363636 3589 0.0168696801180947 2591 0.684054916494625 -0.695818285884946 -1 0.130735286659377 2988 4027 3589 3991 3938 2591 3294 3221 4520 4245 3104 3930 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 5/7 Arthur Liberzon 0.0765897756730953 0.0871115749524574 3180 3671.36363636364 3590 0.00793650793650794 2806 1.2922135710406 -1.2922135710406 -1 0.352295831723345 3176 3548 4178 4332 4054 2806 3590 4230 4153 3281 3037 3931 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 216/504 Jessica Robertson 4.73983317877974e-08 1.89769579972418e-07 3605 3231.54545454545 3590 4.30893934627092e-09 899 1.41937480853423 -1.02709604718464 -1 2.45402855790121 3604 4241 3517 3590 899 1557 3830 3572 2506 3789 4442 3932 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 38/90 Jean Junior 0.0113055178068228 0.0139048967041396 3180 3352.27272727273 3591 0.00103309425987648 1252 0.965610509256325 -0.893957860570173 -1 0.461182838892793 3178 3591 3470 4474 4315 1252 2159 3967 3949 4061 2459 3933 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 10/20 Reactome 0.136015583752472 0.145021393734718 3060 3393.54545454545 3592 0.0132030240435181 2042 0.386790298712793 -0.386790298712793 -1 0.0834279163587442 3056 3904 3592 3772 3978 2042 2279 3030 4474 4437 2765 3934 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 7/29 Jessica Robertson 0.000862114350659274 0.00115523816047737 3970 3451.63636363636 3593 8.62448991908893e-05 2197 1.7385744252024 1.7385744252024 1 1.31354338184269 3422 3970 4576 4043 3376 3980 2197 2299 3969 3593 2543 3935 M11184 REACTOME_ENDOGENOUS_STEROLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOGENOUS_STEROLS.html Genes involved in Endogenous sterols 3/15 Reactome 0.00729886521156349 0.00907950156129188 3810 3154.81818181818 3594 0.00073229496645041 947 1.40122560845476 -1.47084484717251 -1 0.735951472648466 3807 1859 3985 2886 3594 4554 3375 4231 947 1744 3721 3936 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 17/42 Yujin Hoshida 0.0839184282471183 0.0902966141827776 2130 3247.27272727273 3594 0.00793650793650794 2070 1.31998269315602 -0.927869007381074 -1 0.354571487176908 2126 3830 3100 3594 3906 2070 2737 3684 4011 3818 2844 3937 M136 PID_FOXO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FOXO_PATHWAY.html FoxO family signaling 18832364 31/65 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 2735 3546.81818181818 3595 0.00793650793650794 2234 1.02989005135234 1.3391516144101 1 0.276647252322761 2733 4340 3458 3595 4161 3750 2234 2990 4046 4182 3526 3938 M543 REACTOME_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE.html Genes involved in Cell Cycle 258/635 Reactome 0.0839184282471183 0.0902966141827776 2085 3534.45454545455 3595 0.00793650793650794 2083 1.35844709880349 -1.18287901748952 -1 0.364903736076991 2083 4521 3704 3154 4180 2627 3595 3370 4018 4361 3266 3939 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 19/41 Leona Saunders 0.0839184282471183 0.0902966141827776 3600 3619 3596 0.00793650793650794 2313 1.37760902835981 1.71628634395841 1 0.370050983831094 3596 2313 2627 4092 4653 4278 3445 3322 3705 3545 4233 3940 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 7/16 Arthur Liberzon 0.0520817690564341 0.0605295560015998 2475 3284 3596 0.0053344246273108 1849 1.50510212232629 -1.50510212232629 -1 0.471545213994941 2473 3969 4604 4502 4658 1987 1849 2374 3712 3596 2400 3941 M12095 BIOCARTA_IL1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL1R_PATHWAY.html Signal transduction through IL1R 27/52 BioCarta 0.0121051069381641 0.0148415832318779 3650 3633.09090909091 3597 0.00110656643369747 3265 1.19145284919405 -0.948027403417855 -1 0.560370215305481 4642 3796 3265 3648 3634 3374 3458 3646 3595 3309 3597 3942 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 37/74 Reactome 0.0392832816729407 0.0461935904440151 1720 3192.36363636364 3597 0.00363661611663968 1591 0.673582288505426 -0.673582288505426 -1 0.231369583274269 1718 3687 3711 3597 4309 1591 2683 2630 4457 4300 2433 3943 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 85/176 Leona Saunders 0.000111328957996048 0.000164155914779572 4630 3715.54545454545 3597 1.01213265539808e-05 2523 1.12424087378598 -0.993474619592773 -1 1.09444621328024 4628 3586 3597 4475 3054 2523 4357 3700 3571 4214 3166 3944 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 22/48 Arthur Liberzon 0.200129779409236 0.211647065292639 2940 3555.72727272727 3601 0.0200958578641088 2262 0.81691734675041 -0.81691734675041 -1 0.141705212299703 2937 4299 3601 4366 4506 2262 3254 2762 4266 4190 2670 3945 M9461 REACTOME_LAGGING_STRAND_SYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LAGGING_STRAND_SYNTHESIS.html Genes involved in Lagging Strand Synthesis 10/20 Reactome 0.846284865596871 0.860796804902743 2990 3847.36363636364 3602 0.156538724898741 2986 0.460683679265589 -0.460683679265589 -1 0.00771376079914465 2986 4406 3439 4126 4476 3109 3489 3602 4609 4503 3576 3946 M2341 REACTOME_APOPTOTIC_EXECUTION_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOTIC_EXECUTION_PHASE.html Genes involved in Apoptotic execution phase 31/78 Reactome 0.000636106221456388 0.000862498192634443 4505 3445 3602 5.78445653800597e-05 1864 1.96067907523084 1.98750421843384 1 1.54535469760709 4505 3752 2224 3128 3317 3337 4449 3716 1864 3602 4001 3947 M13103 KEGG_AUTOIMMUNE_THYROID_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AUTOIMMUNE_THYROID_DISEASE.html Autoimmune thyroid disease 24/87 KEGG 0.0164241605333461 0.0199129666906235 3240 3384.81818181818 3603 0.00150437023662841 2304 1.4495818103434 -1.10785150530836 -1 0.634177560642217 3236 3860 2493 3837 3664 2304 3603 4407 3763 3025 3041 3948 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 31/80 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2375 3289.72727272727 3603 0.00793650793650794 1949 1.01672687889597 -1.01700106783833 -1 0.273111381383264 2375 4212 3368 3846 4113 1949 2429 3617 4163 3603 2512 3949 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 12/25 Reactome 0.0422944419431843 0.0495479387364404 2510 3206.09090909091 3604 0.0039209202151137 1616 0.386790298712793 -0.386790298712793 -1 0.129830145050169 2506 3833 3604 3979 3800 1616 1886 2615 4419 4533 2476 3950 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 9/28 Leona Saunders 0.00835501817520407 0.0103630532474871 3745 3395.27272727273 3604 0.000838659825804361 1674 1.58775278842828 -1.95725337793883 -1 0.810466834192004 3743 3134 4292 3628 3604 3433 3824 2376 4248 1674 3392 3951 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 7/11 Arthur Liberzon 0.00427568584342521 0.0054194925242874 3350 3551.63636363636 3604 0.000428393486024039 1799 1.15342882334214 1.15342882334214 1 0.672290829268495 3349 3111 4585 4029 3822 4270 2979 1799 3925 3595 3604 3952 M5224 REACTOME_SYNTHESIS_OF_DNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_DNA.html Genes involved in Synthesis of DNA 56/105 Reactome 0.343983923272812 0.359801041173303 1620 3463.18181818182 3605 0.0375994510463513 1618 0.720693621669029 -0.643168201471164 -1 0.0822943756952286 1618 4153 3731 3605 4160 2417 3118 3348 4526 4329 3090 3953 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 41/95 Reactome 0.0117258709922774 0.0143992220832841 2925 3278.54545454545 3605 0.00107171268794482 1799 0.941938310601618 -0.952136085755407 -1 0.446201089649581 2924 4155 3605 4244 3630 1799 3856 2386 4014 3517 1934 3954 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 41/83 Leona Saunders 0.0513990201150185 0.0597657092454036 3275 3483 3605 0.00478551571666647 1864 1.18039661714894 -1.33326661894927 -1 0.371490215538023 3273 4489 3600 3919 4499 1864 3605 2599 4021 4199 2245 3955 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 163/325 Arthur Liberzon 9.60607532754902e-05 0.000142584950854909 4000 3636.54545454545 3607 8.7331770842364e-06 2232 1.1720053433544 -0.933232268109774 -1 1.15938895723516 3999 4325 3607 4525 3032 2232 3481 4306 3348 3753 3394 3956 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 246/542 Broad Institute 0.0839184282471183 0.0902966141827776 2570 3424.27272727273 3609 0.00793650793650794 1996 1.22101230671202 -1.15145813158403 -1 0.327986215696335 2566 4467 3759 3609 4224 1996 3248 2932 3714 4367 2785 3957 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 72/151 Jessica Robertson 0.00126057906778676 0.00166490234262931 3405 3617.90909090909 3609 0.000114663813413606 2372 0.903559998964257 -0.772551811643239 -1 0.645778124446889 3313 3713 3609 4434 3404 2372 3404 4093 4010 4247 3198 3958 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 7/19 Jessica Robertson 3.86277485552123e-05 6.07414864864849e-05 3615 3320.18181818182 3611 3.86284200179705e-06 77 2.81549715119695 -0.850346476135213 -1 3.05356632757205 3611 4105 4353 3108 2878 4118 4325 3850 77 3586 2511 3959 M745 REACTOME_MRNA_CAPPING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_CAPPING.html Genes involved in mRNA Capping 13/31 Reactome 0.0873592929021623 0.0939558518566749 2705 3471.18181818182 3612 0.00827583839234819 1844 0.386790298712793 -0.386790298712793 -1 0.102182377959902 2705 4502 3612 4439 4304 1844 2172 3038 4589 4464 2514 3960 M5109 KEGG_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRIMIDINE_METABOLISM.html Pyrimidine metabolism 57/106 KEGG 0.0415819669165408 0.0487620362790066 2875 3594.90909090909 3617 0.00385357729283394 2605 1.34664481158675 -0.866847571936605 -1 0.454420895545198 2873 4434 3375 3845 3764 2605 3290 4120 3617 4205 3416 3961 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 488/1100 Jessica Robertson 0.00035036868477783 0.000485317072677774 3040 3521.09090909091 3618 3.18567724009867e-05 2260 1.21929235149348 -1.04407469893273 -1 1.03933512007809 3037 4239 3743 3787 3245 2260 3838 3393 3618 4353 3219 3962 M9703 BIOCARTA_ATRBRCA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ATRBRCA_PATHWAY.html Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility 18/27 BioCarta 0.0839184282471183 0.0902966141827776 3900 3534.09090909091 3619 0.00793650793650794 2552 1.76819129719692 -0.591199639996739 -1 0.47496858621318 3897 3449 2552 3253 3937 3526 3708 3619 2613 4121 4200 3963 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 47/120 Reactome 9.1221088309093e-05 0.000135788443397843 4015 3692.54545454545 3619 8.29317008471231e-06 2943 1.22564501625808 -1.11196730310898 -1 1.21913807815551 4015 3463 3038 3383 3025 3978 4431 4141 3619 2943 4582 3964 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 54/121 John Newman 3.78826908849002e-05 5.96299259276595e-05 4430 3540.63636363636 3620 3.44394029254736e-06 2534 1.54191847765456 -1.47112789665607 -1 1.67547917540743 4428 3715 2534 2879 2861 3135 4583 4622 3620 2728 3842 3965 M19283 REACTOME_METABOLISM_OF_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_MRNA.html Genes involved in Metabolism of mRNA 155/349 Reactome 0.053469909548841 0.06205051910497 3025 3486 3621 0.00498322574103694 1675 0.857283014693039 -0.682249837272248 -1 0.266208195724597 3022 4471 3774 3462 4218 1675 3064 3621 4063 4389 2587 3966 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 21/39 KEGG 0.000206546133979916 0.000295534407276301 3385 3601.72727272727 3622 1.87786843665064e-05 2871 0.576082324416053 -0.610829845282276 -1 0.522977437579881 3385 3828 3622 4054 3152 2952 3745 2871 4434 4406 3170 3967 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 71/189 Leona Saunders 1.05328972094087e-07 3.39691371805155e-07 3625 3285.09090909091 3624 9.57536155790013e-09 1255 1.13194826687354 -1.05118715877493 -1 1.88346127799876 3624 1440 3523 3807 1255 4391 2910 4397 3303 3664 3822 3968 M14449 BIOCARTA_ETS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETS_PATHWAY.html METS affect on Macrophage Differentiation 14/27 BioCarta 0.0326297197088629 0.0386020869870567 3500 3590.54545454545 3625 0.0030112697580632 2811 1.03653637231823 1.35477743473133 1 0.376829385663507 3499 3731 3093 3374 3743 4599 3343 2811 3811 3625 3867 3969 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 15/28 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3210 3487.36363636364 3625 0.00793650793650794 1944 1.5518349275434 -1.07648565385426 -1 0.416851274252952 3208 3328 1944 2415 4318 4510 3625 4249 3910 2564 4290 3970 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 8/22 Arthur Liberzon 6.56868706553619e-05 9.96144582171604e-05 4360 3299.09090909091 3625 6.56888123803808e-06 1421 2.08586951378964 -1.32797447675003 -1 2.14697941959038 4356 1421 4672 2574 2986 3625 3807 3629 2826 2113 4281 3971 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 42/72 Jessica Robertson 0.0834896593644223 0.0902966141827776 1790 3255 3626 0.00789430491767798 1789 0.792599489308687 -0.802445465684637 -1 0.212906630118786 1789 4121 3626 4258 3928 1824 2375 2595 4464 4207 2618 3972 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 32/58 Reactome 0.0839184282471183 0.0902966141827776 2670 3593.90909090909 3627 0.00793650793650794 2670 1.27071079085727 -1.47736784720966 -1 0.341336145313128 2670 4259 3532 3849 4138 2890 3627 2901 4128 4270 3269 3973 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 8/41 Jessica Robertson 0.00142036524383696 0.00186961559905056 3630 3331.27272727273 3627 0.000142127390818745 1610 3.71193364655514 -3.71193364655514 -1 2.60484959487467 3627 4359 4479 4041 3713 2744 3373 1610 2616 3687 2395 3974 M751 REACTOME_DARPP_32_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DARPP_32_EVENTS.html Genes involved in DARPP-32 events 14/30 Reactome 1.6779345358208e-05 2.80714074789585e-05 3860 3166 3628 1.52540666683862e-06 183 1.42206656980977 -1.65846489950719 -1 1.66492857725581 3858 2776 2855 1948 2699 4079 4390 3920 183 3628 4490 3975 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 12/92 Arthur Liberzon 4.18513795233539e-06 7.84776168253046e-06 4670 3553.18181818182 3628 3.80467810353892e-07 2403 1.35460927278217 -1.15269126375036 -1 1.77881200593946 4667 3664 2538 4410 2403 3628 4186 2834 3521 2756 4478 3976 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 17/37 Reactome 0.0839184282471183 0.0902966141827776 3475 3689.18181818182 3629 0.00793650793650794 2467 0.804669962937929 -1.01287325957168 -1 0.216148981996578 3475 4624 3629 4518 4549 2467 2838 3585 4165 4094 2637 3977 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) 22/34 Reactome 0.123695666788392 0.132066050255275 2560 3402.27272727273 3630 0.0119320450404828 2011 0.554904359272267 -0.472701998249631 -1 0.125489710711632 2558 3930 3630 3912 4040 2011 2504 3226 4362 4496 2756 3978 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 841/1982 Arthur Liberzon 0.000186215579455383 0.000268087356594899 2330 3501.18181818182 3630 1.86231185604864e-05 2330 1.58687097025433 2.08790956892496 1 1.4578676279907 2330 4412 4150 2883 3150 4186 3630 2797 2839 4292 3844 3979 M125 PID_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IGF1_PATHWAY.html IGF1 pathway 18832364 28/54 Pathway Interaction Database 0.0118356991616665 0.014522672498447 4330 3570.27272727273 3631 0.00108180521410242 2626 1.17981050448044 -1.0986579846316 -1 0.557757335566212 4330 2980 3149 2626 3631 3477 4115 4069 3966 2966 3964 3980 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 60/132 Reactome 0.0309660918650456 0.0367266784306768 2115 3227.27272727273 3631 0.00285552201796236 1529 1.03854179678015 -0.778891544041848 -1 0.383336241797416 2111 3918 3631 3922 4037 1529 2329 3516 3972 4173 2362 3981 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 280/656 Arthur Liberzon 0.0142661804433838 0.0173775205504799 2890 3480.27272727273 3631 0.00130541272537684 1546 1.91667931130681 2.33846900212813 1 0.867688243226059 2886 4465 1546 2981 3655 4086 3622 3631 3274 3968 4169 3982 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 65/142 Arthur Liberzon 0.00372179790212029 0.00474180124234249 3110 3552.09090909091 3632 0.00033891901074944 2422 1.18039964003589 1.30293022559347 1 0.705625613503945 3109 3747 3267 3836 3514 4081 3632 2422 3867 4153 3445 3983 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 16/36 Reactome 0.113711215362881 0.121651372562841 2675 3453.36363636364 3633 0.0109138650037998 1981 0.386790298712793 -0.386790298712793 -1 0.0910204114415668 2674 4352 3633 4486 4221 1981 2247 2798 4522 4511 2562 3984 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 8/22 Arthur Liberzon 0.147859119791321 0.157148522418265 3625 3652.63636363636 3636 0.0158730158730159 2880 1.68027330015041 -1.0476812132427 -1 0.347349557571066 3623 3636 4194 3645 4116 3193 3288 3896 4208 2880 3500 3985 M268 PID_S1P_S1P2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P2_PATHWAY.html S1P2 pathway 18832364 15/36 Pathway Interaction Database 0.0209559036260185 0.0252051756651753 3530 3542.45454545455 3637 0.0019234745839823 2733 1.4394741981968 -1.33275549626065 -1 0.591858444650135 3527 4061 2733 3197 3690 3313 4318 3884 3637 3718 2889 3986 M1045 REACTOME_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IMMUNE_SYSTEM.html Genes involved in Immune System 498/1251 Reactome 4.99961590547933e-08 1.97373210893649e-07 3760 3422.36363636364 3637 4.54510547190749e-09 923 1.31182073185397 -1.18895699171924 -1 2.26231592456089 3756 4368 3637 4141 923 2203 3526 4534 3338 4082 3138 3987 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 17/35 Reactome 0.0839184282471183 0.0902966141827776 2575 3615.54545454545 3638 0.00793650793650794 2574 1.21439333515164 1.28156669367829 1 0.326208237836719 2574 4099 3352 4236 4466 4035 3638 2743 3536 3373 3719 3988 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 19/47 Reactome 0.13876730090213 0.14785438199804 2695 3629.18181818182 3638 0.0134891534869558 2052 0.560208647989583 -0.560208647989583 -1 0.119622413456966 2692 4622 3638 4488 4613 2052 2878 3152 4538 4474 2774 3989 M4864 KEGG_BASAL_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_TRANSCRIPTION_FACTORS.html Basal transcription factors 16/38 KEGG 0.298735036746822 0.313451048409227 3160 3580.45454545455 3640 0.0317460317460317 2413 0.894838747428313 -0.751165001316394 -1 0.115964999263912 3156 3831 3466 3640 4134 2413 3154 4100 4293 4068 3130 3990 M511 REACTOME_SIGNALING_BY_NODAL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NODAL.html Genes involved in Signaling by NODAL 6/22 Reactome 0.00216616092019709 0.00280714327213594 3725 3489.18181818182 3640 0.000216827533545356 2213 1.12669337954414 1.20207617909558 1 0.739503013970421 3723 2213 3917 3479 3469 4426 3123 3879 3640 2470 4042 3991 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 3/12 Arthur Liberzon 0.136160541521561 0.145142924833948 3510 3638.36363636364 3640 0.0145302362032707 2069 0.285529886987833 -0.285529886987833 -1 0.0615599916035397 3507 3640 4270 4458 4638 2442 2069 3122 4557 4585 2734 3992 M7591 REACTOME_G1_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_PHASE.html Genes involved in G1 Phase 20/48 Reactome 0.0839184282471183 0.0902966141827776 3260 3811.81818181818 3641 0.00793650793650794 3021 1.81122770182566 -1.12073856499897 -1 0.486528958378143 3257 4671 3065 3840 4477 4644 3095 4602 3021 3617 3641 3993 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 4/9 Leona Saunders 0.275742742869669 0.289715357194454 2845 3649.45454545455 3641 0.0317460317460317 2845 1.82088697402588 -1.82088697402588 -1 0.251991898213992 2845 4106 4280 4150 4442 2996 3264 3641 4291 3103 3026 3994 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 684/1510 Jessica Robertson 1.6378944761721e-08 9.29197762147999e-08 3645 3008.81818181818 3642 1.63789448824424e-09 501 1.26797232481888 -1.12311878275557 -1 2.29340421181427 3642 3137 4439 4325 501 543 3936 3701 2984 4265 1624 3995 M11480 REACTOME_MEMBRANE_TRAFFICKING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEMBRANE_TRAFFICKING.html Genes involved in Membrane Trafficking 89/177 Reactome 0.00436390913266741 0.00552533861001877 4060 3309.63636363636 3643 0.000397508134223061 1068 1.28788006144116 -1.04665870456369 -1 0.747874779733636 4057 3680 3172 3643 3528 1068 3614 4192 3819 3730 1903 3996 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 10/17 Jessica Robertson 0.0462639616745381 0.0540091989055519 3470 3684.90909090909 3643 0.00429695385364765 2323 0.739338359774914 -0.739338359774914 -1 0.241046354061586 3470 4273 3349 4513 4326 2566 3643 2323 4282 4655 3134 3997 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 39/89 Kevin Vogelsang 0.239049583253411 0.251670713800378 1885 3488.09090909091 3644 0.0245293328906772 1881 0.619284060542889 -0.582140542755732 -1 0.095441166033905 1881 4053 3644 3994 3983 2293 2945 3380 4546 4614 3036 3998 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 50/119 Kevin Vogelsang 0.0416410752349456 0.0488191339882299 2850 3490.72727272727 3645 0.00385916246155295 1609 1.0958418933983 -0.828586363290338 -1 0.369644973509636 2846 4337 3588 4446 4013 1609 2835 3645 4028 4256 2795 3999 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 6/10 Reactome 0.0126626050697172 0.0155007751715503 4105 3316.45454545455 3647 0.00127353427876134 1856 3.95540731868224 -3.85798312434384 -1 1.84112645627378 4101 1856 4051 2527 3647 4305 3016 3678 2364 2474 4462 4000 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 60/141 Jessica Robertson 0.0585846792330955 0.0677846436756261 2855 3568.36363636364 3647 0.00547322843457069 1792 0.935490172024446 -0.896187943470036 -1 0.281256981463077 2852 4533 3647 4588 4610 1792 3480 2774 4377 4312 2287 4001 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 9/18 Arthur Liberzon 0.0152603154509073 0.0185306655099641 2595 3579.90909090909 3650 0.00153661343713537 2591 0.714742124473792 -0.727624004387698 -1 0.318436609124112 2591 2818 4128 4452 3667 3132 2681 3506 4215 4539 3650 4002 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 214/547 Leona Saunders 0.0001460789280069 0.000212585669764079 3185 3449.36363636364 3650 1.32807844071183e-05 2545 1.40821547625344 -1.32194812123764 -1 1.33022626253678 3181 4078 2545 3996 3098 2718 3914 3650 3774 3752 3237 4003 M590 REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT.html Genes involved in Mitochondrial Protein Import 41/74 Reactome 0.0106845011595668 0.0131652833115252 1010 2947.45454545455 3653 0.000976067908613097 1009 0.810305342590985 -0.810305342590985 -1 0.391955362205357 1009 4292 3653 3847 3984 1341 1999 2157 4051 4258 1831 4004 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) 24/49 Reactome 0.557443745451391 0.574863862496747 3655 3823.54545454545 3654 0.0714285714285714 2709 0.590750092130048 -0.493095521719126 -1 0.036534033333313 3152 4618 3654 4562 4238 2709 3234 3651 4427 4473 3341 4005 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 9/17 Arthur Liberzon 0.0765897756730953 0.0871115749524574 3240 3707.54545454545 3654 0.00793650793650794 2322 1.19314175085794 1.24897880728532 1 0.325285892163243 3240 4638 4277 4422 4385 3490 2322 3546 3748 3061 3654 4006 M182 PID_IL3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL3_PATHWAY.html IL3-mediated signaling events 18832364 21/41 Pathway Interaction Database 0.000228797160729576 0.00032548375688488 3655 3543.63636363636 3655 2.08019053458218e-05 2729 1.05840233339636 -1.17087125856514 -1 0.949423430281489 3655 3798 3426 2975 3166 4120 2729 2888 3930 3992 4301 4007 M9546 BIOCARTA_TID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TID_PATHWAY.html Chaperones modulate interferon Signaling Pathway 17/35 BioCarta 0.0144893352798321 0.0176264343513222 3950 3400.54545454545 3656 0.00132596838187245 1688 1.83313135019859 -1.02356315605945 -1 0.826953379444166 3949 3899 2551 2727 3656 3806 3940 3186 1688 3368 4636 4008 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 94/234 Leona Saunders 0.0839184282471183 0.0902966141827776 3490 3603 3656 0.00793650793650794 2194 1.15415363633001 -1.03134513463993 -1 0.310026743506723 3487 4081 3656 3330 4367 2194 4122 3390 3919 4250 2837 4009 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 27/50 Arthur Liberzon 0.0236887723589029 0.0283756613685632 3660 3501 3656 0.00217706879704714 2414 1.52600629301695 -1.50118913421546 -1 0.607239950427892 3656 3532 2414 3442 3700 2903 3945 3639 3768 3709 3803 4010 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 37/81 Itai Pashtan 2.13394254068257e-05 3.5053068842508e-05 3090 3447.72727272727 3656 1.93996658149905e-06 2746 1.27553411761668 1.32942685305571 1 1.46172312983584 3088 3204 2854 3701 2746 4263 2900 3668 3656 3865 3980 4011 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 49/108 Arthur Liberzon 2.74841019284044e-06 5.39323708695574e-06 3945 3416.63636363636 3657 2.49855784215734e-07 2293 1.359650112239 -1.39899230457359 -1 1.84240020841452 3941 3920 3127 3984 2293 2730 4302 3201 3666 3657 2762 4012 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 40/109 Jessica Robertson 0.433464513011472 0.44998110500039 3660 3765.45454545455 3658 0.0503444696877598 2615 0.808834560347432 -0.808834560347432 -1 0.0721511666582653 2615 4611 3658 4203 4080 2712 3331 3658 4550 4657 3345 4013 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 84/171 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2890 3516.45454545455 3658 0.00793650793650794 2309 1.24254322209308 -1.16246222590179 -1 0.333769816743044 2889 4204 3397 3658 4255 2309 4409 2715 3751 4151 2943 4014 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 861/2334 Leona Saunders 5.4994437997721e-08 2.09947262849324e-07 4260 3470.45454545455 3659 5.49944393586956e-09 1024 1.47064939063728 -1.09448761765841 -1 2.52607968767414 4256 4583 4296 3459 1024 1719 4314 3659 3049 4336 3480 4015 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 234/541 Arthur Liberzon 1.51313803672568e-06 3.19128826853215e-06 3240 3433.81818181818 3659 1.37558097949811e-07 1946 1.39286872581108 -1.13257813609755 -1 1.96905676898774 3239 3979 1946 2311 2140 4072 3763 4601 3659 3389 4673 4016 M16647 REACTOME_CELL_CYCLE_CHECKPOINTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE_CHECKPOINTS.html Genes involved in Cell Cycle Checkpoints 71/137 Reactome 0.0839184282471183 0.0902966141827776 2770 3693.72727272727 3661 0.00793650793650794 2766 1.11646845015358 -0.643168201471164 -1 0.299903807330627 2766 4205 3661 3150 4104 2917 3498 4336 4015 4342 3637 4017 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 44/85 Reactome 0.154058506136402 0.163663151157374 1925 3422.72727272727 3661 0.0150944714798413 1921 0.673582288505426 -0.673582288505426 -1 0.136187841656944 1921 4019 3713 3661 4294 2093 3086 3156 4563 4327 2817 4018 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 43/79 Reactome 0.214056938645943 0.226258393611952 1720 3392.81818181818 3662 0.0216593505678115 1719 0.757837899155235 -0.673582288505426 -1 0.125805628302199 1719 4020 3697 3662 4076 2214 3012 3227 4484 4273 2937 4019 M14804 REACTOME_EXTENSION_OF_TELOMERES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTENSION_OF_TELOMERES.html Genes involved in Extension of Telomeres 13/29 Reactome 0.875188267474474 0.889230750517212 2820 3868.36363636364 3662 0.172360135250211 2818 0.629878323864254 -0.629878323864254 -1 0.00826020904343417 2818 4456 3477 4129 4473 3156 3646 3662 4579 4527 3629 4020 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 77/159 Reactome 0.232850105696956 0.245309261532359 4335 3594.36363636364 3663 0.0238095238095238 2061 1.05258867772633 -0.789110830285237 -1 0.165230519525223 2061 4332 3671 3663 4211 2585 3518 3545 4262 4334 3356 4021 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 24/54 Jessica Robertson 0.00109840302897042 0.00145563252085842 3160 3689.54545454545 3663 9.99047106173375e-05 2977 0.916981281922016 0.924605110257319 1 0.669129897316343 3159 3655 3434 3706 3390 4671 3663 2977 3697 4065 4168 4022 M3158 REACTOME_S_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_S_PHASE.html Genes involved in S Phase 63/124 Reactome 0.394610822753497 0.411286991864521 3195 3520.27272727273 3664 0.044600590723161 1822 0.720693621669029 -0.643168201471164 -1 0.0715273660110903 1822 4253 3738 3664 4162 2481 3191 3361 4512 4348 3191 4023 M2044 KEGG_SPLICEOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPLICEOSOME.html Spliceosome 79/188 KEGG 0.456984586115574 0.473662855681836 2480 3659.90909090909 3667 0.0539980876754722 2480 0.826962527905177 -0.826962527905177 -1 0.0690301669956647 2480 4601 3766 3667 4216 2558 3371 3517 4583 4379 3121 4024 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 4/8 Arthur Liberzon 0.000289283566197229 0.000405135323132163 3025 3664.90909090909 3667 2.89321231339906e-05 2173 0.788602549743279 0.748905912168911 1 0.688119352094309 3021 2173 4677 4386 3230 3667 3137 4062 3514 4683 3764 4025 M18937 KEGG_NUCLEOTIDE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NUCLEOTIDE_EXCISION_REPAIR.html Nucleotide excision repair 30/47 KEGG 0.0299448228697884 0.0355604257394396 2290 3361.18181818182 3672 0.00276003185847096 1801 0.574202506780528 -0.512300247464071 -1 0.214013727140677 2286 4213 3672 3988 3726 1801 2684 3126 4411 4402 2664 4026 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 24/48 Reactome 0.0767978069107304 0.087305803780612 2380 3391.54545454545 3674 0.00723795236618875 1798 0.665376741529551 -0.699831779142234 -1 0.181235834399686 2660 4446 3674 3989 4274 1798 2379 3139 4360 4209 2379 4027 M4557 BIOCARTA_NEUROTRANSMITTERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NEUROTRANSMITTERS_PATHWAY.html Biosynthesis of neurotransmitters 2/9 BioCarta 0.13411491204602 0.143059976746563 3195 3635.4 3674.5 0.0158730158730159 2823 0.969861218596682 0.969861218596682 1 0.210667801250615 3194 3877 3818 NA 4339 3131 2823 3032 4197 4412 3531 4028 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 28/71 Reactome 0.475738862655188 0.492556851613392 3280 3682.09090909091 3676 0.0570159798784029 2579 0.914447900242698 -0.863380363541572 -1 0.0723374370820301 3279 4493 3676 3915 4276 2579 3003 3574 4408 4139 3161 4029 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 13/37 John Newman 0.0186906490622516 0.0225558541091195 2370 3338.72727272727 3676 0.00171375953263325 2343 1.31727865656857 1.63693399670368 1 0.557957864805365 2370 3967 2988 4116 3676 2961 2343 3797 3716 3986 2806 4030 M7927 REACTOME_NUCLEOTIDE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEOTIDE_EXCISION_REPAIR.html Genes involved in Nucleotide Excision Repair 28/54 Reactome 0.191069157290909 0.202156258989659 2765 3617.45454545455 3677 0.0190919276016853 2172 0.554904359272267 -0.472701998249631 -1 0.0990994094506993 2763 4669 3677 4606 4058 2172 2765 3320 4458 4479 2825 4031 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 108/260 Yujin Hoshida 6.30018269634131e-06 1.1359236673742e-05 3680 3365.72727272727 3677 5.72745521669919e-07 1799 1.65519846610976 -1.50724249284906 -1 2.10515632495781 3677 3849 1799 2559 2497 4093 3719 4605 3559 2181 4485 4032 M16991 BIOCARTA_IGF1MTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1MTOR_PATHWAY.html Skeletal muscle hypertrophy is regulated via AKT/mTOR pathway 15/32 BioCarta 0.0190838253734026 0.0230066389760135 3325 3560.72727272727 3679 0.00175012782530724 1732 1.35245763498875 -1.48584048044756 -1 0.569868983587457 4504 1732 3325 3072 3679 3323 4537 3788 3865 3715 3628 4033 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 189/425 Arthur Liberzon 0.00488797103781297 0.00616721386192557 3680 3479.72727272727 3680 0.0004453513688753 1076 1.42680280712845 -0.988516060166509 -1 0.81103073355849 3680 4419 3514 4316 3851 1076 3342 4255 3107 4215 2502 4034 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 148/328 Reactome 0.0165028590611036 0.0199980340212908 2965 3424.90909090909 3681 0.00151163343715366 1346 1.06464030253577 -0.867941925262997 -1 0.46526246460389 2965 4280 3725 4260 4446 1346 2916 3389 3681 4321 2345 4035 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 18/33 Jessica Robertson 1.48787672135262e-06 3.15056046825955e-06 3685 3561.63636363636 3681 1.35261611601446e-07 2134 0.960138771614928 -1.18326346408399 -1 1.35869695226272 3681 3695 3200 2722 2134 4676 2840 4198 4294 3476 4262 4036 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 31/83 Reactome 0.321117332266859 0.336258283575977 3150 3635.18181818182 3682 0.0345970734831788 2583 0.868075858056633 -0.81857348619386 -1 0.105685833283517 3146 4392 3682 4321 4513 2583 2861 2889 4328 4183 3089 4037 M19489 REACTOME_SOS_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SOS_MEDIATED_SIGNALLING.html Genes involved in SOS-mediated signalling 8/20 Reactome 0.000348265486906126 0.000482868988743131 3830 3433.36363636364 3682 3.48320078929988e-05 2226 0.86605169316085 -0.568192156212718 -1 0.738718974999343 3827 2819 4077 2226 3259 2808 4246 4051 3997 3682 2775 4038 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 8/18 Jessica Robertson 0.0217020258400883 0.0260825065623631 3210 3457.54545454545 3684 0.00219169255649577 2165 0.913630468529062 0.913630468529062 1 0.372158895784758 3206 3306 4316 4221 4280 3786 2192 2165 4088 3684 2789 4039 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 4/9 Jessica Robertson 0.0808890295004278 0.0902966141827776 3065 3778.72727272727 3684 0.00839936778990656 1900 0.94506185732956 0.94506185732956 1 0.253860834603979 3064 3423 4526 4400 4569 3684 1900 3373 4302 4648 3677 4040 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 61/146 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2175 3496.63636363636 3684 0.00793650793650794 2175 1.39763589486726 1.36222707684076 1 0.37543056960554 2175 4658 3330 3995 4298 3308 2218 2946 3965 3886 3684 4041 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 49/158 Jennifer Shepard 0.0556967058822104 0.0645228093359797 3510 3578.27272727273 3685 0.00519625960958392 1336 2.0649780691884 2.29167554519953 1 0.632216139626015 3508 4154 1336 3318 4226 4413 3685 4233 3625 2384 4479 4042 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 36/81 Kevin Vogelsang 0.0839184282471183 0.0902966141827776 3710 3630.36363636364 3686 0.00793650793650794 3029 1.36391909270441 -1.35062249143009 -1 0.366373614579269 3709 3686 3239 4514 4049 3029 4222 3296 3112 3822 3256 4043 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 6/9 Arthur Liberzon 0.000208712760144554 0.000298543343723254 3730 3209.36363636364 3686 2.08732365193403e-05 165 3.36846092577924 3.36846092577924 1 3.05413607789169 3730 3768 4636 2172 4284 4642 3686 1272 165 3460 3488 4044 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 49/114 John Newman 0.0839184282471183 0.0902966141827776 2815 3612.27272727273 3688 0.00793650793650794 2357 1.13820552437959 -1.0512455617624 -1 0.305742786446048 2815 4659 3688 4206 4669 2357 3140 3183 4071 4201 2746 4045 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 57/115 Reactome 0.0839184282471183 0.0902966141827776 2280 3430.45454545455 3689 0.00793650793650794 1841 0.780605707883416 -0.757916816478516 -1 0.209684879181703 2277 4287 3746 3333 4424 1841 3056 3689 4158 4296 2628 4046 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 152/320 Jessica Robertson 0.0362441111350581 0.0427270200701591 4420 3607.45454545455 3689 0.00335048761638214 1570 1.08637147618994 -0.773209280112006 -1 0.38262609288054 4417 4279 3689 3782 4253 1570 3446 3548 3440 4298 2960 4047 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 30/68 Yujin Hoshida 0.0839184282471183 0.0902966141827776 3270 3722.45454545455 3689 0.00793650793650794 2661 1.39086926339241 -1.00325026193948 -1 0.373612927569055 3267 3689 3238 3498 4103 4633 3515 4396 2661 3824 4123 4048 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 36/88 John Newman 0.0839184282471183 0.0902966141827776 3690 3761.63636363636 3689 0.00793650793650794 2733 1.26659552444082 1.66763905858981 1 0.34023070884039 3689 3436 2813 2733 4232 4421 3966 4444 3676 3556 4412 4049 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 58/125 Reactome 0.0839184282471183 0.0902966141827776 2360 3444.81818181818 3691 0.00793650793650794 2292 0.978119341981307 -1.00895727706854 -1 0.262740684784506 2356 4383 3691 3853 4153 2292 3341 2642 4103 4253 2826 4050 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 1002/2578 Leona Saunders 0.0765897756730953 0.0871115749524574 3290 3670.54545454545 3691 0.00793650793650794 2241 1.29823030955019 -0.988224275627978 -1 0.353936174488758 3286 4581 4295 3087 4128 2241 3691 3787 3481 4591 3208 4051 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 27/62 Jessica Robertson 0.00492415547914122 0.00620785380017642 2635 3464.72727272727 3695 0.000448655603912392 2613 1.14645777622599 1.15003518650205 1 0.650834340072701 2635 3722 3043 4540 3539 3695 2613 3862 3800 2852 3811 4052 M15247 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS.html Ubiquitin mediated proteolysis 77/154 KEGG 0.000372175746898685 0.000514458864297121 2460 3133.63636363636 3696 3.38398839164582e-05 649 0.869321541904825 -0.9400828288576 -1 0.735354193978824 2456 4478 3696 4491 4329 649 2713 1955 4094 4236 1373 4053 M9177 BIOCARTA_DC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DC_PATHWAY.html Dendritic cells in regulating TH1 and TH2 Development 21/83 BioCarta 0.00474767197252822 0.00599181008975687 4195 3674.54545454545 3697 0.000432540787801345 2859 1.39109790982014 -1.48236659459435 -1 0.795218909624336 4194 3962 2859 4191 3536 3118 4638 2910 3986 3697 3329 4054 M18030 ST_TUMOR_NECROSIS_FACTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_TUMOR_NECROSIS_FACTOR_PATHWAY.html Tumor Necrosis Factor Pathway. 21/37 Signaling Transduction KE 0.00337022645541189 0.00430323737603817 3875 3742.90909090909 3698 0.000306854588778183 3297 1.12128852216177 -1.12667680135659 -1 0.682445920425472 3874 3626 3309 4042 3507 3297 4666 3765 4069 3698 3319 4055 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 130/300 Jessica Robertson 0.00208054100696042 0.00269992111842052 3650 3392.45454545455 3698 0.000189319198592166 904 1.19200456317109 -1.11166913836641 -1 0.787555628265937 3646 4472 3698 4383 3788 904 3299 3223 3830 4291 1783 4056 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 10/22 Reactome 0.866037891117523 0.880315305374558 2930 3775.09090909091 3700 0.167019710332725 2588 0.968282296420761 -0.968282296420761 -1 0.0137880783303877 2927 4230 2588 3980 4664 3235 3700 3558 4611 4519 3514 4057 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 32/54 John Newman 0.161385165508919 0.171020100763183 3880 3741.09090909091 3701 0.0158730158730159 2823 1.31248415834767 -1.21511208526815 -1 0.258917295659374 3878 4491 3264 3031 4282 2823 3701 4599 4241 3305 3537 4058 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 14/31 Reactome 0.000198225576684859 0.000284149603042291 4125 3630.72727272727 3702 1.80221308695563e-05 2814 1.15207556470945 1.47899517518934 1 1.05092994874674 4123 2814 3130 4285 3145 3702 4061 3877 3431 3008 4362 4059 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 449/1017 Jessica Robertson 2.35732738340981e-07 6.55574843837293e-07 3275 3421.72727272727 3703 2.14302512363674e-08 1544 1.54438792714194 1.86893076088365 1 2.45629670814595 3274 4240 2798 2567 1544 3703 3813 4117 3220 3800 4563 4060 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 31/73 John Newman 0.0839184282471183 0.0902966141827776 1970 3623.09090909091 3705 0.00793650793650794 1970 1.84114155712481 2.020382440857 1 0.494564371724827 1970 4394 2665 3653 4667 3989 3162 3918 3673 4058 3705 4061 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 7/18 Arthur Liberzon 0.0494654663606901 0.0576031747927917 2900 3342.09090909091 3706 0.0050602322332572 2013 0.751165001316394 -0.751165001316394 -1 0.239496378491778 2898 3706 4206 3757 3923 2013 2483 2735 4218 4561 2263 4062 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 9/28 Reactome 2.57956732416837e-08 1.23361069287334e-07 3710 2659.27272727273 3707 2.57956735411212e-09 594 1.59334604809304 -0.893592036670773 -1 2.83147518433734 3707 594 3911 770 692 4507 3804 3910 621 2296 4440 4063 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 8/24 Reactome 0.0223729795688678 0.0268613328874493 3735 3707.27272727273 3707 0.00226014715137049 2578 1.19907014039842 -1.52931753759891 -1 0.484489095292226 3731 3606 3939 4406 3707 3183 4651 3096 4209 3674 2578 4064 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 74/175 Arthur Liberzon 0.597318307603006 0.614227252452861 1910 3586.90909090909 3708 0.0793650793650794 1908 1.474727732134 -1.42334088302544 -1 0.0802916855760998 1908 4336 2584 3338 4445 3302 3741 3708 4440 4178 3476 4065 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 3/8 Arthur Liberzon 0.018763138555705 0.0226375044469706 3155 3637.90909090909 3708 0.00189234720760136 1523 0.534160549741401 0.534160549741401 1 0.22603789468382 3155 3708 4214 4286 3940 3066 1523 3346 4641 4564 3574 4066 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 27/81 Kevin Vogelsang 0.0547890862288706 0.0635184705760731 2945 3699.09090909091 3708 0.00510937408095987 1777 1.30537242304956 -1.40445942470645 -1 0.401941927797733 2944 4262 3451 4247 4402 3704 1777 4640 3915 3708 3640 4067 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 1271/2834 Arthur Liberzon 0.00258658545289844 0.00332987347040717 3280 3478.27272727273 3708 0.00025896010851293 969 1.10676910224689 -0.977424802528432 -1 0.705313043553976 3276 4580 4631 4208 3489 969 3809 2992 3708 4676 1923 4068 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 14/57 Arthur Liberzon 0.0245114916591948 0.0293236788141401 3710 3843.27272727273 3709 0.00225353871166168 2735 1.218170857431 -0.825132246951933 -1 0.480271664733229 4315 3569 2735 3709 3706 3675 4370 4427 4224 3630 3916 4069 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 8/31 Arthur Liberzon 1.32405952136877e-08 8.23976483019129e-08 4065 2591.72727272727 3709 1.32405952925786e-09 409 1.76029086467256 -1.7506428782044 -1 3.20750151519649 4064 598 4133 1179 409 3988 4343 3709 779 1063 4244 4070 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 14/35 Jean Junior 0.0249237273873757 0.0298016296344073 3525 3589.18181818182 3709 0.00229187715010793 2379 0.994490251703172 -0.973885146056468 -1 0.390288004329072 3522 2775 2379 3750 3709 4518 3499 3785 4223 3016 4305 4071 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 13/18 Jessica Robertson 5.16691925409323e-05 7.96191503606737e-05 4535 3545.81818181818 3709 4.69730964393773e-06 1687 0.869265129487321 -0.919860590106339 -1 0.916488260467749 4534 1687 3125 3876 2924 3709 4521 3911 2930 3534 4253 4072 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 112/249 Kate Stafford 1.61943272362523e-07 4.80903785989088e-07 4190 3577 3711 1.47221167530238e-08 1410 1.09683367174885 -0.817661868483235 -1 1.78244046426222 4189 3711 3583 4361 1410 2289 4326 4487 3474 4222 3295 4073 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 8/25 Vamsi Mootha 0.0229440482973586 0.0275258090940662 3415 3869.81818181818 3711 0.00231844421616171 3239 0.737279518119919 -0.731222645401851 -1 0.295888096292463 3413 3363 4602 4224 3711 4294 3239 3533 4390 3689 4110 4074 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 25/86 Pathway Interaction Database 0.00197231410389958 0.0025665825856355 4420 3851.90909090909 3712 0.000179462228963652 3276 1.04657925596657 -0.831326680905369 -1 0.697394539994214 4418 3691 3468 3592 3444 3712 4634 4285 3276 3888 3963 4075 M17283 REACTOME_G1_S_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_S_TRANSITION.html Genes involved in G1/S Transition 62/126 Reactome 0.33392717611364 0.349515914064891 1670 3501.27272727273 3712 0.0362674677310889 1669 0.770211356619375 -0.71541577812663 -1 0.0904440080805758 1669 4254 3712 3724 4194 2405 3233 3400 4525 4345 3053 4076 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 69/143 Leona Saunders 0.0839184282471183 0.0902966141827776 3385 3617.63636363636 3714 0.00793650793650794 2937 1.12385147015216 -0.945955192368073 -1 0.301887022694948 3381 4047 3431 3145 3861 2937 3714 3845 3784 4131 3518 4077 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 33/69 Reactome 0.0684584193475562 0.0787229823466621 2320 3460.18181818182 3716 0.00642603249591124 1756 0.657993173968921 -0.673374800885106 -1 0.186830901348924 2320 4492 3716 4447 4522 1756 2665 2924 4454 4276 2490 4078 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 44/120 Arthur Liberzon 2.42345887026106e-08 1.19414597960498e-07 4495 3303.09090909091 3716 2.20314445177929e-09 615 1.84104840265985 -1.33727225724668 -1 3.27834456172622 3882 3716 1880 4495 615 4073 4004 2929 3551 2698 4491 4079 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 58/109 Chi Dang 0.0204110989764034 0.0245751309875196 3685 3783.45454545455 3716 0.00187299684618325 3103 1.42236507820064 1.76843891880471 1 0.588845981810247 3578 3682 3103 3716 3685 4288 4147 3833 3129 3952 4505 4080 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 73/159 Reactome 0.00386863219240934 0.00491951437004889 3365 3790.54545454545 3717 0.000352313805258078 3121 1.19804195384667 -0.880204010487196 -1 0.71124794243791 3363 3885 3121 3717 3520 4463 3180 4251 3605 4008 4583 4081 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 43/115 Jessica Robertson 0.00344957251793847 0.00440215054985285 2130 3087.63636363636 3717 0.00031409030071972 1269 1.31427941959292 -1.31427941959292 -1 0.796568877631673 2129 4661 3717 4137 3924 1269 1994 2588 3749 4221 1575 4082 M15434 REACTOME_DNA_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPAIR.html Genes involved in DNA Repair 66/127 Reactome 0.0556567244715146 0.0644924359232239 1250 3186.18181818182 3718 0.00519243063066465 1250 0.750107545487364 -0.755384961421702 -1 0.229693135352889 1250 4334 3718 3998 3973 1689 2333 2725 4358 4255 2415 4083 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 35/108 Yujin Hoshida 0.0839184282471183 0.0902966141827776 3925 3525.09090909091 3718 0.00793650793650794 1795 2.14105350601189 -1.81979217800842 -1 0.575126253595851 3923 4088 2875 3071 4173 3850 3718 3473 1795 3507 4303 4084 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 19/42 Vamsi Mootha 0.0839184282471183 0.0902966141827776 4500 3733.81818181818 3718 0.00793650793650794 2165 1.61822092470748 -1.02781159688773 -1 0.434683777696943 3718 4496 2721 3506 4500 2165 4513 4589 3222 3927 3715 4085 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 57/136 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 2865 3737.18181818182 3719 0.00793650793650794 2660 1.65220607892704 2.12254938103532 1 0.443812817035871 2864 4483 3170 3719 4389 4601 3450 3595 2660 4137 4041 4086 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 40/82 Reactome 0.0679418855749187 0.078148177664229 1850 3325.72727272727 3719 0.00637596053950567 1751 0.673582288505426 -0.673582288505426 -1 0.191808707509424 1849 3958 3719 3918 4374 1751 2902 2729 4493 4315 2575 4087 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 15/30 Reactome 0.0839184282471183 0.0902966141827776 2875 3514.54545454545 3719 0.00793650793650794 2663 1.03589480737568 1.03589480737568 1 0.278260240558849 2872 3863 3536 4374 4007 3798 3001 2663 3804 3719 3023 4088 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 34/67 Reactome 0.0479155803441311 0.0558816350155795 3725 3123.18181818182 3721 0.00445383141840185 1299 0.673582288505426 -0.673582288505426 -1 0.217043462589197 1299 3792 3721 3721 4027 1645 2457 2610 4304 4285 2494 4089 M4076 REACTOME_HIV_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIV_LIFE_CYCLE.html Genes involved in HIV Life Cycle 64/144 Reactome 0.0839184282471183 0.0902966141827776 2330 3503.09090909091 3722 0.00793650793650794 2327 0.936971153728578 -0.950666588832988 -1 0.25168752236959 2327 4381 3722 3855 4094 2430 3508 2828 4134 4290 2965 4090 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 8/15 Arthur Liberzon 0.0227264237960944 0.0272786941363981 4245 3560.45454545455 3724 0.0022962245887597 2035 1.71526217716486 -1.26869414438985 -1 0.690104408304262 4243 3042 4627 4154 4071 2953 4678 3724 3526 2112 2035 4091 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 115/361 Arthur Liberzon 1.58584764703039e-06 3.32198572820045e-06 3860 3531.90909090909 3726 1.44168071833973e-07 2154 1.3402489245659 -1.16661486446217 -1 1.88866041571434 3856 3848 2897 4427 2154 3938 3256 3447 3467 3726 3835 4092 M875 REACTOME_NETRIN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NETRIN1_SIGNALING.html Genes involved in Netrin-1 signaling 18/54 Reactome 0.0839184282471183 0.0902966141827776 3485 3655.72727272727 3728 0.00793650793650794 2723 1.88760610298805 1.69676711688513 1 0.507045605863434 3483 3728 2723 4044 4626 4251 2961 3903 3035 2938 4521 4093 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 326/786 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4295 3494.27272727273 3728 0.00793650793650794 2112 1.42452221785477 -1.00576324527561 -1 0.382652731925195 4293 4519 3728 2633 3905 2112 4184 2854 2591 4337 3281 4094 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 386/821 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2005 3581.63636363636 3729 0.00793650793650794 2005 1.05275956712488 -0.90165795432564 -1 0.282790426127447 2005 4589 3784 3729 4493 2323 3309 3580 4149 4393 3044 4095 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 24/59 Reactome 0.0839184282471183 0.0902966141827776 3115 3638.63636363636 3730 0.00793650793650794 2802 1.1691013779997 -1.34188863006625 -1 0.314041982656418 3115 4397 3389 4320 3995 2846 3730 2802 4067 4208 3156 4096 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 3/8 John Newman 0.00014389544260045 0.000209538236179525 4535 3425.27272727273 3730 1.43904761103972e-05 1748 1.80905299516467 -1.1336417161387 -1 1.71178269396501 4535 2444 4402 3730 3112 4445 4506 2600 1748 1756 4400 4097 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 89/217 Jessica Robertson 0.0839184282471183 0.0902966141827776 4045 3573.36363636364 3731 0.00793650793650794 2500 1.53015178074663 -1.19471156176821 -1 0.411026781039809 4044 4426 3108 3842 3992 2500 3954 3099 2926 3731 3685 4098 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 9/19 Reactome 0.0747238998377854 0.0856336988603234 2295 3349.72727272727 3733 0.00773623006983525 1881 1.17161346877642 -1.41039436697649 -1 0.321656080848212 2295 3733 4031 3588 4011 2494 1881 3902 4375 3778 2759 4099 M814 REACTOME_PURINE_SALVAGE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_SALVAGE.html Genes involved in Purine salvage 8/15 Reactome 0.000344789415981169 0.000478720949122298 4195 3582.90909090909 3734 3.44842923549423e-05 2434 1.00149360549164 -1.38384557945125 -1 0.855212542981629 4195 2434 4017 4326 3256 4425 3734 2500 3636 2878 4011 4100 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 23/71 Leona Saunders 0.0314897673612107 0.0373173198088664 4055 3789.45454545455 3735 0.00290452193969059 3255 0.687274978888454 -0.596916968698141 -1 0.252455186783727 4055 3595 3462 3255 3735 3331 4507 3518 4441 4043 3742 4101 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 142/307 Broad Institute 0.0839184282471183 0.0902966141827776 3735 3808.90909090909 3735 0.00793650793650794 2935 1.14826459704455 -1.0709476998503 -1 0.308444838921028 3735 4245 3734 3270 4531 2935 4358 3492 3885 4287 3426 4102 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 6/11 Reactome 0.562604368603265 0.579802962673169 3370 3779.09090909091 3737 0.0793650793650794 3186 1.63462852340934 -1.63462852340934 -1 0.0995293099388011 3369 4074 4002 3834 4269 3186 3537 3737 4429 3441 3692 4103 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 73/182 Kevin Vogelsang 0.000163530550685226 0.000236732826849233 2560 3623.63636363636 3738 1.48675188649489e-05 2557 1.23364071021225 -0.90741953219982 -1 1.15049342407457 2557 4113 3184 4620 3115 4436 2969 3749 3434 3738 3945 4104 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 9/25 Leona Saunders 0.0102784363896723 0.0126782713666765 3740 3649.54545454545 3739 0.00103262890043817 2078 0.925640126820706 -0.925640126820706 -1 0.451641916406018 3739 3808 4297 4544 3627 2263 3298 3525 4374 4592 2078 4105 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 55/138 Kevin Vogelsang 0.0320039520384196 0.0378809091316076 2840 3701.09090909091 3739 0.00295265725321392 2840 1.26720475657256 1.43968675496535 1 0.463357789218594 2840 4207 3113 4135 3739 4192 3314 3656 3761 3693 4062 4106 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 70/114 Arthur Liberzon 0.0138633552684488 0.0169308529548999 2090 3187 3739 0.00126831764635714 1300 0.784559902949332 -0.836977978257142 -1 0.357455389515563 2087 4250 3739 4202 4048 1300 2510 2484 4104 4280 2053 4107 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) 7/17 Reactome 0.0052566869754332 0.00660752016278969 3920 3776.81818181818 3740 0.000526916327311263 2317 0.382743647383736 -0.252821087831105 -1 0.214612529056146 3918 3607 4050 4593 3560 2317 3567 3740 4395 4498 3300 4108 M1017 REACTOME_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPLICATION.html Genes involved in DNA Replication 119/224 Reactome 0.66489526389376 0.681474017192949 1955 3693.27272727273 3740 0.0946122859595699 1953 0.88010388166531 -0.841629500372165 -1 0.0377030620231471 1953 4377 3740 3668 4316 2844 3575 3770 4536 4370 3477 4109 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 6/12 Arthur Liberzon 0.00491285816205729 0.00619527808057063 3675 3834.09090909091 3740 0.000492375335640274 3055 0.734197700619014 -0.734197700619014 -1 0.416964034168648 3675 3309 4569 4333 3552 3055 3740 4166 3875 4660 3241 4110 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 22/60 Signaling Gateway 0.0251043310537943 0.0300099222750205 2975 3597.27272727273 3741 0.00230867815906896 2272 1.21149194253594 0.822160252508663 1 0.474507838225507 2973 4030 3274 3775 3710 3546 2272 4421 3753 3741 4075 4111 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 144/260 Jessica Robertson 0.0839184282471183 0.0902966141827776 2105 3537.81818181818 3741 0.00793650793650794 2104 0.939089117247581 -0.821831459509367 -1 0.252256446440332 2104 4592 3741 4001 4091 2335 3121 3563 4138 4376 2854 4112 M676 REACTOME_PI_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI_METABOLISM.html Genes involved in PI Metabolism 27/51 Reactome 0.0839184282471183 0.0902966141827776 3485 3634.36363636364 3743 0.00793650793650794 2487 0.982686191414727 -1.05984509817628 -1 0.26396742478584 3482 3890 3515 4469 4010 2487 3743 3458 3968 4129 2827 4113 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 20/39 Arthur Liberzon 0.0126125853403483 0.0154435784961777 3665 3682.45454545455 3746 0.0011532253583023 2984 1.23925808437511 -0.777346046350633 -1 0.577350015410143 3665 4164 2984 3971 3637 3964 3848 3291 3746 3145 4092 4114 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 41/95 John Newman 0.00828031077828954 0.0102731099568612 4515 3753.72727272727 3747 0.000755603749164181 3221 1.0967600052373 -1.12097142259817 -1 0.560907979483813 4512 3285 3404 3762 3596 3221 4211 4168 3747 3796 3589 4115 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 9/13 Jessica Robertson 6.08912303686783e-07 1.43241117222704e-06 4180 3246.72727272727 3749 6.08912470535233e-08 1644 1.75093241243166 -1.28838042936174 -1 2.63192320032196 4177 2504 4476 1644 1923 4187 4473 3802 1709 3070 3749 4116 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 81/214 Reactome 0.514011397665828 0.531360558010604 3145 3789.36363636364 3751 0.0634920634920635 2736 1.03561584346078 -1.10293402537353 -1 0.0731498667837952 3142 4600 3751 3862 4363 2736 3715 3463 4406 4356 3289 4117 M141 PID_PI3KCI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PI3KCI_PATHWAY.html Class I PI3K signaling events 18832364 28/68 Pathway Interaction Database 0.00190055657736387 0.00247802118016892 4260 3644.54545454545 3752 0.000172927312405242 2974 1.05356556744156 -1.06348168458746 -1 0.706182639292952 4257 3441 3033 2974 3438 3765 4135 3460 3860 3975 3752 4118 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 11/49 Reactome 0.036903452539582 0.0434605626037902 4230 3727.09090909091 3752 0.00341249282437268 2858 1.18044475717832 -1.3975445940707 -1 0.413514589828749 4230 3357 2858 4222 3752 4364 2913 4539 3612 3326 3825 4119 M19312 REACTOME_DNA_STRAND_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_STRAND_ELONGATION.html Genes involved in DNA strand elongation 16/31 Reactome 0.947974489701433 0.959854896011434 2800 3841.09090909091 3753 0.235649779251954 2797 0.460683679265589 -0.460683679265589 -1 0.00210834291299271 2797 4405 3450 3526 4441 3370 3569 3753 4617 4530 3794 4120 M2531 REACTOME_MRNA_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_PROCESSING.html Genes involved in mRNA Processing 91/233 Reactome 0.39104015830698 0.407656102742271 2955 3698.72727272727 3754 0.0440896798567647 2474 1.0088616165228 -0.966669272806555 -1 0.101126859638721 2951 4597 3754 3861 4544 2474 3401 3295 4378 4357 3074 4121 M87 PID_LKB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LKB1_PATHWAY.html LKB1 signaling events 18832364 38/103 Pathway Interaction Database 0.0378105125129444 0.0445064209082284 3840 3705.72727272727 3755 0.00349785685694497 2729 1.51223738776775 -1.22957092758164 -1 0.525725911167192 3837 3750 2729 3445 3755 4678 3696 3904 2954 3913 4102 4122 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 101/217 Kevin Vogelsang 0.042234323724825 0.0494898827143111 2250 3480.36363636364 3755 0.00391523610037595 2182 0.725011561980012 -0.692089484632842 -1 0.243452732209339 2250 3952 3755 4072 3768 2182 3249 3343 4353 4358 3002 4123 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 42/127 Reactome 0.0839184282471183 0.0902966141827776 4070 3706.54545454545 3756 0.00793650793650794 3057 1.1239565768013 -1.05829210260139 -1 0.301915256279783 4068 3255 3530 3393 3908 4057 3057 4276 3756 3600 3872 4124 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 26/65 Arthur Liberzon 1.72530225903961e-06 3.56000281191528e-06 4205 3547.18181818182 3757 1.56845782915632e-07 2188 1.07449227677297 -0.90312679209018 -1 1.50585390437619 4390 2696 3092 3245 2188 3828 4202 4203 3757 3222 4196 4125 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 2/13 Yujin Hoshida 0.425141538122303 0.441634504021527 3320 3811.6 3757.5 0.0596607855849708 2903 0.393230208494051 -0.393230208494051 -1 0.0358999841862837 3318 4194 4575 NA 4201 3199 2903 3091 4651 4663 3321 4126 M11844 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY.html Cytosolic DNA-sensing pathway 26/60 KEGG 4.92416109696991e-05 7.62545237951124e-05 3760 3577.18181818182 3759 4.47661028700711e-06 2295 1.77140859600286 1.81867148419062 1 1.87618524740304 3759 4261 2939 3959 2910 3893 3132 4644 2295 3218 4339 4127 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 62/152 Reactome 0.113733389500172 0.121651372562841 2380 3485.81818181818 3760 0.0109161146687719 1982 0.751363255785682 -0.735602808874572 -1 0.176812786621525 2378 4380 3760 4261 4596 1982 2738 2934 4383 4318 2614 4128 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 29/63 Leona Saunders 0.0839184282471183 0.0902966141827776 2295 3617 3760 0.00793650793650794 2291 1.10002527352027 1.18353314588532 1 0.295486866763793 2291 3889 2940 4421 4670 3503 2704 3760 4131 4007 3471 4129 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 26/54 Arthur Liberzon 0.0402292390023854 0.0472229994902751 3760 3860.45454545455 3760 0.00372584300011673 2851 1.46719399437524 -0.954033963936557 -1 0.500356180201053 3757 3533 2851 4594 3760 4500 3247 4258 3809 3646 4510 4130 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 8/18 Leona Saunders 0.00573460171222159 0.00718896298113172 4360 3243.54545454545 3761 0.000574945422929381 260 2.73732394891741 -0.409216788386589 -1 1.50908821661172 4360 2436 4248 3058 4086 3761 3820 1868 260 3683 4099 4131 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 173/354 Broad Institute 0.0839184282471183 0.0902966141827776 3385 3586.72727272727 3761 0.00793650793650794 2121 1.05415629060656 -0.903162680930718 -1 0.283165611819632 3382 4324 3761 3334 4150 2121 3797 3326 3841 4332 3086 4132 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 0.0176000029202445 0.0212780221063637 3405 3735.81818181818 3761 0.00177409688255178 1508 0.666245690281483 0.319803316667102 1 0.28654108892373 3405 3368 4647 4167 4655 3350 1508 3045 4509 4679 3761 4133 M5336 REACTOME_CELL_CYCLE_MITOTIC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE_MITOTIC.html Genes involved in Cell Cycle, Mitotic 191/409 Reactome 0.415320710913563 0.431528348412628 2830 3828 3762 0.0476190476190476 2830 0.959339082507492 -0.804165414194531 -1 0.0900640678568702 2830 4591 3762 3669 4347 2938 3924 3729 4363 4387 3568 4134 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 13/37 Yujin Hoshida 0.0839184282471183 0.0902966141827776 4040 3753.09090909091 3763 0.00793650793650794 2922 1.11880433550562 -0.922540528839363 -1 0.300531269225671 4038 3763 2922 2967 3985 3589 4491 4267 4003 3531 3728 4135 M176 PID_FOXM1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FOXM1_PATHWAY.html FOXM1 transcription factor network 18832364 16/51 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 4455 3869.09090909091 3764 0.00793650793650794 2955 1.76111728243477 -1.60399264833737 -1 0.473068375355504 4453 4399 2955 3441 4089 4429 3751 3016 3707 3764 4556 4136 M525 REACTOME_ENDOSOMAL_VACUOLAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOSOMAL_VACUOLAR_PATHWAY.html Genes involved in Endosomal/Vacuolar pathway 17/38 Reactome 0.0839184282471183 0.0902966141827776 3905 3625 3764 0.00793650793650794 2816 1.53940347068439 -0.927869007381074 -1 0.413511955620678 3902 3597 2816 3201 3914 3410 3952 4181 3764 3372 3766 4137 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 2/10 Jessica Robertson 0.402156176920207 0.418964838827943 3530 3819.7 3767.5 0.0555555555555556 2721 0.806766939053356 0.806766939053356 1 0.0784031168216131 3528 2721 4456 NA 4336 3606 3014 3654 4372 4629 3881 4138 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 14/105 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4355 3955 3768 0.00793650793650794 3295 1.75715021854966 -2.70929878762064 -1 0.472002748816538 4354 4675 3295 3392 4620 3768 4554 3599 3495 4028 3725 4139 M16853 KEGG_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DNA_REPLICATION.html DNA replication 20/36 KEGG 0.924262982095178 0.937061084832973 2795 3853.54545454545 3770 0.209104822609494 2791 0.460683679265589 -0.460683679265589 -1 0.00334516028836352 2791 4401 3544 3780 4431 3287 3629 3751 4606 4399 3770 4140 M8229 REACTOME_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSLATION.html Genes involved in Translation 98/283 Reactome 0.0411622452793143 0.0482819227481519 3130 3519.72727272727 3770 0.00381392663097175 1604 0.513294288527814 -0.513294288527814 -1 0.173776709439966 3128 4596 3770 3728 4023 1604 2689 3863 4443 4434 2439 4141 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 10/84 Leona Saunders 0.000715405343852705 0.000965549954289683 4550 3712.18181818182 3770 6.50580080333251e-05 2249 1.40982299040621 -1.07306912562087 -1 1.09340978096194 4546 3732 2249 4404 3333 3770 4635 3638 3786 2441 4300 4142 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 5/15 Yujin Hoshida 0.0396857919178322 0.0466201105357136 3915 3711.45454545455 3770 0.00404128673167866 2770 1.02122738430962 -0.862733143443307 -1 0.349734228005931 3915 2923 4368 3675 3770 4654 3372 4115 2770 3290 3974 4143 M113 PID_NFAT_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFAT_3PATHWAY.html Role of Calcineurin-dependent NFAT signaling in lymphocytes 18832364 34/74 Pathway Interaction Database 0.0110100388989823 0.0135522810725484 3605 3894.36363636364 3771 0.00100595713699433 3272 1.27817214423097 1.4905470429287 1 0.614132209704668 3602 3719 3272 3650 3623 4439 3789 4552 3771 3971 4450 4144 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 75/217 Reactome 0.121615393493017 0.129933819860529 3440 3635.36363636364 3771 0.0117190392587688 2003 0.525483428368242 -0.525483428368242 -1 0.119791721874581 3437 4481 3771 3666 4050 2003 2842 4201 4425 4447 2666 4145 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 44/108 Jean Junior 0.0338756755153716 0.0400457657580806 4170 3529.45454545455 3771 0.00312807487050864 2237 1.34369504978259 -0.779013564172776 -1 0.482984774565999 4168 3956 3007 4181 3864 3431 3771 2237 2818 3392 3999 4146 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 5/24 Arthur Liberzon 0.399816321388077 0.416619809211592 3345 3767.36363636364 3771 0.0497706989246228 2532 1.09048240252505 -1.09048240252505 -1 0.106658929691326 3343 3771 4592 4287 4250 3542 2532 3386 4490 3302 3946 4147 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 5/16 Reactome 0.000220834082203122 0.000314728865329632 1995 3098.27272727273 3772 2.20856030734279e-05 655 0.690829886862441 0.832742822181803 1 0.622291207980899 1995 3772 4057 4590 3812 1768 655 2247 4370 4500 2315 4148 M140 PID_RANBP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RANBP2_PATHWAY.html Sumoylation by RanBP2 regulates transcriptional repression 18832364 9/19 Pathway Interaction Database 0.000379477194370613 0.000523933451037328 2010 2954.09090909091 3773 3.79542011272432e-05 1133 0.786813033209111 0.856919593754543 1 0.663956724196842 2007 4312 3899 4355 3911 1558 1198 1863 4486 3773 1133 4149 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 14/33 John Newman 0.0839184282471183 0.0902966141827776 3515 3747.72727272727 3773 0.00793650793650794 2410 1.85744894212219 1.85744894212219 1 0.498944836153335 3514 4034 3419 3773 4184 4574 3386 3666 2410 4023 4242 4150 M5415 BIOCARTA_IL4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL4_PATHWAY.html IL 4 signaling pathway 11/20 BioCarta 0.0839184282471183 0.0902966141827776 4510 3713.90909090909 3775 0.00793650793650794 2658 1.23934781777003 1.48935254676759 1 0.332911472197057 4510 2709 2658 3822 4447 3494 4405 3587 3775 3322 4124 4151 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 35/90 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4000 3740 3775 0.00793650793650794 3006 1.10069040087855 -0.84525111600662 -1 0.295665532241664 3158 4339 3185 3651 4192 3006 3688 3999 4151 3996 3775 4152 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 505/1145 Arthur Liberzon 1.98727589864402e-08 1.05897141342484e-07 4435 3125.54545454545 3775 1.98727591641571e-09 570 1.31360716449427 -0.944198765285851 -1 2.35676119182185 4433 3775 4198 2876 570 852 4134 4247 2421 4325 2550 4153 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 4/19 Leona Saunders 0.0158584214411122 0.0192370082508547 3805 3813.63636363636 3776 0.00159727416067493 3101 1.09503466667908 -1.40823202626166 -1 0.483291147926754 3802 3337 4266 3895 3673 4418 3706 3616 3776 3101 4360 4154 M11932 REACTOME_TIE2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TIE2_SIGNALING.html Genes involved in Tie2 Signaling 9/24 Reactome 0.0410587437415627 0.0481725771589792 4090 3763.45454545455 3777 0.00418376966601902 2963 0.796846259398028 -0.796846259398028 -1 0.269975680910354 4088 2963 3972 3138 3774 3238 4501 4385 4297 3777 3265 4155 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 37/89 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3710 3888.81818181818 3778 0.00793650793650794 3463 1.67992676258698 -1.29732048157563 -1 0.45125910402338 3708 4390 3463 3598 4068 3902 3568 3703 3778 4156 4443 4156 M1058 REACTOME_ADAPTIVE_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADAPTIVE_IMMUNE_SYSTEM.html Genes involved in Adaptive Immune System 293/690 Reactome 1.4878491893804e-07 4.47213681939483e-07 3780 3501.27272727273 3779 1.35259026363901e-08 1387 1.25543867257553 -1.06777897242878 -1 2.05037190567936 3779 4077 3641 4205 1387 2113 3937 4293 3371 4224 3487 4157 M10867 OHASHI_AURKB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OHASHI_AURKB_TARGETS.html Candidate substrate proteins of AURKB [GeneID=9212]. 16785988 9/17 Arthur Liberzon 0.0765897756730953 0.0871115749524574 4510 3729.09090909091 3779 0.00793650793650794 2304 1.76104859773366 -0.932154714821524 -1 0.480114274054286 4509 3572 4242 2944 4492 3779 4475 3109 3167 2304 4427 4158 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 11/22 Jessica Robertson 0.0839184282471183 0.0902966141827776 4245 3698.36363636364 3779 0.00793650793650794 2777 1.06240110068141 -0.429009571349449 -1 0.285380319895664 4245 2777 3015 4275 4000 3336 4555 2962 3779 3341 4397 4159 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 10/34 Arthur Liberzon 0.0478718938852648 0.0558445842037219 4055 3436 3779 0.00444967871372298 1651 1.57564505429413 -0.780661335244838 -1 0.507825532051179 4053 2123 1651 2759 3779 4520 4309 3170 3002 3849 4581 4160 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) 12/23 Reactome 0.0625436303263215 0.0721870570712173 3605 3782.90909090909 3780 0.00585416639951836 2261 0.51373959123257 -0.51373959123257 -1 0.150845547741746 3603 4455 3495 4250 3810 2261 3423 3780 4645 4477 3413 4161 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 10/24 Leona Saunders 0.000277514823053262 0.000390169355183794 4340 3704.54545454545 3781 2.52318032561041e-05 2907 1.60507240707094 -1.47157038893948 -1 1.40730425575969 4340 3903 2907 4501 3202 3087 4145 3754 3941 3189 3781 4162 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) 34/86 BioCarta 0.000112074492350368 0.000165203230938604 4215 3475.90909090909 3782 1.01891092875433e-05 2432 1.16026079574331 -1.29101924879327 -1 1.1286872547456 4212 2944 2726 2432 3056 3936 3981 3325 3871 3970 3782 4163 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 9/20 Jean Junior 0.000172004775778892 0.000248463125554835 4225 3323.45454545455 3782 1.72018090768702e-05 24 3.01814812808831 -0.950931996861099 -1 2.79842014383317 4225 3615 4375 2300 3138 4007 4626 2014 24 3782 4452 4164 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 15/27 Arthur Liberzon 0.101532315666763 0.108899160268815 3385 3665.18181818182 3782 0.00968592626431001 1924 0.665134846524455 -0.665134846524455 -1 0.164749100229703 3384 4307 3564 3844 4333 1924 3382 3782 4560 4685 2552 4165 M5316 MODY_HIPPOCAMPUS_PRENATAL http://www.broadinstitute.org/gsea/msigdb/cards/MODY_HIPPOCAMPUS_PRENATAL.html Genes highly expressed in prenatal hippocampus (cluster 1). 11438693 32/88 John Newman 0.0839184282471183 0.0902966141827776 3900 3674 3784 0.00793650793650794 2877 1.69366591896158 -0.661986354256962 -1 0.454949694868344 3896 4545 3276 2931 4042 2877 3054 4520 3422 4067 3784 4166 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 315/696 Leona Saunders 0.0365095602060702 0.0430183050353646 2800 3647.09090909091 3784 0.00337544610695048 2724 1.48195103303021 2.11031498384308 1 0.520826746468045 2798 4370 3323 3784 3751 3997 3906 2724 3067 4328 4070 4167 M3214 KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS.html Primary bile acid biosynthesis 9/26 KEGG 0.00012340665874911 0.000181109803601106 3790 3346.81818181818 3786 1.23413512426323e-05 1359 1.34373946026659 -1.02058662226083 -1 1.29337424208186 3786 1359 3788 2450 3089 4553 3996 4238 2768 2292 4496 4168 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 63/165 Jessica Robertson 6.05436236619454e-06 1.09624196475995e-05 4130 3429.54545454545 3786 5.50398093432763e-07 2265 1.41716107667334 -0.997191090496023 -1 1.80803870596539 4127 3786 3159 3237 2484 2524 3800 3974 2265 4133 4236 4169 M135 PID_IL5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL5_PATHWAY.html IL5-mediated signaling events 18832364 11/23 Pathway Interaction Database 0.0455188612448049 0.0531984204773061 4255 3564.54545454545 3787 0.00422626196288889 2316 1.01338664762393 -1.01338664762393 -1 0.332106620737966 4251 3107 3247 3375 4003 3844 3787 2316 4022 3896 3362 4170 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 29/68 Yujin Hoshida 0.0839184282471183 0.0902966141827776 4155 3723.90909090909 3788 0.00793650793650794 2993 1.22929739007949 -1.27688895176103 -1 0.330211741921677 3079 4263 3157 4378 4391 2993 3788 3405 4152 4154 3203 4171 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 47/120 Kevin Vogelsang 0.0303139866113443 0.035989698824616 4150 3701.45454545455 3789 0.00279453866181952 2218 1.29025477730096 -0.687262538873725 -1 0.479167730169812 4148 3789 3240 3655 4131 3270 4578 2218 3099 4186 4402 4172 M41 PID_ER_NONGENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ER_NONGENOMIC_PATHWAY.html Plasma membrane estrogen receptor signaling 18832364 29/69 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 3590 3877.90909090909 3791 0.00793650793650794 2643 1.56431494598638 1.34493481945422 1 0.420203637422484 3588 4258 2643 3720 4647 4662 3058 4446 3651 3791 4193 4173 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 108/203 Reactome 0.630426031479684 0.647419764083673 3795 3672.81818181818 3791 0.0865177249155573 1851 0.857558723936558 -0.841629500372165 -1 0.0416480461322371 1851 4284 3727 3791 4301 2800 3505 3793 4537 4366 3446 4174 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 4/20 Reactome 0.0482177331899375 0.056206044210957 2740 3525.81818181818 3792 0.00492970708020324 2455 0.471839761817384 0.471839761817384 1 0.151732287992348 2737 2924 3990 3938 3792 2787 2455 4614 4126 4467 2954 4175 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 35/74 Kevin Vogelsang 0.0141027305205894 0.0172052578025207 2940 3757.90909090909 3792 0.00129035940367916 2939 1.00200536785503 1.15181188752011 1 0.454726769960881 2939 3922 3590 4583 3649 4539 3042 3526 3857 3792 3898 4176 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 56/103 John Newman 0.0141941032821385 0.0173077200052306 4205 3637.27272727273 3792 0.00129877432268551 2449 1.31636497971839 -1.21947285488177 -1 0.596515363008291 4205 4083 2814 4053 3652 2449 3792 3883 3554 3489 4036 4177 M12645 ST_GA13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA13_PATHWAY.html G alpha 13 Pathway 28/53 Signaling Transduction KE 0.0839184282471183 0.0902966141827776 4590 3924.72727272727 3793 0.00793650793650794 3213 1.02922899850547 -0.900187483081499 -1 0.276469681333818 4588 3793 3362 3767 4361 3213 4283 4404 3913 3733 3755 4178 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 4/18 Reactome 0.0482177331899375 0.056206044210957 2740 3527 3793 0.00492970708020324 2456 0.471839761817384 0.471839761817384 1 0.151732287992348 2738 2925 3991 3939 3793 2788 2456 4615 4127 4470 2955 4179 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 14/48 Arthur Liberzon 0.0311524836906551 0.0369290509927675 4570 3851.27272727273 3793 0.0028729598008132 2114 1.85644124469857 -2.41086292074595 -1 0.684091769209278 4569 3701 2114 4542 3734 4508 3687 3926 3793 3637 4153 4180 M2920 KEGG_LINOLEIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LINOLEIC_ACID_METABOLISM.html Linoleic acid metabolism 4/62 KEGG 0.000282399612347633 0.000396323624876014 4640 3658.90909090909 3794 2.82435506060976e-05 2034 2.06181276224369 -2.26964057164696 -1 1.80416308526128 4640 3166 3794 4080 3224 4256 3962 3489 3164 2034 4439 4181 M14033 REACTOME_MRNA_SPLICING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_SPLICING.html Genes involved in mRNA Splicing 63/178 Reactome 0.562915088336031 0.579995625317203 3345 3859.09090909091 3794 0.0724781164238979 2704 0.902130308921855 -0.863979420680823 -1 0.0548953603435924 3341 4606 3753 4074 4384 2704 3513 3794 4587 4347 3347 4182 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 26/59 Kevin Vogelsang 0.0306633028227553 0.0363859805083392 4240 3786.18181818182 3794 0.00282720125761678 2687 1.06173525522244 -0.799206270618559 -1 0.393002559882765 4238 3794 3215 4463 3730 3513 4369 3969 4025 3645 2687 4183 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 3/17 Arthur Liberzon 0.0484157294443227 0.0564087787608395 4325 3409.72727272727 3794 0.00495040915079423 857 1.8175028776283 -2.67955053533241 -1 0.583734695964972 4321 2410 4619 2575 3794 4206 4461 4054 857 2821 3389 4184 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 27/62 Reactome 0.0839184282471183 0.0902966141827776 4070 3680.81818181818 3795 0.00793650793650794 2408 1.21761490798003 -0.985287520948843 -1 0.327073611725964 3795 3928 3256 3204 4066 2408 4067 4529 4098 3705 3433 4185 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 28/61 Yujin Hoshida 0.0532952605283065 0.0618784912873251 4150 3767 3795 0.00496653663688858 3260 1.13526802004255 -0.801144386137905 -1 0.35288176122576 4147 3753 3307 3260 3795 3403 4009 4256 3883 3734 3890 4186 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 8/26 KEGG 0.0100029410382965 0.0123449517264834 3625 3930.72727272727 3796 0.00100482548480216 3256 1.02435291416396 -1.29122713395692 -1 0.502854903404126 4299 3765 3796 4609 3622 3256 4129 4055 4416 3667 3624 4187 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 18/40 Reactome 0.839786298611286 0.854372252560245 2870 3833.90909090909 3798 0.153357689059927 2867 0.968282296420761 -0.968282296420761 -1 0.0170236214058115 2867 4453 3311 3850 4595 3093 3798 3596 4622 4506 3482 4188 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 276/626 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3105 3746.18181818182 3798 0.00793650793650794 2411 0.974861499762725 -0.710101332721416 -1 0.261865568268003 3103 4520 3779 4075 4157 2411 3742 3798 4023 4388 3212 4189 M20 PID_P38_MKK3_6PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_MKK3_6PATHWAY.html p38 MAPK signaling pathway 18832364 20/36 Pathway Interaction Database 0.00837658315955484 0.0103870517823959 3465 3702.72727272727 3799 0.000764422579329277 2156 1.18144226859077 -0.832209201954932 -1 0.602760703938452 3464 3799 3321 4185 3597 3939 2156 4658 3931 3614 4066 4190 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 9/19 KEGG 0.0765897756730953 0.0871115749524574 4140 3720.45454545455 3800 0.00793650793650794 2783 1.42551531359308 -0.630124968617653 -1 0.388637871295855 4136 2783 3800 3216 4240 4145 4549 3627 2811 3771 3847 4191 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 44/93 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3805 3631.63636363636 3801 0.00793650793650794 2031 1.15901982546241 -0.741257001951875 -1 0.311333891673048 3801 3886 3372 3647 4368 2031 4010 4288 3689 4149 2707 4192 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 17/76 Arthur Liberzon 0.0029705676030757 0.00380746164879998 3715 3410.63636363636 3801 0.000270416930406366 1720 1.6171993663713 -0.795096383741996 -1 1.00638338158202 3711 3801 1890 2808 4043 4303 3875 1720 3552 3819 3995 4193 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 12/26 Reactome 0.05810202498027 0.0672427979890208 2770 3798.36363636364 3802 0.00542688614554667 2770 0.657251765073594 0.748588787843166 1 0.198193238767963 2770 4175 3359 4611 3802 3951 3006 3624 4472 4483 3529 4194 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 9/23 Arthur Liberzon 0.0557726934149394 0.0645798624331276 2640 3645.36363636364 3808 0.00572239943622906 2106 0.427124623100573 0.365006975686996 1 0.130726641999993 2638 3866 4221 4612 3808 2965 2106 3278 4491 4566 3548 4195 M3494 BIOCARTA_PAR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PAR1_PATHWAY.html Thrombin signaling and protease-activated receptors 24/59 BioCarta 0.0839184282471183 0.0902966141827776 4600 3788.54545454545 3810 0.00793650793650794 2747 2.04907513469798 -1.75637337027736 -1 0.550419166359155 4600 3960 2747 3589 4624 3742 4289 4424 2860 3029 3810 4196 M5248 ST_JAK_STAT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_JAK_STAT_PATHWAY.html Jak-STAT Pathway 5/13 Signaling Transduction KE 0.026350378745387 0.0314513180847894 4625 3728.63636363636 3810 0.00266681489744193 2954 1.30266823538832 -0.739338359774914 -1 0.503392420933147 4624 3165 3885 2954 3722 3810 3927 3946 3319 3267 4396 4197 M143 PID_IL2_PI3K_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_PI3K_PATHWAY.html IL2 signaling events mediated by PI3K 18832364 26/58 Pathway Interaction Database 0.0645652700135813 0.0744470608473528 3835 3619.72727272727 3811 0.00604925692950319 2339 1.30983710379249 -1.15346258701306 -1 0.380087443060828 3834 3183 3146 2339 3811 4322 2516 4519 3826 3640 4681 4198 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 8/59 Jessica Robertson 0.0443300878909114 0.0518937776309795 4375 3868.18181818182 3811 0.00452400629213722 2326 0.997879672927458 -0.785961060969852 -1 0.329792478250163 4374 2326 4427 3811 3781 3538 4383 4433 4082 3686 3709 4199 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 22/59 Reactome 0.747929849048679 0.763905682790346 3520 3923.63636363636 3813 0.117747583652298 3288 0.185568628969767 -0.205408998803771 -1 0.00558245143990349 3519 4623 3684 4067 4196 3288 3364 3813 4592 4475 3539 4200 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 477/1119 Leona Saunders 2.40751577755452e-07 6.67156648942667e-07 3820 3542.36363636364 3814 2.18865094637738e-08 1550 1.41718891292298 -1.04072107398238 -1 2.25121856189509 3818 3814 3086 2882 1550 3240 4252 4429 3321 4165 4409 4201 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 61/115 Yujin Hoshida 2.91305439651119e-07 7.76041665835784e-07 2190 3513 3814 2.64823162021213e-08 1621 1.14990436525226 1.37600077308262 1 1.80721466473411 2190 4116 3476 4379 1621 4042 3208 3814 3759 4108 3930 4202 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 13/40 Yaara Zwang 0.0656818938332907 0.0756787200646177 3770 3661.27272727273 3814 0.00615717677973268 2651 1.31762052006641 -0.888447249664413 -1 0.379930855894649 3767 3997 3288 4505 3814 2651 3392 3924 3934 3989 3013 4203 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 5/10 Arthur Liberzon 0.00664550991016107 0.0082843467515336 4320 3892.09090909091 3815 0.000666546721917417 3285 1.34273638490263 -1.70650500449768 -1 0.718978934274083 4318 3770 4259 3815 3587 4309 3967 3438 3420 3285 4645 4204 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 11/14 Jessica Robertson 0.0135320279419818 0.0165348325778688 4305 3563.45454545455 3815 0.00123781693390256 2611 1.3298506704955 1.3298506704955 1 0.609412932041049 4303 2778 2820 3953 3644 2611 3490 3933 3945 3906 3815 4205 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 9/35 Arthur Liberzon 0.0765897756730953 0.0871115749524574 2830 3602.27272727273 3816 0.00793650793650794 2600 1.99477524996102 1.55452681568719 1 0.543835145827983 2826 4134 4120 4228 3976 3203 2600 4620 3044 3058 3816 4206 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 13/54 Jessica Robertson 0.0255746705141598 0.0305607579064311 3820 3461 3817 0.00235244568954715 2184 1.98642132604389 1.98642132604389 1 0.773990306335419 3817 4062 3017 3951 4321 3870 3177 2184 2268 3985 3419 4207 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 5/18 Arthur Liberzon 0.0104038508109333 0.0128295907631667 3920 3720.45454545455 3818 0.00104528822442947 2006 0.678915893043573 -0.678915893043573 -1 0.330359397720639 3917 3577 4151 3818 3724 3194 4272 2006 4299 4546 3421 4208 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 9/30 Arthur Liberzon 0.0765897756730953 0.0871115749524574 4410 3778.81818181818 3818 0.00793650793650794 2315 1.3824463471626 -1.34463415080541 -1 0.376895983662635 4406 3362 4542 3042 4355 4571 4013 3560 3818 2315 3583 4209 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 7/19 Reactome 0.598881260040338 0.61556428702545 3500 3869.81818181818 3819 0.0873015873015873 3239 1.63462852340934 -1.63462852340934 -1 0.0886004735347188 3497 4277 3932 4121 4270 3239 3819 3644 4448 3576 3745 4210 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 10/35 John Newman 0.232850105696956 0.245309261532359 3560 3764.90909090909 3820 0.0238095238095238 2792 1.28346955769053 1.00567966112461 1 0.201473182843296 3557 3539 2792 3820 4148 4304 3483 3985 4259 3195 4332 4211 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 16/28 John Newman 0.0731709329302799 0.0838950310034969 4470 3703.81818181818 3825 0.00688402525185432 2435 1.14308798449725 0.949193581630435 1 0.316443932696226 4469 3759 2985 3825 4181 3263 4680 2435 3864 3252 4029 4212 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 10/21 Vamsi Mootha 0.039369298721284 0.0462831243873399 3830 3916.09090909091 3826 0.00364472632359257 2590 0.348237896777569 -0.348237896777569 -1 0.119541221215089 3826 4574 3547 4485 3757 2590 3359 4080 4658 4643 3558 4213 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) 72/158 Reactome 0.0272572471404309 0.0325088979638736 4050 3531.63636363636 3827 0.00250917558878761 1490 1.00048719034462 -0.95779876450033 -1 0.382923707214514 4046 3558 3693 3032 4371 1490 3880 4448 3827 4163 2340 4214 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 2/3 Arthur Liberzon 0.728666400991399 0.744717721929268 3815 3990.3 3828 0.134920634920635 3408 0.240223581919033 -0.240223581919033 -1 0.00790934951726695 3744 3813 4227 NA 4296 3408 3843 3690 4500 4570 3812 4215 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 16/33 Kevin Vogelsang 0.378020345089557 0.394346246012837 4160 3746 3828 0.0422495164675961 2976 0.879779641268393 -0.879779641268393 -1 0.0914501426127096 4159 3762 3268 3828 4059 3106 4406 3149 4418 4075 2976 4216 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 122/283 Leona Saunders 0.597318307603006 0.614227252452861 2785 3838.90909090909 3829 0.0793650793650794 2784 0.946436171699761 -0.987021789487094 -1 0.0515287269787176 2784 4651 3686 3790 4375 2916 3829 4025 4442 4362 3368 4217 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 19/52 Yujin Hoshida 0.0839184282471183 0.0902966141827776 4255 3577.18181818182 3829 0.00793650793650794 2239 1.74584466922487 -0.654043919684771 -1 0.468965869717286 4252 3829 2239 4451 3897 2592 2929 4158 3424 3550 4028 4218 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 20/53 Reactome 0.00217998345880624 0.00282271414422935 3855 3509.72727272727 3832 0.000198376964481383 2385 1.8467858268846 -1.52931753759891 -1 1.21099327232529 3853 3929 2385 3832 3457 4509 2703 2803 2519 3956 4661 4219 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 6/11 Arthur Liberzon 0.00032613738111794 0.000454034393321054 4405 3841.09090909091 3833 3.26185255522983e-05 3043 1.67889341841696 -0.59716484701106 -1 1.4435990848485 4403 3043 4682 4083 3249 3385 4532 3566 3833 3462 4014 4220 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 30/83 Arthur Liberzon 6.34017693507373e-05 9.63361514842915e-05 3345 3780.36363636364 3834 5.76396332719714e-06 2968 1.33495030909523 1.2596394983891 1 1.37905063264447 3344 4124 3250 4249 2968 4526 3293 3889 3834 3825 4282 4221 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 9/28 Arthur Liberzon 0.0765897756730953 0.0871115749524574 2650 3684.63636363636 3835 0.00793650793650794 2648 1.64819729797034 1.99982737772359 1 0.449347636474938 2648 3968 4105 3013 4458 3835 3339 4350 4140 3057 3618 4222 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 8/17 Arthur Liberzon 0.0895310152890134 0.0962473818867439 3705 3628.90909090909 3836 0.00933569372139138 1904 0.670709517927351 0.670709517927351 1 0.175382988630846 3702 3836 4130 4229 4381 1904 3084 3262 4333 4540 2517 4223 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 10/20 Reactome 0.123907105544718 0.132261662091697 4515 3750 3837 0.011953720654139 3018 0.925175365139741 -0.971599028300519 -1 0.209072402515963 4513 3508 3018 3439 3894 3124 4062 3315 4455 3837 4085 4224 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. 8/24 SigmaAldrich 0.76527490244494 0.780600390260555 3255 3840.54545454545 3839 0.134920634920635 3078 1.12073856499897 -1.12073856499897 -1 0.0310096006059642 3251 4463 3893 4189 4312 3078 3839 3448 4501 3671 3601 4225 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 137/269 Jennifer Shepard 1.85579387370079e-08 1.01177206773572e-07 3840 3352.81818181818 3839 1.68708535395927e-09 515 1.39009625859642 1.68114652552273 1 2.50107152489377 3839 3883 3061 3198 515 3031 4002 4218 2801 3868 4465 4226 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 31/103 Jessica Robertson 0.0765570282018991 0.0871115749524574 4315 3600.72727272727 3839 0.0072144169298191 2531 1.28175173859028 1.13219183140595 1 0.349443623480374 4312 3438 3186 3952 3839 2641 4485 4103 2531 4059 3062 4227 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 10/23 Leona Saunders 0.118262851455052 0.126409608101819 2315 3588.27272727273 3842 0.011376725000468 1983 0.843962675073231 0.843962675073231 1 0.194986315753261 2312 4505 3453 4304 4555 3062 1983 4096 4327 3842 3032 4228 M648 BIOCARTA_G1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G1_PATHWAY.html Cell Cycle: G1/S Check Point 17/39 BioCarta 0.0839184282471183 0.0902966141827776 3610 3767.72727272727 3843 0.00793650793650794 2487 2.39250505000166 3.1743679111848 1 0.642670776774611 3608 4621 2578 3843 4484 4452 3998 3228 2487 3810 4336 4229 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 67/172 Arthur Liberzon 0.0805217154249528 0.0902966141827776 4620 3734.63636363636 3843 0.00760266621119663 2511 1.40627075572915 -0.824949392934686 -1 0.377750052518141 4618 3853 3573 4130 3843 2511 4078 3461 3082 4103 3829 4230 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 14/34 John Newman 0.000395742655277806 0.000545266122502734 3845 3746.54545454545 3843 3.59830782360485e-05 2404 0.922097132107686 -0.89784919273188 -1 0.774006159142816 3843 3297 3119 4020 3264 4449 3822 4265 4054 2404 4675 4231 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 25/59 Jessica Robertson 0.0839184282471183 0.0902966141827776 2935 3658.81818181818 3843 0.00793650793650794 2603 0.976682989120696 -1.08650973764671 -1 0.262354853910107 2933 4343 3602 4517 4538 2603 4072 3012 3843 4083 2701 4232 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 20/117 Arthur Liberzon 0.00378728358434817 0.00482261165115639 3970 3804.09090909091 3844 0.000344892647403896 2698 1.13701119686632 1.09813036690486 1 0.677542297122699 3970 2698 3112 4337 3516 4082 3716 4372 3844 3618 4580 4233 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 3/8 Arthur Liberzon 0.0345850806710889 0.0408431673449401 3170 3630.36363636364 3844 0.00351354319434094 1689 0.612645635217297 0.855121033419565 1 0.218863084970953 3168 3844 4256 4569 4426 2818 1689 2772 4488 4578 3326 4234 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 64/123 John Newman 0.0839184282471183 0.0902966141827776 3435 3770.36363636364 3845 0.00793650793650794 2790 1.86472111345845 2.07392421854229 1 0.500898275522163 3432 4603 2790 3149 4372 4028 3845 3789 3052 4062 4352 4235 M4732 BIOCARTA_LECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LECTIN_PATHWAY.html Lectin Induced Complement Pathway 7/15 BioCarta 0.0124616393444831 0.0152627396676026 4580 3723.81818181818 3846 0.00125320775127423 1927 1.43662705332685 -1.12591154677038 -1 0.671191294231735 4577 3544 3846 4213 3645 3897 4546 2751 3391 1927 4625 4236 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 28/67 Jessica Robertson 0.0839184282471183 0.0902966141827776 2835 3615.90909090909 3846 0.00793650793650794 2536 1.62764124126903 2.21681462348963 1 0.437214248499576 2833 4395 2661 4310 4248 4255 2536 3202 3846 3384 4105 4237 M26 PID_NFKAPPAB_ATYPICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFKAPPAB_ATYPICAL_PATHWAY.html Atypical NF-kappaB pathway 18832364 13/30 Pathway Interaction Database 0.081774653897659 0.0902966141827776 3680 3765.72727272727 3847 0.00772567901580211 3233 1.13483318825626 1.31749628524341 1 0.304836914754691 3676 3864 3233 3257 3847 4666 3313 3470 3890 3979 4228 4238 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 72/185 Jessica Robertson 0.35943518917414 0.375209021267548 3770 3886.36363636364 3848 0.0396825396825397 2983 1.21132552417785 -1.08188822759259 -1 0.132644661440176 3766 4602 2993 2983 4548 3642 4346 3848 4332 3724 3966 4239 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 88/235 Arthur Liberzon 4.54828769897182e-05 7.08553063742751e-05 3000 3646 3852 4.13489248468417e-06 2241 1.4026704530655 -1.19923754568836 -1 1.49714340542007 2997 3916 2241 4198 2894 4637 3055 4174 3852 3722 4420 4240 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 263/609 Arthur Liberzon 0.0206800446964076 0.0248861554821176 2750 3791.45454545455 3853 0.00189791226003981 2746 1.46431248822099 1.64994441135243 1 0.604154603311123 2746 4200 2848 3457 3687 4341 3853 4571 3785 3883 4335 4241 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 17/40 Jessica Robertson 2.40115839630101e-05 3.90281937047052e-05 1695 2920.54545454545 3854 2.18289509436349e-06 379 0.833748559487754 0.871178288961656 1 0.945445516603782 1692 3898 3336 4177 3854 1139 379 4227 4081 4098 1245 4242 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 230/477 Nikolaos Papanikolaou 0.0839184282471183 0.0902966141827776 2650 3781 3854 0.00793650793650794 2650 1.15003761522589 -0.799916559287557 -1 0.308921104310956 2650 4522 3737 3276 4145 3092 3854 4204 4058 4386 3667 4243 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 79/200 Jessica Robertson 0.015025866620712 0.0182649055731923 3380 3492.18181818182 3855 0.00137540768442074 1322 0.988102803178688 -0.723005459112878 -1 0.441820608194421 3377 4529 3673 4140 3855 1322 2826 3943 4047 4286 2416 4244 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 35/111 Jessica Robertson 0.0406465277517224 0.0477008838078065 3495 3854.54545454545 3856 0.00376522893730742 2944 1.09058535862881 1.09464175828446 1 0.370694877531689 3491 3856 2944 3656 3762 4619 3080 4382 4155 3999 4456 4245 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 313/722 Jessica Robertson 0.00418777079540609 0.00531236977457307 4045 3793.36363636364 3857 0.000381433060050009 2518 1.19267011908166 -0.850936759359743 -1 0.697822963679834 4042 4196 3745 3857 3525 2518 4572 3567 3158 4324 4223 4246 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 6/14 Arthur Liberzon 0.00271012370818927 0.00348412611703016 3455 3986.63636363636 3858 0.000271343453908303 3335 0.435719197768402 -0.435719197768402 -1 0.275467483166003 3454 3335 4612 4503 3491 3858 3657 3843 4361 4670 4069 4247 M19742 REACTOME_COPI_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COPI_MEDIATED_TRANSPORT.html Genes involved in COPI Mediated Transport 10/14 Reactome 0.0533573447977662 0.0619352285663444 4005 3706.81818181818 3859 0.00497246896237581 2358 0.749765037021669 0.925459298486677 1 0.232976861841586 4004 2961 3473 3899 4436 4070 3494 2358 3859 3834 4387 4248 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 14/23 BioCarta 0.0839184282471183 0.0902966141827776 2880 3396.27272727273 3860 0.00793650793650794 2069 2.14410540191132 2.14410540191132 1 0.575946049131992 2876 3935 2392 2789 4615 4144 4037 2623 2069 4019 3860 4249 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 14/25 Jessica Robertson 0.0880260987237513 0.094651284676342 4475 3881.90909090909 3860 0.00834173180960845 2914 1.08155993309569 1.34250254695503 1 0.284836244473416 4474 4271 2964 3591 3860 3560 4627 2914 4311 3636 4493 4250 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 3/19 Leona Saunders 0.0272668445387292 0.0325120695950343 3700 3807 3861 0.00276073052301007 2638 0.888020315717632 -0.888020315717632 -1 0.339868744325071 3699 2638 4253 4392 3727 4019 3230 3374 3861 4576 4108 4251 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 13/20 Reactome 0.0904303481455524 0.0971918833509309 4180 3864.27272727273 3863 0.00857968276359915 3390 0.846826254532197 -0.474577719534452 -1 0.220511808316243 3399 4176 3443 3390 3863 4422 3754 3660 4237 3983 4180 4252 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 4/12 Jessica Robertson 0.000295529779515778 0.000413388819943563 3870 3783.72727272727 3866 2.95569088906232e-05 2457 0.581919486370474 -0.769853131869617 -1 0.506460664197395 3866 3514 4345 4278 3232 2457 3777 4064 4376 4599 3113 4253 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 8/18 Reactome 0.0938296963857262 0.100799164893057 4105 3870.81818181818 3867 0.0098044219234497 3390 0.939371354104657 -1.04641466939113 -1 0.240786252697173 4105 3867 4012 3510 3877 3657 3390 3532 4505 3679 4445 4254 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 80/192 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3970 3784.09090909091 3868 0.00793650793650794 2562 1.60008147549469 -1.40201288964415 -1 0.429811187024552 3966 4479 2662 2562 4646 3533 4560 4297 3868 3393 3659 4255 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 35/68 Leona Saunders 0.0839184282471183 0.0902966141827776 4205 3711.18181818182 3868 0.00793650793650794 2081 1.6225414323066 1.63521857164992 1 0.43584434573738 4202 3381 2081 3251 3868 3918 4631 4498 3703 2724 4566 4256 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 49/107 Arthur Liberzon 1.22838271301063e-06 2.64896520624381e-06 3775 3586.72727272727 3869 1.11671218080523e-07 2087 1.78564836942066 2.17234886159807 1 2.56147016006721 3771 4152 2502 4431 2087 3961 4130 2941 2977 3869 4633 4257 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 33/76 Jessica Robertson 8.41882186008058e-07 1.89211507128717e-06 4220 3646.90909090909 3869 7.65347734704017e-08 1990 1.46308016274725 -1.64705539528022 -1 2.15374605309453 4219 4256 2695 4197 1990 3635 3430 4272 3869 3365 4188 4258 M14314 KEGG_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PURINE_METABOLISM.html Purine metabolism 77/171 KEGG 4.46176892396315e-08 1.81177202579647e-07 4220 3570.18181818182 3870 4.05615364950113e-09 872 1.37244400764745 1.78522187726286 1 2.37999126667781 4220 4331 3150 4186 872 3389 4371 3870 2999 3492 4392 4259 M2699 BIOCARTA_SODD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SODD_PATHWAY.html SODD/TNFR1 Signaling Pathway 8/15 BioCarta 0.000776468206385124 0.00104525424163191 4520 3583.54545454545 3870 7.76739646172714e-05 2471 1.1521236603189 -1.17831778778711 -1 0.883338828362954 4517 2471 3870 2662 3358 3962 4141 3738 3958 2865 3877 4260 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 30/75 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3935 3775.54545454545 3870 0.00793650793650794 2498 0.814893141105381 -0.679915385494827 -1 0.218895116236741 3931 3652 3611 4430 3870 2498 3619 4486 4024 4171 3239 4261 M15216 REACTOME_BOTULINUM_NEUROTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BOTULINUM_NEUROTOXICITY.html Genes involved in Botulinum neurotoxicity 7/20 Reactome 0.00950768818722256 0.0117399280224835 3165 3831.18181818182 3872 0.000954861309447415 3128 0.471839761817384 0.471839761817384 1 0.234274714196989 3163 3872 3923 4233 3615 3128 3147 4321 4564 4445 3732 4262 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 7/18 Reactome 0.00950768818722256 0.0117399280224835 3165 3832.18181818182 3873 0.000954861309447415 3129 0.471839761817384 0.471839761817384 1 0.234274714196989 3164 3873 3924 4234 3616 3129 3148 4322 4565 4446 3733 4263 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 72/177 John Newman 0.0839184282471183 0.0902966141827776 4190 3765.72727272727 3873 0.00793650793650794 2894 1.255486651048 -1.29774989993757 -1 0.337246660524497 4187 4114 3241 3657 4397 2894 4312 3084 4000 3873 3664 4264 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 12/47 Arthur Liberzon 0.0993058340679163 0.106559912627034 3330 3866.18181818182 3873 0.0094630785319316 3327 0.775409041305067 0.775409041305067 1 0.193944186387854 3327 3632 3401 3973 3873 3909 3735 4630 4404 3949 3695 4265 M4072 REACTOME_OLFACTORY_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OLFACTORY_SIGNALING_PATHWAY.html Genes involved in Olfactory Signaling Pathway 16/764 Reactome 0.0839184282471183 0.0902966141827776 3900 3724.81818181818 3875 0.00793650793650794 2644 1.69490660864307 1.69490660864307 1 0.45528296700348 2911 4628 3014 4621 4534 3896 3186 2644 3898 3766 3875 4266 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 5/14 Arthur Liberzon 0.663427224845798 0.680118130743253 3590 3986 3875 0.103174603174603 3284 1.03623098479302 1.03623098479302 1 0.0446220204998266 3589 3875 4250 4342 4583 4053 3681 3854 4466 3284 3869 4267 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 19/57 Jessica Robertson 0.00014110388199016 0.000205664942770105 3910 3765 3876 1.28284484492505e-05 3023 1.1215130970066 -1.02861135487304 -1 1.06354828255792 3907 3023 3219 4212 3094 4125 3709 4657 3876 3548 4045 4268 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 119/361 Arthur Liberzon 0.0447075951341102 0.0523226250745355 4180 3839.63636363636 3876 0.00414934958505674 2595 1.36450538286237 1.49035927985791 1 0.449705410714499 4176 4374 3521 3993 3773 2595 3876 4681 3505 4079 3663 4269 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 110/306 Arthur Liberzon 0.00383142583633936 0.00487484699133485 2340 3232 3877 0.000348919527106371 1469 1.40766926922721 -1.5002631199341 -1 0.837132813937763 2338 4376 3361 4528 3986 1469 3877 2021 3950 4046 1600 4270 M5940 BIOCARTA_NDKDYNAMIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NDKDYNAMIN_PATHWAY.html Endocytotic role of NDK, Phosphins and Dynamin 9/24 BioCarta 0.0943707515125551 0.1013571720348 3650 3905.36363636364 3878 0.00986356029895771 2983 0.598420109881429 0.590464452321791 1 0.153022122029363 3647 3807 3831 4462 3878 4146 2983 3428 4305 4416 4056 4271 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 122/272 John Newman 0.0839184282471183 0.0902966141827776 3110 3814.81818181818 3881 0.00793650793650794 3084 1.3619768805212 1.47547896231622 1 0.365851900559361 3107 4526 3518 3084 3881 4157 3136 4179 3836 4056 4483 4272 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 314/733 Arthur Liberzon 0.000320148153947616 0.000446094037882406 3195 3485.90909090909 3881 2.91086138186543e-05 2100 1.69828903843466 1.96939231630329 1 1.46362356136257 3193 3912 2134 2100 3231 4131 4137 4002 3033 3881 4591 4273 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 50/93 John Newman 0.0839184282471183 0.0902966141827776 2880 3852.72727272727 3882 0.00793650793650794 2880 0.990780230563175 1.13638141844388 1 0.266141633009809 2880 4016 3465 3394 4628 4446 3198 4374 3882 4257 3840 4274 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 5/19 John Newman 0.125196242936103 0.133607286358137 3090 3839.63636363636 3882 0.0132865141095765 3089 1.03788893246413 1.03788893246413 1 0.233369985694918 3089 4361 4405 4464 3907 3707 3165 3882 4329 3293 3634 4275 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 262/606 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3075 3634.27272727273 3883 0.00793650793650794 2684 1.42265192663453 2.01800512039717 1 0.382150337202648 3072 4144 3504 2684 3952 4113 3883 2847 3143 4279 4356 4276 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 10/31 Reactome 0.0839184282471183 0.0902966141827776 4460 3836.72727272727 3884 0.00793650793650794 2669 1.0819014535406 -1.13983521938104 -1 0.290618474391726 4456 3671 3144 4543 4455 3884 4262 2669 3650 3185 4285 4277 M16817 KEGG_OOCYTE_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OOCYTE_MEIOSIS.html Oocyte meiosis 55/119 KEGG 0.0505534819129044 0.058811722006919 1790 3458.36363636364 3885 0.00470490407357948 1749 0.969829847981319 1.07002697618658 1 0.306964599506629 1787 4604 3511 4381 4396 2619 1749 3885 4148 4115 2847 4278 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) 35/65 Reactome 0.0839184282471183 0.0902966141827776 3975 3687.81818181818 3885 0.00793650793650794 2119 0.797210335735319 0.779459955991294 1 0.214145188524099 3975 3408 3659 4370 3885 2119 3821 4268 4056 4225 2780 4279 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 42/93 Arthur Liberzon 3.99951839717363e-07 1.00762060264278e-06 4310 3723.54545454545 3886 3.63592647661039e-08 1753 1.21310738639402 1.20743006212041 1 1.87115784122211 4306 3790 3235 4582 1753 3646 3886 4016 3713 4125 3907 4280 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 7/33 Yujin Hoshida 0.104465941935459 0.111936015920512 4465 3555.81818181818 3887 0.0109728567355738 1077 1.3755062527093 1.43176458192039 1 0.336476912277108 4464 1077 4381 3794 3887 3013 2474 4403 4286 2687 4648 4281 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 544/1244 Jessica Robertson 6.61073258231665e-08 2.38291483697968e-07 4610 3508.72727272727 3887 6.61073277897469e-09 1102 1.43177295669253 -1.03251585327121 -1 2.4390485504701 4608 3977 4423 3528 1102 2334 4331 3887 2435 4134 3837 4282 M234 PID_IL2_STAT5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_STAT5_PATHWAY.html IL2 signaling events mediated by STAT5 18832364 17/46 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 3890 3605.18181818182 3890 0.00793650793650794 2060 1.30158334185841 -1.01338664762393 -1 0.349629082010186 3890 3352 2794 2060 4052 4379 2894 4419 3942 3371 4504 4283 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 13/35 Reactome 0.000224920106827292 0.000320162703703734 4195 3836.09090909091 3893 2.04493731948985e-05 3165 1.01169505454345 -1.18284051816847 -1 0.909388218163228 4191 3386 3225 3427 3165 4597 4356 4535 3899 3523 3893 4284 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 27/58 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4635 3852.54545454545 3894 0.00793650793650794 2849 1.33931712574428 -1.37814353191306 -1 0.359765072427509 4635 4614 2849 4610 4225 3894 3556 3119 3963 3315 3598 4285 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 11/20 Reactome 0.0839184282471183 0.0902966141827776 4550 3733.09090909091 3897 0.00793650793650794 2464 1.295991421774 -0.467943699585684 -1 0.348126989122774 4547 3333 2464 3295 4509 2990 4192 4150 3410 3897 4277 4286 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 11/44 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4030 3484.45454545455 3897 0.00793650793650794 1612 1.81446707187679 -1.92708861384412 -1 0.487399112929718 4028 3039 1612 3739 4118 4416 3367 3932 3897 1970 4211 4287 M16584 LIU_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LIU_BREAST_CANCER.html Low abundance transcripts specific for breast cancer. 18332864 20/57 Jessica Robertson 0.0839184282471183 0.0902966141827776 4190 3773.27272727273 3897 0.00793650793650794 2823 1.13605913730211 -1.21425865447462 -1 0.305166227283176 4190 3897 2868 3964 4635 3189 4504 4010 3806 3620 2823 4288 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 7/18 Pathway Interaction Database 0.284303422744802 0.298642869083645 3950 3941.09090909091 3901 0.0328966358430334 3298 0.639668653970486 -0.639668653970486 -1 0.0863547253847572 3947 3809 3901 3707 4025 3812 4066 3894 4460 4433 3298 4289 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 9/23 Jessica Robertson 5.68136047102517e-06 1.03550584080995e-05 3955 3636.63636363636 3901 5.681374996113e-07 2470 0.854470182632978 -1.03282954404147 -1 1.09558830796253 3952 2470 4553 3563 2495 3975 3106 3901 3994 3785 4209 4290 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 24/59 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3905 3528.90909090909 3901 0.00793650793650794 1741 1.46233396472019 1.37371663033256 1 0.392809664636989 4441 3323 2243 2025 3903 3550 4662 4668 3901 1741 4361 4291 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 20/44 John Newman 0.052864658195918 0.0614241974475754 4425 3562.09090909091 3902 0.00492540111083955 2253 2.11704176825003 -2.99140494957227 -1 0.659794861044543 4422 4095 2647 3902 4264 4207 3262 2507 3663 3961 2253 4292 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 7/27 Arthur Liberzon 0.0631516048150495 0.0728528853183953 4210 3783.09090909091 3904 0.0065021497356388 2423 1.75715021854966 -2.70929878762064 -1 0.514137323920945 4206 3767 4582 3904 4328 4116 4663 2423 2864 3594 3167 4293 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 13/28 John Newman 0.161385165508919 0.171020100763183 2680 3724.72727272727 3905 0.0158730158730159 2677 0.948826769229962 1.10237213414902 1 0.187177560888192 2677 4101 3079 4468 4521 3905 2834 4176 4235 3533 3443 4294 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 8/15 Reactome 0.607306722150855 0.623813963173807 2890 3725.45454545455 3908 0.0892370676576936 2814 0.460683679265589 -0.460683679265589 -1 0.0242848166831306 2890 4072 4024 3908 4497 2814 3125 3269 4580 4487 3314 4295 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 2/15 Leona Saunders 0.560513380565936 0.577902244517486 3500 3847 3908 0.0873015873015873 3010 0.473457995315835 -0.473457995315835 -1 0.0290014386229108 3500 3276 4191 NA 4261 3324 3010 4282 4445 4556 3625 4296 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 65/173 John Newman 0.0839184282471183 0.0902966141827776 3935 3915.72727272727 3908 0.00793650793650794 3106 1.48216165644226 -0.814055984215697 -1 0.398135748389955 3935 4333 3106 3453 4358 3908 3658 3817 3805 4152 4548 4297 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) 11/20 Reactome 0.0282228924954707 0.0335921956397703 4050 3983.36363636364 3910 0.00259923558452082 3343 0.927666551059246 -1.11833150214837 -1 0.351655619635359 4050 3834 3343 3903 3721 4576 3910 3997 4195 3898 4390 4298 M1051 REACTOME_INTEGRATION_OF_PROVIRUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRATION_OF_PROVIRUS.html Genes involved in Integration of provirus 5/13 Reactome 0.34314411236953 0.359002748507171 3785 4002 3910 0.0411580870073246 3356 0.484341082948553 -0.484341082948553 -1 0.0554259190622153 3784 3910 4088 4418 4055 3356 3847 3852 4422 4522 3768 4299 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 87/171 Jessica Robertson 0.35943518917414 0.375209021267548 3115 3892.36363636364 3911 0.0396825396825397 3113 0.89440975439114 -0.826943205190771 -1 0.097941147116363 3113 4528 3699 4262 4176 3125 3911 3815 4334 4317 3536 4300 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 24/59 Yujin Hoshida 0.0839184282471183 0.0902966141827776 4140 3571.63636363636 3911 0.00793650793650794 2420 2.30001394832583 -1.6036763705784 -1 0.617825960704495 4138 4220 2420 3911 3977 4084 3468 2861 2446 3498 4265 4301 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 12/24 Leona Saunders 0.973150198807518 0.982797808537075 3245 3941.45454545455 3913 0.28025863812876 2904 0.591537199317052 -0.591537199317052 -1 0.00114638472603932 3241 4458 2904 3913 4390 3498 4099 3747 4661 4583 3862 4302 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 13/32 Jessica Robertson 0.0839184282471183 0.0902966141827776 4195 3912.81818181818 3914 0.00793650793650794 2922 1.2912621939364 1.40013238583132 1 0.346856631286726 4192 3570 3013 4173 4480 3826 4571 3776 3914 2922 4604 4303 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 2/16 Jessica Robertson 0.108303997696038 0.115949859082393 4465 3977.2 3915.5 0.0126558995930024 2830 0.254582128125352 -0.310637228335091 -1 0.0612739018825175 4461 3486 4622 NA 3902 2830 3803 3424 4642 4673 3929 4304 M261 PID_P53_REGULATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P53_REGULATION_PATHWAY.html p53 pathway 18832364 43/90 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 3420 3805.09090909091 3916 0.00793650793650794 2809 1.22768045942872 1.49169556687515 1 0.329777404521767 3419 4486 3485 3916 4401 4246 3223 2809 3066 4220 4585 4305 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 27/156 Jessica Robertson 0.0314959453359084 0.0373173198088664 3940 3840.63636363636 3918 0.00290510015186618 3175 1.28603565867702 -0.956659981490784 -1 0.47239679936765 3940 4296 3234 4055 3736 4291 3602 3175 3918 4130 3870 4306 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 248/578 Jessica Robertson 0.0839184282471183 0.0902966141827776 3675 3707.18181818182 3921 0.00793650793650794 1847 0.961166505326168 -0.863495946962363 -1 0.258186840134241 3672 4198 3783 4263 4512 1847 3921 3208 3983 4380 3012 4307 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 16/32 Reactome 0.0839184282471183 0.0902966141827776 3530 3738.45454545455 3929 0.00793650793650794 2639 1.45118586597148 -1.85140898805718 -1 0.389815079666923 3530 4270 3003 4428 4189 3243 4435 2639 3929 4073 3384 4308 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 3/10 Arthur Liberzon 0.148608344200712 0.15790900247722 3375 3907.09090909091 3930 0.0159595771288797 3307 0.832328038818185 0.832328038818185 1 0.171611603513749 3375 3618 4228 4170 3930 4190 3307 3420 4368 4571 3801 4309 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 85/222 Jessica Robertson 0.0839184282471183 0.0902966141827776 3410 3776.81818181818 3931 0.00793650793650794 2651 1.53758741007514 -1.33749847065114 -1 0.413024128240623 3410 4429 2651 2934 4672 3471 4152 3686 4122 4087 3931 4310 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 19/42 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3105 3712.27272727273 3932 0.00793650793650794 2641 1.17380551631489 1.3039736155133 1 0.315305600983927 3102 3932 2836 4284 4015 4066 2641 4612 3980 3544 3823 4311 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 32/59 Jessica Robertson 0.166154486805766 0.175954785349564 2800 3796.54545454545 3933 0.0163831422676634 2796 1.07880615803634 1.12715937435018 1 0.209390917960481 2796 3991 2823 4599 3933 3824 2881 4557 4267 3916 4175 4312 M9746 SU_TESTIS http://www.broadinstitute.org/gsea/msigdb/cards/SU_TESTIS.html Genes up-regulated specifically in human testis tissue. 11904358 41/176 John Newman 2.57989432141671e-08 1.23361069287334e-07 3940 3576.90909090909 3938 2.34535850151872e-09 648 1.1953817011409 -0.82122638230843 -1 2.12426769542014 3938 4018 2924 4547 648 3882 4271 4011 3738 2824 4545 4313 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 12/33 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3900 3776.45454545455 3938 0.00793650793650794 2830 1.34207742866553 1.34207742866553 1 0.360506540710767 3067 3938 2914 4415 3898 4085 2830 4450 4096 3948 3900 4314 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 17/34 Reactome 0.0839184282471183 0.0902966141827776 3855 3873 3939 0.00793650793650794 2674 1.45118586597148 -1.85140898805718 -1 0.389815079666923 3852 4349 3097 4369 4554 3497 4647 2674 3939 4095 3530 4315 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 10/29 John Newman 0.161385165508919 0.171020100763183 3205 3616.81818181818 3939 0.0158730158730159 2446 1.46902072530826 -1.2430024094589 -1 0.289797712589687 3201 3939 2613 3830 4275 3950 3025 4294 4187 2446 4025 4316 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 40/92 Kevin Vogelsang 0.0137654263573519 0.0168156381414367 3770 3506.45454545455 3941 0.00125930171976267 1578 0.9920214811221 -0.84876651447053 -1 0.452734243855355 3769 4211 3487 4604 3941 1578 4095 2899 4125 3966 1896 4317 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 7/15 Reactome 0.0608317495260431 0.0702631447569726 3970 3724.63636363636 3942 0.00625641018410995 2414 0.929169266585641 -0.929169266585641 -1 0.275629117174502 3968 3766 3942 4277 4454 2652 3146 2414 4417 4449 3486 4318 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 5/13 Reactome 0.0634928286059114 0.0732284998393553 4590 3715.18181818182 3942 0.00653834136286831 2425 2.33341055335211 -2.33341055335211 -1 0.681409127783406 4590 4040 4010 3942 4093 4673 3178 2425 2889 3273 3754 4319 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 8/11 Arthur Liberzon 0.0497959360318134 0.0579736040360442 2015 3433.81818181818 3942 0.00509482843759976 1776 0.760648731149302 0.760648731149302 1 0.241975439777798 2012 3942 4173 4114 4178 2233 1776 3508 4465 4551 2820 4320 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 36/99 John Newman 0.0839184282471183 0.0902966141827776 3785 3808.36363636364 3944 0.00793650793650794 1943 1.63608914919599 -1.57733797019205 -1 0.439483512405181 3782 4295 1943 3602 4366 3848 4220 3762 4121 4009 3944 4321 M983 REACTOME_INTERFERON_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_SIGNALING.html Genes involved in Interferon Signaling 98/246 Reactome 0.00098222264383466 0.0013086992632952 3950 3947.54545454545 3946 8.93328587278604e-05 3301 1.39952964222596 -1.26143965587477 -1 1.03788555271105 3946 4475 3301 4324 3381 3785 4085 4241 3643 3826 4416 4322 M656 REACTOME_SYNTHESIS_OF_PE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PE.html Genes involved in Synthesis of PE 4/12 Reactome 0.40864260996829 0.425533171180312 3420 3861 3949 0.0511774387947105 3039 0.626194696717993 -0.626194696717993 -1 0.0597665743513621 3420 3811 3949 4097 4123 3367 4334 3039 4412 4451 3468 4323 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 11/41 John Newman 0.35943518917414 0.375209021267548 3625 3755.81818181818 3949 0.0396825396825397 2309 1.18028201561414 -0.838727119095698 -1 0.129245276029891 3622 3269 2309 3949 4419 4583 3694 4331 4318 2621 4199 4324 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 22/68 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3730 3829.27272727273 3952 0.00793650793650794 2155 1.68933096772845 -0.965519641245784 -1 0.453785247001374 3726 4300 2155 3387 4254 4443 3891 4004 3952 3351 4659 4325 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 17/33 Reactome 0.0839184282471183 0.0902966141827776 3695 3809.63636363636 3953 0.00793650793650794 2794 1.45118586597148 -1.85140898805718 -1 0.389815079666923 3692 4350 3082 4308 4190 3404 4527 2794 3953 4096 3510 4326 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 60/158 Kevin Vogelsang 4.95107741670772e-05 7.66207026905297e-05 4290 3648.18181818182 3954 4.5010807670068e-06 1784 1.2536017851943 -0.818411323571761 -1 1.32707987826857 4290 3954 3174 4237 2913 1784 4633 4441 3376 4001 3327 4327 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 22/65 Jessica Robertson 0.0839184282471183 0.0902966141827776 3340 3805.36363636364 3956 0.00793650793650794 2976 1.11791151649024 1.18537151167593 1 0.300291441568532 3340 4556 3460 4242 3956 4552 3103 2976 4110 3349 4215 4328 M13465 KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS.html Terpenoid backbone biosynthesis 8/17 KEGG 0.000236362812838699 0.000335330348459625 4490 3672.63636363636 3957 2.36387956923443e-05 1296 3.57235249104043 -3.57235249104043 -1 3.1926306122538 4488 4104 3803 3957 4214 4461 4429 1296 2346 3669 3632 4329 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 11/25 Jean Junior 0.0839184282471183 0.0902966141827776 4080 3767.09090909091 3958 0.00793650793650794 2516 1.85062189188428 2.39266459360977 1 0.497110964522562 4077 4131 2516 4031 3896 3924 3958 4001 3512 3335 4057 4330 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 218/530 John Newman 4.2047261244744e-05 6.58974803320637e-05 4610 3858.72727272727 3958 3.82255135363317e-06 2833 1.25007184762223 -1.23243474934137 -1 1.34439655061132 4607 4242 3593 4207 2876 2833 4441 3958 3732 4116 3841 4331 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 28/50 Arthur Liberzon 0.034822178830011 0.0411024508809651 2485 3694.54545454545 3959 0.00321689865590967 2187 0.725319176506605 0.796479107000558 1 0.258602171907018 2484 3959 3534 4132 3747 4141 2187 3968 4469 4671 3348 4332 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 81/151 Jessica Robertson 0.0246578091992229 0.0294911929319955 4355 3909.27272727273 3960 0.00226714473952392 3293 1.37649060829707 -1.16133715700628 -1 0.541814374278177 4355 3983 3293 4193 3708 3481 4397 3989 3693 3950 3960 4333 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 4/14 Arthur Liberzon 0.113237081053539 0.121175830513104 3345 3760.54545454545 3962 0.0119458367724184 2004 0.675855645033005 0.675855645033005 1 0.159339819970201 3345 3639 4262 4336 4132 3037 2004 3962 4435 4581 3633 4334 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 4/8 Jessica Robertson 0.0062987722141818 0.00786884739953504 3490 3843 3962 0.000631669730190092 2720 0.79544802733096 0.778782377178748 1 0.430501197060944 3489 2720 4460 3354 3581 4317 3618 4155 3962 4632 3985 4335 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 20/39 John Newman 0.000753639397180257 0.00101510612681422 3270 3719.36363636364 3963 6.85361536644651e-05 3069 1.36036914573101 -0.528299885934831 -1 1.04744921435303 3266 4127 3098 4367 3343 4409 3127 3069 4112 3963 4032 4336 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 6/13 Reactome 0.104483169790081 0.111936015920512 4380 3993.81818181818 3967 0.0109747593950196 3030 0.328789034457426 -0.328789034457426 -1 0.0804283479747208 4376 3512 3967 4103 3888 3030 4264 3914 4585 4457 3836 4337 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 224/539 Leona Saunders 0.00344161087921085 0.00439318675564751 4415 3973.72727272727 3969 0.000313364240745822 2945 1.42448852585319 -1.16949393801941 -1 0.863689651536413 4412 4418 2945 3665 3509 3548 4667 4376 3954 4248 3969 4338 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 70/161 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4605 3698.09090909091 3969 0.00793650793650794 2622 1.48574014371682 -0.845756649199789 -1 0.399096996083354 4605 4150 2622 3254 3969 2878 4108 3335 3350 4136 4272 4339 M963 KEGG_RNA_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_DEGRADATION.html RNA degradation 41/72 KEGG 0.470940036221457 0.48769613474779 3110 3884.18181818182 3970 0.0562345342011552 2571 0.666436886174997 -0.67159422566348 -1 0.053456766408516 3108 4663 3665 4492 4377 2571 3970 3720 4513 4319 3328 4340 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 6/17 Reactome 0.00215401639220892 0.00279294986549281 4485 3744.72727272727 3971 0.00021561071489829 2471 1.23459469095855 -1.02874112477531 -1 0.811022935439093 4481 3971 3930 4409 3467 3668 4125 2628 4033 2471 4009 4341 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 10/18 Jessica Robertson 0.580421948816113 0.597508183688995 3975 3930.72727272727 3971 0.0759185526974877 3162 0.94493713846385 -0.94493713846385 -1 0.0543601605034416 3971 4313 3271 4613 4149 3314 3531 3763 4528 4623 3162 4342 M18448 REACTOME_GLUCOSE_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_TRANSPORT.html Genes involved in Glucose transport 19/44 Reactome 0.0839184282471183 0.0902966141827776 4115 3910.18181818182 3973 0.00793650793650794 2646 1.66093129251642 1.53394616215591 1 0.446156570357789 4115 4303 2646 4299 3970 4200 3973 3839 3372 3922 4373 4343 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 4/12 Leona Saunders 9.58662535705446e-05 0.000142341338476417 4300 3822.36363636364 3976 9.58703894740174e-06 3048 1.11184518089689 -0.826684089072288 -1 1.10008878025795 4298 3114 4113 3930 3048 3652 4016 3976 4446 3096 4357 4344 M15109 BIOCARTA_GLYCOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLYCOLYSIS_PATHWAY.html Glycolysis Pathway 13/35 BioCarta 0.234079676894378 0.246549194409318 3765 3763.18181818182 3977 0.0239518654410988 2760 1.29304160142445 -1.29304160142445 -1 0.20224750346551 3765 4630 3156 4484 4279 2793 4041 2760 4399 3977 3111 4345 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 6/28 John Newman 0.147859119791321 0.157148522418265 3835 3946.90909090909 3977 0.0158730158730159 3353 1.9683837287308 1.9683837287308 1 0.406908375430133 3833 3909 4410 4046 4399 4465 3365 3353 4205 3454 3977 4346 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 190/395 Kate Stafford 0.0839184282471183 0.0902966141827776 2340 3773.18181818182 3979 0.00793650793650794 2339 1.09804066688559 -0.80097114673183 -1 0.294953764812181 2339 4523 3729 3789 4102 3052 3979 4031 4048 4375 3538 4347 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 79/153 Leona Saunders 0.912207156538424 0.925839882074736 3325 3958.63636363636 3980 0.198412698412698 3266 0.969958809432538 -1.02001979369223 -1 0.00834872617073822 3324 4531 3642 3608 4449 3266 3980 4040 4548 4340 3817 4348 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 3/9 Jessica Robertson 0.215558788431648 0.227707051981673 3755 3927.09090909091 3980 0.023986015906435 2829 0.194425671732856 -0.194425671732856 -1 0.0321370513762331 3752 4364 4323 4417 3980 2829 3156 3964 4669 4596 3148 4349 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) 14/22 Reactome 0.0839184282471183 0.0902966141827776 3375 3777 3981 0.00793650793650794 2844 1.00051861067692 -1.11833150214837 -1 0.268757541549799 3371 4224 3384 4119 3981 4052 2844 4023 3682 3629 4238 4350 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 5/14 Arthur Liberzon 0.368793439247142 0.384806514431554 2385 3771.90909090909 3981 0.0449697002720921 2381 0.299914212338121 0.369572563121284 1 0.0319953726664458 2381 4190 4503 3974 4479 2892 2481 3981 4547 4639 3424 4351 M18919 LIU_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LIU_LIVER_CANCER.html Low abundance transcripts specific to hepatocellular carcinoma (HCC). 18332864 20/62 Jessica Robertson 0.00506889029336814 0.00638173560309595 4440 3683.63636363636 3982 0.000461873366936865 2652 1.58222183260549 1.52169264242104 1 0.893331380777188 4436 4165 2652 4407 3545 4060 3982 4627 2840 3148 2658 4352 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 81/218 Reactome 0.0839184282471183 0.0902966141827776 4475 3890.54545454545 3984 0.00793650793650794 2589 1.17240351837896 -0.530488869411046 -1 0.314928998476035 4472 4530 3778 3340 4140 2589 3984 4475 3668 4381 3439 4353 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 9/16 Reactome 0.70512582230239 0.721445328233406 2840 3816.09090909091 3987 0.11495842085276 2837 0.460683679265589 -0.460683679265589 -1 0.01680202917818 2837 4275 3987 4301 4432 2939 3161 3511 4602 4462 3470 4354 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 47/104 Leona Saunders 0.161385165508919 0.171020100763183 4480 4049.27272727273 3987 0.0158730158730159 3435 1.18460797601509 -1.29013083819763 -1 0.233690794896258 4479 4660 3435 4382 4349 3987 3504 3766 4240 3803 3937 4355 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 4/14 Reactome 0.045266760557854 0.0529241616701856 3835 3929 3989 0.00462161809852038 2969 0.286725308515504 -0.278199738870271 -1 0.0941308885887492 3831 2969 3989 3572 3785 4010 3536 4106 4578 4466 4377 4356 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 395/1027 Arthur Liberzon 0.00316234851271551 0.00404442279764871 3990 3875.27272727273 3989 0.000287900303612712 2918 1.58143459558449 -1.38828762093283 -1 0.973461009301348 3989 4588 2918 3275 3502 3762 4428 4119 3642 4060 4345 4357 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 3/9 Arthur Liberzon 0.0188262985623916 0.0227078597331705 3545 3924.45454545455 3990 0.00189877198785313 2894 0.78070960419701 0.78070960419701 1 0.330098228409854 3544 2894 4193 4566 3688 3837 3065 4386 4449 4557 3990 4358 M4791 BIOCARTA_EIF4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF4_PATHWAY.html Regulation of eIF4e and p70 S6 Kinase 21/39 BioCarta 0.0839184282471183 0.0902966141827776 3995 3704.81818181818 3991 0.00793650793650794 2714 1.20632056863715 1.20632056863715 1 0.324039743834644 3300 4344 3492 3325 4639 4029 2856 2714 3991 3991 4072 4359 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 23/82 John Newman 0.0664627185894948 0.0765219408624994 2975 3724.36363636364 3991 0.00623271188907335 2772 1.32640580684397 1.09887700489961 1 0.380822267428957 2974 4161 2796 4413 3820 4211 2772 4426 4004 3400 3991 4360 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 2/12 Arthur Liberzon 0.00247657936690326 0.00319615833470357 3995 3700 3991.5 0.000275478844547364 1860 0.815938877969851 -0.815938877969851 -1 0.523710627476611 3995 1860 4623 NA 3492 3318 4676 3988 4244 4674 2130 4361 M10994 BIOCARTA_SRCRPTP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SRCRPTP_PATHWAY.html Activation of Src by Protein-tyrosine phosphatase alpha 9/18 BioCarta 0.319608281851078 0.334752885282555 3090 3920.63636363636 3992 0.037776627243023 2927 0.888632650572132 0.888632650572132 1 0.108633978577877 3090 4462 3810 4314 4590 3992 3261 2927 4646 4408 3627 4362 M82 PID_RET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RET_PATHWAY.html Signaling events regulated by Ret tyrosine kinase 18832364 28/63 Pathway Interaction Database 0.161385165508919 0.171020100763183 3175 3816.63636363636 3992 0.0158730158730159 3107 0.928309908929494 1.05501143564521 1 0.183130141090497 3175 4157 3571 3992 4297 3906 3107 3260 4214 4138 4166 4363 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 20/39 Reactome 0.0839184282471183 0.0902966141827776 3765 3922.81818181818 3993 0.00793650793650794 3042 1.45118586597148 -1.85140898805718 -1 0.389815079666923 3761 4563 3310 4318 4351 3557 4421 3042 3993 4160 3675 4364 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 21/68 Arthur Liberzon 0.0122924998730976 0.015059517491591 4130 3834.18181818182 3993 0.00112379330442141 2776 0.899852340654533 -0.76459220474643 -1 0.421757803609809 4129 4301 3406 4311 3635 2776 4418 3796 4057 3993 3354 4365 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 22/51 Vamsi Mootha 0.0839184282471183 0.0902966141827776 3355 3814.90909090909 3993 0.00793650793650794 2954 1.26123824019488 -1.14039199150883 -1 0.338791643467462 3996 3993 3050 4357 4335 2954 4558 4145 3873 3352 3351 4366 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 7/13 Leona Saunders 0.435369722646862 0.45165873817206 4650 3917.54545454545 3995 0.0555555555555556 2851 0.611341372788498 0.611341372788498 1 0.0542798263411733 3204 3483 4197 3379 4648 3995 2851 4646 4386 4560 3744 4367 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 46/102 Leona Saunders 0.0839184282471183 0.0902966141827776 3820 3831.36363636364 3999 0.00793650793650794 2807 0.853395874674824 -0.878754774334823 -1 0.229237660723692 3820 4291 3657 4433 4649 2807 3999 3061 4123 4077 3228 4368 M6831 BIOCARTA_KREB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KREB_PATHWAY.html The Citric Acid Cycle 4/11 BioCarta 0.658630986444922 0.675496783208777 4005 4030.63636363636 4002 0.101904728714135 3259 0.19315705984134 -0.253062571077161 -1 0.00846464125343722 4002 4643 3879 4549 4313 3486 3259 3279 4649 4428 3850 4369 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 22/48 BioCarta 0.0839184282471183 0.0902966141827776 4005 3835.18181818182 4003 0.00793650793650794 2836 1.01789246751844 -0.869005328336052 -1 0.273424479988578 4003 4555 3461 2836 4356 3017 4594 4047 4144 3740 3434 4370 M787 REACTOME_POL_SWITCHING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POL_SWITCHING.html Genes involved in Polymerase switching 7/14 Reactome 0.915509204151471 0.928788943635808 3540 4044.54545454545 4004 0.218946217238382 3377 0.238618036497475 -0.317192676797178 -1 0.00196892565787162 3536 4510 4004 4248 4602 3377 3757 3622 4621 4478 3735 4371 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 8/32 Arthur Liberzon 0.275742742869669 0.289715357194454 3685 3986 4004 0.0317460317460317 2776 1.09496761871584 -1.46370832723374 -1 0.151532092660529 3682 4004 4680 4107 4546 3604 2776 3784 4290 3691 4682 4372 M505 REACTOME_CTNNB1_PHOSPHORYLATION_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CTNNB1_PHOSPHORYLATION_CASCADE.html Genes involved in Beta-catenin phosphorylation cascade 6/18 Reactome 0.443794611584386 0.46019507631875 4005 3992.36363636364 4005 0.0569743204243394 2578 0.458886920693445 -0.458886920693445 -1 0.0397838416914054 4005 4408 3915 4553 4593 2578 3964 3582 4648 4441 3229 4373 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 34/80 Kevin Vogelsang 4.59140245413665e-05 7.14654710633222e-05 4620 3742.36363636364 4005 4.17408934505175e-06 1925 1.83569563124232 -1.41241169075659 -1 1.95757554290304 4620 4122 1925 4472 2896 3820 4086 4005 3734 3408 4078 4374 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 8/30 Arthur Liberzon 0.0765897756730953 0.0871115749524574 4665 3939.18181818182 4006 0.00793650793650794 2893 2.29269478264214 -2.41599585399329 -1 0.625056915617368 4662 3868 4613 3817 4006 4353 4034 3832 3234 2893 4019 4375 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 10/22 Reactome 0.0498377423028763 0.0580078639918725 4420 3877.81818181818 4009 0.00463671811406346 2341 0.894460571005017 -0.55732575511993 -1 0.284484294388186 4416 4133 3220 2341 3786 3592 4569 4578 4009 3836 4176 4376 M3656 REACTOME_UNWINDING_OF_DNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNWINDING_OF_DNA.html Genes involved in Unwinding of DNA 6/11 Reactome 0.991385645736031 0.9964130389196 3595 4022.54545454545 4009 0.378383873458798 3320 0.292190479908332 -0.292190479908332 -1 0.00011707500513314 3595 4009 4084 3320 4418 3756 3965 3913 4618 4517 4053 4377 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 3/12 Jessica Robertson 0.000158373846555411 0.000229622476781762 2065 3147.90909090909 4009 1.58385134711541e-05 608 0.547219992970305 0.547219992970305 1 0.512201447741908 2062 3003 4357 4217 4009 1349 608 4153 4432 4603 1834 4378 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 7/16 Reactome 0.141228350282881 0.150408193051268 3555 3989.27272727273 4011 0.0151099047906153 2921 0.550461404809974 0.590464452321791 1 0.11648803307919 3553 2921 4011 3819 3922 4607 4423 3759 4301 4484 4082 4379 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 15/37 Reactome 0.0610298491023327 0.0704745867160008 3605 3919.36363636364 4012 0.00570833504667848 2997 0.929942834708671 -0.991114336297086 -1 0.27554644832997 4012 3601 2997 4618 3806 4450 3604 3603 4229 4051 4142 4380 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 22/48 Reactome 0.10368124044736 0.111127697332189 4450 3761 4013 0.00990148798008159 2347 0.923174076745595 -0.934071793722407 -1 0.226574555162576 3434 4449 3524 4557 4450 2347 4413 3442 4274 4013 2468 4381 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 8/29 John Newman 0.0765897756730953 0.0871115749524574 4155 3893.81818181818 4014 0.00793650793650794 2753 1.87242892903573 1.57465690552939 1 0.510479881662046 4151 2753 4414 3923 4014 4545 3869 4677 2946 2887 4653 4382 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 18/30 Reactome 0.991020386029178 0.9964130389196 3135 3954.45454545455 4016 0.348472854311567 3131 0.460683679265589 -0.460683679265589 -1 0.000184710100558798 3131 4570 3355 3331 4413 3653 3909 4042 4640 4439 4016 4383 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 8/20 Reactome 0.269245961595581 0.283143307010075 3910 3863.63636363636 4016 0.0308809682597126 2847 0.865031143631162 -0.865031143631162 -1 0.121928501840921 3910 4360 4090 4241 4016 2847 3786 3009 4346 4524 3371 4384 M37 PID_NFKAPPAB_CANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFKAPPAB_CANONICAL_PATHWAY.html Canonical NF-kappaB pathway 18832364 17/38 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 4560 3944.81818181818 4017 0.00793650793650794 3369 1.34975004764276 -1.34975004764276 -1 0.362567547702915 4558 3933 3376 3508 4369 4243 4290 4017 4030 3369 3700 4385 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 8/15 Reactome 1.73571761115265e-05 2.89450986685455e-05 4585 3701.63636363636 4019 1.735731168522e-06 2211 1.05903183979478 -1.33479774031212 -1 1.2362684645637 4581 2211 4055 3120 2722 4163 4019 4414 4181 3681 3571 4386 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 58/137 Jessica Robertson 0.0839184282471183 0.0902966141827776 4155 3859.81818181818 4020 0.00793650793650794 2379 1.48909324371931 -0.78130520369082 -1 0.39999770059781 4154 4534 3459 3524 4090 2379 3871 4485 3723 4219 4020 4387 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 38/88 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 4575 3845.09090909091 4021 0.00793650793650794 2718 0.958013796591916 -0.882108270325178 -1 0.257339964410999 4571 4021 3445 4602 4675 2889 3114 4312 4035 3914 2718 4388 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 14/37 Arthur Liberzon 0.698152987361708 0.714467110455769 4475 3864.45454545455 4021 0.103174603174603 2741 0.977089230704963 0.977089230704963 1 0.0366974650625289 2741 4569 3022 4471 4398 3720 3328 4060 4473 4021 3706 4389 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 16/34 Reactome 0.157618006361755 0.167406613284493 3170 4012 4022 0.0154719416662538 3166 0.657251765073594 0.748588787843166 1 0.131225642060417 3166 4561 3398 4375 3925 4573 3395 3705 4531 4481 4022 4390 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 34/133 Leona Saunders 0.0839184282471183 0.0902966141827776 4210 3894.09090909091 4025 0.00793650793650794 2840 1.19957874504038 -0.7788764133935 -1 0.322228765651835 4210 4025 3387 4297 3892 2840 4322 4330 3754 4113 3665 4391 M4217 REACTOME_MITOTIC_PROMETAPHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_PROMETAPHASE.html Genes involved in Mitotic Prometaphase 57/108 Reactome 0.922476804815061 0.935655044883847 3295 3972.45454545455 4027 0.207427057043824 3280 0.937965819246001 -0.916158259030895 -1 0.0069684033560235 3294 4538 3522 3859 4456 3280 4083 4027 4555 4297 3786 4392 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 69/152 John Newman 0.0839184282471183 0.0902966141827776 4290 3494 4027 0.00793650793650794 1502 1.8970543154641 1.94092202198445 1 0.50958357002329 2067 4289 1502 2524 4486 4287 3550 4400 4027 3116 4186 4393 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 46/117 Arthur Liberzon 0.63389956273523 0.650559209587667 4320 4035.27272727273 4027 0.0873015873015873 3283 0.773353958674898 -1.02528473084838 -1 0.0371406464574495 4319 4540 3756 3723 4285 3283 4027 3993 4456 4335 3671 4394 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 7/11 Reactome 0.481063017846562 0.497959200713274 4155 4071 4029 0.0634920634920635 3386 0.595240301241523 -0.595240301241523 -1 0.0463611110166647 4152 3481 4029 4496 4584 3386 3782 4012 4398 4490 3971 4395 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 11/29 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3370 3792.27272727273 4030 0.00793650793650794 2791 1.43764790722844 -1.14949808925226 -1 0.386178534217239 3367 4181 2791 4592 4524 4209 2904 4045 3740 3332 4030 4396 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 105/262 Arthur Liberzon 0.232850105696956 0.245309261532359 2990 3865.54545454545 4030 0.0238095238095238 2989 1.20151695477506 -1.13427024647696 -1 0.188608624305726 2989 4655 3214 3152 4507 3531 4180 4030 4276 4301 3686 4397 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 30/92 Leona Saunders 0.0839184282471183 0.0902966141827776 2785 3917.81818181818 4034 0.00793650793650794 2782 1.32644685693165 1.49881103780624 1 0.356307880809838 2782 4668 3493 3518 4660 4423 3295 4020 4114 4034 4089 4398 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 6/14 Jessica Robertson 0.3081082136534 0.322996664246047 4035 3882.18181818182 4034 0.036162504168484 3059 1.18069291469542 -1.59486697271216 -1 0.149053203629541 3574 3576 4317 4034 4035 3726 3059 4186 4447 3452 4298 4399 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 8/26 Jessica Robertson 0.0456062970244802 0.0532679730450434 4380 3865.63636363636 4034 0.00465702289472915 2889 1.09932949444631 1.14255761188363 1 0.360111339648508 4380 3605 4495 4101 3787 4034 3811 2903 4251 2889 4266 4400 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 22/62 Jessica Robertson 0.991542745017933 0.9964130389196 3750 4019.81818181818 4035 0.35201297278845 3091 1.0476812132427 -1.0476812132427 -1 0.000420337617732282 3750 4626 3091 3456 4666 3827 4035 3865 4643 4188 4071 4401 M2064 BIOCARTA_41BB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_41BB_PATHWAY.html The 4-1BB-dependent immune response 10/25 BioCarta 0.528261683549455 0.545971382689181 3925 3918.45454545455 4036 0.0660223828850958 3150 0.639668653970486 -0.639668653970486 -1 0.0432440884987207 3921 4036 3407 4058 4112 3150 4563 3693 4414 4427 3322 4402 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 9/20 Leona Saunders 0.303037401682437 0.317823022444919 3125 3772.63636363636 4037 0.0354584353511695 2385 0.905258237621621 -0.837658082304428 -1 0.115914574306673 3124 4037 4142 4344 4560 3338 2385 3294 4516 4545 3214 4403 M17406 BIOCARTA_CYTOKINE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CYTOKINE_PATHWAY.html Cytokine Network 8/34 BioCarta 0.0765897756730953 0.0871115749524574 4165 3816.36363636364 4038 0.00793650793650794 2722 2.14843646305736 -1.59486697271216 -1 0.585727785640315 4163 4038 3826 4171 3962 3472 4394 4308 2722 2863 4061 4404 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 3/9 Leona Saunders 0.0171975438358592 0.020818313204556 4285 3722 4038 0.00173321017233122 2112 3.11153501080228 -3.11153501080228 -1 1.34581154649039 4445 3274 4273 3420 3754 4253 4285 2112 4283 2805 4038 4405 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 7/11 Arthur Liberzon 0.550069217913139 0.568008892715066 2685 3731.18181818182 4039 0.0767600885874392 2685 0.853296384175686 -0.853296384175686 -1 0.053914373619979 2685 4039 4210 4112 4230 2735 3351 3319 4619 4563 3180 4406 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 37/100 Reactome 0.0839184282471183 0.0902966141827776 4055 3855.90909090909 4040 0.00793650793650794 2658 0.989686427948178 -0.893612385531751 -1 0.26584781745032 4051 4389 3587 4523 4122 2658 4175 3610 3711 4040 3549 4407 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 48/93 Signaling Gateway 0.0839184282471183 0.0902966141827776 2940 3853.63636363636 4044 0.00793650793650794 2940 1.07590021927717 1.11410205956063 1 0.289006432165317 2940 4435 3565 4526 4511 4044 3101 2975 4117 4197 3979 4408 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 7/24 Reactome 0.214139132665174 0.226258393611952 3920 3950.09090909091 4045 0.0238095238095238 2777 0.799638355827031 -0.710644061081929 -1 0.13274476614292 4086 3839 3918 4360 4045 2777 3916 4390 4271 4442 3407 4409 M17370 BIOCARTA_RANMS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RANMS_PATHWAY.html Role of Ran in mitotic spindle regulation 6/15 BioCarta 0.795268132860435 0.810136189257391 3620 4034.54545454545 4047 0.146666992587309 3489 0.646599912118248 -0.646599912118248 -1 0.0152080590986667 3620 4233 3865 4047 4242 3489 4203 3834 4629 4425 3793 4410 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 57/116 Arthur Liberzon 0.557443745451391 0.574863862496747 3535 3829.90909090909 4048 0.0714285714285714 2754 1.07303034790398 -0.996097241468059 -1 0.0663600903858841 3531 4536 2754 3082 4289 3301 4329 4144 4421 4048 3694 4411 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 152/406 Jessica Robertson 0.0839184282471183 0.0902966141827776 3265 3950.63636363636 4050 0.00793650793650794 3209 1.38624321836203 1.59154762682437 1 0.37237028653841 3262 4423 3353 3209 4541 4050 3583 4506 3825 4169 4536 4412 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 38/92 Reactome 0.232850105696956 0.245309261532359 3400 3880.18181818182 4052 0.0238095238095238 3073 1.1691013779997 -1.34188863006625 -1 0.183520169880602 3398 4612 3635 4204 4589 3073 4052 3144 4263 4306 3406 4413 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 5/17 Arthur Liberzon 0.11891131184528 0.127073753091672 3505 4010.18181818182 4054 0.012579902151185 2879 0.889425699239832 0.889425699239832 1 0.204969312924022 3504 3842 4225 4349 3901 3979 2879 4495 4316 4568 4054 4414 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 15/32 Kate Stafford 0.232850105696956 0.245309261532359 4465 3899.54545454545 4054 0.0238095238095238 2889 1.41008782746642 1.72263794776283 1 0.221349160975899 4462 4172 2889 3644 4496 3232 4103 3551 4258 4054 4034 4415 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 14/55 Jessica Robertson 0.466738071388703 0.483451503653285 4645 4076.81818181818 4054 0.0555555555555556 2479 1.20911467308818 1.39679893634915 1 0.098167338889378 3973 4000 2479 3713 4330 4645 4054 4597 4387 4025 4642 4416 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 15/38 Arthur Liberzon 0.878859116702268 0.892766924098597 3740 4059.45454545455 4055 0.174603174603175 3512 0.888883903800962 0.888883903800962 1 0.011262809162872 3737 4226 3512 3987 4644 3868 3670 4142 4524 4055 4289 4417 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 11/37 Kevin Vogelsang 0.603534685737553 0.620075320624024 4060 4082.09090909091 4058 0.0806662587549397 3381 0.447782864287783 -0.484341082948553 -1 0.0239054342408203 4058 3940 3381 3841 4141 3596 4597 4243 4626 4612 3868 4418 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 7/20 Reactome 0.147859119791321 0.157148522418265 4530 4048.18181818182 4059 0.0158730158730159 3562 1.07378519301828 -1.07378519301828 -1 0.221975009748013 4527 3735 4059 3765 4502 3562 4225 4666 4202 3579 3708 4419 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 5/13 Reactome 0.990368673030401 0.996321941137926 4030 4170.18181818182 4060 0.371408342792295 3649 0.175545807824083 -0.175545807824083 -1 7.20454242975487e-05 4027 4513 3974 3649 4427 3706 3976 4416 4665 4459 4060 4420 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 281/743 Leona Saunders 0.0839184282471183 0.0902966141827776 3980 3952.90909090909 4062 0.00793650793650794 3120 1.16024804071076 -1.01254730896874 -1 0.311663812945333 3980 4647 3701 3461 4062 3120 4218 4109 4091 4331 3762 4421 M105 PID_TELOMERASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TELOMERASE_PATHWAY.html Regulation of Telomerase 18832364 41/89 Pathway Interaction Database 0.00523614164737805 0.00658346116437176 4430 3953.18181818182 4064 0.000477149607827331 3371 1.11653618139154 -0.967595216579327 -1 0.626521042232716 4427 4488 3507 4064 3548 3739 4174 3371 4072 4109 3986 4422 M4495 COLLIS_PRKDC_SUBSTRATES http://www.broadinstitute.org/gsea/msigdb/cards/COLLIS_PRKDC_SUBSTRATES.html Substrates of PRKDC [GeneID=5591]. 15592499 16/40 Jessica Robertson 0.232850105696956 0.245309261532359 4120 3881.45454545455 4064 0.0238095238095238 3307 0.820361902501287 -0.817782490623201 -1 0.12877658349887 4116 3600 3408 3515 4064 3452 4486 4394 4280 4074 3307 4423 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 8/31 Reactome 0.0218384221403079 0.026239704140893 4225 3975.54545454545 4065 0.00220560507645902 3278 0.93019663602881 -0.98081006321927 -1 0.378282594522373 4221 3764 4065 3963 3701 3278 4139 4261 4147 4501 3691 4424 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 54/112 Jean Junior 0.0839184282471183 0.0902966141827776 4690 4029.90909090909 4065 0.00793650793650794 3277 1.10662441180585 1.15088943749705 1 0.297259517039936 4686 4151 3277 4065 3867 3799 4251 4046 4143 4102 3942 4425 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 105/226 Leona Saunders 0.161385165508919 0.171020100763183 3380 3825.09090909091 4068 0.0158730158730159 2771 0.863004750807663 -0.863037942112622 -1 0.170247205494944 3380 4146 3710 4068 4142 2771 4097 3649 4233 4352 3528 4426 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 562/1243 Arthur Liberzon 0.0144654837353721 0.0176059925322505 4370 3970.81818181818 4068 0.00145605181528586 3073 1.5935304033221 -1.02506909473971 -1 0.719072289167177 3453 4367 4649 3274 3661 3931 4068 4188 3073 4368 4647 4427 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 60/160 John Newman 0.0839184282471183 0.0902966141827776 3760 3998.27272727273 4069 0.00793650793650794 3140 0.882544478302403 -0.720536949262782 -1 0.237067513354987 3758 4335 3730 4069 4472 3140 3773 3960 4101 4269 4374 4428 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 28/90 Arthur Liberzon 0.146717879900967 0.156219037767764 3480 3811.18181818182 4070 0.0143205663324625 2075 0.661285978477734 -0.661285978477734 -1 0.13714048960359 3476 4447 3648 4070 4260 2075 3633 4445 4549 4536 2784 4429 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 10/36 Kevin Vogelsang 0.0839184282471183 0.0902966141827776 4070 4113.90909090909 4070 0.00793650793650794 3188 1.05031244272929 -0.667424733187487 -1 0.282133083373306 3924 4069 3188 4538 4518 4513 4151 3965 4070 3847 4470 4430 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 9/37 Arthur Liberzon 0.00253928361729175 0.00327617924852125 4075 3679.90909090909 4071 0.000254218987484226 1704 1.2714212954868 -1.17917232433546 -1 0.812550180136371 4071 2850 4559 4211 3963 4090 4458 1704 3648 2316 4609 4431 M977 REACTOME_KINESINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KINESINS.html Genes involved in Kinesins 16/32 Reactome 0.912207156538424 0.925839882074736 3865 4090.72727272727 4072 0.198412698412698 2804 0.916336367095971 -1.0730550366364 -1 0.00788716993077311 3864 3965 2804 3770 4565 4622 3861 4248 4542 4072 4685 4432 M14663 REACTOME_ETHANOL_OXIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ETHANOL_OXIDATION.html Genes involved in Ethanol oxidation 4/13 Reactome 0.251933792323264 0.265175595423813 3680 4101.54545454545 4073 0.0286091603834348 3574 0.744555506014308 -0.753966422615484 -1 0.110399972002226 3678 4189 4073 4539 4004 3574 4593 3772 4517 4505 3673 4433 M228 PID_SMAD2_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SMAD2_3PATHWAY.html Regulation of cytoplasmic and nuclear SMAD2/3 signaling 18832364 10/22 Pathway Interaction Database 0.891073518496821 0.904978436860881 4525 4076.63636363636 4074 0.182539682539683 3185 0.800907189747059 -0.594906206811403 -1 0.00893259174889403 4010 3905 3299 4473 4523 4486 3185 4074 4533 3833 4522 4434 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 333/805 Jessica Robertson 0.0839184282471183 0.0902966141827776 3270 4089.90909090909 4075 0.00793650793650794 3269 1.16498134516355 -0.955936557612478 -1 0.312935265835421 3269 4590 3767 4564 3959 4075 3692 4481 3687 4378 4527 4435 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 40/80 John Newman 0.514011397665828 0.531360558010604 3890 3942.45454545455 4077 0.0634920634920635 3144 1.18976691824768 -0.949861690019753 -1 0.08403823198397 3888 3857 3148 3144 4376 3788 4268 4225 4405 4191 4077 4436 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 6/19 Reactome 0.660616360224621 0.677384740484152 3775 4107.54545454545 4078 0.10242842551677 3436 0.484341082948553 -0.484341082948553 -1 0.0210743922472637 3775 4234 4078 4551 4175 3436 4069 3935 4593 4509 3828 4437 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 32/80 Jean Junior 0.0839184282471183 0.0902966141827776 3135 3967.90909090909 4078 0.00793650793650794 3132 0.870850724416406 -0.5635054960209 -1 0.233926355349485 3132 4549 3645 3852 4075 4427 3352 4078 4157 4196 4184 4438 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 4/24 Arthur Liberzon 0.161824627403615 0.171447027812195 4445 4092.45454545455 4080 0.0174978947786022 3354 0.46750111935984 -0.247928191512072 -1 0.0920948653850108 4443 3676 4153 4035 3943 3915 4376 3354 4495 4547 4080 4439 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 159/356 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3005 3874.09090909091 4081 0.00793650793650794 2834 1.47883583957627 1.85237628875325 1 0.397242372629247 3005 4422 2834 3033 4164 4348 3919 4652 3655 4081 4502 4440 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 3/12 Jessica Robertson 0.00513253740704418 0.00645839696278438 3905 3952.36363636364 4081 0.000514443040785973 2541 0.787745202159886 0.787745202159886 1 0.443714504020202 3904 2541 4359 4081 3557 4567 4363 3248 4287 4604 3965 4441 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 6/16 Jessica Robertson 0.117996130788865 0.126153289727726 4085 4129 4082 0.0124773873790997 3455 1.32245865772813 -1.98165617905692 -1 0.305836400408941 4414 4410 4505 4465 3900 3942 4082 4082 4231 3455 3933 4442 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 8/14 Jessica Robertson 0.0128564644135085 0.015733975513633 3790 3895.09090909091 4083 0.00129314556535111 2611 0.92288133879708 0.92288133879708 1 0.42803469234528 3787 4461 4343 4577 3650 4312 2611 2965 4083 4598 3459 4443 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 25/72 Jessica Robertson 3.00133051258539e-06 5.83336158522403e-06 4100 3833.90909090909 4084 2.72848600648343e-07 2316 0.966213144315036 -0.743532349470392 -1 1.30080442922847 4098 4217 3510 4479 2316 3543 4260 3594 3644 4084 4428 4444 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 8/19 Kevin Vogelsang 0.429292702193493 0.445847872889785 3790 3975 4085 0.0545439557667401 3071 1.17129621346383 -0.595798636459254 -1 0.105691631537108 3789 4358 4389 4509 4085 3895 3071 3237 4438 3685 4269 4445 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 9/17 Arthur Liberzon 0.0765897756730953 0.0871115749524574 4135 3976.36363636364 4085 0.00793650793650794 3073 1.20431774015452 -1.36892273903237 -1 0.328332800909527 4134 4182 4587 4537 4292 3329 4005 3777 4085 3073 3739 4446 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 26/57 Kate Stafford 0.0839184282471183 0.0902966141827776 4465 3897.36363636364 4087 0.00793650793650794 2157 0.801379448036451 -0.691675688532122 -1 0.215265088994744 4465 3501 3619 4245 4087 2157 3955 4674 4124 4608 3436 4447 M2482 BIOCARTA_ARAP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARAP_PATHWAY.html ADP-Ribosylation Factor 14/22 BioCarta 0.298735036746822 0.313451048409227 3910 4038.81818181818 4090 0.0317460317460317 3312 0.639383170165238 0.759886498202031 1 0.0828596375686377 3906 4306 3582 4478 4607 4021 3312 3416 4300 4409 4090 4448 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 25/55 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4420 4065.63636363636 4090 0.00793650793650794 3377 1.04434318440674 -1.14204948562624 -1 0.280529630474469 4420 4160 3377 4416 4536 3899 4090 4430 3862 3564 3968 4449 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 132/330 Yujin Hoshida 0.0839184282471183 0.0902966141827776 3260 3815.90909090909 4090 0.00793650793650794 2837 1.49661820673991 1.53378375310008 1 0.402019044476236 3258 4281 3457 2837 4557 4221 3478 4240 3016 4090 4540 4450 M14 PID_AURORA_B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AURORA_B_PATHWAY.html Aurora B signaling 18832364 23/52 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 4650 4051.54545454545 4092 0.00793650793650794 2917 1.319169377177 -0.651097998224648 -1 0.35435301550191 3876 4620 2917 3203 4510 4336 4648 3677 4092 4042 4646 4451 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 21/61 Kevin Vogelsang 0.999357683389992 0.999973409262832 4095 4116.36363636364 4094 0.487380199196464 2566 1.17290136053018 -1.17290136053018 -1 3.27042795029606e-06 4019 4632 2566 4071 4601 3976 4396 4094 4657 4177 4091 4452 M243 PID_ARF_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF_3PATHWAY.html Arf1 pathway 18832364 21/33 Pathway Interaction Database 0.0839184282471183 0.0902966141827776 4175 3973.27272727273 4097 0.00793650793650794 3226 0.686867727821985 0.675175475261911 1 0.184505128576365 4459 3727 3606 4113 4171 3226 3923 4685 4097 4175 3524 4453 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 29/96 Kevin Vogelsang 0.0839184282471183 0.0902966141827776 4565 3897.81818181818 4097 0.00793650793650794 2550 0.997829973574814 -0.820547527568616 -1 0.268035324027563 4565 4393 3509 4481 4097 2550 3306 3731 3967 4155 4122 4454 M16563 BIOCARTA_MTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MTOR_PATHWAY.html mTOR Signaling Pathway 18/32 BioCarta 0.0839184282471183 0.0902966141827776 4345 3923.54545454545 4099 0.00793650793650794 2919 1.21907478952994 1.21907478952994 1 0.327465762840338 4345 4059 3615 3142 4287 2919 4681 4457 4099 4120 3435 4455 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 3/10 Reactome 0.987945623895701 0.995235294487095 4100 4207.90909090909 4100 0.357142857142857 3773 0.131255684389294 -0.19461525566921 -1 6.9814756977887e-05 4100 4319 4100 4578 4404 3773 3775 4056 4605 4531 4046 4456 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 55/225 Jessica Robertson 0.0839184282471183 0.0902966141827776 4675 3914.09090909091 4101 0.00793650793650794 2929 1.04582932583415 -0.769426461812598 -1 0.280928835476345 4674 4485 3561 3530 4101 2929 4161 3351 4146 4192 3925 4457 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 200/443 Arthur Liberzon 0.0273721601344465 0.0326293417425633 4265 3831.63636363636 4101 0.00251988857835336 3053 1.59369271415578 -1.23271291079253 -1 0.609307315037998 4261 4372 3417 3085 3718 3267 4311 4383 3053 4180 4101 4458 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 143/318 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3795 4088.72727272727 4101 0.00793650793650794 3550 1.30656724887284 1.72462057744718 1 0.350967851371135 3791 4525 3550 3856 4174 3974 4436 4101 3649 4314 4606 4459 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 13/26 Reactome 0.514011397665828 0.531360558010604 4270 3856.45454545455 4102 0.0634920634920635 2792 0.985363080895312 -0.693679519955372 -1 0.0696002941850515 4266 4102 3179 2792 4158 3368 4207 3827 4396 3982 4144 4460 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 917/1965 Leona Saunders 0.000663572470385842 0.000898959409143699 4470 3789.90909090909 4102 6.63770701490578e-05 1703 1.11607499473183 -0.886222137444341 -1 0.87449819474796 4468 4582 4121 4264 3336 1703 4102 3951 3573 4390 3199 4461 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 2/11 Jessica Robertson 0.319360083389629 0.334567706408182 3440 3979.4 4103.5 0.0418461073350456 2447 0.149360799942404 0.149360799942404 1 0.0182681832526594 3439 3975 4486 NA 4352 3665 2447 4232 4656 4636 3906 4462 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 14/32 Reactome 5.90981259659065e-05 9.02652601943409e-05 4105 3911.09090909091 4104 5.37270123325792e-06 2670 0.674284430157241 -0.746513202252281 -1 0.701462263251299 4103 2670 3430 4104 2954 4182 4541 3978 4118 4482 4460 4463 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 26/57 John Newman 0.0839184282471183 0.0902966141827776 3505 3978.90909090909 4106 0.00793650793650794 3170 0.941362558980429 1.03916425678863 1 0.25286713482738 3505 3859 3496 4305 4537 4572 3170 3635 4142 4106 4441 4464 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 17/68 Leona Saunders 0.0839184282471183 0.0902966141827776 3870 4116.36363636364 4109 0.00793650793650794 3207 1.13891914465679 1.13891914465679 1 0.305934478016478 3870 3760 3207 4467 4508 4332 4088 4556 4109 3815 4568 4465 M1724 KEGG_RNA_POLYMERASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_POLYMERASE.html RNA polymerase 14/29 KEGG 0.595395396258023 0.612787794171995 4090 4019.18181818182 4111 0.0789662828970608 3272 0.865031143631162 -0.865031143631162 -1 0.0473233332722549 4090 4634 3616 4256 4136 3272 4111 3515 4504 4398 3679 4466 M15347 BIOCARTA_AKAPCENTROSOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAPCENTROSOME_PATHWAY.html Protein Kinase A at the Centrosome 13/25 BioCarta 0.0538815914921429 0.0625127847814265 4660 4030 4111 0.00502257630727624 3385 0.703681503408309 -0.637385619611561 -1 0.217927543481828 4660 4225 3418 3385 3797 3916 3684 4206 4506 4422 4111 4467 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 39/99 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3855 3982.90909090909 4111 0.00793650793650794 3266 1.23008106381311 -0.659355362315303 -1 0.330422251142758 3854 4542 3423 3266 4393 3553 4046 4260 4111 4243 4121 4468 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 14/32 Jessica Robertson 0.0839184282471183 0.0902966141827776 4450 4026.72727272727 4115 0.00793650793650794 3330 0.966239690952959 -1.0468587116901 -1 0.25954959137737 4450 3901 3369 4120 4403 4115 4375 4221 3984 4026 3330 4469 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 22/40 Reactome 0.983276066319266 0.991528221814522 3550 3995.72727272727 4117 0.31057772306523 3208 0.632842664372132 -0.460683679265589 -1 0.000601236335925847 3546 4171 3449 3208 4365 3752 4045 4187 4597 4516 4117 4470 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 22/43 Arthur Liberzon 0.35943518917414 0.375209021267548 4650 4036.45454545455 4118 0.0396825396825397 3227 0.946110103883541 -0.998101731245927 -1 0.103602537271745 4650 3961 3319 4118 4645 3227 4328 4303 4324 3743 3783 4471 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 2/8 Arthur Liberzon 0.603432208530886 0.620075320624024 3715 3975.8 4119.5 0.0976633355964392 2822 0.445935703357589 -0.258924364227862 -1 0.0238068204210214 3714 4076 4257 NA 4252 3549 2822 3711 4635 4579 4163 4472 M1128 LANG_MYB_FAMILY_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LANG_MYB_FAMILY_TARGETS.html Myb family target genes. 15608679 30/54 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4225 3965.45454545455 4120 0.00793650793650794 3255 1.45999018964717 -1.61592387630624 -1 0.392180083417348 4224 4548 3255 3259 4527 3525 4127 4474 4120 3823 3738 4473 M14236 REACTOME_SIGNAL_ATTENUATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_ATTENUATION.html Genes involved in Signal attenuation 6/20 Reactome 0.214139132665174 0.226258393611952 4685 4082.36363636364 4121 0.0238095238095238 2475 1.42091093599637 -1.0821915679875 -1 0.23587990900283 4681 3907 4076 4032 4656 4121 4495 3905 4245 2475 4313 4474 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 33/75 Arthur Liberzon 0.978161938897681 0.987646379158486 3475 4011.45454545455 4123 0.293650793650794 3471 0.998063928979198 -0.998063928979198 -1 0.00138568704469458 3471 4215 3503 3601 4539 3634 4377 4123 4588 4202 3873 4475 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 11/21 Reactome 0.547545854501771 0.565527854131651 4260 3930.81818181818 4124 0.0695595183743379 2934 0.637658253365173 -0.637658253365173 -1 0.0406013339493598 4258 4310 3334 4124 4452 2934 3978 3148 4659 4520 3522 4476 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 7/14 Arthur Liberzon 0.0765897756730953 0.0871115749524574 4140 3950 4124 0.00793650793650794 3193 0.611195858606667 -0.611195858606667 -1 0.166630046858524 4139 4005 4124 4461 4334 3223 3594 3679 4161 4537 3193 4477 M14532 ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY.html PI3K Pathway 27/55 Signaling Transduction KE 0.557443745451391 0.574863862496747 3920 4119.36363636364 4127 0.0714285714285714 3542 0.917558361797587 0.894635475088935 1 0.056745107661276 4133 4494 3542 3917 4654 3972 3931 3916 4420 4127 4207 4478 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 11/64 Arthur Liberzon 0.415320710913563 0.431528348412628 4480 4047.63636363636 4127 0.0476190476190476 3212 0.869300632890509 -0.703772242361662 -1 0.0816111147609382 4480 4504 3212 4510 4127 3257 4500 3667 4364 3901 4002 4479 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 9/22 Reactome 0.0765897756730953 0.0871115749524574 4080 4134 4132 0.00793650793650794 3494 0.762517069926823 -0.865031143631162 -1 0.207884732241142 4675 4186 4079 4359 4078 3688 4324 3494 4132 4510 3949 4480 M6682 BIOCARTA_MCM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCM_PATHWAY.html CDK Regulation of DNA Replication 12/19 BioCarta 0.988438980056112 0.995235294487095 4080 4026.90909090909 4133 0.333333333333333 3197 1.02840239039473 1.02840239039473 1 0.000548466047157214 4076 4315 3197 3450 4388 3811 4221 4167 4599 3939 4133 4481 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 133/286 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3425 3903.18181818182 4136 0.00793650793650794 3086 1.2603260658499 -1.05780935605066 -1 0.338546616611752 3423 4474 3296 3086 4295 3397 4497 4208 4136 4302 3821 4482 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 4/10 Arthur Liberzon 0.301332437231886 0.316105619178111 3500 3783.72727272727 4137 0.0352227409874426 2629 0.361261247918275 -0.361261247918275 -1 0.0464765397100315 3496 4137 4683 4179 4394 2629 2937 2898 4581 4686 3001 4483 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 4/16 Arthur Liberzon 0.533864714360933 0.551518970788212 3935 3863.90909090909 4138 0.0734876813493643 2924 0.293016254551054 -0.351296836053853 -1 0.0194780109806973 3934 4138 4571 4231 4205 2924 2941 3164 4483 4661 3251 4484 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 570/1358 Arthur Liberzon 0.0148064857500311 0.0180075764922517 4150 4072.36363636364 4138 0.00149060753320977 3300 1.26189065279119 -0.959248384105018 -1 0.566242364041442 4149 4517 4633 3792 3663 3300 4138 4464 3690 4382 4068 4485 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 1244/2619 Arthur Liberzon 1.8100721901485e-08 9.95539704581677e-08 4655 3305.45454545455 4139 1.81007220489213e-09 533 1.37270342900662 -1.08235129585109 -1 2.47225829623695 4653 4139 4165 3395 533 1025 4557 4440 2717 4216 2520 4486 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 16/36 John Newman 0.776183169580198 0.791210426942094 4120 4160.36363636364 4140 0.127230943693747 3558 0.482983475055286 0.452910089854088 1 0.0126351012253806 4118 4567 3558 3851 4210 4140 3918 3954 4628 4619 4201 4487 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 830/1812 Jessica Robertson 1.38830225239502e-08 8.47729648011404e-08 4480 3367.63636363636 4140 1.38830226106824e-09 431 1.25656976737518 -1.10090938217035 -1 2.28566038699368 4476 4140 4440 4384 431 1031 4515 3939 3262 4261 2165 4488 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 18/48 Jessica Robertson 0.232850105696956 0.245309261532359 4315 3857.54545454545 4140 0.0238095238095238 2438 1.13356000126124 -0.968142956204762 -1 0.177941041148968 4311 4098 3137 2438 4177 4172 3755 4140 4272 3478 4455 4489 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 783/1883 Leona Saunders 8.60193135245328e-06 1.51251971172968e-05 4480 3868.27272727273 4141 8.60196464958502e-07 2581 1.36877122658099 -1.09808575863967 -1 1.69708453511618 4477 4584 4141 3341 2581 3015 4598 4257 3327 4364 3866 4490 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 2/17 Arthur Liberzon 0.980920425136734 0.98936571506473 4060 4162.4 4141 0.355901812505305 3677 0.164472468950442 -0.164472468950442 -1 0.000196214685456442 4059 3677 4223 NA 4392 3751 4293 4028 4624 4567 4010 4491 M13642 REACTOME_PEPTIDE_CHAIN_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEPTIDE_CHAIN_ELONGATION.html Genes involved in Peptide chain elongation 60/185 Reactome 0.557443745451391 0.574863862496747 4300 3918.27272727273 4143 0.0714285714285714 2790 0.497507673018916 -0.497507673018916 -1 0.0307675652292736 4296 4436 3772 3339 4143 2790 3645 4633 4426 4463 3158 4492 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 2/6 Arthur Liberzon 0.979607850803021 0.988893233275088 4250 4171.1 4143 0.351122738448649 3663 0.12171996895485 -0.12171996895485 -1 0.000151650648965416 4247 4010 4286 NA 4408 3663 4039 3941 4633 4587 3897 4493 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 14/43 Arthur Liberzon 0.232850105696956 0.245309261532359 4030 4035.27272727273 4144 0.0238095238095238 2810 0.847238483248693 -0.460358869597575 -1 0.132995550731325 4274 3698 2810 4466 4026 3676 4144 4566 4268 4027 4433 4494 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 102/235 Jean Junior 0.0839184282471183 0.0902966141827776 4280 4110.63636363636 4146 0.00793650793650794 3349 1.0793641724885 1.28500151325078 1 0.289936913896549 4278 4652 3666 3786 3871 3349 4544 4686 4041 4198 4146 4495 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 7/11 Yujin Hoshida 0.0540123711733435 0.0626334994601058 4575 4116.09090909091 4146 0.00553719166377352 3182 0.828779327635385 -0.828779327635385 -1 0.256491306949682 3948 3637 4374 4572 3804 4334 3182 4146 4100 4609 4571 4496 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 92/221 John Newman 0.0839184282471183 0.0902966141827776 3240 3992 4147 0.00793650793650794 2992 1.12135136675779 1.26081277823821 1 0.301215448804447 3238 4594 3652 3607 4147 4197 2992 4649 4084 4218 4534 4497 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 20/54 John Newman 0.0839184282471183 0.0902966141827776 4565 4032.18181818182 4149 0.00793650793650794 2962 1.27244614588359 1.4748777206187 1 0.341802293684855 3263 4562 3570 4253 4643 4149 2962 4562 4107 3962 4321 4498 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 4/8 Arthur Liberzon 0.76527490244494 0.780600390260555 3445 3985.81818181818 4149 0.134920634920635 3113 1.0315129281081 1.0315129281081 1 0.0285408085896122 3444 3455 4609 4152 4439 4088 4149 3734 4502 3113 4159 4499 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 9/35 Arthur Liberzon 0.0765897756730953 0.0871115749524574 4150 3895.09090909091 4150 0.00793650793650794 2709 2.25435938153527 -2.26263042315645 -1 0.61460553938344 3512 4316 4146 2709 4618 4293 2871 4608 4150 3059 4564 4500 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 127/341 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3290 3816.90909090909 4150 0.00793650793650794 1929 1.58816824250917 1.84099930576731 1 0.426611072884241 3289 4282 1929 2565 4234 4386 4150 4623 3927 4047 4554 4501 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 84/191 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4160 3996.81818181818 4150 0.00793650793650794 2753 0.97482344439334 -0.982026204258995 -1 0.261855345893788 4156 4283 3636 4524 4109 2753 4298 4559 4080 4150 3417 4502 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 37/71 Arthur Liberzon 0.980714389232142 0.98936571506473 3920 4046.72727272727 4150 0.301587301587302 3148 0.880631899724238 -0.931127199597976 -1 0.00105151870271659 3919 4443 3266 3148 4530 3919 4296 4019 4590 4234 4150 4503 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 5/18 Arthur Liberzon 0.564088537286601 0.581076914865907 4430 4218.45454545455 4151 0.0796779467757068 3485 0.708477079351539 0.724467474970132 1 0.0429639503684809 4430 3485 4678 4033 4137 4143 4277 3844 4541 4684 4151 4504 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 88/219 Leona Saunders 0.667434366415499 0.683777315483828 3275 3891.72727272727 4152 0.0952380952380952 2739 1.24927878512793 -1.03457151127399 -1 0.0530474776099308 3272 4430 3023 2739 4498 3732 4223 4152 4463 4254 4023 4505 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 12/32 Arthur Liberzon 0.698152987361708 0.714467110455769 4130 4185.90909090909 4153 0.103174603174603 3261 1.40823202626166 -1.40823202626166 -1 0.0528903973642901 4153 4404 3261 4127 4435 4128 4022 4616 4475 3944 4480 4506 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 17/27 Jessica Robertson 0.194010985627076 0.205222455676858 3875 4099.63636363636 4153 0.0194167608927306 3242 1.1721821942665 1.28580472216782 1 0.207367085242315 3875 4400 3242 4196 3953 4153 4169 4038 4321 4097 4652 4507 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 72/229 Reactome 0.455671501492374 0.472406339821519 4480 3938.18181818182 4155 0.053790355866535 2556 0.457918673884831 -0.457918673884831 -1 0.0383602497205202 4381 4605 3773 3727 4155 2556 3759 4371 4479 4476 3038 4508 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 100/250 Chi Dang 0.0839184282471183 0.0902966141827776 3720 4082.45454545455 4156 0.00793650793650794 3273 1.31668536114708 1.78050683763826 1 0.353685762974255 3717 4654 3685 3273 4572 4201 3898 4156 3845 4369 4537 4509 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 7/34 Jessica Robertson 0.00185215672527864 0.00241626013771039 4190 4035.90909090909 4157 0.000185370225658609 3078 0.838622905585366 -0.906706886156692 -1 0.564475532235117 4188 3078 4442 4157 3448 4142 4493 4015 4221 3589 4622 4510 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 20/44 Reactome 0.021591671736911 0.0259565350844446 4495 4085.27272727273 4159 0.00198241264837294 3255 0.820654631698585 -0.452089405640855 -1 0.334729859995998 4493 4128 3533 4309 3694 3255 4402 4583 4317 4159 4065 4511 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 27/61 Arthur Liberzon 0.667434366415499 0.683777315483828 4280 4015.45454545455 4159 0.0952380952380952 3443 0.898270615172327 -0.705285311344362 -1 0.0381427395876022 4280 4159 3471 3599 4290 4104 3443 3702 4461 4235 4426 4512 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 4/14 Arthur Liberzon 0.0118549726467963 0.0145425135662009 4400 3826.45454545455 4160 0.00119186947746434 2174 0.511500950808561 -0.511500950808561 -1 0.241734775516736 4400 2174 4171 4160 3640 3753 4266 3065 4260 4550 3652 4513 M19381 REACTOME_G2_M_CHECKPOINTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G2_M_CHECKPOINTS.html Genes involved in G2/M Checkpoints 24/46 Reactome 0.986245305260063 0.994308412316836 3690 4025.81818181818 4161 0.322719972490665 3265 0.632842664372132 -0.460683679265589 -1 0.000403293372681838 3688 4169 3491 3265 4373 3790 4026 4193 4600 4528 4161 4514 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 32/52 Reactome 0.748422388010251 0.764242168275449 3595 4041 4162 0.117904441183985 2951 0.578568655022456 -0.58837281755578 -1 0.0173770409612325 3593 4615 3700 4527 4550 2951 3870 4162 4518 4491 3474 4515 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 22/54 Jessica Robertson 0.0130177704029647 0.015927225093549 4175 3894.72727272727 4162 0.00119049481373455 2572 1.47180434981152 1.31618596973051 1 0.68061963948217 4172 4162 2572 4541 3639 3876 4276 4458 3799 2839 4508 4516 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 145/299 Jessica Robertson 0.0839184282471183 0.0902966141827776 4305 3965.54545454545 4162 0.00793650793650794 2685 1.31161875143922 -1.07222374627363 -1 0.352324778144256 4305 4373 3191 2685 4082 3774 4462 4301 4002 4162 4284 4517 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 51/116 Joao Pedro de Magalhaes 0.000297313500971507 0.000415635759413031 4595 3811.18181818182 4162 2.70321534786422e-05 1856 1.54758777685901 -1.36715271884451 -1 1.34597179156216 4595 4382 1856 4251 3213 3814 4551 4629 3920 2550 4162 4518 M189 KEGG_RIBOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOSOME.html Ribosome 60/184 KEGG 0.667967214165803 0.684173631820973 4470 3961.36363636364 4163 0.09536997674113 2873 0.497507673018916 -0.497507673018916 -1 0.0210930798487604 4470 4437 3769 3212 4163 2873 3902 4509 4570 4397 3273 4519 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 44/125 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4615 4122.81818181818 4164 0.00793650793650794 3176 1.20205233398359 -1.13421528079555 -1 0.322893217271651 4614 4609 3176 4136 4434 3716 4215 4525 4164 3909 3853 4520 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 15/33 Reactome 0.0839184282471183 0.0902966141827776 3980 3984.90909090909 4166 0.00793650793650794 2930 0.634105563084868 -0.509301442945895 -1 0.170332237837652 3978 4565 3610 4371 4207 2930 3697 4244 4166 4486 3580 4521 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 14/30 Kate Stafford 0.0839184282471183 0.0902966141827776 3970 4081.81818181818 4166 0.00793650793650794 3160 1.15609901821126 1.24141241768295 1 0.310549308965995 3967 4627 3160 4576 4166 4399 4256 3934 3735 3634 4446 4522 M6382 KEGG_REGULATION_OF_AUTOPHAGY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_REGULATION_OF_AUTOPHAGY.html Regulation of autophagy 18/60 KEGG 0.000104808475967183 0.000154931393811426 4170 3986.72727272727 4167 9.52849721806366e-06 3046 0.790199393487997 0.735562886846111 1 0.774362554281994 4167 3696 3363 4598 3046 4232 3584 4412 4343 4119 4294 4523 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 83/197 Jessica Robertson 0.0839184282471183 0.0902966141827776 4425 4012.63636363636 4167 0.00793650793650794 2709 1.32215394201909 -1.06984573690509 -1 0.355154724674008 4425 4480 2709 2738 4464 4167 4448 4076 4156 4142 4334 4524 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 12/33 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3475 3950.09090909091 4168 0.00793650793650794 2361 2.09224647599705 -1.24309783687442 -1 0.562015785002913 3472 4635 2361 3593 4678 4497 3599 4651 4168 3427 4370 4525 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 26/46 John Newman 0.0839184282471183 0.0902966141827776 4345 3820.36363636364 4170 0.00793650793650794 2975 2.15203129463023 2.81365727812765 1 0.57807509012323 3667 4342 3243 3143 4343 4170 4307 3034 2975 4230 4570 4526 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 24/48 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4170 4117.63636363636 4170 0.00793650793650794 3266 0.68095723488034 -0.631256159919104 -1 0.182917461142869 3732 4055 3617 4373 4170 4551 3266 4484 4167 4212 4667 4527 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 25/58 Kevin Vogelsang 0.0839184282471183 0.0902966141827776 4385 3890 4171 0.00793650793650794 2303 1.7919373240853 -1.55777430703054 -1 0.481347207072359 4385 4031 2303 2977 4580 4335 4171 4211 4160 3138 4499 4528 M504 REACTOME_ANDROGEN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANDROGEN_BIOSYNTHESIS.html Genes involved in Androgen biosynthesis 2/16 Reactome 0.0438257470086374 0.0513162045183595 4065 4183.7 4172.5 0.00496707967312621 3796 0.332986110673419 -0.213616311005895 -1 0.110465835179475 4065 3946 3914 NA 3796 4460 3887 4280 4568 4440 4481 4529 M10294 REACTOME_UNFOLDED_PROTEIN_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNFOLDED_PROTEIN_RESPONSE.html Genes involved in Unfolded Protein Response 54/108 Reactome 0.415320710913563 0.431528348412628 4180 3991.45454545455 4178 0.0476190476190476 2576 0.772571669542197 0.770639622234686 1 0.0725300455768328 4178 3984 3694 4490 4293 2576 3992 4242 4350 4322 3785 4530 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 68/184 Leona Saunders 0.0839184282471183 0.0902966141827776 3220 3860.90909090909 4178 0.00793650793650794 2021 1.62920654031696 -1.27219766323728 -1 0.437634716698524 3216 4285 2021 2878 4623 4561 4178 4343 3888 3918 4559 4531 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 10/19 Jessica Robertson 0.0692236374224142 0.0795638864266453 3865 4043.72727272727 4179 0.00650025792357057 2961 0.856511903869324 1.06323738545283 1 0.242181865794267 3863 4179 2961 4573 3826 4385 3836 4195 4402 3844 4417 4532 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 3/7 Arthur Liberzon 0.0736298916961878 0.0844006048161292 4530 4043.72727272727 4179 0.00761897128637624 2364 0.577910798047009 0.577910798047009 1 0.159596529095324 4526 2364 4667 3618 3844 4454 3901 3860 4179 4680 4388 4533 M129 PID_PLK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PLK1_PATHWAY.html PLK1 signaling events 18832364 31/65 Pathway Interaction Database 0.97089578562399 0.980943866199658 4240 4148.63636363636 4182 0.274963908995235 3484 0.712775941542387 -0.638025803909482 -1 0.00153172744458871 4240 4670 3557 4138 4577 3484 4182 3971 4631 4262 3923 4534 M14339 BIOCARTA_ARENRF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARENRF2_PATHWAY.html Oxidative Stress Induced Gene Expression Via Nrf2 9/19 BioCarta 0.7184702227596 0.734938106057954 4670 4179.45454545455 4183 0.119047619047619 3712 0.684431101129569 -0.684431101129569 -1 0.0235459268025493 4666 4183 3853 3712 4516 4295 4077 3992 4489 4420 3771 4535 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 32/83 Jessica Robertson 0.415320710913563 0.431528348412628 3670 3977.90909090909 4183 0.0476190476190476 2980 1.0739966118244 1.15029508353877 1 0.100828299377228 3666 4257 3475 2980 4558 4183 3345 4352 4345 3917 4679 4536 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 2/5 Leona Saunders 0.00467575597326506 0.00590741237280131 4030 4013.4 4184 0.000520611269904391 2859 0.424123556795905 -0.290905229355408 -1 0.243121494724128 4029 2859 4116 NA 3558 4327 3493 4634 4252 4535 4331 4537 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 8/13 John Newman 0.969970560715151 0.980425824389291 3715 4122.90909090909 4188 0.295704810119218 3524 0.344508811671383 -0.348321716644445 -1 0.000760554646499757 3713 4188 4417 3715 4360 3524 4278 3874 4655 4620 4008 4538 M4669 REACTOME_INFLUENZA_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLUENZA_LIFE_CYCLE.html Genes involved in Influenza Life Cycle 90/257 Reactome 0.415320710913563 0.431528348412628 4410 3954.63636363636 4190 0.0476190476190476 2896 0.919308864230203 -1.01048733193075 -1 0.0863059671903521 4409 4598 3776 3537 4241 2896 4190 3931 4348 4383 3192 4539 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 54/110 Itai Pashtan 0.726270090971166 0.742430551110576 4060 4126.72727272727 4190 0.111111111111111 2884 1.47005072203877 -1.41727468157135 -1 0.0489075552590062 4056 4610 2884 3535 4573 4036 4629 4215 4485 4181 4190 4540 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 19/38 Jean Junior 0.35943518917414 0.375209021267548 4305 3982.63636363636 4194 0.0396825396825397 2702 1.29123897146724 -1.45952442345104 -1 0.141395495974346 4301 4558 2702 4194 4451 4059 3660 3527 4322 3547 4488 4541 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 4/8 Jean Junior 0.147859119791321 0.157148522418265 3755 4124.45454545455 4195 0.0158730158730159 3732 0.767758433342683 0.767758433342683 1 0.158712488744077 3753 3773 4363 4341 3991 4477 3939 3732 4199 4606 4195 4542 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 34/99 Reactome 0.653300171007476 0.670322881835129 4205 4138.90909090909 4196 0.0918081453643482 3461 0.356539628344999 -0.356539628344999 -1 0.0159309026342814 4204 4613 3758 3785 4159 3461 4529 4196 4540 4438 3845 4543 M121 PID_MTOR_4PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MTOR_4PATHWAY.html mTOR signaling pathway 18832364 51/104 Pathway Interaction Database 0.298735036746822 0.313451048409227 4070 4132.45454545455 4197 0.0317460317460317 3382 0.829582109649437 -0.603018767507155 -1 0.107508168452728 4069 4535 3650 4529 4582 3382 4197 4033 4306 4266 3908 4544 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 4/27 Reactome 0.147859119791321 0.157148522418265 4320 3991.36363636364 4198 0.0158730158730159 2676 1.50510212232629 -1.50510212232629 -1 0.311137788612922 4320 4075 4044 4289 4683 4406 4205 2676 4198 3094 3915 4545 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 616/1371 Jessica Robertson 3.64280914567073e-08 1.57780713967333e-07 4240 3523.81818181818 4198 3.64280920538599e-09 834 1.37743631256691 -1.01317775287761 -1 2.40992409387003 4343 4238 4424 3397 834 2279 4198 4392 2711 4239 3707 4546 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 41/112 Reactome 0.76576894155592 0.780934332999139 4340 4128.90909090909 4203 0.123614965413647 3334 0.356539628344999 -0.356539628344999 -1 0.00984787786748877 4339 4667 3765 3860 4203 3334 4628 3929 4532 4458 3703 4547 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 5/11 Arthur Liberzon 0.147859119791321 0.157148522418265 3225 3784.72727272727 4204 0.0158730158730159 2754 0.650546857288011 0.650546857288011 1 0.134482255414406 3224 3001 4240 4276 4265 3469 2754 4405 4204 4573 3221 4548 M7963 KEGG_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CELL_CYCLE.html Cell cycle 75/142 KEGG 0.0839184282471183 0.0902966141827776 3280 4112.45454545455 4205 0.00793650793650794 3277 1.32647340129522 1.71422590056735 1 0.356315011115549 3277 4657 3395 4000 4440 4368 4001 4205 4064 4268 4562 4549 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 139/318 Jessica Robertson 0.0839184282471183 0.0902966141827776 4355 4172.09090909091 4206 0.00793650793650794 3624 1.28930689091258 -1.00217617463852 -1 0.346331400825544 3900 4650 3624 4002 4354 3958 4206 4289 4133 4354 4423 4550 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 5/11 Arthur Liberzon 0.0765897756730953 0.0871115749524574 4035 4009.90909090909 4208 0.00793650793650794 3101 1.09920040450279 -0.765200656734479 -1 0.299674673124678 4033 3841 4208 4271 4684 4396 4241 3101 3794 3282 4258 4551 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 4/11 Arthur Liberzon 0.91339562951387 0.926845370268946 4215 4091.36363636364 4211 0.217014028671299 3243 0.334187336805956 -0.3680841848674 -1 0.00283578973021033 4211 4107 4263 4354 4327 3573 3243 3746 4596 4582 4003 4552 M5731 BIOCARTA_AKAP95_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAP95_PATHWAY.html AKAP95 role in mitosis and chromosome dynamics 8/20 BioCarta 0.934081566336537 0.946810776520228 4660 4109.63636363636 4212 0.238095238095238 3535 0.66544312067283 -0.494612970343855 -1 0.0040626471684369 4656 3869 3813 3586 4386 3535 3859 4313 4567 4410 4212 4553 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 128/314 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3610 4140.45454545455 4214 0.00793650793650794 3607 1.07489148798472 1.20237648740763 1 0.288735468332352 3607 4593 3663 3858 4263 4214 3889 4459 4145 4360 4494 4554 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 5/12 Leona Saunders 2.66094562314479e-05 4.29823894865787e-05 4320 3828.27272727273 4216 2.66097748652401e-06 2243 1.52528764835915 -1.0821915679875 -1 1.71318665971789 4317 3674 4239 4172 2815 4394 4216 4546 3124 2243 4371 4555 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 7/36 Arthur Liberzon 0.786767204251786 0.801824949787705 4665 4288.90909090909 4219 0.143188276652983 4007 0.475196102759562 -0.547422437657855 -1 0.0117239722983043 4665 4007 4134 4426 4235 4150 4187 4079 4534 4542 4219 4556 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 9/13 Arthur Liberzon 0.562604368603265 0.579802962673169 4365 4095.54545454545 4219 0.0793650793650794 3256 0.719165974198512 -0.719165974198512 -1 0.0437884795125268 4361 4185 4219 3256 4503 3460 4606 3955 4439 4565 3502 4557 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 219/494 Kate Stafford 0.0839184282471183 0.0902966141827776 4550 3947 4220 0.00793650793650794 2937 1.485187402548 -1.08943494661455 -1 0.398948519609133 4549 4201 3411 2937 4231 3341 4420 4319 3513 4275 4220 4558 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 48/126 Jessica Robertson 0.0839184282471183 0.0902966141827776 4265 3792.27272727273 4223 0.00793650793650794 1716 1.55587289423536 -1.19468025045722 -1 0.417935946593764 4262 3989 1716 1952 4420 4223 4524 4367 3769 4004 4489 4559 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 8/28 Arthur Liberzon 0.187099934314171 0.198001421001853 3155 3704.27272727273 4226 0.020501633946653 2436 0.926197331599731 -0.926197331599731 -1 0.167556719401303 3153 4314 4226 4596 4474 2436 2755 2968 4582 4569 2674 4560 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 4/14 Jessica Robertson 0.141108616719513 0.150314839269752 4625 4164.27272727273 4227 0.0150961738992154 3135 0.661644568467725 -0.661644568467725 -1 0.140062422632436 4625 3135 4509 3627 3921 4227 4589 4499 4183 4640 3852 4561 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 27/75 Arthur Liberzon 0.557443745451391 0.574863862496747 4230 4200 4229 0.0714285714285714 3344 0.966429476622231 -0.855555615099285 -1 0.0597674844671509 4229 4092 3344 4201 4417 4058 4672 4389 4423 3964 4411 4562 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 14/46 Jessica Robertson 0.000336936298939085 0.000468372440471241 4445 3859.36363636364 4231 3.06352647968213e-05 2203 0.790990432523977 -0.713722615751832 -1 0.677387048146333 4288 2203 3300 3556 3238 4231 4444 4435 4292 4022 4444 4563 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 6/17 Arthur Liberzon 0.0227779692244678 0.0273335630693613 2805 3590.09090909091 4232 0.0023014870137756 1575 0.57595439835603 0.57595439835603 1 0.231595308825323 2804 4232 4675 4356 4325 2489 1575 2681 4569 4682 3103 4564 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 11/39 Reactome 0.415320710913563 0.431528348412628 4580 4216.45454545455 4234 0.0476190476190476 3513 0.696003069749136 -0.816795604383953 -1 0.0653416634420315 4579 4229 3513 4059 4542 4107 4049 4234 4359 4453 4257 4565 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 46/123 Kevin Vogelsang 0.161385165508919 0.171020100763183 4490 4058.36363636364 4234 0.0158730158730159 2833 1.20310177583161 -0.937464425628803 -1 0.237339119757655 4486 4120 2833 3327 4311 4022 4410 4553 4234 4078 4268 4566 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 31/63 Arthur Liberzon 0.999878932081991 0.999973409262832 3910 4141.54545454545 4236 0.55953466575818 2902 1.17290136053018 -1.17290136053018 -1 3.27042795029606e-06 3908 4559 2902 3606 4597 4071 4582 4236 4647 4264 4185 4567 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 7/18 Jean Junior 0.147859119791321 0.157148522418265 4335 4100.63636363636 4238 0.0158730158730159 3277 0.517961259008388 0.517961259008388 1 0.107073870589252 4331 3672 4372 3962 4106 4387 3277 3801 4238 4607 4354 4568 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 230/473 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3985 4070.27272727273 4239 0.00793650793650794 3337 1.12329583234413 -0.896367272508027 -1 0.301737768130001 3981 4648 3723 3337 4617 3353 4239 4411 3820 4349 4295 4569 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 35/84 Jessica Robertson 0.0591715591413856 0.068440662112791 4235 4104.36363636364 4245 0.00552960710998594 3246 1.01093271718214 -0.900664415542256 -1 0.302851280718051 4231 4391 3246 4623 3803 3480 4550 4245 4325 4000 4254 4570 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 9/17 Jessica Robertson 0.138233428625008 0.147319046289922 4450 4186.90909090909 4247 0.0147669673160593 3608 0.592517296127967 0.592517296127967 1 0.126761436726947 4448 4184 4457 4423 3918 3759 3608 3872 4510 4630 4247 4571 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 4/11 Leona Saunders 0.164522170207337 0.174265571788332 3025 3693 4249 0.0178145573519577 2384 0.380309162197088 0.420770761520163 1 0.0742258044824499 3025 4318 4249 4546 4364 2670 2384 2677 4630 4575 3185 4572 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 43/112 Jean Junior 0.415320710913563 0.431528348412628 2470 3837.45454545455 4250 0.0476190476190476 2467 0.825039062315026 0.963648210421201 1 0.0774557679994334 2467 4537 3620 4444 4600 4250 2589 3459 4351 4274 3621 4573 M16257 BIOCARTA_MITOCHONDRIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MITOCHONDRIA_PATHWAY.html Role of Mitochondria in Apoptotic Signaling 16/28 BioCarta 0.415320710913563 0.431528348412628 4620 4146.81818181818 4254 0.0476190476190476 3158 0.972257515649913 -0.741594354423538 -1 0.0912768709414451 4616 4033 3158 3966 4568 3767 4254 4516 4356 4069 4312 4574 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 19/50 Arthur Liberzon 0.952384242326998 0.964111592038089 4435 4112.18181818182 4254 0.241779507236709 3445 0.526330154867711 0.435203882297205 1 0.00214864393800861 4431 4268 3527 4254 4314 3445 3881 3922 4644 4652 3896 4575 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 97/210 Jessica Robertson 0.0839184282471183 0.0902966141827776 4255 4119.45454545455 4255 0.00793650793650794 3332 1.41285791878491 -1.11496581351965 -1 0.379519486026652 4255 4427 3366 3332 4380 3999 4443 4399 4045 4204 4464 4576 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 4/20 Arthur Liberzon 0.304324910623461 0.319101931345164 4665 4206.72727272727 4255 0.0356367647830557 3514 0.575433912180618 0.575433912180618 1 0.0734237123409544 4661 3974 4557 4348 4031 4009 3514 3632 4637 4656 4255 4577 M46 PID_ATR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATR_PATHWAY.html ATR signaling pathway 18832364 29/52 Pathway Interaction Database 0.232850105696956 0.245309261532359 3460 4087.09090909091 4257 0.0238095238095238 3292 1.44697798565904 1.7234339444241 1 0.227140015477722 3457 4445 3292 3527 4379 4543 4101 4406 4257 4244 4307 4578 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 116/259 Leona Saunders 0.0020352298722537 0.00264478291219657 4585 3877.09090909091 4259 0.000185192283150756 2071 1.26408903325922 -0.967434509811775 -1 0.83809537682164 4584 4473 3574 4441 3447 2071 4561 4381 3191 4259 3666 4579 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 15/54 Kevin Vogelsang 0.998975885009836 0.999973409262832 4680 4220.09090909091 4259 0.465172758164059 2817 0.259270056355908 -0.298761542598066 -1 5.56551180226679e-07 4017 4680 2817 4259 4535 4003 4670 4044 4676 4613 4107 4580 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 80/213 Itai Pashtan 0.232850105696956 0.245309261532359 4080 4039.27272727273 4265 0.0238095238095238 2403 1.5354033959176 -1.43591491895588 -1 0.241020646794011 4079 4482 2403 2982 4609 4392 4237 4669 4265 3794 4520 4581 M6031 BIOCARTA_SKP2E2F_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SKP2E2F_PATHWAY.html E2F1 Destruction Pathway 7/15 BioCarta 0.988667011007896 0.995251044808378 4680 4272.81818181818 4270 0.361097707163118 3828 0.428724180681131 -0.428724180681131 -1 0.00022776408295236 4680 4512 3828 4060 4517 3959 4209 3880 4672 4414 4270 4582 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 2/10 Arthur Liberzon 0.658487156414159 0.675496783208777 4555 4247.5 4271 0.112524570852377 3393 0.778220703027238 -0.896114552229146 -1 0.0341042881761068 4626 3393 4177 NA 4188 4215 4327 4551 4507 4553 3938 4583 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 2/5 Arthur Liberzon 0.954792354292668 0.966340598750636 4515 4254.7 4273 0.291109593600173 3444 0.122840420484202 -0.0479351465242832 -1 0.000469620313967719 4025 4515 4290 NA 4514 4247 3444 3986 4681 4589 4256 4584 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 47/88 Yujin Hoshida 0.955240661249004 0.966376886574445 4575 4234.09090909091 4273 0.246031746031746 3625 0.893929525274642 -0.53218427599379 -1 0.00341509361019487 4574 4662 3625 4073 4407 3734 4196 4273 4573 4338 4120 4585 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 8/22 Reactome 0.33296556889208 0.348587277888357 4505 4098.90909090909 4278 0.0396825396825397 3142 0.888632650572132 0.888632650572132 1 0.104614055368224 3922 3906 4046 4365 4278 4501 3142 3598 4336 4493 4501 4586 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 48/118 Jean Junior 0.0839184282471183 0.0902966141827776 4630 4129.18181818182 4279 0.00793650793650794 3205 1.51508057993457 -1.06843658455921 -1 0.406978378487056 4627 4607 3205 3781 4579 3485 4538 4328 3989 4003 4279 4587 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 18/61 Reactome 0.232850105696956 0.245309261532359 4395 4033.45454545455 4281 0.0238095238095238 3196 0.651902280515102 -0.711822105486279 -1 0.1023325342416 4395 4347 3598 4131 4306 3196 4534 3330 4281 4452 3798 4588 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 121/263 Arthur Liberzon 0.0839184282471183 0.0902966141827776 3940 4114.63636363636 4283 0.00793650793650794 3210 1.52963310643263 -0.987898328182797 -1 0.410887455551215 3937 4527 3251 3210 4350 3910 4474 4638 4065 4283 4616 4589 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 10/24 Reactome 0.970173825798792 0.980425824389291 4290 4183.81818181818 4286 0.273347034936066 3257 0.210198171398646 -0.165952297766775 -1 0.000463960580513774 4286 4460 3257 3985 4621 4135 3849 3728 4666 4521 4514 4590 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 34/71 Jessica Robertson 0.751985672431077 0.767379107363246 4325 4096.72727272727 4286 0.119047619047619 3357 0.907240210744952 -1.03703990414642 -1 0.0268335237083371 4325 4546 3357 4323 4266 3534 4588 4286 4494 3972 3373 4591 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 4/9 Vamsi Mootha 0.234527104169685 0.246964946098684 3780 4141.72727272727 4288 0.0263721642386969 3274 0.757069269811001 -0.757069269811001 -1 0.118272304737424 3777 4042 4517 4288 3989 3647 4608 4454 4319 4644 3274 4592 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 72/203 Leona Saunders 0.232850105696956 0.245309261532359 4460 4157.18181818182 4289 0.0238095238095238 3211 1.23790706591114 -0.99425694053267 -1 0.194320983623729 4160 4379 3452 3211 4460 4193 4482 4373 4273 4289 4457 4593 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 4/9 Arthur Liberzon 0.435369722646862 0.45165873817206 3915 4134.54545454545 4289 0.0555555555555556 3063 0.544702665121886 -0.0909956190570336 -1 0.0483630801920542 3911 4191 4289 3764 4346 4300 4118 3063 4369 4588 4541 4594 M18241 NIKOLSKY_BREAST_CANCER_7P15_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_7P15_AMPLICON.html Genes within amplicon 7p15 identified in a copy number alterations study of 191 breast tumor samples. 19010930 3/13 Jessica Robertson 0.9980272015559 0.999973409262832 3660 4258 4292 0.463575911799438 3660 0.310281683607488 0.370803633116578 1 7.08077588712236e-07 3660 4192 4352 4292 4540 4180 3808 4229 4654 4601 4330 4595 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 4/6 Arthur Liberzon 0.275742742869669 0.289715357194454 4345 4033.36363636364 4295 0.0317460317460317 3167 0.548975073870972 -0.548975073870972 -1 0.0759723152726829 4341 3167 4532 4497 4125 3511 4456 3230 4295 4650 3563 4596 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 12/36 John Newman 0.998181280012705 0.999973409262832 4485 4125.72727272727 4298 0.436507936507937 2722 1.0476812132427 -1.0476812132427 -1 2.89847041412638e-06 4482 4636 2722 3030 4671 4266 4457 4298 4627 3946 4248 4597 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 2/8 Jessica Robertson 0.99757395991082 0.999973409262832 3775 4284.5 4299.5 0.487807625852277 3773 0.176253248222674 -0.0409330516007103 -1 3.0995565959518e-07 3773 4237 4362 NA 4489 4055 3890 4664 4677 4605 4093 4598 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 9/18 Arthur Liberzon 0.937241593926861 0.949808414606676 4350 4182.36363636364 4300 0.241828961899699 3402 0.902795291110037 -0.902795291110037 -1 0.00519301225011112 4350 4274 4674 4300 4425 3402 3732 3674 4620 4681 3874 4599 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 52/155 Arthur Liberzon 0.466738071388703 0.483451503653285 2855 3969.63636363636 4302 0.0555555555555556 2409 1.58031023703431 1.85669767484202 1 0.128304563104427 2851 4541 2409 3269 4570 4606 3882 4579 4385 4272 4302 4600 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 22/71 Arthur Liberzon 0.35943518917414 0.375209021267548 4540 4208.18181818182 4302 0.0396825396825397 3152 1.1856282593851 1.1856282593851 1 0.12983071059949 4036 4166 3152 4615 4564 4538 3855 4302 4335 4189 4538 4601 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 14/21 Arthur Liberzon 0.35943518917414 0.375209021267548 3850 4144.18181818182 4302 0.0396825396825397 3566 0.684084710300495 -0.361261247918275 -1 0.07490973348501 3848 4454 3566 4315 4302 4596 3620 3919 4331 4030 4605 4602 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 5/13 Reactome 0.998760043397832 0.999973409262832 4340 4328.36363636364 4307 0.487916657988356 3998 0.152390685543906 -0.176756550605639 -1 2.39073615347842e-07 4336 4642 3998 4307 4651 4061 4176 4212 4663 4472 4094 4603 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 141/394 Arthur Liberzon 0.0347819703822428 0.0410653346463063 4605 4122.18181818182 4308 0.00321312371870296 2960 1.05150175083634 -0.893646548305784 -1 0.375004113740343 4603 4470 3707 4607 3746 2960 4459 4656 4020 4308 3808 4604 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 122/272 Jessica Robertson 0.161385165508919 0.171020100763183 3555 4197.18181818182 4308 0.0158730158730159 3317 1.51693913246457 1.90276019145477 1 0.29925071402159 3555 4595 3317 3788 4571 4162 4308 4639 4239 4311 4684 4605 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 9/40 Andrew Gentles 0.275742742869669 0.289715357194454 4090 4196.54545454545 4308 0.0317460317460317 2884 1.60782142289499 -2.26263042315645 -1 0.222505807672146 4087 4575 4679 3936 4614 4464 2884 4594 4308 3786 4235 4606 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 12/26 Kevin Vogelsang 0.597318307603006 0.614227252452861 4310 4146 4309 0.0793650793650794 3402 0.757293070784199 -0.796989992184932 -1 0.0412307862428424 4309 4503 3402 4482 4642 3493 4098 3950 4436 4615 3676 4607 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 6/14 Arthur Liberzon 0.0765897756730953 0.0871115749524574 4020 4006.81818181818 4309 0.00793650793650794 1951 0.728760733954488 -0.799897624885234 -1 0.198681746036768 4500 1951 4637 3471 4378 3575 4543 4018 4016 4677 4309 4608 M13022 BIOCARTA_PTC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTC1_PATHWAY.html Sonic Hedgehog (SHH) Receptor Ptc1 Regulates cell cycle 3/16 BioCarta 0.988197613265395 0.995235294487095 3800 4238.09090909091 4316 0.35849952227827 3606 0.188656999744084 0.197806529337954 1 0.000100439863739851 3796 4514 3872 4115 4575 4267 3606 4468 4664 4426 4316 4609 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 5/13 Jessica Robertson 0.336728826040026 0.352369646901197 3350 4030 4317 0.040225709467039 2434 0.342953092427762 0.45877170290962 1 0.0399604839883913 3348 4317 4430 4550 4488 3343 2434 4290 4614 4625 3891 4610 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 0.94403277046154 0.956277034669861 4350 4200.45454545455 4322 0.250462473990556 3795 0.192767337428759 -0.175295847125102 -1 0.000962502045849033 4346 3876 4356 4225 4322 3795 3934 3808 4595 4602 4346 4611 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 354/745 Arthur Liberzon 0.0839184282471183 0.0902966141827776 2955 3990.81818181818 4323 0.00793650793650794 2954 1.48506955509911 1.79540734204218 1 0.398916863610458 2954 4646 3198 3153 4345 4420 4120 4354 3821 4323 4565 4612 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 2/8 Vamsi Mootha 0.0142464928443112 0.0173580513438487 4605 4108.5 4323.5 0.00159305733220831 2510 0.470825243719012 -0.384308603201621 -1 0.213203232243039 4171 2510 4601 NA 3672 4605 3634 4576 4188 4669 4459 4613 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 6/28 Reactome 0.0765897756730953 0.0871115749524574 4620 4187.54545454545 4327 0.00793650793650794 3444 1.5571957566056 -0.577869192498034 -1 0.42453789615114 4617 4409 4060 4419 4462 4514 4075 4121 3615 3444 4327 4614 M1180 OHASHI_AURKA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OHASHI_AURKA_TARGETS.html Candidate substrate proteins of AURKA [GeneID=6790]. 16785988 2/8 Arthur Liberzon 0.99125724856655 0.9964130389196 3875 4311.2 4327 0.409398920020416 3705 0.242540711081026 -0.1185515722761 -1 9.71450206274958e-05 3873 4195 4241 NA 4547 4239 3705 4665 4660 4574 4413 4615 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 12/32 Reactome 0.997493617109877 0.999973409262832 4180 4272.09090909091 4331 0.41983735126041 3313 0.190392078687021 -0.156512232172201 -1 3.51954049293329e-07 4180 4679 3313 4061 4608 4331 4087 3970 4671 4518 4575 4616 M13492 REACTOME_DEADENYLATION_OF_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEADENYLATION_OF_MRNA.html Genes involved in Deadenylation of mRNA 15/27 Reactome 0.632646649574425 0.649415596912542 4490 4040.45454545455 4332 0.0870180692674384 2821 0.56189700880339 -0.574637850184293 -1 0.0270957166417291 3969 4629 3627 4487 4501 2821 3873 4332 4498 4488 3220 4617 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 14/53 Broad Institute 0.35943518917414 0.375209021267548 4280 4193.72727272727 4337 0.0396825396825397 3379 0.517961259008388 0.517961259008388 1 0.0567185668689816 4279 4566 3568 4436 4471 3379 4636 4307 4337 4610 3542 4618 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 72/203 Jessica Robertson 0.751985672431077 0.767379107363246 4340 4112.54545454545 4338 0.119047619047619 2840 0.981720776504314 -0.753427125904606 -1 0.0290364595040636 4338 4432 3391 2840 4461 3904 4595 4342 4492 4246 4197 4619 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 5/9 Jessica Robertson 0.386086746459241 0.40258177434535 4605 4186.18181818182 4340 0.0476190476190476 3299 0.844575173179012 -0.657747079373799 -1 0.0858407273791178 4604 3739 4516 4568 4262 3689 4440 4543 4340 3299 4048 4620 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 2/16 Jessica Robertson 0.923724736104928 0.936718050938692 4335 4334.2 4341 0.248687848220056 3617 0.480641037346541 -0.286478525785947 -1 0.00350974440955582 4333 4193 4349 NA 4319 4589 3617 4048 4634 4600 4660 4621 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 75/193 Jessica Robertson 0.0839184282471183 0.0902966141827776 4660 4139.45454545455 4343 0.00793650793650794 3321 1.29047518163518 1.34400784829999 1 0.346645225264801 3321 4656 3424 4563 4491 4343 3662 4377 3854 4187 4656 4622 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 37/74 Jessica Robertson 0.9986717983916 0.999973409262832 4350 4284.09090909091 4349 0.452380952380952 3385 0.76597971284595 -0.752972400635042 -1 2.06169615461108e-06 4349 4552 3385 3854 4485 4001 4659 4335 4632 4593 4280 4623 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 194/447 Jessica Robertson 0.0839184282471183 0.0902966141827776 4395 3987.45454545455 4350 0.00793650793650794 2199 1.68542439217588 -1.3983801417884 -1 0.452735868744341 4551 4469 2199 2884 4395 3949 4545 4393 3981 4146 4350 4624 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 21/52 Jessica Robertson 0.993240511078093 0.997497864318891 4185 4091.45454545455 4353 0.365079365079365 2592 1.20177165807981 1.33018891788779 1 0.000336111843585875 4183 4353 2592 3081 4526 4307 4426 4361 4607 3994 4576 4625 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 99/229 Arthur Liberzon 0.988438980056112 0.995235294487095 4600 4283.18181818182 4355 0.333333333333333 3500 1.18776320819297 -1.08660719090805 -1 0.000633489221775766 4553 4599 3500 3538 4576 4155 4581 4341 4598 4355 4319 4626 M7721 BIOCARTA_EIF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF_PATHWAY.html Eukaryotic protein translation 10/40 BioCarta 0.0990819308162709 0.10634400545237 4430 4204.90909090909 4357 0.00944069585811638 3516 1.08501359716727 1.08501359716727 1 0.271627943008787 4434 4357 3516 4429 3872 4268 4442 4388 4288 3831 4429 4627 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 3/19 Jessica Robertson 0.946596086373448 0.95866636281521 4045 4176.45454545455 4358 0.253968253968254 3416 0.806766939053356 0.806766939053356 1 0.00380403359465641 4045 3609 4483 3954 4679 4358 3416 3722 4574 4634 4467 4628 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 6/13 Reactome 0.508732388173577 0.526367845215584 4235 4184.45454545455 4359 0.068609479839363 3142 0.4077194287999 -0.526475678007318 -1 0.0292287663062126 4233 4073 3948 4508 4359 3818 4372 3142 4511 4450 4615 4629 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 5/17 Reactome 0.980707877864739 0.98936571506473 3635 4235.45454545455 4359 0.326189149429756 3535 0.193439521324968 0.236565413107486 1 0.000230809826146481 3632 4644 4013 3983 4588 4359 3535 4277 4675 4485 4399 4630 M3492 REACTOME_MTORC1_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MTORC1_MEDIATED_SIGNALLING.html Genes involved in mTORC1-mediated signalling 6/12 Reactome 0.435369722646862 0.45165873817206 4655 4167.45454545455 4360 0.0555555555555556 2679 0.314751060081156 -0.411723436769525 -1 0.0279460384868747 4652 2679 4089 4102 4551 4360 3753 4618 4381 4523 4134 4631 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 14/35 Yujin Hoshida 0.259502824121389 0.273019810020842 3585 4184.09090909091 4362 0.026942528882832 3415 0.634895684871187 -0.403155276326114 -1 0.0920724346101511 3584 4064 3415 4056 3993 4529 4362 4451 4487 4611 4473 4632 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 6/10 Jessica Robertson 0.314107275451919 0.329138348114421 2510 3737.27272727273 4362 0.0370014801158295 2406 0.303837171050837 0.349574507849818 1 0.037717579301798 2510 4362 4521 4511 4411 2764 2406 3277 4604 4646 3098 4633 M7239 BIOCARTA_DNAFRAGMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DNAFRAGMENT_PATHWAY.html Apoptotic DNA fragmentation and tissue homeostasis 7/18 BioCarta 0.69620750728458 0.712943264671228 4070 4262.27272727273 4363 0.112317406855777 3815 0.860718658949915 -0.765200656734479 -1 0.0325320893251748 4066 4509 3815 4122 4187 4363 3840 4439 4616 4411 4517 4634 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 67/206 Reactome 0.597318307603006 0.614227252452861 4600 4078.81818181818 4365 0.0793650793650794 3103 0.600182663185438 -0.590026503867529 -1 0.0326768730490247 4598 4484 3777 3726 4185 3103 4365 4425 4444 4507 3253 4635 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 12/27 John Newman 0.85882379742199 0.873171689025699 4255 4235.63636363636 4366 0.163038288959203 3424 0.287828503337639 -0.274009392202494 -1 0.00436042800300639 4254 4272 3519 4377 4259 3424 4437 4537 4529 4618 4366 4636 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 8/40 Arthur Liberzon 0.742829351267896 0.759027112961483 4140 4292 4368 0.126984126984127 3520 0.517961259008388 0.517961259008388 1 0.0159528850962145 4140 4639 4131 4368 4249 4570 3879 3520 4497 4541 4678 4637 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 18/28 John Newman 0.962317269026925 0.973115822757913 4625 4187.54545454545 4369 0.257736000704061 3227 0.580104887176765 0.580104887176765 1 0.00176578587617128 3227 4674 3579 4066 4657 4587 3355 4304 4623 4622 4369 4638 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 6/13 Reactome 0.967034090632651 0.977674595189774 4085 4244.81818181818 4372 0.289103287228572 3515 0.163642269468179 -0.190737649392595 -1 0.00041252154874363 4084 4511 4072 4372 4662 3515 4384 4129 4673 4504 3787 4639 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 7/16 Reactome 0.853233160620055 0.867675909432634 4530 4252.27272727273 4372 0.174603174603175 3704 0.805001649478674 0.805001649478674 1 0.0127634521980144 3704 3840 4096 3909 4310 4547 4451 4490 4527 4529 4372 4640 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 60/112 Jessica Robertson 0.980714389232142 0.98936571506473 4595 4233.81818181818 4375 0.301587301587302 3162 1.20942445227375 1.34436444768845 1 0.00144419326505108 4591 4539 3162 3458 4528 4110 4567 4338 4591 4313 4375 4641 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 181/374 Jessica Robertson 0.466738071388703 0.483451503653285 4485 4231 4378 0.0555555555555556 3342 1.18519029149662 -0.890917474000462 -1 0.096224927604701 4483 4649 3649 3342 4468 4106 4368 4325 4389 4384 4378 4642 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 37/94 Leona Saunders 0.698152987361708 0.714467110455769 3165 3930.90909090909 4383 0.103174603174603 2608 1.27363420138833 1.31289550018084 1 0.0478351500341711 3162 4442 2608 3080 4559 4383 3558 4518 4477 3863 4590 4643 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 44/128 Reactome 0.577955125871286 0.595099477001285 3275 4085.18181818182 4384 0.075425963419967 2719 0.888043969266385 -0.67840545751831 -1 0.0514879223102511 3271 4665 3662 3725 4673 4458 2719 4384 4539 4326 4515 4644 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 55/177 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4575 3864.63636363636 4385 0.00793650793650794 1666 1.74960285449587 -1.14292868659802 -1 0.469975387607371 4573 4385 1666 2736 4444 4074 4487 4476 3917 3143 4610 4645 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 45/102 Arthur Liberzon 0.796944161638877 0.811667103116665 2745 4012.81818181818 4386 0.134920634920635 2744 1.2589993527916 1.30126298070138 1 0.029346407547734 2744 4544 2975 2839 4561 4616 4167 4574 4503 4232 4386 4646 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 179/370 Arthur Liberzon 0.0839184282471183 0.0902966141827776 4420 4014.18181818182 4398 0.00793650793650794 2374 1.56219539629591 -1.33086546713897 -1 0.419634287276826 4398 4420 2374 2794 4416 4017 4562 4502 3978 4223 4472 4647 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 24/71 John Newman 0.991130964772011 0.9964130389196 4590 4113.63636363636 4401 0.349206349206349 2631 1.24655144995015 -1.09401748766914 -1 0.000500166403038399 4589 4451 2806 2631 4599 4333 4616 4401 4603 3853 4368 4648 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 14/31 Reactome 0.994718561585481 0.998719910390635 4400 4293 4405 0.379163167415021 3386 0.193941184356008 -0.169561917993919 -1 2.75369539423825e-05 4396 4676 3386 4062 4494 4127 4566 3915 4670 4526 4405 4649 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 5/27 KEGG 0.632427457617131 0.649332836633189 4230 4284.63636363636 4407 0.0952380952380952 3673 0.867995824892017 -0.867995824892017 -1 0.0418688434397998 4227 3973 3809 4506 4277 4623 3673 4662 4462 4407 4512 4650 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 9/26 Arthur Liberzon 0.76912797629705 0.784189229096601 4295 4201.72727272727 4407 0.136351285412181 3406 0.811393732962843 -0.811393732962843 -1 0.0220345504934311 4291 4407 4643 3839 4578 3406 4592 3820 4535 4678 3430 4651 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 37/103 Jessica Robertson 0.514011397665828 0.531360558010604 3360 4160.90909090909 4409 0.0634920634920635 2911 1.14294361876908 -0.645211130335362 -1 0.0807308973753407 3358 4551 2911 3997 4606 4617 4080 4521 4409 4233 4487 4652 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 6/10 Leona Saunders 0.910330139360585 0.924335218427671 3565 4235.90909090909 4411 0.214285714285714 3561 0.805001649478674 0.805001649478674 1 0.00707511779975811 3561 3617 4195 3768 4482 4411 4656 4517 4551 4559 4278 4653 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 7/14 Arthur Liberzon 0.991735043431715 0.9964130389196 4095 4272.72727272727 4413 0.380952380952381 3582 0.977621071686444 -0.94493713846385 -1 0.000392214676404274 4095 4187 4570 3582 4545 4667 4053 4413 4613 3592 4683 4654 M15371 BIOCARTA_ETC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETC_PATHWAY.html Electron Transport Reaction in Mitochondria 6/16 BioCarta 0.997319265801003 0.999973409262832 3665 4305 4415 0.446872341394381 3664 0.0719061398221334 0.063909501441179 1 0 3664 4641 3830 4586 4533 4435 4194 4008 4682 4415 4367 4655 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 4/22 Kevin Vogelsang 0.957744907038273 0.968701194556734 4680 4450.45454545455 4417 0.271234329942703 4131 0.0980577126704918 -0.0822269527759995 -1 0.000348107125276677 4408 4579 4390 4243 4340 4677 4131 4417 4679 4616 4475 4656 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 4/16 John Newman 0.0730705732453113 0.0838004665265611 4505 4158 4419 0.00755907014489861 3038 0.714773282504492 -0.714773282504492 -1 0.197962463229855 4503 3812 4419 4536 3842 3038 4531 4036 4554 4621 3846 4657 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 5/15 Arthur Liberzon 0.750476410737753 0.766172649393706 4580 4369.36363636364 4423 0.129615474992475 3874 0.336483283104729 -0.3680841848674 -1 0.0100112025878198 4302 3874 4261 4350 4213 4437 4564 4423 4577 4580 4482 4658 M17977 BIOCARTA_P27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P27_PATHWAY.html Regulation of p27 Phosphorylation during Cell Cycle Progression 7/17 BioCarta 0.999105795091092 0.999973409262832 4655 4336.09090909091 4424 0.504385841109752 3859 0.14541597356842 -0.170669765360081 -1 2.18355729783156e-07 4654 4577 3859 4520 4592 3940 3935 4347 4685 4424 4164 4659 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 37/107 Reactome 0.569787598019453 0.586818611938276 3390 4119.36363636364 4428 0.0738134971504589 2711 0.888043969266385 -0.67840545751831 -1 0.0528780122499277 3389 4547 3646 3999 4633 4428 2711 4641 4459 4299 4561 4660 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 11/29 Reactome 0.994883598314871 0.998719910390635 4615 4207.27272727273 4435 0.380952380952381 3047 0.606848606588604 -0.606848606588604 -1 8.66188166113464e-05 4091 4573 3047 4435 4611 3747 4499 4228 4612 4443 3994 4661 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 13/22 Reactome 0.989324067175235 0.995484771050709 3990 4245.45454545455 4436 0.338142999791314 3358 0.202486553025468 -0.169561917993919 -1 0.00010214900207367 4507 4633 3358 3986 4438 3986 4516 3835 4667 4436 4338 4662 M715 REACTOME_REGULATORY_RNA_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATORY_RNA_PATHWAYS.html Genes involved in Regulatory RNA pathways 12/30 Reactome 0.557443745451391 0.574863862496747 4340 4385.09090909091 4438 0.0714285714285714 3595 0.620851905672583 -0.620851905672583 -1 0.0383956447042051 4337 4677 3595 4438 4603 4563 4269 4645 4424 4456 4229 4663 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 20/59 Leona Saunders 0.999952225523069 0.999973409262832 4640 4362.54545454545 4438 0.595238095238095 3217 0.715524828573075 0.715524828573075 1 1.9118235115229e-06 4362 4673 3217 4257 4637 4195 4378 4637 4650 4544 4438 4664 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 2/13 Jessica Robertson 0.744805398667964 0.760880335329862 4685 4266.9 4438.5 0.140794929305731 3004 0.0661564449712713 0.0661564449712713 1 0.0020193694071641 3895 4365 4512 NA 4685 4065 3004 4626 4684 4641 4192 4665 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 24/72 Leona Saunders 0.943712354754118 0.956159155541145 4450 4215.90909090909 4446 0.23015873015873 2761 1.2112453675829 -0.822569939764537 -1 0.00606564914396914 4446 4450 2761 3660 4634 4319 4471 4510 4561 4210 4353 4666 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 5/10 Jessica Robertson 0.997600350453749 0.999973409262832 4460 4395.45454545455 4453 0.45296541806381 3857 0.101057235144742 -0.101057235144742 -1 8.65912541050768e-08 4460 4684 4319 4432 4453 3857 4481 4274 4686 4595 4109 4667 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 10/14 Reactome 0.874485177881669 0.888709074724247 3870 4112.63636363636 4454 0.171937374658715 3366 0.199829154029269 -0.238232150905031 -1 0.00263350836657124 3867 4681 3483 4521 4631 3366 4454 3588 4636 4489 3523 4668 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 11/25 Arthur Liberzon 0.298735036746822 0.313451048409227 4485 4193.63636363636 4455 0.0317460317460317 2768 1.58973940667201 -1.63462852340934 -1 0.206019551656229 4484 4678 2768 4554 4574 4161 4234 4455 4310 3343 4569 4669 M712 REACTOME_MICRORNA_MIRNA_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MICRORNA_MIRNA_BIOGENESIS.html Genes involved in MicroRNA (miRNA) Biogenesis 10/27 Reactome 0.955240661249004 0.966376886574445 4560 4344.45454545455 4456 0.246031746031746 3572 0.620851905672583 -0.620851905672583 -1 0.00237178545822615 4556 4682 3572 4561 4505 4456 4155 4053 4572 4455 4222 4670 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 5/14 Jessica Robertson 0.838494417110154 0.853243178844339 4540 4397.18181818182 4458 0.166666666666667 4041 0.293910240580321 -0.324632624420235 -1 0.00521058019152636 4538 4041 4458 4296 4680 4505 4340 4157 4521 4631 4202 4671 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 9/19 Arthur Liberzon 0.836519177325181 0.851418085348783 3575 4300.54545454545 4459 0.16565305239219 3497 0.754254108419245 0.754254108419245 1 0.0135525264077215 3575 4459 4618 3982 4632 4579 4284 3497 4586 4672 4422 4672 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 6/25 Jessica Robertson 0.101290669167954 0.108664852500236 3900 3993.90909090909 4464 0.0106227381194419 2541 0.677967976298358 -0.677967976298358 -1 0.168090903503957 3898 4464 4488 4595 4478 2796 4193 2541 4468 4637 3375 4673 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 20/41 Jessica Robertson 0.972114443288272 0.981963414798199 3755 4333.54545454545 4467 0.277777777777778 3581 0.702154621367277 0.702154621367277 1 0.00142741891500878 3751 4557 3581 4255 4676 4356 4183 4467 4584 4597 4662 4674 M17770 BIOCARTA_CELLCYCLE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELLCYCLE_PATHWAY.html Cyclins and Cell Cycle Regulation 11/30 BioCarta 0.795175608578524 0.810136189257391 3695 4098.90909090909 4469 0.134238370654358 2970 1.26337156305408 1.26337156305408 1 0.0297147598877528 3694 4506 3088 4200 4469 4562 2970 4577 4594 3893 4535 4675 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 39/115 Reactome 0.532087906168332 0.549804614841191 4625 4123.54545454545 4478 0.0667136077444782 2670 0.888043969266385 -0.67840545751831 -1 0.0593412557045163 3429 4666 3660 3722 4630 4550 2670 4621 4478 4310 4623 4676 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 4/13 Reactome 0.999919408912814 0.999973409262832 4645 4422.18181818182 4480 0.610391250391589 4005 0.234514031443804 -0.332300577968228 -1 4.83015169998858e-07 4641 4363 4005 4424 4553 4137 4483 4489 4662 4480 4407 4677 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 15/29 Jessica Robertson 0.987609638983393 0.995235294487095 4485 4253.54545454545 4485 0.329121310951202 3454 0.58583264647594 -0.558345319485373 -1 0.000312343484924031 4485 4568 3454 4558 4563 3729 3988 4349 4608 4628 3859 4678 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 4/19 Jessica Robertson 0.811463530836808 0.826275120708667 3965 4358.63636363636 4486 0.153670387223576 3635 0.223789698121842 0.189726481676558 1 0.0047702876971252 3965 4578 4514 4548 4251 4203 3635 4449 4674 4642 4486 4679 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 7/42 Jessica Robertson 0.992735565696391 0.997204471779912 4145 4467.54545454545 4492 0.388888888888889 4141 0.956236661165351 0.956236661165351 1 0.000298820029681872 4141 4576 4520 4600 4463 4408 4247 4436 4615 4645 4492 4680 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 7/78 Arthur Liberzon 0.822436702569706 0.837266649628859 4680 4311.45454545455 4508 0.158730158730159 2924 0.223804250502508 -0.207914496285821 -1 0.00444021920604637 4678 4508 4583 2924 4587 3819 4338 4483 4515 4665 4326 4681 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 5/17 Reactome 0.98691340421372 0.99476795270929 4670 4429 4513 0.351839338861442 4064 0.0864470944826415 -0.0778470879611839 -1 5.04438984194613e-05 4668 4685 4081 4516 4387 4407 4064 4540 4680 4513 4178 4682 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 22/56 Kevin Vogelsang 0.999942469215142 0.999973409262832 4655 4304.18181818182 4520 0.588342160125139 3320 0.477648324804722 -0.477648324804722 -1 1.20522828566676e-06 4537 4625 3320 3604 4520 4139 4653 4300 4652 4617 4379 4683 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 2/8 Arthur Liberzon 0.989058654350605 0.995431454958534 4680 4406.7 4527.5 0.394493275075445 3676 0.188719720155211 -0.234993750301504 -1 9.63185928034951e-05 4363 4278 4596 NA 4459 4655 3676 4014 4678 4668 4680 4684 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 5/17 Jessica Robertson 0.99955959703778 0.999973409262832 4475 4449.63636363636 4530 0.538273263667508 3714 0.228003938903996 -0.274079335492236 -1 4.63677403403003e-07 4473 4686 4473 3714 4581 4412 4644 4132 4668 4633 4530 4685 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 13/31 Jessica Robertson 0.999646813728965 0.999973409262832 4685 4214.36363636364 4548 0.514507902836732 2826 0.166352331483082 -0.15086154650536 -1 2.80545691023388e-07 3600 4683 2826 3921 4686 4548 3893 4327 4683 4594 4597 4686 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 11/25 Leona Saunders 0.999973409262832 0.999973409262832 3750 4197.90909090909 4558 0.616234086210031 2659 0.315268401709373 0.321072787245994 1 7.22890279951862e-07 3747 4640 2659 3525 4677 4670 4089 4359 4653 4558 4600