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 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 6.93260416353232e-06 0.000112799246910807 5 526.454545454545 12 6.9326257910775e-07 3 1.35873970022419 1.35873970022419 1 11.9717952118748 110 634 4507 12 6 4 3 11 80 420 4 2 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 2.00633218427887e-06 4.03505262469132e-05 5 581.727272727273 19 2.00633399569714e-07 2 2.35459573801311 2.35459573801311 1 23.0924953629245 286 640 4293 75 13 19 5 5 2 1054 7 3 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 1.51693594281884e-12 1.57963596178868e-10 25 80.4545454545455 25 1.3790326752908e-13 2 1.21750923279738 1.21750923279738 1 26.6343336635963 9 24 44 25 146 2 55 14 499 64 3 4 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 4.3447801232505e-25 4.83310462587461e-22 5 138.454545454545 26 3.94980011204591e-26 1 1.40874520235793 1.40874520235793 1 67.0213401545885 1 26 4 235 98 5 12 26 1069 1 46 5 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 7.8620694433412e-10 4.49288505018255e-08 10 82.9090909090909 28 7.14733586013714e-11 6 1.573453361899 1.573453361899 1 25.8030787760378 19 275 79 28 164 6 8 9 253 59 12 6 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 4.80479690034565e-05 0.000543847301328979 265 662.363636363636 61 4.80490079083674e-06 19 1.54692007785211 1.54692007785211 1 11.2711224163717 262 1029 4281 271 19 61 56 27 41 1189 50 7 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 6.35600637545384e-10 3.77015770574389e-08 5 225.090909090909 64 5.77818761571831e-11 4 1.41132740199261 1.41132740199261 1 23.3842938556395 4 1136 206 561 38 31 57 28 284 67 64 8 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 1.99592724053572e-10 1.3361307213072e-08 10 96.9090909090909 68 1.81447930974254e-11 8 1.62150348004237 1.62150348004237 1 28.4971337946281 8 95 68 80 130 8 49 329 209 55 35 9 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 2.74071069754288e-10 1.71854549714628e-08 115 185.727272727273 72 2.49155517989482e-11 2 1.50500684447287 1.54134663496227 1 26.0825760948714 113 2 72 21 704 99 488 35 426 16 67 10 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 4.8876134821607e-06 8.48272473237224e-05 90 122.454545454545 77 4.44329485520388e-07 3 1.44551941443065 1.43965666267675 1 13.1357280764398 87 46 253 77 139 3 53 144 466 58 21 11 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 1.42766049220772e-10 1.01363894946748e-08 20 175.545454545455 79 1.29787317481852e-11 16 1.57907719857346 1.57907719857346 1 28.1743173200297 18 38 64 135 740 16 230 79 450 136 25 12 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 2.50714637440747e-16 5.10803822194495e-14 15 268.545454545455 86 2.27922397673405e-17 12 1.50652402033207 1.50652402033207 1 44.6928082533221 12 249 23 86 741 34 74 181 1353 85 116 13 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 0.000277226923952288 0.00216606544015674 75 521.727272727273 88 2.77261514671092e-05 17 1.69362804863984 1.69362804863984 1 10.0712957784569 190 857 3958 74 45 88 198 72 17 166 74 14 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 4.27232506019821e-05 0.00049310628650465 70 319.818181818182 90 3.8840072995921e-06 50 0.989890888416149 0.989890888416149 1 7.3064915273898 56 108 531 149 68 90 50 77 1306 1013 70 15 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 1.48606205390141e-05 0.000214267285679446 55 163.272727272727 94 1.35097462917199e-06 17 1.29764479318941 1.33353290237066 1 10.626452829311 94 55 300 55 329 27 164 62 520 173 17 16 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 2.16011331476698e-08 8.43524249416505e-07 45 104.636363636364 96 1.96373939634225e-09 30 1.25142658635939 1.25142658635939 1 16.9649562118479 42 62 117 30 135 36 102 52 351 128 96 17 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 8.96990489859681e-08 2.80219829032164e-06 440 214.909090909091 97 8.15445933120037e-09 18 1.33813247877675 1.33813247877675 1 16.5831612112191 23 438 146 439 485 30 97 18 621 35 32 18 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 2.59218684314069e-14 3.79593360842415e-12 105 394.363636363636 103 2.35653349376429e-15 13 1.28466095854139 1.30209556555075 1 32.7461386706058 103 652 32 199 1946 67 381 56 818 13 71 19 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 1.63605674696622e-05 0.000233026198063334 85 213.363636363636 108 1.48733537620709e-06 47 1.74573082976662 1.74573082976662 1 14.153825831895 60 333 303 47 787 84 108 261 181 82 101 20 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 3.50437931597548e-06 6.34035578172243e-05 15 545.454545454545 115 3.50438484229121e-07 1 1.02192717514728 -1.02192717514728 -1 9.57481037484916 187 173 3960 115 15 11 1 284 10 1184 60 21 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 5.2454472592406e-05 0.000582468385232262 40 147.090909090909 117 4.7687021184643e-06 28 1.40563492207994 1.40563492207994 1 10.1482185807372 117 98 371 36 127 28 44 212 204 343 38 22 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 1.03955969749196e-12 1.13287831219705e-10 85 188.363636363636 117 9.45054270447681e-14 42 1.46072313339517 1.52329679448 1 32.4255920531983 82 223 42 78 450 117 243 294 402 46 95 23 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 4.93033405663737e-06 8.52529350162462e-05 35 248.818181818182 126 4.48213191441009e-07 10 1.48664870284902 1.48664870284902 1 13.5022648533481 34 126 254 158 1373 35 10 89 408 202 48 24 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 5.56178644613415e-05 0.000608937646882818 15 148.181818181818 129 5.05629732525977e-06 14 2.02713286821371 2.02713286821371 1 14.5479047199008 215 155 693 15 55 129 63 20 14 131 140 25 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 1.69796037217428e-05 0.000240345480181042 30 244.181818181818 131 1.543612251979e-06 10 1.53977296047476 1.53977296047476 1 12.4378269968324 43 267 436 131 1306 10 24 194 219 30 26 26 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 6.51822356769635e-05 0.000700567891329312 70 372 133 5.92583336319881e-06 67 1.53143725582191 1.53143725582191 1 10.7824175711065 127 1054 381 133 1681 71 159 67 274 68 77 27 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 2.54394404572872e-09 1.24176268732133e-07 105 186.818181818182 134 2.31267640788217e-10 10 1.42117085769211 1.49183852996071 1 21.9053397909893 143 29 92 10 703 134 104 324 263 150 103 28 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 2.17561180340472e-05 0.000291283340307273 180 160.727272727273 137 1.97784847149294e-06 10 1.85539616971103 1.85539616971103 1 14.6416390765346 177 137 614 19 10 220 167 36 54 285 49 29 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 2.48648456606351e-05 0.0003236574076826 45 258.181818181818 142 2.26046606296405e-06 21 1.54962007713558 1.54962007713558 1 12.070341848701 45 488 570 49 232 21 28 142 1053 159 53 30 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 0.000418152819321032 0.00300992951050439 135 431.818181818182 143 3.80211198689383e-05 31 1.65818250371208 1.65818250371208 1 9.33170828998858 135 143 790 124 382 80 31 585 82 2109 289 31 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 2.57077816077947e-11 2.11345025638818e-09 30 269.181818181818 143 2.33707105528138e-12 4 1.50861639301266 1.66327032257981 1 29.2097782316695 29 69 55 4 362 524 312 636 143 7 820 32 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 2.16314285357365e-15 3.57500140874506e-13 20 235 145 1.96649350324877e-16 5 1.55688918786361 1.55688918786361 1 43.250617175512 16 5 28 70 1098 145 148 292 388 11 384 33 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 0.000244002146674522 0.0019747738502881 550 285.545454545455 146 2.21844739246996e-05 8 1.70760480381546 1.7779009888362 1 10.3074472145311 549 146 482 8 39 414 773 98 79 86 467 34 M7098 KEGG_ECM_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ECM_RECEPTOR_INTERACTION.html ECM-receptor interaction 42/94 KEGG 3.829038877839e-06 6.80787920156158e-05 40 368.818181818182 147 3.48095049290093e-07 22 1.62856557886872 1.62856557886872 1 15.1463180606741 37 1725 245 147 1262 22 94 63 170 151 141 35 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 3.70227495502669e-05 0.00044257297038916 65 188.909090909091 147 3.36576114573824e-06 48 1.96480097761565 1.96480097761565 1 14.7083222194319 63 159 350 72 175 65 48 162 106 731 147 36 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 9.44802373071825e-07 2.08836977368612e-05 5 597.090909090909 149 8.589116171116e-08 2 2.11565960589036 2.11565960589036 1 22.0998372084708 149 1539 632 310 2925 9 67 3 93 839 2 37 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 0.000992581094703025 0.00586204055096727 145 409.636363636364 150 9.02753821624332e-05 73 1.56551985739929 1.66231725065415 1 7.79871099684879 753 73 1111 105 91 1232 444 143 150 261 143 38 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 1.25548789833543e-06 2.69872306954121e-05 25 246 153 1.14135328619383e-07 21 1.43644620350148 1.43644620350148 1 14.6478886358807 21 338 250 153 344 66 186 129 1071 27 121 39 M5372 REACTOME_XENOBIOTICS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_XENOBIOTICS.html Genes involved in Xenobiotics 2/46 Reactome 0.000235921214717207 0.00192936616433653 320 620.4 156 2.62162172939459e-05 15 2.01369544572059 2.01369544572059 1 12.2004778906901 320 514 3978 NA 117 81 62 51 15 871 195 40 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 1.06757642242469e-05 0.000161898482701687 625 218.181818181818 156 9.70528730002451e-07 6 1.99009742834135 1.99009742834135 1 16.8375874434923 36 156 625 6 298 51 27 622 9 330 240 41 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 1.37857990065558e-07 4.01243814563482e-06 15 312.181818181818 164 1.25325453367378e-08 14 1.44471433573574 1.44471433573574 1 17.4012759441295 14 139 164 268 824 89 65 366 1094 96 315 42 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 0.000224613260775776 0.00187284295372827 170 365 166 2.04214723981846e-05 43 1.81742651813776 1.81742651813776 1 11.0637144368856 166 79 718 93 1380 361 72 43 286 667 150 43 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 0.000667192097013024 0.00428045072309436 170 387.090909090909 168 6.06722292484746e-05 46 2.06837058612759 2.06837058612759 1 10.9341045412522 168 843 982 328 639 57 46 99 119 915 62 44 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 2.20976210345024e-06 4.37904855231954e-05 815 679.181818181818 170 2.20976430082517e-07 5 1.02192717514728 -1.02192717514728 -1 9.94142256285672 815 632 3944 306 5 103 170 118 25 1294 59 45 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 0.00113353647503798 0.00642291647161789 170 782.909090909091 170 0.000113411509770121 88 1.90919498657043 1.90919498657043 1 9.34164652737445 459 170 4302 700 116 166 133 105 1068 1305 88 46 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 4.21882440642593e-16 8.23725465354663e-14 5 319.090909090909 170 3.83529491493266e-17 3 1.52650275917314 1.52650275917314 1 44.5784437896573 3 244 24 170 1068 161 131 271 1075 5 358 47 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 5.49173603324324e-14 7.14840973660494e-12 215 164.727272727273 171 4.99248730294853e-15 3 1.37519994822926 1.4574148146225 1 34.2102525367622 64 213 36 3 422 114 214 192 360 23 171 48 M5882 NABA_PROTEOGLYCANS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_PROTEOGLYCANS.html Genes encoding proteoglycans 22159717 10/35 Alexandra Naba 7.12065903222286e-05 0.000749829398314524 175 420.909090909091 172 6.47353592219734e-06 13 1.54057722975229 1.54057722975229 1 10.7452931303156 172 506 993 256 2145 25 13 87 61 294 78 49 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 3.073168913904e-07 7.70099974895944e-06 15 290.545454545455 173 2.79379031199409e-08 12 1.1906930921744 1.23015850368649 1 13.5891924139103 75 218 182 156 827 12 83 173 914 541 15 50 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 0.000184016419321046 0.00159685359433041 175 602.818181818182 174 1.84031659016327e-05 6 1.02192717514728 -1.02192717514728 -1 6.37897359875201 291 180 3961 174 62 45 20 670 6 1048 174 51 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 0.000221888153102954 0.00186348869004595 95 294.454545454545 174 2.017368504678e-05 52 1.60216182579999 1.60216182579999 1 9.76105132700552 95 85 527 52 1321 174 152 64 282 310 177 52 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 0.000667735697520695 0.00428045072309436 115 481.545454545455 183 6.07216774818193e-05 58 1.2472921577551 1.2472921577551 1 6.59360703433086 183 496 1811 536 803 130 58 80 115 973 112 53 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 4.34478866764647e-10 2.67890522323571e-08 15 296.727272727273 185 3.94980788045866e-11 13 1.54464397919805 1.54464397919805 1 26.1048379852971 13 47 74 112 1253 332 244 416 185 51 537 54 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 3.48466396814006e-09 1.59331934650797e-07 190 310.818181818182 186 3.16787633969051e-10 29 1.30591963230145 1.30591963230145 1 19.8133457812238 101 432 98 29 418 186 138 186 1404 257 170 55 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 0.000102801304126452 0.00100990966695295 130 363.909090909091 187 9.34600982965835e-06 18 1.12582110247691 1.05998430873567 1 7.5274831447628 126 109 1068 123 331 53 18 1213 260 515 187 56 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 2.26844284624359e-07 6.00560631497033e-06 185 357.727272727273 187 2.06222098195011e-08 72 1.46699768061108 1.46699768061108 1 17.0961978424461 182 72 173 136 575 489 680 187 1129 77 235 57 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 1.09503781712833e-09 5.89810024260157e-08 50 381.636363636364 192 9.95488925157622e-11 46 1.46263939064884 1.46263939064884 1 23.6000181810119 48 78 84 46 2319 192 150 231 418 221 411 58 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 1.76316366694323e-11 1.53003424875852e-09 220 254.727272727273 192 1.60287606087033e-12 2 1.09162977510792 -1.03817082303801 -1 21.477907493733 2 34 217 169 242 23 113 244 192 1346 220 59 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 1.62769775744321e-05 0.000232542429615209 70 390.636363636364 193 1.47973618208652e-06 41 1.43251126162783 1.43251126162783 1 11.6172276662747 41 721 751 862 193 69 66 146 1107 223 118 60 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 2.45370797605442e-06 4.73171834394693e-05 305 824.5 197.5 2.72634516879733e-07 1 2.92908440752761 2.92908440752761 1 28.2745470953074 301 378 4030 NA 2469 70 23 7 1 872 94 61 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 0.000132108912109248 0.00121862669713373 205 309.636363636364 198 1.20106223500986e-05 105 1.28694466456869 1.34566305727654 1 8.37043922920699 205 350 432 107 183 116 105 198 1091 466 153 62 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 0.000207375138394105 0.00176362957988163 50 831.181818181818 199 1.88540625864065e-05 24 1.12814415672294 1.12814415672294 1 6.93336147367071 199 1370 1027 2460 80 47 146 48 2369 1373 24 63 M16519 BIOCARTA_TCAPOPTOSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCAPOPTOSIS_PATHWAY.html HIV Induced T Cell Apoptosis 2/10 BioCarta 0.000225523686917311 0.00187376595194064 480 689 200 2.50606994429905e-05 20 1.86280643978199 1.86280643978199 1 11.3390783085156 480 1032 3841 NA 162 238 73 49 20 870 125 64 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 3.01015415848999e-05 0.000375125209205056 205 334.090909090909 201 2.73654122342739e-06 37 1.56187082501595 1.56187082501595 1 11.9423469186033 201 818 336 37 1107 393 188 122 225 102 146 65 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 8.42806010279008e-07 1.89874469431126e-05 95 271.363636363636 203 7.66187575593459e-08 39 1.5831979538117 1.5831979538117 1 16.6839101868937 119 416 203 195 797 93 222 39 557 253 91 66 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 2.89138476896577e-09 1.35562442784414e-07 210 479.181818181818 210 2.62853161160528e-10 14 1.43374285687123 1.44012256037476 1 21.9771966532913 210 523 95 390 2428 123 611 90 747 14 40 67 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 3.93546193025804e-05 0.000463356145859024 55 444.272727272727 211 3.57775666489776e-06 37 1.55588838160164 1.55588838160164 1 11.5780299730866 53 1644 494 721 219 37 78 151 1100 211 179 68 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 0.00166750296307567 0.00882928687567524 260 349.818181818182 212 0.000151706199960592 124 1.50510637493687 1.50510637493687 1 6.90021962562058 258 353 1004 226 134 212 157 130 172 1078 124 69 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 2.76601171219648e-06 5.26891499323281e-05 40 307.909090909091 214 2.51455926349856e-07 40 1.35620026607193 1.35620026607193 1 12.9500803586228 40 113 230 419 652 106 144 286 1127 56 214 70 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 1.83952657528761e-06 3.73161105272629e-05 10 871.3 214 2.04392008802916e-07 6 1.86235441726781 1.86235441726781 1 18.4060104401713 857 1766 4506 NA 99 247 181 6 8 877 166 71 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 0.000263461192756874 0.00208896641160526 525 367.363636363636 214 2.39538862605299e-05 41 1.15709895756841 1.17819210129122 1 6.92143202891224 525 152 860 505 41 214 87 156 1047 331 123 72 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 4.70993531174572e-06 8.20474233116746e-05 70 413.545454545455 215 4.28176854107344e-07 16 1.67358186647758 1.67358186647758 1 15.2622293463318 70 994 252 695 1449 183 172 16 311 215 192 73 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 0.000135141745232489 0.00123928418426505 85 437.545454545455 216 1.22863679493209e-05 58 1.44680578882827 1.44680578882827 1 9.38662116678706 85 696 448 649 1037 58 100 161 1169 216 194 74 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 0.000523423332114902 0.00358590896826086 110 291.454545454545 217 4.7595264211934e-05 79 1.51632538692123 1.51632538692123 1 8.27602892919664 376 297 546 163 79 614 560 139 217 109 106 75 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 2.67123027027269e-05 0.000343884204574116 25 282.818181818182 219 2.42842064071258e-06 23 1.54389915887131 1.54389915887131 1 11.9350620990058 129 536 328 265 939 24 173 23 436 219 39 76 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 0.00024257105684603 0.00196658818750951 135 302.272727272727 221 2.20543460687331e-05 27 1.36962365922226 1.33937775418441 1 8.27283927975212 134 270 506 294 221 42 195 115 1116 405 27 77 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 0.000353783418762453 0.00263565834709198 120 619.181818181818 221 3.53839754603957e-05 29 1.63379508156065 1.63379508156065 1 9.40474779556357 390 164 4543 118 50 340 221 227 29 610 119 78 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 3.87491761746918e-08 1.365252928982e-06 165 560.818181818182 225 3.52265244156283e-09 129 1.42968501246766 1.42968501246766 1 18.7142382573285 161 887 129 905 1582 146 398 225 1374 145 217 79 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 6.49731228416698e-10 3.80580067045081e-08 145 352.727272727273 225 5.90664753280531e-11 77 1.39983931371509 1.43469985701219 1 23.1811799730863 144 768 77 188 1034 225 334 110 618 81 301 80 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 0.000115004617514697 0.00110887168245652 80 789 226 1.04555118000996e-05 34 0.928874509596461 0.928874509596461 1 6.12648720584824 79 1235 2011 1045 120 56 34 121 1576 2176 226 81 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 0.000392503008427354 0.00286044960729484 230 622.454545454545 228 3.56884593240796e-05 58 1.53482108938407 1.53482108938407 1 8.71325195547291 228 1945 675 476 2170 133 169 58 198 691 104 82 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 2.75068861988555e-06 5.26111300929946e-05 145 275.181818181818 229 2.50062914464848e-07 56 1.36709896660505 1.36709896660505 1 13.0561135063101 141 540 229 56 296 175 357 442 458 181 152 83 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 0.000335149973015638 0.00251684739351166 200 367.636363636364 229 3.04728219050054e-05 36 1.32334911251656 1.3759428655218 1 7.67686986834604 198 664 514 589 668 50 223 183 690 229 36 84 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 2.15777667607973e-05 0.000290347579817706 60 598.181818181818 230 1.96163440000685e-06 4 0.908115098698393 0.908115098698393 1 7.16911510825055 58 355 991 782 144 14 4 230 1883 2050 69 85 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 3.39125204434835e-05 0.000409572347417948 70 382.090909090909 231 3.0830039280796e-06 69 1.50812302227352 1.50812302227352 1 11.4029532081838 69 118 347 298 1213 107 135 323 1190 231 172 86 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 3.05725981788942e-05 0.000379003161551054 50 356.363636363636 232 2.77936573121949e-06 50 1.3886332204367 1.3886332204367 1 10.6038974607643 50 125 454 232 759 195 158 293 1089 187 378 87 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 2.97113751710843e-06 5.59146602617273e-05 215 274.454545454545 233 2.70103775426173e-07 41 1.58320229752153 1.61088785968721 1 15.0264940847814 440 80 233 41 387 626 373 214 215 62 348 88 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 2.37307253429377e-06 4.61419829697121e-05 110 556.181818181818 233 2.15734099459837e-07 107 1.50602132156781 1.50602132156781 1 14.5743873475541 107 1679 226 852 1199 170 134 927 417 174 233 89 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 1.66293075116338e-23 9.74061687493951e-21 235 234.363636363636 235 1.51175522833034e-24 3 1.51211852604585 1.5486216579221 1 67.5372162317617 11 211 8 111 776 235 318 235 252 3 418 90 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 6.75102815208774e-11 5.27255298678053e-09 95 279.727272727273 238 6.13729832026809e-12 50 1.39347730819387 1.47987278870589 1 25.7456451092411 91 451 58 176 251 322 187 777 238 50 476 91 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 4.87608554483578e-15 7.61644562103349e-13 40 355.363636363636 238 4.43280504075981e-16 18 1.35435256893671 1.41194121084091 1 36.6311973281927 38 425 30 452 617 141 68 273 1609 18 238 92 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 1.23552212946007e-13 1.52359386806575e-11 40 297.818181818182 240 1.12320193587284e-14 22 1.43396385478544 1.48615343977443 1 34.6202213023098 39 235 37 240 338 229 301 270 1199 22 366 93 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 2.228200498064e-10 1.45018715748999e-08 235 382 240 2.02563681662698e-11 70 1.39358168393414 1.4215734862556 1 24.3808675316081 234 424 70 564 619 159 730 240 822 209 131 94 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 0.00104907733244668 0.00614188397781582 310 242.454545454545 243 9.54161747902204e-05 33 1.28816706802451 1.31711702862885 1 6.35883636290102 307 60 680 33 321 62 119 396 370 243 76 95 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 6.22000230995057e-06 0.000104096181515816 150 531.181818181818 243 5.65456354151781e-07 88 1.512170193664 1.512170193664 1 13.441357209342 146 149 263 243 3022 208 88 339 237 831 317 96 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 8.1448235843498e-07 1.85274967554676e-05 335 344.636363636364 245 7.40438781792898e-08 45 1.25897665620777 1.28987873025182 1 13.2971566968617 333 245 201 221 384 844 555 45 755 75 133 97 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 3.71710181790966e-08 1.32964420753623e-06 250 353.545454545455 246 3.37918352792137e-09 73 1.27292535967909 1.43722743289588 1 16.6949004324033 246 215 127 85 874 606 599 125 595 73 344 98 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 0.000533868142593123 0.00363092324556078 250 592.272727272727 247 4.8545248998578e-05 36 1.17251984417117 1.17251984417117 1 6.38537701530538 247 1297 1886 693 459 206 36 160 247 1171 113 99 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 1.56703934462526e-05 0.000225249888616993 235 321.909090909091 250 1.42459136964609e-06 40 1.35667199870417 1.35667199870417 1 11.0440946429482 232 99 301 40 476 829 584 218 250 78 434 100 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 4.52881130005508e-05 0.000517609993952636 255 463.181818181818 251 4.11718593692158e-06 102 1.55104006528576 1.55104006528576 1 11.3754812643296 251 562 362 228 2083 168 175 102 534 439 191 101 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 0.000330297715666338 0.00249239145831314 160 401.545454545455 253 3.00315741315446e-05 55 1.51327744725247 1.51327744725247 1 8.79298441567452 466 713 922 253 992 346 177 55 173 160 160 102 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 0.00152230744578886 0.00816193671735311 255 710.818181818182 254 0.000152335129131194 39 1.43991841944783 1.43991841944783 1 6.71105723624475 254 177 4565 533 367 149 122 131 39 1198 284 103 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 2.75055297238521e-10 1.71854549714628e-08 200 335.909090909091 254 2.50050270248099e-11 68 1.31687249988119 1.34737557779489 1 22.8221069635106 89 254 73 389 293 345 459 68 1328 198 199 104 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 0.000564246246100737 0.00380439986939288 165 636.090909090909 258 5.13082739509066e-05 29 1.52469496644993 1.52469496644993 1 8.23429705204775 164 1893 750 1773 684 29 38 95 1248 258 65 105 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 3.30100374096442e-08 1.21799240394955e-06 35 339.545454545455 259 3.00091253681322e-09 35 1.58623958942079 1.58623958942079 1 20.9389914323171 35 59 123 313 885 262 259 948 235 218 398 106 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 0.00379542614410815 0.0167224140546736 2035 1156.90909090909 259 0.000345635440726693 77 1.46581583475631 1.62612528960881 1 5.81263854011102 2031 77 1080 141 207 4025 2657 259 242 236 1771 107 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 0.00169247376014267 0.00893812508280216 425 466.181818181818 261 0.000153979744985905 102 1.4071319103959 1.4071319103959 1 6.43434125118116 422 102 649 261 1316 190 155 246 240 1089 458 108 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 2.56962350984807e-06 4.93494088817543e-05 525 452.636363636364 261 2.33602410109154e-07 50 1.32553642224881 1.35351900723625 1 12.7414149678987 219 449 228 50 1775 537 525 249 521 165 261 109 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 4.40450768068152e-13 5.15988074791841e-11 70 284.545454545455 262 4.00409789152946e-14 6 1.93941493951777 2.03195068691066 1 44.5301587655386 6 282 39 69 1026 267 262 468 68 15 628 110 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 1.82287347049698e-07 5.04959365717082e-06 250 423.636363636364 263 1.6571578377604e-08 20 1.57785424249638 1.57785424249638 1 18.6532875221235 20 299 165 263 1549 287 249 248 1084 43 453 111 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 3.27479503946899e-06 6.08955934720305e-05 265 436.181818181818 264 2.97709083104822e-07 54 1.31151544281471 1.31151544281471 1 12.3393763563117 348 54 236 58 1406 595 794 205 575 263 264 112 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 6.6778543607855e-06 0.000110184596952961 230 428.818181818182 265 6.07079511886632e-07 47 1.31034576420877 1.3015229161291 1 11.5751862851696 229 886 265 673 861 74 228 114 723 617 47 113 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 0.000580557398005584 0.00386983210107278 130 694.545454545455 266 5.27918779784198e-05 128 1.14932202006955 1.14932202006955 1 6.1880528926096 128 907 935 1622 136 199 192 266 1455 1563 237 114 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 1.11970791460546e-06 2.42914411474129e-05 550 754.545454545455 268 1.11970847879148e-07 4 2.06322935667965 2.06322935667965 1 21.2498618278226 546 1325 3797 775 35 268 197 4 45 1286 22 115 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 1.25598002748689e-05 0.000185288548931558 240 375.636363636364 268 1.14180654357667e-06 22 1.31957778760857 1.38475877592183 1 10.9919262714175 238 268 293 101 1350 613 428 22 399 244 176 116 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 0.00182869675184268 0.00946880992169593 250 806.090909090909 268 0.000166383507548235 53 1.41569841822541 1.41569841822541 1 6.39436496862393 250 53 1717 608 2490 189 268 138 1894 1103 157 117 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 7.68536716279772e-06 0.00012418493284438 70 702.818181818182 269 6.986721827815e-07 66 1.48078144982656 1.48078144982656 1 12.9090742071878 66 1625 269 2060 1257 110 147 234 1369 245 349 118 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 1.29570235471089e-06 2.74735802451367e-05 215 379 269 1.17791192529336e-07 9 1.44009883493599 1.446094711469 1 14.6602033673323 231 9 212 212 522 683 636 541 676 178 269 119 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 4.62804519525793e-07 1.11215486076814e-05 275 614.181818181818 272 4.20731469894558e-08 54 1.37447254338677 1.33991410633471 1 15.196974596649 272 1711 191 1207 1452 177 585 111 920 76 54 120 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 0.00016889995040595 0.0014849252675465 120 449.363636363636 272 1.53557198823499e-05 23 1.4287597268294 1.4287597268294 1 9.0191066478222 120 800 455 1082 1478 85 272 38 396 194 23 121 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 0.000615850270282563 0.00405319433503383 1010 513.363636363636 274 5.60020667306597e-05 20 1.61869866559941 1.68279153288838 1 8.64258215500028 1007 148 585 20 65 769 1025 274 120 171 1463 122 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 1.14889349856927e-18 2.99095274127534e-16 20 337.909090909091 275 1.04444863506297e-19 18 1.51637402249538 1.62463947869946 1 52.5405787621091 112 216 18 358 565 165 537 275 1134 19 318 123 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 3.63017918704979e-08 1.30853997465503e-06 125 488.181818181818 276 3.30016295177338e-09 44 1.0879429942435 1.0875472499244 1 14.2856586031202 125 560 126 734 1003 44 220 276 1745 476 61 124 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 2.75318729849067e-07 7.04996485285643e-06 90 377.909090909091 277 2.50289785730728e-08 90 1.43318770744055 1.43318770744055 1 16.4794504131787 90 306 178 277 747 204 372 224 1139 127 493 125 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 1.17891675713568e-07 3.51872861397312e-06 65 348.727272727273 279 1.07174256391859e-08 15 1.67277982763966 1.67277982763966 1 20.3611710002895 15 595 153 567 693 63 21 279 1067 63 320 126 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 9.46630633471202e-05 0.000941807037886635 195 519.363636363636 279 8.60610334706948e-06 147 1.52879217088017 1.62099860332014 1 10.3252931788769 192 298 405 672 2734 182 279 147 244 309 251 127 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 8.79124273583743e-08 2.76481633960632e-06 210 502.909090909091 279 7.99203917012476e-09 145 1.61907987077504 1.74020076015777 1 20.0859531628883 208 279 145 183 1739 646 246 734 320 193 839 128 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 2.27771216923853e-06 4.44723301043822e-05 30 545.818181818182 283 2.07064957037397e-07 26 1.37376943403989 1.37376943403989 1 13.3436094043223 26 1151 276 1097 1184 54 84 283 1254 411 184 129 M695 REACTOME_GLYCOSAMINOGLYCAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSAMINOGLYCAN_METABOLISM.html Genes involved in Glycosaminoglycan metabolism 51/122 Reactome 1.20594388536022e-05 0.000179969842254713 25 334.090909090909 284 1.0963186326077e-06 21 1.49728985821875 1.55709050343331 1 12.5145171089211 403 284 375 73 137 821 796 21 153 21 591 130 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 0.000252398381954301 0.00201832562770965 285 625.363636363636 285 2.2947940308953e-05 33 1.33728223335557 1.33728223335557 1 8.04382866553561 285 1460 1211 701 131 100 224 46 572 2116 33 131 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 0.000115900301373529 0.00111292789392697 80 356.454545454545 285 1.05369461525804e-05 80 1.27697952982241 1.27697952982241 1 8.41793007312946 80 107 542 285 603 127 82 316 1146 264 369 132 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 1.96570043721859e-09 9.79922579660247e-08 25 414.909090909091 285 1.78700039906813e-10 24 1.67884527246153 1.67884527246153 1 26.2623995547347 24 285 90 249 768 581 426 972 187 204 778 133 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 0.000170779916161131 0.00149584053669357 110 464.363636363636 288 1.55266522522449e-05 106 1.49891571339297 1.49891571339297 1 9.45132837144411 106 1080 453 806 641 128 182 288 1099 122 203 134 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 2.35536794939679e-08 9.04692968104372e-07 190 409.090909090909 290 2.14124361328534e-09 7 1.47016478786357 1.47016478786357 1 19.8305158005742 7 480 188 773 978 97 45 290 1079 190 373 135 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 1.20284653320466e-05 0.000179969842254713 295 413.545454545455 291 1.09350282709042e-06 140 1.70933939432575 1.81911939688733 1 14.2868509913723 140 555 291 186 650 295 290 452 1173 273 244 136 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 3.14952311939115e-07 7.85035390290794e-06 225 304.909090909091 291 2.86320324570675e-08 34 1.4942818998537 1.56796884718933 1 17.0261815481227 223 571 183 34 626 291 490 425 316 65 130 137 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 6.51961332867076e-05 0.000700567891329312 65 337.909090909091 291 5.92709685714499e-06 59 1.37341725271728 1.37341725271728 1 9.66984331995736 65 559 575 291 618 59 162 61 544 701 82 138 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 3.01797276718537e-05 0.000375125209205056 155 338.181818181818 295 2.74364924427823e-06 54 1.37571450531698 1.37571450531698 1 10.5189620167616 54 153 337 403 667 118 80 348 1111 154 295 139 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 6.52112372203054e-06 0.000107978748273622 300 456.727272727273 297 5.92831186516457e-07 47 1.51029865916257 1.51029865916257 1 13.3711128952795 47 300 264 522 1276 234 132 640 1160 152 297 140 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 8.58507327754688e-06 0.000135910991143867 10 848.727272727273 298 8.58510644429465e-07 7 1.76895727325323 1.76895727325323 1 15.2666053078366 324 2515 4393 926 7 41 114 37 298 671 10 141 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 1.68271855375187e-07 4.72168810950974e-06 300 298.090909090909 299 1.5297442567803e-08 25 1.5060182228006 1.5060182228006 1 17.9020600597128 299 25 162 299 398 415 489 69 811 158 154 142 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 0.00109945016496701 0.00628295545492121 350 345.363636363636 300 1e-04 32 1.43850168215979 1.43850168215979 1 7.06927539704289 347 66 613 32 142 676 441 165 300 879 138 143 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 2.9890751621199e-05 0.0003744913038617 815 515.909090909091 302 2.717377976887e-06 49 1.37571450531698 1.37571450531698 1 10.5212173335319 49 825 627 811 812 73 52 302 1574 267 283 144 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 0.000262420233075614 0.00208423934269886 100 509.272727272727 303 2.38592309358372e-05 100 0.96957541233836 0.96957541233836 1 5.80184940847321 100 603 647 326 425 293 194 140 303 2290 281 145 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 2.24096352051847e-07 5.96656537338042e-06 150 411 303 2.03723977162498e-08 144 1.41861476197853 1.52929443896144 1 16.541317918239 150 303 172 385 961 180 183 443 1279 144 321 146 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 7.92733330208453e-19 2.32171774084801e-16 525 423.545454545455 304 7.20666663825867e-20 8 1.33337316791034 1.37263482824914 1 46.5271732397613 235 191 16 11 1464 793 524 304 588 8 525 147 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 2.77144649814991e-05 0.000352907562237242 100 569.636363636364 305 2.51952855638074e-06 32 1.60207029731318 1.60207029731318 1 12.3445300757379 99 917 330 1390 1949 218 237 32 581 305 208 148 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 4.32177050542676e-11 3.43251128617454e-09 50 522 305 3.92888227773788e-12 46 1.25298743591891 1.33064169535786 1 23.6712850412089 46 261 57 366 1073 193 101 559 1668 1113 305 149 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 1.2505196912468e-05 0.000185288548931558 270 572.454545454545 306 1.13684254498446e-06 10 1.35837866477468 1.35837866477468 1 11.3151329706249 267 1666 306 1108 542 152 176 10 1481 534 55 150 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 7.99292692205422e-06 0.000128479603313735 270 628.454545454545 308 7.26632360153927e-07 83 1.28758586462293 1.3116790828755 1 11.1824120885521 209 238 270 270 1678 1024 948 308 1255 83 630 151 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 3.23836697968845e-05 0.000394155523813508 180 426.090909090909 311 2.94401331722427e-06 115 1.55371173478559 1.56767057822971 1 11.8054339708207 179 439 344 574 869 115 311 257 1203 274 122 152 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 6.36105782602209e-13 7.27022365188768e-11 75 568.272727272727 311 5.78277984183991e-14 40 1.39235088331617 1.39235088331617 1 31.5064816947999 71 237 40 311 2171 349 226 502 1895 54 395 153 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 2.14019089037568e-05 0.000289018285657073 140 411.090909090909 312 1.94564700976066e-06 101 1.45745475834971 1.43850828060663 1 11.5123600601243 136 312 318 281 433 167 161 628 1560 101 425 154 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 1.30756225899379e-05 0.000190879649397037 15 303.545454545455 318 1.18870002773521e-06 12 1.25507339021652 1.24523703396299 1 10.418445492498 271 82 296 398 318 527 374 12 707 340 14 155 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 2.21990583279204e-05 0.000295524963990441 195 518.727272727273 321 2.0181165754784e-06 49 1.40624608763492 1.40624608763492 1 11.0775184045141 191 969 321 531 1311 49 252 202 739 1085 56 156 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 1.89453426032155e-08 7.58785260159556e-07 30 420.181818181818 321 1.72230388785125e-09 28 1.63318782369334 1.71325374383851 1 22.307899209402 28 1141 114 178 521 321 207 465 1062 107 478 157 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 0.000844484661418526 0.00513929236806132 470 525.454545454545 321 7.68008178904269e-05 73 1.7016016799143 1.7016016799143 1 8.69363885193664 469 1939 591 553 305 834 310 135 321 250 73 158 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 7.45918883861825e-05 0.000773313249950555 130 424.545454545455 324 6.78131068857586e-06 20 1.1900495071369 1.1900495071369 1 8.2648421622123 130 324 840 414 20 240 382 120 501 1636 63 159 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 0.000144593139792185 0.00130551725060921 245 411.363636363636 324 1.31456949025964e-05 31 1.44173438276274 1.54350413472509 1 9.28095785931755 243 704 782 570 866 178 433 31 324 249 145 160 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 0.00036796061817873 0.00272395490803401 470 578 325 3.34565614347884e-05 48 2.05369581223184 2.05369581223184 1 11.7562602566033 467 2398 979 800 48 102 206 325 186 772 75 161 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 9.61148266531031e-05 0.000952207352423766 330 658.818181818182 326 8.73809327528121e-06 17 1.65735694990685 1.65735694990685 1 11.1759622672279 326 621 1315 1531 912 52 17 222 264 1777 210 162 M6487 BIOCARTA_PLATELETAPP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLATELETAPP_PATHWAY.html Platelet Amyloid Precursor Protein Pathway 11/29 BioCarta 5.75653528315699e-05 0.00062732847295055 65 368.909090909091 327 5.23335083143377e-06 38 1.46778240338295 1.46778240338295 1 10.4913420852789 62 363 533 820 307 38 59 333 1135 327 81 163 M15422 BIOCARTA_VITCB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VITCB_PATHWAY.html Vitamin C in the Brain 11/24 BioCarta 6.38567191090547e-06 0.000106110846008876 370 462.454545454545 328 5.80517313262954e-07 7 1.46778240338295 1.46778240338295 1 13.0195311800828 32 1009 368 951 369 26 7 256 1607 328 134 164 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 0.000646994400632135 0.00419919080521078 335 643.909090909091 331 5.88349775030807e-05 78 1.50510637493687 1.50510637493687 1 7.98446226463979 331 1371 1180 1221 659 222 193 78 297 1274 257 165 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 1.03491599124574e-09 5.7054309823265e-08 800 748.727272727273 332 9.40832719756893e-11 26 1.6176909907483 1.65582587008506 1 26.1538885788776 800 274 82 26 332 2504 1587 1374 269 34 954 166 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 6.76408159955881e-07 1.55374933213395e-05 335 507 335 6.14916698112038e-08 111 1.70888831603747 1.70888831603747 1 18.3406028761593 111 698 199 211 1320 241 409 334 1147 335 572 167 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 0.00109945016496701 0.00628295545492121 340 598.181818181818 338 1e-04 68 1.68150639039193 1.68150639039193 1 8.26348130350853 338 1154 1325 68 1884 251 166 503 236 436 219 168 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 0.000123751638401911 0.00116212460431133 105 379.909090909091 339 1.12507818247252e-05 105 1.25915852732872 1.25915852732872 1 8.24765864443965 105 122 425 216 176 236 339 668 1161 361 370 169 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 3.77423270188736e-05 0.00044774821369732 340 846.818181818182 340 3.77429680516585e-06 9 1.8636644772713 1.8636644772713 1 13.9302220238685 340 1258 4190 471 1427 43 9 24 98 1425 30 170 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 0.00257656192064874 0.0126030993321086 300 476.181818181818 340 0.000234507677775332 128 1.49853967449582 1.49853967449582 1 6.35319630496181 300 287 777 356 340 630 707 163 1315 235 128 171 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 3.91629413483077e-17 8.73893062657952e-15 115 445.545454545455 340 3.56026739530068e-18 21 1.39577847484304 1.38877226998744 1 43.7961893660585 115 656 21 340 1248 265 317 582 881 115 361 172 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 3.32891373996924e-06 6.09347257245933e-05 240 1032.36363636364 342 3.02628979736467e-07 116 1.44712430656857 -1.20074158169684 -1 13.6143495126504 2075 342 238 116 263 1669 2211 1640 128 239 2435 173 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 3.32891373996924e-06 6.09347257245933e-05 240 1033.36363636364 343 3.02628979736467e-07 117 1.44712430656857 -1.20074158169684 -1 13.6143495126504 2076 343 239 117 264 1670 2212 1641 129 240 2436 174 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 1.09382556960834e-10 8.13597876061062e-09 125 345.363636363636 345 9.9438688151157e-12 33 1.65360090808337 1.70924026855892 1 29.8563544724956 123 787 61 409 86 655 446 345 334 33 520 175 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 0.00750626439966628 0.0280050596949333 400 505.363636363636 346 0.000684727119901633 133 1.94519725193965 1.94519725193965 1 6.74137544863208 400 346 1179 205 938 211 199 449 133 1269 230 176 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 3.67421863644311e-05 0.000440342417656583 215 627.272727272727 353 3.34025454634597e-06 137 1.46778240338295 1.46778240338295 1 10.9948748661698 214 1312 349 1004 551 330 200 526 1924 353 137 177 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 0.000203700956545062 0.00173869341051031 480 453.545454545455 354 1.85199836305132e-05 92 1.54161259447685 1.54161259447685 1 9.49573954545471 92 476 480 754 724 354 280 213 1131 155 330 178 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 8.57517923926369e-08 2.72023461748668e-06 220 611 356 7.795617794098e-09 143 1.33498184109518 1.34806194821293 1 16.5825303240951 220 1130 143 446 1194 294 242 1048 1362 286 356 179 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 1.04301949971035e-05 0.000158687966741646 380 556.181818181818 357 9.48204040632953e-07 66 1.31354560092654 1.37985633857763 1 11.138998077763 379 1405 287 997 283 151 632 88 1473 357 66 180 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 9.42408079562224e-05 0.000939600906559273 75 377.636363636364 358 8.56771319695191e-06 35 1.29636214929285 1.29636214929285 1 8.75843345178409 72 358 518 814 466 40 35 223 1158 391 79 181 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 0.00109945016496701 0.00628295545492121 290 429 359 1e-04 16 1.35182204554185 1.34248548756684 1 6.64330285201484 289 359 808 16 249 442 163 1079 33 390 891 182 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 3.84626421410015e-05 0.000455141265335185 315 568.818181818182 359 3.4966649636882e-06 107 1.48052120340297 1.48052120340297 1 11.0428616460855 311 799 351 575 1924 209 359 178 597 847 107 183 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 0.000259109047428921 0.0020649404698162 485 337.454545454545 359 2.35581426824096e-05 9 1.84569242858206 1.84569242858206 1 11.0610952218211 202 140 484 9 732 516 481 359 47 98 644 184 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 6.82893124847343e-08 2.25354731199623e-06 340 577 361 6.20811950949775e-09 138 1.56906113920035 1.51930481886094 1 19.7764102169631 337 783 138 175 2502 142 361 863 456 191 399 185 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 1.15340361757011e-09 6.14187426356082e-08 5 405.727272727273 361 1.04854874379528e-10 5 1.5135878907768 1.5135878907768 1 24.3626651405812 5 921 104 361 781 243 120 383 1052 28 465 186 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 4.66629251570384e-06 8.15904728678664e-05 55 666.090909090909 362 4.2420931028508e-07 51 1.31151594040215 1.31151594040215 1 11.9674691637039 51 1407 251 528 2924 140 362 565 622 276 201 187 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 1.09689892236711e-07 3.32061988456738e-06 365 484.909090909091 362 9.97180888234038e-09 150 1.50977095629824 1.49803077708373 1 18.4618215668177 362 901 150 287 680 244 694 1127 459 226 204 188 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 0.00109945016496701 0.00628295545492121 365 464.454545454545 364 1e-04 64 1.2890105193347 1.39040477340632 1 6.33462613485822 181 316 813 64 445 713 399 364 1124 364 326 189 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 7.30407192843711e-05 0.000758910888174197 150 553 368 6.64028585207743e-06 104 1.54623393728817 1.54623393728817 1 10.7667044700752 148 104 394 509 1807 137 202 368 1108 1012 294 190 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 0.00142665288032219 0.00771083667495939 340 446.272727272727 372 0.000129779897722805 42 1.42653469886698 1.42653469886698 1 6.72729586776166 336 42 638 273 372 685 292 243 490 1098 440 191 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 0.0013348303307373 0.00737619685122051 410 908.636363636364 373 0.000121421901430111 107 1.58708857426818 1.58708857426818 1 7.55269660695308 407 1683 2444 350 2455 373 278 112 107 1458 328 192 M666 REACTOME_HYALURONAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HYALURONAN_METABOLISM.html Genes involved in Hyaluronan metabolism 11/23 Reactome 8.68796307608639e-07 1.93865690354956e-05 375 579.636363636364 373 7.89815137002665e-08 2 2.04353376858114 2.04353376858114 1 21.4937725332662 373 2514 824 82 930 596 539 2 70 329 117 193 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 0.000231255030052633 0.00190115977338007 280 535.090909090909 381 2.1025394746947e-05 148 1.50300092147005 1.50300092147005 1 9.1277633522202 279 1228 474 602 300 741 329 381 1154 148 250 194 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 0.000517495876086599 0.00355569747117567 385 898.818181818182 384 5.17616426490349e-05 40 2.09561721618761 2.09561721618761 1 11.4549614613513 384 738 4145 418 1863 307 180 70 40 1607 135 195 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 2.72626358072227e-09 1.30359909584332e-07 95 387.818181818182 391 2.47842144009153e-10 42 1.53391680058278 1.52666237430565 1 23.570902797747 341 302 94 42 856 589 404 725 391 93 429 196 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 9.74513034661633e-13 1.08727811438676e-10 45 521.363636363636 392 8.85920940601876e-14 41 1.29767298937726 1.32396423501159 1 28.8578313384832 147 867 41 462 1943 171 392 490 847 42 333 197 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 8.30343948025651e-05 0.000844032915498525 70 560.363636363636 392 7.54886626614473e-06 26 1.46778240338295 1.46778240338295 1 10.0691849506682 68 941 407 719 1416 176 26 170 1594 392 255 198 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 4.32829937302642e-33 1.01412054310009e-29 5 387.818181818182 392 3.93481761184224e-34 2 1.46551180892967 1.48929869164421 1 94.836533206086 33 392 2 2 1490 484 440 363 448 4 608 199 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 0.0017165558468202 0.00903795584067354 365 495.363636363636 393 0.000156172423541051 134 1.53212608635889 1.76580165720083 1 6.98940222917336 361 147 650 250 1157 915 578 201 134 393 663 200 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 4.52711726110041e-10 2.75507421889825e-08 220 630.636363636364 395 4.11556114730181e-11 75 1.52989567188941 1.52989567188941 1 25.814012046024 218 876 75 395 1245 637 967 328 1683 137 376 201 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 2.29225290822773e-05 0.000302577383886061 1455 675 395 2.08388799301712e-06 44 1.58036988459142 1.58036988459142 1 12.4130283989461 44 1453 395 1297 1455 325 160 285 1246 268 497 202 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 5.20684273992669e-06 8.90484126981622e-05 380 718.636363636364 396 4.73350460295036e-07 161 1.49297839517535 1.49297839517535 1 13.496718341443 377 1499 257 853 786 794 298 335 2149 161 396 203 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 0.00243928976583133 0.0120447964622609 505 750 396 0.000221999870746043 110 1.39930112419729 1.39930112419729 1 5.9939220905228 502 1527 1331 396 2130 272 125 391 308 1158 110 204 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 8.00089464508341e-05 0.000822197199711861 205 536.818181818182 396 7.27380512187163e-06 65 1.25593476632899 1.25593476632899 1 8.64779100363347 204 1566 396 1177 761 79 274 65 819 477 87 205 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 8.19248610413473e-05 0.000837389464982099 305 527.818181818182 397 7.4479919968491e-06 39 1.25807735555051 1.28081525701169 1 8.64021660462234 302 248 397 39 1083 311 650 794 645 1112 225 206 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 0.00318869295657511 0.0146492305828539 325 569.909090909091 397 0.000290302187905138 136 1.50864246462652 1.46778240338295 1 6.17602526363274 397 1222 846 724 291 324 321 369 1125 514 136 207 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 0.000233808972295415 0.00191543504226628 400 551.727272727273 398 2.12576204058072e-05 44 1.71433433560073 1.71433433560073 1 10.3987658092696 398 695 704 145 1848 860 544 44 285 246 300 208 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 0.000600879936591164 0.00397140110418363 195 469.909090909091 399 5.46403741867483e-05 61 1.36587385191605 1.396315342414 1 7.31968648417706 195 61 557 545 1524 276 325 399 507 433 347 209 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 0.000183324410920694 0.00159586284021191 665 404.363636363636 400 1.6667244453984e-05 40 1.59629330942587 1.69119934668786 1 9.96518586919062 662 693 526 53 400 1117 414 40 223 230 90 210 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 0.00048204051461975 0.00339165443169392 165 666.090909090909 400 4.38314696910851e-05 163 1.53793916968323 1.53793916968323 1 8.47702160349955 163 1626 535 939 1411 304 247 210 1180 400 312 211 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 0.00112215486672253 0.00636612313009902 565 726.272727272727 401 0.000112272192396572 104 1.84083109373717 1.84083109373717 1 9.02299143722431 565 1020 3821 401 357 221 512 104 111 668 209 212 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 8.57679003366019e-05 0.000868052658698308 190 472 401 7.79738583780048e-06 84 1.52600922401371 1.52600922401371 1 10.4271216798528 189 84 401 206 562 573 326 710 1283 325 533 213 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 0.000152350392917766 0.00136503621646778 115 433.545454545455 402 1.38509949302411e-05 33 1.40459968537705 1.40459968537705 1 8.98121085238026 349 313 639 796 834 402 115 33 542 635 111 214 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 0.000190815636622977 0.00164670731715519 460 472.636363636364 402 1.73483808099014e-05 286 1.4041997831852 1.4041997831852 1 8.72331425218092 351 286 460 367 1183 459 327 402 580 404 380 215 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 9.33131316664395e-05 0.000934327638865247 100 530.909090909091 403 8.48337179850392e-06 18 1.34037655487012 1.34037655487012 1 9.06311414146797 98 1066 403 1611 473 18 39 76 1357 613 86 216 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 1.8784125691887e-06 3.79406952552511e-05 25 420.272727272727 403 1.70764924820378e-07 25 1.35430913783172 1.35430913783172 1 13.363109762008 25 608 534 849 403 46 25 219 1121 550 243 217 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 0.00352347731967084 0.0157547850381465 205 493.181818181818 405 0.000320830285291696 104 1.57047128517891 1.57047128517891 1 6.31838251069259 545 345 1087 104 202 273 405 497 201 1266 500 218 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 1.72058991573072e-06 3.57463173472032e-05 1170 886 405 1.72059124792552e-07 4 1.22549969020678 1.22549969020678 1 12.1629045883315 1168 376 4370 374 4 728 664 239 112 1306 405 219 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 3.06583532471908e-05 0.000379063438829382 295 445.727272727273 406 2.78716186350338e-06 162 1.46778240338295 1.46778240338295 1 11.208071133044 162 503 338 292 255 406 429 665 1081 291 481 220 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 1.36782085480447e-06 2.87426391283127e-05 605 575.454545454545 409 1.24347427748155e-07 154 1.44167949613553 1.5085548296681 1 14.6131905500708 603 409 214 341 1169 1193 1128 154 768 168 183 221 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 1.16936791051979e-09 6.15691913336602e-08 325 481.545454545455 410 1.06306173740123e-10 85 1.55486751164161 1.3505049652864 1 25.0234133339811 321 258 85 187 1260 427 410 1021 474 175 679 222 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 0.000510832380994707 0.00352542052627569 125 722.363636363636 410 4.64500939161002e-05 33 1.59765669417694 1.59765669417694 1 8.74627685867779 124 1793 968 1200 2770 33 60 92 410 412 84 223 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 1.1642470852398e-06 2.51412988084503e-05 20 679.727272727273 411 1.16424769520233e-07 3 1.25811425780433 1.25811425780433 1 12.9157867112274 443 511 4350 411 3 20 19 474 23 1192 31 224 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 0.00883229442695415 0.0315939936524482 415 684.909090909091 415 0.000806177622152891 34 2.29243283311475 2.29243283311475 1 7.67682993752311 415 1649 1589 1154 411 617 217 355 34 840 253 225 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 0.000117013357117919 0.00111675069542682 210 708.909090909091 418 1.06381437522649e-05 45 1.23403579994088 1.29693759492033 1 8.13074060367559 207 2068 418 904 1773 55 572 113 1502 141 45 226 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 8.89027262177112e-14 1.12594101366539e-11 5 818.181818181818 419 8.89027262177144e-15 1 1.40266459486514 1.46373450231112 1 34.2757835808767 261 383 4554 1 1595 495 463 238 589 2 419 227 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 0.000896851835421337 0.00540186079792338 140 588 420 8.15652413429408e-05 107 1.46778240338295 1.46778240338295 1 7.4281423358147 139 944 619 1056 742 187 107 420 1595 356 303 228 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 0.000121463143939525 0.00114932174295076 180 416.636363636364 421 1.10427136819316e-05 100 1.25807735555051 1.28081525701169 1 8.25408599951369 180 671 421 274 376 150 535 435 682 759 100 229 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 2.89748007449114e-06 5.4788981046456e-05 225 756.818181818182 423 2.63407626416809e-07 221 1.36781279769267 1.37267687732809 1 13.0091529032775 221 1062 231 947 1715 331 519 352 2216 308 423 230 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 2.12264942981167e-06 4.23265328855211e-05 185 465.545454545455 425 1.92968316166626e-07 185 1.42843866563998 1.51701378673411 1 13.9430919686519 185 448 222 425 303 693 204 621 1133 278 609 231 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 0.000862593518050168 0.00524229128440445 995 506.909090909091 426 7.84483560322343e-05 91 1.64768232879319 1.64768232879319 1 8.38646787526036 991 151 1104 426 225 522 511 91 231 914 410 232 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 0.000287613138010867 0.00222769448713872 415 579.909090909091 427 2.61500677720838e-05 50 1.86257814601771 1.86257814601771 1 11.0253203967247 412 1796 988 427 624 610 396 50 230 657 189 233 M15997 BIOCARTA_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTRINSIC_PATHWAY.html Intrinsic Prothrombin Activation Pathway 14/36 BioCarta 2.0120880215015e-05 0.000276499837793432 255 476.272727272727 428 1.82918765818336e-06 195 1.48381875341347 1.46778240338295 1 11.7842947281986 253 829 313 641 539 481 211 263 1086 195 428 234 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 5.62846234243724e-07 1.31874872683305e-05 705 617.909090909091 428 5.11678525674459e-08 63 1.36101499655216 1.46756828218319 1 14.8234012700273 705 63 195 121 2253 1026 896 428 493 213 404 235 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 0.00012993761789799 0.0012081104711706 425 591.909090909091 429 1.18132084527411e-05 142 1.36065430064961 1.36558925954677 1 8.86128628778926 423 242 429 151 628 1266 1412 689 333 142 796 236 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 8.07065635098763e-05 0.000827551327368228 70 587.363636363636 429 7.33722948783755e-06 67 1.46778240338295 1.46778240338295 1 10.0972418969789 67 1164 760 1262 655 144 77 393 1217 429 293 237 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 0.000559925070666842 0.00378616000165198 220 606.727272727273 430 5.09152389796739e-05 65 1.43775902363395 1.52442468789122 1 7.77148686800765 216 65 551 90 3078 271 323 642 430 575 433 238 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 0.000192122838126913 0.00165190388892241 580 564.272727272727 432 1.74672379990715e-05 165 1.70412384147194 1.70412384147194 1 10.5813287949676 579 980 461 336 326 385 165 487 405 1651 432 239 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 1.43102551294072e-08 5.7808496152071e-07 100 562.090909090909 434 1.3009322929537e-09 37 1.60965854575773 1.56359569779051 1 22.4108982890284 96 964 113 364 1614 681 434 742 313 37 825 240 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 0.00139756991324952 0.00760628642681448 440 683.818181818182 438 0.000127132592962131 107 2.24458518468169 2.24458518468169 1 10.6147852367224 438 610 1364 925 107 434 320 504 330 2238 252 241 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 1.00732991872741e-05 0.000154744516940913 4425 1745.81818181818 438 9.15758664628516e-07 27 1.26823828688224 1.45491920842309 1 10.7857225109435 4423 27 284 120 277 1616 4608 3982 438 110 3319 242 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 3.30914112702287e-06 6.09347257245933e-05 440 726.545454545455 439 3.00831464044975e-07 27 1.46739441062581 1.46739441062581 1 13.8050479067293 27 589 439 1640 1646 91 126 489 2205 438 302 243 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 0.00111478734709063 0.00633199213147477 295 599 441 0.000101395694081159 238 1.58889383886159 1.46778240338295 1 7.79637879402169 293 932 612 1257 238 441 258 779 1156 266 357 244 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 1.28684728650747e-06 2.7409847202609e-05 445 754.454545454545 441 1.16986185384038e-07 209 1.55307376270385 1.55307376270385 1 15.8137842215837 441 293 211 209 2516 1422 739 921 314 217 1016 245 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 6.77967821403177e-06 0.000110695373208895 3665 1634.90909090909 442 6.1633628244235e-07 83 1.23973966458594 1.265738386512 1 10.9459162398699 3661 127 267 83 442 3020 4653 1729 163 147 3692 246 M6856 KEGG_HEMATOPOIETIC_CELL_LINEAGE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEMATOPOIETIC_CELL_LINEAGE.html Hematopoietic cell lineage 35/107 KEGG 6.77814931498983e-06 0.000110695373208895 10 523 443 6.16197290763798e-07 1 1.50314197515105 1.50314197515105 1 13.2715493636789 78 1789 443 1012 721 1 15 8 547 1131 8 247 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 6.09412803353895e-22 2.85570839651635e-19 10 433.818181818182 443 5.54011639412629e-23 10 1.54905707129713 1.58684431853208 1 64.1146230430354 10 418 10 451 609 443 367 654 1253 53 504 248 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 0.000672126051252248 0.00428976045951875 570 549.818181818182 444 6.11210437810185e-05 262 1.47451698203415 1.5909990240543 1 7.79168889351137 566 1144 567 262 828 323 315 444 262 342 995 249 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 4.79851473870084e-05 0.000543847301328979 275 843.909090909091 446 4.36238127669844e-06 273 1.72708890821917 1.72708890821917 1 12.5838631143396 382 1521 364 1598 2262 541 273 446 1237 386 273 250 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 3.73544235430156e-05 0.000444271138889774 175 453 446 3.39591434631249e-06 14 1.246250893025 1.246250893025 1 9.32469505032941 175 327 577 278 14 138 452 535 1324 717 446 251 M3005 NABA_COLLAGENS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_COLLAGENS.html Genes encoding collagen proteins 22159717 17/45 Alexandra Naba 6.24921848206639e-06 0.000104212945932253 35 571.818181818182 449 5.68112384852603e-07 31 1.46726266075591 1.46726266075591 1 13.0405893360517 31 826 355 941 813 339 234 492 1569 241 449 252 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 0.00022644610948774 0.00187478174745504 515 427.818181818182 451 2.05881291778509e-05 18 1.37694252489559 1.45492011790452 1 8.38085552412704 514 97 471 18 451 1173 780 184 141 363 514 253 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 0.000254580073203509 0.00203230361674896 290 1073.45454545455 453 2.31463215935156e-05 47 1.30774781221536 1.30774781221536 1 7.85742877813136 287 1461 1309 1726 3527 367 254 47 453 2045 332 254 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 6.9782614487894e-05 0.000739822016946315 260 457.727272727273 453 6.34407527697967e-06 105 1.41989514706111 1.47775660779177 1 9.92204622486228 259 453 386 192 105 670 883 889 460 552 186 255 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 5.05443738244282e-08 1.70396356648396e-06 85 666.363636363636 454 4.59494318051553e-09 83 1.51848659994929 1.51848659994929 1 19.5504340571632 83 454 135 879 1074 278 248 732 2160 865 422 256 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 1.73588897663519e-34 8.1343757445125e-31 90 598.181818181818 454 1.57808088785018e-35 1 1.48902824976591 1.5129005897972 1 100 88 1112 1 454 2071 460 422 613 884 36 439 257 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 8.65686613105064e-05 0.000874268851079812 460 568.090909090909 457 7.87018799293828e-06 17 1.30978505974319 1.37442403698371 1 8.94061679972592 457 389 412 17 685 1772 1021 400 476 32 588 258 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 0.000190118284447785 0.00164670731715519 240 540.909090909091 458 1.7284974178545e-05 124 1.48089481197077 1.48089481197077 1 9.19976699465812 237 124 458 342 149 1020 527 886 1097 387 723 259 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 0.00120174152673077 0.00676754816221133 425 1439.09090909091 464 0.000120239190400309 69 1.1876472081917 1.1876472081917 1 5.75096073688407 425 2338 4534 2759 464 416 69 314 2736 1526 249 260 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 0.000220998789195207 0.00186259051469198 275 659.090909090909 467 2.00928175026485e-05 22 1.72695253772796 1.78236148631409 1 10.5221364423634 275 240 467 22 2078 848 954 1045 212 149 960 261 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 0.00110502456021969 0.00629179233194348 465 552.545454545455 468 0.000100507271533575 119 1.50554140955096 1.50554140955096 1 7.3966798033484 465 468 610 599 977 1048 153 119 1101 201 337 262 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 1.25739988391454e-05 0.000185288548931558 175 717.181818181818 468 1.14309733689388e-06 173 1.38528209150568 1.45887506366387 1 11.5392353205244 173 1129 294 432 2826 319 468 630 608 712 298 263 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 0.000629557126072878 0.00411451142646793 135 546.363636363636 468 5.72488503468404e-05 54 1.46778240338295 1.46778240338295 1 7.81544544156694 132 613 589 1054 997 281 54 307 1151 468 364 264 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 0.000125490529041634 0.0011737497387008 675 842.818181818182 469 1.25497616147701e-05 20 1.69432755403293 1.69432755403293 1 11.0817274241424 672 2109 4395 524 469 191 123 30 66 672 20 265 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 0.000114594643516565 0.00110719690622397 765 412.363636363636 470 1.04182375465486e-05 39 1.65351703051613 1.67028780149623 1 10.9083639289961 487 470 451 98 765 765 562 153 117 39 629 266 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 3.42282414590363e-08 1.24336077113988e-06 120 573.545454545455 470 3.11165836286993e-09 116 1.66471602065399 1.66471602065399 1 21.9416479331647 116 568 125 960 1358 407 285 629 1227 164 470 267 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 2.52870846049497e-08 9.63376247632474e-07 60 658.454545454545 471 2.29882589960025e-09 57 1.46778240338295 1.46778240338295 1 19.7089637326815 57 471 119 1020 1181 301 256 549 1889 945 455 268 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 1.58898128588432e-07 4.51270685191146e-06 175 420.090909090909 471 1.44452854604614e-08 160 1.52975412051456 1.52975412051456 1 18.2513346699714 171 803 160 512 234 564 471 601 617 298 190 269 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 0.000344610918047666 0.00257962741528972 970 922.909090909091 473 3.13331736545173e-05 88 1.35058437148017 1.3838827692098 1 7.80260969750163 967 257 512 473 88 2829 2663 1273 387 362 341 270 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 0.000964142359451199 0.00573346585836081 475 573.090909090909 475 8.768774099238e-05 89 1.37331527974627 1.37331527974627 1 6.87075695920779 475 1053 854 333 89 277 352 1267 736 338 530 271 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 2.53462615146679e-10 1.62702166380457e-08 110 405.909090909091 475 2.304205592508e-11 71 1.66079020917282 1.66079020917282 1 28.8704865141598 108 795 71 152 552 561 592 602 400 157 475 272 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 0.000631874842814688 0.00412390740031982 190 1464.72727272727 475 5.74596727532546e-05 43 0.689861320305099 0.689861320305099 1 3.67175318206867 188 2292 1678 2771 475 98 43 389 3534 4442 202 273 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 0.000238357608477707 0.00193913846063635 155 780.818181818182 478 2.16712215545327e-05 153 1.77795794364836 1.77795794364836 1 10.7634962040346 153 349 478 457 2492 359 261 817 1554 1119 550 274 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 0.0114728635772514 0.0384837786134575 445 647.909090909091 479 0.00104846675843105 212 1.40659842435102 1.46778240338295 1 4.44141012448979 445 1306 837 1140 479 433 293 578 1126 212 278 275 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 0.00550638835918466 0.0221674706624908 835 673.727272727273 479 0.000501838073332059 155 1.41221169300033 1.53738628538886 1 5.21422046396069 834 329 1528 155 271 566 479 1748 393 754 354 276 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 2.33717534845836e-17 5.47600184143793e-15 65 664.363636363636 480 2.12470486223487e-18 20 1.41864393546169 1.41864393546169 1 45.1563962881255 61 1192 20 774 2239 586 388 457 988 123 480 277 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 0.00258130722170794 0.0126131445682204 470 884.909090909091 481 0.000234940082666867 164 1.29912324315874 1.30515339077425 1 5.5067487817051 468 1278 1028 1348 2004 437 354 164 1912 481 260 278 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 6.47214693842323e-20 2.33296004257317e-17 105 528.454545454545 483 5.8837699440211e-21 9 1.40194806487094 1.47969914174708 1 52.0425271071236 104 520 13 241 2064 337 492 757 793 9 483 279 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 7.23770599752151e-05 0.000755365040186766 430 1042.90909090909 486 6.57994919940369e-06 245 1.35980936745317 1.42566808052816 1 9.47476960439965 428 2376 392 1035 3582 696 464 245 1469 299 486 280 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 3.7228383659521e-05 0.000443898742566196 770 772 487 3.72290073528738e-06 9 2.06322935667965 2.06322935667965 1 15.439166162696 769 858 3798 363 122 704 487 17 78 1287 9 281 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 0.000679537237887048 0.00432063975134153 135 655.363636363636 487 6.17952022311065e-05 133 1.31943429260432 1.40748322281163 1 6.96302274103844 133 1077 900 949 995 487 294 321 1565 189 299 282 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 4.90499773812678e-07 1.17269486739092e-05 5 841.818181818182 490 4.90499882078223e-08 1 2.1897291610845 2.1897291610845 1 24.0984252055708 556 2827 3951 181 2 548 634 1 52 490 18 283 M15394 BIOCARTA_AMI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AMI_PATHWAY.html Acute Myocardial Infarction 13/34 BioCarta 0.00013114583457997 0.00121452446806668 305 564.272727272727 491 1.19230593694787e-05 170 1.48381875341347 1.46778240338295 1 9.65578124637747 305 834 430 805 638 491 369 576 1117 170 472 284 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 0.00143920635711816 0.00776557619445582 325 887.454545454545 491 0.000144013929932706 83 2.76431492756404 2.76431492756404 1 13.0170861296918 322 161 4412 827 118 567 491 483 83 1712 586 285 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 5.19906453954507e-06 8.90484126981622e-05 275 749.727272727273 492 4.72643347824821e-07 256 1.36079428330329 1.36079428330329 1 12.3017568249671 274 1208 256 1327 453 1235 822 370 1439 371 492 286 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 0.000283099965331166 0.00220001067585712 585 716.727272727273 493 2.57396728826653e-05 157 1.79426380486278 2.11531861520601 1 10.6426900759303 584 583 493 244 3028 157 916 262 229 1046 342 287 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 0.00139431266473374 0.00760622717921106 495 614.090909090909 493 0.000126836103180147 116 1.40455346425498 1.40455346425498 1 6.64223273038156 493 1170 1120 1501 625 299 303 116 590 394 144 288 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 0.0230639085895143 0.0652383741535136 625 720.090909090909 494 0.00211902824378658 84 1.5459610764906 1.5459610764906 1 4.09052001411191 624 1593 1089 92 2226 408 494 507 84 352 452 289 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 0.000105323625527026 0.00102608421875186 415 872 496 9.57533346979798e-06 167 1.23740151402039 1.23740151402039 1 8.25447623175408 233 1976 413 1090 3185 419 496 167 700 500 413 290 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 0.00163638780426575 0.00868415996691883 400 877.272727272727 498 0.00016375940488506 126 1.60715025417964 1.60715025417964 1 7.39386265312454 396 629 4459 309 126 894 498 421 1037 167 714 291 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 0.000168881117986745 0.0014849252675465 480 749.272727272727 498 1.5354007581337e-05 19 1.38622368568856 1.38622368568856 1 8.75059607587241 479 1986 933 1673 273 256 529 251 1345 498 19 292 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 0.000747739534754296 0.00466565573882641 320 717.545454545455 499 6.79994362422246e-05 85 1.43581252148578 1.43581252148578 1 7.47026195405849 316 1134 1382 499 2069 105 189 85 1211 811 92 293 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 0.00430410785816488 0.0183521832787631 500 554.272727272727 500 0.000392050145962424 208 1.20639644803705 1.29383307824025 1 4.67517031689392 500 208 810 463 228 945 691 641 815 457 339 294 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 0.00105694593078913 0.0061722522978934 375 824.636363636364 500 9.6132187371973e-05 93 0.916457444483748 0.916457444483748 1 4.51956811345273 371 121 1122 1456 93 401 602 500 1675 2604 126 295 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 0.000714464984146893 0.00450603353393316 455 1242.36363636364 501 7.14694795238066e-05 86 0.997293395573521 0.997293395573521 1 5.22238110161826 451 513 4555 1281 501 351 141 86 1057 4491 239 296 M14693 VANTVEER_BREAST_CANCER_POOR_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_POOR_PROGNOSIS.html The optimal set of 70 prognostic markers predicting poor breast cancer clinical outcome (defined as developing metastases with 5 years). 11823860 45/129 Arthur Liberzon 0.000312856019530692 0.00238148759504746 180 948.181818181818 504 2.84455017085802e-05 72 1.22942615175472 1.22942615175472 1 7.19789330624944 178 2753 504 2521 1435 119 81 128 1750 889 72 297 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 0.0132648092162372 0.0425745862926626 510 736 507 0.00121322459497304 101 1.34051551161529 1.4031632732084 1 4.10148565107541 507 101 986 317 1898 1049 909 459 1228 200 442 298 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 3.50217440653694e-09 1.59331934650797e-07 700 713.090909090909 508 3.18379492010187e-10 20 1.43693029933278 1.49746625288449 1 21.801032911985 699 20 99 134 1957 1356 1277 342 508 316 1136 299 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 0.00596118406358015 0.0235929970624464 390 1190.27272727273 509 0.000543399836633752 269 1.18412330342188 1.25472808933965 1 4.3005294418949 387 1504 2328 1912 4086 509 412 269 469 790 427 300 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 0.00151453185649253 0.00812954900289117 260 912.818181818182 510 0.000137779591083502 75 1.20886515090946 1.20886515090946 1 5.63884153184484 260 2200 912 1940 471 358 75 510 632 2235 448 301 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 0.000351285313105383 0.00262121493186596 515 647.636363636364 512 3.19401288345404e-05 128 1.53832836405953 1.53832836405953 1 8.86339876775651 512 128 513 609 214 1576 1186 438 1162 383 403 302 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 0.00382458470284985 0.0167809025445266 395 767.818181818182 512 0.000348295433653415 209 1.55716037813951 1.55716037813951 1 6.16959195668023 391 1676 793 1638 1526 648 309 209 484 260 512 303 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 3.50358275903498e-07 8.64094147833574e-06 75 604.909090909091 512 3.18507574272167e-08 73 1.52768577339553 1.52768577339553 1 17.2647051520961 73 1049 185 424 904 512 275 931 1177 483 641 304 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 9.86300823592996e-05 0.000973011717759322 1415 621.181818181818 512 8.96677312786018e-06 76 1.19989172856267 1.30668396673353 1 8.06602487662142 76 879 643 591 1414 101 474 512 1414 507 222 305 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 0.0383242876775229 0.0945695692769206 875 808.454545454545 513 0.00354624104778396 124 1.45033444021608 -1.38916827744188 -1 3.31553097068535 873 369 1280 130 2470 513 501 1413 124 732 488 306 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 0.000246492830766402 0.00198464846215011 455 576.090909090909 515 2.24109502452053e-05 29 1.29940513081747 1.29940513081747 1 7.83718917945415 452 989 748 349 715 353 171 1476 515 540 29 307 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 0.000365894646191354 0.0027172461363751 275 1053.81818181818 515 3.32686831278522e-05 226 1.16594547686652 1.16594547686652 1 6.67717284287389 273 1140 515 1285 4239 270 425 226 1966 816 437 308 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 8.00598467085163e-06 0.000128479603313735 285 778.545454545455 517 7.2781943685912e-07 165 1.51394314506575 1.51394314506575 1 13.1482774018685 165 1059 271 812 2550 297 281 282 1642 517 688 309 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 0.00175859530874718 0.00917483533446641 520 541.090909090909 518 0.000160000239758192 136 1.47874574172973 1.47874574172973 1 6.72434102393286 244 465 672 803 518 314 299 136 1244 738 519 310 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 0.000290197038124585 0.00223824818670265 285 583.818181818182 519 2.63850294938114e-05 265 1.32076367466076 1.40274601319194 1 7.81206021438282 284 553 497 372 1096 519 510 265 563 1128 635 311 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 0.000228522882131121 0.00188863884597254 295 876.909090909091 520 2.07769657434629e-05 117 1.7837644411093 1.7837644411093 1 10.8442723704307 292 2600 472 1705 1208 629 117 515 1245 520 343 312 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 0.00277896253442089 0.0133287803851548 525 594.272727272727 521 0.000252952640210587 116 1.71312639233516 1.97144246963556 1 7.16999372193518 521 584 1230 191 163 1111 497 375 116 985 764 313 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 0.00109945016496701 0.00628295545492121 645 570.909090909091 522 1e-04 8 1.2809816275141 1.34218429005602 1 6.29516949179854 643 8 939 48 436 1370 648 967 522 348 351 314 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 5.53059309120955e-09 2.37764763535853e-07 525 623.727272727273 523 5.02781191373905e-10 96 1.31433360995766 1.48847123447046 1 19.4310299837066 276 546 106 96 1861 523 470 956 571 935 521 315 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 0.00309488148500607 0.0143821147954926 510 796.545454545455 523 0.00028174944070828 176 1.92478670590569 1.92478670590569 1 7.91395505687736 652 1524 1410 1125 509 506 504 176 495 1338 523 316 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 1.50203824747225e-10 1.03508106289044e-08 200 374.545454545455 528 1.36548931597709e-11 20 1.45523768347528 1.56084858093262 1 25.9352119678529 196 220 66 31 581 724 626 528 573 20 555 317 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 2.94663653306425e-20 1.15066156616159e-17 85 595.727272727273 528 2.67876048460386e-21 12 1.36904367455794 1.40763560463796 1 51.7590109614946 84 522 12 362 1735 528 591 705 1359 79 576 318 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 0.00221397125388205 0.0110662436906653 530 767.727272727273 529 0.000201472948111917 99 1.13072730142469 1.13072730142469 1 4.93635327111014 529 310 1432 345 1666 466 99 255 541 1954 848 319 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 0.000448760393265932 0.0031958832869972 140 715.545454545455 529 4.08047234960795e-05 64 1.31186210253065 1.31186210253065 1 7.3065017654689 137 366 529 669 2667 227 64 679 1384 777 372 320 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 2.07772098042749e-07 5.62786156894984e-06 740 503.363636363636 530 1.88883743331942e-08 15 1.32772929611845 1.35448471175996 1 15.5567899431832 227 15 169 257 1505 740 530 569 586 199 740 321 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 5.1569618287181e-25 4.83310462587461e-22 465 664.545454545455 531 4.68814711701646e-26 5 1.48833186821294 1.54221692777949 1 70.8076920052415 462 1268 5 332 1836 942 531 626 828 45 435 322 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 3.24796931056176e-09 1.50692912765271e-07 535 938.454545454545 532 2.95269937759718e-10 97 1.77891201456686 1.89660961988181 1 27.0856853205925 532 2378 97 1618 3068 348 209 429 692 711 241 323 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 3.23363429340024e-07 8.01735994649393e-06 185 668.909090909091 532 2.93966797153712e-08 184 1.41016621504352 1.45206874395848 1 16.0389748037945 242 769 184 469 1568 1072 700 185 1300 337 532 324 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 0.00181303577151762 0.00942939581057886 1755 1187 535 0.000164957421220892 89 1.4413785824034 1.49410835341058 1 6.51618380360406 1754 535 974 89 155 4351 2382 350 421 99 1947 325 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 2.2484563475015e-08 8.70765821850581e-07 425 651.454545454545 535 2.04405124589209e-09 118 1.14452123282594 1.18527595228334 1 15.4804328862007 442 421 118 421 792 738 879 413 1738 535 669 326 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 0.000913699817714199 0.0054751884217503 435 605.363636363636 536 8.30981376888028e-05 93 1.68439571007378 1.68439571007378 1 8.50236324926963 433 2429 806 658 545 185 573 93 272 536 129 327 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 0.00203194329719639 0.0102825985860284 315 746 537 0.000184892950167502 148 1.55588838160164 1.55588838160164 1 6.90322289809306 313 1790 1139 1063 800 445 336 148 1214 537 421 328 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 0.000147038134032983 0.0013224965375788 310 671.545454545455 537 1.3367996574737e-05 132 1.24185830225235 1.28495761953704 1 7.97872954457902 310 775 442 537 360 623 820 353 1780 1255 132 329 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 0.00201307328542399 0.0102202182183064 250 819.727272727273 537 0.000183174334338561 39 1.62215335213734 1.62215335213734 1 7.20679776844994 248 1970 1195 1419 1560 39 364 523 537 1064 98 330 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 1.59947515816086e-07 4.51514493442277e-06 980 701.090909090909 538 1.45406843131653e-08 43 1.25966296846583 1.40069904191151 1 15.0282461956993 980 518 161 43 538 2152 1267 409 864 91 689 331 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 1.76866543171619e-06 3.60913880064106e-05 35 724.727272727273 538 1.60787895783329e-07 1 1.22541186316176 1.2219197874282 1 12.1506216245975 344 1791 877 1844 1038 32 22 34 1451 538 1 332 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 0.00108293291717487 0.00628295545492121 390 1016.45454545455 539 9.84969409218365e-05 61 1.46778240338295 1.46778240338295 1 7.21317059349672 325 2509 985 2997 1250 539 61 387 1219 522 387 333 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 5.49956504638063e-05 0.000603535405324113 305 851.090909090909 539 4.99972957222305e-06 19 1.38874206389951 1.38874206389951 1 9.97843018607979 303 1446 1113 2494 2392 86 91 19 539 752 127 334 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 1.25028704498914e-05 0.000185288548931558 1555 913.272727272727 539 1.13663104598241e-06 292 1.67023440888973 1.87369274089237 1 13.9128542863761 1552 539 292 516 642 500 1736 2057 394 378 1440 335 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 0.00101904033901465 0.00599902390530482 540 1157 540 0.000101950794027471 101 1.0897164494986 1.0897164494986 1 5.40407495073369 540 374 4329 924 3312 213 185 101 1077 1427 245 336 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 0.00369586526707038 0.0163848861319695 355 502.818181818182 542 0.000336553521488151 147 1.3287205278662 1.39980926415665 1 5.29525420754455 355 681 754 289 746 147 542 204 803 810 200 337 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 0.0115240868742841 0.0386279478489951 310 608.454545454545 543 0.00105317263893549 215 1.18172620290729 1.18172620290729 1 3.72708084802915 308 330 957 215 1356 881 746 390 543 384 583 338 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 3.08220862513807e-05 0.0003800849899315 540 718.090909090909 543 2.80204709804431e-06 97 1.24681293160253 -1.15806984869028 -1 9.51748290885969 537 138 339 308 543 677 1928 1117 1051 97 1164 339 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 0.000669865242480377 0.00428368680306063 1205 1010.27272727273 546 6.70067251937133e-05 75 1.94397009216757 1.94397009216757 1 10.2750575424109 1204 1548 4300 180 75 1580 946 206 92 546 436 340 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 0.0074655824007608 0.0279199673822547 280 682.272727272727 547 0.000681003406414317 274 1.20074158169684 -1.20074158169684 -1 4.16489349414776 278 328 1440 490 325 274 767 618 1061 1377 547 341 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 0.0283756666702954 0.0750347748412546 760 1232.54545454545 547 0.00287446455001888 444 1.47248574116403 1.47248574116403 1 3.69642412136855 758 1809 4562 444 2792 532 473 581 517 547 543 342 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 0.000373618210331133 0.00275279077611901 520 951.545454545455 548 3.39710614253407e-05 59 1.40888143508813 1.54526186441931 1 8.05067768685869 776 548 520 59 2265 2739 1285 517 516 176 1066 343 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 0.014426628288009 0.0452800938764973 385 1102.45454545455 549 0.00132019177050577 302 1.62292126351497 1.62292126351497 1 4.86862384153218 385 1933 1676 549 4181 571 322 519 302 1382 307 344 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 0.00447049589662999 0.0188557549699443 495 721.909090909091 549 0.000407236915171293 55 1.54868944935846 -1.20074158169684 -1 5.96102872252257 495 347 859 380 235 599 1834 1315 55 549 1273 345 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 3.93037111535869e-05 0.000463356145859024 410 560.818181818182 549 3.57312848587769e-06 118 1.32656543646105 1.38469770053361 1 9.87153999361608 410 549 352 381 1187 819 617 199 585 118 952 346 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 0.000967635588465789 0.00574694596647742 155 892.454545454545 551 8.80055863726445e-05 151 1.46778240338295 1.46778240338295 1 7.3400390315991 151 1526 602 1435 1882 162 151 408 2731 551 218 347 M7169 REACTOME_NCAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NCAM1_INTERACTIONS.html Genes involved in NCAM1 interactions 20/60 Reactome 3.63425175364295e-05 0.00043666932609156 55 687.181818181818 552 3.30391980947406e-06 52 1.46726266075591 1.46726266075591 1 11.0028948341967 52 1230 662 1602 925 155 96 552 1587 301 397 348 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 0.000561243585936316 0.00378960726757576 555 588.909090909091 552 5.10351651227439e-05 153 1.46778240338295 1.46778240338295 1 7.93247677160804 158 726 552 555 1418 153 284 766 1202 354 310 349 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 1.20696745793832e-07 3.57965158727784e-06 95 537.181818181818 553 1.09724320377742e-08 93 1.34312901779291 1.42761675853101 1 16.3262943542156 93 444 154 246 594 813 553 980 1164 108 760 350 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 0.00864839460688133 0.031138444998791 385 908 555 0.000789325500235406 213 1.40357105595644 1.40357105595644 1 4.7199960397886 381 1517 1136 1309 2419 555 213 337 1222 479 420 351 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 2.02428164365359e-06 4.05375375306014e-05 1205 629.090909090909 556 1.84025773295841e-07 137 1.50255326219938 1.50927684830679 1 14.7294274608074 386 1201 221 1065 517 1203 612 137 790 232 556 352 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 3.82679652770896e-12 3.89834098453134e-10 170 671.818181818182 559 3.47890593428692e-13 45 1.47271176803371 1.50437983749685 1 30.9276076608112 167 227 45 173 2707 789 559 827 656 184 1056 353 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 0.000103160540016621 0.0010113185994098 410 709.818181818182 560 9.37867069554805e-06 6 1.34653643173223 1.39090146245387 1 9.00141387987816 560 6 409 214 409 1878 1359 1252 561 192 968 354 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 3.31410741757089e-14 4.56761981139329e-12 450 832.545454545455 560 3.01282492506449e-15 34 1.27453541537292 1.27946485541604 1 32.2594078306504 449 1036 34 560 2376 480 625 754 2202 113 529 355 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 0.00677575730290524 0.0260469226590762 1205 1261.54545454545 561 0.000679650629800153 223 1.6584271337134 1.6584271337134 1 5.86405324652432 1205 1550 4523 314 3532 898 561 371 279 421 223 356 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 0.00815550686223044 0.0298102224308985 350 657 562 0.000744172505771241 65 1.77083348285255 1.77083348285255 1 6.02986878288683 350 1452 1198 562 966 920 594 310 65 302 508 357 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 0.00476833759670418 0.0197892545901293 245 604.181818181818 563 0.000434427644196263 135 1.20074158169684 -1.20074158169684 -1 4.56550930824892 241 351 965 801 563 135 615 460 1065 1075 375 358 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 8.28761173217698e-06 0.000132545216986284 1160 915.181818181818 567 7.53422086597513e-07 133 1.42026240819798 1.47514261482327 1 12.2917913288741 1158 281 272 223 141 2084 1643 2437 1128 133 567 359 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 0.00509248674651562 0.0207869276081639 260 907.636363636364 568 0.000464028455283039 233 1.08853605772539 -1.08853605772539 -1 4.08697994169046 395 722 2241 568 258 233 1082 260 1860 2102 263 360 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 8.92252124658058e-12 8.36218691229532e-10 355 626.090909090909 568 8.11138295146981e-13 49 1.39665243301477 1.41132680331424 1 28.2971549149062 352 233 49 102 2320 790 857 568 766 182 668 361 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 0.0115713943247781 0.0387222468477574 1555 763.727272727273 569 0.00105751896783083 120 1.56722812480193 1.56722812480193 1 4.93922263069873 638 120 1552 295 1407 980 569 380 375 1554 531 362 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 6.93529516848352e-05 0.000736934085249746 485 871.545454545455 571 6.93551162042675e-06 31 1.2806995630062 1.36894121062023 1 8.95422057540963 484 380 4308 79 571 784 931 635 825 31 559 363 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 5.89903163764928e-10 3.54395669923392e-08 485 699.545454545455 573 5.36275603566457e-11 76 1.40252690625371 1.4608515860194 1 23.3225939434687 482 206 76 260 1261 1114 1256 573 1640 105 722 364 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 1.90427245238601e-07 5.21837468531043e-06 30 559.090909090909 574 1.73115692474158e-08 25 1.53846358770324 1.53846358770324 1 18.1385841223936 30 579 167 334 1694 656 296 574 1153 25 642 365 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 0.00811505331341604 0.0297086010589893 545 1360.45454545455 576 0.000740467499109639 309 1.44922964151127 1.44922964151127 1 4.93957178953305 544 1848 2475 1716 3913 576 355 309 385 2453 391 366 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 0.000319705429779868 0.00242417418114638 285 683.363636363636 577 2.90683544577359e-05 12 1.28174927888375 1.3000018681775 1 7.48215607865565 281 12 507 387 1020 1043 806 477 1656 577 751 367 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 3.39119627800385e-05 0.000409572347417948 125 621.272727272727 577 3.08295322983978e-06 121 1.59048893985034 1.59048893985034 1 12.025723824516 121 577 346 360 598 756 522 1026 175 1134 1219 368 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 1.38223347822066e-13 1.6608066869082e-11 580 718.181818181818 577 1.25657588929158e-14 12 1.28020311762436 1.32871741954317 1 30.8009662495559 577 387 38 239 527 1474 1525 1312 596 12 1213 369 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 0.00196274726908876 0.01002991679711 125 647.818181818182 579 0.000178590958157692 106 1.56923287836391 1.71685957927007 1 7.0002757226973 968 106 659 122 2592 852 701 159 123 265 579 370 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 0.000579016151911243 0.00386772412125917 585 838.181818181818 581 5.26516908054694e-05 40 0.984762836626545 0.984762836626545 1 5.30257158346847 581 837 2242 1818 67 131 40 853 449 2117 85 371 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 0.000789905089189747 0.00483223922707984 585 700.090909090909 583 7.18353495903588e-05 143 1.33339309732837 -1.54796415353554 -1 6.89205093808546 583 493 588 569 143 688 436 562 1931 971 737 372 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 0.00934126166215202 0.0328874170915435 590 713.818181818182 586 0.000852832937307852 91 1.38931409098269 1.56133705455257 1 4.59846017005758 586 112 803 91 2157 660 1018 493 401 949 582 373 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 0.00136944155130112 0.00750550071274509 840 579.090909090909 587 0.000124572248717756 75 1.33870364705381 1.50790507146072 1 6.34812301450376 837 344 1106 247 106 1178 772 300 75 587 818 374 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 8.55211287560435e-05 0.000867428591668441 315 643.909090909091 587 7.7749503109431e-06 116 1.46778240338295 1.46778240338295 1 10.0302848201557 314 116 400 901 832 1142 411 188 1334 858 587 375 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 0.000745210572150976 0.0046560756547993 765 560.727272727273 587 6.77693744226156e-05 57 1.46778240338295 1.46778240338295 1 7.63951956825693 461 587 765 765 218 678 264 241 1272 860 57 376 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 2.44109466587326e-05 0.000320419316646557 555 776.636363636364 588 2.2192015930903e-06 325 1.28663764275545 1.38483199739115 1 10.034452310338 551 394 325 588 528 1272 1069 1408 1474 333 601 377 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 0.00162151619085564 0.00863457371630629 170 738.181818181818 590 0.000147519324420025 169 1.46726266075591 1.46726266075591 1 6.75843935755185 169 478 1142 1344 590 446 313 814 1632 559 633 378 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 0.000223776288806741 0.00187256125699561 240 659.181818181818 590 2.03453685262139e-05 239 1.37368460182107 1.37368460182107 1 8.36260394877155 239 605 468 493 914 849 500 736 1403 590 454 379 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 0.00037918952179093 0.00278508166005063 440 695.454545454545 592 3.44777176586218e-05 166 1.38148905971698 1.47283622857924 1 7.87853477158705 437 272 521 166 847 715 929 811 1926 434 592 380 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 1.74987399058071e-29 2.73330317328706e-26 185 706 592 1.59079453689157e-30 3 1.48132460035777 1.47729714604866 1 84.5175528502563 184 395 3 113 1106 1385 1097 1621 592 6 1264 381 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 9.05349849862624e-10 5.05055880530506e-08 85 807.727272727273 593 8.23045318395632e-11 81 1.40424898918939 1.51193029477116 1 22.8690339116992 409 778 81 84 3759 474 823 596 724 564 593 382 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 2.57369439824793e-09 1.24333319074121e-07 595 790.636363636364 594 2.33972218296253e-10 23 1.44077319337197 1.42318094412873 1 22.2057169205785 594 23 93 248 894 2199 1761 968 514 143 1260 383 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 1.31136086026983e-06 2.76803468073172e-05 495 737.909090909091 596 1.19214694721585e-07 88 1.63932432911417 1.49749993538318 1 16.6764043211125 494 320 213 836 1296 1084 596 1721 441 88 1028 384 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 0.00042133890698085 0.00301895125093618 320 640.090909090909 596 3.83108747705058e-05 15 1.34194225205979 1.41379830860741 1 7.54811870628297 1379 41 1883 319 596 15 316 912 615 685 280 385 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 0.000750795783299793 0.00467849606455164 600 883.727272727273 597 6.82774664064582e-05 58 1.13547313924477 1.18466348608539 1 5.90462787754584 597 1730 1173 1251 1010 483 314 229 2475 401 58 386 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 1.88185032403754e-09 9.58516371569554e-08 300 694.454545454545 598 1.71077302331567e-10 88 1.34135326321949 1.35670753726225 1 21.0116844475986 297 1402 88 668 1523 363 633 498 1429 140 598 387 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 0.0109515628354739 0.0371070306919962 450 599.818181818182 599 0.00100058750172513 160 1.36371650072081 1.37680117166101 1 4.35416425829944 447 458 822 160 435 691 962 599 413 864 747 388 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 2.69588326145919e-05 0.000346107094882131 600 689.818181818182 599 2.450832997654e-06 6 1.30037474645184 1.30037474645184 1 10.0443830319167 599 687 1818 725 198 377 453 247 1354 1124 6 389 M2602 BIOCARTA_RANKL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RANKL_PATHWAY.html Bone Remodelling 8/19 BioCarta 0.000761284305943741 0.00470079369711562 1065 993.909090909091 601 7.61545230964183e-05 82 0.859207095487099 0.859207095487099 1 4.46404380970289 1062 1863 3819 601 82 347 137 1186 86 1591 159 390 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 0.00182301955484256 0.00944985578981443 225 778.272727272727 601 0.000165866540560241 225 1.46778240338295 1.46778240338295 1 6.63246646006576 225 1309 654 1434 1198 601 598 521 1201 426 394 391 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 7.77230946864221e-10 4.49288505018255e-08 555 548.727272727273 602 7.06573588308005e-11 78 1.50176474816761 1.43073618199442 1 24.6274564206152 359 670 78 683 553 973 751 553 602 116 698 392 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 6.65968855384658e-05 0.000710872450189637 525 711.272727272727 604 6.05444559990736e-06 260 1.3859131642954 1.43149065527552 1 9.73820777718862 524 260 384 498 815 1233 1081 604 1292 368 765 393 M12868 KEGG_PATHWAYS_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PATHWAYS_IN_CANCER.html Pathways in cancer 189/425 KEGG 1.75319166528098e-05 0.000246710394699899 735 701.454545454545 605 1.59382330610381e-06 10 1.49413961962916 1.49966442711271 1 12.031359445212 733 10 307 62 1303 2219 1137 349 605 126 865 394 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 0.00102639709135215 0.00602718893493255 360 674.727272727273 605 9.33523876271892e-05 110 1.46778240338295 1.46778240338295 1 7.27229932874419 357 717 605 660 1212 471 110 652 1633 469 536 395 M6929 KEGG_O_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_O_GLYCAN_BIOSYNTHESIS.html O-Glycan biosynthesis 13/33 KEGG 0.000505501960613425 0.00350411566188537 1430 859.545454545455 606 4.59652862732373e-05 58 1.16140721083475 1.26649718749112 1 6.36487881097478 1427 497 1690 510 58 1238 554 728 180 1967 606 396 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 1.84793794677307e-09 9.58516371569554e-08 880 579.090909090909 607 1.67994358938663e-10 86 1.39236524765699 1.42525197616164 1 21.8107638172489 155 663 86 410 1227 644 607 880 504 315 879 397 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 0.00139671287145702 0.00760628642681448 610 1240.90909090909 609 0.000139759151186896 89 1.41494470965243 1.41494470965243 1 6.69136298199425 607 2776 4327 1084 550 124 639 124 2721 609 89 398 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 6.15837465811627e-08 2.06129597485235e-06 80 695.454545454545 609 5.59852257318662e-09 77 1.63394158176489 1.46931980695816 1 20.735390317214 77 1285 136 1587 1392 609 518 592 728 100 626 399 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 0.0111919429049323 0.0377849023433089 335 653.545454545455 609 0.00102266253799296 121 1.20074158169684 -1.20074158169684 -1 3.81273700170741 332 609 871 795 582 121 762 475 1083 1080 479 400 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 3.71157293572773e-06 6.66376658115715e-05 145 713.545454545455 612 3.37416290677984e-07 87 1.49754221839421 1.46778240338295 1 13.9588056682515 612 144 243 142 634 1702 861 1768 220 87 1436 401 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 0.00142540156095155 0.00771083667495939 340 787.636363636364 612 0.00012966599374301 266 1.29703265342115 1.29703265342115 1 6.11658616970824 280 612 637 266 3352 767 340 311 339 1076 684 402 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 5.8568648125284e-05 0.000636781171960744 75 850.727272727273 614 5.3245643095051e-06 74 1.46778240338295 1.46778240338295 1 10.4700638935411 74 1310 377 1303 648 554 614 860 2592 430 596 403 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 1.27057576454048e-06 2.71868403316743e-05 600 764.090909090909 615 1.15506954394757e-07 210 1.45716148635493 1.52322832973213 1 14.8487201877725 598 440 210 532 1327 1191 1049 615 1352 444 647 404 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 0.000834167866382594 0.0050831087410518 415 720.181818181818 617 7.58622112259808e-05 246 1.50428220890801 -1.20074158169684 -1 7.70154378707216 411 1366 590 630 573 246 1015 920 1144 410 617 405 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 2.89292451524571e-09 1.35562442784414e-07 310 565.636363636364 619 2.62993138095437e-10 21 1.42914411411473 1.45254320715013 1 21.9067046027582 306 21 96 148 631 1245 1381 813 619 44 918 406 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 0.00173760465011784 0.00909767082732089 570 897.363636363636 619 0.000158088960452768 134 1.25396396838912 1.25396396838912 1 5.71245070091637 570 1995 1572 1853 308 619 583 134 1232 689 316 407 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 0.000313059402165863 0.00238148759504746 120 823.818181818182 620 2.84639963009663e-05 118 1.20074158169684 -1.20074158169684 -1 7.02995440685276 118 1233 505 1351 554 216 1046 620 1857 1071 491 408 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 0.012879593859427 0.0416807851003278 320 725.090909090909 624 0.00117778359073946 317 1.4175284526541 1.4175284526541 1 4.36627013127137 317 1200 1094 723 890 450 439 544 1316 624 379 409 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 0.00734416251261071 0.0276645864421976 625 1121.63636363636 625 0.000669890400054823 160 1.47476349360937 1.47476349360937 1 5.128501894767 625 1852 1580 296 4475 1259 622 295 160 284 890 410 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 0.000223780261185989 0.00187256125699561 455 771.272727272727 625 2.03457297250812e-05 42 1.66328783487533 1.66328783487533 1 10.1256266521896 454 926 1011 1162 1528 536 558 42 625 1413 229 411 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 0.000670068806368638 0.00428368680306063 630 899 626 6.0933907345588e-05 73 1.82171513758939 1.82171513758939 1 9.62886617444213 626 2108 1524 227 3080 556 720 81 73 727 167 412 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 0.0021887064558962 0.0109692817671974 945 872.090909090909 627 0.000219086514500809 96 1.35827470555819 1.35827470555819 1 5.94133107568048 944 627 3946 126 951 668 348 179 96 1600 108 413 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 0.00610487973886325 0.0240146466894482 480 688.545454545455 627 0.000556535141216373 251 1.09439428514004 1.13827677035787 1 3.95585810688283 476 911 1274 690 288 386 251 1365 548 758 627 414 M1072 REACTOME_INFLAMMASOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLAMMASOMES.html Genes involved in Inflammasomes 10/20 Reactome 0.00255141146689959 0.01250721517937 630 1242.27272727273 630 0.000232215930438818 77 2.24458518468169 2.24458518468169 1 9.53274063746437 630 3071 1790 1458 3965 77 378 221 197 1763 115 415 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 7.33169942831989e-08 2.39235585517082e-06 60 749.363636363636 632 6.66518152059584e-09 59 1.39521082202543 1.47536774740506 1 17.5043680680412 59 1502 139 677 1671 465 475 632 1166 504 953 416 M8601 BIOCARTA_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAC1_PATHWAY.html Rac 1 cell motility signaling pathway 17/38 BioCarta 7.71569160094893e-05 0.000796408230444888 635 481.909090909091 633 7.01451110342486e-06 21 1.71381840468535 1.91053044415996 1 11.8535083606662 633 141 862 87 21 719 800 1068 59 238 673 417 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 0.000395875978241734 0.00287639031933738 635 629.727272727273 634 3.59952028683408e-05 29 1.53377564944398 1.53377564944398 1 8.69905481767561 634 1247 1020 1155 794 255 29 594 194 773 232 418 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 0.0006197819988604 0.00406764488327708 1010 810.363636363636 636 5.63596974706885e-05 66 1.52767522594989 1.50569731268773 1 8.15131835291401 1009 105 630 878 66 2374 1826 909 325 156 636 419 M4956 BIOCARTA_MONOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MONOCYTE_PATHWAY.html Monocyte and its Surface Molecules 6/16 BioCarta 0.000450966635964855 0.00320672178472126 610 1446.09090909091 637 4.51058179019789e-05 43 2.31622896548935 2.31622896548935 1 12.8927873817657 609 3423 3848 1848 351 482 95 637 3156 1415 43 420 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 7.23990963515961e-09 3.00232004870424e-07 640 987.636363636364 639 6.58173605362292e-10 110 1.67533655983129 1.69703903727656 1 24.3892571325463 639 221 110 242 3096 1553 1278 1494 420 196 1615 421 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 5.63343397418212e-06 9.5300619505478e-05 225 849.181818181818 640 5.1213167268152e-07 222 1.47771797191882 1.47771797191882 1 13.2615670101048 222 1523 260 1511 1530 422 640 758 1919 322 234 422 M10401 BIOCARTA_TEL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TEL_PATHWAY.html Telomeres, Telomerase, Cellular Aging, and Immortality 13/37 BioCarta 0.00109945016496701 0.00628295545492121 695 909.727272727273 641 1e-04 67 1.72985222233658 1.72985222233658 1 8.50106879093347 695 2445 1686 67 2586 641 860 232 152 389 254 423 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 0.000975042345032977 0.005783605606107 215 612.363636363636 641 8.86795230149685e-05 90 1.12647972618936 1.27131778980501 1 5.62632042721892 213 1042 641 535 90 305 709 981 784 1019 417 424 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 0.00239183841318848 0.0118479437676546 820 945.090909090909 642 0.00021767661664599 106 1.75214487306291 1.75214487306291 1 7.53331878716554 818 1365 2320 642 2900 200 106 436 273 1088 248 425 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 0.0117780350586382 0.039115430393181 720 783.272727272727 642 0.00107650611428957 406 1.48447643926148 1.48447643926148 1 4.66388819327893 716 1282 1682 789 417 502 467 1139 642 574 406 426 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 0.00887318806248548 0.0316918896804931 305 729.090909090909 644 0.000809925399471472 246 1.23665236437612 1.29982701509461 1 4.13755562823157 304 1046 945 644 892 667 547 598 1679 452 246 427 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 0.0226483128861375 0.0643602147874108 645 845 644 0.00208044426703107 406 1.12080206218399 1.13474230571192 1 2.98029804643684 538 893 1256 406 635 1729 671 644 1438 641 444 428 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 3.10821542372848e-06 5.82603899023666e-05 645 817.727272727273 645 2.82565437736565e-07 234 1.6567063564413 1.6567063564413 1 15.6581415881073 282 1354 234 645 1177 1291 505 643 1644 358 862 429 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 0.00159056836091853 0.00850845130052993 645 773.181818181818 645 0.000144701771298307 119 1.11163872566728 1.24525198892275 1 5.1362355064498 645 683 1756 899 119 425 385 506 1752 848 487 430 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 0.000244954882518616 0.00197906651634868 100 526.090909090909 645 2.22711055285275e-05 47 1.01834193415176 1.01834193415176 1 6.14477406771542 97 1086 1078 678 645 82 47 54 1080 841 99 431 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 0.0123974707624261 0.0405122370939531 650 794.090909090909 646 0.00113344448605306 304 1.55944478253721 1.55944478253721 1 4.84638450260354 646 889 1219 501 1249 1182 1424 397 529 395 304 432 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 0.00169378042542218 0.00893812508280216 600 1079.27272727273 646 0.000169507281347626 97 1.08991325512181 1.08991325512181 1 4.98380696635164 596 1100 4404 1496 646 517 283 141 1073 1519 97 433 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 0.000158590397179161 0.00140502074883778 650 666.909090909091 646 1.44183482333382e-05 29 1.49853903130491 1.49853903130491 1 9.53993562578395 720 602 801 646 29 1682 1365 646 183 303 359 434 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 0.000979481093570475 0.00580258963902812 595 1630.45454545455 647 9.79913084020349e-05 94 0.617778215060115 0.821494177118194 1 3.08359535705228 591 2169 4530 2376 94 158 308 647 2455 4459 148 435 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 0.00572385137443236 0.0228466503752896 475 1287.63636363636 648 0.00052170889805852 278 1.1712352121029 1.1712352121029 1 4.29021661165852 474 2098 2380 2034 278 400 606 648 2750 2177 319 436 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 0.00324864666430399 0.0148518617257839 495 1029.54545454545 653 0.000325340562599259 130 2.24458518468169 2.24458518468169 1 9.15891206279037 492 1962 4209 831 653 404 130 196 1035 1051 362 437 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 0.00172919569077622 0.00909428844778606 415 659.636363636364 653 0.000157323302971304 124 1.34339871100538 1.34339871100538 1 6.12035616230878 414 436 878 337 124 1296 653 719 1152 501 746 438 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 0.000963046284342806 0.00573346585836081 655 1021.54545454545 654 8.75880104334251e-05 232 1.29691657920732 -1.20074158169684 -1 6.48853088836174 654 481 601 592 1564 1499 2157 1189 232 409 1859 439 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 0.0079232545218296 0.0291202907367008 790 664.181818181818 655 0.000722903151922691 99 1.44933067637142 1.44933067637142 1 4.96801520721636 456 816 789 99 1685 786 655 453 423 277 867 440 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 5.64262937068069e-24 3.77733731871567e-21 20 684.454545454545 657 5.12966306425515e-25 7 1.43367157742125 1.43367157742125 1 65.3498834076582 17 958 7 453 1304 948 657 612 1664 57 852 441 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 0.00110185023184866 0.00628900144511916 265 981.909090909091 658 0.00011023969466759 103 1.90919498657043 1.90919498657043 1 9.38063879073067 264 747 4110 1083 658 252 407 103 1549 1297 331 442 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 8.55241842780379e-07 1.91754223697074e-05 250 734.818181818182 658 7.77492886593323e-08 139 1.4009936257278 1.50958695682335 1 14.7504433217009 249 970 204 519 1886 924 337 658 1233 139 964 443 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 0.000611903824703027 0.00403288512314822 510 1204.36363636364 659 5.56430986157589e-05 73 0.720361760534188 0.814904971630407 1 3.84967471179597 506 617 858 1697 3412 659 393 73 821 3935 277 444 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 0.00128589011156054 0.00713635004796205 660 904.727272727273 659 0.000116967484013985 193 1.47485549353766 1.79182689779031 1 7.06585537944329 656 1069 626 193 1425 1602 1556 659 310 562 1294 445 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 0.0112787632075028 0.0379958910067277 455 671.818181818182 660 0.00103063678314273 313 1.17002306549464 -1.20074158169684 -1 3.708880694768 453 337 1312 749 406 313 726 532 1049 660 853 446 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 1.70283182714695e-05 0.000240345480181042 145 666.454545454545 662 1.54804091586769e-06 142 1.6231429596427 1.6231429596427 1 13.1112649990595 142 927 305 654 1222 662 771 439 1189 324 696 447 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 0.00173493706049577 0.00909767082732089 365 800.272727272727 664 0.000157846068888172 125 1.21340189800944 1.21340189800944 1 5.52766961213211 364 1291 1019 664 125 336 514 721 1748 1628 393 448 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 1.14604342382743e-05 0.000173237402711462 1440 1547.36363636364 664 1.04186308540141e-06 37 1.23181057293926 1.25710431732947 1 10.341134620187 1436 37 288 200 664 4664 3722 2010 612 320 3068 449 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 1.34311580273975e-08 5.47290491446824e-07 180 628.636363636364 665 1.22101437358143e-09 112 1.40590889541487 1.40590889541487 1 19.6487390120173 176 774 112 650 819 869 333 790 1356 665 371 450 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 9.65587950809685e-15 1.45959520564329e-12 665 821.454545454545 665 8.77807228008806e-16 31 1.50585122016169 1.60550000545922 1 39.7793834756804 665 228 31 237 1750 1503 999 1187 643 60 1733 451 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 7.68084411397256e-06 0.00012418493284438 515 942.909090909091 666 6.98260993652656e-07 243 1.43430591576195 1.47021718748388 1 12.5039123798744 515 243 268 576 1230 2457 1410 929 666 447 1631 452 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 0.000297355318499255 0.00227309465332383 3215 1912.27272727273 669 2.70359560999516e-05 19 1.29942687518853 1.4353577817392 1 7.66639879011471 3213 19 502 185 669 2830 4425 3906 331 281 4674 453 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 0.00584593911050999 0.0232350048107293 395 668.909090909091 669 0.000532866476286063 193 1.58290526145842 1.58290526145842 1 5.7722958554254 392 1296 934 848 405 258 669 752 475 1136 193 454 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 0.0029347185799551 0.0139188696049027 670 1201.27272727273 670 0.000293860145674291 121 1.07643464219997 1.07643464219997 1 4.46003074476864 670 1862 4079 2552 493 329 121 708 246 1698 456 455 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 0.00591518123400023 0.0234838468647704 685 700.909090909091 674 0.000539195056209241 197 1.16353727231987 1.2708574633965 1 4.23099444998391 684 703 1095 674 580 378 201 606 791 1801 197 456 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 9.00671380179006e-17 1.91843003978128e-14 160 750.636363636364 674 8.18792163799097e-18 22 1.26706721977793 1.33392080986708 1 38.7918113931065 159 756 22 511 1665 772 978 542 1993 185 674 457 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 0.00134300252578018 0.007407117025692 160 810.727272727273 676 0.000122165733697544 111 1.46778240338295 1.46778240338295 1 6.97898642992208 160 1689 1338 1757 734 232 111 676 1198 656 367 458 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 4.56620765885872e-05 0.000520614333075717 1605 1069.72727272727 678 4.56630148770793e-06 17 2.05369581223184 2.05369581223184 1 15.0504872667845 1605 853 3887 376 17 2460 1108 208 31 544 678 459 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 7.22595668170221e-05 0.000755365040186766 700 624.272727272727 678 6.56926730093213e-06 24 1.43159451180577 1.71671624887831 1 9.97494832065661 725 48 391 24 698 1925 699 678 222 117 1340 460 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 6.42464657302143e-25 5.01764897352974e-22 330 605.272727272727 679 5.84058779365585e-26 6 1.43911755798204 1.52991964833155 1 68.4140387884633 328 650 6 359 1110 1100 837 723 679 17 849 461 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 0.000218683445650081 0.0018463975248942 870 949.090909090909 681 1.98822896502362e-05 49 1.16921597415393 1.16921597415393 1 7.13380350240078 866 500 1874 937 2379 604 638 362 1550 49 681 462 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 0.000473850998372543 0.00334407496743032 685 1111.81818181818 683 4.73952069351727e-05 59 2.31622896548935 2.31622896548935 1 12.7986236616961 683 2401 4567 746 59 520 851 237 206 1718 242 463 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 5.90730239892558e-06 9.95741692135442e-05 145 789.181818181818 684 5.37028932809466e-07 70 1.3240432523517 1.34889765200702 1 11.8261366304662 145 1777 261 1055 1278 684 732 211 1957 70 511 464 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 0.0029197209657901 0.0138871822750554 455 885.454545454545 686 0.000265782097852326 90 1.31573153763134 1.31573153763134 1 5.45442501171871 455 90 686 167 2912 1432 1194 638 1159 153 854 465 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 0.0046980271599489 0.0196150720124687 510 896.545454545455 688 0.000428008157991344 236 1.10898890094407 1.21158821497501 1 4.2261469946931 510 688 1201 280 2209 671 1132 236 867 1586 482 466 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 3.14411902293323e-06 5.86985726751598e-05 510 802.545454545455 689 2.85829410576749e-07 235 1.6048339067262 1.63517406825459 1 15.1562200195186 509 283 235 689 691 1552 1066 494 1915 388 1006 467 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 0.00577234983381785 0.0230010470418966 605 921.272727272727 691 0.000526141015208496 280 1.14927919116672 1.14927919116672 1 4.20228893169837 604 1828 1490 600 280 1058 418 691 1953 761 451 468 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 0.00037421918059473 0.00275289023589781 515 1173.18181818182 692 3.742822135322e-05 11 2.31622896548935 2.31622896548935 1 13.2353923485657 513 2017 4579 1619 1520 692 286 60 11 1312 296 469 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 0.00294117809155051 0.0139188696049027 880 673.454545454545 694 0.000267737956839991 172 1.15840738058051 1.22386898192999 1 4.799671368626 878 315 694 343 578 1029 1213 172 843 637 706 470 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 0.000163018445681365 0.00143861475793386 1630 1358.63636363636 694 1.48209569532987e-05 256 1.46756090982182 1.64544046190514 1 9.3091117320462 4006 694 450 438 256 1626 2387 1629 361 381 2717 471 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 0.00402521650791565 0.0174165877710921 425 1131 694 0.000366600012794105 151 1.19793797626962 1.36114636439247 1 4.70315015222282 424 2124 916 1991 3084 521 233 579 1724 694 151 472 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 0.00309678912263167 0.0143821147954926 405 752.454545454545 695 0.000281923351834292 322 1.50332905110236 1.50104022087764 1 6.18108931736447 405 1349 695 986 1167 505 515 322 1210 351 772 473 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 3.75996221041843e-09 1.69415220365584e-07 700 843.818181818182 698 3.41814746985862e-10 100 1.31865734189308 1.4136531499869 1 19.9281680615404 698 229 100 143 1100 2467 1854 1016 519 224 932 474 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 0.000264105278740667 0.00209053604084251 375 898.636363636364 701 2.40124535765669e-05 169 1.4362232601875 1.48236913937259 1 8.59002739797923 375 1973 486 1131 1562 421 717 169 1896 454 701 475 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 0.00533000876014876 0.0215872264909741 565 815.454545454545 704 0.000485724173516236 253 1.20763157545096 1.20763157545096 1 4.48991060291159 562 1250 1164 979 267 582 618 253 1866 725 704 476 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 0.000655848758743723 0.00422738278331924 895 676.909090909091 704 5.96403961337894e-05 52 1.64220470603604 1.64220470603604 1 8.70110616814994 892 319 1272 614 1108 978 704 94 278 1135 52 477 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 0.00897277497490721 0.0318964689257877 1010 719.636363636364 706 0.000819052825144691 109 1.76670338197494 1.76670338197494 1 5.8999659362864 1008 706 1437 202 1151 1105 768 327 109 478 625 478 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 0.000359431201190276 0.00267348350599624 110 736.909090909091 706 3.26809034282808e-05 76 1.46778240338295 1.46778240338295 1 8.42884242417062 109 827 706 1340 1057 201 76 881 1901 548 460 479 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 0.00379698005850891 0.0167224140546736 560 1390.90909090909 708 0.000345777194963908 207 0.751564534681695 0.751564534681695 1 2.98030139667874 559 1159 1786 2066 3105 428 332 207 708 4445 505 480 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 0.00450442852621761 0.0189817914333235 240 1203.27272727273 708 0.000410334338232928 236 1.30748401878153 1.30748401878153 1 5.02416669668024 236 2504 1022 2870 1639 457 297 675 2190 638 708 481 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 0.003468550381725 0.01558353508031 710 1577.81818181818 709 0.000315821004293518 315 1.08196515182584 1.08196515182584 1 4.36446736720204 498 2983 708 2491 2572 709 495 315 3672 2591 322 482 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 0.00344152969003739 0.0155067385841492 575 683.545454545455 710 0.000313356836743338 106 1.76992266381572 1.76992266381572 1 7.14804899525191 572 710 943 106 1318 1448 859 191 309 805 258 483 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 0.000290750535668821 0.00223824818670265 715 692.454545454545 711 2.64353607433798e-05 44 1.52774904518637 1.52774904518637 1 9.03633841727852 711 276 631 354 44 1562 506 793 841 930 969 484 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 7.01625081348839e-05 0.000741676656414569 355 899.727272727273 712 6.37861326008678e-06 353 1.46778240338295 1.46778240338295 1 10.2531141008306 353 712 387 1295 1322 1538 603 470 1612 663 942 485 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 8.67720166018379e-06 0.000136906959527344 490 1111.63636363636 713 7.88839625894576e-07 275 1.49568951152285 1.66764792998669 1 12.8976411974856 488 1300 275 713 379 2330 1925 2381 347 462 1628 486 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 3.15936767838841e-05 0.00038755591864183 970 953.090909090909 714 2.87219368202588e-06 70 1.34181478224335 1.40489248289276 1 10.2173574336597 966 70 340 177 2781 1860 714 1739 288 295 1254 487 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 0.00211459449452597 0.0106548277433857 540 930.818181818182 715 0.000192420885297284 450 1.46778240338295 1.46778240338295 1 6.46171828530434 539 450 665 715 729 1303 687 563 1929 1581 1078 488 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 1.2976314277769e-10 9.35492441625007e-09 270 663.454545454545 716 1.17966493441222e-11 63 1.52716123956769 1.57601722476479 1 27.366781611322 268 788 63 369 773 1230 716 614 1188 132 1157 489 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 2.72372010525614e-14 3.86768254946372e-12 540 818.363636363636 717 2.47610918659652e-15 33 1.52872227757841 1.56128623583398 1 38.9395394944 536 1271 33 323 2477 1482 939 414 717 52 758 490 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 0.000493430962999937 0.0034562294359009 155 779.272727272727 717 4.48674243468511e-05 17 1.02803005837815 1.02803005837815 1 5.64764137901722 152 1693 959 1453 717 17 33 190 2203 1072 83 491 M19096 KEGG_BLADDER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BLADDER_CANCER.html Bladder cancer 27/58 KEGG 0.00350636854159964 0.0157082628928642 580 787.636363636364 718 0.000319269955178407 142 1.3822738503887 1.3822738503887 1 5.56518140769212 578 1634 1438 822 1136 317 503 916 718 460 142 492 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 6.45683412230735e-05 0.000697159555233462 595 831.181818181818 718 5.87002148482483e-06 186 1.451745705785 1.53832836405953 1 10.2281947158224 595 822 380 635 389 1651 1282 718 1098 186 1387 493 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 0.0165299781852603 0.050528035079015 720 1061.09090909091 718 0.00151413642260409 447 1.64144615939413 1.64144615939413 1 4.74971839203366 718 697 1267 1404 1390 2484 666 447 1229 679 691 494 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 1.26735368633006e-05 0.00018616988633676 5 1083.54545454545 718 1.15214635202865e-06 2 1.51063264943209 1.51063264943209 1 12.5764421713783 543 3209 2136 2340 945 75 2 1634 312 718 5 495 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 0.00104986108967786 0.00614188397781582 220 757.454545454545 719 9.54874934933781e-05 217 1.6298974018777 1.66913489104213 1 8.04573500142895 831 1125 606 218 1474 1375 844 217 525 398 719 496 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 0.0040923858689632 0.017658305876576 500 924 720 0.000372728937147392 394 1.3525532958761 1.46778240338295 1 5.29210538255378 497 707 720 1324 1741 624 483 394 2133 808 733 497 M631 REACTOME_COLLAGEN_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COLLAGEN_FORMATION.html Genes involved in Collagen formation 25/64 Reactome 0.000131687699924128 0.00121713720284904 90 779.272727272727 722 1.19723257411894e-05 86 1.46726266075591 1.46726266075591 1 9.54498807575737 86 484 431 1291 1430 807 564 722 1584 407 766 498 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 0.00479346800625051 0.0198302700490299 725 1172.72727272727 725 0.000436722201832518 205 1.04498612775556 1.13473072187627 1 3.97119226421796 724 2469 2450 2893 248 826 427 272 725 1661 205 499 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 3.40591803950165e-08 1.24336077113988e-06 635 915.090909090909 725 3.0962891747547e-09 124 1.68491225049634 -1.20074158169684 -1 22.2078426229989 635 809 124 321 725 1225 1993 1513 425 705 1591 500 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 2.39938131596237e-07 6.24638935922204e-06 380 834 726 2.18125597967784e-08 176 1.58931010278711 1.58931010278711 1 18.4610518759531 380 1628 176 1169 1252 726 397 662 1301 678 805 501 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 0.00297664474412947 0.0140045755732838 200 1029.18181818182 726 0.000270970895499359 90 1.66369618993404 1.66369618993404 1 6.88335338687693 200 1641 1110 632 4094 640 231 726 90 1079 878 502 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 0.00313799828642828 0.0144873497243379 500 909.181818181818 727 0.00028568028809891 416 1.48544703090304 1.48544703090304 1 6.09706836807288 496 977 697 727 1402 1244 1019 476 1899 416 648 503 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 8.70311329166927e-05 0.00087704922332822 730 1587.54545454545 727 8.7034541592723e-06 16 0.464242254775154 0.464242254775154 1 3.16749731355993 727 171 4502 1632 3848 154 16 1341 486 4418 168 504 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 0.00725671294199579 0.0274143177532568 345 849.818181818182 727 0.00066188730679113 312 1.20074158169684 -1.20074158169684 -1 4.18616561983774 343 1450 843 1250 317 312 570 727 1566 1273 697 505 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 9.18765961432675e-06 0.000144474405881662 860 888.090909090909 728 8.3524527128519e-07 277 1.36639265672756 1.43704889488961 1 11.7114304744948 859 1556 277 716 426 1944 1658 546 772 287 728 506 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 2.27908972630013e-05 0.000301689673939051 315 801.181818181818 729 2.07192121533613e-06 290 1.53854058717623 1.53854058717623 1 12.0888615614261 315 987 323 1253 1122 1224 645 554 1371 290 729 507 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 0.000691636628750513 0.00438566879881584 85 1259.36363636364 730 6.28958328564295e-05 69 1.24121042685321 1.24620302516261 1 6.53224058064196 2183 730 1632 375 83 3188 3695 82 69 111 1705 508 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 5.07485354251946e-09 2.20192256483761e-07 370 881 735 4.61350323111443e-10 105 1.34379283477102 1.33812090443717 1 19.9665645744879 369 1558 105 1758 735 666 456 1676 1005 799 564 509 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 0.00123002209715736 0.00687814265785132 785 866.818181818182 738 0.000111882758405703 100 1.14544964218782 1.14544964218782 1 5.52862915659689 784 597 1916 109 100 1055 738 1866 429 688 1253 510 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 4.27008088065679e-08 1.49325365722073e-06 255 1131.45454545455 738 3.8818917850334e-09 130 1.59706725504045 1.75637903070291 1 20.7664988370967 252 1497 130 1148 3668 366 689 543 2315 1100 738 511 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 0.00116215359366262 0.0065691818334174 290 715.818181818182 740 0.000105706177963556 129 1.20074158169684 -1.20074158169684 -1 5.84899314471533 288 129 616 838 512 423 740 1034 1104 1403 787 512 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 0.005205949263379 0.0211317863291443 640 1000 742 0.000474391752635444 360 1.84663025917948 1.84663025917948 1 6.90384214496306 640 2591 742 1383 1269 730 654 360 1157 861 613 513 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 0.000591139723277215 0.00392362711512327 1190 1159.36363636364 743 5.37544202022087e-05 31 1.34804829891883 1.45796076319464 1 7.23997378209137 1190 31 743 219 63 4495 2505 854 485 162 2006 514 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 0.0056021469526011 0.0224949962466913 660 1042.27272727273 748 0.000510587590424673 185 0.957110715635759 0.957110715635759 1 3.52027260818557 658 1910 1694 1464 401 748 236 624 1434 2111 185 515 M1835 KEGG_GLIOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLIOMA.html Glioma 32/75 KEGG 0.034463851696881 0.0869669407924524 1140 1190.81818181818 749 0.003183262445099 406 1.6157152479086 1.6157152479086 1 3.82485307842062 1140 1574 1403 666 4273 1107 621 603 406 557 749 516 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 0.00764877775744584 0.028378600610761 270 1585.63636363636 749 0.000697772777801259 125 1.20074158169684 -1.20074158169684 -1 4.14592987659705 270 2620 3148 3072 749 125 644 575 2804 3049 386 517 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 7.43504627313309e-12 7.11033200732687e-10 575 967.454545454545 750 6.75913297559836e-13 48 1.35714495226037 1.39871897020262 1 27.7100413720489 575 1273 48 717 2973 831 750 1289 1460 129 597 518 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 0.0104819392749692 0.0359841519725318 1095 1307.81818181818 751 0.00105317119863567 3 3.21934379747048 3.21934379747048 1 10.3748216252743 1091 751 4140 238 4585 1213 574 463 3 1049 279 519 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 2.99688943551296e-05 0.0003744913038617 10 890.545454545455 751 2.72448205508441e-06 6 0.962481346460097 0.962481346460097 1 7.36088438872816 102 916 1117 751 2819 7 6 150 2184 1731 13 520 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 9.44646834496466e-18 2.32979740339497e-15 490 808.727272727273 751 8.5876984954224e-19 19 1.40717263913156 1.4438270535533 1 45.9569149069815 489 210 19 172 2002 1425 1166 1335 751 90 1237 521 M8353 BIOCARTA_HCMV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HCMV_PATHWAY.html Human Cytomegalovirus and Map Kinase Pathways 14/25 BioCarta 0.00396220756109485 0.0171756749595657 755 916.272727272727 752 0.000360851050468722 139 1.1921467147981 1.1921467147981 1 4.69650919996262 752 1532 2510 819 883 320 139 464 356 2034 270 522 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 7.46638878307986e-09 3.06907875767651e-07 3680 1869.36363636364 752 6.78762618947216e-10 111 1.35638805619206 -1.25981903401654 -1 19.717146083019 3680 412 111 351 591 2721 4605 3016 752 270 4054 523 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 0.00475584389086006 0.0197745203838245 505 1025.45454545455 752 0.000433286913263039 475 1.36652326731504 1.36652326731504 1 5.19683788788496 505 686 734 823 2339 1316 1434 558 1658 475 752 524 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 2.54833822877484e-05 0.000330789832134042 505 683.818181818182 754 2.31669795232854e-06 119 1.28309077792731 1.27670012153598 1 9.96717466337438 504 534 326 203 881 1309 754 807 1274 119 811 525 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 0.00726017249931534 0.0274143177532568 1180 1397.63636363636 755 0.000728400168885627 208 0.249370743851551 -0.249370743851551 -1 0.869385428404799 1178 749 4049 2092 1012 375 208 733 550 3673 755 526 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 0.0123251086618383 0.0403558152745448 680 1189.45454545455 757 0.0011267913057166 395 1.07053608042085 1.07053608042085 1 3.33098657729349 676 1424 1337 1225 3990 470 540 395 757 1813 457 527 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 1.29158144152529e-10 9.35492441625007e-09 415 680.090909090909 759 1.1741649469101e-11 62 1.31563114659671 1.34819181046076 1 23.5761551151833 413 527 62 322 844 1688 814 1088 759 183 781 528 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 0.00220732125425374 0.0110507557664883 260 992.818181818182 759 0.000200867185180046 256 1.52754782539778 1.52754782539778 1 6.67080430222495 256 2134 668 2264 905 560 763 759 1712 518 382 529 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 1.93994813988919e-07 5.28523080437253e-06 1400 1098.81818181818 760 1.76358937359345e-08 168 1.36332283713843 1.45064901176628 1 16.0568405556299 1396 214 168 276 602 3495 1547 1357 760 227 2045 530 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 0.00174825673663715 0.0091432266382608 320 906.727272727273 761 0.000159058868879239 85 1.35870350668892 1.35870350668892 1 6.1830148070359 319 914 761 1495 2260 104 85 406 1341 2003 286 531 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 0.00756796634554934 0.028167982760321 615 776.181818181818 764 0.000690375100534316 374 1.36500878471057 1.36500878471057 1 4.72296939430804 615 1714 784 954 882 892 588 410 764 374 561 532 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 4.70457088799738e-08 1.60916928329604e-06 555 909.909090909091 765 4.27688271691078e-09 133 1.49133989989152 1.51659165351333 1 19.2836649468342 554 765 133 370 1802 1420 1080 684 1930 259 1012 533 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 0.00433983688399121 0.0184541521219445 860 816.545454545455 766 0.000395311054063122 273 1.38992017722867 1.38992017722867 1 5.37891819717177 858 273 725 1050 1364 1610 766 281 839 650 566 534 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 3.20272450592952e-05 0.000390832474864212 770 982.454545454545 766 2.9116101196604e-06 71 1.34329096038914 1.42442003661568 1 10.2176359624482 766 552 343 429 1519 2278 1255 891 729 71 1974 535 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 4.2009116054377e-05 0.000488473245237743 270 743.818181818182 770 3.81908347655538e-06 194 1.68900434267256 1.68900434267256 1 12.4821784005088 269 904 358 194 1571 1290 466 770 1115 197 1048 536 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 0.000236440876063414 0.00192996138713548 160 765.909090909091 771 2.14969355388564e-05 157 1.46778240338295 1.46778240338295 1 8.89248822288362 157 1455 476 999 1193 970 486 280 1145 493 771 537 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 0.000181787075894291 0.00158632074048537 450 1007.45454545455 771 1.65274635261083e-05 260 0.987488271888532 1.09583556461856 1 6.17033696403764 446 296 457 518 1674 771 260 898 1983 2921 858 538 M17902 BIOCARTA_CASPASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CASPASE_PATHWAY.html Caspase Cascade in Apoptosis 19/39 BioCarta 0.00188926136270936 0.00969669084956852 775 1317.36363636364 772 0.000171898702627647 90 1.53150662091758 1.53150662091758 1 6.88213865130816 772 2288 2741 2565 569 372 90 717 1737 2316 324 539 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 0.00899693754481094 0.0319391282840789 790 869.454545454545 774 0.000821267519558149 144 1.36163724852233 1.35246023888248 1 4.54546979556375 790 995 2248 691 363 774 696 1291 144 896 676 540 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 0.0175406839753631 0.0529317865278208 360 1106.72727272727 775 0.00160746525265348 358 1.0001184641382 1.0001184641382 1 2.8489061110259 358 1575 2170 991 2578 511 415 697 371 1733 775 541 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 0.00173705601838892 0.00909767082732089 820 1137.81818181818 776 0.000173841532767659 133 1.48034281358945 1.48034281358945 1 6.74372275143772 820 1393 4397 1074 133 742 678 776 292 1710 501 542 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 0.000368715386597005 0.00272523706875957 665 1003.09090909091 776 3.35251997296459e-05 330 1.26116618995449 1.31223309258236 1 7.21889601412214 664 776 517 467 330 1447 1316 1589 1681 441 1806 543 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 0.000719085027616438 0.00452707809785602 780 879.090909090909 777 6.53927430071901e-05 132 1.19122087724416 1.29268140857187 1 6.23251281628301 777 1138 573 1185 1025 1528 567 132 1454 611 680 544 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 0.0106830596810395 0.0364477844743278 780 839.818181818182 778 0.000975935579231242 365 1.2590014857358 1.32013035886476 1 4.04169924915645 778 679 1155 544 1206 1080 753 365 727 1043 908 545 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 1.45888613392263e-07 4.21996322442065e-06 860 1099.54545454545 779 1.32626020969615e-08 121 1.69023553912301 1.57996831061914 1 20.275907984844 856 779 157 682 275 2858 2307 2148 431 121 1481 546 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 0.00228504928559953 0.0113551490436511 1045 824.909090909091 779 0.000207947829910087 114 1.36581055257572 1.36581055257572 1 5.92852374324554 1042 684 2356 1321 145 779 1042 158 640 793 114 547 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 0.000499949609377848 0.00349145137040924 300 1057.18181818182 780 4.54602962724593e-05 296 1.3926906360651 1.3926906360651 1 7.63727285204737 296 2144 536 2351 1482 780 521 1251 1406 385 477 548 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 0.000296130536767504 0.00227114189082246 505 798.727272727273 781 2.69245822608424e-05 271 1.38036454113875 1.46778240338295 1 8.14506727279598 503 923 500 1186 1176 1119 781 287 1627 413 271 549 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 0.00139408470538943 0.00760622717921106 390 985.545454545455 782 0.000126815353302222 389 1.33642347549859 1.40928775112009 1 6.32004119210125 389 1417 636 1594 1798 1556 782 405 655 509 1100 550 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 2.32516560318969e-05 0.000306059719565924 660 870.090909090909 783 2.11380925279674e-06 324 1.29371558598876 1.40977817676359 1 10.1471499024702 657 530 324 783 2232 1025 589 743 915 849 924 551 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 0.00595596366951015 0.0235922618388204 645 1177.36363636364 783 0.000542922669895567 109 1.44395274113808 1.44395274113808 1 5.24422828809451 644 1084 783 1270 3555 109 305 326 2491 2186 198 552 M13191 KEGG_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROSTATE_CANCER.html Prostate cancer 46/121 KEGG 0.0100403555570014 0.0348253931458983 1320 805.909090909091 784 0.000916952058041799 165 1.41311271260707 1.56022004577615 1 4.59880347807438 1320 909 1123 165 383 1598 1271 418 367 527 784 553 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 0.00542038680516936 0.0218964935939859 1410 1142.09090909091 785 0.00049398071525892 88 1.72323311627257 2.03069314115111 1 6.38312966168989 1408 1516 785 88 753 2642 2405 258 216 461 2031 554 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 4.96485206745864e-09 2.17432680262721e-07 195 755.909090909091 785 4.51350188969371e-10 103 1.47563602702444 1.56467222819424 1 21.9435781426408 193 1406 103 1202 799 565 380 785 1391 674 817 555 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 0.000190689327991711 0.00164670731715519 430 906.181818181818 787 1.73368962154828e-05 430 1.32729461554188 1.43721573405288 1 8.24555606348826 430 1063 459 590 2049 1067 759 681 1247 787 836 556 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 1.83040621414978e-05 0.000256804895793589 630 1209 788 1.66401949396234e-06 172 1.68599595693858 1.73318647461325 1 13.5107208122026 628 3119 308 1075 4460 1149 935 193 472 172 788 557 M15798 KEGG_MELANOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOMA.html Melanoma 32/89 KEGG 0.039712244329521 0.0969238706681705 1025 738.272727272727 789 0.00367706787184039 164 1.6157152479086 1.6157152479086 1 3.65508772467142 1025 475 1012 164 949 958 789 1219 368 558 604 558 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 0.00544500644759003 0.0219580896845154 550 886.636363636364 789 0.000496229976001563 182 1.1706334647314 1.19117170264949 1 4.33302510090328 550 1121 1670 932 1338 493 681 769 789 1228 182 559 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 0.00135263575767442 0.00743077510019031 405 834.272727272727 790 0.000123042556479724 104 0.98955805842959 0.98955805842959 1 4.7020748302501 402 295 869 790 104 632 449 1062 933 2439 1202 560 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 0.00760557647592546 0.0282630700762781 755 1255.27272727273 792 0.000693817957112896 227 1.78661574975038 1.78661574975038 1 6.17590534299686 792 1738 1634 753 4334 752 856 773 455 1494 227 561 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 9.57356788414354e-05 0.000950460574260522 475 841.545454545455 792 8.70362228635439e-06 16 1.28776984829647 1.28776984829647 1 8.68603823073939 472 1977 1431 1171 1537 242 866 220 792 533 16 562 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 0.000153684589776362 0.00137174473846101 3025 1845.90909090909 796 1.39723024285663e-05 23 1.50228015619532 1.67277413882291 1 9.5986548044545 3025 89 444 23 796 4186 3889 4168 221 458 3006 563 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 0.00122399775866949 0.00685773981834073 2730 1153.90909090909 797 0.000111334479651338 45 1.39103995783307 1.45447274987848 1 6.71800138675341 2727 45 620 486 529 797 2306 1453 1204 593 1933 564 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 0.0150067730029153 0.046677434268223 435 847 798 0.00137364786079275 433 1.20562879252176 1.34652520861227 1 3.58126381381573 434 798 1161 662 672 1317 741 433 1293 932 874 565 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 2.72222313658002e-05 0.000348533814699835 365 913.727272727273 799 2.4747789284082e-06 329 1.3129933231371 1.36856622604803 1 10.1329593497073 365 1124 329 799 1539 1543 675 551 1695 487 944 566 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 0.00465844034312663 0.0195091861833284 620 1015.36363636364 800 0.000424393982316011 233 1.47034100484392 1.47034100484392 1 5.61090597750326 618 888 800 1765 1413 488 345 233 1800 2537 282 567 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 0.00822822714759813 0.0300291841227763 1390 1481.6 800.5 0.000917608279358104 351 0.496587586046763 -0.496587586046763 -1 1.68740874952184 1387 516 4087 NA 926 675 629 351 1843 3750 652 568 M13247 BIOCARTA_TCYTOTOXIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCYTOTOXIC_PATHWAY.html T Cytotoxic Cell Surface Molecules 4/15 BioCarta 0.00052691717281219 0.00359408132721677 805 1385.27272727273 801 5.27042153290118e-05 41 0.713921463083668 0.713921463083668 1 3.89497270096347 801 2114 3875 1591 777 574 41 107 1555 3330 473 569 M6427 BIOCARTA_THELPER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_THELPER_PATHWAY.html T Helper Cell Surface Molecules 4/15 BioCarta 0.00052691717281219 0.00359408132721677 805 1386.27272727273 802 5.27042153290118e-05 42 0.713921463083668 0.713921463083668 1 3.89497270096347 802 2115 3876 1592 778 575 42 108 1556 3331 474 570 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 0.000262278843172152 0.00208423934269886 480 1015.54545454545 803 2.3846374241897e-05 216 1.093472758285 1.30632518518954 1 6.54323964398981 478 335 485 1010 1936 689 216 1491 2359 1369 803 571 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 0.00122490999316073 0.00685773981834073 2455 1533.72727272727 805 0.000111417502480802 300 1.46372069495104 1.46513174770406 1 7.06901164350901 2452 532 621 585 745 3214 2629 2008 805 300 2980 572 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 6.53325156873473e-05 0.000700567891329312 190 921.272727272727 807 5.93949599286098e-06 186 1.45045803243481 1.45045803243481 1 10.212265710276 186 1565 382 1679 1123 910 807 482 1962 503 535 573 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 5.11799627361952e-07 1.20517238885332e-05 1230 1147.18181818182 809 4.65272496750099e-08 161 1.43621897790972 1.54228809256982 1 15.7678578805757 1226 226 194 161 311 4646 1843 1390 809 471 1342 574 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 0.000252371771799976 0.00201832562770965 325 885.545454545455 809 2.29455206488387e-05 40 0.898980477450584 0.898980477450584 1 5.40741868385098 323 899 841 809 40 92 128 1388 2425 2549 247 575 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 0.00275573917728992 0.0132445064459288 810 853.181818181818 809 0.000250836100520931 81 2.19233975904646 2.19233975904646 1 9.18913704528823 809 1857 1138 417 161 1379 1531 441 81 916 655 576 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 0.00782300560973603 0.0288196574585087 1820 1236.18181818182 810 0.000713723891316483 437 1.59410992842045 1.81260996350999 1 5.48032470088669 1817 810 788 474 611 3164 1180 2189 437 740 1388 577 M6889 KEGG_RIBOFLAVIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOFLAVIN_METABOLISM.html Riboflavin metabolism 4/19 KEGG 5.40793618593708e-05 0.000596272681583557 905 907.454545454545 811 5.40806779642685e-06 11 1.82051220676583 1.82051220676583 1 13.1021615714991 905 861 3801 1631 437 811 267 25 53 1180 11 578 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 9.77787696303729e-19 2.69524302639957e-16 980 915.363636363636 812 8.88897905730662e-20 17 1.49335084197093 1.64302148615145 1 51.8935450429177 976 758 17 508 568 2620 1504 1098 812 40 1168 579 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 9.78234611029224e-07 2.14205952676773e-05 175 761.272727272727 814 8.89304587275968e-08 171 1.54091804839166 1.54091804839166 1 16.0582657314877 174 1155 208 1252 171 814 897 1056 1870 203 574 580 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 0.0333905236281877 0.084668827771476 1880 969.818181818182 814 0.00308257687342881 52 1.24989964178852 1.33633209731061 1 2.99131030645445 804 52 1878 554 814 1547 652 786 833 1880 868 581 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 0.0230866496385186 0.0652497226816032 510 982.181818181818 815 0.0021211399572616 508 1.07881445795077 1.26572216255243 1 2.85429627153748 508 815 925 1157 2028 947 649 749 652 1803 571 582 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 0.0104221576106033 0.0358577316911065 1555 1023.72727272727 817 0.000951987356427209 94 1.2704684134739 1.262573168782 1 4.09861043226417 1553 94 817 254 393 2569 1754 1585 283 442 1517 583 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 0.000486771213309048 0.00341980495587136 1150 901.818181818182 817 4.42617226825327e-05 42 1.62274291485784 1.62274291485784 1 8.93145291505851 1148 997 1088 526 817 2437 1919 268 241 437 42 584 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 0.0105856603262938 0.0362340425778033 330 963.454545454545 818 0.000966994612798124 255 1.34231516676186 1.34231516676186 1 4.31680899192404 330 1133 818 1371 1514 744 255 440 1947 1363 683 585 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 0.0555127400863347 0.124601605911306 1380 1413.18181818182 818 0.00569502956939285 200 1.40918333712617 1.40918333712617 1 2.84475110241187 1376 1025 4598 1199 3667 798 818 750 200 422 692 586 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 0.00124466396423721 0.00693315256676981 1390 904.909090909091 819 0.000113215336275453 102 1.66514321553908 -1.01405746558881 -1 8.02412559305797 1388 1158 1529 703 102 580 627 819 1258 1405 385 587 M2587 BIOCARTA_HSP27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HSP27_PATHWAY.html Stress Induction of HSP Regulation 13/25 BioCarta 0.0296136576589978 0.0776985441153772 820 1071.54545454545 820 0.0027290870443845 162 2.05369581223184 2.05369581223184 1 5.08600846391256 816 1591 967 162 3975 1284 642 820 178 902 450 588 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 0.00565741764583818 0.0226586829815365 2765 1502.81818181818 821 0.00051563805371988 276 1.40657774027322 1.47518979313202 1 5.16353636118825 2763 782 1781 548 276 810 3019 3706 451 821 1574 589 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 4.21941796523856e-05 0.000489410707552175 215 765.272727272727 824 3.83590808396075e-06 120 1.33801644251219 1.39434056125431 1 9.88580045846519 212 461 359 582 918 1870 895 824 1185 120 992 590 M10082 BIOCARTA_TNFR2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR2_PATHWAY.html TNFR2 Signaling Pathway 11/22 BioCarta 0.0576213888996815 0.127968639044506 700 1228.36363636364 825 0.00538075908038871 64 1.06710845596515 1.06710845596515 1 2.12661665949212 696 619 2588 220 4247 364 825 1217 64 1838 834 591 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 0.00479464275833352 0.0198302700490299 830 1249.09090909091 826 0.000480501915087517 163 0.874649861425705 -0.874649861425705 -1 3.32387451978507 826 1813 3790 1691 534 163 239 1120 214 3172 178 592 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 0.00933011420869043 0.0328743726165795 865 887.363636363636 826 0.000851810854347284 96 1.25707923568623 1.25707923568623 1 4.16126233244436 863 96 826 491 368 721 904 1936 1740 1352 464 593 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 4.34432247651983e-07 1.04935541881299e-05 190 1459.27272727273 827 3.94938484944543e-08 54 1.33853405528682 1.46503238571134 1 14.8750302097539 1803 188 190 54 566 4567 2046 3013 827 180 2618 594 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 7.29756940237838e-05 0.000758910888174197 735 1155.18181818182 828 6.63437407237871e-06 74 1.34842882029515 1.34154319902212 1 9.3893519324068 731 2224 393 1183 74 1565 828 1756 2629 592 732 595 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 0.0228522254599018 0.0647825338808831 710 1090.09090909091 828 0.00209937368137343 566 1.63251237725593 1.63251237725593 1 4.33062517079023 708 828 923 627 3270 1409 951 566 683 589 1437 596 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 3.97100477189264e-07 9.69173352140049e-06 830 942.454545454545 829 3.61000498969095e-08 187 1.2003010078049 1.34787413450982 1 13.4313380620463 829 569 187 461 1357 802 854 1462 1888 271 1687 597 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 5.00920472524883e-07 1.18575220388827e-05 365 943.545454545455 829 4.55382351436423e-08 192 1.56864556154969 1.60677143918206 1 17.2464344241826 363 1713 192 1015 671 1572 711 1810 829 415 1088 598 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 8.41589414332056e-06 0.000134139047468028 490 948.727272727273 829 7.65084212518958e-07 273 1.51014750914691 1.51014750914691 1 13.0522132006989 486 2348 273 1003 956 1509 811 829 853 576 792 599 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 0.0024235597908434 0.011979748080055 635 1008.90909090909 830 0.000220566704819291 433 1.30322573467929 1.31893275984107 1 5.58922270679313 631 433 674 815 606 2568 1549 1265 830 845 882 600 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 0.00670608009434271 0.0258426737846134 260 963.272727272727 831 0.000611509941111234 257 1.46726266075591 1.46726266075591 1 5.19930892285226 257 1732 831 1338 1060 1201 826 653 1601 512 585 601 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 0.0112684327529003 0.0379883999137344 725 1383 832 0.00102968792127759 276 1.20474718644447 1.20474718644447 1 3.81918367134949 722 2619 832 2664 2547 618 442 467 3074 952 276 602 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 1.76308695290668e-06 3.60913880064106e-05 835 821.818181818182 832 1.60280760531975e-07 49 1.41213081700438 1.56199828435269 1 14.0020410750733 832 49 219 63 1290 1834 986 1381 746 349 1291 603 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 1.92829759012779e-05 0.000268130638199966 1925 1227 832 1.75301317440223e-06 8 1.79076672618337 1.79076672618337 1 14.2753872323869 1921 491 1163 832 8 3540 2592 690 574 1160 526 604 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 0.00731260387027949 0.0275678694578678 1120 1381 833 0.000733677928853161 140 1.2690931545689 1.35661891752079 1 4.4175898421351 1120 647 4670 140 588 3865 1702 608 855 163 833 605 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 0.00109945016496701 0.00628295545492121 1940 1524.09090909091 834 1e-04 51 2.19853342647778 2.19853342647778 1 10.804324008936 1937 824 834 51 4496 2480 2147 745 121 659 2471 606 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 0.00281450873079987 0.0134388851634452 580 1401.27272727273 837 0.000281807975460184 179 0.967459383376804 -0.967459383376804 -1 4.04141883922274 580 955 4355 1067 179 383 695 837 1844 4131 388 607 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 0.00470522118171556 0.0196162512967252 815 1368.7 838 0.000523898892694624 5 1.91509024629137 1.91509024629137 1 7.29793518915526 812 864 4257 NA 3747 266 174 2398 5 876 288 608 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 9.7831740053596e-05 0.000967172012428588 1085 969.454545454545 839 8.89419007285852e-06 30 1.44436332131058 1.51879362256252 1 9.71786268552794 1085 30 406 57 839 3269 1458 1180 657 366 1317 609 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 1.97905262598735e-05 0.000272760017805198 215 1282.45454545455 840 1.79915493560265e-06 188 1.18196713259558 1.18196713259558 1 9.40263053002597 211 2927 312 3047 1030 188 196 840 2894 2156 306 610 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 0.000495115821488962 0.00346285483507056 900 1046.18181818182 840 4.50206621577393e-05 66 1.69850446179667 1.69850446179667 1 9.32784272498094 900 1957 1624 840 3257 1064 556 66 164 771 309 611 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 1.2962830987979e-21 5.52216600087905e-19 360 709.545454545455 842 1.17843918072536e-22 11 1.48328367449705 1.58607110819858 1 60.444163350027 360 1111 11 729 1547 940 858 508 842 29 870 612 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 0.00234117017768545 0.0116215290811801 150 1185.81818181818 843 0.000213060481344746 140 1.09708043218827 1.09708043218827 1 4.73739829587305 694 2007 2931 1993 148 700 140 1337 2102 843 149 613 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 4.71780253263687e-05 0.000536592783202339 200 1048.27272727273 845 4.28900336987231e-06 197 1.53032795220863 1.53032795220863 1 11.1701495290334 197 1931 363 948 2303 584 731 845 2335 369 925 614 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 0.0169637715758934 0.0515848368621912 505 902.545454545455 845 0.00155418232906202 323 1.23777004229742 1.32341024832561 1 3.55679895652416 501 960 1305 845 1396 461 346 714 1697 1380 323 615 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 4.14704178613597e-09 1.83625817240245e-07 1885 982.272727272727 845 3.77003799450293e-10 24 1.32942410664363 1.46160038936646 1 19.9870847843181 845 198 101 171 1881 2669 1882 861 464 24 1709 616 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 0.0426776322503602 0.102086464892898 825 1006.36363636364 845 0.00395715808311864 50 1.12096553309211 1.22249033368997 1 2.47947320622506 823 845 1685 572 1948 1137 619 1953 50 920 518 617 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 6.35013557114044e-07 1.47310570724575e-05 945 818.090909090909 846 5.7728521855094e-08 197 1.26524668631435 1.30648762615964 1 13.644595477382 941 521 197 598 846 1673 1246 455 939 697 886 618 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 0.0415800128228073 0.100412224897613 700 953.363636363636 846 0.0038533926550804 478 1.31429356913902 1.38062605374941 1 2.92816359863122 697 1193 1839 1424 1161 639 478 826 875 846 509 619 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 5.05156387394198e-08 1.70396356648396e-06 850 750.090909090909 846 4.59233089994021e-09 134 1.47363368156383 1.46069519034301 1 18.9729551230718 277 898 134 846 1333 1324 647 445 1183 314 850 620 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 0.000759006041915958 0.00470079369711562 440 863.090909090909 846 6.90243661485218e-05 439 1.26112455801819 1.26112455801819 1 6.55222158440756 439 1741 579 1007 460 977 846 1395 491 690 869 621 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 0.0472073367556205 0.110446878622571 745 925.181818181818 847 0.00438652924177664 148 1.21339426347673 1.40743815937135 1 2.5913363607236 741 2049 1227 685 979 757 847 1317 148 427 1000 622 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 0.00477205669800387 0.0197892545901293 2030 1561.18181818182 850 0.000434767217207183 138 1.37043690095724 1.45863323676773 1 5.21073187026947 2027 385 850 201 541 4032 2918 2112 722 138 3247 623 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 0.0357044842054838 0.089519108072176 650 842.363636363636 853 0.00329976918227499 458 1.63511889517584 1.63511889517584 1 3.8249440611602 650 464 994 458 853 1236 507 1269 1200 706 929 624 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 4.37853923393117e-05 0.000502888109073565 15 1402.90909090909 855 4.37862550854984e-06 11 0.85322032193671 0.85322032193671 1 6.2814658637969 217 855 4275 1672 2094 13 11 106 2132 4023 34 625 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 0.00201840791119807 0.0102251453749991 630 1229.18181818182 855 0.000183660190727339 98 0.874428728977911 0.891984977416434 1 3.8844467523871 629 594 2166 1530 138 412 98 1347 1368 4384 855 626 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 0.0128768350406984 0.0416807851003278 925 1034.90909090909 856 0.00117752981623265 203 2.46711003640163 2.46711003640163 1 7.59919057881279 924 832 1550 702 443 856 628 1802 203 2172 1272 627 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 0.00398792967061466 0.0172712000337341 1220 870.181818181818 856 0.000363197906426544 113 1.29016890673775 -1.29016890673775 -1 5.0757355071965 224 716 1220 1122 1325 113 184 856 1220 2192 400 628 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 5.08374706091988e-06 8.75824953215829e-05 140 870.272727272727 862 4.62159891677336e-07 138 1.30652461200366 1.34144603336941 1 11.8321734823421 138 1831 255 1088 791 1161 933 862 1390 289 835 629 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 0.0360223222274597 0.0901231190378409 740 1275.45454545455 862 0.00332963900540674 522 1.47097469887605 1.47097469887605 1 3.43138233421008 738 2754 1006 1718 3137 694 862 616 660 1323 522 630 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 1.96577651622396e-15 3.41171435371314e-13 865 1151.36363636364 863 1.7870695602036e-16 27 1.43576089247077 1.56560778672229 1 39.9507177547033 709 388 27 863 2445 2208 1757 1204 862 304 1898 631 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 0.000104503266443108 0.00102234301994238 710 928.727272727273 864 9.50074825759726e-06 215 1.15863869501637 1.1099059725563 1 7.73316640863918 707 482 410 864 215 1354 1095 900 2050 853 1286 632 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 0.0153619781299871 0.0474530187983649 460 950.454545454545 866 0.00140639154304888 394 1.32215050085759 1.40262287898372 1 3.90626658932161 460 1356 866 1646 802 1305 394 448 1677 928 573 633 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 0.00153964510687866 0.00824545939523819 730 836.363636363636 867 0.000140065787907172 131 1.15075421209946 -1.20074158169684 -1 5.35198718794386 728 131 642 980 386 867 1389 970 1223 658 1226 634 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 0.00319560283372104 0.0146665963553544 1450 787.090909090909 867 0.000290932187048022 149 1.63097965253578 1.82702250129526 1 6.67497177708558 1446 947 1039 688 1238 1015 867 180 149 292 797 635 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 3.83542490228821e-06 6.80787920156158e-05 870 1426.45454545455 867 3.48675598989841e-07 246 1.54039145951267 1.54039145951267 1 14.3262631154975 867 813 246 837 456 3750 2685 2441 1212 317 2067 636 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 0.0155179112652478 0.047808633917785 350 1384 867 0.00142076923486647 346 1.76596213505392 1.91698704176158 1 5.20471872675386 346 2682 867 3003 2907 438 686 480 2107 1001 707 637 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 2.19110190055058e-10 1.44612725436338e-08 840 864.909090909091 869 1.99191081888073e-11 69 1.3768069458464 1.4601086613306 1 24.0911330373165 840 219 69 197 2663 1158 1161 955 869 403 980 638 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 1.47705993898314e-07 4.22042858175304e-06 2610 1743.18181818182 871 1.34278185286509e-08 159 1.42104021245603 1.47764342709523 1 17.0465140488776 2607 654 159 231 764 3274 3054 3125 871 482 3954 639 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 0.0131712937075899 0.0423711293341608 2165 1235.36363636364 872 0.00120461972299182 32 1.28186625143775 -1.02597661069573 -1 3.92799250852463 2162 32 872 521 2888 136 1811 2223 587 1819 538 640 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 0.0230687123287179 0.0652383741535136 1640 1278.27272727273 872 0.00211947431099058 204 1.29186272027943 1.32657502813092 1 3.41819104835275 1636 204 1669 293 644 3653 2038 872 780 623 1649 641 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 0.0138722209733162 0.0440116638327418 625 1187.90909090909 873 0.00126913391683399 535 1.40300827499401 1.40300827499401 1 4.24754395886454 623 677 851 1608 2688 2148 1002 1349 535 713 873 642 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 0.00191625316999158 0.00982446647109468 875 1332.63636363636 873 0.000191790758998859 37 1.51935086267539 -1.51935086267539 -1 6.80823454841835 871 1814 4572 873 3157 264 748 910 37 1311 102 643 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 0.0158262505125972 0.0486306950177248 1175 1080 874 0.00144920550742291 397 1.33795703761755 1.42386372504592 1 3.92117350338182 1173 812 874 397 1654 1686 1612 1429 721 666 856 644 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 0.00459070374109318 0.0192760194720095 965 952.636363636364 874 0.000418210105944188 240 1.10619049427982 1.21660168037507 1 4.23417892342398 961 414 1264 530 240 1787 1426 823 874 1474 686 645 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 0.0106869944233304 0.0364477844743278 770 1037.72727272727 875 0.000976296793499586 394 1.2294711097255 1.35105665555181 1 3.94689960046388 768 563 875 684 394 1387 697 1510 1611 1737 1189 646 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 0.000536488377846979 0.00364345585303035 880 892.909090909091 876 4.87835681546874e-05 237 1.23865677968529 1.34796765392169 1 6.74141234947161 876 764 548 282 514 2604 1003 954 975 237 1065 647 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 9.16767308882098e-08 2.84501431087517e-06 880 1157.45454545455 877 8.33424860986304e-09 147 1.28327059985295 1.3559686328731 1 15.8844086332421 877 201 147 540 864 2890 2210 1415 1377 248 1963 648 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 0.0174734766905622 0.0528262656593385 595 1705.9 877 0.00195674306263532 369 0.857185672850884 0.857185672850884 1 2.44341027707084 593 1484 4456 NA 612 369 476 1093 2950 4365 661 649 M19 PID_P73PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P73PATHWAY.html p73 transcription factor network 18832364 63/123 Pathway Interaction Database 0.00903569341056397 0.0320524294639688 2530 1219.18181818182 878 0.000824819909754881 229 1.35824371799646 1.35824371799646 1 4.52947925806986 435 2527 1406 2248 364 703 229 1743 2526 878 352 650 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 9.95325234827211e-12 9.14528245176532e-10 450 944.454545454545 879 9.04841122574286e-13 50 1.48479733107357 1.48382443817123 1 29.9541946830625 450 1403 50 647 2411 1298 1073 879 775 256 1147 651 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 0.000625896657769212 0.00409630131048398 995 821.454545454545 879 5.69158904884868e-05 75 1.30137886665529 1.30137886665529 1 6.93499814355106 481 991 879 1487 793 991 347 75 1143 1638 211 652 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 0.0167996020827353 0.0511520047821298 4600 1833.36363636364 880 0.0015390250311793 88 1.4544705067543 -1.20074158169684 -1 4.19137882761701 4598 88 880 423 540 3255 4638 1060 218 788 3679 653 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 0.0110783591294417 0.0374284000580851 2105 1199.45454545455 880 0.00101223109041579 469 1.25712539755129 1.19009384316858 1 4.00332521013535 2104 680 823 675 962 1459 3098 469 551 880 1493 654 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 0.0293176942932725 0.0770514388436764 425 1161.81818181818 884 0.00270143969195547 421 0.996804943727207 0.996804943727207 1 2.47668312093907 421 884 1340 1060 2259 643 787 761 876 2725 1024 655 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 0.00327453785166968 0.0149265412187978 330 1108.90909090909 884 0.000298129267309046 329 1.52754782539778 1.52754782539778 1 6.22565215263149 329 2533 700 2115 1036 884 957 878 1707 489 570 656 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 2.03508924869316e-05 0.000278842930391116 590 975.909090909091 885 1.85009824939828e-06 291 1.30789897078425 1.46593961028369 1 10.3764648819032 588 472 314 1578 2088 1619 885 291 1361 344 1195 657 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 0.00109945016496701 0.00628295545492121 2785 1539.72727272727 886 1e-04 60 1.39764135027827 1.51136574530028 1 6.86847414496819 2784 199 886 60 342 832 4285 1930 845 1003 3771 658 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 0.0026937218727921 0.0130270977533909 195 984.090909090909 887 0.000245184162002632 132 1.40410888410514 1.48485767606576 1 5.90781368717139 194 2133 887 2223 1566 132 448 451 1687 929 175 659 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 5.11175680573415e-05 0.000571687169252272 460 1230.54545454545 889 4.6471596205338e-06 18 1.14338139147186 1.14338139147186 1 8.27554117910562 458 1237 1841 859 18 701 889 1249 3279 2175 830 660 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 0.00827975366356653 0.030170237688548 1760 1412.27272727273 889 0.000755552718099939 142 1.40917665184157 1.40917665184157 1 4.78199292977619 1757 142 1798 768 346 3043 3431 2411 362 588 889 661 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 0.012782135199306 0.0414799761384679 1185 1159.72727272727 890 0.00116881908549408 288 1.33273220978776 1.47567399076321 1 4.11131962114515 1185 658 1236 288 439 3219 2184 890 865 783 1010 662 M4741 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS.html Systemic lupus erythematosus 64/146 KEGG 2.82000386332379e-05 0.000356187010876961 895 906.181818181818 891 2.56367273758568e-06 333 1.23038222851043 -1.13853737079594 -1 9.46950782847641 470 895 333 1123 1360 773 1509 765 738 891 1111 663 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 0.00161635103562578 0.00861686115238044 1185 1122.72727272727 892 0.000147049072706071 110 1.47406697850764 1.77982051978139 1 6.79271514984588 1183 1016 1795 1027 3926 877 668 127 110 729 892 664 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 0.00175086039381268 0.00914663523456658 1205 1096.63636363636 893 0.000159295942082888 508 1.24698741260489 1.30858692321559 1 5.67418091245195 1203 551 651 692 893 2543 1889 747 1271 508 1115 665 M7253 KEGG_FOCAL_ADHESION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOCAL_ADHESION.html Focal adhesion 101/245 KEGG 5.55772809954383e-06 9.4360557516168e-05 895 953.272727272727 894 5.05249285431706e-07 66 1.62319080972866 1.61684260944243 1 14.5826891740781 894 252 259 66 920 2216 2369 1422 343 104 1641 666 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 3.16760385915111e-05 0.00038755591864183 815 983.636363636364 894 2.8796813344203e-06 313 1.55310116634137 1.55310116634137 1 11.8262147333292 811 894 342 1366 381 2244 1308 313 1465 652 1044 667 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 0.000646722542333145 0.00419919080521078 895 1021.63636363636 895 5.88102485699085e-05 464 1.30084970470145 1.30084970470145 1 6.90089787146855 464 892 562 895 1541 669 1227 1944 1393 1062 589 668 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 0.00520853888394401 0.0211317863291443 535 946.090909090909 896 0.000474628292699482 226 1.06772417951451 -1.07337241505112 -1 3.99181111270411 535 896 2376 1105 987 226 335 250 1308 2029 360 669 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 0.00291822896748264 0.0138871822750554 900 999.545454545455 898 0.000265646100710759 184 1.22697978905454 1.22697978905454 1 5.08650059595858 898 318 685 184 2824 1441 998 1322 338 561 1426 670 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 4.15372100458086e-09 1.83625817240245e-07 255 820.636363636364 899 3.77611001129392e-10 102 1.56109292427359 1.72616572138063 1 23.4700848869466 255 978 102 320 427 899 1058 1888 1710 417 973 671 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 0.000345205255424133 0.00257995506685404 900 1150.81818181818 899 3.13872212721531e-05 37 1.25231655792714 1.25231655792714 1 7.23474171860337 899 2235 2451 1394 897 776 499 496 1332 1643 37 672 M6910 BIOCARTA_INFLAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INFLAM_PATHWAY.html Cytokines and Inflammatory Response 13/44 BioCarta 0.00238548422864243 0.0118289725877444 570 993.545454545455 901 0.000217097706258964 155 1.30149689713263 1.30149689713263 1 5.59778669200019 568 1535 911 958 1997 647 624 155 2342 901 291 673 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 0.000453058128006702 0.00321184627509744 1415 1225.81818181818 901 4.11955868793611e-05 41 1.52518841599199 1.70825945920344 1 8.48727067651906 1414 2974 1586 760 2005 2082 901 472 435 814 41 674 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 0.0151460303419955 0.0469877026803156 810 1734.63636363636 901 0.00138648366535854 210 0.415040243144147 -0.487281287084778 -1 1.23019229221644 810 835 3046 1137 4211 210 289 901 2462 4685 495 675 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 2.16292938202597e-11 1.80990840788816e-09 905 1031.45454545455 902 1.96629943822476e-12 54 1.2556737967963 1.29509081301477 1 24.5010246925954 902 241 54 745 683 2153 1380 1664 1466 440 1618 676 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 0.0176629814406159 0.0532274797625249 1125 1185 902 0.00161876415083914 424 1.18280663879086 1.18280663879086 1 3.36291898860075 1125 902 2276 613 537 2964 1770 556 1234 634 424 677 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 0.000210203777446278 0.00178444728462547 4645 1934 902 1.91112604099712e-05 189 1.24911471951187 1.36526106274606 1 7.66261550152461 4642 189 464 422 855 1604 4092 4432 902 570 3102 678 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 0.0210199639857159 0.0609551505093897 905 1471.90909090909 903 0.00212214794146577 168 0.924440006815576 0.924440006815576 1 2.5068644085234 903 168 3953 1377 647 927 721 874 2307 3499 815 679 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 0.000672849751973171 0.00428976045951875 420 955.909090909091 904 6.11868750029697e-05 360 1.52566378051927 1.52566378051927 1 8.06196041059533 417 1580 568 1296 1139 1295 605 904 1635 360 716 680 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 0.000267248250115132 0.00210829175090826 495 1108.72727272727 907 2.42982472739383e-05 487 1.40729306683085 1.40729306683085 1 8.40545944416619 491 1890 487 1891 535 907 509 1227 2400 999 860 681 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 0.0109785051957605 0.037144603138869 910 1051.18181818182 907 0.00100306148069522 373 1.41235790770474 1.41235790770474 1 4.50808427436648 907 1889 989 798 772 1794 1460 373 720 1037 824 682 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 0.00634117700839232 0.0247282698580666 910 1106.09090909091 909 0.000578138965192864 234 1.33211069264651 1.36922177829024 1 4.7773095904252 909 766 758 571 1502 2589 1859 1014 675 234 1290 683 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 0.0077294464904914 0.028587360895377 735 965.181818181818 910 0.000705157940121283 303 1.05096856795516 1.05096856795516 1 3.62132593362936 735 711 1289 708 1097 631 1306 303 1375 1552 910 684 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 0.000145632599038191 0.00131237376748647 375 1042.54545454545 910 1.32402036654409e-05 374 1.46026109747075 1.46026109747075 1 9.3928064993378 374 1342 441 1657 2305 1071 910 473 1519 525 851 685 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 0.000113156535172738 0.00109556099962696 1210 1028.09090909091 911 1.02874868885777e-05 150 1.34578983182826 1.43364779771546 1 8.89204862523516 1208 200 415 150 911 2553 1821 1300 648 275 1828 686 M4891 BIOCARTA_PML_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PML_PATHWAY.html Regulation of transcriptional activity by PML 11/26 BioCarta 0.0492468471791234 0.113960852287097 915 1309.81818181818 912 0.00458046082146525 151 1.79661288551867 1.79661288551867 1 3.78231991634694 912 1469 1588 639 4466 1540 1477 695 151 768 703 687 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 3.12654738563752e-08 1.16277786103948e-06 400 927.272727272727 912 2.84231584551882e-09 122 1.38562679425632 1.38562679425632 1 18.3531324677254 399 773 122 1143 1022 912 1087 716 2409 995 622 688 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 0.00438378544819183 0.0186072632339012 1020 1071.90909090909 912 0.000399322286913403 154 1.61627084452639 1.78488599757537 1 6.24193861447346 1020 1286 727 154 3909 934 912 1230 266 470 883 689 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 0.0109628005070959 0.037118268190933 775 1542 913 0.00100161939211287 272 1.26424809695537 1.26424809695537 1 4.03620389877405 775 3877 1720 3519 1207 518 702 597 2862 913 272 690 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 0.00761306941750499 0.0282684970605613 830 1615.63636363636 919 0.000694503880184185 253 0.361683886731522 -0.381493615322585 -1 1.25018778579685 830 2047 2817 2726 919 253 462 299 2640 4054 725 691 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 0.000727726087875303 0.00456509296892057 215 927.090909090909 920 6.61788109076286e-05 84 1.49840083701778 1.49840083701778 1 7.82754466003154 920 2096 1684 1764 268 380 215 84 1348 1224 215 692 M16697 BIOCARTA_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CD40_PATHWAY.html CD40L Signaling Pathway 11/19 BioCarta 0.0509404114400669 0.116659769173622 885 1255.90909090909 922 0.00474178493093524 102 1.06710845596515 1.06710845596515 1 2.22231940656035 881 945 2557 224 4517 350 516 964 102 1837 922 693 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 5.01022057980957e-07 1.18575220388827e-05 1315 1131.36363636364 922 4.55474701893094e-08 193 1.36161697580443 1.54946607287842 1 14.9702638120778 1311 1274 193 368 3513 1349 737 922 685 365 1728 694 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 0.0116842911432804 0.03888678146123 1450 1178.45454545455 923 0.00106789202433271 39 1.1839561103186 1.23028385787258 1 3.72644960611323 1448 39 2047 847 414 2554 1037 906 530 2218 923 695 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 8.5914366920194e-08 2.72023461748668e-06 825 1007.63636363636 923 7.81039729775645e-09 144 1.52624370149361 1.57228471725708 1 18.9582971714684 821 1189 144 752 1215 2134 915 729 938 923 1324 696 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 0.00741523721044187 0.0277982412545045 330 1046.27272727273 927 0.000676395391707488 322 1.22400004295079 1.22400004295079 1 4.25075178895057 327 1294 2087 1708 322 697 881 1363 1303 927 600 697 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 0.0162992566943194 0.0498878620963951 2900 1343.72727272727 929 0.00149284376592568 91 1.12150720198569 -1.1223538221809 -1 3.25907465776413 2900 91 2183 629 515 929 2465 1409 637 2152 871 698 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 1.45857863071562e-05 0.000210953687146092 370 986.727272727273 929 1.32598936458184e-06 299 1.46778240338295 1.46778240338295 1 12.0418891943726 370 929 299 821 1469 1521 743 1567 1251 622 1262 699 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 2.46763760500736e-05 0.000322998598242025 965 1231.45454545455 930 2.46766500699469e-06 11 1.49519829363167 1.49519829363167 1 11.6493913554949 963 737 4324 930 11 558 920 1726 1060 1612 705 700 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 0.000942565849473151 0.00561941930105749 1430 1178.63636363636 930 8.57245385322577e-05 108 1.33871346373415 1.44476927641819 1 6.72371440778376 1428 528 600 108 336 3728 1147 930 737 1555 1868 701 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 0.0236423828749534 0.0663402432048095 385 1245.27272727273 930 0.00217275874342677 383 1.46778240338295 1.46778240338295 1 3.85983469864181 383 2733 1102 2666 884 1341 749 706 1613 591 930 702 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 0.0193436447891063 0.0573698224568051 575 1004.63636363636 937 0.00177416805305261 67 1.76503961449764 1.76503961449764 1 4.8900864620375 573 1378 2146 972 572 2075 937 808 67 1021 502 703 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 0.0104747584786787 0.0359841519725318 1430 1052 937 0.000956815132493222 103 2.11565960589036 2.11565960589036 1 6.818032621444 1426 937 1003 103 3945 1248 829 361 213 1161 346 704 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 3.43662710061802e-06 6.24187387344807e-05 2400 1771.72727272727 938 3.12421133545095e-07 95 1.19020422374903 1.21548820479558 1 11.1695199601168 2398 195 241 95 431 3800 2451 4535 926 938 3479 705 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 0.00853293556502159 0.0309244671753218 1340 1418.27272727273 939 0.000856587868105608 24 2.46711003640163 2.46711003640163 1 8.31300591599788 1338 739 4220 475 3866 889 227 939 24 1516 1368 706 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 0.00532832052307624 0.0215872264909741 940 1158.27272727273 939 0.000485569950071824 252 1.05413144572439 1.10929453826245 1 3.91920520398555 939 1411 827 2102 993 729 472 252 1830 2930 256 707 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 0.0125002850535413 0.0407783578492928 1055 1069.45454545455 941 0.00114289829085322 431 1.38190056679364 1.36145438141254 1 4.28584896806313 1052 2511 842 1526 544 1228 736 941 1170 431 783 708 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 0.00306085829003245 0.0142718228329274 500 1041.09090909091 942 0.000278647743020406 156 1.2170462531212 1.2170462531212 1 5.01309026794933 499 1577 1388 1470 2505 436 343 175 1961 942 156 709 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 5.22979657399015e-05 0.000582109898948167 855 1087.72727272727 942 4.75447354529059e-06 370 1.84206129783926 1.84206129783926 1 13.3001717296134 852 1616 370 400 2332 1725 1150 942 565 510 1503 710 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 0.00709146898241789 0.026929192586394 285 1227.18181818182 944 0.000646766479840503 283 1.18045918322006 -1.20074158169684 -1 4.13588447565342 283 2267 774 2443 1072 355 944 547 1809 2354 651 711 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 0.00109031397598248 0.00628295545492121 1820 912.818181818182 945 9.91686098018188e-05 96 1.71783671444025 1.71783671444025 1 8.44202059140113 1818 596 1073 484 96 284 945 1793 523 1371 1058 712 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 0.000931817011102725 0.0055756934813699 160 778.272727272727 946 8.47465381234281e-05 156 1.46778240338295 1.46778240338295 1 7.38307958655322 156 1070 597 987 1028 1003 291 537 1155 946 791 713 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 1.8700050928255e-09 9.58516371569554e-08 265 810.272727272727 947 1.70000463128637e-10 87 1.30235157209998 1.35892113670473 1 20.4007408213365 263 247 87 267 947 1529 1131 1325 1653 228 1236 714 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 0.0029754493096305 0.0140045755732838 690 1248.81818181818 947 0.000270861924775894 689 0.593709647632435 -0.652961244662956 -1 2.45640600637806 689 1363 690 1519 959 743 821 961 763 4282 947 715 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 0.000396955886257019 0.00287946638235354 515 1054.45454545455 947 3.6093411717234e-05 59 1.73888769762328 1.73888769762328 1 9.86057915808376 511 2041 1253 2279 1538 882 1245 59 559 947 285 716 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 0.00693751903127913 0.026430255431361 955 1022.36363636364 947 0.000632681181692707 379 1.21480036212215 1.25893631996541 1 4.27822448728548 955 407 771 379 2151 1758 976 947 846 639 1417 717 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 9.601310848732e-07 2.11228838672104e-05 2165 1624.81818181818 948 8.72846821724506e-08 207 1.29056426804735 1.38132977309206 1 13.4667789628663 2164 762 207 443 859 3993 2438 2465 948 511 3083 718 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 0.000554031938953101 0.00375172495077201 265 1327.45454545455 948 5.03792283202638e-05 265 1.34897775001059 1.34897775001059 1 7.30354626036308 265 2980 550 1945 2291 279 460 1184 2871 948 829 719 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 0.00387021836495638 0.0168862600169326 1640 1440.90909090909 953 0.000352458511880613 14 1.1795962023639 1.23287678311195 1 4.66649669793294 1637 14 713 347 304 4455 2401 1878 953 252 2896 720 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 0.0332228632514068 0.0842893000520261 955 1294 953 0.00306685835342133 251 1.57710718408819 1.57710718408819 1 3.78126445341928 953 251 983 495 3085 2761 1692 899 611 940 1564 721 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 0.0086376177747127 0.0311352899171567 375 1281.45454545455 953 0.000867137639621858 122 1.14505098292374 1.14505098292374 1 3.85074481049647 1292 509 4361 1624 373 122 395 953 2480 1613 374 722 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 4.37700016963427e-05 0.000502888109073565 520 928.909090909091 953 3.97917023133746e-06 283 1.39442484572532 1.39442484572532 1 10.265850265061 519 1191 360 283 2402 1302 953 692 965 443 1108 723 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 0.0454717314945259 0.107501192830193 1055 1129.45454545455 954 0.00422179218416788 492 1.01901974822134 1.01901974822134 1 2.20292983153604 1053 492 1520 617 954 909 575 2147 1209 2237 711 724 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 0.000891216497764095 0.00538175323263215 475 1404.36363636364 956 8.91574119716345e-05 79 1.14672566625037 1.14672566625037 1 5.80748600805394 473 956 4288 1879 4484 198 79 96 1849 1053 93 725 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 0.00511036038729232 0.0208417308745446 245 1079.45454545455 956 0.000465660904215618 245 1.41439407094805 1.41439407094805 1 5.30682543821682 245 1311 956 1150 2246 661 319 1152 2243 838 753 726 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 0.0027125689464985 0.0131042248281361 1475 1277.72727272727 958 0.000246901753676974 159 1.42634797498725 1.42634797498725 1 5.99322364020912 1472 578 958 483 159 3346 2905 2273 344 399 1138 727 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 1.40532916355097e-05 0.000203881500321976 1275 1261.09090909091 958 1.27758012788815e-06 144 1.29582191719355 1.41828117782988 1 10.6739327751505 1271 390 298 144 958 3694 2011 1294 903 925 1984 728 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 0.0116369279287786 0.0387842420158297 1195 970.454545454545 959 0.00106354012041017 236 1.18117335345684 1.21076406225475 1 3.72071401244856 1193 236 938 563 413 959 1163 1657 921 1040 1592 729 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 9.6520830509237e-11 7.29510664139168e-09 605 998.727272727273 959 8.77462095577012e-12 60 1.37370753886491 1.39561930009353 1 24.9480418194303 601 1552 60 970 1717 2026 698 580 959 693 1130 730 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 0.00300783433289678 0.0141371230531136 205 998.545454545455 961 0.000273814047706412 203 1.21540039171038 -1.21540039171038 -1 5.01748279225439 203 1675 1034 1558 688 429 961 527 1507 1787 615 731 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 0.0839184282471183 0.156982736433532 650 1156.63636363636 963 0.00793650793650794 614 1.1931759082029 1.1931759082029 1 2.14150983490499 649 1067 1143 656 2892 1492 1500 884 963 614 863 732 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 0.0226125318875876 0.0642975269570604 705 1137.90909090909 963 0.00207712305034938 669 1.38700090239592 1.38700090239592 1 3.68945117770308 703 1739 921 963 1126 1004 785 669 1179 2502 926 733 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 2.95330667205544e-07 7.4806459812172e-06 720 1185.54545454545 963 2.68482460773726e-08 180 1.62845537233733 1.70094228129226 1 18.6311291891822 719 963 180 1030 1400 2993 2156 775 569 255 2001 734 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 0.000508060681467946 0.00351665044809276 3280 2017.63636363636 968 4.61980044781544e-05 398 1.22472245782224 1.36737628172628 1 6.70762737805202 3279 398 540 962 564 3064 2961 4200 968 817 4441 735 M9131 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROPHOSPHOLIPID_METABOLISM.html Glycerophospholipid metabolism 36/81 KEGG 0.0389220913337042 0.0957422152177101 920 1344.36363636364 969 0.00360256811354544 296 1.00887187857901 -1.00887187857901 -1 2.29427595626943 919 2233 2829 2184 878 296 969 1023 837 1953 667 736 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 2.67537053325429e-08 1.01103115474432e-06 705 938.090909090909 969 2.43215505980806e-09 92 1.32312500904322 1.3396671067862 1 17.7046227652531 704 1709 120 943 1497 1594 1214 437 969 92 1040 737 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 0.0399762381485867 0.0974654796900506 915 1651.27272727273 970 0.00370197101035167 411 1.4630379028186 1.4630379028186 1 3.30179696685337 913 3604 2059 2393 4064 600 451 1990 411 970 709 738 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 0.0221709618961396 0.0634655634974407 1120 1281.81818181818 971 0.00223953168775679 4 2.24458518468169 2.24458518468169 1 5.99897892631564 1119 2705 4234 971 670 1257 836 588 4 1052 664 739 M19118 BIOCARTA_KERATINOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KERATINOCYTE_PATHWAY.html Keratinocyte Differentiation 30/63 BioCarta 0.00770017651837664 0.0285241321463343 660 1181.63636363636 972 0.000702478232923446 104 1.49395446846931 1.49395446846931 1 5.15093037804802 660 1733 2610 300 3335 972 1221 301 104 983 779 740 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 4.89301441661866e-05 0.000549848094874702 975 1098.45454545455 973 4.4482938594698e-06 16 1.14987459781691 1.00313942957215 1 8.36595064172514 973 117 1421 523 16 1268 1091 3918 1206 806 744 741 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 0.0175208020993476 0.0529317865278208 3555 1837.72727272727 973 0.00160562851372344 497 1.237279973933 1.37400920812737 1 3.52447695468702 3554 648 941 497 536 1320 3986 3446 973 579 3735 742 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 0.0122147265583139 0.0402236181674341 820 1801.54545454545 973 0.00111664331008978 263 2.76431492756404 2.76431492756404 1 8.60999275419009 817 3791 973 2871 3669 806 263 454 2668 2803 702 743 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 0.00136924121481673 0.00750550071274509 2160 1522.09090909091 974 0.000124554013608589 231 1.3738129146518 1.48675166472742 1 6.51461090758996 2160 443 633 974 231 4043 1562 2339 796 603 2959 744 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 0.00199024086827198 0.0101372485964375 2130 1056.27272727273 976 0.000181094875741023 174 1.21386892254226 -1.03895190389624 -1 5.40248915863806 2129 976 661 625 174 591 1712 1254 1238 450 1809 745 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 1.11214771644592e-19 3.72251728518968e-17 25 939 976 1.0110433785872e-20 10 1.30175484554248 1.31776744491175 1 47.733601530371 22 1269 14 1146 2474 943 801 976 1400 10 1274 746 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 0.0181331441727303 0.0543298680264798 980 1244.45454545455 977 0.00166221376422432 445 1.45544407565374 1.45544407565374 1 4.10915320262317 977 2582 1793 1810 549 2057 1493 795 620 445 568 747 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 0.0244820352960035 0.0679235153327842 1950 1460.54545454545 977 0.00225079979688904 110 1.30708381749294 1.47261802126269 1 3.40736251462117 1946 763 936 110 676 3638 2809 1442 977 484 2285 748 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 6.00844665526508e-06 0.00010091606102714 360 839.545454545455 978 5.46223915006298e-07 168 1.17926771674323 1.17926771674323 1 10.517723743371 356 1202 262 1260 1055 783 168 978 1495 981 695 749 M1443 REACTOME_GLUTATHIONE_CONJUGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUTATHIONE_CONJUGATION.html Genes involved in Glutathione conjugation 13/32 Reactome 0.0289887257300073 0.0763581611977595 725 1363.63636363636 979 0.00267071815781388 158 0.874649861425705 -0.874649861425705 -1 2.18083673017868 723 158 2040 921 738 687 979 2009 1913 3752 1080 750 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 0.00991641435755648 0.0345232672210324 840 1240 980 0.000905581483883966 538 1.40177063869616 1.35979757981616 1 4.57373130856354 836 3332 811 2037 980 1331 538 1072 1510 642 551 751 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 0.0250667559916793 0.06905515495415 755 1284.36363636364 982 0.00230518243240463 568 1.46778240338295 1.46778240338295 1 3.80277025757761 754 982 1109 2644 678 2042 568 774 2385 1536 656 752 M11358 BIOCARTA_ARF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARF_PATHWAY.html Tumor Suppressor Arf Inhibits Ribosomal Biogenesis 14/28 BioCarta 0.012596468730998 0.0410194944221379 1240 1175.36363636364 983 0.00115174321888949 269 1.31662379339429 1.43857249875286 1 4.07587401166873 1238 3382 1816 1747 532 983 269 843 1344 425 350 753 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 0.000158612030758682 0.00140502074883778 125 1291.63636363636 983 1.44203152059915e-05 122 1.46778240338295 1.46778240338295 1 9.34413408554024 122 1981 447 2605 1966 874 724 983 2482 1108 916 754 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 0.00052489014355958 0.00359070833973751 625 1655.45454545455 984 4.77286742791338e-05 44 1.37174724033726 1.37174724033726 1 7.4851501464213 621 4484 2148 3713 3316 388 288 778 1446 984 44 755 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 0.00686357880746225 0.0262124941253204 920 1184.63636363636 984 0.000625916895922485 310 1.32240646320587 1.29171294134648 1 4.66779121362648 916 2179 984 1178 310 1656 777 1394 2328 749 560 756 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 0.0343621926554303 0.0867571308099926 720 1276.27272727273 987 0.00317372176518944 716 1.49926443738673 1.49926443738673 1 3.55269146339902 1134 1560 987 722 841 3148 1852 720 716 966 1393 757 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 0.00123222595330607 0.00688225365577144 1140 935.454545454545 987 0.000112083333461581 51 1.54996705851844 1.54996705851844 1 7.48017589112927 1136 1541 1742 1011 101 1412 783 987 51 770 756 758 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 0.0117941103207995 0.0391410771694521 990 1248.18181818182 987 0.00107798333815472 265 0.990434628199961 0.990434628199961 1 3.11109164199169 987 1695 2398 1949 495 717 265 384 1871 2123 846 759 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 0.00052887463908286 0.00360218976561378 640 948.272727272727 987 4.80910747330611e-05 169 1.30246243687271 1.35197414545416 1 7.10305651263907 637 234 547 384 1372 2363 987 1103 1289 169 1346 760 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 0.0142303407607809 0.0448048181567649 795 1219.72727272727 987 0.00130211178764846 390 1.35232243471951 1.35232243471951 1 4.07068226708786 793 1841 1957 2344 472 1109 2098 567 859 987 390 761 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 0.0066171803644598 0.0255842468546688 690 1515.90909090909 989 0.000603378890669156 299 1.48194679911884 1.48194679911884 1 5.26577981851213 688 3272 1045 3333 299 989 324 940 2937 2078 770 762 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 0.0135891830646918 0.0432307616029504 615 1349.18181818182 990 0.00136730050355242 490 1.00120791911947 1.00120791911947 1 3.04848554774266 614 954 4432 514 490 1168 557 1685 1916 1521 990 763 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 0.00011577934479776 0.00111292789392697 2565 1913.27272727273 992 1.05259489421272e-05 224 1.21865696537093 1.42446291372671 1 8.03346402823333 2563 224 416 638 990 4400 2564 3466 734 992 4059 764 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 0.00505773859297542 0.0206991817001597 995 1241.27272727273 992 0.00046085488683382 264 1.30464571390902 1.36398276879532 1 4.90372728006559 992 264 739 383 589 2777 1678 2354 1385 715 1778 765 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 2.3607267962389e-07 6.1800926073606e-06 645 1062.72727272727 996 2.14611549959866e-08 175 1.28807913970639 1.29975075221593 1 14.9753464127776 642 391 175 460 1312 2475 1535 1781 996 179 1744 766 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 0.016352286550133 0.0500175031161379 910 1110.90909090909 998 0.00149773734471946 516 1.07070552478632 1.22557201452123 1 3.10875262360891 998 675 909 1243 516 1047 1028 907 2035 1876 986 767 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 0.000116421744716832 0.00111564886655026 85 806.363636363636 998 1.0584355099336e-05 81 1.50268847897339 1.50268847897339 1 9.90226098375587 81 1724 1023 1369 1492 292 142 398 1178 998 173 768 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 0.00255162136395171 0.01250721517937 575 1138.45454545455 1000 0.000232235056357885 571 1.38804246284762 1.38804246284762 1 5.89500852198756 571 1331 676 1000 1629 1523 1448 897 2017 594 837 769 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 3.42793319642861e-06 6.24187387344807e-05 1040 1108.90909090909 1001 3.11630776152668e-07 61 1.24787665075402 1.19899044335441 1 11.7107491976988 1037 676 240 61 2417 2294 817 1507 1001 786 1362 770 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 0.0104473780066086 0.0359181315766455 1555 1141.27272727273 1003 0.000954302088052374 358 1.29584166023452 1.38598818979752 1 4.17835211743309 1551 1003 1445 865 1399 2690 1300 358 481 586 876 771 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 0.00315810121701747 0.0145658093532912 1005 1499.81818181818 1005 0.000316259833593529 127 0.355770648474885 0.378552372989553 1 1.45841025561273 1005 859 4156 1858 1434 316 127 254 2128 3858 503 772 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 0.000674470825726416 0.0042942531105353 725 1140.27272727273 1008 6.13343356545625e-05 322 1.24408964201408 1.38175306474107 1 6.57279522834129 721 322 569 628 1976 2038 1449 1814 478 1008 1540 773 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 0.000646275077641694 0.00419919080521078 2730 1790 1009 5.87695460389481e-05 477 1.54607496249033 1.59837719083981 1 8.20179716322735 2728 477 561 1009 932 4478 3449 2053 511 560 2932 774 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 5.36448572462143e-05 0.000592876889282454 1015 1114.36363636364 1012 4.87692412440597e-06 373 1.29621671305297 1.33682664199367 1 9.33600147475241 713 1113 373 1002 1747 1896 1167 1228 1012 996 1011 775 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 0.000162300342095344 0.00143498000577129 1795 1186.81818181818 1012 1.47556651542031e-05 449 1.43494492481514 1.43494492481514 1 9.10573892255431 619 2231 449 1791 1069 1802 770 1012 1794 791 727 776 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 0.0322171356152554 0.0825301290604009 1015 1388.81818181818 1013 0.00297262121522364 651 1.21023538032318 -1.01545187217586 -1 2.92639678133288 1013 2751 976 994 1791 651 1499 946 2486 720 1450 777 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 0.000318812732129393 0.00242132327837656 1675 1276 1014 2.8987176564824e-05 44 1.6389679011428 1.6389679011428 1 9.56927379046276 1672 332 1014 44 46 4397 2510 1258 497 716 1550 778 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 0.0279457690384754 0.0741948292998843 1400 1744.72727272727 1014 0.0028303552613379 135 0.791760008296744 0.791760008296744 1 1.99621784981244 1399 735 4568 894 1040 975 402 3509 135 4521 1014 779 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 0.0197259576766231 0.05828236927658 3885 1867.45454545455 1015 0.00180955272568952 179 0.255581271769735 -0.30157069288874 -1 0.704184707278689 783 2249 3541 3022 929 179 344 1015 3884 3884 712 780 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 0.0187836522565215 0.0560281314284277 2230 1264.09090909091 1016 0.00172236100973707 322 1.42142986772522 -1.20074158169684 -1 3.97071225152787 2226 918 1016 759 561 1197 2311 1546 322 1009 2040 781 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 0.0035833621356406 0.0159616301973497 680 1312.09090909091 1016 0.000326292005766794 197 1.90919498657043 1.90919498657043 1 7.65701060075915 679 3069 1566 3135 1016 453 484 197 1239 1937 658 782 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 0.0203007028490694 0.0594556834692121 970 1073.27272727273 1017 0.00186277143321052 341 2.46711003640163 2.46711003640163 1 6.74978654034533 969 1232 1652 1094 595 787 533 1017 341 2348 1238 783 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 0.0558028036256912 0.124876761122249 700 1240.45454545455 1018 0.00520642119676934 494 1.86280643978199 1.86280643978199 1 3.75650761981952 700 1800 2158 2091 1065 999 549 798 494 1973 1018 784 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 0.00335863340923945 0.0152063344499479 960 1198.81818181818 1018 0.000305797441633328 139 1.0767729772449 1.0767729772449 1 4.36909733100268 957 908 1032 2239 1018 508 458 1051 2514 2363 139 785 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 1.85276231749437e-05 0.000258443172319334 1075 1051.18181818182 1020 1.68434356453488e-06 309 1.32856211517057 1.51795858215181 1 10.6382370489246 1074 878 309 539 1178 1810 1682 1310 966 797 1020 786 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 0.000125338540257571 0.0011737497387008 570 1020.63636363636 1020 1.13950619656805e-05 426 1.41326797579874 1.52970169619187 1 9.2434608926497 567 988 426 802 1367 1773 1104 1020 1194 516 1470 787 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 0.000107574871232274 0.00104584200538265 525 1403.18181818182 1022 9.78001197752854e-06 414 1.49887655090955 1.48905903038435 1 9.97101773264851 523 2382 414 2333 2009 1022 658 1212 3318 631 933 788 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 0.000760274715416386 0.00470079369711562 1100 1193.18181818182 1022 6.91397798084738e-05 225 1.15585060875781 1.26167608826033 1 6.00526669541987 1096 225 580 339 507 2722 1022 2034 931 1587 2082 789 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 0.0801922566002177 0.156982736433532 550 1416.63636363636 1023 0.00757034543000628 547 1.53026137612659 1.53026137612659 1 2.74651018718667 547 2240 1130 1023 2601 1007 849 1018 1934 2465 769 790 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 0.000764455281732831 0.00470727654428389 1130 984.090909090909 1023 6.95200948817423e-05 524 1.45226120062552 1.45226120062552 1 7.54333941926679 558 1780 583 1112 1130 1098 1023 982 906 1129 524 791 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 0.0153387433578574 0.0474381730647009 940 1277.63636363636 1024 0.00140424937639708 438 1.46013512239617 1.46013512239617 1 4.31438218516025 936 2579 2383 1482 498 2106 1287 1024 778 543 438 792 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 0.00114858516085395 0.00650032616396328 1025 1082.72727272727 1024 0.000104471387058612 557 1.19167131534558 1.32204433222624 1 5.81698175097186 1024 1190 615 1041 1398 1289 876 557 2387 895 638 793 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 6.47879085447401e-12 6.35032291607612e-10 335 793.545454545455 1026 5.88980986772101e-13 46 1.41133836689983 1.49758150172759 1 28.9712031253213 334 526 46 517 1236 1277 1026 1165 1297 135 1170 794 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 0.00683051034809401 0.0261519008395689 605 1194.18181818182 1027 0.000622891836727248 309 1.18810004843625 1.25153193012765 1 4.19638563873749 602 1887 926 1551 309 2018 1349 609 2178 680 1027 795 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 0.0929231831128666 0.171162750026294 795 1100.18181818182 1027 0.00882700566396586 636 1.1000537425841 1.1000537425841 1 1.88216212163182 791 1389 1534 636 1326 785 908 1027 1043 1778 885 796 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 0.0108697827139085 0.0368832742920893 1250 1161.45454545455 1028 0.000993078427170687 593 1.3480375258408 1.45278721926277 1 4.31200649624598 1249 1663 821 893 1913 1028 593 1463 1480 745 928 797 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 6.50481220596786e-12 6.35032291607612e-10 1030 1150.45454545455 1028 5.91346564180646e-13 3 1.53346163460997 1.5539457476779 1 31.478084591984 1028 3 47 7 3217 2329 1488 1707 328 84 2417 798 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 0.00250693953154885 0.0123398305092835 1635 1059.90909090909 1033 0.000228163709080636 139 1.14322869811713 1.09798228248114 1 4.8702163461102 1631 340 2249 565 151 2305 1348 1033 139 321 1577 799 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 0.00749239774109504 0.027975598258782 1035 1189.63636363636 1033 0.000683457858334885 327 1.24002129701395 1.29449692855301 1 4.29874660167735 1033 881 927 652 327 2541 2193 1261 1713 497 1061 800 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 0.0421935420425388 0.101290439554988 770 1264.18181818182 1033 0.00391138041956135 767 1.16426310608688 1.13994412234691 1 2.58407778328758 767 1784 1017 1399 996 865 2251 1001 1312 1481 1033 801 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 0.0205171153702996 0.0598982122796497 1880 1286.81818181818 1034 0.00188281757360614 81 2.56721702188092 2.56721702188092 1 7.00521721398791 1878 598 902 81 3512 2003 932 1779 100 1336 1034 802 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 0.00071973392720929 0.00452707809785602 545 945.818181818182 1036 6.54517724863183e-05 111 1.4726942955414 1.4726942955414 1 7.70519241796018 541 111 574 1036 1086 1801 968 1043 1680 513 1051 803 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 0.0210338195419725 0.0609551505093897 890 1328.72727272727 1036 0.00193069580760793 323 1.47901506611745 1.47901506611745 1 4.0107418563035 887 2764 907 2230 2185 1848 728 1050 658 323 1036 804 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 0.00140331014144911 0.00762777038356254 965 1173.27272727273 1039 0.000140419710556045 12 2.24458518468169 2.24458518468169 1 10.6086486208338 1039 1179 3892 1073 963 1434 964 123 12 1503 724 805 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 0.0940339462362288 0.17264655238743 575 1395.72727272727 1041 0.00893740742909648 574 1.53090795627087 1.53090795627087 1 2.60653332605678 574 2813 1688 1507 3117 603 790 1041 1419 1024 777 806 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 0.0131006563374916 0.0422212349363726 1025 1469.36363636364 1041 0.00131785355273367 427 1.05077947290469 1.05077947290469 1 3.22348835434604 1021 1099 4243 1670 1041 597 528 427 3102 1609 826 807 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 0.00070836938759975 0.00447361044513804 1535 1321.81818181818 1041 6.44179614141002e-05 50 1.16584440274165 1.26855313850324 1 6.11316839580101 1532 50 572 76 236 3211 2095 2752 248 1041 2727 808 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 0.00607990137124181 0.0239415275845707 1145 1059.90909090909 1041 0.000554251730257621 119 1.35294670443351 -1.20074158169684 -1 4.89443507095449 1144 119 820 344 287 1041 3086 1225 1064 753 1776 809 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 0.000226123439662066 0.00187478174745504 170 958.636363636364 1042 2.05587895217116e-05 170 1.46726266075591 1.46726266075591 1 8.93059525246574 170 463 470 1637 1314 1365 1122 617 1590 755 1042 810 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 0.00261006799084691 0.0127271369460027 3905 2058.54545454545 1042 0.000261313867274502 165 1.66151692042374 -1.33403223803043 -1 7.02838020625049 3901 636 4344 633 165 3912 2403 702 1042 419 4487 811 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 0.00906238155681174 0.032122783642375 1045 1262.72727272727 1043 0.000827266237639516 330 1.14338139147186 1.14338139147186 1 3.81052508089749 1043 2142 2206 1713 1532 919 365 330 454 2641 545 812 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 1.00170895515752e-07 3.08816326570274e-06 445 1065.72727272727 1044 9.10644546152332e-09 148 1.57564030682568 1.61723631495019 1 19.3781298117924 444 1194 148 1031 2287 1823 1105 1044 934 486 1227 813 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 0.029012941040088 0.0763790121987934 420 1438.90909090909 1044 0.00267297924115486 418 1.15105234340781 1.15105234340781 1 2.86970923562058 418 979 1044 1128 3783 994 1247 1383 3229 721 902 814 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 0.0839184282471183 0.156982736433532 1050 1130.18181818182 1046 0.00793650793650794 403 1.31141893713294 1.4425230169359 1 2.35373219678303 1046 1284 1298 485 1824 1857 1808 903 403 502 1022 815 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 0.0346529508464584 0.0873970547182477 1590 1165.09090909091 1046 0.00320101179043948 49 1.9476218631361 1.9476218631361 1 4.60125574023218 1587 1174 2485 1033 825 1847 1168 768 49 834 1046 816 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 0.000769620503467232 0.00473286309612526 885 1154.90909090909 1047 6.99899881653469e-05 584 1.21764465805801 1.33551045406455 1 6.31829541284473 885 1047 584 711 1002 1963 1373 950 1458 1244 1487 817 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 0.0264874759294815 0.0719955407224771 1020 1333.54545454545 1048 0.00243744180826439 402 1.39059940208002 1.39059940208002 1 3.54659577917019 1016 1915 1399 1048 4101 901 608 1308 1243 728 402 818 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 0.0297294180622398 0.0779150184785547 1340 1180.63636363636 1048 0.0027399028624431 571 1.53482275857141 1.88668445094058 1 3.79687241637173 685 1583 1048 1813 2447 870 710 571 1339 1340 581 819 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 0.0541207054566284 0.122339423912089 1030 1497.63636363636 1049 0.00504543913189951 815 1.34153821888826 -1.20074158169684 -1 2.73201990519052 1030 2501 1103 2488 1049 824 1875 1013 2739 815 1037 820 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 1.14658792550929e-07 3.44417373008752e-06 865 1283.36363636364 1050 1.04235271387886e-08 152 1.39124885662534 1.38489984029942 1 16.9632403012188 864 1050 152 1021 620 2514 1637 1176 2364 953 1766 821 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 0.0103897509020598 0.0357755682529886 1115 1028.72727272727 1050 0.000949013142717044 245 1.37047945593037 1.45362879893672 1 4.42429970547362 1114 1094 1785 1119 2847 510 245 656 1050 293 603 822 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 7.15280216966649e-05 0.000749844093222755 530 922.545454545455 1053 6.50275885220841e-06 266 1.41019608071543 1.41019608071543 1 9.83587755067749 528 266 390 502 1271 1640 1270 680 1462 1086 1053 823 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 0.000725352763269255 0.00455630435479857 1370 942 1055 6.59629115210806e-05 83 1.94397009216757 1.94397009216757 1 10.1587994590323 1368 1904 1254 681 210 1476 656 83 452 1223 1055 824 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 0.0130837965059125 0.0422212349363726 915 1129.81818181818 1055 0.00119656929950583 292 1.12149278325549 1.19575746705957 1 3.44041639519386 911 1338 1055 1562 455 1154 543 809 2654 1655 292 825 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 0.0130952047203058 0.0422212349363726 555 1776.27272727273 1056 0.00131730188358382 426 0.849254971022537 0.849254971022537 1 2.60526930676845 555 2775 4120 2758 2302 534 563 426 1056 3800 650 826 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 0.0417230737446131 0.100573211711552 1785 1302.81818181818 1057 0.00386691105220005 302 1.10253795573747 1.31181462849754 1 2.45467334257126 1784 403 2988 698 1226 302 1976 1946 937 1014 1057 827 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 6.45628016945514e-05 0.000697159555233462 1060 1195.90909090909 1057 5.86951786176208e-06 202 1.37092395674816 1.47343047687921 1 9.65876951749987 1057 202 379 594 1701 2701 1027 1406 1470 473 2145 828 M18256 KEGG_SULFUR_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SULFUR_METABOLISM.html Sulfur metabolism 4/18 KEGG 0.000993269354986772 0.00586204055096727 180 1209.45454545455 1058 9.93713597277189e-05 97 0.938178160433969 -0.938178160433969 -1 4.67357874902329 1304 179 3805 1066 97 551 1295 177 1058 3188 584 829 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 0.0305208399292878 0.079367733578603 430 1018.45454545455 1061 0.00281387906117707 427 1.20074158169684 -1.20074158169684 -1 2.94891550877979 427 573 1061 595 1328 686 1140 1188 1197 2024 984 830 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 0.0464770131945781 0.109113869654205 1210 1357.27272727273 1064 0.00431717648645483 674 1.34580365212965 1.34580365212965 1 2.88995126313039 1210 2448 1150 2032 971 863 1064 674 3115 726 677 831 M8821 REACTOME_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AXON_GUIDANCE.html Genes involved in Axon guidance 124/342 Reactome 0.054859390953385 0.123473153701999 620 1446.54545454545 1065 0.00511610157188395 423 1.38115413624105 1.38115413624105 1 2.80034768848173 617 3585 1065 3222 1770 938 765 1287 1490 423 750 832 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 0.00742857939306992 0.0278094526034642 1070 993.818181818182 1066 0.000677616559639436 91 1.41296508673787 1.806917851326 1 4.90644418781605 1066 719 2285 355 323 1166 660 1989 91 1067 1211 833 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 0.000574097846221039 0.00384867311500971 760 1505.18181818182 1066 5.22043376232963e-05 71 0.560918262541589 0.801389784978757 1 3.02301522073553 756 1234 1066 2195 3767 310 129 71 2866 4058 105 834 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 0.00425596683116546 0.0182132547244684 1070 1052 1067 0.000426413983381441 27 1.37200307782393 1.37200307782393 1 5.32705455656015 1067 1106 3935 371 244 1353 898 1092 27 345 1134 835 M2398 SERVITJA_LIVER_HNF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_LIVER_HNF1A_TARGETS_DN.html Genes down-regulated in liver tissue upon knockout of HNF1A [GeneID=6927]. 19289501 80/290 Arthur Liberzon 0.00256289944125305 0.0125493696778598 585 1237.36363636364 1067 0.000233262725497435 582 1.23348130831709 1.37206555631081 1 5.23456517975527 582 1496 677 1153 2822 971 1067 1334 1647 802 1060 836 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 0.0444161247164961 0.105437669919707 765 1639.09090909091 1068 0.00453296870304444 254 2.11775562982788 2.11775562982788 1 4.61797768945667 764 3458 4471 2151 1990 854 1068 693 254 1431 896 837 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 1.96164160204911e-05 0.00027115789224785 1810 1211.81818181818 1072 1.96165891843423e-06 9 1.39099953283253 1.37328926738254 1 11.0734407873247 1810 165 3793 252 9 1095 1195 699 1072 605 2635 838 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 0.00173393915244215 0.00909767082732089 805 1580.09090909091 1072 0.000157755206694859 133 0.422331588731399 -0.496396118828829 -1 1.92393756184365 803 1072 2299 2556 1786 371 1000 133 2182 4385 794 839 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 0.0409077205775582 0.0994777263240465 1075 1397.18181818182 1073 0.00378988963472297 548 1.52757719193964 1.52757719193964 1 3.41719096425084 1073 1670 2789 2154 896 1416 1055 936 633 2199 548 840 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 0.00432415038204244 0.0184130018723021 1585 1066.27272727273 1074 0.000393879369091985 81 1.36400327242507 1.36400327242507 1 5.28157263147851 1582 81 1194 182 229 2385 1074 2451 275 989 1287 841 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 0.00923620949818969 0.0326648133649184 1195 1377.45454545455 1076 0.000927482397423315 241 2.24458518468169 2.24458518468169 1 7.44407983291433 1191 1392 4380 1017 2255 888 241 466 1076 1706 540 842 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 0.0362932199351398 0.0906818911270384 685 1777.72727272727 1077 0.00335510453384466 431 1.26844754916662 1.26844754916662 1 2.95134217020689 681 2570 1077 2375 4656 987 431 822 2873 2347 736 843 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 0.00176017434180224 0.00917483533446641 420 1184.45454545455 1078 0.000160144018201246 419 1.24421416467988 1.24421416467988 1 5.65784915823637 419 1360 652 1078 2199 944 797 2288 1435 737 1120 844 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 0.00446838696208824 0.0188557549699443 370 1074 1078 0.000407044411523082 149 0.947269314256406 0.947269314256406 1 3.64611484408577 367 1078 1476 428 1385 223 149 1136 2474 2493 605 845 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 0.0424192033664959 0.10172793601607 1060 1375.45454545455 1079 0.00393271731249229 288 1.32676525305853 1.52721886224564 1 2.93920793271938 1056 561 1079 415 3274 2490 2361 1275 468 288 1863 846 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 0.0100218210062679 0.0348126413901939 480 1836.18181818182 1080 0.000915251584881927 238 0.857185672850884 0.857185672850884 1 2.78991082524655 477 2814 865 2590 4521 764 238 1080 1643 4244 962 847 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 0.0839184282471183 0.156982736433532 740 1192 1082 0.00793650793650794 249 1.50797974409299 1.50797974409299 1 2.70651915668401 740 1938 1759 447 2683 1132 924 1153 249 1005 1082 848 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 0.000334093092625299 0.00251293777213829 855 1021.45454545455 1082 3.03767126325008e-05 47 1.41716624451682 1.41716624451682 1 8.22324717863666 855 1377 1859 1541 47 1220 1454 471 1082 975 355 849 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 0.00871699807512023 0.0313010367662938 950 1209.27272727273 1085 0.000795611818992963 353 1.13416995468368 1.20279805949267 1 3.80831561573352 949 581 1837 388 353 1141 1085 3009 1286 1828 845 850 M276 PID_FGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FGF_PATHWAY.html FGF signaling pathway 18832364 32/84 Pathway Interaction Database 0.0221169203173263 0.0633495651631974 1325 1466.81818181818 1087 0.00203113141162413 409 2.21734841781075 2.21734841781075 1 5.93011667855256 1324 2906 2061 557 3612 988 899 495 409 1797 1087 851 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 1.22762837396048e-07 3.61802928325712e-06 3050 1581.27272727273 1088 1.11602585678521e-08 110 1.45952924231342 1.58892307262171 1 17.7261009153957 3046 110 155 119 220 2407 4427 2913 1088 114 2795 852 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 0.00391133542590746 0.0170339384812289 535 1424.81818181818 1088 0.000391823687333738 130 1.25211502441543 1.36869939343514 1 4.94281386040376 533 646 4547 408 2224 2215 1088 815 1407 130 1660 853 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 0.0267782398172773 0.0724496719305781 895 1167.54545454545 1089 0.00246453158008106 449 1.24678978407767 1.37370327408651 1 3.17222340535806 891 796 1205 449 697 2943 1233 1089 1288 649 1603 854 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 0.000568327353307838 0.00382375418908321 1090 1298.72727272727 1090 5.1679474798418e-05 188 1.35583653639749 1.46078396891037 1 7.31568795896602 1090 2727 553 1384 3507 985 1100 332 1610 188 810 855 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 3.93117855962769e-06 6.95151046430768e-05 1915 1286.36363636364 1091 3.57380507660514e-07 247 1.68355288497271 1.55337246042245 1 15.6236511260808 785 1773 247 857 1091 2897 1911 1942 471 262 1914 856 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 0.0051355819067624 0.0209081987967755 1095 1016 1092 0.000467964500540923 261 1.34983068179167 1.34983068179167 1 5.06041663828145 1286 1147 794 842 261 1665 1092 1369 627 1092 1001 857 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 0.0584219738707174 0.128891416929464 1095 1157.27272727273 1092 0.00545760378512279 138 1.51695614370628 1.51695614370628 1 3.01254309421755 1092 1161 1884 382 2876 1282 1343 741 138 1077 754 858 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 0.00949847176625919 0.0333407031435884 405 1534.45454545455 1093 0.000867248263886664 401 0.985194088120694 -0.985194088120694 -1 3.24779994497843 401 3047 805 2832 1246 593 1093 700 2386 2813 963 859 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 0.0090776637564409 0.0321526321713394 680 1598.72727272727 1094 0.000828667083936043 365 0.633042077535849 0.633042077535849 1 2.10915719795152 680 728 1244 1414 365 921 1764 1094 3748 4578 1050 860 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 0.0225442605453035 0.0641812909570425 995 1902.54545454545 1097 0.00207078636444991 525 1.24571196155165 1.28573180270881 1 3.31580450913821 4310 525 920 993 867 1097 4565 2984 994 1357 2316 861 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 0.0654319106201672 0.140407414664398 840 1208.36363636364 1097 0.00613300613194958 405 1.23847573541057 -1.20074158169684 -1 2.35677138857712 839 1501 1097 1406 1186 405 990 877 2649 1568 774 862 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 0.0975275502458302 0.178034320394219 690 1507 1098 0.00928545018426408 676 1.53977375328965 1.53977375328965 1 2.57576324881647 690 3415 1565 2379 2385 949 676 902 1690 828 1098 863 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 0.00662513422889885 0.0255938821076835 3440 1876.09090909091 1099 0.000604106349319318 286 1.24144834063389 1.3933598453231 1 4.41076706701446 3439 405 1383 286 301 1077 4118 3039 866 1099 4624 864 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 2.97381465515652e-05 0.000373600414854248 1100 1077.45454545455 1100 2.70350441270826e-06 18 1.27601783717943 1.36244545008337 1 9.7617010407903 1100 18 335 324 1401 2156 1579 1992 807 719 1421 865 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 5.41244711872842e-06 9.22280989031322e-05 895 1462.45454545455 1102 4.92041857681291e-07 258 1.35134311580265 1.47384490676852 1 12.1703605636573 893 1923 258 944 2395 3337 1513 1102 967 578 2177 866 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 5.30061046778909e-05 0.000587202379481317 695 1221.09090909091 1103 4.81885289393676e-06 372 1.57003413362655 1.57003413362655 1 11.3228076091205 691 1722 372 762 2007 2211 1103 712 1686 644 1522 867 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 0.00499105262631121 0.0204799234736378 345 984.636363636364 1103 0.000454764702136542 345 1.46778240338295 1.46778240338295 1 5.53205448936614 345 1305 737 1336 713 1642 1355 607 1193 495 1103 868 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 6.08067600263306e-05 0.000659584438618947 345 1359.09090909091 1104 5.52804006872201e-06 304 1.17885078098004 1.17885078098004 1 8.36883760515538 342 2716 378 2625 1104 327 304 1209 3125 2268 552 869 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 0.000459571689423638 0.00324819447456888 815 1142.81818181818 1105 4.17879745726697e-05 448 1.37535428556921 1.44503828982326 1 7.63848091968743 814 653 532 448 1144 2564 1532 1432 950 1105 1397 870 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 1.34952730256831e-15 2.43226343839812e-13 805 1023.36363636364 1105 1.22684300233483e-16 26 1.3231740879208 1.37022161410007 1 37.2519493161762 805 761 26 378 1105 2384 1514 1420 1386 69 1409 871 M5493 WNT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/WNT_SIGNALING.html Genes related to Wnt-mediated signal transduction 53/137 SuperArray 0.0194594328378896 0.0576767250337449 2985 1927.09090909091 1106 0.00178488340195615 284 1.26386883683111 1.47892762998509 1 3.49504409176839 2981 292 895 284 933 2292 4582 3565 808 1106 3460 872 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 0.0618656710229784 0.134650503675651 955 1223.27272727273 1107 0.00578882818660803 954 1.31612588859467 1.31612588859467 1 2.55794631783998 954 1005 1276 1476 1124 1617 1008 1107 1746 1081 1062 873 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 0.0638487935337668 0.137941653526616 825 1219.90909090909 1108 0.00598007232323796 492 1.19929824728735 1.33310072436642 1 2.30281465581529 825 1605 1108 492 1140 1668 1013 1446 2049 1082 991 874 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 0.0106623824013256 0.0364168541782883 370 1146.63636363636 1109 0.000974037400531647 267 1.06047362930485 1.06047362930485 1 3.40524950959855 366 1142 1855 1785 1109 665 579 687 2153 2005 267 875 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 0.0674306442736052 0.144020054268967 645 1553.54545454545 1109 0.00632642646077465 641 1.24775206681785 1.24775206681785 1 2.34369841234017 641 2419 1101 1986 3049 1334 873 2785 898 894 1109 876 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 0.00198977787795418 0.0101372485964375 1375 1158.09090909091 1110 0.000181052709422163 92 3.13200079211126 3.13200079211126 1 13.9393965939802 1373 1514 1301 830 2588 625 92 278 1110 2663 365 877 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 0.000170633542165922 0.00149584053669357 4205 1930.72727272727 1111 1.55133434600277e-05 203 1.54879627460034 1.4562230173394 1 9.76584743286673 4201 533 452 1111 203 2136 3898 3845 844 600 3415 878 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 9.24237777318532e-06 0.000144532965674971 1115 1263.63636363636 1111 8.40219691035414e-07 1 1.27606430406759 1.37222003091545 1 10.9367196874016 1111 1 278 189 1842 3480 2359 1872 609 48 2111 879 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 3.34571231043025e-05 0.000406166007426844 1545 1449.63636363636 1113 3.04160290216468e-06 146 1.33870132163069 1.38516989158929 1 10.1327889961048 1541 557 345 217 489 4275 3318 1966 1113 146 1979 880 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 0.00130601036733995 0.00722545995437428 765 1381 1115 0.000118798755791225 629 1.18200297167431 1.31478529718001 1 5.64861627152555 765 968 629 761 2409 2506 1446 1115 697 1624 2271 881 M9503 BIOCARTA_FAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FAS_PATHWAY.html FAS signaling pathway ( CD95 ) 17/35 BioCarta 0.0568460938134227 0.126606842019819 1365 1287.72727272727 1116 0.00530639838706117 140 1.79661288551867 1.79661288551867 1 3.59906130042992 1365 1907 2483 710 2698 1615 550 915 140 1116 666 882 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 0.000476952785830839 0.00336090339008017 900 1313.90909090909 1116 4.77055184545742e-05 60 1.53756856989626 1.53756856989626 1 8.48855335116587 897 1807 3969 1116 60 1032 1203 2041 1571 545 212 883 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 3.85654745795455e-08 1.365252928982e-06 3110 1911.45454545455 1116 3.50595229596264e-09 13 1.37338684249139 1.29996094800942 1 17.9773085439962 3108 13 128 264 1116 3193 3420 4402 598 282 4502 884 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 0.00303921602081832 0.0142133395943659 210 1142 1116 0.000276674792721865 206 1.20074158169684 -1.20074158169684 -1 4.95070951496727 206 1438 1116 1682 1655 679 902 882 1335 1668 999 885 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 2.21244218637658e-15 3.57500140874506e-13 320 965.909090909091 1117 2.01131107852416e-16 29 1.5150930757114 1.62814128796356 1 42.0895148567238 318 1117 29 1444 1095 1534 1290 1054 1432 80 1232 886 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 0.0205284952883306 0.0598982122796497 530 1556.90909090909 1118 0.00207206367483788 351 0.524869483968619 0.618477787547622 1 1.43222201810198 668 1598 3785 1070 3050 1267 351 530 1118 3161 528 887 M14863 BIOCARTA_P53_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P53_PATHWAY.html p53 Signaling Pathway 15/22 BioCarta 0.0105016280292196 0.0360010905844418 1120 1308 1118 0.000959281344806109 262 1.67526132961391 1.67526132961391 1 5.39801845339174 1118 1750 1038 489 3382 1560 1849 2187 290 463 262 888 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 0.00868932775555679 0.0312495701170676 410 1117.36363636364 1118 0.000793076266226729 222 1.2837778807315 1.34535752690288 1 4.31271683181988 408 564 797 892 2150 1769 1118 1193 1875 222 1303 889 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 0.0618581888467342 0.134650503675651 670 1309.27272727273 1121 0.00578810733265412 513 1.88804590279963 1.88804590279963 1 3.66949704955262 666 1834 1803 1298 2918 1121 580 858 513 2193 618 890 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 0.0200347694339077 0.0588976973445995 555 1295.45454545455 1121 0.00183814371903518 523 1.01213730769283 -0.931951048591966 -1 2.77836554275279 552 606 898 1121 3112 984 523 1132 1637 2331 1354 891 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 0.0366117049694344 0.0911596437230444 1125 1167.72727272727 1121 0.00338505179599375 615 1.27708213803424 1.27708213803424 1 2.96492793031325 1121 1353 998 615 2421 1251 1411 1074 745 681 1175 892 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 0.000138512249563098 0.0012652405486407 1125 1273.81818181818 1122 1.25928155526185e-05 435 1.41050977718043 1.41050977718043 1 9.12279876084816 1122 456 435 902 2860 2434 2220 479 1321 532 1251 893 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 0.00636798056325112 0.0248049517201951 1005 1548.54545454545 1123 0.00063863025294201 313 1.07643464219997 1.07643464219997 1 3.85715549247484 1004 2700 4090 3014 313 731 469 1142 1123 1606 842 894 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 0.000121652493492013 0.00114932174295076 430 1299.81818181818 1124 1.10599291800577e-05 422 1.66972491340613 1.66972491340613 1 10.9548534277499 426 2196 422 888 2318 1346 734 1852 593 2399 1124 895 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 0.0470224670163579 0.110118580928862 615 1181.63636363636 1124 0.00436896913292705 542 1.2303348545442 1.2303348545442 1 2.63106500784559 613 725 1958 1005 2297 1256 1344 1124 1215 919 542 896 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 0.00199429806980936 0.0101468846418314 1000 1196.36363636364 1125 0.000181464381536994 145 1.73542297224509 1.73542297224509 1 7.72213833553286 999 920 1266 1871 1967 1125 677 145 1928 1642 620 897 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 0.0248286700121188 0.0686413850600523 955 1529.18181818182 1126 0.00228303538834525 389 1.37011680037659 1.41462421722507 1 3.5577171532849 1081 3588 1154 2524 953 1567 955 1109 2375 1126 389 898 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 2.26567648828259e-06 4.44554326162095e-05 435 1035.63636363636 1127 2.05970801963597e-07 224 1.22877444993843 1.30171340636809 1 11.9357060360099 432 446 224 612 1061 2155 1127 1210 1326 1251 1548 899 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 0.0330826687086476 0.0840245992242398 1795 1213.72727272727 1130 0.00305371671659368 359 1.35494343399659 -1.20074158169684 -1 3.25273669252493 1795 974 1681 1130 810 559 1442 943 359 1964 1694 900 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 0.0442092660140315 0.105106352380391 925 1141.27272727273 1132 0.00410213474616807 168 1.4910450905656 1.59616163242215 1 3.25592144939945 925 1132 1259 168 943 2108 1693 885 1168 432 1841 901 M4835 BIOCARTA_BCELLSURVIVAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCELLSURVIVAL_PATHWAY.html B Cell Survival Pathway 17/27 BioCarta 0.0410969975520191 0.0997309842199697 1045 1838 1133 0.00380776416391482 455 1.9083122944764 1.9083122944764 1 4.26419233290253 1041 3698 2905 2578 3966 680 455 1057 483 2222 1133 902 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 0.0348209456344982 0.0877735079307469 2995 1686.36363636364 1133 0.00321678287623327 157 1.24905538724657 1.50422253894413 1 2.94568890175554 2993 222 1133 157 829 2462 3068 1832 674 1004 4176 903 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 0.0245761209127754 0.0681442027202755 1290 1283 1133 0.00248522217708836 76 1.20418076991769 -1.20418076991769 -1 3.13532416670249 1290 1030 4331 269 1133 1780 1588 548 76 1191 877 904 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 0.0210019133484236 0.0609551505093897 1125 1203.63636363636 1141 0.00192773868802968 579 1.0851584970176 -1.20074158169684 -1 2.94269524657147 1123 808 905 1006 1141 1227 2096 1372 579 1319 1664 905 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 0.000933620067798245 0.0055756934813699 2785 1707.09090909091 1141 8.49105914794718e-05 58 1.31141707336295 1.34830890391832 1 6.59654769090535 2781 58 598 686 449 3891 2160 2777 1141 626 3611 906 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 0.000225121312765254 0.00187374506504082 1450 1248.81818181818 1142 2.04676683863851e-05 469 1.5076992848588 1.6722465579488 1 9.17752388975305 1450 550 469 670 2861 1468 922 1532 880 1793 1142 907 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 0.00266060486805488 0.0129064124344774 1780 1263.90909090909 1142 0.000266379571432151 7 1.8636644772713 1.8636644772713 1 7.85821569990251 1779 1960 4662 100 168 827 1142 1330 7 1316 612 908 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 0.000758709112995796 0.00470079369711562 635 1089.81818181818 1143 6.89973539747799e-05 77 1.37017743856651 1.46778240338295 1 7.11881005755934 632 1143 1723 1607 77 1662 757 870 1231 1140 1146 909 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 0.000267904259652246 0.00210864599624827 2405 1623.63636363636 1145 2.43578990151156e-05 38 1.34014718100646 1.50598348752553 1 8.00419322996692 2402 212 488 38 1145 4370 2254 2899 647 332 3073 910 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 0.0839184282471183 0.156982736433532 1130 1423 1145 0.00793650793650794 831 1.20838567809848 1.34288375757574 1 2.16880830078556 1127 1127 2128 1515 2598 1895 972 1454 831 1145 861 911 M144 PID_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CERAMIDE_PATHWAY.html Ceramide signaling pathway 18832364 34/69 Pathway Interaction Database 0.0176323493692699 0.053169362383783 930 1565.36363636364 1146 0.00161593397496994 319 1.54295953809263 1.54295953809263 1 4.38852839337682 930 2384 2579 995 4131 1484 1146 462 319 1886 903 912 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 0.0546698124694842 0.123263662723427 730 1313.45454545455 1146 0.00509796176136704 392 1.51604129763343 1.51604129763343 1 3.07633241926873 726 1357 1146 1236 2570 1421 536 3329 392 863 872 913 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 0.00144009511587326 0.00776557619445582 1150 1218.27272727273 1146 0.000131003513694417 86 1.35539504330137 1.37063536958865 1 6.38251953217725 1146 86 1762 546 110 3716 1909 1245 386 530 1965 914 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 6.29766506036403e-09 2.65863589845638e-07 395 1110.63636363636 1147 5.72515007126506e-10 108 1.53325872521754 1.62384427902054 1 22.501594233195 394 2499 108 1147 1768 1507 493 1175 1723 372 1031 915 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 0.00186145278327115 0.00960179022720178 1005 1398.3 1147.5 0.000206999399277485 103 1.98900160281705 1.98900160281705 1 8.95694779727247 1003 1767 4107 NA 1453 836 103 711 1838 873 1292 916 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 0.00221513798161419 0.0110662436906653 375 1383.09090909091 1148 0.000221734916067867 109 1.15343785893321 1.15343785893321 1 5.03549948851107 372 2065 4306 2389 1148 410 302 1534 2300 279 109 917 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 0.0141221793812252 0.0445434210569581 1045 1240.45454545455 1149 0.00129215047529659 519 1.16902989744183 1.2570558643749 1 3.52557607700494 1045 519 853 858 1011 2402 1450 1157 1508 1149 1693 918 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 0.00820474588397716 0.0299668271335284 655 1556.36363636364 1149 0.000748682330195944 236 1.76539055828103 1.76539055828103 1 6.00236891953435 653 3761 1149 3340 2620 440 541 485 2489 1406 236 919 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 2.89963023890762e-06 5.4788981046456e-05 1155 1240.72727272727 1151 2.63603096424289e-07 232 1.27979033332015 1.37598670137366 1 12.1719786204473 1151 870 232 651 1172 2508 1322 1095 2249 785 1613 920 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 1.02544101734024e-05 0.000156521713591412 1445 1502.27272727273 1152 9.32223451863613e-07 247 1.23487307450661 1.31874214695972 1 10.4882997144353 1443 406 286 338 1152 4247 2774 2348 644 247 2640 921 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 0.000320424622828385 0.00242570239511117 810 1488.63636363636 1153 2.9133754673625e-05 508 1.23931093687078 1.23931093687078 1 7.23366703398244 530 806 508 2496 2825 1153 810 1197 3447 1478 1125 922 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 6.74315880077033e-05 0.00071814641228204 1155 1396 1153 6.13033226574939e-06 385 1.23109746088983 1.23975182997315 1 8.63823679039018 1153 2075 385 1134 1128 2473 2150 2000 732 524 1602 923 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 0.00205224267770007 0.0103701088235166 1065 1360.72727272727 1155 0.000205414040975252 152 1.44141515827619 1.44141515827619 1 6.3834834546806 1064 1262 4238 1025 2141 1155 590 152 1841 1187 313 924 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 0.00328903526052936 0.0149780556179209 295 965.818181818182 1156 0.000299451157942506 124 1.55660089776645 1.55660089776645 1 6.33886212947776 295 1639 1174 1156 1769 469 124 511 1887 1271 329 925 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 0.00477739395652648 0.0197938709816827 1160 1244.36363636364 1157 0.000435254538282108 247 1.15561871920577 1.15561871920577 1 4.39368001718036 1157 618 1711 763 247 2340 2004 1082 1218 1925 623 926 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 0.000380562415326164 0.0027907910457252 1260 1019.27272727273 1159 3.46025692790515e-05 57 1.88639818945455 1.88639818945455 1 10.7542513770769 1259 1373 2551 829 1159 1530 960 57 63 1215 216 927 M1076 REACTOME_AMYLOIDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMYLOIDS.html Genes involved in Amyloids 52/136 Reactome 0.00193409357450632 0.00989428219447229 335 1182.45454545455 1160 0.000175981454230624 335 1.3862241508194 -1.20074158169684 -1 6.20217683444518 335 2035 658 1995 1601 788 1248 748 761 1678 1160 928 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 0.0601532380746933 0.132027200757851 1000 1946.72727272727 1160 0.00618463951931276 960 0.743812175910316 0.743812175910316 1 1.45981553237119 997 1817 4666 1659 1160 960 1086 2391 1036 4646 996 929 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 0.00425597821666516 0.0182132547244684 420 1375.63636363636 1161 0.000387657629623345 226 0.847808867288674 0.847808867288674 1 3.29177402188595 416 1390 2051 1161 226 468 513 1533 2830 4034 510 930 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 4.23038691963673e-05 0.000489471434701672 55 1239.81818181818 1162 3.84588024369984e-06 55 1.20074158169684 -1.20074158169684 -1 8.87141449038465 55 1506 937 1709 1633 791 1162 660 2113 2002 1070 931 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 0.0748666605236177 0.156982736433532 885 1498.63636363636 1162 0.00704934516564838 768 1.5292390655962 1.53920247050122 1 2.74467534620454 883 3825 1389 2294 1216 2172 1061 1162 917 798 768 932 M100 PID_SHP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SHP2_PATHWAY.html SHP2 signaling 18832364 38/91 Pathway Interaction Database 0.161385165508919 0.262241686633255 1085 1173.18181818182 1163 0.0158730158730159 301 1.68249249350309 1.68249249350309 1 2.18288934411113 1084 811 1721 301 1680 1247 992 1561 1163 1240 1105 933 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 0.000395918001701368 0.00287639031933738 270 1321.09090909091 1163 3.59990245583284e-05 30 0.986391391541798 0.986391391541798 1 5.59447712562124 266 1163 1614 2048 4079 148 30 343 2611 2110 120 934 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 0.000279433443056022 0.00217874395035028 865 1636.09090909091 1163 2.54062674239668e-05 491 1.20765776438031 1.20765776438031 1 7.17460246986023 861 1630 491 2412 2937 563 635 3292 2904 1109 1163 935 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 8.23372964434978e-05 0.000838766458987458 2995 1552.18181818182 1163 7.4854889240215e-06 14 1.32953391933969 -1.11570623447727 -1 9.12884815302854 2992 136 399 14 284 3571 2379 1427 184 1163 4525 936 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 0.00753601000697173 0.0280713377525195 810 1648.27272727273 1164 0.000687449889057337 298 2.46711003640163 2.46711003640163 1 8.54449027336697 806 3699 1543 3375 2780 1164 601 298 628 2183 1054 937 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 0.00788707777033533 0.0290100835414375 730 1740.18181818182 1164 0.000719590541630655 231 1.30706307349915 1.30706307349915 1 4.48515430774286 730 3670 2043 3435 4021 362 742 518 2226 1164 231 938 M15902 KEGG_GLYCEROLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROLIPID_METABOLISM.html Glycerolipid metabolism 22/70 KEGG 0.104665966121399 0.188278202397265 1575 1401.18181818182 1165 0.0100004242363402 487 0.986364182466095 -0.986364182466095 -1 1.5965209347983 1574 487 1270 956 1403 992 981 3041 1093 2451 1165 939 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 9.14982062216849e-07 2.03204073153941e-05 800 1218.81818181818 1165 8.31802220689969e-08 205 1.30662966588218 1.35542922429443 1 13.6834726542624 796 1717 205 1069 1942 2247 1165 1348 774 682 1462 940 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 0.00564842756557386 0.0226420287188016 1180 1022.90909090909 1166 0.000514816550888904 125 2.31622896548935 2.31622896548935 1 8.5045100083658 1177 1543 1463 1166 1730 1122 637 264 125 1766 259 941 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 0.0010978235970327 0.00628295545492121 1125 1740.45454545455 1166 9.98519823461743e-05 100 1.51677808231454 1.51677808231454 1 7.45395164501239 1124 3403 2039 3275 3533 976 662 100 2048 1166 819 942 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 0.00664660587696552 0.0256556796865407 430 1066 1167 0.000606070167857157 429 1.30526456270129 1.3909518712581 1 4.63444979794212 429 1218 763 1091 972 1585 1184 1504 1167 563 1250 943 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 0.0105653654931474 0.0361910107462636 3585 1514.90909090909 1167 0.000965131709177154 120 1.21983795878073 -0.926180286682885 -1 3.92433434595266 3581 1038 1941 1167 448 120 2821 2384 826 1015 1323 944 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 0.0251450356440922 0.0692301040118778 780 1596.36363636364 1168 0.00231246517383682 517 1.17758752217537 1.35992223441912 1 3.04803735695098 780 3869 2661 2714 1168 777 1222 525 765 2562 517 945 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 0.0118083051898874 0.0391604516063781 1025 1012.54545454545 1171 0.00107928778290528 99 1.50138572221745 1.71890317059642 1 4.71533924722404 1023 1442 1370 204 1598 1335 2291 385 99 220 1171 946 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 0.0689712813640394 0.146708771889191 2010 1550.63636363636 1171 0.00647577349642109 190 1.30097971130382 1.39237618721325 1 2.42035219073739 2010 190 1105 640 1733 2740 3084 1171 771 888 2725 947 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 0.0262955211730067 0.0716400071027381 1145 1590.27272727273 1172 0.00241956187600253 379 1.62518411452666 1.62518411452666 1 4.15268108567831 1145 1464 2595 1540 4655 1078 379 1081 412 1972 1172 948 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 0.00885720655373844 0.0316589396726303 620 1462.81818181818 1172 0.000889270841472668 235 1.25240526293404 1.25240526293404 1 4.19152404112918 620 1920 3912 1974 3388 501 235 346 1172 1292 731 949 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 0.00943670182632657 0.0331720587070463 1390 1374.09090909091 1172 0.00086158404237619 335 1.59747892943138 1.74488183702541 1 5.27411611870913 1390 771 1172 335 370 4318 2047 1305 353 1097 1957 950 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 0.0834937752993042 0.156982736433532 565 1600.81818181818 1173 0.00789470995707692 564 1.4770861862777 1.4770861862777 1 2.65107145828096 564 3439 1366 3789 1845 796 667 839 2388 1173 743 951 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 0.00511976144982606 0.0208619149164217 1210 1300.81818181818 1173 0.000466519539897666 259 1.30445111281024 1.33815028575359 1 4.89309406353889 1209 2074 1084 655 259 3627 1409 1173 631 933 1255 952 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 0.00480671195406768 0.0198626562758035 745 1009.81818181818 1174 0.000437931475170033 242 1.36941754430491 1.40401005031851 1 5.20194161151054 744 1572 1152 1325 1749 1222 1174 242 1264 272 392 953 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 0.0261727195244251 0.071407828404566 930 1426.18181818182 1175 0.00240812500103093 538 1.27325042230805 1.27325042230805 1 3.25742416447272 927 1068 1375 1175 3324 1536 934 538 1986 1799 1026 954 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 2.16242649074647e-05 0.000290347579817706 3175 1898.18181818182 1175 1.96586158725991e-06 270 1.76506330097948 1.43331319421094 1 13.9342931268246 3174 441 319 435 270 3942 4348 2224 1175 625 3927 955 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 0.0679390015135725 0.144973661699727 750 1149.09090909091 1175 0.00637568103404546 146 1.20074158169684 -1.20074158169684 -1 2.24771574667726 746 699 1698 1241 1175 636 1586 1690 146 1895 1128 956 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 1.46420473765026e-10 1.024069164273e-08 560 1813.72727272727 1176 1.33109521613428e-11 65 1.36341265376979 1.47444345641824 1 24.3128435553557 2708 558 65 413 557 4678 2854 3397 1176 89 3456 957 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 0.0520761613830811 0.118633394380709 1180 1461.63636363636 1177 0.00485011990472719 602 1.14751749502539 1.12916104217592 1 2.37111590223646 1078 2218 1054 1919 2111 2352 1177 888 1503 602 1176 958 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 0.00124470006638446 0.00693315256676981 380 1360.54545454545 1179 0.000113218622006951 378 0.964916235402726 -0.810865129405406 -1 4.64981569592714 378 700 622 1022 2508 1607 947 1234 1996 2773 1179 959 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 0.0867928577539195 0.161393385490026 1180 1468 1180 0.00821989792672295 557 1.06710845596515 1.06710845596515 1 1.88658315466439 557 1798 2730 1180 1776 1179 1016 1077 1106 2228 1501 960 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 0.0447540333192976 0.106045430416175 2130 1247.27272727273 1181 0.00415375057156151 526 1.27387958546824 -1.27387958546824 -1 2.77072459277522 2130 586 1181 737 1237 1760 2845 667 526 857 1194 961 M5298 BIOCARTA_STEM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STEM_PATHWAY.html Regulation of hematopoiesis by cytokines 4/15 BioCarta 0.00747359237759033 0.0279276346741533 650 1545.54545454545 1182 0.000749884655714812 212 1.59555088121217 1.59555088121217 1 5.53390477885181 648 2409 3858 1410 2494 456 212 744 3313 1182 275 962 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 0.00865178305344128 0.031138444998791 565 1737.72727272727 1182 0.000868565279679556 341 0.849254971022537 0.849254971022537 1 2.85591533319893 563 1182 4317 1421 3453 550 643 341 1859 4071 715 963 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 0.0305202527076704 0.079367733578603 765 1783.27272727273 1182 0.00281382415174175 739 1.20242805629414 1.26512358068417 1 2.95305734176962 2216 1122 1182 739 762 3524 2912 3065 896 765 2433 964 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 0.00412208121415417 0.0177700759609259 1185 1347.54545454545 1182 0.000375438633470838 507 1.27953049308363 1.27978235614597 1 4.99856503011837 1182 3259 721 1847 739 1866 1630 1036 1471 565 507 965 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 0.000500862722341245 0.00349262309061172 1145 1717.81818181818 1183 4.55433443224969e-05 57 0.865344603401388 0.865344603401388 1 4.74511762065536 1143 1168 2524 494 57 1623 1183 3803 1617 4310 974 966 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 0.0121590062657727 0.0400964837166859 2785 1870.90909090909 1184 0.00122260517876731 454 0.646118488205991 -0.646118488205991 -1 2.01444347266784 2783 1184 4161 712 454 2114 2050 1035 1055 3863 1169 967 M14663 REACTOME_ETHANOL_OXIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ETHANOL_OXIDATION.html Genes involved in Ethanol oxidation 4/13 Reactome 0.0284800836376175 0.0751874208033102 855 1592.63636363636 1185 0.00288518081723237 520 0.713857489204404 0.713857489204404 1 1.79061115028578 853 1185 4073 1771 783 855 520 1340 1096 3713 1330 968 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 0.0156141568619571 0.0480419823080308 1145 1570.63636363636 1185 0.00142964451753693 499 1.52275941807497 1.52275941807497 1 4.48075452778093 1142 2468 1946 2554 506 1169 1009 499 3044 1755 1185 969 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 0.041592003526732 0.100412224897613 1860 1613 1189 0.00385452563408566 128 1.26580170276417 1.26580170276417 1 2.82012676326381 1856 280 1189 128 909 4121 1636 3823 374 1175 2252 970 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 0.0342564357859861 0.0865834186047093 3545 1889.09090909091 1190 0.00316379747397735 664 1.69024700958719 2.0217321625559 1 4.00853193743954 3542 1157 1190 736 820 1546 2882 3369 1066 664 3808 971 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 1.61292304988515e-06 3.3741774159651e-05 960 1458.72727272727 1191 1.46629475672346e-07 215 1.83506961457652 1.61377736865093 1 18.3154497080548 958 897 215 1547 1021 2538 1468 3939 1191 326 1946 972 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 0.000141868329864277 0.00128836239097675 1825 1567.27272727273 1192 1.28979526504811e-05 22 1.22629090506816 1.27655174147185 1 7.909794280683 1821 22 438 198 674 4483 3140 1993 1192 485 2794 973 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 0.0135126108674726 0.043074894234678 2920 1955.81818181818 1193 0.0012360297620045 457 1.23652666814888 1.25960797353518 1 3.76931513982204 2919 1119 1193 610 457 2932 3650 3224 834 692 3884 974 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 0.00102133634160652 0.00600499635730006 405 1561.45454545455 1194 9.28918908236755e-05 404 1.33445169830505 1.33445169830505 1 6.61646834040416 404 2273 604 2873 3200 1146 477 1194 2761 1351 893 975 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 0.0757436996650882 0.156982736433532 850 1216.63636363636 1196 0.00713495759917846 487 1.73041933125535 1.73041933125535 1 3.10575330173203 850 731 1876 487 2015 1135 1220 801 1213 1859 1196 976 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 0.00312238264593841 0.0144437167609747 2025 1277.63636363636 1196 0.000284256632647538 181 1.18280818516914 1.18280818516914 1 4.85833509820281 518 2755 1623 2319 181 1196 416 344 2023 2022 657 977 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 0.00457434070902056 0.0192245386210496 1395 1136.90909090909 1198 0.000416716333324419 162 1.82801883160531 1.82801883160531 1 7.00186874157818 1392 1457 2169 1315 1119 1559 1198 894 171 1070 162 978 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 0.00650176057940731 0.0252212335058797 1200 1343.63636363636 1200 0.000592823219008406 430 1.56658608505435 1.77022538854487 1 5.58822774199912 1200 430 762 957 3074 2214 1358 1805 613 708 1659 979 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 0.0105022387599086 0.0360010905844418 920 1739.63636363636 1200 0.00105522050871012 378 1.14505098292374 1.14505098292374 1 3.68957739701823 918 2342 4603 2234 1972 950 718 378 2834 1200 987 980 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 0.000130208598815204 0.00120823266148128 680 1030.36363636364 1202 1.18378459949429e-05 29 1.85828951839438 1.85828951839438 1 12.1019626697317 678 1838 1202 1288 1297 1326 659 29 705 1806 506 981 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 4.02720347005505e-07 9.77796655993676e-06 1810 1313.36363636364 1204 3.66109473386706e-08 189 1.22878923847718 1.3217984371516 1 13.7395697699027 1076 659 189 1204 1806 2159 1716 1808 1003 648 2179 982 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 0.00361376535530554 0.0160817706124993 1110 1612.36363636364 1206 0.000361965552573866 216 1.35593454827845 1.35593454827845 1 5.42825061384499 1107 2485 4346 1639 1042 1206 631 216 2720 1705 639 983 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 0.000419132360451525 0.00301235313048443 740 1312.90909090909 1206 4.19211433813405e-05 61 1.25051191244786 1.34077488125447 1 7.03649603195199 737 517 4403 365 608 1986 1494 1206 1755 61 1310 984 M4377 KEGG_GALACTOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GALACTOSE_METABOLISM.html Galactose metabolism 12/39 KEGG 0.0112408124580673 0.0379225681630692 1065 1211.18181818182 1207 0.00102715101576474 13 2.51277643597153 2.51277643597153 1 7.97000759686456 1061 2204 2034 1314 2173 1357 1207 376 13 823 761 985 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 0.0062109132606747 0.0243347320564562 1310 1349.72727272727 1207 0.000566228833662241 292 1.12234639950069 1.06407262174262 1 4.0424907373209 1310 593 2219 353 292 1207 971 4078 558 1466 1800 986 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 0.104661745741284 0.188278202397265 2380 1481 1208 0.01 94 1.54605136240993 1.73814578950326 1 2.50242599061858 2379 485 1402 94 2968 570 1004 3942 1208 782 1457 987 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 0.00309240365159984 0.0143821147954926 1425 1381.27272727273 1212 0.000281523547734532 177 0.862825077863568 -0.862825077863568 -1 3.54759250315833 1421 692 2569 696 177 1088 1212 1236 2126 2854 1123 988 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 0.000621616354278611 0.00407397795265675 135 1215.27272727273 1216 5.65265512077076e-05 131 1.20074158169684 -1.20074158169684 -1 6.40506605234713 131 1216 870 1768 1458 917 1433 751 1867 1798 1159 989 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 0.0195474249582466 0.057900906039408 1270 1740 1217 0.00179302720739976 574 1.22170513703986 1.46778240338295 1 3.37385261221652 3602 1073 1156 1217 574 1065 2773 1266 1269 856 4289 990 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 0.00776330112802843 0.0286725049933361 1265 1287.45454545455 1217 0.000708257469526241 451 1.25446623937714 -1.20074158169684 -1 4.31890230419017 1263 1613 787 1851 887 451 1217 1150 1965 2019 959 991 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 3.57835729338672e-06 6.44930087569621e-05 245 1833.63636363636 1217 3.253057376083e-07 72 1.45311215534579 1.61659402683942 1 13.5907437978142 2812 544 242 245 1217 3594 4210 3609 381 72 3244 992 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 0.00467176391473279 0.0195288900128794 1930 1469.36363636364 1218 0.00042561037592181 243 1.3843818172873 1.3843818172873 1 5.28152616290873 1926 288 1218 504 243 4566 1934 938 1909 1146 1491 993 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 0.0191871649168637 0.0570501616753956 1175 1715 1220 0.00193548727862673 169 0.975040667625085 1.28821420152315 1 2.70665545865128 1171 169 4274 797 2206 1129 1544 486 1847 4022 1220 994 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 0.0752251802491593 0.156982736433532 3890 1912.54545454545 1220 0.00708433325430094 451 1.32512200254217 1.39912307427369 1 2.37832643233697 3887 655 1954 883 1220 941 4615 2194 889 451 3349 995 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 0.0213226255770661 0.0615032668662181 1970 1374.09090909091 1221 0.00195746682236672 378 1.51989419843382 1.51989419843382 1 4.10840800754552 1967 1948 1221 1038 614 2886 1524 1005 378 1156 1378 996 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 0.000595074730357886 0.00394415867957151 1050 1450.36363636364 1221 5.41123411106353e-05 556 1.18383879842359 1.11928825122133 1 6.35206346813755 1049 1221 556 1079 3440 1299 1197 1373 2327 944 1469 997 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 0.000504265253999418 0.00350411566188537 1225 1225 1221 4.58528067716367e-05 420 1.33478008810871 1.39143694772073 1 7.31501700770894 1221 420 538 966 1347 2955 1680 949 1291 455 1653 998 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 0.00188622255241681 0.00969170929893112 675 1285.09090909091 1222 0.000171621972200603 132 1.01807455415434 1.01807455415434 1 4.57543361199442 673 2462 1222 1553 132 1677 833 1281 946 2440 917 999 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 0.0276774261242607 0.0739010933437525 2665 1223.81818181818 1222 0.00254835318918472 7 1.45630529814821 1.31450122912212 1 3.67729637681197 2662 7 1265 1053 714 464 2590 1328 918 1239 1222 1000 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 0.00739354158764823 0.0277816720855292 945 1469.63636363636 1222 0.000674409691581828 680 1.60192535451782 1.60192535451782 1 5.564150336245 945 1687 780 680 2788 1033 1006 1222 2318 2468 1239 1001 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 0.0125050149870751 0.0407783578492928 1225 1467.54545454545 1223 0.00125759463303098 26 2.31622896548935 2.31622896548935 1 7.1835903104589 1223 744 3891 318 4062 1957 1558 419 26 1418 527 1002 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 0.000510234891257014 0.00352542052627569 585 1405.45454545455 1223 4.63957514451252e-05 541 1.2549067577187 1.2549067577187 1 6.86991265069781 585 2128 541 1831 1075 1223 1005 923 2416 2089 1644 1003 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 0.00652899536034453 0.0253059323892262 695 1716.09090909091 1226 0.000595313864835751 87 0.493393016758395 -0.493393016758395 -1 1.75839726702277 693 1226 3378 2077 3404 87 218 685 3330 3398 381 1004 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 0.00274626239739798 0.0132396971133816 1230 1356.09090909091 1227 0.00024997241480576 682 1.3194103537409 1.36491115578449 1 5.53073984914656 1227 1708 682 860 1102 2717 1470 2050 911 941 1249 1005 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 5.1826696199712e-19 1.619065989279e-16 1230 1426.45454545455 1228 4.71151783633744e-20 15 1.55666342018024 1.59946081845835 1 54.8626312034521 1228 404 15 621 1823 3491 2567 2074 744 74 2650 1006 M10792 KEGG_MAPK_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MAPK_SIGNALING_PATHWAY.html MAPK signaling pathway 120/294 KEGG 0.0839184282471183 0.156982736433532 1165 1314.45454545455 1229 0.00793650793650794 556 1.28695639053313 1.29185462927796 1 2.30982686499357 1161 1045 2064 556 1579 1964 1775 1508 783 795 1229 1007 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 0.0144061654919148 0.0452461739243382 2805 1838.63636363636 1229 0.00145004185137193 289 1.23761723432965 1.39999770971439 1 3.71364398217841 2804 1033 4336 1229 508 289 2521 3518 2018 813 1156 1008 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 0.00138197010897302 0.00755649000075563 2470 1796.45454545455 1229 0.000125712634809712 94 1.35427372045606 1.46713494697757 1 6.41306830259243 2466 556 634 139 1229 4521 4345 2243 364 94 3170 1009 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 0.0286296239099522 0.0755396495732186 1105 1607.90909090909 1231 0.00263719335558388 408 1.29593200560571 1.39852797374638 1 3.24479226300504 1102 408 963 953 2010 3787 1802 2199 924 1231 2308 1010 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 0.000516343160485086 0.00355569747117567 2745 1474.09090909091 1231 4.69513078910254e-05 253 1.32701139694407 1.40208544844824 1 7.25364550991 2741 253 543 525 1340 1231 3165 2585 726 710 2396 1011 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 0.00110864078150005 0.00630472172586074 2410 1650.54545454545 1234 0.00010083635006197 367 1.41869182172927 1.57777597219218 1 6.96716738899794 2408 872 611 430 1234 3774 1785 2871 750 367 3054 1012 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 0.0160992983200927 0.0493402955709316 1235 1170.45454545455 1234 0.00147439382540963 513 1.50309391562692 1.50309391562692 1 4.38403706053507 1234 1792 1296 804 513 1383 831 911 1890 1464 757 1013 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 0.00297374776052704 0.0140045755732838 1110 1434.09090909091 1235 0.000270706819002984 614 1.42728682008184 1.42728682008184 1 5.90523656090138 1106 2077 689 1929 2160 2863 1036 633 1433 1235 614 1014 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 0.00185938893690455 0.00960179022720178 2010 1345 1237 0.000169178391934817 129 1.13533089743152 -1.41448702878402 -1 5.11266535252372 2009 1856 2516 1237 129 1790 2326 698 176 907 1151 1015 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 0.0034006591796987 0.0153817460579808 1150 1539.81818181818 1238 0.000309629742414886 304 1.32005162734502 1.35497678831016 1 5.3415454157424 1147 413 703 304 3408 3616 2132 1238 1978 448 1551 1016 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 0.061065397651294 0.133466629381513 1010 1643.36363636364 1242 0.00571175719382028 566 1.12198740143433 1.12198740143433 1 2.19023425809902 1555 1242 2903 2193 4184 1006 566 1007 1583 904 934 1017 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 0.0616652252458831 0.134401509535911 685 1031.45454545455 1242 0.00576951848060358 93 1.40428190647113 1.40428190647113 1 2.73180068977208 682 93 1596 213 1468 1998 1723 755 259 1317 1242 1018 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 0.000579415777448557 0.00386772412125917 1155 1242.54545454545 1243 5.26880395400633e-05 203 1.21813861427645 1.30475185921303 1 6.55921096996223 1155 203 554 583 438 3029 1733 1431 1486 1243 1813 1019 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 1.09836978682873e-07 3.32061988456738e-06 985 1672.27272727273 1244 9.9851803787803e-09 151 1.47048563011711 1.52303357267151 1 17.9814316910365 984 3953 151 2317 3141 2047 982 1226 1782 568 1244 1020 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 0.000289192917866305 0.00223623434508499 1190 1426.36363636364 1247 2.62937217869382e-05 429 1.32649679905602 1.4673629238683 1 7.84712792758537 1186 429 496 908 2720 3817 1369 431 1729 1358 1247 1021 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 0.0196539431665556 0.0581568961968204 760 2108.3 1247 0.00220308634970222 363 0.679483240732266 0.679483240732266 1 1.87355079540165 760 1483 4388 NA 4468 842 363 1011 2823 4204 741 1022 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 0.0150888878283765 0.0468607157030558 765 1314.36363636364 1248 0.00138121645331747 761 1.31002507364144 1.31002507364144 1 3.88639180568143 761 1279 861 1248 3186 1541 1048 1285 1467 960 822 1023 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 0.0839184282471183 0.156982736433532 945 1257.36363636364 1249 0.00793650793650794 599 1.28773954351949 1.2991829103646 1 2.31123246647369 942 2023 1967 1249 1424 1898 824 1286 599 819 800 1024 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 0.0249451984139402 0.0688822626798608 875 1170.18181818182 1250 0.00229387438613079 370 1.4836078808557 1.4836078808557 1 3.84737634366958 874 930 1479 1898 1599 1545 370 960 1250 1333 634 1025 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 0.0152614350823516 0.0472835324809122 395 1578.63636363636 1250 0.00139712214817444 326 1.22168558101711 1.22168558101711 1 3.61368216104014 393 2135 863 2657 2717 326 443 1250 3371 2875 335 1026 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 1.47187158215598e-07 4.22042858175304e-06 1860 1436.63636363636 1251 1.33806516420817e-08 158 1.36417898725844 1.49593724693117 1 16.3644181689181 1251 1034 158 741 1644 3409 1858 1860 927 647 2274 1027 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 0.0139403811638865 0.0441959951686474 730 1274.18181818182 1252 0.0012754096870669 422 1.4836078808557 1.4836078808557 1 4.48554516907115 729 2290 1381 2338 2022 1260 587 422 1252 1025 710 1028 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 1.05197781207956e-09 5.73205584581958e-08 1255 1177.27272727273 1252 9.56343465984171e-11 17 1.72784636177238 1.81219504396101 1 27.9270191316881 1252 17 83 312 2061 2895 1879 1626 477 206 2142 1029 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 0.00423465918882803 0.0181551811151401 1255 1489.09090909091 1253 0.000385712025907015 701 1.36771779938172 1.46778240338295 1 5.31465011622595 1253 1895 723 1305 701 3516 1210 945 1672 1133 2027 1030 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 0.00785962156317282 0.0289318041202104 1255 1551.45454545455 1255 0.000717076522016071 305 1.88982393273777 1.88982393273777 1 6.48983325227332 1255 2905 1082 1855 3094 1992 2218 305 567 612 1181 1031 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 0.00682445204010373 0.0261519008395689 315 1666.27272727273 1255 0.000684550098954252 297 0.88359379711774 0.88359379711774 1 3.12086538970466 312 1255 4330 1574 2446 845 871 297 1259 4088 1052 1032 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 0.00470075242637695 0.0196150720124687 255 1701.45454545455 1255 0.000428256972691583 253 1.23382001587673 1.36482199316802 1 4.70185476848651 4493 255 732 1596 253 1096 4013 1255 1667 683 2673 1033 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 1.01049556517113e-05 0.000154744516940913 240 1011.81818181818 1256 9.18636551427696e-07 240 1.45049565860652 1.45049565860652 1 12.3357288917186 240 269 285 900 1447 1835 1651 1256 1285 653 1309 1034 M15285 BIOCARTA_NFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NFKB_PATHWAY.html NF-kB Signaling Pathway 17/37 BioCarta 0.00793006393419607 0.0291224761721338 1260 1432.90909090909 1257 0.000723526684241618 207 1.06710845596515 1.06710845596515 1 3.65775638362572 1257 2242 2802 1046 1832 1204 1599 306 207 2226 1041 1035 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 0.000268193131405029 0.00210864599624827 4610 2208.63636363636 1259 2.43841664845021e-05 42 1.22766042405918 -1.18882366062725 -1 7.33235229250088 4610 134 1243 455 42 2617 4181 4532 1181 1259 4041 1036 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 0.0798048724282454 0.156982736433532 890 2146.45454545455 1259 0.00753235547900942 673 0.52068220311784 0.542332770503336 1 0.934519420901795 886 3068 1127 3383 3395 673 1071 1221 3755 3773 1259 1037 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 0.000366652360154294 0.00271856480962503 845 1260.36363636364 1260 3.3337589159823e-05 353 1.57884033862937 1.57884033862937 1 9.04100947265927 843 2564 516 1688 1763 1901 1260 430 1990 556 353 1038 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 4.30643397900572e-08 1.49481108337932e-06 1685 1447.18181818182 1260 3.91494005754807e-09 66 1.3491563114675 1.37614080778944 1 17.5415754672622 1681 262 131 208 241 4358 2523 2485 1260 66 2704 1039 M12095 BIOCARTA_IL1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL1R_PATHWAY.html Signal transduction through IL1R 27/52 BioCarta 0.02730302400503 0.0733191807951693 415 1173.27272727273 1261 0.00251344308902163 412 1.13224023064161 1.13224023064161 1 2.86768025974461 592 1736 2440 1776 1722 413 423 560 1261 1571 412 1040 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 0.00871408446923959 0.0313010367662938 3015 1724.90909090909 1261 0.000795344829473852 76 1.16201580150283 1.18191876823181 1 3.9018163938485 3015 76 1261 132 352 4061 3063 1727 532 251 4504 1041 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 0.0293084794999186 0.0770514388436764 420 1345.27272727273 1261 0.00270057901709008 420 1.30247509415827 1.30247509415827 1 3.23615778741516 420 1611 1428 1141 2543 1953 813 928 1956 744 1261 1042 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 0.00808503027150136 0.029621932644453 2580 1623 1262 0.000737717876863055 255 1.96647623799944 1.96647623799944 1 6.70813017700251 2576 1082 1317 1213 341 3751 1153 1901 255 1262 3002 1043 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 0.0027537641815407 0.0132445064459288 850 1453.90909090909 1264 0.000275718259265535 44 1.68373715897236 1.68373715897236 1 7.05734201924912 846 3182 4658 1493 1264 1060 1394 174 44 1315 563 1044 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 0.0140103466946143 0.0442999221396509 2145 1621.09090909091 1265 0.0012818520920823 821 1.6785018588368 1.6785018588368 1 5.07096690622418 2141 1213 852 891 821 3603 2040 1568 1265 1138 2300 1045 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 0.00681740746679099 0.0261519008395689 650 1810.36363636364 1265 0.000621693227697754 439 1.74485001602008 1.74485001602008 1 6.16283414740358 647 3355 766 2628 4411 439 1265 650 3283 1868 602 1046 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 0.0202304937400108 0.0593242138083171 1270 1754.18181818182 1267 0.00185626887740532 478 0.755529885595869 0.755529885595869 1 2.06868156644704 1267 1445 980 1780 4046 1012 788 478 2980 3393 1127 1047 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 0.0497620478863187 0.11481287857966 1560 1402.09090909091 1268 0.00462950970746728 272 0.701222236703204 -0.701222236703204 -1 1.47118547437158 1560 361 1542 272 1005 974 1871 2908 295 3367 1268 1048 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 0.0087862114926538 0.0314960098083693 1165 1395.18181818182 1268 0.000801954429839254 354 1.35913722502143 1.35913722502143 1 4.5555298999677 1163 685 1430 1205 354 3227 1331 1724 1268 1176 1784 1049 M45 PID_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD40_PATHWAY.html CD40/CD40L signaling 18832364 19/44 Pathway Interaction Database 0.012633663474785 0.0410835163378505 1050 1646.09090909091 1269 0.00115516380999821 401 1.06710845596515 1.06710845596515 1 3.30183591274804 1047 1850 2716 1001 4309 1079 480 401 1634 2321 1269 1050 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 0.00494715578366555 0.0203532677807347 1130 1317.45454545455 1270 0.000450755967050208 252 1.2759374824445 1.32937767902248 1 4.81666574004474 1128 1270 1561 616 252 3281 1501 1755 1445 598 1085 1051 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 0.0839184282471183 0.156982736433532 850 1197.54545454545 1272 0.00793650793650794 56 2.0458299705554 2.0458299705554 1 3.67185171310917 847 2335 1404 482 2436 1276 1272 1037 56 730 1298 1052 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 0.0106069252720218 0.0362538671223152 2355 1459.90909090909 1272 0.000968946602276212 307 1.04053270638128 1.16004653653813 1 3.34574213718596 2353 334 1229 307 392 3380 2154 2122 376 1272 2140 1053 M7591 REACTOME_G1_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_PHASE.html Genes involved in G1 Phase 20/48 Reactome 0.160263011989341 0.262241686633255 745 1634.81818181818 1275 0.0157533737297506 743 1.39059940208002 1.39059940208002 1 1.80418315589485 743 1996 2103 2157 2661 1036 865 2975 1275 1260 912 1054 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 0.0639679960803579 0.138135497526524 1855 1725.18181818182 1275 0.00599157945472762 469 0.577018634726521 0.577018634726521 1 1.10716830511623 1853 469 1900 922 1142 853 2271 2968 868 4456 1275 1055 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 0.0200110792844474 0.0588649827538736 2740 1697.18181818182 1275 0.00183595010282876 587 1.39071472694174 1.41785374769101 1 3.81832772151845 2738 1275 1204 1107 587 3198 2683 1771 785 762 2559 1056 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 0.00833857824393682 0.0303305908631064 1280 1441.54545454545 1276 0.000760941125528799 347 1.06587114817104 1.20548460870081 1 3.61152074562004 1276 660 838 386 347 3301 2376 2117 1464 867 2225 1057 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 0.0157606807894142 0.0484609909312304 1840 1510 1277 0.00144315772862912 684 1.4214416063327 1.42596877910511 1 4.17065967480825 1839 1198 873 1277 1361 2431 2149 2843 689 684 1266 1058 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 0.036303719111038 0.0906818911270384 1280 1769.45454545455 1278 0.00335609163170289 832 1.32073657875873 1.32073657875873 1 3.07300492100897 1278 2739 2771 3317 849 2043 1263 1207 2136 1029 832 1059 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 2.21867305950875e-07 5.940972546776e-06 795 1368.27272727273 1281 2.01697571205386e-08 171 1.31309215742296 1.31309215742296 1 15.3163755239076 795 1495 171 481 1281 2406 1874 2221 824 1248 2255 1060 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 0.0231562464093449 0.065406974487155 640 1838.54545454545 1282 0.00212760292883779 356 0.872339790410637 0.872339790410637 1 2.30597616167856 636 2243 2702 2418 4159 642 356 1205 1282 3906 675 1061 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 0.02149105047925 0.0618214011944539 1285 1263.27272727273 1283 0.00197308236553497 366 2.24458518468169 2.24458518468169 1 6.05608649692681 1283 931 1937 648 615 1613 706 2086 366 2389 1322 1062 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 0.0839184282471183 0.156982736433532 4190 2104.18181818182 1283 0.00793650793650794 568 1.36708658857183 -0.993691764637665 -1 2.45364439097718 4187 973 1145 794 1283 2709 4356 3889 568 651 2591 1063 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 0.00252237078341968 0.0124027591721979 1465 1195 1284 0.000229569764841541 114 1.01015491360535 0.895785392899615 1 4.29833414523482 1462 114 1284 1127 152 1091 869 1425 1488 1667 2466 1064 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 0.0527859619254296 0.120016990578633 1780 1273.63636363636 1285 0.00491788507811914 101 2.46711003640163 2.46711003640163 1 5.07006153154848 1248 1162 1285 620 1039 1417 1533 1776 101 2052 1777 1065 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 0.0167163335372839 0.0509646967831572 940 1234.81818181818 1286 0.0015313379649185 461 1.49198256055026 1.49198256055026 1 4.30478351089539 940 2541 1286 2282 524 1340 805 666 1331 1407 461 1066 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 0.00453856495616618 0.0190913064493669 1480 1706.09090909091 1287 0.000413450461356735 40 1.09847659295905 1.12592552738805 1 4.21490469250737 1479 40 1168 348 237 4647 3292 2725 1287 1083 2461 1067 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 0.00858989633572966 0.0310557196555006 1030 2084.90909090909 1288 0.00086232819496471 338 0.453578599312491 0.453578599312491 1 1.52648545536765 1029 2703 4202 3013 1288 864 1279 338 3521 3924 773 1068 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 0.0519016166105754 0.118350839628787 1275 1425.90909090909 1288 0.00483346305511244 758 1.30783016458494 1.30783016458494 1 2.70539297492651 1272 1288 1602 983 1031 1696 758 1196 1995 2515 1349 1069 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 0.00012744806221306 0.00118731932312207 1330 1269.90909090909 1289 1.1586858727057e-05 177 1.26939725874971 1.37408301300375 1 8.28833292347158 1326 759 428 808 1289 3208 1773 1166 1731 177 1304 1070 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 0.306202842122068 0.425650109221006 1030 1694.09090909091 1290 0.0326879622443628 1000 1.42052811934811 1.42052811934811 1 1.17609267869998 1027 1290 2525 1228 2381 1000 1141 2078 2279 2477 1209 1071 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 0.00227889909250938 0.01134848155951 1040 1494.45454545455 1292 0.000207387559032427 670 1.36771779938172 1.46778240338295 1 5.93758113593629 1040 2084 670 1438 974 3151 1292 883 1985 1168 1754 1072 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 0.0255911450712233 0.0702108347797146 1955 1613.36363636364 1294 0.00235397908078397 682 1.64202723049307 1.79602472672438 1 4.2277918740824 1954 2238 1176 1028 682 2906 1294 2366 1262 750 2091 1073 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 0.0839184282471183 0.156982736433532 3385 1632.27272727273 1294 0.00793650793650794 16 1.12651980862443 1.22318711969723 1 2.02187559503373 3384 16 1646 709 1294 871 3059 2944 940 1039 2053 1074 M8492 KEGG_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_APOPTOSIS.html Apoptosis 59/107 KEGG 0.0824733396200304 0.156982736433532 1295 1564.45454545455 1295 0.00779434187981105 813 1.49576243043716 1.49576243043716 1 2.68459154553175 1295 1352 2266 1104 3448 1818 1228 832 813 1899 1154 1075 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 0.0132543502757233 0.0425701750459487 1895 1704.09090909091 1295 0.00133340753510377 62 1.22168558101711 1.22168558101711 1 3.73803236374115 1893 1023 4420 405 482 916 2493 4327 62 1429 1295 1076 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 0.0488840534015645 0.113289156399471 1640 1497.81818181818 1295 0.00454593609743489 224 1.9415008500647 2.28398425076776 1 4.09847039298168 1640 1295 1043 866 1196 2601 2182 2793 224 402 2234 1077 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 0.0038089095517419 0.0167277883406397 1300 1295.27272727273 1296 0.000346865457365319 75 1.02649546033437 -1.02649546033437 -1 4.07021010312273 1296 75 964 97 209 1775 1363 2265 610 2964 2630 1078 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 2.21078651432187e-07 5.940972546776e-06 3855 2139.27272727273 1298 2.00980612407681e-08 170 1.26491156874537 1.37734200254724 1 14.7543799434892 3854 256 170 520 889 3089 4659 4022 1298 555 4220 1079 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 1.4672960357157e-12 1.56267027803722e-10 865 1084.45454545455 1298 1.33390548701516e-13 43 1.26328533004831 1.28113625996447 1 27.6489581587882 865 231 43 258 1891 1779 1298 2546 1302 95 1621 1080 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 2.61993692534433e-05 0.000339144321330484 3490 1739.81818181818 1299 2.38178920561854e-06 68 1.50157890217778 -1.61521516397382 -1 11.6281079638067 3490 68 327 687 186 2873 2472 2920 1299 214 4602 1081 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 0.0839184282471183 0.156982736433532 1015 1494.27272727273 1299 0.00793650793650794 684 1.11866354753463 1.14798703265885 1 2.00777519267518 747 1788 1716 2201 3790 1013 684 1299 1015 1318 866 1082 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 7.71594828472e-05 0.000796408230444888 1170 1388.81818181818 1302 7.01474446867684e-06 22 0.50491279453589 -0.50491279453589 -1 3.49219498107391 1170 1315 3093 1882 22 96 1302 411 2209 3581 196 1083 M5539 KEGG_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AXON_GUIDANCE.html Axon guidance 61/153 KEGG 0.0559556489544903 0.125099318225545 1130 1562.45454545455 1304 0.00522106189233612 313 1.21299140356355 1.21299140356355 1 2.44400672686455 1126 682 1304 1227 2037 3034 2619 1306 2246 313 1293 1084 M7407 KONDO_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_HYPOXIA.html Genes up-regulated in HSC-2/8 cells (chondrosarcoma) under hypoxic conditions. 16247469 5/9 Arthur Liberzon 0.0459432179728805 0.108349229703532 680 1656.72727272727 1304 0.00469216616783597 677 1.08196515182584 1.08196515182584 1 2.33076516966439 677 1919 4283 1941 2181 1186 1158 704 2112 1304 759 1085 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 0.0682859157387584 0.145449000523555 1310 1496.45454545455 1307 0.00640930746589775 616 1.53998695706705 -1.42279293755586 -1 2.87787626316655 1307 616 1480 1014 1179 1893 1229 2704 1602 977 2460 1086 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 0.0899671582384847 0.16630615522901 1315 1368.54545454545 1308 0.00853379596607508 230 1.34016355306373 1.4459108240657 1 2.33037558734073 1313 230 2452 1040 1308 2734 1330 1058 1305 748 1536 1087 M4013 KEGG_GAP_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GAP_JUNCTION.html Gap junction 39/107 KEGG 0.0103042817881563 0.035582803580914 1310 1429 1309 0.000941169407290901 390 1.42233913052235 1.73198783511034 1 4.59916627116709 1309 2841 1701 1522 390 2468 1398 539 970 1276 1305 1088 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 0.00499807205721894 0.0204907836046614 950 1459.27272727273 1313 0.000455405743536731 633 1.4127500584962 1.4127500584962 1 5.32391225988584 950 1137 738 2003 845 3492 1725 1490 1313 633 1726 1089 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 0.000739205504841028 0.00463090507444526 1495 1145.45454545455 1313 6.72230906035968e-05 76 1.07606607710567 1.09875256957753 1 5.60636686562839 1494 1313 2119 1290 76 1460 2304 605 189 355 1395 1090 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 0.00848658277706848 0.0307802839731756 1315 2067.09090909091 1314 0.000851916799336898 277 1.08918898596586 1.08918898596586 1 3.67499095114859 799 2996 4638 2599 4408 1312 277 336 3502 1314 557 1091 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 0.142811515112222 0.243350821751225 1670 1646.27272727273 1316 0.0152916222934444 827 1.63639951871907 1.63639951871907 1 2.24167455126676 1669 1662 4444 1316 1774 1308 827 1765 1046 1057 1241 1092 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 0.0578191658025112 0.128164905842274 2025 1214.09090909091 1317 0.00539973731257332 147 1.04801130870732 -1.01405746558881 -1 2.08700155355885 2022 160 1801 465 1317 2823 1462 739 147 776 1643 1093 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 0.00564163035007043 0.022634143681875 1890 1588 1318 0.000514195433911457 67 1.50186190336955 1.50186190336955 1 5.51490126483348 1890 67 745 230 623 3938 3714 1412 1318 954 2577 1094 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 0.000448071028213036 0.00319583080396695 1320 1396.45454545455 1318 4.07420283875938e-05 402 1.33988436390026 1.33988436390026 1 7.46259491122309 1318 402 528 445 1962 3805 1595 1775 887 1034 1610 1095 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 1.8319055094303e-07 5.04959365717082e-06 295 1187.18181818182 1318 1.66536878360929e-08 166 1.57155675652581 1.63997922440344 1 18.5788390633797 294 2071 166 1566 2485 1318 973 763 1450 629 1344 1096 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 0.00224683481875987 0.0112126389357921 410 1542.36363636364 1319 0.000224910977669831 157 1.06124507986413 1.06124507986413 1 4.6194994527061 406 1319 4384 1333 4045 215 595 157 2732 1615 165 1097 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 0.000279982242611562 0.00217939665926541 1115 1356.27272727273 1319 2.54561709822833e-05 197 1.29666034565926 1.39976893798889 1 7.70298352530163 1112 197 492 290 2538 2724 1319 799 1394 2087 1967 1098 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 0.0044007126962796 0.0186622078685667 715 1263.45454545455 1320 0.000400867298040216 228 1.33463874607908 1.45186810779345 1 5.15047833548572 715 2417 1865 1555 1648 966 907 228 1320 1559 718 1099 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 0.0839184282471183 0.156982736433532 985 1423.36363636364 1321 0.00793650793650794 422 1.85880784095809 1.85880784095809 1 3.33618475307142 985 3056 1321 1811 1378 2203 1610 985 422 584 1302 1100 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 0.0186830181113751 0.0558345809119283 1325 1446 1321 0.00171305381074815 43 1.04228334721982 -1.20074158169684 -1 2.91507648129335 1321 43 3210 978 558 718 2437 1290 1360 2611 1380 1101 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 0.000583587639378218 0.00387899528812245 850 1395.63636363636 1321 5.30675003181459e-05 555 1.24527652693821 1.46978440717235 1 6.7018258028113 848 1562 555 1783 2702 2248 1321 583 1479 955 1316 1102 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 0.00110502257315239 0.00629179233194348 1360 1285.18181818182 1322 0.000100507090709434 492 1.19305552184258 1.24844198897955 1 5.86144600651415 1357 1333 609 1322 492 3826 923 855 1526 496 1398 1103 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 8.41363605282875e-07 1.89874469431126e-05 1275 1581.90909090909 1322 7.64876297320421e-08 202 1.10620485986084 1.1800397924747 1 11.6573056993539 739 1359 202 1275 3764 1720 1273 1386 3062 1322 1299 1104 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 0.0268614341915826 0.072552769933493 1800 1449.09090909091 1325 0.00247228395353867 531 1.47120913201575 1.51443812851473 1 3.74118857587285 1798 572 950 1234 788 2795 1633 1708 1325 531 2606 1105 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 0.0765897756730953 0.156982736433532 2635 2032.90909090909 1326 0.00793650793650794 340 1.08023697533246 -1.08023697533246 -1 1.93880725447692 2632 512 4452 1238 3816 1001 1948 3904 340 1193 1326 1106 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 0.000382001238974632 0.00279696532161738 535 1783.45454545455 1326 3.82066921091894e-05 32 0.566840126122949 0.566840126122949 1 3.23030986130471 534 1326 4669 1731 2880 194 32 797 2319 4652 484 1107 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 0.000196250945204943 0.00168430756269297 3075 1835.90909090909 1328 1.78425867229341e-05 33 1.39054003500854 1.39054003500854 1 8.60802520243064 3074 794 2216 1328 33 2505 3897 850 817 1150 3531 1108 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 0.00963067245591846 0.0337037573774712 3095 1494.81818181818 1329 0.000879371970833644 667 1.31809611262803 -1.28017274735121 -1 4.3314104611323 3091 667 807 1455 1576 1157 2389 2270 850 852 1329 1109 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 0.000491710419347067 0.00344933386985084 1795 1442.09090909091 1333 4.47109412141076e-05 56 1.43991841944783 1.43991841944783 1 7.91320091791803 1793 729 1151 626 56 1333 2338 3337 536 1771 2193 1110 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 0.0126644233062325 0.0411549844750383 630 1626.36363636364 1333 0.00115799270695654 287 1.29577623699106 1.29577623699106 1 4.00719435047456 627 2935 1333 3424 2772 318 461 677 3226 1830 287 1111 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 0.0134835425625375 0.0430359473753244 1005 1506.63636363636 1333 0.00123335433852106 789 1.29070591278635 1.39061895307153 1 3.93560192041056 1002 2317 848 1192 1826 2909 1944 913 1333 789 1500 1112 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 1.71759022313847e-11 1.51860901615602e-09 1335 1329.90909090909 1335 1.5614456574108e-12 52 1.38811909792057 1.45011961570475 1 27.3214449373908 1335 399 52 71 3072 2440 1375 2606 753 283 2243 1113 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 0.00441147844494722 0.0186740632276627 3025 1997.36363636364 1337 0.000401849939264242 323 1.53650057396038 -2.17721575502115 -1 5.92853355143622 3023 323 729 931 1033 3289 1885 4110 1337 1011 4300 1114 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 0.0276335089552502 0.0738680108181988 2635 1706.54545454545 1337 0.00254425762045362 550 1.1565609164171 1.26886585032966 1 2.92091795163878 1250 2985 2345 2633 2631 803 1632 550 1310 1337 1296 1115 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 0.087259288588596 0.162003576198954 1090 1573 1338 0.00826595979063162 1088 2.05297122665945 2.05297122665945 1 3.62201942728343 1088 1840 1148 1590 2970 1858 1181 1215 1338 1804 1271 1116 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 0.0363532628611415 0.0907089402381838 1465 1321.18181818182 1338 0.00336074970345321 494 1.39272079860282 1.3776847291263 1 3.24009055345558 1461 1160 1502 587 2019 1960 2120 619 1273 494 1338 1117 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 0.0465941607895948 0.109334119909885 1575 1939.09090909091 1339 0.00432829776694356 946 1.35596671688246 1.40952420929673 1 2.90912482080807 1573 1339 1100 946 973 3852 3366 3573 958 1018 2632 1118 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 0.0531837203612079 0.120745597680533 1435 1650.09090909091 1339 0.00495587955056623 498 0.708876720161269 0.754623609306978 1 1.45262605467913 1433 844 1058 1118 1911 2131 941 1339 498 4647 2231 1119 M6220 BIOCARTA_AGR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGR_PATHWAY.html Agrin in Postsynaptic Differentiation 22/59 BioCarta 0.0240890918573276 0.0670722979884499 1270 1779.18181818182 1343 0.00221427027654234 462 1.42319670393316 1.42319670393316 1 3.72744801343518 1269 3098 1215 1722 665 2725 2581 3804 462 687 1343 1120 M15381 REACTOME_TCR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TCR_SIGNALING.html Genes involved in TCR signaling 25/65 Reactome 0.00465872371727368 0.0195091861833284 530 1185.09090909091 1344 0.000424419853190429 154 1.24300374604446 1.24300374604446 1 4.74337390152345 527 1520 2505 1542 1344 309 154 2055 1304 1486 290 1121 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 0.000123180924425595 0.00115977375308973 4215 1910.27272727273 1345 1.11988929118173e-05 4 1.16354182942751 1.2881997742422 1 7.62364014122064 4214 4 423 137 1345 2143 4336 3597 1018 1238 2558 1122 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 0.000894470993459612 0.0053944544084321 1350 1392.18181818182 1346 8.1348624780058e-05 594 1.35283593711986 1.40929901570837 1 6.84822127023593 946 1346 594 1255 775 2418 2005 2191 1346 640 1798 1123 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 0.0153125583680167 0.0473940875247863 815 1919.54545454545 1346 0.00154191066300257 306 0.573338202093629 0.749492479868813 1 1.69460658128718 813 2614 4511 3006 1346 476 306 586 2461 4431 565 1124 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 0.00508612298970011 0.0207790517260111 310 1258.90909090909 1348 0.000463447242249021 257 0.997661909079786 0.997661909079786 1 3.74615346719729 309 1348 1505 1652 257 455 997 2012 2768 2136 409 1125 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 0.0264717436353585 0.0719945389873997 1035 1385.36363636364 1348 0.00243597627804141 545 1.50946086826303 1.50946086826303 1 3.84976136627949 1032 1975 1184 1523 1348 2810 1746 545 731 801 1544 1126 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 0.00057644390399052 0.00385888019157083 995 1791.45454545455 1349 5.76593488012213e-05 51 0.47290131289661 0.537773828682907 1 2.54744221959995 993 2668 3910 3758 1349 224 729 296 2306 3422 51 1127 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 0.0310949157709414 0.0803182405974565 485 1539.90909090909 1352 0.00315387846147097 420 1.11882204112119 1.11882204112119 1 2.73481767285793 483 1652 3822 1352 1968 876 420 649 3315 1682 720 1128 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 0.0506875936371443 0.116489486897331 940 1769.09090909091 1353 0.00471768561715092 760 1.4806432823923 1.4806432823923 1 3.08562770496001 938 3437 1273 2620 1013 2362 1353 1141 2767 760 1796 1129 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 0.00543410389104455 0.0219329981338801 1355 1478 1354 0.000495233907669275 269 1.82051220676583 1.82051220676583 1 6.74052742880083 1354 1087 992 2016 269 3163 1884 673 1598 2069 1153 1130 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 0.0674819145135769 0.144063895859053 1920 1505.09090909091 1355 0.00633139291134912 857 1.18838851476838 1.18838851476838 1 2.23184307186809 1920 1083 1582 934 1170 2753 1199 1370 857 2333 1355 1131 M10462 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY.html Adipocytokine signaling pathway 32/102 KEGG 0.159409800598657 0.262241686633255 1360 1664.63636363636 1356 0.01566250297806 814 0.653874098340854 0.653874098340854 1 0.848345420300209 1356 814 2388 1190 2754 1419 835 1307 2061 3222 965 1132 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 0.00508311630531941 0.0207790517260111 975 1278.18181818182 1356 0.000463172637684353 674 1.33162841645363 1.53393852430569 1 5.00017527375759 972 674 740 817 1827 2133 1065 1624 1376 1356 1476 1133 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 0.000650400205170125 0.0042096344771094 1360 1435.72727272727 1358 5.91447788003465e-05 70 0.894203045134898 0.894203045134898 1 4.74151864946914 1358 1074 1601 1311 70 1160 747 3080 1405 2574 1413 1134 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 0.0581258274843317 0.128480013014895 925 1267.90909090909 1359 0.00542917104873184 137 1.4621944969237 1.40972244375442 1 2.90832236169351 922 1510 2233 788 1491 1952 2247 990 137 318 1359 1135 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 0.0135328840248105 0.0431101934332168 1365 2072.36363636364 1362 0.00123789572957619 447 1.1511533637635 1.30808939653964 1 3.50815691506575 4050 447 1112 538 461 1361 3745 4638 2358 1362 2724 1136 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 0.0990922017165283 0.180328565919865 1365 1366.72727272727 1363 0.00944172248648601 435 1.18125801460526 1.23698905792595 1 1.96137027555771 1351 435 2160 1446 1363 1946 1428 1320 1422 800 1363 1137 M3618 BIOCARTA_TNFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR1_PATHWAY.html TNFR1 Signaling Pathway 18/35 BioCarta 0.0276543957729547 0.0738816981710752 1310 1697.63636363636 1364 0.00254620543445082 379 1.73041933125535 1.73041933125535 1 4.36989819841442 1306 2882 2797 1742 3902 1364 383 800 379 2278 841 1138 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 0.0154356983328062 0.0476235672353166 1345 1327.54545454545 1364 0.00141318859824256 500 1.13302920780988 1.13302920780988 1 3.34357147910996 1345 1364 2199 1859 500 1373 786 873 1671 1894 739 1139 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 0.0203159870122361 0.0594632824105799 4630 1860.54545454545 1365 0.00186418706242843 181 1.19508751045349 1.25036346539482 1 3.26950165522926 4627 194 1545 1365 1266 181 4629 3141 909 1130 1479 1140 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 6.95268361972897e-09 2.90895316446875e-07 4465 1946.63636363636 1367 6.320621492456e-10 109 1.26958961554488 1.28488917862223 1 18.5213420718251 4464 263 109 302 324 2556 4158 3575 1367 307 3988 1141 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 0.0076949772120882 0.0285241321463343 905 1585.27272727273 1369 0.000702002236621105 228 0.603809180675161 0.672077082520047 1 2.08184326686954 901 2513 1369 3007 1673 590 330 372 2666 3789 228 1142 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 0.00534851886429434 0.0216248139759131 735 1294.18181818182 1369 0.00048741511989699 180 1.69748649654937 1.69748649654937 1 6.30830294771853 734 2291 2165 1983 1369 515 210 534 2137 2118 180 1143 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 0.0271677153275025 0.0730814661450497 1375 1517.45454545455 1372 0.00250082960704637 397 1.4940030260962 1.50854582501127 1 3.78863742495258 1372 669 953 1098 2765 3679 1769 974 1380 397 1636 1144 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 2.11538215286825e-05 0.000287324080241757 1375 1366 1374 1.92309317575581e-06 28 1.30404128802136 1.42385845129443 1 10.3079863834707 1374 28 317 125 1429 2530 2059 3012 560 585 3007 1145 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 0.0168781800469886 0.0513578907144083 1245 1549.63636363636 1375 0.00154627962187958 526 1.12971145825197 1.23683376363916 1 3.25111503316642 1244 1631 1141 938 526 3147 2974 1411 1716 943 1375 1146 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 0.0839184282471183 0.156982736433532 2000 1528.27272727273 1375 0.00793650793650794 490 1.20659898171861 -0.944688806950243 -1 2.16560154154465 1996 1375 1872 634 4217 490 2133 1531 549 1157 857 1147 M17636 KEGG_RENIN_ANGIOTENSIN_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENIN_ANGIOTENSIN_SYSTEM.html Renin-angiotensin system 9/30 KEGG 0.0765897756730953 0.156982736433532 1420 1587.81818181818 1378 0.00793650793650794 162 0.651890080887807 0.566247704365866 1 1.17001106864893 1419 625 3807 1378 2182 690 663 2579 162 3213 748 1148 M7923 REACTOME_SEMAPHORIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMAPHORIN_INTERACTIONS.html Genes involved in Semaphorin interactions 39/106 Reactome 0.00812136533430756 0.0297086010589893 1290 1827.36363636364 1378 0.000741045587169587 736 1.3602063309756 1.3602063309756 1 4.63614366417159 1288 3157 791 2353 3144 2610 1378 1283 2040 736 1321 1149 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 0.0318879604256735 0.0818777986601128 3755 1838.27272727273 1378 0.00294179668758008 486 1.98999443260629 1.98999443260629 1 4.82719195718824 3754 486 975 529 1132 3098 1855 2833 1230 1378 2951 1150 M1386 KEGG_PENTOSE_PHOSPHATE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_PHOSPHATE_PATHWAY.html Pentose phosphate pathway 14/33 KEGG 0.00759089358827192 0.0282308947259065 1660 1271.09090909091 1379 0.000692473861607496 95 1.15105473390125 1.17919760329693 1 3.98019310569526 1660 1379 2327 780 2054 1508 203 2541 95 967 468 1151 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 0.0186182291237625 0.0557120189488833 1305 1367.45454545455 1380 0.001707062228113 556 1.20347814615776 -1.09190043743444 -1 3.36847243301467 1302 1091 1829 1380 556 1795 1968 1505 1120 769 1727 1152 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 0.02058387235399 0.0599850907032322 3165 1818.54545454545 1381 0.00188900203888237 150 0.419637202869499 -0.385352712651176 -1 1.14448300526876 3161 150 3048 1381 601 1170 2580 1202 678 3818 2215 1153 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 0.0243866588595131 0.0677386923476161 760 1331.18181818182 1381 0.00224193201048266 368 1.22168558101711 1.22168558101711 1 3.18796934685454 757 1381 1907 1779 2506 395 368 842 1917 2119 672 1154 M3624 KEGG_GLYCOSAMINOGLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_DEGRADATION.html Glycosaminoglycan degradation 12/28 KEGG 2.42546566848527e-07 6.27941001244309e-06 4525 1782.09090909091 1383 2.20496903262647e-08 1 1.38619679944968 1.35827470555819 1 16.0946512276421 4524 1383 1820 667 1 2638 2762 1353 74 825 3556 1155 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 0.0550967239351003 0.123835591247835 1550 1609.63636363636 1384 0.00565124232331602 38 1.91509024629137 1.91509024629137 1 3.87748446898233 1549 2895 4249 527 3003 861 1384 1401 38 1188 611 1156 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 0.0324138843563306 0.082819772134005 1385 1831.45454545455 1384 0.00299104965505292 643 1.33824660116958 1.39343039985114 1 3.23138841433985 1384 1332 977 718 1225 4089 1648 4066 1791 643 2273 1157 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 0.0363478085920314 0.0907089402381838 1390 1583.18181818182 1386 0.00336023688588956 432 1.24967485985571 1.24967485985571 1 2.9073018169591 1361 1386 1293 1973 1870 1147 432 3500 1387 1922 1144 1158 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 2.35471782378065e-07 6.1800926073606e-06 1390 1188.54545454545 1386 2.14065279619303e-08 174 1.39027331777285 1.46778240338295 1 16.1634669022326 1386 294 174 787 1657 1403 842 2133 1955 988 1455 1159 M19428 KEGG_WNT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_WNT_SIGNALING_PATHWAY.html Wnt signaling pathway 77/178 KEGG 0.0839184282471183 0.156982736433532 3505 2058.45454545455 1389 0.00793650793650794 488 1.45201325922147 1.70737956528213 1 2.60607061681726 3505 793 1166 488 1389 1741 4248 2654 925 1177 4557 1160 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 0.194085819250245 0.304074272486341 835 1688.63636363636 1389 0.0194250379843047 833 1.05953235028159 1.05953235028159 1 1.22264785778316 833 1064 2443 2030 3256 1701 989 1149 2743 1389 978 1161 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 0.0518110757874724 0.118201899289238 1410 1227.90909090909 1391 0.00482482382065697 64 1.14406637407035 1.31725187100225 1 2.36802572063072 1406 64 1362 146 1029 1391 1431 2151 740 2140 1647 1162 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 4.37727415604736e-08 1.50822843347338e-06 340 1275.45454545455 1393 3.97934022103699e-09 132 1.33712292069244 1.46778240338295 1 17.3735369625102 339 1432 132 1393 2327 1864 755 1167 2227 756 1638 1163 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 4.18636741317652e-05 0.0004879929775658 965 1387.72727272727 1393 3.80586097949529e-06 357 1.49210763582452 1.49210763582452 1 11.0284835964318 964 891 357 750 2460 2414 1617 1393 2002 435 1982 1164 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 0.0330054946076508 0.0838871284921277 450 1537.63636363636 1394 0.00335062066647367 448 1.14505098292374 1.14505098292374 1 2.75067704917249 448 1394 4413 1019 1952 1128 779 908 1845 1616 1412 1165 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 0.00108861311327598 0.00628295545492121 1070 1551.90909090909 1395 9.90138326171789e-05 95 0.724095453604658 0.724095453604658 1 3.55844573467519 1070 724 2267 1431 95 1395 1701 1237 2195 3857 1099 1166 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 0.00268842457288536 0.0130270977533909 1240 1508.45454545455 1395 0.000244701408115542 157 1.4628893388006 1.4628893388006 1 6.15513352021651 1236 2752 1041 2510 157 2037 1395 379 1482 2512 1092 1167 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 0.0839184282471183 0.156982736433532 1100 1436.81818181818 1395 0.00793650793650794 383 1.23649481480558 1.39059940208002 1 2.21925852551604 1098 2907 2775 1396 1395 1214 688 1665 383 1463 821 1168 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 0.0662781411042081 0.142076564141957 935 1933.5 1396 0.00759067539199004 768 0.754878325985602 0.754878325985602 1 1.42785700092145 934 1603 4191 NA 1580 768 799 821 3520 3907 1212 1169 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 0.0308163868676923 0.0798261961647353 1400 1571.09090909091 1398 0.00284151865866397 577 1.30176089458974 1.37470663505106 1 3.18974222696655 1398 3589 1702 2250 921 2606 1522 577 836 936 945 1170 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 0.015090230472879 0.0468607157030558 920 1379.63636363636 1398 0.00138134021075693 259 1.08074411889492 -0.827628654622479 -1 3.20619442497607 917 2042 1635 2012 1339 259 1704 958 1398 2601 311 1171 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 0.010298772293821 0.035582803580914 300 1540.18181818182 1398 0.000940663806984718 298 1.12325977396557 1.12325977396557 1 3.63208629734686 298 2197 1398 1554 4528 525 485 536 2483 2295 643 1172 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 0.00160587112495749 0.00857515327147777 935 1310.09090909091 1399 0.000146094956008381 126 1.24349503394725 1.24349503394725 1 5.73605438194629 931 2479 1517 2304 1559 830 1399 126 1663 1220 383 1173 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 0.000212915339893375 0.00180419761797532 2330 1726.45454545455 1399 1.93578135062219e-05 465 1.44230237345848 1.54957395689089 1 8.83232440732175 2327 875 465 623 798 4649 2544 1584 1399 1143 2584 1174 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 0.0303105246496867 0.0790401327258942 885 1715.63636363636 1402 0.00279421500677488 430 1.58403833134116 1.58403833134116 1 3.89660934790421 884 2587 2803 2741 3635 872 713 914 1402 1891 430 1175 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 0.028390238112152 0.0750347748412546 2145 1629.63636363636 1403 0.00261485118487823 555 1.39054003500854 1.39054003500854 1 3.49071341299543 2142 1281 2321 1164 2714 2971 1646 555 712 1017 1403 1176 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 0.000286077071227196 0.00221946548968649 755 1292.72727272727 1404 2.60103889129142e-05 495 1.27025179363296 1.31334534978617 1 7.52366831333476 751 1123 495 1573 708 1674 1404 1100 2324 1438 1630 1177 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 0.000119552810529314 0.00113635795160317 840 1146.63636363636 1405 1.0869027980433e-05 24 0.951253972113462 0.951253972113462 1 6.25151620525751 838 459 1459 229 24 1504 1420 2383 743 2149 1405 1178 M1296 BIOCARTA_IL7_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL7_PATHWAY.html IL-7 Signal Transduction 14/27 BioCarta 0.0267761209745607 0.0724496719305781 1830 1220.63636363636 1406 0.00246433414599184 114 1.92006803294693 1.92006803294693 1 4.88525397933787 1827 1534 1645 159 696 2175 1517 1385 114 969 1406 1179 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 9.27440162535382e-05 0.000930617687717516 790 1393.18181818182 1407 8.43162965776932e-06 402 1.22490770424875 1.22490770424875 1 8.28708178237181 786 913 402 757 2210 1700 1407 2032 2168 1210 1740 1180 M19752 REACTOME_COMPLEMENT_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMPLEMENT_CASCADE.html Genes involved in Complement cascade 13/39 Reactome 0.0385382683067044 0.0950475396237982 1410 1600.81818181818 1408 0.00356639936177263 908 1.23608342732844 1.37200307782393 1 2.81970293612342 1225 1243 1007 1408 3379 1652 1039 1792 2548 908 1408 1181 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 2.21475566986712e-06 4.37904855231954e-05 2120 1822.72727272727 1408 2.01341627225506e-07 223 1.37218200283316 1.38970862738398 1 13.3487409427013 2117 1408 223 714 1195 4409 2393 2666 935 567 3423 1182 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 9.60029953102599e-06 0.000148963588087377 355 1325.27272727273 1409 8.72758311345923e-07 281 1.29305457687444 1.54876772465215 1 11.0444928911871 354 1227 281 1409 2696 1159 727 2054 1673 1490 1508 1183 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 2.11368306679254e-05 0.000287324080241757 1155 1477.18181818182 1410 1.92154852235769e-06 316 1.46394780040916 1.5186228458407 1 11.5719909571596 1152 1965 316 1194 1567 3954 1645 1410 941 499 1606 1184 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 0.0267484649425285 0.0724496719305781 710 1410.81818181818 1411 0.00246175718852255 706 1.48244011309988 1.48244011309988 1 3.77179159141101 706 1420 949 955 1636 2194 1744 1116 2346 1042 1411 1185 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 1.02018482872882e-06 2.22352842205733e-05 3715 2236.27272727273 1413 9.27441183463293e-08 209 1.26587219619778 1.34680169850041 1 13.1461469986553 3713 542 209 466 1044 4005 4020 4273 1413 311 4603 1186 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 0.00840569878301832 0.0305341895327317 1560 1356.90909090909 1415 0.000767089808424302 348 1.52653656684894 1.77616649844852 1 5.1625066868935 1556 2232 1783 1506 348 2005 670 1356 1415 1211 844 1187 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 0.215498203516185 0.329254835890722 1580 1715.63636363636 1416 0.0218225852383734 607 1.66409842843252 1.66409842843252 1 1.79195431272232 1578 607 1358 1271 3375 2337 1416 2983 1619 1218 1110 1188 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 1.85311365555476e-05 0.000258443172319334 1385 1602.18181818182 1416 1.68466296815192e-06 310 1.29866144405729 1.40518227066864 1 10.3988124683228 1385 1879 310 1416 1594 2748 980 3015 1020 886 2391 1189 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 0.0222792330577441 0.0636588329930419 1630 1494.09090909091 1417 0.00204619133477797 415 1.36525179683354 1.50110902348894 1 3.64480927198263 1629 415 918 896 1454 3391 2574 996 1417 449 2296 1190 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 0.00928159261849315 0.0328005603395617 1420 1601.63636363636 1417 0.000847362149266392 802 1.18695090805654 1.18695090805654 1 3.93170531713023 1417 1573 802 982 1189 3261 1898 1913 886 1321 2376 1191 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 0.00090799247533955 0.0054479548520373 2685 1913.54545454545 1419 8.25788583791543e-05 251 2.28524580999216 2.28524580999216 1 11.5463336997392 2682 1215 596 325 1419 4334 2696 3262 251 1132 3137 1192 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 0.000141367780294233 0.00128630955040539 535 1453.45454545455 1419 1.28524422849036e-05 437 1.24500330297055 1.34481743876465 1 8.03241698359581 531 1719 437 1817 1890 1586 1419 1397 2852 956 1384 1193 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 1.75438593586057e-06 3.60913880064106e-05 1460 1495.63636363636 1420 1.59489757717632e-07 218 1.24737017381823 1.3933677427324 1 12.3683501551634 1460 967 218 732 597 3114 2017 2470 1420 1104 2353 1194 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 0.00602103379976678 0.0237547012688006 3290 1893 1421 0.000548870525779084 285 1.32193709281541 1.32193709281541 1 4.79229267085375 3288 1421 2429 861 285 3362 2638 1002 1381 893 3263 1195 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 0.0839184282471183 0.156982736433532 1075 1327.36363636364 1422 0.00793650793650794 440 1.43173600756893 1.54890235164776 1 2.56967704438398 1071 702 1537 1694 2146 2613 925 1469 440 582 1422 1196 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 0.00601053275034713 0.0237481926375436 3020 1764.27272727273 1423 0.00054791063393751 138 1.21829805597304 1.35406103960741 1 4.41690354518075 3019 187 749 138 2499 1709 3910 1423 960 341 4472 1197 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 0.00676827254636294 0.0260395116192584 675 1499.90909090909 1423 0.000617198652768362 671 1.38652876995259 1.38652876995259 1 4.90302687333936 671 2130 764 2481 2266 2041 1345 1151 1423 747 1480 1198 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 7.41960334523081e-08 2.39781112246563e-06 900 1310.09090909091 1424 6.74509417769131e-09 141 1.30061900564127 1.36747702346567 1 16.3147440353008 896 401 141 279 1711 3550 2325 1752 1424 377 1555 1199 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 0.015266748750239 0.0472835324809122 875 1488 1426 0.00139761201119248 222 1.38029039009533 1.49564680855677 1 4.0828269051078 875 397 864 222 1426 3398 2090 1468 814 2403 2411 1200 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 0.0492734241850363 0.113966073904778 1180 1483.63636363636 1427 0.00458299045303843 87 0.976990603895162 0.888929544001141 1 2.05676642594494 1179 87 1069 1117 2719 2284 1724 696 1427 2270 1748 1201 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 0.057799428524495 0.128164905842274 765 1551.36363636364 1427 0.00539784320455719 448 0.896469743250519 -0.871408088998686 -1 1.78522286097702 762 1427 2517 2022 2121 448 843 738 2578 2944 665 1202 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 0.0388849474116983 0.095701083808413 1435 1594.09090909091 1435 0.00359906736071088 305 1.46778240338295 1.46778240338295 1 3.33849591920492 1435 305 1228 607 877 3705 2181 2202 1591 1242 2162 1203 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 0.0257214181565721 0.0704445151850947 1245 1560 1436 0.0023661052510007 812 1.59907249768005 1.59907249768005 1 4.11204438804524 1242 2264 946 1436 1778 3140 1800 812 961 1110 1671 1204 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 1.5793079057613e-05 0.000226319169614601 930 1327.54545454545 1436 1.43574476655378e-06 302 1.28476456092122 1.32550702310166 1 10.4528287710937 928 871 302 919 2080 2063 1481 1477 1436 735 2311 1205 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 0.00187203010954085 0.00963992647616308 955 1801.72727272727 1438 0.000170329542078171 655 1.22750804694095 1.21929938819813 1 5.52304457904373 952 4108 655 3377 700 2408 1438 1501 2392 1327 961 1206 M8066 BIOCARTA_IL22BP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL22BP_PATHWAY.html IL22 Soluble Receptor Signaling Pathway 9/17 BioCarta 0.0096685064616698 0.0338109114025259 910 1641.27272727273 1439 0.000971083187519291 173 0.701222236703204 -0.701222236703204 -1 2.30213673210977 910 734 3844 1664 3714 173 403 1439 1623 3284 266 1207 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 0.0839184282471183 0.156982736433532 1200 1345.54545454545 1439 0.00793650793650794 698 1.12299255866016 1.12299255866016 1 2.01554489355285 1198 1439 1594 1448 1708 1410 1134 994 698 1672 1506 1208 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 2.44480249789859e-06 4.73171834394693e-05 3470 2215.63636363636 1440 2.22255019522539e-07 227 1.34361428115007 1.37933245601338 1 12.9699523757354 3467 777 227 912 1099 3615 3342 4087 1440 890 4516 1209 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 0.0380534502959118 0.0940994554546927 2545 1859.45454545455 1446 0.00352073231796105 546 1.44786559051746 -1.19663412237733 -1 3.31688106388031 2542 1139 1005 1279 2528 4340 1309 1746 546 1446 2574 1210 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 0.000296703471184877 0.00227181775485676 4385 2074.72727272727 1446 2.69766812471796e-05 71 1.30284334384641 1.46778240338295 1 7.68726498277809 4384 71 501 1179 1446 2533 4192 3073 872 792 3779 1211 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 0.0775552837898924 0.156982736433532 1905 1539.54545454545 1448 0.0073120299927114 1171 0.933738422538257 0.933738422538257 1 1.67587193247926 1905 1171 1294 1425 1228 1407 1585 1836 1448 1923 1713 1212 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 0.0170788641746759 0.051867503255043 1435 1998.36363636364 1449 0.00156480987040822 668 1.2759851191679 1.35603327264138 1 3.65985316552683 1432 668 881 1196 2741 4053 2542 1449 2994 1213 2813 1213 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 0.0143897644094903 0.0452249738583982 4620 2049.72727272727 1449 0.00131679600051917 306 1.12429435965836 -1.06834400925129 -1 3.37411355416326 4617 427 1118 577 477 1449 4637 3846 2199 306 2894 1214 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 0.111661364526377 0.1983491865696 960 1334.27272727273 1450 0.0107061191835645 467 1.3367313703346 1.3367313703346 1 2.09610500137833 959 1531 1396 1492 1450 1184 1539 1113 2095 467 1451 1215 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 0.0375117125730347 0.0930052302207623 740 1519.81818181818 1450 0.00346972851358201 335 1.00744291305309 1.00744291305309 1 2.31934913861183 736 2010 1450 2235 2539 335 437 806 3596 1929 645 1216 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 0.0434096492535999 0.103573124441125 605 1691.36363636364 1450 0.00402642076291311 605 0.569376654595611 0.74069391417424 1 1.25142979089835 605 708 1188 1274 937 1806 1485 1450 2838 4512 1802 1217 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 0.00858219583900013 0.0310557196555006 1455 1779.36363636364 1451 0.000783259905500842 318 1.34839498309097 1.34839498309097 1 4.53792426051603 1451 3692 2753 2218 3942 1190 1062 318 630 1541 776 1218 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 0.0162208663892682 0.0496803790196804 4515 2178.09090909091 1452 0.00148561037193718 188 1.52436901329908 -1.27970579708832 -1 4.43594009956945 4512 821 876 731 826 3416 3863 3678 188 1452 3596 1219 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 0.154099884743495 0.257861638609555 1015 1619.54545454545 1453 0.0150988512072948 597 1.15003627356519 1.25439965474365 1 1.51084926027993 1015 1665 1324 2010 2149 3118 1453 1303 2280 597 901 1220 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 0.00392036319294252 0.0170415787774848 990 1690.45454545455 1453 0.000357033335724594 215 1.63956626671578 1.63956626671578 1 6.47159275390938 990 3307 1453 1497 4221 1654 1370 215 327 2642 919 1221 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 0.00618501890171668 0.0242535552915852 1455 1939.72727272727 1453 0.000563861458251778 662 1.61818818502305 1.61818818502305 1 5.83366516374643 1453 3975 753 2446 4160 2161 959 703 3323 662 742 1222 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 0.000870087340587741 0.00526773808526376 490 1401.90909090909 1453 7.91301496162104e-05 417 2.43075392216551 2.43075392216551 1 12.3607810588152 490 3266 593 1805 1808 1601 914 417 531 2543 1453 1223 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 0.00280443162300456 0.0134349503007636 1885 1284.90909090909 1454 0.000255273903798238 159 2.05369581223184 2.05369581223184 1 8.5795942103117 1885 2090 2544 407 1544 2190 872 166 159 1454 823 1224 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 0.0489932274995679 0.113486042542252 825 1733.81818181818 1454 0.00501081328036501 684 1.57416553838995 1.57416553838995 1 3.32038322079274 824 1653 4181 2046 3043 1454 1332 724 684 1701 1430 1225 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 0.027773446772868 0.0740309280874059 775 1302.54545454545 1454 0.00255730834050151 505 2.29602903400914 2.29602903400914 1 5.79376456397708 771 1911 1024 1454 716 1479 1261 1671 505 2071 1465 1226 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 0.0839184282471183 0.156982736433532 1715 1646.09090909091 1455 0.00793650793650794 531 1.29976408886268 1.3647370354902 1 2.33281409742761 1714 531 1455 547 1377 4301 2169 2248 851 994 1920 1227 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 0.00302783475729472 0.0141742594132698 1030 1494.36363636364 1456 0.000275637270780063 692 1.25940092561839 -1.05101944785383 -1 5.1959256647318 1026 2123 692 2406 964 736 1765 1456 2273 1647 1350 1228 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 0.0235586546904627 0.0662640191353589 1830 1456.72727272727 1457 0.00216498001698864 409 1.22325563308004 -1.03523601862632 -1 3.21816458922669 1829 1114 3068 1715 657 409 1581 1143 1457 2093 958 1229 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 3.98460779020207e-05 0.000466796802622172 3525 1944.18181818182 1457 3.62243632787726e-06 47 1.1901260657872 1.35757039204524 1 8.84770190767877 3523 186 354 236 1457 2639 3422 4571 669 47 4282 1230 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 0.00860396801942433 0.0310617828497861 1460 1500.36363636364 1457 0.000785254784517182 108 1.38776161390231 -1.13716001310254 -1 4.67014716367078 1457 2221 2476 2425 1987 108 1211 671 1017 2657 274 1231 M7151 KEGG_SELENOAMINO_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SELENOAMINO_ACID_METABOLISM.html Selenoamino acid metabolism 12/28 KEGG 0.0217629297705201 0.0624501462980141 1375 1789.27272727273 1458 0.00199829485631403 315 0.780328806349212 -0.780328806349212 -1 2.09774132581982 1375 3285 3506 2970 2183 315 386 1458 663 3173 368 1232 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 0.0298632656868822 0.078134708547588 2060 1830.63636363636 1458 0.00275241008260847 752 1.68373715897236 1.68373715897236 1 4.16066424371569 2057 1075 1458 1415 752 3332 1687 3071 1266 2575 1449 1233 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 2.51980758242548e-07 6.48781226991528e-06 3910 2427 1459 2.29073442821454e-08 177 1.2484525007859 1.26435614048225 1 14.4558395417233 3909 1280 177 1264 744 3499 4571 4287 1459 1063 4444 1234 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 0.0839184282471183 0.156982736433532 3255 2009.54545454545 1460 0.00793650793650794 342 1.75894475465316 1.75894475465316 1 3.15695067701776 3253 723 1460 500 1393 3700 3543 2918 342 1027 3246 1235 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 0.0269651197374887 0.0726616164979138 1815 1327.45454545455 1462 0.00248194661701824 245 1.61652873087285 1.62975304503366 1 4.10837781198737 1811 331 952 316 1335 1831 1512 2212 245 1462 2595 1236 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 0.0334680470666626 0.0848195070602384 1155 1507.63636363636 1462 0.00308984570009175 595 1.08029641710859 1.13671493397449 1 2.58354714322447 960 1849 1462 1937 1765 1151 1335 595 1977 2401 1152 1237 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 0.014747652457427 0.0460716662770018 3165 1711.45454545455 1463 0.0013497682625265 100 1.85499113911562 -1.24287224182961 -1 5.53365181713115 3164 100 856 1215 1352 1463 3385 1437 1641 1957 2256 1238 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 0.0545864268666154 0.123154548048609 1465 1397.27272727273 1464 0.00508998406010029 730 1.90919498657043 1.90919498657043 1 3.87575397392147 1464 1466 1648 1706 1054 1967 1463 802 1138 1932 730 1239 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 0.00326174205866871 0.0148971961860834 4665 2090.36363636364 1464 0.000296962546514445 188 1.17792676150608 -1.17792676150608 -1 4.8029884316 4661 1240 1464 676 188 3465 3991 3089 268 1032 2920 1240 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 0.000191389921256044 0.00164862715258423 1485 1355.81818181818 1465 1.74005975755036e-05 32 1.56296497389295 1.69666579578284 1 9.7078464359578 1483 915 1465 882 32 2641 2178 1787 1646 615 1270 1241 M1061 REACTOME_MEIOTIC_SYNAPSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_SYNAPSIS.html Genes involved in Meiotic Synapsis 50/198 Reactome 0.0241969584479106 0.0673319164411575 390 1534.72727272727 1466 0.00222429663443978 388 1.20074158169684 -1.20074158169684 -1 3.14032664950903 388 2229 1025 2361 1466 746 1732 627 2752 2438 1118 1242 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 1.05644608083813e-11 9.52020449001434e-10 1470 1404 1466 9.60405528039274e-13 5 1.38801392591019 1.47403925400368 1 27.9476367424329 1466 192 51 5 2563 3712 2175 2162 487 38 2593 1243 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 0.000456984825982687 0.00323478987092881 1160 1825.8 1471 5.07864075901453e-05 37 0.653320054436723 0.653320054436723 1 3.63104588882173 1159 2171 4186 NA 166 257 37 1783 4331 3903 265 1244 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 0.0412767244378647 0.100063492351699 2425 1579 1472 0.00382473979157539 335 1.19644414824747 -1.20074158169684 -1 2.66963724152791 2422 804 2072 1220 901 1582 3275 1223 335 1472 2063 1245 M17770 BIOCARTA_CELLCYCLE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELLCYCLE_PATHWAY.html Cyclins and Cell Cycle Regulation 11/30 BioCarta 0.103388914262708 0.18669766945474 665 1747.27272727273 1473 0.00987213673146149 663 1.39059940208002 1.39059940208002 1 2.26217587803286 663 1956 1473 1331 4359 1525 692 3305 1904 767 1245 1246 M12718 BIOCARTA_P35ALZHEIMERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P35ALZHEIMERS_PATHWAY.html Deregulation of CDK5 in Alzheimers Disease 10/19 BioCarta 0.0965608444004649 0.176682591511354 1475 1729.18181818182 1474 0.0091890218014288 508 0.493393016758395 -0.493393016758395 -1 0.829002352469507 1474 508 2542 1641 2611 710 830 1260 3451 3259 735 1247 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 0.000144230363465614 0.0013047557590731 1590 1624.72727272727 1475 1.31127109062645e-05 440 1.29434054147473 1.44912724989202 1 8.33286320956608 1586 786 440 694 1475 3364 3220 1101 1767 1044 2395 1248 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 0.0455296209608487 0.107536191442811 1135 1446.18181818182 1475 0.00422728244093907 250 1.07372076815065 1.12717105314373 1 2.32084440766903 1133 250 1768 329 955 2416 1475 2105 524 2751 2202 1249 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 0.00058341158724716 0.00387899528812245 1490 1361.54545454545 1476 5.83564809951119e-05 69 1.24349503394725 1.24349503394725 1 6.69223816871056 1490 1476 4335 1168 69 1718 723 1693 88 670 1547 1250 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 0.00557541693422773 0.0224260976427392 1480 1375.72727272727 1476 0.000508145176395962 274 1.16405023716204 -0.859238213420288 -1 4.28486155671765 1476 673 1974 580 274 1926 1498 1868 1307 2925 632 1251 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 0.0129474933671842 0.0418716038085749 2255 1893 1477 0.0011840296425663 444 1.23336035179737 1.23230347512712 1 3.79353499863324 2251 2026 1373 1368 444 3909 2977 796 1477 1469 2733 1252 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 0.120405867649149 0.211398237468682 1710 1648.54545454545 1478 0.0115954028146266 1204 1.56715355388622 1.56715355388622 1 2.36063943719216 1284 1204 1391 1218 1503 2742 1710 2644 1708 1252 1478 1253 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 0.0765897756730953 0.156982736433532 3105 2210.09090909091 1479 0.00793650793650794 108 1.36581529303493 1.36581529303493 1 2.45136267218221 3105 1261 4151 1449 1479 4432 3678 1198 108 1298 2152 1254 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 0.001012365841217 0.00596722809049415 990 1989.27272727273 1480 9.20756361993659e-05 97 2.31622896548935 2.31622896548935 1 11.4984743828823 989 4379 2675 3396 3934 1480 1323 97 719 2296 594 1255 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 0.0638197393743507 0.137941653526616 1190 2021.18181818182 1481 0.0065730260243402 118 1.08196515182584 1.08196515182584 1 2.07751926122587 2693 1481 4303 436 1190 3939 3778 1720 118 1190 1385 1256 M1053 KEGG_HEDGEHOG_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEDGEHOG_SIGNALING_PATHWAY.html Hedgehog signaling pathway 22/61 KEGG 0.0439457097449881 0.104692219555167 3430 1472 1482 0.00407717281258868 130 1.30268953776633 -0.941280647100138 -1 2.84960382470813 3430 130 1482 315 940 1827 2323 2446 226 686 2387 1257 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 0.116455777147478 0.205696106940476 830 1592.63636363636 1483 0.0111927025613654 828 0.926754241224634 0.926754241224634 1 1.42055461852848 828 919 1567 1463 1483 2036 1969 1064 2986 1805 1399 1258 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 4.31927725907928e-06 7.60907264512989e-05 3035 1939.27272727273 1483 3.92662339924865e-07 248 1.29405622123315 1.44674290303054 1 11.8956865929915 3031 1035 248 441 1593 1315 3990 2434 1483 1127 4635 1259 M1469 BIOCARTA_LYM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LYM_PATHWAY.html Adhesion and Diapedesis of Lymphocytes 6/14 BioCarta 0.0604640200440037 0.132585118355733 750 1950.18181818182 1484 0.00621750720330535 586 0.617571945201239 0.617571945201239 1 1.20953049340071 749 2577 3812 2476 1484 755 586 1086 3784 3238 905 1260 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 0.013817224350691 0.0439263998014504 3120 1803.18181818182 1484 0.00139038958325567 48 1.48034281358945 1.48034281358945 1 4.484453333788 3119 1264 4188 377 496 3566 1793 1484 48 1050 2450 1261 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 0.00996035677211704 0.0346505061871867 4190 1954.36363636364 1485 0.000909612686857069 291 1.11632157451245 1.06004156972285 1 3.63838043792232 4186 291 812 699 1485 2399 3352 3246 473 1036 3519 1262 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 3.91864968588261e-07 9.6140274492387e-06 1035 1711.09090909091 1485 3.56240943988581e-08 186 1.43948053921943 1.54608561903803 1 16.1189833324357 1034 2675 186 2240 1440 3829 2163 1419 1485 373 1978 1263 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 0.0839184282471183 0.156982736433532 1360 1711.63636363636 1486 0.00793650793650794 389 1.16533572062244 1.16533572062244 1 2.09154231955195 1360 1584 2303 1099 2331 1069 1189 3737 389 2281 1486 1264 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 0.000699827364798231 0.00443160950195204 520 1728.45454545455 1486 6.36409164925196e-05 517 1.34108731882781 1.34108731882781 1 7.04432634051401 517 3712 571 3470 1899 1486 984 520 2796 2088 970 1265 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 0.0839184282471183 0.156982736433532 1640 1811.27272727273 1488 0.00793650793650794 352 1.6253539910862 1.77114886650694 1 2.91718223040562 1638 3663 2558 2642 1309 1488 1136 3166 352 899 1073 1266 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 0.0425421525570951 0.101918469776354 2315 1661.18181818182 1489 0.00394434441719973 502 0.529505947752146 -0.529505947752146 -1 1.1720640331453 2315 502 3003 1081 1854 716 1489 1588 1242 3967 516 1267 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 0.0139638479476033 0.0442125618124791 1845 1346.18181818182 1489 0.00127757045513243 196 1.43795835936629 1.87732439546944 1 4.34700587618384 1841 690 1489 225 467 2124 1853 2091 196 962 2870 1268 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 0.0128265728530585 0.0415666116109489 1540 1429.54545454545 1490 0.0011729064785919 306 1.192242826745 1.10502207810623 1 3.67551546430972 1540 785 3033 1490 441 306 1713 1467 1718 2084 1148 1269 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 0.0309244114001044 0.0800617634369554 2085 1657.63636363636 1491 0.00285162304257725 771 1.38415464896347 1.58135927224541 1 3.38768055150048 2084 1000 1618 923 771 3005 1038 2534 1182 1491 2588 1270 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 0.0839184282471183 0.156982736433532 1190 1559.63636363636 1492 0.00793650793650794 444 1.36195127453835 1.36195127453835 1 2.44442753918447 1189 1640 2120 1233 3079 2312 1492 1605 444 618 1424 1271 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 0.000665760474999669 0.0042794973742777 1495 1583.18181818182 1492 6.05420028877957e-05 210 1.3034671435059 1.32768465797087 1 6.89084838855332 1492 1604 566 1144 1200 4213 2029 1790 1443 210 1724 1272 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 0.0319506507494939 0.0819489597220188 1375 1675.90909090909 1492 0.0029476663821238 589 1.58200606812555 1.58200606812555 1 3.83618960559451 1371 2250 1318 1732 3287 2585 1418 589 1618 775 1492 1273 M2064 BIOCARTA_41BB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_41BB_PATHWAY.html The 4-1BB-dependent immune response 10/25 BioCarta 8.8460219268938e-05 0.000889537741403956 1495 1761.54545454545 1493 8.04216148936317e-06 23 0.653874098340854 0.653874098340854 1 4.45238281003339 1493 2251 3219 1261 23 1587 852 1284 2605 3334 1468 1274 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 0.00252654466582859 0.0124102602768058 3925 1574.27272727273 1494 0.000229950081609508 153 1.24227746351936 1.30303158790231 1 5.28531627120997 3922 419 2091 1051 153 197 2851 2523 1494 1045 1571 1275 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 0.0139491841345347 0.0441959951686474 610 1654.90909090909 1494 0.00127622023910126 423 1.57326158207239 1.57326158207239 1 4.75660447765284 608 2759 1494 2480 4509 979 745 423 1775 1670 762 1276 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 1.69951399580741e-05 0.000240345480181042 1615 1737.09090909091 1494 1.54502465891194e-06 304 1.11251142925431 1.26746599162887 1 8.98653570637681 1612 411 304 1494 854 4313 2677 1461 1807 1354 2821 1277 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 0.0021778105715007 0.010926360104981 1350 1639.09090909091 1498 0.000198179037175459 573 1.3610313752518 1.67912614863458 1 5.95856150356698 1346 2310 667 1044 2097 3506 1566 1498 912 573 2511 1278 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 0.060933878494748 0.133365789176268 1655 1303.36363636364 1499 0.00569909684592549 276 1.86280643978199 1.86280643978199 1 3.63775361524593 1654 371 1499 936 2269 2246 565 2047 276 1774 700 1279 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 0.00343352270060616 0.0154855508903181 1500 1320.90909090909 1499 0.000312626646394002 189 0.932484516423559 1.07367039677876 1 3.76718853596341 1499 1797 1806 977 823 1947 888 189 211 2337 2056 1280 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 0.120061017028658 0.211188410584194 2930 1908.27272727273 1499 0.0115601808661397 976 1.28345509699291 1.50960451079176 1 1.93453336260159 2927 1196 1348 976 1499 1136 4530 2513 1661 1246 1959 1281 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 0.0708905282686896 0.149636493453639 1960 1602.27272727273 1500 0.00666213698455523 348 1.50592471725351 1.50592471725351 1 2.77279020920731 1960 1156 2888 854 3100 1563 610 1500 348 1402 2244 1282 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 0.00292205755936932 0.0138871822750554 810 1649.09090909091 1500 0.00026599508107142 171 1.25675177414939 1.25675177414939 1 5.20992171607953 808 3591 1500 2612 2299 1411 1075 171 2026 1833 814 1283 M9726 KEGG_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PANCREATIC_CANCER.html Pancreatic cancer 43/90 KEGG 0.00109945016496701 0.00628295545492121 1505 1394.36363636364 1502 1e-04 65 1.22306464608966 1.22306464608966 1 6.01054619455915 1502 457 1544 65 2642 3087 1957 1844 439 488 1313 1284 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 0.00176916216898199 0.00921143769316625 890 1455.81818181818 1502 0.000160962406399037 653 1.41856303890978 1.41856303890978 1 6.44519589432867 889 1883 653 1441 936 2193 1382 1502 1751 1538 1846 1285 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 0.0605919743934232 0.132803550985772 1440 1712.45454545455 1502 0.00566619188167263 764 0.46058914650926 0.488846619251094 1 0.901340731413083 1438 836 2389 1502 1111 1584 764 788 2326 4081 2018 1286 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 0.0250498249557808 0.0690491057310524 1485 1800.18181818182 1503 0.00230360732470691 677 1.07931485402238 1.07931485402238 1 2.7964096986289 1484 1503 1704 1437 677 2142 804 3000 3070 2898 1083 1287 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 0.0257732360863965 0.0705452011103119 1255 1998.63636363636 1504 0.00260771252291146 387 1.21455215107271 1.21455215107271 1 3.12156175363224 1254 2337 3902 2033 1134 850 387 4548 2591 1504 1445 1288 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 0.00109945016496701 0.00628295545492121 3295 1839.90909090909 1504 1e-04 35 1.31195024575003 1.45820077972264 1 6.44735957519848 3291 393 635 35 1504 2516 3183 2799 787 569 4527 1289 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 0.0478959490148857 0.111661899046644 1500 1764.63636363636 1504 0.0044519653012765 297 1.29274391329344 1.33772615635313 1 2.74708651065672 1497 3043 1386 1504 1383 2827 1863 1470 1998 297 2143 1290 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 0.000304501021074891 0.00232392798820348 845 1500 1505 2.76857431903889e-05 419 1.46892551150462 1.40741216185702 1 8.6349213056759 841 2093 503 1016 3521 1505 1561 2084 419 1219 1738 1291 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 0.0480253411233716 0.111685731267553 780 1536.45454545455 1505 0.00446426571560189 657 1.23190057653592 1.29900125720664 1 2.61753932075739 1958 780 1071 657 988 3898 1542 1565 2159 778 1505 1292 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 0.0936631472446404 0.172187331497993 2110 2034.54545454545 1507 0.0089005390337354 380 1.50529192834922 1.50529192834922 1 2.5668055315426 2110 1507 1223 844 2649 4354 4254 1008 1171 380 2880 1293 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 0.0255670754724765 0.0702012764987435 4245 2352.18181818182 1508 0.00235173877891191 851 1.29363022823277 1.22111377241975 1 3.33093117394217 4244 1341 942 1364 1508 2173 4027 4607 1011 851 3806 1294 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 0.000649373049141342 0.00420879959650945 935 1414.09090909091 1509 5.9051345777124e-05 422 1.25167601467609 1.38777848598963 1 6.63726251603906 935 422 563 1212 1587 2132 1992 1073 2185 1945 1509 1295 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 0.000988975501292588 0.00585143838264781 1510 1717.18181818182 1509 8.99473054288005e-05 504 1.65710293175984 1.17095805733795 1 8.25784411851401 1703 1509 603 1935 504 2428 1506 3847 1311 1091 2452 1296 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 0.00959411130938719 0.0336009010431901 2620 1575.54545454545 1510 0.000876018916600198 375 1.08051553643496 1.03545563767509 1 3.55389544512851 2620 1337 1867 2316 375 627 2416 992 1798 1473 1510 1297 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 0.0179256226529031 0.0538471524519325 1350 1620.36363636364 1511 0.00164303354157997 546 1.17435894638961 1.27175482806694 1 3.32572502303454 1347 1554 2633 1363 546 2685 1400 1511 1754 1441 1590 1298 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 0.0248005626792051 0.0686041539048142 1430 1976.27272727273 1512 0.00228042113486448 940 1.45881951648203 1.5108267338209 1 3.78881447020445 1430 1775 940 1341 1001 4303 2516 2929 1512 1144 2848 1299 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 0.168563944079865 0.271626768211226 785 2064.18181818182 1514 0.0166418670364991 781 1.11115653532883 1.11115653532883 1 1.40375811588679 781 3660 1339 3586 1705 1514 1057 1276 3455 2980 1353 1300 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 0.0386437150852824 0.0952073863773046 1515 1678.27272727273 1514 0.00357633460819753 631 1.42102809493493 1.50397996669576 1 3.23927660509383 1514 2262 1175 2212 1014 4504 1656 631 742 763 1988 1301 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 0.00333997203915292 0.0151511219510848 1175 1553.72727272727 1514 0.000304095771373073 190 1.22655556879527 1.22655556879527 1 4.98117752742662 1172 1429 1842 1994 190 2592 1805 1514 1509 1393 1651 1302 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 0.0650300804286709 0.13993422738454 3350 1870.81818181818 1515 0.00609416585334958 97 1.26556114324707 1.26556114324707 1 2.41245503938831 3350 1648 2587 1086 1149 4419 1515 971 97 830 2927 1303 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 3.98272554208949e-23 2.07367243224793e-20 115 1327.45454545455 1515 3.6206595837177e-24 9 1.40183550993445 1.42392236600448 1 61.5848144705821 114 2414 9 1443 2382 1535 1113 1515 2240 312 1525 1304 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 0.00130426391311255 0.00722432706482909 980 1325.63636363636 1515 0.00011863979861307 500 1.89912963937595 -1.95422089908583 -1 9.07594653094289 978 1515 628 1617 1577 1608 1251 1918 500 986 2004 1305 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 0.0310996020500786 0.0803182405974565 3810 1982 1516 0.00286801217867993 392 1.3836440567664 1.58848878837379 1 3.3821412881934 3810 400 1516 392 774 2109 4105 3286 802 418 4190 1306 M917 BIOCARTA_COMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_COMP_PATHWAY.html Complement Pathway 12/24 BioCarta 0.0236662999027533 0.066367613012748 1520 1642.27272727273 1517 0.00217498085466801 826 1.23608342732844 1.37200307782393 1 3.25004053101307 1517 1173 929 1407 2348 2186 1467 1941 2541 826 1730 1307 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 0.0839184282471183 0.156982736433532 2070 1801.27272727273 1518 0.00793650793650794 792 0.413362459071939 -0.410796906393369 -1 0.741902149814783 2070 922 2446 1998 1515 792 1518 1881 987 4511 1174 1308 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 0.00717133110857955 0.0271225646285745 2020 1877.18181818182 1519 0.000654074064262795 515 1.85327685125833 1.85327685125833 1 6.48033077975381 2019 1205 778 515 3663 3107 1519 3244 662 1236 2701 1309 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 0.0464582714015657 0.109113869654205 1885 1649.09090909091 1520 0.00474591153207508 46 1.9366898762468 1.9366898762468 1 4.15880826698248 1884 1256 4416 1018 2098 2000 1317 709 46 1520 1876 1310 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 0.00895947930147158 0.0318964689257877 785 1472.36363636364 1521 0.000817834190376037 219 1.62625951203323 2.04381891236962 1 5.43094886353677 782 2274 1392 2588 2525 360 219 1521 1732 2023 780 1311 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 0.00105768642663432 0.0061722522978934 1525 1625.27272727273 1522 9.61995699470916e-05 607 1.20991354401041 1.37131173383025 1 5.96676551266878 1522 1606 607 748 999 4559 2604 791 1739 784 1919 1312 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 0.00351838283482543 0.015747031484233 1265 1491.54545454545 1524 0.000320365662882873 201 1.38456010281246 1.38456010281246 1 5.57107789981366 1264 2471 2038 1524 201 2579 2253 740 634 804 1899 1313 M287 BIOCARTA_ERK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK_PATHWAY.html Erk1/Erk2 Mapk Signaling pathway 21/54 BioCarta 0.0278085118798618 0.074082255070513 2290 1799.45454545455 1525 0.00256057880980702 174 1.84083109373717 1.84083109373717 1 4.64388835315756 2287 1525 2468 618 719 3998 2428 1263 174 1330 2984 1314 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 0.0570761030253941 0.127011840748569 1740 1530.81818181818 1525 0.00532845340667262 516 1.09945947580126 1.15096560885139 1 2.19908641826774 516 2495 1508 2755 1737 1568 551 1161 1525 1739 1284 1315 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 0.081512942709462 0.156982736433532 885 1488.81818181818 1525 0.00769997175391155 693 1.62792362819257 1.62792362819257 1 2.92179421016306 882 1882 1525 1226 2227 1590 988 1639 932 2793 693 1316 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 9.85213039723985e-06 0.000151865404741664 850 1512.45454545455 1528 8.95652228884694e-07 283 1.13246668690848 1.231120671785 1 9.65167001149608 849 1335 283 2269 2190 1717 1472 1571 1528 1451 1972 1317 M10277 MULLIGHAN_NPM1_SIGNATURE_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_SIGNATURE_3_UP.html The 'NPM1 signature 3': genes up-regulated in pediatric AML (acute myeloid leukemia) with mutated NPM1 [GeneID=4869] compared to the AML cases with intact NPM1 and MLL [GeneID=4297]. 17597811 235/533 Arthur Liberzon 0.0146974725159962 0.045945534496303 2335 1766.18181818182 1529 0.00134514452322124 484 1.16701842258236 1.21233377763919 1 3.48445129728257 2333 1188 1050 1387 484 3470 1676 2350 1529 882 3079 1318 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 0.0839184282471183 0.156982736433532 1600 1724.63636363636 1530 0.00793650793650794 380 2.18140227549663 2.18140227549663 1 3.91517662638503 1600 3757 2466 1263 2964 1663 802 1156 380 1390 1530 1319 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 0.0363915309619056 0.0907561011641776 2085 1478.72727272727 1530 0.00336434779488231 136 1.36545822260096 1.36545822260096 1 3.17597766891691 2083 838 1773 581 850 2658 1530 2619 136 974 2224 1320 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 0.151440475811012 0.254320272421057 1530 1684.27272727273 1530 0.0148177607048143 980 1.1882728188326 1.22253038329772 1 1.57701024373111 1530 1334 1873 1058 1642 3597 1820 1345 2244 980 1104 1321 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 2.48999599582285e-09 1.22822328804483e-07 1820 1748.09090909091 1532 2.26363272603734e-10 91 1.25829216488581 1.40241041952818 1 19.4081666262514 1820 1118 91 881 1256 4029 2343 2506 1532 375 3278 1322 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 0.0483021008563759 0.112106807633966 2160 1737.90909090909 1533 0.00449058045543568 77 1.29860236402378 1.49513872315112 1 2.75453030657557 2157 1533 2708 744 991 4198 2596 1096 77 1031 1986 1323 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 9.00563255150056e-11 6.91809739939863e-09 2375 1882.36363636364 1534 8.18693868351748e-12 59 1.36345662788492 1.45210940317158 1 24.8320028951158 2372 649 59 373 1534 4387 2971 3301 852 103 4105 1324 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 0.00380784371639428 0.0167277883406397 1525 1540.09090909091 1535 0.000381438434872059 58 1.33239188503372 1.33239188503372 1 5.28313579686744 1521 2370 4212 1535 224 2267 2300 404 58 491 1559 1325 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 0.000775900288844869 0.00476522772415079 2265 1684.36363636364 1536 7.05612790965133e-05 486 1.15233272712668 1.12006015741323 1 5.97178301022225 2261 1345 586 1299 486 1817 3155 1361 1536 2311 2371 1326 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 0.00931423209652209 0.0328743726165795 1540 1398.36363636364 1536 0.000850354680077079 112 1.22249555986577 1.42381182422547 1 4.04678128508687 1536 2120 2174 2072 1546 112 1516 1722 1002 883 699 1327 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 0.00778251291176846 0.0287156342555488 1640 2030.54545454545 1537 0.000780990339234786 317 0.453887475403523 -0.490502992778268 -1 1.56199189396749 1639 1024 4382 1537 3720 925 571 317 3206 4187 828 1328 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 0.06900732014583 0.146718830400798 1160 2204 1537 0.0064792697300242 783 1.02071507325002 1.04822737752204 1 1.89887797235918 1160 3755 3039 3561 3560 1355 1523 783 3178 1537 793 1329 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 0.0146883955620646 0.045945534496303 1215 1408.27272727273 1539 0.00134430816669796 483 1.1395890173864 -0.880581973244883 -1 3.40255333862817 1215 966 914 1539 483 1704 1429 1742 1722 1658 2119 1330 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 0.0101671270081509 0.0351869698376624 1200 1536.18181818182 1542 0.000928583623157614 329 1.82051220676583 1.82051220676583 1 5.90640851280663 1197 1542 2202 2277 415 2790 2641 354 329 1836 1315 1331 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 0.335032276405471 0.455986420922462 1480 1787.72727272727 1542 0.0364129371013393 1196 1.04724017567139 1.16257948866079 1 0.797152608355269 1478 1617 1608 1317 3189 1336 1196 1542 2537 2614 1231 1332 M17673 KEGG_CARDIAC_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CARDIAC_MUSCLE_CONTRACTION.html Cardiac muscle contraction 33/118 KEGG 0.0122951794320832 0.040344087099964 1480 1847.54545454545 1545 0.00112403965551177 411 2.1927370036273 -2.59443856790082 -1 6.82334675324506 1480 3230 835 3452 3181 411 1051 1910 2141 1087 1545 1333 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 0.0784881495936026 0.156982736433532 1060 1729.45454545455 1545 0.00740333584587045 1059 1.1326658119887 1.1326658119887 1 2.0329064301018 1059 1684 2933 2360 1232 1278 1545 2137 2164 1459 1173 1334 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 0.0391422780378039 0.0958811891715364 790 1537.81818181818 1545 0.00362332286998572 447 1.91509024629137 1.91509024629137 1 4.35241494466331 788 2472 1864 1545 2162 800 447 926 2467 2530 915 1335 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 0.0509838441171047 0.116659769173622 1560 1743 1546 0.00521927763211777 546 1.60817712248608 1.60817712248608 1 3.34912839324319 1559 1097 3905 579 4614 553 546 2104 1074 1596 1546 1336 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 0.0204491898914905 0.0597412118650403 1550 1591.09090909091 1548 0.00187652525051408 473 0.991994357949613 0.868544559416011 1 2.70939880047109 1548 473 901 1743 950 2459 1139 1148 3336 1958 1847 1337 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 0.0839184282471183 0.156982736433532 1415 1587.54545454545 1548 0.00793650793650794 675 1.2932315236443 1.38724353457838 1 2.32108946188409 1411 1555 1983 818 1887 2872 1548 1538 858 675 2318 1338 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 0.0794248463995967 0.156982736433532 1435 1920.36363636364 1548 0.00749510125051706 1000 1.12785072559788 1.12785072559788 1 2.02426432226887 1000 2430 1433 3251 1239 1548 1159 1723 3239 2670 1432 1339 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 0.0694379607971128 0.147300264506687 525 1846.81818181818 1551 0.00652105703236297 522 2.46711003640163 2.46711003640163 1 4.58020745625769 522 2770 1171 2031 4641 1510 776 1551 1372 2352 1619 1340 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 0.232850105696956 0.34496857265126 1020 1802.18181818182 1552 0.0238095238095238 1019 1.16186250822327 -1.16186250822327 -1 1.19862536994209 1333 1905 1530 1491 3809 1019 1020 2237 1599 2329 1552 1341 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 0.000517293553729757 0.00355569747117567 1895 1628.90909090909 1553 4.70377478903847e-05 209 1.48519277692885 1.62674730942889 1 8.11828891789918 1894 209 544 534 1553 4476 2248 2527 694 699 2540 1342 M4086 KEGG_PROPANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROPANOATE_METABOLISM.html Propanoate metabolism 16/36 KEGG 0.00642571166351731 0.0250090405774436 2165 1635.81818181818 1554 0.000585868804160354 145 1.12944303899208 -0.967459383376804 -1 4.03812812122024 2381 145 2163 479 294 3201 1554 1028 1149 2161 3439 1343 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 0.00184771340650047 0.00955671636077397 1555 1883.45454545455 1554 0.000184925152691724 32 2.24458518468169 2.24458518468169 1 10.1181390207032 1554 3854 4208 1908 4399 1612 887 149 32 1299 816 1344 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 0.0343452646312131 0.0867571308099926 1500 1808.72727272727 1555 0.00348879251750228 375 0.300355059068805 -0.302684607491424 -1 0.71172824994048 1496 375 4053 2015 1712 621 438 1555 2593 3678 1360 1345 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 0.00354751494233825 0.015847144918777 1055 1612.81818181818 1557 0.000323022571047919 124 1.28764553317412 1.32072403084834 1 5.17321109830939 1054 1822 888 1254 1285 3512 2073 1557 2224 124 1948 1346 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 0.00134674855012582 0.007407117025692 1040 1489.09090909091 1559 0.000122506698258914 103 0.976317039310719 1.03052789434369 1 4.64217540208715 1038 543 2533 907 103 2231 1559 1830 1007 2205 2424 1347 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 0.013349564165025 0.0427880011472688 1110 1780.63636363636 1561 0.00122102400053087 139 0.999239398941921 -1.19351853194667 -1 3.05246287802834 1108 1561 3581 2858 1275 139 672 1595 3254 3055 489 1348 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 0.0464740821855092 0.109113869654205 1115 1909.27272727273 1561 0.0043168982502004 970 1.13062463652535 1.13062463652535 1 2.42788024186152 1115 1422 1722 1561 970 2422 977 3463 3334 2679 1337 1349 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 0.161385165508919 0.262241686633255 2300 1774 1561 0.0158730158730159 1045 0.986369348270618 -0.55936453995665 -1 1.27972941807499 2297 1245 2845 1165 1772 1045 1107 3435 1114 1928 1561 1350 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 0.00120591180440599 0.00676754816221133 1565 1478.90909090909 1562 0.000120656670511389 70 0.62315299528318 0.810314968904444 1 3.01750249078075 1562 642 3945 1695 195 840 70 1877 166 3490 1786 1351 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 0.0839184282471183 0.156982736433532 3755 2083.36363636364 1562 0.00793650793650794 524 1.16764366135614 1.26414127442254 1 2.09568460716088 3755 524 3000 1181 1422 634 4600 2268 930 3041 1562 1352 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 0.00120591180440599 0.00676754816221133 1565 1521.36363636364 1563 0.000120656670511389 71 0.62315299528318 0.810314968904444 1 3.01750249078075 1563 643 4098 1696 196 841 71 1903 167 3770 1787 1353 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 0.0839184282471183 0.156982736433532 1565 1664.27272727273 1563 0.00793650793650794 687 1.28504574290004 1.46778240338295 1 2.30639763828076 1498 2498 1563 1564 1518 3141 1593 1047 687 1998 1200 1354 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 0.0240457237701526 0.0670304946977604 1530 1454.63636363636 1564 0.00221023943314309 352 1.20248455500144 1.20248455500144 1 3.15011471613003 1527 352 1787 1797 663 2150 1864 1564 786 1117 2394 1355 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 2.93170069224285e-05 0.000369299716232527 1835 1632.36363636364 1565 2.6652179641435e-06 334 1.98332619607396 1.98332619607396 1 15.1949600021765 1831 689 334 738 1510 3392 2192 2881 770 1565 2054 1356 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 0.0839184282471183 0.156982736433532 1570 1785.45454545455 1566 0.00793650793650794 583 1.34382182698018 1.43053546088855 1 2.41188884142652 1566 2900 1947 1426 2237 4069 1447 1692 583 743 1030 1357 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 0.00982768653696206 0.0342907960626986 4590 1899.18181818182 1566 0.000897442239078595 83 1.0600067354185 -0.837131918817909 -1 3.46555792102438 4587 83 1549 412 378 1811 4223 1697 1103 1566 3482 1358 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 0.0269574283692368 0.0726616164979138 1140 1486.27272727273 1566 0.00248122981088032 699 1.21772652052584 -1.06103714823757 -1 3.09482938497149 1137 2791 1081 1792 699 758 1659 1566 1831 1818 1217 1359 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 0.0113990552563674 0.0382910200224643 1460 1722.81818181818 1568 0.00104168638328412 408 1.26485411276142 1.26485411276142 1 4.00000129113853 1459 1433 1487 1568 408 2959 2485 1766 668 2075 2643 1360 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 0.00799730763752074 0.0293464241107456 1720 1421.54545454545 1569 0.000729684344064584 335 1.53334444632203 1.53334444632203 1 5.24450038936361 1717 507 1427 1569 335 2355 1715 2635 358 1779 1240 1361 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 0.0595683245505688 0.130988816914109 670 1986.18181818182 1570 0.00612280674654368 582 0.57755077010772 0.57755077010772 1 1.13792912108994 669 2019 4538 2272 1570 598 582 1359 3041 4466 734 1362 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 0.0275461363050119 0.0737100818215015 3000 1571.54545454545 1571 0.00253611003850336 294 1.58868649965987 -1.23889395501682 -1 4.01555572537118 2997 831 1926 870 711 1571 3006 2251 294 1065 1765 1363 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 1.72400079395389e-06 3.57463173472032e-05 1085 1606.54545454545 1574 1.56727467722337e-07 216 1.32776082150113 1.31720169749505 1 13.1778313100418 1083 1772 216 1211 2927 2289 1101 1574 2772 959 1768 1364 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 0.120404889379879 0.211398237468682 1300 1552.63636363636 1574 0.0115953028795523 437 1.1524149390467 1.12939829139593 1 1.73590912411505 1297 437 1577 1043 2795 538 1574 2755 1709 2411 943 1365 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 0.0419898380581918 0.100904810841378 1980 1838.81818181818 1576 0.00389212357718645 709 1.43678471513446 1.43678471513446 1 3.19425083935931 1976 1343 1877 1517 916 4510 1553 1576 1972 709 2278 1366 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 0.000139706371607571 0.00127366548123167 1580 1364.81818181818 1576 1.27013858323272e-05 25 1.61630872602754 -1.33403223803043 -1 10.4434533855548 2244 479 1210 259 25 2888 408 2254 1577 1576 2093 1367 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 0.0237509892344676 0.0665652724597579 1295 1499.72727272727 1577 0.00218284966819747 434 2.01369544572059 2.01369544572059 1 5.28881521093496 1291 1761 930 1272 1046 1577 2871 1820 434 1758 1737 1368 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 2.07295061393478e-11 1.76615392307243e-09 485 1501.63636363636 1578 1.88450055814029e-12 53 1.29604718306991 1.28481689044201 1 25.3195439540986 485 2559 53 1950 2086 1985 1043 1578 2690 601 1488 1369 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 0.0121262051228829 0.0400362982983601 3200 1988.90909090909 1579 0.0011085058231933 424 1.1856222129802 1.32519424432949 1 3.69821384004582 3199 760 1579 742 424 2162 3025 3386 860 1397 4344 1370 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 0.110649668877607 0.197000132355801 1985 1771.81818181818 1581 0.0106037476392858 1137 1.14328439511027 1.14328439511027 1 1.80032726655651 1981 1581 1199 1151 1558 3310 2172 1867 1137 1379 2155 1371 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 0.0839184282471183 0.156982736433532 705 1698.81818181818 1583 0.00793650793650794 702 1.3161894817598 1.41316544213557 1 2.36229436114331 702 2681 1509 2160 3239 1735 1328 1688 810 1583 1252 1372 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 2.48364597506907e-05 0.0003236574076826 570 1485.54545454545 1583 2.48367373374369e-06 13 1.38252049002637 1.50095080694597 1 10.7687653081271 569 185 4648 13 2267 2449 1839 1583 639 26 2123 1373 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 0.0834958354117192 0.156982736433532 1585 2379.45454545455 1585 0.00868096767675125 760 0.56502107390574 0.513540148044672 1 1.01409874127916 1585 1700 4474 1467 1315 801 760 4682 3574 4381 1435 1374 M8719 BIOCARTA_MCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCALPAIN_PATHWAY.html mCalpain and friends in Cell motility 21/49 BioCarta 0.00680562575587344 0.0261402969606745 3580 1733.90909090909 1586 0.000620615487318841 306 1.73206800877509 1.56143222277456 1 6.11843304087976 3576 2439 1170 1109 306 1461 1697 2200 1586 654 2875 1375 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 0.0839184282471183 0.156982736433532 3130 1873.18181818182 1587 0.00793650793650794 239 1.26912097817693 1.35829933889737 1 2.27781590105303 3128 239 2423 720 1498 615 2501 4184 981 2729 1587 1376 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 0.0934726153300119 0.171971996637784 1650 1673.09090909091 1587 0.00888159985461409 798 1.32011624678327 1.5122300018921 1 2.25264746262872 1646 2561 1587 1509 1329 2068 798 2245 1491 1496 1674 1377 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 0.0673215855781973 0.143852690387338 2320 1538.90909090909 1588 0.00631586297800619 394 1.27967581912529 1.51408116398524 1 2.405104263884 2320 910 1471 1588 2073 394 1182 2134 1758 2147 951 1378 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 0.0839184282471183 0.156982736433532 3255 1990.09090909091 1589 0.00793650793650794 291 1.81980715891289 1.81980715891289 1 3.26618640362637 3251 1589 1495 1413 2366 4173 3713 1029 291 910 1661 1379 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 0.000221900701887673 0.00186348869004595 465 1391 1589 2.0174826075564e-05 41 0.628401006665132 0.628401006665132 1 3.8284862247529 463 1638 1860 2088 1589 217 360 41 2258 4410 377 1380 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 0.0614060353319102 0.134023605759353 4500 2183.18181818182 1592 0.00574455528656988 36 1.16213711968396 1.2208946165435 1 2.26391945301067 4497 36 1085 705 1592 2225 4504 4394 709 764 3504 1381 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 0.00432623027345383 0.0184130018723021 2125 1870 1593 0.000433467574355269 156 0.715858725339802 0.715858725339802 1 2.77188473673613 2125 736 4067 871 1929 981 156 1593 2952 3699 1461 1382 M5374 BIOCARTA_SARS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SARS_PATHWAY.html The SARS-coronavirus Life Cycle 8/14 BioCarta 0.0212780339259754 0.0614727909846613 1085 2102.45454545455 1594 0.00214845622374577 358 1.29142669460736 1.29142669460736 1 3.4914606430556 1082 3242 3881 3141 4461 1249 358 661 2309 1594 1149 1383 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 0.0330106412589593 0.0838871284921277 1755 1785.72727272727 1594 0.00304696563958788 808 1.33318817926542 1.49632397535552 1 3.20262606787092 1751 2315 1578 1224 808 3532 1594 1807 2620 1442 972 1384 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 0.0115954979795207 0.0387287979558332 1600 1762.90909090909 1596 0.00105973354186463 410 2.11775562982788 2.11775562982788 1 6.67389905080343 1596 2589 2309 2391 410 1749 1497 1575 1365 2668 1243 1385 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 0.0133666515312304 0.0428063323968036 1265 1681.72727272727 1596 0.0012225965051892 847 1.22504547054706 1.31289399218483 1 3.74174356408886 1261 1197 847 1906 3021 1814 853 1678 2878 1448 1596 1386 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 0.00659874650560628 0.0255340430431635 2855 1831.18181818182 1597 0.000661842334403569 316 1.21455215107271 1.21455215107271 1 4.3179627791164 2851 1252 3906 2245 316 1076 1368 2278 1205 1597 2049 1387 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 0.000568748755823943 0.00382375418908321 835 1532.63636363636 1597 5.68894372095021e-05 74 1.90919498657043 1.90919498657043 1 10.301444458592 835 1804 4169 1669 4435 365 145 74 1597 1608 158 1388 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 7.02741006077825e-05 0.000741676656414569 1600 1611.81818181818 1597 6.3887586779833e-06 232 1.27766851811454 1.37329458208513 1 8.9250839014386 1597 232 388 935 1471 3906 2155 1632 1411 1648 2355 1389 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 0.00226186706121328 0.0112756479243037 720 1468.72727272727 1598 0.000205835989805157 553 1.34815116318878 1.40323611929111 1 5.86105165285169 717 1568 669 2285 1635 1777 1749 1375 2230 553 1598 1390 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 0.0279693756386164 0.0742154554034861 1335 1904.18181818182 1599 0.00257558370296609 416 0.911379274648076 0.911379274648076 1 2.29756130326659 1332 2237 2706 1599 3568 878 508 2479 3670 1553 416 1391 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 0.00939935492294208 0.0330670999766566 1140 2079.18181818182 1600 0.000943934975818195 356 1.38933387508025 1.38933387508025 1 4.59118788919378 1139 2994 4681 2640 2836 1600 1456 356 2104 1530 1535 1392 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 0.214139132665174 0.327605607466211 2200 2110.45454545455 1601 0.0238095238095238 1207 1.21455215107271 1.21455215107271 1 1.31378031500792 2197 1601 3847 1918 4099 2821 1391 1259 1585 1290 1207 1393 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 0.000135648000471958 0.00124149712931952 2085 1666.36363636364 1601 1.35656281354395e-05 27 0.893227070942494 -0.50491279453589 -1 5.79355525547241 2641 1178 3954 586 27 2081 1223 1922 1034 1601 2083 1394 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 0.000152650655571504 0.00136511635879402 1605 1538 1603 1.38782953199924e-05 28 1.09929571317956 -0.616830001680422 -1 7.02899112314695 1603 103 1713 207 28 3515 1910 3477 258 2771 1333 1395 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 0.0302620146709126 0.078957572799497 2800 1682.36363636364 1603 0.00278967997189742 657 1.37480495887437 1.60087936674181 1 3.3833044426764 2800 1824 969 1603 1561 657 2600 2830 816 1111 1735 1396 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 0.00191875893208389 0.00982656213742636 1965 1791.18181818182 1604 0.000174584949921014 468 1.19474867435661 1.11928677432955 1 5.35344015173608 1963 1043 657 468 1604 3845 2432 2360 995 1256 3080 1397 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 0.0216261824783344 0.0621473087148722 1630 1529.45454545455 1605 0.00198561291838107 616 1.06058235615155 1.17532384731078 1 2.856138329788 1628 833 1107 779 616 1458 1706 3147 1882 2063 1605 1398 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 0.00366925304585429 0.0162977438605433 935 1426.09090909091 1608 0.00033412610081516 200 0.978581428872059 -0.950018641782837 -1 3.90492836815124 932 1608 2522 1683 1282 344 2219 200 1720 2681 496 1399 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 0.0327189098957433 0.0834626084765666 3775 2278.18181818182 1609 0.00301962655979349 801 1.40949005116904 1.35697151948269 1 3.39285233872506 3775 1609 1124 1100 801 2612 3211 3961 1513 934 4420 1400 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 0.0839184282471183 0.156982736433532 1080 1555.45454545455 1610 0.00793650793650794 695 1.49716142603433 1.49716142603433 1 2.68710246015036 1080 2070 1385 1922 1610 2557 1696 1216 999 695 1880 1401 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 0.0222706255709617 0.0636588329930419 1750 1818.90909090909 1610 0.00204539264607494 917 1.18018145791437 1.21563513700397 1 3.15072745583336 1749 1051 917 1386 3001 3195 1762 1610 2529 1275 1533 1402 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 0.0266227719132422 0.072206820496027 440 1776.54545454545 1611 0.00269472031096222 391 1.08196515182584 1.08196515182584 1 2.75637931632464 436 2110 4386 1899 1611 706 391 1199 3941 1708 1155 1403 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 0.0103804953413073 0.0357755682529886 1250 2471.36363636364 1611 0.00104293061535176 377 1.50653800334952 1.50653800334952 1 4.86353561571135 1246 4008 4463 3989 4663 1522 918 377 2958 1430 1611 1404 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 0.0463762064020277 0.109113869654205 1725 1796 1614 0.00473734637327165 607 1.31394404283802 1.31394404283802 1 2.82153658913782 1724 1547 4371 1267 1019 2635 1905 1706 607 1614 1361 1405 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 0.0532917306512603 0.120932227521456 1745 1594.45454545455 1614 0.00496619935789591 396 1.27886779891398 1.4203346733261 1 2.61873392280485 1742 789 1059 637 2566 3191 1941 1083 1614 396 2521 1406 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 0.000420880246482102 0.00301895125093618 990 1589.72727272727 1614 3.82691623926031e-05 525 1.31035492168737 1.46778240338295 1 7.37044718658611 986 1728 525 1614 1663 2912 712 2263 2741 1280 1063 1407 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 0.0390145375120237 0.0957827093095062 1075 1586.45454545455 1614 0.0036112815460478 494 1.31558905159867 1.31558905159867 1 2.99124236830877 1075 2623 2747 2404 2020 1614 2188 753 794 739 494 1408 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 9.51580156630722e-06 0.000148143010430949 1005 1761.63636363636 1615 8.650766114423e-07 280 1.29457974381783 1.29176767741948 1 11.06445151084 1001 2494 280 1955 1615 4146 1652 1441 1501 474 2819 1409 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 0.0229234989641403 0.0649393837549897 995 1589.09090909091 1616 0.00210599092118593 714 1.73338970172813 1.73338970172813 1 4.59416299793145 994 3263 924 1928 2164 2053 1616 1882 919 714 1023 1410 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 0.000415894640844136 0.0030048437104538 1930 1602 1617 3.78157530578957e-05 51 0.653874098340854 0.653874098340854 1 3.68086120143418 1928 839 2724 1736 51 995 401 1479 1918 3934 1617 1411 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 0.0236058580286499 0.0663034483294667 1715 2078.36363636364 1617 0.00238604287361085 686 1.07272638267715 -1.07272638267715 -1 2.82153079026236 1712 3241 4445 2886 686 1497 1613 1358 2617 1617 1190 1412 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 0.0839184282471183 0.156982736433532 1580 1670.54545454545 1618 0.00793650793650794 926 1.11054973744747 -0.999806772181872 -1 1.9932125418694 1579 2676 1643 1930 2091 926 1618 1038 1025 2536 1314 1413 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 0.122103048977394 0.213977145664948 975 1883.18181818182 1620 0.0129381787604343 714 1.00744291305309 1.00744291305309 1 1.50569356991545 974 1320 4535 2464 2231 714 774 2027 2868 1620 1188 1414 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 0.190259805944644 0.299481844358952 820 1655.72727272727 1621 0.0190027483355722 819 1.00502828025615 1.03352195711535 1 1.17457822000241 819 1351 1621 909 2776 1745 911 1496 2208 2615 1762 1415 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 0.0550365341116104 0.123812385428232 1625 1837.90909090909 1622 0.00513305449836192 1019 1.08727796406104 1.17429900920557 1 2.2016099153497 1622 1490 1446 2082 1058 3025 1476 1019 2696 2204 2099 1416 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 0.000452013227566258 0.00320929391572043 1405 1941.72727272727 1622 4.11005568344383e-05 530 1.58607878296821 1.58607878296821 1 8.8273317023332 1402 900 530 1615 4438 2914 1622 1279 2481 1790 2388 1417 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 0.00120556826067739 0.00676754816221133 155 1460 1623 0.000109657218360128 154 1.20074158169684 -1.20074158169684 -1 5.81436780540078 154 1829 1714 2208 1623 891 1385 587 2138 2436 1095 1418 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 0.0225599171956176 0.0641868682323401 1625 1874.72727272727 1624 0.00207223951952882 633 1.16751959882986 1.16751959882986 1 3.10757572260013 1624 1249 2597 2416 633 1622 1205 3200 3661 1769 646 1419 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 0.00128685782981817 0.00713635004796205 1680 1360.90909090909 1626 0.000117055561407491 109 1.35336732884391 1.43937684364792 1 6.48382018629127 1677 278 1920 346 3091 3000 1626 109 566 542 1815 1420 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 0.00697522504940837 0.0265523189126951 565 1510.54545454545 1626 0.000636130823888086 561 1.32186312100999 1.32063450059978 1 4.6493690444603 561 1355 772 1626 2980 1450 1708 1985 1946 596 1637 1421 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 0.00736619251695713 0.0277144165444828 2290 1684.63636363636 1627 0.000671906613705065 319 1.53334444632203 1.53334444632203 1 5.329542895902 1523 1317 1541 1627 319 2287 2286 584 3477 1781 1789 1422 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 0.00982005480263968 0.0342896995567582 1165 1797.72727272727 1629 0.000986372169319178 193 1.86280643978199 1.86280643978199 1 6.09026773246435 1162 2162 3909 1629 3981 2666 1350 367 193 1686 670 1423 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 0.156982736433532 1775 1802.45454545455 1629 0.00793650793650794 281 1.28282475167136 1.28282475167136 1 2.30241140747691 1774 1056 2198 1042 1319 3681 1505 2242 281 1629 3100 1424 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 0.00249450481389287 0.0123044732188442 4190 2058.45454545455 1629 0.00022703070415472 150 1.22222585975387 -1.22222585975387 -1 5.21014799051165 4190 846 1377 1796 150 4250 3398 1190 1629 918 2899 1425 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 0.13476916583975 0.232094197399879 905 1643.36363636364 1630 0.0130736913629794 840 1.1843310919607 1.1843310919607 1 1.67676365289818 904 2538 1630 1867 1971 1408 1947 1620 2497 855 840 1426 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 0.0682571024876326 0.145449000523555 2010 2092 1634 0.00704490383704876 347 1.34282134394685 1.45895673867997 1 2.50941974129299 2006 866 4685 915 1634 4484 2128 1543 901 347 3503 1427 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 0.0529336117519756 0.120294328161861 1015 1599.09090909091 1635 0.00493198711427916 569 1.33287994564688 1.33287994564688 1 2.73616746490092 1011 1926 1919 2173 1365 1883 1635 1277 1533 2299 569 1428 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 0.00141151991214783 0.00764668474950837 2040 1536.63636363636 1637 0.000128402396143377 117 1.76539055828103 1.76539055828103 1 8.3395790399156 2039 2152 1637 1886 3920 1658 1611 117 357 972 554 1429 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 0.0567618806956725 0.126539568477603 880 2288.18181818182 1637 0.0058266106487306 379 0.822109601213062 -0.712555328022858 -1 1.6473130158206 880 3779 4494 4107 1637 379 1620 1295 3030 3159 790 1430 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 0.0278694650264351 0.0740900013286198 960 1751.81818181818 1638 0.00256626407249575 384 1.17363481935161 1.17363481935161 1 2.96062475605664 956 2597 2304 1890 3738 1638 384 864 3163 1120 616 1431 M17406 BIOCARTA_CYTOKINE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CYTOKINE_PATHWAY.html Cytokine Network 8/34 BioCarta 0.0115843993944082 0.0387222468477574 1270 1692.81818181818 1640 0.00116452354516411 403 0.580799900060644 0.598045466456658 1 1.83042912820894 1270 628 3826 1661 1092 2387 1640 403 635 3257 1822 1432 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 0.0839184282471183 0.156982736433532 1645 1540.54545454545 1641 0.00793650793650794 379 1.34022806652749 1.47716668706147 1 2.40543876704839 1641 466 1454 399 2791 2263 2062 2711 390 379 2390 1433 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 0.0171230924160052 0.0519465802595754 1320 1861 1641.5 0.00191720290876442 60 0.970079523755056 0.970079523755056 1 2.78100481841972 1319 1031 4132 NA 2390 1405 341 2231 60 3823 1878 1434 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 0.00611698396969721 0.0240146466894482 4295 2157.36363636364 1642 0.000557641674777325 752 1.56099198018953 1.63184787712836 1 5.64244793993018 4294 1187 752 2024 1985 1581 4507 1642 993 1590 3176 1435 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 0.000294165802589937 0.00225977205071548 1840 1885.18181818182 1644 2.67459221247729e-05 499 1.64997024996258 1.64997024996258 1 9.74394670140167 1838 3121 499 1080 2432 4338 1644 1292 1397 1102 1994 1436 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 0.00186257518491814 0.00960179022720178 705 1682.63636363636 1645 0.000169468541762718 89 0.51641185084666 0.586203846809114 1 2.32552552156013 701 1645 1944 2424 3125 260 89 267 2766 4669 619 1437 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 0.0650398521646454 0.13993422738454 2020 1610 1646 0.00609511019404009 533 1.83911281678021 1.83911281678021 1 3.50577844980328 2016 1646 1418 1159 1975 3536 1994 771 533 976 1686 1438 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 0.0828637140980927 0.156982736433532 1420 1897.72727272727 1647 0.0078327263669591 695 0.889829409089437 -0.889829409089437 -1 1.59706411923087 1420 1647 2563 1910 1268 695 1274 1887 2971 4247 993 1439 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 0.061127893927749 0.133540937503698 1650 1711.90909090909 1648 0.00571777379960875 321 1.05994331481352 1.02388395103748 1 2.06854599060772 1648 321 1083 889 1872 3466 2350 3050 806 1047 2299 1440 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 0.00464983156713616 0.0195068135394808 1655 1525.72727272727 1651 0.000423608040265692 575 0.937638291114254 -1.13040952193109 -1 3.57819227396071 2108 575 731 1132 875 1653 2475 1651 1284 2076 2223 1441 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 0.00304309411375217 0.0142172871555759 760 1963.72727272727 1651 0.000277028324163781 116 0.421788296675595 0.480195711411941 1 1.73893786879051 759 1651 2333 3183 4376 196 116 1154 2855 4552 426 1442 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 0.0829451395840252 0.156982736433532 1280 1691 1653 0.00784073459114009 834 1.13236330838015 1.13236330838015 1 2.0323634972045 1279 1426 1653 1723 1838 2608 1608 834 1805 1626 2201 1443 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 0.0839184282471183 0.156982736433532 1615 1760.72727272727 1653 0.00793650793650794 336 1.0845254424348 1.04585690954056 1 1.94650418701942 1614 336 2173 747 2466 2840 1653 3891 465 1410 1773 1444 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 0.161385165508919 0.262241686633255 1195 1773.72727272727 1653 0.0158730158730159 1131 1.03480490076254 1.03480490076254 1 1.34257038278895 1195 1851 2105 2050 2986 1485 1311 1653 1342 2402 1131 1445 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 2.1262257572779e-05 0.000287962251404747 1725 1916.72727272727 1654 2.12624610131373e-06 13 0.970454883618695 0.970454883618695 1 7.66901652838374 1725 1654 3907 1427 3475 3065 1262 13 239 3408 909 1446 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 0.000200122541815404 0.00171439530337656 1010 1836.18181818182 1654 1.81946134763076e-05 462 1.28053278318124 1.33986792066022 1 7.90505704403889 1305 3009 462 2679 2730 1009 1654 1879 3375 1007 1089 1447 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 0.0986215477785938 0.179619651465259 1655 1792 1655 0.00939468917152511 745 1.20000636384879 1.20000636384879 1 1.99708193901386 1655 2881 1960 2515 1617 2099 983 989 3113 1155 745 1448 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 0.135041713933073 0.232478130598965 1445 2091.18181818182 1655 0.0131019574305229 1040 1.38613795957112 1.38613795957112 1 1.96025895324953 1442 3878 1257 2711 4278 1083 1655 1040 2609 1991 1059 1449 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 1.26961360239941e-07 3.71838083802727e-06 1420 1796.54545454545 1655 1.15419425060768e-08 156 1.42895090153864 -1.2610967756572 -1 17.316829763796 1418 1607 156 1115 2736 3695 2203 1655 1984 406 2787 1450 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 0.000387518149795067 0.00283293299522572 1605 1760.18181818182 1655 3.52351296243131e-05 522 1.45037954066291 1.58463072191775 1 8.24746278809001 1601 545 522 1173 1937 4645 1848 1145 1655 2026 2265 1451 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 0.0027232130176248 0.0131420970139957 1910 1653.54545454545 1656 0.000247871793587333 134 1.60735742778023 1.71336702942406 1 6.74929215496014 1908 289 681 506 3434 3972 3040 2359 210 134 1656 1452 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 0.232850105696956 0.34496857265126 1660 1935.27272727273 1657 0.0238095238095238 985 1.11356050197282 1.42364424458003 1 1.14879502452162 1657 985 3062 1306 3305 2926 1789 1192 1639 1832 1595 1453 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 0.0765897756730953 0.156982736433532 2640 1927.09090909091 1658 0.00793650793650794 179 1.27675999939789 -1.27675999939789 -1 2.29152640171101 2636 1105 3959 1269 3067 1742 3088 1658 179 1183 1312 1454 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 0.0339018482653237 0.0857797305460621 690 1955.63636363636 1658 0.0034430434435118 435 0.857185672850884 0.857185672850884 1 2.0406206465375 687 1658 4527 2196 1822 1218 435 792 2724 4451 1002 1455 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 0.0628253375541174 0.136454374060015 3245 2119.72727272727 1658 0.00588132851963867 876 1.26530448687738 1.26530448687738 1 2.44285115256477 3242 1093 1658 876 1131 4116 3936 1183 1048 1866 3168 1456 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 0.0148022433006566 0.0462031002759041 2960 2044.36363636364 1659 0.00135479867948843 490 1.39855421873277 -1.13975148755868 -1 4.16818613662076 2960 490 857 1197 1301 4034 2461 2432 1659 1226 3871 1457 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 0.00415783127439001 0.0178912739685873 370 1973.54545454545 1662 0.000378700919188459 143 0.405479253605357 0.461424794400379 1 1.58135824816008 368 3409 1662 3281 3032 543 143 905 3060 4463 843 1458 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 0.058600915961952 0.129225361034215 1190 1763.81818181818 1666 0.00547478778769364 1049 1.1326658119887 1.1326658119887 1 2.24653500248452 1187 1993 2927 2362 1094 1430 1666 2392 1935 1367 1049 1459 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 0.0301470170395119 0.0787013492184694 1810 1777.72727272727 1666 0.00277893005372795 756 1.7295686678772 1.7295686678772 1 4.26180375968127 1809 3769 1217 1926 756 2711 877 1666 2372 911 1541 1460 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 0.0839184282471183 0.156982736433532 1770 1744.36363636364 1667 0.00793650793650794 305 2.24458518468169 2.24458518468169 1 4.02857719078965 1766 2818 1263 1667 3365 2302 1224 1293 305 1851 1334 1461 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 0.0839184282471183 0.156982736433532 4290 1883.27272727273 1667 0.00793650793650794 265 1.32105188041576 1.36907746394609 1 2.37102138493911 4288 265 1667 755 3302 552 2801 2058 899 1205 2924 1462 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 0.0533511995194655 0.121008577419272 1630 2202.63636363636 1667 0.00546770831174479 529 0.376164333632703 -0.38913040313526 -1 0.770040497979183 1627 2059 4533 2432 1093 529 1238 1667 3570 4462 1019 1463 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 0.0839184282471183 0.156982736433532 1620 1822.54545454545 1668 0.00793650793650794 691 1.76693513116339 1.76693513116339 1 3.17129178947607 1618 2686 1436 1674 2576 2782 1414 2225 691 1278 1668 1464 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 0.00293115758368896 0.013916316552347 1670 1702.18181818182 1668 0.000266824563184036 207 1.34533103165213 1.42864510557789 1 5.57439813556957 1668 207 687 431 2354 4161 2057 2303 989 1395 2472 1465 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 0.0440943272448576 0.104939572102287 475 1580.09090909091 1669 0.00409124789954338 471 1.15930593519789 -1.20074158169684 -1 2.53330358066936 471 1826 2416 2403 1286 1089 1999 663 1669 2201 1358 1466 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 0.018723477610359 0.0558842140650588 3905 2333.90909090909 1669 0.00171679562334151 593 1.402523675024 -0.834340810040004 -1 3.92139504300424 3904 1301 891 593 1669 4399 3509 2507 703 1665 4532 1467 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 0.0631722151686232 0.13692183176696 1975 2001 1669 0.00591478454605879 764 1.42013337349127 1.61373908728807 1 2.7370627873679 1972 2431 1493 1642 3123 3472 2476 764 1330 1669 1639 1468 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 0.00348021644739184 0.0156209715253622 1670 1932.18181818182 1670 0.000316884916648646 428 1.54612341393589 1.54612341393589 1 6.23320858825163 1670 1238 709 1411 1166 3393 2759 3629 2612 428 2239 1469 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 0.241331476497376 0.355175659191804 890 1918.63636363636 1671 0.0247956218689689 890 1.58708494918047 1.58708494918047 1 1.59244449431634 890 3155 1749 3552 2852 1671 1001 1436 2217 1234 1348 1470 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 0.0192622204961597 0.0572370103012075 2585 2099.81818181818 1671 0.00176663351071103 570 1.42521535062189 1.42521535062189 1 3.95179668364348 2585 1671 1625 1301 570 4047 3255 2740 776 1101 3427 1471 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 2.19464451631656e-05 0.000292994421750981 1090 1496.18181818182 1673 1.99515128149366e-06 320 1.36341631171904 1.39220971221843 1 10.7514977036993 1089 1673 320 437 3071 2454 1741 1135 2038 572 1928 1472 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 0.00281625805175058 0.0134388851634452 1075 1583.72727272727 1673 0.000256351787878176 85 1.86963479990731 1.86963479990731 1 7.8101235387591 1072 2330 1810 1379 2874 2574 2620 168 85 836 1673 1473 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 0.0839184282471183 0.156982736433532 2010 1762.63636363636 1675 0.00793650793650794 315 1.86332482731691 1.86332482731691 1 3.34429183153783 2007 1512 1675 611 2180 3045 2739 1631 315 1006 2668 1474 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 0.00496253594579377 0.0203815044593039 4630 2147.18181818182 1675 0.000452160491582575 254 1.22121427890745 1.29691337364956 1 4.60844447538569 4626 396 1047 550 254 1841 4289 4503 1476 1675 2962 1475 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 8.0434177277511e-08 2.58160653919463e-06 1240 1564.90909090909 1676 7.31219820166039e-09 142 1.32961254029597 1.43014353739217 1 16.5832481535192 1240 1412 142 1174 1676 3250 2089 1865 1714 526 2126 1476 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 0.000786544548936216 0.00481797092328772 1050 1685.27272727273 1677 7.86823081243025e-05 51 0.701222236703204 -0.701222236703204 -1 3.62649202134751 1050 1866 3888 1677 2627 64 51 782 3101 3352 80 1477 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 0.031109177696198 0.0803182405974565 1785 2172.45454545455 1678 0.00315534579189174 421 0.553548491170837 0.684632725615625 1 1.35307863157817 1783 1103 4064 1412 1386 1219 421 3738 3398 3695 1678 1478 M6917 BIOCARTA_EPONFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPONFKB_PATHWAY.html Erythropoietin mediated neuroprotection through NF-kB 7/18 BioCarta 0.00250088116057644 0.0123229538574776 1700 1836 1679 0.000250370010947097 160 0.852326785622773 0.852326785622773 1 3.63208909093669 1699 1656 3833 1963 160 1464 1883 2763 1596 1500 1679 1479 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 0.0264436518513814 0.0719599027732712 1010 1637.63636363636 1683 0.00243335946222727 382 1.04495537331979 1.04495537331979 1 2.66556400423522 1006 2660 2788 2386 2759 812 576 1683 382 2561 401 1480 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 0.000744008344669197 0.00465477049815735 585 2085.09090909091 1684 6.76600069799181e-05 553 1.56594789096278 1.15843598159053 1 8.15087722443055 3246 582 576 872 1684 4433 3055 3207 553 583 4145 1481 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 0.172333707938536 0.276617244348736 1110 2042.72727272727 1684 0.0170480306695331 880 1.30189094238941 1.30189094238941 1 1.62174410850859 1110 3023 1809 3993 3828 1684 880 1472 2515 1225 931 1482 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 0.00534576422185538 0.0216248139759131 1835 1802 1686 0.00048716347430044 266 1.1661401648125 1.21583659663497 1 4.33368127171498 1832 1195 2539 1346 266 4243 1686 2590 832 921 2372 1483 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 0.0839184282471183 0.156982736433532 1070 1838.72727272727 1686 0.00793650793650794 708 1.31134033381465 1.31134033381465 1 2.3535911196979 1069 3280 1940 2177 3762 1477 708 1686 964 2400 763 1484 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 0.00403437928096549 0.0174335900228211 925 1780.72727272727 1688 0.000367436055527073 719 2.59443856790082 -2.59443856790082 -1 10.1834109027865 921 2943 719 2905 2408 857 1374 1976 2465 1332 1688 1485 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 0.00086364679290658 0.00524229128440445 70 1839.36363636364 1688 7.854418348632e-05 68 0.914907513141329 -0.914907513141329 -1 4.65674865454108 692 1688 3129 3084 3118 68 240 645 2926 4575 68 1486 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 0.214139132665174 0.327605607466211 2245 2095.09090909091 1689 0.0238095238095238 807 1.53334444632203 1.53334444632203 1 1.65861774478613 2242 851 4042 807 3444 2856 1619 1689 1557 1604 2335 1487 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 0.259125160997559 0.377333904423418 1470 1788.90909090909 1689 0.0268974237130432 1282 1.47495853054486 1.47495853054486 1 1.39341708764285 1470 1434 1425 1916 2793 1782 1689 1704 2859 1324 1282 1488 M13748 REACTOME_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCONEOGENESIS.html Genes involved in Gluconeogenesis 20/48 Reactome 0.0233936328247499 0.0658789443610444 910 1662.18181818182 1690 0.0021496505156002 202 1.23889395501682 -1.23889395501682 -1 3.26630509665164 906 1690 2404 2232 3694 202 719 531 2981 2386 539 1489 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 0.0102023656634073 0.0352828675267354 895 2035.36363636364 1691 0.00102495102940958 250 1.70932184675759 1.70932184675759 1 5.54115680979596 895 3292 3973 2976 4609 612 250 887 2597 1691 607 1490 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 0.0113426254490156 0.0381561685958988 2300 1996.27272727273 1691 0.00103650278951605 407 1.2496970119907 1.39001225204567 1 3.95634174848754 2296 2266 1310 1471 407 4081 2565 1070 1691 1203 3599 1491 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 0.0280954897378075 0.0744236658628412 590 1696.54545454545 1691 0.00258734882992036 590 1.2213237000062 1.2213237000062 1 3.07560579960307 590 2933 961 3232 1691 1728 778 1376 2081 1941 1351 1492 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 0.0581801577199229 0.128539471511343 1690 2540.27272727273 1694 0.00597619835265753 767 1.14672566625037 1.14672566625037 1 2.28033679831082 1689 4237 4018 3677 3823 1526 1487 767 4027 1694 998 1493 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 0.0018208912731813 0.00944927630800395 1610 1894.36363636364 1695 0.000165672739385252 128 1.07643464219997 1.07643464219997 1 4.86414781965453 1609 2158 3621 2935 128 2102 1451 1695 1606 1842 1691 1494 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 0.111353112274416 0.198026825092187 1135 2350 1695 0.0117361205221402 932 1.14672566625037 1.14672566625037 1 1.79996835336418 1135 3387 4020 2950 3842 1145 1623 932 3786 1695 1335 1495 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 0.0205823969428526 0.0599850907032322 3745 1937.27272727273 1695 0.00188886535048082 193 1.18044186220627 1.2539364109259 1 3.21943726829483 3744 193 1405 330 600 645 4193 3409 2382 2714 1695 1496 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 0.00023063985116291 0.00190115977338007 2765 1591.90909090909 1695 2.09694576490947e-05 37 0.93366556579984 -0.748436440339062 -1 5.670175056409 2761 368 1695 179 37 3111 2191 4147 57 733 2232 1497 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 0.0508429928902693 0.116643671146604 1225 2074 1696 0.00473249802594815 1051 1.35155616013995 -1.38916827744188 -1 2.81488014808621 2731 1692 1051 1222 2459 3152 3337 1696 1281 1222 2971 1498 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 0.0225115644917043 0.0641271679076756 1700 1808.54545454545 1696 0.00206775178380352 432 0.394095721377041 -0.407921567878381 -1 1.04931626918413 1696 1513 2402 3054 632 432 930 1813 2229 4124 1069 1499 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 0.00181560405423717 0.00943228447689064 610 1915.18181818182 1696 0.000165191287234288 86 0.417428700921766 0.48765795212621 1 1.88698759387756 610 4333 1696 3979 2355 169 86 277 2954 4387 221 1500 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 0.022935271044496 0.0649393837549897 1340 1897.27272727273 1697 0.00210708391765254 353 1.08918898596586 1.08918898596586 1 2.88677827728172 1339 2740 1334 2205 3789 1697 353 1112 3721 1854 726 1501 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 0.0355095750294474 0.0891735630160721 2435 1692.90909090909 1698 0.00328145640917884 836 1.25096974805379 1.3400914307421 1 2.93101464081241 2435 935 1836 1698 836 1215 2124 2921 1309 1261 2052 1502 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 4.87699261402322e-05 0.000549848094874702 1345 1510.27272727273 1703 4.43372793752178e-06 365 1.11890376958029 1.27523726700082 1 8.14062135724831 1343 426 365 679 1703 1894 1427 2405 1906 2516 1949 1503 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 0.0839184282471183 0.156982736433532 3630 2353 1706 0.00793650793650794 680 1.37379538320067 1.59247971593104 1 2.46568532272911 3630 1044 1367 940 4487 1706 3234 2922 680 1233 4640 1504 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 0.0515731853635258 0.117831275774491 2300 1886.45454545455 1707 0.00480212833872198 713 1.52165234821931 1.70638333650015 1 3.15419743843866 2299 2715 1599 1671 1090 3977 1707 713 1410 1738 1832 1505 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 0.00715075677885406 0.0270665963374072 1425 1561.18181818182 1709 0.000652191410500296 315 1.25168270859685 1.25168270859685 1 4.37925002031805 1422 2185 2150 2074 315 1783 1521 1709 2347 1208 459 1506 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 0.00657997223368142 0.0254824379231662 1230 1571 1709 0.000599975913730617 297 0.900416075626817 0.900416075626817 1 3.20291528404984 1230 1248 1709 1880 297 1748 2072 561 1927 3562 1047 1507 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 0.0555194627068359 0.124601605911306 2140 2160.45454545455 1709 0.00517928633285988 356 0.965339015480038 -0.965339015480038 -1 1.94875227097334 2136 1225 2121 1668 1709 356 838 4634 3782 4261 1035 1508 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 0.0027784804909438 0.0133287803851548 620 1972.90909090909 1710 0.00025290870708234 112 1.10858603309022 1.10858603309022 1 4.63979478279191 616 4385 1710 4013 3129 463 112 803 4118 2129 224 1509 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 0.00582199194509909 0.023159468807075 1710 2018 1711 0.000530677850557547 78 0.671180382603598 -0.671180382603598 -1 2.44967602556139 1706 1416 3226 3693 1067 78 1711 1749 3097 3942 513 1510 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 0.0799886480659046 0.156982736433532 3615 1993.45454545455 1711 0.00755037615628171 57 1.13717702887591 1.0834716564946 1 2.0410031535316 3614 57 1491 480 1244 1879 3530 4363 797 2762 1711 1511 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 0.195477999512875 0.305744294298175 2095 1633.27272727273 1712 0.0195791498370197 975 1.39210461141323 1.39210461141323 1 1.59902902944343 1129 2095 2095 1643 1796 1721 975 1929 1604 1267 1712 1512 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 0.000752113362941978 0.00468048236221263 3015 2248.54545454545 1712 6.83973282592158e-05 578 1.37573203341608 1.52047630600712 1 7.15344354509446 3014 1712 578 767 806 4000 3418 4045 1010 850 4534 1513 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 0.0839184282471183 0.156982736433532 2010 1829.63636363636 1713 0.00793650793650794 208 1.70994404343358 -1.38916827744188 -1 3.06900429436145 2008 2284 2781 1287 3971 1881 1094 1713 208 1404 1495 1514 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 0.155099806926061 0.25883108805396 670 1759.63636363636 1715 0.0152047474475456 667 1.0177635111608 1.0177635111608 1 1.33337519167941 667 2394 1715 2199 3289 1126 868 1314 2790 2039 955 1515 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 0.0839184282471183 0.156982736433532 4075 2133.81818181818 1717 0.00793650793650794 541 1.05749258159007 1.18271947854453 1 1.89798566014556 4074 541 1481 1717 1438 833 3600 4247 929 2298 2314 1516 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 0.052983121589683 0.120348476863429 1950 1718.54545454545 1718 0.00493671624675327 624 1.47300395041997 1.47300395041997 1 3.02317477587265 1449 1718 1057 743 1585 3262 2112 1948 624 1947 2459 1517 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 0.0291372780430488 0.0766632705837881 2020 1786.63636363636 1719 0.00268458990718549 132 0.900416075626817 0.900416075626817 1 2.24160126512679 2017 132 1363 1124 851 3671 1924 564 1719 4371 1917 1518 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 0.0765897756730953 0.156982736433532 1170 2324.18181818182 1724 0.00793650793650794 195 1.77228865595639 1.77228865595639 1 3.18090028552208 1167 4277 4668 3546 3534 1518 870 2649 195 1724 1418 1519 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 0.00054619525979113 0.00370401011198442 3840 2093.45454545455 1725 4.96664464684479e-05 391 1.75970145147917 1.9606351765643 1 9.54909181951662 3838 1126 549 391 1945 3315 2730 1725 1489 1253 4667 1520 M14691 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMINOACYL_TRNA_BIOSYNTHESIS.html Aminoacyl-tRNA biosynthesis 26/41 KEGG 0.172749070454909 0.276847518519735 755 2115.09090909091 1726 0.01709288565641 698 0.262295411198224 -0.303941843726055 -1 0.326525511335617 755 2470 3701 3280 1726 698 1377 1719 3148 3189 1203 1521 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 0.0151511777101914 0.0469877026803156 1730 1824.27272727273 1726 0.00138695814674674 494 1.5944918102954 -1.3261771808088 -1 4.72612371342406 1726 3629 1444 3392 494 2583 1102 657 2074 1751 1215 1522 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 0.170185613911809 0.273863250958357 1975 1911.54545454545 1727 0.016816384121577 902 1.56586485349118 -1.45221947730462 -1 1.96575908809314 1974 3339 1371 2782 1713 902 2434 1168 1727 2359 1258 1523 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 0.0358633740738105 0.0897733818963012 1600 1845.45454545455 1727 0.00331470023610114 629 1.93847904430292 1.93847904430292 1 4.52924823773648 1599 1246 996 1727 1279 3146 2591 2652 629 1867 2568 1524 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 0.00302010351369213 0.0141522050651613 2475 1876.27272727273 1728 0.000274932492706726 173 1.6003108405889 1.6003108405889 1 6.60483729498163 2472 576 1327 1289 173 3929 3093 1527 1728 2009 2516 1525 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 0.138787691361124 0.237270748529088 1770 1771.18181818182 1728 0.0134912768308838 975 1.46863447056767 1.46863447056767 1 2.04787558571748 1767 1358 2499 1557 2197 2129 1728 975 1408 2150 1715 1526 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 0.0930194747475994 0.17127279318949 1140 2169.36363636364 1729 0.00883657148441058 866 1.18063890866154 1.18063890866154 1 2.01930563423527 1138 3929 2125 3919 3047 1198 1226 866 3463 1729 1223 1527 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 0.0839184282471183 0.156982736433532 1730 2096 1730 0.00793650793650794 985 1.67671515683012 1.67671515683012 1 3.00936515232175 1730 2136 1650 1512 3958 2901 1528 2255 985 2859 1542 1528 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 1.37642878695999e-05 0.000200308860114736 690 1495.54545454545 1731 1.25130672604958e-06 297 1.51880842913782 1.51880842913782 1 12.5367415330041 686 2562 297 1978 1973 2119 1739 918 1009 1439 1731 1529 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 3.97781529952951e-05 0.000466796802622172 600 1770.09090909091 1731 3.61626111285783e-06 353 1.10585358248863 1.10585358248863 1 8.22119868865963 600 2076 353 1278 1689 2181 1731 3107 3197 1283 1976 1530 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 0.0841117793000777 0.157281643176442 2850 1868.09090909091 1732 0.00795554503892263 616 1.36385886793935 1.47870497002375 1 2.44533648111883 2850 781 1140 1292 1953 1732 2915 1816 1692 616 3762 1531 M3397 KEGG_BUTANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BUTANOATE_METABOLISM.html Butanoate metabolism 16/48 KEGG 0.012529909052121 0.0408311222658131 3095 2004.72727272727 1734 0.00114562239243206 346 0.89192525733766 -0.89192525733766 -1 2.76511359636459 3094 2244 2106 1423 432 1589 4388 1734 346 3184 1512 1532 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 0.0425903049805498 0.101981690924301 1210 1928.36363636364 1735 0.00394889848335588 465 1.31394404283802 1.31394404283802 1 2.90763183777433 1207 1735 2709 2577 4412 900 465 1229 2071 2691 1216 1533 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 0.0140493109834102 0.0443931701067161 1270 1773.54545454545 1735 0.00128544009224167 338 0.94175740835774 0.94175740835774 1 2.84324904530932 1268 1755 1735 1852 2711 585 532 424 3787 4522 338 1534 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 0.00379655538598577 0.0167224140546736 1740 1613.18181818182 1736 0.000345738454631383 157 0.995816582010741 -0.995816582010741 -1 3.94887386681239 1957 157 1738 828 208 1736 1572 4213 1562 1845 1929 1535 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 0.0472097946822471 0.110446878622571 1440 1861.18181818182 1736 0.0043867627322137 1037 1.08199922774543 1.08199922774543 1 2.31072786934422 1437 2529 1037 1374 3279 2115 1170 1078 2807 1736 1911 1536 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 0.0262514142591815 0.0715614468985017 3655 1987.36363636364 1736 0.00241545391983793 541 1.27608987510979 1.40756534418091 1 3.26203035819466 3655 965 1200 541 690 1994 3932 3007 1736 1449 2692 1537 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 6.49576733892371e-07 1.49946629311313e-05 1740 1893.81818181818 1737 5.90524477898067e-08 198 1.43388255266602 1.43388255266602 1 15.4385366178395 1737 1774 198 945 1613 3923 3036 2016 1699 1206 2685 1538 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 0.0839184282471183 0.156982736433532 1765 1907.36363636364 1738 0.00793650793650794 848 1.38005969488164 -0.726943958260213 -1 2.47692849733742 1761 1498 3172 1738 1656 1014 1953 3183 848 2739 1419 1539 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 0.0144537777203556 0.0453046169883521 1740 2278.18181818182 1739 0.00145486576773685 510 0.282067822188787 0.366295780527207 1 0.846031106732408 1739 3417 3831 3298 510 1515 1235 1637 3223 3263 1392 1540 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 0.00910050542283438 0.0322091906430528 1540 1863.72727272727 1739 0.000830760907084868 287 0.70658926683976 -0.70658926683976 -1 2.35299654963389 1539 2362 3278 1739 3061 906 287 331 1795 4077 1126 1541 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 0.00804189385404136 0.029486944131485 4555 2218.81818181818 1740 0.000733767415177412 339 1.39728213059217 1.32858613161169 1 4.77265640351502 4552 417 1186 1163 339 1495 3862 4474 2523 1740 2656 1542 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 0.00167798790822397 0.00887477577645321 1900 1796.27272727273 1741 0.000152660828585139 419 1.10147061458111 1.07310748111948 1 5.04424897784127 1899 1419 648 1432 419 3069 2231 3506 913 1741 2482 1543 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 3.73656949839633e-06 6.68303995018519e-05 745 1513.54545454545 1742 3.39688713159369e-07 244 1.22490770424875 1.22490770424875 1 11.4141112022901 742 1436 244 1245 2361 1791 1797 1770 2349 1172 1742 1544 M509 REACTOME_DEVELOPMENTAL_BIOLOGY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEVELOPMENTAL_BIOLOGY.html Genes involved in Developmental Biology 192/520 Reactome 0.089822558863864 0.166104384702473 1145 1858.81818181818 1743 0.00851947530013219 940 1.32054746641603 1.32054746641603 1 2.2978196117896 1141 2749 1743 3122 1307 2833 1615 1754 2041 1202 940 1545 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 0.047777674399225 0.111497102706558 1020 1491.09090909091 1743 0.00444072307958322 256 1.55966885201143 1.55966885201143 1 3.31653603104272 1017 1833 1942 1209 2380 1922 1160 682 256 2258 1743 1546 M13 PID_ERBB4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB4_PATHWAY.html ErbB4 signaling events 18832364 25/81 Pathway Interaction Database 0.0460273982044072 0.108438606327729 1545 1678.27272727273 1744 0.00427450430158659 614 1.47141532197542 1.47141532197542 1 3.16854119926501 1545 1579 2143 1744 965 2209 1778 2332 614 1483 2069 1547 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 0.173966996727188 0.27823810013545 1745 1837.63636363636 1744 0.0172245276155275 707 1.16186250822327 -1.16186250822327 -1 1.44073316750078 1744 1467 1992 2372 2728 707 1700 1137 3571 1861 935 1548 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 0.0516512496596516 0.117902549022011 1045 1935.63636363636 1745 0.00480957534339499 715 1.13224258361139 1.23161933002586 1 2.34633542873304 1044 3760 1993 1863 3646 1489 1672 715 1461 1745 1904 1549 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 0.0787932789201679 0.156982736433532 1545 1987.54545454545 1745 0.00743321914388861 1235 1.13796702627236 -0.862559895960135 -1 2.04242103934583 1543 1624 1345 1337 1235 3527 1745 2043 2484 2871 2109 1550 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 0.000598699452851805 0.00396257858201068 1890 1857.18181818182 1746 5.44420402450808e-05 64 1.21907618042887 1.21907618042887 1 6.53562915413369 1886 1095 1746 1556 64 3950 2506 1703 2759 724 2440 1551 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 0.000158504514007448 0.00140502074883778 4030 2354 1746 1.44105395467676e-05 446 1.17351242517724 1.40189336587522 1 7.4707650307022 4026 885 446 975 1746 3522 4329 2995 1700 1201 4069 1552 M10450 REACTOME_GAB1_SIGNALOSOME http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAB1_SIGNALOSOME.html Genes involved in GAB1 signalosome 25/46 Reactome 0.149094250384518 0.251044073769979 915 1669.81818181818 1751 0.0145704367911111 780 1.21038230567078 1.21038230567078 1 1.62156480091018 915 1940 2937 1751 1954 1378 2014 2170 1648 780 881 1553 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 0.00415623424435733 0.0178912739685873 2640 1960.54545454545 1751 0.000378555183784126 722 1.23069946039723 1.46822496281039 1 4.79969499175484 2639 2183 722 1029 2594 3477 1751 1324 1395 866 3586 1554 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 0.0122915788357839 0.040344087099964 1185 1854.36363636364 1752 0.00112370862699063 392 0.849254971022537 0.849254971022537 1 2.64270687249766 1184 1752 2969 2128 1247 1793 733 392 2840 4080 1280 1555 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 0.0445322442092446 0.105659795627605 1945 2032.81818181818 1753 0.00413273318156638 869 1.20779006827473 1.33539709243485 1 2.63124311135355 1944 1768 1029 1219 1481 4380 1753 3581 1004 869 3333 1556 M72 PID_NECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NECTIN_PATHWAY.html Nectin adhesion pathway 18832364 29/55 Pathway Interaction Database 0.041748377909341 0.100582467292119 1395 1876 1754 0.0038693023346089 528 1.806917851326 1.806917851326 1 4.022732600601 1391 3011 2027 1754 4491 1423 1777 651 528 1659 1924 1557 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 0.0119856002580362 0.0396754956838944 795 1803.45454545455 1754 0.00109558183904735 366 1.72479093954639 1.72479093954639 1 5.39513342582339 794 4053 2104 3541 3786 452 366 388 1960 1754 640 1558 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 0.212301187392523 0.326713748479923 1755 2162.90909090909 1755 0.0214608650959966 1030 1.14672566625037 1.14672566625037 1 1.24344256989379 1755 2081 2874 1483 4480 1557 1030 1147 2997 2834 1554 1559 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 0.129282956782165 0.22454408283218 1485 1864.90909090909 1756 0.0125064290446263 1233 1.11350806737479 1.11350806737479 1 1.61218820401517 1482 2434 1247 2023 1756 2930 1569 1233 1932 1550 2358 1560 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 0.0492091674098697 0.113929920198937 3295 2022.36363636364 1758 0.00457687452562022 877 1.13732118014869 1.2321866436778 1 2.39464508650418 3293 877 1360 1389 1000 1900 4222 3002 1027 2418 1758 1561 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 0.000907837040296881 0.0054479548520373 915 1722 1758 8.2564716247657e-05 336 1.31719942932966 1.37448169286346 1 6.65522461240134 914 2617 595 1525 2568 2997 1738 1758 1921 336 1973 1562 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 0.0247381007531003 0.0685122577594727 1845 1743.09090909091 1759 0.00227461181758873 673 1.31212748984869 -0.831099373833084 -1 3.4095339311509 2715 1759 1372 1842 673 2035 1200 1398 1207 1844 3129 1563 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 0.0199491867543651 0.0587566870716248 1395 1622.09090909091 1759 0.00183021932143122 424 0.916470768037738 0.726956892265004 1 2.51788568517737 1394 2025 2856 2005 585 424 2030 780 1759 3090 895 1564 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 0.0707697085438386 0.149448785144852 1760 1758.90909090909 1759 0.00665039478138661 787 1.7159843833992 1.7159843833992 1 3.16165128434816 1759 1055 1861 1280 1849 3613 2209 787 1396 1653 1886 1565 M16650 KEGG_PHENYLALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHENYLALANINE_METABOLISM.html Phenylalanine metabolism 12/27 KEGG 0.0400684980227233 0.0976396160865739 3570 2077.45454545455 1760 0.0037106755625328 154 1.38161079423218 -1.10317666919681 -1 3.11564097768135 3570 620 1013 464 1760 3589 4377 4011 154 824 2470 1566 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 0.00356732653631468 0.015905596021365 1675 2148.18181818182 1760 0.000324829469535736 195 1.24287224182961 -1.24287224182961 -1 4.98889569590775 1671 1650 2385 2483 4226 1456 4130 195 2607 1760 1067 1567 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 0.111184460713496 0.19780196769303 1760 2027.90909090909 1760 0.0106578490025719 1035 1.29350777982016 1.42911232509197 1 2.0317907315919 1760 2558 1234 2233 1448 4534 1570 1556 2255 1035 2124 1568 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 0.000817987148887039 0.00499099971313107 2345 2066.54545454545 1760 7.4390131364777e-05 81 0.736186088956347 -0.736186088956347 -1 3.7821356145286 2342 1643 1955 1760 81 2071 3832 1677 1621 4653 1097 1569 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 0.0869000936692591 0.16146464668285 1150 1761.36363636364 1761 0.00823048599788544 921 1.16295835891775 1.16295835891775 1 2.05554235904684 1094 1146 1147 2753 1761 1851 921 2682 2063 2743 1214 1570 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 0.0680798554952696 0.145142039513573 555 2126.81818181818 1761 0.00702601630483044 553 0.857185672850884 0.857185672850884 1 1.60363537126798 553 2304 4483 2203 1608 622 620 1761 3785 4392 1064 1571 M2220 KEGG_FOLATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOLATE_BIOSYNTHESIS.html Folate biosynthesis 5/12 KEGG 0.0214882246228495 0.0618214011944539 2705 1843.54545454545 1763 0.00216988819227558 36 1.51150060299028 1.51150060299028 1 4.07816038984012 2705 1871 3802 1763 1076 4482 1867 514 36 1288 875 1572 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 0.00877574358053652 0.0314878517751869 3080 1986.45454545455 1763 0.000800995140674487 554 1.39187532599573 1.49361881214129 1 4.66561033707861 3080 1272 798 1103 2110 1763 3022 3238 916 554 3995 1573 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 0.00301967633614681 0.0141522050651613 1935 1702.45454545455 1764 0.000274893551462214 172 1.15288833428217 1.21865306558035 1 4.75822551096889 1931 455 1764 442 172 4623 2255 2107 1236 1534 2208 1574 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 0.161385165508919 0.262241686633255 830 2002.63636363636 1765 0.0158730158730159 827 1.64607149457283 1.64607149457283 1 2.13563622959354 827 2874 1765 2231 3624 2650 1059 2387 1412 1444 1756 1575 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 0.00146455232093965 0.00788838181140597 1765 1887.90909090909 1765 0.000133229835567478 111 1.21822665799619 1.21822665799619 1 5.71806937517334 1765 326 1622 394 111 3331 1975 4594 2618 2573 1458 1576 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 0.032316644030263 0.082706605093289 3310 2237.90909090909 1766 0.0032796458557973 835 1.90919498657043 1.90919498657043 1 4.61255564922437 3309 1180 4086 1766 835 3067 3343 1354 1039 1512 3126 1577 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 0.00348756153089874 0.0156389601280301 3710 2012 1766 0.000317554773400725 89 1.30533272794956 -1.59008010255122 -1 5.26100285003254 3710 364 1925 735 199 3654 1766 4501 89 774 4415 1578 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 0.0138562308624217 0.0439907166811029 1605 2062.45454545455 1766 0.00126766170308698 143 1.48509412128559 1.72502851406272 1 4.49674043416976 1602 3618 3080 3205 1603 143 1675 2155 1766 2946 894 1579 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 0.0839184282471183 0.156982736433532 1535 1845.18181818182 1767 0.00793650793650794 748 1.30251607587498 1.61249062461456 1 2.33775335844698 1534 1877 2593 942 1573 3427 1425 1767 748 2074 2337 1580 M3430 BIOCARTA_CALCINEURIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CALCINEURIN_PATHWAY.html Effects of calcineurin in Keratinocyte Differentiation 8/22 BioCarta 0.276514584370152 0.397103077645888 1405 2464 1769 0.031849268162114 1125 1.05077947290469 1.05077947290469 1 0.940676456788156 1405 3851 3829 4067 3492 1269 1125 1426 3278 1593 1769 1581 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 0.161385165508919 0.262241686633255 1530 2144.45454545455 1769 0.0158730158730159 1074 1.6926090099875 1.6926090099875 1 2.19601465439909 1529 3600 1626 1769 4602 2448 2293 2092 1102 1074 1454 1582 M13950 KEGG_ASTHMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASTHMA.html Asthma 12/39 KEGG 0.121878136117949 0.213693220064719 1750 2038.09090909091 1772 0.011745916990648 933 1.70932184675759 1.70932184675759 1 2.55690045174132 1746 2293 1232 2300 4530 2767 1649 933 1290 1907 1772 1583 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 0.0839184282471183 0.156982736433532 1775 1960.18181818182 1773 0.00793650793650794 892 1.35407352617234 1.35407352617234 1 2.43028857150372 1773 1885 1638 1462 1905 4324 2833 1201 892 1250 2399 1584 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 0.120120074072304 0.211206241254603 1870 1982.18181818182 1774 0.0115662118746485 1391 1.40960629219764 1.40960629219764 1 2.12456388406908 1867 2503 1573 1774 1500 2668 1621 1763 2970 1391 2174 1585 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 0.0190995143418157 0.0568931526672333 1340 1943.7 1776.5 0.00214040232030791 509 1.21455215107271 1.21455215107271 1 3.3747697152361 1337 3362 4222 NA 2742 908 2216 509 2453 875 813 1586 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 0.0107949077087877 0.0367491849053295 1780 1969.09090909091 1778 0.00108477075633531 386 0.461681800815248 0.475776068096846 1 1.47842479058487 1778 1263 4365 1332 733 2435 2060 386 2583 4148 577 1587 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 0.0641809070659994 0.138403925683973 1460 1984.81818181818 1779 0.00601213597767098 766 1.53441258415607 1.53441258415607 1 2.94130344095475 1456 1594 1093 2011 4281 2002 1779 2464 2733 766 1654 1588 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 0.0123029663819566 0.040344087099964 1825 1981.81818181818 1779 0.00112475556915362 836 1.51091402028813 1.51091402028813 1 4.70165380419132 1823 1779 836 1586 1337 4074 1940 3549 905 884 3087 1589 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 0.0227358637049856 0.0645500842264011 1785 1682.36363636364 1781 0.00208857125988359 352 1.66024971690329 -1.59008010255122 -1 4.40998982718614 1781 1571 3473 2244 636 352 2119 1960 1452 2256 662 1590 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 0.000865393884589127 0.00524610057333072 595 1841.81818181818 1781 7.87031349321511e-05 376 1.37403349312836 1.42000852643271 1 6.99266691553844 3172 678 592 559 1781 2773 4173 2757 594 376 2805 1591 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 0.00331944018259443 0.0151018414520752 1870 1757.45454545455 1782 0.000302223570938725 282 1.67592430920918 2.00685773101936 1 6.81140601308569 1866 1795 701 1417 282 3606 3648 1782 1670 751 1814 1592 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 0.00579685132673485 0.023079052945692 2175 2022.72727272727 1782 0.000528380202032275 281 1.41716624451682 1.41716624451682 1 5.17715537154533 2175 1686 1782 1339 281 4602 2911 1342 2317 1376 2439 1593 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 0.0839184282471183 0.156982736433532 2690 2231.81818181818 1782 0.00793650793650794 289 1.23390598342769 1.37307760080408 1 2.21461209591684 2687 936 1628 959 1782 4299 4205 3996 289 1162 2607 1594 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 0.00275512504082609 0.0132445064459288 1785 1939.36363636364 1782 0.000275854683436237 112 1.21884897091422 1.31357450787871 1 5.10877485340625 1782 183 4657 255 833 4048 2895 2612 798 112 3158 1595 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 0.0839184282471183 0.156982736433532 2970 2071.54545454545 1783 0.00793650793650794 595 1.44676928390063 1.5402800092065 1 2.59665873995409 2970 1783 1483 1313 1583 4382 2716 2271 665 595 3026 1596 M1011 REACTOME_MEIOTIC_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_RECOMBINATION.html Genes involved in Meiotic Recombination 54/98 Reactome 0.0042108337403019 0.0180695667647021 230 1672.09090909091 1784 0.000383537727608649 230 1.20074158169684 -1.20074158169684 -1 4.67131886675277 230 2131 1115 2350 2394 1205 1784 1010 2186 2511 1477 1597 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 0.0839184282471183 0.156982736433532 2490 1997.54545454545 1784 0.00793650793650794 754 1.39934214282505 -0.554099100968402 -1 2.51153659797869 2487 1367 2861 1784 1554 3636 1441 1417 754 2558 2114 1598 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 2.26735987948657e-06 4.44554326162095e-05 2375 1705.54545454545 1784 2.06123837842921e-07 225 1.41371915414799 1.46434328197893 1 13.7321672356155 2373 873 225 1189 923 3900 2449 1962 1784 280 2803 1599 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 0.00566570040920022 0.0226724783240924 775 1765.72727272727 1786 0.000516394928750689 188 1.37783121241481 1.54049848018994 1 5.05719519417161 774 3265 1845 3132 4618 526 390 320 2579 1786 188 1600 M11521 KEGG_GLYCOLYSIS_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOLYSIS_GLUCONEOGENESIS.html Glycolysis / Gluconeogenesis 32/81 KEGG 0.0538179360015816 0.121831327586189 3825 2054.09090909091 1788 0.00501649078807646 474 1.32281770007121 1.50049685841841 1 2.69923226694948 3822 474 1429 841 1047 1788 4218 3720 681 1795 2780 1601 M3342 BIOCARTA_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTEGRIN_PATHWAY.html Integrin Signaling Pathway 35/74 BioCarta 0.0165799063571219 0.0506146196674094 1105 1688.54545454545 1788 0.00151874475498664 160 1.9083122944764 1.9083122944764 1 5.51876007132714 1105 2467 1788 2180 3116 160 1171 1111 1971 2784 721 1602 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 0.000142391279364333 0.00129061031934481 1865 1788.45454545455 1788 1.29454996576594e-05 26 1.90919498657043 1.90919498657043 1 12.3114208598097 1862 1635 1989 1645 26 2820 1788 1506 1717 2599 2086 1603 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 2.13429802381542e-08 8.43027075828312e-07 3720 2373.09090909091 1789 1.94027094956455e-09 115 1.24490367679151 1.39937451999745 1 16.8772398713091 3719 205 115 916 1649 2982 4284 4537 1789 1558 4350 1604 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 0.0268627946723453 0.072552769933493 4640 2225.72727272727 1791 0.00247241073340314 219 1.32005112758939 1.4306341511078 1 3.35680365939782 4636 2117 1420 2209 1374 219 4206 4148 972 1791 1391 1605 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 0.232850105696956 0.34496857265126 1150 1952.36363636364 1793 0.0238095238095238 1112 1.05077947290469 1.05077947290469 1 1.08402752090912 1150 2091 3282 2526 2356 1112 1543 1759 1793 2525 1339 1606 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 0.0839184282471183 0.156982736433532 1480 1830.09090909091 1794 0.00793650793650794 317 1.30608083789791 1.30608083789791 1 2.34415138649892 1477 317 1794 478 2998 3445 2496 3363 492 1090 2181 1607 M2130 KEGG_ETHER_LIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ETHER_LIPID_METABOLISM.html Ether lipid metabolism 15/37 KEGG 0.020430402594554 0.0597235599239427 2445 1633.18181818182 1795 0.00187478494646781 318 1.28245506628788 -1.01342649604891 -1 3.50309112826629 2441 2048 1351 1795 599 2596 2093 830 318 1022 2872 1608 M2699 BIOCARTA_SODD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SODD_PATHWAY.html SODD/TNFR1 Signaling Pathway 8/15 BioCarta 0.0100060708300056 0.0347837150663252 1655 2164.27272727273 1797 0.00100514130910026 374 0.46921172998324 0.589727563671725 1 1.5275371490623 1653 1702 3870 2127 4612 1797 874 374 2106 3325 1367 1609 M4629 KEGG_NITROGEN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NITROGEN_METABOLISM.html Nitrogen metabolism 11/23 KEGG 0.131246657314442 0.227196836415026 1650 1910.18181818182 1798 0.0127090971559566 732 0.924440006815576 0.924440006815576 1 1.32792266594946 1647 732 1252 1798 3230 2044 2318 1053 2225 3187 1526 1610 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 0.000100744444165945 0.000991782490255504 3455 1952.81818181818 1798 9.15900525862973e-06 106 1.59700065130476 1.65221133158046 1 10.7059292004051 3452 529 408 129 3360 1798 4226 2349 518 106 4606 1611 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 0.050218114432105 0.115688970943455 2255 2075.81818181818 1800 0.00467294899404982 275 1.32910666695334 1.32910666695334 1 2.77871266153664 2253 1219 1049 275 4404 2793 1351 4426 923 1800 2341 1612 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 0.0701149757102206 0.148333533263248 1635 1815.09090909091 1802 0.00658678686812996 604 1.72130338621463 1.72130338621463 1 3.18394901389133 1634 1744 1802 1980 1840 1180 604 2772 2734 2293 1383 1613 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 0.141086845972788 0.240499439879405 1700 1928.72727272727 1803 0.0137309910418968 701 1.42227651173425 1.6193355577013 1 1.96460028409678 1698 701 1576 1803 2905 2729 2455 988 2596 1139 2626 1614 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 0.0124543537027127 0.0406697571086494 4145 1971 1804 0.00125247092043501 30 1.72130338621463 1.72130338621463 1 5.34292782956836 4145 166 4050 784 465 2025 3468 1804 30 1509 3235 1615 M18928 BIOCARTA_IL5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL5_PATHWAY.html IL 5 Signaling Pathway 4/16 BioCarta 0.0880921915301578 0.1632911430025 810 1962.36363636364 1805 0.00917924921578393 673 0.729152186291554 0.966623954219331 1 1.28083471960532 807 2212 3843 2629 1805 1192 673 979 3162 3280 1004 1616 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 0.00326934550740643 0.0149173836881271 2195 1872.27272727273 1806 0.000297655827559743 699 1.23884648427768 1.29295492224825 1 5.04976202302368 2193 2024 699 1516 1397 3433 2080 1257 1806 1495 2695 1617 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 0.000761927964678488 0.00470079369711562 910 1579.63636363636 1806 6.92901792624715e-05 582 1.52809934656519 1.52809934656519 1 7.93929945940085 908 2078 582 1806 2158 2255 1614 1366 1968 645 1996 1618 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 2.14084980844151e-08 8.43027075828312e-07 1425 1836.18181818182 1807 1.94622711752219e-09 116 1.29710455449603 -1.20393757412829 -1 17.5849305552887 1424 666 116 918 2358 2866 1627 3229 1949 1807 3238 1619 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 0.0455797473756227 0.107600350731571 1690 2186.45454545455 1808 0.00465425405041983 558 0.427131034658915 -0.55892706516751 -1 0.922995579866664 1686 1808 4059 1550 3012 633 1357 3582 2119 3687 558 1620 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 0.0227849580730555 0.0646309403936672 3485 1972 1809 0.00209312878364426 410 1.3421737179448 1.4161838086004 1 3.56348113361056 3483 410 2030 1367 640 449 3502 4564 1814 1809 1624 1621 M19422 BIOCARTA_IL17_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL17_PATHWAY.html IL 17 Signaling Pathway 5/14 BioCarta 0.0158969880646698 0.0487840773222285 1220 2028.09090909091 1812 0.00160118677873358 406 0.839187992563265 0.917292601435508 1 2.45686100220507 1219 1812 3842 2797 3315 754 406 458 3629 3276 801 1622 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 0.0122927901105666 0.040344087099964 1815 2288.81818181818 1812 0.00123613249994946 16 2.11775562982788 2.11775562982788 1 6.5900201333041 1812 2209 4218 1071 458 3577 4269 4524 16 1300 1723 1623 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 0.000619089018802694 0.00406764488327708 2225 1869.63636363636 1812 5.62966637868956e-05 559 1.69046909485309 1.79789030998059 1 9.01994843135503 2224 2460 559 1334 2196 3987 2763 1316 773 1142 1812 1624 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 0.00373181604487269 0.0165286294766289 995 1705.27272727273 1812 0.000339832847609931 712 1.17794902903937 1.25721317858343 1 4.68442216639526 995 1878 712 1184 3704 1821 1193 2003 1812 1949 1507 1625 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 0.0437529303466549 0.104285977418324 1815 1641.09090909091 1813 0.00405891825695385 843 1.82049391928424 1.82049391928424 1 3.98914985523664 1813 1167 1026 843 2403 2313 2309 1160 1911 978 2129 1626 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 0.00443564072109502 0.0187424818927423 520 1463.63636363636 1814 0.000404055380610493 155 1.07856324588695 1.07856324588695 1 4.15777502924906 520 2361 1913 1814 4158 230 342 289 2330 1988 155 1627 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 0.0634920664533103 0.137424398799174 665 2173.36363636364 1815 0.00653826051254136 661 0.88359379711774 0.88359379711774 1 1.69983712792232 661 1815 4326 2122 2096 1569 1469 784 3441 4085 1539 1628 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 0.147859119791321 0.249412467725749 2520 2477.27272727273 1816 0.0158730158730159 1054 1.51150060299028 1.51150060299028 1 2.03453015466121 2517 1816 4531 1206 4537 4422 2772 1516 1054 1196 1683 1629 M17787 REACTOME_GLUCURONIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCURONIDATION.html Genes involved in Glucuronidation 3/23 Reactome 0.0277660029436189 0.0740309280874059 940 1977.54545454545 1818 0.0028119157163909 400 0.569295481499247 0.569295481499247 1 1.4365515148586 937 1818 4085 1160 3030 2298 400 1855 1040 3740 1390 1630 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 0.000337008252409381 0.00252675307326457 2065 1788.72727272727 1818 3.06418080258669e-05 350 1.43465258899989 1.49313034082565 1 8.31708915247612 2062 1876 511 1833 350 4472 1818 1523 1442 1093 2696 1631 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 0.153155395240195 0.256775020427748 1175 1836.18181818182 1819 0.0149989299944717 308 0.815045663152459 0.899509250625694 1 1.0740947238858 1174 308 2178 874 1647 1819 1577 2149 2120 3856 2496 1632 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 0.0238836745918822 0.0667375665698032 1290 2104.72727272727 1819 0.0021951792260466 541 1.30246684754395 1.22428367042401 1 3.41756479137158 1287 4503 932 3211 2207 2522 949 4002 1819 1179 541 1633 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 0.0606314596583584 0.132827966320275 2595 2228.54545454545 1819 0.00566999140056771 800 1.25352121697433 1.39889910290945 1 2.45282994885351 2593 1819 1535 1625 1113 4584 2168 3219 800 1123 3935 1634 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 0.0115697264366594 0.0387222468477574 1535 2421.18181818182 1820 0.00116304079106436 270 1.46518369024774 1.46518369024774 1 4.61762287599736 1535 4527 4451 4079 3883 1820 270 935 2586 1522 1025 1635 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 0.0830932013418934 0.156982736433532 3695 2308.36363636364 1821 0.00785529817180628 858 1.31456737545359 1.46562096608083 1 2.3593830078514 3694 1821 1319 2251 1270 858 4262 4512 1715 1883 1807 1636 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 0.0835322998557535 0.156982736433532 4390 2311 1823 0.00789850114756801 1192 1.36892675765503 1.43615518063277 1 2.45694712292364 4389 1823 1192 1361 1273 1935 3785 3290 1516 1580 3277 1637 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 0.0839184282471183 0.156982736433532 480 1745.09090909091 1823 0.00793650793650794 326 1.78994529371557 1.82923282175383 1 3.21259038515828 1861 2188 1378 477 4177 1968 1823 2701 326 480 1817 1638 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 0.0456068088837068 0.107610023378172 1695 2146.81818181818 1824 0.00465707627685099 332 2.76431492756404 2.76431492756404 1 5.97321986513521 1693 2609 4644 2009 4501 1687 1893 701 332 1722 1824 1639 M95 PID_CIRCADIAN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CIRCADIAN_PATHWAY.html Circadian rhythm pathway 18832364 11/21 Pathway Interaction Database 0.000183561688193389 0.00159586284021191 2395 1917.09090909091 1825 1.66888187130298e-05 31 0.493393016758395 -0.493393016758395 -1 3.08010632470366 2393 1699 2359 1392 31 1667 893 1825 3210 3379 2240 1640 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 0.0774124933451621 0.156982736433532 1710 2175.54545454545 1825 0.0080249318638582 841 0.964916235402726 -0.810865129405406 -1 1.73182981130021 1708 2299 4664 1570 3643 2708 1825 841 1884 1437 1352 1641 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 0.147859119791321 0.249412467725749 1830 2154.09090909091 1826 0.0158730158730159 510 0.691033697677743 0.860598000235519 1 0.930154373042707 1826 510 4168 1430 2946 1752 1034 2565 1090 3873 2501 1642 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 0.00296442156677159 0.0139892038891155 975 1726.27272727273 1827 0.000269856688251397 170 0.968945821733613 0.968945821733613 1 4.00993437608918 971 2833 1075 2266 170 1886 894 1827 2683 2809 1575 1643 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 0.0269112929765249 0.072641888760366 1940 2040.27272727273 1829 0.00272428561816872 254 1.31781506034557 1.47008761331803 1 3.34954941033528 1936 381 4199 566 1754 4193 2860 1829 951 254 3520 1644 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 0.000518968378910531 0.00356059417800109 715 1740.09090909091 1829 4.71900764777435e-05 545 2.59443856790082 -2.59443856790082 -1 14.178133716814 712 3273 545 2879 1829 734 769 2424 2619 2025 1332 1645 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 0.0372869732024742 0.092586989242751 2045 1781.27272727273 1830 0.00344857729332275 552 1.26234542939433 1.26234542939433 1 2.91170419544769 2042 1830 1728 552 862 3584 2578 2214 600 1061 2543 1646 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 0.0127384609863847 0.0413668940971578 1990 1940.81818181818 1831 0.00116480207695914 386 1.15161801807835 1.23649906378136 1 3.55565131516452 1988 386 844 855 1574 3793 2551 1831 1803 2866 2858 1647 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 0.00310625531495777 0.0143975394717034 230 1653.18181818182 1832 0.000282786348391914 226 1.20074158169684 -1.20074158169684 -1 4.9357227620357 226 1832 696 2397 2352 1414 1973 1123 2345 2255 1572 1648 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 0.0839184282471183 0.156982736433532 1450 2004.45454545455 1833 0.00793650793650794 856 1.31315299181176 1.39329519485663 1 2.35684447479972 1447 3748 1833 2105 2633 2904 1679 919 856 2443 1482 1649 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 7.3516697213956e-08 2.39235585517082e-06 1835 1865.81818181818 1833 6.68333633369455e-09 140 1.24035732873892 1.24828047814734 1 15.5615702482896 1833 665 140 503 1982 3935 2541 3947 974 820 3184 1650 M9642 GALLUZZI_PERMEABILIZE_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/GALLUZZI_PERMEABILIZE_MITOCHONDRIA.html Proteins that permeabilize mitochondria. 16892093 29/69 Arthur Liberzon 0.0839184282471183 0.156982736433532 2690 1832.81818181818 1835 0.00793650793650794 127 2.00206450260642 2.00206450260642 1 3.59330153504898 2689 585 2101 433 2214 4408 2576 1529 127 1664 1835 1651 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 0.077431076862824 0.156982736433532 3560 2304.18181818182 1835 0.0072998793580155 657 1.21272672264091 1.33668958548071 1 2.17659959921684 3560 657 1121 973 1835 3181 3612 4313 1023 818 4253 1652 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 0.232850105696956 0.34496857265126 1055 2283.36363636364 1836 0.0238095238095238 804 0.333977935893232 -0.376736246525456 -1 0.344545438073919 1051 2812 3209 2988 4518 804 1231 1405 1836 4149 1114 1653 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 0.00429361929091925 0.0183241347880215 1860 1675.36363636364 1836 0.000391092898137209 227 1.30608253027885 1.26424809695537 1 5.06342199262083 1859 2325 1595 1559 227 2366 1836 3074 554 621 2413 1654 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 0.00713624939981349 0.0270553921420113 675 1690.72727272727 1837 0.000650863934298865 674 1.39463027746372 1.39463027746372 1 4.87993898388307 674 2226 776 2053 2517 2116 1340 1837 2534 931 1594 1655 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 0.190811110739535 0.300047270109216 3490 2327.18181818182 1838 0.0190634856545743 882 1.28403234944772 1.47394840773866 1 1.49830307866152 3489 882 1838 898 1784 2520 3523 3265 1734 1341 4325 1656 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 0.00150079092901666 0.00807428965943983 1215 1790 1839 0.000136528701269687 114 1.14672566625037 1.14672566625037 1 5.35656856368484 1214 1092 2507 1433 114 2273 2899 2019 2833 1839 1467 1657 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 0.0175422672807737 0.0529317865278208 1705 1736.54545454545 1839 0.00160761152393917 416 0.739899500737183 0.739899500737183 1 2.10765452769119 1701 1913 2145 1839 1171 1919 1333 461 416 4047 2157 1658 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 0.00187570154411659 0.0096482298965207 1105 1623.36363636364 1841 0.000170663878453155 506 1.37486722962488 1.53811934251307 1 6.18492445395564 1101 2172 656 1841 2120 2730 2012 1065 1747 506 1907 1659 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 0.107653686310192 0.192764682479771 1845 1958.18181818182 1842 0.0103012096671098 619 1.36860581121049 1.36860581121049 1 2.1839731365216 1842 2286 1733 1110 1428 2996 1609 3192 1939 619 2786 1660 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 0.0691017272706629 0.146852922444592 1550 2256.81818181818 1842 0.00713495193912342 307 1.86280643978199 1.86280643978199 1 3.46380546939334 1550 4034 4392 3756 2448 2315 1842 1801 307 1709 671 1661 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 0.100642079773795 0.182794103031008 2020 1677.90909090909 1844 0.00959676270712901 685 0.932543202286166 0.932543202286166 1 1.53612703303578 798 1844 2020 1684 2017 745 685 2233 2977 2623 831 1662 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 0.2857518135109 0.407248478744549 1580 1868.72727272727 1844 0.0301299267292769 1185 1.44416530821211 -0.989745402399581 -1 1.25752761738692 1577 2277 1449 1585 2370 1683 1185 1859 1981 2746 1844 1663 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 0.0286894047460814 0.0756547837029472 1815 2119.90909090909 1847 0.00264277355556234 237 0.306841605544388 -0.303548383721821 -1 0.767825962631668 1814 2353 3397 3983 865 237 1847 735 3204 4294 590 1664 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 0.0319367456221947 0.0819489597220188 1810 2357.18181818182 1847 0.0032405229757698 424 0.493393016758395 -0.493393016758395 -1 1.19642345271927 1808 2255 4509 2646 4545 747 424 1847 1743 4429 976 1665 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 0.0123323788888494 0.0403558152745448 1940 1746.54545454545 1848 0.00112745973134239 430 0.964856132670061 1.12599180986332 1 3.00216208095383 1940 2187 1591 1429 430 2455 2503 694 1475 2660 1848 1666 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 0.00374893905947568 0.0165887898325808 4270 2295.36363636364 1848 0.000341394797370658 204 1.47707503483361 1.70076842537282 1 5.86877313793494 4267 928 1422 1235 204 2147 4089 4631 1848 655 3823 1667 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 0.0818409257908181 0.156982736433532 2080 1885.63636363636 1848 0.00773218980172418 694 1.21364316535812 -0.518091344145802 -1 2.17824442885061 2080 946 1636 1422 3158 3371 2609 1883 1095 1848 694 1668 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 0.00205366218271946 0.0103701088235166 1300 1642.09090909091 1849 0.000186871068197328 93 1.07250631375009 -1.07250631375009 -1 4.74972548298572 1299 2396 2110 1849 4072 562 93 203 1997 1980 1502 1669 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 0.0473837437990173 0.110798514691714 1380 2040.18181818182 1850 0.00440328839794241 546 1.90919498657043 1.90919498657043 1 4.07141249679469 1380 3003 3050 3893 981 546 1850 833 2884 2990 1032 1670 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 0.151528425223984 0.254320272421057 1595 2246.81818181818 1850 0.0162976027982238 850 1.05077947290469 1.05077947290469 1 1.39453664713708 1591 2894 4551 3237 3366 1527 850 1661 1850 1197 1991 1671 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 0.0201024615300329 0.0590596455985794 2505 1778.90909090909 1851 0.00184441201099383 592 1.03852427879999 -0.780607447819254 -1 2.84803489334227 1260 1902 1851 2503 592 1175 2726 2220 1725 2501 1113 1672 M10066 BIOCARTA_GCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GCR_PATHWAY.html Corticosteroids and cardioprotection 13/35 BioCarta 0.000245760682044647 0.00198215930475252 845 1639.09090909091 1853 2.23443763743237e-05 28 0.756428050260993 0.756428050260993 1 4.56321533319969 842 2397 2239 2331 1853 374 257 610 3845 3254 28 1673 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 0.0862204704251013 0.160647763185696 2600 2270.63636363636 1853 0.00897606755757381 904 0.486453237539005 -0.558267199170518 -1 0.862203327387998 2600 1015 3919 1139 1342 1664 2633 4469 1853 3439 904 1674 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 0.0516547019082776 0.117902549022011 3970 2061.18181818182 1853 0.00480990468622375 928 1.65735694990685 1.65735694990685 1 3.43452488535974 3966 1012 1501 928 1027 3357 1915 2126 1122 1853 3866 1675 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 0.0288925707764299 0.0761476865345055 1190 2152 1853 0.00266174027923249 736 0.857185672850884 0.857185672850884 1 2.13958524008405 1188 3642 1984 3669 736 1853 1099 867 2876 3927 1831 1676 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 0.000250360022215034 0.00200888195907474 2445 1757.72727272727 1856 2.27625925207362e-05 483 1.08622294541485 -1.20074158169684 -1 6.53863076612178 773 1620 483 1925 1856 1767 2441 1572 2501 2445 1952 1677 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 0.316443259437065 0.437161884941652 1635 2166.54545454545 1856 0.0339947062242805 1314 1.06383215852703 1.1349371576449 1 0.853256560811171 1633 1563 1486 1474 3389 2476 1314 4115 2434 2092 1856 1678 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 0.232850105696956 0.34496857265126 4135 2374.90909090909 1857 0.0238095238095238 1293 0.946863186450032 -0.946863186450032 -1 0.976823186124385 4134 1458 1408 1293 3013 1381 1857 3231 1615 3911 2823 1679 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 2.8094592858819e-05 0.000356187010876961 1425 2102.45454545455 1857 2.55408651279594e-06 331 1.33958096556359 1.33277761977597 1 10.3099444598213 1423 3463 331 2908 2292 4411 1906 1751 1821 964 1857 1680 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 0.00309519105034821 0.0143821147954926 1615 1569 1858 0.000281777662429887 178 1.45521273094382 1.45521273094382 1 5.98325420447972 1615 2006 1858 1947 178 3414 2494 529 350 900 1968 1681 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 0.0862106697758171 0.160647763185696 1500 1717.72727272727 1858 0.00816243459251067 646 1.64216404686053 1.64216404686053 1 2.9106174986148 1199 1858 2209 1499 2768 1498 646 1920 2322 1993 983 1682 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 0.0632128019547146 0.136946458603695 2285 2052.81818181818 1859 0.0059186998400873 735 1.21455215107271 1.21455215107271 1 2.34062861770889 2282 1859 2701 2211 1135 1506 735 3985 2727 1843 1597 1683 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 0.0032285149308886 0.01477423922475 1665 2097 1859 0.000323321503305584 125 1.30930432950374 1.44027048785184 1 5.34919802415245 1664 1267 4650 578 1859 4168 2201 2356 944 125 3255 1684 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 0.0278746633253002 0.0740900013286198 1020 1809.45454545455 1860 0.00256674894670419 722 1.17575017336045 1.17575017336045 1 2.96596097252137 1019 1619 3155 1860 722 2560 1206 2369 1982 1174 2238 1685 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 0.106363586027623 0.190843831727646 965 2003.81818181818 1862 0.0101712181055385 705 1.50653800334952 1.50653800334952 1 2.418705054788 965 3236 1862 2561 3941 937 705 1301 2959 2248 1327 1686 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 0.00684213197381806 0.0261519008395689 2815 2154 1862 0.000686329036472643 328 0.577018634726521 0.577018634726521 1 2.03803771843497 2811 1479 4637 1616 328 1929 2236 1817 363 4616 1862 1687 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 0.00286257032128346 0.0136459862925069 3360 1963.27272727273 1863 0.000260572891481775 684 1.19566812492494 1.23381115734328 1 4.97700290554498 3359 1203 684 890 3095 1863 2891 2482 1768 779 2582 1688 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 0.232850105696956 0.34496857265126 1865 1792.81818181818 1864 0.0238095238095238 297 1.29675732249897 -1.20418076991769 -1 1.3377884340172 1864 489 2191 297 3978 1542 1981 2258 1579 1258 2284 1689 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 0.00672595530195543 0.0258979675800848 1395 2154.45454545455 1865 0.000613327880941891 94 0.249976904818191 -0.278722759969053 -1 0.885286120861441 1393 2973 3663 3305 1865 94 1076 1443 4227 3453 207 1690 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 0.0879233796618671 0.163107267258713 3035 2270.72727272727 1865 0.0083315783100807 1257 1.53150662091758 1.53150662091758 1 2.69192969885917 3033 1803 2257 1680 1292 4164 2628 1854 1257 1865 3145 1691 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 0.0839184282471183 0.156982736433532 2740 1776 1868 0.00793650793650794 461 1.39934214282505 -0.554099100968402 -1 2.51153659797869 2740 940 2371 1095 1387 3610 1868 984 461 2105 1975 1692 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 0.0839184282471183 0.156982736433532 2675 2133.36363636364 1868 0.00793650793650794 1013 1.3130212207285 1.39046611428808 1 2.35660797231183 2674 1328 1868 1187 1660 2551 3549 2093 1013 1214 4330 1693 M1001 BIOCARTA_RHO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RHO_PATHWAY.html Rho cell motility signaling pathway 24/53 BioCarta 0.0839184282471183 0.156982736433532 3390 2305.45454545455 1871 0.00793650793650794 576 1.26521609165203 -1.34919956916889 -1 2.27080741819632 3389 1847 2319 1824 1871 4150 1187 2152 576 1456 4589 1694 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 0.00484689832934244 0.0200110709879283 1415 1833.36363636364 1871 0.000441600886948526 250 1.20943470453601 1.25756888338647 1 4.5854953009164 1413 3000 1871 2517 250 2710 1347 2168 2046 1556 1289 1695 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 0.135339782635855 0.232820198763442 1745 1934.72727272727 1872 0.0131328795214797 1006 0.878659028734964 -0.50491279453589 -1 1.24133633812849 1743 1006 1731 1282 1569 2318 1872 2751 2189 2101 2720 1696 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 0.0394013953227244 0.0964603001866255 3245 2275.09090909091 1872 0.00401179539186279 935 0.957944910247095 -0.710694190587221 -1 2.17152461473848 3243 1872 4525 1567 935 3314 2152 1473 1059 1195 3691 1697 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 0.22177224535591 0.337191674801361 1365 1941.36363636364 1873 0.0247618733948541 630 1.46693471565438 1.46693471565438 1 1.54577273675859 1362 630 4056 1420 1928 2509 2224 2491 1873 1421 1441 1698 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 0.0394893180636377 0.0965798248675398 870 1850.09090909091 1873 0.00365604357552811 868 1.02621001772227 1.02621001772227 1 2.32504008643741 868 1721 1010 1355 2337 1936 905 1885 3449 3012 1873 1699 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 0.00317087465340457 0.014610342798283 3645 2149 1873 0.000288677645397372 33 1.02771851778922 0.970561119108649 1 4.20988439791199 3644 33 714 352 184 4620 3254 3753 949 1873 4263 1700 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 0.134476400144158 0.231778848361086 4565 2310.81818181818 1873 0.0130433375360239 772 1.49029667331855 1.59845131278817 1 2.11191062290997 4565 772 1697 1335 1565 1873 3367 3539 1418 1946 3342 1701 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 0.0243299382801272 0.0676617749440215 4030 2100.54545454545 1874 0.0024600492308929 182 1.26877050991147 1.33595627303518 1 3.31223400326187 3629 182 4149 305 1874 1253 4026 4030 910 242 2506 1702 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 0.214139132665174 0.327605607466211 1875 2397 1874 0.0238095238095238 1264 0.528380578657198 0.479859521965756 1 0.571548946983217 1874 2578 4529 2545 2585 1591 1534 1264 1561 4457 1849 1703 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 0.0829849391756604 0.156982736433532 1875 2382.72727272727 1875 0.00784464912968537 836 1.26765771445653 1.37443292069843 1 2.27518963812993 1875 3654 1251 3999 1324 4563 1575 836 3137 1792 2204 1704 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 0.0805300636335172 0.156982736433532 3705 2517.72727272727 1875 0.00836064686841071 1133 1.24457843196923 1.3139522433785 1 2.23376698612054 3702 1875 4378 1686 1295 1133 3269 4619 1535 1254 2949 1705 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 0.0134717756612117 0.0430325431141362 580 1928.90909090909 1875 0.0013554149290172 377 0.636359277453491 0.746775671775114 1 1.94042635853515 576 2575 4528 1875 2330 1301 377 432 2123 4452 649 1706 M7298 BIOCARTA_ASBCELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ASBCELL_PATHWAY.html Antigen Dependent B Cell Activation 4/14 BioCarta 0.0715823482426675 0.150942100745825 2695 2385 1876 0.00739984449725743 810 1.86280643978199 1.86280643978199 1 3.41421393992108 2695 2864 3814 1876 1267 4619 3921 810 1588 1181 1600 1707 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 0.0654177066272899 0.140407414664398 1990 1935.36363636364 1876 0.00613163293737024 848 1.63639951871907 1.63639951871907 1 3.11400494637939 1990 848 1898 2150 1155 3590 1664 1603 1876 1858 2657 1708 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 0.0535513627026571 0.121286459944249 1680 2182.3 1877 0.00609673632096214 674 0.453731770137284 0.453731770137284 1 0.927818849848178 1679 2116 4443 NA 2075 1307 674 772 3311 4340 1106 1709 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 0.117831979607876 0.20781357035849 2180 1930.63636363636 1878 0.011332816290297 434 1.1471990479491 1.28356479635459 1 1.74707003180351 2973 434 2177 1452 1488 1031 2139 4182 2176 1878 1307 1710 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 0.00294151962690427 0.0139188696049027 2475 1989.72727272727 1879 0.000267769088764976 169 1.38614325340753 1.38614325340753 1 5.74325768097542 2474 1610 2562 1869 169 4191 2223 1170 890 1879 2850 1711 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 0.0911835487023413 0.168289133209599 1745 2262.9 1880.5 0.0105673390659537 752 0.43145468075551 -0.43145468075551 -1 0.745288184253251 1741 2020 4656 NA 1443 851 752 2102 3440 4636 988 1712 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 0.213347483464671 0.327605607466211 1885 2423.36363636364 1881 0.0215790990666778 1461 1.28231996638459 1.28231996638459 1 1.38708471916724 1881 4424 1741 3303 1850 2535 1461 3112 2900 1634 1816 1713 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 0.0084371263065884 0.030624611830111 3790 1953.45454545455 1881 0.00076996890636841 42 1.81687673106179 -1.38916827744188 -1 6.13918389563578 3790 1757 2426 740 349 2297 1881 3432 42 837 3937 1714 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 0.0691648438806143 0.146920425396445 1410 1889 1881 0.00649455303872881 1067 1.00397330216119 1.05648611557279 1 1.86639633971903 1407 1881 2372 2158 1185 3105 2608 1067 1823 1247 1926 1715 M17400 BIOCARTA_ALK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ALK_PATHWAY.html ALK in cardiac myocytes 24/51 BioCarta 0.0839184282471183 0.156982736433532 3500 1953.27272727273 1885 0.00793650793650794 382 1.38993071918023 -1.73154548885099 -1 2.49464499284466 3500 2388 1633 1885 1605 1074 2268 3712 762 382 2277 1716 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 0.22252873920066 0.338122461703726 1055 2150.8 1885 0.0275801488296873 1053 0.454077585186079 -0.454077585186079 -1 0.477267945426088 1909 1485 4255 NA 2001 1053 1054 2423 1861 3996 1471 1717 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 0.0325192021009138 0.0829983556889336 1475 2028.45454545455 1885 0.00300091562485636 591 0.997152976973137 0.997152976973137 1 2.40568699666759 1471 2661 1076 2036 4175 1885 1266 591 3481 2531 1140 1718 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 0.0839184282471183 0.156982736433532 2350 1838.81818181818 1887 0.00793650793650794 588 1.69565542546603 1.69565542546603 1 3.04335911019723 2349 588 2187 605 2844 3276 1887 1333 671 1630 2857 1719 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 0.00451704276664468 0.0190178458261428 870 1529.72727272727 1887 0.000411485810137272 161 0.94471558711355 0.94471558711355 1 3.628447088179 870 2105 2272 1887 2435 485 282 2293 2173 1864 161 1720 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 0.0839184282471183 0.156982736433532 1610 1868.09090909091 1889 0.00793650793650794 756 1.4273090025766 1.4273090025766 1 2.56173146430183 1607 1298 2334 2153 1766 3223 1367 2108 756 1889 2048 1721 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 0.00013413065180107 0.00123484525410572 935 1647.63636363636 1890 1.21944391128056e-05 433 1.30034479447807 1.30034479447807 1 8.44093084228073 933 1908 433 1326 1930 2534 1890 2401 2352 1028 1389 1722 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 0.118507661896107 0.208691057363832 1585 2023.81818181818 1891 0.0114016815051048 1047 1.07643464219997 1.07643464219997 1 1.63490642211346 1584 2148 3592 3053 1496 1830 1047 2160 1296 2165 1891 1723 M8395 REACTOME_HEMOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HEMOSTASIS.html Genes involved in Hemostasis 244/615 Reactome 0.000215701199008551 0.00182450508764272 1895 2099.36363636364 1892 1.96111227774202e-05 466 1.37564602118189 1.50033896393952 1 8.40921156897792 1892 1710 466 1837 1368 4383 2721 2287 2086 991 3352 1724 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 0.156982736433532 1960 1843.90909090909 1893 0.00793650793650794 447 2.24458518468169 2.24458518468169 1 4.02857719078965 1956 2571 2022 1372 3838 1621 784 1893 447 2230 1549 1725 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 0.0954076561430513 0.174777277828905 1155 1833.81818181818 1895 0.00907411451195116 871 1.46778240338295 1.46778240338295 1 2.48160402679744 1154 2275 1183 2522 1895 4037 1933 871 2154 1167 981 1726 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 0.0765897756730953 0.156982736433532 2005 1952.81818181818 1895 0.00793650793650794 190 1.37385076578504 1.56441091893074 1 2.46578472328548 2002 382 4537 190 1632 3503 2652 1895 897 599 3192 1727 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 0.00684107292652115 0.0261519008395689 875 1750.09090909091 1897 0.00062385807756468 768 1.22866271715494 1.22866271715494 1 4.33965354004612 872 1894 768 2006 1921 1897 1674 2375 2821 2077 946 1728 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 0.0399548558938664 0.097464057635949 3570 2143.63636363636 1897 0.00369995374185821 869 1.26713150938205 1.33781076455136 1 2.85969159432404 3566 869 1904 1302 888 1115 3953 2520 1774 1897 3792 1729 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 0.000180217185751627 0.00157555547095545 1775 2212.63636363636 1897 1.63847227525963e-05 456 1.27474139041889 1.33707622013723 1 7.97365678041305 1775 1428 456 1897 3283 4308 2790 2948 1522 963 2969 1730 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 0.0570821460982685 0.127011840748569 4190 2259.63636363636 1898 0.00532903292805403 1077 0.883243632105225 -1.00834440938991 -1 1.76662179744854 4189 1898 2682 1223 1077 1517 4306 1131 1733 2700 2400 1731 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 0.177532406275049 0.2824845011222 1525 2103 1900 0.0193548618642393 917 1.70932184675759 1.70932184675759 1 2.09449821559011 1524 2924 3971 2504 2981 1471 917 1900 2590 1185 1166 1732 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 0.275742742869669 0.39623750171336 1905 2071.09090909091 1901 0.0317460317460317 623 1.46693471565438 1.46693471565438 1 1.31632880062026 1258 623 3997 1901 3825 2089 1437 2634 1903 1692 1423 1733 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 0.128568864703176 0.223386614756797 2160 2060.27272727273 1902 0.0124328325856152 938 1.44972391221222 1.44972391221222 1 2.1062393401787 2159 938 1246 1240 3954 3478 2358 1499 1902 1153 2736 1734 M9152 BIOCARTA_CCR3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CCR3_PATHWAY.html CCR3 signaling in Eosinophils 17/52 BioCarta 0.0839184282471183 0.156982736433532 2585 1907.09090909091 1902 0.00793650793650794 578 2.07333958077616 -2.07333958077616 -1 3.72122590885011 2582 1585 1949 1604 1902 1194 3150 2344 578 2223 1867 1735 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 0.147859119791321 0.249412467725749 1735 2086.54545454545 1902 0.0158730158730159 1294 2.46711003640163 2.46711003640163 1 3.32081228025611 1731 2297 4304 1582 1918 2268 2274 1902 1294 1517 1865 1736 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 0.161385165508919 0.262241686633255 1205 1906.54545454545 1903 0.0158730158730159 1087 2.06322935667965 2.06322935667965 1 2.67686268710484 1202 3100 1969 1903 2389 2768 1254 1087 1493 2332 1475 1737 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 0.0273755724530118 0.0733878332464606 1905 1953.54545454545 1903 0.0025202067160447 706 1.53245467196677 1.53245467196677 1 3.879932737245 1903 2225 1225 2106 706 3708 1589 1570 2365 1896 2196 1738 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 0.0128159494696401 0.0415609267922031 1685 2217.54545454545 1904 0.00117192932033859 271 0.897001752184515 0.897001752184515 1 2.76544804504842 1684 1582 2664 1904 3912 1722 271 2378 2673 4030 1573 1739 M9488 KEGG_RETINOL_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RETINOL_METABOLISM.html Retinol metabolism 12/101 KEGG 0.0839184282471183 0.156982736433532 1515 1901.09090909091 1905 0.00793650793650794 545 1.02401096892853 1.02401096892853 1 1.83789292586081 1513 1954 2135 2302 4384 3041 956 1241 545 1905 936 1740 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 0.0331117868429 0.0840529973704384 1755 1937.45454545455 1905 0.00305644606650806 811 0.888450090187472 0.904074553886643 1 2.13256128186985 1753 1888 2280 1951 811 2809 1017 1905 2158 2983 1757 1741 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 0.147859119791321 0.249412467725749 2370 2074.54545454545 1905 0.0158730158730159 1084 1.31212748984869 -0.831099373833084 -1 1.76616730390664 2369 2644 4521 1905 1757 1597 1084 1998 1092 1432 2421 1742 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 0.234570697428545 0.347163660601083 3395 2470.90909090909 1907 0.0240087666114882 1258 1.23018607324356 1.32280441771294 1 1.26154717531788 3394 1778 1767 1258 1907 3683 2573 1853 2397 1904 4666 1743 M86 PID_ARF6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_PATHWAY.html Arf6 signaling events 18832364 33/66 Pathway Interaction Database 0.133274546319106 0.230112204882584 1290 2214.72727272727 1908 0.0129188275531319 962 1.12915939869729 1.12915939869729 1 1.60803894865211 1289 3993 1443 3407 2752 1908 2025 962 3568 1822 1193 1744 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 0.00403658667835273 0.0174335900228211 2470 2090.90909090909 1908 0.000404393779288704 233 0.354428634883974 -0.426959545967613 -1 1.3911651133938 2468 1477 3928 1772 233 1437 2507 1908 2621 3457 1192 1745 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 0.0839184282471183 0.156982736433532 3020 2197.36363636364 1909 0.00793650793650794 885 2.07333958077616 -2.07333958077616 -1 3.72122590885011 3017 2855 1902 3243 2779 1599 3050 1039 885 1909 1893 1746 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 0.0880640061928414 0.1632911430025 2815 2243.18181818182 1910 0.00834547912232888 596 1.08173261267852 1.08173261267852 1 1.90018039269822 2813 1448 1689 596 1293 3834 3351 3306 1910 1408 3027 1747 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 0.0031759273419165 0.0146192490414742 2655 2126.63636363636 1910 0.000318047542420736 200 1.01551528977745 -0.680644994905029 -1 4.15929596468038 2655 1544 4587 1620 200 1910 2530 3441 415 1719 2772 1748 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 0.000201434379709948 0.00172248449511098 765 2104 1912 1.83138932385623e-05 463 1.34854084364781 1.34854084364781 1 8.31873505125971 763 3053 463 2401 4312 1494 1596 1912 3175 2195 1780 1749 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 0.0160668972239547 0.0492732201514738 1915 2032 1914 0.00147140453263134 511 1.52284928454087 1.52284928454087 1 4.44366512442321 1914 1682 1468 903 511 4403 2138 2639 2135 1633 2926 1750 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 0.000290886288028577 0.00223824818670265 2045 1972.18181818182 1914 2.64477051306509e-05 498 1.45983080548926 1.67475834137037 1 8.63461524124407 2044 2964 498 1397 1914 4153 2497 1362 873 885 3107 1751 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 0.0765897756730953 0.156982736433532 1365 2054.72727272727 1915 0.00793650793650794 502 0.653874098340854 0.653874098340854 1 1.17357197937409 1363 2744 3983 2601 2537 1573 839 1915 502 3538 1007 1752 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 0.000570254806363689 0.00382838685189147 2505 1974.09090909091 1917 5.18547885372508e-05 61 0.856278878635482 -0.498005606198256 -1 4.61921944636227 2505 1698 1996 1543 61 3435 1917 1090 3042 1872 2556 1753 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 0.104661745741284 0.188278202397265 2175 1836.54545454545 1918 0.01 154 1.29054757055075 1.29054757055075 1 2.08886965929487 2171 154 1242 661 2751 4237 2795 2140 1224 909 1918 1754 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 0.0410305308745956 0.0996212785898212 2045 1844.36363636364 1918 0.00380148696233185 456 1.41779984091228 1.49040562118216 1 3.16963721915866 2041 1969 1918 1087 899 4618 2076 2599 820 456 1805 1755 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 0.0026407848044231 0.012823541547696 2360 1849.36363636364 1921 0.000240360002315783 156 1.49519829363167 1.49519829363167 1 6.31389924091486 2358 1088 1921 764 156 3244 1912 3044 1879 1984 1993 1756 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 0.136776196163898 0.23467548404327 1105 2389.63636363636 1922 0.0132820312076851 969 0.413535386464399 -0.475342870987107 -1 0.581045624746554 1104 3061 1879 3889 2301 1322 1922 969 3759 4597 1483 1757 M4844 KEGG_CHEMOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHEMOKINE_SIGNALING_PATHWAY.html Chemokine signaling pathway 87/239 KEGG 0.239888283939621 0.353384627016996 1905 2229.54545454545 1923 0.0246271218542544 1199 0.912675857585476 1.03118003827412 1 0.920230312589352 1902 1199 1581 1834 1923 3717 2669 1404 2267 2923 3106 1758 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 0.0295090573558728 0.0774970885603814 2790 2130.18181818182 1923 0.00271931495441431 567 1.21146854664337 1.39206371989953 1 3.0032686546392 2790 567 1844 1829 748 3619 3077 2412 1923 1038 3585 1759 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 0.00859566120213067 0.0310557196555006 930 2300.63636363636 1923 0.000784493666544913 796 1.43583931982769 1.43583931982769 1 4.83221175202066 929 3803 796 2661 3917 1923 1313 4133 2864 1270 1698 1760 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 0.124755590644781 0.217648807803963 1065 2028.45454545455 1924 0.0120407508429617 756 1.08196515182584 1.08196515182584 1 1.59922904273457 1065 2604 2229 1924 4415 1816 756 1597 2488 2062 1357 1761 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 0.236476264093486 0.349456882227081 2185 2101.81818181818 1925 0.0242299050543184 759 0.337412299256329 -0.317393706250111 -1 0.34386063460064 2181 1595 3368 2929 1925 759 1667 1826 2028 3536 1306 1762 M15258 BIOCARTA_AKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKT_PATHWAY.html AKT Signaling Pathway 16/33 BioCarta 0.00140477290674658 0.00762777038356254 1410 1932.54545454545 1927 0.000127788245771422 108 0.653874098340854 0.653874098340854 1 3.09042427916715 1410 2002 3306 2293 108 1226 651 1927 3302 3241 1792 1763 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 0.0505582655028288 0.116301962685241 590 1544.90909090909 1927 0.00470535994630547 341 1.59008010255122 -1.59008010255122 -1 3.31617475869274 589 2283 1927 2174 2033 341 744 1097 2344 2563 899 1764 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 8.83710229540133e-10 4.989236307982e-08 1350 1957.45454545455 1927 8.0337293626828e-11 80 1.63071308545472 1.63071308545472 1 26.5764465796166 1350 1927 80 1532 2580 3430 1781 2563 2072 1589 2628 1765 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 0.0134687931739601 0.0430325431141362 1545 2471.90909090909 1927 0.00123199684402771 415 0.34494863493622 0.471136646557952 1 1.05183887036193 1542 3732 2086 3656 1927 1869 1341 415 4213 4550 1860 1766 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 0.450578966652235 0.573555553184724 1210 1934.09090909091 1930 0.0529889956309465 1206 1.46693471565438 1.46693471565438 1 0.790445081793798 1206 1387 1966 2236 2400 2495 1930 1714 2487 1916 1538 1767 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 0.000328790482932463 0.00248501968229278 2050 1689.27272727273 1930 2.98945119114446e-05 312 1.37870214302981 1.38875326765605 1 8.01498550322978 2047 1930 509 1468 312 3801 2659 1965 673 339 2879 1768 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 0.223126577807433 0.338701374669786 1935 2030.27272727273 1932 0.0249317249743267 856 1.46693471565438 1.46693471565438 1 1.53942062680272 1441 856 4014 2058 1932 2630 1935 2460 1900 1506 1601 1769 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 0.124984977097016 0.217788597952299 2735 2113.90909090909 1932 0.0120642924717741 992 1.15702385788737 1.20799287448596 1 1.70945158523362 2732 1040 1533 992 1527 3690 1932 2331 1944 1810 3722 1770 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 0.00160669751864223 0.00857515327147777 200 1649.54545454545 1933 0.000146170192579861 196 1.3956728289633 1.39209037572801 1 6.43802751744128 2604 196 644 196 1933 2653 3134 2018 730 296 3741 1771 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 0.0134912092817652 0.0430359473753244 1490 1812.18181818182 1934 0.00123405997025436 849 1.12459639064914 -0.880581973244883 -1 3.42910315267231 1486 1135 849 1934 1173 2550 1813 2347 2008 1960 2679 1772 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 0.232850105696956 0.34496857265126 1690 2222.54545454545 1934 0.0238095238095238 1314 1.62371583222612 1.62371583222612 1 1.67509234212791 1687 1314 1613 2222 3415 2498 2215 4337 1605 1934 1608 1773 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 0.086676579835499 0.161241148514946 1935 2039.45454545455 1935 0.00820841835937092 849 1.23719790437856 1.23719790437856 1 2.18842273220894 1342 3048 1856 1932 2281 2120 1814 849 2710 2547 1935 1774 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 0.292888934096137 0.415524536837571 1755 2002.72727272727 1935 0.0310149923214266 1259 1.36581529303493 1.36581529303493 1 1.16266875536243 1752 2427 2994 1259 2056 1644 1326 1935 2355 2786 1496 1775 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 0.101258093362728 0.183699351721929 1935 2066.45454545455 1935 0.00965845236280369 1341 1.44290484918711 1.44290484918711 1 2.36990835146118 1935 2375 2323 2111 1376 3772 2636 1524 1662 1676 1341 1776 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 0.0839184282471183 0.156982736433532 2290 1926.54545454545 1937 0.00793650793650794 145 1.806917851326 1.806917851326 1 3.24305269905356 2290 1751 1707 913 3445 3032 2446 1937 145 1023 2503 1777 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 0.0391110173231175 0.0958547213264272 1740 2276.36363636364 1938 0.00362037597768835 288 1.700555425947 1.700555425947 1 3.86529794501601 1738 4046 3154 4070 1493 288 834 1938 3434 3066 979 1778 M14811 LEE_LIVER_CANCER_ACOX1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_ACOX1_DN.html Genes down-regulated in hepatocellular carcinoma of ACOX1 [GeneID=51] knockout mice. 15565109 38/128 Yujin Hoshida 1.20221215271863e-05 0.000179969842254713 4655 2263 1938 1.09292611125296e-06 265 1.57346113641123 1.17095805733795 1 13.151165222794 4651 1435 290 1032 265 4100 3721 3177 1938 704 3580 1779 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 0.000417889510322634 0.00300992951050439 1185 2077.18181818182 1938 4.17968115366583e-05 53 0.607060817135276 0.54668966435344 1 3.41633954465129 2309 750 4673 1182 53 1185 1242 2035 2825 4657 1938 1780 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 0.0173536392732126 0.0525317529937172 4320 2207.27272727273 1939 0.00159018691740388 370 1.43665710749197 1.43665710749197 1 4.10298076684489 4317 903 1939 1549 531 2347 4569 2422 1130 370 4203 1781 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 6.64623369683697e-05 0.000710872450189637 1880 2061.63636363636 1939 6.0422131718794e-06 383 1.24437059468309 1.29602949728934 1 8.74364982960095 996 3085 383 2952 2245 3471 1878 1407 2445 1877 1939 1782 M923 REACTOME_RAP1_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAP1_SIGNALLING.html Genes involved in Rap1 signalling 12/20 Reactome 0.245825979053622 0.360657651172597 1940 2193 1940 0.0253222509564576 1635 1.61198806678074 1.61198806678074 1 1.59349906588402 1635 2512 2641 2772 1939 1815 2380 1843 2729 1917 1940 1783 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 0.161385165508919 0.262241686633255 1785 2197.36363636364 1942 0.0158730158730159 1105 1.98776016362052 1.98776016362052 1 2.57894789819413 1785 1942 1435 1572 2671 3837 3089 2758 1105 1492 2485 1784 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 0.00103355719716716 0.00606163833031956 2435 1739.81818181818 1943 9.40039164205518e-05 92 2.59443856790082 -2.59443856790082 -1 12.8401159104791 2433 718 726 1943 92 1990 3890 1968 1852 1069 2457 1785 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 6.45407844175769e-08 2.14495117575011e-06 1945 1679.90909090909 1943 5.86734421009018e-09 137 1.24839945505299 1.25096620023728 1 15.7945626064231 1943 874 137 834 1588 3134 2598 2318 1987 233 2833 1786 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 3.37580720681855e-11 2.72741940881926e-09 790 1747.36363636364 1944 3.06891564260941e-12 56 1.41710624309309 1.45986225040807 1 27.0876422290807 787 3147 56 2399 1958 2980 1318 1863 2450 319 1944 1787 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 2.75472627229091e-05 0.000351734259181341 2995 1888.36363636364 1945 2.50432796923085e-06 12 1.4595258986439 -1.16186250822327 -1 11.2508853946369 2995 2101 1791 758 12 2264 1327 4225 1945 829 2525 1788 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 0.161385165508919 0.262241686633255 3840 2078.81818181818 1947 0.0158730158730159 840 1.51935086267539 -1.51935086267539 -1 1.97122710555338 3839 840 1755 961 1963 2749 1688 1947 1184 2107 3834 1789 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 0.249004336506659 0.364863765125143 1850 2329.72727272727 1947 0.0256963899004978 1381 1.29224067598669 1.29224067598669 1 1.26289552307086 1847 2588 2936 2247 1947 2763 1698 4492 1897 1831 1381 1790 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 0.152909400458909 0.256454348801163 1900 2593.54545454545 1948 0.0149729218811221 1004 0.94976353022885 0.94976353022885 1 1.25278090801869 1900 3896 1683 4054 2449 1948 1111 1004 4229 4549 1706 1791 M9546 BIOCARTA_TID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TID_PATHWAY.html Chaperones modulate interferon Signaling Pathway 17/35 BioCarta 0.115617724664069 0.204447040670123 2210 1873.72727272727 1949 0.0111074760456717 766 1.1921467147981 1.1921467147981 1 1.83439398272859 2206 1949 2089 766 1477 3117 1681 1114 1788 2225 2199 1792 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 0.175818059037932 0.28023245736454 1370 2412.81818181818 1949 0.0174249416073716 875 0.473591876160097 0.523072034196165 1 0.583984862332411 1366 2203 1706 3373 4234 1949 875 1309 3819 4510 1197 1793 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 0.00109945016496701 0.00628295545492121 45 1819 1950 1e-04 44 1.31390253588654 1.39814943758314 1 6.45695377783396 2556 44 1832 45 560 3888 2337 2618 506 1950 3673 1794 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 0.104501718479627 0.188278202397265 1950 2403.54545454545 1950 0.0109768079654669 917 0.970454883618695 0.970454883618695 1 1.5707702748281 2886 1251 4616 1741 1969 1429 1949 917 3140 4591 1950 1795 M3126 KEGG_LEISHMANIA_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEISHMANIA_INFECTION.html Leishmania infection 38/98 KEGG 0.161385165508919 0.262241686633255 2475 2034.09090909091 1951 0.0158730158730159 604 1.15718040181069 1.15718040181069 1 1.50134207316044 2475 1065 1951 604 3937 3467 2114 1586 1364 702 3110 1796 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 0.0839184282471183 0.156982736433532 1955 1956.18181818182 1952 0.00793650793650794 228 2.24458518468169 2.24458518468169 1 4.02857719078965 1952 2816 1380 1385 2930 3167 2838 895 228 1910 2017 1797 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 0.000372756810558929 0.0027507691563451 1080 1950.09090909091 1952 3.38927257784302e-05 519 1.33706616283581 1.33706616283581 1 7.64126058632932 1079 2904 519 2116 1404 3136 1598 1952 3157 1279 2307 1798 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 0.0122518997768024 0.0403176982823708 2805 2176.45454545455 1952 0.00112006072050057 304 1.27840814233382 -1.24287224182961 -1 3.97895411587439 2803 304 1952 1345 428 4431 1629 4385 870 2271 3523 1799 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 0.00888582208745182 0.0317128425756277 1645 1912.81818181818 1954 0.000811083297857369 358 1.24188916176471 1.24188916176471 1 4.15428114522262 1645 3514 2296 1967 358 1954 1639 2247 3110 521 1790 1800 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 0.0116278578727546 0.0387842420158297 1955 2278.54545454545 1954 0.00116891529381414 440 0.653874098340854 0.653874098340854 1 2.05971334597052 3002 1186 4279 1954 440 2706 1954 1842 1858 4032 1811 1801 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 0.0951071856280721 0.174294983125986 1295 1960.27272727273 1954 0.00904419655864823 869 1.43053419217618 1.43053419217618 1 2.42245954166124 1294 2036 1300 2694 1591 4576 1988 869 1954 1095 2166 1802 M1870 REACTOME_GLUCOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_METABOLISM.html Genes involved in Glucose metabolism 36/81 Reactome 0.00380352074042444 0.0167277883406397 1215 1671 1955 0.000346373864123903 60 1.47423048862313 -1.23889395501682 -1 5.84554736093707 1211 2425 2805 2129 3357 60 1072 835 2196 1955 336 1803 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 0.209388273829924 0.323079832455391 3180 2234.81818181818 1955 0.0211324493189441 1244 0.522908044083247 0.60288660392483 1 0.572680266587292 1843 2097 1356 3177 3177 1784 1950 1244 2064 3936 1955 1804 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 0.0702665077996493 0.148587028677417 1205 1921 1955 0.00660150473181428 659 1.36303277629485 1.36303277629485 1 2.51898864469057 1201 2939 1620 3155 1955 2110 1106 925 2965 2496 659 1805 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 0.0373035074029693 0.092586989242751 1660 2116.63636363636 1956 0.00345013324738181 625 1.54678721066276 1.54678721066276 1 3.56779270230473 1656 2832 1671 2622 1956 3948 2656 625 971 1815 2531 1806 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 0.055541619844184 0.124601605911306 1215 1831.90909090909 1958 0.00518140800074269 730 1.06710845596515 1.06710845596515 1 2.15419660202308 1213 2321 2412 1958 3327 1442 793 730 2172 2692 1091 1807 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 0.145743996376119 0.247358336478991 3190 2301 1958 0.0142183472023287 1269 1.73380331901047 1.96974416261889 1 2.34765552613713 3187 2418 1269 1284 1862 3764 2479 1815 1958 1475 3800 1808 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 0.182357272039274 0.288957156643142 1170 2181.54545454545 1958 0.0181362317803991 957 0.974408598321829 0.974408598321829 1 1.17258301404625 1166 3110 2620 3769 2699 1715 1958 1126 3105 1772 957 1809 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 0.214139132665174 0.327605607466211 2505 2325.27272727273 1958 0.0238095238095238 1311 1.33403223803043 -1.33403223803043 -1 1.44302185161392 2502 1958 4457 2465 4548 1329 1415 2307 1572 1714 1311 1810 M7146 BIOCARTA_CLASSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CLASSIC_PATHWAY.html Classical Complement Pathway 8/17 BioCarta 0.0998362098982874 0.181611987415906 1100 2078.72727272727 1959 0.0104627351061785 715 1.11882204112119 1.11882204112119 1 1.85000997941914 1099 1959 3823 2145 3830 1241 715 2110 3215 1592 1137 1811 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 0.00342774840677197 0.0154744017669879 3380 2282.09090909091 1959 0.000312100068063259 705 1.50634057005504 1.88937736178133 1 6.08658850970516 3378 984 705 781 2433 4136 3129 1614 1941 1959 4043 1812 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 0.254709357736574 0.372175880995817 1470 2273.45454545455 1961 0.0263715795321161 936 0.653874098340854 0.653874098340854 1 0.626449098227738 1469 1756 3130 1961 3712 936 1032 2582 3164 3644 1622 1813 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 0.161385165508919 0.262241686633255 2660 2223.45454545455 1963 0.0158730158730159 277 1.22653992693785 -1.05907054614109 -1 1.59133009325829 2656 277 1963 1034 1959 4014 1354 4441 1349 2017 3394 1814 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 0.0839184282471183 0.156982736433532 1920 2049.36363636364 1964 0.00793650793650794 982 1.32228409860519 1.48318405576221 1 2.37323296778569 1917 1964 1997 1439 1723 3013 2930 2295 982 1237 3046 1815 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 0.0765897756730953 0.156982736433532 1965 2154.45454545455 1964 0.00793650793650794 379 1.21603194922395 1.27748823102094 1 2.18253181355829 1964 379 4686 835 1351 4140 2111 2641 998 1227 3367 1816 M19043 ST_ADRENERGIC http://www.broadinstitute.org/gsea/msigdb/cards/ST_ADRENERGIC.html Adrenergic Pathway 22/55 Signaling Transduction KE 0.0296414037273978 0.0777278219734674 1510 1950.63636363636 1966 0.00273167933023148 570 1.41986813279968 1.41986813279968 1 3.51580620545941 1507 2693 2263 2260 3422 2764 1943 570 704 1365 1966 1817 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 0.0511701022668975 0.117024450572319 3100 2398.90909090909 1966 0.00476368477571166 1023 1.28984589065016 1.42543241292779 1 2.682281639743 3100 1769 2519 1966 1023 1428 4462 4381 1504 1903 2333 1818 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 0.0419274147184994 0.100806498394504 3190 2362.72727272727 1966 0.00388622322804852 672 1.13576910664916 -1.13365701803285 -1 2.5261079657851 3188 672 1207 1064 915 4050 3228 3698 1329 1966 4673 1819 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 0.00897811406596544 0.0318964689257877 4470 2252.36363636364 1967 0.00081954219167724 414 1.29513471661287 1.48415517346972 1 4.32514636516261 4466 1967 799 985 2233 1306 4332 4224 936 414 3114 1820 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 0.0839184282471183 0.156982736433532 1970 2085.81818181818 1969 0.00793650793650794 450 1.14283854555333 1.14283854555333 1 2.05116443282194 1969 1350 2756 450 4017 2973 1748 1834 638 2016 3193 1821 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 0.161385165508919 0.262241686633255 1905 2238.09090909091 1970 0.0158730158730159 1215 1.07643464219997 1.07643464219997 1 1.39658139284519 1904 3216 3588 3432 1950 1912 1215 2131 1322 1979 1970 1822 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 0.00386085308198942 0.0168610974298252 1095 2121.63636363636 1970 0.000351604119551622 213 0.522536967759313 0.522536967759313 1 2.06791781205214 1093 2792 3706 2532 213 300 1401 1970 4092 4326 913 1823 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 0.0956179249911956 0.175094019737688 1970 2339.90909090909 1970 0.01 174 0.638085500184385 0.671556413365441 1 1.0777018502052 1970 174 4491 1575 3889 2007 1361 1828 1564 4401 2479 1824 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 0.0171270735170815 0.0519465802595754 2610 1779.81818181818 1971 0.00156926181151349 530 1.19290487863563 1.27079642507874 1 3.41979614473611 2609 1971 1929 1548 530 933 2927 2115 2009 698 2309 1825 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 0.0187035464080784 0.0558603049510871 2980 1883.18181818182 1972 0.00171495231003489 559 1.16923296876586 -1.06617321551576 -1 3.26960938946916 2976 2263 1972 1923 559 911 2174 2310 1833 2206 1588 1826 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 0.108981145901483 0.19469525340997 1975 2464.54545454545 1973 0.0114726505367468 770 0.403667128673152 -0.443461547205088 -1 0.640258602845354 1973 1869 4305 3370 3353 770 1972 1105 3535 4056 802 1827 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 9.664853111205e-06 0.000149470302571309 4170 2136.63636363636 1973 8.78626870025255e-07 282 1.32033498881485 1.4213571711459 1 11.2731596897966 4169 1404 282 856 782 2046 3397 4457 1973 566 3571 1828 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 0.0322300760095035 0.0825301290604009 860 1802.18181818182 1975 0.00297383317056917 445 1.02401096892853 1.02401096892853 1 2.47609882525716 860 2484 2455 3691 3147 577 679 825 2686 1975 445 1829 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 0.1785719743933 0.283657041358306 1790 2503.63636363636 1976 0.0177238657968448 884 1.21455215107271 1.21455215107271 1 1.48336120025901 1789 4064 3001 3525 4431 1519 884 1200 3341 1976 1810 1830 M8 PID_ENDOTHELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ENDOTHELIN_PATHWAY.html Endothelins 18832364 46/104 Pathway Interaction Database 0.109908384000399 0.196127451418838 2095 2088.18181818182 1977 0.0105288056252872 926 1.40357105595644 1.40357105595644 1 2.21624025833063 2095 1570 1196 1376 1977 4272 3116 957 2504 926 2981 1831 M10 PID_BCR_5PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BCR_5PATHWAY.html BCR signaling pathway 18832364 44/107 Pathway Interaction Database 0.302992921559434 0.422566913817711 1315 2082.54545454545 1978 0.0322819640718963 1133 1.05547168587539 1.05547168587539 1 0.881290495412232 1314 1978 3305 1266 3401 1660 1133 2164 2510 2254 1923 1832 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 0.0839184282471183 0.156982736433532 2800 1929 1978 0.00793650793650794 123 1.31488673670211 1.48057734419716 1 2.35995619680863 2799 123 1885 327 4383 2961 1978 3086 130 408 3139 1833 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 0.215820186677792 0.329531897938135 3070 2196.90909090909 1980 0.0218590896370799 1188 1.31505585488108 1.31505585488108 1 1.41502194023441 3066 1935 1980 2439 1858 1188 3601 1540 2343 2800 1416 1834 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 1.90512669221732e-10 1.2938295188015e-08 770 1847 1980 1.73193335671118e-11 67 1.32915639070833 1.38225379470614 1 23.4007248094406 770 2493 67 1475 1980 3400 1747 3328 2430 205 2422 1835 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 0.013000805606944 0.0420150172925102 590 1760.90909090909 1981 0.00118893409049478 391 1.05077947290469 1.05077947290469 1 3.22847528229594 587 2153 3055 2655 4398 391 581 407 2719 1981 443 1836 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 0.0240893464606405 0.0670722979884499 1595 1985.54545454545 1982 0.00221429394110772 666 1.22168558101711 1.22168558101711 1 3.19967681164459 1593 3695 1982 2365 666 2112 1152 846 3050 2490 1890 1837 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 0.00629043886042845 0.0246051723705908 1330 2027.45454545455 1983 0.000573499761970277 756 1.12849157547885 -0.791140711360448 -1 4.0525351559302 1329 1361 756 1600 1983 3602 1796 2311 2421 2799 2344 1838 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 0.0192929933306617 0.0572558370788351 930 2096.54545454545 1984 0.00176948098746415 894 0.651603535876874 0.729041829469378 1 1.80654007655511 926 1952 894 2118 2932 1984 1685 1917 2303 4092 2259 1839 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 0.246076811087867 0.360912656262205 1305 2562.18181818182 1984 0.0253517253897304 928 0.26609463327964 -0.280255607918345 -1 0.262860304978388 1303 3964 3603 3863 1940 928 1984 1302 3560 4327 1410 1840 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 0.17539979306514 0.279756102894229 1690 2010.54545454545 1986 0.0173796203103949 938 1.0469657782853 0.989517413316311 1 1.29273721485878 1690 2349 2858 2073 1986 1807 1490 2832 2201 1892 938 1841 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 0.00668526620106376 0.0257836686569422 1990 1995.63636363636 1987 0.000609606177295572 184 0.904374658176375 0.904374658176375 1 3.20669468411695 1987 3097 3014 3492 1231 184 1157 522 3813 3249 206 1842 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 0.0250478014338628 0.0690491057310524 2090 1790.18181818182 1987 0.00230341907652159 371 1.38933387508025 1.38933387508025 1 3.59964166939871 2086 1536 2048 2280 3824 473 371 2865 1660 1987 562 1843 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 0.288190732059453 0.41034997582212 1465 1883.81818181818 1988 0.0304314661143326 772 1.2303348545442 1.2303348545442 1 1.06228373033222 1465 996 1988 772 2048 2563 3004 2364 2161 1543 1818 1844 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 0.209121745053255 0.322774867364806 1990 2289.27272727273 1988 0.0211024545472007 1021 0.916263038179659 0.916263038179659 1 1.00431491325236 1103 1746 1990 3420 4590 2531 1293 1158 1988 4342 1021 1845 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 0.0839184282471183 0.156982736433532 2615 2255.72727272727 1989 0.00793650793650794 234 1.26715109826347 1.26715109826347 1 2.27428036435684 2613 727 2779 1896 3775 1566 4062 3325 234 1847 1989 1846 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 0.0372557536602834 0.092566522615105 2855 2239.63636363636 1990 0.00344563943865098 860 1.38884451320015 1.55182876834609 1 3.20378242020594 2855 1968 1231 1990 860 4254 1886 1870 2241 2031 3450 1847 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 0.0217030183409861 0.0623163872217286 985 2125.27272727273 1991 0.00199273847458717 913 0.684249421628269 0.692277615032315 1 1.8408752716987 982 1914 913 3316 1991 2309 1297 1282 3071 4270 2033 1848 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 0.0544443171031501 0.122893097276186 1025 1702.36363636364 1993 0.00507638955099254 534 1.18159797254922 1.18159797254922 1 2.40113251880205 1022 2289 2509 2134 1993 795 534 2327 1706 2234 1183 1849 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 0.26523693430619 0.385156577055719 1355 2252.63636363636 1996 0.0276299485214755 1355 0.954267778734809 0.962312587885229 1 0.882531975641539 1355 3694 1664 3201 1988 1846 1996 1964 2422 2486 2163 1850 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 0.02600637866118 0.0710588282252416 1860 1879.27272727273 1996 0.00239263528287408 687 1.31394404283802 1.31394404283802 1 3.36777280648223 1860 2008 2297 2407 687 2389 1828 2557 894 1996 1749 1851 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 0.0103906419957997 0.0357755682529886 2250 1988.27272727273 1997 0.000949094924081839 391 1.36169809360883 1.36169809360883 1 4.39595095601542 2248 1941 1970 2283 391 3526 1822 2341 782 2570 1997 1852 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 0.059772269369617 0.131314043256458 1170 2017.72727272727 1998 0.00558734751650954 746 1.65198623575143 1.65198623575143 1 3.25088282557003 1169 1998 1753 2896 3660 2016 1143 746 2848 2380 1586 1853 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 0.200051065301797 0.311234824702596 1665 2438.72727272727 1999 0.020087091802277 1084 1.39998190320723 1.39998190320723 1 1.58392418524056 1665 3747 1863 3172 1811 4592 3221 1435 2237 1084 1999 1854 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 0.243400467145473 0.357771201080203 2150 2397.72727272727 2000 0.0275067247476636 1124 0.412562099886372 0.440529295041985 1 0.411043548649464 2150 1546 4680 2374 2000 1234 1124 1240 4035 4672 1320 1855 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 0.0580214126888094 0.128430958837865 3035 2270.45454545455 2001 0.00541914822014612 414 1.43805443300295 1.43805443300295 1 2.86083979295434 3034 1734 2093 1781 1087 3145 2001 4377 414 1748 3561 1856 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 0.298735036746822 0.4173739958842 2005 2019.36363636364 2001 0.0317460317460317 1014 0.992772228549397 0.992772228549397 1 0.840837168323396 1014 3089 2004 3032 2843 1840 1154 1699 2001 2360 1177 1857 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 0.0539197214239821 0.121943925961766 3880 2358.72727272727 2002 0.00502622173954611 620 1.03979285587352 1.11610209802955 1 2.12078413292971 3880 1002 2002 1273 1048 3537 3332 3824 1221 620 4207 1858 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 0.0283520697756012 0.0750185200273672 1735 1966.63636363636 2002 0.00261128934968451 962 1.14199312084068 1.12877881336218 1 2.86701863293856 1735 2373 962 2762 1727 2662 1436 2015 2939 1020 2002 1859 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 0.232850105696956 0.34496857265126 2005 2189 2003 0.0238095238095238 404 1.36236146820978 1.42210608139987 1 1.4054683814056 2003 566 2841 404 3774 2303 1865 4560 1592 1562 2609 1860 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 0.0412188346259666 0.099974875288447 2870 2278.81818181818 2003 0.00381927164667431 900 1.53820718917955 1.69013236431478 1 3.43353740535431 2869 1057 2161 1902 900 4659 2367 1886 2003 1680 3583 1861 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 0.0141006298708455 0.0445253042956752 1570 1940.72727272727 2003 0.00129016595395355 470 1.58697504743982 1.58697504743982 1 4.78664645433929 1570 2991 2003 2570 470 2077 1296 2044 2730 1931 1666 1862 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 0.0396401722100383 0.0968476782983521 1515 2495.90909090909 2005 0.00367027022608609 450 0.404032221620958 0.42626484337522 1 0.914313851725427 1511 3354 2005 3992 4525 1062 450 1606 3950 4194 806 1863 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 0.102497709771096 0.185445663315581 3120 2155.72727272727 2005 0.00978270827744196 735 1.24573852495283 1.34579752461686 1 2.03464645072311 3118 957 3458 1391 1382 735 3640 2937 1776 2314 2005 1864 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 0.0839184282471183 0.156982736433532 4160 2549.54545454545 2006 0.00793650793650794 749 1.01204873808118 1.01204873808118 1 1.81642313684469 4158 1508 1419 1142 1371 2696 4492 4605 749 2006 3899 1865 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 0.00739896004326514 0.0277816720855292 1300 1948.18181818182 2008 0.000674905614095888 320 0.916569957193614 0.970748814031729 1 3.18362714033923 1300 1418 2008 1714 320 2649 1780 2493 2522 2375 2851 1866 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 0.280537809712687 0.401889796295654 1685 2043.54545454545 2008 0.0294884125062 1232 1.30268536872269 1.30268536872269 1 1.15105727720325 1683 2505 1672 2252 2026 2061 1232 1718 3572 1750 2008 1867 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 0.0751556966791391 0.156982736433532 1165 2005.27272727273 2008 0.00707755136066269 426 1.28409334700263 -1.27675999939789 -1 2.304688279948 1165 2037 1677 2737 2985 426 963 3856 3366 2008 838 1868 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 0.0463940650021574 0.109113869654205 4645 2131.72727272727 2010 0.00430930264043874 447 1.1963737987547 1.41556901115243 1 2.56906864935361 4645 868 2498 996 969 447 4267 3344 2010 1148 2257 1869 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 0.000416163800274118 0.0030048437104538 1245 1752.36363636364 2011 3.78402313550572e-05 206 2.02976440380949 -2.59443856790082 -1 11.4261767840837 2595 1244 524 1242 206 2011 3800 2039 2097 835 2683 1870 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 0.0637580101309217 0.1378726513491 2240 1847.09090909091 2012 0.00597130950670055 492 1.56861719367521 1.63130794353416 1 3.01271770270051 2239 1128 1091 551 2012 4468 2328 2765 503 492 2741 1871 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 0.0839184282471183 0.156982736433532 1220 1899.90909090909 2012 0.00793650793650794 156 1.806917851326 1.806917851326 1 3.24305269905356 2199 1372 2012 769 3338 3570 3016 1218 156 1217 2032 1872 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 0.305997863551899 0.425625354914998 2750 2171.27272727273 2012 0.0326619850924233 1186 1.2748667753726 1.2748667753726 1 1.05556768063268 1948 3625 2713 2511 2750 2012 1406 1599 2749 1385 1186 1873 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 0.0263575099235507 0.0717671653118876 3760 2394.72727272727 2013 0.00266754536391747 569 1.28840473254089 1.48669793622531 1 3.28992547966305 3756 1399 4663 1375 737 569 4032 3750 997 2013 3051 1874 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 0.032870811822167 0.0837133827166711 745 1948.63636363636 2014 0.00333674022542964 343 0.55936453995665 -0.55936453995665 -1 1.34484703721768 745 2014 3979 2587 2697 343 703 838 3526 3532 471 1875 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 0.0231740807273152 0.0654179170410838 2015 2003.90909090909 2014 0.00212925914618862 636 1.48617808816858 1.62399532333239 1 3.92837866482105 2014 1936 2273 2155 649 3236 2238 3741 1256 636 1909 1876 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 0.00634134285574206 0.0247282698580666 3415 2068 2014 0.000578154129669816 208 1.30942315764829 1.4037193720176 1 4.6959459476508 3415 1400 759 1347 2526 2086 3969 2014 908 208 4116 1877 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 0.214139132665174 0.327605607466211 2015 2421.27272727273 2015 0.0238095238095238 1393 1.73041933125535 1.73041933125535 1 1.87179352665719 2015 3323 3859 1881 2881 3030 1393 3311 1631 1502 1808 1878 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 0.229214659568089 0.34496857265126 1995 2543.90909090909 2015 0.0256985595699308 1081 0.330862399978133 -0.365137454091013 -1 0.341331322494241 1992 2015 4062 2558 4224 1176 1445 1520 4220 3690 1081 1879 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 0.319779263122546 0.440213168916642 1530 2585.72727272727 2016 0.0378008104861675 946 0.256649183470734 -0.355720604480839 -1 0.204117539159234 1526 2016 4569 3095 3908 946 1555 1735 3176 4523 1394 1880 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 0.15630127585958 0.260372477311763 1800 2393.63636363636 2016 0.0153321391900189 1071 1.30034479447807 1.30034479447807 1 1.69610191783958 1796 1071 1281 1917 2016 4496 4042 2426 3056 1734 2495 1881 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 0.0316778738550973 0.0814232831662549 435 1749.36363636364 2017 0.00292212880251011 431 1.0337681866745 -0.941930109984975 -1 2.51322192890112 431 651 2548 884 2960 859 2061 2017 2036 3127 1669 1882 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 9.41806661966854e-05 0.000939600906559273 3665 2207.18181818182 2018 8.56224529596019e-06 377 1.24851812919386 -1.20074158169684 -1 8.43519147319325 3662 797 404 1057 377 3740 3492 3359 823 2018 4550 1883 M1840 KEGG_GLUTATHIONE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLUTATHIONE_METABOLISM.html Glutathione metabolism 27/58 KEGG 0.298735036746822 0.4173739958842 2020 2103.45454545455 2020 0.0317460317460317 1254 0.874649861425705 -0.874649861425705 -1 0.740792390836817 2020 1443 1835 2121 2596 1254 2259 2809 2000 3174 1627 1884 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 0.0839184282471183 0.156982736433532 2830 2112.09090909091 2020 0.00793650793650794 735 1.1402443535561 -1.01501733318863 -1 2.04650838199342 2830 906 2800 1979 4073 753 3306 2249 735 1582 2020 1885 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 0.00428393182247495 0.0182994571742184 825 1941.27272727273 2020 0.000390208771404567 724 1.27668630256144 1.33407448259381 1 4.951126378421 822 3228 724 2020 2684 2518 1325 2056 2218 1788 1971 1886 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 0.0703393815044186 0.14867403776712 925 2314.09090909091 2021 0.00660858351578768 579 1.51935086267539 -1.51935086267539 -1 2.80701426248279 923 4633 3359 3771 3675 579 1979 1519 2021 2336 660 1887 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 0.0839184282471183 0.156982736433532 2720 2315.81818181818 2021 0.00793650793650794 664 1.27366405360464 1.35783680994625 1 2.28596980413029 2716 2021 2159 1085 1960 3832 3531 1925 664 1570 4011 1888 M1724 KEGG_RNA_POLYMERASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_POLYMERASE.html RNA polymerase 14/29 KEGG 0.12016129730789 0.211206241254603 1100 2460.54545454545 2023 0.0115704218816016 1097 1.07643464219997 1.07643464219997 1 1.62240632508754 1097 4636 3620 4386 1501 1539 1526 2023 2985 2033 1720 1889 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 0.182927193112453 0.289691391323067 1975 2412.90909090909 2023 0.02 373 1.46693471565438 1.46693471565438 1 1.76167020125284 1971 373 4033 1630 3354 3652 2707 3414 1877 1508 2023 1890 M14025 REACTOME_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTION.html Genes involved in Transcription 123/275 Reactome 0.114984456064274 0.203480801026128 750 2165.18181818182 2024 0.0110431239018072 750 1.10823541582444 -1.20074158169684 -1 1.71036595430103 750 3148 3625 3309 1472 1279 2562 1075 2024 2916 1657 1891 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 0.150345782533875 0.252878800055183 4040 2399.09090909091 2024 0.0161605752978919 761 1.01405746558881 -1.01405746558881 -1 1.35138830884226 1571 4036 4038 3762 2024 761 3300 1063 3494 1420 921 1892 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 0.298735036746822 0.4173739958842 1345 2019.54545454545 2025 0.0317460317460317 796 1.40587491575777 1.47928002000753 1 1.19071812167063 1344 2897 2530 2257 2732 3217 1338 1445 2025 796 1634 1893 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 0.298735036746822 0.4173739958842 2705 2554.36363636364 2025 0.0317460317460317 890 1.10512244861478 1.18788375019806 1 0.93599317510439 2703 890 1796 1546 4465 4390 1838 2025 2016 2506 3923 1894 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 0.161385165508919 0.262241686633255 3400 2196.90909090909 2026 0.0158730158730159 632 1.3647951061432 1.41830870269252 1 1.77070430065303 3400 1567 1575 2026 2993 1472 3757 3129 1351 632 2264 1895 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 0.20088839409017 0.312165923612632 1620 2237.36363636364 2026 0.020180381840618 1414 1.04213269721558 1.13973941646502 1 1.17604002555202 1616 2421 2026 2007 1815 4341 3045 1414 2247 1535 2144 1896 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 0.00987678022675767 0.0344108491766442 2035 1917.81818181818 2027 0.00090194565510338 347 1.1869452599838 1.1869452599838 1 3.87654639403807 2032 2691 1817 2287 2503 2882 2027 347 943 1572 1995 1897 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 8.54089681459864e-06 0.000135669974485455 4410 2443.54545454545 2027 7.76448179315367e-07 274 1.30365716323028 1.34594693169906 1 11.2531756527191 4408 2027 274 1740 1698 1744 3732 3878 2266 1343 3769 1898 M10579 BIOCARTA_EDG1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EDG1_PATHWAY.html Phospholipids as signalling intermediaries 24/51 BioCarta 0.0839184282471183 0.156982736433532 2545 2198.27272727273 2028 0.00793650793650794 349 1.806917851326 1.806917851326 1 3.24305269905356 2543 924 2028 558 3653 4258 3475 1928 349 1455 3010 1899 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 2.87371892746704e-08 1.07729975152884e-06 1825 1919.54545454545 2028 2.61247178636781e-09 121 1.63051826199702 1.54896841814016 1 21.7174856976327 1825 2652 121 1605 2044 4098 2028 2905 1383 225 2229 1900 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 0.0977252901397548 0.178325821493338 890 2215.27272727273 2028 0.00930518619885057 875 1.08991325512181 1.08991325512181 1 1.82149955513125 888 3105 3067 2906 4413 1856 1931 875 1240 2059 2028 1901 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 3.30949870261552e-06 6.09347257245933e-05 1735 2056.54545454545 2028 3.0086397101483e-07 237 1.41562462933735 -1.18263930906901 -1 13.3180048148119 1732 2028 237 1693 3059 3820 3070 1331 2191 334 3127 1902 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 0.105049240847828 0.188822686080907 2030 2264.54545454545 2029 0.010038958931958 767 0.716757573757959 -0.786627043273678 -1 1.15813161009876 2029 1229 3052 1498 4393 782 2594 3102 1437 4027 767 1903 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 0.0310694467211838 0.0803182405974565 1405 2092.63636363636 2029 0.00286519094698127 971 1.31629003703384 -1.13662972446107 -1 3.21750298403115 1404 2029 971 1977 2208 2682 1602 4400 2073 1151 2522 1904 M11266 KEGG_LYSOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSOSOME.html Lysosome 75/155 KEGG 0.122406110531503 0.214428050075 1625 1927.36363636364 2031 0.011799949201594 1384 1.2304816365445 1.2961210300194 1 1.8365297461059 1623 2031 2240 1488 1511 1384 2346 2703 2053 1657 2165 1905 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 0.00312603073477513 0.0144463313837833 3285 2146.18181818182 2032 0.00028458922183733 182 1.11115444406077 -0.940767540772448 -1 4.56382540400974 3284 841 2108 1349 182 3709 1191 4179 1174 2032 3559 1906 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 0.00015613807749586 0.00139099435579012 2340 2471.54545454545 2032 1.41953781823444e-05 445 1.96239312437105 1.96239312437105 1 12.5119887856576 2338 2032 445 1729 4346 4464 1810 3557 849 1961 3656 1907 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 0.000204246002542276 0.00174017594166019 1995 2072.45454545455 2032 1.85695424564235e-05 34 1.48994228118582 1.46945489514707 1 9.17623940816537 1995 2657 2032 1987 34 4011 2206 3721 661 700 2793 1908 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 0.10597909761372 0.190275115485782 1635 2252.81818181818 2033 0.0101325097364463 985 1.02938502993131 -0.625059557561618 -1 1.65562704577933 1632 3202 3230 3336 1412 1010 985 2033 3414 2806 1721 1909 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 0.00356738826684904 0.015905596021365 2770 2065.09090909091 2034 0.000324835099664261 710 1.13099333078049 -1.20074158169684 -1 4.53981316029196 2767 2034 710 2259 1259 1855 3528 2226 1763 1881 2434 1910 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 0.130394954666667 0.226056514083612 2035 2227.90909090909 2034 0.0126211441869642 1513 1.37969593029529 1.37969593029529 1 1.98860958549235 2034 1994 1521 1513 1551 3635 1590 3251 2613 2431 2374 1911 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 0.0143000920894864 0.0449733097525727 4425 2292.81818181818 2035 0.00130853618586596 299 1.71752550330527 1.71752550330527 1 5.16374635943865 4421 604 2035 851 474 3459 3751 4060 299 1339 3928 1912 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 0.00384345409086266 0.0168164573947548 1760 1836.45454545455 2036 0.000350016833502079 212 1.64216404686053 1.64216404686053 1 6.50301415615856 1756 2099 2013 1628 212 2577 2036 2867 480 2058 2475 1913 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 0.0839184282471183 0.156982736433532 2115 2003.90909090909 2037 0.00793650793650794 357 1.46773422057155 1.60338036844898 1 2.63428656814139 2115 962 2245 357 1764 4539 2037 2436 715 1281 3592 1914 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 0.0839184282471183 0.156982736433532 2185 1792.90909090909 2039 0.00793650793650794 157 1.70459369034897 -0.644872453133905 -1 3.05940149089158 2182 1522 2041 402 1812 2860 2039 1587 157 2473 2647 1915 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 0.172577489670102 0.276667162707526 3450 2220.90909090909 2040 0.0170743541707151 897 0.701641921903267 -0.701222236703204 -1 0.873901066357918 3446 1176 2822 897 1725 2040 2486 1607 1898 3700 2633 1916 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 0.100271120746064 0.182190954562255 1775 2329 2040 0.00955963216106096 654 1.13975148755868 -1.13975148755868 -1 1.88110117488246 1772 4389 3016 3929 3262 654 683 2040 2698 1857 1319 1917 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 7.83999713702757e-05 0.000807433551299147 2080 1691.90909090909 2041 7.8402737457602e-06 14 0.967459383376804 -0.967459383376804 -1 6.67847371143548 2079 172 3786 251 2041 3645 14 1071 19 3163 2370 1918 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 0.0560338170605078 0.125214337980706 1930 2217.54545454545 2043 0.0052285502647372 580 1.37423803150174 1.37423803150174 1 2.76767178140753 1927 3302 2364 2818 2043 3197 1408 1861 2889 2004 580 1919 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 0.149210718788284 0.251149938305279 1490 2263.18181818182 2044 0.0145826995048107 1240 0.430736239562367 0.527287132131916 1 0.576886871859088 1488 1382 2592 2227 1631 1902 1240 3462 2626 4301 2044 1920 M19784 BIOCARTA_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCR_PATHWAY.html T Cell Receptor Signaling Pathway 27/73 BioCarta 0.166793319351025 0.269538512855596 1220 2201.63636363636 2045 0.0164516730991565 1046 0.900299882295612 0.900299882295612 1 1.14411143080458 1218 3014 3127 2045 4284 1285 1209 1046 2692 2618 1680 1921 M16743 KEGG_TYROSINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYROSINE_METABOLISM.html Tyrosine metabolism 18/53 KEGG 0.0320363536976768 0.0821238257261016 3335 2172.27272727273 2046 0.00295569130765661 267 1.38161079423218 -1.10317666919681 -1 3.34739862600507 3335 2046 1559 1418 795 2927 3896 3915 267 1152 2585 1922 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 0.264348295296358 0.384104220700383 1840 2441.27272727273 2047 0.0275230975891684 983 0.791140711360448 -0.791140711360448 -1 0.733765919918582 1840 983 1452 1989 1984 3242 2298 3792 3138 4089 2047 1923 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 0.0610231908001264 0.133466629381513 2050 1869.81818181818 2049 0.00570769408593678 233 1.32173001607069 1.32173001607069 1 2.58015228823026 1924 2050 1574 2049 1114 3104 2272 1679 233 2131 2438 1924 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 0.0476695614808322 0.111411254413556 2050 2166.18181818182 2050 0.00443044785654489 982 0.895718906910234 -0.895718906910234 -1 1.90535771119131 2050 998 3213 3178 982 2006 3071 1744 2238 2595 1753 1925 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 0.0213279574600095 0.0615032668662181 2055 2414.54545454545 2051 0.00195796113134447 249 0.361900338834782 -0.433863361879523 -1 0.9782485198084 2051 4218 2010 4213 2812 249 1662 1819 2989 4174 363 1926 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 0.56939322035417 0.686435973907806 1540 2535.45454545455 2051 0.0808040835416152 1457 1.29064118907003 1.29064118907003 1 0.470692234748881 1537 2403 4646 2051 4565 1457 1564 2874 3358 1529 1906 1927 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 0.030358745715308 0.0790778668270892 2095 2031.90909090909 2052 0.00279872323654483 398 0.584451347281639 -0.584451347281639 -1 1.43743382068941 2091 925 3221 2052 758 398 1560 4260 2250 4028 808 1928 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 0.0307621862087636 0.0797298697866517 3470 2041.18181818182 2052 0.00311965127715543 261 1.07629756101333 -0.920562224732071 -1 2.63854259857699 3466 384 4307 706 1277 261 3616 2720 2052 2682 982 1929 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 0.123947893684465 0.216479574369584 1950 2465.54545454545 2052 0.0119579025915951 1521 1.11996455522002 1.19741845388004 1 1.6612427920004 1950 2867 2052 2039 1521 3899 2480 2987 1832 1951 3543 1930 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 0.00781571506579175 0.0288154530277735 1805 2351.18181818182 2053 0.000784334033886105 319 0.449906208579339 0.560698928577176 1 1.54677760361679 1801 2489 4163 3017 1682 1937 2053 319 2957 3866 1579 1931 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 0.011970060352566 0.0396688138699607 3890 2303.36363636364 2054 0.00109415355941722 420 1.25816049855774 -1.12376249562391 -1 3.9357222279891 3890 1770 2054 2146 420 699 3945 4453 2361 1944 1655 1932 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 0.00729796813534592 0.0275348459599283 3735 2117.36363636364 2054 0.000732204665462808 22 1.30107292972974 -0.665455983212677 -1 4.53041995962965 3735 1655 4162 1114 337 2349 2054 3385 22 1515 2963 1933 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 0.161385165508919 0.262241686633255 1475 1940.54545454545 2054 0.0158730158730159 1117 1.31394404283802 1.31394404283802 1 1.70472941835225 1475 2054 1727 2328 2178 3247 1440 2218 1492 2070 1117 1934 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 0.0150022631153259 0.046677434268223 2055 2019.90909090909 2055 0.00151045165708236 519 0.635904278350033 -0.635904278350033 -1 1.88892385050263 2055 1026 4144 1247 519 1017 2162 2352 2456 3841 1400 1935 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 0.117736301962328 0.207767399159385 1355 2510.90909090909 2055 0.0113230687465223 530 0.222211681165667 -0.276065004692397 -1 0.338454146101585 1353 3637 3654 4377 1625 530 2055 1076 3843 4520 950 1936 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 0.187879601784518 0.296432260593351 1330 1975.09090909091 2057 0.0187409517099132 906 1.46376754456424 1.46376754456424 1 1.7252295678811 1328 3198 2478 2998 2194 2239 906 1569 2057 1561 1198 1937 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 0.0255726801074168 0.0702012764987435 1220 2161.54545454545 2057 0.00235226043139685 376 1.26940878519178 -0.781628281319039 -1 3.26856407865885 1217 3172 1001 2543 3004 1217 376 3505 3982 2057 1703 1938 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 0.00295853000734222 0.0139754754177476 3525 2069.09090909091 2058 0.000296247620840027 187 0.964916235402726 -0.810865129405406 -1 3.99417645611119 3522 2058 4563 1702 187 1402 2466 2519 257 1717 2367 1939 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 0.306694946946163 0.426081387900895 2255 2221.09090909091 2059 0.0327503557047827 1218 1.53960170275972 1.53960170275972 1 1.27316551354913 2252 1462 1474 1878 4367 2059 1366 3396 2845 2115 1218 1940 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 0.00649506190844037 0.0252161227033567 710 2172.36363636364 2059 0.000651412399104781 191 0.773301099654384 0.773301099654384 1 2.75862314580994 710 1765 4475 2059 2560 1068 191 2097 3312 4383 1276 1941 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 0.000232126384255597 0.00190498114995049 2550 2110.63636363636 2060 2.11046254537727e-05 475 1.47103298127873 1.5241326903684 1 8.93075802906383 2550 2215 475 1518 1540 3088 3178 2060 1468 1122 4003 1942 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 2.64976753077442e-05 0.000342060899427244 1215 2131.45454545455 2062 2.40890858742453e-06 15 2.31622896548935 2.31622896548935 1 17.9174681405024 1212 4334 2363 3553 4389 2062 1671 15 1276 2073 498 1943 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 0.00418527074820292 0.0179763324711997 2065 2012.72727272727 2063 0.000381204914560752 223 0.577018634726521 0.577018634726521 1 2.24770447674197 2063 986 2726 2068 223 1313 2740 1547 2792 4223 1459 1944 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 0.0669468893976268 0.143313441625071 960 2352.36363636364 2064 0.0062795782628029 957 1.30279269536918 1.44012849088566 1 2.45329429358424 3106 2305 1568 1357 1165 2064 4104 3658 957 958 4634 1945 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 0.131593039360434 0.227597452560442 1235 2325.45454545455 2065 0.0127448894929567 805 0.254406289260776 -0.298377962657826 -1 0.365010445836407 1231 3027 3576 3386 1556 805 2065 1643 3519 3551 1221 1946 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 0.0818174657039037 0.156982736433532 4350 2227.54545454545 2065 0.00772988495069974 133 1.09575622248209 1.14335609063609 1 1.96666116954038 4350 133 2274 786 1258 2065 4446 2749 1865 359 4218 1947 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 0.0502405155505613 0.115688970943455 2065 2172.27272727273 2065 0.00467508313745381 549 0.300046741142004 -0.321878398736623 -1 0.627296288016902 2065 2424 3555 2781 1008 549 1735 1368 3429 4291 690 1948 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 0.0114683539320403 0.0384837786134575 855 1852.90909090909 2066 0.00104805246827695 253 0.865154370270414 0.865154370270414 1 2.73177142302206 851 2282 3117 2807 3973 540 253 959 2066 2586 948 1949 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 0.0075258732462909 0.02805588069381 2070 2220.72727272727 2066 0.000755148284171637 312 1.90919498657043 1.90919498657043 1 6.61324888268164 2066 3077 4518 2138 1643 3703 1743 312 2470 1525 1233 1950 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 1.07118161546519e-07 3.28075624187575e-06 2070 2156.18181818182 2067 9.73801516019192e-09 149 1.41217562760888 1.44523641448716 1 17.2849359484047 1934 2067 149 2078 1202 4655 1727 2919 2070 1212 3705 1951 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 0.0839184282471183 0.156982736433532 3585 2380.45454545455 2073 0.00793650793650794 105 1.4895998979757 1.61495286945514 1 2.6735310440717 3584 1588 2073 1445 2323 3960 1729 4562 105 424 4392 1952 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 0.232850105696956 0.34496857265126 2130 2257.72727272727 2073 0.0238095238095238 1465 0.653874098340854 0.653874098340854 1 0.674563536924583 2128 1916 3164 1996 3106 2202 1989 1465 1563 3233 2073 1953 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 0.0839184282471183 0.156982736433532 3355 2324.72727272727 2073 0.00793650793650794 354 1.55979380434862 -1.38916827744188 -1 2.79951493280242 3352 2056 1705 1068 4198 4096 2297 2073 354 912 3461 1954 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 0.0694731827808467 0.147308296158845 1195 2288.09090909091 2074 0.00652447558233988 403 0.946238441401025 -0.748404803427471 -1 1.75664843531324 1194 4402 3660 3923 2074 403 1923 993 2572 3138 887 1955 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 0.0390497702301207 0.0957827093095062 660 2265.54545454545 2074 0.00361460257517988 308 0.333214952907298 -0.379774584474959 -1 0.757627682883328 659 4049 2074 4442 2546 308 864 634 4063 4600 682 1956 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 0.110513364445478 0.196866367122976 1915 1851.81818181818 2076 0.0105899633484008 1232 1.17628946726973 1.17628946726973 1 1.85307474248466 1911 1303 2149 2189 1444 1280 2391 1232 2110 2285 2076 1957 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 0.0390068543600658 0.0957827093095062 1225 1884.63636363636 2076 0.00361055734834458 286 0.914050857895544 -0.747700200111362 -1 2.07826877972449 1224 2122 3394 2478 2243 286 1063 1757 2076 3121 967 1958 M529 REACTOME_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOSIS.html Genes involved in Meiosis 74/238 Reactome 0.0813487529854298 0.156982736433532 545 1917.27272727273 2077 0.00768384719049908 542 1.20074158169684 -1.20074158169684 -1 2.155088691203 542 2653 1346 2579 2418 1144 2077 1030 2983 2829 1489 1959 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 0.00116698348203574 0.00658853565881866 2080 2086.27272727273 2077 0.0001061457240963 580 1.47728318129556 1.64281874824658 1 7.19185639787201 2077 662 617 1350 3330 4501 2462 3176 1000 580 3194 1960 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 0.177502097587665 0.2824845011222 1565 2537.90909090909 2078 0.0176076277814794 1069 0.399358234670546 0.556526002923739 1 0.489349101429163 1564 3905 2078 3997 4149 1374 1115 1069 3171 3980 1515 1961 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 0.0179975751243337 0.0540087708517784 4035 2389.72727272727 2079 0.0016496833474441 94 1.70010617338384 -0.635897419203641 -1 4.80967577668127 4032 1454 2079 1565 547 3407 4538 1710 94 2239 4622 1962 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 0.280619593145407 0.401889796295654 2865 2434.45454545455 2079 0.0294984422038359 1387 2.02016967911785 1.47248574116403 1 1.78502888436346 2862 3201 1496 3607 2027 2079 3603 1916 1937 1387 2664 1963 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 0.154011438369378 0.257841229081425 2590 2149.27272727273 2079 0.0150894898188028 635 1.08835769074147 -1.13261085290572 -1 1.42990310875606 2586 1785 1901 2500 4036 635 1896 2079 3016 2308 900 1964 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 0.00568990270092006 0.022734251401137 1320 2038.09090909091 2080 0.000518606555658211 746 1.28422789313133 1.36611516812886 1 4.71024633214157 1317 2677 746 2816 2333 2707 1990 2080 1770 1345 2638 1965 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 0.0839184282471183 0.156982736433532 1235 1925.45454545455 2080 0.00793650793650794 986 1.42346328400073 -1.23249347637349 -1 2.55482917596675 1233 2565 1275 3004 2687 1327 1056 2650 986 2080 2317 1966 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 0.0839184282471183 0.156982736433532 3815 2451.90909090909 2083 0.00793650793650794 556 1.44903411468597 1.42552645004176 1 2.60072365391026 3811 1716 2322 2014 1459 2083 4518 3916 556 1125 3451 1967 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 0.0979876413794367 0.17866540369807 2045 2214.72727272727 2083 0.00933137700984714 1172 1.57416553838995 1.57416553838995 1 2.62789530035183 2045 2083 2457 2450 1354 2921 1172 1926 3256 2824 1874 1968 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 0.00368394479213391 0.0163475050150942 2375 2023.45454545455 2083 0.000335466193940079 570 1.08795584252667 1.08795584252667 1 4.33816073430269 2371 570 711 756 1664 4332 2083 1280 2645 2908 2938 1969 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 0.0749770692636691 0.156982736433532 2430 2084.27272727273 2086 0.00706011868667294 1218 0.772086244831543 -0.493393016758395 -1 1.38573891350912 1716 2086 2428 2202 1218 2667 2021 1402 2058 2699 2430 1970 M13143 BIOCARTA_UCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_UCALPAIN_PATHWAY.html uCalpain and friends in Cell spread 24/44 BioCarta 0.0593131263685755 0.130611517933809 3330 1911.45454545455 2088 0.00554321156556401 1035 1.52751898036339 1.52751898036339 1 3.01389095474244 3329 2145 1074 1232 2581 1035 2121 2314 1650 1457 2088 1971 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 0.00269382367115573 0.0130270977533909 1715 2032.36363636364 2090 0.0002451934391207 158 0.755401978283854 -0.806165918255354 -1 3.17836757325216 1713 1437 3030 2090 158 462 2607 3043 2979 4303 534 1972 M706 REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS.html Genes involved in Glycerophospholipid biosynthesis 34/85 Reactome 0.200847722173621 0.312165923612632 2095 2240.72727272727 2092 0.0201758483721634 1674 1.02192717514728 -1.02192717514728 -1 1.15323822425064 2092 2276 2482 1938 1814 1699 2943 3245 1674 2767 1718 1973 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 0.298735036746822 0.4173739958842 2885 2219.27272727273 2093 0.0317460317460317 1300 1.31212748984869 -0.831099373833084 -1 1.11131791497488 2885 1983 2082 3012 2093 1300 2108 2452 1948 2748 1801 1974 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 0.244125344527415 0.358611712995444 2355 2317.72727272727 2093 0.0251226497988355 847 1.72827849287814 1.72827849287814 1 1.71798604572351 2354 981 1761 2093 1934 847 3555 4526 3294 2951 1199 1975 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 0.0270611999881505 0.0728786110025709 2235 2183.18181818182 2094 0.00273964999202762 750 1.62371583222612 1.62371583222612 1 4.12195048788465 2231 1600 4026 1571 750 3755 3341 868 2094 1295 2484 1976 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 0.021211605940937 0.0613186831827456 2075 1955.72727272727 2094 0.00194717495398387 610 1.23257671650446 1.36513538306829 1 3.3353546080571 2073 2390 2094 2147 610 3160 1135 2234 1109 1221 3340 1977 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 0.298735036746822 0.4173739958842 1655 2324.72727272727 2094 0.0317460317460317 1282 1.28387686611089 1.45205104544372 1 1.08739080079213 1652 2459 1744 1775 3472 3771 2103 2094 2042 1282 3178 1978 M12851 BIOCARTA_CELL2CELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELL2CELL_PATHWAY.html Cell to Cell Adhesion Signaling 12/19 BioCarta 0.0938027082524953 0.172308698891099 1405 2210.09090909091 2095 0.00891441391936304 475 0.402982379077559 -0.435839852479004 -1 0.686885431835476 1401 1955 2590 2659 2095 475 665 4152 3925 3251 1143 1979 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 0.0405613502177397 0.098789234470025 2575 2215.72727272727 2095 0.00375718816258398 891 1.12660018196437 1.12660018196437 1 2.52778945829278 2575 1729 2234 2019 891 4288 1903 1702 2419 2095 2518 1980 M16257 BIOCARTA_MITOCHONDRIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MITOCHONDRIA_PATHWAY.html Role of Mitochondria in Apoptotic Signaling 16/28 BioCarta 0.0482714077798595 0.112091088630536 1730 1957.45454545455 2096 0.00448766176769784 688 2.24458518468169 2.24458518468169 1 4.76140678220049 1727 2809 2331 2096 2716 2311 792 688 1863 2162 2037 1981 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 0.0578906663765459 0.128202108998343 4425 2507.54545454545 2097 0.00540659924012852 784 1.23883058836348 1.22618745135201 1 2.46664906356751 4424 784 2793 1703 1085 1636 4063 4100 1431 2097 3467 1982 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 0.256559583040931 0.374179335863617 2100 2153.09090909091 2097 0.0265915630164225 1094 1.1921467147981 1.1921467147981 1 1.13594149799218 2097 3736 2182 2448 2882 2039 1123 1601 2630 1852 1094 1983 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 0.0770532296419488 0.156982736433532 1490 2196.09090909091 2098 0.00798631024809719 641 1.09724913661829 1.09724913661829 1 1.96934064897299 1489 3739 4369 3480 2405 1073 641 2250 2098 1056 1557 1984 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 0.0419013018739063 0.100795431509818 2250 2143.72727272727 2099 0.00388375510588489 303 1.59008010255122 -1.59008010255122 -1 3.53672782705006 2250 2051 1472 3129 4275 303 1376 3392 2521 2099 713 1985 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 0.337321873862228 0.458836081543802 2100 2408 2099 0.0367150279070119 770 1.41268062163693 1.60382551966563 1 1.06679265423279 2814 770 1504 1952 2947 4363 2099 1598 2412 2096 3933 1986 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 0.147859119791321 0.249412467725749 2410 2298.90909090909 2099 0.0158730158730159 1132 1.14338139147186 1.14338139147186 1 1.53902943511106 2409 1870 4472 1984 2251 2898 3113 2099 1132 1308 1752 1987 M18810 REACTOME_PD1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PD1_SIGNALING.html Genes involved in PD-1 signaling 9/21 Reactome 0.153496013186633 0.257254047851416 1700 2287.63636363636 2100 0.0165259597425757 1077 1.70932184675759 1.70932184675759 1 2.24951401164972 1871 3521 4021 2721 1699 2100 1483 2228 2747 1696 1077 1988 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 0.155584763471668 0.259455587768055 1910 2408.45454545455 2101 0.0152561475531786 1658 0.790640563227771 0.790640563227771 1 1.03397383405278 1907 1787 1945 2101 1658 3404 1892 2325 2351 3835 3288 1989 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 2.78948691780946e-07 7.10409548742128e-06 980 2113 2102 2.53589751954739e-08 179 1.166467038645 1.23310803353123 1 13.4039253834249 979 3146 179 2910 1961 2627 1010 3138 3290 1901 2102 1990 M13158 BIOCARTA_LONGEVITY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LONGEVITY_PATHWAY.html The IGF-1 Receptor and Longevity 11/25 BioCarta 0.206854781649601 0.319908088056115 1435 2411.09090909091 2104 0.0208477045150996 1130 0.323512971344329 0.400693838009304 1 0.357399815657994 1434 2104 3145 2789 3820 1558 1430 1130 3948 3337 1827 1991 M4470 BIOCARTA_EXTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EXTRINSIC_PATHWAY.html Extrinsic Prothrombin Activation Pathway 5/13 BioCarta 0.131519707020335 0.227585430981274 2980 2380 2105 0.0140020844642207 1289 1.54796415353554 -1.54796415353554 -1 2.22102704590075 2977 1704 3834 2120 1602 2098 2092 3905 2105 1289 2454 1992 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 0.027863240715315 0.0740900013286198 2945 2271 2105 0.00256568349952625 472 1.16087661992972 1.23550001651241 1 2.92844077477929 2944 1037 960 472 2105 3779 3403 3372 1428 951 4530 1993 M16024 KEGG_ALZHEIMERS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALZHEIMERS_DISEASE.html Alzheimer's disease 89/213 KEGG 0.109094198284773 0.194822947089346 2005 2266.36363636364 2106 0.010446558877462 533 1.39065950045143 1.80382822790103 1 2.20484870515686 2005 1825 3418 2947 1437 533 2106 4368 2251 2938 1102 1994 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 0.102999775701089 0.186079557280833 2305 2470.45454545455 2106 0.00983307845268852 496 0.701404252001585 -0.530468713592533 -1 1.14327325507797 2303 1723 3388 2899 4358 496 2094 2106 2083 4424 1301 1995 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 0.0839184282471183 0.156982736433532 3725 1998.36363636364 2107 0.00793650793650794 428 1.37819508662487 1.56221511345303 1 2.47358190200906 3725 792 1750 513 2107 2584 2643 2555 428 523 4362 1996 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 0.113244929114818 0.200705649709544 1670 2302 2109 0.0108665700346012 989 1.91509024629137 1.91509024629137 1 2.98109558432784 1666 2247 1209 989 4327 2409 2109 4423 1216 2055 2672 1997 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 0.183300777495826 0.290184947076163 1780 2156.27272727273 2111 0.0200448170643099 1119 1.46693471565438 1.46693471565438 1 1.75924969848444 1776 1480 4060 2310 2548 3206 2214 1119 2111 1422 1473 1998 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 0.0429979982420553 0.102695524853349 2255 2226.63636363636 2112 0.00398746484980399 931 1.21455215107271 1.21455215107271 1 2.67947531628166 2255 1380 1828 1960 931 4175 2447 2061 2964 2112 2380 1999 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 0.103965483027766 0.18759424469315 2370 2167.27272727273 2112 0.00993003593378591 1394 1.65718097657825 1.65718097657825 1 2.68814539028826 2366 2332 2112 1633 1394 3419 2414 1438 1840 1869 3023 2000 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 0.0132081545240119 0.0424508999310834 1925 2179.27272727273 2113 0.00120801139923391 412 1.20555776449092 -1.20555776449092 -1 3.69196427062552 1925 1742 2113 2713 4486 1093 3141 412 2931 2467 949 2001 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 0.0508543795040528 0.116643671146604 2115 2246.36363636364 2114 0.00520570768444447 731 1.14672566625037 1.14672566625037 1 2.38828056754505 2114 3322 4019 2991 2820 1789 1364 731 2485 1507 1568 2002 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 0.0269369377057888 0.0726616164979138 2570 2067.45454545455 2114 0.00247932018446705 723 1.23608342732844 1.37200307782393 1 3.1414831234211 2570 1596 951 1310 726 4209 2985 2114 2669 723 2889 2003 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 0.000683395213358138 0.00433928180189192 2490 2033.81818181818 2114 6.21461446947023e-05 71 0.767165047939799 0.675133943148694 1 4.04534234326228 2490 1090 2377 1489 71 1979 1772 2365 2114 4449 2176 2004 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 0.100271120746064 0.182190954562255 1775 2334.90909090909 2116 0.00955963216106096 653 1.13975148755868 -1.13975148755868 -1 1.88110117488246 1771 4388 3015 3928 3261 653 682 2116 2697 1855 1318 2005 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 0.156893679663635 0.261266447371639 2350 2375.63636363636 2116 0.0169214177253405 1260 0.563872894765812 -0.504457938440106 -1 0.733612998367293 2350 1260 4564 1527 1716 2138 1284 2822 2116 4515 1840 2006 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 0.0839184282471183 0.156982736433532 3680 2414.27272727273 2119 0.00793650793650794 950 1.34768931272915 1.52127001549181 1 2.41883019744221 3677 2119 1191 950 1880 2545 4228 3105 956 1726 4180 2007 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 0.0839184282471183 0.156982736433532 2125 2202.72727272727 2121 0.00793650793650794 1026 1.17917267925191 1.33435642957035 1 2.11637686640115 2121 2022 2126 1106 3494 3243 1824 2431 1026 1677 3160 2008 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 0.00598336708350047 0.0236608085681715 1415 2360.27272727273 2121 0.000545427486607446 83 0.512375499107624 -0.512375499107624 -1 1.85943306360457 1412 3229 3491 4134 1903 83 1169 2121 3975 4138 308 2009 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 0.118039209989136 0.208022466344148 1855 1976.81818181818 2121 0.0113539320118863 799 1.16629445480037 1.16629445480037 1 1.77501461542708 1852 2040 2581 1256 2931 2121 1155 2188 2174 2648 799 2010 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 0.298735036746822 0.4173739958842 2125 2429.27272727273 2122 0.0317460317460317 1108 1.54796415353554 -1.54796415353554 -1 1.31106185099862 2122 3175 2671 3925 4138 1108 2321 1536 1936 1911 1879 2011 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 0.00736921959334733 0.0277144165444828 3425 2232 2124 0.000672183658714736 779 1.82051220676583 1.82051220676583 1 6.32767016033104 3422 1085 779 1801 842 3265 2819 1344 3035 2124 4036 2012 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 0.0539031920259558 0.121943925961766 2670 2173 2125 0.00502464142131858 1060 1.25424076622843 1.30349683157862 1 2.55817675692558 2667 2228 1060 2125 1366 4253 2540 1338 1426 1347 3553 2013 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 3.47475275124292e-05 0.000418578184892656 2845 2106.27272727273 2125 3.15891603077318e-06 348 2.31535547495539 -2.59443856790082 -1 17.4576426397487 2844 2466 348 1957 1869 2029 2937 2516 2125 1169 2909 2014 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 0.319541229447084 0.440144092060269 2130 2219 2127 0.03439353436725 897 0.233643437221644 -0.252837182518385 -1 0.185856211141608 1580 1987 3745 2519 2127 897 1507 2129 2269 4115 1534 2015 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 0.00263536093971315 0.012810478592838 1595 2287.09090909091 2127 0.000263849147330874 167 0.849254971022537 0.849254971022537 1 3.58705918528469 1595 1602 4677 2188 167 1969 1079 2753 2339 4662 2127 2016 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 0.0872548363330041 0.162003576198954 4395 2409.72727272727 2128 0.00826552001188405 805 1.03415008052291 -1.03415008052291 -1 1.8245319922827 4395 805 3088 2094 1535 1270 4359 851 3073 2909 2128 2017 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 0.0353689310555002 0.0889045336771751 1160 2360.45454545455 2129 0.00326824423540654 611 0.978920502056381 0.978920502056381 1 2.29647190407228 1156 4119 2129 4147 3173 1726 966 611 4181 2529 1228 2018 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 0.121895428346776 0.213693220064719 3990 2714.45454545455 2130 0.0117476861868685 934 1.28078397138444 1.28078397138444 1 1.91586922099189 3989 1950 1981 1944 4255 4312 2635 934 1573 2130 4156 2019 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 0.0150112875463534 0.046677434268223 3345 2442.09090909091 2131 0.00137406395515711 434 0.999924705187158 -1.38916827744188 -1 2.97022946483867 3341 1627 1374 1580 4646 2426 4467 434 2131 2822 2015 2020 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 0.0407105201455381 0.0991010376114242 1050 1967.63636363636 2131 0.00377127025790539 454 1.00776107410601 1.00776107410601 1 2.25806801005463 1048 1449 2791 2131 2461 886 454 3888 3161 2469 906 2021 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 0.0598958043538761 0.131523776570882 1535 2156.90909090909 2132 0.0055992258852489 376 0.715858725339802 0.715858725339802 1 1.40760461029263 1533 2132 3628 2764 2811 376 1795 951 3064 3667 1005 2022 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 0.063543573270245 0.137472384277178 1140 2363.54545454545 2133 0.00595061417697379 1138 1.347236380865 1.37929349849691 1 2.59132600267223 3613 1330 3126 1836 1138 1140 3653 3818 1802 2133 2410 2023 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 0.0765897756730953 0.156982736433532 950 2104.63636363636 2135 0.00793650793650794 433 1.26828074115038 1.26828074115038 1 2.2763078452469 948 3178 4276 2301 2514 2135 2933 1613 433 1610 1210 2024 M11355 KEGG_TIGHT_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TIGHT_JUNCTION.html Tight junction 69/153 KEGG 0.073727653606187 0.154996763032119 2950 2195.54545454545 2136 0.00693827073649316 418 1.5761542068114 -1.50264531468407 -1 2.8483297251504 2946 1672 1245 2136 4227 418 2634 2324 1994 2761 1794 2025 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 0.00987515642443459 0.0344108491766442 2375 1920.36363636364 2136 0.000901796698754968 380 1.24266909701654 1.33395443592509 1 4.05853965590078 2374 1827 2785 2875 380 2659 2704 789 1703 892 2136 2026 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 0.0155911420787659 0.0480026884238481 2570 2046.81818181818 2136 0.0014275221387449 453 1.31359185193967 1.59350688394343 1 3.86631601698955 2567 2176 868 1304 967 4420 2136 2531 992 453 4101 2027 M11420 BIOCARTA_CTCF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTCF_PATHWAY.html CTCF: First Multivalent Nuclear Factor 17/34 BioCarta 0.475640941275134 0.596268980956468 1895 2285 2137 0.0569999693878179 1115 1.04831594950947 1.04831594950947 1 0.525411845449759 1895 2598 2670 2137 3604 2831 1464 1592 3222 1115 2007 2028 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 0.212169335408355 0.326618103062927 2610 2285.27272727273 2138 0.0214459756358567 1062 0.963068741377366 1.1921467147981 1 1.04456901622276 2606 2138 1708 1062 1844 3078 1929 1894 3180 2764 2935 2029 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 0.214139132665174 0.327605607466211 2840 2442.81818181818 2138 0.0238095238095238 669 1.23340861491086 -1.02540207154554 -1 1.33417734034872 2839 1177 3962 1939 2081 4407 3125 2138 1568 669 2966 2030 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 0.144032934443625 0.245164667926926 1535 1986.72727272727 2138 0.0140390098901306 991 0.938098901476925 -0.993307828801771 -1 1.27833244339071 2688 1292 2405 1534 2261 1367 3007 991 2638 1533 2138 2031 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 0.000701861558799515 0.0044384929345945 2460 2278 2138 6.38259611213963e-05 72 1.16426968034902 1.3102331606547 1 6.11380517315609 2460 2127 2025 1145 72 3710 2876 3775 1534 2138 3196 2032 M96 BIOCARTA_FREE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FREE_PATHWAY.html Free Radical Induced Apoptosis 5/19 BioCarta 0.00080139574368759 0.0048961414014603 2450 2039.09090909091 2139 8.01684896270053e-05 85 0.653874098340854 0.653874098340854 1 3.37142207303681 2448 1183 3837 885 85 2056 1565 2139 2454 3268 2510 2033 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 0.0565016605254117 0.126104426443765 1510 2117.27272727273 2139 0.00527338066493834 1070 1.17340783459439 1.17340783459439 1 2.35514951785931 1509 1720 1598 2176 1070 3264 2085 2319 2901 2139 2509 2034 M1073 REACTOME_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POTASSIUM_CHANNELS.html Genes involved in Potassium Channels 25/106 Reactome 0.35943518917414 0.478362197236587 1950 2387.54545454545 2140 0.0396825396825397 1487 1.44486382660512 -1.42279293755586 -1 1.03272887287554 1947 2633 1956 3378 3063 2954 2043 2076 2140 1487 2586 2035 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 0.00240809833114061 0.0119158910028774 4570 2119.18181818182 2140 0.000219158023475963 271 1.43498591898313 1.52868365389764 1 6.16174472308447 4569 271 673 1092 2140 2432 4612 2443 1355 628 3096 2036 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 0.201379273803562 0.312678355547877 3950 2493.45454545455 2141 0.0202351139751147 1037 0.502799933674464 -0.461252748486026 -1 0.566607100795982 3949 1165 2057 1037 1818 1120 2141 4616 2594 4153 2778 2037 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 0.197916753276957 0.308837131487119 2530 2304.36363636364 2142 0.0198497007631067 1237 1.21455215107271 1.21455215107271 1 1.38323565517497 2526 2156 2849 2142 1801 2091 1237 3796 2728 1912 2110 2038 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 0.313457667340129 0.433676595558265 2315 2333.63636363636 2143 0.0336118973110831 1269 0.435693947974195 0.529101657588531 1 0.352832901871895 2311 1472 2401 1981 2109 3482 1269 1497 2143 4057 2948 2039 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 0.0496517261158665 0.11461477269899 2915 2607.18181818182 2144 0.00461900466024143 1004 0.776975717544185 -0.776975717544185 -1 1.63141919756326 2914 1747 2992 2124 1004 2144 3685 1971 3335 4668 2095 2040 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 0.298232560106884 0.4173739958842 1925 2721.90909090909 2145 0.0347955368791424 990 0.314802328924014 -0.34926065938574 -1 0.266624600439496 1923 2861 4548 3874 2134 990 2145 1581 3963 4483 1439 2041 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 0.199268649250204 0.310120521549803 4685 2480.36363636364 2145 0.02 365 1.44141515827619 1.44141515827619 1 1.63581257367867 4684 365 2117 1450 1999 2375 3402 2712 2145 1935 4100 2042 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 0.199268649250204 0.310120521549803 2145 2285.36363636364 2146 0.02 348 0.746318143268794 -0.839316232100865 -1 0.846970836710361 2143 348 2885 906 2904 1666 3182 3154 2146 4165 1640 2043 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 0.214139132665174 0.327605607466211 2230 2524.36363636364 2146 0.0238095238095238 1553 0.664409341812116 -0.230658898964558 -1 0.718691176457631 2230 2492 4522 1883 2806 1995 2075 1618 1553 4448 2146 2044 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 0.168881925651085 0.27204561828841 2915 2303.72727272727 2148 0.0166760624323364 354 0.955598204248708 0.955598204248708 1 1.20580928832739 2913 354 1999 1039 1707 2141 3309 2367 3169 4195 2148 2045 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 0.0738495338232874 0.155183370177545 675 1909.45454545455 2150 0.00695015039775337 420 0.451540999054126 -0.512141475537328 -1 0.815470716223958 675 2150 2575 2761 2482 420 1301 924 2726 4083 907 2046 M872 REACTOME_L1CAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_L1CAM_INTERACTIONS.html Genes involved in L1CAM interactions 46/131 Reactome 0.298735036746822 0.4173739958842 1690 2438.18181818182 2151 0.0317460317460317 1474 1.42319670393316 1.42319670393316 1 1.20538896247644 1688 4016 2258 3795 2336 3605 1998 1474 2020 1479 2151 2047 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 0.102119305733028 0.184903812467144 2155 2565.36363636364 2151 0.0097447615086167 1178 1.75003199799519 1.75003199799519 1 2.86326530981838 2151 3658 1178 3982 2137 4549 2026 1857 1544 2582 2555 2048 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 0.104661745741284 0.188278202397265 3070 2240.27272727273 2151 0.01 135 1.66983165510287 1.66983165510287 1 2.70277575202046 3070 135 2151 880 1650 4570 3295 2820 1589 1370 3113 2049 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 0.02501797044581 0.0690425262126419 2580 2386.36363636364 2151 0.00230064394178289 365 1.36046414119632 1.36046414119632 1 3.52496839542137 2580 2151 1660 1733 675 4064 4375 3449 365 2060 3138 2050 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 0.0227426779892847 0.0645500842264011 1945 2054.36363636364 2153 0.00208920383044283 637 1.90919498657043 1.90919498657043 1 5.07124342994627 1942 1212 2506 1749 637 2634 2153 2280 2746 2839 1900 2051 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 0.031358016724703 0.0807382782263506 3500 2428.54545454545 2154 0.00318095058890195 822 1.31390839817937 1.42270565782159 1 3.20503828659975 3499 1266 4407 1265 822 1554 3354 2935 2047 2154 3411 2052 M16120 BIOCARTA_SALMONELLA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SALMONELLA_PATHWAY.html How does salmonella hijack a cell 13/24 BioCarta 0.35943518917414 0.478362197236587 2400 2445.72727272727 2155 0.0396825396825397 1597 0.885892611905994 -0.625059557561618 -1 0.633199379539211 2400 2155 1953 2108 2479 3294 1597 3962 2121 1968 2866 2053 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 0.0232696056122897 0.0656085270151561 1590 2344.09090909091 2156 0.00235169218311814 375 0.556898646707547 0.752317551607192 1 1.47046618059157 1590 2301 4025 2156 3841 1583 375 1214 3693 3628 1379 2054 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 0.101046782218696 0.18338699514981 3245 2626.09090909091 2157 0.00963728662979934 1375 1.05946340462454 1.05946340462454 1 1.74187016592735 3245 1912 2256 1756 1375 4417 3761 2135 2157 2036 3837 2055 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 0.0375007763511399 0.0930052302207623 1560 2373.27272727273 2157 0.00346869915325063 741 1.2462343870145 1.23763913013708 1 2.86909820358501 1558 3824 2157 3358 863 4572 2086 2824 2236 741 1887 2056 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 0.108359426501927 0.193732267297989 1395 2222.09090909091 2159 0.0103723929391752 952 1.08556485784445 1.08556485784445 1 1.72703773422338 1395 3970 2623 4099 1433 1570 952 2159 2511 2553 1178 2057 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 0.0258013290437827 0.0705808685926244 3170 2115.36363636364 2159 0.0026105886564427 479 1.16523326848591 1.3554135864349 1 2.994234701991 3169 1327 4337 2141 728 479 2837 2566 2261 2159 1265 2058 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 0.0849178233650938 0.158662248918991 3300 2460.54545454545 2164 0.00883488174987774 865 1.14672566625037 1.14672566625037 1 2.04631219835989 3300 1551 4016 2164 3526 3313 1888 865 2093 1186 3164 2059 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 0.00376966879603156 0.0166647811115131 4595 2397.63636363636 2164 0.000343285782516051 205 1.13518592994862 1.00790319646002 1 4.50533671733997 4594 1685 2164 1576 205 3390 2490 4201 769 1461 3839 2060 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 0.00644323408685029 0.0250564273286145 1925 2630.81818181818 2165 0.000646199254962888 190 0.379960469546853 -0.372997442824569 -1 1.35778571187281 1922 3572 4381 4051 2165 620 190 1892 4253 4186 1707 2061 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 0.0338814105052262 0.0857743325918368 2275 1973.81818181818 2166 0.00312861282741712 338 1.29026877234849 -1.1815031987934 -1 3.07169921833782 2275 3622 1834 2638 1803 338 3633 2166 2494 446 463 2062 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 0.0123727618191855 0.0404597082237985 1405 2116.63636363636 2167 0.00113117262468638 839 1.61112816865721 1.61112816865721 1 5.00903043220018 1403 3377 839 1894 1467 2789 2180 3732 2167 1216 2219 2063 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 0.137956167320621 0.236107596809507 1285 2245 2167 0.0147352734138525 932 0.580651869785827 0.638919247271278 1 0.812431498238728 1282 2167 4022 2430 2604 932 1035 999 3751 3620 1853 2064 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 0.102104345985547 0.184903812467144 1585 2284.81818181818 2167 0.00974326162761755 855 0.485117884297893 0.616477148104334 1 0.793711892550481 1583 2393 1177 2650 2644 1854 855 2167 3402 4513 1895 2065 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 0.286640672587051 0.408371010244963 2170 2241.27272727273 2168 0.0302397136059358 1384 0.997053599744367 1.03823617742115 1 0.865538439237206 2168 1423 1866 1889 2046 2919 2524 1384 3608 2652 2175 2066 M2890 KEGG_CALCIUM_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CALCIUM_SIGNALING_PATHWAY.html Calcium signaling pathway 59/193 KEGG 0.00442258385842404 0.0187041768597248 2170 2288.09090909091 2169 0.000402863593437091 730 1.72327360612593 1.37520761890104 1 6.64649925429705 2169 2380 730 2477 994 3847 1774 3999 1976 1898 2925 2067 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 0.0940603175939198 0.17264655238743 3280 2568 2169 0.0098296253821051 1110 1.18054651416861 1.25798081494101 1 2.01000577435119 3277 1110 4653 1478 1388 2169 3227 3634 1815 1230 4267 2068 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 0.0863422762136531 0.160746883725538 1455 2060.36363636364 2170 0.0081754215480013 832 1.48034281358945 1.48034281358945 1 2.62291594028271 1452 2848 2748 2170 4002 1786 832 847 1280 2424 2275 2069 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 0.222996042741019 0.338701374669786 1120 2203.45454545455 2170 0.0226761986898365 832 1.33324455259183 1.33324455259183 1 1.39912440745731 1116 4157 1813 3544 2686 3283 2415 1179 2170 832 1043 2070 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 0.0451628737918185 0.106831512664544 4400 2418.63636363636 2170 0.00419250512880761 952 1.21670322116821 1.29349560899301 1 2.63765432827553 4399 2174 1847 1401 952 2170 3961 3254 1524 1623 3300 2071 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 0.0202743624816455 0.0594156739143158 965 2291.81818181818 2170 0.00204617454781664 349 0.459171660517881 0.459171660517881 1 1.25655111337232 962 2170 4536 2848 3659 896 349 937 3314 4465 1074 2072 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 0.161385165508919 0.262241686633255 4080 2481.45454545455 2171 0.0158730158730159 1336 1.31394404283802 1.31394404283802 1 1.70472941835225 4077 1642 2514 2042 1900 2055 2423 3783 1336 2171 3353 2073 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 0.0499471567386494 0.115126599349391 4200 2263.09090909091 2175 0.00464713861300063 1007 1.21512026124885 -1.13534241201796 -1 2.54614510287332 4198 2175 1311 1921 1007 1475 3858 2705 2356 1569 2319 2074 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 0.161385165508919 0.262241686633255 3305 2519.54545454545 2178 0.0158730158730159 1119 1.01119429981225 -1.29829314601985 -1 1.31193765817122 3304 3237 3369 2132 1688 2269 4535 1818 1119 2178 2066 2075 M4500 DACOSTA_UV_RESPONSE_VIA_ERCC3_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_DN.html Genes down-regulated in fibroblasts expressing mutant forms of ERCC3 [GeneID=2071] after UV irradiation. 15608684 544/1296 Arthur Liberzon 0.0299657507694727 0.0783591005054403 1420 2322.72727272727 2179 0.00303776658384976 472 1.27422138970255 1.30665369299684 1 3.14517235716997 1416 2999 4260 2179 807 4457 2158 2511 2055 472 2236 2076 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 0.0689246771542157 0.146676220320007 2180 1979.81818181818 2179 0.0064712524604078 399 2.06322935667965 2.06322935667965 1 3.83889080598641 2179 2772 2520 659 2128 399 1758 2856 2466 2242 1799 2077 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 0.00611896887477617 0.0240146466894482 2040 2017.45454545455 2179 0.000557823130193014 290 1.16880562865661 1.16880562865661 1 4.22482946437127 2036 2510 2543 2631 290 3303 2579 683 1645 2179 1793 2078 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 0.013174292667493 0.0423711293341608 2200 2105.81818181818 2180 0.0013253053519331 126 0.405368511468722 0.375523056357185 1 1.24216116491478 2200 860 4377 1077 481 2818 1264 3600 126 4181 2180 2079 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 0.0197173431465443 0.05828236927658 2390 2107.09090909091 2180 0.00180875527639445 577 1.45325029840039 1.40948381616031 1 4.00403609004187 2388 2180 1344 2528 577 4042 2550 1323 2022 812 3412 2080 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 0.00891783117994538 0.0318028591394399 3995 2425.90909090909 2181 0.00081401696590757 359 1.99176057178824 1.95097106729427 1 6.65722643472722 3993 2181 995 1514 359 2552 4167 4023 701 1814 4386 2081 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 0.00647374520294299 0.0251542039975049 2235 1891 2184 0.000590261251762751 295 0.874649861425705 -0.874649861425705 -1 3.12225238156599 2232 1153 2298 778 295 1401 2747 2184 1608 3753 2352 2082 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 0.151498691637608 0.254320272421057 2185 2417.63636363636 2184 0.0148239053412 602 1.14225921611188 -0.554099100968402 -1 1.51594352429072 2184 4110 1780 3171 3742 602 1985 2123 2565 2936 1396 2083 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 0.17798614059489 0.283084408245492 2920 2130.72727272727 2187 0.0176602001629369 663 1.09724913661829 1.09724913661829 1 1.34224552967435 2918 2357 1991 2549 3977 663 2170 1144 2469 2187 1013 2084 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 0.0351807215191927 0.0885850945937329 1765 2137.90909090909 2188 0.00325056646553349 830 0.969053472253738 0.969053472253738 1 2.27670570731382 1763 2684 2188 3277 830 2191 1379 1155 3250 2918 1882 2085 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 0.00344951503392339 0.0155217457473721 2015 2196 2188 0.000314085058458122 197 1.26749052207519 1.49116025113968 1 5.11772694590439 2013 2525 1098 2733 197 4500 3268 1355 2188 1229 3050 2086 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 0.182401892733763 0.288957156643142 2140 2366.45454545455 2188 0.018141103048913 1762 0.988267937766706 1.01201813626383 1 1.18926105449907 2138 2137 1914 2273 1762 4203 1812 2502 2277 2825 2188 2087 M7825 BIOCARTA_ACTINY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACTINY_PATHWAY.html Y branching of actin filaments 18/36 BioCarta 0.28146066725174 0.402848102242411 2495 2471.63636363636 2189 0.0296016494334811 1456 0.885892611905994 -0.625059557561618 -1 0.780732613519517 2493 1456 2189 1968 2034 3967 1952 3756 2122 2279 2972 2088 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 0.281775769837151 0.403052886891602 1675 2325.54545454545 2189 0.0296403435886938 1089 0.825583746957188 0.825583746957188 1 0.727176023504413 1674 2189 2777 2485 2693 2168 1089 1602 2801 4068 2035 2089 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 0.000272702652454797 0.00213693081839996 2955 2075.54545454545 2189 2.47942237621995e-05 43 1.2815413473491 1.2815413473491 1 7.63761073939698 2951 1529 2447 1544 43 2738 1077 3354 2162 2189 2797 2090 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 0.154226297353598 0.257861638609555 3710 2376.45454545455 2191 0.0151122325833494 986 1.42882436135588 1.52397999841027 1 1.87710446972328 3709 1491 2207 2191 1653 986 3590 3967 1975 1952 2420 2091 M6778 BIOCARTA_IL10_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL10_PATHWAY.html IL-10 Anti-inflammatory Signaling Pathway 11/19 BioCarta 0.0839184282471183 0.156982736433532 4480 2401.90909090909 2192 0.00793650793650794 501 0.701222236703204 -0.701222236703204 -1 1.25855232743107 4479 501 2033 1026 4142 2192 3881 1220 570 3282 3095 2092 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 0.232850105696956 0.34496857265126 3860 2359.27272727273 2192 0.0238095238095238 992 1.09702423713368 1.04344597074167 1 1.13173553045784 3858 992 2666 1330 2065 2704 3968 2192 1657 1635 2885 2093 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 0.199268649250204 0.310120521549803 2195 2147.54545454545 2192 0.02 356 0.98466997341672 0.98466997341672 1 1.11746814520688 2192 356 2621 603 2929 2853 1218 2289 1881 4517 2164 2094 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 0.161385165508919 0.262241686633255 2345 2215.63636363636 2192 0.0158730158730159 705 1.02475359367296 1.02475359367296 1 1.32952967608387 2341 705 2618 1911 4326 2336 1782 2951 1537 1673 2192 2095 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 0.298735036746822 0.4173739958842 2955 2717.36363636364 2193 0.0317460317460317 1425 1.40332582496403 1.58766104998936 1 1.18855914680869 2955 1425 1719 2064 2193 3996 4276 3590 2034 1735 3904 2096 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 0.190681444797406 0.299944024948186 4485 2852.90909090909 2193 0.0190491969586543 1783 0.939251733032961 -0.796538314240086 -1 1.09630110831382 4481 2572 2193 1976 1783 1876 4362 4102 2006 2048 3983 2097 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 0.145330270768719 0.247193338955433 1830 2025.36363636364 2195 0.0141749544876204 592 1.10592013775826 1.21180937647392 1 1.49818590727265 1828 1486 2195 1777 2558 592 2487 2292 2443 2992 1629 2098 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 0.0983212090983533 0.17920388402757 2200 2243.45454545455 2196 0.00936468744167058 1169 1.07866220546383 1.10646291098558 1 1.79756079645605 2196 1347 1169 2169 2314 3592 1452 2722 2059 2780 2878 2099 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 0.214508991714299 0.327957303482285 3140 2445.90909090909 2196 0.021710519849483 529 1.35823342054308 1.44036971224005 1 1.46778764874337 3140 2313 2083 2029 2122 4054 2893 2196 1626 529 3920 2100 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 0.0039487232056559 0.0171330712423181 1900 2052.72727272727 2197 0.00035962077525862 717 1.46048142292064 1.77517244746441 1 5.75714028016679 1898 2948 717 1884 2222 2474 1315 2926 2969 1030 2197 2101 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 0.00384070333285304 0.0168164573947548 1060 2056.81818181818 2198 0.000349765887936449 136 0.653874098340854 0.653874098340854 1 2.58935916048316 1060 2198 2314 3062 3766 762 136 1272 2699 4458 898 2102 M648 BIOCARTA_G1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G1_PATHWAY.html Cell Cycle: G1/S Check Point 17/39 BioCarta 0.125581510874102 0.218682630975861 2065 2298.18181818182 2200 0.0121255402226555 519 1.26288057240438 1.26288057240438 1 1.86083538744997 2061 2001 1240 1138 3160 3476 2537 4229 2200 519 2719 2103 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 0.0839184282471183 0.156982736433532 2395 2200.72727272727 2201 0.00793650793650794 604 1.31212748984869 -0.831099373833084 -1 2.35500390584032 2395 2201 1288 2422 2805 4057 1894 1343 604 2181 3018 2104 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 0.232850105696956 0.34496857265126 2025 2597.27272727273 2202 0.0238095238095238 1191 0.946852329508263 0.946852329508263 1 0.976811985654663 2021 3973 3205 4075 4421 2502 2202 1191 1760 1331 1889 2105 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 0.0839184282471183 0.156982736433532 4115 2735.18181818182 2203 0.00793650793650794 336 1.64216404686053 1.64216404686053 1 2.94735288631669 4111 1239 2203 1214 1529 4565 4100 4267 336 2113 4410 2106 M862 BIOCARTA_P38MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P38MAPK_PATHWAY.html p38 MAPK Signaling Pathway 30/62 BioCarta 0.320666723499073 0.441046159764208 1275 2256.63636363636 2205 0.0345388377095142 1274 1.07708428965173 1.07708428965173 1 0.854650088540984 1274 2719 3186 2258 4592 2205 1474 1332 2627 1728 1428 2107 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 0.300609790107206 0.419617955449022 2165 2580.27272727273 2205 0.0319816380587135 1669 1.10858603309022 1.10858603309022 1 0.933164890146295 2161 3639 2205 3330 2072 3248 1669 2562 3412 2121 1964 2108 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 0.215988526536797 0.32968150988646 1855 2281.1 2205.5 0.0266746233884479 874 1.05077947290469 1.05077947290469 1 1.13019384090907 1854 2671 4115 NA 2557 1723 1130 3395 3396 874 1096 2109 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 0.000224191724926999 0.0018726602905667 3010 2083.90909090909 2207 2.0383143138051e-05 36 0.955023857704091 0.955023857704091 1 5.81386660502466 3007 1089 3449 2378 36 1057 1352 3545 1382 3421 2207 2110 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 0.098625984468654 0.179619651465259 4125 2573.81818181818 2207 0.00939513243388808 1191 1.1021820102722 1.06932881979732 1 1.83428009427449 4124 1776 1212 1191 1359 3553 3582 3813 1444 2207 4051 2111 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 0.00109528733308235 0.00628295545492121 2210 2045.54545454545 2208 9.96211828078564e-05 608 1.42687333763417 1.70092610183102 1 7.01212984700009 2208 1494 608 927 2423 3431 2250 2558 1756 1588 3258 2112 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 0.0273395483497876 0.0733603683420227 1400 2274.81818181818 2209 0.00251684816374402 955 1.31369478983561 1.31369478983561 1 3.32654397521655 1397 2713 955 1864 2510 4084 2205 2209 1542 2706 2838 2113 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 0.232850105696956 0.34496857265126 4330 2531.63636363636 2210 0.0238095238095238 1195 1.84083109373717 1.84083109373717 1 1.89907741680686 4329 1726 1583 1195 3029 1924 3546 4189 1688 2210 2429 2114 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 0.0216308707882963 0.0621473087148722 2060 2130.27272727273 2211 0.0019860476853662 491 1.03990117077868 0.978920502056381 1 2.80044409170416 2056 2502 2096 2440 1066 2544 3030 491 3541 2211 1456 2115 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 0.161385165508919 0.262241686633255 2160 2452.81818181818 2212 0.0158730158730159 1277 1.05077947290469 1.05077947290469 1 1.36329601659839 3143 2157 2114 2159 2212 2536 3423 3695 1277 1856 2409 2116 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 0.0813712315829629 0.156982736433532 1380 2265.54545454545 2213 0.0076860545890278 271 1.80556569315371 1.80556569315371 1 3.24062584815543 1377 4186 2895 2514 4673 2130 2468 828 271 1366 2213 2117 M10320 REACTOME_BIOLOGICAL_OXIDATIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BIOLOGICAL_OXIDATIONS.html Genes involved in Biological oxidations 43/219 Reactome 0.00280969938001459 0.0134349503007636 3240 2240 2213 0.000255754016143638 445 1.32035659898489 -1.23330103611277 -1 5.51596967995544 3236 1060 683 507 525 3947 3797 3617 445 2213 4610 2118 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 0.00863325187803545 0.0311352899171567 1285 2450.54545454545 2213 0.000866697628756261 232 0.346081220465826 -0.320722501519605 -1 1.16385251269263 1281 2111 4624 3322 2213 269 232 3700 4101 4604 499 2119 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 0.161385165508919 0.262241686633255 2515 2335.18181818182 2214 0.0158730158730159 1289 1.58905024272725 1.58905024272725 1 2.0616560581942 2515 1289 2071 1843 3205 1446 3429 3320 1392 2963 2214 2120 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 0.0246594174938392 0.0683347311508754 4380 2433.27272727273 2214 0.00226729430470845 205 1.12936685280935 1.31059430246621 1 2.93747475912571 4378 2214 1590 2206 1188 205 4682 3929 2275 2713 1386 2121 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 0.360749621697899 0.479838980209014 2105 2532 2215 0.0398618489664593 1476 1.20190763312073 1.33985635247262 1 0.855482757995379 1844 4107 3285 3045 2215 2975 2101 1687 3014 1476 2103 2122 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 0.102268579382039 0.185102573574443 3275 2511.81818181818 2215 0.00975972909592991 961 1.32189239413733 1.36576295432246 1 2.16140020360436 3273 961 1497 2098 1381 3119 3577 3502 2215 1440 4567 2123 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 1.78704379549086e-07 4.98457572956557e-06 2320 1910.27272727273 2216 1.62458540059193e-08 163 1.19889421957474 1.28325698179155 1 14.1883076903954 2318 2216 163 1246 858 4597 2353 3082 978 350 2852 2124 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 0.112611373684786 0.199809502872741 3640 2380 2218 0.0108023453274221 793 1.18597281846717 1.33411917206854 1 1.85127056636001 3637 1039 1206 793 3170 2218 3489 4516 1430 1114 3568 2125 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 0.0839184282471183 0.156982736433532 2055 2156.36363636364 2219 0.00793650793650794 676 1.44744358403227 1.43721583152407 1 2.59786897253901 2053 2219 1213 2557 1489 4367 2950 2379 991 676 2826 2126 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 0.262186142424503 0.381198964753714 1345 2144.72727272727 2220 0.0272636072103418 581 1.18232068578796 1.18232068578796 1 1.10527815551193 1341 2687 2220 1838 2851 3623 2260 1647 2622 581 1922 2127 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 0.0839184282471183 0.156982736433532 4445 2618.81818181818 2221 0.00793650793650794 538 1.29193164108738 -0.862559895960135 -1 2.31875643516031 4441 1391 1365 929 2221 4304 3848 4300 538 1773 3697 2128 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 0.0700979568174231 0.148333533263248 3525 2319 2221 0.00724125766461875 740 1.0286531864228 1.0286531864228 1 1.90273215326581 3524 740 4481 1312 1224 2221 2433 4149 1581 1523 2321 2129 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 0.35943518917414 0.478362197236587 3370 2364.63636363636 2221 0.0396825396825397 1252 1.80540289925521 1.80540289925521 1 1.29042728244638 3367 1836 2134 3048 3202 1252 2651 1791 2221 2864 1645 2130 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 0.0209356737506483 0.0608211823902902 1510 2003.18181818182 2222 0.00192159977065828 605 0.973376132381195 -1.1155273203918 -1 2.64164363261691 1506 2222 3070 2423 605 904 2520 1364 3029 2978 1414 2131 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 0.186581211965529 0.294681347917247 4020 2250.36363636364 2223 0.018598436810293 1224 1.31394404283802 1.31394404283802 1 1.55618930594269 4018 1224 1328 2181 2345 2223 2296 1582 2005 2662 2890 2132 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 6.08792646232304e-09 2.59345667294961e-07 4415 2288.18181818182 2223 5.53447861742707e-10 107 1.25656551505623 1.37152341359105 1 18.4711696459776 4412 767 107 730 2223 3176 4034 3843 1366 950 3562 2133 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 0.0300111243773233 0.0784287881939467 1800 2191.27272727273 2223 0.00276622837267096 754 1.16112880337275 1.19458109876252 1 2.86502438609987 1799 2259 2223 1787 754 3626 1719 3269 2391 1902 2375 2134 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 0.160414436319909 0.262241686633255 750 2297.09090909091 2225 0.0157695098539759 748 1.10006390028969 -0.694096558555807 -1 1.42723832349712 748 3192 3748 3167 1672 968 2225 2143 2676 3103 1626 2135 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 0.0178529351047017 0.0537307989085628 1225 2352.45454545455 2226 0.00163631625005251 883 1.17181367894184 1.17181367894184 1 3.32097397600491 1222 2474 883 2226 3923 1533 1480 4263 3277 2464 2132 2136 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 0.35943518917414 0.478362197236587 3455 2495.72727272727 2227 0.0396825396825397 1620 1.14672566625037 1.14672566625037 1 0.819632053185331 3451 2695 1778 1690 4500 1620 2834 1969 2147 2227 2542 2137 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 2.23182076504866e-05 0.000296269464731388 2230 2111.18181818182 2227 2.02894855126189e-06 322 1.38541910170788 1.540244104461 1 10.9100777102594 1758 2748 322 2229 2029 4653 2610 2227 895 887 2865 2138 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 0.232850105696956 0.34496857265126 735 2096.36363636364 2227 0.0238095238095238 733 1.18049564801213 1.18049564801213 1 1.217848086844 3096 733 2227 1244 2254 3876 3243 1452 1593 734 2608 2139 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 0.0256555948395689 0.0703464701101345 2230 2050.18181818182 2229 0.00235997805486587 816 1.19833629792411 1.19833629792411 1 3.08316166278967 2229 1622 944 816 3023 3182 2048 2277 854 2446 3111 2140 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 0.267636840125566 0.388040294810767 2865 2302.36363636364 2230 0.027919103989359 1102 0.897202119183888 1.00114037370729 1 0.823269077008548 2861 2230 2672 1610 1992 1102 3463 1939 3049 2370 2038 2141 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 0.0641807548674314 0.138403925683973 3030 2379.18181818182 2234 0.00601212128140412 619 1.61112816865721 1.61112816865721 1 3.08835894284902 3026 2234 2053 619 1143 3137 4017 3871 667 1887 3517 2142 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 0.343156829107247 0.465137817255762 1385 2397.45454545455 2234 0.0411599433425693 1274 0.211863459685407 -0.23248196687267 -1 0.157188439744624 1381 2161 4083 2447 2234 1274 2386 2127 2892 3735 1652 2143 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 0.0113033202446709 0.0380512634098619 1330 2136.63636363636 2235 0.00113612295077013 266 0.245247299930579 -0.274616060720633 -1 0.777068382778823 1327 3113 3806 3238 2129 389 266 2235 3365 3204 431 2144 M17 PID_NOTCH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NOTCH_PATHWAY.html Notch signaling pathway 18832364 31/87 Pathway Interaction Database 0.0624740774881554 0.135785494948746 3395 2209.45454545455 2236 0.00584746127946784 914 1.51549638446077 1.51549638446077 1 2.93310084544567 3395 1223 2236 2846 1129 914 3556 3193 2744 1743 1325 2145 M3462 REACTOME_LIPOPROTEIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIPOPROTEIN_METABOLISM.html Genes involved in Lipoprotein metabolism 14/44 Reactome 0.35943518917414 0.478362197236587 4500 2630 2236 0.0396825396825397 1463 1.90919498657043 1.90919498657043 1 1.36461357141243 4500 1463 2001 2799 2545 1675 2910 2236 2101 2043 4657 2146 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 0.161915653612084 0.262993675156404 3070 2469.63636363636 2236 0.0159296263051762 1120 1.08652964753156 1.09170552124962 1 1.4066630605249 3067 1120 2097 1755 1679 2236 3581 2473 1817 2848 4493 2147 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 0.0583485547986767 0.128790074322468 1710 2412.36363636364 2237 0.00545055413115211 368 0.687195751106563 -0.687195751106563 -1 1.36523499369693 1707 2842 3522 3160 1550 368 2237 2088 3553 4534 975 2148 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 0.000123253804745772 0.00115977375308973 3045 2197.09090909091 2240 1.12055191377158e-05 337 1.48242311380533 -1.13809336905825 -1 9.71298157993426 3043 1058 424 826 3277 3507 2240 4591 337 528 4337 2149 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 0.147859119791321 0.249412467725749 2195 2389 2241 0.0158730158730159 1085 1.07643464219997 1.07643464219997 1 1.44891688081396 2194 2405 4353 2241 4298 2321 1109 3410 1085 1518 1345 2150 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 0.00320826617633718 0.0147103085149863 2395 1814.90909090909 2244 0.000292086761294774 182 1.21455215107271 1.21455215107271 1 4.96719080568954 2394 1758 2409 2390 622 3093 2244 182 446 1906 2520 2151 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 0.0839184282471183 0.156982736433532 3070 2129 2246 0.00793650793650794 432 1.43402817817813 -1.24287224182961 -1 2.57379102780367 3069 2011 2313 1634 2709 2491 1987 2246 432 827 3700 2152 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 0.00951133101919661 0.0333608511646372 2500 2341.72727272727 2246 0.000868427480698077 340 1.41368943892727 1.41368943892727 1 4.65955384648277 2499 3540 2167 3451 4043 3042 2246 340 990 1885 1556 2153 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 0.435369722646862 0.557415989159343 2425 2606.45454545455 2249 0.0555555555555556 1619 1.22168558101711 1.22168558101711 1 0.69209519080507 2425 3646 4524 2249 4015 1951 2177 1694 2463 1619 1908 2154 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 0.0839184282471183 0.156982736433532 2530 2205.81818181818 2251 0.00793650793650794 672 1.41513291157939 -0.967459383376804 -1 2.53987783949831 2527 3379 2251 2972 1876 3009 1900 1211 672 2173 2294 2155 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 0.308903621526571 0.428514615297073 1680 2237.27272727273 2252 0.0330308880638592 1094 1.41325564145404 1.41325564145404 1 1.16088353172174 1676 3440 2252 2855 2351 3924 1457 1622 2748 1094 1191 2156 M14631 KEGG_COLORECTAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_COLORECTAL_CANCER.html Colorectal cancer 42/82 KEGG 0.161385165508919 0.262241686633255 4430 2638.36363636364 2253 0.0158730158730159 914 1.46625125466172 1.46625125466172 1 1.90233492983043 4429 1727 2294 914 4546 2253 4292 1528 1379 1381 4279 2157 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 0.232850105696956 0.34496857265126 1735 2377 2253 0.0238095238095238 1691 0.400850735639594 -0.241081264867744 -1 0.413534181384427 1733 1691 2678 2838 3313 2365 1726 2253 1796 3813 1941 2158 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 4.1730301708488e-05 0.000487651356124625 2460 2276.63636363636 2253 3.79373575301654e-06 356 1.21001845009465 1.34446132072093 1 8.94432404339872 2457 2121 356 1472 1795 4466 2464 1764 2440 2253 3455 2159 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 0.00569084013946514 0.022734251401137 1330 2207.81818181818 2256 0.000518692220609342 76 0.259719602301255 -0.287075184664297 -1 0.952590510268857 1330 3091 3596 3165 2256 76 1190 1444 4248 3622 268 2160 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 0.351701984872748 0.474408062695957 2490 2406.18181818182 2257 0.0424147029809383 1104 0.572412385685472 -0.572845185373919 -1 0.413742099515093 2486 1104 4070 1861 2257 1323 1520 3541 2832 3710 1764 2161 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 0.264490189681394 0.384191267466526 1485 2550.36363636364 2257 0.0275401512512683 1053 0.410305062918177 0.493383682285924 1 0.380458961768065 1481 1760 2835 2047 3361 3007 1053 4596 2257 3774 1883 2162 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 0.0222124251294315 0.0635454359929889 3300 2263.45454545455 2257 0.00203999239480016 431 1.09310073889501 1.00989434300655 1 2.92013737638095 3296 431 2300 933 627 2257 4493 4671 1742 1344 2804 2163 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 0.139053907762619 0.237615006244337 1060 1984.36363636364 2257 0.013519003254534 672 1.04854149074966 -1.04854149074966 -1 1.46062101236945 1058 3301 2876 3397 2584 672 886 977 2662 2257 1158 2164 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 0.0839184282471183 0.156982736433532 2535 2473 2257 0.00793650793650794 577 0.89163686584869 -0.89163686584869 -1 1.60030813916094 2534 3702 2464 3133 2217 1966 2257 2048 577 4283 2022 2165 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 0.037622083340083 0.0932295518411575 2345 2273.54545454545 2258 0.00348011764060609 1002 1.78606414326979 1.78606414326979 1 4.10773117659382 2343 2475 1002 1822 2258 3596 3353 2146 1693 1364 2957 2166 M557 REACTOME_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEFENSINS.html Genes involved in Defensins 10/110 Reactome 0.298735036746822 0.4173739958842 2410 2273.72727272727 2258 0.0317460317460317 722 1.2843873410506 -1.27233357232047 -1 1.08782315203093 2407 3675 2122 3096 2703 1473 2258 2950 1855 722 1750 2167 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 0.00119305288670325 0.00672761230696925 4295 2287 2259 0.000108518215186968 618 1.18972770321952 1.17193697034861 1 5.7678605397896 4293 661 618 833 2063 2259 4216 3974 2551 922 2767 2168 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 0.00162644811902878 0.00864134904761157 3945 2519.09090909091 2260 0.000147968344485249 645 1.24848478160646 1.34681573267837 1 5.749765299254 3944 2651 645 2178 1616 1516 3810 3612 2260 2219 3259 2169 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 0.175565957945494 0.279925851967534 2260 2361.36363636364 2260 0.0173976226381535 1690 1.0989317868129 -0.915429550183146 -1 1.35625591019354 2260 2712 2462 2530 1744 1690 3566 1849 2067 3045 2050 2170 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 0.170580088772484 0.274309641725416 1615 2571.90909090909 2260 0.0168588826781768 1055 0.435843814409893 0.550242757800535 1 0.54646257475221 1611 3452 1807 2897 2021 1845 2753 1055 4004 4586 2260 2171 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 0.169851951493377 0.273420214599095 2890 2198.18181818182 2261 0.0167804514987807 863 1.31212748984869 -0.831099373833084 -1 1.64928087498546 2890 1079 2261 1461 2235 2368 863 3332 1636 2489 3566 2172 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 0.00978039572890741 0.0341766848513498 1885 2214.72727272727 2261 0.000893104395236874 565 1.19735465197263 1.28105334097575 1 3.91846822267094 1882 565 809 1725 2523 3887 2261 2789 2972 1584 3365 2173 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 0.28469859691192 0.406117998517277 3135 2623.72727272727 2261 0.03 234 0.977806706384815 1.07686061021141 1 0.854073843843586 3134 1061 2186 234 4681 3684 1138 4517 2239 2261 3726 2174 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 0.00228508441061951 0.0113551490436511 3250 2227.36363636364 2263 0.000207951029741529 671 1.36858722786284 1.43572548632924 1 5.94057635576652 3249 1487 671 2984 1751 1386 4080 2688 1030 2912 2263 2175 M9367 BIOCARTA_ERYTH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERYTH_PATHWAY.html Erythrocyte Differentiation Pathway 7/15 BioCarta 0.154445388352169 0.258014648776565 2270 2373.90909090909 2268 0.016636314495488 1052 1.00744291305309 1.00744291305309 1 1.32293930297966 2268 1257 3832 2087 3890 2275 2458 1052 3631 1499 1864 2176 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 0.0751978642459046 0.156982736433532 2780 2264.81818181818 2268 0.00778706961417469 755 1.27293921238954 1.3666970832184 1 2.28466886050556 2780 755 4109 1193 1265 1271 2686 3180 2268 1141 4265 2177 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 0.0896272934464921 0.165874208961399 3835 2439.54545454545 2268 0.00850014011109102 259 1.04972036211756 1.13841118675565 1 1.82797767285085 3831 259 2268 584 1305 2020 4654 4543 2193 2897 2281 2178 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 0.00858355441766043 0.0310557196555006 1495 2005.27272727273 2268 0.000783384384291811 552 2.13058595446134 2.15920914130393 1 7.17033051382461 1495 2539 795 2268 4085 2643 2769 1478 552 859 2575 2179 M4052 REACTOME_TELOMERE_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TELOMERE_MAINTENANCE.html Genes involved in Telomere Maintenance 45/93 Reactome 0.00931991180781256 0.0328743726165795 290 1859.72727272727 2269 0.000850875430128463 290 1.20074158169684 -1.20074158169684 -1 3.97476990555916 290 2271 1442 2402 2559 1635 2344 1239 2310 2269 1696 2180 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 0.268903932478882 0.389515866335716 3660 2563.72727272727 2269 0.0308356182355806 952 1.49234186417521 1.49234186417521 1 1.36387668893972 3658 952 4478 1819 2052 1551 2269 4584 2589 1618 2631 2181 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 0.207851560923146 0.321203723924179 4595 2864.72727272727 2271 0.0209596359488402 1133 1.39188427939129 1.39188427939129 1 1.53222611419216 1748 4593 2271 4593 4557 3919 1268 1133 3514 1827 2089 2182 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 0.0699980662456699 0.148287042688612 4090 2336.72727272727 2271 0.00723059391290757 430 1.17071364429621 1.29531671263014 1 2.16586157037099 4086 865 4164 990 1753 430 4143 3217 2271 939 2846 2183 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 0.00391020034636193 0.0170339384812289 2275 2074.72727272727 2272 0.000356106139780569 505 1.34305937056841 1.34305937056841 1 5.30182318936656 2272 2129 715 3038 1612 3557 2615 505 2540 1388 2451 2184 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 0.0323970616830702 0.082819772134005 790 2018.90909090909 2272 0.00298947382883487 447 0.790640563227771 0.790640563227771 1 1.90911507164092 789 3109 2812 3067 1223 825 613 2272 3037 4014 447 2185 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 0.0615199963189971 0.134147372150219 2275 2294.81818181818 2274 0.00575553036689356 965 0.55936453995665 -0.55936453995665 -1 1.08917839793228 2274 1753 1924 2971 1121 2645 965 1022 3697 4304 2567 2186 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 0.027487690125573 0.0736155612891118 2935 2359.09090909091 2276 0.00253066024867567 483 0.97078926890812 0.97078926890812 1 2.45496934501503 2933 483 1979 1428 709 4176 2276 4038 1701 2626 3601 2187 M85 BIOCARTA_BAD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BAD_PATHWAY.html Regulation of BAD phosphorylation 18/40 BioCarta 0.0426400022545553 0.102048544721576 2600 2153.36363636364 2277 0.00395359887373468 304 2.24458518468169 2.24458518468169 1 4.96562539879576 2596 2880 2941 1687 2230 3547 2558 655 304 2277 2012 2188 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 0.0220408160678683 0.0631701921064409 1620 2275.36363636364 2277 0.00202407098536439 915 1.4931426597833 1.4931426597833 1 3.99739158885199 1620 3197 915 2907 2277 3725 3486 1003 1521 2447 1931 2189 M33 PID_GLYPICAN_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_GLYPICAN_1PATHWAY.html Glypican 1 network 18832364 13/37 Pathway Interaction Database 0.232850105696956 0.34496857265126 3135 2331.81818181818 2279 0.0238095238095238 498 1.00744291305309 1.00744291305309 1 1.03931973515913 3131 498 2279 653 1926 3436 3869 3507 1578 1974 2799 2190 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 0.0460023838747246 0.108434190561851 1665 2132.54545454545 2280 0.00427213077154103 261 2.24458518468169 2.24458518468169 1 4.83357138758698 1662 2852 2648 2107 4253 2527 2436 672 261 2280 1760 2191 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 0.278758674132159 0.399835674007744 955 2693.45454545455 2280 0.0292704802866203 837 0.227394358692361 -0.232933935437579 -1 0.202055909290391 951 4323 3717 4358 2280 837 1967 2174 4050 3444 1527 2192 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 0.0088138751936125 0.0315521918695708 2775 2499.90909090909 2281 0.000804489601355464 356 1.07702782168939 1.07702782168939 1 3.60810048126427 2775 1283 1776 2243 356 3036 3977 3952 2281 2090 3730 2193 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 0.0851827225554868 0.159093757630535 1985 2362.45454545455 2282 0.0080610549780033 1280 1.19045135446987 1.19045135446987 1 2.12120591710528 1984 1846 3234 2025 1280 3157 3051 2282 1816 2560 2752 2194 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 0.00627883688009237 0.0245803087887325 1605 2584.63636363636 2282 0.00057243897414321 755 1.43251126162783 1.43251126162783 1 5.14570653503181 1604 4620 755 4409 2887 3871 2146 1594 2428 1835 2282 2195 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 0.0480095992152374 0.111685731267553 2285 2224.18181818182 2283 0.00446276915988675 686 1.26747331848694 1.26747331848694 1 2.69312419552823 2283 2033 2395 2662 2108 3761 2488 686 979 1962 3109 2196 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 0.0839184282471183 0.156982736433532 4140 2576.72727272727 2283 0.00793650793650794 879 1.4365870424641 1.56132083141935 1 2.57838367252367 4136 1414 2046 1402 1710 2283 4102 4004 879 2305 4063 2197 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 0.0878217452386306 0.162983246807217 1770 2218.27272727273 2284 0.00832153304721432 1291 1.55088542876629 1.55088542876629 1 2.7271353163275 1770 2929 1415 2740 1291 2903 2200 1579 2284 2885 2405 2198 M5410 KEGG_ARACHIDONIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARACHIDONIC_ACID_METABOLISM.html Arachidonic acid metabolism 18/108 KEGG 0.0839184282471183 0.156982736433532 2120 2303.54545454545 2285 0.00793650793650794 706 1.08264552524787 -0.874649861425705 -1 1.94313011525252 2120 2392 1144 1623 4283 2879 2285 2517 706 2274 3116 2199 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 0.0795495073584268 0.156982736433532 1325 2332.81818181818 2286 0.00750732031400401 1021 0.620613649093366 -0.620613649093366 -1 1.11387618876133 1322 3223 3702 3041 1240 1021 2354 1336 2286 4569 1567 2200 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 0.136886518733387 0.23467548404327 1880 2727.90909090909 2287 0.0132934960092677 1208 0.73426504557095 0.73426504557095 1 1.03169282758107 1876 3539 2287 4003 1581 3317 1208 1848 3860 4684 1804 2201 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 0.21928319485149 0.334057558866736 1705 2887.81818181818 2288 0.0244504054073813 1702 0.857185672850884 0.857185672850884 1 0.911012677015472 1702 3489 4173 3617 1919 2260 2279 2219 3937 3883 2288 2202 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 0.147322157216645 0.249412467725749 3530 2798 2288 0.0143840448090608 1271 1.14126826551137 -0.55936453995665 -1 1.53618509718693 3526 2199 1271 1583 4289 3542 4684 2118 2206 2288 3072 2203 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 0.0481086740222334 0.111798539165466 2985 2177.54545454545 2288 0.0044721884035585 333 1.31296854530195 1.30131336968609 1 2.78850752628488 2984 2710 3353 2288 3041 333 1936 3258 2242 1121 687 2204 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 0.0272207560814176 0.0731821359710402 4385 2579.54545454545 2289 0.00250577387882173 702 1.34400167146965 1.41738207328826 1 3.40645616071651 4383 2925 1350 2289 702 1978 4151 4520 838 1821 3418 2205 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 0.178030249914525 0.283084408245492 2240 2423.36363636364 2289 0.0176649923180513 1050 1.16537120706009 -0.791140711360448 -1 1.42557805779231 2236 2663 1316 2071 2139 3513 1050 3928 2354 2289 3098 2206 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 0.30609420530592 0.425625354914998 1765 2348.72727272727 2290 0.032674193716385 1311 0.900299882295612 0.900299882295612 1 0.745432759679864 1762 1946 2760 2290 4432 2346 1902 1311 2374 2452 2261 2207 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 0.0512005979679633 0.11703707418433 2780 2364.09090909091 2290 0.00476659274714019 939 0.940767540772448 -0.940767540772448 -1 1.95626209890615 2779 1854 3027 2385 1024 2290 4609 1648 1421 4029 939 2208 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 0.298735036746822 0.4173739958842 4135 2779.18181818182 2290 0.0317460317460317 1231 1.70956702222945 1.70956702222945 1 1.44793282161459 4133 1231 1959 1662 2290 1871 4274 4350 1950 2350 4501 2209 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 0.0328546421738906 0.0837133827166711 2715 2379.45454545455 2291 0.00303234553342309 737 1.13752736102836 -0.874441649465422 -1 2.73488966857106 2713 3886 2042 3727 805 737 2728 4209 2291 1257 1779 2210 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 0.0204290992393255 0.0597235599239427 1795 2087.81818181818 2291 0.00187466421525035 338 1.05919280447021 1.05919280447021 1 2.89323892429243 1794 2945 3467 2862 3418 1264 338 944 2755 2291 888 2211 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 0.0535062074230836 0.121242789160817 3455 2381.90909090909 2291 0.00498669464322448 775 0.985400068065999 -0.82550381394431 -1 2.01535112313112 3453 2073 3424 2291 1045 775 2903 4248 1822 2752 1415 2212 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 0.414279630391322 0.535769969181582 2295 2449.72727272727 2291 0.047465007665062 1303 1.24952268119908 -1.35231969614778 -1 0.755836144296651 2291 2089 1909 2187 2748 3121 1303 4035 2639 1578 3047 2213 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 0.185464750681363 0.293303644412678 1850 2769.63636363636 2292 0.0184760561677112 993 1.3786345671023 1.3786345671023 1 1.6390687896224 1848 4556 2221 4401 4286 3535 993 1084 3587 1663 2292 2214 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 0.335167364008499 0.45603782454815 2295 2710.18181818182 2292 0.04 626 1.21455215107271 1.21455215107271 1 0.924376719375125 2292 626 4282 1913 3910 3434 1661 4657 3274 1703 2060 2215 M9577 MOOTHA_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_MITOCHONDRIA.html Mitochondrial genes 12808457 286/573 Vamsi Mootha 0.0307018749923143 0.0796489342387984 1095 2382.81818181818 2292 0.00283080858041064 766 1.00413735359401 1.21756239367239 1 2.46263045202587 1095 3743 3768 3920 766 822 2292 2124 3082 3147 1452 2216 M13883 BIOCARTA_MPR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MPR_PATHWAY.html How Progesterone Initiates Oocyte Membrane 26/66 BioCarta 0.298735036746822 0.4173739958842 3380 2386.27272727273 2293 0.0317460317460317 1061 1.1895758495521 -0.625059557561618 -1 1.00752172562786 3376 1988 2293 1061 2504 2103 3511 2075 1905 2588 2845 2217 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 0.0268242818798086 0.0725323628902384 2030 2258.81818181818 2293 0.00246882188303282 280 0.330993023813602 -0.386393292236255 -1 0.841783860548507 2030 2986 3284 3597 2828 280 991 1747 2293 4403 408 2218 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 0.164106586186036 0.265999122403239 1820 2453 2294 0.0161637748005134 766 0.253617205258852 -0.332641626189405 -1 0.325549163531982 1816 2294 3526 3144 3585 766 845 1874 3485 4127 1521 2219 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 0.0727789803675596 0.153071051168036 1335 2289.36363636364 2294 0.00684585213011786 859 1.01245311732049 1.01245311732049 1 1.84191279588591 1334 3132 1114 3252 2814 2965 1831 859 4141 2294 1447 2220 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 0.232850105696956 0.34496857265126 1685 2560.63636363636 2296 0.0238095238095238 1682 1.14505098292374 1.14505098292374 1 1.18128190581398 2152 2159 3134 2811 2296 4574 2777 1682 1685 1849 3048 2221 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 0.348730976895065 0.471209157361672 1590 2196.09090909091 2297 0.0382346438208109 1068 1.18063890866154 1.18063890866154 1 0.861113619850332 1588 2546 2603 2297 3140 2471 3298 1377 2211 1068 1558 2222 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 0.136417020286725 0.234191945368432 2300 2592.54545454545 2298 0.014559499261536 1250 0.318210148491367 -0.327938086536269 -1 0.44774331069467 2298 1873 4159 2805 1630 1261 1250 3770 4074 3861 1537 2223 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 0.160436355322012 0.262241686633255 2360 2375.81818181818 2298 0.0173352838586595 1418 1.05077947290469 1.05077947290469 1 1.36329601659839 2356 2298 4626 2868 1740 3127 1567 1418 2587 1435 2112 2224 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 0.151206858498468 0.254144669628343 1510 2414.8 2300 0.0180506302105042 890 0.633042077535849 0.633042077535849 1 0.840562416947071 1508 2707 4486 NA 1893 997 890 2868 3034 4395 1370 2225 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 0.194663651869681 0.304729696016333 1300 2602.09090909091 2300 0.0214168575894974 1146 0.477414342282077 0.519646400483286 1 0.549916105746488 1298 2300 4590 2651 3590 1167 2100 1146 3595 4554 1632 2226 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 0.123992995648306 0.216479574369584 625 2415.72727272727 2301 0.01196252702406 622 0.864828883087338 -0.564322045552235 -1 1.28280019364911 622 2972 3760 3513 2300 955 2008 2301 3681 2933 1528 2227 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 0.208675616166183 0.322298595041111 2850 2415 2301 0.0210522683909431 942 1.17608135842793 1.17608135842793 1 1.29078485155446 2847 2190 2727 2198 4314 2008 942 2645 1765 2628 2301 2228 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 0.0280276114509204 0.0743278931856328 2795 1887.90909090909 2303 0.00258101632295315 228 1.3625470404181 1.5260487703967 1 3.43294302281004 2791 1492 2367 2774 1137 228 2424 1231 2712 2303 1308 2229 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 0.265837686890632 0.385789842294674 2005 2391.27272727273 2304 0.0277022502492881 1247 1.16087976246319 1.30186145517716 1 1.07176358129787 2001 2790 2130 2396 2104 4174 2299 1247 2395 2304 2464 2230 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 0.214139132665174 0.327605607466211 3185 2415.45454545455 2305 0.0238095238095238 1651 1.27675999939789 -1.27675999939789 -1 1.38107050629598 3184 2667 3947 2305 2042 1829 2637 2589 1651 1689 2030 2231 M1986 KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS_AND_CYCLIC_RGD http://www.broadinstitute.org/gsea/msigdb/cards/KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS_AND_CYCLIC_RGD.html Inflammatory cytokines and their receptors moduated in brain tumors in response to treatment with cyclic RGD peptide prior to the oncocytic virus therapy. 18042934 5/25 Jessica Robertson 0.0244009630138233 0.0677386923476161 1770 2393.81818181818 2306 0.00246731114587374 407 0.563173433622882 0.587072054062608 1 1.46959223484504 1769 2062 4580 2306 2681 2419 2151 590 2831 4536 407 2232 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 0.0565128671642991 0.126104426443765 4510 2518.09090909091 2307 0.0052744547721619 778 1.22954159229816 1.3308334108194 1 2.46781570986845 4506 2709 2307 2410 1071 778 3855 3774 2259 2030 2000 2233 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 0.0716056956803178 0.150942100745825 1310 2168.09090909091 2307 0.00673167097157143 1201 1.14964967938937 1.44197676989573 1 2.10711637961864 1308 2307 2729 2326 1201 3063 1413 1503 3240 3060 1699 2234 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 0.232850105696956 0.34496857265126 2570 2390.27272727273 2307 0.0238095238095238 1374 1.52471806479713 -1.29829314601985 -1 1.5729621547965 2569 3099 2264 2307 1944 3345 2690 1396 1665 1374 3640 2235 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 0.0811359185435322 0.156982736433532 2310 2453.72727272727 2307 0.00766294927905102 1239 1.26876572497157 1.38486679574962 1 2.27717829328039 2307 1771 1239 2143 1254 4118 3469 2453 1824 2504 3909 2236 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 0.275742742869669 0.39623750171336 1675 2285.81818181818 2308 0.0317460317460317 1098 1.46693471565438 1.46693471565438 1 1.31632880062026 1673 1098 4032 2308 2899 3023 2575 2413 1907 1602 1614 2237 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 0.232850105696956 0.34496857265126 2310 2579 2308 0.0238095238095238 1547 1.08023697533246 -1.08023697533246 -1 1.11441709755711 2308 1937 1547 1915 2740 4614 2126 3203 1753 2734 3492 2238 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 0.086864397809412 0.161462343567991 4250 2361.81818181818 2308 0.00904592575425407 477 0.319688015612941 -0.367305357868878 -1 0.565056687568548 1175 2552 4248 3131 1525 477 809 2308 4250 3987 1518 2239 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 0.161385165508919 0.262241686633255 3030 2433.45454545455 2308 0.0158730158730159 1400 1.1874442783341 1.35173255772907 1 1.5406068507643 3028 1924 1610 1400 2308 2665 3333 1950 1517 2635 4398 2240 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 0.232850105696956 0.34496857265126 2885 2628.27272727273 2310 0.0238095238095238 1538 1.22606298529464 1.22606298529464 1 1.26485723476438 2883 1837 2310 1538 2155 4522 3235 3342 1694 2011 3384 2241 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 0.386086746459241 0.507632574048261 2060 2751 2311 0.0476190476190476 1703 0.710982301030754 0.762715761560266 1 0.467251459294428 2058 1703 4291 1845 4172 2386 1891 3482 2311 4042 2080 2242 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 0.104661745741284 0.188278202397265 2540 2242.36363636364 2311 0.01 115 0.967459383376804 -0.967459383376804 -1 1.5659217828292 2536 115 1314 631 2311 2699 1466 3922 1235 4254 4183 2243 M19540 KEGG_OXIDATIVE_PHOSPHORYLATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OXIDATIVE_PHOSPHORYLATION.html Oxidative phosphorylation 62/155 KEGG 0.0836619141777488 0.156982736433532 550 2194.54545454545 2312 0.00791125751940731 514 0.918386988900018 -0.6829135458099 -1 1.64831920878467 548 3087 3751 3619 2312 514 994 1943 3468 3020 884 2244 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 0.00879145984407748 0.0314960098083693 3315 2363.90909090909 2312 0.000802435397092576 355 1.35232243471951 1.35232243471951 1 4.53268821745651 3315 2312 1456 1563 355 3050 3360 3907 891 1679 4115 2245 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 0.0408294777868015 0.099339009817732 3205 2369.81818181818 2312 0.0037825016482196 895 1.68636365151441 1.68636365151441 1 3.77467733018891 3201 1131 2067 1752 895 3441 3358 2974 1456 2312 3481 2246 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 0.0478064462472107 0.111508714342673 2315 2352 2312 0.00444345778027619 984 1.52897341091483 1.52897341091483 1 3.25110980200404 2312 2072 2723 2987 984 4493 2070 1032 2556 2508 2135 2247 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 0.232850105696956 0.34496857265126 2435 2394.63636363636 2313 0.0238095238095238 1204 1.36583036967316 1.36583036967316 1 1.40904704348546 2432 2265 2292 2634 2481 4013 2313 1762 1792 1204 3153 2248 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 0.232850105696956 0.34496857265126 2320 2554.54545454545 2316 0.0238095238095238 1241 1.46693471565438 1.46693471565438 1 1.51335046429228 2316 1241 2523 2035 2450 4177 4114 3551 1652 1977 2064 2249 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 0.275845995382549 0.396264357560583 2215 2749.27272727273 2317 0.0289147493482279 1320 0.653874098340854 0.653874098340854 1 0.586699792645114 2212 3730 3181 3740 2008 2317 1320 1980 4103 3364 2287 2250 M456 REACTOME_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRNA_AMINOACYLATION.html Genes involved in tRNA Aminoacylation 27/43 Reactome 0.348251863240569 0.470833303850348 945 2496.90909090909 2317 0.0381703440552285 943 0.238311810617445 -0.271122622382775 -1 0.17399999884078 943 3013 3716 3559 2317 1052 1913 2197 3622 3565 1569 2251 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 0.174555751884839 0.278870535796146 2575 2385.36363636364 2321 0.0172882276535764 1061 0.483197150001952 0.616025958614332 1 0.598110908946582 2574 1468 2368 2320 2655 2066 1540 1061 2321 4640 3226 2252 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 0.0413226056827414 0.100099145839282 2325 2118.36363636364 2322 0.00382907384675127 815 1.29142669460736 1.29142669460736 1 2.88112675695575 2733 2815 2144 3064 902 2322 815 1246 2967 1969 2325 2253 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 0.0839184282471183 0.156982736433532 3000 2320.90909090909 2322 0.00793650793650794 888 0.941363445919324 -0.493393016758395 -1 1.68955730984102 2999 2080 2504 2731 1545 1605 3843 2322 888 2942 2071 2254 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 0.35943518917414 0.478362197236587 2905 2413.09090909091 2322 0.0396825396825397 1236 1.53334444632203 1.53334444632203 1 1.09597115841007 2904 1236 1843 1500 2468 3442 2322 3257 2180 2185 3207 2255 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 0.0933430304620779 0.171801037213392 1015 2257 2323 0.00975125553508717 690 1.14672566625037 1.14672566625037 1 1.95787917216495 1012 2368 4383 3136 3162 1258 690 2323 3359 1707 1429 2256 M13036 KEGG_PRION_DISEASES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRION_DISEASES.html Prion diseases 24/49 KEGG 0.17248732138007 0.276617244348736 2120 2399.09090909091 2324 0.0170646169957947 1386 0.420249329453733 -0.308058886943453 -1 0.523497669324612 2118 2324 2132 2779 1724 2481 1386 2796 3192 3228 2230 2257 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 0.35943518917414 0.478362197236587 4665 2603.36363636364 2324 0.0396825396825397 1172 1.11970026421149 1.33426299290105 1 0.800315414153006 4664 1413 1822 1172 2279 2324 3249 3669 2210 2730 3105 2258 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 0.0042768476168786 0.0182858649020923 3125 2444.63636363636 2324 0.000428510112318127 245 0.613523234585661 -0.490312797593657 -1 2.37975077664159 3121 748 4591 1825 245 1628 1794 3109 2951 4555 2324 2259 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 0.232850105696956 0.34496857265126 2325 2442.81818181818 2325 0.0238095238095238 1405 1.18063890866154 1.18063890866154 1 1.21799588044927 2325 2318 2677 1405 2848 3997 2179 2571 1638 1823 3090 2260 M12524 KEGG_HISTIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HISTIDINE_METABOLISM.html Histidine metabolism 11/36 KEGG 0.0266321222124323 0.072206820496027 4030 2506.54545454545 2326 0.00245091723486283 948 0.967459383376804 -0.967459383376804 -1 2.46466813576404 2326 1470 948 1873 2055 2485 3233 4029 4030 3170 1953 2261 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 0.0771263655605119 0.156982736433532 1180 2188.27272727273 2326 0.00727007704719693 805 1.05077947290469 1.05077947290469 1 1.88593698553323 1176 3840 2938 3888 2669 1262 928 805 2875 2326 1364 2262 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 0.220529041303444 0.335737195434678 3635 2799.90909090909 2327 0.0223945122081599 1654 1.53150662091758 1.53150662091758 1 1.62023224636871 3631 2327 1977 2888 1868 3612 2148 4034 1654 2251 4409 2263 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 0.00602231863152691 0.0237547012688006 3845 2620.90909090909 2329 0.000548987971771587 286 1.39888142350646 1.17406203774989 1 5.07123162645642 3843 1835 1627 2329 286 3501 4521 4018 1006 1383 4481 2264 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 0.197742799507847 0.308668473848692 1955 2302.27272727273 2329 0.0198303778954054 1342 1.56143222277456 1.56143222277456 1 1.77911905314594 1953 2690 1342 2172 2646 3474 1714 2728 2329 1641 2636 2265 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 0.0839184282471183 0.156982736433532 2350 2121.63636363636 2329 0.00793650793650794 331 1.45425102948879 1.56582367699161 1 2.61008696260753 2347 452 1522 331 2329 4662 3201 4598 606 646 2644 2266 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 0.0523733430702613 0.119194504918526 2330 2394.81818181818 2330 0.00536502418497139 638 0.745385806515608 0.884289233841423 1 1.53678174810716 2330 638 4578 1149 1079 3715 3478 893 1548 4533 2402 2267 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 0.275742742869669 0.39623750171336 2080 2669.36363636364 2331 0.0317460317460317 1675 1.46693471565438 1.46693471565438 1 1.31632880062026 2078 1763 4093 2980 3900 3544 3336 1675 1964 1699 2331 2268 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 0.415320710913563 0.535769969181582 1570 2464.54545454545 2331 0.0476190476190476 1398 1.3071874809577 1.3071874809577 1 0.790717575880829 1568 1982 2370 1398 4317 2034 1937 3485 2331 2745 2943 2269 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 0.104752559465436 0.188361662952814 1935 2494.09090909091 2331 0.0100091290771735 504 0.31920526455776 -0.363146255530776 -1 0.516525884110968 1933 2331 3096 3878 2944 504 1760 1428 4075 4374 1112 2270 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 0.0208573116810173 0.0607064363585384 2335 2384.36363636364 2332 0.00191433786097302 604 0.739805811932376 0.791760008296744 1 2.00911175841264 2332 2850 2892 3143 604 885 2233 2276 3511 3854 1648 2271 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 0.00140685770155195 0.00763024906188937 2750 2316.27272727273 2333 0.000127978015115277 109 0.321253997302831 -0.359559441732806 -1 1.51825099229023 2747 2154 3331 3325 109 1050 2069 2333 3466 3488 1407 2272 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 0.171852397399413 0.275976810902553 2105 2512.09090909091 2333 0.0169960795459148 1390 0.595460272904305 -0.595460272904305 -1 0.743092928616485 2105 2355 2208 2895 1721 1390 2333 3059 3640 4238 1689 2273 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 0.0968881626357481 0.177048542352883 3590 2635.81818181818 2334 0.00922166110984731 1167 1.52881424021974 1.69963755790374 1 2.5656580555728 3586 1966 1167 1992 2039 2334 3853 3279 2051 2475 4252 2274 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 0.00311309464364481 0.0144149817194858 1240 1870.45454545455 2334 0.000283409868471801 48 1.01405746558881 -1.01405746558881 -1 4.16715603727532 1239 1081 2339 2498 3018 48 205 3439 4211 2334 163 2275 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 0.0509857463225733 0.116659769173622 1470 2229.27272727273 2335 0.00474610699827414 517 1.19800144227738 1.33102663912009 1 2.49491215198534 1467 3764 1484 2509 4347 1377 517 2564 2754 2335 1404 2276 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 0.0126183788081035 0.0410623077047035 2335 2340.45454545455 2335 0.00115375815110747 434 1.28535286271334 -1.11293806317718 -1 3.97776883601089 2335 3040 3262 2876 434 1292 3628 2203 2290 2704 1681 2277 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 0.156982736433532 2570 2040.36363636364 2336 0.00793650793650794 404 1.93488464960418 1.93488464960418 1 3.47272726353577 2566 1899 2336 606 2396 3184 1856 2418 404 1632 3147 2278 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 0.164808288375236 0.266951828318824 1455 2560.9 2336 0.0198115627155652 927 0.383042264141796 0.383042264141796 1 0.49035485862923 1455 2523 4376 NA 3152 2149 927 1795 3270 4177 1785 2279 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 0.0233244275115888 0.0657235522064371 3585 2594.36363636364 2336 0.00214322247476589 654 1.0973791471732 -1.02985858992326 -1 2.89571771695286 3582 1145 1930 2336 654 4279 2842 4304 1827 1170 4469 2280 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 0.163462325519425 0.26513826839184 1715 2684.54545454545 2339 0.0176900333690942 882 0.468127504880045 0.439484298976979 1 0.602370652402363 1711 1181 4374 2339 4320 1941 882 3314 3236 4171 2061 2281 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 0.0837680713972914 0.156982736433532 1695 2627.72727272727 2339 0.0087104174931322 661 0.499631200742407 -0.487571736202976 -1 0.896737122152854 1691 2339 4556 3319 1408 866 661 4686 3915 4493 971 2282 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 0.0839184282471183 0.156982736433532 3705 2183.63636363636 2340 0.00793650793650794 217 1.0199643972127 1.24817411088064 1 1.83063014669477 3705 217 2917 543 2100 1286 4253 2965 799 2895 2340 2283 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 0.00377853648418342 0.016688239363698 2520 2248.54545454545 2342 0.000378497670353099 222 0.708857239587253 0.815855061952258 1 2.81235283027916 2520 641 4193 1868 222 2342 1817 3632 1112 3910 2477 2284 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 0.0807426066559841 0.156982736433532 2605 2441.72727272727 2342 0.00762434212079057 937 1.21401827160157 1.24964658111409 1 2.17891766881801 2603 1410 1131 1460 2342 3417 4264 4238 1825 937 3232 2285 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 0.036290941945558 0.0906818911270384 3835 2502.45454545455 2342 0.00335489036607493 848 0.884467398417179 -0.650112755713168 -1 2.05792185321133 3835 1743 2912 2062 848 1933 3184 4610 1487 2342 2571 2286 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 0.0266422519499852 0.072206820496027 3430 2521.72727272727 2345 0.00245186100194727 695 1.21602988171798 1.16276200673761 1 3.0979182724671 3426 1974 3244 1485 695 4184 2345 3150 882 1875 4479 2287 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 0.0191222184060803 0.0568931526672333 2470 2336.90909090909 2345 0.00175367984060426 743 1.30532286498139 1.42334279240829 1 3.62698635004106 2469 2345 892 1648 743 3469 3975 2850 2078 1342 3895 2288 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 0.0108315156167397 0.0368067310950269 3305 2511 2346 0.000989564925012272 397 1.07207131821952 1.23530883967623 1 3.43142424850561 3305 2227 2346 2313 397 4350 2724 2478 1472 1348 4661 2289 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 0.0179260686779801 0.0538471524519325 1475 2414.63636363636 2346 0.00180723368130049 345 1.26635987578614 -1.26635987578614 -1 3.58626699275053 1473 3813 4322 3082 2346 1171 3047 1691 3660 1611 345 2290 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 0.376599043923929 0.497671494593212 2205 2541 2348 0.042050761061427 1362 1.50282380330383 1.50282380330383 1 1.01651144987806 2205 3371 2055 3241 2665 4015 1362 1433 3363 1893 2348 2291 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 0.0839184282471183 0.156982736433532 3510 2522.72727272727 2351 0.00793650793650794 933 1.31394404283802 1.31394404283802 1 2.35826425166672 3508 933 1928 1370 1878 4435 2612 4122 984 2351 3629 2292 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 0.415320710913563 0.535769969181582 3145 2555.09090909091 2352 0.0476190476190476 1334 1.1307766002315 -1.0634682405883 -1 0.684006651842027 3142 2352 1775 2228 2520 3287 2885 2082 2348 1334 4153 2293 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 0.174241310652299 0.278572085198456 3370 2357.63636363636 2353 0.0172542017215284 650 0.747686729614264 -0.646118488205991 -1 0.926277341060895 3370 3375 1674 2989 1843 650 1405 2386 2353 4175 1714 2294 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 0.00435832325006098 0.0185159589753271 3465 2212.45454545455 2353 0.000396998305017148 230 1.08292904870686 -0.59277889472046 -1 4.18736884662264 3463 1211 2353 984 230 1574 4603 4187 377 2888 2467 2295 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 0.0557770977960551 0.124876761122249 4380 2501.90909090909 2354 0.00520395910729083 424 2.24458518468169 2.24458518468169 1 4.52639692968682 4379 2354 2676 1342 1064 3061 3301 2195 424 2276 4449 2296 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 0.0356487630012094 0.0894751491289058 2235 2470.09090909091 2354 0.00329453352977643 838 0.650112755713168 -0.650112755713168 -1 1.52108267820939 2235 2328 2925 2354 838 2775 1792 1663 3460 3397 3404 2297 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 0.0206222645862964 0.060059622033179 3595 2189.63636363636 2354 0.00189255892538839 442 1.55155179816711 -1.57303298172666 -1 4.22970363104939 3591 442 903 1129 3126 2354 3636 2844 1790 1532 2739 2298 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 0.232850105696956 0.34496857265126 2325 2660.45454545455 2355 0.0238095238095238 1676 1.46693471565438 1.46693471565438 1 1.51335046429228 2321 2004 2541 2355 2442 4169 3924 3515 1676 2042 2276 2299 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 0.0765897756730953 0.156982736433532 2075 2435.09090909091 2355 0.00793650793650794 142 1.73041933125535 1.73041933125535 1 3.10575330173203 2072 3421 4072 2148 3523 3081 2810 2355 142 1423 1739 2300 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 0.0389722070734409 0.0957827093095062 3900 2660.63636363636 2355 0.00360729163354931 879 1.68636365151441 1.68636365151441 1 3.83426906502008 3900 1781 1649 2140 879 2900 4391 3863 947 2355 4462 2301 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 0.000607020483805571 0.00400633519311677 845 2087.09090909091 2356 5.5198912423103e-05 558 1.3036620028963 1.41537451667822 1 6.97522758176385 844 2422 558 2275 2790 2441 1759 2494 3627 1392 2356 2302 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 0.0224016627259899 0.0638917781704131 1195 2331.63636363636 2356 0.00205755227587415 350 0.298017305875766 0.311195824543841 1 0.794560915799015 1192 2356 3432 3147 2006 1081 350 2550 3219 4673 1642 2303 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 0.193294106729042 0.303036528649144 1460 2242.81818181818 2357 0.0193375047490377 1169 1.12190227680148 1.12190227680148 1 1.29833733988367 1458 2377 2357 2398 1792 3822 1600 1169 2019 2842 2837 2304 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 0.000116825918855424 0.00111675069542682 1350 2191.36363636364 2357 1.0621102098843e-05 417 1.27462864360551 1.27462864360551 1 8.39819628220832 1349 3270 417 2323 1439 3225 2766 3091 2423 1445 2357 2305 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 0.411460049216851 0.534716727292326 3405 2706.81818181818 2357 0.0470490643920919 1245 1.12550541081816 1.29220970268911 1 0.682964894330895 3403 1557 2378 1778 2328 2357 3808 4315 2350 1245 4256 2306 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 0.206455026962468 0.319500745160543 4360 2795 2357 0.0208028507462431 1128 1.53334444632203 1.53334444632203 1 1.69585059427157 4357 3138 1772 2357 2211 1796 4171 1128 4136 1994 3685 2307 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 0.597318307603006 0.711317303539438 2360 2643.54545454545 2358 0.0793650793650794 1822 0.934768526916476 0.968084397128704 1 0.308645071935817 1822 2314 2358 2001 4105 2984 2357 2462 2877 2266 3533 2308 M14933 KEGG_STEROID_HORMONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_HORMONE_BIOSYNTHESIS.html Steroid hormone biosynthesis 14/88 KEGG 0.0454918620107282 0.107501192830193 970 2101.63636363636 2360 0.00422370133487513 482 0.402759885660238 0.506226555671502 1 0.870691435129025 970 2360 2656 2274 4220 962 482 2842 2468 3167 717 2309 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 0.00318204864980227 0.0146330519852536 2575 2226.63636363636 2362 0.000289696405542909 185 1.9083122944764 1.9083122944764 1 7.81422296663633 2571 2599 2362 1609 185 4232 2555 1715 1295 2221 3149 2310 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 0.373537634131977 0.49432289001481 2365 2681.27272727273 2362 0.0416240476151157 1467 1.21501965691307 1.21501965691307 1 0.829791665988506 2362 4170 2288 3845 2244 1467 2970 2065 3773 2414 1896 2311 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 0.292562886705644 0.415313446562451 1325 2165 2363 0.0309743829319066 1167 1.22168558101711 1.22168558101711 1 1.04057812201215 1323 3449 2681 2861 2363 1520 1204 2730 2473 2044 1167 2312 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 0.0839184282471183 0.156982736433532 3305 2517.09090909091 2364 0.00793650793650794 227 1.5131210652793 -1.28490901046479 -1 2.71574679010314 3302 1853 1376 1126 4648 3795 2364 3718 227 1066 4213 2313 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 4.60914503745376e-14 6.17098675585952e-12 1090 2182.90909090909 2364 4.19013185223078e-15 35 1.43327906294773 1.48158703364365 1 35.8593312104258 1087 3500 35 2826 2364 3790 1991 2305 2576 809 2729 2314 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 0.00171204583228925 0.00902434957267426 4225 2540.36363636364 2364 0.000155761782203984 123 2.60557738560654 -3.11553755502548 -1 11.8901821537011 4224 2364 804 1870 123 3796 3960 3684 1856 844 4419 2315 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 0.214139132665174 0.327605607466211 1920 2567.90909090909 2366 0.0238095238095238 1801 1.1896832501922 1.20275914698285 1 1.28687964021483 1918 2672 4676 2738 1917 3682 2082 1846 1801 2366 2549 2316 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 0.00709927920679153 0.0269370221562956 2370 2493.54545454545 2367 0.000647481111344879 775 1.92771852788133 -3.11553755502548 -1 6.75345663965895 2367 975 775 1465 3796 3580 1771 4575 1749 3021 3355 2317 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 0.00334684687631328 0.0151676252054198 3145 2361.36363636364 2367 0.000304722662271176 191 1.17881597565368 1.16389428689663 1 4.78605783450124 3141 1925 1086 1724 191 2367 3162 3697 2658 1396 4628 2318 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 0.107041834214272 0.191889072351981 2620 2428.81818181818 2368 0.0102395376638957 1420 1.57416553838995 1.57416553838995 1 2.51894495345069 2617 3842 2438 3293 1420 3268 2033 1717 1478 2243 2368 2319 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 0.38650304928556 0.508037388205368 1730 2587.54545454545 2368 0.0434443991289035 1464 0.70658926683976 -0.70658926683976 -1 0.463818430972835 1729 3057 2826 2745 2275 1513 2368 1464 4249 4281 1956 2320 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 0.730339207442368 0.832288308870364 1495 2642.27272727273 2369 0.122834017971884 1491 0.695564489726335 0.695564489726335 1 0.123770758677482 1491 2556 3852 1964 3182 2094 1845 2175 4238 3299 2369 2321 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 0.14587511795468 0.247491239223618 655 2436.72727272727 2371 0.0142321035922519 655 1.23123174131809 1.23123174131809 1 1.66650767631224 655 3961 3002 3856 2068 2306 2013 2707 2371 1326 2539 2322 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 0.0505811779668204 0.116301962685241 2945 2241.45454545455 2372 0.00470754351682129 342 1.16593213598038 1.30032364293544 1 2.43159744810323 2941 2372 3731 2084 1473 342 3570 2484 1804 2705 1150 2323 M916 REACTOME_PLATELET_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_HOMEOSTASIS.html Genes involved in Platelet homeostasis 31/91 Reactome 0.318162607299538 0.439019428093532 1900 2538.27272727273 2373 0.0342158491504074 1488 1.6880648511124 1.6880648511124 1 1.34699033841709 1896 2278 1488 2400 2373 3892 2825 4228 2228 1747 2566 2324 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 0.000442242015134513 0.00315906415079318 1905 1949.36363636364 2373 4.02119035683664e-05 52 1.13941737146131 1.13941737146131 1 6.35885759119721 1901 2765 2945 2373 52 2744 609 2624 1165 2393 1872 2325 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 0.0415418382795025 0.100412224897613 3435 2361.36363636364 2373 0.00384978570027748 707 1.20786706143778 1.36182710361716 1 2.69105201784846 3432 757 1915 707 907 2398 3754 3955 1499 2373 4278 2326 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 0.0765897756730953 0.156982736433532 2795 2090.09090909091 2373 0.00793650793650794 21 1.65198623575143 1.65198623575143 1 2.96498173212773 2792 176 4588 210 2471 4343 3693 1125 21 1199 2373 2327 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 0.093743776706077 0.172267975546932 2380 2556.36363636364 2376 0.00890855482199744 1162 1.9873813307682 1.9873813307682 1 3.38795651450023 2376 3164 1162 2286 4506 3199 2632 3805 1347 1666 1977 2328 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 0.161385165508919 0.262241686633255 2190 2678.54545454545 2377 0.0158730158730159 1281 1.17464842867224 -0.983391546104649 -1 1.52400533605627 2187 4042 3691 4151 3993 1281 2826 2377 1545 1450 1921 2329 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 0.591610364223672 0.708060891735058 3170 2408.54545454545 2377 0.0781863057204077 1345 1.08104121333025 1.16369587510112 1 0.361750038887407 3166 2526 1869 2377 3760 1345 2317 2729 3258 1477 1670 2330 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 0.0596211153101366 0.131043408228565 4260 2503.90909090909 2377 0.00557281539628712 1008 1.26715109826347 1.26715109826347 1 2.49611397988301 4256 1008 1379 2185 1103 2415 3090 3731 2377 2126 3873 2331 M13486 KEGG_HUNTINGTONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HUNTINGTONS_DISEASE.html Huntington's disease 92/233 KEGG 0.0587947453050175 0.129591804562235 855 2316.63636363636 2378 0.0054934047797359 498 0.612639895188347 -0.612639895188347 -1 1.21343144975797 854 4045 3752 3861 2378 498 1096 1487 3690 3227 595 2332 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 0.161385165508919 0.262241686633255 3295 2625.54545454545 2378 0.0158730158730159 1099 1.29644110978073 1.29644110978073 1 1.6820208676688 3295 2281 3204 2207 3721 1099 2310 4374 1388 2624 2378 2333 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 0.0439810718924523 0.104723223012211 2380 2289.09090909091 2378 0.00408052166786476 941 1.10858603309022 1.10858603309022 1 2.42468863561193 2378 2607 3174 2942 941 2952 3588 1550 1777 1924 1347 2334 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 0.284566391927094 0.406117998517277 1790 2665.54545454545 2378 0.0329321761053112 1145 0.375193822345573 0.43773097099458 1 0.327716334816195 1788 2997 4430 3926 3136 1705 1145 1660 2378 4323 1833 2335 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 0.0353182826457714 0.0888360024036954 3035 1977.09090909091 2379 0.00326348672427183 275 1.18814112418976 -0.828717545194705 -1 2.78817543210098 3035 1276 3650 1601 831 275 2756 2529 2379 2926 490 2336 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 0.236111699025584 0.349028208717315 2185 2653.9 2379.5 0.0294826188427982 1393 0.296665507807263 0.296665507807263 1 0.302688089356403 2185 3188 4290 NA 2025 1393 1435 2574 3960 4041 1448 2337 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 0.0499061661695122 0.115088727692094 2600 2430.09090909091 2380 0.00464323459282512 1006 1.76519601535094 1.98403766691632 1 3.69932868442947 2597 1972 2433 2027 1006 3453 2802 2380 1925 2155 3981 2338 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 0.161385165508919 0.262241686633255 2405 2438.45454545455 2380 0.0158730158730159 1137 1.61180388191581 1.58166446807331 1 2.09117694861041 2401 1896 1513 2380 2372 4234 2737 3079 1343 1137 3731 2339 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 0.0546912633064166 0.123263662723427 1250 1949.72727272727 2381 0.0051000141180022 552 1.14672566625037 1.14672566625037 1 2.32692166668707 1247 2544 2840 2824 3579 1239 552 1134 2532 2381 575 2340 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 0.0839184282471183 0.156982736433532 3660 2312.36363636364 2382 0.00793650793650794 287 1.56822027466936 1.56822027466936 1 2.81463874559667 3659 1892 2784 597 2135 2469 4058 2382 287 1320 3853 2341 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 0.0135603192172229 0.0431682444646104 3165 2266 2383 0.00124042095561337 323 2.06081593237228 2.06081593237228 1 6.27767898612862 3162 2718 1718 2119 463 4384 3271 2636 323 1749 2383 2342 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 0.344155002071066 0.466101254250004 1575 2637.27272727273 2383 0.0376222700338934 1201 1.31394404283802 1.31394404283802 1 0.972222802608189 1575 3797 1936 3510 3858 1832 1201 4099 2383 2598 2221 2343 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 0.232850105696956 0.34496857265126 3275 2690.27272727273 2383 0.0238095238095238 1304 1.55911809007017 1.55911809007017 1 1.60845064222993 3272 2383 1763 2891 2174 3819 4447 1304 1744 2361 3435 2344 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 0.0109157924622678 0.037012592965403 3750 2456.09090909091 2384 0.000997302986203385 402 1.27675999939789 -1.27675999939789 -1 4.07967745428494 3746 1014 2680 1802 402 4293 2384 3765 710 1770 4451 2345 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 0.514011397665828 0.633523779448203 2330 2622.90909090909 2385 0.0634920634920635 2129 1.29644110978073 1.29644110978073 1 0.573610693010205 2329 2285 2311 3341 3122 3622 2129 2177 2651 2500 2385 2346 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 0.0642815612985483 0.138557219983899 1080 1984 2386 0.00602185560851505 387 0.831342567029314 -0.554099100968402 -1 1.59270200922814 1077 2386 3615 2815 1150 387 995 2775 2715 2701 1208 2347 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 0.0358277477905008 0.0897601311785643 1795 2574.81818181818 2388 0.00331135220094825 430 1.05077947290469 1.05077947290469 1 2.45529222374732 1792 3872 2326 3246 4230 1904 430 2979 4049 2388 1107 2348 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 0.0122842798573631 0.040344087099964 3175 2175.81818181818 2390 0.00112303758316563 429 1.26335308425343 1.26335308425343 1 3.93129506698127 3173 1929 1290 825 429 3730 2640 2741 2390 742 4045 2349 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 0.0944304231492182 0.173190200734731 4635 2472.90909090909 2392 0.00897684414876921 600 0.960500714487355 0.960500714487355 1 1.63242733035833 4635 600 1853 964 1343 2444 2738 3708 2357 2392 4168 2350 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 0.298735036746822 0.4173739958842 1875 2547.90909090909 2392 0.0317460317460317 1752 1.61953060845267 1.61953060845267 1 1.37167568927524 1873 3560 1932 3487 2527 3564 2392 2678 2089 1752 2173 2351 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 0.161396718790078 0.262241686633255 2240 2638.09090909091 2392 0.0174477472112998 1427 0.339953171020477 -0.174266333574512 -1 0.441060009031218 2240 2406 4373 2392 1745 1427 1583 1824 4208 4166 2655 2352 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 0.375948849222223 0.497092637543831 2565 2518.63636363636 2395 0.0419599748338195 1481 1.05077947290469 1.05077947290469 1 0.711933612384811 2564 3020 1943 3488 2252 1481 2872 2022 3470 2395 2198 2353 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 0.391015286225935 0.513092256024759 1770 2686.63636363636 2396 0.0483864021658684 1432 0.548698422658994 0.634022728234571 1 0.354910175509808 1768 2825 4247 2388 3449 2396 1432 1517 3356 3986 2189 2354 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 0.275742742869669 0.39623750171336 2030 2661.90909090909 2397 0.0317460317460317 1018 0.387624796314285 -0.492713334987519 -1 0.347828487298792 3266 1018 4074 2754 2169 2028 2397 3583 2027 3714 2251 2355 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 0.0139952680730731 0.0442821243689536 3985 2787.63636363636 2397 0.00128046362201732 468 1.9083122944764 1.9083122944764 1 5.76599666475884 3982 1997 1931 2076 468 4607 3487 3064 2169 2397 4486 2356 M15743 ST_GA12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA12_PATHWAY.html G alpha 12 Pathway 25/52 Signaling Transduction KE 0.161385165508919 0.262241686633255 2990 2252 2398 0.0158730158730159 303 1.46956407868234 1.46956407868234 1 1.90663303414994 2988 820 1507 303 2398 4657 2791 2873 1389 1482 3564 2357 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 0.0238384185216857 0.0667105481372723 1650 2138.45454545455 2398 0.00219097371262395 516 1.49317273307187 1.49317273307187 1 3.91854726292889 1649 2911 1323 3175 790 2779 2717 516 3280 2398 1985 2358 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 0.00689343243455669 0.0262836650840787 2400 2269.27272727273 2399 0.000628647945136327 770 1.24893519969649 1.29993262991994 1 4.4051719865004 2399 2413 770 1675 1032 4295 2800 2854 1515 1284 3925 2359 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 0.193095859129103 0.30282704012014 1035 2253.45454545455 2400 0.0193155983455713 875 0.55936453995665 -0.55936453995665 -1 0.647707507055948 1031 2400 3303 2839 3026 875 1573 1391 3604 3769 977 2360 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 0.174606519851877 0.278870535796146 1360 2189.36363636364 2400 0.0172937223998385 1308 1.38054735950751 1.47676300019854 1 1.70886859768879 1359 3436 1308 2720 2453 2400 1755 2521 2677 2083 1371 2361 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 0.415320710913563 0.535769969181582 2305 2699 2403 0.0476190476190476 1630 0.454298158905505 0.592269815404069 1 0.274804910605524 2305 2545 2102 3089 4242 2403 3438 1630 2320 3918 1697 2362 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 0.0106014422761192 0.0362538671223152 1325 2175.36363636364 2404 0.00106523602462887 295 0.335872884006568 -0.357186182875437 -1 1.07996995557655 1325 2404 4124 3584 3924 328 295 382 3346 3803 414 2363 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 0.0576204837714006 0.127968639044506 3865 2680.09090909091 2405 0.00538067223461355 1080 1.18149146098025 1.30821520198589 1 2.35456800096999 3861 1922 2901 1721 1080 1743 4159 4399 2405 1656 3634 2364 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 0.105205047658329 0.189030235171369 1630 2262.72727272727 2406 0.010054628141382 892 0.227052227156415 -0.210261220660289 -1 0.366627538230039 1630 3314 3632 3440 2497 1275 1112 892 2406 3178 1514 2365 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 0.161385165508919 0.262241686633255 4655 2616.27272727273 2406 0.0158730158730159 1174 1.06469777730548 1.23653423727076 1 1.38135381981791 4655 1329 2406 1654 1910 1174 4038 4677 1505 2953 2478 2366 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 0.0266186102762082 0.072206820496027 2435 2414.09090909091 2407 0.00244965836909229 694 1.27112445480174 1.27112445480174 1 3.23827541931164 2431 2932 2278 2347 694 4536 3286 963 1892 2789 2407 2367 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 1.93640788853375e-09 9.7569971673862e-08 1295 2233.27272727273 2408 1.76037080930741e-10 89 1.49698495700682 1.61613386155293 1 23.4238011171549 1293 3257 89 2918 769 4667 2408 2846 2253 1249 2817 2368 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 0.0583192471211049 0.128786047129829 1505 2523.09090909091 2408 0.00544774016558849 1072 0.997293395573521 0.997293395573521 1 1.98132862901593 1501 2186 1072 2645 1552 3252 1439 3758 4053 3888 2408 2369 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 0.0839184282471183 0.156982736433532 3965 2370.45454545455 2408 0.00793650793650794 654 1.22109567388454 -0.725336707662805 -1 2.19162017688165 3962 1287 2408 887 1522 1487 4296 2660 654 2483 4429 2370 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 0.0839184282471183 0.156982736433532 1670 2355 2408 0.00793650793650794 1014 1.09793986796278 1.10302657880532 1 1.97058037226726 1667 2899 2479 2489 4573 2938 1835 2408 1014 1783 1820 2371 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 0.37787098760137 0.499211572568373 2225 2449 2408 0.0422286108444231 1394 1.20903024400995 1.17970676197062 1 0.814168195770651 2222 1488 1539 1874 3499 4405 2627 2449 2408 1394 3034 2372 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 0.00574619140782104 0.0229163003719569 4145 2185.36363636364 2410 0.000523750456950726 279 1.17921153659826 1.13710356453275 1 4.31595445693419 4144 1052 1009 810 279 1575 4532 2839 2542 2410 2847 2373 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 0.0839184282471183 0.156982736433532 3575 2362.72727272727 2410 0.00793650793650794 470 1.22735818718378 1.26907959557332 1 2.20286012375786 3573 547 1409 869 2854 2410 4316 4044 470 1033 4465 2374 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 0.0765897756730953 0.156982736433532 4005 2601.72727272727 2411 0.00793650793650794 280 1.31505585488108 1.31505585488108 1 2.36025972979238 4001 850 3938 2411 2273 4494 2522 1856 280 1599 4395 2375 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 0.312264559171656 0.432153492108204 1595 2301.81818181818 2411 0.0367430736221207 1235 1.46693471565438 1.46693471565438 1 1.19295314518293 1594 2642 4009 3185 2773 2411 1576 1672 2530 1693 1235 2376 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 0.000104843434259531 0.00102353402695867 2980 2318.72727272727 2412 9.53167554752523e-06 411 1.38422909778233 1.38422909778233 1 9.23727472709747 2978 554 411 998 1272 4611 2928 4522 1032 2412 3788 2377 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 0.35943518917414 0.478362197236587 2055 2694.81818181818 2413 0.0396825396825397 1000 1.30546907171047 1.39884857749009 1 0.933095270406802 2054 4258 2262 3573 2413 4246 2775 1625 2235 1000 3202 2378 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 0.00078236405932208 0.00479863610207234 4610 2272.27272727273 2413 7.11493111134379e-05 51 1.54151297935923 1.95058757630997 1 7.97820927794037 4606 51 587 459 4306 2656 4136 1559 649 2413 3573 2379 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 0.154223227411042 0.257861638609555 2050 2216.72727272727 2414 0.0151119075937868 607 1.34479422263933 -1.3811115522525 -1 1.76671067098145 2048 3297 2414 2699 1686 607 2689 1668 3007 2868 1401 2380 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 0.0282897206326372 0.0748958366579309 2355 2283 2415 0.00260547125674698 727 1.30935937609962 1.64841985729153 1 3.28927547880823 2352 2456 1226 1720 727 3978 2665 2554 1527 2415 3493 2381 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 4.3787755182713e-06 7.68499703319076e-05 1970 2100.90909090909 2418 3.98071293963857e-07 249 1.26006484679199 1.33261232941093 1 11.5710920536833 1966 2524 249 2004 1652 3338 2484 2469 2418 982 3024 2382 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 0.38350230482981 0.505938006878516 2005 2806.90909090909 2419 0.043020003886761 1002 0.313996582587568 -0.315852108794806 -1 0.207373565933103 2004 3879 2330 3943 2934 1002 2340 2419 4541 3416 2068 2383 M7934 KEGG_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRUVATE_METABOLISM.html Pyruvate metabolism 21/49 KEGG 0.0859410498112857 0.160254579950531 2600 2389.18181818182 2420 0.00813583373767883 601 1.12944303899208 -0.967459383376804 -1 2.00453919203916 3961 601 2403 1459 1284 2680 3895 2598 2599 2420 2381 2384 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 0.0480198212307978 0.111685731267553 1315 2141.90909090909 2420 0.00446374094649342 357 0.791140711360448 -0.791140711360448 -1 1.68101384124344 1315 2638 2836 2420 3089 357 1383 1785 2975 4217 546 2385 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 0.000134570117211344 0.00123646190049482 2985 2547.54545454545 2420 1.22343953938983e-05 434 1.27047259985203 1.34410342764684 1 8.24541021089427 2982 2257 434 1767 2420 3706 3782 3788 1498 746 4643 2386 M2821 BIOCARTA_NTHI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NTHI_PATHWAY.html NFkB activation by Nontypeable Hemophilus influenzae 21/42 BioCarta 0.298735036746822 0.4173739958842 2710 2413 2423 0.0317460317460317 1001 0.975157604060794 0.975157604060794 1 0.825918307227202 2706 1001 2954 1373 2391 3815 2848 1862 1886 2423 3284 2387 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 0.518366378530953 0.637937656498554 1790 2689.27272727273 2423 0.0642581087686115 1451 0.615845475147869 -0.615845475147869 -1 0.268336367362877 1790 2423 2943 2210 4282 1451 3524 1656 3472 4300 1531 2388 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 0.395669980578908 0.517185363735778 1665 2644.72727272727 2424 0.0447526678608039 1331 1.1006318571122 1.1006318571122 1 0.703435926285272 1663 4625 3188 4290 2424 2241 1844 1873 2905 2708 1331 2389 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 9.25307078584963e-06 0.000144532965674971 1805 2154.54545454545 2425 8.41191791268277e-07 279 1.31100216643021 1.39131635743787 1 11.2361604020447 1805 445 279 1528 3124 3937 2425 2714 2785 1470 3188 2390 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 0.232850105696956 0.34496857265126 2055 2524.36363636364 2425 0.0238095238095238 1208 1.20418076991769 -1.20418076991769 -1 1.24228263723846 3935 2053 2916 2095 2425 4141 2649 1208 1702 2054 2590 2391 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 0.307089634979979 0.42650326897338 3475 2768.63636363636 2426 0.0328004268926332 2081 1.58589888969796 1.58589888969796 1 1.30992940356415 3475 2126 2897 2081 2090 2252 3873 3814 2426 2208 3213 2392 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 0.214653039618488 0.328070496951153 1400 2249.09090909091 2427 0.0217268307007885 838 0.653874098340854 0.653874098340854 1 0.706396440345573 1400 3979 3502 2955 2427 838 950 1509 2793 3294 1093 2393 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 0.209694066903703 0.323445160470953 2075 2479.36363636364 2427 0.0211668741648445 1138 1.8636644772713 1.8636644772713 1 2.03901305543515 2071 3696 1515 2850 4625 3108 1288 1138 2427 2434 2121 2394 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 0.0148094444332923 0.0462031002759041 4615 2478.72727272727 2428 0.00135546226573012 341 1.21455215107271 1.21455215107271 1 3.61979490710942 4611 341 2332 1076 487 3296 4620 3302 1241 2428 3532 2395 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 0.16713598731389 0.269789609560071 1800 2451.81818181818 2429 0.0164884525277686 711 0.31886471593594 -0.354742972526786 -1 0.404929144908773 1797 3348 3133 3667 1696 711 1730 2429 3577 3879 1003 2396 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 0.041645606036735 0.100489860910474 1580 2473.81818181818 2431 0.00424472939635799 616 1.10076268176067 1.28280437645879 1 2.4516055371159 1576 3650 4466 3530 960 616 2431 2425 3085 3104 1369 2397 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 0.0410129272069966 0.0996212785898212 2655 2149.54545454545 2431 0.0037998245147561 161 1.64484192015904 2.07644873957905 1 3.67721311524284 2653 4144 2431 1647 898 2600 1717 3319 161 1412 2663 2398 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 0.021118345607565 0.0611245012458614 2840 2317 2432 0.00193853024879335 607 1.37454009721651 1.68120112600609 1 3.72373371271952 2838 2650 1326 2220 607 1406 4084 3022 2432 2755 2147 2399 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 0.35943518917414 0.478362197236587 3660 2854.27272727273 2433 0.0396825396825397 1668 0.605790227089208 0.446763115994329 1 0.432993785860498 3657 2107 1668 2186 2607 2433 3934 4119 2127 4227 2332 2400 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 0.125021623664465 0.217788597952299 3615 2534.72727272727 2435 0.0120680539803644 1000 1.2744643124599 1.36732482992895 1 1.88296466353627 3612 2583 1238 2822 2393 1971 4257 1000 2435 1016 4555 2401 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 0.386086746459241 0.507632574048261 2125 2711.72727272727 2436 0.0476190476190476 1443 0.394989594409129 -0.534557132447245 -1 0.259583767547718 2123 3246 3957 3990 3626 1593 2365 1545 2436 3505 1443 2402 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 0.113931829210477 0.201846711410319 1465 2734 2436 0.0109362495393267 1463 1.28688486166898 1.28688486166898 1 1.99613773603273 4247 2436 2235 3145 1463 2562 3712 2013 2289 1465 4507 2403 M649 REACTOME_PHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHOLIPID_METABOLISM.html Genes involved in Phospholipid metabolism 101/208 Reactome 0.232850105696956 0.34496857265126 2290 2565.72727272727 2437 0.0238095238095238 1769 1.36902790232473 -1.02192717514728 -1 1.41234575028647 2289 2496 3263 2382 1978 1837 2846 3926 1769 3000 2437 2404 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 0.255447662137471 0.37313832443148 3595 2722.09090909091 2437 0.0264593010184537 1131 1.40839380365713 1.40839380365713 1 1.34579672238744 3593 4173 2255 3898 1964 1131 4550 1403 2702 2437 1837 2405 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 0.00213672265984315 0.0107432214420869 985 1776.45454545455 2437 0.000194436431942821 140 1.05077947290469 1.05077947290469 1 4.61750290998081 981 2437 2742 2449 140 1092 1241 2594 2762 2466 637 2406 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 0.0142369556627023 0.0448048181567649 2745 2155.63636363636 2438 0.00143289975798359 156 1.08369382460249 1.21862583502524 1 3.26207206319797 2742 1963 4440 2534 548 156 3368 1796 2438 3074 653 2407 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 0.271611742749983 0.39234667895389 1625 2555.81818181818 2441 0.0311951739223382 1117 0.485917218470386 0.485917218470386 1 0.440677372989803 1621 2783 4008 3423 2441 1433 1117 1698 4017 3604 1969 2408 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 0.0414599227604485 0.100351858499722 4595 2719.54545454545 2441 0.00384204628226064 906 1.2351153717582 1.2351153717582 1 2.75247950715338 4592 2655 1752 2278 906 1862 4142 3960 2441 1360 3967 2409 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 0.0144372232787276 0.0452830175931176 2445 2461.54545454545 2442 0.00132116776490531 478 0.405219610101264 0.425562361251147 1 1.21559852590309 2442 1537 2810 1788 478 4009 2804 2374 3401 3318 2116 2410 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 0.407302164761824 0.530144397188631 1035 2818.09090909091 2442 0.0464389887155858 1035 0.364197609959287 -0.419430629739022 -1 0.224029410809465 1035 3926 1562 3642 3578 2004 2442 1945 3886 4667 2312 2411 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 0.35943518917414 0.478362197236587 2445 2711.45454545455 2443 0.0396825396825397 2217 1.35645621649562 -1.08145551199055 -1 0.969538771587172 2443 2308 2488 3100 3076 3428 2277 2337 2283 2217 3869 2412 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 0.147859119791321 0.249412467725749 2655 2320.90909090909 2443 0.0158730158730159 377 0.650387102874107 -0.858013934048443 -1 0.875442702631947 2651 377 4508 1276 3209 2443 938 3094 1063 4428 1543 2413 M5485 REACTOME_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MUSCLE_CONTRACTION.html Genes involved in Muscle contraction 36/77 Reactome 0.000240006474259169 0.00194916869736303 3090 2238.54545454545 2445 2.18211510445123e-05 479 2.36572981009268 -2.59443856790082 -1 14.3099500343341 3088 3055 479 2445 2386 1637 2463 2601 2130 1165 3175 2414 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 0.00124577773393516 0.00693315256676981 2030 2098.63636363636 2445 0.000113316702821526 366 2.00797681532615 -3.11553755502548 -1 9.67619962283218 2026 2480 623 2643 366 2445 2658 2119 2837 2174 2714 2415 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 0.161385165508919 0.262241686633255 1685 2226.45454545455 2447 0.0158730158730159 1317 1.43881363110877 1.43881363110877 1 1.86673697244544 1685 2322 2827 1748 3011 2447 2478 1548 1317 2619 2489 2416 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 6.26486907437193e-07 1.46055604390581e-05 1915 2190.27272727273 2447 5.69533714399928e-08 196 1.41352619772844 1.35098660523922 1 15.2553848208513 1913 2306 196 2749 870 4082 2554 2802 2447 1002 3172 2417 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 0.0723409796884344 0.152354980143822 3940 2435.18181818182 2448 0.00680321163309212 1116 1.11339871902501 1.17151701811033 1 2.0306193490764 3939 1116 2394 1711 1203 1243 3901 2762 2448 2685 3385 2418 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 0.0739377835314998 0.155299172401886 4000 2573.09090909091 2448 0.00695875298140097 873 1.32747317411853 1.39838371701646 1 2.39642046858604 3997 2788 1434 2525 1211 873 4482 4603 2085 2448 1858 2419 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 0.0284355200535797 0.0751120896116543 4540 2479.90909090909 2449 0.00261907702032252 731 1.38152505238832 1.47326266548086 1 3.46670372797789 4540 3118 2348 2256 731 868 4087 3133 1021 2728 2449 2420 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 0.00634301757776271 0.0247282698580666 1370 2051 2450 0.000636119588948451 95 0.313115127610225 -0.341125899990738 -1 1.12291561819313 1367 2450 4130 2927 3466 95 548 623 2923 3819 213 2421 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 0.0572664845058876 0.127361531274129 2450 2484.18181818182 2450 0.00534671232002673 1078 1.1246091024085 1.1246091024085 1 2.24639235586905 2450 2689 2420 1520 1078 3731 3926 2903 1967 1639 3003 2422 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 0.000236817711823069 0.00192996138713548 4460 2465.09090909091 2451 2.15312007063064e-05 477 1.62170427718469 1.79963847322074 1 9.82501640068932 4459 2347 477 1595 3297 2451 3376 3497 1022 1285 3310 2423 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 0.342479447419434 0.464503238960193 1200 2749.81818181818 2452 0.0373990123278485 1030 0.239917457894644 -0.256741310539316 -1 0.178320106679461 1196 4018 3694 4345 2177 1030 2452 2290 3887 3434 1725 2424 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 0.0409816893488562 0.0996059109381432 1985 2385 2452 0.00379687455566102 298 0.917949216767062 0.998047374026547 1 2.05230705931929 1982 3497 3607 4278 2040 298 2697 1745 2452 3086 553 2425 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 0.000231182263233497 0.00190115977338007 2470 2336.27272727273 2453 2.10187781907644e-05 473 1.55410286758957 1.55410286758957 1 9.43810678871387 2470 1149 473 1268 2708 3631 2453 4528 2150 1671 3198 2426 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 0.0558670552246883 0.124960869108778 2105 2443.09090909091 2454 0.00521257544423539 545 1.14672566625037 1.14672566625037 1 2.31172143808923 2101 2729 3434 2585 4091 2276 545 1182 3458 2454 2019 2427 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 0.0765897756730953 0.156982736433532 2745 2248.90909090909 2454 0.00793650793650794 202 1.9366898762468 1.9366898762468 1 3.47596728085679 2744 624 4318 917 2454 3520 3554 1486 202 1704 3215 2428 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 0.00383864279967094 0.0168164573947548 2450 2122.09090909091 2454 0.00034957791046701 211 1.05091485334912 0.951030367783976 1 4.16165131690177 2446 2711 2454 2705 211 1106 2815 1608 2570 2840 1877 2429 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 0.0253158445116862 0.0696594523674466 4090 2565.18181818182 2456 0.00256089565308488 507 1.21196292046648 1.29858773266738 1 3.12975061045295 4087 2066 4165 2456 720 507 4598 3228 2265 2760 1365 2430 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 0.13453659145159 0.231778848361086 1790 2334.45454545455 2457 0.0143451321954078 803 0.271591012040073 -0.271591012040073 -1 0.3848736654641 1787 3037 4233 2594 3227 954 803 1195 2457 3959 1433 2431 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 0.455698071567819 0.578229397066558 4400 2840.72727272727 2457 0.0537945547714127 1707 1.16440896522276 1.23367114659006 1 0.618271505910576 4397 2457 2453 2216 2416 1707 4162 3451 3008 2215 2766 2432 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 0.105643964711703 0.189746116764676 1590 2454.72727272727 2458 0.0100987825757477 1185 1.00833301536941 0.997152976973137 1 1.62448882087484 1589 2458 1185 3448 2440 4001 1677 1457 2928 3097 2722 2433 M8809 BIOCARTA_PTDINS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTDINS_PATHWAY.html Phosphoinositides and their downstream targets. 25/42 BioCarta 0.00893199698846552 0.031829154287414 2445 2696.81818181818 2459 0.000815315305120395 361 1.0182775376699 -0.889829409089437 -1 3.40265765270369 4254 1900 2459 2441 361 1491 4410 4059 3296 2551 2443 2434 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 0.435369722646862 0.557415989159343 2280 2745.45454545455 2460 0.0555555555555556 1496 1.14672566625037 1.14672566625037 1 0.649629766536305 2279 3571 4046 3300 4503 3092 1496 1731 2460 1605 2117 2435 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 0.35943518917414 0.478362197236587 2465 2521.72727272727 2461 0.0396825396825397 1631 1.47248574116403 1.47248574116403 1 1.05247187437275 2461 2537 2295 1653 3550 4114 2498 2525 2171 1631 2304 2436 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 0.298735036746822 0.4173739958842 3365 2734.27272727273 2461 0.0317460317460317 1740 1.90919498657043 1.90919498657043 1 1.61700948134389 3363 1740 2060 2592 2365 3077 4618 1981 1864 2461 3956 2437 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 0.0652977809712057 0.140360275977555 3690 2527.09090909091 2461 0.00612003968186458 893 1.29961023890636 1.37065073225149 1 2.47353097954045 3686 2461 2853 1942 1154 2427 3316 2990 893 2020 4056 2438 M5113 REACTOME_GLYCOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOLYSIS.html Genes involved in Glycolysis 18/44 Reactome 0.119426449561438 0.210230031046167 2465 2251.18181818182 2462 0.0114954009361031 535 0.385263845399713 -0.353810933963106 -1 0.582401183526912 2462 2000 2512 2723 2954 535 1647 1750 3453 3543 1184 2439 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 0.298735036746822 0.4173739958842 2570 2455.54545454545 2462 0.0317460317460317 1643 1.16690026251726 -1.16690026251726 -1 0.988316437802043 2937 1845 2567 2462 2324 1643 2820 3913 2062 2568 1870 2440 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 0.0839184282471183 0.156982736433532 2725 2442.45454545455 2462 0.00793650793650794 861 1.43637033391577 1.43637033391577 1 2.57799472443615 2722 2381 2023 2901 2289 3437 2623 4072 861 1096 2462 2441 M13266 KEGG_RENAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENAL_CELL_CARCINOMA.html Renal cell carcinoma 41/78 KEGG 0.0839184282471183 0.156982736433532 2210 2394 2463 0.00793650793650794 788 1.33927768552492 1.33927768552492 1 2.40373302504505 2209 2463 2830 1307 4499 4033 2676 1416 788 1349 2764 2442 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 0.165894398931229 0.268432718712618 2640 2540 2463 0.016355254983533 1295 1.37258035693155 1.37258035693155 1 1.74976038062517 2638 2030 1295 2070 2463 3704 2056 3885 2007 2505 3287 2443 M776 REACTOME_PROTEIN_FOLDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROTEIN_FOLDING.html Genes involved in Protein folding 32/70 Reactome 0.415320710913563 0.535769969181582 2400 2699.18181818182 2467 0.0476190476190476 1436 0.379018857694894 -0.398473071014079 -1 0.229268468861619 3297 3093 2397 3210 4018 1436 2467 1736 2399 3579 2059 2444 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 0.18800707692145 0.296533545087147 1235 2662.72727272727 2467 0.0187549549019802 1232 0.551217832507519 0.623405456284234 1 0.649495288565605 1232 2206 1332 2017 3535 2331 2888 2467 4051 4606 2625 2445 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 0.00489917882405065 0.0201735957552736 1685 2159.09090909091 2469 0.000491001333557052 181 0.332694445513436 -0.396985114156869 -1 1.2587814181249 1682 2487 4063 2469 2926 334 1536 481 3900 3691 181 2446 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 0.00310197212558372 0.0143919221588963 1680 2509.90909090909 2471 0.000282395865471902 180 1.05233987867856 1.14839946818118 1 4.32610641208252 1680 3534 2471 4322 180 4413 1945 1705 2813 2913 1633 2447 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 0.0121909316739035 0.0401734921405848 2475 2412.81818181818 2471 0.00111445585881034 126 0.922688875811552 -0.8096244840779 -1 2.87500796547252 2471 3954 3274 3915 2276 126 2335 1772 3021 3063 334 2448 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 0.332416100453422 0.453871800574534 2430 2956.72727272727 2472 0.036068912697357 1614 1.03616185793275 1.16567948637949 1 0.793388401175302 4237 1614 2427 2427 2159 2472 3707 4055 3242 2091 4093 2449 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 0.0725542004205239 0.152666808787865 1745 2439.63636363636 2473 0.00750379720952494 685 1.7354036805309 1.7354036805309 1 3.16159416668148 1745 3581 4323 2593 2743 2167 2473 3920 1551 1055 685 2450 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 0.0839184282471183 0.156982736433532 3015 2316.09090909091 2473 0.00793650793650794 1029 1.08270114446751 -0.855106271162806 -1 1.94322994052143 3013 1664 3010 2473 1667 1371 3127 3268 1029 2970 1885 2451 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 0.0923179027254748 0.170181625559235 2475 2501.54545454545 2473 0.00876689692468415 472 1.04482949391065 -1.04482949391065 -1 1.79349692485872 3281 2473 3307 2849 4657 472 2143 2186 2763 2472 914 2452 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 0.110212989845386 0.196596144048526 2280 2322.18181818182 2475 0.0105595936309859 542 0.542283907280468 -0.542283907280468 -1 0.855012244588691 2280 1148 2921 1956 2475 542 2715 3379 4121 3225 782 2453 M7946 KEGG_NOTCH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NOTCH_SIGNALING_PATHWAY.html Notch signaling pathway 16/52 KEGG 0.485304810938661 0.605790714986299 2480 2579.90909090909 2476 0.0585933048484606 1319 0.361163185251896 -0.289814581167996 -1 0.175467361410164 2476 1748 2900 3376 2473 1319 2841 2406 3636 3212 1992 2454 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 0.000762399319207826 0.00470079369711562 3850 2264.63636363636 2476 6.93330593858692e-05 78 0.894749939838924 -0.646118488205991 -1 4.64870803692473 3850 720 3298 1665 78 2488 3704 3954 496 2182 2476 2455 M17294 BIOCARTA_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAS_PATHWAY.html Ras Signaling Pathway 19/44 BioCarta 0.178377715201159 0.283540696551096 2220 2568.54545454545 2477 0.0177027500576475 1752 0.803760299174553 0.803760299174553 1 0.981971037851588 2220 2477 3217 2334 1752 3824 2275 2648 2516 2317 2674 2456 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 0.0213210474655482 0.0615032668662181 2945 2467.54545454545 2477 0.00195732051904463 613 1.4773970136167 1.69516448222542 1 3.99353437056139 2942 1884 1062 1965 613 4633 2477 3645 2539 1361 4022 2457 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 0.137313342435111 0.235265200238001 2495 2543.90909090909 2479 0.0133378643895128 1260 1.37676019753492 1.49764049711778 1 1.93109336353608 2495 1489 1260 1689 1979 3781 2979 3227 2444 2479 4161 2458 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 0.0223504497971739 0.0637845357792673 1545 2428.72727272727 2481 0.00205279978131171 919 2.06322935667965 2.06322935667965 1 5.50425299840824 1544 2725 919 2463 3899 3047 2481 1799 3114 2564 2161 2459 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 0.108958004686018 0.19469525340997 2265 2287.54545454545 2481 0.0104328076552212 760 1.21632153681227 -0.967459383376804 -1 1.92921412851579 2264 3340 2481 3191 1436 760 1866 3025 2883 2845 1072 2460 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 0.0365580665310366 0.0911229254066157 1965 2797.36363636364 2484 0.00338000752417628 997 1.03466129650679 -0.835195198652305 -1 2.40251749172719 1962 4414 997 3405 2306 2015 3796 3486 3684 2484 2222 2461 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 0.232850105696956 0.34496857265126 3380 2525 2484 0.0238095238095238 1493 1.66688708532377 1.66688708532377 1 1.71962959060028 3379 3018 1814 2484 2117 3049 2407 2798 1666 1493 3550 2462 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 0.0131348799610142 0.0423024381424829 3495 2367.18181818182 2487 0.00120126929609379 357 0.437500327871293 -0.397951388641752 -1 1.34130999053309 3492 357 2487 2061 447 1746 2808 3802 3063 4109 1667 2463 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 0.466738071388703 0.587219019917277 3150 2683.72727272727 2490 0.0555555555555556 1372 1.2765345981333 -1.07272638267715 -1 0.658718348132971 3149 3131 2302 2395 3229 1618 3496 3997 2490 1372 2342 2464 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 0.111161365665586 0.19780196769303 1525 2117 2491 0.0106555120175617 786 1.7354036805309 1.7354036805309 1 2.72590329082426 1525 2726 2090 2648 3403 1376 1014 2626 2602 2491 786 2465 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 0.0839184282471183 0.156982736433532 2700 2377.27272727273 2491 0.00793650793650794 900 1.29960986725232 1.47929592569369 1 2.33253730077668 2699 2261 1262 1176 2640 4526 2491 2656 900 1784 3755 2466 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 0.256866974700671 0.374511090058291 2590 2390.18181818182 2492 0.0292516608060473 1291 1.00744291305309 1.00744291305309 1 0.959080360065597 2588 2340 3869 2624 2018 2492 2765 1650 1878 1291 2777 2467 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 0.0382509870160874 0.0944882051435875 3715 2363.18181818182 2492 0.003539336604537 872 1.46518369024774 1.46518369024774 1 3.35069946770845 3711 2698 2502 3932 872 1710 1768 1821 2492 1927 2562 2468 M875 REACTOME_NETRIN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NETRIN1_SIGNALING.html Genes involved in Netrin-1 signaling 18/54 Reactome 0.466738071388703 0.587219019917277 1870 2767.81818181818 2493 0.0555555555555556 1154 1.23251670030084 1.23251670030084 1 0.636004199221218 1869 4122 3105 3902 4429 2814 2372 2256 2493 1154 1930 2469 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 0.57355327818503 0.690030978581527 2250 2810.72727272727 2495 0.0745534437884667 1637 0.859273688690299 -0.667767904475907 -1 0.309023338108337 2246 1637 1734 2021 4386 3525 2482 4095 2982 2495 3315 2470 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 0.298735036746822 0.4173739958842 3365 2827.27272727273 2496 0.0317460317460317 1294 0.969412552114945 -0.899195830530212 -1 0.821052484965367 3362 2177 2284 2874 2412 1294 4392 2496 2084 3092 4633 2471 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 0.0839184282471183 0.156982736433532 4355 2811.45454545455 2496 0.00793650793650794 293 1.64216404686053 1.64216404686053 1 2.94735288631669 4351 1166 2301 1136 2496 4361 4656 3553 293 2049 4564 2472 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 0.351705849297003 0.474408062695957 2165 2670.27272727273 2497 0.0386348536677557 1746 1.42802375650398 1.42802375650398 1 1.0321816264576 2165 3127 2847 2788 2198 3460 3882 2269 2394 1746 2497 2473 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 0.318124536600005 0.439019428093532 1710 2735.36363636364 2497 0.0342109470025183 893 0.791140711360448 -0.791140711360448 -1 0.631290257442733 1709 2476 2497 2812 4410 893 2954 2404 4215 4343 1376 2474 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 0.0121322116055637 0.0400362982983601 3300 2570.72727272727 2499 0.00121989608140873 452 0.587627690674132 -0.321622659497255 -1 1.83293871740246 3298 863 4157 2167 452 2101 2115 3202 3565 3859 2499 2475 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 0.0762398446739375 0.156982736433532 3435 2621.63636363636 2499 0.007183421652513 917 1.12775224422783 1.12775224422783 1 2.02408756809451 3434 1801 1570 2499 1221 4640 3152 4346 1908 917 3350 2476 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 0.0192796198828423 0.057252407332699 4090 2330.72727272727 2501 0.00176824350351171 56 1.27091864843338 -1.01185884583594 -1 3.52363581880914 4088 56 893 127 2501 4056 3400 3848 1891 1539 3239 2477 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 0.0839184282471183 0.156982736433532 2560 2626.90909090909 2501 0.00793650793650794 904 1.45814194183543 1.8533289605152 1 2.61707036463585 2558 3006 2017 2417 4567 3200 1787 2501 904 2262 3677 2478 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 0.0839184282471183 0.156982736433532 2295 2436.81818181818 2502 0.00793650793650794 653 1.64732154942879 1.71130689280549 1 2.95660956204913 2294 2528 1523 2678 1620 4070 2502 3373 653 1882 3682 2479 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 0.490499721692586 0.611786450852132 1835 2394.09090909091 2503 0.0594610922006302 1617 1.05077947290469 1.05077947290469 1 0.500478984720794 1834 3167 2503 2670 3953 1958 1625 1617 2812 2521 1675 2480 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 0.298735036746822 0.4173739958842 2505 2543.09090909091 2504 0.0317460317460317 1651 1.3400350562862 1.3400350562862 1 1.13495447376064 2501 1681 2964 1651 3380 3753 2504 2679 1885 1660 3316 2481 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 0.0857047241080094 0.15987752275881 3090 2764.63636363636 2504 0.00892014737580465 1019 0.621385674460764 0.567729535954646 1 1.10425616275153 3087 1019 4489 1816 1334 3736 1459 4227 2341 4399 2504 2482 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 0.0896942671547274 0.165932623721695 2505 2647.36363636364 2504 0.00850677142538697 1153 1.15242124850882 1.41421372588732 1 2.00642715474806 2504 3041 1153 2409 1820 2373 3950 3436 2816 2476 3143 2483 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 0.00714680774950583 0.0270665963374072 2530 2466.09090909091 2506 0.000716989691443918 334 0.472313558104112 0.496391869705066 1 1.65247881482881 2506 745 4258 1712 334 1861 2526 4557 2103 3998 2527 2484 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 0.154648409530785 0.258261741646921 2000 2635.63636363636 2506 0.0166599280180023 1706 0.676501319802569 -0.220317591968234 -1 0.88773052834003 1997 2064 4265 2506 1706 2013 1790 2522 3099 4009 3021 2485 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 0.0839184282471183 0.156982736433532 2440 2431 2508 0.00793650793650794 510 2.24458518468169 2.24458518468169 1 4.02857719078965 2438 2801 2212 2508 4369 1210 3277 3057 510 2600 1759 2486 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 0.0442541427585133 0.105159692173627 2510 2423 2510 0.00410638573450498 664 2.19775722972283 2.19775722972283 1 4.79805298304567 2510 3414 1511 2852 3476 3239 2091 664 2192 1915 2789 2487 M6031 BIOCARTA_SKP2E2F_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SKP2E2F_PATHWAY.html E2F1 Destruction Pathway 7/15 BioCarta 0.445287716826522 0.567632818566127 1645 2714.27272727273 2511 0.057227777227134 1396 1.73041933125535 1.73041933125535 1 0.949832100364693 1643 4244 3828 2436 4637 2511 1396 2954 2849 1498 1861 2488 M16517 BIOCARTA_WNT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_WNT_PATHWAY.html WNT Signaling Pathway 19/48 BioCarta 0.111764660334778 0.198457445368992 2280 2656 2512 0.0107165774509489 1451 0.80098952492431 -0.493393016758395 -1 1.25559396830543 3307 2326 2799 2512 1451 2280 3671 2279 3297 2319 2975 2489 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 0.0839184282471183 0.156982736433532 2515 2166.18181818182 2512 0.00793650793650794 574 0.893068756920903 -0.719029057876656 -1 1.60287809451515 2512 574 3212 1170 2321 3179 1304 2821 733 2858 3144 2490 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 0.227140751842141 0.343792494551768 3100 2738.45454545455 2513 0.0231512843581815 1789 1.94337461577111 1.94337461577111 1 2.01129862264754 3099 3268 1789 1969 1888 4398 3444 1958 1999 2513 3798 2491 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 0.0312287309186245 0.0804938575823292 1800 2540.72727272727 2513 0.00288009394649582 972 1.91509024629137 1.91509024629137 1 4.67713922278287 1800 3416 972 1536 3615 2907 2134 3958 3235 1862 2513 2492 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 0.00559593323206937 0.0224893165741656 3555 2267.27272727273 2513 0.000510019816010496 539 1.42750130982906 1.42750130982906 1 5.25072815404816 3553 990 744 1581 2513 3509 3993 2724 603 539 4191 2493 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 0.0464439393346851 0.109113869654205 1860 2500.54545454545 2515 0.00431403688011009 1035 0.990478285128715 1.09900272470116 1 2.12693283053944 1858 3160 1035 3025 2035 3408 2515 1811 3724 1942 2993 2494 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 0.218782498134781 0.333403182523442 2380 2505.18181818182 2516 0.0221955784846936 1159 1.29142669460736 1.29142669460736 1 1.37497639352574 2380 2662 1770 2516 3938 3810 1178 1159 2893 2492 2759 2495 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 0.334536372413391 0.455443765580811 2520 2670.09090909091 2516 0.0363476318445414 1690 1.05077947290469 1.05077947290469 1 0.801059546474807 2516 3519 2961 3896 2163 2478 2664 1835 3719 1930 1690 2496 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 0.161385165508919 0.262241686633255 4510 2767.45454545455 2517 0.0158730158730159 1531 1.36331727637118 1.5633788205492 1 1.76878694359239 4510 2217 2361 2200 2654 1914 3980 3481 1531 2517 3077 2497 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 0.201294812622052 0.312650809395737 1820 2782.18181818182 2517 0.020225694539449 1817 1.26084826947834 1.34990898584332 1 1.42096224160665 2454 2069 3438 2825 1817 3913 2371 3198 2517 1820 4182 2498 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 0.0305458331145508 0.079388671089731 2880 2289.63636363636 2518 0.00281621613138814 306 1.20368890141232 -0.967459383376804 -1 2.95584611353288 2878 592 1506 1013 763 4223 2988 4210 306 2518 4189 2499 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 0.457881026692589 0.580527730270961 2045 2955 2518 0.0541401682774108 1130 0.297882787249615 -0.295174957800389 -1 0.15702276508371 2043 4026 2432 4068 3450 1130 2398 2518 4555 3763 2122 2500 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 0.0855712979785245 0.159755817660305 2520 2863.54545454545 2518 0.00890568516987379 1234 0.301911429711663 0.361799845680553 1 0.536745618568813 2518 4136 4125 4259 1331 1714 1234 1389 4583 3807 2403 2501 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 0.0358389256156837 0.0897601311785643 4450 2586.90909090909 2518 0.00331240264227473 843 1.34725392116451 1.50233447368122 1 3.14804596147531 4447 2961 2518 2314 843 1915 4183 4009 928 1107 3231 2502 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 0.194707910973077 0.304729696016333 2925 2615.09090909091 2518 0.0194938724852061 1108 1.49315035176056 1.49315035176056 1 1.71990523559386 2923 3471 1962 3105 2518 4481 2235 1108 2212 1447 3304 2503 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 0.32038699467049 0.440790797717533 2485 2878.27272727273 2519 0.0378868111038345 1755 0.510702517129058 -0.561341237287854 -1 0.405521422301677 2481 2519 3955 3130 2186 1755 2356 3601 3825 3502 2351 2504 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 0.156982736433532 3550 2670.36363636364 2520 0.00793650793650794 711 1.32638156011368 -0.890693725309109 -1 2.38058708385415 3547 1991 1771 1403 2377 4577 3157 2706 711 2520 4614 2505 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 0.415320710913563 0.535769969181582 2525 2732.36363636364 2521 0.0476190476190476 1649 0.310725328420631 0.359691651498203 1 0.187957719860607 2521 3934 3169 3942 2613 1739 1709 1649 2332 4292 2156 2506 M233 PID_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPO_PATHWAY.html EPO signaling pathway 18832364 24/58 Pathway Interaction Database 0.0839184282471183 0.156982736433532 4445 2604.63636363636 2522 0.00793650793650794 395 2.24458518468169 2.24458518468169 1 4.02857719078965 4445 1302 2698 911 1659 4672 3542 1864 395 2522 4641 2507 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 0.0796151414016891 0.156982736433532 1950 2595.90909090909 2523 0.00751375426025235 818 1.69748649654937 1.69748649654937 1 3.04664551307095 1949 3798 3206 3257 4608 2824 1148 818 2508 2523 1916 2508 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 0.00440923310118323 0.0186740632276627 4040 2476.18181818182 2524 0.000401644995233352 627 1.19281515576998 -1.15000942257907 -1 4.60243542466192 4037 1612 728 2085 3674 2524 3517 3917 922 627 3595 2509 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 0.147859119791321 0.249412467725749 2030 2413.09090909091 2525 0.0158730158730159 1346 0.653874098340854 0.653874098340854 1 0.880136314670596 2028 2743 3977 3023 2724 2525 1346 1851 1378 3529 1420 2510 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 0.255765117322049 0.373252986537254 2530 3159.72727272727 2529 0.0291078220620207 1268 0.246316525508716 -0.0606072869541553 -1 0.235295452427959 2529 4679 4516 4426 2415 2328 2187 1268 3666 4437 2306 2511 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 0.466738071388703 0.587219019917277 2715 2436.63636363636 2530 0.0555555555555556 1478 1.19402984384557 1.47309262659334 1 0.616144182461725 2711 2139 2147 2152 2530 3155 1478 2742 2535 1943 3271 2512 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 0.466738071388703 0.587219019917277 2070 2409.72727272727 2531 0.0555555555555556 1546 1.50240334789498 1.50240334789498 1 0.775271311114668 2067 2724 1736 2309 2957 3366 2531 2864 2555 1546 1852 2513 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 0.435369722646862 0.557415989159343 1980 2597.27272727273 2532 0.0555555555555556 1265 0.67672309647644 0.707414514010884 1 0.383369344616582 1978 1265 4228 2712 2972 2532 1491 2930 2471 3955 2036 2514 M243 PID_ARF_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF_3PATHWAY.html Arf1 pathway 18832364 21/33 Pathway Interaction Database 0.178528961610246 0.283657041358306 3790 2440.72727272727 2533 0.017719189968083 664 0.955443388210537 -0.764161110170704 -1 1.16690555431246 3787 2389 3300 3236 2834 664 1149 3458 2533 2427 1071 2515 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 0.0839184282471183 0.156982736433532 1790 2280.90909090909 2534 0.00793650793650794 980 1.4524648429666 1.91301827372148 1 2.60688111845821 1786 2580 3166 2263 2031 1532 2534 2552 980 3053 2613 2516 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 4.3940620073977e-05 0.000503437030969819 2735 2135.54545454545 2535 3.99468161135671e-06 361 1.75950954745932 -1.51879185355682 -1 12.9517679739642 2734 883 361 1933 2133 1809 2535 3072 2636 2753 2642 2517 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 0.122837871424498 0.214943340364151 2665 2381.36363636364 2536 0.0118441570155101 1516 1.01514929688902 1.17211282698193 1 1.51277814758264 2665 1891 2536 1552 1516 2370 2875 2376 2661 2917 2836 2518 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 9.84489870507721e-16 1.84532781327967e-13 735 2091.81818181818 2536 8.94990791370657e-17 25 1.32509287198843 1.35324540270288 1 37.6606845964757 732 2618 25 1734 3077 2933 1955 2536 3635 924 2841 2519 M18607 REACTOME_STEROID_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_STEROID_HORMONES.html Genes involved in Steroid hormones 10/44 Reactome 0.0133810381015241 0.0428063323968036 800 2180.09090909091 2538 0.00122392048201339 276 0.36700100883727 0.469458887252044 1 1.12095729975604 797 3290 2538 4310 4570 381 276 501 3424 3567 327 2520 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 0.0254944753127147 0.0701098071099655 1510 2320.90909090909 2538 0.00234498175144641 679 1.82051220676583 1.82051220676583 1 4.68988514830443 1510 3165 2222 2777 679 3170 1690 2973 2538 2647 2159 2521 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 0.362866091723066 0.482243478676769 2370 2713 2538 0.0401512743669643 1862 1.14625968082688 1.31553910334678 1 0.81032037358677 2370 2560 2153 2348 2218 3372 1862 3599 3247 2538 3576 2522 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 0.0814254349084259 0.156982736433532 1020 2422.36363636364 2539 0.00769137755816125 953 1.023151511633 -0.842974781513781 -1 1.83635037355273 1018 3652 3766 3579 1255 953 2539 2241 3003 3108 1532 2523 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 0.0108127186516968 0.0367695207560603 1415 2499.90909090909 2540 0.000987839122682207 396 0.994144198272548 0.959138102998357 1 3.1829742986698 1415 3468 1412 2438 396 3949 2020 3772 3542 2540 2547 2524 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 0.282968285773383 0.404265057053071 1865 2705.45454545455 2542 0.0297869227309972 1584 0.980222501913161 0.980222501913161 1 0.860528950178504 1863 2542 2492 3372 2038 2265 1584 3560 3018 4214 2812 2525 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 0.390242552488189 0.512377865217051 985 2696.54545454545 2543 0.0439759261117217 983 0.228832085045537 -0.241803632213901 -1 0.148322658398828 983 3505 3739 4340 2368 1059 2229 2543 3392 3775 1729 2526 M1045 REACTOME_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IMMUNE_SYSTEM.html Genes involved in Immune System 498/1251 Reactome 0.341598309863092 0.463576507390226 4025 2770.54545454545 2544 0.0372818134104959 1263 1.20031492803883 1.33508848979916 1 0.894464936907668 4021 2412 2963 1440 2175 1263 3900 4407 2437 2544 2914 2527 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 0.0146105674385019 0.0457348824427656 1365 2290.45454545455 2544 0.00147075267552536 300 0.94175740835774 0.94175740835774 1 2.81606810869657 1364 2647 4526 2544 2551 1054 300 844 3179 4450 1736 2528 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 0.00546874079886933 0.0220348403985397 1280 2352.63636363636 2546 0.000548224580412156 179 0.633443497940456 0.521050649073834 1 2.34250829768738 1277 1259 4505 2546 4626 712 179 2700 3104 4422 549 2529 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 0.245394799101214 0.360250635522647 2870 2590 2547 0.0252716052629168 1351 0.693810091349027 0.693810091349027 1 0.686611696994059 2868 2547 2984 2431 1938 1351 1541 3097 3186 4256 2291 2530 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 0.202226520990748 0.313682051427555 2420 2637 2548 0.0203296523780496 1347 1.21455215107271 1.21455215107271 1 1.36491028888057 2418 2846 1347 3037 3187 2250 2421 2120 4239 2594 2548 2531 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 0.161385165508919 0.262241686633255 2740 2707.81818181818 2548 0.0158730158730159 1340 2.24458518468169 2.24458518468169 1 2.91215628038114 2737 2464 2643 1650 4345 1987 4676 2548 1340 2862 2534 2532 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 0.375048869340349 0.496042619737193 1875 2575.54545454545 2549 0.0418344530629223 1138 1.02401096892853 1.02401096892853 1 0.695896050011534 1872 3346 2932 3620 2549 1138 3213 1430 3909 2241 2081 2533 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 0.0575740305210421 0.127968639044506 1870 2784.54545454545 2549 0.00537621521291843 1070 0.584382885049943 0.620408076111545 1 1.16460362756254 1870 2102 1070 2470 3333 2549 2165 3736 3864 4642 2829 2534 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 0.331790701516202 0.453271774143138 2550 2914.81818181818 2549 0.0395135300553333 1225 0.456695065755362 0.552285605188841 1 0.350276706764263 2024 1810 4671 2548 4668 1826 1225 2549 3043 4654 3045 2535 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 0.597318307603006 0.711317303539438 1740 2583.36363636364 2552 0.0793650793650794 1680 1.31394404283802 1.31394404283802 1 0.433842541744647 1736 1680 2898 2182 4672 2496 1734 2761 2921 2785 2552 2536 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 0.279354313501495 0.400553676376021 2625 2466.54545454545 2552 0.0293433876558369 1083 0.633042077535849 0.633042077535849 1 0.561401580245492 2624 1441 1548 2171 2552 3447 1083 1382 3705 4273 2906 2537 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 0.292163883977524 0.414872715248084 1700 2817.72727272727 2553 0.0339640872132014 1326 0.34804735276133 0.38241126876061 1 0.296809653106005 1700 2553 4052 4174 2979 2286 2137 1326 4011 3677 2100 2538 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 0.0839184282471183 0.156982736433532 2555 2701.72727272727 2554 0.00793650793650794 1008 1.35866427071877 1.40786471134265 1 2.43852803102399 2554 2831 2217 2002 2066 4541 2778 4465 1008 1816 3441 2539 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 0.00823514393122345 0.0300310384916055 2440 2322.54545454545 2555 0.000751466602804262 345 3.11553755502548 -3.11553755502548 -1 10.5864360554725 2437 2884 889 3434 345 2555 3027 2281 2842 2240 2614 2540 M1326 MANTOVANI_NFKB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_NFKB_TARGETS_DN.html NF-kB-controlled genes down-regulated in endothelial cells in response to viral GPCR protein. 17906691 7/22 Jessica Robertson 0.103006908149057 0.186079557280833 2905 2366.27272727273 2555 0.0108118391690269 611 0.665455983212677 -0.665455983212677 -1 1.08467838035469 2903 1657 4310 2555 1460 611 819 3220 3445 4060 989 2541 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 0.0715297341206415 0.150917755105505 1275 2616.36363636364 2555 0.00739421950145671 435 0.395878231739579 -0.395878231739579 -1 0.725640759494197 1275 2555 4683 3421 4452 435 1444 1488 3540 4678 809 2542 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 0.110532524946767 0.196866367122976 1515 2667.72727272727 2557 0.0105919009091086 1445 1.05077947290469 1.05077947290469 1 1.65535181205669 1515 4221 3528 3583 1445 2031 2557 2030 4114 2620 1701 2543 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 0.0693268017540509 0.147131065679113 1240 2408.09090909091 2557 0.00715896024506277 623 0.358710323475344 0.358710323475344 1 0.666347908730136 1237 2557 4284 3274 1462 817 623 3831 3522 4035 847 2544 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 0.147744824202811 0.249412467725749 2415 2500.54545454545 2559 0.0144284696889675 995 1.8636644772713 1.8636644772713 1 2.50855445886975 2414 3016 1973 2559 1904 3886 3161 995 2248 2590 2760 2545 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 0.0120937160503805 0.0399655524767865 4100 2276.81818181818 2559 0.00110551937499674 177 2.24458518468169 2.24458518468169 1 7.00519789027767 4099 714 3045 496 423 2559 4429 2587 177 2391 4125 2546 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 7.11424884958754e-07 1.62621317605694e-05 3230 2453.54545454545 2559 6.46750104559857e-08 200 1.26674633888135 1.35642491306292 1 13.5393543509048 3230 1553 200 1503 1251 3851 3739 3828 2559 707 4568 2547 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 0.466738071388703 0.587219019917277 2710 2347.36363636364 2560 0.0555555555555556 912 0.811213947375691 0.811213947375691 1 0.418603234202452 2710 912 2857 1008 3414 2325 1942 1659 2560 2832 3602 2548 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 0.339424435265629 0.461294345607523 2385 2852.36363636364 2560 0.036993277990394 1439 0.631262575792853 -0.631262575792853 -1 0.473431489063406 2384 3998 3673 3726 2172 1439 2560 1495 3987 3855 2087 2549 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 1.19256865175533e-05 0.000179690569200176 4335 2363.27272727273 2560 1.08415919676428e-06 289 2.14002406983646 -2.59443856790082 -1 17.8897834019103 4333 2756 289 2560 1441 2207 2582 3375 2124 703 3626 2550 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 0.0765897756730953 0.156982736433532 3005 2404.36363636364 2561 0.00793650793650794 122 1.51430131785667 1.51430131785667 1 2.71786510516871 3001 1917 3862 1052 2561 4402 4227 1118 122 1416 2770 2551 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 0.0666820862361612 0.142811817231559 3865 2758.09090909091 2561 0.00625394332237463 1048 1.07241401869531 -0.851059099641623 -1 2.02311210456782 3862 1048 2894 2043 1164 1906 4501 4612 2561 2442 3306 2552 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 0.0550997028919624 0.123835591247835 3890 2544.45454545455 2561 0.00513910056579447 682 1.31283400655787 1.31283400655787 1 2.65809586810647 3886 1440 2107 2639 1059 682 4321 4450 3170 1674 2561 2553 M17807 KEGG_BASAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_CELL_CARCINOMA.html Basal cell carcinoma 26/60 KEGG 0.00200818755836565 0.0102064716903486 3870 2520.72727272727 2562 0.000182729363921544 663 1.57245504476898 1.66409842843252 1 6.98805282934147 3869 1518 663 1152 2562 3339 3788 4553 795 803 4686 2554 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 0.0555764499717692 0.124608250989335 2265 2311.72727272727 2563 0.00518474326868369 823 1.16614344983449 1.23225642390188 1 2.35406056120111 2265 3224 3529 3029 1063 823 2703 2267 2563 2680 1283 2555 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 0.000652437554088165 0.00421699638407882 3555 2297.90909090909 2563 6.52629186920485e-05 73 1.38975139692581 -1.38975139692581 -1 7.36681387705691 3552 2893 4485 1975 73 4187 2563 600 2595 1309 1045 2556 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 0.0095685653721215 0.0335364976318335 2955 2483.45454545455 2563 0.00087367614347395 374 0.856817625152908 1.04965645171133 1 2.81972989161767 3666 1559 2953 1521 374 1828 3989 3648 2263 2954 2563 2557 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 0.0167888194073546 0.0511520047821298 3465 2386.63636363636 2564 0.00153802957824749 72 1.24641163481477 1.14859695860583 1 3.59181111777556 3465 842 2564 877 4629 4325 4245 450 72 968 3816 2558 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 0.0765897756730953 0.156982736433532 1540 2599.72727272727 2564 0.00793650793650794 301 0.684179230231652 1.05743690813112 1 1.22796357205475 1538 3395 4314 2804 4647 1890 1121 1959 301 4064 2564 2559 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 0.0839184282471183 0.156982736433532 2695 2134 2565 0.00793650793650794 11 1.30703162102277 1.4183229563699 1 2.34585785023057 2691 11 2565 393 1866 2987 3081 2939 677 2265 3999 2560 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 0.200735023569388 0.312165923612632 1890 2650.81818181818 2566 0.0201632875920359 1813 1.1427508546004 1.15275435058944 1 1.28958696703878 1888 2416 3112 2566 1813 3382 2084 3346 3123 2000 3429 2561 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 0.0839184282471183 0.156982736433532 4265 2114 2569 0.00793650793650794 314 1.77228865595639 1.77228865595639 1 3.18090028552208 4261 314 1560 1451 3055 583 3103 2569 688 2801 2869 2562 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 0.0117269690064907 0.0390011190662993 3040 2481.27272727273 2570 0.00107181358358053 830 2.15390727068067 2.15390727068067 1 6.77319836211089 3039 2938 830 1700 2690 4520 3383 2306 1741 1577 2570 2563 M9271 REACTOME_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_METABOLISM.html Genes involved in Purine metabolism 17/39 Reactome 0.0557747468724364 0.124876761122249 1645 2639.09090909091 2571 0.00520373394022909 458 0.292118571307389 -0.306102218176291 -1 0.589081944001667 1644 4489 2571 4533 3797 458 1360 1421 4459 3720 578 2564 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 0.0370488509866576 0.0921501675814636 2955 2525.36363636364 2572 0.00342617145114916 857 1.23062306466498 1.23062306466498 1 2.84417511186094 2953 2125 2127 3033 857 3776 2572 1628 2687 1948 4073 2565 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 0.0447626678111812 0.106045430416175 3600 2518.72727272727 2573 0.00415456889118207 868 1.16448615084999 1.17115159319127 1 2.53279073854459 3600 1277 1467 1719 948 2573 4202 3876 2650 868 4526 2566 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 0.277833372325942 0.398752582762439 2090 2504.72727272727 2573 0.0291573301109863 880 0.288551496442193 -0.323039936151366 -1 0.257157016833583 2087 2573 3208 2943 3570 880 1673 2180 3426 3871 1141 2567 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 0.466738071388703 0.587219019917277 4215 2701.63636363636 2573 0.0555555555555556 1769 1.4627117898207 1.49919198626814 1 0.75478964331512 4215 2420 1769 2383 2729 2021 3521 3534 2573 1785 2768 2568 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 0.452028792738248 0.574563816953485 3175 2564.54545454545 2575 0.0532164500889722 1392 1.24128814102427 -1.12846485370921 -1 0.66674411327856 3171 2182 2828 2575 2406 1392 3457 3480 2815 1650 2254 2569 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 2.0658484714688e-05 0.000282232243070052 2900 2515.18181818182 2575 1.87806170045102e-06 315 1.38527049356965 1.46569183720157 1 10.974083808498 2898 2673 315 2112 1834 2575 3866 2693 2420 1874 4407 2570 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 0.0270893508287256 0.0729125203810501 3010 2162.36363636364 2576 0.00274253548520122 163 1.04831594950947 1.04831594950947 1 2.66077280418975 3008 163 3867 573 751 3412 3854 2884 2092 606 2576 2571 M69 PID_REELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_REELIN_PATHWAY.html Reelin signaling pathway 18832364 20/47 Pathway Interaction Database 0.0420943289146903 0.101104062170292 4595 2734.27272727273 2576 0.00390200099431137 917 1.39951219782993 -0.889829409089437 -1 3.10871071612596 4591 2146 2576 1560 917 3207 4074 3054 1862 2382 3708 2572 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 0.300193102368254 0.419258024676146 1725 2488.90909090909 2576 0.0319292219834546 1126 1.31394404283802 1.31394404283802 1 1.1071202574123 1722 3050 1819 2618 3073 2576 1126 3844 2252 2884 2414 2573 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 0.171266192024271 0.275224065783859 2580 2616.45454545455 2577 0.0186102773924235 903 0.570567968365249 -0.231658193193512 -1 0.713539632573461 2577 3251 4106 3180 1906 1785 903 2416 2163 3786 2708 2574 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 0.107125009715004 0.191964740162336 4015 2617.81818181818 2577 0.0102479191323612 1421 1.12234317535258 1.1681682169479 1 1.79551987090218 4012 1430 2577 2803 1421 2572 3942 3919 1698 1443 2979 2575 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 0.00632874297314137 0.0247282698580666 2855 2464.18181818182 2577 0.000577002048899171 757 1.10483351785852 1.26331033123544 1 3.96223211014041 2852 1401 757 1049 1864 3766 2585 4585 1031 2577 4639 2576 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 0.453838325294813 0.576337775699592 2580 2840.36363636364 2579 0.0586911927098333 1380 0.296729476043797 -0.314789948861326 -1 0.158498269966834 2579 3524 3895 3731 2476 1380 2404 2215 3641 3374 2025 2577 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 0.0654395633006923 0.140407414664398 2635 2627.63636363636 2580 0.00613374597540182 1156 0.792904243146179 -0.792904243146179 -1 1.50886608485957 2631 2603 2470 3085 1156 2319 1946 2286 2580 4564 3264 2578 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 0.0445860340954562 0.10573388449965 4515 2546.90909090909 2581 0.00413783006235941 1030 1.45473886694068 -1.5590810254107 -1 3.1682474658357 4511 2963 1030 3391 1112 1641 4311 2581 2401 1328 2747 2579 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 0.0651845420371608 0.140181167501668 3570 2479.72727272727 2581 0.0061090940753119 1040 1.36818784197274 -1.02066708461929 -1 2.60574722137277 3567 2581 1656 2083 1153 1040 3260 4217 2938 2612 2170 2580 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 0.0700498145944921 0.148329611924894 1180 2290.36363636364 2583 0.00658045863204721 923 1.0829571648177 -0.944877455937817 -1 2.00320768095974 1180 2868 3774 2583 1191 923 2642 2244 3020 3146 1623 2581 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 0.314378972708852 0.4346945606709 3210 2711.54545454545 2583 0.0337298642269718 1485 1.91684460577582 1.91684460577582 1 1.54793949999402 3210 2717 1485 1753 2583 4144 3417 2510 2499 2197 3312 2582 M194 BIOCARTA_PROTEASOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PROTEASOME_PATHWAY.html Proteasome Complex 22/35 BioCarta 0.323668559340002 0.444132026081186 1220 2501 2584 0.034927453151342 1034 0.680644994905029 -0.680644994905029 -1 0.535481454513948 1220 2193 3698 3028 2138 1034 2584 2687 3907 3305 1717 2583 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 0.161385165508919 0.262241686633255 3215 2728.63636363636 2584 0.0158730158730159 1373 1.46118488003261 -1.01405746558881 -1 1.89576174437232 3215 4092 2584 3875 3128 1661 4275 1823 1373 1573 2416 2584 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 0.136263366332541 0.234065298619606 2625 2629.72727272727 2584 0.0132287550401166 1258 1.19463119953769 1.3093281538991 1 1.68155368757673 2622 3432 1258 2584 1789 2998 2459 2717 2282 2474 4312 2585 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 0.048844055007693 0.113289156399471 1160 2322.18181818182 2585 0.00454213044320917 591 0.927790657706714 -1.10317666919681 -1 1.95854796626284 3218 591 1159 1158 998 3487 4486 2959 2805 2585 2098 2586 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 0.00134558293135638 0.007407117025692 2905 2507.81818181818 2586 0.000134639839342231 113 0.686007751272719 -0.686007751272719 -1 3.26181781157667 2901 1096 4184 1660 113 2586 1982 4515 1363 3901 3285 2587 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 0.000504190811173909 0.00350411566188537 655 2482.45454545455 2587 4.58460361383891e-05 537 1.37730083154968 -1.20074158169684 -1 7.5480441289752 651 3298 537 2299 3803 2587 3412 2472 3537 1900 2811 2588 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 0.785759840706654 0.881292829167808 2595 3105.27272727273 2588 0.13069373909264 1799 1.33403223803043 -1.33403223803043 -1 0.163402279648083 2592 4521 1950 4435 4534 1799 2588 2575 4510 2349 2305 2589 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 0.304534694246558 0.424086055643202 2590 2829 2589 0.0356658494915358 1094 0.260301230290752 -0.326343246744106 -1 0.216439084652 2589 3328 4571 3931 2426 1094 1176 1891 4022 4525 1566 2590 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 0.000388693890283046 0.00283710213374821 3530 2269.09090909091 2591 3.53420528489288e-05 49 0.955023857704091 0.955023857704091 1 5.42930249493929 3530 1307 3516 2591 49 1730 2045 2887 907 3591 2807 2591 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 0.144381750936812 0.245669166626688 1850 2470.72727272727 2591 0.0140755430689524 725 0.284464967324789 -0.305292985388255 -1 0.387069059527174 1846 2592 3420 3099 2591 725 2241 1850 3978 3972 864 2592 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 0.39436489956339 0.516199418813979 2660 3043.90909090909 2592 0.0489111205605245 1788 0.53641226035101 -0.319872111297003 -1 0.343824013063501 2659 1865 4665 1909 2353 4447 3976 1788 2584 4645 2592 2593 M18615 KEGG_ALLOGRAFT_REJECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALLOGRAFT_REJECTION.html Allograft rejection 23/70 KEGG 0.0917089107124937 0.169192108503443 3580 2709.90909090909 2594 0.00870645635775022 1157 1.78606414326979 1.78606414326979 1 3.07595533152306 3577 2594 1157 1678 2264 4261 4402 2829 1705 1399 3943 2594 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 0.079884148059008 0.156982736433532 1855 2501.09090909091 2595 0.00754012869000393 1129 0.990478285128715 1.09900272470116 1 1.77770852919488 1851 2876 1129 2946 1718 3505 2595 2087 3667 2079 3059 2595 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 0.0208879531473747 0.0607578823392909 4145 2864.18181818182 2595 0.00191717738056136 904 1.18783911336635 1.18783911336635 1 3.22487324661716 4141 1843 904 2482 2595 3288 3568 4294 2014 1732 4645 2596 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 0.0261798227057286 0.071407828404566 3495 2560.72727272727 2595 0.00240878650525444 689 0.806464722769301 -0.806464722769301 -1 2.06322152317337 3495 1943 3120 1815 689 1836 4421 2595 801 4661 2792 2597 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 0.011989010219461 0.0396754956838944 3225 2530.45454545455 2596 0.00109589525285236 421 0.772086244831543 -0.493393016758395 -1 2.41508011869933 3225 3407 2596 2880 421 1042 1580 3635 4043 2519 2487 2598 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 0.232850105696956 0.34496857265126 2055 2684.18181818182 2596 0.0238095238095238 1696 0.369451190864545 0.441711529811051 1 0.381141113608458 2052 1990 3082 2596 2444 2813 2228 3693 1696 3919 3013 2599 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 0.81903475439031 0.908345999170752 2140 2973.09090909091 2597 0.143931233054893 1964 1.05919280447021 1.05919280447021 1 0.0986955230283206 2139 3976 2400 3457 4474 3172 1964 2296 3839 2390 2597 2600 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 0.49489168137824 0.615952833715387 1115 3023.27272727273 2599 0.0602010478712051 1113 0.680644994905029 -0.680644994905029 -1 0.319708649987511 1113 4592 3499 4565 2599 1325 2586 2172 4546 4354 1905 2601 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 0.0972650878284045 0.177624396556471 3420 2547.90909090909 2600 0.00925926041793086 1353 0.438172034967236 -0.483898016650602 -1 0.733961693810229 3416 1540 2600 2168 1353 1778 2771 3857 3410 3450 1684 2602 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 0.232850105696956 0.34496857265126 2605 2665.09090909091 2601 0.0238095238095238 1271 0.610681132932434 0.610681132932434 1 0.630003889135301 2601 1374 3225 1735 3045 4429 2419 1271 1567 4528 3122 2603 M3075 BIOCARTA_SET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SET_PATHWAY.html Granzyme A mediated Apoptosis Pathway 9/25 BioCarta 0.172429880812206 0.276617244348736 3615 2578.90909090909 2602 0.018748169013957 1470 0.374517384635169 -0.359565544793408 -1 0.466530138735047 3615 1762 3839 2767 1771 1470 2245 1798 3227 3272 2602 2604 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 0.0158405117761642 0.0486426200413535 2605 2746.36363636364 2602 0.00159545725625159 533 1.21455215107271 1.21455215107271 1 3.55922004556429 2533 2163 3927 2602 533 4643 1986 4215 2603 1505 3500 2605 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 0.136014818290415 0.23380977201353 2320 2813.18181818182 2602 0.0145136133300527 1628 0.473861425767653 0.528248466903532 1 0.667505406517391 2319 2956 4118 3813 1628 2602 2022 1897 3567 3797 2226 2606 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 0.35943518917414 0.478362197236587 3085 2944.45454545455 2602 0.0396825396825397 2118 1.21455215107271 1.21455215107271 1 0.868111617791246 3083 2441 2806 2435 2362 4283 2602 4551 2118 2190 3518 2607 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 0.0839184282471183 0.156982736433532 3760 2400.63636363636 2603 0.00793650793650794 509 1.05422615586411 -1.15074581070362 -1 1.89212308550809 3757 823 3089 1047 4269 1975 3428 3440 509 1467 2603 2608 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 0.298735036746822 0.4173739958842 2405 2858.63636363636 2604 0.0317460317460317 1384 1.26001180362053 1.46464290875871 1 1.06717807627018 2404 3200 2021 2487 4391 4641 2645 3591 2077 1384 2604 2609 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 0.0443588383138082 0.105355051362648 4420 2447.72727272727 2604 0.00411630381682298 92 0.986018736463157 -1.01405746558881 -1 2.1508615520103 4417 92 1569 785 944 4492 3839 2604 2231 2863 3089 2610 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 0.0148733688170255 0.0463716608626625 3985 2649.45454545455 2606 0.00136135310759886 488 1.07964590481834 1.20252136740817 1 3.21391558545607 3981 1715 2324 1102 488 3161 3256 3853 2503 2606 4155 2611 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 0.00487810256450378 0.0201044754769259 2280 2237.90909090909 2607 0.000488884391248262 72 1.23033532801839 1.37975931542994 1 4.65918511302837 2278 4076 4198 3001 868 72 2613 1806 2784 2607 314 2612 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 0.0617095365183252 0.134435559332809 3875 2907.54545454545 2607 0.00577378683155605 756 0.940767540772448 -0.940767540772448 -1 1.82987833395049 3871 2003 2607 2194 1816 4239 3144 756 2600 4287 4466 2613 M17906 KEGG_VIBRIO_CHOLERAE_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIBRIO_CHOLERAE_INFECTION.html Vibrio cholerae infection 30/73 KEGG 0.168361369125995 0.2713936620999 3580 2650 2608 0.0166200885431764 1199 0.801505046067566 -0.801505046067566 -1 1.01323291459754 3578 3305 2399 3608 1704 1199 3282 2608 2519 3229 1719 2614 M7897 BIOCARTA_GLEEVEC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLEEVEC_PATHWAY.html Inhibition of Cellular Proliferation by Gleevec 20/42 BioCarta 0.118410688791444 0.208598679577709 2610 2395.72727272727 2608 0.011391795104036 993 0.314564556954276 -0.29239209962835 -1 0.477900759299195 2608 2195 3479 1486 1494 993 3222 3647 2655 3286 1288 2615 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 0.0247678694127643 0.0685541855098721 1900 2587 2608 0.00227738043143807 207 0.30893342178588 -0.384519765319204 -1 0.802573384274973 1897 4666 2608 4603 3455 207 1650 1537 3212 4156 466 2616 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 0.0416823923053512 0.100526860701428 2585 2532.09090909091 2609 0.00386306671406995 457 0.304510971542962 -0.18694923111394 -1 0.678094551131758 2584 2399 3149 2609 1626 1452 457 4051 3132 3641 2753 2617 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 0.0033276283981684 0.0151244099649051 4490 2771.72727272727 2609 0.000302970210406549 189 1.36286765863823 1.4946704170587 1 5.53708707387807 4489 2311 2018 2057 189 2376 4324 3487 2672 2609 3957 2618 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 0.289084814526093 0.411491921044036 2615 2486.18181818182 2611 0.0305422426683975 943 1.53334444632203 1.53334444632203 1 1.31977493112959 2611 943 1451 1388 3424 4060 1334 4365 2988 2053 2731 2619 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 0.103529130485765 0.186878854181932 1780 2549.72727272727 2613 0.00988621416970203 499 0.320068885301424 -0.300459746029038 -1 0.52037533166971 1777 2444 3150 2613 2917 499 2377 2663 4126 4464 1017 2620 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 0.35943518917414 0.478362197236587 2855 2709.90909090909 2614 0.0396825396825397 1580 1.24287224182961 -1.24287224182961 -1 0.88835364674337 2853 2634 3232 2614 4116 1750 4372 1978 2222 2458 1580 2621 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 0.0793394057981334 0.156982736433532 2365 2598.90909090909 2615 0.00748672737114129 816 1.24287224182961 -1.24287224182961 -1 2.23070471932544 2365 3313 3063 2953 4340 1578 4097 816 2615 2167 1281 2622 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 0.35943518917414 0.478362197236587 2855 2710.90909090909 2615 0.0396825396825397 1581 1.24287224182961 -1.24287224182961 -1 0.88835364674337 2854 2635 3233 2615 4117 1751 4373 1979 2223 2459 1581 2623 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 7.14306928753615e-05 0.000749844093222755 4530 2661 2615 6.49391020254643e-06 389 2.03346215453243 -2.59443856790082 -1 14.1830522928662 4526 2970 389 3026 1847 2308 4548 2615 2134 1147 3761 2624 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 0.194358387024314 0.304399532618963 1595 2482.72727272727 2616 0.0194551916835278 1104 0.448041516139884 -0.579011782040659 -1 0.516553417250588 1592 2885 1553 2616 3005 1852 2714 1104 3675 4257 2057 2625 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 0.0191207456619486 0.0568931526672333 4340 2353.63636363636 2617 0.00175354358413217 567 1.20029849708164 -0.831208223470998 -1 3.33516433494881 4336 993 1903 967 567 2878 2892 3272 2308 2617 3157 2626 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 0.079421288985489 0.156982736433532 3905 2676.54545454545 2617 0.00749475258067504 1126 1.26227190138541 1.33844638480305 1 2.26552319114417 3902 3464 1126 2617 1894 1803 4287 2947 2245 2759 2398 2627 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 0.0306165895011092 0.0794843980067577 1315 2621.45454545455 2617 0.00310467737867271 417 0.362913613661914 0.451167430543977 1 0.890767148229021 1312 3706 4484 4112 2617 809 417 1455 4157 4394 1373 2628 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 0.0224858382370105 0.0640928454857853 2620 2484 2618 0.00206536414783129 538 1.27463908196629 1.47692947446309 1 3.39450578095851 2618 538 1857 665 630 4625 2978 4510 2181 3024 3698 2629 M13494 BIOCARTA_BIOPEPTIDES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BIOPEPTIDES_PATHWAY.html Bioactive Peptide Induced Signaling Pathway 28/67 BioCarta 0.104115449000191 0.187792530413739 1575 2451.63636363636 2619 0.00994510111048499 503 0.701222236703204 -0.701222236703204 -1 1.13674812268713 1572 2981 3320 2619 3929 503 1705 2480 3539 3245 1075 2630 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 0.0811197054905129 0.156982736433532 2875 2404.90909090909 2621 0.00842425752604571 631 1.69748649654937 1.69748649654937 1 3.04664551307095 2871 631 4111 1353 1299 3031 2621 4408 1575 1513 3041 2631 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 0.079788995770181 0.156982736433532 4395 2357.45454545455 2621 0.00753079879871354 459 1.80764389061604 -1.54147339981623 -1 3.24435579298089 4393 2621 1557 1294 1241 2797 4249 3194 616 459 3511 2632 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 0.000277345126780633 0.00216606544015674 3320 2687.18181818182 2621 2.52163724303855e-05 490 1.45095084170727 1.42023874664746 1 8.62819619605717 3317 2866 490 2621 1785 2067 3967 3604 2082 2313 4447 2633 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 0.196067292593262 0.306563674705381 2060 2785.72727272727 2622 0.01964445656259 1797 1.25791670772937 1.25791670772937 1 1.44163190898029 2059 3920 2622 3799 1797 4486 1951 1991 2945 2264 2809 2634 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 0.392589000373681 0.514162117314441 1960 2677.81818181818 2622 0.0443109615870022 1752 1.13071048228436 1.36014709874107 1 0.729085400076161 1959 4375 1892 3437 2285 2754 1752 3277 2659 2622 2444 2635 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 0.159980805537259 0.262241686633255 2025 2847 2622 0.0172819771872316 1379 0.434005477459994 -0.434005477459994 -1 0.563084789717221 2025 3818 4313 3936 1738 1756 2622 1379 3756 4062 1912 2636 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 0.194764285012573 0.304729696016333 3190 2413 2623 0.0195001126659548 1609 1.1712352121029 1.1712352121029 1 1.349102969436 3189 3028 3312 2685 1794 1678 1869 1609 2623 2103 2653 2637 M983 REACTOME_INTERFERON_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_SIGNALING.html Genes involved in Interferon Signaling 98/246 Reactome 0.0390611945135438 0.0957827093095062 4630 2869.09090909091 2624 0.00361567944967148 880 1.29194061630317 1.5924441165527 1 2.93747314492054 4629 1493 2601 1676 880 2624 4116 4449 2506 2724 3862 2638 M7272 KEGG_PARKINSONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PARKINSONS_DISEASE.html Parkinson's disease 56/151 KEGG 0.0719363339158358 0.15157089061583 530 2478.63636363636 2625 0.00676383458432462 526 0.622483520228632 -0.622483520228632 -1 1.13840028801279 526 3438 3764 3859 2625 750 1571 2257 4048 3226 1201 2639 M11079 KEGG_N_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_N_GLYCAN_BIOSYNTHESIS.html N-Glycan biosynthesis 30/50 KEGG 0.229219603545927 0.34496857265126 2995 2492.81818181818 2626 0.0233904447738449 956 0.715858725339802 0.715858725339802 1 0.738509439256281 2991 2279 3444 2844 3419 956 2626 1178 2625 3175 1884 2640 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 0.0547137043245257 0.123263662723427 1235 2276.45454545455 2626 0.0051021612577436 246 1.10939596657673 1.11806310303017 1 2.25117269765126 3496 246 1235 1135 1056 2626 3079 3668 2872 1232 4396 2641 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 0.185525978497714 0.293303644412678 2630 2702.72727272727 2627 0.0203121462607949 1122 0.617190280313086 -0.765782969117633 -1 0.733782069433754 2627 1478 4054 2312 3515 2383 3226 1122 3036 3680 2297 2642 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 0.304467560112382 0.424086055643202 4625 2918.36363636364 2627 0.0324682682330342 1209 0.998470431454979 -1.089683506294 -1 0.830222838634562 4621 1731 2556 2627 2082 3424 3490 4630 2363 1209 3369 2643 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 0.0839184282471183 0.156982736433532 3000 2536.63636363636 2627 0.00793650793650794 651 1.53859597974134 1.5128539183364 1 2.76146911779295 2996 2082 2627 2686 1640 3386 2440 4333 651 1241 3821 2644 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 0.156000870033438 0.25996446549669 4400 2955.09090909091 2628 0.0153002717073231 1661 1.18063890866154 1.18063890866154 1 1.54175853478406 4400 2628 3346 2371 1661 2157 4145 3836 2507 1824 3631 2645 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 0.133052727646236 0.229813889329253 2630 2864.54545454545 2629 0.0141762688608358 1549 0.239319954774708 -0.254331322149597 -1 0.341117120399107 2629 2820 4119 3454 1606 1549 2118 2593 4501 3799 2322 2646 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 0.216624271792514 0.330329104334435 4060 2849.63636363636 2631 0.0219503112201855 723 0.710694190587221 -0.710694190587221 -1 0.763054208693088 2217 4300 2631 4056 4417 723 1740 1700 4057 4103 1402 2647 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 0.153747685802684 0.257583716721979 1780 2807.90909090909 2631 0.0150615788601749 1006 3.31598584971361 3.31598584971361 1 4.35981114315953 1780 4457 2215 4128 4121 3711 3128 1006 1580 2631 2130 2648 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 0.0336718241757395 0.0852898205878461 4470 2560.36363636364 2632 0.0031089549719339 816 1.24761700739991 1.41820041845267 1 2.97701009756054 4469 1115 2939 1701 816 1588 4126 4625 962 2632 3191 2649 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 0.0130631628114416 0.0421874437866405 3515 2313.18181818182 2632 0.0011946709335838 446 1.03192577286687 1.09844789254763 1 3.16645150342611 3512 880 3056 771 446 3275 2942 2632 1497 2584 3850 2650 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 0.161228866279139 0.262241686633255 3745 2684.54545454545 2632 0.0158563427880679 1031 1.18638701718937 1.2731547134615 1 1.53923514533572 3741 1979 1659 1948 2913 3258 3763 1031 2632 2153 4453 2651 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 0.514011397665828 0.633523779448203 1870 2684.45454545455 2635 0.0634920634920635 1868 1.46693471565438 1.46693471565438 1 0.649045631549796 1868 2366 2277 2857 3467 3897 3206 2739 2635 1914 2303 2652 M3061 BIOCARTA_FEEDER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FEEDER_PATHWAY.html Feeder Pathways for Glycolysis 6/15 BioCarta 0.0765897756730953 0.156982736433532 2090 2243.90909090909 2636 0.00793650793650794 87 1.70956702222945 1.70956702222945 1 3.06832761742631 2090 3247 3835 2636 2747 3439 808 2890 87 1414 1490 2653 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 0.424713090513952 0.546009750932339 2145 2805.72727272727 2636 0.0490201444571391 1070 0.674350887224881 -0.674350887224881 -1 0.395539800304657 2145 4365 2636 4353 3657 1070 2320 1997 2811 3846 1663 2654 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 0.584886065236649 0.700965754910214 3635 2761.63636363636 2637 0.076816704676273 1010 1.46693471565438 1.46693471565438 1 0.505202242783213 3632 1010 1757 2161 2637 3882 4077 2045 3744 1919 3514 2655 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 0.584886065236649 0.700965754910214 3635 2761.09090909091 2638 0.076816704676273 1011 1.46693471565438 1.46693471565438 1 0.505202242783213 3633 1011 1758 2162 2638 3883 4078 2029 3745 1920 3515 2656 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 0.0612364496375468 0.133715751631661 4515 2802.09090909091 2638 0.00572822547834237 1061 1.20804869587494 1.37434020535588 1 2.35605106388031 4513 2616 2638 3107 1117 1061 3865 4600 2680 2143 2483 2657 M321 KEGG_CHRONIC_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHRONIC_MYELOID_LEUKEMIA.html Chronic myeloid leukemia 39/90 KEGG 0.0839184282471183 0.156982736433532 3730 2489.72727272727 2639 0.00793650793650794 233 1.1106289538885 1.1106289538885 1 1.99335471938604 3729 307 2639 233 2187 4282 3219 4529 714 1277 4271 2658 M12836 BIOCARTA_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPO_PATHWAY.html EPO Signaling Pathway 15/36 BioCarta 0.347591329711232 0.470075893514238 1660 2617.27272727273 2639 0.0380817671376344 952 0.1853303266312 -0.247776624001997 -1 0.135605534528514 1659 4155 3687 3412 2639 952 1508 2274 3766 3264 1474 2659 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 0.298735036746822 0.4173739958842 2925 2594.45454545455 2640 0.0317460317460317 1236 1.07754056151101 -0.989745402399581 -1 0.912632453294044 2925 2640 1564 1589 4335 2660 1236 4160 1940 1995 3495 2660 M3412 BIOCARTA_CACAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CACAM_PATHWAY.html Ca++/ Calmodulin-dependent Protein Kinase Activation 9/15 BioCarta 0.00280913597950828 0.0134349503007636 1185 2568.45454545455 2641 0.000281269337039189 118 0.309472136165763 0.348721407370289 1 1.29286203521829 1181 2641 3820 3601 4679 1195 118 2156 3990 3247 1625 2661 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 0.514011397665828 0.633523779448203 2525 2564.18181818182 2641 0.0634920634920635 1948 1.24287224182961 -1.24287224182961 -1 0.549909133993831 2525 2697 1948 2729 2866 2293 1971 2958 2641 2231 3347 2662 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 0.00503965410764733 0.0206431985563246 3345 3092.09090909091 2641 0.000505111987189248 272 0.796538314240086 -0.796538314240086 -1 2.99601239436925 3342 2371 4610 2271 272 2295 4522 4651 2458 4580 2641 2663 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 0.112388101548761 0.199488880249051 615 2629.09090909091 2645 0.0107797217438342 611 0.564322045552235 -0.564322045552235 -1 0.88176946017694 611 3867 3747 3852 2645 739 1703 2544 4268 3666 1278 2664 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 0.148797659082916 0.250634734170577 1505 2566.54545454545 2645 0.0159814603760246 628 0.434468196704863 -0.434468196704863 -1 0.582749894445017 1505 2645 4315 2938 4210 628 1192 1471 4116 4067 1145 2665 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 0.139090474205765 0.237615006244337 2135 2564.18181818182 2646 0.0148649947606889 812 0.406428081928031 0.479441778078512 1 0.566155370724232 2135 1661 3949 2684 3310 2118 812 1957 3442 3492 2646 2666 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 0.0839184282471183 0.156982736433532 2525 2349.81818181818 2646 0.00793650793650794 457 0.451900038997901 0.428138709932515 1 0.811069324463109 2522 499 2722 1216 3691 2937 1846 2646 457 4344 2968 2667 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 0.683302463845863 0.790606258168324 2265 2774.09090909091 2647 0.0992504325499943 1855 1.46693471565438 1.46693471565438 1 0.334087122962757 2263 1855 2009 2647 3880 4012 3262 1921 3720 2041 2905 2668 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 0.0839184282471183 0.156982736433532 2965 2553.36363636364 2648 0.00793650793650794 699 1.59400404717518 1.74756566414379 1 2.86091541111197 2961 3150 1825 2381 2648 1453 3371 4301 699 2807 2491 2669 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 0.232850105696956 0.34496857265126 3365 2691.54545454545 2649 0.0238095238095238 726 0.993999865251022 0.993999865251022 1 1.02545133159826 3365 801 3012 726 3974 1927 4512 4461 1773 2407 2649 2670 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 0.0249418963550225 0.0688822626798608 3360 2658.90909090909 2649 0.00252263442434109 707 1.24874443271053 1.38431209844888 1 3.23831509098243 3360 2649 4422 1745 707 818 3299 4204 1783 2365 3896 2671 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 0.4329008207048 0.555317067019625 2625 2734.54545454545 2650 0.050258609453421 1085 1.07444863065699 -0.708329498464269 -1 0.612613246205535 2623 3785 1976 3659 3893 1085 3061 2028 3495 2650 1825 2672 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 0.407394360707695 0.530144397188631 3215 2615.18181818182 2651 0.0464524741516012 1492 0.763017140970065 -0.763017140970065 -1 0.469355854886411 3214 2184 2909 2682 2651 2163 3878 1492 2531 2877 2186 2673 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 0.0648373755138044 0.13962681142357 2485 2332.45454545455 2652 0.00607554468083321 631 0.493393016758395 -0.493393016758395 -1 0.941574102768218 2482 1951 3325 2652 3340 1011 775 3206 2974 3310 631 2674 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 0.0839184282471183 0.156982736433532 2615 2732.18181818182 2652 0.00793650793650794 317 2.46711003640163 2.46711003640163 1 4.4279643685023 2614 3974 2652 2827 4068 3641 2599 1591 317 2426 3345 2675 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 0.675098216280473 0.782272562188501 1930 2770.90909090909 2652 0.0971536910683443 1460 1.18063890866154 1.18063890866154 1 0.281011781998892 1929 3931 3118 4279 3715 2652 2067 1977 3569 1460 1783 2676 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 0.512082630237791 0.633523779448203 3390 2897.90909090909 2653 0.0631547836639706 1637 1.58993231593147 1.58993231593147 1 0.703465950539918 3626 3631 2360 2527 2524 2537 3606 3390 2653 1637 3386 2677 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 0.325649790718815 0.446589089642484 1810 2572.36363636364 2653 0.0351848017869788 1807 0.911939656758414 0.982108926999804 1 0.712570285743617 1807 2656 2369 1931 2142 3918 1809 3313 2927 2653 2771 2678 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 0.439387283037208 0.561945635456429 2655 3135.81818181818 2654 0.0562297253673055 1655 0.154590164386752 -0.20665337216709 -1 0.0863638806269486 2654 4395 4039 4215 2438 1655 2614 2592 4468 3650 1774 2679 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 0.35049539869501 0.473183934971138 4430 2999.72727272727 2654 0.0384718105946245 1558 1.74045289762317 2.03704134678686 1 1.26236548213701 4427 3587 1558 2654 2195 2489 3835 3361 2509 2450 3932 2680 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 0.796944161638877 0.890221773883141 3500 2871.36363636364 2655 0.134920634920635 1964 1.08196515182584 1.08196515182584 1 0.121954990857179 3497 2245 1964 2426 3996 3230 2655 2154 3339 2051 4028 2681 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 0.0115852731712667 0.0387222468477574 2900 2221.45454545455 2656 0.00105879411008034 480 1.14696250486499 -0.947519146332811 -1 3.61472785671508 3048 2896 828 2994 480 1139 2896 2539 3028 2656 1932 2682 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 0.466738071388703 0.587219019917277 4015 3058.27272727273 2657 0.0555555555555556 2111 1.40808672019189 1.40808672019189 1 0.726601973595267 4013 3659 2111 2878 2541 2657 4537 2622 2554 2580 3489 2683 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 0.411867919335049 0.535074319380105 1135 2809.90909090909 2657 0.0471091209782093 1113 0.290221176137868 -0.304830995325099 -1 0.175920260186731 1132 4177 2657 4452 2943 1113 2394 2600 4492 3583 1366 2684 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 0.18558371866914 0.293303644412678 3195 2827.81818181818 2658 0.018489089554389 1085 0.347000805272382 -0.426513783766544 -1 0.41255181275865 3193 3759 2658 3914 3345 1865 2569 1085 2546 4158 2014 2685 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 0.557443745451391 0.675680649556446 1445 2757.36363636364 2659 0.0714285714285714 1445 0.791140711360448 -0.791140711360448 -1 0.300636798457576 1445 3545 2659 3320 3269 2307 1582 2576 2738 4547 2343 2686 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 0.0839184282471183 0.156982736433532 3160 2517.09090909091 2660 0.00793650793650794 840 1.26280792819086 1.38190068899811 1 2.26648525102805 3158 972 3572 1649 1828 3130 2660 3861 840 2209 3809 2687 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 0.0555468960197863 0.124601605911306 3580 2409.45454545455 2663 0.00518191323027399 397 1.07611997973469 -0.940659277367857 -1 2.1723883741675 3580 2674 3416 2444 1062 397 4270 2176 2663 2738 1084 2688 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 0.124603796894826 0.217464950558344 2705 2819.36363636364 2664 0.0120251755344764 1237 0.903030302715247 0.903030302715247 1 1.33548908472658 2704 2387 1237 1927 2484 4155 4250 3795 1963 2664 3447 2689 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 0.147859119791321 0.249412467725749 2665 2658.81818181818 2664 0.0158730158730159 1140 1.65198623575143 1.65198623575143 1 2.22362849547444 2664 2208 4504 2589 3052 3936 2964 1803 1140 1524 2863 2690 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 0.0839184282471183 0.156982736433532 4675 2959.63636363636 2664 0.00793650793650794 482 1.64216404686053 1.64216404686053 1 2.94735288631669 4675 1376 2155 1318 2664 4639 4405 4053 482 2246 4543 2691 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 0.161385165508919 0.262241686633255 2415 2368.72727272727 2666 0.0158730158730159 1278 1.13769388754658 -0.701222236703204 -1 1.47605999641582 2415 3010 2833 2845 2830 3112 1551 1321 1278 2666 2195 2692 M5785 KEGG_TASTE_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TASTE_TRANSDUCTION.html Taste transduction 19/88 KEGG 0.750538205254052 0.848905049629493 2670 2858.18181818182 2668 0.1185814511801 2172 1.20418076991769 -1.20418076991769 -1 0.191201147166367 2668 2287 2172 2345 2941 3630 2644 3088 3600 2315 3750 2693 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 0.0615081764556752 0.134147372150219 2780 2255.18181818182 2668 0.00575439199164689 367 1.72130338621463 1.72130338621463 1 3.35167199697241 2776 367 2711 704 1120 4347 2668 4370 1142 1846 2756 2694 M161 PID_IFNG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IFNG_PATHWAY.html IFN-gamma pathway 18832364 25/57 Pathway Interaction Database 0.232850105696956 0.34496857265126 2670 2480.36363636364 2669 0.0238095238095238 590 1.53334444632203 1.53334444632203 1 1.58186148640781 2669 590 3035 663 3319 4423 2549 2886 1600 2554 2996 2695 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 0.101448331634444 0.183973251563081 2530 2707.09090909091 2670 0.0106400963430379 722 1.25240526293404 1.25240526293404 1 2.05521236890964 2530 2670 4057 2924 3263 2377 722 3854 3722 1296 2363 2696 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 0.0210501482716683 0.0609647681094176 3960 2797.72727272727 2670 0.00193220921558051 908 1.10778825710311 1.13352087187104 1 3.00389243517021 3956 2870 908 2103 1800 2090 3860 4332 2670 2605 3581 2697 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 0.705187611027557 0.809135442036026 2380 3032.72727272727 2671 0.114976968000069 1815 0.896585420808603 0.896585420808603 1 0.184059759264429 2377 2669 4434 3384 2945 2671 1815 2504 3632 4331 2598 2698 M980 KEGG_TRYPTOPHAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TRYPTOPHAN_METABOLISM.html Tryptophan metabolism 16/53 KEGG 0.010035831409718 0.0348253931458983 2675 2413.27272727273 2672 0.000916536982401339 814 1.45296921383986 -0.967459383376804 -1 4.72851161448991 2672 1586 814 1656 3235 3103 919 3754 3404 2160 3243 2699 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 0.491835399452222 0.613289164936965 1260 2924.81818181818 2672 0.0596855110936842 1189 0.222084968342895 -0.236884774211063 -1 0.105249419254855 1256 4261 3725 4500 2668 1189 2672 2345 3875 3745 1937 2700 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 0.000643261278756964 0.00419238157476375 2695 2646.54545454545 2672 5.84954036280776e-05 560 1.35143153195385 -0.967459383376804 -1 7.17135609446916 2692 1576 560 1201 4337 4605 2226 3865 1401 2672 3977 2701 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 0.0232344634045281 0.0655488835121123 3670 2660.09090909091 2673 0.002134866900738 651 1.1652032085838 -0.877162226095631 -1 3.07769462636028 3669 2760 1519 2673 651 3285 4587 2577 2219 1409 3912 2702 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 0.0493429850232836 0.114033359656204 4310 2833.81818181818 2674 0.00504741265821439 1050 1.08196515182584 1.08196515182584 1 2.27714045984329 4308 1545 3936 2674 1050 1812 4543 3168 2336 1688 4112 2703 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 0.13035125780697 0.226056514083612 2440 2875.18181818182 2674 0.0126166338457851 557 0.270561568578524 -0.25659284608418 -1 0.389970947085398 2439 3939 2674 4319 3594 557 1722 2440 4586 3748 1609 2704 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 0.295436858370623 0.4173739958842 1535 2805.27272727273 2675 0.0313329253290746 1314 0.219752735854178 -0.234258619574834 -1 0.186121511816965 1531 3892 3744 4212 2059 1314 2675 2299 3620 3531 1981 2705 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 0.0378814012965144 0.0937729775359041 1350 2380.90909090909 2675 0.00350453133043667 283 0.525602276263726 -0.525602276263726 -1 1.20586052206025 1348 3163 3258 3765 2675 283 926 2433 3393 3867 1079 2706 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 0.504223354131933 0.626568718499666 2680 2810.72727272727 2677 0.0617928611631397 1933 1.05077947290469 1.05077947290469 1 0.4761613175002 2089 2329 1933 3159 2509 3284 2679 4683 3538 2038 2677 2707 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 0.301537913699924 0.420788166646171 3220 2619 2677 0.0320984909019625 1612 1.0177635111608 1.0177635111608 1 0.853966637194339 3220 2953 2200 2677 2076 3720 2889 1612 2233 1776 3453 2708 M6981 KEGG_PROTEIN_EXPORT http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEIN_EXPORT.html Protein export 16/39 KEGG 0.3411874541956 0.463153073684988 1550 2603.45454545455 2678 0.0372272147884862 935 0.275347004358992 -0.287539545394304 -1 0.205430248648577 1546 2734 3314 3247 2678 935 2131 2481 4350 3198 2024 2709 M13863 BIOCARTA_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MAPK_PATHWAY.html MAPKinase Signaling Pathway 46/109 BioCarta 0.514011397665828 0.633523779448203 2285 2835.81818181818 2679 0.0634920634920635 2105 0.936014225881437 0.936014225881437 1 0.414139728127744 2284 3558 3494 2538 4193 3074 2105 2136 2679 2306 2827 2710 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 0.0839184282471183 0.156982736433532 3120 2576.72727272727 2679 0.00793650793650794 601 1.4520937689859 1.76342791059926 1 2.60621511558827 3116 2679 1248 2242 2869 3651 3515 2185 601 2610 3628 2711 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 0.298010295949768 0.4173739958842 2685 3002.18181818182 2681 0.0316551046670427 1461 1.00744291305309 1.00744291305309 1 0.853262633563273 2681 2680 1461 2580 4262 4229 2185 1955 4125 2981 3885 2712 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 0.239761302914538 0.353384627016996 1550 2687.36363636364 2681 0.027039975072492 1041 0.45656770228766 0.582442872087981 1 0.46034683163311 1547 3676 4007 3816 2534 2104 1041 2681 2850 3601 1704 2713 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 0.199268649250204 0.310120521549803 3780 2382.18181818182 2684 0.02 290 1.14672566625037 1.14672566625037 1 1.30137958700632 3777 290 2891 1343 1974 1212 4086 3034 2684 2986 1927 2714 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 0.0839184282471183 0.156982736433532 2685 2411.63636363636 2684 0.00793650793650794 132 1.40692097012275 -0.905529645769096 -1 2.52513906269851 2684 2696 2911 1505 2367 4218 2849 2036 132 2249 2881 2715 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 0.0839184282471183 0.156982736433532 3770 2735.36363636364 2685 0.00793650793650794 372 1.2349129073029 1.15114836851811 1 2.21641932095972 3768 1511 2685 1579 3708 3863 3940 2266 372 1753 4644 2716 M913 REACTOME_NEPHRIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEPHRIN_INTERACTIONS.html Genes involved in Nephrin interactions 15/33 Reactome 0.28469859691192 0.406117998517277 3805 2918.27272727273 2686 0.03 494 0.478462076078607 -0.468897779266397 -1 0.417916896795863 3804 494 2154 1862 4407 2622 4647 3333 2417 3675 2686 2717 M15303 REACTOME_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOSIS.html Genes involved in Apoptosis 95/213 Reactome 0.0839184282471183 0.156982736433532 3330 2649.81818181818 2686 0.00793650793650794 976 1.40941625355308 1.62324554169925 1 2.52961759262058 3330 2223 3193 1685 1839 2646 3209 2925 976 2686 4436 2718 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 0.0839184282471183 0.156982736433532 4235 2674.36363636364 2686 0.00793650793650794 182 1.11703822633263 1.16852860670454 1 2.00485806929447 4231 1906 2686 1208 2593 2798 4128 4416 182 1159 4111 2719 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 0.415320710913563 0.535769969181582 3765 2900.36363636364 2688 0.0476190476190476 1756 1.31505585488108 1.31505585488108 1 0.795477154477059 3761 2106 2495 2967 2952 4469 2688 2222 2340 1756 4148 2720 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 0.0887982260413493 0.164534791312678 3755 2699.81818181818 2688 0.00841808778921445 1059 0.480150068614032 -0.406180390874161 -1 0.839904314535815 3752 1217 1657 1059 1298 2688 3580 4555 2520 4275 3097 2721 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 0.415320710913563 0.535769969181582 2610 3122.27272727273 2689 0.0476190476190476 1593 1.73830175663212 1.73830175663212 1 1.0514985579504 3003 3960 1593 2689 2606 4593 2606 4281 2429 2634 3951 2722 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 0.0977774463867009 0.178351542922569 2690 2614.90909090909 2689 0.00931039246258119 876 0.852246096011289 0.852246096011289 1 1.42418308882208 1955 2808 3156 2597 2689 2940 1799 876 2689 4588 2667 2723 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 0.0503032318635957 0.11577649534028 4415 2867.09090909091 2690 0.00468105833278317 638 1.24352787809384 1.3122659621373 1 2.5988847738953 4415 3955 2632 4341 1009 638 4256 4295 1546 2690 1761 2724 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 0.109595119901432 0.195642945469756 2690 2664.90909090909 2690 0.0115407880815216 804 1.0923235667937 1.0923235667937 1 1.72739899039597 2690 1396 4627 3008 4447 3738 1372 2210 3400 1622 804 2725 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 0.190200943615179 0.299481844358952 3235 2921.90909090909 2691 0.01899626568663 1642 1.28616014387759 1.44707946148432 1 1.50313749586992 3232 3496 1642 3520 1780 2356 2597 4256 2691 2141 4430 2726 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 0.349348936550466 0.471772079733569 1265 2696.90909090909 2692 0.0420677062888808 1249 0.381284871900292 0.436208024609609 1 0.277653592271719 1262 2826 3950 3988 2692 2054 1249 1932 4186 3493 2034 2727 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 0.629052925883464 0.742317303120099 2600 2588.54545454545 2692 0.0862097057951093 1172 0.653874098340854 0.653874098340854 1 0.188861277162433 2599 1172 2602 1636 2706 2692 1670 3588 3183 3686 2940 2728 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 0.441499346234167 0.564184874953179 2960 2452.09090909091 2692 0.0515768343745257 1415 1.6112180176146 1.6112180176146 1 0.893917694290376 2959 1415 1724 1789 2464 2712 2692 1541 2996 2750 3931 2729 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 0.0839184282471183 0.156982736433532 3675 2699.09090909091 2692 0.00793650793650794 562 1.75216959283669 2.16227886495905 1 3.14479062956458 3674 2692 1330 1770 4301 3504 2198 3797 562 1549 4313 2730 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 0.161385165508919 0.262241686633255 4455 2656.27272727273 2693 0.0158730158730159 802 1.2047179636419 1.27390153273309 1 1.56301797220425 4451 802 2629 1101 4366 2693 3821 4154 1314 1060 2828 2731 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 0.541771134667345 0.661537691281715 1370 3026.36363636364 2693 0.0684861574148561 1369 0.215397397542489 -0.22526863221015 -1 0.0862685209312356 1369 4454 3709 4560 2569 1388 2693 2617 4224 3633 2074 2732 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 0.0629849974478087 0.136679620044226 3590 2612.63636363636 2693 0.00589672617079003 622 0.458518343325958 -0.444172111946389 -1 0.884502147111643 3590 622 2693 1508 2915 2493 4586 762 2179 4484 2907 2733 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 0.0839184282471183 0.156982736433532 3400 2613 2694 0.00793650793650794 427 1.52086881633862 -1.38975139692581 -1 2.72965243886679 3399 4126 2694 3231 2067 2017 3302 4383 427 903 2194 2734 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 0.225912494172907 0.342154475660712 3385 2736.18181818182 2695 0.0230102547891621 817 1.01912862042896 -0.50491279453589 -1 1.05946670853417 3381 817 3040 1988 1885 4339 2666 2020 2865 2695 4402 2735 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 0.039025435684339 0.0957827093095062 1880 2396.45454545455 2697 0.00361230879381929 852 1.15097570173698 1.37139201081156 1 2.61696255356413 1877 3499 1008 3150 1533 3956 1904 852 3054 2831 2697 2736 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 0.298735036746822 0.4173739958842 2685 3021.36363636364 2698 0.0317460317460317 2075 1.48367074788666 1.64020850865261 1 1.25660798575173 2683 3554 2387 3913 2168 4540 2698 3365 2075 2085 3767 2737 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 6.74770900415305e-06 0.000110695373208895 1220 2379 2698 6.13429972764836e-07 266 1.43445605908482 1.5902657106768 1 12.6651072971682 1216 3154 266 1970 3865 2698 3473 2671 3075 881 2900 2738 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 0.121094879144119 0.212448747161865 3775 2835.81818181818 2700 0.0116658138773496 1507 1.40839380365713 1.40839380365713 1 2.1147287618643 3771 3722 3041 3442 1507 1596 4525 2428 2637 1825 2700 2739 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 0.275520116137161 0.39623750171336 3775 2645.45454545455 2700 0.0288750300452414 828 1.30821074699252 1.30821074699252 1 1.17390055955061 3772 3261 3413 2700 2309 828 1873 3776 2874 1782 2512 2740 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 0.627175175798618 0.741034511798368 2105 2973.90909090909 2700 0.0857901569995513 1896 0.28705209904849 -0.190311786895514 -1 0.0833917416303215 2103 2627 3503 3459 2700 4372 2107 1896 3249 4207 2490 2741 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 0.281641836996481 0.402984320050538 2260 2803.81818181818 2700 0.0296238949384739 843 0.277095774303471 -0.316820388731052 -1 0.24411227843519 2259 4233 2700 3678 2893 843 1807 1633 4540 4427 1829 2742 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 0.271361070652819 0.392105450841539 2620 2583.09090909091 2701 0.0283695323631168 957 0.300097024368703 -0.402606475970312 -1 0.272336305902101 2616 3030 3197 3622 2701 957 2624 1646 3606 3283 1132 2743 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 0.334469357991074 0.455443765580811 1980 2891.90909090909 2701 0.0363388101547052 922 0.858070626841244 -0.858070626841244 -1 0.654148358323844 1979 4515 3512 4219 4418 922 2701 1387 4289 2639 1230 2744 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 0.0234384414624293 0.0659654875032696 1235 2294 2701 0.00236893869298464 419 0.449610517672722 0.571647040272905 1 1.18481190443991 1235 2701 4354 2977 2778 1202 419 533 3476 4128 1431 2745 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 0.082003584215709 0.156982736433532 2705 2516.63636363636 2701 0.00774817175379499 1110 1.15286518606492 1.39497389587572 1 2.06916022801025 2701 3711 2237 3269 1263 1110 2955 2620 2934 2712 2171 2746 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 0.289168351685448 0.411491921044036 1520 2730.63636363636 2702 0.0305525993664519 1288 1.5941190509345 1.5941190509345 1 1.3720846387204 1516 3959 2352 4084 3306 2702 2196 1288 3696 2727 2211 2747 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 0.0239778030438993 0.0669107569086484 3610 2724.27272727273 2702 0.00220392687386412 661 1.44392116083834 1.5385344293411 1 3.78510173753739 3610 3222 1457 2702 661 2078 3841 3979 1543 2649 4225 2748 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 0.235295812343169 0.34804172242427 1615 2582.45454545455 2702 0.024092856169049 1397 1.00040222175546 1.06618932169826 1 1.02345593155007 1613 3861 2813 3404 1912 2588 1397 2702 2920 2997 2200 2749 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 0.161385165508919 0.262241686633255 2555 2684.63636363636 2703 0.0158730158730159 1518 1.75409214154257 1.75409214154257 1 2.27578373107475 2552 2140 3281 3381 2590 3033 2208 2916 1518 2703 3209 2750 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 0.0469948429025824 0.110108916920751 4065 2760.18181818182 2704 0.00436634548407669 976 0.97869468664073 1.06192370868845 1 2.0930170101822 4064 1820 3173 2363 976 1328 4517 4176 2704 3031 2210 2751 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 0.0672502503005387 0.14376581793263 2365 2943 2706 0.00693765609871331 1172 1.18308115364641 1.47096572781637 1 2.22425084087147 2363 4501 4620 4364 1210 1172 3964 2570 2706 3133 1770 2752 M938 REACTOME_CIRCADIAN_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CIRCADIAN_CLOCK.html Genes involved in Circadian Clock 29/72 Reactome 0.0427656726612148 0.102234604257268 2710 2438.27272727273 2707 0.00396548582667586 927 0.966120708920428 1.20248455500144 1 2.13561267484155 2709 1578 2036 2707 927 3881 2960 2897 2068 1662 3396 2753 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 0.527070556673984 0.646219944681918 1970 2941.09090909091 2708 0.0658082404573906 1273 0.27191247406092 -0.256649839643933 -1 0.115077921322826 1968 4361 3579 4101 2544 1273 2646 2708 3736 3438 1998 2754 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 0.35943518917414 0.478362197236587 4350 3062.90909090909 2709 0.0396825396825397 2006 0.938035501432942 -0.649810243057386 -1 0.670468959234844 4348 2280 2283 2709 4632 3785 2006 3250 2175 2673 3551 2755 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 0.0214370917212213 0.0617419863587233 2895 2456.81818181818 2710 0.00196807930420283 604 1.32488498816924 1.42290887023889 1 3.57630595308096 2894 3651 910 2732 1180 2582 3615 2710 1764 604 4383 2756 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 0.659648380205873 0.770907406051987 2635 2948.7 2710 0.112860370268014 1801 0.473208827404109 -0.473208827404109 -1 0.119344472999735 2634 2786 4428 NA 2969 1931 1801 2370 3997 4321 2250 2757 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 0.538603800061203 0.658293533408137 3685 2726.18181818182 2710 0.0679026485285462 1250 1.49234186417521 1.49234186417521 1 0.6048070875201 3685 3063 2529 3188 3802 1250 2710 2085 3040 2128 2508 2758 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 0.175080211909368 0.279531813631107 1705 2616.72727272727 2711 0.017345006109405 652 1.02032688010808 -0.761197380905 -1 1.26063817452936 1704 4407 3732 4081 3416 652 1921 2150 2909 2711 1101 2759 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 0.214139132665174 0.327605607466211 2890 2988.81818181818 2711 0.0238095238095238 1570 0.4126255096798 -0.206512631201288 -1 0.446336760036393 2889 2341 4651 2315 3469 3794 2711 1889 1570 4629 2619 2760 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 0.0273496721070238 0.0733603683420227 3385 2155.90909090909 2712 0.00251779199727673 74 1.22618745135201 1.22618745135201 1 3.10495749114037 3383 74 2712 969 705 2972 3120 3046 1270 1811 3653 2761 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 0.0509072473956659 0.116651032418626 3620 2890.90909090909 2715 0.00473862330711932 1052 1.31212748984869 -0.831099373833084 -1 2.73268196415268 3616 2365 1052 2065 3716 4555 2631 2715 2973 1926 4186 2762 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 0.00833447798347583 0.0303305908631064 1040 2420.90909090909 2715 0.000836590257099887 225 0.309840088255295 0.309840088255295 1 1.04983975633562 1036 2702 4498 2715 3610 494 225 3540 2956 4413 441 2763 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 0.282106559110666 0.403402909976375 1945 2661.09090909091 2716 0.029680980655082 1090 0.842335934484343 -0.842335934484343 -1 0.741222634308851 1941 3958 3363 3826 3676 1362 1090 2261 2716 3038 2041 2764 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 0.161385165508919 0.262241686633255 2890 2948.18181818182 2717 0.0158730158730159 1463 1.16268776010569 1.29381336121016 1 1.50848739700786 2887 2625 2717 2680 4100 3747 2390 3799 1463 1956 4066 2765 M17879 REACTOME_COMMON_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMMON_PATHWAY.html Genes involved in Common Pathway 6/15 Reactome 0.569065562748697 0.686394138234336 2720 2808.63636363636 2718 0.0807341639611571 1419 1.54796415353554 -1.54796415353554 -1 0.564628451618023 2718 2518 3988 2502 3038 2107 2736 4404 3803 1419 1662 2766 M9670 BIOCARTA_STRESS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STRESS_PATHWAY.html TNF/Stress Related Signaling 18/35 BioCarta 0.415320710913563 0.535769969181582 2270 2685.18181818182 2719 0.0476190476190476 1638 0.653874098340854 0.653874098340854 1 0.395528376331611 2267 2883 3304 2358 3850 2719 1638 2069 2323 3338 2788 2767 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 0.0477706848005899 0.111497102706558 985 2234.45454545455 2719 0.00444005874498987 362 1.72130338621463 1.72130338621463 1 3.66024152716199 3423 362 2719 981 983 3046 4239 3056 369 1918 3483 2768 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 0.0839184282471183 0.156982736433532 2550 2487.09090909091 2720 0.00793650793650794 696 1.9083122944764 1.9083122944764 1 3.4250352514408 2549 3343 2720 3074 2757 2771 1550 2454 696 2702 2742 2769 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 0.245744618819855 0.360651200685826 865 2401.54545454545 2720 0.0253126925016576 820 1.03069309216194 -1.03069309216194 -1 1.01888923224099 862 3893 2744 4218 3151 820 1259 1619 4055 2720 1076 2770 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 0.232850105696956 0.34496857265126 2720 2790.54545454545 2720 0.0238095238095238 1726 0.933528639692908 0.936150139411012 1 0.963066716724594 2827 2720 2985 2719 2615 3387 2071 3422 1726 2676 3548 2771 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 0.398712553370309 0.520291569226753 4440 2984 2721 0.0451908814873609 1555 1.14672566625037 1.14672566625037 1 0.726239511065916 4439 2721 1555 2533 3411 2358 2705 3567 3116 2661 3758 2772 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 0.421013275616371 0.541996760862174 1380 3012.54545454545 2721 0.0484657640241864 1063 0.209819302343177 -0.223264402744371 -1 0.124569589138851 1378 4482 3726 4566 2721 1063 2713 2668 4252 3703 1866 2773 M17157 REACTOME_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRUVATE_METABOLISM.html Genes involved in Pyruvate metabolism 8/19 Reactome 0.107322506994122 0.192245132941305 2725 2866.45454545455 2723 0.0112887893237037 1486 1.29142669460736 1.29142669460736 1 2.06419187210203 2723 2451 4035 3587 1486 4462 2347 2052 3228 1603 3557 2774 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 0.0839184282471183 0.156982736433532 3950 2350.45454545455 2723 0.00793650793650794 488 0.97280030978092 -0.719029057876656 -1 1.74598013289551 3947 599 2745 1210 2519 2796 3474 2894 488 2460 2723 2775 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 0.450902453903238 0.573555553184724 1560 2795 2723 0.0530396982606945 1557 0.595460272904305 -0.595460272904305 -1 0.320858616957119 1557 3335 2080 3783 2401 2723 1718 2414 3612 4262 2860 2776 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 0.0303531863229535 0.0790778668270892 2725 2685.90909090909 2724 0.00279820347367736 757 0.459105940757586 0.414450814359764 1 1.12915199799084 2724 1318 2441 2756 757 4634 2559 2326 2962 4046 3022 2777 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 0.00198202185895676 0.010117379554544 2840 2613.36363636364 2725 0.000180346341419813 660 1.32108180111162 1.44150828956841 1 5.88216702202244 2840 3821 660 2217 1405 4006 2725 4335 1530 794 4414 2778 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 0.100935947740148 0.183256819492574 3355 2664 2725 0.00962618683246379 492 0.329277805235423 -0.31752136154417 -1 0.541594265851166 3355 1519 2915 2725 2102 492 2548 3521 4179 4514 1434 2779 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 0.266353049995403 0.386418078104786 2370 2677.81818181818 2726 0.0277643180627858 1248 0.653874098340854 0.653874098340854 1 0.602647471365904 2368 3487 3011 2330 4035 2726 2031 1248 2108 3248 2864 2780 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 0.371215586752492 0.49194463787392 1010 2569.36363636364 2726 0.0413016523071936 1010 1.00702815359401 1.2283812076149 1 0.692452496540398 1010 3151 3758 3464 2241 1221 2430 2861 3388 2726 2013 2781 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 0.0839184282471183 0.156982736433532 2490 2620.27272727273 2731 0.00793650793650794 781 1.45471338835986 1.50767367499242 1 2.61091680342387 2488 3784 1968 3168 2731 4210 2757 2727 781 1325 2884 2782 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 0.298735036746822 0.4173739958842 3915 3025 2734 0.0317460317460317 1681 1.0177635111608 1.0177635111608 1 0.862003754879729 3912 2567 2734 1681 2283 4406 3675 3151 2011 2498 4357 2783 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 0.751985672431077 0.848905049629493 2700 2931.63636363636 2734 0.119047619047619 2039 0.806962431347047 -0.889829409089437 -1 0.128130382420444 2698 2039 2077 2734 3311 2978 2319 2627 3224 4498 3743 2784 M19943 BIOCARTA_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CERAMIDE_PATHWAY.html Ceramide Signaling Pathway 17/33 BioCarta 0.0839184282471183 0.156982736433532 3520 2512.54545454545 2735 0.00793650793650794 169 1.44922964151127 1.44922964151127 1 2.60107458508187 3519 2853 3026 1188 3268 3894 2545 2217 169 2224 2735 2785 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 0.415320710913563 0.535769969181582 2780 2797.63636363636 2735 0.0476190476190476 1985 0.81967232607814 -0.720626733536808 -1 0.495819707642979 2778 1985 2275 2471 3113 4260 2302 2860 2413 2735 3582 2786 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 0.298735036746822 0.4173739958842 1965 2664.63636363636 2735 0.0317460317460317 1668 1.40216611734945 1.40216611734945 1 1.18757692224721 2735 1668 1693 1962 3888 3340 3154 2791 2044 1965 4071 2787 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 0.0520496149738909 0.118630591326679 3335 2973.27272727273 2737 0.00484758639473886 1053 1.75114298357441 1.75114298357441 1 3.61842762001736 3334 2319 1053 1807 2656 4373 3643 4242 2404 2737 4138 2788 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 0.58407513250141 0.700352116402663 2545 2873.90909090909 2740 0.0766528995674462 1587 0.390165719068538 0.467897348380802 1 0.1347016161667 2544 1587 2740 3542 2635 2674 2195 3008 3497 4070 3121 2789 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 3.16491467341374e-05 0.00038755591864183 4245 2237.09090909091 2740 2.87723654974238e-06 35 1.06825565089056 -1.09057381194998 -1 8.1343192518712 4245 35 341 622 718 3097 3830 3531 1920 2740 3529 2790 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 0.394835615659736 0.51638283421198 1940 2613.09090909091 2742 0.0446328469485334 1281 1.86280643978199 1.86280643978199 1 1.19336104640343 1938 3162 2975 2453 4559 2867 1281 1552 2966 2742 2249 2791 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 0.0141566007793443 0.0446118569280479 3155 2188 2743 0.00142476019542555 103 0.849254971022537 0.849254971022537 1 2.55993078379417 3152 178 4460 470 505 1891 3009 3188 103 4369 2743 2792 M9379 REACTOME_SIGNAL_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_AMPLIFICATION.html Genes involved in Signal amplification 13/36 Reactome 0.514011397665828 0.633523779448203 2350 2979.27272727273 2744 0.0634920634920635 1978 1.46693471565438 1.46693471565438 1 0.649045631549796 2348 2202 2436 2939 4164 4648 3495 3184 2634 1978 2744 2793 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 0.0905033799266797 0.167165486139701 1520 2547.90909090909 2744 0.00858691973591591 1310 1.16171285364609 -0.881624310702625 -1 2.01426873304904 1518 3684 3690 3126 1310 1397 2982 2744 2292 3051 2233 2794 M6924 BIOCARTA_EIF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF2_PATHWAY.html Regulation of eIF2 4/16 BioCarta 0.207438229581607 0.320704567409901 2015 2540.27272727273 2745 0.022980319419485 1044 0.260170723339707 -0.334646302876335 -1 0.286795597877891 2011 2745 3857 3057 1883 1044 1110 3394 3942 3311 1589 2795 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 0.275742742869669 0.39623750171336 2850 2802.27272727273 2745 0.0317460317460317 1293 1.54796415353554 -1.54796415353554 -1 1.38903918210564 2849 2646 3925 3176 3777 2745 3558 2458 1854 1293 2544 2796 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 0.0526086044065729 0.119671805946214 1430 2435.27272727273 2745 0.0049009483017071 1056 1.21309609025737 1.2831280647759 1 2.4963732490669 1429 3368 1056 2768 2229 3576 1471 3730 1538 2878 2745 2797 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 0.181844292176137 0.288268725689235 3160 2595.45454545455 2745 0.0180802468079035 1322 1.45582614555272 1.63635472077414 1 1.75527689585894 3156 1505 1322 1699 2745 3986 3727 2038 2869 1386 4117 2798 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 0.514011397665828 0.633523779448203 1985 2892.54545454545 2746 0.0634920634920635 1926 1.58892302450077 1.58892302450077 1 0.703019389294097 1985 4171 2907 3700 4436 2746 1926 2813 2664 1997 2473 2799 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 0.0839184282471183 0.156982736433532 2535 2720.36363636364 2747 0.00793650793650794 1028 1.82051220676583 1.82051220676583 1 3.2674518221626 2532 3793 2619 3894 3163 1343 2969 3459 1028 2747 2377 2800 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 0.232850105696956 0.34496857265126 4260 2776 2749 0.0238095238095238 1703 1.40117763831214 1.65988366522898 1 1.44551274631398 4257 3149 2550 2117 2953 1703 3979 3164 1811 2749 2104 2801 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 0.161385165508919 0.262241686633255 2750 2885.09090909091 2749 0.0158730158730159 1152 1.05077947290469 1.05077947290469 1 1.36329601659839 2749 1152 3189 2367 2652 4249 4188 3427 1500 2593 3670 2802 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 0.633061865972455 0.745034700521015 1955 2942.81818181818 2749 0.0871119298442639 1838 1.00420244794833 -0.664904966411386 -1 0.286491362329171 1951 3634 2749 3593 4571 3189 2230 1838 3637 2327 2652 2803 M12467 KEGG_ERBB_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ERBB_SIGNALING_PATHWAY.html ErbB signaling pathway 41/90 KEGG 0.415320710913563 0.535769969181582 4050 3048.36363636364 2750 0.0476190476190476 1934 1.1326658119887 1.1326658119887 1 0.685149435844269 4046 1934 3391 2008 2338 3992 2750 4395 2380 2144 4154 2804 M7416 ST_GAQ_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GAQ_PATHWAY.html G alpha q Pathway 19/35 Signaling Transduction KE 0.0839184282471183 0.156982736433532 3950 2845.72727272727 2750 0.00793650793650794 650 1.13764843511991 -0.650112755713168 -1 2.04184923255555 3950 2044 2750 1856 4290 4108 2280 2963 650 2320 4092 2805 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 0.31901467892752 0.439838989184391 2750 2563.27272727273 2750 0.0343256307357257 895 0.322405395397993 -0.282823075022067 -1 0.256680339809744 2750 2817 2902 4049 2161 895 2035 1489 4065 3468 1565 2806 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 0.232850105696956 0.34496857265126 2340 2694.81818181818 2750 0.0238095238095238 1424 1.45457890123148 1.51696922221465 1 1.50060369560835 2337 2750 1424 2986 2462 4675 2975 2866 1828 2417 2923 2807 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 0.20659132540229 0.319606124409089 1130 2366 2752 0.0208181415637032 1005 0.554099100968402 -0.554099100968402 -1 0.612646237950021 1340 2806 1510 3493 3552 1005 2752 1129 3159 4151 1129 2808 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 0.0107988962045751 0.0367491849053295 4105 2383 2754 0.000986570063882783 819 1.16152565975617 1.09314191662433 1 3.71950622121895 4105 971 819 850 934 3311 4617 2952 1922 2754 2978 2809 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 0.572974542437215 0.689511737509191 1730 2876.18181818182 2755 0.0744393383266122 1310 0.244243313544383 -0.247536713952958 -1 0.0880162195579895 1728 4183 3461 3968 2755 1310 2249 2330 4402 3449 1803 2810 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 0.0431220065967024 0.102939237346993 4560 2852.81818181818 2755 0.00399919857193683 1021 1.16315579389878 1.22095698022548 1 2.56341514771408 4557 1633 1021 1447 3347 2755 4449 3651 2325 1547 4649 2811 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 0.161385165508919 0.262241686633255 4315 2430.72727272727 2756 0.0158730158730159 440 1.31488673670211 1.48057734419716 1 1.70595248258506 4313 467 2316 440 3591 2756 3680 4269 1196 677 3033 2812 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 0.0745295150828674 0.156471912042257 2385 2747.45454545455 2756 0.00701645424648514 1214 0.99047319569357 1.03268481295226 1 1.78082859874358 2382 3296 3270 3350 1214 4377 1479 2388 2045 2756 3665 2813 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 0.00109945016496701 0.00628295545492121 4315 2224.09090909091 2756 1e-04 27 1.65490954394716 1.77817130287813 1 8.1327755597854 4311 301 1063 27 2756 3745 3697 3685 355 505 4020 2814 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 0.580771018418383 0.69710373778395 3350 2901.72727272727 2757 0.083262219518189 1650 0.964244126337474 -0.964244126337474 -1 0.337242831829997 3349 1764 4095 2337 2676 1650 3387 2699 3443 3762 2757 2815 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 0.563264870660528 0.681307014583125 2760 2650.54545454545 2757 0.0725456191874759 1503 1.29733809947519 1.29733809947519 1 0.482565923322799 2757 2052 1784 1666 4360 3806 1503 3249 3047 2114 2818 2816 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 0.189684028513469 0.29907784576518 2100 2641.45454545455 2759 0.0189393549833277 1639 1.10446083513088 1.10446083513088 1 1.29223037434269 2100 2379 1639 1832 1777 3953 2897 2759 3529 3028 3163 2817 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 0.0839184282471183 0.156982736433532 2760 2732.27272727273 2759 0.00793650793650794 878 1.27307798895182 -1.03465537491335 -1 2.28491793641377 2759 2766 2851 2717 3843 4414 2667 2201 878 1335 3624 2818 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 0.481063017846562 0.600976086811248 2260 3012.54545454545 2759 0.0634920634920635 1705 0.766202821784505 0.863879680911117 1 0.378177879567681 2257 1705 4609 2497 3179 2759 3379 2515 2585 4577 3076 2819 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 0.239824789103714 0.353384627016996 3170 2808.81818181818 2760 0.02461971519306 1922 2.01277540612347 2.01277540612347 1 2.02943567080028 3168 3049 2006 2214 1922 4617 2865 2760 1992 2358 3946 2820 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 0.298735036746822 0.4173739958842 3350 2967.18181818182 2763 0.0317460317460317 1750 1.30405248421144 1.47922930375639 1 1.1044787179468 3347 2173 2919 1750 2763 3582 2760 4052 2029 2684 4580 2821 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 0.47746730603857 0.598078534107655 1320 2671.45454545455 2764 0.0572990348928455 1316 1.12777840085744 -0.921470686114906 -1 0.561925593956274 1316 3820 2764 3688 2456 1511 3185 2125 3305 3004 2212 2822 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 0.316997872904718 0.437799007495286 1465 2616.90909090909 2764 0.0340659854353368 1075 0.343144756110947 -0.41816048125488 -1 0.274738068366014 1463 3511 3436 3491 2764 1075 2420 1329 3326 4263 1708 2823 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 0.19293548927371 0.302676833858924 2535 2808.63636363636 2765 0.0192978810208434 1790 1.10858603309022 1.10858603309022 1 1.28420316176219 2531 2626 2993 2983 1790 3196 4404 1984 2912 2765 2711 2824 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 0.0747957570297809 0.156960554161018 2765 2667.36363636364 2765 0.0077439362864025 746 0.561890593218289 0.539090917821983 1 1.008557126809 2765 746 4240 1982 4607 3016 2793 831 2117 3974 2270 2825 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 0.175167851602395 0.279576482496192 1130 2440.63636363636 2765 0.0190732951947329 913 0.49444485148159 0.49444485148159 1 0.610821815518191 1130 3360 4262 2765 4304 969 913 1318 2824 4005 997 2826 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 0.0196586691369534 0.0581568961968204 2540 2661.81818181818 2765 0.00180332397749177 576 0.812255764615737 0.812255764615737 1 2.23964675308109 2537 2903 2765 2442 576 3024 1938 4062 1781 4188 3064 2827 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 0.0307139616238815 0.0796489342387984 3725 2888.36363636364 2765 0.00283193896581096 767 1.19656361150273 1.2829487886985 1 2.93455270531031 3724 3685 2647 2364 767 2871 2527 4588 2765 1471 4363 2828 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 0.0839184282471183 0.156982736433532 4170 2784.54545454545 2765 0.00793650793650794 1024 1.44339499496624 1.76336270336434 1 2.5906025726367 4166 1928 2460 1920 3372 2765 2864 3723 1024 2654 3754 2829 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 0.0839184282471183 0.156982736433532 2865 2746.63636363636 2766 0.00793650793650794 398 1.31212748984869 -0.831099373833084 -1 2.35500390584032 2863 1528 2766 1761 4305 4231 2413 4319 398 2275 3354 2830 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 0.307392033515668 0.426796761201309 2215 3138.63636363636 2766 0.0360627833792119 1346 0.138751833568008 0.184543675896049 1 0.114514476941289 2213 4533 3990 4390 2766 2237 2513 1346 4661 3549 2327 2831 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 0.156982736433532 3820 2565.45454545455 2766 0.00793650793650794 713 1.13518592994862 1.00790319646002 1 2.03742953299002 3818 999 2484 1621 4606 2766 3446 3092 713 1489 3186 2832 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 0.319152065693524 0.439838989184391 2215 3141.81818181818 2767 0.0377121277144982 1367 0.138751833568008 0.184543675896049 1 0.110466103480137 2214 4534 3991 4391 2767 2238 2514 1367 4662 3554 2328 2833 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 0.00345148507656035 0.0155217457473721 3180 2807.81818181818 2767 0.000314264716887637 707 1.36576071868307 1.47497953358969 1 5.51451100417583 3180 2497 707 1584 3156 4428 2767 3981 2614 1355 4617 2834 M6370 KEGG_P53_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_P53_SIGNALING_PATHWAY.html p53 signaling pathway 47/91 KEGG 0.23812405640344 0.351227361758426 1275 2413.09090909091 2769 0.0244215340201146 1068 1.45679295634334 1.45679295634334 1 1.47749783386322 1273 3005 2049 3040 2769 2893 2267 2801 3023 2356 1068 2835 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 0.124948805738016 0.217788597952299 3875 2660.36363636364 2769 0.0120605798803777 544 1.13582086241524 1.16134365920121 1 1.67812509704012 3873 2344 2351 2769 1998 544 3437 3892 3196 2985 1875 2836 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 0.0839184282471183 0.156982736433532 3975 2976.45454545455 2769 0.00793650793650794 270 2.46711003640163 2.46711003640163 1 4.4279643685023 3973 2769 2007 2507 3791 4200 4524 1774 270 2330 4596 2837 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 0.0725371890548876 0.152666808787865 2510 2329.54545454545 2769 0.00682231085796366 757 1.45205957819474 1.46778240338295 1 2.64539204541788 2507 3891 1125 2831 1204 3438 2938 1243 2769 757 2922 2838 M699 KEGG_FATTY_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FATTY_ACID_METABOLISM.html Fatty acid metabolism 22/56 KEGG 0.16680787180564 0.269538512855596 2715 2698.54545454545 2770 0.0164532347717067 927 0.967459383376804 -0.967459383376804 -1 1.22945849614586 2714 2568 2906 2770 3216 1631 4378 2898 2512 3164 927 2839 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 0.268561230162525 0.389260106570242 2770 2654.81818181818 2770 0.0280307100514835 1253 1.18839467061699 1.18839467061699 1 1.08685077719591 2770 3231 2350 3445 4109 3249 1482 1253 2370 1826 3118 2840 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 0.63389956273523 0.745034700521015 2775 2988.27272727273 2770 0.0873015873015873 2114 1.09314191662433 1.09314191662433 1 0.311865119988315 2774 2658 2513 2114 2715 3229 2751 4621 3017 2770 3709 2841 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 0.0213456445082324 0.061516414615976 1705 2750.18181818182 2770 0.00215534964430368 656 1.17386145337374 1.22276918421266 1 3.1728077790256 1705 2615 4311 2881 656 4632 2603 2797 2770 2158 3124 2842 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 0.34273349471767 0.464713297525175 2540 2946.1 2770 0.045559069069855 1481 0.430882046621367 0.430882046621367 1 0.320066864267915 2538 3253 4367 NA 3002 2338 2122 1481 4131 4152 2077 2843 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 0.00341560391269429 0.01543444545312 4040 2664.18181818182 2771 0.00031099257763463 194 0.839093290538921 -0.55936453995665 -1 3.39258151896074 4038 1629 2960 1914 194 1932 4663 3842 2771 2817 2546 2844 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 0.0820814005603009 0.156982736433532 2500 2485.09090909091 2771 0.00775581848452589 444 1.02842397181928 -0.794509103745665 -1 1.84581337499785 2500 2787 3627 3109 2977 444 2729 2771 2552 3033 807 2845 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 0.0462915972121724 0.109006243485548 2625 2623.36363636364 2773 0.00429957675885484 968 1.1441707465227 1.27121825579722 1 2.45806335934002 2621 2220 2305 2773 968 2806 2996 3003 2665 2811 3689 2846 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 0.466738071388703 0.587219019917277 2225 2976.09090909091 2774 0.0555555555555556 1683 1.19463888943587 1.19463888943587 1 0.616458462627597 2221 3801 3259 3625 4575 2595 1683 3271 2477 2456 2774 2847 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 1.77145096915801e-06 3.60913880064106e-05 3740 2273.54545454545 2774 1.61041126867343e-07 220 1.42067022822832 1.56935556914473 1 14.0867139575539 3740 959 220 1198 2774 3374 3635 3660 1447 269 3733 2848 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 0.0199901606404283 0.0588403849001551 3130 2464.45454545455 2776 0.00183401315738334 497 1.00773969396223 1.16246625514058 1 2.7672448680026 3126 1707 3767 1895 586 497 4408 3771 2776 3116 1460 2849 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 0.0839184282471183 0.156982736433532 2915 2605.45454545455 2776 0.00793650793650794 540 1.64744387553662 1.64744387553662 1 2.9568291127132 2911 2798 3517 2776 3673 4078 1767 2157 540 2012 2431 2850 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 0.93414655179802 0.98846022445738 2260 3033.27272727273 2776 0.219095280951702 2171 0.337438800235958 -0.343334233165864 -1 0.00379641951544264 2258 3170 2776 2877 3652 2171 2512 2572 4200 4502 2676 2851 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 0.0059491862753375 0.0235853526956273 950 2275.18181818182 2776 0.000542303189970234 178 0.94471558711355 0.94471558711355 1 3.43133909774733 947 2659 2965 3198 4154 392 178 4280 2993 2776 485 2852 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 0.622475660662716 0.736843913260302 2390 2863.72727272727 2777 0.0928178514536999 1466 0.212609797127865 -0.212609797127865 -1 0.0629341810976919 2387 3426 3824 4113 2777 1466 2042 1951 4425 3252 1838 2853 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 0.557443745451391 0.675680649556446 2360 2649.72727272727 2777 0.0714285714285714 2132 1.14672566625037 1.14672566625037 1 0.435760577223175 2359 2807 3157 2370 2603 2936 2840 2132 2777 2283 2883 2854 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 0.0607090453280894 0.132935788040854 2895 2652.90909090909 2780 0.00624342748994091 1163 0.646118488205991 -0.646118488205991 -1 1.26378536233066 2895 2780 4398 1707 1163 1595 3270 3155 2610 4237 1372 2855 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 0.604832218088227 0.718803899051846 2340 3022.27272727273 2781 0.0809401892867531 1360 0.315388697736494 -0.319864395503442 -1 0.100935342275818 2339 4296 2290 4467 3359 1360 1939 2781 4436 4159 1819 2856 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 0.081015199517966 0.156982736433532 3315 2907.36363636364 2781 0.00765109800518786 1132 1.4161450122637 1.4161450122637 1 2.54169435586824 3314 2966 1132 2255 2322 4585 2913 2508 2693 2781 4512 2857 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 0.0297514196099984 0.0779290957475978 880 2133.90909090909 2782 0.0030157406781975 413 0.681111565817195 0.681111565817195 1 1.68482688970449 879 2782 3864 2801 3267 547 413 737 4066 3319 798 2858 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 0.161385165508919 0.262241686633255 2275 2674.81818181818 2782 0.0158730158730159 1150 0.497555884531438 0.497325057111023 1 0.645535978624386 2273 3980 1699 3011 4329 2792 1455 1797 1150 4155 2782 2859 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 0.0101423522466062 0.0351531528310627 3295 2676.18181818182 2782 0.000926310376725839 385 1.04657246085035 1.04657246085035 1 3.39643988523762 3294 1369 1971 1997 385 3877 3317 4236 2782 2499 3711 2860 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 0.0765897756730953 0.156982736433532 2785 2709.36363636364 2782 0.00793650793650794 555 1.31394404283802 1.31394404283802 1 2.35826425166672 2782 1017 4605 770 3914 4658 3962 3175 555 1720 2645 2861 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 0.196217873374943 0.306696782733484 2950 2564.81818181818 2783 0.0196611512292189 732 0.756082393928615 -0.769520701083661 -1 0.866187960496852 2947 1880 3448 2437 2582 732 2948 2783 3623 3848 985 2862 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 0.322048702785568 0.442557249634361 2095 2703.63636363636 2783 0.0347175534028078 1730 1.12012404883419 1.17315734045688 1 0.885087901740553 2094 3052 1730 3182 2132 3521 2063 3787 3245 2151 2783 2863 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 0.0839184282471183 0.156982736433532 3855 2735.63636363636 2783 0.00793650793650794 505 0.628598725631089 0.553685285430995 1 1.12820778883912 3853 505 1160 1759 1313 4189 2783 4636 758 4630 4506 2864 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 0.514011397665828 0.633523779448203 3550 3242.27272727273 2784 0.0634920634920635 2141 1.36172616824467 -1.36172616824467 -1 0.602496083447839 3549 2141 2168 2784 4643 4314 2315 4109 2678 2638 4326 2865 M17844 KEGG_OTHER_GLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OTHER_GLYCAN_DEGRADATION.html Other glycan degradation 7/17 KEGG 0.0765897756730953 0.156982736433532 3110 2402.36363636364 2785 0.00793650793650794 71 2.06322935667965 2.06322935667965 1 3.70308009800365 3107 2112 3791 777 3054 3788 3771 1673 71 1497 2785 2866 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 0.00362293865675654 0.0161072965327904 2790 2559.36363636364 2786 0.0003628858803247 217 0.482581210251915 -0.482581210251915 -1 1.93118893879199 2786 2920 4112 2851 217 1918 2217 2528 3486 3790 1328 2867 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 0.514011397665828 0.633523779448203 2790 3186.09090909091 2788 0.0634920634920635 1829 1.0801494289028 1.0801494289028 1 0.477912384736146 2788 2385 2640 2730 4519 3554 4165 4497 2695 1829 3245 2868 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 0.173780088295409 0.278214381193128 3405 2905.72727272727 2788 0.0172043137927126 1734 1.15854686737298 1.26112455801819 1 1.43671744120823 3404 2346 1849 3079 1734 1771 4395 3438 2788 2758 4401 2869 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 0.557443745451391 0.675680649556446 2680 2865.27272727273 2789 0.0714285714285714 1484 1.30628405292381 1.30628405292381 1 0.496393435403948 2680 2192 2070 3163 3518 4395 2741 3232 2789 1484 3254 2870 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 0.431080596982819 0.553285039019855 2630 2917.54545454545 2789 0.0499818862070291 1592 1.01363330904942 1.04677688443947 1 0.581540344371678 2626 2789 1592 2531 2399 3902 2570 3368 3238 2929 4149 2871 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 0.549896454323257 0.669824482703089 3620 2745.36363636364 2791 0.07 934 0.715858725339802 0.715858725339802 1 0.278069536680527 3620 934 2736 1762 3939 2137 3445 2096 3046 3693 2791 2872 M16811 BIOCARTA_ERK5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK5_PATHWAY.html Role of Erk5 in Neuronal Survival 16/34 BioCarta 0.611344812571277 0.725807395923234 2270 2949.54545454545 2792 0.0823275810894427 1578 0.294774995256508 0.385858130295113 1 0.0915677814932766 2270 2737 3374 2792 3856 3381 1578 2483 3924 3316 2734 2873 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 0.0110364196747025 0.037313609376375 2795 2750.63636363636 2793 0.00100837967811491 404 1.51430131785667 1.51430131785667 1 4.8268125167758 2793 3067 2214 2600 404 3617 3231 4574 2500 1990 3267 2874 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 0.0116354377506143 0.0387842420158297 3070 2212.36363636364 2794 0.00106340320051229 412 1.06368982576848 1.20316816416778 1 3.35063911494539 3068 423 1666 1362 412 3001 3174 2936 835 2794 4665 2875 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 0.0424790252215335 0.101819290121793 4185 2809.36363636364 2794 0.00393837439835892 822 1.43454520164166 1.58798837464519 1 3.17672671079365 4182 3365 2365 2794 922 2664 4148 3829 1787 822 4025 2876 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 0.0223475228159713 0.0637845357792673 4180 2449.63636363636 2795 0.00205252816802149 629 1.18236175787136 1.18236175787136 1 3.15428734561507 4179 819 1894 1113 629 3038 3845 2840 2795 1575 4219 2877 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 0.434395662020919 0.556929705124495 2800 2696.72727272727 2796 0.0504864702801919 1150 0.397206042509529 -0.478376500300057 -1 0.225356606182871 2796 3344 1597 3061 2758 1150 2823 2500 3842 4143 1650 2878 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 0.125666670020574 0.218749634367165 3440 2703.36363636364 2796 0.0121342868428069 545 0.909058171142616 1.12484932925378 1 1.33921349785681 3438 4354 2594 4285 1624 545 2796 1982 3067 3110 1942 2879 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 0.35943518917414 0.478362197236587 3060 2718.18181818182 2797 0.0396825396825397 1442 2.24458518468169 2.24458518468169 1 1.60433660615491 3060 2797 2650 1442 4455 1501 3512 3236 2198 2833 2216 2880 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 0.35943518917414 0.478362197236587 2720 2995.36363636364 2797 0.0396825396825397 2164 1.73041933125535 1.73041933125535 1 1.23683213095426 2719 3381 2176 2513 3772 3777 2797 4146 2214 2164 3290 2881 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 0.107781843060647 0.192920441780823 2800 3002.27272727273 2797 0.0103141321736321 896 2.19775722972283 2.19775722972283 1 3.50538322121017 2797 4298 2407 3831 4240 4337 2003 896 2547 2602 3067 2882 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 0.318121584981412 0.439019428093532 2570 3079.18181818182 2798 0.0342105669497387 964 0.252496725925367 -0.244712961600212 -1 0.201479611361952 2568 4434 2798 4597 2123 964 2281 3978 4535 3981 1612 2883 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 0.653783455066693 0.765907317610631 2430 3048.90909090909 2798 0.0919233073364462 1435 0.325038290953723 -0.311884873819382 -1 0.0840256379774768 2430 4373 2142 4149 3099 1435 2798 2673 4106 4420 1913 2884 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 0.232850105696956 0.34496857265126 3825 2963.81818181818 2798 0.0238095238095238 1606 1.08196515182584 1.08196515182584 1 1.11619995583356 3825 2391 2625 2798 3362 3551 1606 4293 1813 2345 3993 2885 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 0.020140571347794 0.0590975061588995 4585 2937.45454545455 2799 0.00184794115548849 899 2.1280738141516 2.1280738141516 1 5.83467883079063 4583 3123 899 2292 2799 3809 4516 2163 1506 2478 4144 2886 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 0.0581072075122561 0.128480013014895 4280 2876.72727272727 2800 0.00542738363427331 906 1.24049609062159 -1.01405746558881 -1 2.46736157707865 4278 2482 2029 2800 1089 3440 4131 3945 1979 906 4565 2887 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 0.281239716970652 0.402654846845242 2805 2599.90909090909 2802 0.0295745262487528 1710 1.00879090831687 1.00879090831687 1 0.889511453237239 2802 2990 2844 1710 2032 2870 2528 3676 3317 1933 1897 2888 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 0.0839184282471183 0.156982736433532 4665 3019.09090909091 2804 0.00793650793650794 564 1.23889395501682 -1.23889395501682 -1 2.22356449777261 4665 2804 3078 2175 3387 4035 4554 2713 564 2462 2773 2889 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 0.209805696591424 0.323510856935642 2135 2812.63636363636 2804 0.0211794439636327 1140 1.29064118907003 1.29064118907003 1 1.41182103901077 2133 4217 2015 4190 4489 1940 2079 1140 2943 2804 2989 2890 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 0.213681482018864 0.327605607466211 2585 2869.90909090909 2805 0.0216168718090618 1357 0.460835813567097 -0.464322103592069 -1 0.498485816111666 2583 4060 1357 3806 3039 1630 2805 2933 2783 4467 2106 2891 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 0.026527807685325 0.0720633662686569 2810 2245.36363636364 2805 0.00244119898150081 384 1.41337415658459 1.41337415658459 1 3.60339065115277 2808 2426 3565 3501 692 384 1495 3468 3086 2805 469 2892 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 0.136437048838203 0.234191945368432 2160 2719.81818181818 2806 0.0132467951107981 568 0.991049482482797 -1.00481146656745 -1 1.39447399312051 2158 3783 3465 4275 4392 568 1983 2471 2806 3002 1015 2893 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 0.31070844165776 0.430508503136684 2145 2782.18181818182 2807 0.0332607310793825 1490 0.680644994905029 -0.680644994905029 -1 0.556036075476442 2144 3054 3380 3395 2101 1490 2617 2807 4052 3456 2108 2894 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 0.237028333449422 0.35016228579571 4245 2896.81818181818 2807 0.0242940656954744 1384 1.68878386369571 1.68878386369571 1 1.71775746858326 4243 2531 1384 2069 2807 3183 3807 3259 2166 2307 4109 2895 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 0.00301501096568015 0.0141522050651613 2810 2930 2808 0.000274468260123139 691 1.59301588539975 1.74940501090549 1 6.57472939914217 2809 2260 691 2708 3682 4506 4308 1638 2808 2416 4404 2896 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 0.20622752103524 0.319254100948508 2180 2846.36363636364 2809 0.0207773330162769 1353 1.09875256957753 1.09875256957753 1 1.2160225072919 2177 2239 1353 3208 2809 4434 2779 4663 3243 1375 3030 2897 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 0.0479233774758325 0.11167028684821 3995 3013.81818181818 2810 0.00445457260873853 985 1.14672566625037 1.14672566625037 1 2.43671359939554 3991 2810 2291 2787 985 3457 4393 2051 3671 2100 4616 2898 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 0.0174124654277678 0.0526757992217689 1055 2415.27272727273 2811 0.00175504265782681 328 0.724095453604658 0.724095453604658 1 2.06603823747971 1055 3357 4264 2568 3337 722 328 2811 3575 4007 544 2899 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 0.0966309362629812 0.176741829558286 2115 2955.63636363636 2811 0.00919601027185944 1165 0.429720194028343 -0.23238410756994 -1 0.721879204565814 2111 3025 1165 3654 4472 2811 2761 1447 4007 4269 2790 2900 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 0.353651444904065 0.476620842916436 2905 2755 2812 0.0388974987825065 1440 1.17163240951516 -0.921158737630447 -1 0.841576048965081 2905 3828 2396 3847 2205 1440 3107 2596 3343 2812 1826 2901 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 0.283262573184701 0.404562151156204 2480 3000.36363636364 2813 0.0327560803364949 1806 0.421122935151296 -0.286501919340572 -1 0.369400347122372 2480 1806 4492 2808 2089 2320 2813 3938 2955 4402 2901 2902 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 0.232850105696956 0.34496857265126 3610 2924.36363636364 2814 0.0238095238095238 1362 2.24458518468169 2.24458518468169 1 2.31560681958926 3606 1362 3161 1477 4523 2014 4460 4334 1630 2787 2814 2903 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 0.232850105696956 0.34496857265126 3560 2928.36363636364 2814 0.0238095238095238 1645 1.21359955867233 1.38747661230396 1 1.25199944888914 3559 2678 2561 2479 3592 2974 3618 2814 1730 1645 4562 2904 M18009 KEGG_CIRCADIAN_RHYTHM_MAMMAL http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CIRCADIAN_RHYTHM_MAMMAL.html Circadian rhythm - mammal 7/14 KEGG 0.000147970512684516 0.00132833299317939 3610 2275.45454545455 2815 1.47980366480654e-05 30 0.493393016758395 -0.493393016758395 -1 3.16786069690228 3609 167 3808 420 30 3083 2410 2815 1148 3216 4324 2905 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 0.161385165508919 0.262241686633255 2385 2761.09090909091 2815 0.0158730158730159 1547 1.25473373235594 -0.839763914023628 -1 1.62790913159434 2385 2898 3664 3066 3473 2815 2566 2551 1547 2828 2579 2906 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 0.397190721982489 0.518901380344198 2820 3151.90909090909 2816 0.0493558220049476 2154 0.366045577558714 -0.410794029808841 -1 0.232771764255643 2816 2516 4582 3388 2357 2154 3401 2611 4089 4540 2217 2907 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 0.00474264309147766 0.0197472522694823 2820 2109.54545454545 2817 0.000432081635687789 164 1.50837308917194 -0.680644994905029 -1 5.73830509658622 1715 3334 3135 2817 3178 172 1291 2817 1539 3043 164 2908 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 0.250140191620232 0.366413547337421 3380 2785.81818181818 2817 0.0258304457874638 1004 0.9282856402567 -0.9282856402567 -1 0.903391586558814 3380 1004 2496 2925 1951 2817 3589 2463 2856 4563 2600 2909 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 0.466792754842479 0.587219019917277 2650 3077.09090909091 2818 0.0555643603522537 1824 2.13935923834372 -3.11553755502548 -1 1.10395377116625 2649 3655 1824 4138 2431 4583 2758 2285 2818 2914 3793 2910 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 0.290474451655906 0.413099629881511 2450 2840.36363636364 2819 0.0307146699598109 1531 1.53334444632203 1.53334444632203 1 1.31397927439654 2447 3341 3711 3904 2050 1531 3137 3564 2376 2819 2364 2911 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 0.11776146226362 0.207767399159385 2510 3026.27272727273 2819 0.0113256319599702 1487 1.3134446444421 1.40274072534865 1 2.00052843021815 2509 4686 3092 4246 1487 2565 2489 2879 2819 2689 3828 2912 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 0.00897432795799184 0.0318964689257877 1120 2267.27272727273 2819 0.000819195167093763 111 0.780328806349212 -0.780328806349212 -1 2.60593454647461 1117 3870 2819 2974 3119 111 577 1839 4039 4135 340 2913 M18933 BIOCARTA_TGFB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TGFB_PATHWAY.html TGF beta signaling pathway 13/26 BioCarta 0.00394789605657151 0.0171330712423181 4465 2575.18181818182 2821 0.000359545308961986 216 1.00744291305309 1.00744291305309 1 3.97128651117058 4463 942 2821 1359 216 3059 3856 4047 1980 1971 3613 2914 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 0.106377312947634 0.190843831727646 2825 2642.72727272727 2821 0.0101726003430377 905 1.1326658119887 1.1326658119887 1 1.81846360245359 2821 905 3260 1479 1417 3946 2967 4380 1496 2435 3964 2915 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 0.385267694019764 0.507632574048261 1665 2678.36363636364 2822 0.047492061922532 1283 0.400991843764993 -0.472586681576832 -1 0.263528394252387 1661 2822 3799 3876 4667 1283 1603 1738 3456 3183 1374 2916 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 0.537389519429773 0.657152215043819 2680 2908 2823 0.0741906836090173 1911 0.247196277627603 -0.265315631035903 -1 0.100597965455316 2676 2823 3789 3286 2616 1911 2536 2407 3934 3168 2842 2917 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 0.0133826882119755 0.0428063323968036 3645 2361.63636363636 2824 0.00134639713495239 43 1.4286533293001 1.38330456261246 1 4.36363753735323 3645 2824 4418 733 1697 3870 3857 456 43 207 4228 2918 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 0.161385165508919 0.262241686633255 2825 2796.36363636364 2824 0.0158730158730159 1520 1.64216404686053 1.64216404686053 1 2.13056665216174 2824 2143 1554 2890 3487 3984 3229 2651 1520 2629 3849 2919 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 0.0441167408383351 0.104939618055045 2825 2390.27272727273 2825 0.00409337079175828 382 0.962655895728519 -0.957021000262823 -1 2.1035854987347 2825 4040 3703 3225 942 382 3323 1483 2667 3093 610 2920 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 0.0842029293648123 0.157389280815122 2750 2912.81818181818 2826 0.00796452082727738 1274 0.906893028416767 0.969525401965631 1 1.62541626953593 2748 2268 2949 2079 1274 4531 2186 2826 3348 3825 4007 2921 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 0.0138458005002723 0.0439874041656108 4355 2755.09090909091 2826 0.0013932832445942 497 1.07312695996487 1.07312695996487 1 3.24941675420225 4353 1254 4604 2086 497 3316 3173 2001 2826 1528 4668 2922 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 0.514011397665828 0.633523779448203 2555 3119.36363636364 2827 0.0634920634920635 1740 1.18252485680283 -0.842384065313259 -1 0.52320841840281 2555 4175 1740 3692 3800 4287 2827 2492 2660 2259 3826 2923 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 0.562604368603265 0.680703349154377 3750 3332.45454545455 2827 0.0793650793650794 2528 0.400899524419008 -0.490612265016718 -1 0.149465537892487 3747 2779 4636 2608 2762 2528 4055 3284 2827 4615 2816 2924 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 0.0839184282471183 0.156982736433532 3350 2724.63636363636 2828 0.00793650793650794 373 1.31505585488108 1.31505585488108 1 2.36025972979238 3348 2732 2253 2303 3231 2828 3038 3413 373 2282 4170 2925 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 0.481063017846562 0.600976086811248 2830 2870.54545454545 2829 0.0634920634920635 1681 0.964916235402726 -0.810865129405406 -1 0.476257676832314 2829 2488 3800 1872 4580 2027 2858 3555 2588 1681 3298 2926 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 0.452020755709807 0.574563816953485 2545 2931.72727272727 2829 0.0532151877008812 1356 0.316123086182784 -0.285996076849723 -1 0.1698019982007 2545 3136 2796 2829 4124 2353 1356 2421 4045 3471 3173 2927 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 0.0154375157128566 0.0476235672353166 1470 2649.54545454545 2829 0.00155458187132619 307 0.236832839668598 0.273354355597119 1 0.698894187795135 1468 2829 4387 4055 2982 1805 307 1526 3999 4202 1585 2928 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 0.0564167239185913 0.126009899086043 3020 2338.27272727273 2830 0.00579023709849997 417 1.23964937559548 -0.973553175042663 -1 2.48900412257029 3020 2830 4621 2332 1125 417 3373 2848 954 2977 1224 2929 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 0.597888529527147 0.711634658207826 3070 2706.63636363636 2831 0.0794836716636962 1350 0.80434330357106 0.85322032193671 1 0.26523305694728 2831 1569 2786 1821 2897 1350 3066 4277 3066 4260 1850 2930 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 0.0839184282471183 0.156982736433532 3375 2614.36363636364 2832 0.00793650793650794 702 1.27517108592419 1.25816905429598 1 2.28867462285132 3371 1782 2843 2968 1409 3928 2832 2736 702 1812 4375 2931 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 0.615276344951224 0.729366292041851 2270 2750.09090909091 2833 0.0911025415481602 1431 0.314354729857548 -0.47555983741253 -1 0.0961595132339499 2266 3035 3883 3506 2833 1431 1956 2260 3857 3343 1881 2932 M565 REACTOME_BETA_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BETA_DEFENSINS.html Genes involved in Beta defensins 8/55 Reactome 0.261603165468169 0.380469408250727 2835 2614 2833 0.0298721269369012 607 1.2843873410506 -1.27233357232047 -1 1.20307890101933 2833 3294 3931 2595 2850 2332 2856 3204 1851 607 2401 2933 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 0.237932784644282 0.351055739560172 3890 2997.54545454545 2834 0.0243992708729487 1607 1.32122805867268 1.48589460062819 1 1.34063214103465 3889 4249 1607 2834 1916 2379 3694 3972 2674 1646 4113 2934 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 0.258776633786509 0.376943520647679 2645 2974.27272727273 2834 0.0268558168536785 1423 1.42267534279842 1.42267534279842 1 1.34545176600679 2642 3703 1423 2982 4520 2834 1443 4613 3901 1850 2806 2935 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 0.161385165508919 0.262241686633255 3515 2799.45454545455 2834 0.0158730158730159 1441 1.254594693849 1.254594693849 1 1.62772874108656 3511 2834 2692 3020 2533 3169 3053 1871 1441 2202 4468 2936 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 0.63389956273523 0.745034700521015 2400 2867.81818181818 2835 0.0873015873015873 1668 0.891470220575415 0.891470220575415 1 0.2543297105865 2397 2835 3633 2539 4208 2812 1668 2870 3004 3008 2572 2937 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 0.046659536545308 0.109432726852509 4360 2444.63636363636 2835 0.00433450468383736 309 0.944200542301551 -0.98680981236176 -1 2.02488634044918 4356 309 1641 813 975 3798 3933 2980 1735 2835 3516 2938 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 0.0117432015685606 0.0390274060640249 3100 2542.63636363636 2835 0.00107330519243615 416 1.1244153084194 1.10540098152967 1 3.53511327456639 3098 1336 1732 2475 416 2861 2835 3977 2915 1884 4440 2939 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 0.00602999616696246 0.0237649806882978 3600 2876 2836 0.000604642131353867 302 1.45023161899474 1.45023161899474 1 5.25677842888623 3599 2610 4408 1469 302 4673 3903 2836 2745 1711 3380 2940 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 0.119930646971085 0.21103830706215 4185 2903.63636363636 2836 0.0115468685506663 1224 0.637090095641508 -0.672409811867713 -1 0.960715791632637 4183 2005 1224 2133 4218 1363 2533 3388 2836 4297 3760 2941 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 0.161047035038019 0.262241686633255 2150 2509 2837 0.0158369496517888 705 0.631262575792853 -0.631262575792853 -1 0.819008914005482 2149 2837 3428 3509 1675 705 3075 1975 3712 3373 1161 2942 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 0.563394084829196 0.681307014583125 2840 3227.81818181818 2838 0.0725705680239102 1287 0.308343061790865 -0.245329864543456 -1 0.114693196994563 3849 4416 2838 4403 2798 1287 2605 2838 4020 4107 2345 2943 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 0.0278439058069627 0.0740900013286198 975 2115 2838 0.00256388005641579 239 0.868067862247035 -0.564322045552235 -1 2.18979801936533 975 2838 3569 4110 3280 239 1070 804 3031 2934 415 2944 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 0.306513760776868 0.425955955812693 1865 2835.54545454545 2839 0.0327273786168122 879 0.233148645969372 -0.236434857241989 -1 0.192867582954514 1865 4116 3214 3868 2839 879 2355 2083 4525 3755 1692 2945 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 0.298735036746822 0.4173739958842 3025 2957.81818181818 2839 0.0317460317460317 1897 2.53484424208856 2.53484424208856 1 2.1469086196452 3024 1897 2679 1985 4596 4148 2839 3275 1952 2696 3445 2946 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 0.355841087724963 0.478362197236587 1245 2476.36363636364 2839 0.0391939499759035 965 1.33403223803043 -1.33403223803043 -1 0.953511039712632 1241 3724 2839 3562 3017 965 1299 3431 3382 2503 1277 2947 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 0.161385165508919 0.262241686633255 4390 2660.81818181818 2840 0.0158730158730159 807 1.17644903982569 -1.04559869458301 -1 1.52634147420555 4386 807 1745 1072 2840 3670 3674 4177 1225 2196 3477 2948 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 0.309505912071452 0.429223055331999 2880 2692 2840 0.0331075287608842 1279 0.743128926420273 -0.743128926420273 -1 0.609234797188859 2876 2840 1477 2569 3611 1332 3180 3425 2774 4249 1279 2949 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 0.415764508288144 0.536123413824502 2840 2837.18181818182 2841 0.052326375369292 1253 0.522536967759313 0.522536967759313 1 0.315748532892113 2836 1253 4414 2841 3102 2951 2116 1553 3165 4284 2694 2950 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 0.401263060761621 0.523037191301518 2755 2920.72727272727 2842 0.05 752 0.628239147489291 0.752293952356203 1 0.394668709616099 2751 752 4402 2190 3713 2842 2695 1741 3395 4250 3397 2951 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 0.14053761102061 0.239824925434296 2845 2920.72727272727 2843 0.0136736737826569 709 0.406183634849478 0.399553057783483 1 0.562170027310217 2843 709 2815 1999 1590 3662 4435 3571 2685 3968 3851 2952 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 0.0211934473135321 0.0613040087106244 2455 2431.18181818182 2843 0.00194549169327071 488 1.16698663784412 1.16954870265455 1 3.15813848742125 2451 2910 1413 2843 3138 3293 3413 488 2274 1468 3052 2953 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 0.128037774727357 0.222628947076956 2170 2923.63636363636 2843 0.0123781324112445 1426 1.25482080313717 1.34561054720661 1 1.82720571146237 2166 3918 1426 3752 1542 4331 2843 3880 2297 2014 3991 2954 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 0.557443745451391 0.675680649556446 3260 3015.09090909091 2844 0.0714285714285714 1544 1.47689902984379 1.47689902984379 1 0.561227844392288 3257 2844 2391 2536 3599 2801 3971 4144 2797 1544 3282 2955 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 0.557443745451391 0.675680649556446 3260 3016.09090909091 2845 0.0714285714285714 1545 1.47689902984379 1.47689902984379 1 0.561227844392288 3258 2845 2392 2537 3600 2802 3972 4145 2798 1545 3283 2956 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 0.371062795504446 0.49188126159373 2100 2899.54545454545 2845 0.0412804765942762 1307 0.976540223220515 0.976540223220515 1 0.671610344983757 2096 2913 3147 2810 2240 2845 1307 4639 3634 4106 2158 2957 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 0.35943518917414 0.478362197236587 4490 3042.45454545455 2846 0.0396825396825397 1679 1.23613809119717 1.35393145042638 1 0.883540354538909 4488 2118 2669 3070 3539 1679 4081 3986 2285 2846 2706 2958 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 0.150528642641348 0.25309552185768 2815 2935.54545454545 2849 0.0147215673813932 998 1.29644110978073 1.29644110978073 1 1.72663164407652 2815 2849 2439 3658 4371 3770 3484 998 2031 2422 3454 2959 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 0.713839205864954 0.817261304344778 2165 3074.27272727273 2850 0.10751500931242 1555 0.342933555008126 -0.380744697543472 -1 0.0670791057060281 2163 3894 2546 4544 3364 1555 2850 2409 4190 3940 2362 2960 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 0.0577219208879126 0.128131180142472 4275 2745.18181818182 2850 0.00539040545409036 1081 1.32923484347124 -1.32923484347124 -1 2.6473669989719 4275 2478 2019 3228 1081 2850 4082 1106 3136 2338 3604 2961 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 0.211290040780327 0.325371387149724 3685 2895.90909090909 2851 0.0213467386791923 1183 1.26233827143394 1.4972606316798 1 1.37384388543643 3681 3331 3215 2703 1841 1183 4053 4125 2800 2851 2072 2962 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 0.0394198623255202 0.0964603001866255 1630 2633.90909090909 2851 0.00364949407376625 290 0.234761244965642 -0.279122091782085 -1 0.532170291320542 1626 2851 3597 3706 4310 290 1253 1906 4384 4426 624 2963 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 0.804956120936968 0.897460000644927 1810 2961.54545454545 2852 0.150793650793651 1806 0.471462821619809 -0.471462821619809 -1 0.0494407783064659 1806 2746 4280 3093 3358 2050 2852 2669 3397 4033 2293 2964 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 0.0839184282471183 0.156982736433532 4605 2587.09090909091 2853 0.00793650793650794 397 1.99082593762628 -2.07333958077616 -1 3.57313058014546 4601 1992 2211 1230 2853 3056 4010 3090 397 1400 3618 2965 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 0.394834547402418 0.51638283421198 2980 2789.54545454545 2853 0.0446326936352489 1459 1.24930768727141 1.24930768727141 1 0.800338187081587 2980 1459 1895 2165 2295 4322 3883 3809 2853 2108 2916 2966 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 0.0479482185688871 0.111672640265311 2770 2672.90909090909 2853 0.00445693402390187 311 0.769573530256952 0.769573530256952 1 1.63527538868501 2768 311 3254 2428 986 4666 3011 4036 1540 2853 3549 2967 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 0.541520751523941 0.661528900051879 1505 2711.54545454545 2854 0.0684398967968689 1503 0.55936453995665 -0.55936453995665 -1 0.22403754236992 1503 2854 3178 3427 3640 1512 2435 2420 3840 3455 1563 2968 M868 REACTOME_CHROMOSOME_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHROMOSOME_MAINTENANCE.html Genes involved in Chromosome Maintenance 78/251 Reactome 0.125833023252279 0.218957871132632 780 2398.09090909091 2855 0.0121513750695152 779 1.20074158169684 -1.20074158169684 -1 1.76781053739388 779 3226 1241 3123 3409 1945 2956 1560 3188 2855 2097 2969 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 0.136119477610161 0.233903876817461 2510 2589 2855 0.0132138120904531 859 0.752029669109221 -0.752029669109221 -1 1.05905406864438 2508 2930 2137 3239 1575 883 2855 3520 3816 4157 859 2970 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 0.751985672431077 0.848905049629493 4045 3000.54545454545 2855 0.119047619047619 1890 1.01294927654863 1.1866959232166 1 0.160837200290972 4045 2038 2855 2080 3944 2835 2995 2788 3233 1890 4303 2971 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 0.0839184282471183 0.156982736433532 4090 2475 2856 0.00793650793650794 384 1.75258517442129 -1.59008010255122 -1 3.14553651459675 4090 2856 1255 1024 3009 2995 4380 2063 384 833 4336 2972 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 0.0274919403021651 0.0736155612891118 4445 2727.54545454545 2856 0.00253105654459517 710 0.924621273085119 -0.74616123595313 -1 2.33821793654667 4443 1886 2780 2856 710 2291 3225 3161 3121 3013 2517 2973 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 0.270837281725213 0.391590096317293 2700 2974.36363636364 2857 0.028306056222079 1996 1.00419156262766 -1.00419156262766 -1 0.912578183075068 2700 4522 3069 4182 1996 2184 3703 3030 2857 2056 2419 2974 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 0.321294572720927 0.441780037491275 2560 2923.90909090909 2858 0.0346199893137465 2131 1.86280643978199 1.86280643978199 1 1.47510673094773 2559 3697 2139 2611 2131 4090 3520 3028 2858 2378 3152 2975 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 0.154399131011011 0.258014648776565 4250 2785.72727272727 2859 0.0151305307906884 608 1.1086912551307 -0.999133560631901 -1 1.45589513538557 4250 1340 3321 2859 3016 608 4056 3563 2773 2364 2493 2976 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 0.0279226380419359 0.0741754432338502 4035 3007.09090909091 2859 0.00257122392625449 723 0.515318167256643 -0.49326043483101 -1 1.29937185745324 4033 1802 2225 1865 723 4498 2994 2859 2735 4664 4680 2977 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 0.690893658813955 0.797777208383085 2840 3098 2860 0.101234953625798 1720 0.852246096011289 0.852246096011289 1 0.186635787104096 2837 2350 2611 2860 3879 4595 1720 2512 3563 3417 3734 2978 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 0.00933054109689518 0.0328743726165795 3080 2572.81818181818 2861 0.00093699507308211 388 0.724095453604658 0.724095453604658 1 2.39694607196312 3077 2369 3964 2139 388 2999 2861 3083 1327 3513 2581 2979 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 0.158599293117378 0.262241686633255 2945 2781.90909090909 2861 0.017120476896617 1059 2.07333958077616 -2.07333958077616 -1 2.68997983356054 2943 3775 4595 3757 4533 2760 1423 1059 1582 1313 2861 2980 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 0.238603129377768 0.35182324237389 3885 3104.27272727273 2862 0.0244773182053194 1920 1.31394404283802 1.31394404283802 1 1.33045970521508 3881 2688 2862 3304 1920 2772 3497 3211 2681 2667 4664 2981 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 0.0328191518956275 0.0836727670200818 3905 2595.09090909091 2862 0.00302901971302874 804 1.25027116253696 -1.2667041641321 -1 3.00654104257616 3903 2839 2609 2889 804 2902 2862 4533 952 961 3292 2982 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 0.230813307365493 0.34496857265126 1695 2743.45454545455 2863 0.0259008234679494 1086 0.307773713321172 0.392940156599671 1 0.317512079346125 1692 2863 4268 3985 3776 1849 1634 1974 3038 4013 1086 2983 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 0.0839184282471183 0.156982736433532 3890 2434.45454545455 2863 0.00793650793650794 428 1.19721741070771 1.31573939758403 1 2.1487635158608 3888 428 2863 434 1831 3302 3326 4611 659 1353 4084 2984 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 0.493535049462591 0.614934717336563 1385 3023.63636363636 2866 0.0599718607747663 1383 0.215527354415815 -0.226253681190779 -1 0.101581869844133 1383 4372 3723 4554 2487 1424 2866 2743 4060 3507 2141 2985 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 0.467199110227247 0.587572471960515 4100 2883.63636363636 2867 0.0556298149486515 781 1.20926352954477 1.20926352954477 1 0.623299763175116 4100 2191 1889 2197 3549 3368 3345 2834 2867 781 4599 2986 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 0.0839184282471183 0.156982736433532 3155 2682.18181818182 2867 0.00793650793650794 537 2.0244123104462 1.66070389558643 1 3.63341133776183 3153 537 1747 1737 2784 4003 3611 3577 804 2867 4684 2987 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 0.0839184282471183 0.156982736433532 4065 2522.72727272727 2867 0.00793650793650794 155 0.685106970905324 -0.646118488205991 -1 1.22962867923916 4061 611 2630 839 1423 3519 2867 3535 155 3869 4241 2988 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 0.392242320632369 0.513851695410478 1890 2923.18181818182 2867 0.0485783154718361 1312 0.401261860556339 0.404669814953153 1 0.258969707756929 1889 3139 4411 3326 2867 2344 1312 2805 3331 4276 2455 2989 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 0.440314204275603 0.562977451905996 4205 3162.09090909091 2869 0.051394050608354 2103 0.650112755713168 -0.650112755713168 -1 0.362038248931753 4203 2438 2869 2204 2375 4543 2830 2103 3706 3649 3863 2990 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 0.415320710913563 0.535769969181582 3325 2727.63636363636 2869 0.0476190476190476 1372 1.41259471624142 1.60286650332445 1 0.854478401920569 3325 2869 2983 2978 2429 1372 3824 3444 2393 2302 2085 2991 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 0.665842649286426 0.775117085755398 4350 3018.63636363636 2869 0.094845281050709 1912 1.08991325512181 1.08991325512181 1 0.269125568908112 4349 2535 1912 2954 2794 2869 3762 2081 3122 2744 4083 2992 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 0.298735036746822 0.4173739958842 3355 2615.63636363636 2871 0.0317460317460317 952 0.934213124706781 0.934213124706781 1 0.791240020413101 3354 1590 1792 952 2871 3833 3175 3377 1942 1970 3916 2993 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 0.345890777475961 0.468181450968328 2680 2996.72727272727 2871 0.0378540992820993 1512 1.29285294335342 -1.23406692774771 -1 0.951036469067696 2679 2871 1512 2819 4200 3123 1877 4635 3087 2015 4146 2994 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 0.134098169299357 0.231307500127953 3200 3066.45454545455 2872 0.0130041365332977 1563 1.08883358125297 -1.08883358125297 -1 1.54514275640478 3196 1786 1893 2224 1563 4656 4370 4178 2414 2872 4579 2995 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 0.865412014258462 0.942878562849373 2860 3161.36363636364 2872 0.166666666666667 2227 0.802213194306554 0.802213194306554 1 0.0457364350106084 2857 2872 2704 3200 3972 2227 4339 2430 3500 4114 2560 2996 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 0.192047467987719 0.301485572861122 1735 2908.63636363636 2872 0.019199832184589 1040 0.267298291019705 0.311009789705364 1 0.310664211660936 1734 4520 2872 4545 3761 2001 1040 1099 4309 4222 1892 2997 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 0.466738071388703 0.587219019917277 4195 3182.90909090909 2872 0.0555555555555556 1654 1.79887914043011 1.79887914043011 1 0.928258973678767 4194 2805 1654 2359 3291 3767 4491 2872 2550 2346 4683 2998 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 0.386086746459241 0.507632574048261 3280 3097.81818181818 2872 0.0476190476190476 1502 1.70820157422404 1.70820157422404 1 1.12261539741644 3280 2699 4654 2429 2872 4152 1502 4534 2305 1723 3926 2999 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 0.136919072423026 0.23467548404327 2595 2625.1 2872.5 0.0162276472330137 848 0.635718651628261 -0.0884034478562228 -1 0.893228374672625 2594 3428 4126 NA 3438 2073 848 1298 3151 3810 1485 3000 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 0.485804975035004 0.60625355872544 2095 2852.54545454545 2873 0.0586765078342446 1611 0.493393016758395 -0.493393016758395 -1 0.239344583451344 2093 3111 2559 2607 4394 3158 2221 1611 3385 3366 2873 3001 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 0.00834317789640293 0.0303305908631064 3155 2748.18181818182 2873 0.000761362471875702 792 1.43956958252211 1.43956958252211 1 4.87773350559469 3155 2873 792 2736 3795 1502 3357 3638 3790 2272 2320 3002 M14857 REACTOME_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPHINGOLIPID_METABOLISM.html Genes involved in Sphingolipid metabolism 41/73 Reactome 0.161385165508919 0.262241686633255 3225 2925.27272727273 2875 0.0158730158730159 1453 2.06322935667965 2.06322935667965 1 2.67686268710484 3221 2875 3007 2550 2744 2310 3388 4396 1453 2857 3377 3003 M81 PID_CDC42_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CDC42_PATHWAY.html CDC42 signaling events 18832364 49/107 Pathway Interaction Database 0.0839184282471183 0.156982736433532 3770 2855.81818181818 2877 0.00793650793650794 641 1.45715085522812 -1.31375712672246 -1 2.61529156429106 3770 3469 2683 1835 3497 4348 2877 2776 641 997 4521 3004 M18799 REACTOME_DIABETES_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DIABETES_PATHWAYS.html Genes involved in Diabetes pathways 87/214 Reactome 0.0155100335047923 0.047808633917785 4540 2587 2877 0.00142004282252205 502 0.783702149742192 0.758399713132473 1 2.30976031359527 4538 2178 3379 2253 502 605 3780 2877 3134 3091 2120 3005 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 0.0153470487336933 0.0474381730647009 2310 2751.18181818182 2877 0.00140501509841193 499 0.362238073650599 0.483293421734994 1 1.07033483933143 2310 3070 2877 3060 499 3593 2639 2532 2384 4104 3195 3006 M7747 BIOCARTA_IL2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL2_PATHWAY.html IL 2 signaling pathway 16/41 BioCarta 0.261183588411643 0.380095122763031 1980 2603.09090909091 2879 0.0271435203859015 1235 0.246094178093803 -0.248235337500758 -1 0.230749909271105 1980 3238 3638 3265 2879 1712 1974 1235 3673 3277 1763 3007 M16763 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NEUROTROPHIN_SIGNALING_PATHWAY.html Neurotrophin signaling pathway 81/152 KEGG 0.298735036746822 0.4173739958842 2630 2743.63636363636 2880 0.0317460317460317 728 1.34839498309097 1.34839498309097 1 1.14203498727686 2630 791 3430 728 4424 4615 1804 3233 2015 2880 3630 3008 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 0.171049118744804 0.274969526736931 3535 2953.63636363636 2880 0.0169094373122801 1302 1.82051220676583 1.82051220676583 1 2.27832491919484 3534 2944 1302 2520 2085 4460 3756 2880 2524 2328 4157 3009 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 0.438822672173402 0.561376751789397 2880 3109.18181818182 2880 0.0511645118786747 1603 1.38933387508025 1.38933387508025 1 0.777534127433994 2880 2632 1603 2663 4579 3658 3775 3281 2846 2567 3717 3010 M576 REACTOME_GLYCOSPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSPHINGOLIPID_METABOLISM.html Genes involved in Glycosphingolipid metabolism 19/36 Reactome 0.0839184282471183 0.156982736433532 4110 3023.72727272727 2883 0.00793650793650794 345 2.06322935667965 2.06322935667965 1 3.70308009800365 4109 2569 2739 1900 4295 3565 4536 2883 345 2323 3997 3011 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 0.472208833919383 0.592759334515465 1090 2971.90909090909 2884 0.0564405178601493 1086 0.24710184350452 -0.254666124131795 -1 0.125260452257947 1086 4212 3623 4288 2884 1187 2787 2538 4364 3739 1983 3012 M10680 KEGG_PROTEASOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEASOME.html Proteasome 28/48 KEGG 0.270560830541163 0.391431939461528 1655 2838.27272727273 2885 0.0282725707845657 1358 0.196126351133035 -0.203381630342918 -1 0.17831034892071 1651 3405 3753 4018 1995 1358 2794 2885 4064 3197 2101 3013 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 0.160269005417701 0.262241686633255 3290 2859.81818181818 2886 0.0157540123529543 1287 1.74050550493129 2.1911001413465 1 2.25815623829424 3290 4325 1287 2914 2500 2160 4141 3240 2886 2094 2621 3014 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 0.225459916288001 0.341579427004712 1520 2857.45454545455 2886 0.0229583407043044 970 0.457607881014885 0.44069969797069 1 0.476466553286369 1519 2886 1585 3441 4666 1382 970 4579 3953 4183 2268 3015 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 0.415320710913563 0.535769969181582 2620 3023.27272727273 2886 0.0476190476190476 1977 1.03999065367122 1.0953297966491 1 0.629090241883041 2619 3195 1986 3502 2886 4185 1977 4070 2381 2709 3746 3016 M2668 KEGG_BETA_ALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BETA_ALANINE_METABOLISM.html beta-Alanine metabolism 11/30 KEGG 0.137921908890336 0.236107596809507 2645 2813.90909090909 2887 0.0134011594767163 973 0.967459383376804 -0.967459383376804 -1 1.35364151440965 2644 2367 1739 3371 4231 3814 1691 973 2887 3171 4065 3017 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 0.273707571574876 0.39500883289186 2550 2667.36363636364 2887 0.0286544067234599 990 1.18887135927513 -1.10077781871531 -1 1.07039232094659 2548 3124 1441 2887 3862 3560 3623 1934 2431 990 2941 3018 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 0.279430210856426 0.400553676376021 2470 2858.27272727273 2891 0.0293526815682 839 0.858070626841244 -0.858070626841244 -1 0.760963959566744 2467 4178 3421 4153 4443 839 1841 2144 3882 2891 1182 3019 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 0.667434366415499 0.775117085755398 3055 2946.54545454545 2891 0.0952380952380952 2301 0.935105340963036 1.0199254563157 1 0.230899803885455 3053 2530 2950 2327 4010 2301 4325 2891 3068 2309 2648 3020 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 0.000109026675009237 0.00105776190288465 3815 2224.90909090909 2892 1.09032024445759e-05 41 1.23047587260953 1.32835652810484 1 8.17201151793568 2892 184 4152 114 1043 3811 3324 3812 670 41 4431 3021 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 0.677565489530034 0.784743421635626 2060 2872.09090909091 2892 0.107015024654084 1550 0.486024034164691 -0.441342325938548 -1 0.114196154291416 2060 2576 4242 2892 3677 1550 1965 2915 3662 3976 2078 3022 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 0.746802677608774 0.846520887100802 2420 2907.36363636364 2893 0.117389662304709 2141 0.276679336221334 0.327530255262504 1 0.044685721119686 2419 2395 3518 2821 2933 3355 2589 2141 3234 3683 2893 3023 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 0.325254055591372 0.446176962675987 3645 2803.54545454545 2893 0.0351333435694763 903 1.08911057142797 1.11208556159529 1 0.851982550505553 3642 2374 3228 3152 2808 903 3369 3727 2688 2893 2055 3024 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 0.0632473318771491 0.13695794693915 1725 2717.18181818182 2894 0.00651230175214233 597 0.204136252815683 0.209339568518517 1 0.393385327119764 1723 3881 4219 3627 2894 939 597 1994 4556 3948 1511 3025 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 0.0201280800730236 0.0590975061588995 4450 2778.90909090909 2896 0.00184678439221688 593 1.10558874190002 1.13384069983906 1 3.03126479209613 4450 2256 2123 1971 593 1524 4640 4245 2906 2896 2964 3026 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 0.597318307603006 0.711317303539438 2820 2883 2897 0.0793650793650794 1488 1.47689902984379 1.47689902984379 1 0.487647577168069 2819 2909 2250 2742 3609 2412 3133 4443 2897 1488 3011 3027 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 0.232850105696956 0.34496857265126 3105 2579 2898 0.0238095238095238 1264 1.50049685841841 1.50049685841841 1 1.54797455750925 3102 2596 1938 2898 3109 3356 3410 1278 1786 1264 3632 3028 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 0.0396293679586307 0.0968476782983521 3775 2915.36363636364 2898 0.00366925123853136 886 1.22644944059247 1.23501872689101 1 2.77542149376172 3773 2258 2226 2113 886 3458 3126 4378 2898 2683 4270 3029 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 0.0839184282471183 0.156982736433532 4040 2651.81818181818 2898 0.00793650793650794 883 1.27503060019828 -1.19369842816534 -1 2.2884224793395 4040 1667 1665 1323 2898 3040 4357 4234 883 1557 3506 3030 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 0.256952407902021 0.374519123928108 2920 3022.81818181818 2899 0.0292628214497399 1270 0.517526920788221 -0.531800306167118 -1 0.492672148434441 2920 2252 4449 3087 2831 2548 4363 1270 2899 4352 2280 3031 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 0.291840911807244 0.414539712861093 870 2725.90909090909 2900 0.0308845210618383 869 0.725321161405422 -0.564322045552235 -1 0.619107745395357 869 3716 3762 3521 2434 1104 2019 2900 3779 4179 1702 3032 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 0.0866099555701248 0.16118119610866 1910 2513.18181818182 2900 0.00820184146038301 848 0.414219320932901 -0.569567975530155 -1 0.732842908904028 1906 3378 2088 3394 2911 1162 2900 848 3275 4267 1516 3033 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 0.161385165508919 0.262241686633255 4480 2861.72727272727 2901 0.0158730158730159 1484 1.38933408833983 1.75894475465316 1 1.80254152011269 4478 2901 3141 2295 1731 3165 4314 2445 1484 2539 2986 3034 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 0.0839184282471183 0.156982736433532 2905 2482.27272727273 2902 0.00793650793650794 296 1.71352929122456 1.71352929122456 1 3.07543909023064 2902 2937 2461 1606 4297 4030 3153 1352 296 854 3417 3035 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 0.0508791429414551 0.116643671146604 3815 2831.45454545455 2902 0.00473594410721767 1017 0.949197695059831 -0.584451347281639 -1 1.97688991933201 3815 1677 1961 2853 1017 1972 3789 3316 3368 2902 4476 3036 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 0.131758583875089 0.227662508863816 1410 2557.90909090909 2903 0.0140292078474914 588 0.303850471034461 0.336716965490698 1 0.43586650923314 1409 3611 4091 2903 3928 588 1129 1789 3811 3756 1122 3037 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 0.706283320918379 0.809995996530476 1850 2859.09090909091 2904 0.115306450142242 1713 0.287428911267952 -0.287428911267952 -1 0.0587100411443778 1849 3036 3998 2904 3931 1713 2400 2198 3951 3569 1901 3038 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 0.00687990044144392 0.0262534311633601 3840 2811.45454545455 2904 0.000627410011296246 769 1.12284967653286 1.16102940212104 1 3.96170311405868 3837 3688 769 2490 1233 3765 3822 2904 1829 2510 4079 3039 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 0.0041706796025144 0.01793009597925 2910 2595.45454545455 2907 0.000417852789693713 239 1.21455215107271 1.21455215107271 1 4.73416912062696 2907 1660 4239 2975 239 2950 2706 4126 2299 1301 3148 3040 M177 PID_EPHA_FWDPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHA_FWDPATHWAY.html EPHA forward signaling 18832364 23/45 Pathway Interaction Database 0.35943518917414 0.478362197236587 2745 2846 2908 0.0396825396825397 1401 1.24511675505387 1.24511675505387 1 0.889957931915301 2745 2908 2281 2455 3423 4145 3250 3496 2220 1401 2982 3041 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 0.202060878367352 0.313528899347487 3280 2949.72727272727 2908 0.0203111622976669 1647 1.08277467778791 1.15038110027963 1 1.21733169118431 3278 2415 2624 3787 1821 1647 3384 3807 2908 2578 4198 3042 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 0.298735036746822 0.4173739958842 4120 3032 2908 0.0317460317460317 1265 1.30765279379691 -1.33376424024472 -1 1.10752803180777 4120 2912 2469 2752 2192 4599 2908 3901 1933 1265 4301 3043 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 0.232850105696956 0.34496857265126 3440 3105.27272727273 2909 0.0238095238095238 1808 1.00706199340117 0.789572496485431 1 1.03892676270713 3440 3152 3527 2909 2895 2446 2630 4185 1808 2688 4478 3044 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 0.380312095596211 0.502011966186998 2565 2802.27272727273 2911 0.0425708672163561 996 1.192242826745 1.10502207810623 1 0.796398758062157 2561 3822 3770 3128 2685 996 3747 2336 2911 3122 1747 3045 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 0.385846481082157 0.507632574048261 1695 2939.09090909091 2912 0.0433513796721811 1500 1.14672566625037 1.14672566625037 1 0.753618254960557 1694 4252 3756 4241 2271 1500 2814 2912 3624 3106 2160 3046 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 0.0243961882973493 0.0677386923476161 1695 2623.27272727273 2914 0.00224281799073529 524 0.325433006643198 0.399945570174445 1 0.849212322435189 1695 3636 2914 4255 3821 2113 1012 524 3432 3872 1582 3047 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 0.0180297789636109 0.0540547307891751 2430 2622.72727272727 2914 0.00165265975116649 885 1.38653101322105 1.18190690852336 1 3.92141453485353 2427 3621 885 3039 2914 3853 2439 3467 2039 1178 2988 3048 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 0.116046505640349 0.205050499785323 3925 2906.72727272727 2915 0.0111510721432801 1041 1.1862015981282 1.1862015981282 1 1.82185721731792 3924 1041 1216 1354 3190 4391 2847 4661 2270 2915 4165 3049 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 0.210031257813395 0.323752129642621 2920 2958.90909090909 2916 0.0212048476824296 1837 1.07125990181195 -0.625059557561618 -1 1.17106764540599 2916 3306 1995 3649 1837 4265 2764 2661 3052 2644 3459 3050 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 0.140833071383176 0.240241635421027 2220 2650.81818181818 2916 0.0137045034020255 986 0.349476550081886 -0.388391975831604 -1 0.483097672975336 2218 2916 3013 3433 4409 1632 1305 986 3319 4482 1446 3051 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 0.00151312159707467 0.00812954900289117 4680 2947.45454545455 2917 0.000137651208989492 640 1.54287828022359 1.68365845545429 1 7.19687065062234 4677 4081 640 3575 2883 1731 3641 2767 2917 2086 3424 3052 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 0.265438972399382 0.385330552869735 2920 2983.27272727273 2918 0.0276542581946303 1546 3.11553755502548 -3.11553755502548 -1 2.87996739039426 3090 3627 1546 4089 1989 2862 3939 2917 2918 2820 3019 3053 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 0.39892282353884 0.520421033157851 2135 2992 2918 0.0452212405558218 1556 0.940464895702508 1.07681339131581 1 0.595384495094711 2132 4054 1556 3850 3737 2022 2000 3877 4073 2693 2918 3054 M185 PID_ALK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK1_PATHWAY.html ALK1 signaling events 18832364 11/33 Pathway Interaction Database 0.514011397665828 0.633523779448203 4120 3049.90909090909 2919 0.0634920634920635 1840 1.00744291305309 1.00744291305309 1 0.445743368622922 4117 3031 2899 2649 2919 2088 4070 4336 2642 1840 2958 3055 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 0.0765897756730953 0.156982736433532 3040 2842.72727272727 2919 0.00793650793650794 626 0.66321577987296 0.699684455162569 1 1.19033841149779 3040 2919 4134 2687 2371 3543 2492 2095 626 3828 3535 3056 M10628 BIOCARTA_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ATM_PATHWAY.html ATM Signaling Pathway 20/32 BioCarta 0.244270780517791 0.358712904263982 2720 2936.36363636364 2920 0.0251397034505707 1935 0.852326785622773 0.852326785622773 1 0.847017816981125 2720 2731 2269 2920 1935 3538 3312 3499 3714 2376 3286 3057 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 0.894525996033541 0.963714889446241 2170 3030.90909090909 2920 0.184929754432789 2146 1.29142669460736 1.29142669460736 1 0.046266119127522 2170 3865 2628 3523 3259 2146 3689 2397 3904 2920 2839 3058 M638 KEGG_ADHERENS_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADHERENS_JUNCTION.html Adherens junction 53/111 KEGG 0.298735036746822 0.4173739958842 2770 3007 2921 0.0317460317460317 1760 1.08595441271056 1.08595441271056 1 0.919758638550581 2766 2793 1760 3741 2921 3830 3723 3399 2060 2481 3603 3059 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 0.514011397665828 0.633523779448203 3360 3164.36363636364 2921 0.0634920634920635 2221 1.14672566625037 1.14672566625037 1 0.507369057593621 3357 2432 3269 2221 2821 4364 2921 3717 2648 2636 4422 3060 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 0.427382347525273 0.548875712587676 2190 2919.72727272727 2921 0.0494221223941336 1324 1.61008259463341 1.61008259463341 1 0.936221818746086 2190 4140 3468 4021 3093 3204 1324 2750 2860 2146 2921 3061 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 0.298735036746822 0.4173739958842 2940 2659.09090909091 2922 0.0317460317460317 580 0.705643609594569 -0.757413120848284 -1 0.597651059774755 2938 580 2922 1320 3693 3420 2295 2780 1989 3214 4099 3062 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 0.70777464031698 0.811110776357391 2210 2926.45454545455 2922 0.105811870640937 1839 1.10858603309022 1.10858603309022 1 0.224961171681552 2210 4384 2816 4114 2922 3060 3037 2456 3307 2046 1839 3063 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 0.110518894508427 0.196866367122976 610 2237.90909090909 2922 0.0105905225591378 594 1.14465333478111 -0.964958726717358 -1 1.8032365693997 606 3366 3128 3636 3222 594 1798 1121 2922 3019 1205 3064 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 0.717420186577186 0.820318829030971 1720 2726.81818181818 2922 0.108536144278903 1624 1.0390842097769 -1.05241966314662 -1 0.199487738153005 1718 3396 3519 2922 2877 1624 3386 1986 3263 3099 2205 3065 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 0.444402034095417 0.566812175223496 3145 2833.72727272727 2925 0.0520260080395425 1611 0.950459745831972 0.950459745831972 1 0.523042965404383 3144 2585 1611 2038 3272 4612 2925 1914 2998 1938 4134 3066 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 0.223791064088403 0.33930536715519 2440 2954.90909090909 2927 0.0227671488396139 1750 0.294402463067704 0.266146201779285 1 0.30844139321337 2436 3871 3396 3940 1879 1973 1750 2927 3053 4495 2784 3067 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 0.0415524676526784 0.100412224897613 4025 2718.54545454545 2928 0.00385079001269261 908 1.1528412386549 1.03438615951945 1 2.56845793761664 4022 2928 1387 3101 908 2654 4597 1466 3340 2541 2960 3068 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 0.032358041821657 0.0827673493320331 2290 2591.09090909091 2929 0.00328390993819645 837 0.492201879232587 -0.222036427684528 -1 1.18879413880626 2288 849 4351 1533 837 3588 2929 1701 3273 4121 3032 3069 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 0.0692024938784801 0.146933795339627 2875 2566.9 2930 0.00793650793650794 190 0.621061479525533 -0.248829048040653 -1 1.15450467798428 2873 1874 4102 NA 2987 2080 761 3654 190 3777 3371 3070 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 0.123295961221671 0.215583908315205 3325 2562.63636363636 2931 0.0118910822681923 812 1.26530448687738 1.26530448687738 1 1.88191039689329 3322 2624 2959 3187 3062 835 2931 3076 2544 2837 812 3071 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 0.0856357828239623 0.159812536166104 3900 3125.72727272727 2931 0.00891267451653059 1332 1.16751959882986 1.16751959882986 1 2.075243548479 3898 2611 4602 2931 1332 2703 3815 4493 2839 1621 3538 3072 M7761 KEGG_MELANOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOGENESIS.html Melanogenesis 48/110 KEGG 0.0640188492693607 0.138181634120785 4230 2518.90909090909 2932 0.00599648893589094 1092 1.31195846197487 -0.959818495517207 -1 2.51692700520438 4226 1293 1092 1286 3702 3185 3224 2932 1818 1560 3390 3073 M15109 BIOCARTA_GLYCOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLYCOLYSIS_PATHWAY.html Glycolysis Pathway 13/35 BioCarta 0.565619547887621 0.683071833577355 2935 2703.09090909091 2932 0.0730013200080529 1293 0.409945421088037 -0.386437671703462 -1 0.151457858942939 2935 2363 2254 2932 3070 1293 3149 2855 3459 3271 2153 3074 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 0.294609172706342 0.4173739958842 2755 2860.90909090909 2932 0.0312295312726255 1482 0.85044611430893 -0.650112755713168 -1 0.720292814392471 2755 2971 3476 2830 2057 3053 2243 1482 3703 2932 3968 3075 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 0.55689571887701 0.675680649556446 2485 3107.72727272727 2933 0.0781705159502164 1546 0.398207563253669 0.541122692905426 1 0.151320549149764 2484 1597 4499 2933 4416 3760 1546 1963 3663 4414 2910 3076 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 0.161385165508919 0.262241686633255 4365 2868 2934 0.0158730158730159 1214 1.08214976033381 0.928348942037812 1 1.40399626721964 4361 1214 2184 1329 3949 2934 4601 4577 1358 2001 3040 3077 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 0.466738071388703 0.587219019917277 4280 3015.90909090909 2934 0.0555555555555556 2272 1.45023161899474 1.45023161899474 1 0.748349616131995 4279 2272 2773 2567 3024 3210 3465 2934 2549 2861 3241 3078 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 0.0312986077025755 0.0806296183036112 3885 2602 2936 0.00288663248369069 784 0.945674107185032 -0.701222236703204 -1 2.30803283661322 3882 1632 1128 2013 784 3003 3164 2999 2936 2665 4416 3079 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 0.0275586989652733 0.0737100818215015 2050 2592.36363636364 2936 0.00253728147744323 712 1.07272638267715 -1.07272638267715 -1 2.71141761989239 2046 2936 3242 2321 712 3298 2981 2943 2156 2698 3183 3080 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 0.232850105696956 0.34496857265126 4450 3162.72727272727 2937 0.0238095238095238 1835 0.50491279453589 -0.50491279453589 -1 0.520888901043075 4448 1980 3287 2937 3750 2686 4439 2447 1835 4364 2617 3081 M5193 SIG_CHEMOTAXIS http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CHEMOTAXIS.html Genes related to chemotaxis 22/63 Signaling Gateway 0.891073518496821 0.961712793370162 2245 2913.36363636364 2939 0.182539682539683 2117 1.09724913661829 1.09724913661829 1 0.0415214507646057 2241 2942 3023 2786 3623 2939 2117 3491 3586 2455 2844 3082 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 0.280441553999587 0.401880465456289 2150 2824.36363636364 2939 0.0294766092951989 1082 2.06479751030715 -2.06479751030715 -1 1.82450865832384 2148 4253 3335 4465 3733 1082 3614 1274 2701 2939 1524 3083 M15955 KEGG_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPHINGOLIPID_METABOLISM.html Sphingolipid metabolism 23/46 KEGG 0.384028421299185 0.506489496821835 2255 2772.72727272727 2940 0.0430942765743097 1676 0.304725366710216 -0.28077070359324 -1 0.200928760430562 2254 2803 3248 3761 2270 1676 3104 2940 3010 3181 2253 3084 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 0.00683646090416844 0.0261519008395689 3450 2809.54545454545 2940 0.000623436179019027 767 1.48531974816698 -1.54796415353554 -1 5.246169687793 3447 2639 767 2796 2940 4524 3992 1434 3213 905 4248 3085 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 0.155909349601475 0.25990438001868 3090 2737.45454545455 2941 0.01529056513734 1279 1.78606414326979 1.78606414326979 1 2.33276414723214 3089 2941 1279 2075 2404 4329 3765 3218 1959 1398 3655 3086 M5467 BIOCARTA_GRANULOCYTES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GRANULOCYTES_PATHWAY.html Adhesion and Diapedesis of Granulocytes 7/21 BioCarta 0.231430430821466 0.34496857265126 1385 2683.81818181818 2941 0.0259790043049965 1224 0.572657872367201 0.698419335822215 1 0.590777522467347 1382 3456 3811 2941 4482 1880 1339 1224 4304 3237 1466 3087 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 0.0799257433238435 0.156982736433532 2715 2910.81818181818 2941 0.00754420747277065 1243 0.966872419807618 0.971076982583996 1 1.73534076732385 2712 3823 2062 4143 1243 2348 2242 2941 3195 3135 4175 3088 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 0.12309568114111 0.215314058166197 2945 3179.27272727273 2943 0.0118705634760904 1517 0.955324262625067 -0.743128926420273 -1 1.42203099274502 4084 4547 3471 4398 1517 1757 4657 2630 2942 2943 2026 3089 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 0.36865853752174 0.489247778767169 2390 2731.36363636364 2944 0.0409478789168801 1239 1.02926052275201 -0.767094350896661 -1 0.713224253439963 2390 3768 2419 2944 3174 3778 1239 1732 3130 2169 3302 3090 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 0.175384416550791 0.279756102894229 2130 2657.27272727273 2944 0.0173779545832643 763 0.284571126352649 -0.273856054016447 -1 0.351373170796955 2127 3466 3653 4077 1851 763 2944 2239 3309 3864 937 3091 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 0.359187141297058 0.478362197236587 2640 2634.81818181818 2944 0.0396487395699386 1400 1.00741281855212 -0.709834088176105 -1 0.720056994591154 2640 3227 3472 3036 2343 1544 3148 1400 2944 3026 2203 3092 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 0.242350917412766 0.356452102635348 2290 3062.81818181818 2945 0.024914822445839 1931 0.50491279453589 -0.50491279453589 -1 0.504862135269644 2286 3794 2109 4132 1931 3010 2366 2637 4236 4245 2945 3093 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 0.35943518917414 0.478362197236587 3595 3018.27272727273 2945 0.0396825396825397 2254 0.916651242069518 0.755529885595869 1 0.655184375549367 3592 3088 2260 3166 3331 2728 4444 2476 2254 2945 2917 3094 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 0.347135082372269 0.469730001731577 2350 3030.81818181818 2946 0.0380206323962124 2188 1.22168558101711 1.22168558101711 1 0.894774630128838 2346 3233 2946 2690 2188 3848 2448 4428 3457 2387 3368 3095 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 0.395395598911524 0.516970919782199 3125 3131.90909090909 2946 0.0447132480568377 2164 1.22834734671781 1.13791415775945 1 0.785555251349163 3124 4541 3400 4469 2298 2164 3550 2535 2946 2841 2583 3096 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 0.366205272535392 0.486267471550254 1805 2879.54545454545 2946 0.0445788252755967 1280 0.39366218808502 0.562261900944939 1 0.275119071043966 1804 3324 4628 3486 2489 1781 1280 2946 3109 4608 2220 3097 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 0.0595011875352349 0.130964098069568 3310 2677.27272727273 2947 0.00556128691667607 599 0.302429743100383 -0.319757342741363 -1 0.595922614386371 3308 2483 3393 3425 1219 2087 3372 1931 2947 4686 599 3098 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 0.162059062856695 0.263135401436754 2205 2777 2948 0.0175253785641547 1066 0.151633392904229 -0.183779984669878 -1 0.196231235206647 2202 3460 3851 3775 2948 1127 2232 1066 4518 3298 2070 3099 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 0.444817275464371 0.567187415734978 1975 2898.72727272727 2948 0.0571478529330807 1560 0.346725123131491 -0.379537448668576 -1 0.19058222612849 1975 3072 3863 2948 4659 2049 2879 1596 3968 3317 1560 3100 M226 PID_VEGFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGFR1_PATHWAY.html VEGFR1 specific signals 18832364 23/43 Pathway Interaction Database 0.311504109475098 0.431483374815344 1930 2805.54545454545 2948 0.033362232819283 1151 0.278762832304077 0.298183193589517 1 0.227117207767486 1930 4430 2948 3978 3180 1833 1151 1822 4347 3400 1842 3101 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 0.0493511851008925 0.114033359656204 4095 2935.36363636364 2948 0.00504827087731691 1051 1.23550170800384 1.3379010493461 1 2.60027868990894 4093 2708 4634 2961 1051 1177 4068 3968 1810 2948 2871 3102 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 0.205713892860512 0.318564210821004 3740 2885.18181818182 2951 0.0207197474195464 1727 1.3925534610232 1.47738997239361 1 1.54410082858332 3739 3258 2848 2951 1825 2609 3888 3743 1820 1727 3329 3103 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 0.668368458116215 0.775817338303836 2450 3283.27272727273 2953 0.0954694129398794 2242 0.193522044157365 -0.198510844889437 -1 0.0476158175074681 2449 4429 3674 4154 2801 2242 2953 2828 4461 3589 2536 3104 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 0.237439842673671 0.350628646629382 2180 3031.72727272727 2954 0.0243419181170648 996 0.9282856402567 -0.9282856402567 -1 0.943014171554817 2178 4056 2308 3900 4402 2456 996 2537 3091 4471 2954 3105 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 0.436457083881943 0.558502975169521 3845 2981.72727272727 2955 0.050801595504706 1209 1.22178399894412 1.22178399894412 1 0.689843774686826 3842 1209 3139 2632 2369 3727 2653 3235 2682 2955 4356 3106 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 0.292740386879742 0.415439567812983 1520 2672.09090909091 2955 0.0340427956480558 890 0.390043234960617 -0.457750934655325 -1 0.332106901944631 1520 2889 4133 3234 2955 890 1387 3068 3533 3826 1958 3107 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 0.541533260904611 0.661528900051879 2285 2919.54545454545 2955 0.0684422074763427 1567 1.32117370675459 1.28688486166898 1 0.529158516924005 2285 4259 2955 4534 2567 3149 2789 1784 3065 1567 3161 3108 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 0.0149417538505475 0.0465538953082884 3530 2786.36363636364 2956 0.00136765539772824 491 0.805929513684816 0.826813715441872 1 2.3960461418674 3527 1210 3124 2562 491 3057 2745 3579 2786 2956 4613 3109 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 0.000934041695022486 0.0055756934813699 3920 2410.81818181818 2956 8.49489537957091e-05 339 1.2021112168736 1.1817307043956 1 6.04672924650348 3920 339 599 867 2956 4208 3202 3352 1323 1411 4342 3110 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 0.0799173833768605 0.156982736433532 1840 2732.36363636364 2957 0.00754338769273838 815 0.966472030706952 -0.970096639526367 -1 1.73462214973275 1836 4580 3237 4563 1242 815 2957 2631 3871 3120 1204 3111 M882 BIOCARTA_CXCR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CXCR4_PATHWAY.html CXCR4 Signaling Pathway 19/45 BioCarta 0.514011397665828 0.633523779448203 4355 3035.72727272727 2958 0.0634920634920635 1304 0.653874098340854 0.653874098340854 1 0.28930675816669 4354 1304 2958 2529 2579 2899 3902 3504 2647 3255 3462 3112 M99 PID_TXA2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TXA2PATHWAY.html Thromboxane A2 receptor signaling 18832364 32/89 Pathway Interaction Database 0.298735036746822 0.4173739958842 3480 2948 2958 0.0317460317460317 1313 1.00379685767875 1.18063890866154 1 0.850174574904176 3480 2934 2586 2958 2965 3361 4295 1313 2080 1796 4660 3113 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 0.216131215024549 0.329684529168306 3535 3206.36363636364 2959 0.024057261513986 1909 1.15344073855914 1.39744912218932 1 1.24060365952328 3533 2959 4347 3495 1909 2507 2746 4157 2705 2810 4102 3114 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 0.551523765128577 0.67163211106874 1585 2939.72727272727 2960 0.0703061703297285 1484 1.39059940208002 1.39059940208002 1 0.536534406864905 1581 3624 2379 2960 4013 3202 1484 4054 3735 2368 2937 3115 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 0.503127204536534 0.625372435134801 1910 2952.09090909091 2961 0.0675522144113015 1684 0.266408682592501 -0.266408682592501 -1 0.121216752487121 1910 3682 4216 3507 2961 1761 2735 1684 3977 3944 2096 3116 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 0.331206518395667 0.452619931525837 4560 3199.54545454545 2962 0.0359102680690843 2154 0.925845428911278 0.910407064201507 1 0.711397910737973 4560 2962 2770 3018 2154 2957 3709 4451 2713 2367 3534 3117 M977 REACTOME_KINESINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KINESINS.html Genes involved in Kinesins 16/32 Reactome 0.605281811337148 0.719155823510618 2000 3206.63636363636 2963 0.0810352966281545 1766 0.862559895960135 -0.862559895960135 -1 0.275639891434156 2000 4386 1766 4447 4223 2243 2963 2778 4269 3698 2500 3118 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 0.000658585567140436 0.0042391922632144 2965 2975.90909090909 2963 5.98893456414708e-05 565 1.54287828022359 1.68365845545429 1 8.17066004142143 4072 3826 565 2964 2963 2032 4625 2960 2567 2142 4019 3119 M15247 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS.html Ubiquitin mediated proteolysis 77/154 KEGG 0.0316623561084191 0.0814232831662549 2750 2665.72727272727 2965 0.00292067621591711 254 0.680878280361112 -0.680644994905029 -1 1.65530168865466 2746 2965 3560 3202 4365 254 2332 1840 3619 3206 1234 3120 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 0.557443745451391 0.675680649556446 2705 3059.09090909091 2965 0.0714285714285714 1994 0.382486323914146 -0.478896522226665 -1 0.145346412063193 2702 4210 1994 4007 2975 2483 2965 2969 2779 4201 2365 3121 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 0.674091414931422 0.781299126977157 2040 2994.90909090909 2966 0.106057510310207 1713 1.21455215107271 1.21455215107271 1 0.290549583294701 2038 3140 4421 3887 4578 2966 2816 1973 3221 1713 2191 3122 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 0.0765897756730953 0.156982736433532 3225 2576.09090909091 2966 0.00793650793650794 489 0.862559895960135 -0.862559895960135 -1 1.54812084928987 3224 633 4437 1809 2976 1672 4219 2966 489 4334 1578 3123 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 0.415320710913563 0.535769969181582 3590 3039.81818181818 2966 0.0476190476190476 1165 1.19018746230139 1.37048309987697 1 0.719944276342971 3587 3533 3342 2966 2753 1165 4014 4290 2396 2947 2445 3124 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 0.54908240606986 0.669042253361007 2970 2863.63636363636 2967 0.0698472183428131 1299 1.05917663339253 1.14385024554408 1 0.412628266022058 2967 1299 1712 1846 2950 3980 3647 3855 3405 1744 4095 3125 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 0.426412636435249 0.547894053834817 2340 2859.27272727273 2967 0.0492758916880072 1525 1.5941190509345 1.5941190509345 1 0.929705475246751 2340 3004 2315 3204 3420 4073 2662 1525 3573 2369 2967 3126 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 0.533016614118031 0.652826935116857 2965 3141.90909090909 2967 0.0668821579439211 1961 0.85044611430893 -0.650112755713168 -1 0.351537675145843 2965 3501 3540 2965 2556 3600 2445 1961 3762 2967 4299 3127 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 0.297388612996758 0.4173739958842 1880 2847.90909090909 2968 0.0315771753556794 1879 0.294531047380891 -0.35100860104018 -1 0.249455660290964 1879 3239 2981 3450 2062 2024 2968 2734 4170 3652 2168 3128 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 0.63389956273523 0.745034700521015 2930 2986.63636363636 2968 0.0873015873015873 1447 0.852246096011289 0.852246096011289 1 0.243139364546679 3148 1447 2926 1823 2928 4470 2989 2818 2968 3827 3509 3129 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 0.129477954070349 0.224799441561191 2985 2767.63636363636 2971 0.0125265355841249 952 1.42267534279842 1.42267534279842 1 2.05824743638887 2983 2630 2971 3024 4216 3563 2571 952 1649 2596 3289 3130 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 4.88184432720768e-05 0.000549848094874702 2345 2616.27272727273 2971 4.43813878152948e-06 366 1.8093897470095 1.8093897470095 1 13.1642749078304 2344 2767 366 1936 3376 4628 3456 2971 3045 661 3229 3131 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 0.570049335571249 0.686873537281273 2315 3119.36363636364 2971 0.0738647371365275 1510 1.10858603309022 1.10858603309022 1 0.403612613241357 2314 4090 3344 4337 2971 4248 1510 1954 4139 2717 2689 3132 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 0.232850105696956 0.34496857265126 2465 2792.09090909091 2973 0.0238095238095238 1622 0.43905895047124 0.508872065586445 1 0.452951354515668 2463 3215 2045 2973 3542 3741 2190 2068 1622 3465 3389 3133 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 0.668823953540495 0.776153800468241 1750 3132.54545454545 2973 0.0955824263684691 1750 0.839316232100865 -0.839316232100865 -1 0.206159784442567 1750 4324 3053 4444 2802 2285 2973 2309 4117 3920 2481 3134 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 0.415320710913563 0.535769969181582 3710 3009.81818181818 2973 0.0476190476190476 2066 1.58518715981072 1.58518715981072 1 0.958879553706555 3708 4085 2066 3263 2589 2076 3691 3742 2373 2542 2973 3135 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 0.662230131557947 0.773024140799122 2100 3127.2 2973.5 0.113610618130545 1899 0.487824731607268 -0.487824731607268 -1 0.121734070188762 2098 3039 4469 NA 2908 1899 3425 2726 4198 4379 2131 3136 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 0.0893599503621072 0.165510168931555 2975 2884.27272727273 2974 0.00847367390236121 1302 1.02921690757326 1.02921690757326 1 1.79446494839453 2974 3593 2382 2695 1302 4212 3060 3524 2791 1652 3542 3137 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 0.223118287649382 0.338701374669786 1995 2641.45454545455 2974 0.0249306844661741 913 0.277859489836103 -0.277859489836103 -1 0.291589411116758 1991 3187 4333 3192 2974 913 1007 1923 4109 4091 1336 3138 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 0.370633057691686 0.491589727807315 1610 2877.09090909091 2974 0.0412209432439423 1244 0.653874098340854 0.653874098340854 1 0.450074197753828 1608 4093 2974 3846 3564 3026 1244 1769 2707 4494 2323 3139 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 0.456120252555975 0.578581547856492 3185 3045.54545454545 2974 0.0590852239301914 2030 0.700597901430259 -0.790147263630164 -1 0.371586187417501 3182 2336 4625 2394 2480 2030 3364 2238 3271 4607 2974 3140 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 0.35943518917414 0.478362197236587 3450 3098.27272727273 2975 0.0396825396825397 2163 1.12180532895237 -0.895625224233574 -1 0.80182002731956 3449 2269 2210 2163 4414 2881 3607 3260 2272 2975 4581 3141 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 0.0630021295978506 0.136679620044226 4615 2944.90909090909 2976 0.00589837854250833 1090 1.96046461039446 1.96046461039446 1 3.78182287061068 4614 2976 1090 2343 4488 3131 3597 2262 2037 2194 3662 3142 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 0.150240801219185 0.252792960327863 3250 2724.18181818182 2976 0.014691221206138 1208 1.14863770201014 1.35757478071806 1 1.53111527918094 3248 3042 3705 3173 1638 1208 2199 3887 2410 2976 2480 3143 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 0.348382467355994 0.470874024237146 4340 3205.72727272727 2977 0.0381878676056998 2191 1.26222330362609 1.49220948032053 1 0.921488688171825 4338 3653 2422 3260 2191 2224 4458 4487 2543 2710 2977 3144 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 0.199268649250204 0.310120521549803 4085 2904.90909090909 2978 0.02 360 0.356061433719072 -0.354026046093333 -1 0.404081896061604 4085 360 3106 1704 2749 2633 4342 3309 2978 4123 2565 3145 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 0.523868673921411 0.64271608967882 4265 3209.45454545455 2979 0.0652350227466444 1597 0.823552784867443 -0.80920612929552 -1 0.352881470745898 4264 1984 2979 1597 2540 4444 2402 4480 2756 4162 3696 3146 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 0.35943518917414 0.478362197236587 3845 3115.45454545455 2979 0.0396825396825397 1980 0.857185672850884 0.857185672850884 1 0.612680847431795 3841 2735 2410 3195 4319 2979 2601 3782 2177 4251 1980 3147 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 0.0839184282471183 0.156982736433532 2980 2717.18181818182 2979 0.00793650793650794 442 1.30764998068512 1.58267290416286 1 2.34696768096836 2979 3557 1514 1826 2875 3816 3799 3127 442 2408 3546 3148 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 2.81717366029821e-05 0.000356187010876961 2070 2872.81818181818 2980 2.56109975981538e-06 332 1.54022284092317 1.54022284092317 1 11.8541636182519 2068 3986 332 2885 3044 4321 2980 3300 2925 1725 4035 3149 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 0.00704838224799582 0.0267872824120912 4605 2535.45454545455 2981 0.000642824157706802 314 0.653874098340854 0.653874098340854 1 2.29427746890494 4603 462 3292 1907 314 1874 4606 2981 945 3707 3199 3150 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 0.726270090971166 0.8280237492927 1995 2860.18181818182 2982 0.111111111111111 1819 0.891470220575415 0.891470220575415 1 0.163069801496507 1994 3369 3509 3118 4248 2105 1819 2735 3199 2982 2384 3151 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 0.441884558094961 0.564369321131912 3860 2870.45454545455 2982 0.0516363213142834 1544 0.88632027725861 0.88632027725861 1 0.491457334612408 3860 2982 2534 3402 3670 1824 3112 1544 2646 4285 1716 3152 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 0.134501630282431 0.231778848361086 2670 2847.81818181818 2983 0.0130459530188278 965 1.06710845596515 1.06710845596515 1 1.51220741766002 2670 4214 3324 3256 3948 3990 1592 965 1511 2873 2983 3153 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 0.22884101127449 0.34496857265126 2180 2820.90909090909 2984 0.0233468461858014 749 2.24458518468169 2.24458518468169 1 2.31560681958926 2176 4321 3241 3865 2823 749 2074 3255 3513 2984 2029 3154 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 0.0185614502716372 0.0555776076504101 3010 2855.81818181818 2985 0.00170181170572841 555 0.757413120848284 -0.757413120848284 -1 2.1217331453364 3010 3287 3587 2864 555 2378 4628 2985 1757 3877 2486 3155 M16929 REACTOME_PI3K_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_CASCADE.html Genes involved in PI3K Cascade 33/105 Reactome 0.466738071388703 0.587219019917277 2990 3134.09090909091 2987 0.0555555555555556 2346 0.355874741897338 -0.28530079202129 -1 0.183638753209708 2987 2799 3192 3345 2817 4040 2374 2346 2564 3781 4230 3156 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 0.0508431243844581 0.116643671146604 3075 2979.63636363636 2987 0.00473251056069789 707 1.57416553838995 1.57416553838995 1 3.27850773391418 3075 3904 2654 4116 3964 3934 2987 707 2553 1921 2961 3157 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 0.684147620011753 0.791388730529517 2245 2968.63636363636 2987 0.0994692243506719 1899 0.312180157591207 0.286537837923466 1 0.0707981472579264 2243 3849 2987 3835 2816 1996 1899 3752 3187 3973 2118 3158 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 0.318424953507746 0.439252084821106 4210 2977.54545454545 2987 0.0342496367495115 1368 0.450310035647998 -0.517021613039392 -1 0.359093367936195 4210 1368 1812 2468 2124 3085 4095 3349 2987 4455 2800 3159 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 0.053453952258126 0.121182980300715 1620 2809.09090909091 2988 0.00498170077868692 526 0.648828184364399 0.648828184364399 1 1.32730090261616 1619 4149 2942 3772 2988 1229 526 4434 3979 4075 1187 3160 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 0.161385165508919 0.262241686633255 4110 2934.45454545455 2988 0.0158730158730159 1523 1.88429669771777 1.82128240336497 1 2.4447129473063 4110 3434 2393 2995 2909 2423 4236 2988 1523 1999 3269 3161 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 0.338769086023809 0.460537260547598 3685 2881.72727272727 2988 0.0369064637109933 930 1.21455215107271 1.21455215107271 1 0.912818164247607 3683 3864 2614 3735 2746 930 3658 2128 3556 2988 1797 3162 M4974 REACTOME_BASIGIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASIGIN_INTERACTIONS.html Genes involved in Basigin interactions 13/30 Reactome 0.495820609510765 0.616945134404525 1505 2780.90909090909 2989 0.0603583024078879 1421 0.318014815911088 0.400543683321213 1 0.148879888337172 1504 3701 2814 3714 3989 1648 1421 2989 3614 3519 1677 3163 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 0.106529561946846 0.19104382980594 3285 2812.54545454545 2989 0.0101879324091012 1187 1.51698751119904 1.23881147641047 1 2.43394128940771 3282 3126 1187 2572 2989 2700 3627 3283 2976 1940 3256 3164 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 0.536909196024653 0.656736228810108 4405 3158.18181818182 2989 0.0675919502341305 1703 1.67949129323189 1.67949129323189 1 0.684509609820106 4401 2989 1703 2928 2657 3153 3340 4207 2903 2127 4332 3165 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 0.441740416759855 0.564339038423305 1650 2944 2990 0.0516140576957877 1103 0.223545266560469 -0.229461338561555 -1 0.123965646478059 1650 4418 3729 4404 2990 1103 2399 2754 3657 3425 1855 3166 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 0.535246695586987 0.655044663233382 2595 2841.63636363636 2990 0.0672881407777514 1246 0.349443450827734 -0.38902867763318 -1 0.143296102244179 2591 2481 3203 3650 3020 1246 2990 1988 3505 4674 1910 3167 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 0.319124871759777 0.439838989184391 3045 3065.90909090909 2991 0.0343398371854858 1777 1.04597300469257 1.05532115521398 1 0.832742597310558 3044 3890 2818 3955 2125 4589 2113 1777 2991 2581 3842 3168 M17681 BIOCARTA_IL3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL3_PATHWAY.html IL 3 signaling pathway 11/29 BioCarta 0.517662708697517 0.637353508396365 2190 2884.18181818182 2992 0.064133907141876 1529 0.175305862950662 -0.228458350231144 -1 0.0765399905475817 2186 4303 3618 3639 2992 1659 2024 2252 4246 3278 1529 3169 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 0.598881260040338 0.712454324587211 3085 2959.90909090909 2992 0.0873015873015873 1609 0.349286498784362 -0.321512349269947 -1 0.114787852506991 3085 2254 4185 3050 3812 1609 2041 2938 2992 3902 2691 3170 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 0.0949246649151314 0.174028552344408 1645 2413.36363636364 2992 0.00992413705886678 693 0.31406400216975 -0.378173965583646 -1 0.532300139344433 1642 2992 4267 3161 3204 846 693 1350 3469 4012 911 3171 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 0.706716390291504 0.810294349132858 1895 3202.45454545455 2992 0.105517975247167 1891 1.16359911442286 -1.16186250822327 -1 0.237260624099471 1891 4316 3370 4512 2857 2281 3145 2992 4275 2881 2707 3172 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 0.115572265258517 0.20444380332254 4635 3032.54545454545 2992 0.0111028551093483 1476 1.49596550925012 1.49596550925012 1 2.30191256478854 4631 2500 2653 2992 1476 3375 3711 3653 1779 2441 4147 3173 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 0.147571447652795 0.249412467725749 3030 2626 2993 0.0144102443330466 1008 0.797095832726204 -0.769520701083661 -1 1.07291753940059 3029 2902 3575 3058 1619 1008 2993 2357 3285 3812 1248 3174 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 0.167067255760832 0.269771592176174 2000 2833.45454545455 2993 0.01811416785215 891 1.05077947290469 1.05077947290469 1 1.3344622419126 1998 3427 4519 2993 3593 2351 891 4458 3870 1058 2010 3175 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 0.000761288304562451 0.00470079369711562 2590 2704.45454545455 2994 6.92319880515279e-05 581 0.831099373833084 -0.831099373833084 -1 4.31800905100921 2587 1076 581 1577 3207 2994 2824 3475 3639 3850 3939 3176 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 0.117907736205742 0.207868943513961 2760 2947.81818181818 2994 0.0113405349792421 531 1.46654554803875 1.81627114660979 1 2.23302425672551 2756 4583 3125 4458 2636 531 2962 3893 3191 2994 1297 3177 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 5.19623210512889e-05 0.000579751039157952 780 2619.45454545455 2994 4.72395894565833e-06 369 1.34935965351481 1.44032755792434 1 9.7480459455238 4184 790 369 776 2994 4192 4580 4353 777 1817 3982 3178 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 0.145644644551109 0.247358336478991 2995 3247.90909090909 2994 0.0142079251584454 1607 1.16822409590693 1.36596855133712 1 1.58183325893597 2994 3860 3551 4539 1607 2277 2327 4289 2913 2971 4399 3179 M14766 REACTOME_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTRINSIC_PATHWAY.html Genes involved in Intrinsic Pathway 7/23 Reactome 0.000266170946730363 0.0021033339905202 2225 2566.27272727273 2995 2.66202833243558e-05 53 1.42267534279842 1.42267534279842 1 8.50058112822514 2225 2995 4071 3049 3625 3348 3974 53 1263 1511 2115 3180 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 0.379627046547251 0.501248898315136 3115 2974.54545454545 2996 0.0424746961410227 1440 1.05077947290469 1.05077947290469 1 0.703452914370668 3111 2741 3114 2996 2858 4326 4412 1440 2631 1757 3334 3181 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 0.234628107794202 0.347163660601083 3575 2808.36363636364 2997 0.0240154216912855 1908 0.32482798381725 -0.437096403201743 -1 0.333108815217979 3575 2009 3301 3479 1908 2140 2997 3136 2287 3525 2535 3182 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 0.289316845425166 0.411578244584799 4415 3021.90909090909 2998 0.0335762324523608 1156 0.333564518585683 -0.243518978221019 -1 0.287036677939817 4411 2998 4334 2814 2495 1216 1156 2623 3848 4094 3252 3183 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 0.20091601058807 0.312165923612632 1860 2755.18181818182 2998 0.0221792637908241 727 1.16584713251892 -1.03796716721555 -1 1.31565096766787 1857 4647 4338 4481 2119 727 3057 1635 3092 2998 1356 3184 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 0.518609134808032 0.638015858679558 3000 3162.27272727273 2998 0.0643009948710193 2166 1.45668638057772 1.45668638057772 1 0.634534729565757 2998 3800 3425 3715 2536 4290 2166 2616 2995 2463 3781 3185 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 0.142993145251713 0.243571747964205 3000 2926.54545454545 3000 0.0139301881641765 1600 0.907946496957157 0.897776925307385 1 1.24298111034261 3000 2309 3116 3699 1600 1999 4668 3714 2234 3057 2796 3186 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 0.285680411775939 0.407248478744549 2970 2971.4 3000.5 0.036690507302287 1965 0.31341232951193 -0.576839951217943 -1 0.27290827278115 2968 3115 4438 NA 2167 1965 3169 2026 3033 4335 2498 3187 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 0.116011032619228 0.205050499785323 1980 2885.09090909091 3002 0.0111474647117189 1480 0.240682236811375 0.273369142933655 1 0.369657797468649 1977 3024 3326 3679 1480 2341 3002 2745 4460 3404 2298 3188 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 0.63389956273523 0.745034700521015 2600 2992.90909090909 3002 0.0873015873015873 1875 1.61718731904454 1.61718731904454 1 0.461371309325229 2598 3086 1875 2692 3947 4310 2002 3501 3002 2082 3827 3189 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 0.361464749863721 0.480653750811974 2910 3269.72727272727 3002 0.0399595445363675 1371 0.24053801895338 0.210697047539851 1 0.170812372179389 2906 4464 2972 4348 2216 3002 1371 2697 4410 4288 3293 3190 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 0.183435650877954 0.2903003917643 3400 3052.72727272727 3005 0.0200610016876631 1809 0.800508376728112 -0.800508376728112 -1 0.959716448692438 3398 2891 4143 3005 1809 2213 2289 4539 3316 3840 2137 3191 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 0.0655459797380641 0.140571378056095 3605 3004.18181818182 3005 0.00614403464124777 1158 1.43991841944783 1.43991841944783 1 2.73848007913182 3605 2359 1498 2586 1158 4525 4673 3005 3828 2064 3745 3192 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 0.328646078987543 0.44977673076391 3825 2982.18181818182 3005 0.0355753082879108 1384 0.633042077535849 0.633042077535849 1 0.490281360820405 3823 1384 3005 2097 2148 3018 4478 2298 3112 4631 2810 3193 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 0.0311544305463196 0.0803835679398411 3040 2491.90909090909 3006 0.0028731419538978 390 1.08777194498467 -1.04077276642597 -1 2.65806242910599 3038 3553 3087 3628 779 390 3852 2396 2802 3006 880 3194 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 0.597318307603006 0.711317303539438 4555 3408.27272727273 3008 0.0793650793650794 2229 1.8636644772713 1.8636644772713 1 0.615351116542755 4551 4059 2373 2809 4263 3008 4364 2580 2888 2229 4367 3195 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 0.0382135147994463 0.0944454273998974 4375 2976.18181818182 3008 0.00353580715141929 871 0.915936714004358 1.00639611726335 1 2.09503951012624 4371 1621 3008 2018 871 2683 4672 4073 3284 2409 3728 3196 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 0.232850105696956 0.34496857265126 2990 3131.36363636364 3008 0.0238095238095238 1799 1.34433363331712 -0.868155059868409 -1 1.38687012204497 2986 3008 2663 3694 2106 4467 3982 3115 1799 2777 3848 3197 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 0.700915966745923 0.805124105272494 1920 2913.18181818182 3009 0.103924013642512 1737 0.891470220575415 0.891470220575415 1 0.187304208260736 1919 3656 3629 3364 4507 1997 1737 2677 3200 3009 2350 3198 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 0.467717607507869 0.588066731629159 1610 2968.18181818182 3009 0.0557133989787484 1580 0.241793534824702 0.256984164622613 1 0.124432383934607 1855 4029 3009 3449 4634 2023 1607 1580 4352 4505 1607 3199 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 0.0543332497183653 0.122701497918198 4310 2861.09090909091 3009 0.00506576591205255 1053 0.923151783692378 -0.703343919440329 -1 1.87733860922101 4309 3556 3675 2963 1053 1444 4200 2297 3009 3015 1951 3200 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 0.00215739485306736 0.0108355329919332 2910 3145.09090909091 3010 0.000196319397902731 666 1.20179337341827 1.20179337341827 1 5.27114549446638 2908 3786 666 4008 4459 3351 2239 2955 2930 3010 4284 3201 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 0.36883418131775 0.489342291521795 1370 2671.72727272727 3010 0.0409721379201909 982 0.943348622268325 0.994445101726886 1 0.653515127956749 1370 3498 3749 3809 3010 982 2474 2317 3306 3142 1732 3202 M19877 KEGG_ENDOMETRIAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOMETRIAL_CANCER.html Endometrial cancer 26/61 KEGG 0.450818149757717 0.573555553184724 4155 3242.63636363636 3015 0.0530264820117817 1562 1.21455215107271 1.21455215107271 1 0.654450920089725 4151 3015 2349 2743 4190 2819 4627 1562 3345 2587 4281 3203 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 0.338535904537642 0.460353815630699 2910 3126.27272727273 3015 0.0404875205671556 1734 0.357709800032325 -0.400345057554644 -1 0.268981271729453 2909 3678 4379 4419 2225 1734 2411 3322 3015 4184 2113 3204 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 0.466738071388703 0.587219019917277 2740 3093.72727272727 3015 0.0555555555555556 1842 0.985608103741814 1.12780103726112 1 0.508594238591555 2736 1842 2347 3015 3371 4588 3498 4143 2498 2719 3274 3205 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 0.557443745451391 0.675680649556446 4110 3286.90909090909 3016 0.0714285714285714 2198 0.852326785622773 0.852326785622773 1 0.323887764080453 4108 2969 3720 3522 2632 2198 4135 4049 2820 2987 3016 3206 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 0.405791627505296 0.528499045717015 3240 2920.90909090909 3017 0.0462183146388734 1038 1.10858603309022 1.10858603309022 1 0.68526635610404 3237 4213 2998 3956 3679 1038 3017 2111 3342 2874 1665 3207 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 0.836613500661709 0.921162553155951 2205 3021.63636363636 3018 0.151847010721974 2201 0.813302707359249 -0.813302707359249 -1 0.0647378804672769 2201 3444 3018 2571 3107 2270 4374 3661 3869 2394 2329 3208 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 0.35943518917414 0.478362197236587 4680 3277 3020 0.0396825396825397 1749 0.382970248821588 -0.320666808018823 -1 0.273731285965233 4679 1749 2973 2637 4624 2891 3395 3020 2197 4163 3719 3209 M8728 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM.html Hypertrophic cardiomyopathy (HCM) 48/137 KEGG 1.95802585100284e-05 0.00027115789224785 2460 2699.54545454545 3021 1.7800393435274e-06 311 1.82447917089839 1.3111729062301 1 14.5242766728719 2456 3470 311 2823 3391 4008 3021 3768 2152 571 3724 3210 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 0.34177449848747 0.463681325973447 3555 3293.54545454545 3022 0.0373052366117826 2176 1.30676629669856 1.43572798238491 1 0.973505261028892 3551 4575 2615 3871 2176 2226 2966 4085 3022 2927 4215 3211 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 0.892966942214243 0.962826298024837 2090 3190.27272727273 3022 0.183841782794538 2052 1.01405746558881 -1.01405746558881 -1 0.0372359385046315 2088 4172 2265 4098 4617 2052 3735 2393 4094 3022 2557 3212 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 0.852549346673383 0.933203980030711 1675 3216.63636363636 3023 0.159723094515952 1675 0.276767379137017 -0.322480633765272 -1 0.0185461847241757 1675 4002 2930 3365 3918 2477 2422 3023 4340 4532 2699 3213 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 0.00776470525747834 0.0286725049933361 2195 2854.63636363636 3024 0.000708386025349929 333 1.25079504528386 -1.03465537491335 -1 4.30626304126603 2191 2654 3521 3647 333 3959 3024 3605 2536 2721 3210 3214 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 0.353330304359445 0.476325030560518 2860 3202.72727272727 3025 0.038854097024878 1808 1.17384020660474 1.20206054068034 1 0.84386829585604 2856 4539 2244 4224 2204 4533 2078 3586 3025 1808 4133 3215 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 0.35943518917414 0.478362197236587 3025 3323.45454545455 3025 0.0396825396825397 2296 1.4090387572199 -1.3305210886483 -1 1.00712259576534 2828 4577 3022 4482 3025 2778 4422 3128 2296 2779 3221 3216 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 0.326981044684344 0.44802139631311 3050 3119.45454545455 3026 0.0353581091003327 1651 0.634409160957587 0.634409160957587 1 0.493744758099679 3047 2967 1651 3206 2144 4276 3026 2561 2700 4649 4087 3217 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 0.233087257403134 0.345210773764565 4230 3074.54545454545 3028 0.0238369615875206 1805 1.49454931704358 1.49454931704358 1 1.54082206842534 4230 2714 1805 3618 1901 2196 4432 4459 3185 2252 3028 3218 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 0.875560374975792 0.950978787567881 4655 3218.63636363636 3029 0.172584756576122 1955 1.49234186417521 1.49234186417521 1 0.0727084865932652 4654 2622 2535 3594 3903 1955 4024 2665 3532 2892 3029 3219 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 0.0839184282471183 0.156982736433532 3030 2626.72727272727 3030 0.00793650793650794 863 1.65221206068581 1.65221206068581 1 2.96538704228748 3030 2730 2156 1812 3683 3306 3096 3592 863 1268 3358 3220 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 0.0386169686350849 0.0951915386764901 2650 2647.18181818182 3030 0.00357381445096705 285 1.22974056687782 -1.10219933532614 -1 2.80342931893935 2646 4202 3441 4286 3238 285 2127 1875 3194 3030 795 3221 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 0.0172646869560697 0.0522962657247205 1835 2338 3031 0.00158197095767068 325 0.246409010992557 -0.265927420767925 -1 0.704798039772739 1835 3065 3594 3031 4601 454 389 1535 3332 3557 325 3222 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 0.700492117901225 0.80493037383157 2230 3070.09090909091 3031 0.113577388920185 1803 0.35664314694863 0.467426644303534 1 0.0750164445649493 2228 2449 4128 3981 3031 2681 1803 2931 3589 3816 3134 3223 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 0.624771041454169 0.738752737889032 1270 2841.72727272727 3033 0.0852557926187401 1266 0.216796516958034 -0.24687099883293 -1 0.0636298015017129 1266 3725 3697 4191 3033 1561 2081 2153 3921 3552 2079 3224 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 0.0177389047340212 0.0534219200408889 2085 2680.09090909091 3033 0.00178821172495205 331 0.234711512650213 0.222889183743774 1 0.666494884233037 2081 3033 4372 3695 2679 961 331 3110 3830 4164 1225 3225 M15216 REACTOME_BOTULINUM_NEUROTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BOTULINUM_NEUROTOXICITY.html Genes involved in Botulinum neurotoxicity 7/20 Reactome 0.160833055199373 0.262241686633255 2205 3209.45454545455 3034 0.0173817253508608 1742 0.1526538897147 0.19822479390761 1 0.198055296130519 2203 4602 3923 4583 1742 2177 3034 2204 4672 3452 2712 3226 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 0.160833055199373 0.262241686633255 2205 3210.54545454545 3035 0.0173817253508608 1743 0.1526538897147 0.19822479390761 1 0.198055296130519 2204 4603 3924 4584 1743 2178 3035 2205 4673 3454 2713 3227 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 0.00322177021210633 0.0147577861328741 2525 2975.36363636364 3035 0.000293318000032073 698 1.40778423115797 1.75491652245998 1 5.75306080143426 2524 3919 698 3413 2112 2436 4076 3816 3797 2903 3035 3228 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 0.549111503718829 0.669042253361007 1425 2740.72727272727 3035 0.0698526751054429 1265 1.0057798248392 1.2316201867746 1 0.391826228066039 1425 3583 3683 3527 3035 1265 2811 2415 3391 3098 1915 3229 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 0.538057989348299 0.65779800106604 3710 3187.45454545455 3037 0.0678024634089653 1338 0.131401606842106 -0.143098073497356 -1 0.0533495446803972 3037 4637 3707 4595 2565 1338 2018 2790 4658 3706 2011 3230 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 0.63389956273523 0.745034700521015 2675 3425.72727272727 3037 0.0873015873015873 2508 1.18597656621885 1.24212451858705 1 0.338350143299662 2673 4612 3488 4519 2761 3818 2508 3037 3026 2958 4283 3231 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 0.372376235588523 0.493203798747264 3545 3022.72727272727 3038 0.0455131753630906 1480 0.278074718955991 -0.172592260107173 -1 0.190520657000743 3544 3038 4176 3428 2507 2960 1960 1480 2753 3891 3513 3232 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 1.29863343782201e-05 0.000190168634051061 1245 2740.81818181818 3038 1.18058282141978e-06 295 1.46305904850203 1.46726266075591 1 12.1502403421451 1245 4084 295 4165 2219 4490 2780 3178 3698 957 3038 3233 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 0.248545185775807 0.364304892256939 3470 2833.90909090909 3039 0.0256422523234045 781 0.945807526217259 0.945807526217259 1 0.925734773457234 3891 3467 1887 3468 4405 781 3804 1448 2451 3039 2532 3234 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 0.0653971851288825 0.140407414664398 3435 2981.63636363636 3039 0.00612964902096836 1096 2.07333958077616 -2.07333958077616 -1 3.94548497249616 3435 3308 1096 3676 4400 2561 3500 2738 3039 2571 2474 3235 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 0.411478557109715 0.534716727292326 1340 3011.63636363636 3040 0.0470517887558346 1046 0.230633272049178 -0.234795153436912 -1 0.139949951966732 1336 4419 3688 4553 3040 1046 2519 2625 4267 3741 1894 3236 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 0.114718318831536 0.203086528917483 3045 2915.27272727273 3041 0.0110160917852212 1214 1.8541326198443 1.8541326198443 1 2.86501253530168 3041 3897 1214 3154 3397 4154 2264 1972 2882 2470 3623 3237 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 0.0116486403614855 0.0387956849565894 3045 3109.90909090909 3042 0.00106461628356023 829 1.51935086267539 -1.51935086267539 -1 4.78554385502398 3042 2758 829 2342 3558 4586 1959 4484 3490 2697 4464 3238 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 0.751985672431077 0.848905049629493 3355 3239 3042 0.119047619047619 2230 0.370157227100753 -0.256221285378388 -1 0.0587739715962408 3353 2773 2662 2820 2983 3920 3042 2230 3211 4656 3979 3239 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 0.298735036746822 0.4173739958842 3420 3046.18181818182 3044 0.0317460317460317 1531 1.6722414479866 1.6722414479866 1 1.41631959830545 3417 4109 1531 3044 4235 1625 3746 4673 2032 2633 2463 3240 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 0.0365975386247668 0.0911596437230444 4015 2914.90909090909 3044 0.00338371953826773 852 1.16002554937187 1.48758192678986 1 2.69316440091451 4014 3502 3044 3063 852 2095 3645 4246 2758 2404 2441 3241 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 0.307751580217675 0.427042909357425 3945 3122.27272727273 3044 0.0328844612868508 1475 1.09658640185324 -0.940767540772448 -1 0.904420363260592 3942 3410 1475 2727 2443 3827 3044 4633 2139 2244 4461 3242 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 0.298735036746822 0.4173739958842 4385 3160.18181818182 3045 0.0317460317460317 2079 1.11141253215191 1.20900534894933 1 0.941320616664936 4381 3045 3672 3616 2374 2092 4431 3253 2079 2904 2915 3243 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 0.419257571735323 0.540181738012572 2475 3001.90909090909 3046 0.0482038151551984 1368 0.328658732492802 -0.334492870108547 -1 0.196193103253793 2473 2323 3250 3815 4555 1368 3046 2674 4009 4126 1382 3244 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 0.122600566194512 0.214608238022966 3985 2852.45454545455 3046 0.0118198569863446 1513 1.01953200625431 -0.571752886235781 -1 1.52085117524332 3984 3046 2728 2576 1513 1913 3946 3247 2069 3076 3279 3245 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 0.00201768693514429 0.0102251453749991 3910 2785.18181818182 3046 0.00018359452697269 664 1.23549499076889 1.46726727422455 1 5.48839984949888 3906 2926 664 1854 3046 2967 4323 3101 3184 979 3687 3246 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 0.347468336832473 0.470045215472566 1680 2905.36363636364 3046 0.0380652829138488 951 1.59008010255122 -1.59008010255122 -1 1.16355649273515 1678 4410 3719 4155 4478 951 2583 2240 3202 3046 1497 3247 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 0.0170023382376698 0.0516685842942418 3555 2507.36363636364 3047 0.00155774341199144 164 1.04806911066368 1.17617592361416 1 3.01003512470446 3555 3191 3132 3460 1336 164 3827 2059 2675 3047 1135 3248 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 0.614098798987246 0.728523284064363 4185 3257.63636363636 3048 0.0829206364033342 2104 0.730986568861182 -0.769819826073411 -1 0.224424501340807 4181 2757 2811 2104 2673 3048 3905 3806 3462 4234 2853 3249 M1519 KEGG_ENDOCYTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOCYTOSIS.html Endocytosis 112/231 KEGG 0.061055580385761 0.133466629381513 3860 2962.54545454545 3051 0.00571081210473346 1115 1.46623973808141 1.62946513455505 1 2.86225005812185 3857 3921 2031 3626 1115 2188 3659 2685 3051 2480 3975 3250 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 0.275742742869669 0.39623750171336 3055 2954.90909090909 3051 0.0317460317460317 1021 1.02401096892853 1.02401096892853 1 0.918878744992325 3051 1021 3904 2969 2465 4523 3617 3864 2043 1685 3362 3251 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 0.466738071388703 0.587219019917277 4590 2981.45454545455 3051 0.0555555555555556 1473 1.28209913597262 1.28209913597262 1 0.661589765154942 4589 2087 2152 1473 3405 3051 4489 3568 2513 1640 3829 3252 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 0.0209263649030545 0.0608211823902902 2845 3061.09090909091 3053 0.00211260776394304 643 0.47807892512553 0.52252353550639 1 1.29745748470922 2845 2554 4114 2865 643 3718 2785 3699 3602 3794 3053 3253 M10960 REACTOME_P2Y_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P2Y_RECEPTORS.html Genes involved in P2Y receptors 5/14 Reactome 0.692053852342561 0.797777208383085 2025 3008.09090909091 3055 0.111111111111111 1914 0.523882108738507 0.778550329372941 1 0.114726427188148 2023 3394 4006 3055 3861 2542 1914 3040 3153 3599 2502 3254 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 0.354780148748656 0.477867139130842 2015 2674.72727272727 3055 0.0390501974395544 963 1.41594741783624 1.41594741783624 1 1.01348175484088 2012 3120 3671 3884 2472 963 3442 2181 3055 3109 1513 3255 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 0.0789416747284595 0.156982736433532 1135 2514.63636363636 3056 0.00744775576225114 630 0.648828184364399 0.648828184364399 1 1.16451558263251 1131 3347 3487 3056 3629 1297 630 1512 3611 4584 1377 3256 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 0.52340095663996 0.642393107075655 3170 3205.63636363636 3057 0.0714285714285714 1887 0.903749173946106 -1.46235772448114 -1 0.387684894930482 3167 3550 4645 2956 3489 1887 2360 2808 2722 4621 3057 3257 M4732 BIOCARTA_LECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LECTIN_PATHWAY.html Lectin Induced Complement Pathway 7/15 BioCarta 0.0765897756730953 0.156982736433532 3060 2552.63636363636 3058 0.00793650793650794 265 1.04153308372933 -0.964244126337474 -1 1.86934158394893 3058 1322 3846 1120 3658 4101 2316 3304 265 1501 3588 3258 M11520 BIOCARTA_TPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TPO_PATHWAY.html TPO Signaling Pathway 18/42 BioCarta 0.560079984871966 0.678525028208385 2490 2888.63636363636 3058 0.0719327887892852 1366 0.26399753553873 -0.306280664929382 -1 0.099245202008843 2489 3726 3508 3046 3058 1366 2926 3296 3428 3339 1593 3259 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 0.43598360485036 0.558049487115211 2420 2976.27272727273 3058 0.0507291231671515 1600 0.994699970241019 0.994699970241019 1 0.562410773111675 2417 3058 1600 2863 3433 4677 3681 3585 3189 2526 1710 3260 M13103 KEGG_AUTOIMMUNE_THYROID_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AUTOIMMUNE_THYROID_DISEASE.html Autoimmune thyroid disease 24/87 KEGG 0.176607104904842 0.281290850942398 3505 2908 3059 0.0175104957947616 1355 1.78606414326979 1.78606414326979 1 2.19586451032675 3504 3059 1355 2135 1748 4477 4179 3791 2502 1453 3785 3261 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 0.378979712990602 0.500535212816787 3060 3191.72727272727 3059 0.0423839084560832 1540 1.46693471565438 1.46693471565438 1 0.984077436893375 3059 2543 1540 3021 3569 4635 4057 2961 3974 2324 3426 3262 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 0.670505057229465 0.777527022563047 3755 3144.09090909091 3060 0.0960007535133046 1899 0.650112755713168 -0.650112755713168 -1 0.158572124417453 3753 3060 2999 2739 3212 2741 4496 1899 4145 3436 2105 3263 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 0.814593149616 0.90626388867535 2480 2881.36363636364 3060 0.142042095792295 1871 1.21455215107271 1.21455215107271 1 0.115873557963356 2478 2295 2081 3139 3060 3222 4085 3357 4042 1871 2065 3264 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 0.048121564980099 0.111798539165466 3475 3073.90909090909 3061 0.00447341403870111 989 0.39812077274297 -0.328508300364651 -1 0.845536456332092 3474 2160 2434 2783 989 3878 2755 3950 3061 4302 4027 3265 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 0.059559294981935 0.130988816914109 4160 2764.54545454545 3061 0.00556687253267615 1101 1.25889229611177 1.37046855842223 1 2.48035372520442 4156 3295 1447 3578 1101 1822 4282 3061 2433 2132 3103 3266 M129 PID_PLK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PLK1_PATHWAY.html PLK1 signaling events 18832364 31/65 Pathway Interaction Database 0.793352056002422 0.888488058719704 1740 2901 3062 0.13354047399314 1708 0.310641774780267 -0.322622184129647 -1 0.0356013419076198 1740 3561 2585 3357 3845 1708 3062 2353 4146 3382 2172 3267 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 0.270215314268674 0.391052798845895 2250 3074.18181818182 3063 0.031009599688702 1116 0.331928827130667 0.363768475091355 1 0.30208839886602 2247 4132 4010 3551 4276 2523 1116 3063 2652 3607 2639 3268 M2482 BIOCARTA_ARAP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARAP_PATHWAY.html ADP-Ribosylation Factor 14/22 BioCarta 0.0049627180085501 0.0203815044593039 2555 2510.81818181818 3064 0.00045217711776788 169 0.2723550839557 -0.284293762687882 -1 1.02777481690129 2551 3064 3497 3935 4188 250 616 2275 3835 3239 169 3269 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 0.698152987361708 0.80243926877041 3215 3157 3064 0.103174603174603 2236 1.08315018934199 1.08315018934199 1 0.231084502657956 3211 2236 2824 2405 3925 4683 3064 2875 3142 2659 3703 3270 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 0.0839184282471183 0.156982736433532 3035 2597.63636363636 3067 0.00793650793650794 808 1.37931964003909 -0.914647255710763 -1 2.47560024832329 3032 3780 3309 3344 1877 808 3356 3336 1019 3067 1646 3271 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 0.0765897756730953 0.156982736433532 3785 2776.63636363636 3069 0.00793650793650794 199 1.70956702222945 1.70956702222945 1 3.06832761742631 3784 3388 3908 2421 2564 1774 4407 3069 199 1598 3431 3272 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 0.475190356368471 0.595990714512035 2305 2847.72727272727 3069 0.0569263321798528 1337 0.577018634726521 0.577018634726521 1 0.289460558339205 2301 3927 2528 3115 3292 1337 3654 1590 3069 4610 1902 3273 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 0.0704416197077838 0.148823007191467 4625 2999.27272727273 3070 0.006618515549919 1192 1.12640531502841 1.29677151331264 1 2.07995039997882 4625 3083 2606 3891 1192 1330 3534 4005 3005 3070 2651 3274 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 0.788646249573679 0.88411395346944 2985 3117.09090909091 3071 0.143946325287601 1310 1.21455215107271 1.21455215107271 1 0.145004863875213 2985 2613 4561 3071 3066 3388 3291 3263 3743 1310 2997 3275 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 0.0936391547088664 0.172187331497993 3210 2797.45454545455 3072 0.00889815393786299 1330 0.329068130494286 -0.429446394581088 -1 0.561122983242551 3209 2914 3072 3156 1330 2249 3102 2171 3416 3413 2740 3276 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 0.242976348614623 0.35725985867842 3455 2991.09090909091 3072 0.024988024677909 1397 0.96957541233836 0.96957541233836 1 0.967350812025081 3455 2508 1397 2040 3346 3861 3767 2902 3072 2432 4122 3277 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 0.00518680505337703 0.0210801114311576 3370 2759 3073 0.00047264310738928 262 0.890211641230575 -0.671837249370926 -1 3.3302725005365 3369 3283 3073 2757 262 4352 3766 2923 1370 1989 3205 3278 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 0.466738071388703 0.587219019917277 3815 3070.45454545455 3074 0.0555555555555556 2066 2.07333958077616 -2.07333958077616 -1 1.0698862575653 3812 3672 2317 3930 3169 2128 3074 4235 2459 2066 2913 3279 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 0.821457247651427 0.910441973153876 3950 3141.27272727273 3075 0.144979424331746 2261 0.373683102167217 -0.400369058327421 -1 0.0339849330405408 3948 2333 2978 2598 3075 2261 3392 3580 3949 3401 3039 3280 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 0.156982736433532 3760 3136.18181818182 3075 0.00793650793650794 443 1.8636644772713 1.8636644772713 1 3.3449014346255 3759 3935 2890 3009 3645 3014 4664 3075 443 2040 4024 3281 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 0.0990044907935832 0.180238944778062 3720 3100.81818181818 3075 0.00943295567914494 1362 0.339124905227972 -0.297611497539034 -1 0.56324912029759 3717 2694 3075 2452 1362 3854 1660 4609 2527 3506 4653 3282 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 0.157449766155067 0.261913242528451 2850 3134.36363636364 3075 0.0154540678739095 1282 0.46318742866322 -0.407314289900538 -1 0.601508530585588 2848 2728 1282 3075 3155 2599 3186 4475 3585 4560 2985 3283 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 0.466738071388703 0.587219019917277 2770 3101.81818181818 3076 0.0555555555555556 2106 1.05077947290469 1.05077947290469 1 0.542224017768719 2769 3171 3492 3076 3779 3850 4204 2395 2528 2106 2750 3284 M19888 KEGG_ACUTE_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ACUTE_MYELOID_LEUKEMIA.html Acute myeloid leukemia 28/71 KEGG 0.122497793393799 0.21450846780394 4020 3012.63636363636 3077 0.0118093349170447 1512 0.653874098340854 0.653874098340854 1 0.975688515861387 4019 3129 2449 3000 1512 4446 1538 2313 3077 3231 4425 3285 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 0.667434366415499 0.775117085755398 4470 3124.27272727273 3078 0.0952380952380952 1907 1.21320581720062 1.21320581720062 1 0.29956944209558 4468 3166 2486 2356 4168 2567 3688 1907 3078 2572 3911 3286 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 0.597318307603006 0.711317303539438 3865 2942.81818181818 3080 0.0793650793650794 1399 1.27616083983238 -0.647449031412981 -1 0.42136715443995 3863 3397 3645 2669 2842 1399 3505 3403 2910 3080 1658 3287 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 0.482206899749667 0.60208407466745 1610 2841.54545454545 3081 0.0636987010238025 1570 0.414467064504262 0.457675684601748 1 0.203830214549536 1610 2862 3898 3284 2532 1579 3236 3081 4219 3386 1570 3288 M1909 BIOCARTA_EGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EGF_PATHWAY.html EGF Signaling Pathway 25/53 BioCarta 0.298735036746822 0.4173739958842 3955 3197.54545454545 3082 0.0317460317460317 1974 0.957887193887956 -0.701222236703204 -1 0.811290981472427 3955 3017 3447 2044 3618 2405 4455 4626 1974 2550 3082 3289 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 0.0839184282471183 0.156982736433532 3760 2806 3084 0.00793650793650794 695 1.1903189876279 1.41231483065504 1 2.13638223932823 3760 1669 3084 1089 4453 2470 3179 4042 695 2778 3647 3290 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 0.153847714919249 0.257659182312938 3475 3198 3085 0.0150721632613625 1651 1.36581529303493 1.36581529303493 1 1.79536675365388 3471 3051 2920 1793 1651 4621 3085 4268 3182 2882 4254 3291 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 0.220415371259523 0.335673197829745 2270 2947.36363636364 3085 0.0223815527080883 1276 0.307720981715758 0.288210644757042 1 0.325605215123351 2269 3691 3530 3991 1867 2266 1276 3085 3181 4496 2769 3292 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 0.0839184282471183 0.156982736433532 3260 2545.45454545455 3086 0.00793650793650794 636 1.2002650676393 1.38484791454241 1 2.15423344468509 3260 1007 1361 1382 3086 3797 3451 4427 636 2072 3521 3293 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 0.196961912485737 0.30755198997273 3110 2731 3088 0.0197436834918354 830 1.46693471565438 1.46693471565438 1 1.67659973184026 3110 830 1341 2149 3088 4450 3892 1940 3898 2166 3177 3294 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 0.659490156734773 0.770907406051987 3795 3087.27272727273 3088 0.0932943255166059 1445 0.346768330730356 -0.348562394022009 -1 0.0874558572756243 3794 1592 2703 3088 3726 1445 4208 2642 4056 4488 2218 3295 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 0.162953983727118 0.264405251989361 3045 3107.72727272727 3089 0.0160405248610262 1292 1.13938478110989 1.28660435982178 1 1.46917940099606 3045 4041 1292 3169 2116 2594 3657 3990 3089 2546 4646 3296 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 0.202989955805576 0.31465793347831 2935 2981.63636363636 3090 0.0224333445970528 733 1.05486585644775 1.22569626941126 1 1.18227918107052 2934 4349 4121 4043 2200 733 3665 2786 3090 3155 1722 3297 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 0.0839184282471183 0.156982736433532 3100 2960.72727272727 3090 0.00793650793650794 584 1.84083109373717 1.84083109373717 1 3.30392012158634 3097 3090 2947 3158 2060 4159 2265 4435 584 2214 4559 3298 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 0.220681274015258 0.335791891999298 2515 2778.54545454545 3091 0.0224118709221487 1038 0.764161110170704 -0.764161110170704 -1 0.808311018048063 2514 3106 2442 3091 4419 1321 3339 1485 3496 4313 1038 3299 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 0.442116177214092 0.564511282404697 2305 3066 3092 0.0566901337763087 1388 0.474627368186203 0.543641914244192 1 0.263061278959196 2302 2455 4659 3092 2531 3159 1388 3323 3996 4638 2183 3300 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 0.111566330075818 0.198255526255322 4530 2842.54545454545 3094 0.0117598350266407 862 0.401866751095377 -0.23113354722477 -1 0.630344180617509 4528 862 4158 1356 1509 3094 3817 2533 1041 3860 4510 3301 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 0.0340039207908378 0.0859915665547036 2170 2573.18181818182 3096 0.00314010530308995 263 1.05541937272273 -0.981276587356977 -1 2.51001352105116 2167 3917 3679 3266 4189 263 2396 1573 3096 3105 654 3302 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 0.232850105696956 0.34496857265126 3955 3121.63636363636 3096 0.0238095238095238 1689 0.332013500091587 0.254856170891547 1 0.342518844933154 3953 2443 3296 2760 3768 2069 4534 3096 1689 4440 2290 3303 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 0.441131447604692 0.563868511586357 1305 3054 3097 0.0515200558698764 1101 0.230530155879369 -0.234259337599635 -1 0.1280254613045 1301 4550 3677 4559 3097 1101 2691 2567 4390 3736 1925 3304 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 0.28269524130317 0.403998139904438 3390 3075.09090909091 3100 0.0326795456212652 1323 0.479116445806455 -0.56275045851996 -1 0.420918961315082 3388 1323 4409 1804 2087 4220 2471 2901 3100 4268 3855 3305 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 0.597318307603006 0.711317303539438 3330 3104.54545454545 3101 0.0793650793650794 2241 1.14672566625037 1.14672566625037 1 0.378629805755001 3328 2241 2884 2262 3101 3893 3544 3561 2863 2425 4048 3306 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 0.493548756274608 0.614934717336563 1940 3191.18181818182 3101 0.0599741735880471 1907 0.225149821324097 -0.231879283482062 -1 0.106117109395023 1939 4421 3722 4463 2488 1907 3101 3006 3935 3487 2634 3307 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 0.0839184282471183 0.156982736433532 4605 2991.81818181818 3101 0.00793650793650794 877 1.28843165593424 1.59435917021471 1 2.31247466851022 4604 3746 3123 3825 2414 1917 3759 2486 877 3101 3058 3308 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 0.466738071388703 0.587219019917277 3375 3215.54545454545 3102 0.0555555555555556 2044 0.923658893572389 -0.796538314240086 -1 0.476627160333759 3375 3102 2044 2894 2959 4359 3311 4276 2495 2180 4376 3309 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 0.597318307603006 0.711317303539438 4065 3171 3103 0.0793650793650794 1804 0.422425736771799 -0.487151567875932 -1 0.139477975676939 4063 4433 1804 3866 3056 2628 2460 3103 2861 3234 3373 3310 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 0.0521583352771251 0.118762856709722 2585 2806.81818181818 3103 0.00485796274455993 1035 0.310972076227453 -0.335696691434446 -1 0.64223297269024 2581 3103 3227 3307 1035 1939 3471 2800 3536 3931 1945 3311 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 0.735626142210112 0.836768188672265 2590 2961.72727272727 3104 0.113916988983276 1551 1.19243325133954 1.19243325133954 1 0.205980274156269 2590 4426 3159 3517 3104 3413 1806 2914 3549 1551 2550 3312 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 0.0541570040279577 0.122362449795087 3130 2701.72727272727 3106 0.00504891027046643 1052 1.17792720355255 1.28211644991974 1 2.39861396046996 3130 3364 1354 3227 1052 1813 3994 3106 3350 2613 2716 3313 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 0.578497707814996 0.69497122925912 2645 3233.63636363636 3107 0.0755340843158237 2556 0.522536967759313 0.522536967759313 1 0.184308276684536 2643 3107 3019 3385 2622 4376 2556 3418 3774 3605 3065 3314 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 0.0198916963590011 0.058661100779282 4430 2967 3108 0.00182489643923523 583 1.25806324710935 1.25806324710935 1 3.45835257932098 4426 3661 1400 3108 583 3267 3818 2827 2924 2973 3650 3315 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 0.0353834731771087 0.0889045336771751 2120 3096.54545454545 3108 0.00326961024928707 990 1.32042978772796 -1.59008010255122 -1 3.09762631641954 2119 3714 990 3475 3876 2918 4021 3062 3971 2808 3108 3316 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 0.522092472704687 0.642132631783245 2300 3103.18181818182 3108 0.0649185474224684 1687 1.90879958106441 -3.11553755502548 -1 0.819575759063232 2300 4264 1687 3270 3661 2836 3833 3108 3324 2790 3062 3317 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 0.454566345198904 0.577105904525079 2495 2986.54545454545 3109 0.0536158713681 1438 0.258063742126776 0.3525012795546 1 0.137511775072753 2492 3671 3109 4200 4352 2229 1851 2070 4046 3394 1438 3318 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 0.226754461320383 0.34331870944986 2675 3412.81818181818 3110 0.0253880270898925 1941 0.268620496098618 0.324404074325782 1 0.278368282757566 2675 3073 4643 3110 1941 3862 2844 4138 3727 4620 2908 3319 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 0.659437309990843 0.770907406051987 1570 2888.18181818182 3111 0.093281533719082 1443 0.241699412350785 -0.249819793272886 -1 0.060957208101545 1567 4380 3111 4156 3318 1443 2023 2089 4475 3433 1775 3320 M16597 REACTOME_EGFR_DOWNREGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EGFR_DOWNREGULATION.html Genes involved in EGFR downregulation 17/36 Reactome 0.838439860076133 0.921799467694876 3705 3304 3111 0.15271331087465 2233 1.21455215107271 1.21455215107271 1 0.0958631157726266 2391 4635 3049 4551 3111 3701 2577 3303 3702 2233 3091 3321 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 0.303483217413262 0.42312477143664 4575 2981 3111 0.0323438676972475 1538 1.49374080912537 1.49374080912537 1 1.24532322913706 4571 1694 1538 2270 2079 3629 3594 3111 3795 2191 4319 3322 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 0.130195344489043 0.225877595066885 4045 3029.72727272727 3112 0.0138518307970396 1049 0.79746726079628 -1.376402735282 -1 1.15003273497837 4042 2211 4647 2635 1597 4031 3284 1049 2096 4623 3112 3323 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 0.389693921402782 0.511944411464378 1435 2817.18181818182 3113 0.0481801239731613 1392 0.348336436221619 0.514136213078316 1 0.226067847611445 1431 3649 4148 3543 2340 1716 1392 3113 4328 3845 1484 3324 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 0.196791191365998 0.307387840913689 2865 3136.90909090909 3114 0.0197247401713393 1394 0.541664143092205 0.352926897180286 1 0.619363040050617 2865 3384 1394 3114 1799 3932 2694 4306 2854 4624 3540 3325 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 0.701004342618817 0.805124105272494 2365 3064.18181818182 3115 0.113729103586989 1889 0.341203484975782 -0.351719061585801 -1 0.0716892691170285 2364 2921 4394 3438 3115 1889 3448 2021 3479 4231 2406 3326 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 0.161385165508919 0.262241686633255 4630 2795.90909090909 3116 0.0158730158730159 1401 1.68921829567976 1.68921829567976 1 2.1916154941293 4628 1674 1401 1510 4381 3318 3416 3116 1514 2134 3663 3327 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 0.300262469230292 0.419258024676146 3210 2960.36363636364 3116 0.0319379458261072 1846 1.28512803435563 1.28512803435563 1 1.08284008588941 3206 3537 1846 3116 2070 2517 3362 3835 3475 2514 3086 3328 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 0.669268552238151 0.776285256383162 3655 3256.45454545455 3117 0.0956928725580425 1898 2.24458518468169 2.24458518468169 1 0.550965085802294 3651 2931 2875 2911 4645 4066 3294 1898 3117 2766 3667 3329 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 0.000405913495921693 0.00293989280044676 1455 2853.27272727273 3117 3.69080371639205e-05 523 1.54678417001237 1.54678417001237 1 8.74009417867832 1454 4080 523 3081 3637 4665 3117 3995 2439 993 3402 3330 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 0.374709928098023 0.495734252701111 4605 3389.45454545455 3117 0.0417872229281324 2247 1.30803339440482 1.4352726234116 1 0.889700079066919 4605 3117 3427 2795 2247 3012 4564 4117 2449 2879 4072 3331 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 0.158678620513505 0.262241686633255 2935 2999.09090909091 3118 0.0155846957891851 1086 1.29648407040111 -0.865167510069464 -1 1.68207660537984 2932 4403 3724 4562 1668 1086 3266 3479 2929 3118 1823 3332 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 0.0298074294096533 0.0780321867115282 3115 2904.63636363636 3118 0.00274719234237132 572 0.316947704205609 -0.345035975399499 -1 0.78360933608377 3115 3504 3077 4445 4061 674 3121 572 3118 4255 2009 3333 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 0.83133244422133 0.918346023955953 3670 2894.81818181818 3118 0.149390671895993 1870 1.08105450907909 -1.08105450907909 -1 0.089259475353137 2434 3286 2733 3670 3443 2074 3118 3452 3669 1870 2094 3334 M543 REACTOME_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE.html Genes involved in Cell Cycle 258/635 Reactome 0.632674741454619 0.745034700521015 1280 3082.90909090909 3119 0.087024416455933 1280 1.03836234754675 -0.862243820280119 -1 0.296236923292984 1280 4447 2751 3811 3605 2195 3563 2583 3888 3119 2670 3335 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 0.332994291586694 0.453871800574534 2720 3021.18181818182 3119 0.0361448385903235 918 0.523746058863399 -0.523746058863399 -1 0.401031986488941 2717 4088 3412 3119 3701 918 3008 2962 4174 3550 1584 3336 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 0.557443745451391 0.675680649556446 2870 3317.27272727273 3120 0.0714285714285714 2052 1.42267534279842 1.42267534279842 1 0.540622615201863 2870 3623 2651 3120 3135 4668 2052 4478 2787 2965 4141 3337 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 0.698152987361708 0.80243926877041 4000 3314.63636363636 3120 0.103174603174603 1953 0.448229418015579 -0.345287024222549 -1 0.0956274329199676 4000 1953 2337 2254 4556 3581 4468 2835 3120 4627 2730 3338 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 0.282442139805901 0.403759568984275 2455 3230.09090909091 3123 0.0297222237396604 2036 0.856646955912648 0.941966558232612 1 0.753081955324278 2453 4478 3546 4405 2036 2220 4604 2684 3517 3123 2465 3339 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 0.16691326447076 0.269615841885551 4595 3100.09090909091 3123 0.0164645455510416 1564 1.30540696670185 1.53056596751522 1 1.65856319781687 4593 3254 2878 3499 1695 1564 4595 4135 2545 2220 3123 3340 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 0.152199924985766 0.255355835475581 2405 2563.27272727273 3124 0.0148979501173386 816 0.650112755713168 -0.650112755713168 -1 0.860233106246885 2403 3447 3140 3512 1645 816 1568 4239 3124 3405 897 3341 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 0.936989803160346 0.989507236660202 3630 3296.72727272727 3125 0.222222222222222 2725 0.791140711360448 -0.791140711360448 -1 0.00808902114794892 3627 2877 2725 2934 3398 3125 3595 2949 3737 4209 3088 3342 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 0.0120387598665659 0.0398120174557006 3270 2518.63636363636 3126 0.00110046791676264 809 0.997293395573521 0.997293395573521 1 3.11620580862975 3267 1207 833 1093 809 4550 3217 3126 1319 3979 4305 3343 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 0.0256965592580426 0.0704175887036186 3240 2719.54545454545 3126 0.00259986279309655 231 1.01248268669639 1.13796318319889 1 2.60399308564215 3240 3190 4439 3687 1118 231 4358 2584 3001 3126 941 3344 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 0.267560432192681 0.388040294810767 1565 2897.27272727273 3126 0.0279098846226652 1060 0.361786844154824 0.476557348007678 1 0.331974161493384 1565 3602 2591 3768 4000 3126 1060 2756 3288 4595 1519 3345 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 0.0839184282471183 0.156982736433532 4085 2751.36363636364 3128 0.00793650793650794 767 1.40157285696625 -1.07272638267715 -1 2.51554027944732 4082 3481 1612 2675 1596 3128 3344 3899 767 1073 4608 3346 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 0.53496705887123 0.654873468618229 4170 3193.54545454545 3128 0.0672371363625942 1700 1.26530448687738 1.26530448687738 1 0.519183361323541 1883 4168 1700 4168 3685 2323 3740 2823 4521 3128 2990 3347 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 0.298735036746822 0.4173739958842 3130 2957.90909090909 3129 0.0317460317460317 1943 1.65198623575143 1.65198623575143 1 1.39916426819859 3129 3169 2804 3181 2659 4182 2068 3223 1943 2343 3836 3348 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 0.340316391247473 0.462104494171446 3055 3222.45454545455 3130 0.0407461093727741 1786 0.52633339147485 0.497891853015859 1 0.393841946771798 3052 2253 4501 2722 2228 4518 1786 3130 3407 4416 3434 3349 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 0.934248897593201 0.98846022445738 2955 3254.81818181818 3130 0.219205689789942 2194 0.793438973180863 -0.50491279453589 -1 0.0089267364833225 2954 3130 2194 2493 3868 2915 3826 4244 4343 2533 3303 3350 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 0.255730019154715 0.373252986537254 2555 3253.09090909091 3131 0.0264928701151344 1907 0.273999034994253 0.332399923443452 1 0.26173934848054 2553 4158 2842 4142 1965 4456 1907 2435 4513 3682 3131 3351 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 0.627877737369431 0.741677609607551 1500 2889.09090909091 3131 0.0941243930811681 1500 0.559072296372983 0.559072296372983 1 0.161946462085844 1500 3580 4215 3422 3131 1747 2546 1880 4028 3943 1788 3352 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 0.0839184282471183 0.156982736433532 3510 2805 3132 0.00793650793650794 939 1.05077947290469 1.05077947290469 1 1.88593698553323 3510 939 2990 1481 3374 3657 3132 4164 942 2163 4503 3353 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 0.740759387871823 0.841502664622391 1440 3098.63636363636 3132 0.115495032712766 1440 0.984964828617036 -0.984964828617036 -1 0.164755556283497 1440 4578 3382 4414 3457 1727 3092 2394 4143 3132 2326 3354 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 0.557443745451391 0.675680649556446 3135 3350.45454545455 3132 0.0714285714285714 2200 0.24361970729185 -0.284292964708684 -1 0.0925765135498906 3132 4523 3456 4216 3000 2200 3915 2893 2822 3989 2709 3355 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 0.0765897756730953 0.156982736433532 3135 2683.09090909091 3133 0.00793650793650794 35 0.697863920415721 0.766926013010973 1 1.25252482778976 3133 1868 4123 1239 4294 3927 1816 1670 35 3802 3607 3356 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 0.691397576194858 0.797777208383085 2425 3078.63636363636 3133 0.101368252642972 1721 0.929712302103307 -0.644872453133905 -1 0.203600331058687 2424 3837 1965 3843 4097 3680 1721 2853 3133 2643 3669 3357 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 0.726270090971166 0.8280237492927 1845 2853.81818181818 3133 0.111111111111111 1845 1.5124231924853 1.5124231924853 1 0.276655960175437 1845 4138 2213 3632 3498 3426 2051 2316 3177 1963 3133 3358 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 0.0839184282471183 0.156982736433532 4615 2939.72727272727 3134 0.00793650793650794 542 0.852246096011289 0.852246096011289 1 1.5296096608935 4612 1013 2865 542 4616 2832 4309 3134 623 3530 4261 3359 M12469 REACTOME_HIV_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIV_INFECTION.html Genes involved in HIV Infection 131/285 Reactome 0.559891222876368 0.678471753400222 1965 3158 3134 0.0718965942632712 1685 1.14672566625037 1.14672566625037 1 0.431178499412843 1965 4505 3769 4605 2597 1685 3290 2851 3958 3134 2379 3360 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 0.933238468813211 0.98846022445738 2020 3418.54545454545 3134 0.237126324623331 2018 0.49485907172355 0.493513744169772 1 0.00556750632158433 2018 3081 4433 3134 4582 2570 3048 3552 4234 4330 2622 3361 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 0.557443745451391 0.675680649556446 2730 3043 3135 0.0714285714285714 2339 0.350628917562627 -0.453360191969414 -1 0.133240463628954 2726 3135 3180 3389 4082 2464 2552 3351 2760 3495 2339 3362 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 0.0059185708807712 0.0234838468647704 4030 3136.45454545455 3135 0.000539504872861894 747 1.18269293147378 1.2565148101219 1 4.30065056629067 4027 3116 747 2265 2873 3209 4461 4643 3135 1644 4381 3363 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 0.327505651040524 0.448488778091161 2245 3107.54545454545 3135 0.0354264898108086 1173 1.27638481739111 1.48524300883569 1 0.992088323140673 2245 4449 2695 4292 4102 3668 1173 2259 3241 2924 3135 3364 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 0.010382422370633 0.0357755682529886 4240 3013.54545454545 3135 0.000948340559112853 816 0.838124715546923 0.838124715546923 1 2.70570632492436 4240 1618 816 2237 2422 3135 4051 3786 2442 4628 3774 3365 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 0.763656845001491 0.860836174086357 1805 2981 3137 0.12289948451877 1802 0.55936453995665 -0.55936453995665 -1 0.0812491143345939 1802 3137 3360 3545 4187 1962 2817 2690 3914 3423 1954 3366 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 0.466738071388703 0.587219019917277 4450 3079.81818181818 3137 0.0555555555555556 1203 0.667767904475907 -0.667767904475907 -1 0.344582098717309 4446 1697 1978 1203 4684 2166 4650 3137 2479 3916 3522 3367 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 0.415320710913563 0.535769969181582 2925 3171.72727272727 3139 0.0476190476190476 2383 1.14672566625037 1.14672566625037 1 0.693654240275479 2921 3235 3333 2793 3778 4515 3139 2613 2411 2383 3768 3368 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 0.204244655345605 0.316393538826282 2500 3138.54545454545 3139 0.0205552100780902 1352 1.14672566625037 1.14672566625037 1 1.27912018105306 2496 3196 1352 3613 3969 4289 2699 2633 3139 2974 4164 3369 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 0.0624319018481053 0.135756794459499 2545 2883.90909090909 3139 0.00642585390245698 396 1.25951571603559 1.47789975729524 1 2.43793239241835 2541 3858 4465 3869 2274 396 3166 3689 3080 3139 1246 3370 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 0.294353962229553 0.4173739958842 2785 3075.1 3139.5 0.0379972289332909 1371 0.187160469167644 -0.187160469167644 -1 0.158517204962674 2785 3494 4574 NA 2238 1694 3646 1371 4534 4527 1888 3371 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 0.138549341260341 0.236949712826992 2460 3065 3140 0.0148030906620745 1641 1.19708811473793 1.4207518902278 1 1.67080024869395 2458 4103 4309 3810 1641 1692 3914 3011 3303 3140 2334 3372 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 0.45477692048205 0.577216860611833 2880 3261.36363636364 3140 0.058853084682928 1956 0.218843288061821 0.0672309384755761 1 0.116571994275781 2879 3981 4458 3140 2478 1956 2749 4254 3530 4366 2084 3373 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 0.966406459437513 0.999999995401952 2560 3332.18181818182 3140 0.265446804155366 2286 1.16186250822327 -1.16186250822327 -1 5.07559893719637e-09 2560 4223 2286 3908 4259 2774 3726 3140 4230 2674 2874 3374 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 0.623870630380473 0.738246912616893 3610 3214.90909090909 3141 0.0850564600681918 1265 1.25385821663403 1.22385152785547 1 0.368839982784175 1265 4312 2944 4172 3606 2486 3608 2972 4026 3141 2832 3375 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 0.33296556889208 0.453871800574534 3835 3214.54545454545 3141 0.0396825396825397 1845 0.989745402399581 -0.989745402399581 -1 0.757847354024689 3833 3141 4539 2225 2294 3963 2409 1845 2129 4468 4514 3376 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 0.0329427489295347 0.0838054948337673 2645 2930.27272727273 3142 0.00304060256271852 593 2.19775722972283 2.19775722972283 1 5.2815948003561 2645 4055 2335 3629 3142 3783 3193 593 2896 2592 3370 3377 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 0.13162677320566 0.227597452560442 3125 2779.27272727273 3142 0.0140142405135056 587 0.312247051907176 -0.264909462803717 -1 0.447997712497031 3122 3142 3952 3533 3927 587 1694 2403 3289 3496 1427 3378 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 0.52340095663996 0.642393107075655 2390 3248.45454545455 3142 0.0714285714285714 2386 0.355313158411369 0.370489181033457 1 0.15242010549045 2386 3319 4399 2766 4285 3238 3142 2553 2737 4239 2669 3379 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 0.730617508246578 0.832403025442126 3290 3069.90909090909 3143 0.11240387636155 1762 0.289499049412845 -0.264536136928409 -1 0.0514756234961128 3289 2811 3143 4111 4535 1762 2204 2011 3911 3577 2415 3380 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 0.0113513134008675 0.0381580018626005 3360 2865 3143 0.00103730083981374 825 1.06842737009334 1.07930135099425 1 3.38242116852359 3358 2836 825 2474 1531 3143 4244 3946 3524 1207 4427 3381 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 0.372108250617054 0.492988199714875 3180 3183.36363636364 3144 0.0414254623561015 2242 1.30043294467946 1.42753854033307 1 0.891532319042808 3178 4167 3302 4014 2242 3144 2362 3070 2814 2616 4108 3382 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 0.678177243318653 0.785257860684756 1720 3148.81818181818 3144 0.0979348881709615 1719 0.282401725549563 0.329514410246275 1 0.066173690001978 1719 4123 3144 4196 4277 2788 1901 1911 3682 4120 2776 3383 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 0.327940725260826 0.448942517841727 2565 2849.81818181818 3144 0.0389615626691509 1267 0.222406652506927 -0.222406652506927 -1 0.172650750648839 2562 3144 4496 3197 3288 1311 1552 2812 3310 4409 1267 3384 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 0.434566473879805 0.556996306510057 3425 2901.81818181818 3145 0.0505125422223227 1090 0.575174557363911 -0.575174557363911 -1 0.326261162325558 2477 2316 3422 2735 3145 1090 4152 3421 3378 4180 1604 3385 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 0.667434366415499 0.775117085755398 3145 3187.27272727273 3145 0.0952380952380952 2210 0.369042250346706 -0.346820981311687 -1 0.0911253304195398 3145 3978 2566 3718 3547 2210 2806 3408 3084 4329 2269 3386 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 0.667434366415499 0.775117085755398 3485 3229.18181818182 3145 0.0952380952380952 2344 1.72130338621463 1.72130338621463 1 0.425030846231503 3482 3874 2881 3446 3619 3124 3941 3145 3076 2344 2589 3387 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 0.00944334748510453 0.0331720587070463 4530 3061.54545454545 3145 0.000862193425050896 371 1.15527319269813 1.39225033376054 1 3.81416296316667 4530 3145 3641 3455 371 1148 4523 4680 2403 3027 2754 3388 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 0.35943518917414 0.478362197236587 2680 3139.09090909091 3146 0.0396825396825397 1563 0.300386900746399 -0.184770590432705 -1 0.214704126163707 2678 4030 3146 3290 4266 2715 1563 4116 2256 3445 3025 3389 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 0.625857448793924 0.739850657176672 2345 3277.09090909091 3146 0.0854968805991929 1980 1.05077947290469 1.05077947290469 1 0.306891290432649 2345 4371 3666 4459 2694 1980 3916 3146 3877 2769 2825 3390 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 0.252594779713638 0.369547030202345 2240 2919.72727272727 3146 0.0286950261174655 1262 1.90919498657043 1.90919498657043 1 1.84223698764475 2237 3774 4599 3146 4183 2388 3814 1262 3438 1433 1843 3391 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 0.0839184282471183 0.156982736433532 3150 2784 3147 0.00793650793650794 1033 0.325902970638244 -0.32111511054135 -1 0.584930027466453 3147 2887 3218 3591 3808 1938 3626 1615 1033 3482 2279 3392 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 0.981993787528594 0.999999995401952 4140 3308.36363636364 3148 0.305931980887986 2547 1.14672566625037 1.14672566625037 1 5.00813485147012e-09 4139 3232 2699 3117 4051 2547 3620 3148 4299 2637 2903 3393 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 0.232850105696956 0.34496857265126 2520 3155.90909090909 3149 0.0238095238095238 1712 0.374241307296949 0.465043793196369 1 0.386082795641153 2519 4269 1985 4311 3149 4342 2947 1712 1834 4264 3383 3394 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 0.0379227160506667 0.0938256850123675 4135 3104 3150 0.00385858593171513 910 0.938433826351083 -1.02061775431493 -1 2.15248620194514 4132 2410 4273 2192 910 3773 2754 2161 3150 4021 4368 3395 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 0.275742742869669 0.39623750171336 2235 3025.81818181818 3150 0.0317460317460317 1549 0.752452616627287 0.884182819534587 1 0.675200497830824 2233 1549 4358 2495 3298 4410 3479 2304 1872 4136 3150 3396 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 0.039712725497842 0.0969238706681705 3155 2846.36363636364 3151 0.0036771132558827 639 0.403552143655121 -0.289198288414714 -1 0.912919828121567 3151 2194 2646 2000 3735 3973 3708 639 2004 3223 4037 3397 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 0.785941684398692 0.881292829167808 3050 3239.54545454545 3151 0.142857142857143 2060 0.478397560735282 -0.499867715123002 -1 0.0585977232677037 3050 2060 4028 3151 4677 2442 4448 2335 3362 3634 2448 3398 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 0.0839184282471183 0.156982736433532 4175 3112.81818181818 3151 0.00793650793650794 512 1.81829142039364 1.81829142039364 1 3.26346595903479 4175 3693 1729 2842 4674 4516 3151 2716 512 1548 4685 3399 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 0.0647614223110635 0.13952736779294 3510 3090.72727272727 3153 0.00606820624317548 1146 0.971814793230189 1.1326658119887 1 1.8552487459871 3507 3153 3171 2747 1146 4393 2909 2591 3544 2608 4229 3400 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 0.232850105696956 0.34496857265126 4545 3015.72727272727 3153 0.0238095238095238 1010 1.16312116290335 -1.06806590925483 -1 1.19992385011594 4541 2320 1975 2346 3153 3933 4533 3627 1762 1010 3973 3401 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 0.0839184282471183 0.156982736433532 3365 2351.63636363636 3153 0.00793650793650794 325 1.31182939412448 1.51000545628412 1 2.35446888420539 3364 325 1800 643 3437 4201 3537 3153 467 897 4044 3402 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 0.715758869558456 0.818882123967867 2780 3252 3154 0.108060957179781 1761 1.90919498657043 1.90919498657043 1 0.36977924040023 2777 4069 2312 3569 4437 4499 4599 1983 3154 1761 2612 3403 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 0.201806434297743 0.313237810904016 2335 3094.90909090909 3155 0.022288277571128 958 0.281822243225654 -0.113675882216529 -1 0.317098190143753 2334 3492 4340 3328 3350 3006 958 3051 3155 4097 2933 3404 M9052 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM.html Phosphatidylinositol signaling system 37/77 KEGG 0.597318307603006 0.711317303539438 3565 3194.63636363636 3158 0.0793650793650794 2597 0.995816582010741 -0.995816582010741 -1 0.328802127741428 3562 3158 2846 3194 3509 2597 3335 4468 2932 2814 2726 3405 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 0.0239043758974738 0.0667556051582611 3565 2553.36363636364 3158 0.00219710299654044 203 1.1500438502368 1.25481551858099 1 3.01731824348323 3563 3495 2887 3271 1197 203 3322 2773 3298 3158 920 3406 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 0.63389956273523 0.745034700521015 3320 3177.36363636364 3159 0.0873015873015873 2098 0.302919131321607 -0.342181273370168 -1 0.0864205367285644 3318 3092 3445 3465 2837 2578 4009 2098 2984 3966 3159 3407 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 0.514011397665828 0.633523779448203 3405 2978.63636363636 3159 0.0634920634920635 988 0.838969195239275 -0.680644994905029 -1 0.371202130060344 3405 1431 1852 988 3159 4507 3349 2845 2657 4112 4460 3408 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 0.456222539336265 0.578581547856492 2650 3072.27272727273 3160 0.0538774752836924 1123 0.236028564514687 -0.240435716072904 -1 0.125185865077317 2650 3843 3583 4536 3730 1123 2015 2410 4318 3160 2427 3409 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 0.0427831965319041 0.102234604257268 2265 2813.18181818182 3160 0.00396714349291229 928 0.997293395573521 0.997293395573521 1 2.20451999057728 2262 3635 3160 3820 928 3685 2164 1627 3423 4199 2042 3410 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 0.698152987361708 0.80243926877041 3960 3540.09090909091 3161 0.103174603174603 2109 1.14672566625037 1.14672566625037 1 0.244648002543483 3958 3161 3065 2458 4658 4561 4665 2109 3126 2741 4439 3411 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 0.667434366415499 0.775117085755398 3750 3261 3162 0.0952380952380952 1837 0.318977844295621 -0.247261180148954 -1 0.0787632349019623 3748 2358 3131 2775 3815 4059 1837 3642 3057 3162 4287 3412 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 0.323176670479632 0.443803039246024 2535 2714.81818181818 3162 0.0382824707723661 1181 0.246473454402279 -0.268409431544716 -1 0.194084233934962 2535 2777 3894 3283 3546 1181 1527 3162 3333 3369 1256 3413 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 0.161385165508919 0.262241686633255 3910 3127.90909090909 3162 0.0158730158730159 1425 1.38933387508025 1.38933387508025 1 1.80254124342672 3908 1623 3162 1893 3562 2910 4149 4590 1425 2950 4235 3414 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 0.753908069096075 0.850665353186662 2550 3115.45454545455 3163 0.119670580228904 1633 0.282221128801644 -0.265887076015181 -1 0.0442447089230793 2546 2977 3091 3361 3504 1633 3163 4118 4474 3221 2182 3415 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 0.61198198815398 0.726379837003432 2975 3087.45454545455 3163 0.0903272429794216 1641 0.273652347205264 -0.396225422865165 -1 0.0847971998381843 2972 3419 3996 3030 4135 1892 1641 3163 4306 3563 1845 3416 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 0.829759366264352 0.917040658093102 2965 3426.27272727273 3163 0.148672510554551 1877 0.228382724284021 -0.224461343488398 -1 0.0191717785604869 2964 4595 3163 4456 3092 1877 2870 3832 4377 4279 2184 3417 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 0.87081626062541 0.947664885576097 4475 3356.36363636364 3164 0.169765619558408 2784 0.331635766742597 -0.188558880543045 -1 0.017279800472046 4471 2952 2997 3721 3164 3035 2828 2784 3868 3235 3865 3418 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 0.616255951273166 0.730342788989897 3285 3244.09090909091 3165 0.083387860171432 1777 0.291948865901276 -0.380515011511055 -1 0.0889270518617181 3285 4563 1777 4437 3165 1988 2936 2695 4524 3889 2426 3419 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 0.862280689279697 0.941436931492232 2550 3468.27272727273 3165 0.16492245906014 2359 1.05413324400306 1.13733135458513 1 0.0616625788560742 2547 4648 3733 4306 3146 2359 4279 3165 3781 3156 3031 3420 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 0.692053852342561 0.797777208383085 3055 3329.72727272727 3165 0.111111111111111 2166 0.437540160685528 -0.316250039873972 -1 0.0958181593541726 3054 2210 4429 2166 2966 4147 3218 3798 3152 4322 3165 3421 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 0.557443745451391 0.675680649556446 3165 3178 3165 0.0714285714285714 1774 0.425200929423567 -0.378873840413107 -1 0.161578141852496 3165 2534 1774 3660 3896 2085 3328 4243 2817 4602 2854 3422 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 0.481452186915777 0.601301958392146 3900 3266.45454545455 3166 0.0579548679437107 1794 0.767094350896661 -0.767094350896661 -1 0.378214841777564 3899 1794 2721 1877 2467 4608 2684 4420 3166 4197 4098 3423 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 0.630563991183118 0.743913107422983 2940 3372 3167 0.086548729935875 1398 0.256024504862151 -0.238762174739499 -1 0.0734157337426324 2939 4467 2415 4582 4372 1398 2881 3167 4613 3744 2514 3424 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 0.667434366415499 0.775117085755398 3160 3645.54545454545 3167 0.0952380952380952 2731 1.41842081901975 1.41842081901975 1 0.35024191889555 3157 4618 3167 4511 3654 2976 4566 3117 3081 2731 4523 3425 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 0.816521443770307 0.906472278016503 4215 3020.81818181818 3168 0.142857142857143 2122 1.13172731109781 1.13172731109781 1 0.107719489690888 4213 3555 3184 3363 3168 2122 2976 2389 3384 2157 2718 3426 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 0.817393003518111 0.907010091045671 2070 3142.18181818182 3169 0.143228089908913 2007 0.322503055812126 0.387574204731656 1 0.0305109053711467 2069 3995 2472 4009 3757 2752 2007 2193 3943 4198 3169 3427 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 0.198838752782564 0.30996619944747 2040 2858.63636363636 3170 0.0199521805612871 702 0.851166116214458 -0.764324581788544 -1 0.966369862783825 2040 3782 3761 3170 3571 702 3481 2444 3658 3154 1682 3428 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 0.794027274505754 0.888641991099861 2240 3006.63636363636 3171 0.133798233521413 1764 0.304401591135176 -0.32304862323341 -1 0.0348350654360372 2238 3211 3115 4314 3171 1764 2803 3610 3373 3458 2016 3429 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 0.0413341543318418 0.100099145839282 2495 3213.36363636364 3171 0.0038301647902393 903 1.10384421376173 1.10384421376173 1 2.46263695263582 2491 4207 2868 4431 903 4528 3171 3350 2881 3032 3485 3430 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 0.167549209113571 0.270277037968227 4120 3040.09090909091 3171 0.0165328229813455 1692 1.21455215107271 1.21455215107271 1 1.54024553073302 4118 4125 1692 3773 1700 3171 4156 2004 3111 2065 3526 3431 M5415 BIOCARTA_IL4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL4_PATHWAY.html IL 4 signaling pathway 11/20 BioCarta 0.571842866388748 0.688503512820574 2850 3075.27272727273 3172 0.0742166189655299 1740 0.36024080179842 0.464442497938781 1 0.130328370302272 2846 2917 3024 3299 3167 3702 3172 1740 3325 3279 3357 3432 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 0.878859116702268 0.952656447112382 2880 3093.27272727273 3174 0.174603174603175 2273 0.896585420808603 0.896585420808603 1 0.0421507845256391 2877 3174 2343 2660 3483 3721 2273 3690 3543 3261 3001 3433 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 0.832801005042335 0.919318141255214 2230 3225.81818181818 3174 0.150066634675166 2228 1.53334444632203 1.53334444632203 1 0.125031234903942 2328 4670 2228 4578 3447 3174 3812 2229 3815 2250 2953 3434 M15181 BIOCARTA_PGC1A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PGC1A_PATHWAY.html Regulation of PGC-1a 15/30 BioCarta 0.00262350054797216 0.0127660680870172 715 2303.27272727273 3175 0.000238784936917169 109 0.298649814846066 0.332537014889193 1 1.26243397245035 714 3875 3175 4205 3906 370 109 1110 4044 3313 515 3435 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 0.63389956273523 0.745034700521015 3375 3079.63636363636 3175 0.0873015873015873 1767 1.16186250822327 -1.16186250822327 -1 0.331470584956591 3374 3570 2140 3184 3175 3823 3159 3532 3012 1767 3140 3436 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 0.461884741466404 0.585445468896827 2975 3200.27272727273 3176 0.0547773524109847 1352 0.272144542289068 -0.279084158909717 -1 0.141230160372175 2971 4630 3295 4609 3176 1352 2919 1577 4258 4473 1943 3437 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 0.0896043681121927 0.165874208961399 3795 3185.90909090909 3177 0.00934367539452907 1355 0.272061378416083 -0.174573267728597 -1 0.473766293631275 3795 2890 4077 3077 1355 3177 1961 2964 3789 3721 4239 3438 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 0.372590599293215 0.493348275865501 3820 3230.09090909091 3179 0.0455457806909442 1434 1.17181367894184 1.17181367894184 1 0.802526033312011 3817 2828 4607 3179 2310 3925 2213 3095 4285 1434 3838 3439 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 0.198348346983145 0.309304610303833 3700 2930.45454545455 3180 0.0218655180880595 1029 0.967459383376804 -0.967459383376804 -1 1.10040691525184 3697 3180 3804 2641 3755 3073 3223 2779 1868 3186 1029 3440 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 0.88079455664788 0.954533601399622 3445 3035.18181818182 3180 0.175810804354711 1802 0.998429914123333 0.998429914123333 1 0.0450336567170377 3442 3274 2341 2921 4027 1970 2718 3691 4021 1802 3180 3441 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 0.884274638578228 0.957198188121408 2725 3291.45454545455 3181 0.178027779078535 1982 0.241273318642065 -0.237426508398771 -1 0.0102305681346042 3181 3972 3170 3745 3322 1982 2782 2721 4404 4206 2721 3442 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 0.0141253785084592 0.0445434210569581 3610 2892.45454545455 3182 0.00142159769088061 503 0.446398780771204 -0.461079844196492 -1 1.34625544279135 4116 1321 3796 2837 503 3607 3105 2475 3609 3182 3266 3443 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 0.391224633114909 0.513092256024759 2900 3164.72727272727 3182 0.0441160087550629 1018 0.237061336106011 -0.238758950272672 -1 0.153336472090132 2897 4224 3622 4090 2660 1018 3018 3182 3897 4423 1781 3444 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 0.253102487457564 0.370058738292089 2825 3114.81818181818 3183 0.02618093231635 1029 0.290352290901329 0.260620415538976 1 0.279779810533715 2823 2055 3235 3880 3183 3027 1029 3527 3991 4679 2834 3445 M1084 REACTOME_TRYPTOPHAN_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRYPTOPHAN_CATABOLISM.html Genes involved in Tryptophan catabolism 5/11 Reactome 0.255672587233021 0.373252986537254 1935 2824.72727272727 3184 0.0290957517175702 1078 0.496549131803598 -0.496549131803598 -1 0.474331766432851 1932 3184 4097 3588 3226 1426 1078 2487 4197 3767 2090 3446 M504 REACTOME_ANDROGEN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANDROGEN_BIOSYNTHESIS.html Genes involved in Androgen biosynthesis 2/16 Reactome 0.412541442006245 0.535769969181582 3015 3228.8 3184.5 0.0573926890198812 2336 0.235388219438878 -0.0514359777127211 -1 0.142386310201742 3012 3778 3914 NA 2457 3075 2336 3010 3983 3429 3294 3447 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 0.415320710913563 0.535769969181582 4270 2981.81818181818 3185 0.0476190476190476 910 0.633042077535849 0.633042077535849 1 0.382927089038296 4269 1530 3185 910 3069 3500 4090 1919 2316 4367 3645 3448 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 0.165486073738915 0.267864504849932 3020 3157.18181818182 3188 0.0163114892602266 1042 0.94175740835774 0.94175740835774 1 1.20248324256831 3016 3062 2883 4048 3188 3383 3346 1042 3461 4598 2702 3449 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 0.783182390322491 0.879883164960727 1515 3191 3189 0.129748141782385 1512 0.724699651325126 -0.643179695930235 -1 0.0898911658397183 1512 4406 3593 4294 3584 1842 2878 3189 4298 3144 2361 3450 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 0.0316935698880173 0.0814232831662549 4130 3039.27272727273 3190 0.00292359809966562 789 0.481449101090274 -0.481449101090274 -1 1.17046399187948 4128 3488 2866 3282 789 2816 3190 2858 2914 3571 3530 3451 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 0.531415970655876 0.651206913831965 2725 3345.36363636364 3190 0.0665918484122633 2363 1.28028989446095 -1.08023697533246 -1 0.532299951165137 2721 4293 2582 4130 2554 4636 2363 4194 3190 2678 3458 3452 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 0.131672363186376 0.227597452560442 3195 3247.63636363636 3191 0.0127530880060583 1557 1.0177635111608 1.0177635111608 1 1.4602402877803 3191 3898 3151 3780 1557 3370 4681 2849 3761 2340 3146 3453 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 0.748189019419366 0.847682240086835 2335 3098.27272727273 3192 0.117830086160554 1829 0.651716405074945 -0.650112755713168 -1 0.104390863434908 2331 3007 3216 2349 3192 3405 1829 4569 3417 4095 2671 3454 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 0.0822651061242987 0.156982736433532 4525 3142.36363636364 3192 0.00777387290392747 1135 2.07333958077616 -2.07333958077616 -1 3.72122590885011 4523 1944 1135 2653 3719 3192 4150 4309 3011 2488 3442 3455 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 0.514011397665828 0.633523779448203 3195 3306.27272727273 3192 0.0634920634920635 1797 1.03313393875872 1.29724451087013 1 0.457110369368741 3192 3269 1797 2451 4147 4660 2647 4623 2656 2371 4556 3456 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 0.706022047848321 0.809894569453423 2410 3307.8 3192.5 0.127181661985265 2090 0.311046939946055 0.311046939946055 1 0.0635720003987533 2406 3741 4454 NA 3505 2747 2880 2090 4339 4362 2554 3457 M963 KEGG_RNA_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_DEGRADATION.html RNA degradation 41/72 KEGG 0.741653791909222 0.842221149478473 1620 3067.27272727273 3193 0.115772889070147 1603 0.262282411913844 -0.245283287692067 -1 0.0436551342241083 1617 3967 3404 4086 3665 1603 2904 2770 4218 3193 2313 3458 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 0.156982736433532 4600 3181.18181818182 3193 0.00793650793650794 983 1.54233408141681 1.53039757613321 1 2.7681782555213 4600 3193 2075 2790 3328 2892 4297 4310 983 2198 4327 3459 M4864 KEGG_BASAL_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_TRANSCRIPTION_FACTORS.html Basal transcription factors 16/38 KEGG 0.090030810535813 0.166358193285023 1065 2538.90909090909 3194 0.00854010054455181 649 0.203107489209267 -0.215111520100443 -1 0.353116743064228 1063 4153 3514 4328 3273 649 1422 857 4336 3194 1139 3460 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 0.476135256688821 0.596569468674817 2445 3120.81818181818 3194 0.0570808194888736 1163 0.266682782427603 -0.231013724273752 -1 0.133530128453882 2444 3810 3090 4372 3194 1163 2370 3326 4303 4406 1851 3461 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 0.626051103243577 0.739892930592535 1905 3110.72727272727 3194 0.0855399218695987 1903 0.630361842887751 -0.630361842887751 -1 0.184068951084047 3673 2685 3194 2322 2695 1903 4251 3222 3833 4537 1903 3462 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 0.171712090412205 0.275846025255945 3690 2919.18181818182 3195 0.0169809404244956 691 1.74485001602008 1.74485001602008 1 2.17825293910246 3690 691 1303 1360 3195 4264 4028 3221 2870 2907 4582 3463 M2044 KEGG_SPLICEOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPLICEOSOME.html Spliceosome 79/188 KEGG 0.666591621483788 0.775117085755398 1335 3202.72727272727 3196 0.0950299048486911 1331 0.192709283561327 -0.214065952344889 -1 0.0475845166910321 1331 4589 3755 4479 3728 1768 2972 2662 4467 3196 2283 3464 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 0.415320710913563 0.535769969181582 3390 3200.63636363636 3196 0.0476190476190476 2130 0.846898746177843 -0.829059636361518 -1 0.512288966427629 3390 3001 3290 3196 2512 4225 2406 2130 2398 4082 4577 3465 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 0.7406131901063 0.841502664622391 3335 3150.81818181818 3196 0.126234709465962 1870 0.38950619553026 0.253069113634458 1 0.0651528947986617 3333 2490 4497 2413 3368 2180 1870 3196 4152 4411 2749 3466 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 0.323208972225974 0.443803039246024 4050 3023.27272727273 3198 0.0348678538132534 1124 1.52740838862628 1.65055102504002 1 1.20274975600477 4048 4288 3198 3644 2136 1124 3840 3261 3000 3082 1635 3467 M2529 BIOCARTA_PDGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PDGF_PATHWAY.html PDGF Signaling Pathway 26/52 BioCarta 0.0839184282471183 0.156982736433532 4670 2823.72727272727 3199 0.00793650793650794 158 1.58416613655242 -0.701222236703204 -1 2.84325834796668 4670 2435 3034 824 3236 3215 3837 3199 158 2589 3864 3468 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 0.285729226575285 0.407248478744549 3915 3039.09090909091 3199 0.0301271385364951 847 0.483021087624012 0.533328799513338 1 0.420597527107664 3913 847 2099 2384 2045 4681 3199 2461 3844 3372 4585 3469 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 0.0186509282960065 0.0557742501564048 1915 3131.09090909091 3199 0.00171008615066168 890 1.22334499728723 1.22334499728723 1 3.42275488868279 1915 3617 890 3314 3199 4661 3136 3963 3013 2782 3952 3470 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 0.0839184282471183 0.156982736433532 3200 2911.54545454545 3200 0.00793650793650794 955 1.61003262351327 -2.07333958077616 -1 2.88968346922747 3200 2878 2531 2668 3278 3643 3338 3544 955 1730 4262 3471 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 0.0839184282471183 0.156982736433532 4420 2807.81818181818 3200 0.00793650793650794 495 1.05077947290469 1.05077947290469 1 1.88593698553323 4416 495 2197 1820 4150 3389 4140 4326 686 2067 3200 3472 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 0.471092930469578 0.591834174847304 1710 3227.54545454545 3201 0.0562593320895963 1156 0.276054554105078 -0.279936934876009 -1 0.140355073222725 1710 4557 2737 4561 3799 1156 2708 3201 4504 4531 2039 3473 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 0.68813018720656 0.795799125678662 2860 3234.09090909091 3203 0.100507438297266 1933 0.353652388771683 0.456385646594728 1 0.0782983633819031 2858 2629 2879 2744 3807 4622 3203 1933 3723 3399 3778 3474 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 0.668345811792535 0.775817338303836 3875 3218.27272727273 3204 0.09546379782078 1465 0.337668654557875 -0.294857586819229 -1 0.0830828814269767 3875 2100 2807 2604 4182 1465 3114 4438 3665 3947 3204 3475 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 0.273363956944955 0.394634473889113 2655 2984 3205 0.0286126383231819 1329 0.950753591852095 0.950753591852095 1 0.856878407205107 2652 3205 1779 3648 2003 4305 1329 3589 3847 2791 3676 3476 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 0.614911558754323 0.729302851005507 4380 3274.72727272727 3206 0.0830963949392498 2674 0.304596355988668 -0.295346583727887 -1 0.0932001584788439 4380 2949 3355 3624 2674 2923 2886 2696 4005 3324 3206 3477 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 0.35943518917414 0.478362197236587 2795 3215.09090909091 3207 0.0396825396825397 1967 1.14672566625037 1.14672566625037 1 0.819632053185331 2795 4117 3207 3862 4179 4197 2998 1967 2278 2555 3211 3478 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 0.71316321097091 0.816729013328207 1600 3161.27272727273 3207 0.10732355037796 1598 0.204536789082926 -0.213488899979127 -1 0.0401373436494309 1598 4422 3736 4462 2863 1740 3207 2568 4015 3625 2538 3479 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 0.233985440506584 0.346431524238184 3060 2881.81818181818 3207 0.026303290348389 1031 0.718360016479216 0.887544688955203 1 0.738143166018508 3056 1108 4251 2063 3736 3838 1031 3679 3207 3990 1741 3480 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 0.21248296682159 0.326778858722013 4060 3264.18181818182 3207 0.021481396356746 1846 0.339935292709679 -0.357311640737435 -1 0.368540386494676 4060 3207 3255 4053 1846 3109 3056 2737 3149 4169 3265 3481 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 0.726420322949699 0.8280237492927 4515 3241 3208 0.111155472311945 2085 0.852246096011289 0.852246096011289 1 0.155894833603078 4514 2085 2532 2433 2890 2581 3208 4642 3304 3782 3680 3482 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 0.7184702227596 0.82095865980285 3040 3238.18181818182 3208 0.119047619047619 1428 1.21455215107271 1.21455215107271 1 0.232256913046725 3036 3327 4410 3951 4246 3689 2331 3060 3208 1428 2934 3483 M6391 KEGG_PEROXISOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PEROXISOME.html Peroxisome 45/92 KEGG 0.12999051123613 0.225605753945372 3415 2876.36363636364 3209 0.0125794058560252 1478 0.50491279453589 -0.50491279453589 -1 0.728727396306355 3412 2532 3515 3334 1548 1478 4184 3143 3264 3209 2021 3484 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 0.928434699254604 0.986317161801649 2970 3276.9 3209 0.253989874219678 2479 0.20073585882093 -0.20073585882093 -1 0.00268073121530091 2966 2747 4227 NA 3452 2479 3522 2675 3923 3954 2824 3485 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 0.172470965555504 0.276617244348736 970 2663 3209 0.0187530405504367 966 0.960186285948682 0.960186285948682 1 1.19608824485326 1109 3548 4589 3705 3471 967 1252 1924 3209 4553 966 3486 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 0.232850105696956 0.34496857265126 3210 3050.36363636364 3210 0.0238095238095238 1308 1.18063890866154 1.18063890866154 1 1.21799588044927 3910 3210 2767 1308 3206 3618 4073 4008 1625 1329 4500 3487 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 0.0311687885076166 0.0803835679398411 4180 3088.45454545455 3210 0.0028744853338889 780 0.822357965266513 0.822357965266513 1 2.009500999545 4180 1932 2759 2902 780 3485 3197 3210 3351 4168 4009 3488 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 0.155025635996481 0.258799476408802 4580 3117.27272727273 3211 0.0151968885026293 1277 0.453067046178108 0.31408172132598 1 0.593618207995657 4579 3559 1277 3351 2865 1981 4353 2621 2879 3211 3614 3489 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 0.597318307603006 0.711317303539438 3525 3351.45454545455 3211 0.0793650793650794 1888 1.01826314245602 1.0681704076301 1 0.336213609906434 3525 3744 3737 4471 3211 1888 4319 3084 2948 3124 2815 3490 M11911 KEGG_ABC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ABC_TRANSPORTERS.html ABC transporters 17/50 KEGG 0.956888510373196 0.999999995401952 3195 3380.63636363636 3212 0.248598437937882 2453 0.28683898754631 -0.264651529450714 -1 1.17566644684386e-09 3441 4229 2867 4395 3524 2453 3191 2653 4031 3191 3212 3491 M11932 REACTOME_TIE2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TIE2_SIGNALING.html Genes involved in Tie2 Signaling 9/24 Reactome 0.823112378277618 0.911629544932385 3125 3115.45454545455 3212 0.159050833842086 2149 0.376561931564973 -0.373308454931723 -1 0.0337709502910114 3123 2774 3972 3254 3744 2372 3212 2655 3492 3523 2149 3492 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 0.114298592713754 0.202419956710752 3490 2999.54545454545 3212 0.0109734743331521 965 1.14713173282107 1.25020492785887 1 1.77620775295828 3488 4351 2445 3567 1465 3212 3909 3131 2424 965 4038 3493 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 0.654574366953918 0.766642210333931 3250 3259.90909090909 3213 0.0921120897415464 2560 1.22168558101711 1.22168558101711 1 0.314682202161186 3250 3756 2560 3732 2771 3213 3170 3494 3952 2919 3042 3494 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 0.707068885879006 0.810500195506121 3470 3203.63636363636 3213 0.10561576249037 1537 0.522536967759313 0.522536967759313 1 0.106417874355376 3470 3213 2612 3663 4464 1537 2768 2459 4082 4290 2682 3495 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 0.247920425253005 0.363502851293987 4070 3055.90909090909 3214 0.0255686362925565 1026 1.18063890866154 1.18063890866154 1 1.15810462608691 4066 3214 1407 2913 2203 3468 4636 3636 2476 1026 4570 3496 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 0.751985672431077 0.848905049629493 3120 3194 3214 0.119047619047619 1986 1.13596515691048 1.13596515691048 1 0.180369797094619 3120 3673 2329 2985 3878 4199 3507 2402 3214 1986 3841 3497 M9494 BIOCARTA_BCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCR_PATHWAY.html BCR Signaling Pathway 21/57 BioCarta 0.908598649933573 0.974077619214991 3220 3345.45454545455 3216 0.19547203155529 2421 1.14672566625037 1.14672566625037 1 0.0291936917746848 3216 3633 2970 2582 4425 4222 3111 2455 3638 2421 4127 3498 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 0.690612954829238 0.797777208383085 3220 3083.72727272727 3216 0.110696068108441 1811 0.399695412352041 -0.379038967843259 -1 0.087530430692319 2940 1811 3993 2763 3218 1934 4198 3216 4421 3556 1871 3499 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 0.145701697109101 0.247358336478991 4325 2499.81818181818 3216 0.0142139098585834 464 1.24259159315252 1.34854084364781 1 1.68253053178516 4322 614 1604 791 3961 3586 4350 3404 1186 464 3216 3500 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 0.698152987361708 0.80243926877041 4675 3380.72727272727 3216 0.103174603174603 2012 0.653874098340854 0.653874098340854 1 0.139500664135688 4672 2012 2552 2318 4111 4134 3216 3121 3106 4221 3725 3501 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 0.145701697109101 0.247358336478991 4325 2500.81818181818 3217 0.0142139098585834 465 1.24259159315252 1.34854084364781 1 1.68253053178516 4323 615 1605 792 3962 3587 4351 3405 1187 465 3217 3502 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 0.637943669378222 0.749224068848708 3220 2864.36363636364 3220 0.0882227737092992 1624 0.724095453604658 0.724095453604658 1 0.202643332059781 2610 2045 3435 2213 3441 3220 1624 4114 3220 3511 2075 3503 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 0.902157871246138 0.969168222067722 3620 3380.72727272727 3220 0.19047619047619 2852 1.1921467147981 1.1921467147981 1 0.0361888523202235 3914 3002 2852 3220 3413 3194 4125 3190 3617 3042 3619 3504 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 0.390092477424906 0.512324369174078 990 2922.81818181818 3221 0.0439545376779288 988 0.245822328768802 -0.258872045855672 -1 0.159360146050309 988 4364 3614 4161 3221 1016 2733 2142 4439 3643 1830 3505 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 0.452073579408344 0.574563816953485 3225 3235.36363636364 3222 0.0532234851065622 1118 0.229603600360875 -0.22969869073014 -1 0.123329019076823 3222 4597 2626 4504 4370 1118 3015 2206 4620 3847 1464 3506 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 0.0235813204378977 0.0662879829466038 3055 2755.45454545455 3222 0.00216708570742069 513 0.646118488205991 -0.646118488205991 -1 1.69959456924552 3055 3735 3222 3296 3951 1389 1827 513 3947 4336 1039 3507 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 0.657249817422587 0.769006902482458 2650 3193.4 3223 0.112167875718974 2007 0.13194654867645 0.13194654867645 1 0.0335929484698408 2648 3950 4101 NA 3621 2825 2044 2007 4287 3776 2675 3508 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 0.816521443770307 0.906472278016503 3225 3338.45454545455 3223 0.142857142857143 2430 0.89160854114137 1.07872523342085 1 0.0848646278032698 3223 3862 3183 3746 3729 2430 4029 3001 3386 3136 2998 3509 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 0.000655249307737107 0.00422738278331924 2930 2834.63636363636 3223 5.95858680905775e-05 564 1.9327424049922 1.9327424049922 1 10.2404997377857 2928 3338 564 1457 3223 4545 3655 4094 1449 1654 4274 3510 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 0.104661745741284 0.188278202397265 4115 2876.72727272727 3224 0.01 162 0.352581846973266 -0.320417224555621 -1 0.570686070990713 4114 162 3224 2472 1810 2424 3935 1669 3645 3615 4574 3511 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 0.334404252965593 0.455443765580811 2160 3140.90909090909 3225 0.0363302405886531 1503 1.17541203944299 -0.94491829980495 -1 0.896072924461706 2156 3225 1503 3409 4146 2672 3786 3696 4168 2870 2919 3512 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 0.859981833188057 0.939145856518116 3150 3465.54545454545 3225 0.163664755850136 2663 1.31412529102136 1.48815205361691 1 0.0799747592254934 3150 4405 2714 3924 3143 2663 4199 4033 3554 3111 3225 3513 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 0.232850105696956 0.34496857265126 2570 3255.63636363636 3225 0.0238095238095238 1629 1.82051220676583 1.82051220676583 1 1.87811561345875 4154 2566 1629 2352 3225 3976 4531 4544 1682 2566 4587 3514 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 0.0765897756730953 0.156982736433532 3870 2513.27272727273 3226 0.00793650793650794 113 1.59555088121217 1.59555088121217 1 2.86369166587924 3326 1473 3926 968 1702 3867 3867 3226 113 1687 3491 3515 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 0.117750784145379 0.207767399159385 4345 3108.90909090909 3226 0.0124499209422978 1023 1.15920300182878 1.2810175616869 1 1.76560053090159 4341 3429 4400 3226 1543 1023 3955 3859 2694 3048 2680 3516 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 0.000425700178544476 0.00304554356741896 3230 2642.54545454545 3228 4.25781749826683e-05 54 0.993519398986551 -0.989745402399581 -1 5.57987404925786 3228 1102 4147 624 54 4204 3232 4498 1616 3844 2519 3517 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 0.00211239173024432 0.0106548277433857 4220 2887.27272727273 3228 0.000211440241022006 147 1.08991325512181 1.08991325512181 1 4.79819923835117 4425 1921 4259 2387 147 3228 4520 4218 1136 1303 4216 3518 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 0.865412014258462 0.942878562849373 3785 3308.45454545455 3231 0.166666666666667 2179 0.340953365213698 -0.292463403424186 -1 0.019438712169058 3783 3168 3231 3157 4197 2179 2958 3559 3482 4185 2494 3519 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 0.850621352955467 0.931311135502177 3615 3378.27272727273 3232 0.158730158730159 2795 1.14672566625037 1.14672566625037 1 0.0790989475906276 3207 3159 3097 3221 3232 3614 3303 3611 3465 2795 4457 3520 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 0.0387843978934505 0.0955037774717337 4230 2699.45454545455 3233 0.00358959135303159 582 1.26715109826347 1.26715109826347 1 2.88469154149532 4229 3133 3451 3233 876 3305 3450 1360 582 2170 3905 3521 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 0.742829351267896 0.843036652952618 3235 3496.45454545455 3233 0.126984126984127 1983 1.19006192860293 1.28996405194021 1 0.196961354643315 3233 4646 4295 4527 3098 1983 4160 3215 3308 3153 2843 3522 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 0.0671868814626624 0.143695904397095 2235 2938.72727272727 3233 0.00630281701623766 1099 1.30662214601286 -1.42279293755586 -1 2.45713005447571 2234 3924 1099 3708 3233 3579 3583 1812 3731 2406 3017 3523 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 0.210179123341356 0.323873519229725 4460 3023.27272727273 3233 0.0233187263190854 1027 0.526557743138504 -0.489901116356241 -1 0.57542503408707 4458 1027 4406 1096 3014 3233 4396 1177 2334 4258 3857 3524 M13720 KEGG_LYSINE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSINE_DEGRADATION.html Lysine degradation 20/50 KEGG 0.415320710913563 0.535769969181582 4685 3398.09090909091 3234 0.0476190476190476 2046 0.967459383376804 -0.967459383376804 -1 0.58521608376443 4682 3234 2924 3651 3718 2770 4666 4153 2366 3169 2046 3525 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 0.0305958506312559 0.0794745876153355 1230 2650.27272727273 3234 0.0028208933487334 245 0.680878280361112 -0.680644994905029 -1 1.67128910463914 1229 4250 3686 4472 3234 245 1763 1876 3856 3757 785 3526 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 0.00700163223314835 0.0266312083153678 1165 2992.72727272727 3234 0.000638546831019521 773 1.39320310030882 1.39320310030882 1 4.89628570668891 1164 3400 773 2882 3867 4075 3010 4129 3427 2959 3234 3527 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 0.259457074149325 0.37769986003844 3560 3179 3235 0.0269370637460374 1882 1.25430664371455 1.41148834354889 1 1.18378511349021 3556 4287 1882 3621 1970 3235 2792 4025 2778 2783 4040 3528 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 0.583789516977794 0.700188808947516 4640 3145.09090909091 3237 0.0765952755272235 1753 1.3691571693485 -0.874649861425705 -1 0.473000138037148 4637 3790 1891 3812 2634 1753 4379 2100 3237 2798 3565 3529 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 0.877076420273514 0.952045426314961 2190 3261.81818181818 3237 0.173506269414775 1961 0.220935448627397 -0.244520184978467 -1 0.0105241435693051 2189 4390 3366 3858 3237 1961 2874 2573 4417 4633 2382 3530 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 0.298735036746822 0.4173739958842 3240 3032.90909090909 3239 0.0317460317460317 2087 1.4452219372308 1.5530130551413 1 1.22404342748597 3239 3398 2306 3355 2272 3328 3143 3274 2087 2297 4663 3531 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 0.667434366415499 0.775117085755398 2925 3522.63636363636 3239 0.0952380952380952 1897 1.16885970375432 1.28290578524525 1 0.288619329360853 2922 4359 3239 4260 2939 4511 1897 4198 3094 3040 4290 3532 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 0.35943518917414 0.478362197236587 3760 3015.36363636364 3240 0.0396825396825397 1613 1.21455215107271 1.21455215107271 1 0.868111617791246 4209 1947 3240 1613 3470 3757 3760 2340 2165 2322 4346 3533 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 0.33296556889208 0.453871800574534 2890 3245.09090909091 3240 0.0396825396825397 1702 1.07312695996487 1.07312695996487 1 0.821692553639334 2888 3240 4277 3540 4155 3686 2923 4456 2276 1702 2553 3534 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 0.578834139003627 0.695135001376473 1720 3056.45454545455 3240 0.0756011888929048 1720 0.386450741736354 0.500292523821211 1 0.136219930440302 1720 4111 1737 3950 3240 3110 2288 2439 3579 4059 3388 3535 M79 PID_TRAIL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TRAIL_PATHWAY.html TRAIL signaling pathway 18832364 17/31 Pathway Interaction Database 0.514011397665828 0.633523779448203 4370 3334 3241 0.0634920634920635 2486 0.321362070586419 -0.281456604719397 -1 0.142186728363812 4370 2665 3177 2486 4299 2887 3670 3241 2708 3375 3796 3536 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 0.180318106290512 0.286236668725387 3585 2965.90909090909 3241 0.0179138722866605 715 0.849254971022537 0.849254971022537 1 1.02976270254089 3585 715 2179 2505 1758 4271 3241 3596 2360 3870 4545 3537 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 0.231165731916005 0.34496857265126 1565 2952.18181818182 3243 0.0259454637703887 1024 0.332884145493358 0.395792000668527 1 0.343417038703493 1561 3243 4593 3430 3373 2010 1024 2768 4180 4558 1734 3538 M1473 BIOCARTA_BLYMPHOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BLYMPHOCYTE_PATHWAY.html B Lymphocyte Cell Surface Molecules 4/18 BioCarta 0.148151538822404 0.249636142007115 2635 3088.63636363636 3244 0.0159067922020747 841 0.234932992874065 -0.080938187914688 -1 0.316023501149284 2635 4400 3817 4197 3725 2733 841 2603 4480 3244 1300 3539 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 0.868241595864952 0.945082489715021 1915 3324.27272727273 3244 0.168274823599589 1912 0.291106934175644 -0.318917616910739 -1 0.0159380309490621 1912 3805 2056 3526 4114 2803 3244 3045 4526 4355 3181 3540 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 0.0238455331049789 0.0667105481372723 4235 2945.45454545455 3245 0.00219163483817018 660 0.373510936501693 -0.286950680168868 -1 0.980208267516773 4232 1696 3245 2547 660 2279 4178 4288 2148 3483 3644 3541 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 0.52340095663996 0.642393107075655 3540 3357.63636363636 3245 0.0714285714285714 2520 0.53753854132261 -0.432044091537761 -1 0.230590056272114 3537 2520 4266 3190 2647 3245 3699 4206 2751 4011 2862 3542 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 0.591248115293131 0.707866292351459 4520 3161.81818181818 3245 0.0781120024668492 2048 1.13376173748063 -1.2745195582153 -1 0.379694043258157 4519 3715 2384 3245 2643 2048 4473 3293 3352 2722 2386 3543 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 0.35943518917414 0.478362197236587 3340 2849.18181818182 3245 0.0396825396825397 1316 1.0055452326564 -0.796538314240086 -1 0.71872212147594 3337 1316 2289 1663 3245 4196 3279 3988 2151 1780 4097 3544 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 0.433235118302916 0.555593805245612 2875 3052.36363636364 3246 0.0503095194788957 1087 0.22519099575256 -0.254511730859218 -1 0.128287323487677 2874 4302 3246 4429 4081 1087 2266 1987 4310 3441 1553 3545 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 0.373027120392078 0.493786747502056 3080 3065.27272727273 3246 0.041553074338537 1237 0.242683470890827 -0.276268843237413 -1 0.165994751752458 3079 4230 3276 3977 3246 1237 3028 1424 4412 4289 1520 3546 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 0.00474507171477529 0.0197472522694823 3395 3033.27272727273 3246 0.000432303376107707 733 1.42286613413055 1.58852054679859 1 5.41301091079182 3393 3255 733 2671 1852 4039 3138 4342 3246 2200 4497 3547 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 0.0839184282471183 0.156982736433532 3830 2717.27272727273 3247 0.00793650793650794 591 1.11882204112119 1.11882204112119 1 2.00805965666081 3827 1465 3247 1730 3421 2206 4498 3677 591 1908 3320 3548 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 0.481063017846562 0.600976086811248 3250 3252.81818181818 3247 0.0634920634920635 1395 0.324097706488072 -0.208302428899017 -1 0.159966238549627 3247 1395 4558 2434 2804 4562 2283 3902 2628 4499 3469 3549 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 0.35943518917414 0.478362197236587 4150 3391.45454545455 3248 0.0396825396825397 2182 0.385703565344314 -0.297198623341237 -1 0.275684947507609 4146 2334 2668 2806 4382 4401 3248 2182 2207 4545 4387 3550 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 0.0917638480728264 0.169226836705732 3130 3299.54545454545 3248 0.00871190720820774 1158 1.05077947290469 1.05077947290469 1 1.8094408154516 3127 3592 1158 2706 3836 2988 4655 3784 4210 2991 3248 3551 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 0.78418912456294 0.880380986512203 2700 3109.36363636364 3249 0.130116263052699 1691 0.701222236703204 -0.701222236703204 -1 0.0865945911793808 2696 3373 2783 3249 3751 1691 3078 3867 3728 3809 2178 3552 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 0.681907584007771 0.789187191568391 2140 3270.18181818182 3249 0.0988904880153912 1850 0.305468377894873 -0.342504419766469 -1 0.0701008515694255 2140 3771 1850 3312 3967 2922 3094 2841 4527 4299 3249 3553 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 0.893541128049031 0.963002236899209 4545 3361 3249 0.184240787066762 2123 1.12416859127964 -1.12416859127964 -1 0.0410800925338486 4543 4044 2527 3967 3249 3462 2123 3213 3919 3029 2895 3554 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 0.0628400638543559 0.136454374060015 3690 2927 3250 0.0064691167530282 781 0.27890293599174 -0.26320379543945 -1 0.538461979393727 3687 3250 3982 3482 1391 2727 2992 781 3321 3535 3049 3555 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 0.176662179753196 0.281290850942398 2505 2799.36363636364 3252 0.0175164701994024 658 0.852246096011289 0.852246096011289 1 1.04778821256313 2503 3342 3681 3566 4137 658 2303 2664 3252 3597 1090 3556 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 0.431339030695081 0.553465141795496 3255 3065.18181818182 3252 0.0548835067879115 1143 0.314281058746446 -0.254538886528363 -1 0.180209760240715 3252 3906 4479 3882 2677 1143 2167 2312 3674 4389 1836 3557 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 0.069754399150348 0.147837681781334 1355 2635.27272727273 3253 0.00655177389832121 600 0.277521703709088 0.316178432790729 1 0.514241365314874 1352 3932 3272 4093 3727 1255 600 1604 4280 3253 1620 3558 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 0.35943518917414 0.478362197236587 3955 3140.63636363636 3253 0.0396825396825397 1663 1.25240526293404 1.25240526293404 1 0.895167455740434 3951 3476 1663 3068 3253 3598 3772 2609 2142 2569 4446 3559 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 0.214503405671472 0.327957303482285 3685 3167.36363636364 3253 0.0217098873847153 1857 1.08128203590063 -1.05397803871103 -1 1.16849754472982 3684 2794 2232 3230 1857 4018 3637 3525 3253 2362 4249 3560 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 0.0238249796559907 0.0667105481372723 3280 3079.72727272727 3254 0.00218972491251508 931 1.9083122944764 1.9083122944764 1 5.00800192285376 3276 3667 931 2778 3254 3864 4049 2997 2314 2430 4317 3561 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 0.693865559029984 0.799668964489549 3255 3254.54545454545 3255 0.111635451278582 1791 0.300657027367684 0.193015646091263 1 0.0651514874683253 3255 2922 3885 2724 4636 2452 1791 3602 4018 3348 3167 3562 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 0.423145495799646 0.544293108239677 3260 3290.09090909091 3256 0.0487848614198501 1404 1.19851050335346 1.19851050335346 1 0.706643280942188 3256 4353 3712 4592 2349 1404 3574 4513 2949 3071 2418 3563 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 0.0839184282471183 0.156982736433532 4315 2590.18181818182 3256 0.00793650793650794 243 1.24287224182961 -1.24287224182961 -1 2.23070471932544 4314 504 1299 875 4315 4300 3559 3256 243 1775 4052 3564 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 0.751985672431077 0.848905049629493 4665 3363.81818181818 3257 0.119047619047619 1939 1.04561534110608 1.17760887099959 1 0.166023953954692 4662 3304 2537 3111 3161 2526 4662 4347 3257 1939 3496 3565 M15513 BIOCARTA_D4GDI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_D4GDI_PATHWAY.html D4-GDI Signaling Pathway 10/26 BioCarta 0.0577592895639135 0.128153423719933 2845 3104.63636363636 3258 0.00539399133953058 1082 0.327592303678484 0.284495929406719 1 0.652393209920137 2841 3289 3086 3707 1082 3559 2625 3735 3729 3258 3240 3566 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 0.577885189977191 0.694529366564021 2920 3442.63636363636 3258 0.0826331149820474 2670 0.217198007980246 -0.20223784589137 -1 0.076743580509006 3933 2918 4339 2981 2670 2920 3258 4307 3328 4096 3119 3567 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 0.514011397665828 0.633523779448203 4490 3041.54545454545 3258 0.0634920634920635 1574 1.12024552872844 1.28209913597262 1 0.495652914127415 4486 2590 1935 1827 3258 3309 4683 3423 2624 1574 3748 3568 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 0.000117377629968085 0.00111795035372042 3520 2585.09090909091 3258 1.06712629945042e-05 419 1.59191006153021 1.38791674055612 1 10.4870242149805 3517 3584 419 3258 946 1649 3773 4618 1350 696 4626 3569 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 0.417296990576389 0.53780354726099 2835 3041.45454545455 3259 0.0479121483404113 1056 0.523746058863399 -0.523746058863399 -1 0.314890650806673 2832 3925 3310 2701 3698 1056 3259 3123 4173 3558 1821 3570 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 0.275742742869669 0.39623750171336 3260 3184.09090909091 3259 0.0317460317460317 1893 0.463042686157666 -0.189670691393022 -1 0.41550344204026 3259 2860 4075 3138 2810 3926 3532 1909 1893 3717 3906 3571 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 0.0310309815080998 0.0802933072042824 3630 2857.90909090909 3259 0.00314730085850414 818 1.29092067091405 1.48573184080352 1 3.15587931297526 3628 3431 4166 3259 818 998 4327 3724 2402 2723 1961 3572 M10570 BIOCARTA_RNA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RNA_PATHWAY.html Double Stranded RNA Induced Gene Expression 8/17 BioCarta 0.575490016031746 0.692005700570891 2515 3115.36363636364 3260 0.0821139048475412 1676 0.653874098340854 0.653874098340854 1 0.233343593585386 2511 3909 3827 4206 3684 1867 1997 3156 4176 3260 1676 3573 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 0.0199436176907654 0.0587566870716248 4240 3122.81818181818 3260 0.00182970368428645 584 1.22196003002012 -1.05090527905824 -1 3.35717818263382 4239 3260 3489 3027 584 2876 3447 4068 2810 2850 3701 3574 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 0.232850105696956 0.34496857265126 3320 2745.09090909091 3260 0.0238095238095238 807 1.16933234042285 1.16933234042285 1 1.20633155748238 3320 1636 2133 1830 3950 3260 4503 3433 1704 807 3620 3575 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 0.147938718947773 0.24945694026242 4105 2874.81818181818 3261 0.0144488559120212 1039 1.32028415226883 -1.14782656326293 -1 1.77691826911887 4104 3586 3570 3261 1621 1039 4155 3618 2891 1531 2247 3576 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 0.74980083822241 0.848905049629493 2180 3042.36363636364 3262 0.118344921100617 1833 0.270642017693669 0.289597484069319 1 0.0429728371779737 2180 3477 3336 3262 3731 2637 1833 2399 4172 3354 3085 3577 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 0.698152987361708 0.80243926877041 3945 3293 3262 0.103174603174603 2151 1.24128814102427 -1.12846485370921 -1 0.2648224184998 3945 3262 2494 3911 2855 2151 4221 3764 3144 2310 4166 3578 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 0.363285915639346 0.48266453095718 3265 3089.09090909091 3262 0.0402087887778268 1901 0.316236305752447 0.316424917086439 1 0.223288037254189 3262 1901 3478 2215 2220 3895 2104 2831 3504 4311 4259 3579 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 0.00772358103895589 0.028587360895377 3535 3189.45454545455 3262 0.000704620944009738 786 1.26983255622736 1.31325234254829 1 4.37546631504177 3531 3781 786 2836 2249 3216 4320 4415 3262 2203 4485 3580 M9134 BIOCARTA_TRKA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TRKA_PATHWAY.html Trka Receptor Signaling Pathway 13/25 BioCarta 0.791271312574107 0.886632561148318 3085 3138.45454545455 3264 0.132750953357283 2113 0.293279595858898 0.34284789685026 1 0.0342058395397961 3084 2637 3264 2408 3601 4126 2282 2113 3767 3341 3900 3581 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 0.726270090971166 0.8280237492927 3265 3403.72727272727 3264 0.111111111111111 2647 0.852326785622773 0.852326785622773 1 0.155909593534068 4223 3264 3693 3313 2901 2647 3493 4391 3201 3054 3261 3582 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 0.410256429028727 0.533572474723456 4100 3349.63636363636 3264 0.0468720583901948 2174 0.302983293832707 0.31565884955904 1 0.184481610799424 2174 4100 3031 4120 2326 3154 3264 4098 3763 4328 2488 3583 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 0.825204003616126 0.913298526439577 3210 3533.1 3264.5 0.176171463731342 2350 0.24295956409716 -0.415283752611218 -1 0.0213584206439772 3208 3532 4655 NA 3191 2350 3091 3321 4293 4634 3056 3584 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 0.909721540676125 0.974835385229435 2100 3102.45454545455 3265 0.19637562032419 2060 0.229744011429085 -0.28599601522572 -1 0.00567571980678346 2099 3125 3699 3215 3265 2060 3315 3298 4127 3466 2458 3585 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 0.0300258740972984 0.0784287881939467 3900 3056.09090909091 3265 0.0027676069283635 755 1.13415999438805 1.3514807389124 1 2.79848026525507 3897 3885 1890 3474 755 2093 4466 3662 3265 3129 3101 3586 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 0.298735036746822 0.4173739958842 4495 3290.72727272727 3266 0.0317460317460317 2056 0.937110025477263 -0.757444483325528 -1 0.793693575993138 4492 4320 2637 2623 3490 3266 3441 3839 2056 2960 3074 3587 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 0.450079426250026 0.573123021313162 2930 3250 3266 0.0529107521325155 1616 1.73041933125535 1.73041933125535 1 0.933686869665463 2926 3605 1616 2573 3266 4441 3978 4525 3127 2035 3658 3588 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 0.751985672431077 0.848905049629493 3745 3232.81818181818 3266 0.119047619047619 2267 0.758917203788738 0.795185353147261 1 0.120501708338078 3745 2563 3637 2267 3281 3365 3196 3185 3266 3087 3969 3589 M7561 KEGG_MTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MTOR_SIGNALING_PATHWAY.html mTOR signaling pathway 34/78 KEGG 0.751985672431077 0.848905049629493 4500 3473.09090909091 3267 0.119047619047619 2843 0.333107902652481 -0.337518548616287 -1 0.0528912391053874 4499 2843 3387 3212 3065 2983 4008 4186 3267 3210 3544 3590 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 0.51091172750409 0.633523779448203 2400 3385.81818181818 3267 0.0629506209511309 2097 0.216436737423209 0.255637915317098 1 0.0957624884760186 2396 4189 3267 4538 2522 2651 2097 4061 4355 4507 2661 3591 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 0.751985672431077 0.848905049629493 4435 3529.90909090909 3268 0.119047619047619 2916 0.339684079676397 -0.353717266346123 -1 0.0539354117271637 4431 3173 3119 3980 3103 2916 3702 3132 3268 4683 3322 3592 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 0.0769508472635019 0.156982736433532 3810 2894.18181818182 3269 0.00725291452768814 431 1.01850752302452 1.11432938074852 1 1.82801535169187 3808 3952 3275 3921 2383 431 3634 3019 3269 3025 1119 3593 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 0.0765897756730953 0.156982736433532 3270 2919.90909090909 3270 0.00793650793650794 527 0.374894962534612 -0.157184959349696 -1 0.672860760698163 3270 2165 4040 2284 2619 3518 1927 4232 527 3654 3883 3594 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 0.120381081764296 0.211398237468682 3430 3197.27272727273 3270 0.0127447403728807 1555 0.227330105504822 -0.189951192544582 -1 0.342432565620191 3429 2408 4532 3279 1555 3091 1880 4163 3103 4460 3270 3595 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 0.726270090971166 0.8280237492927 4070 3201.09090909091 3271 0.111111111111111 2092 1.29142669460736 1.29142669460736 1 0.2362307679129 4067 2092 2458 2854 3296 3271 3806 3488 3173 2471 4236 3596 M5576 BIOCARTA_PLCE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLCE_PATHWAY.html Phospholipase C-epsilon pathway 6/16 BioCarta 0.0568298355264673 0.126606842019819 2155 2902.90909090909 3272 0.00583377332307791 760 0.858982002181133 0.858982002181133 1 1.72075404036027 2153 3527 3854 3767 3210 2640 3485 760 3272 3302 1962 3597 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 0.232850105696956 0.34496857265126 3675 3225.36363636364 3272 0.0238095238095238 1761 0.904374658176375 0.904374658176375 1 0.932990264789698 3675 2246 2820 2930 3886 4454 3272 1996 1761 4045 4394 3598 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 0.10828939826483 0.193732267297989 4140 3036.18181818182 3273 0.0113959324431205 1495 0.423969089933683 0.330831375536073 1 0.67449734679671 4140 2013 4037 2606 1495 3273 3828 1711 3525 3645 3125 3599 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 0.807016049167552 0.899114885021196 2650 3443.81818181818 3273 0.138912308926586 2117 0.839385191942424 0.872392052885933 1 0.0865246879755947 2647 4650 3765 4604 3042 2117 4304 3273 3625 3157 2698 3600 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 0.161385165508919 0.262241686633255 4535 2951.63636363636 3274 0.0158730158730159 1150 0.337723060041706 -0.340788315189181 -1 0.438166631788365 4534 1150 3389 1866 3502 3232 3274 3683 1541 3347 2950 3601 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 0.261435260583062 0.380343257091658 3315 2872.36363636364 3275 0.0271736519729817 898 1.19812360617127 1.19812360617127 1 1.12266124344407 3313 3275 2344 3337 4449 4637 1045 1652 2633 898 4013 3602 M181 PID_BMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BMP_PATHWAY.html BMP receptor signaling 18832364 26/54 Pathway Interaction Database 0.148037609321618 0.249533898302555 4210 3099.63636363636 3276 0.0144592549360409 1542 1.35402956563856 -1.38975139692581 -1 1.82193004749401 4207 3276 2859 3483 1622 3510 4134 3174 2525 1542 3764 3603 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 0.223814103686874 0.33930536715519 3155 3344.27272727273 3276 0.0250180520106005 1203 0.46095096936929 -0.228197326706443 -1 0.482931962358396 3154 2551 4608 2926 4353 3994 3276 1203 2313 4576 3833 3604 M4557 BIOCARTA_NEUROTRANSMITTERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NEUROTRANSMITTERS_PATHWAY.html Biosynthesis of neurotransmitters 2/9 BioCarta 0.830419975031952 0.917554351096375 2775 3315.7 3276.5 0.178939865395547 2102 0.395417675398988 0.395417675398988 1 0.0329790257814341 2773 3857 3818 NA 4339 2404 2102 3307 4596 3246 2715 3605 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 0.35943518917414 0.478362197236587 3815 3191.09090909091 3277 0.0396825396825397 1206 0.653874098340854 0.653874098340854 1 0.467362147260217 3814 1206 3277 1484 3870 4356 3192 4330 2288 3215 4070 3606 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 0.232850105696956 0.34496857265126 3870 3082.54545454545 3278 0.0238095238095238 1571 2.16779355016341 2.16779355016341 1 2.23638539649542 3866 4360 1571 3278 1981 3401 4645 2294 1721 2137 4654 3607 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 0.156982736433532 4365 3181.54545454545 3281 0.00793650793650794 407 1.42010235024591 1.42010235024591 1 2.54879697850007 4362 3281 2850 2466 3057 3464 4451 4043 407 2232 4384 3608 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 0.545766023802268 0.665658403835874 2340 3227.63636363636 3281 0.0692273756547515 1920 1.05077947290469 1.05077947290469 1 0.414521508492567 2336 4370 3659 4406 2577 1920 3281 3406 4024 2797 2728 3609 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 0.882869193116509 0.95633958366712 2945 3278.18181818182 3282 0.193011931730908 1417 1.05077947290469 1.05077947290469 1 0.0454696058247186 2945 3248 3890 3073 3282 4151 3135 3450 3863 1417 3606 3610 M13465 KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS.html Terpenoid backbone biosynthesis 8/17 KEGG 0.386086746459241 0.507632574048261 3190 3288.90909090909 3283 0.0476190476190476 2302 0.372309775325291 0.191385109344737 1 0.244678785313386 3190 3389 3803 3382 3110 3402 3283 3252 2302 3185 3880 3611 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 0.397335740791165 0.518928450765719 3125 3221.72727272727 3285 0.0449923337385255 1475 0.653874098340854 0.653874098340854 1 0.415771515515795 2411 3762 3122 3473 4250 3523 3123 1475 4195 3285 2820 3612 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 0.386086746459241 0.507632574048261 3065 3401.63636363636 3285 0.0476190476190476 2367 0.332592779837473 0.307281235209887 1 0.218577117131703 3065 3245 4271 3285 3264 3601 2924 4056 2367 4019 3321 3613 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 0.742829351267896 0.843036652952618 3920 3384 3286 0.126984126984127 2486 0.433595730579087 -0.43529601948157 -1 0.0717623178525988 3916 2486 4031 3244 4141 3486 3115 2667 3286 3638 3214 3614 M765 BIOCARTA_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INSULIN_PATHWAY.html Insulin Signaling Pathway 17/44 BioCarta 0.746213833503 0.846058074956462 3695 3437.90909090909 3287 0.117203256733093 2037 0.268186773357887 -0.202034760063861 -1 0.0434562737187718 3695 3728 3534 2833 3132 4638 3108 2037 3276 3287 4549 3615 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 0.173940720288065 0.27823810013545 2605 3001.09090909091 3287 0.0172216856130252 1736 0.284883524207475 0.357515641949967 1 0.353261370605505 2605 2205 3390 2936 1736 3451 3348 3004 3287 3694 3356 3616 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 0.664523961265175 0.774616736937466 2685 3293.72727272727 3287 0.103467266871351 2411 0.322170234612187 0.400580728267791 1 0.0797531607141569 2685 2411 4294 3287 2841 3418 3715 2852 4256 4049 2423 3617 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 0.741751319653789 0.842221149478473 4375 3241.27272727273 3287 0.115803239983488 1892 1.05913550091286 1.05913550091286 1 0.176285943835766 4375 2847 1905 1892 3081 3343 4497 3287 3487 2534 4406 3618 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 0.466738071388703 0.587219019917277 3870 3019.81818181818 3288 0.0555555555555556 1724 1.29644110978073 1.29644110978073 1 0.668990521320214 3867 3411 3288 3623 4212 1724 3605 2368 2496 2168 2456 3619 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 0.622523566685069 0.736843913260302 3765 3396.18181818182 3288 0.0847590562496811 2691 0.950136767809547 -0.66598687983005 -1 0.281247996548003 3763 3686 3081 3792 2691 2781 3288 4172 3203 3114 3787 3620 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 0.474665924841646 0.595524638235061 4080 3347.81818181818 3288 0.0568406988691053 1390 0.940767540772448 -0.940767540772448 -1 0.472648068489177 4078 3288 2413 3104 3154 4418 1390 2578 4001 4312 4090 3621 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 0.902157871246138 0.969168222067722 2615 3418.54545454545 3288 0.19047619047619 2327 0.953273050371831 -0.723188492201251 -1 0.0289375939957617 2612 4617 3110 4602 3456 2327 3700 3288 3621 3143 3128 3622 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 0.00611768932574777 0.0240146466894482 4415 3055.90909090909 3289 0.00055770615675272 289 0.35282425524668 -0.286950680168868 -1 1.27533806535519 4413 2149 3289 3010 289 2369 4315 4343 2183 3489 3766 3623 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 0.16459784363514 0.266703144977271 4255 3181.72727272727 3289 0.0162163528431331 1687 1.26957306351628 -0.74026698660245 -1 1.62640184120011 4253 3662 2196 3289 1687 3326 2748 3924 3128 2876 3910 3624 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 0.597318307603006 0.711317303539438 2500 3273.90909090909 3291 0.0793650793650794 2263 0.896590546013716 1.01075436102882 1 0.296039335513678 2497 4289 3308 3529 2713 4538 2263 3291 2916 3117 3552 3625 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 0.410630843181632 0.533911246156805 2960 3331.54545454545 3293 0.0514969310068936 1342 0.358266041451505 0.425621424463721 1 0.217921961737138 2956 3293 4461 4183 3919 3178 1342 1681 4132 4370 3132 3626 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 0.553337219309713 0.673665422105823 2975 3332 3294 0.0774328712931481 1760 0.36922123832066 0.421509982272882 1 0.141374633271535 2975 2522 4332 3294 3636 3748 3023 1760 4071 4090 3201 3627 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 0.00518573973898874 0.0210801114311576 4250 2805.18181818182 3294 0.00047254580174236 460 1.55333852437627 -2.04149846920114 -1 5.81102328056672 4246 460 741 1529 3294 4217 3686 4546 1678 2886 3574 3628 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 0.139381885606318 0.238026062664434 4360 3251.90909090909 3295 0.0135531728470227 1586 1.31223962978039 -1.35231969614778 -1 1.82575468918904 4359 4453 2645 3193 1586 2393 4528 3640 3295 1888 3791 3629 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 0.579398164809953 0.695634076428245 2415 3117.72727272727 3295 0.0757137989087223 1821 0.955598204248708 0.955598204248708 1 0.336173801668227 2413 2761 1821 3763 2626 3583 2807 3317 4088 3821 3295 3630 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 0.662332890590797 0.773024140799122 3430 3297.90909090909 3296 0.0939850961683108 2420 0.26206175816069 -0.253325985348142 -1 0.0653961194903247 3428 2802 3559 3944 2785 2420 3296 3278 3939 3603 3223 3631 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 0.414740390963609 0.535769969181582 3085 3277.54545454545 3297 0.0475331518146538 1051 0.263330166773387 -0.244266740291935 -1 0.159288391338884 3082 4276 2425 4535 4145 1051 2470 3297 4595 3749 2428 3632 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 0.155288221829803 0.259053260054986 2965 3083.36363636364 3297 0.015224714186076 1278 0.701222236703204 -0.701222236703204 -1 0.918090283159337 2962 2987 1278 3297 3697 3534 1557 2477 4058 4476 3594 3633 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 0.232850105696956 0.34496857265126 3515 2965.90909090909 3299 0.0238095238095238 1231 1.06381156318509 1.25788359667354 1 1.09747196371043 3514 1615 2325 1231 3854 3299 4064 4230 1797 2081 4615 3634 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 0.391605327809005 0.513304214297342 3300 3377.45454545455 3299 0.0484786436528823 1518 0.302871664820164 -0.268825069702821 -1 0.195782784596925 3299 4163 4319 4430 2407 2678 4584 1518 2919 4074 2761 3635 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 0.468319057056118 0.588664995001333 2365 3224.09090909091 3299 0.0558104480551281 1152 1.33403223803043 -1.33403223803043 -1 0.685208106927216 2361 4658 3655 4624 3576 1152 3001 3299 4333 3011 1795 3636 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 0.345193879478399 0.467373163604675 2175 2944.36363636364 3300 0.0377609548359868 1202 0.268514430117209 0.304349242757417 1 0.197971826591146 2172 3933 3437 4033 3300 2695 1202 1378 3866 3312 3060 3637 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 0.0239884915933695 0.0669107569086484 4510 3216.72727272727 3300 0.00220492024227227 662 1.03187434100902 1.15676574664845 1 2.70496026165548 4509 3827 1291 3250 662 3019 3959 4629 3300 2928 4010 3638 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 0.734324886771352 0.836017108700329 4010 3356.54545454545 3301 0.113521389164358 1897 1.29064118907003 1.29064118907003 1 0.224068088529668 4008 3134 1897 3827 3295 3240 4271 4173 3588 2188 3301 3639 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 0.435369722646862 0.557415989159343 3710 2916.81818181818 3303 0.0555555555555556 1397 0.405617633005248 -0.265649598556367 -1 0.22978581182164 3707 1397 3855 1746 3551 1415 3770 4354 2464 3303 2523 3640 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 0.927367965619105 0.985407321290505 2445 3177.54545454545 3303 0.212108889003273 2445 1.17181367894184 1.17181367894184 1 0.0166972767169083 2445 3303 2882 3362 3780 2942 3562 2526 3920 2844 3387 3641 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 0.816521443770307 0.906472278016503 3275 3179.09090909091 3303 0.142857142857143 2180 1.73041933125535 1.73041933125535 1 0.164703887188851 3271 4147 2180 2610 3303 2736 3668 3850 3361 2247 3597 3642 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 0.631467118677363 0.744791069247955 2670 3255.63636363636 3304 0.0950019899414842 1890 0.435192438651738 0.434232842377409 1 0.124295076988691 2666 2819 3856 2683 3454 4188 4346 1890 3601 3304 3005 3643 M619 REACTOME_TRIGLYCERIDE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRIGLYCERIDE_BIOSYNTHESIS.html Genes involved in Triglyceride Biosynthesis 22/42 Reactome 0.232850105696956 0.34496857265126 3410 3279.90909090909 3304 0.0238095238095238 1778 1.27675999939789 -1.27675999939789 -1 1.31715836924422 4576 2440 2738 3273 3410 3304 4365 4329 1778 2457 3409 3644 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 0.000121349666975688 0.00114932174295076 3305 3133.45454545455 3306 1.1032396455597e-05 420 1.34361960559484 1.34361960559484 1 8.81531785489323 3301 4106 420 3306 2878 4172 2916 4622 3709 673 4365 3645 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 0.513536909878567 0.633523779448203 3310 3206.54545454545 3308 0.0634089780234695 1680 0.497706168989802 0.249669458139274 1 0.22021021878572 4531 3515 1680 3840 3309 2256 4071 2607 2847 3308 3308 3646 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 0.00138108353594764 0.00755649000075563 3490 2602.27272727273 3308 0.000138194261374633 115 0.50491279453589 -0.50491279453589 -1 2.39097915673484 3487 948 3911 1358 115 3869 3308 2438 1409 3424 4358 3647 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 0.888972625035748 0.960951723395044 1985 3242.09090909091 3309 0.181118771728095 1983 0.264379658454649 0.302696345153871 1 0.0102073798429017 1983 4118 3079 4032 3537 2401 2884 3620 4438 3309 2262 3648 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 0.567047963175321 0.68431283941271 3310 3126.36363636364 3310 0.0732788568698889 2084 0.456723645422965 0.517898172905464 1 0.167936893225482 3310 2549 2084 2656 2610 3975 3407 2183 3752 3617 4247 3649 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 0.925957382722952 0.984758809861691 3120 3368.45454545455 3310 0.210729965381841 2566 0.259475339243992 -0.23186918496738 -1 0.00386286577804445 3117 3022 3564 3664 3299 2566 3572 3310 3955 3734 3250 3650 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 0.0368096323179604 0.0916037902506439 3825 3051 3310 0.00340366751065423 999 1.1104939338591 1.31065956541062 1 2.57293794577726 3824 3256 999 3310 1875 2925 4505 3767 3381 2300 3419 3651 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 0.594857736562784 0.711279243055168 2295 3096.63636363636 3310 0.0788550848080468 1645 0.264469546403591 -0.238431940903016 -1 0.0873371771320449 2293 3310 3549 4129 4442 1645 3080 1773 3354 4501 1987 3652 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 0.181732228645457 0.288188569689547 1530 2699.36363636364 3311 0.0180680208017268 751 0.250159729908667 -0.244668290985489 -1 0.301682840262739 1528 2888 3311 3589 4651 751 3334 1091 4047 3547 956 3653 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 0.391141452188437 0.513092256024759 4520 3342.90909090909 3312 0.0441041359807125 2049 0.261311089021773 -0.171450144535995 -1 0.169021744200424 4520 3312 3595 2748 2282 3231 4624 2049 3367 3291 3753 3654 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 0.120668029488718 0.211779170855481 2215 3409.54545454545 3312 0.0116221875936455 1506 0.271504511785159 0.260763055965623 1 0.408499686890009 2211 4058 3057 4549 1506 3312 2742 4308 4278 4421 3063 3655 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 0.202856897984455 0.31455573261256 2360 3029 3313 0.0204000509862919 1349 0.375034066196789 0.311873256185984 1 0.420451128688889 2357 3442 1349 3722 2521 3129 1832 3646 4025 3983 3313 3656 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 0.298735036746822 0.4173739958842 3315 3238.36363636364 3313 0.0317460317460317 2030 1.80148879049739 1.80148879049739 1 1.52578677151816 4305 3128 3313 3603 2430 2482 3313 4604 2030 2675 3739 3657 M18053 BIOCARTA_LEPTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LEPTIN_PATHWAY.html Reversal of Insulin Resistance by Leptin 6/35 BioCarta 0.243547084649487 0.357874455524458 1445 2644.90909090909 3314 0.0275255718346423 1242 0.469829136043097 0.438141164327592 1 0.467968382458337 1444 3391 3861 4063 3639 1462 1286 1242 4135 3314 1257 3658 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 0.0295203378318995 0.0774970885603814 3990 3177.63636363636 3315 0.00272036876597249 966 1.21455215107271 1.21455215107271 1 3.01091300706744 3986 3315 966 3103 2030 4163 3970 3794 2963 1985 4679 3659 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 0.0313932613974387 0.0807846364131783 3660 3055.27272727273 3316 0.00289549013930216 785 1.08498581287936 1.02700505937693 1 2.6460199881348 3660 3433 3316 3580 785 2839 2734 4471 2571 2576 3643 3660 M9043 BIOCARTA_GH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GH_PATHWAY.html Growth Hormone Signaling Pathway 20/53 BioCarta 0.543041156948591 0.6628525296851 3640 3353.09090909091 3319 0.0687211603443806 2541 0.284707016176201 -0.219833066329177 -1 0.113479663102257 3639 3597 3510 2541 2573 4328 3319 2586 2907 3273 4611 3661 M15926 BIOCARTA_TFF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TFF_PATHWAY.html Trefoil Factors Initiate Mucosal Healing 19/40 BioCarta 0.163808686138096 0.265608132610075 3320 2943.36363636364 3319 0.0161319049921907 1655 1.21455215107271 1.21455215107271 1 1.56076019197264 3319 1999 3349 1655 1683 4067 4099 3626 2012 2318 4250 3662 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 0.304275214702922 0.423976704162323 1945 3074.54545454545 3320 0.0356298760243643 1175 0.531747351129235 0.472526291702893 1 0.442278008155914 1945 3320 4364 3189 3581 3349 1175 2643 3403 4146 2705 3663 M4085 KEGG_PRIMARY_IMMUNODEFICIENCY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_IMMUNODEFICIENCY.html Primary immunodeficiency 11/48 KEGG 0.855640829765787 0.935713635538501 4375 3433.27272727273 3321 0.161340149301181 2291 0.321435619356247 -0.252046325137411 -1 0.0207026224312053 3506 4031 2553 4371 3224 3321 4041 2291 4374 3232 2822 3664 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 0.427410899537437 0.548875712587676 2150 3262.81818181818 3322 0.054232670578153 1442 0.210064888645512 -0.135415881128005 -1 0.122147356051202 2146 3681 4345 4181 3133 3322 2227 2909 4403 4102 1442 3665 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 0.734025592451589 0.835879447443049 2115 3168.63636363636 3322 0.113430648722055 1681 0.296038855864895 -0.298915098303091 -1 0.0514425309466908 2113 3484 3322 3728 2906 1681 3957 2747 4193 4539 2185 3666 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 0.0280731147161662 0.0744064567646804 3315 3268.18181818182 3323 0.00284341962821423 770 0.295047772049444 -0.255369321493264 -1 0.743071976030572 3312 2778 4441 3323 770 2097 4381 4485 3399 4337 2627 3667 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 0.578549459099408 0.69497122925912 2565 3225.90909090909 3324 0.0755444034592614 2033 0.653874098340854 0.653874098340854 1 0.230633267468387 2565 3789 3728 3961 2623 2033 4106 3324 3205 3470 2681 3668 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 0.270968638352722 0.391659173140301 2355 3033.63636363636 3325 0.0311096707262188 1297 0.404159748523634 0.39928456873451 1 0.367218758659514 2351 3325 4041 3565 4026 2953 1665 1297 3985 3657 2505 3669 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 0.214139132665174 0.327605607466211 3330 3027.18181818182 3327 0.0238095238095238 1302 1.44141515827619 1.44141515827619 1 1.55917789042492 3327 2063 4244 1850 4610 4170 3791 3393 1558 1302 2991 3670 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 0.0123193077804428 0.0403558152745448 3220 3103.45454545455 3327 0.00123881398391953 462 0.73426504557095 0.73426504557095 1 2.28467499196903 3217 2452 4285 3379 462 4487 2727 2024 3327 4036 3742 3671 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 0.323239388166171 0.443803039246024 2765 3198.45454545455 3327 0.03487179702066 1492 0.349945609571083 0.369346841259938 1 0.275562841961417 2762 4427 1492 4199 3048 3473 2125 1794 4161 4375 3327 3672 M5500 KEGG_BASE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASE_EXCISION_REPAIR.html Base excision repair 21/35 KEGG 0.929545109497602 0.986602125278769 2605 3356.18181818182 3328 0.214285714285714 2602 0.55936453995665 -0.55936453995665 -1 0.00731341786533047 2602 3666 3328 3598 4605 2705 3147 3614 3715 3200 2738 3673 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 0.510203026324398 0.633159793791347 2965 3307 3328 0.0688886733138329 2324 0.303703351108608 0.364125072616423 1 0.134542807633573 2963 3176 4462 3443 2575 3611 2324 2746 3377 4372 3328 3674 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 0.988255865026905 0.999999995401952 3095 3619.18181818182 3329 0.332380236022211 2709 0.285849703293833 -0.219849003570727 -1 1.17125726045371e-09 4234 3316 3094 3162 4041 4190 2709 3093 4292 3329 4351 3675 M12 PID_RHOA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHOA_PATHWAY.html RhoA signaling pathway 18832364 31/67 Pathway Interaction Database 0.220779944355492 0.335791891999298 4130 2912.45454545455 3329 0.0224231236999443 1164 1.57323327037052 -2.07333958077616 -1 1.66412785151987 4127 3994 1815 2919 3393 3517 3329 1164 2144 1742 3893 3676 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 0.128403093992411 0.223181342154466 2305 2997.81818181818 3330 0.0136488210920913 791 0.281172602725936 0.331696523356382 1 0.408753717703548 2304 3425 4230 3938 3051 2240 791 3330 4216 3957 1494 3677 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 0.274419798056415 0.395792912801589 2760 3317.18181818182 3332 0.0315693134796575 1120 0.653874098340854 0.653874098340854 1 0.587454297909768 2760 4128 3877 4543 3891 3282 1120 2862 4358 3332 2336 3678 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 0.97530599069028 0.999999995401952 3795 3332 3332 0.285714285714286 2104 1.25240526293404 1.25240526293404 1 5.47914309631721e-09 3792 3448 2381 3332 3689 3156 4506 3234 3906 2104 3104 3679 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 0.165461139989955 0.267864504849932 4625 3415.72727272727 3333 0.0163088174044624 1692 0.70206160710333 0.70206160710333 1 0.89642758344728 4622 3203 2918 2368 1692 3333 4484 4393 3248 3410 3902 3680 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 0.834367499525838 0.919531068386189 4260 3397.63636363636 3333 0.150793650793651 2675 1.43355846665554 1.43355846665554 1 0.116572728550472 4258 3333 2823 2835 3242 2675 4485 3875 3437 2910 3501 3681 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 0.514011397665828 0.633523779448203 3930 3291.45454545455 3334 0.0634920634920635 2183 1.06054007585721 1.06054007585721 1 0.469236221579088 3929 3336 3505 2183 3271 2716 4440 3334 2644 2482 4366 3682 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 0.63389956273523 0.745034700521015 4370 3436.27272727273 3335 0.0873015873015873 2733 1.14850667862738 0.927719966665454 1 0.327660267798777 4369 3718 3513 3164 3672 3100 4300 2733 2990 2905 3335 3683 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 0.224600874909218 0.340388001236933 3410 2988.45454545455 3335 0.0228598780049153 1172 1.01405746558881 -1.01405746558881 -1 1.05928269152787 3406 3475 3343 3335 3622 2618 4607 1172 2643 2527 2125 3684 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 0.169611592577034 0.273127121242606 2725 3346.36363636364 3336 0.0184145149145646 900 0.262537057226387 -0.170079286454063 -1 0.330269336697467 2725 4526 3880 4150 4256 2580 900 2945 4547 3336 2965 3685 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 0.0165523574194306 0.0505634594963833 3340 3089.72727272727 3336 0.00151620198263784 520 1.10285884552099 1.12691409664067 1 3.19050316038347 4465 2968 3338 3458 520 2732 4025 4314 2803 2028 3336 3686 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 0.874372219897219 0.949990313572541 3065 3434.36363636364 3337 0.171869654989908 1950 0.29824001756409 -0.254438127473496 -1 0.0148312137705074 4039 2736 3061 3065 4031 1950 3314 4545 3754 3946 3337 3687 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 0.180517480494409 0.286456117032442 2035 3023.81818181818 3338 0.0179355907221137 1759 0.375579602938426 0.406064642264592 1 0.455129421367432 2035 3766 2355 3666 1759 4179 2256 3338 3853 3540 2515 3688 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 0.33296556889208 0.453871800574534 3340 3014.63636363636 3338 0.0396825396825397 1706 0.381535928887229 -0.551186867451401 -1 0.292141790615063 3338 1706 3999 2276 4268 3406 3706 1833 2109 3573 2947 3689 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 0.796944161638877 0.890221773883141 3820 3296.81818181818 3338 0.134920634920635 1991 0.665455983212677 -0.665455983212677 -1 0.0750076637577516 3820 3156 3099 3112 3781 1991 3462 4096 3338 4061 2349 3690 M1749 KEGG_VEGF_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VEGF_SIGNALING_PATHWAY.html VEGF signaling pathway 32/89 KEGG 0.722482692623301 0.824940033536255 4250 3303.90909090909 3341 0.11 1220 1.14672566625037 1.14672566625037 1 0.213909014730033 4248 1220 3261 1612 4572 3341 4648 3282 3409 2732 4018 3691 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 0.0495661597895613 0.114473644541096 3400 3241.90909090909 3341 0.0046108576364906 1046 0.957499771176985 -0.962459145282916 -1 2.01160983422579 3396 3399 1046 3268 3723 2880 4602 3053 3872 3081 3341 3692 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 0.480224530283359 0.600976086811248 2960 3272.18181818182 3342 0.0577523328776554 1647 1.18950771485677 1.23337027717375 1 0.587110217539693 2958 3044 1647 3342 3566 4360 2702 4031 3498 2507 4339 3693 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 0.00740954679120118 0.0277982412545045 3230 2618.18181818182 3343 0.000743436897666245 343 0.620893507665358 0.586885763089849 1 2.15626151616112 3229 635 3913 1133 343 3561 3698 3343 1226 3427 4292 3694 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 0.0108460585383354 0.0368294422540866 4655 3076 3344 0.000990900172082013 399 0.724095453604658 0.724095453604658 1 2.31721015398688 4652 2442 3542 2366 399 3734 4400 3014 2013 3344 3930 3695 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 0.493063572728597 0.614657063529185 4650 3406.54545454545 3344 0.0598923409635221 2417 1.06532251051669 1.11035529877623 1 0.50257177554583 4647 3084 3652 3034 2486 2417 3567 4653 3344 2972 3616 3696 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 0.751017133201056 0.848905049629493 3540 3158.2 3345 0.143144244713791 2173 0.401131982881682 -0.608830464812057 -1 0.0636921773919533 3540 2706 3795 NA 3785 2985 2173 2190 3718 3180 3510 3697 M12705 SIG_CD40PATHWAYMAP http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CD40PATHWAYMAP.html Genes related to CD40 signaling 21/36 Signaling Gateway 0.902157871246138 0.969168222067722 4140 3386.18181818182 3345 0.19047619047619 1903 0.303974622380825 -0.290904349450387 -1 0.009227465454225 4137 1903 3257 2693 4191 4016 2873 3017 3607 3345 4209 3698 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 0.232850105696956 0.34496857265126 3345 3180.90909090909 3345 0.0238095238095238 1771 1.32827622002797 1.32827622002797 1 1.37030463102564 3345 3122 3351 1972 3484 4297 2561 4064 1771 2651 4372 3699 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 0.864290333985705 0.942878562849373 2110 3160.54545454545 3345 0.166037668735087 2009 0.831595203603502 -0.824099235974244 -1 0.0474115861689883 2107 3956 3554 3456 3150 2009 3886 3345 3507 3017 2779 3700 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 0.0578820107051954 0.128202108998343 2635 3233.09090909091 3345 0.00540576852804784 1084 1.10140055249504 1.10140055249504 1 2.19301062383309 2633 3987 3345 3802 1084 4286 2457 3964 3259 2792 3955 3701 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 0.161385165508919 0.262241686633255 3990 3023.72727272727 3346 0.0158730158730159 1078 1.14672566625037 1.14672566625037 1 1.48777795270266 3987 1860 3357 2246 4174 2519 4273 4656 1078 1765 3346 3702 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 0.726270090971166 0.8280237492927 4190 3445.90909090909 3347 0.111111111111111 1993 0.961393616868723 0.961393616868723 1 0.175860351419012 4188 3690 3076 3347 4361 1993 4138 3830 3193 2838 3251 3703 M5489 BIOCARTA_IL6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL6_PATHWAY.html IL 6 signaling pathway 17/36 BioCarta 0.330695683265066 0.452053667380426 4290 3377.36363636364 3348 0.0358433470167077 2153 0.30939188646291 -0.288523371002946 -1 0.238104899200018 4287 3598 3348 3042 2153 2868 4170 3869 2960 3281 3575 3704 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 0.42332866383472 0.544379286149698 4440 3348.36363636364 3348 0.0488123234195007 2350 0.976083622180352 -1.29829314601985 -1 0.57535032669946 4440 2796 3238 3348 2350 3062 3984 3536 3758 2883 3437 3705 M2909 REACTOME_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_METABOLISM.html Genes involved in Pyrimidine metabolism 17/29 Reactome 0.87309029841288 0.949037610383381 4565 3405.81818181818 3348 0.171104981998478 1943 0.26727280601316 -0.253894953997133 -1 0.0135511826574412 2661 4561 2493 4339 3348 1943 3005 4405 4563 3780 2366 3706 M9174 ST_STAT3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_STAT3_PATHWAY.html STAT3 Pathway 8/19 Signaling Transduction KE 0.692053852342561 0.797777208383085 4060 3257.81818181818 3350 0.111111111111111 1963 0.433983221546397 0.347308918776492 1 0.0950392151743335 4057 2821 3886 2658 3407 2800 1963 3898 3174 3350 3822 3707 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 0.937138949274003 0.989507236660202 4595 3345.09090909091 3351 0.22238976729788 2382 0.311010810473798 -0.315015891528533 -1 0.00317993112691584 4595 3753 2761 3224 3351 2382 3613 3171 4097 3403 2446 3708 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 0.214139132665174 0.327605607466211 2765 3092.81818181818 3351 0.0238095238095238 1351 0.858982002181133 0.858982002181133 1 0.929160303555844 2764 3321 4000 3477 3847 4171 2444 1351 1711 3584 3351 3709 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 0.944354839374935 0.993990740635882 3355 3609.45454545455 3351 0.230961742117402 2492 0.224647271611446 -0.262820407787916 -1 0.00131248425585547 3351 4337 3223 4441 4569 2619 2720 3124 4512 4316 2492 3710 M19358 BIOCARTA_MET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MET_PATHWAY.html Signaling of Hepatocyte Growth Factor Receptor 29/65 BioCarta 0.179307154474165 0.284728338145014 4280 3178.63636363636 3353 0.0178038201044845 1755 1.9083122944764 1.9083122944764 1 2.32369397666894 4276 4142 2063 2298 1755 3353 3906 4550 1914 2658 4050 3711 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 0.624362153060808 0.738534215091017 1840 3098.72727272727 3353 0.0932721937570644 1634 0.35255926362906 0.35255926362906 1 0.10357728416886 1837 3552 4254 3984 3339 1634 1663 3353 4337 3994 2139 3712 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 0.343245107142643 0.465137817255762 3065 3208.81818181818 3354 0.037500967689637 2179 0.28267813192741 0.320816260406753 1 0.209728164454836 3063 3596 3354 3264 2179 2791 2831 3680 3581 3391 3567 3713 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 0.223565295920252 0.339147613040564 4225 3473 3355 0.0227413124376288 1368 1.30797528369001 1.41015524709925 1 1.37093723038516 4221 4576 1368 4171 2733 3297 4500 3335 3355 2940 3707 3714 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 0.840135001633771 0.923281570744806 2665 3317 3356 0.16751706681182 2190 0.247662525651166 -0.288983662280986 -1 0.0191620289543852 2663 4529 4003 4385 3356 2361 2426 2373 4609 3592 2190 3715 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 0.554370849097497 0.674748519187239 3915 3389.09090909091 3356 0.0708442722947347 2587 0.934213124706781 0.934213124706781 1 0.356255017383567 3915 3267 2715 3356 2587 3173 3380 4558 3713 2962 3654 3716 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 0.785941684398692 0.881292829167808 2810 3359.63636363636 3357 0.142857142857143 2183 0.408777224498258 0.584516849371713 1 0.0500701020200001 2807 4499 4224 4373 4139 2546 2183 2351 3357 3951 2526 3717 M814 REACTOME_PURINE_SALVAGE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_SALVAGE.html Genes involved in Purine salvage 8/15 Reactome 0.0190955429169431 0.0568931526672333 1390 2332.45454545455 3358 0.00192616431509568 248 0.290358014105606 -0.290358014105606 -1 0.806792389786863 1389 3358 4017 3380 4130 248 1044 484 3527 3618 462 3718 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 5.08692391767632e-05 0.000570270944455293 4130 2592.45454545455 3358 4.62458322116294e-06 367 1.59293002124275 2.15526094263491 1 11.5331043285081 4130 1500 367 868 4675 3742 3518 3358 463 1627 4269 3719 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 0.158964687690461 0.262241686633255 1765 2986.27272727273 3358 0.0156151297802222 840 0.260499752586953 0.300793498238131 1 0.33797603027373 1764 4553 3358 4234 4330 2222 840 1025 4061 4176 2286 3720 M3115 KEGG_LONG_TERM_POTENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_POTENTIATION.html Long-term potentiation 27/89 KEGG 0.808400973959046 0.900443775605441 3930 3339 3359 0.139475921317639 2158 0.260991079869415 -0.258937224965232 -1 0.0265295976559426 3926 3372 3584 3359 3203 2503 4371 2158 4205 3217 2831 3721 M1 PID_FANCONI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FANCONI_PATHWAY.html Fanconi anemia pathway 18832364 34/62 Pathway Interaction Database 0.979582813869625 0.999999995401952 2280 3476 3359 0.297957728812651 2277 0.257053168869353 -0.292533523918839 -1 1.04291266449965e-09 2277 4112 3142 4352 3831 2714 3214 3447 4462 3359 3326 3722 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 0.145718749171301 0.247358336478991 4485 3367.81818181818 3360 0.0156261060635534 1670 0.623720220433303 -0.735943006824022 -1 0.844548055765252 4483 2648 4426 3016 1670 3360 2305 2343 3988 4319 4488 3723 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 0.466738071388703 0.587219019917277 3075 3341.36363636364 3361 0.0555555555555556 2103 0.313079905424683 -0.213248091149551 -1 0.161555729345327 3071 2103 3334 2563 4492 3802 3361 3643 2574 4141 3671 3724 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 0.0198285301400139 0.0585485143264684 3435 3032.18181818182 3362 0.00181904837493403 896 1.20378528543315 1.30734079226523 1 3.31138683340786 3431 3619 896 3899 1442 3280 3432 3362 2718 2757 4518 3725 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 0.660009733462017 0.771080930192722 4250 3490.90909090909 3364 0.0934201876458364 2559 1.51746024606229 1.51746024606229 1 0.382376296692951 4249 3562 3103 3291 2783 2929 4549 4039 3364 2559 3972 3726 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 0.0255441765614835 0.0702012764987435 3715 3011 3364 0.00234960748666437 681 1.36817005830577 1.43018481349059 1 3.52286163311005 3712 4313 2069 3854 681 2345 3575 3364 2714 2509 3985 3727 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 0.113165911025652 0.200641490376922 3955 3032.36363636364 3364 0.0108585575455811 1116 1.08266449562403 -0.919782616310716 -1 1.68564845327416 3952 4314 3364 4164 1461 1116 4386 2723 3436 2273 2167 3728 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 0.478231970981605 0.598876273655745 2795 3299.27272727273 3365 0.0574245303578423 2458 0.650112755713168 -0.650112755713168 -1 0.323084474067268 2794 3723 2649 3860 2458 2865 2670 4253 4222 3365 3433 3729 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 0.232850105696956 0.34496857265126 3575 3121.63636363636 3365 0.0238095238095238 1620 1.06103007659061 -0.680644994905029 -1 1.09460246721237 3574 4127 3365 3153 3717 3555 2611 2766 1620 1983 3867 3730 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 0.232850105696956 0.34496857265126 4055 3236.72727272727 3367 0.0238095238095238 1684 1.31212748984869 -0.831099373833084 -1 1.35364493372936 4055 2147 2598 3086 4357 3367 4335 4071 1684 2325 3579 3731 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 0.775485941583084 0.872282074473915 3830 3446.36363636364 3367 0.126984126984127 2498 0.373856376082348 -0.263213404066566 -1 0.0495169886866742 3829 3277 2545 3946 3367 3604 3252 2498 3301 3921 4370 3732 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 0.0631616952846956 0.13692183176696 1850 2854.45454545455 3367 0.0059137697473682 486 0.261390916126039 -0.288604150725979 -1 0.503786026524158 1850 4097 3367 4531 4564 486 1529 1616 4067 4671 621 3733 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 0.157352879472823 0.261845025997745 4055 3276.09090909091 3368 0.0169749744556296 1288 1.30075121165843 1.3954673556245 1 1.68952140687798 4051 4538 4312 3368 1720 1288 3846 4675 2577 3075 2587 3734 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 0.944003618297321 0.99384429461722 4305 3290 3369 0.230521728977709 2047 1.29644110978073 1.29644110978073 1 0.00775951569250088 4301 3450 2473 3901 3369 2677 3795 3181 3806 2047 3190 3735 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 0.572825312598283 0.689509225490766 1440 3094.63636363636 3369 0.0815393570800573 1439 0.368923288262551 0.423560325383773 1 0.132947554979441 1439 4193 4573 3814 3495 2992 1962 2006 3369 4526 1672 3736 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 0.203209323922605 0.314893813459434 2225 2697.54545454545 3370 0.0204394309156115 708 0.242631666794461 -0.223423881202589 -1 0.271762005007999 2223 3370 3704 3798 3425 708 1783 1319 3561 4357 1425 3737 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 0.185873231421982 0.293662158612073 3865 3366 3371 0.0185208139884465 1767 0.653874098340854 0.653874098340854 1 0.776621480135318 3865 3965 2908 4031 1767 2631 4592 3021 3905 3371 2970 3738 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 0.193887843696222 0.303865697511872 3495 3243.63636363636 3372 0.0194031421047585 1793 0.724095453604658 0.724095453604658 1 0.836051897083626 3494 2738 3372 2696 1793 4684 3087 3367 3528 3522 3399 3739 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 0.504936043664042 0.62728799061763 3375 3111.45454545455 3372 0.0619155497901154 1209 0.931796716572437 -0.781628281319039 -1 0.421207973470848 3372 4083 2792 3739 2903 1209 3887 3687 3583 3035 1936 3740 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 0.58834661854412 0.704752621292879 4085 3412.45454545455 3372 0.0775190080956318 2641 1.92386779320347 1.92386779320347 1 0.652519500885592 4081 3887 3511 3080 2641 2691 4398 3785 3088 3003 3372 3741 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 0.0382956522589132 0.0945486967783284 2860 3289.27272727273 3373 0.00354354372155775 873 0.825380008545052 -0.801505046067566 -1 1.88703310966629 2859 4662 3373 4226 873 3113 2681 2953 4078 3804 3560 3742 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 0.494875594976771 0.615952833715387 3230 3261.90909090909 3374 0.0601983269850755 2057 0.374345784798007 -0.318452524924561 -1 0.175835547680051 3227 2057 2757 3374 2491 4020 3533 2676 3515 4339 3892 3743 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 0.298735036746822 0.4173739958842 4430 3106.54545454545 3376 0.0317460317460317 1480 1.14672566625037 1.14672566625037 1 0.97122938609837 4428 2605 3376 1480 4028 3595 4583 1680 1880 2037 4480 3744 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 0.358876491966646 0.478362197236587 2495 3280.45454545455 3376 0.0396064258749681 1399 0.38575774179462 0.501138195108117 1 0.275723670592397 2494 3376 1617 3836 4426 4330 3146 1399 4188 4043 3230 3745 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 0.843963796367308 0.926620044465137 4275 3537 3377 0.155388768494717 2133 0.197793470799353 -0.213568010237131 -1 0.0146115845395861 3377 4275 3520 4274 4654 2776 2906 3294 4428 3270 2133 3746 M87 PID_LKB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LKB1_PATHWAY.html LKB1 signaling events 18832364 38/103 Pathway Interaction Database 0.891318536407728 0.961712793370162 3805 3383.27272727273 3377 0.182707016004905 2385 0.274022269605127 -0.29451625075017 -1 0.0103693880555575 3805 4216 2752 4102 4110 2990 2427 2385 4458 3377 2594 3747 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 0.664369326497077 0.774616736937466 4195 3309.27272727273 3377 0.0944831979890781 1884 0.377897158032946 0.299292097509412 1 0.0935483466373932 4193 2446 2768 3242 3479 3377 4642 1884 3531 3655 3185 3748 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 0.220711688174854 0.335791891999298 2465 3049.27272727273 3377 0.0224153393418705 1121 0.229158313838683 -0.229861345845501 -1 0.242398085211074 2465 4156 3377 3848 4032 1400 3029 1163 4379 4572 1121 3749 M735 REACTOME_NEURONAL_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEURONAL_SYSTEM.html Genes involved in Neuronal System 98/338 Reactome 0.597318307603006 0.711317303539438 3140 3318.36363636364 3378 0.0793650793650794 2216 1.28666434015716 -1.22657421499143 -1 0.424835236131888 3138 3745 2230 4214 2782 3539 3378 3821 2941 2216 4498 3750 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 0.737299158470412 0.83818143051731 2835 3272 3378 0.125124718218912 1398 0.556773986355242 -0.361230421103292 -1 0.0952661110647144 2834 1398 4630 2123 4483 3825 1860 3160 3692 4609 3378 3751 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 0.251962438671308 0.368787034048893 2775 3102.54545454545 3380 0.0260458971502631 1414 1.03535367828569 0.946754248625666 1 1.00110850425555 2771 3594 1414 3554 4251 3347 2812 3953 3380 1564 3488 3752 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 0.147859119791321 0.249412467725749 4295 3098.81818181818 3381 0.0158730158730159 1087 1.26530448687738 1.26530448687738 1 1.70314198238624 4291 3291 3860 1828 4112 3890 3381 2046 1087 1683 4618 3753 M14033 REACTOME_MRNA_SPLICING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_SPLICING.html Genes involved in mRNA Splicing 63/178 Reactome 0.778741083851366 0.875513794437566 2110 3307.18181818182 3381 0.128142464530176 1680 0.955023857704091 0.955023857704091 1 0.123068821318258 2106 4622 3696 4564 3381 1680 3278 2967 4100 3588 2397 3754 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 0.422656082694046 0.543812851044564 4590 3499.36363636364 3382 0.0487115236076419 2347 0.368079992545706 -0.35949524126506 -1 0.217335368525723 4588 4095 2570 4065 2347 3058 3198 3382 3261 4235 3694 3755 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 0.562602523845002 0.680703349154377 3385 3210.63636363636 3382 0.0724178376823374 1599 0.931951048591966 -0.931951048591966 -1 0.347455051296718 3382 3509 2687 3203 3488 1838 4180 3018 4105 4308 1599 3756 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 0.63389956273523 0.745034700521015 4440 3486 3383 0.0873015873015873 2430 1.38933387508025 1.38933387508025 1 0.396366445286603 4438 2722 2430 3148 3383 4345 3682 4483 2999 2669 4047 3757 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 0.138423126886026 0.236820289371273 3375 3511.09090909091 3383 0.013453320098984 1584 0.686007751272719 -0.686007751272719 -1 0.95783828467578 4330 3383 2860 3102 1584 3373 3642 4292 3372 4599 4085 3758 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 0.298735036746822 0.4173739958842 4215 3443 3385 0.0317460317460317 2084 1.0871635362997 1.0871635362997 1 0.920782716406236 4211 3626 3385 3346 2084 2986 4542 4563 2090 2836 4204 3759 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 0.37081961460371 0.491697994915955 2525 3195.27272727273 3385 0.0412467832013124 2034 0.750092992699933 -0.750092992699933 -1 0.516143412719626 2523 3066 2085 3602 2236 3385 2034 3948 4392 4228 3649 3760 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 0.51337480396989 0.633523779448203 3390 2940 3386 0.0633806092550289 1319 1.03923524778171 1.12627933352179 1 0.459809895071201 3386 1344 1679 1319 3519 4285 3394 4318 2885 1794 4417 3761 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 0.931198374717606 0.987685736515776 2035 3468.72727272727 3386 0.234826589998559 2033 0.329895932260096 0.329895932260096 1 0.00396220633389533 2033 4135 4352 4176 3386 2450 3210 3078 4381 4125 2830 3762 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 0.22185501935045 0.337208115691278 4165 3365 3386 0.0225458137619063 1863 1.53150662091758 1.53150662091758 1 1.61374257374013 4165 3386 2354 2869 1873 4502 4436 3866 3108 1863 4593 3763 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 0.136895161541798 0.23467548404327 4375 3016.72727272727 3387 0.0132943942324682 572 0.285523053797977 -0.278476124653294 -1 0.401179503836046 2124 3930 2929 4323 4375 572 1657 3387 4373 4398 1116 3764 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 0.214139132665174 0.327605607466211 2375 3153.72727272727 3390 0.0238095238095238 1324 0.50098802279829 0.321699261996803 1 0.541918436151535 4035 1324 4278 2414 3390 4221 2375 2372 1624 4026 4632 3765 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 0.237493667179185 0.350628646629382 3395 3362.54545454545 3391 0.0243481788450311 1915 0.372975009030383 0.319023639528503 1 0.378892771622657 3391 3977 2754 3353 1915 3691 4660 2804 2304 4008 4131 3766 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 0.865412014258462 0.942878562849373 3395 3165.90909090909 3392 0.166666666666667 2066 0.904443386244114 0.892522259237821 1 0.0515648663719513 3392 2771 2181 3595 3528 4436 2066 2863 3499 2286 4208 3767 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 0.399525073361804 0.521061645915228 2425 3087.18181818182 3393 0.0453082475929743 1674 0.318665267038259 -0.192420501306188 -1 0.201358915847884 2421 3765 3265 3939 2307 4227 1699 1674 3464 3805 3393 3768 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 0.0580610033465049 0.128457913919604 4020 3382.63636363636 3393 0.00542294842835132 1088 0.254754045860545 -0.338713097651312 -1 0.506751325104972 4017 4032 2832 4336 1088 2837 3393 3276 4469 4349 2580 3769 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 0.154243741575455 0.257861638609555 2110 2733.90909090909 3394 0.0151140792799665 1009 0.21188738592365 -0.245913207986821 -1 0.278365045996825 2109 4227 3634 4424 3707 1066 1052 1009 3394 3669 1782 3770 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 0.302735454552699 0.422333533799925 2900 3354.72727272727 3395 0.0322494727308538 1466 0.73426504557095 0.73426504557095 1 0.613484774252848 2896 3284 1466 3717 2803 4571 3877 4139 2337 4417 3395 3771 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 0.924790804238268 0.984007654100936 4580 3503 3398 0.209607495356659 2667 0.670476327300891 0.7649899404062 1 0.0104774487115071 4577 2979 2667 2915 3293 3687 4259 3398 4108 2772 3878 3772 M11480 REACTOME_MEMBRANE_TRAFFICKING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEMBRANE_TRAFFICKING.html Genes involved in Membrane Trafficking 89/177 Reactome 0.0911823107309272 0.168289133209599 3345 3016.72727272727 3399 0.00865422263793806 467 0.272518510807458 -0.264756440587428 -1 0.470744287031737 3344 4356 3399 4289 2680 467 2171 3827 4209 3448 994 3773 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 0.581415801598385 0.697698961918062 4045 3458.63636363636 3399 0.0761177552560326 1689 0.288238881236849 -0.253301189376046 -1 0.100572625631041 4041 3351 3182 3399 2629 1689 4559 4650 4314 4044 2187 3774 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 0.131063570490949 0.226963744020911 3975 3350.54545454545 3399 0.0126901836756224 1250 1.17361346683533 1.34487051333645 1 1.68701851567576 3975 4174 1250 4177 2910 3399 4389 2101 3251 2899 4331 3775 M11792 BIOCARTA_SHH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SHH_PATHWAY.html Sonic Hedgehog (Shh) Pathway 7/19 BioCarta 0.933921556273989 0.98846022445738 2845 3369.18181818182 3402 0.237910495439976 2288 0.210036785475422 -0.219227056209226 -1 0.00236305883523291 2842 3947 3871 3729 3402 2288 2383 3927 4538 3326 2808 3776 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 0.231432032336753 0.34496857265126 3935 3205.90909090909 3402 0.0236456174816656 1606 0.87593205932852 0.87593205932852 1 0.903647704609164 3932 3402 1606 2691 1896 3962 4643 2208 3791 2796 4338 3777 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 0.450083806750413 0.573123021313162 3405 3259 3402 0.0529114379736808 1558 0.25804585543857 0.155744046578561 1 0.139234474841711 3402 4023 3252 4330 3064 2262 4213 1558 3890 4272 1583 3778 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 0.775485941583084 0.872282074473915 4670 3599.27272727273 3403 0.126984126984127 2883 0.997343507657918 1.07651813584614 1 0.132097378589623 4668 3687 3485 2883 4136 3066 3347 4659 3292 2966 3403 3779 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 0.597318307603006 0.711317303539438 4565 3373.45454545455 3405 0.0793650793650794 2459 1.24287224182961 -1.24287224182961 -1 0.410375811200655 4561 3094 3405 2459 2856 3840 3596 4097 2880 2733 3587 3780 M6467 REACTOME_OPIOID_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OPIOID_SIGNALLING.html Genes involved in Opioid Signalling 35/93 Reactome 0.834367499525838 0.919531068386189 4475 3347.63636363636 3406 0.150793650793651 1678 1.05852373568377 -0.650112755713168 -1 0.0860760149904701 4472 1678 2995 2100 3286 3749 4186 4075 3406 2788 4089 3781 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 0.872067877500771 0.948366227423674 2325 3273.90909090909 3406 0.170500119585562 1860 1.34349992948527 1.34349992948527 1 0.0690393150071694 2323 4675 2068 4581 3638 3335 3406 3495 4099 1860 2533 3782 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 0.698152987361708 0.80243926877041 3825 3348 3407 0.103174603174603 1754 0.298481067867757 0.324609456039837 1 0.0636793952667875 3821 1754 3407 2564 3915 4430 2483 2991 3129 3658 4676 3783 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 0.25601463193865 0.373500798650222 3220 3168.09090909091 3408 0.0291403774220418 1690 1.21455215107271 1.21455215107271 1 1.15942742272218 3594 3219 3968 3408 2013 3497 2529 4214 3218 1690 3499 3784 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 0.689922762588757 0.797478555868504 3410 3226.81818181818 3409 0.11049787772469 1776 0.457756806149229 -0.394892874461297 -1 0.100411596121958 3409 3179 4179 3496 3968 1930 1776 2957 4294 3895 2412 3785 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 0.656050517267862 0.767987190586361 2930 3061.27272727273 3410 0.0924654849440447 1745 0.276627567522233 -0.322704691313859 -1 0.0707838218816585 2929 3846 3059 3410 3587 1765 3718 2328 3793 3494 1745 3786 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 0.588322618542426 0.704752621292879 3435 3089.36363636364 3411 0.0775141189517607 1339 0.252241583453198 -0.271408082802693 -1 0.0855529431633299 3433 3729 3268 3673 3544 1339 2525 3139 4155 3411 1767 3787 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 0.656050517267862 0.767987190586361 2930 3062.72727272727 3411 0.0924654849440447 1746 0.276627567522233 -0.322704691313859 -1 0.0707838218816585 2930 3847 3060 3411 3588 1766 3719 2329 3794 3500 1746 3788 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 0.603667233386678 0.717661362899568 3415 3170.72727272727 3411 0.080694204349426 1359 1.10858603309022 1.10858603309022 1 0.356495429821443 3411 4209 3577 4268 2662 1359 3510 3631 3032 2952 2267 3789 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 0.914113997105443 0.976638894308278 3780 3362.72727272727 3412 0.200011297762084 2359 0.650112755713168 -0.650112755713168 -1 0.0148959712500159 3776 3412 2940 3069 3982 3325 3752 2505 4317 3553 2359 3790 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 0.0258569201548378 0.0706916731887807 3595 3014.81818181818 3413 0.00261628024800484 730 0.322399987568355 -0.300162392089926 -1 0.827962982810334 3595 2061 4513 2716 730 3835 2342 1730 3413 4433 3795 3791 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 0.386086746459241 0.507632574048261 4660 3371.81818181818 3414 0.0476190476190476 1700 1.59008010255122 -1.59008010255122 -1 1.04498698114609 4658 4304 4180 3489 4554 2751 3414 2442 2362 1700 3236 3792 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 0.00162647670934558 0.00864134904761157 1990 3169.09090909091 3414 0.000147970947453999 646 0.409021960922758 -0.432502745360468 -1 1.88370760469674 1989 3628 646 3414 3834 3052 3602 2906 4322 4278 3189 3793 M10654 REACTOME_PYRIMIDINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_CATABOLISM.html Genes involved in Pyrimidine catabolism 10/16 Reactome 0.642907804954545 0.754486845483846 2910 3095.81818181818 3415 0.0893664035565032 1418 0.319324614525182 -0.293500288787739 -1 0.0871986956537569 2910 3812 2411 3657 3705 1418 2341 3715 4316 3415 2354 3794 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 0.0925113342900095 0.170471141361771 4360 3439.63636363636 3415 0.0087861021213552 1323 0.24715306943508 -0.242300326615557 -1 0.423842172935898 4358 3413 3415 3398 1323 2843 4614 3048 4359 3600 3465 3795 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 0.581780299025345 0.697957624483555 2480 3072.09090909091 3415 0.0761909209562403 1753 0.955023857704091 0.955023857704091 1 0.332884835505422 2479 3804 1881 3564 3540 3415 2284 1753 3408 4213 3452 3796 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 0.162491626936131 0.263746367794496 2630 3227.63636363636 3417 0.0175761079136018 878 0.275975208286903 0.248180208744551 1 0.356523602059376 2628 3034 4368 4047 3417 2300 878 4192 4259 4154 2227 3797 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 0.793496057563372 0.888488058719704 1610 3223.27272727273 3418 0.145931243667191 1606 0.505950515893818 0.487360651501784 1 0.0579848519648829 1606 3418 4103 4173 4059 2204 2674 2556 4148 3778 2737 3798 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 0.0179217102212965 0.0538471524519325 2730 3296.81818181818 3418 0.00164267196960657 884 1.2898510862431 1.34539093566373 1 3.65279291029955 2730 4286 884 3418 3087 4105 3774 4357 2940 2098 4586 3799 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 0.834367499525838 0.919531068386189 4160 3387 3418 0.150793650793651 2058 1.49234186417521 1.49234186417521 1 0.121352820334494 4157 3542 3229 3945 4173 2058 4177 2803 3418 2671 3084 3800 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 0.679192491585116 0.786239134280597 3655 3286.72727272727 3419 0.0981939624315511 1483 1.17600646720956 1.36365185670306 1 0.274143748449508 3653 4404 3741 3419 2835 1483 4502 3572 3141 3115 2289 3801 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 0.570420511177471 0.686973943452077 3230 3364.63636363636 3419 0.0739374502964393 1304 0.791031902152567 -0.791031902152567 -1 0.287885828038084 3226 4582 3361 4550 3459 1304 3419 3195 3558 4503 1854 3802 M676 REACTOME_PI_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI_METABOLISM.html Genes involved in PI Metabolism 27/51 Reactome 0.834367499525838 0.919531068386189 3980 3440.18181818182 3420 0.150793650793651 2800 0.283459462857931 -0.333323453234972 -1 0.0230500838781321 3980 2800 3590 3253 4613 2826 3014 3790 3420 3501 3055 3803 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 0.894613693788124 0.963714889446241 3420 3485.18181818182 3420 0.184991386904823 2735 0.280449015726908 -0.254680354749025 -1 0.0100472504719866 3700 3026 3419 3829 3219 2735 4001 3327 3936 3725 3420 3804 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 0.174543939348258 0.278870535796146 3005 3259.54545454545 3421 0.0172869491967413 1307 1.46693471565438 1.46693471565438 1 1.81580056141242 3005 2593 1307 3986 3481 4560 3951 2998 4068 2485 3421 3805 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 0.834367499525838 0.919531068386189 4420 3675.18181818182 3422 0.150793650793651 3028 0.320080690668636 -0.283272473484644 -1 0.0260280136604347 4419 3754 3107 4004 3134 3028 4470 3270 3422 4611 3208 3806 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 0.232850105696956 0.34496857265126 3645 2906 3423 0.0238095238095238 1409 1.02639765970063 1.06873745576773 1 1.05887423498481 3641 1409 3483 1794 3563 3423 3067 3584 1826 2301 3875 3807 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 0.161385165508919 0.262241686633255 4465 3360.72727272727 3424 0.0158730158730159 1195 0.386399286388025 -0.399334642967919 -1 0.501319850134494 4461 2988 2976 2847 2316 4682 3424 3659 1195 4412 4008 3808 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 0.594846286193547 0.711279243055168 2425 3134.72727272727 3425 0.0788527181166275 1348 0.918857543130349 0.94096020169886 1 0.303439186711767 2423 4477 3608 3870 3628 1348 3729 2597 3425 3131 2246 3809 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 5.6988662474792e-05 0.00062249154395542 3425 3132.90909090909 3425 5.18092170537098e-06 376 1.46427224650531 1.46427224650531 1 10.4772383731788 3425 3194 376 2335 2896 3723 4232 4606 3430 1625 4620 3810 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 0.949494806717981 0.997544330001665 2755 3469.63636363636 3426 0.237707831611918 2501 0.220135032982292 -0.236826614281534 -1 0.000524634367474942 2753 4219 3649 4281 3400 2501 3560 3058 4163 3426 3156 3811 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 0.610539724259016 0.725035263020211 4345 3426.45454545455 3427 0.0899896816324147 1918 0.181020540066274 -0.151875157030245 -1 0.0564182950189022 3427 3852 4343 4489 2739 2981 1918 2605 4345 4100 2892 3812 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 0.0812716413792261 0.156982736433532 3640 2865.36363636364 3427 0.007676275203033 862 1.22865233110218 0.947089914544191 1 2.20518285078422 3638 3719 1134 3952 4055 862 3427 3437 2415 2148 2732 3813 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 0.196585664396715 0.307169197520176 3570 2888.09090909091 3428 0.0216506570564444 852 1.02401096892853 1.02401096892853 1 1.17160627614795 3568 852 3896 2751 1855 3931 4137 3428 1991 1595 3765 3814 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 0.94331293292587 0.993760920084898 2940 3527.09090909091 3429 0.229663701372178 2334 0.266887848574038 -0.202214844159623 -1 0.00161909198113504 2936 4428 3191 3748 4670 3429 2334 2672 4119 3266 4005 3815 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 0.391732792348676 0.513327702725362 3850 3297.18181818182 3430 0.0441885725671239 1551 0.419324628884886 -0.335939667755227 -1 0.271041896652213 3846 3595 1551 3124 3430 3448 4424 2002 3225 3295 4329 3816 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 0.0671692428215624 0.143695904397095 3480 3176.36363636364 3430 0.00692903188485471 1209 1.09917635728409 1.13721767890851 1 2.06702394481225 3476 3430 4423 3581 1209 2911 3535 3031 2054 3044 4246 3817 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 0.390380513583823 0.512415430435236 3205 3219.90909090909 3431 0.0439955923063598 1460 0.268650490014557 -0.282832624286472 -1 0.174112761316557 3202 3962 3667 4236 2666 2254 3610 1460 3431 4277 2654 3818 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 0.850621352955467 0.931311135502177 4405 3190.45454545455 3432 0.158730158730159 1861 0.274629133842009 -0.288212991770273 -1 0.0189433933628111 4405 1861 3531 2688 4510 1989 2142 3688 3448 3432 3401 3819 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 0.893395120299363 0.963002236899209 3740 3485.18181818182 3432 0.184139140489483 2720 0.293476647134388 -0.271287031252825 -1 0.0107244125382648 3738 2947 3340 3987 3215 2720 3973 3331 3912 3742 3432 3820 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 0.00477033046212981 0.0197892545901293 4100 3188.09090909091 3432 0.000434609602880598 735 1.07683034478502 1.22724281484529 1 4.09436887790684 4096 3717 735 3094 3432 3782 4494 3152 3083 1480 4004 3821 M15347 BIOCARTA_AKAPCENTROSOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAPCENTROSOME_PATHWAY.html Protein Kinase A at the Centrosome 13/25 BioCarta 0.518409431486661 0.637937656498554 4285 3523.18181818182 3433 0.0642657132081305 2535 0.33518882403212 0.278405884499913 1 0.146048570659673 4284 2606 2957 2780 2535 3849 4301 4554 3433 3306 4150 3822 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 0.0958593597971534 0.175467562503696 2405 2963.45454545455 3433 0.00911910780482269 478 0.235244260190743 -0.277803580344751 -1 0.396832553771906 2405 4326 3433 4030 4308 478 2593 1539 4441 4218 827 3823 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 0.452607796927715 0.575086804881582 4455 3400.54545454545 3434 0.0533074394597168 1619 1.29644110978073 1.29644110978073 1 0.695225584473657 4454 4185 1619 3849 2846 2896 3434 4666 3616 2524 3317 3824 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 0.554775818606808 0.675066083093093 3275 3461.1 3434.5 0.0859852720414027 1700 0.168209614202584 -0.282167489195931 -1 0.0640687287273681 3275 3363 4623 NA 3506 2512 4263 2588 4178 4603 1700 3825 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 0.859554868903118 0.938898395263405 3805 3355.09090909091 3435 0.163433233105296 2037 1.46693471565438 1.46693471565438 1 0.0896491221870414 3803 2043 2037 2900 3435 4512 4469 3173 3829 2429 4276 3826 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 0.173659068569063 0.278115651166995 4315 3475.27272727273 3435 0.0171912279362397 1732 0.359846954227293 -0.402190379506164 -1 0.446371088182749 4312 2946 2758 3822 1732 4676 3131 3341 3435 4346 3729 3827 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 0.0839184282471183 0.156982736433532 4095 2876.63636363636 3436 0.00793650793650794 277 1.1712352121029 1.1712352121029 1 2.10213071556304 4094 3454 3548 3436 1470 3432 4037 1459 277 1764 4672 3828 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 0.21243434115645 0.326778858722013 3440 3239.09090909091 3436 0.0235979623306865 1181 1.0897164494986 1.0897164494986 1 1.18141461083259 3436 3677 4117 3331 4587 3812 2678 1181 3217 1514 4080 3829 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 0.0132943754955589 0.0426402762301089 2540 3330.72727272727 3436 0.00121594530383824 845 1.34349992948527 1.34349992948527 1 4.10860909957111 2539 3787 845 4393 4056 4291 3436 3360 3415 2901 3615 3830 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 0.157237667576629 0.261746255866459 3140 3161.72727272727 3438 0.0169615347598474 639 0.59131221708147 -0.614937080119854 -1 0.768260616975327 3136 639 3929 2750 1719 4160 4457 3179 3913 3459 3438 3831 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 0.415320710913563 0.535769969181582 3320 3439.27272727273 3439 0.0476190476190476 2238 1.44106467339063 1.44106467339063 1 0.871699876141613 3316 4480 2238 4166 3427 3528 3439 3519 2446 2707 4566 3832 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 0.691828648934415 0.797777208383085 3735 3508.09090909091 3439 0.111046127359225 2468 0.295994975160013 -0.318052139704545 -1 0.0648207781405366 3732 3177 4552 3439 2889 3072 3864 2468 4069 4487 2840 3833 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 0.00294357656390494 0.0139188696049027 4635 3407.18181818182 3439 0.00026795658466465 688 3.11553755502548 -3.11553755502548 -1 12.9087198956229 4634 4225 688 4448 3439 3403 3842 3417 2961 2603 3819 3834 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 0.493865446231429 0.615165731270727 2355 3165.36363636364 3440 0.0600276259895074 1417 0.688984775972756 0.688984775972756 1 0.324479918842933 2355 4015 3668 3416 4332 2296 1417 3838 3649 3440 2393 3835 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 0.215761358335164 0.329531897938135 1795 3060.18181818182 3440 0.0218524190373061 720 0.270250914973231 -0.241508878047755 -1 0.290794472743336 1791 4548 3440 4567 3197 720 2654 3476 3895 4212 1162 3836 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 0.721636913812816 0.824175134810348 3620 3256 3442 0.109753757410742 1896 0.393095217390972 -0.400936556934308 -1 0.0736810370191055 3618 4459 1896 4432 3442 2339 4397 1995 3419 3473 2346 3837 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 0.565393330979043 0.683019631082185 4280 3464.45454545455 3443 0.0799537942955649 2491 0.305594440747467 -0.303081271493414 -1 0.112927131088729 4280 2491 4225 3538 2653 2731 4195 3225 3376 3952 3443 3838 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 0.216713654693072 0.330357900420213 3180 3138.18181818182 3444 0.0219604567584116 1841 1.26530448687738 1.26530448687738 1 1.35841821288251 3179 3809 3179 3444 1860 3674 3561 4231 2187 1841 3555 3839 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 0.0166224414759574 0.0507114327840732 3855 3325.09090909091 3446 0.00152267088197212 523 0.392203514636091 0.377232470398061 1 1.13350983909089 3855 3021 2076 3106 523 4463 3656 4348 3446 3412 4670 3840 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 0.291743983203057 0.41452768504837 4030 3149.90909090909 3446 0.0308724630153892 1684 0.319342109324794 -0.286538992880733 -1 0.272587783501336 4030 3446 2904 3697 2053 4479 1684 2207 3851 4003 2295 3841 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 0.920306459094924 0.981194289668571 3175 3529.54545454545 3447 0.223498476127538 2421 0.447711734814182 -0.387078609147964 -1 0.00823887763105816 3175 3491 4415 3447 3349 2421 4337 2994 3902 4286 3008 3842 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 0.910442316279742 0.97526870534772 3450 3633 3448 0.196961026915049 2138 0.298921656903046 -0.292812743110453 -1 0.00725595532562567 3448 4145 2138 4557 4307 3334 3717 3187 4430 3361 3339 3843 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 0.667434366415499 0.775117085755398 3450 3353.63636363636 3450 0.0952380952380952 2261 0.933018448622291 0.933018448622291 1 0.230384500409671 3450 2584 2366 2261 3545 4036 3947 4312 3079 2802 4508 3844 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 0.783748957483022 0.880235431717247 4570 3365 3450 0.129955120416478 2065 0.417827278752896 -0.374718811883537 -1 0.0516648478909798 4570 2602 2065 2324 2991 3226 3885 3744 3450 4341 3817 3845 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 0.319225864749491 0.439838989184391 3565 3468.45454545455 3452 0.034352859394803 1839 0.280807495298468 0.288696951537053 1 0.223562522026293 3565 1839 3452 2959 2126 4385 3204 4410 4133 3409 4671 3846 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 0.514011397665828 0.633523779448203 3915 3429.27272727273 3452 0.0634920634920635 1759 1.02001141650513 -1.23889395501682 -1 0.451304306117214 3911 2296 2790 3272 4633 4642 3452 3921 2601 1759 4445 3847 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 0.721139301357392 0.823807597796377 3025 3616.18181818182 3454 0.119886401807998 2176 0.250523607123616 0.267656806515722 1 0.0470659948938751 3022 3359 4503 3255 2949 3454 2176 4454 4397 4419 3790 3848 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 0.988890278056681 0.999999995401952 3490 3633.27272727273 3455 0.335742214067772 2982 0.271940580907008 0.271199783133833 1 1.10926505449941e-09 3486 3350 3455 3308 3859 4362 3365 2982 4140 3355 4304 3849 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 0.401921766762084 0.523750110969723 3830 3279 3455 0.0456552858009488 1786 0.309760216559295 -0.407404693593698 -1 0.194186765305022 3830 3282 2772 3877 2313 3907 3455 1786 3778 3970 3099 3850 M2842 BIOCARTA_FIBRINOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FIBRINOLYSIS_PATHWAY.html Fibrinolysis Pathway 5/15 BioCarta 0.258608565819356 0.376815839374846 3460 3355.45454545455 3456 0.0294794036533327 2023 0.479283707644261 -0.382963543264146 -1 0.453425323571091 3456 2407 3836 3051 2023 3804 3983 3032 4279 3267 3772 3851 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 0.743270044646143 0.843332549445963 3550 3326.27272727273 3456 0.116277221042091 2031 0.296081217537373 -0.321422260522999 -1 0.0489022459598127 3548 2940 3384 2791 3829 3456 4426 2031 3852 3709 2623 3852 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 0.0863089499420638 0.160746883725538 3460 3215.09090909091 3457 0.00817213274257713 1287 0.257943604321027 -0.332424717061363 -1 0.457032239513151 3457 3349 3442 3463 1287 3665 4678 1522 4134 3791 2578 3853 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 0.0685753497123314 0.145999131645609 4205 3335.81818181818 3457 0.00643737104171701 1182 1.13121356210756 1.06622568920714 1 2.10983471401778 4205 2960 3038 4020 1182 2158 4445 4470 3646 3113 3457 3854 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 0.698152987361708 0.80243926877041 3955 3535.54545454545 3458 0.103174603174603 2357 1.09875256957753 1.09875256957753 1 0.234413189957364 3954 3401 3293 2923 3922 4142 3458 4422 3143 2357 3876 3855 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 0.52340095663996 0.642393107075655 3460 3627.63636363636 3458 0.0714285714285714 2775 0.724095453604658 0.724095453604658 1 0.31061812051918 3458 3326 4269 3599 2868 4674 4539 3049 2775 4015 3332 3856 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 0.23792740709108 0.351055739560172 3460 3297.27272727273 3459 0.0268055258937792 799 1.06138507083871 1.25675814705144 1 1.07697299539907 3459 4573 4631 4367 2341 799 4610 3616 3147 3151 1576 3857 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 0.407578924020521 0.530237323142744 2485 3385.72727272727 3460 0.0510069102342398 1337 0.132212043106495 0.140973762156549 1 0.0813053266785143 2483 4680 3930 4450 3019 2877 1337 4103 4663 3460 2241 3858 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 0.957322512515482 0.999999995401952 2115 3541.18181818182 3460 0.249289272047151 2112 0.84968443665508 -0.789047941657043 -1 3.68423816195404e-09 2112 4352 3586 4485 3431 2807 3928 3460 4360 3152 3280 3859 M13088 KEGG_PPAR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PPAR_SIGNALING_PATHWAY.html PPAR signaling pathway 26/91 KEGG 0.448878937397006 0.57189959234431 3325 3409.54545454545 3461 0.0527229822967859 1615 0.417825455687753 0.397466106430956 1 0.226312643481739 3324 3096 1615 3821 3461 4270 2532 4507 3772 3199 3908 3860 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 0.497775823998138 0.619049233348003 2390 3164.63636363636 3461 0.0665527910339586 1825 0.369886564396058 0.412637891156639 1 0.171943141660661 2389 3461 3963 3764 2553 1825 4113 2825 4450 3508 1960 3861 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 0.94734463076205 0.996242580734059 2275 3500.90909090909 3461 0.234813120298689 2271 1.05077947290469 1.05077947290469 1 0.0038342664186331 2271 4545 3582 4415 3385 2499 3461 3608 4473 3052 3219 3862 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 0.0765897756730953 0.156982736433532 3525 2696.72727272727 3461 0.00793650793650794 693 1.51341879904055 1.51341879904055 1 2.71628116208765 3521 953 4577 1692 3543 3461 2469 3595 693 1527 3633 3863 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 0.71756015369141 0.820318829030971 1820 3255.18181818182 3462 0.108576295034982 1819 0.644872453133905 -0.644872453133905 -1 0.123805314162145 1819 4336 1880 3462 3882 2621 3506 2892 4511 4010 2888 3864 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 0.0943398270790021 0.173091789229524 2895 3257.09090909091 3462 0.00896783136597893 1341 0.310703804443798 -0.231577663451394 -1 0.528230530282255 2891 3541 3462 4257 1341 4630 3638 1869 2562 4232 3405 3865 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 0.822564360000116 0.911237964766086 2140 3226.45454545455 3463 0.145462773026917 1792 0.653874098340854 0.653874098340854 1 0.0589132545214374 2137 4099 3200 4080 4006 1792 3020 3471 4054 3463 2169 3866 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 0.716424518650034 0.81942037939811 4100 3427.72727272727 3464 0.108251049097013 2235 0.271034742918695 -0.236058561487941 -1 0.0523222823846217 4098 3996 2705 4262 2870 2235 3464 2731 4323 3824 3197 3867 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 0.918352404502699 0.980049958437634 2415 3404.27272727273 3464 0.221615211951002 2412 0.271837076534793 -0.256038874784348 -1 0.00530988233747814 2412 3390 4194 3574 4011 2458 3261 3464 4329 3912 2442 3868 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 0.94043803945563 0.992080919874473 3465 3524.90909090909 3464 0.226191414339117 2316 0.227969496123669 -0.275116396730677 -1 0.00175687403607131 3462 4564 3243 4587 3464 2316 2682 3711 4110 4167 2468 3869 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 0.312214161491892 0.432153492108204 2970 3299.18181818182 3465 0.0334529028076892 2103 0.857384049986611 0.963016830876921 1 0.697249160500169 2969 3465 3771 3917 2103 2282 4122 4024 3518 3125 2995 3870 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 0.110260245983061 0.196605598430984 2395 3167.27272727273 3466 0.0105643708989591 1197 0.386954750191065 0.500510167861513 1 0.610088670739272 2392 3866 1197 3466 3108 3839 2770 2889 3562 4182 3569 3871 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 0.902157871246138 0.969168222067722 3235 3373.81818181818 3468 0.19047619047619 2510 0.326439392391044 -0.242338033295035 -1 0.00990940689358365 3234 2915 2980 3818 3468 2510 4075 3957 3618 3702 2835 3872 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 0.999188161260485 0.999999995401952 2950 3589.27272727273 3471 0.476348072478352 2950 0.268432476297197 -0.29723627823217 -1 1.09362962205209e-09 2950 3443 3095 3471 4077 3162 4015 3523 4354 4017 3375 3873 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 0.801693838687628 0.895100626183042 3650 3455.45454545455 3471 0.136780040847572 2246 0.831740250885542 -0.791140711360448 -1 0.0893441955076359 3646 2795 2246 3490 3027 2590 3321 4388 3471 4546 4490 3874 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 0.907040023776002 0.973297355487599 2675 3418.36363636364 3472 0.19423439030984 2450 1.21455215107271 1.21455215107271 1 0.0318638521829734 2671 3441 3102 3472 4244 4110 3784 2450 3770 2931 3627 3875 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 0.911756120862818 0.97526870534772 2280 3306 3472 0.198039192164164 2276 0.275468332001072 -0.181884821062568 -1 0.00668665472058002 2276 3472 3482 3744 3837 3640 3033 2466 3717 3351 3348 3876 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 0.883781089295491 0.957106120739236 3080 3392.45454545455 3472 0.177709706672684 2092 1.29142669460736 1.29142669460736 1 0.0548800025520455 3078 2683 2092 2535 4129 4544 3472 3729 3707 2935 4413 3877 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 0.735089153045955 0.83668393761801 3475 3423.81818181818 3472 0.113753522731587 1592 1.17181367894184 1.17181367894184 1 0.202532831003969 3472 4322 3443 4091 4445 1592 3459 3719 3550 2949 2620 3878 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 0.663384324820014 0.773723239329868 2775 3274 3473 0.0942419295562513 1455 0.612253049866341 -0.542728541212628 -1 0.152248027973819 2772 3473 2688 2665 3559 1455 4577 3671 4013 4393 2748 3879 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 0.362782848586011 0.482243478676769 3475 3491.63636363636 3473 0.0440641574119668 1275 0.292685093596752 0.267131258401283 1 0.206906600891518 3473 2704 4661 3137 3082 3044 1275 3987 4451 4641 3953 3880 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 0.466738071388703 0.587219019917277 4650 3652.63636363636 3474 0.0555555555555556 2581 0.885892611905994 -0.625059557561618 -1 0.457138975121488 4649 3831 3474 3801 4551 3270 4418 3348 2581 2843 3413 3881 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 0.0839184282471183 0.156982736433532 4355 3032.36363636364 3475 0.00793650793650794 479 0.738696985995612 -0.743128926420273 -1 1.3258119356937 4355 1451 3475 2281 2962 3713 4154 1728 479 4626 4132 3882 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 0.514011397665828 0.633523779448203 3970 3556.09090909091 3476 0.0634920634920635 2709 0.331651089988497 -0.280876740345761 -1 0.146739107570359 3967 3199 3383 3217 4680 4386 2784 3514 2709 3476 3802 3883 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 0.166179207745394 0.268707994304665 3570 3211.1 3476.5 0.0199904625116763 1778 0.362619613087036 -0.264643750416215 -1 0.461905879037494 3569 2213 3965 NA 1804 4663 3320 1778 3439 3514 3846 3884 M16 PID_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INSULIN_PATHWAY.html Insulin Pathway 18832364 29/68 Pathway Interaction Database 0.850621352955467 0.931311135502177 4130 3471.09090909091 3477 0.158730158730159 2271 0.481449101090274 -0.481449101090274 -1 0.0332094399446504 4126 3969 3201 3963 3607 2271 3477 4208 3474 3362 2524 3885 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 0.93003651267817 0.986827090301926 4575 3544.18181818182 3477 0.214785495104018 2348 0.223085958556753 -0.196562656668261 -1 0.00286743833769591 4572 3385 3536 3516 3314 4068 2348 3415 4098 3477 3257 3886 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 0.896882020175095 0.965714417863166 3895 3425.18181818182 3477 0.186601949974089 2019 0.268423718918334 -0.232591134889632 -1 0.00907715802367062 3892 4274 3101 4439 3477 2019 3072 2503 4221 3564 3115 3887 M15371 BIOCARTA_ETC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETC_PATHWAY.html Electron Transport Reaction in Mitochondria 6/16 BioCarta 0.954822860459364 0.99961092867638 3115 3461.90909090909 3478 0.266345014770683 2697 0.150668857082861 -0.181265539354317 -1 5.6832962722445e-05 3113 3575 3830 3949 3478 2697 3440 3740 4095 3262 2902 3888 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 0.785655668948816 0.881292829167808 3480 3559.18181818182 3478 0.130655321224207 2968 0.237155873987978 0.265891756388214 1 0.0290486310781125 3478 4124 2968 3970 2995 4087 3000 3118 4478 3396 3537 3889 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 0.570425867258223 0.686973943452077 1700 3142.09090909091 3478 0.0739384999685948 1511 0.308024619452522 0.294137890738273 1 0.112101575595454 1697 3991 2697 4141 3810 2607 1511 3478 3878 3811 2942 3890 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 0.35943518917414 0.478362197236587 3625 3215.90909090909 3478 0.0396825396825397 2124 1.16479889230599 1.16479889230599 1 0.832550047277106 3625 3478 2124 2130 4581 4404 2680 3562 2232 2396 4163 3891 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 0.931888078502017 0.988193603951223 4545 3566.54545454545 3479 0.216697747065152 2542 0.650112755713168 -0.650112755713168 -1 0.00748421617540671 4544 3479 3108 3302 3709 4072 3215 2542 4326 3561 3374 3892 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 0.966887219108041 0.999999995401952 2320 3548 3480 0.266408736658663 2317 0.143465630333916 0.155717703327027 1 5.36659150661753e-10 2317 4639 3480 4617 4113 3011 2648 2719 4665 3964 2855 3893 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 0.207898184947084 0.321203723924179 2085 2953 3480 0.0230370346008834 1174 0.364626536903354 0.437461049990774 1 0.401391344048762 2082 3853 4341 4121 3480 2364 1188 1174 3792 4098 1990 3894 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 0.912207156538424 0.97526870534772 4285 3537.54545454545 3481 0.198412698412698 2616 0.352030260604213 -0.297799844255168 -1 0.00854510133569352 4282 3451 2616 4252 3556 3481 3297 3594 3652 3464 3268 3895 M1441 REACTOME_P38MAPK_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P38MAPK_EVENTS.html Genes involved in p38MAPK events 10/15 Reactome 0.809680642156294 0.901654821564732 4655 3411.36363636364 3481 0.14 1471 0.610681132932434 0.610681132932434 1 0.0612798044069644 4653 1471 3199 2028 3999 3378 3167 4303 3788 3481 4058 3896 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 0.667434366415499 0.775117085755398 3485 3411.09090909091 3481 0.0952380952380952 2219 0.724095453604658 0.724095453604658 1 0.178796431680942 3481 2595 3580 2219 3121 4557 3285 4237 3059 3651 3737 3897 M7860 BIOCARTA_NGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NGF_PATHWAY.html Nerve growth factor pathway (NGF) 16/34 BioCarta 0.751985672431077 0.848905049629493 3975 3476.90909090909 3482 0.119047619047619 2461 0.257044601732436 -0.232646323413035 -1 0.0408138245142347 3972 3482 3557 2704 3662 2461 4570 4123 3260 3293 3162 3898 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 8.20234239066973e-05 0.000837389464982099 3185 3133.45454545455 3483 7.45695292512378e-06 398 1.49240205291497 1.48341911632816 1 10.249510446637 3183 3889 398 2603 3392 3791 3483 3976 3725 1359 4669 3899 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 0.936989803160346 0.989507236660202 3735 3449.09090909091 3484 0.222222222222222 2500 1.41016629318858 1.41016629318858 1 0.014418250593782 3734 3863 3484 3223 3460 2500 4124 3574 3740 2957 3281 3900 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 0.0839184282471183 0.156982736433532 4555 3284 3484 0.00793650793650794 779 0.980222501913161 0.980222501913161 1 1.75930146912032 4553 2762 2580 2867 3378 3484 3753 3624 779 4562 3782 3901 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 0.415320710913563 0.535769969181582 3485 3239.81818181818 3485 0.0476190476190476 1342 1.22635373731493 1.71859815318811 1 0.7418212524674 3485 4655 3635 4598 3193 1342 3696 3937 2389 2135 2573 3902 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 0.912207156538424 0.97526870534772 3020 3422.36363636364 3485 0.198412698412698 2333 1.32484166512252 1.32484166512252 1 0.0321589012341029 3018 4613 2690 4303 3485 2333 3790 3512 3647 3018 3237 3903 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 0.00258400407120354 0.0126131698725623 2430 3227.81818181818 3485 0.000235185827848065 678 1.20790310614176 1.34587913491666 1 5.12008074803759 2428 3404 678 3485 3754 4135 3200 3639 3966 2775 4042 3904 M19553 BIOCARTA_AHSP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AHSP_PATHWAY.html Hemoglobin's Chaperone 6/21 BioCarta 0.52340095663996 0.642393107075655 4405 3425.63636363636 3486 0.0714285714285714 2453 0.478468403645272 -0.676044538048459 -1 0.205250503235462 4404 2453 3840 3229 3486 3697 4225 2497 2757 3274 3820 3905 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 0.166142097145851 0.268707994304665 4500 3177.63636363636 3488 0.016381813637419 1263 0.938853735140482 -0.760060047820356 -1 1.19591451820568 3723 4256 3029 4498 1693 1627 3488 4499 3855 3023 1263 3906 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 0.33961001247819 0.461412733683038 1485 2971.36363636364 3489 0.0406434434442757 1285 0.31861387689727 0.358578033602495 1 0.238873362649069 1485 4239 3970 4188 2384 1808 2270 4046 3489 3521 1285 3907 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 0.135100100689682 0.232493232402442 3340 3312.54545454545 3490 0.0144093276800345 1618 0.255854612503236 0.340739415502849 1 0.361810280807387 3340 3943 3920 3742 1618 4601 2135 1858 4348 3443 3490 3908 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 0.416002468261522 0.536282686732735 2820 3385.45454545455 3490 0.0523649813315808 1554 0.32199458639706 0.255510183936635 1 0.194475951501752 2820 4073 3995 4186 3463 3490 3391 1554 3699 3560 3009 3909 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 0.001638587024357 0.00868599411327703 3615 3094 3490 0.000149073521656112 121 0.682955064130999 0.785694668736354 1 3.14186632200709 3611 2079 3490 2325 121 4302 2983 3925 2295 4280 4623 3910 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 0.18068736390799 0.286628634824929 4150 3226.36363636364 3491 0.0179541004271892 1320 0.852246096011289 0.852246096011289 1 1.03225912685343 4147 2951 1320 1786 3491 2679 3584 4202 2835 4651 3844 3911 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 0.00385500575693867 0.0168512658367673 4305 3012.3 3492 0.000429069639229636 246 0.920480148425561 -0.704045079123503 -1 3.64328142100002 4302 644 4187 NA 246 3637 3110 3347 2091 3904 4655 3912 M835 KEGG_DILATED_CARDIOMYOPATHY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DILATED_CARDIOMYOPATHY.html Dilated cardiomyopathy 51/122 KEGG 0.000127118700841338 0.00118661002418827 3445 2996.90909090909 3493 1.15569133191051e-05 427 1.82447917089839 1.3111729062301 1 11.9137111568571 3444 3538 427 2523 3493 4440 3919 3672 2338 630 4542 3913 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 0.0236151206278019 0.0663034483294667 3370 3315.72727272727 3493 0.00217022589097655 928 0.522886301913839 0.535084185916552 1 1.37531790438292 3368 2540 928 2630 4406 4445 4471 1999 3493 3938 4255 3914 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 0.328792125328131 0.449845226069379 3465 3373.63636363636 3493 0.0390833815405132 1219 0.184505896298479 0.173407444939532 1 0.142869747639955 3464 3493 4357 3555 4584 2661 1219 2042 4283 4134 3318 3915 M6382 KEGG_REGULATION_OF_AUTOPHAGY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_REGULATION_OF_AUTOPHAGY.html Regulation of autophagy 18/60 KEGG 0.126982284407564 0.220875643924962 3980 3252.54545454545 3494 0.0122695109207417 1536 0.757413120848284 -0.757413120848284 -1 1.10871095726541 3978 1745 2787 3097 1536 3808 3494 3762 3817 3208 4546 3916 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 0.232850105696956 0.34496857265126 4170 3395.27272727273 3494 0.0238095238095238 1772 1.22168558101711 1.22168558101711 1 1.26034132364336 4168 3835 3408 3494 2705 4616 2822 3548 1772 2640 4340 3917 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 0.298735036746822 0.4173739958842 3335 3192.72727272727 3494 0.0317460317460317 1493 0.377863204138944 -0.269693717913122 -1 0.320034563197694 3332 3632 2613 3886 4108 3494 2189 1493 1951 4220 4202 3918 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 0.463391455121929 0.587196419335143 4365 3267.36363636364 3497 0.055018259855311 1579 1.21791174813949 1.21791174813949 1 0.62851317754824 4365 2723 1631 3497 4497 2655 3734 3862 3255 1579 4143 3919 M14449 BIOCARTA_ETS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETS_PATHWAY.html METS affect on Macrophage Differentiation 14/27 BioCarta 0.784949784237514 0.881023877589698 2885 3360.36363636364 3498 0.130395441822593 1895 0.241573476403878 0.274015000833399 1 0.0296612037324417 2884 3876 3498 3962 3819 3859 1895 2692 3726 3289 3464 3920 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 0.471293999995028 0.591928084689547 4005 3394.36363636364 3498 0.0562919534391406 2439 1.14672566625037 1.14672566625037 1 0.58285609701706 4004 3563 2589 2672 2439 3359 4266 4685 3711 2552 3498 3921 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 0.834367499525838 0.919531068386189 4015 3365.72727272727 3498 0.150793650793651 1982 1.08315018934199 1.08315018934199 1 0.0880785652643266 4011 2548 2424 3498 4511 4112 3571 2499 3411 1982 4456 3922 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 0.635872231772522 0.746978510425179 1285 3459.36363636364 3499 0.0877497695324673 1285 0.242050686245597 -0.265078650780438 -1 0.0684438915488426 1285 4584 3495 4416 3852 2463 3499 3355 4482 3646 2976 3923 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 0.865412014258462 0.942878562849373 4565 3665.72727272727 3501 0.166666666666667 3136 0.263426175090008 -0.324394297989155 -1 0.0150186685624717 4562 4549 3136 4105 3678 3352 3176 3285 3501 3838 3141 3924 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 0.498948720553379 0.620343248743204 3920 3258.27272727273 3501 0.0608897917621481 1200 1.43889558694762 1.80504874700154 1 0.665963532685881 3919 4043 2501 3794 4088 1200 3501 3667 3146 3036 2946 3925 M278 PID_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAC1_PATHWAY.html RAC1 signaling pathway 18832364 37/83 Pathway Interaction Database 0.751985672431077 0.848905049629493 4210 3454.81818181818 3502 0.119047619047619 2429 0.885892611905994 -0.625059557561618 -1 0.140663003314283 4208 4017 3493 3216 3739 3502 2429 3569 3232 2818 3780 3926 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 0.878859116702268 0.952656447112382 4545 3528.27272727273 3503 0.174603174603175 2144 0.653874098340854 0.653874098340854 1 0.030740301550146 4542 3206 3453 2144 3396 4071 3503 3722 3555 3360 3859 3927 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 0.562604368603265 0.680703349154377 3315 3332.90909090909 3504 0.0793650793650794 1742 0.40491046352525 0.332282825103514 1 0.150960917993647 3311 2402 3956 3535 4264 2593 1742 4565 2843 3504 3947 3928 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 0.422597341197723 0.543812851044564 3560 3367.63636363636 3505 0.0534405885691538 2290 0.433052814655083 -0.505321373833 -1 0.255699019172181 3557 3080 4289 3505 2410 2629 2290 4159 4423 4040 2662 3929 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 0.389403382959547 0.511706184113415 3880 3258.27272727273 3506 0.0438563905269294 2118 1.51746024606229 1.51746024606229 1 0.985505433812586 3878 3506 2118 3604 2278 2883 4164 3909 2368 2597 4536 3930 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 0.466738071388703 0.587219019917277 3730 3390.63636363636 3508 0.0555555555555556 1485 1.5279603264104 1.5279603264104 1 0.788459242486202 3730 3508 2732 3354 3832 3205 4201 4620 2478 1485 4152 3931 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 0.953306659670705 0.99959610812641 2050 3377.63636363636 3508 0.243126714555406 2049 0.336804281881896 0.414998617256777 1 0.000131884563319638 2049 3569 2421 4136 3508 3079 3621 2794 4341 4298 3338 3932 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 0.0422538194859721 0.101383204358047 2575 3343.72727272727 3508 0.00391707936868643 1018 1.65870060756586 1.65870060756586 1 3.6800082456478 2572 4328 1018 3035 4252 4394 3476 4425 3508 2010 3763 3933 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 0.173973033161944 0.27823810013545 4345 3380.90909090909 3510 0.01722518051479 1306 0.460133002226651 -0.445529006069879 -1 0.570574291713133 4342 2768 1306 3292 3957 3620 3396 2910 3510 4535 3554 3934 M12975 BIOCARTA_VEGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VEGF_PATHWAY.html VEGF, Hypoxia, and Angiogenesis 18/64 BioCarta 0.844884351825241 0.927413462790602 4585 3594.54545454545 3513 0.155842977975416 2395 0.281727285253556 0.26598104295691 1 0.0205782957155508 4581 3513 3414 3912 3120 2395 4619 3992 4023 3342 2629 3935 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 0.33296556889208 0.453871800574534 3990 3241.54545454545 3513 0.0396825396825397 1022 0.489224472319026 -0.577260873465286 -1 0.374598832104484 3990 1022 4272 1644 2786 4519 3513 3339 2115 4020 4437 3936 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 0.775485941583084 0.872282074473915 4560 3401.36363636364 3513 0.126984126984127 1540 1.55088103516806 1.60459091458215 1 0.205412997361397 4559 3713 2016 3213 4621 2808 4529 3513 3282 1540 3621 3937 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 0.836464725162727 0.921162553155951 2625 3473.81818181818 3514 0.165625266143864 2127 0.226032134171076 -0.205682655381632 -1 0.0179918757075027 2625 3946 4583 3514 3148 2127 3809 2911 4320 4541 2688 3938 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 0.157770235634798 0.262241686633255 3515 3039.54545454545 3515 0.0154881172583831 1283 1.38916827744188 -1.38916827744188 -1 1.80232639472955 3515 3900 1283 1840 2397 3625 4069 4181 1869 2184 4572 3939 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 0.954267830976752 0.99961092867638 4170 3585.36363636364 3515 0.244556512129404 2638 0.530468713592533 -0.530468713592533 -1 0.000200095416111465 4170 4098 3318 3515 3681 2956 3205 2638 3961 4644 3253 3940 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 0.848641242322945 0.930665308103281 2210 3337.54545454545 3516 0.157722436366304 1868 0.955023857704091 0.955023857704091 1 0.0665178932878674 2207 4291 3721 4468 3301 1868 3525 3042 4159 3516 2615 3941 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 0.865412014258462 0.942878562849373 2430 3261.09090909091 3517 0.166666666666667 2061 1.05077947290469 1.05077947290469 1 0.0599078990966637 2426 3517 2162 4076 3873 4284 3660 3623 3512 2061 2678 3942 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 0.849902933224503 0.931311135502177 2755 3311.09090909091 3517 0.158363142877937 1875 0.905955195328801 1.081883242509 1 0.062491060067005 2754 4105 3604 4473 3517 1875 4561 2363 3776 3084 2310 3943 M136 PID_FOXO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FOXO_PATHWAY.html FoxO family signaling 18832364 31/65 Pathway Interaction Database 0.978161938897681 0.999999995401952 3090 3527.27272727273 3518 0.293650793650794 2922 0.552037074845415 -0.493393016758395 -1 2.35763997395199e-09 3086 3095 3176 3518 3710 4421 2922 3657 3933 3385 3897 3944 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 0.83249395350659 0.919318141255214 4130 3655.18181818182 3518 0.163621136867696 1909 0.300859595293453 -0.299223873430064 -1 0.0245325482449956 4129 3422 3967 4175 3462 1909 4515 3402 4448 3518 3260 3945 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 0.937382057088752 0.989540959566995 2990 3525 3518 0.222663641561571 2786 0.325686300674925 -0.250139463217748 -1 0.00331922197883534 2990 3518 2795 3406 3344 4569 2786 3837 4010 3580 3940 3946 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 0.832656756310386 0.919318141255214 3520 3425.36363636364 3518 0.15 1538 0.292011828964365 0.24630831326021 1 0.0238110879404762 3518 1538 3273 3235 4508 3957 2197 3389 4165 3685 4214 3947 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 0.692053852342561 0.797777208383085 4620 3602.90909090909 3519 0.111111111111111 2448 0.579867866244599 -0.64564188335255 -1 0.126986906847046 4618 2955 3939 3098 4566 4022 3519 2448 3158 3474 3835 3948 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 0.836410282516912 0.921162553155951 2310 3486.45454545455 3520 0.1517511628623 1995 0.117051029695619 0.121543174258919 1 0.00931711579082828 2306 4628 3773 4570 3817 2857 1995 3318 4636 3520 2931 3949 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 0.873054493017489 0.949037610383381 3480 3409.36363636364 3520 0.171083724859755 1942 0.202760911074314 -0.193928463271391 -1 0.0102803206061777 3477 3520 3605 3716 4257 1942 2731 2547 4091 4438 3179 3950 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 0.594486461331301 0.711198253203594 4190 3252.27272727273 3522 0.0787783764186153 1347 0.634409160957587 0.634409160957587 1 0.209574317118278 3704 4188 3074 4189 2942 1347 1840 3522 4232 4348 2389 3951 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 0.278206851557682 0.399166352234935 4265 3445.27272727273 3524 0.0292029850036112 1989 0.330375331412846 -0.33889769013499 -1 0.294098282734255 4262 1989 3524 3558 2014 3951 3188 3295 3389 4556 4172 3952 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 0.979766696542568 0.999999995401952 2285 3553 3525 0.298534893803172 2281 0.957172730471711 -0.523746058863399 -1 4.163307672067e-09 2281 4614 3525 4368 3794 2529 4031 3412 4262 3137 3130 3953 M902 REACTOME_CGMP_EFFECTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CGMP_EFFECTS.html Genes involved in cGMP effects 5/21 Reactome 0.964123794279472 0.999999995401952 2530 3356.81818181818 3525 0.283063567313097 2528 0.196164465942892 0.209739618237203 1 7.7153500981145e-10 2528 2958 4048 3556 3525 3279 2538 3606 4204 3671 3012 3954 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 0.932120067585876 0.988215981155524 3105 3437.63636363636 3525 0.216940662109874 2190 1.86280643978199 1.86280643978199 1 0.0214040789244111 3104 4485 2190 3964 4157 2989 2650 4321 3802 2627 3525 3955 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 0.63389956273523 0.745034700521015 4165 3691.27272727273 3527 0.0873015873015873 2967 0.764161110170704 -0.764161110170704 -1 0.218009384377019 4162 4465 2967 4573 3015 3425 3189 3886 3027 4368 3527 3956 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 0.102594355720401 0.185548881090622 3675 2912.45454545455 3528 0.010766353028209 743 0.653874098340854 0.653874098340854 1 1.06761029346727 3672 743 3976 2067 1456 3546 3453 4211 1249 3528 4136 3957 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 0.352163681299136 0.474888923904389 2800 3297.45454545455 3528 0.0424829209069021 1258 0.420765553844167 -0.49242977822665 -1 0.303717934596843 2798 3528 4263 3760 4631 2425 1258 2698 4124 4006 2781 3958 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 0.929545109497602 0.986602125278769 4390 3501.81818181818 3528 0.214285714285714 2574 0.73426504557095 0.73426504557095 1 0.00960015649285726 4390 2763 2574 3393 3769 3350 2935 3528 3700 4024 4094 3959 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 0.0757355169817229 0.156982736433532 2515 3266.36363636364 3528 0.00713415850288984 1119 0.536834350269052 0.452947529830324 1 0.963509263676035 2513 2858 1119 3557 3936 2784 2914 4258 3986 4477 3528 3960 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 0.509252096406123 0.632177784692738 3530 3232.27272727273 3528 0.0626620017821928 1523 0.203755901852043 -0.158459669119384 -1 0.0905719143908045 3528 3844 3612 4010 2608 1698 3076 2658 4363 4635 1523 3961 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 0.0378616278036345 0.0937729775359041 1245 2640.72727272727 3529 0.00350266952897154 282 0.680878280361112 -0.680644994905029 -1 1.56210175585261 1243 4079 3730 4446 3529 282 1920 1645 3626 3759 789 3962 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 0.675490580516311 0.782533710828043 4535 3469.09090909091 3530 0.106442034250506 2207 0.256473380412143 -0.246050695252566 -1 0.0609619705898282 4533 2207 3943 2785 2859 4573 2330 3530 4062 3486 3852 3963 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 0.589080226407465 0.705451045475436 1990 3255.72727272727 3530 0.0850956257286505 1601 0.5166158967085 0.626138149332484 1 0.174724932462702 1986 3530 4155 4052 3574 2841 1601 3214 4120 3853 2887 3964 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 0.0604285261176545 0.132569322746877 3705 3239.81818181818 3531 0.00621375294123105 1162 0.496896027143009 0.469928169664623 1 0.973240997713667 3701 2168 4213 2626 1162 3531 4594 3443 2604 3939 3657 3965 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 0.97482276682907 0.999999995401952 3030 3558.63636363636 3531 0.284454769771316 2477 1.25590635170379 1.5717828996862 1 5.49474725954496e-09 3027 4579 2477 3922 3531 2854 4384 4014 3928 3065 3364 3966 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 0.252730864778953 0.369630721708543 3340 3292.36363636364 3531 0.0261368942152287 1416 1.26257828214407 1.41924849787918 1 1.21802085741174 3336 4078 1416 3531 3596 2616 3929 3547 3892 2847 3428 3967 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 0.277436485141711 0.398304953852345 4200 3313.54545454545 3536 0.0291088372993984 2011 0.85044611430893 -0.650112755713168 -1 0.758843261761978 4197 3536 3558 2884 2011 3846 3576 2748 3701 3016 3376 3968 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 0.577538463951111 0.694290723980222 3540 3373.81818181818 3538 0.0753430204887493 1854 0.408649394836292 -0.405986655591907 -1 0.144526115690928 3538 2950 1854 3563 2621 2945 4187 4376 3965 3822 3291 3969 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 0.000505131865335759 0.00350411566188537 2660 3187.45454545455 3538 4.59316257847177e-05 539 1.49922205635305 1.49922205635305 1 8.21621099855563 2658 3435 539 2542 3538 4137 3667 4104 3678 2583 4181 3970 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 0.761018366226684 0.858274865015221 2500 3421.09090909091 3538 0.122013811415875 2228 0.842802333908373 0.842802333908373 1 0.124853492614168 2498 4290 3727 4568 2958 2228 3538 3705 4096 3112 2912 3971 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 0.0619239867896876 0.134714857055003 3445 3106.90909090909 3539 0.00637204146056703 1174 0.318096268947785 -0.181509882176844 -1 0.618086222656104 3445 3613 3984 3709 1174 4349 3377 1327 1969 3539 3690 3972 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 0.871745323913244 0.948235512501732 1725 3378.81818181818 3539 0.17031020920332 1721 0.23255313340435 -0.245452894306062 -1 0.0119814325246169 1721 4215 3678 4466 3260 2189 3539 3503 4079 3668 2849 3973 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 0.907495524126236 0.973561117410739 4125 3454.45454545455 3539 0.194594121407681 2494 1.31505585488108 1.31505585488108 1 0.0341551784009618 4125 3309 2526 3892 3243 2946 4631 3652 3642 2494 3539 3974 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 0.735345643019206 0.836768188672265 3545 3450 3541 0.124476303840256 2071 0.288870656049539 -0.322496681372759 -1 0.0498993606301179 3541 4242 3942 4195 4427 2201 2700 2071 4207 3485 2939 3975 M11184 REACTOME_ENDOGENOUS_STEROLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOGENOUS_STEROLS.html Genes involved in Endogenous sterols 3/15 Reactome 0.303574927018323 0.423126742417568 4455 3600.90909090909 3541 0.0355328504711893 2147 0.468874281307361 0.216621539611461 1 0.390895708308426 4453 3186 3985 4046 2147 4238 3467 3047 3360 3541 4140 3976 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 0.796944161638877 0.890221773883141 4620 3614.54545454545 3543 0.134920634920635 2670 0.680644994905029 -0.680644994905029 -1 0.0767197113042971 4616 3029 3543 3338 3172 3860 4454 2670 3347 4173 3558 3977 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 0.615106534446036 0.729349499092643 3065 3501.81818181818 3544 0.083138608399437 1809 0.261523512728391 0.302318261461007 1 0.0800045491793384 3062 4483 3544 4589 2862 3995 2553 1809 3198 4582 3843 3978 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 0.775485941583084 0.872282074473915 4050 3607.36363636364 3545 0.126984126984127 3036 0.248060892629006 -0.286621630875959 -1 0.0328554738846677 4049 3643 3545 3712 3276 3324 4338 3036 3281 4118 3359 3979 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 0.130679040779212 0.22646523117285 1570 2776.72727272727 3547 0.0139066839891257 795 0.373159856159067 0.462010566329089 1 0.537196473137313 1569 3850 4142 3547 3741 905 795 3158 3989 3839 1009 3980 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 0.825713880556426 0.913394985037899 3960 3430.27272727273 3547 0.146852954882941 2571 0.872339790410637 0.872339790410637 1 0.0765975353374066 3957 3845 3017 3288 3083 2571 3585 2816 3580 4444 3547 3981 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 0.976460745335598 0.999999995401952 4660 3702.27272727273 3548 0.288817346445189 2783 0.493393016758395 -0.493393016758395 -1 2.0962665798714e-09 4660 4139 3460 3807 3548 2783 3769 3429 4362 3407 3361 3982 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 0.147859119791321 0.249412467725749 3485 3334.36363636364 3548 0.0158730158730159 1070 0.337575908310543 -0.151257481192625 -1 0.4543884160321 3484 3579 3989 3429 3500 4122 3851 2145 1070 3548 3961 3983 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 0.825750004642297 0.913394985037899 3505 3508.63636363636 3548 0.146869031926602 2213 0.822128263809292 0.822128263809292 1 0.0721886120822369 3501 3380 2718 3548 3308 4514 4112 2213 3584 3566 4151 3984 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 0.00261398050279568 0.0127329653181918 1825 3197.72727272727 3548 0.000237917412727088 679 1.23632977637006 1.36611213255288 1 5.22924803753824 1824 3367 679 3127 4125 4651 3710 3757 3548 2372 4015 3985 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 0.406730878868955 0.52957513153096 2830 3240.90909090909 3549 0.0508711502031972 1336 0.404229248699446 -0.412516090727276 -1 0.249075096269442 2826 3549 4154 4250 3894 2174 1336 2417 4509 3851 2690 3986 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 0.425800950828285 0.547258161157801 4275 3197.36363636364 3549 0.0491837661405847 1444 0.795869587349046 0.795869587349046 1 0.465054624619987 4272 1444 1584 1782 2493 3549 4217 4664 2902 3978 4286 3987 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 0.208932374551752 0.322588832668701 1625 3041.27272727273 3549 0.0231646645389818 974 0.296310665013234 -0.31053992458947 -1 0.324951384176991 1625 3075 4542 3549 4387 1037 974 4076 4505 4478 1206 3988 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 0.0811768296307382 0.156982736433532 3540 3483.18181818182 3550 0.00843042203917707 1300 1.1292569021246 1.17628713595526 1 2.02678812520606 3539 4476 4424 4515 1300 2962 3679 3550 2671 3007 4192 3989 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 0.659696691905349 0.770907406051987 4530 3507.27272727273 3553 0.0933443356210451 1827 1.86280643978199 1.86280643978199 1 0.469804534751918 4527 3483 1827 3218 3553 3548 3787 4162 3753 2287 4435 3990 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 0.816521443770307 0.906472278016503 4005 3344.90909090909 3554 0.142857142857143 2457 0.944927296335322 -0.743128926420273 -1 0.0899395862756898 4005 2465 2511 2457 3758 3677 4050 3554 3374 2823 4120 3991 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 0.950760096026441 0.997818994396395 3650 3521.36363636364 3555 0.26 2113 0.431680709479592 -0.425462314886249 -1 0.000913602481724556 3647 2113 3992 2802 4522 2847 4652 3490 4422 3555 2693 3992 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 0.943712354754118 0.993760920084898 4220 3432.90909090909 3557 0.23015873015873 2623 0.344977670474283 -0.296351542477348 -1 0.0020928288453158 4219 3212 2870 3207 3627 2623 3557 4063 3777 3570 3037 3993 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 0.00134358879110151 0.007407117025692 3585 2797.09090909091 3558 0.000134440183691745 112 1.14338139147186 1.14338139147186 1 5.43653009934078 3583 1918 4639 1466 112 3769 4456 3558 2099 1436 3732 3994 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 0.445413174735316 0.567638329292817 2690 3097.63636363636 3559 0.057249101844357 1472 0.261754391216712 -0.350294486953792 -1 0.143675267724881 2686 3609 3994 3611 4536 1657 2049 2647 4254 3559 1472 3995 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 0.624428630002264 0.738534215091017 2465 3197.27272727273 3559 0.0851799385568206 1604 0.688984775972756 0.688984775972756 1 0.202414684070258 2464 3963 3644 3174 4058 2614 1604 3793 3559 3701 2596 3996 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 0.548138890901311 0.66820469374702 3060 3332.27272727273 3560 0.0763647558698123 2064 0.252194822312306 0.263127257568807 1 0.098554906148014 3057 2643 4131 3560 2630 3369 3834 2064 3984 3820 3563 3997 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 0.926127203384651 0.984758809861691 3565 3475.45454545455 3561 0.229365488803955 2494 0.196165590172541 -0.235377289171227 -1 0.00292035975676742 3561 4306 4200 4029 3363 2494 2661 2694 4471 3922 2529 3998 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 0.617532623191814 0.731670764166079 4650 3386.63636363636 3564 0.0836655041228464 1884 0.318630040839819 -0.282966148537843 -1 0.0964930125632064 4650 3767 2568 2574 2682 1884 3564 4324 3831 4243 3166 3999 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 0.987275669980646 0.999999995401952 2700 3482.54545454545 3564 0.32749721988552 2418 0.50491279453589 -0.50491279453589 -1 2.14760960617238e-09 2697 3564 2418 3121 3869 2889 3871 4000 4391 4559 2929 4000 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 0.891921024925976 0.962141326612138 3795 3218.90909090909 3565 0.183119944847426 2072 0.311273303738689 -0.304233764225643 -1 0.0116446044698933 3793 3565 3211 3734 3250 2072 3586 2390 3644 3716 2447 4001 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 0.920266534412945 0.981194289668571 3575 3350.72727272727 3565 0.205398923334806 2096 0.338465597760245 -0.353425737370713 -1 0.00622850913702523 3572 2536 2794 3352 3565 2096 4247 4523 3738 3894 2541 4002 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 0.0839184282471183 0.156982736433532 4460 3227 3566 0.00793650793650794 646 1.40839380365713 1.40839380365713 1 2.52778250150541 4460 4268 3064 3605 2845 3329 3794 3566 646 1368 4552 4003 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 0.176426948775486 0.281107338307354 3570 3178.09090909091 3566 0.0174909553711922 1118 1.18063890866154 1.18063890866154 1 1.45227538980333 3323 3566 1313 3568 2387 4346 4115 4593 2616 1118 4014 4004 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 0.191239380341305 0.300519026250622 3605 3306.54545454545 3566 0.021001560307752 1833 0.409392773441088 -0.240850881656799 -1 0.477086066503292 3604 2612 4235 2467 1833 2429 4394 4389 3566 3961 2882 4005 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 0.54182280391362 0.661537691281715 4000 3467.54545454545 3567 0.0684957066496365 2247 0.631262575792853 -0.631262575792853 -1 0.252826122306715 3996 2506 2247 2454 2571 3567 4527 4531 3337 4240 4167 4006 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 0.466738071388703 0.587219019917277 4115 3476.81818181818 3569 0.0555555555555556 2558 1.77523817066847 1.77523817066847 1 0.916059742592631 4112 4408 2755 3683 2614 3569 4174 3489 2558 2969 3914 4007 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 0.617883267982668 0.731901161215061 1490 3020.18181818182 3570 0.0837419079995015 1487 0.849254971022537 0.849254971022537 1 0.256926776782695 1487 3638 2474 3570 3586 2304 1591 4444 3894 3874 2360 4008 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 0.0260443043830498 0.0711209850460206 2540 3461.36363636364 3570 0.00239616672742345 947 1.19647646248054 1.19647646248054 1 3.06567737266929 2540 4254 947 3476 4321 3344 4326 3725 4495 3077 3570 4009 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 0.865412014258462 0.942878562849373 3575 3869.90909090909 3571 0.166666666666667 3217 0.276491775320307 0.250876046599044 1 0.0157635752548465 3571 3217 3347 3766 4623 4475 3548 4667 3509 3512 4334 4010 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 0.284511311424937 0.406117998517277 2865 3108.63636363636 3575 0.0329247310069225 1144 0.755476726132346 0.853006089489494 1 0.659877772555841 2864 1482 4299 2415 3575 2874 1144 3911 3962 4052 3617 4011 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 0.191871995741502 0.301311049612829 4390 3559.81818181818 3575 0.0191804694110415 1336 1.43148206821771 1.43148206821771 1 1.66452620833912 4388 3510 1336 2912 3905 3575 4341 4669 3545 2565 4412 4012 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 0.102764104076789 0.185784178898083 3600 3452.45454545455 3576 0.0098094313132421 1384 0.409819990952962 -0.448903376501283 -1 0.668628502590859 3598 3445 1823 3576 1384 4267 3987 4670 3320 3349 4558 4013 M2531 REACTOME_MRNA_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_PROCESSING.html Genes involved in mRNA Processing 91/233 Reactome 0.836634192537714 0.921162553155951 2420 3382.54545454545 3576 0.151856776125928 1839 0.955023857704091 0.955023857704091 1 0.0760187071782348 2416 4409 3734 4474 3745 1839 3389 2888 4169 3576 2569 4014 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 0.52340095663996 0.642393107075655 3665 3577.63636363636 3577 0.0714285714285714 2723 0.458039388512538 -0.423104987561745 -1 0.196486986968238 3204 3577 4250 3052 3664 3483 3664 4349 2723 3988 3400 4015 M2623 BIOCARTA_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1_PATHWAY.html IGF-1 Signaling Pathway 17/41 BioCarta 0.891073518496821 0.961712793370162 4310 3630.63636363636 3578 0.182539682539683 2540 0.254654576695791 -0.202034760063861 -1 0.00963648731067499 4307 3999 3539 3125 3355 4131 3811 2540 3578 3275 4277 4016 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 0.466738071388703 0.587219019917277 4300 3494.54545454545 3578 0.0555555555555556 1899 0.432301547243621 -0.479865323722256 -1 0.223076571073992 4299 3841 1899 3267 4148 2941 4302 3510 2518 3578 4137 4017 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 0.294968627689105 0.4173739958842 3245 3543.72727272727 3578 0.031274420643902 2058 0.277252594275317 -0.290079242022774 -1 0.234821522503585 3241 4096 3568 4273 2058 4065 2894 3578 3769 3995 3444 4018 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 0.231856978220961 0.34496857265126 4520 3244.45454545455 3578 0.0236947054789706 1897 0.390325750892599 -0.386174237070782 -1 0.402676172241525 4517 1909 2204 2728 1897 4488 2732 3603 3708 4325 3578 4019 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 0.794202445310759 0.888641991099861 4380 3666.27272727273 3578 0.13386522912961 2485 0.233011727937214 -0.248460636567404 -1 0.0266653625312899 2485 4552 3578 4410 3008 2591 4376 3407 4378 4500 3044 4020 M5872 KEGG_STEROID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_BIOSYNTHESIS.html Steroid biosynthesis 5/21 KEGG 0.275742742869669 0.39623750171336 3605 3497.81818181818 3579 0.0317460317460317 1874 0.548913543759486 0.593142592187552 1 0.492558188783804 3603 3181 3787 3083 4627 4598 3579 2474 1874 3165 4505 4021 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 0.663427224845798 0.773723239329868 3580 3703.63636363636 3579 0.103174603174603 2990 0.2774055082045 -0.184386185447191 -1 0.068982002699736 3579 3490 3901 2990 4552 4374 3273 4069 3119 3392 4001 4022 M101 PID_HDAC_CLASSI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HDAC_CLASSI_PATHWAY.html Signaling events mediated by HDAC Class I 18832364 38/88 Pathway Interaction Database 0.820238404980819 0.909306166486898 3640 3476.81818181818 3582 0.144450436800964 1970 0.653874098340854 0.653874098340854 1 0.0602583364029542 3640 4051 3137 4140 3514 3762 1970 2691 3582 3380 4378 4023 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 0.652031355207377 0.764045744061457 4080 3459.36363636364 3582 0.0915064917736181 2110 0.351681116677631 -0.297026843144376 -1 0.0917426290563423 4080 2574 3006 2110 2760 3964 4036 3943 3483 3582 4515 4024 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 0.453032694922497 0.575470644729417 1070 3312.54545454545 3583 0.0533742670241919 1068 0.674350887224881 -0.674350887224881 -1 0.361189229470992 1068 4611 3746 4606 3583 1738 3390 2602 4301 4551 2242 4025 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 0.775485941583084 0.872282074473915 4050 3517.27272727273 3585 0.126984126984127 2212 1.39059940208002 1.39059940208002 1 0.184183818627197 3418 4050 3585 3638 3252 2851 4560 4048 3293 2212 3783 4026 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 0.466738071388703 0.587219019917277 4345 3556.81818181818 3585 0.0555555555555556 2566 0.361723232573386 -0.284738675250011 -1 0.18665669578912 4345 2636 2934 3585 3641 3187 4268 4538 2566 3977 3448 4027 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 0.765361970080957 0.862550791678538 2805 3421 3585 0.123476647314897 2067 0.363188457824668 -0.206789802546504 -1 0.0520535383133379 2801 3807 2116 3948 3036 3585 4433 2067 4225 4253 3360 4028 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 0.0349988561432972 0.0881745375739198 4590 3033.4 3586.5 0.00395061927851411 645 0.498677132836101 -0.467578951863978 -1 1.17384341895458 4586 645 4566 NA 924 3397 3776 1904 1839 4519 4178 4029 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 0.876192392002808 0.95130619761936 3495 3656.45454545455 3587 0.188525768482005 2665 0.134954777851543 -0.148499374923187 -1 0.0065301109087038 3491 4283 3897 4347 3228 2852 3587 3971 4517 3383 2665 4030 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 0.963562471059566 0.999999995401952 4610 3532.18181818182 3589 0.26 2094 0.610681132932434 0.610681132932434 1 2.61901336803259e-09 4607 2094 3402 2109 4476 3621 3124 4424 3929 3479 3589 4031 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 0.0238617334335581 0.0667160398983611 2325 2975.54545454545 3589 0.00241218958752983 540 0.375881758783165 0.343889409088572 1 0.986400046136177 2322 3707 4183 3724 3589 2466 1605 540 4072 3899 2624 4032 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 0.290566035716738 0.413104503449221 4430 3677.63636363636 3590 0.0337462383336112 2114 0.170179687891859 -0.180525770676808 -1 0.145831290024114 4430 3457 4080 3577 2114 4503 3194 3248 4531 3730 3590 4033 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 0.123529809534452 0.215912229570474 1150 2710.81818181818 3590 0.0130987137619705 943 0.896585420808603 0.896585420808603 1 1.33218528113403 1149 3680 4467 3590 3647 1959 943 966 4034 4376 1008 4034 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 0.891073518496821 0.961712793370162 2900 3516.27272727273 3591 0.182539682539683 2294 0.891470220575415 0.891470220575415 1 0.0337344871053339 2899 3689 3256 3582 4075 4106 2294 4083 3591 3078 4026 4035 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 0.961201780719665 0.999999995401952 2360 3552 3591 0.255764875263648 2360 0.240205870230613 -0.253061765827135 -1 9.67825165954399e-10 2360 3992 3591 4507 3446 2515 3625 3381 4444 4196 3015 4036 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 0.329266976412624 0.450231996343611 4590 3588.27272727273 3591 0.0356564280380164 2152 1.366823019083 1.50884151185319 1 1.05724305513488 4590 4543 2769 4293 2152 3251 3816 4479 3093 2894 3591 4037 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 0.0418049588314328 0.100615324645143 4060 2613.09090909091 3591 0.00387464952629349 205 1.92506082905628 2.02870228482674 1 4.28514428537797 4056 1737 1015 965 3911 3981 3591 4028 205 862 4393 4038 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 0.803551919136523 0.896747866890627 3795 3471.09090909091 3593 0.137518478571802 1737 0.235588520908488 -0.217473302315617 -1 0.0248866792462815 3791 3641 3469 3895 4603 1737 2898 2857 4319 3593 3379 4039 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 0.0356908102892423 0.089519108072176 4020 3158.72727272727 3594 0.0032984843340095 840 0.50491279453589 -0.50491279453589 -1 1.18111484152351 4016 1175 2243 1635 840 4679 4626 4283 3594 3428 4227 4040 M15434 REACTOME_DNA_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPAIR.html Genes involved in DNA Repair 66/127 Reactome 0.949859752553868 0.997544330001665 3660 3415.81818181818 3595 0.238210234149545 2102 0.699340386028758 -0.699340386028758 -1 0.00166669541574625 2102 4411 3656 4354 3595 2251 3331 3197 4308 3659 2710 4041 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 0.275742742869669 0.39623750171336 3600 2997.09090909091 3596 0.0317460317460317 1475 1.62371583222612 1.62371583222612 1 1.4570136565655 3596 1475 4034 1658 2268 4215 4382 3801 1846 1697 3996 4042 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 0.516017692820707 0.63549511394424 4320 3363.36363636364 3597 0.07 949 0.482982341650948 -0.321381215677201 -1 0.212241144396789 4319 949 3934 2054 2725 2785 4632 4645 3597 3469 3888 4043 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 0.516017692820707 0.63549511394424 4320 3364.72727272727 3598 0.07 950 0.482982341650948 -0.321381215677201 -1 0.212241144396789 4320 950 3937 2055 2726 2786 4633 4646 3598 3472 3889 4044 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 0.631943138674209 0.745034700521015 3600 3572.90909090909 3598 0.0868592590028572 2712 0.522536967759313 0.522536967759313 1 0.149075844235471 3635 3599 2935 3343 2712 3591 3325 4001 4270 3598 4293 4045 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 0.667434366415499 0.775117085755398 4105 3538.36363636364 3598 0.0952380952380952 2185 1.13256556794377 1.33235416971512 1 0.279657441884148 4102 4251 3317 3971 3598 2185 4235 4373 3098 3089 2703 4046 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 0.516017692820707 0.63549511394424 4325 3366.09090909091 3599 0.07 951 0.482982341650948 -0.321381215677201 -1 0.212241144396789 4321 951 3940 2056 2727 2787 4634 4647 3599 3475 3890 4047 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 0.509276811185465 0.632177784692738 3310 3296.45454545455 3599 0.0626662933083512 1644 0.931951048591966 -0.931951048591966 -1 0.414263291993447 3306 4562 2508 4194 4103 2233 3599 1644 4162 3796 2154 4048 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 0.0417934029372694 0.100615324645143 4425 3201.27272727273 3599 0.00387355741081241 913 1.26530448687738 1.26530448687738 1 2.81654076032285 4422 3971 3599 4127 913 2145 4040 4367 2568 2532 2530 4049 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 0.999610180498914 0.999999995401952 3640 3702.09090909091 3600 0.510132637386357 3085 0.249110788213525 -0.271412238950315 -1 1.0075139036224e-09 3520 3640 3085 3469 4374 3246 4101 3637 4479 3572 3600 4050 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 0.659196075169681 0.770907406051987 2680 3431.63636363636 3601 0.0932231646302842 1826 0.36128971268265 0.401213946633147 1 0.0911181868380788 2677 3601 1826 4254 4505 4026 2207 2837 4273 4506 3036 4051 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 0.286713748123331 0.408371010244963 3180 3293.45454545455 3602 0.0302487450167939 1693 0.266482948330786 -0.270688746169632 -1 0.231332834228391 3177 4004 2831 3737 2047 1693 4349 3883 4452 3602 2453 4052 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 0.816351931542927 0.906472278016503 4250 3418.09090909091 3602 0.142785182397203 1770 0.233333714612682 -0.254841479147643 -1 0.0222090501192002 3185 4513 3602 4237 4249 1770 2087 3401 4247 3876 2432 4053 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 0.994254297222932 0.999999995401952 3345 3793.45454545455 3603 0.374389652458018 2490 0.334392982885412 -0.195937444574594 -1 1.38761203126147e-09 3343 3603 2490 4422 4652 4281 3370 3461 4192 3503 4411 4054 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 0.415320710913563 0.535769969181582 3930 3370.81818181818 3603 0.0476190476190476 2308 1.23497519652913 1.23497519652913 1 0.747036372280437 3927 4012 2465 4034 3603 3842 2308 3454 2407 3079 3948 4055 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 0.694807562361729 0.800360923605472 2460 3362.72727272727 3605 0.111909188331208 2005 0.858982002181133 0.858982002181133 1 0.185418694132648 2459 4129 3825 3719 3992 3411 4197 2005 3605 3256 2392 4056 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 0.139751929577627 0.238571053552189 3910 3166.90909090909 3606 0.013591739214945 578 0.687391531885301 0.687391531885301 1 0.954862706590309 3125 3829 3636 3909 4639 578 3187 3237 3910 3606 1180 4057 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 0.628961507433683 0.742317303120099 2120 3175.36363636364 3608 0.0861892353581482 1396 0.182768856540761 -0.198420445793694 -1 0.0527899173724441 2116 4262 3735 4449 3608 1396 3251 2300 4149 3660 2003 4058 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 0.667434366415499 0.775117085755398 4535 3638.63636363636 3608 0.0952380952380952 3095 0.326430719895891 -0.265371264465646 -1 0.0806035275832966 4532 3337 3395 3800 4170 3608 3100 4088 3095 3718 3182 4059 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 0.964006867586055 0.999999995401952 2820 3643.18181818182 3609 0.260825050378241 2456 0.204728674185237 -0.17948724747875 -1 8.09705222599129e-10 2818 3644 3538 4378 4280 3055 2456 4506 4281 3510 3609 4060 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 0.15145370749808 0.254320272421057 4685 3452.45454545455 3609 0.0162889405052493 1690 1.20004986420299 1.28109121269671 1 1.59264008975371 4681 4609 4594 4480 1690 2187 3609 3815 2557 2827 2928 4061 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 0.902157871246138 0.969168222067722 3880 3534.72727272727 3610 0.19047619047619 2335 0.978904771416766 1.08042273281406 1 0.0297156715249183 3879 4205 2521 4558 3307 2335 4157 3205 3610 3050 4055 4062 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 0.885874722822563 0.958487405021133 3425 3770.2 3610 0.214285714285714 2543 0.157666197594205 -0.0755700763534843 -1 0.00647972538842746 3424 3082 4635 NA 4451 4262 2543 3526 3694 4614 3471 4063 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 0.000906401627346594 0.0054479548520373 4665 3073.18181818182 3610 8.24341164571934e-05 87 0.801505046067566 -0.801505046067566 -1 4.04964957524646 4663 1308 2115 1728 87 4631 3644 4655 2742 4622 3610 4064 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 0.838589656590537 0.921799467694876 3005 3329.90909090909 3611 0.152784758580469 1844 0.19757040207996 -0.219802310878034 -1 0.015593990102939 3004 4094 3713 4264 4029 1844 3158 2986 3689 3611 2237 4065 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 0.450913072542152 0.573555553184724 3800 3166 3611 0.053041363061416 1563 0.246378956887545 -0.325612259012506 -1 0.132759169529196 3796 3795 3611 4133 2838 1882 3280 1563 3818 3808 2302 4066 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 0.990351228665784 0.999999995401952 3240 3738.1 3613.5 0.402892610228345 3039 0.259425821662606 -0.455707081722148 -1 1.0534874496318e-09 3238 3330 4586 NA 3826 3039 3793 3434 4288 4548 3299 4067 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 0.9147653459064 0.977112015253566 3745 3581.72727272727 3614 0.218261285512697 2513 0.205336862204626 -0.250992634598991 -1 0.00460846671268015 3743 3614 4011 3782 3326 2513 3920 3587 4233 3609 3061 4068 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 0.251996603291625 0.368787034048893 4625 3330.3 3614.5 0.0317460317460317 753 0.851101291017547 -0.963468558268422 -1 0.822950416144168 4624 753 4632 NA 3213 2497 4016 2810 1837 4612 4309 4069 M14236 REACTOME_SIGNAL_ATTENUATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_ATTENUATION.html Genes involved in Signal attenuation 6/20 Reactome 0.663427224845798 0.773723239329868 3325 3558.18181818182 3615 0.103174603174603 2343 0.441514074146974 -0.328886960168017 -1 0.109790628415314 3321 3615 4076 4370 3465 2343 4139 4448 3107 3719 2537 4070 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 0.921309192177062 0.981194289668571 4380 3610 3615 0.206349206349206 2433 0.311224829827102 -0.323358067614858 -1 0.00572721926918288 4376 2433 3299 3704 3329 2676 4621 3615 3680 4441 3536 4071 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 0.0839184282471183 0.156982736433532 3810 2877.63636363636 3616 0.00793650793650794 165 2.76431492756404 2.76431492756404 1 4.96138713798758 3806 3733 2185 2099 3616 4491 3879 1662 165 1936 4082 4072 M18155 KEGG_INSULIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INSULIN_SIGNALING_PATHWAY.html Insulin signaling pathway 60/174 KEGG 0.391576420876007 0.513304214297342 3410 3418.81818181818 3619 0.0441662372608318 2051 0.273346889223842 -0.243125017372541 -1 0.176697332059417 3407 4257 3619 4244 2284 2051 3923 4398 3653 3220 2551 4073 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 0.739004502830274 0.83991634738362 3885 3422 3619 0.114952381721609 1872 0.19907810263979 -0.199847362972692 -1 0.0336640021966051 3885 4558 3640 4283 2920 1872 3330 2689 4516 3619 2330 4074 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 0.0329127551153126 0.0837746716297419 4010 3339.90909090909 3620 0.0030377915800029 981 1.07516182151552 1.0965159262945 1 2.58418517410266 4007 3620 981 2866 4194 3396 3798 4240 2781 2545 4311 4075 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 0.0488665088006016 0.113289156399471 3265 3477.90909090909 3622 0.00454426679537548 1042 1.05077947290469 1.05077947290469 1 2.21817495419471 3265 3750 1042 3369 4030 3446 4651 3622 4361 3083 3638 4076 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 0.943712354754118 0.993760920084898 3625 3579.72727272727 3622 0.23015873015873 2625 1.21455215107271 1.21455215107271 1 0.00736815766008182 3622 4425 2634 4346 3429 2757 3460 3630 3768 2625 4681 4077 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 0.614047863186712 0.728523284064363 4325 3602.63636363636 3622 0.0829096327933913 2438 1.29345980778089 1.45086476152059 1 0.397112730642425 4324 3859 2689 4295 2672 2438 4667 4518 3552 2993 3622 4078 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 0.190245220991837 0.299481844358952 3780 3030.3 3623 0.0231743438423769 754 1.0737736766931 -0.525845567846613 -1 1.25492107897824 3780 754 4349 NA 1889 4083 3466 1780 2298 4110 3794 4079 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 0.316176825710432 0.436922620253342 3625 3443.18181818182 3624 0.0339604827167134 2118 1.53334444632203 1.53334444632203 1 1.23064698464202 3624 4369 2896 4103 2118 3661 2917 2970 3679 2887 4651 4080 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 0.466738071388703 0.587219019917277 2810 3499.45454545455 3624 0.0555555555555556 1537 0.204911517594534 0.242453835723098 1 0.105738596094892 2806 4493 3624 4220 4653 3609 1537 3114 2472 4252 3714 4081 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 0.796944161638877 0.890221773883141 3715 3564.27272727273 3626 0.134920634920635 2518 0.724095453604658 0.724095453604658 1 0.0816172815162178 3715 2586 3626 2581 3370 4600 2518 4589 3349 3648 4625 4082 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 0.949776431494504 0.997544330001665 2250 3471.72727272727 3630 0.238095238095238 2249 1.01242236214617 1.01242236214617 1 0.00241284469718975 2249 3590 2837 4094 3630 4041 2568 4615 3801 2989 3775 4083 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 0.400208568811657 0.521807833458938 3950 3615.36363636364 3630 0.0454070883447294 1289 0.21741264651314 -0.196562656668261 -1 0.137077609344387 3946 3486 3566 3630 3510 4058 1289 4089 4144 3478 4573 4084 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 0.622527753435241 0.736843913260302 1920 3064.63636363636 3630 0.0847599791018738 1394 0.299094399892286 -0.330628843277906 -1 0.0885343074086715 1916 4068 3104 3910 4467 1394 1628 3710 3630 4093 1791 4085 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 0.0839184282471183 0.156982736433532 4225 3106.81818181818 3630 0.00793650793650794 168 0.955023857704091 0.955023857704091 1 1.71407499075146 4222 2601 3630 1888 1572 4582 2932 3879 168 4190 4511 4086 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 0.232850105696956 0.34496857265126 1800 3054.72727272727 3631 0.0238095238095238 1448 1.72317199106608 1.72317199106608 1 1.77769542497899 4382 1799 1448 1799 3631 4294 4368 4298 1603 2236 3744 4087 M832 REACTOME_ZINC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ZINC_TRANSPORTERS.html Genes involved in Zinc transporters 5/15 Reactome 0.190025111324371 0.299433703035486 3865 3181 3631 0.0208546732013884 1695 0.415149358523271 0.465019553982209 1 0.485250436622636 3864 3816 4027 3592 1830 3150 1695 1841 3659 3631 3886 4088 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 0.597318307603006 0.711317303539438 4350 3461.90909090909 3631 0.0793650793650794 1923 0.442525780645566 0.192763560126773 1 0.146114676967965 4347 3937 1923 3631 4293 2970 4630 2334 2841 4001 3174 4089 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 0.988743594644416 0.999999995401952 3025 3661.63636363636 3631 0.361530769360357 2855 0.315916717791899 -0.333959139928835 -1 1.3052643173591e-09 3021 3079 4570 3788 4024 2855 3631 3067 4491 4524 3228 4090 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 0.999195775457736 0.999999995401952 3440 3754.63636363636 3632 0.476796469773315 3142 0.228792985214527 -0.234110115727084 -1 9.16958554907811e-10 3437 4148 3280 3804 4348 3142 3998 3517 4488 3632 3507 4091 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 0.698152987361708 0.80243926877041 4320 3553.45454545455 3634 0.103174603174603 2518 0.264619586950582 0.281212863888283 1 0.0564552230721258 4318 2550 3450 2518 3634 4424 3230 3900 3131 3653 4280 4092 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 0.273249024668811 0.394590116979368 4680 3326.36363636364 3635 0.0285986716293424 1439 1.72317199106608 1.72317199106608 1 1.55321777281626 4676 3374 1439 2551 3711 4104 3859 3834 2851 2556 3635 4093 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 0.749038168034588 0.848439172204515 3640 3659.27272727273 3636 0.118100940131198 2910 1.09578116527076 1.20827046216093 1 0.174572407016973 3636 4166 2910 4040 2936 3514 3716 4266 3615 3094 4359 4094 M1979 KEGG_GNRH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GNRH_SIGNALING_PATHWAY.html GnRH signaling pathway 44/116 KEGG 0.873972706880523 0.94977646206914 3785 3563.18181818182 3637 0.171630585421387 2338 1.21455215107271 1.21455215107271 1 0.0606636570723694 3782 4086 2962 3637 3384 4465 3293 2338 3903 2890 4455 4095 M16563 BIOCARTA_MTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MTOR_PATHWAY.html mTOR Signaling Pathway 18/32 BioCarta 0.969222668099115 0.999999995401952 3290 3701.90909090909 3639 0.271270330696537 2499 0.215861721632944 -0.195007583508983 -1 8.59324612743475e-10 3286 4152 3639 4600 3620 3905 2499 2978 4277 3290 4475 4096 M4217 REACTOME_MITOTIC_PROMETAPHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_PROMETAPHASE.html Genes involved in Mitotic Prometaphase 57/108 Reactome 0.847469372415931 0.929815377930474 1660 3405.54545454545 3639 0.1571316767145 1658 0.263584270054242 -0.291177361507918 -1 0.0185922152058736 1658 4591 2644 4413 3857 2397 3639 3119 4514 3743 2886 4097 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 0.145631054752032 0.247358336478991 4485 3398.72727272727 3641 0.0142064996690629 1268 1.70932184675759 1.70932184675759 1 2.31450640074626 4484 4511 1268 4097 2618 3450 3764 2782 3956 2815 3641 4098 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 0.52340095663996 0.642393107075655 4260 3371.63636363636 3642 0.0714285714285714 1716 1.43991841944783 1.43991841944783 1 0.617687559004602 4259 2954 4559 3090 3642 4097 4121 1800 2740 1716 4110 4099 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 0.564368709191277 0.682133549463586 3645 3629.36363636364 3643 0.0727589662916764 2602 0.195582941323128 -0.214444261358697 -1 0.0725203905994482 3643 4431 3648 4615 2602 2913 3119 4156 4453 3207 3136 4100 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 0.884136482961328 0.957198188121408 3925 3591.63636363636 3644 0.177938619316136 2671 0.307227099494058 -0.267376434588485 -1 0.0130271668605472 3925 3453 3037 3401 3196 4024 2671 3644 3881 3672 4604 4101 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 0.000872199663854825 0.00527371306428866 4275 3201.63636363636 3644 7.93223312081059e-05 84 0.388552878669791 -0.398482938689209 -1 1.97542795321398 4271 2447 2491 2041 84 3644 3454 4355 3992 4031 4408 4102 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 0.562604368603265 0.680703349154377 4650 3712.72727272727 3645 0.0793650793650794 2787 1.28574791132464 1.33570377984002 1 0.479359519145625 2949 4104 4649 3645 2787 4045 3553 4648 2933 2869 4658 4103 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 0.420570179056654 0.541575119279879 4615 3709.90909090909 3646 0.0483995865056319 2344 0.653874098340854 0.653874098340854 1 0.388697902743243 4613 4355 3563 4569 2344 3132 3965 2928 3387 4307 3646 4104 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 0.838494417110154 0.921799467694876 2915 3814.72727272727 3646 0.166666666666667 2915 0.362532246993863 0.410259268820635 1 0.0286142267720948 2915 3424 4660 3646 3887 4551 3604 3391 3488 4639 3757 4105 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 0.711850032937866 0.815581724779178 2135 3180.45454545455 3648 0.106952794467564 1756 1.0264160158726 1.12087939885344 1 0.202817662278703 2134 4047 2318 3916 2916 4244 1756 4013 3730 2263 3648 4106 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 0.00304653138653934 0.0142191693997244 4065 2387.27272727273 3649 0.000305071607209267 131 1.04004576141948 1.04736760635646 1 4.28774027828793 4065 372 3941 671 192 4194 3649 4463 131 608 3974 4107 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 0.962119338030589 0.999999995401952 3390 3578.18181818182 3650 0.279155223126205 2611 0.302068992797062 -0.209994564893807 -1 1.2435457562591e-09 3387 3546 3916 4369 3650 2611 3938 3833 3995 3431 2684 4108 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 0.912207156538424 0.97526870534772 3650 3659.54545454545 3650 0.198412698412698 2165 0.262078049128176 -0.250906886933861 -1 0.0063616220792324 3737 3543 3647 4318 3394 2165 4593 3733 3650 4358 3117 4109 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 0.481063017846562 0.600976086811248 3790 3492.63636363636 3651 0.0634920634920635 2303 0.529429040108502 -0.281959428788791 -1 0.26131246982247 3788 2303 3900 2718 4336 4671 3651 3142 2582 3390 3938 4110 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 0.601313038178008 0.715165709873641 3720 3632 3651 0.0878564251050603 2390 1.0855675271585 1.25009110723774 1 0.352758785263493 3718 4446 4633 4523 2718 2390 4088 3641 3651 3150 2994 4111 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 0.102047560156696 0.184903812467144 3365 3239.63636363636 3651 0.0107060948473562 725 0.301427040779075 -0.220963455235967 -1 0.493171319235188 3361 2957 4675 3937 3846 2670 725 1185 3970 4659 3651 4112 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 0.90309825964203 0.969733832420384 2925 3573.3 3651.5 0.228439163565175 2329 0.488097034187669 0.488097034187669 1 0.0145406592789237 2924 3856 4138 NA 3935 3218 2329 3465 4565 3833 3470 4113 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 0.0144790369416076 0.0453534539494474 3945 3323 3652 0.00132501966891571 855 1.27178585866397 -1.27166129041429 -1 3.8132522823219 3943 4450 855 3652 2483 4480 3894 3613 3383 1834 3966 4114 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 0.298735036746822 0.4173739958842 4550 3255.54545454545 3652 0.0317460317460317 1169 0.531357981456853 -0.531357981456853 -1 0.450038314528226 4546 1169 3283 2341 4004 2684 3908 4037 2065 4122 3652 4115 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 0.912207156538424 0.97526870534772 2825 3435.81818181818 3654 0.198412698412698 2245 0.871218161253435 -0.650112755713168 -1 0.0211477488156299 2822 4013 2655 4399 4066 2245 2991 4150 3654 3100 3699 4116 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 0.778919549511355 0.875513794437566 4095 3644 3655 0.128206418278163 2386 0.324824623344577 -0.246706401340065 -1 0.0418584134238368 4092 4000 2386 3461 2984 3655 4641 4183 3576 3442 3664 4117 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 0.320044496819455 0.440448902230827 1890 3294.09090909091 3655 0.0344584800796822 1164 0.693810091349027 0.693810091349027 1 0.551439142051913 1887 4626 3778 4305 3644 2217 1164 3655 4576 3723 2660 4118 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 0.0839184282471183 0.156982736433532 4525 2892.27272727273 3655 0.00793650793650794 191 0.852246096011289 0.852246096011289 1 1.5296096608935 4522 370 3021 697 3655 2805 3875 4252 191 3806 4621 4119 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 0.314306427292237 0.4346945606709 3735 3346.81818181818 3655 0.0337205700521769 1830 0.610681132932434 0.610681132932434 1 0.493152884998935 3731 2428 3297 3655 2113 3327 1830 4223 3821 3908 4482 4120 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 0.912207156538424 0.97526870534772 4585 3729.18181818182 3655 0.198412698412698 3102 0.998026665218183 -0.881800518798107 -1 0.0242258692243055 4582 4502 3757 4106 3284 3102 3907 3469 3655 3149 3508 4121 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 0.557443745451391 0.675680649556446 4310 3594.18181818182 3660 0.0714285714285714 2384 1.29644110978073 1.29644110978073 1 0.492653075601383 4306 3512 2928 2828 4446 3660 4596 4188 2764 2384 3924 4122 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 0.544255037599953 0.66398831194829 3095 3453.72727272727 3661 0.0755739235185873 2599 0.210699746358518 -0.260737589397384 -1 0.0836318984204174 3095 3949 4153 3661 2624 2694 3737 3356 4274 3849 2599 4123 M14314 KEGG_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PURINE_METABOLISM.html Purine metabolism 77/171 KEGG 0.0999147202001719 0.181684275847111 4070 3357 3662 0.00952397192911832 1370 1.14386582177135 1.18192501111007 1 1.89097947340097 4068 3535 3138 3662 1370 3672 4437 3749 2717 2374 4205 4124 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 0.543292558953224 0.662986700847606 2755 3352.09090909091 3662 0.0687677497672284 1850 0.225272173018215 -0.269814015998778 -1 0.0897456905336578 2752 4627 3662 4596 2574 1850 4414 2657 3742 4065 1934 4125 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 0.33296556889208 0.453871800574534 4570 3113.63636363636 3662 0.0396825396825397 742 0.461937822341295 -0.356923208912428 -1 0.353705463528596 4566 742 4342 1946 3482 1629 3662 3933 2100 4099 3749 4126 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 0.867162992659326 0.944347149338044 3410 3535.63636363636 3663 0.167658143526048 1928 0.523746058863399 -0.523746058863399 -1 0.0290701236343031 3408 4176 3319 3972 3892 1928 4039 3663 4414 3656 2425 4127 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 0.496118254062533 0.617151616282726 4495 3097.27272727273 3663 0.0662451672865221 1107 0.526664091701105 -0.822708096576692 -1 0.246389039985777 4494 1107 4045 1800 4169 3916 1465 2640 2953 3663 3818 4128 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 0.102017799379192 0.184903812467144 3805 3146.72727272727 3663 0.00973458481401709 1211 1.24757627948785 1.27943610807732 1 2.04118661055935 3802 4201 3670 4230 1379 1211 3663 4093 2799 2655 2911 4129 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 0.00743009702508262 0.0278094526034642 3665 3401.63636363636 3664 0.000677755464660425 781 1.04458815474116 1.07200953091195 1 3.62727538603663 3664 4358 781 4287 4106 2123 4459 4124 3592 3068 2856 4130 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 0.161244734371544 0.262241686633255 3635 3517 3664 0.0158580353742548 1677 0.758499848375418 -0.792904243146179 -1 0.984088334912159 3779 3664 1848 3142 1677 4629 3632 3713 3633 4378 4592 4131 M745 REACTOME_MRNA_CAPPING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_CAPPING.html Genes involved in mRNA Capping 13/31 Reactome 0.991130964772011 0.999999995401952 4270 3812.63636363636 3665 0.349206349206349 3021 0.176836197504304 -0.208004617182553 -1 6.85389963095919e-10 4268 4062 3665 4202 4547 3021 3622 3511 4059 3546 3436 4132 M899 REACTOME_IL1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL1_SIGNALING.html Genes involved in Interleukin-1 signaling 25/45 Reactome 0.35943518917414 0.478362197236587 3385 3458.45454545455 3665 0.0396825396825397 2194 1.7354036805309 1.7354036805309 1 1.24039473755779 3385 3665 3398 3781 4107 4233 2547 4174 2194 2557 4002 4133 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 0.865412014258462 0.942878562849373 3500 3724.36363636364 3665 0.166666666666667 2339 0.94175740835774 0.94175740835774 1 0.0536922439360836 3498 3796 3158 3665 4563 4129 2339 3656 3503 4170 4491 4134 M1017 REACTOME_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPLICATION.html Genes involved in DNA Replication 119/224 Reactome 0.97272795985555 0.999999995401952 2195 3605.90909090909 3666 0.279236954637526 2195 1.39059940208002 1.39059940208002 1 6.09506689778802e-09 2195 4581 3371 4302 3960 2864 3988 3666 4264 3058 3416 4135 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 0.00333796394394968 0.0151511219510848 3670 3372.18181818182 3666 0.000303912661362442 702 1.16186250822327 -1.16186250822327 -1 4.71845186891866 2410 3888 702 3315 4186 3666 4072 3670 4498 3062 3625 4136 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 0.690835384304405 0.797777208383085 3670 3471.09090909091 3668 0.101219551275794 2465 1.14672566625037 1.14672566625037 1 0.251124702530209 3668 4452 3375 4160 2827 2465 3741 4134 3716 2768 2876 4137 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 0.191605624748562 0.300993616349904 4305 3467.36363636364 3668 0.0191510835694255 1787 0.257431332032482 -0.259358904006533 -1 0.299603969343705 4303 3208 3532 3668 1787 2394 3876 3966 3867 4447 3093 4138 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 0.751985672431077 0.848905049629493 4445 3427 3669 0.119047619047619 2224 1.38933387508025 1.38933387508025 1 0.220599960875992 4442 3669 2224 2296 4323 3696 4475 2792 3230 2292 4258 4139 M19829 BIOCARTA_AGPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGPCR_PATHWAY.html Attenuation of GPCR Signaling 9/21 BioCarta 0.8904762546915 0.961712793370162 4635 3724 3671 0.198412698412698 2993 0.332342657012385 -0.207251436899518 -1 0.0125763135563233 4632 2993 3816 3671 3343 3952 3624 4261 3628 3243 3801 4140 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 0.964710728006694 0.999999995401952 4105 3418.36363636364 3671 0.262150957391371 2371 0.324254399549421 -0.283481113127933 -1 1.34242491385966e-09 4103 3799 2746 3853 3671 2371 2781 3625 4012 3711 2930 4141 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 0.000246993695879444 0.00198527008386119 4660 3434.27272727273 3672 2.24564936533502e-05 481 1.27733479785135 1.27733479785135 1 7.70368716000147 4659 4048 481 3672 3573 3633 4153 3508 3704 2405 3941 4142 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 0.804956120936968 0.897460000644927 3840 3756.27272727273 3672 0.150793650793651 2427 0.322183639686553 0.334318411679242 1 0.0337863542105948 3840 3647 4576 3606 3901 4461 3238 2427 3421 4530 3672 4143 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 0.394478066955808 0.516203357094364 3265 3388.36363636364 3673 0.0445815462991664 1606 0.610681132932434 0.610681132932434 1 0.391423594966097 3264 4486 3556 4357 2293 1606 3749 3673 4255 3798 2235 4144 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 0.962541620667541 0.999999995401952 2895 3503.18181818182 3673 0.258138839012951 2360 0.243450224207629 -0.268304733662326 -1 9.82285076101021e-10 2893 4516 3152 3867 3687 2360 3673 2769 4589 4271 2758 4145 M14091 KEGG_OLFACTORY_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OLFACTORY_TRANSDUCTION.html Olfactory transduction 35/833 KEGG 0.875687893375033 0.950978787567881 3150 3576.09090909091 3675 0.172661873086064 2342 0.73612050976123 -0.650112755713168 -1 0.0358645759541658 3146 4052 3236 3675 3827 4365 3012 2342 4142 3219 4321 4146 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 0.667434366415499 0.775117085755398 3730 3475.36363636364 3676 0.0952380952380952 1992 1.29644110978073 1.29644110978073 1 0.320122220376 3728 3731 2599 3832 3428 3676 4318 4437 3048 1992 3440 4147 M2920 KEGG_LINOLEIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LINOLEIC_ACID_METABOLISM.html Linoleic acid metabolism 4/62 KEGG 0.796644820540539 0.890221773883141 2760 3564.27272727273 3680 0.147242546886021 2216 0.322890518284786 -0.086986725441967 -1 0.0363949893033408 2758 4474 3794 4374 3680 3256 4035 2216 4214 3179 3227 4148 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 0.514011397665828 0.633523779448203 3690 3452.36363636364 3681 0.0634920634920635 2021 1.39059940208002 1.39059940208002 1 0.61527105297616 3689 4297 3553 3736 2891 2615 4639 4151 2703 2021 3681 4149 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 0.124931700622956 0.217788597952299 3880 3456 3681 0.0132566797665224 1578 0.237235314590666 -0.328443365257143 -1 0.350504686434368 3877 4006 4055 3301 1578 2908 3415 4180 3946 3681 3069 4150 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 0.343389030106653 0.465198321792361 2950 3599.81818181818 3683 0.0411938447448093 1243 0.345403837743631 0.442271032703359 1 0.256222871952368 2948 3683 4606 4118 3323 3639 1243 4086 4016 4573 3363 4151 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 0.816521443770307 0.906472278016503 4265 3672 3684 0.142857142857143 1804 1.04245820145563 -0.641507698556005 -1 0.0992227229780119 4263 4504 3684 4470 4600 1804 4120 3516 3390 3085 2956 4152 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 0.952274404737792 0.999059787558938 2810 3489.81818181818 3685 0.241620671512502 2380 0.284705716534134 -0.332323887921132 -1 0.000259591291753415 2810 4327 2956 3685 3916 2380 4552 2628 4260 4072 2802 4153 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 0.903480638057396 0.969922169515913 3990 3682.36363636364 3686 0.191477291801428 2161 0.310355130003349 0.335406473188957 1 0.00918721705449396 3988 3674 2966 3572 4620 3961 2161 3686 3812 3384 4682 4154 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 0.921309192177062 0.981194289668571 3520 3762.90909090909 3686 0.206349206349206 3073 0.978702497151459 -0.978702497151459 -1 0.0180102720987486 3516 4014 3356 3966 4380 3649 3156 4251 3686 3073 4345 4155 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 0.63456456852902 0.745629279871361 2040 3163.63636363636 3686 0.0874524280362362 1799 0.349740117185609 0.407528157932719 1 0.0995077707839229 2037 3806 1799 3830 3686 2625 1916 4166 4484 4408 2043 4156 M984 BIOCARTA_TOLL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TOLL_PATHWAY.html Toll-Like Receptor Pathway 37/78 BioCarta 0.557443745451391 0.675680649556446 4140 3639.09090909091 3687 0.0714285714285714 2794 0.975157604060794 0.975157604060794 1 0.370563991822863 4138 3832 3610 3219 4420 4166 3687 3169 2794 2816 4179 4157 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 0.392859293123783 0.51437235193575 4080 3322 3687 0.0443496306389509 2288 1.12773021404976 1.12773021404976 1 0.7267168411052 2295 3751 2825 4263 2288 4079 2301 4079 3687 3059 3915 4158 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 0.747273770518605 0.846850033530878 4040 3331.72727272727 3688 0.117539076325829 1611 0.229437605348545 -0.227856748149378 -1 0.0369693825788079 2375 4208 3743 4037 3114 1611 3547 3820 4037 3688 2469 4159 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 0.743918127093577 0.843863554480877 2420 3574.09090909091 3689 0.116480258385249 1908 0.262798993782237 -0.261047448498544 -1 0.0432448451607778 2420 4146 1908 3689 4126 3263 4000 3455 4557 4265 3486 4160 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 0.929210832462149 0.986602125278769 3160 3525.27272727273 3690 0.21394754623929 2139 0.15571334821285 -0.163385143387731 -1 0.00203587581954978 3160 4022 3715 4282 3690 2139 4004 2876 4550 3575 2765 4161 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 0.0469359938652921 0.110026046649704 2190 3392.18181818182 3690 0.0043607564236484 1036 1.90919498657043 1.90919498657043 1 4.0843597923841 2188 4292 1036 3690 4092 3237 3825 3858 4389 3095 3612 4162 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 0.871073509305853 0.947724742188815 3755 3590.18181818182 3691 0.16991605381941 2601 0.197682093371016 -0.219159596792938 -1 0.0102880745663908 3751 4331 3669 4487 3166 2644 3836 3702 3691 3614 2601 4163 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 0.661195777455086 0.772081588127219 3695 3501.27272727273 3691 0.0937081510532534 1831 0.857185672850884 0.857185672850884 1 0.214919846781737 3691 2984 1831 2999 3251 4113 3831 3628 3749 3842 4595 4164 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 0.936989803160346 0.989507236660202 3695 3797.36363636364 3692 0.222222222222222 2962 0.274700077496894 0.256022804235359 1 0.00280867189772778 3692 3352 3410 2962 4229 4458 4331 3529 3733 3621 4454 4165 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 0.0371613215642233 0.0923808768434749 4175 3419.72727272727 3692 0.00343675361593365 1000 2.76431492756404 2.76431492756404 1 6.38209271709632 4172 3808 1000 2979 3692 3910 3672 4490 3160 2122 4612 4166 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 0.755534517163407 0.85229531714678 3550 3736.72727272727 3692 0.120201102451338 2951 0.525602276263726 -0.525602276263726 -1 0.0814250804083159 3546 3567 3271 3698 2951 2963 3692 4278 4036 4613 4489 4167 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 0.890758762530111 0.961712793370162 3695 3658.45454545455 3693 0.182325223313785 2326 0.254134988561277 -0.247103949762861 -1 0.00961682536474268 3693 4413 3417 4475 3208 2326 3731 3457 4375 4105 3043 4168 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 0.838494417110154 0.921799467694876 4465 3594.63636363636 3693 0.166666666666667 1857 0.792904243146179 -0.792904243146179 -1 0.0625829620793701 4462 3221 4546 1857 3321 4320 2385 3777 3478 4481 3693 4169 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 0.694779557867937 0.800360923605472 4125 3427.54545454545 3694 0.1022680280849 2270 0.347010157468714 -0.332253057105737 -1 0.0749051435683468 4123 2270 2583 2872 2832 4211 3847 3694 3837 4111 3323 4170 M18937 KEGG_NUCLEOTIDE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NUCLEOTIDE_EXCISION_REPAIR.html Nucleotide excision repair 30/47 KEGG 0.957188941990313 0.999999995401952 3105 3611.63636363636 3695 0.249075979991363 2314 0.18351417320962 -0.209160015166288 -1 7.15153339516701e-10 3101 4514 3695 4455 3798 2314 3598 3868 4325 3201 2859 4171 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 0.704041650910282 0.808216358688285 2790 3424.27272727273 3695 0.10477942686845 1759 0.243833794351201 -0.321611830704637 -1 0.050325188290515 2789 4634 2989 4506 3695 1759 3904 2610 4431 4516 1834 4172 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 0.949776431494504 0.997544330001665 4525 3807.27272727273 3700 0.238095238095238 3319 0.194678181390124 -0.22705591052514 -1 0.000463964597343598 4525 3700 3680 3615 4313 3319 4127 3400 3798 3729 3674 4173 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 0.817384088451729 0.907010091045671 2915 3483.36363636364 3701 0.156366413255349 2264 0.359284045053362 0.505615757280959 1 0.0339906283249344 2912 3551 4325 3701 3863 3841 2890 2264 4019 4084 2867 4174 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 0.186793248027163 0.29491683297011 3010 3550.18181818182 3701 0.0186216963466723 1329 1.16186250822327 -1.16186250822327 -1 1.37516964947 3009 3271 1329 3043 4350 4624 3701 4137 4113 2937 4538 4175 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 0.240390831218397 0.354013650248085 2820 3454.09090909091 3703 0.0246857637551393 1390 1.05738358203104 1.05738358203104 1 1.0643130615576 2817 4204 1390 3753 3895 3015 4472 3703 4332 2968 3446 4176 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 0.954765347077066 0.99961092867638 3415 3648.18181818182 3705 0.26625166927131 2637 0.160169165720581 -0.193220170566225 -1 6.04165278556723e-05 3413 4601 4069 4343 3991 2848 3043 3033 4447 3705 2637 4177 M8232 KEGG_LONG_TERM_DEPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_DEPRESSION.html Long-term depression 17/94 KEGG 0.894891364205019 0.963792446027285 4230 3560.63636363636 3706 0.185186836884017 2400 0.27058441395532 0.284622533668214 1 0.00967273867690698 2866 4228 3043 4228 3793 4117 3168 2400 4400 3218 3706 4178 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 0.943712354754118 0.993760920084898 3340 3597.63636363636 3707 0.23015873015873 3028 0.306931698029991 -0.252612224645628 -1 0.0018620205371154 3339 3317 3028 3711 3997 3707 4185 3208 3775 3378 3929 4179 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 0.912207156538424 0.97526870534772 4685 3731.09090909091 3707 0.198412698412698 2314 0.321434135339926 -0.263728840155637 -1 0.00780241804034782 4685 4519 2854 4315 4134 2977 2314 3707 3643 4676 3218 4180 M7239 BIOCARTA_DNAFRAGMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DNAFRAGMENT_PATHWAY.html Apoptotic DNA fragmentation and tissue homeostasis 7/18 BioCarta 0.715254186816829 0.818681270010664 4550 3684.90909090909 3708 0.118046405252633 2857 0.353396210451781 -0.42428651158356 -1 0.0685309850634413 4550 3708 3815 3612 2935 3971 2857 2942 4407 3242 4495 4181 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 0.923812829511494 0.983190306402648 4285 3789.81818181818 3708 0.208678628620577 2514 0.162660533946613 -0.164800451138688 -1 0.00267289467437916 4285 4672 3113 4620 3557 3241 3239 2514 4604 3708 4135 4182 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 0.315075439460682 0.435529058794323 4415 3305.36363636364 3710 0.0338191377646251 887 0.862559895960135 -0.862559895960135 -1 0.694952948927925 3597 4319 2374 4411 3722 887 3404 4414 3710 3836 1685 4183 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 0.331876964806894 0.453271774143138 4670 3646.63636363636 3713 0.0359981692656019 2156 1.20766374081474 1.2745565488468 1 0.92625585386763 4666 4401 3646 4167 2156 2780 4196 4305 3019 3064 3713 4184 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 2.99026143300443e-07 7.53352961024664e-06 3165 3299.63636363636 3720 2.71841985403977e-08 181 1.1321379982938 1.1321379982938 1 12.9450402395349 3163 3957 181 3640 2201 4093 3720 3983 4164 2830 4364 4185 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 0.0272968343522446 0.0733191807951693 3720 3555 3720 0.00251286605445228 954 0.506871665096219 -0.480334792309214 -1 1.2837786794878 3720 2507 954 3478 3458 4513 4147 3903 3231 4666 4528 4186 M139 PID_MYC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_PATHWAY.html C-MYC pathway 18832364 14/39 Pathway Interaction Database 0.926696972586041 0.985093909948563 3725 3651.09090909091 3721 0.211449948078786 2125 0.262683032263178 -0.267277691547653 -1 0.00382398973041894 3721 4383 3329 4492 3451 2125 4007 3811 4520 3387 2936 4187 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 0.35943518917414 0.478362197236587 4330 3446.36363636364 3721 0.0396825396825397 2155 1.29644110978073 1.29644110978073 1 0.926642456807828 4326 3278 2480 4022 4033 3336 4005 4057 2155 2497 3721 4188 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 0.386086746459241 0.507632574048261 3140 3180.45454545455 3722 0.0476190476190476 1283 0.744241777517181 -0.621226037364227 -1 0.48910930147213 3139 1701 4292 1283 4611 3722 1486 4632 2301 4048 3770 4189 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 0.99951171875 0.999999995401952 3845 3656.09090909091 3723 0.5 2762 0.301138230175399 -0.332967274753923 -1 1.2393973976113e-09 3844 2978 2762 3400 4128 3286 4230 3681 4371 3814 3723 4190 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 0.923772620365396 0.983190306402648 4150 3746.90909090909 3724 0.208640670993637 3243 0.258516027769468 -0.273218492418198 -1 0.00424802567009591 4148 4001 3409 3360 3290 3724 4540 3243 3954 3307 4240 4191 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 0.90020157410859 0.968621027846809 3245 3678.09090909091 3724 0.205832026705835 2234 0.208377888765257 -0.191557163896951 -1 0.00643959963036344 3244 4102 3933 4208 3724 3139 2234 4291 4434 3467 3683 4192 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 0.97530599069028 0.999999995401952 4280 3690.90909090909 3724 0.285714285714286 2664 0.288110663897239 -0.271287031252825 -1 1.18133423953858e-09 4277 2664 3423 3702 4084 3166 4465 3383 3908 3724 3804 4193 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 0.321751419053176 0.442278424665058 4015 3474.54545454545 3725 0.0380801443934904 1961 0.711100515280854 -0.621834831913594 -1 0.562324369413807 4015 1961 4500 2553 2189 4311 3725 3029 3444 4415 4078 4194 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 0.397204278978796 0.518901380344198 3750 3552.54545454545 3726 0.0449733974311654 2248 0.276357305511364 0.290076060585562 1 0.175738163505831 3750 2248 3339 3295 2304 4508 3861 3726 3896 3692 4459 4195 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 0.977234824456997 0.999999995401952 3730 3399.54545454545 3727 0.290975895020055 1768 1.21455215107271 1.21455215107271 1 5.31043382471417e-09 3727 2608 2338 2940 4089 4296 3130 4197 4070 1768 4232 4196 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 0.21609611559472 0.329684529168306 2085 3394.36363636364 3727 0.0218903835426408 1359 1.05077947290469 1.05077947290469 1 1.13018451303826 2085 3727 1359 3311 4303 4076 3109 4509 4566 2433 3860 4197 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 0.926862793205979 0.985093909948563 3085 3507.72727272727 3728 0.211612278596902 2126 0.955023857704091 0.955023857704091 1 0.0139026927770925 3081 4412 3763 4355 3822 2126 3728 3087 3873 3537 2801 4198 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 0.888829124559905 0.960951723395044 3195 3541.63636363636 3728 0.181022611277244 2100 0.367158811195753 -0.358591259014627 -1 0.0141755590464524 3195 2975 2100 3508 4397 4449 2587 3728 3764 3785 4470 4199 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 0.857741086655343 0.937791584709971 2885 3512 3730 0.177174109054285 1976 0.175054522999248 -0.214935731085278 -1 0.0108982941576673 2882 4133 4545 3730 3617 1976 2934 3884 4104 4480 2347 4200 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 0.311759600088712 0.431709658988093 3295 3620 3731 0.0366723713332751 2166 0.177287596765626 0.178614786263796 1 0.144351911767391 3292 4131 4081 4060 2166 3190 3738 3498 4335 3731 3598 4201 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 0.737078244663006 0.838133621570212 3610 3705.45454545455 3733 0.125051174895132 2077 0.267117755746812 0.259079991313566 1 0.0457196157824665 3608 4342 3849 4152 3554 3733 3504 2077 4558 3292 4091 4202 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 0.642204767037117 0.753850585755494 2735 3536.81818181818 3734 0.089203563578134 1876 0.357913771806185 -0.294501319635729 -1 0.0980290144653085 3543 3734 2735 4309 2735 4077 1876 4077 3613 3886 4320 4203 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 0.936989803160346 0.989507236660202 2835 3538.36363636364 3734 0.222222222222222 2443 0.329741631678131 0.2943983218776 1 0.00337144448046899 2835 4020 2604 4532 3406 4604 2443 3766 3734 4101 2877 4204 M2164 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION.html Leukocyte transendothelial migration 64/141 KEGG 0.00125714952011322 0.00698814074881443 3855 2893.36363636364 3735 0.000114351679118544 624 1.64774574603087 1.43494882865823 1 7.92767169165542 3852 1564 624 1300 4163 3735 4094 4112 2033 2027 4323 4205 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 0.0508319732671811 0.116643671146604 3740 2932.09090909091 3736 0.00473144758043951 1015 1.46415804325365 1.28067143083456 1 3.04939560128989 3736 4203 1532 4232 1015 1344 4240 3973 2262 1649 4067 4206 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 0.26987693142682 0.39068375059193 3875 3420.27272727273 3737 0.0281897823393714 1994 0.768915333877956 -0.680644994905029 -1 0.700493495951967 3874 3406 2731 2698 1994 3737 2869 4020 3885 3896 4513 4207 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 0.952800902066922 0.999289397288629 3010 3622.90909090909 3738 0.242385081328051 2272 0.208497559627921 -0.216393613312825 -1 0.000143663268486048 3006 4363 3738 4510 4008 2272 4169 2882 4217 3732 2955 4208 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 0.84342973867464 0.92625070434248 3215 3613 3738.5 0.186189567457045 2130 0.11011300912291 0.11011300912291 1 0.00817692270338977 3212 4246 4116 NA 4039 3138 2130 3682 4476 3795 3296 4209 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 0.307539909213428 0.426875596734041 4080 3606.09090909091 3739 0.0328575815681689 2092 0.264214656773166 -0.284617758447638 -1 0.218013983565992 4076 4184 3446 3528 2092 3789 3922 4660 3739 3363 2868 4210 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 0.937081454779076 0.989507236660202 4540 3851.90909090909 3739 0.222325137406981 2884 0.176364692078723 -0.186353208145962 -1 0.00180324137074056 4536 4616 3783 4524 3342 2884 3619 3739 4311 3635 3382 4211 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 0.147859119791321 0.249412467725749 3745 3223.90909090909 3740 0.0158730158730159 1267 0.653874098340854 0.653874098340854 1 0.880136314670596 3742 1659 4211 1959 3740 2750 3355 4652 1267 3933 4195 4212 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 0.0107811923705302 0.036742303598767 3445 3233.63636363636 3741 0.000984944672900237 395 1.08196515182584 1.08196515182584 1 3.46492925311682 3443 3749 2175 3855 395 2762 3943 3890 3741 3069 4548 4213 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 0.921309192177062 0.981194289668571 4095 3675.45454545455 3742 0.206349206349206 2560 0.680644994905029 -0.680644994905029 -1 0.0125253604296931 4095 4260 3742 4233 3632 3076 3956 2560 3688 4425 2763 4214 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 0.917370055074399 0.979224619152308 3765 3753.72727272727 3743 0.202817142348563 3017 0.276711851192909 -0.252702794390868 -1 0.00563107710571074 3762 4270 3266 3960 3275 3017 3743 3965 3732 3664 4637 4215 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 0.513826273089878 0.633523779448203 4475 3370.18181818182 3743 0.0634596383726203 1646 0.94976353022885 0.94976353022885 1 0.420223111273373 4473 3788 2014 3743 2529 1646 4406 4325 2895 4266 2987 4216 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 0.253376821004151 0.370344286720353 4600 3700.09090909091 3743 0.0262134542239521 1417 0.701222236703204 -0.701222236703204 -1 0.675164638139896 4597 3606 1417 3349 2923 3743 3963 4641 4507 4475 3480 4217 M258 PID_BARD1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BARD1_PATHWAY.html BARD1 signaling events 18832364 17/36 Pathway Interaction Database 0.999053975880483 0.999999995401952 3505 3790.81818181818 3746 0.469015285714473 2871 0.243655462919811 -0.268406289378103 -1 9.83199813937206e-10 3502 4272 2871 4088 4292 3115 4352 3746 4606 3406 3449 4218 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 0.59171285788188 0.708060891735058 3945 3141 3746 0.0782073397413069 1385 1.46693471565438 1.46693471565438 1 0.490882016272212 3941 1385 1751 2419 4355 3828 4277 2977 3746 1913 3959 4219 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 0.943712354754118 0.993760920084898 3655 3725.54545454545 3747 0.23015873015873 3051 0.247809920606819 -0.196892775184072 -1 0.00150335451944891 3652 4340 3051 4074 3970 3444 4108 3649 3747 3868 3078 4220 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 0.993300279421106 0.999999995401952 3790 3794.54545454545 3747 0.393814325216529 3358 0.339458214738759 -0.435668332476155 -1 1.41018749558814e-09 3786 3710 4195 3733 3804 3358 3666 3470 4357 3914 3747 4221 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 0.858962512942732 0.938470117894531 3800 3751.36363636364 3748 0.163113083605011 3068 0.245044165099148 -0.237103098124198 -1 0.01508381211053 3798 4120 3401 4440 3139 3068 3652 3748 4523 3900 3476 4222 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 0.878859116702268 0.952656447112382 4025 3660 3748 0.174603174603175 2141 0.359309653648881 -0.384559989331463 -1 0.0168920700495741 4024 4063 2141 3824 4132 3739 3748 3212 3551 4434 3392 4223 M9664 BIOCARTA_GPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GPCR_PATHWAY.html Signaling Pathway from G-Protein Families 22/55 BioCarta 0.921309192177062 0.981194289668571 4300 3836.63636363636 3749 0.206349206349206 3022 0.261474171840467 -0.185931292381912 -1 0.00481169806110247 4296 4267 3589 3749 4074 3022 4423 4472 3677 3323 3311 4224 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 0.35943518917414 0.478362197236587 3750 3670.45454545455 3749 0.0396825396825397 2294 0.303263761259275 0.335416111674256 1 0.216760387010211 3749 4115 3042 4421 3248 4091 3724 3172 2294 4130 4389 4225 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 0.645390474649684 0.757210757187887 3065 3693.36363636364 3749 0.0899437891589046 1808 0.301835813678141 -0.316253463652728 -1 0.0813686188025112 3064 4638 1808 4591 3749 2931 4417 2806 4489 4660 3474 4226 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 0.310160304042109 0.429876126809028 4505 3451.63636363636 3750 0.0331908682144844 1639 1.06652134565326 1.17959543354241 1 0.872787865857678 4501 4350 3750 4036 2099 1639 4387 4017 3024 3145 3020 4227 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 0.415376077259216 0.535769969181582 4455 3426.09090909091 3752 0.0476272466940543 2058 0.372715717262119 -0.326703301013876 -1 0.225455699846698 4455 3101 2058 3879 2335 2176 3529 3944 4199 4259 3752 4228 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 0.981879729775546 0.999999995401952 2615 3637.63636363636 3753 0.305533447625509 2615 0.117785309135989 0.125864054505484 1 4.22203348462287e-10 2615 4629 3772 4363 3753 3295 2618 3779 4617 3419 3154 4229 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 0.980110580272407 0.999999995401952 3050 3708.45454545455 3754 0.299627181127098 2521 0.199454081890602 -0.205139021706709 -1 7.86196650112651e-10 3049 4362 3754 4412 4156 2521 4272 3135 4251 3726 3155 4230 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 0.97819350834065 0.999999995401952 3590 3734 3754 0.317883460768125 2605 0.143734535022672 -0.144162300551985 -1 5.37857644311017e-10 3588 4443 4089 4495 4291 2605 3408 2996 4607 3754 2798 4231 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 0.833377693957047 0.919531068386189 4245 3549.36363636364 3755 0.150333555203111 2000 1.13429110438601 -1.13429110438601 -1 0.0922371930086232 4242 3204 2000 3387 3666 4505 3755 3970 4290 2007 4017 4232 M189 KEGG_RIBOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOSOME.html Ribosome 60/184 KEGG 0.420122477112216 0.541147313839429 4250 3470.45454545455 3756 0.0483327678713472 1310 0.1135353213318 0.115089762299877 1 0.0675784631265245 2154 4661 3776 4248 3756 2905 1310 4249 4651 3192 3273 4233 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 0.00466941602402062 0.0195288900128794 4505 2961.81818181818 3756 0.000467925668897733 260 1.21455215107271 1.21455215107271 1 4.63361254965031 4502 1101 4232 2126 260 3756 4241 4275 2725 1426 3936 4234 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 0.523938425645133 0.64271608967882 4650 3671.18181818182 3756 0.0652474726751338 1691 0.758511437749222 -0.667767904475907 -1 0.325012114149951 4648 3485 1691 3324 4558 3979 2920 3755 4194 4073 3756 4235 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 0.855298073652137 0.935557136585881 4225 3839.45454545455 3757 0.175771872208018 2358 0.182346683251 0.171293722494839 1 0.0117739207742866 3679 3709 4612 4062 3285 3744 4224 2358 3757 4583 4221 4236 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 0.90790910863955 0.973561117410739 3995 3584 3759 0.194922147090696 2201 0.351577382647236 -0.253393714655587 -1 0.00913131414341253 3995 3516 2201 3759 3244 2413 4303 4142 4240 3190 4421 4237 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 0.190344988951642 0.299515318410811 3650 3566.90909090909 3760 0.0208933487657567 940 0.248411878021002 0.317148028976125 1 0.290292462024719 3648 3740 4092 4253 3988 3552 940 3024 4367 3760 3872 4238 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 0.598874229946632 0.712454324587211 4230 3672.18181818182 3763 0.0796890344187141 2262 0.246999757517471 0.208184862241681 1 0.0811728246678412 4227 3763 3165 3209 2650 4606 2262 3709 4464 4116 4223 4239 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 5.43453538333927e-05 0.00059779889216732 3420 3493.18181818182 3765 4.94060875839217e-06 374 1.41969994821831 -1.38916827744188 -1 10.2140121797668 3420 3657 374 2540 4192 4497 4066 4504 3765 2763 4647 4240 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 0.304703237593498 0.424194703316439 3770 3394.54545454545 3766 0.0324980767334904 1469 1.16400075421342 -1.01405746558881 -1 0.967571399177525 3766 3503 1469 2667 4070 3784 4123 3808 3353 2260 4537 4241 M7963 KEGG_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CELL_CYCLE.html Cell cycle 75/142 KEGG 0.563871046466187 0.681707875062062 3375 3613.27272727273 3768 0.0726627185401101 1725 1.26288057240438 1.26288057240438 1 0.4690288608797 3373 3752 1725 3684 4025 4102 3768 4566 3820 2353 4578 4242 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 0.0839184282471183 0.156982736433532 3770 3417.36363636364 3769 0.00793650793650794 1016 1.9083122944764 1.9083122944764 1 3.4250352514408 3769 4181 2050 3755 3522 3868 3937 4338 1016 2646 4509 4243 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 0.480960399002688 0.600976086811248 1995 3464.81818181818 3769 0.0578736819853851 1403 0.214194540885031 -0.137122878302296 -1 0.105720880851744 1993 4061 3504 4271 4368 3308 1403 3769 4418 4680 2338 4244 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 0.987127930609906 0.999999995401952 4145 3841.27272727273 3773 0.326791095047849 2952 0.140578248482591 -0.164869320207959 -1 5.23790245966114e-10 4143 4479 3779 4300 3633 3443 2952 3773 4553 3461 3738 4245 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 0.783871629653451 0.880235431717247 4580 3439.81818181818 3773 0.13 1388 0.694957063565193 -0.694957063565193 -1 0.0859322807153757 4580 1388 2660 2676 3773 2928 4278 3780 4338 3626 3811 4246 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 0.0101595545376288 0.0351867498620313 3665 3611 3773 0.000927888793964398 815 1.05949018680426 1.05949018680426 1 3.43738071267147 3665 4448 815 3754 3921 3452 4616 3781 4424 3072 3773 4247 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 0.52340095663996 0.642393107075655 4410 3776 3774 0.0714285714285714 2780 0.246298740319211 -0.177823567934415 -1 0.105655754879061 4409 3737 3975 3774 3703 2859 4265 4386 2780 3527 4121 4248 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 0.443927954001021 0.566361664157033 3775 3577.27272727273 3774 0.0519525014240551 1549 0.325706307490601 -0.191462230687282 -1 0.17948891508119 3774 4065 2696 4425 4222 3673 2744 1549 3454 4129 4619 4249 M16227 REACTOME_CHOLESTEROL_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHOLESTEROL_BIOSYNTHESIS.html Genes involved in Cholesterol biosynthesis 9/24 Reactome 0.386086746459241 0.507632574048261 4245 3700 3776 0.0476190476190476 2333 0.409998719380432 0.178936197131041 1 0.269447635518761 4241 3610 4099 3539 4683 3915 4047 2686 2333 3771 3776 4250 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 0.845709567191349 0.928101880997344 2740 3752.18181818182 3777 0.156252233680843 2010 0.12078461797456 0.108691453824202 1 0.00873563451588106 2739 4659 3777 4247 3656 3558 2010 4429 4597 3545 4057 4251 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 0.0352564582215 0.08872812203327 1965 2993.45454545455 3777 0.0035828634503248 445 0.202247201275207 0.202247201275207 1 0.474845702834224 1961 3884 4214 3777 4458 1496 445 2457 4544 3941 1751 4252 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 0.264222314623017 0.384040250100328 3265 3469.45454545455 3777 0.0302167890986841 1098 0.265057282435172 -0.367467814193467 -1 0.245877696582204 3263 3777 4435 4307 3771 2183 1098 4339 4000 4332 2659 4253 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 0.903866164811352 0.970113799428767 1830 3584.63636363636 3778 0.191771415086365 1830 0.214177186153108 -0.231122160811189 -1 0.0062991184331074 1830 4415 3658 4296 3839 2598 3899 3778 4380 3587 3151 4254 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 0.899831543644595 0.968445248855897 2885 3740.72727272727 3779 0.205538056963093 2495 0.206257621442677 -0.0202030443922601 -1 0.00641036094923472 2881 4571 4044 4388 4396 3752 3779 2495 3850 3662 3330 4255 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 0.323553394611178 0.444104044272988 3065 3363 3779 0.0383360139887489 1380 0.210114287440698 0.193407117853635 1 0.165315309938355 3061 3944 4316 3779 4550 3168 2373 1380 3846 4069 2507 4256 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 0.989148258671398 0.999999995401952 4290 3939.27272727273 3780 0.36386404456258 3224 0.189010883211934 -0.15379859276372 -1 7.39651878609095e-10 4289 4570 3809 4541 3732 3780 3508 3665 4502 3224 3712 4257 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 0.472114919245153 0.592759334515465 4410 3566.36363636364 3780 0.0564252558121932 1640 0.960712294109597 1.05228047505522 1 0.487002665850474 4406 4082 1640 3641 2997 3133 3931 4614 3780 3088 3918 4258 M8229 REACTOME_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSLATION.html Genes involved in Translation 98/283 Reactome 0.973178959134239 0.999999995401952 3975 3838.54545454545 3781 0.280328759122654 3041 0.150292268915658 0.122436531695391 1 5.67085109479674e-10 3974 4585 3781 4571 3520 3511 3041 3537 4493 3414 3797 4259 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 0.95383620120374 0.99961092867638 4400 3672.36363636364 3781 0.264758260370345 2381 0.349758877911943 -0.34659703617431 -1 0.000131930739460334 4396 3143 4419 3186 4237 2381 3781 3026 3862 4305 3660 4260 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 0.39767054841001 0.519221005809224 3785 3612 3781 0.0494315188607121 2359 0.226111272659198 -0.215915240029748 -1 0.143651285841761 3781 3244 4585 3339 2359 2689 3952 4341 4123 4544 2775 4261 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 0.480630743883817 0.600976086811248 1815 3364.54545454545 3782 0.0578193005790052 1402 0.116578395817115 0.117540437818743 1 0.0575400784404355 1815 4623 3782 4417 3853 2234 1402 3897 4642 3590 2755 4262 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 0.805832897881312 0.898010216283431 3115 3460.45454545455 3782 0.151176167289714 1916 0.181209683565786 -0.194866920196426 -1 0.0188952182760197 3114 4641 4446 4494 3782 1916 2140 2524 4554 4347 2107 4263 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 0.63909175097802 0.750384351060637 3885 3702.18181818182 3783 0.088485994055939 2723 1.05077947290469 1.05077947290469 1 0.292492082381768 3883 4357 2982 4451 2723 3667 3783 4296 3516 3096 3970 4264 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 0.935710590109709 0.989507236660202 4340 3840.90909090909 3784 0.220799827623315 2737 0.183182314152566 -0.194372312942281 -1 0.00187294817389544 4339 4615 3784 4525 3336 2737 4048 3593 4334 3642 3297 4265 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 0.93384802756002 0.98846022445738 3665 3594.18181818182 3784 0.218774127037394 2192 1.33781152956556 1.5717828996862 1 0.0150513038159011 3663 4318 2192 3366 3784 3101 4280 4106 3967 2865 3894 4266 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 0.510836595187287 0.633523779448203 4490 3642.54545454545 3784 0.0629375357922358 1673 0.421903362441997 -0.280423222760327 -1 0.1866712480791 4487 3940 1673 3784 3855 3879 3669 3474 3168 4567 3572 4267 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 0.35943518917414 0.478362197236587 3480 3388.90909090909 3785 0.0396825396825397 2218 1.82051220676583 1.82051220676583 1 1.30122679021286 3479 3966 2218 3785 2829 3821 3819 3840 2264 2860 4397 4268 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 0.0437112301543049 0.104239605345075 2130 2964.81818181818 3786 0.00445956159587092 502 0.125090971080421 0.162921525853239 1 0.274159007025231 2126 3985 4229 3786 3130 1027 502 4430 3826 3956 1616 4269 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 0.992079140046057 0.999999995401952 4065 3838.90909090909 3787 0.383579272809805 2999 0.253051575838626 0.154318977345789 1 1.02507778085947e-09 4062 3112 4375 3511 3787 3628 2999 3745 4449 4172 4388 4270 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 0.056680010862822 0.126417197002943 3940 3260.27272727273 3788 0.00581798190179574 1127 0.50491279453589 -0.50491279453589 -1 1.01219923426863 3937 1474 3788 1593 1127 4547 4182 4413 3322 3166 4314 4271 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 0.656494462614554 0.768314948004945 3790 3719.27272727273 3789 0.092572036610465 2775 0.26678603679163 0.242365004251689 1 0.0681552182210367 3789 3811 3083 3720 2775 4125 2939 3456 4272 4315 4627 4272 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 0.597318307603006 0.711317303539438 4300 3833.81818181818 3790 0.0793650793650794 2935 0.275903012244583 -0.251555730983029 -1 0.0910986009282296 4298 3721 3643 3790 4422 3084 4110 4540 2935 3747 3882 4273 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 0.415005792965329 0.535769969181582 4405 3593.09090909091 3791 0.0475724255636849 2334 0.268613897554614 0.271452482901845 1 0.162484519557937 4403 4033 2952 3791 2334 3545 2941 3100 4212 3865 4348 4274 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 0.989444360105343 0.999999995401952 3960 3798.63636363636 3792 0.365621498697704 2769 0.288421836346743 -0.24447140014155 -1 1.18272111831069e-09 3959 3704 3792 4313 4241 2769 3541 4193 4455 3176 3642 4275 M12294 KEGG_VIRAL_MYOCARDITIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIRAL_MYOCARDITIS.html Viral myocarditis 41/116 KEGG 0.167689370996947 0.270403438572503 4610 3512.27272727273 3792 0.0165478776700343 1297 1.42802375650398 1.42802375650398 1 1.81031432039449 4608 4551 1297 4239 3792 2794 4243 4352 3006 2145 3608 4276 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 0.97530599069028 0.999999995401952 4505 3770.45454545455 3792 0.285714285714286 2603 0.249969234100927 -0.279316605296188 -1 1.01133995049815e-09 4503 3792 3631 4335 3649 2603 4450 3144 3916 4230 3222 4277 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 0.949776431494504 0.997544330001665 4025 3827.27272727273 3796 0.238095238095238 3078 0.27183721973527 -0.280232077199917 -1 0.000647853052795637 4023 3507 3609 3078 4171 4127 3527 4226 3796 3676 4360 4278 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 0.822436702569706 0.911237964766086 3800 3752.45454545455 3797 0.158730158730159 2883 0.273083902925656 -0.278396255280035 -1 0.0246045247555445 3797 3612 4206 4108 3788 4269 2883 3239 3452 3929 3994 4279 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 0.333210580588789 0.454034539296035 2150 3261.36363636364 3801 0.0397178194072031 1230 0.155810516732733 0.190265261919565 1 0.1192498595132 2147 4197 4122 4085 4311 2299 1230 3384 4237 3801 2062 4280 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 0.792722909630113 0.888046749827088 3715 3603.72727272727 3802 0.133300990303713 2287 1.0177635111608 1.0177635111608 1 0.117131706252695 3714 3802 3294 4192 3006 3903 2287 4674 4160 2341 4268 4281 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 0.298735036746822 0.4173739958842 4040 3441.72727272727 3803 0.0317460317460317 2077 1.10496445483283 -0.932831861493612 -1 0.935859360881532 4036 3922 3032 4025 2077 2949 4334 4592 2088 3001 3803 4282 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 0.0448138007628148 0.106112920856266 2220 3461.27272727273 3805 0.00415941506953307 1031 0.313811710148163 -0.328529741701415 -1 0.682355931043579 2219 4151 1031 4464 4067 2917 3805 3378 4610 4208 3224 4283 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 0.130987515738768 0.226915896026569 2200 3326.90909090909 3805 0.0126823280307414 1249 0.365985569752681 0.381020211281498 1 0.526163197769849 2198 4226 1249 4329 3805 4241 3049 1654 4349 4504 2992 4284 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 0.850621352955467 0.931311135502177 3715 3902.45454545455 3807 0.158730158730159 3175 0.955023857704091 0.955023857704091 1 0.0658757227398994 4452 4113 3714 4272 4526 3175 4144 3542 3467 3715 3807 4285 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 0.355334867731202 0.478362197236587 4180 3465.63636363636 3808 0.0429526652734571 1451 0.97975757930076 -0.97975757930076 -1 0.7002901739828 4178 4130 4066 4058 4538 3254 1861 1451 3808 3697 3081 4286 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 0.993932717884054 0.999999995401952 3400 3779.6 3808.5 0.432891677139641 3086 0.293576810681047 -0.293576810681047 -1 1.20569656001965e-09 3397 3742 4241 NA 3875 3086 3918 3621 4543 3975 3398 4287 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 0.955240661249004 0.99961092867638 2860 3759 3809 0.246031746031746 2712 0.27975174953364 -0.145530843768785 -1 0.000105523691657933 2860 4463 3004 4210 4477 3678 2712 4481 3809 4241 3414 4288 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 0.966127175188938 0.999999995401952 3900 3748.54545454545 3810 0.287171358108974 2795 0.345517030614082 -0.309195051564517 -1 1.43719131014498e-09 3896 3076 4105 3614 4078 3300 4234 2795 4542 3784 3810 4289 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 0.00487149586996049 0.020094920463587 3975 3311.27272727273 3811 0.000443846951080452 736 1.17952576784896 -1.09190043743444 -1 4.46731673950863 3971 3353 736 3276 3811 4115 3872 4322 3484 842 4642 4290 M125 PID_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IGF1_PATHWAY.html IGF1 pathway 18832364 28/54 Pathway Interaction Database 0.978161938897681 0.999999995401952 4500 3778.36363636364 3813 0.293650793650794 3202 0.286540134916822 -0.243664139071396 -1 1.17433447684303e-09 4496 4114 3202 3974 3813 3836 3802 3370 3938 3381 3636 4291 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 0.481063017846562 0.600976086811248 4370 3610.90909090909 3813 0.0634920634920635 1424 1.46584243959724 1.46584243959724 1 0.723501884746395 4367 3393 4167 3481 4245 4459 3813 3230 2608 1424 4533 4292 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 0.853356858894554 0.93365170226007 2430 3512.45454545455 3813 0.160142482197735 2032 0.701222236703204 -0.701222236703204 -1 0.046662886532733 2429 4508 2489 4438 4005 3562 2032 2283 4413 4665 3813 4293 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 0.632431976984906 0.745034700521015 4155 3701 3814 0.0952392076646094 2797 0.330750335997829 -0.168006328191388 -1 0.0943605689024583 4152 3817 3866 4073 2797 3699 3944 3445 3783 3321 3814 4294 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 0.955240661249004 0.99961092867638 4030 3635.54545454545 3814 0.246031746031746 2351 0.368150059974342 -0.296970427110306 -1 0.000138867987639405 4028 2351 2782 3248 4243 3508 4060 4270 3814 3402 4285 4295 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 0.235674942744545 0.348492515525699 4490 3345 3814 0.0265182598646851 1033 0.30132991996747 0.32559485284673 1 0.307895830488371 2256 4472 4490 4586 3814 2392 1033 2321 4486 4400 2545 4296 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 0.274129650394943 0.395496164332113 2075 3062.27272727273 3815 0.0315305944865082 1119 0.311456409724332 0.302215610048096 1 0.28004545099294 2074 3815 4389 4117 4615 1695 1119 1737 4153 4216 1755 4297 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 0.7184702227596 0.82095865980285 3820 3638.09090909091 3816 0.119047619047619 2315 0.257267589783274 0.12804617931673 1 0.0491968797543115 3816 4444 4170 3996 3765 2648 4679 2315 3216 3878 3092 4298 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 0.815614188102356 0.906472278016503 3370 3621.09090909091 3817 0.155552313927011 1859 0.158608361011636 -0.174187818842914 -1 0.015096579751452 3366 4640 4129 4547 4378 1859 3526 2490 4676 3817 2404 4299 M477 BIOCARTA_GABA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GABA_PATHWAY.html Gamma-aminobutyric Acid Receptor Life Cycle 4/14 BioCarta 0.990852368426112 0.999999995401952 3515 3900.54545454545 3819 0.374638894793036 3269 0.11278191093695 0.11699045157485 1 3.99903473387491e-10 3513 4475 3838 4493 3770 4086 3304 3819 4655 3269 3684 4300 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 0.645577054453981 0.757240069379563 3820 3603.27272727273 3819 0.0985281222316502 2813 0.273277003270264 -0.180497970780269 -1 0.0736595072382226 3819 4035 3868 3857 2813 3071 4420 3312 3899 3322 3220 4301 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 0.669198906141322 0.776285256383162 4150 3538.36363636364 3822 0.0956755623219069 1469 0.911131724554558 0.911131724554558 1 0.223650130137769 4149 3923 3562 4618 2999 1469 3985 4627 3822 3102 2666 4302 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 0.326977906302657 0.44802139631311 4485 3562.36363636364 3823 0.0388239691459634 2166 0.555851743372547 0.5203700809741 1 0.432605487834434 4485 2166 3850 2813 2202 3533 4428 4599 3823 3297 3990 4303 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 0.829242618414225 0.916685753689327 3785 3703 3823 0.14843791436246 2487 1.21455215107271 1.21455215107271 1 0.102412303534693 3785 4632 2864 4163 3090 3901 3823 3419 3931 2487 4638 4304 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 0.911174835031856 0.97526870534772 4530 3734 3824 0.197560376084538 2549 0.724095453604658 0.724095453604658 1 0.0175765261071023 4529 3300 2549 3113 3247 4552 3569 4440 3838 4113 3824 4305 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 0.223483099047557 0.339132707945871 2385 3201.36363636364 3829 0.0249764818616448 1011 0.263472972511378 0.263472972511378 1 0.276166983115971 2383 4642 4135 4610 4318 1800 1011 2320 4668 3829 1499 4306 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 0.546648075057926 0.666560728524965 4070 3822.54545454545 3829 0.0760604743249733 2628 0.339176145046687 -0.189732541491564 -1 0.133356085517963 4069 3392 4640 3696 2628 4167 3829 3157 3244 4617 4609 4307 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 0.566993112338148 0.68431283941271 4340 3711.36363636364 3830 0.0732681841563834 2609 0.648828184364399 0.648828184364399 1 0.238573567694574 4340 3830 3573 3953 2609 2758 4146 3473 4265 4219 3659 4308 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 0.187038091383415 0.295203939448529 2175 3172.63636363636 3831 0.0204941824801664 936 0.252764837590434 0.252764837590434 1 0.298931705306139 2173 4605 4136 4611 4001 1905 936 2165 4667 3831 1869 4309 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 0.597488804057064 0.711339567025254 3535 3709.81818181818 3831 0.0794005224750103 1754 1.05077947290469 1.05077947290469 1 0.346918084659939 3535 4255 1754 3872 4020 3650 4591 3747 4497 3056 3831 4310 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 0.866732909936791 0.944098190600605 3080 3590 3832 0.167413516931208 2058 0.28405016589429 -0.179752355818317 -1 0.0158385825962763 3076 4439 2547 4327 4454 3541 2058 3170 4077 3969 3832 4311 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 0.960158985072255 0.999999995401952 3410 3784.45454545455 3833 0.253968253968254 2677 1.39059940208002 1.39059940208002 1 6.09506689778802e-09 3410 4506 3574 4104 3833 3090 4635 4175 3841 2677 3784 4312 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 0.670796580850186 0.77767263183176 2920 3473.27272727273 3833 0.0960734938153099 1840 1.29142669460736 1.29142669460736 1 0.314763682474294 2917 3833 1840 4072 4322 4580 2378 3483 3893 2774 4114 4313 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 0.946596086373448 0.995678846407626 3940 3819.18181818182 3834 0.253968253968254 3315 0.460998398797293 -0.511872399269155 -1 0.00193509808690354 3938 3455 3893 3609 4034 4654 3426 3315 3834 3357 4496 4314 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 0.715779167685101 0.818882123967867 2575 3496.45454545455 3834 0.118209144555602 2066 0.305657400515968 0.460533234945809 1 0.0592007427296666 2573 4072 4139 4427 2938 3921 2984 2066 3930 3834 3577 4315 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 0.86802593958647 0.945067275302556 2955 3660.45454545455 3834 0.183325758438082 2952 0.297742467997129 0.416191545469931 1 0.0163059709024207 2952 3459 4160 3834 3214 3966 3287 4016 4312 3862 3203 4316 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 0.35943518917414 0.478362197236587 4335 3605.63636363636 3834 0.0396825396825397 2213 1.49234186417521 1.49234186417521 1 1.06666420942985 4332 3834 2834 4145 4485 3463 4207 3191 2213 2715 4243 4317 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 0.000333793566536445 0.00251293777213829 4080 3259.54545454545 3836 3.03494747189162e-05 510 1.57157302434315 1.57157302434315 1 9.11920777711822 4079 3299 510 2369 3930 3410 4546 4058 3836 1789 4029 4318 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 0.999712772522011 0.999999995401952 3605 3884.72727272727 3837 0.557592380133044 3320 0.257581192195245 -0.268646444213724 -1 1.04526603589556e-09 3601 3679 3865 3837 4144 3530 4340 4362 4530 3320 3524 4319 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 0.997092948387618 0.999999995401952 3840 3756.90909090909 3839 0.411962808418632 3082 0.205427531448782 -0.188795223090187 -1 8.1281999161255e-10 4204 4003 3463 3839 3840 3082 4499 3267 4369 3484 3276 4320 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 0.824303683279996 0.912733237204646 2135 3403.54545454545 3839 0.146227701186945 1980 0.771426592705555 0.771426592705555 1 0.0682785888882773 2131 3839 2540 3453 4063 4292 1980 3989 4405 4489 2258 4321 M8344 NAKAJIMA_EOSINOPHIL http://www.broadinstitute.org/gsea/msigdb/cards/NAKAJIMA_EOSINOPHIL.html Top 30 increased eosinophil specific transcripts. 11493461 15/52 Kevin Vogelsang 0.0450917610233045 0.106717167755154 3540 3355.09090909091 3840 0.0041857631669152 1033 1.26530448687738 1.26530448687738 1 2.74432898675903 3536 3901 1033 4179 4007 4670 3069 2179 4372 2120 3840 4322 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 0.185194037436664 0.292984219928497 4175 3579 3841 0.0202722261416175 1819 0.462136560506253 -0.291595566009326 -1 0.549925674367212 4174 2343 4597 2311 1819 3278 4119 3841 3760 4566 4561 4323 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 0.569854443324427 0.686815309006755 4510 3779.8 3841.5 0.0894776626669511 2737 0.212361997263603 -0.23362788102027 -1 0.0773339405057974 4507 2865 4601 NA 2737 3768 3013 3800 3883 4571 4053 4324 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 0.989862840805202 0.999999995401952 2790 3707.72727272727 3842 0.341251467692318 2437 0.322047781530271 0.346099368942573 1 1.33259013673273e-09 2787 3356 2437 3842 4373 4162 2901 4542 4411 4306 3668 4325 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 0.790224149222121 0.88567097901336 3810 3605.7 3843 0.159302997370172 2150 0.368012066658459 -0.637549163902204 -1 0.0433091339179815 3809 4165 4177 NA 3877 2439 3661 3472 4415 3892 2150 4326 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 0.562604368603265 0.680703349154377 4575 3469.45454545455 3843 0.0793650793650794 1790 0.653874098340854 0.653874098340854 1 0.243780892457059 4573 2164 4197 1790 2800 3843 3545 4107 2828 3917 4400 4327 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 0.0415276073267799 0.100412224897613 4045 3318.27272727273 3844 0.00423246970115315 957 1.25309527076868 1.39179190343982 1 2.79181763011986 4044 4685 4296 4170 957 1438 3844 4482 2575 2996 3014 4328 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 0.878859116702268 0.952656447112382 3735 3700 3844 0.174603174603175 2487 0.709534985824837 -0.667767904475907 -1 0.0333570629050729 3733 4182 3054 3844 4498 2487 4252 3895 3557 4593 2605 4329 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 0.999752945540485 0.999999995401952 3360 3946.72727272727 3845 0.564207983654568 3288 0.234654083187947 -0.134779677498295 -1 9.43081151472981e-10 3356 4531 3845 4324 4127 3813 3551 4417 4621 3288 3541 4330 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 0.816521443770307 0.906472278016503 4320 3597.90909090909 3847 0.142857142857143 2024 0.38427969375026 -0.297316514050609 -1 0.0365763130628947 3847 4089 2024 4392 4040 3259 2088 4320 3370 3830 4318 4331 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 0.882433011271664 0.956088113484166 2730 3536 3848 0.176847141961869 2098 0.401024125090861 -0.382229754966337 -1 0.0174554484438875 2729 3848 2098 3995 4595 4007 2986 2362 4086 4345 3845 4332 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 0.972692764502083 0.999999995401952 4550 3967 3851 0.302365782681676 3240 0.181618327363431 -0.203861883632644 -1 7.06703657150983e-10 4548 4279 3813 4082 3580 3719 4215 3851 4632 3240 3678 4333 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 0.403620301352108 0.525817273321095 4205 3692.54545454545 3852 0.045901997799089 2315 0.729890307791734 -0.55936453995665 -1 0.454776855808032 4202 4367 2996 3633 2315 3455 3573 4282 4040 3852 3903 4334 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 0.096787670199205 0.176959431351336 2455 3497.54545454545 3856 0.010128123098543 1410 0.34704156164118 0.351648627454702 1 0.582574955422062 2455 3573 4520 4308 1410 3856 2788 3984 4235 4446 2898 4335 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 0.0477483013548705 0.111497102706558 3930 3565.36363636364 3857 0.00443793131398954 1040 1.2815413473491 1.2815413473491 1 2.72511568609219 3928 3720 1040 3002 4071 3857 4354 3761 4393 2900 4193 4336 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 0.147859119791321 0.249412467725749 4395 3237.27272727273 3858 0.0158730158730159 886 0.843946822682246 0.520920570236399 1 1.13598053233459 4394 1109 4172 886 3746 3858 3733 4369 1044 3881 4418 4337 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 0.141001650002859 0.240441678279984 2230 3021.45454545455 3859 0.0150839085503302 816 0.430141860657645 0.487943089205701 1 0.594258047712627 2227 4245 4391 4312 4096 1413 816 1600 3859 4226 2051 4338 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 0.268685326785879 0.389319555138722 4675 3696.63636363636 3860 0.0308066430627322 2051 1.19383512831952 1.26552952984869 1 1.09164965179331 4674 4610 4141 4366 2051 2969 4098 3860 3145 3061 3688 4339 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 0.949776431494504 0.997544330001665 3220 3997.18181818182 3864 0.238095238095238 3219 0.234885234349824 0.263891800226589 1 0.000559787627614719 3219 4180 3661 4552 3864 4686 3411 3810 3800 4443 4343 4340 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 0.952368773159577 0.999059787558938 4680 3769.27272727273 3865 0.24175711719258 2555 0.343069802806926 -0.277151085040587 -1 0.000312806993669972 4680 3480 2555 4123 4495 3775 3405 2629 3865 4574 3881 4341 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 0.298735036746822 0.4173739958842 4220 3390.36363636364 3868 0.0317460317460317 1970 1.90919498657043 1.90919498657043 1 1.61700948134389 4216 4490 2893 3958 2815 2212 3868 4644 1970 2125 4103 4342 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 0.108337110004758 0.193732267297989 3190 3236.45454545455 3868 0.0103701412399328 1432 0.850934469142744 0.850934469142744 1 1.35376152508736 3186 3868 1609 2957 1432 3874 2009 4111 3994 4317 4244 4343 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 0.979624863145402 0.999999995401952 3610 3649.81818181818 3870 0.298089293734551 2500 0.308969241222177 -0.336129507479398 -1 1.27429979016643e-09 3884 3607 2500 3941 3567 2838 4175 3872 4286 3608 3870 4344 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 0.996109202762694 0.999999995401952 3830 3812.36363636364 3870 0.396172900750403 2743 0.219206318506832 -0.276165186235641 -1 8.74231300058025e-10 3828 4492 2743 4454 3844 2875 3870 3914 4598 4147 3171 4345 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 0.93583281560457 0.989507236660202 3680 3618.90909090909 3871 0.220934616581507 2182 0.31520503999144 -0.356938933597458 -1 0.00322281504277476 3676 4335 2873 4087 3871 2182 4231 4130 3880 3301 3242 4346 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 0.0680710021472547 0.145142039513573 4650 2780.72727272727 3872 0.00702507297221585 28 1.66203447267612 -1.6720827096008 -1 3.10935816258855 4646 2018 4182 920 2248 3872 4045 4082 28 346 4201 4347 M1389 BIOCARTA_SPRY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SPRY_PATHWAY.html Sprouty regulation of tyrosine kinase signals 9/30 BioCarta 0.481063017846562 0.600976086811248 3970 3401.81818181818 3873 0.0634920634920635 1684 1.21455215107271 1.21455215107271 1 0.599471502980574 3970 4392 3873 4157 2738 4309 3433 1956 2606 1684 4302 4348 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 0.466738071388703 0.587219019917277 4660 3547.81818181818 3873 0.0555555555555556 2339 1.00744291305309 1.00744291305309 1 0.519861453396854 4656 3873 3066 3947 2967 4103 3540 3936 2569 2339 4030 4349 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 0.878859116702268 0.952656447112382 4155 3869.54545454545 3874 0.174603174603175 2924 0.955023857704091 0.955023857704091 1 0.0448981256159955 4155 4143 3708 4394 4513 2924 3874 4091 3546 3612 3605 4350 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 0.96855221189793 0.999999995401952 3470 3752.54545454545 3874 0.26984126984127 3036 0.264007482165595 -0.197909415817883 -1 1.07390766261253e-09 3468 3936 3036 4122 3743 4226 3095 3374 3874 4274 4130 4351 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 0.380880192499814 0.502620270924846 3925 3706.81818181818 3874 0.0468144063051811 2325 0.31087274497818 0.192084848765295 1 0.20729300789729 3921 2785 4641 3534 2325 3922 4622 2869 3664 4618 3874 4352 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 0.995659262979588 0.999999995401952 4420 3873.90909090909 3875 0.39013593638052 2948 0.199892094561548 0.148995849024694 1 7.88148848889304e-10 4418 4301 3552 4433 4481 2948 3565 3149 4189 3875 3702 4353 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 0.0839184282471183 0.156982736433532 4200 3118.81818181818 3879 0.00793650793650794 741 1.42279293755586 -1.42279293755586 -1 2.55362603945126 4200 4236 2435 4045 2250 4195 3884 2680 741 1762 3879 4354 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 0.158964914550334 0.262241686633255 4480 3755.54545454545 3880 0.0171631952003449 1729 0.383652778958439 -0.310303325384694 -1 0.497756492898133 4480 3529 4113 4050 1729 3203 3880 3734 4330 3792 4471 4355 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 0.532549113358359 0.652424874561377 4635 3552.18181818182 3880 0.0667972736862034 1748 0.393958009968302 -0.34158988213348 -1 0.163080474144823 4633 2857 1748 3431 2555 3880 4464 3934 4008 3898 3666 4356 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 0.3543901238671 0.477479045555271 4005 3556.90909090909 3881 0.0428125043063248 2263 0.48236113133686 0.561327735573945 1 0.345635780010337 2657 4005 4137 3881 2263 4130 4023 2718 4002 3832 3478 4357 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 0.775485941583084 0.872282074473915 3095 3746.36363636364 3881 0.126984126984127 2889 0.333600394458478 0.358757661797614 1 0.044185114955737 3093 3012 2889 3934 3881 4652 2945 4561 3299 4637 4307 4358 M7968 BIOCARTA_CARM1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARM1_PATHWAY.html Transcription Regulation by Methyltransferase of CARM1 6/15 BioCarta 0.980479820544289 0.999999995401952 4620 3881 3882 0.325396825396825 3099 0.20923875872511 -0.164849070621917 -1 8.29806425384719e-10 4620 3574 3882 3723 4204 4336 3099 3751 4003 3340 4159 4359 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 0.133604989879398 0.230597783637148 3620 3588.45454545455 3882 0.0142390857543375 1609 0.187260064765849 0.211555905917691 1 0.266294940640842 3617 3882 3922 4001 1609 4558 2743 3940 3945 3451 3805 4360 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 0.98182085523805 0.999999995401952 2315 3649.72727272727 3882 0.305328623577747 2313 0.715858725339802 0.715858725339802 1 3.0877842069801e-09 2313 4590 2710 4362 4115 2935 4046 3424 4508 3882 3262 4361 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 0.306065069117517 0.425625354914998 1880 3120.63636363636 3882 0.0358782621236267 1134 0.31167237393088 -0.385479367527298 -1 0.258059344806731 1880 3773 4495 3994 4152 1134 1179 3882 3927 4407 1504 4362 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 0.913189391115034 0.975873543161927 4685 3830.72727272727 3884 0.216827769034504 3027 0.244286856085263 0.16289753711972 1 0.00578295670005741 4683 3582 3884 4115 3320 4471 3253 3027 4029 3346 4428 4363 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 0.847919277466084 0.930091229917151 2440 3741.90909090909 3885 0.157357991971842 2016 0.693810091349027 0.693810091349027 1 0.0487391920187028 2440 4586 3775 4304 3511 3885 2016 4608 4395 3722 3919 4364 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 0.19246001050737 0.302032019168633 4490 3749.18181818182 3885 0.0192453699309828 1788 0.212037989632003 0.170458041778372 1 0.246066403060855 4490 3938 3571 3885 1788 4214 4452 3426 3590 3727 4160 4365 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 0.339785186232095 0.461516922516985 3845 3387.45454545455 3885 0.0370411001806589 931 0.293322744819471 -0.312266748242077 -1 0.219847729430766 3845 4554 2977 4400 4162 931 1908 4455 3917 3885 2228 4366 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 0.853233160620055 0.93365170226007 4090 3762.18181818182 3885 0.174603174603175 2539 0.31517797286904 -0.278396255280035 -1 0.0209735418760829 4089 3576 4207 3318 3885 2539 4317 4676 3523 3930 3324 4367 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 0.597318307603006 0.711317303539438 3135 3458.81818181818 3890 0.0793650793650794 1263 1.35570769085078 1.35570769085078 1 0.447632206007319 3135 4458 2951 3890 4201 4333 2418 4462 2890 1263 4046 4368 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 0.161385165508919 0.262241686633255 4345 3209.09090909091 3891 0.0158730158730159 1416 1.48034281358945 1.48034281358945 1 1.92061751590168 4343 2088 1917 1953 4669 3914 3891 4467 1416 2630 4012 4369 M11650 BIOCARTA_NOS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NOS1_PATHWAY.html Nitric Oxide Signaling Pathway 10/27 BioCarta 0.814179706164943 0.90610577659284 3895 3759 3893 0.141868346183937 2178 0.230930326523688 -0.13076993136512 -1 0.0220708139899717 3893 4391 3190 4221 3987 3493 3592 2178 4446 3296 4662 4370 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 0.232850105696956 0.34496857265126 3985 3536.63636363636 3894 0.0238095238095238 1785 0.388461027965246 0.408284303685855 1 0.400752447021879 3985 3568 2617 3537 4364 4023 2388 3894 1785 4145 4597 4371 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 0.990112694306776 0.999999995401952 4365 3806.63636363636 3895 0.342744301542973 2687 0.207878072773798 -0.207904545683241 -1 8.2374192171677e-10 4363 3895 3523 3750 4644 2687 4111 4019 4619 3358 2904 4372 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 0.506517317819797 0.629085648370944 3895 3713.45454545455 3895 0.0621883385519872 2467 0.345315767839095 -0.34051497919575 -1 0.155138162725649 3895 3630 2467 3214 2511 3698 4430 4165 4102 4205 4531 4373 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 0.930178245382759 0.986827090301926 3900 3707.18181818182 3896 0.233699558379738 2351 0.305050156097571 0.344386165264818 1 0.00392096627952655 3137 3772 4221 4326 3898 3896 2351 3371 4107 3949 3751 4374 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 0.349099132028211 0.471570634962294 4000 3721.36363636364 3897 0.0382840815483742 1518 0.385975421504939 -0.407016508413538 -1 0.281229060941801 3999 3311 1518 3770 3933 4553 3676 3870 4151 3897 4257 4375 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 0.428305819677745 0.549874266030113 4170 3519.36363636364 3897 0.049561589780148 1530 0.264955970175374 -0.277948293729571 -1 0.153598305056427 4167 3836 3323 3897 4338 2111 4558 1530 4112 4225 2616 4376 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 0.962382958830255 0.999999995401952 3095 3698 3899 0.279658454620139 2687 0.328088181125006 0.311875797683411 1 1.35951187092336e-09 3092 2742 3899 3484 4048 4548 4255 4617 3918 3388 2687 4377 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 0.950651536813798 0.997818994396395 4140 3677.45454545455 3899 0.239311774710191 2258 0.314250205062682 -0.303101360837259 -1 0.000665074321960641 3461 3899 2774 4137 4640 2258 3181 4549 4137 4472 2944 4378 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 0.269705277636953 0.390555911930396 3535 3634.81818181818 3901 0.0309418995510407 1114 0.244776373860799 0.195396185755233 1 0.223072627757411 3532 4011 4557 4320 3334 3080 1114 3104 4533 4497 3901 4379 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 0.16755330672166 0.270277037968227 2000 2968.27272727273 3903 0.0181714800329639 892 0.15661366688978 0.15661366688978 1 0.198611068414746 1999 4284 4390 3903 3955 1242 892 1623 4641 4224 1498 4380 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 0.574235920956999 0.690674929569943 3590 3532.09090909091 3905 0.0818431010880196 1369 0.232521244718433 -0.250643591445037 -1 0.0834121204817945 3589 4162 4189 4211 3835 1369 2687 4010 4648 3905 2248 4381 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 0.972114443288272 0.999999995401952 4335 3981.90909090909 3906 0.277777777777778 3272 0.18455989579993 -0.197741439150222 -1 7.19814068525096e-10 4334 4231 3676 3906 4662 3272 4613 4284 3889 3629 3305 4382 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 0.443870977248942 0.566361664157033 3965 3801.54545454545 3907 0.0569872687405472 2451 0.156917564983809 -0.159394245871091 -1 0.086473497230612 3963 3907 4082 3681 2451 3988 4589 3822 4602 3733 2999 4383 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 0.557443745451391 0.675680649556446 3920 3592.36363636364 3907 0.0714285714285714 1922 1.45127279439026 -0.839316232100865 -1 0.551489767113146 3917 4374 1922 3500 3907 3982 4209 4576 2809 2645 3675 4384 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 0.53608852978127 0.655903616332906 3765 3484.09090909091 3907 0.0674418559473721 1473 0.250088270748914 -0.262568892219407 -1 0.102235906592057 3764 4025 3352 3907 4649 2230 1473 4170 4122 4361 2272 4385 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 0.443870977248942 0.566361664157033 3965 3809.18181818182 3908 0.0569872687405472 2452 0.156917564983809 -0.159394245871091 -1 0.086473497230612 3964 3908 4104 3682 2452 3989 4590 3826 4603 3783 3000 4386 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 0.825098771234019 0.913298526439577 4165 3614.09090909091 3909 0.16 1599 0.738966098018225 -0.514772766976538 -1 0.0649620395588517 4161 1599 4192 2710 4473 3096 3927 3308 3750 3909 4630 4387 M7772 BIOCARTA_BARRESTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARRESTIN_PATHWAY.html fl-arrestins in GPCR Desensitization 6/23 BioCarta 0.596717267037759 0.711317303539438 3800 3923 3910 0.0868103875114919 2710 0.319567097447492 -0.20192817867956 -1 0.105515758047764 3799 3910 3874 4381 2710 4542 4012 4366 3858 3328 4373 4388 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 0.533662629236255 0.653447368853173 3270 3810.81818181818 3912 0.0734475217979029 1733 0.421658572860892 0.424067532895633 1 0.173907179818174 3269 3912 4682 3596 4395 4128 4343 1733 3480 4677 3704 4389 M842 REACTOME_PURINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_CATABOLISM.html Genes involved in Purine catabolism 5/15 Reactome 0.973423420138585 0.999999995401952 3980 3742.45454545455 3914 0.304255296140179 2540 0.353035913128648 -0.388990962339196 -1 1.4707025627191e-09 3979 3914 4036 4251 3818 2540 3350 4140 4429 3639 3071 4390 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 0.529009021904234 0.648426962239927 3870 3720 3915 0.0725270357606946 2509 0.252750852789668 -0.205500764330547 -1 0.106133103841957 3870 4009 3915 4005 2600 4396 3997 2509 3879 3430 4310 4391 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 0.838494417110154 0.921799467694876 4135 3668.90909090909 3916 0.166666666666667 2528 0.226802574716879 -0.263717931208339 -1 0.0179012497379471 4135 3916 4058 4109 4119 4389 3246 2683 3491 3684 2528 4392 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 0.918911786623302 0.980423641192348 4235 3959.45454545455 3917 0.222150148442971 3341 0.218725618650952 0.162683442073427 1 0.00419161576238581 4233 3616 3917 3778 3341 3889 4176 4442 4183 3435 4544 4393 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 0.990600877727737 0.999999995401952 3995 3762.63636363636 3918 0.37294053161374 2799 0.160925229217817 -0.171958898911116 -1 6.14475638272475e-10 3994 4471 3918 3680 4583 2799 2868 3994 4503 3437 3142 4394 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 0.135978159110576 0.23380977201353 3770 3698.90909090909 3921 0.014509431958235 1627 0.511401852745991 0.412467658162972 1 0.720386769321452 3767 3114 4253 3019 1627 4273 4578 3760 4383 3993 3921 4395 M121 PID_MTOR_4PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MTOR_4PATHWAY.html mTOR signaling pathway 18832364 51/104 Pathway Interaction Database 0.878859116702268 0.952656447112382 3925 3763.18181818182 3923 0.174603174603175 2444 1.14251740338152 1.14251740338152 1 0.0537126790089523 3923 3990 3481 4238 4069 3292 4367 4171 3564 2444 3856 4396 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 0.00213516972665528 0.0107432214420869 4675 2802.5 3926 0.000237466517190149 154 0.546151384968707 -0.494904876803336 -1 2.39998560531448 4673 181 4455 NA 154 3675 4438 357 1552 4363 4177 4397 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 0.838494417110154 0.921799467694876 4260 3965.81818181818 3928 0.166666666666667 3379 0.303444768298777 -0.295500020601296 -1 0.0239505243432377 4260 3525 4205 3817 4341 3379 4481 4446 3506 3928 3736 4398 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 0.794710641731201 0.888998344987445 2660 3282.36363636364 3928 0.134059887081235 1711 0.31492812487266 -0.304732522516027 -1 0.0359173102407535 2660 3928 2673 3969 4095 1711 4052 2819 4115 3992 2092 4399 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 0.933040924329561 0.98846022445738 3620 3885.09090909091 3930 0.236900893607556 3236 0.301293229972336 0.316939843366695 1 0.00338975687924325 3619 4071 3810 4135 3399 3763 3930 3969 4578 3236 4226 4400 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 0.891073518496821 0.961712793370162 4235 3682.36363636364 3931 0.182539682539683 2578 1.1115341439332 1.1115341439332 1 0.042062015536608 4235 4137 2578 4039 3496 3070 4360 3931 3593 3034 4033 4401 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 0.849715647263787 0.931311135502177 3180 3629.63636363636 3932 0.158267727387455 2070 0.245285025270295 -0.244048672468432 -1 0.0169192927628719 3176 4368 3507 4240 3127 2070 4588 3932 4191 3965 2762 4402 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 0.99021359116607 0.999999995401952 3670 3835.27272727273 3932 0.343356883631671 2891 0.208297291095697 -0.223435793265755 -1 8.25610355096547e-10 3670 4232 3426 4461 3932 3257 4132 3533 4537 4117 2891 4403 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 0.885379224278357 0.958172527706324 4270 3736.72727272727 3932 0.178744131856339 2371 0.998601224481488 -0.998601224481488 -1 0.0413583007080798 4270 4438 2684 3550 3904 4085 4220 2371 3932 4178 3472 4404 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 0.916456839248998 0.978695703901733 2745 3626.54545454545 3934 0.202020195571424 2222 1.29142669460736 1.29142669460736 1 0.0269568151565297 2743 4455 3600 4356 4022 3799 2222 3949 4076 2736 3934 4405 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 0.960158985072255 0.999999995401952 4330 3857.72727272727 3935 0.253968253968254 2849 1.39059940208002 1.39059940208002 1 6.09506689778802e-09 4327 4317 3454 4038 3763 3498 4293 3935 3832 2849 4129 4406 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 0.021030073118333 0.0609551505093897 3075 3382.63636363636 3941 0.00193034857823609 906 1.4630379028186 1.4630379028186 1 3.96741553796007 3073 4087 906 3467 4456 4046 4261 3941 2505 2267 4200 4407 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 0.991469684762736 0.999999995401952 4600 3793.90909090909 3942 0.35150606842098 2718 0.255835884778794 -0.281407349970581 -1 1.03748729516662e-09 4599 3942 3195 4028 4279 2718 4646 3453 4203 3356 3314 4408 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 0.954502900480847 0.99961092867638 4345 3842 3944 0.265827063779441 2454 0.25306101672375 -0.290936988957019 -1 9.54558103789988e-05 4344 2454 4615 3059 3474 4255 3195 3763 3944 4590 4569 4409 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 0.999438241476716 0.999999995401952 4475 4053.09090909091 3945 0.526897800592138 3374 0.303902938701931 -0.282871605056529 -1 1.25171955393533e-09 4474 3911 4201 3793 4628 3904 3374 3998 4433 3923 3945 4410 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 0.143170964671981 0.243786024873875 4405 3503.90909090909 3945 0.0153329224051605 1662 0.427661514887977 -0.266408682592501 -1 0.585105203408547 4402 3526 4217 3321 1662 3958 4513 2361 2204 3945 4434 4411 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 0.891288754723551 0.961712793370162 3455 3648 3945 0.199009349110329 2278 0.276763756325545 -0.128730993805062 -1 0.0104731297696009 3454 3945 4226 3841 3255 4055 2278 3066 3993 3953 4062 4412 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 0.933575174018083 0.98846022445738 4485 3833.09090909091 3948 0.237511948441652 2614 0.277947983074327 -0.314519178240747 -1 0.00312710672385685 4482 4397 3948 4266 4540 2846 3470 2614 4263 3491 3847 4413 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 0.210318143553892 0.323981203383806 4240 3596.36363636364 3948 0.0233359187228341 1721 1.13830914051267 1.13830914051267 1 1.2435833366252 4236 4341 4629 3503 1892 4307 3948 2907 3603 1721 4473 4414 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 0.825875917969607 0.913394985037899 3665 3725.45454545455 3949 0.160373989497698 2284 0.214879062430297 -0.200192585281867 -1 0.018867884614624 4436 2892 4047 3390 4104 3664 4419 2284 4130 3665 3949 4415 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 0.0180029236172595 0.0540087708517784 4005 2922.09090909091 3949 0.00181504559278336 579 1.26530448687738 1.26530448687738 1 3.57960251888433 4003 1028 4405 2089 579 4443 3949 4559 1559 1307 4222 4416 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 0.968686883175159 0.999999995401952 4525 3783.63636363636 3950 0.270126080557332 2642 0.316148958711634 -0.280572785752356 -1 1.30629940257345e-09 4521 3032 2642 3600 4638 4245 4283 2732 4409 3568 3950 4417 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 0.768733897840249 0.866142593238617 4265 3665.72727272727 3951 0.124629315666229 1934 1.14334471693578 1.24866952053185 1 0.159263087268047 4265 4542 1934 4245 3436 3330 4413 3951 3969 2449 3789 4418 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 0.692053852342561 0.797777208383085 3730 3875.45454545455 3955 0.111111111111111 3172 0.73426504557095 0.73426504557095 1 0.160798782596266 3726 3705 4174 3199 4331 3955 4061 4316 3172 3887 4104 4419 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 0.170251715239145 0.273875570755452 3960 3332.36363636364 3956 0.0168235042347003 1714 0.259981073895061 -0.215115328557401 -1 0.32636431336154 3960 4027 3121 4024 1714 1719 4011 3956 4300 3509 2315 4420 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 0.999256272183612 0.999999995401952 4680 4035.45454545455 3956 0.480502941088175 3416 0.16050414900761 -0.176723230960758 -1 6.1259890655724e-10 4678 4440 3501 4349 3956 3556 4294 3416 4638 3704 3858 4421 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 0.987646006853145 0.999999995401952 3565 3893.81818181818 3957 0.355562601782428 3052 0.284020843904386 -0.326295540971099 -1 1.16310613310153e-09 3564 4497 4473 3957 4016 3291 3578 3052 4385 4380 3639 4422 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 0.475291784065615 0.595990714512035 4285 3684.36363636364 3958 0.0624557244567046 2515 0.346491138565638 -0.249771707454097 -1 0.173816775350146 4283 3249 4231 2945 2515 4371 2949 3546 3964 3958 4517 4423 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 0.993153147291999 0.999999995401952 4125 3904 3958 0.364337702569073 2707 0.230909030663467 -0.224485368392922 -1 9.26389654989555e-10 4122 4565 2707 4497 3734 3384 3958 3366 4653 4492 3466 4424 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 0.980714389232142 0.999999995401952 4420 3881.72727272727 3959 0.301587301587302 3344 0.989745402399581 -0.989745402399581 -1 4.30848230857371e-09 4420 4294 3411 4350 3998 3911 3375 3448 3959 4189 3344 4425 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 0.816521443770307 0.906472278016503 4535 3663.45454545455 3960 0.142857142857143 2385 1.29142669460736 1.29142669460736 1 0.122919914690195 4535 3279 3431 4125 3983 2743 4161 4317 3379 2385 3960 4426 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 0.963099518004121 0.999999995401952 4165 3882 3960 0.259150170341648 2450 0.207317721361907 -0.206118669715825 -1 8.21244465790605e-10 4164 4667 3617 4407 3884 3394 2450 3908 4187 3960 4064 4427 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 0.650526422053442 0.76247293990556 2580 3519 3962 0.0997949713349561 1493 0.194003082521469 -0.239788942804534 -1 0.0509968533655855 2578 4348 4236 4491 3959 1493 2352 4486 4670 3962 2134 4428 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 0.190037523010571 0.299433703035486 3075 3466.63636363636 3962 0.0189782700304175 1779 1.09724913661829 1.09724913661829 1 1.28252787043168 3072 4376 2231 4332 1779 4590 2723 4384 4156 2528 3962 4429 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 0.564854987527216 0.682545247950627 4355 3705 3963 0.0728531089094159 1726 1.37414648862793 1.37414648862793 1 0.508717458352015 4352 4540 1726 3417 3963 3573 4355 4065 3547 2922 4295 4430 M8560 BIOCARTA_G2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G2_PATHWAY.html Cell Cycle: G2/M Checkpoint 20/43 BioCarta 0.992176927850876 0.999999995401952 4580 3644.90909090909 3965 0.356588455994912 2377 1.05077947290469 1.05077947290469 1 4.58050785869515e-09 4578 3997 2463 3747 4120 3290 3065 4364 4128 2377 3965 4431 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 0.241256065308492 0.355175659191804 4080 3621.63636363636 3965 0.0247868100197427 1393 0.343492652853839 -0.366304915119713 -1 0.344652618645191 4385 3318 1393 3797 3986 3965 3073 4080 4490 4079 3272 4432 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 0.0548104828578274 0.123422355921086 3965 3753.63636363636 3965 0.00511142148591699 1064 0.4151421291861 -0.41644477566257 -1 0.841883588735453 3965 3345 1064 3796 3874 4317 3177 4302 4291 4561 4598 4433 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 0.99969380125868 0.999999995401952 3945 3957.63636363636 3968 0.520768050732292 3020 0.242698198179205 -0.231142608752089 -1 9.78933336779119e-10 3968 3941 3020 4144 4023 3944 4091 3570 4394 3787 4652 4434 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 0.980714389232142 0.999999995401952 3970 4020.27272727273 3969 0.301587301587302 3496 0.234513992997605 -0.237759630216092 -1 9.4245677707391e-10 3969 3903 3496 4256 3752 4381 4328 4113 3957 3515 4553 4435 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 0.994416491485565 0.999999995401952 3160 3874.81818181818 3970 0.404761904761905 3159 0.219514110079668 0.327556190062541 1 8.75603110445741e-10 3159 4535 4203 4012 4122 3970 3850 3264 4177 3925 3406 4436 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 0.900849582143098 0.96887333989501 4155 3641.63636363636 3971 0.206349206349206 1864 0.342944475199914 -0.30703109802924 -1 0.0105115945037347 4153 1864 4029 2840 4012 3323 4190 4372 3668 3636 3971 4437 M7739 BIOCARTA_PYK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PYK2_PATHWAY.html Links between Pyk2 and Map Kinases 20/47 BioCarta 0.775485941583084 0.872282074473915 4470 3788.27272727273 3973 0.126984126984127 2379 1.14672566625037 1.14672566625037 1 0.151882930329777 4467 4432 3350 3973 4619 3422 4168 3209 3291 2379 4361 4438 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 0.982992683943975 0.999999995401952 3685 3906.90909090909 3973 0.30952380952381 2804 0.210708550576186 -0.266450778223008 -1 8.36357208144971e-10 3682 4191 3567 4383 4529 2804 4575 4541 3973 3498 3233 4439 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 0.960109383155593 0.999999995401952 3670 3760.90909090909 3974 0.275418777355401 2509 0.299897902731234 0.326019426179526 1 1.23386932529797e-09 3667 2784 4175 3610 4328 3974 2509 4108 4257 3890 4068 4440 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 0.80541090720264 0.897753451748709 4495 3822.63636363636 3975 0.138263658684861 3025 0.258268180814823 0.163359804736658 1 0.0270019036026046 4495 3880 3025 4002 3037 3354 4059 3975 4346 4382 3494 4441 M105 PID_TELOMERASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TELOMERASE_PATHWAY.html Regulation of Telomerase 18832364 41/89 Pathway Interaction Database 0.56572808069008 0.683071833577355 3530 3882.18181818182 3976 0.0730223784629607 2605 0.958306879088019 0.958306879088019 1 0.354054712425098 3529 4664 3439 4408 2605 4416 3677 4595 3976 2856 4539 4442 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 0.81425766650287 0.90610577659284 3850 3786.54545454545 3976 0.141901082110886 1754 0.264326455792449 -0.254776220035632 -1 0.0252625981596963 3848 4510 3535 3976 4090 1754 4476 4167 3656 4453 3187 4443 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 0.00391672636264775 0.0170415782129688 3780 3699.36363636364 3978 0.000356701532591115 716 0.982363058786336 0.982363058786336 1 3.87752165536669 3778 4315 716 4044 4215 3688 4562 3896 4353 3148 3978 4444 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 0.975368714677481 0.999999995401952 4565 3995.36363636364 3980 0.30952380952381 3183 0.207212036152957 -0.15449579983248 -1 8.20773432532188e-10 4563 3183 4127 3776 4302 4485 3801 3759 3980 3815 4158 4445 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 0.946596086373448 0.995678846407626 3625 3961.45454545455 3980 0.253968253968254 3329 0.460362929691006 0.600985128484183 1 0.00193243062619137 3623 3329 4287 3703 4470 3807 4330 3980 3824 4039 4184 4446 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 0.319732204030256 0.440213168916642 3285 3579.27272727273 3980 0.0377941539982944 2184 0.696516803986324 0.390180435788397 1 0.55395187366398 3283 3078 4468 2492 2184 4627 4065 4220 2598 4377 3980 4447 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 0.692053852342561 0.797777208383085 4660 3848.45454545455 3981 0.111111111111111 2958 0.461890253064473 -0.41528149787014 -1 0.101150655074568 4657 3218 3981 3819 4206 2958 4189 4530 3167 3534 4074 4448 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 0.111506339054693 0.198224091354435 2560 3560.45454545455 3981 0.0106904255791593 1203 0.31143066107703 -0.323599180539456 -1 0.488539400040274 2557 3988 1203 3532 4195 3224 3981 4015 4496 4469 3505 4449 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 0.801535257937178 0.895100626183042 4515 3653.45454545455 3981 0.136717309410092 1733 0.230816707304306 -0.253725951878011 -1 0.0247939581379139 3287 3544 3459 4064 4512 1733 4361 4514 3981 4675 2058 4450 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 0.999857875616158 0.999999995401952 4160 4020.81818181818 3984 0.587649182894724 3526 0.184889303981596 -0.168458241688486 -1 7.21282222968844e-10 4159 3984 3974 3674 4167 3669 4567 3692 4630 3526 4187 4451 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 0.470078661721897 0.590718318269995 4380 3793.27272727273 3984 0.0560949496607494 2437 0.277500709830941 -0.212942191558937 -1 0.141597974165723 4567 4377 2880 4344 2437 4379 3097 4050 3891 3984 3720 4452 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 0.49430524396364 0.615549926445287 4180 3721.18181818182 3984 0.06010190754629 1661 0.452855307411088 -0.467054254170305 -1 0.21299981438138 4176 3108 1661 3653 3984 4139 4511 3055 3854 4650 4142 4453 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 0.991917884165381 0.999999995401952 4085 3848.54545454545 3987 0.354680176405963 2635 0.273713009873331 -0.316806017827152 -1 1.11716467450877e-09 4083 4332 2635 4223 3700 3647 3684 4158 4570 3315 3987 4454 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 0.732782658058693 0.83466687789573 4220 3673.54545454545 3989 0.113054804710576 2515 0.354666070568009 -0.306806043964533 -1 0.0621292244230639 4220 2666 2515 3426 2902 4268 2829 4662 4327 4605 3989 4455 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 0.899282779447187 0.968076982423505 2695 3826 3991 0.188342013098249 2144 0.134403238503493 0.125885774105314 1 0.00422672051360638 2694 4654 3780 4484 3648 3991 2144 4328 4574 3758 4031 4456 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 0.973402363843062 0.999999995401952 4460 3857.54545454545 3991 0.304200192790907 2616 0.358312377375011 -0.289825460354129 -1 1.49421947839316e-09 4456 3776 4252 3883 4363 3746 2616 2976 4368 3991 4006 4457 M6831 BIOCARTA_KREB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KREB_PATHWAY.html The Citric Acid Cycle 4/11 BioCarta 0.990520723309469 0.999999995401952 2935 3776.45454545455 3993 0.372407825047552 2859 0.280652029003521 -0.230750516348172 -1 1.14809150735101e-09 2931 4200 3879 4375 4044 4019 2859 3993 4419 3335 3487 4458 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 0.921309192177062 0.981194289668571 3870 3715.45454545455 3996 0.206349206349206 2284 1.73041933125535 1.73041933125535 1 0.0318435103300514 3868 4024 2456 2917 4343 4353 3996 4573 3676 2284 4380 4459 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 0.985023615986936 0.999999995401952 4515 3861.45454545455 3998 0.317460317460317 2448 0.332374008382339 -0.307360134914329 -1 1.37861357113364e-09 4515 3838 2448 3959 4261 2947 4579 4421 3998 4037 3473 4460 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 0.996772412416914 0.999999995401952 4000 4003.18181818182 3998 0.436507936507937 3420 0.392960947152563 -0.471374560391635 -1 1.64864627930381e-09 3998 3523 4679 4376 4049 3969 3536 3420 4231 4670 3584 4461 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 0.980003901083321 0.999999995401952 4565 3868.45454545455 3999 0.299286508143709 2923 0.229524683074444 -0.258562185635061 -1 9.20219692682487e-10 4564 4387 2923 4276 3572 3253 3516 4081 4485 3999 3497 4462 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 0.956930203251513 0.999999995401952 4020 3925.81818181818 4002 0.26984126984127 3504 0.348088760626903 -0.363873630454869 -1 1.44865337167409e-09 4020 3738 4002 3504 4014 3632 4519 4233 3876 3586 4060 4463 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 0.993240511078093 0.999999995401952 4005 3809.54545454545 4002 0.365079365079365 2631 0.28188841703651 -0.268713447696415 -1 1.15360202192187e-09 4346 2631 3392 3725 4003 3648 4366 3411 4087 4002 4294 4464 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 0.366781496658606 0.486894644006297 2875 3326.18181818182 4004 0.0446657244043837 1283 0.349105451106824 -0.384938593709349 -1 0.243543494986374 2872 4346 4261 4607 4439 1921 1283 2488 4158 4004 2209 4465 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 0.0324828230014784 0.0829506858773448 3815 3568.27272727273 4004 0.00299750758832534 978 1.73041933125535 1.73041933125535 1 4.17569648260059 3813 3474 978 2746 4401 4004 4514 4092 4315 2718 4196 4466 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 0.902487371923958 0.969299982772328 4180 3688.81818181818 4006 0.190724408366476 2159 0.610681132932434 0.610681132932434 1 0.0184573900209964 4177 3019 3561 2916 4494 4119 2159 4597 4006 3480 4049 4467 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 0.96908319439447 0.999999995401952 4445 4136.63636363636 4007 0.293650793650794 3462 0.311181408653306 -0.357009556579696 -1 1.28415930072232e-09 4444 4007 3932 3838 4448 3945 4557 4581 3940 3462 4349 4468 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 0.191032065018368 0.300293947224446 2805 3761.18181818182 4007 0.0190878387757791 1335 0.271060111094233 -0.283040312768466 -1 0.31607689048292 2805 4588 1335 4572 4296 3475 4191 4007 4584 3793 3727 4469 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 0.943712354754118 0.993760920084898 4010 3911.81818181818 4010 0.23015873015873 2548 1.39059940208002 1.39059940208002 1 0.00843615948939046 4010 4546 3651 4243 3994 3363 4487 4340 3771 2548 4077 4470 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 0.386086746459241 0.507632574048261 4035 3309.90909090909 4010 0.0476190476190476 1715 1.23081245443276 -0.874649861425705 -1 0.808879369670843 4031 3074 4553 2238 4019 4010 4103 2169 2312 1715 4185 4471 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 0.858169883154676 0.937822778093007 3425 3703.27272727273 4011 0.177422462100597 2232 0.308087094585636 -0.228925797973827 -1 0.01917051270144 3421 4343 4540 4011 4685 2232 2417 4567 3805 4470 2245 4472 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 0.568524949221977 0.685918617933621 4365 3752.63636363636 4012 0.0806189057753348 2658 0.218256618826412 -0.195208938098173 -1 0.0797569184615962 4364 4196 4012 3803 2658 2991 2776 4128 4568 3610 4173 4473 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 0.963779718014981 0.999999995401952 4630 3950.90909090909 4012 0.260402182963576 2454 0.230179214720219 0.163122356786346 1 9.2313690481565e-10 4630 4466 2808 4453 3995 3930 2454 4012 4506 4000 4206 4474 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 0.980479820544289 0.999999995401952 4555 4021.45454545455 4014 0.325396825396825 2923 0.376686850585722 -0.311116383918003 -1 1.57611351138112e-09 4555 2923 4171 3828 4178 3754 4443 4006 4014 3880 4484 4475 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 0.986384898950065 0.999999995401952 3875 3784.54545454545 4016 0.34926811531679 2885 0.214522442213825 -0.264319384943777 -1 8.53355516831353e-10 3872 4445 4301 4016 4342 2885 2946 3035 4615 4053 3120 4476 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 0.703591024317746 0.807896971319029 2155 3631.09090909091 4018 0.104655597629051 1870 0.872339790410637 0.872339790410637 1 0.180377610134131 2155 4021 1870 3833 4539 4587 3122 4418 4427 4018 2952 4477 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 0.0277191862400653 0.0739704480187619 4135 2945.72727272727 4018 0.00280711398682022 175 0.766631130249494 -0.547115261877079 -1 1.93511260713412 4131 175 4550 416 760 4575 4018 3598 1038 4486 4656 4478 M3896 KEGG_INOSITOL_PHOSPHATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INOSITOL_PHOSPHATE_METABOLISM.html Inositol phosphate metabolism 30/55 KEGG 0.992250758218665 0.999999995401952 4300 3948.54545454545 4019 0.357142857142857 3153 0.268293378617115 0.186622867071945 1 1.09300967121755e-09 4297 4019 3153 4006 4490 3529 4322 4358 4083 3177 4000 4479 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 0.999146851798674 0.999999995401952 3380 3885.81818181818 4019 0.473980038187989 3309 0.217408045433049 -0.225963489422318 -1 8.66216494259952e-10 4292 3408 3616 4019 4553 3376 4109 3376 4494 4192 3309 4480 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 0.925085915180653 0.984098206251201 4075 3873.72727272727 4021 0.209889944550771 2171 0.263361287904517 -0.294835204058541 -1 0.00409202274446275 4071 4150 2171 3864 4385 3572 4242 3704 4594 3837 4021 4481 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 0.936265840597278 0.989507236660202 4645 3780.90909090909 4023 0.240658342000039 2381 0.209619680655863 -0.226793703179244 -1 0.00214325712954278 4643 4194 4023 4026 4057 3234 2381 3484 4166 3623 3759 4482 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 0.950435952164341 0.997818994396395 2990 3741.27272727273 4023 0.259514298721189 2611 0.297394364529095 -0.327886242166358 -1 0.000629400873652749 2989 4241 4146 4023 4050 3120 4344 3186 4601 3843 2611 4483 M18448 REACTOME_GLUCOSE_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_TRANSPORT.html Genes involved in Glucose transport 19/44 Reactome 0.713199983469702 0.816729013328207 4025 3801.27272727273 4025 0.107333954728871 2864 0.300603957688842 -0.271287031252825 -1 0.0589891159243537 4025 2879 3098 4059 2864 3624 4409 4649 4084 3640 4483 4484 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 0.0765897756730953 0.156982736433532 4375 2699.90909090909 4027 0.00793650793650794 18 1.62518411452666 1.62518411452666 1 2.91687733628189 4372 637 4470 456 1431 4027 4568 4155 18 1194 4371 4485 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 0.6954985110626 0.800959946630461 3710 3726.90909090909 4027 0.102460473005194 1910 0.342996197533599 -0.187720412400372 -1 0.0737899540490585 3706 4382 1910 4027 3503 4532 3744 1949 4081 4643 4519 4486 M853 REACTOME_MYOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MYOGENESIS.html Genes involved in Myogenesis 17/38 Reactome 0.974853520105573 0.999999995401952 4185 3898.63636363636 4030 0.284534270121942 2787 0.229685386374159 0.213133324420358 1 9.20935938594804e-10 4185 4381 3196 4342 3952 3578 4030 2787 4499 3647 4288 4487 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 0.933284547569581 0.98846022445738 4035 3802.45454545455 4032 0.218171506453903 2554 0.345189973993316 0.389912500076165 1 0.00388362557501833 4075 4329 2554 4359 3325 4120 4033 3674 4032 3368 3958 4488 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 0.569226376032234 0.686411425138201 4435 3835.45454545455 4032 0.0737037229886049 2612 0.201901123403528 0.155030175777917 1 0.0736396180041514 4435 3902 3500 4204 2612 4028 4288 2659 4443 4087 4032 4489 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 0.0969119742072437 0.177048542352883 3840 3684.18181818182 4037 0.010141746989476 1415 0.296941913737647 0.27425680309404 1 0.498328307552988 3836 4037 4108 4379 1415 4603 3430 2211 4366 3788 4353 4490 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 0.270655388235677 0.391447885577896 3350 3493.45454545455 4038 0.0310680475044375 1296 0.470552903854205 0.47154422118428 1 0.42778957467911 3346 2302 4348 2681 4390 4344 4194 1296 4038 4108 3381 4491 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 0.628509822512544 0.742237154307909 4540 3878 4038 0.0942783824312858 2789 0.49295952323979 -0.431921305818508 -1 0.142435220913286 4537 4038 4560 3329 2789 4165 4581 2993 3695 4508 3463 4492 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 0.962214689415515 0.999999995401952 3765 3763.27272727273 4039 0.257552538075831 2270 1.2815413473491 1.2815413473491 1 5.60900104820866e-09 3765 4179 2270 3415 4133 3726 4551 4169 4297 2852 4039 4493 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 0.524338477672995 0.643038499444034 3625 3697.45454545455 4040 0.0653189096829607 2542 0.886958345514679 -0.55936453995665 -1 0.379618745810965 3621 4211 2605 4159 2542 4298 3593 4040 4185 2941 4477 4494 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 0.310075970547294 0.429876126809028 2640 3806.27272727273 4042 0.0331801239709656 1478 0.266512364599418 -0.30207834373421 -1 0.21810042413987 2637 4366 1478 4042 4493 3634 4416 3873 4587 4682 3661 4495 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 0.996406113259591 0.999999995401952 4060 4113 4051 0.4304177607507 3409 0.379544679718366 -0.314879788992731 -1 1.58885070120849e-09 4058 3883 4051 3998 3872 4527 3409 4464 4629 3674 4678 4496 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 0.998875257134218 0.999999995401952 4645 4147.72727272727 4052 0.492886321877632 3696 0.137995740836306 -0.143821323594718 -1 5.12280149107755e-10 4641 4442 4065 4225 3980 4052 4006 4003 4654 3696 3861 4497 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 0.666429430758931 0.775117085755398 4055 3714.90909090909 4052 0.0949898924086386 2417 0.653320054436723 0.653320054436723 1 0.161320298159735 4052 4295 2417 3686 2796 3037 4611 4084 4388 4191 3307 4498 M7721 BIOCARTA_EIF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF_PATHWAY.html Eukaryotic protein translation 10/40 BioCarta 0.326912997633081 0.44802139631311 4055 3735 4053 0.0353492429418825 2143 0.191493293766013 -0.220315897814195 -1 0.149034433582239 4053 4468 3613 4146 2143 4517 2349 3910 4171 3265 4450 4499 M994 REACTOME_DSCAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DSCAM_INTERACTIONS.html Genes involved in DSCAM interactions 7/19 Reactome 0.214139132665174 0.327605607466211 4480 3184.45454545455 4053 0.0238095238095238 854 1.14672566625037 1.14672566625037 1 1.24041244807521 4476 854 4068 1395 4053 4474 3705 4654 1628 1510 4212 4500 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 0.998163526420609 0.999999995401952 4055 3959.54545454545 4054 0.436010089196815 3187 0.244850031084077 -0.185331241752055 -1 9.88523939615746e-10 4054 4067 3187 4331 4038 3943 4291 3280 4435 3389 4540 4501 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 0.934081566336537 0.98846022445738 4465 4024.18181818182 4054 0.238095238095238 3197 0.443068667602371 -0.289753647371759 -1 0.0049848284964416 3197 3948 4464 4249 4054 3866 4463 4067 3799 4373 3786 4502 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 0.946596086373448 0.995678846407626 4360 4134.18181818182 4057 0.253968253968254 3648 0.194972101090179 -0.203048743953128 -1 0.000818419572533843 4360 3648 4043 4057 4598 4228 4541 3912 3827 3661 4601 4503 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 0.912207156538424 0.97526870534772 4200 3893.72727272727 4060 0.198412698412698 2545 0.294699932209959 -0.337938826280545 -1 0.00715347815310723 4199 3968 3327 3905 4060 4452 4258 2545 3648 4203 4266 4504 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 0.992252573160635 0.999999995401952 3700 3930.27272727273 4061 0.384942457890929 2902 0.217906317665996 0.225917457077967 1 8.68437266644226e-10 3698 3420 4061 4126 4316 4453 2902 4331 4324 3689 3913 4505 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 0.351194509854888 0.473991207713135 1750 3030.90909090909 4065 0.0423397714660338 1240 0.272223865707555 0.369982089485276 1 0.196996524775052 1747 4195 4447 4423 4065 1240 1257 1716 4456 4350 1444 4506 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 0.972017821556483 0.999999995401952 3200 3888.36363636364 4070 0.300660349467057 2847 0.340057661648798 -0.193089161416146 -1 1.41285919803437e-09 3198 4070 4618 3403 4388 4451 3265 2847 4228 4594 3710 4507 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 0.929027482837731 0.986602125278769 3700 3856.18181818182 4071 0.232445855868834 2500 0.249254734092012 -0.224965472568991 -1 0.00325888372116204 3699 4240 4425 4071 3377 3574 2500 4265 4150 4318 3799 4508 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 0.0557067762499281 0.124840723819781 3660 3763.54545454545 4074 0.00519722406166362 1067 1.06105082832197 1.06105082832197 1 2.13999608644313 3656 4263 1067 3808 4153 4644 3803 4074 4522 2821 4588 4509 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 0.689685894515795 0.797401456131511 2870 3562 4074 0.110429951983666 1776 0.267402741763982 -0.267402741763982 -1 0.0586813941515995 2867 4074 4544 4317 2885 1776 3160 4222 4652 4479 2206 4510 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 0.8926258176 0.962679995690127 4600 3644.81818181818 4076 0.2 1805 0.209638510779349 -0.183242455979577 -1 0.00772875358375786 4596 1805 4320 2949 4213 3106 3039 4136 4167 4076 3686 4511 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 0.978210715749944 0.999999995401952 3995 4022.18181818182 4076 0.293794365004377 2342 0.231222899842209 -0.204553036358131 -1 9.27788552937977e-10 3992 4600 2342 4508 4076 3729 4544 3607 4579 4490 3777 4512 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 0.000269922279163639 0.00211868643243018 4440 3651.90909090909 4077 2.45414001947928e-05 489 1.34233833141235 1.43064344543844 1 8.01109937043044 4437 4077 489 3367 4228 4038 4574 4299 3861 2419 4382 4513 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 0.649582398914856 0.76174752785661 3110 3736.81818181818 4080 0.090927083452235 1642 0.693810091349027 0.693810091349027 1 0.183019358348375 3109 4598 3286 4443 4678 4080 1642 2530 4420 4356 3963 4514 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 0.241659553412378 0.355546834314098 4255 3289.81818181818 4080 0.0248339671517561 1395 0.982440522443698 -0.786711002772732 -1 0.984763528948705 4255 4481 1395 4083 2498 2045 4383 4637 4080 1585 2746 4515 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 0.828932189583757 0.916558810851696 3680 3786.81818181818 4081 0.148297294203461 1998 0.337949805076738 0.362130800057672 1 0.0285416461506389 3678 4462 1998 4069 3184 4178 2836 4196 4386 4587 4081 4516 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 0.999979749224984 0.999999995401952 3895 4220.09090909091 4084 0.660652882238026 3738 0.182454970699779 0.14639345044584 1 7.10432531236259e-10 3894 3915 4084 4015 4661 4581 3758 4624 4588 3738 4563 4517 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 0.981707346833934 0.999999995401952 4560 3930.27272727273 4085 0.329764125196878 2956 0.228963385710863 -0.248144365959073 -1 9.1771802070082e-10 4558 4161 4245 4321 3651 4099 3363 2956 4085 3982 3812 4518 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 0.955240661249004 0.99961092867638 4585 3896.81818181818 4086 0.246031746031746 2697 0.299153465155666 0.291550446489583 1 0.000112842118277446 4584 3104 3337 2697 4333 4242 4488 4508 3807 3679 4086 4519 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 0.96908319439447 0.999999995401952 4050 3876.72727272727 4086 0.293650793650794 2719 0.509957405609988 0.597573852115177 1 2.17009316480158e-09 4047 2781 4328 3327 4430 4368 2719 4257 3922 4086 4379 4520 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 0.842000839817822 0.924898250207763 4035 3917.9 4087 0.185367669455849 3189 0.287187081563147 -0.262762512201988 -1 0.02173309362647 4034 3189 4360 NA 3220 4556 3257 3650 4382 4140 4391 4521 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 0.993240511078093 0.999999995401952 4070 4012.45454545455 4090 0.365079365079365 2809 0.298537458767331 -0.326188147581209 -1 1.22780590015481e-09 4070 4330 2809 4284 3943 3342 4572 4105 4090 4063 4529 4522 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 0.997094909560606 0.999999995401952 2710 3791.18181818182 4091 0.411998883596631 2707 0.78209152973017 -0.78209152973017 -1 3.38298023276158e-09 2707 4091 2801 3634 4271 3180 4510 4132 4426 4543 3408 4523 M11773 REACTOME_PECAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PECAM1_INTERACTIONS.html Genes involved in PECAM1 interactions 8/17 Reactome 0.863727966370256 0.942797402844402 4120 3844.09090909091 4092 0.180704303399292 2110 0.242531181421962 0.18549743504548 1 0.0138476226329144 4119 4308 3966 4092 4209 3792 2110 3077 4560 3517 4535 4524 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 0.803980542435745 0.896983495368286 3550 3908.36363636364 4092 0.137689722900722 2999 1.10858603309022 1.10858603309022 1 0.116824516238573 3550 4656 3220 4476 3034 4092 3482 4397 4457 2999 4629 4525 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 0.957351816938788 0.999999995401952 3560 3879.54545454545 4093 0.249336147973093 2412 0.226145136072568 0.223927128830224 1 9.05157234538401e-10 3558 4665 3550 4509 3688 4158 2412 2924 4093 4518 4600 4526 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 0.251426185371998 0.368182220204119 3835 3900.45454545455 4096 0.0259824443340024 1411 0.237708308546313 -0.282265502978215 -1 0.230224101304009 3832 4280 1411 4096 4356 3884 4576 3789 4599 3913 4169 4527 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 0.99938831159193 0.999999995401952 4060 4096.72727272727 4098 0.522852090917227 3359 0.0728889430837564 -0.100014985915767 -1 2.22102673990815e-10 4059 4608 4359 4542 4098 3831 3359 3849 4675 4139 3545 4528 M46 PID_ATR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATR_PATHWAY.html ATR signaling pathway 18832364 29/52 Pathway Interaction Database 0.998653797993313 0.999999995401952 2875 3906.18181818182 4100 0.451710383580378 2875 0.232904866392349 0.204333648487241 1 9.35284986852691e-10 2875 4222 3100 4100 4151 4591 3838 3874 4549 3370 4298 4529 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 0.603717689404631 0.717661362899568 4305 3927.63636363636 4101 0.0884080767469807 2722 0.260128945735218 0.162085851220379 1 0.0836514059023338 4304 4101 4614 3851 2722 3395 4107 3825 4365 4589 3331 4530 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 0.73569887693763 0.836768188672265 4110 3836 4106 0.12459323014951 2072 0.296378039643466 0.150072974923953 1 0.0511961820076733 4106 4010 4321 4185 4676 2894 4310 2072 4201 4078 3343 4531 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 0.978941741456183 0.999999995401952 4110 3954.45454545455 4107 0.320260910663081 3185 0.368493827720739 0.348453624597607 1 1.53959765173814e-09 4107 3185 4178 3240 3613 4206 3480 4679 4466 3893 4452 4532 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 0.994113976280303 0.999999995401952 4555 3905.18181818182 4111 0.373015873015873 2694 1.29142669460736 1.29142669460736 1 5.65305950611285e-09 4554 4141 3315 3975 3806 4529 3245 4390 4111 2694 4197 4533 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 0.976037008886707 0.999999995401952 3270 4003.63636363636 4111 0.311420478312838 3268 0.209690945540649 -0.159895137327728 -1 8.31821797556962e-10 3268 4238 4674 4269 3597 4111 3491 3380 4529 4658 3825 4534 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 0.999947317181426 0.999999995401952 4115 4151.27272727273 4113 0.626606373887347 3646 0.11045738254837 -0.101034049350131 -1 3.89543176123302e-10 4113 4310 4088 4333 4428 3646 4390 4026 4637 3751 3942 4535 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 0.940634982288152 0.992080919874473 4395 3932.81818181818 4118 0.246031746031746 2944 0.257309286638843 -0.196271700941123 -1 0.00198298463451233 4391 3578 4385 3710 4588 2944 4203 3340 3804 4200 4118 4536 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 0.997264838759285 0.999999995401952 3115 3957.09090909091 4118 0.415212004984846 2573 0.211984741058022 -0.236195741088461 -1 8.42045120076917e-10 3112 4487 2573 4242 4118 3642 4658 4021 4616 4229 3830 4537 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 0.977408490260954 0.999999995401952 4470 3815.90909090909 4119 0.315466785612387 2517 0.353999161622264 -0.389163955690828 -1 1.47499570914061e-09 4470 2517 4210 3536 3602 2849 4214 4205 4321 3932 4119 4538 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 0.999742039672145 0.999999995401952 3810 4106.45454545455 4119 0.52817870507412 3496 0.759980613502947 -0.759980613502947 -1 3.2844330754014e-09 3807 4587 3533 4477 4037 3496 4677 4250 4472 4119 3716 4539 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 0.912784548526958 0.975663411130777 3420 3960.09090909091 4120 0.216463299695865 3237 0.168699250460057 0.188636180923379 1 0.00402880010588211 3419 4528 4431 4436 3317 3449 3237 4120 4585 4324 3715 4540 M523 KEGG_THYROID_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_THYROID_CANCER.html Thyroid cancer 19/43 KEGG 0.964917814973681 0.999999995401952 4125 3799.81818181818 4121 0.262545638307017 2282 0.304775202634027 -0.227318625381968 -1 1.25560718708868e-09 4121 4435 2282 4158 4219 3714 3820 3099 4196 3230 4524 4541 M3158 REACTOME_S_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_S_PHASE.html Genes involved in S Phase 63/124 Reactome 0.921309192177062 0.981194289668571 4220 3927.45454545455 4123 0.206349206349206 2687 1.39059940208002 1.39059940208002 1 0.0255900784222366 4217 4624 3606 4361 3851 3421 4415 4212 3685 2687 4123 4542 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 0.850621352955467 0.931311135502177 4620 3823.90909090909 4123 0.158730158730159 2259 1.80148879049739 1.80148879049739 1 0.124263258149511 4619 4265 2259 4576 4403 4123 4480 3556 3473 2716 3593 4543 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 0.96194028883667 0.999999995401952 4510 3918.54545454545 4124 0.278815226505694 3120 0.32762226090843 -0.163083961759665 -1 1.35743528972572e-09 4508 4164 4256 4184 3516 4124 3263 3120 4470 3997 3502 4544 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 0.364488442661269 0.484124955303488 4545 3976 4124 0.044320334709946 2286 0.264912082272249 -0.195768163114144 -1 0.186273256616687 4545 3522 4401 4124 2286 4021 4238 4041 4399 4242 3917 4545 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 0.275742742869669 0.39623750171336 4690 3293.54545454545 4124 0.0317460317460317 1059 1.3261771808088 -1.3261771808088 -1 1.19002243193271 4686 2521 4619 1808 2388 4235 4411 4536 1842 1059 4124 4546 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 0.99139981453481 0.999999995401952 4165 3965 4129 0.351024975704851 2713 0.791140711360448 -0.791140711360448 -1 3.42331194570082e-09 4163 4621 3537 4517 3699 2713 4166 4027 4129 4568 3475 4547 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 0.066650977021751 0.142810461053464 4435 3419.81818181818 4131 0.00687387224463039 741 0.473745802275883 -0.363337426245684 -1 0.893727167736471 4432 741 4442 2501 1205 4366 4043 4131 2844 4338 4575 4548 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 0.628849626981053 0.742317303120099 3720 3806.36363636364 4132 0.086164189304005 2632 0.200158093553517 -0.194728997020588 -1 0.0578125257327225 3716 4518 3466 4622 2704 2632 4281 4255 4647 4132 2897 4549 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 0.0172320197488125 0.0522310766771896 3675 3782.27272727273 4133 0.00157895386525209 882 1.51746024606229 1.51746024606229 1 4.34219138263227 3671 4417 882 3751 4225 4280 4133 4090 4536 2961 4659 4550 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 0.997190465291851 0.999999995401952 3895 4245.63636363636 4133 0.444270514146584 3634 0.0976604878578264 0.0973226499443154 1 3.32508108836586e-10 3634 4681 4617 4577 3897 4133 3893 4101 4686 4592 3891 4551 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 0.972143872465712 0.999999995401952 3460 4005.09090909091 4134 0.300976020403602 3240 0.212129799392691 0.188893365993029 1 8.4269163722646e-10 3460 4134 4667 4574 3577 3277 3240 4409 4645 4648 3425 4552 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 0.971159012971408 0.999999995401952 3305 3878.81818181818 4137 0.275562505413112 2511 0.26822123908625 0.296763943060276 1 1.09268814923144e-09 3303 4235 2986 4203 4444 3999 2511 4521 4342 4137 3986 4553 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 0.977821744788343 0.999999995401952 2325 3743.45454545455 4138 0.292657486182637 2324 0.648828184364399 0.648828184364399 1 2.78903271239898e-09 2324 4266 2340 4217 4574 4138 2940 4241 3926 4314 3898 4554 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 0.999918333415095 0.999999995401952 3505 4016.90909090909 4139 0.575020802337215 3418 0.133030544660956 0.129681325225278 1 4.90150538385703e-10 3503 4566 3657 4397 4434 4224 3514 3716 4618 3418 4139 4555 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 0.327513572050353 0.448488778091161 3255 3470.27272727273 4140 0.0389004976255736 1216 0.308368840606097 0.360454069765148 1 0.239684084077068 3254 4159 4453 4270 4140 2636 1216 2489 4445 4360 2751 4556 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 0.858108538997981 0.937822778093007 4400 3754.63636363636 4141 0.177386891018849 1977 0.26161847905033 -0.31720247439453 -1 0.0162790342696313 3509 4282 4488 4119 4516 1977 2818 4141 4396 4397 2658 4557 M203 PID_ALK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK2_PATHWAY.html ALK2 signaling events 18832364 5/13 Pathway Interaction Database 0.900849582143098 0.96887333989501 4145 4098.27272727273 4142 0.206349206349206 3395 0.266630551494345 -0.251777596316322 -1 0.00817249565003177 4142 3982 3903 4180 3940 4369 4333 4477 3683 3395 4677 4558 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 0.999829773269693 0.999999995401952 4075 4170.18181818182 4143 0.580141668342362 3353 0.0995578537836266 0.0817885596528927 1 3.4096456611489e-10 4073 4572 3889 4614 4686 4143 3690 3675 4678 3353 4499 4559 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 0.290659738891416 0.413112385940301 3705 3649.36363636364 4150 0.0337590015267319 2115 1.2759757520036 1.39778573479469 1 1.09339237949289 3703 4574 4150 4301 2115 2844 4172 4473 2711 2889 4211 4560 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 0.987638412269225 0.999999995401952 3275 3884.36363636364 4154 0.355522996122563 2799 0.419949540919091 -0.419144189550308 -1 1.7689329815602e-09 3274 3252 4480 3927 4185 4489 2799 4371 4154 4390 3407 4561 M6034 REACTOME_SEROTONIN_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEROTONIN_RECEPTORS.html Genes involved in Serotonin receptors 2/12 Reactome 0.999240802698035 0.999999995401952 4410 4110 4155.5 0.549833949296109 3443 0.133357412272391 -0.266310876825266 -1 4.91607369645387e-10 4410 4075 4001 NA 4441 4236 3443 4356 4519 3585 4034 4562 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 0.796944161638877 0.890221773883141 4340 3970.54545454545 4160 0.134920634920635 3149 0.25326697642056 -0.266371882890256 -1 0.0285472888442993 4337 3645 3362 3149 4543 4609 3849 4505 3329 4160 4188 4563 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 0.819178444834741 0.908345999170752 3015 3849.27272727273 4161 0.143993049706179 1966 0.241780890532162 0.243678833453808 1 0.0225291290354487 3011 4594 3332 4590 3614 4278 1966 4297 4515 4161 3984 4564 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 0.475830668277167 0.596347288458626 3760 3854.18181818182 4162 0.0570309928903838 1644 1.05077947290469 1.05077947290469 1 0.526512799318915 4671 3758 1644 4162 4287 3758 4347 4494 4243 2906 4126 4565 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 0.93976485154045 0.991832904125799 4685 3951.81818181818 4165 0.244933854441496 2395 0.201518436550672 0.227751008946917 1 0.00160186460098179 3235 4347 4684 4488 4165 3599 2395 3442 4580 4681 3854 4566 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 0.997069626653558 0.999999995401952 3335 4001.7 4166.5 0.476945437086327 3327 0.136427173625385 0.136427173625385 1 5.05289129912706e-10 3331 4500 4515 NA 3946 3479 3327 4387 4674 4436 3422 4567 M16817 KEGG_OOCYTE_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OOCYTE_MEIOSIS.html Oocyte meiosis 55/119 KEGG 0.967940167991264 0.999999995401952 4550 3867.45454545455 4173 0.268560693892264 2391 0.266840403650934 -0.260425582402043 -1 1.08653384040343e-09 4173 3989 3251 4235 4549 2391 4547 4547 4561 3205 3094 4568 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 0.998444025612634 0.999999995401952 4505 3992.81818181818 4174 0.444444444444444 2979 1.59067727499171 1.59067727499171 1 6.98680315256348e-09 4505 4169 2991 4041 4176 3489 4680 4476 4241 2979 4174 4569 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 0.996676483027122 0.999999995401952 4220 4010 4175 0.404761904761905 3116 0.210835608056143 -0.21247064910645 -1 8.36923496458964e-10 4218 4420 3710 4556 4660 3116 4403 3633 4175 3524 3695 4570 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 0.984261846274646 0.999999995401952 4200 3914.63636363636 4178 0.33976981136802 2673 0.324679913942306 -0.300223347802675 -1 1.34432140848719e-09 4196 3814 4672 4178 3748 2673 4661 3038 4351 4655 3075 4571 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 0.725264309022383 0.827914385402896 3610 3937.36363636364 4180 0.110814687958796 1888 0.317512095362651 0.304906477691931 1 0.0581207014300973 3607 4460 1888 4000 4324 4180 3917 3991 4182 4295 4467 4572 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 0.0303825307220489 0.0790958549797341 2215 3500.63636363636 4180 0.00280094699277206 970 0.331939535379707 -0.363322190162136 -1 0.816318322088507 2215 4206 970 4298 4180 3054 4305 3122 4477 4405 3275 4573 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 0.970704948492414 0.999999995401952 3940 3895.90909090909 4181 0.274533002541928 2722 0.88632027725861 0.88632027725861 1 3.84752212141897e-09 3940 4669 3047 4503 3501 4181 2722 3242 4261 4248 4541 4574 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 0.704222772942836 0.808226283127634 3700 4036.72727272727 4184 0.10482924631473 2849 0.254638169724294 -0.226315276814755 -1 0.0525520871758157 3696 3668 3403 3954 2849 4442 4573 4580 4184 4461 4594 4575 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 0.999472702634496 0.999999995401952 4370 4136.18181818182 4187 0.529883428594538 3327 0.254528658488893 -0.300415223382555 -1 1.03166105831726e-09 4368 4039 3872 4187 4042 4252 4003 4285 4532 3327 4591 4576 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 0.999998599951862 0.999999995401952 4160 4153.45454545455 4190 0.706349206349206 3457 0.16668747025596 -0.183459166410931 -1 6.40157634825564e-10 4160 4192 3457 4402 4479 3917 4495 4190 4571 3764 4061 4577 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 0.999587315232174 0.999999995401952 4330 4076.36363636364 4193 0.507587636087454 3305 0.154871538481714 -0.181267194315978 -1 5.87494666183849e-10 4328 4339 3406 4229 4093 4157 3305 4264 4582 4193 3944 4578 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 0.999637123173813 0.999999995401952 3470 4100.90909090909 4194 0.547127527280498 3435 0.234699421281751 0.190888886547882 1 9.43283220904145e-10 3469 4199 4013 4078 4577 4256 3435 4665 4611 3613 4194 4579 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 0.983782121345666 0.999999995401952 4150 4104.63636363636 4195 0.312500817549009 2375 0.199409432715164 -0.224274667108582 -1 7.85997651153373e-10 4150 4496 2375 4460 4650 4109 4260 4195 4635 3746 4075 4580 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 0.305146779163431 0.424686013412485 4575 3914.36363636364 4199 0.0325542008136113 1470 1.72130338621463 1.72130338621463 1 1.42889584070374 4574 4507 1470 4478 4199 4002 4246 3930 4539 3037 4076 4581 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 0.13411491204602 0.231307500127953 4240 3372 4200.5 0.0158730158730159 515 0.822403992524824 -0.811086454570772 -1 1.16705766036204 4238 515 4477 NA 4202 3855 2194 4199 1045 4388 4607 4582 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 0.137788267054508 0.235992624056075 4225 3914.54545454545 4201 0.0147160850957791 997 0.200749007772643 0.171820116479388 1 0.280977051288586 4225 4568 4015 4201 4166 4219 4022 997 4573 3616 4458 4583 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 0.997531259367701 0.999999995401952 4295 4011.81818181818 4202 0.420634920634921 3099 0.205383077818045 -0.214458460235575 -1 8.12621864185424e-10 4295 4299 3642 4139 4515 3099 4479 4572 4202 3497 3391 4584 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 0.916888107157732 0.978933167040586 4115 4106.90909090909 4202 0.220230368578936 3307 0.239468384822349 -0.173653289559912 -1 0.00494227115019833 4115 4498 4510 4198 3332 4202 3307 4495 4577 4430 3512 4585 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 0.999092118093309 0.999999995401952 4105 4059.18181818182 4203 0.47099812099681 3122 0.13663215558031 -0.146899872812777 -1 5.06202723395691e-10 4101 4560 3692 4514 4433 3122 4229 4203 4659 3670 3468 4586 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 0.753888300277806 0.850665353186662 3690 4036.72727272727 4204 0.13081299237382 2996 0.363740012732875 -0.375696068767747 -1 0.0570246850891565 3688 4305 4204 3738 2996 4626 4096 4382 4226 3926 4217 4587 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 0.0198875778764203 0.058661100779282 4205 3710 4205 0.00182451513082553 897 1.90919498657043 1.90919498657043 1 5.24828097591306 3650 4190 897 3524 4205 4205 4526 4681 4302 2245 4385 4588 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 0.804145895015401 0.896983495368286 4210 4013.45454545455 4206 0.150441542241346 2232 0.31421326059689 -0.273752793508262 -1 0.0331122808583674 4206 4278 4611 4193 3985 3307 4453 2232 4206 4581 4096 4589 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 0.976317899121715 0.999999995401952 3405 3988.90909090909 4207 0.312231909296456 2895 0.145801294275518 0.181559067872559 1 5.47069078483298e-10 3401 4606 4514 4387 4207 3844 3267 2895 4454 4435 3868 4590 M84 PID_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATM_PATHWAY.html ATM pathway 18832364 29/48 Pathway Interaction Database 0.995744470417072 0.999999995401952 4195 4160.90909090909 4210 0.391234084462607 3330 0.239671375277381 -0.24926681364603 -1 9.65442950865568e-10 4191 4555 3330 4619 3801 3908 4686 4519 4575 3376 4210 4591 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 0.488503504615039 0.60945884521461 3495 3868.90909090909 4210 0.0591266853069956 1655 0.353396640989034 -0.317898982408019 -1 0.169626132054971 3493 4057 1655 4131 4254 4650 4298 3266 4313 4210 4231 4592 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 0.793793760752682 0.888609069012677 4285 3701.81818181818 4211 0.133709004643906 2274 0.23421396657657 -0.204682659355201 -1 0.0268113550973742 4281 4631 3341 4502 3007 2274 4553 2559 4295 4211 3066 4593 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 0.08327538321501 0.156982736433532 4325 3857.54545454545 4211 0.00787322079311997 1137 1.46491767614715 1.72843993912124 1 2.6292314396024 4325 4653 1137 4169 4300 3759 4211 4489 4138 2911 4341 4594 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 0.999997953160831 0.999999995401952 4640 4234.18181818182 4212 0.73015873015873 3761 0.156916225751078 -0.150875866238348 -1 5.96607726719906e-10 4640 3913 4094 4384 4524 3985 4212 4345 4590 3761 4128 4595 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 0.329032843441313 0.450043171151778 4215 3452.81818181818 4212 0.0391178488616807 1392 0.687555096536048 -0.396806601193795 -1 0.532106175662585 4212 1867 4642 2461 4531 4335 2517 1392 2829 4619 4576 4596 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 0.886776127944857 0.959019832806277 4395 4022.63636363636 4215 0.179659101794871 2665 0.254106351527439 -0.243739665411737 -1 0.010306415125581 4392 4154 2665 4382 3201 4062 3925 4578 4442 4215 4233 4597 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 0.17336488807249 0.277739441199209 3205 3419.72727272727 4216 0.0171594254785813 1728 1.26715109826347 1.26715109826347 1 1.57349643816668 3205 4456 1906 4325 1728 4426 2252 4216 4244 2621 4238 4598 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 0.923085831045639 0.982863032101764 4275 3902.45454545455 4219 0.226250047812122 2197 0.280999788673333 0.164466485659459 1 0.00470816772664962 4273 4393 3980 4258 4267 2197 3999 4219 4483 3533 3325 4599 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 0.998444025612634 0.999999995401952 4375 4056.45454545455 4220 0.444444444444444 3488 0.20539724732233 -0.182955116822876 -1 8.12685016899415e-10 4374 4220 3685 4280 3976 3488 4675 4323 4245 3637 3718 4600 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 0.74540666974079 0.84534744782317 3650 3975.90909090909 4223 0.116948377346299 1911 0.31165414049021 0.304906477691931 1 0.0507534511121877 3649 4461 1911 4066 4450 4427 4054 3701 4223 4246 4547 4601 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 0.37615401724356 0.497223617716029 4165 4007.18181818182 4227 0.0419886130102118 1536 0.348852717806144 -0.377255851940158 -1 0.236268760994807 4377 4028 1536 4227 4083 4375 4163 4161 4416 4359 4354 4602 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 0.992297154002643 0.999999995401952 4370 3964.27272727273 4233 0.35749371071339 2853 0.554099100968402 -0.554099100968402 -1 2.36683031282057e-09 4366 4657 3740 4522 3706 3095 2853 4500 4569 4233 3366 4603 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 0.988438980056112 0.999999995401952 3265 3959.63636363636 4233 0.333333333333333 2887 1.10416511485725 1.10416511485725 1 4.81844477655996e-09 3261 4619 3547 4365 4233 4680 2887 4286 4033 2995 4650 4604 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 0.991814770382281 0.999999995401952 4460 4181.27272727273 4234 0.353936012755752 3682 0.148686698082289 -0.1676920709393 -1 5.59929167141378e-10 4457 4234 3682 4207 3696 4044 4669 4419 4562 3779 4245 4605 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 0.838301695638289 0.921799467694876 3235 3652.72727272727 4236 0.152647464633021 1843 0.292769030735831 -0.266732050569557 -1 0.0231079014339226 3231 4338 2763 4334 4236 1843 3421 4684 4266 4454 2610 4606 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 0.940634982288152 0.992080919874473 4520 3918.18181818182 4237 0.246031746031746 2764 0.392957656605097 0.266771460748616 1 0.00302837499252307 4516 2859 4487 3873 4560 4546 3052 2764 3810 4396 4237 4607 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 0.358607532199511 0.478362197236587 4230 3934.54545454545 4238 0.039569805787387 1526 1.16098276490417 1.32794323271334 1 0.829822437326425 4228 4649 1526 4418 4238 4049 4401 4488 3972 3005 4306 4608 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 0.999547892229453 0.999999995401952 3170 4032.90909090909 4240 0.503486469092608 3168 0.189201768759204 0.185526927294657 1 7.4050264516582e-10 3170 4524 3168 4555 4260 4240 3289 4640 4581 3937 3998 4609 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 0.0591979304732683 0.130419135965085 3940 3750.45454545455 4242 0.0060836692943501 1147 0.343177394662724 -0.304362827491873 -1 0.677600895333935 3936 3547 4436 3823 1147 4266 2673 4262 4242 4333 4590 4610 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 0.992735565696391 0.999999995401952 4585 4176.72727272727 4242 0.388888888888889 3462 0.249686850210703 -0.153248277788837 -1 1.0100813807772e-09 4585 3462 4450 3933 4214 3568 4545 4445 4147 4353 4242 4611 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 0.397934486738188 0.519420892717311 4435 3937.36363636364 4246 0.0494731806027424 2360 0.206815875004044 0.176124755300138 1 0.131315520530502 4434 4525 4246 4490 2360 3320 3736 3098 4625 3985 4492 4612 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 0.992393253415676 0.999999995401952 4255 4133.54545454545 4251 0.386068531386666 2907 0.205104228625545 -0.253927616566549 -1 8.11379048421001e-10 4251 4394 3921 4017 4630 4685 2907 4221 4548 3447 4448 4613 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 0.99923315100791 0.999999995401952 4520 4265.18181818182 4251 0.511942506598835 3619 0.134967899042871 -0.0840671497052242 -1 4.9878522204942e-10 4518 4678 4196 4616 4009 4378 4093 3619 4644 3915 4251 4614 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 0.0220140337314505 0.0631320453277706 4255 3421 4252 0.00202158642411994 621 1.41942828239076 1.41942828239076 1 3.8008770248255 4252 4451 2778 4546 621 3186 4399 4496 3058 1350 4494 4615 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 0.986541753778373 0.999999995401952 3415 4110.5 4256 0.380402252921398 3004 0.281930646440434 -0.392916938177496 -1 1.15379023609043e-09 3414 4247 4575 NA 4265 3941 4685 3852 4593 4529 3004 4616 M16853 KEGG_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DNA_REPLICATION.html DNA replication 20/36 KEGG 0.999990583197867 0.999999995401952 4195 4171.90909090909 4259 0.650793650793651 3195 0.184342181520367 -0.177671491910956 -1 7.18843727760056e-10 4192 4187 3470 3918 4440 4259 4508 4672 4528 3195 4522 4617 M6682 BIOCARTA_MCM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCM_PATHWAY.html CDK Regulation of DNA Replication 12/19 BioCarta 0.999961576753993 0.999999995401952 4550 4021.81818181818 4259 0.603174603174603 2886 0.222338333768983 -0.244251220891935 -1 8.88190522630342e-10 4547 3770 2886 3635 4527 4149 4313 4259 4481 3250 4423 4618 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 0.472498538894012 0.592964154594895 3760 3864.90909090909 4260 0.0619578213196116 1636 0.163619243802572 -0.103585258698719 -1 0.0828868007105283 3758 4399 3986 4499 3241 4537 4385 1636 4271 3542 4260 4619 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 0.762153238218856 0.859347948578815 4270 3649.36363636364 4266 0.122393665341177 2062 1.15547920299127 1.15547920299127 1 0.169774259888107 4266 4517 2691 4548 3561 3004 4286 2062 4296 2535 4377 4620 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 0.999478524659733 0.999999995401952 3855 4184.90909090909 4270 0.530405093541372 3538 0.166997749146658 0.170645975330565 1 6.41540531054416e-10 3851 4285 4270 4530 4586 4257 4312 3538 4649 4016 3740 4621 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 0.886397100990223 0.958831213121003 4300 3945.45454545455 4271 0.179409829599226 3058 0.554099100968402 -0.554099100968402 -1 0.0225796037584263 4300 4271 3386 4338 3198 3693 3058 4552 4408 4309 3887 4622 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 0.965264098472603 0.999999995401952 3910 4052.90909090909 4271 0.285375572182593 3106 0.425911248184927 -0.380063715366639 -1 1.79550398829841e-09 3907 3220 4600 4420 3536 4156 3106 4271 4406 4570 4390 4623 M11675 KEGG_HOMOLOGOUS_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HOMOLOGOUS_RECOMBINATION.html Homologous recombination 22/27 KEGG 0.9999966994683 0.999999995401952 4435 4126.63636363636 4272 0.682539682539683 3203 0.204395364029043 -0.189525519257963 -1 8.08219677266018e-10 4433 4121 3486 3805 4504 3873 4555 4582 4559 3203 4272 4624 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 0.605855660321274 0.719655164579339 2065 3456.72727272727 4272 0.0889010850999949 1631 0.360643396486437 0.360643396486437 1 0.115004667020535 2064 4530 4678 4428 4272 1974 1631 2896 4622 4663 2266 4625 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 0.964580988386728 0.999999995401952 4605 4106.09090909091 4273 0.261904761904762 3107 1.35899249204575 1.527238677239 1 5.95419660979055e-09 4602 4651 3598 4483 4052 3732 4441 4379 3849 3107 4273 4626 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 0.776416537599186 0.873119245305924 4440 3956.09090909091 4273 0.127313711448066 2913 0.255778752452387 -0.271226117542666 -1 0.033639862711273 4398 4273 2913 4095 2978 4251 3082 4439 4440 4296 4352 4627 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 0.999996585487256 0.999999995401952 4100 4181.72727272727 4274 0.681558335536022 3249 0.174372810279073 -0.203144812289697 -1 6.7441077950944e-10 4097 4488 3249 4520 4274 3940 4563 4279 4628 3737 4224 4628 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 0.90970552045718 0.974835385229435 4275 3889.36363636364 4274 0.19636265719949 2068 1.16533572062244 1.16533572062244 1 0.0287890817527206 4274 4674 2131 4575 4080 4509 3629 4511 4041 2068 4291 4629 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 0.359971725490797 0.478940234426427 4410 3979.18181818182 4275 0.0397556912422697 1527 0.252718638804891 -0.258372938933186 -1 0.18033699810196 4407 4671 1527 4621 3530 3786 3742 4527 4660 4025 4275 4630 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 0.990816480149934 0.999999995401952 3665 4101.54545454545 4276 0.374393983225229 2863 0.264101607673873 0.106158905337181 1 1.07432717491046e-09 4575 3855 4549 4486 4258 3663 2863 3664 4276 4485 4443 4631 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 0.812557005489034 0.904642938399052 4640 3938.72727272727 4277 0.14118978539705 2173 0.129802154334835 -0.168290620733586 -1 0.0126089320589651 4638 4676 3253 4351 3541 4277 3247 2173 4669 4579 3922 4632 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 0.123824160230315 0.216346015972877 4070 4025.18181818182 4282 0.0119452169603623 1233 0.355683584866374 -0.283030328295468 -1 0.527798033137623 4539 4066 1233 4148 4471 4315 4509 4274 4282 4066 4374 4633 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 0.907896750461653 0.973561117410739 4290 3768.54545454545 4286 0.212179104838251 2312 0.170091222892871 -0.153180145095164 -1 0.00441767999672776 4286 4311 4652 4529 3304 2558 2312 2774 4612 4632 3484 4634 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 0.198277076649789 0.309296398528933 4335 3998.72727272727 4291 0.0198897377769929 1343 0.30868067294804 -0.289560537449825 -1 0.351107279762085 4335 4378 1343 4291 4232 4415 3750 4272 4567 3971 4432 4635 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 0.999992062386588 0.999999995401952 3995 4232.27272727273 4293 0.690992518551053 3875 0.190855979855087 -0.210434574550156 -1 7.47875374522561e-10 3918 4604 4417 4505 4351 3875 3995 3959 4646 4293 3992 4636 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 0.999493225603366 0.999999995401952 3545 4198.72727272727 4296 0.531746031746032 3545 0.257543341746908 -0.245105959539089 -1 1.04509733849514e-09 3545 4345 4096 3965 4288 4437 4474 4587 4387 3766 4296 4637 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 0.999424653733305 0.999999995401952 4670 4225 4297 0.563492063492063 3531 0.163069785960715 -0.143346099627912 -1 6.24033811648845e-10 4667 3531 4237 NA 4514 4357 4644 3817 4432 3963 4088 4638 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 0.999500097829989 0.999999995401952 4500 4226.45454545455 4297 0.53238492642894 3543 0.0948850758720406 -0.100461173691263 -1 3.20138247773759e-10 4498 4677 4297 4599 4196 4535 3777 3543 4682 4050 3637 4639 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 0.954114728178669 0.99961092867638 3195 4023.36363636364 4298 0.265203073834484 2709 0.165246745153256 -0.132726881507797 -1 6.23318168541663e-05 3194 4495 4298 4613 4682 4392 3382 2709 4465 4051 3976 4640 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 0.996208265229547 0.999999995401952 2960 4061.63636363636 4305 0.397586966884377 2951 0.184735591508611 0.173830578443602 1 7.2059713479304e-10 2957 4509 3759 4518 4047 4448 2951 4121 4305 4625 4438 4641 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 0.998444987429173 0.999999995401952 4315 4147.45454545455 4307 0.476190476190476 3361 0.139928596765586 -0.135817537477717 -1 5.2089478341146e-10 4414 3361 4100 4061 4379 4017 4585 4311 4307 3772 4315 4642 M6705 BIOCARTA_TH1TH2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TH1TH2_PATHWAY.html Th1/Th2 Differentiation 5/21 BioCarta 0.999907012929453 0.999999995401952 4315 4224 4315 0.604776957973579 3333 0.288343259807644 -0.250807941903534 -1 1.18237090692715e-09 4315 4398 3878 4528 4161 4613 4044 4032 4487 3333 4675 4643 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 0.999641042439079 0.999999995401952 4320 4068.63636363636 4316 0.547619047619048 3300 0.222917910354355 0.21910966286985 1 8.90773664114575e-10 4316 3608 3853 3571 4593 4388 3913 4460 4398 3300 4355 4644 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 0.95702913700236 0.999999995401952 4005 4073.09090909091 4316 0.270009165039574 2495 0.163413744979572 0.126490466276268 1 6.25566818386713e-10 4002 3983 4363 4316 4349 4323 2495 3881 4545 4144 4403 4645 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 0.841987472010029 0.924898250207763 4595 4095.45454545455 4316 0.168486791894369 2064 0.248836260448906 0.215134401628598 1 0.0188308670174871 4043 4198 4592 4380 4270 4316 2064 3576 4591 4557 4463 4646 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 0.94224815003518 0.993558692858878 3905 4119.36363636364 4320 0.24810605052164 3003 0.239314922895347 -0.21218089381389 -1 0.00149902924472434 3905 4344 4427 4209 3426 4578 3003 4583 4356 4320 4162 4647 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 0.99988584203849 0.999999995401952 4450 4298.7 4320.5 0.63529213094048 3923 0.0849092119111581 -0.10468680979835 -1 2.75676361823215e-10 4449 3951 4448 NA 4203 4216 4290 3923 4605 4351 4551 4648 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 0.999998995721183 0.999999995401952 4570 4337.72727272727 4322 0.748704084217777 4063 0.162770065275978 -0.146949093535849 -1 6.22697972772727e-10 4568 4309 4366 4265 4377 4063 4237 4431 4627 4150 4322 4649 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 0.997166209592146 0.999999995401952 3980 4037.18181818182 4325 0.413325697067487 2572 0.252237803480043 -0.265865937565498 -1 1.0214508414847e-09 3976 4494 2572 4267 4325 4530 3242 4375 4551 3446 4631 4650 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 0.99999958286702 0.999999995401952 4550 4319.09090909091 4335 0.76984126984127 3544 0.138280289165056 -0.131102140515857 -1 5.13548365614108e-10 4549 4281 3987 4222 4576 4230 4670 4502 4614 3544 4335 4651 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 0.993051537324278 0.999999995401952 4505 4141.4 4336 0.424281932709403 3289 0.081970406270937 -0.083499136583562 -1 2.62578264082639e-10 4504 4248 4622 NA 3860 3803 3399 3289 4664 4601 4424 4652 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 0.999814005098638 0.999999995401952 4495 4295.5 4337.5 0.61496508295545 3630 0.0473610770397741 -0.0473610770397741 -1 1.08326356164214e-10 4491 4645 4223 NA 4457 4207 3630 4411 4677 3950 4264 4653 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 0.999993327972671 0.999999995401952 4355 4341.4 4339.5 0.733978011678933 4029 0.0534199738908701 -0.0152297017899041 -1 1.35330531625695e-10 4029 4644 4286 NA 4354 4263 4442 4351 4679 4038 4328 4654 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 0.660710072031033 0.771706729196766 4560 3964 4344 0.0935901144524639 1830 1.2815413473491 1.2815413473491 1 0.321920660948558 4556 4423 1830 3643 4469 4319 4477 4344 4284 2826 4433 4655 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 0.817915168716253 0.907374640294593 3655 3984.45454545455 4344 0.143451101887167 1987 1.18839561747551 1.31175525595309 1 0.111967129843021 3654 4652 1987 4526 4362 4306 3954 4360 4344 3130 4554 4656 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 0.994317226872501 0.999999995401952 3935 4239 4354 0.437002194515835 3083 0.0589274215569446 0.0589274215569446 1 1.59876927904533e-10 3931 4537 4596 NA 4568 4132 3083 4127 4680 4565 4171 4657 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 0.999948002986097 0.999999995401952 4390 4217.54545454545 4355 0.592109593203018 3429 0.140370215091622 -0.10428251360143 -1 5.22863052397773e-10 4387 4567 3429 4588 4143 4355 3911 4452 4634 3630 4297 4658 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 0.998842148461521 0.999999995401952 4610 4324.90909090909 4356 0.491412961669722 3430 0.115179659100049 0.115250730032784 1 4.10590107225311e-10 4171 4607 4356 4608 4591 4610 4079 3430 4681 4133 4308 4659 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 0.999999851309753 0.999999995401952 4360 4176.45454545455 4359 0.76050392102599 3071 0.159154191398578 -0.170684156795216 -1 6.06582218530399e-10 4195 4436 3071 4360 4423 4088 4623 4359 4650 3420 4316 4660 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 0.803353596879969 0.896740103615897 4555 4099.7 4361 0.165318731377183 2302 0.177444714477557 -0.155740721597737 -1 0.0187460767124635 4331 3819 4482 NA 3979 4554 4067 2302 4552 4391 4520 4661 M5109 KEGG_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRIMIDINE_METABOLISM.html Pyrimidine metabolism 57/106 KEGG 0.999762700877767 0.999999995401952 4610 4102.27272727273 4370 0.531746031746032 2579 1.05306144797759 -1.0296882537552 -1 4.5906784981336e-09 4609 4660 3477 4623 4087 3656 4556 4601 4370 2579 3907 4662 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 0.999999516850327 0.999999995401952 4375 4265.27272727273 4373 0.733421200302973 3624 0.143274289937542 -0.152040587013884 -1 5.35806356867185e-10 4373 4491 3689 4501 4589 3983 4299 4570 4600 3624 4199 4663 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 0.780564174459818 0.87715197158722 4390 4033.45454545455 4376 0.140727815876553 3053 0.315243229937465 0.223456721551776 1 0.0400524929367036 3103 4469 4476 4389 3053 4568 3310 4361 4376 4386 3877 4664 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 0.999999252623323 0.999999995401952 4400 4299.45454545455 4396 0.756020153285788 3728 0.112033797096523 -0.101034049350131 -1 3.96569170475831e-10 4475 4396 4078 4396 4594 4051 4129 4556 4657 3728 4234 4665 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 0.999837614436726 0.999999995401952 4480 4180.72727272727 4401 0.547619047619048 3058 0.257465488179538 -0.278661494306079 -1 1.04475034935748e-09 4477 4544 3058 4601 4123 3968 3792 4412 4401 4596 4016 4666 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 0.650458609694588 0.76247293990556 4405 4194.90909090909 4403 0.0997775051513636 2818 0.224721631295623 0.197066549394979 1 0.0590717216111578 3722 4243 4493 4261 2818 4669 4671 4403 4437 4404 4023 4667 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 0.99999750175699 0.999999995401952 4670 4308.36363636364 4405 0.69047619047619 3279 0.182488963478065 -0.189722304396854 -1 7.10584035209975e-10 4669 4596 3279 4521 4344 4183 4674 4392 4564 3765 4405 4668 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 0.999999995401952 0.999999995401952 4290 4297 4425 0.825396825396825 3464 0.133613284847734 -0.131102140515857 -1 4.92747779870243e-10 4290 4441 3464 4231 4635 4425 4369 4586 4640 3712 4474 4669 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 0.99999995288804 0.999999995401952 4010 4265.81818181818 4426 0.784264798133106 3574 0.14382839983569 -0.151652346755372 -1 5.38275994704282e-10 4009 4559 3700 4513 4599 4327 4083 4491 4643 3574 4426 4670 M13515 KEGG_MISMATCH_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MISMATCH_REPAIR.html Mismatch repair 14/23 KEGG 0.999512287920737 0.999999995401952 3835 4049.72727272727 4434 0.50005301271583 3202 0.150340998808868 -0.155525397794195 -1 5.67302295977283e-10 3834 4599 3601 4457 4561 3221 4434 4602 4626 3202 3410 4671 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 0.996183343814057 0.999999995401952 3880 4234.36363636364 4434 0.426981947982146 2968 0.230816075486666 -0.21060130862036 -1 9.25975358795696e-10 3876 4307 4613 4434 4671 2968 4649 4406 4639 4585 3430 4672 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 0.99999990324893 0.999999995401952 3930 4277 4437 0.769679633202421 3381 0.151928917042251 -0.161971108188807 -1 5.74379561632499e-10 3930 4437 3381 4035 4665 4596 4307 4668 4624 3768 4636 4673 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 0.991583869433661 0.999999995401952 3205 3861.18181818182 4439 0.379829296680807 2822 0.125945480831882 0.136106176407019 1 4.58572792221979e-10 3203 4532 4517 4537 4604 2822 2959 3159 4631 4439 3070 4674 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 0.113070305257069 0.20054786163309 3830 3963.63636363636 4439 0.0108488639220112 1208 1.67949129323189 1.67949129323189 1 2.61563446625111 3826 4663 1208 4299 4541 4439 4117 4447 4463 3014 4583 4675 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 0.982272517742261 0.999999995401952 3860 4125.90909090909 4442 0.30691564390825 2878 0.202449644243645 -0.188966914534137 -1 7.99547709451569e-10 3859 4673 3291 4594 4544 4412 3683 2878 4500 4509 4442 4676 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 0.999997132089852 0.999999995401952 4615 4418 4452 0.757800105872053 4019 0.0673347147952197 -0.0960932887671069 -1 1.9734777900863e-10 4615 4536 4362 NA 4562 4438 4019 4466 4671 4142 4369 4677 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 0.995815327304447 0.999999995401952 4685 4186.18181818182 4462 0.421682746096615 3031 0.0566063318634903 0.0736626328809211 1 1.49531956718476e-10 3800 4682 4581 4579 4462 4094 3031 3492 4683 4538 4106 4678 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 0.995815327304447 0.999999995401952 4685 4187.63636363636 4463 0.421682746096615 3032 0.0566063318634903 0.0736626328809211 1 1.49531956718476e-10 3801 4683 4584 4580 4463 4095 3032 3493 4684 4542 4107 4679 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 0.999995833189353 0.999999995401952 4685 4450.4 4469 0.747535442203532 4002 0.0230560128399708 -0.0230560128399708 -1 0 4644 4684 4512 NA 4502 4274 4002 4436 4685 4432 4333 4680 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 0.999999414526698 0.999999995401952 3985 4412.81818181818 4470 0.761904761904762 3983 0.268180916455125 -0.220288460953509 -1 1.09250843344609e-09 3983 4470 4396 4612 4597 4107 4483 4401 4608 4236 4648 4681 M787 REACTOME_POL_SWITCHING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POL_SWITCHING.html Genes involved in Polymerase switching 7/14 Reactome 0.999998292930827 0.999999995401952 4625 4291.63636363636 4473 0.735012668340787 3594 0.13547615025455 -0.129682229059235 -1 5.01050470202012e-10 3856 4473 4004 4277 4622 4594 3966 4628 4623 3594 4571 4682 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 0.985100311749474 0.999999995401952 3935 4207.27272727273 4473 0.317778819845641 2390 0.23013708713812 -0.256101868143179 -1 9.22949144461461e-10 3934 4512 2390 4297 4532 4473 4233 4678 4592 4055 4584 4683 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 0.995650118201147 0.999999995401952 4625 4272.72727272727 4474 0.419439150454645 3552 0.102993790331859 0.0838612137809716 1 3.56278349416252e-10 4623 4569 4541 4496 3849 3692 3552 4191 4666 4474 4347 4684 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 0.999982441783833 0.999999995401952 4640 4259.36363636364 4490 0.630444189039327 3595 0.141058692190939 -0.144849371647137 -1 5.25931557580825e-10 4639 4668 3718 4516 4664 3659 4490 4433 4656 3595 3815 4685 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 0.999995232268502 0.999999995401952 3980 4317.63636363636 4542 0.706349206349206 3596 0.212004125690087 -0.157555862510508 -1 8.42131516333267e-10 3977 4643 4005 4540 4542 4579 3912 4568 4572 3596 4560 4686 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 0.99997213547563 0.999999995401952 4095 4301.72727272727 4564 0.649647546298374 3627 0.147856422144518 -0.150875866238348 -1 5.56228672207064e-10 4091 4160 4024 4585 4642 4564 3730 4658 4633 3627 4605