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 M2578 LIM_MAMMARY_LUMINAL_MATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_MATURE_UP.html Genes consistently up-regulated in mature mammary luminal cells both in mouse and human species. 20346151 153/201 Daniel Hollern 1.22058093976404e-24 2.30445681427451e-22 5 103.636363636364 36 1.10961903614913e-25 1 1.46444682508333 -1.51425933943162 -1 47.5466751578995 1 569 25 1 68 3 102 36 232 9 94 2 M2580 LIM_MAMMARY_LUMINAL_MATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_MATURE_DN.html Genes consistently down-regulated in mature mammary luminal cells both in mouse and human species. 20346151 161/176 Daniel Hollern 2.74188071070646e-19 2.5883353909069e-17 5 541.363636363636 36 2.49261882791496e-20 1 1.30022462386906 1.31399791436677 1 32.3613090664508 2 1762 36 1687 118 1 14 5 2266 54 10 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 233/268 Arthur Liberzon 9.63131869657914e-14 4.94128524433191e-12 20 910 75 8.7557442696178e-15 2 1.31826501710011 1.29022012761964 1 22.3644185033867 17 1732 69 2820 2592 2 81 38 2575 75 9 4 M11756 WOTTON_RUNX_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WOTTON_RUNX_TARGETS_UP.html Common target genes up-regulated by all three Runx family members (RUNX1, RUNX2, and RUNX3 [GeneID=861;860;864]) in MEF cells (embryonic fibroblasts). 18560354 27/31 Jessica Robertson 2.00399769145229e-05 0.000182603650649707 960 273.909090909091 110 1.82183267841928e-06 25 1.40682110065413 1.5009991694195 1 7.89171048916315 110 304 959 264 46 37 57 25 186 960 65 5 M2456 WANG_MLL_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WANG_MLL_TARGETS.html Genes requiring MLL [GeneID=4297] for H3K4me3 and expression in MEF cells (embryonic fibroblast). 19703992 344/461 Arthur Liberzon 4.27919816869117e-32 1.55367810432479e-29 45 777.272727272727 137 3.89018015335561e-33 9 1.44214371534124 1.4465233119983 1 62.3407974797212 42 2235 9 1684 1177 137 317 68 2803 20 58 6 M2498 PHONG_TNF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_TARGETS_DN.html Genes down-regulated in Calu-6 cells (lung cancer) at 1 h time point after TNF [GeneID=7124] treatment. 20516219 6/8 Arthur Liberzon 2.81184992650429e-06 3.40305939823083e-05 140 674.818181818182 140 2.81185348443563e-07 2 1.64743901787295 1.64743901787295 1 11.0451810959159 140 451 4709 710 15 19 2 70 76 949 282 7 M12289 REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEPTIDE_LIGAND_BINDING_RECEPTORS.html Genes involved in Peptide ligand-binding receptors 69/226 Reactome 8.37177668826478e-13 3.55989062780268e-11 50 992.454545454545 141 7.6107060802436e-14 14 2.00378460562077 1.95470288369262 1 31.4157882544232 48 3288 86 2803 1827 14 141 40 2337 271 62 8 M8689 CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_DN.html Top 200 marker genes down-regulated in the 'CTNNB1' subclass of hepatocellular carcinoma (HCC); characterized by activated CTNNB1 [GeneID=1499]. 18701503 218/315 Yujin Hoshida 2.22152300862314e-21 2.75936542123716e-19 125 628.727272727273 141 2.01956637147558e-22 27 1.41591132638161 1.46599003004157 1 39.4308132850673 33 1210 27 672 1643 122 345 124 2550 49 141 9 M2041 GERHOLD_RESPONSE_TO_TZD_DN http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_RESPONSE_TO_TZD_DN.html Genes down-regulated in 3T3-L1 cells (fibroblast) induced to differentiate to mature adipocytes and then treated with a TZD derivative AD-5075 [PubChem=128440], a PPARG [GeneID=5468] activator. 12021175 12/13 Arthur Liberzon 0.000130244646985335 0.00081532458059785 130 586.909090909091 145 1.18411234893362e-05 13 1.26646288673371 1.35917949315556 1 5.86945638678942 130 1580 1356 1696 406 79 13 34 145 928 89 10 M2581 DURAND_STROMA_S_UP http://www.broadinstitute.org/gsea/msigdb/cards/DURAND_STROMA_S_UP.html Genes up-regulated in the HSC supportive stromal cell lines. 439/546 Charles Durand 1.90031007888807e-24 3.44979368167373e-22 155 821.818181818182 155 1.72755461717097e-25 16 1.31826167838272 1.33380867265736 1 42.4538156692678 100 1690 16 1682 1990 152 588 155 2505 44 118 11 M18334 REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_A1_RHODOPSIN_LIKE_RECEPTORS.html Genes involved in Class A/1 (Rhodopsin-like receptors) 108/346 Reactome 3.84802280192027e-19 3.56130737746347e-17 125 1276.18181818182 166 3.49820254720023e-20 13 1.86127173107928 1.7913174002579 1 45.938202543499 121 3236 37 3266 4325 13 279 147 2344 166 104 12 M1266 SHANK_TAL1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHANK_TAL1_TARGETS_DN.html Genes down-regulated in preleukemic thymocytes from transgenic mice which overexpress TAL1 [GeneID=6886] in thymus. 16407836 7/16 Leona Saunders 1.95064796170667e-05 0.000180719086242143 120 785.727272727273 167 1.95066508454183e-06 5 1.6402763117416 1.6402763117416 1 9.2124086162415 116 1628 4405 736 279 24 5 12 167 1137 134 13 M1306 GROSS_HIF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HIF1A_TARGETS_UP.html Genes up-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 14/23 Jessica Robertson 0.000137623724260576 0.000853592613022232 70 467.363636363636 175 1.25120303851934e-05 40 1.54408210354026 1.54408210354026 1 7.10995989894545 66 1033 749 1255 154 40 45 64 743 817 175 14 M2142 HOELZEL_NF1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOELZEL_NF1_TARGETS_UP.html Genes up-regulated in SH-SY5Y cells (neuroblastoma) after knockdown of NF1 [GeneID=4763] by RNAi. 20655465 170/230 Arthur Liberzon 5.06772940323388e-09 1.1959841391632e-07 100 700.818181818182 176 4.60702674082497e-10 55 1.40502832006249 1.43035089644496 1 14.5939400935651 97 1232 161 242 3900 55 159 176 1219 143 325 15 M16944 WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN.html Genes down-regulated in esophageal adenocarcinoma (EAC) and Barret's esophagus (BE) relative to normal esophagi. 16449976 44/80 Leona Saunders 8.68170057985064e-07 1.23426586556913e-05 140 350.090909090909 179 7.89245818713557e-08 19 1.65310055485867 -1.86557590362174 -1 12.1757066730395 136 179 275 19 510 71 496 170 1773 198 24 16 M2575 LIM_MAMMARY_LUMINAL_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_PROGENITOR_UP.html Genes consistently up-regulated in mammary luminal progenitor cells both in mouse and human species. 20346151 79/91 Daniel Hollern 2.16787880251645e-23 3.19762123371176e-21 5 287.818181818182 180 1.97079891137858e-24 3 1.8486332802219 1.89292305317606 1 56.8516868560863 3 696 21 1150 290 41 180 142 308 13 322 17 M12602 WOO_LIVER_CANCER_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WOO_LIVER_CANCER_RECURRENCE_UP.html Genes positively correlated with recurrence free survival in patients with hepatitis B-related (HBV) hepatocellular carcinoma (HCC). 18381945 176/200 Yujin Hoshida 6.94285174622905e-08 1.30558805745821e-06 55 877.454545454545 209 6.3116836048495e-09 51 1.36324791152138 1.35480924213775 1 12.0364883914077 55 2295 209 2384 1404 84 366 181 2459 164 51 18 M2352 WINZEN_DEGRADED_VIA_KHSRP http://www.broadinstitute.org/gsea/msigdb/cards/WINZEN_DEGRADED_VIA_KHSRP.html Transcripts (mRNA molecules) rapidly degraded upon interaction with KHSRP [GeneID=8570]. 17908789 110/146 Arthur Liberzon 5.29703343258738e-09 1.24388048765236e-07 210 1119.09090909091 210 4.81548495031023e-10 93 1.523380134919 1.39273235421085 1 15.7842804564101 210 1823 162 2270 4431 93 505 129 2391 154 142 19 M13265 KEGG_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI_ANCHOR_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI_ANCHOR_BIOSYNTHESIS.html Glycosylphosphatidylinositol(GPI)-anchor biosynthesis 24/25 KEGG 0.000298179966549146 0.00158174292324708 175 915.818181818182 219 2.71109444039351e-05 34 0.592683220606697 -0.601301237607648 -1 2.49079523250365 171 324 3700 151 219 34 65 166 337 4480 427 20 M5825 VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_DN.html Angiogenic markers down-regulated in lymph endothelial cells upon infection with KSHV (Kaposi's sarcoma herpes virus). 17483315 155/220 Jessica Robertson 2.55791700431011e-13 1.2319763530963e-11 130 1007.36363636364 226 2.32537909482764e-14 75 1.48679993475296 1.33049590210833 1 24.3384672592183 126 2779 75 3326 1429 120 343 187 2331 226 139 21 M17844 KEGG_OTHER_GLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OTHER_GLYCAN_DEGRADATION.html Other glycan degradation 16/17 KEGG 0.000314143909153174 0.00164385726297448 825 703.636363636364 230 2.85626159613853e-05 22 0.955771488038427 -0.787368654319551 -1 3.99277463549643 824 380 2420 61 230 125 214 1028 22 2320 116 22 M4263 CHEBOTAEV_GR_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEBOTAEV_GR_TARGETS_UP.html Genes up-regulated in follicular epithelial stem cells after transgenic expression of GR [GeneID=2908] under control of the keratin5 (K5) [GeneID=3852] promoter. 17146443 106/124 Leona Saunders 3.32725796890562e-07 5.37830740179265e-06 120 494 230 3.02478042919717e-08 18 1.33373549609288 1.33307469994707 1 10.545436642203 118 661 241 1158 1562 18 204 29 1180 230 33 23 M5931 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_1 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_1.html Amplification hot spot 1: colocolized fragile sites and cancer genes in the Xp22.3-p11.1 region. 16751803 3/18 Arthur Liberzon 1.40799925249921e-06 1.87204407656233e-05 515 875.454545454545 236 1.40800014460786e-07 1 0.810495358831243 0.810495358831243 1 5.74953577954485 512 1105 4376 133 151 88 1 236 10 2686 332 24 M9946 LU_TUMOR_ANGIOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_ANGIOGENESIS_UP.html Up-regulated genes of putative pathways stimulated in tumor endothelial cells by papillary serous ovarian epithelial tumor cells. 17308118 37/40 Jessica Robertson 0.000129428845130072 0.000813454259672359 240 367.363636363636 236 1.17669509294208e-05 102 1.64814972362296 1.77340254791711 1 7.64089286219649 492 236 497 160 1309 168 170 138 238 531 102 25 M10660 YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAO_HOXA10_TARGETS_VIA_PROGESTERONE_UP.html Genes up-regulated in the uteri of ovariectomized mice 6 h after progesterone [PubChem=5994] injection: HOXA10 [GeneID=3206] knockout vs wild type animals. 12554760 92/127 Kevin Vogelsang 2.98900864017295e-07 4.8817026926008e-06 90 1103.45454545455 238 2.71728095115617e-08 8 1.35825881703316 1.35938257292847 1 10.8250883429754 90 1316 238 3709 3649 8 67 74 2564 380 43 26 M1983 SCHOEN_NFKB_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SCHOEN_NFKB_SIGNALING.html Genes down-regulated in A375 cells (melanoma) treated with KINK-1, a small molecule inhibitor of NFKB. 18544741 51/67 Jessica Robertson 3.39372091135578e-09 8.29966979357476e-08 125 496.363636363636 239 3.08520083326449e-10 73 1.56407098807551 1.4925038456889 1 16.6182913059754 122 801 156 538 776 73 125 961 1521 239 148 27 M9162 UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN http://www.broadinstitute.org/gsea/msigdb/cards/UZONYI_RESPONSE_TO_LEUKOTRIENE_AND_THROMBIN.html Genes up-regulated in HUVEC cells (primary endothelium) after stimulation with leukotriene LTD4 [PubChem=3908] or thrombin (F2) [GeneID=2147] for 1 h. 16606835 53/80 Arthur Liberzon 4.56651576107688e-07 7.09011657640885e-06 175 1061.81818181818 253 4.15137882631255e-08 147 1.40342458232549 1.48324975706622 1 10.8437320167591 173 1931 253 2867 1200 147 234 992 3480 221 182 28 M8519 DAVICIONI_MOLECULAR_ARMS_VS_ERMS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_MOLECULAR_ARMS_VS_ERMS_DN.html Genes down-regulated in mARMS (molecular ARMS) compared to the mERMS (molecular ERMS) class of rhabdomyosarcoma tumors. 16849537 255/354 Arthur Liberzon 8.51045555709909e-09 1.91282620140513e-07 130 903.090909090909 258 7.73677780910986e-10 12 1.23744979124907 1.26494736639674 1 12.474601663962 129 2259 171 1708 1792 12 309 109 3082 258 105 29 M1348 SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_UP.html Genes up-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 12 h. 18794802 178/214 Jessica Robertson 1.25882962475949e-10 3.90899725583211e-09 55 865.727272727273 260 1.14439056802865e-11 52 1.2853635951055 1.25091749079363 1 16.2163943217666 188 2289 119 1812 677 54 657 260 3318 97 52 30 M589 GOUYER_TATI_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOUYER_TATI_TARGETS_UP.html Genes up-regulated in constitutively invasive HT-29 5M21 cells (colon cancer) vs those expressing functionally inactive TATI [GeneID=6690]. 18317448 10/14 Jessica Robertson 0.000181336032331594 0.00107173965007642 265 526.363636363636 261 1.6486452796742e-05 12 1.7552366009721 1.58103268525146 1 7.82194918535288 261 1062 989 779 1716 92 20 41 88 730 12 31 M9257 KEGG_DRUG_METABOLISM_CYTOCHROME_P450 http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DRUG_METABOLISM_CYTOCHROME_P450.html Drug metabolism - cytochrome P450 41/122 KEGG 1.20486639129874e-07 2.15415506323109e-06 270 363.636363636364 266 1.09533314298659e-08 80 1.44844460038305 -1.50099916106237 -1 12.3160644426306 266 182 277 660 224 80 136 723 790 128 534 32 M528 REACTOME_ER_PHAGOSOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ER_PHAGOSOME_PATHWAY.html Genes involved in ER-Phagosome pathway 77/109 Reactome 0.000213004650825929 0.00122907329082932 45 1689.63636363636 266 1.93659342541006e-05 44 0.64888586312742 -0.646845683974408 -1 2.83367408929246 44 2385 4009 2716 185 115 167 266 4181 4323 195 33 M14787 CLAUS_PGR_POSITIVE_MENINGIOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CLAUS_PGR_POSITIVE_MENINGIOMA_DN.html Genes down-regulated in meningioma samples positive for PGR [GeneID=5241] compared to those without the receptor. 18172325 16/16 Jessica Robertson 6.16548991102937e-06 6.6899108919675e-05 20 405.090909090909 274 5.60500653623123e-07 17 1.2814438785745 1.57495006816425 1 8.0269106148563 576 383 1010 274 19 276 168 17 119 1370 244 34 M11319 GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_UP.html Up-regulated genes from the set E (Fig. 5a): specific signature shared by cells expressing either MLL-AF4 [GeneID=4297;4299] or AF4-MLL fusion proteins alone, and those expressing both fusion proteins. 17130830 133/170 Arthur Liberzon 5.84012074047468e-10 1.66056445150846e-08 280 1018.45454545455 277 5.30920067456817e-11 15 1.39819806930532 1.39955507324034 1 16.3219863987501 277 1802 132 2537 1662 157 669 21 3687 244 15 35 M14228 RICKMAN_HEAD_AND_NECK_CANCER_A http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_A.html Cluster a: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 120/228 Jessica Robertson 8.83002750217709e-12 3.20597921617507e-10 75 740.727272727273 287 8.02729772928415e-13 27 1.44901008552203 1.4735230204444 1 20.6424867795462 75 1801 102 1956 601 27 287 375 2573 195 156 36 M17079 VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_UP.html Up-regulated genes distinguishing between two subtypes of gastric cancer: advanced (AGC) and early (EGC). 17297478 251/324 Arthur Liberzon 5.68558690924533e-24 9.2537828315993e-22 15 725.272727272727 295 5.1687153720412e-25 12 1.46056662928282 1.48933457463178 1 46.0975094305618 12 1723 19 1694 650 295 528 146 2770 46 95 37 M17095 REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SCF_BETA_TRCP_MEDIATED_DEGRADATION_OF_EMI1.html Genes involved in SCF-beta-TrCP mediated degradation of Emi1 53/63 Reactome 0.000403520390735433 0.00196757876474302 35 1002.90909090909 304 3.66904020722335e-05 34 0.61874202107432 -0.619020095803494 -1 2.51230181128344 34 132 3937 155 278 171 304 482 711 4308 520 38 M821 SCHLESINGER_METHYLATED_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SCHLESINGER_METHYLATED_IN_COLON_CANCER.html Genes expressed in normal colon; they undergo down-regulation in tumors through DNA methylation. 17200670 5/11 Leona Saunders 1.97483155664422e-05 0.000182054784128139 310 1345.63636363636 310 1.97484910668226e-06 6 1.64295695755486 1.64295695755486 1 9.21958012466616 310 3136 4417 1996 161 288 25 6 2254 2095 114 39 M806 REACTOME_POST_TRANSLATIONAL_MODIFICATION_SYNTHESIS_OF_GPI_ANCHORED_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_TRANSLATIONAL_MODIFICATION_SYNTHESIS_OF_GPI_ANCHORED_PROTEINS.html Genes involved in Post-translational modification: synthesis of GPI-anchored proteins 27/27 Reactome 0.000263983223977075 0.00143805682462909 885 1083.81818181818 312 2.40013550248368e-05 41 0.791395884966914 -0.569478133623185 -1 3.37505048610686 883 306 3280 115 207 78 312 1451 41 3969 1280 40 M884 REACTOME_RNA_POL_I_PROMOTER_OPENING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_PROMOTER_OPENING.html Genes involved in RNA Polymerase I Promoter Opening 23/75 Reactome 8.24503519721657e-05 0.000568125053005288 45 527.545454545455 312 7.4957674692566e-06 7 1.60673665858041 -1.60673665858041 -1 7.82473704939549 45 1504 934 1592 312 7 11 377 198 717 106 41 M3323 KANG_DOXORUBICIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_DOXORUBICIN_RESISTANCE_DN.html Genes down-regulated in gastric cancer cell lines: doxorubicin [PubChem=31703] resistant vs sensitive. 14734480 30/32 John Newman 0.000930754231169433 0.00376126709856141 235 817.818181818182 318 8.46498398954172e-05 162 0.882949718527626 0.924458642690156 1 3.21229457738466 232 272 2715 318 389 474 278 173 162 3040 943 42 M7346 KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_UP.html Top 25 most highly expressed genes in embryonic carcinoma relative to seminoma tumors. 16424014 21/29 Arthur Liberzon 8.44627276673648e-05 0.000579453596787736 45 523.727272727273 325 7.67872459520802e-06 19 1.25719804397938 1.19763521273475 1 6.10630051432253 325 1518 1203 122 497 155 44 19 737 1096 45 43 M12618 KESHELAVA_MULTIPLE_DRUG_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/KESHELAVA_MULTIPLE_DRUG_RESISTANCE.html Genes up-regulated in multiple drug resistant neuroblastoma cell lines. 17623797 105/144 Jessica Robertson 0.000594979002895234 0.00263442860568997 275 853.636363636364 330 5.41036339038832e-05 24 0.962892163561831 -0.90812588278282 -1 3.72658704659964 274 24 3195 94 330 26 379 1566 471 2840 191 44 M18107 WILENSKY_RESPONSE_TO_DARAPLADIB http://www.broadinstitute.org/gsea/msigdb/cards/WILENSKY_RESPONSE_TO_DARAPLADIB.html Atherosclerotic process genes whose coronary expression changed after darapladib [PubChem=9939609] treatment. 18806801 20/39 Jessica Robertson 0.000206187047625453 0.00119542176884588 340 907.272727272727 337 1.87460340270075e-05 18 1.64626897029304 1.7679412670607 1 7.21917566598968 160 3044 832 1967 337 75 18 336 2124 1020 67 45 M12828 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_UP.html Genes up-regulated in reverted NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845] which then reverted to normal cells upon stable over-expression of a dominant negative form of CDC25 [GeneID=5923]) vs normal fibroblasts. 16607279 177/214 Lauren Kazmierski 2.91973509710404e-06 3.5066538570817e-05 50 838.272727272727 338 2.65430815640403e-07 50 1.34935750147803 1.38075352866349 1 9.02031886360528 50 2768 338 2297 390 202 269 133 2100 194 480 46 M730 REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_ORNITHINE_DECARBOXYLASE_ODC.html Genes involved in Regulation of ornithine decarboxylase (ODC) 47/55 Reactome 0.000374494429999814 0.00186654034804554 35 1001.27272727273 341 3.40507448557641e-05 31 0.680046092646606 -0.61243578741344 -1 2.7845898744058 31 154 3812 346 341 209 239 822 73 4171 816 47 M828 MASSARWEH_TAMOXIFEN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MASSARWEH_TAMOXIFEN_RESISTANCE_DN.html Genes down-regulated in breast cancer tumors (formed by MCF-7 xenografts) resistant to tamoxifen [PubChem=5376]. 18245484 305/377 Jessica Robertson 4.48601673931574e-07 6.9881184850067e-06 1175 668.545454545455 341 4.07819786732637e-08 22 1.23120437535792 1.234426191641 1 9.52466469401854 259 1172 252 1175 2369 22 341 225 947 157 435 48 M19437 ALONSO_METASTASIS_NEURAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_NEURAL_UP.html Neural-related genes up-regulated in melanoma tumors that developed metastases compared to primary melanoma that did not. 17409456 25/34 Jessica Robertson 0.000249498452537351 0.00138219799997218 900 445.181818181818 342 2.26842502043489e-05 47 1.40511663563263 1.62496602417204 1 6.02873216543871 899 308 840 239 951 342 119 47 93 629 430 49 M17033 LINDSTEDT_DENDRITIC_CELL_MATURATION_A http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_A.html Maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli: genes up-regulated only at 8 hr after the stimulation (cluster A). 12356685 73/96 Arthur Liberzon 4.85349793809495e-06 5.49364754623697e-05 95 930.727272727273 344 4.4122805869107e-07 94 1.27498118161446 1.2553861717725 1 8.15011495664706 94 1870 337 2280 1475 183 344 196 2692 327 440 50 M14437 VALK_AML_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_5.html Top 40 genes from cluster 5 of acute myeloid leukemia (AML) expression profile; 96% of the samples are FAB M4 or M5 subtype. 15084694 32/69 Jessica Robertson 6.00483235186434e-05 0.000439423390710073 25 488.272727272727 345 5.45908750743661e-06 5 1.18924239957071 1.21476815134328 1 5.99060901877507 24 887 1078 1192 345 5 7 63 937 803 30 51 M1811 MATZUK_FERTILIZATION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_FERTILIZATION.html Genes important for fertilization, based on mouse models with female fertility defects. 18989307 7/11 Jessica Robertson 2.06195036505355e-05 0.00018644455408147 930 1072.36363636364 350 2.06196949768029e-06 53 0.830680859942677 -0.69696370335957 -1 4.64847980720259 927 445 4566 986 53 350 160 343 299 3363 304 52 M2318 KASLER_HDAC7_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/KASLER_HDAC7_TARGETS_1_DN.html Genes down-regulated in DO11.10 cells (hybridoma) by expression of transciptionally activating form of HDAC7 [GeneID=51564] and up-regulated by its transcriptionally repressing form. 17470548 26/28 Arthur Liberzon 0.00236278938169535 0.00758148598341404 350 635.454545454545 350 0.000215030075291902 122 1.37182271701637 1.486172754688 1 4.364308595672 329 930 1043 349 540 126 122 1852 350 1192 157 53 M1011 REACTOME_MEIOTIC_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_RECOMBINATION.html Genes involved in Meiotic Recombination 42/98 Reactome 0.00249894747890845 0.00790391091608911 225 698.909090909091 351 0.000227435501686486 45 1.36599713235192 -1.51298515083321 -1 4.30870019609099 203 221 1238 2077 1398 45 221 369 351 1355 210 54 M1362 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_UP.html Early prostate development genes (up-regulated at 12 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 18/20 Jessica Robertson 4.60079713637507e-05 0.000355413461271527 90 694.636363636364 351 4.18263032213454e-06 87 1.38669825611288 1.29859199586481 1 7.177018694591 367 1001 569 765 87 351 274 108 3696 333 90 55 M15472 VECCHI_GASTRIC_CANCER_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_EARLY_DN.html Down-regulated genes distinguishing between early gastric cancer (EGC) and normal tissue samples. 17297478 383/696 Arthur Liberzon 3.2562720071095e-34 1.53696038735568e-31 145 814.181818181818 354 2.96024727919048e-35 8 1.46911322709874 1.44640565450156 1 67.9258589497444 145 2227 8 1152 2043 354 459 50 2190 23 305 56 M6469 DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/DUNNE_TARGETS_OF_AML1_MTG8_FUSION_DN.html Genes down-regulated in Kasumi-1 cells (acute myeloid leukaemia (AML) with the t(8;21) translocation) after knockdown of the AML1 MTG8 fusion [GeneID=861;862] by RNAi. 16652140 27/39 Leona Saunders 0.000316294446797387 0.00165131475363624 185 770.363636363636 355 2.87581754244743e-05 90 1.58842656212253 1.60410584584349 1 6.63110192195531 182 933 610 1752 2267 217 355 90 1560 337 171 57 M2024 NAKAMURA_ADIPOGENESIS_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_EARLY_UP.html Genes up-regulated in mesenchymal stem cells during early phase of adipogenesis, defined as days 1 to 5 of culturing with adipogenic hormones. 12646203 81/96 Arthur Liberzon 0.00258103051280596 0.00808928553814352 320 1062 356 0.000234914868138871 48 1.15270169831085 1.1632802958331 1 3.61848160499462 317 83 1414 991 3556 48 182 356 3265 1401 69 58 M2375 EHRLICH_ICF_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/EHRLICH_ICF_SYNDROM_DN.html Down-regulated in B lymphocytes from patients with ICF syndrom caused by mutations in DNMT3B [GeneID=1789] compared to normals. 11741835 20/26 John Newman 0.00081014566084463 0.00338397125591739 155 1068.72727272727 362 7.36767408438708e-05 43 1.20598139540312 1.12764298417833 1 4.47064191575211 151 362 1094 1977 2591 154 43 172 3095 1761 356 59 M1322 INGRAM_SHH_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/INGRAM_SHH_TARGETS_DN.html Genes down-regulated in 10T1/2 cells (multipotent mesoderma) by expression of SHH [GeneID=6469]. 17873912 117/144 Jessica Robertson 6.36266674234066e-06 6.87226247685307e-05 85 1061.36363636364 365 5.78425922183531e-07 84 1.23817768787924 1.24870270908382 1 7.7341901516279 84 1811 348 2395 2163 199 297 365 3129 733 151 60 M18702 MARSON_FOXP3_TARGETS_STIMULATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_STIMULATED_DN.html Genes with promoters bound by FOXP3 [GeneID=50943], dependent on it, and down-regulated in hybridoma cells stimulated by PMA [PubChem=4792] and ionomycin [PubChem=3733]. 17237765 15/21 Arthur Liberzon 0.000319365133220855 0.00166253722973015 245 1259.81818181818 366 2.90374094176659e-05 61 0.954956079914586 1.00388754304839 1 3.98233635960489 241 2620 2530 2862 366 149 78 61 1300 3410 241 61 M212 PID_INTEGRIN5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN5_PATHWAY.html Beta5 beta6 beta7 and beta8 integrin cell surface interactions 18832364 23/26 Pathway Interaction Database 0.000659018684168274 0.00286424326820833 220 716.727272727273 367 5.99287435132552e-05 99 1.46524663976592 1.65107558349417 1 5.59099355103219 216 959 687 1008 367 116 99 103 3148 938 243 62 M510 REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CROSS_PRESENTATION_OF_SOLUBLE_EXOGENOUS_ANTIGENS_ENDOSOMES.html Genes involved in Cross-presentation of soluble exogenous antigens (endosomes) 46/55 Reactome 0.000137283022432122 0.00085259982352581 190 1188.18181818182 368 1.24810536208909e-05 20 0.678067479153728 -0.643911595544494 -1 3.12271927835302 20 161 3645 150 368 189 186 401 3260 3997 693 63 M1162 BAKER_HEMATOPOESIS_STAT1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BAKER_HEMATOPOESIS_STAT1_TARGETS.html STAT1 [GeneID=6772] targets in hematopoetic signaling. 17934481 10/11 Arthur Liberzon 3.18628710746139e-05 0.000268558484771746 860 657.363636363636 371 2.89666659616899e-06 8 1.39775698306041 1.46773575398952 1 7.48949377755059 859 1060 1390 1764 157 325 17 8 371 1090 190 64 M1404 LEI_HOXC8_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEI_HOXC8_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) by overexpression of HOXC8 [GeneID=3224]. 15699330 26/30 Kate Stafford 1.13247138457836e-05 0.00011421506271816 410 730.909090909091 372 1.02952474011537e-06 169 1.83323384028502 1.84595470259648 1 10.844325123908 410 942 372 760 3430 226 169 315 841 306 269 65 M12820 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_18 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_18.html Amplification hot spot 18: colocolized fragile sites and cancer genes in the 18q11.2-q23 region. 16751803 5/5 Arthur Liberzon 0.000433039907432841 0.00205835686111079 375 1193.36363636364 374 4.33124316186231e-05 30 1.16948588292489 1.16948588292489 1 4.71422759882194 374 1648 4375 2312 300 261 30 102 36 3085 604 66 M9435 GRADE_COLON_VS_RECTAL_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_VS_RECTAL_CANCER_DN.html Genes down-regulated in rectal but up-regulated in colon carcinoma compared to normal mucosa samples. 17210682 71/101 Jessica Robertson 0.000311948624791063 0.0016373254660183 95 626.727272727273 378 2.83629878432601e-05 93 1.1290234510905 -1.19501075872307 -1 4.71949029513154 978 93 1601 95 228 109 1267 591 378 1385 169 67 M14829 HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN http://www.broadinstitute.org/gsea/msigdb/cards/HESS_TARGETS_OF_HOXA9_AND_MEIS1_DN.html Genes down-regulated in hematopoietic precursor cells conditionally expressing HOXA9 and MEIS1 [GeneID=3205;4211]. 16507773 97/178 Kevin Vogelsang 3.34687165650013e-10 9.8119467196774e-09 255 738.272727272727 383 3.04261059728117e-11 33 1.43037202158127 1.39687054810459 1 17.1880054371318 255 1299 127 1208 2074 33 97 431 1936 278 383 68 M6937 CUI_TCF21_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_DN.html Genes most strongly down-regulated in kidney glomeruli isolated from TCF21 [GeneID=6943] knockout mice. 16207825 63/82 John Newman 1.49642599333763e-06 1.98402547431281e-05 50 1077.63636363636 385 1.36038819199821e-07 21 1.34652867464394 1.33958399763875 1 9.50116845730902 47 2430 294 2420 1694 21 32 385 3905 597 29 69 M19164 RICKMAN_HEAD_AND_NECK_CANCER_D http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_D.html Cluster d: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 19/70 Jessica Robertson 1.24918660501363e-05 0.000124391577545662 555 708.636363636364 388 1.13563063463875e-06 230 2.0478139637458 1.87006197178878 1 11.9997655937791 553 991 376 266 1910 1749 833 259 230 388 240 70 M733 REACTOME_REGULATION_OF_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_APOPTOSIS.html Genes involved in Regulation of Apoptosis 65/77 Reactome 0.000111758488734448 0.000722602831269311 300 1076.09090909091 392 1.01603787629726e-05 106 0.667383717593148 -0.628813813778313 -1 3.14546323713451 296 106 3866 392 142 302 387 742 752 4246 606 71 M15940 NAKAMURA_METASTASIS_MODEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_METASTASIS_MODEL_DN.html Bottom genes down-regulated in subcutaneous tumors from highly metastatic pancreatic cancer cells. 17210693 51/63 Jessica Robertson 0.000413233923857111 0.00200252989795233 300 611.181818181818 392 3.75737784991662e-05 71 1.43196083497305 1.44751251218612 1 5.79795349898204 297 167 868 753 1758 688 392 71 280 1340 109 72 M2445 PLASARI_TGFB1_TARGETS_10HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_10HR_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 10 h. 19752192 268/318 Arthur Liberzon 1.28968550445847e-14 6.99691446097011e-13 65 1260.18181818182 393 1.17244136768953e-15 63 1.24715329932904 1.25557585633832 1 22.746675356285 131 2735 65 3270 3013 63 356 624 3059 153 393 73 M11773 REACTOME_PECAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PECAM1_INTERACTIONS.html Genes involved in PECAM1 interactions 16/17 Reactome 0.000794537070453625 0.00333352442003654 310 910.545454545455 396 7.22567422945375e-05 41 1.39383912819461 1.42505310157524 1 5.18070054478192 307 396 1376 1336 2807 329 41 304 331 2326 463 74 M2526 BOSCO_ALLERGEN_INDUCED_TH2_ASSOCIATED_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_ALLERGEN_INDUCED_TH2_ASSOCIATED_MODULE.html Genes representing a co-expression network in atopic CD4 [GeneID=920] T lymphocyte responses. 19414752 168/248 Antony Bosco 1.17168388761682e-06 1.60765928766029e-05 560 543.909090909091 396 1.06516773785172e-07 210 1.40837515186303 1.35117982988549 1 10.1306212559878 557 592 285 269 1566 235 534 396 1068 210 271 75 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 2.37164275087636e-06 2.93040674977394e-05 5 749.909090909091 398 2.37164528199037e-07 2 1.53897316432266 1.53897316432266 1 10.467936773259 398 454 4582 683 13 42 4 332 630 1109 2 76 M14791 SABATES_COLORECTAL_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_DN.html Genes down-regulated in colorectal adenoma compared to normal mucosa samples. 18171984 280/566 Leona Saunders 6.56807345354183e-36 3.87516333758968e-33 85 1240.18181818182 400 5.97097586685625e-37 7 1.56450996289227 1.4968698792024 1 76.0889308386369 83 2731 7 2798 2795 400 596 287 3601 41 303 77 M1246 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_DN.html Genes down-regulated in Wilm's tumor vs fetal kidney. 15531917 89/104 Arthur Liberzon 2.9909449912183e-09 7.46944992515894e-08 20 854.181818181818 400 2.71904090480414e-10 19 1.50848467499978 1.62806032700935 1 16.1312875402264 19 1314 153 1877 1544 338 475 298 2915 400 63 78 M63 PID_AVB3_OPN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AVB3_OPN_PATHWAY.html Osteopontin-mediated events 18832364 48/54 Pathway Interaction Database 0.000312634336679337 0.0016377736616276 350 718.818181818182 407 2.84253429906102e-05 60 1.2899070680672 1.42123351131526 1 5.39179337362821 348 823 1485 1659 892 279 235 60 289 1430 407 79 M671 REACTOME_REVERSIBLE_HYDRATION_OF_CARBON_DIOXIDE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REVERSIBLE_HYDRATION_OF_CARBON_DIOXIDE.html Genes involved in Reversible Hydration of Carbon Dioxide 6/12 Reactome 0.000220988686172808 0.00127048306788752 160 1269.36363636364 411 2.21010665448816e-05 19 1.74391159439934 1.74391159439934 1 7.57815410768541 157 1091 4214 1700 4553 300 19 212 361 945 411 80 M7439 DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_DN.html Genes down-regulated in fibroblasts expressing different mutant forms of ERCC3 [GeneID=2071]: XP/CS (xeroderma pigmentosum (XP) and Cockraine's syndrome (CS)) vs TTD (trichothiodystrophy). 15608684 63/72 Arthur Liberzon 3.61223109982487e-07 5.76241950559762e-06 115 939.818181818182 413 3.28384699356875e-08 112 1.75088198339298 1.65548842165949 1 13.7650088571186 112 2427 245 1808 760 369 624 246 2969 365 413 81 M16574 PACHER_TARGETS_OF_IGF1_AND_IGF2_UP http://www.broadinstitute.org/gsea/msigdb/cards/PACHER_TARGETS_OF_IGF1_AND_IGF2_UP.html Genes up-regulated in MCF7 cells (breast cancer) by IGF1 and IGF2 [GeneID=3479;3481]. 16774935 41/51 Arthur Liberzon 5.27598661071572e-05 0.000398442508841251 345 719.727272727273 414 4.79646649308591e-06 94 1.20013977857821 1.15566335000503 1 6.12207066739859 772 204 723 1168 94 344 414 1353 2137 367 341 82 M1483 SCHURINGA_STAT5A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHURINGA_STAT5A_TARGETS_DN.html Genes down-regulated in hematopoietic stem cells (HSC) overexpressing a constitutively active form of STAT5 [GeneID=6776] off retroviral vector. 15353555 13/96 Kevin Vogelsang 2.68670247016078e-05 0.000231832461776214 555 616.272727272727 416 2.44248661954112e-06 33 1.82040774323377 1.72570075209397 1 9.92863281701701 555 1573 671 1691 60 131 33 416 408 1053 188 83 M10450 REACTOME_GAB1_SIGNALOSOME http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAB1_SIGNALOSOME.html Genes involved in GAB1 signalosome 46/46 Reactome 0.00303312828691272 0.00912795565581309 375 980 418 0.000276119830372239 105 0.833488757950809 0.904109191455492 1 2.55078690260468 373 191 3240 418 595 105 164 277 724 3998 695 84 M10680 KEGG_PROTEASOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEASOME.html Proteasome 41/48 KEGG 4.30354849001876e-05 0.000339110999547388 15 1004.09090909091 422 3.912393342318e-06 14 0.633902971291761 -0.630093557970461 -1 3.30017791590739 14 178 3910 773 458 172 236 422 33 4215 634 85 M13596 YANAGISAWA_LUNG_CANCER_RECURRENCE http://www.broadinstitute.org/gsea/msigdb/cards/YANAGISAWA_LUNG_CANCER_RECURRENCE.html Genes defining a 25-signal proteomic signature associated with a high risk of cancer recurrence and poor survival of NSCLC (non-small cell lung cancer) patients. 17551146 11/31 Jessica Robertson 0.000376719548984851 0.0018717013381142 430 1008 430 3.42530974965529e-05 31 1.46728603073059 -1.46728603073059 -1 6.00558950681871 430 2642 1969 2173 260 135 31 1375 199 1722 152 86 M17636 KEGG_RENIN_ANGIOTENSIN_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENIN_ANGIOTENSIN_SYSTEM.html Renin-angiotensin system 10/30 KEGG 2.34212767088005e-05 0.000206632572085118 605 601.909090909091 432 2.12922964147685e-06 54 1.62450551663182 1.60309588948278 1 8.98197715433489 602 432 1255 308 54 269 205 1207 519 1590 180 87 M2574 LIM_MAMMARY_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_STEM_CELL_DN.html Genes consistently down-regulated in mammary stem cells both in mouse and human species. 20346151 572/695 Daniel Hollern 5.77271821425446e-05 0.000426617300967481 5 920.818181818182 432 5.77286817897739e-06 4 1.08612829488622 -1.08450955047726 -1 5.49211359957998 211 488 4715 4 1207 4 1929 327 432 686 126 88 M697 KONDO_COLON_CANCER_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_COLON_CANCER_HCP_WITH_H3K27ME3.html Genes with high histone H3 tri-methylation mark at K27 (H3K27me3) in SW48 cells (colon cancer), by ChIP-chip assay on a 12K CpG array (high-CpG-density promoters, HCP). 18488029 5/21 Jessica Robertson 8.21770364983543e-07 1.17833070041186e-05 85 1128.81818181818 433 8.21770668871641e-08 5 1.00398196133994 -1.11653367653691 -1 7.42500590534467 1749 1645 4528 550 5 433 123 83 127 3089 85 89 M4957 FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_UP.html Genes up-regulated in thyroid tumors of uncertain malignancy (T-UM) compared to other thyroid tumors. 17968324 40/58 Arthur Liberzon 0.00536668299074281 0.0140648216081655 1555 914.363636363636 433 0.00048907448812142 109 1.14577559768381 -1.14149189784104 -1 3.18373158352823 1555 222 1332 109 2849 377 426 389 1118 1248 433 90 M17695 REACTOME_PACKAGING_OF_TELOMERE_ENDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PACKAGING_OF_TELOMERE_ENDS.html Genes involved in Packaging Of Telomere Ends 20/64 Reactome 0.000560870419168357 0.00252364955050014 290 880 435 5.10012235587133e-05 25 1.53145597484765 -1.61930476635573 -1 5.96998056896327 288 2582 1366 2168 323 158 1000 320 435 1015 25 91 M19632 ZHAN_MULTIPLE_MYELOMA_MS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MS_UP.html Top 50 up-regulated genes in cluster MS of multiple myeloma samples with characteristic expression spike of WHSC1 [GeneID=7468]. 16728703 67/75 Kevin Vogelsang 0.00304490178827526 0.00913942469514037 250 923 438 0.000277193114293427 116 0.96850803251941 1.01780925603733 1 2.96322093515947 247 750 2095 1713 1652 127 116 434 438 2448 133 92 M507 REACTOME_GPCR_LIGAND_BINDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPCR_LIGAND_BINDING.html Genes involved in GPCR ligand binding 162/454 Reactome 7.63307316048306e-23 1.02937443764229e-20 400 1239.09090909091 440 6.93915741862093e-24 5 1.73633371234335 1.67638275585646 1 52.0752070769996 400 2301 23 3265 3822 11 440 981 2286 96 5 93 M1962 MIKKELSEN_MEF_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the bivalent tri-methylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MEF cells (embryonic fibroblasts). 18509334 27/63 Jessica Robertson 3.91722654231595e-05 0.00031284787275349 1650 535.636363636364 440 3.56117844775129e-06 77 1.55492061803245 -1.63169289271242 -1 8.17694626174682 1647 299 432 440 173 548 781 276 480 739 77 94 M12882 KEGG_TAURINE_AND_HYPOTAURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TAURINE_AND_HYPOTAURINE_METABOLISM.html Taurine and hypotaurine metabolism 8/12 KEGG 6.74727465482434e-06 7.18896983538847e-05 1225 917.636363636364 443 6.74729514148376e-07 25 1.8564725814837 -1.49054323223628 -1 11.5418716427713 1225 439 4181 252 25 943 225 443 419 827 1115 95 M713 REACTOME_NEGATIVE_REGULATION_OF_THE_PI3K_AKT_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEGATIVE_REGULATION_OF_THE_PI3K_AKT_NETWORK.html Genes involved in Negative regulation of the PI3K/AKT network 8/8 Reactome 4.97263365663857e-05 0.000379118705621224 1135 1543.09090909091 443 4.97274493202769e-06 95 0.699747399217744 0.769829188839179 1 3.59212893390677 1132 443 4222 375 95 848 144 270 4523 4534 388 96 M4562 LENAOUR_DENDRITIC_CELL_MATURATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LENAOUR_DENDRITIC_CELL_MATURATION_UP.html Genes up-regulated during in vitro maturation of CD14+ [GeneID=929] monocytes (day 0) into immature (day 7) and mature dendritic cells (day 14). 11279020 133/177 Kevin Vogelsang 1.66893052965311e-11 5.83507562960197e-10 350 577.545454545455 448 1.51720957242343e-12 72 1.51911423898462 1.53540645474589 1 21.0483347920227 347 623 106 448 2334 72 522 284 965 180 472 97 M2143 HOELZEL_NF1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOELZEL_NF1_TARGETS_DN.html Genes down-regulated in SH-SY5Y cells (neuroblastoma) after knockdown of NF1 [GeneID=4763] by RNAi. 20655465 134/179 Arthur Liberzon 1.24926166202112e-09 3.2577431186407e-08 170 1390.81818181818 448 1.1356924206641e-10 98 1.35750601222799 1.38761708558779 1 15.2508206411247 98 3646 145 3759 2286 166 448 641 3666 276 168 98 M2231 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_UP.html Genes from the black module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 54/61 Arthur Liberzon 0.001365258709171 0.00497992357595605 455 947.272727272727 451 0.000124191517046042 135 1.04170234575465 1.11029026500505 1 3.59935452511855 234 149 2455 135 3615 251 451 174 996 1507 453 99 M11064 HALMOS_CEBPA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HALMOS_CEBPA_TARGETS_UP.html Genes up-regulated in H358 cells (lung cancer) by inducible expression of CEBPA [GeneID=1050] off plasmid vector. 15205324 77/99 Kevin Vogelsang 5.64043890817536e-05 0.000419657465953116 235 836.181818181818 451 5.12780320451093e-06 58 1.33876399791726 1.25304295882004 1 6.78396545927621 233 1331 451 554 2331 58 229 595 2945 403 68 100 M2576 LIM_MAMMARY_LUMINAL_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_LUMINAL_PROGENITOR_DN.html Genes consistently down-regulated in mammary luminal progenitor cells both in mouse and human species. 20346151 28/33 Daniel Hollern 0.000622218292584117 0.00273337113055396 290 589.545454545455 454 5.6581303828723e-05 98 1.356328927703 -1.27597547356375 -1 5.21672203764395 287 282 707 454 398 179 569 98 1799 1041 671 101 M15122 OZEN_MIR125B1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OZEN_MIR125B1_TARGETS.html Potential targets of MIR125B1 [GeneID=406911] microRNA which are up-regulated in prostate cancer. 17891175 39/45 Jessica Robertson 0.000677138289153999 0.00293334130328078 660 971.636363636364 455 6.15769814081108e-05 105 1.02875242869602 -1.15599404823334 -1 3.90943450764351 659 242 2773 1097 1174 455 232 105 293 3537 121 102 M3815 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_27 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_27.html Amplification hot spot 27: colocalized fragile sites and cancer genes in the 5p15.3-p15.1; 5p12-q35 region. 16751803 16/22 Arthur Liberzon 3.74275271824097e-05 0.000304058396387218 980 671 456 3.4025603576222e-06 76 1.27694475644999 1.31030501917071 1 6.738834261999 976 386 1490 323 76 456 134 89 955 1798 698 103 M4680 DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_UP.html Genes up-regulated in RD cells (embryonal rhabdomyosarcoma, ERMS) by expression of PAX3- or PAX7-FOXO1 [GeneID=5077;5081;2308] fusions off retroviral vectors. 16849537 366/462 Arthur Liberzon 7.43556909441125e-13 3.19053510232919e-11 680 630.454545454545 458 6.75960826764887e-14 43 1.21424833880465 1.25601207244607 1 19.1238968204505 246 1158 85 680 669 43 677 458 2527 91 301 104 M259 MANALO_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANALO_HYPOXIA_UP.html Genes up-regulated in response to both hypoxia and overexpression of an active form of HIF1A [GeneID=3091]. 15374877 342/437 Kate Stafford 2.03851717984013e-07 3.48615981479907e-06 265 1046.27272727273 458 1.85319760793536e-08 94 1.19739139972031 1.24625452615091 1 9.8057124164427 263 2240 228 2414 1317 169 815 94 3356 458 155 105 M2108 VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_ADVANCED_VS_EARLY_DN.html Down-regulated genes distinguishing between two subtypes of gastric cancer: advanced (AGC) and early (EGC). 17297478 114/210 Arthur Liberzon 3.53653038577277e-07 5.67769504110458e-06 300 484 459 3.21502814025003e-08 5 1.37016692482631 -1.30995778491633 -1 10.785122151131 298 13 244 5 616 459 1543 492 499 207 948 106 M14418 MARTINELLI_IMMATURE_NEUTROPHIL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINELLI_IMMATURE_NEUTROPHIL_UP.html Neutrophil-specific genes up-regulated in comparison of immature with mature neutrophils. 15302890 2/65 Arthur Liberzon 1.15341493480082e-05 0.000115341493480082 555 994.9 462.5 1.2815787195351e-06 3 2.3541600858457 2.3541600858457 1 13.9107901642794 551 1107 4597 NA 106 144 3 1732 66 1269 374 107 M9325 MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_DN.html Down-regulated 'cooperation response genes': responded synergystically to the combination of mutant TP53 and HRAS [GeneID=7157;3265] in YAMC cells (colon). 18500333 99/122 Jessica Robertson 1.97295622180174e-05 0.000182054784128139 405 1005.09090909091 463 1.79361265041945e-06 234 1.31753287097146 1.43444965940007 1 7.393416714944 404 1292 418 740 3697 316 330 463 2359 234 803 108 M1325 MANTOVANI_NFKB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_NFKB_TARGETS_UP.html NF-kB-controlled genes up-regulated in endothelial cells in response to viral GPCR protein. 17906691 66/77 Jessica Robertson 6.43722324962071e-06 6.90538494050222e-05 370 926.363636363636 464 5.85203825916466e-07 99 1.66328119269757 1.8075331323017 1 10.3843941461681 370 120 351 99 3986 726 1079 1306 464 341 1348 109 M15780 GRADE_COLON_AND_RECTAL_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_AND_RECTAL_CANCER_DN.html Down-regulated genes in both rectal and colon carcinoma compared to normal mucosa samples. 17210682 150/198 Jessica Robertson 3.67206820863446e-05 0.000300384089163859 205 798.545454545455 464 3.33829954669261e-06 17 1.29076298510793 1.25272057561258 1 6.82198502716977 204 2304 426 955 478 17 441 464 2547 920 28 110 M17879 REACTOME_COMMON_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMMON_PATHWAY.html Genes involved in Common Pathway 10/15 Reactome 6.91120982274013e-05 0.000492762996424976 465 609.454545454545 465 6.2831154046482e-06 144 2.061632325376 -2.20757969903286 -1 10.2312866411602 334 1059 464 939 144 454 465 1084 355 480 926 111 M568 REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_EVENTS_IN_ERBB4_SIGNALING.html Genes involved in PI3K events in ERBB4 signaling 44/44 Reactome 0.00331188768840174 0.00980425330377675 570 1115.09090909091 466 0.00030153490443827 141 0.892084720491378 0.947651208706161 1 2.68856866692507 567 195 2616 407 3368 141 203 290 889 3124 466 112 M10778 CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY http://www.broadinstitute.org/gsea/msigdb/cards/CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY.html Genes down-regulated in T cell acute lymphocytic leukemia (T-ALL) patients refractory to chemotherapy treatment. 14684422 36/69 Arthur Liberzon 0.000260438681398777 0.00142441549965496 760 621.727272727273 469 2.36790470507291e-05 23 1.32075116189535 -1.37567636271204 -1 5.64085575849797 756 250 1016 399 2099 359 469 49 614 805 23 113 M6679 BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_DN.html Genes down-regulated in SaOS-2 cells (osteosarcoma) upon expression of PAX3-FOXO1 [GeneID=5077;2308] fusion protein off an adenoviral vector. 15688035 78/91 Leona Saunders 1.10524955639939e-05 0.000111708306342722 165 1410.90909090909 471 1.00477737187206e-06 94 1.26777968294012 1.29722095302635 1 7.51773522872869 161 2395 371 2939 4071 94 400 1170 3317 471 131 114 M547 REACTOME_SULFUR_AMINO_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SULFUR_AMINO_ACID_METABOLISM.html Genes involved in Sulfur amino acid metabolism 22/27 Reactome 0.00169505363045588 0.00590003483362169 485 698.545454545455 481 0.000154214640367032 211 1.15726143003466 -1.25219888047706 -1 3.87079182821921 338 345 2105 509 481 408 481 211 306 1919 581 115 M5014 TSUNODA_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSUNODA_CISPLATIN_RESISTANCE_DN.html Genes down-regulated in bladder cancer cells resistant to cisplatin [PubChem=2767] compared to the parental cells sensitive to the drug. 15608674 64/80 Leona Saunders 1.98494297942964e-07 3.40688395014832e-06 110 590.909090909091 484 1.80449378047319e-08 109 1.390900299345 1.3366988583557 1 11.4112679859008 508 109 259 925 517 484 1335 309 1806 138 110 116 M986 SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_UP.html Genes up-regulated in circulating endothelial cells (CEC) from cancer patients compared to those from healthy donors. 16540638 227/329 Arthur Liberzon 8.04874841379265e-11 2.54967063846318e-09 490 1157.18181818182 487 7.31704401280646e-12 37 1.27412773244439 1.23836438125157 1 16.4294439535184 487 2753 117 2346 2023 123 995 329 3299 220 37 117 M12383 OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_UP.html Genes up-regulated in hematopoietic stem cells (HSC, CD34+ [GeneID=947]) cultured in a three-dimentional collagen gel compared to the cells grown in suspension. 16166251 306/392 Leona Saunders 4.52124398576132e-06 5.15465497893561e-05 380 1114.45454545455 487 4.11023025222351e-07 90 1.26624700453816 1.17292446409688 1 8.14683945747947 376 2250 335 3377 1450 90 487 395 2637 277 585 118 M257 PID_EPHRINB_REV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHRINB_REV_PATHWAY.html Ephrin B reverse signaling 18832364 44/52 Pathway Interaction Database 0.00105756577062811 0.00414593890146566 490 469.272727272727 489 9.61885906624031e-05 98 1.40224567169604 1.41285730379027 1 5.01264852510322 489 185 882 841 919 117 98 145 173 799 514 119 M3210 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 3 days after transduction. 16818636 27/55 Arthur Liberzon 0.000118053963946468 0.000758115251465756 280 976.090909090909 489 1.07327544821374e-05 208 1.47519558579844 1.36375208637362 1 6.90678926432876 276 919 489 1185 4039 208 316 467 1847 446 545 120 M8696 VALK_AML_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_7.html Top 40 genes from cluster 7 of acute myeloid leukemia (AML) expression profile; 61% of the samples are FAB M1 or M2 subtype. 15084694 33/47 Jessica Robertson 3.19624941092381e-05 0.000268677072551052 435 1291.45454545455 490 2.90572349843525e-06 1 1.36207515629586 1.22428302924417 1 7.29790802568348 432 3392 2296 860 4201 490 184 22 309 2019 1 121 M552 REACTOME_PROLACTIN_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROLACTIN_RECEPTOR_SIGNALING.html Genes involved in Prolactin receptor signaling 14/41 Reactome 6.0790090958483e-05 0.000443488091257858 1145 1004.36363636364 492 5.52652461515637e-06 23 0.818116580521999 -0.901000913161318 -1 4.11618304119382 1144 395 2768 492 100 833 951 415 23 3880 47 122 M8831 BRUECKNER_TARGETS_OF_MIRLET7A3_UP http://www.broadinstitute.org/gsea/msigdb/cards/BRUECKNER_TARGETS_OF_MIRLET7A3_UP.html Genes up-regulated in A549 cells (lung cancer) expressing MIRLET7A3 [GeneID=406883] microRNA off a plasmid vector. 17308078 156/201 Jessica Robertson 0.000125108476429993 0.000793698936491356 545 895.818181818182 495 1.13741446910376e-05 266 1.21056755171432 1.12971722230754 1 5.63161021673734 542 1767 495 326 3126 317 918 473 1303 321 266 123 M4904 REACTOME_G_ALPHA_S_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_S_SIGNALLING_EVENTS.html Genes involved in G alpha (s) signalling events 59/145 Reactome 1.33460064299086e-05 0.000132338551153716 560 1017.27272727273 503 1.21328067203303e-06 19 1.38407016729094 1.26602366914227 1 8.05447310842374 559 777 378 1205 4688 98 360 232 2371 503 19 124 M554 REACTOME_SPHINGOLIPID_DE_NOVO_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPHINGOLIPID_DE_NOVO_BIOSYNTHESIS.html Genes involved in Sphingolipid de novo biosynthesis 33/37 Reactome 0.00073335372332447 0.00312968315921474 800 1038 504 6.6690754136991e-05 14 1.13315536565354 -1.13406661543657 -1 4.25835090704345 799 281 2507 521 4004 504 357 215 201 2015 14 125 M1525 ZHENG_RESPONSE_TO_ARSENITE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_RESPONSE_TO_ARSENITE_DN.html Down-regulated in HEK293 cells (kidney epithelium) by treatment with sodium arsenite [PubChem=26435]. 12679051 25/29 John Newman 0.000589793083841552 0.00262093635000982 935 681.090909090909 504 5.36319326837792e-05 139 1.41380143470175 1.44553651477573 1 5.47647722528145 931 316 789 504 1515 315 139 562 1685 384 352 126 M597 REACTOME_ACTIVATION_OF_NF_KAPPAB_IN_B_CELLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_NF_KAPPAB_IN_B_CELLS.html Genes involved in Activation of NF-kappaB in B Cells 65/77 Reactome 0.000370329314074983 0.00185164657037491 505 1161.90909090909 505 3.36719697146448e-05 100 0.649002988996541 -0.62631775058784 -1 2.66086088845712 505 100 3946 166 256 390 1038 459 1069 4311 541 127 M703 REACTOME_ACYL_CHAIN_REMODELLING_OF_PS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PS.html Genes involved in Acyl chain remodelling of PS 8/16 Reactome 0.00161560674226942 0.00569079389814302 385 940.272727272727 505 0.000161678252884882 15 1.55798812759251 -1.65724750113886 -1 5.2478341239454 785 437 4220 15 505 1339 1247 201 385 828 381 128 M10276 LEE_NEURAL_CREST_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_NEURAL_CREST_STEM_CELL_DN.html Genes down-regulated in the neural crest stem cells (NCS), defined as p75+/HNK1+ [GeneID=4804;27087]. 18037878 178/239 Arthur Liberzon 1.55402850464503e-05 0.000149389298206203 390 1237.45454545455 505 1.41276316549745e-06 104 1.26340969890127 1.34197340380193 1 7.25251067149243 387 3197 384 2333 1790 258 873 104 3378 505 403 129 M18215 BIOCARTA_TOB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TOB1_PATHWAY.html Role of Tob in T-cell activation 12/22 BioCarta 7.70583814709218e-05 0.00053566356486414 120 669 506 7.00555279013972e-06 117 1.025059515043 1.15055406961215 1 5.0312584102356 1255 416 1796 119 117 1000 472 506 163 633 882 130 M19056 REACTOME_AMINO_ACID_AND_OLIGOPEPTIDE_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINO_ACID_AND_OLIGOPEPTIDE_SLC_TRANSPORTERS.html Genes involved in Amino acid and oligopeptide SLC transporters 34/55 Reactome 0.000128979763112953 0.000812796371018879 1160 1007.63636363636 511 1.1726120495593e-05 240 1.41880577813479 1.32239278363122 1 6.57837783365828 1156 247 496 240 483 1303 870 2971 511 452 2355 131 M4913 IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_DN.html Genes down-regulated in adipose tissue mesenchymal stem cells (ASC) vs bone marrow mesenchymal stem cells (rBMSC) 18519682 192/245 Leona Saunders 2.11197339002995e-10 6.34937222989897e-09 230 1158.18181818182 511 1.91997580930246e-11 123 1.23241527423268 1.23493317485957 1 15.1588078120371 226 2287 123 2388 1415 511 797 195 4153 502 143 132 M1991 MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_DN.html Genes down-regulated in derivatives of MCF-7aro cells (breast cancer) that developed resistance to tamoxifen [PubChem=5376] or inhibitors of aromatase (CYP19A1) [GeneID=1588]. 18559539 31/34 Leona Saunders 0.000119466726801135 0.000765105767301707 105 1044.09090909091 514 1.086120133663e-05 30 1.78651793235095 1.87242493284482 1 8.3537207440455 104 2999 514 3518 2224 238 172 30 1065 585 36 133 M17002 REACTOME_BILE_SALT_AND_ORGANIC_ANION_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BILE_SALT_AND_ORGANIC_ANION_SLC_TRANSPORTERS.html Genes involved in Bile salt and organic anion SLC transporters 6/12 Reactome 0.000327162359437224 0.00168261410046973 355 1444.90909090909 515 3.27210535263936e-05 65 1.37332353169264 1.37332353169264 1 5.71630653304705 353 3133 4244 3715 515 397 121 65 1477 1546 328 134 M19779 FARMER_BREAST_CANCER_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_6.html Cluster 6: selected luminal genes clustered together across breast cancer samples. 15897907 22/26 Leona Saunders 0.00075555240595505 0.0032003023509053 520 686.454545454545 517 6.87101829406137e-05 32 1.31721031621449 -1.40088321128073 -1 4.93088542324127 517 947 2292 524 1118 174 143 112 32 1534 158 135 M1813 MATZUK_IMPLANTATION_AND_UTERINE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_IMPLANTATION_AND_UTERINE.html Genes important for implantation and uterine, based on mouse models with female fertility defects. 18989307 20/32 Jessica Robertson 0.000172435263942985 0.00102764450228647 2860 1460.90909090909 518 1.56771618949577e-05 171 1.64844856620612 -2.15211513919664 -1 7.39119086234443 2858 360 1302 518 171 4083 3771 337 425 1762 483 136 M5522 ROZANOV_MMP14_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_TARGETS_DN.html Genes down-regulated in HT1080 cells (fibrosarcoma) over-expressing MMP14 [GeneID=4323] compared to those with knockdown of the gene by RNAi. 18519667 34/48 Jessica Robertson 0.00904375456428074 0.0202114211853244 325 680.727272727273 519 0.000825558816700496 268 1.12424457754921 1.22990516306882 1 2.85827018998507 324 275 1535 756 869 358 268 519 1260 903 421 137 M11516 ADDYA_ERYTHROID_DIFFERENTIATION_BY_HEMIN http://www.broadinstitute.org/gsea/msigdb/cards/ADDYA_ERYTHROID_DIFFERENTIATION_BY_HEMIN.html Selected genes changed in K562 (immortalized erythroleukemia) cells induced by hemin [PubChem=26945] treatment to express erythroid properties. 15252187 91/129 Kevin Vogelsang 5.21154592939558e-06 5.8428733460207e-05 275 761 519 4.73778024998815e-07 47 1.29053794773596 1.10351431761185 1 8.1977292561996 275 1312 341 826 1660 47 185 926 1855 425 519 138 M570 REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_EVENTS_IN_ERBB2_SIGNALING.html Genes involved in PI3K events in ERBB2 signaling 47/47 Reactome 0.00335136941378961 0.00985574058136258 525 1106.63636363636 521 0.000305135057830697 148 0.895204574435473 0.949160133352255 1 2.69491606978523 521 181 2657 414 2850 148 165 293 1081 3284 579 139 M16650 KEGG_PHENYLALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHENYLALANINE_METABOLISM.html Phenylalanine metabolism 20/27 KEGG 0.000564610155351697 0.00253323187572244 395 589.272727272727 524 5.13413735944955e-05 121 1.40607462128531 -1.45702669335138 -1 5.47773290408768 395 1532 914 953 324 121 132 708 329 550 524 140 M11885 NIELSEN_SCHWANNOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SCHWANNOMA_DN.html Top 20 negative significant genes associated with schwannoma tumors. 11965276 28/31 Arthur Liberzon 8.1333699237903e-05 0.000561306651401695 470 697.727272727273 524 7.39424602629857e-06 154 1.24742432680735 1.19816956549921 1 6.08469326696198 723 291 470 935 1037 909 524 505 1659 468 154 141 M9128 KIM_WT1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_UP.html Genes up-regulated in UB27 cells (osteosarcoma) at any time point after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 289/336 Arthur Liberzon 0.000121002085564948 0.000772841466666513 170 1128.81818181818 526 1.10007946642608e-05 87 1.14469778614457 1.10603957009423 1 5.34504077669294 167 2251 518 2285 2398 87 380 1434 2083 288 526 142 M12784 RHEIN_ALL_GLUCOCORTICOID_THERAPY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RHEIN_ALL_GLUCOCORTICOID_THERAPY_UP.html Genes up-regulated in ALL (acute lymphoblastic leukemia) blasts after 1 week of treatment with glucocorticoids. 17330098 104/190 Arthur Liberzon 0.000154010330439874 0.000940399430370252 445 1010.09090909091 528 1.40019193584504e-05 36 1.34858239897533 1.27048672851169 1 6.12462347998023 445 36 504 528 2782 686 837 523 3198 311 1261 143 M6951 ELLWOOD_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELLWOOD_MYC_TARGETS_DN.html Genes down-regulated in transgenic mice expressing human MYC [GeneID=4609] in prostate. 14522256 55/73 Arthur Liberzon 0.00124180394247061 0.00464078749680228 530 589.363636363636 529 0.000112955040089989 56 1.39163586311028 -1.5274568407488 -1 4.87246501544073 529 131 1170 56 437 321 564 1413 334 897 631 144 M5574 CAFFAREL_RESPONSE_TO_THC_24HR_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_3_DN.html Genes down-regulated in EVSA-T cells (breast cancer) after treatment with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 19/26 Jessica Robertson 0.000181423724663361 0.00107173965007642 535 926.272727272727 532 1.64944261416447e-05 39 1.06183248314048 -1.16690104802714 -1 4.73185571706842 532 1537 2226 1010 1443 306 131 42 312 2611 39 145 M17669 XU_CREBBP_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_CREBBP_TARGETS_UP.html Genes up-regulated in pro-B lymphocytes after knockout of CREBBP [GeneID=1387]. 16424387 32/34 Kevin Vogelsang 0.00023861099535869 0.00135041234783336 960 702.818181818182 534 2.16942617207834e-05 58 1.29889510060796 -1.3822081027952 -1 5.59266728533313 960 252 1220 58 195 534 1285 394 120 1950 763 146 M15326 HUANG_FOXA2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_FOXA2_TARGETS_UP.html Genes up-regulated in H358 cells (lung cancer) by inducible expression of FOXA2 [GeneID=3170] in a Tet-off system. 18593902 65/77 Leona Saunders 0.000730238278485116 0.00311920785018077 305 1254.27272727273 535 6.64073433281431e-05 281 1.44650458183946 1.3456042491839 1 5.43909392757776 304 3298 595 2909 2441 296 281 445 2230 463 535 147 M3238 SMID_BREAST_CANCER_RELAPSE_IN_BONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BONE_UP.html Genes up-regulated in bone relapse of breast cancer. 18451135 119/168 Jessica Robertson 2.71464662436213e-07 4.52760850423649e-06 3850 1399.72727272727 536 2.46786087211878e-08 11 1.37866866207392 -1.54517729884423 -1 11.0554051070421 3849 11 291 249 1490 1946 4171 2296 413 145 536 148 M2458 SANDERSON_PPARA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANDERSON_PPARA_TARGETS.html Hepatic genes regulated by fasting or in response to WY14643 [PubChem=5694] and which require intact PPARA [GeneID=5465]. 19805517 16/18 Arthur Liberzon 0.000845232540455916 0.00349037409532102 295 862 538 7.68688591551496e-05 123 1.03482761641867 -1.11083631307034 -1 3.81527245670235 292 379 1817 690 538 156 307 123 2046 2332 802 149 M19752 REACTOME_COMPLEMENT_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COMPLEMENT_CASCADE.html Genes involved in Complement cascade 22/39 Reactome 0.000258601698024236 0.00141930234264464 145 1305.27272727273 539 2.3512009152845e-05 72 1.5796821382452 1.56517126824054 1 6.75045843744269 72 2576 539 2800 3038 500 261 144 3404 879 145 150 M2030 NAKAMURA_ADIPOGENESIS_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_LATE_DN.html Genes down-regulated in mesenchymal stem cells during late phase of adipogenesis, defined as days 7 to 14 of culturing with adipogenic hormones. 12646203 53/61 Arthur Liberzon 0.000703894337006014 0.00302860644545888 135 1545.81818181818 543 6.40108773016771e-05 133 1.46276044730197 1.51230334938307 1 5.52831780194196 133 3745 592 3819 2999 242 301 430 4002 543 198 151 M13104 REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VIF_MEDIATED_DEGRADATION_OF_APOBEC3G.html Genes involved in Vif-mediated degradation of APOBEC3G 53/64 Reactome 0.00022388682491224 0.00128557884864449 30 1097.45454545455 545 2.03554193082639e-05 26 0.620888930264109 -0.617320837965962 -1 2.69322056505607 26 146 3974 580 340 190 166 545 1163 4309 633 152 M6154 MAHAJAN_RESPONSE_TO_IL1A_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAHAJAN_RESPONSE_TO_IL1A_UP.html Genes up-regulated in corneal fibroblasts after treatment with IL1A [GeneID=3552]. 12091409 111/143 John Newman 6.98355638965807e-10 1.92762492158983e-08 225 1144.36363636364 545 6.34868762897719e-11 136 1.44966338698281 1.43473396644078 1 16.781891234013 221 1812 136 1789 3009 545 680 302 3332 237 525 153 M4001 DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_TARGETS_OF_PAX_FOXO1_FUSIONS_DN.html Genes down-regulated in RD cells (embryonal rhabdomyosarcoma, ERMS) by expression of PAX3- or PAX7-FOXO1 [GeneID=5077;5081;2308] fusions off retroviral vectors. 16849537 111/139 Arthur Liberzon 3.23820371085451e-06 3.79263561172042e-05 480 771.545454545455 546 2.94382588837389e-07 284 1.27756086059243 1.33859463139641 1 8.47508929436408 479 655 326 546 1587 537 844 1029 1791 409 284 154 M13639 CORRE_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CORRE_MULTIPLE_MYELOMA_UP.html Genes up-regulated in multiple myeloma (MM) bone marrow mesenchymal stem cells. 17344918 77/139 Leona Saunders 2.90301793337252e-06 3.4954705728363e-05 455 913 546 2.63911069460671e-07 215 1.50551602944214 1.27658854592663 1 10.0673690004642 454 1861 317 1201 379 558 546 447 2357 215 1708 155 M8701 KRISHNAN_FURIN_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRISHNAN_FURIN_TARGETS_DN.html Genes down-regulated in naive T lymphocytes lacking FURIN [GeneID=5045]: Cre-Lox knockout of FURIN in CD4+ [GeneID=920] cells. 18690214 17/23 Jessica Robertson 6.12049037884974e-05 0.000445126573007254 1135 578.363636363636 546 5.56423696367154e-06 38 1.49048749204786 -1.52177491096433 -1 7.49558220691189 1135 371 791 38 103 546 872 502 693 421 890 156 M1278 MCLACHLAN_DENTAL_CARIES_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCLACHLAN_DENTAL_CARIES_DN.html Genes down-regulated in pulpal tissue extracted from carious teeth. 15869869 125/178 John Newman 6.82135844638409e-08 1.28787247467732e-06 550 924.909090909091 547 6.20123514353485e-09 208 1.33237902146521 1.26943590007546 1 11.7757983613762 253 1804 208 1767 1235 514 549 547 2303 529 465 157 M4303 WOTTON_RUNX_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WOTTON_RUNX_TARGETS_DN.html Common target genes down-regulated by all three Runx family members (RUNX1, RUNX2, and RUNX3 [GeneID=861;860;864]) in MEF cells (embryonic fibroblasts). 18560354 41/53 Jessica Robertson 6.0791693865219e-05 0.000443488091257858 1985 1048.27272727273 548 5.52667034200409e-06 52 1.49751581391779 1.48176413536819 1 7.53452654937577 1981 220 548 52 101 1431 1334 2611 523 280 2450 158 M2253 NIKOLSKY_BREAST_CANCER_17P11_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_17P11_AMPLICON.html Genes within amplicon 17p11 identified in a copy number alterations study of 191 breast tumor samples. 19010930 7/10 Jessica Robertson 1.91500644226989e-05 0.000177929732431376 790 1271.63636363636 549 1.91502294509357e-06 50 1.70207461060381 -1.70207461060381 -1 9.57674860809226 787 446 4463 467 50 526 914 137 4511 1138 549 159 M7140 ZHOU_INFLAMMATORY_RESPONSE_FIMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_FIMA_UP.html Genes up-regulated in macrophages by P.gingivalis FimA pathogen. 18025224 563/856 Arthur Liberzon 4.35511719555225e-09 1.04345955142166e-07 265 1439.27272727273 551 4.35511720408742e-10 89 1.32043916841766 1.32737654747075 1 13.8327058920997 264 2704 4311 2255 1879 180 551 194 2918 89 487 160 M2025 NAKAMURA_ADIPOGENESIS_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_EARLY_DN.html Genes down-regulated in mesenchymal stem cells during early phase of adipogenesis, defined as days 1 to 5 of culturing with adipogenic hormones. 12646203 54/62 Arthur Liberzon 0.000335786766906415 0.00171713276251168 385 1497.54545454545 551 3.0530729919261e-05 122 1.5505226528039 1.6013825719699 1 6.43337281507062 207 3338 551 3398 3019 382 383 361 4014 698 122 161 M18274 VANHARANTA_UTERINE_FIBROID_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_UP.html Genes up-regulated in uterine fibroids vs normal myometrium samples. 15940248 69/88 Leona Saunders 0.000342125632086234 0.00174576538751029 40 802.363636363636 552 3.11071680176805e-05 38 1.32196009924963 1.36929566693526 1 5.47076726766763 38 1888 552 1266 794 264 492 282 2421 779 50 162 M17535 CAMPS_COLON_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAMPS_COLON_CANCER_COPY_NUMBER_DN.html Genes from chromosomal copy number losses in a panel of 51 primary colon carcinoma samples. 18316590 63/215 Jessica Robertson 0.00248890068288712 0.00788430283438068 315 705.272727272727 553 0.000226520080912771 44 1.40348666739657 -1.40978299754159 -1 4.42922635155923 314 1368 1264 560 1245 44 435 539 553 1251 185 163 M1798 JONES_TCOF1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/JONES_TCOF1_TARGETS.html Genes up-regulated in E8.5 embryos with heterozygous knockout of TCOF1 [GeneID=6949] compared to wild type. 18246078 5/5 Jessica Robertson 5.69417663213374e-05 0.000422586693453951 505 1407.72727272727 553 5.69432254380963e-06 8 1.11828349115759 -1.11828349115759 -1 5.66163044529392 501 3134 4562 1493 553 437 8 86 1257 3091 363 164 M11011 ASTON_MAJOR_DEPRESSIVE_DISORDER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ASTON_MAJOR_DEPRESSIVE_DISORDER_DN.html Genes down-regulated in the temporal cortex samples from patients with major depressive disorder. 15303102 240/304 Jean Junior 0.000107993033731639 0.000707482804573066 235 769 555 9.81803047547453e-06 25 1.25496588460774 1.32790839427904 1 5.93219889368287 235 1729 483 1285 1104 25 295 702 1967 555 79 165 M13387 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_6.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 6. 12554760 85/111 Arthur Liberzon 0.0134877740796518 0.0277274798153121 465 1028 556 0.00123374379950706 66 1.09298436195202 1.23708455737206 1 2.55359114228939 461 66 1566 503 3087 192 395 1292 1629 1561 556 166 M1845 RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_DN.html Down-regulated genes in breast tumors from transgenic mice overexpressing ERBB2 and CDC25A [GeneID=2064;993] compared to those from mice overexpressing ERBB2 only. 17283130 228/267 Jessica Robertson 0.00157378841061969 0.00558097768454166 1040 1051.18181818182 557 0.000143174123830446 181 1.19562552260244 1.26353369415562 1 4.04243132277583 1038 557 848 248 4144 543 1363 1729 473 439 181 167 M6714 HAHTOLA_MYCOSIS_FUNGOIDES_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_UP.html Genes up-regulated in monocytes isolated from peripheral blood samples of patients with mucosis fungoides compared to those from normal healthy donors. 16914566 17/56 Arthur Liberzon 7.25736073785344e-06 7.71503213573609e-05 1100 947.272727272727 563 6.59762243504368e-07 23 1.40151069152433 -1.46745123583148 -1 8.64880201136203 1099 1004 1228 1551 23 220 296 3641 354 563 441 168 M2256 MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_DN.html Genes commonly down-regulated in UET-13 cells (mesenchymal progenitor) by expression of EWSR1 [GeneID=2130] fusions with ETS transcription factors FLI1 and ERG [GeneID=2313 ,2078]. 18212050 323/415 Arthur Liberzon 2.29948258237227e-24 4.019836218073e-22 140 733.818181818182 563 2.09043871124751e-25 17 1.36815409737233 1.37640927355096 1 43.9242280133531 139 1167 17 1685 844 563 583 310 2410 43 311 169 M1450 WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_UP.html Up-regulated genes in myeloid progenitors immortalized by HOXA9 [GeneID=3205] vs those immortalized by HOXA9 and MEIS1 [GeneID=4211]. 15755900 39/63 Kevin Vogelsang 0.000903521017045918 0.00366691246814852 565 1061.81818181818 564 8.21720271658307e-05 178 1.25318675526773 1.29093040277014 1 4.58006107203329 564 849 609 317 4461 714 494 178 2722 484 288 170 M15842 NIELSEN_LIPOSARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LIPOSARCOMA_UP.html Top 20 positive significant genes associated with liposarcomas, versus other soft-tissue tumors. 11965276 17/21 John Newman 0.00239228622548969 0.00765531592156702 505 1223 564 0.000217717415586308 94 1.72961752066875 1.50231082979239 1 5.49169928850838 503 2608 917 2267 1179 536 94 249 4080 564 456 171 M13449 CAIRO_HEPATOBLASTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_DN.html Genes down-regulated in hepatoblastoma samples compared to normal liver tissue. 19061838 267/467 Arthur Liberzon 1.30143865146059e-09 3.37515957961208e-08 1105 810 570 1.18312604748225e-10 146 1.29063857500156 1.31853640782059 1 14.4698167117399 1105 1187 146 241 2015 422 1426 570 1225 168 405 172 M1435 GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN http://www.broadinstitute.org/gsea/msigdb/cards/GALINDO_IMMUNE_RESPONSE_TO_ENTEROTOXIN.html Genes up-regulated in macrophages by aerolysin-related cytotoxic enterotoxin (Act) from Aeromonas hydrophila. 12824169 110/135 Kevin Vogelsang 7.98071691104531e-05 0.000552331141057681 125 1432.90909090909 572 7.25546039465805e-06 123 1.25733070926192 1.26094748387981 1 6.1462233067794 123 2347 469 3395 3062 249 482 1285 3377 401 572 173 M2551 KEGG_ARGININE_AND_PROLINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARGININE_AND_PROLINE_METABOLISM.html Arginine and proline metabolism 51/66 KEGG 0.00867317827351948 0.0195966498090052 505 899.454545454545 573 0.000791596448076782 285 1.3987447548109 -1.6912246885754 -1 3.58433907091964 913 806 1048 514 3480 285 527 501 573 744 503 174 M9399 BOYLAN_MULTIPLE_MYELOMA_PCA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA1_UP.html Top up-regulated genes from principal component 1 (PCA1) which captures variation between normal plasma cells and tumors arising from aberrant expression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 112/199 Arthur Liberzon 7.00749440203559e-09 1.60560065910718e-07 225 797.636363636364 574 6.3704494766873e-10 16 1.43364770603821 1.55775392702151 1 14.6160432555007 223 16 167 1179 2236 574 713 410 1524 469 1263 175 M1975 MIKKELSEN_IPS_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_LCP_WITH_H3K4ME3.html Table 2S. Genes in MEF, MCV6, MCV8.1 and ES cells by epigenetic mark of their promoter 18509334 179/284 Jessica Robertson 1.37412194365711e-09 3.54418337380414e-08 835 842.818181818182 575 1.24920176774126e-10 9 1.33952331683225 -1.39270764769811 -1 14.9752296998037 833 575 147 9 2168 165 2071 1748 1110 126 319 176 M2514 FOSTER_KDM1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_KDM1A_TARGETS_DN.html Genes down-regulated in ES cells (embryonic stem) heterozygotic for KDM1A [GeneID=23028] loss of function mutant compared to the homozygotic loss of the gene. 20713442 274/326 Arthur Liberzon 0.000431375049935312 0.00205665680373199 575 1317.90909090909 575 3.92236051813935e-05 10 0.968466361116462 -1.00102686718666 -1 3.90441603294958 575 550 3668 530 3164 10 456 582 850 3862 250 177 M7054 SU_LIVER http://www.broadinstitute.org/gsea/msigdb/cards/SU_LIVER.html Genes up-regulated specifically in human liver tissue. 11904358 45/140 John Newman 8.57314236608461e-07 1.22251456096433e-05 2120 1087.81818181818 576 7.79376882449056e-08 35 1.65617733600729 -1.65485111057494 -1 12.2086934227335 2116 193 274 35 576 2294 3521 1008 479 374 1096 178 M7847 REACTOME_SIGNALING_BY_WNT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_WNT.html Genes involved in Signaling by Wnt 69/79 Reactome 0.000247260010109296 0.00137764531438843 185 1111.54545454545 577 2.24807094782893e-05 89 0.671047444197677 -0.653912616807175 -1 2.88055437157046 185 89 3930 386 199 262 639 799 890 4271 577 179 M13276 MARZEC_IL2_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARZEC_IL2_SIGNALING_DN.html Genes down-regulated by IL2 [GeneID=3558] in cells derived from CD4+ [GeneID=920] cutaneous T-cell lymphoma (CTCL). 18281483 50/59 Jessica Robertson 0.000418767519093747 0.00201148183802017 580 1105.45454545455 579 3.80770229334132e-05 88 1.07256369604446 1.19950469692429 1 4.33962437185821 579 812 1624 1756 286 96 88 476 3879 2126 438 180 M19476 GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_UP.html Genes up-regulated in dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the dividing cells from normal donors. 17717066 15/54 Arthur Liberzon 6.39764987532112e-05 0.000461726413020118 585 744.909090909091 581 5.81621448000415e-06 323 1.86163760671594 -2.22471317391735 -1 9.31768392028964 581 1030 459 1491 348 523 471 930 1416 323 622 181 M1003 REACTOME_IKK_COMPLEX_RECRUITMENT_MEDIATED_BY_RIP1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IKK_COMPLEX_RECRUITMENT_MEDIATED_BY_RIP1.html Genes involved in IKK complex recruitment mediated by RIP1 12/22 Reactome 0.00134248718068867 0.00491585686024092 585 966.090909090909 584 0.000122118826882196 64 0.983808227559249 1.01298307878638 1 3.40761076805327 584 424 2088 403 573 450 64 1040 1794 2455 752 182 M709 REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CDK_MEDIATED_PHOSPHORYLATION_AND_REMOVAL_OF_CDC6.html Genes involved in CDK-mediated phosphorylation and removal of Cdc6 50/60 Reactome 0.000396605509429085 0.00194592308160632 35 1146.90909090909 589 3.60615477844932e-05 32 0.615477469979935 -0.61117684417367 -1 2.50348500942406 32 156 3964 589 371 216 245 597 1449 4291 706 183 M9251 SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_UP.html Genes bound by EWSR1-FLT1 [GeneID=2130;2321] fusion and up-regulated in STA-ET-7.2 cells (Ewing's sarcoma) after knockdown of EWSR1-FLT1 by RNAi. 15735734 19/24 Arthur Liberzon 0.000281207448881665 0.00150719795511485 590 1059 590 2.55675817901993e-05 54 1.44068381191769 1.70502151548966 1 6.10005500302948 590 1550 1983 567 2787 593 202 54 341 2609 373 184 M14566 PEREZ_TP53_AND_TP63_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/PEREZ_TP53_AND_TP63_TARGETS.html Genes up-regulated in HMEC cells (primary mammary epithelium) upon expression of both of TP53 [GeneID=7157] and the transcriptionally active isoform of TP63 [GeneID=8626] off adenoviral vectors. 17563751 283/385 Leona Saunders 1.31759498605327e-06 1.77180864221409e-05 330 862.363636363636 596 1.19781434106414e-07 101 1.21923794933035 1.18066817532394 1 8.69287289926813 330 1717 290 1699 1527 101 533 746 1694 596 253 185 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 0.00167819537745615 0.00585445837516116 395 1519.09090909091 603 0.000152679718243517 28 1.43803191069589 -1.49351701310938 -1 4.81720181558617 391 4464 2662 4120 1188 28 347 603 392 2435 80 186 M10158 LEE_SP4_THYMOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_SP4_THYMOCYTE.html Genes enriched in the single positive 4 (SP4) thymocytes compared to all other T lymphocyte differentiation stages. 15210650 21/31 Arthur Liberzon 0.000618174940646763 0.00272181503717604 420 909.727272727273 603 5.62135190113893e-05 97 1.56206635444794 1.34411459644549 1 6.01235963886787 416 2070 765 1714 2383 463 660 97 416 603 420 187 M10102 NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_UP.html Top 20 positive significant genes associated with malignant fibrous histiocytoma tumors. 11965276 31/44 John Newman 0.000239805211311733 0.00135230656797059 70 1506.36363636364 604 2.1802850421587e-05 67 1.59239180242613 1.49946347220538 1 6.85494868393219 67 3417 530 3176 2540 604 199 1194 3825 584 434 188 M850 REACTOME_PI_3K_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI_3K_CASCADE.html Genes involved in PI-3K cascade 44/61 Reactome 5.71751193833431e-05 0.000423652375964489 525 1140 605 5.19787321308165e-06 97 0.852265049855038 0.789610586539165 1 4.31341189257804 525 200 2845 877 97 119 251 1764 1296 3961 605 189 M3015 HUANG_DASATINIB_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_DASATINIB_RESISTANCE_UP.html Genes whose expression positively correlated with sensitivity of breast cancer cell lines to dasatinib [PubChem=3062316]. 17332353 131/159 Jessica Robertson 2.05307074420429e-08 4.25021662835273e-07 260 843.545454545455 605 1.86642796669438e-09 187 1.30579567561479 1.3503473712179 1 12.4842110567558 257 625 187 1251 467 741 605 572 2982 394 1198 190 M1081 REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SCFSKP2_MEDIATED_DEGRADATION_OF_P27_P21.html Genes involved in SCF(Skp2)-mediated degradation of p27/p21 57/69 Reactome 0.00057123625364788 0.00255114612524251 330 1260.90909090909 606 5.19440573368049e-05 79 0.593223297618743 -0.604565282016515 -1 2.30827176272328 79 129 4014 606 326 330 484 937 1608 4331 1026 191 M19724 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_UP.html Genes from the lightyellow module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 18/18 Arthur Liberzon 0.00187149812526367 0.00636020284346217 350 1448.18181818182 606 0.000170281097430544 120 0.827357515613077 0.827357515613077 1 2.72681150713145 606 1009 3230 2330 502 347 120 349 3270 4007 160 192 M2496 PHONG_TNF_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_TARGETS_UP.html Genes up-regulated in Calu-6 cells (lung cancer) at 1 h time point after TNF [GeneID=7124] treatment. 20516219 89/104 Arthur Liberzon 9.47087425880235e-05 0.000630501079006306 45 1240.72727272727 611 8.61025636281863e-06 41 1.37837156408882 1.29019837832653 1 6.61902137505998 41 2376 479 3392 1499 175 100 1351 3092 611 532 193 M1228 OXFORD_RALB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALB_TARGETS_DN.html Genes down-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALB [GeneID=5899] by RNAi. 17496927 11/13 Arthur Liberzon 0.00299290383514 0.00905545262939795 765 656.545454545455 613 0.000272453016862686 27 1.22563625533577 -1.26965289450683 -1 3.75732393452299 763 423 1413 49 1129 754 613 273 27 1234 544 194 M1422 MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_UP.html Up-regulated genes discriminating multiple myeloma samples by the ype of immunoglobulin light chain they produce: Ig lambda (IGLL) vs Ig kappa (IGLK). 12623842 63/77 Kate Stafford 0.00879873877890986 0.019823411473248 500 1303.81818181818 613 0.000803102454063952 127 1.05528332922592 1.14536776934317 1 2.69626759235952 496 127 2285 856 4101 613 580 508 2055 2245 476 195 M2455 PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_DN.html Genes down-regulated after 10 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 38/51 Arthur Liberzon 3.73808132147517e-05 0.000304058396387218 620 1095 618 3.39831348887977e-06 154 1.47358903760364 1.36215604873737 1 7.77660353352243 618 2947 429 972 939 420 217 154 3936 572 841 196 M11266 KEGG_LYSOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSOSOME.html Lysosome 120/155 KEGG 0.0014426936364881 0.00521801836338991 815 1058.18181818182 619 0.000131240052812589 52 0.980417014094008 -0.95911426122567 -1 3.35775249235336 811 619 2434 229 457 69 871 2845 52 2951 302 197 M19439 DOANE_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_ESR1_UP.html Genes up-regulated in breast cancer samples positive for ESR1 [GeneID=2099] compared to the ESR1 negative tumors. 16491124 125/174 Arthur Liberzon 1.1236575398235e-08 2.45539980924395e-07 180 929.818181818182 620 1.02150685960238e-09 14 1.42759473186608 -1.52864131746518 -1 14.1591417102133 2086 620 177 14 2450 411 2232 1111 836 178 113 198 M5868 REACTOME_AMINE_LIGAND_BINDING_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINE_LIGAND_BINDING_RECEPTORS.html Genes involved in Amine ligand-binding receptors 9/45 Reactome 2.66974899477382e-05 0.000230791488192902 2170 1663.90909090909 621 2.66978106933478e-06 32 1.97032400083323 -2.17691126693236 -1 10.7520738034696 2168 431 4235 32 63 4070 4651 417 58 621 1557 199 M833 REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AUTODEGRADATION_OF_THE_E3_UBIQUITIN_LIGASE_COP1.html Genes involved in Autodegradation of the E3 ubiquitin ligase COP1 52/62 Reactome 0.000741640725850554 0.00315648712895818 790 1476.72727272727 621 6.7444623453158e-05 74 0.615477469979935 -0.61117684417367 -1 2.30947002524692 74 789 3918 610 354 275 385 621 4125 4305 788 200 M4065 ZHU_CMV_24_HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_24_HR_DN.html Down-regulated at 24 h following infection of primary human foreskin fibroblasts with CMV 9826724 136/180 John Newman 4.20396775067048e-08 8.40793550134097e-07 125 1207.27272727273 622 3.82178893727624e-09 124 1.27084725551781 1.36211044736736 1 11.5850972736691 124 2320 195 2096 1794 398 529 622 4039 498 665 201 M8637 STREICHER_LSM1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STREICHER_LSM1_TARGETS_DN.html Genes down-regulated in MCF10A cells (breast cancer) by expression of LSM1 [GeneID=27257] off a letiviral vector. 17001308 26/29 Arthur Liberzon 3.84744098233341e-05 0.000308842201302954 625 1003.72727272727 625 3.49773479040455e-06 9 1.33343301050735 1.52704881456435 1 7.02338002029121 625 3019 1347 2030 620 140 130 9 1246 1848 27 202 M1666 BURTON_ADIPOGENESIS_9 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_9.html Strongly down-regulated at 8-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 129/142 John Newman 0.00103721344717774 0.00408993105319876 605 904.272727272727 626 9.43366159564536e-05 322 1.20925839473899 1.30858135970958 1 4.33347489630787 604 626 725 322 3515 381 1010 1005 763 420 576 203 M998 REACTOME_DESTABILIZATION_OF_MRNA_BY_AUF1_HNRNP_D0 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_AUF1_HNRNP_D0.html Genes involved in Destabilization of mRNA by AUF1 (hnRNP D0) 60/72 Reactome 0.000150939244231907 0.000922840975096633 220 1525.54545454545 627 1.37226909981078e-05 160 0.614071605189129 -0.612156853996255 -1 2.7963075101925 218 768 3862 627 160 333 476 557 4566 4342 872 204 M1034 REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AUTODEGRADATION_OF_CDH1_BY_CDH1_APC_C.html Genes involved in Autodegradation of Cdh1 by Cdh1:APC/C 62/74 Reactome 0.00198300963393859 0.00663345533110572 75 1243.90909090909 627 0.00018043630129357 71 0.595288522087041 -0.597349662509515 -1 1.9456084768282 71 122 4084 1107 627 229 188 589 1501 4347 818 205 M852 REACTOME_TAK1_ACTIVATES_NFKB_BY_PHOSPHORYLATION_AND_ACTIVATION_OF_IKKS_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TAK1_ACTIVATES_NFKB_BY_PHOSPHORYLATION_AND_ACTIVATION_OF_IKKS_COMPLEX.html Genes involved in TAK1 activates NFkB by phosphorylation and activation of IKKs complex 24/27 Reactome 0.00217598822772434 0.00711757757093479 240 1501.09090909091 628 0.000198013041020595 195 1.23847758471784 1.28622408077577 1 3.99103509927447 240 3466 2360 3572 530 628 195 423 582 3501 1015 206 M1056 REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VOLTAGE_GATED_POTASSIUM_CHANNELS.html Genes involved in Voltage gated Potassium channels 15/43 Reactome 2.37968886900578e-05 0.00020916445924967 1020 1255.45454545455 630 2.16337691812456e-06 117 2.1265242596806 -2.14584574181904 -1 11.7408211301393 1020 2113 407 1962 3450 248 424 117 3187 630 252 207 M188 REACTOME_AMINO_ACID_TRANSPORT_ACROSS_THE_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINO_ACID_TRANSPORT_ACROSS_THE_PLASMA_MEMBRANE.html Genes involved in Amino acid transport across the plasma membrane 24/36 Reactome 0.000579784611786975 0.0025865627293332 1025 938.181818181818 631 5.27215876117205e-05 262 1.33043649454863 1.2890820141763 1 5.16499594008608 1023 317 631 262 327 1357 972 2422 494 454 2061 208 M2560 HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_DN.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 11/16 Arthur Liberzon 0.000968583447008649 0.00387436429519473 635 1148.45454545455 631 8.80918312384963e-05 338 1.15405404741842 1.15405404741842 1 4.17636224627212 631 2140 2561 2336 393 587 508 601 338 1723 815 209 M4741 KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS.html Systemic lupus erythematosus 54/146 KEGG 6.84660764679872e-07 1.01622604065692e-05 480 734.272727272727 633 6.22419070684415e-08 163 1.58328289243794 -1.5471321139954 -1 11.8620257104439 812 163 266 479 180 633 1796 1295 920 476 1057 210 M10387 NIELSEN_SYNOVIAL_SARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SYNOVIAL_SARCOMA_UP.html Top 20 positive significant genes associated with synovial sarcoma tumors. 11965276 37/100 Arthur Liberzon 0.000768512766567009 0.0032474308488776 50 1183.36363636364 633 6.98892143521562e-05 46 1.30169722215278 1.33176334901925 1 4.86041116667409 46 2505 633 2466 1461 223 264 407 3716 1062 234 211 M1091 REACTOME_DIGESTION_OF_DIETARY_CARBOHYDRATE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DIGESTION_OF_DIETARY_CARBOHYDRATE.html Genes involved in Digestion of dietary carbohydrate 3/13 Reactome 0.000235941226700141 0.00134012345369996 2685 1558 635 2.35966281162202e-05 21 1.17446037675888 1.17446037675888 1 5.06273079992193 522 2693 4269 2826 2682 635 21 93 629 2685 83 212 M707 WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_DN.html Genes down-regulated in mucinous ovarian carcinoma tumors of grades 1 and 2 compared to the normal ovarian survace epithelium tissue. 16467078 86/119 Arthur Liberzon 0.00100550831998419 0.0039882346809457 160 845.909090909091 636 9.14516528247022e-05 47 1.43488525734751 1.54655197762858 1 5.16559115538993 156 1319 662 2809 1521 57 47 441 1304 636 353 213 M640 REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P53_INDEPENDENT_G1_S_DNA_DAMAGE_CHECKPOINT.html Genes involved in p53-Independent G1/S DNA damage checkpoint 55/65 Reactome 0.000394608288881493 0.00194420785336184 240 1189.81818181818 637 3.58799169568022e-05 136 0.635072113684903 -0.61117684417367 -1 2.58355551267218 236 136 3914 180 268 512 701 637 1082 4324 1098 214 M19141 WONG_IFNA2_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WONG_IFNA2_RESISTANCE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) cell lines resistant to IFNA2 [GeneID=3440]. 15709204 30/37 Yujin Hoshida 8.81702755634833e-05 0.000597936351522473 640 964.363636363636 637 8.01580085427151e-06 20 1.21259959284267 -1.36084838504333 -1 5.86486725725128 637 903 1910 573 3295 312 262 20 860 1801 35 215 M12338 GERY_CEBP_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GERY_CEBP_TARGETS.html Genes changed in NIH 3T3 cells (embryonic fibroblast) by expression of one or more of C/EBP proteins: CEBPA, CEBPB, CEBPG, and CEBPD [GeneID=1050;1051;1054;1052]. 15985538 170/229 Kevin Vogelsang 3.51213094279623e-08 7.08429831196504e-07 530 1607.54545454545 643 3.19284636260428e-09 39 1.33305206753377 1.25341804909443 1 12.3009693986248 527 3202 193 3540 3801 39 643 1993 3416 287 42 216 M2450 PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_UP.html Genes up-regulated after 1 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 42/57 Arthur Liberzon 0.000521202390544681 0.00238379387923536 175 1399.90909090909 644 4.73932645150547e-05 35 1.29733254856312 1.22640723556391 1 5.10549575683091 175 2931 644 2828 2943 65 35 85 4349 1114 230 217 M2039 GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_E_DN.html Down-regulated genes from the set E (Fig. 5a): specific signature shared by cells expressing either MLL-AF4 [GeneID=4297;4299] or AF4-MLL fusion proteins alone, and those expressing both fusion proteins. 17130830 30/35 Arthur Liberzon 4.39364139623932e-05 0.000342776651078505 770 1083.54545454545 646 3.99429922230214e-06 11 1.41417136723235 1.31309289166683 1 7.35257441187803 770 2983 646 2273 264 391 308 11 3003 695 575 218 M11585 NAGASHIMA_NRG1_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAGASHIMA_NRG1_SIGNALING_UP.html Genes up-regulated in MCF7 cells (breast cancer) after stimulation with NRG1 [GeneID=3084]. 17142811 231/284 Arthur Liberzon 7.86770491240273e-05 0.000546111282155013 180 1152.18181818182 647 7.15271481243209e-06 68 1.17099950784875 1.14957660707757 1 5.7328444228911 176 2264 468 1583 4028 68 155 1041 1941 303 647 219 M9709 TAVOR_CEBPA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAVOR_CEBPA_TARGETS_UP.html Genes up-regulated in KCL22 cells (chronic myelogenous leukemia, CML, with BCR-ABL1 [GeneID=613;25] fusion) by expression of CEBPA [GeneID=1050]. 14517214 51/67 Kevin Vogelsang 0.000110588896711166 0.000718980154926588 345 985.545454545455 647 1.00540414681565e-05 28 1.27974960730897 1.31889866057357 1 6.035909172266 342 813 647 1721 1802 97 153 28 3576 1339 323 220 M15975 LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_UP.html Genes up-regulated between two breast carcinoma subtypes: metaplastic (MCB) and ductal (DCB). 17603561 100/130 Arthur Liberzon 3.19536760739218e-06 3.76789534971322e-05 250 1118.54545454545 649 2.90488386225525e-07 248 1.37503339993631 1.46276862134616 1 9.1275755531263 248 1303 324 2268 2542 343 495 604 2877 651 649 221 M8713 REACTOME_AMINE_DERIVED_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINE_DERIVED_HORMONES.html Genes involved in Amine-derived hormones 3/15 Reactome 1.57611243380081e-05 0.000150248278081907 1360 1214.81818181818 650 1.57612361249922e-06 1 2.59308222901147 -3.09194425198329 -1 14.8758210575236 1358 455 4233 7 42 3121 2571 95 1 830 650 222 M12393 LIU_VAV3_PROSTATE_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_VAV3_PROSTATE_CARCINOGENESIS_DN.html Selected genes down-regulated in prostate tumors developed by transgenic mice overexpressing VAV3 [GeneID=10451] in prostate epithelium. 18676865 25/44 Jessica Robertson 0.00193901154790671 0.00652326051754787 410 1895.90909090909 651 0.000176429331279613 217 0.990515242458877 1.06512027811591 1 3.24822902744165 651 4535 1843 4619 525 399 407 217 4597 2652 410 223 M11218 TURJANSKI_MAPK7_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK7_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK7 [GeneID=5598] phosphorylation. 17496919 9/9 Arthur Liberzon 1.34511870720159e-05 0.000132823437196475 655 1625.45454545455 652 1.34512684932047e-06 9 0.842787152086399 0.801771956820706 1 4.90247476342175 652 2167 4358 3315 34 198 9 318 3911 2754 164 224 M4717 LI_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_CISPLATIN_RESISTANCE_UP.html Genes consistently up-regulated in ACRP cells (ovarian cancer, resistant to cisplatin [PubChem=2767]) compared to the parental sensitive A2780 cells, regardless of cisplatin exposure. 17072341 58/69 Arthur Liberzon 0.00106091032183034 0.00415215316669916 55 1328.18181818182 652 9.64929338511624e-05 54 1.26330184191433 1.373981617538 1 4.51471844233584 54 2881 652 2987 1121 326 376 426 4183 1455 149 225 M1399 KHETCHOUMIAN_TRIM24_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KHETCHOUMIAN_TRIM24_TARGETS_UP.html Retinoic acid-responsive genes up-regulated in hepatocellular carcinoma (HCC) samples of TRIM24 [GeneID=8805] knockout mice. 18026104 73/82 Leona Saunders 3.82383062491448e-07 6.07692947797856e-06 415 1185.63636363636 656 3.47621026321498e-08 247 1.4226315134525 1.51835193443404 1 11.1350964181904 414 2403 247 2444 397 569 656 1414 3133 911 454 226 M2612 ZWANG_CLASS_2_TRANSIENTLY_INDUCED_BY_EGF http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_CLASS_2_TRANSIENTLY_INDUCED_BY_EGF.html Class II of genes transiently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 49/64 Yaara Zwang 0.000126405309603751 0.000798705570722499 660 1041 660 1.14920520957007e-05 32 1.2302154656585 1.16965469263082 1 5.71797367271126 660 1946 867 2808 599 324 179 32 2683 1026 327 227 M1804 WANG_SMARCE1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_SMARCE1_TARGETS_UP.html Genes up-regulated in BT549 cells (breast cancer) by expression of SMARCE1 [GeneID=6605] off a retroviral vector. 16135788 377/460 John Newman 3.74129042927781e-20 4.10671879678867e-18 125 728.545454545455 661 3.40117311752528e-21 31 1.29636161964064 1.31286875945474 1 33.8204128457378 125 1157 31 919 1312 311 700 661 2267 67 464 228 M13597 GRADE_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_METASTASIS_DN.html Down-regulated genes in colon carcinoma tumors with lymph node metastases. 17210682 54/64 Jessica Robertson 0.00882023392873019 0.0198623588471405 535 1355 663 0.000805072341014532 129 0.690441708399457 -0.717213993666655 -1 1.76317106906848 534 1390 3799 1593 1044 129 270 657 509 4317 663 229 M72 PID_NECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NECTIN_PATHWAY.html Nectin adhesion pathway 18832364 51/55 Pathway Interaction Database 0.00102004769611119 0.00403234935146132 160 1163.45454545455 664 9.27746324238568e-05 48 1.17629753006126 1.2046510801355 1 4.22622303483193 159 1413 2041 2949 2228 82 48 202 664 2506 506 230 M1443 REACTOME_GLUTATHIONE_CONJUGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUTATHIONE_CONJUGATION.html Genes involved in Glutathione conjugation 20/32 Reactome 0.00577426225782821 0.0142024584976285 670 794.090909090909 666 0.000526315789473684 19 1.1886179340776 -1.05925757394197 -1 3.29523708099817 666 328 1151 23 3106 130 489 785 19 1014 1024 231 M11695 STOSSI_RESPONSE_TO_ESTRADIOL http://www.broadinstitute.org/gsea/msigdb/cards/STOSSI_RESPONSE_TO_ESTRADIOL.html Genes up-regulated by estradiol (E2) [PubChem=5757] in U2OS cells (osteosarcoma) expressing ESR1 or ESR2 [GeneID=2099;2100]. 15033914 61/92 Kevin Vogelsang 2.16486641215607e-06 2.70032494210536e-05 585 740.272727272727 667 1.96806231132082e-07 66 1.49304504453521 1.3528601104147 1 10.2350941049882 583 761 308 746 1477 462 667 66 1713 399 961 232 M6250 KORKOLA_YOLK_SAC_TUMOR http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_YOLK_SAC_TUMOR.html Genes predicting the yolk sac tumor (YS) subtype of nonseminomatous male germ cell tumors (NSGCT). 15870693 95/124 Leona Saunders 1.60200339045266e-09 4.1094869581177e-08 260 1422.72727272727 668 1.45636671965383e-10 148 1.40392686230959 1.46292400448117 1 15.5598401162705 256 1840 148 2843 3585 1060 598 668 3782 546 324 233 M16794 KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450.html Metabolism of xenobiotics by cytochrome P450 40/110 KEGG 8.77146706231379e-07 1.24328301904267e-05 705 703.909090909091 669 7.97406414502398e-08 198 1.3648512145259 -1.44602858463217 -1 10.0461492637463 702 198 276 1164 462 335 962 1060 1692 223 669 234 M1840 KEGG_GLUTATHIONE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLUTATHIONE_METABOLISM.html Glutathione metabolism 43/58 KEGG 0.00577426225782821 0.0142024584976285 520 735.090909090909 679 0.000526315789473684 30 1.22458869375137 -1.19888077229006 -1 3.39496297643782 516 184 1329 30 1943 240 679 923 47 929 1266 235 M10761 PEREZ_TP63_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/PEREZ_TP63_TARGETS.html Genes up-regulated in the HMEC cells (primary mammary epithelium) upon expression of the transcriptionally active isoform of TP63 [GeneID=8626] off adenoviral vector. 17563751 486/644 Leona Saunders 1.19375609146371e-15 7.04316093963587e-14 50 726.545454545455 679 1.08523281042155e-16 46 1.28622854138086 1.23589318895936 1 25.3838570808047 375 2216 58 679 1019 46 961 693 1747 149 49 236 M4385 XU_RESPONSE_TO_TRETINOIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_UP.html Genes up-regulated in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin [PubChem=444795] alone. 16140955 24/71 Kevin Vogelsang 0.00860956031156703 0.0195089412724899 680 894.545454545455 679 0.000785767185480138 247 1.20590160399657 1.21680244018496 1 3.09368133837556 679 1490 1774 783 1577 308 247 596 349 589 1448 237 M727 REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES.html Genes involved in Metabolism of amino acids and derivatives 158/214 Reactome 0.00157708989294733 0.00558486928494095 220 893 682 0.000143474689093151 219 1.08912743611384 -1.05655354719065 -1 3.68185522345049 219 594 2468 682 470 250 694 719 366 2634 727 238 M17961 NIKOLSKY_BREAST_CANCER_14Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_14Q22_AMPLICON.html Genes within amplicon 14q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 18/21 Jessica Robertson 0.00176090165925168 0.00608007010363419 685 1259.18181818182 683 0.000160210243971488 199 0.977257243894159 1.01567215952259 1 3.24955756103886 683 1545 2082 1256 585 646 334 199 3367 2537 617 239 M34 PID_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_PATHWAY.html TCR signaling in naïve CD4+ T cells 18832364 66/94 Pathway Interaction Database 0.0025012012982281 0.00790391091608911 440 1234.27272727273 684 0.000227640861144927 118 0.936481792666254 0.82648908951776 1 2.95386698369428 436 118 2115 390 684 758 331 242 3798 2982 1723 240 M2597 GHANDHI_BYSTANDER_IRRADIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_BYSTANDER_IRRADIATION_UP.html Genes significantly (FDR < 10%) up-regulated in IMR-90 cells (fibroblast) in response to bystander irradiation. 19108712 82/108 Itai Pashtan 3.94768528668272e-07 6.25270958159142e-06 60 908.181818181818 684 3.58880545005135e-08 56 1.53773162059209 1.47737578964108 1 12.0074314811417 56 1855 248 1234 2549 218 480 892 1577 197 684 241 M6121 REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INITIAL_TRIGGERING_OF_COMPLEMENT.html Genes involved in Initial triggering of complement 13/18 Reactome 1.95268504202315e-05 0.000180719086242143 615 1347.27272727273 685 1.77518397632788e-06 44 1.66603484914774 1.65428365131892 1 9.35707991107777 611 3090 863 3278 44 410 685 483 3651 1473 232 242 M15593 MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_DN.html Genes down-regulated in FSHD (facioscapulohumeral muscular dystrophy) mesoangioblasts. 17761758 16/20 Arthur Liberzon 4.49829915206704e-05 0.000349210065752573 840 686.363636363636 685 4.08944648235231e-06 85 1.62396075604728 1.65409394621901 1 8.42365095653972 1290 1013 655 486 85 971 178 838 685 510 839 243 M18292 MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_UP.html Top genes up-regulated in mesenchyme stem cells (MSC) grown in a tumor conditioned medium, which leads to carcinoma-associated fibroblast phenotype. 18519693 31/39 Leona Saunders 0.000901120451627445 0.0036603171529101 690 1278.63636363636 686 8.19536147767757e-05 304 1.48095855588549 1.29423815807481 1 5.41426245461059 686 2017 608 3716 967 304 352 648 3179 1241 347 244 M2376 IKEDA_MIR1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR1_TARGETS_DN.html Genes down-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-1 microRNA. 19188439 10/11 Arthur Liberzon 0.00453399683775625 0.0123345620024262 1220 1090.09090909091 686 0.000413033457832365 37 1.37159584965828 1.38593614552055 1 3.92856596932574 1216 2663 2330 1306 686 586 348 593 37 1601 625 245 M5409 MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOROSETTI_FACIOSCAPULOHUMERAL_MUSCULAR_DISTROPHY_UP.html Genes up-regulated in FSHD (facioscapulohumeral muscular dystrophy) mesoangioblasts. 17761758 29/36 Arthur Liberzon 0.000538589932911549 0.00244289233894981 150 1207.54545454545 687 4.89747120240348e-05 150 1.71760313717475 1.77512338210311 1 6.7320430663791 150 2547 576 1994 687 606 510 1561 3063 647 942 246 M2194 OHGUCHI_LIVER_HNF4A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OHGUCHI_LIVER_HNF4A_TARGETS_DN.html Genes down-regulated in liver samples of liver-specific knockout of HNF4A [GeneID=3172]. 18426912 90/243 Arthur Liberzon 6.39963694859346e-07 9.58929726900354e-06 1130 1138.54545454545 688 5.81785346381925e-08 143 1.40183092674325 1.71876123492175 1 10.5555824226242 1128 688 264 230 3384 2428 2524 143 426 200 1109 247 M19133 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_UP.html Genes from the grey module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 26/29 Arthur Liberzon 0.00412921340536597 0.0114578996315858 1020 820.545454545455 689 0.00037608945591569 285 1.36867713072108 1.46060776674197 1 3.985963585165 1019 318 824 689 2949 631 323 341 755 892 285 248 M15057 HENDRICKS_SMARCA4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HENDRICKS_SMARCA4_TARGETS_UP.html Genes up-regulated in ALAB cells (breast cancer) upon reintroduction of SMARCA4 [GeneID=6597] expressed off adenoviral vector. 14673169 82/109 John Newman 0.00888937538572837 0.0199762539201158 165 956.090909090909 691 0.000811408957248919 163 1.14593331767536 1.20912804772041 1 2.92215336512248 163 1321 1090 1834 3326 185 259 691 826 644 178 249 M9911 WOO_LIVER_CANCER_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WOO_LIVER_CANCER_RECURRENCE_DN.html Genes negatively correlated with recurrence free survival in patients with hepatitis B-related (HBV) hepatocellular carcinoma (HCC). 18381945 78/146 Yujin Hoshida 0.000247509158178259 0.00137764531438843 3485 1533.90909090909 695 2.25033643977777e-05 76 1.32874931830037 -1.31747964325681 -1 5.70392495154444 3483 76 695 659 200 2391 3151 2376 612 416 2814 250 M17421 DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_UP.html Genes up-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071], after low dose UVC irradiation. 15608684 16/35 Arthur Liberzon 3.80008741469947e-05 0.000306022854083954 830 726.181818181818 696 3.4546845960639e-06 79 1.49368242477883 -1.49827615247495 -1 7.87637564168425 826 398 1527 1284 79 696 672 819 97 1367 223 251 M7030 ELVIDGE_HYPOXIA_BY_DMOG_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_BY_DMOG_DN.html Genes down-regulated in MCF7 cells (breast cancer) treated with hypoxia mimetic DMOG [PubChem=3080614]. 16565084 76/89 Arthur Liberzon 0.000748362090195899 0.00317936009516169 700 1477.54545454545 697 6.80560707068232e-05 111 1.11010886701206 -1.09703540048158 -1 4.16034839119157 697 2854 2757 1562 4406 188 315 111 625 2358 380 252 M591 REACTOME_SIGNALING_BY_HIPPO http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_HIPPO.html Genes involved in Signaling by Hippo 26/26 Reactome 0.00459254425693424 0.0124722720901781 640 1732.45454545455 698 0.000418378127067109 206 0.762279223672163 0.610089853477529 1 2.17778070267838 638 3462 3691 3361 689 698 206 615 458 4179 1060 253 M14520 REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYCLIN_E_ASSOCIATED_EVENTS_DURING_G1_S_TRANSITION_.html Genes involved in Cyclin E associated events during G1/S transition 67/79 Reactome 0.00585084353265323 0.0143536324110837 230 1298.81818181818 698 0.000533314716647643 107 0.689528181141552 -0.623036025616446 -1 1.90679523577719 229 107 3968 619 744 428 698 1327 695 4185 1287 254 M10508 HARRIS_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/HARRIS_HYPOXIA.html Genes known to be induced by hypoxia 11902584 116/148 John Newman 2.06543542065594e-06 2.606645771523e-05 160 1309.36363636364 699 1.87767032705461e-07 144 1.40648194042143 1.50949071194335 1 9.67404394829689 158 3654 306 3812 1101 282 801 398 3048 699 144 255 M15807 BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_POOR_SURVIVAL_DN.html Top highly correlated genes negatively associated with poor survival of patients with suboptimally debulked ovarian tumors. 18593951 32/41 Jessica Robertson 0.0102155324919433 0.0222302044084704 700 1358.45454545455 699 0.000933025292195223 206 0.989742624792461 -1.11121319024533 -1 2.45489584127608 699 2525 3293 1805 913 385 687 636 206 3176 618 256 M19259 IYENGAR_RESPONSE_TO_ADIPOCYTE_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/IYENGAR_RESPONSE_TO_ADIPOCYTE_FACTORS.html Genes up-regulated in MCF-7 cells (breast cancer) in response to growth medium from L3T3-L1 cells (differentiated to pre-adipocytes). 14508521 15/17 John Newman 0.00238596416345619 0.00764026516384887 285 1350.45454545455 704 0.000217141431540018 239 1.39559932552833 1.43668269590396 1 4.4329292964001 283 2621 924 3061 1339 475 375 239 4203 631 704 257 M17937 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_DN.html Top 100 probe sets contrubuting to the negative side of the 1st principal component; predominantly associated with synovial sarcoma and myxoid/round cell liposarcoma samples. 17464315 105/190 Nikolaos Papanikolaou 2.4603697180019e-09 6.21013105292458e-08 150 1121.27272727273 704 2.23669974613951e-10 146 1.30092592768956 1.39118850950013 1 14.0682332608877 146 2349 151 1495 1752 704 790 461 3411 390 685 258 M18559 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP.html Genes up-rgulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 6h. 16818636 84/135 Arthur Liberzon 6.61923773143689e-06 7.08453562185535e-05 400 943.545454545455 705 6.01750695192308e-07 352 1.25781973410665 1.43635679729261 1 7.8319490422657 558 705 352 1182 1757 838 792 397 2959 441 398 259 M14383 SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_UP.html Genes up-regulated in brain relapse of breast cancer. 18451135 42/112 Jessica Robertson 0.000168447824763127 0.00100897681837812 765 1243.09090909091 707 1.53146112475419e-05 192 1.61620942288707 1.66234326718004 1 7.26594571396443 765 2483 507 2822 2479 438 523 192 2183 575 707 260 M1076 REACTOME_AMYLOIDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMYLOIDS.html Genes involved in Amyloids 35/136 Reactome 1.1707455166179e-07 2.10110982450056e-06 1845 1170.27272727273 709 1.0643141626545e-08 203 1.83082516853887 -1.68434381541928 -1 15.5972056586952 1841 878 220 1240 709 256 622 3795 697 203 2412 261 M10541 YANG_BREAST_CANCER_ESR1_LASER_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_LASER_UP.html Genes up-regulated in laser microdissected (LCM) samples of early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 38/49 Leona Saunders 0.000316618612720507 0.00165131475363624 1220 1031 709 2.87876535344621e-05 216 1.06870602037575 -1.15098063604714 -1 4.46142347016585 1218 227 2263 709 231 361 1032 2502 216 2002 580 262 M3447 AMIT_SERUM_RESPONSE_60_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_60_MCF10A.html Genes whose expression peaked at 60 min after stimulation of MCF10A cells with serum. 17322878 76/82 Leona Saunders 0.000599952930861856 0.00264899703804299 165 1390.45454545455 709 5.45560549131207e-05 165 1.4052826190336 1.46993154453303 1 5.4337257226633 165 1875 709 3526 4415 186 333 529 2420 387 750 263 M1612 BURTON_ADIPOGENESIS_1 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_1.html Strongly up-regulated at 2 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 41/47 John Newman 7.46297777619081e-07 1.09056517348671e-05 545 933.636363636364 709 6.78452755257278e-08 69 1.25121671279802 1.23204278912894 1 9.31658309884191 541 1437 812 1762 69 480 511 1612 2178 159 709 264 M2467 KRIEG_HYPOXIA_VIA_KDM3A http://www.broadinstitute.org/gsea/msigdb/cards/KRIEG_HYPOXIA_VIA_KDM3A.html Genes dependent on KDM3A [GeneID=55818] for hypoxic induction in RCC4 cells (renal carcinoma) expressing VHL [GeneID=7428]. 19858293 87/103 Arthur Liberzon 0.000467300714828081 0.00219468594426721 490 1044.36363636364 709 4.24909094024506e-05 100 1.24562194044849 1.14343852786903 1 4.9690837939126 490 709 567 1556 2655 100 162 1228 2167 571 1283 265 M12922 REACTOME_REGULATION_OF_RHEB_GTPASE_ACTIVITY_BY_AMPK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_RHEB_GTPASE_ACTIVITY_BY_AMPK.html Genes involved in Regulation of Rheb GTPase activity by AMPK 13/32 Reactome 0.00203912500136304 0.00676840366134566 1130 1289.63636363636 710 0.000185547042865659 57 0.80968913947877 0.89248937026146 1 2.6357553216387 1127 414 2722 387 4109 797 425 222 57 3216 710 266 M871 REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEPOSITION_OF_NEW_CENPA_CONTAINING_NUCLEOSOMES_AT_THE_CENTROMERE.html Genes involved in Deposition of New CENPA-containing Nucleosomes at the Centromere 36/81 Reactome 0.00395310877050299 0.0110668288237094 360 1199.81818181818 710 0.00036002090037657 107 1.34329186045323 -1.45475009293724 -1 3.94243221306657 357 1981 2045 3141 1812 107 148 362 710 2240 295 267 M8463 DAZARD_UV_RESPONSE_CLUSTER_G3 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G3.html Cluster G3: genes increasingly up-regulated in NHEK cells (normal keratinocyte) after 6 h time point upon UV-B irradiation. 12771951 13/27 John Newman 0.00426257827525354 0.0117245742769211 470 1502 711 0.000388259967697675 150 1.15202506702492 1.15202506702492 1 3.33772388348935 469 422 2302 1547 4140 150 157 683 3366 2575 711 268 M14447 MASSARWEH_RESPONSE_TO_ESTRADIOL http://www.broadinstitute.org/gsea/msigdb/cards/MASSARWEH_RESPONSE_TO_ESTRADIOL.html Genes rapidly up-regulated in breast cancer cell cultures by estradiol [PubChem=5757]. 18245484 84/105 Jessica Robertson 0.000482350157919859 0.00225192160769707 715 695.818181818182 713 4.38596314272364e-05 142 1.18963161367208 1.09670516247944 1 4.72576161373863 713 1318 1036 985 303 142 373 258 1015 1142 369 269 M4697 ZHAN_MULTIPLE_MYELOMA_HP_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_HP_DN.html Top 50 down-regulated genes in cluster HP of multiple myeloma samples characterized by a hyperploid signature. 16728703 47/60 Arthur Liberzon 9.80764658272871e-06 0.000100199333052986 975 1031.63636363636 713 8.91608209608884e-07 27 1.09739422194794 1.18893983605548 1 6.58511830217253 973 180 1564 460 27 1829 2412 344 591 2255 713 270 M265 ODONNELL_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_METASTASIS_UP.html Up-regulated genes in the signature set for lymph node metastasis in head and neck squamous cell carcinoma (HNSCC). 15558013 119/204 Leona Saunders 5.26222370768881e-05 0.000398442508841251 225 1086.63636363636 714 4.78395416370747e-06 31 1.21519663886179 1.26677936888735 1 6.19887901736209 225 1807 446 2316 1086 50 714 321 3460 1497 31 271 M1973 HORIUCHI_WTAP_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HORIUCHI_WTAP_TARGETS_UP.html Genes up-regulated in primary endothelial cells (HUVEC) after knockdown of WTAP [GeneID=9589] by RNAi. 17088532 417/531 Leona Saunders 1.19894908673595e-12 4.9640699029769e-11 90 744.454545454545 715 1.08995371521509e-13 88 1.23963155816493 1.23069749325452 1 19.1665840021479 744 516 88 261 908 715 1119 379 2430 88 941 272 M143 PID_IL2_PI3K_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_PI3K_PATHWAY.html IL2 signaling events mediated by PI3K 18832364 52/58 Pathway Interaction Database 0.00194683744759837 0.00654083560642565 820 945 716 0.000177142035663572 162 1.0683228038716 0.927331083668898 1 3.50152105183608 819 162 2297 634 506 725 444 716 353 1917 1822 273 M18256 KEGG_SULFUR_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SULFUR_METABOLISM.html Sulfur metabolism 8/18 KEGG 0.00264339937125921 0.00824098086680545 1425 1334.72727272727 718 0.000264654904768493 300 1.02143706858555 -1.02143706858555 -1 3.19404583694077 1421 2171 4183 1036 586 664 443 537 718 2623 300 274 M1069 REACTOME_PIP3_ACTIVATES_AKT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PIP3_ACTIVATES_AKT_SIGNALING.html Genes involved in PIP3 activates AKT signaling 30/30 Reactome 0.000477660321120498 0.00223444669542988 720 1614.18181818182 718 4.34330964968672e-05 301 0.665496850564573 0.687656139271577 1 2.64699016156116 718 911 3628 1873 301 409 650 587 3516 4617 546 275 M14134 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_DN.html Genes down-regulated in ductal carcinoma vs normal ductal breast cells. 17389037 245/315 Arthur Liberzon 8.70688647702859e-12 3.18577551717635e-10 720 1438.63636363636 720 7.9153513427846e-13 101 1.44151574636428 1.38994244817683 1 20.5416611002677 720 3621 101 2811 3776 346 987 414 2662 112 275 276 M12228 BOYAULT_LIVER_CANCER_SUBCLASS_G12_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G12_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G12, defined by unsupervised clustering 17187432 16/33 Yujin Hoshida 0.00122151800330708 0.00458867425062877 1105 763.454545454545 720 0.000111108796462717 162 1.31500237016372 1.28970863446422 1 4.61382358066768 1103 385 1098 332 1842 721 628 162 418 989 720 277 M12027 RODRIGUES_NTN1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_NTN1_TARGETS_UP.html Genes up-regulated in HCT8/S11 cells (colon cancer) engineered to stably express NTN1 [GeneID=1630] off a plasmid vector. 17334389 35/43 Arthur Liberzon 4.41711266912308e-05 0.000344039138585164 750 586.181818181818 721 4.01563759768535e-06 84 1.46388449413263 1.13425573731654 1 7.6075400192728 747 870 873 457 84 182 104 1287 172 951 721 278 M2003 MIKKELSEN_ES_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 K27 trimethylation mark (H3K27me3) in embryonic stem cells (ES). 17603471 63/100 Arthur Liberzon 2.4319091717482e-07 4.09950403237554e-06 90 1114.27272727273 724 2.21082676415882e-08 89 1.39035949006566 1.28927371747255 1 11.2391498193876 89 1902 232 2562 940 355 567 1109 3528 724 249 279 M12138 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_UP.html Genes up-regulated in erythroid lineage cells by RUNX1-RUNX1T1 [GeneID=861;862] fusion . 17898786 228/342 Arthur Liberzon 3.13431487769074e-11 1.04182860723242e-09 450 888 726 2.84937716157764e-12 112 1.27117538399432 1.34524951977378 1 17.1327666931079 448 1206 112 1004 2085 679 932 255 2171 150 726 280 M1597 BURTON_ADIPOGENESIS_PEAK_AT_2HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_2HR.html Cluster 2: genes maximally expressed at 2 h time point during differentiation of 3T3-L1 fibroblasts into adipocytes (cluster 2) in response to adipogenic hormones. 12137940 75/83 John Newman 2.75271443806483e-07 4.55355684590915e-06 550 1411.45454545455 727 2.50246798408531e-08 146 1.41177806834163 1.41724827541035 1 11.3156509908191 547 3699 466 2948 727 298 884 2448 2955 146 408 281 M4629 KEGG_NITROGEN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NITROGEN_METABOLISM.html Nitrogen metabolism 16/23 KEGG 0.000562235629638081 0.00252716251395888 1125 1042.18181818182 728 5.11253969939139e-05 91 1.6592944044699 1.74868273775519 1 6.46682993181091 1124 369 728 1160 3563 1916 1163 91 168 703 479 282 M8565 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREY_DN.html Genes from the grey module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 77/102 Arthur Liberzon 0.00450738634882884 0.0122692408111143 665 776.636363636364 731 0.000410604337416599 552 1.28782598375858 1.26095640286367 1 3.69307955902969 663 731 834 1180 685 552 755 980 808 627 728 283 M1259 SASAI_RESISTANCE_TO_NEOPLASTIC_TRANSFROMATION http://www.broadinstitute.org/gsea/msigdb/cards/SASAI_RESISTANCE_TO_NEOPLASTIC_TRANSFROMATION.html Genes down-regulated in MEF and REF cells (mouse and rat fibroblasts) but not in TIG3/T cells (human lung fibroblasts expressing TERT [GeneID=7015]) by co-expression of the SV40 early region and the activated HRAS (H-RasV12) [GeneID=3265]. 16832346 79/80 Arthur Liberzon 2.31325681646991e-06 2.86576697473438e-05 55 1434.63636363636 732 2.10296295347057e-07 52 1.37977176191427 1.41703768494126 1 9.40511009449462 52 2849 310 2705 3209 665 732 997 3314 256 692 284 M1902 SCHRAETS_MLL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAETS_MLL_TARGETS_UP.html Genes up-regulated in fibroblasts from MLL [GeneID=4297] knockout mice. 12789274 59/77 Arthur Liberzon 2.71146243607869e-05 0.000233542020041814 105 1207.27272727273 732 2.46499623178808e-06 103 1.29600820858041 1.34137919425706 1 7.06228503626752 103 1917 413 2184 910 732 579 1529 3692 504 717 285 M1141 SAENZ_DETOX_PATHWAY_AND_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAENZ_DETOX_PATHWAY_AND_CARCINOGENESIS_DN.html Detoxification pathway genes down-regulated in enterocytes of transgenic mice expressing SV40 T antigen. 17334401 20/56 Arthur Liberzon 0.00654943362533484 0.0156364829092466 735 786.727272727273 733 0.000597183003782379 355 1.40470109362636 -1.43919108049678 -1 3.80625565375195 733 355 839 720 1153 1292 1220 435 564 755 588 286 M1527 MCDOWELL_ACUTE_LUNG_INJURY_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCDOWELL_ACUTE_LUNG_INJURY_UP.html Genes up-regulated in the mouse model of acute lung injury induced by inhaling nickel sulfate [PubChem=24586]. 12540486 72/112 John Newman 8.48801857051626e-05 0.000581472389736382 25 1508.90909090909 734 7.71667824737453e-06 22 1.41913577710319 1.4383910263885 1 6.88964087581067 22 3701 471 3805 3421 64 79 837 3336 734 128 287 M990 CORRE_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CORRE_MULTIPLE_MYELOMA_DN.html Genes down-regulated in multiple myeloma (MM) bone marrow mesenchymal stem cells. 17344918 83/104 Leona Saunders 0.000179436555244027 0.00106266065338997 150 962.909090909091 735 1.63137447393069e-05 149 1.2820878293822 1.32459774224902 1 5.72051183310225 149 1327 513 1056 735 502 741 952 3357 669 591 288 M19766 WU_SILENCED_BY_METHYLATION_IN_BLADDER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WU_SILENCED_BY_METHYLATION_IN_BLADDER_CANCER.html Genes silenced by DNA methylation in bladder cancer cell lines. 17456585 78/106 Jessica Robertson 1.99327508970673e-10 6.03093488680499e-09 105 1267.81818181818 736 1.81206826353394e-11 102 1.41811781582981 1.4278995502176 1 17.4905307667916 102 2399 122 3077 810 608 604 1107 4096 285 736 289 M19245 COULOUARN_TEMPORAL_TGFB1_SIGNATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/COULOUARN_TEMPORAL_TGFB1_SIGNATURE_DN.html 'Early-TGFB1 signature': genes overexpressed in primary hepatocytes at an early phase of TGFB1 [GeneID=7040] treatment; is associated with a less invasive phenotype. 18506891 182/254 Yujin Hoshida 1.39861840742209e-06 1.86482454322945e-05 4555 1819.09090909091 736 1.27147208779495e-07 176 1.25732705218047 -1.35814936603369 -1 8.92251890405127 4555 573 434 234 736 2413 4660 2794 646 176 2789 290 M1797 ZHENG_GLIOBLASTOMA_PLASTICITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_GLIOBLASTOMA_PLASTICITY_DN.html The glioblastoma multiforme (GBM) plasticity signature: genes down-regulated in neural stem cells (NSC) with double knockout of TP53 and PTEN [GeneID=7157;5728] vs those with knockout of TP53 alone. 18948956 98/115 Jessica Robertson 5.29651465544176e-08 1.0330392220531e-06 315 846.727272727273 737 4.81501343905063e-09 34 1.27622315437589 1.24728848795374 1 11.4628512339797 313 34 202 737 1607 486 751 1470 2493 343 878 291 M1679 ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_UP.html Genes up-regulated in CD-1 compared to CD-2 cluster of multiple myeloma samples. 16728703 70/94 Kevin Vogelsang 2.84641882011628e-06 3.43608614602272e-05 2940 2156.36363636364 740 2.58765682081429e-07 91 1.42274581012053 1.25727900997275 1 9.5297664217937 2940 740 316 664 91 4462 4326 4547 569 418 4647 292 M19675 FARMER_BREAST_CANCER_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_3.html Cluster 3: selected apocrine, basal and hypoxia genes clustered together across breast cancer samples. 15897907 22/23 Arthur Liberzon 0.000276666359544392 0.00149071371809307 500 742.909090909091 741 2.51546507748469e-05 53 1.15979403232379 1.29310364686574 1 4.91901982819522 499 943 1415 741 1110 374 198 53 1099 1201 539 293 M10161 BROWNE_HCMV_INFECTION_4HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_4HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 4 h time point that were not up-regulated at the previous time point, 2 h. 11711622 76/108 Arthur Liberzon 9.04483748420228e-05 0.000610752974612801 180 1236.09090909091 743 8.22291760462273e-06 130 1.22608286052176 1.31136150301194 1 5.91313632282966 178 2850 474 2929 771 206 743 571 3893 852 130 294 M12300 CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LVAD_SUPPORT_OF_FAILING_HEART_UP.html Up-regulated genesin the left ventricle myocardium of patients with heart failure following implantation of LVAD (left ventricular assist device). 12824457 116/140 John Newman 6.85386121809012e-05 0.000490898709398868 350 1677.45454545455 744 6.23097704728256e-06 286 1.27092616283223 1.16089356806502 1 6.31033879389322 346 4035 462 4190 2873 297 744 1081 3770 368 286 295 M6386 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_4 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_4.html The 'group 4 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 but not ERBB2 [GeneID=2099;2064]. 18794137 396/488 Jessica Robertson 5.78451042049304e-05 0.000426617300967481 635 874.818181818182 744 5.25878410868193e-06 320 1.1753241575087 1.16406118249062 1 5.9431498646647 633 1155 453 744 1524 320 940 480 1862 396 1116 296 M2613 ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF.html Class III of genes transiently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 305/365 Yaara Zwang 1.49698056634446e-07 2.61694380486883e-06 70 995 750 1.36089151655079e-08 69 1.19389830211805 1.20000684734692 1 10.0002389032527 69 1175 357 2254 2916 153 364 750 1991 131 785 297 M2232 BHAT_ESR1_TARGETS_NOT_VIA_AKT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_NOT_VIA_AKT1_DN.html Genes bound by ESR1 [GeneID=2099] and down-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer). 18838536 135/157 Arthur Liberzon 0.00423922993670527 0.0116875965544678 170 1056.27272727273 752 0.000386129155437305 168 1.12996394580841 1.19124507224483 1 3.27613095729968 168 1258 752 795 2696 204 427 685 2513 1513 608 298 M7012 SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_DN.html Genes down-regulated in invasive ductal carcinoma (IDC) relative to ductal carcinoma in situ (DCIS, non-invasive). 16707453 123/148 Arthur Liberzon 5.3109900230029e-07 8.16543091484485e-06 4060 1993.63636363636 753 4.82817391374745e-08 218 1.24668974526754 -1.43134201959444 -1 9.51796826774739 4056 621 256 218 4378 4578 4138 753 2010 295 627 299 M2712 TRAYNOR_RETT_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/TRAYNOR_RETT_SYNDROM_UP.html Genes up-regulated in primary fibroblasts from Rett syndrom patients who carry mutations inactivating MECP2 [GeneID=4204]. 12418965 48/68 John Newman 0.000375332862164024 0.00186874589600653 365 1074 756 3.4126991949386e-05 67 1.23894069216643 1.30315284460779 1 5.07223333568304 362 824 677 3016 520 1061 547 67 3011 973 756 300 M2391 WANG_THOC1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_THOC1_TARGETS_DN.html Genes down-regulated in testis tissue expressing hypomorphic allele of THOC1 [GeneID=9984]. 19307311 18/47 Arthur Liberzon 0.00821135901848897 0.0186873744297338 1320 942.454545454545 756 0.00074928804570168 228 1.42110179316586 1.12720921070417 1 3.68563036266906 1319 368 1013 320 2904 756 238 1575 228 1196 450 301 M4995 LINDGREN_BLADDER_CANCER_CLUSTER_2B http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_2B.html Genes specifically up-regulated in Cluster IIb of urothelial cell carcinom (UCC) tumors. 16532037 508/674 Arthur Liberzon 1.59225018941113e-10 4.84865864130357e-09 565 1681.90909090909 757 1.59225018952521e-11 70 1.27986830025204 1.28237630391071 1 15.9673923929687 224 3604 4362 3280 1465 345 757 565 3266 70 563 302 M19918 ABE_VEGFA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ABE_VEGFA_TARGETS.html Genes most profoundly induced in HUVEC cells (endothelium) by VEGFA [GeneID=7422]. 12197474 20/29 John Newman 0.000428030608391428 0.0020432814817571 700 1244.90909090909 757 3.89194462223871e-05 73 1.50519085907217 1.4696963277345 1 6.07470376827652 1806 364 700 700 4487 774 1271 73 2212 757 550 303 M518 REACTOME_ANTIGEN_PROCESSING_CROSS_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_PROCESSING_CROSS_PRESENTATION.html Genes involved in Antigen processing-Cross presentation 93/132 Reactome 0.00141008062903584 0.0051275659237667 320 1657.81818181818 758 0.0001282713841845 320 0.851164175243755 -0.670400055134903 -1 2.92477016185819 320 1837 3321 2693 456 395 758 650 3211 4109 486 304 M1387 SHIN_B_CELL_LYMPHOMA_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_3.html Cluster 3 of genes distinguishing among different B lymphocyte neoplasms. 19010892 34/44 Jessica Robertson 0.0035429501884808 0.0102467677019788 550 871.818181818182 758 0.000322606251435423 135 1.18788702180261 1.17201136658535 1 3.54592021829507 549 258 1191 178 1516 465 135 954 2160 1426 758 305 M12524 KEGG_HISTIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HISTIDINE_METABOLISM.html Histidine metabolism 27/36 KEGG 0.000854291836578609 0.00351835553102581 1280 783.636363636364 759 7.76930682652159e-05 259 1.73240913089947 -1.62783593116973 -1 6.37822005373486 1279 309 759 724 376 933 1176 1376 259 566 863 306 M13254 GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_DN.html Genes down-regulated in quescent CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloblastic leukemia) patients compared to the dividing cells from normal donors. 17717066 9/24 Arthur Liberzon 0.00169384944915955 0.00590003483362169 760 1180.63636363636 760 0.000169514194260531 206 1.6626739507975 -1.85159734963915 -1 5.56133476961447 760 1616 4316 475 1264 834 729 206 412 2035 340 307 M1627 JACKSON_DNMT1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JACKSON_DNMT1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon Cre-lox knockout of DNMT1 [GeneID=1786]. 11137995 49/53 John Newman 3.72007402026775e-05 0.000303259920132362 95 1262.45454545455 762 3.38194266007125e-06 91 1.39571188268968 1.46458598311105 1 7.36800678511078 91 2458 428 2406 1081 857 762 495 3891 673 745 308 M6100 SENESE_HDAC1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC1 [GeneID=3065] by RNAi. 17470557 364/452 Leona Saunders 5.37643158423319e-09 1.25627510285053e-07 765 906.818181818182 764 4.88766508852025e-10 122 1.22113296006742 1.27142898140113 1 12.6446793530542 764 1159 163 952 1128 356 2064 592 2186 122 489 309 M2212 TAKADA_GASTRIC_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKADA_GASTRIC_CANCER_COPY_NUMBER_UP.html Candidate genes in the regions of copy number gain in gastric cancer cell lines. 16103878 14/14 Arthur Liberzon 0.00205365184239699 0.00680704824165296 3460 1437.27272727273 764 0.000186870126409568 265 1.2793365432378 -1.20835833050932 -1 4.15989844033683 3457 415 1626 405 518 3036 3826 265 764 1161 337 310 M8341 PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_DN.html Antigen processing and presentation genes down-regulated in JY cells (B lymphocytes) treated with trichostatin A (TSA) [PubChem=5562]. 18829567 69/89 Jessica Robertson 0.00077409176063901 0.00326515916909395 70 1390 765 7.03967515207896e-05 62 0.820995298334416 -0.828744574778171 -1 3.06256492188464 68 1350 3842 1636 765 62 72 114 3097 4110 174 311 M2377 IKEDA_MIR133_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR133_TARGETS_UP.html Genes up-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-133 microRNA. 19188439 66/94 Arthur Liberzon 0.00394431418658463 0.0110618912422338 365 1401.36363636364 766 0.000359218511865599 363 0.8652876984441 0.91855325568139 1 2.53975002180151 363 766 3405 2390 647 485 442 881 2197 3273 566 312 M2286 REACTOME_PEROXISOMAL_LIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEROXISOMAL_LIPID_METABOLISM.html Genes involved in Peroxisomal lipid metabolism 23/24 Reactome 0.000105888027328479 0.00069664684542787 1670 1244.18181818182 769 9.62664765093235e-06 137 1.12173999917299 -1.17583015262003 -1 5.31371434121958 1668 2556 2510 769 137 313 724 158 1654 2971 226 313 M16518 ST_WNT_CA2_CYCLIC_GMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_WNT_CA2_CYCLIC_GMP_PATHWAY.html Wnt/Ca2+/cyclic GMP signaling. 17/28 Signaling Transduction KE 0.00269114988176669 0.00835672858022288 465 866.363636363636 771 0.000244949770854462 186 1.1469611643712 1.31012186912823 1 3.57614917781928 465 1546 1579 1006 750 259 771 252 1259 1457 186 314 M10797 AMIT_EGF_RESPONSE_60_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_60_HELA.html Genes whose expression peaked at 60 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 60/71 Leona Saunders 0.00517025759859397 0.013690005497996 420 1206.72727272727 771 0.000471131676191095 220 1.48828145718378 1.38206750911441 1 4.16167051071002 420 2433 1028 1861 3737 611 574 380 1239 771 220 315 M847 BOYLAN_MULTIPLE_MYELOMA_C_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_UP.html Genes up-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 61/69 Jessica Robertson 0.010616786148637 0.0228524359067621 775 1420.45454545455 774 0.000969851782232527 142 0.959777145675898 0.996994813152056 1 2.36330193361 774 142 2826 1763 3174 497 584 696 1633 3331 205 316 M12671 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN.html Genes down-regulated in nsopharyngeal carcinoma relative to the normal tissue. 16912175 302/528 Leona Saunders 3.15191182407904e-20 3.54214852610788e-18 1600 867.909090909091 775 2.8653743855264e-21 3 1.45384756798332 -1.54838506626257 -1 38.0691477903948 1600 532 30 3 2293 215 2296 775 863 45 895 317 M8043 ROSS_AML_WITH_AML1_ETO_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_AML1_ETO_FUSION.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtype t(8;21) ; has AML1 ETO fusion [GeneID=861;862]. 15226186 86/177 Kate Stafford 0.00318208739494185 0.00948796746944128 70 691.727272727273 776 0.000289699938048599 68 1.35054874941986 -1.35757484074471 -1 4.0992042959373 1067 68 1180 134 1333 76 1165 776 696 1044 70 318 M4953 REACTOME_CDT1_ASSOCIATION_WITH_THE_CDC6_ORC_ORIGIN_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CDT1_ASSOCIATION_WITH_THE_CDC6_ORC_ORIGIN_COMPLEX.html Genes involved in CDT1 association with the CDC6:ORC:origin complex 57/67 Reactome 0.00104629101373514 0.0041188436904336 105 1459.09090909091 778 9.51626315929446e-05 105 0.615477469979935 -0.61117684417367 -1 2.20273574596773 105 778 4045 1628 401 360 363 658 2404 4330 978 319 M1541 DELASERNA_MYOD_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELASERNA_MYOD_TARGETS_DN.html Genes down-regulated in NIH 3T3 cells (fibroblasts) 24 h after inducing MyoD [GeneID=4654] differentiation program. 15870273 117/154 John Newman 0.00104915861591659 0.0041266905559386 55 1500 778 9.54235712512405e-05 53 1.17280765163268 1.20584520603921 1 4.19600901095813 53 2806 778 2952 4250 146 226 175 3899 1104 111 320 M12085 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINDED_IN_ERYTHROCYTE_UP.html Genes up-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing erythroid lineage. 17898786 57/83 Arthur Liberzon 0.000121538793339371 0.000775220411570039 690 1122.45454545455 780 1.10495916598135e-05 31 1.40430074839126 1.61692639037123 1 6.55443970906948 689 780 584 1480 4032 1092 903 31 1559 541 656 321 M5547 LU_AGING_BRAIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_AGING_BRAIN_UP.html Age up-regulated genes in the human frontal cortex. 15190254 372/458 John Newman 2.61917050315406e-09 6.57578977387615e-08 780 788.636363636364 780 2.38106409661115e-10 152 1.19219468896521 1.18393040332928 1 12.8479537297364 780 520 152 270 841 722 1306 817 2013 186 1068 322 M6815 AMIT_EGF_RESPONSE_60_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_60_MCF10A.html Genes whose expression peaked at 60 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 56/58 Leona Saunders 0.00495618731484682 0.0132370379104381 630 1249.72727272727 781 0.000451580728857998 396 1.45864354037042 1.51316581877978 1 4.11077552039494 627 2450 781 1629 4020 441 396 638 1446 520 799 323 M17148 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_DN.html Genes down-regulated in granulocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 17/30 Arthur Liberzon 0.000135694479366905 0.000843844456669029 850 864.363636363636 783 1.23366226937628e-05 153 1.38436638606117 1.28924957805868 1 6.38487567416543 847 1548 783 696 153 1264 1837 210 1231 562 377 324 M2591 GHANDHI_DIRECT_IRRADIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_DIRECT_IRRADIATION_UP.html Genes significantly (FDR < 10%) up-regulated in IMR-90 cells (fibroblast) in response to direct irradiation. 19108712 113/143 Itai Pashtan 1.41137584059997e-05 0.000137638305116361 470 1175.54545454545 784 1.28307717740351e-06 380 1.48940769904668 1.49205903852961 1 8.62937216983585 470 1813 380 1766 3731 471 784 625 1546 558 787 325 M16743 KEGG_TYROSINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYROSINE_METABOLISM.html Tyrosine metabolism 33/53 KEGG 0.00279088153996433 0.0085744699659703 630 737.363636363636 785 0.000254038936745919 107 1.42481830799649 -1.39156268570082 -1 4.4186318252151 626 880 1326 785 1257 252 107 1117 286 517 958 326 M15569 KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY.html NOD-like receptor signaling pathway 56/72 KEGG 0.00577426225782821 0.0142024584976285 780 1359.36363636364 785 0.000526315789473684 173 1.16396879311438 1.18150538190118 1 3.2268994179444 704 785 1409 173 3123 695 798 3455 779 776 2256 327 M12895 CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_DN.html Genes down-regulated in basal-like breast cancer cell lines as compared to the mesenchymal-like ones. 16288205 87/104 Arthur Liberzon 2.64590035225176e-05 0.000229149535094097 700 1081 785 2.40539288595842e-06 64 1.17124703390068 1.12192021811042 1 6.39691110157708 700 64 412 510 785 1326 2049 1937 2327 570 1211 328 M1522 ONGUSAHA_TP53_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ONGUSAHA_TP53_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblast) lacking TP53 and BRCA1 [GeneID=7157;672] by expression of TP53; most genes are further up-regulated by simultaneous expression of BRCA1. 12802282 45/47 John Newman 0.00409994441461085 0.0113833750805666 680 1227.09090909091 786 0.000373418646469985 340 1.28057890369702 1.31605518984878 1 3.7348361142449 1521 1421 786 730 3149 1137 676 340 2593 676 469 329 M9334 VALK_AML_CLUSTER_11 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_11.html Top 40 genes from cluster 11 of acute myeloid leukemia (AML) expression profile; 67% of the samples are FAB M4 or M5. 15084694 57/75 Jessica Robertson 0.000204452861262303 0.00118698340117844 865 951 786 1.85883512887986e-05 313 1.3476163217774 1.38738405037449 1 5.91573377572185 861 786 703 1038 2235 663 725 888 1933 313 316 330 M2118 SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN.html Genes down-regulated in pleura relapse of breast cancer. 18451135 26/84 Jessica Robertson 0.00590521920303632 0.0144417796053531 180 1095.18181818182 787 0.000538284523503963 179 1.70108321569341 1.83876870127807 1 4.69747979326971 179 3457 787 2318 1373 253 193 479 1290 1191 527 331 M4791 BIOCARTA_EIF4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF4_PATHWAY.html Regulation of eIF4e and p70 S6 Kinase 35/39 BioCarta 0.00776560996477927 0.0178189980718319 790 1814 788 0.000708468856398938 204 0.634687532737691 0.708961892466135 1 1.66568538530815 788 274 3736 2761 4375 337 704 472 2162 4141 204 332 M8448 BENPORATH_PRC2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_PRC2_TARGETS.html Set 'PRC2 targets': Polycomb Repression Complex 2 (PRC) targets; identified by ChIP on chip on human embryonic stem cells as genes that: posess the trimethylated H3K27 mark in their promoters and are bound by SUZ12 [GeneID=23512] and EED [GeneID=8726] Polycomb proteins. 18443585 489/952 Jessica Robertson 6.83738188859495e-50 3.22724425141682e-46 550 1081.09090909091 789 6.21580171690452e-51 1 1.46497954929204 1.39196343453257 1 100 548 2217 1 1953 1626 292 1115 789 2888 11 452 333 M251 PID_SYNDECAN_3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_3_PATHWAY.html Syndecan-3-mediated signaling events 18832364 22/26 Pathway Interaction Database 0.000403280639586832 0.00196757876474302 2245 1206.18181818182 791 3.66685985171546e-05 55 1.32055488584559 -1.28321617025272 -1 5.36201937132244 2244 333 1646 791 277 2301 3181 633 55 1198 609 334 M503 REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_STEROID_HORMONES_AND_VITAMINS_A_AND_D.html Genes involved in Metabolism of steroid hormones and vitamins A and D 21/53 Reactome 4.62448678961788e-05 0.00035607793877645 145 859.909090909091 791 4.20416727365032e-06 88 1.75147079147702 2.03528926133706 1 9.06283745514252 1907 967 1204 142 88 1953 791 159 143 1438 667 335 M1982 ONO_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONO_FOXP3_TARGETS_DN.html Genes down-regulated in CD4+ [GeneID=920] T lymphocytes transduced with FOXP3 [GeneID=50943]. 17377532 30/53 Jessica Robertson 0.000506517177701238 0.00233472761596664 795 923.545454545455 791 4.60576212116178e-05 84 1.21066254588892 1.32632485005901 1 4.78081796067643 791 287 1285 319 2250 672 1236 84 754 1467 1014 336 M1592 SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_UP.html Genes up-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] which continued to respond normally to insulin in the insulin resistant cells. 14530283 47/52 John Newman 0.00353508949602473 0.0102303019136951 295 1471.54545454545 794 0.000321889336133826 118 1.29071413989613 1.20888483984534 1 3.8542277300554 293 3352 1148 3371 3201 118 149 794 2678 499 584 337 M18685 ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_LIVE_UP.html Genes up-regulated in macrophage by live P.gingivalis. 18025224 524/771 Arthur Liberzon 1.32815702215083e-08 2.87564272685867e-07 270 1655.09090909091 796 1.32815703008883e-09 101 1.27311199857293 1.27752739418562 1 12.495869756358 267 2706 4287 2802 3105 287 796 354 2831 101 670 338 M10290 KOBAYASHI_EGFR_SIGNALING_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_24HR_UP.html Genes up-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 24h. 17145885 138/193 Arthur Liberzon 1.38179486879569e-05 0.000135594007915086 2790 1393.90909090909 797 1.25618504342521e-06 224 1.28313883557239 -1.40497937183044 -1 7.44678384340402 2789 616 648 511 556 1099 3746 3156 797 224 1191 339 M600 REACTOME_G_ALPHA_I_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_I_SIGNALLING_EVENTS.html Genes involved in G alpha (i) signalling events 84/229 Reactome 2.50393389964787e-07 4.20589608766476e-06 800 1495.18181818182 798 2.27630380421236e-08 55 1.53560359872755 1.66121178593134 1 12.3876209272489 798 3687 233 4549 1924 644 880 55 3029 440 208 340 M6856 KEGG_HEMATOPOIETIC_CELL_LINEAGE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEMATOPOIETIC_CELL_LINEAGE.html Hematopoietic cell lineage 52/107 KEGG 1.1470050395358e-05 0.000115188591204447 155 1205 799 1.04273729061174e-06 155 1.42593439224824 1.37666403539954 1 8.42707251582424 155 799 373 1702 4679 764 827 707 1365 518 1366 341 M1402 LEI_HOXC8_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEI_HOXC8_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) by overexpression of HOXC8 [GeneID=3224]. 15699330 17/28 Kate Stafford 0.000450425371470485 0.00212813588922992 330 1363.36363636364 799 4.09561470422572e-05 78 1.91832760278728 2.02829568511764 1 7.69121881265511 326 2606 799 1971 2332 701 423 78 3685 1904 172 342 M17037 PETRETTO_HEART_MASS_QTL_CIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_HEART_MASS_QTL_CIS_UP.html Up-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that colocalize with previously mapped cardiac mass QTLs. 18443592 40/45 Jessica Robertson 0.00257882725000101 0.00808775057807626 1055 1032.90909090909 801 0.000234714100586781 268 1.17511721056848 -1.16017848207338 -1 3.6889942151137 1052 859 2177 775 564 281 1650 801 421 2514 268 343 M2210 WIERENGA_STAT5A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_UP.html Genes up-regulated in CD34+ [GeneID=947] cells by intermediate activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 269/369 Arthur Liberzon 1.10643160518554e-06 1.5313818861979e-05 785 1442.09090909091 801 1.0058474196694e-07 283 1.23294345441605 1.28083034234193 1 8.90776123401139 781 2734 283 2288 3207 712 1452 566 2499 540 801 344 M702 REACTOME_ACYL_CHAIN_REMODELLING_OF_PE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PE.html Genes involved in Acyl chain remodelling of PE 13/22 Reactome 0.00577426225782821 0.0142024584976285 680 732 807 0.000526315789473684 21 1.27135072193284 -1.37099017239182 -1 3.5246067530849 677 411 1167 21 807 845 1425 432 907 1050 310 345 M3228 KEGG_SMALL_CELL_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SMALL_CELL_LUNG_CANCER.html Small cell lung cancer 112/124 KEGG 0.010798954284384 0.0231758044221638 570 1241.54545454545 809 0.00098657539624005 214 1.12952180220482 1.20932479280642 1 2.77094782808183 570 656 853 1386 4118 214 390 809 3119 942 600 346 M288 PID_HES_HEY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HES_HEY_PATHWAY.html Notch-mediated HES/HEY network 18832364 61/75 Pathway Interaction Database 0.00265048474138513 0.00825216885180595 260 823.272727272727 809 0.000241243941003637 250 1.19812318311214 1.29589115973837 1 3.74550445183789 260 1365 1193 809 1725 367 277 250 816 1615 379 347 M583 REACTOME_RIP_MEDIATED_NFKB_ACTIVATION_VIA_DAI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RIP_MEDIATED_NFKB_ACTIVATION_VIA_DAI.html Genes involved in RIP-mediated NFkB activation via DAI 22/35 Reactome 0.00201418740934376 0.00669976361670371 410 1322.45454545455 812 0.000183275804096084 112 1.32226932913927 1.38645810525712 1 4.31319143771849 409 3037 2014 3173 514 349 112 299 812 2878 950 348 M286 PID_TGFBR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TGFBR_PATHWAY.html TGF-beta receptor signaling 18832364 79/85 Pathway Interaction Database 0.0228928034714687 0.0422086064005204 675 1051.90909090909 814 0.00210314100840899 79 1.06515097842577 0.986822426456363 1 2.19688881737205 674 79 2409 389 2008 683 997 814 263 1527 1728 349 M1941 MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation at K4 (H3K4me2) and trimethylation at K27 (H3K27me3) in brain. 18600261 1102/1553 Jessica Robertson 9.19295701817875e-31 2.89271714172025e-28 820 1391.81818181818 816 9.19295701817867e-32 5 1.32935833317228 1.30667860834108 1 54.9321218569633 816 1113 4613 654 2860 134 1475 712 2451 5 477 350 M7585 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_DUCTAL_NORMAL_UP.html Genes up-regulated in ductal carcinoma vs normal ductal breast cells. 17389037 88/114 Arthur Liberzon 0.0038730139052546 0.0109072945303113 140 1636 820 0.000352713549710077 137 1.37158605209536 1.35787328799369 1 4.03845381250839 137 3683 745 3394 2183 494 594 820 3638 1680 628 351 M14958 PRAMOONJAGO_SOX4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PRAMOONJAGO_SOX4_TARGETS_UP.html Genes up-regulated in ACC3 cells (adenoid cystic carcinoma) after knockdown of SOX4 [GeneID=6659] by RNAi. 16636670 66/71 Leona Saunders 0.00902738917536458 0.0202035452383693 355 1309.54545454545 821 0.000824058727023297 236 1.30645963175643 1.22576974796131 1 3.32188122884788 354 3301 1546 3101 2248 236 415 513 1442 821 428 352 M10728 BASSO_HAIRY_CELL_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_HAIRY_CELL_LEUKEMIA_DN.html Genes down-regulated in hairy cell leukemia (HCL) compared with normal and other neoplastic B cell populations. 14707115 101/147 Arthur Liberzon 0.00163553830668697 0.00573355297131115 670 1255.63636363636 821 0.000148795952384177 448 1.24506674219337 1.37046505916659 1 4.18771354914739 775 669 667 942 3883 821 1124 2133 1632 448 718 353 M13486 KEGG_HUNTINGTONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HUNTINGTONS_DISEASE.html Huntington's disease 188/233 KEGG 0.000937375868915786 0.00378155051391667 55 1484.27272727273 823 8.52523185798001e-05 51 0.765719086423825 -0.742886371595329 -1 2.78309538850324 51 1748 3875 1514 410 110 124 823 2525 4379 768 354 M1523 NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_DN.html Top 20 genes whose down-regulation correlated with gastrointestinal stromal tumors (GIST) and synovial sarcoma compared to other tumors. 11965276 24/32 John Newman 7.6187383416883e-05 0.000531350806929073 730 1562.09090909091 824 6.92636563289132e-06 320 1.76723191419692 1.70829159154152 1 8.68341970864316 726 2567 467 2560 3562 824 320 2283 2910 455 509 355 M1692 YANG_MUC2_TARGETS_COLON_3MO_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_COLON_3MO_DN.html Genes down-regulated in colon of 3 month old MUC2 [GeneID=4583] knockout mice. 18794118 8/18 Jessica Robertson 0.000324138065914754 0.00167571924547387 385 1554.81818181818 824 3.24185355091515e-05 23 2.09780835281195 -2.09780835281195 -1 8.73756326357381 383 3119 4506 2570 824 487 23 564 3241 829 557 356 M5076 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_UP.html Genes specifically up-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and high dose methotrexate (HDMTX) [PubChem=4112]. 12704389 9/9 Arthur Liberzon 0.000171459898384287 0.0010244186333846 2355 1113.90909090909 824 1.71473129144594e-05 6 1.7776253081991 1.65785531187757 1 7.9740343135614 2354 440 4614 329 176 1128 66 824 6 1449 867 357 M12391 DAUER_STAT3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAUER_STAT3_TARGETS_UP.html Top 50 genes up-regulated in A549 cells (lung cancer) expressing STAT3 [GeneID=6774] off an adenovirus vector. 15735721 67/84 Arthur Liberzon 0.000319474844780773 0.00166253722973015 805 1147.45454545455 825 2.90473860929273e-05 501 1.37879695506231 1.40715184718219 1 5.74987501127179 804 1891 549 2825 512 989 702 1070 1954 501 825 358 M7804 ROSS_ACUTE_MYELOID_LEUKEMIA_CBF http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_ACUTE_MYELOID_LEUKEMIA_CBF.html Top 100 probe sets for core-binding factor (CBF) acute myeloid leukemia (AML): contains CBFB MYH11 [GeneID=865;4629] or AML1 ETO [GeneID=861;862] fusions. 15226186 98/176 Kate Stafford 0.00258674044666669 0.00809106355749953 940 1027.81818181818 825 0.000235435175373811 37 1.18299372335131 -1.16301751194382 -1 3.71340559135931 938 37 865 66 3716 49 670 1227 2649 825 264 359 M3008 NABA_ECM_GLYCOPROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_ECM_GLYCOPROTEINS.html Genes encoding structural ECM glycoproteins 22159717 150/221 Alexandra Naba 4.55599514569555e-19 4.05741454484585e-17 10 1598.54545454545 825 4.14181376881414e-20 10 1.62660778411239 1.63556540288186 1 40.0081844681657 10 3214 39 3769 3136 986 775 825 4032 61 737 360 M6225 WANG_BARRETTS_ESOPHAGUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_UP.html Genes up-regulated in Barrett's esophagus compared to the normal tissue. 16449976 62/102 Arthur Liberzon 0.00223781564893293 0.00727945545345515 1565 1486.72727272727 831 0.000203645016099792 442 1.4428937834443 -1.32989941521341 -1 4.62864478806695 1562 767 690 719 4234 781 2010 2972 442 831 1346 361 M14553 LIANG_SILENCED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_SILENCED_BY_METHYLATION_UP.html Genes up-regulated in LD419 cells (fibroblast) after treatment with decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 11861364 48/98 John Newman 3.29131276669201e-07 5.33848668686814e-06 420 942.272727272727 833 2.99210296280852e-08 126 1.5253492460812 -1.39332953195443 -1 12.0678699336411 417 1411 240 2061 126 530 1584 833 1882 438 843 362 M1360 ZEMBUTSU_SENSITIVITY_TO_FLUOROURACIL http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_FLUOROURACIL.html Top genes associated with chemosensitivity to 5-fluorouracil [PubChem=3385] across 85 tumor xenografts. 11809704 29/41 Arthur Liberzon 0.00118520544675724 0.0044933090029672 430 1398.54545454545 833 0.000107804039470875 59 0.834934252765071 0.879853950001579 1 2.94084270375141 427 900 2775 833 3382 59 110 157 3166 3392 183 363 M2216 WIERENGA_STAT5A_TARGETS_GROUP2 http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_GROUP2.html Genes up-regulated in a linear fashion in CD34+ [GeneID=947] cells upon increasing activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 59/93 Arthur Liberzon 0.00139848424044936 0.00509324507324151 750 1192.72727272727 834 0.00012721581939867 350 1.33046010132358 1.39462067278239 1 4.57760912111641 746 1392 649 2038 1787 731 829 834 2248 1516 350 364 M10280 ZHAN_LATE_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_LATE_DIFFERENTIATION_GENES_UP.html B lymphocyte late differentiation genes (LDG): top genes up-regulated in plasma cells from tonsils (TPC) compared to those from bone marrow (BPC). 12393520 37/48 Arthur Liberzon 8.95003485903472e-05 0.000605217256943322 1725 1195.09090909091 836 8.13672634989325e-06 118 1.46937673989294 -1.52814079869985 -1 7.09523037969713 1724 1973 836 118 125 1794 2600 768 346 667 2195 365 M11106 BIOCARTA_GSK3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GSK3_PATHWAY.html Inactivation of Gsk3 by AKT causes accumulation of b-catenin in Alveolar Macrophages 44/55 BioCarta 0.0016655128035854 0.00581451215452893 115 1320.90909090909 839 0.000151525001833299 113 0.803386241970849 0.856974457796984 1 2.69476710396845 113 839 3011 2973 479 243 303 976 1874 3121 598 366 M4732 BIOCARTA_LECTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LECTIN_PATHWAY.html Lectin Induced Complement Pathway 10/15 BioCarta 5.54434344058929e-06 6.14302841304729e-05 840 829.636363636364 840 5.04032492113598e-07 17 2.00946371312192 2.08063193182945 1 12.6989343003494 840 1602 851 271 17 550 938 1241 765 1593 458 367 M2422 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_UP.html Genes from the magenta module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 73/117 Arthur Liberzon 0.00442759792414521 0.0120849478034359 550 1782 840 0.000403321259066304 162 0.963868243406563 0.996259994110708 1 2.77355053478825 550 3277 2489 3722 678 162 668 840 3729 2734 753 368 M12971 KYNG_DNA_DAMAGE_BY_GAMMA_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_GAMMA_RADIATION.html Genes specifically responding to gamma radiation. 15897889 118/154 Jessica Robertson 0.00800362823086137 0.0182498189611911 780 1072.36363636364 840 0.000730263154773228 167 1.18301788304541 1.21216200591683 1 3.08640725949139 777 645 975 1296 840 167 518 2072 2991 646 869 369 M10010 VALK_AML_WITH_FLT3_ITD http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_FLT3_ITD.html Genes that best predicted acute myeloid leukemia (AML) with internal tandem duplications (IDT) in FLT3 [GeneID=2322]. 15084694 58/73 Jessica Robertson 0.000247476814547237 0.00137764531438843 200 1347.81818181818 841 2.25004234059729e-05 192 1.2265068363101 1.35817418302622 1 5.26502029421977 198 2436 531 2943 1848 432 557 1059 3789 841 192 370 M1850 MATTHEWS_AP1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MATTHEWS_AP1_TARGETS.html Known targets of AP1 that were down-regulated by overexpression of TAM67, a dominant-negative form of JUN [GeneID=3725]. 17363560 20/22 Jessica Robertson 0.00988529112343332 0.0216513104884479 735 1314.36363636364 842 0.000902726389291844 248 1.47149294600501 1.75299068535531 1 3.67515290281849 731 2088 842 2824 952 495 374 3625 516 1763 248 371 M10953 BOYAULT_LIVER_CANCER_SUBCLASS_G2 http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G2.html Genes in hepatocellular carcinoma (HCC) subclass G2, defined by unsupervised clustering. 17187432 41/52 Yujin Hoshida 0.00284439201702495 0.00868404289803219 845 1045.27272727273 843 0.000258916019761771 254 1.3430276151757 1.47792043289883 1 4.153863901767 820 843 1300 845 2394 1504 2141 262 295 840 254 372 M10814 BECKER_TAMOXIFEN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BECKER_TAMOXIFEN_RESISTANCE_UP.html Genes up-regulated in a breast cancer cell line resistant to tamoxifen [PubChem=5376] compared to the parental line sensitive to the drug. 15657362 58/83 Jean Junior 0.00149146344107184 0.00535746380658986 1445 1300.81818181818 845 0.000135679592855951 183 1.05171671420266 1.20722698011339 1 3.58387363215259 1443 779 1459 788 4257 1181 610 183 2072 692 845 373 M1911 OKUMURA_INFLAMMATORY_RESPONSE_LPS http://www.broadinstitute.org/gsea/msigdb/cards/OKUMURA_INFLAMMATORY_RESPONSE_LPS.html Genes up-regulated in mast cells (MC) after stimulation with a bacterial lipopolysaccharide (LPS). 12855579 242/375 Kate Stafford 0.00577426225782821 0.0142024584976285 605 1056.18181818182 845 0.000526315789473684 148 1.17470619653891 1.18586478942521 1 3.25666796275464 603 1203 968 148 3516 666 845 403 1243 580 1443 374 M1988 GYORFFY_MITOXANTRONE_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/GYORFFY_MITOXANTRONE_RESISTANCE.html Genes associated with resistance to mitoxantrone [PubChem=4212]. 16044152 85/111 Arthur Liberzon 0.000289653558212574 0.00154831800086449 1165 1106.36363636364 847 2.63356092032819e-05 216 1.21462354058716 1.10263803277069 1 5.12156230117598 1162 713 1080 478 216 453 1067 4054 1289 847 811 375 M95 PID_CIRCADIAN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CIRCADIAN_PATHWAY.html Circadian rhythm pathway 18832364 21/21 Pathway Interaction Database 0.0110855230176886 0.0236224237668127 595 1225.27272727273 848 0.0010128889842823 288 0.941170581176485 0.975337527044329 1 2.29715913739806 595 965 2881 848 1654 468 288 1959 336 2796 688 376 M10550 AMIT_DELAYED_EARLY_GENES http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_DELAYED_EARLY_GENES.html Delayed early genes (DEG) which are coordinately down-regulated in multiple epithelial tumor types. 17322878 20/21 Arthur Liberzon 0.00302058030709301 0.0091041756382369 90 1211.63636363636 849 0.000274975956920287 87 1.07862741584694 1.10229127989362 1 3.30286747013352 87 2085 1862 1777 708 510 127 832 2277 2214 849 377 M1032 REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_MITOTIC_PROTEINS.html Genes involved in APC/C:Cdc20 mediated degradation of mitotic proteins 73/85 Reactome 0.000508257232788594 0.00234046257440211 40 1172.63636363636 854 4.62158810385261e-05 36 0.626135788412269 -0.626079371540183 -1 2.47151234679635 36 86 4071 191 854 221 190 876 1145 4343 886 378 M4502 GAL_LEUKEMIC_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAL_LEUKEMIC_STEM_CELL_DN.html Genes down-regulated in leukemic stem cells (LSC), defined as CD34+CD38- [GeneID=947;952] cells from AML (acute myeloid leukemia patients) compared to the CD34+CD38+ cells. 17039238 251/464 Leona Saunders 7.41618714312732e-07 1.09047985406732e-05 650 1338.45454545455 854 6.74199058465532e-08 134 1.30308693970921 1.41314205634371 1 9.70288060538003 648 1726 267 2540 3395 553 854 134 2504 436 1666 379 M8510 POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_DN.html Top down-regulated marker genes for medulloblastoma classification: desmoplastic vs classic morphology. 11807556 84/113 Jean Junior 0.00940937640034958 0.0207935728475375 140 1424.27272727273 854 0.000859078439522399 138 1.30328955194707 1.45493381906797 1 3.28937238923823 138 3264 854 3449 1251 658 531 530 3012 1308 672 380 M16369 HUANG_DASATINIB_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_DASATINIB_RESISTANCE_DN.html Genes whose expression negatively correlated with resistance of breast cancer cell lines to dasatinib [PubChem=3062316]. 17332353 82/100 Jessica Robertson 0.00457050671069661 0.0124195691850823 2080 1031.63636363636 855 0.000416366332855323 70 1.09160162437016 -1.10099269235533 -1 3.12169077303567 2080 70 1964 92 2471 629 1307 855 536 1245 99 381 M2452 PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_10HR_UP.html Genes up-regulated after 10 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 90/119 Arthur Liberzon 2.19518900653437e-08 4.52458170779137e-07 205 1192.54545454545 855 1.99562638948933e-09 188 1.38927169370314 1.29093816484272 1 13.225666063308 201 1846 188 2013 2593 567 855 869 3440 347 199 382 M1163 BAKER_HEMATOPOIESIS_STAT3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BAKER_HEMATOPOIESIS_STAT3_TARGETS.html STAT3 [GeneID=6774] targets in hematopoietic signaling. 17934481 18/20 Arthur Liberzon 0.00184901608769563 0.00632875702242448 730 1174.27272727273 856 0.000168233813290535 111 1.36764283227082 1.46669986556477 1 4.51197467542043 729 1560 1311 2159 1141 429 111 205 3736 856 680 383 M6244 OHM_EMBRYONIC_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/OHM_EMBRYONIC_CARCINOMA_UP.html Genes with a high basal transcription state in undifferentiated embryonic carcinoma cells. 17211412 10/14 Leona Saunders 0.00862916068643029 0.0195345987721587 2135 1365.45454545455 856 0.000787563115790188 224 1.39545020069295 1.60931118540615 1 3.57878040168201 2131 436 1603 495 856 3337 3245 790 224 1091 812 384 M13879 VANHARANTA_UTERINE_FIBROID_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_DN.html Genes down-regulated in uterine fibroids vs normal myometrium samples. 15940248 98/122 Leona Saunders 8.29018236064515e-06 8.63789420358612e-05 860 1006.18181818182 857 7.53655781855599e-07 110 1.22875520630481 1.24525477906428 1 7.49223091893736 857 678 362 1693 407 1255 1133 110 2971 289 1313 385 M1458 ABBUD_LIF_SIGNALING_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_1_UP.html Genes up-regulated in AtT20 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 51/73 Kevin Vogelsang 0.0011394819171326 0.00439695967188244 1140 976.363636363636 859 0.000103642957811077 59 1.4113895779584 -1.33892469487665 -1 4.99126917978949 1140 157 756 59 1430 373 1682 2416 859 422 1446 386 M1561 LINDVALL_IMMORTALIZED_BY_TERT_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDVALL_IMMORTALIZED_BY_TERT_DN.html Genes down-regulated in BJ cells (foreskin fibroblasts) immortalized by expression of TERT [GeneID=7015]. 12702554 122/152 John Newman 7.77556046744264e-12 2.88981459892356e-10 860 1130.81818181818 860 7.06869133406376e-13 99 1.43949183025372 1.43799813312549 1 20.6042850933458 109 2332 99 2090 860 892 856 710 3417 121 953 387 M2449 PLASARI_NFIC_TARGETS_BASAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_NFIC_TARGETS_BASAL_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon knockout of NFIC [GeneID=4782]. 19752192 29/37 Arthur Liberzon 0.000696094947988284 0.00300326156718894 110 1585.18181818182 860 6.3301390433869e-05 107 1.36259394811413 1.35505454327057 1 5.15720610289236 177 4171 860 4058 1463 210 108 107 4501 1395 387 388 M12107 MAHAJAN_RESPONSE_TO_IL1A_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAHAJAN_RESPONSE_TO_IL1A_DN.html Genes down-regulated in corneal fibroblasts after treatment with IL1A [GeneID=3552]. 12091409 134/175 John Newman 0.0002205607754722 0.00126956934174242 560 1102 861 2.0052990079486e-05 187 1.13859100710264 1.14944304126577 1 4.94823534951127 556 1795 1304 1384 187 700 861 588 2341 1645 761 389 M2026 NAKAMURA_ADIPOGENESIS_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_ADIPOGENESIS_LATE_UP.html Genes up-regulated in mesenchymal stem cells during late phase of adipogenesis, defined as days 7 to 14 of culturing with adipogenic hormones. 12646203 153/185 Arthur Liberzon 0.00568664061299535 0.0142024584976285 790 1261.45454545455 861 0.000518308460313571 599 1.19438227563853 1.25666314922165 1 3.31121823149368 790 1242 777 1048 1967 599 712 1512 3577 791 861 390 M736 REACTOME_NFKB_IS_ACTIVATED_AND_SIGNALS_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NFKB_IS_ACTIVATED_AND_SIGNALS_SURVIVAL.html Genes involved in NF-kB is activated and signals survival 16/19 Reactome 0.00080264612786209 0.00336157029592641 365 2043.09090909091 863 7.2994464932122e-05 42 0.721109637501279 0.721109637501279 1 2.67627317393766 365 4242 3048 4437 706 151 42 863 4502 3942 176 391 M1298 GROSS_ELK3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_ELK3_TARGETS_UP.html Genes up-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 39/43 Jessica Robertson 0.0176137563404979 0.0341986548445702 1230 1178.72727272727 863 0.00161421615634003 345 1.2711912906923 1.19488160333275 1 2.79619579051178 1226 863 913 556 1873 507 646 4083 345 766 1188 392 M14560 CHO_NR4A1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CHO_NR4A1_TARGETS.html Genes up-regulated in RKO cells (colon cancer) after treatment with the NR4A1 [GeneID=3164] agonist, DIM-C-pPhOCH3. 17234778 38/54 Jessica Robertson 0.00102760582855128 0.00405882804247871 435 1102.63636363636 864 9.34623755207489e-05 49 1.22433306537018 1.12174675816543 1 4.39358823411816 431 864 1179 1730 3734 89 49 500 1963 711 879 393 M14043 PETRETTO_CARDIAC_HYPERTROPHY http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_CARDIAC_HYPERTROPHY.html Genes that correlated most highly with left ventricular mass (LVM) index. 18443592 66/74 Jessica Robertson 1.19908266593253e-06 1.63574282751489e-05 15 1312.36363636364 866 1.09007574498012e-07 13 1.44301576839931 1.50669438426231 1 10.3635131611083 13 2869 287 2993 1166 596 514 1014 3776 342 866 394 M6046 BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_UP.html Up-regulated genes in tumor samples from colon cancer patients who developed recurrence of the disease. 16091735 17/19 Leona Saunders 0.00464869066632365 0.0125741088510302 390 1273.54545454545 867 0.000423503881680033 82 0.987035115408095 -1.01571603869951 -1 2.81469384921558 1314 388 2874 1561 695 1081 867 780 82 3977 390 395 M1655 HAN_JNK_SINGALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAN_JNK_SINGALING_DN.html Genes down-regulated in 3T3 cells (fibroblast) upon activation of JNK pathway. 12354774 56/65 John Newman 0.000117025794491811 0.000753092837001957 405 1704.72727272727 868 1.06392745429144e-05 310 1.56630950851691 1.81515018379503 1 7.34017105338209 403 2888 488 3031 4536 588 310 1275 3733 632 868 396 M9945 UDAYAKUMAR_MED1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/UDAYAKUMAR_MED1_TARGETS_DN.html Genes down-regulated in HeLa cells after knockdown of MED1 [GeneID=5469] by RNAi. 16574658 346/406 Leona Saunders 0.00279215261391872 0.0085744699659703 350 1442.36363636364 870 0.000254154782948798 53 1.17349373737478 1.10667179284053 1 3.6392079947683 350 3609 922 3407 2430 53 682 635 2714 870 194 397 M9152 BIOCARTA_CCR3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CCR3_PATHWAY.html CCR3 signaling in Eosinophils 38/52 BioCarta 3.46897306337033e-05 0.000287231415822982 1255 1282.09090909091 872 3.15366160322828e-06 74 0.932943489846401 -0.897171172582859 -1 4.95801680257834 1251 872 3225 1126 74 749 1574 802 606 3145 679 398 M14557 DORSEY_GAB2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/DORSEY_GAB2_TARGETS.html Genes up-regulated by expression of GAB2 [GeneID=9846] in K562 cells (chronic myeloid leukemia (CML) cell line with p210 BCR-ABL [GeneID=613;25]). 11830491 48/76 Kevin Vogelsang 1.02149203550188e-05 0.000104134825217471 25 1573 874 9.28633434971801e-07 21 1.55453904728087 1.62493266752789 1 9.28931761359738 21 3757 369 4281 1628 625 874 631 3708 972 437 399 M2208 CARD_MIR302A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CARD_MIR302A_TARGETS.html Potential targets of MIR302A [GeneID=407028]. 18710938 108/130 Arthur Liberzon 0.0395453844062933 0.0661190982634448 715 1370 874 0.00366133080496366 426 1.06766790123728 1.07823029677075 1 1.88979781753928 715 665 1661 838 3166 426 602 1693 2596 1834 874 400 M625 REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES.html Genes involved in Chemokine receptors bind chemokines 21/74 Reactome 0.00152900592087656 0.00545694030563126 170 1510.63636363636 875 0.000139097238112098 142 1.7415593686022 1.60919677776548 1 5.91379986281277 169 3488 659 2813 3924 272 142 875 2942 1095 238 401 M7815 RADMACHER_AML_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/RADMACHER_AML_PROGNOSIS.html The 'Bullinger validation signature' [PMID=15084693] used to validate prediction of prognostic outcome of acute myeloid leukemia (AML) patients with a normal karyotype. 16670265 143/181 Kevin Vogelsang 6.2908073471969e-06 6.81023180705719e-05 565 1273.63636363636 877 5.71893212324325e-07 347 1.21778648215968 1.20949617452495 1 7.61401184460087 561 1781 347 1341 2824 759 1351 594 3105 877 470 402 M1912 ZHANG_TLX_TARGETS_36HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_36HR_UP.html Genes up-regulated in neural stem cells (NSC) at 36 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 305/403 Jessica Robertson 4.36149002341136e-05 0.000341691152421599 2555 1470.45454545455 877 3.96506953832112e-06 70 1.12122051791137 -1.1249847138894 -1 5.83175692244324 2552 534 780 70 2440 877 3468 3288 1050 252 864 403 M1320 INGRAM_SHH_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/INGRAM_SHH_TARGETS_UP.html Genes up-regulated in 10T1/2 cells (multipotent mesoderma) by expression of SHH [GeneID=6469]. 17873912 146/288 Jessica Robertson 1.78418129653619e-05 0.000168090533326364 880 1033 878 1.62199615114465e-06 170 1.26550894788405 1.33681200228775 1 7.16729151379293 879 2306 389 2259 878 294 953 268 2659 308 170 404 M602 REACTOME_REGULATION_OF_COMPLEMENT_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_COMPLEMENT_CASCADE.html Genes involved in Regulation of Complement cascade 12/20 Reactome 7.48465753895147e-05 0.000524628503121043 40 786.818181818182 879 6.80446562535603e-06 15 1.39308406041019 1.39308406041019 1 6.85655372652891 40 1578 891 2264 879 193 145 15 1707 927 16 405 M6750 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_DN.html Genes down-regulated in nasopharyngeal carcinoma (NPC) positive for LMP1 [GeneID=9260], a latent gene of Epstein-Barr virus (EBV). 16912175 150/300 Arthur Liberzon 3.3016447681247e-21 3.89594082638715e-19 30 885.272727272727 880 3.00149524374973e-22 26 1.63345134609781 1.54554052910711 1 45.1217916309356 613 1240 29 1154 2042 880 1110 549 1765 26 330 406 M4737 VERRECCHIA_EARLY_RESPONSE_TO_TGFB1 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_EARLY_RESPONSE_TO_TGFB1.html ECM related genes up-regulated early (within 30 min) in dermal fibroblasts after addition of TGFB1 [GeneID=7040]. 11279127 137/173 John Newman 7.524329294043e-06 7.94515308006331e-05 195 1099.36363636364 882 6.84032275318058e-07 192 1.30671397730787 1.40258491086304 1 8.03877089141025 192 1791 356 2219 1087 603 882 487 3149 978 349 407 M897 REACTOME_BIOSYNTHESIS_OF_THE_N_GLYCAN_PRECURSOR_DOLICHOL_LIPID_LINKED_OLIGOSACCHARIDE_LLO_AND_TRANSFER_TO_A_NASCENT_PROTEIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BIOSYNTHESIS_OF_THE_N_GLYCAN_PRECURSOR_DOLICHOL_LIPID_LINKED_OLIGOSACCHARIDE_LLO_AND_TRANSFER_TO_A_NASCENT_PROTEIN.html Genes involved in Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein 29/32 Reactome 0.000524313212873835 0.00239570025630639 530 1528.36363636364 883 4.76762010093189e-05 315 0.800040980085144 -0.800862778451039 -1 3.14582664000655 530 2535 3800 2331 315 505 644 883 395 3780 1094 408 M962 REACTOME_IRON_UPTAKE_AND_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IRON_UPTAKE_AND_TRANSPORT.html Genes involved in Iron uptake and transport 37/51 Reactome 0.0187344087468195 0.0359603128446473 810 1349.27272727273 887 0.00171780659082199 648 1.1124818147821 1.31157149962759 1 2.41065993032247 806 1446 2179 2291 2720 667 887 729 834 1635 648 409 M14555 ZHU_CMV_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_ALL_DN.html Down-regulated at any timepoint following infection of primary human foreskin fibroblasts with CMV 9826724 186/248 John Newman 9.85758741929602e-08 1.81042072447771e-06 280 1226.36363636364 888 8.96144350998827e-09 215 1.21402006558277 1.3041218717624 1 10.4602760004321 279 1753 215 1538 2198 777 928 703 3805 406 888 410 M6051 DORSAM_HOXA9_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORSAM_HOXA9_TARGETS_DN.html HOXA9 [GeneID=3205] targets down-regulated in hematopoietic stem cells. 14604967 38/53 Broad Institute 0.00129984275459711 0.00479217899694665 1235 1668.36363636364 890 0.000118237398768864 138 0.758657006747937 0.746745401444114 1 2.64032912846185 1235 871 2973 2633 447 670 211 890 4456 3828 138 411 M1843 LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TARGETS_OF_TGFB1_AND_WNT3A_DN.html Down-regulated genes in NMuMG cells (mammary epithelium) after stimulation with both TGFB1 and WNT3A [GeneID=7040;89780]. 17210685 134/200 Jessica Robertson 1.44949326194247e-07 2.55283887924196e-06 1505 1141 890 1.31772123403989e-08 224 1.37799271142644 1.28689309992292 1 11.5645238587757 1504 2318 224 1469 890 234 862 1609 2506 319 616 412 M2448 SWEET_KRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_KRAS_TARGETS_UP.html Genes upregulated in KRAS [GeneID=3845] knockdown vs control in a human cell line. 15608639 129/150 Aravind Subramanian 0.000170281573485417 0.00101866796812569 220 1612.54545454545 891 1.54813413481235e-05 150 1.16405998585379 1.20348723738038 1 5.22594969003564 220 3216 508 3387 2605 648 891 854 3766 1493 150 413 M1714 LEIN_OLIGODENDROCYTE_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_OLIGODENDROCYTE_MARKERS.html Genes enriched in oligodendrocytes in the adult mouse brain identified through correlation-based searches seeded with the oligodendrocyte cell-type specific gene expression patterns. 17151600 82/114 Jessica Robertson 0.00648331772809748 0.0155415234518131 635 1189.18181818182 891 0.00059113663849909 378 1.4456423827783 1.53515130074734 1 3.92293414600197 635 2379 889 1246 3097 831 986 891 1204 545 378 414 M17758 KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM.html Alanine, aspartate and glutamate metabolism 28/35 KEGG 0.00371652842932188 0.0106186526552054 1420 1065 894 0.000338438342325109 298 1.01552845686749 -1.0099913051207 -1 3.00781071488501 1416 298 1831 950 634 392 558 678 2043 2021 894 415 M6753 ODONNELL_TFRC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TFRC_TARGETS_UP.html Genes up-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) upon knockdown of TFRC [GeneID=7037] by RNAi. 16508012 545/822 Leona Saunders 4.88736240435984e-09 1.15921359540595e-07 895 1164.81818181818 894 4.88736241510866e-10 93 1.21869678499566 1.23204657370781 1 12.6833126767363 894 1141 4306 485 973 352 1200 749 1854 93 766 416 M7048 GENTILE_UV_HIGH_DOSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_HIGH_DOSE_UP.html Selected genes up-regulated in WS1 (fibroblast) in response to irradiation with high dose UV-C. 12907719 32/73 John Newman 0.00314244626396213 0.00938756099107673 1200 1192.72727272727 894 0.000286085807513872 283 1.1316838735617 -1.17010531085626 -1 3.44273143278982 1196 283 970 1085 596 709 2887 894 2903 801 796 417 M13273 DELYS_THYROID_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELYS_THYROID_CANCER_DN.html Genes down-regulated in papillary thyroid carcinoma (PTC) compared to normal tissue. 17621275 292/388 Aravind Subramanian 2.86987079997533e-24 4.8377822056727e-22 890 1237.36363636364 895 2.60897345452302e-25 18 1.43214572378234 1.38507176115565 1 45.8058091055335 890 2247 18 1161 2891 895 1308 695 2981 32 493 418 M1269 KREPPEL_CD99_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KREPPEL_CD99_TARGETS_DN.html Genes down-regulated in ESFT cells (Ewing's sarcoma family of tumors) after knockdown of CD99 [GeneID=4267] by RNAi. 16314831 13/14 Arthur Liberzon 0.00129468594751237 0.00478912043280437 895 1195.18181818182 895 0.000117768044568074 160 1.34320096152786 1.52093967166001 1 4.67533868945926 895 2128 2389 2345 445 936 338 848 160 1963 700 419 M18077 ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_UP.html Genes up-regulated in immunoglobulin light chain amyloidosis plasma cells (ALPC) compared to multiple myeloma (MM) cells. 15388584 32/42 Kevin Vogelsang 0.000940005837950714 0.00378711778960274 1515 1191.54545454545 895 8.54916108839614e-05 467 1.34918273489127 1.55466958022522 1 4.9025493032988 1512 895 614 526 681 1241 904 3081 2567 619 467 420 M3649 BROWNE_HCMV_INFECTION_2HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_2HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 2 h time point that were not up-regulated at the previous time point, 1 h. 11711622 38/49 Arthur Liberzon 0.0105715146893191 0.0228050956734855 690 2203.54545454545 895 0.000965696152613996 556 1.3150807572545 1.19635311546051 1 3.23999814905947 690 4141 849 4598 4006 556 597 2974 4350 895 583 421 M2273 ZHU_SKIL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_SKIL_TARGETS_UP.html Genes up-regulated in A549 cells (lung adenocarcinoma) upon SKIL [GeneID=6498] knockdown by RNAi. 17074815 33/36 Arthur Liberzon 0.000309057297227983 0.00162444370035198 1345 1121.54545454545 896 2.81000656654644e-05 227 1.27472727881197 1.42422731549877 1 5.33512960408085 1344 896 774 2575 227 1043 2195 493 1624 664 502 422 M15243 REACTOME_GAP_JUNCTION_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_DEGRADATION.html Genes involved in Gap junction degradation 10/11 Reactome 0.00718646381861914 0.0168087756312598 900 1049.81818181818 897 0.000655458805326842 69 1.13261305482065 1.22424183555534 1 3.01561089823542 897 1055 2250 1450 912 671 462 453 69 2898 431 423 M9673 ZHOU_INFLAMMATORY_RESPONSE_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_LPS_UP.html Genes up-regulated in macrophages by P.gingivalis LPS (lipopolysaccharide). 18025224 433/673 Arthur Liberzon 3.04681750510257e-11 1.01992756199178e-09 385 1262.36363636364 897 2.76983409558615e-12 111 1.31518089210887 1.2888120208115 1 17.7440808912303 385 2714 111 2263 2413 518 721 897 2591 132 1141 424 M893 REACTOME_RESPIRATORY_ELECTRON_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESPIRATORY_ELECTRON_TRANSPORT.html Genes involved in Respiratory electron transport 79/93 Reactome 5.7016462935782e-08 1.10748026772383e-06 5 1493.18181818182 900 5.18331494667759e-09 4 0.591968828030372 -0.591968828030372 -1 5.29007887010163 4 1313 3977 1430 491 70 63 900 2882 4415 880 425 M16734 KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_PROSTATE_CANCER_HCP_WITH_H3K27ME3.html Genes with high histone H3 trimethylation mark at K27 (H3K27me3) in PC3 cells (prostate cancer) by ChIP-chip assay on a 12K CpG array (high-CpG-density promoters, HCP). 18488029 97/143 Jessica Robertson 4.97994909926184e-05 0.000379118705621224 45 1614.72727272727 900 4.52732893601896e-06 42 1.41008899069236 -1.43373488475602 -1 7.23875021519218 4341 42 445 43 2106 3481 2712 2650 900 397 645 426 M5002 DAZARD_UV_RESPONSE_CLUSTER_G24 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G24.html Cluster G24: genes induced in NHEK (normal keratinocyte) but not in SCC12B2 cells (squamous cell carcinoma) by UV-B radiation. 12771951 34/102 Arthur Liberzon 0.00040524132912219 0.00197393093235989 640 1072.45454545455 900 3.68469085522918e-05 359 1.45823650787165 -1.54661292867545 -1 5.91801388004001 1277 1460 636 2112 359 802 1698 1557 637 359 900 427 M19540 KEGG_OXIDATIVE_PHOSPHORYLATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OXIDATIVE_PHOSPHORYLATION.html Oxidative phosphorylation 126/155 KEGG 9.02138831079955e-07 1.27107321871564e-05 10 1460 901 8.2012654637638e-08 7 0.647939770691466 -0.606711005918651 -1 4.75984783504477 7 1256 3985 1432 473 83 39 788 2676 4420 901 428 M2103 STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_UP.html Genes induced in SKBR3 cells (breast cancer) by 25-hydroxyvitamin D3 [PubChem=1593]. 20227041 127/173 Arthur Liberzon 3.20111448143009e-06 3.76789534971322e-05 600 1035.54545454545 902 2.91010830838884e-07 211 1.39414554528207 1.41754824460319 1 9.25444488824809 598 628 325 253 3760 902 967 1226 1377 211 1144 429 M5319 APPEL_IMATINIB_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/APPEL_IMATINIB_RESPONSE.html Genes up-regulated by imatinib [PubChem=5291] during dendritic cell differentiation. 15756019 36/65 Kevin Vogelsang 0.00111840485389707 0.00433404836649769 4335 1659.36363636364 904 0.000101724892518432 11 1.40742277057671 1.52273611048309 1 4.99045817460302 2450 213 904 226 4333 4335 4389 152 11 1004 236 430 M5884 NABA_CORE_MATRISOME http://www.broadinstitute.org/gsea/msigdb/cards/NABA_CORE_MATRISOME.html Ensemble of genes encoding core extracellular matrix including ECM glycoproteins, collagens and proteoglycans 22159717 207/301 Alexandra Naba 3.382358335691e-29 9.39101843791853e-27 905 1513.09090909091 904 3.07487121426457e-30 6 1.63757942024933 1.63553389527209 1 63.9546855048279 6 3632 12 3334 2478 904 717 904 3945 39 673 431 M13626 MCCABE_HOXC6_TARGETS_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_CANCER_DN.html Genes whose promoters were bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and which were down-regulated in comparison of tumor vs normal prostate tissue samples. 18339881 30/32 Jessica Robertson 0.0020461239766636 0.00678686238218708 1310 1355 905 0.000186184497166394 223 0.969813475424873 -0.878001995477167 -1 3.15530268475808 1310 905 3015 513 2612 639 1284 223 576 3439 389 432 M16334 BIOCARTA_EPHA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPHA4_PATHWAY.html Eph Kinases and ephrins support platelet aggregation 30/36 BioCarta 0.000167807905265539 0.00100642098202458 110 1384.54545454545 906 1.52564278547391e-05 16 1.3283654948341 1.29118714445145 1 5.97407085194889 107 2021 1159 1939 4190 81 16 438 4177 906 196 433 M12029 BILD_HRAS_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_HRAS_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing activated HRAS [GeneID=3265] oncogene from control cells expressing GFP. 16273092 373/465 Arthur Liberzon 5.27022543114822e-05 0.000398442508841251 2725 1525.36363636364 906 4.79122880603413e-06 260 1.18085059840533 1.10929614382342 1 6.02367232449552 472 2723 499 3309 3376 501 809 906 2725 260 1199 434 M18658 WIKMAN_ASBESTOS_LUNG_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WIKMAN_ASBESTOS_LUNG_CANCER_UP.html Genes positively correlated with the asbestos exposure of lung cancer patients. 17297452 22/26 Arthur Liberzon 0.00379480297376009 0.0107576396613499 2450 955.363636363636 908 0.000345578592711416 31 1.27899345288135 -1.49726321168349 -1 3.77733502359473 2449 957 2174 945 640 702 908 338 31 1199 166 435 M7343 LUI_THYROID_CANCER_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_2.html Cluster 2: genes with similar expression profiles across follicular thyroid carcinoma (FTC) samples. 15608688 64/74 Leona Saunders 0.00629677023045754 0.0152257968687293 4385 1914.90909090909 908 0.000574078654121032 132 1.1216866822493 1.01076080512912 1 3.05881803421406 4383 758 1269 493 3768 3677 4696 425 555 908 132 436 M7404 FRIDMAN_IMMORTALIZATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_IMMORTALIZATION_DN.html Genes down-regulated in immortalized cell lines. 18711403 51/63 Jessica Robertson 0.00689697161277311 0.0162768530061445 300 1733.36363636364 908 0.000628971718779769 173 1.32375948795064 1.31029893799538 1 3.55230130461166 300 4459 908 3655 2935 173 337 449 4257 1338 256 437 M17312 ZIRN_TRETINOIN_RESPONSE_WT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_WT1_UP.html Genes up-regulated in MZ128 cells (Wilms tumor with mutated WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 31/34 Leona Saunders 0.000193293857114431 0.00113335031749082 310 784.272727272727 909 1.75737129241064e-05 43 1.3693514035241 1.37894579709889 1 6.05240776337377 309 909 920 743 1074 991 346 43 1961 963 368 438 M5312 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transformed by activated KRAS [GeneID=3845] vs those reverted to normal cells upon over-expression of a dominant negative form of CDC25 [GeneID=5923]. 16607279 71/75 Lauren Kazmierski 9.38752191088131e-08 1.73082435231874e-06 500 921.727272727273 910 8.53411119222918e-09 192 1.41087896145935 1.46048758662339 1 12.1978133200837 500 1337 214 1235 192 812 910 1140 1842 222 1735 439 M892 REACTOME_SYNTHESIS_OF_SUBSTRATES_IN_N_GLYCAN_BIOSYTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_SUBSTRATES_IN_N_GLYCAN_BIOSYTHESIS.html Genes involved in Synthesis of substrates in N-glycan biosythesis 15/18 Reactome 0.00126257044233919 0.00469238778570156 645 1579.72727272727 911 0.000114845055339605 441 0.78874954778617 -0.78874954778617 -1 2.75587989367859 641 3070 3468 2572 441 461 678 911 530 3402 1203 440 M1090 REACTOME_SIGNALING_BY_FGFR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR.html Genes involved in Signaling by FGFR 110/136 Reactome 0.00591454088398308 0.0144570859515278 915 1375.90909090909 911 0.000539136527770538 451 0.930392274911405 0.82712289942221 1 2.56855441722506 911 663 3088 911 748 451 570 2163 1299 3262 1069 441 M1317 GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_UP.html Genes up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] and HIF1A [GeneID=3091] by RNAi. 17704799 193/210 Jessica Robertson 0.0164046373480896 0.032411003885719 305 1450.90909090909 913 0.00150256849551774 230 1.16117374107372 1.14814903991623 1 2.59481072250723 302 3194 1542 2666 3235 230 590 913 1955 891 442 442 M2058 NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_DN.html Top 20 genes whose down-regulation correlated with gastrointestinal stromal tumors (GIST) compared to synovial sarcoma. 11965276 27/45 Arthur Liberzon 6.39370438084659e-06 6.89001933278445e-05 455 1910.81818181818 914 5.81247542044815e-07 349 1.62261454446176 -1.8117937145388 -1 10.1328522447118 3465 914 349 453 452 3892 3548 4202 862 447 2435 443 M10845 GOLDRATH_IMMUNE_MEMORY http://www.broadinstitute.org/gsea/msigdb/cards/GOLDRATH_IMMUNE_MEMORY.html 'Memory genes' expressed uniquely in CD8+ [GeneID=925] memory T lymphocytes (compared with effector or naive cells) 15548615 78/90 Kate Stafford 0.0198909913776181 0.0376294506221874 1155 985.818181818182 915 0.00182483116865309 69 1.12838482823131 1.0566358504403 1 2.41175920277517 1155 69 1133 233 2831 1278 1158 756 534 915 782 444 M8321 WEST_ADRENOCORTICAL_TUMOR_MARKERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_MARKERS_DN.html Top down-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 23/40 Arthur Liberzon 1.92686774581413e-07 3.31927582490609e-06 410 1148.54545454545 916 1.75169810416242e-08 181 1.84709614652727 1.87952942418532 1 15.1853969447379 407 2565 227 2508 181 974 490 1368 2757 241 916 445 M15822 OZANNE_AP1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OZANNE_AP1_TARGETS_UP.html Cancer motility and invasion genes up-regulated by the AP-1 transcription factor. 16799638 26/40 Arthur Liberzon 0.00344207033547574 0.0100225613716505 2840 1355.90909090909 916 0.000313406140620157 357 1.4238500858751 1.50007666200591 1 4.27083437039904 2836 916 879 357 622 1578 2014 568 628 1189 3328 446 M4594 GENTILE_UV_LOW_DOSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_LOW_DOSE_DN.html Selected genes down-regulated in WS1 (fibroblast) in response to irradiation with low dose UV-C. 12907719 102/123 John Newman 0.00200671118584835 0.00669156600814588 695 1098.63636363636 917 0.000182594902830444 456 1.27671281003413 1.3188513757011 1 4.16560280888308 695 1298 813 776 1502 917 818 984 2763 456 1063 447 M9914 YAMASHITA_LIVER_CANCER_WITH_EPCAM_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_WITH_EPCAM_DN.html Down-regulated genes distinguishing hepatocellular carcinoma (HCC) samples positive for EPCAM [GeneID=4072] from the negative ones. 18316609 12/49 Yujin Hoshida 5.72619210543383e-07 8.69055522110858e-06 2215 1213.18181818182 917 5.20563054168728e-08 3 1.41592689674785 1.38843809065349 1 10.7525290558436 2213 413 1064 51 3 2216 917 4560 101 1345 462 448 M11636 GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_DN.html Genes down-regulated in quiescent (G0) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the quiescent cells from normal donors. 17717066 52/82 Arthur Liberzon 0.000745643474347227 0.00317066414317019 1275 960.181818181818 918 6.78087558558926e-05 243 1.39275087808429 -1.50384903005 -1 5.22211694860579 1275 791 596 487 1132 927 2373 243 918 789 1031 449 M1448 NEMETH_INFLAMMATORY_RESPONSE_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NEMETH_INFLAMMATORY_RESPONSE_LPS_UP.html Genes up-regulated in RAW 264.7 cells (macrophage) 3 hr after stimulation with bacterial lipopolysaccharide (LPS). 12766259 111/147 Kevin Vogelsang 0.00361760541418845 0.0104081532879602 95 1240.72727272727 918 0.000329415255683626 95 1.10010330523507 1.17104915537038 1 3.2726691431662 95 2342 1284 3761 1950 159 196 364 2128 918 451 450 M1477 MARCINIAK_ER_STRESS_RESPONSE_VIA_CHOP http://www.broadinstitute.org/gsea/msigdb/cards/MARCINIAK_ER_STRESS_RESPONSE_VIA_CHOP.html Endoplasmic retuculum (ER) stress response (caused by tunicamycin [PubChem=5282055]) genes dependent on CHOP [GeneID=13198]. 15601821 35/36 Kevin Vogelsang 0.00781785470111889 0.0179127544608161 1280 1101.72727272727 918 0.00071325227273767 184 1.41265876669985 1.37309100842172 1 3.7027057706623 1278 885 1977 483 832 1523 788 1441 184 1810 918 451 M14309 REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_PROTEIN_BETA_GAMMA_SIGNALLING.html Genes involved in G-protein beta:gamma signalling 24/34 Reactome 0.00188236293058028 0.00638731346681448 1270 1345.90909090909 920 0.000171270495359078 209 0.893449585208208 -0.945805877001672 -1 2.94217021799588 1270 343 2414 2129 839 920 803 209 2802 2565 511 452 M1925 BOYAULT_LIVER_CANCER_SUBCLASS_G56_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G56_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G56, defined by unsupervised clustering. 17187432 19/34 Yujin Hoshida 0.000130116163627791 0.00081532458059785 3115 1461.45454545455 922 1.18294418016179e-05 85 1.87934038535385 -2.28508577825227 -1 8.70990488764557 3112 357 498 85 922 1891 4699 1835 255 507 1915 453 M5882 NABA_PROTEOGLYCANS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_PROTEOGLYCANS.html Genes encoding proteoglycans 22159717 19/35 Alexandra Naba 0.000176500837486284 0.00104790434331479 175 1596.81818181818 925 1.60468181204512e-05 172 1.69537115435554 1.71204369825399 1 7.58001249388247 172 3498 511 3015 2577 1247 438 694 4006 925 482 454 M13950 KEGG_ASTHMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASTHMA.html Asthma 12/39 KEGG 0.00126961823603381 0.00471486866568025 4365 2183.90909090909 926 0.000115486502201846 419 1.75545730714238 -1.54491009802153 -1 6.12820538534128 4364 419 654 462 442 3994 4353 4672 642 926 3095 455 M15112 WONG_MITOCHONDRIA_GENE_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_MITOCHONDRIA_GENE_MODULE.html Genes that comprise the mitochondria gene module 18199530 242/284 Jessica Robertson 0.00205888907321081 0.00681961854424913 75 1409.27272727273 930 0.000187347130065618 73 0.82177934509115 -0.705016867799412 -1 2.67107681430091 73 1192 4065 930 734 340 263 1403 463 4411 1628 456 M1970 MIKKELSEN_IPS_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 70/120 Jessica Robertson 7.67375279122152e-08 1.43162502666267e-06 4265 1870.27272727273 931 6.97613914444304e-09 211 1.57277013136688 1.2730226414891 1 13.7919801267611 4265 747 211 931 267 4300 2936 2407 3306 281 922 457 M7272 KEGG_PARKINSONS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PARKINSONS_DISEASE.html Parkinson's disease 123/151 KEGG 2.73485887481474e-05 0.000234274662234584 15 1701.27272727273 932 2.48626624810942e-06 11 0.611549566978541 -0.60232093227024 -1 3.3311881359536 11 1796 4056 2007 380 111 75 932 3988 4443 915 458 M2070 YAGUE_PRETUMOR_DRUG_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAGUE_PRETUMOR_DRUG_RESISTANCE_DN.html Down-regulated genes common to all pretumorigenic cells with acquired drug resistance. 17283147 25/27 Jessica Robertson 0.000357621832599189 0.00180339214729506 440 966 932 3.25163617440743e-05 227 1.35394061661924 1.33660068299263 1 5.57446271754354 440 945 932 2269 250 922 1123 231 2188 1099 227 459 M2446 PLASARI_TGFB1_TARGETS_10HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_10HR_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 10 h. 19752192 326/413 Arthur Liberzon 3.9793276906118e-13 1.85964620788987e-11 935 1284.90909090909 935 3.61757062782956e-14 78 1.23413930850962 1.26317692915014 1 19.8713082042239 935 2238 78 2243 1484 652 1437 865 3289 170 743 460 M816 BONOME_OVARIAN_CANCER_POOR_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_POOR_SURVIVAL_UP.html Top highly correlated genes positively associated with poor survival of patients with suboptimally debulked ovarian tumors. 18593951 40/45 Jessica Robertson 0.0104298785967167 0.0225821224662858 710 1124.09090909091 936 0.000952695983963154 201 1.1000294646973 1.04316431364259 1 2.71719687627982 709 234 1975 770 1066 508 936 2342 1479 2145 201 461 M13903 NELSON_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/NELSON_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in LNCaP cells (prostate cancer) in response to synthetic androgen R1881 [PubChem=13766]. 12185249 123/158 Broad Institute 0.000320602378503337 0.00166290464454478 3400 1786.45454545455 937 2.91499189903999e-05 4 1.19402226975342 1.18244100762638 1 4.97913935950454 3396 4 626 72 937 2472 2778 3832 567 340 4627 462 M8646 BOYLAN_MULTIPLE_MYELOMA_C_D_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_D_DN.html Genes down-regulated both in group C and D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 288/419 Jessica Robertson 9.96044059605615e-08 1.81771189497532e-06 940 1264 937 9.05494640637493e-09 216 1.28577464470855 1.43014515677327 1 11.0751684886848 937 542 216 703 3418 1548 1802 759 1532 262 2185 463 M13158 BIOCARTA_LONGEVITY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LONGEVITY_PATHWAY.html The IGF-1 Receptor and Longevity 22/25 BioCarta 0.00169542336019927 0.00590003483362169 1280 1159 939 0.000154248304045854 256 0.991646972797613 0.943791494895618 1 3.31683176555098 1276 1521 2638 1387 482 365 256 939 719 2388 778 464 M815 REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_GLUCOSE_AND_OTHER_SUGARS_BILE_SALTS_AND_ORGANIC_ACIDS_METAL_IONS_AND_AMINE_COMPOUNDS.html Genes involved in Transport of glucose and other sugars, bile salts and organic acids, metal ions and amine compounds 57/102 Reactome 0.00476043187731973 0.0127956938843674 940 1395.81818181818 939 0.000433705815328119 497 1.2865729175407 1.40371255467392 1 3.65426134192299 939 1399 760 1964 4442 906 746 497 1846 814 1041 465 M7362 HASLINGER_B_CLL_WITH_6Q21_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_6Q21_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 6q21 region. 15459216 23/53 Kevin Vogelsang 0.00330730220806852 0.00979941394983266 825 1034.72727272727 939 0.000301116784393054 215 1.35903414342203 -1.54687184259611 -1 4.09635544430523 821 2059 1768 1891 606 266 1297 1128 215 939 392 466 M10773 LI_WILMS_TUMOR http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR.html 'Wilm's tumor signature': genes highly expressed in Wilm's tumor samples compared to normal fetal kidney and a heterologous tumor, Burkit lymphoma. 12057921 40/109 Arthur Liberzon 0.000715010893943337 0.00306247860200776 45 1452.72727272727 940 6.50221256195387e-05 43 1.27908998380306 1.26319275798826 1 4.82487462174448 43 2495 747 2182 2657 339 420 940 4225 1523 409 467 M19982 WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_LMP_UP.html Genes up-regulated in mucinous ovarian carcinoma tumors of low malignant potential (LMP) compared to normal ovarian surface epithelium tissue. 16467078 345/404 Arthur Liberzon 0.00577426225782821 0.0142024584976285 1655 1288.45454545455 941 0.000526315789473684 110 1.02274609781294 -1.01506634941239 -1 2.83537141372471 1652 526 2626 110 941 419 2919 1742 713 1836 689 468 M10770 ZHAN_MULTIPLE_MYELOMA_MF_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MF_UP.html Top 50 up-regulated genes in cluster MF of multiple myeloma samples with characteristic expression spike of MAF family transcription factors. 16728703 65/98 Kevin Vogelsang 0.0171182395874029 0.0334983792920986 370 1267.18181818182 941 0.00156844601837379 299 1.20765606597719 1.33977880400628 1 2.67271649274444 366 1372 941 2353 4126 299 377 743 1345 1571 446 469 M23 PID_WNT_NONCANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_NONCANONICAL_PATHWAY.html Noncanonical Wnt signaling pathway 18832364 48/51 Pathway Interaction Database 0.00019431803677062 0.00113794185304879 1070 1133.63636363636 942 1.76668365729199e-05 177 1.05839976197193 0.984122031894827 1 4.67521732814253 1066 196 2621 1611 177 323 617 1390 942 2656 871 470 M8825 DORN_ADENOVIRUS_INFECTION_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_24HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 24 h after infection with adenovirus Ad12. 15681441 76/104 Arthur Liberzon 0.00123332710234234 0.00462008247861574 25 1475.36363636364 943 0.000112183550239257 22 1.22458538343832 1.08578055491065 1 4.29113519493353 132 3697 943 3896 588 23 152 1801 3762 1213 22 471 M1511 GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_DN.html Genes down-regulated in glioblastoma cell lines displaying spherical growth (cluster-1) compared to those displaying semiadherent or adherent growth phenotype (cluster-2). 18037961 31/34 Jessica Robertson 7.22605779995488e-05 0.000512117009246051 915 1081.18181818182 944 6.56935923265548e-06 111 1.23837597208244 1.3291393425374 1 6.11457064525026 914 2528 1176 1025 111 372 521 451 2612 1239 944 472 M17299 CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_UP.html Genes up-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. 16288205 583/712 Arthur Liberzon 0.000163882648346854 0.00098627269465891 945 1169.72727272727 945 1.63894735486519e-05 6 1.10499727091779 -1.12458508860764 -1 4.98405929707644 945 490 4294 25 2231 6 1987 1048 1097 688 56 473 M9167 ROZANOV_MMP14_TARGETS_SUBSET http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_TARGETS_SUBSET.html Genes linked to the ECM maintenance and angiogenesis that were changed in HT1080 cells (fibrosarcoma) over-expressing MMP14 [GeneID=4323] compared to those with knockdown of the gene by RNAi. 18519667 66/72 Jessica Robertson 3.3457920877722e-05 0.000279231961935975 20 1404.63636363636 945 3.04167542922698e-06 16 1.28989656944851 1.32229372335918 1 6.87878442748567 16 2868 420 3199 945 713 885 1015 3886 983 521 474 M12459 CHIBA_RESPONSE_TO_TSA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIBA_RESPONSE_TO_TSA_DN.html Cancer related genes down-regulated in any of four hepatoma cell lines following 24 h treatment with TSA [PubChem=5562]. 15452378 48/53 John Newman 0.0014570561596697 0.00525787849666741 140 1152.90909090909 945 0.000132547460103666 137 1.25598788238674 1.24282165919283 1 4.2953344433644 1208 159 945 137 521 1647 1454 2369 137 437 3668 475 M18264 MOOTHA_VOXPHOS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_VOXPHOS.html Genes involved in oxidative phosphorylation; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 93/111 Vamsi Mootha 2.07893544977122e-06 2.61280437037737e-05 10 1357.54545454545 946 1.8899431039153e-07 8 0.620081762714276 -0.60200224903249 -1 4.26402474096682 8 1293 4039 941 582 257 150 1010 946 4409 1298 476 M930 REACTOME_TRANSPORT_OF_ORGANIC_ANIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_ORGANIC_ANIONS.html Genes involved in Transport of organic anions 6/16 Reactome 0.00759854202772558 0.0175671011637266 950 1399.45454545455 947 0.000762464978524908 62 1.79913101086094 -1.87450882091514 -1 4.73855827630675 1553 1096 4253 669 850 1495 947 3236 62 946 287 477 M7388 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 10 days after transduction. 16818636 151/278 Arthur Liberzon 6.21165323317951e-13 2.74009376267358e-11 950 1030.72727272727 947 5.64695748471023e-14 82 1.41216695552788 1.46313234526777 1 22.3811092983456 947 1771 82 668 808 1473 1226 507 2309 148 1399 478 M17702 KERLEY_RESPONSE_TO_CISPLATIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/KERLEY_RESPONSE_TO_CISPLATIN_DN.html Genes genes down-regulated in NT2/D1 cells (embryonal carcinoma) in response to treatment with cisplatin [PubChem=2767]. 15940259 6/10 Leona Saunders 0.00270292041581881 0.00837674613438264 3270 1740.72727272727 947 0.000270621365519651 85 1.4073151741364 -1.4878353781851 -1 4.38574563005043 3270 448 4343 108 737 2095 2626 272 85 947 4217 479 M12861 GENTILE_UV_RESPONSE_CLUSTER_D2 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D2.html Cluster d2: genes down-regulated consistently in WS1 cells (fibroblast) between 6 h and 24 h after irradiation with high dose UV-C. 12907719 52/56 John Newman 0.00344707135707257 0.0100309351451187 265 1320.63636363636 947 0.000313862207311053 265 1.2212100602992 1.1903245162992 1 3.66233648990846 265 820 2145 1841 3863 609 641 301 1436 1659 947 480 M2155 MCBRYAN_PUBERTAL_BREAST_6_7WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_6_7WK_UP.html Genes up-regulated during pubertal mammary gland development between week 6 and 7. 17486082 280/343 Arthur Liberzon 0.0306753068527889 0.0536051271177947 1260 1318.36363636364 949 0.00282832387716773 404 1.16501279342526 1.40627833309928 1 2.22140045413702 1259 546 1596 404 2970 949 2017 2525 774 750 712 481 M16718 DING_LUNG_CANCER_MUTATED_FREQUENTLY http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_MUTATED_FREQUENTLY.html The lung adenocarcinoma TSP (tumor sequencing project) genes with significantly higher frequencies of nonsense, splice site, and frame-shift mutations. 18948947 24/25 Jessica Robertson 0.00647174761919582 0.0155259884964326 1100 1214.45454545455 949 0.00059007857801341 187 1.11225056982407 1.07871818086818 1 3.01893360161093 1097 949 2022 866 779 786 406 1928 2228 2111 187 482 M1879 PIONTEK_PKD1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PIONTEK_PKD1_TARGETS_UP.html Genes up-regulated during later stages of renal maturation (days P14-P16) in kidney specific knockout of PKD1 [GeneID=5310]. 17965720 36/67 Jessica Robertson 0.00096091212709874 0.00385344540348858 485 946.363636363636 949 8.73938263119119e-05 56 1.34045303315036 1.26529155391687 1 4.85566076715304 485 1449 969 949 980 177 56 2497 1544 412 892 483 M5071 IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_UP.html Genes up-regulated during transition from G1 (well differentiated tumor, infected with HCV) to G2 (moderately differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 18/22 Yujin Hoshida 0.0111329456702371 0.023712772366209 665 1544.90909090909 950 0.00101724414086545 509 0.947676309763056 -0.990144392874403 -1 2.31068119352529 662 2600 2999 3150 950 705 509 1092 869 2538 920 484 M1466 AFFAR_YY1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/AFFAR_YY1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) expressing ~25% of YY1 [GeneID=7528]. 16611997 280/415 Kevin Vogelsang 3.26538168964695e-09 8.06942490844692e-08 3455 1446.18181818182 952 2.96852881317603e-10 126 1.31298543804785 -1.36694709717827 -1 13.9745562784381 3455 1185 154 126 920 952 4188 2634 1328 232 734 485 M13256 RIGGI_EWING_SARCOMA_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIGGI_EWING_SARCOMA_PROGENITOR_DN.html Genes down-regulated in mesenchymal stem cells (MSC) engineered to express EWS-FLI1 [GeneID=2130;2321] fusion protein. 18381423 216/259 Jessica Robertson 1.86415988816088e-13 9.07096357950448e-12 465 1079.27272727273 952 1.69469080741912e-14 73 1.45534594307973 1.4834280818024 1 24.113903343554 464 2269 73 1408 2000 924 1260 902 1518 102 952 486 M18053 BIOCARTA_LEPTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LEPTIN_PATHWAY.html Reversal of Insulin Resistance by Leptin 15/35 BioCarta 0.000110855204446736 0.000719720171923787 2325 1031.27272727273 955 1.00782536994277e-05 56 0.925129267713524 1.03832003432625 1 4.36270108982908 2324 393 1797 331 140 1478 502 56 1151 2217 955 487 M8467 JISON_SICKLE_CELL_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/JISON_SICKLE_CELL_DISEASE_UP.html Genes up-regulated in peripheral blood mononuclear cells (PBMC) from sickle cell disease patients compared to those from healthy subjects. 15031206 265/378 Jessica Robertson 0.00118240205155873 0.00448988569632661 2885 1423.81818181818 955 0.000107548910781413 426 1.12608259465428 -1.0710273049265 -1 3.96693459146334 2882 551 955 571 426 580 2550 3414 1865 1103 765 488 M2776 IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_UP.html Cluster 1: genes up-regulated in lung tissue samples from mice with oncogenic form of KRAS [GeneID=3845] and inactivated PTEN [GeneID=5728]. 18281487 226/300 Jessica Robertson 0.0155196481674596 0.0310656231341856 595 1434.81818181818 957 0.00142092939622398 593 1.30212399566627 1.31483262102367 1 2.94577264197496 593 2756 957 1851 3344 668 760 651 2111 1284 808 489 M138 PID_THROMBIN_PAR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_THROMBIN_PAR4_PATHWAY.html PAR4-mediated thrombin signaling events 18832364 22/29 Pathway Interaction Database 4.25653932131423e-05 0.00033596765211711 1080 1175.72727272727 958 3.86965607151614e-06 81 1.18796227151722 -1.29608132323258 -1 6.19198163501827 1077 958 2349 2087 81 414 793 368 1087 3380 339 490 M851 REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_MITOTIC_CELL_CYCLE.html Genes involved in Regulation of mitotic cell cycle 85/99 Reactome 0.000607848897586256 0.00267884854958649 40 1253.09090909091 959 5.52742643783068e-05 39 0.626692864410193 -0.629998689653508 -1 2.41856226570019 39 54 4082 593 1056 224 218 1131 1052 4376 959 491 M13095 SU_THYMUS http://www.broadinstitute.org/gsea/msigdb/cards/SU_THYMUS.html Genes up-regulated specifically in human thymus. 11904358 12/22 John Newman 0.00577426225782821 0.0142024584976285 1945 1000.36363636364 960 0.000526315789473684 13 1.51160188657324 -2.01593432627482 -1 4.19068283102918 1945 412 1740 116 1107 960 1927 643 13 1842 299 492 M15267 FUJII_YBX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FUJII_YBX1_TARGETS_UP.html Genes up-regulated in MCF-7 cells (breast cancer) after knockdown of YBX1 [GeneID=4904] by RNAi. 18316615 55/70 Jessica Robertson 0.00577426225782821 0.0142024584976285 1630 1362.09090909091 960 0.000526315789473684 113 1.25666993089675 1.39358194669616 1 3.48390549892416 1626 783 829 113 960 4350 2279 818 1609 604 1012 493 M980 KEGG_TRYPTOPHAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TRYPTOPHAN_METABOLISM.html Tryptophan metabolism 31/53 KEGG 0.0166065039233244 0.0327003331322866 2755 1169.36363636364 961 0.00152119977700156 286 1.73617173147058 -2.08878451068754 -1 3.86972420421816 2753 286 933 749 1704 1338 1693 674 374 961 1398 494 M14970 SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_ACTIVATED_DENDRITIC_CELL.html IRF4 [GeneID=3662] target genes up-regulated in plasmacytoid dendritic cells compared to monocytes. 18568025 90/97 Jessica Robertson 0.00886149614790888 0.0199362544414347 1475 1125.54545454545 961 0.000808853856711388 60 1.08130103636361 1.05794906931906 1 2.75874612790358 1473 60 1992 345 862 961 807 1768 491 1358 2264 495 M160 PID_AVB3_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AVB3_INTEGRIN_PATHWAY.html Integrins in angiogenesis 18832364 104/117 Pathway Interaction Database 3.71052948822439e-05 0.000303005176201023 290 1270.18181818182 962 3.37326551968411e-06 289 1.34263167419061 1.51246083684443 1 7.08852595825951 289 1824 427 2215 1124 915 945 962 3217 1173 881 496 M944 REACTOME_REGULATION_OF_MRNA_STABILITY_BY_PROTEINS_THAT_BIND_AU_RICH_ELEMENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_MRNA_STABILITY_BY_PROTEINS_THAT_BIND_AU_RICH_ELEMENTS.html Genes involved in Regulation of mRNA Stability by Proteins that Bind AU-rich Elements 99/115 Reactome 5.99607246441218e-05 0.000439423390710073 965 1691.27272727273 962 5.45112353895697e-06 39 0.632285120461352 -0.593190039298578 -1 3.18498062710464 962 39 4046 1130 99 627 783 879 4221 4378 1440 497 M1718 SIG_IL4RECEPTOR_IN_B_LYPHOCYTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_IL4RECEPTOR_IN_B_LYPHOCYTES.html Genes related to IL4 rceptor signaling in B lymphocytes 33/36 Signaling Gateway 0.00165718487811386 0.00579830439191804 1045 1497.45454545455 963 0.000150766772446158 417 0.802480938686384 0.814106018151305 1 2.69319010500519 1042 2508 3322 2221 477 647 840 433 417 3602 963 498 M14827 FERRARI_RESPONSE_TO_FENRETINIDE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FERRARI_RESPONSE_TO_FENRETINIDE_UP.html Genes up-regulated in HUVEC cells (umbilical vein endothelium) by fenretinide [PubChem=1744]. 15958647 31/31 Arthur Liberzon 0.00502108263644629 0.0133744413341007 485 2067.63636363636 965 0.000457507186870626 174 1.48474354014381 1.47263341624471 1 4.17434119073106 481 4507 876 4574 4651 176 174 1546 4375 965 419 499 M2230 BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP.html Genes bound by ESR1 [GeneID=2099] and up-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer). 18838536 238/310 Arthur Liberzon 0.000525912366248073 0.00240068314186741 840 1200.27272727273 966 4.78216480232593e-05 450 1.22241463320855 1.09141179782941 1 4.80503513111493 838 1731 574 1955 2697 617 1224 966 800 450 1351 500 M2361 TERAO_AOX4_TARGETS_HG_DN http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_HG_DN.html Genes down-regulated in Harderian gland tissue upon knockout of AOX4 [GeneID=71872]. 18981221 9/10 Arthur Liberzon 0.000601205983055849 0.00265204882245197 2245 1585.72727272727 966 6.01368696900132e-05 315 0.892657821804667 1.06080394680412 1 3.45088042739458 2242 433 4690 966 339 2330 601 931 315 3567 1029 501 M977 REACTOME_KINESINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KINESINS.html Genes involved in Kinesins 28/32 Reactome 0.0160578647952127 0.0319397900688596 870 1393 967 0.00147057122572477 78 1.35729022358343 -1.4259804367757 -1 3.04603315542124 866 2541 2555 967 2752 383 359 1452 78 2440 930 502 M5125 KHETCHOUMIAN_TRIM24_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KHETCHOUMIAN_TRIM24_TARGETS_DN.html Retinoic acid-responsive genes down-regulated in hepatocellular carcinoma (HCC) samples of TRIM24 [GeneID=8805] knockout mice. 18026104 9/13 Leona Saunders 0.000355243691339423 0.00179523578492728 1895 1441.54545454545 968 3.55300493255676e-05 177 1.67932757918048 -1.78039964977841 -1 6.91913657897293 1891 1614 4423 1023 265 825 177 3185 885 968 601 503 M546 REACTOME_O_LINKED_GLYCOSYLATION_OF_MUCINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_O_LINKED_GLYCOSYLATION_OF_MUCINS.html Genes involved in O-linked glycosylation of mucins 38/61 Reactome 3.02498133487011e-06 3.60553330822902e-05 4260 1844.54545454545 969 2.74998681291071e-07 13 1.62223826172708 -1.72535519683556 -1 10.8151237322605 4256 233 320 13 343 3799 3734 3737 969 240 2646 504 M2658 BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_UP.html Genes from cluster 3: up-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 30/39 Jessica Robertson 0.0100395923178423 0.0219180738853912 2445 1513.72727272727 969 0.000916882033237124 296 1.00412200501876 -1.20768371843463 -1 2.49981587760855 2444 296 2340 969 904 2087 2952 654 460 3041 504 505 M13077 WANG_RECURRENT_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RECURRENT_LIVER_CANCER_DN.html Genes down-regulated in samples from patients with recurrent hepatocellular carcinoma (HCC). 17975138 16/21 Yujin Hoshida 2.87440802754322e-05 0.000245338262025389 450 1156.09090909091 970 2.61313234889318e-06 62 1.15898918657572 1.06446416593059 1 6.27840475091868 446 2107 2143 2337 62 348 77 767 970 2330 1130 506 M7727 RICKMAN_HEAD_AND_NECK_CANCER_B http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_B.html Cluster b: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 84/167 Jessica Robertson 2.88207602622878e-07 4.72340237631939e-06 415 1557.72727272727 974 2.62006945799161e-08 237 1.60875088181575 1.57209361841349 1 12.8560456000625 412 3684 237 2924 2125 1419 648 816 3301 595 974 507 M19735 CHANG_POU5F1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_POU5F1_TARGETS_DN.html Genes down-regulated by POU5F1 [GeneID=5460] in bladder cancer cell lines. 18676852 7/9 Jessica Robertson 0.00352405324902042 0.0102046204511511 675 1612.81818181818 974 0.00035296542821 272 1.30239854258072 1.34926226811269 1 3.89125299624641 675 2675 4476 1013 3819 723 305 330 974 2479 272 508 M16024 KEGG_ALZHEIMERS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALZHEIMERS_DISEASE.html Alzheimer's disease 163/213 KEGG 0.000325550008859196 0.00167750659586834 40 1345.27272727273 975 2.95998357132217e-05 37 0.76505716087408 -0.709532653987961 -1 3.18593417913952 37 1227 3707 1431 236 86 70 975 2143 4265 621 509 M1695 TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_UP http://www.broadinstitute.org/gsea/msigdb/cards/TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_UP.html Genes up-regulated in small intestine tissue from transgenic mice expressing a mutant form of COL13A1 [GeneID=1305], compared to normal controls. 19074901 23/40 Leona Saunders 0.0118515770177274 0.0249500130927305 2170 1173.63636363636 975 0.00108326437475765 191 1.48310355385423 1.27401000313728 1 3.56709557610409 2167 331 919 292 975 1884 1661 857 191 1623 2010 510 M1145 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_1.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 1. 12554760 102/114 Arthur Liberzon 0.0222482115448855 0.0413428582381618 760 1803.72727272727 976 0.00204331287857781 384 1.26579419024227 1.1013114134467 1 2.62783331239777 758 3670 960 4023 3225 384 909 1523 2717 696 976 511 M1398 ZEILSTRA_CD44_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZEILSTRA_CD44_TARGETS_UP.html Genes implicated in apoptosis that were up-regulated in duodenum of CD44 [GeneID=960] knockout mice. 18483247 9/12 Jessica Robertson 0.000234134236975175 0.00133146216689497 2040 1339.72727272727 977 2.34158909112177e-05 135 1.56939415699563 -1.493914916007 -1 6.77183357108914 2036 1063 4471 302 205 1308 977 2374 135 969 897 512 M14650 NGUYEN_NOTCH1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NGUYEN_NOTCH1_TARGETS_DN.html Genes down-regulated in primary keratinocytes by expression of constantly active NOTCH1 [GeneID=4851]. 16618808 137/163 Kevin Vogelsang 0.000260353871581708 0.00142441549965496 460 1241.54545454545 977 2.36713352417682e-05 206 1.11862925590043 1.0056742428623 1 4.77758799062364 458 2316 1406 2436 206 273 690 1476 2823 977 596 513 M4535 CHEOK_RESPONSE_TO_HD_MTX_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_HD_MTX_DN.html Genes specifically down-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by high-dose methotrexate (HDMTX) [PubChem=4112]. 12704389 35/42 Jean Junior 0.000416160734272539 0.00200500415506367 2480 1402.63636363636 978 3.78399525221483e-05 59 1.13336647947298 -1.23300627806924 -1 4.58802254858934 2478 879 2376 1225 284 978 2604 813 59 2953 780 514 M17694 REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BRANCHED_CHAIN_AMINO_ACID_CATABOLISM.html Genes involved in Branched-chain amino acid catabolism 20/20 Reactome 7.35731466181494e-05 0.000518306346324873 2260 1559.27272727273 980 6.68869156286275e-06 114 0.702720052374575 -0.64825623292238 -1 3.46418376097752 2257 980 3532 832 114 1447 1779 665 736 4568 242 515 M1304 GROSS_HYPOXIA_VIA_ELK3_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_DN.html Genes down-regulated in SEND cells (skin endothelium) at hypoxia with ELK3 [GeneID=2004] knockdown by RNAi. 17704799 224/258 Jessica Robertson 0.000354469904673443 0.00179324539127401 170 1612.45454545455 983 3.2229730063845e-05 166 1.30098438103265 1.30512501002288 1 5.36121010057941 166 3627 554 3780 3490 319 412 1143 2891 372 983 516 M2884 WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_UP.html Genes specifically up-regulated via JNK (MAPK8) [GeneID=5599] signaling pathway activated by paclitaxel [PubChem=4666] in BR cells (ovarian cancer). 16547493 20/35 Arthur Liberzon 0.000704555583121024 0.00302869066696834 1410 1044.45454545455 985 6.40710290955424e-05 347 1.13918278781506 -1.3465037883986 -1 4.30535297591985 1407 985 1616 579 347 829 1330 946 433 1759 1258 517 M1099 GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_UP.html Genes up-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) upon serum deprivation for 22 hr in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 313/538 Arthur Liberzon 7.29828039661578e-10 1.99120713711136e-08 665 964.181818181818 986 6.63480036276084e-11 107 1.2411545875625 1.29051999991961 1 14.3418454213405 665 1174 138 1213 1890 443 1449 357 2184 107 986 518 M15 PID_LYSOPHOSPHOLIPID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LYSOPHOSPHOLIPID_PATHWAY.html LPA receptor mediated events 18832364 91/103 Pathway Interaction Database 0.0362330988485613 0.0613635545623284 985 1301.54545454545 987 0.00334945233602364 51 0.918350714703089 0.945570386135408 1 1.67015794891785 984 51 2140 629 2645 680 582 987 2477 1803 1339 519 M14859 COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_DN.html Genes down-regulated in pilocytic astrocytoma compared to glioblastoma samples. 16314830 49/60 Jessica Robertson 0.000691575921290657 0.00299196915535463 135 1467.63636363636 987 6.28903105242611e-05 134 1.43423252104677 1.67119865246087 1 5.43187344675291 134 2902 591 2985 987 736 876 1265 3802 1494 372 520 M8478 DER_IFN_GAMMA_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_GAMMA_RESPONSE_DN.html Genes down-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon gamma for 6 h. 9861020 11/12 Yujin Hoshida 0.000421151687540215 0.00201810757887291 990 1423.81818181818 987 3.82938483009411e-05 6 1.06771070541107 1.2777938892315 1 4.3177004035739 987 1590 2373 963 2004 363 58 80 3510 3728 6 521 M15258 BIOCARTA_AKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKT_PATHWAY.html AKT Signaling Pathway 30/33 BioCarta 0.00173696135462496 0.0060150092397871 355 1169.81818181818 988 0.000158030386528394 101 0.721091254230237 0.695647098446121 1 2.40278692063387 352 294 3218 1118 486 203 101 1439 1235 3434 988 522 M1030 REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_C_CDH1_MEDIATED_DEGRADATION_OF_CDC20_AND_OTHER_APC_C_CDH1_TARGETED_PROTEINS_IN_LATE_MITOSIS_EARLY_G1.html Genes involved in APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 69/82 Reactome 0.00219764025887472 0.00717845122622055 80 1372.09090909091 989 0.0001999853288126 76 0.597307190584946 -0.595028849505213 -1 1.92147254737223 76 101 4088 1601 989 293 231 898 1396 4372 1048 523 M7552 BIOCARTA_CARDIACEGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARDIACEGF_PATHWAY.html Role of EGF Receptor Transactivation by GPCRs in Cardiac Hypertrophy 31/34 BioCarta 0.025079910714983 0.0455822790045129 590 1343.90909090909 990 0.00230640624391284 468 1.25384340860457 1.24455418389538 1 2.52325837769609 587 2012 1105 1920 2688 577 468 859 2615 962 990 524 M4991 DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_UP.html 'PAX-FKHR signature': genes up-regulated by PAX3- or PAX7-FOXO1 [GeneID=5081;5077;2308] fusion in primary alveolar rhabdomyosarcoma(ARMS) tumors. 16849537 76/95 Arthur Liberzon 0.000756003627385469 0.0032003023509053 1395 1007.63636363636 991 6.87512312747378e-05 357 1.3051036517038 1.34635941982258 1 4.88556399199717 1393 734 817 723 357 1427 1683 991 1126 612 1221 525 M16289 REACTOME_CYTOSOLIC_SULFONATION_OF_SMALL_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOSOLIC_SULFONATION_OF_SMALL_MOLECULES.html Genes involved in Cytosolic sulfonation of small molecules 5/18 Reactome 0.000327254183099834 0.00168261410046973 1290 1317 992 3.27302385975869e-05 13 0.963916442399465 -0.963916442399465 -1 4.01216348750464 1286 2185 4260 1537 252 992 615 136 132 3079 13 526 M16692 COWLING_MYCN_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/COWLING_MYCN_TARGETS.html Genes down-regulated by MYCN [GeneID=4613] but not by its transactivation-defficient, trunkated form N-Myc-delta-73. 17704800 71/86 Jessica Robertson 4.70208273202346e-07 7.276665736115e-06 195 1250.18181818182 994 4.27462157909524e-08 194 1.39309413399162 1.45360288768423 1 10.7403344245252 194 2408 254 2516 1408 1293 976 681 2580 994 448 527 M6117 GARCIA_TARGETS_OF_FLI1_AND_DAX1_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARCIA_TARGETS_OF_FLI1_AND_DAX1_UP.html Genes up-regulated in the A673 cells (Ewing sarcoma) after double knockdown of both FLI1 and DAX1 [GeneID=2313;190] by RNAi. 18591936 91/113 Jessica Robertson 0.00586276262014419 0.0143677256319214 485 1120.90909090909 994 0.00053440407172895 95 1.12285181103115 -1.01243050994074 -1 3.10444047241736 483 2370 2074 994 1381 95 707 862 1048 2020 296 528 M4781 PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_DN.html Down-regulated genes in angioimmunoblastic lymphoma (AILT) compared to normal T lymphocytes. 18006812 174/221 Arthur Liberzon 0.00112180955097583 0.00434367603002948 100 1124.63636363636 995 0.000102034725947712 51 1.07030924040728 0.967774854586698 1 3.79354355812709 96 1234 2199 1590 3483 67 51 995 933 1577 146 529 M13240 WAGNER_APO2_SENSITIVITY http://www.broadinstitute.org/gsea/msigdb/cards/WAGNER_APO2_SENSITIVITY.html Genes whose expression most significantly correlated with cancer cell line sensitivity to the proapoptotic ligand APO2 [GeneID=8797]. 17767167 18/28 Jessica Robertson 0.00187709034896585 0.00637400463821497 1320 1198.63636363636 995 0.000170790349193486 208 1.39826905094669 1.28798396787417 1 4.60652413191881 1318 377 995 244 2278 2103 550 208 3032 1193 887 530 M106 PID_HNF3B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HNF3B_PATHWAY.html FOXA2 and FOXA3 transcription factor networks 18832364 40/64 Pathway Interaction Database 0.000472968956349731 0.00221469590671699 2580 1263.36363636364 996 4.30064244196453e-05 223 1.25112171434285 -1.36539578588373 -1 4.98362425107377 2579 223 1126 360 299 2473 3449 373 747 996 1272 531 M2414 PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2.html Genes up-regulated in MCF7 cells (breast cancer) more than three-fold by the truncated form 611-CTF of ERBB2 [GeneID=2064] and less than two-fold by the full-length ERBB2 [GeneID=2064]. 19364815 103/133 Arthur Liberzon 1.10031064718707e-05 0.000111447773706502 1505 937.454545454545 996 1.0002874093932e-06 19 1.25460233925412 1.22332540208226 1 7.44150358519891 1505 19 370 284 1125 996 1921 1405 914 360 1413 532 M2844 REACTOME_FORMATION_OF_FIBRIN_CLOT_CLOTTING_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_FIBRIN_CLOT_CLOTTING_CASCADE.html Genes involved in Formation of Fibrin Clot (Clotting Cascade) 21/39 Reactome 1.57888021035224e-05 0.000150248278081907 780 929.454545454545 997 1.43535594696388e-06 39 1.96771527692931 -2.2090167094101 -1 11.2882321444034 778 997 491 1449 39 1059 665 1775 1088 601 1282 533 M9192 CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_MESENCHYMAL_DN.html Genes down-regulated in luminal-like breast cancer cell lines compared to the mesenchymal-like ones. 16288205 657/762 Arthur Liberzon 8.39475212931865e-11 2.6415486700256e-09 290 1489.81818181818 998 8.39475212963575e-12 69 1.18272357716812 1.2125105736198 1 15.2235256604429 290 1673 4295 1698 2547 488 998 494 2870 69 966 534 M1048 REACTOME_BINDING_AND_ENTRY_OF_HIV_VIRION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BINDING_AND_ENTRY_OF_HIV_VIRION.html Genes involved in Binding and entry of HIV virion 3/8 Reactome 0.000261043864518021 0.00142607296357067 1000 1455.18181818182 999 2.61074534343358e-05 38 1.49122192391867 1.49122192391867 1 6.36781057412426 999 3587 4259 2563 1242 436 38 57 64 2684 78 535 M12110 KANG_FLUOROURACIL_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_FLUOROURACIL_RESISTANCE_DN.html Genes down-regulated in gastric cancer cell lines resistant to 5-fluorouracil [PubChem=3385]. 14734480 22/26 John Newman 0.00200516428765111 0.00669156600814588 4045 2288.27272727273 1000 0.000182454018784867 481 1.20836868964062 -1.11440444022392 -1 3.94260693201439 4045 960 963 1000 511 4205 4564 3604 481 655 4183 536 M1644 SAFFORD_T_LYMPHOCYTE_ANERGY http://www.broadinstitute.org/gsea/msigdb/cards/SAFFORD_T_LYMPHOCYTE_ANERGY.html Genes up-regulated in anergic mouse T helper cells (A.E7), versus non-anergic stimulated controls 15834410 113/156 John Newman 0.00153640681583066 0.00547722067274978 575 1334.90909090909 1001 0.000139770985588866 189 1.26821230204009 1.2360443481837 1 4.30336431085036 572 2341 1150 2323 2170 379 1001 189 2939 851 769 537 M14801 HOOI_ST7_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOOI_ST7_TARGETS_DN.html Genes down-regulated in PC-3 cells (prostate cancer) stably expressing ST7 [GeneID=7982] off a plasmid vector. 16474848 172/228 Leona Saunders 1.99707417844042e-05 0.000182396771335444 725 1474.09090909091 1002 1.81553846121014e-06 394 1.36765147303221 1.35465648902943 1 7.67299172051632 722 2773 394 3096 1076 872 1002 964 3279 536 1501 538 M19977 SU_SALIVARY_GLAND http://www.broadinstitute.org/gsea/msigdb/cards/SU_SALIVARY_GLAND.html Genes up-regulated specifically in human salivary gland tissue. 11904358 18/35 John Newman 0.00792013395306878 0.0181119342337619 2775 1790.81818181818 1002 0.000722617405294576 624 1.68592981436898 -1.76531317706955 -1 4.40684512775676 2774 1002 821 970 3632 3313 2944 928 624 857 1834 539 M4862 REACTOME_RECYCLING_OF_BILE_ACIDS_AND_SALTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECYCLING_OF_BILE_ACIDS_AND_SALTS.html Genes involved in Recycling of bile acids and salts 9/27 Reactome 0.0135963491000616 0.0279020729357786 1185 1511.18181818182 1003 0.0013680259883624 267 1.59242645483626 -1.59631222966385 -1 3.71399586103535 1181 1075 4205 537 3592 2324 1003 655 818 966 267 540 M13319 ABE_VEGFA_TARGETS_2HR http://www.broadinstitute.org/gsea/msigdb/cards/ABE_VEGFA_TARGETS_2HR.html Genes up-regulated in HUVEC cells (endothelium) at 2 h after VEGFA [GeneID=7422] stimulation. 12197474 36/49 John Newman 0.0162423484931323 0.0322117163393211 365 1307.90909090909 1005 0.0014875925613797 362 1.25756090300232 1.10685562027635 1 2.81526510341737 672 1447 1727 1793 1614 362 362 887 3524 1005 994 541 M16490 GALI_TP53_TARGETS_APOPTOTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/GALI_TP53_TARGETS_APOPTOTIC_UP.html Apoptosis genes up-regulated by TP53 [GeneID=7157] in HCT116 cells (colon cancer) treated with thymoquinone [PubChem=10281]. 18632613 13/14 Jessica Robertson 5.15854923864094e-05 0.000392082969507009 1160 1393.09090909091 1005 4.68970018183817e-06 39 1.31924097937999 -1.40945363712302 -1 6.74346450013643 1160 392 1005 73 93 3463 4301 3147 39 1054 597 542 M1803 GEORGANTAS_HSC_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/GEORGANTAS_HSC_MARKERS.html Genes up-regulated in HSC (hematopoietic stem cells) compared to HPC (hematopoietic progenitor cells). 15231652 102/161 John Newman 0.00241093433383911 0.00768892571332473 450 1222.09090909091 1006 0.00021941640794842 447 1.25745387239958 -1.36842857973754 -1 3.98891634659093 447 677 701 1591 642 1033 2086 1153 3173 934 1006 543 M13907 TSENG_IRS1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_IRS1_TARGETS_DN.html Down-regulated in brown preadipocytes with IRS1 [GeneID=3667] knockout vs wild type controls; the knockouts have severe defects in adipocyte differentiation. 15895078 194/236 John Newman 5.16043564438826e-06 5.79934672416967e-05 1010 1435.90909090909 1006 4.69131613547011e-07 340 1.37345951254597 1.45321367649118 1 8.73116132975234 1006 2764 340 2539 871 944 1889 1033 3517 395 497 544 M7657 AMUNDSON_GAMMA_RADIATION_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_GAMMA_RADIATION_RESISTANCE.html Gene predicting resistance of the NCI-60 cell lines to gamma radiation. 18199535 42/64 Jessica Robertson 0.00202911412915619 0.00673991463027249 85 1255.18181818182 1007 0.000184635277381742 82 1.39183632394666 1.29616339491925 1 4.53470242831091 82 2482 683 1905 1252 840 825 1007 2844 1112 775 545 M8943 TING_SILENCED_BY_DICER http://www.broadinstitute.org/gsea/msigdb/cards/TING_SILENCED_BY_DICER.html Epigenetically silenced genes up-regulated in HCT116 cells (colon cancer) hypomorphic for DICER1 [GeneID=23405]. 18413723 43/68 Jessica Robertson 0.00030882007600964 0.00162444370035198 600 1384.90909090909 1007 2.80784940416125e-05 26 1.35188756581221 1.39625405358305 1 5.65807577772349 597 2477 1007 3275 3285 196 368 59 2765 1179 26 546 M9343 BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G5, defined by unsupervised clustering. 17187432 36/56 Yujin Hoshida 0.00131517820027586 0.00483084910918447 1460 988.727272727273 1008 0.000119633189393666 169 1.29235878598697 1.49773387399954 1 4.4910596961773 1456 246 1086 359 1335 1162 763 169 335 1008 2957 547 M6413 RUTELLA_RESPONSE_TO_HGF_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_DN.html Genes down-regulated in peripheral blood monocytes by HGF [GeneID=3082]. 16527888 281/404 Arthur Liberzon 0.020646249568841 0.0387939084255293 785 1026.90909090909 1009 0.0018947811022575 267 1.13472406063522 1.14634771215181 1 2.4027729477467 783 547 1022 771 2554 267 1009 1037 1434 768 1104 548 M1987 GYORFFY_DOXORUBICIN_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/GYORFFY_DOXORUBICIN_RESISTANCE.html Genes associated with resistance to doxorubicin [PubChem=31703]. 16044152 64/77 Arthur Liberzon 0.0139368757466178 0.0285512385086961 740 1432.90909090909 1009 0.0012750869202316 737 1.22774374594859 1.22259550683012 1 2.84502548303819 1009 1373 883 2277 1571 870 737 737 3383 910 2012 549 M18607 REACTOME_STEROID_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_STEROID_HORMONES.html Genes involved in Steroid hormones 19/44 Reactome 3.76702347010277e-05 0.000304458061282279 2215 1102.54545454545 1011 3.42462543069676e-06 77 1.62698351547004 1.8958614256366 1 8.58473385241349 2214 999 1360 149 77 2652 1011 213 208 1668 1577 550 M1874 LUDWICZEK_TREATING_IRON_OVERLOAD http://www.broadinstitute.org/gsea/msigdb/cards/LUDWICZEK_TREATING_IRON_OVERLOAD.html Genes changed in liver in response to nifedipine [PubChem=4485] treatment of iron overload. 17293870 8/10 Jessica Robertson 0.000341379160818509 0.00174384160071792 1015 1200.18181818182 1011 3.41431615038972e-05 46 1.36066438385797 1.46756891799103 1 5.63192088813462 1011 1067 4591 705 258 1008 1211 1053 46 1296 956 551 M2176 ROY_WOUND_BLOOD_VESSEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROY_WOUND_BLOOD_VESSEL_DN.html Genes down-regulated in blood vessel cells from wound site. 17728400 38/64 Leona Saunders 0.00209204748746344 0.00691005188301429 1840 1314.45454545455 1012 0.000190367230192274 402 1.29742978567606 -1.27338486831313 -1 4.20603394323125 1837 854 866 1012 1094 1121 1934 4102 402 460 777 552 M12596 SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_DN.html Genes down-regulated in prostate cancer samples bearing the fusion of TMPRSS2 with ERG [GeneID=7113;2078]. 18505969 15/42 Jessica Robertson 0.000516650438537096 0.00236986401350349 3970 1153 1012 4.69792553822342e-05 67 1.30744967692038 -1.35743246535917 -1 5.15030477778824 3967 1012 1248 446 313 1355 1781 795 67 1260 439 553 M1262 REACTOME_GRB2_SOS_PROVIDES_LINKAGE_TO_MAPK_SIGNALING_FOR_INTERGRINS_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GRB2_SOS_PROVIDES_LINKAGE_TO_MAPK_SIGNALING_FOR_INTERGRINS_.html Genes involved in GRB2:SOS provides linkage to MAPK signaling for Intergrins 20/22 Reactome 6.92628564006172e-07 1.0248297247991e-05 1275 889.454545454545 1013 6.29662529152115e-08 4 1.66446004741885 1.6239326313315 1 12.4610694493654 1274 359 1110 1314 4 708 290 1994 256 1013 1462 554 M10855 XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_REPRESSED_BY_AKT1_DN.html Genes down-regulated in DU-145 cells (prostate cancer) in the presence but not in the absence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 98/188 Arthur Liberzon 1.49915624489344e-05 0.000145000358112644 4055 1641.90909090909 1013 1.36287860069192e-06 43 1.43097155160151 -1.63853435401164 -1 8.24220837230584 4051 43 382 254 673 3758 2924 1013 2568 461 1934 555 M362 LE_SKI_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LE_SKI_TARGETS_UP.html Selected genes implicated in metastasis and epithelial-to-mesenchymal transition (EMT) which were up-regulated in MDA-MB-231 cells (breast cancer) upon knockdown of SKI [GeneID=6497] by RNAi. 18451154 36/54 Jessica Robertson 3.37827823989536e-08 6.87304883289056e-07 770 1695.18181818182 1013 3.07116208342869e-09 191 1.66038243978597 1.70291755931685 1 15.3542491743278 768 2504 191 2517 4231 1013 635 496 3995 411 1886 556 M366 LANDIS_ERBB2_BREAST_TUMORS_324_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_324_UP.html Up-regulated genes from the 324 genes identified by two analytical methods as changed in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 205/218 Leona Saunders 0.0220302205155362 0.0410187932281385 800 1503.27272727273 1014 0.00202308804286334 462 1.02198094342748 1.06370806041052 1 2.12688897089932 621 1216 2801 797 4358 998 1014 796 462 1541 1932 557 M1641 BURTON_ADIPOGENESIS_PEAK_AT_8HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_8HR.html Cluster 3: genes maximally expressed at 8 hr time point during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 67/78 John Newman 0.00181464355358596 0.00622725344253624 275 992.090909090909 1014 0.00016510382465826 271 1.19270635073314 1.27082342497835 1 3.94739713119115 271 1889 835 1293 492 1014 306 1087 1340 848 1538 558 M11736 SA_MMP_CYTOKINE_CONNECTION http://www.broadinstitute.org/gsea/msigdb/cards/SA_MMP_CYTOKINE_CONNECTION.html Cytokines can induce activation of matrix metalloproteinases, which degrade extracellular matrix. 10/15 SigmaAldrich 7.37644653708088e-06 7.80646359978066e-05 1185 1146.18181818182 1016 6.70588297264333e-07 24 1.28196642144996 1.53100928876562 1 7.90123613533792 1184 427 952 258 24 1878 1997 1016 2271 728 1873 559 M8629 NADERI_BREAST_CANCER_PROGNOSIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NADERI_BREAST_CANCER_PROGNOSIS_DN.html Down-regulated genes in the breast cancer prognostic signature of 70 genes that significantly correlated with survival. 16936776 20/23 Arthur Liberzon 0.00286949071237136 0.00873355338068671 285 1744.81818181818 1016 0.000261203661619058 81 1.40847718528198 1.38928798304623 1 4.35108056271414 285 4215 1680 3748 3889 318 109 705 3147 1016 81 560 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 0.00534922448114963 0.0140268553061257 1200 1461.63636363636 1016 0.000536214466536582 128 0.532567444977264 -0.532567444977264 -1 1.48071032600966 1200 456 4465 1016 747 568 322 1049 128 4667 1460 561 M12801 DORN_ADENOVIRUS_INFECTION_32HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_32HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 32 h after infection with adenovirus Ad12. 15681441 16/29 Arthur Liberzon 0.000547586477251572 0.00247330925610279 4380 2158.18181818182 1016 4.97929836955559e-05 194 1.55093290779112 -1.69098094109932 -1 6.06627214610929 4378 1016 986 827 579 4661 2978 4255 194 378 3488 562 M770 REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P53_DEPENDENT_G1_DNA_DAMAGE_RESPONSE.html Genes involved in p53-Dependent G1 DNA Damage Response 59/69 Reactome 0.000325456828659145 0.00167750659586834 145 1600 1018 2.95913622785145e-05 134 0.606713409476071 -0.61117684417367 -1 2.52652001692055 144 134 3973 1620 235 402 562 1018 4133 4340 1039 563 M982 REACTOME_REGULATION_OF_IFNA_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_IFNA_SIGNALING.html Genes involved in Regulation of IFNA signaling 16/31 Reactome 0.00105306272249196 0.00413859787690428 1405 1125.27272727273 1018 9.57788295159104e-05 121 1.06150065973075 -1.15259576914886 -1 3.79577759854882 1401 1011 2306 1018 402 1806 1570 574 121 1364 805 564 M8124 SMID_BREAST_CANCER_BASAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_BASAL_UP.html Genes up-regulated in basal subtype of breast cancer samles. 18451135 828/1212 Jessica Robertson 4.88886242374233e-13 2.24033307185086e-11 490 1538.18181818182 1019 4.8888624237434e-14 51 1.36333235854655 1.37923779235129 1 21.7860402667214 488 2203 4553 1209 3452 200 1019 797 2246 51 702 565 M7096 NIELSEN_SYNOVIAL_SARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SYNOVIAL_SARCOMA_DN.html Top 20 negative significant genes associated with synovial sarcoma tumors. 11965276 20/30 Arthur Liberzon 5.80056630458633e-05 0.000427124383114625 4645 1756.90909090909 1021 5.27338113562184e-06 57 1.32783267181734 -1.1326708346194 -1 6.71331099252548 4644 981 994 57 98 2782 3063 116 2112 1021 3458 566 M60 PID_NFAT_TFPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFAT_TFPATHWAY.html Calcineurin-regulated NFAT-dependent transcription in lymphocytes 18832364 49/61 Pathway Interaction Database 0.00240377418148009 0.00768674965726008 435 1060.45454545455 1022 0.000218764057178143 95 1.14435955337992 1.05375451584914 1 3.63035820910437 434 1941 1517 2305 1684 133 95 663 1393 1022 478 567 M12369 RICKMAN_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_METASTASIS_DN.html Genes down-regulated in metastatic vs non-metastatic HNSCC (head and neck squamous cell carcinoma) samples. 18679425 335/416 Jessica Robertson 0.00577426225782821 0.0142024584976285 1935 1312.09090909091 1023 0.000526315789473684 83 1.15301752421557 -1.15793551178127 -1 3.19653794915587 1935 529 1023 83 2695 1285 2794 583 1964 865 677 568 M1439 ABBUD_LIF_SIGNALING_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_2_UP.html Genes up-regulated in GH3 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 38/45 Kevin Vogelsang 0.00148410585931964 0.00533509493982384 65 1308.09090909091 1023 0.000135009815831748 61 1.33586321648229 1.36139552123074 1 4.55581401216141 61 2494 669 2753 1023 623 432 1334 3568 1126 306 569 M17487 RIGGINS_TAMOXIFEN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIGGINS_TAMOXIFEN_RESISTANCE_UP.html Genes up-regulated SUM44/LCCTam cells (breast cancer) resistant to 4-hydroxytamoxifen [PubChem=63062] relative to the parental SUM44 cells sensitive to the drug. 18974135 93/145 Leona Saunders 3.37928256135189e-09 8.29966979357476e-08 4235 1702.81818181818 1025 3.07207506049327e-10 41 1.52128446799299 -1.74109913690334 -1 16.1636806213452 4231 41 155 232 317 4152 3977 3059 1025 147 1395 570 M2398 SERVITJA_LIVER_HNF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_LIVER_HNF1A_TARGETS_DN.html Genes down-regulated in liver tissue upon knockout of HNF1A [GeneID=6927]. 19289501 148/290 Arthur Liberzon 1.8398447143772e-13 9.04590317902121e-12 1335 1082.63636363636 1025 1.67258610397941e-14 72 1.48838908363284 1.46649067595272 1 24.6640871708723 1334 601 72 220 3593 1223 1755 1319 675 92 1025 571 M2111 KIM_ALL_DISORDERS_CALB1_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_CALB1_CORR_DN.html Genes whose expression significantly and negatively correlated with the density of CALB1-positive [GeneID=793] GABAergic interneurons in the BA9 brain region across all subjects with psychiatric disorders. 18762803 24/82 Jessica Robertson 2.05588203332173e-05 0.000186252652538936 1625 1179.27272727273 1026 1.86900113238435e-06 54 2.07897481034172 -2.31571613202147 -1 11.6354715008912 1621 1489 397 1178 351 1026 786 3925 1888 257 54 572 M16789 SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_AND_SERUM_RESPONSE_SYNERGY.html Cluster 3: genes strongly up-regulated in B493-6 cells (B lymphocytes) by a combination of MYC [GeneID=4609] and serum but not by each of them alone. 15516975 45/50 Leona Saunders 0.00577426225782821 0.0142024584976285 1350 1298.90909090909 1027 0.000526315789473684 152 1.09494854122516 -1.16095524588191 -1 3.03554659455263 1346 205 3101 152 2825 832 1257 836 220 2487 1027 573 M3185 HELLER_SILENCED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_SILENCED_BY_METHYLATION_DN.html Genes down-regulated in at least one of three multiple myeloma (MM) cell lines treated with the DNA hypomethylating agent decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 18172295 126/163 Jessica Robertson 0.0363346533549713 0.0614914176534474 505 1485.72727272727 1027 0.00335900002403607 416 1.12372031874623 1.17390053509976 1 2.04215262830668 504 2797 1027 1822 2162 416 572 1553 3781 935 774 574 M13191 KEGG_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROSTATE_CANCER.html Prostate cancer 96/121 KEGG 0.0531937440662047 0.0851099905059275 1030 1428.54545454545 1030 0.00495683721708157 519 0.944499678877787 1.04619258972596 1 1.51636932267623 1030 693 2703 909 1962 519 728 1857 1661 2716 936 575 M571 REACTOME_NUCLEAR_SIGNALING_BY_ERBB4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEAR_SIGNALING_BY_ERBB4.html Genes involved in Nuclear signaling by ERBB4 42/70 Reactome 0.000104663145190581 0.000690923140279081 1160 802.909090909091 1031 9.51528407119414e-06 100 1.32205300787198 -1.12209831425126 -1 6.26972938126589 1157 202 1461 100 136 1031 1740 1096 326 1354 229 576 M9951 WANG_METHYLATED_IN_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METHYLATED_IN_BREAST_CANCER.html Genes up-regulated in MDA468 cells (breast cancer) vs DU99 cells (normal breast) after treatment with azacytidine [PubChem=9444]. 15735726 67/88 Leona Saunders 0.0158081098105499 0.0315276564969975 565 1258.09090909091 1031 0.00144753227546436 222 1.22444921693965 1.20642300160288 1 2.75826387891129 563 1356 1031 1637 3120 222 693 2505 1601 714 397 577 M2662 SINGH_NFE2L2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SINGH_NFE2L2_TARGETS.html Selected electrophile and drug detoxication genes down-regulated in A549 and H460 cells (lung cancer) upon knockdown of NFE2L2 [GeneID=4780] by RNAi. 18829555 32/38 Jessica Robertson 0.00577426225782821 0.0142024584976285 2120 984.272727272727 1031 0.000526315789473684 107 1.14524265486569 -1.20870679588421 -1 3.17498278004422 2118 261 1187 107 896 1153 2063 659 257 1031 1095 578 M1540 VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_UP.html Genes up-regulated after heat shock in peripheral lympocytes from old donors, compared to those from the young ones. 12618007 22/30 John Newman 0.000694373966125732 0.00300132337006727 1120 1004.54545454545 1032 6.31448385884754e-05 187 1.11349161672158 -1.2195595483812 -1 4.2148416311226 1120 1507 1874 1032 344 621 187 573 382 1923 1487 579 M14072 WINTER_HYPOXIA_METAGENE http://www.broadinstitute.org/gsea/msigdb/cards/WINTER_HYPOXIA_METAGENE.html Genes regulated by hypoxia, based on literature searches. 17409455 311/364 Jessica Robertson 3.53183381399515e-06 4.09588589731132e-05 635 1522.18181818182 1032 3.21076316721796e-07 91 1.26248675686226 1.292187910365 1 8.31180411750785 632 3611 330 3249 2508 91 1064 1032 3451 576 200 580 M12314 KANG_GIST_WITH_PDGFRA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_GIST_WITH_PDGFRA_UP.html Genes up-regulated in gastrointestinal stromal tumors (GIST) with PDGFRA [GeneID=5156] mutations. 15690055 68/116 Arthur Liberzon 4.61748352510388e-05 0.00035607793877645 645 1875.27272727273 1034 4.1978004020805e-06 347 1.70191627650963 1.6940430475239 1 8.80641881502373 643 3703 441 3737 4069 1034 661 347 3156 743 2094 581 M1025 REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_.html Genes involved in Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins. 98/117 Reactome 1.5450822770535e-07 2.69106581095665e-06 5 1513.90909090909 1037 1.40462035051473e-08 5 0.633247068984629 -0.577141844299767 -1 5.29257972569271 5 1287 3899 1444 463 103 55 724 3218 4418 1037 582 M15148 LE_EGR2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LE_EGR2_TARGETS_DN.html Genes down-regulated in P14 nerves of transgenic mice having hypomorhic (reduced function) allele of EGR2 [GeneID=1959]. 15695336 132/159 Kate Stafford 2.33793044706948e-05 0.000206632572085118 405 1143.45454545455 1037 2.12541390229497e-06 2 1.23693873673666 1.1956315354877 1 6.83907462648335 1257 2 405 287 899 1037 1120 2856 2106 405 2204 583 M17668 BIOCARTA_AKAP13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAP13_PATHWAY.html Rho-Selective Guanine Exchange Factor AKAP13 Mediates Stress Fiber Formation 14/15 BioCarta 0.000129813293669432 0.000814785566648562 1775 1345.54545454545 1039 1.18019049155442e-05 150 1.16908234591628 -1.23098455991338 -1 5.41863933845281 1774 1039 2601 1870 150 413 692 334 2347 2672 909 584 M15545 VALK_AML_CLUSTER_15 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_15.html Top 40 genes from cluster 15 of acute myeloid leukemia (AML) expression profile; 88% of the samples are FAB M1 or M2 subtype, 63% have mutations in CEBPA [GeneID=1050]. 15084694 45/59 Jessica Robertson 0.000161207200445971 0.000975620660869223 2460 1521.18181818182 1039 1.46562740251618e-05 166 1.21060745708002 1.29617191245675 1 5.46898804777206 2460 192 1381 367 166 4204 3376 1039 431 835 2282 585 M264 PID_TOLL_ENDOGENOUS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TOLL_ENDOGENOUS_PATHWAY.html Endogenous TLR signaling 18832364 29/47 Pathway Interaction Database 0.00120626001702259 0.0045548378242773 620 1049.54545454545 1042 0.000109720174322099 160 1.43558550096397 1.61520227939376 1 5.04383585672427 620 314 1042 2100 1884 1047 709 160 1776 1079 814 586 M183 PID_IL6_7_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL6_7_PATHWAY.html IL6-mediated signaling events 18832364 68/74 Pathway Interaction Database 0.00607494430327986 0.0147875967918264 685 1241.27272727273 1044 0.000553798583417978 209 1.03045213244156 0.948262761359299 1 2.82962431579024 684 737 1571 1342 762 469 209 1044 3730 1482 1624 587 M12362 DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_UP.html Genes up-regulated in RMS cells (rhabdomyosarcoma) expressing PAX3 or PAX7 fusions with FOXO1 [GeneID=5077;5081;2308] compared to the fusion negative cell lines. 16849537 78/95 Arthur Liberzon 0.000353772094853832 0.00179163550183486 1700 959.909090909091 1045 3.21662723783705e-05 285 1.35751122266517 1.43654250722784 1 5.59494999568335 1699 722 589 285 524 1251 1111 1093 1045 348 1892 588 M2700 SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BONE_DN.html Genes down-regulated in bone relapse of breast cancer. 18451135 400/649 Jessica Robertson 1.08664982867955e-18 8.99822314274992e-17 730 1290.54545454545 1045 9.87863480617768e-20 42 1.43223183689767 1.45028274527239 1 34.4838973756303 727 2226 42 1790 2870 634 1338 1045 3006 58 460 589 M945 MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_UP.html Genes up-regulated in normal bone marrow plasma cells (BMPC) compared to polyclonal plasmablasts (PPC) that also distinguished multiple myeloma (MM) samples by expression of levels of TACI (TNFRSF13B) [GeneID=23495]. 15827134 142/185 Kevin Vogelsang 2.75311784841724e-05 0.000235411526169011 1050 1416.90909090909 1046 2.50286572910115e-06 415 1.27957599477638 1.06764896389458 1 6.96609182958989 1046 1255 415 2164 970 746 965 2282 2666 587 2490 590 M2464 DELACROIX_RAR_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RAR_TARGETS_UP.html Genes bound by RARG [GeneID=5916] and up-regulated by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] in MEF cells (embryonic fibroblast). 19884340 62/85 Arthur Liberzon 0.0505602168582384 0.0815320203521986 520 1369.27272727273 1046 0.0047055459096912 363 1.25311067176286 1.35677159654942 1 2.0469430318995 518 1367 1246 363 4613 509 1046 2730 484 832 1354 591 M12889 LINDGREN_BLADDER_CANCER_CLUSTER_2A_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_2A_UP.html Genes whose expression profile is specific to Cluster IIa of urothelial cell carcinoma (UCC) tumors. 16532037 9/10 Leona Saunders 0.000591179224706783 0.00262252438027821 2290 1661 1050 5.91336555410794e-05 101 1.50928129685675 0.849982025953726 1 5.84573779051774 2287 441 4335 999 629 3319 2154 101 203 2753 1050 592 M924 REACTOME_PLATELET_CALCIUM_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_CALCIUM_HOMEOSTASIS.html Genes involved in Platelet calcium homeostasis 13/19 Reactome 0.00568409002433079 0.0142024584976285 1995 1384.27272727273 1051 0.000518075383644824 125 1.07996723570583 -1.1201212481361 -1 2.99401218934908 1992 417 1478 520 984 2842 2628 989 2201 1051 125 593 M1000 REACTOME_TRAF6_MEDIATED_INDUCTION_OF_TAK1_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_INDUCTION_OF_TAK1_COMPLEX.html Genes involved in TRAF6 mediated induction of TAK1 complex 18/31 Reactome 0.000104314522973025 0.000689586202286665 270 1775.18181818182 1051 9.4835881315186e-06 12 1.02028416718113 1.02028416718113 1 4.83987872647777 270 3504 2741 3597 1051 138 12 675 3738 3071 730 594 M2384 SCHMIDT_POR_TARGETS_IN_LIMB_BUD_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHMIDT_POR_TARGETS_IN_LIMB_BUD_DN.html Genes down-regulated in E12.5 forelimb buds with POR [GeneID=5447] knockout. 19273610 22/35 Arthur Liberzon 0.00785586630803065 0.0179911154652618 1055 1302.63636363636 1051 0.000716732678089222 468 1.63208361572598 -1.76705382153584 -1 4.27321192229677 1051 953 1125 582 3329 1423 1161 477 2880 880 468 595 M19218 LIU_CDX2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CDX2_TARGETS_DN.html Genes down-regulated in HET1A cells (esophagus epithelium) engineered to stably express CDX2 [GeneID=1045]. 16990345 13/19 Arthur Liberzon 0.000556594055843751 0.00251081449716114 80 1241.54545454545 1052 5.0612265684818e-05 27 2.47201766978192 -2.47201766978192 -1 9.64479329915389 77 3085 587 2507 1944 219 27 1208 2565 1052 386 596 M18843 JI_METASTASIS_REPRESSED_BY_STK11 http://www.broadinstitute.org/gsea/msigdb/cards/JI_METASTASIS_REPRESSED_BY_STK11.html Adenocarcinoma metastatic program genes up-regulated in A549 and H2126 cells (lung cancer) lacking functional STK11 [GeneID=6794] but down-regulated by the normal gene. 17676035 33/42 Jessica Robertson 0.00221955259140602 0.00724000568862227 1520 1270.90909090909 1052 0.000201981367120965 532 1.26028818060875 1.28800965222359 1 4.04731561539191 1741 892 903 2506 532 1648 1052 1516 828 846 1516 597 M2337 BILANGES_SERUM_RESPONSE_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_RESPONSE_TRANSLATION.html Genes translationally repressed upon serum deprivation in MEF cells (embryonic fibroblast). 17562867 43/69 Arthur Liberzon 0.000112763650118597 0.00072810455343335 250 1143.81818181818 1052 1.02517663972824e-05 65 1.24315959702337 1.42247267599953 1 5.85311378916405 249 1960 2790 1770 143 205 369 1273 65 2706 1052 598 M17776 REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR.html Genes involved in Downstream signaling of activated FGFR 94/117 Reactome 0.0033934708381391 0.00993621734244202 1265 1321.63636363636 1053 0.000308974232131904 52 0.935007513103542 0.824551793928496 1 2.80978806246816 1262 52 2745 428 619 966 899 2294 1053 2850 1370 599 M16596 WATTEL_AUTONOMOUS_THYROID_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATTEL_AUTONOMOUS_THYROID_ADENOMA_UP.html Up-regulated genes characteristic for autonomous thyroid adenoma. 16027733 94/124 Arthur Liberzon 1.15280371287135e-05 0.000115341493480082 525 1228.09090909091 1053 1.04800886693325e-06 117 1.30282627358278 1.3658880936213 1 7.69838540762121 524 1306 374 1245 3393 1053 1409 221 3140 727 117 600 M4861 VERHAAK_AML_WITH_NPM1_MUTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_AML_WITH_NPM1_MUTATED_UP.html Genes up-regulated in acute myeloid leukemia (AML) patients with mutated NPM1 [GeneID=4869]. 16109776 199/356 Kevin Vogelsang 9.2913589113906e-19 7.97367528395702e-17 650 1313.09090909091 1054 8.44668991944599e-20 41 1.3818288325119 1.24506276063822 1 33.3791917490221 646 1743 41 476 3276 440 1054 1840 3013 80 1835 601 M4470 BIOCARTA_EXTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EXTRINSIC_PATHWAY.html Extrinsic Prothrombin Activation Pathway 9/13 BioCarta 0.000243359375350487 0.00136582194013591 1080 1383.54545454545 1055 2.43386030162328e-05 176 1.99808217485652 -2.39805581469616 -1 8.58844792547616 1080 1607 4190 929 208 862 1055 2531 176 620 1961 602 M65 PID_FRA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FRA_PATHWAY.html Validated transcriptional targets of AP1 family members Fra1 and Fra2 18832364 54/66 Pathway Interaction Database 0.000125084495526106 0.000793698936491356 65 1516.81818181818 1055 1.13719643609085e-05 55 1.59841078592089 1.50880379907205 1 7.4359068557107 65 3742 494 4271 1980 85 69 1271 3598 1055 55 603 M12101 REACTOME_P130CAS_LINKAGE_TO_MAPK_SIGNALING_FOR_INTEGRINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P130CAS_LINKAGE_TO_MAPK_SIGNALING_FOR_INTEGRINS.html Genes involved in p130Cas linkage to MAPK signaling for integrins 19/21 Reactome 1.57456005335595e-05 0.000150248278081907 1365 1137.45454545455 1056 1.43142847521699e-06 38 1.78310160964915 1.8149139990341 1 10.2291452455201 1364 996 1056 1295 38 1284 782 2373 261 923 2140 604 M16929 REACTOME_PI3K_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_CASCADE.html Genes involved in PI3K Cascade 61/105 Reactome 0.00113431621496812 0.00438131958645625 420 1363.45454545455 1057 0.000103172862633943 130 0.868456564797314 0.887519796885596 1 3.07320487584036 1057 130 2799 419 416 442 731 2281 1454 3596 1673 605 M13910 CLIMENT_BREAST_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/CLIMENT_BREAST_CANCER_COPY_NUMBER_UP.html Genes from the most frequent genomic gains and amplifications in a panel of patients with lymph node negative breast cancer (NNBC). 17234794 34/41 Jessica Robertson 0.0236780020218172 0.043418869286316 2875 1527.72727272727 1057 0.00217606810688643 243 1.34757202126511 -1.26647325099765 -1 2.7545884154983 2871 243 979 552 1563 2676 4310 1057 715 705 1134 606 M2137 GREGORY_SYNTHETIC_LETHAL_WITH_IMATINIB http://www.broadinstitute.org/gsea/msigdb/cards/GREGORY_SYNTHETIC_LETHAL_WITH_IMATINIB.html Genes identified as synthetic lethal with imatinib [PubChem=5291] in RNAi screen in K562 cells (CML, chronic myelogenous leukemia). 20609354 197/291 Arthur Liberzon 0.0176691786571269 0.0342921559463976 2635 1289.27272727273 1058 0.00161933673737183 336 1.04541089091971 1.15373477586569 1 2.29767554520287 336 571 1567 1327 2633 1058 674 706 2632 1766 912 607 M4987 KIM_WT1_TARGETS_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_12HR_DN.html Genes down-regulated in UB27 cells (osteosarcoma) at 12 hr after inducing the expression of a mutated form of WT1 [GeneID=7490]. 17430890 258/315 Arthur Liberzon 0.0309905174523583 0.0539960289313884 720 1187.90909090909 1061 0.00285780696648528 406 1.15231671914928 1.18538706242008 1 2.1917348482296 717 554 1895 406 2329 1122 982 920 1061 1287 1794 608 M1626 BURTON_ADIPOGENESIS_PEAK_AT_0HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_0HR.html Cluster 1: genes progressively down-regulated over 24 h (peak at 0 h timepoint) during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 118/149 John Newman 0.00129417364303933 0.00478912043280437 510 1552 1061 0.000117721416561222 493 1.25968068732049 1.43044454692876 1 4.38461941565047 510 3228 640 3248 493 1394 1760 672 3312 754 1061 609 M1887 WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_UP http://www.broadinstitute.org/gsea/msigdb/cards/WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_UP.html Genes up-regulated in gastric mucosal tissue of mice on 2% cholesterol [PubChem=5997] diet and infected with H. pylori vs those infected with H. pylori while on 0% cholesterol diet. 16951684 84/197 Jessica Robertson 0.00592521791632272 0.0144756876630658 1065 1188.18181818182 1064 0.000540112420460458 62 1.16089148525308 -1.18728353498031 -1 3.20395210416069 1064 62 788 289 1119 2024 3460 996 1265 693 1310 610 M12432 PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_DN.html Genes down-regulated in unstable ateroslerotic plaques compared to the stable ones. 16741146 61/71 Arthur Liberzon 0.00274593847628039 0.00848221832987135 455 1567.45454545455 1066 0.000249942893724174 221 1.16688992579516 1.25169491303441 1 3.62695347021242 451 3305 1066 3116 921 828 1801 254 3902 1377 221 611 M5374 BIOCARTA_SARS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SARS_PATHWAY.html The SARS-coronavirus Life Cycle 11/14 BioCarta 0.00270085592196273 0.00837584753723001 845 1599.81818181818 1068 0.000245834306329317 253 0.931146803595835 1.15222748711786 1 2.9018476594761 845 2645 2677 3749 1068 976 342 253 1207 3013 823 612 M10355 JI_RESPONSE_TO_FSH_UP http://www.broadinstitute.org/gsea/msigdb/cards/JI_RESPONSE_TO_FSH_UP.html Genes up-regulated in MCV152 cells (ovarian cancer) treated with follicle stimulating hormone (FSH). 15386376 128/208 John Newman 7.56320818828686e-05 0.000528864335536504 2520 1640.63636363636 1069 6.87588019129946e-06 3 1.1614967394514 -1.23706797418033 -1 5.71061086428931 2516 3 702 1069 115 860 3579 4174 2933 769 1327 613 M7919 BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transfrormed by expression of constitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression did NOT reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 27/31 Leona Saunders 0.000395993926394189 0.00194592308160632 2515 1327.09090909091 1070 3.60059292886014e-05 270 1.37364398743447 -1.56055026609674 -1 5.58749512952926 2512 931 1045 1070 270 3124 1566 1234 1339 737 770 614 M1373 GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP.html Genes up-regulated in MMH-RT cells (hepatocytes displaying an invasive, metastatic phenotype) during epithelial to mesenchymal transition (EMT). 16607286 113/135 Jessica Robertson 0.00272789919696741 0.00843201323489599 330 1488.54545454545 1070 0.000248298868218682 328 1.20416476455837 1.16782949127623 1 3.74747376359212 328 2346 712 2737 1900 479 966 1370 3482 984 1070 615 M12899 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GLOBO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GLOBO_SERIES.html Glycosphingolipid biosynthesis - globo series 10/15 KEGG 5.28711656367732e-05 0.000398645210552028 100 1080 1071 4.8065851179798e-06 13 1.88532282963607 2.36784638414665 1 9.61671496429594 1071 1613 1395 98 2757 1070 1313 13 277 2175 98 616 M2437 HUANG_GATA2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_GATA2_TARGETS_UP.html Genes up-regulated in G1ME cells (megakaryocyte/erythroid progenitor lacking GATA1 [GeneID=2623]) upon knockdown of GATA2 [GeneID=2624] by RNAi. 19620289 178/247 Arthur Liberzon 0.0181686951844398 0.035088478424941 1250 1129.63636363636 1071 0.00166549994413176 245 1.05387722941162 -1.03065375442666 -1 2.30051850344723 1249 587 1737 482 1692 245 1903 1800 1071 1000 660 617 M11673 KEGG_BIOSYNTHESIS_OF_UNSATURATED_FATTY_ACIDS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BIOSYNTHESIS_OF_UNSATURATED_FATTY_ACIDS.html Biosynthesis of unsaturated fatty acids 27/33 KEGG 0.00163356814990458 0.00573355297131115 475 1207 1072 0.000148616580663577 445 1.19482749704334 1.33077826397366 1 4.01873233939556 474 1483 1314 936 2755 822 1072 1704 581 445 1691 618 M18788 REACTOME_PHASE_II_CONJUGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHASE_II_CONJUGATION.html Genes involved in Phase II conjugation 38/95 Reactome 0.0163035298819807 0.0322788007730489 1375 868.090909090909 1073 0.00149323808548547 219 1.06919917622718 -1.04109120671951 -1 2.39211974475027 1372 219 1350 256 1073 270 1384 701 400 1398 1126 619 M15821 AMIT_SERUM_RESPONSE_120_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_120_MCF10A.html Genes whose expression peaked at 120 min after stimulation of MCF10A cells with serum. 17322878 95/127 Leona Saunders 0.00652112819881399 0.015598091841524 680 1021.90909090909 1073 0.000594594399284919 547 1.23134969236954 1.31632553187114 1 3.33849263368894 714 683 1073 1272 1993 676 1101 1138 1366 547 678 620 M2607 ELLWOOD_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELLWOOD_MYC_TARGETS_UP.html Genes up-regulated in transgenic mice expressing human MYC [GeneID=4609] in prostate. 14522256 16/17 Arthur Liberzon 0.000417848380880201 0.00201044277039199 850 1464 1073 3.79934331258672e-05 24 1.30733160367443 -1.36575924966483 -1 5.28996562134743 846 2610 2396 1417 4322 1073 808 72 24 2329 207 621 M2602 BIOCARTA_RANKL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RANKL_PATHWAY.html Bone Remodelling 17/19 BioCarta 0.000245639665726213 0.00137607566270606 345 1466.72727272727 1074 2.23333724329201e-05 114 1.13606479893774 1.09209735310242 1 4.877616370138 343 2611 1933 2364 198 241 114 1074 4537 1902 817 622 M7013 KAYO_CALORIE_RESTRICTION_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_CALORIE_RESTRICTION_MUSCLE_UP.html Upregulated in the vastus lateralis muscle of middle aged rhesus monkeys subjected to caloric restriction since young adulthood vs age matched controls 11309484 137/232 John Newman 3.76465482747765e-05 0.000304458061282279 495 1216 1076 3.42247204549832e-06 407 1.27752553206212 1.35464822847986 1 6.7408056663146 494 1792 431 1117 1240 1076 857 1498 3390 407 1074 623 M201 PID_ERBB_NETWORK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB_NETWORK_PATHWAY.html ErbB receptor signaling network 18832364 16/18 Pathway Interaction Database 0.00332906959311373 0.00982075529968551 3890 1860.09090909091 1077 0.000303101625822142 410 1.39711892795721 -1.18754402029571 -1 4.20917164402554 3890 410 1077 572 612 2093 1899 3733 493 986 4696 624 M1020 REACTOME_PKB_MEDIATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PKB_MEDIATED_EVENTS.html Genes involved in PKB-mediated events 35/56 Reactome 0.00771351453804192 0.0177572727940038 1925 1603.09090909091 1077 0.00070369933850952 271 0.715365601467815 0.788358541457541 1 1.87904947329403 1921 271 3605 884 825 1141 866 1077 901 4143 2000 625 M1144 OZANNE_AP1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OZANNE_AP1_TARGETS_DN.html Cancer motility and invasion genes down-regulated by the AP-1 transcription factor. 16799638 8/8 Arthur Liberzon 0.000264151539608776 0.00143805682462909 2495 1777 1077 2.64182944078889e-05 218 1.49827459291846 1.31015819424447 1 6.38975675329875 2495 1077 4348 549 218 1021 738 2239 643 1882 4337 626 M11716 REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_ATP_BY_CHEMIOSMOTIC_COUPLING.html Genes involved in Formation of ATP by chemiosmotic coupling 16/21 Reactome 0.00125473557005959 0.00466694396428785 235 1892.18181818182 1080 0.000114131978252373 60 0.498770644580857 -0.498770644580857 -1 1.74442599286378 231 2110 3449 3086 569 233 60 777 4613 4606 1080 627 M14181 YAMASHITA_METHYLATED_IN_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_METHYLATED_IN_PROSTATE_CANCER.html Genes up-regulated in prostate cancer cell lines after treatment with 5-aza-2'-deoxycytidine (decitabine) [PubChem=451668]. 18381416 72/104 Jessica Robertson 1.21469129369471e-11 4.31078414002935e-10 200 1551.72727272727 1081 1.10426481245583e-12 105 1.66923768986387 1.61240087809268 1 23.4577519562899 196 3700 105 3304 1856 839 1081 1468 3396 386 738 628 M18009 KEGG_CIRCADIAN_RHYTHM_MAMMAL http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CIRCADIAN_RHYTHM_MAMMAL.html Circadian rhythm - mammal 14/14 KEGG 0.00903684899558 0.0202114211853244 1090 1365.18181818182 1086 0.000824925833437761 159 1.01561297431011 1.09322365577854 1 2.58207586744858 1086 1031 2645 527 867 1333 748 3023 159 2072 1526 629 M804 REACTOME_PROSTANOID_LIGAND_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROSTANOID_LIGAND_RECEPTORS.html Genes involved in Prostanoid ligand receptors 3/9 Reactome 0.00122202617225431 0.00458867425062877 1090 1417.45454545455 1087 0.000122269869939953 87 1.82691576719443 1.82691576719443 1 6.40996656161479 1087 3143 4241 2526 450 478 87 576 179 1618 1207 630 M2223 KANG_AR_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_AR_TARGETS_UP.html Genes up-regulated in osteoblasts from wild type male mice compared to those with AR [GeneID=367] knockout. 18838539 29/35 Arthur Liberzon 0.000249237999996393 0.00138219799997218 65 1692.63636363636 1087 2.26605673316955e-05 64 1.27780064365054 1.29883487509944 1 5.48246613304604 64 3002 534 3226 2246 837 812 1870 4114 1087 827 631 M17941 BIOCARTA_VIP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VIP_PATHWAY.html Neuropeptides VIP and PACAP inhibit the apoptosis of activated T cells 32/34 BioCarta 0.00303882039171816 0.00913000143151477 620 1418 1088 0.000276638726785309 115 0.818751054102238 0.725250627113416 1 2.50556258545463 619 1463 2761 2936 855 516 115 1088 2217 2353 675 632 M2064 BIOCARTA_41BB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_41BB_PATHWAY.html The 4-1BB-dependent immune response 19/25 BioCarta 0.00125208988404568 0.00466077622452334 315 1770 1088 0.000113891186952851 59 0.730249542024581 0.851975029021332 1 2.55469058599651 311 3047 3272 3359 623 388 59 929 3232 3162 1088 633 M556 REACTOME_TERMINATION_OF_O_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TERMINATION_OF_O_GLYCAN_BIOSYNTHESIS.html Genes involved in Termination of O-glycan biosynthesis 10/22 Reactome 0.0138586802556759 0.0284033742105037 1380 1339 1088 0.00126788721796539 300 1.86048750882361 1.78308138254598 1 4.31761953646197 1380 1064 976 474 3498 1905 327 1550 300 1088 2167 634 M19757 SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_DN.html Genes down-regulated in pilocytic astrocytoma (PA) from supratentorial regions compared to the infratentorial PA tumors. 17283119 6/8 Jessica Robertson 8.65336624094186e-05 0.000590229604873491 1370 1511.45454545455 1088 8.65370322277302e-06 128 1.13802271097403 0.711388542931348 1 5.51378241547451 1366 1088 4575 715 131 654 128 2929 1481 3242 317 635 M3254 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FLI1 http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FLI1.html Genes whose expression is coregulated with that of FLI1 [GeneID=2313] in hematopoietic stem cells (HSC). 15711547 7/9 Jean Junior 0.000246060987144898 0.00137607566270606 855 1444.81818181818 1089 2.46088237095817e-05 51 0.741896294417024 -0.741896294417024 -1 3.18524418680146 855 1089 4479 1467 1279 403 194 51 2454 3362 260 636 M601 REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS.html Genes involved in Antigen Activates B Cell Receptor Leading to Generation of Second Messengers 38/47 Reactome 0.00545562140007981 0.0142024584976285 610 1312.36363636364 1090 0.000497199778080524 181 0.905456900127953 0.747314367669463 1 2.51019701177672 607 866 2516 1651 1123 614 181 402 2643 2743 1090 637 M9972 NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_VS_SYNOVIAL_SARCOMA_UP.html Top 20 genes whose up-regulation correlated with gastrointestinal stromal tumors (GIST) compared to synovial sarcoma. 11965276 37/110 John Newman 5.55602318170944e-05 0.000414943503444123 30 1696.72727272727 1091 5.05105772917831e-06 29 1.33977574503984 1.36919762462917 1 6.7989551974716 29 3393 449 3230 1781 1091 1090 827 4546 1636 592 638 M11290 SOUCEK_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SOUCEK_MYC_TARGETS.html Chemokine genes up-regulated within 2 hr of c-Myc [GeneID=4609] activation in a mouse model of Myc-induced pancreatic beta-cell tumorigenesis. 17906636 10/13 Jessica Robertson 0.00552973160420053 0.0142024584976285 415 1440.27272727273 1092 0.000503970888296089 183 1.66677063951349 1.440032748357 1 4.62087510307352 413 2158 921 2052 3640 800 183 2678 1266 1092 640 639 M689 REACTOME_SIGNALING_BY_FGFR3_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR3_MUTANTS.html Genes involved in Signaling by FGFR3 mutants 5/14 Reactome 1.76782223592652e-06 2.29865591007526e-05 2335 1530.27272727273 1093 1.76782364226605e-07 8 1.33548755139821 -1.53758199962462 -1 9.29515650283845 2331 1093 4217 1007 8 1955 3390 44 107 2091 590 640 M13897 REACTOME_CD28_DEPENDENT_PI3K_AKT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CD28_DEPENDENT_PI3K_AKT_SIGNALING.html Genes involved in CD28 dependent PI3K/Akt signaling 25/29 Reactome 9.65831899973547e-05 0.000641171106592847 1065 1512 1093 8.7806754909152e-06 132 0.673127256460677 0.739627711225877 1 3.22498126701543 1063 332 3004 642 132 1093 653 1144 3485 3919 1165 641 M1366 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_DN.html Early prostate development genes (down-regulated at 48 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 6/7 Jessica Robertson 0.000109436598059954 0.00071305430343848 1410 1383.18181818182 1094 1.09441987799568e-05 146 1.80286243268025 -1.8388402882288 -1 8.512925276969 1406 1094 4445 973 146 1693 1681 660 700 1552 865 642 M2357 RAFFEL_VEGFA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAFFEL_VEGFA_TARGETS_UP.html Genes up-regulated in hearts of E18.5 embryos upon knockout of VEGFA [GeneID=7422]. 18981216 13/14 Arthur Liberzon 0.0172401559271599 0.0336671642433573 750 1064.18181818182 1095 0.00157970530149502 103 1.38989915174547 1.61440597611504 1 3.07151034710432 749 1044 1470 1462 1095 1170 1058 1186 103 1968 401 643 M19162 WANG_RESPONSE_TO_FORSKOLIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_FORSKOLIN_DN.html Genes down-regulated in LNCaP cells (prostate cancer) treated with forskolin [PubChem=47936], an activator of PKA pathway. 16751804 14/14 Arthur Liberzon 0.000131443182725563 0.000821737513198222 1690 1156.09090909091 1096 1.19500942459436e-05 33 1.0508614795702 1.12793631415423 1 4.86486252129424 1690 1028 2042 1229 223 2905 1096 33 298 1584 589 644 M1745 MARSON_FOXP3_CORE_DIRECT_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_CORE_DIRECT_TARGETS.html Direct FOXP3 [GeneID=50943] targets that exhibit consistent transcriptional behavior in hybridoma and in ex vivo T lymphocytes. 17237765 20/32 Jessica Robertson 7.28130588836481e-05 0.000514141233550908 1420 1295.81818181818 1096 6.6195880798034e-06 113 1.49606014289595 -1.55714458173281 -1 7.38308085167188 1420 970 1096 995 113 1865 740 2361 1660 1019 2015 645 M19553 BIOCARTA_AHSP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AHSP_PATHWAY.html Hemoglobin's Chaperone 10/21 BioCarta 0.00012548161970429 0.000794735871803309 1100 1390.18181818182 1098 1.14080706712296e-05 147 1.25386146183526 -1.42043576953513 -1 5.83195224606018 1098 2150 2335 1558 147 170 445 3758 672 2176 783 646 M5321 VERRECCHIA_RESPONSE_TO_TGFB1_C3 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C3.html Cluster 3: ECM related genes up-regulated in dermal fibroblasts within 30 min after TGFB1 [GeneID=7040] addition; returned rapidly to basal level after that. 11279127 25/28 John Newman 8.6804573851307e-05 0.00059122307154137 1850 1473.27272727273 1098 7.89163627781706e-06 121 1.38432438499897 1.60100951760409 1 6.70563327254956 1847 938 1436 1061 121 2882 2849 528 322 1098 3124 647 M1711 DASU_IL6_SIGNALING_SCAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_SCAR_DN.html Genes down-regulated in hypertrophic scar fibroblasts in response to IL6 [GeneID=3569]. 15095275 28/34 John Newman 0.00745658866387921 0.0172948886945995 470 1219.18181818182 1099 0.000680180208480669 462 1.37721674800167 1.33880919553646 1 3.64130999432962 467 1486 1099 2099 1908 1526 621 462 2618 607 518 648 M15055 MATTIOLI_MULTIPLE_MYELOMA_SUBGROUPS http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MULTIPLE_MYELOMA_SUBGROUPS.html Genes differentially expressed in multiple myeloma (MM) patients: comparison of MGUS-like vs PCL-like samples; MGUS=monoclonal gammopathy of undetermined significance, PCL=plasma cell leukemia. 15735737 17/41 Leona Saunders 0.0147456604870676 0.0298617253421183 1480 1402.90909090909 1100 0.00134958471196545 89 1.03577023713561 -1.1520573879376 -1 2.36986149261054 1478 384 2106 738 4714 1185 1100 950 89 2423 265 649 M194 BIOCARTA_PROTEASOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PROTEASOME_PATHWAY.html Proteasome Complex 31/35 BioCarta 0.00358913679264872 0.0103486412103249 285 1534.54545454545 1102 0.000326818691982499 284 0.532253076645353 -0.532253076645353 -1 1.58532035153084 284 1994 3991 1871 630 404 349 1102 456 4503 1296 650 M1272 WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_PACLITAXEL_VIA_MAPK8_DN.html Genes specifically down-regulated via JNK (MAPK8) [GeneID=5599] signaling pathway activated by paclitaxel [PubChem=4666] in BR cells (ovarian cancer). 16547493 4/5 Arthur Liberzon 1.13276171766401e-06 1.55878580389916e-05 1670 1494.63636363636 1102 1.13276229508152e-07 3 0.838684517094691 -0.838684517094691 -1 6.04959432466245 1667 1102 4412 1453 7 277 117 149 2597 4657 3 651 M13796 THUM_MIR21_TARGETS_HEART_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/THUM_MIR21_TARGETS_HEART_DISEASE_UP.html Genes up-regulated in a mouse model of heart disease whose expression reverted to normal by silencing of MIR21 [GeneID=406991] microRNA. 19043405 32/34 Jessica Robertson 2.44374321963341e-06 2.9959657134207e-05 10 1631.09090909091 1102 2.22158721284451e-07 9 1.59172414283365 1.64454740815521 1 10.8037970070959 9 2998 312 2762 2596 1102 1040 1312 4524 802 485 652 M9858 VALK_AML_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_3.html Top 40 genes from cluster 3 of acute myeloid leukemia (AML) expression profile; 84% of the samples are FAB M1 or M2 subtypes, 52% bear intern tandem duplication in FLT3 [GeneID=2322]. 15084694 55/76 Jessica Robertson 0.00271081546227658 0.00839019605373472 390 1350.72727272727 1102 0.000246741952032856 388 1.0985347657488 1.07279421846811 1 3.42229312941924 388 1389 711 1268 2132 492 497 2193 3609 1077 1102 653 M3102 SMID_BREAST_CANCER_ERBB2_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_ERBB2_UP.html Genes up-regulated in the erbb2 subype of breast cancer samples, characterized by higher expression of ERBB2 [GeneID=2064]. 18451135 187/290 Jessica Robertson 2.21774045311319e-10 6.62514869537611e-09 1875 1311 1103 2.01612768485159e-11 12 1.39958465408406 -1.29983678803592 -1 17.1762409909981 1875 567 124 12 1793 2017 3052 3301 498 79 1103 654 M2100 STAMBOLSKY_BOUND_BY_MUTATED_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_BOUND_BY_MUTATED_TP53.html Gene promoters preferentially bound by a mutated form of TP53 [GeneID=7157] in SKBR3 cells (breast cancer). 20227041 24/32 Arthur Liberzon 0.00577426225782821 0.0142024584976285 1560 1223.90909090909 1104 0.000526315789473684 157 0.957575425237799 -1.06732378958418 -1 2.6546912240956 1557 1488 2479 157 1644 1104 988 517 377 2116 1036 655 M2218 BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G123_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G123, defined by unsupervised clustering. 17187432 50/80 Yujin Hoshida 0.0150765131921828 0.0303718063453278 1045 1699.72727272727 1105 0.00138007583598235 642 1.05635754651143 1.02631221488228 1 2.40530828615864 1041 3333 2809 2618 1105 934 652 642 1935 2771 857 656 M557 REACTOME_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEFENSINS.html Genes involved in Defensins 6/110 Reactome 0.00227605557493395 0.00735820706417003 1110 1735.45454545455 1106 0.000227839013394917 215 1.43601184963494 1.1058956195583 1 4.5964983386491 1106 2181 4208 3352 554 808 215 866 3616 1542 642 657 M565 REACTOME_BETA_DEFENSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BETA_DEFENSINS.html Genes involved in Beta defensins 6/55 Reactome 0.00227605557493395 0.00735820706417003 1110 1736.45454545455 1107 0.000227839013394917 216 1.43601184963494 1.1058956195583 1 4.5964983386491 1107 2182 4209 3353 555 809 216 867 3617 1543 643 658 M515 LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_UP.html Up-regulated genes displaying alternative splicing in MDA-MB-435 cells (breast cancer) whose metastatic potential has been reduced by expression of NME1 [GeneID=4830]. 18245461 127/152 Jessica Robertson 0.000178569510912874 0.00105885438631754 835 1442.90909090909 1107 1.62349096984509e-05 512 1.22826965950382 1.33506677780437 1 5.48324972932322 835 639 512 873 3811 1488 1262 1679 2721 1107 945 659 M37 PID_NFKAPPAB_CANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFKAPPAB_CANONICAL_PATHWAY.html Canonical NF-kappaB pathway 18832364 33/38 Pathway Interaction Database 0.00385545810899315 0.0108773235352347 425 1146.72727272727 1108 0.000351111940883448 292 1.03849466528656 0.920524802228843 1 3.0595466949728 424 1453 2197 2327 644 579 292 1108 596 1373 1621 660 M13333 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN.html Genes down-regulated in peripheral blood mononucleocytes by HGF [GeneID=3082] compared to those regulated by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 291/368 Arthur Liberzon 0.00577426225782821 0.0142024584976285 1360 1269.72727272727 1108 0.000526315789473684 80 1.12370913822893 1.09200934553979 1 3.11528292249211 1356 1176 939 80 2743 332 1057 2860 1108 998 1318 661 M1733 GAVIN_FOXP3_TARGETS_CLUSTER_P3 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P3.html Cluster P3 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 196/250 Jessica Robertson 0.00341604784952051 0.00997139508332517 1575 1532.63636363636 1109 0.00031103306126112 496 1.15158535602785 1.08313547672909 1 3.45799778225566 1573 570 1109 677 4371 1748 1631 540 1029 496 3115 662 M12225 PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/PICCALUGA_ANGIOIMMUNOBLASTIC_LYMPHOMA_UP.html Up-regulated genes in angioimmunoblastic lymphoma (AILT) compared to normal T lymphocytes. 18006812 277/361 Arthur Liberzon 9.89222262835479e-22 1.26192677853607e-19 145 1575.81818181818 1110 8.99292966214072e-23 26 1.37639869863552 1.38218081647364 1 39.0321904588162 141 3619 26 3279 1817 1110 1048 1212 4066 106 910 663 M9126 BEIER_GLIOMA_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BEIER_GLIOMA_STEM_CELL_UP.html Genes up-regulated in cancer stem cells derived from glyoblastoma tumors: CD133+ [GeneID=8842] vs. CD133- cells. 17483311 54/71 Jessica Robertson 0.00195827537002031 0.00657401119949918 345 1465.09090909091 1111 0.000178183695957508 61 1.28377814605495 1.25311903400564 1 4.20348349334074 341 2447 1111 4188 2193 61 83 306 3737 1509 140 664 M2508 KINNEY_DNMT1_METHYLATION_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KINNEY_DNMT1_METHYLATION_TARGETS.html Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. 20584988 4/18 Arthur Liberzon 1.40402163270527e-05 0.000137435409859693 3480 1932.36363636364 1111 1.4040305035295e-06 36 2.61331125577481 2.76357555743828 1 15.1436683209571 3478 1099 4711 938 36 3024 2609 793 245 1111 3212 665 M16563 BIOCARTA_MTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MTOR_PATHWAY.html mTOR Signaling Pathway 32/32 BioCarta 0.0311513712823805 0.0542162509044381 705 1830 1112 0.00287285572103399 414 0.554959693495617 0.560133673514089 1 1.0540201959777 703 1465 3927 2452 3670 435 727 974 1112 4251 414 666 M6813 IVANOVA_HEMATOPOIESIS_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL.html Genes in the expression cluster 'HSC Shared': up-regulated in hematopoietic stem cells (HSC) from adult bone marrow and fetal liver. 12228721 340/530 John Newman 5.80420304369191e-07 8.78071742507238e-06 1150 1035.54545454545 1113 5.27654961363667e-08 261 1.17547284438135 1.09635527751225 1 8.9186000860084 1146 528 261 267 1231 286 1113 2297 2392 473 1397 667 M16141 CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_UP.html All marker genes up-regulated in the 'interferon' subclass of hepatocellular carcinoma (HCC). 18701503 16/132 Yujin Hoshida 9.85376777200559e-05 0.000652311134416078 405 1520.36363636364 1115 8.95837195317974e-06 117 1.45438102503473 -1.57919685990767 -1 6.95179840764143 3070 401 1115 117 133 2262 1015 3419 401 1371 3420 668 M7137 WEINMANN_ADAPTATION_TO_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEINMANN_ADAPTATION_TO_HYPOXIA_DN.html Genes most down-regulated in hypoxia tolerant NCI H460 cells (lung cancer). 15897868 65/74 Arthur Liberzon 0.000276580950129301 0.00149071371809307 195 1718 1116 2.51468843294663e-05 195 1.30771917239361 1.1142468186551 1 5.54642636020821 195 3716 544 3872 1116 594 386 2620 4082 1129 644 669 M255 PID_HIF1_TFPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF1_TFPATHWAY.html HIF-1-alpha transcription factor network 18832364 93/113 Pathway Interaction Database 0.00456858557719201 0.0124195691850823 380 1549.54545454545 1119 0.000416190955663174 360 1.28166415076686 1.3329319231512 1 3.66523755382684 377 3253 1341 3823 2489 375 881 360 2610 1119 417 670 M12827 BOQUEST_STEM_CELL_CULTURED_VS_FRESH_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_CULTURED_VS_FRESH_DN.html Genes down-regulated in cultured stromal stem cells from adipose tissue, compared to the freshly isolated cells. 15635089 35/44 Arthur Liberzon 1.76975369950139e-08 3.74117482174022e-07 1110 1400.45454545455 1119 1.60886701248899e-09 158 1.76585140549436 2.16957921098556 1 17.0294657693002 1108 1988 183 1960 2987 1827 994 504 2577 158 1119 671 M1401 BYSTROEM_CORRELATED_WITH_IL5_DN http://www.broadinstitute.org/gsea/msigdb/cards/BYSTROEM_CORRELATED_WITH_IL5_DN.html Genes whose expression in bone marrow samples correlated inversely with increased levels of serum IL5 [GeneID=3567]. 14525773 87/136 Kate Stafford 0.00587767605421477 0.0143818719418837 420 1842.36363636364 1122 0.00053576711437069 367 1.04986948232712 1.13473650721792 1 2.90198007432274 419 2830 3224 2972 4182 875 367 405 1122 2838 1032 672 M15069 ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_UP.html Genes up-regulated in A549 cells (lung carcinoma) upon infection with RSV (respiratory syncytial virus) and up-regulated by further treatment with ribavirin [PubChem=5064]. 12719586 52/82 John Newman 0.00404456384106226 0.011249464543202 895 2027.45454545455 1122 0.000368365337808248 88 1.18080686592915 1.16224034178745 1 3.45294631026512 893 4105 1000 4616 3764 423 419 1122 4467 1405 88 673 M8236 KANG_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_CISPLATIN_RESISTANCE_DN.html Genes down-regulated in gastric cancer cell lines resistant to cisplatin [PubChem=2767]. 14734480 15/15 Arthur Liberzon 0.001058845255804 0.00414751004763061 645 1552.72727272727 1124 9.63050195070972e-05 391 1.75159091253159 1.75159091253159 1 6.26105703361696 645 3540 1799 2692 405 878 391 543 3373 1690 1124 674 M1514 KANG_IMMORTALIZED_BY_TERT_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_IMMORTALIZED_BY_TERT_DN.html Down-regulated genes in the signature of adipose stromal cells (ADSC) immortalized by forced expression of telomerase (TERT) [GeneID=7015]. 15579653 126/211 Kevin Vogelsang 7.36339271523616e-09 1.67899582685578e-07 1125 1136.36363636364 1125 6.69399339989217e-10 139 1.43512057418302 1.47375478675776 1 14.589256760744 1125 1266 168 992 704 2377 2100 139 1948 208 1473 675 M17951 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP.html Top 100 probe sets contrubuting to the positive side of the 1st principal component; predominantly associated with spindle cell and pleomorphic sarcoma samples. 17464315 75/136 Nikolaos Papanikolaou 3.04261673527202e-12 1.19676258254033e-10 425 1192.27272727273 1125 2.76601521388748e-13 94 1.533107161334 1.51411495079265 1 22.8250206673585 423 1878 94 1429 247 1068 1290 1438 3898 225 1125 676 M2485 GUILLAUMOND_KLF10_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUILLAUMOND_KLF10_TARGETS_UP.html Genes up-regulated in the liver tissue from 10 week old male mice with KLF10 [GeneID=7071] compared to wild-type littermates. 20385766 69/96 Arthur Liberzon 4.36524925657255e-05 0.000341691152421599 450 1197.18181818182 1125 3.96848715858011e-06 439 1.43364106366227 1.49040371794954 1 7.4567661994218 450 752 439 1053 1456 1125 1598 2060 2169 462 1605 677 M1549 LINDVALL_IMMORTALIZED_BY_TERT_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDVALL_IMMORTALIZED_BY_TERT_UP.html Genes up-regulated in BJ cells (foreskin fibroblasts) immortalized by expression of TERT [GeneID=7015]. 12702554 102/119 John Newman 0.000828004542763865 0.00344157552593309 1120 1130.54545454545 1127 7.53014854160085e-05 40 1.18037389116905 1.22354158566791 1 4.36272734492301 1118 40 1127 1722 1994 590 1188 120 1639 1078 1820 678 M8729 AMIT_EGF_RESPONSE_480_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_480_HELA.html Genes whose expression peaked at 480 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 249/275 Leona Saunders 0.0128642435442169 0.0266410066897217 580 1409 1128 0.00117637157477582 580 1.10111259276004 1.12222869007498 1 2.60126482692953 580 3175 1319 2461 1511 642 971 600 2120 992 1128 679 M6181 DORN_ADENOVIRUS_INFECTION_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_48HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 48 h after infection with adenovirus Ad12. 15681441 20/33 Arthur Liberzon 0.00115804887536208 0.0044402848835979 3130 1456.81818181818 1129 0.000105332627773599 187 1.47990103528215 1.29897540172457 1 5.22410355523834 3126 1536 1129 824 433 2375 1027 2355 187 424 2609 680 M1769 JI_CARCINOGENESIS_BY_KRAS_AND_STK11_UP http://www.broadinstitute.org/gsea/msigdb/cards/JI_CARCINOGENESIS_BY_KRAS_AND_STK11_UP.html Cluster A: genes up-regulated in primary lung tumors driven by KRAS [GeneID=3845] activation and loss of STK11 [GeneID=6794]; also up-regulated in human squamous cell carcinoma (SCC) vs adenocarcinoma subtype of NSCLC (non-small cell lung cancer). 17676035 21/24 Jessica Robertson 0.00021215695984947 0.0012256803555563 740 1686.81818181818 1131 1.92888565422403e-05 526 2.24028125069228 -2.45095492153205 -1 9.78756737149781 738 3487 526 2821 1824 1145 1131 1129 4224 602 928 681 M512 REACTOME_DAG_AND_IP3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DAG_AND_IP3_SIGNALING.html Genes involved in DAG and IP3 signaling 32/37 Reactome 0.098357034915009 0.142275576095263 2035 1373.63636363636 1132 0.00936826571249925 277 1.07038576459678 0.891730929245015 1 1.36008142510157 2032 277 1597 388 2113 2949 1132 1787 867 1030 938 682 M1734 GAVIN_FOXP3_TARGETS_CLUSTER_P4 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P4.html Cluster P4 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 124/154 Jessica Robertson 0.000193066670156674 0.00113335031749082 2835 1677.81818181818 1134 1.75530559365309e-05 31 1.23624031237113 1.17632340332713 1 5.46405864695788 2835 629 520 31 731 2269 2329 3577 1134 356 4045 683 M53 PID_INTEGRIN3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN3_PATHWAY.html Beta3 integrin cell surface interactions 18832364 66/73 Pathway Interaction Database 3.43201745115738e-08 6.95241303410423e-07 210 1576.09090909091 1135 3.12001591336102e-09 192 1.54303484643904 1.63665339042003 1 14.2575348663003 208 2870 192 2763 2632 1123 1135 982 3551 681 1200 684 M5283 REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HOST_INTERACTIONS_OF_HIV_FACTORS.html Genes involved in Host Interactions of HIV factors 160/201 Reactome 0.0255599628274719 0.0462908087403151 590 1940.90909090909 1135 0.00235107677202473 586 0.701578533437833 -0.657709928251257 -1 1.40477142701261 586 1236 4111 1135 3967 770 820 846 2655 4393 831 685 M3206 SANCHEZ_MDM2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANCHEZ_MDM2_TARGETS.html Genes up-regulated in BJ cells (forskin fibroblasts) upon overexpression of the most abundant alternative splicing forms of MDM2 [GeneID=4193], HDM2-A and HDM2-B, off a retroviral vector. 16331255 21/48 Arthur Liberzon 4.52630513860316e-05 0.000350807229133118 1380 1331 1135 4.11490751454974e-06 86 1.50949857716024 -1.54560917337395 -1 7.82542764011565 1379 977 1135 2654 86 939 2352 2205 617 818 1479 686 M14136 FOURNIER_ACINAR_DEVELOPMENT_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_EARLY_DN.html Genes down-regulated early in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 11/12 Arthur Liberzon 0.000298252373239385 0.00158174292324708 395 1134.27272727273 1136 2.71175286153613e-05 58 1.82414278611069 1.82414278611069 1 7.66631535972133 392 3927 1394 1833 1618 449 365 58 1136 1232 73 687 M18359 RODRIGUES_DCC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_DCC_TARGETS_UP.html Genes up-regulated in HCT8/S1 cells (colon cancer) which normally lack DCC [GeneID=9423] compared to those stably expressing wild type DCC off a plasmid vector. 17334389 7/7 Arthur Liberzon 8.04860485380819e-06 8.42337359422941e-05 580 1178.09090909091 1136 8.04863400497482e-07 3 1.52159356602082 1.31605291437648 1 9.30274975819877 577 1636 4297 1545 2260 1310 37 3 141 1136 17 688 M12112 VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VART_KSHV_INFECTION_ANGIOGENIC_MARKERS_UP.html Angiogenic markers up-regulated in lymph endothelial cells upon infection with KSHV (Kaposi's sarcoma herpes virus). 17483315 186/272 Jessica Robertson 1.90385265213791e-19 1.91195415278531e-17 305 1345 1136 1.73077513830718e-20 33 1.5797751366345 1.432940435872 1 39.6308892858432 305 2765 33 2852 1455 1330 1023 1127 2645 124 1136 689 M12676 FOSTER_TOLERANT_MACROPHAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_TOLERANT_MACROPHAGE_DN.html Class NT (non-tolerizeable) genes: induced during the first LPS stimulation and induced at equal or greater degree in tolerant macrophages. 17538624 569/651 Jessica Robertson 0.00159875831794815 0.0056483078298767 185 1562.54545454545 1138 0.000159990969661573 181 1.07948068221092 1.10270823363945 1 3.64129731260475 181 1138 4523 1214 3689 576 461 1051 2129 451 1775 690 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 0.00468240683952952 0.012643569955709 825 2044.72727272727 1139 0.000469230241794988 176 1.86331295501014 1.86331295501014 1 5.30694968065876 823 3572 4512 3726 1000 763 176 2056 4392 1139 333 691 M563 REACTOME_SIGNALING_BY_EGFR_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_EGFR_IN_CANCER.html Genes involved in Signaling by EGFR in Cancer 132/143 Reactome 0.0356589006918889 0.0605867571150884 1145 1604.09090909091 1141 0.00329548606276277 6 0.923852315590011 0.893662168056534 1 1.68783396084495 1141 6 3299 907 2872 894 883 979 1737 3352 1575 692 M12621 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_UP.html Genes up-regulated in Wilm's tumor samples compared to fetal kidney. 12057921 277/342 Kevin Vogelsang 5.34388921637991e-05 0.000402283207357467 1095 1325 1141 4.85819911457316e-06 447 1.14092842898439 1.19717798593569 1 5.81288803237525 1094 1184 447 1222 2211 1106 1362 676 3094 1141 1038 693 M16701 HUANG_FOXA2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_FOXA2_TARGETS_DN.html Genes down-regulated in H358 cells (lung cancer) by inducible expression of FOXA2 [GeneID=3170] in a Tet-off system. 18593902 45/57 Leona Saunders 0.000128814688387168 0.000812796371018879 1045 1197.72727272727 1142 1.17111119436379e-05 294 1.50958545657846 1.4975278679287 1 6.99929001249809 1044 1947 540 1500 1172 1853 1581 1043 1142 294 1059 694 M2821 BIOCARTA_NTHI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NTHI_PATHWAY.html NFkB activation by Nontypeable Hemophilus influenzae 32/42 BioCarta 0.000540328683095525 0.00244755411152676 345 1195.45454545455 1143 4.91328577819358e-05 310 0.916694722544305 0.888937418520044 1 3.59174205615236 344 1995 2365 1904 320 310 479 1217 1143 1946 1127 695 M2603 VALK_AML_CLUSTER_13 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_13.html Top 40 genes from cluster 13 of acute myeloid leukemia (AML) expression profile; 91% of the samples are FAB M2 subtype, all bear the t(8;21) translocation producing the AML1-ETO fusion [GeneID=861;862]; indicate good survival. 15084694 37/50 Jessica Robertson 0.00763784897785704 0.0176217623138166 1880 1234.81818181818 1143 0.000696772298162679 161 1.3246846258803 -1.34991081713884 -1 3.48624972924305 1878 1451 1384 982 3092 255 1143 489 803 1945 161 696 M773 REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPVI_MEDIATED_ACTIVATION_CASCADE.html Genes involved in GPVI-mediated activation cascade 49/59 Reactome 0.0173870733447978 0.0338699901722846 410 1590.90909090909 1146 0.00159327518475714 186 0.963974389359835 0.931064857541386 1 2.12646215390775 408 186 1296 1146 4612 503 382 2168 3916 2385 498 697 M7559 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_15 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_15.html Amplification hot spot 15: colocalized fragile sites and cancer genes in the 6p25-p11.1 region. 16751803 18/23 Arthur Liberzon 0.000295987493271402 0.00157650536937468 865 1578.09090909091 1146 2.69115748057185e-05 22 1.32746656945424 0.834608366346978 1 5.58177721344633 862 3508 1979 2679 239 533 22 1146 2835 2535 1021 698 M19068 CERVERA_SDHB_TARGETS_2 http://www.broadinstitute.org/gsea/msigdb/cards/CERVERA_SDHB_TARGETS_2.html Genes present but differentially expressed between Hep3B cells (hepatocellular carcinoma, HCC) with RNAi knockdown of SDHB [GeneID=6390] and control cells. 18519664 159/210 Jessica Robertson 2.86671120810009e-13 1.36675524264974e-11 515 1239.45454545455 1146 2.60610109827314e-14 76 1.50249559626767 1.4183610028996 1 24.4937487666289 511 2299 76 2257 1535 1146 1117 1418 2553 161 561 699 M3062 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_2.html The 'group 2 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [GeneID=2099;2064]. 18794137 456/685 Jessica Robertson 0.00187167833677308 0.00636020284346217 1070 1141.27272727273 1148 0.000170297508219448 32 1.20911352076872 -1.25035670773292 -1 3.98505482817537 1070 1148 1299 688 2428 32 1460 1976 1360 862 231 700 M13186 MCBRYAN_PUBERTAL_BREAST_3_4WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_3_4WK_UP.html Genes up-regulated during pubertal mammary gland development between weeks 3 and 4. 17486082 310/374 Arthur Liberzon 3.27920421756357e-21 3.89594082638715e-19 30 1725.63636363636 1149 2.98109474323961e-22 28 1.48202298873007 1.55723531972789 1 40.9387868357208 2369 530 28 225 3216 1149 2297 4062 780 29 4297 701 M1548 KEEN_RESPONSE_TO_ROSIGLITAZONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KEEN_RESPONSE_TO_ROSIGLITAZONE_UP.html Genes up-regulated in aorta biopsies from mice treated with rosiglitazone [PubChem=77999]. 15054141 41/55 John Newman 0.0190515786983101 0.036418538071044 835 1547.81818181818 1150 0.00174714455136569 364 0.769689877075074 -0.781559339491457 -1 1.66147331576283 834 842 3347 1460 1150 364 1042 736 2045 3648 1558 702 M2214 CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN.html Genes down-regulated in CD4+ [GeneID=920] T lymphocytes after stimulation with prostaglandin E2 [PubChem=5280360]. 16424048 428/562 Arthur Liberzon 0.00227388233132165 0.00735820706417003 3110 1611.09090909091 1151 0.000206930543967556 443 1.15680606552453 -1.13173744391665 -1 3.70277418808764 3108 1151 693 443 2947 820 3730 1737 1475 792 826 703 M165 PID_SYNDECAN_4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_4_PATHWAY.html Syndecan-4-mediated signaling events 18832364 49/62 Pathway Interaction Database 0.00283485914362514 0.00867176614252148 1380 1295.63636363636 1153 0.000258047151653697 607 1.35156708456058 1.37282453553096 1 4.18152242879624 1376 817 715 1112 607 1873 2542 1428 1606 1023 1153 704 M19432 MCBRYAN_PUBERTAL_BREAST_4_5WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_4_5WK_UP.html Genes up-regulated during pubertal mammary gland development between week 4 and 5. 17486082 397/469 Arthur Liberzon 1.86883025082569e-28 4.90048821327625e-26 15 1225.09090909091 1153 1.69893659165973e-29 11 1.52889313832393 1.56084318644932 1 58.0638978028142 1246 1153 13 11 3156 728 1660 2014 846 16 2633 705 M12135 MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_DN.html Genes down-regulated in apoptotic tissues (neuroepithelium) after MDM4 [GeneID=4194] knockout. 15608685 144/231 Arthur Liberzon 0.00409575994921984 0.0113784502415054 1015 2047.27272727273 1153 0.000373036817826055 618 1.21780382321656 1.23966812486253 1 3.55208945866953 1012 4017 751 4550 4046 869 1153 618 3567 1307 630 706 M10748 YANG_BREAST_CANCER_ESR1_BULK_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_BULK_UP.html Genes up-regulated in bulk samples from early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative samples. 16261164 34/39 Leona Saunders 0.00104515329219707 0.0041177992814442 1685 1234.72727272727 1153 9.50591039382922e-05 33 1.21679970567123 -1.36900303857739 -1 4.35511573123932 1681 254 1448 33 2410 2887 3221 141 42 1153 312 707 M3471 AMIT_EGF_RESPONSE_120_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_120_MCF10A.html Genes whose expression peaked at 120 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 59/73 Leona Saunders 0.0012510800498964 0.00466069284570717 335 1351.54545454545 1154 0.000113799279269442 333 1.14745123206081 1.03243120722819 1 4.01429458267097 333 1906 1728 1853 440 620 464 1001 3853 1515 1154 708 M9065 KUNINGER_IGF1_VS_PDGFB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUNINGER_IGF1_VS_PDGFB_TARGETS_UP.html Genes up-regulated in C2AS12 cells (myoblast) by IGF1 [GeneID=3479] vs PDGFB [GeneID=5155]. 15475267 94/160 John Newman 0.00169626001466624 0.00590003483362169 1005 1676.54545454545 1156 0.000154324480991946 197 1.2031330485019 1.21147806255138 1 4.02422677022088 1001 3250 964 3740 1985 710 1577 197 3315 1156 547 709 M3005 NABA_COLLAGENS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_COLLAGENS.html Genes encoding collagen proteins 22159717 38/45 Alexandra Naba 2.82436131707078e-07 4.64494265385857e-06 25 1293.81818181818 1157 2.56760152696593e-08 25 1.65718684146505 1.59167447415348 1 13.2612054095148 25 2493 236 2115 1306 865 1157 1175 3418 713 729 710 M11367 MAHADEVAN_IMATINIB_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_IMATINIB_RESISTANCE_DN.html Top genes down-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] compared to the parental cell line sensitive to the drug. 17325667 26/33 Arthur Liberzon 3.58386437681708e-06 4.13590216591115e-05 995 1160.45454545455 1158 3.25806383186394e-07 191 1.90759163460895 1.94845783600451 1 12.5469337437317 992 1484 332 1202 1158 2875 1669 191 2081 414 367 711 M13354 KONDO_COLON_CANCER_HCP_WITH_H3K27ME1 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_COLON_CANCER_HCP_WITH_H3K27ME1.html Genes with high levels of histone H3 monomethylation mark at K27 (H3K27me1) in SW48 cells (colon cancer) by ChIP-chip assay on a 12K CpG array (CpG promoters only, HCP=high-CpG-density promoters). 18488029 28/37 Jessica Robertson 0.00368532950337038 0.0105550699368375 890 1438.63636363636 1158 0.000335592499934129 316 1.45055978644732 1.46269040154215 1 4.30201698924419 888 929 1852 1034 4557 1158 501 316 1399 1655 1536 712 M2562 HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_DN.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 26/48 Arthur Liberzon 0.00393555472446816 0.0110504570490718 710 2170.72727272727 1158 0.000358419334152722 260 0.927675856417307 1.01472271320011 1 2.72350151997508 708 4207 2835 4266 915 965 260 333 4278 3953 1158 713 M755 REACTOME_REGULATION_OF_INSULIN_LIKE_GROWTH_FACTOR_IGF_ACTIVITY_BY_INSULIN_LIKE_GROWTH_FACTOR_BINDING_PROTEINS_IGFBPS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_LIKE_GROWTH_FACTOR_IGF_ACTIVITY_BY_INSULIN_LIKE_GROWTH_FACTOR_BINDING_PROTEINS_IGFBPS.html Genes involved in Regulation of Insulin-like Growth Factor (IGF) Activity by Insulin-like Growth Factor Binding Proteins (IGFBPs) 14/52 Reactome 0.000391983606955279 0.0019332942788181 485 2006 1159 3.5641224164795e-05 405 1.63647654381093 1.43555947439955 1 6.66356834007443 482 3541 559 3949 4099 1210 405 1123 4402 1159 1137 714 M15346 LEE_LIVER_CANCER_E2F1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_E2F1_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by overexpression of E2F1 [GeneID=1869]. 15565109 61/118 Yujin Hoshida 0.000991548359870773 0.00394945844606755 1610 1142.90909090909 1159 9.01814124247125e-05 484 1.24347957511334 1.19518336067192 1 4.48443318089726 1609 764 620 1232 749 1010 1159 484 1815 1170 1960 715 M11079 KEGG_N_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_N_GLYCAN_BIOSYNTHESIS.html N-Glycan biosynthesis 46/50 KEGG 0.00037633727299744 0.0018717013381142 945 1511 1160 3.42183332341006e-05 98 0.988139292436879 -1.02991377233188 -1 4.04441133810916 944 826 3082 728 259 1160 2024 1962 98 3533 2005 716 M1342 FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_DN.html Genes commonly down-regulated in both non-tumorous and tumorous liver tissues of PARK2 [GeneID=5071] knockout mice. 18574468 10/15 Jessica Robertson 0.00143258436617296 0.00519738524852911 1165 1428.54545454545 1161 0.000130319825473743 53 1.49806333006389 -1.5067516666598 -1 5.13452209301175 2888 428 1161 251 1165 3589 2833 179 53 731 2436 717 M77 PID_WNT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_SIGNALING_PATHWAY.html Wnt signaling network 18832364 28/34 Pathway Interaction Database 0.00118335123013354 0.00448988569632661 3575 1533.09090909091 1163 0.000107635292637829 62 1.48665644329533 -1.60749255165295 -1 5.23718869044635 3571 288 635 62 1163 2167 2351 2949 899 1037 1742 718 M10454 MCLACHLAN_DENTAL_CARIES_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCLACHLAN_DENTAL_CARIES_UP.html Genes up-regulated in pulpal tissue extracted from carious teeth. 15869869 225/455 John Newman 7.06983445944491e-22 9.26933851349444e-20 720 1504.36363636364 1163 6.42712223585898e-23 24 1.47473112374706 1.51197922915277 1 42.1172201112195 190 1737 24 2252 4391 718 718 1163 3918 95 1342 719 M8406 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_21 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_21.html Amplification hot spot 21: colocolized fragile sites and cancer genes in the 12q13-q21 region. 16751803 7/10 Arthur Liberzon 0.00250265641785209 0.00790391091608911 1335 1605.63636363636 1164 0.000250547937342453 253 0.973785100905496 1.1799462989191 1 3.07153393587295 1333 1084 4370 2362 577 1164 253 878 854 2475 2312 720 M2462 DE_YY1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DE_YY1_TARGETS_UP.html Genes up-regulated in SaOS-2 cells (osteosarcoma) upon knockdown of YY1 [GeneID=7528] by RNAi. 18339860 14/26 Jessica Robertson 0.00020145770356209 0.00117392637137416 3040 1588.81818181818 1164 1.83160139771373e-05 183 1.52083542195297 1.38444788876887 1 6.68710287943504 3039 1034 1015 473 183 1644 2326 2676 520 1164 3403 721 M2062 NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_MALIGNAT_FIBROUS_HISTIOCYTOMA_DN.html Top 20 negative significant genes associated with malignant fibrous histiocytoma tumors. 11965276 46/48 Arthur Liberzon 0.00905042339737045 0.020216752690766 190 1874.18181818182 1164 0.000826170103937568 189 1.06267670652932 1.13136919428212 1 2.70155209291761 189 3359 1164 4111 2169 417 684 514 4419 3246 344 722 M15935 PARK_TRETINOIN_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/PARK_TRETINOIN_RESPONSE.html Genes up-regulated in U937 cells (acute promyelocytic leukemia, APL) by tretinoin (ATRA) [PubChem=444795]. 12893766 14/18 Arthur Liberzon 5.36382724299325e-05 0.000403141155842805 255 1282.45454545455 1165 4.87632547555078e-06 6 1.2680193841371 1.23672738821307 1 6.45865195521809 254 2125 1405 3078 1436 139 6 96 4157 1165 246 723 M1999 WONG_ADULT_TISSUE_STEM_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ADULT_TISSUE_STEM_MODULE.html The 'adult tissue stem' module: genes coordinately up-regulated in a compendium of adult tissue stem cells. 18397753 955/1207 Arthur Liberzon 5.53007112683937e-16 3.43446522614234e-14 865 1540.90909090909 1165 5.53007112683937e-17 36 1.18310766147199 1.19191748843305 1 23.9024709629765 865 1118 4642 1165 2202 212 1377 1851 2723 36 759 724 M454 ROSS_AML_WITH_MLL_FUSIONS http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_MLL_FUSIONS.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtypes with chimeric MLL fusions [GeneID=4297]. 15226186 88/138 Kate Stafford 0.0207277748421525 0.038931594610012 2385 1421.45454545455 1167 0.0019023346807653 57 1.08370247949433 -1.06094135133718 -1 2.29222819188902 2381 57 1477 451 1167 867 2668 3897 626 1491 554 725 M952 OLSSON_E2F3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OLSSON_E2F3_TARGETS_DN.html Genes down-regulated in the 5637 cell line (bladder cancer) after knockdown of E2F3 [GeneID=1871] by RNAi. 16909110 61/100 Arthur Liberzon 0.0167086559944056 0.0328193326232186 915 1712.63636363636 1168 0.00153062923031458 232 1.34417087661017 -1.46497622870458 -1 2.99279425990885 915 2431 1093 3658 3099 232 647 1808 3412 1168 376 726 M5823 BROWNE_HCMV_INFECTION_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_1HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 1 h time point that were not up-regulated at the previous time point, 30 min. 11711622 81/179 Arthur Liberzon 0.00495828030204545 0.0132370379104381 595 1634.36363636364 1168 0.000451771861971889 592 1.28486296719251 1.35076813350599 1 3.62101136817635 592 2842 762 2365 3360 795 814 1168 3057 1034 1189 727 M8544 GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_UP.html Up-regualted genes from the set F (Fig. 5a): specific signature shared by cells expressing AF4-MLL [GeneID=4299;4297] alone and those expressing both AF4-MLL and MLL-AF4 fusion proteins. 17130830 283/339 Arthur Liberzon 3.81359903403233e-12 1.4876187967465e-10 535 1146.36363636364 1169 3.46690821276268e-13 95 1.16511161062204 1.21000224444433 1 17.1810651460922 535 1714 95 934 1219 1126 1390 1169 3038 196 1194 728 M1834 BOQUEST_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_UP.html Genes up-regulated in freshly isolated CD31- [GeneID=5175] (stromal stem cells from adipose tissue) versus the CD31+ (non-stem) counterparts. 15635089 381/494 Arthur Liberzon 1.52141321325894e-41 2.39369012219406e-38 60 1428.72727272727 1169 1.3831029211445e-42 3 1.48037891996849 1.5520377213077 1 83.5687106734354 57 2721 3 1987 2175 1636 1169 1020 3777 15 1156 729 M940 REACTOME_TRAF6_MEDIATED_NFKB_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_NFKB_ACTIVATION.html Genes involved in TRAF6 mediated NF-kB activation 23/29 Reactome 0.00770634356973087 0.0177520457047973 540 1609.54545454545 1171 0.000703042829191132 227 1.23241332405401 1.38846500316521 1 3.23749068345198 537 2574 1956 3537 1036 910 227 782 1526 3449 1171 730 M1969 MIKKELSEN_IPS_ICP_WITH_H3K4ME3_AND_H327ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_ICP_WITH_H3K4ME3_AND_H327ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the bivalent tri-methylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 149/250 Jessica Robertson 1.73899456350085e-16 1.15606399151042e-14 695 1341.27272727273 1171 1.58090414863713e-17 53 1.36375645693208 1.27967959870929 1 28.5198266533479 694 2303 53 1695 926 912 1171 1793 3130 120 1957 731 M2160 MARSON_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_DN.html Genes down-regulated by FOXP3 [GeneID=50943] in both ex vivo and hybridoma cells. 17237765 61/84 Arthur Liberzon 0.00364992734981469 0.010466377333612 260 1313.36363636364 1171 0.0003323633538971 138 1.32004299265142 1.34213893286858 1 3.92218446165345 258 1377 1112 1761 2007 197 138 1827 3958 1171 641 732 M19043 ST_ADRENERGIC http://www.broadinstitute.org/gsea/msigdb/cards/ST_ADRENERGIC.html Adrenergic Pathway 44/55 Signaling Transduction KE 0.00577426225782821 0.0142024584976285 1725 1187.63636363636 1172 0.000526315789473684 183 0.93066945964514 1.24753949731943 1 2.58009670522162 1722 187 2342 183 1978 1172 1953 509 444 2058 516 733 M13262 SYED_ESTRADIOL_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/SYED_ESTRADIOL_RESPONSE.html Genes responsive to estradiol [PubChem=5757] both in normal and cancer ovarian cell lines. 16116479 35/47 Arthur Liberzon 0.00469076230955878 0.0126588897090437 1175 1400.45454545455 1174 0.000427344885840578 269 1.01996944138262 1.04855885609533 1 2.90414848993145 1174 269 2725 1094 696 813 340 1342 2118 3349 1485 734 M1276 XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_UP.html Genes up-regulated synergistically in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin and NSC682994 [PubChem=444795;388304]. 16140955 30/48 Kevin Vogelsang 0.00517145758536586 0.013690005497996 990 1208.36363636364 1175 0.000471241281248177 381 1.23642564644264 -1.35407844646092 -1 3.45739004764666 989 1466 1585 574 2845 1551 1373 381 470 1175 883 735 M675 REACTOME_SIGNALING_BY_ACTIVATED_POINT_MUTANTS_OF_FGFR1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ACTIVATED_POINT_MUTANTS_OF_FGFR1.html Genes involved in Signaling by activated point mutants of FGFR1 6/15 Reactome 1.83288979734414e-06 2.35088039224575e-05 3590 1832.54545454545 1176 1.83289130911415e-07 9 1.48037202328997 -1.53758199962462 -1 10.2819090707667 3587 1085 4215 1029 9 2767 4205 37 504 1544 1176 736 M8582 RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_DN.html Genes down-regulated in peripheral blood monocytes by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 364/541 Arthur Liberzon 4.78532911666586e-06 5.42950803621704e-05 2105 1421.81818181818 1176 4.35030865954933e-07 204 1.18915342918467 1.19037466337182 1 7.61056827590388 2104 523 354 316 2306 911 2088 2708 1176 204 2950 737 M1087 REACTOME_FGFR2C_LIGAND_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FGFR2C_LIGAND_BINDING_AND_ACTIVATION.html Genes involved in FGFR2c ligand binding and activation 6/16 Reactome 1.83288979734414e-06 2.35088039224575e-05 3590 1839 1177 1.83289130911415e-07 10 1.48037202328997 -1.53758199962462 -1 10.2819090707667 3588 1086 4267 1030 10 2768 4206 45 505 1547 1177 738 M15908 BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_UP.html Genes up-regulated in D-341 MED (OBR) cells (medulloblastoma) resistant to both carmustine and O6-BG [PubChem=2578;4578]. 12479369 45/57 John Newman 0.0226582677239349 0.0418743240630278 685 2116.27272727273 1177 0.00208136830151736 343 1.21130988755119 1.24354632048073 1 2.5046346618248 685 4476 1177 4644 2734 517 458 915 4504 2826 343 739 M1092 REACTOME_FGFR1_LIGAND_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FGFR1_LIGAND_BINDING_AND_ACTIVATION.html Genes involved in FGFR1 ligand binding and activation 6/18 Reactome 1.83288979734414e-06 2.35088039224575e-05 3590 1840.18181818182 1178 1.83289130911415e-07 11 1.48037202328997 -1.53758199962462 -1 10.2819090707667 3589 1087 4270 1031 11 2769 4207 46 506 1548 1178 740 M6241 VALK_AML_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_8.html Top 40 genes from cluster 8 of aculte myeloid leukemia (AML) expression profile; 69% of the samples are FAB M2 subtype. 15084694 31/38 Jessica Robertson 0.00771613697044531 0.0177572727940038 760 1502.27272727273 1178 0.000703939425895014 274 0.993298051735249 0.940940037127202 1 2.60913523107607 759 2529 3119 1856 826 1178 1412 605 857 3110 274 741 M16948 CROMER_TUMORIGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_TUMORIGENESIS_DN.html Tumorigenesis markers of head and neck squamous cell carcinoma (HNSCC): down-regulated in the 'early' tumors vs normal samples. 14676830 47/90 Arthur Liberzon 6.69838168650914e-07 9.97361563417133e-06 3925 1796 1179 6.08943975088998e-08 41 1.5362284484412 -1.50613382097695 -1 11.5282471151421 3924 177 408 41 4167 1179 2676 2579 465 156 3984 742 M2157 DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_24HR_DN.html Genes down-regulated in MCF7 cells (breast cancer) at 24 h of estradiol [PubChem=5757] treatment. 20406972 682/817 Jessica Robertson 4.89839519191335e-06 5.53120222627536e-05 445 1558 1179 4.89840598937081e-07 206 1.12768280364361 1.13859423116229 1 7.2035146926421 441 1124 4664 671 3206 997 1179 1464 1385 206 1801 743 M19391 LIU_PROSTATE_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_PROSTATE_CANCER_DN.html Genes down-regulated in prostate cancer samples. 16618720 646/808 Arthur Liberzon 4.94430866820206e-26 1.0146581266919e-23 635 1465.72727272727 1181 4.94430866820208e-27 8 1.35913021426224 1.3330670155359 1 46.8932554265728 634 1675 4276 1153 2177 602 1700 1181 2408 8 309 744 M15303 REACTOME_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOSIS.html Genes involved in Apoptosis 173/213 Reactome 0.0174765539864596 0.0340021990173493 955 1870.90909090909 1183 0.00160154088033382 239 0.856661009032227 -0.845545152153411 -1 1.88754945557131 953 589 3522 639 4496 239 1275 1183 3443 3923 318 745 M1124 MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_TGFB1_TARGETS_UP.html Pubertal genes up-regulated by TGFB1 [GeneID=7040]. 17486082 292/366 Arthur Liberzon 0.000191329995250889 0.00112462961093922 1185 1357.81818181818 1184 1.73951488089579e-05 453 1.11356244518507 1.16056088284015 1 4.92742960313168 639 1183 519 1383 3060 1184 1312 1345 2851 453 1007 746 M2699 BIOCARTA_SODD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SODD_PATHWAY.html SODD/TNFR1 Signaling Pathway 14/15 BioCarta 0.00577426225782821 0.0142024584976285 1300 1142.72727272727 1186 0.000526315789473684 56 1.30288529136257 -1.37269317659778 -1 3.61203368546564 1298 1019 1824 101 2867 1186 1256 1380 56 1157 426 747 M17572 SMID_BREAST_CANCER_LUMINAL_B_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_B_DN.html Genes down-regulated in the luminal B subtype of breast cancer. 18451135 617/967 Jessica Robertson 5.94989504870602e-36 3.87516333758968e-33 425 1793.36363636364 1186 5.94989504870598e-37 1 1.48242079946336 1.46062052125177 1 72.0965718801136 425 2208 4551 2241 3245 780 1073 544 3473 1 1186 748 M3837 WEST_ADRENOCORTICAL_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_DN.html Down-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 681/905 Jessica Robertson 6.27191860202698e-12 2.34948061917201e-10 810 1482.36363636364 1186 6.27191860204468e-13 59 1.24496915272666 1.26023053402163 1 17.9878931707865 810 1670 4572 1186 1084 66 1193 1970 2807 59 889 749 M10150 LI_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_CISPLATIN_RESISTANCE_DN.html Genes consistently down-regulated in ACRP cells (ovarian cancer, resistant to cisplatin [PubChem=2767]) compared to the parental sensitive A2780 cells, regardless of cisplatin exposure. 17072341 39/61 Arthur Liberzon 3.04237127291448e-06 3.61712655117288e-05 1120 1335.36363636364 1187 2.76579589109617e-07 321 1.58316122015526 1.44431284532979 1 10.5512907140601 1119 862 321 1187 1090 1485 1790 1340 3381 483 1631 750 M615 KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION.html Intestinal immune network for IgA production 26/53 KEGG 0.00875478937895403 0.0197432421732743 4540 1972.72727272727 1188 0.000799074905896948 340 1.60607545323379 -1.30652903760984 -1 4.10784778143712 4536 340 827 469 4659 2593 1783 1110 1037 1188 3158 751 M1271 CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_DN http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_DN.html Genes down-regulated in neuroblastoma xenografts: resistant vs those that reverted to be sensitive to the topoisomerase inhibitor irinotecan [PubChem=3750]. 16501609 6/9 Arthur Liberzon 0.000141678615967982 0.000874775187163762 1190 1534.63636363636 1188 1.41687649552174e-05 129 1.46315269140579 -1.9218469763508 -1 6.71392985286998 1188 1643 4411 2625 162 341 154 787 3144 2297 129 752 M12746 KOYAMA_SEMA3B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOYAMA_SEMA3B_TARGETS_UP.html Genes up-regulated in NCI-H1299 cells (large cell neuroendocrine carcinoma) stably expressing SEMA3B [GeneID=7869]. 18985860 347/474 Jessica Robertson 0.000415414388091204 0.00200500415506367 1145 1328.72727272727 1188 3.77720772127154e-05 361 1.18750755750568 1.15934340327093 1 4.80719809413781 1142 2236 706 1188 2477 565 1353 2083 1350 361 1155 753 M7602 ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_VS_CD2_DN.html Genes down-regulated in CD-1 compared to CD-2 cluster of multiple myeloma samples. 16728703 70/81 Kevin Vogelsang 0.00268314782786438 0.00833736520574052 2205 1497.90909090909 1190 0.000244220529755186 251 1.31547313717134 1.29069930957994 1 4.10356257204133 2204 746 1190 281 4117 1977 1806 251 798 1152 1955 754 M1824 MATZUK_LUTEAL_GENES http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_LUTEAL_GENES.html Luteal genes, based on mouse models with female fertility defects. 18989307 7/34 Jessica Robertson 0.0118921936775173 0.0249916091531086 2640 1649.27272727273 1190 0.00119563180963789 247 1.29086379274662 1.19972874685697 1 3.10331393839556 2636 447 4569 1233 1007 1408 1190 1161 247 1140 3104 755 M9210 LINDSTEDT_DENDRITIC_CELL_MATURATION_C http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_C.html Maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli: genes up-regulated only at 48 hr after the stimulation (cluster C). 12356685 94/118 Arthur Liberzon 0.0202175313629221 0.0381706992131969 1540 1258.54545454545 1191 0.0018550683874809 49 1.21381582833789 1.18525285660709 1 2.5830671324947 1538 49 926 321 3629 1464 1673 978 1191 842 1233 756 M2611 ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF.html Class I of genes transiently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 645/861 Yaara Zwang 0.000409102323684804 0.00198863333449256 325 1372.54545454545 1191 4.09177657324402e-05 322 1.11365937119384 1.09742893721784 1 4.51419358027639 322 1676 4717 1191 1599 476 773 711 1902 369 1362 757 M2402 KOHOUTEK_CCNT2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KOHOUTEK_CCNT2_TARGETS.html Genes down-regulated in E14 ES (embryonic stem) cells upon knockdown of CYCT2 [GeneID=905] by RNAi. 19364821 64/179 Arthur Liberzon 0.00224646694799918 0.00730020588604876 1195 1337.27272727273 1193 0.000204433104365345 234 1.36594718759871 1.38656094857405 1 4.37926912925582 1193 3293 1262 2807 1020 737 437 234 1710 1521 496 758 M319 RAY_TARGETS_OF_P210_BCR_ABL_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TARGETS_OF_P210_BCR_ABL_FUSION_DN.html Genes down-regulated in HL-60 cells (acute myeloid leukemia, AML) by expression of p210 BCR-ABL [GeneID=613;25] fusion protein. 15155749 18/21 Arthur Liberzon 0.000348078525628186 0.00176849369318088 2195 1242.54545454545 1194 3.16485099952892e-05 81 1.42054606972749 -1.48897306279256 -1 5.86678660550528 2194 1557 1671 790 246 1869 2625 81 527 1194 914 759 M746 REACTOME_SIGNALING_BY_GPCR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_GPCR.html Genes involved in Signaling by GPCR 358/1438 Reactome 1.21728099885407e-15 7.09329174640889e-14 1395 1448.90909090909 1195 1.10661908986734e-16 59 1.35404259744606 1.37927143731051 1 26.7159219971051 1395 1163 59 1195 4437 322 1550 2601 2113 108 995 760 M1171 RASHI_NFKB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_NFKB1_TARGETS.html Known and putative targets of NFKB1 [GeneID=4790] identified among the ATM [GeneID=472] dependent, late responders to ionizing radiation. 16314843 28/29 Arthur Liberzon 0.0220681472390306 0.0410570181191267 500 1766.54545454545 1195 0.00202660652503982 434 1.45181658683072 1.15998690185815 1 3.02060187549733 497 2543 1195 3357 2698 610 434 4060 772 795 2471 761 M5218 SILIGAN_BOUND_BY_EWS_FLT1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/SILIGAN_BOUND_BY_EWS_FLT1_FUSION.html Genes bound by EWSR1-FLT1 [GeneID=2130;2321] fusion but whose expression did not change in STA-ET-7.2 cells (Ewing's sarcoma) after knockdown of EWSR1-FLT1 by RNAi. 15735734 62/89 Leona Saunders 0.0257538237468311 0.0465918160540602 745 1367.81818181818 1195 0.00236912187969634 424 1.36170603425542 1.44949807034028 1 2.72089345110466 745 1897 1160 1227 4650 583 474 1274 1195 1417 424 762 M17377 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_LACTO_AND_NEOLACTO_SERIES.html Glycosphingolipid biosynthesis - lacto and neolacto series 14/26 KEGG 9.37446519483579e-05 0.000625848312865982 2080 1225.63636363636 1196 8.52260425084504e-06 130 1.48446393103115 -1.443219815982 -1 7.13565651438344 2076 2103 885 438 130 1928 1415 1196 526 816 1969 763 M895 REACTOME_ASSEMBLY_OF_THE_PRE_REPLICATIVE_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASSEMBLY_OF_THE_PRE_REPLICATIVE_COMPLEX.html Genes involved in Assembly of the pre-replicative complex 66/76 Reactome 0.00190890907450306 0.00644495767643381 70 1731.90909090909 1196 0.000173687947538108 70 0.643093186682459 -0.640301601222655 -1 2.11394035467063 70 1355 4012 2163 1196 380 388 1193 2809 4318 1167 764 M2523 ZHAN_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_DN.html Genes most significantly down-regulated in multiple myeloma samples, compared to normal bone marrow plasma cells. 11861292 63/90 Kevin Vogelsang 4.05669776518634e-10 1.17470021175948e-08 215 1309.81818181818 1196 3.68790705994033e-11 129 1.67266630754194 1.61876387070139 1 19.9033413230119 215 1898 129 2341 2421 856 1196 1776 2951 432 193 765 M12486 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_RUNX1 http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_RUNX1.html Genes whose expression is coregulated with that of RUNX1 [GeneID=861] in hematopoietic stem cells (HSC). 15711547 15/22 Jean Junior 0.0706695075956277 0.107600024468181 1190 1594 1197 0.0066406575245558 209 1.31512120128799 1.21034087521421 1 1.91048248607391 1189 400 1197 377 4228 3025 1586 2873 209 899 1551 766 M768 REN_ALVEOLAR_RHABDOMYOSARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/REN_ALVEOLAR_RHABDOMYOSARCOMA_UP.html Genes commonly up-regulated in human alveolar rhabdomyosarcoma (ARMS) and its mouse model overexpressing PAX3-FOXO1 [GeneID=5077;2308] fusion. 18701482 121/192 Jessica Robertson 0.000406567722260763 0.00197835015368124 1605 1273.54545454545 1197 3.69675342589109e-05 335 1.29601278169212 1.23385141044237 1 5.25775499856539 1603 643 560 335 1488 2762 2487 1707 1197 617 610 767 M13748 REACTOME_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCONEOGENESIS.html Genes involved in Gluconeogenesis 32/48 Reactome 0.000970739618976955 0.00387967061945066 1200 1606.36363636364 1198 8.82880198218971e-05 228 0.940959020758592 -0.989886122263355 -1 3.40434197483445 1198 2526 3258 2903 394 228 398 1417 1040 3548 760 768 M6891 HOUSTIS_ROS http://www.broadinstitute.org/gsea/msigdb/cards/HOUSTIS_ROS.html Genes known to modulate ROS or whose expression changes in response to ROS 16612386 39/53 Nick Houstis 0.0002510719911081 0.00138603485149735 1200 1289.54545454545 1199 2.2827331721323e-05 202 1.10937235565596 1.07355023066784 1 4.75779834098981 1199 228 1162 701 202 2010 2230 2317 768 1452 1916 769 M18320 WINNEPENNINCKX_MELANOMA_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WINNEPENNINCKX_MELANOMA_METASTASIS_DN.html Genes from the 254-gene classifier which were down-regulated in melanoma patients with a reported distant metastasis within 4 years. 16595783 32/51 Arthur Liberzon 0.00015461903192744 0.000942896422089813 355 1144.90909090909 1199 1.40572636214039e-05 300 1.70631063511297 1.91065849778959 1 7.74633544187104 1954 1467 656 1199 353 1906 2624 353 450 300 1332 770 M999 HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_DN.html Genes down-regulated in hematopoietic progenitor cells (HPC) of T lymphocyte and NK (natural killer) lineage. 15331438 51/109 Kevin Vogelsang 1.58652263988404e-05 0.000150671767811925 870 1817.36363636364 1200 1.44230371014045e-06 386 1.42157807658685 1.4309703781443 1 8.15255894903395 869 811 386 1200 4635 2662 858 1717 3076 747 3030 771 M8244 BROCKE_APOPTOSIS_REVERSED_BY_IL6 http://www.broadinstitute.org/gsea/msigdb/cards/BROCKE_APOPTOSIS_REVERSED_BY_IL6.html Genes changed in INA-6 cells (multiple myeloma, MM) by re-addition of IL6 [GeneID=3569] after its initial withdrawal for 12h. 12969979 223/330 Kate Stafford 0.0067774191740066 0.0160589450307787 1360 1333.81818181818 1201 0.000618035317417351 429 1.19129414129313 1.21015454518691 1 3.20728404723961 1359 1735 804 761 2913 1201 1907 1891 1027 645 429 772 M649 REACTOME_PHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHOLIPID_METABOLISM.html Genes involved in Phospholipid metabolism 180/208 Reactome 0.00577426225782821 0.0142024584976285 2035 1253.54545454545 1202 0.000526315789473684 42 1.04960878145271 -1.06120070497509 -1 2.90984593703708 2031 579 2683 42 1719 405 2622 1202 234 1744 528 773 M685 REACTOME_HS_GAG_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HS_GAG_BIOSYNTHESIS.html Genes involved in HS-GAG biosynthesis 24/30 Reactome 0.0218400604773144 0.0407129089466525 685 1514.45454545455 1202 0.00200544866560236 430 1.3799202870571 1.13295152945715 1 2.87858015224273 682 1495 1318 1189 3833 1202 430 2908 588 2109 905 774 M1154 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_DN.html Apoptotic genes dependent on MAPK1 [GeneID=5594] and down-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 8/8 Arthur Liberzon 0.0046303182454771 0.0125364889794405 255 2015.27272727273 1202 0.000463999456486939 252 0.998115269328612 0.998115269328612 1 2.84824086352497 252 3947 4353 3553 714 520 401 392 4207 2627 1202 775 M1478 LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS http://www.broadinstitute.org/gsea/msigdb/cards/LIAN_NEUTROPHIL_GRANULE_CONSTITUENTS.html Granule constituents expressed during mouse promyelocytic cell line differentiation to neutrophils. 11468144 23/68 Kevin Vogelsang 0.000295555561579099 0.00157629632842186 4690 2130.45454545455 1203 2.68722977271475e-05 169 1.60533085626881 -1.44276688193798 -1 6.75031142672363 4686 319 545 246 1203 4592 4090 2770 169 720 4095 776 M12868 KEGG_PATHWAYS_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PATHWAYS_IN_CANCER.html Pathways in cancer 338/425 KEGG 0.0372256406945507 0.0628191004927706 1205 1546.72727272727 1204 0.00344280579827346 412 1.07167872614984 1.08529166010285 1 1.93265336418339 1204 1704 1024 1663 3241 412 1091 2219 2300 1073 1083 777 M7876 CHEBOTAEV_GR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEBOTAEV_GR_TARGETS_DN.html Genes down-regulated in follicular epithelial stem cells after transgenic expression of GR [GeneID=2908] under control of the keratin5 (K5) [GeneID=3852] promoter. 17146443 176/216 Leona Saunders 3.73604006439423e-10 1.08852525332968e-08 675 1337.27272727273 1208 3.39640005911697e-11 128 1.31104409939615 1.23032694129579 1 15.665407548299 671 2291 128 1458 2086 1208 1378 1135 2746 534 1075 778 M1336 RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_UP http://www.broadinstitute.org/gsea/msigdb/cards/RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_UP.html Angiogenic genes up-regulated in hepatocytes after knockout of VHL and HIF2A [GeneID=7428;2034]. 18490920 7/13 Jessica Robertson 5.87282443876088e-06 6.3870348734911e-05 860 1844.18181818182 1208 5.8728399593487e-07 2 1.71442249565498 -1.71442249565498 -1 10.790868138143 856 3125 4438 3063 3722 1109 189 2 1208 2478 96 779 M9326 VALK_AML_CLUSTER_9 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_9.html Top 40 genes from cluster 9 of acute myeloid leukemia (AML) expression profile; 87% of the samples are FAB M4 or M5 subtype, all have inv(16) inversion producing the CBFB-MYH11 fusion [GeneID=865;4629]; indicate good survival. 15084694 37/49 Jessica Robertson 0.00277433961702816 0.00855027668618352 715 1750.09090909091 1208 0.000252531311328434 106 1.74025838915067 2.12819816300029 1 5.40009913287159 712 3385 1208 3502 4181 290 106 679 2033 2700 455 780 M11857 RODRIGUES_NTN1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_NTN1_TARGETS_DN.html Genes down-regulated in HCT8/S11 cells (colon cancer) engineered to stably express NTN1 [GeneID=1630] off a plasmid vector. 17334389 222/305 Arthur Liberzon 0.000699826989380583 0.00301660583550352 2485 1966.09090909091 1209 6.3640882341915e-05 398 1.18838558534627 1.26302563280759 1 4.49440764147482 2483 1209 1104 488 2653 4389 3592 1145 1024 398 3142 781 M14973 SENESE_HDAC1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC1 [GeneID=3065] by RNAi. 17470557 590/714 Leona Saunders 0.0375653340537942 0.0632366735049933 865 1629.90909090909 1209 0.00382158853890613 384 1.11317833086489 1.07527921062982 1 2.002691290229 384 493 4307 865 3208 1347 1209 1030 2315 861 1910 782 M970 REACTOME_ACTIVATION_OF_IRF3_IRF7_MEDIATED_BY_TBK1_IKK_EPSILON http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_IRF3_IRF7_MEDIATED_BY_TBK1_IKK_EPSILON.html Genes involved in Activation of IRF3/IRF7 mediated by TBK1/IKK epsilon 18/31 Reactome 0.00423206046629018 0.0116746495621798 830 1767.27272727273 1210 0.000385474865513782 156 0.905072632749579 0.982329321035849 1 2.62473096212938 830 3060 2588 2677 905 431 156 1210 3542 3070 971 783 M276 PID_FGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FGF_PATHWAY.html FGF signaling pathway 18832364 68/84 Pathway Interaction Database 0.0451715308933721 0.0739028165742517 1325 1363.36363636364 1211 0.00419332591059354 102 1.10579962186474 1.25495387963556 1 1.87709616963501 1322 102 1278 413 3672 1211 654 3145 592 1704 904 784 M2920 KEGG_LINOLEIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LINOLEIC_ACID_METABOLISM.html Linoleic acid metabolism 18/62 KEGG 0.0307567604863292 0.0536878363518764 1030 1857.45454545455 1213 0.00283594177289843 488 2.03071170469295 -2.19221511216499 -1 3.87011937122178 1028 4226 1229 3514 4511 1051 525 1083 1213 1564 488 785 M553 REACTOME_SIGNALING_BY_ERBB2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ERBB2.html Genes involved in Signaling by ERBB2 118/128 Reactome 0.0248091478736799 0.0452469775748721 1045 1435.27272727273 1214 0.00228121963361853 433 0.955187733398495 0.912237079020201 1 1.92680854704738 1043 651 3017 433 2837 804 467 1214 1280 2659 1383 786 M823 REACTOME_TRANSPORT_OF_INORGANIC_CATIONS_ANIONS_AND_AMINO_ACIDS_OLIGOPEPTIDES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_INORGANIC_CATIONS_ANIONS_AND_AMINO_ACIDS_OLIGOPEPTIDES.html Genes involved in Transport of inorganic cations/anions and amino acids/oligopeptides 62/101 Reactome 9.26169581790977e-07 1.30104774584923e-05 1815 1194.81818181818 1214 8.41972701541631e-08 113 1.42447399712724 1.43418506378574 1 10.4428569912392 1811 113 279 227 1214 2596 2594 1387 670 334 1918 787 M12636 RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP.html Genes up-regulated in peripheral blood monocytes by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 407/507 Arthur Liberzon 0.000271225906702338 0.00146978906961543 1000 1025.27272727273 1215 2.4659940947812e-05 260 1.13425649461595 1.16201206667279 1 4.82115428249396 996 515 543 260 1377 1309 1575 1420 1215 429 1639 788 M13713 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_13.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 13. 12554760 193/223 Arthur Liberzon 0.00154773512957697 0.00550513173444108 65 1719.81818181818 1215 0.000140802278145679 63 0.769684981924738 -0.744110992304072 -1 2.60914425825772 63 1215 4091 481 4143 601 592 1488 330 4259 1655 789 M2434 GUO_TARGETS_OF_IRS1_AND_IRS2 http://www.broadinstitute.org/gsea/msigdb/cards/GUO_TARGETS_OF_IRS1_AND_IRS2.html Transcripts dependent upon IRS1 and IRS2 [GeneID=3667, 8660] for normal expression in liver. 19596788 130/168 Arthur Liberzon 0.0455209641860192 0.0743713918165492 1140 1544.81818181818 1215 0.00422646141020648 814 1.12530619870215 1.07756321049444 1 1.90557555640376 1139 1798 1583 814 3390 1200 1154 1073 1549 1215 2078 790 M684 REACTOME_SYNTHESIS_OF_PC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PC.html Genes involved in Synthesis of PC 14/19 Reactome 0.00577426225782821 0.0142024584976285 4200 2209.63636363636 1216 0.000526315789473684 20 1.49711965758786 -1.42919701817531 -1 4.15053207339641 4198 1021 1216 20 4119 3770 4359 1080 25 573 3925 791 M4047 BIOCARTA_NKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NKT_PATHWAY.html Selective expression of chemokine receptors during T-cell polarization 9/30 BioCarta 0.00143770279410864 0.00521045958612891 1220 1373.27272727273 1217 0.000143863378712746 267 1.25330490051048 1.39432148512008 1 4.29355801042457 1217 1065 4196 1716 472 1136 1320 627 267 1442 1648 792 M17749 DORN_ADENOVIRUS_INFECTION_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_12HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 12 h after infection with adenovirus Ad12. 15681441 62/84 Arthur Liberzon 0.00930783395302441 0.0206255440972881 295 1729.36363636364 1217 0.000849768063095806 291 1.1528622120149 1.08579250619458 1 2.91579225494469 291 4094 1368 3905 886 557 351 1595 3925 1217 834 793 M6905 JAATINEN_HEMATOPOIETIC_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAATINEN_HEMATOPOIETIC_STEM_CELL_DN.html Genes down-regulated in CD133+ [GeneID=8842] cells (hematopoietic stem cells, HSC) compared to the CD133- cells. 16210406 206/410 Arthur Liberzon 6.96913518733029e-20 7.4759813827725e-18 860 1366.81818181818 1218 6.33557744302753e-21 32 1.52691597020755 1.48421495406494 1 39.2391984961567 860 1218 32 732 3963 1677 1695 699 2876 55 1228 794 M2102 STAMBOLSKY_TARGETS_OF_MUTATED_TP53_DN http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_TARGETS_OF_MUTATED_TP53_DN.html Genes repressed in SKBR3 cells (breast cancer) by mutated TP53 [GeneID=7157]. 20227041 86/125 Arthur Liberzon 0.0112850049669203 0.0239286718076657 465 1646.81818181818 1218 0.00103121009891954 463 0.923219396093655 -0.901914859288076 -1 2.24559321063406 463 1848 3071 2125 957 493 1218 1104 2696 3296 844 795 M2104 STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_DN http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_RESPONSE_TO_VITAMIN_D3_DN.html Genes repressed in SKBR3 cells (breast cancer) by 25-hydroxyvitamin D3 [PubChem=1593]. 20227041 52/61 Arthur Liberzon 0.00166084592289673 0.00580251129242974 425 1690.63636363636 1218 0.000151100097456466 422 1.44046772181723 1.35535029418025 1 4.83372800303185 422 3739 665 2424 2264 1506 1127 1218 3759 790 683 796 M812 REACTOME_GPCR_DOWNSTREAM_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GPCR_DOWNSTREAM_SIGNALING.html Genes involved in GPCR downstream signaling 266/1312 Reactome 4.86879926932967e-15 2.76154050948597e-13 1020 1379.81818181818 1220 4.42618115393607e-16 61 1.39386917337797 1.41813147461503 1 26.2670860180709 1017 2258 61 2251 3387 247 1305 1220 2417 183 832 797 M19062 DODD_NASOPHARYNGEAL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DODD_NASOPHARYNGEAL_CARCINOMA_UP.html Genes up-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. 17119049 1758/2621 Arthur Liberzon 1.25551040413132e-26 2.82190909880945e-24 2940 1712.27272727273 1220 1.25551040413133e-27 2 1.22856289781659 -1.24938159879398 -1 43.4129244630559 2936 459 4318 2 1955 254 3871 3280 1220 7 533 798 M12299 SEMENZA_HIF1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SEMENZA_HIF1_TARGETS.html Genes that are transcriptionally regulated by HIF1A [GeneID=3091]. 11516994 47/68 John Newman 0.00380288657533652 0.0107740844151191 995 2013.72727272727 1221 0.000346316012698783 326 1.42255066700903 1.48889921052451 1 4.19990778234097 995 3758 1019 3792 1221 2485 3026 326 3827 1151 551 799 M1960 MIKKELSEN_MCV6_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K4 (H3K4me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 186/271 Jessica Robertson 0.000445446662314294 0.00211307361419444 1935 1501.90909090909 1221 4.05033527307748e-05 444 1.21514326488033 -1.19800901272893 -1 4.87750267523141 1932 1221 564 920 2173 541 2731 3425 990 444 1580 800 M2840 CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_UP.html Genes up-regulated in luminal-like breast cancer cell lines compared to the basal-like ones. 16288205 502/589 Arthur Liberzon 0.00382924434489334 0.010829259022107 2185 1407.90909090909 1222 0.000383585879232835 40 1.07737284756804 -1.10034559272008 -1 3.17720032802118 2184 502 4292 40 1552 145 2976 1222 842 1641 91 801 M1238 DAWSON_METHYLATED_IN_LYMPHOMA_TCL1 http://www.broadinstitute.org/gsea/msigdb/cards/DAWSON_METHYLATED_IN_LYMPHOMA_TCL1.html Genes hypermethylated in at least one of the lymphoma tumors of transgenic mice overexpressing TCL1 [GeneID=8115] in germinal center B lymphocytes. 17260020 65/94 Arthur Liberzon 0.00552621482130045 0.0142024584976285 765 1386.45454545455 1222 0.000503649565568212 745 1.3015967305235 1.25066205264552 1 3.60846125928757 1389 762 773 745 761 1222 1662 3037 1565 1130 2205 802 M26 PID_NFKAPPAB_ATYPICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFKAPPAB_ATYPICAL_PATHWAY.html Atypical NF-kappaB pathway 18832364 27/30 Pathway Interaction Database 0.000818522007587231 0.0034159362297186 455 1630.81818181818 1223 7.44387910807187e-05 256 0.765820626015545 0.885532882073316 1 2.83421018051908 455 2031 2977 2759 370 761 703 256 3592 2812 1223 803 M2222 ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_DN.html Genes down-regulated in K562 cells (lymphoblast) by MYC [GeneID=4609] in the presence of CKN1B [GeneID=1027]. 18838534 140/188 Arthur Liberzon 0.00661283624346816 0.0157383759234373 2425 1644.18181818182 1223 0.000602981580577443 340 1.17727278937535 -1.16625209724442 -1 3.18500315298148 2421 615 855 340 1223 799 3816 2969 3249 553 1246 804 M1533 CUI_TCF21_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_2_DN.html All significantly down-regulated genes in kidney glomeruli isolated from TCF21 [Gene ID=6943] knockout mice. 16207825 1137/1393 John Newman 1.70313644079385e-06 2.22066408854889e-05 565 1569.36363636364 1225 1.70313774609844e-07 185 1.13962580584275 1.13019408580238 1 7.95755455181448 565 1112 4492 674 1995 1345 1225 1201 2437 185 2032 805 M13008 DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_DN.html Genes exclusively down-regulated in fibroblasts expressing the TTD mutant form of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 144/151 Arthur Liberzon 0.0140169018551579 0.0286158203963431 245 1244.09090909091 1227 0.00128245571058511 245 1.10048037988014 1.05759606796161 1 2.54848938679493 245 1248 1766 2135 1227 366 335 948 2930 1463 1022 806 M16154 NICK_RESPONSE_TO_PROC_TREATMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/NICK_RESPONSE_TO_PROC_TREATMENT_UP.html Genes up-regulated in neutrophils upon treatment with activated protein C (PROC) [GeneID=5624] of pulmonary inflammation induced by bacterial lipopolysaccharide (LPS). 15339848 5/6 Arthur Liberzon 6.48532172757405e-05 0.000467339214567168 2740 1726.09090909091 1228 6.48551100263892e-06 26 0.797552344968502 -0.757951287048459 -1 3.98548949299889 2739 2183 4598 564 110 1228 26 1027 136 4697 1679 807 M2113 KIM_ALL_DISORDERS_DURATION_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_DURATION_CORR_DN.html Genes whose expression in brain significantly and negatively correlated with the duration of all psychiatric disorders studied. 18762803 180/208 Jessica Robertson 0.030166856781429 0.0527947957020188 450 1587.63636363636 1228 0.00278078457966472 446 0.88633676446649 -0.756482174256069 -1 1.69880469062452 449 1228 3971 608 1320 446 991 1924 1095 4085 1347 808 M9483 SUNG_METASTASIS_STROMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SUNG_METASTASIS_STROMA_UP.html Genes up-regulated in metastatic vs non-metastatic stromal cells originated from either bone or prostate tissues. 19047182 174/236 Jessica Robertson 6.12108333953438e-07 9.23051545131063e-06 1060 1519.81818181818 1230 5.56462276600959e-08 262 1.26692961189898 1.24348712022028 1 9.57126803063603 1060 1230 262 813 1028 2573 2277 2431 2654 283 2107 809 M11262 MORI_IMMATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_IMMATURE_B_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature based on expression profiling of lymphomas from the Emu-myc transgenic mice: the immature B stage. 18922927 68/84 Jessica Robertson 0.0594683531574979 0.0931907791843925 4265 1961.09090909091 1230 0.00555813082954332 116 1.18131295263122 -1.31472882661203 -1 1.82676699025632 4261 116 1230 343 2053 3320 3963 1195 3017 884 1190 810 M2443 PLASARI_TGFB1_TARGETS_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_1HR_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 1 h. 19752192 44/46 Arthur Liberzon 0.00773083963177094 0.0177739961223967 275 1132.81818181818 1230 0.000705285485960326 228 1.19691219642192 1.24122633670019 1 3.14326401461596 273 1433 1250 2864 1542 260 228 485 2588 1230 308 811 M2196 GABRIELY_MIR21_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GABRIELY_MIR21_TARGETS.html Genes significantly de-regulated (p < 0.05) by MIR21 [GeneID=406991] in A172 cells (glioma). 18591254 411/461 Arthur Liberzon 0.0188567149198866 0.0361362949337657 315 1428.54545454545 1232 0.00172911879024738 312 1.00044550356893 0.996849820088465 1 2.16469270369008 312 519 3227 836 1612 1232 633 731 1931 3207 1474 812 M19620 COLLER_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/COLLER_MYC_TARGETS_DN.html Genes down-regulated in 293T (transformed fetal renal cell) upon expression of MYC [GeneID=4609]. 10737792 29/34 Yujin Hoshida 0.001465190272912 0.00527129893559473 60 1789.45454545455 1233 0.00013328790854233 60 1.239979164018 1.239979164018 1 4.23852522935876 60 3444 958 3686 1270 871 1012 1233 4565 2104 481 813 M13438 STEARMAN_TUMOR_FIELD_EFFECT_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEARMAN_TUMOR_FIELD_EFFECT_UP.html Up-regulated genes in the 'Field Effect' signature of normal lung tissue adjacent to the tumor. 18172294 33/69 Jessica Robertson 1.10008813197238e-05 0.000111447773706502 1380 968.727272727273 1233 1.00008512081114e-06 29 1.32432617700818 1.61886356951279 1 7.85506695193286 1053 262 682 84 29 1233 1717 1377 1538 1376 1305 814 M215 LIU_VAV3_PROSTATE_CARCINOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_VAV3_PROSTATE_CARCINOGENESIS_UP.html Selected genes up-regulated in prostate tumors developed by transgenic mice overexpressing VAV3 [GeneID=10451] in prostate epithelium. 18676865 118/208 Jessica Robertson 2.36565364541323e-11 8.03301093982046e-10 1235 1551.81818181818 1233 2.15059422312605e-12 110 1.49942818027492 1.57053234655733 1 20.4632091404384 1233 2804 110 3087 680 930 1756 1984 2964 393 1129 815 M10320 REACTOME_BIOLOGICAL_OXIDATIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BIOLOGICAL_OXIDATIONS.html Genes involved in Biological oxidations 79/219 Reactome 1.19397766430384e-06 1.63349987696061e-05 2315 1483.45454545455 1234 1.08543482936041e-07 73 1.33083829313971 -1.35473267018593 -1 9.55905390188877 2311 73 286 1166 1712 521 2541 4575 1697 202 1234 816 M12518 BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BACOLOD_RESISTANCE_TO_ALKYLATING_AGENTS_DN.html Genes down-regulated in D-341 MED (OBR) cells (medulloblastoma) resistant to both carmustine and O6-BG [PubChem=2578;4578]. 12479369 109/140 John Newman 0.00338672558007783 0.00992456922039141 330 1432.90909090909 1234 0.000308359130875977 296 1.2252261445961 1.18256254443597 1 3.68289253611842 327 2351 2086 2487 1234 984 1170 296 2144 1682 1001 817 M11951 HINATA_NFKB_TARGETS_KERATINOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HINATA_NFKB_TARGETS_KERATINOCYTE_UP.html Genes up-regulated in primary keratinocytes by expression of p50 (NFKB1) and p65 (RELA) [GeneID=4790;5970] components of NFKB. 12673201 122/152 Arthur Liberzon 2.48293630561382e-12 9.93174522245529e-11 880 1219.27272727273 1237 2.25721482328783e-13 92 1.54086146192648 1.40513206985432 1 23.1277068018665 878 1269 92 1697 2779 859 1237 190 2424 104 1883 818 M11948 WEINMANN_ADAPTATION_TO_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEINMANN_ADAPTATION_TO_HYPOXIA_UP.html Genes most up-regulated in hypoxia tolerant NCI H460 cells (lung cancer). 15897868 56/64 Arthur Liberzon 0.00119608532520503 0.00452365603763441 295 1774.90909090909 1238 0.000108794191132809 294 1.29071577273888 1.14005247005631 1 4.54061282758591 294 3734 782 3444 427 947 864 2159 4026 1609 1238 819 M1488 HANSON_HRAS_SIGNALING_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/HANSON_HRAS_SIGNALING_VIA_NFKB.html Genes changed by expression of activated form of HRas[GeneID=3265] in MEF cells (embryonic fibroblast) with or without p65/c-Rel complex [GeneID=5970;5966]. 15492243 27/36 Kevin Vogelsang 0.000316294446797387 0.00165131475363624 2110 1606.63636363636 1239 2.87581754244743e-05 338 1.54709818437316 1.27916697624769 1 6.45856825540285 2110 921 657 1204 3814 1633 828 1239 2838 338 2091 820 M7732 RAGHAVACHARI_PLATELET_SPECIFIC_GENES http://www.broadinstitute.org/gsea/msigdb/cards/RAGHAVACHARI_PLATELET_SPECIFIC_GENES.html Genes in this set correspond to the most abuntant transcripts that are also specific to platelets. 17353439 105/163 Arthur Liberzon 0.000825904148023503 0.00343762573075038 3415 1531.81818181818 1239 7.51103967782292e-05 27 1.20653266945421 -1.20749932023628 -1 4.46031686876613 3411 27 1239 192 372 1305 3330 3627 892 1043 1412 821 M508 REACTOME_SIGNALING_BY_SCF_KIT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_SCF_KIT.html Genes involved in Signaling by SCF-KIT 97/107 Reactome 0.109079280712756 0.155064688083556 900 1633.27272727273 1240 0.0104450525839038 434 0.804646246129744 0.788610187024406 1 0.97725904205418 896 679 3661 434 1886 893 1008 1586 1240 4150 1533 822 M10091 WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_LMP_DN.html Genes down-regulated in mucinous ovarian carcinoma tumors of low malignant potential (LMP) compared to normal ovarian surface epithelium tissue. 16467078 255/317 Arthur Liberzon 0.0279150433532969 0.0498898162164186 645 1280.72727272727 1241 0.00257051549647225 368 1.11742292238571 1.15305509692875 1 2.18295782013315 642 1721 1241 1734 2749 368 761 1326 2153 1002 391 823 M10196 WILLIAMS_ESR1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR1_TARGETS_DN.html The 'ER-alpha profile': genes down-regulated in T47D cells (breast cancer, ESR2 [GeneID=2100] Tet-Off) upon activation of ESR1 [GeneID=2099] by estradiol (E2) [PubChem=5757]. 17700529 8/10 Jessica Robertson 0.000741571373266745 0.00315648712895818 2305 1655.09090909091 1241 7.41818957201128e-05 369 1.10753761473906 1.31576893419759 1 4.15592303768815 2302 1069 4427 1241 369 990 457 972 2840 1885 1654 824 M1193 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 25/33 Arthur Liberzon 0.000597450304594847 0.00264289169417777 1000 1405.45454545455 1242 5.43284195348663e-05 485 1.57002877500865 1.6010918545471 1 6.07311346635889 998 2050 583 1242 775 2807 1873 1323 2656 485 668 825 M1689 YANG_MUC2_TARGETS_DUODENUM_6MO_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_DUODENUM_6MO_UP.html Genes up-regulated in duodenum of 6 month old MUC2 [GeneID=4583] knockout mice. 18794118 7/16 Jessica Robertson 0.000495860415127077 0.00229456976411745 690 1785.45454545455 1244 4.95971094785123e-05 322 2.57798958662657 -2.59391046807005 -1 10.2095597411632 1756 1082 4505 1174 322 3306 3599 688 1244 690 1274 826 M11120 HASLINGER_B_CLL_WITH_MUTATED_VH_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_MUTATED_VH_GENES.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with mutations in the variable immunoglobulin veriable heavy chain (VH) genes. 15459216 22/44 Kevin Vogelsang 0.0105853370193971 0.0228244818325967 1245 1392.18181818182 1245 0.000966964935534446 541 0.972386023653621 0.905325983521613 1 2.39512633432805 1245 971 2432 1265 927 659 541 734 1947 1922 2671 827 M2683 WINTER_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WINTER_HYPOXIA_DN.html Genes down-regulated in head and neck tumor samples which clustered around known hypoxia genes. 17409455 70/115 Arthur Liberzon 1.60008034234746e-05 0.000151654201122089 1025 1544 1246 1.45462907272568e-06 387 1.42078349525362 1.44946509612609 1 8.1419846134132 1024 1349 387 1207 4205 1625 1246 516 3395 477 1553 828 M2139 LU_EZH2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_EZH2_TARGETS_UP.html Genes up-regulated in SKOV3ip1 cells (ovarian cancer) upon knockdown of EZH2 [GeneID=2146] by RNAi. 20708159 346/459 Arthur Liberzon 0.0048701714054121 0.0130534974636826 875 1626.72727272727 1246 0.000443726009560891 77 1.00995556602427 -1.06237690490445 -1 2.85543205439723 871 1703 3447 2559 1236 77 964 1246 1858 3585 348 829 M677 REACTOME_ABACAVIR_TRANSPORT_AND_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABACAVIR_TRANSPORT_AND_METABOLISM.html Genes involved in Abacavir transport and metabolism 9/16 Reactome 0.000623274116107516 0.00273337113055396 1250 1794.45454545455 1247 6.23448996924677e-05 36 1.1158368763648 -1.1896495683213 -1 4.29172102263203 1247 3115 4216 2022 865 489 36 288 4384 2032 1045 830 M19826 ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_UP.html Genes up-regulated in BxPC3 cells (pancreatic cancer) after treatment with TNF [GeneID=7124] or IKI-1, an inhibitor of IkappaB kinase (IKK). 19010928 261/341 Jessica Robertson 1.27148410429215e-10 3.92248690997317e-09 285 1488.27272727273 1247 1.15589464033239e-11 99 1.28225189437732 1.19604133497281 1 16.1742576155085 281 1720 120 2246 4621 854 981 1247 2450 99 1752 831 M7488 PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PELLICCIOTTA_HDAC_IN_ANTIGEN_PRESENTATION_UP.html Antigen processing and presentation genes up-regulated in JY cells (B lymphocytes) treated with TSA [PubChem=5562]. 18829567 80/89 Jessica Robertson 2.26305957041519e-05 0.000201540399478485 270 1585.27272727273 1248 2.05734804546991e-06 52 0.696563762016866 -0.664057181793104 -1 3.86260410049932 269 717 3952 525 52 980 1386 1248 2457 4332 1520 832 M6972 MONTERO_THYROID_CANCER_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MONTERO_THYROID_CANCER_POOR_SURVIVAL_DN.html Down-regulated genes predicting poor survival of patients with thyroid carcinoma. 17873908 15/16 Arthur Liberzon 0.00261480923517682 0.008173443437109 1425 1541.54545454545 1248 0.000237992931543092 565 0.924685354969733 0.98039906754906 1 2.89645079691269 1422 1027 2529 781 565 1248 1083 2421 1168 2792 1921 833 M16441 REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRIN_CELL_SURFACE_INTERACTIONS.html Genes involved in Integrin cell surface interactions 97/114 Reactome 3.00136927299209e-06 3.58644632114498e-05 360 1584.90909090909 1249 2.72852124331294e-07 319 1.40587433431802 1.47663836969453 1 9.37751936406947 358 3246 319 3236 787 1249 1261 1136 3402 807 1633 834 M18467 MATTIOLI_MULTIPLE_MYELOMA_WITH_14Q32_TRANSLOCATIONS http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MULTIPLE_MYELOMA_WITH_14Q32_TRANSLOCATIONS.html Genes expressed in multiple myeloma (MM) patients carrying specific translocations involving the immunoglobulin heavy chain (IGH) locus at 14q32. 15735737 61/80 Leona Saunders 0.0171815008803732 0.033566508342451 1295 1284.27272727273 1250 0.00157428820070417 138 1.01159241837937 1.01601623899873 1 2.23744290726497 1292 138 1569 846 1156 681 1250 3276 1784 1846 289 835 M4095 SHI_SPARC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHI_SPARC_TARGETS_UP.html Genes up-regulated in glioma cell lines after knockdown of SPARC [GeneID=6678] by RNAi. 17213807 29/35 Arthur Liberzon 0.00199504424019498 0.00666898641198323 315 1021.27272727273 1251 0.000181532338448404 84 1.32380561945789 1.30101663361481 1 4.3221749739029 315 1479 1558 1494 651 102 84 1251 2445 1736 119 836 M2184 KAPOSI_LIVER_CANCER_MET_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAPOSI_LIVER_CANCER_MET_DN.html Selected down-regulated MET [GeneID=4233] target genes from a classifier of hepatocellular carcinoma (HCC) cases; associated with poor survival. 16710476 9/10 Yujin Hoshida 0.00163468450118435 0.00573355297131115 1660 1544.63636363636 1251 0.0001635888234635 422 1.49338370607436 1.23508490404453 1 5.02293511414495 1657 2159 4622 1338 490 2542 1251 849 690 971 422 837 M17115 SCHEIDEREIT_IKK_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SCHEIDEREIT_IKK_TARGETS.html Genes encoding substrates of IkappaB kinase (IKK) complex. 17072322 25/32 Arthur Liberzon 0.00373386067144154 0.0106488352684012 385 1481 1252 0.000340019355773568 382 1.25406623578199 0.95427160645384 1 3.71202149556976 382 3034 2457 2745 635 727 498 1252 782 2206 1573 838 M516 REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT.html Genes involved in The citric acid (TCA) cycle and respiratory electron transport 136/157 Reactome 4.64056242603931e-05 0.000356733789102696 15 1641.63636363636 1253 4.21878210406711e-06 15 0.67427364737389 -0.562908110728752 -1 3.48809828676162 15 2307 4038 1555 409 136 192 1036 2700 4417 1253 839 M18938 SENESE_HDAC1_AND_HDAC2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_AND_HDAC2_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of both HDAC1 and HDAC2 [GeneID=3065;3066] by RNAi. 17470557 285/454 Leona Saunders 8.01713281378987e-06 8.4090815291307e-05 510 1581.09090909091 1253 7.28832911780338e-07 325 1.21142884869586 1.13616905501861 1 7.40777742279594 506 1716 360 2284 4184 1253 1187 842 2989 325 1746 840 M12084 WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_UP.html Genes up-regulated in non-neoplastic rectal mucosa samples from patients having cancer associated with ulcerative collitis, compared to those who did not have the cancer. 17255260 32/34 Arthur Liberzon 0.00627617352765218 0.0152071555700813 1655 1266.63636363636 1253 0.000572195461110907 382 1.28278321514745 1.21215900837752 1 3.49916448162328 1651 1999 1244 382 768 2287 1894 1253 533 1299 623 841 M3258 LIU_TARGETS_OF_VMYB_VS_CMYB_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_TARGETS_OF_VMYB_VS_CMYB_DN.html Gene regulated in the opposite directions by v-MYB (DN) and c-MYB (UP) variants of CMYB [GeneID=4602] overexpressed in primary monocyte cultures off adenoviral vectors. 16205643 64/80 Arthur Liberzon 0.000935116498617751 0.00377566285156184 195 1805.63636363636 1254 8.50467463032032e-05 193 1.21849010396483 1.21298109990924 1 4.43004432742282 193 3718 613 4073 1783 1254 538 1238 4355 1519 578 842 M1632 BURTON_ADIPOGENESIS_11 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_11.html Strongly down-regulated at 2-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 110/129 John Newman 0.000569844281620053 0.00254944550639493 185 1265.90909090909 1254 5.18174487550317e-05 184 1.11473335379919 1.06480001784652 1 4.33807992316556 184 1283 1468 1614 325 649 506 1254 3589 1914 1139 843 M4336 OSADA_ASCL1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OSADA_ASCL1_TARGETS_DN.html Genes down-regulated in A549 cells (lung cancer) upon expression of ASCL1 [GeneID=429] off a viral vector. 18339843 37/45 Jessica Robertson 6.56598808148047e-05 0.000472430849765058 2600 1454.54545454545 1254 5.96925823110189e-06 344 1.60935962056089 1.62831624907227 1 8.03095627717842 1254 2496 460 3023 2598 684 559 575 2598 344 1409 844 M12353 FONTAINE_PAPILLARY_THYROID_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_PAPILLARY_THYROID_CARCINOMA_UP.html Genes up-regulated in papillary thyroid carcinoma (PTC) compared to other thyroid tumors. 17968324 87/119 Arthur Liberzon 0.00981072555709766 0.0215179482479094 3210 1800.54545454545 1254 0.000895886437656681 534 1.21459307126751 -1.11713166386527 -1 3.03840008358204 3207 708 841 823 3934 2637 3347 534 1169 1254 1352 845 M610 REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION.html Genes involved in Extracellular matrix organization 71/134 Reactome 1.12115644166192e-07 2.0275319558024e-06 80 1469.90909090909 1256 1.01923318072537e-08 80 1.5364116970804 1.55402914459357 1 13.1247052404317 80 2412 218 2122 2172 1256 1888 1198 3302 590 931 846 M18536 FALVELLA_SMOKERS_WITH_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/FALVELLA_SMOKERS_WITH_LUNG_CANCER.html Genes that distinguish normal from cancer (lung adenocarcinoma) samples and smokers from non-smoking subjects. 17724461 107/126 Jessica Robertson 0.00586675563764403 0.0143700501347586 240 1730.45454545455 1256 0.00053476901959541 238 1.35680810742689 1.34231918243167 1 3.75115764091334 238 4039 1476 4283 2018 483 554 404 3276 1256 1008 847 M7997 SA_CASPASE_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/SA_CASPASE_CASCADE.html Apoptosis is mediated by caspases, cysteine proteases arranged in a proteolytic cascade. 18/30 SigmaAldrich 0.000164030522310857 0.00098627269465891 2650 1663.27272727273 1258 1.49129775993802e-05 34 1.10159002871364 -1.17254351503614 -1 4.9686907000558 2647 363 2382 381 169 4026 4579 1258 34 1984 473 848 M1583 VISALA_AGING_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_AGING_LYMPHOCYTE_DN.html Genes down-regulated in peripheral lymphocytes from old individuals compared to those from young donors. 12618007 26/31 John Newman 0.00334670901926939 0.00984817117889746 4170 2213.36363636364 1259 0.000304710091560107 86 1.30429799786641 -1.09392919131571 -1 3.92714876082546 4169 285 1259 86 613 4492 3596 4683 91 894 4179 849 M2122 VERHAAK_GLIOBLASTOMA_MESENCHYMAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_MESENCHYMAL.html Genes correlated with mesenchymal type of glioblastoma multiforme tumors. 20129251 280/399 Arthur Liberzon 1.50546938990801e-08 3.22991614562083e-07 785 1298.45454545455 1259 1.36860854564546e-09 180 1.28843326680356 1.34319976064761 1 12.5487043825071 784 1186 180 1707 1689 1098 1462 1259 2719 233 1966 850 M3346 RODRIGUES_NTN1_AND_DCC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_NTN1_AND_DCC_TARGETS.html Genes down-regulated in HCT8/S11 cells (colon cancer) which lack DCC [GeneID=9423] and stably express NTN1 [GeneID=1630]. 17334389 48/49 Leona Saunders 0.0465848613746668 0.0758208778235957 1115 1670.27272727273 1260 0.00432741489163302 194 1.18939399675925 1.1017897186363 1 1.99914579765555 1114 194 1345 1219 3778 1260 666 4216 1109 1431 2041 851 M517 REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_EXPRESSION.html Genes involved in BMAL1:CLOCK/NPAS2 Activates Circadian Expression 38/44 Reactome 0.0230936801292077 0.042512546883721 440 1480.45454545455 1261 0.00212179281138361 439 0.955875183402086 1.05103375239554 1 1.96702563371926 439 1444 3316 1274 2938 566 450 1261 618 2742 1237 852 M1492 BRUNO_HEMATOPOIESIS http://www.broadinstitute.org/gsea/msigdb/cards/BRUNO_HEMATOPOIESIS.html Genes that are rapidly down-regulated as multipotential cells of the FDCP-mix hematopoiesis model undergo differentiation and loose their self-renewal and proliferation properties. 14701746 81/112 Kevin Vogelsang 0.0212758640197383 0.0398026469176238 1365 1446.63636363636 1261 0.00195313175000872 724 1.13512194768349 1.08718315187648 1 2.38462670691179 1363 724 1261 1757 3073 1872 2303 784 1013 864 899 853 M19929 BROWNE_HCMV_INFECTION_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_48HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 48 h time point that were not up-regulated at the previous time point, 24 h. 11711622 261/381 John Newman 0.00314964010604982 0.00940310012685337 1240 1417.54545454545 1261 0.000286741669216979 283 1.153107615487 1.12833207093712 1 3.506664454021 1236 1194 1620 1261 3608 1367 1909 283 1474 919 722 854 M12809 BOYAULT_LIVER_CANCER_SUBCLASS_G23_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G23_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G23, defined by unsupervised clustering. 17187432 9/12 Yujin Hoshida 0.000344604259396577 0.00175461931429541 1265 1833.90909090909 1261 3.44657709505415e-05 89 1.12920151403902 0.791858715483446 1 4.66932181351683 1261 2164 4621 2302 261 237 89 4028 1205 2765 1240 855 M6900 MAHADEVAN_GIST_MORPHOLOGICAL_SWITCH http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_GIST_MORPHOLOGICAL_SWITCH.html Genes up-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] that may correlate with the morphological switch in these cells. 17325667 23/32 Arthur Liberzon 0.00357346456178036 0.0103100299727517 950 1911.27272727273 1263 0.00032538928921671 265 2.17607639567183 2.46361181982031 1 6.48708984807005 946 4195 735 3745 4706 907 265 1556 2304 1263 402 856 M18825 KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN.html Genes down-regulated in AIDS-related primary effusion lymphoma (PEL) samples compared to other tumor subtypes and normal B lymphocytes. 12531789 58/78 Kate Stafford 6.67933774171954e-05 0.000479125746822435 4375 1887 1263 6.07230958110476e-06 107 1.25108901733257 -1.28668038659754 -1 6.23163378817406 4375 121 585 437 107 4117 4565 3284 1263 478 1425 857 M11825 BRUECKNER_TARGETS_OF_MIRLET7A3_DN http://www.broadinstitute.org/gsea/msigdb/cards/BRUECKNER_TARGETS_OF_MIRLET7A3_DN.html Genes down-regulated in A549 cells (lung cancer) expressing MIRLET7A3 [GeneID=406883] microRNA off a plasmid vector. 17308078 110/144 Jessica Robertson 7.96675788376135e-06 8.37485461277362e-05 340 1239.72727272727 1263 7.24253339414376e-07 340 1.24641607162176 1.21338179616495 1 7.62503695938476 340 1285 359 1758 928 1323 1263 2102 2455 672 1152 858 M2542 GENTLES_LEUKEMIC_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/GENTLES_LEUKEMIC_STEM_CELL_UP.html Genes up-regulated in LSC (leukemic stem) cells compared to LPC (leukemia progenitor) cells from AML (acute myeloid leukemia) tumor samples. 21177505 37/51 Andrew Gentles 5.97790765627311e-05 0.000438813750196098 3585 1882.36363636364 1264 5.43460917817979e-06 240 1.4749786150162 -1.68938314084156 -1 7.43131713607507 3581 240 456 716 2992 4697 4439 468 1321 532 1264 859 M1569 BRACHAT_RESPONSE_TO_METHOTREXATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_METHOTREXATE_UP.html Genes up-regulated in FL5.12 cells (pro-B lymphocyte) in response to methotrexate [PubChem=4112]. 12447701 30/54 John Newman 0.000420732844196518 0.00201810757887291 2675 1909.90909090909 1265 3.82557570564945e-05 287 1.2993446727398 -1.3951971055517 -1 5.25442472640633 2672 303 1492 576 287 3264 4604 4701 669 1176 1265 860 M17609 WU_ALZHEIMER_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_ALZHEIMER_DISEASE_UP.html Genes up-regulated in brain endothelial cells from patients with Alzheimer disease. 16116430 23/45 Jessica Robertson 0.000224995078005272 0.0012893480608063 1890 1452.72727272727 1265 2.04561901506618e-05 177 1.28047709390073 -1.19887918802198 -1 5.55197568960788 1887 1517 1068 3045 188 656 578 4162 1437 1265 177 861 M2154 DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_6HR_DN.html Genes down-regulated in MCF7 cells (breast cancer) at 6 h of estradiol [PubChem=5757] treatment. 20406972 128/150 Jessica Robertson 0.00291561931270186 0.00884998273694713 1470 1438.18181818182 1265 0.000265408228505896 512 1.23289069968824 1.31746625435297 1 3.79800395618758 873 1265 719 2296 3566 775 1467 1466 887 512 1994 862 M2199 THILLAINADESAN_ZNF217_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/THILLAINADESAN_ZNF217_TARGETS_DN.html Genes bound and repressed by ZNF217 [GeneID=7764] in MCF7 cells (breast cancer). 18625718 14/15 Arthur Liberzon 0.00255335913998161 0.0080185330277533 920 1417.63636363636 1265 0.000232393403475523 60 1.10296900446606 -1.24906213592371 -1 3.46867393040091 916 409 1703 519 1813 2028 1265 488 3714 2679 60 863 M15196 TIEN_INTESTINE_PROBIOTICS_2HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_2HR_UP.html Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 2h. 16394013 54/79 Arthur Liberzon 0.00931208357443239 0.0206255440972881 1035 1482.81818181818 1271 0.000850157691372408 170 1.02865270848004 1.08267371356021 1 2.60163306971928 1033 170 2067 895 887 1271 896 1373 2595 2998 2126 864 M10540 KANG_FLUOROURACIL_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_FLUOROURACIL_RESISTANCE_UP.html Genes up-regulated in gastric cancer cell lines resistant to 5-fluorouracil [PubChem=3385]. 14734480 31/37 John Newman 0.0017311899955914 0.00599942494801132 2835 1634 1271 0.000157504889048734 485 1.18830250935583 -1.1857299782564 -1 3.96168416126527 2833 908 1712 1271 485 1269 3467 1463 1206 2259 1101 865 M11521 KEGG_GLYCOLYSIS_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOLYSIS_GLUCONEOGENESIS.html Glycolysis / Gluconeogenesis 52/81 KEGG 7.06723494340143e-05 0.000502369712844198 2815 1443.27272727273 1272 6.42496543638183e-06 109 1.18060684570149 -1.2396425105583 -1 5.84411118424014 2815 781 1743 147 109 1272 2357 2918 274 788 2672 866 M12950 BIOCARTA_ACE2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACE2_PATHWAY.html Angiotensin-converting enzyme 2 regulates heart function 19/27 BioCarta 4.90223612398923e-05 0.000375017090846502 50 1508.09090909091 1272 4.45667760308418e-06 49 1.60501539196197 1.48405427757118 1 8.25080504527119 49 2598 443 1930 2078 1113 894 1795 3788 1272 629 867 M16311 NAGASHIMA_EGF_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAGASHIMA_EGF_SIGNALING_UP.html Genes up-regulated in MCF7 cells (breast cancer) after stimulation with EGF [GeneID=1950]. 17142811 78/109 Arthur Liberzon 0.00224883460981248 0.00730020588604876 80 1859.09090909091 1273 0.000204648787102045 78 1.18874490136608 1.18168272477533 1 3.81113936429243 78 3268 1002 3838 4451 791 575 1574 2947 653 1273 868 M2546 DUNNE_TARGETS_OF_AML1_MTG8_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/DUNNE_TARGETS_OF_AML1_MTG8_FUSION_UP.html Genes up-regulated in Kasumi-1 cells (acute myeloid leukaemia (AML) with the t(8;21) translocation) after knockdown of the AML1 MTG8 fusion [GeneID=861;862] by RNAi. 16652140 47/93 Leona Saunders 0.0139632491323874 0.0285658268596144 2115 1685.63636363636 1275 0.00127751531700821 832 1.26036934861822 1.20586866989095 1 2.92021137715676 2113 832 884 1275 2941 955 941 851 3946 1381 2423 869 M1576 GERHOLD_ADIPOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_ADIPOGENESIS_DN.html Selected genes down-regulated during differentiation of 3T3-L1 cells (fibroblast) into adipocytes in response to adipogenic hormones. 12021175 98/116 John Newman 0.00401194600321804 0.0112049616184551 1120 1389.45454545455 1276 0.000365389178981424 614 1.28213769199074 1.41996355302895 1 3.75258154834746 1116 2357 748 1632 1474 954 1276 1696 2401 614 1016 870 M1582 BURTON_ADIPOGENESIS_2 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_2.html Strongly up-regulated at 8 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 116/131 John Newman 0.0112201092422091 0.0238661179014093 220 1596 1276 0.00102524948154885 217 1.10381166487655 1.14298560797176 1 2.68676050816193 217 1276 857 1260 3936 1502 905 1674 3228 1065 1636 871 M19496 ZEMBUTSU_SENSITIVITY_TO_CISPLATIN http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_CISPLATIN.html Top genes associated with chemosensitivity to cisplatin [PubChem=2767] across 85 tumor xenografts. 11809704 19/28 Arthur Liberzon 0.00400415482335786 0.0111898228337769 3010 1914.18181818182 1276 0.000364678299210674 87 1.53743729301504 -1.78811984674631 -1 4.50117222327067 3007 2592 1145 1985 1114 4034 4226 546 1044 1276 87 872 M166 PID_ATF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATF2_PATHWAY.html ATF-2 transcription factor network 18832364 77/92 Pathway Interaction Database 8.72840858262159e-05 0.000593245147751871 885 1694.63636363636 1278 7.93523172531017e-06 326 1.42288738631924 1.43598058640252 1 6.88926852147454 881 2853 473 2225 4027 389 326 1821 3742 626 1278 873 M12455 JAZAG_TGFB1_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_DN.html Genes down-regulated in PANC-1-puro cells (pancreatic cancer) stimulated by TGF1B [GeneID=7040] for 2 h. 15592526 41/68 Leona Saunders 0.00802766285470056 0.0182957840049187 1315 1177.54545454545 1279 0.000732464165090852 165 1.29540773578337 -1.14114144832941 -1 3.37751071600597 1311 858 1614 1279 1018 711 1743 2522 427 1305 165 874 M6967 HU_ANGIOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HU_ANGIOGENESIS_UP.html Up-regulated genes that separate angiogenic from non-angiogenic non-small cell lung carcinoma (NSCLC) samples. 15592519 45/48 Leona Saunders 0.00567495377260745 0.0142024584976285 205 1556.54545454545 1280 0.000517240503536775 202 1.32152292790359 1.26289611819222 1 3.66370495985042 202 2927 775 2764 1670 378 324 2217 4091 1280 494 875 M1327 MANTOVANI_VIRAL_GPCR_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_VIRAL_GPCR_SIGNALING_UP.html Up-regulated genes in the expression signature of direct and paracrine viral GPCR signaling in endothelial cells. 17906691 109/156 Jessica Robertson 1.02668815255447e-08 2.26447106544724e-07 1065 1372.63636363636 1281 9.33352870314348e-10 176 1.55422021935893 1.60043468782149 1 15.4970328558638 1061 1281 176 456 2427 1665 1702 3163 1026 247 1895 876 M12993 KLEIN_PRIMARY_EFFUSION_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KLEIN_PRIMARY_EFFUSION_LYMPHOMA_UP.html Genes up-regulated in AIDS-related primary effusion lymphoma (PEL) samples compared to other tumor subtypes and normal B lymphocytes. 12531789 59/72 Kate Stafford 0.00652571374064968 0.015598091841524 1510 1217.90909090909 1281 0.000595013754400026 164 1.14177014321286 -1.00810489838981 -1 3.0956126891534 1507 2429 1924 1281 781 164 353 1845 631 1767 715 877 M19488 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_WITH_LMP1_UP.html Genes up-regulated in nasopharyngeal carcinoma (NPC) positive for LMP1 [GeneID=9260], a latent gene of Epstein-Barr virus (EBV). 16912175 474/643 Arthur Liberzon 0.0326957281084811 0.0563431313150898 400 1666.54545454545 1282 0.00301745444181049 397 1.22949991301687 1.20908909324298 1 2.30445427573339 397 2221 998 1735 4694 1479 1053 1282 1146 954 2373 878 M538 REACTOME_VITAMIN_B5_PANTOTHENATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VITAMIN_B5_PANTOTHENATE_METABOLISM.html Genes involved in Vitamin B5 (pantothenate) metabolism 12/12 Reactome 0.000566983054557693 0.00254146250476003 2020 1561.81818181818 1283 5.15572027209754e-05 79 0.817884535904985 -0.98390574168966 -1 3.18451079853795 2016 1052 3072 1270 2726 1514 1283 92 79 3798 278 879 M7914 HENDRICKS_SMARCA4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HENDRICKS_SMARCA4_TARGETS_DN.html Genes down-regulated in ALAB cells (breast cancer) upon reintroduction of SMARCA4 [GeneID=6597] expressed off adenoviral vector. 14673169 45/89 John Newman 0.00524262314520611 0.0138068808911899 600 1432.72727272727 1283 0.000477741655543098 273 1.32132465649693 1.37657188605877 1 3.68747861771572 599 1952 1283 2311 4709 421 273 387 1716 1535 574 880 M1125 MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_TGFB1_TARGETS_DN.html Pubertal genes down-regulated by TGFB1 [GeneID=7040]. 17486082 86/106 Arthur Liberzon 2.75914673290258e-07 4.55355684590915e-06 3240 1453.09090909091 1285 2.50831552631193e-08 75 1.50117082784393 1.59149912573388 1 12.0321564746114 3239 75 235 394 2141 2248 3038 2122 917 290 1285 881 M1418 KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_UP.html Up-regulated genes predicting response of patients with hepatocellular carcinoma (HCC) to combination chemotherapy with 5-fluorouracil (5-FU) [PubChem=3385] and IFN1@ [GeneID=3438]. 15447987 11/15 Yujin Hoshida 0.00010573898598725 0.00069664684542787 1285 1724.54545454545 1285 9.61309713460746e-06 24 0.909734225104931 -0.835461623447788 -1 4.30941694699164 1285 3105 3151 2604 4513 370 24 26 821 3023 48 882 M4038 PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN.html Genes down-regulated in CD38+ [GeneID=952] CLL (chronic lymphocytic leukemia) cells. 17287849 16/31 Arthur Liberzon 0.00658730582212104 0.0156942368933109 1785 1254.54545454545 1286 0.000600646619049045 96 1.01565860066286 -1.17743091289247 -1 2.74961517463847 1781 382 1860 291 3046 826 1286 2729 96 1366 137 883 M511 REACTOME_SIGNALING_BY_NODAL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NODAL.html Genes involved in Signaling by NODAL 13/22 Reactome 0.00304793353983226 0.00913942469514037 1290 1902.09090909091 1288 0.000277469493601814 112 0.952685845366688 1.03981945184955 1 2.91481007116829 1288 3918 2885 3364 3492 851 500 278 1021 3214 112 884 M6875 LANDIS_BREAST_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_BREAST_CANCER_PROGRESSION_UP.html Genes up-regulated in preneoplastic mammary tissues and whose expression is maintained in tumors. 16434967 55/57 Lauren Kazmierski 0.0286592132063908 0.0507389380646563 1290 1405.27272727273 1288 0.00263995530856499 237 1.02750958281702 1.13341728234213 1 1.99599722432144 237 1395 2659 1490 2859 768 697 1286 681 2098 1288 885 M17086 BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_UP.html Genes up-regulated in microdissected endothelial samples from ovarian cancer tumors with tumor-infiltrating lymphocytes (TIL) vs those without TILs. 18157142 31/41 Jessica Robertson 0.000347165357548977 0.00176575483580945 1455 1447.81818181818 1288 3.15654684721687e-05 245 1.03252080171739 1.01098490412555 1 4.26527496005944 1455 904 2304 1288 245 1267 869 2516 1028 2261 1789 886 M14233 MARSON_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_UP.html Genes up-regulated by FOXP3 [GeneID=50943] in both ex vivo and hybridoma cells. 17237765 84/108 Arthur Liberzon 0.00402683217263873 0.01122078039025 1740 1215.54545454545 1288 0.000366747431058287 90 1.16617136093555 1.18292022510807 1 3.41208770102467 1739 710 1184 90 1922 1288 1835 2263 451 509 1380 887 M12692 FINETTI_BREAST_CANCER_KINOME_GREEN http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCER_KINOME_GREEN.html Genes in the green cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 21/27 Jessica Robertson 0.000381894251168264 0.00189342527890148 380 1731.72727272727 1289 3.47236872414236e-05 53 1.07529956912968 1.07529956912968 1 4.3930776191032 379 3042 2295 4228 1289 274 53 69 4308 2805 307 888 M8513 SMID_BREAST_CANCER_NORMAL_LIKE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_NORMAL_LIKE_UP.html Genes up-regulated in the normal-like subtype of breast cancer. 18451135 492/820 Jessica Robertson 1.51085565395311e-40 1.78280967166467e-37 545 1699.72727272727 1289 1.37350513995739e-41 4 1.45980165857993 1.40104723255794 1 80.4969406856441 543 3162 4 3267 3042 1289 955 612 3875 19 1929 889 M3958 ZHAN_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_UP.html Genes most significantly up-regulated in multiple myeloma samples, compared to normal bone marrow plasma cells. 11861292 106/151 Kevin Vogelsang 0.00118698634539408 0.00449644907725525 630 1408 1290 0.000107966114116443 20 1.08159200132921 -1.12644626588929 -1 3.80917050987792 630 1290 3153 2721 1302 20 336 1097 1497 3335 107 890 M1818 MATZUK_STEROIDOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_STEROIDOGENESIS.html Genes important for steroidogenesis, based on mouse models with female fertility defects. 18989307 4/8 Jessica Robertson 3.22651744854262e-06 3.78834884505502e-05 1885 1666.54545454545 1290 3.22652213323888e-07 16 1.45245183995846 1.01670998110279 1 9.63636682926282 1882 1097 4568 685 16 1290 963 3376 115 1860 2480 891 M250 ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_FIMA_DN.html Genes down-regulated in macrophages by P.gingivalis FimA pathogen. 18025224 355/510 Arthur Liberzon 0.0113576355226268 0.0240610590964087 3210 1655.63636363636 1291 0.00103788157576356 191 1.24552063246839 -1.31365812885168 -1 3.02510151979832 3206 1701 1291 924 1762 191 3657 3595 809 859 217 892 M8760 MCGARVEY_SILENCED_BY_METHYLATION_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/MCGARVEY_SILENCED_BY_METHYLATION_IN_COLON_CANCER.html Genes silenced in HCT116 cells (colon cancer) by methylation of CpG islands in their promoters. 18632628 53/86 Jessica Robertson 0.000184951234525627 0.00109030925664755 630 1191.54545454545 1291 1.68151622703348e-05 228 1.45756045305565 1.51098917230498 1 6.47906540764018 628 1407 515 2018 1374 1291 1567 228 2622 392 1065 893 M1968 MIKKELSEN_IPS_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) without H3 methylation marks at either H3K4 or H3K27 in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 79/162 Jessica Robertson 4.45590095423574e-06 5.0968216852712e-05 3120 1626.27272727273 1291 4.05082725389596e-07 333 1.54352988134308 -1.64942544762166 -1 9.94220748191724 3117 728 333 933 358 2083 2568 1291 1520 1125 3833 894 M9197 ELVIDGE_HYPOXIA_BY_DMOG_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_BY_DMOG_UP.html Genes up-regulated in MCF7 cells (breast cancer) treated with hypoxia mimetic DMOG [PubChem=3080614]. 16565084 178/201 Arthur Liberzon 2.34166061441482e-05 0.000206632572085118 1150 1352 1292 2.12880503565043e-06 406 1.31282438879746 1.2934567121345 1 7.25865536473117 1149 1759 406 1503 2195 1005 1932 1067 2151 413 1292 895 M16533 SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SILIGAN_TARGETS_OF_EWS_FLI1_FUSION_DN.html Genes bound by EWSR1-FLT1 [GeneID=2130;2321] fusion and down-regulated in STA-ET-7.2 cells (Ewing's sarcoma) after knockdown of EWSR1-FLT1 by RNAi. 15735734 25/32 Arthur Liberzon 0.00182555112735361 0.00625751729928036 1765 1441.45454545455 1292 0.000166097065860174 93 1.32783381661498 -1.36321557068401 -1 4.39043369653443 1763 2046 2470 1292 1022 1165 2765 204 388 2648 93 896 M4138 REACTOME_ORC1_REMOVAL_FROM_CHROMATIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ORC1_REMOVAL_FROM_CHROMATIN.html Genes involved in Orc1 removal from chromatin 68/79 Reactome 0.00537425422799555 0.0140732978253488 115 1536 1294 0.000489766160154853 114 0.676120364740951 -0.614593300846646 -1 1.87840613125218 114 1344 3982 1364 1059 425 491 1139 1357 4327 1294 897 M2000 MIKKELSEN_ES_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 K27 trimethylation mark (H327me3) in embryonic stem cells (ES). 17603471 39/81 Arthur Liberzon 0.0012020076671595 0.00454241488310075 540 1158.27272727273 1294 0.000109333173401434 214 1.16369468894327 1.17845569479485 1 4.09061635161222 539 1972 1294 1719 428 376 890 1517 2027 1765 214 898 M12095 BIOCARTA_IL1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL1R_PATHWAY.html Signal transduction through IL1R 34/52 BioCarta 0.000891390022632667 0.00363066378484564 230 1433.18181818182 1295 8.10683089660585e-05 230 0.958013463188639 1.05736758806696 1 3.50745921349501 230 1991 2450 2156 385 935 1295 533 2928 1748 1114 899 M1188 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment with 2 nM docetaxel [PubChem=148124]. 17099726 120/163 Arthur Liberzon 3.0170507200798e-09 7.49498915725087e-08 920 1272.18181818182 1298 2.74277338565213e-10 87 1.36373093898328 1.4141928256411 1 14.5802904606232 920 642 175 1298 597 2321 1972 1992 2522 87 1468 900 M2206 CHYLA_CBFA2T3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHYLA_CBFA2T3_TARGETS_DN.html Genes down-regulated in immature bone marrow progenitor cells upon knock out of CBFA2T3 [GeneID=863]. 18710942 295/395 Arthur Liberzon 6.63540132550773e-10 1.86423180097598e-08 3060 1841.81818181818 1298 6.03218302500819e-11 134 1.22589408081923 1.28367223220647 1 14.2181447180718 3056 533 134 212 2340 3604 4064 1298 1093 173 3753 901 M2513 ELVIDGE_HIF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) after knockdown of HIF1A [GeneID=3091] by RNAi. 16565084 124/150 Arthur Liberzon 0.00106870153043465 0.00417918079838572 2000 1570.45454545455 1299 9.72019118702388e-05 539 1.30931948164517 1.32152146782499 1 4.67364159182671 1997 635 624 539 1698 3716 3198 1179 1712 678 1299 902 M229 PID_P38_ALPHA_BETA_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_ALPHA_BETA_DOWNSTREAM_PATHWAY.html Signaling mediated by p38-alpha and p38-beta 18832364 50/52 Pathway Interaction Database 0.000428136734207155 0.0020432814817571 1730 1613.54545454545 1300 3.89290977799574e-05 289 0.825031542336511 0.943377796750549 1 3.32964434993348 1726 821 2687 1329 289 1050 716 1300 3999 2770 1062 903 M14024 GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_UP.html Genes up-regulated in erythroid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 36/39 Arthur Liberzon 0.0114142119016736 0.0241385596508837 1305 2092.18181818182 1301 0.00104307870556548 247 1.05796339083213 1.1408491871493 1 2.56733229958188 1301 4492 2749 4556 959 1261 636 870 2912 3031 247 904 M9940 HONRADO_BREAST_CANCER_BRCA1_VS_BRCA2 http://www.broadinstitute.org/gsea/msigdb/cards/HONRADO_BREAST_CANCER_BRCA1_VS_BRCA2.html Genes distinguishing between breast cancer tumors bearing mutations in BRCA1 [GeneID=672] and those with mutated BRCA2 [GeneID=675]. 16998498 32/36 Arthur Liberzon 0.0459862095547002 0.0749498995504783 905 2047.27272727273 1301 0.00427059607196559 711 2.01499322238251 -2.10731739399736 -1 3.40206638564142 901 3404 1063 3194 2910 1275 711 3170 3867 1301 724 905 M10202 TSUNODA_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSUNODA_CISPLATIN_RESISTANCE_UP.html Genes up-regulated in bladder cancer cells resistant to cisplatin [PubChem=2767] compared to the parental cells sensitive to the drug. 15608674 18/21 Leona Saunders 0.00226896841936293 0.00735039872298765 550 1584.63636363636 1301 0.000206482900249155 90 1.38962714860965 1.36609716727282 1 4.44898464737099 546 3063 1301 3110 2888 106 90 971 3219 1567 570 906 M10922 WANG_RECURRENT_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RECURRENT_LIVER_CANCER_UP.html Genes up-regulated in samples from patients with recurrent hepatocellular carcinoma (HCC). 17975138 24/28 Yujin Hoshida 0.0106345990288739 0.0228784445835392 2110 1789.90909090909 1302 0.000971486937785524 206 0.785829358612127 -0.843018209911994 -1 1.93438088832657 2108 1497 3637 1302 3471 811 733 1132 894 3898 206 907 M15662 WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_ULCERATIVE_COLITIS_WITH_CANCER_DN.html Genes down-regulated in non-neoplastic rectal mucosa samples from patients having cancer associated with ulcerative collitis, compared to those who did not have the cancer. 17255260 18/27 Arthur Liberzon 0.000622481487237194 0.00273337113055396 335 1387.09090909091 1303 5.66052441605341e-05 332 1.29486452787647 -1.39218407630644 -1 4.98031242697167 335 1544 2269 1972 332 1204 1191 1303 838 2533 1737 908 M1482 IGLESIAS_E2F_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IGLESIAS_E2F_TARGETS_DN.html Genes down-regulated in pancreatic cells from mice with double knockout of E2F1 [GeneID=1869] and E2F2 [GeneID=1870] compared to wild type. 15146237 15/36 Kevin Vogelsang 0.00171733350332521 0.00596454314620675 1835 1408.81818181818 1304 0.000156243230114655 484 1.62618861689881 -2.29669005837202 -1 5.42777202607331 1831 2114 819 1304 484 2313 2162 671 1634 1258 907 909 M7245 SEKI_INFLAMMATORY_RESPONSE_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SEKI_INFLAMMATORY_RESPONSE_LPS_UP.html Genes up-regulated in hepatic stellar cells after stimulation with bacterial lipopolysacharide (LPS). 17952090 96/123 Jessica Robertson 2.12607474161839e-06 2.66182301868403e-05 85 1607.72727272727 1304 1.93279708750429e-07 81 1.31607080628999 1.25799769497826 1 9.03420759162072 81 2359 307 2587 4507 645 736 1304 3305 242 1612 910 M1313 GROSS_HYPOXIA_VIA_ELK3_ONLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_ONLY_UP.html Genes specifically up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 45/48 Jessica Robertson 0.0144504296983598 0.0293731982169771 1310 1485.27272727273 1306 0.00132238433351145 467 1.35592215099724 1.25936832171692 1 3.11698281478413 1306 1426 1155 1759 1033 467 603 3602 1630 1047 2310 911 M10156 BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_UP.html Genes up-regulated in SaOS-2 cells (osteosarcoma) upon expression of PAX3-FOXO1 [GeneID=5077;2308] fusion protein off an adenoviral vector. 15688035 96/118 Leona Saunders 0.000163371574381374 0.000986079067877346 925 1344.54545454545 1307 1.48530643258466e-05 495 1.26594900697669 1.20124666366124 1 5.71020499436586 922 1307 505 2319 1379 554 1144 2404 2058 495 1703 912 M11733 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_DN.html Genes exclusively down-regulated in B lymphocytes from WM (Waldenstroem's macroblobulinemia) patients but with a similiar expression pattern in the normal cells and in the cells from CLL (chronic lymphocytic leukemia) patients. 17252022 12/15 Arthur Liberzon 0.000569020871891497 0.0025481769595141 430 1716.09090909091 1307 5.17425545539793e-05 29 1.5941784947969 1.5941784947969 1 6.20444414737063 429 3104 1307 3320 3888 393 29 130 3998 1843 436 913 M15762 RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_DN.html Neuroblastoma markers down-regulated in neuroblastoma cell lines expressing ESWR1-FLI1 [GeneID=2130;2313] fusion protein. 14973077 22/43 Kevin Vogelsang 0.00145620941108398 0.00525787849666741 1150 1927.18181818182 1308 0.000132470380883549 182 1.55542670672566 1.49553482862861 1 5.31940609471023 1148 4194 972 3930 1308 1846 1747 182 3718 1200 954 914 M8526 CHEN_LUNG_CANCER_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LUNG_CANCER_SURVIVAL.html Protein profiles associated with survival in lung adenocarcinoma. 14573703 45/62 Kate Stafford 0.00950872695713435 0.0209627236047053 875 1553.09090909091 1310 0.000868188682361324 143 1.23343581682041 -1.36074719361741 -1 3.10655069158486 874 3348 1310 1594 1739 143 999 1249 3481 2138 209 915 M3804 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_UP.html Genes up-regulated in normal hematopoietic progenitors by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 262/368 Arthur Liberzon 6.31913225059392e-09 1.45494166940504e-07 690 1176.45454545455 1311 5.7446656988587e-10 111 1.2536190231949 1.24683183324834 1 12.8611320436207 688 1191 166 1325 1553 1452 1504 774 2866 111 1311 916 M1299 GROSS_ELK3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_ELK3_TARGETS_DN.html Genes down-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 47/58 Jessica Robertson 0.0126376774663291 0.0262453776840711 1315 1852.45454545455 1312 0.00115553296119705 782 1.26870207733914 1.34545387047848 1 3.00956374498944 1312 1948 871 3960 2447 782 1181 1283 3415 1150 2028 917 M2237 JOHNSTONE_PARVB_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_1_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) upon overexpression of PARVB [GeneID=29780] under all three culture conditions. 17998334 84/108 Arthur Liberzon 0.000343589120759366 0.00175133979479936 3610 1821.54545454545 1312 3.12402539245072e-05 216 1.12833136664663 1.02953567915152 1 4.66709922882863 3606 707 1552 759 244 4192 3298 216 647 1312 3504 918 M1253 INAMURA_LUNG_CANCER_SCC_UP http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_UP.html Up-regulated genes characteristic to the squamous cell carcinoma (SCC) type of non-small cell lung cancer (NSCLC). 16007138 28/33 Arthur Liberzon 0.0230389961948063 0.0424284284196198 495 2020.27272727273 1313 0.00211671495238207 449 1.8876964105906 -2.19849319273312 -1 3.88709203273099 493 3829 1025 4356 3530 472 449 1500 4253 1313 1003 919 M2804 HAHTOLA_CTCL_CUTANEOUS http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_CTCL_CUTANEOUS.html Genes showing similar expression profiles in all subtypes of cutaneous T cell lymphoma (CTCL). 16914566 25/65 Arthur Liberzon 2.7266746643674e-05 0.000234274662234584 2810 1425.27272727273 1313 2.47882587208496e-06 61 1.42504352961054 -1.60726916557363 -1 7.76253380851339 2809 1494 1690 603 61 1727 4147 1313 364 1100 370 920 M3642 DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_PAX_FOXO1_SIGNATURE_IN_ARMS_DN.html 'PAX-FKHR signature': genes down-regulated by PAX3- or PAX7-FOXO1 [GeneID=5081;5077;2308] fusion in primary alveolar rhabdomyosarcoma(ARMS) tumors. 16849537 23/28 Arthur Liberzon 0.000587234407473458 0.00261485509742898 4570 2185.27272727273 1314 5.33992012236541e-05 328 1.28097365613244 -1.18221493036318 -1 4.96388698685914 4569 1508 973 480 328 3732 4560 1147 1314 718 4709 921 M13380 KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION.html Neuroactive ligand-receptor interaction 89/344 KEGG 4.44495328154742e-12 1.70570564950438e-10 1870 1355.54545454545 1315 4.04086661959673e-13 97 1.57408893782651 1.38503875374542 1 23.0716682522184 1870 1315 97 3264 875 562 1955 1687 2458 329 499 922 M18395 URS_ADIPOCYTE_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/URS_ADIPOCYTE_DIFFERENTIATION_DN.html Genes down-regulated in primary adipocytes compared to preadipocytes. 15051823 56/64 John Newman 0.00257758842034142 0.00808775057807626 150 1813.72727272727 1315 0.000234601215093725 148 1.41752677714015 1.41292137580116 1 4.45000182726996 148 3322 708 3434 1209 1444 1315 2253 4097 932 1089 923 M10558 LU_IL4_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/LU_IL4_SIGNALING.html Genes up-regulated in peripheral B lymphocytes after incubation with IL4 [GeneID=3565] for 4 h. 15591113 120/180 Kate Stafford 0.0191953938460605 0.0366069733145072 970 1604.27272727273 1317 0.00176045017633657 647 1.07880395138172 1.08881175639459 1 2.32514962422165 967 647 1293 2281 2115 1317 1232 739 2641 2081 2334 924 M14833 GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_UP.html Up-regulated genes from the set B (Fig. 5a): specific signature shared by cells expressing either AF4-MLL or MLL-AF4 [GeneID=4299;4297] fusion proteins. 17130830 46/59 Arthur Liberzon 0.000225089576717032 0.0012893480608063 240 1648 1320 2.04647827005556e-05 239 1.44180631909266 1.44730612000986 1 6.25149074821892 239 1957 527 2653 2730 1387 1139 1270 3732 1320 1174 925 M9143 FRIDMAN_SENESCENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_SENESCENCE_UP.html Genes up-regulated in senescent cells. 18711403 122/146 Jessica Robertson 0.000998193152969509 0.00396922635384674 465 1793.63636363636 1321 9.07860313836288e-05 462 1.27370031513464 1.28862777547898 1 4.58927846043473 462 2803 622 3687 2026 1301 1214 1372 4186 736 1321 926 M1618 LIU_SMARCA4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LIU_SMARCA4_TARGETS.html Genes up-regulated in SW-13 cells (kidney cancer) by transient expression of SMARCA4 [GeneID=6597] at 24 h off a plasmid vector. 11509180 82/109 John Newman 2.73216276862872e-05 0.000234274662234584 990 1635.54545454545 1323 2.48381518157645e-06 414 1.26289174199985 1.29199020384289 1 6.87924437388541 986 1323 414 993 1554 1197 1491 3289 3255 544 2945 927 M2088 LI_INDUCED_T_TO_NATURAL_KILLER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_INDUCED_T_TO_NATURAL_KILLER_DN.html Genes down-regulated in ITNK cells (T-lymphocyte progenitors (DN3 cells) reprogrammed to natural killer (NK) cells by ablation of BCL11B [GeneID=64919] gene), compared to the parental DN3 cells. 20538915 159/199 Arthur Liberzon 5.48128161016222e-06 6.08744687058016e-05 1070 1602.09090909091 1324 4.98299569707015e-07 304 1.27814314278536 1.28931908248964 1 8.0848392469372 1069 2298 344 1541 4614 1019 1324 1503 2594 304 1013 928 M8601 BIOCARTA_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAC1_PATHWAY.html Rac 1 cell motility signaling pathway 35/38 BioCarta 0.00577426225782821 0.0142024584976285 4310 1990.09090909091 1326 0.000526315789473684 97 1.23776501397841 -1.131745913362 -1 3.43149321225043 4307 230 1324 97 1326 3245 3130 3860 218 1220 2934 929 M10914 STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN.html Genes down-regulated in prefrontal cortex (PFC) of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 609/707 Jessica Robertson 0.0356534567150173 0.0605867571150884 280 1704.09090909091 1326 0.00362387428440629 278 0.802213348763137 -0.731545667469451 -1 1.46559145684291 278 1135 4456 612 1936 525 599 1765 1326 4470 1643 930 M11572 BROWNE_HCMV_INFECTION_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_12HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 12 h time point that were not up-regulated at the previous time point, 10 h. 11711622 174/220 John Newman 0.00429092104086834 0.0117887935465067 1020 1492.36363636364 1327 0.000390846641581477 346 1.2412534484204 1.19389754105346 1 3.59183206769882 1016 2292 1739 1309 2414 2094 1327 346 508 1288 2083 931 M16312 REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_SURFACE_INTERACTIONS_AT_THE_VASCULAR_WALL.html Genes involved in Cell surface interactions at the vascular wall 99/131 Reactome 3.25860044879986e-06 3.7976775600828e-05 445 1431 1329 2.96236843217297e-07 328 1.28976562835385 1.21637675141068 1 8.55493773089248 443 2356 328 1662 2274 886 772 1329 3070 1166 1455 932 M4275 GOLUB_ALL_VS_AML_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOLUB_ALL_VS_AML_UP.html Up-regulated genes highly correlated with acute lymphoblastic leukemia (ALL) vs acute myeloid leukemia (AML). 10521349 33/38 Jean Junior 0.0007841829101412 0.0033018227795419 320 1715.63636363636 1330 7.13147790163003e-05 195 0.882229013755724 -0.94554398043771 -1 3.28457375283019 316 2518 2975 2907 360 195 488 1330 3544 3604 635 933 M7169 REACTOME_NCAM1_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NCAM1_INTERACTIONS.html Genes involved in NCAM1 interactions 43/60 Reactome 0.000210682877742886 0.00121865586145395 60 1879.45454545455 1331 1.91548233165818e-05 59 1.29824286138871 1.38167821712466 1 5.67671283892553 59 3370 525 4449 1112 888 1620 1331 4404 2705 211 934 M15669 GNATENKO_PLATELET_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/GNATENKO_PLATELET_SIGNATURE.html Top 50 most up-regulated genes in human platelet cells. 12433680 88/172 Kate Stafford 0.0019174539493394 0.00646756881262531 1005 1527.63636363636 1332 0.000174466107879174 36 1.22818648358601 -1.35592059611103 -1 4.03451990509665 1004 3680 1419 3865 682 36 878 1332 1959 1490 459 935 M15380 KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONIC_CARCINOMA_VS_SEMINOMA_DN.html Top 25 most highly expressed genes in seminoma relative to embryonic carcinoma tumors. 16424014 24/90 Arthur Liberzon 0.00957941068957405 0.0210988420227669 1025 1430 1333 0.000874670741816042 189 1.46174759821547 1.43100256671279 1 3.67543449199976 1022 3030 1604 1459 2784 1774 868 554 1113 1333 189 936 M1778 ZHANG_GATA6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_GATA6_TARGETS_DN.html Genes down-regulated after cre-lox knockout of GATA6 [GeneID=2627] in airway epithelium. 18536717 108/129 Jessica Robertson 0.000307700889362163 0.00162092432788996 630 1625.18181818182 1334 2.79767212800599e-05 547 1.24366490632459 1.22309508255788 1 5.20687911369079 629 2350 547 2918 1773 1334 886 1826 3645 980 989 937 M566 VERRECCHIA_RESPONSE_TO_TGFB1_C4 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C4.html Cluster 4: ECM related genes up-regulated in dermal fibroblasts later than 30 min after TGFB1 [GeneID=7040] addition; kept increasing with time. 11279127 45/55 John Newman 0.0144563431055165 0.0293731982169771 210 1795.81818181818 1335 0.00132292907835084 209 1.21312280890394 1.25066996822196 1 2.78870570310326 209 2928 1143 3464 2503 999 1249 1335 4126 1536 262 938 M6034 REACTOME_SEROTONIN_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEROTONIN_RECEPTORS.html Genes involved in Serotonin receptors 3/12 Reactome 0.0027752169244138 0.00855027668618352 2495 1731.63636363636 1336 0.000277868885139705 104 1.5442804018578 -1.47426023309742 -1 4.79195880972183 2492 1104 4236 471 1336 4401 2440 279 104 1617 568 939 M2631 FARMER_BREAST_CANCER_APOCRINE_VS_BASAL http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_APOCRINE_VS_BASAL.html Genes which best discriminate between two groups of breast cancer according the status of ESR1 and AR [GeneID=2099;367]: apocrine (ESR1- AR+) vs basal (ESR1- AR-). 15897907 439/571 Leona Saunders 2.16826939207189e-06 2.70032494210536e-05 2330 1246.63636363636 1337 1.97115593551934e-07 27 1.2016794503814 -1.24797084417386 -1 8.2377095514635 2329 510 309 27 1337 1483 3054 1862 1496 213 1093 940 M7061 CROMER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_METASTASIS_UP.html Metastatic propensity markers of head and neck squamous cell carcinoma (HNSCC): up-regulated in metastatic vs non-metastatic tumors. 14676830 124/157 Kevin Vogelsang 0.0126500496252673 0.0262453776840711 945 1723.54545454545 1337 0.00115667078914401 872 1.17220041640772 1.20167075713183 1 2.78063835911114 941 1806 872 1372 3107 1337 1287 1325 3368 1181 2363 941 M11067 KENNY_CTNNB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KENNY_CTNNB1_TARGETS_UP.html Genes up-regulated in HC11 cells (mammary epithelium) by expression of constantly active CTNNB1 [GeneID=1499]. 15642117 63/72 Yujin Hoshida 0.0891923821520341 0.130944959178103 1340 1517.36363636364 1340 0.00845708872476673 128 1.19479430092443 1.27211317875242 1 1.58278872409795 1340 128 1499 531 4405 765 916 3461 712 1470 1464 942 M973 REACTOME_INTERFERON_ALPHA_BETA_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_ALPHA_BETA_SIGNALING.html Genes involved in Interferon alpha/beta signaling 74/120 Reactome 0.0179074971112438 0.0346976134503574 460 1379 1341 0.00164135845932594 460 1.05552814326074 -1.02421841155476 -1 2.3118277432641 460 1341 2201 1589 1278 1038 1535 713 2015 1745 1254 943 M17044 WANG_HCP_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WANG_HCP_PROSTATE_CANCER.html Genes with the high-CpG-density promoters (HCP) that were up-regulated in 1542-CP3TX cells (prostate cancer) compared to 1542-NPTX (normal prostate). 17486081 166/220 Arthur Liberzon 0.00725884546348775 0.0169444859483987 755 2098.09090909091 1341 0.000662082460427219 456 1.15930321783579 1.10461051161755 1 3.08060153739146 754 4718 1972 4467 3559 1235 1173 456 2650 1341 754 944 M2346 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_UP http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_UP.html Top 20 up-regulated genes in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 22/36 Arthur Liberzon 0.00213856633138209 0.00702581017691599 1975 1426.45454545455 1341 0.000194604364824276 227 1.72869186717555 -1.98954151253536 -1 5.58542767633641 1972 1523 897 2266 692 2016 1341 227 3689 656 412 945 M1792 WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_UP.html Protease genes up-regulated at tumor-bone interface compared to the tumor alone area. 18632634 20/35 Jessica Robertson 0.000226271231541273 0.00129454571257552 760 1542.81818181818 1343 2.05722279105113e-05 189 1.11704145242614 1.00756526589681 1 4.84039873088492 757 988 2866 1724 189 1343 913 1118 1718 3256 2099 946 M2002 MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) without H3 methylation marks at K4 and K27 in embryonic stem cells (ES). 17603471 70/135 Arthur Liberzon 9.09895154446994e-06 9.34833590801027e-05 1500 1095.90909090909 1343 8.27180834265804e-07 366 1.57175609338914 1.37847916390095 1 9.50272213228256 1499 1343 366 1418 454 430 811 1877 1404 957 1496 947 M4976 DIRMEIER_LMP1_RESPONSE_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DIRMEIER_LMP1_RESPONSE_LATE_UP.html Cluster 3: genes up-regulated in B2264-19/3 cells (primary B lymphocytes) within 60-180 min after activation of LMP1 (an oncogene encoded by Epstein-Barr virus, EBV). 15674340 71/89 Arthur Liberzon 0.00529760395250617 0.0139146859520474 965 1526.54545454545 1345 0.000482763978539782 722 1.12744088138909 1.02414970566389 1 3.14066870508061 965 1345 1411 763 722 2134 1513 3302 1325 837 2475 948 M1978 ONO_AML1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONO_AML1_TARGETS_DN.html Genes down-regulated in CD4+ [GeneID=920] T lymphocytes by expression of AML1 [GeneID=861] off a viral vector. 17377532 31/54 Jessica Robertson 0.00288812963596177 0.00878348703720332 1345 1480.45454545455 1345 0.000262902555977338 267 1.33428713795261 1.34612294739516 1 4.11692918588665 1345 1473 990 1965 4095 1441 1797 267 1106 753 1053 949 M14811 LEE_LIVER_CANCER_ACOX1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_ACOX1_DN.html Genes down-regulated in hepatocellular carcinoma of ACOX1 [GeneID=51] knockout mice. 15565109 65/128 Yujin Hoshida 0.00211088434091605 0.00696739446791871 2400 1846.81818181818 1346 0.000192082949479162 226 1.38458830020735 -1.27022096082554 -1 4.48113657098031 2398 3708 696 3752 1346 427 931 226 3167 1131 2533 950 M3002 FRASOR_RESPONSE_TO_ESTRADIOL_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_ESTRADIOL_DN.html Genes down-regulated in MCF-7 cells (breast cancer) by estradiol (E2) [PubChem=5757]. 14973112 122/178 Arthur Liberzon 1.74652018616214e-08 3.71332219760598e-07 2870 1957.27272727273 1346 1.58774563638844e-09 103 1.34632352988288 -1.48869485026881 -1 12.9901663053349 2869 632 182 347 1009 3950 3547 2871 1346 103 4674 951 M5887 NABA_BASEMENT_MEMBRANES http://www.broadinstitute.org/gsea/msigdb/cards/NABA_BASEMENT_MEMBRANES.html Genes encoding structural components of basement membranes 22159717 49/56 Alexandra Naba 7.64344197858834e-05 0.000532109825058067 20 1794.09090909091 1346 6.94882504271295e-06 18 1.31335379032294 1.36159416006673 1 6.45200837271478 18 3355 517 3442 1834 1133 1336 1346 4539 1496 719 952 M3126 KEGG_LEISHMANIA_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEISHMANIA_INFECTION.html Leishmania infection 68/98 KEGG 0.0150998311679456 0.0303928371482744 625 1508.36363636364 1347 0.00138222515344798 592 1.11833414134693 1.19889420420396 1 2.54592968758973 623 1353 894 1347 4350 592 1141 1515 2441 883 1453 953 M11509 HASLINGER_B_CLL_WITH_11Q23_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_11Q23_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 11q23 region. 15459216 35/49 Kevin Vogelsang 0.0227803444560181 0.0420834543375364 1680 1677.54545454545 1347 0.00209270048392002 446 1.20767379232783 0.890343767012067 1 2.4931952713411 1676 882 1863 1778 4715 816 446 1126 1347 952 2852 954 M16496 CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_CTNNB1_UP.html Top 200 marker genes up-regulated in the 'CTNNB1' subclass of hepatocellular carcinoma (HCC); characterized by activated CTNNB1 [GeneID=1499]. 18701503 198/302 Yujin Hoshida 6.4429657195954e-13 2.81581464782318e-11 3520 1828.18181818182 1347 5.85724156327028e-14 78 1.39767935296372 -1.40878692198218 -1 22.1266689927845 3518 563 83 213 1347 3967 3694 1461 759 78 4427 955 M19509 MORI_PLASMA_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PLASMA_CELL_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: plasma cell. 18922927 41/60 Jessica Robertson 0.00118119689577413 0.00448988569632661 1350 1742.63636363636 1349 0.00010743923332488 425 0.907522755592311 0.994501379195308 1 3.19697711260606 1347 850 2076 2844 425 1349 1242 2153 3252 2582 1049 956 M2133 QI_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/QI_HYPOXIA.html Genes up-regulated by hypoxia in TRAMP-C cells (prostatic cancer). 20609350 187/201 Arthur Liberzon 0.0378377669431346 0.0636246027686481 1350 1513.81818181818 1349 0.00350042292188265 581 1.1287436116488 1.18664217746694 1 2.02619728909748 1349 581 1482 2282 3047 1156 2179 1115 1427 787 1247 957 M5754 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_DN http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_DN.html Genes down-regulated more than two-fold in lymphoblastoid cell lines from European population compared to those from Asian population. 17206142 20/30 Leona Saunders 0.000256757738225173 0.00141370404955761 3110 1915 1350 2.33443371654969e-05 204 1.20262723042459 0.970297512769356 1 5.14226117122776 3107 982 1287 1212 204 2254 1483 3957 962 1350 4267 958 M17321 REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_AND_INTERCONVERSION_OF_NUCLEOTIDE_DI_AND_TRIPHOSPHATES.html Genes involved in Synthesis and interconversion of nucleotide di- and triphosphates 21/22 Reactome 0.0223962770285979 0.0415201993617369 1100 1521.27272727273 1353 0.00205705247936687 544 0.84995051840249 -0.982362186829423 -1 1.76212161742213 1100 1535 3094 1075 2418 1462 544 807 548 2798 1353 959 M15535 KIM_WT1_TARGETS_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_12HR_UP.html Genes up-regulated in UB27 cells (osteosarcoma) at 12 hr after inducing the expression of a mutated form of WT1 [GeneID=7490]. 17430890 223/253 Arthur Liberzon 0.000952706614751842 0.00383030257378935 1310 1494.90909090909 1354 8.66472211986922e-05 335 1.15802225004631 1.15855880341977 1 4.19935446912829 1309 2270 616 2837 2617 559 1548 1354 2114 885 335 960 M5636 LEE_LIVER_CANCER_MYC_E2F1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_E2F1_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) from MYC and E2F1 [GeneID=4609;1869] double transgenic mice. 15565109 54/107 Yujin Hoshida 0.00222779659079689 0.00725686674158822 1530 1274.09090909091 1354 0.000202732339872823 271 1.26052142437207 1.31684794353369 1 4.04615387142347 1527 1919 689 1753 1354 271 319 525 2879 1270 1509 961 M1352 NIKOLSKY_BREAST_CANCER_15Q26_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_15Q26_AMPLICON.html Genes within amplicon 15q26 identified in a copy number alterations study of 191 breast tumor samples. 19010930 31/44 Jessica Robertson 0.00618281462550111 0.0150194982153192 4330 1735 1355 0.000563659936281115 627 1.4049623065389 1.30815343136845 1 3.84382205097389 4326 1998 1315 777 766 2011 1355 1676 627 1240 2994 962 M9387 KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION.html Vascular smooth muscle contraction 97/140 KEGG 0.00572859049119059 0.0142024584976285 1025 1619.36363636364 1356 0.000522141981928135 127 1.17192472853479 1.13348690443255 1 3.2489565774555 1021 2818 984 2670 1964 1356 989 1184 3271 1429 127 963 M1930 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_UP.html Genes from the yellow module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 42/51 Arthur Liberzon 0.00124418561068746 0.00464523632089661 1910 1216.36363636364 1356 0.000113171800334322 217 1.18816393406711 -1.10433003242425 -1 4.15930155368206 1909 217 1918 742 438 2019 1839 1061 264 1356 1617 964 M10165 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_UP.html Genes up-regulated in lobular carcinoma vs normal ductal breast cells. 17389037 113/129 Arthur Liberzon 4.29113556895108e-08 8.54605902339624e-07 85 1666.09090909091 1357 3.90103241150034e-09 85 1.35830826204433 1.38347241043005 1 12.367979652389 85 3234 196 2966 991 1572 1344 1357 4187 850 1545 965 M5888 RASHI_RESPONSE_TO_IONIZING_RADIATION_2 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_2.html Cluster 2: late ATM [GeneID=472] dependent genes induced by ionizing radiation treatment. 16314843 181/231 Arthur Liberzon 0.0260700594281801 0.04710975516884 905 1800.63636363636 1357 0.0023985649735841 853 1.19603916801692 1.07017869873999 1 2.38123662504969 903 1755 971 1357 4188 1250 1049 2925 1802 853 2754 966 M1625 BRACHAT_RESPONSE_TO_CAMPTOTHECIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_CAMPTOTHECIN_DN.html Genes specifically down-regulated in FL5.12 cells (pro-B lymphocyte) by camptothecin [PubChem=2538]. 12447701 66/92 John Newman 0.0429080029930517 0.0707884565282083 980 1600.54545454545 1357 0.00397895032739874 444 1.07712584014043 -1.10004288395787 -1 1.85864115442686 979 1357 3097 1653 2100 444 735 1301 671 3511 1758 967 M174 PID_UPA_UPAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_UPA_UPAR_PATHWAY.html Urokinase-type plasminogen activator (uPA) and uPAR-mediated signaling 18832364 49/84 Pathway Interaction Database 4.09582497173577e-05 0.000324454462245657 175 1282.54545454545 1358 3.72354657025344e-06 174 1.43451612319653 1.58371315084813 1 7.50970630854395 1835 175 436 369 174 1643 2328 1358 2203 539 3048 968 M2347 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_DN http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_TOP20_DN.html Top 20 down-regulated genes in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 23/32 Arthur Liberzon 0.00577426225782821 0.0142024584976285 2985 1714 1358 0.000526315789473684 145 1.1510718008489 -1.17365314970418 -1 3.19114359533131 2982 948 1272 145 4488 1429 2538 1555 873 1266 1358 969 M19891 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_12 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_12.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 12. 12554760 97/134 Arthur Liberzon 0.014484775040426 0.0294183038686793 955 1449.18181818182 1359 0.00132554827820465 207 1.09730799430411 -1.09075548703756 -1 2.52136527111468 951 1835 2663 1609 1359 207 853 1580 825 3005 1054 970 M2599 GHANDHI_BYSTANDER_IRRADIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_BYSTANDER_IRRADIATION_DN.html Genes significantly (FDR < 10%) down-regulated in IMR-90 cells (fibroblast) in response to bystander irradiation. 19108712 20/32 Itai Pashtan 0.000599558817511816 0.00264899703804299 1430 1356 1360 5.45202068807041e-05 331 1.3834388678105 1.21766206599852 1 5.34926209736346 1428 1533 1070 844 331 2126 1360 2273 817 758 2376 971 M594 REACTOME_SIGNALING_BY_NOTCH4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH4.html Genes involved in Signaling by NOTCH4 16/16 Reactome 0.00990954572124941 0.0216742612624176 2295 1475.36363636364 1361 0.000904951381476725 188 1.31796056844726 -1.50191407062004 -1 3.29077445281203 2294 404 1960 499 3698 1689 2743 535 188 1361 858 972 M14353 CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_INTERFERON_DN.html All marker genes down-regulated in the 'interferon' subclass of hepatocellular carcinoma (HCC). 18701503 55/68 Yujin Hoshida 0.0108699027104253 0.0232798164037958 3005 1907 1361 0.000993089444872295 273 1.2282014521378 1.22257087017445 1 3.00945439338521 3003 784 935 273 3757 2565 1361 1141 2711 605 3842 973 M6917 BIOCARTA_EPONFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPONFKB_PATHWAY.html Erythropoietin mediated neuroprotection through NF-kB 15/18 BioCarta 0.00152956186956571 0.00545694030563126 115 1330.72727272727 1362 0.000139147849269486 115 0.923403674802633 0.930832026933134 1 3.13554509842212 115 2102 2237 2124 465 331 210 1362 2775 2216 701 974 M64 PID_S1P_S1P4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P4_PATHWAY.html S1P4 pathway 18832364 15/18 Pathway Interaction Database 0.000141780300461923 0.000874775187163762 400 1522.27272727273 1362 1.2889948945606e-05 156 0.712134022769164 -0.746435472209205 -1 3.26769613603404 3149 399 3267 1362 156 396 671 1605 2049 3399 292 975 M604 REACTOME_SIGNALING_BY_NOTCH2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH2.html Genes involved in Signaling by NOTCH2 16/16 Reactome 0.00990954572124941 0.0216742612624176 2295 1476.36363636364 1362 0.000904951381476725 189 1.31796056844726 -1.50191407062004 -1 3.29077445281203 2295 405 1961 500 3699 1690 2744 536 189 1362 859 976 M618 REACTOME_SIGNALING_BY_NOTCH3 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH3.html Genes involved in Signaling by NOTCH3 16/16 Reactome 0.0133528414044047 0.0274979980055803 2300 1483.72727272727 1363 0.0012213255941961 190 1.31796056844726 -1.50191407062004 -1 3.08637338386336 2296 406 1962 501 3700 1691 2745 607 190 1363 860 977 M2585 SMIRNOV_RESPONSE_TO_IR_2HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_2HR_UP.html Genes up-regulated in B lymphocytes at 2 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 68/87 Itai Pashtan 0.00234513427612528 0.00753508085998047 390 1519.27272727273 1363 0.00021342162329452 92 1.1471065811264 1.05429383426966 1 3.65397027940218 386 2864 1363 3963 2497 181 92 490 2024 1705 1147 978 M1837 LABBE_WNT3A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_WNT3A_TARGETS_DN.html Down-regulated genes in NMuMG cells (mammary epithelium) after stimulation with WNT3A [GeneID=89780]. 17210685 120/248 Jessica Robertson 8.17699749177082e-06 8.53881154007926e-05 2115 1628.27272727273 1364 7.43366171302964e-07 361 1.31289842889961 1.31752275944804 1 8.015165090491 2112 1275 361 857 3114 1364 2031 1757 3207 912 921 979 M18117 XU_AKT1_TARGETS_48HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_AKT1_TARGETS_48HR.html Genes up-regulated in DU-145 cells (prostate cancer) expressing a dominant negative form of AKT1 [GeneID=207] upon sham-treatment for 48 h (as a control for the HGF [GeneID=3082] experiments). 17099727 10/13 Arthur Liberzon 0.00114484595609372 0.00441116156143865 2600 1304.81818181818 1365 0.000104131104600831 123 1.35895972379827 -1.42050367260339 -1 4.80299537013298 2597 429 2209 370 418 2259 1435 248 123 2900 1365 980 M8535 KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIO_SERIES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSPHINGOLIPID_BIOSYNTHESIS_GANGLIO_SERIES.html Glycosphingolipid biosynthesis - ganglio series 12/16 KEGG 3.88563371470994e-06 4.4732173496173e-05 2465 1406.72727272727 1367 3.53240052502006e-07 1 1.76993380701936 2.28001548363458 1 11.5510697725992 2463 1587 1367 127 184 3787 3325 1 60 2449 124 981 M676 REACTOME_PI_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI_METABOLISM.html Genes involved in PI Metabolism 47/51 Reactome 0.0029025621667738 0.00882169570326614 2335 1690.36363636364 1367 0.000264218067289438 66 0.832855979200007 -1.03836322352003 -1 2.56737290074278 2332 833 3715 635 1367 1966 2640 983 197 3860 66 982 M14371 NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN.html Down-regulated genes in peripheral zone of human pancreatic cancer growing in the pancreas of nude mice compared to that of the tumor from the central zone. 17699763 846/1057 Arthur Liberzon 0.00144146781088373 0.00521758287375093 970 1564.45454545455 1368 0.000144240368863964 442 1.18812816439307 1.23719462224038 1 4.06921298374422 970 2202 4274 600 1913 819 1691 2088 1368 442 842 983 M7617 BENPORATH_EED_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_EED_TARGETS.html Set 'Eed targets': genes identified by ChIP on chip as targets of the Polycomb protein EED [GeneID=8726] in human embryonic stem cells. 18443585 848/1581 Jessica Robertson 2.60125948384789e-28 6.46207619145369e-26 1000 1569.72727272727 1368 2.60125948384789e-29 6 1.40094233851849 1.36552130852258 1 52.9520713736134 997 2201 4452 1403 1368 445 1634 1278 2664 6 819 984 M1538 YANAGIHARA_ESX1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/YANAGIHARA_ESX1_TARGETS.html Genes down-regulated in U2-OS Tet-On cells (osteosarcoma) after induction of ESX1 [GeneID=80712] expression. 15897875 45/70 Arthur Liberzon 0.0202260526048539 0.03817151871048 960 1718.72727272727 1369 0.00185585756711483 414 1.36804566273561 1.45663962413075 1 2.91127104635779 957 1953 2188 2415 3707 1369 708 762 414 3182 1251 985 M1464 VALK_AML_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_2.html Top 40 genes from cluster 2 of acute myeloid leukemia (AML) expression profile; 71% of the samples are FAB M4 or M5 subtypes, and 82% bear internal tundem duplications in FLT3 [GeneID=2322]. 15084694 36/51 Jessica Robertson 0.0557394025260937 0.088326644245669 4280 2122.18181818182 1370 0.00520034878635194 245 1.07283993254877 -1.15557774589571 -1 1.69649451575542 4276 245 1370 295 3564 4002 4082 1167 735 1007 2601 986 M16848 KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_EPITHELIAL_CELL_SIGNALING_IN_HELICOBACTER_PYLORI_INFECTION.html Epithelial cell signaling in Helicobacter pylori infection 82/91 KEGG 0.131050187108253 0.1809704163695 1030 1505.72727272727 1371 0.0126888012695874 77 0.98269719726375 1.07814726500613 1 1.09459400429291 1026 77 2471 1371 3550 970 1098 1856 728 1853 1563 987 M11187 REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NCAM_SIGNALING_FOR_NEURITE_OUT_GROWTH.html Genes involved in NCAM signaling for neurite out-growth 78/96 Reactome 0.0163185880032709 0.0322815320098235 295 1859.81818181818 1371 0.00149462762539543 280 1.12505839480418 1.29422880650465 1 2.51703709239782 295 3272 1219 3257 1371 1004 1061 1573 4158 2968 280 988 M19806 REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_TRANSLATIONAL_PROTEIN_MODIFICATION.html Genes involved in Post-translational protein modification 168/203 Reactome 6.14058451584001e-05 0.000445900906380998 1670 1205 1371 5.58250537907649e-06 104 1.16505571125232 -1.11206786245736 -1 5.85766041666028 1670 585 1371 219 104 868 1715 2626 367 1407 2323 989 M612 REACTOME_CIRCADIAN_REPRESSION_OF_EXPRESSION_BY_REV_ERBA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CIRCADIAN_REPRESSION_OF_EXPRESSION_BY_REV_ERBA.html Genes involved in Circadian Repression of Expression by REV-ERBA 26/30 Reactome 0.0508461711510804 0.0818812445694642 755 1877.18181818182 1375 0.00473280099570198 210 0.870410646962774 0.967891351808351 1 1.4193499032243 752 3442 3558 1838 2665 1198 877 1116 210 3618 1375 990 M1720 LEIN_MIDBRAIN_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_MIDBRAIN_MARKERS.html Top 100 ranked genes most specific to midbrain region of adult mouse brain. 17151600 102/141 Jessica Robertson 0.00190697580626747 0.00644303923091086 1375 1574.36363636364 1375 0.000173511890484075 101 1.38273447847484 1.46990706326973 1 4.54563827809485 1375 1832 678 2001 3962 1079 1893 812 3069 516 101 991 M11410 LUCAS_HNF4A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LUCAS_HNF4A_TARGETS_UP.html Genes up-regulated in Tet-On HEK293 cells (embryonic kidney) by expression of HNF4A [GeneID=3172]. 16007190 79/96 Leona Saunders 0.0243788567920947 0.0445827989378872 2045 1290.54545454545 1377 0.00224120663486617 325 1.12908033583034 -1.17444821339898 -1 2.28848528712834 2041 721 1731 325 1460 1377 2702 1000 1670 812 357 992 M4740 BENPORATH_ES_CORE_NINE http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_CORE_NINE.html Set 'Core 9': 'embryonic stem cell' transcription regulators that are preferentially and coordinately overexpressed in the high-grade, ER-negative breast cancer tumors. 18443585 12/16 Jessica Robertson 0.00175988357230485 0.00608007010363419 540 1767.54545454545 1378 0.000160117542244956 73 0.895974411331348 0.895974411331348 1 2.97926860000752 536 3102 3040 2142 2465 1095 73 466 1378 3803 1343 993 M1609 LEE_CALORIE_RESTRICTION_NEOCORTEX_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_NEOCORTEX_DN.html Down-regulated in the neocortex of aged (30-month) mice subjected to caloric restriction since young adulthood. 10888876 141/204 John Newman 0.0328903335075595 0.0565958345445428 1690 1589.90909090909 1378 0.00303569030676472 999 1.10857825010766 1.12663573460801 1 2.07456725572693 1688 1251 999 1366 1613 1130 1277 1952 2690 1378 2145 994 M635 REACTOME_SIGNALING_BY_FGFR_IN_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR_IN_DISEASE.html Genes involved in Signaling by FGFR in disease 130/165 Reactome 0.0359017679993725 0.0609555197687187 1340 1571 1380 0.00331830849063677 7 0.90376704525313 0.818956278268517 1 1.64756300563904 1337 7 3175 912 1392 983 806 2287 1380 3288 1714 995 M8776 HELLER_SILENCED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_SILENCED_BY_METHYLATION_UP.html Genes up-regulated in at least one of three multiple myeloma (MM) cell lines treated with the DNA hypomethylating agent decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 18172295 311/565 Jessica Robertson 3.30620086046424e-14 1.73391867348791e-12 1360 1390.90909090909 1380 3.00563714587661e-15 67 1.330478488561 1.29401515195044 1 23.4796109951717 1357 2245 67 2265 1462 619 1380 1245 2630 136 1894 996 M2407 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_1 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_1.html Genes regulated in MCF7 cells (breast cancer) by expression of full-length and truncated (611-CTF) forms of ERBB2 [GeneID=2064] at both 15 h and 60 h time points. 19364815 69/82 Arthur Liberzon 1.63161463686268e-06 2.13922807944219e-05 1450 1249.45454545455 1380 1.4832871335814e-07 182 1.21262373866571 1.1769455678892 1 8.49680079388306 1446 736 535 1181 1386 1380 2095 2108 579 182 2116 997 M984 BIOCARTA_TOLL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TOLL_PATHWAY.html Toll-Like Receptor Pathway 56/78 BioCarta 0.0118827853381379 0.0249829607109181 560 2223.54545454545 1382 0.00108613245338429 560 0.88019661564305 0.994339738706885 1 2.11621028921834 560 3729 2852 4270 977 1088 754 1221 3950 3676 1382 998 M11790 ONDER_CDH1_TARGETS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_3_DN.html Genes down-regulated in HMLE cells (immortalized nontransformed mammary epithelial) cells after loss of function of E-cadhedrin (CDH1) [GeneID=999], which was achieved either by RNAi knockdown or by expression of a dominan-negative form of CDH1. 18483246 60/94 Jessica Robertson 6.02168926917835e-08 1.16485136682466e-06 1385 1560.54545454545 1382 5.47426312181809e-09 193 1.81646995357044 1.40432655136698 1 16.1731616908973 1258 1385 203 1742 2703 1382 1112 1381 3203 193 2604 999 M917 BIOCARTA_COMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_COMP_PATHWAY.html Complement Pathway 17/24 BioCarta 0.00152294713401449 0.00544981840223533 575 1898.18181818182 1383 0.000138545674095403 490 1.88373937275956 1.91023079517085 1 6.39821121989073 574 3061 658 2804 4532 1350 1383 1158 3414 1456 490 1000 M2038 CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_UP.html Genes up-regulated in APL (acute promyeolocytic leukemia) blasts expressing PML-RARA fusion [GeneID=5371;5914] compared to normal promyeloblasts. 16990782 260/396 Leona Saunders 0.0151508443814741 0.0304435868371894 2970 1647.09090909091 1383 0.00138692742063236 319 1.13644230501742 1.15024132432146 1 2.58591972910843 319 2739 1383 2970 3659 464 517 647 2968 1575 877 1001 M19971 RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_UP.html Genes up-regulated in peripheral blood mononucleocytes by HGF [GeneID=3082] compared to those regulated by CSF2RB (GM-CSF) and IL4 [GeneID=1437;3565]. 16527888 480/678 Arthur Liberzon 1.11332773899366e-08 2.44414275723258e-07 1485 1202.27272727273 1383 1.01211613147976e-09 98 1.18250271313816 1.22468592651224 1 11.7317977683984 1483 505 201 279 1383 1777 2380 1491 1189 98 2439 1002 M4716 CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/CONCANNON_APOPTOSIS_BY_EPOXOMICIN_UP.html Genes up-regulated in SH-SY5Y cells (neuroblastoma) after treatment with epoxomicin [PubChem=3035402], a protease inhibitor causing apoptosis. 16983338 322/404 Leona Saunders 0.00673891494020238 0.0159993765303422 1180 1555.09090909091 1384 0.000614513287254661 222 1.12885361493437 1.07536036131484 1 3.04190564080716 1177 3173 801 2438 1728 491 1745 1211 2736 1384 222 1003 M1229 OXFORD_RALB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALB_TARGETS_UP.html Genes up-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALB [GeneID=5899] by RNAi. 17496927 26/28 Arthur Liberzon 0.000246003718371424 0.00137607566270606 30 1793.72727272727 1384 2.23664755257114e-05 27 1.11008476554738 1.11008476554738 1 4.76607045683511 27 3032 1290 3007 1384 937 897 1578 4559 2727 293 1004 M1985 KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS http://www.broadinstitute.org/gsea/msigdb/cards/KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS.html Inflammatory cytokines and their receptors modulated in brain tumors after treatment with an oncocytic virus, a potential anticancer therapy. 18042934 27/57 Jessica Robertson 1.91826284877084e-06 2.43392490489203e-05 415 1454.72727272727 1384 1.74387683761681e-07 304 1.82073374662518 1.86671271087512 1 12.604722245611 411 2539 304 1203 3424 1434 1444 2443 1384 339 1077 1005 M2161 FIGUEROA_AML_METHYLATION_CLUSTER_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_1_DN.html Cluster 1 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 57/122 Arthur Liberzon 0.00157001247499118 0.00557177359545742 2455 1671.27272727273 1384 0.000142830365689486 469 1.25975120196886 -1.35011120697314 -1 4.26060207159516 2451 1384 1235 1795 469 1556 3811 2229 1010 1205 1239 1006 M184 PID_ECADHERIN_KERATINOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ECADHERIN_KERATINOCYTE_PATHWAY.html E-cadherin signaling in keratinocytes 18832364 34/40 Pathway Interaction Database 0.0300927545936189 0.0527375425762961 1270 1620.72727272727 1385 0.00277385803117175 255 0.794836106488486 0.807809869269735 1 1.52398028693807 1267 255 3207 432 2658 2098 1786 907 967 2866 1385 1007 M2849 TIMOFEEVA_GROWTH_STRESS_VIA_STAT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIMOFEEVA_GROWTH_STRESS_VIA_STAT1_DN.html Genes down-regulated in SK-NEP-1 cells (Wilm's tumor ) stably expressing inactivated forms of STAT1 [GeneID=6772] under growth stress (hypoxia or nutritional deprivation). 16799645 25/33 Arthur Liberzon 0.00262215087444979 0.00819075462055376 1385 1891.72727272727 1385 0.00023866194603136 103 0.805707236370708 -0.704274575875163 -1 2.5226435699502 1385 3848 3562 2734 566 163 103 390 4182 3579 297 1008 M19492 GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_DN.html Genes exclusively down-regulated in B lymphocytes from CLL (chronic lymphocytic leukemia) patients but with a similiar expression pattern in the normal cells and in the cells from WM (Waldenstroem's macroblobulinemia) patients. 17252022 71/90 Arthur Liberzon 0.00577426225782821 0.0142024584976285 3640 2101.09090909091 1386 0.000526315789473684 64 1.19098210186494 1.18433587044886 1 3.30179153666441 3636 96 874 64 1212 4122 3240 3635 1115 1386 3732 1009 M16774 WILCOX_RESPONSE_TO_PROGESTERONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILCOX_RESPONSE_TO_PROGESTERONE_DN.html Genes down-regulated in primary cultures of ovarian surface epithlium cells exposed to progesterone [PubChem=5994] for 5 days. 18070364 97/163 Arthur Liberzon 5.49000133139812e-05 0.000410662540161634 305 1700.45454545455 1387 4.99103485155055e-06 301 1.41930459406069 1.40352403247606 1 7.21213813747295 301 3247 448 3391 2292 926 996 1646 3386 685 1387 1010 M3010 HECKER_IFNB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HECKER_IFNB1_TARGETS.html Genes transcriptionally modulated in the blood of multiple sclerosis patients in response to subcutaneous treatment with recombinant IFNB1 [GeneID = 3456]. 23636981 87/145 Michael Hecker 0.00156552003110051 0.00556415069774526 1390 1393.45454545455 1387 0.000142421378752482 529 1.30497161744748 1.41936179785308 1 4.41471001193097 1387 703 660 529 1983 1766 1789 2292 1190 661 2368 1011 M14690 REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_FATTY_ACID_BETA_OXIDATION.html Genes involved in Mitochondrial Fatty Acid Beta-Oxidation 17/17 Reactome 8.85904165654105e-06 9.19003881733489e-05 2115 1603.63636363636 1388 8.05370666423629e-07 26 0.601431315199896 -0.605319975065502 -1 3.64283782554592 2115 389 3686 172 26 1381 2073 1388 63 4548 1799 1012 M15368 ROSS_AML_WITH_PML_RARA_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_PML_RARA_FUSION.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtype t(15;17): has PML RARA fusion [GeneID=5371;5914]. 15226186 112/135 Kate Stafford 0.0103674617162314 0.022467593801934 725 1685.45454545455 1389 0.00094696754353057 724 1.26382285277202 1.28413243572862 1 3.12598838255023 724 3232 847 2459 1480 1168 1389 1525 3370 1101 1245 1013 M15040 CONRAD_GERMLINE_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/CONRAD_GERMLINE_STEM_CELL.html Genes enriched in pluripotent adult germline stem cells. 18849962 9/17 Jessica Robertson 0.00370338332215929 0.0105875041069606 1335 2082.81818181818 1389 0.000370956960849532 339 1.26805935699623 1.26805935699623 1 3.75821522969025 1331 4268 4579 3579 2715 1389 416 339 898 2761 636 1014 M18227 BOYLAN_MULTIPLE_MYELOMA_PCA3_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA3_UP.html Top up-regulated genes from principal component 3 (PCA3) which captures variation among different plasma cell tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 90/124 Arthur Liberzon 0.00577426225782821 0.0142024584976285 55 1585.54545454545 1389 0.000526315789473684 53 1.23081624036097 1.14991523503692 1 3.41222832383853 2576 53 896 53 2619 2325 2770 1389 732 860 3168 1015 M6220 BIOCARTA_AGR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGR_PATHWAY.html Agrin in Postsynaptic Differentiation 50/59 BioCarta 0.00279416772644618 0.00857507910846942 985 1330.72727272727 1390 0.000254338441408285 552 1.11502954795295 1.36094876024669 1 3.45784349289524 981 1939 2284 1390 581 1263 552 1391 1557 1060 1640 1016 M1595 BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_UP.html Up-regulated genes in non-neoplastic mucosa samples from colon cancer patients who developed recurrence of the disease. 16091735 29/38 Leona Saunders 0.000416293235585253 0.00200500415506367 3485 1527.54545454545 1391 3.78520026557457e-05 82 1.29671380991709 1.10252798440797 1 5.24929013994298 3482 926 1939 815 285 2045 3387 82 1667 1391 784 1017 M1131 DARWICHE_SKIN_TUMOR_PROMOTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SKIN_TUMOR_PROMOTER_UP.html Genes up-regulated during skin tumor progression: epidermis treated with the carcinogen DMBA [PubChem=6001] followed by 20 weekly applications of the tumor promoter TPA [PubChem=4792], compared to the untreated skin. 17525749 163/260 Arthur Liberzon 0.0353947479492369 0.0602463794880628 1700 1678.27272727273 1392 0.00327066935764881 698 1.35131695934203 1.50466117586255 1 2.47380160186004 1696 2777 1008 1277 2808 1392 2012 2632 698 886 1275 1018 M714 REACTOME_PI3K_AKT_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PI3K_AKT_ACTIVATION.html Genes involved in PI3K/AKT activation 44/47 Reactome 0.000275545695279576 0.0014880728623794 215 1707 1393 2.50527466264975e-05 211 0.756474951003412 0.776145792437543 1 3.20926497431194 948 215 3274 2434 211 544 1393 1666 3441 3960 691 1019 M9556 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_DN.html Genes down-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 184/308 John Newman 0.000968591073798681 0.00387436429519473 1850 1424.36363636364 1394 8.8092525194123e-05 581 1.209868638017 1.14231312011476 1 4.37835266103504 1849 1226 618 767 2283 1787 1677 1076 1394 581 2410 1020 M13308 MURAKAMI_UV_RESPONSE_1HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_1HR_UP.html Genes up-regulated in primary keratinocytes at 1 h after UVB irradiation. 11532376 29/39 Arthur Liberzon 0.00873657699826284 0.019711588638528 565 1960.81818181818 1394 0.00079740596048062 249 2.00719785815835 -2.17113753642855 -1 5.13592092608133 562 3820 901 3947 4013 353 249 1678 4268 1394 384 1021 M1103 GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP.html Genes up-regulated in ME-A cells (breast cancer) undergoing apoptosis in response to doxorubicin [PubChem=31703]. 17160024 1500/1799 Arthur Liberzon 0.0121899974624542 0.0254925954908213 4450 2301 1395 0.00122573865306918 444 1.08334777091642 -1.08264662492846 -1 2.59040369551196 4446 1108 4337 444 2581 677 4586 4204 1395 625 908 1022 M4844 KEGG_CHEMOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHEMOKINE_SIGNALING_PATHWAY.html Chemokine signaling pathway 161/239 KEGG 0.0850586507447121 0.126131583887855 1215 1974.63636363636 1396 0.00804882560343013 902 1.0097135501122 1.02289749707236 1 1.36223186301056 1213 1237 1943 1137 3845 1396 902 3115 2638 1347 2948 1023 M862 BIOCARTA_P38MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P38MAPK_PATHWAY.html p38 MAPK Signaling Pathway 57/62 BioCarta 0.0308596541844854 0.0538276303587477 920 1822.63636363636 1396 0.00284556566809296 548 0.930370072523314 0.971013436934677 1 1.77146027413605 917 1396 3285 1918 4568 1325 548 917 1072 1910 2193 1024 M2049 REACTOME_SIGNALING_BY_PDGF http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_PDGF.html Genes involved in Signaling by PDGF 143/154 Reactome 0.00235873578890043 0.00757362783919048 215 1276.63636363636 1397 0.000214660774196142 57 1.04591697177117 1.07137955981329 1 3.32815569198447 214 1782 1483 1397 2693 124 626 831 2517 2319 57 1025 M5876 REACTOME_CTLA4_INHIBITORY_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CTLA4_INHIBITORY_SIGNALING.html Genes involved in CTLA4 inhibitory signaling 20/24 Reactome 0.0539255892801848 0.0859313914255476 1400 1909.81818181818 1397 0.005026782750896 902 0.584745633763767 0.676690519646514 1 0.935093388394835 1397 979 3425 902 2806 1850 1357 1150 1313 4064 1765 1026 M3389 LIU_TARGETS_OF_VMYB_VS_CMYB_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_TARGETS_OF_VMYB_VS_CMYB_UP.html Genes regulated in the opposite directions by v-MYB (UP) and c-MYB (DN) variants of CMYB [GeneID=4602] overexpressed in primary monocyte cultures off adenoviral vectors. 16205643 19/25 Arthur Liberzon 0.00085499021061157 0.00351835553102581 2615 1363.18181818182 1397 7.77566061811391e-05 314 1.48149834618616 1.70711819842376 1 5.4544251351306 2615 2093 1369 750 377 1397 1533 1860 580 2107 314 1027 M2451 PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_SIGNALING_VIA_NFIC_1HR_DN.html Genes down-regulated after 1 h of TGFB1 [GeneID=7040] stimulation in MEF cells (embryonic fibroblast) with NFIC [GeneID=4782] knockout vs wild type MEFs. 19752192 161/189 Arthur Liberzon 0.0171654593258398 0.0335490550799023 650 2121 1397 0.00157280673030296 650 1.14906743723925 1.12143059619852 1 2.5419143689118 650 2778 911 3804 4642 1239 1080 1397 3852 1664 1314 1028 M2533 BOSCO_EPITHELIAL_DIFFERENTIATION_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_EPITHELIAL_DIFFERENTIATION_MODULE.html Genes representing epithelial differentiation module in sputum during asthma exacerbations. 20336062 54/95 Antony Bosco 3.8097528250038e-09 9.26908934743193e-08 2785 1668.09090909091 1397 3.46341166509196e-10 110 1.84794106946469 -2.0778615817728 -1 19.5014048095233 2784 792 157 1404 4235 1940 3569 1113 1397 110 848 1029 M7669 LEE_TARGETS_OF_PTCH1_AND_SUFU_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_TARGETS_OF_PTCH1_AND_SUFU_UP.html Genes up-regulated in medulloblastoma tumors from animals with inactivating mutations of one copy of PTCH1 or SUFU [GeneID=5727;51684] in conjunction with TP53 [GeneID=7157] loss. 17452975 73/93 Jessica Robertson 0.0218099870640818 0.0406729114747001 830 2178.27272727273 1399 0.00200265932039591 278 1.18181452882901 1.22337129662803 1 2.46606379870201 828 3280 1399 4215 3720 278 664 1337 4180 2735 1325 1030 M2293 PASINI_SUZ12_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PASINI_SUZ12_TARGETS_DN.html Genes down-regulated in ES (embryonic stem cells) with defficient SUZ12 [GeneID=23512]. 17339329 456/529 Arthur Liberzon 3.97596245633668e-11 1.28537964341843e-09 890 1415.90909090909 1399 3.61451132400776e-12 85 1.18042798143551 1.1706136901976 1 15.7480745168789 886 1147 115 727 3082 1399 1637 2766 1889 85 1842 1031 M4577 MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/MISHRA_CARCINOMA_ASSOCIATED_FIBROBLAST_DN.html Top genes down-regulated in mesenchyme stem cells (MSC) grown in a tumor conditioned medium, which leads to carcinoma-associated fibroblast phenotype. 18519693 38/40 Leona Saunders 0.00376555695626896 0.0107004810454229 855 1951.63636363636 1400 0.000342910693964173 327 1.33884478241079 1.25643851486338 1 3.95875094291231 853 3783 740 3300 3185 327 706 1951 4433 1400 790 1032 M86 PID_ARF6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_PATHWAY.html Arf6 signaling events 18832364 55/66 Pathway Interaction Database 0.00766091645741377 0.0176646437122584 625 1256.18181818182 1401 0.000698884031841864 114 1.25305108034325 1.27153615145688 1 3.29573716781054 624 1401 1717 1912 2058 114 246 1724 619 2097 1306 1033 M167 PID_AP1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AP1_PATHWAY.html AP-1 transcription factor network 18832364 106/143 Pathway Interaction Database 0.0246950500565042 0.0451086053663698 775 1788.45454545455 1403 0.00227060805285746 301 1.18984769286963 1.17787569925094 1 2.40256644220867 773 3676 1026 3705 1947 301 537 1652 4123 1403 530 1034 M1729 GAVIN_FOXP3_TARGETS_CLUSTER_T4 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_T4.html Cluster T4 of genes with similar expression profiles in thymic T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 107/126 Jessica Robertson 0.0224583091345682 0.0416188532057959 1480 1299.63636363636 1403 0.00206280925407139 23 1.09769938937141 1.1757373443144 1 2.27408899700039 1480 23 1650 276 1403 2559 1914 808 448 1093 2642 1035 M17082 HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HADDAD_T_LYMPHOCYTE_AND_NK_PROGENITOR_UP.html Genes up-regulated in hematopoietic progenitor cells (HPC) of T lymphocyte and NK (natural killer) lineage. 15331438 137/161 Kevin Vogelsang 0.0515829756911774 0.0829263096942634 1125 1695.45454545455 1405 0.00480306226413583 766 1.04693637338402 1.1475545733024 1 1.6985734028805 766 1793 1124 1356 1579 1684 1178 1125 3720 2920 1405 1036 M11835 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION.html Valine, leucine and isoleucine degradation 52/60 KEGG 0.00156668565197107 0.00556415069774526 1980 1484.36363636364 1406 0.000142527495378339 468 1.02132134711967 -1.0423510314503 -1 3.45510009427716 1976 1406 2825 1830 468 687 1245 522 586 3204 1579 1037 M1053 KEGG_HEDGEHOG_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HEDGEHOG_SIGNALING_PATHWAY.html Hedgehog signaling pathway 40/61 KEGG 0.00577426225782821 0.0142024584976285 2330 1526.72727272727 1410 0.000526315789473684 89 1.26003744079026 -1.24923676931579 -1 3.49324163590259 2327 232 1429 89 4213 1155 2928 1410 531 1816 664 1038 M15381 REACTOME_TCR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TCR_SIGNALING.html Genes involved in TCR signaling 47/65 Reactome 0.00573281282561604 0.0142024584976285 475 1757.90909090909 1410 0.000522527841259461 471 0.893845805002042 0.924456056497116 1 2.47800623045967 471 829 2539 1876 741 1410 802 847 4334 3590 1898 1039 M11288 SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SCHLESINGER_METHYLATED_DE_NOVO_IN_CANCER.html Genes bearing H3K27me3 mark or whose promoters are bound by the polycomb proteins SUZ12 or EED [GeneID=23512;8726]; their DNA is methylated de novo in cancer. 17200670 88/126 Leona Saunders 2.72652387417357e-10 8.04324542881204e-09 1325 1455.18181818182 1410 2.47865806773771e-11 126 1.52607601083101 1.31114715518682 1 18.5357091639398 1324 2369 126 1410 816 1321 2219 2101 2200 134 1987 1040 M1634 WENG_POR_DOSAGE http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_DOSAGE.html Genes up-regulated in liver from mice with liver specific knockout of POR [GeneID=5447] vs mice with reduced expression of POR in all tissues. 16006652 28/69 John Newman 0.00773093517781364 0.0177739961223967 1185 1316.27272727273 1410 0.000705294233464023 470 1.19321016233275 1.22338649112441 1 3.13354161196528 1183 2032 1410 542 2038 1701 634 470 1675 1040 1754 1041 M18322 ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION.html Genes up-regulated in RD-EF cells (rhabdomyosarcoma) engineered to express EWSR1-FLI1 fusion [GeneID=2130;2313] and which are also highly expressed in Ewing's famliy tumors. 15930281 128/188 Kevin Vogelsang 0.0412541178105101 0.0684251500784001 2100 1643.63636363636 1411 0.00382260438332506 802 1.20270618920754 1.26518530847343 1 2.1019625575092 2098 2324 1243 802 3537 1025 1510 1031 1411 866 2233 1042 M643 REACTOME_ACYL_CHAIN_REMODELLING_OF_PC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PC.html Genes involved in Acyl chain remodelling of PC 14/23 Reactome 0.00577426225782821 0.0142024584976285 1915 1467.90909090909 1412 0.000526315789473684 44 1.21210009293658 -1.3305646899433 -1 3.36033938465555 1912 408 1412 44 2009 2205 3029 2403 1212 1158 355 1043 M1751 ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_DN.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are down-regulated only in mature (peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 48/62 Jessica Robertson 0.00246888033066411 0.00783139459726787 1110 1612.90909090909 1412 0.000224695937654832 550 1.10640360119601 1.12677676232338 1 3.49650206487183 1109 818 1609 1969 550 1939 1300 1412 3661 794 2581 1044 M281 PID_FAK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FAK_PATHWAY.html Signaling events mediated by focal adhesion kinase 18832364 102/118 Pathway Interaction Database 0.00577426225782821 0.0142024584976285 1415 1391.27272727273 1416 0.000526315789473684 198 1.04766407304969 1.11489955290632 1 2.90445439711358 1411 667 2492 198 1489 1978 1350 1416 544 1628 2131 1045 M2506 LEE_NEURAL_CREST_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_NEURAL_CREST_STEM_CELL_UP.html Genes up-regulated in the neural crest stem cells (NCS), defined as p75+/HNK1+ [GeneID=4804;27087]. 18037878 188/284 Arthur Liberzon 3.0300291079597e-18 2.42402328636776e-16 610 1488 1416 2.75457191632698e-19 44 1.57147915498977 1.70804711611879 1 36.8217187377271 609 2286 44 1223 2764 1346 1416 1475 2694 116 2395 1046 M1267 HOWLIN_PUBERTAL_MAMMARY_GLAND http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_PUBERTAL_MAMMARY_GLAND.html Genes up-regulated in pubertal mammary glands compared to mammary glands from other developmental stages. 16278680 71/115 Arthur Liberzon 1.04361429395818e-10 3.26215858773682e-09 4310 2417.45454545455 1417 9.48740267279711e-12 118 1.84997164790016 -1.89871093597596 -1 23.5577216516931 4309 742 118 1411 836 4676 4396 4351 1417 140 4196 1047 M11333 WEIGEL_OXIDATIVE_STRESS_BY_TBH_AND_H2O2 http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_BY_TBH_AND_H2O2.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to tert-butyl hydroperoxide (tBH) and H2O2 [PubChem=6410;784]. 12419474 81/118 John Newman 0.00718170860462542 0.016805981464468 980 1935.36363636364 1417 0.000655023670354099 108 1.21672177921993 -1.16904324633853 -1 3.23969217909913 980 4412 1417 4101 2900 108 637 561 4031 1822 320 1048 M4623 KORKOLA_TERATOMA http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_TERATOMA.html Genes predicting the teratoma (T) subtype of nonseminomatous male germ cell tumors (NSGCT). 15870693 63/87 Leona Saunders 0.0112334788237746 0.0238837928145119 1295 1731 1418 0.00102647743720871 629 1.39815515088447 1.36113827735156 1 3.40256836147853 1293 2424 858 3042 1768 1129 629 1344 3667 1469 1418 1049 M17843 NIELSEN_SCHWANNOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_SCHWANNOMA_UP.html Top 20 positive significant genes associated with schwannoma tumors. 11965276 15/25 John Newman 0.00577426225782821 0.0142024584976285 2710 1527.27272727273 1418 0.000526315789473684 75 1.8268642252134 1.54323261923838 1 5.06472105831228 2709 2617 996 75 2126 1418 586 2084 140 1259 2790 1050 M15456 MCCABE_HOXC6_TARGETS_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_CANCER_UP.html Genes whose promoters were bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and which were up-regulated in comparison of tumor vs normal prostate tissue samples. 18339881 33/50 Jessica Robertson 0.000836016660407473 0.00346140231326603 1775 1622.18181818182 1418 7.60304111080186e-05 122 1.33588651259979 1.55493292259324 1 4.93252372091572 1773 2514 1418 996 4619 1085 1850 122 543 2018 906 1051 M12641 JIANG_TIP30_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_TIP30_TARGETS_UP.html Up-regulated genes in HepG2 cells (liver cancer) overexpressing an oncogenic variant of tumor suppressor TIP30 [GeneID=10553] compared to its wild type form. 17440068 63/76 Jessica Robertson 0.0260020987232198 0.0470049429236298 1170 1796.36363636364 1418 0.00239223676532101 699 1.27844477345493 1.31729195707604 1 2.54716378317731 1169 2421 1209 1566 4145 699 1418 2685 2503 723 1222 1052 M19 PID_P73PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P73PATHWAY.html p73 transcription factor network 18832364 102/123 Pathway Interaction Database 0.0944866037457841 0.137647151135834 1420 1784.45454545455 1419 0.00898243358347279 672 0.957546779966596 0.916739321031351 1 1.23732906029547 1419 672 2894 1360 3017 735 990 2200 1175 2956 2211 1053 M499 REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BILE_ACID_AND_BILE_SALT_METABOLISM.html Genes involved in Bile acid and bile salt metabolism 25/53 Reactome 0.00357356123631817 0.0103100299727517 1160 1691 1419 0.000325398106459836 314 1.45348177826415 -1.46668762280962 -1 4.33293170973138 1158 3449 743 2527 628 1929 1905 314 4135 1419 394 1054 M1111 GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN.html Down-regulated genes from the set A (Fig. 5a): specific to cells expressing MLL-AF4 [GeneID=4297;4299] fusion protein alone. 17130830 148/206 Arthur Liberzon 8.15896852124329e-10 2.18890068241138e-08 1955 1398.63636363636 1419 7.41724411297197e-11 139 1.37006737716096 1.41647573015046 1 15.7469615805368 1953 1244 139 477 829 2047 1761 1419 2084 214 3218 1055 M3603 OUILLETTE_CLL_13Q14_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUILLETTE_CLL_13Q14_DELETION_DN.html Genes down-regulated in chronic lymphocytic leukemia (CLL) samples bearing deletions in the 13q14 region. 18281475 81/98 Jessica Robertson 0.0417948612186299 0.0691586158425896 1035 1403.63636363636 1420 0.00387369522827581 78 1.08605456022381 1.11128552604845 1 1.89053479067461 1818 78 1491 286 1951 2598 2856 1035 874 1033 1420 1056 M2510 ZHANG_RESPONSE_TO_CANTHARIDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_CANTHARIDIN_DN.html Genes down-regulated in HL-60 cells (promyeloid leukemia) by cantharidin [PubChem=6708701]. 14639605 95/114 John Newman 0.0298566623112248 0.0524463885779609 670 2078.90909090909 1421 0.00275179300182605 667 0.911553194372058 -0.949278051613679 -1 1.75107213500366 667 2826 3847 3881 1796 981 1421 903 1330 3810 1406 1057 M3988 ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_DN.html Genes down-regulated in 3 out of 4 NSCLC cell lines (non-small cell lung cancer) after treatment with azacitidine [PubChem=9444] and TSA [PubChem=5562]. 17043644 90/121 Leona Saunders 0.00911077118548708 0.0203216181671883 1520 2316.09090909091 1422 0.000831701951295645 542 0.883471212534306 -0.782946930377603 -1 2.2429768235554 1518 4401 4017 4614 874 542 1403 1311 1090 4285 1422 1058 M3518 WU_HBX_TARGETS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_3_DN.html Genes down-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] both in SK-Hep-1 cells (hepatocellular carcinoma) and normal primary hepatocytes. 11439330 18/23 John Newman 0.00369556031976837 0.0105736808285861 1425 1656.09090909091 1424 0.000336525705536094 113 0.751528115716162 -0.783100305324024 -1 2.22794074131227 1424 1008 2383 1622 2323 113 378 317 4478 3613 558 1059 M769 REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ELEVATION_OF_CYTOSOLIC_CA2_LEVELS.html Genes involved in Elevation of cytosolic Ca2+ levels 6/9 Reactome 0.00627941473630753 0.0152072024399033 4150 2135.45454545455 1427 0.000629722959851021 242 1.22550224755539 -1.64650612470235 -1 3.34290678797752 4147 1092 4234 968 795 3750 4517 773 242 1545 1427 1060 M3495 AGARWAL_AKT_PATHWAY_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/AGARWAL_AKT_PATHWAY_TARGETS.html Angiogenic and metastatic genes changed in RKO cells (colorectal cancer) upon perturbation of key components of AKT pathway. 15592509 10/11 Leona Saunders 0.0312673722005007 0.0543980821180845 1365 1899 1428 0.00288370965033223 359 2.58797441519899 2.58797441519899 1 4.91001196728887 1365 3938 1428 3971 3494 772 1162 1803 359 2182 415 1061 M17977 BIOCARTA_P27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P27_PATHWAY.html Regulation of p27 Phosphorylation during Cell Cycle Progression 16/17 BioCarta 0.00556612251769318 0.0142024584976285 1765 1851.45454545455 1429 0.00050729592746497 397 0.764748558602902 -0.544882537405795 -1 2.12009500999315 1761 403 3120 1300 738 1386 1429 2911 397 3940 2981 1062 M11984 FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_DN.html Genes down-regulated in genomically unstable Ewing's sarcoma tumors compared to the stable ones. 17952124 106/142 Jessica Robertson 0.00577426225782821 0.0142024584976285 2750 1662.63636363636 1430 0.000526315789473684 26 0.96808203288264 -0.957532825910552 -1 2.68381990708471 2750 26 2569 55 791 751 3068 4286 1430 2198 365 1063 M47 PID_INTEGRIN_CS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_CS_PATHWAY.html Integrin family cell surface interactions 18832364 22/27 Pathway Interaction Database 0.00276015085437032 0.00851497518472413 260 1483.90909090909 1431 0.000251238170278636 257 1.58826119361056 1.68588098426772 1 4.9327179589008 1431 973 967 1471 4038 1957 1943 257 260 1197 1829 1064 M1436 GUO_HEX_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUO_HEX_TARGETS_UP.html Genes up-regulated in day 6 embryoid bodies derived from embryonic stem cells (ES) with HEX [GeneID=3087] knockout. 12791650 122/141 Kevin Vogelsang 0.0567313817826178 0.0897359658223713 1140 1902.09090909091 1431 0.0052954007589136 742 1.06945273124887 1.1599131044368 1 1.68010570877366 1137 3650 2497 2707 2397 942 742 1431 1388 3036 996 1065 M6939 HOSHIDA_LIVER_CANCER_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SURVIVAL_UP.html Survival signature genes defined in adjacent liver tissue: genes correlated with poor survival of hepatocellular carcinoma (HCC) patients. 18923165 120/169 Yujin Hoshida 4.72030009414515e-08 9.28325685181879e-07 860 1375.27272727273 1432 4.29118199583953e-09 199 1.40453786118379 1.31526254425784 1 12.7131903414058 858 1273 199 1513 645 2081 1865 1432 3344 218 1700 1066 M1408 KIM_GERMINAL_CENTER_T_HELPER_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GERMINAL_CENTER_T_HELPER_DN.html Genes down-regulated in germinal center T helper cells compared to other CD4+ [GeneID=920] T lymphocyte types. 15213097 29/40 Kate Stafford 0.0136918308874623 0.0280858069486406 1230 1434.27272727273 1433 0.0012525266122523 613 1.26516686371212 1.32206882184014 1 2.94529945945858 1228 1475 1835 1196 1919 1117 1537 613 1433 1083 2341 1067 M15902 KEGG_GLYCEROLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROLIPID_METABOLISM.html Glycerolipid metabolism 53/70 KEGG 0.00577426225782821 0.0142024584976285 3195 1705.18181818182 1435 0.000526315789473684 46 1.38950344210151 -1.30780964292777 -1 3.85217519824181 3194 160 890 46 4585 1435 2334 2973 114 542 2484 1068 M9239 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_9 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_9.html Amplification hot spot 9: colocolized fragile sites and cancer genes in the 8p23-q12; 8q23 region. 16751803 16/17 Arthur Liberzon 0.00124126753933745 0.00464078749680228 1295 1376.27272727273 1436 0.000112906221065169 423 1.08267255203979 1.09869346705284 1 3.79068373843467 1295 1567 2294 870 436 1436 662 2090 423 2327 1739 1069 M11782 SMID_BREAST_CANCER_RELAPSE_IN_LIVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LIVER_DN.html Genes down-regulated in liver relapse of breast cancer. 18451135 11/14 Jessica Robertson 0.000472758282445655 0.00221469590671699 2000 1660.72727272727 1437 4.29872640097698e-05 298 1.71206324663325 1.56473872132804 1 6.81974311360923 1999 2637 936 1437 298 2106 2040 3910 734 1238 933 1070 M18806 TOOKER_GEMCITABINE_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOOKER_GEMCITABINE_RESISTANCE_DN.html Down-regulated genes in Calu3 cells (non-small cell lung cancer, NSCLC) resistant to gemcitabine [PubChem=3461] which became up-regulated in response to bexarotene [PubChem=82146]. 17483357 163/171 Jessica Robertson 0.113276262723158 0.160174943095658 1285 1708.72727272727 1437 0.0108697474639331 599 1.13841104659437 1.17932436437119 1 1.35861257152125 1281 599 2275 1237 1959 2759 3335 1913 1000 1001 1437 1071 M198 PID_SYNDECAN_1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_1_PATHWAY.html Syndecan-1-mediated signaling events 18832364 52/61 Pathway Interaction Database 0.000172020435807284 0.00102646834008898 365 1761.36363636364 1438 1.56394443407448e-05 361 1.32190057919473 1.41627815390247 1 5.92800486580489 361 1933 509 2432 1314 2470 2454 1404 3880 1180 1438 1072 M1766 TESAR_JAK_TARGETS_MOUSE_ES_D3_DN http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_JAK_TARGETS_MOUSE_ES_D3_DN.html Genes down-regulated in mES cells (mouse embryonic stem cells) after tratment with JAK inhibitor I [PubChem=5494425]. 17597760 9/15 Jessica Robertson 7.39771283703732e-05 0.000520375627284891 2905 2077.63636363636 1438 7.3979591162746e-06 18 1.75239753240077 -2.86731811328857 -1 8.63436393172478 2901 1068 4527 1438 400 4368 3698 18 358 2758 1320 1073 M19610 CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_UP.html Marker genes up-regulated in the 'unannotated' subclass of hepatocellular carcinoma (HCC) samples. 18701503 102/161 Yujin Hoshida 0.00149365118843078 0.00536124228851201 190 1428.81818181818 1438 0.000135878749227197 184 1.08228599482895 1.17188801660135 1 3.68754861252161 187 1828 2062 2334 4360 551 659 184 1438 1630 484 1074 M631 REACTOME_COLLAGEN_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COLLAGEN_FORMATION.html Genes involved in Collagen formation 57/64 Reactome 1.27302757714508e-06 1.72663510463356e-05 90 1569.18181818182 1439 1.15729846707426e-07 88 1.50192872026031 1.5156281691242 1 10.7336923124063 88 2443 288 2131 2147 1439 1883 1280 3478 813 1271 1075 M1543 HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_24HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_24HR.html Genes discriminating between direct (cisplatin, MMS, mitomycin C [PubChem=2767;4156;5746]) and indirect (paclitaxel, hydroxyurea, etoposide [PubChem=4666;3657;36462]) acting genotoxins at 24 h time point. 15120960 83/114 John Newman 0.0152097503289298 0.0305359513196719 1440 1622.54545454545 1439 0.00139235749525871 211 1.05093122141664 -0.93670140504119 -1 2.38926073165015 1439 2380 3192 1900 1400 211 823 1478 983 3422 620 1076 M1129 MCBRYAN_TERMINAL_END_BUD_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_TERMINAL_END_BUD_UP.html The 'TEB profile genes': up-regulated during pubertal mammary gland development specifically in the TEB (terminal end bud) structures. 17486082 16/17 Arthur Liberzon 0.00677622049807718 0.0160589450307787 2620 1797.18181818182 1440 0.000617925671167096 391 1.5391763925021 1.32662667802656 1 4.14390748180829 2620 391 803 712 1440 2915 1923 2521 940 987 4517 1077 M2619 ZWANG_EGF_INTERVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_INTERVAL_UP.html Genes induced in the time interval between two pulses of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 85/171 Yaara Zwang 0.00121714341302473 0.00457762303543962 780 1903.81818181818 1440 0.000110710665090935 161 1.09344715867907 1.00508656492821 1 3.83817426620193 779 3681 1440 3721 2713 849 1075 161 3643 2248 632 1078 M9177 BIOCARTA_DC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DC_PATHWAY.html Dendritic cells in regulating TH1 and TH2 Development 25/83 BioCarta 0.00113040669812467 0.00437104989901119 750 1670.72727272727 1441 0.000102817085749288 153 1.22253559201332 1.28939374404481 1 4.32809611331317 748 3471 1493 2914 1441 1166 623 153 3665 2204 500 1079 M5053 EHRLICH_ICF_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/EHRLICH_ICF_SYNDROM_UP.html Up-regulated in B lymphocytes from patients with ICF syndrom caused by mutations in DNMT3B [GeneID=1789] compared to normals. 11741835 18/23 John Newman 0.00186952983533755 0.00636020284346217 1445 1520.18181818182 1442 0.000170101857164579 367 0.969353442118352 -1.01137484054758 -1 3.19482097843725 1442 1547 1801 1465 498 539 850 367 3972 3073 1168 1080 M5060 SA_FAS_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SA_FAS_SIGNALING.html The TNF-type receptor Fas induces apoptosis on ligand binding. 9/11 SigmaAldrich 3.88122244119568e-05 0.000310497795295654 4325 1727.54545454545 1443 3.88129023035639e-06 28 1.32121272296748 -1.22047604857707 -1 6.95440992524868 4322 434 4201 366 82 3775 1528 164 28 1443 2660 1081 M110 PID_IL1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL1_PATHWAY.html IL1-mediated signaling events 18832364 40/47 Pathway Interaction Database 0.00645784247019794 0.0155205260015678 290 1480.09090909091 1443 0.000588806998173241 200 0.930217504162127 0.981267162672694 1 2.52504512067591 286 1443 3122 1630 3168 314 200 781 2166 2512 659 1082 M1675 GERHOLD_ADIPOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_ADIPOGENESIS_UP.html Selected genes up-regulated during differentiation of 3T3-L1 cells (fibroblast) into adipocytes in response to adipogenic hormones. 12021175 62/71 John Newman 0.000364426523176625 0.00182760746255676 3720 2021.45454545455 1443 3.3135173077952e-05 115 1.15595904026232 1.31052068772769 1 4.74926705203157 3719 115 604 313 255 4001 4462 2976 1443 479 3869 1083 M14857 REACTOME_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPHINGOLIPID_METABOLISM.html Genes involved in Sphingolipid metabolism 65/73 Reactome 0.00577426225782821 0.0142024584976285 2700 1629.18181818182 1445 0.000526315789473684 102 1.07863148728304 -0.956127319319356 -1 2.9903089395775 2700 112 2480 102 2277 1445 3565 1360 106 2359 1415 1084 M2621 ZWANG_EGF_PERSISTENTLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_PERSISTENTLY_DN.html Genes persistently repressed by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 83/110 Yaara Zwang 0.0102892725488697 0.0223289041060529 1575 1341.72727272727 1445 0.000939792031726483 197 1.16464362743371 -1.18267508318078 -1 2.88536583080381 1571 1856 1581 1528 2952 246 1394 704 1445 1285 197 1085 M244 SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_BRAIN_DN.html Genes down-regulated in brain relapse of breast cancer. 18451135 156/196 Jessica Robertson 0.0415048886127785 0.0687861918020767 4230 2339.81818181818 1446 0.00384629460338062 350 1.20233895687061 -1.2829487377886 -1 2.09719735382501 4227 1239 1082 350 1446 3081 4638 4704 1390 1068 2513 1086 M3034 BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 43/52 Leona Saunders 0.00443921254537945 0.0120976231028816 1450 2024.54545454545 1447 0.000404381407374645 355 1.09090841156905 1.14214894236193 1 3.13837991189303 1447 3771 1274 3810 2615 2013 1405 355 4265 763 552 1087 M1294 GALIE_TUMOR_ANGIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/GALIE_TUMOR_ANGIOGENESIS.html Angiogenic genes up-regulated in A17 carcinomas (high vascularization) compared to the syngeneic BB1 and spontaneous tumors (little vascularization). 17998939 9/9 Jessica Robertson 0.00549244665076565 0.0142024584976285 960 1976.18181818182 1447 0.000550606919799354 411 1.1970810094073 1.24558332113832 1 3.3187002431077 958 2166 4425 3714 1428 2765 1235 411 2293 1447 896 1088 M14693 VANTVEER_BREAST_CANCER_POOR_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_POOR_PROGNOSIS.html The optimal set of 70 prognostic markers predicting poor breast cancer clinical outcome (defined as developing metastases with 5 years). 11823860 82/129 Arthur Liberzon 0.0513136847123535 0.0825496223048086 805 1706.72727272727 1447 0.00477737707517416 801 1.22975637195992 1.35048368052315 1 1.99885177589262 801 2390 1333 2751 1927 1314 1398 1124 2642 1647 1447 1089 M9740 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 8 days after transduction. 16818636 186/354 Arthur Liberzon 2.88009985043474e-15 1.65781357244536e-13 805 1499 1448 2.61827259130431e-16 60 1.41340626008212 1.45945437362939 1 27.1052710819385 805 1223 60 1688 3945 1694 1448 988 2957 77 1604 1090 M19341 KRIGE_AMINO_ACID_DEPRIVATION http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_AMINO_ACID_DEPRIVATION.html The 'amino acid deprivation response' (AADR): genes up-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after amino acid deprivation or treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703]. 18701491 35/39 Jessica Robertson 3.20406241525154e-05 0.000268677072551052 1450 1592.54545454545 1448 2.91282643628357e-06 66 1.26879857398216 0.993329205993789 1 6.79813105906362 1313 1448 805 2294 66 729 954 3981 1448 1500 2980 1091 M16708 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_5.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 5. 12554760 52/62 Arthur Liberzon 0.00089938602536771 0.00365641863887648 345 1856.36363636364 1448 8.17958105080551e-05 345 1.18440553480578 1.3183991863642 1 4.33089035765452 345 2895 607 3417 1448 1074 849 2814 4118 1918 935 1092 M14105 DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_LOW_DOSE_UV_RESPONSE_VIA_ERCC3_XPCS_DN.html Genes down-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071], after low dose UVC irradiation. 15608684 16/28 Arthur Liberzon 7.08456602256756e-05 0.000502844385361186 405 1480.45454545455 1449 6.44072197646076e-06 10 1.50548560882519 1.40374556763385 1 7.45139316077929 401 3527 1638 3181 1673 178 10 1449 2849 1368 11 1093 M1191 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_2NM_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment with 2 nM docetaxel [PubChem=148124]. 17099726 33/54 Arthur Liberzon 0.00241470631411378 0.00769575543728363 1450 2052.27272727273 1450 0.000219760069140417 544 1.26776144254107 1.12213753760207 1 4.02088154776117 1450 4146 784 3074 544 1177 1316 2732 4229 2016 1107 1094 M1333 RAHMAN_TP53_TARGETS_PHOSPHORYLATED http://www.broadinstitute.org/gsea/msigdb/cards/RAHMAN_TP53_TARGETS_PHOSPHORYLATED.html Proteins phosporylated in HCT116 cells (colon cancer) upon p53 [GeneID=7157] activation. 18438429 35/44 Jessica Robertson 0.0269237459603144 0.0483746025628793 620 1740.45454545455 1450 0.00247809079971333 616 0.984788907954448 -0.948972660651799 -1 1.94362913265642 616 1990 3080 1586 1259 678 1318 1382 2834 2952 1450 1095 M1694 HARRIS_BRAIN_CANCER_PROGENITORS http://www.broadinstitute.org/gsea/msigdb/cards/HARRIS_BRAIN_CANCER_PROGENITORS.html Genes from the brain cancer stem (cancer stem cell, CSC) signature. 19074870 38/60 Leona Saunders 9.5396002114562e-05 0.0006341818732123 1095 2283.81818181818 1450 8.67273990089868e-06 480 1.63715303213186 1.46717053687118 1 7.8555148708624 1092 3799 480 4548 4158 1089 1013 1450 4441 1684 1368 1096 M2381 KUWANO_RNA_STABILIZED_BY_NO http://www.broadinstitute.org/gsea/msigdb/cards/KUWANO_RNA_STABILIZED_BY_NO.html Transcripts stabilized by NO [PubChem=145068] identified as up-regulated by NO [PubChem=145068] in the presence of actinomycin D [PubChemiD=2019] in IMR-90 and NIH 3T3 cells (fibroblast). 19289500 9/9 Arthur Liberzon 2.19547925420475e-05 0.000197008784787955 1490 1741.63636363636 1450 2.19550094508756e-06 56 1.43427768790075 -1.60405305400911 -1 7.97476315735961 1490 1621 4695 2335 56 899 851 4350 383 1450 1028 1097 M4665 BAELDE_DIABETIC_NEPHROPATHY_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAELDE_DIABETIC_NEPHROPATHY_DN.html Genes down-regulated in glomeruli of kidneys from patients with diabetic nephropathy (type 2 diabetes mellitus). 15042541 639/758 John Newman 0.0544411254998531 0.0866651306439482 1205 1800.36363636364 1451 0.00558227335472018 1133 1.07292885155613 1.10951111934646 1 1.70991294031622 1201 1133 4498 1380 1755 1451 1848 1199 2177 1212 1950 1098 M5032 DER_IFN_ALPHA_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_ALPHA_RESPONSE_DN.html Genes down-regulated in HT1080 cells (fibrosarcoma) by treatment with interferon alpha for 6 h. 9861020 5/5 Yujin Hoshida 4.32079037952109e-05 0.000339902176522326 1945 1893.90909090909 1454 4.32087439335291e-06 89 1.45763722917889 -0.996458910829422 -1 7.58656509052901 1943 1647 4540 1454 89 864 983 1279 4544 3090 400 1099 M17557 DANG_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DANG_MYC_TARGETS_DN.html Genes down-regulated by MYC [GeneID=4609] and whose promoters are bound by MYC, according to MYC Target Gene Database. 14519204 39/42 Chi Dang 0.002320241415633 0.00746827961275641 3455 1667 1454 0.000211153826318911 188 0.999225978569381 -0.895774800379021 -1 3.18869927425157 3451 237 2614 188 536 1313 1925 4137 387 1454 2095 1100 M12480 LINDSTEDT_DENDRITIC_CELL_MATURATION_B http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_B.html Maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli: genes up-regulated both at 8 hr and 48 hr after the stimulation (cluster B). 12356685 70/83 Arthur Liberzon 0.00781715019989499 0.0179127544608161 230 1481.54545454545 1455 0.000713187768589101 228 1.14755522348485 1.09224323559699 1 3.00782566392771 228 1883 1455 2338 4574 767 404 474 1516 956 1702 1101 M240 PID_SYNDECAN_2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SYNDECAN_2_PATHWAY.html Syndecan-2-mediated signaling events 18832364 58/68 Pathway Interaction Database 0.000493956585373491 0.00228800302547878 1755 1345.27272727273 1456 4.49152296550949e-05 152 1.22781006845419 1.32527912620992 1 4.8647089495211 1755 152 2125 905 307 2054 1676 2486 640 1242 1456 1102 M501 REACTOME_SIGNALING_BY_RHO_GTPASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_RHO_GTPASES.html Genes involved in Signaling by Rho GTPases 115/130 Reactome 0.0198323595768434 0.0375335754621896 2315 1703.45454545455 1456 0.00181940290266945 250 1.18210458656859 1.23561074536073 1 2.52854768010989 2312 637 1205 250 3842 1954 2483 1456 1036 680 2883 1103 M7581 NAKAMURA_CANCER_MICROENVIRONMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_CANCER_MICROENVIRONMENT_UP.html Genes up-regulated in pancreatic cancer cells grown in orthotopic xenograft tumors compared to those grown in vitro. 17210693 35/63 Arthur Liberzon 0.000118895168498601 0.000762479884936677 615 1761.18181818182 1457 1.08092358606466e-05 490 1.6401583321432 1.64386923246408 1 7.67301224005414 612 1984 490 1378 843 2830 3125 1457 3854 950 1850 1104 M10462 KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADIPOCYTOKINE_SIGNALING_PATHWAY.html Adipocytokine signaling pathway 70/102 KEGG 0.0950066331537353 0.138191466405433 1460 1533.45454545455 1458 0.00903418653075539 105 0.944748394709436 1.01800362426777 1 1.21835995717209 1458 105 1949 588 4456 898 942 1567 1895 1336 1674 1105 M5483 YANG_BREAST_CANCER_ESR1_BULK_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_BULK_DN.html Genes down-regulated in bulk samples from early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative samples. 16261164 27/44 Leona Saunders 0.028473187172684 0.0506107131215275 1130 1330 1458 0.00262259235600122 502 1.38361086387629 1.37018490919247 1 2.69006288511796 1126 1485 1685 502 1663 1458 1919 1692 931 738 1431 1106 M16941 DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_ERCC3_ALLELE_XPCS_VS_TTD_UP.html Genes up-regulated in fibroblasts expressing different mutant forms of ERCC3 [GeneID=2071]: XP/CS (xeroderma pigmentosum (XP) and Cockraine's syndrome (CS)) vs TTD (trichothiodystrophy). 15608684 25/33 Arthur Liberzon 0.00135386014866097 0.00494599063597506 1460 1419.54545454545 1459 0.000123154001862608 171 1.44272765236429 1.41492764925256 1 4.99147102215132 1459 2554 792 687 1604 1654 1024 171 2538 833 2299 1107 M2061 NIELSEN_LEIOMYOSARCOMA_CNN1_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_CNN1_DN.html Top 20 negative significant genes associated with leiomyosarcoma tumors expressing muscle gene cluster with CNN1 [GeneID=1264]. 11965276 33/43 John Newman 0.00186625097222999 0.00636020284346217 1345 1897.09090909091 1459 0.000169803271634408 662 1.40735182407744 1.53994980277419 1 4.63843556808431 1342 1459 675 2502 4718 1866 847 1356 3939 662 1502 1108 M10084 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_DN.html Genes down-rgulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 6h. 16818636 49/66 Arthur Liberzon 0.0150301837294366 0.0303043431024949 1205 2220.45454545455 1461 0.00137580558868893 640 1.134774933455 1.07425208089101 1 2.58551563673401 1202 4460 1119 4370 2139 1131 1374 640 4482 2047 1461 1109 M737 LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIEN_BREAST_CARCINOMA_METAPLASTIC_VS_DUCTAL_DN.html Genes down-regulated between two breast carcinoma subtypes: metaplastic (MCB) and ductal (DCB). 17603561 148/223 Arthur Liberzon 0.00498371499854327 0.0132899066627821 3215 1855.90909090909 1461 0.000454094606171471 449 1.13638277179133 -1.01601679746039 -1 3.19959918991924 3211 602 763 449 3505 1461 4118 3130 1562 882 732 1110 M2339 DUAN_PRDM5_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/DUAN_PRDM5_TARGETS.html Direct targets of PRDM5 [GeneID=11107]. 17636019 95/174 Arthur Liberzon 0.00364678760735826 0.0104637310071313 2290 1562.63636363636 1461 0.000332076972769947 548 1.30544430956333 1.38582746406816 1 3.8790220026237 2286 690 737 1461 2585 2327 2390 1307 1171 548 1687 1111 M1807 MATZUK_OVULATION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_OVULATION.html Genes important for ovulation, based on mouse models with female fertility defects. 18989307 24/27 Jessica Robertson 0.0109817794520787 0.0234807748378332 1635 1650.90909090909 1463 0.00100336214306038 895 1.42671654358363 1.16111152346464 1 3.48790039712141 1632 2058 1463 2860 944 1052 1097 895 3251 1703 1205 1112 M12898 REACTOME_GAP_JUNCTION_TRAFFICKING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_TRAFFICKING.html Genes involved in Gap junction trafficking 16/27 Reactome 0.075797568065841 0.114155877878357 2280 1675.81818181818 1464 0.00714021838599543 781 1.27129969797067 1.25983713929435 1 1.79782055132249 2276 1010 1464 1436 1697 2380 2764 1422 781 1365 1839 1113 M17990 BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_DN.html Genes from cluster 2: down-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 38/69 Jessica Robertson 0.00036474708256959 0.00182760746255676 2095 1740.63636363636 1467 3.31643245031317e-05 327 1.58910867064042 1.48455127615848 1 6.52890546112045 2092 865 555 1416 3389 3241 2595 1467 327 712 2488 1114 M7098 KEGG_ECM_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ECM_RECEPTOR_INTERACTION.html ECM-receptor interaction 85/94 KEGG 1.54311781091484e-08 3.29570862783623e-07 130 1478.90909090909 1468 1.40283438339867e-09 128 1.55985165152725 1.66124451984513 1 15.1717099918925 128 2377 181 2425 1806 1468 1988 912 3323 522 1138 1115 M13166 REACTOME_DOWNSTREAM_TCR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_TCR_SIGNALING.html Genes involved in Downstream TCR signaling 32/42 Reactome 0.00240699491386237 0.00768674965726008 515 1504.09090909091 1470 0.000219057492760765 191 0.855785223783276 0.870238368920563 1 2.71486034617152 513 1472 2698 1874 543 481 191 1154 2975 3174 1470 1116 M5465 MCCABE_HOXC6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_DN.html Genes with promoters bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and down-regulated upon loss of function (LOF) of HOXC6. 18339881 30/38 Jessica Robertson 0.0101846108861016 0.0221731380915127 2360 2005.27272727273 1470 0.000930187914459643 626 1.19557166010933 1.21121324521922 1 2.96744595272262 2358 1470 880 713 911 4690 3849 3935 1719 907 626 1117 M18149 RUTELLA_RESPONSE_TO_HGF_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUTELLA_RESPONSE_TO_HGF_UP.html Genes up-regulated in peripheral blood monocytes by HGF [GeneID=3082]. 16527888 489/649 Arthur Liberzon 6.10535660407704e-08 1.1762156396426e-06 2020 1579.09090909091 1470 5.55032433955509e-09 151 1.1684637853364 1.18411198253361 1 10.3961293242895 2017 503 204 666 1470 2673 2486 2816 1149 151 3235 1118 M4723 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_HSC_DN.html Genes down-regulated in normal hematopoietic progenitors by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 182/303 Arthur Liberzon 2.1664220542087e-07 3.67824176110254e-06 1495 1513.72727272727 1471 1.96947478867672e-08 139 1.32060836200952 1.31718015976588 1 10.768617880811 1493 1225 231 944 4713 2032 1624 656 2123 139 1471 1119 M6656 HASINA_NOL7_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HASINA_NOL7_TARGETS_UP.html Genes up-regulated in SiHa cells (cervical carcinoma) by stable expression of NOL7 [GeneID=51406] off a plasmid vector. 16205646 14/17 Leona Saunders 0.000410214308522095 0.0019904230216429 885 1584.18181818182 1472 3.72991652259613e-05 281 1.07665474981108 1.09318103915948 1 4.36356150544723 885 2129 2149 2648 281 734 663 1472 2701 3317 447 1120 M19586 VALK_AML_WITH_CEBPA http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_CEBPA.html Genes that best predicted acute myeloid leukemia (AML) with mutations in CEBPA [GeneID=1050]. 15084694 49/66 Jessica Robertson 0.00569404657382569 0.0142024584976285 2400 1952 1472 0.000518985231350775 674 1.36186280906198 1.37123459216965 1 3.77554387587373 2400 815 828 1248 739 4623 4115 1825 1472 674 2733 1121 M1189 DING_LUNG_CANCER_BY_MUTATION_RATE http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_BY_MUTATION_RATE.html The lung adenocarcinoma TSP (tumor sequencing project) genes mutations in which show positive correlation with the higher overall mutation rate. 18948947 43/47 Arthur Liberzon 0.00189122391669539 0.00640816718363405 2440 1796.63636363636 1473 0.000172077423767619 676 1.39470566150881 1.58103050691566 1 4.58992615172528 2440 1428 676 1473 4058 1258 1406 2380 1796 764 2084 1122 M12073 HAHTOLA_MYCOSIS_FUNGOIDES_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_DN.html Genes down-regulated in monocytes isolated from peripheral blood samples of patients with mucosis fungoides compared to those from normal healthy donors. 16914566 13/24 Arthur Liberzon 7.04180352413818e-05 0.000501316932638495 1820 1537.27272727273 1474 6.40184448152666e-06 108 1.19297213814757 1.29630358676005 1 5.90695250958048 1816 1040 1747 298 108 2581 2463 3990 272 1474 1121 1123 M10457 LUCAS_HNF4A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LUCAS_HNF4A_TARGETS_DN.html Genes down-regulated in Tet-On HEK293 cells (embryonic kidney) by expression of HNF4A [GeneID=3172]. 16007190 13/18 Leona Saunders 0.00577426225782821 0.0142024584976285 2595 1735.45454545455 1475 0.000526315789473684 171 1.59753860947504 -1.30055207667136 -1 4.42893514263607 2593 1038 1067 171 4229 3084 1728 874 241 1475 2590 1124 M10544 BOYAULT_LIVER_CANCER_SUBCLASS_G56_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G56_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G56, defined by unsupervised clustering. 17187432 24/27 Yujin Hoshida 0.0062097456406571 0.0150771601974802 1205 1507.45454545455 1476 0.00056612208353242 418 1.22216742578189 1.34419439305934 1 3.3406498133442 1203 1501 1280 2028 2702 1213 1476 418 1750 783 2228 1125 M8583 STEIN_ESTROGEN_RESPONSE_NOT_VIA_ESRRA http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESTROGEN_RESPONSE_NOT_VIA_ESRRA.html Genes up-regulated by estradiol [PubChem=5757] and not modulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 21/24 Arthur Liberzon 0.00123130693277782 0.00461617849301931 1465 1713 1476 0.000111999692475439 165 0.856042797092551 0.825677526771293 1 3.00014512960326 1463 2082 2521 2584 1476 1144 794 165 2067 3328 1219 1126 M1194 NAISHIRO_CTNNB1_TARGETS_WITH_LEF1_MOTIF http://www.broadinstitute.org/gsea/msigdb/cards/NAISHIRO_CTNNB1_TARGETS_WITH_LEF1_MOTIF.html Genes regulated by CTNNB1 [GeneID=1499] and whose promoters contain binding sites for LEF1 [GeneID=51176]. 15735679 8/11 Leona Saunders 0.0102533756942837 0.0222714833304275 1190 2085.18181818182 1477 0.0010300994484531 294 1.38895791337907 1.44095341186805 1 3.44344803602792 1190 2676 4382 2619 4455 1404 294 1477 2792 1294 354 1127 M9634 SESTO_RESPONSE_TO_UV_C4 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C4.html Cluster 4: genes changed in primary keratinocytes by UVB irradiation. 11867738 32/37 John Newman 0.0616108064234547 0.0959268337625045 985 1619.27272727273 1477 0.00576427675516954 777 1.32353067569138 -1.40024266127694 -1 2.02174517157945 983 1477 2080 1843 2516 985 777 2823 805 2737 786 1128 M9270 VALK_AML_WITH_11Q23_REARRANGED http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_11Q23_REARRANGED.html Genes that best predicted acute myeloid leukemia (AML) with the 11q23 rearrangements. 15084694 19/39 Jessica Robertson 0.0952890973679581 0.138431683464685 1670 1612.45454545455 1477 0.00906230849471623 372 1.5680076682884 1.77462948864744 1 2.0204184516628 1477 372 1186 523 4085 2555 1668 2714 483 1669 1005 1129 M779 REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_SIGNAL_TRANSDUCTION.html Genes involved in Downstream signal transduction 106/111 Reactome 0.251230993714363 0.313374812455548 1470 1779.90909090909 1478 0.0259593583042012 35 0.872781381408772 0.794394146198139 1 0.659861735403274 1469 35 3343 430 2687 1379 1459 2304 1478 3334 1661 1130 M13206 KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN.html Genes down-regulated in TC71 and EWS502 cells (Ewing's sarcoma) by EWSR1-FLI1 [GeneID=2130;2314] as inferred from RNAi knockdown of this fusion protein. 17114343 485/623 Leona Saunders 1.83136326431715e-11 6.35590779968894e-10 1240 1553.90909090909 1478 1.66487569484764e-12 107 1.18760885942905 1.28560611148717 1 16.3889161443581 1237 2218 107 1455 1984 2075 2547 682 3036 274 1478 1131 M16009 ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN.html Genes whose DNA is hyper-methylated in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 780/1587 Jessica Robertson 2.30075066202852e-06 2.85777450651964e-05 1170 1697.54545454545 1478 2.30075304408611e-07 189 1.24622978136467 1.17701282277985 1 8.49708916276359 1168 1123 4547 721 2191 1270 1478 1628 2665 189 1693 1132 M2023 YIH_RESPONSE_TO_ARSENITE_C5 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C5.html Genes in cluster 5: slowly down-regulated in HFW cells (fibroblast) by sodium arsenite [PubChem=26435]. 12016162 13/17 Arthur Liberzon 0.0105548696303204 0.0227900204277732 1870 1605.27272727273 1478 0.000964168286411023 203 1.58747408017085 2.10901437879955 1 3.91180655964062 1868 2126 1047 1976 2378 1306 515 955 3806 1478 203 1133 M1280 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM4.html Cluster PAM4: genes down-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 242/403 Leona Saunders 0.0199805151874682 0.0377836665404045 1990 1507.18181818182 1480 0.00183312005688818 675 1.12216830759401 1.19053344215838 1 2.39548084039201 1989 1200 1021 675 1152 1581 2490 2126 1807 1058 1480 1134 M1719 LEIN_CHOROID_PLEXUS_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_CHOROID_PLEXUS_MARKERS.html Genes enriched in choroid plexus cells in the brain identified through correlation-based searches seeded with the choroid plexus cell-type specific gene expression patterns. 17151600 115/154 Jessica Robertson 4.34669258387002e-09 1.04345955142166e-07 4115 2072.63636363636 1480 3.95153872041644e-10 22 1.43612645664144 -1.25954165590081 -1 15.0446363729954 4111 638 159 22 2931 4235 4000 757 1480 187 4279 1135 M2092 KAMIKUBO_MYELOID_CEBPA_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/KAMIKUBO_MYELOID_CEBPA_NETWORK.html Network of differentially expressed myeloid genes centered around CEBPA [GeneID=1050]. 20478528 27/48 Arthur Liberzon 0.000357339798925857 0.00180339214729506 2080 1782.45454545455 1480 3.24907139840158e-05 249 1.89863867437928 1.95130282745581 1 7.81714354281297 2079 1480 602 755 249 4053 4413 3287 496 567 1626 1136 M2411 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_5 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_5.html Genes regulated in MCF7 cells (breast cancer) by expression of the truncated (611-CTF) form of ERBB2 [GeneID=2064] at 15 h time point. 19364815 13/13 Arthur Liberzon 0.0196870525443779 0.0373117551581051 1055 1769.81818181818 1480 0.00180595131803862 972 1.53451239475552 1.63402254292967 1 3.28831467491887 1813 3086 1055 3710 1149 1446 1521 1055 972 1480 2181 1137 M2470 MALIK_REPRESSED_BY_ESTROGEN http://www.broadinstitute.org/gsea/msigdb/cards/MALIK_REPRESSED_BY_ESTROGEN.html Genes consistently and robustly repressed by estradiol [PubChem=5757] in MCF7 cells (breast cancer); this reperession was prevented by fulvestrant [PubChem=3478439]. 19917725 13/15 Arthur Liberzon 0.00950190548432517 0.0209620623225621 990 1674.81818181818 1481 0.00086756314069752 257 1.72233480683804 1.67998907982352 1 4.33797666950003 990 3919 1520 3068 2701 929 257 1052 1509 1481 997 1138 M18356 XU_HGF_TARGETS_INDUCED_BY_AKT1_6HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_INDUCED_BY_AKT1_6HR.html Genes changed in DU-145 cells (prostate cancer) in the absence but not presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 6 h. 17099727 27/36 Arthur Liberzon 0.111649484843448 0.158111481686491 1485 1757.54545454545 1482 0.0107049164863742 737 1.09696989881777 1.22977679369381 1 1.31842070662176 737 1481 1518 1749 3852 1438 1551 1482 2965 1252 1308 1139 M17372 LEE_LIVER_CANCER_MYC_TGFA_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_TGFA_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) tissue of MYC and TGFA [GeneID=4609;7039] double transgenic mice. 15565109 60/113 Yujin Hoshida 6.89988203136416e-05 0.000492699594372751 2180 1449.81818181818 1482 6.27281676596145e-06 377 1.24271593201792 1.2320487781607 1 6.16730293134796 2180 765 463 706 2219 2023 1482 610 2446 377 2677 1140 M2084 WANG_METASTASIS_OF_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METASTASIS_OF_BREAST_CANCER.html Genes whose expression in primary ER(-) [GeneID=2099] breast cancer tumors negatively correlates with developing distant metastases. 15721472 31/45 Arthur Liberzon 0.0454801768102471 0.0743304828754731 360 2011.54545454545 1482 0.00422259312193823 356 1.01259266880443 1.00660516558265 1 1.71506073582172 356 3822 1398 3419 1482 815 795 2114 4551 2262 1113 1141 M17340 DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS http://www.broadinstitute.org/gsea/msigdb/cards/DEBOSSCHER_NFKB_TARGETS_REPRESSED_BY_GLUCOCORTICOIDS.html NF-kB-driven pro-inflammatory genes that are negatively regulated by glucocorticoids. 17072333 17/29 Arthur Liberzon 0.00129813051247843 0.00479217899694665 570 1980.18181818182 1483 0.000118081556349731 566 1.57493114393522 1.37067631870844 1 5.48129513348263 566 3887 642 3529 1483 923 1092 2166 4439 1458 1597 1142 M1334 HASEGAWA_TUMORIGENESIS_BY_RET_C634R http://www.broadinstitute.org/gsea/msigdb/cards/HASEGAWA_TUMORIGENESIS_BY_RET_C634R.html Genes up-regulated in salivary, thyroid and mammary gland carcinomas developed in transgenic mice carrying RET [GeneID=5979] allele with the MEN2A mutation (C634R). 18542059 32/35 Jessica Robertson 0.000270226281091843 0.00146744372235182 245 1482.18181818182 1484 2.45690435208504e-05 243 1.31032103001792 1.18851756838676 1 5.5708962090419 243 2001 541 1365 1053 1484 1536 2207 3509 618 1747 1143 M1390 SHIN_B_CELL_LYMPHOMA_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_6.html Cluster 6 of genes distinguishing among different B lymphocyte neoplasms. 19010892 6/16 Jessica Robertson 0.000231366652182497 0.00131890168876979 1485 1578.81818181818 1484 2.3139074445035e-05 48 1.64437576881138 1.58160479668136 1 7.10553629697373 1484 2174 4460 1489 480 1152 1611 48 2398 948 1123 1144 M1839 LABBE_TGFB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TGFB1_TARGETS_DN.html Down-regulated genes in NMuMG cells (mammary epithelium) after stimulation with TGFB1 [GeneID=7040]. 17210685 140/235 Jessica Robertson 2.22301806896807e-05 0.000198724342528964 1385 1816.18181818182 1484 2.02094593823232e-06 400 1.36942834854987 1.35102065239172 1 7.60645043528084 1381 2315 400 2556 3416 874 1099 3194 2708 551 1484 1145 M12242 PENG_GLUCOSE_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUCOSE_DEPRIVATION_UP.html Genes up-regulated in BJAB cells (B-lymphoma) after glucose [PubChem=206] deprivation. 12101249 51/80 Broad Institute 0.00577426225782821 0.0142024584976285 2325 1500.54545454545 1486 0.000526315789473684 158 1.08385948547662 -1.1378252374268 -1 3.00480312335177 2322 164 2121 158 2243 1273 2606 569 1486 2170 1394 1146 M8276 REACTOME_NUCLEAR_RECEPTOR_TRANSCRIPTION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEAR_RECEPTOR_TRANSCRIPTION_PATHWAY.html Genes involved in Nuclear Receptor transcription pathway 35/50 Reactome 0.000372689306943132 0.00186147463362072 3830 2320 1487 3.38865870059935e-05 185 1.34199952055713 1.13968359474289 1 5.49757527588995 3830 263 1487 711 257 4521 4423 4169 185 1221 4453 1147 M8924 WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP.html Genes up-regulated in esophageal adenocarcinoma (EAC) and Barret's esophagus (BE) relative to normal esophagi. 16449976 44/59 Leona Saunders 0.00114871229771809 0.00441524596517052 225 1647.09090909091 1487 0.000104482957037658 222 1.18230128479679 1.12944873924512 1 4.17790150499523 222 2476 630 2208 1894 881 879 2136 4206 1487 1099 1148 M11078 YANG_BREAST_CANCER_ESR1_LASER_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_LASER_DN.html Genes down-regulated in laser microdissected (LCM) samples of early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 69/75 Leona Saunders 0.10177465500804 0.146233294258128 1310 1616.54545454545 1487 0.00971021220774187 819 1.22992512609322 1.2198565390936 1 1.54082411612729 1307 1887 2429 839 2127 1174 969 1487 819 2274 2470 1149 M1869 VILIMAS_NOTCH1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VILIMAS_NOTCH1_TARGETS_UP.html Genes up-regulated in bone marrow progenitors by constitutively active NOTCH1 [GeneID=4851]. 17173050 44/80 Jessica Robertson 0.00506711692929817 0.0134742489612886 335 1549 1489 0.000461711405648841 175 1.17366478531631 1.06630872090635 1 3.29403782784146 332 2480 1062 3982 1999 265 175 725 2896 1489 1634 1150 M4508 ENK_UV_RESPONSE_EPIDERMIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_EPIDERMIS_DN.html Genes down-regulated in epidermis after to UVB irradiation. 16434974 729/857 Lauren Kazmierski 8.07917969680063e-07 1.16261366368594e-05 890 1748.09090909091 1491 8.07918263409363e-08 163 1.15223796071588 1.11543780217767 1 8.53154011427896 889 1667 4326 1301 1491 938 1164 2951 2377 163 1962 1151 M1311 WONG_ENDMETRIUM_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ENDMETRIUM_CANCER_DN.html Genes down-regulated in cancer endometrium samples compared to the normal endometrium. 17043662 124/156 Arthur Liberzon 1.36582508059635e-10 4.1861651820875e-09 120 1623.54545454545 1491 1.24165916425558e-11 119 1.44953479318103 1.44037948396289 1 18.2229131644129 119 3224 121 3136 1131 1491 1084 1954 3811 265 1523 1152 M7409 MODY_HIPPOCAMPUS_NEONATAL http://www.broadinstitute.org/gsea/msigdb/cards/MODY_HIPPOCAMPUS_NEONATAL.html Genes highly expressed in the neonatal hippocampus (clusters 4 and 8). 11438693 69/85 John Newman 0.0157255115206716 0.0313845303922073 270 1878.81818181818 1491 0.00143991406597396 268 1.25666257335959 1.21297391157866 1 2.83455844393461 268 3710 898 3697 1776 940 1036 1558 3990 1303 1491 1153 M2116 VERHAAK_GLIOBLASTOMA_NEURAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_NEURAL.html Genes correlated with neural type of glioblastoma multiforme tumors. 20129251 140/198 Arthur Liberzon 0.00577426225782821 0.0142024584976285 3440 2216.27272727273 1492 0.000526315789473684 28 1.24158196336311 -0.975377543933422 -1 3.44207538228767 3436 610 1060 28 4045 4440 3893 1492 566 721 4088 1154 M2225 KANG_AR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_AR_TARGETS_DN.html Genes down-regulated in osteoblasts from wild type male mice compared to those with AR [GeneID=367] knockout. 18838539 31/38 Arthur Liberzon 0.00180323580669424 0.00620355175480818 210 1644.36363636364 1492 0.000164065048360573 206 1.59345048787939 1.7144930643105 1 5.27770074385682 206 3407 672 1924 1492 1262 1438 2449 2528 1540 1170 1155 M2317 KASLER_HDAC7_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/KASLER_HDAC7_TARGETS_1_UP.html Genes up-regulated in DO11.10 cells (hybridoma) by expression of transciptionally activating form of HDAC7 [GeneID=51564] and down-regulated by its transcriptionally repressing form. 17470548 232/263 Arthur Liberzon 0.0221007420173986 0.041101458755761 1495 1440.72727272727 1492 0.00202963045896834 283 1.11258147365907 -1.02528493489946 -1 2.31399135949925 1492 558 1955 782 2347 283 1684 3193 1545 1410 599 1156 M155 PID_S1P_META_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_META_PATHWAY.html Sphingosine 1-phosphate (S1P) pathway 18832364 25/30 Pathway Interaction Database 0.000911221678400623 0.00369498824918465 1475 1687.81818181818 1493 8.28726652573147e-05 128 0.944686653372227 -1.05281993237102 -1 3.44785442395785 1475 1493 2124 2147 1747 921 1414 128 4226 2646 245 1157 M19152 PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN http://www.broadinstitute.org/gsea/msigdb/cards/PUIFFE_INVASION_INHIBITED_BY_ASCITES_DN.html Genes down-regulated in OV-90 cells (ovarian cancer) exposed to ascites which inhibited invasion. 17971902 179/201 Arthur Liberzon 0.037566871294068 0.0632366735049933 480 1690.27272727273 1494 0.00347492043198362 478 1.0646252537088 1.10183569230653 1 1.91533604776813 478 1760 3422 1862 2815 1027 752 998 886 3099 1494 1158 M2386 GILDEA_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/GILDEA_METASTASIS.html Top genes down-regulated in metastatic (T24T) vs non-metastatic (T24) bladder cancer cell lines. 12438227 60/78 Kevin Vogelsang 9.20942907763007e-05 0.000617604867008724 420 1781.36363636364 1494 8.37255874228688e-06 418 1.56430470793881 1.65918999964349 1 7.53296459601798 418 3308 476 2456 753 1430 1494 1927 3734 1319 2280 1159 M6285 REACTOME_OPSINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OPSINS.html Genes involved in Opsins 4/8 Reactome 0.00181347153558159 0.00622725344253624 1495 1910.45454545455 1495 0.0001814953143093 219 2.39308722849978 2.39308722849978 1 7.92030048990114 1495 3959 4242 2815 1569 1221 530 219 1281 2913 771 1160 M5392 BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins; the changes did not depend on expression of constitutively active (Q63L) form of RHOA [GeneID=387]. 17213802 36/41 Leona Saunders 0.000432128347966011 0.0020581693263366 680 1647.09090909091 1496 3.92921137107793e-05 186 1.59998674831062 1.67924178297124 1 6.44972158860222 678 2967 562 2062 4671 1496 2368 186 1795 410 923 1161 M9898 BENPORATH_SUZ12_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_SUZ12_TARGETS.html Set 'Suz12 targets': genes identified by ChIP on chip as targets of the Polycomb protein SUZ12 [GeneID=23512] in human embryonic stem cells. 18443585 834/1473 Jessica Robertson 9.36388775769467e-35 4.91083891292432e-32 915 1590.45454545455 1496 9.36388775769465e-36 2 1.42256385872242 1.3776400861054 1 66.8313029947474 912 2200 4451 1401 1573 280 1496 2016 2456 2 708 1162 M305 CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70 http://www.broadinstitute.org/gsea/msigdb/cards/CHIARETTI_ACUTE_LYMPHOBLASTIC_LEUKEMIA_ZAP70.html Differentially expressed genes between high vs low ZAP70 [GeneID=7535] acute lymphoblastic leukemia (ALL) cases with no known molecular aberrations. 16160012 73/90 Kevin Vogelsang 0.00577426225782821 0.0142024584976285 1500 1473.45454545455 1496 0.000526315789473684 82 1.03118544301555 1.1448211112178 1 2.85876878605956 1496 87 1821 82 4494 2231 1622 406 565 1928 1476 1163 M1296 BIOCARTA_IL7_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL7_PATHWAY.html IL-7 Signal Transduction 25/27 BioCarta 0.00577426225782821 0.0142024584976285 1500 1401 1497 0.000526315789473684 179 0.977094712635785 1.07515420732789 1 2.70880680107429 1497 315 2183 179 3380 879 719 1568 181 2645 1865 1164 M1138 CROONQUIST_NRAS_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_SIGNALING_UP.html Genes up-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing a constantly active form of NRAS [GeneID=4893] off a plasmid vector compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 37/65 Arthur Liberzon 0.00704630999913295 0.0165712920756889 615 1767.72727272727 1497 0.000642634556341474 450 1.26017280174901 1.40271520997685 1 3.36693916894077 615 2503 1497 1895 4470 919 1259 450 2922 1638 1277 1165 M3952 BIOCARTA_LAIR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LAIR_PATHWAY.html Cells and Molecules involved in local acute inflammatory response 15/23 BioCarta 0.000803400013037078 0.00336174473540338 1500 2282 1498 7.30630500184096e-05 598 2.03248970416704 1.71675338746084 1 7.54335624878447 1498 3530 598 3953 1444 1860 1114 4346 4296 1257 1206 1166 M700 REACTOME_ACYL_CHAIN_REMODELLING_OF_PG http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PG.html Genes involved in Acyl chain remodelling of PG 9/18 Reactome 0.0523533159741375 0.0839645434583517 2725 2086.09090909091 1498 0.00536292214819519 707 1.57770695011465 1.01267508676934 1 2.54696896021405 2724 1622 4219 707 4166 1498 1311 1176 879 1445 3200 1167 M1614 DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_RHABDOMYOSARCOMA_PAX_FOXO1_FUSION_DN.html Genes down-regulated in RMS cells (rhabdomyosarcoma) expressing PAX3 or PAX7 fusions with FOXO1 [GeneID=5077;5081;2308] compared to the fusion negative cell lines. 16849537 34/41 Arthur Liberzon 0.000149860878574249 0.0009174362475622 335 1640.63636363636 1498 1.36246443507548e-05 331 1.37518721292387 1.46339293241644 1 6.26760669808458 331 2515 503 2672 1049 1360 1498 1939 3767 902 1511 1168 M1264 WANG_RESPONSE_TO_BEXAROTENE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_BEXAROTENE_DN.html Genes down-regulated in the mouse lung cancer model and which reverted to normal levels upon treatment with bexarotene [PubChem=82146]. 16247446 35/51 Leona Saunders 0.0554511426105023 0.087976266595486 2920 1931 1498 0.00517274459236421 260 1.24514530018235 -1.31238025742252 -1 1.97220521242341 2920 260 1211 1009 3229 3107 2578 1288 3522 1498 619 1169 M8349 MARCHINI_TRABECTEDIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARCHINI_TRABECTEDIN_RESISTANCE_DN.html Genes down-regulated in chondrosarcoma and ovarian carcinoma cell lines which developed resistance to trabectedin [PubChem=3199]. 15661559 117/164 John Newman 0.0147663701162085 0.0298617253421183 640 1921.63636363636 1498 0.00135149302192391 268 1.07367448047244 1.1388446581849 1 2.45659097641758 640 3659 1498 3688 1042 268 1184 1972 4138 2194 855 1170 M1289 HUI_MAPK14_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUI_MAPK14_TARGETS_UP.html Genes up-regulated in fetal liver (days E13.5 and E15.5) samples from embryo-specific Cre-lox knockout of MAPK14 [GeneID=1432]. 17468757 25/34 Leona Saunders 0.0295750985034367 0.0520098602593968 4365 2090.54545454545 1500 0.00272548461511922 919 1.31090913681805 -1.408221026862 -1 2.52541200347337 4362 1500 1171 1033 1310 3974 4175 919 1555 1097 1900 1171 M15171 SASAKI_ADULT_T_CELL_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/SASAKI_ADULT_T_CELL_LEUKEMIA.html Genes up-regulated in adult T-cell leukemia (ATL) cells compared to T lymphocytes from healthy controls. 15471956 234/286 Kate Stafford 0.0679012496683101 0.104293491192458 1505 1947.09090909091 1502 0.00637202243025242 599 1.03514137353558 -1.03478147480829 -1 1.52478656543585 1502 1204 3013 599 4484 616 1892 2071 1425 3249 1363 1172 M3004 CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_DN.html Genes down-regulated in type 2B (EDL) vs type 1 (soleus) myofibers. 21364395 24/45 Emmanuelle Fouilloux-Meugnier 0.00685746515293038 0.016216049860637 1685 1505.81818181818 1502 0.000625357619942621 446 1.01732128920716 1.02894639763374 1 2.73243273151985 1683 1502 2281 880 1102 1657 920 446 1413 3055 1625 1173 M12428 MCBRYAN_PUBERTAL_BREAST_4_5WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_4_5WK_DN.html Genes down-regulated during pubertal mammary gland development between week 4 and 5. 17486082 257/319 Arthur Liberzon 0.00508030806462622 0.0134941215897782 1645 1352.81818181818 1503 0.000462916157932338 337 1.12584197319155 1.30339613736457 1 3.15873150877784 1645 553 1268 337 2186 1949 2057 1524 1333 526 1503 1174 M7778 EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_DN.html Genes down-regulated in Rh4 cells (alveolar rhabdomyosarcoma, ARMS) after knockdown of the PAX3-FOXO1 [GeneiD=5077;2308] fusion protein by RNAi for 72 hr. 17525748 51/71 Leona Saunders 0.00824207801778231 0.0187482449368349 4075 2421.54545454545 1503 0.000752101732996873 167 1.24608171440033 -1.44682252428786 -1 3.22906166678481 4071 1415 1484 980 3762 3875 4001 4257 1503 1122 167 1175 M5304 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_8 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_8.html Amplification hot spot 8: colocolized fragile sites and cancer genes in the 9q11-34 region. 16751803 15/17 Arthur Liberzon 0.0276489335356554 0.0494704193662978 1260 2388.09090909091 1503 0.00254569604622644 739 0.974091536638039 0.974091536638039 1 1.90829597285726 1260 3910 2843 4389 1274 1503 739 968 4570 3405 1408 1176 M16956 YAMASHITA_LIVER_CANCER_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_STEM_CELL_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) cells with hepatic stem cell properties. 19150350 81/95 Yujin Hoshida 0.00222165043096087 0.00724184394622604 3430 2023.63636363636 1504 0.00020217246562276 146 1.23881655015765 1.47782889863534 1 3.97815442397457 3426 723 688 146 1504 4370 3262 2567 957 1219 3398 1177 M1281 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5.html Cluster PAM5: genes changed exclusively in hepatocellular carcinoma (HCC) samples from 27 month old mice deficient for TXNIP [GeneID=10628]. 16607285 108/185 Leona Saunders 0.00044603698353511 0.00211374956052783 2500 1631.63636363636 1505 4.05570400519121e-05 21 1.28881029616443 1.1817628804091 1 5.1729349366611 2500 21 565 36 2675 1448 1651 4173 1505 843 2531 1178 M8344 NAKAJIMA_EOSINOPHIL http://www.broadinstitute.org/gsea/msigdb/cards/NAKAJIMA_EOSINOPHIL.html Top 30 increased eosinophil specific transcripts. 11493461 20/52 Kevin Vogelsang 0.0318731757005155 0.0553093343038356 1895 1531.36363636364 1505 0.00294041244423071 237 1.61909817839601 -2.0606175238255 -1 3.05425194392337 1895 2588 993 1980 1646 1505 2239 1294 237 1351 1117 1179 M2302 VANDESLUIS_COMMD1_TARGETS_GROUP_4_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_4_DN.html Genes down-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout and in normal 8.5 dpc embryos compared to normal 9.5 dpc embryos. 17371845 27/41 Arthur Liberzon 0.0035221291050344 0.0102046204511511 95 1873.90909090909 1505 0.000320707326480068 93 1.317575240906 1.3157445327553 1 3.93659854679459 93 3464 877 2990 1971 973 1182 1505 4543 2376 639 1180 M1290 DIERICK_SEROTONIN_FUNCTION_GENES http://www.broadinstitute.org/gsea/msigdb/cards/DIERICK_SEROTONIN_FUNCTION_GENES.html Genes involved in serotonin [PubChem=5202] function, orthologs computed from D. melanogaster genes using InsParanoid resource. 17450142 3/7 Leona Saunders 0.0126073541185762 0.0262028672125407 2765 2072.63636363636 1506 0.00126794559165731 328 1.09698423106099 1.09698423106099 1 2.60336612773929 2763 1106 4416 1259 1506 1470 328 4057 600 2687 2607 1181 M1604 JACKSON_DNMT1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JACKSON_DNMT1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon Cre-lox knockout of DNMT1 [GeneID=1786]. 11137995 131/165 John Newman 0.0166652727514808 0.0327670595443356 600 2005.72727272727 1506 0.00152662450116548 231 1.16441142685701 1.24426497682272 1 2.59375554506825 600 3218 1506 3901 4212 231 689 2002 3514 1380 810 1182 M6929 KEGG_O_GLYCAN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_O_GLYCAN_BIOSYNTHESIS.html O-Glycan biosynthesis 23/33 KEGG 0.00202449361644789 0.0067293027250944 2980 1846.18181818182 1507 0.000184214455315141 54 1.47402830242791 -1.60923157736956 -1 4.80400963696802 2976 344 794 54 516 3724 1507 3475 2321 716 3881 1183 M10597 WHITEHURST_PACLITAXEL_SENSITIVITY http://www.broadinstitute.org/gsea/msigdb/cards/WHITEHURST_PACLITAXEL_SENSITIVITY.html Genes that reduced viability of NCI-H1155 cells (non-small-cell lung cancer, NSCLC) in the presence of otherwise sublethal concentrations of paclitaxel [PubChem=4666], based on RNAi synthetic lethal screen. 17429401 47/65 Jessica Robertson 0.00394720945077845 0.0110634374154835 3605 1954.63636363636 1507 0.000359482665405179 648 1.1702357089898 -1.12639433886886 -1 3.43474917953878 3602 1423 1898 1507 648 3244 3440 662 1379 2254 1444 1184 M1445 GUO_HEX_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUO_HEX_TARGETS_DN.html Genes down-regulated in day 6 embryoid bodies derived from embryonic stem cells (ES) with HEX [GeneID=3087] knockout. 12791650 80/106 Kevin Vogelsang 0.0311053437645077 0.0541561130831709 1010 2024.54545454545 1507 0.0028685493633216 458 1.12077893822693 -1.17685517461001 -1 2.12958414505387 1008 2847 1507 4013 2911 458 800 922 4262 2272 1270 1185 M1501 SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1A.html Genes basally silent, with hypermethylated promoters, up-regulated by the combination of TSA and decitabine [PubChem=5562;451668] in RKO cells (colorectal cancer). 11992124 29/38 John Newman 0.00719628801727057 0.0168234172568188 1075 2045.36363636364 1507 0.000656357793459181 331 1.26201174159615 1.41743773988915 1 3.35943419742211 1075 4168 1337 4557 1620 1507 1060 454 4285 2105 331 1186 M2205 CHYLA_CBFA2T3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHYLA_CBFA2T3_TARGETS_UP.html Genes up-regulated in immature bone marrow progenitor cells upon knock out of CBFA2T3 [GeneID=863]. 18710942 461/721 Arthur Liberzon 5.06581627403644e-11 1.61558464955757e-09 3560 2050.54545454545 1508 4.60528752195736e-12 18 1.2601438931351 -1.26877315548326 -1 16.6238103196688 3558 507 116 18 1498 4133 3814 2618 1508 123 4663 1187 M16407 IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL_LONG_TERM.html Genes in the expression cluster 'LT-HSC Shared': up-regulated in long term hematopoietic stem cells (LT-HSC) from adult bone marrow and fetal liver. 12228721 348/476 John Newman 0.000484111091684076 0.00225345596918031 1730 1439.81818181818 1509 4.40197866727285e-05 570 1.18724234154708 1.16197153368233 1 4.71574314062389 1729 1164 570 704 2225 1509 2346 943 2308 591 1749 1188 M10 PID_BCR_5PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BCR_5PATHWAY.html BCR signaling pathway 18832364 85/107 Pathway Interaction Database 0.00933974170718776 0.0206771017157252 795 1752.45454545455 1510 0.00085269357570947 452 0.816418309901825 0.839737495315322 1 2.0635070269372 793 1850 3057 908 1510 1049 452 524 4040 3481 1613 1189 M4333 LUI_THYROID_CANCER_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_4.html Cluster 4: genes with similar expression profiles across follicular thyroid carcinoma (FTC) samples. 15608688 13/15 Leona Saunders 0.00623411017895129 0.0151132860242952 2805 1554.36363636364 1510 0.000568349644881774 233 1.279613816823 -1.22127302507372 -1 3.49568204329177 2804 1041 1346 1510 2948 1576 1935 419 1810 1476 233 1190 M1357 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_DN.html Early prostate development genes (down-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 11/11 Jessica Robertson 0.000277645703623556 0.00149428474470146 820 1638.18181818182 1510 2.5243704493031e-05 212 1.22246854290196 1.29175242919599 1 5.18294007155136 817 3555 2193 2624 212 1003 1558 598 929 3021 1510 1191 M1759 WANG_LSD1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LSD1_TARGETS_UP.html Genes up-regulated after Cre-lox knockout of LSD1 [GeneID=23028] in pituitary. 17392792 24/34 Jessica Robertson 0.0143725878247658 0.0292533913466557 1445 1393.54545454545 1510 0.00131521379377484 460 1.38908365177812 1.39763936451633 1 3.19691653990679 1444 1510 1684 2034 1030 1316 460 1812 766 1702 1571 1192 M16033 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_8.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 8. 12554760 63/77 Arthur Liberzon 0.00130205106983754 0.00479382297163275 2150 1835.09090909091 1511 0.000118438392424854 433 1.26619269950249 1.16303947531295 1 4.40647675433332 2148 773 1511 861 3096 3364 3537 1385 1060 433 2018 1193 M11640 LEE_LIVER_CANCER_CIPROFIBRATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_CIPROFIBRATE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by ciprofibrate [PubChem=2763]. 15565109 57/117 Yujin Hoshida 1.84855094118338e-06 2.36454212530774e-05 2805 1663.45454545455 1512 1.68050226766448e-07 301 1.56461504953862 -1.48178821664209 -1 10.8611160590559 2803 1386 301 2258 570 1540 1512 1442 2906 815 2765 1194 M3274 POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_DESMOPLASIC_VS_CLASSIC_UP.html Top up-regulated marker genes for medulloblastoma classification: desmoplastic vs classic morphology. 11807556 98/133 Jean Junior 0.000324999853438721 0.00167750659586834 810 1480.81818181818 1512 2.9549806790092e-05 234 1.15093082942167 1.31967548396304 1 4.79288462474371 807 1834 1452 1934 234 1512 1636 1386 2561 1857 1076 1195 M1737 GAVIN_PDE3B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_PDE3B_TARGETS.html Genes changed in peripheral regulatory T lymphocytes that depend on PDE3B [GeneID=5140]. 17220874 17/35 Jessica Robertson 0.00212991334760886 0.00700570801443472 1250 2081.27272727273 1513 0.000193816200576843 86 1.11940754782642 -0.882431746448848 -1 3.6188743684133 1248 2602 1513 3040 838 807 86 4535 4295 2425 1505 1196 M12710 AMIT_EGF_RESPONSE_120_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_120_HELA.html Genes whose expression peaked at 120 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 99/122 Leona Saunders 0.0139660093218192 0.0285658268596144 575 1948.63636363636 1515 0.00127776947190499 289 1.2263481134579 1.02773853172156 1 2.84138305712649 571 3244 1942 3219 3606 289 332 4262 1462 993 1515 1197 M7846 BROWNE_HCMV_INFECTION_8HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_8HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 8 h time point that were not down-regulated at the previous time point, 6 h. 11711622 52/77 John Newman 0.00310307687296858 0.00927582193819614 1720 1443 1515 0.00028249658115871 281 1.25249860130495 1.35303452029052 1 3.8200506174381 1718 1932 1530 2029 3291 1331 734 281 1515 941 571 1198 M1812 MATZUK_MATERNAL_EFFECT http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_MATERNAL_EFFECT.html Maternal effect genes, based on mouse models wih female fertility defects. 18989307 5/12 Jessica Robertson 0.0041681878345506 0.0115347199959706 2165 1764.90909090909 1515 0.000417602674145189 12 1.62494548995867 1.62494548995867 1 4.72523127782051 2163 2688 4567 1515 688 2257 1208 630 12 3092 594 1199 M6189 ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) after knockdown of both HIF1A and HIF2A [GeneID=3091;2034] by RNAi. 16565084 141/165 Arthur Liberzon 0.000488430077168892 0.00226908461046966 1535 1447.45454545455 1516 4.44125953672907e-05 393 1.36562098281831 1.36642479756651 1 5.41813076043889 1535 624 571 1516 3622 1958 2675 393 1672 642 714 1200 M5370 FONTAINE_FOLLICULAR_THYROID_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_FOLLICULAR_THYROID_ADENOMA_DN.html Genes down-regulated in follicular thyroid adenoma (FTA) compared to other thyroid tumors. 17968324 87/119 Arthur Liberzon 0.00424645704222997 0.0116958488352629 1225 1446.09090909091 1517 0.00038678870950793 63 1.18513198353079 1.19595634898056 1 3.43554099388543 1222 63 753 311 3049 1967 2033 2465 1517 660 1867 1201 M2395 SERVITJA_ISLET_HNF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_ISLET_HNF1A_TARGETS_UP.html Genes up-regulated in pancreatic islets upon knockout of HNF1A [GeneID=6927]. 19289501 229/327 Arthur Liberzon 8.06131607629679e-19 7.04618738520757e-17 520 1416.09090909091 1517 7.3284691602698e-20 40 1.34239010446233 1.29610741396416 1 32.5346901815681 519 2266 40 1993 1517 803 1470 1809 3540 76 1544 1202 M9488 KEGG_RETINOL_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RETINOL_METABOLISM.html Retinol metabolism 24/101 KEGG 0.000237412944831968 0.00134524501753528 2805 1492.63636363636 1518 2.15853244650347e-05 194 1.74709809948641 -1.70699103176076 -1 7.52690142223125 2801 2558 807 1968 194 1790 2183 1121 699 780 1518 1203 M16977 CHIBA_RESPONSE_TO_TSA http://www.broadinstitute.org/gsea/msigdb/cards/CHIBA_RESPONSE_TO_TSA.html Genes up-regulated in more than one of several human hepatoma cell lines by TSA [PubChem=5562]. 15336447 73/90 John Newman 0.0044229271939667 0.0120811437242609 1795 1511.18181818182 1518 0.000402894931786209 97 0.965646762538945 -1.02308037393071 -1 2.77886657023054 1792 1340 2515 2923 847 305 1518 1804 1016 2466 97 1204 M16643 VERRECCHIA_DELAYED_RESPONSE_TO_TGFB1 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_DELAYED_RESPONSE_TO_TGFB1.html ECM related genes up-regulated later than 30 min following addition of TGFB1 [GeneID=7040] in dermal fibroblasts. 11279127 84/98 John Newman 0.00292458700697401 0.00887149786177207 680 1769.54545454545 1518 0.000266225643670428 507 1.33566974728749 1.43952083473659 1 4.11251716459716 676 2382 720 2482 3074 1518 2535 1066 3196 1309 507 1205 M1848 MATTHEWS_SKIN_CARCINOGENESIS_VIA_JUN http://www.broadinstitute.org/gsea/msigdb/cards/MATTHEWS_SKIN_CARCINOGENESIS_VIA_JUN.html Genes up-regulated by skin tumor promoters but completely blocked by expression of TAM67, a dominan-negative form of JUN [GeneID=3725]. 17363560 20/23 Jessica Robertson 0.0154531985494538 0.0309457348975061 1165 1597.27272727273 1519 0.00141480219863076 207 1.73428681645399 1.73052924034328 1 3.92785227076772 1163 998 1519 2350 4142 1613 354 2157 207 2215 852 1206 M178 CROMER_TUMORIGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_TUMORIGENESIS_UP.html Tumorigenesis markers of head and neck squamous cell carcinoma (HNSCC): up-regulated in the 'early' tumors vs normal samples. 14676830 72/110 Arthur Liberzon 2.57691228766855e-06 3.14290077462417e-05 245 1866.45454545455 1519 2.34265027824737e-07 244 1.35457584395681 1.48201460311756 1 9.15187684156549 244 2860 313 3233 3224 1205 1519 2066 3740 868 1259 1207 M16227 REACTOME_CHOLESTEROL_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHOLESTEROL_BIOSYNTHESIS.html Genes involved in Cholesterol biosynthesis 22/24 Reactome 1.73376975068355e-05 0.000163667864464527 935 1483.90909090909 1520 1.57616674025245e-06 43 0.962943915745764 -1.02244881034138 -1 5.47040154893479 934 1520 2942 1794 43 1042 1788 760 290 3382 1828 1208 M19693 DAZARD_RESPONSE_TO_UV_NHEK_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_NHEK_UP.html Genes up-regulated in NHEK cells (normal keratinocytes) by UV-B irradiation. 12771951 306/538 John Newman 0.114373583272315 0.161533008092558 1360 2084.27272727273 1522 0.0109810872523913 1286 1.12735005497096 1.1213363893863 1 1.33920840161304 1360 3613 1393 3466 1932 1522 1371 1490 3206 1286 2288 1209 M15188 KAAB_FAILED_HEART_VENTRICLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_FAILED_HEART_VENTRICLE_DN.html Genes down-regulated in the ventricles of failing hearts (DCM and ICM) compared to the healthy controls. 15103417 62/95 Arthur Liberzon 0.0283054493859538 0.050434775802832 1695 1543.36363636364 1522 0.00260693894897997 406 1.04819211325856 -1.00891510427342 -1 2.04028348113668 1694 1379 1888 1522 2174 406 923 882 2977 2192 940 1210 M1074 REACTOME_NUCLEOTIDE_BINDING_DOMAIN_LEUCINE_RICH_REPEAT_CONTAINING_RECEPTOR_NLR_SIGNALING_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEOTIDE_BINDING_DOMAIN_LEUCINE_RICH_REPEAT_CONTAINING_RECEPTOR_NLR_SIGNALING_PATHWAYS.html Genes involved in Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways 49/56 Reactome 0.00577426225782821 0.0142024584976285 2210 1653 1524 0.000526315789473684 120 1.14796320932835 1.21024485250747 1 3.18252528769046 2210 169 1654 120 3230 1524 1365 2254 344 1246 4067 1211 M254 PID_MYC_REPRESS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_REPRESS_PATHWAY.html Validated targets of C-MYC transcriptional repression 18832364 88/110 Pathway Interaction Database 0.00270990858854372 0.00839019605373472 530 1402.27272727273 1525 0.000246659305302429 51 1.15543443990755 1.13278291075776 1 3.5995596043393 528 2374 1525 1946 3227 51 220 1686 2492 1106 270 1212 M18761 SMITH_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SMITH_LIVER_CANCER.html Potential marker genes specifically up-regulated in the majority of hepatocellular carcinoma (HCC) tumors. 12591738 57/66 Yujin Hoshida 0.00124869337369857 0.00465547608519528 2250 1408.09090909091 1525 0.000113582061876399 321 1.00184900020403 -1.07324187468322 -1 3.50563098624406 2248 769 2904 578 439 571 1877 1736 321 2521 1525 1213 M1611 WENG_POR_TARGETS_GLOBAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_GLOBAL_UP.html Genes up-regulated in liver from transgenic mice with reduced expression of POR [GeneID=5447] in all tissues. 16006652 20/49 John Newman 0.00402711906378889 0.01122078039025 3335 1787.18181818182 1526 0.000366773607920036 335 1.30222782309298 -1.23937349133233 -1 3.81018612400649 3333 1526 1848 2313 3091 1196 1231 335 488 1352 2946 1214 M1616 BURTON_ADIPOGENESIS_7 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_7.html Down-regulated at 48-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 74/94 John Newman 0.00909222327438862 0.0202909190804323 1400 1679.45454545455 1526 0.000830001703721315 792 1.19357704454995 1.12190881225649 1 3.03149361910885 1398 1877 1009 2360 873 1586 2732 792 2917 1526 1404 1215 M8759 ROPERO_HDAC2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ROPERO_HDAC2_TARGETS.html Genes up-regulated genes in cell lines with HDAC2 [GeneID=3066] loss of function (LOS). 18264134 143/222 Jessica Robertson 0.0396206206364765 0.066221433924989 3340 2173.27272727273 1528 0.00366842625495837 613 1.12641030643162 1.07898596940168 1 1.99264386952349 3340 613 1033 951 1528 4471 4052 1844 1086 876 4112 1216 M11654 LIEN_BREAST_CARCINOMA_METAPLASTIC http://www.broadinstitute.org/gsea/msigdb/cards/LIEN_BREAST_CARCINOMA_METAPLASTIC.html Genes up-regulated in metaplastic carcinoma of the breast (MCB) subclass 2 compared to the MCB subclass 1. 17603561 64/78 Arthur Liberzon 2.02048898814373e-06 2.55675818338831e-05 65 1841.09090909091 1529 1.83680985797405e-07 62 1.4641389971566 1.42396652263264 1 10.089061996692 62 3721 305 3227 1891 1585 1529 1409 4277 909 1337 1217 M10837 NIKOLSKY_BREAST_CANCER_20Q11_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_20Q11_AMPLICON.html Genes within amplicon 20q11 identified in a copy number alterations study of 191 breast tumor samples. 19010930 39/52 Jessica Robertson 0.00340628608985987 0.00995521383537993 1530 1715.54545454545 1529 0.000310142867591363 72 0.902426739263457 -0.899986554008107 -1 2.71075274858603 1529 2489 3383 2003 1438 184 831 1459 1944 3539 72 1218 M19837 RICKMAN_HEAD_AND_NECK_CANCER_E http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_E.html Cluster e: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 87/189 Jessica Robertson 2.67182193654068e-19 2.57367337560653e-17 1535 1352 1531 2.4289290332188e-20 35 1.75979589093617 -1.75006574145359 -1 43.8061369438495 1531 695 35 657 1630 1582 2805 3330 791 38 1778 1219 M6890 HELLER_HDAC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_DN.html Genes down-regulated in at least one of three multiple myeloma (MM) cell lines by TSA [PubChem=5562]. 18172295 358/493 Jessica Robertson 0.0544366160633329 0.0866651306439482 680 2259.18181818182 1531 0.00507565290691088 680 1.06067268411488 1.1070422795297 1 1.69037923468596 680 4682 1504 4600 2640 1056 1033 1155 3230 2740 1531 1220 M1785 POS_HISTAMINE_RESPONSE_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/POS_HISTAMINE_RESPONSE_NETWORK.html Genes corresponding to the histamine [PubChem=774] response network. 18339882 44/55 Jessica Robertson 0.000460804898739239 0.0021663337869016 2725 1819.81818181818 1531 4.19001314325914e-05 297 1.25464901112092 1.17656594782798 1 5.01572691066655 2725 1432 1364 1733 297 2688 2016 1531 878 1229 4125 1221 M15371 BIOCARTA_ETC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETC_PATHWAY.html Electron Transport Reaction in Mitochondria 13/16 BioCarta 0.00702061148007119 0.0165273247810155 710 1709 1532 0.000640283288379773 561 0.553405771032331 -0.568950530597551 -1 1.47949246768717 707 1577 3571 1559 801 561 939 1532 1338 4497 1717 1222 M19387 TCGA_GLIOBLASTOMA_MUTATED http://www.broadinstitute.org/gsea/msigdb/cards/TCGA_GLIOBLASTOMA_MUTATED.html Genes significantly mutated in 91 glioblastoma samples. 18772890 14/14 Arthur Liberzon 0.0252720498406733 0.0458693338746506 1535 1588.45454545455 1532 0.00232428306103622 562 1.13090122287175 1.30683172169166 1 2.27121026873661 1532 1572 2138 888 3582 1017 581 841 2680 2080 562 1223 M9118 IWANAGA_CARCINOGENESIS_BY_KRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_UP.html Cluster 3: genes up-regulated in lung tissue samples from mice with tumor-bearing genotypes (activated KRAS [GeneID=3845] alone or together with inactivated PTEN [GeneID=5728]). 18281487 249/309 Jessica Robertson 0.0181423964224597 0.0350683826331752 1695 1910.90909090909 1533 0.00166306899127764 702 1.17122630331879 1.19627177578933 1 2.55712993518362 1691 1197 1206 702 1120 2770 2484 4411 1533 1434 2472 1224 M2270 STEGER_ADIPOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEGER_ADIPOGENESIS_UP.html Genes up-regulated during adipogenesis of 3T3-L1 cells (fibroblast). 18285465 22/32 Arthur Liberzon 0.0119561966686745 0.0250925959431496 535 1648.90909090909 1533 0.00109287935929512 299 1.54663111895285 1.70230045565452 1 3.71415038990518 531 2074 948 2816 4504 738 299 1565 2476 1533 654 1225 M10080 REACTOME_M_G1_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_M_G1_TRANSITION.html Genes involved in M/G1 Transition 81/91 Reactome 0.00386954991427665 0.0109040451315736 100 1970.27272727273 1535 0.000352397529056971 99 0.639380951135847 -0.636762051632813 -1 1.88264033935244 99 1329 4081 2202 2468 482 593 1497 3018 4369 1535 1226 M1867 WANG_NEOPLASTIC_TRANSFORMATION_BY_CCND1_MYC http://www.broadinstitute.org/gsea/msigdb/cards/WANG_NEOPLASTIC_TRANSFORMATION_BY_CCND1_MYC.html Selected genes changed in NMuMG cells (mammary epithelium) transformed by overexpression of CCND1 [GeneID=595] vs those transformed by overexpression of CCND1 and MYC [GeneID=4609]. 17440082 36/42 Jessica Robertson 5.59283498780068e-05 0.000417032877447381 120 1847.27272727273 1535 5.08452470344078e-06 117 1.25973031888396 1.21026103354886 1 6.38861938472309 117 3396 450 4078 2156 959 750 1535 4558 1876 445 1227 M15422 BIOCARTA_VITCB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VITCB_PATHWAY.html Vitamin C in the Brain 22/24 BioCarta 0.00607756298882487 0.0147875967918264 155 1907.27272727273 1536 0.000554037968437277 154 1.28072593589808 1.17284276627266 1 3.51690255363454 154 3046 790 3003 1536 1374 1844 1938 4531 1529 1235 1228 M620 REACTOME_INSULIN_RECEPTOR_SIGNALLING_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INSULIN_RECEPTOR_SIGNALLING_CASCADE.html Genes involved in Insulin receptor signalling cascade 82/127 Reactome 0.00140395109042122 0.00510921291194153 2020 1883.27272727273 1536 0.000127713439685904 431 0.863925005156448 0.862068186372717 1 2.97063923215699 2019 726 3366 431 455 1536 1431 3028 1242 3824 2658 1229 M14079 BENPORATH_ES_CORE_NINE_CORRELATED http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_CORE_NINE_CORRELATED.html Breast cancer compendium: 100 transcription regulators showing most correlated expression with the 9 'embryonic stem cell' transcription factors that are preferentially and coordinately overexpressed in the high-grade, ER-negative breast cancer tumors. 18443585 117/141 Jessica Robertson 0.115604972414244 0.16297953100216 910 2220 1536 0.0111061797611233 909 0.96748164091081 1.06827686939708 1 1.14366078761054 909 3226 3505 2951 4097 1277 1031 1536 1402 3060 1426 1230 M7547 JIANG_HYPOXIA_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_HYPOXIA_CANCER.html Genes up-regulated in 786-0 cells (renal carcinoma, RCC) by hypoxia and in the absensce of VHL [GeneID=7428]. 12692265 107/138 John Newman 0.034024829670104 0.0582084798995617 1540 1955.27272727273 1537 0.00314206686085897 703 0.986553867336178 -1.06115147878269 -1 1.82813920330416 1537 2811 3492 2652 2559 703 1321 960 776 3760 937 1231 M2369 GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_DN.html Genes down-regulated during differentiation of Oli-Neu cells (oligodendroglial precursor) in response to PD174265 [PubChem=4709]. 19139271 1433/1785 Arthur Liberzon 2.96226233931641e-05 0.000251925734082404 1855 1574.09090909091 1537 2.962301827549e-06 16 1.10736354779443 1.14457380245591 1 5.97961612206601 1854 461 4693 16 1832 1227 2199 1745 1506 245 1537 1232 M7253 KEGG_FOCAL_ADHESION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOCAL_ADHESION.html Focal adhesion 214/245 KEGG 6.68126128049131e-06 7.13474055292285e-05 685 1539.36363636364 1538 6.07389233740619e-07 353 1.23763530301396 1.29769948431904 1 7.70057148811872 681 2272 353 1945 1531 1538 1346 1908 2830 443 2086 1233 M678 REACTOME_CHONDROITIN_SULFATE_DERMATAN_SULFATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHONDROITIN_SULFATE_DERMATAN_SULFATE_METABOLISM.html Genes involved in Chondroitin sulfate/dermatan sulfate metabolism 43/50 Reactome 0.0582284475866955 0.0916300724123046 1955 1750.90909090909 1539 0.00543902258808173 751 1.30565488561041 1.34871137757998 1 2.03342915632886 751 1951 1102 2256 3860 1924 1951 1514 1539 1412 1000 1234 M6318 GRANDVAUX_IFN_RESPONSE_NOT_VIA_IRF3 http://www.broadinstitute.org/gsea/msigdb/cards/GRANDVAUX_IFN_RESPONSE_NOT_VIA_IRF3.html Genes up-regulated in Jurkat cells (T lymphocyte) by IFN1@, and IFNB1 [GeneID=3438;3456] but not by overexpression of a constitutively active form of IRF3 [GeneID=3661]. 11991981 21/27 Yujin Hoshida 0.000623695065170893 0.00273337113055396 875 1793 1539 5.6715631957498e-05 99 0.812739997564972 -0.844206425715785 -1 3.12592398702641 875 1539 2695 3339 1870 1135 699 99 3494 3325 653 1235 M5133 GRANDVAUX_IRF3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRANDVAUX_IRF3_TARGETS_UP.html Genes up-regulated in Jurkat cells (T lymphocyte) by expression of a constitutively active form of IRF3 [GeneID=3661]. 11991981 22/30 Yujin Hoshida 0.00870988882175253 0.0196701795400344 2935 2142.54545454545 1540 0.000794960360777974 347 1.06868379537012 1.09560964285429 1 2.73591154908621 2935 347 1540 752 859 3769 3107 3825 769 1532 4133 1236 M5360 KANG_IMMORTALIZED_BY_TERT_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_IMMORTALIZED_BY_TERT_UP.html Up-regulated genes in the signature of adipose stromal cells (ADSC) immortalized by forced expression of telomerase (TERT) [GeneID=7015]. 15579653 137/177 Kevin Vogelsang 8.89912134178555e-06 9.21137121342715e-05 785 1884 1540 8.09014303584188e-07 364 1.30028159533187 1.20613473228551 1 7.87389552774188 782 3212 364 3348 948 1032 1912 2868 3863 855 1540 1237 M1499 WHITESIDE_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WHITESIDE_CISPLATIN_RESISTANCE_UP.html Genes up-regulated in NCI-H2170 cells (lung cancer) upon induction of resistance to cisplatin [PubChem=2767]. 14737109 19/25 John Newman 0.0167592532591443 0.0328913411156594 3365 2103.54545454545 1540 0.0015353000923933 1088 1.01087499136714 1.03544489420316 1 2.24924149375254 3363 1540 1982 1101 1088 1187 2092 3772 1138 1274 4602 1238 M1562 YIH_RESPONSE_TO_ARSENITE_C2 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C2.html Genes in cluster 2: moderately up-regulated in HFW cells (fibroblast) upon treatment with sodium arsenite [PubChem=26435] at all time points. 12016162 31/36 John Newman 0.0151507386475286 0.0304435868371894 2795 2283.81818181818 1541 0.00138691767411946 646 1.32841068965783 -1.47215951902674 -1 3.02275241879968 2793 1476 1541 1059 3461 3285 4201 646 3928 1539 1193 1239 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 0.00114022852508138 0.00439695967188244 555 1539.81818181818 1542 0.000103710901670217 417 1.56499526300447 1.43919886835284 1 5.5344952240519 2464 1592 1092 553 417 4172 1776 553 1542 634 2143 1240 M1093 REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_GLYCOSYLPHOSPHATIDYLINOSITOL_GPI.html Genes involved in Synthesis of glycosylphosphatidylinositol (GPI) 18/18 Reactome 0.0102305082535732 0.0222422841809606 2795 1981.90909090909 1543 0.000934399502463513 17 0.930730595367625 -0.526112368651848 -1 2.30819028238313 2791 1543 3025 540 914 589 1107 4267 17 3611 3397 1241 M4008 FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL.html Genes which best discriminate between two groups of breast cancer according to the status of ESR1 and AR [GeneID=2099;367]: apocrine (ESR1- AR+) and luminal (ESR1+ AR+). 15897907 406/551 Leona Saunders 1.27010065696584e-06 1.72663510463356e-05 3080 2026.90909090909 1543 1.15463762747183e-07 174 1.23088626313134 1.26658018081186 1 8.79663965273211 3077 1152 293 663 1543 3099 3149 3505 1158 174 4483 1242 M1414 MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_DN.html Down-regulated genes discriminating multiple myeloma samples by type of immunoglobulin they produce: IgG vs IgA. 12623842 31/46 Kate Stafford 9.15608355288888e-05 0.000615622711818169 2870 2006.63636363636 1544 8.32405876192797e-06 127 1.31569104959452 1.11626081346942 1 6.33849608295136 2866 293 1544 1066 127 3946 2848 3874 1023 583 3903 1243 M2469 KRIEG_HYPOXIA_NOT_VIA_KDM3A http://www.broadinstitute.org/gsea/msigdb/cards/KRIEG_HYPOXIA_NOT_VIA_KDM3A.html Genes induced under hypoxia independently of KDM3A [GeneID=55818] in RCC4 cells (renal carcinoma) expressing VHL [GeneID=7428]. 19858293 951/1187 Arthur Liberzon 0.000107829272910778 0.000707482804573066 1710 1858.63636363636 1544 1.07834505486567e-05 286 1.12110329669337 1.10963555108844 1 5.29942180225668 1708 1119 4705 725 2744 1544 2620 1216 1147 286 2631 1244 M2544 ROESSLER_LIVER_CANCER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROESSLER_LIVER_CANCER_METASTASIS_UP.html Genes up-regulated in liver samples containing tumor thrombi in the major branches of the portal vein at surgery (PT) compared to those from metastasis-free HCC patients (PN) at the time of surgery and at follow-up. 21159642 158/214 Yujin Hoshida 0.0143062519071691 0.0291435084168486 1005 1513.54545454545 1544 0.00130910355150252 259 1.20143841709203 1.16514034693557 1 2.76799121864638 1003 1241 1342 1910 3429 572 1544 1752 1866 1731 259 1245 M15694 WATTEL_AUTONOMOUS_THYROID_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATTEL_AUTONOMOUS_THYROID_ADENOMA_DN.html Down-regulated genes characteristic for autonomous thyroid adenoma. 16027733 59/85 Arthur Liberzon 1.43322215900092e-07 2.53363617621136e-06 905 1435.45454545455 1545 1.30292932033662e-08 223 1.4989077901311 1.53122555623501 1 12.5866636566251 905 1911 223 1706 3133 1609 1545 970 2236 357 1195 1246 M2616 ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY.html Genes transiently induced only by the second pulse of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 1222/2731 Yaara Zwang 3.94859915927843e-23 5.64769334296793e-21 1545 1847.81818181818 1545 3.94859915927843e-24 14 1.37008187117018 1.30962343745638 1 41.6267131926721 1545 1660 4718 1149 1459 1413 2056 1401 2363 14 2548 1247 M15891 GESERICK_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GESERICK_TERT_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) with TERT [GeneID=7015] knockout, after expression of the gene off a retroviral vector. 16501597 26/26 Lauren Kazmierski 0.0703057498897203 0.107219108070914 515 1622.72727272727 1547 0.00660531655545467 514 1.24756746171002 1.27507046514454 1 1.81522464553723 514 2034 1217 1745 3511 1480 1547 1831 746 893 2332 1248 M5395 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_UP.html Genes up-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing granulocytes. 17898786 23/36 Arthur Liberzon 0.00304628527986038 0.00913942469514037 1490 1627.90909090909 1548 0.000277319235498583 592 1.5206693103446 1.80590134478768 1 4.65265895431427 1489 2067 1199 2120 592 2251 2089 889 1548 1261 2402 1249 M12227 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_5 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_5.html Amplification hot spot 5: colocolized fragile sites and cancer genes in the 17q22-q25 region. 16751803 7/7 Arthur Liberzon 0.0219301047093554 0.0408484981168734 2180 1572.63636363636 1549 0.00221495774520924 3 1.45839453884016 -1.34304705166014 -1 3.0391273486456 2178 1634 4374 330 1216 2148 1039 1101 3 1727 1549 1250 M3955 GU_PDEF_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GU_PDEF_TARGETS_UP.html Integrin, VEGF, Wnt and TGFbeta signaling pathway genes up-regulated in PC-3 cells (prostate cancer) after knockdown of PDEF [GeneID=25803] by RNAi. 17483333 109/138 Jessica Robertson 4.09692498937313e-05 0.000324454462245657 670 1666.81818181818 1549 3.72454662352923e-06 437 1.1363591128424 1.27759558282815 1 5.94882936986248 670 1286 437 1363 1549 1715 1992 1922 3779 1510 2112 1251 M3576 MCCLUNG_CREB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_CREB1_TARGETS_DN.html Genes down-regulated in the nucleus accumbens (a major reward center in the brain) 8 weeks after induction of CREB1 [GeneID=1385] expression in a transgenic Tet-Off system. 14566342 90/118 John Newman 0.0229499738276145 0.0422809822272991 1295 1655.45454545455 1550 0.0021084490364286 741 1.12805237264854 1.16006355430979 1 2.32537063864603 1294 1842 1260 1035 3051 1550 2079 815 2948 741 1595 1252 M12985 BIOCARTA_TALL1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TALL1_PATHWAY.html TACI and BCMA stimulation of B cell immune responses. 17/23 BioCarta 0.000701342881129442 0.00302038175084942 840 1611.81818181818 1552 6.3778778510953e-05 346 0.69943959164099 0.83153225941465 1 2.64462759571816 836 1552 3185 1860 346 1280 984 1596 1793 2986 1312 1253 M7623 HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_DN.html Genes down-regulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562]. 18172295 350/450 Jessica Robertson 0.0182066383099785 0.0351330060601385 1320 1769.90909090909 1552 0.00166900735990728 675 1.06148149513075 1.09439693719812 1 2.31624143032139 1317 2237 918 2904 2049 675 1240 1946 3120 1511 1552 1254 M1876 JU_AGING_TERC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JU_AGING_TERC_TARGETS_DN.html Cytokines, growth factors, and secreted proteins that show decreased expression on a protein array of samples from aged TERC [GeneID=7012] knockout mice. 17486088 6/7 Jessica Robertson 0.0162811990262213 0.0322481155701907 1150 1770.90909090909 1553 0.00164017285774839 164 1.84678281126777 1.52889038325838 1 4.13302950322249 1150 1638 4593 1443 2663 968 389 3047 164 1553 1872 1255 M13686 GENTILE_UV_RESPONSE_CLUSTER_D9 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D9.html Cluster d9: genes progressively down-regulated in WS1 cells (fibroblast) through 24 h after irradiation with high dose UV-C. 12907719 35/42 John Newman 0.0161998520769461 0.0321632424179588 400 1572 1555 0.00148367138447054 399 1.18268688185256 1.20129945670184 1 2.64880119644505 399 2964 2175 3289 1869 630 519 669 1412 1811 1555 1256 M31 PID_BETA_CATENIN_DEG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BETA_CATENIN_DEG_PATHWAY.html Degradation of beta catenin 18832364 24/26 Pathway Interaction Database 0.0284845733739821 0.0506107131215275 1475 1985 1556 0.00262365501328009 503 0.904824756977238 0.882137677945158 1 1.75915417477134 1474 954 3033 2627 4100 1067 503 2400 622 3499 1556 1257 M1351 SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN.html Genes down-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 48 h. 18794802 534/749 Jessica Robertson 1.42849427796852e-11 5.03171118806821e-10 935 1961 1557 1.4284942779777e-12 60 1.29214430151001 1.30710164612936 1 18.0282302543154 933 3158 4443 3268 2391 328 1557 1338 3594 60 501 1258 M4078 ABE_VEGFA_TARGETS_30MIN http://www.broadinstitute.org/gsea/msigdb/cards/ABE_VEGFA_TARGETS_30MIN.html Genes up-regulated in HUVEC cells (endothelium) at 30 min after VEGFA [GeneID=7422] stimulation. 12197474 34/42 John Newman 0.0108246114226215 0.0232026184899062 555 2016.63636363636 1557 0.000988931028030197 285 1.10872452558713 1.30528755356892 1 2.71909044782642 554 3815 1557 4216 2436 527 285 1427 3878 2501 987 1259 M12695 ROSS_LEUKEMIA_WITH_MLL_FUSIONS http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_LEUKEMIA_WITH_MLL_FUSIONS.html Top 100 probe sets associated with MLL fusions [GeneID=4297] irrespective of the lineage of the pediatric acute leukemia. 15226186 95/157 Arthur Liberzon 0.0146966872663318 0.0297974071722879 3880 2174 1557 0.00134507216952237 47 1.12448485478951 1.14470220478415 1 2.57443128042872 3879 47 1083 352 1038 4035 3425 1277 3452 1557 3769 1260 M6724 REACTOME_NA_CL_DEPENDENT_NEUROTRANSMITTER_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NA_CL_DEPENDENT_NEUROTRANSMITTER_TRANSPORTERS.html Genes involved in Na+/Cl- dependent neurotransmitter transporters 10/23 Reactome 0.00442944061439492 0.0120849478034359 1345 1502.09090909091 1559 0.000403489453637256 263 1.28429759001693 1.5489706979881 1 3.69562769837783 1341 1599 1321 1703 3128 1559 766 352 2312 2179 263 1261 M17923 BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_CULTURED_VS_FRESH_UP.html Genes up-regulated in cultured stromal stem cells from adipose tissue, compared to the freshly isolated cells. 15635089 593/758 Arthur Liberzon 1.14840908296769e-19 1.20455352702389e-17 540 1687.27272727273 1559 1.14840908296769e-20 21 1.31938931475126 1.28575890414212 1 33.4959695375155 540 2209 4571 2253 2096 473 946 1559 3268 21 624 1262 M2408 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_3 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_3.html Genes regulated in MCF7 cells (breast cancer) by expression of the truncated (611-CTF) form of ERBB2 [GeneID=2064] at both 15 h and 60 h time points. 19364815 24/27 Arthur Liberzon 0.00414363723402566 0.0114844202845573 1335 2114.72727272727 1559 0.000377405663447824 330 1.02029841065551 -1.00559386274416 -1 2.96982496522779 3597 330 1559 534 659 3157 2663 3943 1335 1334 4151 1263 M15484 ONDER_CDH1_SIGNALING_VIA_CTNNB1 http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_SIGNALING_VIA_CTNNB1.html Genes changed in HMLE cells (mmortalized nontransformed mammary epithelium) after RNAi knockdown of both CDH1 and CTNNB1 [GeneID=999;1499], compared to the knockdown of CDH1 alone. 18483246 144/178 Jessica Robertson 1.63114350934558e-12 6.69478031661836e-11 1790 1542.36363636364 1560 1.48285773576981e-13 89 1.3422178221139 1.28022367589982 1 20.4911133091299 622 1786 89 2148 1560 1352 1501 2371 3635 115 1787 1264 M1697 TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_DN http://www.broadinstitute.org/gsea/msigdb/cards/TUOMISTO_TUMOR_SUPPRESSION_BY_COL13A1_DN.html Genes down-regulated in small intestine tissue from transgenic mice expressing a mutant form of COL13A1 [GeneID=1305], compared to normal controls. 19074901 6/22 Leona Saunders 0.00130842959475721 0.00480980349474613 1415 2115.90909090909 1560 0.000130920062836992 180 1.16989926545231 -1.16989926545231 -1 4.06882072613275 1412 3575 4513 1477 1397 1560 1838 180 3123 3238 962 1265 M8857 KIM_WT1_TARGETS_8HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_8HR_UP.html Genes up-regulated in UB27 cells (osteosarcoma) at 8 hr after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 244/284 Arthur Liberzon 0.0351424924569925 0.0599034179837502 425 1397.72727272727 1561 0.00324697614550017 421 1.08139809843186 1.01192284855956 1 1.98367400266513 421 2745 1653 1869 1561 581 563 977 2097 1698 1210 1266 M4175 FERRANDO_LYL1_NEIGHBORS http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_LYL1_NEIGHBORS.html Nearest neighbors of LYL1 [GeneID=4066], based on the close agreement of their expression profiles with that of LYL1 in pediatric T cell acute lymphoblastic leukemia (T-ALL). 12086890 15/18 Jean Junior 0.00150280000014569 0.00538998176344045 1565 1574.81818181818 1561 0.000136711593814101 185 1.33113730525116 1.54870826476233 1 4.53081771739592 1561 3075 1675 2078 796 1437 1034 185 3098 1688 696 1267 M14940 BILBAN_B_CLL_LPL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BILBAN_B_CLL_LPL_DN.html Genes down-regulated in B-CLL (B-cell chronic leukemia) samples expressing high levels of LPL [GeneID=4023] compared with those expressing low levels of the gene. 16617321 56/81 Arthur Liberzon 0.182738473184491 0.239657014012447 2250 1932 1562 0.0181778555318724 1063 1.24306084509317 1.21813947065497 1 1.15710605307933 2246 1398 1538 1570 2678 1562 1417 3203 1063 1149 3428 1268 M1696 WOOD_EBV_EBNA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WOOD_EBV_EBNA1_TARGETS_UP.html Genes up-regulated in the Ad/AH cells (adenocarcinoma) engineered to stably express the Epstein-Barr virus (EBV) gene EBNA1. 17486072 150/175 Arthur Liberzon 0.00241936208660815 0.00770539072118114 2525 1727.63636363636 1562 0.000220184253349434 545 1.14954873858794 1.1266693931902 1 3.64500633027572 2521 1775 899 852 545 2334 3408 1562 1057 637 3414 1269 M10941 PENG_RAPAMYCIN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_RAPAMYCIN_RESPONSE_UP.html Genes up-regulated in BJUB cells (B-lymphoma) in response to rapamycin (sirolimus) [PubChem=6610346] treatment. 12101249 278/380 Broad Institute 0.00193109314739109 0.00650125510391294 1095 1516.45454545455 1562 0.000175708208019936 46 1.00861521389264 -0.978110441522045 -1 3.30980779687337 1093 2730 2577 2742 1431 52 1562 370 1949 2129 46 1270 M527 GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_DN.html Down-regulated genes from the set D (Fig. 5a): specific signature shared by cells expressing MLL-AF4 [GeneID=4297;4299] alone and those expressing both MLL-AF4 and AF4-MLL fusion proteins. 17130830 15/17 Arthur Liberzon 0.00577426225782821 0.0142024584976285 3385 2145.63636363636 1563 0.000526315789473684 128 1.52852981990427 1.22543903129424 1 4.23761409755485 3381 1563 1106 128 1558 3533 4671 4514 213 898 2037 1271 M16050 KAYO_AGING_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_AGING_MUSCLE_UP.html Upregulated in the vastus lateralis muscle of aged vs young adult rhesus monkeys 11309484 319/538 John Newman 9.11524557720046e-05 0.00061375120006257 1565 2168.54545454545 1563 8.28693024589235e-06 475 1.30799009817226 1.27405900167794 1 6.30399041789779 1563 3981 475 4189 1340 1440 1803 4516 2376 659 1512 1272 M2587 BIOCARTA_HSP27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HSP27_PATHWAY.html Stress Induction of HSP Regulation 18/25 BioCarta 7.43965882739004e-05 0.000522547465257157 755 1904.45454545455 1565 6.76355493045372e-06 14 1.15338999145419 1.2089468164567 1 5.67978415666275 753 3876 2093 4230 2648 1401 561 14 2952 1565 856 1273 M10735 REACTOME_PLATELET_AGGREGATION_PLUG_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_AGGREGATION_PLUG_FORMATION.html Genes involved in Platelet Aggregation (Plug Formation) 41/51 Reactome 1.6122770297412e-05 0.000152503959526622 3930 2044.81818181818 1567 1.46571713226014e-06 40 1.48004887769001 -1.6465284809785 -1 8.4762277481965 3926 848 988 1567 40 3495 2009 3430 485 1304 4401 1274 M18424 FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_EARLY_UP.html Genes up-regulated early in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 29/33 Arthur Liberzon 0.000386817101453836 0.00191180808257812 1455 1759.36363636364 1567 3.51713755169642e-05 263 1.0032099624036 1.12480846174731 1 4.09223579920907 1454 305 2103 2289 263 1567 2452 4464 2099 1390 967 1275 M4276 NIKOLSKY_BREAST_CANCER_6P24_P22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_6P24_P22_AMPLICON.html Genes within amplicon 6p24-p22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 25/26 Jessica Robertson 0.0226157046177879 0.0418448160705445 1570 1846.90909090909 1567 0.0020774175408638 342 1.00837223407078 -0.955176235957595 -1 2.0854644281697 1567 923 2077 681 2898 853 3043 4157 1124 2651 342 1276 M706 REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCEROPHOSPHOLIPID_BIOSYNTHESIS.html Genes involved in Glycerophospholipid biosynthesis 69/85 Reactome 0.00577426225782821 0.0142024584976285 2980 1477.27272727273 1568 0.000526315789473684 24 1.10759123859555 -1.14952136148982 -1 3.07059740603031 2977 743 1818 24 2143 1568 2482 1688 449 1102 1256 1277 M1286 HOSHIDA_LIVER_CANCER_SUBCLASS_S3 http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SUBCLASS_S3.html Genes from 'subtype S3' signature of hepatocellular carcinoma (HCC): hepatocyte differentiation. 19723656 294/490 Jessica Robertson 0.000125608678043489 0.000794735871803309 4605 2351.45454545455 1568 1.14196227478072e-05 293 1.23378309417295 -1.30713902674872 -1 5.7385621788182 4601 1178 580 1280 1237 1894 4504 4589 1568 293 4142 1278 M2083 WANG_METASTASIS_OF_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METASTASIS_OF_BREAST_CANCER_ESR1_DN.html Genes whose expression in primary ER(+) [GeneID=2099] breast cancer tumors negatively correlates with developing distant metastases. 15721472 34/46 Arthur Liberzon 0.0566058994100976 0.0895674975580492 2685 1902.90909090909 1568 0.00528337195302175 508 1.37193264852749 1.37414771710351 1 2.15701034439734 2685 886 1458 508 1568 2996 2337 3821 537 1427 2709 1279 M2093 KAMIKUBO_MYELOID_MN1_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/KAMIKUBO_MYELOID_MN1_NETWORK.html Network of differentially expressed myeloid genes centered around MN1 [GeneID=4330]. 20478528 29/31 Arthur Liberzon 0.00362968417640983 0.0104273337265091 1570 1817.09090909091 1569 0.000330516954817176 633 0.96429597409814 -1.03718732007063 -1 2.86748935981352 1569 2542 3140 2573 633 962 2379 1172 976 2963 1079 1280 M9271 REACTOME_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_METABOLISM.html Genes involved in Purine metabolism 34/39 Reactome 0.00603320219081929 0.0147090466635677 1570 1868.18181818182 1570 0.000549982839407655 758 1.05201180445872 -0.850289950909876 -1 2.89248078523172 1570 2513 3252 2889 758 1114 1364 1166 945 3290 1689 1281 M13133 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_CIS.html Genes associated with the same cis-regulatory QTL (quantitative trait loci) in both brain and hematopoietic stem cells (HSC). 15711547 81/91 Jean Junior 0.01215999814948 0.0254524129780691 1390 1838.63636363636 1570 0.00111161222770135 461 0.795014307320582 -0.831213166732264 -1 1.90175577139038 1390 2391 3841 1604 1570 555 1289 585 2490 4049 461 1282 M1550 SIMBULAN_PARP1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_PARP1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) from PARP1 [GeneID=142] knockout mice. 11016956 48/53 John Newman 0.000257656899233679 0.00141576317157504 415 1682.72727272727 1571 2.34260981933435e-05 415 1.45425413377215 1.35157349822562 1 6.21682443523178 415 1945 538 2172 897 1571 1203 3364 3112 640 2653 1283 M5058 FUNG_IL2_TARGETS_WITH_STAT5_BINDING_SITES_T1 http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_TARGETS_WITH_STAT5_BINDING_SITES_T1.html Genes with putative STAT5 [GeneID=6777] binding sites; up-regulated by IL2 [GeneID=3558] only in T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 6/11 Arthur Liberzon 0.013344750195552 0.0274933308262792 3235 2025.81818181818 1573 0.00134255711706837 476 1.59371095211502 -1.84907453620131 -1 3.7323184822939 3234 2178 4393 1573 1126 2847 3022 632 476 1551 1252 1284 M16830 NELSON_RESPONSE_TO_ANDROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/NELSON_RESPONSE_TO_ANDROGEN_DN.html Genes down-regulated in LNCaP cells (prostate cancer) in response to synthetic androgen R1881 [PubChem=13766]. 12185249 28/30 Broad Institute 0.0397035341919466 0.0662963096882347 4605 2078.18181818182 1574 0.00367624633078028 95 1.39897060049748 1.36634336612238 1 2.47380422876746 4604 311 1521 328 3595 4298 2763 2975 95 796 1574 1285 M7363 ELVIDGE_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_UP.html Genes up-regulated in MCF7 cells (breast cancer) under hypoxia conditions. 16565084 225/258 Arthur Liberzon 1.30141544242631e-05 0.000129319597647414 1730 1608.45454545455 1575 1.18311194640483e-06 298 1.28148668412385 1.29506006265268 1 7.47676114605571 1730 1213 377 1468 2810 1575 2551 1486 1975 298 2210 1286 M2134 REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS.html Genes involved in Metabolism of lipids and lipoproteins 453/619 Reactome 0.00577426225782821 0.0142024584976285 3525 1811.72727272727 1576 0.000526315789473684 48 1.0693592054123 -1.05637847806428 -1 2.96460232062603 3522 509 1803 48 1250 1721 3733 3118 1277 1576 1372 1287 M197 PID_HIV_NEF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIV_NEF_PATHWAY.html HIV-1 Nef: Negative effector of Fas and TNF-alpha 18832364 43/52 Pathway Interaction Database 0.0957196153256206 0.138928838971995 1770 1798.45454545455 1577 0.00910518595629989 304 0.98884900944689 0.97241285004162 1 1.27180832791663 1769 834 2666 1317 3983 1376 943 1577 304 1990 3024 1288 M14387 DAIRKEE_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_TERT_TARGETS_DN.html Genes down-regulated in non-spontaneously immortalizing (NSI) primary breast cancer tumor cultures upon expression of TERT [GeneID=7015] off a retroviral vector. 17471242 199/295 Arthur Liberzon 0.0169522912417527 0.0332287436300136 910 1522.18181818182 1578 0.00155312230794582 906 1.01973098128123 1.01765960995346 1 2.26216534847866 906 1750 2439 2505 1091 1055 1029 999 1578 1807 1585 1289 M16991 BIOCARTA_IGF1MTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1MTOR_PATHWAY.html Skeletal muscle hypertrophy is regulated via AKT/mTOR pathway 29/32 BioCarta 0.0261206876272318 0.0471831785688994 1120 1865.18181818182 1579 0.00240327951444279 753 0.703953013860743 0.655628205545712 1 1.40076695637806 1117 2025 3805 2469 1241 1209 1579 884 753 3777 1658 1290 M2512 FOSTER_KDM1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_KDM1A_TARGETS_UP.html Genes up-regulated in ES cells (embryonic stem) heterozygotic for KDM1A [GeneID=23028] loss of function mutant compared to the homozygotic loss of the gene. 20713442 254/576 Arthur Liberzon 4.27210944159428e-13 1.97689770238481e-11 3575 2129 1579 3.88373585599556e-14 79 1.38177834922097 -1.46670140876736 -1 22.1934522210697 3573 1196 79 447 858 3938 3492 4584 1579 84 3589 1291 M7880 SPIRA_SMOKERS_LUNG_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SPIRA_SMOKERS_LUNG_CANCER_UP.html Up-regulated genes that distinguished smokers with and without lung cancer. 17334370 49/72 Jessica Robertson 0.00201020875451571 0.00669596705809045 1580 1938.54545454545 1580 0.000182913445289503 159 1.36324253472566 1.12916738392752 1 4.44735129176688 1580 810 1456 159 3836 3193 3104 3260 1018 457 2451 1292 M587 REACTOME_DEGRADATION_OF_THE_EXTRACELLULAR_MATRIX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEGRADATION_OF_THE_EXTRACELLULAR_MATRIX.html Genes involved in Degradation of the extracellular matrix 14/70 Reactome 0.00283995526292218 0.00867610928219591 1255 1752.18181818182 1581 0.000258511633493675 64 1.67434360436075 1.69995285137719 1 5.17961791670429 1253 3536 1297 2574 2607 1547 1816 873 2126 1581 64 1293 M5077 MARTINEZ_RESPONSE_TO_TRABECTEDIN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RESPONSE_TO_TRABECTEDIN.html Genes down-regulated by trabectedin [PubChem=3199] and its synthetic analog phthalascidin Pt 650 in HCT116 cells (colon cancer). 11755394 72/76 John Newman 0.0120076955566152 0.0251782865514099 1335 1591.63636363636 1581 0.00109761266293892 275 1.10913724463957 1.25458260987889 1 2.66103864368487 1335 1339 3092 1581 1740 1412 1887 580 275 2414 1853 1294 M2201 PHESSE_TARGETS_OF_APC_AND_MBD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/PHESSE_TARGETS_OF_APC_AND_MBD2_UP.html Genes up-regulated in small intestine upon loss of both APC and MBD2 [GeneID=324, 8932]. 18644872 15/31 Arthur Liberzon 0.000109526349574767 0.00071305430343848 930 1854.72727272727 1581 9.95743660834338e-06 27 1.17226859847182 1.17226859847182 1 5.53529102838729 929 4239 2829 3159 3300 394 413 27 1581 3411 120 1295 M277 PID_INTEGRIN_A4B1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_A4B1_PATHWAY.html Alpha4 beta1 integrin signaling events 18832364 46/61 Pathway Interaction Database 0.00461229999778193 0.0125067320625315 1040 1934.90909090909 1582 0.000420181651069841 363 1.25134373028355 1.3765838921432 1 3.57282319953463 1039 3354 2038 4057 3741 1138 1269 363 1582 1868 835 1296 M33 PID_GLYPICAN_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_GLYPICAN_1PATHWAY.html Glypican 1 network 18832364 30/37 Pathway Interaction Database 0.00275799628935401 0.00851389305804509 1585 1737 1583 0.000251041808144801 290 1.34770547073826 1.51431212946269 1 4.18571128627567 1583 290 714 569 3729 2153 1767 3646 1554 694 2408 1297 M161 PID_IFNG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IFNG_PATHWAY.html IFN-gamma pathway 18832364 55/57 Pathway Interaction Database 0.0867621828761546 0.128134387726987 1585 1818.09090909091 1584 0.00821686941250992 787 0.831369909852647 0.904820852067147 1 1.11306982281624 1584 787 3251 1361 3112 931 907 2447 1083 2402 2134 1298 M11023 GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_DN.html Down-regulated genes from the set G (Fig. 5a): specific to cells expressing both MLL-AF4 [GeneID=4297;4299] and AF4-MLL fusion proteins. 17130830 54/64 Arthur Liberzon 0.00106993376972817 0.00418053592145444 430 1480.45454545455 1584 9.7314042632589e-05 148 1.11462293464612 1.10843101837318 1 3.97841721940832 426 2889 2558 2612 1584 466 173 148 2804 2364 261 1299 M10970 CHUANG_OXIDATIVE_STRESS_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHUANG_OXIDATIVE_STRESS_RESPONSE_UP.html Genes up-regulated in MCF7 cells (breast cancer) after treatment with the oxydants: hydrogen peroxyde, menadione, and t-butyl hydroperoxyde [PubChem=784;4055;6410]. 12414654 42/43 John Newman 0.0385200899465398 0.0646108118506282 895 1804.36363636364 1584 0.00356468668799989 595 1.10900676368684 1.12445198991817 1 1.97964971358856 892 2944 1584 2183 2256 739 595 1879 3989 1357 1430 1300 M260 ABE_INNER_EAR http://www.broadinstitute.org/gsea/msigdb/cards/ABE_INNER_EAR.html Genes prefentially expressed in human inner ear tissue (cochlea and vestibule), at least 10-fold higher from a mixture of 29 other tissues. 12471561 60/83 John Newman 0.00540107881527573 0.0141235966803886 1590 1885.45454545455 1586 0.000492216764707546 391 1.44349513573039 1.70555464791736 1 4.00710046446906 1586 2434 1495 3051 3481 2448 2247 391 904 1560 1143 1301 M10175 ELVIDGE_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HYPOXIA_DN.html Genes down-regulated in MCF7 cells (breast cancer) under hypoxia conditions. 16565084 189/212 Arthur Liberzon 0.0342205659703398 0.0585009313219863 1265 2218.45454545455 1587 0.00316043165227118 963 0.969584882041298 -0.910649949501493 -1 1.79352632735628 1263 3633 3809 2935 2955 1087 1587 963 985 3784 1402 1302 M2466 DELACROIX_RAR_BOUND_ES http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RAR_BOUND_ES.html Genes with DNA sequences bound by RARA and RARG [GeneID=5914, 5916] in ES cells. 19884340 510/658 Arthur Liberzon 0.00525070999993344 0.0138068808911899 4360 2405 1587 0.000526315789473684 121 1.10729962856231 -1.02870689931951 -1 3.09017245222404 4356 1144 4704 121 2290 873 3910 4619 1275 1587 1576 1303 M2096 ABDULRAHMAN_KIDNEY_CANCER_VHL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABDULRAHMAN_KIDNEY_CANCER_VHL_DN.html Genes down-regulated in the RCC4 cells (renal cell carcinoma, RCC) expressing VHL [GeneID=7428] mutants Type 1 and 2B (associated with RCC) but not those of Type 2A and 2C (not associated with RCC). 17001320 26/40 Arthur Liberzon 0.000999522359160159 0.00397116627545114 4695 2019.81818181818 1588 9.09069781410459e-05 325 1.31447071638014 -1.48486659929906 -1 4.73576341226117 4692 325 1303 376 3403 2207 2612 715 1588 415 4582 1304 M18299 YANG_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_UP.html Genes up-regulated in early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 51/67 Leona Saunders 0.0598091522238487 0.0936937266832279 2695 1562.81818181818 1588 0.00559089379768284 153 0.99835563009945 -0.994807677488408 -1 1.54032597169472 2692 153 2009 497 1588 882 2397 3323 320 2169 1161 1305 M11404 CERVERA_SDHB_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/CERVERA_SDHB_TARGETS_1_DN.html Genes turned off in Hep3B cells (hepatocellular carcinoma, HCC) upon knockdown of SDHB [GeneID=6390] by RNAi. 18519664 43/73 Jessica Robertson 0.0100332496462141 0.0219143629477697 2460 2087.72727272727 1589 0.000916300114860032 903 1.38492361093824 -1.61392205642012 -1 3.44803496016001 2456 3767 906 3511 903 1096 2539 973 4047 1178 1589 1306 M1633 SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_UP.html Genes up-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] but displayed blunted response to insulin the insulin resistant cells. 14530283 25/26 John Newman 0.0599183776778682 0.0938025680396477 1265 1772.27272727273 1589 0.00560139655139351 750 1.18461235951682 0.967051482639028 1 1.82681807400378 1265 2559 1662 1798 1589 2647 1151 3114 750 1421 1539 1307 M7281 KONDO_PROSTATE_CANCER_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_PROSTATE_CANCER_WITH_H3K27ME3.html Top 200 genes with high histone H3 trimethylation mark at K27 (H3K27me3) in PC3 cells (prostate cancer), by ChIP-chip assay on an 88K microarray (all promoters). 18488029 102/442 Jessica Robertson 1.0694707965296e-13 5.4278517845373e-12 1540 1718 1589 9.72246178663313e-15 70 1.93116951114893 1.97651067030031 1 32.6442229134971 1539 2817 70 3478 1457 2305 1549 1589 1595 130 2369 1308 M2047 KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP.html Genes up-regulated in response to hydorgen peroxyde [PubChem=784] in CS-B cells (Cockaine syndrome fibroblast, CS) with defficient ERCC6 [GeneID=2074]. 12606941 69/85 Arthur Liberzon 0.00345765048706022 0.0100555208249687 2415 1888.90909090909 1589 0.000314826974808977 515 0.948207408514335 1.10964606148099 1 2.84208143205203 693 2413 2411 2480 624 1318 1589 1429 3922 3384 515 1309 M1565 WESTON_VEGFA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS.html Genes up-regulated in MMEC cells (myometrial endothelium) by VEGFA [GeneID=7422] stimulation. 12200464 137/171 John Newman 9.79840116607797e-12 3.53041629800672e-10 285 1695.27272727273 1591 8.9076374237469e-13 103 1.43638800574403 1.48582621842413 1 20.3724393581689 282 2789 103 2846 2298 2021 1546 1591 3433 358 1381 1310 M2336 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_17.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 17. 12554760 225/259 Arthur Liberzon 0.010337537863906 0.0224233358077372 150 1890.09090909091 1591 0.000944221335549446 147 0.792969906397197 -0.790693478861222 -1 1.96234197899431 147 1730 4089 1310 2464 773 804 1570 1591 4341 1972 1311 M11420 BIOCARTA_CTCF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTCF_PATHWAY.html CTCF: First Multivalent Nuclear Factor 30/34 BioCarta 0.0721047562804974 0.10939712299709 1845 1486.09090909091 1593 0.00678022227120046 280 1.03230232267717 1.11342125005613 1 1.48846476063512 1845 280 2131 391 2262 1593 1323 2358 1499 905 1760 1312 M8475 WANG_ESOPHAGUS_CANCER_VS_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ESOPHAGUS_CANCER_VS_NORMAL_UP.html Up-regulated genes specific to esophageal adenocarcinoma (EAC) relative to normal tissue. 16449976 174/224 Arthur Liberzon 0.000426052893836099 0.00203952298063528 1245 1956.54545454545 1593 3.87395841627206e-05 561 1.22951235658792 1.29404132607258 1 4.96356628453344 1241 3205 561 3152 2330 1011 1047 2537 3932 913 1593 1313 M13965 GOUYER_TUMOR_INVASIVENESS http://www.broadinstitute.org/gsea/msigdb/cards/GOUYER_TUMOR_INVASIVENESS.html Genes up-regulated in constitutively invasive HT-29 5M21 cells (colon cancer) vs the parental non-invasive cells. 18317448 11/15 Jessica Robertson 0.0216594864968959 0.0404561837219424 1850 1579.54545454545 1593 0.00198870138317209 83 1.29157991469573 -1.15256809108804 -1 2.69961533624675 1850 1593 1851 1442 1418 582 428 4569 83 1719 1840 1314 M16834 BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_REVERSIBLY_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 10/10 Leona Saunders 9.30288801934043e-05 0.000621949453984233 4430 1670 1595 8.45752856654606e-06 38 0.934472753365383 0.908374776218667 1 4.49567513810252 4428 421 1905 60 129 4150 3305 140 38 1595 2199 1315 M19661 WANG_ESOPHAGUS_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ESOPHAGUS_CANCER_PROGRESSION_UP.html Candidate progression biomarkers up-regulated in transition from non-tumor-risk associated to tumor-risk associated Barrett's esophagus and then to esophageal adenocarcinoma (EAC). 16449976 10/11 Arthur Liberzon 0.0191804848016 0.036593325894726 1600 2017.81818181818 1596 0.00175907072495127 587 1.29796827881358 -1.49958109633007 -1 2.79785210029921 3689 1600 1501 808 1139 3051 4707 803 587 1596 2715 1316 M1555 RUAN_RESPONSE_TO_TNF_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_DN.html Adipocyte abundant genes down-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to TNF [GeneID=7124]. 12732648 104/126 John Newman 0.163108371384131 0.216987461367841 1255 1923.72727272727 1596 0.0160570248700867 1151 1.0051649680315 1.0485621745874 1 1.00073003695558 1252 2353 2649 1311 3243 1151 1212 2498 1596 2570 1326 1317 M1165 BAKER_HEMATOPOESIS_STAT5_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BAKER_HEMATOPOESIS_STAT5_TARGETS.html STAT5 [GeneID=6777] targets in hematopoietic signaling. 17934481 10/10 Arthur Liberzon 0.000173017351480017 0.00102981323957841 1305 1762.72727272727 1597 1.57300872543912e-05 172 1.49825335440482 1.64838342973481 1 6.71568877767598 1304 3110 1776 3166 172 1354 411 1225 3401 1597 1874 1318 M6122 BROWNE_HCMV_INFECTION_20HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_20HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 20 h time point that were not up-regulated at the previous time point, 18 h. 11711622 406/539 John Newman 0.00923539988327665 0.0205006564524236 930 2010.90909090909 1597 0.000843127149439784 520 0.958943877991484 0.997589887626137 1 2.42911606763627 928 2719 3202 3002 917 1062 1597 520 3227 3639 1307 1319 M1810 DAZARD_UV_RESPONSE_CLUSTER_G6 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G6.html Cluster G6: genes increasingly down-regulated in NHEK cells (normal keratinocyte) after UV-B irradiation. 12771951 222/252 John Newman 0.0105975610822322 0.0228299809713082 835 1667.45454545455 1597 0.00096808702331886 552 1.04994461286412 1.04243133092675 1 2.58600788267343 831 564 3131 1824 2604 1597 1234 552 1254 2459 2292 1320 M935 REACTOME_IRAK1_RECRUITS_IKK_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IRAK1_RECRUITS_IKK_COMPLEX.html Genes involved in IRAK1 recruits IKK complex 11/11 Reactome 0.000322578256054362 0.00167131654069878 1900 1577.27272727273 1598 2.93295967527417e-05 232 0.884536233871025 0.84722559766538 1 3.68562940386988 1900 1598 2708 792 232 1194 1503 2188 291 2339 2605 1321 M18742 SENGUPTA_EBNA1_ANTICORRELATED http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_EBNA1_ANTICORRELATED.html Genes whose reduced expression in nasopharyngeal carinoma (NPC) correlated most with the increased expression of EBNA1 [GeneID=3783774], a latent gene of Epstein-Barr virus (EBV). 16912175 185/254 Arthur Liberzon 0.00939792505345131 0.0207935728475375 2260 1959.27272727273 1598 0.000858028427824111 583 1.03990224336079 -1.04572564594975 -1 2.62458779634506 2258 583 2456 787 888 1018 3655 4536 1598 2558 1215 1322 M16304 NEBEN_AML_WITH_FLT3_OR_NRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NEBEN_AML_WITH_FLT3_OR_NRAS_UP.html Genes up-regulated in acute myeloid leukemia (AML) samples with constitutively activated FLT3 [GeneID=2322] or with activating point mutations within NRAS [GeneID=4893]. 15674343 10/14 Arthur Liberzon 0.079970022971229 0.11944889507095 1600 2001.54545454545 1599 0.00754854966714764 913 1.44800317596762 -1.93370380036852 -1 2.00495390593499 2526 1597 1152 1423 2514 3090 2660 3605 938 1599 913 1323 M2145 DEMAGALHAES_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/DEMAGALHAES_AGING_DN.html Genes consistently underexpressed with age, based on meta-analysis of microarray data. 19189975 28/35 Joao Pedro de Magalhaes 0.0116709760023005 0.0246253941577373 310 1856.36363636364 1601 0.0010666685617309 306 1.01402014649026 1.14529488657357 1 2.44749727199722 306 2022 1316 2455 969 1601 1559 1982 4536 2442 1232 1324 M195 PID_CMYB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CMYB_PATHWAY.html C-MYB transcription factor network 18832364 121/152 Pathway Interaction Database 0.000643147801394935 0.00280559854212948 430 1738.90909090909 1602 5.84850814683894e-05 15 1.13124391077342 1.12924617927609 1 4.33175393618535 428 3223 1602 2997 3024 15 118 1931 3713 1387 690 1325 M18437 REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_Q_SIGNALLING_EVENTS.html Genes involved in G alpha (q) signalling events 104/199 Reactome 1.39266907928109e-06 1.86482454322945e-05 1920 1768.27272727273 1603 1.26606360080466e-07 292 1.45727441282275 -1.36362142136943 -1 10.341445874581 1920 1826 292 2498 4577 719 1563 2321 1603 748 1384 1326 M1940 BIOCARTA_CHREBP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CHREBP2_PATHWAY.html Regulation And Function Of ChREBP in Liver 41/64 BioCarta 0.00652674393792582 0.015598091841524 1605 1454.18181818182 1605 0.00059510796782623 122 0.880924341067715 0.933818472859845 1 2.3883729837321 1605 844 3049 831 782 1828 1950 652 122 2580 1753 1327 M894 REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASPARAGINE_N_LINKED_GLYCOSYLATION.html Genes involved in Asparagine N-linked glycosylation 87/94 Reactome 8.7352834255837e-05 0.000593245147751871 1420 1756.90909090909 1605 7.94148207870609e-06 122 0.919363439232447 -0.907704270564256 -1 4.45129275571179 1418 701 3386 731 122 1605 2107 2737 398 3554 2567 1328 M13 PID_ERBB4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB4_PATHWAY.html ErbB4 signaling events 18832364 51/81 Pathway Interaction Database 0.00577426225782821 0.0142024584976285 2230 1702.18181818182 1606 0.000526315789473684 172 1.15317085434817 1.16491782035503 1 3.1969630440082 2230 172 2127 194 2335 1373 1527 4208 568 1606 2384 1329 M9012 GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_B_DN.html Down-regulated genes from the set B (Fig. 5a): specific signature shared by cells expressing either AF4-MLL or MLL-AF4 [GeneID=4299;4297] fusion proteins. 17130830 10/11 Arthur Liberzon 0.0266385689569189 0.0479445951605065 3420 1980 1606 0.00245151786392673 174 1.34675284081826 -1.38951930054309 -1 2.66589461221269 3416 1606 1373 498 3671 2453 1198 3439 174 729 3223 1330 M14648 CAFFAREL_RESPONSE_TO_THC_8HR_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_3_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 36/40 Jessica Robertson 0.0069559384558165 0.0163914276143055 810 1935.45454545455 1607 0.000634366320201456 605 1.01795917512844 1.10256852650375 1 2.72701021461438 809 2959 2771 2340 799 605 1607 4385 1324 3033 658 1331 M8556 OSADA_ASCL1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OSADA_ASCL1_TARGETS_UP.html Genes up-regulated in A549 cells (lung cancer) upon expression of ASCL1 [GeneID=429] off a viral vector. 18339843 56/87 Jessica Robertson 5.53008564095445e-07 8.44725055835113e-06 1895 1824 1607 5.02735184639901e-08 258 1.46004290522725 1.52579353706845 1 11.1145662649451 1894 1921 258 2262 4163 1607 1506 927 3484 521 1521 1332 M9809 KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION.html Cytokine-cytokine receptor interaction 144/310 KEGG 1.04386424833175e-09 2.767999579846e-08 1545 1912.81818181818 1608 9.48967498933681e-11 142 1.34899811162636 1.32368977245934 1 15.2984521870622 605 2784 142 2499 4152 1543 1608 1541 3755 391 2021 1333 M660 REACTOME_HYALURONAN_UPTAKE_AND_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HYALURONAN_UPTAKE_AND_DEGRADATION.html Genes involved in Hyaluronan uptake and degradation 12/13 Reactome 0.00226464727119291 0.00734143895606492 3795 2091.27272727273 1608 0.000206089257320156 235 1.61219768111122 2.30562372652859 1 5.16285753605911 3795 1584 1608 1710 663 4535 4555 235 761 2452 1106 1334 M12892 SMID_BREAST_CANCER_LUMINAL_B_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_B_UP.html Genes up-regulated in the luminal B subtype of breast cancer. 18451135 189/288 Jessica Robertson 7.29642259297052e-10 1.99120713711136e-08 4445 2150.90909090909 1609 6.63311145035494e-11 137 1.30710169636006 -1.3727948321174 -1 15.1038860477602 4445 568 137 236 4014 2903 4457 3983 1120 188 1609 1335 M13656 NAKAMURA_LUNG_CANCER_DIFFERENTIATION_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_LUNG_CANCER_DIFFERENTIATION_MARKERS.html 14 candidate differentiation markers in lung adenocarcinoma cells, noncancerous lung cells and peripheral blood cells. 16491115 10/27 Arthur Liberzon 0.000656799003891024 0.00285722700310197 1845 1793.27272727273 1610 5.97268336314411e-05 338 1.20212077229581 1.10635350159666 1 4.58887717916721 1842 1610 1157 1768 338 3743 1879 478 4213 1598 1100 1336 M2169 FIGUEROA_AML_METHYLATION_CLUSTER_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_3_DN.html Cluster 3 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 56/108 Arthur Liberzon 0.000622593288195637 0.00273337113055396 2615 1449.09090909091 1610 5.6615413639538e-05 150 1.21802261125127 -1.30887565559776 -1 4.68475650120092 2612 150 1081 1867 333 916 2556 1788 2487 1610 540 1337 M777 REACTOME_METABOLISM_OF_NUCLEOTIDES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_NUCLEOTIDES.html Genes involved in Metabolism of nucleotides 74/85 Reactome 0.0443651821412884 0.0727601319342881 700 2141.81818181818 1611 0.00411690481584336 698 0.966704741345018 -0.919276390058661 -1 1.65078581542057 698 3696 3496 3563 2690 953 1146 1063 1308 3336 1611 1338 M18175 REACTOME_P75NTR_SIGNALS_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P75NTR_SIGNALS_VIA_NFKB.html Genes involved in p75NTR signals via NF-kB 20/23 Reactome 0.00350977819167917 0.0101757696957774 695 2306.72727272727 1614 0.000319580915226394 133 0.721109637501279 0.721109637501279 1 2.15578505407997 691 4567 3394 4463 724 515 133 1614 4507 4063 703 1339 M1097 GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP.html Genes up-regulated in ME-A cells (breast cancer) undergoing apoptosis upon serum starvation (5% to 0% FCS) for 22 hr. 17160024 759/1097 Arthur Liberzon 1.31534856230406e-06 1.77180864221409e-05 1060 1984.54545454545 1615 1.31534934086854e-07 177 1.22615011907227 1.2259367261242 1 8.74215560454869 1056 3152 4336 3306 1385 1545 1615 709 2498 177 2051 1340 M19231 EPPERT_HSC_R http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_HSC_R.html Genes up-regulated in human hematopoietic stem cell (HSC) enriched populations compared to committed progenitors and mature cells. 21873988 169/206 Kolja Eppert 0.000249004794214284 0.00138219799997218 1055 2017.18181818182 1615 2.26393620035394e-05 533 1.16134047084382 1.08178351606088 1 4.98277842264556 1054 3638 533 3578 1002 1615 1703 1502 3596 1167 2801 1341 M2071 REACTOME_PURINE_RIBONUCLEOSIDE_MONOPHOSPHATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_RIBONUCLEOSIDE_MONOPHOSPHATE_BIOSYNTHESIS.html Genes involved in Purine ribonucleoside monophosphate biosynthesis 12/12 Reactome 0.0941560379087166 0.137250308501897 1395 2202 1616 0.00894954995732056 944 0.515941910419781 -0.515941910419781 -1 0.667615130197411 1616 2135 3801 3142 3058 1140 1045 1394 944 4556 1391 1342 M12456 VERNELL_RETINOBLASTOMA_PATHWAY_DN http://www.broadinstitute.org/gsea/msigdb/cards/VERNELL_RETINOBLASTOMA_PATHWAY_DN.html Cluster 2: genes down-regulated by RB1, CDNK2A [GeneID=1029;5925], and one of the E2Fs (E2F1, E2F2, or E2F3 [GeneID=1869;1870;1871]). 12923195 28/44 Kevin Vogelsang 0.000134418815949042 0.000837014262901686 2760 1862.36363636364 1617 1.22206390517225e-05 152 1.53874413176941 1.31458635168893 1 7.105046897995 2760 2029 1500 1535 152 2976 2256 1617 310 1039 4312 1343 M1989 WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_UP.html Selected genes with immunologic function which were reciprocally changed in evasion and tolerogenic tumor models. 18381452 23/40 Arthur Liberzon 0.0252714542863302 0.0458693338746506 3040 1718.36363636364 1617 0.00232422764511305 556 1.34014424561949 1.01411186422004 1 2.6914565608288 3038 1496 961 974 2279 1959 1617 1034 556 1626 3362 1344 M12653 HUTTMANN_B_CLL_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUTTMANN_B_CLL_POOR_SURVIVAL_DN.html Down-regulated genes in B-CLL (B-cell chronic leukemia) patients expressing high levels of ZAP70 and CD38 [GeneID=7535;952], which are associated with poor survival. 16932341 82/112 Leona Saunders 0.0139889115548295 0.0285834036964482 2925 1728.18181818182 1618 0.0012798783067044 80 1.21913900082942 1.11966104434747 1 2.82419060921076 2924 80 1618 543 1025 2037 1408 2202 1789 773 4611 1345 M988 RUIZ_TNC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUIZ_TNC_TARGETS_UP.html Genes up-regulated in T98G cells (glioblastoma) by TNC [GeneID=3371]. 15492259 231/287 Arthur Liberzon 1.7963821429299e-05 0.000168902862841218 2020 1524.81818181818 1618 1.63308801020773e-06 390 1.21475531574974 1.34197012548018 1 6.87602437795372 1110 2262 390 1740 1324 2020 2020 1069 2652 568 1618 1346 M2344 FARDIN_HYPOXIA_9 http://www.broadinstitute.org/gsea/msigdb/cards/FARDIN_HYPOXIA_9.html Genes in the hypoxia signature, based on analysis of nine neuroblastoma cell lines in hypoxia and normal oxygen conditions. 19832978 10/11 Paolo Fardin 0.00384042933657273 0.0108526230711268 1550 1978.09090909091 1618 0.000349740891896665 147 0.812268629692346 -0.611833239187495 -1 2.39423431456495 1547 1618 2875 2639 2699 513 147 965 3948 3663 1145 1347 M1939 MEISSNER_BRAIN_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in brain. 18600261 39/57 Jessica Robertson 0.025938829467711 0.0469085345163203 2285 1619.27272727273 1619 0.00238634576542413 395 1.24667323365555 -1.38689742652777 -1 2.48552777484394 2282 1442 1678 979 1972 1619 3457 852 1683 1453 395 1348 M1377 HE_PTEN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HE_PTEN_TARGETS_UP.html Genes up-regulated in the intestine after the tissue specific knockout of PTEN [GeneID=5728] by Cre-lox. 17237784 23/26 Jessica Robertson 0.00581672526658741 0.0142845698534301 1715 1547.36363636364 1620 0.000530196514502288 743 1.08973428666934 1.16665072496259 1 3.0169966442196 1711 1503 1633 1307 743 1676 848 1250 3109 1621 1620 1349 M14515 COATES_MACROPHAGE_M1_VS_M2_DN http://www.broadinstitute.org/gsea/msigdb/cards/COATES_MACROPHAGE_M1_VS_M2_DN.html Down-regulated genes distinguishing between M1 (pro-inflammatory) and M2 (anti-inflammatory) macrophage subtypes. 18199539 98/138 Jessica Robertson 0.00262381800556722 0.00819075462055376 1410 1978.27272727273 1620 0.000238813865706125 525 1.35986875490255 1.38201723103325 1 4.25777833599189 1409 3671 710 3311 3280 1620 2164 1510 1993 525 1568 1350 M12533 WALLACE_PROSTATE_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_DN.html Genes down-regulated in prostate tumor vs normal tissue samples. 18245496 9/10 Jessica Robertson 0.000143754327002817 0.000883490134704811 1750 1574.63636363636 1620 1.43763627237502e-05 163 1.44470338238213 1.21086439581258 1 6.61993771920765 1750 1620 4539 2274 163 1813 466 558 840 970 2328 1351 M18168 CASTELLANO_NRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_NRAS_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) isolated from NRAS [GeneID=4893] knockout mice. 16909116 89/117 Leona Saunders 0.000673092617753912 0.00292003415055006 3075 2084.72727272727 1621 6.12089672265686e-05 58 1.17940307750972 1.38091419052191 1 4.48544274165657 3071 58 590 96 1402 3341 2943 4640 1621 609 4561 1352 M159 PID_AMB2_NEUTROPHILS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AMB2_NEUTROPHILS_PATHWAY.html amb2 Integrin signaling 18832364 53/76 Pathway Interaction Database 0.0197628490074285 0.0374320414586928 535 2059.90909090909 1622 0.00181296783786054 533 1.08498473307631 1.12782373356921 1 2.32271275256909 533 1934 1392 3641 3621 1622 1445 754 4401 1975 1341 1353 M1424 LEE_LIVER_CANCER_DENA_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_DENA_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by diethylnitrosamine (DENA) [PubChem=5921]. 15565109 74/159 Yujin Hoshida 7.65804944746131e-07 1.11218441206207e-05 3500 1955.90909090909 1622 6.96186555743384e-08 88 1.42040032024236 -1.50142158431443 -1 10.5581716723465 3498 88 270 662 1043 3016 4286 4565 1622 345 2120 1354 M2978 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_DN.html Genes specifically down-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and low-dose methotrexate (LDMTX) [PubChem=4112]. 12704389 23/38 Jean Junior 0.010617667784646 0.0228524359067621 3345 2223.09090909091 1622 0.000969932712479789 796 1.53621539781799 1.42043711327415 1 3.78275502766161 3345 1516 1407 796 929 3451 2353 4038 1011 1622 3986 1355 M1542 YAMAZAKI_TCEB3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMAZAKI_TCEB3_TARGETS_UP.html Genes up-regulated in embryonic stem cells from TCEB3 [GeneID=6924] knockout mice. 12604609 245/290 John Newman 2.24543029175366e-05 0.000200348411664977 1535 1704 1622 2.04132110006217e-06 401 1.20422112730919 1.21009488674247 1 6.68241160408739 1533 1202 401 1744 852 2784 2855 1622 2469 762 2520 1356 M5493 WNT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/WNT_SIGNALING.html Genes related to Wnt-mediated signal transduction 98/137 SuperArray 0.0381308461099021 0.0640489657077359 1520 1687.81818181818 1623 0.00352802115090443 591 1.05621970506269 1.01101460889289 1 1.89142788692273 1517 1302 1971 1527 2446 1044 591 3008 1623 1856 1681 1357 M249 PID_PI3KCI_AKT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PI3KCI_AKT_PATHWAY.html Class I PI3K signaling events mediated by Akt 18832364 46/49 Pathway Interaction Database 0.00413799697853035 0.0114755262859361 1335 2057.90909090909 1623 0.000376890975100926 658 0.71035755910502 0.723096762832115 1 2.06799374696079 1332 3756 3896 1944 658 1623 1725 1094 1144 3996 1469 1358 M19118 BIOCARTA_KERATINOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KERATINOCYTE_PATHWAY.html Keratinocyte Differentiation 58/63 BioCarta 0.0403100827139536 0.0670650653541984 765 1689.81818181818 1624 0.00373347224468542 612 0.85611856166027 1.0214962748545 1 1.50740404643173 761 2880 3352 903 1624 1045 612 1670 1059 2579 2103 1359 M5301 KONDO_EZH2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KONDO_EZH2_TARGETS.html Genes up-regulated in PC3 cells (prostate cancer) after EZH2 [GeneID=2146] knockdown by RNAi. 18488029 276/457 Jessica Robertson 9.46230917855744e-07 1.32136388528968e-05 1140 1513.18181818182 1624 8.60210295304183e-08 281 1.23886441561187 1.24297252830343 1 9.0696252110976 1136 1718 281 2020 1054 1624 2105 1537 2839 297 2034 1360 M9440 DUTTA_APOPTOSIS_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/DUTTA_APOPTOSIS_VIA_NFKB.html NF-kB target genes involved in the regulation of programmed cell death. 17072329 38/51 Arthur Liberzon 0.0537820909639131 0.0858034012101577 1400 2071 1627 0.00501306413569719 722 1.27061881548724 1.16845342922725 1 2.03326278925939 1399 3779 1729 2620 3705 1570 722 1626 2605 1399 1627 1361 M2554 HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_DN.html Genes distinguishing asparaginase resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 23/36 Arthur Liberzon 4.35573333524582e-05 0.000341691152421599 1875 1242.09090909091 1627 3.9598359780697e-06 83 1.32366231990013 -1.5523685504877 -1 6.8847280242295 1874 339 1802 1238 83 2764 2005 1658 150 1627 123 1362 M705 REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION.html Genes involved in MHC class II antigen presentation 110/131 Reactome 0.0915089381945921 0.133846355214898 1830 1549 1628 0.00868661774061902 17 1.11031158844271 -1.12472630850127 -1 1.45500680755205 1826 17 2329 294 2423 1628 1618 2427 325 3261 891 1363 M18669 MOOTHA_TCA http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_TCA.html Tricarboxylic acid related genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 19/21 Vamsi Mootha 0.0401460575955437 0.0668628764470594 795 2015.63636363636 1630 0.00371799375633302 795 0.54375266550762 -0.54375266550762 -1 0.958439532716734 795 2587 3808 2373 1433 830 1354 1630 824 4692 1846 1364 M17607 DER_IFN_BETA_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_BETA_RESPONSE_DN.html Genes down-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon beta for 6 h. 9861020 10/11 Yujin Hoshida 0.000538781975603125 0.00244289233894981 1635 1666.45454545455 1631 4.89921790045849e-05 88 1.20185452640427 1.50785475493088 1 4.71056536616165 1631 1071 2196 1014 3437 2701 2226 88 475 2906 586 1365 M1741 ZHENG_BOUND_BY_FOXP3 http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_BOUND_BY_FOXP3.html Genes whose promoters are bound by FOXP3 [GeneID=50943] based an a ChIP-chip analysis. 17237761 635/805 Jessica Robertson 0.0359296629200606 0.0609809453371759 1225 1910.36363636364 1631 0.00365241596867069 385 1.08717296789727 1.11114214436777 1 1.98163714717898 1224 487 4517 385 1426 2236 1852 1631 3134 1290 2832 1366 M8728 KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HYPERTROPHIC_CARDIOMYOPATHY_HCM.html Hypertrophic cardiomyopathy (HCM) 79/137 KEGG 0.00206269848821576 0.00682744520643646 960 1566.90909090909 1632 0.000187694090594365 224 1.30090647801286 1.36052485697407 1 4.22750068891794 959 2394 692 1813 3304 2046 1632 224 1911 683 1578 1367 M595 REACTOME_DOWNSTREAM_SIGNALING_EVENTS_OF_B_CELL_RECEPTOR_BCR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNSTREAM_SIGNALING_EVENTS_OF_B_CELL_RECEPTOR_BCR.html Genes involved in Downstream Signaling Events Of B Cell Receptor (BCR) 98/111 Reactome 0.000644558634104857 0.00280829563220865 2495 2004.72727272727 1632 5.86134141054734e-05 33 0.655401738265153 -0.623416558058836 -1 2.50920639301082 2494 33 4019 875 336 1236 2398 1582 3046 4401 1632 1368 M9150 GRESHOCK_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRESHOCK_CANCER_COPY_NUMBER_UP.html Genes from common genomic gains observed in a meta analyis of copy number alterations across a panel of different cancer cell lines and tumor samples. 17440070 384/483 Jessica Robertson 0.00515830402190266 0.0136781994288655 355 1495.18181818182 1633 0.000470039860337581 351 1.10263912858866 1.10497805436963 1 3.0838942153446 351 1697 1901 1941 3809 424 453 378 2644 1633 1216 1369 M529 REACTOME_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOSIS.html Genes involved in Meiosis 75/238 Reactome 0.0113297957109874 0.0240128584444816 1530 1766.81818181818 1634 0.0010353242982979 216 1.21845251591566 -1.44259606027194 -1 2.96094883021575 1530 2400 1952 3404 1597 674 2384 1634 1616 2028 216 1370 M760 REACTOME_INTEGRIN_ALPHAIIB_BETA3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRIN_ALPHAIIB_BETA3_SIGNALING.html Genes involved in Integrin alphaIIb beta3 signaling 37/42 Reactome 3.36950477175736e-05 0.000280494929853523 2395 1736.54545454545 1634 3.06323307269619e-06 71 1.35707202276454 1.31356927440153 1 7.23303349981754 2394 259 1277 2149 71 2343 1229 3198 833 1634 3715 1371 M16679 SHAFFER_IRF4_MULTIPLE_MYELOMA_PROGRAM http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_MULTIPLE_MYELOMA_PROGRAM.html Direct targets of IRF4 [GeneID=3662] that constitute a multiple myeloma program. 18568025 55/62 Jessica Robertson 0.00121448264504987 0.00457125844069806 3020 1872.81818181818 1636 0.000110468509427502 148 1.21524049259467 1.24157803035251 1 4.26680196581395 3018 148 1130 489 1636 3543 2891 2325 604 428 4389 1372 M3961 KYNG_DNA_DAMAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_UP.html Genes with GO annotation and up-regulated after DNA damage in cell lines from young donors. 15897889 300/392 Jessica Robertson 0.00441416214410194 0.0120641837406839 1195 1639.18181818182 1637 0.000402094894789107 499 1.16811664611498 1.18733027794533 1 3.36261094697449 1192 1711 838 2324 3250 499 927 2772 2367 514 1637 1373 M9331 YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAUCH_HEDGEHOG_SIGNALING_PARACRINE_DN.html Genes down-regulated in mouse stroma of pancreatic adenocarcinoma zenografts after treatment with HhAntag, a hedgehog (Hh) pathway inhibitor. 18754008 263/465 Jessica Robertson 0.00099755569971614 0.00396922635384674 1340 2079.09090909091 1640 9.07280284676381e-05 621 1.20340778931491 1.15826160372196 1 4.33600113158645 1339 3990 621 3097 1631 1945 2021 1599 3882 1640 1105 1374 M9450 REACTOME_PLATELET_ADHESION_TO_EXPOSED_COLLAGEN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_ADHESION_TO_EXPOSED_COLLAGEN.html Genes involved in Platelet Adhesion to exposed collagen 29/34 Reactome 0.0014255509683527 0.00517584659278828 60 1623.54545454545 1642 0.000129679593859388 58 1.32359726177762 1.24219012357097 1 4.54011972737398 58 2038 856 2784 1642 1090 919 1948 4036 1733 755 1375 M1955 MIKKELSEN_MCV6_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the bivalent trimethylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 42/64 Jessica Robertson 2.79962003644823e-06 3.39696827044618e-05 275 1569.72727272727 1642 2.54511236283984e-07 272 1.33162168162005 1.23822307196783 1 8.92933224465427 272 2485 315 2668 770 1698 1105 1761 3836 715 1642 1376 M1406 JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP http://www.broadinstitute.org/gsea/msigdb/cards/JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_UP.html Genes up-regulated during epithelial to mesenchymal transition (EMT) induced by TGFB1 [GeneID=7040] in the EpH4 cells (mammary epithelium cell line transformed by HRAS [GeneID=3265]). 14562044 107/132 Arthur Liberzon 4.20288412244483e-08 8.40793550134097e-07 350 1740.27272727273 1643 3.82080382066983e-09 194 1.43529682404748 1.54615719463203 1 13.0842401825254 349 3662 194 2931 1388 2155 2054 1643 3199 355 1213 1377 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 0.00866951880459115 0.0195966498090052 3135 2018.54545454545 1644 0.000791261124668886 616 1.25894404644652 -1.36445901562453 -1 3.22608361780939 3132 1515 925 1644 857 1912 616 2290 3521 1329 4463 1378 M1461 PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_UP.html Genes up-regulated in LEC (lymphatic endothelial cells) compared to BEC (blood endothelial cells). 12198161 171/224 Kevin Vogelsang 0.000770915447754527 0.00325466986887421 1150 2054.81818181818 1644 7.01077928681628e-05 527 1.38405768201658 1.50119103227669 1 5.16593549406369 1147 4003 597 3292 4138 1348 2378 1160 2369 527 1644 1379 M1701 HOWLIN_CITED1_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_1_UP.html Genes up-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs. heterozygotic animals. 16278680 42/50 Arthur Liberzon 0.0115188944583401 0.0243480438170019 2820 1921.36363636364 1644 0.00105269560197018 212 1.3106777941374 -1.12193271710754 -1 3.17323258839721 2818 212 1267 338 964 3697 2573 3652 615 1644 3355 1380 M16402 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_24 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_24.html Amplification hot spot 24: colocalized fragile sites and cancer genes in the 1q21-q24 region. 16751803 18/23 Arthur Liberzon 0.0126489249510122 0.0262453776840711 965 2073.54545454545 1645 0.00115656735590886 313 1.04819952484266 1.19299390411125 1 2.48647811692672 963 4222 2557 4004 1645 913 313 1608 3537 2534 513 1381 M7102 BILD_CTNNB1_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_CTNNB1_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing activated beta-catenin (CTNNB1) [GeneID=1499] oncogene from control cells expressing GFP. 16273092 113/126 Arthur Liberzon 0.0184879207189575 0.035573985239902 480 1749.18181818182 1646 0.00169501260273584 455 1.19840815002778 1.22288564064373 1 2.60529907939744 476 2336 2625 2275 4506 1415 455 722 507 1646 2278 1382 M233 PID_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPO_PATHWAY.html EPO signaling pathway 18832364 47/58 Pathway Interaction Database 0.0167881215101022 0.032934303211838 2165 1559.09090909091 1648 0.00153796514895196 183 1.02535134932152 -1.12922753332131 -1 2.28058133864451 2162 183 2225 417 3846 1150 372 1818 597 1648 2732 1383 M1036 REACTOME_INNATE_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INNATE_IMMUNE_SYSTEM.html Genes involved in Innate Immune System 233/416 Reactome 0.0405708942652769 0.0674514339317038 950 1741.36363636364 1648 0.00375808909012583 925 1.14985441889259 1.26332891401665 1 2.02032892751562 949 2750 1648 1842 3881 1195 925 1024 1896 1696 1349 1384 M6487 BIOCARTA_PLATELETAPP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLATELETAPP_PATHWAY.html Platelet Amyloid Precursor Protein Pathway 21/29 BioCarta 0.00363937115985985 0.0104488028433933 110 1983 1649 0.000331400509526517 108 1.44419639892381 1.21581073738569 1 4.29266748070618 108 3493 736 2783 1304 1537 1649 1932 4527 2302 1442 1385 M17427 DOANE_BREAST_CANCER_CLASSES_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_CLASSES_UP.html Genes up-regulated in ER(-) / PR(-) breast tumors (do not express ESR1 and PGR [GeneID=2099;5241]) with molecular similarity to ER(+) (class A) relative to the rest of the ER(-) / PR(-) samples (class B). 16491124 90/126 Arthur Liberzon 0.000124769430194963 0.000793681550566344 50 1602.18181818182 1651 1.13433188047841e-05 50 1.31446752711906 -1.25462183176688 -1 6.11498503760075 2205 50 588 50 2207 2060 3397 4577 1651 291 548 1386 M12166 KRASNOSELSKAYA_ILF3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRASNOSELSKAYA_ILF3_TARGETS_DN.html Down-regulated in GHOST(3)CXCR4 cells (osteosarcoma) upon ectopic expression of ILF3 [GeneID=3609]. 12036489 77/90 John Newman 0.000859247771786622 0.00352765438085475 660 1836 1651 7.81439590338039e-05 603 1.28303441487525 1.18096333749232 1 4.72152039392706 657 2852 603 3114 1679 1171 1248 1735 3856 1651 1630 1387 M4500 DACOSTA_UV_RESPONSE_VIA_ERCC3_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_DN.html Genes down-regulated in fibroblasts expressing mutant forms of ERCC3 [GeneID=2071] after UV irradiation. 15608684 1167/1296 Arthur Liberzon 0.0762791764477977 0.11473477145749 370 1861.72727272727 1652 0.00790314383527192 369 0.966915237262315 0.958984955790556 1 1.36415978503171 369 462 4391 429 2182 1652 1213 1907 1418 4001 2455 1388 M659 KOBAYASHI_EGFR_SIGNALING_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_6HR_DN.html Genes down-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 6h. 17145885 28/34 Leona Saunders 0.000777562315067882 0.0032768697563575 310 1643.63636363636 1653 7.07124791585769e-05 40 1.27351620203725 1.25719341983728 1 4.74769420686587 308 3425 1700 2728 3381 284 40 1545 2195 1653 821 1389 M3737 PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP http://www.broadinstitute.org/gsea/msigdb/cards/PUIFFE_INVASION_INHIBITED_BY_ASCITES_UP.html Genes up-regulated in OV-90 cells (ovarian cancer) exposed to ascites which inhibited invasion. 17971902 122/157 Arthur Liberzon 0.156232357846374 0.209612486934305 2025 2132.90909090909 1653 0.0153248273562452 1124 0.98034206303729 -1.02491972689381 -1 0.998105110314487 2025 1277 3392 1124 4189 1244 2576 1653 1590 3035 1357 1390 M216 SHARMA_ASTROCYTOMA_WITH_NF1_SYNDROM http://www.broadinstitute.org/gsea/msigdb/cards/SHARMA_ASTROCYTOMA_WITH_NF1_SYNDROM.html Genes up-regulated in pilocytic astrocytoma (PA) samples from patients with type 1 neurofibromatosis syndrom (NF1) compared to the PA tumors from non-NF1 patients. 17283119 3/5 Jessica Robertson 0.00134652180577609 0.00492680846764584 1795 1844.27272727273 1654 0.000134733840669508 461 1.31178388815161 1.31178388815161 1 4.54175109295128 1795 1654 4574 1802 461 1616 888 728 2801 2689 1279 1391 M2362 TERAO_AOX4_TARGETS_SKIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_SKIN_UP.html Genes up-regulated in skin upon knockout of AOX4 [GeneID=71872]. 18981221 46/80 Arthur Liberzon 0.0421386440126851 0.0696408962674627 1240 1858.54545454545 1654 0.00390619035241147 616 1.30759273003001 -1.3378727227276 -1 2.27027431070495 1240 3350 2599 2409 1453 1782 1654 1447 616 2549 1345 1392 M5686 MARKEY_RB1_CHRONIC_LOF_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_CHRONIC_LOF_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) isolated from RB1 [GeneID=5925] knockout mice: chronic loss of function (LOF) of RB1. 17452985 127/188 Arthur Liberzon 1.66851133336134e-06 2.18154390400707e-05 1395 1678.18181818182 1655 1.51682963525949e-07 12 1.32334503110717 1.29535801332322 1 9.25573751042362 1392 12 298 1226 4176 2277 1655 2110 3064 255 1995 1393 M1662 REACTOME_SIGNALING_BY_BMP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_BMP.html Genes involved in Signaling by BMP 23/27 Reactome 0.0600818759059226 0.0939961731110225 1020 1706 1656 0.00561712006653824 373 1.24088926254296 1.17575470227855 1 1.91194171473189 1018 2073 2546 2081 3850 827 1197 1656 373 2494 651 1394 M1160 MARKS_ACETYLATED_NON_HISTONE_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/MARKS_ACETYLATED_NON_HISTONE_PROTEINS.html Non-histone proteins that are acetylated. 17322921 21/27 Leona Saunders 0.0101106359267372 0.0220425873321937 980 2356.45454545455 1656 0.000923400272402119 275 1.32465086943788 1.32465086943788 1 3.29293353007871 977 4229 3212 3668 1656 1320 275 1495 4421 3795 873 1395 M3993 PARK_APL_PATHOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARK_APL_PATHOGENESIS_UP.html Genes up-regulated in U937 cells (acute promyelocytic leukemia, APL) expressing RARA [GeneID=5914] fused with either PML or PLZF [GeneID=5371;7704]. 12893766 11/18 Arthur Liberzon 0.00680037632701554 0.0160891109090292 1065 1838.36363636364 1656 0.000620135295826398 244 0.853351300352775 -0.853351300352775 -1 2.29637743266011 1065 1596 2754 3484 1926 244 1656 442 3630 3026 399 1396 M15374 VERRECCHIA_RESPONSE_TO_TGFB1_C6 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C6.html Cluster 6: ECM related genes up-regulated in dermal fibroblasts later than 30 min after TGFB1 [GeneID=7040] addition; slowly increased up to 120 min time point, then reached a plateau. 11279127 14/19 Arthur Liberzon 0.00577426225782821 0.0142024584976285 3945 2452.54545454545 1657 0.000526315789473684 190 1.29207755203515 -1.43844005552384 -1 3.58207014030064 3943 1569 1657 190 1050 4698 3986 4312 415 1585 3573 1397 M7883 CUI_TCF21_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_UP.html Genes most strongly up-regulated in kidney glomeruli isolated from TCF21 [GeneID=6943] knockout mice. 16207825 71/87 John Newman 7.94121560117806e-12 2.92832325293441e-10 2410 1649.54545454545 1658 7.21928691018794e-13 100 1.69807823091218 1.72608124825334 1 24.2909533424672 303 2409 100 2400 1295 1558 1658 2408 3532 435 2047 1398 M8104 KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM.html Amino sugar and nucleotide sugar metabolism 42/54 KEGG 3.43408142121556e-05 0.000284865805063927 3180 1827.81818181818 1659 3.12194093322459e-06 72 1.0182125831676 -0.884873447084971 -1 5.41666634111968 3177 210 2350 293 72 1659 3309 3322 457 1642 3615 1399 M1292 GROSS_HYPOXIA_VIA_HIF1A_ONLY http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_HIF1A_ONLY.html Genes uniquely up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 9/9 Jessica Robertson 0.000279010629722616 0.00149821407541609 1970 1681.90909090909 1659 2.79045667033277e-05 116 1.42285757219634 1.62996289649194 1 6.03011835534655 1970 2154 4424 1784 226 1574 1345 1659 116 1446 1803 1400 M9487 FRIDMAN_SENESCENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRIDMAN_SENESCENCE_DN.html Genes down-regulated in senescent cells. 18711403 36/38 Jessica Robertson 0.000537975816656299 0.00244289233894981 365 1902.63636363636 1660 4.89188559398217e-05 364 1.45402191575822 1.46939166930307 1 5.69893594759577 364 3388 575 3246 2021 1712 1339 1660 4260 1279 1085 1401 M19128 HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/HELLEBREKERS_SILENCED_DURING_TUMOR_ANGIOGENESIS.html Genes down-regulated in tumor-conditioned vs quiescent endothelial cells and up-regulated upon treatment with decitabine and TSA [PubChem=451668;5562]. 17483324 138/176 Jessica Robertson 1.17311048109386e-08 2.55165044735623e-07 780 1593.63636363636 1660 1.06646407940842e-09 178 1.23805438195819 1.32323961095177 1 12.2482102397141 776 2317 178 2127 1592 1463 1817 1960 3326 314 1660 1402 M2547 HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_UP.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 32/35 Arthur Liberzon 2.04781450216949e-05 0.00018587854712 1455 2143.72727272727 1661 1.86166687634782e-06 48 0.655168866232352 -0.708725056281984 -1 3.66759261347048 1451 2987 3864 2930 48 1661 2661 1106 1127 4094 1652 1403 M231 PID_KIT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_KIT_PATHWAY.html Signaling events mediated by Stem cell factor receptor (c-Kit) 18832364 74/85 Pathway Interaction Database 0.194014757558968 0.251579575735805 1330 1967.72727272727 1664 0.0194171780765196 98 0.861599909601187 0.828439909202962 1 0.774729781546388 1329 98 3339 904 4193 1664 1302 1902 665 3575 2674 1404 M856 REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE.html Genes involved in Phospholipase C-mediated cascade 39/61 Reactome 0.0322295343493182 0.0557228579226307 2340 1682.09090909091 1664 0.00297378244013797 226 1.14630914583626 0.954584195437889 1 2.15679183998697 2336 226 1020 806 1669 3106 1664 4095 771 765 2045 1405 M6239 NEWMAN_ERCC6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NEWMAN_ERCC6_TARGETS_DN.html Genes down-regulated in Cockayne syndrome fibroblasts rescued by expression of ERCC6 [GeneID=2074] off a plasmid vector. 16772382 63/82 Leona Saunders 5.13326226893858e-10 1.46842411572061e-08 265 1568.81818181818 1664 4.6666020637603e-11 131 1.36715737761455 1.30287521890441 1 16.0691837916712 262 1904 131 2628 1423 1754 1325 1664 4127 364 1675 1406 M7566 CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN.html Down-regulated genesin the left ventricle myocardium of patients with heart failure following implantation of LVAD (left ventricular assist device). 12824457 46/80 John Newman 0.000927899410554039 0.00375294363137537 995 1857.54545454545 1665 8.43900912926143e-05 612 1.59715193082842 1.67435121617731 1 5.81305353542785 991 2924 612 2317 3378 1577 1665 2132 2749 710 1378 1407 M6541 WU_HBX_TARGETS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_3_UP.html Genes up-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] both in SK-Hep-1 cells (hepatocellular carcinoma) and normal primary hepatocytes. 11439330 29/36 John Newman 0.00577426225782821 0.0142024584976285 4275 2215.72727272727 1665 0.000526315789473684 140 1.02870580417778 0.865389084795616 1 2.85189419665121 4274 284 1665 140 972 4091 3462 4644 486 1084 3271 1408 M1121 JOHANSSON_GLIOMAGENESIS_BY_PDGFB_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_GLIOMAGENESIS_BY_PDGFB_DN.html Genes down-regulated in brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 29/35 Arthur Liberzon 0.0555616740193935 0.0881220098694681 2270 1760.18181818182 1666 0.00518332833743506 253 1.22806121055455 1.21280460158144 1 1.94381932638743 2267 915 1666 373 4521 1925 1215 1164 253 1734 3329 1409 M7484 DAZARD_RESPONSE_TO_UV_SCC_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_SCC_DN.html Genes down-regulated in SCC12B2 cells (squamous cell carcinoma) by UV-B irradiation. 12771951 180/230 John Newman 0.03225193678496 0.0557411723269905 460 2257.36363636364 1667 0.00297588061334656 457 0.950868321222202 0.96186494689369 1 1.78884635218262 457 3196 3794 2963 4323 1406 832 936 1255 4002 1667 1410 M18519 WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_DN.html Down-regulated genes in pediatric adrenocortical carcinoma (ACC) compared to the adenoma (ACA) tumors. 17234769 24/38 Jessica Robertson 0.037279700763791 0.0628429241446762 4405 2335.81818181818 1667 0.00344789292680008 334 1.22416128686479 1.30222157773263 1 2.20735127549168 4404 334 1018 470 1667 3835 3435 1544 3238 1332 4417 1411 M1956 MIKKELSEN_MCV6_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 57/125 Jessica Robertson 1.06954707842054e-06 1.4847830029838e-05 510 1964.63636363636 1667 9.72315998535913e-08 282 1.47259875901073 1.3846737074597 1 10.668896606905 509 2441 282 3115 3055 2256 1471 1095 4347 1667 1373 1412 M4204 AMIT_EGF_RESPONSE_40_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_40_HELA.html Genes whose expression peaked at 40 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 52/55 Leona Saunders 0.12645447237027 0.175703594226575 1070 2146 1668 0.0122152380631028 884 1.15908425366393 1.23116665285808 1 1.3133937138849 884 3343 1668 3412 4678 1069 1069 1989 2624 1658 1212 1413 M1451 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN.html Top 100 probe sets contrubuting to the negative side of the 2nd principal component; associated with adipocytic differentiation. 17464315 85/131 Nikolaos Papanikolaou 6.75427870230717e-10 1.88640209910591e-08 790 1656.72727272727 1668 6.14025336761894e-11 135 1.52554800382042 1.56727686523437 1 17.6818586848091 789 2834 135 2805 1668 2169 1808 471 3664 331 1550 1414 M2130 KEGG_ETHER_LIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ETHER_LIPID_METABOLISM.html Ether lipid metabolism 26/37 KEGG 0.00201305766603368 0.00669976361670371 1595 1681.27272727273 1669 0.000183172911790401 220 1.45428942361904 1.34968407089868 1 4.7438464487296 1594 2040 1140 1183 4280 1733 1706 220 1742 1187 1669 1415 M1564 BURTON_ADIPOGENESIS_5 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_5.html Up-regulated at 48-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 160/197 John Newman 0.00128803926928505 0.00477201361932922 1305 1457.72727272727 1670 0.00011716309085606 29 0.968930087125297 -0.873575310023305 -1 3.3748275817668 1302 584 2047 29 444 964 1670 1963 1841 2846 2345 1416 M994 REACTOME_DSCAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DSCAM_INTERACTIONS.html Genes involved in DSCAM interactions 15/19 Reactome 0.00305986724119395 0.00915825832494322 1675 1660.54545454545 1671 0.000278557396278442 77 0.927041711178184 -0.887217302649393 -1 2.83510353437448 1671 1564 2437 1316 4169 2401 1785 280 77 2221 345 1417 M13522 DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_DN.html Common down-regulated transcripts in fibroblasts expressing either XP/CS or TDD mutant forms of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 707/799 Arthur Liberzon 0.0836504998659297 0.124434402573964 390 1819 1671 0.00869769792931928 390 0.981138701356145 0.988636945824706 1 1.33233938992866 390 482 4392 899 1875 1671 1282 1915 1319 3484 2300 1418 M10371 BENPORATH_ES_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_WITH_H3K27ME3.html Set 'H3K27 bound': genes posessing the trimethylated H3K27 (H3K27me3) mark in their promoters in human embryonic stem cells, as identified by ChIP on chip. 18443585 889/1630 Jessica Robertson 1.92081873657971e-33 8.24205857877841e-31 1240 1786.81818181818 1671 1.92081873657969e-34 3 1.41373543019174 1.35296588741066 1 63.8181624231804 1238 2199 4453 1402 2488 371 1829 1671 2526 3 1475 1419 M19520 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_DN.html Genes from the green module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 33/42 Arthur Liberzon 0.000250728213344218 0.00138575780677366 4375 1957.90909090909 1673 2.27960720672066e-05 201 1.13018118164192 1.15191528501271 1 4.84719098825534 4371 889 2050 958 201 3421 3382 2828 332 1673 1432 1420 M2461 DELACROIX_RARG_BOUND_MEF http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RARG_BOUND_MEF.html Genes with DNA sequences bound by RARG [GeneID=5916] in MEF cells (embryonic fibroblast). 19884340 484/602 Arthur Liberzon 0.000556953978501635 0.00251081449716114 2560 2059.72727272727 1673 5.0645002496869e-05 379 1.14443555853486 1.18055996654731 1 4.46505866290198 2557 1146 717 536 1603 2972 3247 4247 1673 379 3580 1421 M749 REACTOME_CA_DEPENDENT_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CA_DEPENDENT_EVENTS.html Genes involved in Ca-dependent events 28/33 Reactome 0.0335210967922536 0.0575134775933977 3120 2039.18181818182 1674 0.00309482010456682 849 1.13048467684884 1.02743912179758 1 2.10371548720773 3118 918 1674 849 1363 4593 2760 2260 986 1038 2872 1422 M2151 DUTERTRE_ESTRADIOL_RESPONSE_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_6HR_UP.html Genes up-regulated in MCF7 cells (breast cancer) at 6 h of estradiol [PubChem=5757] treatment. 20406972 271/303 Jessica Robertson 0.0339946054579609 0.0581778599570614 1675 1702.90909090909 1674 0.00313923140145833 452 1.17317283361433 1.15785369804075 1 2.1743768216607 1674 548 1202 692 3296 2149 2563 2103 452 772 3281 1423 M17072 RUNNE_GENDER_EFFECT_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUNNE_GENDER_EFFECT_UP.html Up-regulated genes detecting gender effects in global expression profiling studies. 17724341 15/40 Arthur Liberzon 0.0428469173973091 0.0707123951452094 390 1915.27272727273 1675 0.00397317138505412 389 0.617596854129911 0.566664874451771 1 1.06608560169422 389 2106 3547 2328 1675 1054 638 1613 883 4632 2203 1424 M2555 MATTIOLI_MGUS_VS_MULTIPLE_MYELOMA http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MGUS_VS_MULTIPLE_MYELOMA.html Genes distinguishing between MGUS (monoclonal gammopathy of undetermined significance) and multiple myeloma (MM) samples. 15735737 22/24 Leona Saunders 0.000301094982817586 0.00159323802567153 3195 1783.18181818182 1676 2.73760180893312e-05 45 1.29937868217729 -1.3498842314951 -1 5.45473007454724 3193 955 2245 136 220 4375 4092 286 45 2392 1676 1425 M9138 CHANG_POU5F1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_POU5F1_TARGETS_UP.html Genes up-regulated by POU5F1 [GeneID=5460] in bladder cancer cell lines. 18676852 33/36 Jessica Robertson 0.0039522135791312 0.0110668288237094 105 1903.09090909091 1676 0.000359939225806419 101 1.2477138343184 1.22123300674159 1 3.66191238339158 101 2978 1054 3438 2791 925 901 2030 4065 1676 975 1426 M15285 BIOCARTA_NFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NFKB_PATHWAY.html NF-kB Signaling Pathway 28/37 BioCarta 0.00340509075022154 0.00995521383537993 600 1659.45454545455 1677 0.000310033862811646 596 0.889905981503397 0.913846495960248 1 2.67314082722033 596 2028 2652 1595 621 1116 1121 2005 2821 2022 1677 1427 M14435 TIAN_TNF_SIGNALING_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/TIAN_TNF_SIGNALING_VIA_NFKB.html Genes modulated in HeLa cells (cervical carcinoma) by TNF [GeneID=7124] via NFKB pathway. 15722553 29/31 Arthur Liberzon 0.0222988033542315 0.0413882626157974 215 1999.18181818182 1677 0.00204800728638807 213 1.12806084040335 1.02446958903714 1 2.34107561682514 213 3453 1153 3864 1677 941 770 2577 4364 1086 1893 1428 M8617 WEI_MIR34A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WEI_MIR34A_TARGETS.html Potential direct target genes for MIR34A [GeneID=407040] microRNA in IMR32 cells (neuroblastoma). 18504438 188/211 Jessica Robertson 0.0631928378007512 0.0979862662350676 1390 1941.90909090909 1678 0.00591677393457794 1224 1.10692737154709 1.18055211136655 1 1.67553520170727 1388 1752 2612 1615 3669 1459 1678 1224 2117 2301 1546 1429 M2271 STEGER_ADIPOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEGER_ADIPOGENESIS_DN.html Genes down-regulated during adipogenesis of 3T3-L1 cells (fibroblast). 18285465 33/34 Arthur Liberzon 1.40638353733542e-05 0.000137435409859693 200 1755 1678 1.27853866176094e-06 199 1.58226015623986 1.59709807494209 1 9.16887103931661 199 2980 379 2567 1678 1533 1381 2183 3957 663 1785 1430 M6754 ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_UP.html Genes whose promoters display higher histone H3 trimethylation mark at K9 (H3K9me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 105/208 Jessica Robertson 8.34287502749543e-06 8.67364980832124e-05 2860 1928.36363636364 1679 7.58446060513356e-07 263 1.43380994171538 1.3343819704879 1 8.7386927537077 2859 666 363 263 1232 2632 1679 4408 2268 577 4265 1431 M8754 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_7 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_7.html Amplification hot spot 7: colocalized fragile sites and cancer genes in the 3q26.3-q29 region. 16751803 13/13 Arthur Liberzon 0.00223521612004642 0.00727601385284076 670 1789.90909090909 1680 0.000203408213777346 171 0.944349171227767 0.944349171227767 1 3.02962288072616 669 3089 2747 2916 1680 336 171 233 4113 3218 517 1432 M4621 ROSS_AML_OF_FAB_M7_TYPE http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_OF_FAB_M7_TYPE.html Top 100 probe sets for pediatric acute myeloid leukemia (AML) subtype FAB M7 (also known as acute megakaryoblastic leukemia, AMKL). 15226186 94/126 Jean-Pierre Bourquin 0.311525251906094 0.375580891186912 3315 1982.72727272727 1680 0.0333649313707516 684 1.08649459433947 -1.04713984409477 -1 0.693258028680142 3313 684 1508 1028 2998 1409 3189 2654 1637 1710 1680 1433 M196 PID_IL23_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL23_PATHWAY.html IL23-mediated signaling events 18832364 37/54 Pathway Interaction Database 0.0575607699172759 0.0907740841996466 845 1833.72727272727 1681 0.0053749429424958 843 1.13059885751019 1.10547917264338 1 1.76769754805795 843 1975 1100 1081 1982 1681 1641 2706 3587 1061 2514 1434 M274 PID_LYMPH_ANGIOGENESIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LYMPH_ANGIOGENESIS_PATHWAY.html VEGFR3 signaling in lymphatic endothelium 18832364 53/57 Pathway Interaction Database 0.0848935096060914 0.125926261892128 375 2088.18181818182 1681 0.00803255049082148 371 1.01901598147074 1.17677695353205 1 1.37586486325594 371 2894 1590 3261 2683 1442 1093 1681 4053 2601 1301 1435 M1878 HUNSBERGER_EXERCISE_REGULATED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HUNSBERGER_EXERCISE_REGULATED_GENES.html Exercise regulated genes in hyppocampus. 18059283 40/53 Jessica Robertson 0.00221587578104292 0.00723301084821757 930 2086.81818181818 1682 0.000201646436310004 529 1.20188006742437 1.43991695725802 1 3.86049475409157 926 4125 1682 4203 531 972 768 3472 3930 1817 529 1436 M16088 LIAN_LIPA_TARGETS_3M http://www.broadinstitute.org/gsea/msigdb/cards/LIAN_LIPA_TARGETS_3M.html Genes up-regulated at 3 months of age in lungs from LIPA [GeneID=3988] knockout mice, which display pulmonary pathology. 16127159 59/122 John Newman 0.00290916085231123 0.00883606127600321 815 2279.81818181818 1683 0.000264819536900563 269 1.17713683070955 1.17804628669431 1 3.62745321072787 813 4445 1339 4052 3688 1683 1051 269 4322 2621 795 1437 M9577 MOOTHA_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_MITOCHONDRIA.html Mitochondrial genes 12808457 501/573 Vamsi Mootha 0.0197957935130261 0.0374794004739202 1685 1888 1684 0.00199743796617398 212 0.80168396165019 -0.741731853275025 -1 1.71554015764506 212 1684 4589 1065 2590 560 673 1571 1684 4441 1699 1438 M5576 BIOCARTA_PLCE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PLCE_PATHWAY.html Phospholipase C-epsilon pathway 15/16 BioCarta 0.000828311397766946 0.00344157552593309 2225 1676 1686 7.53294023440132e-05 121 1.08517566552191 0.930595203674239 1 4.01086088978054 2225 2116 2232 2877 4479 1358 403 121 578 1686 361 1439 M10850 CHUNG_BLISTER_CYTOTOXICITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHUNG_BLISTER_CYTOTOXICITY_DN.html Genes down-regulated in blister cells from patients with adverse drug reactions (ADR). 19029983 65/120 Jessica Robertson 0.00577426225782821 0.0142024584976285 2645 1759 1686 0.000526315789473684 119 1.21720030790399 1.18036687746966 1 3.37447930021953 2645 119 1686 167 909 3258 2740 2275 403 1132 4015 1440 M14118 ZHANG_RESPONSE_TO_CANTHARIDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_CANTHARIDIN_UP.html Genes up-regulated in HL-60 cells (promyeloid leukemia) by cantharidin [PubChem=6708701]. 14639605 19/31 John Newman 0.0742044701799261 0.112138240657187 1435 1997.27272727273 1688 0.00698475413198344 1000 0.97897311955199 1.06167587640226 1 1.3957762954006 1434 1000 1958 1723 1688 1139 1490 3195 3652 3169 1522 1441 M9433 MOOTHA_HUMAN_MITODB_6_2002 http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_HUMAN_MITODB_6_2002.html Mitochondrial genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 463/545 Vamsi Mootha 0.0302595949752095 0.0529374678587802 245 1851.72727272727 1688 0.00278945376807871 242 0.812240839617986 -0.725015740724343 -1 1.55535080059508 242 1688 4144 1090 2351 650 822 1739 1272 4449 1922 1442 M2899 LINDGREN_BLADDER_CANCER_HIGH_RECURRENCE http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_HIGH_RECURRENCE.html Genes up-regulated among the high recurrence rate urothelial cell carcinoma (UCC) tumors. 16532037 83/87 Arthur Liberzon 2.58233490069002e-05 0.000224882301314703 525 1831.09090909091 1689 2.34760473849144e-06 410 1.26559989275901 1.24144146280573 1 6.92774282743704 523 2383 410 2655 1301 1588 1689 2280 3858 671 2784 1443 M2258 IVANOVSKA_MIR106B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVSKA_MIR106B_TARGETS.html A consensus set of genes that were significantly down-regulated by MIR106B [GeneID=406900]. 18212054 122/153 Arthur Liberzon 0.0588113744165265 0.0922531363396494 4335 2245.54545454545 1689 0.00549500214108815 14 0.959635245339601 -0.985353425777097 -1 1.49027159249359 4332 14 3488 1027 1583 3017 4617 1689 500 3247 1187 1444 M252 PID_IL8_CXCR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL8_CXCR1_PATHWAY.html IL8- and CXCR1-mediated signaling events 18832364 44/52 Pathway Interaction Database 0.00577426225782821 0.0142024584976285 4250 2144.27272727273 1690 0.000526315789473684 193 0.911153495529499 -0.935503477080344 -1 2.52599034176276 4250 199 2444 193 1690 4226 4186 444 1170 3123 1662 1445 M6906 SENESE_HDAC2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC2_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC2 [GeneID=3066] by RNAi. 17470557 169/210 Leona Saunders 6.72475057782965e-15 3.73421443851246e-13 945 1505.18181818182 1690 6.11340961620877e-16 63 1.56157010298767 1.58084803050289 1 29.1203102239117 942 2294 63 1690 3839 1805 2344 718 2256 135 471 1446 M14386 MCCOLLUM_GELDANAMYCIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCCOLLUM_GELDANAMYCIN_RESISTANCE_DN.html Genes down-regulated in A549GARS cells (lung cancer) resistant to the geldanamycin and 17-AAG [PubChem=5476289;6440175]. 18794130 8/13 Jessica Robertson 0.00548747797726329 0.0142024584976285 710 1748.36363636364 1690 0.000550107584572086 512 0.980435733630794 0.980435733630794 1 2.71806949981715 710 2170 4508 2104 759 745 512 850 1721 3463 1690 1447 M5840 SMID_BREAST_CANCER_RELAPSE_IN_LUNG_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LUNG_UP.html Genes up-regulated in lung relapse of breast cancer. 18451135 39/105 Jessica Robertson 0.00504479114833738 0.0134300136605485 395 1908.18181818182 1690 0.000459672415183578 393 1.49982458246515 1.49517730378381 1 4.21268972046692 393 2951 766 2957 2487 1589 1329 1690 3845 2446 537 1448 M6391 KEGG_PEROXISOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PEROXISOME.html Peroxisome 78/92 KEGG 0.00659024947511487 0.0156942368933109 1895 1765.09090909091 1691 0.000600915836911349 84 0.971222751076972 -0.922772831790743 -1 2.62931275334906 1892 84 3177 365 784 1183 2076 1691 2518 3993 1653 1449 M5457 YAMANAKA_GLIOBLASTOMA_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMANAKA_GLIOBLASTOMA_SURVIVAL_UP.html Genes whose expression most strongly and consistently associated with the long term survival of patients with high grade glioma tumors. 16652150 15/17 Arthur Liberzon 1.13880930927485e-05 0.000114609380379046 1775 1384 1691 1.03528654932441e-06 30 1.26932632081787 1.36311671641412 1 7.50569898169395 1772 1015 1421 1748 30 1963 2018 1876 393 1691 1297 1450 M13867 ONDER_CDH1_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_2_UP.html Genes up-regulated in HMLE cells (immortalized nontransformed mammary epithelium) after E-cadhedrin (CDH1) [GeneID=999] knockdown by RNAi. 18483246 369/443 Jessica Robertson 7.70720969015222e-24 1.21260099125062e-21 470 1463.09090909091 1692 7.00655426377475e-25 20 1.36219506638676 1.40584086373301 1 42.7527963904054 466 2232 20 2249 1685 1692 1862 1203 2832 47 1806 1451 M16091 DISTECHE_ESCAPED_FROM_X_INACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/DISTECHE_ESCAPED_FROM_X_INACTIVATION.html Genes that escape X inactivation. 12900543 24/53 Broad Institute 0.0326621566598231 0.0563058361703306 590 2106.72727272727 1693 0.00301430890338284 540 0.610932623130243 0.554057898842004 1 1.14528267713262 588 2562 3796 2895 1693 1006 540 1554 1655 4676 2209 1452 M1709 HILLION_HMGA1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HILLION_HMGA1_TARGETS.html Genes changed in Rat1a cells (fibroblasts) by overexpression of HMGA1 isoform a [GeneID=3159] off a plasmid vector. 19074878 116/175 Leona Saunders 0.0147613421116099 0.0298617253421183 4105 2465.45454545455 1693 0.0013510297079457 864 1.17055282760869 -1.20133758133226 -1 2.67826032790786 4102 1279 1693 1105 1040 3712 4062 3642 864 921 4700 1453 M1838 LABBE_TGFB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TGFB1_TARGETS_UP.html Up-regulated genes in NMuMG cells (mammary epithelium) after stimulation with TGFB1 [GeneID=7040]. 17210685 144/206 Jessica Robertson 1.22504876419672e-05 0.000122245880909271 1695 1792.54545454545 1693 1.11368689619609e-06 259 1.32313474331547 1.30105837875864 1 7.76826111957727 1693 2311 375 854 4162 793 1442 3432 2339 259 2058 1454 M2571 ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_DN.html Genes down-regulated during prostate cancer progression in the JOCK1 model due to inducible activation of FGFR1 [GeneID=2260] gene in prostate. 18068632 392/587 Yujin Hoshida 1.14593318454324e-29 3.38050289440255e-27 1400 1383.63636363636 1694 1.04175744049386e-30 11 1.44612005412782 1.29554637260635 1 57.4402090156365 1396 1694 11 445 1888 1735 2401 608 2703 33 2306 1455 M10183 BIOCARTA_RELA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RELA_PATHWAY.html Acetylation and Deacetylation of RelA in The Nucleus 19/19 BioCarta 0.00300114943460712 0.00907458381252121 650 1604.72727272727 1695 0.000273204665011282 447 0.787537577235438 0.782067633013124 1 2.41316289331951 647 2583 3091 1820 587 643 447 1905 1695 2605 1629 1456 M16393 BIOCARTA_NUCLEARRS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NUCLEARRS_PATHWAY.html Nuclear Receptors in Lipid Metabolism and Toxicity 12/24 BioCarta 0.000819759805890199 0.00341807975600861 1050 1913.36363636364 1695 7.4551402060712e-05 118 1.21536364714486 -1.26677455895623 -1 4.49748020586111 1047 3093 1586 2646 2739 1695 1077 118 4057 2451 538 1457 M14765 REACTOME_PLC_BETA_MEDIATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLC_BETA_MEDIATED_EVENTS.html Genes involved in PLC beta mediated events 39/48 Reactome 0.00213900195428565 0.00702581017691599 4095 2257.45454545455 1695 0.000194644044064224 398 1.02774694025672 -1.05723482029752 -1 3.32062187251919 4091 846 1695 398 523 3542 3844 3230 1098 1206 4359 1458 M1063 REACTOME_THE_NLRP3_INFLAMMASOME http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THE_NLRP3_INFLAMMASOME.html Genes involved in The NLRP3 inflammasome 11/16 Reactome 0.043825912364362 0.0720008027705495 1560 1919.81818181818 1696 0.00406582863452839 1042 1.23854683130695 1.38473342942845 1 2.12349202295521 1559 2648 2559 1550 1696 2725 2476 1056 1042 2340 1467 1459 M11238 LINDGREN_BLADDER_CANCER_CLUSTER_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_3_DN.html Genes whose expression profile is specific to Cluster III of urothelial cell carcinoma (UCC) tumors. 16532037 315/375 Leona Saunders 0.345243795657155 0.412127140996908 1665 1887.72727272727 1697 0.0377676234248123 364 1.10609000749415 1.18790495389986 1 0.638830810132393 1661 1170 1967 364 4510 1797 1697 2164 1405 1578 2452 1460 M1806 BOCHKIS_FOXA2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BOCHKIS_FOXA2_TARGETS.html Direct targets of FOXA2 [GeneID=3170] in liver, according to a ChIP-chip analysis. 18660816 505/732 Jessica Robertson 0.00525070999993344 0.0138068808911899 4690 2253.36363636364 1698 0.000526315789473684 87 1.09688606715982 -1.04625793789899 -1 3.06111003606431 4689 497 4564 87 827 1467 4608 3707 1823 820 1698 1461 M2487 FORTSCHEGGER_PHF8_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FORTSCHEGGER_PHF8_TARGETS_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) upon knockdown of PHF8 [GeneID=23133] by RNAi. 20421419 334/415 Arthur Liberzon 0.00658655829373563 0.0156942368933109 2315 1711.63636363636 1698 0.000600578252412604 549 1.2086259667805 1.13823692929795 1 3.27204113453649 2314 1166 826 686 2454 2038 2322 1698 1356 549 3419 1462 M1787 WORSCHECH_TUMOR_REJECTION_UP http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_REJECTION_UP.html Up-regulated genes defining rejection of mammary carcinoma (MMC) tumors. 18381452 53/115 Jessica Robertson 3.99034865318458e-05 0.000317643429777192 655 1812.45454545455 1699 3.6276554834187e-06 307 1.50710101367597 1.39624103598633 1 7.91053087546814 653 802 433 2002 3363 1699 1337 3011 3786 307 2544 1463 M2121 VERHAAK_GLIOBLASTOMA_CLASSICAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_CLASSICAL.html Genes correlated with classical type of glioblastoma multiforme tumors. 20129251 272/331 Arthur Liberzon 0.00509679751030731 0.0135303061016032 4545 2100.45454545455 1699 0.000464422166795573 69 1.08739111013157 -1.02757147689147 -1 3.04895017117006 4545 543 767 69 2101 1565 4148 4494 1699 1148 2026 1464 M1954 MIKKELSEN_MCV6_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 345/697 Jessica Robertson 2.66619129461961e-43 6.29221145530227e-40 1590 1528.54545454545 1700 2.42381026783601e-44 2 1.57995591258188 1.51698924388698 1 92.9363489797015 1587 1700 2 655 2793 1596 2281 1819 2066 18 2297 1465 M83 PID_CDC42_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CDC42_REG_PATHWAY.html Regulation of CDC42 activity 18832364 40/42 Pathway Interaction Database 0.0200178833917036 0.0378391708485547 1705 2106.81818181818 1701 0.00183658013190777 970 1.01983131415358 1.05450829836737 1 2.17603792013953 1701 2943 3146 3312 1154 1304 1332 2682 1033 3598 970 1466 M15351 SUZUKI_AMPLIFIED_IN_ORAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_AMPLIFIED_IN_ORAL_CANCER.html High-level amplifications detected in oral squamous cell carcinoma (OSCC) lines by array-CGH analysis. 17599052 17/24 Leona Saunders 0.0088919723487634 0.0199762539201158 1820 1789.90909090909 1701 0.000811646969293375 252 1.02759311722098 0.904522337729432 1 2.62037250813507 1817 1553 2085 1571 1701 1071 252 3012 1370 2422 2835 1467 M2109 KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_DN.html Genes whose expression significantly and negatively correlated with oligodendrocyte density in layer VI of BA9 brain region in patients with bipolar disorder. 18762803 70/174 Jessica Robertson 0.000143501153974621 0.000883084024459204 3805 2124.27272727273 1701 1.30464104630598e-05 419 1.48056675088224 -1.82797178778381 -1 6.78471752203473 3801 1352 501 1978 1029 3958 4078 3757 1701 419 793 1468 M6729 REACTOME_RECRUITMENT_OF_NUMA_TO_MITOTIC_CENTROSOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECRUITMENT_OF_NUMA_TO_MITOTIC_CENTROSOMES.html Genes involved in Recruitment of NuMA to mitotic centrosomes 13/13 Reactome 0.012592973367665 0.0261845085001669 1410 1950.45454545455 1702 0.00115142177603056 99 1.84167275171511 -1.84167275171511 -1 4.37157607570727 1408 3548 3196 1354 999 1702 1140 2628 99 3215 2166 1469 M12461 FINAK_BREAST_CANCER_SDPP_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/FINAK_BREAST_CANCER_SDPP_SIGNATURE.html Genes in the stroma-derived prognostic predictor of breast cancer disease outcome. 18438415 18/33 Arthur Liberzon 3.87242029725172e-05 0.000310319589185537 2255 1641.72727272727 1705 3.52044405538793e-06 80 1.86583276268588 1.91149807465391 1 9.8218444075751 2252 394 806 1705 80 2536 2554 3681 977 1195 1879 1470 M2573 LIM_MAMMARY_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIM_MAMMARY_STEM_CELL_UP.html Genes consistently up-regulated in mammary stem cells both in mouse and human species. 20346151 691/782 Daniel Hollern 4.97522235084531e-11 1.59748636027142e-09 115 1901.45454545455 1705 4.9752223509567e-12 66 1.30421824327235 1.28392405750259 1 17.2148173373852 111 3599 4714 3739 1998 213 1705 238 3881 66 652 1471 M1073 REACTOME_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POTASSIUM_CHANNELS.html Genes involved in Potassium Channels 45/106 Reactome 4.98264366910204e-06 5.61290647211495e-05 2035 1867.36363636364 1707 4.52968632183518e-07 339 1.66251839444049 -1.71443128043956 -1 10.604149723388 2034 1434 339 3479 4336 1707 2097 448 2697 675 1295 1472 M13123 LEE_LIVER_CANCER_HEPATOBLAST http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_HEPATOBLAST.html Fig.5, Supplementary Fig.2 Genes overexpressed in human hepatocellular carcinoma with hepatoblast property 16532004 19/21 Yujin Hoshida 0.00107267555076372 0.00418778213366811 2085 1922.09090909091 1707 9.75635384531444e-05 350 1.37498036735388 -1.14230016842082 -1 4.90618245996513 2085 3496 1630 3075 408 733 1122 350 3924 2613 1707 1473 M6744 COLDREN_GEFITINIB_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/COLDREN_GEFITINIB_RESISTANCE_DN.html Genes down-regulated in NSCLC (non-small cell lung carcinoma) cell lines resistant to gefitinib [PubChem=123631] compared to the sensitive ones. 16877703 320/386 Arthur Liberzon 0.134191112214851 0.184469445828226 3150 2285.18181818182 1708 0.0130137679787865 956 1.17141870598554 -1.17716189470379 -1 1.29020614308884 3146 1708 1632 956 3785 2266 4317 3658 1174 1056 1439 1474 M17471 SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHUETZ_BREAST_CANCER_DUCTAL_INVASIVE_UP.html Genes up-regulated in invasive ductal carcinoma (IDC) relative to ductal carcinoma in situ (DCIS, non-invasive). 16707453 439/604 Arthur Liberzon 7.78658467469484e-31 2.6251914046114e-28 255 1687.36363636364 1709 7.07871334063173e-32 10 1.27325790854417 1.31622233772525 1 52.6944398234093 251 2715 10 2859 2192 1984 1525 1064 4152 100 1709 1475 M1172 IWANAGA_E2F1_TARGETS_INDUCED_BY_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_E2F1_TARGETS_INDUCED_BY_SERUM.html Genes up-regulated in REF52 cells (embryonic fibroblast) by expression of E2F1 [GeneID=1869] that were also induced at 16 hr after serum stimulation. 16288221 35/37 Arthur Liberzon 0.00348403395315137 0.0101135548947568 1085 1760.81818181818 1710 0.000317233064888498 303 0.975813186403566 0.992185717172311 1 2.9211683810796 1084 2966 3113 2326 1974 1115 645 303 786 3347 1710 1476 M12570 DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_DN.html Genes down-regulated in T-PLL cells (T-cell prolymphocytic leukemia) bearing the inv(14)/t(14:14) chromosomal aberration. 17713554 379/534 Leona Saunders 0.0522853181156124 0.0839410549339084 1705 1757.81818181818 1711 0.00487008345484795 521 1.14350848649086 1.01746468536059 1 1.84620065668969 1705 521 1711 764 1534 2066 1751 2591 1749 1154 3790 1477 M19541 REN_ALVEOLAR_RHABDOMYOSARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/REN_ALVEOLAR_RHABDOMYOSARCOMA_DN.html Genes commonly down-regulated in human alveolar rhabdomyosarcoma (ARMS) and its mouse model overexpressing PAX3-FOXO1 [GeneID=5077;2308] fusion. 18701482 575/636 Jessica Robertson 0.00376557182551852 0.0107004810454229 1435 1913.54545454545 1711 0.000377196787351494 450 1.08809632534694 1.2307259759496 1 3.21730784210655 1435 489 4487 450 1157 3003 3238 2033 1711 511 2535 1478 M15491 HAN_SATB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAN_SATB1_TARGETS_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of SATB1 [GeneID=6304] by RNAi. 18337816 600/767 Jessica Robertson 0.0205150640623002 0.0386242929294205 1470 1970.81818181818 1711 0.00207069525187689 697 1.13281442249765 1.15328879381884 1 2.40196384967769 1468 1136 4606 858 1425 1711 2196 3098 2031 697 2453 1479 M8342 CROONQUIST_IL6_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_IL6_DEPRIVATION_UP.html Genes up-regulated in the ANBL-6 cell line (multiple myeloma, MM) after withdrawal of IL6 [GeneID=3569]. 12791645 26/42 Arthur Liberzon 0.0109842268732915 0.0234807748378332 1580 1634.54545454545 1712 0.00100358688092873 212 1.20485719113229 1.37378496377985 1 2.94550337658797 1576 323 1808 1712 4572 1722 2434 745 593 2283 212 1480 M2001 WU_CELL_MIGRATION http://www.broadinstitute.org/gsea/msigdb/cards/WU_CELL_MIGRATION.html Genes associated with migration rate of 40 human bladder cancer cells. 18724390 257/340 Jessica Robertson 3.99700851866297e-19 3.628053886171e-17 40 1576 1713 3.63364410787543e-20 38 1.36306176770038 1.27806683323871 1 33.625318772077 907 1195 38 1447 1713 1892 1918 2902 2914 40 2370 1481 M10319 WALLACE_PROSTATE_CANCER_RACE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_RACE_UP.html Genes up-regulated in prostate cancer samples from African-American patients compared to those from the European-American patients. 18245496 291/525 Jessica Robertson 2.7494919464899e-17 1.99655415191267e-15 985 1955.72727272727 1713 2.49953813317264e-18 48 1.36417362825685 1.36381005069208 1 30.089776408565 982 3615 48 2522 2650 1637 1713 1437 4048 118 2743 1482 M117 PID_CONE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CONE_PATHWAY.html Visual signal transduction: Cones 18832364 11/34 Pathway Interaction Database 0.000874017442046216 0.00357483737128088 3055 1644.45454545455 1714 7.94877150471204e-05 111 2.12662594828399 2.47890952167639 1 7.8075632467493 3055 2133 1563 557 2880 2702 2681 126 111 1714 567 1483 M2284 LINSLEY_MIR16_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LINSLEY_MIR16_TARGETS.html Transcripts down-regulated by overexpression of MIR16 family of microRNA molecules in DLD-1 and HCT116 (colon cancer) cells hypomorphic for DICER1 [GeneID=23405]. 17242205 289/325 Arthur Liberzon 0.0179195723712939 0.0347009724692308 2610 2267.63636363636 1715 0.00164247439823475 917 0.934994147183134 -0.921669174312783 -1 2.04776197489337 2606 1715 3908 1346 1115 1148 2727 3973 1613 3876 917 1484 M10272 REACTOME_IONOTROPIC_ACTIVITY_OF_KAINATE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IONOTROPIC_ACTIVITY_OF_KAINATE_RECEPTORS.html Genes involved in Ionotropic activity of Kainate Receptors 11/15 Reactome 0.0758450250115688 0.114170127187883 3945 2319.90909090909 1716 0.00714485326122689 1047 1.30956518366526 -1.27154713618288 -1 1.85183071930882 3944 1605 1623 1047 1699 2218 4131 3944 1456 1716 2136 1485 M10198 FUNG_IL2_SIGNALING_2 http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_SIGNALING_2.html Genes up-regulated by IL2 [GeneID=3558] in T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 10/15 Arthur Liberzon 0.000327834093342212 0.00168376161107208 2805 1762.63636363636 1716 2.98075414451499e-05 237 1.78817791004543 -1.84907453620131 -1 7.44232929373428 2805 3108 1716 2066 237 1457 1155 2831 282 1600 2132 1486 M13061 BILD_E2F3_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_E2F3_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing E2F3 [GeneID=1871] from control cells expressing GFP. 16273092 332/390 Arthur Liberzon 0.152580980133212 0.205355639072929 1845 1645.45454545455 1716 0.0149382099219608 766 1.1047285678345 1.096954427752 1 1.13952950517149 1716 1168 1715 766 2080 1842 1842 1779 1049 1183 2960 1487 M17228 SASAI_TARGETS_OF_CXCR6_AND_PTCH1_DN http://www.broadinstitute.org/gsea/msigdb/cards/SASAI_TARGETS_OF_CXCR6_AND_PTCH1_DN.html Down-regulated genes in medulloblastoma tumors from heterozygotic CXCR6 [GeneID=10663] knockout mice compared to those from PTCH1 [GeneID=5727] heterozygotic knockout mice. 17413002 5/9 Jessica Robertson 2.62167649647821e-05 0.000227887901719653 1045 1948.18181818182 1716 2.6217074263362e-06 7 2.43029084539932 2.43029084539932 1 13.2821926982079 1045 3581 4586 3297 2733 1716 1258 7 92 3094 21 1488 M1216 LI_WILMS_TUMOR_ANAPLASTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_ANAPLASTIC_DN.html Selected down-regulated genes distinguishing between Wilms tumors of different histological types: anaplastic vs favorable histology. 15531917 11/19 Leona Saunders 0.132895237993155 0.18298294146082 1695 1858.81818181818 1717 0.0128795644490259 793 1.32601049462835 1.60209455350798 1 1.46747974480344 1692 1051 1595 1827 1991 2409 1264 2660 793 1717 3448 1489 M7330 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE.html Glycosaminoglycan biosynthesis - heparan sulfate 22/28 KEGG 0.0617762203447267 0.0961053922304252 1140 1761.36363636364 1718 0.00578021059832005 780 1.23384450589086 -1.19235256850576 -1 1.88324356633061 1138 1522 2025 1441 3372 1745 780 1718 820 2875 1939 1490 M236 PID_DELTA_NP63_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_DELTA_NP63_PATHWAY.html Validated transcriptional targets of deltaNp63 isoforms 18832364 80/93 Pathway Interaction Database 0.00545538464719397 0.0142024584976285 1105 2174.81818181818 1718 0.000497178147787768 201 1.26196107489653 1.08061862588816 1 3.49857474911691 1102 3691 772 3835 3758 201 642 2438 4198 1568 1718 1491 M1673 WESTON_VEGFA_TARGETS_3HR http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS_3HR.html Genes up-regulated in MMEC cells (myometrial endothelium) at 3 h after VEGFA [GeneID=7422] stimulation. 12200464 85/110 John Newman 3.75438644473127e-05 0.000304458061282279 1560 1943.09090909091 1718 3.41313683303813e-06 430 1.39444461825647 1.46840504348834 1 7.35773361978197 1558 1853 430 1718 4238 3391 2792 1151 2669 523 1051 1492 M3879 LEE_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER.html Genes down-regulated in tumor compared to non-tumor liver samples from patients with hepatocellular carcinoma (HCC). 18519680 29/95 Leona Saunders 0.0420514241740047 0.0695210935556224 1720 2020 1718 0.00389794513316995 512 1.20136328371782 -1.33090353813748 -1 2.08717552276826 2669 2533 1443 1221 4591 1718 1716 3279 801 1737 512 1493 M1059 REACTOME_NOD1_2_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOD1_2_SIGNALING_PATHWAY.html Genes involved in NOD1/2 Signaling Pathway 36/37 Reactome 0.27371139051449 0.337051334001668 3565 1996.54545454545 1719 0.028654871039195 146 1.09207082552215 1.08969017997489 1 0.773846464562617 3561 235 1644 296 2705 1719 2465 4572 146 1278 3341 1494 M10664 XU_GH1_AUTOCRINE_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_AUTOCRINE_TARGETS_UP.html Genes up-regulated in MFCF-7 cells (breast cancer) upon stable autocrine expression of HG1 [GeneID=2688]. 15845533 268/405 John Newman 6.20169061387994e-07 9.32228652787049e-06 1980 1671.63636363636 1719 5.63790214736945e-08 263 1.2541549015368 1.24293597747748 1 9.46667240560793 1978 1719 263 1197 1700 2843 1913 951 2535 493 2796 1495 M154 SCHAVOLT_TARGETS_OF_TP53_AND_TP63 http://www.broadinstitute.org/gsea/msigdb/cards/SCHAVOLT_TARGETS_OF_TP53_AND_TP63.html Genes up-regulated by TP53 [GeneID=7157] and down-regulated by an isoform of TP63 [GeneID=8626] in primary HEK cells (epidermal keratinocytes). 17404570 24/30 Leona Saunders 0.000198533730761626 0.0011583179347279 2660 1794.09090909091 1720 1.8050149929682e-05 182 1.11285437207026 1.16980882647237 1 4.90289165097063 2656 341 1720 867 182 2789 3255 1865 368 1699 3993 1496 M5149 MARTINELLI_IMMATURE_NEUTROPHIL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINELLI_IMMATURE_NEUTROPHIL_DN.html Neutrophil-specific genes down-regulated in comparison of immature with mature neutrophils. 15302890 11/19 Arthur Liberzon 0.0308997865294353 0.0538777216176338 1625 2164.09090909091 1720 0.00284931959469725 526 1.61314583168146 1.42857350436308 1 3.07059134110682 1623 3553 1087 3041 2634 1541 526 1569 2819 1720 3692 1497 M16973 BIOCARTA_CBL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CBL_PATHWAY.html CBL mediated ligand-induced downregulation of EGF receptors 20/21 BioCarta 0.0106844302329238 0.0229751757172667 900 1768.54545454545 1721 0.000976061397461831 555 1.23376629416535 1.42454701790865 1 3.03368106890471 898 3043 1721 3764 3644 693 576 555 2122 1756 682 1498 M18608 MURATA_VIRULENCE_OF_H_PILORI http://www.broadinstitute.org/gsea/msigdb/cards/MURATA_VIRULENCE_OF_H_PILORI.html Selected genes up-regulated in WT-A10 cells (gastric epithelium) expressing the H. pilori virulence gene CagA. 17237808 26/38 Arthur Liberzon 0.000824707771455419 0.00343567579988489 1725 1788.63636363636 1721 7.50015536063222e-05 119 1.43946494633232 1.52078389001836 1 5.32197491666674 1721 2042 776 3026 3328 1599 1976 119 2738 1190 1160 1499 M6162 BOWIE_RESPONSE_TO_EXTRACELLULAR_MATRIX http://www.broadinstitute.org/gsea/msigdb/cards/BOWIE_RESPONSE_TO_EXTRACELLULAR_MATRIX.html Genes up-regulated by growing HMEC-E6 cells (mammary epithelial cells damaged by expression of HPV-16 E6 [GeneID=1489078]) in extracellular matrix (ECM). 17016442 31/52 Arthur Liberzon 0.0941897861590527 0.137257113513655 3800 2261.36363636364 1723 0.00895290662464312 823 1.20398747736588 -1.03226961514063 -1 1.55803004992022 3800 890 1445 1022 3352 4033 4435 1723 823 964 2388 1500 M13941 DIRMEIER_LMP1_RESPONSE_EARLY http://www.broadinstitute.org/gsea/msigdb/cards/DIRMEIER_LMP1_RESPONSE_EARLY.html Clusters 1 and 2: genes up-regulated in B2264-19/3 cells (primary B lymphocytes) within 30-60 min after activation of LMP1 (an oncogene encoded by Epstein-Barr virus, EBV). 15674340 78/103 Arthur Liberzon 0.0164477509195865 0.0324825875901457 755 2046.63636363636 1723 0.00150654737191734 654 1.24522221480882 1.03431219467221 1 2.78084659968519 755 2397 980 2600 4330 1219 889 4425 1723 654 2541 1501 M647 REACTOME_ACTIVATED_POINT_MUTANTS_OF_FGFR2 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_POINT_MUTANTS_OF_FGFR2.html Genes involved in Activated point mutants of FGFR2 7/20 Reactome 5.84915051517949e-06 6.38233623047543e-05 25 2094.81818181818 1724 5.84916591088931e-07 21 1.48037202328997 -1.53758199962462 -1 9.31840997802422 4559 1080 4211 1042 21 4655 3139 23 638 1724 1951 1502 M1651 RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMPON_ENRICHED_LEARNING_ENVIRONMENT_LATE_UP.html Genes up-regulated in the brain cortex of mice that were exposed to an enriched learning environment for 2 or 14 days. 11070096 31/38 John Newman 0.0248057924676353 0.0452469775748721 1575 2134.63636363636 1724 0.00228090755052187 303 0.958442784198676 -0.854626888017434 -1 1.93337500928103 1572 2989 2628 2683 1724 303 695 1702 4111 3854 1220 1503 M9134 BIOCARTA_TRKA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TRKA_PATHWAY.html Trka Receptor Signaling Pathway 22/25 BioCarta 0.00707122568135596 0.0165968101521632 1290 1859.09090909091 1725 0.000644914252015422 705 0.775568983115317 0.698717872705171 1 2.07135266000703 1289 2572 3194 2483 804 1725 705 2064 1491 3379 744 1504 M3661 REACTOME_FGFR_LIGAND_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FGFR_LIGAND_BINDING_AND_ACTIVATION.html Genes involved in FGFR ligand binding and activation 7/24 Reactome 5.84915051517949e-06 6.38233623047543e-05 4560 2101.63636363636 1725 5.84916591088931e-07 22 1.48037202328997 -1.53758199962462 -1 9.31840997802422 4560 1081 4265 1043 22 4656 3140 35 639 1725 1952 1505 M14050 KORKOLA_CHORIOCARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CHORIOCARCINOMA_UP.html Genes from the 12p region that were up-regulated in choriocarcinoma cells compared to normal testis. 16424014 7/17 Arthur Liberzon 0.000329818149862735 0.00169148966560177 2075 1834.72727272727 1726 3.29867111095693e-05 254 0.988810869225671 -0.947486540986899 -1 4.11239562584388 2074 444 4275 1472 254 1864 2395 2861 1671 1726 1146 1506 M6362 NAKAMURA_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_LUNG_CANCER.html Genes up-regulated in lung adenocarcinoma cell lines and not expressed in non-cancerous lung epithelial cells. 16491115 23/26 Arthur Liberzon 0.0140741550389555 0.0287078702609637 170 2086.54545454545 1726 0.00128772790757943 170 1.36627623584798 1.36627623584798 1 3.16118478722313 170 3857 947 3244 2013 1421 1493 1726 4545 2496 1040 1507 M10376 MOOTHA_GLYCOGEN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_GLYCOGEN_METABOLISM.html Genes involved in glycogen metabolism; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 20/25 Vamsi Mootha 0.0363171337232805 0.0614838131900588 1665 2029.81818181818 1726 0.00335735284348745 673 0.803135031694817 0.780158217036898 1 1.45958304609888 1664 2081 3408 1807 1395 1606 2669 1552 673 3747 1726 1508 M12484 REACTOME_GAMMA_CARBOXYLATION_TRANSPORT_AND_AMINO_TERMINAL_CLEAVAGE_OF_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAMMA_CARBOXYLATION_TRANSPORT_AND_AMINO_TERMINAL_CLEAVAGE_OF_PROTEINS.html Genes involved in Gamma-carboxylation, transport, and amino-terminal cleavage of proteins 9/13 Reactome 0.000147531406979144 0.000904348364859169 2505 1780.27272727273 1727 1.47541202376625e-05 29 1.87748705578546 1.21634107977733 1 8.57452640035471 2505 2161 4207 1727 167 3211 2110 853 29 1444 1169 1509 M8818 BIDUS_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BIDUS_METASTASIS_DN.html Genes down-regulated in endometroid endometrial tumors from patients with lymph node metastases compared to those without the metastases. 16397028 216/275 Arthur Liberzon 0.0821313550702801 0.122367422958246 2145 1915.54545454545 1727 0.00776072764413616 780 1.25530040763287 1.32441408843455 1 1.7183699964343 2143 2274 1660 780 3538 2826 2039 1333 1459 1292 1727 1510 M2493 PEDRIOLI_MIR31_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PEDRIOLI_MIR31_TARGETS_UP.html Genes up-regulated in primary LEC cells (lymphatic endothelum) upon overexpression of MIR31 [GeneID=407035]. 20479124 252/454 Arthur Liberzon 0.00181320618619595 0.00622725344253624 2780 1894.54545454545 1727 0.000164972939044387 641 1.1349304704381 1.16318226023181 1 3.75617616697213 2779 1727 673 2500 1705 747 1659 2338 2534 641 3537 1511 M3645 DELYS_THYROID_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELYS_THYROID_CANCER_UP.html Genes up-regulated in papillary thyroid carcinoma (PTC) compared to normal tissue. 17621275 569/768 Aravind Subramanian 5.95593170189953e-18 4.68533293882763e-16 1555 1884.81818181818 1729 5.95593170189956e-19 27 1.30378457431674 1.39904078186975 1 29.9893664869618 1552 1137 4330 1167 2584 1729 2285 1675 2064 27 2183 1512 M2129 CHICAS_RB1_TARGETS_CONFLUENT http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_CONFLUENT.html Genes up-regulated in confluent IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 721/968 Arthur Liberzon 1.94914584000052e-17 1.43749505700038e-15 1075 1857.54545454545 1729 1.94914584000053e-18 28 1.29383534523248 1.36486362426971 1 28.8153016225463 1072 1666 4662 1155 2496 1815 2234 1289 2287 28 1729 1513 M15410 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN.html Genes down-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 16 days after transduction. 16818636 177/287 Arthur Liberzon 9.79975375697795e-05 0.000649646597372695 1730 1565.72727272727 1730 8.90926391610836e-06 481 1.28787573304185 1.36581501243198 1 6.15934258317317 1287 588 481 1726 2084 2128 1730 2418 1818 538 2425 1514 M6641 BROWNE_HCMV_INFECTION_18HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_18HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 18 h time point that were not down-regulated at the previous time point, 16 h. 11711622 254/356 John Newman 2.93714529007361e-05 0.000250240537349232 1355 1807.54545454545 1730 2.67016773057808e-06 416 1.16214378480121 1.27651645159577 1 6.28051037002401 1351 1725 416 1832 1445 2965 2718 1730 3171 459 2071 1515 M1430 BROWN_MYELOID_CELL_DEVELOPMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWN_MYELOID_CELL_DEVELOPMENT_UP.html Genes defining differentiation potential of the bipotential myeloid cell line FDB. 16769770 167/326 Kevin Vogelsang 7.32939381018948e-06 7.77409860316727e-05 1195 1453.54545454545 1731 6.66310748044671e-07 355 1.21627059983983 1.35779482028939 1 7.49961582142301 1195 1763 355 1731 1831 1741 2933 475 2270 613 1082 1516 M10024 WENDT_COHESIN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WENDT_COHESIN_TARGETS_UP.html Cohesin targets identified by ChIP-chip which were up-regulated after knockdown of CTCF and RAD21 [GeneID=10664;5885] by RNAi. 18235444 46/49 Jessica Robertson 0.0132296999571842 0.0272801152459194 2570 2067.09090909091 1731 0.00120999391364653 477 1.00612151648728 0.937932566204828 1 2.36130580851379 2566 836 3411 1324 1012 1731 1385 3038 477 2861 4097 1517 M5485 REACTOME_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MUSCLE_CONTRACTION.html Genes involved in Muscle contraction 51/77 Reactome 0.00952558581231007 0.0209900863838018 1615 2229.09090909091 1732 0.000869734687339466 526 1.17949995087586 1.16473883239369 1 2.969699691499 1614 2910 1627 3195 974 4218 3532 526 2585 1607 1732 1518 M12769 LU_TUMOR_VASCULATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_VASCULATURE_UP.html Genes up-regulated in endothelial cells derived from invasive ovarian cancer tissue. 17308118 51/59 Arthur Liberzon 6.68118662937603e-08 1.2664739313516e-06 230 1687.27272727273 1732 6.07380621116111e-09 207 1.61647745881908 1.65266317598342 1 14.3043823285883 227 3340 207 2195 1548 1732 1800 1943 3388 746 1434 1519 M1147 DARWICHE_PAPILLOMA_PROGRESSION_RISK http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_PROGRESSION_RISK.html Genes that classify progression risk of benign papilloma samples: low vs high risk. 17525749 69/112 Arthur Liberzon 0.0797693168137794 0.119186823476112 1735 2387.54545454545 1732 0.00752886934318619 759 1.32336473953416 -1.36126813845557 -1 1.83426040107632 4189 759 1450 1732 1732 4669 3450 3531 1229 916 2606 1520 M1459 PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_ENDOTHELIUM_LYMPHATIC_VS_BLOOD_DN.html Genes down-regulated in BEC (blood endothelial cells) compared to LEC (lymphatic endothelial cells). 12198161 237/274 Kevin Vogelsang 5.09556847080792e-10 1.46652946233008e-08 920 1693.18181818182 1733 4.63233497453469e-11 130 1.28387623023837 1.2932759204417 1 15.0913943411351 918 1733 130 2883 2461 2386 2114 901 3325 172 1602 1521 M13479 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_10D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 10 days after transduction. 16818636 226/350 Arthur Liberzon 5.60600598735236e-09 1.30346543154203e-07 1510 1751.36363636364 1734 5.09636909239771e-10 164 1.36606183199464 1.35591019571256 1 14.1125851721276 1509 1734 164 1170 2059 3096 2530 2978 1156 248 2621 1522 M18122 DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_UP.html Genes exclusively up-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071] after high dose UVC irradiation. 15608684 38/42 Arthur Liberzon 0.0349485642259956 0.0595943725240966 1685 2199.18181818182 1734 0.00322876517636404 753 1.02472854957163 0.886354274973394 1 1.88317012081875 1684 3380 2656 3198 1378 1734 753 1142 3915 3147 1204 1523 M9221 BROWNE_INTERFERON_RESPONSIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_INTERFERON_RESPONSIVE_GENES.html Genes up-regulated in primary fibroblast culture after treatment with interferon alpha for 6 h. 11711622 114/192 John Newman 0.00847681619318838 0.019217373886575 3515 2379.45454545455 1734 0.00077360504384833 853 1.14279716375822 -1.0663748651314 -1 2.94299860528187 3512 1284 1734 1089 853 3991 4554 3076 1441 1503 3137 1524 M5056 REACTOME_HDL_MEDIATED_LIPID_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HDL_MEDIATED_LIPID_TRANSPORT.html Genes involved in HDL-mediated lipid transport 15/27 Reactome 0.0017413289740672 0.00602571316539383 1735 2079.36363636364 1735 0.000158428071647563 198 1.39237533022905 -1.42769891039828 -1 4.6380939287022 1735 3890 1486 3030 3478 653 745 198 4476 2786 396 1525 M12037 SHAFFER_IRF4_TARGETS_IN_PLASMA_CELL_VS_MATURE_B_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_PLASMA_CELL_VS_MATURE_B_LYMPHOCYTE.html IRF4 [GeneID=3662] target genes up-regulated in plasma cells compared to mature B lymphocytes. 18568025 83/93 Jessica Robertson 0.0175642230700875 0.0341165155929271 2375 1955.81818181818 1737 0.00160963989855682 720 0.98292430532211 0.965542164732323 1 2.16362112880595 2371 720 2026 1239 1109 1672 1737 4548 1137 1908 3047 1526 M784 REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CITRIC_ACID_CYCLE_TCA_CYCLE.html Genes involved in Citric acid cycle (TCA cycle) 22/23 Reactome 0.0571759843528324 0.0903483917460224 880 1953.36363636364 1738 0.00533803230545905 876 0.54375266550762 -0.54375266550762 -1 0.851771003161372 876 2060 3884 1868 1572 950 1310 1791 881 4557 1738 1527 M10263 LOPEZ_MESOTHELIOMA_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_DN.html Top genes associated with unfavorable survival after surgery of patients with epithelioid mesothelioma. 16540645 34/37 Arthur Liberzon 0.0274705538784416 0.0492072160555006 405 2055.90909090909 1738 0.00252906244284685 402 1.10457239365281 1.29518181265345 1 2.167768868118 402 2981 1403 3895 1271 1802 1366 1738 4532 2502 723 1528 M247 PID_INSULIN_GLUCOSE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INSULIN_GLUCOSE_PATHWAY.html Insulin-mediated glucose transport 18832364 34/41 Pathway Interaction Database 0.00461318231374309 0.0125067320625315 1485 1876.72727272727 1739 0.000420262199454385 691 0.815132141872048 0.840235127840968 1 2.32731965919305 1482 2004 3563 1925 691 1739 1542 1583 822 2867 2426 1529 M2385 KATSANOU_ELAVL1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KATSANOU_ELAVL1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) with ELAVL1 [GeneID=1994] knocked out. 19307312 212/297 Arthur Liberzon 9.91801922611722e-13 4.142747853741e-11 2770 2174.27272727273 1739 9.01638111465606e-14 73 1.24841272642764 1.2934006793469 1 19.4494990128597 2769 1739 87 923 1375 4239 3328 1276 3397 73 4711 1530 M1240 JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_DN.html Genes down-regulated in early vs late brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 70/85 Leona Saunders 0.00895657769510505 0.020092702814114 2285 1987.36363636364 1741 0.000817568241294818 810 1.22230424895857 1.35781109756288 1 3.11227803385125 2281 1881 974 1247 863 3021 3118 4544 1381 810 1741 1531 M13283 HSIAO_LIVER_SPECIFIC_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HSIAO_LIVER_SPECIFIC_GENES.html Liver selective genes 11773596 212/467 Kevin Vogelsang 3.34450074784044e-17 2.35612589997117e-15 4345 2203.27272727273 1741 3.04045522530949e-18 50 1.54494183916735 -1.53174834229403 -1 33.9103011057425 4343 1741 50 1163 842 3238 4601 2842 1401 86 3929 1532 M1758 SANSOM_WNT_PATHWAY_REQUIRE_MYC http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_WNT_PATHWAY_REQUIRE_MYC.html Wnt target genes up-regulated after Cre-lox knockout of APC [GeneID=324] in the small intestine that require functional MYC [GeneID=4609]. 17377531 80/97 Jessica Robertson 0.00211316463028876 0.00697004685881408 1000 1806.81818181818 1741 0.000192290647335866 685 1.38536526545543 1.42397739148344 1 4.48330761435843 1000 2387 685 2896 1434 1590 1822 1741 3001 838 2481 1533 M692 REACTOME_HEPARAN_SULFATE_HEPARIN_HS_GAG_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HEPARAN_SULFATE_HEPARIN_HS_GAG_METABOLISM.html Genes involved in Heparan sulfate/heparin (HS-GAG) metabolism 43/53 Reactome 0.0470931255833667 0.0764635544387653 1540 1796.81818181818 1742 0.00437568036936417 207 1.18028669536607 1.20809968682903 1 1.9773452704318 1536 207 1071 694 1742 3002 2319 3748 1792 1991 1663 1534 M10253 BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_ROCK_SIGNALING_NOT_VIA_RHOA_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins; the changes did not depend on expression of constitutively active (Q63L) form of RHOA [GeneID=387]. 17213802 91/107 Leona Saunders 0.00879021906277018 0.0198136742962155 145 1819.27272727273 1743 0.000802321689715553 128 0.971997183820745 0.90196839208605 1 2.48377287307539 142 3254 1937 3461 1743 128 266 1511 4280 3007 283 1535 M1723 LEIN_CEREBELLUM_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_CEREBELLUM_MARKERS.html Top 100 ranked genes most specific to the cerebellum region of adult mouse brain. 17151600 84/121 Jessica Robertson 0.170774261903554 0.225596002290729 1745 1860.36363636364 1744 0.0168798085745389 461 1.06732146376472 1.0727481517632 1 1.03555804157766 1744 719 1335 461 2818 2481 2252 1711 3030 1310 2603 1536 M778 BIERIE_INFLAMMATORY_RESPONSE_TGFB1 http://www.broadinstitute.org/gsea/msigdb/cards/BIERIE_INFLAMMATORY_RESPONSE_TGFB1.html Inflammatory genes down-regulated in mammary carcinoma cells after stimulation with TGFB1 [GeneID=7040] for 1 hr. 18339861 10/10 Jessica Robertson 0.00689047926795112 0.0162696659053173 1025 1890.18181818182 1744 0.000628377782230747 208 1.45193539828677 1.21582229150245 1 3.8966887829537 1025 2143 985 2680 2268 977 208 4337 3693 732 1744 1537 M2215 WIERENGA_STAT5A_TARGETS_GROUP1 http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_GROUP1.html Genes up-regulated to their maximal levels in CD34+ [GeneID=947] cells by intermediate activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 187/243 Arthur Liberzon 0.00690211456460433 0.0162808499474925 1230 2150.54545454545 1745 0.00062944221186253 667 1.20046212153898 1.2472969819782 1 3.22123156462508 1229 4001 808 3718 4439 1474 2113 667 2481 981 1745 1538 M1070 REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_PROCESSING_UBIQUITINATION_PROTEASOME_DEGRADATION.html Genes involved in Antigen processing: Ubiquitination & Proteasome degradation 198/234 Reactome 0.0498564462071184 0.080617480677492 1040 1998.90909090909 1746 0.00463849937404806 496 0.719659502787842 -0.706418261458725 -1 1.18080136909901 1037 1746 4151 2151 2840 496 1168 1348 1817 4394 840 1539 M1713 LEIN_ASTROCYTE_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_ASTROCYTE_MARKERS.html Genes enriched in astrocytes in the adult mouse brain identified through correlation-based searches seeded with the astrocyte cell-type specific gene expression patterns. 17151600 49/75 Jessica Robertson 0.00331996772471707 0.00980425330377675 1690 1982.09090909091 1746 0.000302271674507814 292 1.33265840143255 1.43459116173966 1 4.01642373689866 1687 1944 800 1746 3249 3993 4063 292 2601 1024 404 1540 M1518 KUMAMOTO_RESPONSE_TO_NUTLIN_3A_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUMAMOTO_RESPONSE_TO_NUTLIN_3A_UP.html Genes up-regulated in response to nutlin-3a [PubChem=216345], an inhibitor of MDM2 [GeneID=4193], in skin fibroblast cultures after knockdown of TP53 [GeneID=7157] by RNAi. 18451145 12/13 Jessica Robertson 0.000951357921577958 0.00382814099731284 1080 1781.54545454545 1746 8.65245065161618e-05 91 1.17341887930333 1.00442742162245 1 4.25562057476814 1078 2635 2157 3064 1746 1243 91 131 3547 3129 776 1541 M96 BIOCARTA_FREE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FREE_PATHWAY.html Free Radical Induced Apoptosis 13/19 BioCarta 0.000707428524640212 0.00303827355441474 1750 1570.72727272727 1748 6.43323733362685e-05 112 1.38384442607205 1.18921419540415 1 5.22718506581565 1748 2112 1263 1243 349 2200 2175 3136 112 725 2215 1542 M12645 ST_GA13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA13_PATHWAY.html G alpha 13 Pathway 47/53 Signaling Transduction KE 0.00243406609429501 0.00774699390766853 1550 1852.18181818182 1749 0.000221523937128647 546 0.868375819871626 -0.758171466771481 -1 2.75038598519962 1549 825 3246 1115 546 2272 1244 1749 2056 3586 2186 1543 M1429 REACTOME_SMOOTH_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SMOOTH_MUSCLE_CONTRACTION.html Genes involved in Smooth Muscle Contraction 34/38 Reactome 0.00165370237393708 0.00579041187313279 745 1828 1749 0.000150449703949593 38 1.19324507955139 1.28677234488159 1 4.00573646603819 741 3412 1854 3652 1391 2506 1152 328 3285 1749 38 1544 M97 BAELDE_DIABETIC_NEPHROPATHY_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAELDE_DIABETIC_NEPHROPATHY_UP.html Genes up-regulated in glomeruli of kidneys from patients with diabetic nephropathy (type 2 diabetes mellitus). 15042541 108/162 John Newman 8.94029694814656e-07 1.26341920943868e-05 2730 1877.63636363636 1749 8.12754598298263e-08 269 1.30750035582041 1.1947481013671 1 9.61031769969104 2730 659 278 1169 923 2190 1749 4415 2616 269 3656 1545 M1126 HUMMERICH_MALIGNANT_SKIN_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_MALIGNANT_SKIN_TUMOR_UP.html Genes up-regulated in malignant skin tumors (squamous cell carcinoma, SCC) formed by treatment with DMBA and TPA [PubChem=6001;4792] in the two stage skin carcinogenesis model. 16247483 34/40 Leona Saunders 0.00111128275562006 0.00431353174878838 2995 2065 1750 0.000101076772139046 127 1.44546307607314 1.52268669044063 1 5.12981451694177 127 2995 627 4302 2995 1229 1711 2278 4191 1750 510 1546 M735 REACTOME_NEURONAL_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEURONAL_SYSTEM.html Genes involved in Neuronal System 192/338 Reactome 8.5725824539099e-05 0.000585565690049996 4180 2218.72727272727 1751 7.79356046710494e-06 472 1.22023026377843 -1.35006477838618 -1 5.91839855760469 4180 1751 472 1563 3031 1557 4625 1958 3138 1337 794 1547 M16649 ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_DN.html Genes commonly down-regulated in CD-1 and CD-2 clusters of multiple myeloma samples and which were higher expressed in the CD-1 group. 16728703 69/92 Kevin Vogelsang 0.00577426225782821 0.0142024584976285 3245 2265.54545454545 1753 0.000526315789473684 110 1.0947422984376 -1.15655182383306 -1 3.03497480383 3244 110 1348 154 849 4483 4260 4033 3084 1753 1603 1548 M1820 MATZUK_CENTRAL_FOR_FEMALE_FERTILITY http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_CENTRAL_FOR_FEMALE_FERTILITY.html Genes central for female fertility pathways, based on mouse models with female fertility defects. 18989307 24/37 Jessica Robertson 0.0768952948244818 0.11555103201896 1755 1830.45454545455 1753 0.0072474831205522 335 0.983504563610452 0.942978386333491 1 1.38302287920231 1753 335 1613 1739 2054 1755 859 3899 1514 2113 2501 1549 M2052 ZEMBUTSU_SENSITIVITY_TO_VINCRISTINE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_VINCRISTINE.html Top genes associated with chemosensitivity to vincristine [PubChem=5978] across 85 tumor xenografts. 11809704 17/33 Arthur Liberzon 0.00122657762692346 0.00460210365586546 3025 1753.36363636364 1753 0.000111569274681236 76 0.990294798481709 1.00632157331767 1 3.47264098679786 3023 373 1753 76 1032 3575 2776 163 1331 1906 3279 1550 M1773 JEPSEN_SMRT_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/JEPSEN_SMRT_TARGETS.html Genes up-regulated in neural progenitor cells (NPC) isolated from E13 cortical tissue of SMRT [GeneID=9612] knockout mice. 17928865 39/47 Jessica Robertson 0.00752091565226291 0.017426962139755 910 1969.54545454545 1754 0.000686068215495247 532 1.0328732052133 0.909258886999095 1 2.72573141582362 908 3368 2033 3508 818 752 532 1754 4090 2445 1457 1551 M9815 AKL_HTLV1_INFECTION_DN http://www.broadinstitute.org/gsea/msigdb/cards/AKL_HTLV1_INFECTION_DN.html Genes down-regulated in WE17/10 cells (CD4+ [GeneID=920] T lymphocytes) infected by HTLV1 (and thus displaying low CD7 [GeneID=924]) compared to the uninfected (i.e., CD7+) cells. 17287851 93/136 Arthur Liberzon 0.00117563123088493 0.00448332685672388 700 1890.72727272727 1755 0.000106932721141256 423 1.18667326539104 1.21554021734375 1 4.18151802003352 696 2827 1328 2748 423 1934 1645 1755 3492 1485 2465 1552 M3069 LENAOUR_DENDRITIC_CELL_MATURATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LENAOUR_DENDRITIC_CELL_MATURATION_DN.html Genes down-regulated during in vitro maturation of CD14+ [GeneID=929] monocytes (day 0) into immature (day 7) and mature dendritic cells (day 14). 11279020 145/235 Kevin Vogelsang 1.99471021000288e-05 0.000182396771335444 995 1664.90909090909 1755 1.81338935999985e-06 393 1.3168152063572 1.25261874307452 1 7.38777897379236 994 1784 393 2879 3508 573 875 2196 2798 559 1755 1553 M889 REACTOME_DCC_MEDIATED_ATTRACTIVE_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DCC_MEDIATED_ATTRACTIVE_SIGNALING.html Genes involved in DCC mediated attractive signaling 20/22 Reactome 0.061965263153802 0.0963677239162918 1760 1795.72727272727 1756 0.00579842367109026 546 0.940511213788107 0.910715690983394 1 1.43382674641396 2325 974 2550 558 1606 2136 1322 4222 546 1758 1756 1554 M9378 ST_INTERLEUKIN_4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTERLEUKIN_4_PATHWAY.html Interleukin 4 (IL-4) Pathway 28/32 Signaling Transduction KE 0.004358401777085 0.0119325153061724 1830 1640.18181818182 1758 0.000397005472240748 154 0.775795067582905 0.569995111338034 1 2.23876288910582 1827 297 3073 189 672 1795 1758 1171 154 3734 3372 1555 M2396 SERVITJA_ISLET_HNF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_ISLET_HNF1A_TARGETS_DN.html Genes down-regulated in pancreatic islets upon knockout of HNF1A [GeneID=6927]. 19289501 97/171 Arthur Liberzon 2.07809114614132e-11 7.15955489765477e-10 4030 1833.45454545455 1759 1.88917376923723e-12 108 1.46244421243723 -1.40374815471586 -1 20.0681781976032 4026 673 108 918 1362 2288 3505 2824 1759 246 2459 1556 M1931 MEISSNER_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone trimethylation marks at K4 (H3K4me3) and K27 (H3K27me3)ES cells (embryonic stem). 18600261 15/23 Jessica Robertson 0.00449657465707591 0.0122468738496239 2955 2337.18181818182 1760 0.000409617416338908 358 1.17831411033459 -1.24289662685327 -1 3.38042608873142 2951 1568 1514 1760 4580 4288 4354 358 1687 2226 423 1557 M2172 FIGUEROA_AML_METHYLATION_CLUSTER_5_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_5_UP.html Cluster 5 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 14/20 Arthur Liberzon 0.0170449580419904 0.0333735764076643 1760 1825.72727272727 1760 0.0015616788927533 690 0.957723841121491 -1.03701813099099 -1 2.12188822528879 1760 2626 2639 2583 1406 823 1205 690 2289 3320 742 1558 M489 REACTOME_INHIBITION_OF_THE_PROTEOLYTIC_ACTIVITY_OF_APC_C_REQUIRED_FOR_THE_ONSET_OF_ANAPHASE_BY_MITOTIC_SPINDLE_CHECKPOINT_COMPONENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_THE_PROTEOLYTIC_ACTIVITY_OF_APC_C_REQUIRED_FOR_THE_ONSET_OF_ANAPHASE_BY_MITOTIC_SPINDLE_CHECKPOINT_COMPONENTS.html Genes involved in Inhibition of the proteolytic activity of APC/C required for the onset of anaphase by mitotic spindle checkpoint components 20/22 Reactome 0.0124931641250033 0.0260458192005369 1470 1949.72727272727 1762 0.00114224349050521 688 0.681847219738652 -0.709464661381345 -1 1.62079290151156 1466 2089 3830 2671 994 1265 835 1785 688 4062 1762 1559 M17275 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_8D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 8 days after transduction. 16818636 168/298 Arthur Liberzon 2.27816139337692e-10 6.76284388474155e-09 2255 1657.45454545455 1764 2.07105581237531e-11 125 1.32243088009439 1.24327356478711 1 16.2116468693734 2253 1764 125 1177 1503 2894 2633 614 2255 169 2845 1560 M6303 SCHEIDEREIT_IKK_INTERACTING_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/SCHEIDEREIT_IKK_INTERACTING_PROTEINS.html Genes encoding IkappaB kinase (IKK) interacting proteins. 17072322 81/88 Arthur Liberzon 0.0270029614717963 0.048480022117489 440 2171.72727272727 1766 0.00248547339710608 437 0.968198845907004 1.07174853336667 1 1.90951088753535 437 4411 3743 4639 1260 591 504 1355 1830 3353 1766 1561 M2255 MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP.html Genes commonly up-regulated in UET-13 cells (mesenchymal progenitor) by expression of EWSR1 [GeneID=2130] fusions with ETS transcription factors FLI1 and ERG [GeneID=2313 ,2078]. 18212050 357/464 Arthur Liberzon 9.11066635102696e-06 9.34833590801027e-05 370 1645.63636363636 1766 8.2824582549512e-07 366 1.1731897145454 1.13898644525127 1 7.09299218454041 1766 1162 367 1194 2563 1266 2130 1830 2826 366 2632 1562 M870 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_DN.html Genes down-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic B.D. chr3 (BD, large HSC size) vs parental B6 strain (tiny HSC size). 17220891 54/65 Leona Saunders 0.081308820665531 0.121256756253177 4115 2113.27272727273 1767 0.00767992595733053 212 1.18334828900891 -1.21895665480459 -1 1.62690058151941 4115 1402 2481 1244 1730 957 3752 3813 212 1773 1767 1563 M18073 THUM_MIR21_TARGETS_HEART_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/THUM_MIR21_TARGETS_HEART_DISEASE_DN.html Genes down-regulated in a mouse model of heart disease whose expression reverted to normal by silencing of MIR21 [GeneID=406991] microRNA. 19043405 13/16 Jessica Robertson 0.000162840583650285 0.000984132592611195 1770 1501.54545454545 1767 1.48047852824168e-05 168 1.48151290533998 1.2202625079912 1 6.68445580301103 1767 2632 1864 2287 168 1066 749 1042 279 1965 2698 1564 M1192 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_2_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer, mutated TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 80/123 Arthur Liberzon 0.0103665152618346 0.022467593801934 1865 1606.90909090909 1768 0.000946880683216479 599 1.33533291588177 1.23674664643663 1 3.30287012968104 1862 1860 850 1817 1218 1519 1768 2402 2041 599 1740 1565 M8699 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_CIS.html Transcripts in hematopoietic stem cells (HSC) which are cis-regulated (i.e., modulated by a QTL (quantitative trait locus) in close proximity to the gene). 15711547 154/211 Jean Junior 0.0986425805184343 0.142557556658607 1680 2122.81818181818 1768 0.00939679053534829 753 1.00513727262871 -0.904537371476868 -1 1.27587032523073 1680 1768 2313 1041 3856 753 1534 3349 2090 3426 1541 1566 M17004 LU_TUMOR_ENDOTHELIAL_MARKERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_ENDOTHELIAL_MARKERS_UP.html Genes specifically up-regulated in tumor endothelium. 17308118 43/48 Jessica Robertson 3.38499302577898e-07 5.45295804835385e-06 250 1817.36363636364 1768 3.07726686055032e-08 243 1.51753971901195 1.45795093079699 1 11.9851027919497 250 2948 243 2210 1170 1768 1724 2226 4081 1415 1956 1567 M1928 MIKKELSEN_PARTIALLY_REPROGRAMMED_TO_PLURIPOTENCY http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_PARTIALLY_REPROGRAMMED_TO_PLURIPOTENCY.html Genes up-regulated in cells that have been partially reprogrammed to pluripotency: comparison with the parental lineage-committed cell lines, fully reprogrammed stem cells, and embryonic stem cells. 18509334 8/12 Jessica Robertson 0.0190580061515845 0.036418538071044 4300 2112.27272727273 1768 0.00192234500140273 126 1.46175564967961 -1.48721471544027 -1 3.15548030210303 4299 1074 4610 1508 2564 3020 1599 778 126 1889 1768 1568 M15476 URS_ADIPOCYTE_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/URS_ADIPOCYTE_DIFFERENTIATION_UP.html Genes up-regulated in primary adipocytes compared to preadipocytes. 15051823 111/149 John Newman 7.81027652834759e-06 8.22868419950907e-05 1400 1796.27272727273 1769 7.10027659631708e-07 358 1.33999081553459 1.54799602966416 1 8.21287035965908 1400 1820 358 1610 1769 2704 2461 956 3612 809 2260 1569 M1722 LEIN_MEDULLA_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_MEDULLA_MARKERS.html Top 100 ranked genes most specific to medulla (myelencephalon) hindbrain region of adult mouse brain. 17151600 89/121 Jessica Robertson 0.00225251502534734 0.00730712777982093 695 2275.63636363636 1769 0.000204984056386483 65 1.37887665765211 -1.20213126012726 -1 4.41987081394626 4584 692 691 65 3348 4097 4150 1769 437 610 4589 1570 M1067 REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NONSENSE_MEDIATED_DECAY_ENHANCED_BY_THE_EXON_JUNCTION_COMPLEX.html Genes involved in Nonsense Mediated Decay Enhanced by the Exon Junction Complex 128/218 Reactome 0.00843283814409881 0.0191360557885319 155 2485.27272727273 1770 0.00076957605984404 152 0.69455606141254 0.652120826107991 1 1.79053951171524 152 4390 4163 4542 1099 535 242 1770 4485 4446 1514 1571 M11383 BROWNE_HCMV_INFECTION_16HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_16HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 16 h time point that were not up-regulated at the previous time point, 14 h. 11711622 329/382 John Newman 0.0184867592167177 0.035573985239902 805 2128.81818181818 1770 0.0016949052050991 721 1.01993244216111 1.02483340058954 1 2.21728312251074 803 3980 3726 1942 1770 1516 1463 721 1761 3733 2002 1572 M3896 KEGG_INOSITOL_PHOSPHATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INOSITOL_PHOSPHATE_METABOLISM.html Inositol phosphate metabolism 50/55 KEGG 0.0190319699866288 0.0363982570246709 3265 2102.36363636364 1771 0.00174533051153646 168 0.752582276161517 -0.825274797851445 -1 1.62481522768801 3265 168 3481 1771 1136 1425 2466 3709 1091 4083 531 1573 M2005 MIKKELSEN_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_ICP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing bivalent histone H3 methylation mark (H3K4me3 and H3K27me3) in embryonic stem cells (ES). 17603471 153/277 Arthur Liberzon 8.1926110192657e-16 4.89482582416887e-14 1235 1659 1772 7.44782819933244e-17 57 1.46035617557411 1.3468755824815 1 29.1665897517641 1232 1772 57 2248 891 1405 1975 2212 3214 152 3091 1574 M513 ZHAN_MULTIPLE_MYELOMA_MF_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MF_DN.html Top 50 down-regulated genes in cluster MF of multiple myeloma samples with characteristic expression spike of MAF family transcription factors. 16728703 55/66 Arthur Liberzon 0.00671880301818408 0.015968152188232 1825 1733.36363636364 1773 0.000612673674077493 439 1.33768496937599 1.19188868470737 1 3.6063629934255 1825 2883 1773 1542 3794 1838 1118 439 951 2100 804 1575 M645 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_GOLGI_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_GOLGI_MEMBRANE.html Genes involved in Synthesis of PIPs at the Golgi membrane 18/19 Reactome 0.000953777632666242 0.00383134504356141 1780 2038.72727272727 1774 8.6744670915639e-05 40 0.727440495032735 -0.724981825149542 -1 2.63776066443396 1778 3878 3813 4024 392 771 1774 798 1153 4005 40 1576 M1431 NADLER_OBESITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/NADLER_OBESITY_UP.html Genes up-regulated in adipose tissue from obese mouse strains compared to the lean ones. 11027337 87/125 Kevin Vogelsang 0.000493171301592738 0.00228660957123549 1845 1729.81818181818 1774 4.48438081733363e-05 396 1.16781312963756 1.20754529214002 1 4.6274534022352 396 1845 572 2361 1501 1674 1639 2124 3298 1844 1774 1577 M189 KEGG_RIBOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOSOME.html Ribosome 98/184 KEGG 0.017780012501924 0.0344875996234788 195 2507.54545454545 1776 0.00162957769049471 191 0.649401043844756 0.584363444785452 1 1.4248528446743 191 4430 4149 4540 1113 615 410 1244 4680 4435 1776 1578 M866 REACTOME_ROLE_OF_DCC_IN_REGULATING_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ROLE_OF_DCC_IN_REGULATING_APOPTOSIS.html Genes involved in Role of DCC in regulating apoptosis 14/16 Reactome 0.0322094085322955 0.0557084676703681 1780 1925.81818181818 1776 0.00297189752872585 686 0.759138421432255 0.799249486999405 1 1.42841837420831 1776 2118 2832 1333 4156 1035 686 935 723 3313 2277 1579 M13339 CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP.html Genes up-regulated in secondary APL (acute promyelocytic leukemia) compared to the de novo tumors. 16990782 50/65 Leona Saunders 0.0193808465815103 0.036826729414142 2620 2062.18181818182 1776 0.00177761068524667 738 1.18644665517208 1.25186783945681 1 2.5525352989646 2617 822 1643 1776 1146 3714 3089 2145 738 1298 3696 1580 M1358 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_UP.html Early prostate development genes (up-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in localized vs metastatic prostate cancers. 18794802 13/15 Jessica Robertson 0.0797448961751798 0.119186823476112 2345 1889.90909090909 1776 0.00752647503381318 1028 1.07761383600888 1.22401223742984 1 1.49361572115445 2344 1048 2128 1534 1818 1776 1028 1322 3800 2574 1417 1581 M9160 ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_RESPONSE_TO_IKK_INHIBITOR_AND_TNF_DN.html Genes down-regulated in BxPC3 cells (pancreatic cancer) after treatment with TNF [GeneID=7124] or IKI-1, an inhibitor of IkappaB kinase (IKK). 19010928 151/182 Jessica Robertson 0.033369364355617 0.05727396354855 2200 2007.45454545455 1776 0.0030805930095758 949 1.14350264967205 1.16728691915968 1 2.1310515979721 2200 1776 1655 1433 2977 2246 2998 949 1751 1231 2866 1582 M2583 TOMIDA_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOMIDA_METASTASIS_DN.html Down-regulated genes associated with the acquision of metastatic potential in LNM35 cells (large cell lung cancer). 17260014 26/37 Arthur Liberzon 0.00484069421933909 0.0129892420211942 2365 1780.90909090909 1777 0.00044103438182035 103 1.41608199326933 1.06810778353193 1 4.00826344280596 2361 3448 1911 1057 2920 1542 1777 1366 380 2725 103 1583 M17860 TAKAO_RESPONSE_TO_UVB_RADIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKAO_RESPONSE_TO_UVB_RADIATION_DN.html Genes down-regulated in primary tissue culture of epidermal kerationcytes after UVB irradiation. 11982916 127/173 John Newman 0.0681384323206496 0.104589723757225 1175 2183.90909090909 1777 0.00639501049223072 819 1.12164453765714 1.18022811593424 1 1.65014332019283 1171 3648 2640 3827 3620 890 819 2686 1728 1777 1217 1584 M14142 BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_DN.html Genes down-regulated in the invasive ductal carcinoma (IDC) compared to the invasive lobular carcinoma (ILC), the two major pathological types of breast cancer. 18490921 64/81 Jessica Robertson 4.87522363106665e-09 1.15921359540595e-07 455 1925 1778 4.43202149260927e-10 160 1.54336837458428 1.49324690463386 1 16.0622874126615 452 2873 160 2880 4285 2395 1778 452 4289 302 1309 1585 M13055 DAVIES_MULTIPLE_MYELOMA_VS_MGUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVIES_MULTIPLE_MYELOMA_VS_MGUS_UP.html Genes up-regulated in multiple myeloma (MM) compared to monoclonal gammopathy of uncertain significance (MGUS). 12947006 24/40 Arthur Liberzon 0.000281322330181394 0.00150719795511485 4490 2205.27272727273 1779 2.55780282158567e-05 214 1.40028442195582 1.18936959660801 1 5.92899541716322 4489 346 1003 1779 214 4600 3791 2467 924 782 3863 1586 M2525 BOUDOUKHA_BOUND_BY_IGF2BP2 http://www.broadinstitute.org/gsea/msigdb/cards/BOUDOUKHA_BOUND_BY_IGF2BP2.html Transcripts bound to IGF2BP2 [GeneID=10644] complexes and differentially regulated in myoblasts with IGF2BP2 [GeneID=10644] knockdown by RNAi. 20956565 145/205 Arthur Liberzon 0.0299224968065495 0.0525229397273758 1300 1954.18181818182 1779 0.00275794535956934 686 0.959194132185657 -1.02593292273275 -1 1.84168308101469 1297 1779 3376 1051 3835 789 2080 905 2520 3178 686 1587 M1218 BORLAK_LIVER_CANCER_EGF_UP http://www.broadinstitute.org/gsea/msigdb/cards/BORLAK_LIVER_CANCER_EGF_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) developed by transgenic mice overexpressing a secretable form of EGF [GeneID=1950] in liver. 15674348 100/134 Leona Saunders 0.000108394678429597 0.000708618950398475 855 2092.09090909091 1780 9.85454722156798e-06 485 1.41192271857765 1.49612002326879 1 6.67266756729275 852 3668 485 4075 3921 1057 1511 2127 2887 650 1780 1588 M18532 KIM_MYCN_AMPLIFICATION_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCN_AMPLIFICATION_TARGETS_UP.html Genes positively correlated with amplifications of MYCN [GeneID=4613] in the SCLC (small cell lung cancer) cell lines. 16116477 122/163 Arthur Liberzon 0.0354508745789862 0.0603201615042592 1170 1973.45454545455 1780 0.00327594184300743 449 1.10366494854071 1.1791065758297 1 2.01953536003727 1167 3649 1687 2857 2874 2006 1328 1206 2705 1780 449 1589 M3475 CHEN_HOXA5_TARGETS_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_6HR_UP.html Genes up-regulated 6 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 11/11 Arthur Liberzon 0.00183301886509951 0.00627855518379514 2675 1963.72727272727 1781 0.000166777082061564 282 1.9544019133399 -2.6284472354512 -1 6.45793325711641 2671 2148 1475 3081 494 1781 282 872 1369 3024 4404 1590 M19428 KEGG_WNT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_WNT_SIGNALING_PATHWAY.html Wnt signaling pathway 144/178 KEGG 0.0268909195146903 0.0483340213668463 2300 2081.45454545455 1782 0.00247503165455628 586 1.00701610497346 1.00102921974616 1 1.98805098709603 2298 1246 2436 586 1258 1454 1782 4273 1323 2941 3299 1591 M14663 REACTOME_ETHANOL_OXIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ETHANOL_OXIDATION.html Genes involved in Ethanol oxidation 9/13 Reactome 0.00554145446002807 0.0142024584976285 4530 2325.81818181818 1782 0.000555532162574784 622 1.3519805022839 -1.62943729468942 -1 3.74814601434978 4528 1612 4256 1782 763 2480 3233 1496 872 622 3940 1592 M8795 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP.html Genes up-regulated in transformed NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845]) vs normal cells. 16607279 163/210 Lauren Kazmierski 0.0577200572506406 0.0909644975702917 1710 2081.36363636364 1782 0.00539022662347605 1180 1.20454391646709 1.22532094852641 1 1.88167311592196 1707 1770 1782 1642 2618 2547 3129 1180 1778 1867 2875 1593 M9131 KEGG_GLYCEROPHOSPHOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCEROPHOSPHOLIPID_METABOLISM.html Glycerophospholipid metabolism 64/81 KEGG 0.0996360577518321 0.143729276463523 3530 1787.09090909091 1783 0.0094960988488993 340 1.13044089729654 -1.19626157964921 -1 1.42890743080373 3530 1359 2160 1172 1826 1783 2292 2345 340 1517 1334 1594 M11763 MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_UP.html Genes commonly up-regulated in SK-N-BE cells (neuroblastoma) after RNAi knockdown of CCND1 and CDK4 [GeneID=595;1019]. 18413728 77/136 Jessica Robertson 0.00146497652584149 0.00527129893559473 4570 2394.63636363636 1783 0.000133268451073452 459 1.21136192873776 -1.31318643739277 -1 4.14070269673409 4568 733 1353 1783 459 4560 3778 4069 1337 1244 2457 1595 M3464 VANTVEER_BREAST_CANCER_BRCA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_BRCA1_DN.html Down-regulated genes from the optimal set of 100 markers discriminating ER(-) breast cancer tumors by BRCA1 [GeneID=672] mutation status. 11823860 56/71 Arthur Liberzon 0.0196580200940354 0.0372933500176234 1935 1821.36363636364 1784 0.00180326389894677 850 1.19419322513417 -0.977944254786996 -1 2.55940344131907 1934 1916 923 2272 1422 2337 1638 1784 3600 1359 850 1596 M2252 CERIBELLI_PROMOTERS_INACTIVE_AND_BOUND_BY_NFY http://www.broadinstitute.org/gsea/msigdb/cards/CERIBELLI_PROMOTERS_INACTIVE_AND_BOUND_BY_NFY.html Transcriptionally inactive genes whose promoters (regions between -2 kb to +0.5 kb relative to trascription start sites) where bound by NF-Y transcription factor. 18212061 30/92 Arthur Liberzon 0.0270364614218068 0.048521710232292 1680 2248.54545454545 1784 0.00248859563493321 703 1.7083993932878 1.63281779215203 1 3.36848065320975 1679 4160 1615 4209 4364 1784 2090 871 703 2173 1086 1597 M28 PID_IL4_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL4_2PATHWAY.html IL4-mediated signaling events 18832364 76/106 Pathway Interaction Database 0.000111046131941532 0.000719742812472241 1225 1878.63636363636 1786 1.00956124952998e-05 486 1.35902203805268 1.30890231925841 1 6.40886336420497 1221 1864 486 2689 1786 1909 1520 1753 3358 1009 3070 1598 M19751 MORI_SMALL_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_SMALL_PRE_BII_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Small Pre-BII stage. 18922927 115/144 Jessica Robertson 0.00962814091565148 0.0211866184824382 2515 1956.18181818182 1786 0.000879139797469599 593 1.26326220800087 1.1831993724274 1 3.17292851338062 2513 653 861 789 1321 3707 2797 3201 1786 593 3297 1599 M16026 VERRECCHIA_RESPONSE_TO_TGFB1_C1 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C1.html Cluster 1: ECM related genes up-regulated in dermal fibroblasts within 30 min after TGFB1 [GeneID=7040] addition, and which kept increasing with time. 11279127 58/82 John Newman 7.49151718439794e-05 0.000524628503121043 955 1897.54545454545 1786 6.81070209121065e-06 16 1.16083196585548 1.28313474778822 1 5.71342562078505 954 2878 1425 2959 3725 1786 1606 16 2994 1970 560 1600 M1857 MALONEY_RESPONSE_TO_17AAG_UP http://www.broadinstitute.org/gsea/msigdb/cards/MALONEY_RESPONSE_TO_17AAG_UP.html Up-regulated genes in A2780 cells (ovarian cancer) treated with 17AAG [PubChem=6440175], a chemical with anticancer properties. 17409432 73/107 Jessica Robertson 0.0523383519510512 0.0839645434583517 1270 2061.18181818182 1786 0.00487514605435487 710 1.22584853087822 1.30482529020011 1 1.97892322238679 1269 2401 1786 1902 3251 801 710 4688 3294 1695 876 1601 M5487 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_UP http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_UP.html Hepatic graft versus host disease (GVHD), day 7: up-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 138/204 Arthur Liberzon 9.27720590586105e-06 9.49857090578398e-05 1790 2164.09090909091 1786 8.43385911568257e-07 368 1.18428975994066 1.28675719375926 1 7.1477987661722 1786 1252 368 1308 1211 3408 3072 3428 3170 775 4027 1602 M7761 KEGG_MELANOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOGENESIS.html Melanogenesis 86/110 KEGG 0.00577426225782821 0.0142024584976285 1790 1936.27272727273 1787 0.000526315789473684 164 0.99955616668092 0.962611317720073 1 2.77107928677776 1787 704 1735 164 4670 1206 778 4358 1886 2040 1971 1603 M1226 OXFORD_RALA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_TARGETS_DN.html Genes down-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALA [GeneID=5898] by RNAi. 17496927 30/32 Arthur Liberzon 0.0139682051677945 0.0285658268596144 190 2015.36363636364 1788 0.00127797166320239 186 1.24000460754731 1.18038025029228 1 2.87302560277476 186 3428 1046 3222 1024 1788 1439 2125 4542 2172 1197 1604 M8416 BROWNE_HCMV_INFECTION_10HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_10HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 10 h time point that were not down-regulated at the previous time point, 8 h. 11711622 72/92 John Newman 0.00760744804632567 0.0175671011637266 1790 1830.90909090909 1788 0.00069398928502171 97 0.992995881178687 1.0866995885898 1 2.61530900821834 1788 97 2190 977 4253 2994 2341 465 919 2981 1135 1605 M2862 FINETTI_BREAST_CANCERS_KINOME_BLUE http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCERS_KINOME_BLUE.html Genes in the blue cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 39/50 Jessica Robertson 0.0920300089409755 0.13448348055771 2140 1536.81818181818 1788 0.0087383197672827 216 1.11976412022487 1.08336739210374 1 1.46392948167418 2140 216 1543 395 1788 2342 1895 2151 229 1207 2999 1606 M3732 SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN.html Genes down-regulated in response to UVB radiation in HFK cells (keratinocytes) immortalized by overexpression of HPV E6 and E7 viral oncogenes. 16007217 58/61 Leona Saunders 0.0118183060029107 0.0248917466906463 1710 2094.09090909091 1789 0.00108020682295832 579 1.14620897883204 1.33723492796813 1 2.75853389579985 1231 2440 2205 3229 1707 1789 1560 579 3472 1709 3114 1607 M2021 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_2.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 2. 12554760 108/141 Arthur Liberzon 0.00278496830054287 0.00856913323243961 1280 1815.90909090909 1789 0.000253500003438334 475 1.41180731568772 1.36475604545622 1 4.37885410640871 1280 3233 900 1828 1789 1804 1106 3143 1251 475 3166 1608 M2842 BIOCARTA_FIBRINOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FIBRINOLYSIS_PATHWAY.html Fibrinolysis Pathway 10/15 BioCarta 0.000117112318296491 0.000753092837001957 2020 1865.63636363636 1790 1.06471411805624e-05 145 2.0587238580303 -2.52786201966617 -1 9.64779776827675 2018 2664 1012 2039 145 993 1309 2968 3992 1592 1790 1609 M10381 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_DN.html Genes down-regulated in transformed NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845]) vs normal cells. 16607279 215/252 Lauren Kazmierski 5.8549821775336e-06 6.38233623047543e-05 1790 1855.63636363636 1790 5.32272523616444e-07 209 1.23714313808691 1.29359317254453 1 7.78735415184292 1790 1736 388 547 2161 3647 3535 1665 2032 209 2702 1610 M15412 OSAWA_TNF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OSAWA_TNF_TARGETS.html Genes up-regulated in Hc cells (normal hepatocyte) by TNF [GeneID=7124]. 12682234 26/29 Yujin Hoshida 0.00775105949244994 0.0178029200994471 175 1838.63636363636 1791 0.000707136687031714 174 1.416903911199 1.20612472292023 1 3.71951206493097 174 3027 818 3245 1791 707 408 2977 4131 1850 1097 1611 M10880 STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN.html Down-regulated genes classifying non-tumor lung tissues by age after incution of lung cancer by urethane injection [PubChem=5641]: early (24-26 weeks) vs late (46 weeks). 18172294 70/107 Jessica Robertson 0.00622826936394265 0.0151132860242952 2515 1798.63636363636 1791 0.000567815635829754 306 1.0939590719159 1.35281260084017 1 2.9884902664399 2511 738 942 306 767 3836 2422 2106 1740 1791 2626 1612 M7375 DORN_ADENOVIRUS_INFECTION_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_48HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 48 h after infection with adenovirus Ad12. 15681441 76/94 Arthur Liberzon 0.00334323172086984 0.00984679437295289 95 2004.81818181818 1791 0.000304393009166811 60 1.06666328110966 1.04925031035304 1 3.21172538779479 92 4074 1791 4679 2455 60 151 1751 4316 2600 84 1613 M2435 WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/WAMUNYOKOLI_OVARIAN_CANCER_GRADES_1_2_UP.html Genes up-regulated in mucinous ovarian carcinoma tumors of grades 1 and 2 compared to the normal ovarian survace epithelium tissue. 16467078 194/221 Arthur Liberzon 0.00577426225782821 0.0142024584976285 2240 1871.54545454545 1792 0.000526315789473684 74 1.05366199449628 -1.0465266766611 -1 2.92108312812908 2237 566 1792 74 2721 2497 3851 2549 1177 1402 1721 1614 M16336 PODAR_RESPONSE_TO_ADAPHOSTIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/PODAR_RESPONSE_TO_ADAPHOSTIN_UP.html Up-regulated genes in MM1.S cells (multiple myeloma) treated with adaphostin [PubChem=387042], a tyrosine kinase inhibitor with anticancer properties. 17308109 193/252 Jessica Robertson 0.000285991244733543 0.00153047468836998 595 1877.81818181818 1792 2.60025844749777e-05 4 1.02853099030357 0.931348561707071 1 4.34464034780404 594 3999 1139 3874 1933 16 516 2745 4044 1792 4 1615 M15549 CERVERA_SDHB_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/CERVERA_SDHB_TARGETS_1_UP.html Genes turned on in Hep3B cells (hepatocellular carcinoma, HCC) upon knockdown of SDHB [GeneID=6390] by RNAi. 18519664 133/199 Jessica Robertson 5.81445407776672e-09 1.34530506113034e-07 1520 1922.72727272727 1794 5.28586735739449e-10 165 1.28788102375565 1.43123978273959 1 13.2783883975517 1520 1794 165 2501 1045 3395 3059 1299 3599 305 2468 1616 M15382 BROWNE_HCMV_INFECTION_10HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_10HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 10 h time point that were not up-regulated at the previous time point, 8 h. 11711622 178/261 John Newman 0.0172584826112471 0.0336750880219456 640 2349 1795 0.00158139792702572 636 0.985940305550758 1.05082665315529 1 2.17862781174372 636 4351 2920 4636 1096 1001 1041 1395 3450 3518 1795 1617 M2124 HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_DN.html Down-regulated genes in the cancer gene signature, representing a gene signature of cellular transformation. 20385360 155/181 Arthur Liberzon 0.119122625131815 0.167090279531104 1035 2008.36363636364 1795 0.0114643999889911 835 1.13463493002121 1.15385259044472 1 1.32285279048356 1032 4013 1965 2979 2220 835 1443 1777 2986 1795 1047 1618 M6322 REACTOME_ACTIVATION_OF_RAC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_RAC.html Genes involved in Activation of Rac 16/20 Reactome 0.0640593883346496 0.0991535536326427 2145 2083.54545454545 1797 0.00600040284207646 843 1.20414788477135 -1.22209574162195 -1 1.81341260954774 2142 1024 1923 843 4669 2664 4075 1231 1148 1797 1403 1619 M9206 YAMASHITA_LIVER_CANCER_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_STEM_CELL_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) cells with hepatic stem cell properties. 19150350 73/175 Yujin Hoshida 3.17895396023535e-08 6.49552497502633e-07 2925 1500.90909090909 1797 2.88995818742778e-09 190 1.41738380712081 -1.34437321722629 -1 13.159305665247 2922 730 190 695 293 2059 3534 1797 2091 273 1926 1620 M1842 LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_TARGETS_OF_TGFB1_AND_WNT3A_UP.html Up-regulated genes in NMuMG cells (mammary epithelium) after stimulation with both TGFB1 and WNT3A [GeneID=7040;89780]. 17210685 152/219 Jessica Robertson 5.45404027242693e-06 6.07308559367971e-05 1070 1752.36363636364 1798 4.95823072148668e-07 342 1.38676021584896 1.53915981086359 1 8.77403535453977 1068 3207 342 1501 4482 1798 2190 1864 2040 426 358 1621 M1072 REACTOME_INFLAMMASOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLAMMASOMES.html Genes involved in Inflammasomes 14/20 Reactome 0.00349082708426451 0.0101270459973746 970 1586 1799 0.000317852586700783 305 1.48447563884008 1.65559778931449 1 4.44265232931912 968 3084 2112 2050 2154 1799 834 305 980 2076 1084 1622 M1984 NAKAYAMA_FGF2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_FGF2_TARGETS.html Genes down-regulated in S-17 cells (bone marrow stroma) after stimulation with FGF2 [GeneID=2247]. 17284717 48/57 Jessica Robertson 0.0434767307175932 0.0716692298844914 460 2265 1799 0.00403277035041769 456 1.25355454992775 1.16009371314897 1 2.15299470257105 456 4116 1049 3674 1799 1773 1770 2450 4148 1979 1701 1623 M211 PID_HEDGEHOG_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HEDGEHOG_2PATHWAY.html Signaling events mediated by the Hedgehog family 18832364 30/34 Pathway Interaction Database 0.0955054680741711 0.138660661122758 4480 2491.18181818182 1801 0.00908385562896022 594 1.10751586430354 1.16934080297916 1 1.42583894834116 4480 906 1692 594 1801 4506 2916 3984 913 1464 4147 1624 M19170 MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_UP.html The 'NPM1-mutated signature 1': genes up-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to all AML cases with the intact gene. 17597811 317/448 Arthur Liberzon 0.0794852494541637 0.118902134420816 1740 1901.36363636364 1801 0.00750102167136399 538 1.09215141784396 1.09830173936139 1 1.51546886024164 1736 538 2016 1801 1721 2571 2450 1504 2626 1739 2213 1625 M8645 MCCLUNG_DELTA_FOSB_TARGETS_2WK http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_DELTA_FOSB_TARGETS_2WK.html Genes up-regulated in the nucleus accumbens (a major reward center in brain) 2 weeks after induction of deltaFosB, a FOSB [GeneID=2354] splice variant. 14566342 79/105 John Newman 0.000460311857662425 0.00216617344782318 695 2129.27272727273 1803 4.18552907418009e-05 566 1.40158613573929 1.29612851977559 1 5.60321939151518 692 3695 566 4417 1305 1803 1605 2301 3663 1959 1416 1626 M16101 BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transfrormed by expression of constitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector; their expression did NOT reverted completely after treatment with Y27632 [PubChem=123862], an inhibitor of ROCK proteins. 17213802 65/71 Leona Saunders 0.000483947639586917 0.00225345596918031 35 1799.90909090909 1804 4.40049208496657e-05 35 1.12003943402124 1.04628127234767 1 4.44880626427291 35 4088 937 4330 2072 56 93 1839 4254 1804 291 1627 M5549 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_UP.html Genes up-regulated in lobular carcinoma vs normal lobular breast cells. 17389037 126/168 Arthur Liberzon 1.00128197604573e-07 1.81771189497532e-06 1600 1927.18181818182 1805 9.10256383288089e-09 217 1.52288224742825 1.45771226589104 1 13.1175417408162 1491 1805 217 2524 4113 2684 2186 1600 2753 227 1599 1628 M1917 ZHANG_TLX_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_UP.html Genes up-regulated in neural stem cells (NSC) at both 36 h and 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 141/204 Jessica Robertson 6.25699430620582e-08 1.19566854758265e-06 3135 2011.90909090909 1805 5.68817680378206e-09 119 1.22401147206575 -1.27294244503635 -1 10.8772726638475 3131 607 314 678 4220 2018 3924 4236 1079 119 1805 1629 M813 REACTOME_SYNTHESIS_SECRETION_AND_DEACYLATION_OF_GHRELIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_SECRETION_AND_DEACYLATION_OF_GHRELIN.html Genes involved in Synthesis, Secretion, and Deacylation of Ghrelin 14/20 Reactome 0.0627123090782691 0.0973370926831404 1535 2335.09090909091 1806 0.00587042945893806 787 1.08864407285706 -1.00840314769982 -1 1.652574111844 1534 1581 1754 3931 4122 1216 787 1806 3817 2674 2464 1630 M14171 KEGG_STARCH_AND_SUCROSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STARCH_AND_SUCROSE_METABOLISM.html Starch and sucrose metabolism 27/58 KEGG 0.0155998141934444 0.0311864138047681 665 1660.54545454545 1807 0.00142832185909109 371 1.1710091648223 1.24435032214109 1 2.64618176895031 661 2033 1807 2819 2560 1281 1078 653 2192 2811 371 1631 M14766 REACTOME_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTRINSIC_PATHWAY.html Genes involved in Intrinsic Pathway 10/23 Reactome 3.63052846366851e-05 0.000297501637995058 2950 1922.90909090909 1807 3.30053488863026e-06 75 2.04867636822624 -2.6309859058707 -1 10.8406700147786 2948 2656 1276 2530 75 1997 1807 3846 1154 1594 1269 1632 M6761 GOLUB_ALL_VS_AML_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOLUB_ALL_VS_AML_DN.html Down-regulated genes highly correlated with acute lymphoblastic leukemia (ALL) vs acute myeloid leukemia (AML). 10521349 20/35 Jean Junior 0.021036975026623 0.0394182302999843 1870 1971.72727272727 1807 0.00193098826798339 422 1.11522597280353 1.01245334387133 1 2.34988122391947 1867 1527 1605 1017 1807 1493 422 4005 3406 2713 1827 1633 M1802 ZHENG_IL22_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_IL22_SIGNALING_DN.html Genes down-regulated in ex-vivo colonic tissue after treatment with IL22 [GeneID=50616]. 18264109 73/105 Jessica Robertson 0.000891512569202564 0.00363066378484564 910 2038 1807 8.10794585994655e-05 605 1.42865161557088 1.37875150423645 1 5.23060193933412 910 3287 605 3788 690 2115 1626 1807 3490 1484 2616 1634 M7494 REACTOME_TOLL_RECEPTOR_CASCADES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TOLL_RECEPTOR_CASCADES.html Genes involved in Toll Receptor Cascades 141/182 Reactome 0.089171022788648 0.130944959178103 1035 2232.72727272727 1808 0.00845497486657325 956 0.99868819897767 1.1257096371104 1 1.32298226192613 1035 1787 2910 2961 4495 1486 956 1374 1808 3762 1986 1635 M11954 XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_UP.html Genes up-regulated in DU-145 cells (prostate cancer) in the absence and presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 48/61 Arthur Liberzon 0.0961763370787425 0.1394202429397 1805 1985.36363636364 1810 0.00915069347760144 828 1.24388511491252 1.23492727824724 1 1.59698824826239 1802 828 1694 1055 1810 2457 2068 2774 2394 1209 3748 1636 M15473 SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_DN.html Selected genes down-regulated in peripheral blood monocytes (PBMC) of patients with hepatocellular carcinoma (HCC) compared to those with chronic hepatitis. 19074895 46/62 Arthur Liberzon 0.00360453877058606 0.0103867051264751 1765 1806.72727272727 1810 0.000328223465950693 311 1.11921018152218 1.04265315606247 1 3.33101607210813 1764 2467 2154 2932 2439 1668 1356 311 773 2200 1810 1637 M7396 SWEET_LUNG_CANCER_KRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_LUNG_CANCER_KRAS_DN.html Genes down-regulated in the Kras2LA mouse lung cancer model with mutated KRAS [GeneID=3845]. 15608639 543/758 Arthur Liberzon 3.40324534436593e-17 2.36225265079517e-15 1075 2038.90909090909 1812 3.40324534436593e-18 31 1.35116689325816 1.30356997121841 1 29.6547881349289 1073 1681 4602 2799 1622 1812 2126 1424 3283 31 1975 1638 M1186 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_UP.html Genes up-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 39/141 Arthur Liberzon 3.99073207326006e-05 0.000317643429777192 1815 1833.54545454545 1814 3.62800405976922e-06 251 1.84149527302612 1.88122902767658 1 9.66573605238764 1814 3785 523 3936 600 2745 2754 1918 968 251 875 1639 M7141 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP.html Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs moderately differentiated tumors. 18679425 145/165 Jessica Robertson 0.00577426225782821 0.0142024584976285 3915 1922.54545454545 1814 0.000526315789473684 68 1.07962083558094 -1.09708976577151 -1 2.99305182423728 3914 605 1814 68 3342 1724 4368 1985 705 1823 800 1640 M8991 ZERBINI_RESPONSE_TO_SULINDAC_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZERBINI_RESPONSE_TO_SULINDAC_UP.html Selected genes up-regulated in DU145 and PC-3 cells (prostate cancer) after treatment with the NSAID (non-steroid anti-inflammatory drug) sulindac [PubChem=5352]. 17178890 12/12 Arthur Liberzon 0.00702922344832431 0.0165393492901749 3535 2262.09090909091 1816 0.000641071228206658 802 1.24612098259612 -1.4116261541641 -1 3.33096106197594 3535 1591 1374 1852 802 4069 4190 1655 1543 2456 1816 1641 M7284 SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_UP.html Genes up-regulated in CT60/4 cells (breast cancer reverted to normal by transfer of chromosome 8p region) vs parental MDA-MB-231 cells (deleted chromosome 8p). 15580292 106/147 Arthur Liberzon 4.47602895828182e-07 6.9881184850067e-06 845 1503.27272727273 1816 4.06911806268765e-08 251 1.32549660677572 1.30870437194659 1 10.2541226818319 841 1816 251 2025 798 1937 1904 1721 2797 335 2111 1642 M17812 TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_DN.html Genes down-regulated in plasma cells compared with B lymphocytes. 12663452 46/64 Kate Stafford 0.00344184876500246 0.0100225613716505 485 1386.90909090909 1817 0.000313385934614268 300 1.01094475695079 0.917354018130564 1 3.03229529609117 484 1950 2020 1821 1006 549 600 300 2508 2201 1817 1643 M2235 BHAT_ESR1_TARGETS_VIA_AKT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_VIA_AKT1_DN.html Genes bound by ESR1 [GeneID=2099] and down-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer) expressing constitutevly active form of AKT1 [GeneID=207]. 18838536 108/125 Arthur Liberzon 0.0438051948153434 0.0719918243483359 1565 1825.54545454545 1817 0.00406386692330742 847 1.15128049296428 1.15162123564718 1 1.97395974561445 1565 1817 1053 1231 3792 847 1369 2848 1821 1835 1903 1644 M1432 SANSOM_APC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS_DN.html Top genes down-regulated at day 5 of Cre-Lox induced APC [GeneID=324] knockout in the intestine. 15198980 423/653 Kevin Vogelsang 1.2315852543763e-14 6.75939814029783e-13 3750 1884.36363636364 1818 1.11962295852391e-15 6 1.20607322861188 -1.17154022861215 -1 22.0245609304141 3750 512 64 6 2261 1961 4248 4559 1382 167 1818 1645 M13547 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_LOBULAR_NORMAL_DN.html Genes down-regulated in lobular carcinoma vs normal lobular breast cells. 17389037 116/135 Arthur Liberzon 7.45489006720746e-07 1.09056517348671e-05 2470 1762.54545454545 1819 6.77717508487506e-08 268 1.52497699655455 1.60892486274782 1 11.3550304582113 339 2340 268 2711 1360 2468 2470 1474 3611 528 1819 1646 M19930 BILBAN_B_CLL_LPL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BILBAN_B_CLL_LPL_UP.html Genes up-regulated in B-CLL (B-cell chronic leukemia) samples expressing high levels of LPL [GeneID=4023] compared with those expressing low levels of the gene. 16617321 108/156 Arthur Liberzon 0.0159866423999168 0.0318383764251507 2110 1890.81818181818 1819 0.00146400068802102 979 1.10258107581939 1.14883715945401 1 2.4766795964936 2107 1819 1548 1487 1067 2780 2877 1012 2140 979 2983 1647 M16005 IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_INTERMEDIATE_PROGENITOR.html Genes in the expression cluster 'Intermediate Progenitors Shared': up-regulated in hematopoietic intemediate progenitor cells from adult bone marrow and fetal liver. 12228721 166/189 John Newman 0.0857209705257422 0.126834790244985 1860 2193.18181818182 1819 0.00811412588067072 597 0.831433212275371 -0.773960995997859 -1 1.11867800708509 1856 597 4024 1819 1754 901 1613 3061 1741 4241 2518 1648 M11850 TANG_SENESCENCE_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TANG_SENESCENCE_TP53_TARGETS_UP.html Genes up-regulated in WI-38 cells (senescent primary fibroblasts) after inactivation of TP53 [GeneID=7157] by GSE56 polypeptide. 17533371 41/61 Leona Saunders 0.0938548123253706 0.136952912197702 1370 2229.45454545455 1820 0.00891959450358068 1362 1.49249256306309 1.41927620997508 1 1.9335557984807 1368 3376 1362 3165 1797 1820 1648 1790 4324 1877 1997 1649 M4342 BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G6_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G6, defined by unsupervised clustering. 17187432 102/123 Yujin Hoshida 0.0033873900453497 0.00992456922039141 2550 1915.72727272727 1821 0.000308419723411653 30 1.10420525755452 1.17813660365317 1 3.31910685383595 2550 30 931 71 618 4066 3608 1710 2916 1821 2752 1650 M17651 FRASOR_TAMOXIFEN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_TAMOXIFEN_RESPONSE_UP.html Genes preferentially up-regulated in MCF-7 cells (breast cancer) by tamoxifen [PubChem=5376] but not by estradiol or fulvestrant (ICI 182780) [PubChem=5757;3478439]. 16849584 64/76 Arthur Liberzon 0.0132089716684271 0.0272611920747599 2830 1697.09090909091 1822 0.00120808658849093 305 1.21275278331782 -1.08770434039365 -1 2.84682691714403 2826 757 1822 305 1010 2291 1791 2471 532 1996 2867 1651 M14238 BALLIF_DEVELOPMENTAL_DISABILITY_P16_P12_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/BALLIF_DEVELOPMENTAL_DISABILITY_P16_P12_DELETION.html Candidate genes in the pericentromeric microdeletion in 16p11.2-p12.2 associated with developmental disabilities. 17704777 21/28 Leona Saunders 0.036066302553252 0.0611249364636802 990 1981.90909090909 1823 0.00333377289934267 986 1.1460526672403 1.33916692464988 1 2.08720404263926 1751 989 1823 2840 2919 3719 2688 986 1031 1825 1230 1652 M5955 COLLER_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/COLLER_MYC_TARGETS_UP.html Genes up-regulated in 293T (transformed fetal renal cell) upon expression of MYC [GeneID=4609]. 10737792 29/35 Yujin Hoshida 0.0442923502257239 0.072677643535517 440 2533.63636363636 1824 0.00411000511281236 438 0.970554745412779 0.970554745412779 1 1.65807811666942 438 4513 3420 4248 1472 1384 1186 1661 3941 3783 1824 1653 M10759 LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_UP.html Top genes associated with favorable overall survival of mesothelioma patients after surgery. 16540645 7/12 Arthur Liberzon 0.000206412868985041 0.00119542176884588 3545 2171.90909090909 1824 2.0643204431446e-05 190 1.22639723419291 -1.4966157668386 -1 5.37793811073635 3545 1632 4637 1425 190 2150 1824 4000 702 1729 2057 1654 M5436 KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY.html B cell receptor signaling pathway 76/110 KEGG 0.00923832548184428 0.0205006564524236 1130 1987.18181818182 1825 0.000843395366150135 429 0.821743162228206 0.783268769443294 1 2.08155559987844 1130 2392 3221 1664 884 1107 429 2723 3072 3412 1825 1655 M881 REACTOME_TRANSPORT_OF_VITAMINS_NUCLEOSIDES_AND_RELATED_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_VITAMINS_NUCLEOSIDES_AND_RELATED_MOLECULES.html Genes involved in Transport of vitamins, nucleosides, and related molecules 24/37 Reactome 0.219920441698574 0.279941878321809 2320 1914.27272727273 1826 0.0223251458985945 348 1.42181412037003 -1.37032794091184 -1 1.1795530933681 2318 348 1388 1407 4653 2263 2185 2324 1017 1328 1826 1656 M2105 KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP.html Genes whose expression was significantly and positively correlated with the number of perineuronal oligodendrocytes in the layer III of BA9 brain region. 18762803 941/1159 Jessica Robertson 0.0910109687850011 0.133241864970597 1710 2207.81818181818 1826 0.00949684260905466 470 0.957478548884536 -0.860853075033998 -1 1.25753668604885 1710 470 4658 890 3162 757 1826 2621 1775 4353 2064 1657 M14162 REACTOME_CHYLOMICRON_MEDIATED_LIPID_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHYLOMICRON_MEDIATED_LIPID_TRANSPORT.html Genes involved in Chylomicron-mediated lipid transport 12/19 Reactome 0.00758520779774805 0.0175500886300837 3910 2097.09090909091 1828 0.000691953379916747 118 1.34911233849554 1.46793885853238 1 3.55412270145933 3909 1054 1828 828 820 3788 4176 1103 118 1838 3606 1658 M2207 FUKUSHIMA_TNFSF11_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/FUKUSHIMA_TNFSF11_TARGETS.html Genes up-regulated in RAW 264.7 cells (macrophage) upon stimulation with TNFSF11 [GeneID=8600]. 18710934 14/16 Arthur Liberzon 0.00301702159929785 0.00909926003110916 3405 1993.45454545455 1828 0.000274651547610123 346 1.6337210753308 1.52961969997687 1 5.00325047969071 3401 2124 1365 2548 589 3007 1828 1100 4034 1586 346 1659 M17534 LEE_DOUBLE_POLAR_THYMOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_DOUBLE_POLAR_THYMOCYTE.html Genes enriched in the double polar (DP) thymocyte compared to all other T lymphocyte differentiation stages. 15210650 21/34 Arthur Liberzon 0.170291366920293 0.225021067151115 2755 1954.27272727273 1829 0.016827775568163 358 1.2064677062281 1.09557734705996 1 1.17258333875997 2755 358 1359 733 4586 2292 1233 2271 830 1829 3251 1660 M2035 BAUS_TFF2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAUS_TFF2_TARGETS_UP.html Genes up-regulated in pyloric atrium with knockout of TFF2 [GeneID=7032]. 16121031 27/53 Arthur Liberzon 0.00231867459650032 0.00746827961275641 3045 1858.27272727273 1832 0.000211011087204744 388 0.955915852363835 -0.977831231585202 -1 3.05048474183096 3041 925 2240 1451 535 2438 4197 388 1832 2375 1019 1661 M10500 XU_HGF_TARGETS_REPRESSED_BY_AKT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_REPRESSED_BY_AKT1_UP.html Genes up-regulated in DU-145 cells (prostate cancer) in the presence but not in the absence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 9/12 Arthur Liberzon 0.0295630497180348 0.0520080487026181 1385 1957.72727272727 1833 0.00299638631730564 86 1.29307158317719 1.06147089099777 1 2.49107660824216 1383 2668 4381 1476 2536 1833 2623 941 86 2755 853 1662 M636 REACTOME_HS_GAG_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HS_GAG_DEGRADATION.html Genes involved in HS-GAG degradation 19/21 Reactome 0.000914826816222615 0.0037064228090736 3165 1909.90909090909 1836 8.32006773278659e-05 91 0.913496621595464 -0.96683779943097 -1 3.33217626267757 4304 356 1836 91 387 1142 3165 2586 1019 3165 2958 1663 M13327 VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_DN.html Genes down-regulated in uterine fibroids with deletions in the 7q region vs those without the deletion. 15940248 53/68 Leona Saunders 0.0684379675331422 0.104981217665398 1840 2091.36363636364 1836 0.00642404944993588 1132 1.28043535391107 1.39429762455688 1 1.88065098953319 1836 3326 2487 3384 1647 1402 1189 2765 1132 2290 1547 1664 M2572 ANASTASSIOU_CANCER_MESENCHYMAL_TRANSITION_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/ANASTASSIOU_CANCER_MESENCHYMAL_TRANSITION_SIGNATURE.html Genes in the 'mesenchymal transition signature' common to all invasive cancer types. 22208948 105/125 Dimitris Anastassiou 7.52127177814716e-16 4.55133369139161e-14 25 1720.36363636364 1836 6.83751979831558e-17 23 1.59393993323019 1.57964948139366 1 31.9101423391014 23 2820 56 2214 2204 1836 1274 2255 4145 324 1773 1665 M1247 CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/CEBALLOS_TARGETS_OF_TP53_AND_MYC_UP.html Genes up-regulated in K562 cells (chronic myelogenous leukemia, CML) expressing TP53 and MYC [GeneID=7157;4609]. 15856024 42/43 Arthur Liberzon 0.0506822032690913 0.0816450510000379 1625 2285.09090909091 1837 0.00471717185542877 826 1.04368216677237 1.03660803632158 1 1.70388385685907 1622 3794 2730 4109 1837 1324 826 1114 4279 2639 862 1666 M3923 YU_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YU_MYC_TARGETS_DN.html Genes down-regulated in B cell lymphoma tumors expressing an activated form of MYC [GeneID=4609]. 16382050 69/100 Kevin Vogelsang 0.136503978081221 0.18713295862427 2565 2176 1837 0.0132537478040962 954 1.05696108606341 -1.12723767798987 -1 1.15425750539058 2565 1351 1254 954 2437 2112 3860 1837 4171 1754 1641 1667 M15837 CHANG_IMMORTALIZED_BY_HPV31_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_IMMORTALIZED_BY_HPV31_UP.html Genes up-regulated in normal keratinocytes immortalized by infection with the high risk HPV31 (human papilloma virus) strain. 10756030 85/128 John Newman 0.0224831277755199 0.0416484941524544 1685 1989.27272727273 1837 0.00206511259509428 810 1.10950177497897 1.17504079649973 1 2.29802622161787 1682 1857 2752 1837 3882 1935 1569 810 891 3482 1185 1668 M15315 BERNARD_PPAPDC1B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERNARD_PPAPDC1B_TARGETS_UP.html Genes up-regulated in ZR-75-1 cells (breast cancer, amplified 8p11-12 region) upon knockdown of PPAPDC1B [GeneID=84513] by RNAi. 18757432 54/63 Jessica Robertson 0.0073237281196191 0.0170790497651196 2165 1989.45454545455 1837 0.000668020255123595 153 1.04787766141894 -1.09391955341207 -1 2.77910012447839 2161 809 3155 1580 1355 1837 2590 1349 3595 3300 153 1669 M11303 SABATES_COLORECTAL_ADENOMA_SIZE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_SIZE_DN.html A selection of genes whose expression displayed significant negative correlation with size of colorectal adenoma. 18171984 12/21 Leona Saunders 0.00117477303879697 0.00448332685672388 1950 2188.72727272727 1839 0.000106854620233933 422 1.33601883427185 1.52756781843404 1 4.70778503101214 1946 1042 1622 1463 422 3426 2733 4283 3653 1839 1647 1670 M2380 IKEDA_MIR30_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR30_TARGETS_DN.html Genes down-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-30 microRNA. 19188439 43/48 Arthur Liberzon 0.0939547428518291 0.136999192542673 1840 1724.54545454545 1839 0.00892953111628664 575 1.13136792522865 1.04487628155741 1 1.46543645326071 1839 835 1759 2261 1970 2359 1219 1392 575 2363 2398 1671 M1926 REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_7ALPHA_HYDROXYCHOLESTEROL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_7ALPHA_HYDROXYCHOLESTEROL.html Genes involved in Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol 13/28 Reactome 0.000636656108544727 0.00277984905858567 1355 2115.72727272727 1840 5.78945840534202e-05 241 1.33706301595538 -1.33706301595538 -1 5.12792856443627 1354 3900 1574 3285 335 1840 1977 241 4422 3213 1132 1672 M18615 KEGG_ALLOGRAFT_REJECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALLOGRAFT_REJECTION.html Allograft rejection 29/70 KEGG 0.0119234727749773 0.0250461911428095 880 2024.81818181818 1841 0.00108987179680133 880 1.23017053783499 -1.09358580675115 -1 2.95564980823011 880 3422 1841 1600 978 956 2376 3222 2925 2525 1548 1673 M11536 XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_SIGNALING_NOT_VIA_AKT1_48HR_DN.html Genes down-regulated in DU-145 cells (prostate cancer) in the absence and presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 31/57 Arthur Liberzon 0.0306920217928686 0.0536144866255884 4295 2229.45454545455 1841 0.00282988708312285 214 1.79648367547969 -1.91245059212923 -1 3.42531720341603 4294 902 991 1305 1841 4666 4587 2237 214 751 2736 1674 M3115 KEGG_LONG_TERM_POTENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_POTENTIATION.html Long-term potentiation 65/89 KEGG 0.0678481258318307 0.104245818335365 1845 2465.45454545455 1844 0.00636687432543065 816 0.791047357612282 0.827866578859079 1 1.16544131585135 1843 1358 3374 1389 4026 1424 816 4251 2750 4045 1844 1675 M14507 CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN.html Genes down-regulated in luminal-like breast cancer cell lines compared to the basal-like ones. 16288205 644/782 Arthur Liberzon 6.85457713630153e-10 1.90315318137313e-08 1305 1954.45454545455 1844 6.85457713841586e-11 81 1.18173763224064 1.16666473055833 1 13.6900937153162 1305 1126 4293 1190 2133 1844 2156 1782 2771 81 2818 1676 M2081 KARLSSON_TGFB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KARLSSON_TGFB1_TARGETS_DN.html Genes down-regulated by TGFB1 [GeneID=7040] in MEF cells (embryonic fibroblast) via TGFB1R [GeneID=7046]. 15769904 307/385 Arthur Liberzon 0.00577426225782821 0.0142024584976285 3435 2043.54545454545 1844 0.000526315789473684 163 1.04492017943226 -0.980236719645603 -1 2.89684718363044 3431 535 2338 163 1844 975 3915 4673 1004 2265 1336 1677 M2582 DURAND_STROMA_NS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DURAND_STROMA_NS_UP.html Genes up-regulated in the HSC non-supportive stromal cell lines. 212/268 Charles Durand 1.51447426996767e-06 1.99117508474858e-05 3220 1802.09090909091 1844 1.37679573866256e-07 212 1.22165546697815 1.14609502901715 1 8.61718382067138 3218 1214 297 665 725 2333 2475 2170 1844 212 4670 1678 M18134 COLDREN_GEFITINIB_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/COLDREN_GEFITINIB_RESISTANCE_UP.html Genes up-regulated in NSCLC (non-small cell lung carcinoma) cell lines resistant to gefitinib [PubChem=123631] compared to the sensitive ones. 16877703 105/123 Arthur Liberzon 0.00577426225782821 0.0142024584976285 1755 1852.90909090909 1845 0.000526315789473684 156 1.2311915052682 -1.29430904707095 -1 3.41326871412331 1754 1825 1845 156 1981 3329 2753 2314 1200 1211 2014 1679 M1979 KEGG_GNRH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GNRH_SIGNALING_PATHWAY.html GnRH signaling pathway 90/116 KEGG 0.0319936637811467 0.055436891720636 1850 1918.72727272727 1846 0.00295169389184102 536 0.890810108824505 0.966498843140856 1 1.67903114382987 1846 706 2888 646 4544 1245 536 1448 2360 2964 1923 1680 M19612 LEE_LIVER_CANCER_ACOX1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_ACOX1_UP.html Genes up-regulated in hepatocellular carcinoma of ACOX1 [GeneID=51] knockout mice. 15565109 86/148 Yujin Hoshida 1.10960297686373e-06 1.5313818861979e-05 925 1815 1846 1.00873048773547e-07 284 1.33773431468753 1.23053223930038 1 9.66486250190614 923 1324 284 1519 2674 2068 1846 3027 2586 537 3177 1681 M4835 BIOCARTA_BCELLSURVIVAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCELLSURVIVAL_PATHWAY.html B Cell Survival Pathway 26/27 BioCarta 0.259514206361011 0.322343961585255 3990 2147.09090909091 1847 0.0269438886143312 296 1.14485353616057 0.921876522617877 1 0.844540091711634 3990 941 2595 1133 3654 1819 1488 3537 296 1847 2318 1682 M13642 REACTOME_PEPTIDE_CHAIN_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEPTIDE_CHAIN_ELONGATION.html Genes involved in Peptide chain elongation 99/185 Reactome 0.0189983815067827 0.036348747755174 200 2578.45454545455 1847 0.00174222325291916 197 0.634486088572088 0.584363444785452 1 1.37039330090755 197 4429 4148 4703 1135 632 417 1847 4683 4436 1736 1683 M12802 SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS http://www.broadinstitute.org/gsea/msigdb/cards/SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS.html Genes from the recurrent amplicons in 89 samples of oral squamous cell carcinoma (SCC). 15824737 54/61 Leona Saunders 0.00577426225782821 0.0142024584976285 3330 2223.36363636364 1847 0.000526315789473684 145 1.09510753518396 -1.01829133637628 -1 3.03598739188507 3328 145 1847 181 4379 3738 3868 3237 570 1508 1656 1684 M2123 HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HIRSCH_CELLULAR_TRANSFORMATION_SIGNATURE_UP.html Up-regulated genes in the cancer gene signature, representing a gene signature of cellular transformation. 20385360 326/397 Arthur Liberzon 0.0991666347857643 0.143139607397189 1630 1972 1847 0.00944916276576963 976 1.07980857423316 1.08999304046299 1 1.36779495117927 1629 1169 1509 1439 3218 2804 2948 2181 1972 976 1847 1685 M232 PID_ECADHERIN_STABILIZATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ECADHERIN_STABILIZATION_PATHWAY.html Stabilization and expansion of the E-cadherin adherens junction 18832364 70/82 Pathway Interaction Database 0.214693788635445 0.274919881269479 1740 1876.72727272727 1848 0.0217314452923679 409 1.05328656148529 0.909060311356888 1 0.886216307439612 1737 745 2399 409 2861 2498 1818 1848 932 2333 3064 1686 M16932 CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_DN.html Top 200 marker genes down-regulated in the 'proliferation' subclass of hepatocellular carcinoma (HCC); characterized by increased proliferation, high levels of serum AFP [GeneID=174], and chromosomal instability. 18701503 146/313 Yujin Hoshida 4.71092535813486e-06 5.35796811816784e-05 4590 2244.81818181818 1848 4.28266858709957e-07 259 1.33268750142754 -1.3373431616223 -1 8.54071658433114 4587 611 336 259 657 3349 4612 4500 1848 362 3572 1687 M8451 SENESE_HDAC3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC3_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC3 [GeneID=8841] by RNAi. 17470557 696/930 Leona Saunders 1.83796403298724e-05 0.000171785945261382 795 1755.63636363636 1849 1.83797923466724e-06 238 1.13484038961195 1.14603401255817 1 6.41114842337184 794 480 4308 278 3361 2026 1849 1930 1662 238 2386 1688 M18090 NUYTTEN_NIPP1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_NIPP1_TARGETS_DN.html Genes down-regulated in PC3 cells (prostate cancer) after knockdown of NIPP1 [GeneID=5511] by RNAi. 17724462 1112/1300 Jessica Robertson 0.095437595097977 0.138604753496139 3980 2224.63636363636 1849 0.00998026159712843 272 1.06335900891601 -1.04732694627896 -1 1.36926573003256 3976 464 4429 272 1849 1964 3987 3294 1422 999 1815 1689 M11816 KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY.html Fc epsilon RI signaling pathway 65/94 KEGG 0.00577426225782821 0.0142024584976285 2655 1923.63636363636 1851 0.000526315789473684 126 0.86315114767073 0.798685470039643 1 2.3929078834873 2654 126 2868 203 1836 2523 1294 1695 1851 2637 3473 1690 M12212 WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ESOPHAGUS_CANCER_VS_NORMAL_DN.html Down-regulated genes specific to esophageal adenocarcinoma (EAC) relative to normal tissue. 16449976 140/168 Arthur Liberzon 0.045979627821689 0.0749498995504783 1855 2142.18181818182 1852 0.00426997157131731 361 1.24433376914818 -1.37616371083718 -1 2.1008629132823 3916 622 1496 361 2348 1851 3393 4608 1852 819 2298 1691 M1914 ZHANG_TLX_TARGETS_60HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_60HR_UP.html Genes up-regulated in neural stem cells (NSC) at 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 395/528 Jessica Robertson 1.91347610705492e-12 7.71932241478564e-11 2180 1728.81818181818 1853 1.7395237336878e-13 62 1.24365009887717 1.26374887990119 1 18.8709044490095 2177 518 91 216 2456 4546 3543 1853 745 62 2810 1692 M10619 KAAB_FAILED_HEART_ATRIUM_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_FAILED_HEART_ATRIUM_DN.html Genes down-regulated in atria of failing hearts (DCM and ICM) compared to healthy controls. 15103417 216/274 John Newman 0.0859806375420094 0.127139288595954 2245 2060.72727272727 1854 0.00813973903827007 562 0.939378476805611 -0.894582801349836 -1 1.26246221685113 2241 562 2841 851 3770 692 1854 1682 2911 3516 1748 1693 M11720 BEIER_GLIOMA_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BEIER_GLIOMA_STEM_CELL_DN.html Genes down-regulated in cancer stem cells derived from glyoblastoma tumors: CD133+ [GeneID=8842] vs. CD133- cells. 17483311 82/103 Jessica Robertson 0.00283271903022846 0.00867083905491461 4180 2183.72727272727 1854 0.000257852093321776 47 1.12423343129559 -1.15236104032771 -1 3.47825066895028 4179 718 1691 47 584 4184 3154 3791 1336 1854 2483 1694 M2588 SMIRNOV_RESPONSE_TO_IR_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_6HR_UP.html Genes up-regulated in B lymphocytes at 6 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 223/276 Itai Pashtan 0.0189912141101912 0.036348747755174 1395 2159.81818181818 1854 0.00174156021206838 735 1.02140471405614 1.07215960264993 1 2.20614312839713 1391 3626 2222 4187 1854 1036 1541 735 3183 2334 1649 1695 M2334 BILANGES_SERUM_SENSITIVE_VIA_TSC2 http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_SENSITIVE_VIA_TSC2.html Genes translationally up-regulated by serum in MEF cells (embryonic fibroblast) lacking TSC2 [GeneID=7249]. 17562867 74/98 Arthur Liberzon 0.0399716255495207 0.0666900221257468 720 1884.90909090909 1855 0.00370153583993721 719 1.23112149042259 1.1395344350709 1 2.17223300567986 719 2402 1034 1932 1855 1476 2459 1597 3704 1974 1582 1696 M623 REACTOME_NGF_SIGNALLING_VIA_TRKA_FROM_THE_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NGF_SIGNALLING_VIA_TRKA_FROM_THE_PLASMA_MEMBRANE.html Genes involved in NGF signalling via TRKA from the plasma membrane 156/169 Reactome 0.217735029630064 0.277684231249365 1605 2289.90909090909 1857 0.022076464218397 606 0.853495657741259 0.828096917730666 1 0.712531095204898 1602 606 3747 1398 4597 1708 1379 2258 1857 3637 2400 1697 M1755 SANSOM_APC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS.html Genes up-regulated after Cre-lox knockout of APC [GeneID=324] in the small intestine. 17377531 275/346 Arthur Liberzon 0.0379173739329107 0.0637357567533256 1600 2011.81818181818 1857 0.00350791847460334 1002 1.10312513206515 1.08044618893446 1 1.97895259773712 1599 2257 2397 1840 3056 1857 1413 1002 1528 2484 2697 1698 M8916 TIEN_INTESTINE_PROBIOTICS_2HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_2HR_DN.html Genes down-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 2h. 16394013 124/139 Arthur Liberzon 0.0203388692622038 0.0383537606542557 595 1968.45454545455 1860 0.00186630646896022 591 0.935773737555863 0.959240437377324 1 1.98843637228758 591 3220 3647 2440 1860 1390 1156 764 651 4021 1913 1699 M938 REACTOME_CIRCADIAN_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CIRCADIAN_CLOCK.html Genes involved in Circadian Clock 61/72 Reactome 0.0330084255125136 0.0567576569832656 1015 1987 1863 0.00304675796663962 542 0.909108629075993 1.00518952611181 1 1.69957394228372 1013 1907 3519 1788 3506 1065 542 1399 1925 3330 1863 1700 M17730 GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_DIVIDING_UP.html Genes up-regulated in quescent CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloblastic leukemia) patients compared to the dividing cells from normal donors. 17717066 80/146 Arthur Liberzon 3.6137207069002e-07 5.76241950559762e-06 1955 1731.27272727273 1863 3.28520118226384e-08 148 1.39985827663827 1.11159639912186 1 11.0053245229375 1955 1863 246 3149 148 1481 2038 1324 3582 267 2991 1701 M7735 BOYLAN_MULTIPLE_MYELOMA_C_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_DN.html Genes down-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 78/102 Jessica Robertson 1.65414127763918e-07 2.87042162884446e-06 1925 1423.27272727273 1863 1.50376491091924e-08 59 1.2969326016697 1.37592625441804 1 10.7851386209513 1923 59 226 214 3485 2674 1863 1873 266 162 2911 1702 M11403 KANNAN_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANNAN_TP53_TARGETS_DN.html Primary down-regulated targets of TP53 [GeneID=7157] in the H1299 (lung cancer) cell line. 11402317 31/37 Broad Institute 0.138840245274006 0.189674662139887 3755 2196.63636363636 1864 0.0134967497007287 279 1.15626332720189 -1.11205061203541 -1 1.25254535196155 3753 279 1516 1211 4035 2488 2536 1588 845 1864 4048 1703 M2069 BILD_MYC_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_MYC_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing c-Myc [GeneID=4609] from control cells expressing GFP. 16273092 275/338 Arthur Liberzon 0.107498442068352 0.153152021298708 2420 1984 1864 0.0102855580909022 1116 1.02332071161537 -1.03959711122449 -1 1.25114902485101 2420 1188 1857 1116 1864 2002 2349 1493 2628 1782 3125 1704 M3911 GEISS_RESPONSE_TO_DSRNA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GEISS_RESPONSE_TO_DSRNA_UP.html Genes up-pregulated by dsRNA in GRE cells (glioma; no interferon system). 11487589 48/55 John Newman 0.0950431157949022 0.138201942868743 3930 2250.09090909091 1865 0.00903781827135334 982 1.19948327313532 1.3148030130183 1 1.54683868511623 3929 1417 1183 1751 1865 2594 2711 3637 982 1432 3250 1705 M16864 REACTOME_METABOLISM_OF_CARBOHYDRATES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_CARBOHYDRATES.html Genes involved in Metabolism of carbohydrates 218/287 Reactome 0.0488294208246556 0.0790651342340908 2765 2466.63636363636 1866 0.00454073810764034 327 1.12209799183581 -1.05432875553387 -1 1.85539047972037 2762 565 1474 327 1513 4408 4322 4334 1432 1866 4130 1706 M2733 NOJIMA_SFRP2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NOJIMA_SFRP2_TARGETS_DN.html Cellular proliferation, growth, apoptosis and Wnt signaling genes down-regulated in SNU638 cells (gastric cancer) by overexpression of SFRP2 [GeneID=6423] off a plasmid vector. 17297461 33/40 Arthur Liberzon 0.18007085514369 0.23655286286619 3665 2067.18181818182 1866 0.0178869451406537 478 1.23006375445332 -1.06619408379576 -1 1.15545700932706 3661 888 1866 1353 3127 2310 2083 1744 478 1374 3855 1707 M1337 RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_DN http://www.broadinstitute.org/gsea/msigdb/cards/RANKIN_ANGIOGENIC_TARGETS_OF_VHL_HIF2A_DN.html Angiogenic genes down-regulated in hepatocytes after knockout of VHL and HIF2A [GeneID=7428;2034]. 18490920 18/22 Jessica Robertson 0.0581334387764242 0.0915242932037099 2500 1763.18181818182 1866 0.00542990169997561 747 1.23152669499841 -1.23734364060924 -1 1.91890278393938 2497 1006 1573 1893 2833 818 747 1866 2175 2536 1451 1708 M17 PID_NOTCH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NOTCH_PATHWAY.html Notch signaling pathway 18832364 77/87 Pathway Interaction Database 0.00916780501472207 0.0204209720007023 1940 1969.36363636364 1867 0.000836930302430876 877 1.0861503013814 1.04428061973523 1 2.7541152895235 1938 1867 2186 1060 877 1612 1554 4041 2543 1650 2335 1709 M16842 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_CDC25_DN.html Genes down-regulated in reverted NIH3T3 cells (fibroblasts transformed by activated KRAS [GeneID=3845] which then reverted to normal cells upon stable over-expression of a dominant negative form of CDC25 [GeneID=5923]) vs normal fibroblasts. 16607279 223/271 Lauren Kazmierski 5.6458154847506e-05 0.000419657465953116 3825 2253.72727272727 1867 5.13269125216066e-06 153 1.18275452533779 -1.14109767731063 -1 5.99340088996484 3823 560 452 153 1277 3535 4143 4628 1867 318 4035 1710 M16530 ZHAN_MULTIPLE_MYELOMA_CD1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_DN.html Top 50 down-regulated genes in cluster CD-1 of multiple myeloma samples with the characteristic expression spike of CCND1 [GeneID=595]. 16728703 66/101 Kevin Vogelsang 0.00577426225782821 0.0142024584976285 2920 1835.09090909091 1867 0.000526315789473684 77 1.02182765825866 -0.884831252330981 -1 2.83282511757226 2919 108 1683 77 4419 1913 1784 1867 971 2396 2049 1711 M1375 LASTOWSKA_COAMPLIFIED_WITH_MYCN http://www.broadinstitute.org/gsea/msigdb/cards/LASTOWSKA_COAMPLIFIED_WITH_MYCN.html Genes co-amplified within MYCN [GeneID=4613] in primary neuroblastoma tumors. 17533364 43/50 Leona Saunders 0.0576888250312568 0.0909456426678463 3970 2256.63636363636 1868 0.00538722969489181 658 1.39042655216054 -1.42433579837662 -1 2.17225304245372 3970 840 1868 1217 1578 2575 3092 3909 658 1414 3702 1712 M18513 ZHAN_MULTIPLE_MYELOMA_CD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD2_UP.html Top 50 up-regulated genes in cluster CD-2 of multiple myeloma samples with the characteristic expression spike of CCND3 [GeneID=896]. 16728703 49/60 Kevin Vogelsang 0.00595073194098869 0.01452298591596 1465 1956.54545454545 1868 0.000542444469424719 752 1.18455914613163 1.27890056472189 1 3.2667566538437 1462 1420 2057 2847 752 1579 2413 1855 3220 2049 1868 1713 M6416 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_UP.html Genes up-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 19/24 John Newman 0.00787635880026385 0.0180205591552329 1870 2483.90909090909 1869 0.000718609054730831 599 0.533767969346388 -0.541302462582252 -1 1.39690091314336 1869 3871 3687 3624 834 1475 1016 599 4702 4681 965 1714 M13569 ZHAN_MULTIPLE_MYELOMA_LB_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_LB_DN.html Top 50 down-regulated genes in cluster LB of multiple myeloma samples belonging to the low bone disease group. 16728703 49/56 Arthur Liberzon 0.00263419640647536 0.00821771780473478 3360 2070.18181818182 1869 0.000239759617320708 171 1.00908809696197 -0.936081846352856 -1 3.15728808028735 3359 171 1869 1427 567 3662 3609 1699 1725 2050 2634 1715 M6822 ONDER_CDH1_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_1_DN.html Genes down-regulated in HMLE cells (mmortalized nontransformed mammary epithelial) by expression of a dominant-negative form of E-cadhedrin (CDH1) [GeneID=999]. 18483246 212/280 Jessica Robertson 0.0205492103242076 0.0386731549961164 570 1855.72727272727 1870 0.00188579084957062 568 1.31490732814301 1.08608640208578 1 2.78699835704746 568 3631 928 3388 2218 891 821 2222 3175 701 1870 1716 M1546 APPIERTO_RESPONSE_TO_FENRETINIDE_UP http://www.broadinstitute.org/gsea/msigdb/cards/APPIERTO_RESPONSE_TO_FENRETINIDE_UP.html Genes up-regulated in A2780 cells (ovarian carcinoma) exposed to fenretinide [PubChem=1744]. 17213814 56/71 Arthur Liberzon 0.0550823098714866 0.0874498831461207 1875 2243.90909090909 1871 0.00513743579263166 615 1.18687195912548 1.07269103541484 1 1.88454181450634 1871 1923 1325 1339 4318 637 1495 4671 4339 2150 615 1717 M961 REACTOME_TRANSPORT_TO_THE_GOLGI_AND_SUBSEQUENT_MODIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_TO_THE_GOLGI_AND_SUBSEQUENT_MODIFICATION.html Genes involved in Transport to the Golgi and subsequent modification 36/38 Reactome 0.0769961173791334 0.115628913149701 3475 2562.90909090909 1872 0.00725734084346075 317 1.25617506344769 -1.39487869276197 -1 1.76593512330144 3472 869 1645 673 1708 4473 4624 4126 317 1872 4413 1718 M6145 LEE_LIVER_CANCER_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_SURVIVAL_UP.html Genes highly expressed in hepatocellular carcinoma with good survival. 15349906 170/349 Yujin Hoshida 0.000248589564810655 0.00138202914712166 3010 1873.72727272727 1872 2.26016053360653e-05 238 1.1868919492061 -1.17023746821443 -1 5.09250489945221 3006 586 532 238 1872 2681 2968 2847 1444 652 3785 1719 M17866 KYNG_DNA_DAMAGE_BY_UV http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_UV.html UV only responding genes in primary fibroblasts from young donors. 15897889 77/99 Jessica Robertson 0.0738981244975473 0.111794598598854 1080 2144.45454545455 1873 0.00695488692563208 842 1.01564447449712 0.954718294929 1 1.45009600411718 1079 1873 1764 3284 3865 1082 842 2363 4130 2134 1173 1720 M8910 LY_AGING_OLD_UP http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_OLD_UP.html Genes up-regulated in fibroblasts from old individuals, compared to those from young donors. 10741968 9/11 Arthur Liberzon 0.00280551954049186 0.00860432243737594 1055 2450.27272727273 1874 0.000280906776966371 400 1.30479928801954 1.30479928801954 1 4.0434659582179 1055 4270 4650 4246 593 1874 1407 400 4627 2767 1064 1721 M1493 NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON.html Genes within amplicon 11q12-q14 identified in a copy number alterations study of 191 breast tumor samples. 19010930 157/230 Jessica Robertson 0.0373945839254565 0.062991590338385 2265 1793.09090909091 1875 0.00345870445622485 415 1.0081703642402 -0.926417468017395 -1 1.81631531858387 2261 596 2333 472 4468 415 1780 2562 1875 2397 565 1722 M3941 HASLINGER_B_CLL_WITH_13Q14_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_13Q14_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 13q14 region. 15459216 36/43 Kevin Vogelsang 0.00926672489119504 0.0205443595521093 1380 2040.81818181818 1875 0.000845999040388974 283 1.42937104576787 1.5791384110171 1 3.61883096726206 1378 3384 1783 1884 4530 2851 2951 521 283 1875 1009 1723 M10605 BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN.html Genes down-regulated in medullary breast cancer (MBC) relative to ductal breast cancer (DBD). 16651414 229/309 Arthur Liberzon 1.64935015488619e-09 4.20807174652044e-08 2145 1529.45454545455 1876 1.49940923283883e-10 144 1.28367916038351 1.39970180357649 1 14.2072844967574 2141 556 149 247 3369 2752 3320 382 1876 144 1888 1724 M10765 BIOCARTA_TCRA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCRA_PATHWAY.html Lck and Fyn tyrosine kinases in initiation of TCR Activation 10/20 BioCarta 0.0019183466817109 0.00646756881262531 1105 2289.72727272727 1877 0.000174547407128819 214 1.0072988071463 1.0072988071463 1 3.30889792884789 1104 3564 1811 4037 2538 1361 325 214 4704 3652 1877 1725 M1368 SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_UP.html Predicted targets of SOX9 [GeneID=6662] that are up-regulated during early prostate development. 18794802 24/29 Jessica Robertson 0.0135446534634645 0.0278080749663124 1665 2032.45454545455 1877 0.00123897901989709 656 1.2715838692851 1.23498068435371 1 2.96847379107157 1663 3455 1936 3338 1017 1877 1126 2854 656 1700 2735 1726 M12139 GALE_APL_WITH_FLT3_MUTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/GALE_APL_WITH_FLT3_MUTATED_DN.html Genes down-regulated in acute promyelocytic leukemia (APL) patients with mutated FLT3 [GeneID=2322]. 16105978 34/50 Kevin Vogelsang 0.00466567904227237 0.0126128322334053 650 2166.45454545455 1878 0.000425054847371394 74 0.714556569211137 -0.663057902423464 -1 2.03621517445893 649 3403 3690 3654 1878 74 230 1296 4585 3928 444 1727 M8108 FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by selective estrogen receptor modulators (SERM) 4-hydroxytamoxifen, raloxifene, or ICI 182780 but not by estradiol [PubChem=44959;5035;3478439;5757]. 14973112 25/33 Arthur Liberzon 0.00577426225782821 0.0142024584976285 1915 1716.27272727273 1878 0.000526315789473684 186 1.05186353790672 0.952541750089463 1 2.91609705901544 1915 342 3238 186 1774 2340 1473 2152 443 3138 1878 1728 M11778 BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_DN.html Genes down-regulated in B lymphocytes from patients with primary immunodefiency syndrom. 17195838 74/103 Jessica Robertson 0.0201306646096507 0.0380219035444384 1515 2036.27272727273 1879 0.0018470237339462 761 1.02081008246166 1.03649785247645 1 2.17492165546976 1514 1879 1770 2141 4416 1901 1125 761 3282 2250 1360 1729 M16003 LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_OVERALL_DN.html Top genes associated with unfavorable overall survival of mesothelioma patients after surgery. 16540645 37/40 Arthur Liberzon 0.0708344196905708 0.107781579928915 690 2192 1879 0.00665668374270184 687 1.0600892441587 1.04178409739982 1 1.53881123159482 687 2961 1245 3440 1666 1879 852 2681 4021 3097 1583 1730 M2327 BILANGES_SERUM_SENSITIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_SENSITIVE_GENES.html Genes translationally regulated in MEF cells (embryonic fibroblasts) in response to serum starvation but not by rapamycin (sirolimus) [PubChem=6610346]. 17562867 101/137 Arthur Liberzon 0.229329494034811 0.28988623777298 1700 1903.45454545455 1879 0.0234031033796197 38 1.07424010357352 1.21804182995343 1 0.866739635751442 1698 38 1879 355 2318 2660 1793 3563 1652 2231 2751 1731 M17175 MURAKAMI_UV_RESPONSE_24HR http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_24HR.html Genes down-regulated in primary keratinocytes at 24 h after UVB irradiation. 11532376 35/40 John Newman 0.023804103640883 0.0436162147457174 1265 2194.45454545455 1880 0.00218778504988231 951 1.54799734065018 -1.86330222823827 -1 3.15972132594256 1264 1989 951 3496 4194 1167 1956 1880 4407 1812 1023 1732 M6794 BUSA_SAM68_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUSA_SAM68_TARGETS_UP.html Genes up-regulated in LNCaP cells (prostate cancer) after knockdown of SAM68 [GeneID=10657] by RNAi. 17237817 8/10 Arthur Liberzon 2.21224995001872e-05 0.000198136997421031 4015 2216.81818181818 1881 2.21227197355158e-06 57 1.05166064638354 -1.01433011195416 -1 5.84342285664807 4014 442 4346 161 57 4325 4054 1813 405 1881 2887 1733 M1146 CORRADETTI_MTOR_PATHWAY_REGULATORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CORRADETTI_MTOR_PATHWAY_REGULATORS_DN.html Major antagonists linked to the mTOR [GeneID=2475] signaling network. 17041621 11/29 Leona Saunders 0.000143212785307548 0.000882459982573926 2200 1658.45454545455 1881 1.30201917127212e-05 158 0.860396801240639 0.977371055840197 1 3.94313222046572 2199 2137 2689 1881 158 2079 1004 515 258 3725 1598 1734 M19130 BROWNE_HCMV_INFECTION_16HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_16HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 16 h time point that were not down-regulated at the previous time point, 14 h. 11711622 142/194 John Newman 5.77649738365643e-06 6.34071340717636e-05 1885 2067.18181818182 1881 5.25137504631769e-07 346 1.23130762131848 1.24594561151567 1 7.75587131674055 1881 1788 346 2657 639 3680 3146 1733 3603 588 2678 1735 M19053 KYNG_DNA_DAMAGE_BY_4NQO_OR_GAMMA_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_4NQO_OR_GAMMA_RADIATION.html Genes responding to 4NQO treatment and gamma irradiation. 15897889 24/30 Jessica Robertson 0.000514244822841432 0.00236112408931085 1300 1937.09090909091 1881 4.67604605190495e-05 311 0.9259935156019 1.13237206420834 1 3.64987164613151 1299 2062 2499 3826 311 1532 1279 1881 1415 3054 2150 1736 M2468 KRIEG_KDM3A_TARGETS_NOT_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/KRIEG_KDM3A_TARGETS_NOT_HYPOXIA.html Genes not induced under hypoxia, but dependent on KDM3A [GeneID=55818] for hypoxic expression in RCC4 cells (renal carcinoma) expressing VHL [GeneID=7428]. 19858293 255/310 Arthur Liberzon 0.0993116071509098 0.143305039973187 1945 2169.63636363636 1881 0.00946365570983934 755 1.01056281713086 -0.901539899374966 -1 1.27931379629449 1942 1198 3570 1847 1881 755 2442 4580 928 3677 1046 1737 M14385 WANG_CISPLATIN_RESPONSE_AND_XPC_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CISPLATIN_RESPONSE_AND_XPC_DN.html Genes down-regulated in fibroblasts with defective XPC [GeneID=7508] in response to cisplatin [PubChem=2767]. 15107491 312/382 John Newman 0.0307538810570617 0.0536878363518764 1180 2124.36363636364 1882 0.0028356724663096 724 1.05728737378037 1.10196060007745 1 2.01492182346699 1178 3984 2925 3824 2572 724 968 914 1743 2654 1882 1738 M17673 KEGG_CARDIAC_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CARDIAC_MUSCLE_CONTRACTION.html Cardiac muscle contraction 71/118 KEGG 0.00110167990496031 0.00428683359555867 475 1613.27272727273 1883 0.000100202906656798 35 0.995097028790158 -0.982649945112772 -1 3.5355002992146 473 2404 1883 2046 2480 35 50 856 3351 3711 457 1739 M762 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_29 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_29.html Amplification hot spot 29: colocolized fragile sites and cancer genes in the 7p22-p13 region. 16751803 8/11 Arthur Liberzon 0.00567877263827741 0.0142024584976285 2420 1980.36363636364 1883 0.000569333685304524 18 1.21329016236424 1.56143362005908 1 3.36363875170772 2419 1073 4366 801 3712 2668 1810 421 18 1883 2613 1740 M15394 BIOCARTA_AMI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AMI_PATHWAY.html Acute Myocardial Infarction 24/34 BioCarta 5.55848451183856e-06 6.14427327772319e-05 380 1741.63636363636 1884 5.05318050533231e-07 345 1.57733127181184 1.16744125691275 1 9.96781469600748 378 2068 345 1652 902 2422 1884 2596 3258 1035 2618 1741 M10867 OHASHI_AURKB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OHASHI_AURKB_TARGETS.html Candidate substrate proteins of AURKB [GeneID=9212]. 16785988 10/17 Arthur Liberzon 0.212180889092815 0.272219025963057 1885 2190.09090909091 1885 0.0214472802516717 235 2.39920782728752 -2.39920782728752 -1 2.03422127889751 1885 2653 1732 1278 4146 1723 1359 4349 235 2181 2550 1742 M2195 LEE_LIVER_CANCER_CIPROFIBRATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_CIPROFIBRATE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by ciprofibrate [PubChem=2763]. 15565109 72/99 Yujin Hoshida 8.23832904948971e-07 1.17833070041186e-05 985 1824 1885 7.48939284954028e-08 273 1.47933325426432 1.36797070509371 1 10.940543632438 985 1885 273 2098 814 1835 2091 3991 2247 615 3230 1743 M5929 CROONQUIST_STROMAL_STIMULATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_STROMAL_STIMULATION_UP.html Genes up-regulated in ANBL-6 cell line (multiple myeloma, MM) co-cultured with bone marrow stromal cells compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 104/137 Arthur Liberzon 1.99786294026323e-05 0.000182396771335444 540 1986.63636363636 1885 1.81625553043382e-06 395 1.24932797563323 1.21686772686847 1 7.00914734518304 538 3242 395 3690 2401 1740 1402 1885 4050 556 1954 1744 M1106 GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP.html Genes up-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) exposed to doxorubicin [PubChem=31703] in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 816/970 Arthur Liberzon 0.001147315386283 0.00441347076059963 3845 2275.18181818182 1887 0.000114790816673023 10 1.10046145587387 -1.0908504497776 -1 3.88898492795413 3841 476 4339 10 2647 1083 4031 4709 1573 431 1887 1745 M16309 RAY_TARGETS_OF_P210_BCR_ABL_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TARGETS_OF_P210_BCR_ABL_FUSION_UP.html Genes up-regulated in HL-60 cells (acute myeloid leukemia, AML) by expression of p210 BCR-ABL [GeneID=613;25] fusion protein. 15155749 34/54 Arthur Liberzon 0.000129371280022637 0.000813454259672359 3830 2346.45454545455 1887 1.17617171221458e-05 149 1.37301285121938 1.06660798591378 1 6.36532884550198 3828 1457 1503 1887 149 4111 4455 3154 684 706 3877 1746 M9230 LIU_CMYB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CMYB_TARGETS_DN.html Genes down-regulated in MCF-7 cells (breast cancer) by overexpression of CMYB [GeneID=4602] off adenovirus vector. 16205643 9/9 Arthur Liberzon 0.0858470664197103 0.126981558602643 1890 2197 1888 0.00893557811085427 139 1.86145042765479 1.64201307994 1 2.5032753411984 1888 1070 4291 1005 4204 4078 1531 3016 139 2034 911 1747 M2185 PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP http://www.broadinstitute.org/gsea/msigdb/cards/PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP.html Genes up-regulated in ovarian tumors from mouse models for the BMP SMAD signaling (gonad specific double knockout of SMAD1 and SMAD5 [GeneID=4086, 4090]). 17967875 184/227 Arthur Liberzon 6.61816267913891e-05 0.000475460088973146 1640 1876.09090909091 1888 6.01669252616761e-06 461 1.14622214049897 1.10368464742818 1 5.71502313220221 1640 1757 461 1428 2930 2229 2533 1888 2677 582 2512 1748 M1002 REACTOME_RIG_I_MDA5_MEDIATED_INDUCTION_OF_IFN_ALPHA_BETA_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RIG_I_MDA5_MEDIATED_INDUCTION_OF_IFN_ALPHA_BETA_PATHWAYS.html Genes involved in RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways 67/95 Reactome 0.00517668185928815 0.0136961537981166 1760 2286.72727272727 1889 0.00047171846027686 719 1.12226335817757 1.28212463010236 1 3.1378223828662 1426 3711 3165 3622 719 1758 1974 1563 1757 3570 1889 1749 M15798 KEGG_MELANOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MELANOMA.html Melanoma 67/89 KEGG 0.211332020019809 0.271351233540124 2470 2181.54545454545 1890 0.0213514741581528 1129 1.07497711590794 -1.02703393633997 -1 0.913621390743629 2466 1890 1467 1129 4334 1881 1352 3399 2314 1425 2340 1750 M8570 DOANE_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_ESR1_DN.html Genes down-regulated in breast cancer samples positive for ESR1 [GeneID=2099] compared to the ESR1 negative tumors. 16491124 54/77 Arthur Liberzon 3.36976987203752e-11 1.11225970601518e-09 3170 1986.72727272727 1890 3.06342715644467e-12 109 1.91537001278842 1.74654989206887 1 25.73355546937 3169 774 113 667 1775 2372 2350 4595 1890 109 4040 1751 M5672 SU_KIDNEY http://www.broadinstitute.org/gsea/msigdb/cards/SU_KIDNEY.html Genes up-regulated specifically in human kidney tissue. 11904358 11/32 John Newman 0.000415178838534369 0.00200500415506367 2100 1963.90909090909 1890 3.77506555288932e-05 282 1.62056915748541 -1.73682380930011 -1 6.56033112880545 2100 2643 1761 1521 282 2856 2480 1229 3604 1237 1890 1752 M1551 ULE_SPLICING_VIA_NOVA2 http://www.broadinstitute.org/gsea/msigdb/cards/ULE_SPLICING_VIA_NOVA2.html Genes whose splicing in neocortex was most affected by knock out of NOVA2 [GeneID=4858]. 16041372 78/102 John Newman 0.101161571323258 0.145618364332351 1405 2004.90909090909 1892 0.00964878378466232 1405 1.03108791281015 1.12189183810982 1 1.2945394588896 1405 1868 2168 1892 2944 1632 1757 1435 2500 2163 2290 1753 M18567 ZHAN_MULTIPLE_MYELOMA_MS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_MS_DN.html Top 50 down-regulated genes in cluster MS of multiple myeloma samples with characteristic expression spike of WHSC1 [GeneID=7468]. 16728703 64/96 Kevin Vogelsang 0.019269894303742 0.0367045605785561 1805 2005.90909090909 1892 0.00176734357707696 133 0.891764345713303 0.832105333457571 1 1.92045708101743 1804 133 3247 1792 2416 2896 2208 741 1892 3444 1492 1754 M2285 CHENG_TAF7L_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CHENG_TAF7L_TARGETS.html Genes down-regulated in testis tissues upon knockout of TAF7L [GeneID=54457]. 17242199 8/8 Arthur Liberzon 0.000415227395869406 0.00200500415506367 4370 2511.72727272727 1892 4.15305002484591e-05 243 1.40599511736982 -0.952323096694673 -1 5.69168602583083 4370 1076 4679 937 294 4494 4470 1318 243 1892 3856 1755 M92 PID_ANGIOPOIETIN_RECEPTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ANGIOPOIETIN_RECEPTOR_PATHWAY.html Angiopoietin receptor Tie2-mediated signaling 18832364 72/84 Pathway Interaction Database 0.13817250339971 0.18887176833091 1490 1888 1894 0.0134272348328684 99 1.03203642008596 1.03324663737528 1 1.12081563032086 1487 99 1704 886 3733 2516 2053 1585 2011 1894 2800 1756 M11771 DOANE_BREAST_CANCER_CLASSES_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_BREAST_CANCER_CLASSES_DN.html Genes down-regulated in ER(-) / PR(-) breast tumors (do not express ESR1 and PGR [GeneID=2099;5241]) with molecular similarity to ER(+) (class A) relative to the rest of the ER(-) / PR(-) samples (class B). 16491124 51/53 Arthur Liberzon 0.172716346237296 0.227906389220027 1570 2015.90909090909 1894 0.0170893510261371 1286 1.32109033846246 1.27327707106842 1 1.2730279539128 2058 1412 1568 1286 3467 2177 2859 1719 1894 2168 1567 1757 M1489 FIRESTEIN_CTNNB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/FIRESTEIN_CTNNB1_PATHWAY.html Genes required for CTNNB1 [GeneID=1499] activity in DLD-1 cell (colon cancer with APC [GeneID=324] deletions), based on shRNA screen. 18794900 62/72 Jessica Robertson 0.188855186229631 0.2461061510226 1435 1941.72727272727 1895 0.0188481709426125 459 0.995308956217364 1.02060326147951 1 0.909241235859608 1433 1371 3079 613 3953 2105 1288 1895 459 2780 2383 1758 M5827 GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_UP.html Genes up-regulated in non-metastatic breast cancer tumors having type 1 amplification in the 20q13 region; involves ZNF217 [GeneID=7764] locus only. 16899599 96/109 Leona Saunders 0.0609720357851869 0.0951365318697792 1720 2219.81818181818 1896 0.0057027697917703 694 0.807230472636407 0.753430431248721 1 1.23738684693106 1719 694 3900 1109 1598 2188 1896 3513 1245 3931 2625 1759 M10394 FARMER_BREAST_CANCER_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_7.html Cluster 7: selected apocrine and luminal genes clustered together across breast cancer samples. 15897907 29/31 Leona Saunders 0.0159978161798886 0.0318471920578129 4285 1849 1896 0.00146503148326135 664 1.17715294603526 -1.29120176595754 -1 2.64398190707448 4281 2008 1896 983 2044 3040 2497 664 687 1082 1157 1760 M13968 BIOCARTA_HIVNEF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HIVNEF_PATHWAY.html HIV-I Nef: negative effector of Fas and TNF 75/87 BioCarta 0.337646202093891 0.403772504150789 1900 2096.27272727273 1897 0.0367578966602208 741 1.00804665537675 1.04945526115493 1 0.595649467471772 1897 741 2685 872 4226 2663 1794 2504 1125 1346 3206 1761 M1245 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_2_UP.html Genes up-regulated in Wilm's tumor vs fetal kidney. 15531917 35/44 Arthur Liberzon 0.00331842527624848 0.00980425330377675 1650 2207.72727272727 1897 0.000302131027460028 291 1.42469728221124 1.53227800974231 1 4.29382181981543 1646 3391 1697 3111 3781 1897 1037 291 3496 2161 1777 1762 M1598 CHEN_PDGF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_PDGF_TARGETS.html Up-regulated PDGF targets identified by a gene-trap screen. 14981515 30/37 John Newman 0.000279004581200149 0.00149821407541609 1895 2024.72727272727 1897 2.53672700834901e-05 213 1.01886897374015 0.954543134075683 1 4.31797100926614 1893 3408 2344 2650 213 1630 1897 3797 785 1466 2189 1763 M1791 NADELLA_PRKAR1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NADELLA_PRKAR1A_TARGETS_DN.html Epithelial and mesenchymal markers down-regulated in MEF cells (embryonic fibroblasts) after knockout of PRKAR1A [GeneID=5573]. 18413734 16/22 Jessica Robertson 0.00323947139991199 0.00964079760881751 610 2388.27272727273 1897 0.000294931939644856 126 1.17811302373296 1.00848978550872 1 3.56354346024526 610 4606 1897 4484 4093 810 126 1157 4616 2895 977 1764 M1952 MEISSNER_BRAIN_HCP_WITH_H3K4ME2 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K4ME2.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark (H3K4me2) in brain. 18600261 20/29 Arthur Liberzon 0.00577426225782821 0.0142024584976285 4215 2084.90909090909 1897 0.000526315789473684 79 1.28846921346512 -1.47199327161643 -1 3.57206632614133 4214 993 1488 79 3290 2818 4218 2365 219 1353 1897 1765 M8191 ALONSO_METASTASIS_EMT_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_EMT_UP.html EMT (epithelial-mesenchymal transition) genes up-regulated genes in melanoma tumous that developed metastatic disease compared to primary melanoma that did not. 17409456 56/69 Jessica Robertson 0.112059936180139 0.158550029607391 1270 2471.09090909091 1899 0.0107464789907087 1268 1.29542051361771 1.21200989258535 1 1.55461444686418 1268 3731 1451 3847 3745 1433 1382 1485 3838 3103 1899 1766 M19270 PARK_TRETINOIN_RESPONSE_AND_PML_RARA_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/PARK_TRETINOIN_RESPONSE_AND_PML_RARA_FUSION.html Genes up-regulated by tretinoin (ATRA) [PubChem=444795] in U937 cells (acute promyelocytic leukemia, APL) made sensitive to the drug by expression of the PML-RARA fusion [GeneID=5371;5914]. 12893766 35/43 Arthur Liberzon 0.00117592344250512 0.00448332685672388 670 1823.27272727273 1899 0.000106959314260599 52 1.07383939110927 1.02395126840704 1 3.78391167522929 668 2509 2107 3294 1899 99 52 3975 2984 1501 968 1767 M12313 KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_UP.html Genes up-regulated in MEWO cells (melanoma) after 96 h of methionine [PubChem=876] deprivation. 16908595 147/191 Arthur Liberzon 0.111322974275252 0.157720983569215 1670 2037.36363636364 1900 0.0106718663310785 883 1.14086863726814 1.11474817561519 1 1.37302419816803 1669 2783 1212 3405 2969 883 1900 2806 2272 1404 1108 1768 M6889 KEGG_RIBOFLAVIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIBOFLAVIN_METABOLISM.html Riboflavin metabolism 17/19 KEGG 0.0220418233621945 0.04102421382869 4695 2405.27272727273 1901 0.00202416443190808 276 1.42325084233707 -1.35748749299033 -1 2.9619081959281 4695 1554 1670 533 1183 3026 3533 4388 276 1901 3699 1769 M5248 ST_JAK_STAT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_JAK_STAT_PATHWAY.html Jak-STAT Pathway 11/13 Signaling Transduction KE 0.114661083698458 0.161890611742962 3145 2150 1901 0.0110102792580368 175 1.15098472221524 -1.26974353017387 -1 1.36562820016044 3141 1595 2572 1554 1901 3229 1180 1528 175 3015 3760 1770 M919 REACTOME_PLATELET_SENSITIZATION_BY_LDL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_SENSITIZATION_BY_LDL.html Genes involved in Platelet sensitization by LDL 22/23 Reactome 0.00686374010148568 0.0162227607806772 1795 1954.09090909091 1902 0.000625931651112135 792 0.840046891791134 -0.578307911412807 -1 2.2560448298105 1793 1519 2890 1367 792 2164 1696 2272 2220 2880 1902 1771 M17268 SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAMOLS_TARGETS_OF_KHSV_MIRNAS_DN.html Genes down-regulated in 293 cells (embryonic kidney) upon expression of KHSV (Kaposi sarcoma-associated herpesvirus) microRNAs. 17500590 84/111 Arthur Liberzon 7.90957018000689e-08 1.46980989171782e-06 3510 1725.54545454545 1903 7.19051860397861e-09 72 1.52705263822548 -1.36015391929951 -1 13.3648752103979 3506 72 212 106 253 3033 3142 2492 1903 316 3946 1772 M1363 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX5_DN.html Early prostate development genes (down-regulated at 12 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 17/20 Jessica Robertson 0.078388846674535 0.117570815476265 1325 2492.90909090909 1903 0.00739361240573057 1310 1.220074073022 1.10305976178825 1 1.70193924597139 1321 3884 1876 4045 4275 1728 1468 1310 3538 1903 2074 1773 M5889 NABA_MATRISOME http://www.broadinstitute.org/gsea/msigdb/cards/NABA_MATRISOME.html Ensemble of genes encoding extracellular matrix and extracellular matrix-associated proteins 22159717 595/1178 Alexandra Naba 9.49919498767228e-33 3.73635002848443e-30 1485 2124.09090909091 1903 9.49919498767229e-34 4 1.56478757201032 1.55894449975633 1 69.0956447454051 162 3155 4720 3011 2507 1903 1485 1481 3621 4 1316 1774 M16104 ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_DN.html The vEDG down-regulated set: most variable early differentiation genes (EDG) with similar expression patterns in tonsil B lymphocytes (TBC) and multiple myeloma (MM) cells compared to the plasma cells from tonsil (TPC) and bone marrow (BPC). 12393520 45/48 Arthur Liberzon 0.201242956593918 0.259739336921874 2445 2160 1906 0.0202199118044764 625 0.758372994534204 -0.720216870241928 -1 0.666123247401892 2445 831 3852 625 2631 1808 2585 1906 1576 4146 1355 1775 M16517 BIOCARTA_WNT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_WNT_PATHWAY.html WNT Signaling Pathway 43/48 BioCarta 0.13243019624192 0.182509985418988 1490 2216.54545454545 1908 0.0128314481757508 1108 0.784264830522898 0.692149446240828 1 0.869215846004832 1488 1962 3587 2720 2638 1600 1108 1829 1607 3935 1908 1776 M18311 REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS.html Genes involved in Metabolism of vitamins and cofactors 55/56 Reactome 0.00640546799757314 0.0154350763241603 1910 1671.54545454545 1908 0.000584017671273818 151 0.988646937509577 1.02044031135115 1 2.68721344521446 1908 151 2367 722 3262 2268 2736 429 645 2718 1181 1777 M1065 MIDORIKAWA_AMPLIFIED_IN_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/MIDORIKAWA_AMPLIFIED_IN_LIVER_CANCER.html Candidate genes in genomic amplification regions in hepatocellular carcinoma (HCC) samples. 16785998 57/76 Arthur Liberzon 0.00828414062477823 0.0188348476632723 955 1659.09090909091 1912 0.000755954559378148 240 1.04998497728661 1.03667483233836 1 2.71773195575013 952 1918 2357 2836 3320 547 240 1119 1939 1912 1110 1778 M15590 DORN_ADENOVIRUS_INFECTION_32HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_32HR_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) 32 h after infection with adenovirus Ad12. 15681441 73/90 Arthur Liberzon 0.00154454495968991 0.00549792775998217 35 2010.90909090909 1912 0.000140511854458428 31 1.05732475252953 1.03945079851275 1 3.58515204887165 86 4079 1912 4673 2864 31 105 1668 4200 2468 34 1779 M2500 PHONG_TNF_RESPONSE_VIA_P38_COMPLETE http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_RESPONSE_VIA_P38_COMPLETE.html Genes whose expression changes in Calu-6 cells (lung cancer) by TNF [GeneID=7124] were blocked completely by p38 inhibitor LY479754. 20516219 317/382 Arthur Liberzon 0.0664508474546483 0.102365535243453 1090 2000.90909090909 1912 0.0062315630741373 607 1.03328746062117 1.02571093525792 1 1.53461965562763 1089 2726 3147 2942 2689 607 906 1649 1708 2635 1912 1780 M19131 MAHADEVAN_RESPONSE_TO_MP470_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_RESPONSE_TO_MP470_DN.html Bottom genes down-regulated in the GIST (gastrointestinal stromal tumor) cell line sensitive to imatinib [PubChem=5291] after treatment with MP470, a protein kinase inhibitor. 17325667 26/26 Arthur Liberzon 0.0152463995288783 0.0305835128671082 1850 2241.27272727273 1913 0.00139573604490717 966 1.11623986567733 1.18225300777155 1 2.53661244554404 966 2055 1842 1913 1055 1847 2472 3504 4199 1849 2952 1781 M187 PID_TRKR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TRKR_PATHWAY.html Neurotrophic factor-mediated Trk receptor signaling 18832364 89/98 Pathway Interaction Database 0.035187367054222 0.0599582572187465 2650 2168.09090909091 1914 0.00325119060069655 429 1.04259630618106 0.943264515180256 1 1.91187202517219 2650 1310 2750 1641 1382 1914 1222 4428 429 2166 3957 1782 M3146 MARSON_FOXP3_TARGETS_STIMULATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_FOXP3_TARGETS_STIMULATED_UP.html Genes with promoters bound by FOXP3 [GeneID=50943], dependent on it, and up-regulated in hybridoma cells stimulated by PMA [PubChem=4792] and ionomycin [PubChem=3733]. 17237765 25/41 Arthur Liberzon 0.311759090715329 0.375766830484258 1915 2017.63636363636 1914 0.0333947828251095 458 1.33296055509003 -1.08712259337793 -1 0.850114277162339 1914 936 1575 458 4490 2469 1856 2095 1386 2208 2807 1783 M858 REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_RNA_POL_III_AND_MITOCHONDRIAL_TRANSCRIPTION.html Genes involved in RNA Polymerase I, RNA Polymerase III, and Mitochondrial Transcription 85/143 Reactome 0.0139607291073046 0.0285658268596144 1285 2278.18181818182 1915 0.00127728327671834 251 1.29189860495444 -1.3952517604456 -1 2.99326570034861 1282 4419 3740 4684 2352 564 1915 1371 767 3715 251 1784 M2310 DANG_REGULATED_BY_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/DANG_REGULATED_BY_MYC_DN.html Genes down-regulated by MYC [GeneID=4609], according to the MYC Target Gene Database. 14519204 334/435 Chi Dang 0.00338116516723962 0.0099186448659857 1785 1762 1915 0.000307852078707878 617 1.07616543887857 1.12151233571827 1 3.23523863713912 1782 2239 878 1915 617 1756 2616 1941 2935 722 1981 1785 M666 REACTOME_HYALURONAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HYALURONAN_METABOLISM.html Genes involved in Hyaluronan metabolism 20/23 Reactome 0.0578667490194555 0.0911652387756442 4075 2619.63636363636 1916 0.00540430383283173 829 1.53290516536463 -1.0577209221093 -1 2.39244803188662 4075 1528 1101 1249 1916 4445 3862 4171 829 1757 3883 1786 M19104 REACTOME_REGULATION_OF_AMPK_ACTIVITY_VIA_LKB1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_AMPK_ACTIVITY_VIA_LKB1.html Genes involved in Regulation of AMPK activity via LKB1 18/38 Reactome 0.000139483796345872 0.000863994119097792 3005 1647.63636363636 1917 1.26811491494824e-05 61 0.835799654313576 -0.674905968005715 -1 3.84192062805861 3002 366 2921 378 155 1917 1990 1003 61 3610 2721 1787 M15107 JAATINEN_HEMATOPOIETIC_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAATINEN_HEMATOPOIETIC_STEM_CELL_UP.html Genes up-regulated in CD133+ [GeneID=8842] cells (hematopoietic stem cells, HSC) compared to the CD133- cells. 16210406 410/523 Arthur Liberzon 3.3990500718832e-05 0.000282456273579027 3055 1990.27272727273 1917 3.09009326283309e-06 421 1.12986850119267 1.16393706031084 1 6.01691725653955 1917 1692 421 1198 3756 2145 2370 1644 3054 643 3053 1788 M108 PID_NETRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NETRIN_PATHWAY.html Netrin-mediated signaling events 18832364 54/58 Pathway Interaction Database 0.307806663817375 0.371572238674683 1920 2128.90909090909 1919 0.0328914574789404 630 0.844737922475551 0.859367831977029 1 0.544884207881948 1919 788 3007 630 4178 2348 2222 3834 1051 1771 1670 1789 M6161 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_GRANULOCYTE_DN.html Genes down-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing granulocytes. 17898786 7/10 Arthur Liberzon 0.00101128052327285 0.0040010428079194 935 1936.81818181818 1920 0.000101174102797672 18 1.10711864309729 1.10711864309729 1 3.98329292115448 932 3127 4303 2536 432 1077 1920 359 4129 2472 18 1790 M1545 WESTON_VEGFA_TARGETS_12HR http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS_12HR.html Genes up-regulated in MMEC cells (myometrial endothelium) at 12 h after VEGFA [GeneID=7422] stimulation. 12200464 49/62 John Newman 3.54777315890618e-05 0.000292753309616034 135 2082.81818181818 1920 3.22530033858645e-06 135 1.345792865456 1.3029591470045 1 7.13540225936869 135 3754 423 3202 1661 1920 1748 2265 4360 1495 1948 1791 M7151 KEGG_SELENOAMINO_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SELENOAMINO_ACID_METABOLISM.html Selenoamino acid metabolism 26/28 KEGG 0.00577426225782821 0.0142024584976285 2730 1622.45454545455 1923 0.000526315789473684 71 1.3649674080664 -1.20419362097287 -1 3.78415111460055 2728 935 2084 139 988 1923 2510 2440 71 2279 1750 1792 M2234 BHAT_ESR1_TARGETS_VIA_AKT1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BHAT_ESR1_TARGETS_VIA_AKT1_UP.html Genes bound by ESR1 [GeneID=2099] and up-regulated by estradiol [PubChem=5757] in MCF-7 cells (breast cancer) expressing constitutevly active form of AKT1 [GeneID=207]. 18838536 338/425 Arthur Liberzon 0.00118250662901006 0.00448988569632661 3010 2361.18181818182 1923 0.000107558428053666 592 1.19109495104672 1.05888644138421 1 4.19596454608509 3009 1705 634 1409 1923 3279 3695 4601 795 592 4331 1793 M1645 LI_ADIPOGENESIS_BY_ACTIVATED_PPARG http://www.broadinstitute.org/gsea/msigdb/cards/LI_ADIPOGENESIS_BY_ACTIVATED_PPARG.html Adipocyte genes induced in 3T3-L1 cells (adipocyte) by constitutively active PPARG [GeneID=5468] or its agonist, TZD [PubChem=5437]. 11981038 15/22 John Newman 0.00795385727375634 0.0181626542487324 1225 2290.81818181818 1925 0.000725705451427065 481 1.07663902456846 1.1182420420084 1 2.81222212916311 1223 3528 1925 3744 4295 1108 765 481 3512 3409 1209 1794 M1717 ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_VARIABLE_EARLY_DIFFERENTIATION_GENES_UP.html The vEDG up-regulated set: most variable early differentiation genes (EDG) with similar expression patterns in tonsil B lymphocytes (TBC) and multiple myeloma (MM) cells compared to the plasma cells from tonsil (TPC) and bone marrow (BPC). 12393520 22/35 Arthur Liberzon 0.0273235100818456 0.0489809979439085 2105 1960 1925 0.00251535294120295 1001 1.18963741505388 -1.22762492245411 -1 2.3382928609333 2102 1509 1306 1001 1267 3122 3095 3064 1927 1925 1242 1795 M9806 ZHU_CMV_8_HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_8_HR_DN.html Down-regulated at 8 h following infection of primary human foreskin fibroblasts with CMV 9826724 72/93 John Newman 0.0135206767324357 0.02777092871066 2330 1811.72727272727 1927 0.00123677215045198 611 1.15303382706988 1.14748327941006 1 2.69271685432789 2326 748 1154 1257 2287 3323 3184 611 2245 867 1927 1796 M8773 HO_LIVER_CANCER_VASCULAR_INVASION http://www.broadinstitute.org/gsea/msigdb/cards/HO_LIVER_CANCER_VASCULAR_INVASION.html Gene expression signature of vascular invasion of hepatocellular carcinoma (HCC). 17009164 18/40 Yujin Hoshida 0.0472330100021934 0.0766643078440002 1835 1919.90909090909 1927 0.00438896809568284 1017 1.301583417847 1.281752666194 1 2.17834166101583 1833 2096 1927 3037 2144 2692 1017 1089 1567 1986 1731 1797 M13088 KEGG_PPAR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PPAR_SIGNALING_PATHWAY.html PPAR signaling pathway 52/91 KEGG 0.129392241681575 0.178975386299497 1185 2058.81818181818 1929 0.0125176971131995 1088 1.11404420547872 1.07374000348688 1 1.24895901617472 1182 1929 1426 2278 4312 2100 1088 2561 2608 1657 1506 1798 M1021 REACTOME_SIGNALING_BY_INSULIN_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_INSULIN_RECEPTOR.html Genes involved in Signaling by Insulin receptor 100/149 Reactome 0.0290921393510948 0.0513518690116558 1300 2085.90909090909 1930 0.00268037467200286 913 0.862600252013356 0.908104339607277 1 1.6688843808717 2090 1300 3540 913 1300 1618 1930 2906 1111 3891 2346 1799 M11581 COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/COLIN_PILOCYTIC_ASTROCYTOMA_VS_GLIOBLASTOMA_UP.html Genes up-regulated in pilocytic astrocytoma compared to glioblastoma samples. 16314830 65/104 Jessica Robertson 0.00542709110615342 0.0141680697019049 1885 2047.18181818182 1930 0.000494593217962373 491 1.42834423311725 1.68774426580991 1 3.96211453113855 1883 3294 771 3290 2622 2736 3318 491 1930 1570 614 1800 M279 PID_RB_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RB_1PATHWAY.html Regulation of retinoblastoma protein 18832364 77/92 Pathway Interaction Database 0.0437520408503718 0.0719295133450905 1050 1824 1931 0.00405883403703888 649 1.09574786447994 1.24381420748258 1 1.87935795012703 1048 1872 2872 2412 2380 720 649 2162 1361 2657 1931 1801 M14718 TURJANSKI_MAPK14_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK14_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK14 [GeneID=1432] phosphorylation. 17496919 13/13 Arthur Liberzon 0.00086456391291121 0.00354538807032225 1935 2122.90909090909 1931 7.8627623581164e-05 61 0.844702312492 0.75884790816118 1 3.10567762159696 1931 3913 2418 4235 381 861 61 1398 4512 3217 425 1802 M1777 ZHANG_GATA6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_GATA6_TARGETS_UP.html Genes up-regulated after cre-lox knockout of GATA6 [GeneID=2627] in airway epithelium. 18536717 17/29 Jessica Robertson 0.0668144060426188 0.102791393911721 2615 2068.18181818182 1931 0.00626675204960546 946 1.50594205833714 -1.77163313266132 -1 2.23257181768366 2613 2100 1457 946 1640 1175 1931 2651 4089 1461 2687 1803 M1061 REACTOME_MEIOTIC_SYNAPSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEIOTIC_SYNAPSIS.html Genes involved in Meiotic Synapsis 47/198 Reactome 0.000472662838501043 0.00221469590671699 2070 2065.90909090909 1932 4.29785835571416e-05 7 1.26682625766837 -1.48771553605988 -1 5.04618187760008 2069 3347 1932 2982 574 1911 3883 1714 2657 1649 7 1804 M3278 DE_YY1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DE_YY1_TARGETS_DN.html Genes down-regulated in SaOS-2 cells (osteosarcoma) upon knockdown of YY1 [GeneID=7528] by RNAi. 18339860 146/162 Jessica Robertson 0.0599609816228722 0.0938381410013119 870 1893.54545454545 1933 0.00560549350475146 683 1.08078881497675 1.15086885532759 1 1.66643306506329 868 2310 2947 896 4034 1933 1082 1200 683 2603 2273 1805 M699 KEGG_FATTY_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FATTY_ACID_METABOLISM.html Fatty acid metabolism 42/56 KEGG 0.00507706074667405 0.0134930893717914 2685 1833.27272727273 1935 0.000462619577585468 168 1.01203479559788 -1.11431233489636 -1 2.83946684191012 2683 841 2805 168 713 1814 2515 4136 297 1935 2259 1806 M5958 VARELA_ZMPSTE24_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VARELA_ZMPSTE24_TARGETS_DN.html Top genes down-regulated in liver tissue from mice with knockout of ZMPSTE24 [GeneID=10269]. 16079796 48/80 John Newman 0.00087347147388896 0.00357483737128088 2865 1946.36363636364 1935 7.94380421208532e-05 382 1.3725194952269 -1.60792151982769 -1 5.0389458332691 2861 1935 862 1228 382 2183 3881 2214 3533 639 1692 1807 M2894 AMIT_EGF_RESPONSE_240_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_240_MCF10A.html Genes whose expression peaked at 240 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 27/28 Leona Saunders 0.00567006659898648 0.0142024584976285 655 1865.72727272727 1938 0.00051679391143232 258 1.0133127387385 0.95328775601387 1 2.8092182218201 655 3433 1938 3282 4133 334 329 399 3391 2371 258 1808 M2460 KANG_GLIS3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KANG_GLIS3_TARGETS.html Genes downregulated in the postnatal day 3 pancreata with impaired function of GLIS3 [GeneID=169792]. 19805515 19/49 Arthur Liberzon 0.053863937635363 0.0858621363184443 3150 2322.45454545455 1938 0.00502088854620934 924 1.59227484746762 1.78675669466512 1 2.54729821063056 3150 1549 1091 2121 3247 1938 1771 4498 1604 924 3654 1809 M17906 KEGG_VIBRIO_CHOLERAE_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIBRIO_CHOLERAE_INFECTION.html Vibrio cholerae infection 55/73 KEGG 0.0716283943936776 0.108779286209189 1555 2257.18181818182 1939 0.00673387870941713 929 0.886601652349308 0.912982204732734 1 1.28163800525435 1554 1926 3331 3192 3289 2329 1939 1268 1717 3355 929 1810 M16702 REACTOME_ACTIVATED_AMPK_STIMULATES_FATTY_ACID_OXIDATION_IN_MUSCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_AMPK_STIMULATES_FATTY_ACID_OXIDATION_IN_MUSCLE.html Genes involved in Activated AMPK stimulates fatty-acid oxidation in muscle 23/44 Reactome 2.35764533771876e-05 0.000207613544664787 4660 1989.54545454545 1940 2.14333691269861e-06 49 0.953073466747877 -0.789189223283437 -1 5.2666084149177 4659 310 1940 277 55 3863 3781 958 49 2006 3987 1811 M5388 BROWNE_HCMV_INFECTION_18HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_18HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 18 h time point that were not up-regulated at the previous time point, 16 h. 11711622 249/313 John Newman 0.156388299004334 0.209762083347671 1210 2136.36363636364 1940 0.0153413726574378 1185 1.112177408274 1.12642668947545 1 1.1318263726805 1209 2744 3044 1940 3738 1531 1185 2184 1372 2704 1849 1812 M651 REACTOME_CS_DS_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CS_DS_DEGRADATION.html Genes involved in CS/DS degradation 11/13 Reactome 0.0186930911258831 0.0359102116866781 1650 1939 1942 0.00171398537942727 726 1.41442774681564 1.570875419649 1 3.06626665077744 1650 2636 1226 2814 2499 2824 1942 726 2264 1715 1033 1813 M2584 KAAB_HEART_ATRIUM_VS_VENTRICLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_HEART_ATRIUM_VS_VENTRICLE_DN.html Genes down-regulated in the ventricles of healthy hearts, compared to atria. 15103417 354/447 John Newman 0.13863837694993 0.189453717198514 3750 2054.45454545455 1942 0.0134757291535451 342 1.12495740352468 -1.08610653014106 -1 1.21948417593955 3747 525 1256 342 2924 1283 3259 3445 1942 1486 2390 1814 M2553 HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_B_ALL_UP.html Genes distinguishing asparaginase resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 33/47 Arthur Liberzon 0.00837155240403721 0.0190152682132125 905 2204.81818181818 1942 0.000763961728216848 241 0.920143714208184 0.994653832538669 1 2.37592727476182 902 4170 3731 4279 1414 706 241 1942 2537 3606 725 1815 M16488 DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_MUTATED_SIGNIFICANTLY.html The lung adenocarcinoma TSP (tumor sequencing project) genes that were found significantly mutated by at least one method. 18948947 50/58 Jessica Robertson 0.0672615326379193 0.103411867769049 2010 1954.63636363636 1943 0.00631004669792412 716 1.32168353421578 1.50300978886255 1 1.95421067353231 2006 2460 1214 1943 1853 2255 1590 2727 3182 1555 716 1816 M18757 ONDER_CDH1_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_1_UP.html Genes up-regulated in HMLE cells (mmortalized nontransformed mammary epithelial) by expression of a dominant-negative form of E-cadhedrin (CDH1) [GeneID=999]. 18483246 200/263 Jessica Robertson 0.000924385689933652 0.00374193864192696 2720 2159.90909090909 1945 8.40703929646758e-05 487 1.31434035462366 1.17130060148206 1 4.78621856698181 2719 1747 611 998 1945 3314 2507 3223 1785 487 4423 1817 M14728 BROWNE_HCMV_INFECTION_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_6HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 6 h time point that were not up-regulated at the previous time point, 4 h. 11711622 110/171 John Newman 0.00018502917681667 0.00109030925664755 1210 1966.90909090909 1945 1.6822249124984e-05 516 1.19662842947671 1.34216613265026 1 5.31916616777809 1206 2348 516 2201 2433 1898 2583 1945 3961 900 1645 1818 M5224 REACTOME_SYNTHESIS_OF_DNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_DNA.html Genes involved in Synthesis of DNA 93/105 Reactome 0.0156594804224688 0.0312924418264407 180 1957.90909090909 1946 0.00143382430051981 180 0.668820408137163 -0.61533057346681 -1 1.50983870572906 180 698 4080 2194 2354 794 979 2087 1836 4389 1946 1819 M7933 SESTO_RESPONSE_TO_UV_C1 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C1.html Cluster 1: genes changed in primary keratinocytes by UVB irradiation. 11867738 97/129 John Newman 0.124083374081889 0.173020243919207 1845 2050.63636363636 1946 0.0119717944330515 687 1.32897183216905 1.08256063944896 1 1.51924236520593 1844 687 1837 1092 1946 2562 2354 2898 2229 1639 3469 1820 M15125 FARMER_BREAST_CANCER_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_4.html Cluster 4: selected stromal genes clustered together across breast cancer samples. 15897907 44/55 Leona Saunders 7.9606784237172e-07 1.1525890233112e-05 30 2159.63636363636 1948 7.23698300389303e-08 30 1.44025927516785 1.47549111474142 1 10.6722968485519 30 3373 271 3252 2936 1948 1612 2085 4574 1770 1905 1821 M1273 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1.html Cluster PAM1: genes up-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 307/408 Leona Saunders 0.000124035893038678 0.000790080182378623 2660 2187.72727272727 1949 1.12766260662117e-05 315 1.13049570486354 1.15489024918263 1 5.26247227050859 2660 1709 493 315 4601 3296 3205 1949 1824 533 3480 1822 M875 REACTOME_NETRIN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NETRIN1_SIGNALING.html Genes involved in Netrin-1 signaling 43/54 Reactome 0.0196914368853474 0.0373117551581051 1005 1645.72727272727 1950 0.00180635716542842 313 0.954289982981522 0.814925425605135 1 2.0449130044738 1002 1435 2464 2071 2899 598 493 2886 1950 1992 313 1823 M4052 REACTOME_TELOMERE_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TELOMERE_MAINTENANCE.html Genes involved in Telomere Maintenance 47/93 Reactome 0.120516914968631 0.168795204347756 615 2128.36363636364 1950 0.0116067475077151 614 1.23466001999443 -1.3542611385765 -1 1.43131167546163 614 3744 2783 4033 3108 945 1552 1950 701 2938 1044 1824 M18095 GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP.html Up-regulated genes from the set G (Fig. 5a): specific to cells expressing both MLL-AF4 [GeneID=4297;4299] and AF4-MLL fusion proteins. 17130830 257/379 Arthur Liberzon 8.09813702921053e-09 1.82886156831932e-07 1955 1753.63636363636 1951 7.36194278092686e-10 170 1.37113637344772 1.39667845060847 1 13.8624022171087 1951 1724 170 1692 2149 2787 2065 1894 2406 231 2221 1825 M15981 RIGGI_EWING_SARCOMA_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIGGI_EWING_SARCOMA_PROGENITOR_UP.html Genes up-regulated in mesenchymal stem cells (MSC) engineered to express EWS-FLI1 [GeneID=2130;2321] fusion protein. 18381423 564/830 Jessica Robertson 2.35083208612701e-14 1.26090084619539e-12 1215 2028.45454545455 1954 2.35083208612703e-15 42 1.30477782604965 1.26960241042663 1 23.2969202338746 1214 1680 4542 1954 1808 2173 2041 1189 3333 42 2337 1826 M2159 FIGUEROA_AML_METHYLATION_CLUSTER_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_1_UP.html Cluster 1 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 136/191 Arthur Liberzon 0.0129427044311132 0.0267467447087803 4400 2369.45454545455 1954 0.00118358909721925 1003 1.17211348294369 -1.21669035903811 -1 2.76597829361466 4400 1261 1954 1536 1003 3252 4267 2588 1881 2276 1646 1827 M2567 NATSUME_RESPONSE_TO_INTERFERON_BETA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NATSUME_RESPONSE_TO_INTERFERON_BETA_DN.html Genes down-regulated in T98 cells (glioma) 48 h after treatment with interferon beta. 16140920 63/112 John Newman 0.233403974581063 0.294013013083165 1960 2218.09090909091 1956 0.023873616895904 1353 0.9623255552537 -0.94196035233131 -1 0.767566920227218 1956 1369 2498 1481 4519 1353 2495 1904 1958 3142 1724 1828 M2536 ABRAMSON_INTERACT_WITH_AIRE http://www.broadinstitute.org/gsea/msigdb/cards/ABRAMSON_INTERACT_WITH_AIRE.html Proteins interacting with AIRE [GeneID=326], based on massspectroscopy analysis of co-immunoprecipitates in 293T cells (embryonic kidney). 20085707 63/101 Arthur Liberzon 0.251395059518701 0.313496613191088 1865 2471.54545454545 1956 0.0259787625990002 589 0.820769025944871 -0.946049164540858 -1 0.620323913904919 1863 3302 3853 3450 2718 1703 1709 1956 589 4140 1904 1829 M2600 WARTERS_RESPONSE_TO_IR_SKIN http://www.broadinstitute.org/gsea/msigdb/cards/WARTERS_RESPONSE_TO_IR_SKIN.html Genes displaying an ionizing radiation response in the human skin cell samples. 19580510 100/132 Itai Pashtan 0.0439766427575343 0.0722232963867648 2185 2440.45454545455 1957 0.00408010221511524 1469 1.12520969130993 1.19314626736889 1 1.9269030925116 2182 4043 1748 4221 1469 1675 1986 1957 3753 1954 1857 1830 M500 VANTVEER_BREAST_CANCER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_METASTASIS_UP.html Genes whose expression is significantly and positively correlated with poor breast cancer clinical outcome (defined as developing distant metastases in less than 5 years). 11823860 79/109 Jean Junior 0.0207590392259832 0.0389748071386797 4075 2323.09090909091 1958 0.00190523157803234 91 1.21069676194437 -1.06185378680397 -1 2.55998139692602 4074 91 1708 965 1169 3363 4352 2608 1286 1958 3980 1831 M13767 LEE_EARLY_T_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_EARLY_T_LYMPHOCYTE_DN.html Genes down-regulated at early stages of progenitor T lymphocyte maturation compared to the late stages. 15210650 73/109 Arthur Liberzon 0.0177844952295652 0.0344875996234788 3420 2208.63636363636 1958 0.00162999191282496 915 1.28780328739064 -1.18681168847973 -1 2.82567722281096 3420 1348 915 1273 1958 2825 3820 3342 1353 1066 2975 1832 M6470 VERRECCHIA_RESPONSE_TO_TGFB1_C5 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C5.html Cluster 5: ECM related genes up-regulated in dermal fibroblasts later than 30 min after TGFB1 [GeneID=7040] addition; decreased slowly after the peak at 120 min time point. 11279127 43/50 John Newman 0.00863464709361681 0.0195376482655184 1995 1990.45454545455 1959 0.000788065826496652 499 1.40528404325133 1.57140588612756 1 3.6038581337392 1551 1959 1165 2386 3812 1992 2889 499 1819 1993 1830 1833 M8511 SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_DN.html Genes that were inversely correlated in H1299 cells (lung cancer): down-regulated by P53 [GeneID=7157] and up-regulated by P73 [GeneID=7161]. 17982488 43/63 Jessica Robertson 0.00151240512563911 0.00542031297875216 360 2086.72727272727 1960 0.000137585985518563 68 0.850237260669011 0.801251411036774 1 2.89082152171965 360 2932 3359 3786 4689 227 68 1519 1960 3416 638 1834 M972 MMS_MOUSE_LYMPH_HIGH_4HRS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MMS_MOUSE_LYMPH_HIGH_4HRS_UP.html Up-regulated at 4 hours following treatment of mouse lymphocytes (TK 3.7.2C) with a high dose of methyl methanesulfonate (MMS) 15515172 53/77 John Newman 0.021382536245868 0.039954699556808 1030 2327.18181818182 1960 0.00196302117014448 786 0.995427475541808 1.02499464747225 1 2.08867477616123 1029 3334 3320 3409 3656 1960 1314 786 1914 2935 1942 1835 M7146 BIOCARTA_CLASSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CLASSIC_PATHWAY.html Classical Complement Pathway 13/17 BioCarta 0.00587582030835925 0.0143818719418837 730 2230 1961 0.000535597503815323 730 1.92792028240223 1.92792028240223 1 5.32911877208847 730 3545 785 1970 4594 1634 1420 2864 3868 1961 1159 1836 M11685 SHIPP_DLBCL_CURED_VS_FATAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_CURED_VS_FATAL_DN.html Top 50 down-regulated markers for the diffused large B-cell lymphoma (DLBCL) that distinguished between cured and fatal/refractory clinical outcomes. 11786909 63/90 Jean Junior 0.00866333981487015 0.0195931786900753 1855 2162.72727272727 1961 0.000790694935808066 173 0.957241913126768 0.976416020836764 1 2.45304757709392 1852 2871 2271 3365 1777 1311 1811 1961 3257 3141 173 1837 M695 REACTOME_GLYCOSAMINOGLYCAN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSAMINOGLYCAN_METABOLISM.html Genes involved in Glycosaminoglycan metabolism 99/122 Reactome 2.01620321958757e-05 0.000183361834228388 1515 2121 1962 1.83292881585473e-06 396 1.33326095127145 1.41992201051408 1 7.47546155365552 1511 1296 396 1689 3951 2939 2907 3045 1962 854 2781 1838 M899 REACTOME_IL1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL1_SIGNALING.html Genes involved in Interleukin-1 signaling 43/45 Reactome 0.0240615154736747 0.0440365851243677 1585 2043.27272727273 1962 0.00221170717291429 837 0.830621401689244 0.936545753119695 1 1.6901961489612 1581 837 3024 1479 1215 2755 1962 2112 2159 3415 1937 1839 M6670 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_3D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 3 days after transduction. 16818636 207/331 Arthur Liberzon 2.16021663591876e-11 7.38856704459171e-10 2110 1890.27272727273 1966 1.96383330539998e-12 109 1.27051282700362 -1.22952604201381 -1 17.4083448661469 2106 1217 109 943 1956 3159 2730 1966 2482 228 3897 1840 M202 YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) samples from patients with early recurrence (within 2 years after surgery) after resection. 19167881 41/52 Yujin Hoshida 0.00172233846472652 0.00597752761287438 660 1693.09090909091 1966 0.000156698939156698 29 0.9942721241388 -1.01191715409248 -1 3.31715781172333 656 1966 2969 2564 2777 29 85 1230 2816 3308 224 1841 M11358 BIOCARTA_ARF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARF_PATHWAY.html Tumor Suppressor Arf Inhibits Ribosomal Biogenesis 25/28 BioCarta 0.364773970655067 0.433140412953941 2575 2189.72727272727 1968 0.0404129251595175 1102 1.23698576994409 1.08294856895114 1 0.674355614869741 2573 1499 1929 1102 2768 1968 1733 4310 2762 1418 2025 1842 M15638 RIZ_ERYTHROID_DIFFERENTIATION_APOBEC2 http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_APOBEC2.html Selected genes whose expression profile follows that of APOBEC2 [GeneID=10930] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 30/48 Leona Saunders 0.00123937765541898 0.00463906624391559 4250 2142.81818181818 1968 0.000112734219482141 295 1.23783792999149 -1.24082696924782 -1 4.33426755464332 4246 295 1950 1974 435 4159 3194 1968 949 3437 964 1843 M14414 BOYAULT_LIVER_CANCER_SUBCLASS_G6_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G6_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G6, defined by unsupervised clustering. 17187432 25/30 Yujin Hoshida 0.000835676688114685 0.00346140231326603 1615 2031.54545454545 1969 7.59994810325075e-05 374 1.19531245325467 1.48971350626265 1 4.41346783379141 1615 4530 2500 3968 374 1969 1068 581 844 2653 2245 1844 M12347 REACTOME_NEF_MEDIATES_DOWN_MODULATION_OF_CELL_SURFACE_RECEPTORS_BY_RECRUITING_THEM_TO_CLATHRIN_ADAPTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEF_MEDIATES_DOWN_MODULATION_OF_CELL_SURFACE_RECEPTORS_BY_RECRUITING_THEM_TO_CLATHRIN_ADAPTERS.html Genes involved in Nef-mediates down modulation of cell surface receptors by recruiting them to clathrin adapters 41/60 Reactome 0.0700971417504749 0.107039310599237 1710 2394.18181818182 1970 0.00658505485177133 788 0.684539566967353 -0.62916553313841 -1 0.996713672741072 1706 1970 3604 3402 1659 788 1254 2481 4337 4322 813 1845 M16651 RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_DN.html Genes down-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to normal thyroid tissue. 17406368 1047/1230 Arthur Liberzon 0.28527118031441 0.349372073452002 1640 1956.27272727273 1970 0.0330274862080929 324 1.09399232855018 1.12135267328422 1 0.749612848212309 1637 1115 4321 324 2500 1970 2111 2541 1302 1428 2270 1846 M11193 AMIT_SERUM_RESPONSE_20_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_20_MCF10A.html Genes whose expression peaked at 20 min after stimulation of MCF10A cells with serum. 17322878 25/33 Leona Saunders 0.00577426225782821 0.0142024584976285 145 1871.18181818182 1970 0.000526315789473684 144 0.853721697532879 0.963960572828762 1 2.3667655287795 3618 307 3209 144 845 2630 1970 3341 144 2650 1725 1847 M1423 ABBUD_LIF_SIGNALING_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_1_DN.html Genes down-regulated in AtT20 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 31/42 Kevin Vogelsang 0.01044360999171 0.0226014851723389 3640 2506.45454545455 1970 0.000953956255687421 924 1.32030531537076 1.35798952704786 1 3.26058684783164 3639 2002 1970 1818 924 3224 4503 1836 1152 1865 4638 1848 M1782 POS_RESPONSE_TO_HISTAMINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/POS_RESPONSE_TO_HISTAMINE_UP.html Genes gradually up-regulated by histamine [PubChem=774] in B16-F10 melanoma tumors. 18339882 16/17 Jessica Robertson 0.113548852977834 0.160464247321969 3210 2327 1973 0.010897394175626 270 1.0082242472999 -0.998533960418084 -1 1.20204615228893 3210 1570 3315 1584 1973 1904 2903 4383 270 3475 1010 1849 M16922 YAGI_AML_WITH_T_9_11_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_T_9_11_TRANSLOCATION.html Genes specifically expressed in samples from patients with pediatric acute myeloid leukemia (AML) bearing t(9;11) translocation. 12738660 164/231 Arthur Liberzon 0.0450654768551793 0.0737851207284991 1805 2185.90909090909 1973 0.00418327136905714 600 0.940533256817136 0.910758415632603 1 1.59751739438303 1805 600 2633 1526 1478 2655 1973 4010 1600 3187 2578 1850 M8155 MCBRYAN_PUBERTAL_BREAST_3_4WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_3_4WK_DN.html Genes down-regulated during pubertal mammary gland development between weeks 3 and 4. 17486082 38/47 Arthur Liberzon 0.024772096087827 0.0452143439808753 1220 1980 1974 0.00227777353669252 362 0.953375580815625 0.944709755227794 1 1.92360111667461 1220 1974 2502 2354 3702 669 785 1832 3234 3146 362 1851 M8066 BIOCARTA_IL22BP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL22BP_PATHWAY.html IL22 Soluble Receptor Signaling Pathway 12/17 BioCarta 0.0382222417809837 0.064179644683829 2335 1871.72727272727 1976 0.00353662912184187 285 0.89877736015445 -1.00223688926257 -1 1.60827807425329 2335 1046 2714 1568 1411 2312 3027 1465 285 2450 1976 1852 M2742 LEE_LIVER_CANCER_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by overexpression of MYC [GeneID=4609]. 15565109 61/99 Yujin Hoshida 0.123766369848588 0.172680244068973 4155 2446.45454545455 1976 0.0119392926253498 998 1.27816424158012 -1.40858738656034 -1 1.46279494992181 4152 1380 1232 1523 1976 4256 3785 3101 998 1169 3339 1853 M8512 TSAI_RESPONSE_TO_IONIZING_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_RESPONSE_TO_IONIZING_RADIATION.html Genes up-regulated in TK6, WTK1, and NH32 cell lines (lymphoblast) in response to ionizing radiation. 16247478 215/274 Arthur Liberzon 0.0917200212931301 0.134113537950302 1610 1876.27272727273 1979 0.00870755871841814 1155 1.12032579841822 1.06906421958208 1 1.46667494873102 1607 1742 1178 2445 2088 1257 1979 2323 2436 1155 2429 1854 M7405 HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_DN.html Genes down-regulated during differentiation from pre-BI to large pre-BII lymphocyte. 11779835 90/132 Arthur Liberzon 0.00534867305754064 0.0140268553061257 4600 2228.18181818182 1979 0.000487429205973092 45 1.21346153848833 -1.18290829072961 -1 3.37395217199034 4600 45 769 290 1979 3419 3394 2599 1012 1973 4430 1855 M9834 DORN_ADENOVIRUS_INFECTION_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_24HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 24 h after infection with adenovirus Ad12. 15681441 19/21 Arthur Liberzon 0.0749055500061404 0.11299271205784 1940 2364.36363636364 1979 0.00705313981029373 846 1.15530784239376 1.17428378302782 1 1.64149052925121 1937 4211 2189 3756 3025 1407 846 3382 1979 1670 1606 1856 M3019 ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_RESPONSE_TO_AZACITIDINE_AND_TSA_UP.html Genes up-regulated in 3 out of 4 NSCLC cell lines (non-small cell lung cancer) after treatment with azacitidine [PubChem=9444] and TSA [PubChem=5562]. 17043644 255/350 Leona Saunders 0.00085384966004904 0.00351835553102581 1980 1750.54545454545 1980 7.76528391626787e-05 499 1.12644822187163 0.993203741456302 1 4.14721348591302 1980 1722 601 1816 499 2471 2263 1995 2393 679 2837 1857 M1516 HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_4HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIN_ACTION_DIRECT_VS_INDIRECT_4HR.html Genes discriminating between direct (cisplatin, MMS, mitomycin C [PubChem=2767;4156;5746]) and indirect (paclitaxel, hydroxyurea, etoposide [PubChem=4666;3657;36462]) acting genotoxins at 4 h time point. 15120960 55/65 John Newman 0.0114146748179602 0.0241385596508837 1060 2174.63636363636 1980 0.00104312123036409 219 1.18851537169008 1.03613647905072 1 2.88415246193505 1059 3740 1980 4091 1168 1234 535 3823 3669 2403 219 1858 M7705 AKL_HTLV1_INFECTION_UP http://www.broadinstitute.org/gsea/msigdb/cards/AKL_HTLV1_INFECTION_UP.html Genes up-regulated in WE17/10 cells (CD4+ [GeneID=920] T lymphocytes) infected by HTLV1 (and thus displaying low CD7 [GeneID=924]) compared to the uninfected (i.e., CD7+) cells. 17287851 42/47 Arthur Liberzon 0.19450697891119 0.252079335656457 2965 2313.72727272727 1981 0.0194716340520935 855 0.890088545715713 -0.858505061615947 -1 0.799198469182512 2963 855 3599 1114 4634 1295 1981 3082 1589 3010 1329 1859 M15510 NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP.html Genes up-regulated in K562 cells (bone marrow) after treatment with dasatinib [PubChem=3062316] or imatinib [PubChem=5291]. 17213809 36/39 Arthur Liberzon 0.00463212643647125 0.0125364889794405 1780 1895 1983 0.000421991661874907 694 0.992448692951701 1.02609944467992 1 2.8320700117509 1780 1983 2751 3400 694 1366 726 944 2388 2242 2571 1860 M1936 MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) that have no histone H3 methylation marks in neural precursor cells (NPC). 18600261 525/913 Jessica Robertson 1.39982105312054e-13 7.02888869226482e-12 4720 2740.45454545455 1984 1.39982105312062e-14 48 1.37077724144094 -1.41193021448648 -1 22.9404961048451 4716 1682 4612 915 3957 1910 4372 4178 1771 48 1984 1861 M5714 WILLIAMS_ESR2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR2_TARGETS_DN.html Genes uniquely down-regulated in T47D cells (breast cancer) by induction of ESR2 [GeneID=2100] expression in the Tet-Off system. 17700529 18/19 Jessica Robertson 3.34841717067293e-05 0.000279231961935975 4375 2365.81818181818 1985 3.04406194084505e-06 70 1.09801017416147 -1.20471568360007 -1 5.85547334510378 4374 378 1736 772 70 4518 4623 3806 2869 1985 893 1862 M9811 SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_UP.html Genes up-regulated in 293 cells (embryonic kidney) expressing polymorphic variants S427G (SNP ID=rs2070235) or I624M (SNP ID=rs11556379) of BMYB [GeneID=4605]. 18026132 14/18 Jessica Robertson 0.00187001097132708 0.00636020284346217 1985 2265.54545454545 1985 0.000170145671281178 486 0.884181602567189 1.0677634973746 1 2.91410005510145 1985 3905 3757 4241 500 1738 486 2709 562 3318 1720 1863 M950 ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_ANTIVIRAL_RESPONSE_TO_RIBAVIRIN_DN.html Genes up-regulated in A549 cells (lung carcinoma) upon infection with RSV (respiratory syncytial virus) and down-regulated by further treatment with ribavirin [PubChem=5064]. 12719586 73/97 John Newman 0.106771490393044 0.152438425485531 1460 2611.63636363636 1985 0.0102123004304276 973 1.12808341276916 1.04597395636508 1 1.38267982905743 1460 4075 1985 4632 4265 1276 1472 4194 2702 1694 973 1864 M1873 VILIMAS_NOTCH1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VILIMAS_NOTCH1_TARGETS_DN.html Genes down-regulated in bone marrow progenitors by constitutively active NOTCH1 [GeneID=4851]. 17173050 10/42 Jessica Robertson 0.00629150952116519 0.0152208738800101 1355 2063.90909090909 1985 0.000573597654780571 769 1.60716634197489 1.60716634197489 1 4.38309623625649 1355 2149 1931 3733 769 1986 1441 821 3625 2908 1985 1865 M16637 LIU_CDX2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CDX2_TARGETS_UP.html Genes up-regulated in HET1A cells (esophagus epithelium) engineered to stably express CDX2 [GeneID=1045]. 16990345 34/58 Arthur Liberzon 1.53053886213485e-05 0.000147431498556663 3595 2285.18181818182 1986 1.39140864562682e-06 229 1.29301603402137 1.15702133019156 1 7.4335819334658 2962 1986 568 1422 4268 1697 1961 3593 3591 229 2860 1866 M1255 INAMURA_LUNG_CANCER_SCC_DN http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_DN.html Down-regulated genes characteristic to the squamous cell carcinoma (SCC) type of non-small cell lung cancer (NSCLC). 16007138 20/24 Arthur Liberzon 0.00251578120268264 0.00792689404316561 3635 2517 1986 0.000228969336868135 560 1.51150535120656 1.44564611626048 1 4.76482112608168 3631 1538 869 1986 560 4488 4216 3029 1898 1018 4454 1867 M2948 SESTO_RESPONSE_TO_UV_C8 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C8.html Cluster 8: genes changed in primary keratinocytes by UVB irradiation. 11867738 146/168 John Newman 0.00920445193409931 0.020473615989137 1990 2433.72727272727 1986 0.000840289908467593 881 1.11378006161198 1.10236503538707 1 2.82230915170811 1986 1780 1174 1671 881 4115 4066 2739 3877 1528 2954 1868 M638 KEGG_ADHERENS_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ADHERENS_JUNCTION.html Adherens junction 96/111 KEGG 0.108425311643189 0.154332771699594 1285 2194.63636363636 1987 0.0103790409445669 1284 0.938630465499644 0.962453252479656 1 1.14289717686721 1284 1833 2293 1656 1868 1501 1999 3529 3574 1987 2617 1869 M1190 ZHAN_MULTIPLE_MYELOMA_CD1_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_UP.html Top 50 up-regulated genes in cluster CD-1 of multiple myeloma samples with the characteristic expression spike of CCND1 [GeneID=595]. 16728703 45/75 Kevin Vogelsang 3.13954174506308e-05 0.000265259274643481 1990 2015.45454545455 1987 2.85416959021974e-06 64 1.32305662275201 1.16690893088973 1 7.09988446595876 1987 816 482 670 64 3668 2817 4633 2949 1048 3036 1870 M16473 KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION.html Aldosterone-regulated sodium reabsorption 40/55 KEGG 0.0403049539844497 0.0670650653541984 1785 2313 1988 0.00373298822763417 611 1.2844902374943 1.11427230092821 1 2.26170906916903 1783 3788 1988 4264 1909 1120 611 4468 1080 2143 2289 1871 M15209 LANDIS_ERBB2_BREAST_PRENEOPLASTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_PRENEOPLASTIC_UP.html Up-regulated genes from top 82 genes out of the 324-gene signature identified in the pre-neoplastic tissue adjacent to the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 27/27 Leona Saunders 0.0301229692342573 0.0527375425762961 1575 1899.18181818182 1988 0.00277668222402109 1150 1.0449690329519 1.12692346923366 1 2.00360635943917 1574 2041 2585 2709 1319 1988 1150 1205 1178 2813 2329 1872 M16884 BIOCARTA_ACH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACH_PATHWAY.html Role of nicotinic acetylcholine receptors in the regulation of apoptosis 18/21 BioCarta 0.0265688232837957 0.0478461830978694 2330 1846.27272727273 1991 0.00244502000439281 148 0.724313148951439 0.751463642693578 1 1.43469740533163 2330 352 2876 577 3548 1023 483 3913 148 3068 1991 1873 M2289 MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_UP.html Up-regulated target genes shared by acute myeloid leukemia (AML) translocation products PML RARA [GeneID=5371;5914], AML1 ETO [GeneID=861;862], and PLZF RARA [GeneID=5914;7704]. 15024077 21/22 Arthur Liberzon 3.20477101369157e-05 0.000268677072551052 3910 2086.90909090909 1991 2.91347063544983e-06 67 0.743519482596836 -0.529975666200878 -1 3.98367983872943 3906 354 3427 863 67 1991 2619 3875 221 3796 1837 1874 M987 REACTOME_NFKB_AND_MAP_KINASES_ACTIVATION_MEDIATED_BY_TLR4_SIGNALING_REPERTOIRE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NFKB_AND_MAP_KINASES_ACTIVATION_MEDIATED_BY_TLR4_SIGNALING_REPERTOIRE.html Genes involved in NFkB and MAP kinases activation mediated by TLR4 signaling repertoire 82/99 Reactome 0.0111975983545136 0.0238397222522796 370 2097.09090909091 1995 0.00102318195865137 291 0.903489807451781 1.09148474189295 1 2.19979439234526 368 3692 3576 3910 2324 744 291 828 1995 4056 1284 1875 M19457 GRABARCZYK_BCL11B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRABARCZYK_BCL11B_TARGETS_DN.html Genes down-regulated in Jurkat cells (transformed T lymphocytes) after knockdown of BCL11B [GeneID=64919] by RNAi. 17173069 61/97 Arthur Liberzon 0.0455725667016515 0.0744299359279568 1510 2067.54545454545 1995 0.00423135562526514 850 1.25187840753399 1.14413889382575 1 2.11928087758518 1506 2422 2191 850 3597 3187 1995 1075 1570 2431 1919 1876 M18306 KEGG_REGULATION_OF_ACTIN_CYTOSKELETON http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_REGULATION_OF_ACTIN_CYTOSKELETON.html Regulation of actin cytoskeleton 193/251 KEGG 0.042328466316418 0.0699301228608656 3635 2308.45454545455 1996 0.00392413732779805 422 1.17443513918501 1.22125184737619 1 2.03590011734519 3632 576 1352 422 1996 4711 3942 2406 910 806 4640 1877 M10885 DAZARD_UV_RESPONSE_CLUSTER_G4 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G4.html Cluster G4: genes increasingly up-regulated in NHEK cells (normal keratinocyte) after 12 h time point after UV-B irradiation. 12771951 37/83 John Newman 0.0200652706202892 0.0379135617805304 2585 2116 1996 0.00184096808190794 1155 1.29964141996538 -1.51041824669025 -1 2.771440902741 2585 2501 1812 2206 1155 2739 3206 1610 1522 1944 1996 1878 M9564 SMID_BREAST_CANCER_NORMAL_LIKE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_NORMAL_LIKE_DN.html Genes down-regulated in the normal-like subtype of breast cancer. 18451135 23/24 Jessica Robertson 0.0402302009840561 0.0669793822380052 300 1960.63636363636 1996 0.0037259337791722 299 1.28497734741509 1.36627623584798 1 2.26363733245259 299 2579 1040 2218 1435 1886 1996 2041 4534 2011 1528 1879 M2363 TERAO_AOX4_TARGETS_SKIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_SKIN_DN.html Genes down-regulated in skin upon knockout of AOX4 [GeneID=71872]. 18981221 32/39 Arthur Liberzon 0.0249634283708982 0.0454580948729319 3790 2293.27272727273 1997 0.00229557016907251 1226 1.37250179914326 -1.73009277589136 -1 2.76449886481037 3786 1997 1286 1725 1226 3648 2915 3367 1653 2356 1267 1880 M16300 HAEGERSTRAND_RESPONSE_TO_IMATINIB http://www.broadinstitute.org/gsea/msigdb/cards/HAEGERSTRAND_RESPONSE_TO_IMATINIB.html Genes with the highest differential expression in primary tissue cultures of high grade glioma: responders vs non-responders to imatinib [PubChem=5291] treatment. 16547494 30/32 Arthur Liberzon 0.000250406193551157 0.00138560050827839 30 2004.90909090909 1998 2.27667908705728e-05 28 1.39916110981166 1.39916110981166 1 6.00093743922156 28 3014 573 3008 2462 1351 1500 1998 4548 2171 1401 1881 M1746 ZHENG_FOXP3_TARGETS_IN_THYMUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_THYMUS_UP.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are up-regulated only in developing (located in the thymus) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 258/299 Jessica Robertson 0.0815168574242483 0.121528606141014 1775 2106 1999 0.00770035623788815 1193 1.00964393741395 0.951168819512349 1 1.38659797268737 1771 1193 3327 1289 1733 2626 2144 1999 1512 2189 3383 1882 M1384 SHIN_B_CELL_LYMPHOMA_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_2.html Cluster 2 of genes distinguishing among different B lymphocyte neoplasms. 19010892 36/41 Jessica Robertson 0.00332139852388539 0.00980425330377675 3095 1768.72727272727 2000 0.000302402141071834 71 1.06568662230415 -1.10997516470557 -1 3.21179140003682 3095 264 1891 2000 756 2129 3362 295 3349 2244 71 1883 M2504 PHONG_TNF_RESPONSE_NOT_VIA_P38 http://www.broadinstitute.org/gsea/msigdb/cards/PHONG_TNF_RESPONSE_NOT_VIA_P38.html Genes whose expression changes in Calu-6 cells (lung cancer) by TNF [GeneID=7124] were not affected by p38 inhibitor LY479754. 20516219 487/583 Arthur Liberzon 0.00675310115043352 0.0160174057437418 1135 1900.72727272727 2000 0.000615810903110077 802 1.07019117513022 1.12955073445952 1 2.88303785987208 1133 2708 802 2314 2565 1499 1886 2000 2439 914 2648 1884 M3001 CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEMELLO_SOLEUS_VS_EDL_MYOFIBERS_UP.html Genes up-regulated in type 1 (soleus) vs type 2B (EDL) myofibers. 21364395 40/85 Emmanuelle Fouilloux-Meugnier 0.00097365186356803 0.0038880175939434 2000 2230.54545454545 2000 8.85530035369292e-05 395 1.1186372956132 -1.19305675011288 -1 4.04562624826403 2000 3372 1466 3382 395 1336 2492 4021 3739 1524 809 1885 M2401 KOHOUTEK_CCNT1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KOHOUTEK_CCNT1_TARGETS.html Genes down-regulated in E14 ES (embryonic stem) cells upon knockdown of CYCT1 [GeneID=904] by RNAi. 19364821 71/86 Arthur Liberzon 0.032486249191075 0.0560640205418186 975 2178.63636363636 2001 0.0029978285527999 972 1.19982567959731 1.16824706511569 1 2.25271615778285 972 3283 1382 3380 1353 2001 1292 2922 3421 2088 1871 1886 M11725 REACTOME_CD28_CO_STIMULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CD28_CO_STIMULATION.html Genes involved in CD28 co-stimulation 35/41 Reactome 0.000159468494647869 0.000969901022834412 2105 1803.54545454545 2003 1.44981868184733e-05 164 0.815549182129792 0.784744672698224 1 3.6873802124428 2103 256 2850 641 164 1859 2003 2533 1620 3709 2101 1887 M4203 LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_UP.html Genes with copy number gains in primary neuroblastoma tumors. 17533364 208/279 Arthur Liberzon 0.0365450509940665 0.0617301454239838 1645 2228.81818181818 2003 0.00337878355413402 932 0.885720793057658 -0.920551384016621 -1 1.60737384840899 1644 1220 4002 2188 1399 932 2094 2003 3209 4256 1570 1888 M13630 GENTILE_UV_HIGH_DOSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_HIGH_DOSE_DN.html Selected genes down-regulated in WS1 (fibroblast) in response to irradiation with high dose UV-C. 12907719 407/485 John Newman 0.134248420851686 0.184469445828226 1425 2325 2003 0.0130197072001838 1425 1.04383248445727 1.04278142053171 1 1.14967054458362 1425 3167 3494 3453 2003 1907 1874 1616 1868 2055 2713 1889 M2236 JOHNSTONE_PARVB_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_1_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) upon overexpression of PARVB [GeneID=29780] under all three culture conditions. 17998334 13/13 Arthur Liberzon 0.00706248832399278 0.0165845496961423 2030 2271.09090909091 2003 0.000644114809193732 212 1.28669790016245 1.0891875312221 1 3.43714079296732 2026 3550 1113 3944 3710 1335 212 1006 4604 1479 2003 1890 M598 REACTOME_RORA_ACTIVATES_CIRCADIAN_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RORA_ACTIVATES_CIRCADIAN_EXPRESSION.html Genes involved in RORA Activates Circadian Expression 30/34 Reactome 0.142641371235597 0.194249068733993 1600 2054 2004 0.013893399550368 155 0.883575170545343 0.967891351808351 1 0.943403734835739 1598 2015 3573 1809 2882 2176 1343 1603 155 3436 2004 1891 M11361 KYNG_DNA_DAMAGE_BY_4NQO http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_4NQO.html Genes specifically responding to 4NQO treatment of primary fibroblasts. 15897889 57/66 Jessica Robertson 0.000204452861262303 0.00118698340117844 3810 2045 2004 1.85883512887986e-05 312 1.41226296375679 -1.32588624985789 -1 6.19952312931593 3806 776 606 516 3411 3470 4141 2004 722 312 2731 1892 M1932 MEISSNER_NPC_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the H3K27 tri-methylation (H3K27me3) mark in neural precursor cells (NPC). 18600261 36/125 Jessica Robertson 0.00116176736133185 0.00445092690380385 1995 2151.27272727273 2004 0.000105671028802492 156 1.43157938693456 1.4770256013854 1 5.05128971642816 1991 2960 1039 3723 2972 2446 2004 156 3424 1563 1386 1893 M13526 AMIT_EGF_RESPONSE_20_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_20_HELA.html Genes whose expression peaked at 20 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 11/15 Leona Saunders 0.0588077773463508 0.0922531363396494 1500 1934.54545454545 2006 0.00549465661107955 756 1.40611480225734 1.35147058199665 1 2.1836840671194 1500 2151 2233 1627 2964 784 756 1518 3394 2347 2006 1894 M14487 HOEGERKORP_CD44_TARGETS_DIRECT_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_DIRECT_UP.html Genes directly up-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 32/48 Kevin Vogelsang 0.00818120730394674 0.0186277368425608 1545 2292.81818181818 2006 0.000746526395538632 237 0.900711371328635 0.975932583909945 1 2.33783419548848 1542 2519 2006 4172 3748 506 237 1641 3614 3550 1686 1895 M15008 PIEPOLI_LGI1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PIEPOLI_LGI1_TARGETS_UP.html Up-regulated genes in U87 cells (glioblastoma multiforme, GBM) engineered to stably express LGI1 [GeneID=9211]. 16533756 23/33 Arthur Liberzon 0.00283765153296101 0.00867468603340413 1050 1955.18181818182 2007 0.000258301661546231 261 1.34276671205005 1.16915016955459 1 4.15400027320371 1050 3476 1707 2426 3529 1555 587 261 2635 2007 2274 1896 M19948 HOQUE_METHYLATED_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HOQUE_METHYLATED_IN_CANCER.html Genes whose DNA was methylated both in primary tumors and across a panel of cancer cell lines. 18413733 48/73 Jessica Robertson 0.00657322691492842 0.0156774285186772 2355 2188.27272727273 2007 0.000599359013551998 437 1.44167073380317 1.56113763397106 1 3.90397648933767 2353 3336 1001 2528 1935 4274 4002 437 2007 1707 491 1897 M7184 GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUENTHER_GROWTH_SPHERICAL_VS_ADHERENT_UP.html Genes up-regulated in glioblastoma cell lines displaying spherical growth (cluster-1) compared to those displaying semiadherent or adherent growth phenotype (cluster-2). 18037961 23/35 Jessica Robertson 0.020569881004401 0.0386750584715373 2565 2004.90909090909 2008 0.00188770582791188 678 1.62475762686616 1.7529997361765 1 3.44371120871555 2561 966 1069 758 4241 3266 3212 771 678 2008 2524 1898 M15592 NGUYEN_NOTCH1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NGUYEN_NOTCH1_TARGETS_UP.html Genes up-regulated in primary keratinocytes by expression of constantly active NOTCH1 [GeneID=4851]. 16618808 41/56 Kevin Vogelsang 0.269635454237613 0.332726625882754 1925 2171.09090909091 2008 0.0281605674977005 1482 1.04590786271878 -0.971909102447815 -1 0.749932704359548 1922 1967 1772 2157 2821 1482 2008 2795 2069 3305 1584 1899 M18491 STEIN_ESRRA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_UP.html Genes up-regulated by ESRRA [GeneID=2101] only. 18974123 540/727 Leona Saunders 0.0702032608776822 0.107166685427768 2010 2284 2008 0.00725250044603858 657 0.939260841584241 -0.873845980685923 -1 1.36690824381158 2008 1683 4522 2167 2616 657 1595 3355 895 4038 1588 1900 M8817 ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K9ME3_DN.html Genes whose promoters display lower histone H3 trimethylation mark at K9 (H3K9me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 117/203 Jessica Robertson 0.0145041817575622 0.0294450485572876 2040 1834.09090909091 2010 0.00132733609856907 644 1.1463256072516 -1.30359613755835 -1 2.63332254916886 2039 644 1991 2010 1035 1608 2309 2031 2744 2195 1569 1901 M1851 QI_PLASMACYTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/QI_PLASMACYTOMA_UP.html Up-regulated genes that best disciminate plasmablastic plasmacytoma from plasmacytic plasmacytoma tumors. 17363561 277/394 Jessica Robertson 5.35215264521238e-06 5.98629395388683e-05 1885 2009 2011 4.8656051508689e-07 205 1.21334184747239 1.19419191858213 1 7.68818517566481 1884 1190 404 2011 4711 1594 2047 2649 2336 205 3068 1902 M16161 LOPEZ_MESOTHELIOMA_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_UP.html Top genes associated with favorable survival after surgery of patients with epithelioid mesothelioma. 16540645 16/17 Arthur Liberzon 0.217188384271004 0.27727618004239 3515 2268.81818181818 2011 0.0220143592868214 225 1.20536604310439 -1.33209239964063 -1 1.00748481630612 3513 1566 2011 1215 3391 3588 3937 2718 225 1372 1421 1903 M13143 BIOCARTA_UCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_UCALPAIN_PATHWAY.html uCalpain and friends in Cell spread 32/44 BioCarta 0.00272081145137183 0.00841561602259177 2450 1982 2012 0.000247652927719468 575 1.32823470678365 1.46189829072907 1 4.13528682627502 2446 2522 1997 1670 575 2868 2102 2012 762 1029 3819 1904 M15114 DAZARD_UV_RESPONSE_CLUSTER_G5 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G5.html Cluster G5: genes up-regulated in NHEK cells (normal keratinocyte) at 3 h and 24 h time points after UV-B irradiation. 12771951 16/33 Arthur Liberzon 0.000402696036130179 0.00196757876474302 2015 1942.54545454545 2012 3.66154332707618e-05 276 1.31308146872416 -1.31686693971028 -1 5.33167349270794 2012 3888 2247 3794 276 2634 2806 1215 370 1800 326 1905 M4767 VERRECCHIA_RESPONSE_TO_TGFB1_C2 http://www.broadinstitute.org/gsea/msigdb/cards/VERRECCHIA_RESPONSE_TO_TGFB1_C2.html Cluster 2: ECM related genes up-regulated in dermal fibroblasts within 30 min after TGFB1 [GeneID=7040] addition; reached a plateau after that. 11279127 64/76 John Newman 0.00165985851031693 0.00580251129242974 590 2169.18181818182 2013 0.000151010196969443 589 1.40794475478891 1.43483368671317 1 4.72458941150617 589 3299 664 3234 996 1947 2338 2862 3920 1999 2013 1906 M5785 KEGG_TASTE_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TASTE_TRANSDUCTION.html Taste transduction 33/88 KEGG 0.259737106124598 0.322451115441374 3100 2242.09090909091 2014 0.0269705202295096 901 1.1842881172548 0.960383932740439 1 0.873377487738319 3099 901 1434 1505 2759 2595 1765 3306 1334 2014 3951 1907 M4661 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_GRANULOCYTE_UP.html Genes up-regulated in granulocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 78/109 Arthur Liberzon 0.00236513513522495 0.00758385722708001 4590 2392 2014 0.00021524378493629 698 1.3628597611891 -1.23184331113113 -1 4.33551547472351 4590 1333 698 2014 712 2815 4452 2905 1910 1076 3807 1908 M657 REACTOME_GASTRIN_CREB_SIGNALLING_PATHWAY_VIA_PKC_AND_MAPK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GASTRIN_CREB_SIGNALLING_PATHWAY_VIA_PKC_AND_MAPK.html Genes involved in Gastrin-CREB signalling pathway via PKC and MAPK 135/232 Reactome 0.000584445980934821 0.00260489615676332 2185 2161.63636363636 2015 5.3145572820441e-05 581 1.32272677287718 -1.18681344878264 -1 5.12897668055722 2183 2791 581 2632 4548 1592 2015 1824 1768 1214 2630 1909 M9775 HAHTOLA_MYCOSIS_FUNGOIDES_CD4_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_CD4_UP.html Genes up-regulated in T helper cells (defines as CD4+) isolated from patients with mucosis fungoides compared to those from normal control donors. 16914566 78/116 Arthur Liberzon 0.00269549432375063 0.00836471611315119 4405 2621.54545454545 2015 0.000245345689641633 470 1.22552775946349 -1.39320415003383 -1 3.82035889401351 4403 1859 739 2015 1619 4701 4181 4049 1919 470 2882 1910 M4864 KEGG_BASAL_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_TRANSCRIPTION_FACTORS.html Basal transcription factors 31/38 KEGG 0.0156717475285487 0.0313037022152984 1810 2225.72727272727 2016 0.0014349556150997 1058 0.7383800818158 -0.685977523540565 -1 1.66670512753288 1807 2016 3919 2702 1058 1319 1281 2663 1349 4239 2130 1911 M2281 ISSAEVA_MLL2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ISSAEVA_MLL2_TARGETS.html Genes down-regulated in HeLa cells upon knockdown of MLL2 [GeneID=8085] by RNAi. 17178841 90/125 Arthur Liberzon 4.7105707371684e-08 9.28325685181879e-07 1595 2043.45454545455 2016 4.28233712548151e-09 198 1.4146636240632 1.52261505483612 1 12.8048445616172 1592 2372 198 2016 1060 2714 2982 1923 3831 292 3498 1912 M619 REACTOME_TRIGLYCERIDE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRIGLYCERIDE_BIOSYNTHESIS.html Genes involved in Triglyceride Biosynthesis 37/42 Reactome 0.0637245000259572 0.098713370568598 4310 2394.45454545455 2017 0.00596807515798581 804 0.991350408240318 -0.979764110095284 -1 1.49580131478545 4310 867 2017 926 1623 2960 3506 3895 804 1942 3489 1913 M1821 MATZUK_EMBRYONIC_GERM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_EMBRYONIC_GERM_CELL.html Genes important for embryonic germ cell, based on mouse models with female fertility defects. 18989307 21/31 Jessica Robertson 0.137123743493887 0.187764452942021 4350 2500.18181818182 2017 0.0133181530916043 166 1.44120735831183 -1.15040365629593 -1 1.57074923940838 4347 976 1634 517 2017 3911 4475 3348 166 1828 4283 1914 M14744 ZHAN_MULTIPLE_MYELOMA_LB_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_LB_UP.html Top 50 up-regulated genes in cluster LB of multiple myeloma samples belonging to the low bone disease group. 16728703 59/68 Kevin Vogelsang 0.0249422201851214 0.0454370047370794 1740 2071.54545454545 2018 0.0022935973487408 1116 1.10155491698807 1.11175683537677 1 2.21906875025993 1738 1909 1156 2271 1225 2495 1116 2018 3505 2337 3017 1915 M308 TSAI_RESPONSE_TO_RADIATION_THERAPY http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_RESPONSE_TO_RADIATION_THERAPY.html Genes up-regulated in response to both single dose and fractionated radiation that were common to all three cell lines studied. 17440099 57/76 Jessica Robertson 2.55990858777424e-05 0.000223455227185849 715 2123 2019 2.32721670474821e-06 409 1.28567881700599 1.4241029461371 1 7.04298787825739 711 3728 409 3644 1389 2328 2468 2019 4210 982 1465 1916 M1959 HINATA_NFKB_TARGETS_KERATINOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HINATA_NFKB_TARGETS_KERATINOCYTE_DN.html Genes down-regulated in primary keratinocytes by expression of p50 (NFKB1) and p65 (RELA) [GeneID=4790;5970] components of NFKB. 12673201 29/44 Arthur Liberzon 0.088953973515629 0.130798366041673 3215 2284.36363636364 2019 0.00843349684796473 1085 1.22236869283036 -1.27335326830484 -1 1.62021226559049 3212 2019 1169 1456 2588 1705 2671 3882 3493 1085 1848 1917 M7634 REACTOME_MITOTIC_M_M_G1_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_M_M_G1_PHASES.html Genes involved in Mitotic M-M/G1 phases 187/203 Reactome 0.0949341538133026 0.138128608507641 395 2309.36363636364 2020 0.00902697181850818 394 0.751578373482719 -0.771147031819772 -1 0.969446550652775 394 2767 4143 2996 2827 918 1020 2020 1943 4405 1970 1918 M1185 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_DN.html Genes down-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment wiht 4 nM docetaxel [PubChem=148124]. 17099726 11/11 Arthur Liberzon 0.00105461730698816 0.00414125930863905 1430 1979.18181818182 2021 9.59202909108585e-05 308 0.922679083239108 1.00546535902085 1 3.2989707114102 1429 1604 2021 3724 403 2304 2059 308 4312 2345 1262 1919 M1205 SCHRAMM_INHBA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAMM_INHBA_TARGETS_UP.html Genes up-regulated in Kelly cells (neuroblastoma) by overexpressing INHBA [GeneID=3624] off a plasmid vector. 15580313 7/8 Arthur Liberzon 0.00211993277854191 0.00698261180371097 2025 2180 2021 0.000212195784972371 237 1.34457181814388 1.73910474650337 1 4.34971094742752 2021 2175 4389 1579 3396 1604 1734 237 3197 2476 1172 1920 M2410 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4.html Genes regulated in MCF7 cells (breast cancer) by expression of the full-length and truncated (611-CTF) forms of ERBB2 [GeneID=2064] at 60 h time point. 19364815 131/188 Arthur Liberzon 9.99852084889276e-08 1.81771189497532e-06 2460 1942.09090909091 2022 9.08956482118525e-09 125 1.35722123846541 1.30283446429699 1 11.6905878610337 2458 1259 242 684 2685 2022 2362 4391 749 125 4386 1921 M2494 PEDRIOLI_MIR31_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PEDRIOLI_MIR31_TARGETS_DN.html Genes down-regulated in primary LEC cells (lymphatic endothelum) upon overexpression of MIR31 [GeneID=407035]. 20479124 547/811 Arthur Liberzon 3.60625259103115e-05 0.000296026299646383 1040 2297.63636363636 2022 3.6063111151277e-06 249 1.19958506921959 1.17816072738968 1 6.3515048281254 1040 2211 4708 3269 3646 1426 1723 2022 3201 249 1779 1922 M4013 KEGG_GAP_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GAP_JUNCTION.html Gap junction 85/107 KEGG 0.184986435986408 0.242067085626794 1605 1994.81818181818 2023 0.0184236724690331 1400 1.03702617514757 1.00994799033247 1 0.958538573593175 1601 2375 2023 2229 2184 1669 1400 2401 1764 2504 1793 1923 M11405 TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAKADA_GASTRIC_CANCER_COPY_NUMBER_DN.html Candidate genes in the regions of copy number loss in gastric cancer cell lines. 16103878 28/41 Arthur Liberzon 0.0166950364936111 0.032806233243066 3360 2224 2023 0.00152937198999367 680 1.60063466466133 -1.25005973633271 -1 3.56424707113178 3358 3000 1679 1799 1530 2568 2359 680 1403 2023 4065 1924 M8224 ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_DN.html Genes in discrete regions of loss within 16q region detected in individual invasive breast cancer tumors. 16702952 29/64 Arthur Liberzon 0.0409814533673422 0.0680381498043811 2220 2309.54545454545 2023 0.00379685227098883 630 1.40871214500318 1.56845717712878 1 2.46722293424049 2220 2023 1041 1990 4211 1460 630 3932 2899 1081 3918 1925 M3985 KEGG_CITRATE_CYCLE_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CITRATE_CYCLE_TCA_CYCLE.html Citrate cycle (TCA cycle) 30/33 KEGG 0.00187047388201751 0.00636020284346217 1190 2193.72727272727 2024 0.000170187825749201 501 0.557544001749396 -0.571367921145816 -1 1.8375234614648 1186 2006 3947 2403 501 1214 2123 1920 2329 4478 2024 1926 M3058 WALLACE_JAK2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_JAK2_TARGETS_UP.html Genes up-regulated more than 7-fold by expressing JAK2 [GeneID=3717] in the JAK2 null cell line. 15189810 29/50 Arthur Liberzon 0.00152761022948348 0.00545694030563126 1100 1861.18181818182 2024 0.000138970180533982 188 0.766979418416668 -0.754702165799564 -1 2.60436693897874 1096 2024 3396 2392 2339 595 675 188 3045 4024 699 1927 M15699 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_0 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_0.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 0. 12554760 92/110 Arthur Liberzon 0.00470046335229132 0.0126705808239949 1175 1970.81818181818 2025 0.000428230580423566 677 1.29591479260077 1.30516030994129 1 3.6890938954411 1172 2368 758 3272 3445 1641 2025 1816 2413 677 2092 1928 M220 PID_CASPASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CASPASE_PATHWAY.html Caspase cascade in apoptosis 18832364 63/81 Pathway Interaction Database 0.139358623736361 0.190327750010308 4135 2546.18181818182 2027 0.0135507489743632 1250 1.07048458925863 -0.995553561909885 -1 1.15721811804071 4133 1903 2508 1890 2027 4301 3498 1935 1307 1250 3256 1929 M14036 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_DN.html Genes down-regulated in monocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 50/74 Arthur Liberzon 0.0238410023861706 0.0436668728221674 3075 2450.63636363636 2027 0.00219121381877559 708 1.34547185932428 1.33925461394182 1 2.74530135076995 3075 1424 1778 2027 1243 4067 4056 1834 2237 708 4508 1930 M1552 MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_DN.html Cluster 10: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate and TSA [PubChem=5222465;5562] with the same kinetics with which each alters the level of histone H4 acetylation. 10969808 85/101 John Newman 0.0352323956477681 0.0600133191834953 435 2067.18181818182 2029 0.00325541969777555 435 0.935295737893678 0.905135169758316 1 1.71453810743309 435 2837 2670 3406 2029 685 565 1098 3970 3716 1328 1931 M11718 BOYLAN_MULTIPLE_MYELOMA_D_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_DN.html Genes down-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 95/120 Jessica Robertson 0.0737688547123965 0.111670620347181 1590 2150.45454545455 2029 0.00694228644813022 762 1.02972104484784 1.09068420965248 1 1.47094000723022 1589 1839 2686 2004 4324 2064 2387 2029 1772 2199 762 1932 M1170 HUMMERICH_SKIN_CANCER_PROGRESSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_SKIN_CANCER_PROGRESSION_DN.html Selected genes down-regulated during progression through benign to malignant skin tumors formed by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 155/194 Arthur Liberzon 0.0175119383783289 0.0340570041803512 1310 2147 2030 0.00160480967122928 912 1.11400972843233 1.1374500376675 1 2.45344900908646 1308 2781 912 2460 1556 2466 2635 1590 4085 1794 2030 1933 M3003 MEINHOLD_OVARIAN_CANCER_LOW_GRADE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MEINHOLD_OVARIAN_CANCER_LOW_GRADE_UP.html Genes up-regulated in low grade (LMP and G1) serous ovarian carcinomas vs the higher grade invasive tumors (G2 and G3). 15558012 24/31 Arthur Liberzon 0.00286207475417677 0.00872110577128104 2870 2070 2031 0.000260527722376269 235 0.808537727174547 -0.950594705866632 -1 2.49844854509909 2867 1506 3086 1323 2985 2031 4136 264 835 3502 235 1934 M17400 BIOCARTA_ALK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ALK_PATHWAY.html ALK in cardiac myocytes 38/51 BioCarta 0.0702900020558536 0.107219108070914 1920 2377.45454545455 2032 0.00660378685469649 814 1.11958579759182 1.10609371678656 1 1.62899903287883 1918 2490 2324 2032 3569 3675 4107 1264 814 2000 1959 1935 M4306 ONDER_CDH1_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_2_DN.html Genes down-regulated in HMLE cells (immortalized nontransformed mammary epithelium) after E-cadhedrin (CDH1) [GeneID=999] knockdown by RNAi. 18483246 600/793 Jessica Robertson 1.7764598574796e-23 2.70480339590442e-21 1820 2239.09090909091 2032 1.77645985747961e-24 12 1.35404804730955 1.28443790015201 1 41.7891927586825 1819 1134 4470 656 3876 1817 2032 2810 2549 12 3455 1936 M10620 REACTOME_EICOSANOID_LIGAND_BINDING_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EICOSANOID_LIGAND_BINDING_RECEPTORS.html Genes involved in Eicosanoid ligand-binding receptors 5/14 Reactome 0.00114649795893423 0.00441347076059963 2035 1936 2033 0.000114708989469952 82 1.82691576719443 1.82691576719443 1 6.45631405291629 2033 3956 4240 3490 1198 866 82 167 1129 2092 2043 1937 M1089 REACTOME_FGFR4_LIGAND_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FGFR4_LIGAND_BINDING_AND_ACTIVATION.html Genes involved in FGFR4 ligand binding and activation 3/13 Reactome 0.000483440438014243 0.00225345596918031 4305 2581.18181818182 2033 4.8354564182256e-05 87 2.01956705969763 -1.97922420853824 -1 8.02182272188915 4303 1653 4268 1492 2033 3973 4658 87 1102 1619 3205 1938 M11792 BIOCARTA_SHH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SHH_PATHWAY.html Sonic Hedgehog (Shh) Pathway 16/19 BioCarta 0.0261985525131896 0.0473005077701794 1465 2007.09090909091 2034 0.00241053079356824 858 1.02735996804899 -1.26252792615706 -1 2.0426869283266 1464 2619 2615 3323 1417 1950 2034 858 2557 2322 919 1939 M690 REACTOME_KERATAN_SULFATE_KERATIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_KERATIN_METABOLISM.html Genes involved in Keratan sulfate/keratin metabolism 25/32 Reactome 0.00431776872623358 0.0118487606905945 3790 2534.36363636364 2034 0.000393296930209423 468 1.45468739478512 -1.31614410009908 -1 4.20465707572163 3789 1491 754 468 3446 4584 3480 2034 1946 1420 4466 1940 M13462 LUI_THYROID_CANCER_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_5.html Cluster 5: genes with similar expression profiles across follicular thyroid carcinoma (FTC) samples. 15608688 11/14 Leona Saunders 0.122203833038762 0.17085370022007 4675 2316.90909090909 2034 0.0117792448963542 318 1.72275728698352 -2.19441234045909 -1 1.98358459325048 4672 2141 1536 1738 2034 3972 2873 1522 318 1233 3447 1941 M4163 PALOMERO_GSI_SENSITIVITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/PALOMERO_GSI_SENSITIVITY_UP.html Up-regulated genes associated with sensitivity and resistance to gamma-secretase (GSI) in T-cell acute lymphoblastic leukemia (T-ALL) cell lines. 17873882 9/9 Jessica Robertson 0.000410313898317488 0.0019904230216429 2770 2027.81818181818 2035 4.103896788838e-05 9 1.15525663948301 0.957814896613589 1 4.68213391535425 2766 2652 4594 807 3335 1855 1410 79 9 2764 2035 1942 M2565 HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_UP.html Genes distinguishing asparaginase resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 27/41 Arthur Liberzon 0.0193248715558522 0.0367499571892112 2125 1805.54545454545 2036 0.00177243083405839 134 1.05615234990648 1.04131283812594 1 2.27364328034146 2124 2036 2824 1466 3186 876 402 1587 134 2819 2407 1943 M18660 ROETH_TERT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROETH_TERT_TARGETS_UP.html Genes up-regulated in T lymphocytes overexpressing TERT [GeneID=7015] off a retrovirus vector. 15741219 14/19 Kevin Vogelsang 0.145525436365148 0.197689403849974 1660 1981.63636363636 2037 0.0141954216288116 1163 1.38298397253661 1.2506524641566 1 1.46086606245369 1659 1579 2037 2542 2047 2610 2383 1618 1626 1163 2534 1944 M13251 BROWNE_HCMV_INFECTION_14HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_14HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 14 h time point that were not down-regulated at the previous time point, 12 h. 11711622 388/510 John Newman 0.00050149860308728 0.00231611879312325 2890 2155.63636363636 2037 4.5601178013762e-05 314 1.17882258722871 1.16869554861002 1 4.66122893919093 2890 1154 713 314 2037 3261 3345 3571 1453 373 4601 1945 M13148 CHEN_HOXA5_TARGETS_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_6HR_DN.html Genes down-regulated 6 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 9/14 Arthur Liberzon 0.0316307652316847 0.0549290698651772 2145 2290.63636363636 2037 0.00320902240164434 528 1.07095516631579 -1.22257619025903 -1 2.02501900961015 2145 3114 4578 3120 1934 2975 1916 969 528 2037 1881 1946 M1994 KYNG_NORMAL_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_NORMAL_AGING_UP.html Genes distinctly up-regulated in primary fibroblast cultures from normal old donors compared to those from normal young donors. 14527998 28/32 Arthur Liberzon 0.00390613630850621 0.0109743829619936 2720 2032.18181818182 2037 0.000355735364238218 250 1.14100235494506 -1.16886530118554 -1 3.35495337209833 2718 2037 2764 1811 4252 1660 2701 331 250 2873 957 1947 M1767 JI_CARCINOGENESIS_BY_KRAS_AND_STK11_DN http://www.broadinstitute.org/gsea/msigdb/cards/JI_CARCINOGENESIS_BY_KRAS_AND_STK11_DN.html Cluster B: genes down-regulated in primary lung tumors driven by KRAS [GeneID=3845] activation and loss of STK11 [GeneID=6794]; also up-regulated in human squamous cell carcinoma (SCC) vs adenocarcinoma subtype of NSCLC (non-small cell lung cancer). 17676035 25/30 Jessica Robertson 5.92077011928331e-05 0.000435296494751047 470 1732.45454545455 2038 5.3826631532314e-06 385 1.53999593111039 1.59926326873633 1 7.76697192513986 468 2056 455 2661 598 2162 1984 2552 3698 385 2038 1948 M389 NAKAJIMA_MAST_CELL http://www.broadinstitute.org/gsea/msigdb/cards/NAKAJIMA_MAST_CELL.html Top 50 most-increased mast cell specific genes. 11493461 48/75 Kevin Vogelsang 0.0145267242348899 0.0294781334431129 2350 2259.81818181818 2042 0.00132941283723311 626 1.14597517473339 1.32559758008174 1 2.63167886977766 2349 1418 1147 988 3717 4203 2802 626 3860 1706 2042 1949 M19233 EPPERT_CE_HSC_LSC http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_CE_HSC_LSC.html Shared human hematopoietic stem cell (HSC) and acute myeloid leukemia (AML) stem cell (LSC) genes: HSC genes that are highly expressed in LSC versus other leukemic cells. 21873988 54/67 Kolja Eppert 0.0748856241594485 0.11299271205784 1625 2645.72727272727 2043 0.00705119552595089 1141 1.11860685884164 1.03327829040885 1 1.58934148404874 1624 3317 1141 4177 3899 1880 1859 1715 4035 2043 3413 1950 M10573 SWEET_KRAS_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_KRAS_ONCOGENIC_SIGNATURE.html Genes that contributed maximally to the GSEA score of the up-regulated gene set from the KrasLA mouse model in two human lung cancer expression data sets comparing mutant vs normal KRAS [GeneID=3845]. 15608639 108/149 Arthur Liberzon 0.259672677287482 0.322451115441374 2120 2051.54545454545 2044 0.0269628216527463 881 1.02455929801969 1.1355145644638 1 0.755567930617839 2119 1289 2490 881 3609 1667 1489 2592 1461 2044 2926 1951 M2007 MIKKELSEN_ES_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in embryonic stem cells (ES). 17603471 137/229 Arthur Liberzon 1.12271432702512e-09 2.94400645753254e-08 3885 2260.72727272727 2044 1.02064938872552e-10 144 1.46469586897158 -1.62569719096522 -1 16.551702337859 3884 1250 144 439 3723 4109 4230 3702 1164 179 2044 1952 M2046 MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_2 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_2.html Cluster 2: genes up-regulated in SW260 cells (colon cancer) by sodium butyrate, curcumin, sulindac and TSA [PubChem=5222465;969516;5352;5562]. 10969808 13/17 Arthur Liberzon 0.00188994506606032 0.00640816718363405 2890 2052.09090909091 2044 0.000171960964441585 239 0.892969900166333 -0.739652293218922 -1 2.93869374237748 2889 3087 3199 2044 503 1680 4360 351 1001 3220 239 1953 M17183 BENPORATH_OCT4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_OCT4_TARGETS.html Set 'Oct4 targets': genes upregulated and identified by ChIP on chip as OCT4 [GeneID=5460] transcription factor targets in human embryonic stem cells. 18443585 372/499 Jessica Robertson 0.0984842379569595 0.142372313371163 2830 2495.63636363636 2045 0.00938097175493083 1161 1.15636335773668 1.13047009432992 1 1.468824817027 2828 1161 1790 1872 1821 3975 2941 3173 1488 2045 4358 1954 M11025 HOEGERKORP_CD44_TARGETS_TEMPORAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_TEMPORAL_DN.html Genes temporally down-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 27/40 Kevin Vogelsang 0.0108887472602404 0.0233083388065009 965 2213.45454545455 2045 0.0009948197070651 543 0.970428478663419 0.998913451677959 1 2.37703832830145 964 2045 2317 3935 3981 1112 543 563 4382 3279 1227 1955 M10412 ZHAN_MULTIPLE_MYELOMA_PR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_PR_DN.html Top 50 down-regulated genes in cluster PR of multiple myeloma samples characterized by increased expression of proliferation and cell cycle genes. 16728703 57/69 Arthur Liberzon 0.021914470057799 0.0408354909880818 1135 2128.45454545455 2046 0.00201235057868963 433 1.05277959170241 1.12428589505972 1 2.19406126951601 1131 2439 3061 3293 3708 618 433 2046 1233 3428 2023 1956 M219 PID_HEDGEHOG_GLI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HEDGEHOG_GLI_PATHWAY.html Hedgehog signaling events mediated by Gli proteins 18832364 65/86 Pathway Interaction Database 0.00185546767192086 0.0063416418620322 2050 2145.90909090909 2048 0.00016882131029122 281 0.799144811502092 -0.757286471745532 -1 2.63534624780266 2048 1894 3675 3160 495 748 2410 1898 3246 3750 281 1957 M19861 REACTOME_ENERGY_DEPENDENT_REGULATION_OF_MTOR_BY_LKB1_AMPK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENERGY_DEPENDENT_REGULATION_OF_MTOR_BY_LKB1_AMPK.html Genes involved in Energy dependent regulation of mTOR by LKB1-AMPK 21/41 Reactome 0.0583308715605287 0.0916822223661989 2585 1845.54545454545 2048 0.00544885627221086 68 0.793587823781576 0.89248937026146 1 1.23559928400737 2581 350 3229 397 2280 1975 2048 1188 68 3792 2393 1958 M3462 REACTOME_LIPOPROTEIN_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIPOPROTEIN_METABOLISM.html Genes involved in Lipoprotein metabolism 26/44 Reactome 0.0969178484463387 0.140322774437644 2240 2082.63636363636 2048 0.00922462183221238 908 1.3776892737329 -1.32611808241891 -1 1.76299382199935 2240 2048 1330 1039 2558 908 948 3859 3888 2280 1811 1959 M15228 KRISHNAN_FURIN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRISHNAN_FURIN_TARGETS_UP.html Genes up-regulated in naive T lymphocytes lacking FURIN [GeneID=5045]: Cre-Lox knockout of FURIN in CD4+ [GeneID=920] cells. 18690214 18/25 Jessica Robertson 0.0285401739498584 0.0506617604525504 1420 2131.72727272727 2048 0.00262884429519771 1110 1.437599921288 -1.69317275049048 -1 2.79408991689212 1417 3511 1361 1110 1287 1535 3080 2140 3420 2540 2048 1960 M56 PID_LPA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LPA4_PATHWAY.html LPA4-mediated signaling events 18832364 16/19 Pathway Interaction Database 0.0101697864975739 0.0221510808807332 2050 1903.09090909091 2050 0.000928827651783067 276 0.982408285294599 0.930355427366112 1 2.43898614808079 2050 2105 2217 1804 3340 2077 276 758 2494 1796 2017 1961 M674 REACTOME_ALPHA_LINOLENIC_ACID_ALA_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ALPHA_LINOLENIC_ACID_ALA_METABOLISM.html Genes involved in alpha-linolenic acid (ALA) metabolism 15/17 Reactome 0.000270482211535187 0.00146744372235182 2195 1944.18181818182 2050 2.45923156446042e-05 209 1.19327994880831 1.45408872060521 1 5.07328067295264 2192 3515 1989 2342 209 1931 1166 1473 2301 2218 2050 1962 M1433 MA_MYELOID_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/MA_MYELOID_DIFFERENTIATION_DN.html Genes down-regulated during myeloid differentiation induced by tretinoin (ATRA) [PubChem=444795] and IL3 [GeneID=3652] in the EML cell line (myeloid progenitor). 12130493 55/71 Kevin Vogelsang 0.108830564061387 0.154816233384493 2655 2365 2052 0.0104199419354025 1845 1.26843335605836 1.05033323701679 1 1.54192429774356 2653 1924 1877 1907 1871 2052 2934 3283 3570 2099 1845 1963 M11837 RODWELL_AGING_KIDNEY_NO_BLOOD_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_NO_BLOOD_DN.html Genes whose expression decreases with age in normal kidney, excluding those with higher expression in blood. 15562319 189/251 John Newman 0.14776958316108 0.200135561698794 2055 2157.54545454545 2052 0.0144310726275447 393 0.99318486740916 0.961857083463401 1 1.04112630712906 2052 2283 2893 393 4410 1852 2305 1621 1734 2151 2039 1964 M6349 SU_PLACENTA http://www.broadinstitute.org/gsea/msigdb/cards/SU_PLACENTA.html Genes up-regulated specifically in human placenta. 11904358 25/52 John Newman 0.0030497020963657 0.00913942469514037 2635 2240.54545454545 2052 0.000277630718389582 486 1.61036980513362 -1.70959011400764 -1 4.92711395925496 2633 2052 732 2026 4719 2443 2863 1758 3954 486 980 1965 M15997 BIOCARTA_INTRINSIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTRINSIC_PATHWAY.html Intrinsic Prothrombin Activation Pathway 25/36 BioCarta 1.86913692024342e-06 2.38441250366188e-05 580 1701 2054 1.69921682570765e-07 302 1.65900854687132 1.24842673141308 1 11.5073282344796 578 2054 302 1123 716 2792 2084 2615 2845 628 2974 1966 M9826 VANTVEER_BREAST_CANCER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_METASTASIS_DN.html Genes whose expression is significantly and negatively correlated with poor breast cancer clinical outcome (defined as developing distant metastases in less than 5 years). 11823860 162/263 Jean Junior 0.0254388650007825 0.0461280994251607 855 2237.09090909091 2054 0.00233980630919434 776 1.19652086659624 1.19178295092053 1 2.39861517767398 851 4354 2421 4260 3282 776 1583 844 2054 2387 1796 1967 M18 PID_INTEGRIN1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN1_PATHWAY.html Beta1 integrin cell surface interactions 18832364 79/86 Pathway Interaction Database 8.7567800282682e-09 1.94962272327481e-07 2055 1909.36363636364 2055 7.96070914829392e-10 173 1.55990390605688 1.62307092501457 1 15.7058862046255 200 3275 173 3231 2123 2053 2055 1352 3934 494 2113 1968 M1207 NIKOLSKY_BREAST_CANCER_1Q32_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_1Q32_AMPLICON.html Genes within amplicon 1q32 identified in a copy number alterations study of 191 breast tumor samples. 19010930 11/15 Jessica Robertson 0.00194700720911611 0.00654083560642565 2055 2206.45454545455 2055 0.000177157495894762 507 0.948010459885299 1.13758910351786 1 3.10717494585023 2055 1589 2454 1499 507 3736 3571 1672 547 3727 2914 1969 M2313 DELPUECH_FOXO3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELPUECH_FOXO3_TARGETS_UP.html Genes up-regulated in DL23 cells (colon cancer) upon expression of an activated form of FOXO3 [GeneID=2309]. 17452451 117/143 Arthur Liberzon 7.28729841621943e-05 0.000514141233550908 2060 1815.36363636364 2056 6.62503619317882e-06 131 1.19048997153043 1.14206019510393 1 5.87506552919114 2056 634 465 131 2470 2108 3062 3929 3180 320 1614 1970 M16626 BIOCARTA_CK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CK1_PATHWAY.html Regulation of ck1/cdk5 by type 1 glutamate receptors 23/32 BioCarta 0.00493093460691878 0.0131864086938564 2470 1925.36363636364 2057 0.000449274662002249 204 1.02554077738832 -1.29248897990624 -1 2.89272715295187 2468 2057 2897 1844 3083 2938 1580 374 204 2970 764 1971 M1376 GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN.html Genes down-regulated in MMH-RT cells (hepatocytes displaying an invasive, metastatic phenotype) during epithelial to mesenchymal transition (EMT). 16607286 271/350 Jessica Robertson 0.239349026695182 0.300299682615965 3305 2254 2058 0.0245642354818647 1119 1.09415505358273 -1.11048976895993 -1 0.857645425932244 3302 1189 2058 1119 2780 2625 3727 1925 1994 1814 2261 1972 M3559 ZHANG_INTERFERON_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_INTERFERON_RESPONSE.html Interferon-inducible genes up-regulated in A549 cells (lung cancer) infected with a respiratory syncytial virus (RSV) that had its NS1 [GeneID=1494468] gene knocked down by RNAi. 15619625 36/61 Jessica Robertson 0.116376955341311 0.16382649748992 2225 2118.72727272727 2058 0.0111846835753094 257 1.2872540306481 1.57760404871714 1 1.5173508723841 2224 257 1572 2058 2951 1956 2304 4476 1107 1006 3395 1973 M1018 REACTOME_APOPTOSIS_INDUCED_DNA_FRAGMENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOSIS_INDUCED_DNA_FRAGMENTATION.html Genes involved in Apoptosis induced DNA fragmentation 14/16 Reactome 0.0112838778188572 0.0239286718076657 950 2116.18181818182 2059 0.0010311065682892 215 1.66076465992781 -1.88783937979851 -1 4.03964638665028 950 3912 2059 4219 1917 1566 2112 804 3449 2075 215 1974 M4856 MORI_LARGE_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_LARGE_PRE_BII_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Large Pre-BII stage. 18922927 76/100 Jessica Robertson 1.98966859383682e-05 0.000182396771335444 2090 1561.36363636364 2059 1.80880598956751e-06 82 1.31570382823594 -1.44780760114 -1 7.38154367707714 2534 82 477 282 2089 3000 3261 1068 2059 235 2088 1975 M2296 BERGER_MBD2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BERGER_MBD2_TARGETS.html Genes strongly up-regulated in colon tissue upon MBD2 [GeneID=8932] knockout. 17353267 4/23 Arthur Liberzon 0.00340844253526566 0.0099553519594393 2060 1965.45454545455 2059 0.000341368171475132 322 1.34293869065542 1.00568979531536 1 4.03402320586491 2059 1103 4680 717 2925 3379 2418 322 632 1110 2275 1976 M2444 PLASARI_TGFB1_TARGETS_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_TGFB1_TARGETS_1HR_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) upon stimulation with TGFB1 [GeneID=7040] for 1 h. 19752192 6/7 Arthur Liberzon 1.86213946098551e-05 0.000173701546558332 3820 2244.36363636364 2059 1.86215506520471e-06 49 1.37232370961077 1.13450866678962 1 7.74288766835927 3820 1639 4703 1715 49 2526 2534 2059 1666 565 3412 1977 M1825 REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_ACETYLCHOLINE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_ACETYLCHOLINE.html Genes involved in Regulation of Insulin Secretion by Acetylcholine 11/13 Reactome 2.67654164721658e-07 4.47988531023484e-06 3605 2019.54545454545 2060 2.43321997531575e-08 1 1.01424808450495 -0.858565482540991 -1 8.14012897411278 3603 425 2060 1019 1 2517 3780 1086 131 3016 4577 1978 M1498 BRACHAT_RESPONSE_TO_METHOTREXATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_METHOTREXATE_DN.html Genes down-regulated in FL5.12 cells (pro-B lymphocyte) in response to methotrexate [PubChem=4112]. 12447701 37/59 John Newman 0.00200746980244376 0.00669156600814588 2700 2053.09090909091 2062 0.00018266399405275 513 1.09017387526947 -0.950069628681025 -1 3.55695625540508 2698 2497 2919 3163 513 1015 1532 1983 756 3446 2062 1979 M971 REACTOME_ION_TRANSPORT_BY_P_TYPE_ATPASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ION_TRANSPORT_BY_P_TYPE_ATPASES.html Genes involved in Ion transport by P-type ATPases 29/39 Reactome 0.295941055462827 0.360103578701867 4530 2540.27272727273 2063 0.0313959634964006 1075 1.20119526834619 -1.27223539306674 -1 0.799397169003561 4529 2014 1592 1780 3892 4087 3254 2063 1075 1389 2268 1980 M1257 INAMURA_LUNG_CANCER_SCC_SUBTYPES_DN http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_SUBTYPES_DN.html Down-regulated genes discriminating between two subtypes of squamous cell carcinoma (SCC) type of non-small cell lung cancer: SSC-A vs SSC-B. 16007138 6/7 Arthur Liberzon 0.00469991788374269 0.0126705808239949 1090 2462.45454545455 2063 0.000470988772558844 553 0.478044425115866 0.478044425115866 1 1.36078716530741 1088 3130 4402 3787 718 806 553 1494 4390 4656 2063 1981 M1680 SUZUKI_RESPONSE_TO_TSA http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_RESPONSE_TO_TSA.html Genes up-regulated by TSA alone [PubChem=5562], with non-hypermethylated promoters, in RKO cells (colorectal cancer). 11992124 23/32 John Newman 0.149475714071112 0.201867058774148 1890 2604.54545454545 2064 0.0146106059889899 1166 0.865668842309623 -0.831706541933923 -1 0.902581811099513 1886 3850 3129 3777 2064 1428 1735 1716 4448 3451 1166 1982 M2183 WANG_ADIPOGENIC_GENES_REPRESSED_BY_SIRT1 http://www.broadinstitute.org/gsea/msigdb/cards/WANG_ADIPOGENIC_GENES_REPRESSED_BY_SIRT1.html Adipogenic genes (group 2) that are selectively repressed by SIRT1 [GeneID=23411] in mature 3T3-L1 adipocytes. 17954559 35/62 Arthur Liberzon 0.00322585823381591 0.00960634123887135 990 2148.54545454545 2065 0.000293690730906929 285 1.10819891775797 1.13826441482557 1 3.35464744974024 988 2507 2065 3062 3917 1826 3182 285 2038 2556 1208 1983 M1521 WESTON_VEGFA_TARGETS_6HR http://www.broadinstitute.org/gsea/msigdb/cards/WESTON_VEGFA_TARGETS_6HR.html Genes up-regulated in MMEC cells (myometrial endothelium) at 6 h after VEGFA [GeneID=7422] stimulation. 12200464 75/93 John Newman 2.22327020307832e-08 4.5625371124042e-07 165 1925.18181818182 2067 2.02115475049654e-09 164 1.49504947577243 1.50826152138952 1 14.2245245199498 164 3274 189 3095 1617 2143 2067 1964 3815 689 2160 1984 M10695 BROWNE_HCMV_INFECTION_8HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_8HR_UP.html Genes up-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 8 h time point that were not up-regulated at the previous time point, 6 h. 11711622 165/217 John Newman 0.0250108988436435 0.0454918853726386 2070 2461 2067 0.00229998609192666 1128 1.2507825009655 1.20765773801446 1 2.51871629857851 2067 4717 1128 4061 1230 1403 1640 3423 2871 1468 3063 1985 M19460 WOOD_EBV_EBNA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WOOD_EBV_EBNA1_TARGETS_DN.html Genes down-regulated in the Ad/AH cells (adenocarcinoma) engineered to stably express the Epstein-Barr virus (EBV) gene EBNA1. 17486072 60/74 Arthur Liberzon 0.0556267814323603 0.0881956359962178 2945 2588.36363636364 2068 0.0051895631128626 1165 1.10119239832168 -1.11126374224954 -1 1.74239657206561 2943 1388 1688 2068 4549 4051 4232 1165 3039 1318 2031 1986 M3506 MOREIRA_RESPONSE_TO_TSA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOREIRA_RESPONSE_TO_TSA_DN.html Down-regulated in CD4+ [GeneID=920] T lymphocytes after 4 h treatment with 100 nM TSA [PubChem=5562]. 14606959 16/24 John Newman 0.0121138369045374 0.0253783001284584 4030 1953 2068 0.00110736890599346 161 1.21154463704596 0.929976291079307 1 2.90049679820026 4030 402 2068 353 1545 3362 2814 584 161 2328 3836 1987 M15955 KEGG_SPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPHINGOLIPID_METABOLISM.html Sphingolipid metabolism 39/46 KEGG 0.00237834253604135 0.00762102971494582 4595 2043.45454545455 2069 0.000216447052414282 100 1.05786074219935 -1.00915033802781 -1 3.36186131494113 4595 224 2442 494 541 4448 2699 3682 100 2069 1184 1988 M16894 KEGG_COMPLEMENT_AND_COAGULATION_CASCADES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_COMPLEMENT_AND_COAGULATION_CASCADES.html Complement and coagulation cascades 47/95 KEGG 1.25653908642304e-07 2.2296483037281e-06 1075 1893.81818181818 2069 1.14230832562799e-08 159 1.65637198662182 1.41740852052881 1 14.046897198139 1074 2915 222 3013 159 2859 2069 2595 3231 760 1935 1989 M16515 CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_AKT1_SIGNALING_VIA_MTOR_UP.html Genes in the AKT1 [GeneID=207] pathway which are independent of MTOR [GeneID=2475], insensitive to RAD001 (everolimus) [PubChem=6442177]. 17213801 52/58 Arthur Liberzon 0.00355824691439456 0.0102784121394996 960 1919.45454545455 2069 0.000324001366786723 76 0.863153566859298 -0.80605171409941 -1 2.57480632764034 956 2445 3329 2069 4676 104 300 1611 2343 3205 76 1990 M8432 NIKOLSKY_BREAST_CANCER_12Q24_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_12Q24_AMPLICON.html Genes within amplicon 12q24 identified in a copy number alterations study of 191 breast tumor samples. 19010930 15/18 Jessica Robertson 0.000490540401515945 0.00227664768451845 4185 2268.45454545455 2069 4.46045284447493e-05 15 1.13076826510582 -1.22834625611196 -1 4.48387730454007 4182 1035 3003 551 306 3780 4253 1843 15 3916 2069 1991 M2701 ST_MYOCYTE_AD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_MYOCYTE_AD_PATHWAY.html Myocyte Adrenergic Pathway is a specific case of the generalized Adrenergic Pathway. 39/54 Signaling Transduction KE 0.00577426225782821 0.0142024584976285 2640 2247.81818181818 2070 0.000526315789473684 195 1.09177912148197 1.14046030408615 1 3.02675964579813 2638 856 1859 195 4417 4508 3187 2198 1064 2070 1734 1992 M2817 STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/STARK_PREFRONTAL_CORTEX_22Q11_DELETION_UP.html Genes up-regulated in prefrontal cortex (PFC) of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 285/347 Jessica Robertson 0.0930327200414549 0.135864615902125 2075 1966.36363636364 2072 0.0088378873729451 545 1.02423299103275 0.972141616221898 1 1.33220753247931 585 545 2299 1754 4254 1443 935 3381 2073 2289 2072 1993 M1594 BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_CAMPTOTHECIN_UP.html Genes specifically up-regulated in FL5.12 cells (pro-B lymphocyte) by camptothecin [PubChem=2538]. 12447701 35/56 John Newman 0.000829100071442801 0.00344182263606862 2950 2104.09090909091 2072 7.54011540084148e-05 373 1.11173688743435 -1.13489985315499 -1 4.10898300291143 2946 876 2072 1785 373 2880 4124 3670 434 1499 2486 1994 M3009 HORTON_SREBF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HORTON_SREBF_TARGETS.html Genes up-regulated in liver from mice transgenic for SREBF1 or SREBF2 [GeneID = 6720, 6721] and down-regulated in mice lacking SCAP [GeneID=22937]. 14512514 33/35 Arthur Liberzon 0.00214753076189217 0.00704891877338738 1700 1947.27272727273 2072 0.000195420904010386 180 1.14931416193093 1.13155396006576 1 3.71095531561045 1697 1464 2417 1337 526 3140 2072 3474 180 2412 2701 1995 M8702 DAZARD_RESPONSE_TO_UV_NHEK_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_NHEK_DN.html Genes down-regulated in NHEK cells (normal keratinocytes) by UV-B irradiation. 12771951 438/494 John Newman 0.0607601479143522 0.0948686398133452 940 2177.27272727273 2073 0.00568237559638115 940 1.02138075795872 0.994414568832038 1 1.56755834074461 940 2222 3758 1899 1595 2080 1667 2073 1298 3263 3155 1996 M1708 HOWLIN_CITED1_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_2_DN.html Genes down-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs wild type (WT) animals. 16278680 22/26 Arthur Liberzon 0.0112125615895404 0.0238608163672817 3565 2142.81818181818 2073 0.0010245562591284 404 1.35238051190257 0.780704081542105 1 3.29201537638443 3563 2577 1838 2553 953 3611 2471 1604 404 1924 2073 1997 M2091 NOUSHMEHR_GBM_SILENCED_BY_METHYLATION http://www.broadinstitute.org/gsea/msigdb/cards/NOUSHMEHR_GBM_SILENCED_BY_METHYLATION.html Top 50 most differentially hypermethylated and down-regulated genes in proneural G-CIMP (a CpG island methylator phenotype) GBM (glyoblastoma multiforme) tumors. 20399149 51/75 Arthur Liberzon 2.16873925305716e-05 0.000194979986179615 4295 2360.54545454545 2074 1.97160057507205e-06 399 1.51864118529834 -1.42326809333194 -1 8.4540852261446 4291 800 399 1412 1390 4381 3682 3863 2074 500 3174 1998 M2085 VARELA_ZMPSTE24_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VARELA_ZMPSTE24_TARGETS_UP.html Top genes up-regulated in liver tissue from mice with knockout of ZMPSTE24 [GeneID=10269]. 16079796 52/57 John Newman 0.00138070909858259 0.00503239146355971 2075 2316.09090909091 2075 0.000125597853354099 453 1.17260602169506 1.08115595493679 1 4.04366544948392 2075 3321 1844 2594 453 1471 1252 4615 2979 1660 3213 1999 M18159 BIOCARTA_RB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RB_PATHWAY.html RB Tumor Suppressor/Checkpoint Signaling in response to DNA damage 20/23 BioCarta 0.0356114807264608 0.0605715996500522 2040 2277.90909090909 2077 0.00329103058182797 568 0.845158361931858 1.01116527990081 1 1.54419266550369 2040 2077 2503 1914 1828 1477 568 2381 3926 3743 2600 2000 M19784 BIOCARTA_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCR_PATHWAY.html T Cell Receptor Signaling Pathway 61/73 BioCarta 0.0073324306949668 0.0170909001877745 810 2018.45454545455 2077 0.000668816705977383 219 0.839407731215366 0.779363819311087 1 2.22581181948469 808 3303 3442 3258 1262 778 219 2077 2131 3595 1330 2001 M12090 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_ERYTHROCYTE_DN.html Genes down-regulated in erythroid lineage cells by RUNX1-RUNX1T1 [GeneID=861;862] fusion . 17898786 14/25 Arthur Liberzon 0.0361949164194991 0.0613208921392807 1415 2092.72727272727 2077 0.00334586283608464 1037 1.46831986912122 1.32812876250011 1 2.67108785850206 1415 2627 1037 3712 1394 1614 1223 2858 2905 2077 2158 2002 M537 REACTOME_REGULATION_OF_KIT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_KIT_SIGNALING.html Genes involved in Regulation of KIT signaling 22/24 Reactome 0.0108704905410945 0.0232798164037958 325 1701.18181818182 2078 0.000993143417647414 286 0.920374649992267 0.888503816925027 1 2.25516176727806 323 2078 2729 3184 2303 524 286 629 2259 3381 1017 2003 M2304 VANDESLUIS_NORMAL_EMBRYOS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_NORMAL_EMBRYOS_DN.html Genes down-regulated in normal 9.5 days post coitus (dpc) embryos compared to normal 8.5 dpc and 9.5 dpc embryos. 17371845 21/62 Arthur Liberzon 0.0203190685185006 0.0383317359741499 4060 2462.18181818182 2079 0.00186447247599195 691 1.45807893570634 1.04405949486647 1 3.09889356017995 4057 2079 1058 2551 1159 4318 4203 1339 691 1441 4188 2004 M6862 NADERI_BREAST_CANCER_PROGNOSIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NADERI_BREAST_CANCER_PROGNOSIS_UP.html Up-regulated genes in the breast cancer prognostic signature of 70 genes that significantly correlated with survival. 16936776 58/147 Arthur Liberzon 0.200302190347314 0.258824327799352 1245 2294.54545454545 2080 0.0201150612915781 1157 0.944546894036916 -0.753024533862045 -1 0.831848843299153 1244 2435 3233 1606 4002 1157 1319 2419 2080 3752 1993 2005 M2767 KANG_CISPLATIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_CISPLATIN_RESISTANCE_UP.html Genes up-regulated in gastric cancer cell lines resistant to cisplatin [PubChem=2767]. 14734480 21/30 Arthur Liberzon 0.0119474507507202 0.0250853948146794 2130 2060.27272727273 2080 0.00109207553731689 225 1.23837051826169 1.19219382702734 1 2.97408988470641 2129 2080 2070 2858 3212 1529 2559 2924 1250 1827 225 2006 M2379 IKEDA_MIR30_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR30_TARGETS_UP.html Genes up-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-30 microRNA. 19188439 209/261 Arthur Liberzon 0.103496354493399 0.14834582241386 665 2073.54545454545 2080 0.00988292334405825 664 1.0365666012689 1.06734385666961 1 1.28888341264389 664 2276 2571 1359 4224 2089 1419 1443 2613 2071 2080 2007 M1346 SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_UP.html Genes up-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 6 h. 18794802 228/305 Jessica Robertson 0.0322041530299125 0.0557084676703681 385 2293.54545454545 2081 0.00297140532320115 381 1.06735880020558 1.08210657845608 1 2.00841835598887 381 4338 2081 3855 3862 994 817 933 3534 2930 1504 2008 M8626 SIG_BCR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/SIG_BCR_SIGNALING_PATHWAY.html Members of the BCR signaling pathway 52/63 Signaling Gateway 0.0168019412751318 0.0329477203234824 2085 1966.09090909091 2082 0.00153924098593755 165 0.82890972820455 0.779436435103663 1 1.84341657669383 2082 165 2808 898 1089 2137 1074 1506 4154 3494 2220 2009 M11911 KEGG_ABC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ABC_TRANSPORTERS.html ABC transporters 35/50 KEGG 0.0011153631609224 0.00432581275230379 1095 1976.45454545455 2083 0.000101448093913792 151 1.21244518822744 -1.20128130192314 -1 4.30059224506422 1095 2511 1175 2083 1737 2405 3377 151 4270 2552 385 2010 M10082 BIOCARTA_TNFR2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR2_PATHWAY.html TNFR2 Signaling Pathway 21/22 BioCarta 0.00962824081458263 0.0211866184824382 850 1899.54545454545 2084 0.000879148959419471 848 0.87279373106238 0.894415364865588 1 2.19215834659418 848 2084 2929 1096 894 1513 973 3177 2682 2303 2396 2011 M234 PID_IL2_STAT5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_STAT5_PATHWAY.html IL2 signaling events mediated by STAT5 18832364 34/46 Pathway Interaction Database 0.00577426225782821 0.0142024584976285 3015 1863.63636363636 2085 0.000526315789473684 199 1.11417131427873 1.07714272121252 1 3.08884011053578 3014 276 2192 199 1162 3742 2693 953 742 2085 3442 2012 M672 CHIN_BREAST_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIN_BREAST_CANCER_COPY_NUMBER_UP.html Genes from common regions of gains observed in more than 15% of 148 primary breast cancer tumors. 17001317 34/37 Arthur Liberzon 0.0689531232531163 0.105634125853524 4455 2477.81818181818 2086 0.00647401196857179 249 1.12133504012001 -0.77183203310851 -1 1.6424272246596 4451 249 2069 602 4273 3785 3617 1256 439 2086 4429 2013 M4435 YAO_HOXA10_TARGETS_VIA_PROGESTERONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAO_HOXA10_TARGETS_VIA_PROGESTERONE_DN.html Genes down-regulated in the uteri of ovariectomized mice 6 h after progesterone [PubChem=5994] injection: HOXA10 [GeneID=3206] knockout vs wild type animals. 12554760 25/36 Kevin Vogelsang 0.000589793083841552 0.00262093635000982 2835 2251.45454545455 2086 5.36319326837792e-05 383 1.50900048972967 -1.74752754511881 -1 5.8452457939284 2834 3458 639 2086 1960 2930 4220 1709 1724 383 2823 2014 M11814 GRANDVAUX_IRF3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRANDVAUX_IRF3_TARGETS_DN.html Genes down-regulated in Jurkat cells (T lymphocyte) by expression of a constitutively active form of IRF3 [GeneID=3661]. 11991981 20/33 Yujin Hoshida 0.0470237707430041 0.0763845939961505 3080 2147.18181818182 2087 0.00436909295836955 1003 1.46851852344801 -1.15525340635668 -1 2.46123732105063 3076 2087 1472 1003 3080 2501 1138 1085 4073 1760 2344 2015 M1393 SHIN_B_CELL_LYMPHOMA_CLUSTER_9 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_9.html Cluster 9 of genes distinguishing among different B lymphocyte neoplasms. 19010892 8/25 Jessica Robertson 0.00305976281374163 0.00915825832494322 2665 2169.63636363636 2088 0.000306398396280679 614 1.25040199076977 1.03770132094812 1 3.82404942641697 2662 3122 4461 2088 614 2483 1238 909 1829 1886 2574 2016 M20 PID_P38_MKK3_6PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_MKK3_6PATHWAY.html p38 MAPK signaling pathway 18832364 34/36 Pathway Interaction Database 0.0725811132503135 0.110013761895144 2090 2267.72727272727 2089 0.00682658698825764 839 0.895402062187694 0.945789976710046 1 1.28777602087345 2089 1993 3273 2162 3409 1225 839 2036 1705 3668 2546 2017 M1800 ZHENG_IL22_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_IL22_SIGNALING_UP.html Genes up-regulated in ex-vivo colonic tissue after treatment with IL22 [GeneID=50616]. 18264109 74/114 Jessica Robertson 1.6925372438776e-12 6.88687568198471e-11 4565 2194.90909090909 2092 1.53867022170809e-13 68 1.72794108422723 -1.88272028629455 -1 26.347974510675 4564 1330 90 917 2338 2092 3894 3585 871 68 4395 2018 M1453 NADLER_HYPERGLYCEMIA_AT_OBESITY http://www.broadinstitute.org/gsea/msigdb/cards/NADLER_HYPERGLYCEMIA_AT_OBESITY.html Genes correlated with the development of hyperglycemia in obese mice. 11027337 69/86 Kevin Vogelsang 0.0895313437531435 0.131360877374833 1090 1952.81818181818 2094 0.00849064055023541 513 0.996405718006662 0.892036057405277 1 1.31789919963755 1090 1347 2865 1078 1771 2819 3216 2094 513 2275 2413 2019 M266 PID_NCADHERIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NCADHERIN_PATHWAY.html N-cadherin signaling events 18832364 64/76 Pathway Interaction Database 0.43119990772354 0.499814448548158 2100 2236.54545454545 2096 0.05 125 1.03263367903611 0.940933901702702 1 0.466586179588357 2096 125 2035 621 4057 3828 3337 3257 1556 1518 2172 2020 M17374 SASAKI_TARGETS_OF_TP73_AND_TP63 http://www.broadinstitute.org/gsea/msigdb/cards/SASAKI_TARGETS_OF_TP73_AND_TP63.html Genes up-regulated in DLD1 cells (colon cancer) by p73 beta [GeneID=7161] or by and p63 gamma [GeneID=8626] but not by p53 [GeneID=7157]. 15856012 12/13 Arthur Liberzon 0.0347002543578534 0.0592351539128636 1170 2175.27272727273 2096 0.00320545231711662 555 1.10954284643328 0.987535169053493 1 2.04341585905529 1170 3556 2096 3585 2691 905 555 4128 1698 2457 1087 2021 M758 REACTOME_ABC_FAMILY_PROTEINS_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABC_FAMILY_PROTEINS_MEDIATED_TRANSPORT.html Genes involved in ABC-family proteins mediated transport 30/45 Reactome 0.0029717582625344 0.00900301604567547 820 2065.63636363636 2097 0.000270525465374132 271 1.29191540564756 -1.20961875112146 -1 3.96540502656262 818 3410 1117 3056 1471 2097 3064 271 4302 2593 523 2022 M9291 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_16 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_16.html Amplification hot spot 16: colocolized fragile sites and cancer genes in the 8q11.1-q24.3 region. 16751803 12/15 Arthur Liberzon 0.00607795291867442 0.0147875967918264 3185 2183.90909090909 2101 0.000554073613607874 202 1.20958820914173 1.49924281886711 1 3.32155085955344 3184 2136 2632 2101 1487 4264 4199 413 202 1840 1565 2023 M16061 STANELLE_E2F1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/STANELLE_E2F1_TARGETS.html Genes up-regulated by induction of E2F1 expression in Saos2 (osteosarcoma) cells. 11937641 41/59 Yujin Hoshida 0.00577426225782821 0.0142024584976285 2340 1880.63636363636 2102 0.000526315789473684 169 1.18818114352034 1.31042588390921 1 3.29402611604116 2339 860 2102 169 2578 2504 1065 2379 1332 3304 2055 2024 M17359 XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_UP.html Genes up-regulated in DU-145 cells (prostate cancer) in the absence but not in the presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 27/37 Arthur Liberzon 0.00327626204014133 0.00973187969129456 4095 2096.36363636364 2103 0.000298286479907279 604 1.44721120595567 -1.63496446761331 -1 4.36866470671755 4095 3009 1222 2103 604 2293 3133 2353 1714 1253 1281 2025 M549 REACTOME_DOWNREGULATION_OF_ERBB2_ERBB3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNREGULATION_OF_ERBB2_ERBB3_SIGNALING.html Genes involved in Downregulation of ERBB2:ERBB3 signaling 16/19 Reactome 0.0189021559360551 0.0361939862142718 2560 1917.18181818182 2104 0.00173332199416087 399 1.09874597810529 1.49149560019507 1 2.37625646171938 2556 2104 2265 1648 3167 1569 399 1458 524 2324 3075 2026 M18441 THUM_SYSTOLIC_HEART_FAILURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/THUM_SYSTOLIC_HEART_FAILURE_DN.html Genes down-regulated in samples with systolic heart failure compared to normal hearts. 17606841 290/337 Arthur Liberzon 0.0657974822687977 0.101458384942413 1155 2109.18181818182 2104 0.00616835490737411 1154 1.08549400800665 1.08784701362552 1 1.61845787666356 1154 2727 3462 1294 1632 2171 1594 2104 1211 3257 2595 2027 M6452 KAUFFMANN_MELANOMA_RELAPSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_MELANOMA_RELAPSE_DN.html DNA repair and replication genes down-regulated in melanoma patients who will relapse vs patients who will not. 17891185 8/9 Jessica Robertson 0.00743121341231496 0.0172529893291326 4665 2456.09090909091 2104 0.000745618132227688 80 0.886385871054483 -0.644182497063505 -1 2.34493473397791 4665 1079 4426 561 848 3023 2104 4699 80 1884 3648 2028 M923 REACTOME_RAP1_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAP1_SIGNALLING.html Genes involved in Rap1 signalling 19/20 Reactome 0.143808626313424 0.195669275352943 1385 2290.54545454545 2105 0.0140155242024062 1384 1.28715953109154 1.14254865555557 1 1.36825352148376 1384 4213 2013 2921 2877 1767 1451 1606 2252 2607 2105 2029 M14742 HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_UP.html Genes up-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrom (MDS) compared to the low risk patients. 12411319 29/43 Arthur Liberzon 0.0173387963518437 0.0337898921472759 2430 2023.18181818182 2106 0.00158881592417262 960 0.922811884529009 -0.778314832686407 -1 2.03707977609719 2426 2994 2908 2343 1100 1342 960 1762 1398 2106 2916 2030 M9719 CAVARD_LIVER_CANCER_MALIGNANT_VS_BENIGN http://www.broadinstitute.org/gsea/msigdb/cards/CAVARD_LIVER_CANCER_MALIGNANT_VS_BENIGN.html Genes identified by subtractive hybridization comparing malignant and benign components of a hepatocellular carcinoma (HCC) in a pre-existing liver adenoma in a morphologically normal liver. 16314847 56/108 Arthur Liberzon 0.000365363936687624 0.00182875692594442 2490 2254.45454545455 2107 3.32204207671258e-05 556 1.63545844722028 -1.43622243509956 -1 6.71866803319071 2490 2887 556 2107 2276 1704 4089 3877 1800 931 2082 2031 M1234 OXFORD_RALA_AND_RALB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_AND_RALB_TARGETS_DN.html Genes down-regulated in the UMUC-3 cells (bladder cancer) after knockdown of both RALA and RALB [GeneID=5898;5899] by RNAi. 17496927 24/25 Arthur Liberzon 0.0041943240089639 0.0115840897146341 110 2311 2107 0.00038203108567521 106 1.17507507107811 1.17507507107811 1 3.41373878639867 106 3486 1188 3685 1784 2222 1971 2107 4591 3052 1229 2032 M4648 ZEMBUTSU_SENSITIVITY_TO_NIMUSTINE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_NIMUSTINE.html Top genes associated with chemosensitivity to nimustine [PubChem=39214] across 85 tumor xenografts. 11809704 17/30 Arthur Liberzon 0.026567842802301 0.0478461830978694 1760 2181.81818181818 2107 0.00244492866079639 1254 1.08530366348901 1.0746521800587 1 2.14978915549904 1757 3069 2133 3728 1254 1456 1571 2336 2107 1905 2684 2033 M10949 AMUNDSON_GENOTOXIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_GENOTOXIC_SIGNATURE.html Genes discriminating genotoxic (DNA damaging) agents from other kinds of stresses. 15824734 119/151 Arthur Liberzon 0.152981785254791 0.205836381528681 1735 2005.18181818182 2108 0.0149805741433698 654 1.01064019591527 1.10219035571363 1 1.04092816719877 1731 654 2753 2108 3588 988 1172 2147 2540 2492 1884 2034 M1497 LEE_AGING_NEOCORTEX_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_NEOCORTEX_DN.html Downregulated in the neocortex of aged adult mice (30-month) vs young adult (5-month) 10888876 94/137 John Newman 0.0301073452348698 0.0527375425762961 2110 1948.72727272727 2108 0.00277522182309812 673 1.2013010816015 -1.33276953314611 -1 2.3033706789952 2338 4046 2110 2193 1835 673 2108 908 1884 2636 705 2035 M1252 CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/CEBALLOS_TARGETS_OF_TP53_AND_MYC_DN.html Genes down-regulated in K562 cells (chronic myelogenous leukemia, CML) expressing TP53 and MYC [GeneID=7157;4609]. 15856024 44/62 Arthur Liberzon 0.0105965018647378 0.0228299809713082 1810 2259.72727272727 2109 0.000967989793688749 551 1.24877860402833 1.25108193321666 1 3.07575496488924 1808 3766 2195 3303 3050 2109 2235 551 2092 1768 1980 2036 M8139 HOEGERKORP_CD44_TARGETS_TEMPORAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_TEMPORAL_UP.html Genes temporally up-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 12/15 Kevin Vogelsang 0.00776288043808395 0.0178189980718319 1130 2303.72727272727 2109 0.000708218953065295 163 1.0053643298221 1.0053643298221 1 2.63855805036034 1129 3925 2974 3993 2109 1237 681 1099 4227 3804 163 2037 M10959 REACTOME_OTHER_SEMAPHORIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OTHER_SEMAPHORIN_INTERACTIONS.html Genes involved in Other semaphorin interactions 24/29 Reactome 0.0109984757677751 0.0235005910474869 2585 2022.36363636364 2110 0.00100489531559 567 1.38826873923126 1.55676581942996 1 3.39314084788179 882 3028 1358 2582 2958 2582 1085 567 3702 2110 1392 2038 M2535 PECE_MAMMARY_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PECE_MAMMARY_STEM_CELL_DN.html The '3/3 signature': genes consistently down-regulated in all three pools of normal mammary stem cells (defined by their ability to retain the dye PKH26). 20074520 195/217 Arthur Liberzon 0.429479906129099 0.499814448548158 1135 2171.72727272727 2110 0.0497392022090864 1134 1.04061723417059 1.22188743258375 1 0.470194294882929 1134 1222 2807 2040 2729 2110 1864 2702 1571 3351 2359 2039 M781 REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_3_UTR_MEDIATED_TRANSLATIONAL_REGULATION.html Genes involved in 3' -UTR-mediated translational regulation 124/229 Reactome 0.00580500889379023 0.0142632181044716 120 2518.81818181818 2111 0.000529125731681085 120 0.647482055082471 0.602013181403964 1 1.79318225927073 120 4405 4166 4545 1063 448 298 2111 4674 4458 1419 2040 M2543 GENTLES_LEUKEMIC_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/GENTLES_LEUKEMIC_STEM_CELL_DN.html Genes down-regulated in LSC (leukemic stem) cells compared to LPC (leukemia progenitor) cells from AML (acute myeloid leukemia) tumor samples. 21177505 12/40 Andrew Gentles 0.159731438621763 0.213397223406375 2835 2508.27272727273 2112 0.0156967489859419 1483 1.20368956056039 -1.51649393263461 -1 1.21148682328999 2831 1588 2348 2023 2112 4605 3331 2097 1483 3133 2040 2041 M1677 WENG_POR_TARGETS_LIVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_LIVER_DN.html Genes down-regulated in liver from mice with liver specific knockout of POR [GeneID=5447]. 16006652 27/35 John Newman 0.0152380281442824 0.0305797163439681 870 2102.18181818182 2113 0.00139496430888876 277 1.13490024691409 1.25577655920972 1 2.57911103218546 867 4186 2167 2113 1866 817 350 3712 3952 2817 277 2042 M3485 MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MONNIER_POSTRADIATION_TUMOR_ESCAPE_DN.html The postradiation tumor escape signature: genes down-regulated in tumors from irradiated stroma vs those from non-irradiated stroma. 18794119 516/596 Jessica Robertson 0.0412906945753712 0.0684552435531268 4240 2338.18181818182 2113 0.00420785931163743 268 1.02887391312728 -0.926199874106037 -1 1.79784679688905 4240 495 4507 268 1481 2113 4337 2813 1194 1505 2767 2043 M393 VANTVEER_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_ESR1_UP.html Up-regulated genes from the optimal set of 550 markers discriminating breast cancer samples by ESR1 [GeneID=2099] expression: ER(+) vs ER(-) tumors. 11823860 217/252 Arthur Liberzon 0.00577426225782821 0.0142024584976285 3275 1743.90909090909 2113 0.000526315789473684 26 1.04344430380323 -1.03112557231024 -1 2.89275544300561 3271 559 2159 26 2775 1362 3671 2113 284 2317 646 2044 M9070 BIOCARTA_CREB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CREB_PATHWAY.html Transcription factor CREB and its extracellular signals 42/45 BioCarta 0.0193455589179604 0.0367744817127559 2770 2134.72727272727 2114 0.00177434518252429 958 0.787639239423983 0.824662951631895 1 1.69522948658606 2770 2479 3431 1677 1145 2114 958 1767 1294 3008 2839 2045 M1617 KEEN_RESPONSE_TO_ROSIGLITAZONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KEEN_RESPONSE_TO_ROSIGLITAZONE_DN.html Genes down-regulated in aorta biopsies from mice treated with rosiglitazone [PubChem=77999]. 15054141 154/202 John Newman 0.000195841059435782 0.00114402203036744 940 2137 2114 1.78053177380098e-05 522 1.42614215798201 1.35394270573433 1 6.29471200354455 936 4012 522 3852 1778 2198 1291 3407 2688 709 2114 2046 M1942 MEISSNER_BRAIN_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) that have no histone H3 methylation marks in brain. 18600261 24/152 Jessica Robertson 0.0341293527443226 0.0583661394757981 4655 2503.54545454545 2114 0.00315187322818135 445 1.33737173246691 -1.68110508335316 -1 2.47590450312819 4653 1512 1789 1979 1369 4446 3718 2352 445 2114 3162 2047 M2131 WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_UP.html Genes up-regulated in RS4;11 cells (MLL, mixed lineage leukemia) in response to SB216763 [PubChem=176158], an inhibitor of GSK3B [GeneID=2932]. 20541704 458/675 Arthur Liberzon 0.160679020551735 0.214299230574792 1570 2136.27272727273 2114 0.0157977109082007 1496 1.04926411235264 1.04297684509239 1 1.05316332338621 1568 1689 2739 1496 2114 2622 2151 2171 2076 1955 2918 2048 M6364 HEIDENBLAD_AMPLIFIED_IN_SOFT_TISSUE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLIFIED_IN_SOFT_TISSUE_CANCER.html Genes from selected recurrently amplified regions in soft tissue tumors with supernumerary ring chromosomes. 16732325 15/18 Arthur Liberzon 0.00339710946742982 0.00994070470320445 1035 1821.09090909091 2115 0.000309306040941303 129 1.12562528172801 1.33473302055996 1 3.38230327797874 1034 2115 2545 2421 907 946 129 3001 2992 2223 1719 2049 M2056 RUAN_RESPONSE_TO_TROGLITAZONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TROGLITAZONE_DN.html Adipocyte abundant genes down-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591]. 12732648 24/31 Arthur Liberzon 0.020574803352125 0.0386750584715373 945 2001.27272727273 2115 0.00188816185070121 943 1.18244083939104 1.19175128806738 1 2.50618178093356 943 3477 2164 3324 1164 1710 950 2456 2461 2115 1250 2050 M835 KEGG_DILATED_CARDIOMYOPATHY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DILATED_CARDIOMYOPATHY.html Dilated cardiomyopathy 80/122 KEGG 0.00185310986563078 0.00633817287375167 1525 1936.63636363636 2117 0.000168606602297394 307 1.32562842248787 1.30289536636335 1 4.37207787095003 1523 2846 674 2117 3144 3418 2298 307 1872 598 2506 2051 M5899 LOPEZ_MESOTELIOMA_SURVIVAL_TIME_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTELIOMA_SURVIVAL_TIME_DN.html Top genes higher expressed in long term mesothelioma survivors. 16540645 10/13 Arthur Liberzon 0.0338816587542456 0.0580055964164089 1175 2099.27272727273 2117 0.00312863611388394 959 1.60463627431934 1.42050585111949 1 2.97719767040249 1175 2662 1123 3566 2600 3432 2117 959 3010 1089 1359 2052 M13183 ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TARGETS_OF_MYC_AND_TFRC_UP.html Genes down-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) by MYC [GeneID=4609] and up-regulated by RNAi knockdown of TFRC [GeneID=7037]. 16508012 123/186 Leona Saunders 0.0640716819024492 0.0991535536326427 2120 2202 2117 0.00600158977387403 1116 1.28272343390608 1.25270506890001 1 1.93175206674814 2117 1808 1116 2681 2203 3704 2302 1637 1992 1145 3517 2053 M19652 CHEOK_RESPONSE_TO_MERCAPTOPURINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_UP.html Genes specifically up-regulated in pediadric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490]. 12704389 18/20 Jean Junior 0.0074495369276173 0.0172870276786399 875 2636.36363636364 2118 0.000679534766865027 223 0.545005382994047 0.545005382994047 1 1.44107153532153 872 4575 3477 4605 2118 401 223 1986 4697 4675 1371 2054 M15887 IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/IZADPANAH_STEM_CELL_ADIPOSE_VS_BONE_UP.html Genes up-regulated in adipose tissue mesenchymal stem cells (ASC) vs bone marrow mesenchymal stem cells (rBMSC) 18519682 172/244 Leona Saunders 0.00318001172647391 0.00948777202841774 1930 1937.09090909091 2118 0.000289510693566768 721 1.16369330157923 1.22235847751134 1 3.5320590283122 1926 2293 726 1709 721 2230 2342 2118 2440 784 4019 2055 M67 PID_ARF6_TRAFFICKING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_TRAFFICKING_PATHWAY.html Arf6 trafficking events 18832364 64/75 Pathway Interaction Database 0.162773264375206 0.216724910536241 1825 2469.63636363636 2119 0.0160212141957029 1270 1.00944066190299 1.02423292873659 1 1.00578374774169 1823 1899 2960 1888 2119 1996 1270 4599 2510 3181 2921 2056 M1747 ZHENG_FOXP3_TARGETS_IN_THYMUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_THYMUS_DN.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are down-regulated only in developing (located in the thymus) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 15/34 Jessica Robertson 0.000324125752019861 0.00167571924547387 4515 2427.63636363636 2119 2.94703195711273e-05 233 1.3042749904972 1.28493651000283 1 5.43238434982812 4512 2119 1639 1549 233 3260 3295 1011 4164 1689 3233 2057 M19988 GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_DN.html Genes down-regulated in metastatic breast cancer tumors having type 2 amplification in the 20q13 region; involves MYBL2, STK6 and ZNF217 [GeneID=4605;6790;7764] 16899599 235/259 Leona Saunders 0.0338403787153436 0.0579587697097999 1405 2455.18181818182 2120 0.00312476400312271 1366 0.867228276054126 0.908565166227445 1 1.60943908860342 1404 3181 4094 3451 1366 1778 1464 2120 1376 4245 2528 2058 M1685 ZHONG_SECRETOME_OF_LUNG_CANCER_AND_MACROPHAGE http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_SECRETOME_OF_LUNG_CANCER_AND_MACROPHAGE.html Proteins secreted in co-culture of LKR-13 tumor cells (non-small cell lung cancer, NSCLC) and MHS stroma cells (macrophages). 18757440 104/143 Jessica Robertson 0.0175450340975911 0.0341073150496828 2970 2392.72727272727 2120 0.00160786713265808 1083 1.16972008390199 1.33086930966175 1 2.5750232530095 2968 1291 1469 1083 1108 3944 4704 3218 1482 2120 2933 2059 M842 REACTOME_PURINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_CATABOLISM.html Genes involved in Purine catabolism 10/15 Reactome 0.000537416189226214 0.00244289233894981 3635 2216.18181818182 2121 4.88679558375863e-05 193 1.45103692197024 1.72441798295489 1 5.68723625853857 3635 2651 2073 1276 319 4509 4677 744 193 2180 2121 2060 M3158 REACTOME_S_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_S_PHASE.html Genes involved in S Phase 111/124 Reactome 0.101341838638759 0.145833377553336 410 2079.72727272727 2121 0.00966684186196948 406 0.694264071777637 -0.622745407715204 -1 0.870952208440185 406 662 4092 2212 2121 1176 1348 2565 1657 4362 2276 2061 M19580 KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_AND_GLUCURONATE_INTERCONVERSIONS.html Pentose and glucuronate interconversions 14/32 KEGG 0.0108197906073042 0.0232026184899062 1875 2131.54545454545 2122 0.000988488415356846 397 0.892580974757062 0.958769182945199 1 2.18898876356419 1872 2122 2690 2561 1615 2144 397 559 3903 3879 1705 2062 M13324 BIOCARTA_HIF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HIF_PATHWAY.html Hypoxia-Inducible Factor in the Cardiovascular System 21/24 BioCarta 0.0137519256312699 0.0281968240571651 1640 2500.18181818182 2123 0.00125805882527239 1021 1.04849560046056 1.15071573423915 1 2.43817667911732 1636 4212 2341 4586 1021 2123 1129 1508 4388 2794 1764 2063 M848 REACTOME_MITOTIC_G1_G1_S_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_G1_G1_S_PHASES.html Genes involved in Mitotic G1-G1/S phases 141/159 Reactome 0.164922645529833 0.21903063784491 545 2112.54545454545 2123 0.0162511310061998 544 0.740542595660941 -0.67610654900051 -1 0.732724521175258 544 1257 4096 1393 2771 1012 1399 2191 2136 4316 2123 2064 M10389 FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH_REARRANGEMENTS_DN.html Genes down-regulated in B-CLL (B-cell chronic lymphocytic leukemia) patients with mutated immunoglobulin variable heavy chain (VH) genes. 15817677 66/76 Kevin Vogelsang 0.0393160595647596 0.0658289468413145 2890 2221.63636363636 2123 0.00363970653644403 756 0.867450846498717 -0.817702363450486 -1 1.53787510598943 2887 756 3666 853 1421 982 2077 2123 3212 4058 2403 2065 M16335 MELLMAN_TUT1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MELLMAN_TUT1_TARGETS_DN.html Genes down-regulated in HEK293 cells (embryo kidney) after knockdown of TUT1 [GeneID=64852] by RNAi. 18288197 66/77 Jessica Robertson 0.000449537935180118 0.00212607119644304 2265 1855 2123 4.08754379991951e-05 291 1.12956617171773 1.15702543934755 1 4.52948065663607 2265 1360 1698 2359 291 2063 2191 503 3382 2123 2170 2066 M15130 MILI_PSEUDOPODIA_CHEMOTAXIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_CHEMOTAXIS_UP.html Transcripts enriched in pseudopodia of NIH/3T3 cells (fibroblast) in response to the chemotactic migration stimulus by lysophosphatidic acid (LPA) [PubChem=3988]. 18451862 89/95 Jessica Robertson 0.109044129903924 0.155064688083556 925 2210.27272727273 2125 0.0104415033411481 921 0.837877978988189 0.797720406569727 1 1.01762402034518 921 2373 3685 2393 2362 1752 1007 1579 2065 4051 2125 2067 M7714 AMIT_EGF_RESPONSE_240_HELA http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_240_HELA.html Genes whose expression peaked at 240 min after stimulation of HeLa cells with EGF [GeneID=1950]. 17322878 80/85 Leona Saunders 0.0222568226235528 0.0413428582381618 800 2135.09090909091 2126 0.00204411188392143 797 1.08397046560172 1.01490976113844 1 2.25034565582214 797 2388 2210 2126 1186 1941 1841 4219 2342 1781 2655 2068 M13984 MARZEC_IL2_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARZEC_IL2_SIGNALING_UP.html Genes up-regulated by IL2 [GeneID=3558] in cells derived from CD4+ [GeneID=920] cutaneous T-cell lymphoma (CTCL). 18281483 136/169 Jessica Robertson 0.267796159885096 0.330802898366305 2050 2586.81818181818 2127 0.0279383302941785 1286 1.22388522086083 1.18475681338736 1 0.882188007659847 2049 4025 1681 3671 2750 1286 1642 4687 3158 1379 2127 2069 M10117 VERHAAK_AML_WITH_NPM1_MUTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_AML_WITH_NPM1_MUTATED_DN.html Genes down-regulated in acute myeloid leukemia (AML) patients with mutated NPM1 [GeneID=4869]. 16109776 298/470 Kevin Vogelsang 1.16496298013687e-16 7.85517895178004e-15 1705 1972.90909090909 2128 1.05905725466988e-17 52 1.41709808875944 1.46952930780473 1 29.992210316089 1702 2248 52 2801 3475 2602 2052 1914 2563 165 2128 2070 M1623 SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_DN.html Down-regulated in murine dorsal skin cells at 6 h after treatment with the phorbol ester carcinogen TPA [PubChem=4792]. 12640676 47/68 John Newman 0.0298717766849801 0.0524534173932686 1935 2084.72727272727 2128 0.00275320543499044 491 1.18369516227537 1.14995066920629 1 2.27377864371042 491 2472 1074 2462 1315 2187 2128 2735 4204 1931 1933 2071 M8941 HEDENFALK_BREAST_CANCER_BRACX_DN http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_BRACX_DN.html Down-regulated genes distinguishing between two groups of non-BRCA1/BRCA2 [GeneID=672;675] breast tumors (BRACx): group A vs group B. 12610208 25/27 John Newman 0.235047929575261 0.295846994025395 2240 2256.90909090909 2129 0.0240641017433146 171 0.928603188676546 1.08581944759202 1 0.736902695251928 2239 1514 3398 1108 2976 3715 2129 1910 171 3581 2085 2072 M3430 BIOCARTA_CALCINEURIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CALCINEURIN_PATHWAY.html Effects of calcineurin in Keratinocyte Differentiation 21/22 BioCarta 0.0397216024996457 0.0662963096882347 1915 2442.63636363636 2130 0.00367795054294543 606 0.657693289913364 0.564649262793192 1 1.16294509231779 1911 995 3561 2437 3960 2130 606 4543 1690 4090 946 2073 M204 PID_RHODOPSIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHODOPSIN_PATHWAY.html Visual signal transduction: Rods 18832364 12/35 Pathway Interaction Database 0.00130002841347842 0.00479217899694665 3335 1991.45454545455 2130 0.000118254296819598 168 2.12662594828399 2.47890952167639 1 7.40141744643768 3334 2130 1539 2533 3065 2892 3081 168 196 1837 1131 2074 M15927 RODRIGUES_DCC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_DCC_TARGETS_DN.html Genes down-regulated in HCT8/S1 cells (colon cancer) which normally lack DCC [GeneID=9423] compared to those stably expressing wild type DCC off a plasmid vector. 17334389 182/207 Arthur Liberzon 0.298526242571303 0.362688253522922 2270 2064.09090909091 2130 0.0317198273550777 582 1.06075968927349 1.04318761525649 1 0.700980840714143 2270 582 2551 847 2469 1709 1901 3685 1270 2130 3291 2075 M5488 REACTOME_TRAFFICKING_OF_GLUR2_CONTAINING_AMPA_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAFFICKING_OF_GLUR2_CONTAINING_AMPA_RECEPTORS.html Genes involved in Trafficking of GluR2-containing AMPA receptors 12/16 Reactome 0.00196620837961462 0.0065959513516567 2135 2117 2131 0.000178906167548398 508 0.818940746372169 -0.7318264273635 -1 2.67964679084074 2796 2131 3116 2133 508 1224 865 2045 3348 4562 559 2076 M1770 GAZIN_EPIGENETIC_SILENCING_BY_KRAS http://www.broadinstitute.org/gsea/msigdb/cards/GAZIN_EPIGENETIC_SILENCING_BY_KRAS.html Genes required for epigenetic silencing of FAS [GeneID=355] by activated KRAS [GeneID=3845] in NIH 3T3 cells, based on RNAi screen. 17960246 28/36 Jessica Robertson 0.0162285388428241 0.0321978576452836 2230 2150.90909090909 2131 0.00148631831746681 279 0.725835887073821 -0.776875378038902 -1 1.62506654058835 2226 2030 3654 2158 2131 1876 2400 1861 839 4206 279 2077 M1225 OXFORD_RALA_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_TARGETS_UP.html Genes up-regulated in the UMUC-3 cells (bladder cancer) after knockdown of RALA [GeneID=5898] by RNAi. 17496927 12/14 Arthur Liberzon 0.0525302980023656 0.0842197712537927 4195 2733.90909090909 2132 0.00489347133999125 709 1.13944564919773 -1.16667675558877 -1 1.83717937667234 4193 2132 1915 2391 2048 4490 4591 1133 709 1841 4630 2078 M2541 PARK_APL_PATHOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARK_APL_PATHOGENESIS_DN.html Genes down-regulated in U937 cells (acute promyelocytic leukemia, APL) expressing RARA [GeneID=5914] fused with either PML or PLZF [GeneID=5371;7704]. 12893766 72/116 Arthur Liberzon 0.0028698604435265 0.00873355338068671 1105 2167.54545454545 2133 0.000261237361469768 718 1.45619839083351 1.5036255823889 1 4.49850493159982 1101 3281 718 3645 2519 1465 993 2802 4141 1045 2133 2079 M50 PID_PTP1B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PTP1B_PATHWAY.html Signaling events mediated by PTP1B 18832364 74/115 Pathway Interaction Database 0.00529519594916592 0.0139146859520474 3595 2318 2134 0.000482544009760074 622 1.39318360706078 1.55514417074213 1 3.8809629403167 3592 729 768 622 4078 3692 3619 2134 848 798 4618 2080 M2019 MIKKELSEN_MEF_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in MEF cells (embryonic fibroblast). 17603471 427/986 Arthur Liberzon 2.13530204197562e-36 1.67977093968749e-33 3590 1948 2134 1.94118367452331e-37 6 1.47669409228958 -1.54540629225794 -1 72.6224840211722 3590 514 6 1151 3367 2651 4662 2989 2134 30 334 2081 M2387 KATSANOU_ELAVL1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KATSANOU_ELAVL1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) with ELAVL1 [GeneID=1994] knocked out. 19307312 185/232 Arthur Liberzon 2.09227251646935e-07 3.56517194142069e-06 740 1953 2135 1.90206610495581e-08 229 1.45382360325028 1.48279834736894 1 11.8844842613585 740 3200 229 2626 2434 2192 1710 2092 3531 594 2135 2082 M10792 KEGG_MAPK_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MAPK_SIGNALING_PATHWAY.html MAPK signaling pathway 233/294 KEGG 0.0630906387971739 0.0978599458175027 1330 2509.45454545455 2136 0.00590691556750465 651 1.0233449007357 0.968975221371499 1 1.54987026592056 1330 3624 2064 4136 4542 651 789 3090 3442 2136 1800 2083 M1688 YANG_MUC2_TARGETS_DUODENUM_3MO_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_DUODENUM_3MO_DN.html Genes down-regulated in duodenum of 3 month old MUC2 [GeneID=4583] knockout mice. 18794118 21/66 Jessica Robertson 0.166854667908466 0.221160918991283 4440 2626.09090909091 2136 0.0164582567860087 227 1.25609601917238 -1.46573893608598 -1 1.23498602755962 4438 969 1804 1253 2136 3766 4257 3830 227 1826 4381 2084 M6946 SHI_SPARC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHI_SPARC_TARGETS_DN.html Genes down-regulated in glioma cell lines after knockdown of SPARC [GeneID=6678] by RNAi. 17213807 15/16 Arthur Liberzon 0.0245932355164486 0.0449574251114009 1445 2497.18181818182 2137 0.00226113982176071 360 1.14509995939901 1.29837731576572 1 2.31471201311413 1445 4590 1889 4357 2240 2042 1192 2137 4427 2790 360 2085 M2193 OHGUCHI_LIVER_HNF4A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OHGUCHI_LIVER_HNF4A_TARGETS_UP.html Genes up-regulated in liver samples of liver-specific knockout of HNF4A [GeneID=3172]. 18426912 65/91 Arthur Liberzon 0.000240551187027923 0.00135409472095923 2140 2005.45454545455 2137 2.18706812063803e-05 322 1.37256444230579 1.34511629122889 1 5.90743647498504 2137 2866 563 1755 1830 2298 2809 4034 2689 322 757 2086 M5410 KEGG_ARACHIDONIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARACHIDONIC_ACID_METABOLISM.html Arachidonic acid metabolism 39/108 KEGG 4.83733424709867e-05 0.000371255571484646 3550 2271.18181818182 2138 4.39767328464739e-06 442 1.74989398513679 -1.81169652169401 -1 9.00707892340909 3547 1969 442 1406 2569 3867 4122 1426 2138 600 2897 2087 M4493 REN_BOUND_BY_E2F http://www.broadinstitute.org/gsea/msigdb/cards/REN_BOUND_BY_E2F.html Genes whose promoters were bound by E2F1 and E2F4 [GeneID=1869;1874] in the primary fibroblasts WI-38, by ChIP on chip assay. 11799067 76/110 Yujin Hoshida 0.0771900626972026 0.115883300232442 510 2284 2138 0.00727630621061588 507 1.06772176568792 -1.11083887267723 -1 1.49946186916859 507 3276 3323 2787 4082 787 860 2138 1798 3642 1924 2088 M7600 DOANE_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in MDA-MB-453 cells (class A ER(-) [GeneID=2099] breast cancer) after exposure to the androgen R1881 [PubChem=13766]. 16491124 231/341 Arthur Liberzon 0.00416911701549276 0.0115347199959706 2825 2325.45454545455 2139 0.000379730794444815 513 1.11866749500715 1.02554717585019 1 3.25297623293603 2821 1205 983 997 4524 2139 2807 4393 1123 513 4075 2089 M4391 PEREZ_TP53_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/PEREZ_TP53_TARGETS.html Genes up-regulated in the HMEC cells (primary mammary epithelium) upon expression of TP53 [GeneID=7157] off adenoviral vector. 17563751 1337/1775 Leona Saunders 2.49437233866414e-06 3.05011332603491e-05 1595 2105.09090909091 2141 2.49437513852058e-07 192 1.17395080453581 1.16419176028276 1 7.95443749656924 1595 1659 4357 1159 3093 2371 2426 2141 2294 192 1869 2090 M2213 WIERENGA_STAT5A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_STAT5A_TARGETS_DN.html Genes down-regulated in CD34+ [GeneID=947] cells by intermediate activity levels of STAT5A [GeneID=6776]; predominant long-term growth and self-renewal phenotype. 18779318 247/340 Arthur Liberzon 4.79444784754135e-08 9.38995595037144e-07 2775 2023.27272727273 2141 4.35858904729682e-09 200 1.24314089323742 1.27576928687192 1 11.2430335772417 2772 1201 200 922 2660 3729 3150 1780 2141 370 3331 2091 M7416 ST_GAQ_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GAQ_PATHWAY.html G alpha q Pathway 31/35 Signaling Transduction KE 0.0283309276412608 0.0504611239497173 1145 2040.63636363636 2142 0.00260931643926769 899 0.740089977615116 0.7665641365569 1 1.44028627778865 1145 899 3264 2138 1281 2151 2142 2559 2148 3105 1615 2092 M267 PID_ANTHRAX_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ANTHRAX_PATHWAY.html Cellular roles of Anthrax toxin 18832364 14/18 Pathway Interaction Database 0.00577426225782821 0.0142024584976285 4200 2505.72727272727 2142 0.000526315789473684 177 1.07683155223178 -0.942760833133841 -1 2.98531877155359 4197 1571 2142 177 1718 3001 4509 4422 303 2074 3449 2093 M19636 MCBRYAN_PUBERTAL_BREAST_6_7WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_6_7WK_DN.html Genes down-regulated during pubertal mammary gland development between week 6 and 7. 17486082 98/121 Arthur Liberzon 0.00010807099620703 0.000707482804573066 4590 2379.45454545455 2142 9.82511866937878e-06 46 1.31409802205665 -1.33079854152693 -1 6.21172032329002 4588 46 484 948 4582 1943 3415 3657 2142 524 3845 2094 M2364 PURBEY_TARGETS_OF_CTBP1_AND_SATB1_UP http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_AND_SATB1_UP.html Genes up-regulated in HEK-293 cells (fibroblast) upon knockdown of both CTBP1 and SATB1 [GeneID=1487, 6304] by RNAi. 19103759 154/216 Arthur Liberzon 0.109481917179563 0.155555282687398 1240 2360.27272727273 2142 0.0104857166223901 984 1.11101608174831 1.1360790968548 1 1.34710463916428 1239 4014 1829 4329 2252 1041 1273 2142 3797 3063 984 2095 M1870 REACTOME_GLUCOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_METABOLISM.html Genes involved in Glucose metabolism 62/81 Reactome 0.00039996742296764 0.00195631734342721 3365 2137.45454545455 2143 3.63672869916287e-05 274 0.874851455519727 -0.884174783450702 -1 3.55550892078291 3365 1376 3670 1858 274 1022 2143 3075 610 3628 2491 2096 M15743 ST_GA12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GA12_PATHWAY.html G alpha 12 Pathway 44/52 Signaling Transduction KE 0.0698673451015973 0.106792055984307 2800 2447.63636363636 2144 0.00656273993174816 1263 1.24790898346137 1.25144047126337 1 1.81896711048289 2800 2920 1944 1658 3211 4645 2381 1263 1901 2057 2144 2097 M1263 WANG_RESPONSE_TO_BEXAROTENE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_BEXAROTENE_UP.html Genes up-regulated in the mouse lung cancer model and which reverted to normal levels upon treatment with bexarotene [PubChem=82146]. 16247446 36/53 Leona Saunders 0.375524799872432 0.443896081992957 4610 2594.27272727273 2144 0.0419008114399595 420 1.26913097193688 -0.922034575721994 -1 0.671596296547179 4608 3792 2144 1530 4063 1500 1938 2655 420 1874 4013 2098 M2107 KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_BIPOLAR_DISORDER_OLIGODENDROCYTE_DENSITY_CORR_UP.html Genes whose expression significantly and positively correlated with oligodendrocyte density in layer VI of BA9 brain region in patients with bipolar disorder. 18762803 862/1054 Jessica Robertson 0.159275513304011 0.212848364324726 2065 2307.27272727273 2145 0.0171994979224866 475 0.949478297513512 -0.827050791654262 -1 0.957199944252565 2063 475 4659 649 2990 1040 2145 2609 1923 4382 2445 2099 M4891 BIOCARTA_PML_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PML_PATHWAY.html Regulation of transcriptional activity by PML 22/26 BioCarta 0.0301173243353756 0.0527375425762961 2150 2415.81818181818 2146 0.00277615458356956 520 1.03850061630337 1.20319503895033 1 1.99120326914516 2146 3862 2945 1332 4056 1982 520 1863 3499 2876 1493 2100 M4592 JEON_SMAD6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JEON_SMAD6_TARGETS_UP.html Genes up-regulated in H1299 cells (lung cancer) upon knockdown of SMAD6 [GeneID=4091] by RNAi. 19047146 29/36 Jessica Robertson 0.00355301727452345 0.0102695906526336 2440 1944.90909090909 2146 0.000323524402996433 648 1.21856383665291 1.29688007083215 1 3.63572848987777 2438 912 734 1446 2146 2544 3050 2233 1769 648 3474 2101 M13806 ZHAN_V1_LATE_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_V1_LATE_DIFFERENTIATION_GENES_DN.html The v1LDG down-regulated set: most variable late differentiation genes (LDG) with similar expression patterns in tonsil plasma cells (TPC) and multiple myeloma (MM) samples. 12393520 22/42 Arthur Liberzon 0.00161067395611213 0.00567765576762455 2040 2241.27272727273 2147 0.000146532216372691 74 1.2166036477821 -1.19765552104667 -1 4.09974432370031 2038 3482 2446 4578 475 1302 3082 2144 2147 2886 74 2102 M2275 ZHU_SKIL_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_SKIL_TARGETS_DN.html Genes down-regulated in A549 cells (lung adenocarcinoma) upon SKIL [GeneID=6498] knockdown by RNAi. 17074815 10/11 Arthur Liberzon 0.182915483608747 0.239756140976871 2070 2336.27272727273 2147 0.0181971894861113 1079 1.10527772642149 1.15943105917367 1 1.02854073123087 2066 2147 2665 1079 3362 1821 1663 2409 4291 2910 1286 2103 M6175 CAIRO_LIVER_DEVELOPMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_LIVER_DEVELOPMENT_DN.html Genes down-regulated at early fetal liver stage (embryonic days E11.5 - E12.5) compared to the late fetal liver stage (embryonic days E14.5 - E16.5). 19061838 233/344 Arthur Liberzon 6.08230275701803e-14 3.15477681462913e-12 3990 2358.36363636364 2148 5.5293661427438e-15 68 1.45648229500473 -1.38774697061785 -1 25.1351786952584 3989 555 68 221 2148 4691 4178 4210 1440 74 4368 2104 M521 BROWNE_HCMV_INFECTION_2HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_2HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 2 h time point that were not down-regulated at the previous time point, 1 h. 11711622 67/89 Arthur Liberzon 0.0564385153444832 0.0893325930335214 850 2204.45454545455 2149 0.00526732869286576 847 1.25466320786878 -1.21137741924827 -1 1.97477250006843 2823 1361 1136 2140 3810 2840 3432 2149 2862 849 847 2105 M13519 KEGG_GRAFT_VERSUS_HOST_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GRAFT_VERSUS_HOST_DISEASE.html Graft-versus-host disease 29/73 KEGG 0.0192171172175246 0.0366188103620169 1085 2273.36363636364 2150 0.00176246015381584 1083 1.23017053783499 -1.09358580675115 -1 2.6511461836246 1083 3432 1798 2150 1140 1279 2841 3483 3545 2526 1730 2106 M17641 FRASOR_RESPONSE_TO_ESTRADIOL_UP http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_ESTRADIOL_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by estradiol (E2) [PubChem=5757]. 14973112 42/51 Arthur Liberzon 0.000272854598214486 0.00147637965137618 1430 2060.45454545455 2150 2.48080404393903e-05 52 1.03610319180606 0.877300641890973 1 4.40092393821946 1427 4120 2150 3549 3417 1064 371 52 3320 2640 555 2107 M11615 CHANDRAN_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_DN.html Genes down-regulated in metastatic tumors from the whole panel of patients with prostate cancer. 17430594 387/480 Arthur Liberzon 1.20109349519088e-11 4.29481916462192e-10 2850 2187.81818181818 2151 1.09190317745221e-12 104 1.2745308932861 1.2761843173022 1 17.9140047567088 2151 1695 104 1162 1897 4637 2846 3546 2848 155 3025 2108 M2365 PURBEY_TARGETS_OF_CTBP1_AND_SATB1_DN http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_AND_SATB1_DN.html Genes down-regulated in HEK-293 cells (fibroblast) upon knockdown of both CTBP1 and SATB1 [GeneID=1487, 6304] by RNAi. 19103759 198/356 Arthur Liberzon 0.14867915514412 0.20112038286315 3125 2531.36363636364 2151 0.0145267446913853 574 1.0648441706754 1.07267570213097 1 1.11284600087192 3125 574 2968 1315 2151 3514 4529 1627 2089 1927 4026 2109 M6782 BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP.html Genes up-regulated in T24 (bladder cancer) cells in response to the photodynamic therapy (PDT) stress. 17952126 1112/1329 Jessica Robertson 0.041817518986176 0.0691586158425896 280 2185.09090909091 2152 0.00426259304330205 280 1.02664779128236 1.00334596439498 1 1.78711747217077 280 2698 4432 3009 4218 697 838 1347 2152 2936 1429 2110 M16587 SASSON_RESPONSE_TO_GONADOTROPHINS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_GONADOTROPHINS_UP.html Genes up-regulated in primary granulosa cells after stimulation with LH or FSH gonadotrophic hormones for 24 h. 15026540 126/157 Arthur Liberzon 0.172122335052989 0.227186079823856 4570 2488.09090909091 2152 0.0170252123734749 617 0.962129104263918 -0.913243807041557 -1 0.929082043904916 4566 640 3106 617 2152 2055 4239 4006 1678 2118 2192 2111 M7578 REACTOME_SEMA3A_PLEXIN_REPULSION_SIGNALING_BY_INHIBITING_INTEGRIN_ADHESION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA3A_PLEXIN_REPULSION_SIGNALING_BY_INHIBITING_INTEGRIN_ADHESION.html Genes involved in SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion 32/34 Reactome 0.0037212729815588 0.01062577645067 340 1922.27272727273 2153 0.00033887112867565 224 1.0238379153431 1.06663974129384 1 3.0319752270699 337 2992 2153 3846 3184 225 224 319 4354 3175 336 2112 M5451 HOSHIDA_LIVER_CANCER_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SURVIVAL_DN.html Survival signature genes defined in adjacent liver tissue: genes correlated with good survival of hepatocellular carcinoma (HCC) patients. 18923165 120/179 Yujin Hoshida 0.0861346233219925 0.127327097425557 3385 1902.45454545455 2153 0.00815493108495432 9 1.0308240995735 -0.957740766930683 -1 1.38437777919082 3383 9 2229 283 3691 694 2153 2309 807 2082 3287 2113 M1786 YAMASHITA_SILENCED_BY_METHYLATION http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_SILENCED_BY_METHYLATION.html Genes silenced by DNA methylation in prostate cancer cell lines. 18381416 10/12 Jessica Robertson 0.000185423473032145 0.0010912703151019 3115 2431.27272727273 2154 1.68581002724201e-05 175 0.945860112362366 -0.718086265760219 -1 4.2039037223385 3114 2144 1930 3022 175 2154 892 1933 4363 2907 4110 2114 M1860 ZHOU_PANCREATIC_EXOCRINE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_PANCREATIC_EXOCRINE_PROGENITOR.html Transcription factors expressed in progenitors of exocrine pancreatic cells. 18754011 3/14 Jessica Robertson 0.00798756908406032 0.0182220039037046 2140 2299.54545454545 2155 0.000801642573820224 250 1.6949288660346 1.6949288660346 1 4.42367615137711 2136 2191 4581 2155 3261 1899 250 1026 4519 2690 587 2115 M2036 BAUS_TFF2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAUS_TFF2_TARGETS_DN.html Genes down-regulated in pyloric atrium with knockout of TFF2 [GeneID=7032]. 16121031 10/14 Arthur Liberzon 0.000164826079702122 0.000989795287778645 4030 2508.09090909091 2155 1.49853118112047e-05 39 1.29108583793185 -1.39045732297941 -1 5.82042473619861 4027 2155 1816 2008 733 4144 3926 39 2063 2186 4492 2116 M2527 BOSCO_TH1_CYTOTOXIC_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_TH1_CYTOTOXIC_MODULE.html Genes representing Th1 / cytotoxic module in sputum during asthma exacerbations. 20336062 104/233 Antony Bosco 1.80340958139879e-06 2.33848714950612e-05 2155 2058.27272727273 2155 1.6394645997385e-07 299 1.35676679829809 1.27651389755521 1 9.42807478222321 2155 1830 299 3482 1449 2794 2642 1489 2483 557 3461 2117 M3261 KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY.html Toll-like receptor signaling pathway 95/144 KEGG 0.0450839593603795 0.0737851207284991 1630 2116.27272727273 2156 0.00418502354533376 1305 0.966014564360415 1.12918497723259 1 1.64080084913081 1628 1305 1914 2768 1479 2156 2287 2384 1877 2926 2555 2118 M4381 LUI_THYROID_CANCER_PAX8_PPARG_UP http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_PAX8_PPARG_UP.html Top up-regulated genes distinguishing between follicular thyroid carcinoma (FTC) samples by the presence or absence of the PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 67/84 Leona Saunders 0.146107781474741 0.198340157768414 1300 2246.18181818182 2156 0.0142565178027869 1145 1.11191306710063 1.2338878018716 1 1.17212787093585 1300 4425 2822 3132 2467 1328 1145 2866 1871 2156 1196 2119 M10991 NIKOLSKY_OVERCONNECTED_IN_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_OVERCONNECTED_IN_BREAST_CANCER.html Overconnected mutated transcription factors regulating genes within the breast cancer amplicome. 19010930 26/38 Leona Saunders 0.0987572178422926 0.142679543377907 2160 2122.09090909091 2156 0.00940824464021234 816 0.90983097279365 -0.971886291385062 -1 1.15437616795368 2156 928 2139 816 1822 2747 1066 3346 3243 2730 2350 2120 M2999 MOOTHA_ROS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_ROS.html Reactive oxidative species (ROS) genes; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 9/9 Vamsi Mootha 0.00430675876145441 0.0118254225445403 3570 2431.72727272727 2157 0.000431512827625538 699 0.797415526256705 -0.734000445653216 -1 2.30584226289367 3569 2157 4590 1511 699 1854 2172 3417 770 4693 1317 2121 M6767 POOLA_INVASIVE_BREAST_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/POOLA_INVASIVE_BREAST_CANCER_DN.html Genes down-regulated in atypical ductal hyperplastic tissues from patients with (ADHC) breast cancer vs those without the cancer (ADH). 15864312 185/269 Jessica Robertson 2.53728528913667e-14 1.34561646794664e-12 3755 2056.63636363636 2158 2.30662299012427e-15 66 1.43440979373553 -1.59912494407123 -1 25.5507372386493 3751 580 66 505 2024 4105 3520 3340 2158 133 2441 2122 M10154 SA_G2_AND_M_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/SA_G2_AND_M_PHASES.html Cdc25 activates the cdc2/cyclin B complex to induce the G2/M transition. 13/13 SigmaAldrich 0.0086140212334288 0.0195096834077658 1620 2243.27272727273 2159 0.000786175925069424 248 0.626666247451558 0.626666247451558 1 1.60761511238623 1618 1582 3319 2965 2989 740 248 1526 3020 4510 2159 2123 M11 PID_PRL_SIGNALING_EVENTS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PRL_SIGNALING_EVENTS_PATHWAY.html Signaling events mediated by PRL 18832364 35/41 Pathway Interaction Database 0.153573383123973 0.206514634856169 2280 2064.72727272727 2159 0.0150431380528777 558 1.12740938681165 1.06566140905991 1 1.15879212816968 2278 1987 2586 2222 3568 1240 1526 1639 558 2159 2949 2124 M12494 REACTOME_PHOSPHORYLATION_OF_CD3_AND_TCR_ZETA_CHAINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHORYLATION_OF_CD3_AND_TCR_ZETA_CHAINS.html Genes involved in Phosphorylation of CD3 and TCR zeta chains 10/18 Reactome 0.00258465545495085 0.00808990301549603 1515 2068.63636363636 2160 0.000235245184019599 247 2.00910958313106 2.00910958313106 1 6.30683681160733 1515 2160 1173 2830 649 2131 2423 247 4459 2899 2269 2125 M11216 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_14 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_14.html Amplification hot spot 14: colocolized fragile sites and cancer genes in the 8q24.1-q24.3 region. 16751803 4/4 Arthur Liberzon 0.268209989812251 0.331227407617432 3210 2451.09090909091 2161 0.0307436662400858 316 1.06542345617866 -1.04786312841486 -1 0.767063166247727 3209 1100 4367 2136 2452 4178 1853 2161 316 1858 3332 2126 M4196 NUYTTEN_EZH2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_EZH2_TARGETS_UP.html Genes up-regulated in PC3 cells (prostate cancer) after knockdown of EZH2 [GeneID=2146] by RNAi. 17724462 1328/1657 Jessica Robertson 4.06987702668901e-06 4.67392203551633e-05 1610 1994.27272727273 2161 4.06988448046278e-07 201 1.12295012759838 1.16377043597365 1 7.29652075685095 1606 1110 4430 307 2344 2467 2602 1581 2161 201 3128 2127 M13976 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_1_UP.html Genes exclusively up-regulated in B lymphocytes from WM (Waldenstroem's macroblobulinemia) patients but with a similiar expression pattern in the normal cells and in the cells from CLL (chronic lymphocytic leukemia) patients. 17252022 13/16 Arthur Liberzon 0.00628861015950012 0.0152208738800101 1330 2199.09090909091 2163 0.000573332560139202 424 0.966549646499561 0.966549646499561 1 2.63595137111252 1327 2634 2163 3344 4512 689 619 424 4443 2577 1458 2128 M1202 TERAMOTO_OPN_TARGETS_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_6.html Cluster 6: genes exhibiting prolonged up-regulation (>72 h) after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 38/44 Arthur Liberzon 0.213308050144321 0.273442150103529 2930 2421.36363636364 2165 0.0215746404149369 1378 1.23261640318175 1.40913930418705 1 1.04144847336937 2930 1971 1378 2513 2975 3644 3554 2054 1450 2001 2165 2129 M2499 BIOCARTA_CARM_ER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARM_ER_PATHWAY.html CARM1 and Regulation of the Estrogen Receptor 35/48 BioCarta 0.00643451703573847 0.0154795720737439 2010 2288.72727272727 2166 0.000586674000746779 135 0.950668314752806 -0.998364797565899 -1 2.58219739053389 2009 3387 3402 3584 4239 1395 2166 755 396 3708 135 2130 M18968 HAHTOLA_SEZARY_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_SEZARY_SYNDROM_DN.html Genes down-regulated in monocytes isolated from peripheral blood samples of Sezary syndrom patients compared to those from healthy normal donors. 16914566 40/79 Arthur Liberzon 0.00115339523200005 0.00442603698783758 3680 2131.63636363636 2166 0.000104909124306123 238 1.43826055585045 1.31487316811828 1 5.0801205179659 3679 238 666 1435 3890 2166 2229 2764 1702 423 4256 2131 M1822 MATZUK_EARLY_ANTRAL_FOLLICLE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_EARLY_ANTRAL_FOLLICLE.html Genes important for early anral follicle, based on mouse models with female fertility defects. 18989307 19/23 Jessica Robertson 0.0139824093971414 0.0285824912752305 1340 2778.81818181818 2166 0.00127927958429754 616 1.55424467982144 1.55424467982144 1 3.60053948480488 1336 4579 2166 4474 4180 2033 1928 616 4493 3170 1592 2132 M3624 KEGG_GLYCOSAMINOGLYCAN_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_DEGRADATION.html Glycosaminoglycan degradation 22/28 KEGG 0.0191069300862346 0.0364824878669204 3410 1952.54545454545 2168 0.00175226539314881 70 0.953022768829852 -0.967917069234771 -1 2.05615625002519 3407 338 2243 464 1138 1398 2168 2771 70 3834 3647 2133 M16 PID_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INSULIN_PATHWAY.html Insulin Pathway 18832364 60/68 Pathway Interaction Database 0.195846673345781 0.253614673990272 1635 2303.72727272727 2168 0.0196200019685629 621 1.01291694908987 0.848384938166978 1 0.905490852141319 2646 2426 2984 1631 3264 2168 1635 1796 621 2065 4105 2134 M1638 ZAMORA_NOS2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZAMORA_NOS2_TARGETS_DN.html Down-regulated in hepatocytes upon expression of NOS2 [GeneID=4843]. 12381414 135/193 John Newman 0.00635395540762367 0.0153483467369415 2170 2171.72727272727 2169 0.000579307382167494 359 0.905768823755322 -0.918075602822729 -1 2.46526192391211 2169 1262 2931 1640 4552 928 2898 427 3465 3258 359 2135 M15537 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_UP.html Genes from the turquoise module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphocholine (oxPAPC). 16912112 108/122 Arthur Liberzon 0.0387954855156495 0.06504962402624 480 2128.54545454545 2170 0.00359063623071925 477 1.00491418536765 1.01793776353206 1 1.78939511620104 477 3230 3184 3313 3844 896 926 1009 2170 2954 1411 2136 M9544 BOYLAN_MULTIPLE_MYELOMA_PCA3_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA3_DN.html Top down-regulated genes from principal component 3 (PCA3) which captures variation among different plasma cell tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 89/116 Arthur Liberzon 0.314614869072136 0.378918648129748 3915 2285.27272727273 2170 0.0337600923317431 61 1.15354977475092 -1.24471917088298 -1 0.729399299373692 3913 61 2098 512 4434 2170 3134 3205 1686 1317 2608 2137 M5278 NIKOLSKY_BREAST_CANCER_7Q21_Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_7Q21_Q22_AMPLICON.html Genes within amplicon 7q21-q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 81/105 Jessica Robertson 0.0635564322419254 0.0984853447740932 905 2494.63636363636 2171 0.00595185507659574 904 1.11863375960716 1.22313137506197 1 1.6895525463548 904 3694 2132 4284 1621 1686 1630 2476 3489 3354 2171 2138 M7636 REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLUENZA_VIRAL_RNA_TRANSCRIPTION_AND_REPLICATION.html Genes involved in Influenza Viral RNA Transcription and Replication 118/206 Reactome 0.0172670983993391 0.033677977043339 1100 2703.18181818182 2173 0.0015821936784314 405 0.6545588365739 0.620692770243255 1 1.44630352353611 405 4413 4162 4544 1098 1100 560 2173 4676 4452 2152 2139 M14030 WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_CARCINOMA_VS_ADENOMA_UP.html Up-regulated genes in pediatric adrenocortical carcinoma (ACC) compared to the adenoma (ACA) tumors. 17234769 18/26 Jessica Robertson 0.00380980823481347 0.0107872194770963 3750 2268.63636363636 2173 0.000346947439785108 390 1.18624944820825 -0.964644749386215 -1 3.5012977357976 3746 390 2173 1750 641 3663 3686 1499 1150 2539 3718 2140 M1935 MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 trimethylation marks at k4 (H3K4me3) and K27 ((H3K27me3) in neural precursor cells (NPC). 18600261 159/261 Jessica Robertson 5.67023152691912e-13 2.52485781198663e-11 2770 2153.18181818182 2174 5.15475593356416e-14 37 1.34006649997877 1.15122050973077 1 21.3098409437442 2767 1235 81 37 2166 3412 3444 4158 2174 113 4098 2141 M1584 LIU_VMYB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_VMYB_TARGETS_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by overexpression of v-MYB oncogenic varian of CMYB [GeneID=4602] off adenovirus vector. 16205643 179/224 Arthur Liberzon 0.0329884992429669 0.0567440657532084 1015 2225.54545454545 2176 0.00304489037746544 945 0.981350207589807 1.03209655519204 1 1.83479077098915 1014 3198 3268 2964 2671 1294 1657 945 2176 3419 1875 2142 M19384 YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAUCH_HEDGEHOG_SIGNALING_PARACRINE_UP.html Genes up-regulated in mouse stroma of pancreatic adenocarcinoma zenografts after treatment with HhAntag, a hedgehog (Hh) pathway inhibitor. 18754008 165/243 Jessica Robertson 0.00647155907576408 0.0155259884964326 2030 2712.36363636364 2176 0.000590061336232588 796 1.37866262227712 1.35657255180777 1 3.74206965801874 2030 4356 796 4587 3806 1466 2176 4632 3931 1202 854 2143 M15247 KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS.html Ubiquitin mediated proteolysis 140/154 KEGG 0.231058805939491 0.291681616484193 2430 2369.81818181818 2177 0.0236025242540462 428 0.760241888370032 -0.808750420988683 -1 0.610303557670743 2428 1785 4125 2177 3234 1584 2617 1899 428 4310 1481 2144 M100 PID_SHP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SHP2_PATHWAY.html SHP2 signaling 18832364 80/91 Pathway Interaction Database 0.0097438074128018 0.0214010102319332 1655 2119.72727272727 2178 0.000889748388070486 531 1.11143684914688 1.10557115800197 1 2.78428452468316 1653 1865 1453 2983 2515 2680 1719 531 3469 2271 2178 2145 M2919 KIM_MYCN_AMPLIFICATION_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCN_AMPLIFICATION_TARGETS_DN.html Genes negatively correlated with amplifications of MYCN [GeneID=4613] in the SCLC (small cell lung cancer) cell lines. 16116477 192/256 Arthur Liberzon 0.0794337485336297 0.118873586898774 1630 2294.81818181818 2178 0.00749597377327328 1317 1.06037915813536 1.07930985822912 1 1.47154453443679 1630 2282 2178 2093 2580 3360 2170 1317 2515 2066 3052 2146 M12208 TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_DN.html Genes down-regulated in ductal vs lobular carcinoma breast tumor cells. 17389037 11/11 Arthur Liberzon 1.98954108085268e-05 0.000182396771335444 2150 2122.90909090909 2179 1.8086900665761e-06 45 1.09357354529715 1.12739860276681 1 6.13529975966754 2150 1056 1724 506 45 2179 2728 3787 3848 2341 2988 2147 M1155 ABDULRAHMAN_KIDNEY_CANCER_VHL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ABDULRAHMAN_KIDNEY_CANCER_VHL_UP.html Genes up-regulated in the RCC4 cells (renal cell carcinoma, RCC) expressing VHL [GeneID=7428] mutants Type 1 and 2B (associated with RCC) but not those of Type 2A and 2C (not associated with RCC). 17001320 6/9 Arthur Liberzon 0.0185098104684143 0.0356015914469909 1620 1808.45454545455 2179 0.00186658183514137 333 1.17949013393983 1.33370804618464 1 2.56357403005259 1619 2179 4355 2525 2512 2228 607 765 333 2296 474 2148 M1591 BURTON_ADIPOGENESIS_PEAK_AT_24HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_24HR.html Cluster 5: genes progressively up-regulated (peak at 24 h time point) during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 59/99 John Newman 0.012524737386032 0.0260885968499872 660 1940.72727272727 2179 0.00114514682184723 311 1.34566851949246 -1.09718009145996 -1 3.19740102335427 658 2886 2423 2769 2165 844 311 2983 1198 2932 2179 2149 M181 PID_BMP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BMP_PATHWAY.html BMP receptor signaling 18832364 47/54 Pathway Interaction Database 0.101554988566427 0.14609556416749 1830 2313.36363636364 2180 0.0096881981676623 762 1.25478861934594 1.06272313311017 1 1.57274523247576 1828 3746 2853 3151 2180 762 1688 3699 1114 2937 1489 2150 M6984 GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_UP.html Genes up-regulated in common hematopoietic progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 64/87 Arthur Liberzon 0.0585327458343261 0.0919382896299565 2335 2308.72727272727 2180 0.00546824098649287 1375 0.900941924627332 -0.809790720236384 -1 1.40112412317643 2333 1375 2938 2180 1580 1655 2708 1680 3823 3442 1682 2151 M14877 BASAKI_YBX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BASAKI_YBX1_TARGETS_DN.html Genes down-regulated in SKOC-3 cells (ovarian cancer) after YB-1 (YBX1) [GeneID=4904] knockdown by RNAi. 17072343 525/667 Arthur Liberzon 0.000527982868453647 0.00240548179449924 1675 1945.36363636364 2180 5.28108355076264e-05 368 1.21605886908944 1.27568107215844 1 4.77846905578338 1673 501 4296 368 2801 2862 2321 2180 855 382 3160 2152 M15343 REACTOME_ACTIVATED_TLR4_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_TLR4_SIGNALLING.html Genes involved in Activated TLR4 signalling 104/124 Reactome 0.0282682220386376 0.0503874652652452 570 2225.90909090909 2181 0.00260346520011111 499 0.916022951134369 1.09883887042131 1 1.78356592294696 569 3238 3509 3889 3086 967 499 1178 2181 3839 1530 2153 M1801 GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_D_UP.html Up-regulated genes from the set D (Fig. 5a): specific signature shared by cells expressing MLL-AF4 [GeneID=4297;4299] alone and those expressing both MLL-AF4 and AF4-MLL fusion proteins. 17130830 36/59 Arthur Liberzon 0.216281027668514 0.276352585434593 1525 2402.09090909091 2181 0.0219113605662196 1376 1.26620781277634 1.2864676940914 1 1.06109683631881 1524 2957 1430 3515 2978 2181 1376 3202 3628 1873 1759 2154 M1736 GAVIN_FOXP3_TARGETS_CLUSTER_P7 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P7.html Cluster P7 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 130/177 Jessica Robertson 0.000296262767507487 0.00157650536937468 2365 1839.63636363636 2181 2.69366064750045e-05 300 1.22797264000785 1.26145066553538 1 5.16341377571221 2364 1263 546 300 3217 2353 2181 1257 2785 811 3159 2155 M9565 AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_UP.html Up-regulated genes whose expression correlates with copy number gains in pancreatic adenocarcinoma cell lines and primary tumor specimens. 15199222 364/425 Arthur Liberzon 0.0226438276464309 0.0418743240630278 2180 2187.72727272727 2181 0.00208002793796385 291 0.877072795848822 -0.8449832885958 -1 1.81350088566037 2179 2233 4120 2181 2370 291 2318 2131 1463 4210 569 2156 M13135 ENGELMANN_CANCER_PROGENITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ENGELMANN_CANCER_PROGENITORS_UP.html Up-regulated genes in the cancer progenitor (stem) cells corresponding to side population (SP) MCF7 cells (breast cancer) positive for MUC1 [GeneID=4582]. 18381450 58/66 Jessica Robertson 0.000857801298498688 0.00352684854435001 830 1928.81818181818 2182 7.80123587471869e-05 125 1.02173967363767 1.13533626007762 1 3.76009573022414 829 1394 2187 3287 4662 2295 1255 125 2182 2270 731 2157 M9371 MILICIC_FAMILIAL_ADENOMATOUS_POLYPOSIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MILICIC_FAMILIAL_ADENOMATOUS_POLYPOSIS_UP.html Top genes up-regulated in colon epithelium biopsies from FAP (familial adenomatous polyposis) patients with mutated APC [GeneID=324]. 18829530 10/58 Jessica Robertson 0.000432693389747291 0.00205835686111079 2340 1972.90909090909 2183 3.93435013463584e-05 75 1.5096455065195 -1.2584803679362 -1 6.08545055010302 2340 3560 1741 3035 1180 2000 2441 75 925 2183 2222 2158 M16591 MCCABE_HOXC6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_HOXC6_TARGETS_UP.html Genes with promoters bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer) and up-regulated upon loss of function (LOF) of HOXC6. 18339881 10/14 Jessica Robertson 0.000718905093561758 0.00307636631152448 3300 2418.27272727273 2184 6.53763746666367e-05 350 1.17951336184994 -1.37710740499219 -1 4.44577411278108 3299 1611 1640 957 350 3651 3630 4354 757 2184 4168 2159 M5601 BROWNE_HCMV_INFECTION_20HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_20HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 20 h time point that were not down-regulated at the previous time point, 18 h. 11711622 161/203 John Newman 0.0150483275946579 0.0303279702163901 2990 2183 2185 0.00137747791077003 595 1.12085131839766 1.01530237072975 1 2.55322096853918 2990 595 893 1020 1323 4233 3944 2185 2815 761 3254 2160 M12457 LY_AGING_MIDDLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_MIDDLE_DN.html Genes down-regulated in fibroblasts from middle-age individuals, compared to those from the young donors. 10741968 24/36 John Newman 0.01266087570081 0.026256297586917 805 2219.90909090909 2186 0.00115766643937174 314 1.27111833283174 -1.28399199764904 -1 3.01495111193827 802 3026 2760 2186 4412 1414 314 3704 897 3053 1851 2161 M2308 WANG_TNF_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TNF_TARGETS.html Representative genes up-regulated in MEF cells (embryonic fibroblast) in response to TNF [GeneID=7124]. 17438126 22/31 Arthur Liberzon 0.0321226878377886 0.055630931436807 1175 2164.72727272727 2188 0.00296377598891219 651 0.941238096108857 0.962351296032958 1 1.77194245186546 1173 2571 1257 2550 1344 836 651 4165 4682 2395 2188 2162 M2548 HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_B_ALL_DN.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 10/32 Arthur Liberzon 0.0112525317222575 0.0239027676548404 1385 2068.27272727273 2188 0.00102822741443388 293 0.945789526809374 0.920038036986766 1 2.30116185284959 1382 3111 2343 3501 1261 641 293 3961 3321 2188 749 2163 M7455 REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTRINSIC_PATHWAY_FOR_APOPTOSIS.html Genes involved in Intrinsic Pathway for Apoptosis 40/55 Reactome 0.0847713547117378 0.125897864457703 1305 2259.36363636364 2189 0.00802051350848258 846 0.898351668738633 -0.926461706400772 -1 1.21306465551259 1303 1439 2705 1358 4649 1192 2991 2308 2189 3873 846 2164 M1534 VIETOR_IFRD1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/VIETOR_IFRD1_TARGETS.html Genes down-regulated in c-JunER cells (mammary gland epithelum) by overexpression of IFRD1 [GeneID=3475] off an adenovirus vector. 12198164 26/44 John Newman 0.186001315146791 0.243192855261179 4090 2662.54545454545 2189 0.0185348525103001 94 1.51279183248572 -1.32182456853491 -1 1.3937701743524 4090 1498 1760 2024 2189 4678 4345 1990 94 2728 3892 2165 M4552 TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_B_LYMPHOCYTE_UP.html Genes up-regulated in plasma cells compared with B lymphocytes. 12663452 101/118 Kate Stafford 0.00647098238553396 0.0155259884964326 2190 2099.27272727273 2190 0.000590008599507809 685 0.993579684993043 -1.0020846402913 -1 2.69681906183327 2190 685 2241 1806 778 1653 2215 3262 2316 3771 2175 2166 M7337 ROY_WOUND_BLOOD_VESSEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROY_WOUND_BLOOD_VESSEL_UP.html Genes up-regulated in blood vessel cells from wound site. 17728400 79/92 Leona Saunders 0.000940360603689494 0.00378711778960274 575 2268.63636363636 2191 8.55238899052065e-05 573 1.20861958342304 1.30536158033869 1 4.39177145389881 573 2398 615 3785 3281 2051 1798 1916 4115 2232 2191 2167 M1449 NADLER_OBESITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/NADLER_OBESITY_DN.html Genes down-regulated in adipose tissue from obese mouse strains compared to the lean ones. 11027337 62/80 Kevin Vogelsang 0.000788881907613082 0.00331400263363004 2810 1986.09090909091 2191 7.17422662815746e-05 135 1.09473193726102 -1.02396384542359 -1 4.07312931830574 2806 135 1850 1814 362 1078 2414 3436 3508 2191 2253 2168 M19622 LEONARD_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/LEONARD_HYPOXIA.html Genes up-regulated in HK-2 cells kidney tubular epithelium) under hypoxia and down-regulated on re-oxygenation. 12885785 69/105 John Newman 0.021261204195932 0.0397909927854079 1450 2547.27272727273 2191 0.0019517727365853 329 1.40148264315564 1.32036235757145 1 2.94448074555926 1449 4432 2030 4439 4048 1834 2388 2899 2191 1981 329 2169 M13954 NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_8Q12_Q22_AMPLICON.html Genes within amplicon 8q12-q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 125/161 Jessica Robertson 0.204309355605171 0.263480917611041 2330 2163.36363636364 2194 0.020562449931703 1575 1.15304707333201 1.18729415137446 1 1.00209674420815 1924 2327 2478 1736 2328 2683 2194 1817 1575 2922 1813 2170 M17309 GALI_TP53_TARGETS_APOPTOTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/GALI_TP53_TARGETS_APOPTOTIC_DN.html Apoptosis genes down-regulated by TP53 [GeneID=7157] in HCT116 cells (colon cancer) treated with thymoquinone [PubChem=10281]. 18632613 12/13 Jessica Robertson 0.0105268384769443 0.0227398982202184 1865 2342.81818181818 2194 0.000961595332305471 283 0.99499848150392 0.680622205208802 1 2.45323387746405 1864 3923 2797 3358 1507 661 283 2194 3763 3805 1616 2171 M5407 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_24HR_DN.html Genes down-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 13/20 John Newman 0.00475061529593351 0.012783867843105 4415 1869.54545454545 2194 0.000432809523146131 7 1.07176381284694 0.835257796128214 1 3.04476579465983 4411 418 2562 354 700 2611 3217 1513 7 2578 2194 2172 M11457 GHO_ATF5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GHO_ATF5_TARGETS_DN.html Genes down-regulated in HEP3B cells (liver cancer) overexpressing ATF5 [GeneID=22809] off a plasmid vector. 18701499 28/32 Jessica Robertson 0.004000999276878 0.0111876283097536 2415 2235.72727272727 2195 0.000364390383517309 86 1.08669106773852 1.18891148700984 1 3.18162536783634 2412 2544 2031 3370 4164 2195 2834 843 2088 2026 86 2173 M1663 SASSON_FSH_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_FSH_RESPONSE.html Genes up-regulated in rFSH-17 cells (primary granulosa) after stimulation with FSH. 12832290 11/12 John Newman 0.00373155218120381 0.0106486857891669 435 1760.45454545455 2196 0.000339808778336231 82 1.02524895880545 1.02524895880545 1 3.03471508200032 433 3109 2248 2402 3989 457 161 1940 2196 2348 82 2174 M5775 BROWNE_HCMV_INFECTION_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_12HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 12 h time point that were not down-regulated at the previous time point, 10 h. 11711622 169/225 John Newman 0.0313188439318518 0.0544675546640901 1355 2302.90909090909 2196 0.00288852611595498 924 1.10101619562299 1.07294400389653 1 2.08791686323291 1352 4712 2309 2196 3488 1932 1423 924 2824 2415 1757 2175 M16463 MANN_RESPONSE_TO_AMIFOSTINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANN_RESPONSE_TO_AMIFOSTINE_DN.html Genes down-regulated in HCT116 cells (colon cancer) after treatment with amifostine [PubChem=2141] depending on the presence of TP53 [GeneID=7157]: TP53-positive vs TP53-null cells. 15750621 19/24 Leona Saunders 0.112893165645637 0.159681073373511 995 2515 2197 0.0108309059604381 993 0.844016364800038 -0.948793727222815 -1 1.00894460022333 993 4565 3530 4072 2714 1714 1018 2197 1897 3689 1276 2176 M9032 MOHANKUMAR_TLX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOHANKUMAR_TLX1_TARGETS_DN.html Down-regulated in MCF7 cells (breast cancer) by TLX1 (HOX11) [GeneID=3195]. 17213808 226/353 Arthur Liberzon 2.7096545187463e-12 1.07475372508257e-10 2200 1738.09090909091 2197 2.46332228977241e-13 93 1.39014307029143 1.46549200152402 1 20.7939613936946 2197 2755 93 2810 2786 2057 2449 748 2743 117 364 2177 M14573 BENPORATH_NOS_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_NOS_TARGETS.html Set 'NOS targets': genes upregulated and identified by ChIP on chip as targets of the transcription factors NANOG , OCT4, and Sox2 [GeneID=79923;5460;6657] (NOS) in human embryonic stem cells. 18443585 243/323 Jessica Robertson 0.132165625957333 0.182297415113563 2200 2340.54545454545 2198 0.0128040844599975 1663 1.16495021978964 1.14184581762334 1 1.29207289156501 2198 2748 1663 2938 1986 2524 2474 2148 2053 1677 3337 2178 M16524 LEE_LIVER_CANCER_DENA_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_DENA_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by diethylnitrosamine (DENA) [PubChem=5921]. 15565109 87/123 Yujin Hoshida 2.99163553071703e-06 3.58388824999603e-05 585 1970.18181818182 2198 2.71967236259407e-07 318 1.47429186921161 1.47603088244982 1 9.83457140763188 582 2835 318 2733 2809 2007 1985 2246 3174 785 2198 2179 M55 PID_S1P_S1P3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P3_PATHWAY.html S1P3 pathway 18832364 39/42 Pathway Interaction Database 0.00154344506644506 0.00549792775998217 3145 2057.72727272727 2200 0.000140411723606722 466 1.13033510362352 1.49498179669831 1 3.83272114786879 3142 861 1529 2200 466 3948 2489 770 2478 2824 1928 2180 M18496 LEE_LIVER_CANCER_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) induced by overexpression of MYC [GeneID=4609]. 15565109 69/119 Yujin Hoshida 0.017792434321542 0.0344888254610589 2245 2268.45454545455 2200 0.00163072552154411 631 1.25261392272569 1.31807356242372 1 2.74843338025022 2243 3706 916 4247 2291 841 631 2139 3987 1752 2200 2181 M2605 ONKEN_UVEAL_MELANOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONKEN_UVEAL_MELANOMA_DN.html Genes down-regulated in uveal melanoma: class 2 vs class 1 tumors. 16651410 769/1035 Arthur Liberzon 0.147455570438122 0.199767592556813 1210 2735.81818181818 2201 0.0158264203853011 1207 1.03707843256098 1.05559930329667 1 1.08838703478504 1207 4305 4278 4527 2116 1990 1465 2201 2472 3772 1761 2182 M11893 RAY_ALZHEIMERS_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/RAY_ALZHEIMERS_DISEASE.html A biomarker of plasma signaling proteins that predicts clinical Alzheimer's diagnosis. 17934472 13/20 Jessica Robertson 0.0617312586705291 0.0960671087784034 1325 2247.54545454545 2201 0.00577587931795801 662 1.81089934764203 1.56350916072855 1 2.764534538202 1325 4608 1198 4373 2238 662 779 2576 3286 1477 2201 2183 M7094 MARKEY_RB1_ACUTE_LOF_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_ACUTE_LOF_DN.html Genes down-regulated in adult fibroblasts with inactivated RB1 [GeneID=5925] by Cre-lox: acute loss of function (LOF) of RB1. 17452985 297/446 Arthur Liberzon 5.59791269293638e-07 8.52327351956765e-06 4325 2326.27272727273 2202 5.08901283393545e-08 260 1.30763068753246 -1.26969905880484 -1 9.94668356158871 4321 1177 260 1483 1299 3336 4246 3586 2202 261 3418 2184 M18400 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_16 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_16.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 16. 12554760 119/149 Arthur Liberzon 0.00248230277897759 0.00786868308715529 2270 2357.81818181818 2202 0.000225918912890763 480 1.10331639802199 1.20261598046731 1 3.48333015444501 480 3229 704 4307 2063 2073 2268 2049 4293 2268 2202 2185 M2144 DEMAGALHAES_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/DEMAGALHAES_AGING_UP.html Genes consistently overexpressed with age, based on meta-analysis of microarray data. 19189975 85/116 Joao Pedro de Magalhaes 4.08969023816171e-05 0.000324454462245657 2205 2108 2202 3.71796933221951e-06 435 1.44393573412441 -1.20734069000442 -1 7.55901876123865 2202 1322 435 1512 537 2578 3932 4072 2296 616 3686 2186 M3283 BOWIE_RESPONSE_TO_TAMOXIFEN http://www.broadinstitute.org/gsea/msigdb/cards/BOWIE_RESPONSE_TO_TAMOXIFEN.html Genes up-regulated by tamoxifen [PubChem=5376] in HMEC-E6 cells (mammary epithelial cells damaged by expression of HPV-16 E6 [GeneID=1489078]). 17016442 31/52 Arthur Liberzon 0.50225662963245 0.570966110757506 2745 2578.81818181818 2203 0.0614551218036823 1474 1.16777533057074 1.3947851020606 1 0.426378663933817 2742 1474 1689 2610 3612 2122 2203 4400 1720 1537 4258 2187 M1481 ABBUD_LIF_SIGNALING_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABBUD_LIF_SIGNALING_2_DN.html Genes down-regulated in GH3 cells (pituitary cancer) after treatment with LIF [GeneID=3976]. 14576184 7/16 Kevin Vogelsang 9.0682839471835e-05 0.00061146143186723 2205 2408 2203 9.06865402041976e-06 24 1.96664870615752 -2.34518650229621 -1 9.48330571956538 2203 3571 4485 3934 1567 2014 618 24 3438 2480 2154 2188 M12051 CHANG_IMMORTALIZED_BY_HPV31_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_IMMORTALIZED_BY_HPV31_DN.html Genes down-regulated in normal keratinocytes immortalized by infection with the high risk HPV31 (human papilloma virus) strain. 10756030 94/164 John Newman 0.000571305392877402 0.00255114612524251 2790 2006.54545454545 2203 5.19503459873212e-05 530 1.44123211969101 -1.62112970652195 -1 5.60808242291171 2787 691 579 2529 2294 2203 3972 2075 2790 530 1622 2189 M2004 MIKKELSEN_ES_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density (ICP) promoters bearing histone H3 K4 trimethylation mark (H3K4me3) in embryonic stem cells (ES). 17603471 801/1213 Arthur Liberzon 5.46924970207295e-05 0.0004100215460166 3615 2331.90909090909 2204 5.4693843138511e-06 132 1.24056263846436 -1.20543854027725 -1 6.30511774010993 3615 2204 4643 1413 3153 132 3531 4292 1912 264 492 2190 M13103 KEGG_AUTOIMMUNE_THYROID_DISEASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AUTOIMMUNE_THYROID_DISEASE.html Autoimmune thyroid disease 29/87 KEGG 0.00649180910910453 0.0155539791852657 735 2087.81818181818 2205 0.000591913163357335 735 1.23505104922621 -1.09358580675115 -1 3.35080762744174 735 3434 1784 2651 780 885 2205 2488 3723 2957 1324 2191 M519 REACTOME_GROWTH_HORMONE_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GROWTH_HORMONE_RECEPTOR_SIGNALING.html Genes involved in Growth hormone receptor signaling 25/54 Reactome 5.47274521166225e-05 0.0004100215460166 3145 2089.63636363636 2205 4.97534668821891e-06 96 1.03395206340328 -1.11886082225468 -1 5.25500884045224 3145 1487 2531 618 96 3377 3819 4332 554 2205 822 2192 M3270 ST_INTEGRIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTEGRIN_SIGNALING_PATHWAY.html Integrin Signaling Pathway 109/127 Signaling Transduction KE 0.463179682913755 0.532442304762037 1490 2169 2206 0.054984362624635 660 0.991990791879205 0.968258538358741 1 0.407338047110216 1486 660 2518 1379 3975 2206 1944 3532 1315 2318 2526 2193 M14455 TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/TANAKA_METHYLATED_IN_ESOPHAGEAL_CARCINOMA.html Genes with hypermethylated DNA in all four esophageal squamous cell carcinoma (ESCC) lines analyzed. 17438526 97/177 Arthur Liberzon 0.0394838812294198 0.0660396596041324 3465 2639.81818181818 2206 0.00365553088017668 1032 1.46227253279214 1.21550049062479 1 2.58944216923479 3464 1836 1032 2021 4098 4439 3224 1712 2206 1072 3934 2194 M120 PID_ARF6_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF6_DOWNSTREAM_PATHWAY.html Arf6 downstream pathway 18832364 26/29 Pathway Interaction Database 0.0203759405080663 0.0384083223634476 2485 2038.36363636364 2208 0.00186974018838729 281 0.873163882035473 0.946020307995112 1 1.85457999303869 2484 940 3344 885 1160 3702 3293 1402 281 2723 2208 2195 M18919 LIU_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LIU_LIVER_CANCER.html Low abundance transcripts specific to hepatocellular carcinoma (HCC). 18332864 40/62 Jessica Robertson 0.0107748706171597 0.0231380297147379 4015 2335.81818181818 2208 0.000984364278424133 571 1.24949016382072 -1.10923030580491 -1 3.06659422670915 4013 2952 2208 2866 936 3368 4343 1501 571 1522 1414 2196 M16004 KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ANTIGEN_PROCESSING_AND_PRESENTATION.html Antigen processing and presentation 67/124 KEGG 0.0109042885770266 0.0233310254231939 1215 2307.63636363636 2209 0.000996246696728052 739 1.1063492268506 -1.1564664890772 -1 2.70928595004789 1215 4084 2278 2209 942 1298 2854 2174 3778 3813 739 2197 M1951 MEISSNER_NPC_HCP_WITH_H3K4ME2 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K4ME2.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark at K4 (H3K4me2) in neural precursor cells (NPC). 18600261 559/753 Arthur Liberzon 4.69331588698264e-12 1.78648798278694e-10 1760 2311.90909090909 2210 4.69331588699255e-13 57 1.31790485714669 1.32291380544402 1 19.276980088978 1759 2210 4625 1681 1702 3028 3003 1720 2581 57 3065 2198 M4281 REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Neurotransmitter Release Cycle 37/61 Reactome 0.364097607918074 0.432554923074078 2215 2547.63636363636 2211 0.0403200856167882 1726 0.998743788777658 0.871389366258039 1 0.545335515660541 2211 1977 1726 2321 2790 1908 1731 4148 4128 3096 1988 2199 M1907 CASTELLANO_HRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) isolated from HRAS [GeneID=3265] knockout mice. 16909116 6/9 Leona Saunders 0.0998295807934562 0.14392047078348 3790 2275.72727272727 2211 0.0104620063805181 102 0.897763683830177 -0.683735247084844 -1 1.13399771699122 3787 1095 4331 575 1874 3443 2211 3331 102 3228 1056 2200 M4420 LEE_LIVER_CANCER_MYC_E2F1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_E2F1_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) from MYC and E2F1 [GeneID=4609;1869] double transgenic mice. 15565109 83/125 Yujin Hoshida 8.9364064235585e-06 9.22972392104948e-05 770 1812 2212 8.12403883952173e-07 365 1.55883416775997 1.45590540328859 1 9.43756774575849 769 2843 365 2719 2212 1534 1147 2362 2822 430 2729 2201 M13618 REACTOME_CD28_DEPENDENT_VAV1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CD28_DEPENDENT_VAV1_PATHWAY.html Genes involved in CD28 dependent Vav1 pathway 17/22 Reactome 0.0071320951052482 0.0167147412595688 2730 2004.45454545455 2213 0.000650483804984094 422 1.05931673617895 -1.13237780949095 -1 2.82432350393275 2726 1005 2213 624 805 2434 2147 3540 422 2989 3144 2202 M668 BIOCARTA_BARR_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARR_MAPK_PATHWAY.html Role of fl-arrestins in the activation and targeting of MAP kinases 22/26 BioCarta 0.00403338076219786 0.0112249747627205 2270 1913.18181818182 2214 0.000367344946922136 383 0.800693295714113 -0.681912859199696 -1 2.34251135490716 2269 3854 3456 2767 655 790 2214 383 706 3378 573 2203 M3340 PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/PEPPER_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP.html Genes up-regulated in CD38+ [GeneID=952] CLL (chronic lymphocytic leukemia) cells. 17287849 39/87 Arthur Liberzon 0.000727544523450807 0.00311051644084041 4205 2402.63636363636 2214 6.61622941248637e-05 482 1.39958546482289 -1.52870963809776 -1 5.26521187525501 4203 851 594 708 2102 4294 4409 2606 2214 482 3966 2204 M8364 TSENG_ADIPOGENIC_POTENTIAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_ADIPOGENIC_POTENTIAL_DN.html Genes showing decreasing expression in brown preadipocytes with increasing ability of the cells to differentiate. 15895078 73/93 John Newman 1.21664055898905e-07 2.16699752393522e-06 645 1981.27272727273 2215 1.10603693297411e-08 221 1.55796091053264 1.64867783183795 1 13.2412502972626 644 3282 221 3539 1071 2215 2394 2305 3943 326 1854 2205 M2447 PLASARI_NFIC_TARGETS_BASAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PLASARI_NFIC_TARGETS_BASAL_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) upon knockout of NFIC [GeneID=4782]. 19752192 43/64 Arthur Liberzon 6.26964456216471e-05 0.000453876109408243 735 2266.63636363636 2215 5.69983931275851e-06 458 1.30334021154077 1.10236967454485 1 6.53788221332112 734 3363 458 4034 1204 2552 2096 2215 4251 1416 2610 2206 M8353 BIOCARTA_HCMV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HCMV_PATHWAY.html Human Cytomegalovirus and Map Kinase Pathways 25/25 BioCarta 0.000509886465873305 0.00234567652916374 1925 1915.27272727273 2216 4.63640617156428e-05 249 0.786225682248807 0.952327530211191 1 3.10231355677564 1925 320 2917 889 310 2760 2216 4270 249 2644 2568 2207 M17283 REACTOME_G1_S_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_S_TRANSITION.html Genes involved in G1/S Transition 113/126 Reactome 0.0740774713266577 0.112030011106 355 2269.72727272727 2216 0.00697237127454855 355 0.669624506125335 -0.620817719634159 -1 0.95510873781227 355 1288 4112 3446 3069 760 1025 2216 2297 4383 2016 2208 M206 PID_PDGFRA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PDGFRA_PATHWAY.html PDGFR-alpha signaling pathway 18832364 31/35 Pathway Interaction Database 0.0223579118919511 0.0414816604284628 1155 1897.54545454545 2217 0.00205349224011625 418 1.0708509777184 0.952479864518122 1 2.22076907924441 1153 2531 2680 2217 4377 1080 439 2236 636 3106 418 2209 M4339 HANN_RESISTANCE_TO_BCL2_INHIBITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HANN_RESISTANCE_TO_BCL2_INHIBITOR_DN.html Genes down-regulated in SCLC (small cell lung cancer) cells with acquired resistance to ABT-737 [PubChem=11228183], an inhibitor of the BCL2 [GeneID=596] family proteins. 18381439 44/76 Jessica Robertson 0.00382696754134633 0.010829259022107 2080 2382.54545454545 2217 0.000348512811502008 742 1.21070935259119 1.11313992519132 1 3.57042621927041 2078 1958 742 987 3704 3049 2217 3286 3678 1488 3021 2210 M2013 MIKKELSEN_NPC_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in neural progenitor cells (NPC). 17603471 625/901 Arthur Liberzon 0.0254874236459061 0.0461984023074796 3105 2619.81818181818 2217 0.00257845552573897 735 1.19054310149229 1.269659003864 1 2.38544973504387 3105 1677 4647 1765 2082 2217 4009 3002 1978 735 3601 2211 M2372 IKEDA_MIR1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR1_TARGETS_UP.html Genes up-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-1 microRNA. 19188439 70/76 Arthur Liberzon 0.0291555591425758 0.0514445753842833 870 2343.09090909091 2217 0.00268629712152071 870 1.01096096026604 0.905917413278359 1 1.95474976331076 870 2859 3283 2922 4420 2124 2026 896 997 3160 2217 2212 M8292 ZIRN_TRETINOIN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_DN.html Genes down-regulated in MS427 cells (Wilms tumor with normal WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 5/7 Leona Saunders 0.0459518252909376 0.0749456169223308 1950 2702.63636363636 2218 0.00469306411919822 992 1.13118326792099 1.13118326792099 1 1.90985849151849 1948 4289 4345 3979 1523 1322 992 1980 4049 3084 2218 2213 M8411 LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_WITH_LOH_IN_CHR9Q.html Genes down-regulated in urothelial cell carcinoma (UCC) tumors with LOH on 9q as compared to the tumors showing retention. 16532037 152/181 Arthur Liberzon 0.00421681725071128 0.0116394020019633 3145 2466.18181818182 2218 0.000384083775274021 664 0.783953518063369 -0.784036332900527 -1 2.27501339669326 3144 1777 4076 2190 664 1549 3176 2722 2218 4289 1323 2214 M830 REACTOME_RECEPTOR_LIGAND_BINDING_INITIATES_THE_SECOND_PROTEOLYTIC_CLEAVAGE_OF_NOTCH_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECEPTOR_LIGAND_BINDING_INITIATES_THE_SECOND_PROTEOLYTIC_CLEAVAGE_OF_NOTCH_RECEPTOR.html Genes involved in Receptor-ligand binding initiates the second proteolytic cleavage of Notch receptor 15/18 Reactome 0.0328114467121356 0.0565219082048468 2220 2216.90909090909 2219 0.00302829766920633 944 1.32000531391715 1.13400706627449 1 2.47137141896864 2855 2622 2219 2109 1356 1824 944 4052 1861 2219 2325 2215 M16389 ZEMBUTSU_SENSITIVITY_TO_METHOTREXATE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_METHOTREXATE.html Top genes associated with chemosensitivity to methotrexate [PubChem=4112] across 85 tumor xenografts. 11809704 32/41 Arthur Liberzon 0.0666929627954145 0.102638012518538 2220 2224 2219 0.00625499612500717 827 1.26395966542348 1.27616715753673 1 1.87504385600078 827 2532 1502 2220 1639 2111 2027 2507 4525 2355 2219 2216 M860 REACTOME_SHC_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_MEDIATED_CASCADE.html Genes involved in SHC-mediated cascade 15/33 Reactome 0.00215120321152981 0.00705606612815894 4555 2256.09090909091 2220 0.000195755416760136 229 1.3960477891235 -1.62629399529316 -1 4.50672025402061 4554 3519 1884 1132 2649 3969 1643 229 551 2220 2467 2217 M5082 FRASOR_TAMOXIFEN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_TAMOXIFEN_RESPONSE_DN.html Genes preferentially down-regulated in MCF-7 cells (breast cancer) by tamoxifen [PubChem=5376] but not by estradiol or fulvestrant (ICI 182780) [PubChem=5757;3478439]. 16849584 17/18 Arthur Liberzon 0.170038062630835 0.22474927348573 4130 2409.09090909091 2220 0.0168004924759049 810 1.30769973278895 -1.25886627177498 -1 1.27201102493195 4126 1561 2048 1068 2551 3626 2220 1708 810 2419 4363 2218 M2018 MIKKELSEN_NPC_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in neural progenitor cells (NPC). 17603471 72/107 Arthur Liberzon 0.127652750281546 0.176899877078361 3725 2175.09090909091 2222 0.0123384953457481 744 1.17842582955599 1.18980926294 1 1.33010117420304 3721 744 1422 1420 2222 2399 2748 3080 958 1046 4166 2219 M4655 HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_DN.html Genes down-regulated during differentiation of immature to mature B lymphocyte. 11779835 52/64 Arthur Liberzon 0.00434986475997586 0.0119229742549861 2725 2229.90909090909 2223 0.000396226294945089 348 1.29019587237813 -0.95874838144884 -1 3.72394586201981 2723 2453 2044 3941 2107 584 1087 348 3523 3496 2223 2220 M691 REACTOME_KERATAN_SULFATE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_DEGRADATION.html Genes involved in Keratan sulfate degradation 9/12 Reactome 0.000841023410138652 0.0034760337091545 2065 2132.27272727273 2224 8.41341873950278e-05 388 1.28068016780399 1.73632396133165 1 4.72515938612417 2064 1626 4218 2511 388 2766 2224 498 3748 2751 661 2221 M8976 WATANABE_COLON_CANCER_MSI_VS_MSS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_COLON_CANCER_MSI_VS_MSS_DN.html Down-regulated genes discriminating between MSI (microsatellite instability) and MSS (microsatellite stability) colon cancers. 17047040 80/123 Leona Saunders 0.0140150294884726 0.0286158203963431 2320 1830.72727272727 2224 0.00128228329717012 617 1.47003618405913 1.57599230013343 1 3.4043412231745 2320 2839 1061 2279 2868 2224 1411 617 1236 990 2293 2222 M4397 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLACK_DN.html Genes from the black module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 16/17 Arthur Liberzon 4.33139442834391e-07 6.79208694411404e-06 2330 1998.18181818182 2224 3.9376320737417e-08 2 1.03858029244706 1.07932196203344 1 8.05375496412804 2328 2614 2438 3711 2 1883 1603 835 2224 2893 1449 2223 M1992 KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_UP.html Genes up-regulated similarly in primary fibroblast cultures from Werner syndrom patients and normal old donors compared to those from normal young donors. 14527998 118/142 Arthur Liberzon 0.197155413390312 0.255231363467437 2375 2203.45454545455 2226 0.0197651588982692 1591 1.01769898932306 1.08051546040322 1 0.905552007771821 2373 2334 2678 1835 2226 1591 1947 2405 2115 2849 1885 2224 M2010 MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the bivalent histone H3 trimethylation mark at K4 and K27 (H3K4me3 and H3K27me3) in neural progenitor cells (NPC). 17603471 196/329 Arthur Liberzon 3.1177655887927e-17 2.22967478471236e-15 3560 2277.18181818182 2226 2.83433235344792e-18 8 1.44717868052595 1.3277155666977 1 31.8164903141585 3556 1219 49 8 1638 4677 3772 4681 2226 127 3096 2225 M2650 CAIRO_HEPATOBLASTOMA_POOR_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_POOR_SURVIVAL.html Genes whose expression classifies hepatoblastoma tumors as belonging to either rC1 or rC2 subtypes and whose expression predicts poor survival. 19061838 15/25 Yujin Hoshida 0.0754481595207009 0.113702207195948 2320 2057.36363636364 2227 0.0071061001139634 397 1.15079125689039 0.861329291991287 1 1.63037863543761 2319 397 1793 1046 3410 2452 2979 1293 2050 2227 2665 2226 M16355 BIOCARTA_NKCELLS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NKCELLS_PATHWAY.html Ras-Independent pathway in NK cell-mediated cytotoxicity 41/65 BioCarta 0.050457946450233 0.0813949101999657 790 2190.18181818182 2228 0.00469580004900342 612 0.794832949323421 -0.780757730222649 -1 1.29918429951127 786 2939 3302 2228 2589 612 1553 1112 4095 3645 1231 2227 M2086 LI_INDUCED_T_TO_NATURAL_KILLER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_INDUCED_T_TO_NATURAL_KILLER_UP.html Genes up-regulated in ITNK cells (T-lymphocyte progenitors (DN3 cells) reprogrammed to natural killer (NK) cells by ablation of BCL11B [GeneID=64919] gene), compared to the parental DN3 cells. 20538915 347/480 Arthur Liberzon 0.00333664779337912 0.00983696288866299 2230 1881.72727272727 2229 0.000303792647142398 492 1.17488406165184 1.16926435494098 1 3.53835394842645 2229 1165 820 729 2346 2556 3191 3207 993 492 2971 2228 M1835 KEGG_GLIOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLIOMA.html Glioma 66/75 KEGG 0.0835601537601375 0.124339194750268 2135 2285.36363636364 2230 0.00790124233250998 893 0.88385199672893 0.970065218110801 1 1.20065907193973 2132 1893 2748 2230 3948 1639 893 2420 3042 2695 1499 2229 M11028 ROVERSI_GLIOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROVERSI_GLIOMA_COPY_NUMBER_UP.html Genes in the most frequently gained loci in a panel of glioma cell lines. 16247447 101/137 Arthur Liberzon 0.127085924628786 0.176373291457768 3555 2512.72727272727 2230 0.0122801713449159 1073 1.1101281217253 -1.17517457882745 -1 1.25516341670981 3554 2814 2218 1475 2050 2836 3955 3866 1569 2230 1073 2230 M1227 TRAYNOR_RETT_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/TRAYNOR_RETT_SYNDROM_DN.html Genes down-regulated in primary fibroblasts from Rett syndrom patients who carry mutations inactivating MECP2 [GeneID=4204]. 12418965 24/31 John Newman 0.00240940809033035 0.00768892571332473 4480 2521.54545454545 2230 0.000219277353828547 114 1.45411611804647 -1.20819001219019 -1 4.6127881847162 4479 939 699 114 2230 4673 3353 4353 1020 1331 4546 2231 M15588 TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_UP.html Genes up-regulated in CD34+ [GeneID=947] hematopoetic cells by expression of NUP98-HOXA9 fusion [GeneID=4928;3205] off a retroviral vector at 16 days after transduction. 16818636 160/276 Arthur Liberzon 4.36020133358691e-12 1.68689756512543e-10 1625 2077.72727272727 2231 3.96381939417778e-13 96 1.45458286407897 1.51660472329036 1 21.3305511548653 1625 1766 96 2245 3838 2456 2570 4374 1525 129 2231 2232 M1668 JIANG_AGING_HYPOTHALAMUS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_HYPOTHALAMUS_UP.html Up-regulated in the hypothalamus of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 66/78 John Newman 0.0586278479553903 0.092057033383048 2840 2195 2231 0.00547737435324006 114 0.919366163940782 -0.826534060530829 -1 1.42900593863851 2840 114 2231 811 1581 1368 1769 4557 2239 3272 3363 2233 M129 PID_PLK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PLK1_PATHWAY.html PLK1 signaling events 18832364 63/65 Pathway Interaction Database 0.572836302531731 0.639949668153792 2140 2389.63636363636 2232 0.0744121032897933 1141 0.887772038301326 -1.05224399899956 -1 0.258131158442306 2139 1366 3716 1343 2966 1890 2340 3014 1141 4139 2232 2234 M3335 HELLER_HDAC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_UP.html Genes up-regulated in at least one of three multiple myeloma (MM) cell lines by TSA [PubChem=5562]. 18172295 445/635 Jessica Robertson 0.000384482558288576 0.00190226171396444 4465 2380.45454545455 2232 3.4959069886426e-05 354 1.14590425333756 -1.19998172213848 -1 4.67805924838999 4463 1691 825 1077 1494 3350 4256 4152 2232 354 2291 2235 M2399 MADAN_DPPA4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MADAN_DPPA4_TARGETS.html Genes differentially expressed in ES cells with DPPA4 [GeneID=55211] knockout. 19332562 38/76 Arthur Liberzon 0.135752498605316 0.186265056225899 2210 2553.90909090909 2232 0.0131757112927066 1253 0.969212596481061 -1.05571384160738 -1 1.06135884690554 2207 1445 1253 2059 2068 3240 2914 2232 4241 2746 3688 2236 M7089 OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/OSWALD_HEMATOPOIETIC_STEM_CELL_IN_COLLAGEN_GEL_DN.html Genes down-regulated in hematopoietic stem cells (HSC, CD34+ [GeneID=947]) cultured in a three-dimentional collagen gel compared to the cells grown in suspension. 16166251 358/496 Leona Saunders 0.0162751120973867 0.0322481155701907 1620 2207.63636363636 2234 0.00149061578939568 1072 1.16481492588556 1.11176052414278 1 2.60677230371236 1620 2724 2234 2457 1072 2866 1926 1975 1849 2633 2928 2237 M4345 LIAN_LIPA_TARGETS_6M http://www.broadinstitute.org/gsea/msigdb/cards/LIAN_LIPA_TARGETS_6M.html Genes up-regulated at 6 months of age in lungs from LIPA [GeneID=3988] knockout mice, which display pulmonary pathology. 16127159 79/156 John Newman 0.00212532860793923 0.00699550280995341 1830 2571.36363636364 2234 0.000193398598256467 510 1.38854576086635 1.39382706294717 1 4.49030181024891 1830 4415 686 4554 3674 2686 1875 510 3684 2234 2137 2238 M11156 ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_DN.html Genes down-regulated in normal tissue adjacent to liver tumor, compared to the normal liver samples. 18413731 436/547 Jessica Robertson 0.00577426225782821 0.0142024584976285 2790 1922.81818181818 2234 0.000526315789473684 103 1.06430872484712 -1.05390911700751 -1 2.9506002894949 2786 513 2406 103 2722 1610 3183 1846 999 2749 2234 2239 M1950 MEISSNER_BRAIN_HCP_WITH_H3K4ME2_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K4ME2_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing bivalent histone H3 dimethylation mark at K4 (H3K4me2) and trimethlation mark at K27 (H3K27me3) in brain. 18600261 63/106 Arthur Liberzon 6.67801401435099e-07 9.97361563417133e-06 865 2018.09090909091 2234 6.07092367403356e-08 265 1.40639656388319 1.38824607950329 1 10.5539468475367 545 2879 265 4043 2234 2387 2657 864 4205 863 1257 2240 M13814 GENTILE_UV_RESPONSE_CLUSTER_D5 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D5.html Cluster d5: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 52/57 John Newman 0.0142749694161791 0.0290923383611249 735 2084.36363636364 2238 0.00130622223167909 623 1.15912964787964 1.19771091825317 1 2.67183985182722 732 3741 2828 3816 2731 887 1207 623 3200 2238 925 2241 M14863 BIOCARTA_P53_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P53_PATHWAY.html p53 Signaling Pathway 21/22 BioCarta 0.129640940282656 0.179181621708385 2430 2253.72727272727 2240 0.0125433445426197 987 1.20355425176153 1.40857919908253 1 1.34841430041825 2427 987 2137 1369 4588 1717 1089 2489 2240 2795 2953 2242 M15626 OUYANG_PROSTATE_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUYANG_PROSTATE_CANCER_PROGRESSION_UP.html Genes up-regulated during prostate cancer progression in mice heterozygotic for both NKX3.1 and PTEN [GeneID=4824;5728]. 18381418 26/29 Jessica Robertson 0.335937117615584 0.401988114345051 1930 2466.72727272727 2240 0.0365322091964302 1498 1.14534641051983 1.25314141249333 1 0.680099391003208 1930 3463 2699 2189 3652 2449 2140 2143 1498 2731 2240 2243 M1035 REACTOME_MYD88_MAL_CASCADE_INITIATED_ON_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MYD88_MAL_CASCADE_INITIATED_ON_PLASMA_MEMBRANE.html Genes involved in MyD88:Mal cascade initiated on plasma membrane 95/113 Reactome 0.0129899030213778 0.0268325349063033 445 2148.27272727273 2241 0.00118793108991244 421 0.915767043121992 1.09366776944646 1 2.159112279866 444 3248 3457 3888 3503 792 421 602 2241 3809 1226 2244 M19107 GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_UP.html Genes up-regulated in myeloid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 36/46 Arthur Liberzon 0.0134152982536683 0.0275905044694181 1440 2474.45454545455 2241 0.00122707346866193 609 1.22596644179234 1.26211865032085 1 2.86825285537164 1438 3797 2534 4199 4132 1642 2202 609 3015 2241 1410 2245 M12522 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1.html The 'group 1 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [GeneID=2099;2064]. 18794137 663/837 Jessica Robertson 0.0627064147403749 0.0973370926831404 2780 2605.72727272727 2241 0.00645494884032942 887 1.1127269374255 1.10318205546587 1 1.68913451588368 2776 1674 4509 961 2241 4431 3612 2176 1610 887 3786 2246 M13608 ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_V1_LATE_DIFFERENTIATION_GENES_UP.html The v1LDG up-regulated set: most variable late differentiation genes (LDG) with similar expression patterns in tonsil plasma cells (TPC) and multiple myeloma (MM) samples. 12393520 43/48 Arthur Liberzon 0.00230142179452137 0.00743003479489799 2465 1827.36363636364 2241 0.000209439349596453 233 1.50812118527815 1.50841959762161 1 4.81776972100843 2462 827 694 265 3021 3032 2810 2241 233 491 4025 2247 M5311 HOSHIDA_LIVER_CANCER_SUBCLASS_S1 http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SUBCLASS_S1.html Genes from 'subtype S1' signature of hepatocellular carcinoma (HCC): aberrant activation of the WNT signaling pathway. 19723656 326/406 Jessica Robertson 2.28735064803606e-05 0.000202937877043801 1405 2196.09090909091 2241 2.07943130007057e-06 403 1.16076623339336 1.34861141576494 1 6.43155565346896 1402 2241 403 1901 3270 3538 2965 1967 3408 749 2313 2248 M8023 MARKS_HDAC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARKS_HDAC_TARGETS_UP.html Genes whose transcription is up-regulated by histone deacetylase inhibitors. 17322921 36/53 Arthur Liberzon 0.000215104908769745 0.00123967664150573 3345 2348.72727272727 2243 1.9556903956607e-05 186 0.999408716386999 -1.1463905557807 -1 4.35886431239055 3341 1980 1755 3098 186 1839 3661 2267 3498 2243 1968 2249 M5883 NABA_SECRETED_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_SECRETED_FACTORS.html Genes encoding secreted soluble factors 22159717 161/379 Alexandra Naba 1.82472442009478e-18 1.48494814876679e-16 1030 2423.81818181818 2243 1.65884038190434e-19 43 1.60445591956925 1.55012841892892 1 38.106789010391 1027 4008 43 3925 3873 2243 2136 4268 3491 82 1566 2250 M11798 PARK_TRETINOIN_RESPONSE_AND_RARA_PLZF_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/PARK_TRETINOIN_RESPONSE_AND_RARA_PLZF_FUSION.html Genes up-regulated by tretinoin (ATRA) [PubChem=444795] in U937 cells (acute promyelocytic leukemia, APL) made resistant to the drug by expression of the PLZF-RARA fusion [GeneID=7704, 5914]. 12893766 33/41 Arthur Liberzon 0.00327239344395452 0.00972650948077161 445 1991.72727272727 2244 0.000297933739198666 146 0.988837021497128 1.04081743656729 1 2.98530278167404 442 2979 2244 4223 603 407 146 3966 3660 2823 416 2251 M1910 VANASSE_BCL2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANASSE_BCL2_TARGETS_DN.html Genes down-regulated in primary B lymphocytes engineered to overexpress BCL2 [GeneID=12043]. 15561778 103/141 Arthur Liberzon 0.0125679281972704 0.0261486548926751 2395 2367.45454545455 2244 0.00114911858616534 870 1.18330988628751 -1.1277971513239 -1 2.80983981674507 2393 1831 870 1848 2145 3567 2244 2339 3275 1124 4406 2252 M271 PID_PI3K_PLC_TRK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PI3K_PLC_TRK_PATHWAY.html Trk receptor signaling mediated by PI3K and PLC-gamma 18832364 54/60 Pathway Interaction Database 0.0286797180730086 0.0507389380646563 2245 2291 2245 0.00264186933870109 507 0.900417941066094 0.804565509175892 1 1.74910121650984 2245 2444 2789 1931 1410 1800 507 3947 3016 2997 2115 2253 M14495 VETTER_TARGETS_OF_PRKCA_AND_ETS1_UP http://www.broadinstitute.org/gsea/msigdb/cards/VETTER_TARGETS_OF_PRKCA_AND_ETS1_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PRKCA and ETS1 [GeneID=5578;2113] by RNAi. 15531915 19/21 Leona Saunders 0.000448234366462721 0.00212203230662392 1325 2088.09090909091 2245 4.07568833715986e-05 77 1.06714213962805 1.31793886795033 1 4.28048119059108 1323 3879 2782 4579 2245 447 289 77 3746 2610 992 2254 M12664 SESTO_RESPONSE_TO_UV_C3 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C3.html Cluster 3: genes changed in primary keratinocytes by UVB irradiation. 11867738 28/52 John Newman 7.62128170108013e-05 0.000531350806929073 2610 2165.72727272727 2245 6.92867793797343e-06 116 1.4042424822123 -1.58414255288316 -1 6.89982357915941 2608 3012 1298 3828 116 3735 4296 2245 689 606 1390 2255 M7923 REACTOME_SEMAPHORIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMAPHORIN_INTERACTIONS.html Genes involved in Semaphorin interactions 85/106 Reactome 0.0984339459096015 0.142343206094767 1285 2624.18181818182 2246 0.00937594799404879 1283 1.12555788647686 1.26190362287725 1 1.42984253982549 1283 3255 1993 3203 4321 2841 1954 1423 4239 2246 2108 2256 M3362 MARKS_HDAC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARKS_HDAC_TARGETS_DN.html Genes whose transcription is down-regulated by histone deacetylase inhibitors. 17322921 18/23 Arthur Liberzon 0.0871962608758672 0.128654689382336 4075 2411.81818181818 2247 0.00825973430795838 677 1.58956231428097 -1.56027705451398 -1 2.12406560132683 4072 2603 1719 1099 3398 4549 3236 1364 677 1566 2247 2257 M2412 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_6 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_6.html Genes regulated in MCF7 cells (breast cancer) by expression of the full-length form of ERBB2 [GeneID=2064] at 60 h time point. 19364815 36/65 Arthur Liberzon 3.23309949311574e-05 0.000270571446941601 3020 2361.27272727273 2247 2.93922455220191e-06 419 1.70364695535046 -1.68080949071008 -1 9.12025317345249 3016 881 419 2247 683 4169 3710 3852 2004 624 4369 2258 M103 PID_S1P_S1P1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P1_PATHWAY.html S1P1 pathway 18832364 38/45 Pathway Interaction Database 0.0113668838757094 0.024069848314647 3130 2413.18181818182 2248 0.00103873111485267 244 1.2009965254797 -1.00131884923316 -1 2.91667242390499 3127 244 859 1638 3052 2910 4687 4205 2179 1396 2248 2259 M16338 NIELSEN_LEIOMYOSARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_UP.html Top 20 positive significant genes associated with CNN1 [GeneID=1264] negative leiomyosarcoma tumors. 11965276 38/41 John Newman 0.0400982846783044 0.0668540811309066 555 2217.54545454545 2248 0.00371348604200037 552 1.08838595368383 1.09800054146136 1 1.91863058899452 552 2963 1035 2776 1843 2389 1538 2248 4541 2004 2504 2260 M8382 MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_5.html Cluster 5: genes up-regulated in SW260 cells (colon cancer) by curcumin and sulindac [PubChem=969516;5352]. 10969808 36/40 John Newman 0.00027306767704479 0.00147637965137618 2935 2116.27272727273 2249 2.48274160501946e-05 210 1.01190410931094 0.826471054532453 1 4.29813409719661 2934 1452 3363 1297 210 2748 2249 2129 474 3965 2458 2261 M1704 HOWLIN_CITED1_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_2_UP.html Genes up-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs wild type (WT) animals. 16278680 22/27 Arthur Liberzon 0.00158055003393243 0.00559235094464848 2250 2107.09090909091 2249 0.000143789699528594 75 1.11859554516973 -1.12236442417077 -1 3.78050077760151 2249 3033 2010 3485 3459 2226 2579 193 984 2885 75 2262 M12004 SENESE_HDAC1_AND_HDAC2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC1_AND_HDAC2_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of both HDAC1 and HDAC2 [GeneID=3065;3066] by RNAi. 17470557 306/422 Leona Saunders 9.87827482654371e-18 7.64351757070267e-16 2250 2325.45454545455 2250 8.98024984231245e-19 45 1.4152180493864 1.41237040090617 1 32.1011745532556 2764 2246 45 2250 1370 3263 3269 3672 1965 64 4672 2263 M1585 FERRARI_RESPONSE_TO_FENRETINIDE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FERRARI_RESPONSE_TO_FENRETINIDE_DN.html Genes down-regulated in HUVEC cells (umbilical vein endothelium) by fenretinide [PubChem=1744]. 15958647 11/12 Arthur Liberzon 0.0191452836378347 0.0365409376346866 1530 2586.45454545455 2250 0.00175581383168677 738 1.23296930133791 1.23296930133791 1 2.65888854716802 1528 4264 1907 3877 2773 1583 2250 738 4644 3025 1862 2264 M616 REACTOME_SIGNALING_BY_NOTCH1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH1.html Genes involved in Signaling by NOTCH1 75/86 Reactome 0.111340321451827 0.157720983569215 4160 2636.72727272727 2251 0.0106736219747444 1072 1.10601271671227 -1.05296633564013 -1 1.33107220691231 4160 2851 2251 1072 1885 3085 4536 4271 1354 1788 1751 2265 M17772 MACLACHLAN_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MACLACHLAN_BRCA1_TARGETS_UP.html Genes up-regulated in SW480 cells (colon cancer with mutated p53 [GeneID=7157]) upon expression of BRCA1 [GeneID=672] off an adenovirus vector. 10644742 35/51 John Newman 0.00777717980647797 0.0178368749691817 4650 2586.81818181818 2251 0.000709528146625075 831 1.4124217680792 0.959879016896499 1 3.70599183372611 4646 891 1547 2712 831 3915 4540 3710 2251 1222 2190 2266 M1690 YANG_MUC2_TARGETS_DUODENUM_6MO_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_MUC2_TARGETS_DUODENUM_6MO_DN.html Genes down-regulated in duodenum of 6 month old MUC2 [GeneID=4583] knockout mice. 18794118 21/59 Jessica Robertson 0.0228722060029554 0.0421944982759789 3860 2372 2253 0.00210122868894732 1193 1.4319148019997 -1.62474493573656 -1 2.95369273150203 3858 2071 1533 2315 1193 2085 2543 3125 2253 1439 3677 2267 M6509 PARK_HSC_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_MARKERS.html Genes in a cCDNA library from hematopoietic stem cells (HSC) after subtraction of lineage-specific markers. 11781229 50/59 Kevin Vogelsang 0.119414608794954 0.167400342593461 2125 2333.36363636364 2254 0.0114941925727812 808 1.00191784110607 1.03422821230313 1 1.1668972009774 2790 808 2589 1464 2883 2685 2254 1509 2125 2124 4436 2268 M1572 LEE_CALORIE_RESTRICTION_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_MUSCLE_UP.html Up-regulated in the gastrocnemius muscle of aged (30-month) mice subjected to caloric restriction diet since young adulthood. 10464095 47/68 John Newman 0.134386841648956 0.184605905874002 1735 2339.09090909091 2254 0.013034054012415 1423 1.24061988774763 1.23411515853279 1 1.36583306555808 1733 2465 2204 3172 2254 4052 2652 1572 2273 1930 1423 2269 M2051 ZEMBUTSU_SENSITIVITY_TO_CYCLOPHOSPHAMIDE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_CYCLOPHOSPHAMIDE.html Top genes associated with chemosensitivity to cyclophosphamide [PubChem=2907] across 85 tumor xenografts. 11809704 20/29 Arthur Liberzon 0.0095039858835345 0.0209620623225621 1695 2287.45454545455 2254 0.000867753916734861 258 1.07084692636118 0.752479659379997 1 2.69705983949974 1695 4205 2254 3978 1364 1118 258 2506 4393 2715 676 2270 M269 PID_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAS_PATHWAY.html Regulation of Ras family activation 18832364 36/38 Pathway Interaction Database 0.00980043277665033 0.0215053662044582 1145 2304.63636363636 2256 0.000894942310475237 267 1.15195919541686 1.02438418155124 1 2.88215013715219 1143 3795 2256 4197 3946 624 267 1625 3765 2615 1118 2271 M17395 KEGG_LIMONENE_AND_PINENE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LIMONENE_AND_PINENE_DEGRADATION.html Limonene and pinene degradation 13/14 KEGG 0.229585186465355 0.290067744917256 3995 2505.81818181818 2257 0.0234325636882243 726 1.52308842381143 -1.88651954979506 -1 1.22831125658185 3992 3088 2185 1626 2319 1849 2257 4482 726 1960 3080 2272 M8 PID_ENDOTHELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ENDOTHELIN_PATHWAY.html Endothelins 18832364 88/104 Pathway Interaction Database 0.327842846011257 0.39324478606687 1765 2203.36363636364 2258 0.035470467671247 702 0.963695269121426 -0.75437849368459 -1 0.586029385097222 1762 702 1664 1141 3799 2980 1653 2285 3613 2380 2258 2273 M25 ASTON_MAJOR_DEPRESSIVE_DISORDER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ASTON_MAJOR_DEPRESSIVE_DISORDER_UP.html Genes up-regulated in the temporal cortex samples from patients with major depressive disorder. 15303102 65/77 Jean Junior 0.00754381950817962 0.01746822176572 2005 2393.63636363636 2260 0.000688164745356153 159 1.10491129812276 1.2205416458893 1 2.9141431401135 2001 4082 2260 4359 889 3778 2926 1191 2631 2054 159 2274 M15913 KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY.html RIG-I-like receptor signaling pathway 56/79 KEGG 0.126270870160077 0.175500149339094 2645 2445.63636363636 2262 0.0121963659508986 667 1.06573475851539 -0.874591403822285 -1 1.20841265509952 2644 1391 2262 2035 1957 2773 2975 4336 667 2148 3714 2275 M797 REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS.html Genes involved in Class B/2 (Secretin family receptors) 50/92 Reactome 0.000194947944946347 0.00114021598531197 4060 2136.09090909091 2262 1.7724111086721e-05 189 1.4900298464753 -1.59973672482721 -1 6.57994029903964 4059 189 521 465 1409 4468 3627 2690 2262 707 3100 2276 M8751 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_14 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_14.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 14. 12554760 186/227 Arthur Liberzon 0.0855239430548956 0.126582944878993 710 2074.72727272727 2262 0.00809469580434306 706 0.910198657813014 -0.926633500356085 -1 1.22584441634463 706 2288 3786 2435 1753 1173 974 2417 1043 3985 2262 2277 M2204 TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_UP.html Genes up-regulated in normal ductal and normal lobular breast cells. 17389037 91/102 Arthur Liberzon 0.00130058925743404 0.00479217899694665 2305 2173.63636363636 2263 0.000118305342978923 448 1.17100867350244 1.06125302362307 1 4.07548064679841 2304 1844 2135 2299 448 2519 2221 2192 3023 2263 2662 2278 M17163 CAIRO_LIVER_DEVELOPMENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_LIVER_DEVELOPMENT_UP.html Genes up-regulated at early fetal liver stage (embryonic days E11.5 - E12.5) compared to the late fetal liver stage (embryonic days E14.5 - E16.5). 19061838 230/273 Arthur Liberzon 0.000255325403826494 0.00140786904913674 1180 2072.72727272727 2263 2.32140946311704e-05 536 1.21982941356006 1.21459374370452 1 5.21910454763737 1179 2263 536 2295 1653 2895 2638 2079 3463 1143 2656 2279 M3293 REACTOME_SHC_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_MEDIATED_SIGNALLING.html Genes involved in SHC-mediated signalling 19/20 Reactome 0.12922084701011 0.178862873280856 2265 2511.63636363636 2264 0.0125000256480304 598 0.736507030126097 -0.801122681378655 -1 0.825966670750831 2264 4570 3838 3260 2613 1611 1958 1549 598 4034 1333 2280 M4974 REACTOME_BASIGIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASIGIN_INTERACTIONS.html Genes involved in Basigin interactions 22/30 Reactome 0.15071890898536 0.20331330391852 2190 2698.45454545455 2265 0.0147416316689864 2051 1.07146367715012 1.16837400625789 1 1.11219251374529 2189 4199 2051 3318 2073 2174 2167 3664 2265 2391 3192 2281 M2301 VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_4_UP.html Genes up-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout and in normal 8.5 dpc embryos compared to normal 9.5 dpc embryos. 17371845 13/23 Arthur Liberzon 0.0547202729894119 0.0869921483698297 3125 2484.18181818182 2265 0.00510278975142857 240 1.66583119500409 1.78670578576169 1 2.6507837580203 3123 3914 1981 2887 3661 4346 2265 1159 240 1967 1783 2282 M13220 OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_DN.html Genes down-regulated in pirmary cultures of epithelial ovarian cancer (EOC): invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 83/134 Leona Saunders 4.30112858988465e-09 1.041093689449e-07 850 2228.72727272727 2266 3.91011690753963e-10 158 1.35712454882653 1.37773224800229 1 14.2190263942246 850 2838 158 2664 4314 3067 1619 2266 4110 574 2056 2283 M3434 NIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_17Q11_Q21_AMPLICON.html Genes within amplicon 17q11-q21 identified in a copy number alterations study of 191 breast tumor samples. 19010930 119/185 Jessica Robertson 0.26545464755426 0.328129744789461 3315 2332.36363636364 2266 0.027656144518245 650 1.12906010177245 -1.11458862502303 -1 0.819798749921917 3311 650 2465 1044 2404 2245 3163 4377 1968 2266 1763 2284 M273 PID_EPHA2_FWD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHA2_FWD_PATHWAY.html EPHA2 forward signaling 18832364 38/46 Pathway Interaction Database 0.0700887455086046 0.107039310599237 4280 2354.81818181818 2268 0.00658423942760186 192 1.15487714802729 1.07684934126575 1 1.68161443701505 4280 241 2268 427 1658 4303 4654 3556 192 1397 2927 2285 M2295 BAKKER_FOXO3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAKKER_FOXO3_TARGETS_DN.html Genes down-regulated in I/11 erythroblast cells upon expression of an activated form of FOXO3 [GeneID=2309]. 17353275 224/308 Arthur Liberzon 0.0627332440988485 0.0973375779574507 1860 2452.54545454545 2268 0.00587244808183358 674 1.00319893073771 -1.03669396127299 -1 1.52285584668844 1860 3183 3389 2926 3754 1009 2209 2268 1813 3893 674 2286 M8009 KAAB_FAILED_HEART_ATRIUM_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_FAILED_HEART_ATRIUM_UP.html Genes up-regulated in atria of failing hearts (DCM and ICM) compared to healthy controls. 15103417 60/91 John Newman 0.0213697999960169 0.0399467152400791 4355 2229.45454545455 2270 0.00196184036024047 482 1.09310151176612 -1.10696935098455 -1 2.29377394242649 4352 771 2270 596 1178 3158 3887 2877 482 1806 3147 2287 M9780 CUI_GLUCOSE_DEPRIVATION http://www.broadinstitute.org/gsea/msigdb/cards/CUI_GLUCOSE_DEPRIVATION.html Representative genes up-regulated in MiaPaCa2 cells (pancreatic cancer) under glucose-deprived conditions. 17409444 79/162 Jessica Robertson 0.200147469038322 0.258749946277973 2675 2508.72727272727 2271 0.0200978279922419 1282 1.10738942765689 -1.18394186996656 -1 0.975487581048019 2673 3685 2707 3363 4539 1282 2271 1997 1494 2235 1350 2288 M11213 SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_BY_DEACETYLATION_IN_PANCREATIC_CANCER.html 50 most interesting genes up-regulated in pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by TSA [PubChem=5562]. 12839967 56/89 John Newman 1.77547279675807e-08 3.74117482174022e-07 2390 2127 2272 1.61406619189702e-09 184 1.65540385083357 1.52813854149747 1 15.964328275875 2388 1404 184 3274 2524 1497 2138 3477 3462 777 2272 2289 M1574 LEE_AGING_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_MUSCLE_DN.html Downregulated in the gastrocnemius muscle of aged adult mice (30-month) vs young adult (5-month) 10464095 80/102 John Newman 0.00837981684447441 0.0190248848032319 1665 2443.45454545455 2273 0.000764718807784966 851 1.06989795657061 1.13329988987778 1 2.76227634973843 1662 1862 1295 1935 851 3188 3598 3618 4174 2273 2422 2290 M721 REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_THE_MRNA_UPON_BINDING_OF_THE_CAP_BINDING_COMPLEX_AND_EIFS_AND_SUBSEQUENT_BINDING_TO_43S.html Genes involved in Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S 66/112 Reactome 0.0105706473727765 0.0228050956734855 185 2583.63636363636 2274 0.000965616540205417 183 0.604480789954925 0.58236129359754 1 1.48921762304781 183 4463 4131 4691 1711 386 284 2274 4500 4537 1260 2291 M8231 HEIDENBLAD_AMPLICON_12P11_12_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_12P11_12_UP.html Up-regulated genes whose expression is associated with amplification of the 12p11-12 chromosome in pancreatic cancer cell lines. 15688027 44/48 Arthur Liberzon 0.015594448159231 0.0311864138047681 2275 2158.09090909091 2274 0.00142782701631641 1057 0.920463464581613 -0.85283497456053 -1 2.0799898049087 2274 2469 2884 2663 1057 1769 1964 1406 2727 3454 1072 2292 M177 PID_EPHA_FWDPATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHA_FWDPATHWAY.html EPHA forward signaling 18832364 37/45 Pathway Interaction Database 0.383914049226499 0.452566012075193 2275 2227.27272727273 2275 0.0430781255848605 248 1.10097504467871 0.908176523990165 1 0.568719718209383 2275 248 2165 638 4700 2307 1773 3311 716 2698 3669 2293 M1369 SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_SOX9_TARGETS_IN_PROSTATE_DEVELOPMENT_DN.html Predicted targets of SOX9 [GeneID=6662] that are down-regulated during early prostate development. 18794802 64/77 Jessica Robertson 0.283276388236558 0.347136781885113 1995 2190.72727272727 2275 0.0298248294401673 1363 1.01069249791101 1.03480203651288 1 0.696754543277858 1995 1363 2576 1850 2438 2661 1815 2411 2275 2855 1859 2294 M1484 IGLESIAS_E2F_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IGLESIAS_E2F_TARGETS_UP.html Genes up-regulated in pancreatic cells from mice with double knockout of E2F1 [GeneID=1869] and E2F2 [GeneID=1870] compared to wild type. 15146237 217/271 Kevin Vogelsang 1.15661734987485e-07 2.08367705778981e-06 775 1752.36363636364 2275 1.05147037334754e-08 219 1.22834839376535 1.20461753443191 1 10.4712067606034 771 2275 219 2453 611 2402 1759 2367 3629 301 2489 2295 M1921 REACTOME_REGULATION_OF_INSULIN_SECRETION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_SECRETION.html Genes involved in Regulation of Insulin Secretion 96/133 Reactome 0.0451914562080533 0.0739097967089438 3740 2594.72727272727 2278 0.00419521505995817 686 1.13820001202972 -1.18627611549718 -1 1.93202891812028 3736 686 1059 2070 3766 4344 4515 2039 2278 1602 2447 2296 M3412 BIOCARTA_CACAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CACAM_PATHWAY.html Ca++/ Calmodulin-dependent Protein Kinase Activation 15/15 BioCarta 0.00993578003067527 0.0217215756112956 795 2053.72727272727 2279 0.000907358038016806 272 0.943851208313746 1.04638908834268 1 2.35530123810245 792 3072 2279 3943 2095 357 272 2341 3431 3397 612 2297 M2082 WANG_METASTASIS_OF_BREAST_CANCER_ESR1_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_METASTASIS_OF_BREAST_CANCER_ESR1_UP.html Genes whose expression in primary ER(+) [GeneID=2099] breast cancer tumors positively correlates with developing distant metastases. 15721472 24/41 Arthur Liberzon 0.0884159320503792 0.130169432089142 2500 2505.27272727273 2279 0.00838027523467237 951 0.968825242419525 0.687984844813975 1 1.28716936654397 2498 951 3271 1320 1765 2279 2238 4092 1247 3899 3998 2298 M8245 REACTOME_CRMPS_IN_SEMA3A_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CRMPS_IN_SEMA3A_SIGNALING.html Genes involved in CRMPs in Sema3A signaling 26/29 Reactome 0.0604320230775186 0.0944500493132079 1115 2776.36363636364 2280 0.00565080185181772 769 1.18618842977326 1.30426218456077 1 1.82393132910421 1113 4192 2280 4290 3958 1663 769 2234 4568 3621 1852 2299 M12595 FOSTER_TOLERANT_MACROPHAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOSTER_TOLERANT_MACROPHAGE_UP.html Class T (tolerizeable) genes: induced during the first LPS stimulation and either not re-induced or induced to a much lesser degree in tolerant macrophages. 17538624 195/269 Jessica Robertson 0.0519207787807055 0.0834125513427264 2240 2272.72727272727 2280 0.0048352915693847 836 1.16480098259886 1.18000183066421 1 1.88537374405917 2236 2280 1095 1966 3057 2984 2850 2351 1782 836 3563 2300 M2322 KASLER_HDAC7_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/KASLER_HDAC7_TARGETS_2_DN.html Genes down-regulated in DO11.10 cells (hybridoma) by expression of transciptionally activating and by transcriptionally repressive forms of HDAC7 [GeneID=51564]. 17470548 49/62 Arthur Liberzon 0.0372770280296229 0.0628429241446762 2280 2408.09090909091 2280 0.00344764141265476 1017 1.24339571804842 -1.2593762255727 -1 2.24203557910248 2280 1414 1017 2260 3655 3203 3916 2313 3021 1775 1635 2301 M15068 NOUZOVA_TRETINOIN_AND_H4_ACETYLATION http://www.broadinstitute.org/gsea/msigdb/cards/NOUZOVA_TRETINOIN_AND_H4_ACETYLATION.html Genes whose CpG islands showed greatly increased histone H4 acetylation in NB4 cells (acute promyelocytic leukemia, APL) upon treatment with tretinoin [PubChem=444795]. 15302897 184/239 Kevin Vogelsang 0.174197644240513 0.229732573572288 1245 2768 2281 0.017249477476384 1242 0.931678851034841 -0.9926685849465 -1 0.892906805893913 1243 4711 4075 4668 2281 1242 2436 1722 2231 4356 1483 2302 M1467 BIOCARTA_CTLA4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTLA4_PATHWAY.html The Co-Stimulatory Signal During T-cell Activation 13/29 BioCarta 0.0188497625081598 0.0361362949337657 2190 2170.63636363636 2282 0.00172847572155467 730 0.892067611712351 0.797643044106406 1 1.93018087841871 2186 1047 2944 2192 2282 2477 2419 730 2414 3212 1974 2303 M19727 NIELSEN_LIPOSARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LIPOSARCOMA_DN.html Top 20 negative significant genes associated with liposarcomas, versus other soft-tissue tumors. 11965276 26/28 John Newman 0.000965544061166508 0.00386873341995409 2235 2221.54545454545 2282 8.78152802945248e-05 135 1.17757351967913 1.08916959364001 1 4.26259423143806 2231 2043 2398 3295 2788 3217 1564 135 2806 2282 1678 2304 M5314 MILI_PSEUDOPODIA_HAPTOTAXIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_HAPTOTAXIS_DN.html Transcripts depleted from pseudopodia of NIH/3T3 cells (fibroblast) in response to haptotactic migratory stimulus by fibronectin, FN1 [GeneID=2335]. 18451862 878/998 Jessica Robertson 0.122678404412469 0.171394778258172 4100 2293.72727272727 2283 0.0130028878292259 304 1.02746595134008 -0.933632896883328 -1 1.18086558578988 4096 472 4618 304 2555 897 3526 3107 1343 2030 2283 2305 M17761 ST_WNT_BETA_CATENIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_WNT_BETA_CATENIN_PATHWAY.html Wnt/beta-catenin Pathway 42/54 Signaling Transduction KE 0.199850107937496 0.258436303963008 2810 2230.81818181818 2284 0.0200647155747654 845 1.03779016039005 1.05138042696646 1 0.914991938254338 2807 845 2118 1524 2760 2951 2767 1805 1273 2284 3405 2306 M1168 SHIRAISHI_PLZF_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHIRAISHI_PLZF_TARGETS_UP.html Genes up-regulated in A375 and 397 cells (melanoma) by forced expression of PLZF [GeneID=7704] off adenovirus vector. 16862184 15/17 Arthur Liberzon 0.0037462666158754 0.0106648844553268 2285 2540.45454545455 2284 0.000341151017273521 638 0.876634981319692 -0.797035558216054 -1 2.59393717724205 2284 3522 2873 3942 638 1743 2159 1794 4588 3404 998 2307 M11504 TOMLINS_PROSTATE_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_PROSTATE_CANCER_DN.html Genes down-regulated in prostate cancer vs benign prostate tissue, based on a meta-analysis of five gene expression profiling studies. 17173048 57/67 Leona Saunders 0.1248162773464 0.173990794174544 3550 2396.27272727273 2284 0.0120469784933316 790 1.04217059930972 -1.05775178042671 -1 1.18755759526383 3548 790 1233 1218 2227 2974 4433 2284 2940 1204 3508 2308 M1047 YAGI_AML_WITH_INV_16_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_INV_16_TRANSLOCATION.html Genes specifically expressed in samples from patients with pediatric acute myeloid leukemia (AML) bearing inv(16) translocation. 12738660 561/770 Arthur Liberzon 0.280451886250614 0.344273836957841 1770 2589.81818181818 2284 0.0323774431753118 1422 1.09528335170582 1.08947443954914 1 0.760989938323974 1770 3157 4624 3420 2822 1998 1989 2082 2920 1422 2284 2309 M69 PID_REELIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_REELIN_PATHWAY.html Reelin signaling pathway 18832364 42/47 Pathway Interaction Database 0.164897242545394 0.21903063784491 2025 2311.27272727273 2285 0.0162484105383904 1104 1.01144865390379 1.18257409169303 1 1.00080927732336 2023 2937 3182 3415 3101 1344 1340 1684 1104 3009 2285 2310 M18887 YAGI_AML_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_SURVIVAL.html Genes differentially expressed in pediatric AML (acute myeloid leukemia) samples from patients with good survival (>3 years without relapse) compared to those with poor survival (relapsed within one year after treatment). 12738660 188/221 Kevin Vogelsang 0.168362909764881 0.222909658931343 2090 2621.63636363636 2285 0.0166202541564773 1578 0.913086111913999 0.970200742710711 1 0.893025414356817 2088 2285 3269 1654 4505 1918 1578 1703 2843 4016 2979 2311 M2279 MAEKAWA_ATF2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MAEKAWA_ATF2_TARGETS.html Genes down-regulated in MEF cells (embryonic fibroblast) upon knockout of ATF2 [GeneID=1386]. 17189429 23/46 Arthur Liberzon 0.139495144011349 0.190404013803807 4620 2661.36363636364 2286 0.0135649751547462 389 1.37616249441209 -1.39658084903647 -1 1.48733381159318 4616 3031 1702 2286 4339 3762 3538 1593 389 2012 2007 2312 M4619 LIU_PROSTATE_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_PROSTATE_CANCER_UP.html Genes up-regulated in prostate cancer samples. 16618720 133/169 Arthur Liberzon 0.344131279168107 0.411111019406091 1785 2504 2288 0.0376191054809869 1260 1.129532155482 -1.14921661866348 -1 0.654189330775079 3433 1260 1565 1502 2608 3457 4316 3549 2288 1785 1781 2313 M7988 BORCZUK_MALIGNANT_MESOTHELIOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BORCZUK_MALIGNANT_MESOTHELIOMA_DN.html Genes down-regulated in biphasic (mixed) vs epithelial subtypes of malignant peritoneal mesothelioma. 16862182 112/198 Arthur Liberzon 0.017006017820444 0.0333202175643402 2310 2259 2289 0.00155808317578671 909 1.24062363583764 1.2110865439563 1 2.74999271311671 2309 1821 909 2568 1975 1472 2289 4164 2800 1977 2565 2314 M12824 SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A4.html Cluster 4 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts good survival outcome. 18641660 278/338 Arthur Liberzon 2.55879077350018e-05 0.000223455227185849 2845 1924.09090909091 2289 2.32620048630941e-06 217 1.17800855135687 1.11857258429606 1 6.45315800762279 2843 539 632 217 2289 4077 3277 3217 777 243 3054 2315 M13096 SA_PROGRAMMED_CELL_DEATH http://www.broadinstitute.org/gsea/msigdb/cards/SA_PROGRAMMED_CELL_DEATH.html Programmed cell death, or apoptosis, eliminates damaged or unneeded cells. 11/19 SigmaAldrich 0.00301333388375627 0.00909926003110916 2855 1947.45454545455 2290 0.000274315379154784 274 0.861399379677459 -0.644527729547306 -1 2.63797486096193 2854 430 2560 2290 1008 4320 1134 274 319 3723 2510 2316 M1966 MIKKELSEN_MEF_LCP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_LCP_WITH_H3K4ME3.html Genes with low-CpG-density promoters (LCP) bearing tri-methylation mark at H3K4 (H3K4me3) in MEF cells (embryonic fibroblasts). 18509334 170/230 Jessica Robertson 8.7042046349531e-09 1.94710170033074e-07 2030 2026.27272727273 2290 7.91291333580991e-10 172 1.24741820826031 1.39352236938846 1 12.5606558428283 2029 2290 172 932 391 3755 2960 3005 2735 219 3801 2317 M2349 BIOCARTA_CCR5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CCR5_PATHWAY.html Pertussis toxin-insensitive CCR5 Signaling in Macrophage 20/27 BioCarta 0.00577426225782821 0.0142024584976285 2295 1931.36363636364 2291 0.000526315789473684 185 0.80742014531433 1.0588792124903 1 2.23839838287773 2291 984 2776 185 3180 2926 2308 1445 288 3742 1120 2318 M1307 GROSS_HIF1A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HIF1A_TARGETS_DN.html Genes down-regulated in SEND cells (skin endothelium) at normal oxygen (normoxia) conditions after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 27/46 Jessica Robertson 0.0125701902439576 0.0261486548926751 2015 2599.27272727273 2291 0.00114932660504808 998 0.883074036029032 1.02598880588448 1 2.09688505357015 2015 3440 3034 3575 998 2056 2291 1328 3976 3699 2180 2319 M9246 ENGELMANN_CANCER_PROGENITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ENGELMANN_CANCER_PROGENITORS_DN.html Down-regulated genes in the cancer progenitor (stem) cells corresponding to side population (SP) MCF7 cells (breast cancer) positive for MUC1 [GeneID=4582]. 18381450 84/118 Jessica Robertson 3.47476988209582e-05 0.000287231415822982 3380 2229.63636363636 2291 3.15893160476778e-06 317 1.25428831882621 -1.33404908691438 -1 6.66580198574163 3378 714 422 1704 2251 3471 3644 2669 2291 317 3665 2320 M2089 NOUSHMEHR_GBM_SOMATIC_MUTATED http://www.broadinstitute.org/gsea/msigdb/cards/NOUSHMEHR_GBM_SOMATIC_MUTATED.html Genes showing significantly elevated somatic mutation frequencies in proneural G-CIMP (a CpG island methylator phenotype) GBM (glyoblastoma multiforme) tumors. 20399149 23/29 Arthur Liberzon 0.00266257657073541 0.00828435162417345 930 2070.54545454545 2291 0.000242345859703329 197 1.19638804393679 1.20137773730586 1 3.73704535923617 930 3474 2291 4236 571 622 197 2330 3553 2978 1594 2321 M14511 NAKAMURA_BRONCHIAL_AND_BRONCHIOLAR_EPITHELIA http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_BRONCHIAL_AND_BRONCHIOLAR_EPITHELIA.html Differentiation markers for normal bronchiolar and bronchial epithelial cells. 16491115 6/18 Arthur Liberzon 2.08138653233451e-06 2.61280437037737e-05 2295 2229.72727272727 2292 2.08138848181354e-07 12 1.09795266257436 0.935540265068346 1 7.55021058692848 2292 452 4364 820 12 4719 3760 686 3233 1550 2639 2322 M11616 ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP.html Genes whose promoters display higher levels of histone H3 trimethylation mark at K27 (H3K27me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 307/615 Jessica Robertson 8.1620025445848e-10 2.18890068241138e-08 1580 1879.09090909091 2293 7.42000231601174e-11 140 1.23625915428396 1.24814577789223 1 14.2090174322811 1578 1173 140 698 3214 3054 2293 2578 3008 349 2585 2323 M11184 REACTOME_ENDOGENOUS_STEROLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOGENOUS_STEROLS.html Genes involved in Endogenous sterols 6/15 Reactome 0.0800929068423835 0.119594596740288 1745 2834.54545454545 2295 0.00831351001916271 1436 1.16181129540742 1.16181129540742 1 1.60773913213256 1742 4294 4226 4021 1761 2520 2163 2028 4694 2295 1436 2324 M1504 RUAN_RESPONSE_TO_TROGLITAZONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TROGLITAZONE_UP.html Adipocyte abundant genes up-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591]. 12732648 33/38 John Newman 0.000228299682860365 0.00130456961634494 4530 2121.54545454545 2295 2.07566706864231e-05 191 1.03443502315036 -1.02090803011679 -1 4.47723852411508 4526 251 1909 297 191 4479 2826 3759 394 2410 2295 2325 M14275 FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_PAPILLARY_THYROID_CARCINOMA_DN.html Genes down-regulated in papillary thyroid carcinoma (PTC) compared to other thyroid tumors. 17968324 76/137 Arthur Liberzon 0.156504493908108 0.209858298649508 2120 2394.36363636364 2295 0.0153537027030287 94 1.08857587508781 1.16547886382489 1 1.1074803090245 2120 94 1281 804 2295 4151 3416 4189 2764 2063 3161 2326 M9874 OUYANG_PROSTATE_CANCER_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/OUYANG_PROSTATE_CANCER_MARKERS.html Mouse orthologs of human prostate cancer tumor markers which were deregulated in mice heterozygotic for both NKX3.1 and PTEN [GeneID=4824;5728]. 18381418 25/27 Jessica Robertson 0.0791930341615683 0.118663848013525 3135 2245.63636363636 2299 0.00747238339253136 973 1.21371329556641 1.27145774532745 1 1.68574652398257 3134 2049 2216 2401 3242 2299 2385 1315 973 2209 2479 2327 M44 PID_HIF2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF2PATHWAY.html HIF-2-alpha transcription factor network 18832364 39/51 Pathway Interaction Database 0.00376503168575666 0.0107004810454229 2300 1957.36363636364 2300 0.000342862778055401 271 1.20333185146216 1.1329060185835 1 3.5580500616453 842 4128 2300 4198 2300 434 271 323 3503 2443 789 2328 M641 REACTOME_REGULATION_OF_HYPOXIA_INDUCIBLE_FACTOR_HIF_BY_OXYGEN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_HYPOXIA_INDUCIBLE_FACTOR_HIF_BY_OXYGEN.html Genes involved in Regulation of Hypoxia-inducible Factor (HIF) by Oxygen 26/35 Reactome 0.00739185142776357 0.0171785025795392 2300 2477.45454545455 2300 0.000674255000712342 813 0.985285775650463 1.17728366009135 1 2.60936440487416 2300 3456 3016 3582 813 2282 1514 1731 3338 3620 1600 2329 M5103 YAGI_AML_FAB_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_FAB_MARKERS.html Genes specifically expressed in FAB subtypes M2, M4, M5 and M7 of pediatric AML (acute myeloid leukemia). 12738660 293/403 Kevin Vogelsang 0.0205668525675755 0.0386750584715373 2355 2480.81818181818 2300 0.00188742526441046 929 1.14055187246366 1.0615344000025 1 2.41739442240263 2351 2252 929 1903 1564 4423 3380 2300 2810 1144 4233 2330 M1948 YAMANAKA_GLIOBLASTOMA_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMANAKA_GLIOBLASTOMA_SURVIVAL_DN.html Genes whose expression most strongly and consistently associated with the short term survival of patients with high grade glioma tumors. 16652150 11/12 Arthur Liberzon 0.0360129389166559 0.0610783584932145 4260 2609.09090909091 2301 0.0033287570511492 1393 1.09357047235307 -0.817764305352502 -1 1.99216128218925 4260 1608 2301 2850 1393 3982 4473 1694 1547 2350 2242 2331 M2465 DELACROIX_RAR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELACROIX_RAR_TARGETS_DN.html Genes bound by RARG [GeneID=5916] and down-regulated by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] in MEF cells (embryonic fibroblast). 19884340 29/35 Arthur Liberzon 0.143852411547472 0.195672444525668 1825 2410.27272727273 2301 0.0140201081993036 1137 1.43373154712881 1.53544597925582 1 1.52405682756334 1821 4173 2036 3158 3088 2043 1137 2551 2467 1738 2301 2332 M9626 BOYERINAS_ONCOFETAL_TARGETS_OF_LET7A1 http://www.broadinstitute.org/gsea/msigdb/cards/BOYERINAS_ONCOFETAL_TARGETS_OF_LET7A1.html Embryonic genes targeted by LET7A1 [GeneID=406881] and which are up-regulated in many human cancers. 18413726 27/36 Jessica Robertson 0.0125064083650905 0.0260619194186434 380 2330.27272727273 2303 0.0011434613594131 380 1.24253967723186 1.17276750652771 1 2.95318010787224 380 3465 1275 3669 995 2888 1813 2303 4535 2372 1938 2333 M1990 WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_EVASION_AND_TOLEROGENICITY_DN.html Selected genes with immunologic function which were reciprocally changed in evasion and tolerogenic tumor models. 18381452 17/27 Arthur Liberzon 0.00543856706452601 0.0141901805110905 1930 2277.81818181818 2303 0.000495641666405895 730 0.998193378751435 1.03441814093277 1 2.76786366252909 1929 2612 2303 3328 730 1999 952 2366 4223 2427 2187 2334 M14301 REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PI3KGAMMA.html Genes involved in G beta:gamma signalling through PI3Kgamma 21/30 Reactome 0.0171452166647182 0.0335233730975435 985 1996.09090909091 2304 0.00157093731047859 692 0.921424423764024 -1.00820834285004 -1 2.03877178587238 2405 983 2463 2146 2178 2360 2389 692 3052 2304 985 2335 M10153 CLAUS_PGR_POSITIVE_MENINGIOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CLAUS_PGR_POSITIVE_MENINGIOMA_UP.html Genes up-regulated in meningioma samples positive for PGR [GeneID=5241] compared to those without the receptor. 18172325 9/18 Jessica Robertson 0.00179022751777442 0.00616779115612794 3090 2253 2304 0.000179167136664914 218 1.03977822918387 -1.24059630890335 -1 3.44775177697063 3088 2666 4531 2304 1111 2069 2603 218 2105 3566 522 2336 M1075 REACTOME_INWARDLY_RECTIFYING_K_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INWARDLY_RECTIFYING_K_CHANNELS.html Genes involved in Inwardly rectifying K+ channels 21/39 Reactome 0.000954710575800006 0.00383183156273472 2420 2352 2305 8.68295575697119e-05 132 1.38714477685721 -1.40456032266334 -1 5.0298852924482 2416 2083 1460 2603 3928 3878 3896 132 1674 2305 1497 2337 M11619 VETTER_TARGETS_OF_PRKCA_AND_ETS1_DN http://www.broadinstitute.org/gsea/msigdb/cards/VETTER_TARGETS_OF_PRKCA_AND_ETS1_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PRKCA and ETS1 [GeneID=5578;2113] by RNAi. 15531915 21/27 Leona Saunders 0.0786567700488321 0.117935182538274 2155 2705.72727272727 2306 0.00741984883076918 798 1.28441053675659 1.22177544236857 1 1.7891008277357 2154 4560 2071 3813 2579 2238 3141 2017 4086 2306 798 2338 M939 HADDAD_B_LYMPHOCYTE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/HADDAD_B_LYMPHOCYTE_PROGENITOR.html Genes up-regulated in hematopoietic progenitor cells (HPC) of B lymphocyte lineage CD34+CD45RA+CD10+ [GeneID=947;5788;4311]. 15331438 431/684 Kevin Vogelsang 0.0289128019719641 0.0510926339601912 1575 2360.81818181818 2306 0.00266362917580308 1296 1.03889746444934 0.972726500120655 1 2.01341698668865 1575 2716 1881 3831 1296 1974 1430 2306 2623 3251 3086 2339 M2433 IM_SREBF1A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/IM_SREBF1A_TARGETS.html Genes differentially expressed in liver tissue upon knockout of the 1a isoform of SREBF1 [GeneID=6720]. 19564420 7/7 Arthur Liberzon 0.000259431160106972 0.00142220101707887 4000 2547.72727272727 2306 2.59461452121338e-05 215 0.84126688410575 -0.674061002232837 -1 3.59381926118625 3999 1633 4702 1533 215 4223 2306 1811 497 3367 3739 2340 M1110 GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_UP.html Up-regulated genes from the set A (Fig. 5a): specific to cells expressing MLL-AF4 [GeneID=4297;4299] fusion protein alone. 17130830 281/360 Arthur Liberzon 0.0538089126233193 0.0858034012101577 1215 2510.27272727273 2307 0.00501562817553633 1148 1.16076395707434 1.19163608446043 1 1.85746229048285 1212 4690 2184 4261 2684 1658 1965 1148 3152 2352 2307 2341 M15181 BIOCARTA_PGC1A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PGC1A_PATHWAY.html Regulation of PGC-1a 29/30 BioCarta 0.00298369285561658 0.00903337413631189 115 2125.36363636364 2308 0.00027161337377397 112 0.866454649415949 0.931508702344628 1 2.65756020938073 502 3823 2784 4213 2308 112 113 2074 3726 3386 338 2342 M2750 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_13 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_13.html Amplification hot spot 13: colocolized fragile sites and cancer genes in the Xq12-q28 region. 16751803 8/9 Arthur Liberzon 8.32740261893615e-05 0.000572964145209601 1655 2272.72727272727 2308 8.32771469074969e-06 128 1.08986652926699 0.899606347004704 1 5.30154426763118 1654 3116 4377 2592 128 1627 1701 1430 3439 2628 2308 2343 M13616 SUH_COEXPRESSED_WITH_ID1_AND_ID2_UP http://www.broadinstitute.org/gsea/msigdb/cards/SUH_COEXPRESSED_WITH_ID1_AND_ID2_UP.html Genes whose expression positively correlates with that of both ID1 and ID2 [GeneID=3397;3398] genes in a cohort of 285 patients with primaly AML (acule myelogenous leukemia) [PMID=15084694]. 18542061 21/22 Jessica Robertson 0.00185691047450986 0.0063419807812493 1200 2407.54545454545 2308 0.000168952695887583 496 1.06338026423352 1.0389082276377 1 3.50671557533607 1197 3869 2211 4358 496 2588 2098 1462 3242 2308 2654 2344 M12627 REACTOME_DOPAMINE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOPAMINE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Dopamine Neurotransmitter Release Cycle 14/20 Reactome 0.16026281189869 0.213804542725217 3425 2449.63636363636 2309 0.0157533524093816 133 1.2521302917196 -1.70109724658941 -1 1.2586896094428 3423 1036 2147 1728 4665 2309 1206 3357 133 2673 4269 2345 M1852 QI_PLASMACYTOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/QI_PLASMACYTOMA_DN.html Down-regulated genes that best disciminate plasmablastic plasmacytoma from plasmacytic plasmacytoma tumors. 17363561 149/179 Jessica Robertson 0.0406153711018223 0.067501602676268 1585 2490.27272727273 2309 0.00376228766860354 1038 1.12070684028517 -0.991056861683582 -1 1.96857007070756 1582 2309 1038 2925 1903 3189 3044 2302 3486 2140 3475 2346 M12942 MAINA_VHL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAINA_VHL_TARGETS_UP.html Genes up-regulated in RCC4 cells (renal cell carcinoma) engineered to stably express VHL [GeneID=7428] off a plasmid vector. 15824735 17/18 Leona Saunders 0.00979205696426451 0.0214969808703853 3035 2211.72727272727 2310 0.000894174027851022 532 1.26826342843709 -1.26647827970191 -1 3.17347111082842 3034 1559 927 2310 3626 3375 3821 532 2514 1070 1561 2347 M1531 HU_GENOTOXIC_DAMAGE_24HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIC_DAMAGE_24HR.html Genes most consistently regulated at 24 h by all six genotoxins tested: cisplatin, methyl methanesulfonate, mitomycin C, taxol, hydroxyurea and etoposide [PubChem=2767;4156;5746;4666;3657;36462]. 15120960 48/88 John Newman 0.0657107396484346 0.101357742202814 1700 2586 2310 0.00615996623349135 1243 1.08294644812144 1.02771805648906 1 1.61535964373038 1700 3752 2310 4063 3798 2270 2599 1243 1906 1978 2827 2348 M15468 GENTILE_UV_RESPONSE_CLUSTER_D4 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D4.html Cluster d4: genes progressively down-regulated in WS1 cells (fibroblast) through 12 h after irradiation with high dose UV-C. 12907719 84/89 John Newman 0.0117045885350383 0.0246742554200003 865 2358.90909090909 2311 0.00106975708033686 577 0.957769131768035 0.946889969331719 1 2.31048352674146 863 2836 3436 3796 3912 1511 957 577 2311 3453 2296 2349 M2323 DORMOY_ELAVL1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/DORMOY_ELAVL1_TARGETS.html Genes down-regulated in HeLa cells upon knockdown of ELAVL1 [GeneID=1994] by RNAi. 17548472 21/31 Arthur Liberzon 0.0756493742377121 0.113969054070221 1805 2655.81818181818 2311 0.00712574645137428 1297 1.37093108187534 1.31825580578695 1 1.94018680656052 1801 4224 2202 3857 2273 2772 2658 1297 3986 2311 1833 2350 M15411 BARIS_THYROID_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARIS_THYROID_CANCER_DN.html Genes down-regulated in oncocytic follicular carcinoma (FTC) vs mitochondrial-rich papillary carcinoma (PTC) types of thyroid cancer. 15806164 91/108 Arthur Liberzon 0.0377703510282806 0.0635338762842069 4525 2478.09090909091 2312 0.00349407568467844 626 1.11568016756319 -1.06879317512939 -1 2.00378348759405 4523 1308 2374 626 1407 4485 4614 2312 1597 1228 2785 2351 M2254 CERIBELLI_GENES_INACTIVE_AND_BOUND_BY_NFY http://www.broadinstitute.org/gsea/msigdb/cards/CERIBELLI_GENES_INACTIVE_AND_BOUND_BY_NFY.html Transcriptionally inactive genes which where bound by NF-Y transcription factor. 18212061 30/65 Arthur Liberzon 0.150430560794132 0.203040390891708 2845 2352.72727272727 2312 0.0147112258847352 963 1.08604068528165 -1.14911188367178 -1 1.1282757214281 2842 2985 2312 1973 2915 963 1881 4199 995 3043 1772 2352 M1167 HUMMERICH_SKIN_CANCER_PROGRESSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_SKIN_CANCER_PROGRESSION_UP.html Selected genes up-regulated during progression through benign to malignant skin tumors formed by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 128/168 Arthur Liberzon 5.17840413514199e-07 7.98760376400987e-06 2315 1878.72727272727 2313 4.7076412309505e-08 255 1.28061310733387 1.34343868137718 1 9.79533754239436 2313 633 255 864 551 3104 3008 3881 2453 586 3018 2353 M3468 NABA_ECM_REGULATORS http://www.broadinstitute.org/gsea/msigdb/cards/NABA_ECM_REGULATORS.html Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix 22159717 142/319 Alexandra Naba 1.71072231742032e-13 8.4995887770778e-12 1330 2094.54545454545 2313 1.55520210674586e-14 71 1.49981597719698 1.49297797415036 1 24.91432815359 1326 2313 71 3012 1349 3305 3274 2050 3717 272 2351 2354 M15926 BIOCARTA_TFF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TFF_PATHWAY.html Trefoil Factors Initiate Mucosal Healing 34/40 BioCarta 0.00577426225782821 0.0142024584976285 2965 1979.72727272727 2315 0.000526315789473684 149 0.832102222707766 -0.847976565357852 -1 2.30682735940463 2965 884 3360 206 1586 2315 3845 2995 149 2865 607 2355 M185 PID_ALK1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK1_PATHWAY.html ALK1 signaling events 18832364 29/33 Pathway Interaction Database 8.88413986574876e-05 0.000601623244854148 3655 2173.90909090909 2315 8.07681695400163e-06 113 1.06760590855162 1.16051362716233 1 5.1593005008562 3651 300 2315 545 123 4523 4648 2518 113 1388 3789 2356 M4479 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_UP.html Genes up-regulated in ductal carcinoma vs normal lobular breast cells. 17389037 105/146 Arthur Liberzon 0.216937793198624 0.277116748010151 1910 2415.27272727273 2315 0.0219859025602057 1121 1.33434930598113 1.36698465025984 1 1.1158047497272 1910 3663 1444 1121 3061 2989 2949 2315 2208 1210 3698 2357 M12315 TSAI_DNAJB4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_DNAJB4_TARGETS_DN.html Genes down-regulated in CL1-5 cells (lung cancer) overexpressing DNAJB4 [GeneID=11080] off a plasmid vector. 16788156 8/9 Jessica Robertson 0.0180418525226449 0.034900632748723 360 2456.63636363636 2315 0.00181900272685209 359 2.3900973713473 2.3900973713473 1 5.22586089874738 359 3945 4630 4178 2315 843 409 1900 3436 3465 1543 2358 M239 PID_A6B1_A6B4_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_A6B1_A6B4_INTEGRIN_PATHWAY.html a6b1 and a6b4 Integrin signaling 18832364 56/64 Pathway Interaction Database 0.0025210680068666 0.00793825283016034 1960 2330.18181818182 2316 0.000229451058447115 244 1.07879987386922 1.20222208642198 1 3.3997372580146 1960 3319 2567 2995 3909 2316 2050 244 2485 2149 1638 2359 M18876 MAHADEVAN_IMATINIB_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_IMATINIB_RESISTANCE_UP.html Top genes up-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] compared to the parental cell line sensitive to the drug. 17325667 20/31 Arthur Liberzon 0.000882045450285098 0.00360454937259365 1560 2241.90909090909 2316 8.02181170156587e-05 127 1.38420677929831 1.281935951125 1 5.07438811081 1556 3866 733 4180 2651 2814 2316 127 4609 1017 792 2360 M16664 SIMBULAN_UV_RESPONSE_NORMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_UV_RESPONSE_NORMAL_UP.html Genes up-regulated in HFK cells (primary keratinocytes) in response to UVB irradiation. 16007217 11/12 Leona Saunders 0.11201323944459 0.158531481312883 2105 2310.45454545455 2316 0.0107417495758925 1550 1.39199278424422 1.25080276037152 1 1.67062337578291 2101 2646 1550 3147 1889 2619 1831 2316 2864 1718 2734 2361 M14032 ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN.html Genes down-regulated in macrophage by live P.gingivalis. 18025224 483/706 Arthur Liberzon 0.000418916662452082 0.00201148183802017 2170 1853.27272727273 2317 3.80905865852041e-05 9 1.14689861991693 -1.10592518977444 -1 4.64039300238438 2166 2711 2387 2503 2659 9 2317 3247 832 1514 41 2362 M925 REACTOME_SIGNAL_REGULATORY_PROTEIN_SIRP_FAMILY_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_REGULATORY_PROTEIN_SIRP_FAMILY_INTERACTIONS.html Genes involved in Signal regulatory protein (SIRP) family interactions 10/15 Reactome 0.00010934221842093 0.00071305430343848 3175 2233.63636363636 2318 9.94069574705527e-06 139 0.674011423065669 -0.6928343732754 -1 3.18254422116026 3928 1603 3325 1569 139 3173 3172 2318 365 3656 1322 2363 M1557 DELASERNA_MYOD_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DELASERNA_MYOD_TARGETS_UP.html Genes up-regulated in NIH 3T3 cells (fibroblasts) 24 h after inducing MyoD [GeneID=4654] differentiation program. 15870273 114/146 John Newman 0.0633129336876147 0.0981402453220169 4630 2357.81818181818 2318 0.00592835992859729 20 1.14900181554445 -1.11738891652448 -1 1.73805080519358 4627 20 1114 1236 2709 3405 3431 3309 2318 1678 2089 2364 M15844 DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_TTD_UP.html Genes exclusively up-regulated in fibroblasts expressing the TTD mutant form of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 112/131 Arthur Liberzon 0.171930680981822 0.226996591394182 2320 2531.45454545455 2319 0.0170045273565197 658 0.843344503720897 0.975466024078601 1 0.814822950869032 1820 658 2319 2467 2316 4213 3488 1897 4092 3321 1255 2365 M209 PID_P38_GAMMA_DELTA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_GAMMA_DELTA_PATHWAY.html Signaling mediated by p38-gamma and p38-delta 18832364 12/12 Pathway Interaction Database 0.0353925974312136 0.0602463794880628 3225 2423.36363636364 2320 0.00327046734545846 566 0.771319115707167 0.720384308279631 1 1.41197745721463 3223 1585 2886 2320 1840 1650 566 4132 975 3126 4354 2366 M1197 TERAMOTO_OPN_TARGETS_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_1.html Cluster 1: genes whose up-regulation peaked one day after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 17/19 Arthur Liberzon 0.00482346026944038 0.0129503597677808 3700 1945.72727272727 2320 0.000439460744913014 374 0.912147282106494 -0.784735863403515 -1 2.58360515931284 3697 374 2320 817 701 2863 2824 2042 563 2424 2778 2367 M6206 HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2 http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_BRCA1_VS_BRCA2.html Genes differentially expressed in hereditary breast cancer tumors with mutated BRCA1 [GeneID=672] compared to those with mutated BRCA2 [GeneID=675]. 11207349 232/254 John Newman 0.498453538509392 0.567599686794772 1745 2472.81818181818 2320 0.0608054560389243 1232 1.00020837366423 1.07225989346728 1 0.369035769971485 1745 2265 3588 1678 3935 2320 2013 2544 1232 3188 2693 2368 M1476 ZHAN_EARLY_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_EARLY_DIFFERENTIATION_GENES_DN.html B lymphocyte early differentiation genes (EDG): top genes down-regulated in tonsil B lymphocytes (TBC) compared to the tonsil plasma cells (TPC). 12393520 50/58 Arthur Liberzon 0.241486990405557 0.302821093175937 1930 2578.72727272727 2321 0.0248137962904386 1344 0.878386358936527 0.870573054564049 1 0.683709726266221 1928 1937 3465 3389 3719 2700 2210 1929 1344 3424 2321 2369 M757 REACTOME_ACETYLCHOLINE_BINDING_AND_DOWNSTREAM_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACETYLCHOLINE_BINDING_AND_DOWNSTREAM_EVENTS.html Genes involved in Acetylcholine Binding And Downstream Events 2/14 Reactome 0.00941437821508214 0.0207935728475375 3775 2483.1 2321.5 0.00105044496114992 467 0.876678217475806 -0.876678217475806 -1 2.21261343744086 3772 2192 4231 NA 961 1791 1479 2451 467 4550 2937 2370 M559 REACTOME_SIGNALING_BY_CONSTITUTIVELY_ACTIVE_EGFR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_CONSTITUTIVELY_ACTIVE_EGFR.html Genes involved in Signaling by constitutively active EGFR 30/35 Reactome 0.000665082594166235 0.00288793913934188 850 2085 2322 6.04803400547395e-05 34 0.894551625713187 0.820685993612785 1 3.40852822923743 849 3832 3446 3255 3660 498 34 386 2322 3435 1218 2371 M14582 REACTOME_P75NTR_RECRUITS_SIGNALLING_COMPLEXES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P75NTR_RECRUITS_SIGNALLING_COMPLEXES.html Genes involved in p75NTR recruits signalling complexes 16/19 Reactome 0.00511169334959444 0.013562221815675 4625 2583.54545454545 2322 0.000465782648409149 321 0.653282629126554 0.653282629126554 1 1.83070244221105 1604 4600 3404 4623 715 1007 658 2322 4625 4540 321 2372 M1827 MATZUK_PREOVULATORY_FOLLICLE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_PREOVULATORY_FOLLICLE.html Genes important for preovulatory follicle, based on mouse models with female fertility defects. 18989307 16/19 Jessica Robertson 0.0888493992435637 0.130685311445815 3480 2501.90909090909 2322 0.00842315040577212 988 1.4479209635263 -1.44516231087672 -1 1.92001033441132 3476 2108 1168 2047 3775 2322 1750 3351 2502 988 4034 2373 M36 PID_IL27_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL27_PATHWAY.html IL27-mediated signaling events 18832364 16/27 Pathway Interaction Database 0.0961724342754465 0.1394202429397 2790 2365.90909090909 2323 0.00915030451573282 1026 0.954887786184714 -0.975780955345642 -1 1.22592831985965 2788 1026 2496 1598 1809 2319 3428 2211 3405 2323 2622 2374 M708 REACTOME_A_TETRASACCHARIDE_LINKER_SEQUENCE_IS_REQUIRED_FOR_GAG_SYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_A_TETRASACCHARIDE_LINKER_SEQUENCE_IS_REQUIRED_FOR_GAG_SYNTHESIS.html Genes involved in A tetrasaccharide linker sequence is required for GAG synthesis 22/26 Reactome 0.058320789046343 0.0916822223661989 2160 2227.27272727273 2323 0.00544788821097211 341 1.35392811775203 1.3916984639938 1 2.10811187153232 2160 956 1103 341 3202 3840 2705 4013 2323 1530 2327 2375 M210 PID_IL8_CXCR2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL8_CXCR2_PATHWAY.html IL8- and CXCR2-mediated signaling events 18832364 57/67 Pathway Interaction Database 0.231420955720346 0.291982601176165 2780 2125.72727272727 2325 0.0236443382865696 144 0.93074849485496 -0.936960920522287 -1 0.746580256691404 2777 144 2778 628 2325 2071 2260 3041 916 2829 3614 2376 M4939 MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_UP.html Genes correlated with the early tumor onset in the Emu-myc transgenic mouse lymphoma model. 18922927 132/151 Jessica Robertson 0.189653708343989 0.247078527017287 1115 2381.81818181818 2325 0.0189360178542251 1115 0.922885294391468 -0.879153813727804 -1 0.840701059268873 1115 2325 3939 3186 2196 1230 1505 2357 1584 4227 2536 2377 M929 SABATES_COLORECTAL_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_UP.html Genes up-regulated in colorectal adenoma compared to normal mucosa samples. 18171984 130/249 Leona Saunders 3.38529082719773e-16 2.21924620894074e-14 2230 2400.72727272727 2326 3.07753711563429e-17 54 1.70355231387458 1.64027133909952 1 34.9019208041095 2227 1800 54 2244 4603 2893 2608 4586 2926 141 2326 2378 M14665 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP.html Genes up-regulated in lymphoblastoid cells from the European population compared to those from the Asian population. 17206142 668/882 Leona Saunders 0.038121400128835 0.0640489657077359 1620 2559.72727272727 2326 0.00387915972938869 439 0.875387515851143 -0.862169894949582 -1 1.56758410617949 1617 3600 4414 3262 3255 439 1739 1760 2326 4454 1291 2379 M1710 HILLION_HMGA1B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/HILLION_HMGA1B_TARGETS.html Genes changed in Rat1a cells (fibroblasts) by overexpression of HMGA1 isoform b [GeneID=3159] off a plasmid vector. 19074878 127/192 Leona Saunders 0.215187406232015 0.275253267592171 4500 2310.54545454545 2327 0.0217873619397699 609 1.11217207573982 -1.18096723885906 -1 0.934889064984767 4498 631 1380 609 2327 2715 4676 2395 1392 1411 3382 2380 M15801 SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC.html Cluster 2: genes up-regulated in B493-6 cells (B lymphocytes) by serum alone or in combination with MYC [GeneID=4609] but not by MYC alone. 15516975 128/146 Leona Saunders 0.146633050586556 0.198938775156236 1965 2586.63636363636 2328 0.0143116584044835 948 0.789228255590249 -0.773807732147862 -1 0.830387664946929 1964 2328 3980 2954 4425 948 1729 1919 2751 4292 1163 2381 M11033 MENSE_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MENSE_HYPOXIA_UP.html Hypoxia response genes up-regulated in both astrocytes and HeLa cell line. 16507782 123/142 Kevin Vogelsang 0.00924653372846894 0.020509228946604 3770 2460.09090909091 2329 0.000844147895966631 885 1.26073364328156 -1.24710272555619 -1 3.19327437444107 3766 2329 1628 1540 885 3800 4025 3890 1237 1146 2815 2382 M883 REACTOME_HIGHLY_CALCIUM_PERMEABLE_POSTSYNAPTIC_NICOTINIC_ACETYLCHOLINE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIGHLY_CALCIUM_PERMEABLE_POSTSYNAPTIC_NICOTINIC_ACETYLCHOLINE_RECEPTORS.html Genes involved in Highly calcium permeable postsynaptic nicotinic acetylcholine receptors 2/11 Reactome 0.00941437821508214 0.0207935728475375 3775 2490.1 2331 0.00105044496114992 468 0.876678217475806 -0.876678217475806 -1 2.21261343744086 3773 2193 4247 NA 962 1792 1480 2469 468 4579 2938 2383 M17466 SANA_TNF_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/SANA_TNF_SIGNALING_UP.html Genes up-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by TNF [GeneID=7124]. 15749026 120/173 Yujin Hoshida 0.00124496270040979 0.00464523632089661 1950 2171 2331 0.000113242524879008 519 1.24747333747173 1.25986646856502 1 4.36692607689259 1950 2331 637 1073 2284 2754 2525 3111 2932 519 3765 2384 M2177 FIGUEROA_AML_METHYLATION_CLUSTER_6_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_6_UP.html Cluster 6 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 152/199 Arthur Liberzon 0.00116761322008739 0.00446245700308704 4705 2458.18181818182 2331 0.000106203033829275 421 0.997812527133403 -1.04474439795659 -1 3.51904057529833 4701 1238 2331 463 421 4247 3034 4520 1885 2430 1770 2385 M886 REACTOME_PRESYNAPTIC_NICOTINIC_ACETYLCHOLINE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRESYNAPTIC_NICOTINIC_ACETYLCHOLINE_RECEPTORS.html Genes involved in Presynaptic nicotinic acetylcholine receptors 2/12 Reactome 0.00941437821508214 0.0207935728475375 3775 2491.1 2332 0.00105044496114992 469 0.876678217475806 -0.876678217475806 -1 2.21261343744086 3774 2194 4248 NA 963 1793 1481 2470 469 4580 2939 2386 M913 REACTOME_NEPHRIN_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEPHRIN_INTERACTIONS.html Genes involved in Nephrin interactions 27/33 Reactome 0.110970869517241 0.157339292316425 3380 2474.81818181818 2332 0.0106362378413808 321 0.796048486657277 -0.843223901549734 -1 0.959261487943761 3380 321 3087 1625 1883 1973 2332 4011 1038 3277 4296 2387 M17434 LIN_APC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LIN_APC_TARGETS.html Genes up-regulated by forced expression of APC [GeneID=324] in the APC-deficient SW480 cell line (colon cancer). 11522623 121/156 Yujin Hoshida 0.00424965693908388 0.0116958488352629 1195 1996.18181818182 2333 0.000387080737213056 92 1.11792775833281 -1.1987272657037 -1 3.24071882563139 1191 2333 2574 3390 3817 597 1370 409 2985 3200 92 2388 M94 PID_FAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FAS_PATHWAY.html FAS (CD95) signaling pathway 18832364 47/54 Pathway Interaction Database 0.106717873826936 0.152421112367631 3665 2483.72727272727 2335 0.0102068994334052 174 0.812833292081006 -0.899728689498484 -1 0.996311701666837 3664 174 3070 1113 1857 2335 1870 4014 1689 3587 3948 2389 M5408 RODWELL_AGING_KIDNEY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_DN.html Genes whose expression decreases with age in normal kidney. 15562319 171/233 John Newman 0.139491470498619 0.190404013803807 2365 2415.36363636364 2336 0.0135645923271998 1267 1.03779250524074 0.993814236102318 1 1.12160306636144 2365 2296 2565 1267 3813 2982 2336 1592 1611 2133 3609 2390 M2425 YANG_BCL3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BCL3_TARGETS_DN.html Genes down-regulated in neonatal cardiac myocytes upon knockdown of BCL3 [GeneID=602] by RNAi. 19451226 9/24 Arthur Liberzon 0.0585204387926497 0.0919382896299565 2340 2261.27272727273 2337 0.00601211843813046 734 2.30127850068741 2.59032428858297 1 3.57905979033658 2337 2661 4701 734 3455 2928 3342 1232 851 1451 1182 2391 M19336 ST_TYPE_I_INTERFERON_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_TYPE_I_INTERFERON_PATHWAY.html Type I Interferon (alpha/beta IFN) Pathway 11/14 Signaling Transduction KE 0.0117177623320716 0.0246909991997224 3375 1921.90909090909 2338 0.00107096759288875 246 0.938809624141446 -0.900000161093552 -1 2.26432926534341 3373 1049 2591 871 1452 2606 3358 578 246 2338 2679 2392 M15676 BECKER_TAMOXIFEN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BECKER_TAMOXIFEN_RESISTANCE_DN.html Genes down-regulated in a breast cancer cell line resistant to tamoxifen [PubChem=5376] compared to the parental line sensitive to the drug. 15657362 113/132 Jean Junior 0.02106202420372 0.0394495056514121 3630 2600.36363636364 2339 0.0019333099359648 674 1.48581968986097 -1.43685236997598 -1 3.1300226799595 3626 2339 949 2145 1175 4538 3454 4571 674 742 4391 2393 M8697 NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST_AND_SYNOVIAL_SARCOMA_UP.html Top 20 genes whose up-regulation correlated with gastrointestinal stromal tumors (GIST) and synovial sarcoma compared to other tumors. 11965276 44/52 John Newman 0.000113227478766416 0.000730100682756127 1185 2399.90909090909 2339 1.02939369699134e-05 487 1.23664821701501 1.27094032486331 1 5.82024964931091 1185 2478 487 3196 1949 3790 3060 2007 4139 1769 2339 2394 M11205 IVANOVA_HEMATOPOIESIS_MATURE_CELL http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_MATURE_CELL.html Genes in the expression cluster 'MBC Shared': up-regulated in mature blood cell populations from adult bone marrow and fetal liver. 12228721 368/466 John Newman 0.0659250002908318 0.101588639037782 3920 2506.18181818182 2340 0.00618068815972439 524 1.08672327999245 -1.05801504644308 -1 1.61938223145433 3917 524 2258 855 1634 3720 3934 2529 2340 2229 3628 2395 M836 OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_UP.html Genes up-regulated in pirmary cultures of epithelial ovarian cancer (EOC): invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 84/95 Leona Saunders 0.129337854980952 0.178972346968658 2175 2453.09090909091 2344 0.0125120892877856 941 1.03204602495023 -1.07340445970972 -1 1.15703418924074 2174 3257 3538 1645 3824 2344 2902 2311 941 2967 1081 2396 M7081 FARMER_BREAST_CANCER_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_8.html Cluster 8: selected ERBB2 [GeneID=2064] amplicon genes clustered together across breast cancer samples. 15897907 11/12 Leona Saunders 0.0410323343117499 0.0680986701657735 4150 2139.27272727273 2344 0.00380165727611944 84 1.00652296175387 -0.884319532687722 -1 1.7622141205186 4146 420 2155 830 1442 2410 2735 2630 84 2344 4336 2397 M1455 WANG_TARGETS_OF_MLL_CBP_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TARGETS_OF_MLL_CBP_FUSION_DN.html Top 50 genes down-regulated in granulocyte/macrophage progenitors (GMP) upon expression of MLL-CBP fusion [GeneID=4297;1387]. 15635450 55/65 Kevin Vogelsang 0.0262056838599617 0.0473005077701794 2315 2574 2344 0.00241119493680724 1244 0.811402040653669 -0.798264286855993 -1 1.61327824645254 2315 2884 3721 2344 1244 1621 2184 2413 3328 4160 2100 2398 M1395 MORI_PRE_BI_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PRE_BI_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Pre-BI stage. 18922927 112/185 Jessica Robertson 0.146719264010213 0.198998541990864 825 2242.36363636364 2345 0.0143207116844768 825 1.01090852513085 -1.00052598842046 -1 1.06346072501248 825 2345 2810 2216 3991 1422 1148 2453 1230 3707 2519 2399 M10570 BIOCARTA_RNA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RNA_PATHWAY.html Double Stranded RNA Induced Gene Expression 17/17 BioCarta 0.0102481339745322 0.0222703463903279 610 2544.90909090909 2346 0.00093601690329919 608 0.811942804246369 0.811942804246369 1 2.01291866483328 608 4574 3250 4447 916 1515 614 2346 4516 3520 1688 2400 M1920 CHEN_METABOLIC_SYNDROM_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_METABOLIC_SYNDROM_NETWORK.html Genes forming the macrophage-enriched metabolic network (MEMN) claimed to have a causal relationship with the metabolic syndrom traits. 18344982 1395/1952 Jessica Robertson 1.48104754495732e-19 1.51968356786925e-17 1805 2057.81818181818 2348 1.48104754495732e-20 22 1.20249843639366 1.25979251870075 1 30.3462852792998 1803 1109 4607 436 3170 2362 2500 1421 2348 22 2858 2401 M4625 AMIT_EGF_RESPONSE_20_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_20_MCF10A.html Genes whose expression peaked at 20 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 28/30 Leona Saunders 0.148052668663287 0.200461444661708 4465 2541.54545454545 2349 0.0144608386288742 1279 1.49349698091478 1.65846888063575 1 1.56405851410402 4464 2536 1279 2349 3601 1617 1775 1624 3672 1314 3726 2402 M75 TSENG_ADIPOGENIC_POTENTIAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_ADIPOGENIC_POTENTIAL_UP.html Genes showing increasing expression in brown preadipocytes with decreasing ability of the cells to differentiate. 15895078 47/52 John Newman 0.00706086653933448 0.0165845496961423 1180 2234.36363636364 2349 0.000643966421311544 810 1.09624915066359 1.13699832820168 1 2.9283816502478 1180 1954 810 2754 983 2654 3049 2540 4373 1932 2349 2403 M9884 BRUNEAU_HEART_GREAT_VESSELS_AND_VALVULOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/BRUNEAU_HEART_GREAT_VESSELS_AND_VALVULOGENESIS.html Genes for which mutations result in developmental defects in the great vessels formation and valvulogenesis, a major class of congenital heart disease. 18288184 11/14 Jessica Robertson 0.0209512800064715 0.0392888524555207 4670 2485.81818181818 2349 0.00192304608473647 779 1.04112899303746 -1.14673490950446 -1 2.19597573075858 4668 1061 2448 1552 1540 3549 3863 779 943 2349 4592 2404 M882 BIOCARTA_CXCR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CXCR4_PATHWAY.html CXCR4 Signaling Pathway 41/45 BioCarta 0.123430250594341 0.172262206624864 1800 2629.45454545455 2350 0.0119048426666907 1460 0.768184409022107 0.876062603327988 1 0.880319714265189 1796 3765 3629 3239 1941 2350 2177 3110 1460 3643 1814 2405 M1419 MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGG_VS_IGA_UP.html Up-regulated genes discriminating multiple myeloma samples by type of immunoglobulin they produce: IgG vs IgA. 12623842 41/51 Kate Stafford 0.0360529123335436 0.0611241904505481 975 2258.09090909091 2350 0.00333251427868646 975 1.19357968727883 1.2907983109362 1 2.17377466933694 975 1968 1011 2752 2350 2959 2106 2652 4335 2583 1148 2406 M2586 SMIRNOV_RESPONSE_TO_IR_2HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_2HR_DN.html Genes down-regulated in B lymphocytes at 2 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 70/81 Itai Pashtan 0.0229301422248618 0.0422609415467972 2350 2445.72727272727 2350 0.00210660772322526 1195 1.17436668493811 1.18502274586039 1 2.42121027722711 2350 3285 2040 4207 1195 1487 1948 2713 3749 2591 1338 2407 M19895 KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NICOTINATE_AND_NICOTINAMIDE_METABOLISM.html Nicotinate and nicotinamide metabolism 23/31 KEGG 0.0250437835603236 0.0455341519278611 3800 2445.36363636364 2351 0.00230304529491564 839 1.52362392652272 1.63813366746851 1 3.06724148723082 3799 3029 2046 2351 3886 1747 980 839 1101 2493 4628 2408 M17726 KEGG_DRUG_METABOLISM_OTHER_ENZYMES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DRUG_METABOLISM_OTHER_ENZYMES.html Drug metabolism - other enzymes 28/80 KEGG 0.000760740567079455 0.00321746906506723 2225 2310.27272727273 2351 6.91821592605816e-05 113 1.27285529038759 -1.15130510079784 -1 4.76040439043105 2222 3427 1598 3486 4135 1757 2528 113 2351 2869 927 2409 M1479 MA_MYELOID_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/MA_MYELOID_DIFFERENTIATION_UP.html Genes up-regulated during myeloid differentiation induced by tretinoin (ATRA) [PubChem=444795] and IL3 [GeneID=3652] in the EML cell line (myeloid progenitor). 12130493 53/86 Kevin Vogelsang 0.000290139820004764 0.00154916283984444 1445 2399.45454545455 2352 2.6379826474035e-05 217 0.892553840472511 0.99569050803193 1 3.76318297567909 1441 2891 3340 3366 217 1930 1492 2348 3195 3822 2352 2410 M2312 AZARE_STAT3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/AZARE_STAT3_TARGETS.html Genes up-regulated in RPWE-1 cells by activated STAT3 [GeneID=6774]. 17438134 40/48 Arthur Liberzon 0.109687528931325 0.155753651190088 1510 2539.36363636364 2353 0.0105064887105147 1471 1.32746843888127 1.47573512178742 1 1.60847082354627 1508 3790 1775 3818 2353 2953 2365 1471 3502 2146 2252 2411 M17019 REACTOME_NEF_MEDIATED_DOWNREGULATION_OF_MHC_CLASS_I_COMPLEX_CELL_SURFACE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEF_MEDIATED_DOWNREGULATION_OF_MHC_CLASS_I_COMPLEX_CELL_SURFACE_EXPRESSION.html Genes involved in Nef mediated downregulation of MHC class I complex cell surface expression 30/45 Reactome 0.105116148468885 0.150439120913626 1365 2842.36363636364 2354 0.0100456874066794 1315 0.678002615370927 -0.63786534674702 -1 0.83681154841247 1361 4161 3531 4267 1852 1315 1832 2354 4598 4224 1771 2412 M12763 RAMALHO_STEMNESS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMALHO_STEMNESS_DN.html Genes depleted in embryonic, neural and hematopoietic stem cells. 12228720 103/149 John Newman 0.000628362216424843 0.00274872072430515 1660 2281.81818181818 2354 5.71401600481378e-05 586 1.22066649449242 1.29392556088342 1 4.69047106975241 1658 2354 586 2105 2928 3052 2881 1685 3917 975 2959 2413 M630 REACTOME_GLUTAMATE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUTAMATE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Glutamate Neurotransmitter Release Cycle 18/28 Reactome 0.0623493324437852 0.0969330860127359 3000 2418.63636363636 2355 0.00583543658382513 1130 0.924304060247234 0.817645611490469 1 1.40559339072331 2996 1551 2469 2355 4480 1737 1130 1219 2778 3609 2281 2414 M12123 REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EFFECTS_OF_PIP2_HYDROLYSIS.html Genes involved in Effects of PIP2 hydrolysis 20/25 Reactome 0.24338451255709 0.305038475642449 4055 2172.27272727273 2356 0.0250358269909591 959 1.19118631161389 -1.37946358167177 -1 0.921558187947432 4054 986 1462 959 2356 3267 2995 2892 979 1349 2596 2415 M1904 SCHRAETS_MLL_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAETS_MLL_TARGETS_DN.html Genes down-regulated in fibroblasts from MLL [GeneID=4297] knockout mice. 12789274 34/47 Arthur Liberzon 0.000270266184977427 0.00146744372235182 1125 2484.09090909091 2356 2.45726720382719e-05 542 1.61799509491985 1.73524296992346 1 6.87901292468256 1121 3809 542 3753 4701 3330 2356 806 4011 904 1992 2416 M6924 BIOCARTA_EIF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF2_PATHWAY.html Regulation of eIF2 15/16 BioCarta 0.104769168827602 0.150033518466712 1415 2440.27272727273 2357 0.0100107988294108 1367 0.650420313944516 0.653173824930757 1 0.803908640163187 1413 2623 3767 2678 1850 1902 1367 3007 1375 4504 2357 2417 M2341 REACTOME_APOPTOTIC_EXECUTION_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOTIC_EXECUTION_PHASE.html Genes involved in Apoptotic execution phase 67/78 Reactome 0.330106665343441 0.395759070465085 2600 2517.63636363636 2357 0.0357662413785407 1354 1.09761407752873 -1.23286218893492 -1 0.662922277161824 2599 1354 2255 1623 3500 2357 3853 2963 3550 1897 1743 2418 M1570 MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP.html Genes up-regulated in non-apoptotic tissues (fetal liver) after MDM4 [GeneID=4194] knockout. 15608685 286/354 Arthur Liberzon 0.15830656791092 0.211853416654251 3535 2694.27272727273 2358 0.0155451280887394 1179 1.08635774230753 1.10185142586775 1 1.09852482314581 3531 1179 1282 1184 2358 3956 4189 3894 2094 1423 4547 2419 M4359 SWEET_KRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_KRAS_TARGETS_DN.html Genes upregulated in control vs KRAS [GeneID=3845] knockdown in a human cell line. 15608639 95/144 Aravind Subramanian 0.134675385158362 0.184840889196706 2375 2305.18181818182 2358 0.0130639672042033 314 1.42259759673893 1.22732798168176 1 1.56501363078468 2374 2358 1327 1588 2006 4246 3256 3174 314 1360 3354 2420 M17902 BIOCARTA_CASPASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CASPASE_PATHWAY.html Caspase Cascade in Apoptosis 25/39 BioCarta 0.0011788400361959 0.00448988569632661 4010 2159.36363636364 2359 0.000107224743257931 90 1.09594177588266 -1.10632714532712 -1 3.86075246334826 4009 326 2359 372 424 3628 3303 4534 90 2203 2505 2421 M1149 MOTAMED_RESPONSE_TO_ANDROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOTAMED_RESPONSE_TO_ANDROGEN_DN.html Genes down-regulated in ovarian epithelial cells in response to dihydrotestosterone (DHT) [PubChem=10635]. 16832351 6/6 Arthur Liberzon 0.00525070999993344 0.0138068808911899 2360 2246.45454545455 2359 0.000526315789473684 111 1.31453202587609 -1.32679710901948 -1 3.66852158176115 2359 449 4351 111 4033 3551 4212 3088 178 1549 830 2422 M19979 CASORELLI_APL_SECONDARY_VS_DE_NOVO_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_APL_SECONDARY_VS_DE_NOVO_DN.html Genes down-regulated in secondary APL (acute promyelocytic leukemia) compared to the de novo tumors. 16990782 13/15 Leona Saunders 0.0112735074712656 0.023925789237578 2360 2434.18181818182 2360 0.00103015403775395 594 1.46924434595458 -2.54058966338042 -1 3.57389523819334 2360 4604 3005 3774 956 2141 929 2119 594 3846 2448 2423 M1579 BURTON_ADIPOGENESIS_8 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_8.html Progressively down-regulated 8-96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 145/182 John Newman 0.359486162623401 0.427722381543346 975 2450.54545454545 2360 0.0396894870263932 974 1.00424776742792 1.04632637489526 1 0.555693951051498 974 2312 1872 3237 2595 2308 2360 3032 3682 2585 1999 2424 M2577 NUTT_GBM_VS_AO_GLIOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUTT_GBM_VS_AO_GLIOMA_DN.html Top 50 marker genes for anaplastic oligodendroglioma (AO), a class of high grade glioma. 12670911 65/82 Arthur Liberzon 0.193639384864218 0.251438210882836 2530 2122.09090909091 2360 0.0193756697463148 1105 1.00221672167398 -0.94790929570175 -1 0.901553379326406 2528 1370 2814 1599 3063 1105 1446 2622 1269 2360 3167 2425 M1816 KYNG_DNA_DAMAGE_BY_4NQO_OR_UV http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_4NQO_OR_UV.html 4NQO treatment and UV irradiation responding genes. 15897889 87/98 Jessica Robertson 0.366693850692457 0.435201150432083 1655 2451.90909090909 2361 0.0406769439784493 1655 1.13921164713095 1.08033074838831 1 0.617521018065741 1655 1851 2459 2615 4105 2074 1738 2937 2825 2351 2361 2426 M2970 WILLIAMS_ESR1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR1_TARGETS_UP.html The 'ER-alpha profile': genes up-regulated in T47D cells (breast cancer, ESR2 [GeneID=2100] Tet-Off) upon activation of ESR1 [GeneID=2099] by estradiol (E2) [PubChem=5757]. 17700529 31/50 Jessica Robertson 0.334835497157784 0.400919215267565 2365 2248.45454545455 2362 0.036387018080237 649 1.29595173638544 1.27889911401617 1 0.771790410360478 2362 2000 1510 1548 3767 2909 3046 2491 649 1863 2588 2427 M10861 LI_PROSTATE_CANCER_EPIGENETIC http://www.broadinstitute.org/gsea/msigdb/cards/LI_PROSTATE_CANCER_EPIGENETIC.html Genes affected by epigenetic aberrations in prostate cancer. 15657340 35/46 Jessica Robertson 0.0164677046639731 0.0324941630478106 4625 2545 2362 0.00150838892189589 877 1.27539653160734 -1.26313362821533 -1 2.84793871516407 4623 877 1192 964 1079 4699 4508 3427 2362 1223 3041 2428 M17787 REACTOME_GLUCURONIDATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCURONIDATION.html Genes involved in Glucuronidation 6/23 Reactome 0.00389211766940026 0.0109415100652586 1475 2387.18181818182 2363 0.000389895138155535 158 0.837531767784681 0.679742238932269 1 2.46425092772614 1472 2683 4257 2841 2363 1393 158 1235 4564 3226 2067 2429 M9546 BIOCARTA_TID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TID_PATHWAY.html Chaperones modulate interferon Signaling Pathway 30/35 BioCarta 0.0267044296223948 0.0480171077400776 520 1988.09090909091 2364 0.00245765416508157 485 0.899148801720144 0.969539825404809 1 1.778942590504 520 3416 2372 2428 1280 538 485 2364 4590 3039 837 2430 M912 MUELLER_METHYLATED_IN_GLIOBLASTOMA http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_METHYLATED_IN_GLIOBLASTOMA.html Genes up-regulated in short-term cultured glioblastomas after azacitidine [PubChem=9444] treatment. 16909125 46/104 Leona Saunders 0.00692148327651273 0.0163183821504196 4455 2436.72727272727 2366 0.000631214141196713 809 1.30534947710554 -1.44275601910556 -1 3.50072905565693 4454 1949 809 3299 3650 3500 2692 1446 1564 1075 2366 2431 M12498 UEDA_PERIFERAL_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/UEDA_PERIFERAL_CLOCK.html Molecular timetable composed of 162 time-indicating genes (182 probes) in the peripheral (liver) clock. 15273285 232/267 Kate Stafford 0.247167751323696 0.308877888866255 2370 2573.63636363636 2366 0.0254800219200653 1652 1.00302473289396 0.978908771383131 1 0.767794978331492 2054 2752 1652 2366 2366 2382 2116 3782 3495 2101 3244 2432 M2117 THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP http://www.broadinstitute.org/gsea/msigdb/cards/THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP.html Genes up-regulated in polymorphonuclear neutrophilic granulocytes (PMNs) attracted to skin wounds. 15187151 95/117 Kevin Vogelsang 0.00985969089277395 0.0216096841865588 145 1815.09090909091 2366 0.000900378009412923 143 1.0368629361946 1.10578684963742 1 2.59090419030221 143 2366 2441 2913 4335 160 431 1072 2609 2668 828 2433 M15847 MORI_MATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_MATURE_B_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the mature B 18922927 92/109 Jessica Robertson 0.0607806655418584 0.0948692927769747 1095 2504.18181818182 2367 0.00568435023394385 987 1.03342216593593 -1.01680684404139 -1 1.58603543596085 1091 2367 3423 3583 4471 987 1461 1209 3280 3980 1694 2434 M91 PID_TCPTP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCPTP_PATHWAY.html Signaling events mediated by TCPTP 18832364 64/71 Pathway Interaction Database 0.281242179618488 0.345064488640308 1165 2517.36363636364 2368 0.0295748285141409 1161 1.01744008712933 1.05335610063932 1 0.705376875583101 1161 2420 2368 3636 4546 1580 1568 2043 3240 2293 2836 2435 M8604 HALMOS_CEBPA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HALMOS_CEBPA_TARGETS_DN.html Genes down-regulated in H358 cells (lung cancer) by inducible expression of CEBPA [GeneID=1050] off plasmid vector. 15205324 55/78 Kevin Vogelsang 0.00036328608319563 0.00182610256941787 4365 2351.18181818182 2368 3.30314624102214e-05 140 1.30872812595157 -1.38142148138404 -1 5.37763661013258 4365 140 729 691 2368 4648 4276 4622 244 350 3430 2436 M3903 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_QTL http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_QTL.html Genes changed in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of reciprocal congenic strains D.B. Chr3 (DB), B.D. Chr3 (BD) and the parental strains B6 and D2. 17220891 23/33 Arthur Liberzon 0.00105575500447795 0.0041422806493233 4335 2502.09090909091 2368 9.60238172688585e-05 404 1.34960687195474 -1.39761660594266 -1 4.82525148145815 4331 1511 1636 2368 404 3608 3722 4343 852 1625 3123 2437 M766 KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCINE_SERINE_AND_THREONINE_METABOLISM.html Glycine, serine and threonine metabolism 26/34 KEGG 0.102061997211941 0.146556929370357 2570 2230.90909090909 2369 0.00973901581543134 796 1.1636760478709 -1.37466932014201 -1 1.45614653765513 2568 2552 2101 2515 2884 2369 2689 1440 796 2278 2348 2438 M3395 MARTORIATI_MDM4_TARGETS_FETAL_LIVER_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_FETAL_LIVER_DN.html Genes down-regulated in non-apoptotic tissues (fetal liver) after MDM4 [GeneID=4194] knockout. 15608685 684/902 Arthur Liberzon 0.162985897442898 0.216885659974762 1210 2649.36363636364 2370 0.0176341028158437 1210 1.05084867258046 1.04495959299265 1 1.04653834488943 1210 3965 4396 2491 2167 2370 2078 2299 2005 2923 3239 2439 M1151 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_DN.html Apoptotic genes dependent on SMAD4 [GeneID=4089] and down-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 14/15 Arthur Liberzon 0.106566781728453 0.152330469339278 2375 2345.90909090909 2374 0.0101916809470822 779 1.12896768068692 1.20620798508759 1 1.38428496174849 1036 3904 2769 3762 2953 779 1195 1987 2374 2675 2371 2440 M2262 KIM_GLIS2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GLIS2_TARGETS_DN.html Partial list of genes down-regulated in the kidney of GLIS2 [GeneID=84662] knockout mice compared to the wild type. 18227149 7/9 Arthur Liberzon 0.000399147310215626 0.00195433122844165 2375 1974 2375 3.99219021703336e-05 8 1.30548986636413 -1.30548986636413 -1 5.30659508670368 2375 3124 4675 2385 3067 1300 1266 76 72 3366 8 2441 M12144 BROWNE_HCMV_INFECTION_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_48HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 48 h time point that were not down-regulated at the previous time point, 24 h. 11711622 630/965 John Newman 2.39442060509202e-06 2.95082643760688e-05 1960 2034.63636363636 2376 2.39442318505845e-07 191 1.19040585434679 1.25989862136443 1 8.09160706960958 1958 484 4494 693 2376 1926 2513 2535 2774 191 2437 2442 M1794 WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WILSON_PROTEASES_AT_TUMOR_BONE_INTERFACE_DN.html Protease genes down-regulated at tumor-bone interface compared to the tumor alone area. 18632634 4/7 Jessica Robertson 0.0435026151735313 0.0716692298844914 3705 2283.18181818182 2377 0.0044378459519314 54 1.02890624841347 0.807195913926853 1 1.76713963376435 3703 453 4557 356 2377 3936 4595 2661 54 1859 564 2443 M15383 CONRAD_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/CONRAD_STEM_CELL.html Supplementary Table 2. Genelist comparing microarray expression profiles of spermatogonial cells, haGSCs and hES (H1) cells. Examples of expression rates of different hES cell enriched and germ cell specific genes, surface markers for germ cell selection and signal transduction in all three cell types (spermatogonial cells = SC). 18849962 40/84 Jessica Robertson 0.00189916832382284 0.00642585984834681 3105 2149.81818181818 2377 0.000172800889167404 44 0.974750251142428 -1.13751200448919 -1 3.20608476177583 3104 1441 2377 2662 751 3698 4437 1090 1181 2863 44 2444 M4448 BOYAULT_LIVER_CANCER_SUBCLASS_G23_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G23_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G23, defined by unsupervised clustering. 17187432 61/68 Yujin Hoshida 0.470238720997395 0.54016226894809 2210 2504.72727272727 2377 0.0561208714333566 1305 1.09454647831544 -1.32292433761622 -1 0.439193398799954 2209 2432 2991 1772 4365 1670 2324 2775 1305 3332 2377 2445 M979 REACTOME_N_GLYCAN_ANTENNAE_ELONGATION_IN_THE_MEDIAL_TRANS_GOLGI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_N_GLYCAN_ANTENNAE_ELONGATION_IN_THE_MEDIAL_TRANS_GOLGI.html Genes involved in N-glycan antennae elongation in the medial/trans-Golgi 17/19 Reactome 0.0167185394118374 0.0328250857004461 2380 2037.09090909091 2379 0.00153154159605355 539 1.37771406152427 1.15345279118936 1 3.06732337875331 2379 2589 907 658 1239 3909 2885 2857 539 1069 3377 2446 M5755 KAPOSI_LIVER_CANCER_MET_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAPOSI_LIVER_CANCER_MET_UP.html Selected up-regulated MET [GeneID=4233] target genes from a classifier of hepatocellular carcinoma (HCC) cases; associated with poor survival. 16710476 37/40 Yujin Hoshida 0.0292792073203667 0.0516048762330586 2380 2397.54545454545 2379 0.00269784500296895 899 1.10407818335808 1.15567094315765 1 2.13256844348256 1476 3786 2379 2727 4018 2379 2644 899 1500 2316 2249 2447 M14098 BROWNE_HCMV_INFECTION_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_24HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 24 h time point that were not down-regulated at the previous time point, 20 h. 11711622 223/276 John Newman 3.22884362929279e-07 5.25522135526275e-06 2380 2293.54545454545 2380 2.93531282106921e-08 239 1.24508507056078 1.34128051764603 1 9.86328271321831 2380 1738 239 2381 933 4469 3641 2025 3310 363 3750 2448 M520 REACTOME_TRIF_MEDIATED_TLR3_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRIF_MEDIATED_TLR3_SIGNALING.html Genes involved in TRIF mediated TLR3 signaling 85/102 Reactome 0.0184410316338786 0.0355127169775222 675 2474.63636363636 2381 0.00169067712225608 393 0.838489572676955 1.01686933174214 1 1.82375828582475 673 4057 3777 4669 2968 914 393 1548 2381 4255 1586 2449 M1603 ZHOU_TNF_SIGNALING_30MIN http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_TNF_SIGNALING_30MIN.html Genes up-regulated in HeLa cells (cervical carcinoma) at 30 min after stimulation with TNF [GeneID=7124]. 12673210 82/102 John Newman 0.0487707705608771 0.0789972673463761 3125 2636.09090909091 2381 0.00453515815907629 1512 1.11268494840515 -1.04416672082817 -1 1.84044778214665 3121 2381 2094 2439 1512 3670 3795 1601 2009 2368 4007 2450 M18193 REACTOME_ACTIVATION_OF_KAINATE_RECEPTORS_UPON_GLUTAMATE_BINDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_KAINATE_RECEPTORS_UPON_GLUTAMATE_BINDING.html Genes involved in Activation of Kainate Receptors upon glutamate binding 27/38 Reactome 0.028603075449499 0.0507161968901711 2665 2213.36363636364 2383 0.00263471530837988 687 1.14272387319879 -1.06521305276435 -1 2.22015340025099 2661 3010 1744 2557 1291 1602 3765 2383 2710 1937 687 2451 M3578 KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION.html Progesterone-mediated oocyte maturation 80/92 KEGG 0.207908652191864 0.267537851239258 1690 2529.90909090909 2384 0.0209660507804931 1379 0.760619319785033 -0.729883983959068 -1 0.653433464017238 1689 2384 3717 2233 3181 1682 2938 2154 2706 3766 1379 2452 M19888 KEGG_ACUTE_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ACUTE_MYELOID_LEUKEMIA.html Acute myeloid leukemia 64/71 KEGG 0.0228370015261433 0.0421551220975347 2620 2448.45454545455 2384 0.00209796030387517 1192 0.811178345271239 -0.717026080180017 -1 1.67371172927325 2618 1364 3555 1674 1192 2384 2251 3379 1831 3180 3505 2453 M10431 GRUETZMANN_PANCREATIC_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRUETZMANN_PANCREATIC_CANCER_DN.html Genes down-regulated in pancreatic ductal adenocarcinoma (PDAC) identified in a meta analysis across four independent studies. 15897887 241/350 Leona Saunders 0.0554148730602935 0.0879482854218511 2385 2572.36363636364 2384 0.00516927190927054 1555 1.09251331063893 0.972618289394068 1 1.73066250862076 2384 2747 1968 1619 1555 2985 2566 4338 1777 2190 4167 2454 M151 PID_AR_TF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_TF_PATHWAY.html Regulation of Androgen receptor activity 18832364 70/92 Pathway Interaction Database 0.387313955589647 0.456004457566259 2385 2712.09090909091 2385 0.0435594094645069 1594 0.774111245672922 -0.743269402193562 -1 0.396025264441505 2385 2858 3858 1919 3365 2015 1952 2250 1594 4124 3513 2455 M4710 ZHU_CMV_8_HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_8_HR_UP.html Up-regulated at 8 h following infection of primary human foreskin fibroblasts with CMV 9826724 82/121 John Newman 0.0310074235761798 0.0540055495496564 2770 2155.27272727273 2386 0.00285938851992411 1059 1.15887604020773 -1.18538318080149 -1 2.20407829521338 2768 2386 1194 1624 1330 2442 3824 2647 2718 1059 1716 2456 M16476 KEGG_CELL_ADHESION_MOLECULES_CAMS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CELL_ADHESION_MOLECULES_CAMS.html Cell adhesion molecules (CAMs) 108/183 KEGG 4.22046961028465e-07 6.64020552018118e-06 2595 2314.27272727273 2387 3.83679129085251e-08 250 1.55068493260991 -1.47799485059441 -1 12.0478175389034 2591 3664 250 2565 2387 2050 2984 1833 3947 1133 2053 2457 M1017 REACTOME_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPLICATION.html Genes involved in DNA Replication 206/224 Reactome 0.165330597015636 0.219448936421204 515 2449 2387 0.016294829838252 515 0.768074764517342 -0.76846056744634 -1 0.759014975777107 515 3190 4145 3001 2908 1188 1278 2387 1643 4413 2271 2458 M19993 HUTTMANN_B_CLL_POOR_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUTTMANN_B_CLL_POOR_SURVIVAL_UP.html Up-regulated genes in B-CLL (B-cell chronic leukemia) patients expressing high levels of ZAP70 and CD38 [GeneID=7535;952], which are associated with poor survival. 16932341 364/551 Leona Saunders 0.00402262029775185 0.01122078039025 3650 2357.27272727273 2387 0.000366363126975754 508 1.14648472590544 -1.10473528328851 -1 3.35448500994312 3649 1699 764 2031 653 4443 3559 3159 2387 508 3078 2459 M453 MURAKAMI_UV_RESPONSE_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_6HR_UP.html Genes up-regulated in primary keratinocytes at 6 h after UVB irradiation. 11532376 60/71 John Newman 0.00330659072314196 0.00979941394983266 2390 2391.18181818182 2387 0.000301051908879606 605 1.29005298155614 -1.50117700297234 -1 3.88842935249259 2387 2423 1292 2611 605 4189 4225 2370 3901 1559 741 2460 M494 REACTOME_PTM_GAMMA_CARBOXYLATION_HYPUSINE_FORMATION_AND_ARYLSULFATASE_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PTM_GAMMA_CARBOXYLATION_HYPUSINE_FORMATION_AND_ARYLSULFATASE_ACTIVATION.html Genes involved in PTM: gamma carboxylation, hypusine formation and arylsulfatase activation 22/27 Reactome 7.2623487126334e-05 0.00051391733018935 3615 2132.54545454545 2389 6.6023531443213e-06 40 1.46537843107936 1.3298803868671 1 7.2320798975814 3612 353 1749 757 112 3332 3997 4397 40 2389 2720 2461 M10179 REACTOME_FORMATION_OF_THE_TERNARY_COMPLEX_AND_SUBSEQUENTLY_THE_43S_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_THE_TERNARY_COMPLEX_AND_SUBSEQUENTLY_THE_43S_COMPLEX.html Genes involved in Formation of the ternary complex, and subsequently, the 43S complex 55/99 Reactome 0.0160575065908684 0.0319397900688596 325 2689.72727272727 2389 0.00147053817892554 321 0.576251773122861 0.523428146081404 1 1.29316436588208 321 4479 4127 4688 1862 522 358 2389 4671 4519 1651 2462 M241 PID_RAC1_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAC1_REG_PATHWAY.html Regulation of RAC1 activity 18832364 48/51 Pathway Interaction Database 0.00577426225782821 0.0142024584976285 4330 2015.90909090909 2392 0.000526315789473684 67 1.24227929818975 -1.225782943545 -1 3.44400868424291 4328 173 1218 67 2431 2872 2392 3438 446 793 4017 2463 M5624 KIM_MYCL1_AMPLIFICATION_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCL1_AMPLIFICATION_TARGETS_DN.html Genes negatively correlated with amplifications of MYCL1 [GeneID=4610] in SCLC (small cell lung cancer) cell lines. 16116477 32/37 Arthur Liberzon 0.0331601466113593 0.0569977756757523 2620 1993.27272727273 2392 0.00306097917073858 270 0.777492719865464 -0.839068949222805 -1 1.4513643696248 2616 270 3291 362 3273 2392 3287 1527 599 3877 432 2464 M11363 NIELSEN_GIST http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_GIST.html A cluster of genes specifically up-regulated in gastrointestinal stromal tumors (GIST). 11965276 139/182 Arthur Liberzon 0.0140542760393866 0.0286797159126264 4465 2697.18181818182 2392 0.00128589730531993 886 1.27282844279737 -1.26946131821896 -1 2.9457791056873 4462 1254 886 962 2392 4658 4018 4583 2225 1042 3187 2465 M2590 SMIRNOV_RESPONSE_TO_IR_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_RESPONSE_TO_IR_6HR_DN.html Genes down-regulated in B lymphocytes at 6 h after exprosure to 10 Gy dose of ionizing radiation. 21844125 130/177 Itai Pashtan 0.0231341891283366 0.0425705156669586 2505 2334 2393 0.00212555457613533 700 1.19056962555863 1.22300813580157 1 2.44895493405752 2502 1268 954 2823 4584 2070 3367 2393 2333 700 2680 2466 M5539 KEGG_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AXON_GUIDANCE.html Axon guidance 133/153 KEGG 0.270677826568697 0.333925598903358 2125 2620.90909090909 2394 0.0282867406418717 1733 1.1739677835698 1.29791718967513 1 0.839014840103944 2125 2321 1733 2394 4114 3773 2799 2006 2397 2154 3014 2467 M16021 KORKOLA_TERATOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_TERATOMA_UP.html Genes from the 12p region that up-regulated in teratoma cells compared to normal testis. 16424014 19/25 Arthur Liberzon 0.00190519979257423 0.00644164972847448 1675 2132.09090909091 2395 0.00017335015441207 80 0.935668316506825 -0.883715477724284 -1 3.07603832456217 1675 3050 2395 3567 1197 263 80 2672 4201 3687 666 2468 M5415 BIOCARTA_IL4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL4_PATHWAY.html IL 4 signaling pathway 17/20 BioCarta 0.000806335757446639 0.00337104054486106 2810 2058.36363636364 2396 7.33301313038391e-05 365 0.869401975750543 -0.931861177497192 -1 3.22506231677221 2810 381 2596 1098 365 3174 2396 1728 541 3521 4032 2469 M10575 DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_XPCS_DN.html Genes exclusively down-regulated in fibroblasts expressing the XP/CS mutant form of ERCC3 [GeneID=2071] after high dose UVC irradiation. 15608684 131/142 Arthur Liberzon 0.19388531417715 0.251579575735805 1165 2268.36363636364 2396 0.0194028623743493 1164 1.03401093578239 0.971934399580717 1 0.929778779374242 1164 1797 2702 2396 3414 2061 1301 2429 1615 2921 3152 2470 M1520 ZHOU_TNF_SIGNALING_4HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_TNF_SIGNALING_4HR.html Genes up-regulated in HeLa cells (cervical carcinoma) at 4 h after stimulation with TNF [GeneID=7124]. 12673210 78/93 John Newman 0.448426729858185 0.516867927943988 2190 2762.54545454545 2396 0.0526523483973793 989 1.13659699103524 1.19921227022791 1 0.488721448527128 2187 2396 1941 1863 4636 4039 3751 3648 989 1492 3446 2471 M2050 VISALA_AGING_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_AGING_LYMPHOCYTE_UP.html Genes up-regulated in peripheral lymphocytes from old individuals compared to those from young donors. 12618007 12/14 Arthur Liberzon 0.00175042412884177 0.006052748635995 1930 2486.09090909091 2396 0.000159256218406001 487 0.869630598881546 0.926905797592373 1 2.89422010665266 1927 3554 2504 4206 487 2258 1050 2396 4447 2458 2060 2472 M321 KEGG_CHRONIC_MYELOID_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CHRONIC_MYELOID_LEUKEMIA.html Chronic myeloid leukemia 83/90 KEGG 0.100425666439237 0.144647282756546 3705 2718 2398 0.00957509947158575 1134 0.846717964548748 -0.77992777172779 -1 1.06673448727594 3704 1849 3279 1134 1833 3226 2099 4077 1938 2398 4361 2473 M14127 HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/HELLER_HDAC_TARGETS_SILENCED_BY_METHYLATION_UP.html Genes up-regulated in multiple myeloma (MM) cell lines treated with both decitabine [PubChem=451668] TSA [PubChem=5562]. 18172295 587/881 Jessica Robertson 5.66387629000896e-13 2.52485781198663e-11 2680 2324.81818181818 2398 5.66387629001041e-14 52 1.25356654850279 1.17294589469521 1 19.9343052059916 2679 1678 4530 1176 872 2398 3016 3299 1909 52 3964 2474 M1613 MILI_PSEUDOPODIA_CHEMOTAXIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_CHEMOTAXIS_DN.html Transcripts depleted in pseudopodia of NIH/3T3 cells (fibroblast) in response to the chemotactic migration stimulus by lysophosphatidic acid (LPA) [PubChem=3988]. 18451862 650/764 Jessica Robertson 0.0570267072619387 0.0901426852901375 2350 2512.09090909091 2398 0.00585452690758933 1131 1.01506435665601 1.1273336987726 1 1.59166508081299 2347 1131 4616 1885 1609 3219 3241 2398 2548 2660 1979 2475 M7897 BIOCARTA_GLEEVEC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLEEVEC_PATHWAY.html Inhibition of Cellular Proliferation by Gleevec 41/42 BioCarta 0.127861429726702 0.177137055565023 2905 2437.90909090909 2399 0.012359976269144 866 0.706243750647196 -0.712579624156148 -1 0.796485425104147 2902 1965 3745 1147 2321 2447 4303 2399 866 3644 1078 2476 M12890 ROZANOV_MMP14_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_TARGETS_UP.html Genes up-regulated in HT1080 cells (fibrosarcoma) over-expressing MMP14 [GeneID=4323] compared to those with knockdown of the gene by RNAi. 18519667 375/525 Jessica Robertson 5.89852453914924e-10 1.66712789369967e-08 2400 2306.90909090909 2399 5.36229503702793e-11 133 1.24027014389514 1.35587547170523 1 14.4752007975343 2399 2231 133 2534 1332 4343 3830 1400 3430 266 3478 2477 M2333 KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION.html Pathogenic Escherichia coli infection 82/116 KEGG 0.386101414861433 0.454690288958574 1545 2674.45454545455 2400 0.043387486734952 1544 1.08006854324589 1.06941586217025 1 0.554622228982915 1544 3689 2400 2492 4153 2817 2347 2247 3043 2367 2320 2478 M2267 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_UP http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_2FC_UP.html Genes up-regulated more than two-fold in lymphoblastoid cell lines from European population compared to those from Asian population. 17206142 19/37 Leona Saunders 0.00181540269850209 0.00622725344253624 900 1874.18181818182 2400 0.000165172951903277 194 1.02541591973118 -1.11897469072521 -1 3.39371560600365 900 3057 2837 3325 3520 194 233 203 2400 3690 257 2479 M1475 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN.html Genes down-regulated in kidney biopsies from patients with acute transplant rejection compared to the biopsies from patients with well functioning kidneys more than 1-year post transplant. 15307835 736/974 Jean Junior 0.100487135889041 0.144691666075739 4505 2646.72727272727 2400 0.0105343137705603 410 1.11115905049472 -1.08960012642748 -1 1.39970051056246 4502 479 4480 410 1880 2400 4371 4035 1696 1976 2885 2480 M3672 TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_LOBULAR_CARCINOMA_VS_DUCTAL_NORMAL_DN.html Genes down-regulated in lobular carcinoma vs normal ductal breast cells. 17389037 112/150 Arthur Liberzon 3.45439122432316e-06 4.0159425070949e-05 2475 2441.36363636364 2403 3.14036058940327e-07 268 1.62993705198574 1.56085763656473 1 10.7519452471401 2475 2337 329 1720 4198 3449 2403 4105 2257 268 3314 2481 M12617 KEGG_TYPE_I_DIABETES_MELLITUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYPE_I_DIABETES_MELLITUS.html Type I diabetes mellitus 33/78 KEGG 0.0886575771086082 0.130484491410237 1645 2588.63636363636 2404 0.00840417457965403 1641 1.21653123939462 -1.09358580675115 -1 1.61437908703307 1641 3817 1890 2687 1766 1921 3474 3258 3761 2404 1856 2482 M1589 ZHENG_RESPONSE_TO_ARSENITE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_RESPONSE_TO_ARSENITE_UP.html Up-regulated in HEK293 cells (kidney epithelium) by treatment with sodium arsenite [PubChem=26435]. 12679051 19/33 John Newman 0.000485207583400641 0.00225633477206998 3355 2056.09090909091 2404 4.41195116776161e-05 304 1.28745568033639 1.07606501074696 1 5.11272971837233 3351 2596 1427 2404 304 3440 3490 457 740 1275 3133 2483 M661 REACTOME_SIGNALING_BY_FGFR1_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR1_MUTANTS.html Genes involved in Signaling by FGFR1 mutants 33/51 Reactome 0.289726076452136 0.354001315261217 3875 2431.18181818182 2405 0.0306217728547409 265 0.912208073809615 -1.00998024927583 -1 0.617210219923071 3873 265 2274 882 3407 4308 2872 2051 849 2405 3557 2484 M7678 CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_DN.html Marker genes down-regulated in the 'chromosome 7 polysomy' subclass of hepatocellular carcinoma (HCC); characterized by polysomy of chromosome 7 and by a lack of gains of chromosome 8q. 18701503 31/39 Yujin Hoshida 0.00575296649245653 0.0142024584976285 4595 2067 2406 0.000524369610832527 130 1.26797215494858 1.29744192921754 1 3.51523996125553 4594 253 779 228 2509 2775 4655 3656 130 752 2406 2485 M88 PID_CD8_TCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD8_TCR_PATHWAY.html TCR signaling in naïve CD8+ T cells 18832364 74/109 Pathway Interaction Database 0.365611720438912 0.434025986034121 2580 2657.63636363636 2407 0.0405280418320813 894 0.88500860104768 0.819189085694072 1 0.481263553123442 2578 1342 2407 894 3534 2358 2134 2203 4258 3573 3953 2486 M2492 TURJANSKI_MAPK11_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK11_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK11 [GeneID=5600] phosphorylation. 17496919 5/5 Arthur Liberzon 0.000132310624012991 0.000824975092921158 1650 2451.18181818182 2407 1.32318502418736e-05 15 0.822977124300981 0.822977124300981 1 3.80776192941119 1648 4292 4359 2407 3332 852 15 769 4626 4643 20 2487 M1293 YANG_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BREAST_CANCER_ESR1_DN.html Genes down-regulated in early primary breast tumors expressing ESR1 [GeneID=2099] vs the ESR1 negative ones. 16261164 46/54 Leona Saunders 0.0356416271954217 0.0605867571150884 2695 2282 2407 0.00329386305804169 1035 1.25604282224156 1.20944554808998 1 2.2947681689349 2695 2907 1531 2363 1387 2558 2407 2625 1035 1870 3724 2488 M8834 WHITESIDE_CISPLATIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WHITESIDE_CISPLATIN_RESISTANCE_DN.html Genes down-regulated in NCI-H2170 cells (lung cancer) upon induction of resistance to cisplatin [PubChem=2767]. 14737109 41/64 John Newman 0.00069534165203689 0.00300275626497175 1670 2535.09090909091 2407 6.32328656424155e-05 106 1.1629721721872 1.18800748148078 1 4.40178075747019 1666 4151 2242 4328 3240 2407 1349 106 4300 2584 1513 2489 M10911 KEGG_CYSTEINE_AND_METHIONINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYSTEINE_AND_METHIONINE_METABOLISM.html Cysteine and methionine metabolism 27/39 KEGG 0.00197729509972245 0.00662843243656959 3025 2323.45454545455 2408 0.00017991586123443 509 1.3554423416313 -1.79134098479736 -1 4.43085791181613 3025 4177 2939 4019 509 2408 1940 826 650 2810 2255 2490 M10679 REACTOME_INHIBITION_OF_INSULIN_SECRETION_BY_ADRENALINE_NORADRENALINE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_INSULIN_SECRETION_BY_ADRENALINE_NORADRENALINE.html Genes involved in Inhibition of Insulin Secretion by Adrenaline/Noradrenaline 27/36 Reactome 0.31233133452415 0.376264394832565 4705 2801.36363636364 2408 0.0334678733801692 934 1.12058590849681 -1.08434951535485 -1 0.713686202449513 4702 934 1594 1982 3590 4378 2408 4654 3308 1580 1685 2491 M5126 PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_DN.html Down-regulated genes in head and neck cancer compared to cervical carcinoma samples. 17510386 38/83 Arthur Liberzon 0.010221146679927 0.022232171580302 1125 2336.54545454545 2408 0.000933540460758751 846 1.40644836417807 1.12519508418525 1 3.48843020698759 1123 2491 846 3276 2408 2039 2299 2827 4330 1127 2936 2492 M16647 REACTOME_CELL_CYCLE_CHECKPOINTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE_CHECKPOINTS.html Genes involved in Cell Cycle Checkpoints 125/137 Reactome 0.0853633478484902 0.126424537761178 375 2500.63636363636 2409 0.00807886135003043 372 0.640274615731837 -0.632288025886222 -1 0.86280510807973 372 2795 4126 3251 2409 1002 1063 2013 3965 4430 2081 2493 M1495 PETROVA_PROX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_PROX1_TARGETS_UP.html Genes specific to LEC (lymphatic endothelium cells) induced in BEC (blood endothelium cells) by expression of PROX1 [GeneID=5629] off adenovirus vector. 12198161 33/37 Kevin Vogelsang 0.289830789428746 0.35403761027528 3640 2752.63636363636 2409 0.0306347657014621 1451 1.24749694694082 -0.964667950687391 -1 0.844025985866402 3637 1992 1987 1999 4354 3309 3400 2052 1451 2409 3689 2494 M2609 ZWANG_EGF_PERSISTENTLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_PERSISTENTLY_UP.html Genes persistently induced by EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 32/40 Yaara Zwang 0.0145766671765306 0.029566767973023 2030 2256.72727272727 2409 0.00133401401323393 628 0.906940988133222 0.921691053118631 1 2.0809514476315 2028 913 3415 3337 2965 2916 1680 628 981 3552 2409 2495 M1854 RIZ_ERYTHROID_DIFFERENTIATION_6HR http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_6HR.html Selected genes down-regulated in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts) at 6 h time point. 17213805 32/53 Leona Saunders 0.0696098187536547 0.106501894495057 2410 2213.36363636364 2410 0.00653773821175787 733 1.30785421178029 -0.979260881369562 -1 1.9086679512185 2410 2977 1553 2833 2712 3338 1819 1886 2786 1300 733 2496 M10184 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP.html Genes up-regulated in monocytes by RUNX1-RUNX1T1 [GeneID=861;862] fusion. 17898786 286/354 Arthur Liberzon 0.0712481246466672 0.108376135459964 1610 2544.36363636364 2411 0.00669689912568077 1137 1.12759823692866 1.15132970293256 1 1.63277076912004 1608 3987 1137 3436 3095 2411 2201 2098 3247 1907 2861 2497 M3456 FERNANDEZ_BOUND_BY_MYC http://www.broadinstitute.org/gsea/msigdb/cards/FERNANDEZ_BOUND_BY_MYC.html Genes identified by ChIP within the high-affinity group of MYC [GeneID=4609] targets. 12695333 251/334 Yujin Hoshida 0.195852857350538 0.253614673990272 1580 2695.63636363636 2411 0.0196206873529816 1577 1.09395227170854 1.1326718975752 1 0.977940344845957 1577 4335 2257 4324 2223 3059 2061 2493 3169 1743 2411 2498 M1753 ZHENG_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_UP.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are up-regulated both in developing (located in the thymus) and mature (from peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 33/39 Jessica Robertson 0.0116852704443351 0.0246445382025297 2345 2155.09090909091 2411 0.0010679820080659 893 1.26775752856881 1.34499409763807 1 3.05931686014127 2345 893 1439 1701 971 2726 2458 2441 2776 2411 3545 2499 M13714 LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_METASTASIS_AND_ALTERNATIVE_SPLICING_DN.html Down-regulated genes displaying alternative splicing in MDA-MB-435 cells (breast cancer) whose metastatic potential has been reduced by expression of NME1 [GeneID=4830]. 18245461 69/87 Jessica Robertson 0.0605302546933342 0.094572261553306 2505 2102.54545454545 2412 0.00566025311732889 87 1.40506269725387 -1.2596597760228 -1 2.15931678187194 2503 117 1108 522 2412 4200 2869 4117 87 1755 3438 2500 M2837 BARIS_THYROID_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARIS_THYROID_CANCER_UP.html Genes up-regulated in oncocytic follicular carcinoma (FTC) vs mitochondrial-rich papillary carcinoma (PTC) types of thyroid cancer. 15806164 29/39 Arthur Liberzon 3.14152403656157e-05 0.000265259274643481 2415 2248.27272727273 2414 2.85597172485174e-06 65 0.723752999103885 -0.735509927678123 -1 3.88380902543325 3788 289 3337 835 65 3294 4174 2412 342 3781 2414 2501 M4377 KEGG_GALACTOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GALACTOSE_METABOLISM.html Galactose metabolism 29/39 KEGG 0.0656469155268552 0.101325520368462 3165 2493.36363636364 2415 0.00615379440560576 177 1.07807710832005 1.29073351297351 1 1.60831927245598 3163 2013 2415 1021 3914 4364 4501 1242 177 2524 2093 2502 M7429 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_DN.html Genes down-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 40/64 Arthur Liberzon 0.126061173050694 0.175342501834413 2415 2420.72727272727 2415 0.0121748160047276 1022 1.3618116586241 1.21310896412036 1 1.54495452014772 2415 3776 1779 2878 3023 2378 2074 1538 1022 2516 3229 2503 M2242 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A.html Category A genes: p53-dependent genes whose expression in the absence of S389 phosphorylation is similar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 992/1481 Arthur Liberzon 8.14467619872139e-10 2.18890068241138e-08 2210 2103.90909090909 2415 8.14467620170649e-11 83 1.20453239374623 1.23670022568942 1 13.8443613247341 2208 467 4672 231 2871 2341 2840 2460 2555 83 2415 2504 M5880 NABA_ECM_AFFILIATED http://www.broadinstitute.org/gsea/msigdb/cards/NABA_ECM_AFFILIATED.html Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins 22159717 89/185 Alexandra Naba 9.8884409194874e-09 2.1912413680742e-07 3700 2264.45454545455 2415 8.98949178539404e-10 174 1.44398439773487 -1.4907462398349 -1 14.42880425961 3698 699 174 441 4313 1785 3874 4664 2415 330 2516 2505 M16966 BIOCARTA_STATHMIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STATHMIN_PATHWAY.html Stathmin and breast cancer resistance to antimicrotubule agents 17/22 BioCarta 0.203833441969918 0.26293901232523 2935 2636.45454545455 2416 0.0205092084763552 1555 1.07911196603031 -1.00782465282811 -1 0.939281830089429 2933 1555 2169 1880 2917 4299 3969 1815 2345 2416 2703 2506 M3432 LEE_LIVER_CANCER_MYC_TGFA_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_MYC_TGFA_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) tissue of MYC and TGFA [GeneID=4609;7039] double transgenic mice. 15565109 81/124 Yujin Hoshida 0.0126420428307591 0.0262453776840711 2685 2529.18181818182 2416 0.00115593442834302 623 1.24616904455533 1.20362997435122 1 2.95610991657599 2682 1858 944 1497 3933 3209 2416 4118 1996 623 4545 2507 M2126 CHICAS_RB1_TARGETS_LOW_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_LOW_SERUM.html Genes up-regulated in IMR90 cells (fibroblast) grown under low serum conditions and after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 100/154 Arthur Liberzon 0.193513681536333 0.251413315951415 2040 2694.90909090909 2416 0.0193617735264974 1296 0.980066862603627 -0.971757233448278 -1 0.881689167280304 2037 3667 3232 4025 2213 1296 1949 2128 2927 3754 2416 2508 M2298 VANDESLUIS_COMMD1_TARGETS_GROUP_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_2_UP.html Genes up-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout compared to normal 8.5 dpc and 9.5 dpc embryos. 17371845 22/26 Arthur Liberzon 8.36031757964235e-05 0.000574391542589692 4600 2716.63636363636 2416 7.6005775460749e-06 119 1.06925670468822 0.886745719044764 1 5.19955413786261 3930 2072 2416 1093 119 4598 4596 3113 2173 2394 3379 2509 M2404 BIOCARTA_PPARA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PPARA_PATHWAY.html Mechanism of Gene Regulation by Peroxisome Proliferators via PPARa(alpha) 74/86 BioCarta 0.292700303520315 0.356804089002036 2005 2649.36363636364 2417 0.0309914962001967 1962 0.966668986487337 0.951567347702298 1 0.649097495629911 2005 3278 2532 2991 3594 1962 1983 2058 4074 2249 2417 2510 M9814 RODRIGUES_THYROID_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_DN.html Genes down-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to anaplastic thyroid carcinoma (ATC). 17406368 132/154 Arthur Liberzon 0.165715715818585 0.21983647517249 1440 2456.27272727273 2417 0.0163361007059138 1115 1.32859209735611 1.35396772131846 1 1.31147036011678 1437 2794 1849 2417 4388 3308 2283 2461 1726 1115 3241 2511 M8323 KRASNOSELSKAYA_ILF3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRASNOSELSKAYA_ILF3_TARGETS_UP.html Up-regulated in GHOST(3)CXCR4 cells (osteosarcoma) upon ectopic expression of ILF3 [GeneID=3609]. 12036489 82/150 John Newman 0.0151725476678428 0.0304742234009439 1495 2386.72727272727 2418 0.001388928041047 895 1.27854601477548 -1.15200524130575 -1 2.90844506248558 1494 2840 895 3632 2153 2418 3422 3224 3229 901 2046 2512 M11458 WONG_PROTEASOME_GENE_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_PROTEASOME_GENE_MODULE.html Genes that comprise the proteasome gene module 18199530 61/72 Jessica Robertson 0.140227796323216 0.191238138874771 825 2622.09090909091 2418 0.0136413567162531 822 0.696279469475128 -0.703731340095074 -1 0.750491703818221 822 2418 3988 3121 3820 1378 1609 1594 3942 4287 1864 2513 M2642 KEGG_TGF_BETA_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TGF_BETA_SIGNALING_PATHWAY.html TGF-beta signaling pathway 74/94 KEGG 0.0376562909063186 0.0633645964626823 2195 2348.45454545455 2422 0.00348333779598304 1120 1.06773743521448 1.15662892888341 1 1.91952924311889 2195 1871 2422 2893 1405 3547 3109 2750 1249 1120 3272 2514 M6382 KEGG_REGULATION_OF_AUTOPHAGY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_REGULATION_OF_AUTOPHAGY.html Regulation of autophagy 23/60 KEGG 0.00492285268239131 0.0131722588780538 2910 2374.90909090909 2424 0.000448536635231393 538 0.71130578368833 -0.509751376081316 -1 2.00683456387017 2907 963 3553 1643 707 2271 3231 3756 538 4131 2424 2515 M918 REACTOME_N_GLYCAN_TRIMMING_IN_THE_ER_AND_CALNEXIN_CALRETICULIN_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_N_GLYCAN_TRIMMING_IN_THE_ER_AND_CALNEXIN_CALRETICULIN_CYCLE.html Genes involved in N-glycan trimming in the ER and Calnexin/Calreticulin cycle 14/16 Reactome 5.57682473691473e-06 6.15014316781251e-05 1900 2491.45454545455 2424 5.0698535216103e-07 18 0.521390616919612 -0.532706191059251 -1 3.29448964916809 1896 2625 3650 2872 18 2424 2330 2320 2443 4584 2244 2516 M1784 KAN_RESPONSE_TO_ARSENIC_TRIOXIDE http://www.broadinstitute.org/gsea/msigdb/cards/KAN_RESPONSE_TO_ARSENIC_TRIOXIDE.html Genes changed in U373-MG cells (malignant glioma) upon treatment with arsenic trioxide [PubChem=14888], a chemical that can cause autophagic cell death. 15592527 141/179 Arthur Liberzon 4.13206191025056e-07 6.52285358407446e-06 2405 1950.72727272727 2425 3.75642062394431e-08 249 1.339884832444 1.26072802312805 1 10.425592190515 2404 2785 249 1787 728 2463 2575 2425 2466 351 3225 2517 M19682 TRACEY_RESISTANCE_TO_IFNA2_DN http://www.broadinstitute.org/gsea/msigdb/cards/TRACEY_RESISTANCE_TO_IFNA2_DN.html Genes down-regulated in huT78R cells (cutaneous T-cell lymphoma, CTCL) resistant to IFNA2 [GeneID=3440] compared to the IFN2A sensitive parental cell line. 12414529 41/45 Arthur Liberzon 0.0872578587574393 0.128705341667223 3330 2447.90909090909 2425 0.0082658185565338 852 0.870878615782288 0.814362074032022 1 1.16344740852318 3326 852 2425 1344 1759 2675 1633 2310 4162 2949 3492 2518 M759 REACTOME_PKA_MEDIATED_PHOSPHORYLATION_OF_CREB http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PKA_MEDIATED_PHOSPHORYLATION_OF_CREB.html Genes involved in PKA-mediated phosphorylation of CREB 14/16 Reactome 0.016642083231441 0.0327430733023767 4525 2527 2426 0.00152448393068759 1085 1.05841886343521 0.883724316137879 1 2.35814991721882 4522 1576 1893 1815 1085 4550 2664 2426 2566 1582 3118 2519 M19523 HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_DN.html Genes down-regulated during differentiation from large pre-BII to small pre-BII lymphocyte. 11779835 105/133 Arthur Liberzon 3.58362409157134e-05 0.000295195562167831 3410 2372.81818181818 2426 3.25789315206694e-06 424 1.24519894749194 -1.23518686025759 -1 6.59530338849027 3406 668 424 825 1938 4662 3477 3584 2426 578 4113 2520 M3501 ST_B_CELL_ANTIGEN_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/ST_B_CELL_ANTIGEN_RECEPTOR.html B Cell Antigen Receptor 58/69 Signaling Transduction KE 0.00326109740132485 0.00969904205056919 1355 1987.27272727273 2427 0.000296903766998525 602 0.821861679286524 0.794795883504739 1 2.48270031591362 1353 772 2935 1139 602 2608 1026 2751 2496 3751 2427 2521 M2311 AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_DN http://www.broadinstitute.org/gsea/msigdb/cards/AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_DN.html Genes down-regulated in RWPE-1 cells (prostate cancer) upon expression of constitutively active form of STAT3 [GeneID=6774]. 17438134 17/19 Arthur Liberzon 0.0234565276573967 0.0430796928182539 620 2256 2428 0.00215549277527784 454 1.16245189782032 0.93789322889014 1 2.38210844541592 617 3071 1270 4350 2553 742 454 3739 4343 2428 1249 2522 M2429 SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A12.html Cluster 12 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts good survival outcome. 18641660 317/534 Arthur Liberzon 0.001794645152641 0.00617850118195881 3285 2667.27272727273 2429 0.00016328280041697 670 1.16446675360824 1.17924062722363 1 3.8598967376365 3284 2243 670 1711 3297 4572 3802 1841 2429 1289 4202 2523 M1963 MIKKELSEN_MEF_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MEF cells (embryonic fibroblasts). 18509334 169/379 Jessica Robertson 5.92164690019047e-12 2.23601386951192e-10 1425 2124.09090909091 2429 5.38331536382401e-13 98 1.42786843405043 1.44516354794251 1 20.6765816701384 1423 3204 98 3927 2429 1651 1625 2809 3269 279 2651 2524 M9575 WAKASUGI_HAVE_ZNF143_BINDING_SITES http://www.broadinstitute.org/gsea/msigdb/cards/WAKASUGI_HAVE_ZNF143_BINDING_SITES.html DNA repair genes whose promoters contain putative ZNF143 [GeneID=7702] binding sites. 17297437 65/67 Leona Saunders 0.0651455745621117 0.100617510449335 1520 2831.45454545455 2430 0.00610532778161199 1189 0.725854498631838 -0.707560408970106 -1 1.08614147381545 1519 4083 3865 4446 1629 1189 1573 2430 4292 4312 1808 2525 M18724 XU_AKT1_TARGETS_6HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_AKT1_TARGETS_6HR.html Genes up-regulated in DU-145 cells (prostate cancer) expressing a dominant negative form of AKT1 [GeneID=207] upon sham-treatment for 6 h (as a control for the HGF [GeneID=3082] experiments). 17099727 35/54 Arthur Liberzon 0.0321292201476135 0.055630931436807 3185 2361.27272727273 2430 0.00296438772774431 441 1.0501082536418 0.919416930628557 1 1.97690990499983 3183 1456 2787 1287 1345 2430 3132 3554 441 1809 4550 2526 M163 PID_LIS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LIS1_PATHWAY.html Lissencephaly gene (LIS1) in neuronal migration and development 18832364 47/57 Pathway Interaction Database 0.00110265859370257 0.00428710754717969 3345 2506.54545454545 2431 0.00010029196760169 414 1.09460307631164 -0.915208522585249 -1 3.88900234098268 3342 2911 3043 3611 414 2306 2286 1871 2431 3588 1769 2527 M19146 LY_AGING_MIDDLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_MIDDLE_UP.html Genes up-regulated in fibroblasts from middle-age individuals, compared to those from the young donors. 10741968 17/21 John Newman 0.00250039847526612 0.00790391091608911 1155 2417 2432 0.000227567710916659 705 2.32403245848093 1.61739062328664 1 7.33065996925952 1152 3537 705 3643 1238 2432 1890 3039 4479 1460 3012 2528 M903 REACTOME_REGULATION_OF_SIGNALING_BY_CBL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_SIGNALING_BY_CBL.html Genes involved in Regulation of signaling by CBL 23/26 Reactome 0.01511413217618 0.0304086546767134 1615 2227.45454545455 2433 0.00138354336137234 381 0.940975446166479 0.829109424364513 1 2.14183012135039 1612 2570 2696 3200 1052 1215 381 3523 2433 3448 2372 2529 M6510 PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_UP.html Genes up-regulated in post-GC, BCL6 [GeneID=604] dependent B cell non-Hodgkin's lymphoma (B-NHL) vs MYC [GeneID=4609] driven pre-GC lymphoma. 18066064 361/414 Jessica Robertson 0.00577426225782821 0.0142024584976285 3110 2394 2433 0.000526315789473684 63 0.989756955504647 -0.902853937751654 -1 2.74391180079696 3109 522 1928 63 1229 3497 2812 3904 2298 2433 4539 2530 M1967 MIKKELSEN_IPS_WITH_HCP_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_WITH_HCP_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV8.1 (induced pluripotent cells, iPS). 18509334 80/196 Jessica Robertson 3.81606729491264e-13 1.80118376319877e-11 3840 2284.45454545455 2433 3.46915208628483e-14 77 1.54660365808546 -1.82224458579982 -1 24.9346262587531 3836 727 77 2496 631 4618 3839 2388 3769 315 2433 2531 M2053 ZEMBUTSU_SENSITIVITY_TO_VINBLASTINE http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_VINBLASTINE.html Top genes associated with chemosensitivity to vinblastine [PubChem=13342] across 85 tumor xenografts. 11809704 27/47 Arthur Liberzon 0.00577426225782821 0.0142024584976285 3475 2242.09090909091 2433 0.000526315789473684 162 1.00015099736128 1.1509134330161 1 2.77272840463826 3474 312 2433 162 2181 3169 3115 3231 1070 3281 2235 2532 M1001 BIOCARTA_RHO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RHO_PATHWAY.html Rho cell motility signaling pathway 48/53 BioCarta 0.04357290007999 0.0717269306412464 2435 1902.09090909091 2434 0.0040418739554916 188 0.909425917453011 0.843368799958874 1 1.56144372737611 2434 188 3341 402 1715 2670 2752 1054 1182 2655 2530 2533 M275 PID_ALPHA_SYNUCLEIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALPHA_SYNUCLEIN_PATHWAY.html Alpha-synuclein signaling 18832364 41/48 Pathway Interaction Database 0.166430788373123 0.220723046114398 3835 2543.27272727273 2434 0.0164127766890195 853 0.716699209251932 -0.613139404549904 -1 0.705534514095751 3832 853 3008 1613 2767 1020 2188 2368 3812 4081 2434 2534 M19695 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP.html Genes up-regulated in kidney biopsies from patients with acute transplant rejection compared to the biopsies from patients with well functioning kidneys more than 1-year post transplant. 15307835 117/208 Jean Junior 0.00286135035624392 0.00872110577128104 4550 2566.63636363636 2435 0.000260461696225585 592 1.22546371866236 -1.18085953023075 -1 3.78683896171766 4550 1280 716 592 1741 4023 4700 2435 3821 834 3541 2535 M885 GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_CHRONIC_LYMPHOCYTIC_LEUKEMIA_UP.html Genes exclusively up-regulated in B lymphocytes from CLL (chronic lymphocytic leukemia) patients but with a similiar expression pattern in the normal cells and in the cells from WM (Waldenstroem's macroblobulinemia) patients. 17252022 10/17 Arthur Liberzon 0.205914582537798 0.265333559808465 2115 2360.27272727273 2435 0.0207422437800655 515 0.977739502844913 1.03052204906681 1 0.845258885037564 2114 3929 2673 2012 2637 2435 2274 3096 515 2909 1369 2536 M8293 NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_8P12_P11_AMPLICON.html Genes within amplicon 8p12-p11 identified in a copy number alterations study of 191 breast tumor samples. 19010930 59/85 Jessica Robertson 0.305666968766275 0.369636274265296 2440 2420.09090909091 2437 0.0326200651591661 607 0.949009409555114 0.829144030209042 1 0.615386477305477 2437 775 3380 2329 2486 1573 1821 3802 607 3774 3637 2537 M2419 WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_8D.html Genes with promoters bound by PPARG [GeneID=5468] at 8 day time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 872/1046 Arthur Liberzon 0.219443315574054 0.279409886568529 4460 2735.18181818182 2437 0.0244704152398129 473 1.02324476029125 -0.962724685708226 -1 0.850134171506364 4456 473 4699 794 2345 1989 4703 4067 1407 2437 2717 2538 M3582 ALONSO_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_UP.html Up-regulated genes in melanoma tumous that developed metastatic disease compared to primary melanoma that did not. 17409456 260/333 Jessica Robertson 0.00577426225782821 0.0142024584976285 2600 2057.81818181818 2438 0.000526315789473684 170 1.04762172773672 -0.913698507987363 -1 2.90433699830711 2600 552 2541 170 2676 1029 2150 3479 1727 3274 2438 2539 M193 PID_NEPHRIN_NEPH1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NEPHRIN_NEPH1_PATHWAY.html Nephrin/Neph1 signaling in the kidney podocyte 18832364 39/46 Pathway Interaction Database 0.165430954495171 0.219520411924994 2305 2326.36363636364 2439 0.0163055828781532 868 0.82145481242729 0.783301373590201 1 0.811598410515079 2305 868 3128 2718 3577 2439 1293 3963 877 3198 1224 2540 M834 CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_POLYSOMY7_UP.html Marker genes up-regulated in the 'chromosome 7 polysomy' subclass of hepatocellular carcinoma (HCC); characterized by polysomy of chromosome 7 and by a lack of gains of chromosome 8q. 18701503 90/144 Yujin Hoshida 0.00892655608164123 0.0200348762269837 1275 2394.90909090909 2440 0.000814816627551727 511 1.11099240846936 1.15649110401173 1 2.83092857410147 1272 3679 1948 4185 4015 2440 1621 511 2833 2463 1377 2541 M12816 DOANE_RESPONSE_TO_ANDROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOANE_RESPONSE_TO_ANDROGEN_DN.html Genes down-regulated in MDA-MB-453 cells (class A ER(-) [GeneID=2099] breast cancer) after exposure to the androgen R1881 [PubChem=13766]. 16491124 396/480 Arthur Liberzon 0.415376358277077 0.486012992332128 2575 2602.90909090909 2442 0.0476272883111446 1436 1.07291240524828 1.10017142976017 1 0.504368085572702 2574 2229 2253 2442 3315 2366 2729 3687 1981 1436 3620 2542 M2539 KUMAR_AUTOPHAGY_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/KUMAR_AUTOPHAGY_NETWORK.html Genes defining the Mycobacterium tuberculosis strain-independent regulatory axis of the host macrophage cells. 20211141 86/126 Arthur Liberzon 0.423094706162904 0.494186343253874 4490 2667.18181818182 2442 0.0487772480398528 515 1.16537395390634 -1.23680963335832 -1 0.535177336079898 4487 715 1588 515 3966 3740 3917 3678 2249 2042 2442 2543 M1338 FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_HEPATOCYTE_PROLIFERATION_UP.html Genes commonly up-regulated in both non-tumorous and tumorous liver tissues of PARK2 [GeneID=5071] knockout mice. 18574468 20/31 Jessica Robertson 0.393620837705156 0.46296794267838 2620 3037.09090909091 2444 0.0444586641667687 1676 1.50238782726874 1.28604244926421 1 0.753863832007485 2619 4559 1676 4607 4684 2178 2192 2261 3975 2213 2444 2544 M5497 NIKOLSKY_BREAST_CANCER_1Q21_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_1Q21_AMPLICON.html Genes within amplicon 1q21 identified in a copy number alterations study of 191 breast tumor samples. 19010930 39/50 Jessica Robertson 0.117254204169667 0.164812341775113 3120 2269.09090909091 2444 0.0112739677164071 214 0.994589516604182 -0.909789397509717 -1 1.16845989690238 3119 214 1762 455 4432 1094 3515 4404 2491 2444 1030 2545 M14532 ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_PHOSPHOINOSITIDE_3_KINASE_PATHWAY.html PI3K Pathway 46/55 Signaling Transduction KE 0.00639005787144209 0.0154197715507191 1630 2149 2445 0.000582608552685073 428 0.855128939199046 0.828397419569554 1 2.32484046523014 1627 830 3249 1916 2445 3501 2532 428 1753 2858 2500 2546 M19529 RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_DN.html Genes down-regulated in anaplastic thyroid carcinoma (ATC) compared to normal thyroid tissue. 17406368 645/761 Arthur Liberzon 0.00525070999993344 0.0138068808911899 2970 2284.09090909091 2445 0.000526315789473684 78 1.09085921760985 1.08682048639265 1 3.04429016023286 2966 1129 4323 78 1816 2445 3193 3000 1406 1216 3553 2547 M2246 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_D.html Category D genes: p53-independent genes whose expression in the absence of S389 phosphorylation is similar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 324/496 Arthur Liberzon 0.00377483501666019 0.0107139033545617 2920 2300 2446 0.000343757055359679 658 1.2390369442489 -1.28078348029639 -1 3.66261497071755 2918 2244 741 1250 1217 3824 2940 2446 2611 658 4451 2548 M2618 ZWANG_TRANSIENTLY_UP_BY_1ST_EGF_PULSE_ONLY http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_TRANSIENTLY_UP_BY_1ST_EGF_PULSE_ONLY.html Genes transiently induced only by the first pulse of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 1886/2790 Yaara Zwang 0.000520230169917615 0.00238165509409422 2575 2465.36363636364 2447 5.20351997802634e-05 381 1.14162436949368 1.11850115086872 1 4.49338009275083 2308 1658 4719 2242 2573 2710 2447 2571 1966 381 3544 2549 M7068 BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_SURVIVAL_OPTIMAL_DEBULKING.html Genes whose expression in optimally debulked ovarian tumors is associated with survival prognosis. 18593951 335/433 Jessica Robertson 0.141033968565677 0.192226489064394 3325 2751 2448 0.0137254713930925 1088 1.06019961232308 1.16037035765566 1 1.13924045886288 3322 1707 1714 1088 2035 4559 3436 3135 2448 2251 4566 2550 M4319 BIOCARTA_IL12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL12_PATHWAY.html IL12 and Stat4 Dependent Signaling Pathway in Th1 Development 16/29 BioCarta 0.00336565850105248 0.0098854437616476 3770 2729.09090909091 2449 0.00030643804464395 615 0.719946596010127 -0.707982350322161 -1 2.16588841331445 3770 1017 3075 1633 615 4654 4465 2359 2044 3939 2449 2551 M16093 GENTILE_UV_RESPONSE_CLUSTER_D7 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D7.html Cluster d7: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 52/70 John Newman 0.00121016700794093 0.00456593787168759 2490 2072.09090909091 2449 0.000110075745887379 429 0.902670151001437 0.958062853273094 1 3.1700015228881 2486 2449 3460 2080 429 2586 2527 1341 661 2857 1917 2552 M141 PID_PI3KCI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PI3KCI_PATHWAY.html Class I PI3K signaling events 18832364 54/68 Pathway Interaction Database 0.0615888498273227 0.0959268337625045 1960 2165.45454545455 2451 0.00576216193192542 166 0.916714236898206 0.816746705934376 1 1.400284529673 1959 166 3135 901 3918 2451 776 1977 2558 2663 3316 2553 M17507 MILI_PSEUDOPODIA http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA.html Transcripts significantly enriched in pseudopodia of NIH/3T3 cells (fibroblast) in response to both chemotactic (lysophosphatidic acid, LPA [PubChem=3988]) and haptotactic (fibronectin, FN1 [GeneID=2335) migratory stimuli. 18451862 52/56 Jessica Robertson 0.00419032041909519 0.0115798081839164 2800 2325.45454545455 2451 0.000381665730250794 662 0.908974092088704 0.859909485728764 1 2.64087745701197 2798 2451 3388 2134 662 2833 1809 1530 1617 3786 2572 2554 M5622 DAZARD_UV_RESPONSE_CLUSTER_G2 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G2.html Cluster G2: genes increasingly up-regulated in NHEK cells (normal keratinocyte) and reaching maximum levels at 12 h and 24 h after UV-B irradiation. 12771951 45/79 John Newman 0.000510999698154075 0.00234850883669643 2025 2172.63636363636 2452 4.64653116352767e-05 375 1.38904690554016 -1.54830398901647 -1 5.47993295286727 2452 2919 628 3208 539 2609 3909 3215 2023 375 2022 2555 M750 REACTOME_ADENYLATE_CYCLASE_INHIBITORY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADENYLATE_CYCLASE_INHIBITORY_PATHWAY.html Genes involved in Adenylate cyclase inhibitory pathway 12/14 Reactome 0.00253607023326732 0.00797485109994788 2960 2194.90909090909 2453 0.00023081803985139 302 0.929459351086635 0.998428666395115 1 2.92630379323941 2959 2631 2194 2874 562 3080 302 916 4172 2453 2001 2556 M4872 TARTE_PLASMA_CELL_VS_PLASMABLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_PLASMABLAST_UP.html Genes up-regulated in mature plasma cells compared with plasmablastic B lymphocytes. 12663452 493/952 Kate Stafford 1.3249112581797e-17 9.92631926763203e-16 1905 1916.54545454545 2453 1.20446478016336e-18 47 1.35446197018494 1.28187066348896 1 30.492382277103 1901 2219 47 2578 2511 2530 2453 1632 2629 90 2492 2557 M7057 LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_DN.html Genes higher expressed in the best 25 mesothelioma survivors compared to the 25 worst ones. 16540645 5/8 Arthur Liberzon 0.0319119903633136 0.0553563375651746 1705 2407.45454545455 2454 0.00323797409739392 248 3.737017547879 3.737017547879 1 7.04754534189974 1704 3954 4305 3507 4351 2454 1304 1130 248 3082 443 2558 M14767 AMUNDSON_GAMMA_RADIATION_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_GAMMA_RADIATION_RESPONSE.html Genes down-regulated across the entire panel of NCI-60 cell lines in response to gamma radiation. 18199535 53/62 Jessica Robertson 0.0365423667518847 0.0617301454239838 845 2648.90909090909 2454 0.00337853113214872 577 0.923185998180653 -1.0098614694843 -1 1.67536881507183 844 2454 3677 4263 4294 1111 577 3404 2198 3974 2342 2559 M19248 REACTOME_CELL_JUNCTION_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_JUNCTION_ORGANIZATION.html Genes involved in Cell junction organization 76/101 Reactome 0.188023752328019 0.245225783638643 2195 2772.09090909091 2455 0.0187567868495198 1336 1.21883027962469 1.23009581414344 1 1.11630403628684 2193 2406 1336 2375 4256 2233 2455 4302 3135 3153 2649 2560 M12210 YOKOE_CANCER_TESTIS_ANTIGENS http://www.broadinstitute.org/gsea/msigdb/cards/YOKOE_CANCER_TESTIS_ANTIGENS.html Genes up-regulated in both colorectal cancer cells and normal testis relative to normal colon epithelium. 18281482 48/74 Jessica Robertson 0.0147623029957117 0.0298617253421183 4605 2618.63636363636 2455 0.00135111825006847 1041 1.16108504302924 -1.10768575014537 -1 2.65659689402595 4602 2455 1372 1264 1041 3316 4641 3397 1535 1433 3749 2561 M1350 SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP.html Genes up-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 48 h. 18794802 601/800 Jessica Robertson 1.65304113595504e-20 1.90301321017264e-18 4500 2521.45454545455 2456 1.65304113595505e-21 17 1.33427849500649 -1.32719790422135 -1 35.4784303459535 4497 1132 4442 210 1997 3089 4127 4711 1058 17 2456 2562 M15262 YAGI_AML_RELAPSE_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_RELAPSE_PROGNOSIS.html Genes associated with clinical prognosis of pediatric AML (acute myeloid leukemia): good prognosis=no relapse > 3 years; poor prognosis=relapse < 1 year or no response to therapy. 12738660 49/57 Kate Stafford 0.118425751918081 0.16626101994448 4670 2672.45454545455 2456 0.0113933307238588 1243 0.88789496751757 -0.792065028185833 -1 1.03803835510566 4670 2456 3574 1578 1921 3853 3012 2096 1312 3682 1243 2563 M1397 TOMIDA_LUNG_CANCER_POOR_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/TOMIDA_LUNG_CANCER_POOR_SURVIVAL.html Metastatic signature genes that best distinguished between favorable and unfavorable prognosis for the non-small cell lung cancer (NSCLC) patients. 17260014 2/5 Arthur Liberzon 0.000246891944003659 0.00137764531438843 3250 2366.4 2456.5 2.74354488453096e-05 221 0.663634223683726 -0.663634223683726 -1 2.84873103408871 3248 2694 4462 NA 221 1492 895 2269 1073 4666 2644 2564 M10382 IIZUKA_LIVER_CANCER_EARLY_RECURRENCE http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_EARLY_RECURRENCE.html Genes down-regulated in hepatocellular carcinoma (HCC) tumors with higher risk of early intrahepatic recurrence. The single up-regulated gene (GenBank Accession=AC000063) has been excluded from the signature. 12648972 20/27 Yujin Hoshida 0.0777978430479818 0.116721493701994 1560 2737.90909090909 2458 0.00733576282093796 863 1.19589800262967 1.19962852343131 1 1.67386303399383 1560 4583 2458 4481 3278 1987 863 1654 4603 2714 1936 2565 M19522 REACTOME_ADENYLATE_CYCLASE_ACTIVATING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADENYLATE_CYCLASE_ACTIVATING_PATHWAY.html Genes involved in Adenylate cyclase activating pathway 9/11 Reactome 0.0128565316280693 0.0266386432328741 2460 2235 2459 0.001293152365542 339 0.997670949554049 0.998428666395115 1 2.35694236250707 2459 2667 4228 2590 2157 2513 339 805 3896 2033 898 2566 M14279 DOUGLAS_BMI1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DOUGLAS_BMI1_TARGETS_DN.html Genes down-regulated in A4573 cells (Ewing's sarcoma, ESFT) after knockdown of BMI1 [GeneID=648] by RNAi. 18701473 411/491 Jessica Robertson 0.0276867591138678 0.0495193266454929 4510 2564.81818181818 2459 0.00254922357433915 374 0.969941681041405 -0.926260252258597 -1 1.89954116342605 4507 517 3115 374 1275 2459 4480 3775 2332 3206 2173 2567 M2521 RAO_BOUND_BY_SALL4 http://www.broadinstitute.org/gsea/msigdb/cards/RAO_BOUND_BY_SALL4.html Loci bound by both isoforms (a and b) of SALL4 [GeneID=57167] in ES cells (embryonic stem). 20837710 315/435 Arthur Liberzon 0.0401404211857031 0.0668628764470594 1725 2844.90909090909 2460 0.00371746191038634 1432 1.07499346041657 1.03474060408398 1 1.89492854974012 1725 4325 2227 4637 1432 3803 2421 1633 3284 2460 3347 2568 M76 PID_P38_ALPHA_BETA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_ALPHA_BETA_PATHWAY.html Regulation of p38-alpha and p38-beta 18832364 35/37 Pathway Interaction Database 0.489227971953791 0.558847054119529 2220 2557.09090909091 2461 0.0592479109166776 1982 0.992351656735374 1.13440260640181 1 0.376185958029358 2216 1982 2461 3179 3358 2566 1998 2717 2060 3345 2246 2569 M800 REACTOME_G_ALPHA1213_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA1213_SIGNALLING_EVENTS.html Genes involved in G alpha (12/13) signalling events 83/97 Reactome 0.43119990772354 0.499814448548158 4500 2617.09090909091 2461 0.05 71 1.16665728923683 -1.1553262403501 -1 0.527157269742269 4496 71 2003 401 4600 3834 3908 4075 1258 1681 2461 2570 M6897 NATSUME_RESPONSE_TO_INTERFERON_BETA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NATSUME_RESPONSE_TO_INTERFERON_BETA_UP.html Genes up-regulated in T98 cells (glioma) 48 h after treatment with interferon beta. 16140920 124/170 John Newman 0.259197531953797 0.322120155561328 4160 2937.18181818182 2461 0.0269060655225012 1486 1.03118392658552 1.11335544948686 1 0.761144066021163 1936 4030 2180 4159 3664 1867 1486 4063 4159 2461 2304 2571 M2353 VANLOO_SP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANLOO_SP3_TARGETS_UP.html Genes up-regulated in E12.5 hearts from mice with SP3 [GeneID=6670] knockout compared to the wild type organ. 17923686 6/10 Arthur Liberzon 0.00160306231760594 0.0056592775909499 2300 2758.63636363636 2461 0.000160421990700517 74 2.09759975717108 -2.84009789002957 -1 7.0730576579568 2461 4296 4687 4031 2297 1520 74 3048 4630 2299 1002 2572 M1600 MCCLUNG_COCAIN_REWARD_4WK http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_COCAIN_REWARD_4WK.html Genes up-regulated in the nucleus accumbens (a major reward center in the brain) after 4 weeks of cocaine [PubChem=5760] treatment. 14566342 96/125 John Newman 0.0967298535117733 0.140093558936965 1230 2272.18181818182 2462 0.00920587360025514 743 1.17687735842341 1.15884274893816 1 1.50725831028771 1230 3674 2004 3811 2979 743 1160 2462 3437 2490 1004 2573 M2188 LI_DCP2_BOUND_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/LI_DCP2_BOUND_MRNA.html Genes encoding mRNA transcripts specifically bound by DCP2 [GeneID=167227]. 18039849 104/114 Arthur Liberzon 0.0988343684566284 0.142747313070773 2290 2655.72727272727 2463 0.00941595396801634 1772 0.729350114807293 -0.69199178156215 -1 0.925138807598746 2289 1829 4087 2197 1823 1772 2680 2965 2463 4306 2802 2574 M14942 WANG_RESPONSE_TO_FORSKOLIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_FORSKOLIN_UP.html Genes up-regulated in LNCaP cells (prostate cancer) treated with forskolin [PubChem=47936], an activator of PKA pathway. 16751804 33/50 Arthur Liberzon 1.33836982983643e-05 0.00013243407959807 4095 2417.09090909091 2464 1.21670724716145e-06 31 0.948712229763867 1.03219627833833 1 5.5204669463854 4093 268 2007 141 31 4324 4551 2464 1274 2821 4614 2575 M17096 GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_2 http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_WALDENSTROEMS_MACROGLOBULINEMIA_2.html Genes exclusively up-regulated in B lymphocytes from WM (Waldenstroem's macroglobulinemia) but with a similar expression profile in MM (macroglobulinemia) and normal cells. 17252022 7/24 Arthur Liberzon 0.0012843804797743 0.0047621962800744 1915 2394.63636363636 2464 0.000128512341913039 177 1.85136352738927 -1.85136352738927 -1 6.4509643905035 1913 3949 4640 2549 2700 1673 2464 177 2438 2482 1356 2576 M2055 DAZARD_UV_RESPONSE_CLUSTER_G28 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G28.html Cluster G28: genes differentially up-regulated in NHEK (normal keratinocyte) compared to SCC12B2 cells (squamous cell carcinoma) by UV-B radiation. 12771951 27/41 Arthur Liberzon 0.00015966379125897 0.000969901022834412 4710 2416.63636363636 2465 1.45159436316703e-05 165 1.22140798465225 -1.3512214523013 -1 5.52246104063157 4707 932 750 2169 165 4082 3355 3942 2465 740 3276 2577 M747 REACTOME_METABOLISM_OF_POLYAMINES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_POLYAMINES.html Genes involved in Metabolism of polyamines 16/17 Reactome 0.0185369111294906 0.0356391936990614 2060 2478.45454545455 2466 0.00169954257808891 394 1.28318545610102 -1.4815701348443 -1 2.78807818059472 2057 4232 3239 3576 4155 958 394 2466 1908 2889 1389 2578 M1315 SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_PIP3_SIGNALING_IN_B_LYMPHOCYTES.html Genes related to PIP3 signaling in B lymphocytes 46/60 Signaling Gateway 0.00922161428646131 0.0204988685776508 1835 2217.09090909091 2467 0.000841863305821265 190 0.837762247085255 0.804447273935811 1 2.1221831817203 1832 190 2467 879 3470 2753 1440 518 4412 3245 3182 2579 M1866 WANG_TUMOR_INVASIVENESS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TUMOR_INVASIVENESS_DN.html Down-regulated genes in the subpopulation of invasive PyMT cells (breast cancer) compared to the general population of PyMT cells. 17440055 292/318 Jessica Robertson 0.431360963451023 0.499814448548158 1675 2577.54545454545 2468 0.0500244570086952 1410 1.03784394308506 1.13121298990362 1 0.468940924196129 1672 2729 3714 2468 3473 2290 1866 2645 1410 3764 2322 2580 M225 BIOCARTA_MTA3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MTA3_PATHWAY.html Downregulated of MTA-3 in ER-negative Breast Tumors 27/43 BioCarta 0.0188689115494829 0.0361449929032303 2470 2614.18181818182 2470 0.00173024693693078 732 1.13026139891341 -1.1940075532596 -1 2.44541555463947 2470 4518 2602 4079 1611 1823 1966 732 3774 3275 1906 2581 M314 NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_UP.html Up-regulated genes in lung tissue of smokers with chronic obstructive pulmonary disease (COPD) vs smokers without disease (GOLD-2 vs GOLD-0). 15469929 212/280 Kate Stafford 0.011073237089742 0.0236069011127291 4600 2663.90909090909 2470 0.00101176071185081 949 1.09204385387178 -1.12886496776686 -1 2.66588735752239 4596 2759 2019 2137 949 3372 4321 1433 2470 2827 2420 2582 M1796 ZHENG_GLIOBLASTOMA_PLASTICITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_GLIOBLASTOMA_PLASTICITY_UP.html The glioblastoma multiforme (GBM) plasticity signature: genes up-regulated in neural stem cells (NSC) with double knockout of TP53 and PTEN [GeneID=7157;5728] vs those with knockout of TP53 alone. 18948956 342/447 Jessica Robertson 2.28253036080216e-05 0.000202891587626858 1905 2381.18181818182 2471 2.07504912973967e-06 402 1.23838092782911 1.2685811816986 1 6.86179312995056 1905 2725 402 2701 4573 2281 3152 2165 2471 427 3391 2583 M19096 KEGG_BLADDER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BLADDER_CANCER.html Bladder cancer 51/58 KEGG 0.0818655573777656 0.122009924478388 2665 2163.72727272727 2473 0.00773460980512335 829 1.12686481343831 1.23658179283834 1 1.54469331218294 2665 2898 1810 2473 2802 2012 1968 2524 2699 1121 829 2584 M12002 MAYBURD_RESPONSE_TO_L663536_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAYBURD_RESPONSE_TO_L663536_UP.html Genes up-regulated in H720 cells (lung cancer) after treatment with L663536 (MK886) [PubChem=105049], an inhibitor of leukotriene biosynthesis. 16551867 36/42 Arthur Liberzon 0.0128689608585944 0.0266410066897217 2475 2562.45454545455 2473 0.00117680550010584 1001 0.934724247695775 0.952798808224858 1 2.20817354728308 2473 2955 3068 2325 1001 4580 3611 1120 1056 3757 2241 2585 M3397 KEGG_BUTANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BUTANOATE_METABOLISM.html Butanoate metabolism 36/48 KEGG 0.0294917423788001 0.0519019478105654 3000 2428.81818181818 2474 0.00271769742705582 1307 1.24021658186539 -1.45521643489711 -1 2.39089867681602 2998 3381 2474 3129 1307 1432 2300 1507 2732 3029 2428 2586 M1530 SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1B http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_RESPONSE_TO_TSA_AND_DECITABINE_1B.html Genes with some basal expression and partially methylated promoters, up-regulated by the combination of TSA and decitabine [PubChem=5562;451668] in RKO cells (colorectal cancer). 11992124 31/44 John Newman 0.0147622070129344 0.0298617253421183 3455 2451.90909090909 2474 0.00135110940558637 634 1.57473172550377 -2.03556985647328 -1 3.60307043079347 3452 2530 930 2017 4516 2474 1243 634 3641 1538 3996 2587 M4950 ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_UP.html Genes up-regulated in liver tumor compared to the normal adjacent tissue. 18413731 1080/1311 Jessica Robertson 0.11526715136912 0.162600404800432 1460 2733.18181818182 2474 0.0121722658160976 863 0.884956124946495 -0.867891082257974 -1 1.0474413722705 1457 3149 4546 4142 2200 863 1878 2474 3293 4453 1610 2588 M19469 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_DN http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_D7_DN.html Hepatic graft versus host disease (GVHD), day 7: down-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 43/66 Arthur Liberzon 0.00534230834521615 0.0140243022188099 3375 2426.63636363636 2474 0.000486847769562148 723 1.47851477661851 -1.80874971440186 -1 4.11111424520411 3374 2474 1166 3483 723 3415 3983 3050 1320 1697 2008 2589 M17728 BLALOCK_ALZHEIMERS_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_DN.html Genes down-regulated in brain from patients with Alzheimer's disease. 14769913 1572/1930 John Newman 0.317558828009876 0.382269234431679 3230 2579.09090909091 2476 0.0374871815631653 460 0.979490675791391 -0.923964780360352 -1 0.613704910549937 3226 460 4490 1394 2566 1530 3200 2439 2199 4390 2476 2590 M1537 MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_8 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_8.html Cluster 8: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate, curcumin, sulindac and TSA [PubChem=5222465;969516;5352;5562]. 10969808 15/19 John Newman 0.156052153071226 0.209430242393001 2480 2540.81818181818 2476 0.0153057111558588 935 0.909608270512608 1.0247584469908 1 0.926597632654928 2476 3898 3370 3596 2094 1825 1602 2691 935 3408 2054 2591 M6831 BIOCARTA_KREB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_KREB_PATHWAY.html The Citric Acid Cycle 11/11 BioCarta 3.79623533955918e-05 0.000306022854083954 2310 2532.09090909091 2477 3.4511825886526e-06 78 0.512796315273373 -0.512796315273373 -1 2.70397009085776 2306 2647 3653 2423 78 1889 2042 2477 3164 4508 2666 2592 M19025 MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_MULTIPLE_MYELOMA_BY_TACI_UP.html Up-regulated genes distinguishing in multiple myeloma (MM) samples with higher expression of TACI [GeneID=23495]. 15827134 500/758 Kevin Vogelsang 1.18446995898737e-17 9.01725517164578e-16 2480 2155.54545454545 2477 1.0767908718067e-18 46 1.27793138048549 -1.39174355694566 -1 28.8494671045415 3833 504 46 312 2028 3737 3544 4679 2479 72 2477 2593 M2063 HOFFMAN_CLOCK_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMAN_CLOCK_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) upon knockdown of CLOCK [GeneID=9575] by RNAi that also belong to the highest confidence network (according to Ingenuity Pathway Analysis). 20124474 10/23 Jessica Robertson 0.0913617222419069 0.13367245163726 2480 2734 2477 0.00867201546598506 1201 1.62683571094066 -1.71155030653426 -1 2.13331293685007 2477 4634 2097 4048 2550 2284 2868 1383 4345 2187 1201 2594 M3574 REACTOME_SIGNALLING_BY_NGF http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_BY_NGF.html Genes involved in Signalling by NGF 254/279 Reactome 0.68618940391 0.690284310838704 2370 2743.54545454545 2478 0.1 914 0.954969867052129 0.953864833306499 1 0.230559229464777 2366 2261 3566 914 4399 2296 2478 3620 1663 3140 3476 2595 M8202 AMIT_SERUM_RESPONSE_480_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_480_MCF10A.html Genes whose expression peaked at 480 min after stimulation of MCF10A cells with serum. 17322878 47/67 Leona Saunders 0.000677402970461029 0.00293334130328078 3685 2459.63636363636 2478 6.16010581696458e-05 342 1.52810125224435 -1.8804059686722 -1 5.8070964840473 3682 1419 1030 1210 342 4638 4552 4155 2633 917 2478 2596 M2288 BIOCARTA_NFAT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NFAT_PATHWAY.html NFAT and Hypertrophy of the heart (Transcription in the broken heart) 72/91 BioCarta 0.23640513573209 0.297317410246594 2065 2477.81818181818 2479 0.0242216416939941 1427 0.960422416628635 0.98356221076295 1 0.759053780554604 2061 1880 2668 2479 4610 2572 1427 2796 2096 2702 1965 2597 M8897 AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/AGUIRRE_PANCREATIC_CANCER_COPY_NUMBER_DN.html Down-regulated genes whose expression correlates with copy number losses in pancreatic adenocarcinoma cell lines and primary tumor specimens. 15199222 294/354 Arthur Liberzon 0.431521864476871 0.499824098240695 3165 2471.90909090909 2479 0.0500488968142554 583 0.919833567027319 -0.923438297576283 -1 0.415595337282425 3162 1181 3998 821 2758 2479 3784 2343 583 4104 1978 2598 M58 PID_AR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_PATHWAY.html Coregulation of Androgen receptor activity 18832364 87/113 Pathway Interaction Database 0.00710742995922956 0.0166652108333649 2425 2480.90909090909 2480 0.000648226906441023 147 0.777480611957307 -0.790234470299482 -1 2.07437459815296 2424 711 3831 3601 3279 1182 3173 2480 2335 4127 147 2599 M966 REACTOME_N_GLYCAN_ANTENNAE_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_N_GLYCAN_ANTENNAE_ELONGATION.html Genes involved in N-Glycan antennae elongation 12/14 Reactome 0.00899979061440448 0.020160897816796 2480 2519.45454545455 2480 0.000821529029638068 866 1.52183605115213 -1.42611082496332 -1 3.87162309395749 2480 3091 1144 1961 866 4635 3669 3036 2163 1344 3325 2600 M17966 VALK_AML_WITH_T_8_21_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_T_8_21_TRANSLOCATION.html Genes that best predicted acute myeloid leukemia (AML) with the t(8;21) translocation producing the AML1-ETO fusion [GeneID=861;862]. 15084694 7/9 Jessica Robertson 0.0153728014914854 0.0308239690058671 1945 2634 2481 0.00154801939227745 542 2.12016520033282 -2.12016520033282 -1 4.80726920751546 1944 4642 4620 4179 3955 1190 898 684 3839 2481 542 2601 M5109 KEGG_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRIMIDINE_METABOLISM.html Pyrimidine metabolism 93/106 KEGG 0.291431816190597 0.35562517384168 1080 2993.90909090909 2482 0.0308336392197748 1076 0.801213202072899 -0.80839834741716 -1 0.539707377461153 1076 4404 4100 4486 4563 1385 1593 2334 2213 4297 2482 2602 M18325 OLSSON_E2F3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OLSSON_E2F3_TARGETS_UP.html Genes up-regulated in the 5637 cell line (bladder cancer) after knockdown of E2F3 [GeneID=1871] by RNAi. 16909110 33/42 Arthur Liberzon 0.0024465093433581 0.00778135047213627 3610 2205.63636363636 2482 0.000222657656961427 547 1.42410709297949 -1.53077105256123 -1 4.50650147840188 3608 898 953 748 547 4410 2504 2482 3610 1375 3127 2603 M2348 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_UP.html Genes up-regulated in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 345/424 Arthur Liberzon 0.00717693645977726 0.0168031448859864 4145 2483.72727272727 2482 0.000654586987995852 527 1.11597358447545 1.05929688967019 1 2.97154999202247 3500 527 887 714 2482 3659 4144 4142 2442 560 4264 2604 M2011 MIKKELSEN_NPC_ICP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_ICP_WITH_H3K27ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in neural progenitor cells (NPC). 17603471 7/16 Arthur Liberzon 0.00159801040984753 0.0056483078298767 3945 2653.27272727273 2483 0.000159916071097872 450 2.06324581212151 -1.33601370630977 -1 6.95982398233965 3945 450 4646 1983 488 4591 3610 1050 3921 2483 2019 2605 M238 PID_THROMBIN_PAR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_THROMBIN_PAR1_PATHWAY.html PAR1-mediated thrombin signaling events 18832364 56/67 Pathway Interaction Database 0.00577426225782821 0.0142024584976285 4050 2273.45454545455 2484 0.000526315789473684 143 0.990682677755488 -1.12208943148405 -1 2.74647828761099 4048 143 2345 184 2484 2717 3806 2468 2507 2774 1532 2606 M17316 WU_HBX_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_2_UP.html Genes up-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in primary hepatocytes. 11439330 41/42 John Newman 0.545967947355217 0.614295282840673 2125 2676 2484 0.0692649980160776 1128 0.957072343547025 0.992044129964542 1 0.303807028045985 2121 2484 2728 1128 4453 2356 2103 3241 3557 2948 2317 2607 M1712 LEIN_NEURON_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_NEURON_MARKERS.html Genes enriched in neurons in the adult mouse brain identified through correlation-based searches seeded with neuron cell-type specific gene expression patterns. 17151600 78/110 Jessica Robertson 0.214874367969118 0.275076489507523 3855 2720.81818181818 2485 0.021751897482423 1332 1.17617486358503 -1.0632681172711 -1 0.989188155951955 3853 1332 1379 1531 3275 3519 4235 4669 1487 2164 2485 2608 M12367 LEE_NAIVE_T_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_NAIVE_T_LYMPHOCYTE.html Genes enriched in the naive circulating T lymphocytes compared to the earlier differentiation stages. 15210650 20/30 Arthur Liberzon 0.243953887284903 0.305589795112724 2075 3046.45454545455 2485 0.0251025487567805 2071 0.771412118128903 -0.937051849721309 -1 0.595855926651565 2071 3868 2453 3945 2359 2204 2485 4483 3226 4070 2347 2609 M1943 IRITANI_MAD1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IRITANI_MAD1_TARGETS_UP.html Genes up-regulated by overexpression of MAD1 [GeneID=4084] in primary thymocytes from RAG2 [GeneID=5897] knockout mice. 12234922 16/22 Jessica Robertson 0.0165401211731498 0.0325832103244019 2900 2641.72727272727 2485 0.00151507259547579 673 1.0867044282886 -0.661999187807385 -1 2.42463878698341 2896 4235 2485 3987 2259 3895 4485 673 1648 1799 697 2610 M1965 MIKKELSEN_MEF_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MEF cells (embryonic fibroblasts). 18509334 42/127 Jessica Robertson 0.000132033450180874 0.000824335826526091 3080 2043 2486 1.20037613510231e-05 59 1.74468416844285 -1.51967355048379 -1 8.07332869745169 3078 2486 500 2510 3706 1191 3405 1874 2551 1113 59 2611 M14512 BIOCARTA_RACCYCD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RACCYCD_PATHWAY.html Influence of Ras and Rho proteins on G1 to S Transition 44/48 BioCarta 0.00547728416953509 0.0142024584976285 2590 2137.54545454545 2487 0.000499178958750455 608 0.838876907034513 0.943469179145811 1 2.32560959995037 2586 1429 3455 653 732 2368 2516 3557 608 3122 2487 2612 M18342 ST_G_ALPHA_I_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_G_ALPHA_I_PATHWAY.html G alpha i Pathway 46/60 Signaling Transduction KE 0.0181995681033539 0.0351330060601385 2490 1986 2488 0.00166835378937653 201 0.892957103881963 0.945612435768479 1 1.94849030760297 2488 201 2815 1145 1122 3464 3291 1620 655 2547 2498 2613 M15652 REACTOME_DOUBLE_STRAND_BREAK_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOUBLE_STRAND_BREAK_REPAIR.html Genes involved in Double-Strand Break Repair 26/32 Reactome 0.131669306407281 0.181719042760926 1525 2812.63636363636 2489 0.0127527720600778 1102 0.841036930732404 -0.86782789976619 -1 0.934525479143286 1522 4179 3631 4416 4655 1199 1102 2295 2489 3951 1500 2614 M292 DASU_IL6_SIGNALING_SCAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_SCAR_UP.html Genes up-regulated in hypertrophic scar fibroblasts in response to IL6 [GeneID=3569]. 15095275 45/49 John Newman 0.00135234840347701 0.00494429470519869 4285 2662 2489 0.000123016401209986 451 1.05223785619379 1.08482705628052 1 3.64068208631951 4283 838 2403 1576 451 4031 3914 4473 1715 2489 3109 2615 M2128 CHICAS_RB1_TARGETS_GROWING http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_GROWING.html Genes up-regulated in growing IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 343/431 Arthur Liberzon 8.01789682632268e-07 1.15732333395239e-05 1645 2528.36363636364 2490 7.2889997713141e-08 272 1.29523640532762 1.29937015010325 1 9.59420925430496 1643 3172 272 2912 4433 2490 2311 2390 3475 1277 3437 2616 M1386 KEGG_PENTOSE_PHOSPHATE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PENTOSE_PHOSPHATE_PATHWAY.html Pentose phosphate pathway 28/33 KEGG 0.000454759468279482 0.00214646469027915 4495 2510.45454545455 2491 4.13503180271398e-05 74 1.15731338755508 0.925751667549851 1 4.63354790254481 4492 910 2491 112 292 3852 4577 4638 74 1652 4525 2617 M8599 CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by activated KRAS [GeneID=3845] vs those reverted to normal cells upon over-expression of a dominant negative form of CDC25 [GeneID=5923]. 16607279 64/102 Lauren Kazmierski 0.188779047545612 0.246074870040124 4560 2625.81818181818 2491 0.0188397988895152 124 1.31187350132081 -1.34347215087799 -1 1.19857370537205 4558 124 1338 751 2491 4426 4134 4232 363 1997 4470 2618 M1726 LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES.html Transcripts showing subcellular localization only to proximal dendrites in the adult mouse brain. 17151600 38/54 Jessica Robertson 0.568580000823487 0.635796636789116 4015 2627.36363636364 2492 0.0735774539732233 727 1.15574719614359 -0.994562064603017 -1 0.340984004220919 4015 2492 2024 1981 3318 2267 3783 2560 727 1685 4049 2619 M2 PID_SMAD2_3NUCLEAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SMAD2_3NUCLEAR_PATHWAY.html Regulation of nuclear SMAD2/3 signaling 18832364 111/130 Pathway Interaction Database 0.00198061441831471 0.00663014188258543 705 1937.36363636364 2493 0.000180218161372043 38 0.9802071070063 1.05732978754242 1 3.2040429240412 701 3657 2514 2493 3535 38 470 1038 3350 3287 228 2620 M1291 THEODOROU_MAMMARY_TUMORIGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/THEODOROU_MAMMARY_TUMORIGENESIS.html Candidate mammary tumorigenesis genes from the common insertion sites (CIS) of MMTV virus that induced breast tumors in mice. 17468756 33/53 Leona Saunders 0.0181434301674182 0.0350683826331752 2560 2569.18181818182 2494 0.0016631645454283 298 1.1456588476198 1.33300429500995 1 2.50130638349751 2560 3813 1447 4217 4443 1563 1391 2494 4361 1674 298 2621 M15672 RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_UP.html Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: moderately vs poorly differentiated tumors. 18679425 163/186 Jessica Robertson 0.0688819309291218 0.10555932272255 1965 2787.63636363636 2494 0.00646710586519604 1650 0.966551128818314 0.926316347267799 1 1.41614573680066 1965 2302 2494 4055 1650 2005 2036 3319 3631 3340 3867 2622 M17967 REACTOME_TIGHT_JUNCTION_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TIGHT_JUNCTION_INTERACTIONS.html Genes involved in Tight junction interactions 23/35 Reactome 0.520080557571751 0.588394111155001 2895 2339.09090909091 2495 0.0645613626619908 406 1.78592126370247 -1.69847863317149 -1 0.617139479019201 2895 2064 1672 989 3427 2837 2125 2656 406 2495 4164 2623 M142 PID_AJDISS_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AJDISS_2PATHWAY.html Posttranslational regulation of adherens junction stability and dissassembly 18832364 75/87 Pathway Interaction Database 0.44616736217465 0.51527035709918 2720 2536.72727272727 2496 0.0523002264225523 1336 1.07468125944218 1.05934755360256 1 0.464260745667172 2720 1336 2134 1373 4225 1631 2496 2545 3712 1787 3945 2624 M3021 KOBAYASHI_RESPONSE_TO_ROMIDEPSIN http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_RESPONSE_TO_ROMIDEPSIN.html Genes up-regulated in MM-LH cells (malignant melanoma) after treatment with the HDAC inhibitor romidepsin (FK228) [PubChem=5352062]. 16186804 23/24 Arthur Liberzon 0.105777987347405 0.151248742889958 3320 2407.36363636364 2497 0.0101122689891993 818 1.2228091401448 1.1463005651545 1 1.50503643848638 3319 2065 1710 818 3178 2560 2382 1455 3619 2497 2878 2625 M10775 REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS.html Genes involved in G alpha (z) signalling events 36/47 Reactome 0.383537033236496 0.45223452332657 3680 2774 2498 0.0430249047738445 1562 1.05395194013711 -1.15420118332318 -1 0.544928201830978 3680 2498 1742 2054 2639 4126 2307 2458 3721 1562 3727 2626 M1615 WENG_POR_TARGETS_GLOBAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_GLOBAL_DN.html Genes down-regulated in liver from transgenic mice with reduced expression of POR [GeneID=5447] in all tissues. 16006652 31/39 John Newman 0.0166681588910911 0.0327670595443356 750 2032.63636363636 2498 0.00152689091718876 370 1.27042858558272 1.44668859507086 1 2.82992105025547 750 4169 2506 2934 2498 528 370 877 3884 3108 735 2627 M1135 DARWICHE_PAPILLOMA_RISK_HIGH_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_UP.html Genes up-regulated during skin tumor progression from normal skin to high risk papilloma. 17525749 151/262 Arthur Liberzon 0.499804054275769 0.568863066356795 1825 2682.36363636364 2499 0.0610356444777955 1468 1.27450129146351 1.36153520845396 1 0.468420991697346 1822 4015 1656 3736 4346 2653 2424 2882 1468 2005 2499 2628 M1929 MEISSNER_ES_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_ES_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in ES cells (embryonic stem). 18600261 37/56 Jessica Robertson 0.184577167459614 0.241665528546291 2500 2621.72727272727 2499 0.0183788726981598 1290 1.26909200395345 -1.45238383024292 -1 1.1744371860888 3424 2499 1746 1509 3938 3466 4323 2510 2497 1637 1290 2629 M10401 BIOCARTA_TEL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TEL_PATHWAY.html Telomeres, Telomerase, Cellular Aging, and Immortality 34/37 BioCarta 0.0440681540322094 0.0723484128807055 2525 2188.54545454545 2500 0.00408876897416553 906 1.01531487477931 1.34809577513657 1 1.73755447247437 2523 1996 2566 906 3377 2969 2646 1058 1458 2500 2075 2630 M7928 MITSIADES_RESPONSE_TO_APLIDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/MITSIADES_RESPONSE_TO_APLIDIN_UP.html Genes up-regulated in the MM1S cells (multiple myeloma) after treatment with aplidin [PubChem=44152164], a marine-derived compound with potential anti-cancer properties. 18593922 569/742 Jessica Robertson 0.0150295286839995 0.0303043431024949 1855 2841 2500 0.00151321559485136 1082 1.08998204921281 1.05012063866383 1 2.48345359823095 1853 4314 4548 4144 1082 2082 1993 2500 2330 3006 3399 2631 M1139 DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SQUAMOUS_CELL_CARCINOMA_UP.html Genes up-regulated in squamous cell carcinoma (SCC) compared to normal skin. 17525749 167/272 Arthur Liberzon 0.00207928858190158 0.00687753476284193 2055 2066.63636363636 2503 0.000189205126056269 684 1.32768929595098 1.40787142586741 1 4.30821339932277 2051 2772 684 754 2672 2727 2591 4369 741 869 2503 2632 M843 STEIN_ESRRA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS.html Genes regulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 752/981 Arthur Liberzon 0.022876212094964 0.0421944982759789 2115 2442.36363636364 2503 0.00231151761043184 307 0.956876775763563 -0.927530863691884 -1 1.97376945987733 2111 3963 4636 2755 2641 307 1674 2503 1283 4059 934 2633 M1899 BASSO_CD40_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_CD40_SIGNALING_DN.html Gene down-regulated by CD40 [GeneID=958] signaling in Ramos cells (EBV negative Burkitt lymphoma). 15331443 76/105 Kevin Vogelsang 0.00250513786662485 0.00790391091608911 3045 2448.63636363636 2504 0.000227999547321522 558 1.27483707303149 -1.41321556995743 -1 4.0211512668682 3043 1874 755 2504 558 2981 2087 4342 3623 1613 3555 2634 M6840 XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_SIGNALING_NOT_VIA_AKT1_6HR.html Genes changed similarly in DU-145 cells (prostate cancer) in the absence and presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 6 h. 17099727 40/48 Arthur Liberzon 0.0538002386368017 0.0858034012101577 1465 2440.72727272727 2505 0.00501479897102852 723 1.19935438245072 1.3100951062623 1 1.91921846701596 1461 4137 2393 4193 2505 2027 723 2741 1327 2513 2828 2635 M10579 BIOCARTA_EDG1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EDG1_PATHWAY.html Phospholipids as signalling intermediaries 43/51 BioCarta 0.00577426225782821 0.0142024584976285 200 2354.81818181818 2508 0.000526315789473684 197 0.987634730881755 -0.752813634370935 -1 2.73802811213535 4032 197 1973 200 3155 3042 4631 2508 843 2361 2961 2636 M10547 BIOCARTA_MAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MAL_PATHWAY.html Role of MAL in Rho-Mediated Activation of SRF 34/42 BioCarta 0.148412702718851 0.200833703220463 2510 2536.45454545455 2508 0.0144987086437155 1149 0.978139819667659 -0.909023442566236 -1 1.02313374818512 2508 3400 3169 2224 3465 1327 3442 2270 2863 2084 1149 2637 M17162 NAKAMURA_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_METASTASIS.html Genes up-regulated in highly metastatic pancreatic cancer cells. 17210693 51/70 Jessica Robertson 0.157057297036506 0.210539744962314 3885 2756.63636363636 2508 0.0154123846744202 1026 1.13177916602053 1.05071093364095 1 1.14904702461634 3881 1410 1556 1026 2097 4434 4067 3171 1957 2508 4216 2638 M1182 LA_MEN1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LA_MEN1_TARGETS.html Genes up-regulated in cells expressing MEN1 [GeneID=4221]. 16449969 29/35 Arthur Liberzon 6.36178361021615e-05 0.000459841020524046 4350 2648.72727272727 2509 5.78360689329262e-06 105 1.25717750847849 1.32962632948835 1 6.29561800774949 4346 917 1163 2509 105 3873 4126 4643 1566 1735 4153 2639 M1686 ZHONG_SECRETOME_OF_LUNG_CANCER_AND_ENDOTHELIUM http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_SECRETOME_OF_LUNG_CANCER_AND_ENDOTHELIUM.html Proteins secreted in co-culture of LKR-13 tumor cells (non-small cell lung cancer, NSCLC) and MEC stroma cells (endothelium). 18757440 124/177 Jessica Robertson 0.00129715968531141 0.00479217899694665 740 2220.36363636364 2509 0.000117993195090619 641 1.24193524568971 1.27539188326178 1 4.32233396635967 739 3651 641 3882 1760 2540 2509 2689 2842 1316 1855 2640 M16297 SCHLESINGER_H3K27ME3_IN_NORMAL_AND_METHYLATED_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SCHLESINGER_H3K27ME3_IN_NORMAL_AND_METHYLATED_IN_CANCER.html Genes bearing the H3K27me3 mark in normal cells; their DNA is methylated in cancer cells. 17200670 36/73 Leona Saunders 1.91616157357008e-06 2.43392490489203e-05 1220 2185.63636363636 2510 1.74196658410489e-07 303 1.67989611173931 1.21488097242814 1 11.6297119360153 1219 2510 303 1616 958 3307 2777 2893 3735 1003 3721 2641 M17954 STARK_HYPPOCAMPUS_22Q11_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/STARK_HYPPOCAMPUS_22Q11_DELETION_DN.html Genes down-regulated in hyppocampus of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 20/21 Jessica Robertson 0.00640621070318431 0.0154350763241603 2510 2682.63636363636 2510 0.000584085585579472 774 0.630681589486245 -0.672057063232977 -1 1.71419957921036 2510 2090 3504 2073 774 1638 2269 2825 4593 4663 2570 2642 M32 PID_HDAC_CLASSIII_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HDAC_CLASSIII_PATHWAY.html Signaling events mediated by HDAC Class III 18832364 40/49 Pathway Interaction Database 0.00653212035402053 0.0156030405217494 2345 2485.09090909091 2511 0.000595599652358375 783 1.08630984517262 0.816291412976942 1 2.94501682146921 2341 3772 1995 2974 783 1383 1396 3490 3686 2511 3005 2643 M4605 FONTAINE_FOLLICULAR_THYROID_ADENOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_FOLLICULAR_THYROID_ADENOMA_UP.html Genes up-regulated in follicular thyroid adenoma (FTA) compared to other thyroid tumors. 17968324 98/122 Arthur Liberzon 0.142536996172496 0.194162950053154 3025 2497.81818181818 2511 0.0138824866201689 1028 0.99772870924362 -0.857347231542678 -1 1.06558881935333 3022 1838 2511 3122 3805 1028 2506 1602 3007 3704 1331 2644 M18837 BIOCARTA_EGFR_SMRTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EGFR_SMRTE_PATHWAY.html Map Kinase Inactivation of SMRT Corepressor 17/18 BioCarta 0.076930207998039 0.115566703294317 3115 2565.36363636364 2512 0.00725089657522844 1439 0.787894017680892 -0.576747879300956 -1 1.10786091995764 3111 1558 2756 2161 1706 2318 2512 4630 1439 2985 3043 2645 M214 PID_ERBB1_INTERNALIZATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_INTERNALIZATION_PATHWAY.html Internalization of ErbB1 18832364 57/64 Pathway Interaction Database 0.249596062339576 0.31158249517133 3505 2387.54545454545 2512 0.0257662035462684 265 0.936699217303056 -0.69717219045602 -1 0.711695467555719 3503 2437 3487 648 2375 2512 2552 2377 265 2830 3277 2646 M12921 BLALOCK_ALZHEIMERS_DISEASE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_UP.html Genes up-regulated in brain from patients with Alzheimer's disease. 14769913 2149/2922 John Newman 0.162824648300523 0.216732188375203 2540 2621.09090909091 2512 0.0176151793679393 1374 1.08168885918723 1.09124602273021 1 1.07775411396968 2540 1657 4493 1374 2164 3339 2766 2512 2070 1435 4482 2647 M576 REACTOME_GLYCOSPHINGOLIPID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOSPHINGOLIPID_METABOLISM.html Genes involved in Glycosphingolipid metabolism 32/36 Reactome 0.00577426225782821 0.0142024584976285 2815 1892.72727272727 2513 0.000526315789473684 51 1.02751535131069 1.30052073811388 1 2.8485937665456 2811 273 2513 138 930 3382 2648 3119 51 3173 1782 2648 M3063 DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN http://www.broadinstitute.org/gsea/msigdb/cards/DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_DN.html Genes down-regulated in HEK293 cells (embryonic kidney) at 6 h, 12 h or 24 h after infection with reovirus strain T3A (known as a strong inducer of apoptosis). 12885910 434/538 John Newman 0.315148957527809 0.379465071308994 3125 2583.45454545455 2513 0.0338285661706447 607 1.06469867500913 -1.00216918274912 -1 0.672210021922797 3122 1150 1593 607 2513 3573 4714 3350 1645 1632 4519 2649 M4090 BOYAULT_LIVER_CANCER_SUBCLASS_G3_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G3_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G3, defined by unsupervised clustering. 17187432 57/77 Yujin Hoshida 0.000735346972537967 0.0031353547519234 3015 2593.09090909091 2514 6.68720796663194e-05 352 1.33719538920434 -1.28983819919979 -1 5.02356618689997 3011 795 1189 2514 352 4282 3628 4617 2030 1913 4193 2650 M11542 YE_METASTATIC_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/YE_METASTATIC_LIVER_CANCER.html Genes up-regulated in hepatocellular carcinoma (HCC) with intra-hepatic metastasis compared to the non-metastatic tumors. 12640447 40/71 Yujin Hoshida 0.064665973729674 0.0999749086158079 3620 2472.36363636364 2515 0.00605898497150599 966 1.4904983745335 -1.40130334400756 -1 2.23666064145619 3620 3367 1621 3117 1726 3854 3798 1236 966 2515 1376 2651 M16384 XU_GH1_AUTOCRINE_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_AUTOCRINE_TARGETS_DN.html Genes down-regulated in MFCF-7 cells (breast cancer) upon stable autocrine expression of HG1 [GeneID=2688]. 15845533 198/237 John Newman 0.127210617020461 0.176494448070716 2155 2720.36363636364 2516 0.0122929987185895 1542 1.06205631410291 1.06274195774236 1 1.20033130396277 2152 2281 2452 2411 3193 3690 2908 1542 2516 2750 4029 2652 M10122 REACTOME_RETROGRADE_NEUROTROPHIN_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RETROGRADE_NEUROTROPHIN_SIGNALLING.html Genes involved in Retrograde neurotrophin signalling 17/19 Reactome 0.00698520572502159 0.0164521811487534 3820 2260.09090909091 2517 0.000637043954284116 800 0.850957693348431 -0.682758557993788 -1 2.27756112025363 3817 1014 2838 1529 800 2921 2517 1453 2780 3524 1668 2653 M13447 LANDIS_ERBB2_BREAST_PRENEOPLASTIC_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_PRENEOPLASTIC_DN.html Down-regulated genes from top 82 genes out of the 324-gene signature identified in the pre-neoplastic tissue adjacent to the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 63/74 Leona Saunders 0.000105972973520595 0.00069664684542787 2160 2120.63636363636 2517 9.63437077577788e-06 123 0.896502876311556 -0.871293653951651 -1 4.24673842243862 3208 123 2535 132 138 2159 3258 2160 3680 3417 2517 2654 M15025 LIAO_HAVE_SOX4_BINDING_SITES http://www.broadinstitute.org/gsea/msigdb/cards/LIAO_HAVE_SOX4_BINDING_SITES.html Genes up-regulated in the samples with intrahepatic metastatic hepatocellular carcinoma (HCC) vs primary HCC that also have putative binding sites for SOX4 [GeneID=6659]. 18504433 63/66 Jessica Robertson 0.0269932364451467 0.048480022117489 2310 2737.54545454545 2518 0.00248456703059123 868 1.3698338335864 1.46653679016175 1 2.70167139169108 2307 4434 1771 4374 4343 2518 1969 868 3334 2545 1650 2655 M1699 BAFNA_MUC4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAFNA_MUC4_TARGETS_UP.html Genes up-regulated in NIH3T3 cells (fibroblast) engineered to stably express MUC4 [GeneID=4585]. 19010895 9/10 Leona Saunders 1.41569060500494e-05 0.000137774425889141 1800 2433.72727272727 2518 1.4156996238953e-06 37 1.10305201593951 -1.07712751773809 -1 6.3901557603599 1797 1619 4514 2518 37 3366 4005 2701 1976 2756 1482 2656 M4785 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_DN.html Genes down-regulated in monocyte-derived dendritic cells (MDDC) after stimulation with galecin-1 (lectin, LGALS1) [GeneID=3956] compared to that with bacterial lipopolysaccharide (LPS). 16785517 556/774 Arthur Liberzon 0.000139875586024501 0.000865285407648291 2520 2229.09090909091 2520 1.39884391135342e-05 45 1.14940186123459 1.18438764765737 1 5.28237710512863 2520 494 4284 45 2320 3100 2832 3009 1447 299 4170 2657 M2358 RAFFEL_VEGFA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAFFEL_VEGFA_TARGETS_DN.html Genes down-regulated in hearts of E18.5 embryos upon knockout of VEGFA [GeneID=7422]. 18981216 3/5 Arthur Liberzon 0.0365457589935392 0.0617301454239838 3885 2453.27272727273 2520 0.00371610659469355 75 1.95526267513806 -0.798455115489714 -1 3.54846730773542 3885 3585 4689 2520 2081 2450 609 1022 75 2694 3376 2658 M19990 TIEN_INTESTINE_PROBIOTICS_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_6HR_DN.html Genes down-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 6h. 16394013 224/273 Arthur Liberzon 0.18490634628507 0.242029382824606 2745 2751.81818181818 2522 0.0184149039988309 909 0.953408384850966 1.04548208465628 1 0.88133766287364 2745 2268 3696 2433 4463 2522 2327 1759 909 4099 3049 2659 M4000 TSUDA_ALVEOLAR_SOFT_PART_SARCOMA http://www.broadinstitute.org/gsea/msigdb/cards/TSUDA_ALVEOLAR_SOFT_PART_SARCOMA.html Protein kinase genes most significantly up-regulated in ASPS (alveolar soft part sarcoma) tumors compared to four other types of primitive sarcomas. 17283122 17/18 Jessica Robertson 0.0100599854492818 0.0219524416646372 2430 2688.90909090909 2522 0.000918753056100661 906 0.924875125457634 0.958759341933065 1 2.30157382806316 2429 2095 2522 1826 906 4137 3170 3954 2039 2994 3506 2660 M16713 DIRMEIER_LMP1_RESPONSE_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/DIRMEIER_LMP1_RESPONSE_LATE_DN.html Cluster 4: genes down-regulated in B2264-19/3 cells (primary B lymphocytes) within 60-180 min after activation of LMP1 (an oncogene encoded by Epstein-Barr virus, EBV). 15674340 33/59 Arthur Liberzon 0.00443772297080199 0.0120976231028816 4435 2353.27272727273 2523 0.000404245442779951 619 1.12990007476259 -1.16195858538476 -1 3.25055686240347 4435 2523 2679 2544 679 3730 3736 619 992 2407 1542 2661 M1805 WILLERT_WNT_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/WILLERT_WNT_SIGNALING.html Genes up-regulated in NCCIT cell line (embryonic teratocarcinoma) after stimulation with WNT3A [GeneID=89780]. 12095419 36/43 Yujin Hoshida 0.00488440212152621 0.0130842099963699 1435 2445.54545454545 2523 0.000445025473996978 371 1.16735594343171 1.05618501817834 1 3.29867649338428 1432 3798 2523 4423 3932 1453 1303 371 3101 2616 1949 2662 M3848 LINDSTEDT_DENDRITIC_CELL_MATURATION_D http://www.broadinstitute.org/gsea/msigdb/cards/LINDSTEDT_DENDRITIC_CELL_MATURATION_D.html Genes down-regulated during the course of maturation of monocyte-derived dendritic cells (DC) in response to inflammatory stimuli (cluster D). 12356685 85/129 Arthur Liberzon 0.00709913318070989 0.016654030125721 4230 2602.27272727273 2523 0.000647467749986799 716 1.22132008191402 1.33835640338259 1 3.25916501798796 4230 716 811 976 1061 3955 4680 3987 2523 1186 4500 2663 M902 REACTOME_CGMP_EFFECTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CGMP_EFFECTS.html Genes involved in cGMP effects 9/21 Reactome 0.00378225898346127 0.0107285230780873 2525 2276.36363636364 2525 0.000378871191373652 342 2.13993728673304 2.16737412055847 1 6.32386753991474 2525 1072 4250 452 4500 4003 3315 342 923 967 2691 2664 M7327 LIN_NPAS4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIN_NPAS4_TARGETS_DN.html Genes down-regulated in neurons after NPAS4 [GeneID=266743] knockdown by RNAi. 18815592 71/113 Jessica Robertson 1.52630130803233e-05 0.000147323970836659 3765 2153.09090909091 2525 1.3875562701877e-06 253 1.50129685535189 -1.67863624997046 -1 8.6317245059836 3762 1338 383 1405 2594 2525 2691 4059 1915 253 2759 2665 M15835 RIGGINS_TAMOXIFEN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIGGINS_TAMOXIFEN_RESISTANCE_DN.html Genes down-regulated SUM44/LCCTam cells (breast cancer) resistant to 4-hydroxytamoxifen [PubChem=63062] relative to the parental SUM44 cells sensitive to the drug. 18974135 319/395 Leona Saunders 0.0952262937916857 0.138383037776095 3615 2525.45454545455 2526 0.00905605511918422 1185 1.12022840075247 1.20089173421803 1 1.44366963512258 2010 1710 1185 3351 2379 3614 2900 2526 2716 1778 3611 2666 M1847 LIN_TUMOR_ESCAPE_FROM_IMMUNE_ATTACK http://www.broadinstitute.org/gsea/msigdb/cards/LIN_TUMOR_ESCAPE_FROM_IMMUNE_ATTACK.html Genes up-regulated in highly immune-resistant cancer cell line developed from a susceptible cancer using an in vivo selection strategy. 17308126 23/33 Jessica Robertson 0.00131795273263497 0.00483411801679895 2980 2265.81818181818 2526 0.000119885721876725 643 1.83440397910834 1.83829344826691 1 6.37394985139793 2978 4191 643 1424 1925 3094 2526 1255 2793 1264 2831 2667 M4857 UROSEVIC_RESPONSE_TO_IMIQUIMOD http://www.broadinstitute.org/gsea/msigdb/cards/UROSEVIC_RESPONSE_TO_IMIQUIMOD.html Interferon cluster genes up-regulated in skin tumors treated with imiquimod [PubChem=57469]. 16077073 32/44 Jessica Robertson 0.321110029473335 0.385855228898713 3050 2664 2526 0.0345961294046882 1468 1.15325563772656 -1.18368231047543 -1 0.715579829389626 3050 1468 1554 2074 2526 3990 4194 2386 3362 1611 3089 2668 M17693 GARY_CD5_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARY_CD5_TARGETS_UP.html Genes up-regulated in Daudi cells (B lymphocytes) stably expressing CD5 [GeneID=921] off a plasmid vector. 17878328 610/741 Arthur Liberzon 0.044299487383831 0.072677643535517 4550 2559.63636363636 2527 0.00452081882846493 491 0.934713992043231 -0.883373828611095 -1 1.59684451591433 4546 491 4285 620 1508 1332 4300 2667 1970 3910 2527 2669 M896 ZHAN_MULTIPLE_MYELOMA_SPIKED http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_SPIKED.html 'Spiked' genes: genes most highly up-regulated in multiple myeloma samples; were not differentially expressed as compared to the normal plasma cells. 11861292 20/30 Kevin Vogelsang 0.00384210448132476 0.0108526230711268 3060 2244.90909090909 2528 0.000349893711531984 365 1.55525556372857 -1.81597389350138 -1 4.5843514461554 3058 365 744 978 2528 3954 4211 2830 4137 756 1133 2670 M5967 REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS.html Genes involved in Synthesis of bile acids and bile salts 17/32 Reactome 0.00131811650161446 0.00483411801679895 2455 2418.72727272727 2529 0.000119900627827348 449 1.31453710169204 -1.33706301595538 -1 4.56755362673321 2454 3885 1355 3938 449 2591 2529 469 4508 2987 1441 2671 M10395 DAIRKEE_TERT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_TERT_TARGETS_UP.html Genes up-regulated in non-spontaneously immortalizing (NSI) primary breast cancer tumor cultures upon expression of TERT [GeneID=7015] off a retroviral vector. 17471242 468/574 Arthur Liberzon 0.109652406241299 0.155750634203711 1465 2599.63636363636 2529 0.0105029401044374 798 1.02531122938291 -0.946255882867655 -1 1.24234095025388 1465 3607 3575 3673 2529 798 1991 2189 2846 3956 1967 2672 M1356 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX2_UP.html Early prostate development genes (up-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 8/9 Jessica Robertson 0.00100950809887024 0.0040007373859509 1815 2798.36363636364 2529 0.000100996699026272 150 1.31320486935803 1.31320486935803 1 4.72485386161077 1815 4283 4444 4398 1750 2529 1834 150 4707 2629 2243 2673 M208 MIZUKAMI_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIZUKAMI_HYPOXIA_UP.html Genes up-regulated in DLD-1 cells (colon cancer) in response to hypoxia; might not be direct targets of HIF1A [GeneID=3091]. 16127434 14/20 Jessica Robertson 0.00377443879501089 0.0107139033545617 2530 2529.18181818182 2529 0.000343720911160044 324 1.8930015397372 -2.54389502195767 -1 5.59580165771902 2529 4248 987 3964 3954 2317 2906 324 3722 2079 791 2674 M5988 REACTOME_SLC_MEDIATED_TRANSMEMBRANE_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SLC_MEDIATED_TRANSMEMBRANE_TRANSPORT.html Genes involved in SLC-mediated transmembrane transport 170/268 Reactome 1.82339687335381e-05 0.000171102052529424 3405 2023.09090909091 2530 1.65764726013461e-06 391 1.29770385373209 1.39100515079845 1 7.3346151576956 2530 1233 391 442 3405 2932 3404 2572 1217 465 3663 2675 M16257 BIOCARTA_MITOCHONDRIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MITOCHONDRIA_PATHWAY.html Role of Mitochondria in Apoptotic Signaling 24/28 BioCarta 0.148805893921174 0.201135114349353 2535 2178.63636363636 2531 0.0145400829088076 124 1.08349535977902 -1.05362287521822 -1 1.13228809930226 2531 329 2352 819 3690 3131 4719 2556 124 2563 1151 2676 M19872 TAVOR_CEBPA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TAVOR_CEBPA_TARGETS_DN.html Genes down-regulated in KCL22 cells (chronic myelogenous leukemia, CML, with BCR-ABL1 [GeneID=613;25] fusion) by expression of CEBPA [GeneID=1050]. 14517214 41/60 Kevin Vogelsang 0.0547515316584934 0.0870125351609728 2945 2385.63636363636 2531 0.0051057806535093 532 1.27681590511036 -1.09632560800338 -1 2.03153651720321 1732 2942 1780 3144 3676 532 1857 3923 2531 2945 1180 2677 M7517 SMID_BREAST_CANCER_LUMINAL_A_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_A_UP.html Genes up-regulated in the luminal A subtype of breast cancer. 18451135 109/160 Jessica Robertson 6.91897435567348e-13 2.99610632649347e-11 2410 2405 2531 6.28997668697785e-14 84 1.53190857673825 1.57857003700668 1 24.1897065509633 2406 2810 84 2531 1892 3507 3076 2038 3744 175 4192 2678 M2491 BRIDEAU_IMPRINTED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BRIDEAU_IMPRINTED_GENES.html List of genomically imprinted genes. 20421412 56/85 Arthur Liberzon 0.000988119271877762 0.00394245389963063 2390 2520.72727272727 2531 8.98693963726746e-05 619 1.17552154700503 1.36491271185676 1 4.2407062123592 2389 1393 619 1957 2946 3794 2531 4367 3483 778 3471 2679 M11788 CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_DN.html Selected genes down-regulated during invasion of lymphatic vessels during metastasis. 18794116 70/84 Jessica Robertson 7.57854213960444e-08 1.41947297217988e-06 205 2341.45454545455 2532 6.88958400060861e-09 205 1.58145295344795 1.57337038824009 1 13.8769075777624 205 3717 210 3694 3187 2186 1814 2853 4403 955 2532 2680 M2426 LOPEZ_TRANSLATION_VIA_FN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_TRANSLATION_VIA_FN1_SIGNALING.html Genes translationally up-regulated in HUVEC cells (endothelium) grown on FN1 [GeneID=2335] compared to those grown on laminin 1. 19451229 46/54 Arthur Liberzon 0.000786085249663691 0.00330688269020733 2535 2609.45454545455 2532 7.14878425027921e-05 361 0.934598040997507 1.02557129206342 1 3.47861938276066 2532 2464 3083 2091 361 3846 2488 4471 1828 2550 2990 2681 M8901 LANDIS_ERBB2_BREAST_TUMORS_324_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_324_DN.html Down-regulated genes from the 324 genes identified by two analytical methods as changed in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 203/229 Leona Saunders 3.07479963753085e-05 0.000261026156279597 2535 2491.63636363636 2533 2.79531146625866e-06 417 1.14697096953997 -1.15256155288698 -1 6.16697072560206 2533 2277 417 1488 990 3908 3168 3588 3866 808 4365 2682 M1134 DARWICHE_PAPILLOMA_RISK_LOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_LOW_DN.html Genes down-regulated during skin tumor progression from low risk papilloma vs normal skin. 17525749 213/288 Arthur Liberzon 0.0286596912837792 0.0507389380646563 2635 2434.27272727273 2534 0.00263999993435897 1278 1.2105544571682 1.23026081405688 1 2.35159140899842 2632 2757 1904 3354 1293 3793 3374 2534 1278 1335 2523 2683 M19768 LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT http://www.broadinstitute.org/gsea/msigdb/cards/LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT.html Genes downregulated in MCF10A cells (breast cancer) co-cultured with cancer-associated fibroblasts (CAF). 19074894 132/209 Jessica Robertson 1.08353714527386e-09 2.85714822664393e-08 3790 2364.36363636364 2534 9.85033768915929e-11 114 1.34004775641253 1.31486793130092 1 15.1692673067817 3790 1249 143 676 4332 2534 4459 2952 2008 114 3751 2684 M4210 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_3.html The 'group 3 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 and ERBB2 [GeneID=2099;2064]. 18794137 885/1090 Jessica Robertson 8.83954370377559e-13 3.72523627516257e-11 2535 2160.63636363636 2535 8.83954370377911e-14 53 1.22104833670743 1.17294026088576 1 19.1077047109724 2535 471 4510 209 2852 3317 2514 2807 577 53 3922 2685 M6315 IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_DN.html Cluster 2: genes down-regulated in lung tissue samples from mice with oncogenic form of KRAS [GeneID=3845] and inactivated PTEN [GeneID=5728]. 18281487 443/575 Jessica Robertson 1.80880594601221e-06 2.33905864799388e-05 2675 2556.27272727273 2535 1.64437039380561e-07 300 1.17946653584371 1.15357265762991 1 8.19582637752324 2674 2223 300 2535 1533 4571 3530 2227 3555 336 4635 2686 M530 REACTOME_NEGATIVE_REGULATION_OF_FGFR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEGATIVE_REGULATION_OF_FGFR_SIGNALING.html Genes involved in Negative regulation of FGFR signaling 29/49 Reactome 0.0162042776419293 0.0321632424179588 1505 2292.81818181818 2537 0.00148407972756229 361 1.09285596717495 0.997741781605326 1 2.44760361445924 1501 3835 3002 3661 2537 655 361 3808 1693 3387 781 2687 M942 REACTOME_REGULATION_OF_IFNG_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_IFNG_SIGNALING.html Genes involved in Regulation of IFNG signaling 18/20 Reactome 0.149931316810398 0.202424432306945 3740 2575.72727272727 2538 0.0146586037052982 252 0.928551819791004 -1.05806347234237 -1 0.966485413707895 3739 2086 2901 1565 2067 3942 4169 2538 252 2531 2543 2688 M17211 YEMELYANOV_GR_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YEMELYANOV_GR_TARGETS_DN.html Transcription factors down-regulated in LNCaP cells (prostate cancer) by expression of GR [GeneID=2908] off a lentiviral vector. 17016446 19/26 Aravind Subramanian 0.00045774515778134 0.00215839874598194 2470 2455.72727272727 2538 4.1621856975348e-05 295 1.0066795795079 1.03815836781163 1 4.02680266728231 2467 2599 2347 2476 295 2538 1474 4323 2729 2608 3157 2689 M11031 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_LD_MTX_UP.html Genes specifically up-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and low-dose methotrexate (LDMTX) [PubChem=4112]. 12704389 15/18 Jean Junior 0.00426750752956362 0.0117312961791149 2540 2148 2538 0.0003887098263066 436 0.539271288511639 0.582569602477417 1 1.56215504580555 2538 1023 3619 1062 667 2852 3127 893 436 4673 2738 2690 M9823 REN_MIF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/REN_MIF_TARGETS_DN.html Genes down-regulated in SK-N-DZ cells (neuroblastoma) after knockdown of MIF [GeneID=4282] by antisense RNA. 16449971 7/9 Leona Saunders 0.0281719842700769 0.050253879725912 3815 2519 2539 0.00285356369780278 50 1.32279259716269 -1.822735044262 -1 2.57791255893015 3812 2677 4403 2382 2539 3390 1885 918 50 2477 3176 2691 M116 BILD_SRC_ONCOGENIC_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/BILD_SRC_ONCOGENIC_SIGNATURE.html Genes selected in supervised analyses to discriminate cells expressing c-Src (CSK) [GeneID=1445] from control cells expressing GFP. 16273092 100/109 Arthur Liberzon 0.132935077686288 0.182984417229303 2540 2555.09090909091 2539 0.0128836876161759 1304 1.2158865821232 -1.18184129799776 -1 1.34559176615288 2539 1304 1599 1647 1992 3563 2981 3003 3459 1953 4066 2692 M2366 PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_UP.html Genes up-regulated in HEK-293 cells (fibroblast) upon knockdown of CTBP1 but not of SATB1 [GeneID=1487, 6304] by RNAi. 19103759 488/737 Arthur Liberzon 0.225382178938807 0.285922373936904 2260 2461.54545454545 2541 0.0229494264213825 1788 1.10698206718781 1.1446096360471 1 0.903092549351051 2256 2710 1788 2725 2541 2913 2258 1883 3047 2068 2888 2693 M2471 TIAN_BHLHA15_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TIAN_BHLHA15_TARGETS.html Genes up-regulated in both AGS and HGC-27 cells (gastric cancer) by BHLHA15 [GeneID=168620] transfection. 20038531 18/22 Arthur Liberzon 0.00577426225782821 0.0142024584976285 4490 2359.36363636364 2542 0.000526315789473684 124 1.0337723166573 -1.02078291563599 -1 2.86594067491187 4488 375 2212 124 1220 3138 4535 2697 391 2542 4231 2694 M14590 AIGNER_ZEB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/AIGNER_ZEB1_TARGETS.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of ZEB1 [GeneID=6935] by RNAi. 17486063 43/55 Leona Saunders 0.179500227766635 0.23586889617442 3680 2887 2543 0.0178248285324728 1320 1.40499396264827 -1.38729408446641 -1 1.32244342993511 3676 2475 1320 2543 4595 2107 4172 2992 4197 1413 2267 2695 M16075 WANG_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in LNCaP cells (prostate cancer) treated with synthetic androgen R1881 [PubChem=13766]. 16751804 39/55 Arthur Liberzon 1.35627970165284e-05 0.000133645933022994 2965 2340 2544 1.23298914824021e-06 32 0.848353824201092 0.914199069060429 1 4.9314437953019 2961 229 2544 1452 32 4290 3284 2099 1998 3199 3652 2696 M4786 OKAWA_NEUROBLASTOMA_1P36_31_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/OKAWA_NEUROBLASTOMA_1P36_31_DELETION.html Genes in the smallest region of deletion (SRD) in 1p36.3 area in neuroblastoma samples. 17667943 22/25 Jessica Robertson 0.0873598797334157 0.128815567741869 3280 2281.18181818182 2545 0.00827589636347411 313 1.24705879873532 -1.32756771093808 -1 1.66535410480707 3276 3479 2709 2545 1931 2058 3234 1365 313 2883 1300 2697 M16256 ZHAN_EARLY_DIFFERENTIATION_GENES_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_EARLY_DIFFERENTIATION_GENES_UP.html B lymphocyte early differentiation genes (EDG): top genes up-regulated in tonsil B lymphocytes (TBC) compared to the tonsil plasma cells (TPC). 12393520 7/7 Arthur Liberzon 0.102156695109654 0.146648297116048 2250 2968.45454545455 2545 0.0107181191422253 1483 1.61712124620441 -1.61712124620441 -1 2.02294205148679 2247 4639 4615 3561 3350 2404 2335 1483 2110 3364 2545 2698 M1809 MATZUK_CUMULUS_EXPANSION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_CUMULUS_EXPANSION.html Genes important for cumulus expansion, based on mouse models with female fertility defects. 18989307 7/10 Jessica Robertson 1.36121225914973e-05 0.00013385253881639 3865 2214 2546 1.36122059726627e-06 35 2.13635103197104 2.01568517635489 1 12.4165255312506 3865 1631 4565 491 35 3057 2654 2546 223 691 4596 2699 M2068 ONGUSAHA_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ONGUSAHA_BRCA1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) lacking TP53 and BRCA1 [GeneID=7157;672] by expression of BRCA1. 12802282 26/28 Arthur Liberzon 0.00578934968778342 0.0142321513158009 1250 2560.72727272727 2546 0.00052769462333274 742 0.884111434843823 0.809852037978295 1 2.44981522871147 1250 2546 2779 2367 742 1720 1644 3731 4028 3952 3409 2700 M2477 ALFANO_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ALFANO_MYC_TARGETS.html Genes up-regulated hT-RPE cells (immortalized retinal pigment epithelium) by MYC [GeneID=4609]. 20123981 362/489 Arthur Liberzon 0.395257938127785 0.464546182261739 2830 2537.63636363636 2547 0.0446934767643669 1602 1.02711334945201 1.09811484528423 1 0.513070635284398 2827 2234 2287 1602 2661 2138 3296 2547 2418 2587 3317 2701 M9880 ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/ABRAHAM_ALPC_VS_MULTIPLE_MYELOMA_DN.html Genes down-regulated in immunoglobulin light chain amyloidosis plasma cells (ALPC) compared to multiple myeloma (MM) cells. 15388584 25/26 Kevin Vogelsang 0.00035848612820931 0.00180582126483238 3640 2352 2549 3.25949596565885e-05 217 0.807920339919072 -0.827766805950789 -1 3.32562923397064 3640 937 3219 408 251 3682 4266 4496 217 2207 2549 2702 M3268 CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP.html Top 200 marker genes up-regulated in the 'proliferation' subclass of hepatocellular carcinoma (HCC); characterized by increased proliferation, high levels of serum AFP [GeneID=174], and chromosomal instability. 18701503 212/260 Yujin Hoshida 0.669979151771311 0.690284310838704 2035 2832.27272727273 2549 0.0958696786437992 1209 1.18726789748733 -1.22667216544992 -1 0.286668893569095 2035 3996 2549 2370 4717 2539 3102 4226 1209 1712 2700 2703 M2179 FIGUEROA_AML_METHYLATION_CLUSTER_7_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_7_UP.html Cluster 7 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 154/215 Arthur Liberzon 0.0308565889954396 0.0538276303587477 2505 2611.36363636364 2551 0.00284527896016218 1328 0.993848986855706 0.918040507996227 1 1.89233378042558 2501 2780 2724 2376 1328 2551 2127 3363 2475 3427 3073 2704 M2332 BILANGES_SERUM_SENSITIVE_VIA_TSC1 http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_SENSITIVE_VIA_TSC1.html Genes translationally up-regulated by serum in MEF cells (embryonic fibroblast) lacking TSC1 [GeneID=7248]. 17562867 27/35 Arthur Liberzon 0.00736865402206061 0.0171414721459468 2555 2788.36363636364 2551 0.000672131896268396 812 0.974750055768419 -1.03831094617822 -1 2.58283194309715 2551 3438 1892 3998 812 2510 1422 3393 4515 2377 3764 2705 M592 REACTOME_ACTIVATED_NOTCH1_TRANSMITS_SIGNAL_TO_THE_NUCLEUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_NOTCH1_TRANSMITS_SIGNAL_TO_THE_NUCLEUS.html Genes involved in Activated NOTCH1 Transmits Signal to the Nucleus 30/38 Reactome 0.0582748832455085 0.0916552645514163 3815 2702 2552 0.0054434807363442 1187 1.35116950627273 -1.52997094524765 -1 2.10407534466731 3811 3418 1900 2552 2309 3411 4584 1187 3352 1465 1733 2706 M704 REACTOME_SIGNALING_BY_FGFR_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR_MUTANTS.html Genes involved in Signaling by FGFR mutants 41/63 Reactome 0.108085445336954 0.153941853346536 1970 2316.27272727273 2552 0.010344752219191 225 0.884009529403503 0.787108975655555 1 1.07784439909114 1966 225 2552 893 4605 2623 1005 4339 954 2944 3373 2707 M62 PID_EPHB_FWD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_EPHB_FWD_PATHWAY.html EPHB forward signaling 18832364 66/76 Pathway Interaction Database 0.635791113262311 0.690284310838704 2015 2149.81818181818 2553 0.0877312962747066 501 1.01253817754527 1.15552327210679 1 0.244464377772629 2013 760 2933 645 3507 3078 2288 2674 501 2696 2553 2708 M5872 KEGG_STEROID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_BIOSYNTHESIS.html Steroid biosynthesis 19/21 KEGG 0.125556128207419 0.174815612135404 4140 2386.63636363636 2554 0.0121229333413548 20 1.79624746022105 -1.17309155998167 -1 2.04137177990844 4139 1530 1236 699 2704 3161 4593 2554 20 1271 4346 2709 M285 PID_HNF3A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HNF3A_PATHWAY.html FOXA1 transcription factor network 18832364 35/84 Pathway Interaction Database 0.00467013897222926 0.0126176622489537 2585 2202.63636363636 2554 0.000425462023791515 100 1.26662132728663 -1.37259034304286 -1 3.60915605822475 2583 1461 1935 1836 2851 2624 3616 372 4297 2554 100 2710 M73 TAKAO_RESPONSE_TO_UVB_RADIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/TAKAO_RESPONSE_TO_UVB_RADIATION_UP.html Genes up-regulated in primary tissue culture of epidermal kerationcytes after UVB irradiation. 11982916 112/160 John Newman 0.22302086687745 0.283353564377272 2010 2625.54545454545 2554 0.0226790372821084 1814 0.865769305243951 -0.755311662208697 -1 0.711376293775988 2007 1814 3582 2928 2302 2044 2694 2047 2570 4339 2554 2711 M15514 REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSMISSION_ACROSS_CHEMICAL_SYNAPSES.html Genes involved in Transmission across Chemical Synapses 149/243 Reactome 0.0794149655964909 0.118873586898774 4005 2545.63636363636 2556 0.00749413281468221 1103 1.08880505632665 -1.1632808010193 -1 1.51099550161808 4001 1245 1149 1103 2556 3074 3847 3065 3380 2523 2059 2712 M3169 RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/RORIE_TARGETS_OF_EWSR1_FLI1_FUSION_UP.html ES/PNET (Ewing sarcoma; primitive neuroectodermal tumors) markers up-regulated in neuroblastoma cell lines expressing ESWR1-FLI1 [GeneID=2130;2313] fusion protein. 14973077 52/73 Kevin Vogelsang 0.0124587580528574 0.0259988287465373 2500 2884.09090909091 2557 0.00113907976301293 590 1.13762786248274 1.41915263250858 1 2.70562106577405 2499 4108 2221 4444 1205 4404 3486 590 4266 2557 1945 2713 M997 REACTOME_ION_CHANNEL_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ION_CHANNEL_TRANSPORT.html Genes involved in Ion channel transport 33/63 Reactome 0.43119990772354 0.499814448548158 4275 2568.63636363636 2558 0.05 292 1.20119526834619 -1.27223539306674 -1 0.542766482501376 4272 292 1699 2306 4353 3849 2558 2759 1161 1672 3334 2714 M1113 GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_UP.html Up-regulated genes from the set C (Fig. 5a): specific to cells expressing AF4-MLL [GeneID=4299;4297] fusion protein alone. 17130830 226/262 Arthur Liberzon 0.561851886483688 0.629018241034869 2710 2609.18181818182 2559 0.0722732354270407 1212 1.08259578570985 1.08424592137262 1 0.326957021905093 2710 1212 1886 1321 3618 3564 2723 2553 2354 2559 4201 2715 M18213 WANG_BARRETTS_ESOPHAGUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_BARRETTS_ESOPHAGUS_DN.html Genes down-regulated in Barrett's esophagus compared to the normal tissue. 16449976 33/44 Arthur Liberzon 0.00330531177448103 0.00979941394983266 3640 2823.81818181818 2559 0.000300935290280057 289 1.29526378265299 -1.65909790029739 -1 3.90413598134567 3638 2520 1750 4202 3657 2491 3281 289 4269 2406 2559 2716 M1587 YIH_RESPONSE_TO_ARSENITE_C4 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C4.html Genes in cluster 4: immediate down-regulation in HFW cells (fibroblast) by sodium arsenite [PubChem=26435]. 12016162 24/28 John Newman 0.0806802844930523 0.120395492509392 2500 2655.27272727273 2561 0.00761822600891942 525 1.33990033008531 -1.32888856450686 -1 1.84837082941405 2496 3469 2445 3618 4043 2561 2473 4191 525 2567 820 2717 M2511 ZHANG_ADIPOGENESIS_BY_BMP7 http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_ADIPOGENESIS_BY_BMP7.html Genes up-regulated in C3H10T1/2 cells (mesenchyme multipotent cells) upon their differentiation to brown adipocytes in response to BMP7 [GeneID=655]. 20584981 24/30 Arthur Liberzon 0.0698662554007891 0.106792055984307 2750 2334.45454545455 2561 0.00656263412584236 1262 0.820696776626078 0.85840379310464 1 1.19622124150074 2747 2561 2980 1650 3130 3506 1596 1262 1580 2569 2098 2718 M906 REACTOME_AMINO_ACID_SYNTHESIS_AND_INTERCONVERSION_TRANSAMINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINO_ACID_SYNTHESIS_AND_INTERCONVERSION_TRANSAMINATION.html Genes involved in Amino acid synthesis and interconversion (transamination) 19/20 Reactome 0.484733493259643 0.554383835276355 2565 2168.81818181818 2562 0.0584983552510532 292 1.09077166666813 -1.3273672447765 -1 0.419205778433969 2562 990 2230 960 2785 2810 3019 3182 292 2606 2421 2719 M8213 LEE_INTRATHYMIC_T_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/LEE_INTRATHYMIC_T_PROGENITOR.html Genes enriched in the intrathymic T progenitor (ITTP) cells compared to all other T lymphocyte differentiation stages. 15210650 38/63 Arthur Liberzon 0.106706774508306 0.152421112367631 2360 2788.27272727273 2562 0.0102057813943902 1207 1.14014415545594 1.2306762231101 1 1.39754807448397 2356 3369 1207 3314 4459 2687 2537 2496 2562 2384 3300 2720 M17331 ALONSO_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_DN.html Down-regulated genes in melanoma tumors that developed metastatic disease compared to primary melanoma that did not. 17409456 25/41 Jessica Robertson 0.0171411542388279 0.0335233730975435 1590 2353.09090909091 2563 0.00157056214764382 531 1.12226655087084 1.17059156871179 1 2.48318426969601 1588 2563 910 4174 2950 531 1177 3792 4405 3137 657 2721 M2020 MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED.html Genes with high-CpG-density promoters (HCP) with unmethylated histone H3 in MEF cells (embryonic fibroblast). 17603471 171/480 Arthur Liberzon 4.53087281228022e-08 8.98559650166497e-07 2565 2265.09090909091 2563 4.11897536872089e-09 197 1.45696845449279 1.21309007688677 1 13.2187128290768 2563 3203 197 3480 1464 1203 2632 4340 1952 472 3410 2722 M16173 BIOCARTA_PS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PS1_PATHWAY.html Presenilin action in Notch and Wnt signaling 24/27 BioCarta 0.57227975738829 0.639479274354339 2260 2372.45454545455 2564 0.0743025377504148 347 0.859400938131893 0.829738980049897 1 0.250290323985237 2259 950 3275 581 4385 2484 2564 2568 347 3498 3186 2723 M18647 REACTOME_STRIATED_MUSCLE_CONTRACTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_STRIATED_MUSCLE_CONTRACTION.html Genes involved in Striated Muscle Contraction 24/48 Reactome 0.0143926215291851 0.0292689244367746 3780 2626 2564 0.00131705918414323 1031 1.15276747975543 -1.39084882841211 -1 2.65262820517943 3778 3849 2246 2635 1031 2376 2815 2513 2675 2564 2404 2724 M991 REACTOME_TRANSFERRIN_ENDOCYTOSIS_AND_RECYCLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSFERRIN_ENDOCYTOSIS_AND_RECYCLING.html Genes involved in Transferrin endocytosis and recycling 24/29 Reactome 0.125789415279537 0.175037158054073 2350 2428.36363636364 2566 0.0121468952618514 407 1.06975014658381 1.38466195632033 1 1.21480753559561 2348 2063 2772 3330 3711 3485 3094 1869 407 2566 1067 2725 M12527 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN.html Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs poorly differentiated tumors. 18679425 505/587 Jessica Robertson 0.107137215801515 0.152821897426156 2015 2674.27272727273 2566 0.0112682687693932 1011 1.14419858138254 1.0740458318757 1 1.40056017258559 2011 2215 4440 2827 4065 1553 2405 2566 3290 1011 3034 2726 M1454 NUMATA_CSF3_SIGNALING_VIA_STAT3 http://www.broadinstitute.org/gsea/msigdb/cards/NUMATA_CSF3_SIGNALING_VIA_STAT3.html Target genes for STAT3 [GeneID=20848] in CSF3 [GeneID=12985] signaling during myeloblast differentiation to neutrophils. 15664994 26/36 Kevin Vogelsang 0.0104802194684478 0.022659933985833 3580 2604.81818181818 2566 0.000957316362602788 548 1.41086436731732 -1.26733565071552 -1 3.48186146244829 3576 4164 1673 2292 1194 3353 3946 548 3060 2281 2566 2727 M15898 KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM.html Fructose and mannose metabolism 36/41 KEGG 0.000990865842463865 0.00394945844606755 2570 2237.18181818182 2567 9.01193094243485e-05 269 1.19479742243588 -1.32088777201707 -1 4.30886374085658 2567 3802 3355 3577 396 979 2587 2327 269 3028 1722 2728 M4960 SMID_BREAST_CANCER_BASAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_BASAL_DN.html Genes down-regulated in basal subtype of breast cancer samles. 18451135 858/1156 Jessica Robertson 9.99740592231108e-19 8.4263849916622e-17 4500 2542.72727272727 2567 9.9974059223111e-20 17 1.28895142969234 -1.3055847148565 -1 31.0892709602668 4499 1121 4554 17 3152 2567 4526 3494 2052 24 1964 2729 M1977 ONO_AML1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONO_AML1_TARGETS_UP.html Genes up-regulated in CD4+ [GeneID=920] T lymphocytes by expression of AML1 [GeneID=861] off a viral vector. 17377532 16/29 Jessica Robertson 0.00498801062776663 0.0132938510237484 1370 2343.09090909091 2568 0.000454486896418529 108 1.07288724845204 -1.07288724845204 -1 3.02060781197185 1370 4236 2568 4001 3904 470 608 666 4367 3476 108 2730 M4308 SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1 http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_1.html Genes up-regulated in the pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 12839967 527/867 John Newman 1.39698232920157e-06 1.86482454322945e-05 1720 2447.72727272727 2569 1.39698320740418e-07 181 1.30005526387661 1.24906606785328 1 9.22573977070043 1717 3160 4499 2606 1723 2464 2270 2569 2881 181 2855 2731 M11548 AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_8G http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_8G.html Genes with basal expression distinguishing NCI-60 cell lines with poor survival after 8 Gy gamma irradiation. 18199535 134/152 Jessica Robertson 0.049965225183158 0.080738056441118 4110 2677.27272727273 2569 0.0046488595348269 541 1.10576231479209 1.20089464260729 1 1.81329014032473 4108 627 1880 541 1520 3870 3777 4691 2569 1815 4052 2732 M7090 TOMLINS_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_METASTASIS_DN.html Top genes down-regulated in hormone refractory metastatic prostate cancer compared to localized prostate cancer. 17173048 29/35 Leona Saunders 0.00284909540811609 0.00869277978429733 2570 1907.72727272727 2570 0.000259344710343052 263 0.955636667146023 -1.115560334147 -1 2.95504170311046 2570 322 2578 3082 1206 2758 3272 263 1193 3390 351 2733 M12469 REACTOME_HIV_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIV_INFECTION.html Genes involved in HIV Infection 235/285 Reactome 0.11555815792785 0.162962206578862 920 2420.09090909091 2571 0.0111014211468883 919 0.700390285511987 -0.642688843103765 -1 0.827951195779171 919 2751 4161 2794 3557 1072 1030 1799 2571 4448 1519 2734 M135 PID_IL5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL5_PATHWAY.html IL5-mediated signaling events 18832364 22/23 Pathway Interaction Database 0.244373728982653 0.305998658047696 2410 2652.45454545455 2573 0.025151776868987 1447 1.08859984316915 0.910858866697362 1 0.839953802300119 2407 2573 2162 3148 2829 1764 1447 2550 4586 2877 2834 2735 M1187 HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_MITOTIC_ARREST_BY_DOCETAXEL_1_DN.html Genes down-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing mitotic arrest and apoptosis after treatment with 100 nM docetaxel [PubChem=148124]. 17099726 57/85 Arthur Liberzon 0.132731046792532 0.182810195757442 4330 2747.63636363636 2574 0.0128625734706252 1249 1.30893002651447 -1.46591881424439 -1 1.44938128060315 4329 1915 1249 1865 3939 3220 4087 2574 3093 1666 2287 2736 M1199 TERAMOTO_OPN_TARGETS_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_4.html Cluster 4: genes whose up-regulation peaked 4 days after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 30/33 Arthur Liberzon 0.0147606792806021 0.0298617253421183 455 2354.36363636364 2574 0.00135096863042304 453 1.25524308358723 1.33760430674167 1 2.87204185572343 453 3439 1489 3675 1039 2574 2627 1969 4540 2595 1498 2737 M581 ZIRN_TRETINOIN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_UP.html Genes up-regulated in MS427 cells (Wilms tumor with normal WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 22/25 Leona Saunders 0.00110415009540077 0.00428937321011659 2885 2599.36363636364 2575 0.000100427694819268 415 1.28209694269298 1.2675998664475 1 4.55472378008561 2885 2575 1763 1743 415 4266 3762 3450 2295 1920 3519 2738 M15936 NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_17Q21_Q25_AMPLICON.html Genes within amplicon 17q21-q25 identified in a copy number alterations study of 191 breast tumor samples. 19010930 351/497 Jessica Robertson 0.0248391014492489 0.0452841092469892 3300 2346.81818181818 2576 0.00228400563019592 690 1.07687126553617 -1.07076043049416 -1 2.17170687946558 3296 1702 1946 2576 1224 690 3251 3434 3124 3118 1454 2739 M6335 AUJLA_IL22_AND_IL17A_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/AUJLA_IL22_AND_IL17A_SIGNALING.html Genes changed in HBE cells (bronchial epithelium) after treatment with IL22 and IL17A [GeneID=50616;3605]. 18264110 9/19 Jessica Robertson 0.289201774046266 0.353452194070009 1215 2749 2576 0.033560585590214 1211 1.88949701672915 1.58584265720689 1 1.28047975715785 1211 4265 4563 4036 2576 2161 1628 3124 2541 1448 2686 2740 M18438 LEE_LIVER_CANCER_E2F1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_E2F1_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) induced by overexpression of E2F1 [GeneID=1869]. 15565109 90/147 Yujin Hoshida 6.41043632550307e-06 6.89231422696457e-05 1085 2291 2577 5.82768636775548e-07 350 1.38902606070418 1.33459633505717 1 8.6738295536095 1085 3252 350 3161 2051 3225 2577 2414 3259 466 3361 2741 M7715 FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_DN.html Top 100 genes negatively associated with T-cell acute lymphoblastic leukemia MLL T-ALL) expressing MLL-ENL fusion [GeneID=4297;4298]. 12637319 106/152 Kevin Vogelsang 0.68618940391 0.690284310838704 2225 2362.90909090909 2577 0.1 670 0.98217955066719 -0.925041887612733 -1 0.237131503044392 2223 670 3378 1605 3413 2393 2709 2947 960 3117 2577 2742 M2033 TRACEY_RESISTANCE_TO_IFNA2_UP http://www.broadinstitute.org/gsea/msigdb/cards/TRACEY_RESISTANCE_TO_IFNA2_UP.html Genes up-regulated in huT78R cells (cutaneous T-cell lymphoma, CTCL) resistant to IFNA2 [GeneID=3440] compared to the IFN2A sensitive parental cell line. 12414529 5/7 Arthur Liberzon 0.0875475878770005 0.129011743608942 3035 2337.36363636364 2577 0.009120091959568 735 1.75486375701808 -1.83222596798952 -1 2.34179261374673 3033 2687 4651 735 1804 2577 2820 4192 744 1326 1142 2743 M18841 MULLIGHAN_MLL_SIGNATURE_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_1_DN.html The 'MLL signature 1': genes down-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to all AML cases with the intact gene. 17597811 296/408 Arthur Liberzon 0.00135692124075236 0.0049533397187557 3250 2426.18181818182 2578 0.000123432626296591 645 1.17833653568655 -1.12315148312343 -1 4.07558543106367 3246 1712 645 1989 2087 3135 2895 3822 2578 767 3812 2744 M11121 REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PLC_BETA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_BETA_GAMMA_SIGNALLING_THROUGH_PLC_BETA.html Genes involved in G beta:gamma signalling through PLC beta 16/23 Reactome 0.0166346548467069 0.0327421062870962 2520 2429.09090909091 2579 0.00152379824353278 677 0.975882562732325 -0.927656997151994 -1 2.17427013890131 2517 3507 2380 2601 1559 2579 2997 677 3772 2890 1241 2745 M1637 NIELSEN_LEIOMYOSARCOMA_CNN1_UP http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_CNN1_UP.html Top 20 positive significant genes associated with leiomyosarcoma tumors expressing muscle gene cluster with CNN1 [GeneID=1264]. 11965276 26/32 John Newman 0.00145034218990719 0.00524166549491726 1970 2380.90909090909 2579 0.000131936291476102 653 1.51940054435708 1.30615508088471 1 5.19925560670234 1968 3841 653 2579 2609 2541 3473 1192 3701 682 2951 2746 M12848 CASTELLANO_NRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_NRAS_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) isolated from NRAS [GeneID=4893] knockout mice. 16909116 22/24 Leona Saunders 0.374992850744803 0.443482504398213 4430 2699.81818181818 2580 0.04182664548496 1052 1.15452067426102 -1.14643724269392 -1 0.611638785244493 4426 2580 1920 1052 3321 2734 4398 2230 2139 1531 3367 2747 M18517 MATSUDA_NATURAL_KILLER_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/MATSUDA_NATURAL_KILLER_DIFFERENTIATION.html Genes changed between developmental stages of Valpha14i natural killer T lymphocyte cells (NKT). 16357323 614/792 Kevin Vogelsang 0.0129408671981282 0.0267467447087803 2580 2701.90909090909 2580 0.00130168504111577 492 1.22639191031908 1.29176400484617 1 2.89407058013629 2580 492 4482 1883 3791 4627 3761 2021 2104 635 3345 2748 M2186 PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_DN http://www.broadinstitute.org/gsea/msigdb/cards/PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_DN.html Genes down-regulated in ovarian tumors from mouse models for the BMP SMAD signaling (gonad specific double knockout of SMAD1 and SMAD5 [GeneID=4086, 4090]). 17967875 192/257 Arthur Liberzon 0.00577426225782821 0.0142024584976285 4175 2460.09090909091 2580 0.000526315789473684 143 1.07287422594522 -1.05052294602689 -1 2.97434741840305 4175 578 2288 143 1004 3232 4588 3805 3037 1631 2580 2749 M11787 GRADE_COLON_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_CANCER_DN.html Down-regulated genes in colon carcinoma tumors compared to the matched normal mucosa samples. 17210682 44/64 Jessica Robertson 0.0143522019454485 0.0292245009415516 3480 2464.90909090909 2581 0.00131333599807064 532 1.48736176383231 -1.52615659993816 -1 3.42406460504384 3479 1436 1142 532 4208 3517 2581 3706 1599 638 4276 2750 M3656 REACTOME_UNWINDING_OF_DNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNWINDING_OF_DNA.html Genes involved in Unwinding of DNA 11/11 Reactome 0.212137428367464 0.272219025963057 770 2488 2582 0.0214423728555885 767 0.671348973520444 -0.671348973520444 -1 0.569141821162438 767 2644 3208 1618 2582 2088 1358 2517 3248 4608 2730 2751 M14812 SEMBA_FHIT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SEMBA_FHIT_TARGETS_UP.html Genes up-regulated in H1299 cells (non-small cell lung cancer, NSCLC) expressing the Y144F mutant form of FHIT [GeneID=2272]. 16407838 30/40 Leona Saunders 0.09185116850782 0.13426370868904 745 2608.72727272727 2583 0.00872057170389852 742 1.03350469468909 1.09563727953916 1 1.3522511493516 742 3423 1610 4288 1785 2583 2610 2249 4547 2596 2263 2752 M2601 WARTERS_IR_RESPONSE_5GY http://www.broadinstitute.org/gsea/msigdb/cards/WARTERS_IR_RESPONSE_5GY.html Genes up-regulated in the human skin cells at 4 h after exprosure to 5 Gy dose of ionizing radiation. 19580510 54/90 Itai Pashtan 0.0598725435075177 0.0937619128584882 1595 2667.81818181818 2583 0.00559698915605609 764 0.996702218835084 1.01261296502113 1 1.53730229023877 1593 4101 2583 4569 4509 1084 764 1281 3419 3000 2443 2753 M4035 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_UP.html Genes from the red module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 20/21 Arthur Liberzon 0.0365541856906853 0.0617301454239838 1965 2452.18181818182 2584 0.00337964257167292 990 1.28654048205087 1.20316961775734 1 2.3348147179153 1961 2584 1522 1781 4372 2645 2273 990 3263 2712 2871 2754 M15542 BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_UP.html Genes up-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes are independent of ATM [GeneID=472] signaling. 18849970 74/103 Jessica Robertson 0.0715267978305675 0.10872994710476 3655 2848.27272727273 2584 0.00672399753642354 1188 1.10209902741098 -1.01731957468236 -1 1.59350445810887 3654 2405 2584 2298 1671 4407 2893 4260 1188 1746 4225 2755 M1309 GROSS_HYPOXIA_VIA_HIF1A_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_HIF1A_DN.html Genes down-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 142/182 Jessica Robertson 0.0263381213172549 0.0475032222458705 2975 2658.81818181818 2585 0.00242352965777489 1116 1.10931987068642 -1.14907173283292 -1 2.20256369053273 2975 2314 1512 2585 1248 3781 2670 3887 2460 1116 4699 2756 M11932 REACTOME_TIE2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TIE2_SIGNALING.html Genes involved in Tie2 Signaling 21/24 Reactome 0.012071301290054 0.0253004183343938 3770 2743.45454545455 2586 0.00110345902595092 982 1.03812909459787 0.971462281808607 1 2.4873957105555 3768 2586 2495 2198 982 4182 2511 2664 2222 2797 3773 2757 M6311 ODONNELL_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_METASTASIS_DN.html Down-regulated genes in the signature set for lymph node metastasis in head and neck squamous cell carcinoma (HNSCC). 15558013 31/40 Leona Saunders 0.238618815504634 0.299622455222632 3155 2644 2586 0.0244791452677568 1490 1.34464402813541 -1.58061101813824 -1 1.05599195234386 3155 3409 1709 2045 4340 2285 2586 2329 3071 2665 1490 2758 M1249 YU_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YU_MYC_TARGETS_UP.html Genes up-regulated in B cell lymphoma tumors expressing an activated form of MYC [GeneID=4609]. 16382050 49/54 Kevin Vogelsang 0.356137519517152 0.423951851732903 1320 2454.54545454545 2586 0.0392341536426384 609 1.03434167941388 -0.896730170493398 -1 0.578317708771715 1316 2901 3503 1100 2586 2193 2498 3492 609 3902 2900 2759 M1394 BIOCARTA_GATA3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GATA3_PATHWAY.html GATA3 participate in activating the Th2 cytokine genes expression 14/17 BioCarta 0.0851978873850859 0.126245203824895 3385 2549.63636363636 2587 0.0080625498317538 851 0.915809323021287 -0.976468107860831 -1 1.23499592683972 3384 1043 2587 2380 3990 4123 3709 2135 1173 2671 851 2760 M12403 WATANABE_COLON_CANCER_MSI_VS_MSS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_COLON_CANCER_MSI_VS_MSS_UP.html Up-regulated genes discriminating between MSI (microsatellite instability) and MSS (microsatellite stability) colon cancers. 17047040 29/42 Leona Saunders 0.027504889688242 0.0492500300942724 3645 2498.81818181818 2587 0.00253226398386408 1149 0.923658498445162 0.877761291277225 1 1.81217706867082 3641 2027 2654 1845 1272 2587 1565 1149 2734 3389 4624 2761 M13760 HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_UP.html Genes up-regulated during differentiation from small pre-BII to immature B lymphocyte. 11779835 67/90 Arthur Liberzon 0.16919497834222 0.22388570164712 3950 2778.81818181818 2587 0.0167097394022089 1389 1.25575083643228 -1.35668179713876 -1 1.22462607111117 3946 3290 1389 2541 2587 2906 4454 1706 3456 1898 2394 2762 M7955 SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_INSULIN_RECEPTOR_PATHWAY_IN_CARDIAC_MYOCYTES.html Genes related to the insulin receptor pathway 64/82 Signaling Gateway 0.111200193737379 0.157617091423553 2590 2678.27272727273 2588 0.0106594410569043 1479 0.809271270933844 0.779013103840241 1 0.974266767291206 2588 2416 3730 1669 3751 2823 2275 1479 2078 3441 3211 2763 M10064 REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HORMONE_SENSITIVE_LIPASE_HSL_MEDIATED_TRIACYLGLYCEROL_HYDROLYSIS.html Genes involved in Hormone-sensitive lipase (HSL)-mediated triacylglycerol hydrolysis 11/13 Reactome 0.655323044041804 0.690284310838704 2235 2720.63636363636 2588 0.0922911535296548 1057 1.22255017712451 0.960743956437272 1 0.295191035817 2232 1057 2049 2839 3929 2363 2588 4168 3278 3019 2405 2764 M17143 SASSON_RESPONSE_TO_GONADOTROPHINS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_GONADOTROPHINS_DN.html Genes down-regulated in primary granulosa cells after stimulation with LH or FSH gonadotrophic hormones for 24 h. 15026540 151/168 Arthur Liberzon 0.053346564148205 0.0852966743833088 2905 2738 2588 0.00497143881579997 1539 0.984054969978727 1.02892366922443 1 1.57847366798849 2905 1774 2182 1933 1539 4590 3885 1991 2668 2588 4063 2765 M16845 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_12 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_12.html Amplification hot spot 12: colocolized fragile sites and cancer genes in the 17q11.1-q21; 17q25 region. 16751803 14/14 Arthur Liberzon 0.38563699862658 0.454256709138372 3320 2210.27272727273 2590 0.0433217202181982 35 1.01780012392781 -0.946311320710278 -1 0.523273663803529 3320 407 2590 383 2644 4342 2734 3544 35 2078 2236 2766 M18326 WILLIAMS_ESR2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILLIAMS_ESR2_TARGETS_UP.html Genes uniquely up-regulated in T47D cells (breast cancer) by induction of ESR2 [GeneID=2100] expression in the Tet-Off system. 17700529 47/70 Jessica Robertson 0.0263976020592523 0.0475923154009437 3455 2774.36363636364 2590 0.00242906996416221 861 1.1752293535858 1.48247196410282 1 2.33199875950878 3454 3346 1953 3322 2104 4516 3732 861 2210 2590 2430 2767 M7641 ZIRN_TRETINOIN_RESPONSE_WT1_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZIRN_TRETINOIN_RESPONSE_WT1_DN.html Genes down-regulated in MZ128 cells (Wilms tumor with mutated WT1 [GeneID=7490]) after treatment with 10 microM tretinoin (ATRA) [PubChem=444795] for 24 h. 15897880 25/46 Leona Saunders 0.018001994331179 0.0348378078077756 2130 2471.54545454545 2592 0.00165009178242685 714 1.18766234140801 1.30162858330933 1 2.59812170529312 2126 3858 2055 3801 1184 2779 1241 714 4188 2649 2592 2768 M1471 AFFAR_YY1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/AFFAR_YY1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) expressing ~25% of YY1 [GeneID=7528]. 16611997 284/397 Kevin Vogelsang 0.000320523837121774 0.00166290464454478 2405 2421.54545454545 2593 2.91427767833838e-05 550 1.32662712974797 1.38485107234409 1 5.53212076333079 2403 3174 550 2851 2221 1750 2593 3485 3065 881 3664 2769 M169 PID_INTEGRIN2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN2_PATHWAY.html Beta2 integrin cell surface interactions 18832364 24/38 Pathway Interaction Database 0.000594050916805006 0.00263278903973674 2195 2517.81818181818 2594 5.40192168151547e-05 582 1.93259870651718 1.6405138822767 1 7.48043774671253 2191 3856 582 3556 1078 2802 2546 4218 3237 1036 2594 2770 M17287 LIU_SOX4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_SOX4_TARGETS_DN.html Genes down-regulated in LNCaP cells (prostate cancer) by overexpression of SOX4 [GeneID=6659] and up-regulated by its RNAi knockdown. 16618720 412/471 Arthur Liberzon 0.409528371576875 0.479437159440884 3505 2817.54545454545 2594 0.0467651486262589 652 0.873585274340938 -0.868511107227375 -1 0.418401362887301 3504 1693 4137 652 4369 2381 3499 2594 1899 4354 1911 2771 M4357 XU_CREBBP_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_CREBBP_TARGETS_DN.html Genes down-regulated in pro-B lymphocytes after knockout of CREBBP [GeneID=1387]. 16424387 67/87 Kevin Vogelsang 0.232784749667306 0.293389591035964 2595 2527.09090909091 2595 0.0238019636580747 749 1.05928671934973 -1.06933323949228 -1 0.846380690226687 2595 749 1795 868 4697 3606 3775 3753 912 1227 3821 2772 M6712 ROVERSI_GLIOMA_LOH_REGIONS http://www.broadinstitute.org/gsea/msigdb/cards/ROVERSI_GLIOMA_LOH_REGIONS.html Genes in the most frequently heterozygous deleted loci of a panel of glioma cell lines. 16247447 63/83 Arthur Liberzon 0.0644969633732096 0.0997462867370738 2600 2597.54545454545 2596 0.00604265900717815 1118 1.2536848357668 -1.23891488692374 -1 1.88314886358405 2596 1895 1118 1797 4116 3630 2717 3959 1202 1708 3835 2773 M1674 JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP.html Genes up-regulated in H460 cells (non-small cell lung carcinoma, NSCLC) after treatment with sodium butyrate [PubChem=5222465]. 15318170 44/58 John Newman 0.00786287667598626 0.01799843739605 3940 2931 2596 0.000717374572168329 833 1.01442302723505 -1.12883849708682 -1 2.65570964904668 3937 2471 2542 2416 833 2776 2596 2220 4432 3765 4253 2774 M3444 REACTOME_TRANSMEMBRANE_TRANSPORT_OF_SMALL_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSMEMBRANE_TRANSPORT_OF_SMALL_MOLECULES.html Genes involved in Transmembrane transport of small molecules 304/475 Reactome 1.31073690762816e-06 1.77180864221409e-05 3035 2287.54545454545 2597 1.19157971686554e-07 289 1.22906454520791 -1.16594403265646 -1 8.76293501386117 3035 540 289 1171 3312 2597 3039 4487 1953 296 4444 2775 M2557 HOLLEMAN_DAUNORUBICIN_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_B_ALL_DN.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 19/21 Arthur Liberzon 0.000306723837892976 0.00161758269816184 3295 2482.81818181818 2597 2.78878736051471e-05 225 0.826312251724661 -0.971574367038004 -1 3.46061535150231 3295 2597 3606 2171 225 3402 4279 2208 360 3696 1472 2776 M11682 BONCI_TARGETS_OF_MIR15A_AND_MIR16_1 http://www.broadinstitute.org/gsea/msigdb/cards/BONCI_TARGETS_OF_MIR15A_AND_MIR16_1.html Potential targets of MIR15A and MIR16-1 [GeneID=406948;406950] microRNAs in prostate cancer. 18931683 115/140 Jessica Robertson 0.0128828539624861 0.0266564534587849 460 2137.90909090909 2598 0.00117808347754625 309 0.985492186297595 0.977626090045981 1 2.32774018556731 459 3655 2598 4208 2986 309 318 763 3515 3900 806 2777 M12 PID_RHOA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHOA_PATHWAY.html RhoA signaling pathway 18832364 58/67 Pathway Interaction Database 0.429085126262397 0.499814448548158 2745 2810.54545454545 2600 0.0496794439936924 1914 0.976499369281514 -0.965188814214415 -1 0.441216647072548 2743 1914 2941 2405 4087 3441 1945 2337 2600 2269 4234 2778 M17936 NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_8Q23_Q24_AMPLICON.html Genes within amplicon 8q23-q24 identified in a copy number alterations study of 191 breast tumor samples. 19010930 172/226 Jessica Robertson 0.121916442695207 0.170552937024712 4345 2824.18181818182 2600 0.0117498362418683 846 1.10304760523347 -1.01053200971068 -1 1.27127862503611 4344 2770 2267 3933 3423 846 3776 2600 2435 2519 2153 2779 M524 REACTOME_ABCA_TRANSPORTERS_IN_LIPID_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABCA_TRANSPORTERS_IN_LIPID_HOMEOSTASIS.html Genes involved in ABCA transporters in lipid homeostasis 19/26 Reactome 0.00373882717021857 0.0106565605334732 2640 2558.81818181818 2601 0.000340472394750844 636 1.37771762432296 -1.21382542810062 -1 4.07738751578793 2639 2601 1576 2051 636 3772 4521 697 4381 3164 2109 2780 M10651 SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHWAB_TARGETS_OF_BMYB_POLYMORPHIC_VARIANTS_DN.html Genes down-regulated in 293 cells (embryonic kidney) expressing polymorphic variants S427G (SNP ID=rs2070235) or I624M (SNP ID=rs11556379) of BMYB [GeneID=4605]. 18026132 24/28 Jessica Robertson 0.00485491153552772 0.0130199900270971 2605 2426.36363636364 2602 0.000442332587687863 702 0.755467118844737 -0.587689889466721 -1 2.1371594206268 2602 952 2412 2845 702 2873 1183 3149 3608 3895 2469 2781 M8537 HOFMANN_CELL_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_CELL_LYMPHOMA_DN.html Genes down-regulated in lymph nodes from patients with mantle cell lymphoma (MCL) compared to the non-malignant hyperplastic lymph nodes. 11468180 53/91 Kevin Vogelsang 0.300961688502412 0.364895753848288 3240 2491.54545454545 2602 0.0320259262550118 805 1.18870759578198 -1.13164464192739 -1 0.780844736243005 3236 805 2032 1322 3808 2629 4099 3730 1485 2602 1659 2782 M8215 IVANOVA_HEMATOPOIESIS_STEM_CELL_AND_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL_AND_PROGENITOR.html Genes in the expression cluster 'HSC and Progenitors Shared': up-regulated in hematopoietic stem cells (HSC) and progenitors from adult bone marrow and fetal liver. 12228721 826/1015 John Newman 0.0575558992598412 0.0907740841996466 2840 2406.09090909091 2602 0.00591033195943772 275 1.11308181180199 -1.03947268908102 -1 1.74030791084878 2838 477 4497 275 2602 3984 3243 1223 1766 1730 3832 2783 M2182 WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CLASSIC_ADIPOGENIC_TARGETS_OF_PPARG.html Classic adipogenic genes (group 1) that are induced by PPARG [GeneID=5468] during adipogenesis in 3T3-L1 preadipocytes. 17954559 22/34 Arthur Liberzon 0.0435984245783339 0.0717269306412464 3315 2566.18181818182 2602 0.00404429030084062 1467 1.31257831297632 1.40150810277507 1 2.25368531822629 3314 1534 1696 3489 1467 2801 1502 3784 3646 2393 2602 2784 M18030 ST_TUMOR_NECROSIS_FACTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_TUMOR_NECROSIS_FACTOR_PATHWAY.html Tumor Necrosis Factor Pathway. 35/37 Signaling Transduction KE 0.298777944941808 0.362900643367301 2605 2716.36363636364 2603 0.0317514177514226 802 1.08205288464733 0.898234386240843 1 0.714641319935185 2603 2965 2911 2123 3919 1856 1610 4427 802 2158 4506 2785 M1062 REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIGEN_PRESENTATION_FOLDING_ASSEMBLY_AND_PEPTIDE_LOADING_OF_CLASS_I_MHC.html Genes involved in Antigen Presentation: Folding, assembly and peptide loading of class I MHC 45/62 Reactome 0.0727542318143642 0.110240762171364 2130 2885.09090909091 2603 0.00684344230651666 1495 0.764515368836079 -0.67305373722979 -1 1.09849108871643 2128 4126 3648 3241 1682 1713 2457 2603 4499 4144 1495 2786 M13606 AIYAR_COBRA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/AIYAR_COBRA1_TARGETS_DN.html Genes down-regulated in T47D cells (breast cancer) after COBRA1 [GeneID=25920] knockdown by RNAi. 17043641 45/55 Arthur Liberzon 0.0121816721708 0.0254864772367802 4630 2562.45454545455 2603 0.00111360465047981 390 1.01614662670759 -1.07060211367487 -1 2.42987074799013 4628 1431 2603 1106 986 3239 3828 3503 390 2488 3985 2787 M17411 KEGG_JAK_STAT_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_JAK_STAT_SIGNALING_PATHWAY.html Jak-STAT signaling pathway 101/186 KEGG 0.180434138804818 0.236856964274484 2930 2423.18181818182 2604 0.0179265114753851 1095 1.09414549330085 1.03807453947503 1 1.02685483465341 2927 1297 1322 1095 2723 2604 2282 3659 2874 1588 4284 2788 M3342 BIOCARTA_INTEGRIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INTEGRIN_PATHWAY.html Integrin Signaling Pathway 62/74 BioCarta 0.0021534600605419 0.00705856353177624 2605 2431.54545454545 2604 0.000195960987123888 527 1.04866764170308 -1.02202193458173 -1 3.3850398004698 2604 2874 3047 1148 527 3286 1604 4090 1309 1909 4349 2789 M45 PID_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD40_PATHWAY.html CD40/CD40L signaling 18832364 37/44 Pathway Interaction Database 0.0212441197001185 0.039774789759841 3330 2507.45454545455 2604 0.00195018897151719 663 0.921676777926777 -0.979765512762939 -1 1.93662875766259 3330 873 2604 1120 1176 3913 3225 4537 663 1941 4200 2790 M16697 BIOCARTA_CD40_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CD40_PATHWAY.html CD40L Signaling Pathway 18/19 BioCarta 0.00679714260639938 0.0160891109090292 800 2209.36363636364 2605 0.000619839492389055 790 0.811671097035247 0.851691611152696 1 2.18421039293378 796 2605 2964 2715 790 1539 1530 2758 3549 3067 1990 2791 M162 PID_RXR_VDR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RXR_VDR_PATHWAY.html RXR and RAR heterodimerization with other nuclear receptor 18832364 32/36 Pathway Interaction Database 0.000481522105488875 0.00225028152268068 2290 2528.90909090909 2605 4.3784320937473e-05 302 1.02406050943856 1.08307182353445 1 4.06850883723998 2290 2005 2905 2875 302 3181 2605 1955 4147 3172 2381 2792 M16523 REACTOME_GENERATION_OF_SECOND_MESSENGER_MOLECULES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GENERATION_OF_SECOND_MESSENGER_MOLECULES.html Genes involved in Generation of second messenger molecules 17/33 Reactome 0.0469987399131235 0.0763845939961505 1815 2898.81818181818 2605 0.00436671560532655 1496 0.959212715240217 1.02578838705898 1 1.60760398811262 1812 2109 2435 3808 1496 4331 2345 2605 3914 3975 3057 2793 M16763 KEGG_NEUROTROPHIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NEUROTROPHIN_SIGNALING_PATHWAY.html Neurotrophin signaling pathway 139/152 KEGG 0.0735759146779351 0.111414282091708 1430 2320.90909090909 2606 0.00692348273323488 841 0.856358987739631 0.884633382467867 1 1.22455976469573 1430 2788 3429 1947 3165 1220 841 2755 2606 3185 2164 2794 M186 PID_PDGFRB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PDGFRB_PATHWAY.html PDGFR-beta signaling pathway 18832364 184/200 Pathway Interaction Database 0.279880970099467 0.343841275083156 3620 2802.27272727273 2607 0.0294078970525568 650 1.04353596560242 -1.04554821642318 -1 0.725886435382488 3616 1754 2607 650 2435 4452 3204 4469 1223 1994 4421 2795 M14236 REACTOME_SIGNAL_ATTENUATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_ATTENUATION.html Genes involved in Signal attenuation 15/20 Reactome 0.346529043321227 0.413484767517603 2820 2573.18181818182 2608 0.0379394863859601 1074 1.09888353843537 1.00211040369804 1 0.632312851601069 2820 3083 2608 2750 2571 3399 1871 2206 1074 2222 3701 2796 M2538 KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES http://www.broadinstitute.org/gsea/msigdb/cards/KUMAR_PATHOGEN_LOAD_BY_MACROPHAGES.html Genes indentified by RNAi screen as regulating infection of THP-1 cells (macrophage) with Mycobacterium tuberculosis. 20211141 355/569 Arthur Liberzon 0.142729997074782 0.194313696623297 3815 2796.18181818182 2608 0.0139026667693389 1393 1.11134062270084 -1.11295937424146 -1 1.18637798719417 3815 3171 1577 2608 2039 2570 4590 3444 3239 2312 1393 2797 M13036 KEGG_PRION_DISEASES http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRION_DISEASES.html Prion diseases 41/49 KEGG 0.0549946592924364 0.0873401049328061 2275 2520.09090909091 2610 0.00512904674030999 613 1.03205694433178 1.35974494619483 1 1.63955408169462 2271 2938 1375 2686 2610 1885 2261 3551 4228 3303 613 2798 M509 REACTOME_DEVELOPMENTAL_BIOLOGY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEVELOPMENTAL_BIOLOGY.html Genes involved in Developmental Biology 398/520 Reactome 0.300411851684741 0.364603363889993 1715 2749.09090909091 2610 0.031956735406494 1677 1.06018919058962 1.17568732328072 1 0.696965253725014 1713 3975 1677 4156 2473 2646 2228 2610 3699 2239 2824 2799 M9726 KEGG_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PANCREATIC_CANCER.html Pancreatic cancer 83/90 KEGG 0.270946259053575 0.334169412786223 2730 2407.09090909091 2611 0.0283192593860702 1325 0.900200127576915 -0.732338051323218 -1 0.642904897080308 2729 1325 2871 1665 2417 3046 2611 2867 1870 2142 2935 2800 M7871 ST_GRANULE_CELL_SURVIVAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_GRANULE_CELL_SURVIVAL_PATHWAY.html Granule Cell Survival Pathway is a specific case of more general PAC1 Receptor Pathway. 37/47 Signaling Transduction KE 0.116662608827281 0.164176360663317 2170 2647.54545454545 2611 0.0112137478051669 1253 1.07005022856942 1.03732713186537 1 1.25981642046972 2170 3378 2611 2778 1907 2658 2477 3864 1253 2315 3712 2801 M17742 SMITH_TERT_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMITH_TERT_TARGETS_UP.html Genes consistently up-regulated in HMEC cells (primary mammary epithelium) upon expression of TERT [GeneID=7015] off a retroviral vector. 12717449 206/229 Broad Institute 0.0959651792871226 0.139199645431843 1860 2679 2612 0.00912965122579319 1805 1.01278153338663 1.10761930005187 1 1.30130646511136 1859 2760 2912 2481 1805 4058 3280 3166 2384 2152 2612 2802 M7047 MCCOLLUM_GELDANAMYCIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCOLLUM_GELDANAMYCIN_RESISTANCE_UP.html Genes up-regulated in A549GARS cells (lung cancer) resistant to the geldanamycin and 17-AAG [PubChem=5476289;6440175]. 18794130 19/28 Jessica Robertson 0.0217788555586213 0.0406630530999575 1320 2594.90909090909 2612 0.00199977191798508 940 1.38782473481709 1.24528650816817 1 2.89617799815168 1320 3049 940 3283 3750 2494 1424 3278 4450 2612 1944 2803 M17496 LEE_RECENT_THYMIC_EMIGRANT http://www.broadinstitute.org/gsea/msigdb/cards/LEE_RECENT_THYMIC_EMIGRANT.html Candidate genes specific for recent thymic emigrants (RTEs). 15210650 294/387 Arthur Liberzon 0.0642572198932139 0.0994080884614781 3050 2439.18181818182 2613 0.00601950500448894 541 1.14073456281716 1.13920011923223 1 1.71600250160722 3047 541 2015 1015 4444 3617 2613 2959 1172 871 4537 2804 M17243 REACTOME_ACTIVATED_TAK1_MEDIATES_P38_MAPK_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATED_TAK1_MEDIATES_P38_MAPK_ACTIVATION.html Genes involved in activated TAK1 mediates p38 MAPK activation 17/17 Reactome 0.226712807938721 0.287425316537943 1810 2720 2614 0.0231021243690752 1401 0.642199018510413 0.670172430956647 1 0.521677070964426 1809 2101 3552 3345 3183 1887 1401 2177 3274 4577 2614 2805 M976 REACTOME_GABA_RECEPTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_RECEPTOR_ACTIVATION.html Genes involved in GABA receptor activation 29/59 Reactome 0.0423713016650592 0.0699519216016368 2680 2570.45454545455 2614 0.00392818769398228 933 0.986701779855945 -0.921613435352935 -1 1.71024433000562 2678 2538 2224 3513 2247 2614 933 1047 3869 2961 3651 2806 M2540 KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_BY_GAMMA_AND_UV_RADIATION.html Gamma and UV responding genes. 15897889 131/185 Jessica Robertson 0.0282229137004176 0.0503257093562415 3560 2266 2614 0.00259923756307315 630 1.33002581193683 -1.24757872668155 -1 2.59077155398141 3559 630 982 1318 2614 3456 2703 3167 961 824 4712 2807 M9367 BIOCARTA_ERYTH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERYTH_PATHWAY.html Erythrocyte Differentiation Pathway 8/15 BioCarta 0.0450698284753868 0.0737851207284991 1440 2751.45454545455 2615 0.00460108841159964 1436 1.18999582457024 1.25230384526591 1 2.0212633793278 1436 3946 4189 3952 1518 2135 1484 2635 4477 1879 2615 2808 M9702 SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_2 http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_BY_METHYLATION_IN_PANCREATIC_CANCER_2.html 50 most interesting genes up-regulated in the pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 12839967 43/61 John Newman 0.138125599008491 0.188862348586349 1650 2713.45454545455 2615 0.0134223537199891 1584 1.02451146805841 1.02860666378609 1 1.11267588381926 1649 3358 1785 3750 2846 2615 2374 1584 4460 3062 2365 2809 M1671 KYNG_RESPONSE_TO_H2O2 http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2.html Genes up-regulated in response to hydrogen peroxide [PubChem=784] in CS-B cells (Cockayne syndrome fibroblast, CS) expressing ERCC6 [GeneID=2074] off a plasmid vector. 12606941 92/120 John Newman 0.59906259976225 0.665430043573571 2280 2466.27272727273 2616 0.0797283319601827 700 1.05024759627513 -0.901282120187544 -1 0.278670204881073 2277 700 1999 2849 3740 3383 2947 2616 2079 1833 2706 2810 M1684 DURCHDEWALD_SKIN_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DURCHDEWALD_SKIN_CARCINOGENESIS_DN.html Genes down-regulated upon skin specific knockout of FOS [GeneID=2353] by cre-lox in the K5-SOS-F mice (express a constitutively active form of SOS1 [GeneID=6654] in the skin). 18757399 374/460 Jessica Robertson 0.126083146446186 0.175342501834413 1375 2383.18181818182 2616 0.0121770739245195 1237 1.15341739573133 1.11915217229737 1 1.30851821834643 1374 2722 1237 2372 4196 2616 2160 2763 2640 1249 2886 2811 M7934 KEGG_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PYRUVATE_METABOLISM.html Pyruvate metabolism 41/49 KEGG 0.00490005030915852 0.0131186826200954 3540 2196.63636363636 2617 0.000446454393011176 208 0.928944599803988 -0.951580388983624 -1 2.62336701519778 3726 208 2617 380 705 2240 3539 3582 686 2942 3538 2812 M12272 MISSIAGLIA_REGULATED_BY_METHYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/MISSIAGLIA_REGULATED_BY_METHYLATION_UP.html Genes up-regulated in PaCa44 and CFPAC1 cells (pancreatic cancer) after treatment with decitabine [PubChem=451668], a DNA hypomethylating agent similar to azacitidine [PubChem=9444]. 15637593 191/288 Leona Saunders 4.39128759530503e-05 0.000342776651078505 4715 2387.63636363636 2617 3.99215931782122e-06 440 1.20840386972496 -1.22108838887394 -1 6.28273051040561 4711 577 440 1091 979 4147 3989 4144 2617 490 3079 2813 M4967 KORKOLA_CORRELATED_WITH_POU5F1 http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CORRELATED_WITH_POU5F1.html Genes whose expression pattern in adult male germ cell tumors (GCT) correlates with POU5F1 [GeneID=5460]. 16424014 36/57 Arthur Liberzon 0.68618940391 0.690284310838704 3325 2567.45454545455 2617 0.1 975 1.02669463499378 0.955008221597568 1 0.247883752749054 3323 1979 2440 975 3543 2750 2451 3112 1252 2617 3800 2814 M7890 WAESCH_ANAPHASE_PROMOTING_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/WAESCH_ANAPHASE_PROMOTING_COMPLEX.html Subunits of the anaphase promoting complex (APC). 15637585 16/18 Leona Saunders 0.0130130923288291 0.0268686770743978 2175 2765.36363636364 2618 0.00119006443895577 321 0.521701201803472 -0.516186499373043 -1 1.22951650233458 2173 2618 3698 3995 4293 1097 321 1750 4461 4652 1361 2815 M1472 PETROVA_PROX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETROVA_PROX1_TARGETS_DN.html Genes specific to BEC (blood endothelium cells) repressed in BEC by expression of PROX1 [GeneID=5629] off adenovirus vector. 12198161 93/111 Kevin Vogelsang 0.00294135151251175 0.00891662115546272 2140 2453.54545454545 2618 0.000267753764655735 721 1.27811991324875 1.28223801222083 1 3.93109138880465 2138 2823 721 1791 4428 3397 2618 1272 3706 1291 2804 2816 M2307 WANG_NFKB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WANG_NFKB_TARGETS.html Representative genes up-regulated in C2C12 cells (myoblast) lacking NFkB activity due to expression of a super repressor form of NFKBIA [GeneID=4792]. 17438126 36/61 Arthur Liberzon 0.154755004390282 0.20798508562703 4235 2701.81818181818 2618 0.0151682184499301 1086 1.12816550316858 -1.0422020256928 -1 1.15435312965716 4233 1454 1659 1086 3666 3254 3964 1645 1510 2618 4631 2817 M17043 CHANDRAN_METASTASIS_TOP50_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_TOP50_DN.html Top 50 genes down-regulated in metastatic vs primary prostate cancer tumors. 17430594 59/61 Arthur Liberzon 0.00251421563358627 0.00792689404316561 3110 2683.27272727273 2619 0.000228826686216451 141 0.966006549593296 1.11075943707396 1 3.04516995780177 3110 141 2430 1457 559 4465 4085 4303 2350 2619 3997 2818 M8804 GILMORE_CORE_NFKB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/GILMORE_CORE_NFKB_PATHWAY.html Genes encoding the NF-kB core signaling proteins. 17072321 14/14 Arthur Liberzon 0.0064022837494775 0.0154350763241603 730 2184.90909090909 2619 0.000583726498557881 627 0.771027232799596 0.811942804246369 1 2.09568414952205 728 3081 2798 3551 773 969 627 2619 3632 3316 1940 2819 M15531 MOOTHA_FFA_OXYDATION http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_FFA_OXYDATION.html Genes involved in free fatty acid oxidation; based on literature and sequence annotation resources and coverted to Affymetrix HG-U133A probe sets. 12808457 26/29 Vamsi Mootha 0.000331306197896234 0.00169605775929525 2405 2036.45454545455 2619 3.01232819138715e-05 44 0.834856888991618 -0.767759456407562 -1 3.47062795674369 2402 327 3620 176 242 2657 3035 3654 44 3625 2619 2820 M19166 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_CHONDROITIN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_CHONDROITIN_SULFATE.html Glycosaminoglycan biosynthesis - chondroitin sulfate 20/24 KEGG 0.0218065485641915 0.0406729114747001 1900 2570.18181818182 2620 0.00200234040036661 1182 1.1226284911398 -0.948092967025858 -1 2.34255642517112 1898 2595 2460 3038 1182 3744 3009 2257 2760 2709 2620 2821 M153 PID_P75_NTR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P75_NTR_PATHWAY.html p75(NTR)-mediated signaling 18832364 88/106 Pathway Interaction Database 0.061283717204489 0.0955118881457092 2745 2562.18181818182 2620 0.0057327767147467 1164 0.999540673078527 -1.08716748946 -1 1.52963549251728 2744 2371 2620 2744 4136 1770 3699 1213 2579 3144 1164 2822 M11620 WIELAND_UP_BY_HBV_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/WIELAND_UP_BY_HBV_INFECTION.html Genes induced in the liver during hepatitis B (HBV) viral clearance in chimpanzees. 15100412 120/193 Kate Stafford 0.0938649726609252 0.136952912197702 2865 2617.09090909091 2620 0.0089206047531663 1181 1.1922794700505 -1.06493472319668 -1 1.54460207636323 2865 1278 1181 2898 2620 3925 4102 2228 3256 1895 2540 2823 M2356 KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3 http://www.broadinstitute.org/gsea/msigdb/cards/KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3.html Genes with promoters occupied by SMAD2 or SMAD3 [GeneID=4087, 4088] in HaCaT cells (keratinocyte) according to a ChIP-chip analysis. 18955504 1120/1317 Arthur Liberzon 0.522336105651706 0.590804317919016 2435 2818.27272727273 2620 0.0712213117895402 1114 1.05875665978769 1.03232576027562 1 0.362998340981779 2435 1114 4688 1878 2921 2620 2589 4176 2755 1671 4154 2824 M5459 NEWMAN_ERCC6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NEWMAN_ERCC6_TARGETS_UP.html Genes up-regulated in Cockayne syndrome fibroblasts rescued by expression of ERCC6 [GeneID=2074] off a plasmid vector. 16772382 29/44 Leona Saunders 0.00734454129572288 0.017102237254964 2740 2331.45454545455 2621 0.000669925066417008 815 1.34448441784435 1.22524686278682 1 3.56457887514769 2740 3421 815 2597 1034 2621 1718 3018 3031 1080 3571 2825 M18973 NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON.html Genes within amplicon 20q12-q13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 134/193 Jessica Robertson 0.151857170506552 0.204498101224229 3280 2589.45454545455 2621 0.0148617509625575 1039 1.1624607418185 -1.19450436150681 -1 1.20225587825136 3278 4026 2536 2621 3219 1039 2171 4096 1527 2809 1162 2826 M1462 BIOCARTA_CTL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CTL_PATHWAY.html CTL mediated immune response against target cells 26/57 BioCarta 0.011038716137783 0.0235439404294333 1910 2906 2622 0.00100859056461918 947 1.03302934275552 -0.950294161969689 -1 2.52361379136511 1906 4532 2622 4443 947 1979 2259 3374 4240 3191 2473 2827 M2563 HOLLEMAN_DAUNORUBICIN_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_ALL_UP.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 9/11 Arthur Liberzon 0.150950783348554 0.203567913544336 2625 2621.18181818182 2622 0.0162306525660031 584 1.04664790932101 0.999039508217878 1 1.08557737081738 2622 1624 4713 1769 3681 3450 3594 1683 584 2039 3074 2828 M10487 HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN.html Genes down-regulated during differentiation from small pre-BII to immature B lymphocyte. 11779835 78/114 Arthur Liberzon 0.0561703627152746 0.0889379778651781 2940 2395 2623 0.00524163246015153 717 1.03508177754055 -0.885326515763897 -1 1.63213084768772 2938 2845 2091 2623 1565 717 2548 3977 3300 2969 772 2829 M6778 BIOCARTA_IL10_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL10_PATHWAY.html IL-10 Anti-inflammatory Signaling Pathway 16/19 BioCarta 0.376232289937839 0.444621033677166 3630 2824.72727272727 2624 0.0419995408836337 1007 0.926031486043994 -0.930796294568103 -1 0.489022209895836 3629 1007 2385 1049 2624 4128 3384 3716 2544 2321 4285 2830 M6786 REACTOME_NUCLEOTIDE_LIKE_PURINERGIC_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEOTIDE_LIKE_PURINERGIC_RECEPTORS.html Genes involved in Nucleotide-like (purinergic) receptors 8/18 Reactome 0.000362292811410771 0.00182305124718427 1475 2583.72727272727 2624 3.62351890203515e-05 273 0.976590729866283 0.953364096660825 1 4.01390303301929 1471 2680 4239 3302 273 1765 1752 3575 4556 2624 2184 2831 M873 REACTOME_ROLE_OF_SECOND_MESSENGERS_IN_NETRIN1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ROLE_OF_SECOND_MESSENGERS_IN_NETRIN1_SIGNALING.html Genes involved in Role of second messengers in netrin-1 signaling 8/13 Reactome 0.00162287859000187 0.00570788893055798 865 2097.54545454545 2625 0.000162406499030612 76 0.901687172747222 0.652706452332714 1 3.03538212603551 864 2673 4246 2863 3487 1024 76 4409 644 2625 162 2832 M596 HASINA_NOL7_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HASINA_NOL7_TARGETS_DN.html Genes down-regulated in SiHa cells (cervical carcinoma) by stable expression of NOL7 [GeneID=51406] off a plasmid vector. 16205646 23/25 Leona Saunders 0.0249861536225831 0.0454643967226648 4465 2500.09090909091 2625 0.00229768415266692 719 1.23482937834601 -0.98783080096304 -1 2.48707633616408 4465 946 1251 799 2625 3523 4534 4147 775 719 3717 2833 M2282 ITO_PTTG1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ITO_PTTG1_TARGETS_UP.html Genes up-regulated in HSA/c and KYSE140 cells (esophageal squamous cell carcinoma, ESCC) after knockdown of PTTG1 [GeneID=9232] by RNAi. 18451147 18/30 Jessica Robertson 0.00101079354470938 0.0040010428079194 2625 2629.63636363636 2625 9.19325685796228e-05 623 1.69340872924607 -1.82483145937586 -1 6.09275716890517 2625 4223 623 3992 830 3474 4698 670 4386 858 2547 2834 M2397 SERVITJA_LIVER_HNF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SERVITJA_LIVER_HNF1A_TARGETS_UP.html Genes up-regulated in liver tissue upon knockout of HNF1A [GeneID=6927]. 19289501 165/232 Arthur Liberzon 2.44148879174178e-09 6.19560596614043e-08 4385 2364.54545454545 2626 2.21953526768297e-10 150 1.31551017960242 1.30875875689878 1 14.2279562338493 4384 590 150 223 2626 4251 4627 4375 875 236 3673 2835 M639 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_EARLY_ENDOSOME_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_EARLY_ENDOSOME_MEMBRANE.html Genes involved in Synthesis of PIPs at the early endosome membrane 15/15 Reactome 0.0452472556120463 0.0739754230997085 3250 2955.45454545455 2627 0.00420050567697018 655 0.555414440515709 0.540809961909781 1 0.942408576001215 3247 4588 3679 4392 1596 2548 655 2627 2061 4531 2586 2836 M16325 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_4.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 4. 12554760 12/18 Arthur Liberzon 0.0546192363087804 0.0868900557389428 2300 2383.81818181818 2627 0.00509312294204601 836 0.969787581807473 -0.778100342726451 -1 1.54388977604116 2297 3092 2627 2873 1547 1942 836 3741 1389 3132 2746 2837 M954 REACTOME_GABA_B_RECEPTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_B_RECEPTOR_ACTIVATION.html Genes involved in GABA B receptor activation 26/42 Reactome 0.0359720515795094 0.0610309430105264 2810 2534.63636363636 2628 0.00332491406789209 985 0.986701779855945 -0.921613435352935 -1 1.79796721651093 2808 2555 2063 3516 1814 2628 1043 985 3897 2724 3848 2838 M12718 BIOCARTA_P35ALZHEIMERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P35ALZHEIMERS_PATHWAY.html Deregulation of CDK5 in Alzheimers Disease 15/19 BioCarta 0.0089877002467253 0.0201433737723378 3830 2663.72727272727 2629 0.000820420840889619 512 1.12205975194873 -1.71155030653426 -1 2.85518127843575 3829 2629 3357 2446 2069 3634 2562 512 561 3398 4304 2839 M1077 REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_ACTIVATION_SIGNALING_AND_AGGREGATION.html Genes involved in Platelet activation, signaling and aggregation 227/310 Reactome 0.00192010708284139 0.0064688832484021 1600 2513.18181818182 2629 0.000174707723331615 679 1.12817847567885 1.03845930366425 1 3.70584149850316 1596 3182 679 3702 2629 2383 1704 3594 3607 1424 3145 2840 M2432 VERNOCHET_ADIPOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/VERNOCHET_ADIPOGENESIS.html Genes up-regulated during adipogenic differentiation of 3T3-L1 cells (preadipocyte) and down-regulated by troglitazone [PubChem=5591]. 19564408 17/26 Arthur Liberzon 0.00656362968508478 0.0156624530402427 1880 2507 2629 0.000598481295426208 436 1.12218117528234 1.36034027921443 1 3.03948923012099 1880 3514 1555 3301 3829 1858 691 436 4353 3531 2629 2841 M3654 THUM_SYSTOLIC_HEART_FAILURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/THUM_SYSTOLIC_HEART_FAILURE_UP.html Genes up-regulated in samples with systolic heart failure compared to normal hearts. 17606841 522/717 Arthur Liberzon 0.0389405643445477 0.065269695918418 1415 2668.36363636364 2630 0.00396402484947367 1190 1.13804428086985 1.22828081105135 1 2.023961744057 1414 3966 4288 4088 1458 2677 2630 1190 4083 1255 2303 2842 M8334 ZEMBUTSU_SENSITIVITY_TO_DOXORUBICIN http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_DOXORUBICIN.html Top genes associated with chemosensitivity to doxorubicin [PubChem=31703] across 85 tumor xenografts. 11809704 24/24 Arthur Liberzon 0.324625235237368 0.389781508603505 3945 2666.63636363636 2630 0.0350516332288695 430 1.5251165060979 1.24367676045445 1 0.936286657986179 3941 3025 2261 2630 2530 2241 2399 3191 430 3507 3178 2843 M2006 MIKKELSEN_ES_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters bearing H3 trimethylation mark at K27 (H3K27me3) in embryonic stem cells (ES). 17603471 8/24 Arthur Liberzon 0.221198571602544 0.281341217451902 2985 2682.90909090909 2631 0.0246900071560501 147 1.34608859284054 -1.24258333176048 -1 1.11235077347837 2984 1629 4644 1434 2411 3966 4418 1926 147 2631 3322 2844 M1470 SESTO_RESPONSE_TO_UV_C5 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C5.html Cluster 5: genes changed in primary keratinocytes by UVB irradiation. 11867738 77/82 John Newman 0.534966211650186 0.603382398044421 2320 2465.45454545455 2633 0.0672369818758504 574 0.919657926402466 -0.972080819923749 -1 0.302668692767699 2316 732 3452 636 2963 2633 2082 4437 574 3189 4106 2845 M19832 REACTOME_CELL_DEATH_SIGNALLING_VIA_NRAGE_NRIF_AND_NADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_DEATH_SIGNALLING_VIA_NRAGE_NRIF_AND_NADE.html Genes involved in Cell death signalling via NRAGE, NRIF and NADE 76/83 Reactome 0.68618940391 0.690284310838704 3820 2958.18181818182 2635 0.1 834 1.06348356045919 -1.01759285032595 -1 0.256769812810585 3816 1866 2355 834 4084 4064 4559 4264 1706 2357 2635 2846 M6467 REACTOME_OPIOID_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OPIOID_SIGNALLING.html Genes involved in Opioid Signalling 74/93 Reactome 0.381051592049618 0.449753316947786 2855 2307.45454545455 2635 0.042674790465586 420 1.02751807234372 1.01263614787567 1 0.534942267833669 2852 739 2384 420 2635 3661 3202 3071 1519 1525 3374 2847 M4910 ST_ERK1_ERK2_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_ERK1_ERK2_MAPK_PATHWAY.html ERK1/ERK2 MAPK Pathway 39/41 Signaling Transduction KE 0.22476667802638 0.285349262847724 2325 2771.63636363636 2636 0.0228788745122858 1732 0.803064596541183 -0.695768953280299 -1 0.656173103408342 2321 3782 3706 2489 2305 2636 1732 3259 1816 3536 2906 2848 M6740 SABATES_COLORECTAL_ADENOMA_SIZE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SABATES_COLORECTAL_ADENOMA_SIZE_UP.html A selection of genes whose expression displayed significant positive correlation with size of colorectal adenoma. 18171984 18/20 Leona Saunders 0.218086191462943 0.277981858953576 1800 2835.18181818182 2636 0.0221163808853277 1798 1.45657936694882 1.45657936694882 1 1.21506658213858 1798 4578 3105 4385 3059 2275 1861 1858 2636 3612 2020 2849 M18377 MELLMAN_TUT1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MELLMAN_TUT1_TARGETS_UP.html Genes up-regulated in HEK293 cells (embryo kidney) after knockdown of TUT1 [GeneID=64852] by RNAi. 18288197 24/26 Jessica Robertson 0.0196476897722587 0.0372887397366549 2640 2560.81818181818 2636 0.00180230767937316 751 0.760442999113035 -0.840525682206814 -1 1.62980968899225 3317 3851 3534 2636 1514 2640 1812 751 1641 3897 2576 2850 M1361 DAZARD_RESPONSE_TO_UV_SCC_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_RESPONSE_TO_UV_SCC_UP.html Genes up-regulated in SCC12B2 cells (squamous cell carcinoma) by UV-B irradiation. 12771951 152/186 John Newman 0.35903999894988 0.427299242320584 2735 2853 2637 0.039628694915973 1469 1.04776075620158 -1.12138262252261 -1 0.580451974708486 2732 3642 3301 2465 4458 1469 2132 3732 2386 2429 2637 2851 M3854 MARTINEZ_RB1_AND_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_AND_TP53_TARGETS_DN.html Genes down-regulated in mice with skin specific double knockout of both RB1 and TP53 [GeneID=5925;7157] by Cre-lox. 18245467 760/992 Jessica Robertson 0.533881762223389 0.602563825369296 2180 2602.90909090909 2638 0.0734910699180944 1382 1.11589953438484 1.10537831484826 1 0.368263578305195 2176 1663 4537 1382 3199 2798 2448 2638 2791 1614 3386 2852 M17026 RIZKI_TUMOR_INVASIVENESS_3D_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_3D_UP.html Genes up-regulated in three-dimentional (3D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 276/374 Jessica Robertson 0.115102435696427 0.162416590878068 4635 2727.81818181818 2638 0.0110551097045457 1532 1.0873879057282 -0.913905735856013 -1 1.2878670238217 4632 2255 1532 1639 1902 2721 4068 3453 2857 2638 2309 2853 M1388 SHIN_B_CELL_LYMPHOMA_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_5.html Cluster 5 of genes distinguishing among different B lymphocyte neoplasms. 19010892 11/25 Jessica Robertson 0.239938281175317 0.300958992066835 3275 2563.63636363636 2639 0.0246329544186391 1236 1.1301967260344 -1.0616310900551 -1 0.884284668389554 3274 2639 1534 3717 3066 3061 3463 2509 1835 1236 1866 2854 M13917 BIOCARTA_PARKIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PARKIN_PATHWAY.html Role of Parkin in the Ubiquitin-Proteasomal Pathway 12/15 BioCarta 0.225003560058441 0.285565152857177 1880 2763.72727272727 2641 0.0229060211303931 1558 0.725365308646164 0.797376192951253 1 0.592318339583689 1876 3924 3493 2641 3392 3014 2505 1882 1558 3797 2319 2855 M1130 MCBRYAN_TERMINAL_END_BUD_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_TERMINAL_END_BUD_DN.html The 'TEB profile genes': down-regulated during pubertal mammary gland development specifically in the TEB (terminal end bud) structures. 17486082 11/15 Arthur Liberzon 0.00585092982180615 0.0143536324110837 4025 2740 2641 0.000533322603075082 745 1.01757173282468 -1.18595908930833 -1 2.81400485342674 4022 2641 2223 2634 745 2665 2791 4639 1985 2343 3452 2856 M2415 WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_36HR.html Genes with promoters bound by both PPARG and RXRA [GeneID=5468, 6256] at 36 h time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 197/236 Arthur Liberzon 0.0228093387494227 0.0421205316499512 2485 2606.63636363636 2641 0.00209539216565268 1191 0.977964798745167 0.969520229001625 1 2.01838866831105 2482 3192 3472 1299 1191 2641 1576 3452 2086 3393 3889 2857 M9054 TOMLINS_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_METASTASIS_UP.html Top genes up-regulated in hormone refractory metastatic prostate cancer compared to localized prostate cancer. 17173048 24/28 Leona Saunders 0.38511585870675 0.453869376553273 3670 2549.18181818182 2642 0.0432479747863672 424 1.02177640246045 0.587356546491479 1 0.525886372446747 3669 2560 2978 1577 2642 1888 2161 3765 424 3503 2874 2858 M2785 EHLERS_ANEUPLOIDY_DN http://www.broadinstitute.org/gsea/msigdb/cards/EHLERS_ANEUPLOIDY_DN.html Down-regulated genes in the expression signature of aneuploidy in uveal melanoma tumors: low vs high aneuploidy. 18172260 14/18 Jessica Robertson 0.235986236961464 0.296869679759624 4395 2642.72727272727 2642 0.0241729901852264 251 1.52232714597565 -1.53517750444436 -1 1.20470274990988 4395 3539 2054 3028 2336 2184 2432 2642 251 2678 3531 2859 M3644 BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_DN http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_DN.html Genes down-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes depend on ATM [GeneID=472] but not NFKB signaling. 18849970 65/85 Jessica Robertson 0.0184407020000694 0.0355127169775222 1275 2144.72727272727 2642 0.00169064664416736 477 0.982790912190715 -0.991160404555052 -1 2.13763939210104 1271 3707 2902 2642 1127 477 1021 2698 3874 3211 662 2860 M8821 REACTOME_AXON_GUIDANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AXON_GUIDANCE.html Genes involved in Axon guidance 271/342 Reactome 0.0338420273983493 0.0579587697097999 1375 2402.90909090909 2643 0.00312491864842703 1004 1.12090903739605 1.23844278265561 1 2.08026158258409 1371 2733 1004 2785 2789 2828 2375 2457 3634 1813 2643 2861 M1379 HE_PTEN_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HE_PTEN_TARGETS_DN.html Genes down-regulated in the intestine after the tissue specific knockout of PTEN [GeneID=5728] by Cre-lox. 17237784 7/8 Jessica Robertson 0.176705537632967 0.232455445269677 2565 2722.63636363636 2643 0.0192563171785068 1319 1.2541146819401 -1.42792832080594 -1 1.19233144526058 2564 2682 4447 2643 2448 3134 2262 3206 1883 3361 1319 2862 M14365 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_UP.html All common up-regulated stress response genes (Human Environmental Stress Response, H-ESR). 15897889 96/114 Jessica Robertson 0.135907914824197 0.186424108680677 1800 2840.81818181818 2643 0.0131918452481475 1551 1.05279545430281 1.18899191322081 1 1.15231173997038 1799 2363 1551 3452 2012 4132 2643 3150 4038 2491 3618 2863 M18161 KORKOLA_YOLK_SAC_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_YOLK_SAC_TUMOR_UP.html Genes from the 12p region that were up-regulated in yolk sac tumor cells compared to normal testis. 16424014 31/42 Arthur Liberzon 0.00573024184366711 0.0142024584976285 3465 2674.81818181818 2644 0.000522292891105201 740 1.15195651176534 -1.1070630349449 -1 3.19359638168186 3461 3402 2366 2644 740 1736 2835 4574 2769 2258 2638 2864 M2392 JUBAN_TARGETS_OF_SPI1_AND_FLI1_UP http://www.broadinstitute.org/gsea/msigdb/cards/JUBAN_TARGETS_OF_SPI1_AND_FLI1_UP.html Genes up-regulated in 745A cells (erythroleukemia) upon knockdown of FLI1 [GeneID=2313] by RNAi and down-regulation of SPI1 [GeneID=6688] by HMBA [PubChem=3616]. 19289502 169/224 Arthur Liberzon 0.0112443679284351 0.0238961803792047 3420 2668.81818181818 2644 0.00102747757971507 584 1.07540265430155 -1.05056273281619 -1 2.61672591914118 3417 1231 2644 584 954 4604 3360 4629 2102 1896 3936 2865 M7772 BIOCARTA_BARRESTIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARRESTIN_PATHWAY.html fl-arrestins in GPCR Desensitization 19/23 BioCarta 0.00039731961153963 0.0019474024573905 3630 2238.45454545455 2649 3.61264895944813e-05 272 0.936060200374594 -0.84536973735228 -1 3.80706264960703 3628 2094 3051 2649 272 3249 4162 747 725 3161 885 2866 M1506 WEBER_METHYLATED_HCP_IN_SPERM_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_SPERM_UP.html Methylated germline-specific genes with high-CpG-density promoters (HCP) in sperm. 17334365 10/41 Jessica Robertson 0.00230432265756427 0.00743431506746642 2975 2230.18181818182 2649 0.000209703617727167 53 0.831245353730568 0.989925308518047 1 2.65509603364229 2974 2649 2763 1478 3633 2553 937 2964 868 3660 53 2867 M11519 AMIT_SERUM_RESPONSE_40_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_40_MCF10A.html Genes whose expression peaked at 40 min after stimulation of MCF10A cells with serum. 17322878 40/49 Leona Saunders 0.00337237808783316 0.00989902025781872 1395 2394.09090909091 2650 0.000307050793148961 731 1.39634283795429 1.30632626244306 1 4.19961044859958 1394 2954 731 2905 3974 2650 2231 3402 3139 804 2151 2868 M10277 MULLIGHAN_NPM1_SIGNATURE_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_SIGNATURE_3_UP.html The 'NPM1 signature 3': genes up-regulated in pediatric AML (acute myeloid leukemia) with mutated NPM1 [GeneID=4869] compared to the AML cases with intact NPM1 and MLL [GeneID=4297]. 17597811 400/533 Arthur Liberzon 0.127358496611524 0.176647694389184 2655 2757.72727272727 2651 0.012308213568864 1156 1.06309369890071 1.02950415463207 1 1.20090258686262 2651 1156 2937 2378 1968 3952 3041 3220 2299 2522 4211 2869 M19134 KENNY_CTNNB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KENNY_CTNNB1_TARGETS_DN.html Genes down-regulated in HC11 cells (mammary epithelium) by expression of constantly active CTNNB1 [GeneID=1499]. 15642117 75/91 Yujin Hoshida 2.56121351499035e-05 0.000223455227185849 3995 2845.81818181818 2651 2.32840302983249e-06 59 1.06200860820901 -0.843936781265939 -1 5.81769722327316 3991 1346 2651 1908 59 4675 4139 3621 1850 2561 4503 2870 M9377 ALCALAY_AML_BY_NPM1_LOCALIZATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/ALCALAY_AML_BY_NPM1_LOCALIZATION_UP.html Genes up-regulated in acute myeloid leukemia (AML) with respect to cellular localization of NPM1 [GeneID=4869]: cytoplasmic vs. nucleolar. 15831697 186/271 Kevin Vogelsang 0.00016394335730832 0.00098627269465891 2655 2477 2652 1.49050523267397e-05 506 1.22403028050456 1.18911070783944 1 5.52096575892408 2652 2284 506 1800 2326 4503 3275 3044 2681 770 3406 2871 M15967 SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMIRNOV_CIRCULATING_ENDOTHELIOCYTES_IN_CANCER_DN.html Genes down-regulated in circulating endothelial cells (CEC) from cancer patients compared to those from healthy donors. 16540638 6/8 Arthur Liberzon 0.00770017627546152 0.0177465000098527 2085 2619.45454545455 2654 0.000772698884871237 244 1.01234997316449 1.01234997316449 1 2.65958204592425 2084 3574 4299 3531 2654 1983 244 1105 4654 3227 1459 2872 M17386 REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY.html Genes involved in Costimulation by the CD28 family 55/72 Reactome 0.00347569373677211 0.0100955535000396 2550 2225.09090909091 2655 0.000316472456825205 158 0.928545134901232 1.01299472629906 1 2.78074087273716 2546 158 2655 423 626 2885 3334 4324 1183 3356 2986 2873 M2564 HOLLEMAN_DAUNORUBICIN_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_ALL_DN.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 10/10 Arthur Liberzon 8.53365997804375e-05 0.000583751812990819 4380 2376.09090909091 2655 7.75817364659989e-06 16 0.853074716399512 -0.999030408478245 -1 4.13930224722533 4380 2655 3407 1071 120 4524 3018 1978 16 3664 1304 2874 M9908 LANDIS_BREAST_CANCER_PROGRESSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_BREAST_CANCER_PROGRESSION_DN.html Genes down-regulated in preneoplastic mammary tissues and whose expression is maintained in tumors. 16434967 101/108 Lauren Kazmierski 0.00014619170212139 0.000897301474659246 2045 2609.18181818182 2656 1.32910379615413e-05 434 1.24984036674505 -1.31548729142685 -1 5.71438568780678 2045 2355 502 2656 434 3616 3100 4362 3909 1057 4665 2875 M19548 STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_UP.html Genes up-regulated by estradiol [PubChem=5757] and up-regulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 38/42 Leona Saunders 0.00540622750592541 0.0141292324628837 1825 2640.90909090909 2656 0.000492687138733541 115 1.177759512257 1.26405767131289 1 3.26910042961545 1824 4481 2913 4376 2656 2617 2469 2769 2085 2745 115 2876 M15964 CHESLER_BRAIN_D6MIT150_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_D6MIT150_QTL_TRANS.html Neurologically relevant genes modulated in brain tissue by a trans-regulatory QTL (quantitative trait locus) near D6Mit150 marker. 15711545 8/17 Jean Junior 0.00116298653060299 0.00445198412363837 2660 2485.81818181818 2657 0.000116359562123317 443 1.38541858694516 1.5296223768567 1 4.88819472891227 2657 2671 4477 2043 443 2881 1216 4064 3994 1887 1011 2877 M716 REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_PYRUVATE_DEHYDROGENASE_PDH_COMPLEX.html Genes involved in Regulation of pyruvate dehydrogenase (PDH) complex 12/13 Reactome 0.00246445132794196 0.00782786693666625 4600 2531.45454545455 2659 0.000224292396030963 81 1.16119538565502 -0.436814011003817 -1 3.67000349070025 4598 3538 3295 3108 548 2659 1456 2539 81 3799 2225 2878 M10952 KAAB_HEART_ATRIUM_VS_VENTRICLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAAB_HEART_ATRIUM_VS_VENTRICLE_UP.html Genes up-regulated in the atria of healthy hearts, compared to venticles. 15103417 389/507 John Newman 1.45523649910791e-07 2.55342612482875e-06 2660 2513.18181818182 2659 1.3229423594251e-08 225 1.2247645175982 1.20640442415183 1 10.2783920264247 2659 1696 225 1574 2093 3953 3897 3781 2773 310 4684 2879 M9362 IWANAGA_CARCINOGENESIS_BY_KRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_CARCINOGENESIS_BY_KRAS_DN.html Cluster 4: genes down-regulated in lung tissue samples from mice with tumor-bearing genotypes (activated KRAS [GeneID=3845] alone or together with inactivated PTEN [GeneID=5728]). 18281487 183/239 Jessica Robertson 0.0848131537844228 0.125897864457703 1755 2929.09090909091 2659 0.00802463216964591 1751 1.10913144723747 -1.09247470889957 -1 1.49771020650524 3402 1758 1752 2659 1751 4373 3359 3780 2338 2505 4543 2880 M1098 GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN.html Genes down-regulated in ME-A cells (breast cancer) undergoing apoptosis upon serum starvation (5% to 0% FCS) for 22 hr. 17160024 299/346 Arthur Liberzon 0.00661545293052957 0.0157383759234373 4555 2645.63636363636 2661 0.000603220900650848 554 1.20114243780333 -1.17485904194527 -1 3.24958243508147 4551 1713 881 1959 3451 3291 4403 3613 2025 554 2661 2881 M3053 MULLIGHAN_MLL_SIGNATURE_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_2_UP.html The 'MLL signature 2': genes up-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to the AML cases with intact MLL and NPM1 [GeneID=4869]. 17597811 506/649 Arthur Liberzon 0.00525070999993344 0.0138068808911899 3555 2397.45454545455 2662 0.000526315789473684 104 0.913661371298497 -0.909347120432451 -1 2.54976217378657 3553 498 4302 104 2662 884 3852 3752 1945 3982 838 2882 M14146 BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G1_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G1, defined by unsupervised clustering 17187432 194/241 Yujin Hoshida 0.338319590815667 0.404475296010625 2125 2742.81818181818 2662 0.0368469641799385 1692 0.899946622221644 0.914277515975869 1 0.530742483399126 2123 2763 3664 3433 2557 2003 1692 2662 1859 4079 3336 2883 M10336 OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_DN.html Genes down-regulated in epithelial ovarian cancer (EOC) biopsies: invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 14/15 Leona Saunders 0.0285713459890128 0.0506789752229014 3735 2466.72727272727 2664 0.00263175374468183 254 1.25468522042464 1.6351457181859 1 2.4382893813991 3735 3897 2664 3146 1290 2902 1428 1540 254 3881 2397 2884 M12224 MARTINEZ_RB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_TARGETS_UP.html Genes up-regulated in mice with skin specific knockout of RB1 [GeneID=5925] by Cre-lox. 18245467 873/1078 Jessica Robertson 0.133449357228251 0.183638765631879 4185 2890.09090909091 2666 0.0142213797215544 1064 1.11492846398007 1.12627018618937 1 1.23126157500225 2666 1661 4532 2448 2407 2808 2523 4185 3316 1064 4181 2885 M8445 KIM_MYC_AMPLIFICATION_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYC_AMPLIFICATION_TARGETS_UP.html Genes positively correlated with amplifications of MYC [GeneID=4609] in SCLC (small cell lung cancer) cell lines. 16116477 234/298 Arthur Liberzon 0.019298033479776 0.0367137114165831 3960 2532.63636363636 2667 0.00176994737107453 788 1.1798159754688 -1.05504186441472 -1 2.54063253962809 3958 3177 2667 1773 1143 2160 3483 3394 788 2147 3169 2886 M11840 SHEPARD_BMYB_MORPHOLINO_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_BMYB_MORPHOLINO_DN.html Human orthologs of genes down-regulated in zebra fish after knockdown of BMYB [GeneID=4605] by morpholino. 16150706 250/360 Jennifer Shepard 0.000541852630248591 0.00244975518656451 1935 2470.27272727273 2668 4.92714666156599e-05 577 1.34084519415981 1.34839076712772 1 5.25288826903372 1933 3993 577 3851 3466 2213 2782 1713 2967 1010 2668 2887 M18155 KEGG_INSULIN_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_INSULIN_SIGNALING_PATHWAY.html Insulin signaling pathway 129/174 KEGG 0.217528152358922 0.27757039176375 2045 2519.72727272727 2669 0.0220529560437359 1163 0.839111549422078 0.80435899517591 1 0.700745124381983 2042 2793 3601 2772 3071 1163 1685 2633 1856 3432 2669 2888 M3214 KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_BILE_ACID_BIOSYNTHESIS.html Primary bile acid biosynthesis 14/26 KEGG 0.00240541814402274 0.00768674965726008 545 2493.54545454545 2670 0.00021891383576968 541 1.47181240397473 -1.53928862237457 -1 4.66919761436205 2439 3903 1357 4175 542 2891 3014 541 4490 2670 1407 2889 M4023 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP.html Genes up-regulated in kidney biopsies from patients with well functioning kidneys more than 1-year post transplant compared to the biopsies from normal living kidney donors. 15307835 775/962 Jean Junior 0.11394062047705 0.160969688312385 1950 2900.09090909091 2670 0.0120242549543173 1948 0.996945147152427 1.0014792900662 1 1.18655438497208 1974 2205 4481 1950 1948 3136 2371 2670 3131 4012 4023 2890 M18367 PYEON_HPV_POSITIVE_TUMORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_HPV_POSITIVE_TUMORS_DN.html Down-regulated genes in cervical carcinoma and head and neck tumors positive for human papilloma virus (HPV) compared to those negative for HPV. 17510386 8/17 Arthur Liberzon 0.0316053123915621 0.0549050697416905 3510 2630.90909090909 2672 0.00320640244425672 1112 1.1909579309071 -1.1909579309071 -1 2.25227765874519 3510 2672 4273 2084 1376 1528 1326 3072 4529 3458 1112 2891 M7331 KOBAYASHI_EGFR_SIGNALING_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_6HR_UP.html Genes up-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 6h. 17145885 8/12 Leona Saunders 0.000299594008586018 0.00158707488274523 4685 3016.63636363636 2674 2.99634406707975e-05 240 1.00405421674136 -1.07389723414976 -1 4.21748390632846 4681 2674 4279 1995 240 4377 4514 2666 720 2626 4411 2892 M1268 KREPPEL_CD99_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KREPPEL_CD99_TARGETS_UP.html Genes up-regulated in ESFT cells (Ewing's sarcoma family of tumors) after knockdown of CD99 [GeneID=4267] by RNAi. 16314831 5/5 Arthur Liberzon 0.0236008813306337 0.0433111041526403 1660 2433.27272727273 2674 0.00238553438919862 477 1.06193251993493 1.06193251993493 1 2.17240653090085 1656 3580 4407 2674 4278 1132 477 3506 602 3087 1367 2893 M8780 MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_COMMON_TARGETS_OF_AML_FUSIONS_DN.html Down-regulated target genes shared by acute myeloid leukemia (AML) translocation products PML RARA [GeneID=5371;5914], AML1 ETO [GeneID=861;862], and PLZF RARA [GeneID=5914;7704]. 15024077 46/71 Arthur Liberzon 0.245559736747469 0.307112336366733 2175 2772.90909090909 2674 0.0252909754619396 1508 1.35665693557847 1.16099116555874 1 1.04359850053223 2171 4115 1589 3967 3744 2855 2460 3548 2674 1871 1508 2894 M13453 DER_IFN_BETA_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_BETA_RESPONSE_UP.html Genes up-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon beta for 6 h. 9861020 167/237 Yujin Hoshida 0.215352705262829 0.275321917766767 3740 2823.36363636364 2675 0.0218060940415909 1507 1.0926512213517 -0.901346757698454 -1 0.918300458949897 3738 2300 2675 3180 2887 3935 4578 1850 1507 1824 2583 2895 M15615 DER_IFN_GAMMA_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_GAMMA_RESPONSE_UP.html Genes up-regulated in HT1080 (fibrosarcoma) cells by treatment with interferon gamma for 6 h. 9861020 128/230 Yujin Hoshida 0.123405185878872 0.172262206624864 4270 2811.18181818182 2675 0.0119022741834222 1111 1.00060491310359 -0.805846659268075 -1 1.14669969525269 4266 1264 1815 1111 1940 3926 3900 4453 3399 2174 2675 2896 M9630 KOMMAGANI_TP63_GAMMA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KOMMAGANI_TP63_GAMMA_TARGETS.html Genes changed in H1299 cells (non-small cell lung cancer, NSCLC) transiently transfected to express the TP63 [GeneID=8626] gamma splice variant. 16462763 14/16 Arthur Liberzon 0.162688137851698 0.216672689238152 4110 2922.45454545455 2676 0.0160121193614569 1045 0.969182633334457 0.921844006309855 1 0.96581954479216 4110 1045 2509 2622 2533 3688 3326 1677 3870 2676 4091 2897 M12053 NIKOLSKY_BREAST_CANCER_22Q13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_22Q13_AMPLICON.html Genes within amplicon 22q13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 24/28 Jessica Robertson 0.186439231283641 0.243495620270832 2680 2780.63636363636 2676 0.0185828651592031 1280 0.888038242526208 -0.980591174373944 -1 0.817406491903443 2676 2569 3052 2933 4522 1971 1280 1988 2602 3504 3490 2898 M1660 MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_DN.html Genes similarly down-regulated in 3T3-L1 cells (fibroblasts able to differentiate to adipocytes) upon stimulation of INSR or IGFR1 by NTF3 [GeneID=3643;3480;4908]. 12213819 14/16 John Newman 0.203316730528706 0.262344168424136 2825 2683.09090909091 2677 0.0204514356338624 1226 1.49949963912793 -1.01672524330744 -1 1.30745051701744 2825 3896 2593 2870 2242 4061 2725 2069 1226 2677 2330 2899 M17552 MAINA_VHL_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAINA_VHL_TARGETS_DN.html Genes down-regulated in RCC4 cells (renal cell carcinoma) engineered to stably express VHL [GeneID=7428] off a plasmid vector. 15824735 23/27 Leona Saunders 0.0151388013827786 0.0304435868371894 2090 2691.54545454545 2678 0.00138581730793444 406 1.13457582828294 1.28035990252573 1 2.58167247738675 2087 4196 2661 4395 1641 3552 2678 645 4371 2975 406 2900 M13944 GOZGIT_ESR1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOZGIT_ESR1_TARGETS_UP.html Genes up-regulated in TMX2-28 cells (breast cancer) which do not express ESR1 [GeneID=2099]) compared to the parental MCF7 cells which do. 17726467 191/244 Arthur Liberzon 6.33824521492444e-08 1.20631118606627e-06 4715 2621.72727272727 2679 5.76204127048234e-09 206 1.43412522595447 -1.63848102242157 -1 12.7362011392057 4712 1749 206 1686 2679 4573 3691 4317 2783 216 2227 2901 M7952 GALLUZZI_PREVENT_MITOCHONDIAL_PERMEABILIZATION http://www.broadinstitute.org/gsea/msigdb/cards/GALLUZZI_PREVENT_MITOCHONDIAL_PERMEABILIZATION.html Proteins acting on mitochondria to prevent membrane permeabilization. 16892093 33/38 Arthur Liberzon 0.00577426225782821 0.0142024584976285 4655 2427 2679 0.000526315789473684 81 0.95338096769863 -0.686163282980322 -1 2.64306244455992 4651 239 2111 81 1329 2679 3260 4156 472 3225 4494 2902 M1037 KANG_DOXORUBICIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANG_DOXORUBICIN_RESISTANCE_UP.html Genes up-regulated in gastric cancer cell lines: doxorubicin [PubChem=31703] resistant vs sensitive. 14734480 67/71 John Newman 0.310143583816059 0.374106239614567 725 2652.63636363636 2679 0.033188737931802 725 0.989629339874161 -0.988643915944687 -1 0.633979027345793 725 3297 3835 3457 3232 1809 1847 2679 1658 4186 2454 2903 M7298 BIOCARTA_ASBCELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ASBCELL_PATHWAY.html Antigen Dependent B Cell Activation 3/14 BioCarta 0.00282427592372216 0.00865622231166792 4290 2828.18181818182 2680 0.0002827871797881 594 1.27226626252672 1.27226626252672 1 3.93766020008916 4288 2190 4185 2042 594 3621 3865 1091 2536 2680 4018 2904 M9948 KIM_WT1_TARGETS_8HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_8HR_DN.html Genes down-regulated in UB27 cells (osteosarcoma) at 8 hr after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 144/204 Arthur Liberzon 0.0957528547231875 0.138934360373023 2755 2500.27272727273 2680 0.00910849720774085 1709 1.13358814151653 1.17718075090408 1 1.45795072008116 2752 2308 1873 1810 1803 3064 3090 2680 1709 2738 3676 2905 M6177 REACTOME_NOTCH_HLH_TRANSCRIPTION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOTCH_HLH_TRANSCRIPTION_PATHWAY.html Genes involved in Notch-HLH transcription pathway 14/14 Reactome 0.393762634366651 0.463019340859639 1860 2630.09090909091 2681 0.0444789795349315 1139 0.950813425238211 0.96755410879807 1 0.476988781173608 1857 3533 3282 2910 4024 2008 1924 2262 1139 3311 2681 2906 M1871 BENPORATH_ES_1 http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_1.html Set 'ES exp1': genes overexpressed in human embryonic stem cells according to 5 or more out of 20 profiling studies. 18443585 502/629 Jessica Robertson 0.56808230650823 0.635390636663234 2295 2869.18181818182 2682 0.0805246315888983 1752 1.13765086840663 1.07569488537701 1 0.336116893790047 2293 3161 4448 2447 3002 2799 2682 2624 1752 2662 3691 2907 M2637 UEDA_CENTRAL_CLOCK http://www.broadinstitute.org/gsea/msigdb/cards/UEDA_CENTRAL_CLOCK.html Molecular timetable composed of 96 time-indicating genes (103 probes) in the central (suprachiasmatic nucleus (SCN)) clock. 15273285 121/147 Kate Stafford 0.0222292110833106 0.0413240946487696 4010 2672.45454545455 2682 0.00204154988510802 1185 1.12099313262195 -1.12069607700921 -1 2.32754073336948 4007 2801 1494 2682 1185 2533 4024 3762 2796 1916 2197 2908 M15031 STREICHER_LSM1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STREICHER_LSM1_TARGETS_UP.html Genes up-regulated in MCF10A cells (breast cancer) by expression of LSM1 [GeneID=27257] off a letiviral vector. 17001308 59/62 Arthur Liberzon 0.478969123731595 0.54898840796822 2815 2685.81818181818 2683 0.0575456689523316 1553 1.07461385212465 1.10624930901922 1 0.419843254199077 2812 1913 1637 1553 3922 4633 2925 2683 1703 2336 3427 2909 M1215 LI_WILMS_TUMOR_ANAPLASTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_ANAPLASTIC_UP.html Selected up-regulated genes distinguishing between Wilms tumors of different histological types: anaplastic vs favorable histology. 15531917 21/24 Leona Saunders 0.588235720932249 0.654828444056654 1710 2568.18181818182 2683 0.0774964188320464 157 1.25709249968819 -1.25512260237934 -1 0.34673142695989 1709 3867 3578 2165 3004 2584 2180 2999 157 3324 2683 2910 M1885 YOSHIMURA_MAPK8_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIMURA_MAPK8_TARGETS_DN.html Genes down-regulated in vascular smooth muscle cells (VSMC) by MAPK8 (JNK1) [GeneID=5599]. 16311603 508/619 Jessica Robertson 0.501211526888425 0.570006875284145 3220 2578.63636363636 2683 0.0671933342641727 1145 1.08001614247403 1.17015384808142 1 0.395511448914812 1851 1145 4600 1370 2878 3801 2683 3219 1860 1742 3216 2911 M19590 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_TURQUOISE_DN.html Genes from the turquoise module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphocholine (oxPAPC). 16912112 79/90 Arthur Liberzon 0.00172553307694906 0.00598421463864773 765 2366.18181818182 2684 0.000156989814349173 30 0.945971921300977 -0.950023820573821 -1 3.1553210280187 762 4067 3760 4082 4017 30 163 1640 2684 4129 694 2912 M19848 ENK_UV_RESPONSE_EPIDERMIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_EPIDERMIS_UP.html Genes up-regulated in epidermis after to UVB irradiation. 16434974 377/554 Lauren Kazmierski 0.0447698141450814 0.0733727509599945 3240 2436.45454545455 2684 0.00415524617818847 460 1.15814371161528 -1.26155059848023 -1 1.97138807915461 3238 3608 2012 3593 3135 460 2684 3151 2132 1605 1183 2913 M5740 JAEGER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAEGER_METASTASIS_UP.html Genes up-regulated in metastases from malignant melanoma compared to the primary tumors. 17289871 57/79 Leona Saunders 0.0149472242772781 0.0301886600722091 1455 2439.63636363636 2685 0.00136815956347251 892 1.51840811481449 1.65839489469674 1 3.46342078430842 1453 3314 892 2685 4157 3207 2772 2286 2018 1203 2849 2914 M18773 CASTELLANO_HRAS_AND_NRAS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_AND_NRAS_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) isolated from HRAS and NRAS [GeneID=3265;4893] double knockout mice. 16909116 5/10 Leona Saunders 1.82798389006473e-05 0.000171192142085427 4065 2570.72727272727 2685 1.82799892710178e-06 47 0.800294616664644 -0.555590568570221 -1 4.52294575383775 4062 2685 4333 1532 47 2444 1708 2397 3110 3083 2877 2915 M2239 JOHNSTONE_PARVB_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_2_DN.html Genes down-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D collagen I and 3D Matrigel only. 17998334 471/524 Arthur Liberzon 0.0373155502800889 0.0628808987226061 1165 2770 2685 0.00345126655989828 994 0.932483828791718 1.01358297910714 1 1.68101960562496 1165 3163 4053 3418 4704 2419 1869 994 1780 4220 2685 2916 M1528 INGRAM_SHH_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/INGRAM_SHH_TARGETS.html Genes up-regulated by in C3H/10T1/2 cells (embryonic pluripotent cell) in response to SSH [GeneID=6469]. 12444557 6/8 John Newman 0.00343607498302758 0.0100174638171033 2715 2407.54545454545 2686 0.000344139954898223 184 1.44580830090793 -1.15363641487351 -1 4.33717893274657 2712 2686 4491 1445 3020 3060 1592 325 4670 2298 184 2917 M18850 JIANG_VHL_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_VHL_TARGETS.html Genes up-regulated in 786-0 cells (renal carcinoma, RCC) upon expression of VHL [GeneID=7428] off a retroviral vector under normoxia (normal oxygen) condition. 12692265 185/212 John Newman 0.409553098912213 0.479437159440884 4285 2712.36363636364 2686 0.0467687776831594 987 0.922028401397603 -0.922951940625472 -1 0.441608939300646 4285 1756 3867 1612 2686 1649 3731 2575 987 3909 2779 2918 M9096 IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_UP.html Genes up-regulated during transition from G2 (moderately differentiated tumor, infected with HCV) to G3 (poorly differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 37/49 Yujin Hoshida 0.000752925798387967 0.00319587209387698 4410 2353.81818181818 2688 6.84712365900957e-05 231 1.02889436655103 -0.844980772786444 -1 3.8525003353415 4409 231 2688 348 355 2599 3430 3847 492 3788 3705 2919 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 0.000232065538822041 0.00132128991946928 2825 2415.90909090909 2689 2.32089776870939e-05 203 0.685194546851836 -0.871073896563054 -1 2.95993468099779 2824 1101 4559 1290 203 2998 1455 3870 896 4690 2689 2920 M569 REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC1_EVENTS_IN_ERBB4_SIGNALING.html Genes involved in SHC1 events in ERBB4 signaling 29/30 Reactome 0.373256100392373 0.44187830294758 3585 2596.63636363636 2691 0.0415849013812081 307 1.10244643416483 -0.865342059387288 -1 0.586649735058779 3583 3003 2691 651 3439 3333 4642 2224 307 2103 2587 2921 M724 REACTOME_RESPONSE_TO_ELEVATED_PLATELET_CYTOSOLIC_CA2_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESPONSE_TO_ELEVATED_PLATELET_CYTOSOLIC_CA2_.html Genes involved in Response to elevated platelet cytosolic Ca2+ 100/153 Reactome 0.0122772073781858 0.0256408932854145 4045 2915.90909090909 2691 0.00112238736722889 864 1.24053831939294 1.14861064916861 1 2.96158976547426 1983 4044 864 4331 2492 2691 2343 4567 4042 1952 2766 2922 M17456 CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_UP http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_UP.html Genes up-regulated in neuroblastoma xenografts: sensitive vs resistant to the topoisomerase inhibitor irinotecan [GeneID=3750]. 16501609 4/6 Arthur Liberzon 0.206395427754168 0.26588057287109 2490 2773.09090909091 2691 0.0228518454993549 1671 2.45643437560646 -2.45643437560646 -1 2.12045854103294 2489 2691 4408 2095 2304 3461 2852 3724 1893 2916 1671 2923 M1863 ZHOU_PANCREATIC_BETA_CELL http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_PANCREATIC_BETA_CELL.html Transcription factors expressed in adult pancreatic beta cells. 18754011 3/13 Jessica Robertson 1.57127701042066e-05 0.000150248278081907 2695 2615.81818181818 2691 1.57128812063272e-06 41 1.39179576777346 -1.8015119287108 -1 7.98431203954677 4605 2692 4583 1729 41 2396 3145 3569 922 2691 2401 2924 M16478 LEE_TARGETS_OF_PTCH1_AND_SUFU_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_TARGETS_OF_PTCH1_AND_SUFU_DN.html Genes down-regulated in medulloblastoma tumors from animals with inactivating mutations of one copy of PTCH1 or SUFU [GeneID=5727;51684] in conjunction with TP53 [GeneID=7157] loss. 17452975 112/167 Jessica Robertson 1.51320092859903e-06 1.99117508474858e-05 4180 2757 2692 1.37563815400708e-07 296 1.31680717640997 -1.35619427499 -1 9.28836310392711 4177 2344 296 3020 2692 4216 4210 2289 3784 943 2356 2925 M17621 CHEN_HOXA5_TARGETS_9HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_9HR_UP.html Genes up-regulated 9 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 330/394 Arthur Liberzon 0.0588535078395517 0.0922885571437488 4115 2808.18181818182 2692 0.00549904951376832 318 0.997203271514233 0.943959091928749 1 1.54836777648083 318 3983 3779 4114 3732 1746 1392 2511 2512 4111 2692 2926 M1788 NIKOLSKY_BREAST_CANCER_16P13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_16P13_AMPLICON.html Genes within amplicon 16p13 identified in a study of 191 breast tumor samples. 19010930 110/165 Jessica Robertson 0.292546113129115 0.356708254706645 2605 2997.27272727273 2693 0.03097229423354 1340 0.99437382554219 -1.0512973590182 -1 0.667877804534664 2601 3231 3434 3966 4648 1340 2499 2693 2034 4191 2333 2927 M19467 SANA_TNF_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/SANA_TNF_SIGNALING_DN.html Genes down-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by TNF [GeneID=7124]. 15749026 122/138 Yujin Hoshida 0.000849313438999234 0.00350416034272411 2695 2682.54545454545 2693 7.72401359180804e-05 600 1.14440186712988 1.0598132019832 1 4.21632959020371 2693 3221 600 4173 3973 2557 2402 1393 4243 1105 3148 2928 M5336 REACTOME_CELL_CYCLE_MITOTIC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE_MITOTIC.html Genes involved in Cell Cycle, Mitotic 361/409 Reactome 0.438990850028578 0.507852159836982 1170 2857.81818181818 2694 0.0511903657804705 1166 0.814981435215251 -0.841273897833958 -1 0.359746846224245 1166 3977 4165 3474 2732 1870 2456 2694 1917 4425 2560 2929 M17406 BIOCARTA_CYTOKINE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CYTOKINE_PATHWAY.html Cytokine Network 5/34 BioCarta 0.00642271115114513 0.0154669370578597 2775 2526.18181818182 2696 0.000644135006208942 213 1.77639266178901 1.26435894503554 1 4.82606020873897 2773 3135 4188 3504 2501 2563 213 2696 1987 1324 2904 2930 M1789 WORSCHECH_TUMOR_REJECTION_DN http://www.broadinstitute.org/gsea/msigdb/cards/WORSCHECH_TUMOR_REJECTION_DN.html Down-regulated genes defining rejection of mammary carcinoma (MMC) tumors. 18381452 13/13 Jessica Robertson 0.163526378110691 0.217482249840084 2920 2393.63636363636 2696 0.0161017127664294 8 1.19219182809053 1.50415743097151 1 1.18518185011016 2917 3908 2954 1334 2122 2791 2085 2939 8 2576 2696 2931 M10668 DORN_ADENOVIRUS_INFECTION_12HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORN_ADENOVIRUS_INFECTION_12HR_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) 12 h after infection with adenovirus Ad12. 15681441 48/77 Arthur Liberzon 0.0348088315931016 0.0593990184813592 2400 2634.63636363636 2696 0.00321564554564604 974 1.37180700981568 1.21242523370139 1 2.52397629217143 2396 2904 1006 3765 3054 2426 2696 4452 2077 974 3231 2932 M1833 MATZUK_SPERMATOZOA http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATOZOA.html Spermatozoa genes, based on mouse models with male reproductive defects. 18989307 119/220 Jessica Robertson 0.0301189470505636 0.0527375425762961 1370 2314.54545454545 2697 0.00277630626185087 910 1.02793014628262 1.13814492527817 1 1.97093455405743 1369 3225 2697 3763 3771 1119 1044 910 3389 2925 1248 2933 M959 REACTOME_DESTABILIZATION_OF_MRNA_BY_KSRP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_KSRP.html Genes involved in Destabilization of mRNA by KSRP 20/20 Reactome 0.279022870641801 0.342876321121921 2230 2655.27272727273 2698 0.0293028116744095 370 0.540010234468436 -0.543807482151316 -1 0.376570491758204 2228 370 3824 2698 3468 1896 1556 3221 2545 4590 2812 2934 M2072 BAE_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAE_BRCA1_TARGETS_UP.html Genes concordantly up-regulated in DU-145 and MCF-7 cells (lprostate, breast cancer) upon expression of BRCA1. 15520196 108/139 Arthur Liberzon 0.0496284380783595 0.0803313538168234 4495 2821 2699 0.00461678727106296 844 1.19601933771534 -1.28502050950902 -1 1.96524326834175 4493 2343 1079 1864 4356 2699 3434 3928 2269 844 3722 2935 M17946 KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_BIOSYNTHESIS.html Valine, leucine and isoleucine biosynthesis 10/11 KEGG 0.00103665602055938 0.00408993105319876 3760 2911.81818181818 2703 9.42858929921638e-05 399 0.502801019568745 -0.497451208987496 -1 1.80176614266874 3757 2153 3418 2703 399 2406 2369 2542 4165 4479 3639 2936 M4151 HINATA_NFKB_TARGETS_FIBROBLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/HINATA_NFKB_TARGETS_FIBROBLAST_UP.html Genes up-regulated in primary fibroblast cells by expression of p50 (NFKB1) and p65 (RELA) [GeneID=4790;5970] components of NFKB. 12673201 114/141 Arthur Liberzon 3.18335078887346e-06 3.76576835175005e-05 3340 2352.45454545455 2703 2.89395945010924e-07 323 1.32335499593608 1.15702081098632 1 8.78501338723723 2703 652 323 1067 4501 2388 3339 2817 3339 449 4299 2937 M13194 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_23 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_23.html Amplification hot spot 23: colocolized fragile sites and cancer genes in the 11q12-q25 region. 16751803 26/28 Arthur Liberzon 0.132109457527584 0.182273206527389 2705 2690.81818181818 2704 0.0127982761027101 1104 1.34778672704038 0.877350996882494 1 1.49499429115761 2704 2551 2327 1894 3449 1763 1104 2784 3691 2726 4606 2938 M16912 BALDWIN_PRKCI_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BALDWIN_PRKCI_TARGETS_UP.html Genes up-regulated in U87MG cells (glioblastoma multiforme) after knockdown of PRKCI [GeneID=5584] by RNAi. 16331246 49/80 Jessica Robertson 0.548160915322289 0.616175165592094 2530 2676.09090909091 2704 0.0696745740124432 1834 1.146133813834 1.15700196253405 1 0.361560230321642 2527 2457 2727 2897 3749 2839 2704 2520 1834 2048 3135 2939 M2438 TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA http://www.broadinstitute.org/gsea/msigdb/cards/TAYLOR_METHYLATED_IN_ACUTE_LYMPHOBLASTIC_LEUKEMIA.html Genes whose DNA methylation differed between primary ALL cells (acute lymphoblastic leukemia) and normal peripheral blood samples. 17363581 108/146 Jessica Robertson 0.554482966096755 0.621653111633417 2880 2753.63636363636 2704 0.0708655264264423 671 1.14625433500372 -1.15675150002554 -1 0.354986802406946 2876 671 1701 2418 3780 2671 4675 2704 2235 2955 3604 2940 M2200 LEE_DIFFERENTIATING_T_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/LEE_DIFFERENTIATING_T_LYMPHOCYTE.html Genes enriched at every T lymphocyte differentiation stage compared to the early passage fetal thymic stromal cultures (TSC). 15210650 264/361 Arthur Liberzon 0.262786503279931 0.325507985276411 1160 2707.81818181818 2705 0.0273355900081627 1159 1.04045407640931 1.07445745676392 1 0.760893760987973 1159 3989 2426 3321 3603 2487 1499 2335 3053 3209 2705 2941 M4779 IGARASHI_ATF4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IGARASHI_ATF4_TARGETS_DN.html Genes down-regulated in A549 cells (lung cancer) after knockdown of ATF4 [GeneID=468] by RNAi. 17297441 121/145 Leona Saunders 0.00889834213603711 0.0199810537022337 3820 2383.54545454545 2706 0.00081223076363547 1 1.18321626325051 -1.10689524538408 -1 3.01704383632853 3819 1 831 237 2706 4619 3728 4627 375 1067 4209 2942 M1137 DARWICHE_PAPILLOMA_RISK_HIGH_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_DN.html Genes down-regulated during skin tumor progression from normal skin to high risk papilloma. 17525749 241/333 Arthur Liberzon 0.0292033504072652 0.0515096464582554 4520 2737.90909090909 2706 0.00269076033534959 1303 1.22150997465764 -1.21263284038823 -1 2.36087391197312 4518 2746 1827 2706 1303 3318 4589 3992 1310 1506 2302 2943 M287 BIOCARTA_ERK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK_PATHWAY.html Erk1/Erk2 Mapk Signaling pathway 49/54 BioCarta 0.0194358288976586 0.0369163430168806 2800 2602.18181818182 2707 0.00178269893416638 1147 0.940186278112417 -0.802741267622049 -1 2.02121676256997 2799 4109 3406 2239 1147 2937 2158 2473 1374 2707 3275 2944 M5275 OSMAN_BLADDER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/OSMAN_BLADDER_CANCER_UP.html Genes up-regulated in blood samples from bladder cancer patients. 16740760 514/594 Leona Saunders 0.440284922031513 0.509099664867403 1785 2909.81818181818 2707 0.0563809484846078 1735 0.893531230709227 0.894633995187409 1 0.393001687869601 1785 2707 4300 2458 2763 3087 2393 2673 1735 4345 3762 2945 M15015 FARMER_BREAST_CANCER_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_1.html Cluster 1: interferon, T and B lymphocyte genes clustered together across breast cancer samples. 15897907 32/84 Leona Saunders 0.222340872124651 0.282630815662221 3390 2931.90909090909 2707 0.0226013109755638 1391 1.46080818315728 -1.28168167246232 -1 1.20280563398984 3389 2521 1391 2595 2848 4238 4538 2707 2016 1949 4059 2946 M9402 SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_DN.html Cell cycle genes down-regulated in H1299 cells (lung cancer) after overexpression of either P53 or P73 [GeneID=7157;7161]. 17982488 26/31 Jessica Robertson 0.0525847781197565 0.0842784898897286 655 2288.27272727273 2708 0.00489867322736803 654 1.23971625618206 -1.29196041359526 -1 1.99829642527738 654 2553 3391 3185 3032 1510 715 2734 1066 3623 2708 2947 M4780 WANG_SMARCE1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_SMARCE1_TARGETS_DN.html Genes down-regulated in BT549 cells (breast cancer) by expression of SMARCE1 [GeneID=6605] off a retroviral vector. 16135788 488/682 John Newman 0.131518685564047 0.181564257344926 3490 2888.45454545455 2709 0.0127372052753359 1172 1.10910843078524 1.16905886178805 1 1.23304508906655 3486 2709 1247 2118 2270 4330 3836 3626 2698 1172 4281 2948 M505 REACTOME_CTNNB1_PHOSPHORYLATION_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CTNNB1_PHOSPHORYLATION_CASCADE.html Genes involved in Beta-catenin phosphorylation cascade 18/18 Reactome 0.00401930073986495 0.0112188642768554 3055 2323.36363636364 2710 0.000366060241610566 652 0.827963713567749 0.792741985957803 1 2.42259119365763 3054 1018 3256 1879 652 3448 3528 1308 1096 3608 2710 2949 M1012 REACTOME_IL_2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_2_SIGNALING.html Genes involved in Interleukin-2 signaling 48/57 Reactome 0.312159715466559 0.376153652540761 2360 2723.72727272727 2711 0.0334459473188085 1142 0.944201041076746 -1.05460500768419 -1 0.601513501396747 2357 2905 2711 1142 2544 2140 2917 3837 4094 3631 1683 2950 M1391 SHIN_B_CELL_LYMPHOMA_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_7.html Cluster 7 of genes distinguishing among different B lymphocyte neoplasms. 19010892 35/37 Jessica Robertson 0.68618940391 0.690284310838704 2715 2763.63636363636 2711 0.1 884 1.06091520283061 0.984376789032156 1 0.256149447310415 2711 2506 2742 2358 4528 2576 2651 3063 884 3348 3033 2951 M1676 SHEN_SMARCA2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHEN_SMARCA2_TARGETS_DN.html Genes whose expression negatively correlated with that of SMARCA2 [GeneID=6595] in prostate cancer samples. 19074882 283/664 Jessica Robertson 3.54008684148272e-17 2.42162462199978e-15 3845 2752.54545454545 2712 3.21826076498428e-18 51 1.3989718418402 -1.41013380472814 -1 30.681362631684 3845 2254 51 2497 2457 4057 4044 4380 2712 94 3887 2952 M6434 FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP.html Top 100 genes positively associated with T-cell acute lymphoblastic leukemia MLL T-ALL) expressing MLL-ENL fusion [GeneID=4297;4298]. 12637319 133/194 Kevin Vogelsang 0.0840404207070383 0.124935680547156 2900 2452 2712 0.00794851873592678 1175 1.05721475533564 -1.06403980396294 -1 1.43288539840064 3275 4027 2900 2771 1745 1252 2896 2712 2603 1616 1175 2953 M90 PID_WNT_CANONICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_WNT_CANONICAL_PATHWAY.html Canonical Wnt signaling pathway 18832364 31/33 Pathway Interaction Database 0.175042348098204 0.230653233674908 2435 2740.90909090909 2713 0.0173409058444279 487 0.949741971178166 0.838090880482273 1 0.907744908885165 2432 2534 3342 2713 4640 2521 1253 3375 487 3852 3001 2954 M2987 ROZANOV_MMP14_CORRELATED http://www.broadinstitute.org/gsea/msigdb/cards/ROZANOV_MMP14_CORRELATED.html Genes whose expression most uniformly correlated with that of MMP14 [GeneID=4323] both in HT1080 cells (fibrosarcoma) and in 190 human tumors. 18519667 21/23 Jessica Robertson 0.552432476640544 0.61994324530275 4550 2864 2713 0.0704775795502974 583 0.909228015988376 0.871533684164567 1 0.283191521752872 4547 975 2713 583 3713 4626 4567 2530 654 2309 4287 2955 M12039 KEGG_ONE_CARBON_POOL_BY_FOLATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ONE_CARBON_POOL_BY_FOLATE.html One carbon pool by folate 18/19 KEGG 0.145895049622757 0.198108352767379 1455 2230.45454545455 2716 0.0142341948562661 183 1.22957723247485 -1.26950549017428 -1 1.29711226636693 1452 3503 2976 2067 3248 1455 1142 2716 183 3065 2728 2956 M18795 REACTOME_METAL_ION_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METAL_ION_SLC_TRANSPORTERS.html Genes involved in Metal ion SLC transporters 19/24 Reactome 0.295604490444914 0.359802072451198 3180 2797.81818181818 2716 0.03135387928492 1341 1.07825649638162 -0.630694983430016 -1 0.718158980423723 3180 3501 2648 3746 2463 2627 2716 2150 1341 3166 3238 2957 M19618 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_UP http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_UP.html Hepatic graft versus host disease (GVHD), day 35: genes up-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 144/220 Arthur Liberzon 2.42266136569352e-06 2.97785459533161e-05 4120 2312.09090909091 2716 2.20242184868714e-07 311 1.25522703276033 -1.21458720851455 -1 8.52476687068852 4120 1247 311 718 4357 2716 3870 1887 2956 481 2770 2958 M4447 SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHARMA_PILOCYTIC_ASTROCYTOMA_LOCATION_UP.html Genes up-regulated in pilocytic astrocytoma (PA) from supratentorial regions compared to the infratentorial PA tumors. 17283119 22/32 Jessica Robertson 0.015810585366185 0.0315276564969975 3130 2531.72727272727 2717 0.00144776061000316 1046 1.1529053868295 0.931092301113436 1 2.59709399865758 3130 2069 2717 2053 1062 4285 2977 3692 1046 3383 1435 2959 M7534 YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIOKA_LIVER_CANCER_EARLY_RECURRENCE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) samples from patients with early recurrence (within 2 years after surgery) after resection. 19167881 96/124 Yujin Hoshida 0.187088067770268 0.24420787607181 3285 2557.09090909091 2717 0.0186540460969932 680 1.07128592347941 1.07496908132187 1 0.98406195399418 3285 680 2029 1216 2816 4692 3813 1771 880 2717 4229 2960 M5190 MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RESPONSE_TO_TRABECTEDIN_UP.html Genes up-regulated in at least 8 of 11 sarcoma cell lines by trabectedin [PubChem=3199]. 15897246 82/105 John Newman 0.0149989542788276 0.0302801814354432 815 2239.18181818182 2718 0.00137292723232656 418 1.02548073280811 -1.00404347288957 -1 2.33701828482818 815 3258 2718 3126 4413 418 1210 639 4136 3150 748 2961 M927 REACTOME_GABA_SYNTHESIS_RELEASE_REUPTAKE_AND_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_SYNTHESIS_RELEASE_REUPTAKE_AND_DEGRADATION.html Genes involved in GABA synthesis, release, reuptake and degradation 23/36 Reactome 0.431330057314255 0.499814448548158 2970 3096.18181818182 2719 0.0500197632899524 2096 0.816702433676045 0.724730232124059 1 0.3689974718214 2969 2581 2363 2431 2719 2096 2665 4447 4612 3866 3309 2962 M2338 KIM_TIAL1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KIM_TIAL1_TARGETS.html Top scoring genes whose transcripts bound TIAR1 [GeneID=7073] in extracts from RKO cells (colon cancer). 17682065 48/66 Arthur Liberzon 0.614355163648415 0.680374559460469 3745 2612.72727272727 2719 0.0829760386584802 301 0.958804284674218 -1.13171081372347 -1 0.240520377746982 3741 1416 2719 878 3693 1972 2339 4578 301 3633 3470 2963 M19938 SU_PANCREAS http://www.broadinstitute.org/gsea/msigdb/cards/SU_PANCREAS.html Genes up-regulated specifically in human pancreas. 11904358 41/94 John Newman 0.0116653663595994 0.0246245658395837 3040 2548.18181818182 2721 0.00106615312382984 968 1.2157098935655 -1.14627034710349 -1 2.93435492884895 3037 4133 2721 2558 968 2120 1217 1607 2784 2947 3938 2964 M1381 PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_UP.html Up-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that were identified as candidate genes for the regulation of left ventricle mass (LVM). 18443592 7/8 Jessica Robertson 0.511926362962969 0.580979185666077 3395 2846.63636363636 2722 0.0692168020360771 805 1.83777507636023 -1.53318739903215 -1 0.650249310501017 3392 1637 4457 805 4620 3281 2722 4104 2385 1728 2182 2965 M16756 MURAKAMI_UV_RESPONSE_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_6HR_DN.html Genes down-regulated in primary keratinocytes at 6 h after UVB irradiation. 11532376 28/31 John Newman 0.213454855235039 0.273481790637726 3170 2830.36363636364 2723 0.0215912404217401 1420 1.41459390104927 -1.62595527806164 -1 1.19508486171646 3166 3007 1420 3937 2272 2723 3383 2062 4503 2025 2636 2966 M2277 KIM_PTEN_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_PTEN_TARGETS_DN.html Genes down-regulated in HCT116 cells (colorectal carcinoma) upon knockout of PTEN [GeneID=5728]. 17060456 5/7 Arthur Liberzon 0.0233800630046841 0.0429559740685516 1840 3045.09090909091 2724 0.00236297505499378 473 0.225146356090085 0.225146356090085 1 0.461708876361333 1840 4295 4677 4220 2724 1706 473 2221 4061 4717 2562 2967 M16586 LAIHO_COLORECTAL_CANCER_SERRATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/LAIHO_COLORECTAL_CANCER_SERRATED_UP.html Genes up-regulated in serrated vs conventional colorectal carcinoma (CRC) samples. 16819509 156/175 Arthur Liberzon 0.372615377398675 0.441230451912129 3020 2408.72727272727 2725 0.0414958707544291 609 0.93528153818706 -0.877722973552631 -1 0.498573738276135 3020 609 3541 623 2725 1811 2989 3297 2412 3638 1831 2968 M2040 GERHOLD_RESPONSE_TO_TZD_UP http://www.broadinstitute.org/gsea/msigdb/cards/GERHOLD_RESPONSE_TO_TZD_UP.html Genes up-regulated in 3T3-L1 cells (fibroblast) induced to differentiate to mature adipocytes and then treated with a TZD derivative AD-5075 [PubChem=128440], a PPARG [GeneID=5468] activator. 12021175 6/8 Arthur Liberzon 0.382673752871135 0.451442167845977 4710 3192.81818181818 2725 0.047090900234475 1825 0.713442792545591 -0.713442792545591 -1 0.369654767617745 2914 3576 4652 2697 2694 2528 1825 2725 4710 4710 2090 2969 M256 PID_TAP63_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TAP63_PATHWAY.html Validated transcriptional targets of TAp63 isoforms 18832364 63/73 Pathway Interaction Database 0.5890270371842 0.655400192246446 3995 2728.45454545455 2726 0.0776577270380115 1374 1.02508001133239 -1.09035972904152 -1 0.282135174395284 3993 1374 2108 2853 3015 1915 2193 4676 2726 1956 3204 2970 M2294 BAKKER_FOXO3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BAKKER_FOXO3_TARGETS_UP.html Genes up-regulated in I/11 erythroblast cells upon expression of an activated form of FOXO3 [GeneID=2309]. 17353275 84/100 Arthur Liberzon 0.0766415235218572 0.115206366567887 3510 2789.27272727273 2726 0.00722267547244434 779 1.00817800453964 -1.00969181256976 -1 1.41968441543375 3508 1326 2272 3291 4683 1919 4053 2726 3923 2202 779 2971 M2345 FARDIN_HYPOXIA_11 http://www.broadinstitute.org/gsea/msigdb/cards/FARDIN_HYPOXIA_11.html Genes in the hypoxia signature, based on analysis of 11 neuroblastoma cell lines in hypoxia and normal oxygen conditions. 20624283 47/53 Paolo Fardin 0.539844532719154 0.608314116013006 4360 2780.63636363636 2726 0.0681307899886362 1816 1.11729704597191 -1.02612152516633 -1 0.361809508173378 4359 2908 2322 2690 3317 1816 2726 3634 1984 1933 2898 2972 M1937 MEISSNER_NPC_ICP_WITH_H3_UNMETHYLATED http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_ICP_WITH_H3_UNMETHYLATED.html Genes with intermediate-CpG-density promoters (ICP) that have no histone H3 methylation marks in neural precursor cells (NPC). 18600261 30/45 Jessica Robertson 0.0128877175408786 0.0266564534587849 4190 2836.27272727273 2728 0.00117853086476782 875 1.3134475380703 -1.61032578591841 -1 3.1024084871218 4188 2540 875 3751 2728 3896 3979 1701 3453 1802 2286 2973 M11472 RIZKI_TUMOR_INVASIVENESS_3D_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_3D_DN.html Genes down-regulated in three-dimentional (3D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 377/565 Jessica Robertson 0.00141518658150193 0.00514217141238577 3935 2378.63636363636 2730 0.000128736158588801 650 1.17349360294733 -1.24274683133032 -1 4.03022337698293 3934 1160 650 874 2091 3110 3451 3431 2730 1118 3616 2974 M5736 BARRIER_COLON_CANCER_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_COLON_CANCER_RECURRENCE_DN.html Down-regulated genes from the 70-gene prognosis predictor for stage 2 colon cancer, based on non-neoplastic mucosa gene expression profiles. 17043639 40/56 Arthur Liberzon 0.00919816811636899 0.0204692850114388 1085 2448.27272727273 2731 0.000839713831503788 880 0.790120565587732 -0.733205783839799 -1 2.00223693581594 1082 2950 3428 2731 880 1180 2019 3536 4068 3265 1792 2975 M9400 REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P75_NTR_RECEPTOR_MEDIATED_SIGNALLING.html Genes involved in p75 NTR receptor-mediated signalling 103/116 Reactome 0.68618940391 0.690284310838704 4290 3146.36363636364 2732 0.1 1612 1.08248061889289 -1.04699114441723 -1 0.261358394838975 4289 2352 2732 2383 3834 4227 4449 3631 1612 2544 2557 2976 M78 EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/EBAUER_TARGETS_OF_PAX3_FOXO1_FUSION_UP.html Genes up-regulated in Rh4 cells (alveolar rhabdomyosarcoma, ARMS) after knockdown of the PAX3-FOXO1 [GeneiD=5077;2308] fusion protein by RNAi for 72 hr. 17525748 268/388 Leona Saunders 9.36089967913433e-07 1.31108149808647e-05 2925 2561.18181818182 2732 8.50991242014257e-08 190 1.24342004714392 1.19065289217584 1 9.10930710960609 2921 2732 280 1546 1895 4526 3705 2657 3118 190 4603 2977 M1490 GREENBAUM_E2A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GREENBAUM_E2A_TARGETS_UP.html Genes up-regulated in pre-B lymphocytes upon Cre-Lox knockout of E2A [GeneID=6929]. 15310760 45/58 Kevin Vogelsang 0.274967170176518 0.338332910123348 2630 2750 2732 0.0288076722017396 799 1.32263749330781 -1.27498087287438 -1 0.933978342200246 2627 3349 2123 2732 4465 3912 2621 3473 799 1281 2868 2978 M8077 SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_DN.html Down-regulated genes whose expression correlated with histologic grade of invasive breast cancer tumors: comparison of grade 1 vs grade 3. 16478745 69/78 Arthur Liberzon 0.00189377177113781 0.00641219710170049 2735 2271.09090909091 2733 0.000172309446116561 504 1.0023725163828 1.13385979330936 1 3.29833145860683 2733 753 2895 1011 504 3624 3114 2089 1084 2834 4341 2979 M2012 DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DAVICIONI_MOLECULAR_ARMS_VS_ERMS_UP.html Genes up-regulated in mARMS (molecular ARMS) compared to the mERMS (molecular ERMS) class of rhabdomyosarcoma tumors. 16849537 444/551 Arthur Liberzon 0.539878777961543 0.608314116013006 2735 2660.54545454545 2734 0.06813709480769 1603 1.09172863952587 1.00418688346579 1 0.353527379047488 2734 3969 2916 1603 2889 2091 2146 2844 1649 2131 4294 2980 M6384 LANDIS_ERBB2_BREAST_TUMORS_65_UP http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_65_UP.html Up-regulated genes from the 65 most significantly changed (p<0.01) genes identified by two analytical methods in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 29/32 Leona Saunders 0.43119990772354 0.499814448548158 2530 2541.72727272727 2734 0.05 182 0.977911275625133 0.986733368363626 1 0.441854748868942 3010 302 2734 984 4096 3987 4613 2527 182 2527 2997 2981 M9526 ST_T_CELL_SIGNAL_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/ST_T_CELL_SIGNAL_TRANSDUCTION.html T Cell Signal Transduction 55/72 Signaling Transduction KE 0.0429598182644688 0.0708491761734076 880 2586.09090909091 2735 0.00398385252272704 640 0.882815933287445 0.846408118909054 1 1.52283614097142 877 3310 2735 3866 2738 1371 640 2319 4435 4014 2142 2982 M590 REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT.html Genes involved in Mitochondrial Protein Import 69/74 Reactome 0.0793747286601074 0.118860634287978 530 2713.63636363636 2735 0.00749018921552215 526 0.597791592322521 -0.555014852199113 -1 0.829583457523738 526 4081 4068 3892 2735 1218 1056 1316 4637 4530 1791 2983 M93 REACTOME_ACETYLCHOLINE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACETYLCHOLINE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Acetylcholine Neurotransmitter Release Cycle 10/18 Reactome 0.265307746296145 0.328121163123698 4215 2809.36363636364 2736 0.0276384680859969 1008 0.912591023419735 -1.2038858494158 -1 0.662618076453918 4212 1615 2804 2581 3796 2423 1509 2736 1008 3654 4565 2984 M1066 REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_I_MHC_MEDIATED_ANTIGEN_PROCESSING_PRESENTATION.html Genes involved in Class I MHC mediated antigen processing & presentation 262/328 Reactome 0.123997275697587 0.172951282887888 1510 2526.81818181818 2736 0.0119629658809149 903 0.805639841643001 -0.711195237329802 -1 0.921151911610999 1510 2736 4115 2760 3639 903 1727 1822 3141 4384 1058 2985 M4170 ST_INTERFERON_GAMMA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_INTERFERON_GAMMA_PATHWAY.html Interferon gamma pathway. 11/15 Signaling Transduction KE 0.00110136049396137 0.00428683359555867 2990 2444.27272727273 2737 0.000100173840185159 413 0.946600304654658 -0.93958370655631 -1 3.36319015253743 2988 1053 2737 2130 413 3753 2662 4294 549 3014 3294 2986 M1463 TIEN_INTESTINE_PROBIOTICS_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_24HR_UP.html Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 24h. 16394013 673/786 Arthur Liberzon 0.445129399196737 0.514197445963925 1485 2795.54545454545 2737 0.0572008734966309 714 0.89154802034478 -0.859547822903286 -1 0.386340440056652 1481 2702 4310 2994 4429 1687 2255 2986 714 4456 2737 2987 M1882 MARSHALL_VIRAL_INFECTION_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARSHALL_VIRAL_INFECTION_RESPONSE_DN.html Genes down-regulated in the influenza-specific CD8+ [GeneID=925] T lymphocytes from bronchoalveolar lavage (BAL) compared to those from spleen. 15831586 40/60 Arthur Liberzon 0.00651490424413684 0.0155956758650023 1205 2355.90909090909 2739 0.000594025211517099 201 1.13924287030827 0.978469245289016 1 3.08887541180638 1205 2945 1834 3085 4622 750 201 4313 2974 1247 2739 2988 M5885 NABA_MATRISOME_ASSOCIATED http://www.broadinstitute.org/gsea/msigdb/cards/NABA_MATRISOME_ASSOCIATED.html Ensemble of genes encoding ECM-associated proteins including ECM-affilaited proteins, ECM regulators and secreted factors 22159717 391/882 Alexandra Naba 4.88092210213914e-39 4.60759046441935e-36 1550 2265 2741 4.43720191103561e-40 5 1.52797221089551 1.4952463886343 1 81.017819302086 1546 2230 5 1952 2839 3922 3179 3092 3384 25 2741 2989 M2904 SUNG_METASTASIS_STROMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SUNG_METASTASIS_STROMA_DN.html Genes down-regulated in metastatic vs non-metastatic stromal cells originated from either bone or prostate tissues. 19047182 60/67 Jessica Robertson 0.0285576372410615 0.050673702172109 1380 2463.63636363636 2742 0.00263047422506603 1143 0.960722419999486 1.00904726540277 1 1.86705785963206 1377 4092 3480 3783 1288 1143 1175 1635 3099 3286 2742 2990 M1897 RASHI_RESPONSE_TO_IONIZING_RADIATION_1 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_1.html Cluster 1: ATM [GeneID=472] dependent genes induced at 30 min after ionizing radiation treatment. 16314843 65/89 Arthur Liberzon 0.526359152020132 0.594784581645924 4615 2730.72727272727 2745 0.0656805769036956 1351 1.1192415800977 -1.13039373847638 -1 0.378844519177212 4611 1362 1813 1351 3942 3568 3754 3793 1530 1569 2745 2991 M965 REACTOME_INTERFERON_GAMMA_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_GAMMA_SIGNALING.html Genes involved in Interferon gamma signaling 83/110 Reactome 0.0192891865326598 0.0367116775944171 2175 2619.81818181818 2746 0.00176912873183127 1142 1.0196738853191 -1.00762313564835 -1 2.19580272695452 2175 3259 2083 2740 1142 2832 3421 2746 3264 2399 2757 2992 M820 REACTOME_CELL_CELL_JUNCTION_ORGANIZATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CELL_JUNCTION_ORGANIZATION.html Genes involved in Cell-cell junction organization 46/69 Reactome 0.0654298681279327 0.10102354516318 2750 2925.81818181818 2748 0.00613280866945584 1121 1.67932980443441 1.67071562524722 1 2.5086178651921 2748 4461 1121 4176 4478 2163 1686 1415 2892 2548 4496 2993 M5793 CHANG_CORE_SERUM_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_CORE_SERUM_RESPONSE_DN.html Down-regulated genes in the canonical gene expression signature of the fibroblast core serum response (CSR) defined by the Stanford group. 14737219 276/325 Arthur Liberzon 0.0523031921997194 0.0839411993140686 3050 2302.18181818182 2748 0.00487178968262961 549 1.1230821758368 1.28348804474635 1 1.81321911807232 3046 549 1354 1448 3988 3522 3601 2923 1306 839 2748 2994 M14698 HOEBEKE_LYMPHOID_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOEBEKE_LYMPHOID_STEM_CELL_UP.html Genes up-regulated in the common lymphoid progenitor (CLP, defined as CD34+CD38-CD7+ [GeneID=947;952;924]) compared to a multipotent cord blood cell (defined as CD34+CD38+CD7-). 17170726 127/163 Arthur Liberzon 0.102688713835752 0.147277644881419 1345 2544.27272727273 2750 0.00980186789693719 985 1.0395308942312 0.880153125482989 1 1.29746509684566 1343 2796 2629 2885 1845 1951 985 4027 3205 3571 2750 2995 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 0.00385839643730599 0.0108791106237063 2755 2579.72727272727 2751 0.000386511210424917 345 1.61879321118159 1.61879321118159 1 4.76907106236708 2751 2187 4363 3719 2066 3114 912 345 4481 2915 1524 2996 M2043 RICKMAN_HEAD_AND_NECK_CANCER_F http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_F.html Cluster f: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 53/93 Jessica Robertson 0.000644956030786902 0.00280829563220865 1235 2037.81818181818 2751 5.86495622651812e-05 100 1.49025823117088 1.63917480000178 1 5.70559034788855 1234 3737 617 2832 3119 3636 2751 100 2817 822 751 2997 M2328 BILANGES_SERUM_AND_RAPAMYCIN_SENSITIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_SERUM_AND_RAPAMYCIN_SENSITIVE_GENES.html Genes translationally regulated in MEF cells (embryonic fibroblasts) in response to serum starvation and by rapamycin (sirolimus) [PubChem=6610346]. 17562867 79/117 Arthur Liberzon 0.00266637629825911 0.00829070891158302 155 2437.18181818182 2753 0.000242692128329525 153 0.614529134927296 0.571758240744319 1 1.91918847835767 153 4090 4138 3924 572 452 418 2753 4494 4387 1428 2998 M2115 VERHAAK_GLIOBLASTOMA_PRONEURAL http://www.broadinstitute.org/gsea/msigdb/cards/VERHAAK_GLIOBLASTOMA_PRONEURAL.html Genes correlated with proneural type of glioblastoma multiforme tumors. 20129251 232/333 Arthur Liberzon 0.00127269249511537 0.00472256963596268 2785 2302.54545454545 2754 0.000115766303656242 638 1.31534579959423 1.32448460228821 1 4.59037476451304 2785 2754 638 1737 3048 2978 2139 2801 1135 704 4609 2999 M268 PID_S1P_S1P2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_S1P_S1P2_PATHWAY.html S1P2 pathway 18832364 32/36 Pathway Interaction Database 0.0535185667180825 0.0855137558934832 2185 2300.72727272727 2756 0.00498787581948285 575 0.732258240939824 -0.648541645903336 -1 1.17333905949612 2181 907 3132 2756 2836 575 1845 2811 4117 3546 602 3000 M1754 ZHENG_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_DN.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are down-regulated both in developing (located in the thymus) and mature (from peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 9/11 Jessica Robertson 0.00117967331294935 0.00448988569632661 3405 2505.72727272727 2757 0.000118030001433156 446 0.954491795530029 0.863003514609226 1 3.3624428437761 3404 1066 4521 800 446 3407 3518 1766 2352 2757 3526 3001 M2300 VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN.html Genes down-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout compared to normal 9.5 dpc embryos. 17371845 35/54 Arthur Liberzon 0.000229251662620664 0.00130842545050729 1785 2801.72727272727 2757 2.08432323040851e-05 528 1.54677602544758 1.51847874134505 1 6.69182886844449 1784 4145 528 3975 3631 3825 2757 2344 4445 1224 2161 3002 M12530 NEBEN_AML_WITH_FLT3_OR_NRAS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NEBEN_AML_WITH_FLT3_OR_NRAS_DN.html Genes down-regulated in acute myeloid leukemia (AML) samples with constitutively activated FLT3 [GeneID=2322] or with activating point mutations within NRAS [GeneID=4893]. 15674343 20/29 Arthur Liberzon 0.0902910216401426 0.132317335066652 1615 2750.45454545455 2758 0.00856587788233172 1022 0.891717529729348 0.949663188196254 1 1.17520614541805 1611 4227 2758 3663 3878 1274 1022 1378 4602 3746 2096 3003 M18631 ROME_INSULIN_TARGETS_IN_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROME_INSULIN_TARGETS_IN_MUSCLE_DN.html Genes down-regulated by 3 h of euglycemic hyperinsulinemic clamp in the vastus lateralis muscle of healthy lean subjects. 12621037 214/353 Jessica Robertson 0.297367799948196 0.361466911088201 2760 2749.81818181818 2758 0.0315745674793195 2067 1.09549582427447 1.01954024164336 1 0.726347046004052 2686 2758 2854 2357 3116 2756 3098 2067 2554 3203 2799 3004 M18834 FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_DN http://www.broadinstitute.org/gsea/msigdb/cards/FONTAINE_THYROID_TUMOR_UNCERTAIN_MALIGNANCY_DN.html Genes down-regulated in thyroid tumors of uncertain malignancy (T-UM) compared to other thyroid tumors. 17968324 27/65 Arthur Liberzon 0.318274538382573 0.383033100756182 3075 2748.54545454545 2758 0.0342302633220333 1492 1.11471814193832 0.984677888451999 1 0.696996858319516 3072 1492 1647 3730 2518 3422 2315 3204 2758 2373 3703 3005 M12517 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_DN.html Genes from the blue module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 65/73 Arthur Liberzon 0.00394250528982703 0.0110618912422338 2760 2550.81818181818 2759 0.000359053474955835 646 1.08431518926519 -1.13593307388551 -1 3.18265556034586 2759 3709 2669 3032 646 2465 4312 1623 2953 3210 681 3006 M1005 REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_INCISION_COMPLEX_IN_GG_NER.html Genes involved in Formation of incision complex in GG-NER 21/21 Reactome 0.323108620617095 0.388059208476511 2560 3132.09090909091 2761 0.0348548450930076 1490 0.563226371216554 -0.550794179499174 -1 0.347329827826168 2558 3865 3848 3592 2527 1490 2700 3879 2761 4593 2640 3007 M7995 HOSHIDA_LIVER_CANCER_SUBCLASS_S2 http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_SUBCLASS_S2.html Genes from 'subtype S2' signature of hepatocellular carcinoma (HCC): proliferation, MYC and AKT1 [GeneID=4609;207] activation. 19723656 178/210 Jessica Robertson 0.256478979572379 0.318993618862089 1300 2831.81818181818 2761 0.0265819692623306 1296 0.917396124322362 -0.734274146927856 -1 0.6829736336274 1296 3199 3243 4326 2727 2036 1477 2146 3960 3979 2761 3008 M2152 IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_UP.html Genes up-regulated during transition from L0 (non-tumor, not infected with HCV) to L1 (non-tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 24/37 Yujin Hoshida 0.00577426225782821 0.0142024584976285 4020 2622.72727272727 2762 0.000526315789473684 175 1.19535514519449 1.09156254643427 1 3.31391543023214 4016 3020 2000 175 2762 4261 4665 1636 831 1701 3783 3009 M8659 IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_DN.html Genes down-regulated during transition from L1 (non-tumor, infected with HCV) to G1 (well differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 12/15 Yujin Hoshida 0.0222711347264305 0.041353169122247 3100 2491.72727272727 2766 0.00204543989043328 436 0.802914632403554 -0.734589744698297 -1 1.66670987332491 3097 3549 3584 3976 1819 730 436 2040 2766 4672 740 3010 M1760 WANG_LSD1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LSD1_TARGETS_DN.html Genes down-regulated after Cre-lox knockout of LSD1 [GeneID=23028] in pituitary. 17392792 31/76 Jessica Robertson 0.245478085929291 0.307091589076664 3255 2607.09090909091 2766 0.0252813859474185 545 1.37994720954215 -1.66182680679607 -1 1.0615769444664 3255 3814 1570 768 2766 4234 3589 4370 545 2260 1507 3011 M16399 WEBER_METHYLATED_ICP_IN_SPERM_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_ICP_IN_SPERM_DN.html Unmethylated germline-specific genes with intermediate-CpG-density promoters (ICP) in sperm. 17334365 9/78 Arthur Liberzon 0.0626435357296562 0.0972943365067381 4365 3008.54545454545 2766 0.00644828377348063 384 1.06050864770101 -1.62795876528777 -1 1.61016511875816 4363 2669 4634 1661 1649 4432 4556 2068 384 2766 3912 3012 M603 REACTOME_YAP1_AND_WWTR1_TAZ_STIMULATED_GENE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_YAP1_AND_WWTR1_TAZ_STIMULATED_GENE_EXPRESSION.html Genes involved in YAP1- and WWTR1 (TAZ)-stimulated gene expression 26/30 Reactome 0.0390688359615045 0.0654614503863335 1770 2651.72727272727 2767 0.00361639975345734 1416 0.761963608413198 0.795569107625688 1 1.35362716601578 1768 3021 3741 3381 1416 2127 2223 2767 1748 3949 3028 3013 M7591 REACTOME_G1_PHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_PHASE.html Genes involved in G1 Phase 40/48 Reactome 0.0574267732362179 0.0906839644278851 2345 2586.81818181818 2767 0.00536208772790225 1575 0.939063387667455 1.0704421338974 1 1.46882070433724 2343 3778 3421 1928 1575 1775 1671 3004 2767 3264 2929 3014 M14262 LU_TUMOR_VASCULATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_VASCULATURE_DN.html Genes down-regulated in endothelial cells derived from invasive ovarian cancer tissue. 17308118 14/17 Arthur Liberzon 2.15437580067059e-05 0.000194058278228343 4360 2653.72727272727 2768 1.95854263448865e-06 51 1.43166573316354 1.37370725742083 1 7.97431850609596 4358 1575 852 2519 51 3907 4331 2768 4217 1160 3453 3015 M19261 YAGI_AML_WITH_T_8_21_TRANSLOCATION http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_T_8_21_TRANSLOCATION.html Genes specifically expressed in samples from patients with pediatric AML (acute myeloid leukemia ) bearing t(8;21) translocation. 12738660 488/708 Arthur Liberzon 0.68618940391 0.690284310838704 3775 2939.81818181818 2768 0.1 591 1.07393106352862 -1.0350540905827 -1 0.259293320594342 3771 1686 2323 591 3565 2535 4478 4431 2768 2067 4123 3016 M738 REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHASE1_FUNCTIONALIZATION_OF_COMPOUNDS.html Genes involved in Phase 1 - Functionalization of compounds 41/126 Reactome 3.54938211703814e-06 4.10614793931863e-05 4520 2574.81818181818 2769 3.22671622133296e-07 199 1.59247741005224 -1.71019299544788 -1 10.4817865955625 4520 1438 331 3271 2769 3357 4320 2279 2660 199 3179 3017 M11350 KYNG_DNA_DAMAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_DNA_DAMAGE_DN.html Genes with GO annotation and down-regulated after DNA damage in cell lines from young donors. 15897889 289/346 Jessica Robertson 0.00143839594083177 0.00521045958612891 2160 2654.45454545455 2769 0.000130848840848124 651 1.20964347664528 1.25715363098722 1 4.14397950267696 2158 2728 651 3385 2393 3796 2769 3464 3106 875 3874 3018 M9869 SASSON_RESPONSE_TO_FORSKOLIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_FORSKOLIN_UP.html Genes up-regulated in primary granulosa cells in response to forskolin [PubChem=47936]. 15026540 127/158 Arthur Liberzon 0.656221704203981 0.690284310838704 4540 2619.81818181818 2772 0.0925065568347234 636 0.961244093243497 -0.915303771879943 -1 0.232074716804263 4539 636 3170 883 3072 2543 3659 4364 1039 2141 2772 3019 M10145 BIOCARTA_PTEN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTEN_PATHWAY.html PTEN dependent cell cycle arrest and apoptosis 23/25 BioCarta 0.51563343543924 0.584049956666007 3090 2760.09090909091 2773 0.0637766494210698 357 0.665444658021135 0.607417705984374 1 0.233096902361901 3089 2568 3656 1673 3949 3687 2045 2699 357 3865 2773 3020 M4361 KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROXIMAL_TUBULE_BICARBONATE_RECLAMATION.html Proximal tubule bicarbonate reclamation 21/32 KEGG 0.13250651104755 0.182554212534861 4010 2676.27272727273 2774 0.0128393425982656 1528 1.81558413494118 -2.00298867688693 -1 2.01209942152265 4010 3039 1528 3729 1988 2857 2774 2452 1551 2793 2718 3021 M1563 MA_PITUITARY_FETAL_VS_ADULT_DN http://www.broadinstitute.org/gsea/msigdb/cards/MA_PITUITARY_FETAL_VS_ADULT_DN.html Down-regulated in human fetal pituitary tissue, compared to adult pituitary tissue 15894316 30/32 John Newman 0.102469874941017 0.147008452802919 1550 2504.09090909091 2774 0.00977991647484093 975 0.863350403194627 0.790097338560134 1 1.0785810696276 1548 3004 3667 3821 2774 1134 975 1740 3215 3438 2229 3022 M115 PID_REG_GR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_REG_GR_PATHWAY.html Glucocorticoid receptor regulatory network 18832364 95/143 Pathway Interaction Database 0.217694643116641 0.277684231249365 3910 3125 2775 0.0220718745162677 1385 1.15570622552508 -1.17083226409981 -1 0.964865605804912 3908 2361 1385 4244 4248 2592 4656 1878 3662 2666 2775 3023 M17778 DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_DN.html Genes down-regulated in CD34+ [GeneID=947] cells isolated from bone marrow of CML (chronic myelogenous leukemia) patients, compared to those from normal donors. 17252012 160/301 Leona Saunders 0.00334415495335667 0.00984679437295289 2955 2643 2775 0.000304477195334307 730 1.22690464680292 1.30443709585152 1 3.69422837581554 2952 2775 730 2602 2090 3137 2894 3779 2720 823 4571 3024 M10427 TSENG_IRS1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSENG_IRS1_TARGETS_UP.html Up-regulated in brown preadipocytes with IRS1 [GeneID=3667] knockout vs wild type controls; the knockouts have severe defects in adipocyte differentiation. 15895078 155/177 John Newman 0.184035652497237 0.241157212600489 2460 2912.36363636364 2775 0.0183196282382564 1331 1.07906248641071 1.2117173317949 1 1.00004575053675 2457 2305 1331 2775 2906 4359 4045 2433 3826 2543 3056 3025 M17428 GAL_LEUKEMIC_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAL_LEUKEMIC_STEM_CELL_UP.html Genes up-regulated in leukemic stem cells (LSC), defined as CD34+CD38- [GeneID=947;952] cells from AML (acute myeloid leukemia patients) compared to the CD34+CD38+ cells. 17039238 161/232 Leona Saunders 0.318976218726166 0.383681894084481 2895 2659.27272727273 2776 0.0343206728024956 1582 1.11717749139644 1.20477961626789 1 0.69730272894114 2892 2776 1582 1607 2523 3494 3148 2105 2868 2155 4102 3026 M3652 DER_IFN_ALPHA_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/DER_IFN_ALPHA_RESPONSE_UP.html Genes up-regulated in HT1080 cells (fibrosarcoma) by treatment with interferon alpha for 6 h. 9861020 144/205 Yujin Hoshida 0.340945765646273 0.407511778640266 4250 2964.54545454545 2777 0.037195111248348 1600 1.10441482522652 -0.876906672002473 -1 0.645968567387328 4247 1783 1600 2207 2562 4425 3742 4019 2777 1789 3459 3027 M14523 IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_STEM_CELL_SHORT_TERM.html Genes in the expression cluster 'ST-HSC Shared': up-regulated in short term hematopoietic stem cells (ST-HSC) from adult bone marrow and fetal liver. 12228721 34/52 John Newman 0.417178828965892 0.488001009347958 2780 2578 2778 0.0478945984886692 1420 0.90805479309454 -0.986114203729451 -1 0.424437903513378 2778 1462 2989 2037 3477 2199 1833 2881 1420 3291 3991 3028 M8417 CROMER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROMER_METASTASIS_DN.html Metastatic propensity markers of head and neck squamous cell carcinoma (HNSCC): down-regulated in metastatic vs non-metastatic tumors. 14676830 119/149 Kevin Vogelsang 0.0241109225408357 0.0441099048033894 3200 2704.90909090909 2779 0.00221629938929492 830 1.06728657214121 -1.19335124908673 -1 2.17064913589768 3199 4034 2405 3825 3619 1981 2779 830 3876 2267 939 3029 M15693 GENTILE_UV_RESPONSE_CLUSTER_D8 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D8.html Cluster d8: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 62/67 John Newman 0.0457981820753865 0.0747725421638963 3155 2572.72727272727 2779 0.00425275682925178 1381 0.993286709460143 1.08774733357666 1 1.67852140798119 3154 1381 2563 2675 1485 3079 3307 3142 1680 2779 3055 3030 M2164 KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION.html Leukocyte transendothelial migration 100/141 KEGG 0.120115470841759 0.168332845122655 3160 2744.72727272727 2780 0.0115657417714766 681 1.14052346794042 1.1012212765811 1 1.3242120273433 3160 681 1225 2669 4569 3287 2780 3343 2473 1556 4449 3031 M8809 BIOCARTA_PTDINS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTDINS_PATHWAY.html Phosphoinositides and their downstream targets. 39/42 BioCarta 0.00577426225782821 0.0142024584976285 3260 2186.36363636364 2781 0.000526315789473684 129 0.826650660359781 0.761971296949638 1 2.29171336287999 3258 203 2781 129 943 4065 2955 2080 676 3197 3763 3032 M1658 LEE_AGING_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_MUSCLE_UP.html Upregulated in the gastrocnemius muscle of aged adult mice (30-month) vs young adult (5-month) 10464095 70/85 John Newman 0.101648147666505 0.146185026503932 4070 2773.45454545455 2782 0.0096975335803685 949 1.27817508067855 1.30993142618103 1 1.60154976631364 2782 4069 1387 2399 4068 4634 3557 2093 2997 1573 949 3033 M719 REACTOME_SHC1_EVENTS_IN_EGFR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC1_EVENTS_IN_EGFR_SIGNALING.html Genes involved in SHC1 events in EGFR signaling 24/25 Reactome 0.237124495017132 0.297983923450709 2785 2830.90909090909 2783 0.0243052457588986 495 0.867839595101755 -0.764440112859766 -1 0.684605905169777 2783 4193 3559 2238 4076 2152 2333 4325 495 3500 1486 3034 M1877 REACTOME_GOLGI_ASSOCIATED_VESICLE_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GOLGI_ASSOCIATED_VESICLE_BIOGENESIS.html Genes involved in Golgi Associated Vesicle Biogenesis 76/88 Reactome 0.00439610450208504 0.0120217921493867 4470 2581.18181818182 2783 0.000400446689131344 90 0.724493474673174 0.780016854979071 1 2.08719227635294 4470 90 3755 590 675 2678 3639 2783 4149 4098 1466 3035 M16114 SIMBULAN_UV_RESPONSE_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_UV_RESPONSE_NORMAL_DN.html Genes down-regulated in HFK cells (primary keratinocytes) in response to UVB irradiation. 16007217 54/56 Leona Saunders 0.214936490387244 0.275081408521636 2520 2797.18181818182 2783 0.0217589343786334 1772 1.0121187076209 1.10258797102754 1 0.851186872761436 2518 2892 1865 3189 4088 2783 2742 1849 4027 1772 3044 3036 M5369 POOLA_INVASIVE_BREAST_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/POOLA_INVASIVE_BREAST_CANCER_UP.html Genes up-regulated in atypical ductal hyperplastic tissues from patients with (ADHC) breast cancer vs those without the cancer (ADH). 15864312 286/518 Jessica Robertson 4.90111388291739e-16 3.08443433698268e-14 2255 2549.36363636364 2783 4.45555807537942e-17 55 1.42850919059707 1.45263078642154 1 28.9604370700754 2251 2253 55 3021 4414 3152 2783 2259 3579 376 3900 3037 M19016 GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_ERYTHROID_DN.html Genes down-regulated in erythroid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 678/930 Arthur Liberzon 0.0175604218322123 0.0341165155929271 4545 2852.81818181818 2786 0.00177007508378063 993 1.05760138945423 -1.17596468562789 -1 2.32800898562787 4544 3153 4280 2779 1144 2478 4533 2786 1767 2924 993 3038 M17450 LIU_SOX4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_SOX4_TARGETS_UP.html Genes up-regulated in LNCaP cells (prostate cancer) by overexpression of SOX4 [GeneID=6659] and down-regulated by its RNAi knockdown. 16618720 164/194 Arthur Liberzon 0.00634918650294801 0.0153446801300126 3390 2272.18181818182 2788 0.000578871326798721 598 1.02253537980829 -0.984993477565897 -1 2.783242293656 3390 598 2788 793 772 3178 2844 3418 1391 1174 4648 3039 M5315 TAKAYAMA_BOUND_BY_AR http://www.broadinstitute.org/gsea/msigdb/cards/TAKAYAMA_BOUND_BY_AR.html Genes whose promoters bound AR [GeneID=367] in LNCaP cells (prostate cancer) after exposure to the synthetic androgen R1881 [PubChem=13766], based on ChIP-chip analysis. 17297473 15/26 Leona Saunders 0.0154190162770431 0.0308903891458589 2790 3169.72727272727 2789 0.00141165046032088 649 1.24650794722185 -1.1286308179374 -1 2.82454391333189 3368 4599 2129 4563 4643 2786 2746 649 4471 2789 2124 3040 M1636 YIH_RESPONSE_TO_ARSENITE_C3 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C3.html Genes in cluster 3: delayed up-regulation in HFW cells (fibroblast) by sodium arsenite [PubChem=26435]. 12016162 46/51 John Newman 0.00385231402192358 0.0108749534590187 3310 2440 2789 0.000350825109687429 206 0.999379991141274 1.04553983598839 1 2.94444747299344 3306 206 2592 1340 643 2761 2789 3017 3615 2860 3711 3041 M4388 BIOCARTA_CDMAC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CDMAC_PATHWAY.html Cadmium induces DNA synthesis and proliferation in macrophages 26/29 BioCarta 0.000382414514020497 0.00189401522159155 2575 2971.63636363636 2791 3.47710003018152e-05 262 0.820257528297775 -0.68007489167102 -1 3.3509256786531 2575 4183 3349 2791 262 4565 2935 4078 2468 2722 2760 3042 M158 PID_INTEGRIN4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN4_PATHWAY.html Alpha6 beta4 integrin-ligand interactions 18832364 12/12 Pathway Interaction Database 0.00187163746139243 0.00636020284346217 2840 2328.18181818182 2791 0.000170293785941731 207 1.42724424533193 1.70562356556384 1 4.70399971336254 2839 3096 1825 3049 1811 3751 4265 207 633 1343 2791 3043 M11545 KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_CHEMOTHERAPY_DN.html Down-regulated genes predicting response of patients with hepatocellular carcinoma (HCC) to combination chemotherapy with 5-fluorouracil (5-FU) [PubChem=3385] and IFN1@ [GeneID=3438]. 15447987 55/68 Yujin Hoshida 0.0973910558784538 0.140964668428795 3835 2694.27272727273 2791 0.00927182925372351 797 0.954669227730213 -1.0630843304918 -1 1.21879398990514 3835 797 2791 2387 3773 4217 4037 2204 1619 3045 932 3044 M1923 MIKKELSEN_PLURIPOTENT_STATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_PLURIPOTENT_STATE_DN.html Genes down-regulated in the induced pluripotent cells (iPS) and embryonic stem cells (ES) compared to the parental lineage-committed and partially reprogrammed cell lines. 18509334 15/17 Jessica Robertson 0.292072876870709 0.356223250343603 3870 2706.36363636364 2791 0.030913383915242 1022 0.940039671314467 -0.85662760083033 -1 0.63221161490961 3868 1022 1966 1058 3641 3555 4219 2057 3807 2791 1786 3045 M16169 ALCALA_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/ALCALA_APOPTOSIS.html Genes able to induce cell death in an expression cDNA library screen. 17621274 130/200 Jessica Robertson 0.00151912771655749 0.00544027528236067 2005 2473.27272727273 2792 0.000138197973506409 32 0.793252787655921 -0.691100998654702 -1 2.69516591174893 2004 2792 3965 3225 1249 585 1830 3232 4029 4263 32 3046 M4229 SESTO_RESPONSE_TO_UV_C6 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C6.html Cluster 6: genes changed in primary keratinocytes by UVB irradiation. 11867738 50/61 John Newman 0.43119990772354 0.499814448548158 4395 2442.63636363636 2793 0.05 176 1.20786661188742 1.15532654387441 1 0.545781552387036 4391 176 1756 333 3379 2793 3667 4233 356 2125 3660 3047 M793 REACTOME_CLASS_C_3_METABOTROPIC_GLUTAMATE_PHEROMONE_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLASS_C_3_METABOTROPIC_GLUTAMATE_PHEROMONE_RECEPTORS.html Genes involved in Class C/3 (Metabotropic glutamate/pheromone receptors) 4/16 Reactome 0.0179239345084713 0.0347009724692308 3925 2555.54545454545 2794 0.00180701676173725 510 1.38469477786149 -2.01235375091173 -1 3.03271727664311 3925 2186 4238 1992 2031 3284 3487 752 510 2912 2794 3048 M19358 BIOCARTA_MET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MET_PATHWAY.html Signaling of Hepatocyte Growth Factor Receptor 60/65 BioCarta 0.0407857931865516 0.0677371371711905 2545 2909.27272727273 2795 0.00377837701787371 1439 0.936076754149957 -0.868165524916541 -1 1.64211708240349 2541 3723 3330 2795 1439 2711 1843 4613 3044 2064 3899 3049 M1078 REACTOME_CREATION_OF_C4_AND_C2_ACTIVATORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CREATION_OF_C4_AND_C2_ACTIVATORS.html Genes involved in Creation of C4 and C2 activators 7/11 Reactome 0.006179244588444 0.0150185553333963 2685 2935.81818181818 2795 0.000619649451341875 789 1.52093226149258 -1.72479083829181 -1 4.16117402685475 2684 4282 4263 3948 789 2795 1522 1798 4635 2471 3107 3050 M12482 CADWELL_ATG16L1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CADWELL_ATG16L1_TARGETS_DN.html Genes down-regulated in Paneth cell (part of intestiinal epithelium) of mice with hypomorphic (reduced function) form of ATG16L1 [GeneID=55054]. 18849966 94/111 Jessica Robertson 0.361023577573347 0.429227024218186 2795 2687.63636363636 2795 0.0398992630646681 1805 1.17865625354783 1.21032435689662 1 0.649522873840208 2795 4045 1805 2899 2599 2201 2444 2948 3136 2851 1841 3051 M2269 MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_DN.html Proteins significantly repressed by oxidative stress (hydrogen peroxide [PubChem=784] in 786-O cells (renal clear cell carcinoma, RCC) expressing VHL [GeneID=7428]. 18285459 12/14 Arthur Liberzon 0.0172557072924924 0.0336750880219456 840 2279.36363636364 2795 0.00158114160083235 290 0.754290646101199 -0.784467351249497 -1 1.66672774764507 839 3551 2795 3319 4061 842 1174 860 3535 3807 290 3052 M1687 ZHONG_SECRETOME_OF_LUNG_CANCER_AND_FIBROBLAST http://www.broadinstitute.org/gsea/msigdb/cards/ZHONG_SECRETOME_OF_LUNG_CANCER_AND_FIBROBLAST.html Proteins secreted in co-culture of LKR-13 tumor cells (non-small cell lung cancer, NSCLC) and MLg stroma cells (fibroblasts). 18757440 192/257 Jessica Robertson 0.030962133031926 0.0539664947971532 3245 2823.27272727273 2796 0.00285515168461743 992 1.16227386217474 -0.938003747859312 -1 2.2110888907881 3241 2762 992 2676 1627 2796 4304 3713 2855 1915 4175 3053 M18983 GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_NORMAL_QUIESCENT_UP.html Genes up-regulated in quiescent (G0) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the quiescent cells from normal donors. 17717066 124/198 Arthur Liberzon 0.0484018181180372 0.0784265642008704 3400 2723.90909090909 2798 0.00450006343045576 1075 1.31642658300795 -1.53864408957927 -1 2.18368812771112 3397 2798 1075 2451 3084 2618 2756 3680 3342 1832 2930 3054 M14278 SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP.html Cluster 5: genes up-regulated in B493-6 cells (B lymphocytes) by MYC [GeneID=4609] alone or in combination with serum but not by serum alone. 15516975 66/88 Leona Saunders 0.127078100015117 0.176373291457768 1635 2734.81818181818 2799 0.0122793664656769 1063 0.843207093888661 -0.80424460416086 -1 0.953344419088737 1633 3712 3756 3629 2263 1063 1076 2799 3841 4057 2254 3055 M1544 LEE_AGING_CEREBELLUM_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_CEREBELLUM_DN.html Downregulated in the cerebellum of aged adult mice (30-month) vs young adult (5-month) 10888876 118/167 John Newman 0.136339470673392 0.186961737820572 3200 2897.18181818182 2799 0.013236659446926 1293 1.25166144339993 1.08422088355081 1 1.3676467569997 3200 4031 1349 4060 2014 3869 2502 2791 2799 1293 3961 3056 M10654 REACTOME_PYRIMIDINE_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_CATABOLISM.html Genes involved in Pyrimidine catabolism 10/16 Reactome 0.00518901635878273 0.0137210964781258 1550 2313 2800 0.000472845087975993 384 0.935095951074067 -0.935095951074067 -1 2.61338024874399 1550 3932 2816 3316 2800 1231 759 384 4051 3653 951 3057 M19909 AMIT_EGF_RESPONSE_40_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_40_MCF10A.html Genes whose expression peaked at 40 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 21/22 Leona Saunders 0.482480942531983 0.552075163333566 2960 2790.36363636364 2800 0.0581249248966288 1877 1.12523880901687 1.36065300184383 1 0.43551559638633 1877 3872 2078 2724 2960 2956 1982 2919 3927 2800 2599 3058 M11355 KEGG_TIGHT_JUNCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TIGHT_JUNCTION.html Tight junction 114/153 KEGG 0.68618940391 0.690284310838704 2575 2872.81818181818 2801 0.1 1345 1.02433448289881 -1.02428531861378 -1 0.247313677570044 2572 1810 2819 1345 3680 4569 2801 3683 1668 2721 3933 3059 M1308 GROSS_HYPOXIA_VIA_HIF1A_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_HIF1A_UP.html Genes up-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of HIF1A [GeneID=3091] by RNAi. 17704799 120/154 Jessica Robertson 0.3185042725227 0.383211870075744 2325 2867.63636363636 2802 0.0342598545824996 1431 0.941995519849883 1.00377101515234 1 0.588696206656272 2323 2802 3546 3642 2520 2899 1937 2782 1431 3869 3793 3060 M12948 CHUANG_OXIDATIVE_STRESS_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHUANG_OXIDATIVE_STRESS_RESPONSE_DN.html Genes down-regulated in MCF7 cells (breast cancer) after treatment with the oxydants: hydrogen peroxyde, menadione, and t-butyl hydroperoxyde [PubChem=784;4055;6410]. 12414654 21/38 John Newman 0.192993142173989 0.250875139372412 4615 3074.81818181818 2802 0.0193042500236474 927 1.10968812539367 -1.41454962546549 -1 0.999862864410405 4612 3035 2402 2746 2210 4102 4464 2514 927 2802 4009 3061 M1659 CARDOSO_RESPONSE_TO_GAMMA_RADIATION_AND_3AB http://www.broadinstitute.org/gsea/msigdb/cards/CARDOSO_RESPONSE_TO_GAMMA_RADIATION_AND_3AB.html Down-regulated synergystically by gamma-irradiation and 3-aminobenzamine [PubChem=1645], an inhibitor of PARP1 [GeneID=142]. 12379459 21/42 John Newman 0.000541507325640154 0.00244975518656451 3850 2247.63636363636 2803 4.92400598213923e-05 156 0.818036614327355 -0.800772519589443 -1 3.20469478961906 3847 964 3022 1224 321 3586 2870 3352 156 2803 2579 3062 M17204 CHIARETTI_T_ALL_RELAPSE_PROGNOSIS http://www.broadinstitute.org/gsea/msigdb/cards/CHIARETTI_T_ALL_RELAPSE_PROGNOSIS.html Genes whose expression predicted relapse in less than 2 years after chemotherapy for adult patients with T-ALL (T cell lymphoblastic leukemia). 14684422 32/68 Arthur Liberzon 0.68618940391 0.690284310838704 3415 2704.81818181818 2803 0.1 666 1.16978258961126 -1.07582323879552 -1 0.282445462359416 3415 2003 2307 1825 4489 3414 3136 2803 666 1951 3744 3063 M874 REACTOME_SIGNALING_BY_ILS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ILS.html Genes involved in Signaling by Interleukins 118/135 Reactome 0.68618940391 0.690284310838704 1950 2511.90909090909 2804 0.1 649 0.926921557027368 0.879779935147066 1 0.223784392625934 1949 649 2701 1125 3117 2878 2391 2804 3379 3104 3534 3064 M1739 GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_UP.html FOXP3 [GeneID=50943] target genes up-regulated in T lymphocytes after stimulation with IL2 [GeneID=3558]. 17220874 21/28 Jessica Robertson 0.43119990772354 0.499814448548158 4150 2851.81818181818 2804 0.05 367 0.951088027854704 0.734655051524103 1 0.429732158256064 4149 367 2582 1230 2754 3992 4650 3978 1803 2804 3061 3065 M1599 LEE_AGING_CEREBELLUM_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_CEREBELLUM_UP.html Upregulated in the cerebellum of aged adult mice (30-month) vs young adult (5-month) 10888876 114/161 John Newman 0.000714753784019091 0.00306247860200776 3665 2713 2805 6.49987367893299e-05 593 1.23629802242295 1.2787625818852 1 4.66345487828078 3665 2805 593 2005 3915 4347 3804 2055 1745 873 4036 3066 M6041 DAIRKEE_CANCER_PRONE_RESPONSE_E2 http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_CANCER_PRONE_RESPONSE_E2.html 'Cancer prone response profile' (CPRP): genes changed in response to estradiol [PubChem=5757] in epithelial cell cultures from patients at high risk of breast cancer. 18381411 46/58 Jessica Robertson 0.436282130351812 0.504966075345893 4125 2859.45454545455 2805 0.050774810066753 1604 1.10081849637371 -1.09258340600992 -1 0.490045739518202 4125 2918 1990 3372 3527 2482 4048 2805 2620 1604 1963 3067 M12322 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_3.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 3. 12554760 19/24 Arthur Liberzon 0.175601520653217 0.231196423286802 4435 2879.54545454545 2805 0.0174014759356936 1312 1.72821382447039 -1.24025960611253 -1 1.64923077454747 4432 2591 1312 1560 2805 2029 3625 4423 3185 2108 3605 3068 M840 REACTOME_CELL_EXTRACELLULAR_MATRIX_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_EXTRACELLULAR_MATRIX_INTERACTIONS.html Genes involved in Cell-extracellular matrix interactions 20/22 Reactome 0.0517021982662137 0.0830896751162848 740 2511 2806 0.00481443592617049 593 0.757130822118345 0.788627876349145 1 1.22738594472235 736 3048 2806 3355 4664 1411 1128 1743 4072 4065 593 3069 M17405 ZHAN_MULTIPLE_MYELOMA_SUBGROUPS http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_SUBGROUPS.html Top genes up-regulated in MM4 vs MM1 subgroup of multiple myeloma samples. 11861292 33/37 Kevin Vogelsang 0.0891874505549726 0.130944959178103 1730 2862.45454545455 2806 0.00845660065861363 915 0.529543889884266 -0.507507741869611 -1 0.701447684553868 1727 2973 4037 2757 3950 1564 915 2454 3627 4677 2806 3070 M2171 FIGUEROA_AML_METHYLATION_CLUSTER_4_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_4_DN.html Cluster 4 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 21/34 Arthur Liberzon 0.163723894082566 0.217683600019637 2215 2830.27272727273 2806 0.0161228356938776 2099 1.01556338388514 1.27300011372279 1 1.00896385047225 2215 3036 2099 3386 2124 2373 2284 3720 3513 2806 3577 3071 M14702 KIM_GASTRIC_CANCER_CHEMOSENSITIVITY http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GASTRIC_CANCER_CHEMOSENSITIVITY.html Genes up-regulated in gastric cancer patients refractory to chemotherapy treatment with 5-fluorouracil and cisplatin [PubChem=3385;2767] compared to the sensitive state. 15033468 122/169 John Newman 0.00883421118421695 0.0198843475391054 4065 2698 2807 0.000806353283986241 641 1.02084200889657 0.987923783359922 1 2.6062241512764 4063 641 2443 798 861 4430 4284 4107 1094 2807 4150 3072 M4034 YEGNASUBRAMANIAN_PROSTATE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/YEGNASUBRAMANIAN_PROSTATE_CANCER.html Genes expressed in at least one prostate cancer cell line but not in normal prostate epithelial cells or stromal cells 18974140 116/278 Leona Saunders 0.0831945356502615 0.123834187407516 3625 2722.36363636364 2807 0.00786526680153461 870 1.33988349170456 1.26571207388009 1 1.82375824938254 3624 2807 1433 1520 4561 4165 3634 2394 870 922 4016 3073 M19251 TIEN_INTESTINE_PROBIOTICS_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_6HR_UP.html Genes up-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 6h. 16394013 85/131 Arthur Liberzon 0.0535710718804909 0.0855352980421861 4325 2514.09090909091 2808 0.00499289388752528 682 0.928444465284223 0.871755536310628 1 1.48757536856096 971 4064 3381 4322 1557 682 720 2808 4325 3271 1554 3074 M11038 GEORGES_CELL_CYCLE_MIR192_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GEORGES_CELL_CYCLE_MIR192_TARGETS.html Experimentally validated direct targets of MIR192 [GeneID=406967] microRNA; MIR192 caused cell cycle arrest in HCT116 cells (colon cancer). 19074876 76/85 Jessica Robertson 0.205563842535713 0.264953942318014 1570 2451.36363636364 2808 0.0207029308659559 1140 1.10977304180268 1.14663492173698 1 0.960452027552109 1566 3271 3067 3360 4186 1212 1333 1868 1140 3154 2808 3075 M13788 MCBRYAN_PUBERTAL_BREAST_5_6WK_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_5_6WK_UP.html Genes up-regulated during pubertal mammary gland development between week 5 and 6. 17486082 150/174 Arthur Liberzon 8.85697281437106e-08 1.63940830132672e-06 3105 2151 2811 8.05179379176695e-09 184 1.59059539433073 1.6661725667089 1 13.8078179027823 3101 603 213 245 2811 3467 3513 3768 1241 184 4515 3076 M11298 CAFFAREL_RESPONSE_TO_THC_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated THC (delta-9-tetrahydrocannabinol) [PubChem=6610319]. 18454173 47/71 Jessica Robertson 0.00039096125144516 0.00193026894018949 3860 2423.90909090909 2811 3.55482496660564e-05 266 1.00356626588201 -0.977482149872153 -1 4.08740445133275 3859 1425 2811 1823 266 2968 3093 3052 748 1929 4689 3077 M1023 REACTOME_LIPID_DIGESTION_MOBILIZATION_AND_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIPID_DIGESTION_MOBILIZATION_AND_TRANSPORT.html Genes involved in Lipid digestion, mobilization, and transport 38/63 Reactome 0.0725754562586274 0.110013761895144 4135 2696.36363636364 2812 0.00682603625563802 874 1.32920830604278 -1.44407520460073 -1 1.911731683757 4132 874 1138 1024 2962 2812 2491 4420 3659 2381 3767 3078 M19508 HATADA_METHYLATED_IN_LUNG_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/HATADA_METHYLATED_IN_LUNG_CANCER_UP.html Genes with hypermethylated DNA in lung cancer samples. 16407832 450/744 Arthur Liberzon 2.030138377873e-08 4.22125689143638e-07 2845 2854.27272727273 2812 1.84558036055174e-09 186 1.2889959940022 -1.25473114185894 -1 12.3293374722139 2845 2713 186 2812 2055 4715 3461 4634 2672 800 4504 3079 M2259 KIM_GLIS2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GLIS2_TARGETS_UP.html Partial list of genes up-regulated in the kidney of GLIS2 [GeneID=84662] knockout mice compared to the wild type. 18227149 123/190 Arthur Liberzon 9.26237548364122e-10 2.46996679563766e-08 1010 2284.81818181818 2813 8.42034135230986e-11 141 1.3719774101241 1.49323205369327 1 15.6609060731807 1007 3227 141 3178 1247 2813 2929 2332 4252 506 3501 3080 M9464 WONG_ENDOMETRIAL_CANCER_LATE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ENDOMETRIAL_CANCER_LATE.html Genes down-regulated in late stage (stage 3) endometrial cancers compared to the earlier stages (stage 1 and 2). 17043662 13/28 Arthur Liberzon 0.0101095929742309 0.0220425873321937 2990 2853.81818181818 2814 0.000923304578609326 478 1.53865348636826 -1.33606180206897 -1 3.82493713682442 2989 4613 844 4360 2814 2455 478 1480 4664 2573 4122 3081 M11749 HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP.html Genes up-regulated in SCLC (small cell lung cancer) cells with acquired resistance to ABT-737 [PubChem=11228183], an inhibitor of the BCL2 [GeneID=596] family proteins. 18381439 75/114 Jessica Robertson 0.226342642949928 0.287033120559822 2815 2794.27272727273 2814 0.0230596216685986 1092 1.31261589845087 1.10770806593036 1 1.06755480286366 2814 2848 1400 2111 2425 4528 3509 4058 1092 1572 4380 3082 M4932 GAJATE_RESPONSE_TO_TRABECTEDIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GAJATE_RESPONSE_TO_TRABECTEDIN_UP.html Genes up-regulated in HeLa cells (cervical carcinoma) by trabectedin [PubChem=3199]. 12198119 100/142 John Newman 0.00233074641359465 0.00749395304643513 3795 2542.36363636364 2815 0.000212110849576534 561 1.35329586356702 -1.28723830060809 -1 4.31560725014222 3791 2815 697 2586 1419 2961 4431 3790 2042 561 2873 3083 M13863 BIOCARTA_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MAPK_PATHWAY.html MAPKinase Signaling Pathway 102/109 BioCarta 0.130393098141437 0.180168449422595 1730 2875.09090909091 2816 0.0126209525543073 1094 0.814674088102846 0.903705508402919 1 0.909778395766001 1728 2816 3913 3898 4606 2133 1094 2583 1956 3607 3292 3084 M1620 SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_BLUNTED_BY_INSULIN_RESISTANCE_DN.html Genes down-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] but displayed blunted response to insulin the insulin resistant cells. 14530283 27/28 John Newman 0.00278861755916367 0.0085744699659703 4615 3170 2816 0.000253832596937261 580 1.06509780504732 1.09083984609548 1 3.30304359758849 4613 2549 2706 2413 580 4554 4347 3612 2075 2816 4605 3085 M1725 LEIN_LOCALIZED_TO_DISTAL_AND_PROXIMAL_DENDRITES http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_LOCALIZED_TO_DISTAL_AND_PROXIMAL_DENDRITES.html Transcripts showing subcellular localization to both distal and proximal dendrites in the adult mouse brain. 17151600 29/31 Jessica Robertson 0.176790749114116 0.232502740545731 3440 2703.54545454545 2816 0.0175304185495694 1313 1.10645619798348 1.12005270688485 1 1.05178812343239 3439 2991 1313 1984 3356 3166 2816 2731 3840 1392 2711 3086 M1223 DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_DN.html Genes that classify skin lesions into low risk papilloma. 17525749 47/58 Arthur Liberzon 0.38784590159194 0.456516871699241 1765 2763.45454545455 2818 0.0436349302203881 1560 1.05138391989056 1.07261160761375 1 0.537142793964459 1765 2462 1560 3204 3404 3029 2818 2777 4160 2253 2966 3087 M13337 ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN http://www.broadinstitute.org/gsea/msigdb/cards/ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_DN.html Hepatic graft versus host disease (GVHD), day 35: genes down-regulated in allogeneic vs syngeneic bone marrow transplant. 12663442 47/96 Arthur Liberzon 0.00918405212569448 0.0204475122798481 3520 2581 2818 0.000838419742258317 833 1.3660526498559 -1.47367627669847 -1 3.46272544134323 3520 2906 833 2818 1887 1753 1876 3574 3244 1383 4597 3088 M1996 KYNG_WERNER_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_UP.html Genes distinctly up-regulated in primary fibroblast cultures from Werner syndrom patients compared to those from normal young donors. 14527998 27/29 Arthur Liberzon 0.0572892275733071 0.0904970395401639 4320 2839.36363636364 2818 0.00534889376313616 1423 1.0460815318108 0.977077323882803 1 1.63763007034229 4318 3435 2630 2580 1574 2864 4562 2888 1423 2818 2141 3089 M3910 RODRIGUES_THYROID_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_UP.html Genes up-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to anaplastic thyroid carcinoma (ATC). 17406368 17/18 Arthur Liberzon 0.43119990772354 0.499814448548158 4055 2719.09090909091 2819 0.05 117 1.25926007428814 -0.942339410100982 -1 0.569008490086548 4052 387 1917 697 4485 4459 4306 2819 117 2420 4251 3090 M6998 FURUKAWA_DUSP6_TARGETS_PCI35_UP http://www.broadinstitute.org/gsea/msigdb/cards/FURUKAWA_DUSP6_TARGETS_PCI35_UP.html Genes up-regulated in PCI-35 cells (pancreatic cancer, lack endogenous DUSP6 [GeneID=1848]) upon expression of DUSP6 off an adenoviral vector. 16532023 99/159 Arthur Liberzon 0.00108142361533506 0.00421844583833179 3365 2630.36363636364 2819 9.8359596537834e-05 535 1.4832158104864 -1.33952515595953 -1 5.28534315813891 3361 2822 625 3524 2819 2208 3911 4655 1822 535 2652 3091 M543 REACTOME_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CYCLE.html Genes involved in Cell Cycle 434/635 Reactome 0.494812503953661 0.56413406247857 1405 3050.09090909091 2821 0.0601876564034653 1403 0.883415051323798 -0.943763987721561 -1 0.329457292848393 1403 4318 4141 3476 3553 2035 2821 2437 2501 4406 2460 3092 M1417 JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN http://www.broadinstitute.org/gsea/msigdb/cards/JECHLINGER_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN.html Genes down-regulated during epithelial to mesenchymal transition (EMT) induced by TGFB1 [GeneID=7040] in the EpH4 cells (mammary epithelium cell line transformed by HRAS [GeneID=3265]). 14562044 102/124 Arthur Liberzon 0.0336652062585888 0.057739743292347 2825 2589.63636363636 2821 0.00310833431681597 957 1.14184380339117 1.14441817029379 1 2.12193305888806 1775 2821 1343 3806 4596 2886 2866 957 2582 2029 2825 3093 M1700 BAFNA_MUC4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAFNA_MUC4_TARGETS_DN.html Genes down-regulated in NIH3T3 cells (fibroblast) engineered to stably express MUC4 [GeneID=4585]. 19010895 6/7 Leona Saunders 0.0196874172164641 0.0373117551581051 2740 2766 2821 0.00198640409793695 791 0.940285180053862 0.940598947439369 1 2.01490107284009 2736 3951 4515 2854 2056 2821 2233 791 2365 3239 2865 3094 M1884 YOSHIMURA_MAPK8_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YOSHIMURA_MAPK8_TARGETS_UP.html Genes up-regulated in vascular smooth muscle cells (VSMC) by MAPK8 (JNK1) [GeneID=5599]. 16311603 1201/2045 Jessica Robertson 2.94838159295747e-11 9.94025794197089e-10 4300 2785.63636363636 2822 2.94838159299658e-12 63 1.27463102406795 -1.23659684868245 -1 17.2183563315224 4297 1111 4599 1156 2367 2822 4330 4451 2576 63 2870 3095 M126 KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP.html Genes up-regulated in glioma cell lines treated with both decitabine [PubChem=451668] and TSA [PubChem=5562]. 16885346 147/241 Arthur Liberzon 6.15616658597725e-08 1.18118318235011e-06 3445 2023.45454545455 2823 5.59651523476605e-09 205 1.28161754641223 -1.35924467109291 -1 11.3993784705438 3442 1243 205 507 895 3004 2823 3043 2841 464 3791 3096 M7223 REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS.html Genes involved in Trafficking of AMPA receptors 25/32 Reactome 0.0384820207610289 0.0645699033032551 4060 2634.45454545455 2825 0.00356110009596069 475 1.08326350145023 -1.17877909082815 -1 1.93414094973575 4058 2047 2136 3047 3373 1810 2825 1974 3656 3578 475 3097 M17915 KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_UP.html Genes up-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 24 h. 18701491 940/1166 Jessica Robertson 0.00525070999993344 0.0138068808911899 2830 2601.18181818182 2829 0.000526315789473684 39 1.04452490224315 1.04400286195925 1 2.91497924501214 2829 469 4503 39 2371 3452 2958 4274 1293 1786 4639 3098 M1496 KIM_HYPOXIA http://www.broadinstitute.org/gsea/msigdb/cards/KIM_HYPOXIA.html Genes up-regulated in normal fibroblasts under hypoxia conditions. 14499499 38/42 John Newman 0.00227861146780361 0.00736142787681933 3470 2737.09090909091 2830 0.000207361357046354 533 1.23006705509327 1.23555644246302 1 3.93692826158134 3469 4134 2120 4015 533 2412 2028 3234 3330 2003 2830 3099 M2042 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_48HR_UP.html Genes up-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 26/39 John Newman 0.483121136208115 0.552673718589991 4050 2972.36363636364 2830 0.0582309063756582 1210 1.17337364012777 1.12704844682851 1 0.453321786412134 4049 2044 1641 2089 2830 4512 4483 3663 1210 1851 4324 3100 M6787 SCIBETTA_KDM5B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCIBETTA_KDM5B_TARGETS_DN.html Genes down-regulated in HB2 cells (mammary epithelium) upon expression of KDM5B [GeneID=10765] off an adenoviral vector. 17709396 100/109 Leona Saunders 0.68618940391 0.690284310838704 3000 2322 2831 0.1 559 1.18603173009524 0.995156922169904 1 0.286370307580154 2997 674 2346 778 3911 3083 2831 2903 559 2400 3060 3101 M4551 SANA_RESPONSE_TO_IFNG_UP http://www.broadinstitute.org/gsea/msigdb/cards/SANA_RESPONSE_TO_IFNG_UP.html Genes up-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by IFNG [GeneID=3458]. 15749026 105/166 Yujin Hoshida 0.19393304052643 0.251579575735805 2835 2778.63636363636 2832 0.0194081403940376 1740 1.14755122845486 -1.15054561919405 -1 1.03188540782993 2832 3237 1840 2092 2215 3105 4097 3543 2779 1740 3085 3102 M5505 HUPER_BREAST_BASAL_VS_LUMINAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUPER_BREAST_BASAL_VS_LUMINAL_DN.html Genes down-regulated in basal mammary epithelial cells compared to the luminal ones. 17409405 85/112 Jessica Robertson 0.00309498205898973 0.00925748752752315 3395 2484.18181818182 2832 0.000281758609598692 724 1.36748257982029 -1.25470445060212 -1 4.1725181915934 3395 2832 724 2019 2770 2883 4532 2991 3210 726 1244 3103 M683 REACTOME_LATENT_INFECTION_OF_HOMO_SAPIENS_WITH_MYCOBACTERIUM_TUBERCULOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LATENT_INFECTION_OF_HOMO_SAPIENS_WITH_MYCOBACTERIUM_TUBERCULOSIS.html Genes involved in Latent infection of Homo sapiens with Mycobacterium tuberculosis 26/38 Reactome 0.0586942915614051 0.0921307137245866 2150 2736.72727272727 2833 0.00548375592657026 637 1.11534578487225 1.33788543752886 1 1.73306559772836 2147 3842 2318 4000 2061 3184 3316 2833 2572 3194 637 3104 M18483 NAKAMURA_METASTASIS_MODEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_METASTASIS_MODEL_UP.html Top genes up-regulated in orthotopic tumors from highly metastatic pancreatic cancer cells. 17210693 50/65 Jessica Robertson 0.46957579314882 0.539663438924381 2650 2836.63636363636 2834 0.0560135558361427 1629 1.12852254662017 1.09239277319572 1 0.453509249070097 2649 1940 1629 2834 4264 3011 3575 3526 2057 2127 3591 3105 M877 REACTOME_INTERACTION_BETWEEN_L1_AND_ANKYRINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERACTION_BETWEEN_L1_AND_ANKYRINS.html Genes involved in Interaction between L1 and Ankyrins 16/27 Reactome 0.0204113714523645 0.0384488191464814 2820 2628.54545454545 2835 0.00187302208549525 766 1.36060548455086 -1.02312941515855 -1 2.8890194358574 2819 3062 1713 2835 1591 4015 3438 766 3654 2892 2129 3106 M1938 MEISSNER_BRAIN_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_BRAIN_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing the H3K27 tri-methylation (H3K27me3) mark in brain. 18600261 140/357 Jessica Robertson 1.39044673131176e-08 2.99676190492763e-07 4245 2516.81818181818 2835 1.2640424909997e-09 171 1.44817486618753 -1.43441063653699 -1 14.175229641588 4243 2786 179 1415 2895 2835 4385 4145 3186 171 1445 3107 M17034 REACTOME_INTEGRATION_OF_ENERGY_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRATION_OF_ENERGY_METABOLISM.html Genes involved in Integration of energy metabolism 128/186 Reactome 0.224772999844881 0.285349262847724 3695 2479.45454545455 2836 0.0228795988930661 10 1.06665600138116 -1.12914945793974 -1 0.871584772859714 3695 10 1396 587 4625 2853 2836 3265 1812 1793 4402 3108 M16639 KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_DN.html Genes down-regulated in MEWO cells (melanoma) after 48h of methionine [PubChem=876] deprivation. 16908595 82/93 Arthur Liberzon 0.636584470459662 0.690284310838704 2655 2475.90909090909 2836 0.0879121297020752 542 0.96656046958878 1.07560625986573 1 0.233358843451515 2655 712 2836 876 3037 2898 2964 4341 542 2604 3770 3109 M16963 RAMASWAMY_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMASWAMY_METASTASIS_DN.html Down-regulated genes in metastatic vs primary solid tumors. 12469122 74/105 John Newman 0.0510236463767004 0.0821110163307283 2935 2754.81818181818 2836 0.00474972039942499 933 1.27970491224327 -1.28276429723831 -1 2.08448541442301 2931 4065 1084 2094 2185 2829 4112 2836 2998 933 4236 3110 M888 REACTOME_ORGANIC_CATION_ANION_ZWITTERION_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ORGANIC_CATION_ANION_ZWITTERION_TRANSPORT.html Genes involved in Organic cation/anion/zwitterion transport 5/14 Reactome 0.119331461116205 0.167333480828428 2920 2740.54545454545 2838 0.012626997624053 760 0.697021106979675 -0.892805298490766 -1 0.811944339758515 2916 2184 4249 2293 2838 2283 1095 3175 760 4581 3772 3111 M7999 RIZ_ERYTHROID_DIFFERENTIATION_HEMGN http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_HEMGN.html Selected gradually up-regulated genes whose expression profile follows that of HEMGN [GeneID=55363] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 33/47 Leona Saunders 0.00996615698310013 0.0217778985927003 4340 2815.36363636364 2838 0.000910144800578621 641 1.12559506270816 -1.10294186815402 -1 2.80694860169086 4338 2516 2075 2838 900 3236 4149 4061 641 2822 3393 3112 M17537 JI_RESPONSE_TO_FSH_DN http://www.broadinstitute.org/gsea/msigdb/cards/JI_RESPONSE_TO_FSH_DN.html Down-regulated in ovarian epithelial cells (MCV152) 72 hours following FSH treatment, compared to untreated 15386376 103/115 John Newman 0.00217305369152287 0.007112908061018 2680 2582.45454545455 2839 0.000197745736532543 48 0.956788619741615 -0.800632688645009 -1 3.08366818401222 2680 48 2839 910 529 3768 3652 3329 2788 3636 4228 3113 M7 PID_FCER1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FCER1_PATHWAY.html Fc-epsilon receptor I signaling in mast cells 18832364 78/97 Pathway Interaction Database 0.0188051768652328 0.0360814775625605 2070 2504.09090909091 2841 0.00172435183653758 1133 0.842233602325269 0.790957223848446 1 1.82318155399671 2070 2841 3384 1143 1133 2918 1646 2743 3115 3248 3304 3114 M2170 FIGUEROA_AML_METHYLATION_CLUSTER_4_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_4_UP.html Cluster 4 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 129/172 Arthur Liberzon 0.0328555716992411 0.0565566369148133 4170 2910.45454545455 2841 0.00303243264142658 746 1.03107523779101 -1.10456525661561 -1 1.92998806744473 4615 1799 2109 2588 1358 4168 4292 4170 3329 2841 746 3115 M2247 BRUINS_UVC_RESPONSE_LATE http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_LATE.html Late response genes: differentially expressed only 12 h after UV-C irradiation of MEF cells (embryonic fibroblast). 18195040 1444/1740 Arthur Liberzon 0.305733053968583 0.369636274265296 4335 3226.36363636364 2841 0.0358321433724826 1420 1.03920357478728 -1.00266186991816 -1 0.673883067642752 4333 2695 4674 2211 2736 1420 3890 4693 2789 3208 2841 3116 M2476 LIU_IL13_PRIMING_MODEL http://www.broadinstitute.org/gsea/msigdb/cards/LIU_IL13_PRIMING_MODEL.html Genes up-regulated in BEAS-2B cells (bronchial epithelium) stimulated with IL13 [GeneID=3596] on days 1 to 3, rested on days 4 and 5, and then restimulated on day 6 for 1 h before lysis (priming model). 20123980 26/30 Arthur Liberzon 0.0891320405879698 0.130944959178103 4275 2875.63636363636 2842 0.00845111705670049 884 1.20101225784988 -1.23904920488229 -1 1.59102643508552 4273 3836 2176 3965 2110 4326 2842 3411 1077 2732 884 3117 M2520 RAO_BOUND_BY_SALL4_ISOFORM_B http://www.broadinstitute.org/gsea/msigdb/cards/RAO_BOUND_BY_SALL4_ISOFORM_B.html Loci bound exclusively by SALL4 [GeneID=57167] isoform b in ES cells (embryonic stem). 20837710 608/939 Arthur Liberzon 0.175407389572386 0.231005267517205 1880 2912.90909090909 2842 0.019101785828169 1781 1.10611959542376 1.05031068233302 1 1.05612571202468 1879 4312 4712 3396 3673 2352 2062 1781 2048 2842 2985 3118 M776 REACTOME_PROTEIN_FOLDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROTEIN_FOLDING.html Genes involved in Protein folding 62/70 Reactome 0.68618940391 0.690284310838704 3910 3046.18181818182 2843 0.1 1936 0.968212307589986 -1.11352949386925 -1 0.23375783123126 3910 2428 3416 1936 4564 3082 3707 2843 2185 2778 2659 3119 M4100 PROVENZANI_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PROVENZANI_METASTASIS_UP.html Genes up-regulated in polysomal and total RNA samples from SW480 cells (primary colorectal carcinoma, CRC) compared to the SW620 cells (lymph node metastasis from the same individual). 16531451 261/336 Arthur Liberzon 0.2097752122485 0.269572284729899 4475 3320.90909090909 2844 0.021176011185582 2258 1.12639557841731 -1.18380987020484 -1 0.962155024020231 4474 2737 2634 2454 2258 3214 4580 4719 2728 2844 3888 3120 M5839 COLLIS_PRKDC_REGULATORS http://www.broadinstitute.org/gsea/msigdb/cards/COLLIS_PRKDC_REGULATORS.html Proteins that regulate activity of PRKDC [GeneID=5591]. 15592499 24/24 Jessica Robertson 0.0017869785863009 0.00616109490674964 2845 2725.09090909091 2844 0.000162584703238282 489 0.733232025060486 0.675756500468956 1 2.43177746697582 2844 2557 3669 1859 489 3125 1917 4552 2095 3896 2973 3121 M8673 MARTINEZ_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_TP53_TARGETS_DN.html Genes down-regulated in mice with skin specific knockout of TP53 [GeneID=7157]. 18245467 748/997 Jessica Robertson 0.186069257309937 0.243202376833676 2600 2776.63636363636 2846 0.0203775140278661 1185 1.12773692754877 -1.1381454871787 -1 1.03895445727125 2598 1664 4535 1350 3351 3540 2888 2846 2724 1185 3862 3122 M156 PID_ECADHERIN_NASCENT_AJ_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ECADHERIN_NASCENT_AJ_PATHWAY.html E-cadherin signaling in the nascent adherens junction 18832364 67/73 Pathway Interaction Database 0.0574677149655259 0.0907182657649774 2715 2510.09090909091 2847 0.00536601537067999 643 0.949807656236594 0.816664250921444 1 1.48539331007156 2714 751 3164 643 1576 3198 2847 4016 1839 3037 3826 3123 M11665 PRAMOONJAGO_SOX4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PRAMOONJAGO_SOX4_TARGETS_DN.html Genes down-regulated in ACC3 cells (adenoid cystic carcinoma) after knockdown of SOX4 [GeneID=6659] by RNAi. 16636670 64/70 Leona Saunders 0.68618940391 0.690284310838704 2220 2966.72727272727 2847 0.1 2166 0.92278384764732 -0.781210835498904 -1 0.222784963216046 2217 2419 2847 2166 4282 2289 2788 3127 3597 3713 3189 3124 M2135 LUI_THYROID_CANCER_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_1.html Cluster 1: genes with similar expression profiles across follicular thyrorid carcinoma (FTC) samples. 15608688 72/82 Leona Saunders 0.0104267445167924 0.0225821224662858 1010 2443.72727272727 2847 0.000952408339356511 280 0.935144063512631 1.03522619658683 1 2.30989547130382 1010 4421 3373 4400 3271 578 280 2695 2847 3259 747 3125 M12924 SASSON_RESPONSE_TO_FORSKOLIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/SASSON_RESPONSE_TO_FORSKOLIN_DN.html Genes down-regulated in primary granulosa cells in response to forskolin [PubChem=47936]. 15026540 142/157 Arthur Liberzon 0.0266948439633722 0.0480171077400776 3220 2838.36363636364 2847 0.00245676103659645 1253 0.980117903705 1.04245477799248 1 1.93914738923602 3217 1253 2238 1922 1256 4705 3864 2740 2860 2847 4320 3126 M14091 KEGG_OLFACTORY_TRANSDUCTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OLFACTORY_TRANSDUCTION.html Olfactory transduction 29/833 KEGG 0.103892128806294 0.148822715619334 3310 2665.18181818182 2848 0.00992266780153579 1201 1.27037678557044 1.08246414385665 1 1.57697349184054 3308 3414 1201 2848 3679 2719 1516 3010 3575 1732 2315 3127 M522 REACTOME_CELL_CELL_COMMUNICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CELL_CELL_COMMUNICATION.html Genes involved in Cell-Cell communication 124/162 Reactome 0.600952045680011 0.667096344216758 3660 2789.27272727273 2848 0.080123437713021 1271 1.0594762329048 -1.01994546790348 -1 0.279393106680307 3656 1271 1738 1596 4284 2696 3101 2900 2432 2848 4160 3128 M2354 VANLOO_SP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANLOO_SP3_TARGETS_DN.html Genes down-regulated in E12.5 hearts from mice with SP3 [GeneID=6670] knockout compared to the wild type organ. 17923686 94/134 Arthur Liberzon 0.663859354256986 0.690284310838704 4180 2728.90909090909 2848 0.0943582040491267 1561 1.0337709664851 -1.09625653468741 -1 0.249592981976373 4178 1841 2859 1998 3684 2848 3484 3290 1561 1711 2564 3129 M1647 WENG_POR_TARGETS_LIVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WENG_POR_TARGETS_LIVER_UP.html Genes up-regulated in liver from mice with liver specific knockout of POR [GeneID=5447]. 16006652 46/96 John Newman 0.0649032281104004 0.100276018553548 4065 2400.36363636364 2850 0.00608190765786656 209 1.24192644989763 -1.24834891265766 -1 1.86119892949399 4064 209 1258 358 3394 2850 4196 3871 1227 874 4103 3130 M15137 TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_CARCINOMA_DUCTAL_VS_LOBULAR_UP.html Genes up-regulated in ductal vs lobular carcinoma breast tumor cells. 17389037 27/38 Arthur Liberzon 0.374006418186546 0.442544571030458 1115 2928.72727272727 2851 0.0416892658187828 1111 1.1295324434975 1.10150306345141 1 0.599956702344801 1111 4519 3216 3604 3331 2778 1753 2528 2827 3698 2851 3131 M7435 HOEBEKE_LYMPHOID_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOEBEKE_LYMPHOID_STEM_CELL_DN.html Genes down-regulated in the common lymphoid progenitor (CLP, defined as CD34+CD38-CD7+ [GeneID=947;952;924]) compared to a multipotent cord blood cell (defined as CD34+CD38+CD7-). 17170726 114/150 Arthur Liberzon 0.00645811717522864 0.0155205260015678 4130 2851.72727272727 2851 0.000588832118882182 777 1.21418646424632 -1.16862349422414 -1 3.29590192100278 4129 3660 1819 3770 777 3437 2851 2789 3526 2060 2551 3132 M15096 REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOCHONDRIAL_TRNA_AMINOACYLATION.html Genes involved in Mitochondrial tRNA aminoacylation 27/27 Reactome 0.0902953678495096 0.132317335066652 2055 2702.18181818182 2852 0.0085663084885354 922 0.684160483202142 -0.70709411904638 -1 0.901639378189777 2053 3833 3843 3562 3283 1147 922 2852 1783 4195 2251 3133 M12605 CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_DN.html Genes specifically down-regulated in pediadric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490]. 12704389 19/25 Jean Junior 0.000415549625088675 0.00200500415506367 3715 2713.54545454545 2853 3.7784376130736e-05 283 0.860304962384395 1.00712940020613 1 3.48260667674367 3715 2091 2860 1786 283 4630 2131 1436 4372 3692 2853 3134 M951 REACTOME_TRAF6_MEDIATED_INDUCTION_OF_NFKB_AND_MAP_KINASES_UPON_TLR7_8_OR_9_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_INDUCTION_OF_NFKB_AND_MAP_KINASES_UPON_TLR7_8_OR_9_ACTIVATION.html Genes involved in TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation 104/132 Reactome 0.0150973608874942 0.0303928371482744 605 2417.63636363636 2854 0.0013819974549523 463 0.928768512162738 1.10396961230201 1 2.11435847238901 601 4040 3433 4325 3663 1075 463 644 2854 3937 1559 3135 M731 WEBER_METHYLATED_ICP_IN_FIBROBLAST http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_ICP_IN_FIBROBLAST.html Germline-specific genes with intermediate-CpG-density promoters (ICP) that are methylated in primary fibroblasts. 17334365 17/105 Arthur Liberzon 0.450386115941751 0.518999625792253 3705 2815.90909090909 2854 0.0529587815755559 837 0.908070635722565 0.61771015088107 1 0.388001351468796 3702 1025 2849 1391 2854 3640 4445 2372 837 3530 4330 3136 M8123 BERNARD_PPAPDC1B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERNARD_PPAPDC1B_TARGETS_DN.html Genes down-regulated in ZR-75-1 cells (breast cancer, amplified 8p11-12 region) upon knockdown of PPAPDC1B [GeneID=84513] by RNAi. 18757432 75/91 Jessica Robertson 0.00130731891844966 0.0048094663250837 4290 2178.54545454545 2855 0.000118917856468372 81 1.27327780274025 -1.17510172336849 -1 4.42843094115926 4290 81 845 301 3385 3282 4673 2855 268 434 3550 3137 M2187 TSUTSUMI_FBXW8_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TSUTSUMI_FBXW8_TARGETS.html Genes differentially expressed in E18.5 whole embryos upon knockout of FBXW8 [GeneID=26259]. 17998335 10/15 Arthur Liberzon 0.208797484720493 0.268535184708645 3955 2962 2855 0.0210659751359638 2026 0.721715929038988 -0.776651012448147 -1 0.618256889483743 3954 2146 2759 2855 2255 3410 4217 2026 2037 3662 3261 3138 M19976 HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP.html Genes up-regulated during differentiation of immature to mature B lymphocyte. 11779835 50/72 Arthur Liberzon 0.0305130043298866 0.0533610153527472 2860 3003.09090909091 2856 0.00281314637889223 1322 1.04456405264667 -0.947238658790058 -1 1.9948295539821 2856 2461 2431 4226 1322 4166 4012 2276 3581 2436 3267 3139 M13448 MOOTHA_GLUCONEOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_GLUCONEOGENESIS.html Genes involved in gluconeogenesis; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 34/51 Vamsi Mootha 0.0030152322402443 0.00909926003110916 965 2069.09090909091 2856 0.000274488431289756 275 0.950468026875021 0.957709379849125 1 2.91075225514264 961 2972 2856 2920 665 3163 3201 275 1276 3292 1179 3140 M121 PID_MTOR_4PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MTOR_4PATHWAY.html mTOR signaling pathway 18832364 93/104 Pathway Interaction Database 0.00728078741951829 0.0169873043104925 3020 2868.36363636364 2857 0.000664090458808455 809 0.739432414219552 0.829256758034943 1 1.96362979571338 3017 2365 4004 2486 809 3943 2857 2839 1192 4190 3850 3141 M2517 RAO_BOUND_BY_SALL4_ISOFORM_A http://www.broadinstitute.org/gsea/msigdb/cards/RAO_BOUND_BY_SALL4_ISOFORM_A.html Loci bound exclusively by SALL4 [GeneID=57167] isoform a in ES cells (embryonic stem). 20837710 178/360 Arthur Liberzon 0.134558830521148 0.18473463643392 3240 2582.27272727273 2858 0.013051882939464 812 1.22796024486907 -1.20833743566714 -1 1.35133681010249 3237 2769 1515 812 2005 3910 2858 3413 3004 1980 2902 3142 M9043 BIOCARTA_GH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GH_PATHWAY.html Growth Hormone Signaling Pathway 44/53 BioCarta 0.254115780304443 0.316406580043773 2475 2557.45454545455 2859 0.026301111020469 1100 0.848230473251736 0.825250121860739 1 0.635975118816993 2471 2929 3607 2235 2902 2300 1469 3140 1100 3120 2859 3143 M6977 BROWNE_HCMV_INFECTION_30MIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_30MIN_UP.html Genes up-regulated in primary fibroblast cell culture at 30 min time point after infection with HCMV (AD169 strain). 11711622 70/94 Arthur Liberzon 0.00320175018410091 0.0095405687304017 1640 2558.90909090909 2861 0.000291492667132963 727 1.22488802727464 1.26857541161556 1 3.71337417628344 1638 2861 727 3211 1780 3387 3244 2231 3971 1574 3524 3144 M4707 IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G2_G3_DN.html Genes down-regulated during transition from G2 (moderately differentiated tumor, infected with HCV) to G3 (poorly differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 11/11 Yujin Hoshida 0.0716661092667202 0.108801555400103 4090 2840.09090909091 2862 0.00673754706780443 426 0.732700175078171 -0.685151726883654 -1 1.05904770884187 4086 426 2862 1045 1674 4672 4599 2778 2529 3022 3548 3145 M2067 ONGUSAHA_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONGUSAHA_BRCA1_TARGETS_UP.html Genes up-regulated in MEF cells (embryonic fibroblast) lacking TP53 and BRCA1 [GeneID=7157;672] by expression of BRCA1. 12802282 17/20 Arthur Liberzon 0.000120993136238535 0.000772841466666513 3635 2499.81818181818 2862 1.09999809996305e-05 492 1.54104729438676 -1.4361247317733 -1 7.1957879815685 3634 3502 492 3731 1106 2601 2862 1727 3850 786 3207 3146 M87 PID_LKB1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_LKB1_PATHWAY.html LKB1 signaling events 18832364 68/103 Pathway Interaction Database 0.155970429085248 0.209380098203178 3295 2838 2863 0.0152970430631073 1591 0.827939340566674 -0.84757107828672 -1 0.843523014376793 3292 2863 3632 2205 4232 2252 3587 1651 1951 3962 1591 3147 M11584 HEIDENBLAD_AMPLICON_8Q24_DN http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_8Q24_DN.html Down-regulated genes whose expression is associated with amplification of the 8q24 chromosome region in pancreatic cancer cell lines. 15688027 67/76 Arthur Liberzon 0.00115240653344876 0.00442584120250459 3085 2733.54545454545 2865 0.000104819148311604 419 1.06656873026203 -0.908935142734112 -1 3.76726077480224 3085 2865 1606 1635 419 4493 3525 2360 4019 2157 3905 3148 M1442 STONER_ESOPHAGEAL_CARCINOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/STONER_ESOPHAGEAL_CARCINOGENESIS_UP.html Genes up-regulated in esophagus by the carcinogen NMBA [PubChem=13643] and brought back to normal by a diet with PEITC [PubChem=16741] or black raspberries. 18676871 48/57 Jessica Robertson 0.061037024547694 0.0952064626123978 2845 2767.27272727273 2865 0.00570902579477584 1362 1.09989771378719 1.02123310622682 1 1.68552208729392 2841 1422 3014 1796 1600 2865 3512 4252 1362 3632 4144 3149 M18899 BIOCARTA_DREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DREAM_PATHWAY.html Repression of Pain Sensation by the Transcriptional Regulator DREAM 14/17 BioCarta 0.192106085511939 0.249859664815749 2960 2909.63636363636 2867 0.0192063012835378 2073 1.08468858753946 -1.2617173073905 -1 0.980202103125303 2956 3922 2766 3423 2208 2867 3128 3614 2837 2073 2212 3150 M18120 GEORGES_TARGETS_OF_MIR192_AND_MIR215 http://www.broadinstitute.org/gsea/msigdb/cards/GEORGES_TARGETS_OF_MIR192_AND_MIR215.html Genes down-regulated in HCT116 cells (colon cancer) by expression of MIR192 or MIR215 [GeneID=406967;406997] at 24 h. 19074876 1117/1300 Jessica Robertson 0.175811102021812 0.231343295662937 2855 3052.27272727273 2867 0.0191498202257474 1165 1.07159414079372 1.08322677331334 1 1.02213631600206 2851 2697 4458 2829 3558 3129 2867 1783 1165 3938 4300 3151 M1524 RUAN_RESPONSE_TO_TNF_TROGLITAZONE_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_TROGLITAZONE_DN.html Adipocyte abundant genes down-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591] and TNF [GeneID=7124]. 12732648 53/67 John Newman 0.0580081092665678 0.0913574493620954 2860 3161.09090909091 2867 0.00541787129051336 1182 1.09363553534586 -1.04973120435021 -1 1.70533625944888 2860 4450 2694 4184 4311 3358 2035 1182 2867 2291 4540 3152 M593 REACTOME_TRAFFICKING_AND_PROCESSING_OF_ENDOSOMAL_TLR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAFFICKING_AND_PROCESSING_OF_ENDOSOMAL_TLR.html Genes involved in Trafficking and processing of endosomal TLR 34/64 Reactome 0.0397204049342469 0.0662963096882347 4035 2805.09090909091 2868 0.00367783758705308 1017 1.24776844975499 1.15222171698099 1 2.2064215395611 4033 3379 1408 1539 3795 4059 2614 1017 2307 2868 3837 3153 M152 REACTOME_NUCLEAR_EVENTS_KINASE_AND_TRANSCRIPTION_FACTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEAR_EVENTS_KINASE_AND_TRANSCRIPTION_FACTOR_ACTIVATION.html Genes involved in Nuclear Events (kinase and transcription factor activation) 31/31 Reactome 0.153795019898218 0.206753772121785 2070 2980.36363636364 2869 0.0150665872906501 1652 0.644464173138918 0.842957914148039 1 0.661872206275192 2068 3413 3886 3878 2083 2869 1652 2834 3347 4078 2676 3154 M863 LEI_MYB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LEI_MYB_TARGETS.html Myb-regulated genes in MCF7 (breast cancer) and lung epithelial cell lines overexpressing MYBL2, MYBL1 or MYB [GeneID=4605;4603;4602]. 15105423 440/532 Kevin Vogelsang 5.78464136905059e-05 0.000426617300967481 2725 2442.63636363636 2869 5.25890315908569e-06 353 1.20527655639107 -1.1848692415085 -1 6.09461000782642 2721 2224 454 1385 3827 3223 3273 2869 2976 353 3564 3155 M16097 NOUZOVA_METHYLATED_IN_APL http://www.broadinstitute.org/gsea/msigdb/cards/NOUZOVA_METHYLATED_IN_APL.html Genes whose CpG islands are hyper-methylated in the NB4 cell line (APL, acute promyelocytic leukemia) compared to PBMC (normal peripheral peripheral blood mononuclear cells). 15302897 73/112 Kevin Vogelsang 0.298967956074618 0.363038012007254 3660 2998.54545454545 2871 0.0317752722977809 1738 1.06130002728085 1.02068910687844 1 0.700671328183664 3657 1882 2693 2871 2472 1831 4448 3967 1738 3293 4132 3156 M3190 WU_HBX_TARGETS_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_1_UP.html Genes up-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in SK-Hep-1 cells (hepatocellular carcinoma). 11439330 21/24 John Newman 0.611907690684925 0.678141418180992 3655 2835.09090909091 2871 0.0824484823851628 992 1.09314235903809 1.13159652506136 1 0.276576504980022 3652 992 1745 2593 3927 3655 2871 3596 3096 2310 2749 3157 M5098 CLIMENT_BREAST_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/CLIMENT_BREAST_CANCER_COPY_NUMBER_DN.html Genes from the most frequent genomic losses and homozygous deletions in a panel of patients with lymph node negative breast cancer (NNBC). 17234794 10/12 Jessica Robertson 0.0605891494623632 0.0946329534951536 2875 2477.54545454545 2873 0.00566592005472102 435 1.21009766850886 -0.840527798420301 -1 1.85917165009968 2873 435 1718 2276 3272 3009 3494 4159 3177 2185 655 3158 M19867 ALCALAY_AML_BY_NPM1_LOCALIZATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/ALCALAY_AML_BY_NPM1_LOCALIZATION_DN.html Genes down-regulated in acute myeloid leukemia (AML) with respect to cellular localization of NPM1 [GeneID=4869]: cytoplasmic vs. nucleolar. 15831697 218/279 Kevin Vogelsang 0.68618940391 0.690284310838704 3810 3130.54545454545 2874 0.1 2027 1.04447097439698 -1.12451778789534 -1 0.252177480212214 3807 2273 2027 2397 4367 2874 4121 3908 2811 2828 3023 3159 M2383 SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHMIDT_POR_TARGETS_IN_LIMB_BUD_UP.html Genes up-regulated in E12.5 forelimb buds with POR [GeneID=5447] knockout. 19273610 28/31 Arthur Liberzon 1.47459243742505e-05 0.000142917377918814 4270 2862.36363636364 2874 1.34054756478005e-06 33 1.06285477409569 -1.00457339893136 -1 6.13189881087811 4269 2026 2813 1829 33 3560 4643 4521 305 2874 4613 3160 M13266 KEGG_RENAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RENAL_CELL_CARCINOMA.html Renal cell carcinoma 74/78 KEGG 0.0271884849990676 0.0487574654998477 3290 2778.72727272727 2875 0.00250276565329159 1265 0.925342342387146 -0.792917911632346 -1 1.82154219340806 3289 1876 3000 1666 1265 3726 2875 4246 2216 2517 3890 3161 M2579 ST_DIFFERENTIATION_PATHWAY_IN_PC12_CELLS http://www.broadinstitute.org/gsea/msigdb/cards/ST_DIFFERENTIATION_PATHWAY_IN_PC12_CELLS.html Differentiation Pathway in PC12 Cells; this is a specific case of PAC1 Receptor Pathway. 62/73 Signaling Transduction KE 0.230963254525063 0.291638994477876 3600 3147.18181818182 2875 0.0235914948149707 2048 0.936830529221356 -1.05890258580039 -1 0.752178388915525 3599 4431 3139 4495 2322 2048 2698 2875 3674 2777 2561 3162 M2687 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_15 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_15.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 15. 12554760 63/75 Arthur Liberzon 0.000562721991985335 0.00252716251395888 2265 2642.54545454545 2875 5.11696343738691e-05 578 1.38883515440539 1.31820732600335 1 5.41274176576781 2263 2875 578 2766 1190 3268 3239 3516 3959 1471 3943 3163 M200 PID_ERA_GENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERA_GENOMIC_PATHWAY.html Validated nuclear estrogen receptor alpha network 18832364 74/121 Pathway Interaction Database 0.0253623275456938 0.046006989245071 3865 2461.36363636364 2876 0.00233268369557217 92 0.957925332331819 -0.91934721550934 -1 1.92193275063993 3863 92 3211 412 2876 4606 4605 2818 652 3574 366 3164 M3026 CHUNG_BLISTER_CYTOTOXICITY_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHUNG_BLISTER_CYTOTOXICITY_UP.html Genes up-regulated in blister cells from patients with adverse drug reactions (ADR). 19029983 141/182 Jessica Robertson 0.00577426225782821 0.0142024584976285 2895 2190.63636363636 2876 0.000526315789473684 165 1.00934165750736 -0.992197831801598 -1 2.79820873424659 2894 618 3265 165 3236 1048 2467 3774 708 3046 2876 3165 M15493 CHEN_HOXA5_TARGETS_9HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_HOXA5_TARGETS_9HR_DN.html Genes down-regulated 9 h after induction of HoxA5 [GeneID=3205] expression in a breast cancer cell line. 15757903 59/69 Arthur Liberzon 0.137482866068023 0.188147036196309 4450 3088 2877 0.013355491930824 1833 1.09161514641759 -0.961701516342244 -1 1.1882605218159 4450 2877 1833 3512 2020 3763 3933 2793 2290 2622 3875 3166 M15195 REACTOME_MAPK_TARGETS_NUCLEAR_EVENTS_MEDIATED_BY_MAP_KINASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MAPK_TARGETS_NUCLEAR_EVENTS_MEDIATED_BY_MAP_KINASES.html Genes involved in MAPK targets/ Nuclear events mediated by MAP kinases 36/37 Reactome 0.0911638621391276 0.133424319161762 2085 3065.09090909091 2878 0.00865239321163621 924 0.620817104043418 -0.398676293938796 -1 0.814780220959 2081 4142 3943 4315 2534 2390 924 2878 3993 4163 2353 3167 M7918 SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_INVERSED_TARGETS_OF_TP53_AND_TP73_UP.html Genes that were inversely correlated in H1299 cells (lung cancer): up-regulated by P53 [GeneID=7157] and down-regulated by P73 [GeneID=7161]. 17982488 10/20 Jessica Robertson 0.117943054487384 0.165681909875135 2445 2884.36363636364 2879 0.0113441336946202 1136 0.92365976186133 0.81513913070591 1 1.08195548017624 2441 3113 1957 2865 1918 2879 1136 4485 4498 2903 3533 3168 M2260 CAFFAREL_RESPONSE_TO_THC_8HR_5_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_5_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 24/27 Jessica Robertson 0.0297524935045007 0.0522828627480429 2695 3218.45454545455 2879 0.00274205900574335 1313 0.821950765588132 0.897936019195803 1 1.58061029517997 2694 4552 2610 4320 1313 2009 2879 3437 4638 4156 2795 3169 M9905 FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN.html Genes downregulated in peripheral blood lymphocytes (PBL) from patients with well functioning kidneys more than 1-year post transplant compared to those from normal living kidney donors. 15307835 47/52 Jean Junior 0.0447541849316898 0.0733726130175671 2545 3126.27272727273 2880 0.00415376494031605 1065 0.774000451602136 0.774029446725425 1 1.31746664380031 2544 4114 3705 4610 2745 2564 2227 1065 3913 4022 2880 3170 M18762 COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP.html 'Late-TGFB1 signature': genes overexpressed in primary hepatocytes at a late phase of TGFB1 [GeneID=7040] treatment; is associated with a more invasive phenotype. 18506891 138/156 Yujin Hoshida 0.563781635334667 0.630879402271131 4400 3018 2880 0.0726454370479227 1288 1.10620478332133 -1.07662607674025 -1 0.331959723416237 4396 2319 2408 1498 4695 4421 4364 2880 1288 1608 3321 3171 M12825 YAGUE_PRETUMOR_DRUG_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAGUE_PRETUMOR_DRUG_RESISTANCE_UP.html Up-regulated genes common to all pretumorigenic cells with acquired drug resistance. 17283147 9/15 Jessica Robertson 0.0989594803539133 0.142884290997391 2885 2952.90909090909 2881 0.0103663996878606 979 1.33806101608232 -1.36340640244242 -1 1.69650568455939 2881 2659 4576 2033 3129 2954 4619 2328 3564 2760 979 3172 M3061 BIOCARTA_FEEDER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FEEDER_PATHWAY.html Feeder Pathways for Glycolysis 10/15 BioCarta 0.000499184261201064 0.00230768825942118 4625 2905.81818181818 2882 4.53906875518381e-05 308 0.849768330882698 -0.785400494820663 -1 3.36209232479525 4624 2650 3201 2882 308 2722 2212 3850 1863 3651 4001 3173 M1203 TERAMOTO_OPN_TARGETS_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_7.html Cluster 7: genes down-regulated early (within 24 h) after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 22/27 Arthur Liberzon 0.264142161740769 0.326888044944004 4650 2827.72727272727 2882 0.0274983286303757 447 1.80185700273927 -1.60764949950799 -1 1.31282446561729 4650 1524 1642 1506 2400 3897 3967 3583 447 2882 4607 3174 M8716 HEDVAT_ELF4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEDVAT_ELF4_TARGETS_UP.html Genes up-regulated in HEL cells (erythroleukemia) upon expression of ELF4 [GeneID=2000]. 14625302 17/21 Kevin Vogelsang 0.0280192323763109 0.0500381297072218 1375 2577.54545454545 2882 0.00258023464948258 978 1.27165379484593 1.21865335276047 1 2.48181248453026 1373 3877 978 4194 1412 2957 2882 3021 3518 1459 2682 3175 M1650 MCDOWELL_ACUTE_LUNG_INJURY_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCDOWELL_ACUTE_LUNG_INJURY_DN.html Genes down-regulated in the mouse model of acute lung injury induced by inhaling nickel sulfate [PubChem=24586]. 12540486 57/75 John Newman 0.000176456412350799 0.00104790434331479 3215 2741.72727272727 2882 1.60427788237207e-05 510 1.47887596549211 1.30453499861982 1 6.61204796091131 3213 2882 510 1988 4641 4499 3226 2668 1733 665 4134 3176 M5940 BIOCARTA_NDKDYNAMIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NDKDYNAMIN_PATHWAY.html Endocytotic role of NDK, Phosphins and Dynamin 21/24 BioCarta 0.00577426225782821 0.0142024584976285 4630 2626.27272727273 2883 0.000526315789473684 110 0.779978418248748 -0.683797151912614 -1 2.16231851053572 4630 962 3464 174 2798 3932 3496 2883 110 3790 2650 3177 M3871 REACTOME_ASSOCIATION_OF_TRIC_CCT_WITH_TARGET_PROTEINS_DURING_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASSOCIATION_OF_TRIC_CCT_WITH_TARGET_PROTEINS_DURING_BIOSYNTHESIS.html Genes involved in Association of TriC/CCT with target proteins during biosynthesis 34/35 Reactome 0.0105166978508757 0.0227283946227717 2885 2165.81818181818 2883 0.000960664549772048 202 0.832941445148011 -0.967109158853981 -1 2.05392907171297 2883 894 3840 869 3173 2950 3086 2027 231 3669 202 3178 M12795 CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHARAFE_BREAST_CANCER_BASAL_VS_MESENCHYMAL_UP.html Genes up-regulated in basal-like breast cancer cell lines as compared to the mesenchymal-like ones. 16288205 173/215 Arthur Liberzon 0.00725356351990833 0.0169405342968666 3490 2639.63636363636 2883 0.000661599094134025 814 1.29622441581845 -1.29148003901825 -1 3.444649994132 3489 3201 814 3488 4692 1807 4332 1979 2883 888 1463 3179 M838 REACTOME_UNBLOCKING_OF_NMDA_RECEPTOR_GLUTAMATE_BINDING_AND_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNBLOCKING_OF_NMDA_RECEPTOR_GLUTAMATE_BINDING_AND_ACTIVATION.html Genes involved in Unblocking of NMDA receptor, glutamate binding and activation 10/19 Reactome 0.481733506741817 0.551353577066289 2885 3065.36363636364 2884 0.0580013406193529 1700 0.685411495938153 0.829201032896194 1 0.265826416093676 2884 2654 2358 3754 3761 1700 2075 4665 4056 3655 2157 3180 M878 REACTOME_SIGNAL_TRANSDUCTION_BY_L1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_TRANSDUCTION_BY_L1.html Genes involved in Signal transduction by L1 49/53 Reactome 0.68618940391 0.690284310838704 3950 2697.63636363636 2884 0.1 323 1.13232397441082 -0.702894542291611 -1 0.273397644292377 3950 814 1916 640 4079 4214 4263 2884 323 2386 4205 3181 M1318 GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_AND_HIF1A_DN.html Genes down-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] and HIF1A [GeneID=3091] by RNAi. 17704799 169/214 Jessica Robertson 0.567191587719678 0.634544748527348 2945 2823.36363636364 2884 0.0733068087328469 1765 0.979537843004252 1.0561698880998 1 0.290238349455466 2942 1765 1947 2730 2940 3170 2884 2744 3313 2781 3841 3182 M17987 CAFFAREL_RESPONSE_TO_THC_8HR_5_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_5_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 22/32 Jessica Robertson 0.0418043321771417 0.0691586158425896 3880 2784.72727272727 2884 0.00387459030262882 205 1.42004701527664 -1.96253891821348 -1 2.4719601857524 3877 3485 2206 2861 2389 3887 3841 4489 205 2884 508 3183 M9066 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_DN.html Genes down-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 46/67 John Newman 0.246177031288506 0.307802804683907 2680 2693 2884 0.0253635044228419 1323 1.13062521375394 1.12368694402081 1 0.868052967211664 2677 2921 1423 2884 4041 2078 2022 2920 3477 1323 3857 3184 M2351 TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/TORCHIA_TARGETS_OF_EWSR1_FLI1_FUSION_DN.html Genes down-regulated in leukemic progenitor cells expressing activated fusion of ESWR1 and FLI1 [GeneID=2130, 2313] compared to normal hematopoetic progenitors. 17875932 430/516 Arthur Liberzon 0.000629008757470179 0.00274900123635115 3100 2352.72727272727 2885 5.71989701196185e-05 389 1.15348555358865 -1.17034391867009 -1 4.43224246687422 3098 1149 823 661 3902 3574 3407 2885 1282 389 4710 3185 M12467 KEGG_ERBB_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ERBB_SIGNALING_PATHWAY.html ErbB signaling pathway 84/90 KEGG 0.00577426225782821 0.0142024584976285 4390 2353.09090909091 2886 0.000526315789473684 74 0.88426037306224 -0.837851722418221 -1 2.45143142937006 4390 74 3136 204 2886 3155 2417 2790 653 2965 3214 3186 M9893 RODWELL_AGING_KIDNEY_NO_BLOOD_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_NO_BLOOD_UP.html Genes whose expression increases with age in normal kidney, excluding those with higher expression in blood. 15562319 279/355 John Newman 4.91460599145809e-15 2.76154050948597e-13 1590 2399.09090909091 2886 4.46782362859826e-16 62 1.37483353642367 1.50194548841402 1 25.9083631642084 1590 2256 62 3018 2875 3587 2886 3660 3061 284 3111 3187 M2009 MIKKELSEN_NPC_HCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_HCP_WITH_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 trimethylation mark at K27 (H3K27me3) in neural progenitor cells (NPC). 17603471 247/551 Arthur Liberzon 1.74039943717286e-27 4.10734267172794e-25 2380 2672.90909090909 2886 1.58218130652078e-28 14 1.54759211890234 1.43790307224292 1 56.6299130592561 2378 2740 14 2240 3440 3947 3033 4119 2886 50 4555 3188 M9174 ST_STAT3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_STAT3_PATHWAY.html STAT3 Pathway 17/19 Signaling Transduction KE 0.000626833945884168 0.00274457905804571 1705 2287.45454545455 2887 5.70011470473655e-05 334 0.886916516509858 -0.915184973762272 -1 3.40886294848298 1703 1556 2887 3143 334 1751 620 3031 3602 3522 3013 3189 M6590 MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_UP.html The 'NPM1-mutated signature 2': genes up-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to the AML cases with the intact gene and without recurring cytogenetic anomalities or M7 phenotype. 17597811 180/214 Arthur Liberzon 0.0313524913634542 0.0545059886686939 2860 2923.72727272727 2888 0.00289167479905564 591 0.992798061151165 -1.01435700985936 -1 1.88223016608712 2857 591 2600 2888 1334 4683 3485 2483 3157 3429 4654 3190 M967 REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION_IN_TLR7_8_OR_9_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION_IN_TLR7_8_OR_9_SIGNALING.html Genes involved in TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling 29/50 Reactome 0.0073892989495818 0.0171785025795392 2160 2779.45454545455 2889 0.000674021387131907 460 0.975148590010571 1.03281157573293 1 2.58251667721674 2159 4167 2308 3374 3875 2889 2294 460 3969 2960 2119 3191 M7514 BERENJENO_TRANSFORMED_BY_RHOA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_DN.html Genes down-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector. 17213802 558/655 Leona Saunders 0.0213391795474807 0.0399052802948134 2470 2715.72727272727 2889 0.0021546904731379 702 1.07691867085941 1.16302076475648 1 2.26054247463458 2469 1139 4342 981 1509 4641 3489 3640 2889 702 4072 3192 M16646 WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_FIBROBLAST_DN.html Unmethylated germline-specific genes with high-CpG-density promoters (HCP) in primary fibroblasts. 17334365 29/79 Jessica Robertson 0.011009181893573 0.0235128228677214 1580 2329 2889 0.00100587843935192 213 0.826403771424061 0.912420646157994 1 2.01953398231835 1579 3011 2889 3331 4031 855 683 1629 3375 4023 213 3193 M1123 HUMMERICH_BENIGN_SKIN_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_BENIGN_SKIN_TUMOR_DN.html Genes down-regulated in benign skin tumors (papilloma) induced by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 22/41 Leona Saunders 0.00278006894620145 0.00855963824270765 4255 3032.81818181818 2890 0.000253053477931985 578 1.06817429709773 -1.01850287111123 -1 3.31378972637344 4253 2075 2008 2890 578 3623 4469 4545 2583 2881 3456 3194 M2777 AMIT_SERUM_RESPONSE_240_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_SERUM_RESPONSE_240_MCF10A.html Genes whose expression peaked at 240 min after stimulation of MCF10A cells with serum. 17322878 104/123 Leona Saunders 0.0256776968528765 0.0464719053472304 2670 2580.27272727273 2890 0.00236203538978037 966 1.29678480416471 1.15359495979956 1 2.59334374291048 2668 1294 966 1076 2918 4309 3323 2890 3584 1512 3843 3195 M1681 BURTON_ADIPOGENESIS_PEAK_AT_16HR http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_PEAK_AT_16HR.html Cluster 4: genes maximally expressed at 16 h time point during differentiation of 3T3-L1 fibroblasts into adipocytes in response to adipogenic hormones. 12137940 58/73 John Newman 0.169422339778658 0.224121575888641 1545 2879.36363636364 2890 0.0167342052783635 1227 1.28149345716071 1.63570007627512 1 1.24885344771147 1541 2890 2785 4084 4535 1370 1227 2835 3407 3753 3246 3196 M19667 CHENG_RESPONSE_TO_NICKEL_ACETATE http://www.broadinstitute.org/gsea/msigdb/cards/CHENG_RESPONSE_TO_NICKEL_ACETATE.html Genes down-regulated in HPL1D cells (lung epithelium) upon exposure to nickel acetate [PubChem=9756]. 12915101 58/71 John Newman 0.0236239064318889 0.0433365092726449 3950 2954.36363636364 2891 0.0021710421462864 1121 1.12972449686264 -0.963418648840721 -1 2.31066433614487 3948 3722 2891 2708 1210 4436 3807 1237 1121 2856 4562 3197 M18160 STEIN_ESRRA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_DN.html Genes down-regulated by ESRRA [GeneID=2101] only. 18974123 171/207 Leona Saunders 0.0160654622324224 0.0319414413382618 2875 2614.27272727273 2891 0.00147127214381479 276 0.932175294606404 -0.998153298605677 -1 2.09192491783156 2875 3639 3491 3209 1756 951 3402 2891 2752 3515 276 3198 M118 PID_INTEGRIN_A9B1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_INTEGRIN_A9B1_PATHWAY.html Alpha9 beta1 integrin signaling events 18832364 28/34 Pathway Interaction Database 0.00342358367454501 0.00998721566369126 2425 2594.18181818182 2892 0.000311720273084806 297 1.53618603439593 1.7316694768639 1 4.61133075701142 2422 4172 1076 3094 1735 3433 3550 297 3427 2438 2892 3199 M907 REACTOME_CALNEXIN_CALRETICULIN_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CALNEXIN_CALRETICULIN_CYCLE.html Genes involved in Calnexin/calreticulin cycle 12/14 Reactome 6.10449391688284e-05 0.000444648322340849 2270 2686.18181818182 2892 5.54969391738797e-06 102 0.486875367451927 -0.48664795663242 -1 2.44874010564297 2268 2138 3623 2892 102 2977 2956 2169 3343 4583 2497 3200 M2570 ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_FGFR1_TARGETS_IN_PROSTATE_CANCER_MODEL_UP.html Genes up-regulated during prostate cancer progression in the JOCK1 model due to inducible activation of FGFR1 [GeneID=2260] gene in prostate. 18068632 356/499 Yujin Hoshida 3.57240010189573e-16 2.30982581930792e-14 3265 2311.45454545455 2892 3.24763645626884e-17 34 1.35612770961146 -1.3704837084009 -1 27.7486037601561 3262 1698 74 1157 3980 2920 2892 3949 861 34 4599 3201 M15513 BIOCARTA_D4GDI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_D4GDI_PATHWAY.html D4-GDI Signaling Pathway 13/26 BioCarta 0.00362080247856583 0.0104081532879602 3025 2729.18181818182 2894 0.000329706857481774 632 0.864987409457376 0.95364062129838 1 2.57320626973174 3021 3907 3297 2886 632 2600 1933 2894 1452 3841 3558 3202 M18679 SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCIAN_CELL_CYCLE_TARGETS_OF_TP53_AND_TP73_UP.html Cell cycle genes up-regulated in H1299 cells (lung cancer) after overexpression of either P53 or P73 [GeneID=7157;7161]. 17982488 16/17 Jessica Robertson 0.169468200073423 0.224121575888641 2545 3217.36363636364 2894 0.016739140944128 1228 1.1370767589106 1.20273012698948 1 1.10810315843284 2543 4598 2447 4273 3675 2500 1228 4605 4317 2894 2311 3203 M16673 VALK_AML_CLUSTER_16 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_16.html Top 40 genes from cluster 16 of acute myeloid leukemia (AML) expression profile; 81% of the samples are FAB M5 subtype, 45% have 11q23 abnormalities. 15084694 23/39 Jessica Robertson 0.303946449299658 0.368136320424528 3890 2807 2895 0.0324023906936183 548 1.14920857361188 1.22045467547354 1 0.748273395699783 3886 2061 1767 548 2481 4073 3214 3844 2895 2498 3610 3204 M1888 WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_DN http://www.broadinstitute.org/gsea/msigdb/cards/WUNDER_INFLAMMATORY_RESPONSE_AND_CHOLESTEROL_DN.html Genes down-regulated in gastric mucosal tissue of mice on 2% cholesterol [PubChem=5997] diet and infected with H. pylori vs those infected with H. pylori while on 0% cholesterol diet. 16951684 30/52 Jessica Robertson 0.168715767341421 0.22331419569588 1940 3022.45454545455 2897 0.0166581924632079 1030 0.965478272085984 -0.891602434513311 -1 0.943131794458173 1940 4527 2483 4148 2266 1030 2897 3460 4514 3440 2542 3205 M1437 WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_IMMORTALIZED_BY_HOXA9_AND_MEIS1_DN.html Down-regulated genes in myeloid progenitors immortalized by HOXA9 [GeneID=3205] vs those immortalized by HOXA9 and MEIS1 [GeneID=4211]. 15755900 24/33 Kevin Vogelsang 0.00963592456161276 0.021193645820509 2255 2484.09090909091 2899 0.000879853655213503 781 1.54390001611764 1.6804335112982 1 3.8774947534488 2255 3853 837 3273 3040 1645 1868 3116 3758 781 2899 3206 M2287 CHANGOLKAR_H2AFY_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANGOLKAR_H2AFY_TARGETS_UP.html Genes up-regulated in liver tissue upon knockout of H2AFY [GeneID=9555]. 17242180 67/73 Arthur Liberzon 0.43119990772354 0.499814448548158 2900 2510.81818181818 2899 0.05 104 1.06796780166201 -0.916265421709586 -1 0.48255520417945 2899 104 2158 459 3504 4354 3311 4224 692 1662 4252 3207 M11268 WHITE_NEUROBLASTOMA_WITH_1P36.3_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/WHITE_NEUROBLASTOMA_WITH_1P36.3_DELETION.html Genes within the smallest region of consistend deletion (SRD) within 1p36.3 area across a large collection of neuroblastoma cell lines and biopsy samples. 15829979 21/23 Leona Saunders 0.0204137162671784 0.0384488191464814 4070 2730.09090909091 2900 0.00187323928478244 908 1.12064097635124 -1.16668454204092 -1 2.37947605177649 4068 3490 3084 2638 1161 2900 3848 2115 908 3323 2496 3208 M5871 MOOTHA_PYR http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_PYR.html Genes involved in pyruvate metabolism; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 7/8 Vamsi Mootha 9.24781343605156e-05 0.000619144388910119 3220 2313.36363636364 2900 9.24819830783356e-06 30 1.54098954297304 -0.47202095098864 -1 7.41818790147956 3219 2173 4649 2900 135 3977 3717 687 30 3365 595 3209 M2482 BIOCARTA_ARAP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARAP_PATHWAY.html ADP-Ribosylation Factor 21/22 BioCarta 0.00031220188970688 0.0016373254660183 3890 2609.90909090909 2901 2.8386018460505e-05 229 0.701916323450031 -0.634073355542631 -1 2.93407729799716 3888 2076 3811 1896 229 2901 2364 3269 827 4089 3359 3210 M9670 BIOCARTA_STRESS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STRESS_PATHWAY.html TNF/Stress Related Signaling 32/35 BioCarta 0.132435741538143 0.182509985418988 1795 2659.36363636364 2901 0.0128320217903697 1109 0.745635510146673 0.907897021648374 1 0.82639701219174 1794 2976 3581 3187 2137 2180 1109 2570 3273 3545 2901 3211 M8395 REACTOME_HEMOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HEMOSTASIS.html Genes involved in Hemostasis 435/615 Reactome 4.93162961854459e-05 0.000376655207112143 2585 2707 2901 4.48340015625537e-06 444 1.16114013488784 1.06794472939277 1 5.9656751774396 2584 2225 444 3664 2611 3473 2901 3429 3245 1012 4189 3212 M8268 AMBROSINI_FLAVOPIRIDOL_TREATMENT_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/AMBROSINI_FLAVOPIRIDOL_TREATMENT_TP53.html Genes down-regulated by flavopiridol [PubChem=5287969] in the HCT116 cells (colon cancer) depending on their TP53 [GeneID=7157] status: wild-type vs loss of the gene's function (LOF). 18381438 165/209 Jessica Robertson 0.547097266383461 0.615359735048218 3905 3014 2901 0.0694756933928101 1779 1.10094618415714 1.09422831555177 1 0.348251219610681 3903 2297 1903 2060 2901 3605 3905 4207 2207 1779 4387 3213 M18597 BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_AND_PAX3 http://www.broadinstitute.org/gsea/msigdb/cards/BEGUM_TARGETS_OF_PAX3_FOXO1_FUSION_AND_PAX3.html Genes up-regulated in SaOS-2 cells (osteosarcoma) upon expression of PAX3-FOXO1 [GeneID=5077;2308] but down-regulated by PAX3 expression off adenoviral vectors. 15688035 9/10 Leona Saunders 0.528484164322048 0.596900037233804 2905 2806.81818181818 2903 0.0724237328731377 2036 1.43644098659968 -1.344838548183 -1 0.48291776190169 2903 2168 4383 3044 2927 2101 3209 3424 2155 2036 2525 3214 M128 PID_TNF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TNF_PATHWAY.html TNF receptor signaling pathway 18832364 57/60 Pathway Interaction Database 0.43119990772354 0.499814448548158 3370 2512.81818181818 2904 0.05 139 0.946941829503387 -1.02599475534681 -1 0.42785831114989 3366 139 2802 555 3715 3709 2904 3442 379 1911 4719 3215 M18415 REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA4D_INDUCED_CELL_MIGRATION_AND_GROWTH_CONE_COLLAPSE.html Genes involved in Sema4D induced cell migration and growth-cone collapse 35/48 Reactome 0.653775839592309 0.690284310838704 4120 2902.90909090909 2904 0.0919214915087112 1127 0.975943583820473 -0.947776526387709 -1 0.235625256932535 4116 1450 2681 1127 3703 3468 4390 3139 2904 2555 2399 3216 M12143 CHESLER_BRAIN_D6MIT150_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_D6MIT150_QTL_CIS.html Cis-regulatory QTLs (quantitative trait loci) found at the D6Mit150 region. 15711545 10/16 Jean Junior 0.0326394707013655 0.0562872859738564 4035 2904.18181818182 2905 0.00301218335710535 942 0.798426658580149 0.882764213076241 1 1.49697163080126 4034 1609 2214 3288 2188 4522 4308 942 4592 2905 1344 3217 M13669 TSAI_DNAJB4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TSAI_DNAJB4_TARGETS_UP.html Genes up-regulated in CL1-5 cells (lung cancer) overexpressing DNAJB4 [GeneID=11080] off a plasmid vector. 16788156 21/34 Jessica Robertson 0.0793687279451611 0.118860634287978 3595 3026.36363636364 2906 0.00748960110230311 807 0.927629484263253 -0.915680920388904 -1 1.28737337681887 3594 1529 2314 2906 4299 4310 4633 4649 2419 1830 807 3218 M4752 WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN.html Genes down-regulated in rectal cancer patients resistant to radiotherapy (non-responders) relative to the sensitive ones (responders). 16585155 174/204 Arthur Liberzon 0.27189971202625 0.335082673828695 1035 3068.27272727273 2907 0.0284348516978884 1031 0.931847214877893 0.981605599186559 1 0.663853013563833 1031 4713 3108 4685 2444 2907 2312 2010 4142 4161 2238 3219 M18630 ROVERSI_GLIOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROVERSI_GLIOMA_COPY_NUMBER_DN.html Genes in the most frequently homozygous deleted loci in a panel of glioma cell lines. 16247447 57/83 Arthur Liberzon 0.0274159498491894 0.04912804984365 3645 2633.45454545455 2907 0.00252397126330007 794 1.26620954208731 -1.17690608378732 -1 2.48633251728744 3645 794 1725 3296 1269 3310 4042 2851 3464 1665 2907 3220 M10351 BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN.html Genes down-regulated in T24 (bladder cancer) cells in response to the photodynamic therapy (PDT) stress. 17952126 810/943 Jessica Robertson 0.0827378175004247 0.123193217224607 3940 2686.36363636364 2909 0.0085990086322866 1259 1.08915346588504 -0.949739995637651 -1 1.48614510838812 3936 1662 4433 1657 1779 1259 2909 3653 1880 3004 3378 3221 M1222 DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_HIGH_VS_LOW_UP.html Genes that classify skin lesions into high risk papilloma. 17525749 9/9 Arthur Liberzon 0.14461796424604 0.196657099176407 2910 3091.45454545455 2910 0.0154993379598891 1662 1.11846176420848 -1.11846176420848 -1 1.18524316727926 2910 4628 4397 4567 2797 1927 1978 1662 3679 3560 1901 3222 M16962 IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L0_L1_DN.html Genes down-regulated during transition from L0 (non-tumor, not infected with HCV) to L1 (non-tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 41/61 Yujin Hoshida 0.0546775235533636 0.0869534741145135 1965 2638.27272727273 2910 0.00509869953163022 529 0.976457536440658 -0.805151998851733 -1 1.5540447236246 1962 4131 3486 4112 1686 529 1070 2910 4088 3647 1400 3223 M4406 GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_UP.html Genes up-regulated in quiescent vs dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors. 17717066 83/142 Arthur Liberzon 0.000353091659821628 0.00179011024098613 3450 2546.27272727273 2911 3.21043947664685e-05 553 1.23120711291578 -1.40604447916809 -1 5.07506412532632 3446 1320 553 2911 870 4283 3455 2350 3471 670 4680 3224 M2094 MARTENS_BOUND_BY_PML_RARA_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/MARTENS_BOUND_BY_PML_RARA_FUSION.html Genes with promoters occupied by PML-RARA fusion [GeneID=5371,5914] protein in acute promyelocytic leukemia(APL) cells NB4 and two APL primary blasts, based on Chip-seq data. 20159609 581/739 Arthur Liberzon 0.209971029248578 0.269750478512055 4680 3041.36363636364 2911 0.0232929967496378 1087 1.01634387799434 -1.01658250150521 -1 0.867702038265133 4678 1679 4655 1087 2314 3043 4506 4166 1825 2911 2591 3225 M66 PID_MYC_ACTIV_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_ACTIV_PATHWAY.html Validated targets of C-MYC transcriptional activation 18832364 107/136 Pathway Interaction Database 0.246610167530742 0.308262709413428 1370 3094.81818181818 2912 0.0254144279640262 1367 0.949722848916035 0.940132705295075 1 0.728221723432474 1367 4386 3846 4683 2857 1679 1453 2779 4100 3981 2912 3226 M1233 OHM_METHYLATED_IN_ADULT_CANCERS http://www.broadinstitute.org/gsea/msigdb/cards/OHM_METHYLATED_IN_ADULT_CANCERS.html Genes showing frequent DNA methylation and which are silenced in adult cancers but remain unmethylated in embryonic carcinoma and embryonic stem (ES) cells. 17211412 33/42 Leona Saunders 0.447221513375445 0.516108934751125 3075 2988.90909090909 2912 0.0524643528384291 1675 1.29266635052269 1.40078762073249 1 0.557081621973096 3073 4144 1855 2128 2741 4125 2912 4376 3700 1675 2149 3227 M16130 RICKMAN_HEAD_AND_NECK_CANCER_C http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_HEAD_AND_NECK_CANCER_C.html Cluster c: genes identifying an intrinsic group in head and neck squamous cell carcinoma (HNSCC). 18679425 120/231 Jessica Robertson 2.29868660896715e-19 2.26037516548436e-17 2900 2740.63636363636 2912 2.08971509906104e-20 34 1.84364707224296 -2.27322549237708 -1 46.0493790783512 2898 2800 34 3926 1590 4000 3313 2912 3808 217 4649 3228 M226 PID_VEGFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGFR1_PATHWAY.html VEGFR1 specific signals 18832364 38/43 Pathway Interaction Database 0.513297727434139 0.581975804345217 2525 3109.54545454545 2913 0.0633671237632228 2500 0.853458351728403 0.660590570478987 1 0.300964298322213 2524 2500 2820 3662 2844 3649 2565 2913 4093 3486 3149 3229 M792 REACTOME_PERK_REGULATED_GENE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PERK_REGULATED_GENE_EXPRESSION.html Genes involved in PERK regulated gene expression 31/34 Reactome 0.125675785137521 0.174930612164287 2210 2906.45454545455 2913 0.0121352230942409 1954 1.02233059632369 0.952225830376768 1 1.16135888997044 2206 2996 3030 2187 1954 2790 2784 4197 3426 3488 2913 3230 M4280 REACTOME_EARLY_PHASE_OF_HIV_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EARLY_PHASE_OF_HIV_LIFE_CYCLE.html Genes involved in Early Phase of HIV Life Cycle 13/19 Reactome 0.0072034114187117 0.0168317336120392 2725 2771.90909090909 2914 0.000657009643373276 455 1.09638167432026 1.26050791310502 1 2.91816535651078 2722 4249 2914 4011 1989 3206 2755 455 815 3845 3530 3231 M18387 KORKOLA_SEMINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_SEMINOMA_UP.html Genes from the 12p region that were up-regulated in seminoma tumors compared to normal testis. 16424014 63/79 Arthur Liberzon 0.551620340480049 0.61932635753231 4315 3310.36363636364 2914 0.0703243722262023 2196 1.06619045203268 -1.09082853596395 -1 0.332789613662914 4312 4086 2726 3990 2914 2196 4079 4285 2324 2832 2670 3232 M9639 HAN_SATB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAN_SATB1_TARGETS_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of SATB1 [GeneID=6304] by RNAi. 18337816 507/684 Jessica Robertson 7.19149406778654e-07 1.06074537499851e-05 4605 2762.72727272727 2914 7.191496395079e-08 125 1.22672894727688 -1.20248481261306 -1 9.15640795215218 4324 2214 4605 125 2570 3119 4602 2914 2715 160 3042 3233 M13746 ZHAN_MULTIPLE_MYELOMA_HP_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_HP_UP.html Top 50 up-regulated genes in cluster HP of multiple myeloma samples characterized by a hyperploid signature. 16728703 66/96 Kevin Vogelsang 0.0545853825845843 0.0868654773429663 1195 2631.72727272727 2915 0.00508988415518133 1156 1.0989085516218 1.27079681262141 1 1.74966544211604 1194 3713 2915 4259 4677 2030 1201 1156 2954 3510 1340 3234 M1554 MEDINA_SMARCA4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MEDINA_SMARCA4_TARGETS.html Genes up-regulated in H1299 cells (lung cancer) by expression of SMARCA4 [GeneID=6597] off a plasmid vector. 15731117 66/89 John Newman 0.010802281722195 0.0231758044221638 3620 2826.18181818182 2918 0.000986880891646003 938 1.20448627790862 -1.11685633843698 -1 2.9548580315391 3617 2414 1377 2569 938 4157 2918 2933 3695 2122 4348 3235 M6910 BIOCARTA_INFLAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INFLAM_PATHWAY.html Cytokines and Inflammatory Response 13/44 BioCarta 0.0647314295468404 0.100043335776387 1615 2548.45454545455 2919 0.00606530855500465 1049 1.37424998321227 1.16324360494134 1 2.06159584044863 1613 3546 1120 3072 4064 2221 1199 3572 3658 1049 2919 3236 M4113 SENESE_HDAC2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC2_TARGETS_UP.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC2 [GeneID=3066] by RNAi. 17470557 137/166 Leona Saunders 0.617411617374346 0.682798227274347 2920 2932.90909090909 2919 0.0836391522943188 2083 1.06404128379995 1.08916908038709 1 0.264465485964593 2083 2790 2966 2919 3006 3632 3306 2687 2395 2919 3559 3237 M9538 GRADE_COLON_VS_RECTAL_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_VS_RECTAL_CANCER_UP.html Genes up-regulated in rectal but down-regulated in colon carcinoma compared to normal mucosa samples. 17210682 44/52 Jessica Robertson 0.0879227198693727 0.129524106673982 2780 3292.45454545455 2919 0.00833151309474961 1367 1.08644373873596 1.16735047179645 1 1.44696740691978 2780 4474 2704 4604 3841 2919 2639 1367 4483 2748 3658 3238 M14174 NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_DN.html Genes down-regulated in K562 cells (bone marrow) after treatment with dasatinib [PubChem=3062316] or imatinib [PubChem=5291]. 17213809 17/18 Arthur Liberzon 0.43119990772354 0.499814448548158 4410 2731.09090909091 2920 0.05 376 0.789699245111037 -0.809941289797497 -1 0.356793558148544 4410 376 2830 595 2847 4013 3573 4419 1067 2992 2920 3239 M12050 STARK_HYPPOCAMPUS_22Q11_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/STARK_HYPPOCAMPUS_22Q11_DELETION_UP.html Genes up-regulated in hyppocampus of mice carrying a hemizygotic microdeletion in the 22q11.2 region. 18469815 76/98 Jessica Robertson 0.68618940391 0.690284310838704 2160 2987.81818181818 2921 0.1 1679 1.02297882044999 0.872497395552019 1 0.246986228540451 2157 3267 2716 3720 3815 2908 2921 3161 1679 2599 3923 3240 M13013 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_IL3RA.html Genes whose expression is coregulated with that of IL3RA [GeneID=3563] in hematopoietic stem cells (HSC). 15711547 18/24 Arthur Liberzon 0.325133590399784 0.390292611059761 1715 2752.81818181818 2921 0.0351176846905991 1715 1.08865167963396 1.16847415409223 1 0.667375922747268 1715 3051 2581 2980 2532 2991 2290 2921 3677 2541 3002 3241 M140 PID_RANBP2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RANBP2_PATHWAY.html Sumoylation by RanBP2 regulates transcriptional repression 18832364 15/19 Pathway Interaction Database 0.00830363536452002 0.018870081329097 2735 2730.09090909091 2922 0.000757740277671019 486 0.706602340442176 -0.751509727522515 -1 1.82804122645923 2731 3892 3660 3376 2011 2922 3111 486 1408 4514 1920 3242 M16737 VANTVEER_BREAST_CANCER_BRCA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_BRCA1_UP.html Up-regulated genes from the optimal set of 100 markers discriminating ER(-) breast cancer tumors by BRCA1 [GeneID=672] mutation status. 11823860 44/54 Arthur Liberzon 0.00674170535126638 0.0159993765303422 495 2129.36363636364 2923 0.000614768525454125 207 0.916892345916363 0.987705343581267 1 2.47071677920263 495 2923 3369 2946 3995 796 207 921 3554 3125 1092 3243 M1473 BIOCARTA_BLYMPHOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BLYMPHOCYTE_PATHWAY.html B Lymphocyte Cell Surface Molecules 10/18 BioCarta 0.0532473748856513 0.0851669296713908 2630 2984.27272727273 2924 0.00496196127146974 1446 1.43266807908016 0.885269828688773 1 2.29954111936058 2630 4258 1446 3983 1538 3177 3411 1912 4651 2897 2924 3244 M1683 DURCHDEWALD_SKIN_CARCINOGENESIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DURCHDEWALD_SKIN_CARCINOGENESIS_UP.html Genes up-regulated upon skin specific knockout of FOS [GeneID=2353] by cre-lox in the K5-SOS-F mice (express a constitutively active form of SOS1 [GeneID=6654] in the skin). 18757399 108/170 Jessica Robertson 2.06683848842172e-05 0.000186529209662534 4700 2480.90909090909 2924 1.87896173276984e-06 398 1.39301570086022 -1.56273020524308 -1 7.79495816770461 4697 1818 398 1486 815 2924 4377 4025 2943 474 3333 3245 M626 REACTOME_ACYL_CHAIN_REMODELLING_OF_PI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACYL_CHAIN_REMODELLING_OF_PI.html Genes involved in Acyl chain remodelling of PI 8/16 Reactome 0.0192871723490106 0.0367116775944171 2925 2677.90909090909 2925 0.00194566439352484 783 1.29177573348475 -1.34929685189075 -1 2.78178495590784 2925 2169 4210 1470 3920 3885 3229 783 3154 1880 1832 3246 M16424 BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_INVASIVE_CARCINOMA_DUCTAL_VS_LOBULAR_UP.html Genes up-regulated in the invasive ductal carcinoma (IDC) compared to the invasive lobular carcinoma (ILC), the two major pathological types of breast cancer. 18490921 43/48 Jessica Robertson 0.238037379275733 0.299051485275874 3995 2826.63636363636 2925 0.0244114445742762 631 0.9850344905832 -0.925130646966014 -1 0.77477520150546 3994 2925 2370 631 2342 3731 3304 3164 3885 2362 2385 3247 M490 REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE.html Genes involved in Pyruvate metabolism and Citric Acid (TCA) cycle 42/44 Reactome 0.113525839744573 0.160464247321969 2495 2633.72727272727 2926 0.0108950598234931 1116 0.817123901153341 -0.502342772145121 -1 0.974188450877508 2491 2926 3797 2953 1898 1268 1629 3538 1116 4102 3253 3248 M17157 REACTOME_PYRUVATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRUVATE_METABOLISM.html Genes involved in Pyruvate metabolism 18/19 Reactome 0.000111163667434802 0.000719742812472241 2275 2440.54545454545 2926 1.01062986194941e-05 141 1.05144210313539 1.52538144142184 1 4.95835684426786 2272 3053 2926 4195 141 3699 4380 700 978 3069 1433 3249 M10332 MODY_HIPPOCAMPUS_POSTNATAL http://www.broadinstitute.org/gsea/msigdb/cards/MODY_HIPPOCAMPUS_POSTNATAL.html Genes up-regulated in hyppocampus at late postnatal stages (clusters 11 and 15). 11438693 95/117 John Newman 0.302626791847379 0.366632047617974 4355 2575.27272727273 2927 0.0322357631903244 410 1.14667893816637 -1.03941016563936 -1 0.749685735822195 4355 682 1984 822 2942 3035 4530 2081 410 2927 4560 3250 M14722 GAUTSCHI_SRC_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/GAUTSCHI_SRC_SIGNALING.html Genes down-regulated in A549 cells (lung cancer) after treatment with AZD0530 [PubChem=10302451], a SRC [GeneID=6714] kinase inhibitor. 18381431 8/8 Jessica Robertson 0.0319661696366912 0.055429731553528 4545 2969.45454545455 2927 0.00324355264003223 659 1.44722663111459 -1.41788022384234 -1 2.72797307037631 4100 2678 4543 1575 1380 4541 2927 4558 659 1295 4408 3251 M9904 KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY.html T cell receptor signaling pathway 103/137 KEGG 0.0845358365264456 0.125593058987983 2930 2815.63636363636 2928 0.00799730997878932 1144 0.795378002405123 -0.839091682621733 -1 1.07526125230703 2928 1295 3368 1144 1749 2846 1902 3273 4168 3635 4664 3252 M567 REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE.html Genes involved in SRP-dependent cotranslational protein targeting to membrane 126/217 Reactome 0.0150207873076427 0.0303043431024949 745 3010.81818181818 2928 0.00137493953045131 743 0.599052562418865 0.558556848072219 1 1.36485485132863 743 4396 4160 4543 1048 1985 1368 2928 4678 4459 2811 3253 M11189 SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE.html IRF4 [GeneID=3662] target genes induced after activation of primary B lymphocytes by anti-IgM crosslinking. 18568025 114/132 Jessica Robertson 0.000518603875395437 0.00237651484647229 3140 2504.63636363636 2928 4.71569241587634e-05 314 1.08874587422169 1.20777122769622 1 4.28678085431214 3140 1282 2928 1080 314 4603 4084 3812 409 1679 4220 3254 M222 PID_CXCR3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CXCR3_PATHWAY.html CXCR3-mediated signaling events 18832364 54/62 Pathway Interaction Database 0.301727121091662 0.365635946483349 3780 2975.18181818182 2929 0.0321223298576068 1925 0.922592337374433 -0.849917146337222 -1 0.604795451390636 3776 1925 2903 2231 2929 3476 3580 2078 2486 3297 4046 3255 M4572 LOCKWOOD_AMPLIFIED_IN_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LOCKWOOD_AMPLIFIED_IN_LUNG_CANCER.html Overexpressed genes with amplified copy number across 27 non-small cell lung cancer (NSCLC) cell lines. 18391978 284/320 Jessica Robertson 0.243789854547872 0.305465387169088 3700 2875.18181818182 2929 0.0250833220160121 544 0.830970617499766 -0.793012078918103 -1 0.642088911133372 3699 544 3995 1122 2357 2929 4553 3615 2389 4262 2162 3256 M27 BENPORATH_MYC_TARGETS_WITH_EBOX http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_MYC_TARGETS_WITH_EBOX.html Set 'Myc targets1': targets of c-Myc [GeneID=4609] identified by ChIP on chip in cultured cell lines, focusing on E-box-containing genes; high affinity bound subset 18443585 294/414 Jessica Robertson 0.496194610236714 0.565300159381436 1685 3026.81818181818 2929 0.0604216898800419 1685 1.0403195815348 1.02539703476473 1 0.386591540869677 1685 4327 3312 4298 3638 2666 2011 3056 2560 2929 2813 3257 M242 PID_AURORA_A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AURORA_A_PATHWAY.html Aurora A signaling 18832364 44/47 Pathway Interaction Database 0.512441822113376 0.58128464320479 2320 3031.72727272727 2930 0.0632175028991098 1762 0.763327439941795 -0.717088222138563 -1 0.269760390258811 2317 2930 3727 3447 3110 1762 2747 2874 3466 4242 2727 3258 M3996 JIANG_HYPOXIA_NORMAL http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_HYPOXIA_NORMAL.html Genes up-regulated in RPTEC cells (normal kidney) by hypoxia. 12692265 410/525 John Newman 0.290273965713381 0.354487223329149 2995 3015.45454545455 2930 0.0306897745620319 1593 1.07815498549147 1.04833590897799 1 0.728547277356792 2991 2717 2930 1923 2449 4099 3750 3623 1593 2378 4717 3259 M4270 KAYO_CALORIE_RESTRICTION_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_CALORIE_RESTRICTION_MUSCLE_DN.html Downregulated in the vastus lateralis muscle of middle aged rhesus monkeys subjected to caloric restriction since young adulthood vs age matched controls 11309484 132/169 John Newman 0.0367628688061082 0.0620603507742599 4575 2714.45454545455 2931 0.00339926893563871 5 1.17000837022659 -1.29277608629859 -1 2.11925491671322 4571 5 1014 1886 2710 3073 4679 3422 3804 1764 2931 3260 M18719 BIOCARTA_HER2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HER2_PATHWAY.html Role of ERBB2 in Signal Transduction and Oncology 35/37 BioCarta 0.00577426225782821 0.0142024584976285 4195 2567.27272727273 2932 0.000526315789473684 205 0.889577332298399 -0.940388853694054 -1 2.46617225012701 4192 1455 2970 205 1727 3976 3801 3839 590 2553 2932 3261 M1214 PATTERSON_DOCETAXEL_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/PATTERSON_DOCETAXEL_RESISTANCE.html Genes up-regulated in DU145-RD cells (prostate cancer) resistant to docetaxel [PubChem=148124] vs the parental, docetaxel-sensitive cells. 16652143 53/80 Arthur Liberzon 0.0188259779799002 0.036106711119516 2640 2577.72727272727 2934 0.0017262757845687 1134 1.08210638872594 -0.949178888959514 -1 2.34197089036155 2637 1922 1832 1608 1134 3012 3713 3263 3307 2934 2993 3262 M18328 POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP.html Top marker genes in medulloblastoma associated with good response to treatment (good outcome). 11807556 64/80 Jean Junior 0.265493113421812 0.328129744789461 4165 2513.63636363636 2934 0.0276607735956552 343 1.25137545120249 -1.09884141331291 -1 0.908622112605548 4161 763 1442 947 3125 2934 4499 4258 343 1998 3180 3263 M1657 LEE_CALORIE_RESTRICTION_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_MUSCLE_DN.html Down-regulated in the gastrocnemius muscle of aged (30-month) mice subjected to caloric restriction diet since young adulthood. 10464095 68/90 John Newman 0.00258304110906716 0.00808990301549603 3350 2759.81818181818 2936 0.000235098079721198 61 1.1759078611885 -1.26881354511185 -1 3.69127242856561 3348 4427 2936 4412 2737 1226 3936 3347 1419 2509 61 3264 M12176 CAIRO_HEPATOBLASTOMA_CLASSES_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_CLASSES_DN.html Genes down-regulated in robust Cluster 2 (rC2) of hepatoblastoma samples compared to those in the robust Cluster 1 (rC1). 19061838 252/372 Arthur Liberzon 1.45365666279237e-05 0.000141178177950206 4580 2528.54545454545 2936 1.32151478905605e-06 381 1.20858477270505 -1.26168907144896 -1 6.98231265023023 4576 1199 381 1426 1966 3940 3920 3211 2936 940 3319 3265 M22 PID_GMCSF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_GMCSF_PATHWAY.html GMCSF-mediated signaling events 18832364 50/57 Pathway Interaction Database 0.188543734336041 0.245836029300031 2940 2914.72727272727 2937 0.0188139288476726 647 0.947200730648653 0.863908259954025 1 0.865965841194959 2937 2897 2793 647 3872 3572 2404 1773 4167 3115 3885 3266 M15226 LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTHELIOMA_SURVIVAL_WORST_VS_BEST_UP.html Genes higher expressed in the worst 25 mesothelioma survivors compared to the 25 best ones. 16540645 22/24 Arthur Liberzon 0.0416666251140044 0.0690057791361758 1955 2674.72727272727 2937 0.00386157677681397 625 0.83693186174715 0.96370910196493 1 1.45806018727651 1952 3483 2609 4225 2937 1656 625 3100 4016 3837 982 3267 M10169 WU_APOPTOSIS_BY_CDKN1A_VIA_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/WU_APOPTOSIS_BY_CDKN1A_VIA_TP53.html Genes downstream of both CDKN1A and TP53 [GeneID=1026;7157] in 2774qw1 cells (ovarian cancer). 12138103 98/116 Arthur Liberzon 0.367227701703326 0.435615670278888 1870 3130.72727272727 2937 0.0407504876020845 1866 1.18862066696891 -1.47602872631128 -1 0.643570834033102 1866 4392 3266 4168 4206 2642 2937 2210 2260 3705 2786 3268 M1927 MIKKELSEN_DEDIFFERENTIATED_STATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_DEDIFFERENTIATED_STATE_DN.html Genes down-regulated in partially reprogrammed and pluripotent cell populations (induced, iPS; and embryonic stem cells, ES) compared to parental lineage-commited cell lines. 18509334 8/9 Jessica Robertson 0.0742203101298842 0.112138240657187 2400 3141.54545454545 2938 0.00768223845793828 1731 0.659402421798197 -0.659402421798197 -1 0.940112074235822 2397 2172 4609 3732 1731 2803 2236 2938 4629 3464 3846 3269 M311 KEGG_ALPHA_LINOLENIC_ACID_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ALPHA_LINOLENIC_ACID_METABOLISM.html alpha-Linolenic acid metabolism 10/21 KEGG 0.0059327668053233 0.0144866318267594 3860 2609.27272727273 2939 0.000540802403102967 408 1.64312639972729 -1.96793987299205 -1 4.53411016344349 3857 3937 2005 2577 2939 3610 2996 408 1614 1589 3170 3270 M16644 PARENT_MTOR_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARENT_MTOR_SIGNALING_DN.html Genes down-regulated in HepaRG cells (liver cancer) expressing constituvely active form of MTOR [GeneID=2475]. 17483347 51/81 Arthur Liberzon 0.00459627749750863 0.0124752327706962 2940 2636.72727272727 2939 0.000418718936342408 745 1.3718148974201 -1.39378331601743 -1 3.91905574690097 2939 819 757 1484 4531 3747 3527 4678 1297 745 4480 3271 M14183 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_17 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_17.html Amplification hot spot 17: colocalized fragile sites and cancer genes in the 1q11-q44 region. 16751803 24/31 Arthur Liberzon 0.0358258226110182 0.0608484644562814 1410 2354.81818181818 2940 0.0033111712824275 571 0.960552169516405 1.1075394807879 1 1.75218899762687 1410 3467 2940 2688 3146 1238 571 3026 3376 3050 991 3272 M605 KEGG_ASCORBATE_AND_ALDARATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ASCORBATE_AND_ALDARATE_METABOLISM.html Ascorbate and aldarate metabolism 11/30 KEGG 0.228132822873698 0.28852811467413 4580 2815.90909090909 2941 0.0232653436095133 1402 1.50184268549073 -1.88651954979506 -1 1.21638454345433 4577 3098 1402 2119 3495 1525 2796 3807 2941 1713 3502 3273 M19613 BIOCARTA_IGF1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1R_PATHWAY.html Multiple antiapoptotic pathways from IGF-1R signaling lead to BAD phosphorylation 40/44 BioCarta 0.0499054503964007 0.0806690842024012 4585 2797.90909090909 2941 0.00464316642258573 806 0.800773484558519 -0.855931814285567 -1 1.31356939792441 4582 2941 3510 1680 1519 4045 3186 2584 806 2862 3062 3274 M16859 SENESE_HDAC3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SENESE_HDAC3_TARGETS_DN.html Genes down-regulated in U2OS cells (osteosarcoma) upon knockdown of HDAC3 [GeneID=8841] by RNAi. 17470557 657/789 Leona Saunders 0.0801515019080365 0.119644240672338 2945 2751.27272727273 2941 0.00831982691801754 739 1.1194887519438 -1.01711412679082 -1 1.54886567475597 2941 1128 4309 739 3897 4502 3913 1814 1502 936 4583 3275 M1105 GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN.html Genes down-regulated in ME-A cells (breast cancer) undergoing apoptosis in response to doxorubicin [PubChem=31703]. 17160024 2335/2619 Arthur Liberzon 0.50424050095182 0.573083352875654 4515 3172.27272727273 2941 0.0677613502209407 1399 0.963035813122319 -0.918471607450264 -1 0.349282654016369 4511 1656 4338 1399 2885 2712 4545 3939 1635 4334 2941 3276 M13537 KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP.html Genes up-regulated in MEWO cells (melanoma) after 48h of methionine [PubChem=876] deprivation. 16908595 161/209 Arthur Liberzon 0.195630622427934 0.253465972511625 3175 2864.72727272727 2942 0.0195960596624842 1344 1.16637922596116 1.06617190569893 1 1.0431393343524 3174 3641 1344 3858 2896 2346 2878 3589 3340 1504 2942 3277 M14971 BIOCARTA_DEATH_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DEATH_PATHWAY.html Induction of apoptosis through DR3 and DR4/5 Death Receptors 41/48 BioCarta 0.0348299533165327 0.0594135813711725 1725 2467.90909090909 2943 0.00321762857370684 556 1.05851200977017 0.962505313488348 1 1.94735416440747 1723 3774 3031 3844 3029 1207 556 2837 1221 2943 2982 3278 M1732 GAVIN_FOXP3_TARGETS_CLUSTER_P2 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P2.html Cluster P2 of genes with similar expression profiles in peripheral T ymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 91/145 Jessica Robertson 0.00176735407334028 0.00609788832322085 1970 2735 2944 0.000160797769391481 200 0.999017651625238 1.02059145195993 1 3.32001211228064 1969 3678 2028 3738 3617 2462 2124 200 3857 3468 2944 3279 M16431 DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DEURIG_T_CELL_PROLYMPHOCYTIC_LEUKEMIA_UP.html Genes up-regulated in T-PLL cells (T-cell prolymphocytic leukemia) bearing the inv(14)/t(14:14) chromosomal aberration. 17713554 485/702 Leona Saunders 0.161477660238887 0.215242743950169 3835 2505.36363636364 2945 0.0158828839988117 1269 1.15948916412194 -1.11130390913832 -1 1.16048965523718 3831 1685 1288 1269 3018 3180 4476 2945 1291 1283 3293 3280 M6520 BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_UP.html Genes up-regulated in patients at the incipient stage of Alzheimer's disease. 14769913 584/826 John Newman 0.0703927037799928 0.107282390003735 2060 2810 2945 0.00727272919122259 1305 1.07546918042659 1.13092770551527 1 1.56439159129118 2060 3154 4488 2945 3028 3409 2679 1305 1495 2739 3608 3281 M2417 WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D.html Genes with promoters bound by both PPARG and RXRA [GeneID=5468, 6256] at 8 day time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 1101/1344 Arthur Liberzon 0.029457166517011 0.0518655500702428 4200 3135.90909090909 2945 0.00298550866562519 1348 0.962449582439655 -0.918443147824195 -1 1.85583369855084 4196 2196 4698 1649 1348 2945 4262 4564 1940 4159 2538 3282 M10066 BIOCARTA_GCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GCR_PATHWAY.html Corticosteroids and cardioprotection 29/35 BioCarta 0.0326186531468836 0.0562719454873139 925 2296.90909090909 2946 0.00301023290960647 539 0.799043932937334 0.808143605197381 1 1.49827097492163 924 3005 2946 3656 3079 600 539 1973 4284 2958 1302 3283 M1500 BURTON_ADIPOGENESIS_10 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_10.html Strongly down-regulated at 8-48 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 41/42 John Newman 0.269370128492237 0.332486141862803 3155 2878 2946 0.0281284774887274 1879 0.945038845451569 0.932152368901291 1 0.678043073979361 3153 2488 2840 3542 2841 3392 3329 2001 1879 2946 3247 3284 M1947 CHEN_LIVER_METABOLISM_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_LIVER_METABOLISM_QTL_CIS.html Cis-regulated expression quantitative loci (cis-eQTL) in the liver that contribute to metabolic quantitative traits (weight, fat mass, and plasma glucose and cholesterol levels). 18344982 123/185 Arthur Liberzon 0.20037960716986 0.258824327799352 4435 2879.63636363636 2946 0.0201236853351956 1274 1.17443755313302 -0.967404733938527 -1 1.0343359922824 4434 1274 1351 2056 3944 3356 4255 3690 2946 1983 2387 3285 M656 REACTOME_SYNTHESIS_OF_PE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PE.html Genes involved in Synthesis of PE 9/12 Reactome 0.00525070999993344 0.0138068808911899 2950 2513.54545454545 2947 0.000526315789473684 21 1.31032447422856 1.44193675478651 1 3.65677904601685 2947 2163 4212 105 3357 3277 4057 3878 21 2031 1601 3286 M653 REACTOME_SYNTHESIS_OF_PA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PA.html Genes involved in Synthesis of PA 22/29 Reactome 0.68618940391 0.690284310838704 4715 2851.27272727273 2948 0.1 747 1.11008984564835 -1.42116294276561 -1 0.268027174752977 4715 972 2364 747 4498 2948 3562 4018 1076 2390 4074 3287 M119 PID_ERB_GENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERB_GENOMIC_PATHWAY.html Validated nuclear estrogen receptor beta network 18832364 34/50 Pathway Interaction Database 0.452111834545933 0.520479965623611 1680 2887.45454545455 2949 0.0532294945755781 1640 0.989570564258071 1.21761680273038 1 0.420997478506091 1677 3382 2949 2869 4674 3536 3223 2375 1640 3289 2148 3288 M16376 KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ARRHYTHMOGENIC_RIGHT_VENTRICULAR_CARDIOMYOPATHY_ARVC.html Arrhythmogenic right ventricular cardiomyopathy (ARVC) 67/95 KEGG 0.0162653021407828 0.0322436900900861 1865 2531.63636363636 2950 0.00148971057609989 800 1.34853281085313 1.3537629767289 1 3.01805705906223 1865 3704 902 3570 4111 3204 3010 800 2950 1028 2704 3289 M3782 NAKAYAMA_FRA2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_FRA2_TARGETS.html Genes down-regulated in ST1 cells (adult T-cell leukemia, ATL) after knockdown of FRA2 [GeneID=2355] by RNAi. 18071306 51/56 Jessica Robertson 0.0319777879280205 0.055429731553528 3840 2778.45454545455 2950 0.00295020734311294 1342 1.05682692370193 -1.08217672537864 -1 1.99205432709825 3840 3330 2146 2547 1342 4074 2950 3180 1352 2507 3295 3290 M10445 DORSAM_HOXA9_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DORSAM_HOXA9_TARGETS_UP.html HOXA9 [GeneID=3205] targets up-regulated in hematopoietic stem cells. 14604967 54/66 Broad Institute 0.184242173577388 0.241293856627434 4705 2629.27272727273 2952 0.0183422184653043 994 1.06988142092081 -1.22030502572335 -1 0.991141150232426 4703 1403 2952 1063 3420 3965 3590 3178 994 2365 1289 3291 M8719 BIOCARTA_MCALPAIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCALPAIN_PATHWAY.html mCalpain and friends in Cell motility 39/49 BioCarta 0.00986170757157788 0.0216096841865588 4240 2786.45454545455 2953 0.0009005630029278 898 1.16983463719925 -1.16638893532719 -1 2.92318630531211 4237 2953 2156 1667 898 3764 4187 4282 2219 937 3351 3292 M8493 BASSO_CD40_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_CD40_SIGNALING_UP.html Gene up-regulated by CD40 [GeneID=958] signaling in Ramos cells (EBV negative Burkitt lymphoma). 15331443 126/201 Kevin Vogelsang 0.0854052743510881 0.126446955751925 3320 2888.72727272727 2953 0.00808299499853774 1158 1.08443328539599 -1.09030223193075 -1 1.4612813502785 3318 1803 1158 2339 4207 3739 2953 3693 2670 1558 4338 3293 M12707 MILI_PSEUDOPODIA_HAPTOTAXIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MILI_PSEUDOPODIA_HAPTOTAXIS_UP.html Transcripts enriched in pseudopodia of NIH/3T3 cells (fibroblast) in response to haptotactic migratory stimulus by fibronectin, FN1 [GeneID=2335]. 18451862 697/805 Jessica Robertson 0.218881160021001 0.278919836743824 955 3028.72727272727 2953 0.0244001805297803 955 0.839048326253833 0.846167176299524 1 0.698040513533865 955 3598 4617 3475 2341 2800 2425 2953 2187 4472 3493 3294 M796 REACTOME_ACTIVATION_OF_GENES_BY_ATF4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_GENES_BY_ATF4.html Genes involved in Activation of Genes by ATF4 23/26 Reactome 0.0124596081831922 0.0259988287465373 2955 2505.54545454545 2954 0.00113915793349283 273 1.10043041024439 1.06476358905526 1 2.61715088127063 2954 968 2906 2048 992 3428 3391 4188 273 2972 3441 3295 M3284 KUMAR_TARGETS_OF_MLL_AF9_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/KUMAR_TARGETS_OF_MLL_AF9_FUSION.html Myeloid leukemia model in mice with germ-line MLL-AF9 fusion knock-in [GeneID=4297;4300]: genes changed in comparison among the leukemic, preleukemic and wild-type animals. 14615372 448/605 Kevin Vogelsang 3.60273079107685e-05 0.000296026299646383 3055 2090.63636363636 2954 3.27526344629606e-06 280 1.23520681283251 -1.14485071173636 -1 6.54011625062182 3053 511 425 280 3400 3629 2954 3074 1466 309 3896 3296 M99 PID_TXA2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TXA2PATHWAY.html Thromboxane A2 receptor signaling 18832364 74/89 Pathway Interaction Database 0.0729939027568245 0.11056842779596 4635 2923.63636363636 2955 0.0068667820771284 95 0.957414878421295 -0.871484162027859 -1 1.37383304102159 4634 95 1794 1655 1683 4513 3834 4402 4077 2518 2955 3297 M6921 NUTT_GBM_VS_AO_GLIOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUTT_GBM_VS_AO_GLIOMA_UP.html Top 50 marker genes for glioblastoma multiforme (GBM), a class of high grade glioma. 12670911 86/110 Arthur Liberzon 0.0289605832466677 0.0511533820699591 3285 2763.45454545455 2955 0.00266809044251879 1297 1.07471742651139 -0.750064973870497 -1 2.08200866646 3281 2831 2126 2955 1297 3384 3529 1917 3085 2041 3952 3298 M6455 MORI_PRE_BI_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PRE_BI_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Pre-BI stage. 18922927 103/138 Jessica Robertson 0.579551927480388 0.646686784327998 4280 2863.45454545455 2956 0.0757445220566606 675 1.00657828534262 -0.928345089465863 -1 0.285820256861449 4279 675 1769 1564 2956 4312 4384 2966 3919 1845 2829 3299 M17807 KEGG_BASAL_CELL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASAL_CELL_CARCINOMA.html Basal cell carcinoma 45/60 KEGG 0.125126376870913 0.174320100009064 4610 2665.90909090909 2957 0.0120788069392171 484 1.32469970903769 -1.53223573301391 -1 1.50789702041519 4606 1427 1234 484 3742 4405 4191 2957 1201 1818 3260 3300 M4235 GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_DN.html Genes down-regulated in quiescent CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors compared to the dividing cells from CML (chronic myeloid leukemia) patients. 17717066 118/196 Arthur Liberzon 4.4597189746123e-06 5.0968216852712e-05 4180 2267.54545454545 2957 4.0542981955772e-07 334 1.35948459331023 -1.44042543349324 -1 8.75671963429001 4176 648 334 1040 1026 3782 2957 3447 3117 497 3919 3301 M2073 BAE_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BAE_BRCA1_TARGETS_DN.html Genes concordantly down-regulated in DU-145 and MCF-7 cells (lprostate, breast cancer) upon expression of BRCA1. 15520196 50/58 Arthur Liberzon 0.68618940391 0.690284310838704 2960 2799.45454545455 2957 0.1 611 1.12418017752499 1.12200225477623 1 0.271430577645527 2957 807 2505 611 3580 4708 4429 3440 660 2772 4325 3302 M1412 PARK_HSC_VS_MULTIPOTENT_PROGENITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_VS_MULTIPOTENT_PROGENITORS_UP.html Genes up-regulated in long term hematopoietic stem cells (LT-HSC) compared to multipotent progenitor (MPP) cells. 11781229 27/30 Kate Stafford 0.0164742652909768 0.0324941630478106 3085 2527.90909090909 2958 0.00150899441579874 927 0.921220963853816 0.712959627610904 1 2.05704132132716 3081 927 3009 1504 1080 4030 2206 1734 2958 3972 3306 3303 M7603 BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOHN_PRIMARY_IMMUNODEFICIENCY_SYNDROM_UP.html Genes up-regulated in B lymphocytes from patients with primary immunodefiency syndrom. 17195838 56/84 Jessica Robertson 0.68618940391 0.690284310838704 2520 3154.72727272727 2959 0.1 1489 1.08479930441756 1.00850108862281 1 0.261918454111577 2519 4448 3121 2927 4421 2788 2959 3186 1489 2775 4069 3304 M1502 SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHLINGEMANN_SKIN_CARCINOGENESIS_TPA_UP.html Up-regulated in murine dorsal skin cells at 6 h after treatment with the phorbol ester carcinogen TPA [PubChem=4792]. 12640676 45/82 John Newman 0.218992961469604 0.278986984652235 3470 2791.36363636364 2960 0.0222195291169671 934 1.24269310056001 1.34412071041694 1 1.03370599699433 3468 1961 1386 2599 3161 4076 4021 2960 934 2139 4000 3305 M2589 SESTO_RESPONSE_TO_UV_C2 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C2.html Cluster 2: genes changed in primary keratinocytes by UVB irradiation. 11867738 91/103 John Newman 0.68618940391 0.690284310838704 2960 2924.36363636364 2960 0.1 952 0.954889316022291 -0.972147012551719 -1 0.230539773031078 2960 1843 3430 2175 4493 3006 2813 3415 952 2741 4340 3306 M1763 TESAR_ALK_AND_JAK_TARGETS_MOUSE_ES_D4_UP http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_AND_JAK_TARGETS_MOUSE_ES_D4_UP.html Genes up-regulated in mES cells (mouse embryonic stem cells) after tratment with the ALK [GeneID=238] inhibitor SB-431542 and JAK inhibitor I [PubChem=4521392;5494425]. 17597760 2/6 Jessica Robertson 0.0506427345589737 0.0816093230175336 2690 3145.1 2960 0.00575781389095835 978 1.04720827897613 -1.04720827897613 -1 1.70993953663171 2689 4654 4526 NA 1605 1832 978 2870 4561 4686 3050 3307 M1831 MATZUK_SPERMATOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATOCYTE.html Genes important for spermatocyte, based on mouse models with male reproductive defects. 18989307 90/225 Jessica Robertson 0.0616207966033715 0.0959268337625045 1660 2492.54545454545 2960 0.00576523900776622 570 1.07334663793938 -1.15021779171121 -1 1.63955920791156 1660 3251 3076 3212 2506 570 2152 3310 2960 3666 1055 3308 M11250 FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN http://www.broadinstitute.org/gsea/msigdb/cards/FRASOR_RESPONSE_TO_SERM_OR_FULVESTRANT_DN.html Genes down-regulated in MCF-7 cells (breast cancer) by selective estrogen receptor modulators (SERM) 4-hydroxytamoxifen, raloxifene, or ICI 182780 but not by estradiol [PubChem=44959;5035;3478439;5757]. 14973112 61/71 Arthur Liberzon 0.68618940391 0.690284310838704 1865 2919 2960 0.1 1814 1.1126726190454 -1.15354416691869 -1 0.268651022262553 1861 1912 3193 2960 4102 3524 2715 4263 1814 2719 3046 3309 M5193 SIG_CHEMOTAXIS http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CHEMOTAXIS.html Genes related to chemotaxis 50/63 Signaling Gateway 0.191080162680609 0.248662356728005 3300 2751.90909090909 2961 0.0190931408015138 796 0.856763939234611 0.834032245956301 1 0.776892751592519 3297 796 2961 1082 2201 3149 2655 4566 2000 3114 4450 3310 M646 REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TGF_BETA_RECEPTOR_SIGNALING_ACTIVATES_SMADS.html Genes involved in TGF-beta receptor signaling activates SMADs 34/38 Reactome 0.28612378260641 0.350168225676438 1975 2767.54545454545 2961 0.0301758551396198 1388 0.758449140513882 0.839144023532927 1 0.518538307731168 1971 3399 3597 3175 2932 1388 1872 3603 2961 3926 1619 3311 M1085 REACTOME_APOBEC3G_MEDIATED_RESISTANCE_TO_HIV1_INFECTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOBEC3G_MEDIATED_RESISTANCE_TO_HIV1_INFECTION.html Genes involved in APOBEC3G mediated resistance to HIV-1 infection 7/10 Reactome 0.120952315857173 0.169304546514192 2200 3214.18181818182 2961 0.0128088725471428 1564 0.605748071899956 0.605748071899956 1 0.700985908955327 2196 4644 4266 4074 2961 2118 1627 1564 4379 4624 2903 3312 M11701 CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_UP.html Selected genes up-regulated during invasion of lymphatic vessels during metastasis. 18794116 28/35 Jessica Robertson 0.193622975740767 0.251438210882836 2540 2892.81818181818 2961 0.0193738556429164 1404 1.2150651857124 1.30267981156249 1 1.09304567151399 2537 3846 1404 4378 3341 3583 2961 1789 4012 1654 2316 3313 M16812 KERLEY_RESPONSE_TO_CISPLATIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/KERLEY_RESPONSE_TO_CISPLATIN_UP.html Genes genes up-regulated in NT2/D1 cells (embryonal carcinoma) in response to treatment with cisplatin [PubChem=2767]. 15940259 65/77 Leona Saunders 0.122338561261257 0.170991415206732 3960 2953.36363636364 2962 0.0117930346493312 1128 1.12106809493896 1.05102895577944 1 1.29017342232637 3957 3292 1231 3957 2365 4339 2785 2677 2962 1128 3794 3314 M11105 NIELSEN_LEIOMYOSARCOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/NIELSEN_LEIOMYOSARCOMA_DN.html Top 20 negative significant genes associated with CNN1 [GeneID=1264] negative leiomyosarcoma tumors. 11965276 29/32 John Newman 0.000795579980677502 0.00333493562060196 3875 2643.54545454545 2962 7.23516208937683e-05 364 1.01823670516767 -0.993357331386229 -1 3.78433073326909 3874 2010 2305 2308 364 3005 3918 3094 1186 2962 4053 3315 M2594 GHANDHI_DIRECT_IRRADIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GHANDHI_DIRECT_IRRADIATION_DN.html Genes significantly (FDR < 10%) down-regulated in IMR-90 cells (fibroblast) in response to direct irradiation. 19108712 35/45 Itai Pashtan 0.168073611425902 0.222589070126335 3160 2804.45454545455 2962 0.0165891604852217 1435 1.15186199817237 -0.991549124474915 -1 1.12766335280883 3158 2962 1435 2806 2142 3312 2240 3285 3979 1502 4028 3316 M3977 WEBER_METHYLATED_ICP_IN_SPERM_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_ICP_IN_SPERM_UP.html Methylated germline-specific genes with intermediate-CpG-density promoters (ICP) in sperm. 17334365 8/27 Arthur Liberzon 0.6513215599 0.690284310838704 2915 3244.72727272727 2963 0.1 1083 0.755632623744122 0.700811231392287 1 0.182410970331719 2912 1083 4633 2427 4623 2963 3831 3616 2180 4708 2716 3317 M8873 ST_FAS_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_FAS_SIGNALING_PATHWAY.html Fas Signaling Pathway 84/100 Signaling Transduction KE 0.68618940391 0.690284310838704 4425 2892.81818181818 2966 0.1 897 1.02798988766032 -1.01661828022267 -1 0.248196610296376 4423 1317 2823 897 4681 3496 3020 3535 1820 2966 2843 3318 M182 PID_IL3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL3_PATHWAY.html IL3-mediated signaling events 18832364 36/41 Pathway Interaction Database 0.68618940391 0.690284310838704 3195 3151.63636363636 2967 0.1 1985 1.07348232442478 0.997678747375709 1 0.259184931382691 3195 1985 2526 2179 4403 3431 2967 2788 4356 2614 4224 3319 M5466 WINTER_HYPOXIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/WINTER_HYPOXIA_UP.html Genes up-regulated in head and neck tumor samples which clustered around known hypoxia genes. 17409455 141/174 Arthur Liberzon 0.0104646883096719 0.0226367226497027 3095 2841.81818181818 2967 0.000955890861231442 925 1.10485231680551 1.10761752320977 1 2.72737158686061 3092 1789 1619 3599 925 2967 4088 3745 2938 2252 4246 3320 M6663 HOLLMANN_APOPTOSIS_VIA_CD40_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLMANN_APOPTOSIS_VIA_CD40_DN.html Genes down-regulated in DLBCL (diffuse large B-cell lymphoma) cell lines sensitive to stimulation of CD40 [GeneID=958] relative to the resistant ones. 16585179 390/543 Arthur Liberzon 0.00585413957721163 0.014354046132176 4105 3020.81818181818 2967 0.000533615960239847 746 0.907460000944935 -0.933637378504577 -1 2.50947207685466 4101 2228 3793 2967 746 1980 4706 4607 2685 4052 1364 3321 M1602 HEIDENBLAD_AMPLICON_12P11_12_DN http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_12P11_12_DN.html Down-regulated genes whose expression is associated with amplification of the 12p11-12 chromosome in pancreatic cancer cell lines. 15688027 34/38 Arthur Liberzon 0.0091597242486232 0.0204126055021253 3245 2737.45454545455 2968 0.000836189513464787 294 0.741560164316611 -0.812687487798282 -1 1.88051396398692 3245 2968 3608 2566 876 3658 4269 2478 2223 3927 294 3322 M2263 MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIKHAYLOVA_OXIDATIVE_STRESS_RESPONSE_VIA_VHL_UP.html Proteins significantly induced by oxidative stress (hydrogen peroxide [PubChem=784] in 786-O cells (renal clear cell carcinoma, RCC) expressing VHL [GeneID=7428]. 18285459 9/9 Arthur Liberzon 0.000871860273899964 0.00357220528889569 2510 2912.81818181818 2968 8.72202526050985e-05 46 0.498549829006842 -0.498549829006842 -1 1.83050334971978 2507 3120 4676 2968 1825 783 46 4611 4642 4716 2147 3323 M1519 KEGG_ENDOCYTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOCYTOSIS.html Endocytosis 203/231 KEGG 0.0638572991188041 0.0988866311813501 2440 2814.90909090909 2970 0.00598089335959525 1376 0.984477342482426 1.0904849685282 1 1.48430508235223 2436 3630 3495 1376 1625 3365 2582 2970 2234 3514 3737 3324 M1044 REACTOME_CONVERSION_FROM_APC_C_CDC20_TO_APC_C_CDH1_IN_LATE_ANAPHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CONVERSION_FROM_APC_C_CDC20_TO_APC_C_CDH1_IN_LATE_ANAPHASE.html Genes involved in Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase 19/21 Reactome 0.0612935400833375 0.0955118881457092 2970 3018.27272727273 2970 0.00573372255314235 1298 0.526346968992574 -0.521993708359421 -1 0.805438887912502 2970 3052 3926 4406 1602 2274 1298 2613 3690 4612 2758 3325 M19875 SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SENGUPTA_NASOPHARYNGEAL_CARCINOMA_UP.html Genes up-regulated in nsopharyngeal carcinoma relative to the normal tissue. 16912175 405/518 Leona Saunders 0.0372763379791285 0.0628429241446762 1645 3134.18181818182 2970 0.00344757647646064 993 1.07657257847914 1.21364966637076 1 1.94121335218628 1642 4681 2877 4687 3871 2546 2970 993 3434 4019 2756 3326 M1828 MATZUK_MALE_REPRODUCTION_SERTOLI http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_MALE_REPRODUCTION_SERTOLI.html Genes important for Sertoli, peritubular, Leydig and interstitial cells, based on mouse models with male reproductive defects. 18989307 25/40 Jessica Robertson 0.560762212865877 0.628096261207152 3895 2768.72727272727 2970 0.072063721720586 944 0.8878422628988 -1.11604227197266 -1 0.268968733981409 3891 944 2462 1482 3238 2970 2135 4179 1550 3583 4022 3327 M648 BIOCARTA_G1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G1_PATHWAY.html Cell Cycle: G1/S Check Point 34/39 BioCarta 0.00949538881481984 0.0209620623225621 4075 3051.54545454545 2971 0.00086696555371782 893 0.964942709855856 1.05218440016073 1 2.43031656393123 4073 2971 3110 2463 893 2612 2845 3962 3309 2864 4465 3328 M14981 REACTOME_GAP_JUNCTION_ASSEMBLY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GAP_JUNCTION_ASSEMBLY.html Genes involved in Gap junction assembly 7/18 Reactome 0.0337827749552767 0.0578993092915418 2975 2906.27272727273 2972 0.00343076138352563 1135 1.4793296626957 -1.49316833093115 -1 2.7464670643797 2972 3569 4271 3492 1401 2326 3549 2896 2934 1135 3424 3329 M2545 ROESSLER_LIVER_CANCER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROESSLER_LIVER_CANCER_METASTASIS_DN.html Genes down-regulated in liver samples containing tumor thrombi in the major branches of the portal vein at surgery (PT) compared to those from metastasis-free HCC patients (PN) at the time of surgery and at follow-up. 21159642 61/68 Yujin Hoshida 0.00670374322757501 0.0159403869189693 4460 2758 2972 0.000611296195419784 595 1.17633321547047 -1.12988795752865 -1 3.17268428317157 4459 3304 2972 2300 786 4460 3419 2182 595 2720 3141 3330 M811 REACTOME_ADP_SIGNALLING_THROUGH_P2RY1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADP_SIGNALLING_THROUGH_P2RY1.html Genes involved in ADP signalling through P2Y purinoceptor 1 23/29 Reactome 0.402198779919123 0.471646768004537 3535 3004.63636363636 2973 0.0456954784321308 1513 0.830758432583026 -0.786461627943749 -1 0.406753501937123 3532 1513 2736 2082 3294 2890 1805 4146 3639 2973 4441 3331 M4042 NIKOLSKY_BREAST_CANCER_10Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_10Q22_AMPLICON.html Genes within amplicon 10q22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 14/19 Jessica Robertson 0.0867465369150784 0.128134387726987 2720 2864.81818181818 2974 0.00821532473078652 903 0.974481703751992 -1.066665111715 -1 1.30469158153368 2717 4240 2767 3565 3855 2227 2974 1361 3585 3319 903 3332 M14736 BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_UP.html Genes up-regulated in ALL (acute lymphoblastic leukemia) patients who developed t-ML (treatment related myeloid leukemia). 16341039 33/63 Arthur Liberzon 0.670952112302409 0.690284310838704 3125 3006.45454545455 2975 0.0961123256230401 1990 1.06569564709351 -1.05258415613015 -1 0.257304124004653 3124 2975 2618 3088 3982 4048 2804 2724 1990 3223 2495 3333 M19666 TIEN_INTESTINE_PROBIOTICS_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TIEN_INTESTINE_PROBIOTICS_24HR_DN.html Genes down-regulated in Caco-2 cells (intestinal epithelium) after coculture with the probiotic bacteria L. casei for 24h. 16394013 299/389 Arthur Liberzon 0.215646515532689 0.275616450938069 1975 2880.72727272727 2977 0.0218393982172131 1159 0.944466994435112 0.904350439690061 1 0.793089076503895 1973 3612 3523 2977 3747 1159 1722 4413 2921 3179 2462 3334 M1934 MEISSNER_NPC_ICP_WITH_H3K4ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_ICP_WITH_H3K4ME3.html Genes with intermediate-CpG-density promoters (ICP) bearing histone H3 trimethylation mark at K4 (H3K4me3) in neural precursor cells (NPC). 18600261 23/32 Jessica Robertson 0.000887960575242545 0.00362558297157856 3025 2483.36363636364 2977 8.07562886505954e-05 383 0.931488584486618 -0.874858335437649 -1 3.41119401276919 3024 4188 3066 3139 383 3570 1623 556 2411 2977 2380 3335 M70 PID_PS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_PS1_PATHWAY.html Presenilin action in Notch and Wnt signaling 18832364 75/83 Pathway Interaction Database 0.150542975705065 0.203134032397915 3000 2779.90909090909 2979 0.0147230787135178 1335 0.957908950619757 0.948099642925312 1 0.994860756052359 2999 1335 2979 1617 2070 4387 3112 3555 1435 2560 4530 3336 M4925 STEARMAN_LUNG_CANCER_EARLY_VS_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/STEARMAN_LUNG_CANCER_EARLY_VS_LATE_UP.html Up-regulated genes classifying non-tumor lung tissues by age after incution of lung cancer by urethane injection [PubChem=5641]: early (24-26 weeks) vs late (46 weeks). 18172294 164/192 Jessica Robertson 0.617297000658651 0.682798227274347 1980 3108.45454545455 2979 0.0836141988276211 1977 0.861107177363234 1.00263804618341 1 0.214006407031157 1977 2774 3906 2956 3338 2979 2237 3371 3618 4269 2768 3337 M13014 ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_TUMOR_VS_NORMAL_ADJACENT_TISSUE_DN.html Genes down-regulated in liver tumor compared to the normal adjacent tissue. 18413731 287/408 Jessica Robertson 0.00389007849518341 0.0109415100652586 2985 2546.81818181818 2980 0.00035427037055793 88 1.18578397422851 -1.11343305198451 -1 3.48894958460527 2985 1180 746 88 3598 4177 2980 4417 2221 1032 4591 3338 M941 REACTOME_FACTORS_INVOLVED_IN_MEGAKARYOCYTE_DEVELOPMENT_AND_PLATELET_PRODUCTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FACTORS_INVOLVED_IN_MEGAKARYOCYTE_DEVELOPMENT_AND_PLATELET_PRODUCTION.html Genes involved in Factors involved in megakaryocyte development and platelet production 112/159 Reactome 0.265210607288926 0.328121163123698 3255 2668.63636363636 2981 0.0276267812436753 856 1.07136672448861 -1.2601981744053 -1 0.777921043278134 3253 2338 2981 2076 3542 3160 3877 2589 856 3111 1572 3339 M4557 BIOCARTA_NEUROTRANSMITTERS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NEUROTRANSMITTERS_PATHWAY.html Biosynthesis of neurotransmitters 3/9 BioCarta 9.09079019084144e-06 9.34833590801027e-05 2645 2673.90909090909 2983 9.09082738016537e-07 4 3.28492587122926 -3.28492587122926 -1 19.8605363844642 2641 3586 4187 1975 3851 2983 3604 4 3104 2681 797 3340 M15009 SCHRAMM_INHBA_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHRAMM_INHBA_TARGETS_DN.html Genes down-regulated in Kelly cells (neuroblastoma) by overexpressing INHBA [GeneID=3624] off a plasmid vector. 15580313 32/37 Arthur Liberzon 0.00497824163061425 0.0132828154304688 2985 2592.54545454545 2983 0.000453594763386298 711 1.2667308094556 -1.09159638483834 -1 3.56705982870494 2983 2984 3154 2704 711 2695 1395 3336 893 3549 4114 3341 M1568 APRELIKOVA_BRCA1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/APRELIKOVA_BRCA1_TARGETS.html Genes down-regulated in embryonic stem cells with BRCA1 [GeneID=672] loss of function (LOF). 11384963 70/85 John Newman 0.375080965584251 0.443482504398213 1810 3135.09090909091 2983 0.0418389267557128 1810 1.24490892428448 -1.31478943149046 -1 0.659532708894579 1810 4426 2983 4151 2623 3328 1855 4329 3165 2854 2962 3342 M8229 REACTOME_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSLATION.html Genes involved in Translation 171/283 Reactome 0.0110278255332215 0.0235313456224257 475 2902.09090909091 2984 0.00100759047344729 475 0.611260962891263 0.583121822057655 1 1.49343497383917 475 4371 4169 4706 946 1561 1239 2984 4506 4473 2493 3343 M487 BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BUCKANOVICH_T_LYMPHOCYTE_HOMING_ON_TUMOR_DN.html Genes down-regulated in microdissected endothelial samples from ovarian cancer tumors with tumor-infiltrating lymphocytes (TIL) vs those without TILs. 18157142 32/39 Jessica Robertson 0.00335986240106331 0.00987456446638781 2290 2882.27272727273 2986 0.000305909510457787 294 1.07795735549506 1.21272016247132 1 3.24375466123578 2288 2986 2079 3742 2853 4547 3047 294 4112 3551 2206 3344 M18506 CROONQUIST_IL6_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_IL6_DEPRIVATION_DN.html Genes down-regulated in the ANBL-6 cell line (multiple myeloma, MM) after withdrawal of IL6 [GeneID=3569]. 12791645 121/145 Arthur Liberzon 0.68618940391 0.690284310838704 2050 2884.81818181818 2986 0.1 1758 1.2726054833912 1.28840603541952 1 0.307281480217242 2047 1809 2762 1938 3642 3578 2986 4382 1758 3201 3630 3345 M1015 REACTOME_INHIBITION_OF_REPLICATION_INITIATION_OF_DAMAGED_DNA_BY_RB1_E2F1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_REPLICATION_INITIATION_OF_DAMAGED_DNA_BY_RB1_E2F1.html Genes involved in Inhibition of replication initiation of damaged DNA by RB1/E2F1 13/13 Reactome 0.159241988352653 0.212848364324726 2985 2835.72727272727 2987 0.0156446401069034 138 1.01309761946157 -0.556486502690815 -1 1.02134374223952 2981 3542 3328 1854 2111 3565 4151 2692 138 3844 2987 3346 M1344 FUJIWARA_PARK2_IN_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_IN_LIVER_CANCER_DN.html Genes down-regulated in tumorous liver tissues from PARK2 [GeneID=5071] knockout mice compared to the normal, non-tumorous tissue from wild type mice. 18574468 11/16 Jessica Robertson 0.0527416034760135 0.0844724697681655 2990 2542.36363636364 2987 0.00491364879261448 751 1.83499038470402 1.59362295705604 1 2.95511938479048 2987 3106 1221 2891 4607 3172 3065 1134 751 1235 3797 3347 M8615 BIOCARTA_IL2RB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL2RB_PATHWAY.html IL-2 Receptor Beta Chain in T cell Activation 52/61 BioCarta 0.297184911691323 0.361337656667451 3815 2843 2988 0.0315516545879804 847 0.996026989337391 -0.973369975075808 -1 0.66061871554834 3814 3327 2988 2780 4197 3066 1827 2065 847 2236 4126 3348 M19681 FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_OK_VS_DONOR_UP.html Genes upregulated in peripheral blood lymphocytes (PBL) from patients with well functioning kidneys more than 1-year post transplant compared to those from normal living kidney donors. 15307835 196/253 Jean Junior 0.0946419713660133 0.137788434561253 3450 2763.81818181818 2988 0.00899789282473041 1224 0.862624220468632 -0.950439011222898 -1 1.11408421709097 3448 1224 3925 2988 3743 2278 4411 1396 1628 4026 1335 3349 M456 REACTOME_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRNA_AMINOACYLATION.html Genes involved in tRNA Aminoacylation 43/43 Reactome 0.474936290153051 0.544630536813022 2870 3087.09090909091 2990 0.0568848365369717 1317 0.668450706426564 -0.71731113920948 -1 0.264590132642807 2868 3768 4062 3626 4259 1678 2242 2990 1317 4329 2819 3350 M1115 GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_C_DN.html Down-regulated genes from the set C (Fig. 5a): specific to cells expressing AF4-MLL [GeneID=4299;4297] fusion protein alone. 17130830 17/26 Arthur Liberzon 0.000890827890169983 0.00363066378484564 3525 2856.18181818182 2991 8.10171645812091e-05 384 1.05866816121014 -1.0707358755325 -1 3.8759852453081 3525 3058 2130 2303 384 2693 3385 4660 1681 2991 4608 3351 M16817 KEGG_OOCYTE_MEIOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_OOCYTE_MEIOSIS.html Oocyte meiosis 104/119 KEGG 0.43119990772354 0.499814448548158 2995 2636.27272727273 2992 0.05 31 0.741850635675739 -0.737117792683784 -1 0.335168693458627 2992 31 3836 1381 3346 2580 3061 3138 2396 4136 2102 3352 M662 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_PLASMA_MEMBRANE.html Genes involved in Synthesis of PIPs at the plasma membrane 33/36 Reactome 0.010138491486468 0.0220931116417954 2995 2268 2993 0.000925956131386848 152 0.961989288498611 -1.28606014885795 -1 2.38993325027538 2993 897 3188 1587 4262 4060 3670 542 152 3222 375 3353 M2250 LINDGREN_BLADDER_CANCER_CLUSTER_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_1_UP.html Up-regulated genes whose expression profile is specific to Custer I of urothelial cell carcinoma (UCC) tumors. 16532037 152/189 Leona Saunders 0.604846777928497 0.670946367055818 3205 2705.36363636364 2993 0.0809432677462573 859 0.949005919251854 1.01133761165698 1 0.246691157691661 3202 1773 3816 859 2993 2417 2437 3054 1014 3838 4356 3354 M7202 FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH_REARRANGEMENTS_UP.html Genes up-regulated in B-CLL (B-cell chronic lymphocytic leukemia) patients with mutated immunoglobulin variable heavy chain (VH) genes. 15817677 96/138 Kevin Vogelsang 0.029984694927442 0.0526125502072588 4460 3210.45454545455 2993 0.00276375823997807 1316 0.981977456840108 -0.908525096273538 -1 1.88433944342361 4457 2825 2907 3646 1316 4647 4014 2916 2993 3202 2392 3355 M10480 GU_PDEF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GU_PDEF_TARGETS_DN.html Integrin, VEGF, Wnt and TGFbeta signaling pathway genes down-regulated in PC-3 cells (prostate cancer) after knockdown of PDEF [GeneID=25803] by RNAi. 17483333 53/92 Jessica Robertson 0.00162596937714611 0.00571450145951575 3530 2527.81818181818 2993 0.000147924758054209 661 1.69520749355969 1.62897358297057 1 5.70545234451335 3526 1928 661 1054 3302 2993 2245 3108 3062 1225 4702 3356 M9788 MOOTHA_PGC http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_PGC.html Genes up-regulated in differentiating C2C12 cells (myoblasts) upon expression of PPARGC1A [GeneID=10891] off an adenoviral vector. 12808457 536/643 Vamsi Mootha 0.015545195684987 0.0311035708491475 3350 2699.54545454545 2994 0.00156550224135785 496 0.927489848481213 -0.754654134902371 -1 2.0974759659452 3350 496 4588 1921 1093 1760 2994 4110 1677 4273 3433 3357 M868 REACTOME_CHROMOSOME_MAINTENANCE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHROMOSOME_MAINTENANCE.html Genes involved in Chromosome Maintenance 96/251 Reactome 0.364298506951895 0.432684688679653 1890 3114.81818181818 2996 0.040347652234516 1809 1.05763824353707 -1.23412840323351 -1 0.577292654630806 1890 4385 3401 4459 3894 1882 2739 2988 2996 3820 1809 3358 M1128 LANG_MYB_FAMILY_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LANG_MYB_FAMILY_TARGETS.html Myb family target genes. 15608679 49/54 Arthur Liberzon 0.103002208789095 0.147682389272336 3540 2928 2996 0.00983332261663184 769 1.10001703272646 1.02751068577131 1 1.370998238027 3536 4104 2996 1909 3869 769 1582 3916 2737 2708 4082 3359 M7034 MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCMURRAY_TP53_HRAS_COOPERATION_RESPONSE_UP.html Up-regulated 'cooperation response genes': responded synergystically to the combination of mutant TP53 and HRAS [GeneID=7157;3265] in YAMC cells (colon). 18500333 32/35 Jessica Robertson 0.0247147095933493 0.0451270519460769 2700 2959.81818181818 2997 0.00227243639266085 956 2.02004251139847 1.51685427050834 1 4.07844957362845 2696 2997 956 3986 2036 4237 2481 4309 4246 1302 3312 3360 M2442 STEINER_ERYTHROCYTE_MEMBRANE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/STEINER_ERYTHROCYTE_MEMBRANE_GENES.html Major erythrocyte membrane genes. 19687298 17/27 Arthur Liberzon 0.00476014924365144 0.0127956938843674 2730 2701.81818181818 2997 0.000433680009659084 366 1.16058170668431 1.16569214964306 1 3.29639733100088 2727 3067 2390 3379 4646 2997 4101 366 3818 1462 767 3361 M3634 REACTOME_CASPASE_MEDIATED_CLEAVAGE_OF_CYTOSKELETAL_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CASPASE_MEDIATED_CLEAVAGE_OF_CYTOSKELETAL_PROTEINS.html Genes involved in Caspase-mediated cleavage of cytoskeletal proteins 17/20 Reactome 0.675805335932468 0.690284310838704 4205 3131.54545454545 2998 0.0973325011386804 2417 0.860670980850706 -0.861173204306665 -1 0.207782114995659 4204 2607 2998 3138 3572 2724 3786 2733 3448 2417 2820 3362 M9224 SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_CHRONIC_HEPATITIS_VS_LIVER_CANCER_UP.html Selected genes up-regulated in peripheral blood monocytes (PBMC) of patients with hepatocellular carcinoma (HCC) compared to those with chronic hepatitis. 19074895 110/146 Arthur Liberzon 0.147400237283589 0.199749962669693 840 2716.45454545455 2998 0.0143922499929118 837 0.929430640401922 0.947398152499832 1 0.975455926661426 837 3235 3591 2998 3113 1936 1434 1619 4151 4123 2844 3363 M2370 GOBERT_CORE_OLIGODENDROCYTE_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/GOBERT_CORE_OLIGODENDROCYTE_DIFFERENTIATION.html Oligodendrocyte core differentiation genes: up-regulated in Oli-neo cells (oligodendroglial precursor) at 10 h after treatment with PD174265, dexamethasone or isotretinoin [PubChem=4709, 5743, 5282379]. 19139271 54/66 Arthur Liberzon 0.553224119252202 0.620536559617489 3010 2791 2999 0.0706271642593203 1405 1.06003515205551 -1.08962714932471 -1 0.329519220882929 3008 1405 1978 1997 3651 3031 2121 3665 2902 2999 3944 3364 M16811 BIOCARTA_ERK5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ERK5_PATHWAY.html Role of Erk5 in Neuronal Survival 31/34 BioCarta 0.124924066577821 0.174089635148307 2750 2991.09090909091 3000 0.0120580407585463 1062 0.767760485226287 0.707738748659522 1 0.87455415544801 2746 2988 3497 3000 3576 3404 1062 3883 2282 3487 2977 3365 M17370 BIOCARTA_RANMS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RANMS_PATHWAY.html Role of Ran in mitotic spindle regulation 11/15 BioCarta 0.295617041730031 0.359802072451198 2610 2545.63636363636 3000 0.0313554483739725 26 1.58337069948169 -1.90373920734863 -1 1.05463342540846 2610 3112 3228 2369 3176 2260 1601 3608 26 3012 3000 3366 M16229 KANNAN_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KANNAN_TP53_TARGETS_UP.html Primary up-regulated targets of TP53 [GeneID=7157] in the H1299 (lung cancer) cell line. 11402317 72/111 Broad Institute 0.0125522229191799 0.0261343150324345 4585 2796.18181818182 3000 0.00114767433331264 997 1.14915075041378 -1.10096171602794 -1 2.72913464676915 4581 3284 1537 3807 997 4577 3000 1934 3080 1656 2305 3367 M764 REACTOME_INSULIN_SYNTHESIS_AND_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INSULIN_SYNTHESIS_AND_PROCESSING.html Genes involved in Insulin Synthesis and Processing 29/35 Reactome 0.0520965103105735 0.0836663928771374 3905 2823.81818181818 3001 0.00485206198924788 461 0.936656012902425 -1.10437291781506 -1 1.51421758791793 3902 3001 3143 2609 1532 2705 1666 3647 461 3779 4617 3368 M1808 WEBER_METHYLATED_HCP_IN_SPERM_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_SPERM_DN.html Unmethylated germline-specific genes with high-CpG-density promoters (HCP) in sperm. 17334365 22/45 Jessica Robertson 0.0676225384233626 0.103933045053166 1945 2669.36363636364 3001 0.00634501615613384 813 0.773738974130904 0.779825339891263 1 1.14145385969026 1941 3481 3001 3779 4320 1287 813 1425 3984 4118 1214 3369 M1004 REACTOME_LIGAND_GATED_ION_CHANNEL_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LIGAND_GATED_ION_CHANNEL_TRANSPORT.html Genes involved in Ligand-gated ion channel transport 4/24 Reactome 0.0549266283573937 0.0872614223651627 2895 3072 3005 0.00563334412872849 767 0.511425658113819 0.489986905711236 1 0.812711876576158 2891 2689 4255 2348 3682 3618 767 3708 3005 4592 2237 3370 M16909 PARENT_MTOR_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARENT_MTOR_SIGNALING_UP.html Genes up-regulated in HepaRG cells (liver cancer) expressing constituvely active form of MTOR [GeneID=2475]. 17483347 716/856 Arthur Liberzon 0.0939033555882925 0.136966575518152 4070 2743.90909090909 3005 0.00981247114824356 637 0.995729742111247 -0.911180645958915 -1 1.289889060945 4069 1668 4272 637 3005 766 3843 4080 1676 4138 2029 3371 M5542 SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER.html 50 genes up-regulated in the pancreatic cancer cell lines (AsPC1, Hs766T, MiaPaCa2, Panc1) but not in the non-neoplastic cells (HPDE) by the combination of decitabine and TSA [PubChem=451668;5562]. 12839967 47/66 John Newman 0.0149270815475804 0.0301738008156657 3650 2863.54545454545 3005 0.00136630318077055 1046 1.19887748812672 1.2234973439323 1 2.73494813674822 3648 2909 1097 2617 1046 3044 3005 4293 3764 1382 4694 3372 M11507 IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_UP http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_L1_G1_UP.html Genes up-regulated during transition from L1 (non-tumor, infected with HCV) to G1 (well differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 29/37 Yujin Hoshida 0.238392165538064 0.299417514991927 2240 3278.90909090909 3006 0.0244527492364466 2238 0.757956875851405 0.836922163752777 1 0.595539562568356 2238 3006 2967 4218 2343 4170 2874 3134 4457 3782 2879 3373 M15804 TURJANSKI_MAPK1_AND_MAPK2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK1_AND_MAPK2_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK1 and MAPK3 [GeneID=5594;5595] phosphorylation. 17496919 17/17 Arthur Liberzon 0.0172958617525649 0.0337201435242075 4715 3067.81818181818 3007 0.00158485029837656 698 1.11747486115802 1.03670040299057 1 2.46831956806644 4714 3065 2321 2684 4192 4116 2922 698 3606 2421 3007 3374 M2592 ZEMBUTSU_SENSITIVITY_TO_MITOMYCIN http://www.broadinstitute.org/gsea/msigdb/cards/ZEMBUTSU_SENSITIVITY_TO_MITOMYCIN.html Top genes associated with chemosensitivity to mitomycin [PubChem=5746] across 85 tumor xenografts. 11809704 21/30 Arthur Liberzon 0.0790631048574268 0.118506781494778 3330 2892.81818181818 3007 0.00745965244941196 1314 1.19604796335598 1.14312497571117 1 1.66224166206733 3329 4203 1635 4352 3007 2429 1397 1314 4426 1831 3898 3375 M17454 MASSARWEH_TAMOXIFEN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MASSARWEH_TAMOXIFEN_RESISTANCE_UP.html Genes up-regulated in breast cancer tumors (formed by MCF-7 xenografts) resistant to tamoxifen [PubChem=5376]. 18245484 763/965 Jessica Robertson 1.86614180500805e-08 3.89742890249469e-07 3660 2296.18181818182 3008 1.86614182067923e-09 105 1.09855616260223 -1.13346323070011 -1 10.5648910763557 3659 478 4538 215 1451 3008 3248 3746 1625 105 3185 3376 M14137 NIKOLSKY_BREAST_CANCER_19P13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_19P13_AMPLICON.html Genes within amplicon 19p13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 6/7 Jessica Robertson 0.0246442659189646 0.0450332695073607 4160 2897.36363636364 3010 0.00249219122811022 382 0.799929399165609 -1.1574672056084 -1 1.61607156008321 4156 2681 4464 2596 4627 3010 1860 3213 1646 3236 382 3377 M10628 BIOCARTA_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ATM_PATHWAY.html ATM Signaling Pathway 31/32 BioCarta 0.0013200478145203 0.00483744230165825 890 2473.18181818182 3011 0.000120076412535499 62 0.805834982097859 0.744303181914132 1 2.79959090632841 887 2990 3039 4621 3011 387 62 3153 4233 3850 972 3378 M6319 KIM_MYC_AMPLIFICATION_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYC_AMPLIFICATION_TARGETS_DN.html Genes negatively correlated with amplifications of MYC [GeneID=4609] in SCLC (small cell lung cancer) cell lines. 16116477 152/196 Arthur Liberzon 0.0582394528044309 0.0916300724123046 1315 2780.27272727273 3011 0.00544007914794471 1185 1.08162856798177 1.14718074363667 1 1.68451202726037 1315 3643 3118 3782 4578 3359 2198 1185 1704 3011 2690 3379 M2360 TERAO_AOX4_TARGETS_HG_UP http://www.broadinstitute.org/gsea/msigdb/cards/TERAO_AOX4_TARGETS_HG_UP.html Genes up-regulated in Harderian gland tissue upon knockout of AOX4 [GeneID=71872]. 18981221 39/44 Arthur Liberzon 0.000236342307826329 0.00134078809247629 4445 2916.27272727273 3011 2.14879728639179e-05 193 0.784704386647119 -0.710137534710323 -1 3.38232614151284 4444 2940 3834 1621 193 2941 4632 4099 328 4036 3011 3380 M7062 ELVIDGE_HIF1A_AND_HIF2A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_AND_HIF2A_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) after knockdown of both HIF1A and HIF2A [GeneID=3091;2034] by RNAi. 16565084 50/59 Arthur Liberzon 0.271615711334792 0.33490624385138 3015 2794.54545454545 3012 0.0284004063599889 1400 1.05847930112339 -1.12096948928791 -1 0.754444061897784 3012 3339 3102 2614 3570 2436 3083 2008 1400 3423 2753 3381 M13167 FREDERICK_PRKCI_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/FREDERICK_PRKCI_TARGETS.html Genes down-regulated in H1703 cells (non-small cell lung cancer, NSCLC) after knockdown of PRKCI [GeneID=5584] by RNAi. 18427549 13/23 Jessica Robertson 0.0226523496598786 0.0418743240630278 3015 2888.45454545455 3013 0.00208081897006082 811 1.62725348284304 -1.8808319091191 -1 3.36472073492124 3013 3921 1809 3834 3637 4293 2187 811 4331 1964 1973 3382 M5863 BOYLAN_MULTIPLE_MYELOMA_D_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_UP.html Genes up-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 103/121 Jessica Robertson 0.00245131862499789 0.00779139657238386 4320 2251.90909090909 3013 0.00022309584001246 15 1.06786155992533 -1.03533534966261 -1 3.37825953410916 4319 15 1625 235 3306 3832 3907 3013 324 467 3728 3383 M6376 MCCABE_BOUND_BY_HOXC6 http://www.broadinstitute.org/gsea/msigdb/cards/MCCABE_BOUND_BY_HOXC6.html Genes whose promoters where bound by HOXC6 [GeneID=3223] in LNCaP cells (prostate cancer), according to a ChIP-chip analysis. 18339881 503/926 Jessica Robertson 0.110047020115662 0.156170154824391 4255 3279.63636363636 3014 0.0115909660385992 1928 1.15084755745556 -1.08594825152638 -1 1.39244540749863 4251 3603 4541 3014 1928 2845 4412 4416 2772 1934 2360 3384 M1132 DARWICHE_SKIN_TUMOR_PROMOTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SKIN_TUMOR_PROMOTER_DN.html Genes down-regulated during skin tumor progression: epidermis treated with the carcinogen DMBA [PubChem=6001] followed by 20 weekly applications of the tumor promoter TPA [PubChem=4792], compared to the untreated skin. 17525749 236/344 Arthur Liberzon 0.173768064546037 0.229230090737087 4350 3268.18181818182 3015 0.0172030135873842 2155 1.15241379748339 -1.23005316809475 -1 1.10612529031945 4349 3623 2404 4613 2155 3015 4274 3761 2447 2369 2940 3385 M5354 FIRESTEIN_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/FIRESTEIN_PROLIFERATION.html Genes required for proliferation of DLD-1 cell (colon cancer with APC [GeneID=324] deletions), based on shRNA screen. 18794900 216/296 Jessica Robertson 0.68618940391 0.690284310838704 3070 2802.54545454545 3015 0.1 615 1.01900994233738 0.990867477268132 1 0.246027578924043 3066 1211 2277 615 4215 3711 3015 4433 1348 2287 4650 3386 M2378 IKEDA_MIR133_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IKEDA_MIR133_TARGETS_DN.html Genes down-regulated in hypertrophic hearts (due to expression of constitutively active form of PPP3CA [GeneID=5530]) and predicted to be targets of miR-133 microRNA. 19188439 9/11 Arthur Liberzon 0.164920771561709 0.21903063784491 2045 3025.90909090909 3015 0.0178614268811343 1268 0.710387082252591 0.890256279062796 1 0.702883056901501 2043 2657 4694 2374 3491 2234 1268 3392 4549 3568 3015 3387 M18895 SA_TRKA_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/SA_TRKA_RECEPTOR.html The TrkA receptor binds nerve growth factor to activate MAP kinase pathways and promote cell growth. 25/28 SigmaAldrich 0.0966482755972553 0.140061363469157 3580 2978.81818181818 3016 0.00919773915665874 1411 0.760320816393416 -0.885245528282399 -1 0.973839628221817 3579 3016 3241 2792 2673 2476 4498 1411 3425 3577 2079 3388 M7399 KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM.html Porphyrin and chlorophyll metabolism 25/48 KEGG 0.0306032962259617 0.0534990956246442 4580 3076.81818181818 3017 0.00282158961686721 1325 0.913663978836105 -0.720607206887696 -1 1.74329449784374 4580 3017 2971 2057 1325 2433 3375 3525 2495 3576 4491 3389 M18954 MANN_RESPONSE_TO_AMIFOSTINE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MANN_RESPONSE_TO_AMIFOSTINE_UP.html Genes up-regulated in HCT116 cells (colon cancer) after treatment with amifostine [PubChem=2141] depending on the presence of TP53 [GeneID=7157]: TP53-positive vs TP53-null cells. 15750621 26/28 Leona Saunders 0.0318720498231233 0.0553093343038356 3665 2503.18181818182 3018 0.00294030703296108 372 0.901772506715404 0.913784814435758 1 1.70104849442378 3662 1482 3018 1543 1341 3034 2325 3239 372 3196 4323 3390 M13115 REACTOME_G_PROTEIN_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G_PROTEIN_ACTIVATION.html Genes involved in G-protein activation 18/30 Reactome 0.527214168714883 0.595608156135531 4675 3245.54545454545 3020 0.0658340332164373 2072 0.970525245938862 -0.886892188268697 -1 0.327617334415607 4674 2097 2369 2072 2866 4164 3465 4477 3967 2530 3020 3391 M8455 HOOI_ST7_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOOI_ST7_TARGETS_UP.html Genes up-regulated in PC-3 cells (prostate cancer) stably expressing ST7 [GeneID=7982] off a plasmid vector. 16474848 125/167 Leona Saunders 0.452072197427365 0.520479965623611 4270 2958.45454545455 3021 0.0532232680194123 1612 1.09545084997378 1.04553184429089 1 0.466053930251458 2582 2330 1612 2605 4270 4270 3021 3022 3694 1692 3445 3392 M13015 REACTOME_NOREPINEPHRINE_NEUROTRANSMITTER_RELEASE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOREPINEPHRINE_NEUROTRANSMITTER_RELEASE_CYCLE.html Genes involved in Norepinephrine Neurotransmitter Release Cycle 14/21 Reactome 0.304593861204568 0.368825814490909 3485 2756.54545454545 3022 0.0324842416598884 704 0.945366759146183 -1.11729964545891 -1 0.614376248343016 3485 1037 2605 2006 4040 3022 1616 3826 704 3312 4669 3393 M17333 FARMER_BREAST_CANCER_CLUSTER_2 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_2.html Cluster 2: selected proliferation and 8q amplicon genes clustered together across breast cancer samples. 15897907 45/72 Leona Saunders 0.0343043858502799 0.0586017738738043 1905 2710.72727272727 3022 0.00316829701576699 1160 0.828819258921072 -0.883103106314407 -1 1.53219418921894 1902 3356 3785 3426 1372 1845 1714 4091 1160 4145 3022 3394 M1829 MATZUK_SPERMATOGONIA http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATOGONIA.html Genes important for spermatogonia, based on mouse models with male reproductive defects. 18989307 18/32 Jessica Robertson 0.175132037091738 0.230707009509629 3770 3175.27272727273 3024 0.0173506185260015 1878 1.04531448776729 -0.973602997020797 -1 0.998943111482941 3769 2604 1878 3024 2160 2590 4639 2385 4283 3075 4521 3395 M2890 KEGG_CALCIUM_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CALCIUM_SIGNALING_PATHWAY.html Calcium signaling pathway 114/193 KEGG 3.14338612686723e-06 3.72783480372194e-05 3575 2354.90909090909 3025 2.8576278347124e-07 22 1.22250182140415 -1.265582480268 -1 8.12356322569661 3574 22 322 1421 2364 3394 3155 3057 3025 872 4698 3396 M2238 JOHNSTONE_PARVB_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_2_UP.html Genes up-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D collagen I and 3D Matrigel only. 17998334 206/250 Arthur Liberzon 0.137480905801078 0.188147036196309 4510 3279.45454545455 3025 0.0133552880787874 2019 1.00251857389882 -0.944171901478311 -1 1.09126720967092 4508 3997 2624 4428 2019 2509 4702 3025 3369 2153 2740 3397 M16867 MULLIGHAN_MLL_SIGNATURE_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_2_DN.html The 'MLL signature 2': genes down-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to the AML cases with intact MLL and NPM1 [GeneID=4869]. 17597811 404/552 Arthur Liberzon 0.00647354774597022 0.0155259884964326 3030 2905.27272727273 3026 0.000590243194830066 759 1.20443590224149 -1.11414338248191 -1 3.26915703230471 3026 2718 797 3517 3605 3416 2695 4269 2488 759 4668 3398 M2895 MARKEY_RB1_CHRONIC_LOF_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_CHRONIC_LOF_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) isolated from RB1 [GeneID=5925] knockout mice: chronic loss of function (LOF) of RB1. 17452985 148/168 Arthur Liberzon 0.227127534670178 0.287719260237048 3880 3049.36363636364 3026 0.0231497656673151 1401 1.13011862745673 1.18196184911984 1 0.917356084504317 3878 1778 1401 2332 2442 4183 3901 3766 3026 2292 4544 3399 M17256 HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_HEREDITARY_VS_SPORADIC.html Genes distinguishing between sporadic breast cancer tumors and hereditary breast cancer tumors that have mutated BRCA1 and BRCA2 [GeneID=672;675]. 11207349 76/83 John Newman 0.00577426225782821 0.0142024584976285 3565 2737.36363636364 3026 0.000526315789473684 182 1.0586640540339 1.10686342114933 1 2.93495091604779 3565 1334 3026 182 2890 4671 3715 4209 311 2062 4146 3400 M15103 DOUGLAS_BMI1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DOUGLAS_BMI1_TARGETS_UP.html Genes up-regulated in A4573 cells (Ewing's sarcoma, ESFT) after knockdown of BMI1 [GeneID=648] by RNAi. 18701473 766/940 Jessica Robertson 0.282703950263847 0.34658770006373 2265 2894.09090909091 3026 0.0326807200735081 1315 1.12445203394061 1.13075344641703 1 0.77635035187122 2262 3151 4500 1889 3026 4036 3403 2086 2621 1315 3546 3401 M15687 LE_SKI_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LE_SKI_TARGETS_DN.html Selected genes implicated in metastasis and epithelial-to-mesenchymal transition (EMT) which were down-regulated in MDA-MB-231 cells (breast cancer) upon knockdown of SKI [GeneID=6497] by RNAi. 18451154 8/11 Jessica Robertson 0.0738725878729669 0.111791796973518 1270 3033.54545454545 3026 0.00764497336464974 1266 1.83655189237028 -1.35117403229976 -1 2.62226986372963 1266 3948 4555 4354 1729 3123 2218 2298 4222 2630 3026 3402 M5650 REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOCHROME_P450_ARRANGED_BY_SUBSTRATE_TYPE.html Genes involved in Cytochrome P450 - arranged by substrate type 21/99 Reactome 0.00643061807435148 0.0154780812396425 3745 2631.45454545455 3027 0.00058631746414987 795 1.64732266565093 -1.51800836535791 -1 4.4746251047749 3743 2585 795 3027 4008 2942 3067 1384 3189 1094 3112 3403 M606 REACTOME_AMINE_COMPOUND_SLC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AMINE_COMPOUND_SLC_TRANSPORTERS.html Genes involved in Amine compound SLC transporters 15/33 Reactome 0.0437005274029593 0.0718698569135776 4475 2723.81818181818 3027 0.00405395672593746 928 1.28540153566981 -1.0877246639311 -1 2.20535335470978 4473 1562 1052 928 4001 3939 4058 1673 3562 1687 3027 3404 M4217 REACTOME_MITOTIC_PROMETAPHASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_PROMETAPHASE.html Genes involved in Mitotic Prometaphase 102/108 Reactome 0.472877814040091 0.542797490824229 2025 3025.36363636364 3027 0.0565493051201198 1287 0.87240636677935 -0.997921685885266 -1 0.34727003822993 2024 3245 4079 3421 2765 3027 3663 2849 1287 4252 2667 3405 M262 AMUNDSON_RESPONSE_TO_ARSENITE http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_RESPONSE_TO_ARSENITE.html Genes discriminating responses to sodium arsenite [PubChem=26435] from other stresses. 15824734 313/376 Arthur Liberzon 0.210302377609967 0.270102645528992 1450 3075.18181818182 3027 0.0212353911406329 1448 0.997261067421787 0.939791908050491 1 0.850560243537982 1448 4686 3784 4506 3645 2276 1946 1838 3027 4087 2584 3406 M19097 SWEET_LUNG_CANCER_KRAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SWEET_LUNG_CANCER_KRAS_UP.html Genes up-regulated in the Kras2LA mouse lung cancer model with mutated KRAS [GeneID=3845]. 15608639 627/808 Arthur Liberzon 0.00525070999993344 0.0138068808911899 3030 2563.90909090909 3027 0.000526315789473684 130 1.08294783085274 1.14328217356167 1 3.02221087290271 3027 485 4601 130 2982 3601 3164 3457 1264 1117 4375 3407 M2015 CROONQUIST_STROMAL_STIMULATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_STROMAL_STIMULATION_DN.html Genes down-regulated in ANBL-6 cell line (multiple myeloma, MM) co-cultured with bone marrow stromal cells compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 14/20 Arthur Liberzon 0.232981496742131 0.293559173684692 2425 3302.72727272727 3027 0.0238247244270475 1477 0.577523279594724 -0.575888713712769 -1 0.461181276144142 2425 2123 3027 3775 4052 2811 2930 4359 4648 4703 1477 3408 M1416 HAHTOLA_CTCL_PATHOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_CTCL_PATHOGENESIS.html Differentially expressed genes relevant to pathogenesis of cutaneous T cell lymphoma (CTCL). 16914566 11/46 Arthur Liberzon 0.0796215650488786 0.119041427630886 4090 2956.18181818182 3027 0.00751438397723224 1321 1.34125542418148 -1.56470241194201 -1 1.86012626651424 4087 2640 1894 3734 2194 3293 4271 1321 3488 3027 2569 3409 M17814 REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS.html Genes involved in Activation of BH3-only proteins 24/26 Reactome 0.257206400601736 0.319814070295098 2390 3264.36363636364 3028 0.0266685841430431 1552 0.779239657820192 -0.691700830581291 -1 0.578799992701959 2390 4187 2786 4573 2390 1552 3028 4163 4173 4155 2511 3410 M1993 KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_AND_NORMAL_AGING_DN.html Genes down-regulated similarly in primary fibroblast cultures from Werner syndrom patients and normal old donors compared to those from normal young donors. 14527998 324/433 Arthur Liberzon 0.20042434705649 0.258824327799352 4385 2750.18181818182 3028 0.0201286695946142 416 1.0503840896223 -0.991198095005097 -1 0.925069994931538 3550 531 3028 416 2237 4383 4105 4474 1162 1982 4384 3411 M8397 ELVIDGE_HIF2A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF2A_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) after knockdown of HIF2A [GeneID=2034] by RNAi. 16565084 9/9 Arthur Liberzon 3.14073437209466e-05 0.000265259274643481 3030 2630.54545454545 3029 3.14077876193342e-06 73 0.935086312475617 -0.706222403355141 -1 5.01789841198227 3029 438 4314 1002 73 3767 3884 3233 3799 2752 2645 3412 M2569 KLEIN_TARGETS_OF_BCR_ABL1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/KLEIN_TARGETS_OF_BCR_ABL1_FUSION.html Genes changed in pre-B lymphoblastic leukemia cells with BCR-ABL1 fusion [GeneID=613, 25] vs normal pre-B lymphocytes. 16205638 40/75 Arthur Liberzon 0.00113073134040099 0.00437104989901119 2510 2609.18181818182 3029 0.000102846629049368 629 1.81860785296591 1.98145883138858 1 6.43839959543226 2509 2946 629 3029 846 4307 3653 3095 3385 997 3305 3413 M2189 WAGSCHAL_EHMT2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WAGSCHAL_EHMT2_TARGETS_UP.html Genes up-regulated in placenta of mice with EHMT2 [GeneID=10919] knocked out. 18039842 7/18 Arthur Liberzon 0.029218952582254 0.0515179141532458 2375 3111.81818181818 3029 0.00296104024354819 1343 0.545112773772093 0.587176811120405 1 1.0534513265808 2372 1635 4667 2631 1343 4180 3426 1705 4528 4714 3029 3414 M17294 BIOCARTA_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAS_PATHWAY.html Ras Signaling Pathway 42/44 BioCarta 0.00424786339353861 0.0116958488352629 2805 2856.27272727273 3032 0.000386917055272737 666 0.769318820607144 0.804373068506221 1 2.23011645769438 2802 1963 3776 2793 666 4455 3032 4120 930 3373 3509 3415 M11215 REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK.html Genes involved in NRAGE signals death through JNK 56/60 Reactome 0.448293696940057 0.516840803506856 4200 2761.09090909091 3032 0.0526315789473684 371 1.10775268276459 -1.00555413864497 -1 0.476353981995783 4200 782 1751 371 3687 4314 4307 4616 1457 1855 3032 3416 M910 REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GIP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GIP.html Genes involved in Synthesis, Secretion, and Inactivation of Glucose-dependent Insulinotropic Polypeptide (GIP) 9/17 Reactome 0.00399742143898505 0.0111842496692409 2895 2983.72727272727 3033 0.000400463041683024 676 1.05687827056492 -0.518468932428221 -1 3.09454427548292 2893 2660 4251 3033 676 2211 1906 4677 3387 3558 3569 3417 M9016 PROVENZANI_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PROVENZANI_METASTASIS_DN.html Genes down-regulated in polysomal and total RNA samples from SW480 cells (primary colorectal carcinoma, CRC) compared to the SW620 cells (lymph node metastasis from the same individual). 16531451 205/239 Arthur Liberzon 0.0435889437782461 0.0717269306412464 2405 2713.72727272727 3033 0.00404339276853392 1051 1.1479808498742 1.08956970028974 1 1.97105966357821 2401 1745 1051 1377 3448 3927 3249 4250 3033 1408 3962 3418 M5290 BIOCARTA_MEF2D_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MEF2D_PATHWAY.html Role of MEF2D in T-cell Apoptosis 20/26 BioCarta 0.12894956532731 0.178592120993223 4090 2781.90909090909 3036 0.0124720619010831 514 0.899367459396397 -1.1349893566306 -1 1.00952016144581 4088 1541 3178 1906 4077 2923 3036 1547 514 3744 4047 3419 M6195 HWANG_PROSTATE_CANCER_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/HWANG_PROSTATE_CANCER_MARKERS.html Proteins implicated in prostate carcinogenesis. 16799640 37/47 Arthur Liberzon 0.250822373313951 0.312947819730862 970 2962.27272727273 3036 0.0259110469875868 969 0.95171037219583 0.991498216764557 1 0.720390786556253 969 4494 3036 4276 3947 2189 1457 2536 4571 3445 1665 3420 M19287 MORI_LARGE_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_LARGE_PRE_BII_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Large Pre-BII stage. 18922927 126/203 Jessica Robertson 0.47444770997933 0.544334757195536 1125 2841.36363636364 3037 0.0568050899217023 1122 0.960671775752002 -0.954406316558333 -1 0.380645160759881 1122 2799 3732 3254 3956 2065 1967 3305 1826 4192 3037 3421 M14933 KEGG_STEROID_HORMONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_STEROID_HORMONE_BIOSYNTHESIS.html Steroid hormone biosynthesis 21/88 KEGG 0.00303113197660271 0.00912795565581309 3425 2588.54545454545 3038 0.000275937845910688 560 1.74773621351607 -2.07005473493474 -1 5.34884166441869 3425 3038 843 3498 590 4629 4083 560 4208 1437 2163 3422 M1102 GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN.html Genes down-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) upon serum deprivation for 22 hr in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 110/129 Arthur Liberzon 0.0170473925251862 0.0333735764076643 3710 2700.09090909091 3038 0.00156190369578898 1050 0.997773338817731 1.07808171461909 1 2.21062444786958 3706 1815 3062 1050 1092 3019 3373 4308 1638 3038 3600 3423 M957 REACTOME_NFKB_ACTIVATION_THROUGH_FADD_RIP1_PATHWAY_MEDIATED_BY_CASPASE_8_AND10 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NFKB_ACTIVATION_THROUGH_FADD_RIP1_PATHWAY_MEDIATED_BY_CASPASE_8_AND10.html Genes involved in NF-kB activation through FADD/RIP-1 pathway mediated by caspase-8 and -10 12/15 Reactome 0.217935777022627 0.277865172216855 3040 3294.09090909091 3039 0.0220992812375919 1424 0.676944301596582 -0.64328533592134 -1 0.564829964169893 3971 2134 2834 3036 4187 3039 4050 2391 4580 4589 1424 3424 M9052 KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM.html Phosphatidylinositol signaling system 67/77 KEGG 0.30043210214701 0.364603363889993 4150 2476.09090909091 3040 0.0319592828249722 111 0.876162466308345 0.782819073468655 1 0.575968257297558 4150 111 3090 810 3433 2958 3782 3040 905 3301 1657 3425 M16409 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_OLD.html Human environmental stress response genes not changed in primary fibroblasts from old donors in response to UV radiation. 15897889 31/34 Jessica Robertson 0.0061106282161901 0.0148594359507559 3040 2907.36363636364 3040 0.000557060648758681 764 0.922127466854629 -0.752971830009974 -1 2.52924112382218 3040 2009 2796 3973 764 2414 3301 3296 4466 3491 2431 3426 M5589 HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_PRE_BI_TO_LARGE_PRE_BII_LYMPHOCYTE_UP.html Genes up-regulated during differentiation from pre-BI to large pre-BII lymphocyte. 11779835 46/61 Arthur Liberzon 0.0383271488443959 0.0643329098668381 1860 2953.81818181818 3040 0.00354651056070573 1004 1.10779382577659 1.26228504781177 1 1.98059619196349 1858 4117 3284 4419 4581 1994 2225 1004 3040 3831 2139 3427 M13494 BIOCARTA_BIOPEPTIDES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BIOPEPTIDES_PATHWAY.html Bioactive Peptide Induced Signaling Pathway 59/67 BioCarta 0.292947132811488 0.357012772236051 3895 2963.18181818182 3041 0.0310222427951864 911 0.852801639118768 -0.848506296889883 -1 0.572300606474412 3892 1378 3041 1140 2458 4714 2719 4122 911 3773 4447 3428 M19193 REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOGEN_BREAKDOWN_GLYCOGENOLYSIS.html Genes involved in Glycogen breakdown (glycogenolysis) 16/17 Reactome 0.00523679953941343 0.0138068808911899 3870 2626.81818181818 3042 0.000477209702337985 278 0.909448941080359 -0.850143925766642 -1 2.53800602281078 3869 1020 3042 570 720 4009 3982 3995 278 2888 4522 3429 M9112 LU_AGING_BRAIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_AGING_BRAIN_DN.html Age down-regulated genes in the human frontal cortex. 15190254 222/295 John Newman 0.673945022458768 0.690284310838704 2765 3153.09090909091 3042 0.0968628393050904 2066 0.976359526594197 0.964476346931134 1 0.235725724462443 2765 2271 2066 3403 3514 4190 3042 2728 3688 2931 4086 3430 M1664 CHEN_ETV5_TARGETS_TESTIS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_ETV5_TARGETS_TESTIS.html Genes down-regulated in testis from 4 week old ETV5 [GeneID=2119] knockout mice. 16107850 24/41 John Newman 0.374216476852247 0.442682148055791 3045 2650.54545454545 3042 0.0417185040193242 522 0.911019399070042 1.02339621669502 1 0.483687419790854 3042 2051 3089 1831 3634 2004 1754 4082 522 3505 3642 3431 M18970 CHANDRAN_METASTASIS_TOP50_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_TOP50_UP.html Top 50 genes up-regulated in metastatic vs primary prostate cancer tumors. 17430594 56/90 Arthur Liberzon 0.490207824342184 0.559695435630167 2125 2858.54545454545 3044 0.0594121191972927 1003 0.871733918059679 -1.04014914079256 -1 0.329586934187312 2122 3320 3769 2203 3044 2607 2001 4017 1003 4028 3330 3432 M19202 CHENG_IMPRINTED_BY_ESTRADIOL http://www.broadinstitute.org/gsea/msigdb/cards/CHENG_IMPRINTED_BY_ESTRADIOL.html Genes whose CpG islands became hypermethylated in breast progenitor cells pre-exposed to estradiol [PubChem=5757]. 18339859 159/198 Jessica Robertson 0.0184272151221415 0.0355127169775222 1745 2445.63636363636 3044 0.00168939964940927 505 1.15843917630207 1.27331578348807 1 2.51970564069274 1743 4009 3130 3162 3198 3625 2518 720 1248 3044 505 3433 M579 REACTOME_PPARA_ACTIVATES_GENE_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PPARA_ACTIVATES_GENE_EXPRESSION.html Genes involved in PPARA Activates Gene Expression 115/156 Reactome 0.167818163016504 0.222375555709686 3115 3086.36363636364 3045 0.0165617131617271 1893 1.00285705105646 1.04490582741404 1 0.982402241023245 3113 3656 3045 2902 2140 3696 3031 1893 3296 3001 4177 3434 M12008 GHO_ATF5_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GHO_ATF5_TARGETS_UP.html Genes up-regulated in HEP3B cells (liver cancer) overexpressing ATF5 [GeneID=22809] off a plasmid vector. 18701499 20/29 Jessica Robertson 0.398795188233573 0.468005042573937 2515 2959.36363636364 3045 0.0452028112603524 1602 1.0128903742952 -1.08911403508654 -1 0.501067967735991 2514 3045 3364 3164 2670 2744 3085 4079 1602 3255 3031 3435 M7189 CHESLER_BRAIN_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_QTL_TRANS.html Best trans-regulated quantitative trait loci (QTLs) in the mouse genome which modulate transcription in brain tissue. 15711545 10/19 Jean Junior 0.0415279280961363 0.0688002178356488 3120 2872.63636363636 3046 0.0038484714170136 1342 0.631330635100937 -0.717341779553844 -1 1.1010735748354 3116 1617 2334 3046 1447 2421 1342 4141 4385 4674 3076 3436 M9752 RICKMAN_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_METASTASIS_UP.html Genes up-regulated in metastatic vs non-metastatic HNSCC (head and neck squamous cell carcinoma) samples. 18679425 433/504 Jessica Robertson 0.086628768620655 0.128017466465088 2000 3250.81818181818 3047 0.00820369857037535 1359 0.962535033266866 1.00510715528457 1 1.28926802443557 1996 4679 4035 4642 3567 3047 2839 1359 2748 4258 2589 3437 M670 REACTOME_KERATAN_SULFATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_KERATAN_SULFATE_BIOSYNTHESIS.html Genes involved in Keratan sulfate biosynthesis 20/27 Reactome 0.00795149823542425 0.0181626542487324 3750 2669.18181818182 3048 0.000725489431066759 822 1.60641572570597 -1.6037159491337 -1 4.19607111987002 3749 2092 822 1419 1413 4296 3048 4373 3088 1348 3713 3438 M1743 MARSON_BOUND_BY_FOXP3_UNSTIMULATED http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_BOUND_BY_FOXP3_UNSTIMULATED.html Genes with promoters bound by FOXP3 [GeneID=50943] in unstimulated hybridoma cells. 17237765 1434/1812 Jessica Robertson 0.102315054532825 0.146830969107611 3050 3077.45454545455 3049 0.0107355692410119 999 0.926551389460934 -0.954530955333718 -1 1.1582750332612 3049 3593 4519 4143 2826 1299 3584 2629 2787 4424 999 3439 M722 REACTOME_TRANSLOCATION_OF_ZAP_70_TO_IMMUNOLOGICAL_SYNAPSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSLOCATION_OF_ZAP_70_TO_IMMUNOLOGICAL_SYNAPSE.html Genes involved in Translocation of ZAP-70 to Immunological synapse 7/16 Reactome 0.0223895959586776 0.0415201993617369 2300 2900 3051 0.00226184298841076 1222 1.70195855194524 1.70195855194524 1 3.52861496929062 2299 3952 4223 4003 1222 2827 1540 1240 4185 3358 3051 3440 M12026 LUND_SILENCED_BY_METHYLATION http://www.broadinstitute.org/gsea/msigdb/cards/LUND_SILENCED_BY_METHYLATION.html Genes up-regulated in FE-8 cells (fibroblasts) upon treatment with azacitidine [PubChem=9444]. 16568090 24/29 Arthur Liberzon 0.599545138071076 0.665691143659252 4440 3189.63636363636 3051 0.079829075288622 165 1.12913932823388 -1.40168211883395 -1 0.299322435013364 4437 2564 2476 2613 2984 3504 4507 4698 165 3051 4087 3441 M17330 MARCHINI_TRABECTEDIN_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARCHINI_TRABECTEDIN_RESISTANCE_UP.html Genes up-regulated in chondrosarcoma and ovarian carcinoma cell lines which developed resistance to trabectedin [PubChem=3199]. 15661559 28/37 John Newman 0.015390652154912 0.0308466573975306 3190 2862.54545454545 3052 0.00140903525358595 273 1.27377857085361 -1.28904367907221 -1 2.88751650212082 3190 4166 1649 3052 2781 3576 3959 2901 3500 2441 273 3442 M1389 BIOCARTA_SPRY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SPRY_PATHWAY.html Sprouty regulation of tyrosine kinase signals 28/30 BioCarta 0.226947269654684 0.28756808396513 3700 3118.90909090909 3053 0.023129055058006 1600 0.949440688596319 -0.771653306531349 -1 0.771001859225913 3696 3446 3035 2788 3830 3053 1600 1889 3566 2870 4535 3443 M1028 REACTOME_RAF_MAP_KINASE_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAF_MAP_KINASE_CASCADE.html Genes involved in RAF/MAP kinase cascade 14/14 Reactome 0.101929301542393 0.146410926135147 4605 2824.81818181818 3053 0.00972571316403021 970 0.43735358107194 -0.43735358107194 -1 0.547493100798301 1979 4605 3928 3695 3053 1161 970 1444 4102 4602 1534 3444 M1319 HESS_TARGETS_OF_HOXA9_AND_MEIS1_UP http://www.broadinstitute.org/gsea/msigdb/cards/HESS_TARGETS_OF_HOXA9_AND_MEIS1_UP.html Genes up-regulated in hematopoietic precursor cells conditionally expressing HOXA9 and MEIS1 [GeneID=3205;4211]. 16507773 72/85 Kevin Vogelsang 0.617188265914734 0.682798227274347 3965 3297.72727272727 3053 0.0835905322175673 1980 1.06779044558475 -1.12177335901795 -1 0.265397706051965 3965 2857 3053 3766 4477 3400 4145 2646 1980 2980 3006 3445 M846 REACTOME_FRS2_MEDIATED_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FRS2_MEDIATED_CASCADE.html Genes involved in FRS2-mediated cascade 26/43 Reactome 0.019206392585416 0.036613155494008 4120 2901.72727272727 3054 0.00176146784104677 740 0.9825657782772 -0.987467790348278 -1 2.11760961398707 4117 4180 3054 2789 1473 3577 4421 740 1062 3622 2884 3446 M3898 ENK_UV_RESPONSE_KERATINOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_KERATINOCYTE_DN.html Genes down-regulated in NHEK cells (normal epidermal keratinocytes) after UVB irradiation. 16434974 649/741 Lauren Kazmierski 0.6513215599 0.690284310838704 2095 3278.90909090909 3055 0.1 2095 0.947581539450048 0.972226449775019 1 0.22877464016254 2095 2207 4328 3010 4579 3120 2607 3055 2878 4365 3824 3447 M2316 WIEDERSCHAIN_TARGETS_OF_BMI1_AND_PCGF2 http://www.broadinstitute.org/gsea/msigdb/cards/WIEDERSCHAIN_TARGETS_OF_BMI1_AND_PCGF2.html Genes up-regulated in DAOY cells (medulloblastoma) upon knockdown of both BMI1 and PCGF2 [GeneID=648, 7703] by RNAi. 17452456 95/110 Arthur Liberzon 2.75849695633735e-07 4.55355684590915e-06 2765 2790.36363636364 3055 2.50772482019539e-08 234 1.29188092510172 1.16780633612764 1 10.3546451878802 2761 2364 234 3055 2077 4175 3250 3372 4001 1027 4378 3448 M2615 ZWANG_DOWN_BY_2ND_EGF_PULSE http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_DOWN_BY_2ND_EGF_PULSE.html Genes down-regulated by second pulse of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 284/454 Yaara Zwang 0.265754604986427 0.328366946475376 3430 3353.45454545455 3055 0.0276922479784119 1650 1.14855315148315 1.1046908186686 1 0.833413407401329 3430 4329 3010 4371 2406 4596 3055 2936 1650 2833 4272 3449 M1122 HUMMERICH_BENIGN_SKIN_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_BENIGN_SKIN_TUMOR_UP.html Genes up-regulated in benign skin tumors (papilloma) induced by treatment with DMBA and TPA [PubChem=6001;4792] chemicals in the two stage skin carcinogenesis model. 16247483 18/33 Leona Saunders 0.186706004857137 0.243776581722182 4040 3106.63636363636 3056 0.0186121254406604 1334 1.47568819832293 -1.98255827538718 -1 1.35727767535485 4037 3056 1334 2309 2980 4680 4519 4281 2082 3072 1823 3450 M1349 SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_12HR_DN.html Genes down-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 12 h. 18794802 67/94 Jessica Robertson 0.0281310425772423 0.0501998188902017 1960 2617.81818181818 3056 0.00259066578891481 981 1.12078143118135 1.02413339574126 1 2.18499486685777 1957 3289 981 3112 2239 2142 3056 3691 3793 1226 3310 3451 M18937 KEGG_NUCLEOTIDE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NUCLEOTIDE_EXCISION_REPAIR.html Nucleotide excision repair 45/47 KEGG 0.22074813357945 0.280843986656336 1750 2989.36363636364 3058 0.0224194957246711 1169 0.571126422597804 -0.592951555147965 -1 0.472552198411116 1747 3762 4066 4054 3195 1169 1707 2998 3058 4486 2641 3452 M18201 GOTTWEIN_TARGETS_OF_KSHV_MIR_K12_11 http://www.broadinstitute.org/gsea/msigdb/cards/GOTTWEIN_TARGETS_OF_KSHV_MIR_K12_11.html Genes down-regulated in BJAB cell line (B lymphocyte) after expression of the viral microRNA miR-K12-11 which functions as an ortholog of cellular MIR155 [GeneID=406947]. 18075594 80/94 Jessica Robertson 0.12553920029154 0.174815612135404 4700 2908.63636363636 3058 0.0121211948283226 1797 0.999155457022012 0.880304455319727 1 1.13545791682866 4696 3266 3276 2153 1953 3098 4618 2156 1924 3058 1797 3453 M6669 HEDENFALK_BREAST_CANCER_BRACX_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEDENFALK_BREAST_CANCER_BRACX_UP.html Up-regulated genes distinguishing between two groups of non-BRCA1/BRCA2 [GeneID=672;675] breast tumors (BRACx): group A vs group B. 12610208 22/33 John Newman 0.00416147134717621 0.0115270802574365 2425 2907.81818181818 3058 0.000379033091243175 660 0.703581134203794 -0.709058374695678 -1 2.0462099918919 2423 4231 3543 4624 660 1841 2207 772 4510 4117 3058 3454 M1596 HAN_JNK_SINGALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAN_JNK_SINGALING_UP.html Genes up-regulated in 3T3 cells (fibroblast) upon activation of JNK pathway. 12354774 46/58 John Newman 0.127003883659148 0.176363145298963 2670 2941.45454545455 3058 0.0122717325229836 1240 1.20630379363469 1.27069767270639 1 1.36395857694451 2667 3761 1240 4191 3499 2345 2280 3058 3752 1322 4241 3455 M11280 PENG_LEUCINE_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_LEUCINE_DEPRIVATION_UP.html Genes up-regulated in BJAB cells (B-lymphoma) after leucine [PubChem=857] deprivation. 12101249 172/216 Broad Institute 0.0685590826373228 0.105132836272958 3290 3027.36363636364 3059 0.00643579357263121 794 1.02989325383467 1.05151977007637 1 1.51167570718611 3287 1761 2956 1839 1648 4717 4406 4626 794 3059 4208 3456 M2778 TAVAZOIE_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/TAVAZOIE_METASTASIS.html Putative metastasis genes: up-regulated in metastatic cell lines LM2 (lung) and BoM2 (bone) relative to the parental MDA-MB-231 line (breast adenocarcinoma). 18185580 140/262 Jessica Robertson 3.25856119983354e-06 3.7976775600828e-05 4245 2840.54545454545 3059 2.9623327511888e-07 327 1.43962812926495 -1.51221520439669 -1 9.54897896978854 4242 2787 327 3059 1352 4713 3647 3803 2829 552 3935 3457 M1980 SEKI_INFLAMMATORY_RESPONSE_LPS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SEKI_INFLAMMATORY_RESPONSE_LPS_DN.html Genes down-regulated in hepatic stellar cells after stimulation with bacterial lipopolysacharide (LPS). 17952090 23/30 Jessica Robertson 0.00217235437855094 0.007112908061018 3285 2372.90909090909 3062 0.00019768203679477 303 1.32682864806206 -1.30233524269156 -1 4.27632432465144 3283 961 1029 303 528 3886 3084 3062 3624 1624 4718 3458 M10172 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_YELLOW_DN.html Genes from the yellow module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 31/32 Arthur Liberzon 0.0715704109578391 0.108754597149833 3230 2921.81818181818 3063 0.0067282391820898 1267 0.906236115659809 1.04152930057049 1 1.3101572431966 3228 2982 3063 2114 2030 4262 4202 1267 2012 3489 3491 3459 M19582 REACTOME_MRNA_DECAY_BY_3_TO_5_EXORIBONUCLEASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_DECAY_BY_3_TO_5_EXORIBONUCLEASE.html Genes involved in mRNA Decay by 3' to 5' Exoribonuclease 11/11 Reactome 0.16965923137053 0.224311364725182 3065 2842.54545454545 3064 0.0167597031515171 1058 0.549709164785617 -0.549709164785617 -1 0.535344258206263 3064 1058 3544 2075 2443 2239 1230 4235 3346 4572 3462 3460 M1080 REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G2_M_DNA_DAMAGE_CHECKPOINT.html Genes involved in G2/M DNA damage checkpoint 16/16 Reactome 0.0706358925234662 0.107583547179981 2095 2853.36363636364 3066 0.00663739111666585 830 0.765632184590292 0.765632184590292 1 1.11226951240929 2091 3066 3191 3849 4202 1193 830 1996 3565 4621 2783 3461 M14666 TIAN_TNF_SIGNALING_NOT_VIA_NFKB http://www.broadinstitute.org/gsea/msigdb/cards/TIAN_TNF_SIGNALING_NOT_VIA_NFKB.html Genes modulated in HeLa cells (cervical carcinoma) by TNF [GeneID=7124] not via NFKB pathway. 15722553 30/31 Arthur Liberzon 0.426051362900793 0.497141513925751 855 3059.27272727273 3066 0.0492214697391038 854 0.937586162352884 0.906127527715214 1 0.426906356547522 854 4174 2264 4105 3789 2225 1898 3599 4636 3042 3066 3462 M1084 REACTOME_TRYPTOPHAN_CATABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRYPTOPHAN_CATABOLISM.html Genes involved in Tryptophan catabolism 5/11 Reactome 0.000713576065919509 0.00306189002830917 1530 2421.63636363636 3067 7.13805305387661e-05 115 2.89990617497491 -2.89990617497491 -1 10.9392771541481 1526 4290 4264 3067 4587 1666 255 115 3176 3081 611 3463 M18181 HUMMEL_BURKITTS_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMEL_BURKITTS_LYMPHOMA_DN.html Down-regulated genes constituting the molecular signature of Burkitt 's lymphoma. 16760442 18/23 Arthur Liberzon 0.000395919516004974 0.00194592308160632 4505 2713 3067 3.59991622718601e-05 269 1.04100439323435 -0.950260130090365 -1 4.23440995464565 4503 1003 1580 1252 269 3205 4550 3359 3067 2532 4523 3464 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 0.29433596864655 0.358427701757408 3340 3124 3067 0.034260937700617 2047 1.17257489827597 -1.17257489827597 -1 0.78391221189523 3336 3584 4682 3091 2521 2247 2182 4689 2047 2918 3067 3465 M11896 LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_2A_DN.html Genes whose expression profile is specific to Cluster IIa of urothelial cell carcinoma (UCC) tumors. 16532037 193/246 Leona Saunders 0.069701307014165 0.106607313385243 3070 2848.72727272727 3068 0.0065466195488384 890 1.14193168460158 1.11393786821657 1 1.66577279852188 3068 3193 2172 2379 3045 4124 3122 3628 1470 890 4245 3466 M235 PID_TCR_CALCIUM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_CALCIUM_PATHWAY.html Calcium signaling in the CD4+ TCR pathway 18832364 24/34 Pathway Interaction Database 0.578733638340088 0.64623202577838 2850 3303.36363636364 3069 0.0755811379241637 2437 0.775771266010917 0.843738461518085 1 0.220613428957072 2846 3478 3069 4245 3607 2437 2963 2581 4328 3894 2889 3467 M18988 LIU_NASOPHARYNGEAL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/LIU_NASOPHARYNGEAL_CARCINOMA.html Low abundance transcripts specific to nasopharyngeal carcinoma (NPC). 18332864 100/167 Jessica Robertson 0.010731062846536 0.0230649438231558 3845 2927.36363636364 3069 0.000980342419148727 934 0.946120997224651 -0.916500716895192 -1 2.32396733844972 3844 2819 3214 2185 934 3069 4043 3318 2923 3343 2509 3468 M1815 MATZUK_POST-IMPLANTATION_AND_POST-PARTUM http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_POST-IMPLANTATION_AND_POST-PARTUM.html Genes important for post-implantation and post-partum, based on mouse models with female fertility defects. 18989307 19/25 Jessica Robertson 0.120513479176913 0.168795204347756 3610 3023.72727272727 3069 0.0116063964846511 1043 0.728538855920951 -0.728538855920951 -1 0.844534197253867 3609 2594 3127 2647 2301 2117 3069 4101 4618 4035 1043 3469 M3042 KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_KERATAN_SULFATE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_KERATAN_SULFATE.html Glycosaminoglycan biosynthesis - keratan sulfate 13/15 KEGG 0.145488877078917 0.197689403849974 4555 2644 3070 0.0141915873095717 211 1.5089222091155 -1.583917845609 -1 1.59390608836234 4553 1574 1265 927 3898 3857 4585 3070 211 1472 3672 3470 M11166 IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_LATE_PROGENITOR.html Genes in the expression cluster 'Late Progenitors Shared': up-regulated in hematopoietic late progenitor cells from adult bone marrow and fetal liver. 12228721 660/849 John Newman 0.620090642835043 0.685600335952543 4255 3148.45454545455 3070 0.0922463600617969 1084 1.01042309591375 -0.973316815999234 -1 0.248436753876824 4255 1130 4489 1084 3070 2728 4268 4549 2651 3433 2976 3471 M18308 REACTOME_THROMBOXANE_SIGNALLING_THROUGH_TP_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THROMBOXANE_SIGNALLING_THROUGH_TP_RECEPTOR.html Genes involved in Thromboxane signalling through TP receptor 19/26 Reactome 0.0741208728276722 0.112059743672842 4045 3198.09090909091 3071 0.00697660290758133 1687 0.906193960047153 -0.93519972363973 -1 1.29241666397166 4041 2593 2833 3071 1687 3851 4640 2747 3938 3167 2611 3472 M2388 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_QTL_TRANS.html Transcripts in hematopoietic stem cells (HSC) which are trans-regulated (i.e., modulated by a QTL (quantitative trait locus) not in a close proximity to the gene). 15711547 1053/1453 Jean Junior 0.10355265264019 0.148381457335063 4145 2857.45454545455 3072 0.0108720393928192 466 1.10656325859231 -1.13373213667967 -1 1.37575231575687 4144 466 4478 1355 1896 3571 4193 3550 2511 2196 3072 3473 M1735 GAVIN_FOXP3_TARGETS_CLUSTER_P6 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_P6.html Cluster P6 of genes with similar expression profiles in peripheral T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 94/126 Jessica Robertson 0.281932513758046 0.345821586522344 4050 3001.18181818182 3073 0.0296595972703212 1417 1.08434391090603 -1.0288964485046 -1 0.750218606970828 1516 4049 3288 4049 4427 1417 1572 3073 2756 4010 2856 3474 M14524 GRADE_COLON_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_CANCER_UP.html Up-regulated genes in colon carcinoma tumors compared to the matched normal mucosa samples. 17210682 1119/1490 Jessica Robertson 0.304785375796616 0.368963060723269 2645 3273.09090909091 3074 0.0357006147052286 1416 0.865097705174912 -0.855817411636901 -1 0.561992155628135 2642 3595 4570 4339 4342 1416 3074 2752 2988 4450 1836 3475 M9172 MURAKAMI_UV_RESPONSE_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/MURAKAMI_UV_RESPONSE_1HR_DN.html Genes down-regulated in primary keratinocytes at 1 h after UVB irradiation. 11532376 16/18 Arthur Liberzon 0.0102747193034287 0.0223075782484744 3165 2961 3074 0.000938456520171643 918 1.20742727273262 -1.11531804183853 -1 2.99211663020397 3164 3074 2148 3574 918 2911 4200 1369 4685 2896 3632 3476 M15132 BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_MGMT_24HR_UP.html Genes up-regulated in T98G cells (glioma, express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 24 h. 15980968 13/14 Arthur Liberzon 0.0459485964761457 0.0749456169223308 3075 2824.54545454545 3074 0.0042670272482807 981 0.541302462582252 -0.541302462582252 -1 0.913864895484618 3074 3544 3693 3155 2138 2656 1763 1079 4275 4712 981 3477 M15193 GRUETZMANN_PANCREATIC_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRUETZMANN_PANCREATIC_CANCER_UP.html Genes up-regulated in pancreatic ductal adenocarcinoma (PDAC) identified in a meta analysis across four independent studies. 15897887 515/686 Leona Saunders 7.96728103500331e-05 0.000552210961603754 4190 2571.81818181818 3077 7.96756669846974e-06 275 1.18127623887731 -1.15698185983335 -1 5.77460653082155 4186 499 4401 862 1965 3077 4487 3409 1383 275 3746 3478 M14215 HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_UP.html Genes up-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 14/15 Arthur Liberzon 0.085215512581804 0.126245203824895 3355 2807 3077 0.00806428724136419 1350 0.866992139708568 0.587989701755325 1 1.16915887184839 3355 1583 2623 2102 3077 4186 3246 1350 1541 3887 3927 3479 M5784 SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE http://www.broadinstitute.org/gsea/msigdb/cards/SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE.html IRF4 [GeneID=3662] target genes up-regulated in primary myeloma vs. mature B lymphocytes. 18568025 125/146 Jessica Robertson 0.00108701755296652 0.00423676535920891 3205 2499.45454545455 3077 9.88686380866376e-05 411 0.934323006719667 -0.922377587229452 -1 3.32672173922871 3205 1270 3300 598 411 3706 3077 4401 784 2061 4681 3480 M2090 NOUSHMEHR_GBM_GERMLINE_MUTATED http://www.broadinstitute.org/gsea/msigdb/cards/NOUSHMEHR_GBM_GERMLINE_MUTATED.html Genes with significantl germline mutation differences in proneural G-CIMP (a CpG island methylator phenotype) GBM (glyoblastoma multiforme) tumors. 20399149 9/17 Arthur Liberzon 0.00200021911613951 0.00668155288618436 3695 2675.36363636364 3077 0.000200202179463225 230 2.16132638068519 -1.58004152031101 -1 7.05406384540065 3693 1625 4654 1220 1266 3502 3479 230 3077 2038 4645 3481 M14025 REACTOME_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTION.html Genes involved in Transcription 182/275 Reactome 0.370725931769992 0.439213453301798 2285 3181.54545454545 3078 0.0412338063418514 1373 0.949733199773568 -1.12699717990282 -1 0.509114884150407 2285 4719 4146 4537 4003 1494 2861 3078 1373 4397 2104 3482 M168 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_MAGENTA_DN.html Genes from the magenta module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 14/15 Arthur Liberzon 0.00714533282994407 0.0167374545693975 3165 2764.45454545455 3081 0.000651695098036284 129 0.949638522890377 -1.27100665738087 -1 2.53105089758458 3161 3078 3081 2512 806 3289 2800 3845 129 3315 4393 3483 M1407 WELCH_GATA1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/WELCH_GATA1_TARGETS.html Genes up-regulated after GATA1 [GeneID=2623] activation in G1E-ER4 cells (erythroid precursors engineered to express GATA1 upon addition of estradiol [PubChem=5757]). 15297311 22/30 Jean-Pierre Bourquin 9.76485827852613e-07 1.35959088715762e-05 4540 2800.45454545455 3081 8.87714782975585e-08 6 0.793989848748854 0.840215881844711 1 5.79794040828221 4537 351 2842 1717 6 3482 4711 3738 3081 1921 4419 3484 M790 REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_XBP1S http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_XBP1S.html Genes involved in Activation of Chaperone Genes by XBP1(S) 61/65 Reactome 0.00250509019952169 0.00790391091608911 3975 2930.72727272727 3083 0.000227995204056129 557 0.705560637676168 -0.714166312385915 -1 2.22546540796816 3972 2872 4049 2441 557 3101 3004 4330 707 4122 3083 3485 M19511 WANG_CISPLATIN_RESPONSE_AND_XPC_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CISPLATIN_RESPONSE_AND_XPC_UP.html Genes up-regulated in fibroblasts with defective XPC [GeneID=7508] in response to cisplatin [PubChem=2767]. 15107491 253/404 John Newman 0.000831653581415641 0.00344938919532674 3085 2890.18181818182 3083 7.56334666553293e-05 599 1.25123167685967 -1.17390550367681 -1 4.62277886543549 4541 2743 599 2736 3085 3276 4597 2705 3083 649 3778 3486 M14539 BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP.html Genes up-regulated in medullary breast cancer (MBC) relative to ductal breast cancer (DBD). 16651414 255/307 Arthur Liberzon 0.68618940391 0.690284310838704 4425 3071.54545454545 3084 0.1 1525 1.03352902162 -1.08962010278665 -1 0.249534542199304 4424 2260 2564 1525 3561 4660 3766 4231 1755 1957 3084 3487 M1515 JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_DN.html Genes down-regulated in H460 cells (non-small cell lung carcinoma, NSCLC) after treatment with sodium butyrate [PubChem=5222465]. 15318170 93/171 John Newman 0.117227509511691 0.164812341775113 2260 2869.36363636364 3084 0.0112712496127359 1223 1.08569759133985 0.902309048459256 1 1.27550483513407 2260 3675 1223 4562 3169 2175 2060 3084 4143 2119 3093 3488 M1605 BURTON_ADIPOGENESIS_4 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_4.html Progressively up-regulated from 8-48 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 87/108 John Newman 0.0116279084217686 0.0245564777408267 1635 2748.45454545455 3085 0.00106271139688431 966 1.12342918269479 1.07137536281496 1 2.71363635254115 1635 1854 1305 3454 966 4146 3591 3085 3847 2839 3511 3489 M1198 TERAMOTO_OPN_TARGETS_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_3.html Cluster 3: genes whose up-regulation peaked 3 days after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 5/5 Arthur Liberzon 4.46720582096985e-05 0.000347367569604245 4670 2743.09090909091 3086 4.46729562518594e-06 90 0.932302891682278 -1.00333905171915 -1 4.83911966076312 4669 1650 4386 490 90 4181 3190 2967 1089 3086 4376 3490 M1761 TESAR_ALK_TARGETS_EPISC_3D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_EPISC_3D_UP.html Genes up-regulated in EpiSC cells (mouse epiblast embryonic stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=4521392]. 17597760 5/11 Jessica Robertson 0.00872865893870465 0.0197031421284964 3650 2998.36363636364 3088 0.000876313494957773 527 1.33564828625505 1.33564828625505 1 3.41792996234227 3650 3132 4524 2049 2804 4075 4622 527 2673 3088 1838 3491 M10595 BUDHU_LIVER_CANCER_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BUDHU_LIVER_CANCER_METASTASIS_UP.html Genes up-regulated in tumor-adjacent liver tissue, which is asociated with intrahepatic metastasis of hepatocellular carcinoma 16904609 5/9 Yujin Hoshida 0.0412580460006624 0.0684251500784001 2555 2913.36363636364 3089 0.00420446822158494 1071 2.80046009529594 -2.80046009529594 -1 4.89448828280621 2555 3958 4623 4009 3089 3215 2786 1071 2524 3095 1122 3492 M2197 THILLAINADESAN_ZNF217_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/THILLAINADESAN_ZNF217_TARGETS_UP.html Genes bound and activated by ZNF217 [GeneID=7764] in MCF7 cells (breast cancer). 18625718 55/58 Arthur Liberzon 0.43119990772354 0.499814448548158 3965 2442.18181818182 3091 0.05 147 0.952194087998241 -1.01236954371511 -1 0.430232034871605 3962 147 3296 351 4331 2354 2367 3091 151 3626 3188 3493 M5681 MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP.html Genes up-regulated in apoptotic tissues (neuroepithelium) after MDM4 [GeneID=4194] knockout. 15608685 227/276 Arthur Liberzon 0.0088771492519261 0.0199619554402531 3435 2792.27272727273 3093 0.000810288437903664 830 1.1624041972932 1.23311500670632 1 2.96469835928529 3432 1208 830 2283 4668 4279 3720 3093 1907 1063 4232 3494 M8144 KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP.html Genes up-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 6 h. 18701491 1143/1374 Jessica Robertson 0.137037549899011 0.187700880883149 4505 2727 3094 0.0146303312304715 299 1.02650789178682 1.03799037427937 1 1.11897088423922 3094 463 4501 299 2065 3691 3188 4399 1363 2432 4502 3495 M2423 PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_DN.html Genes down-regulated in M2-10B4 cells (osteoblast) in response to phenylamil [PubChem=4755]. 19433444 8/13 Arthur Liberzon 0.639034916872905 0.690284310838704 3560 2835.54545454545 3094 0.0968777970779616 105 1.54424645467981 -0.937487687313803 -1 0.372894105633912 3557 2152 4700 1173 3094 3132 2762 4272 105 1893 4351 3496 M10546 REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_CAMKII http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_CAMKII.html Genes involved in CREB phosphorylation through the activation of CaMKII 12/19 Reactome 0.160125527695357 0.213742220226834 2350 2893.72727272727 3095 0.015738725378794 1127 0.666724137512319 0.781823195611199 1 0.670293979163019 2346 3095 3037 3781 4108 1127 1204 3521 3822 3801 1989 3497 M7577 ACEVEDO_LIVER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) compared to normal liver samples. 18413731 607/821 Jessica Robertson 0.0163165723985956 0.0322815320098235 4265 2510.36363636364 3095 0.0016437629004884 222 1.1161303455884 -1.1106972777691 -1 2.49706197290394 4264 486 4545 222 2045 3095 4607 3228 1322 666 3134 3498 M2110 KIM_ALL_DISORDERS_CALB1_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_CALB1_CORR_UP.html Genes whose expression significantly and positively correlated with the density of CALB1-positive [GeneID=793] GABAergic interneurons in the BA9 brain region across all subjects with psychiatric disorders. 18762803 697/844 Jessica Robertson 0.6513215599 0.690284310838704 4125 3134.81818181818 3097 0.1 1669 0.971772713377156 -0.882873668369357 -1 0.234617817742635 4123 1669 4660 2226 3724 2355 3829 3097 1760 4231 2809 3499 M2568 ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION http://www.broadinstitute.org/gsea/msigdb/cards/ALTEMEIER_RESPONSE_TO_LPS_WITH_MECHANICAL_VENTILATION.html Genes up-regulated in lung tissue upon LPS aspiration with mechanical ventilation (MV) compared to control (PBS aspiration without MV). 16116230 137/218 Jernej Godec 1.50468531379425e-06 1.98938786585682e-05 1540 2775.36363636364 3097 1.36789667538323e-07 295 1.16714191644507 1.18788307816452 1 8.23334018277226 1540 3644 295 3974 4402 3097 3121 2710 4346 408 2992 3500 M19828 PASTURAL_RIZ1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PASTURAL_RIZ1_TARGETS_UP.html Genes up-regulated in K562 (chronic myelogenous leukemia, CML) cells engineered to stably express RIZ1 [GeneID=7799]. 16953217 28/43 Aravind Subramanian 0.00922449085994285 0.0204988685776508 3465 2954.72727272727 3098 0.000842127024606265 882 1.25167469187685 -1.01840238066761 -1 3.17074061612433 3324 3452 1902 2723 882 3462 4712 2614 3461 2872 3098 3501 M14735 REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY.html Genes involved in Resolution of AP sites via the single-nucleotide replacement pathway 12/13 Reactome 0.0839919365246348 0.124902942783956 3040 3125 3099 0.00794374503899777 1744 0.677628570246197 -0.677628570246197 -1 0.918494806492784 3036 3099 3556 3145 1744 2420 2659 3293 4632 4623 2168 3502 M7076 NAM_FXYD5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAM_FXYD5_TARGETS_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of FXYD5 [GeneID=53827] by RNAi. 16849564 21/29 Arthur Liberzon 0.000527469193665332 0.00240546337594238 2855 2738.54545454545 3099 4.79632455883899e-05 316 0.929172419137718 0.991293432973835 1 3.65113650560404 2853 3040 3335 3099 316 4271 3420 3128 694 3794 2174 3503 M10694 SASAI_TARGETS_OF_CXCR6_AND_PTCH1_UP http://www.broadinstitute.org/gsea/msigdb/cards/SASAI_TARGETS_OF_CXCR6_AND_PTCH1_UP.html Up-regulated genes in medulloblastoma tumors from heterozygotic CXCR6 [GeneID=10663] knockout mice compared to those from PTCH1 [GeneID=5727] heterozygotic knockout mice. 17413002 12/19 Jessica Robertson 0.272244220756845 0.33533212995102 2430 3158.45454545455 3100 0.028476652218913 1587 1.15820108255708 1.29361540785107 1 0.824572761716267 2430 3100 2104 4349 4315 3557 2923 3042 3530 3806 1587 3504 M2479 SUZUKI_CTCFL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SUZUKI_CTCFL_TARGETS_UP.html Genes up-regulated in testis tissue upon knockout of CTCFL [GeneID=140690]. 20231363 12/17 Arthur Liberzon 0.00362010320910959 0.0104081532879602 1640 2548.09090909091 3100 0.000329643077576489 137 0.716700162476702 0.80959942158244 1 2.13205607219317 1639 3547 2985 3100 3759 660 137 4187 3892 3808 315 3505 M2561 HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_ALL_UP.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 35/41 Arthur Liberzon 0.00623423048502179 0.0151132860242952 3400 2198.54545454545 3100 0.000568360644152549 255 1.05048754196031 -1.15821713861352 -1 2.86973002397113 3100 267 3162 566 3397 2729 3540 420 3398 3350 255 3506 M13883 BIOCARTA_MPR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MPR_PATHWAY.html How Progesterone Initiates Oocyte Membrane 56/66 BioCarta 0.571228523198956 0.638455749348585 3300 3086 3101 0.0740959372498632 2197 0.964480019428972 -1.08937696720562 -1 0.281913089462387 2376 3730 3298 3005 4466 2197 2890 3360 3297 3101 2226 3507 M6267 ZAIDI_OSTEOBLAST_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/ZAIDI_OSTEOBLAST_TRANSCRIPTION_FACTORS.html An assortment of osteoblast transcriptional regulators. 17618270 13/16 Jessica Robertson 0.0043474168286968 0.0119229742549861 3985 2752.27272727273 3101 0.000396002872304116 670 1.49225868423272 -1.70873634958123 -1 4.30718471127297 3983 3101 1587 3329 670 2242 1317 3668 3859 1966 4553 3508 M4086 KEGG_PROPANOATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROPANOATE_METABOLISM.html Propanoate metabolism 33/36 KEGG 0.43119990772354 0.499814448548158 4190 2653.63636363636 3102 0.05 278 1.0580504457396 -1.19105236259384 -1 0.478073120322994 4187 278 2473 1319 3532 3227 3810 3102 623 2013 4626 3509 M921 REACTOME_IL_RECEPTOR_SHC_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_RECEPTOR_SHC_SIGNALING.html Genes involved in Interleukin receptor SHC signaling 30/37 Reactome 0.278566552146125 0.342493911469058 3985 2936.45454545455 3102 0.0292469758721338 922 1.09559599846923 -1.4130117682202 -1 0.764908024533806 3981 922 2043 1104 2432 4278 4417 3368 4060 2594 3102 3510 M1513 LEE_CALORIE_RESTRICTION_NEOCORTEX_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_CALORIE_RESTRICTION_NEOCORTEX_UP.html Up-regulated in the neocortex of aged (30-month) mice subjected to caloric restriction since young adulthood. 10888876 123/187 John Newman 0.581808045947987 0.64859092510026 3105 3373.36363636364 3102 0.0761964929801909 2273 1.03505885567884 -1.01800014389179 -1 0.291927216261509 3102 4375 2273 4482 2959 2672 3162 3067 4146 2413 4456 3511 M7963 KEGG_CELL_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CELL_CYCLE.html Cell cycle 132/142 KEGG 0.294140573430097 0.358282195249047 2645 3141.27272727273 3103 0.0311710429847878 2326 0.793815234308717 -0.777185362340803 -1 0.530872414689419 2643 2326 3970 3004 2459 3529 3213 3122 3009 4176 3103 3512 M5467 BIOCARTA_GRANULOCYTES_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GRANULOCYTES_PATHWAY.html Adhesion and Diapedesis of Granulocytes 12/21 BioCarta 0.00163624912126189 0.00573355297131115 3090 3146.36363636364 3103 0.000148860668141877 663 2.13231068057203 1.77787624256709 1 7.17198517991038 3087 3103 663 3093 3800 4215 4542 2879 4202 1342 3684 3513 M11575 REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION.html Genes involved in Glucagon signaling in metabolic regulation 27/36 Reactome 0.666386147413842 0.690284310838704 3685 3093.63636363636 3103 0.0949792174003244 1936 1.07388100932249 -1.20045242916103 -1 0.259281230415672 3683 3013 2152 3103 3525 3619 2431 2721 3559 1936 4288 3514 M1844 RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAY_TUMORIGENESIS_BY_ERBB2_CDC25A_UP.html Up-regulated genes in breast tumors from transgenic mice overexpressing ERBB2 and CDC25A [GeneID=2064;993] compared to those from mice overexpressing ERBB2 only. 17283130 133/174 Jessica Robertson 0.0063591903551714 0.0153531347705417 2830 2730.09090909091 3103 0.000579786053389738 496 1.24081006871515 1.19985730030347 1 3.37694205327815 2830 1790 793 496 4454 4121 3767 4195 3103 668 3814 3515 M2017 MIKKELSEN_NPC_WITH_LCP_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_NPC_WITH_LCP_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing histone H3 trimethylation mark at K27 in neural progenitor cells (NPC). 17603471 8/11 Arthur Liberzon 0.268635844561358 0.331666541022655 3675 2693.45454545455 3103 0.0308000855048307 784 2.53743565871467 -3.44670340029887 -1 1.82480971705533 3674 1078 4648 784 4173 3103 3222 3971 1669 1297 2009 3516 M2162 FIGUEROA_AML_METHYLATION_CLUSTER_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_2_UP.html Cluster 2 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 68/98 Arthur Liberzon 0.0225503402902804 0.041740237713774 3105 2852.81818181818 3103 0.00207135064689654 1189 1.10768543664772 -1.10803705770284 -1 2.29267567480154 3103 4080 3513 4067 1189 1363 3354 2955 2243 3830 1684 3517 M2413 PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 http://www.broadinstitute.org/gsea/msigdb/cards/PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7.html Genes regulated in MCF7 cells (breast cancer) by expression of the truncated (611-CTF) form of ERBB2 [GeneID=2064] at 60 h time point. 19364815 508/662 Arthur Liberzon 0.0182911803647851 0.0352817210142155 4015 2616.72727272727 3103 0.00184435031986833 255 1.12988860718381 -1.18787586871357 -1 2.46240812637441 4011 1142 4697 255 1468 4702 4016 3103 1316 684 3390 3518 M3862 REACTOME_AKT_PHOSPHORYLATES_TARGETS_IN_THE_CYTOSOL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AKT_PHOSPHORYLATES_TARGETS_IN_THE_CYTOSOL.html Genes involved in AKT phosphorylates targets in the cytosol 14/14 Reactome 0.00208802826196973 0.00690160601995596 4505 2874.09090909091 3104 0.000190001150426191 519 0.547506115391131 -0.604558806620314 -1 1.77529151296762 4505 1032 3611 1917 519 4276 4575 3104 876 4536 2664 3519 M1371 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX3 http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX3.html Early prostate development genes (up-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in lower grade vs higher grade locally invasive prostate cancers. 18794802 10/12 Jessica Robertson 0.288157448543576 0.352358330861574 4255 3305.81818181818 3107 0.0304273447391167 1473 1.01583097227274 -0.489297655463055 -1 0.690414197908683 4252 3107 3261 2699 4288 4621 4672 2048 1473 2904 3039 3520 M14966 REACTOME_REGULATION_OF_GENE_EXPRESSION_IN_BETA_CELLS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_GENE_EXPRESSION_IN_BETA_CELLS.html Genes involved in Regulation of gene expression in beta cells 6/22 Reactome 0.0249324949019086 0.0454368246861037 3175 3082.81818181818 3109 0.00252167266668163 1268 0.636148739463174 -0.524542925164156 -1 1.28147069492698 3173 1641 4227 3109 1268 3727 2876 2829 4620 4545 1896 3521 M6222 GRABARCZYK_BCL11B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRABARCZYK_BCL11B_TARGETS_UP.html Genes up-regulated in Jurkat cells (transformed T lymphocytes) after knockdown of BCL11B [GeneID=64919] by RNAi. 17173069 112/127 Arthur Liberzon 0.214999825320834 0.275087876257614 2960 3092.63636363636 3112 0.0217661091432766 1642 1.05018386782893 1.01555958835491 1 0.883187375264106 2958 4036 3512 2199 2275 4196 3349 2838 1642 3112 3902 3522 M1184 HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP http://www.broadinstitute.org/gsea/msigdb/cards/HERNANDEZ_ABERRANT_MITOSIS_BY_DOCETACEL_4NM_UP.html Genes up-regulated in MCF7 cells (breast cancer, normal TP53 [GeneID=7157]) undergoing aberrant mitosis and necrosis after treatment wiht 4 nM docetaxel [PubChem=148124]. 17099726 27/109 Arthur Liberzon 0.000789181983093256 0.00331400263363004 4495 2773.54545454545 3113 7.17695654531279e-05 363 1.35979738568998 -1.81756335060011 -1 5.05937431928232 4491 3830 1200 3946 363 2709 3113 4196 2280 959 3422 3523 M1457 GREENBAUM_E2A_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GREENBAUM_E2A_TARGETS_DN.html Genes down-regulated in pre-B lymphocytes upon Cre-Lox knockout of E2A [GeneID=6929]. 15310760 27/36 Kevin Vogelsang 0.186264451924546 0.24333468394239 3570 3074.27272727273 3113 0.0185636997238087 1763 1.05914831312 0.883597310676799 1 0.975383741273845 3566 2018 1899 2301 4430 3376 4689 1763 3113 2815 3847 3524 M8655 DAIRKEE_CANCER_PRONE_RESPONSE_BPA http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_CANCER_PRONE_RESPONSE_BPA.html 'Cancer prone response profile' (CPRP): genes changed in response to bisphenol A [PubChem=6623] in epithelial cell cultures from patients at high risk of breast cancer. 18381411 62/87 Jessica Robertson 0.548525750156405 0.616291725955304 4200 2960.72727272727 3113 0.0697428887108288 271 1.14245201860778 -1.05821883780783 -1 0.360257606745144 4199 1905 3152 1634 2907 4394 4684 4116 271 2193 3113 3525 M2140 LU_EZH2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_EZH2_TARGETS_DN.html Genes down-regulated in SKOV3ip1 cells (ovarian cancer) upon knockdown of EZH2 [GeneID=2146] by RNAi. 20708159 536/670 Arthur Liberzon 0.114733744578841 0.161944759094537 1390 2919.90909090909 3115 0.0121127256824127 1386 1.0225170624133 1.06584725633754 1 1.21296837025561 1386 3159 4663 4282 2954 3115 2122 1534 2546 3155 3203 3526 M12086 SCHURINGA_STAT5A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHURINGA_STAT5A_TARGETS_UP.html Genes up-regulated in hematopoietic stem cells (HSC) overexpressing a constitutively active form of STAT5 [GeneID=6776] off retroviral vector. 15353555 23/32 Kevin Vogelsang 0.621459981785593 0.686792581135097 2905 3321.90909090909 3116 0.0845249195467541 2009 1.07557431429169 1.22862537345027 1 0.263244745463933 2904 3480 2053 3772 3012 4685 3116 4356 4119 2009 3035 3527 M1204 TERAMOTO_OPN_TARGETS_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_8.html Cluster 8: genes showing sustained pattern of down-regulation after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 8/8 Arthur Liberzon 0.0966903037969226 0.140079261486027 1780 2774.63636363636 3117 0.0101174527849189 142 4.84006070973806 4.84006070973806 1 6.1994465218638 1779 3117 4388 3039 4411 3804 1432 3979 142 3461 969 3528 M6920 MCCLUNG_CREB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_CREB1_TARGETS_UP.html Genes up-regulated in the nucleus accumbens (a major reward center in the brain) 8 weeks after induction of CREB1 [GeneID=1385] expression in a transgenic Tet-Off system. 14566342 112/159 John Newman 0.0143857714603677 0.0292676040055757 4050 2496.72727272727 3117 0.0013164281911121 25 1.26266578898993 -1.25411201668408 -1 2.90556193501848 4046 25 888 344 4663 3168 4195 4603 1471 944 3117 3529 M19654 TOOKER_GEMCITABINE_RESISTANCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOOKER_GEMCITABINE_RESISTANCE_UP.html Up-regulated genes in Calu3 cells (non-small cell lung cancer, NSCLC) resistant to gemcitabine [PubChem=3461] which became down-regulated in response to bexarotene [PubChem=82146]. 17483357 100/134 Jessica Robertson 0.253368735245252 0.315707610970853 3615 2908.09090909091 3119 0.0262124955117262 689 1.07787483740927 -0.993708502804035 -1 0.80973692264577 3613 689 2992 3349 3979 3491 4691 2109 2428 3119 1529 3530 M10456 OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_UP.html Genes up-regulated in both the patients in the multicentric hepatocellular carcinoma (HCC) group and those with multicentric recurrence. 16788756 39/52 Yujin Hoshida 0.194383489443827 0.251988483981012 2760 3191.72727272727 3119 0.0194579691869538 1667 1.2765227999401 1.56947713514574 1 1.14651837294771 2758 1976 1667 3119 2217 4286 3469 4720 4313 2447 4137 3531 M13671 COATES_MACROPHAGE_M1_VS_M2_UP http://www.broadinstitute.org/gsea/msigdb/cards/COATES_MACROPHAGE_M1_VS_M2_UP.html Up-regulated genes distinguishing between M1 (pro-inflammatory) and M2 (anti-inflammatory) macrophage subtypes. 18199539 102/119 Jessica Robertson 0.5822476279362 0.648927698667973 3125 3182.81818181818 3121 0.0762848129131296 1629 1.10752668208902 -0.903051931135889 -1 0.311998738764913 4218 1827 1765 3025 4617 4579 4003 3105 3121 1629 3122 3532 M2668 KEGG_BETA_ALANINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BETA_ALANINE_METABOLISM.html beta-Alanine metabolism 24/30 KEGG 0.305033382487172 0.369073972145463 4055 3207.27272727273 3123 0.0325398489269945 1359 1.43685504442592 -1.88651954979506 -1 0.933210554162904 4053 4536 2517 4431 2630 1359 1799 3123 4107 3047 3678 3533 M544 REACTOME_SIGNALING_BY_ERBB4 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ERBB4.html Genes involved in Signaling by ERBB4 105/137 Reactome 0.00577426225782821 0.0142024584976285 3575 2558.54545454545 3123 0.000526315789473684 32 1.00315230420002 1.0231265570314 1 2.78104927455308 3572 32 3123 197 3517 2698 3053 4371 730 3485 3366 3534 M1208 YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_DN http://www.broadinstitute.org/gsea/msigdb/cards/YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_DN.html Genes down-regulated in HUVEC cells (endothelium) by ETS1 [GeneID=2113] which were up-regulated by SP100 [GeneID=6672]. 15592518 148/206 Arthur Liberzon 0.349497259656135 0.41678298776578 2305 3174.36363636364 3123 0.03833757275078 1846 1.2125071819159 1.15689184880665 1 0.691426664130788 2301 4366 1846 4518 3223 3933 3123 2175 3871 2503 3059 3535 M2329 BILANGES_RAPAMYCIN_SENSITIVE_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_RAPAMYCIN_SENSITIVE_GENES.html Genes translationally regulated in MEF cells (embryonic fibroblasts) by rapamycin (sirolimus) [PubChem=6610346] but not in response to serum deprivation. 17562867 46/63 Arthur Liberzon 0.0611800090790732 0.095397965924422 2110 2777.81818181818 3123 0.00572279127805576 774 0.975221688841141 0.871664202605199 1 1.49317511395536 2109 3763 3354 3123 2756 1246 774 2941 3160 3535 3795 3536 M127 PID_ERBB1_RECEPTOR_PROXIMAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_RECEPTOR_PROXIMAL_PATHWAY.html EGF receptor (ErbB1) signaling pathway 18832364 52/54 Pathway Interaction Database 0.68618940391 0.690284310838704 3860 2742.81818181818 3124 0.1 804 0.873313038359471 -0.91909810538629 -1 0.210835699217081 3860 804 3223 1138 3124 4532 3414 3034 926 2237 3879 3537 M7176 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_UP.html Genes up-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing monocytes. 17898786 23/30 Arthur Liberzon 0.252949030807117 0.315267870454078 3335 2907.90909090909 3124 0.0261627449533619 1262 1.45522705812189 -1.677037010557 -1 1.09457584979123 3335 3855 1481 3124 4047 2690 1466 2675 4179 1262 3873 3538 M2290 CHANGOLKAR_H2AFY_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHANGOLKAR_H2AFY_TARGETS_DN.html Genes down-regulated in liver tissue upon knockout of H2AFY [GeneID=9555]. 17242180 41/47 Arthur Liberzon 0.140030767244401 0.191024630460571 2335 2984.36363636364 3125 0.013620809931957 1517 1.10979423276515 -1.23376201473526 -1 1.19707341508226 2334 3371 2855 2665 2032 3164 1517 3933 3125 3650 4182 3539 M122 PID_IL2_1PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL2_1PATHWAY.html IL2-mediated signaling events 18832364 74/87 Pathway Interaction Database 0.00577426225782821 0.0142024584976285 4330 2681.63636363636 3126 0.000526315789473684 103 0.929517952365286 -0.895771855452594 -1 2.5769042484698 4327 103 3126 207 4221 4187 3689 2331 1002 2782 3523 3540 M542 REACTOME_IL_7_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_7_SIGNALING.html Genes involved in Interleukin-7 signaling 12/13 Reactome 0.0574949810826621 0.0907309631261 4115 2833 3127 0.00536863116372425 1047 0.869382530613036 -0.70216000868062 -1 1.35952912542456 4114 2127 2419 1544 4473 3879 4117 1177 1047 3127 3139 3541 M10504 SEMBA_FHIT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SEMBA_FHIT_TARGETS_DN.html Genes down-regulated in H1299 cells (non-small cell lung cancer, NSCLC) expressing the Y144F mutant form of FHIT [GeneID=2272]. 16407838 9/9 Leona Saunders 0.231210980721902 0.291795676205181 1850 3135.09090909091 3127 0.0259511966017416 1458 1.09484625653042 -1.09484625653042 -1 0.878683378141719 1848 4269 4404 4212 4139 2244 1458 2499 3127 3562 2724 3542 M1428 SANSOM_APC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS_UP.html Top genes up-regulated at day 5 of Cre-Lox induced APC [GeneID=324] knockout in the intestine. 15198980 181/216 Kevin Vogelsang 0.519817389006387 0.588237371400179 3215 3210.72727272727 3127 0.0645147418254622 2056 1.23630994319047 1.11634259064646 1 0.427398937436263 3215 4347 2056 4092 2856 3127 2990 3216 2156 2784 4479 3543 M8472 REACTOME_FACILITATIVE_NA_INDEPENDENT_GLUCOSE_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FACILITATIVE_NA_INDEPENDENT_GLUCOSE_TRANSPORTERS.html Genes involved in Facilitative Na+-independent glucose transporters 7/11 Reactome 0.160185280847027 0.213761528300246 4565 2834.90909090909 3128 0.0173059008770179 158 1.76197703034401 -2.19722218687385 -1 1.77148131440886 4565 3128 4243 2571 2159 4140 3471 1823 158 1134 3792 3544 M13661 CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5 http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5.html The 'group 5 set' of genes associated with acquired endocrine therapy resistance in breast tumors expressing ESR1 but not ERBB2 [GeneID=2099;2064]. 18794137 609/708 Jessica Robertson 6.87083476200706e-05 0.000491368789040505 3130 2506.72727272727 3128 6.87104720891829e-06 211 1.07993169777798 1.03840523213894 1 5.36133317092631 3128 1127 4511 211 3191 3048 3169 3580 956 270 4383 3545 M1033 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_10.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 10. 12554760 93/111 Arthur Liberzon 0.032823987996722 0.056522883379981 2900 2903.45454545455 3128 0.00302947290113319 657 0.950281070260601 -1.01873904551411 -1 1.77911726722453 2900 1311 3956 2917 1357 3128 3581 4316 657 4250 3565 3546 M2550 HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_UP.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 54/60 Arthur Liberzon 0.327284919353179 0.392675348080073 3990 3209.18181818182 3128 0.0353977122550628 2429 1.06551159997339 -1.08322031256181 -1 0.648961937106367 3090 3324 2870 3128 2535 2904 2429 3334 3709 3989 3989 3547 M15216 REACTOME_BOTULINUM_NEUROTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BOTULINUM_NEUROTOXICITY.html Genes involved in Botulinum neurotoxicity 15/20 Reactome 0.515184336920849 0.583834350604179 3045 3248.27272727273 3129 0.0636977686248111 2043 0.656306338991184 0.587386731252189 1 0.230052325908276 3044 3076 3528 3969 3333 2531 2043 3478 3074 4526 3129 3548 M3828 REACTOME_PROTEOLYTIC_CLEAVAGE_OF_SNARE_COMPLEX_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROTEOLYTIC_CLEAVAGE_OF_SNARE_COMPLEX_PROTEINS.html Genes involved in Proteolytic cleavage of SNARE complex proteins 15/18 Reactome 0.515184336920849 0.583834350604179 3045 3240.63636363636 3130 0.0636977686248111 2044 0.656306338991184 0.587386731252189 1 0.230052325908276 3045 3077 3529 3970 3334 2532 2044 3384 3075 4527 3130 3549 M12434 DONATO_CELL_CYCLE_TRETINOIN http://www.broadinstitute.org/gsea/msigdb/cards/DONATO_CELL_CYCLE_TRETINOIN.html Genes involved in cell cycle regulation which were up-regulated in MCF-7 cells (breast cancer) by tretinoin (retinoic acid) [PubChem=444795]. 17234770 6/6 Jessica Robertson 0.000442920388381614 0.00210320345388452 4215 2859.54545454545 3130 4.4300869346533e-05 305 0.610411171913395 -0.544167485866527 -1 2.45195879634066 4213 1644 4573 2065 305 3130 2508 2993 3519 3241 3264 3550 M1974 MIKKELSEN_IPS_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 12/30 Jessica Robertson 0.261289644183695 0.324207970701115 2775 3106.36363636364 3131 0.027156216832943 1560 1.25383971225959 -1.05808557059858 -1 0.920236185575669 2771 3552 1631 3544 2865 3810 4373 2738 4195 3131 1560 3551 M3618 BIOCARTA_TNFR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TNFR1_PATHWAY.html TNFR1 Signaling Pathway 33/35 BioCarta 0.68618940391 0.690284310838704 3425 3103.18181818182 3132 0.1 1358 0.765130459385913 -0.572381914593125 -1 0.184705093818605 3422 3398 3710 2443 3132 2273 4285 3006 1358 4113 2995 3552 M1213 KANG_GIST_WITH_PDGFRA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KANG_GIST_WITH_PDGFRA_DN.html Genes down-regulated in gastrointestinal stromal tumors (GIST) with PDGFRA [GeneID=5156] mutations. 15690055 8/10 Arthur Liberzon 0.110588727506841 0.156891732441326 3135 2948.54545454545 3132 0.0116511462063018 585 0.800365617832738 -0.778450820652022 -1 0.965950084026222 4118 1627 4390 1291 1929 4366 3131 4403 585 3462 3132 3553 M16927 BOYLAN_MULTIPLE_MYELOMA_C_D_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_D_UP.html Genes up-regulated both in group C and D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 176/197 Jessica Robertson 0.405385070799528 0.474911276786739 2355 3151.54545454545 3134 0.046159007956799 2146 1.06051570166411 1.00681862020839 1 0.514508844605879 2355 4350 3134 4201 2681 2475 2276 4112 2146 3344 3593 3554 M19367 GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_DIVIDING_DN.html Genes down-regulated in dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients compared to the dividing cells from normal donors. 17717066 7/23 Arthur Liberzon 0.00232117927794781 0.00746827961275641 3060 3071.72727272727 3135 0.000232360739118763 245 1.44234507058467 -1.63643857316791 -1 4.60281425094022 3059 4274 4317 3053 3861 3728 3135 245 4054 2473 1590 3555 M7775 EHLERS_ANEUPLOIDY_UP http://www.broadinstitute.org/gsea/msigdb/cards/EHLERS_ANEUPLOIDY_UP.html Up-regulated genes in the expression signature of aneuploidy in uveal melanoma tumors: low vs high aneuploidy. 18172260 44/54 Jessica Robertson 0.101708697376755 0.146227551513336 3210 2970.18181818182 3135 0.00970360169928307 1838 1.02385019097482 0.879778487232948 1 1.28266627852434 2465 3353 3206 3135 1838 3208 2569 2815 2873 3455 3755 3556 M8731 BIOCARTA_SPPA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SPPA_PATHWAY.html Aspirin Blocks Signaling Pathway Involved in Platelet Activation 36/42 BioCarta 0.0119976567498355 0.0251684177152104 3140 3055.27272727273 3136 0.00109668997064488 981 0.994404136619505 -0.859808893527468 -1 2.38601442583995 3136 4135 2922 2777 981 4481 3424 2961 1421 3396 3974 3557 M2530 SHIRAISHI_PLZF_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHIRAISHI_PLZF_TARGETS_DN.html Genes down-regulated in A375 and 397 cells (melanoma) by forced expression of PLZF [GeneID=7704] off adenovirus vector. 16862184 8/12 Arthur Liberzon 0.0557468375440356 0.088326644245669 4020 2997.90909090909 3137 0.00571967682946628 1601 0.74743969433305 -0.820516940804168 -1 1.18190315951618 4017 1630 4349 2009 1601 1830 2837 3137 4288 3459 3820 3558 M1535 JIANG_AGING_HYPOTHALAMUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_HYPOTHALAMUS_DN.html Down-regulated in the hypothalamus of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 64/71 John Newman 0.440991310715453 0.509791571534886 2640 3098.72727272727 3137 0.0514984372098277 1977 0.915284779133184 -0.898174924295687 -1 0.401762035941977 3900 2867 2637 3188 3137 1993 4441 2639 3864 3443 1977 3559 M9693 FINETTI_BREAST_CANCERS_KINOME_GRAY http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCERS_KINOME_GRAY.html Genes in the gray cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 31/32 Jessica Robertson 0.107407523596602 0.153068693048297 2955 2932.72727272727 3137 0.0102763929265401 362 0.836479997005216 -0.990638930811164 -1 1.02298813396519 2953 2524 3655 2410 1863 3594 3137 3562 362 3492 4708 3560 M19422 BIOCARTA_IL17_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL17_PATHWAY.html IL 17 Signaling Pathway 5/14 BioCarta 0.0118785660371847 0.0249829607109181 2625 2915.27272727273 3138 0.00119425430182642 1005 1.63253635958792 1.0485744917339 1 3.92511150198539 2621 3138 4192 3939 1005 2461 1891 3235 3184 2089 4313 3561 M1071 REACTOME_TANDEM_PORE_DOMAIN_POTASSIUM_CHANNELS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TANDEM_PORE_DOMAIN_POTASSIUM_CHANNELS.html Genes involved in Tandem pore domain potassium channels 5/12 Reactome 0.6513215599 0.690284310838704 3890 3290.54545454545 3139 0.1 1587 1.31926748461582 -1.75924737619781 -1 0.318552299906258 3887 3139 4262 2831 3843 2917 3370 2754 1587 3080 4526 3562 M4120 LOPEZ_MBD_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MBD_TARGETS.html Genes up-regulated in HeLa cells (cervical cancer) after simultaneus knockdown of all three MBD (methyl-CpG binding domain) proteins MeCP2, MBD1 and MBD2 [GeneID=4204;4152;8932] by RNAi. 18223687 1273/1612 Jessica Robertson 0.120874352209299 0.169245607365141 3140 2990.36363636364 3139 0.0128001173963975 889 1.02072753636141 -1.00075225316964 -1 1.18151400443749 3139 3961 4434 3923 2257 889 3017 2580 3216 3990 1488 3563 M6591 REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOSOLIC_TRNA_AMINOACYLATION.html Genes involved in Cytosolic tRNA aminoacylation 29/29 Reactome 0.596370626611462 0.662790053592207 3370 3153.27272727273 3140 0.0791683220404919 858 0.604785069036677 -0.661089388683307 -1 0.161994063118821 3370 4506 4048 2770 4279 2191 2363 2612 858 4549 3140 3564 M17074 AIYAR_COBRA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/AIYAR_COBRA1_TARGETS_UP.html Genes up-regulated in T47D cells (breast cancer) after COBRA1 [GeneID=25920] knockdown by RNAi. 17043641 46/63 Arthur Liberzon 0.353189921403238 0.42086756602456 3730 3030.81818181818 3140 0.0388351305920324 1493 1.48003739681819 1.63782722409307 1 0.834601641734923 3729 4466 1526 3980 3140 4224 3873 2252 1493 1869 2787 3565 M18219 BREUHAHN_GROWTH_FACTOR_SIGNALING_IN_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/BREUHAHN_GROWTH_FACTOR_SIGNALING_IN_LIVER_CANCER.html Growth factor signaling components up-regulated in hepatocellular carcinoma (HCC). 16799620 29/31 Arthur Liberzon 0.187953179399358 0.245201494407122 3360 3037.09090909091 3141 0.0187490339949242 1772 0.92788620547031 1.06045675704064 1 0.849868390617844 3360 2537 2034 3771 3469 3141 3412 1772 4365 2528 3019 3566 M15305 PUJANA_BRCA_CENTERED_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BRCA_CENTERED_NETWORK.html Genes constituting the BRCA-centered network (BCN). 17922014 143/153 Leona Saunders 0.68618940391 0.690284310838704 1995 2922.09090909091 3141 0.1 521 0.863766036898703 -0.777001648393037 -1 0.208529700134077 1994 3209 4116 2474 3141 2648 2597 3725 521 4398 3320 3567 M16111 MOOTHA_GLYCOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/MOOTHA_GLYCOLYSIS.html Genes involved in glycolysis; based on literature and sequence annotation resources and converted to Affymetrix HG-U133A probe sets. 12808457 28/42 Vamsi Mootha 0.00331314135329203 0.00980425330377675 4185 2726.09090909091 3141 0.000301649218267664 609 1.02918063619406 -1.09299306765098 -1 3.10176517550813 4183 3450 3141 3177 609 2194 2962 1260 1238 3339 4434 3568 M14314 KEGG_PURINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PURINE_METABOLISM.html Purine metabolism 139/171 KEGG 0.579914166634822 0.646938044555981 3175 2846.54545454545 3142 0.0758169410544437 964 1.08867066846481 -0.943425764107043 -1 0.308863618884695 3171 3210 3142 2629 4012 1900 2493 3931 964 2379 3481 3569 M13424 JAZAG_TGFB1_SIGNALING_VIA_SMAD4_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_VIA_SMAD4_UP.html Genes up-regulated in PANC-1-S4KD cells (pancreatic cancer; SMAD4 [GeneID=4089] knocked down by RNAi) after stimulation by TGF1B [GeneID=7040] for 2 h. 15592526 142/199 Leona Saunders 0.149099935593182 0.201474862868542 3735 2482.18181818182 3142 0.0145710353393701 336 1.10800220997863 -1.11305456690867 -1 1.15668232874648 3731 617 1271 336 2415 3142 3560 3246 3319 1899 3768 3570 M915 REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NITRIC_OXIDE_STIMULATES_GUANYLATE_CYCLASE.html Genes involved in Nitric oxide stimulates guanylate cyclase 14/27 Reactome 0.000381047044985633 0.00189121141149547 2570 2715.63636363636 3143 3.46466417783731e-05 558 1.93115394415536 1.84733989823559 1 7.89118043616323 2569 3894 558 1963 4383 3884 3799 733 3363 1583 3143 3571 M17083 MORI_MATURE_B_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_MATURE_B_LYMPHOCYTE_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the mature B 18922927 119/156 Jessica Robertson 0.033753877649154 0.0578707964053784 3755 2776.36363636364 3143 0.00311665060053003 18 1.0378242389822 -1.09692899566618 -1 1.92708647765787 3755 18 2039 1557 1365 3334 4497 4234 3843 3143 2755 3572 M5202 BIOCARTA_P53HYPOXIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_P53HYPOXIA_PATHWAY.html Hypoxia and p53 in the Cardiovascular system 40/44 BioCarta 0.0363617843739243 0.0615045528329881 2945 3256 3146 0.00336155091258756 1396 0.808026967645069 -0.782198991664219 -1 1.46829649429627 2945 4485 2846 4659 1396 1779 1647 4239 4621 4053 3146 3573 M6616 BENPORATH_NANOG_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_NANOG_TARGETS.html Set 'Nanog targets': genes upregulated and identified by ChIP on chip as Nanog [GeneID=79923] transcription factor targets in human embryonic stem cells. 18443585 1238/1499 Jessica Robertson 0.0870250155042715 0.128482350071993 4455 3287.90909090909 3146 0.00906335770615707 1800 0.983009227311492 -0.91675312495638 -1 1.31437239592213 4455 3146 4449 2781 1800 2185 4645 4123 1845 4363 2375 3574 M12717 LOPES_METHYLATED_IN_COLON_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LOPES_METHYLATED_IN_COLON_CANCER_DN.html Genes un-methylated aberrantly in HCT116 and Colo320 (colon cancer) cells. 18794111 34/46 Jessica Robertson 0.027698081097236 0.0495208116586947 3840 2989.09090909091 3146 0.00255027946123204 1276 1.27491552136057 1.35954641309329 1 2.49681261139067 3837 3389 1922 2079 1276 4433 4668 2223 3146 1751 4156 3575 M911 REACTOME_PASSIVE_TRANSPORT_BY_AQUAPORINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PASSIVE_TRANSPORT_BY_AQUAPORINS.html Genes involved in Passive Transport by Aquaporins 4/10 Reactome 0.07585540653839 0.114170127187883 3180 3187.36363636364 3147 0.00785763939106366 1738 1.11459678042491 -1.11459678042491 -1 1.57611392721868 3178 3582 4252 1991 1738 4139 3147 2987 4434 2914 2699 3576 M14780 KUNINGER_IGF1_VS_PDGFB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUNINGER_IGF1_VS_PDGFB_TARGETS_DN.html Genes down-regulated in C2AS12 cells (myoblast) by IGF1 [GeneID=3479] vs PDGFB [GeneID=5155]. 15475267 53/67 John Newman 0.00198023087199248 0.00663014188258543 3560 2698 3147 0.000180183230630145 681 1.49347894288185 -1.53717583211282 -1 4.88185091020078 4168 1409 681 1474 4545 3147 3735 3559 2405 995 3560 3577 M16992 ZHANG_PROLIFERATING_VS_QUIESCENT http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_PROLIFERATING_VS_QUIESCENT.html Genes up-regulated in HDMEC cells (microvascular endothelium): proliferating vs quiescent cells. 14517420 83/97 John Newman 0.68618940391 0.690284310838704 2865 3122.72727272727 3147 0.1 2250 1.18253692756098 1.28279937750572 1 0.285526166990839 2864 3686 2282 3240 3147 3876 2966 3298 2250 2661 4080 3578 M5516 VALK_AML_CLUSTER_12 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_12.html Top 40 genes from cluster 12 of acute myeloid leukemia (AML) expression profile; 89% of the samples are FAB M3 subtype, 95% bear the t(15;17) translocation, all have the PML-RARA fusion [GeneID=5371;5914]; indicate good survival. 15084694 36/47 Jessica Robertson 0.148788523159725 0.201135114349353 3670 3085 3148 0.0145382546717862 1150 1.32092806213959 -1.33987215144721 -1 1.38043623191644 3670 4138 1730 3510 3910 3092 4466 3148 2087 3034 1150 3579 M2132 WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_RESPONSE_TO_GSK3_INHIBITOR_SB216763_DN.html Genes down-regulated in RS4;11 cells (MLL, mixed lineage leukemia) in response to SB216763 [PubChem=176158], an inhibitor of GSK3B [GeneID=2932]. 20541704 463/609 Arthur Liberzon 0.68618940391 0.690284310838704 2370 3149 3148 0.1 1428 1.12366294659751 1.13533942428091 1 0.271305644801496 2370 3968 2955 3899 4515 3148 3228 2826 1428 2264 4038 3580 M1405 KIM_GERMINAL_CENTER_T_HELPER_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_GERMINAL_CENTER_T_HELPER_UP.html Genes up-regulated in germinal center T helper cells compared to other CD4+ [GeneID=920] T lymphocyte types. 15213097 82/100 Kate Stafford 0.00152724479393925 0.00545694030563126 3795 2460.72727272727 3149 0.00013893691292324 67 0.91612954310184 0.828449932967422 1 3.11084394287472 3794 67 2484 339 464 3667 3401 4003 1887 3149 3813 3581 M11672 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_BLUE_UP.html Genes from the blue module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 183/193 Arthur Liberzon 0.0110275442805802 0.0235313456224257 500 2338.09090909091 3150 0.00100756464597024 161 0.965049720464595 0.968256566931954 1 2.35787418497899 498 4710 3517 4240 3970 161 589 689 3150 3371 824 3582 M3835 BENPORATH_SOX2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_SOX2_TARGETS.html Set 'Sox2 targets': genes upregulated and identified by ChIP on chip as SOX2 [GeneID=6657] transcription factor targets in human embryonic stem cells. 18443585 958/1168 Jessica Robertson 0.300488789307643 0.364603363889993 4710 3366.27272727273 3150 0.035106306442726 1267 1.05926910640454 -1.00767633440704 -1 0.696360301247105 4706 3150 4450 2477 2531 2707 4571 4518 1267 3995 2657 3583 M16542 YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP http://www.broadinstitute.org/gsea/msigdb/cards/YAMASHITA_LIVER_CANCER_WITH_EPCAM_UP.html Up-regulated genes distinguishing hepatocellular carcinoma (HCC) samples positive for EPCAM [GeneID=4072] from the negative ones. 18316609 66/108 Yujin Hoshida 0.0459250552415605 0.0749456169223308 835 2468.36363636364 3150 0.00426479366169469 626 0.92478015494857 0.819683790335129 1 1.56135388370381 832 3720 3771 3876 3150 626 799 1078 3981 3512 1807 3584 M427 CHESLER_BRAIN_HIGHEST_GENETIC_VARIANCE http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_HIGHEST_GENETIC_VARIANCE.html Neurologically relevant transcripts with highest variance accounted for by mouse strain (genotype) differences. 15711545 54/64 Jean Junior 0.13407873459557 0.184397327299269 1505 3128.90909090909 3151 0.0130021226816039 1503 1.06087452548298 1.12000416488002 1 1.16871260136076 1503 4457 1561 4494 2001 3513 3138 2850 4452 3298 3151 3585 M11884 GOLDRATH_ANTIGEN_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/GOLDRATH_ANTIGEN_RESPONSE.html Genes up-regulated at the peak of an antigen response of naive CD8+ [GeneID=925;926] T-cells. 15548615 401/541 Arthur Liberzon 0.6816038821958 0.690284310838704 3155 2912.72727272727 3151 0.0988123089354707 1741 1.13412642653627 -1.13561263157805 -1 0.273833011665632 3151 3166 1963 1866 3560 3503 3603 4625 1774 1741 3088 3586 M1919 COLINA_TARGETS_OF_4EBP1_AND_4EBP2 http://www.broadinstitute.org/gsea/msigdb/cards/COLINA_TARGETS_OF_4EBP1_AND_4EBP2.html Genes up-regulated in MEF cells (embryonic fibroblast) with double knockout of the translation repressors 4EBP1 [GeneID=1978] and 4EBP2 [GeneID=1979]. 18272964 480/630 Jessica Robertson 0.0252767240271115 0.0458693338746506 4680 3049.72727272727 3151 0.0023247179919474 962 1.13735260852762 -1.08895088985059 -1 2.28416731201162 4680 2220 962 2176 2967 3645 4471 4621 3151 1218 3436 3587 M16955 ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN.html Genes whose promoters display lower levels of histone H3 trimethylation mark at K27 (H3K27me3) in hepatocellular carcinoma (HCC) compared to normal liver. 18413731 171/413 Jessica Robertson 0.0053806404032557 0.0140779505007577 4465 2815.54545454545 3154 0.000490349574312361 770 1.2610089567928 -1.36528371904545 -1 3.5031709169894 4461 3636 770 3491 797 3154 4720 4491 2119 953 2379 3588 M10311 BROWNE_HCMV_INFECTION_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_6HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 6 h time point that were not down-regulated at the previous time point, 4 h. 11711622 218/254 John Newman 0.460949078847672 0.530136367485626 3155 3033.63636363636 3155 0.0546280583939713 1936 1.04278470539547 1.04725215199729 1 0.4311502385759 2003 3186 3568 4083 3913 2503 1936 3155 2310 3151 3562 3589 M477 BIOCARTA_GABA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GABA_PATHWAY.html Gamma-aminobutyric Acid Receptor Life Cycle 8/14 BioCarta 0.00545812108125173 0.0142024584976285 3160 2717.09090909091 3156 0.0005471573595955 733 1.1281771651015 -0.674469151147213 -1 3.12767014991673 3156 3121 4191 3568 757 1598 1436 4448 733 3457 3423 3590 M12170 AMIT_EGF_RESPONSE_480_MCF10A http://www.broadinstitute.org/gsea/msigdb/cards/AMIT_EGF_RESPONSE_480_MCF10A.html Genes whose expression peaked at 480 min after stimulation of MCF10A cells with EGF [GeneID=1950]. 17322878 50/56 Leona Saunders 0.256268519145583 0.318815869891183 4480 3001.45454545455 3156 0.0265569238592482 1554 1.25062816281575 -1.20898050097641 -1 0.931547491512957 4476 3335 1974 4182 2388 2505 3156 3689 2026 1554 3731 3591 M5389 RODWELL_AGING_KIDNEY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODWELL_AGING_KIDNEY_UP.html Genes whose expression increases with age in normal kidney. 15562319 568/819 John Newman 0.000262536706535363 0.00143257023681724 4410 3173.36363636364 3156 2.62567728178582e-05 332 1.24197402250442 -1.1805012535353 -1 5.29977628931573 4406 3156 4495 3017 2753 2831 4451 3565 3304 332 2597 3592 M687 LIN_NPAS4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIN_NPAS4_TARGETS_UP.html Genes up-regulated in neurons after NPAS4 [GeneID=266743] knockdown by RNAi. 18815592 200/291 Jessica Robertson 0.208743521759241 0.268535184708645 3970 2883.63636363636 3156 0.0210599056013915 572 1.01915209582776 -0.946446857107711 -1 0.873098758541131 3966 572 2512 829 2253 3228 4701 3851 2292 3156 4360 3593 M17681 BIOCARTA_IL3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL3_PATHWAY.html IL 3 signaling pathway 27/29 BioCarta 0.11874522823384 0.166659969451004 2595 3055.63636363636 3157 0.0114259055549313 1035 0.810383752794297 -0.864002826450651 -1 0.946145045354794 2594 4185 3365 3677 2717 1893 3157 2347 4675 3967 1035 3594 M15884 NIKOLSKY_BREAST_CANCER_7P22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_7P22_AMPLICON.html Genes within amplicon 7p22 identified in a copy number alterations study of 191 breast tumor samples. 19010930 51/58 Jessica Robertson 0.310345889002347 0.374254623426438 2795 3102.09090909091 3157 0.0332145162880927 1375 1.01714542941916 -1.12228548721818 -1 0.65134654759225 2792 4106 3313 4056 4319 1375 1880 2665 3657 3157 2803 3595 M13696 DAUER_STAT3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAUER_STAT3_TARGETS_DN.html Top 50 genes down-regulated in A549 cells (lung cancer) expressing STAT3 [GeneID=6774] off an adenovirus vector. 15735721 71/106 Arthur Liberzon 0.68618940391 0.690284310838704 3030 3122.36363636364 3159 0.1 2207 1.02202584128445 1.0220785634645 1 0.246756044320739 3028 2410 2207 3170 4529 3196 3171 3969 3159 2643 2864 3596 M5236 ROSS_AML_WITH_CBFB_MYH11_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/ROSS_AML_WITH_CBFB_MYH11_FUSION.html Top 63 probe sets for pediatric acute myeloid leukemia (AML) subtype inv(16); has a CBFB-MYH11 fusion [GeneID=865;4629]. 15226186 59/91 Kate Stafford 0.0683699849830033 0.104911030273009 3160 3164.90909090909 3159 0.00641745801981981 1131 1.11009121236783 1.29012920181338 1 1.63092622734382 3159 2876 1131 3487 2922 4100 2942 4042 3894 2620 3641 3597 M15187 GENTILE_UV_RESPONSE_CLUSTER_D6 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D6.html Cluster d6: genes progressively down-regulated in WS1 cells (fibroblast) through 18 h after irradiation with high dose UV-C. 12907719 51/54 John Newman 0.385259243810611 0.453925020166272 3500 3208.72727272727 3159 0.0432682592480103 682 1.13348435134901 -1.1464596603488 -1 0.583301072442878 3496 2900 3148 2915 2643 4552 3614 3767 682 3159 4420 3598 M611 REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NOTCH1_INTRACELLULAR_DOMAIN_REGULATES_TRANSCRIPTION.html Genes involved in NOTCH1 Intracellular Domain Regulates Transcription 50/56 Reactome 0.46036232838753 0.529590589809686 4070 3090.27272727273 3160 0.0545345568267122 648 0.993649188163719 -0.83281036197513 -1 0.411496635973374 4070 3736 2899 2660 3160 4348 3372 2382 648 3116 3602 3599 M732 REACTOME_SLBP_DEPENDENT_PROCESSING_OF_REPLICATION_DEPENDENT_HISTONE_PRE_MRNAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SLBP_DEPENDENT_PROCESSING_OF_REPLICATION_DEPENDENT_HISTONE_PRE_MRNAS.html Genes involved in SLBP Dependent Processing of Replication-Dependent Histone Pre-mRNAs 11/14 Reactome 0.215357737371801 0.275321917766767 2410 3260 3160 0.0218066643490993 1372 0.489172308929783 -0.489172308929783 -1 0.411058242770031 2409 4251 3724 4558 3001 2303 1372 3160 3771 4542 2769 3600 M1619 RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_UP.html Genes up-regulated in the brain cortex of mice that were exposed to an enriched learning environment for one day. 11070096 30/36 John Newman 0.00418856270490341 0.0115798081839164 3090 3267.45454545455 3160 0.000381505327025996 661 0.831351002678724 0.910807111810792 1 2.41534706684591 3086 4515 3160 4496 661 2367 3058 2487 4601 4044 3467 3601 M17500 CHESLER_BRAIN_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_QTL_CIS.html Best cis-regulated quantitative trait loci (QTLs) in the mouse genome which modulate transcription in brain tissue. 15711545 84/108 Jean Junior 0.0280926803479239 0.0501503219524209 3120 3011.54545454545 3161 0.0025870867281023 716 0.886312325192558 -0.863696410790169 -1 1.72843839739085 3120 4055 3161 3999 4394 716 2706 880 4336 4096 1664 3602 M15147 BOYAULT_LIVER_CANCER_SUBCLASS_G12_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G12_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G12, defined by unsupervised clustering 17187432 53/64 Yujin Hoshida 0.00121406298770379 0.00457125844069806 4610 2719.63636363636 3163 0.00011043031659688 430 0.900183836871203 -0.824891363126668 -1 3.16058660523521 4607 1400 3163 837 430 4652 3962 3277 1184 3541 2863 3603 M2424 YANG_BCL3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/YANG_BCL3_TARGETS_UP.html Genes up-regulated in neonatal cardiac myocytes upon knockdown of BCL3 [GeneID=602] by RNAi. 19451226 458/593 Arthur Liberzon 2.21118417544065e-07 3.7407846982365e-06 3885 2969 3164 2.01016763425745e-08 230 1.24795253842669 1.34004948814727 1 10.1624438724985 3883 3164 230 1958 2783 4583 4251 4135 2709 250 4713 3604 M17905 ELVIDGE_HIF1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ELVIDGE_HIF1A_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) after knockdown of HIF1A [GeneID=3091] by RNAi. 16565084 83/93 Arthur Liberzon 0.0713571783621245 0.108507049571272 3165 2749.18181818182 3165 0.00670750271867378 1266 1.05153303632645 -1.05994376182879 -1 1.52179338936406 3165 3265 3174 2139 3653 2731 3482 1266 1583 3421 2362 3605 M1539 MCCLUNG_COCAINE_REWARD_5D http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_COCAINE_REWARD_5D.html Genes up-regulated in the nucleus accumbens (a major reward center in the brain) after 5 days of cocaine [PubChem=5760] treatment. 14566342 121/143 John Newman 0.239066435604419 0.300104674482142 3295 2928.54545454545 3167 0.0245312968389193 562 1.07776948978881 1.0479768439971 1 0.84525637434582 3293 1272 1416 562 4554 3459 3167 4320 2484 2983 4704 3606 M4491 CROONQUIST_NRAS_VS_STROMAL_STIMULATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_VS_STROMAL_STIMULATION_DN.html Genes down-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing an activated form of NRAS [GeneID=4893] off a plasmid vector compared to those co-cultured with bone marrow stromal cells. 12791645 148/194 Arthur Liberzon 0.0237635186665994 0.0435587604296501 2235 2855.54545454545 3167 0.00218401387891735 950 1.29953101824037 1.29853182750521 1 2.65365932490465 2233 4020 950 4147 2812 3167 3553 2243 3795 1147 3344 3607 M14899 BIOCARTA_AT1R_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AT1R_PATHWAY.html Angiotensin II mediated activation of JNK Pathway via Pyk2 dependent signaling 50/56 BioCarta 0.213405387842831 0.273481790637726 4000 3162.18181818182 3168 0.021585646574611 903 0.916029163353483 -0.808125837334026 -1 0.773847408250619 3996 2899 3168 2786 2271 3891 2522 3955 903 3718 4675 3608 M1050 REACTOME_PHOSPHORYLATION_OF_THE_APC_C http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PHOSPHORYLATION_OF_THE_APC_C.html Genes involved in Phosphorylation of the APC/C 22/24 Reactome 0.059064420264202 0.092588529939234 1990 2952.54545454545 3168 0.00551931241824356 1103 0.50790275061058 -0.495950330305711 -1 0.787499820114877 1988 3484 3944 4095 1585 1861 1103 3168 3768 4613 2869 3609 M17788 LINDGREN_BLADDER_CANCER_CLUSTER_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_1_DN.html Down-regulated genes whose expression profile is specific to Custer I of urothelial cell carcinoma (UCC) tumors. 16532037 527/653 Leona Saunders 0.185479252247409 0.242644698062021 2450 2840.18181818182 3168 0.0203065259516252 1184 1.17277506230057 1.23371650128199 1 1.08220564493349 2447 3601 4334 3168 3194 1871 3324 2475 1729 1184 3915 3610 M789 BROWNE_HCMV_INFECTION_4HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_4HR_DN.html Genes down-regulated in primary fibroblast cell culture point after infection with HCMV (AD169 strain) at 4 h time point that were not down-regulated at the previous time point, 2 h. 11711622 398/570 Arthur Liberzon 0.606640383584477 0.67277786901286 3520 3253.81818181818 3168 0.0813232897750328 2279 1.09356815966299 1.09589973573865 1 0.282343114369904 3519 3168 2579 2673 2994 4693 3570 3471 2279 2592 4254 3611 M2226 PILON_KLF1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PILON_KLF1_TARGETS_UP.html Genes up-regulated in erythroid progenitor cells from fetal livers of E13.5 embryos with KLF1 [GeneID=10661] knockout compared to those from the wild type embryos. 18852285 672/853 Arthur Liberzon 0.0284237401640941 0.0505882554956728 2700 2878.54545454545 3168 0.00287939818269013 774 1.17300957819693 1.14423182820163 1 2.28092792762382 2699 2206 4668 1313 1331 4336 3253 3669 3168 774 4247 3612 M751 REACTOME_DARPP_32_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DARPP_32_EVENTS.html Genes involved in DARPP-32 events 29/30 Reactome 0.68618940391 0.690284310838704 2935 2961.90909090909 3172 0.1 352 0.974880329985759 0.884339477169656 1 0.235368436780373 2932 924 3310 1911 4409 3637 4291 4684 352 2959 3172 3613 M12591 ROME_INSULIN_TARGETS_IN_MUSCLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROME_INSULIN_TARGETS_IN_MUSCLE_UP.html Genes up-regulated by 3 h of euglycemic hyperinsulinemic clamp in the vastus lateralis muscle of healthy lean subjects. 12621037 576/722 Jessica Robertson 0.286143823397038 0.350168225676438 4435 3160.27272727273 3173 0.0331456129475028 1140 0.878832113491109 -0.821933471966927 -1 0.600858821534285 4433 1140 4619 1396 2502 2669 3840 4667 1920 4404 3173 3614 M7946 KEGG_NOTCH_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NOTCH_SIGNALING_PATHWAY.html Notch signaling pathway 47/52 KEGG 0.585694277557355 0.652153099804368 4355 3380.90909090909 3175 0.0769802499722001 1891 1.06685986364318 0.936241862990998 1 0.29709167870728 4353 3351 3166 3133 3175 4438 4528 2598 1891 2589 3968 3615 M14577 HAHTOLA_SEZARY_SYNDROM_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_SEZARY_SYNDROM_UP.html Genes up-regulated in monocytes isolated from peripheral blood samples of Sezary syndrom patients compared to those from healthy normal donors. 16914566 111/196 Arthur Liberzon 0.536918903205719 0.605268025586576 3910 2638.09090909091 3175 0.0675937270582493 604 1.13074814918489 -1.215258829637 -1 0.369865699145806 3907 664 2286 604 3274 4657 3175 3567 1364 1579 3942 3616 M11048 RIZ_ERYTHROID_DIFFERENTIATION_CCNE1 http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_CCNE1.html Selected gradually up-regulated genes whose expression profile follows that of CCNE1 [GeneID=898] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 46/57 Leona Saunders 0.47247688674097 0.542469205890873 2980 3100.36363636364 3175 0.0564840926341543 679 0.800580421739596 0.88783982767582 1 0.318985921001261 2980 2917 3744 3383 4565 2777 1963 3921 679 4000 3175 3617 M10209 SHEPARD_BMYB_MORPHOLINO_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_BMYB_MORPHOLINO_UP.html Human orthologs of genes up-regulated in zebra fish after knockdown of BMYB [GeneID=4605] by morpholino. 16150706 254/302 Jennifer Shepard 0.66830989366731 0.690284310838704 4635 3348.09090909091 3176 0.0954548926948743 2084 1.03178822708703 -0.963206037936929 -1 0.249114067706529 4633 3176 3065 2881 3930 2084 4375 3982 2733 3282 2688 3618 M2371 WACKER_HYPOXIA_TARGETS_OF_VHL http://www.broadinstitute.org/gsea/msigdb/cards/WACKER_HYPOXIA_TARGETS_OF_VHL.html Genes down-regulated by VHL [GeneID=7428] and re-expressed under hypoxia conditions in renal carcinoma cells. 19158274 21/23 Arthur Liberzon 0.280419597346548 0.344273836957841 2185 3142.90909090909 3176 0.0294739170949377 1608 1.44469857401209 1.48510436612524 1 1.00379326941461 2185 4217 2362 4399 3016 3176 3219 3918 3143 3329 1608 3619 M916 REACTOME_PLATELET_HOMEOSTASIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PLATELET_HOMEOSTASIS.html Genes involved in Platelet homeostasis 64/91 Reactome 0.0279598072418256 0.0499509046863804 3150 2644.36363636364 3178 0.00257469112821847 977 1.17392141696539 -1.06442905757953 -1 2.29240047487037 3148 1896 977 1037 3408 3710 3218 3188 3178 1071 4257 3620 M614 REACTOME_PRE_NOTCH_PROCESSING_IN_GOLGI http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRE_NOTCH_PROCESSING_IN_GOLGI.html Genes involved in Pre-NOTCH Processing in Golgi 22/24 Reactome 0.342046111985023 0.408723455334002 4405 3235.72727272727 3181 0.0373413571356827 2158 1.10474247186671 -1.06865387072145 -1 0.644022822975608 4405 3041 2336 3118 3583 3756 3624 2158 3181 2879 3512 3621 M7825 BIOCARTA_ACTINY_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ACTINY_PATHWAY.html Y branching of actin filaments 29/36 BioCarta 0.0124829399505833 0.0260360037855736 4230 3160.45454545455 3182 0.00114130334070839 993 1.05949290378675 -1.17614175422489 -1 2.51879884276643 4229 3443 2844 2735 993 3182 4080 3833 2782 2102 4542 3622 M11190 KEGG_DORSO_VENTRAL_AXIS_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DORSO_VENTRAL_AXIS_FORMATION.html Dorso-ventral axis formation 25/28 KEGG 0.68618940391 0.690284310838704 3785 2968.81818181818 3183 0.1 634 0.830952021632064 -0.706516494763916 -1 0.200603746689376 3783 1505 3183 1131 3345 4319 4173 2863 634 3134 4587 3623 M10245 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP.html Genes up-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic D.B. Chr 3 (DB, small HSC population) vs parental D2 strain (huge HSC population). 17220891 45/53 Leona Saunders 0.148709774617032 0.20112038286315 3765 2796.72727272727 3183 0.0145299669745378 411 1.18957800282977 -1.19880520611012 -1 1.24321507308384 3764 1955 3371 1855 2060 3733 4522 3755 411 3183 2155 3624 M5536 TCGA_GLIOBLASTOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/TCGA_GLIOBLASTOMA_COPY_NUMBER_UP.html Genes up-regulated and displaying increased copy number in glioblastoma samples. 18772890 89/106 Jessica Robertson 0.585631938389896 0.652153099804368 3085 3217.27272727273 3183 0.0769676250510762 2597 0.93623741811845 -0.877009511347478 -1 0.260703895818483 3083 2828 3524 3217 3828 3183 3075 2597 2627 3617 3811 3625 M1367 BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_C_CLUSTER_UP.html Genes from cluster 1: up-regulated in group C of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 45/52 Jessica Robertson 0.620691351259255 0.686103788745593 3915 3068.36363636364 3184 0.084356085835247 906 1.23455646207063 1.16886963841965 1 0.302978230921488 3912 2922 2524 3755 4392 2210 2243 4507 906 3184 3197 3626 M10582 STAEGE_EWING_FAMILY_TUMOR http://www.broadinstitute.org/gsea/msigdb/cards/STAEGE_EWING_FAMILY_TUMOR.html Genes up-regulated in Ewing family tumors (EFT) compared with normal bone marrow samples. 15548687 28/44 Kevin Vogelsang 0.00506443516843006 0.0134742489612886 3880 2763.18181818182 3186 0.000461466481006641 376 1.55010115765095 -1.26302583094572 -1 4.35058779266614 3880 3431 1215 3493 4247 3186 1795 376 2890 2024 3858 3627 M15912 HAMAI_APOPTOSIS_VIA_TRAIL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAMAI_APOPTOSIS_VIA_TRAIL_DN.html Genes down-regulated in T1 cells (primary melanoma, sensitive to TRAIL [GeneID=8743]) compared to G1 cells (metastatic melanoma, resistant to TRAIL). 16983347 213/337 Leona Saunders 0.0233079966184411 0.0428736336862985 3830 2953.90909090909 3187 0.00214169637456021 1201 1.11108095402546 -1.0994390291903 -1 2.28030551680458 3827 3187 1309 3054 1201 3902 4338 3267 2474 2211 3723 3628 M525 REACTOME_ENDOSOMAL_VACUOLAR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOSOMAL_VACUOLAR_PATHWAY.html Genes involved in Endosomal/Vacuolar pathway 22/38 Reactome 0.116973960153942 0.164565452139078 1230 3167.54545454545 3189 0.0112454364327745 1227 0.687432425654149 -0.687432425654149 -1 0.808245656997259 1227 4557 3189 4125 1911 2132 3561 3024 4677 4116 2324 3629 M562 REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GRB2_EVENTS_IN_ERBB2_SIGNALING.html Genes involved in GRB2 events in ERBB2 signaling 28/28 Reactome 0.540813415483948 0.6090764307049 4490 3075.09090909091 3189 0.0683093338529523 635 1.04167846892376 -0.718615213257072 -1 0.33646495904267 4486 3827 2831 1668 2892 4127 3996 3189 635 2439 3736 3630 M8516 BIOCARTA_PITX2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PITX2_PATHWAY.html Multi-step Regulation of Transcription by Pitx2 20/25 BioCarta 0.287521510867051 0.351671814276361 1790 3048.81818181818 3190 0.0303486325498515 1329 0.558523348479821 0.497829645530122 1 0.380265158954938 1789 3873 3598 4596 3190 1329 1792 2459 4699 4500 1712 3631 M144 PID_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CERAMIDE_PATHWAY.html Ceramide signaling pathway 18832364 64/69 Pathway Interaction Database 0.68618940391 0.690284310838704 3875 2670.18181818182 3190 0.1 455 0.900086428961715 -0.747814508047154 -1 0.217302589835185 3872 755 2792 616 3551 4071 3574 3190 455 1995 4501 3632 M9728 BARRIER_COLON_CANCER_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_COLON_CANCER_RECURRENCE_UP.html Up-regulated genes from the 70-gene prognosis predictor for stage 2 colon cancer, based on non-neoplastic mucosa gene expression profiles. 17043639 47/59 Arthur Liberzon 0.00246651581024886 0.00782915576622368 3510 2815.81818181818 3190 0.000224480497889828 549 1.1785665133987 -1.12623996569879 -1 3.72478075986317 3509 3748 3190 3153 549 3210 3392 2797 939 3591 2896 3633 M10839 BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_DN.html Down-regulated genes in MDA-MB-435 cells (breast cancer) undergoing G2/M arrest after treatment with 2-methoxyestradiol (2ME2) [PubChem=1573]. 17234781 183/294 Jessica Robertson 0.252818151293656 0.315187975199699 2380 3023.09090909091 3190 0.0261472360690673 1527 1.03662330551394 1.05123341333041 1 0.779856096647387 2377 4348 3213 4382 3359 1801 2647 3391 3019 3190 1527 3634 M2278 ISHIDA_TARGETS_OF_SYT_SSX_FUSIONS http://www.broadinstitute.org/gsea/msigdb/cards/ISHIDA_TARGETS_OF_SYT_SSX_FUSIONS.html Genes down-regulated in synovial sarcoma samples with SYT-SSX fusions resulting from translocation of SS18 [GeneID=SS18] to one of the SSX genes. 17101797 8/8 Arthur Liberzon 0.612198124898186 0.678304025708788 4145 3344.81818181818 3191 0.0903779269690955 2382 0.783013818339731 -0.689237118123634 -1 0.197958362543471 3196 3118 4678 2598 4159 4143 2553 4143 3191 2632 2382 3635 M17770 BIOCARTA_CELLCYCLE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELLCYCLE_PATHWAY.html Cyclins and Cell Cycle Regulation 26/30 BioCarta 0.107206840049249 0.152875010583823 2915 3238.81818181818 3192 0.0102561657431459 1861 0.98653778220133 -0.76634206388054 -1 1.20733695309661 2915 3445 3038 1929 1861 4063 3697 4576 2995 3192 3916 3636 M1640 YIH_RESPONSE_TO_ARSENITE_C1 http://www.broadinstitute.org/gsea/msigdb/cards/YIH_RESPONSE_TO_ARSENITE_C1.html Genes in cluster 1: strongly up-regulated in HFW cells (fibroblast) upon treatment with sodium arsenite [PubChem=26435] at all time points. 12016162 47/53 John Newman 0.118179661610894 0.165964892235471 3195 3147.27272727273 3192 0.0113682458821841 1800 1.45883197204245 -2.15256674647439 -1 1.70728383638351 4495 3760 1800 3220 1920 3195 3192 3187 4264 2940 2647 3637 M15659 RASHI_RESPONSE_TO_IONIZING_RADIATION_5 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_5.html Cluster 5: early responding genes activated in ATM [GeneID=472] deficient but not in the wild type tissues. 16314843 203/258 Arthur Liberzon 0.0235859580018523 0.0433005530022337 3945 3061.18181818182 3193 0.00216751655128299 1208 1.05034995816976 -1.10647469559865 -1 2.14887757648373 3942 2761 2684 3193 1208 3200 3768 4596 2346 2733 3242 3638 M1922 MIKKELSEN_PLURIPOTENT_STATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_PLURIPOTENT_STATE_UP.html Genes up-regulated in the induced pluripotent cells (iPS) and embryonic stem cells (ES) compared to the parental lineage-committed and partially reprogrammed cell lines. 18509334 11/22 Jessica Robertson 0.424364110062401 0.495423843555413 4145 3395.90909090909 3193 0.0489677149808509 1587 0.411346272498631 0.411346272498631 1 0.188164595560108 4145 2638 3626 2944 4292 1587 3006 3184 3193 4699 4041 3639 M12175 BENNETT_SYSTEMIC_LUPUS_ERYTHEMATOSUS http://www.broadinstitute.org/gsea/msigdb/cards/BENNETT_SYSTEMIC_LUPUS_ERYTHEMATOSUS.html Genes significantly up-regulated in the blood mononuclear cells from patients with systemic lupus erythematosus compared to those from healthy persons. 12642603 33/109 Kevin Vogelsang 0.68618940391 0.690284310838704 3090 3220.81818181818 3194 0.1 1469 0.976003087359181 -0.860789739398619 -1 0.23563962951918 4078 1469 2356 3090 3858 4281 4091 3905 3090 2017 3194 3640 M711 REACTOME_ENOS_ACTIVATION_AND_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENOS_ACTIVATION_AND_REGULATION.html Genes involved in eNOS activation and regulation 26/31 Reactome 0.0695771762129826 0.106486469431024 4065 3122.18181818182 3195 0.00653456958854971 1655 1.04392493866244 -0.875624809622863 -1 1.52356967321836 4061 3451 2200 4027 1655 3070 3294 2760 3586 3195 3045 3641 M14027 NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/NING_CHRONIC_OBSTRUCTIVE_PULMONARY_DISEASE_DN.html Down-regulated genes in lung tissue of smokers with chronic obstructive pulmonary disease (COPD) vs smokers without disease (GOLD-2 vs GOLD-0). 15469929 184/270 Kate Stafford 0.68618940391 0.690284310838704 2635 3225.36363636364 3195 0.1 1994 1.02459710272417 1.09891956795967 1 0.247377111212423 2635 3195 1994 2976 4104 4155 3396 2787 3640 3057 3540 3642 M1748 ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHENG_FOXP3_TARGETS_IN_T_LYMPHOCYTE_UP.html Genes with promoters bound by FOXP3 [GeneID=50943] and which are up-regulated only in mature (peripheral blood) regulatory CD4+ [GeneID=920] T lymphocytes. 17237761 11/14 Jessica Robertson 0.0506422695875908 0.0816093230175336 4115 3128.36363636364 3197 0.00471336581629597 696 0.728227486392016 -0.850084997454869 -1 1.18905783943654 4112 4619 3197 4379 2317 2041 696 2593 4415 3729 2314 3643 M3698 SEIKE_LUNG_CANCER_POOR_SURVIVAL http://www.broadinstitute.org/gsea/msigdb/cards/SEIKE_LUNG_CANCER_POOR_SURVIVAL.html The 'CLASS-11' set of pro- and anti-inflammatory cytokines whose expression identifies stage I lung adenocarcinoma patients with poor prognosis. 17686824 4/10 Jessica Robertson 0.6513215599 0.690284310838704 3730 3093.90909090909 3197 0.1 529 1.98847250391376 -2.80046009529594 -1 0.480193226346252 3727 3142 4629 3073 3648 4094 2377 3197 529 1861 3756 3644 M2909 REACTOME_PYRIMIDINE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PYRIMIDINE_METABOLISM.html Genes involved in Pyrimidine metabolism 22/29 Reactome 0.122053015294475 0.170693402130347 1480 2867.18181818182 3198 0.0117638106249881 1479 0.903832040368871 -0.903832040368871 -1 1.04117574569644 1479 4544 3198 4366 3402 1726 1694 1521 3479 3836 2294 3645 M772 REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_II_TRANSCRIPTION_PRE_INITIATION_AND_PROMOTER_OPENING.html Genes involved in RNA Polymerase II Transcription Pre-Initiation And Promoter Opening 40/47 Reactome 0.0909209986835184 0.133151447032642 1750 3128.72727272727 3199 0.00862831317663481 1742 0.596954264003038 -0.551064170452275 -1 0.784254207190382 1746 4490 4099 4127 1782 1742 1772 3199 3837 4553 3069 3646 M1906 VANASSE_BCL2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANASSE_BCL2_TARGETS_UP.html Genes up-regulated in primary B lymphocytes engineered to overexpress BCL2 [GeneID=12043]. 15561778 45/78 Arthur Liberzon 0.0893746344839719 0.13117172722772 3855 2883.36363636364 3199 0.00847512740552464 1172 1.38465618903683 1.39470819957227 1 1.83276139300276 3851 3759 1172 3069 3512 3199 2037 2378 3773 1282 3685 3647 M2483 REICHERT_MITOSIS_LIN9_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/REICHERT_MITOSIS_LIN9_TARGETS.html Genes with known mitosis function that were down-regulated in MEF cells (embryonic fibroblast) upon knockout of LIN9 [GeneID=286826]. 20404087 33/33 Arthur Liberzon 0.505399553773003 0.574262372125319 2065 3162.63636363636 3202 0.0619954286852964 1682 1.00196727321957 -1.34409368267741 -1 0.362065000702293 2065 4150 3821 3809 2832 2732 2155 4084 1682 4257 3202 3648 M2661 REACTOME_REGULATED_PROTEOLYSIS_OF_P75NTR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATED_PROTEOLYSIS_OF_P75NTR.html Genes involved in Regulated proteolysis of p75NTR 13/13 Reactome 0.431168420677291 0.499814448548158 3975 2919.81818181818 3204 0.0499952192915804 1330 0.980486088438818 0.759592592706303 1 0.443018418604697 3974 3529 2927 1330 3239 2223 3516 3651 3204 2572 1953 3649 M19844 VALK_AML_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_1.html Top 40 genes from cluster 1 of acute myeloid leukemia (AML) expression profile; 57% of the samples are FAB M1 subtype, 43% have 11q23 abnormalities, and 36% have up-regulated EVI1 [GeneID=2122] expression. 15084694 30/45 Jessica Robertson 0.018589508800369 0.035725766098429 3510 2610.09090909091 3204 0.00170440633327015 1107 1.40692583527967 -1.37470014578047 -1 3.05472441431322 3204 3411 1107 3506 1130 3510 1614 4161 2542 1177 3349 3650 M6355 BIOCARTA_ECM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ECM_PATHWAY.html Erk and PI-3 Kinase Are Necessary for Collagen Binding in Corneal Epithelia 45/51 BioCarta 0.197987627975274 0.256238443664188 3785 3013.27272727273 3205 0.01985757465076 1534 1.00171850180805 -0.971555671169968 -1 0.888760183513064 3784 2470 3205 1672 2229 4412 4095 3938 1534 1819 3988 3651 M12751 MIZUKAMI_HYPOXIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MIZUKAMI_HYPOXIA_DN.html Genes down-regulated in DLD-1 cells (colon cancer) in response to hypoxia; might not be direct targets of HIF1A [GeneID=3091]. 16127434 11/13 Jessica Robertson 0.0434896750008112 0.0716692298844914 4305 2732.72727272727 3205 0.00403399563650542 200 1.76494204662979 -1.7457733613084 -1 3.03135192315436 4301 1594 1050 1254 3205 3518 4436 4140 200 1721 4641 3652 M1079 REACTOME_APC_CDC20_MEDIATED_DEGRADATION_OF_NEK2A http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_CDC20_MEDIATED_DEGRADATION_OF_NEK2A.html Genes involved in APC-Cdc20 mediated degradation of Nek2A 26/31 Reactome 0.0149360697437206 0.0301790450301204 2525 3110.63636363636 3207 0.00136713154148454 1047 0.681847219738652 -0.709464661381345 -1 1.55534615423885 2522 3472 3879 3637 1047 2990 3207 2564 4245 4180 2474 3653 M19805 LI_CYTIDINE_ANALOGS_CYCTOTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/LI_CYTIDINE_ANALOGS_CYCTOTOXICITY.html Genes whose expression in a panel of lymphoblastoid cell lines was associated with cytotoxicity of the anti-cancer analogs of cytidine, gemcitabine and cytarabine [PubChem=596;3461;6253]. 18757419 17/18 Jessica Robertson 0.0901803074150744 0.132230832867086 3875 2754.27272727273 3208 0.00855490936068711 921 0.747628999160231 -0.695447443960215 -1 0.985611508138925 3875 3513 3508 2174 2025 2157 921 4348 1041 3527 3208 3654 M16036 CHANDRAN_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANDRAN_METASTASIS_UP.html Genes up-regulated in metastatic tumors from the whole panel of patients with prostate cancer. 17430594 267/361 Arthur Liberzon 0.359816382232124 0.428007390155147 1085 2986.81818181818 3208 0.0397345059529555 1081 0.961317620210857 0.976615956003611 1 0.531517014007863 1081 4333 3948 4153 4251 1546 1720 2659 3208 4158 1798 3655 M16720 GOERING_BLOOD_HDL_CHOLESTEROL_QTL_CIS http://www.broadinstitute.org/gsea/msigdb/cards/GOERING_BLOOD_HDL_CHOLESTEROL_QTL_CIS.html Top scoring cis-regulated QTL (quantitative trait loci) influencing blood levels of high-density lipoprotein (HDL) cholesterol. 17873875 15/25 Leona Saunders 0.253460878610891 0.315739072853895 4225 3296.45454545455 3209 0.0262234213250348 2382 1.1186471355646 -0.913701517821771 -1 0.840297845159927 4225 3525 2613 2591 2382 2944 4137 4410 2818 3407 3209 3656 M5813 WU_HBX_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_1_DN.html Genes down-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in SK-Hep-1 cells (hepatocellular carcinoma). 11439330 39/40 John Newman 0.146863578079288 0.199137055022763 1275 2821 3210 0.0143358679800619 1149 0.778135491616975 0.847147738088925 1 0.818209755206108 1273 3374 3466 3210 3434 1626 1149 3089 4578 3849 1983 3657 M969 SCHUHMACHER_MYC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHUHMACHER_MYC_TARGETS_DN.html Genes down-regulated in P493-6 cells (Burkitt's lymphoma) induced to express MYC [GeneID=4609]. 11139609 7/8 Yujin Hoshida 0.00100084474114526 0.00397307584373897 2270 3243 3212 0.000100129578766376 412 0.634497927478686 0.507072762000595 1 2.28570997011035 2266 3570 4475 3058 412 3212 1922 4710 4665 4671 2712 3658 M1918 WEST_ADRENOCORTICAL_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_UP.html Up-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 429/516 Jessica Robertson 0.664039181668259 0.690284310838704 3275 3256.09090909091 3212 0.094402259968179 2103 1.00994316910982 -0.986209896622776 -1 0.243837574990924 3272 3972 3849 3917 3081 2302 2811 3212 2103 4134 3164 3659 M936 REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF6_MEDIATED_IRF7_ACTIVATION.html Genes involved in TRAF6 mediated IRF7 activation 18/36 Reactome 0.534328664070222 0.602924048389062 2625 3343.45454545455 3213 0.067120800573743 2081 0.67704203377788 0.703894896138709 1 0.223128721287613 2623 4219 3217 4186 3213 2771 2081 2897 4567 4006 2998 3660 M7182 KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) with early recurrence. 15288478 24/42 Yujin Hoshida 0.405002846176058 0.474581289461518 2095 3249.90909090909 3213 0.0461032843411083 2049 0.950969283105231 -0.690739927684359 -1 0.461782257078613 2093 4533 3046 3213 2680 2049 3289 4151 4327 3506 2862 3661 M278 PID_RAC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RAC1_PATHWAY.html RAC1 signaling pathway 18832364 73/83 Pathway Interaction Database 0.442770867747966 0.511723431873262 3460 3150 3215 0.0517733329216947 1921 0.873593134444709 -0.932566279996038 -1 0.381303507298341 3456 2856 3636 3215 3103 3374 4325 2356 1921 4041 2367 3662 M5652 FARMER_BREAST_CANCER_BASAL_VS_LULMINAL http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_BASAL_VS_LULMINAL.html Genes which best discriminated between two groups of breast cancer according to the status of ESR1 and AR [GeneID=2099;367]: basal (ESR1- AR-) and luminal (ESR1+ AR+). 15897907 450/582 Leona Saunders 6.19263826514921e-05 0.000448990055476256 3740 2405.90909090909 3215 5.629829622367e-06 257 1.22835041394173 -1.28284123611556 -1 6.17037242551166 3740 508 457 257 3215 4428 4020 4539 1271 417 3613 3663 M2245 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_C http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_C.html Category C genes: p53-independent genes whose expression in the absence of S389 phosphorylation is dissimilar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 141/201 Arthur Liberzon 0.0692272350830967 0.105985257733447 3220 3116.72727272727 3216 0.00650060702424741 1134 1.32495632814035 -1.39376182365416 -1 1.93782663868157 3216 4368 1134 4059 2424 3068 2267 4412 3470 1693 4173 3664 M12001 SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_GOOD_SURVIVAL_A5.html Cluster 5 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts good survival outcome. 18641660 128/191 Arthur Liberzon 0.0161446846870605 0.0320773375078651 3400 3205.36363636364 3217 0.00147858127678974 1069 0.823858796694791 -0.850477353284571 -1 1.84655670119408 3400 3217 3837 3793 1069 2741 4443 3087 2858 3889 2925 3665 M2552 HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_VINCRISTINE_RESISTANCE_B_ALL_DN.html Genes distinguishing vincristine [PubChem=5978] resistant and sensitive B-lineage ALL; here - genes down-regulated in the drug resistant samples. 15295046 18/27 Arthur Liberzon 0.108145846331122 0.153981416193935 2825 2953.90909090909 3217 0.0103508451388498 1351 0.951988384195271 -0.691111405047367 -1 1.16057755292618 2822 3500 2672 3725 1867 3963 3606 2155 1351 3615 3217 3666 M15109 BIOCARTA_GLYCOLYSIS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GLYCOLYSIS_PATHWAY.html Glycolysis Pathway 19/35 BioCarta 0.00537588050404745 0.0140732978253488 2575 2928.72727272727 3218 0.000489914729583368 726 0.903868548032226 1.11485994279516 1 2.51117465628639 2571 3512 3482 3218 726 3905 4510 2179 3041 3684 1388 3667 M2420 WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_WITH_H4K20ME1_MARK.html Genes with promoters bound by both PPARG and RXRA [GeneID=5468, 6256] at 8 (but not 0) day time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte) and that were newly modified by H4K20me1. 19414603 200/219 Arthur Liberzon 0.68618940391 0.690284310838704 4640 3188.63636363636 3218 0.1 1216 0.9555074213236 -0.842893223062259 -1 0.230689071244122 4637 1744 3657 1282 4418 3218 4290 4517 1216 3002 3094 3668 M2761 NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_UP.html Top 100 probe sets contrubuting to the positive side of the 2nd principal component; associated with adipocytic differentiation. 17464315 132/209 Nikolaos Papanikolaou 0.0449762498276438 0.073685490866532 2000 2800.54545454545 3219 0.00417481291258119 1057 1.3194517297921 1.31074163107165 1 2.24232358788015 1998 3219 1057 3250 3721 2682 3935 1648 3525 2137 3634 3669 M12836 BIOCARTA_EPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EPO_PATHWAY.html EPO Signaling Pathway 31/36 BioCarta 0.050091168198028 0.0808585204838208 3220 2681.27272727273 3220 0.0046608557538735 582 0.682715834244881 -0.756592126587734 -1 1.1188513415683 3220 3825 3881 3253 1665 1685 4034 2240 1034 4075 582 3670 M1316 GROSS_HYPOXIA_VIA_ELK3_ONLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_ONLY_DN.html Genes specifically down-regulated in SEND cells (skin endothelium) at hypoxia after knockdown of ELK3 [GeneID=2004] by RNAi. 17704799 55/59 Jessica Robertson 0.0705804426903123 0.107533792607577 3950 2686.18181818182 3220 0.00663200323940531 454 1.203424022559 1.12867206526224 1 1.74869337689886 3947 1397 1562 1741 4316 3798 3220 3566 454 896 4651 3671 M712 REACTOME_MICRORNA_MIRNA_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MICRORNA_MIRNA_BIOGENESIS.html Genes involved in MicroRNA (miRNA) Biogenesis 23/27 Reactome 0.264043083579197 0.326888044944004 2850 3503.63636363636 3221 0.027486425666584 2399 0.577490719893951 -0.577490719893951 -1 0.420685089172649 2848 4563 4001 4646 2399 2496 2503 2943 4387 4533 3221 3672 M1558 BURTON_ADIPOGENESIS_12 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_12.html Strongly down-regulated at 2 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 49/54 John Newman 0.68618940391 0.690284310838704 1515 3162.63636363636 3221 0.1 1513 0.84692524974279 0.694199913314466 1 0.20446194756295 1513 2468 3979 3221 3786 2952 2544 3083 3295 4194 3754 3673 M15425 VANTVEER_BREAST_CANCER_ESR1_DN http://www.broadinstitute.org/gsea/msigdb/cards/VANTVEER_BREAST_CANCER_ESR1_DN.html Down-regulated genes from the optimal set of 550 markers discriminating breast cancer samples by ESR1 [GeneID=2099] expression: ER(+) vs ER(-) tumors. 11823860 317/450 Arthur Liberzon 0.000374407224981601 0.00186654034804554 3225 2493.18181818182 3221 3.40428144271937e-05 309 1.26219926572773 1.15993351153444 1 5.16842746508776 3221 1171 680 309 4602 3272 3719 3934 1762 352 4403 3674 M17837 DASU_IL6_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_DN.html Genes down-regulated in normal fibroblasts in response to IL6 [GeneID=3569]. 15095275 13/15 Arthur Liberzon 0.0114081870494596 0.0241385596508837 1970 2791.81818181818 3221 0.00104252524726181 218 1.034426763953 0.889106720673476 1 2.51021422370064 1967 4247 2883 4007 1327 3622 1299 3610 4309 3221 218 3675 M715 REACTOME_REGULATORY_RNA_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATORY_RNA_PATHWAYS.html Genes involved in Regulatory RNA pathways 26/30 Reactome 0.164712079912699 0.218935797574751 3225 3330 3222 0.0162285832910019 2128 0.577490719893951 -0.577490719893951 -1 0.571533706691975 3222 3864 4030 3891 2128 2431 2439 2915 4219 4535 2956 3676 M16975 NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_UP.html Up-regulated genes in peripheral zone of human pancreatic cancer growing in the pancreas of nude mice compared to that of the tumor from the central zone. 17699763 373/439 Arthur Liberzon 0.296680627660467 0.36081746007663 4720 3388 3222 0.031488504157736 1479 1.106686392119 -1.02344798150739 -1 0.735064751136564 4717 3170 1479 3206 4497 2871 4280 3798 3222 2335 3693 3677 M15671 WALLACE_PROSTATE_CANCER_RACE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_RACE_DN.html Genes down-regulated in prostate cancer samples from African-American patients compared to those from the European-American patients. 18245496 121/165 Jessica Robertson 0.635402455201431 0.690284310838704 3230 3151 3222 0.087642838366413 936 1.20267852338239 -1.28927670575099 -1 0.290391202539986 3227 3222 2653 1597 3035 4617 3664 4241 936 2984 4485 3678 M17123 YAGI_AML_WITH_11Q23_REARRANGED http://www.broadinstitute.org/gsea/msigdb/cards/YAGI_AML_WITH_11Q23_REARRANGED.html Genes specifically expressed in samples from patients with pediatric acute myeloid leukemia (AML) bearing 11q23 rearrangements. 12738660 471/627 Arthur Liberzon 0.361613552312748 0.429820188092715 2950 3281.81818181818 3223 0.0399798853377071 2597 1.00010199976292 -0.956080301146238 -1 0.550210800029605 2950 2712 2597 2694 2601 4566 3314 3282 3223 3829 4332 3679 M9936 PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PAPASPYRIDONOS_UNSTABLE_ATEROSCLEROTIC_PLAQUE_UP.html Genes up-regulated in unstable ateroslerotic plaques compared to the stable ones. 16741146 76/108 Arthur Liberzon 0.0748799506539016 0.11299271205784 3960 3086.63636363636 3224 0.00705064193495784 1524 1.12062871246469 -1.18006716175417 -1 1.59221436988929 3959 4061 1524 2658 1691 3113 3978 4115 4018 1612 3224 3680 M16468 SEIDEN_MET_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SEIDEN_MET_SIGNALING.html Genes down-regulated both in vivo and in vitro upon activation of MET [GeneID=4233] signaling. 16158056 33/41 Arthur Liberzon 0.228127181426225 0.28852811467413 3900 3323.09090909091 3224 0.0232646946308104 1892 1.23219984887053 -1.23516794300398 -1 0.99797424151745 3897 3807 2965 2984 3968 4419 4214 1892 1988 3224 3196 3681 M1410 SCHLOSSER_SERUM_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_SERUM_RESPONSE_DN.html Cluster 4: genes down-regulated in B493-6 cells (B lymphocytes) upon serum stimulation but not affected by MYC [GeneID=4609]. 15516975 937/1138 Leona Saunders 0.6513215599 0.690284310838704 2590 3338.54545454545 3226 0.1 2198 0.983374467350855 1.03294918605472 1 0.237420125266575 2589 2198 4378 2494 3226 3945 3185 3591 2647 4253 4218 3682 M11865 BRUNEAU_SEPTATION_VENTRICULAR http://www.broadinstitute.org/gsea/msigdb/cards/BRUNEAU_SEPTATION_VENTRICULAR.html Genes for which mutations result in developmental defects in ventricular septation and atrioventricular cushion formation, a major class of congenital heart disease. 18288184 11/18 Jessica Robertson 0.209251264891406 0.268972214130566 4165 3149.09090909091 3228 0.0211170293787298 1117 0.858846301327735 -1.04924723943367 -1 0.734839410795304 4164 4623 3634 3228 2711 2964 1347 3015 1117 3730 4107 3683 M16082 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_25 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_25.html Amplification hot spot 25: colocalized fragile sites and cancer genes in the 2q13-q36 region. 16751803 6/11 Arthur Liberzon 4.55976343539212e-05 0.000352821039590997 4545 2525.72727272727 3229 4.55985699958577e-06 14 1.5439983178608 1.85422840756954 1 7.99852155977918 4543 1640 4365 786 92 4085 3858 1062 14 3229 4109 3684 M0 BROWNE_HCMV_INFECTION_30MIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_30MIN_DN.html Genes down-regulated in primary fibroblast cell culture at 30 min time point after infection with HCMV (AD169 strain). 11711622 204/317 Arthur Liberzon 0.0946200093776231 0.137788434561253 3235 2886.18181818182 3229 0.0089957074374825 1182 1.2486811334263 1.20091070965164 1 1.61272633602802 3231 2278 1182 2554 3447 3429 3556 3229 2667 1661 4514 3685 M16516 TESAR_ALK_TARGETS_HUMAN_ES_4D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_HUMAN_ES_4D_DN.html Genes down-regulated in hES cells (human embryonic stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=16079008]. 17597760 2/7 Jessica Robertson 0.00016122544819449 0.000975620660869223 4575 2612.8 3229.5 1.79152224553941e-05 4 1.06542345617866 -1.04786312841486 -1 4.81309837395355 4572 457 4467 NA 178 4694 2972 3487 4 1267 4030 3686 M2098 MARTENS_TRETINOIN_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTENS_TRETINOIN_RESPONSE_UP.html Genes up-regulated in NB4 cells (acute promyelocytic leukemia, APL) in response to tretinoin [PubChem=444795]; based on Chip-seq data. 20159609 683/1518 Arthur Liberzon 6.9425528132173e-16 4.25569471147866e-14 4660 3017.45454545455 3230 6.94255281321734e-17 37 1.41221050248164 -1.47029572635699 -1 28.3337769869189 4500 1672 4656 1683 3233 3230 4659 4386 3068 37 2068 3687 M2811 TESAR_ALK_TARGETS_HUMAN_ES_5D_DN http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_HUMAN_ES_5D_DN.html Genes down-regulated in hES cells (human embryonic stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=4521392]. 17597760 2/10 Jessica Robertson 0.00016122544819449 0.000975620660869223 4575 2613.9 3230.5 1.79152224553941e-05 5 1.06542345617866 -1.04786312841486 -1 4.81309837395355 4573 458 4469 NA 179 4695 2973 3488 5 1268 4031 3688 M879 REACTOME_FATTY_ACID_TRIACYLGLYCEROL_AND_KETONE_BODY_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FATTY_ACID_TRIACYLGLYCEROL_AND_KETONE_BODY_METABOLISM.html Genes involved in Fatty acid, triacylglycerol, and ketone body metabolism 185/250 Reactome 0.0626364084305088 0.0972943365067381 3350 3150.18181818182 3231 0.00586311121485259 1262 0.934620200455767 0.97001764518731 1 1.41901673959743 3346 2766 3231 1262 1610 4519 3985 3694 2480 3098 4661 3689 M14139 FUNG_IL2_SIGNALING_1 http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_SIGNALING_1.html Genes up-regulated by IL2 [GeneID=3558] in both primary thymocytes and T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 10/14 Arthur Liberzon 0.382895558421629 0.451590963455795 1330 3140.63636363636 3231 0.0429344200552803 1328 1.31442896695941 1.31442896695941 1 0.680849466786497 1328 4629 2898 4427 3388 3231 1908 2604 4619 3657 1858 3690 M2382 LIU_TOPBP1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LIU_TOPBP1_TARGETS.html Genes up-regulated in U2OS cells (osteosarcoma) upon knockdown of TOPBP1 [GeneID=11073]. 19289498 18/22 Arthur Liberzon 0.569867540713244 0.637085455273925 4515 3308.36363636364 3231 0.0738291444105062 2099 0.958917703571505 -0.642601379746864 -1 0.281629271432921 4514 2099 2353 2710 3231 4112 3660 2563 4431 3076 3643 3691 M2515 YU_BAP1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/YU_BAP1_TARGETS.html Genes deregulated in U2OS cells (osteosarcoma) upon knockdown of BAP1 [GeneID=8314] by RNAi. 20805357 41/46 Arthur Liberzon 0.168000325433773 0.222554458615608 2020 3108 3232 0.016581285296178 1700 0.941588442209213 1.0412181339525 1 0.921883384355648 2020 3773 3104 4255 3677 1922 1911 1700 4377 4217 3232 3692 M1750 CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_UP http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_REVERTED_UP.html Genes up-regulated in neuroblastoma xenografts: resistant vs those that reverted to be sensitive to the topoisomerase inhibitor irinotecan [PubChem=3750]. 16501609 6/7 Arthur Liberzon 0.00328918466019279 0.00976412050069808 2305 2779.81818181818 3234 0.0003294063257191 136 1.2595105762753 1.2595105762753 1 3.7993285289085 2303 3955 4410 3615 4149 2209 2310 313 3944 3234 136 3693 M2314 DELPUECH_FOXO3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DELPUECH_FOXO3_TARGETS_DN.html Genes down-regulated in DL23 cells (colon cancer) upon expression of an activated form of FOXO3 [GeneID=2309]. 17452451 46/50 Arthur Liberzon 0.68618940391 0.690284310838704 2710 3152.90909090909 3234 0.1 601 1.16721034435592 -1.41950553495172 -1 0.28182415783522 2706 4118 3234 3614 3426 3221 3166 4439 601 3534 2623 3694 M673 REACTOME_SIGNALING_BY_FGFR1_FUSION_MUTANTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_FGFR1_FUSION_MUTANTS.html Genes involved in Signaling by FGFR1 fusion mutants 27/36 Reactome 0.43119990772354 0.499814448548158 3320 2879 3235 0.05 313 0.722820090649496 0.669405608232242 1 0.326567963656346 3316 313 3235 1375 3039 4544 2574 3861 1490 3276 4646 3695 M844 ONDER_CDH1_TARGETS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONDER_CDH1_TARGETS_3_UP.html Genes up-regulated in HMLE cells (immortalized nontransformed mammary epithelial) cells after loss of function of E-cadhedrin (CDH1) [GeneID=999], which was achieved either by RNAi knockdown or by expression of a dominan-negative form of CDH1. 18483246 24/28 Jessica Robertson 0.105599443805346 0.151039204473101 3235 2968.09090909091 3235 0.0100943029379376 1454 1.12230924134636 0.939550480051301 1 1.38234616130483 3235 4184 1820 3048 2385 3960 3773 1454 3410 2112 3268 3696 M2180 PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_UP.html The XPRSS-Int network genes up-regulated in breast tumors from patients with germline mutations in BRCA1 [GeneID=672] compared to those with the wild type allele. 17922014 68/75 Arthur Liberzon 0.68618940391 0.690284310838704 1950 3205.90909090909 3235 0.1 1947 0.707043880990429 -0.753065654119441 -1 0.170674762194038 1947 2417 4047 3235 3386 2757 3106 3400 3409 4366 3195 3697 M2306 SUMI_HNF4A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SUMI_HNF4A_TARGETS.html Genes up-regulated in HepG2 cells (hepatocellular carcinoma, HCC) upon expression of HNF4A [GeneID=3172] and down-regulated upon knockdown of HNF4A [GeneID=3172] in these cells by RNAi. 17403900 24/60 Arthur Liberzon 0.285976081861679 0.350144515275519 4700 3146.18181818182 3235 0.0301576153746277 1465 1.33097695582999 -1.18773157548222 -1 0.9101041003822 4698 3024 1465 2546 3667 3748 3356 2434 3235 2117 4318 3698 M1400 ZEILSTRA_CD44_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZEILSTRA_CD44_TARGETS_DN.html Genes implicated in apoptosis that were down-regulated in duodenum of CD44 [GeneID=960] knockout mice. 18483247 6/8 Jessica Robertson 0.000155370505979866 0.000946256500935444 3685 2778.63636363636 3237 1.55381370046278e-05 2 0.904118101002821 1.02944936119854 1 4.10238373247178 3685 2176 4472 396 170 4558 4600 4361 2 3237 2908 3699 M2299 VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP.html Genes up-regulated in 9.5 days post coitus (dpc) embryos with COMMD1 [GeneID=150684] knockout compared to normal 9.5 dpc embryos. 17371845 96/143 Arthur Liberzon 0.0233778749012945 0.0429559740685516 3895 2622.90909090909 3237 0.0021481868260289 55 1.29568874106592 -1.29846888536959 -1 2.65757925725679 3894 55 946 1193 3237 4684 4355 4522 466 1406 4094 3700 M644 FOURNIER_ACINAR_DEVELOPMENT_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_LATE_UP.html Genes up-regulated late in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 17/24 Arthur Liberzon 0.331371650294078 0.397073924698667 2155 3152.45454545455 3238 0.0359319108199888 1607 1.30863946173498 1.19080537619193 1 0.787566308142504 2153 4582 1607 4566 2545 3288 1741 3238 4624 2990 3343 3701 M109 REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VIRAL_MESSENGER_RNA_SYNTHESIS.html Genes involved in Viral Messenger RNA Synthesis 15/17 Reactome 0.191807438960564 0.249539997765673 1740 3235.45454545455 3240 0.0191733467486329 1740 0.577490719893951 -0.577490719893951 -1 0.522294170721443 1740 4596 3857 4077 2206 2250 2157 2671 4193 4603 3240 3702 M8315 MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_2_DN.html The 'NPM1-mutated signature 2': genes down-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to the AML cases with the intact gene and without recurring cytogenetic anomalities or M7 phenotype. 17597811 98/115 Arthur Liberzon 0.145544635249716 0.197689403849974 3935 3047.81818181818 3240 0.01419743525773 1123 1.31139274836547 -1.26314232032713 -1 1.38523773401831 3931 3240 1266 2842 3139 3784 3904 3304 2987 1123 4006 3703 M2037 KAMMINGA_SENESCENCE http://www.broadinstitute.org/gsea/msigdb/cards/KAMMINGA_SENESCENCE.html Genes down-regulated on serial passage of MEF cells (embryonic fibroblast). 16293602 42/47 Arthur Liberzon 0.680555773550607 0.690284310838704 4450 3325.36363636364 3240 0.098543023944283 2642 1.01138121971134 -0.967099172960027 -1 0.244184924196018 4448 2936 3058 3298 3104 3325 4241 3240 3447 2642 2840 3704 M2244 BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B.html Category B genes: p53-dependent genes whose expression in the absence of S389 phosphorylation is dissimilar to loss of TP53 [GeneID=7157] in MEF (embryonic fibroblast) cells in response to UV-C irradiation. 18195040 677/874 Arthur Liberzon 5.17346164865424e-05 0.000392584228000772 3240 2769.63636363636 3240 5.1735820937751e-06 263 1.19754012907346 1.12823224044398 1 6.12036862765874 3240 1671 4673 466 1651 4668 3593 3989 2900 263 3352 3705 M346 LIN_MELANOMA_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIN_MELANOMA_COPY_NUMBER_UP.html Candidate genes in significant regions of chromosomal copy number gains in a panel of melanoma samples. 18245465 99/112 Jessica Robertson 0.136781841283889 0.187405019117548 2980 3164.90909090909 3241 0.0132826178203197 1811 0.869907300324069 0.906880550505467 1 0.949142565584498 2979 3241 3817 2717 2016 3271 2932 4715 1811 3720 3595 3706 M791 REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1.html Genes involved in Regulation of Insulin Secretion by Glucagon-like Peptide-1 42/55 Reactome 0.487923853968386 0.557762313085682 3245 3107.27272727273 3242 0.059029804327288 1643 1.09344411081198 0.948902103418701 1 0.415903856636574 3242 2933 1787 3527 4631 2249 1994 4113 3754 1643 4307 3707 M7300 BLUM_RESPONSE_TO_SALIRASIB_UP http://www.broadinstitute.org/gsea/msigdb/cards/BLUM_RESPONSE_TO_SALIRASIB_UP.html Selected genes up-regulated in response to the Ras inhibitor salirasib [PubChem=5469318] in a panel of cancer cell lines with constantly active HRAS [GeneID=3265]. 17409441 327/391 Jessica Robertson 0.0762789073535056 0.11473477145749 2205 3038.72727272727 3242 0.00718723834779849 1521 0.92505627602218 0.853440693173584 1 1.3050990326473 2201 3982 3891 3242 1703 1521 1712 4405 2671 4232 3866 3708 M1868 MIKI_COEXPRESSED_WITH_CYP19A1 http://www.broadinstitute.org/gsea/msigdb/cards/MIKI_COEXPRESSED_WITH_CYP19A1.html Nuclear receptors whose expression correlated with that of aromatase (CYP19A1) [GeneID=1588] in a panel of breast cancer biopsies. 17440110 6/9 Jessica Robertson 0.127552423014106 0.176812756718526 3245 3182.54545454545 3243 0.013552596331292 1111 1.23967119392286 1.23967119392286 1 1.3996328905728 2749 4291 4587 4238 3244 2515 2002 2495 4533 3243 1111 3709 M18153 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 9. 12554760 77/91 Arthur Liberzon 0.43119990772354 0.499814448548158 4105 2636.54545454545 3243 0.05 85 0.949147049103386 -0.855315628114267 -1 0.428854945660784 4103 85 2643 310 3412 3850 3597 4215 1409 2135 3243 3710 M783 REACTOME_PROCESSING_OF_CAPPED_INTRONLESS_PRE_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSING_OF_CAPPED_INTRONLESS_PRE_MRNA.html Genes involved in Processing of Capped Intronless Pre-mRNA 27/30 Reactome 0.335983709976954 0.401988114345051 2970 3375.54545454545 3244 0.0365383547906579 1489 0.584070629618989 -0.471839859898434 -1 0.346765552616046 2967 4516 4015 4612 2974 1489 1675 3244 4190 4555 2894 3711 M14985 BASAKI_YBX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BASAKI_YBX1_TARGETS_UP.html Genes up-regulated in SKOC-3 cells (ovarian cancer) after YB-1 (YBX1) [GeneID=4904] knockdown by RNAi. 17072343 348/437 Arthur Liberzon 0.68618940391 0.690284310838704 2690 3067.27272727273 3248 0.1 2204 1.05494526047515 -1.04340945989599 -1 0.25470745720977 2690 3610 3478 2790 3831 2264 2549 3662 2204 3414 3248 3712 M9642 GALLUZZI_PERMEABILIZE_MITOCHONDRIA http://www.broadinstitute.org/gsea/msigdb/cards/GALLUZZI_PERMEABILIZE_MITOCHONDRIA.html Proteins that permeabilize mitochondria. 16892093 53/69 Arthur Liberzon 0.68618940391 0.690284310838704 3745 3264.63636363636 3249 0.1 1927 1.09487234617525 -1.13308592004201 -1 0.264351513868796 3745 1927 2090 2389 3874 4027 4541 4395 2741 2933 3249 3713 M1744 MARSON_BOUND_BY_E2F4_UNSTIMULATED http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_BOUND_BY_E2F4_UNSTIMULATED.html Genes with promoters bound by E2F4 [GeneID=1874] in unstimulated hybridoma cells. 17237765 788/969 Jessica Robertson 0.479406454078573 0.549356266873238 1715 3437.36363636364 3251 0.0631935376406321 1712 0.899668600394157 -0.971761761731402 -1 0.351083561215559 1712 4668 4520 4547 4266 1761 2781 3251 3049 4476 2780 3714 M13930 JIANG_TIP30_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_TIP30_TARGETS_DN.html Down-regulated genes in HepG2 cells (liver cancer) overexpressing an oncogenic variant of tumor suppressor TIP30 [GeneID=10553] compared to its wild type form. 17440068 32/42 Jessica Robertson 0.451763133458819 0.520332354789074 3255 3509.63636363636 3251 0.0531747315025429 2332 1.25713803462643 -0.968079725696222 -1 0.535090904035379 3251 4508 2332 4390 2746 2820 2905 3406 4400 3177 4671 3715 M841 REACTOME_ADP_SIGNALLING_THROUGH_P2RY12 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADP_SIGNALLING_THROUGH_P2RY12.html Genes involved in ADP signalling through P2Y purinoceptor 12 16/23 Reactome 0.68618940391 0.690284310838704 4650 3547.36363636364 3252 0.1 2528 0.990153465868393 -0.921382843281913 -1 0.239057536178197 4648 3068 2528 2637 4137 4229 3110 4289 4232 2891 3252 3716 M18933 BIOCARTA_TGFB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TGFB_PATHWAY.html TGF beta signaling pathway 24/26 BioCarta 1.08440834088015e-05 0.000110310503641257 3255 2713.27272727273 3253 9.85830623732222e-07 28 0.742389586280299 0.860584600195432 1 4.40830213280798 3310 2053 3253 2144 28 3569 3648 3253 1904 3049 3635 3717 M506 REACTOME_INSULIN_RECEPTOR_RECYCLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INSULIN_RECEPTOR_RECYCLING.html Genes involved in Insulin receptor recycling 20/27 Reactome 0.250623372717113 0.312782210265672 3140 2895.18181818182 3254 0.025887527758508 611 0.915584567644404 1.1495134380154 1 0.693357413409863 3138 3492 3385 3595 2792 4194 3738 1953 611 3254 1695 3718 M12294 KEGG_VIRAL_MYOCARDITIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VIRAL_MYOCARDITIS.html Viral myocarditis 70/116 KEGG 0.0276395460038887 0.0494704193662978 4585 3040.36363636364 3255 0.00254482060550848 1273 1.19599481542337 -1.21184116080906 -1 2.34304014304634 4585 3286 1591 2758 1273 3255 4369 3974 3091 1790 3472 3719 M1924 MIKKELSEN_DEDIFFERENTIATED_STATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_DEDIFFERENTIATED_STATE_UP.html Genes up-regulated in partially reprogrammed and pluripotent cell populations (induced, iPS; and embryonic stem cells, ES) compared to parental lineage-commited cell lines. 18509334 5/8 Jessica Robertson 0.6513215599 0.690284310838704 2945 3137.72727272727 3255 0.1 535 0.61441017591415 0.648908266325289 1 0.148299858425672 2944 1649 4608 1303 3145 4665 3792 3919 535 4700 3255 3720 M1041 REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_TGF_BETA_RECEPTOR_COMPLEX.html Genes involved in Signaling by TGF-beta Receptor Complex 85/100 Reactome 0.152302026982522 0.205038667244012 2310 2880.81818181818 3256 0.0149087359355837 1167 0.85487543925025 -0.86711761359602 -1 0.882642173309863 2310 3256 3897 3425 2903 1508 1167 4008 1827 3984 3404 3721 M5520 TCGA_GLIOBLASTOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/TCGA_GLIOBLASTOMA_COPY_NUMBER_DN.html Genes down-regulated and displaying decreased copy number in glioblastoma samples. 18772890 33/43 Jessica Robertson 0.01185654223877 0.0249500130927305 3670 2695.72727272727 3257 0.0010837206784693 294 1.37639057128335 -1.29158201683974 -1 3.31042657936282 3667 3401 3257 3310 976 3388 4667 1746 294 2408 2539 3722 M8813 SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_DN.html Top 50 down-regulated markers distinguishing diffuse large B-cell lymphoma (DLBCL) from follicular lymphoma (FL) samples. 11786909 71/124 Jean Junior 0.68618940391 0.690284310838704 2030 3267.18181818182 3257 0.1 2027 1.08343413104732 1.14479146040601 1 0.261588707797739 2027 4424 2114 4122 3257 3280 2435 3152 4329 3712 3087 3723 M2340 DALESSIO_TSA_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/DALESSIO_TSA_RESPONSE.html Top genes up-regulated in HEK293 cells (fibroblast) in response to trichostatin A (TSA) [PubChem=5562]. 17709385 27/59 Arthur Liberzon 0.000428124086291301 0.0020432814817571 3565 2881.90909090909 3258 3.8927947521725e-05 288 1.18586618147753 -1.31677448148182 -1 4.7859392212473 3562 3015 1273 2430 288 4451 3960 3380 4144 1940 3258 3724 M2623 BIOCARTA_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IGF1_PATHWAY.html IGF-1 Signaling Pathway 36/41 BioCarta 0.541393492086221 0.609438894025033 4055 3407 3259 0.0684163932327722 2423 0.869452159030654 -0.824614094232645 -1 0.280480817222933 4055 3812 3612 3259 2894 4050 2853 4480 2423 3030 3009 3725 M3590 ASTIER_INTEGRIN_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/ASTIER_INTEGRIN_SIGNALING.html Integrin signaling signature in precursor B leukemia (PBL) cells: fibronectin (FN1) [GeneID=2335] vs control treatment with poly-L-lysine. 12393420 72/81 Kevin Vogelsang 0.290527114436101 0.354704599104604 4645 3403.09090909091 3260 0.0307212104357443 1884 0.99648087099679 -1.12610940967482 -1 0.67295110425664 4642 1884 2646 2645 4686 4505 4106 2053 3908 3260 3099 3726 M12701 MARTINEZ_RB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_TARGETS_DN.html Genes down-regulated in mice with skin specific knockout of RB1 [GeneID=5925] by Cre-lox. 18245467 675/937 Jessica Robertson 0.050185344937484 0.0809828472153588 3260 2971.63636363636 3260 0.00513560877260184 845 1.17875572836447 -1.16068911509505 -1 1.93067029739909 3260 1125 4533 1849 3584 3498 3954 2780 2812 845 4448 3727 M2440 LE_NEURONAL_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/LE_NEURONAL_DIFFERENTIATION_UP.html Genes up-regulated during neuronal differentiation of SH-SY5Y cells (neuroblastoma) in response to stimulation by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] and BDNF [GeneID=627]. 19635812 20/34 Arthur Liberzon 0.0313707836509282 0.0545177094375483 2890 3347.72727272727 3260 0.00289338660936376 925 0.915565613496606 1.01307158898495 1 1.73566986914495 2886 4551 2472 4355 3260 4613 3117 925 4406 4071 2169 3728 M14691 KEGG_AMINOACYL_TRNA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMINOACYL_TRNA_BIOSYNTHESIS.html Aminoacyl-tRNA biosynthesis 41/41 KEGG 0.403808572373864 0.473299344823601 3265 3096.18181818182 3261 0.045929383461925 1284 0.690526785583663 -0.762135908162066 -1 0.33650187865554 3261 3364 4042 3606 4359 1554 2169 3183 1284 4321 2915 3729 M765 BIOCARTA_INSULIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_INSULIN_PATHWAY.html Insulin Signaling Pathway 37/44 BioCarta 0.310009311389458 0.374039864457628 3555 3186.81818181818 3262 0.0331716323155235 1853 0.892736469844145 -0.824614094232645 -1 0.57200012142738 3552 3806 3592 2797 2504 3262 2295 4221 1853 2697 4476 3730 M13763 RADAEVA_RESPONSE_TO_IFNA1_UP http://www.broadinstitute.org/gsea/msigdb/cards/RADAEVA_RESPONSE_TO_IFNA1_UP.html Genes up-regulated in primary hepatocytes and Hep3B (hepatocyte) cells in response to IFNA [GeneID=3439]. 11910354 85/136 Yujin Hoshida 0.0875337841392367 0.129011743608942 3670 2916.90909090909 3262 0.00829307729989556 870 1.05283192878876 -0.966105441192122 -1 1.40491803428009 3267 3262 2606 3667 2307 3527 3522 3666 3145 2247 870 3731 M6792 ODONNELL_TARGETS_OF_MYC_AND_TFRC_DN http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TARGETS_OF_MYC_AND_TFRC_DN.html Genes up-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) by MYC [GeneID=4609] and down-regulated by RNAi knockdown of TFRC [GeneID=7037]. 16508012 53/59 Leona Saunders 0.614558367591634 0.680439947227894 3460 3105.18181818182 3263 0.0830199762906742 1196 1.10543599560644 1.11342273526943 1 0.277250559096411 3458 2896 3332 2947 3003 2554 3263 3976 1196 3269 4263 3732 M1509 BRACHAT_RESPONSE_TO_CISPLATIN http://www.broadinstitute.org/gsea/msigdb/cards/BRACHAT_RESPONSE_TO_CISPLATIN.html Genes up-regulated in FL5.12 cells (pro-B lymphocyte) in response to cisplatin [PubChem=2767]. 12447701 23/27 John Newman 0.68618940391 0.690284310838704 4605 3126.27272727273 3263 0.1 1476 1.22818297854798 -1.38137325216398 -1 0.296551592319546 4603 2066 2052 1774 3263 4631 3443 4381 1476 2010 4690 3733 M19703 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_WS http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_UV_IN_WS.html Human environmental stress response genes not changed in primary fibroblasts from patients with Warner syndrom (WS) . 15897889 17/19 Jessica Robertson 0.661675612292901 0.690284310838704 3265 3244.90909090909 3263 0.093824912130151 2477 0.901898472488583 -0.843839745854008 -1 0.217740273931966 3263 2613 2477 3598 3943 2603 3510 2715 4475 3529 2968 3734 M16740 GRADE_COLON_AND_RECTAL_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRADE_COLON_AND_RECTAL_CANCER_UP.html Up-regulated genes in both rectal and colon carcinoma compared to normal mucosa samples. 17210682 400/477 Jessica Robertson 0.68618940391 0.690284310838704 3205 3500.27272727273 3265 0.1 2361 0.983837836230434 -0.859395142802188 -1 0.237532048179313 3203 4324 4074 4345 3228 2361 2775 3914 2619 4395 3265 3735 M7968 BIOCARTA_CARM1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CARM1_PATHWAY.html Transcription Regulation by Methyltransferase of CARM1 14/15 BioCarta 0.0569140856276978 0.0899948020645674 3270 2661.27272727273 3266 0.00531291744637909 239 0.841487659200916 -1.05918859693679 -1 1.32037153492674 3266 2121 3345 1898 4562 3858 4362 1174 239 3309 1140 3736 M82 PID_RET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RET_PATHWAY.html Signaling events regulated by Ret tyrosine kinase 18832364 53/63 Pathway Interaction Database 0.223534715942272 0.283929994415372 2485 2902.63636363636 3266 0.0227378134588409 1508 0.888109213260284 0.862071630621099 1 0.728558879989485 2485 3331 3414 3682 3436 2146 1508 1875 3529 3266 3257 3737 M253 BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING http://www.broadinstitute.org/gsea/msigdb/cards/BONOME_OVARIAN_CANCER_SURVIVAL_SUBOPTIMAL_DEBULKING.html Genes whose expression in suboptimally debulked ovarian tumors is associated with survival prognosis. 18593951 632/779 Jessica Robertson 0.0703019916824613 0.107219108070914 3655 3216.72727272727 3266 0.00726304247519871 1709 1.05900287064326 -1.09053543088552 -1 1.54084505578088 3655 2703 4556 2097 1709 4291 3668 4378 2403 2658 3266 3738 M1547 BIOCARTA_HDAC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_HDAC_PATHWAY.html Control of skeletal myogenesis by HDAC and calcium/calmodulin-dependent kinase (CaMK) 38/43 BioCarta 0.220699133552363 0.280843986656336 2225 2812.27272727273 3267 0.0224139076023639 1387 0.719443673106115 0.738951084622853 1 0.595297944519128 2221 2487 3485 3401 3305 1400 1387 3390 3267 4017 2575 3739 M914 REACTOME_IL_3_5_AND_GM_CSF_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_3_5_AND_GM_CSF_SIGNALING.html Genes involved in Interleukin-3, 5 and GM-CSF signaling 53/66 Reactome 0.607191853849339 0.673231277934902 3555 3110.72727272727 3267 0.0814404497480089 1660 1.05896950023634 -1.37173054118666 -1 0.272941980698883 3551 2448 2311 1660 2996 3765 2741 3366 3796 3267 4317 3740 M12730 KORKOLA_EMBRYONAL_CARCINOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONAL_CARCINOMA_UP.html Genes from the 12p region that were up-regulated in embryonic carcinoma tumors compared to normal testis. 16424014 53/69 Arthur Liberzon 0.579397921458538 0.646667814917072 4690 3394.72727272727 3268 0.0757137502930403 1895 1.02049349568728 -0.894903426696367 -1 0.289792483898195 4687 4103 2821 4051 3068 1895 3790 3053 2592 3268 4014 3741 M14614 SAKAI_TUMOR_INFILTRATING_MONOCYTES_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_TUMOR_INFILTRATING_MONOCYTES_UP.html Selected genes up-regulated in inflammatory monocytes infiltrating hepatocellular carcinoma (HCC). 19074895 42/47 Jessica Robertson 0.0165300506489997 0.0325769682936445 4160 2759.36363636364 3268 0.00151414311079814 226 1.09264172378317 -1.04479092684851 -1 2.43802299058256 4159 2481 2692 1074 1083 4037 3662 3268 226 3701 3970 3742 M2780 REACTOME_SIGNALING_BY_ROBO_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_ROBO_RECEPTOR.html Genes involved in Signaling by Robo receptor 32/36 Reactome 0.68618940391 0.690284310838704 4295 3133 3269 0.1 1471 1.11160577281087 -1.10678401921146 -1 0.268393334395986 4293 1471 2519 1846 3443 4486 4182 4315 2285 2354 3269 3743 M10334 WANG_CLIM2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CLIM2_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) engineered to conditionally express a dominant negative form of CLIM2 [GeneID=8861] by a Tet Off system. 17452977 340/426 Arthur Liberzon 0.148380676843988 0.200833703220463 4295 3095.45454545455 3269 0.0144953394272345 1843 1.05788201927455 -1.06893902136699 -1 1.10655267548508 4292 3979 3403 3638 2057 3269 4467 2100 2150 2852 1843 3744 M2292 ITO_PTTG1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ITO_PTTG1_TARGETS_DN.html Genes down-regulated in HSA/c and KYSE140 cells (esophageal squamous cell carcinoma, ESCC) after knockdown of PTTG1 [GeneID=9232] by RNAi. 18451147 16/17 Jessica Robertson 0.000239590672341677 0.00135230656797059 3270 2796.18181818182 3269 2.17833426279192e-05 196 0.904648906116782 -0.594479566155789 -1 3.89429852421222 3269 2615 2746 2616 196 3453 3361 3998 1054 3947 3503 3745 M6031 BIOCARTA_SKP2E2F_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SKP2E2F_PATHWAY.html E2F1 Destruction Pathway 13/15 BioCarta 0.0191040773265912 0.0364824878669204 3365 2804.54545454545 3270 0.00175200146325081 376 0.970277937448507 -0.516209252702792 -1 2.09338636669795 3362 1586 3157 1857 1137 3520 3270 4493 376 3842 4250 3746 M13585 CAFFAREL_RESPONSE_TO_THC_24HR_5_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_5_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 53/76 Jessica Robertson 0.226912226028899 0.28756808396513 3770 2965.18181818182 3270 0.0231250294130025 489 1.02743754567113 -1.20746662256541 -1 0.834348603018317 3767 1408 2573 1582 2310 4450 4261 3951 489 3270 4556 3747 M1652 MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_6.html Cluster 6: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate and sulindac [PubChem=5222465;5352]. 10969808 73/95 John Newman 0.68618940391 0.690284310838704 4010 3120.72727272727 3270 0.1 633 0.96932136165229 -1.07739900171203 -1 0.234025714048832 4008 3270 3100 633 4708 3924 3210 4124 721 2467 4163 3748 M12104 PENG_LEUCINE_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_LEUCINE_DEPRIVATION_DN.html Genes down-regulated in BJAB cells (B-lymphoma) after leucine [PubChem=857] deprivation. 12101249 256/307 Broad Institute 0.40630096327653 0.475866140611717 3095 3366.63636363636 3271 0.0462926663512071 2288 0.885924346663427 -0.865246446151854 -1 0.428628864324595 3091 3622 4095 3467 4396 2730 3271 2288 2695 4168 3210 3749 M19002 STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_DN http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESRRA_TARGETS_RESPONSIVE_TO_ESTROGEN_DN.html Genes down-regulated by estradiol [PubChem=5757] and down-regulated by ESRRA [GeneID=2101] in MCF-7 cells (breast cancer). 18974123 49/58 Leona Saunders 0.68618940391 0.690284310838704 2850 3402 3272 0.1 2397 0.892472131120193 -0.935318081282082 -1 0.215463419294318 2847 3749 3096 3778 4483 2397 3174 3272 3725 4055 2846 3750 M1997 KYNG_WERNER_SYNDROM_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_WERNER_SYNDROM_DN.html Genes distinctly down-regulated in primary fibroblast cultures from Werner syndrom patients compared to those from normal young donors. 14527998 40/63 Arthur Liberzon 0.00252794940433012 0.00795461412562544 3275 2606.72727272727 3273 0.00023007807921762 561 1.11868755671146 -1.44034979860963 -1 3.5239424864439 3273 3777 3055 3414 561 3486 4123 1820 605 3600 960 3751 M5618 TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_DUCTAL_CARCINOMA_VS_LOBULAR_NORMAL_DN.html Genes down-regulated in ductal carcinoma vs normal lobular breast cells. 17389037 90/118 Arthur Liberzon 7.61632745550917e-07 1.10953906141985e-05 2415 2634.45454545455 3274 6.92393644750717e-08 269 1.52527192552081 1.24534879534983 1 11.3400819346551 2413 4053 269 4183 4599 3561 1515 3274 3724 346 1042 3752 M11362 REACTOME_THE_ROLE_OF_NEF_IN_HIV1_REPLICATION_AND_DISEASE_PATHOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THE_ROLE_OF_NEF_IN_HIV1_REPLICATION_AND_DISEASE_PATHOGENESIS.html Genes involved in The role of Nef in HIV-1 replication and disease pathogenesis 57/79 Reactome 0.0252475437735661 0.0458692866094042 3280 2642.63636363636 3277 0.00232200281372411 644 0.82292973536057 -0.725815650262681 -1 1.65267705137987 3277 793 3353 644 1233 3290 3779 3674 3225 3714 2087 3753 M14132 SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP http://www.broadinstitute.org/gsea/msigdb/cards/SLEBOS_HEAD_AND_NECK_CANCER_WITH_HPV_UP.html Genes up-regulated in head and neck squamous cell carcinoma (HNSCC) samples positive for HPV compared to the HPV-negative tumors. 16467079 86/105 Leona Saunders 0.506679679014006 0.57557835979449 2850 3200.54545454545 3277 0.062216392773496 603 1.23885824902026 1.05842311275586 1 0.445843593016283 2849 4400 3277 3333 2834 3065 3586 4327 603 3056 3876 3754 M13658 HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_DN.html Genes whose expression correlated with lower risk of late recurrence of hepatocellular carcinoma (HCC). 18923165 64/119 Yujin Hoshida 0.046870577302092 0.0762333304155322 3915 3038.72727272727 3277 0.00435454399480366 1493 1.22536076842133 -1.22317671272946 -1 2.05527023888676 3915 1900 1505 3277 1493 4679 4549 4614 1779 1520 4195 3755 M4495 COLLIS_PRKDC_SUBSTRATES http://www.broadinstitute.org/gsea/msigdb/cards/COLLIS_PRKDC_SUBSTRATES.html Substrates of PRKDC [GeneID=5591]. 15592499 27/40 Jessica Robertson 0.133772906154446 0.184030345977553 3005 3196.18181818182 3278 0.012970437712442 1091 0.9101760398898 -1.0016320966053 -1 1.00386216400498 3001 4523 3458 4107 3926 3361 2634 2558 3221 3278 1091 3756 M1981 ONO_FOXP3_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONO_FOXP3_TARGETS_UP.html Genes up-regulated in CD4+ [GeneID=920] T lymphocytes transduced with FOXP3 [GeneID=50943]. 17377532 22/32 Jessica Robertson 0.659421648387361 0.690284310838704 3550 3128.63636363636 3278 0.093277743102533 1867 1.46506211976028 -1.43488409353918 -1 0.353767785766562 3549 4209 1867 4211 3940 2067 3278 3176 3428 1926 2764 3757 M1648 HU_GENOTOXIC_DAMAGE_4HR http://www.broadinstitute.org/gsea/msigdb/cards/HU_GENOTOXIC_DAMAGE_4HR.html Genes most consistently regulated at 4 h by all six genotoxins tested: cisplatin, methyl methanesulfonate, mitomycin C, taxol, hydroxyurea and etoposide [PubChem=2767;4156;5746;4666;3657;36462]. 15120960 47/65 John Newman 0.0515172943351834 0.0828489367162063 3720 3202.45454545455 3280 0.00479679691258705 1523 0.932347307716469 -1.13692866626471 -1 1.51321706866035 3717 2914 3215 3157 1529 3928 4155 4217 1523 3592 3280 3758 M175 PID_ERBB2_ERBB3_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB2_ERBB3_PATHWAY.html ErbB2/ErbB3 signaling events 18832364 60/65 Pathway Interaction Database 0.00577426225782821 0.0142024584976285 4415 2896.72727272727 3285 0.000526315789473684 208 0.847013154391414 -0.723369086523329 -1 2.34816665908797 4413 1901 3595 208 4393 4209 2985 3518 236 3285 3121 3759 M10292 HONMA_DOCETAXEL_RESISTANCE http://www.broadinstitute.org/gsea/msigdb/cards/HONMA_DOCETAXEL_RESISTANCE.html Genes up-regulated in MCF7-ADR cell line (breast cancer) resistant to docetaxel [PubChem=148124]. 18724378 62/83 Jessica Robertson 0.21262588839977 0.272715813382313 3430 2942.81818181818 3285 0.0214975418039107 1842 0.907034804377954 -0.971260493843496 -1 0.767905927016571 3429 2425 3107 1926 2933 3297 3427 1842 3324 3376 3285 3760 M19829 BIOCARTA_AGPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AGPCR_PATHWAY.html Attenuation of GPCR Signaling 18/21 BioCarta 0.68618940391 0.690284310838704 3440 3093.45454545455 3286 0.1 613 1.06128388795705 0.813216542314662 1 0.256238500147267 3438 3509 3254 3416 3286 2816 3679 4443 613 3066 2508 3761 M540 LOPEZ_MESOTELIOMA_SURVIVAL_TIME_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MESOTELIOMA_SURVIVAL_TIME_UP.html Top genes higher expressed in short term mesothelioma survivors. 16540645 30/57 Arthur Liberzon 0.661343469176321 0.690284310838704 4565 3580.36363636364 3286 0.0937440737386926 2331 0.81364337947823 -0.715073297847569 -1 0.196422987620804 4561 4162 3255 4262 3078 2331 3286 2876 2634 4225 4714 3762 M17006 RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_MODERATELY_VS_POORLY_DN.html Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: moderately vs poorly differentiated tumors. 18679425 16/38 Jessica Robertson 0.242982599367767 0.304615635860787 3805 3159.72727272727 3286 0.0249887565611363 1932 0.887576945758014 -1.15789373237205 -1 0.687446952122458 3802 2616 3286 3378 2355 4103 4283 3030 1932 3945 2027 3763 M1217 SMITH_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMITH_TERT_TARGETS_DN.html Genes consistently down-regulated in HMEC cells (primary mammary epithelium) upon expression of TERT [GeneID=7015] off a retroviral vector. 12717449 127/169 Broad Institute 0.00478126918064838 0.0128443884648039 4045 3206.54545454545 3286 0.000435608369059205 761 1.21496803464082 1.34613281879736 1 3.44786830087874 4043 2322 761 3286 4398 3638 3994 3252 3190 1776 4612 3764 M1610 CUI_TCF21_TARGETS_2_UP http://www.broadinstitute.org/gsea/msigdb/cards/CUI_TCF21_TARGETS_2_UP.html All significantly up-regulated genes in kidney glomeruli isolated from TCF21 [Gene ID=6943] knockout mice. 16207825 543/664 John Newman 0.140817200897582 0.19198647840456 4015 3187 3286 0.0150627619043125 1074 1.23729925031528 -1.20448313628755 -1 1.33056841904957 4012 2212 4496 2817 3971 1952 3640 4511 3086 1074 3286 3765 M295 SIG_PIP3_SIGNALING_IN_CARDIAC_MYOCTES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_PIP3_SIGNALING_IN_CARDIAC_MYOCTES.html Genes related to PIP3 signaling in cardiac myocytes 81/93 Signaling Gateway 0.68618940391 0.690284310838704 3290 2845.81818181818 3287 0.1 725 0.888080585301354 -0.91557488464773 -1 0.214402677796285 4154 725 3289 1388 3287 4429 3310 3750 1005 2836 3131 3766 M1508 JIANG_AGING_CEREBRAL_CORTEX_UP http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_CEREBRAL_CORTEX_UP.html Up-regulated in the cerebral cortex of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 79/99 John Newman 0.0344803983455542 0.0588811433397308 3755 2813.27272727273 3287 0.00318481543105221 967 1.00842823056352 0.90393239648402 1 1.86112529505293 1242 4414 3287 4513 3753 1863 1433 967 3751 3741 1982 3767 M8492 KEGG_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_APOPTOSIS.html Apoptosis 90/107 KEGG 0.307697839046501 0.371535891608976 3690 2874.09090909091 3288 0.0328776360849199 1309 0.978507691760696 0.957480975973537 1 0.631249319714746 3688 1309 2220 1368 2495 3592 3288 4276 3501 1972 3906 3768 M18394 ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ROYLANCE_BREAST_CANCER_16Q_COPY_NUMBER_UP.html Genes in discrete regions of gain within 16q region detected in individual invasive breast cancer tumors. 16702952 66/97 Arthur Liberzon 0.0331782121934913 0.057008067547608 3470 3257.63636363636 3291 0.00306267263881834 1361 1.06742526754485 1.11427371750305 1 1.99250230549 3467 3291 2682 3127 1361 4079 4419 3261 2233 3509 4405 3769 M8880 MCBRYAN_PUBERTAL_BREAST_5_6WK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCBRYAN_PUBERTAL_BREAST_5_6WK_DN.html Genes down-regulated during pubertal mammary gland development between week 5 and 6. 17486082 193/226 Arthur Liberzon 0.68618940391 0.690284310838704 2395 3453.54545454545 3292 0.1 2395 0.873168062035949 1.12049758084535 1 0.210800681387611 2395 4344 3999 4327 3462 2844 3158 3292 2970 4182 3016 3770 M15154 MARTIN_INTERACT_WITH_HDAC http://www.broadinstitute.org/gsea/msigdb/cards/MARTIN_INTERACT_WITH_HDAC.html Interaction partners of class IIa histone deacetylases (HDAC). 17694086 54/63 Leona Saunders 0.68618940391 0.690284310838704 2495 3050.18181818182 3292 0.1 1586 0.874639408200158 1.11006329410141 1 0.211156072859938 2493 2446 3292 2377 4486 3455 3322 3592 1586 3840 2663 3771 M814 REACTOME_PURINE_SALVAGE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PURINE_SALVAGE.html Genes involved in Purine salvage 15/15 Reactome 0.0067817029107605 0.0160610324830856 1735 2514.81818181818 3294 0.000618427163819775 440 1.08930030160828 -1.08930030160828 -1 2.93258788768659 1734 3532 3294 3569 3303 1771 1858 440 3741 3401 1020 3772 M2243 REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA4D_IN_SEMAPHORIN_SIGNALING.html Genes involved in Sema4D in semaphorin signaling 41/55 Reactome 0.68618940391 0.690284310838704 4520 3425.54545454545 3295 0.1 1964 1.01755663390412 -0.947776526387709 -1 0.24567654431614 4517 1964 2337 2738 4673 3295 4525 3776 4454 2581 2821 3773 M1642 SIMBULAN_PARP1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SIMBULAN_PARP1_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) from PARP1 [GeneID=142] knockout mice. 11016956 21/25 John Newman 0.548349550462412 0.616240447186329 3230 3028.09090909091 3295 0.0697098893561223 386 1.81723373455144 1.82179587589068 1 0.573202420425903 3230 4197 1934 4181 3431 3062 2109 3295 386 3327 4157 3774 M1998 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_SCP2_QTL_TRANS.html Genes trans-regulated by the hematopoietic stem cell (HSC) proliferation QTL (quantitative trait locus) Scp2. 15711547 45/62 Arthur Liberzon 0.00403227285720712 0.0112249747627205 1485 2812.09090909091 3297 0.000367243857604294 654 1.21737661416179 1.21630579511833 1 3.5616167311193 1485 3769 1085 3650 654 4681 3297 3403 4273 1820 2816 3775 M1392 SHIN_B_CELL_LYMPHOMA_CLUSTER_8 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_8.html Cluster 8 of genes distinguishing among different B lymphocyte neoplasms. 19010892 45/65 Jessica Robertson 0.68618940391 0.690284310838704 4665 3424 3299 0.1 2249 1.02418883515144 -1.16304393777345 -1 0.247278497563708 4661 3751 2249 3832 3196 4188 3299 3799 2754 2825 3110 3776 M6370 KEGG_P53_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_P53_SIGNALING_PATHWAY.html p53 signaling pathway 79/91 KEGG 0.319171406925053 0.383818863869108 3250 3407.27272727273 3300 0.0343458372913535 1391 0.876301862523807 0.854421621526982 1 0.546730027824141 3250 4060 3077 4653 2652 1391 2241 3300 4348 4018 4490 3777 M1749 KEGG_VEGF_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VEGF_SIGNALING_PATHWAY.html VEGF signaling pathway 68/89 KEGG 0.304951075797807 0.369068994298884 3300 3299.45454545455 3300 0.0325294332330072 2336 0.809086316836645 -0.824376692711095 -1 0.525447348141042 3300 2411 3103 3445 2483 3237 4259 4305 3814 3601 2336 3778 M18979 HAMAI_APOPTOSIS_VIA_TRAIL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAMAI_APOPTOSIS_VIA_TRAIL_UP.html Genes up-regulated in T1 cells (primary melanoma, sensitive to TRAIL [GeneID=8743]) compared to G1 cells (metastatic melanoma, resistant to TRAIL). 16983347 759/869 Leona Saunders 0.350305612409923 0.417641447480383 800 2993.63636363636 3302 0.0422086478280157 800 1.11282432948177 1.13580518341431 1 0.633082112655058 800 4306 4344 3462 3769 2860 2204 2463 1218 4202 3302 3779 M1326 MANTOVANI_NFKB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_NFKB_TARGETS_DN.html NF-kB-controlled genes down-regulated in endothelial cells in response to viral GPCR protein. 17906691 19/22 Jessica Robertson 0.00116694740444593 0.00446245700308704 4245 2813.54545454545 3302 0.000106142440832081 420 0.847830047986406 0.573706016162038 1 2.99007317145189 3630 1542 2181 1747 420 3302 2148 4242 3803 3691 4243 3780 M2220 KEGG_FOLATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FOLATE_BIOSYNTHESIS.html Folate biosynthesis 8/12 KEGG 0.00902144673929769 0.0201998238185413 1995 2841.72727272727 3303 0.000905828129704249 538 0.982182555538333 0.982182555538333 1 2.49744686970226 1993 4275 4182 3767 1526 3303 3869 538 2646 3456 1704 3781 M963 KEGG_RNA_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_DEGRADATION.html RNA degradation 70/72 KEGG 0.650677183297569 0.690284310838704 3205 3581.45454545455 3303 0.0911856463749734 2235 0.517028999686426 -0.481886312384112 -1 0.12477824234488 3201 4085 4113 4522 3064 2235 2615 3109 4667 4482 3303 3782 M7561 KEGG_MTOR_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MTOR_SIGNALING_PATHWAY.html mTOR signaling pathway 56/78 KEGG 0.0393946550829259 0.0659371531884433 3305 3081.90909090909 3303 0.00364711720053799 1424 0.713544338936365 -0.660228095312394 -1 1.26423683287487 3303 2442 3754 2999 1424 3304 2685 3416 2390 4164 4020 3783 M2101 STAMBOLSKY_TARGETS_OF_MUTATED_TP53_UP http://www.broadinstitute.org/gsea/msigdb/cards/STAMBOLSKY_TARGETS_OF_MUTATED_TP53_UP.html Genes induced in SKBR3 cells (breast cancer) by mutated TP53 [GeneID=7157]. 20227041 53/63 Arthur Liberzon 0.00844159326555526 0.0191467180266318 490 2325 3303 0.000770378134412321 243 0.982560646617288 1.00581317961473 1 2.53269176268584 486 3328 3303 4214 3959 691 243 1302 3393 3823 833 3784 M19818 KEGG_NON_SMALL_CELL_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NON_SMALL_CELL_LUNG_CANCER.html Non-small cell lung cancer 58/64 KEGG 0.65963125117329 0.690284310838704 3805 3090.27272727273 3304 0.0933284869185335 1136 0.800019957520163 0.886230701914406 1 0.193132362949616 3804 1387 3304 1136 3075 4392 3290 4044 1983 3478 4100 3785 M7014 BIOCARTA_MYOSIN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MYOSIN_PATHWAY.html PKC-catalyzed phosphorylation of inhibitory phosphoprotein of myosin phosphatase 42/49 BioCarta 0.186111649390516 0.243202376833676 4225 2572 3306 0.0185469472235266 218 0.855470643291887 0.875942160663159 1 0.788097119892533 3385 218 3306 384 2190 4222 3507 3353 783 4221 2723 3786 M13422 HUPER_BREAST_BASAL_VS_LUMINAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUPER_BREAST_BASAL_VS_LUMINAL_UP.html Genes up-regulated in basal mammary epithelial cells compared to the luminal ones. 17409405 61/100 Jessica Robertson 5.12689420076348e-13 2.32682121419266e-11 2485 2836.18181818182 3307 4.66081290978606e-14 80 1.91269514966383 -2.03613035137412 -1 30.5176826163963 2481 3307 80 3481 3547 3531 4349 3225 3819 142 3236 3787 M19312 REACTOME_DNA_STRAND_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_STRAND_ELONGATION.html Genes involved in DNA strand elongation 30/31 Reactome 0.670868751918822 0.690284310838704 1190 3151.54545454545 3308 0.096091510816878 1187 0.6446969892538 -0.633606982356623 -1 0.155615387188849 1187 2545 3774 3183 3308 2858 2361 3783 3583 4622 3463 3788 M10593 MACLACHLAN_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MACLACHLAN_BRCA1_TARGETS_DN.html Genes down-regulated in SW480 cells (colon cancer with mutated p53 [GeneID=7157]) upon expression of BRCA1 [GeneID=672] off an adenovirus vector. 10644742 44/51 John Newman 9.39272510521818e-05 0.000626181673681212 3195 2938.63636363636 3308 8.53920558556419e-06 478 1.64040863458148 -1.98715783635066 -1 7.88470758869403 3192 3357 478 3223 703 4511 3308 3867 4170 985 4531 3789 M4772 CAIRO_HEPATOBLASTOMA_CLASSES_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_CLASSES_UP.html Genes up-regulated in robust Cluster 2 (rC2) of hepatoblastoma samples compared to those in the robust Cluster 1 (rC1). 19061838 736/821 Arthur Liberzon 0.6513215599 0.690284310838704 4710 3644 3308 0.1 2133 0.78945202800088 -0.80409913299561 -1 0.190579767154919 2545 4309 4639 4707 4349 2943 3232 3210 2133 4709 3308 3790 M10961 GOZGIT_ESR1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOZGIT_ESR1_TARGETS_DN.html Genes down-regulated in TMX2-28 cells (breast cancer) which do not express ESR1 [GeneID=2099]) compared to the parental MCF7 cells which do. 17726467 975/1368 Arthur Liberzon 1.20996330960037e-24 2.30445681427451e-22 3310 2504 3309 1.20996330960036e-25 10 1.26234348686413 -1.26074129809286 -1 40.9849052157095 3309 1116 4324 435 1594 3996 3519 4046 1311 10 3884 3791 M905 CHOW_RASSF1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHOW_RASSF1_TARGETS_DN.html Genes down-regulated in C666-1 cells (nasopharyngeal carcinoma) by stable expression of RASSF1 [GeneID=11186]. 16116475 36/39 Lauren Kazmierski 0.498296423326974 0.567557702245009 3865 3035.90909090909 3309 0.0607787131680657 262 0.928885743030964 -1.04712410236247 -1 0.342757881773517 3864 3791 3309 2352 4036 3532 3497 2442 262 3032 3278 3792 M14 PID_AURORA_B_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AURORA_B_PATHWAY.html Aurora B signaling 18832364 47/52 Pathway Interaction Database 0.68618940391 0.690284310838704 2705 3490.72727272727 3311 0.1 2701 0.874755923484619 -1.01798217436363 -1 0.21118421616129 2701 2912 3798 3845 4702 3311 3108 4026 2978 4170 2847 3793 M19849 HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_CD4_DN.html Genes down-regulated in T helper cells (defines as CD4+) isolated from patients with mucosis fungoides compared to those from normal control donors. 16914566 152/191 Arthur Liberzon 0.68618940391 0.690284310838704 3295 2889.18181818182 3311 0.1 612 0.803355816389908 -0.86067851745796 -1 0.193938112013997 3294 612 4083 887 3311 3881 2501 4029 729 4162 4292 3794 M1243 WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_UP.html Genes up-regulated by telomere shortening due to the knockout of TERC [GeneID=7012] in the presence of chronic liver damage. 15608677 16/28 Leona Saunders 0.180452890578611 0.236856964274484 4475 3133.09090909091 3311 0.0179285542211299 1323 1.41258390035064 1.0056028823456 1 1.32573987272695 4472 3064 1323 1882 2233 4280 4240 4198 3311 1369 4092 3795 M663 REACTOME_THE_ACTIVATION_OF_ARYLSULFATASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THE_ACTIVATION_OF_ARYLSULFATASES.html Genes involved in The activation of arylsulfatases 9/10 Reactome 0.0014641548755211 0.00527129893559473 3315 2798.81818181818 3312 0.000146512045829921 48 1.18949618384912 1.44341969395687 1 4.06595883969183 3312 2156 4213 535 474 4197 4513 4662 48 3557 3120 3796 M5355 CASTELLANO_HRAS_AND_NRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_AND_NRAS_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) isolated from HRAS and NRAS [GeneID=3265;4893] double knockout mice. 16909116 11/12 Leona Saunders 0.68618940391 0.690284310838704 4130 3209.09090909091 3312 0.1 1312 1.23024064097058 -1.44343208911887 -1 0.297048603625048 4130 3558 2289 1312 3441 3299 4315 3312 2931 2342 4371 3797 M4241 BENPORATH_ES_2 http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_ES_2.html Set 'Set 'ES exp2': genes overexpressed in human embryonic stem cells according to a meta-analysis of 8 profiling studies. 18443585 39/66 Jessica Robertson 0.68618940391 0.690284310838704 3140 3354.72727272727 3313 0.1 2347 1.22857534749712 1.03708648593612 1 0.29664636578749 3137 4487 2803 3621 4092 2347 2749 3313 2378 3538 4437 3798 M190 PID_TCR_JNK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_JNK_PATHWAY.html JNK signaling in the CD4+ TCR pathway 18832364 12/18 Pathway Interaction Database 0.00740011923921866 0.017189253350941 1760 2767.45454545455 3314 0.000675011709475048 222 0.676934364191207 -0.360699343992909 -1 1.79243821258672 1758 4257 3453 4103 3314 1527 222 1642 4633 4515 1018 3799 M947 REACTOME_INHIBITION_OF_VOLTAGE_GATED_CA2_CHANNELS_VIA_GBETA_GAMMA_SUBUNITS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INHIBITION_OF_VOLTAGE_GATED_CA2_CHANNELS_VIA_GBETA_GAMMA_SUBUNITS.html Genes involved in Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits 14/28 Reactome 0.23513145033813 0.295873219300446 3525 3181 3314 0.0240737892137624 1911 1.12026744698433 -1.04778319236935 -1 0.888956987476399 3524 3534 2283 3060 3772 3118 2248 1911 3536 3314 4691 3800 M523 KEGG_THYROID_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_THYROID_CANCER.html Thyroid cancer 36/43 KEGG 0.585612860969561 0.652153099804368 2640 3503 3315 0.0769637618391302 2173 0.890926025997505 -0.589980967907671 -1 0.248081401328638 2640 4502 3615 4515 3188 3156 2173 3315 4473 3755 3201 3801 M11980 REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADHERENS_JUNCTIONS_INTERACTIONS.html Genes involved in Adherens junctions interactions 23/34 Reactome 0.0322078088455865 0.0557084676703681 3465 3213.72727272727 3315 0.00297174770936882 934 1.55751099384235 1.468067356261 1 2.93077223963035 3462 4202 1424 4560 3284 3315 2580 934 4178 2974 4438 3802 M2202 JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_UP.html Up-regulated genes distinguishing between breast cancer tumors with mutated BRCA1 [GeneID=672] from those with mutated BRCA2 [GeneID=675]. 12096084 71/77 John Newman 0.0401187587027279 0.0668628764470594 3690 2945.18181818182 3316 0.00371541788676947 1021 0.759363573468423 -0.779218624841408 -1 1.33852564280235 3687 1886 3804 2464 3316 3888 4111 1021 1977 4013 2230 3803 M1355 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_DN.html Early prostate development genes (down-regulated at 6 h dihydrotestosterone [PubChem=10635]) which are also down-regulated in normal epithelium vs high grade prostatic intraepithelial neoplasia (PIN). 18794802 10/12 Jessica Robertson 0.0665108276932586 0.102424504636927 2015 3191.90909090909 3317 0.00623736772626418 1524 0.45713562601202 0.455526606265797 1 0.678698908920151 2014 4622 3317 4568 1635 2809 1524 3539 4513 4661 1909 3804 M11234 THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN http://www.broadinstitute.org/gsea/msigdb/cards/THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_DN.html Genes down-regulated in polymorphonuclear neutrophilic granulocytes (PMNs) attracted to skin wounds. 15187151 309/390 Kevin Vogelsang 0.00577426225782821 0.0142024584976285 3160 2785.18181818182 3317 0.000526315789473684 196 0.86097471078342 -0.891012443791813 -1 2.38687389589784 3157 536 3921 196 1616 3488 3317 4214 1787 3933 4472 3805 M1790 NADELLA_PRKAR1A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NADELLA_PRKAR1A_TARGETS_UP.html Epithelial and mesenchymal markers up-regulated in MEF cells (embryonic fibroblasts) after knockout of PRKAR1A [GeneID=5573]. 18413734 12/14 Jessica Robertson 0.126716885299937 0.176016391587906 1340 3185.27272727273 3320 0.0122422172359536 1071 0.639986378216449 0.639986378216449 1 0.724398875773965 1338 4633 2553 4473 4291 2034 1071 3320 4712 4688 1925 3806 M124 PID_CXCR4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CXCR4_PATHWAY.html CXCR4-mediated signaling events 18832364 119/141 Pathway Interaction Database 0.43119990772354 0.499814448548158 4195 2813.63636363636 3321 0.05 8 1.0012438142364 -0.93254906953756 -1 0.452399736409764 4195 8 2575 415 3701 4474 4686 3321 2172 2046 3357 3807 M17181 REACTOME_SIGNALLING_TO_P38_VIA_RIT_AND_RIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_P38_VIA_RIT_AND_RIN.html Genes involved in Signalling to p38 via RIT and RIN 18/20 Reactome 0.129415888440717 0.178975386299497 3325 3124.36363636364 3321 0.0125201354353991 1551 0.637977230375102 -0.43735358107194 -1 0.715193372936997 3321 4237 3751 4141 2402 1976 2314 1551 4282 4004 2389 3808 M12705 SIG_CD40PATHWAYMAP http://www.broadinstitute.org/gsea/msigdb/cards/SIG_CD40PATHWAYMAP.html Genes related to CD40 signaling 33/36 Signaling Gateway 0.68618940391 0.690284310838704 3150 3442.81818181818 3323 0.1 2416 0.650467116984543 -0.591232976985127 -1 0.157009113722838 3147 2970 3662 4053 3323 2416 2790 4659 2856 3906 4089 3809 M170 KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN.html Genes down-regulated in MEWO cells (melanoma) after 96 h of methionine [PubChem=876] deprivation. 16908595 95/107 Arthur Liberzon 0.68618940391 0.690284310838704 4220 3101.27272727273 3324 0.1 697 0.974475304904472 -1.0039597645378 -1 0.235270606328594 4217 697 2993 900 3324 4670 4563 4129 3361 2667 2593 3810 M1908 BIOCARTA_FCER1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FCER1_PATHWAY.html Fc Epsilon Receptor I Signaling in Mast Cells 53/61 BioCarta 0.0718776955956032 0.109087692350883 3100 3106.72727272727 3325 0.0067581296438476 1676 0.811312268015653 -0.911693914500732 -1 1.17129667363173 3096 3325 3610 1949 1676 4228 1736 4023 2884 3973 3674 3811 M12771 SA_PTEN_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/SA_PTEN_PATHWAY.html PTEN is a tumor suppressor that dephosphorylates the lipid messenger phosphatidylinositol triphosphate. 20/22 SigmaAldrich 0.00577426225782821 0.0142024584976285 3840 2437 3325 0.000526315789473684 109 0.60289342733592 -0.704817992617374 -1 1.67136531833552 3839 361 3643 201 3325 2884 3953 3507 109 4061 924 3812 M14151 DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP http://www.broadinstitute.org/gsea/msigdb/cards/DEBIASI_APOPTOSIS_BY_REOVIRUS_INFECTION_UP.html Genes up-regulated in HEK293 cells (embryonic kidney) at 6 h, 12 h or 24 h after infection with reovirus strain T3A (known as a strong inducer of apoptosis). 12885910 431/530 John Newman 0.553158734338489 0.620536559617489 1440 3105.27272727273 3325 0.0706148003378987 1440 1.03863169031903 1.01633736173812 1 0.3228636707334 1440 3970 3765 3902 3523 2751 2120 3325 2305 3252 3805 3813 M15709 ACEVEDO_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_LIVER_CANCER_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) compared to normal liver samples. 18413731 1238/1528 Jessica Robertson 0.258663349199133 0.321540955549094 3325 3257.27272727273 3325 0.0294865753259446 1312 0.925645830883383 -0.892254920305037 -1 0.68431838800277 3325 3147 4544 4161 2863 1312 3595 3502 3035 4466 1880 3814 M3630 REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ABORTIVE_ELONGATION_OF_HIV1_TRANSCRIPT_IN_THE_ABSENCE_OF_TAT.html Genes involved in Abortive elongation of HIV-1 transcript in the absence of Tat 25/27 Reactome 0.0981262079199714 0.141985193556795 1900 3306.45454545455 3326 0.00934521305392062 1820 0.532168413261368 -0.57629280008551 -1 0.676853001211391 1899 4539 4008 4469 1820 2280 2320 2748 4362 4600 3326 3815 M10783 HOFMANN_CELL_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_CELL_LYMPHOMA_UP.html Genes up-regulated in lymph nodes from patients with mantle cell lymphoma (MCL) compared to the non-malignant hyperplastic lymph nodes. 11468180 73/116 Kevin Vogelsang 0.648822768106665 0.690284310838704 4340 3204.27272727273 3326 0.0907481073129973 1166 1.22580084138468 -1.41966129493737 -1 0.295976206829481 4339 3279 2963 3886 3604 3998 2301 3326 1166 2465 3920 3816 M1724 KEGG_RNA_POLYMERASE http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_RNA_POLYMERASE.html RNA polymerase 27/29 KEGG 0.601842514051631 0.667927737202845 2610 3519.45454545455 3327 0.0803102352691053 2213 0.514537111304024 -0.577490719893951 -1 0.135215855204327 2609 4546 4064 4655 2988 2339 2213 3060 4430 4483 3327 3817 M13408 REACTOME_ERK_MAPK_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ERK_MAPK_TARGETS.html Genes involved in ERK/MAPK targets 26/26 Reactome 0.110816908370928 0.15716821139146 3060 3278 3327 0.0106206629769811 1882 0.650400032477978 -0.406271683927973 -1 0.784192631450599 3057 3460 3775 3435 1882 3777 3177 3255 3327 3950 2963 3818 M1721 LEIN_PONS_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/LEIN_PONS_MARKERS.html Top 100 ranked genes most specific to pons region (P) of the adult mouse brain. 17151600 109/143 Jessica Robertson 4.17594539548843e-05 0.000330158496929739 4100 2338.72727272727 3330 3.79638605781335e-06 438 1.40345389100167 -1.33535201969841 -1 7.33115385555783 4098 657 438 921 3330 3367 3835 3868 1055 569 3588 3819 M5914 LANDEMAINE_LUNG_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/LANDEMAINE_LUNG_METASTASIS.html Genes associated with metastasis of breast cancer in the lung compared to the non-lung metastasis. 18676831 27/31 Jessica Robertson 0.68618940391 0.690284310838704 3505 2910.36363636364 3331 0.1 1283 1.58480143797719 -1.47482298860251 -1 0.382689825753919 3505 3436 1870 1283 3143 3331 4222 3632 2157 1938 3497 3820 M16128 XU_GH1_EXOGENOUS_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_EXOGENOUS_TARGETS_UP.html Genes up-regulated in MFCF-7 cells (breast cancer) by exogenous HG1 [GeneID=2688]. 15845533 63/121 John Newman 0.348716303214885 0.415956773104437 3510 3215.72727272727 3331 0.038232673891584 2170 1.13493696667144 0.916746167076662 1 0.648653447176597 3507 4087 2170 4552 2597 3590 2178 2172 3331 2546 4643 3821 M4322 AUNG_GASTRIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/AUNG_GASTRIC_CANCER.html Selected genes specifically expressed in gastric cancer. 16331256 51/111 Arthur Liberzon 0.262208351284841 0.325091520374166 2390 2998.27272727273 3332 0.0272662690867462 1629 1.03303546963451 1.14249695322946 1 0.756329568890412 2386 3332 3413 3758 2396 1629 2409 4712 3572 3467 1907 3822 M17811 PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN.html Genes down-regulated in post-GC, BCL6 [GeneID=604] dependent B cell non-Hodgkin's lymphoma (B-NHL) vs MYC [GeneID=4609] driven pre-GC lymphoma. 18066064 207/276 Jessica Robertson 0.0284202848665838 0.0505882554956728 3615 3037.90909090909 3332 0.00261765521074032 1131 1.16203002227338 0.999783247603371 1 2.25957708945027 3611 2279 2252 3332 1282 3941 4295 4657 1131 2197 4440 3823 M8876 PODAR_RESPONSE_TO_ADAPHOSTIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/PODAR_RESPONSE_TO_ADAPHOSTIN_DN.html Down-regulated genes in MM1.S cells (multiple myeloma) treated with adaphostin [PubChem=387042], a tyrosine kinase inhibitor with anticancer properties. 17308109 28/33 Jessica Robertson 0.0397035341919466 0.0662963096882347 4485 2944.18181818182 3332 0.00367624633078028 797 1.39730881222709 -1.4434176109842 -1 2.47086555749561 4483 3424 1432 3327 4547 3484 3332 1792 2372 797 3396 3824 M1536 HASLINGER_B_CLL_WITH_CHROMOSOME_12_TRISOMY http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_CHROMOSOME_12_TRISOMY.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with trisomy of chromosome 12. 15459216 28/33 Kevin Vogelsang 0.68618940391 0.690284310838704 4115 2874.09090909091 3333 0.1 557 1.02135595590883 0.869354964178434 1 0.246594239059865 4113 920 3179 563 4436 3162 3333 3552 557 3338 4462 3825 M4866 FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_DN.html Down-regulated genes significantly associated with positive minimal residual disease (MRD) on day 46 after chemotherapy treatment of children with acute lymphoblastic leukemia (ALL). 16627760 33/38 Arthur Liberzon 0.401006824691211 0.470482777166919 3330 3268.81818181818 3335 0.0455226543917878 865 1.16541562258466 1.03757158204971 1 0.572526621588209 3327 2974 3244 3335 3513 4548 4093 2277 865 3605 4176 3826 M1127 HUMMERICH_MALIGNANT_SKIN_TUMOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUMMERICH_MALIGNANT_SKIN_TUMOR_DN.html Genes down-regulated in malignant skin tumors (squamous cell carcinoma, SCC) formed by treatment with DMBA and TPA [PubChem=6001;4792] in the two stage skin carcinogenesis model. 16247483 25/49 Leona Saunders 0.00231749943020692 0.00746827961275641 3340 3041.72727272727 3337 0.000210904028270711 534 0.942549405456762 -1.01850287111123 -1 3.00782873107222 3337 3470 2636 3588 534 2514 3753 4366 3262 3580 2419 3827 M4389 RIZ_ERYTHROID_DIFFERENTIATION_12HR http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_12HR.html Selected genes down-regulated in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts) at 12 h time point. 17213805 47/63 Leona Saunders 0.68618940391 0.690284310838704 3115 3293.45454545455 3337 0.1 2127 0.951283169058723 1.00332046442576 1 0.22966873811762 3115 3337 2676 3070 3893 4047 3568 3500 2127 2939 3956 3828 M17300 KARAKAS_TGFB1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/KARAKAS_TGFB1_SIGNALING.html Genes up-regulated by TGFB1 [GeneID=7040] in MCF10A cells (breast cancer): both wild-type and those lacking p21 [GeneID=1026]. 16619041 25/28 Arthur Liberzon 0.0255678259292376 0.0462908087403151 4575 3244.72727272727 3338 0.00235180862766245 965 1.674269513251 1.52150949086616 1 3.35253831022864 4575 3023 965 3034 2751 3559 4133 4706 3824 1784 3338 3829 M1880 PIONTEK_PKD1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PIONTEK_PKD1_TARGETS_DN.html Genes down-regulated during later stages of renal maturation (days P14-P16) in kidney specific knockout of PKD1 [GeneID=5310]. 17965720 24/48 Jessica Robertson 0.68618940391 0.690284310838704 3340 3119 3338 0.1 1355 1.11465006224385 0.677410347820634 1 0.269128657279271 3338 3473 1906 3214 3489 3247 3837 3405 1355 2568 4477 3830 M17387 XU_GH1_EXOGENOUS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_GH1_EXOGENOUS_TARGETS_DN.html Genes down-regulated in MFCF-7 cells (breast cancer) by exogenous HG1 [GeneID=2688]. 15845533 172/268 John Newman 0.00374322107805349 0.0106626454365796 4620 3075 3340 0.000340873204275312 637 1.20040097562591 -1.33767994841704 -1 3.55215458363986 4620 3635 1196 3340 637 4163 3688 4466 2452 2520 3108 3831 M5244 KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM.html Glyoxylate and dicarboxylate metabolism 16/18 KEGG 0.424963892886058 0.496001378442679 1780 3087.90909090909 3341 0.0490578418969962 1777 0.632618857807203 -0.675662268281412 -1 0.28895926575071 1777 3524 3527 3341 4066 1995 1851 3688 3161 4481 2556 3832 M19745 TARTE_PLASMA_CELL_VS_PLASMABLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/TARTE_PLASMA_CELL_VS_PLASMABLAST_DN.html Genes down-regulated in mature plasma cells compared with plasmablastic B lymphocytes. 12663452 408/494 Kate Stafford 0.638174110234688 0.690284310838704 2410 3301.90909090909 3342 0.088275545893307 2261 0.892371959369114 -0.848072427774171 -1 0.215439223638008 2408 3973 4117 3473 4445 2261 2278 3086 2590 4348 3342 3833 M459 SESTO_RESPONSE_TO_UV_C0 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C0.html Cluster 0: genes changed in primary keratinocytes by UVB irradiation. 11867738 157/177 John Newman 0.204918478877285 0.26419426940748 1050 2865.27272727273 3342 0.0206306360822908 1049 1.04540399383879 1.0086824734434 1 0.906693852459501 1049 4361 3474 3915 3895 1517 1331 3373 3022 3342 2239 3834 M19708 KEGG_TYPE_II_DIABETES_MELLITUS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TYPE_II_DIABETES_MELLITUS.html Type II diabetes mellitus 46/67 KEGG 0.540336242267755 0.608684263366063 3955 3041.45454545455 3343 0.0682213585289688 1603 1.05054941176665 -1.11589217089581 -1 0.339772141396086 3953 2466 1926 4388 3254 3346 3343 3636 3365 1603 2176 3835 M535 DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_UP http://www.broadinstitute.org/gsea/msigdb/cards/DIAZ_CHRONIC_MEYLOGENOUS_LEUKEMIA_UP.html Genes up-regulated in CD34+ [GeneID=947] cells isolated from bone marrow of CML (chronic myelogenous leukemia) patients, compared to those from normal donors. 17252012 1707/1965 Leona Saunders 0.6513215599 0.690284310838704 3375 3359 3343 0.1 2532 0.847023483225624 -0.803771642574809 -1 0.204485675046628 3371 3145 4290 3477 3343 2643 3577 3051 2532 4629 2891 3836 M9729 WIKMAN_ASBESTOS_LUNG_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/WIKMAN_ASBESTOS_LUNG_CANCER_DN.html Genes negatively correlated with the asbestos exposure of lung cancer patients. 17297452 27/41 Arthur Liberzon 0.000840317700432923 0.0034760337091545 4555 2977 3343 7.64217129183639e-05 375 0.839815662612034 -0.821065153294613 -1 3.09852241401715 4552 2035 2858 3079 375 3343 4125 829 4067 3970 3514 3837 M125 PID_IGF1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IGF1_PATHWAY.html IGF1 pathway 18832364 50/54 Pathway Interaction Database 0.68618940391 0.690284310838704 3575 3167.09090909091 3344 0.1 1030 0.909909113589417 -0.984416714857595 -1 0.219675177902465 3575 3344 3603 2782 4147 3701 2798 3117 1030 2769 3972 3838 M10219 DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN.html Genes down-regulated in multiple myeloma (MM) compared to monoclonal gammopathy of uncertain significance (MGUS). 12947006 35/123 Arthur Liberzon 0.280828061391456 0.344645982778907 3450 2720.09090909091 3344 0.029524012871743 266 0.962063589162412 0.830527245182158 1 0.66774021228222 3447 266 1454 568 4005 3721 3097 3344 3432 2162 4425 3839 M2626 CHOW_RASSF1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHOW_RASSF1_TARGETS_UP.html Genes up-regulated in C666-1 cells (nasopharyngeal carcinoma) by stable expression of RASSF1 [GeneID=11186]. 16116475 35/36 Lauren Kazmierski 0.157537211300045 0.211063195383541 3805 3328.18181818182 3346 0.0154633576165919 1192 0.919363162499599 -1.02318992386031 -1 0.931882571025183 3803 3386 3176 3543 4474 3151 4611 2821 3107 3346 1192 3840 M5075 SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM.html Cluster 7: genes up-regulated in B493-6 cells (B lymphocytes) by MYC [GeneID=4609] and down-regulated by the combination of MYC and serum. 15516975 194/226 Leona Saunders 0.68618940391 0.690284310838704 2965 3349 3347 0.1 1371 0.793402776207956 -0.801222580455877 -1 0.191534037642898 2964 4000 4157 3458 3347 3257 3541 3126 1371 4403 3215 3841 M8887 LEE_METASTASIS_AND_RNA_PROCESSING_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_METASTASIS_AND_RNA_PROCESSING_UP.html Components of RNA post-transcriptional modification machinery up-regulated in MDA-MB-435 cells (breast cancer) whose metastatic potential has been reduced by expression of NME1 [GeneID=4830]. 18245461 24/29 Jessica Robertson 0.158193152338053 0.211821752917903 2075 3402.36363636364 3347 0.0155330695333825 1663 0.679054798567488 0.7673995564094 1 0.686686600096656 2073 4540 3871 4606 3319 3347 2358 1663 4255 4687 2707 3842 M2566 HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_ASPARAGINASE_RESISTANCE_ALL_DN.html Genes distinguishing asparaginase resistant and sensitive ALL (B- and T-lineage ALL); here - genes down-regulated in the drug resistant samples. 15295046 31/38 Arthur Liberzon 0.000240696074339999 0.00135409472095923 3515 3067.18181818182 3347 2.18838556621326e-05 197 0.765589059716327 0.774879703843442 1 3.29500339802646 3511 2993 3759 3347 197 4245 3096 3281 2003 3856 3451 3843 M9694 REACTOME_ACTIVATION_OF_THE_PRE_REPLICATIVE_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_THE_PRE_REPLICATIVE_COMPLEX.html Genes involved in Activation of the pre-replicative complex 30/30 Reactome 0.68618940391 0.690284310838704 1680 3484 3348 0.1 1678 0.628773078098588 -0.628773078098588 -1 0.15176909841717 1678 4521 3885 4130 3122 2718 2687 3337 4378 4520 3348 3844 M627 REACTOME_TGF_BETA_RECEPTOR_SIGNALING_IN_EMT_EPITHELIAL_TO_MESENCHYMAL_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TGF_BETA_RECEPTOR_SIGNALING_IN_EMT_EPITHELIAL_TO_MESENCHYMAL_TRANSITION.html Genes involved in TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) 26/32 Reactome 0.000755382632817597 0.0032003023509053 4510 3331.27272727273 3348 6.86947384115354e-05 356 0.886258748377168 -0.828343343725194 -1 3.3176135072627 4509 3447 3314 3167 356 3348 4071 4512 3102 3619 3199 3845 M6176 HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOSHIDA_LIVER_CANCER_LATE_RECURRENCE_UP.html Genes whose expression correlated with higher risk of late recurrence of hepatocellular carcinoma (HCC). 18923165 84/110 Yujin Hoshida 0.000256982642906871 0.00141370404955761 3520 2698.27272727273 3350 2.33647878213106e-05 537 1.42320280762525 -1.55579804980062 -1 6.08543004373539 3516 3682 537 3350 2799 3786 4492 1786 3649 1311 773 3846 M5968 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_GREEN_UP.html Genes from the green module which are up-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 45/79 Arthur Liberzon 0.0296695464951176 0.0521565212130187 3690 3110.63636363636 3351 0.00273430874811399 1311 0.939052647177315 0.970841957833452 1 1.80729271141474 3686 2916 3078 3356 1311 4649 3351 1872 2781 3815 3402 3847 M3889 ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD1_AND_CD2_UP.html Genes commonly up-regulated in CD-1 and CD-2 clusters of multiple myeloma samples and which were higher expressed in the CD-1 group. 16728703 126/158 Kevin Vogelsang 0.599169001099084 0.665430043573571 4005 3237.18181818182 3351 0.0797505367299704 1267 0.957180716222077 -1.00632046870048 -1 0.253966681942212 4002 1267 3351 2371 4502 3722 4159 2617 2449 2950 4219 3848 M17842 REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_24_HYDROXYCHOLESTEROL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_BILE_ACIDS_AND_BILE_SALTS_VIA_24_HYDROXYCHOLESTEROL.html Genes involved in Synthesis of bile acids and bile salts via 24-hydroxycholesterol 10/20 Reactome 0.00705447226912144 0.0165822256525165 3355 2921.27272727273 3352 0.000643381369080107 803 1.59921113130016 -1.73164566494175 -1 4.27212542326381 3352 3563 1431 3500 803 4622 4425 1407 4332 2178 2521 3849 M4956 BIOCARTA_MONOCYTE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MONOCYTE_PATHWAY.html Monocyte and its Surface Molecules 10/16 BioCarta 0.0165248221930705 0.0325769682936445 2625 3373.27272727273 3353 0.0015136605405527 905 2.09683354656511 1.8815180299162 1 4.67878404602998 2624 4263 905 3125 3353 3899 4388 4563 4646 2177 3163 3850 M7528 KEGG_PANTOTHENATE_AND_COA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PANTOTHENATE_AND_COA_BIOSYNTHESIS.html Pantothenate and CoA biosynthesis 17/20 KEGG 0.0540588776653766 0.0861147156869988 3300 3052.27272727273 3354 0.00503952697879939 1029 0.999833817331614 -0.532739162073881 -1 1.59756639771362 3298 1029 1996 3727 3354 4707 4135 1152 3561 3519 3097 3851 M9524 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN.html Down-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs moderately differentiated tumors. 18679425 152/229 Jessica Robertson 1.86586935492928e-08 3.89742890249469e-07 3410 2572.72727272727 3355 1.69624488250376e-09 185 1.44835262599101 1.1776142333988 1 13.9289417080492 3408 1769 185 1414 3355 3642 3815 3451 2276 282 4703 3852 M865 REACTOME_RNA_POL_II_PRE_TRANSCRIPTION_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_II_PRE_TRANSCRIPTION_EVENTS.html Genes involved in RNA Polymerase II Pre-transcription Events 61/69 Reactome 0.062487306500927 0.0971156031229422 2445 3243 3356 0.00584873656454335 1608 0.566493564501846 -0.581209590258979 -1 0.860733919226915 2442 3725 4133 4137 1608 2102 2555 3356 3810 4578 3227 3853 M19275 LAU_APOPTOSIS_CDKN2A_DN http://www.broadinstitute.org/gsea/msigdb/cards/LAU_APOPTOSIS_CDKN2A_DN.html Genes down-regulated by UV-irradiation in cervical cancer cells after knockdown of CDKN2A [GeneID=1029]. 17369842 7/8 Leona Saunders 9.21173360962165e-05 0.000617604867008724 3650 2903.09090909091 3359 9.2121154840632e-06 134 0.656111967737878 -0.524542925164156 -1 3.15946892377178 3646 1090 4329 2422 134 4491 4110 4581 550 3359 3222 3854 M1783 POS_RESPONSE_TO_HISTAMINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/POS_RESPONSE_TO_HISTAMINE_DN.html Genes gradually down-regulated by histamine [PubChem=774] in B16-F10 melanoma tumors. 18339882 14/14 Jessica Robertson 0.534990537249132 0.603382398044421 2910 3251.09090909091 3359 0.0672414176353737 2415 0.759819418215492 -1.17368463859458 -1 0.250045835638419 2908 3917 3708 3630 2879 3072 2415 2532 3359 3885 3457 3855 M872 REACTOME_L1CAM_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_L1CAM_INTERACTIONS.html Genes involved in L1CAM interactions 100/131 Reactome 0.301696350378342 0.365635946483349 4470 2758.63636363636 3360 0.0321184525391177 632 1.15415166127736 -0.887117005035924 -1 0.756618228949467 4469 676 1480 632 4249 3776 4697 4100 1159 1747 3360 3856 M12398 MAINA_HYPOXIA_VHL_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAINA_HYPOXIA_VHL_TARGETS_UP.html Genes up-regulated by hypoxia in RCC4 cells (renal cell carcinoma) engineered to stably express VHL [GeneID=7428] off a plasmid vector. 15824735 7/8 Leona Saunders 0.0157066808404315 0.0313602087846179 2695 3155.09090909091 3360 0.00158188128203057 1097 1.05335797025745 1.05335797025745 1 2.37649471716633 2691 4278 4395 3954 1097 3579 3196 1543 3985 3360 2628 3857 M801 REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_ATF6_ALPHA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_CHAPERONE_GENES_BY_ATF6_ALPHA.html Genes involved in Activation of Chaperone Genes by ATF6-alpha 17/18 Reactome 0.0286503710446241 0.0507389380646563 1155 2735.45454545455 3362 0.0026391299468602 949 0.717330885526434 0.717330885526434 1 1.39342508807244 1151 4241 3362 4293 1292 1103 949 3638 4689 3976 1396 3858 M4988 JAERVINEN_AMPLIFIED_IN_LARYNGEAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/JAERVINEN_AMPLIFIED_IN_LARYNGEAL_CANCER.html Genes whose expression was increased due to copy number gain in laryngeal cancer tumors (both in primary cultures and cell lines). 16715129 44/50 Arthur Liberzon 0.287409392152716 0.351625798590155 3635 3045.27272727273 3362 0.0303347618549681 1944 0.852117800012235 -0.990554124252471 -1 0.580284363794165 3633 3362 3923 4609 3371 1944 1957 2044 2320 4128 2207 3859 M10702 JAEGER_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAEGER_METASTASIS_DN.html Genes down-regulated in metastases from malignant melanoma compared to the primary tumors. 17289871 327/478 Leona Saunders 5.11308844796612e-23 7.09816984541179e-21 3460 2656.36363636364 3364 4.64826222542375e-24 22 1.44634192922886 -1.51491872801889 -1 43.7282477970974 3459 1706 22 726 4492 4041 3025 4279 3364 56 4050 3860 M11592 MAHADEVAN_RESPONSE_TO_MP470_UP http://www.broadinstitute.org/gsea/msigdb/cards/MAHADEVAN_RESPONSE_TO_MP470_UP.html Top genes up-regulated in the GIST (gastrointestinal stromal tumor) cell line resistant to imatinib [PubChem=5291] after treatment with MP470, a protein kinase inhibitor. 17325667 21/29 Arthur Liberzon 0.68618940391 0.690284310838704 2880 3338.54545454545 3364 0.1 1882 1.16536979065968 -1.21816020700097 -1 0.281379587343304 2879 3494 1882 4028 4368 3233 3364 4355 3335 2307 3479 3861 M17173 MCCLUNG_DELTA_FOSB_TARGETS_8WK http://www.broadinstitute.org/gsea/msigdb/cards/MCCLUNG_DELTA_FOSB_TARGETS_8WK.html Genes up-regulated in the nucleus accumbens (a major reward center in brain) 8 weeks after induction of deltaFosB, a FOSB [GeneID=2354] splice variant. 14566342 74/99 John Newman 0.495281719945073 0.564532653499334 3080 3345.63636363636 3365 0.060267043897284 2202 0.990968411899497 1.04450475051644 1 0.369124580710483 3079 4418 2391 4408 2803 2202 3365 4087 3743 3812 2494 3862 M18008 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_RED_DN.html Genes from the red module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 38/50 Arthur Liberzon 0.643815124343072 0.690284310838704 3480 3138.27272727273 3366 0.0895769912174698 1465 1.30494269647221 1.17634697932102 1 0.315092266045456 3480 3366 2228 2356 4277 4453 3952 3121 1465 1683 4140 3863 M12275 BROWNE_HCMV_INFECTION_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_24HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 24 h time point that were not up-regulated at the previous time point, 20 h. 11711622 209/260 John Newman 0.68618940391 0.690284310838704 2630 3494.27272727273 3366 0.1 2361 1.09947160906591 1.112816747489 1 0.265462427704092 2629 4703 3099 4296 4550 3597 3366 2985 2361 3064 3787 3864 M19946 LI_CYTIDINE_ANALOG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/LI_CYTIDINE_ANALOG_PATHWAY.html The 'cytidine analog pathway': genes involved in transport and metabolism of the anti-cancer analogs of cytidine: gemcitabine and cytarabine [PubChem=596;3461;6253]. 18757419 13/18 Jessica Robertson 0.54947320048981 0.617209306594932 4030 3474.63636363636 3366 0.0699205318376984 2523 1.15893682593506 -0.571145604297814 -1 0.364333783389858 4029 3097 2986 3591 3366 3133 2983 2523 4530 3847 4136 3865 M752 REACTOME_NEUROTRANSMITTER_RECEPTOR_BINDING_AND_DOWNSTREAM_TRANSMISSION_IN_THE_POSTSYNAPTIC_CELL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEUROTRANSMITTER_RECEPTOR_BINDING_AND_DOWNSTREAM_TRANSMISSION_IN_THE_POSTSYNAPTIC_CELL.html Genes involved in Neurotransmitter Receptor Binding And Downstream Transmission In The Postsynaptic Cell 94/156 Reactome 0.369158860801121 0.437576550221319 4655 3187.81818181818 3368 0.0410169971160551 1821 1.00153418813797 -0.982821269784403 -1 0.539326111175649 4652 2824 2266 2722 3718 2946 3712 3561 3476 3368 1821 3866 M12399 BIOCARTA_CFTR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CFTR_PATHWAY.html Cystic Fibrosis Transmembrane Conductance Regulator And Beta 2 Adrenergic Receptor Pathway 15/17 BioCarta 0.288304851142976 0.352447266872533 4625 3303.54545454545 3369 0.0304455983904826 953 0.964333665998032 -1.23699136721265 -1 0.65524985583521 4625 3079 2951 3369 4560 4709 3558 4127 953 2785 1623 3867 M3686 SA_REG_CASCADE_OF_CYCLIN_EXPR http://www.broadinstitute.org/gsea/msigdb/cards/SA_REG_CASCADE_OF_CYCLIN_EXPR.html Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases. 13/24 SigmaAldrich 0.68618940391 0.690284310838704 3370 3158.63636363636 3369 0.1 1050 1.05388749975082 -0.973333773384366 -1 0.254451963872898 3369 1050 2896 2640 3782 4363 4038 4666 1700 2571 3670 3868 M18086 DAIRKEE_CANCER_PRONE_RESPONSE_BPA_E2 http://www.broadinstitute.org/gsea/msigdb/cards/DAIRKEE_CANCER_PRONE_RESPONSE_BPA_E2.html 'Cancer prone response profile' (CPRP): genes common to estradiol and bisphenol A [PubChem=5757;6623] response of epithelial cell cultures from patients at high risk of breast cancer. 18381411 155/217 Jessica Robertson 0.501292063411967 0.570006875284145 3310 3463 3369 0.0612899230843332 2205 1.0120902339654 0.920862376114186 1 0.370629725504326 3307 3208 3617 4274 2823 3369 3357 3673 2205 3767 4493 3869 M4911 JISON_SICKLE_CELL_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/JISON_SICKLE_CELL_DISEASE_DN.html Genes down-regulated in peripheral blood mononuclear cells (PBMC) from sickle cell disease patients compared to those from healthy subjects. 15031206 227/300 Jessica Robertson 0.0497378190896116 0.0804532234759996 725 2854.45454545455 3370 0.00462720250070148 638 0.907397712979501 0.845616223875224 1 1.49007171293047 721 4700 4067 4670 3370 638 688 2994 3511 4344 1696 3870 M497 REACTOME_PROCESSING_OF_INTRONLESS_PRE_MRNAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSING_OF_INTRONLESS_PRE_MRNAS.html Genes involved in Processing of Intronless Pre-mRNAs 18/18 Reactome 0.245234829862807 0.306868610008603 3375 3219.63636363636 3372 0.0252528222277839 1341 0.631519789963593 -0.454507410867085 -1 0.48606218066049 3372 3510 3912 4254 2909 1341 1450 2711 4298 4521 3138 3871 M14636 OUYANG_PROSTATE_CANCER_PROGRESSION_DN http://www.broadinstitute.org/gsea/msigdb/cards/OUYANG_PROSTATE_CANCER_PROGRESSION_DN.html Genes down-regulated during prostate cancer progression in mice heterozygotic for both NKX3.1 and PTEN [GeneID=4824;5728]. 18381418 25/28 Jessica Robertson 0.368403306255452 0.436790657002194 2615 3248.27272727273 3372 0.040912638641278 1744 0.749504332572292 0.870419776661168 1 0.404459426643781 2611 4181 3372 3791 3266 3435 1744 2637 4557 3921 2216 3872 M19304 TESAR_ALK_TARGETS_HUMAN_ES_5D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_HUMAN_ES_5D_UP.html Genes up-regulated in hES cells (human embryonic stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=4521392]. 17597760 3/9 Jessica Robertson 0.6513215599 0.690284310838704 3625 3301.09090909091 3373 0.1 1869 1.0947324972575 -0.889529436077018 -1 0.264317734521698 3622 2188 4468 2055 4306 3373 2987 3486 1869 4668 3290 3873 M2031 RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RAMPON_ENRICHED_LEARNING_ENVIRONMENT_EARLY_DN.html Genes down-regulated in the brain cortex of mice that were exposed to an enriched learning environment for one day. 11070096 14/16 Arthur Liberzon 0.0469190665420741 0.0762859090866654 3535 3196.36363636364 3373 0.00435914884572398 1495 0.834505740618487 -0.64363242946232 -1 1.39928913006128 3534 2630 3324 3373 1495 3526 3988 2199 4281 3888 2922 3874 M14772 NOJIMA_SFRP2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NOJIMA_SFRP2_TARGETS_UP.html Cellular proliferation, growth, apoptosis and Wnt signaling genes up-regulated in SNU638 cells (gastric cancer) by overexpression of SFRP2 [GeneID=6423] off a plasmid vector. 17297461 42/48 Arthur Liberzon 0.0161474054912473 0.0320773375078651 2635 3218.36363636364 3374 0.00147883231006757 1070 1.07845412859098 1.22418116036261 1 2.41722689532287 2634 4477 1875 4430 1070 3596 3878 2720 4344 3374 3004 3875 M855 REACTOME_MAP_KINASE_ACTIVATION_IN_TLR_CASCADE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MAP_KINASE_ACTIVATION_IN_TLR_CASCADE.html Genes involved in MAP kinase activation in TLR cascade 55/56 Reactome 0.15761410750919 0.211106296096304 2065 3204.09090909091 3375 0.0154715274165213 1194 0.631948352827608 0.782350405992315 1 0.64043672372061 2062 3732 4032 4319 3375 2638 1194 2931 3861 4325 2776 3876 M7357 LEE_EARLY_T_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_EARLY_T_LYMPHOCYTE_UP.html Genes up-regulated at early stages of progenitor T lymphocyte maturation compared to the late stages. 15210650 123/177 Arthur Liberzon 0.68618940391 0.690284310838704 1875 3331.72727272727 3375 0.1 1873 1.04096291574841 -1.03833554791714 -1 0.251330137718347 1873 4032 3375 3856 3265 2746 2545 4481 2990 4101 3385 3877 M5291 BIOCARTA_CDC42RAC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CDC42RAC_PATHWAY.html Role of PI3K subunit p85 in regulation of Actin Organization and Cell Migration 26/29 BioCarta 0.51215524302135 0.581099218043455 4680 3236.18181818182 3377 0.0631674593462489 991 0.869290653429653 0.887637695391243 1 0.307403280452638 4676 2039 3377 2471 2842 3633 3502 4484 991 3193 4390 3878 M15841 FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_OK_VS_DONOR_DN.html Genes down-regulated in kidney biopsies from patients with well functioning kidneys more than 1-year post transplant compared to the biopsies from normal living kidney donors. 15307835 26/42 Jean Junior 2.52423940473934e-05 0.000221457434765236 4595 2541 3377 2.29478942532885e-06 58 0.74585563399812 -0.784092075582545 -1 4.09014059035618 4593 301 3382 774 58 4682 3888 3377 153 3624 3119 3879 M1776 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_DN.html All common down-regulated stress response genes (Human Environmental Stress Response, H-ESR). 15897889 23/24 Jessica Robertson 0.12907792945198 0.178717461722895 2280 3328.54545454545 3378 0.0124852927027935 1086 0.985626931126042 1.09690779759778 1 1.10590404235956 2279 4538 3144 4404 4307 2415 1086 3378 4470 3867 2726 3880 M2309 AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_UP http://www.broadinstitute.org/gsea/msigdb/cards/AZARE_NEOPLASTIC_TRANSFORMATION_BY_STAT3_UP.html Genes up-regulated in RWPE-1 cells (prostate cancer) upon expression of constitutively active form of STAT3 [GeneID=6774]. 17438134 175/256 Arthur Liberzon 5.45548366889872e-06 6.07308559367971e-05 1755 2953.36363636364 3378 4.95954290660437e-07 343 1.32983031348397 1.40379084181342 1 8.41383537538488 1752 4353 343 4289 3010 3378 3045 3901 3980 657 3779 3881 M9011 KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION.html Vasopressin-regulated water reabsorption 50/62 KEGG 0.68618940391 0.690284310838704 3380 3274.18181818182 3379 0.1 1943 0.894452259285243 0.855955213736631 1 0.215941702842466 3379 1943 3171 2408 4423 4211 2656 3553 2919 3717 3636 3882 M6110 BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN.html Genes down-regulated in patients at the incipient stage of Alzheimer's disease. 14769913 259/311 John Newman 0.178571403449208 0.234713735527781 3675 2998.45454545455 3379 0.0177238037292614 1672 0.978856142422006 -1.01251329752116 -1 0.92444298950013 3672 2738 3379 1948 2171 2311 4006 3465 3474 4147 1672 3883 M13247 BIOCARTA_TCYTOTOXIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TCYTOTOXIC_PATHWAY.html T Cytotoxic Cell Surface Molecules 7/15 BioCarta 0.00972267310882028 0.0213645330882829 2370 3395.72727272727 3380 0.000976547557695974 931 1.95020163417402 -2.52746457986293 -1 4.88774023651938 2367 4284 4197 4363 931 3380 4493 3249 4656 2469 2964 3884 M6427 BIOCARTA_THELPER_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_THELPER_PATHWAY.html T Helper Cell Surface Molecules 7/15 BioCarta 0.00972267310882028 0.0213645330882829 2370 3396.72727272727 3381 0.000976547557695974 932 1.95020163417402 -2.52746457986293 -1 4.88774023651938 2368 4285 4198 4364 932 3381 4494 3250 4657 2470 2965 3885 M16201 WONG_ENDMETRIUM_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WONG_ENDMETRIUM_CANCER_UP.html Genes up-regulated in cancer endometrium samples compared to the normal endometrium. 17043662 32/52 Arthur Liberzon 2.64075486666454e-05 0.000229124319313541 3965 2991.72727272727 3381 2.40071505937874e-06 411 2.01998949435724 -1.76166432920814 -1 11.0326449813 3963 3810 411 3019 4571 4611 4221 3046 1387 489 3381 3886 M17122 NUYTTEN_EZH2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_EZH2_TARGETS_DN.html Genes down-regulated in PC3 cells (prostate cancer) after knockdown of EZH2 [GeneID=2146] by RNAi. 17724462 1197/1509 Jessica Robertson 0.6513215599 0.690284310838704 4435 3239 3382 0.1 1467 0.94565232761416 -0.950719159583707 -1 0.228308655031736 3382 2696 4431 2962 3818 2121 3666 3856 1467 4432 2798 3887 M7084 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_LARGE_VS_TINY_UP.html Genes up-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic B.D. chr3 (BD, large HSC size) vs parental B6 strain (tiny HSC size). 17220891 65/89 Leona Saunders 0.518804932155067 0.587232441192306 3785 3164.54545454545 3385 0.0643355993843429 1669 1.21456080679679 -1.02888491930039 -1 0.421231601477797 3782 2415 1669 3154 3879 4024 3703 3385 2358 1805 4636 3888 M9025 OUILLETTE_CLL_13Q14_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUILLETTE_CLL_13Q14_DELETION_UP.html Genes up-regulated in chronic lymphocytic leukemia (CLL) samples bearing deletions in the 13q14 region. 18281475 95/129 Jessica Robertson 0.43119990772354 0.499814448548158 3890 2772.54545454545 3385 0.05 56 1.02138745899591 -0.91993771144523 -1 0.461503524323917 3889 56 3262 565 3454 4090 3066 3466 560 3385 4705 3889 M658 REACTOME_CHONDROITIN_SULFATE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CHONDROITIN_SULFATE_BIOSYNTHESIS.html Genes involved in Chondroitin sulfate biosynthesis 16/21 Reactome 0.0285006939569958 0.0506107131215275 2235 3183.36363636364 3387 0.00262515954274503 1286 1.78604438489534 -1.57333998487222 -1 3.47251848408771 2234 4597 1757 4396 1286 3865 3340 3387 4238 2325 3592 3890 M15066 LIU_CMYB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_CMYB_TARGETS_UP.html Genes up-regulated in MCF-7 cells (breast cancer) by overexpression of CMYB [GeneID=4602] off adenovirus vector. 16205643 227/304 Arthur Liberzon 0.68618940391 0.690284310838704 3390 2967.63636363636 3387 0.1 544 1.01515264385635 -0.931254552856117 -1 0.245095880442936 3387 1207 2141 544 4272 4403 3823 4642 1664 2128 4433 3891 M740 SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SEITZ_NEOPLASTIC_TRANSFORMATION_BY_8P_DELETION_DN.html Genes down-regulated in CT60/4 cells (breast cancer reverted to normal by transfer of chromosome 8p region) vs parental MDA-MB-231 cells (deleted chromosome 8p). 15580292 36/43 Arthur Liberzon 0.0249774240953447 0.0454643967226648 4625 3184.90909090909 3387 0.00229687209575194 1228 1.09856227311016 -1.03039676533554 -1 2.2126083654407 4622 1458 1839 3066 1228 3322 4094 3999 4261 3758 3387 3892 M145 PID_P53_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P53_DOWNSTREAM_PATHWAY.html Direct p53 effectors 18832364 160/185 Pathway Interaction Database 0.626146298318279 0.690284310838704 3390 3378.36363636364 3388 0.0855610871753484 1758 1.07818310003447 -0.848234334433141 -1 0.260320364773992 3388 4355 1758 4232 4527 3444 3235 3243 2168 2510 4302 3893 M13709 NIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_12Q13_Q21_AMPLICON.html Genes within amplicon 12q13-q21 identified in a copy number alterations study of 191 breast tumor samples. 19010930 51/63 Jessica Robertson 0.109103777357095 0.155064688083556 4140 3106.45454545455 3388 0.0104475261310643 1469 0.973225837739455 -0.875751350776302 -1 1.1820245168074 4140 1930 2957 1485 3840 3819 3388 1469 4189 3158 3796 3894 M1380 DEN_INTERACT_WITH_LCA5 http://www.broadinstitute.org/gsea/msigdb/cards/DEN_INTERACT_WITH_LCA5.html Proteins shown to interact with LCA5 [GeneID=167691] in vivo. 17546029 36/41 Jessica Robertson 0.367069007838203 0.435536882100634 3760 3397.27272727273 3390 0.0407286199538681 2209 0.658435060301509 -0.747986527214515 -1 0.356535736832508 3759 3390 3557 2475 4074 3165 3312 2209 4631 4283 2515 3895 M1420 MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAGRANGEAS_MULTIPLE_MYELOMA_IGLL_VS_IGLK_DN.html Down-regulated genes discriminating multiple myeloma samples by the ype of immunoglobulin light chain they produce: Ig lambda (IGLL) vs Ig kappa (IGLK). 12623842 29/32 Kate Stafford 0.018324256819708 0.0353310834105481 3225 2958 3391 0.00167988065313459 717 0.843574622395245 -0.777187644224914 -1 1.83763804296913 3225 3831 3473 4039 1722 4010 3381 717 1224 3391 3525 3896 M16121 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS.html Fc gamma R-mediated phagocytosis 96/116 KEGG 0.120990235511752 0.169307415243246 3690 2889.09090909091 3392 0.0116551169648888 44 0.894177729141106 0.863390495195566 1 1.03480400575082 3690 44 2723 400 1930 4349 3970 4650 3392 1988 4644 3897 M3075 BIOCARTA_SET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SET_PATHWAY.html Granzyme A mediated Apoptosis Pathway 12/25 BioCarta 0.227626460826311 0.288206935572104 3415 3351.36363636364 3394 0.0232071100928031 2001 0.528335744210042 -0.545930218659569 -1 0.428228824754976 3414 2633 3702 3362 2312 4525 4158 2865 2001 4499 3394 3898 M9990 REACTOME_APOPTOTIC_CLEAVAGE_OF_CELL_ADHESION_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOTIC_CLEAVAGE_OF_CELL_ADHESION_PROTEINS.html Genes involved in Apoptotic cleavage of cell adhesion proteins 15/19 Reactome 0.00439480485361332 0.0120217921493867 4695 3349 3394 0.000400328065169744 674 0.814966934580427 -1.08782588540925 -1 2.34785036084001 3394 3080 2959 3105 674 3700 2649 4692 4491 3400 4695 3899 M12678 BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_D_CLUSTER_DN.html Genes from cluster 4: down-regulated in group D of tumors arising from overexpression of BCL2L1 and MYC [GeneID=598;4609] in plasma cells. 17483317 56/61 Jessica Robertson 0.326854258898696 0.392258352911733 2475 3437.27272727273 3394 0.035341590261446 2121 0.886279006003157 0.934958815099047 1 0.540394144839326 2472 3724 2817 3281 3826 4663 3980 2121 4176 3394 3356 3900 M2191 SUBTIL_PROGESTIN_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SUBTIL_PROGESTIN_TARGETS.html Genes responding to progestin R5020 [PubChem=36709] treatment of T47D-MTVL cells (breast cancer). 18378698 56/62 Arthur Liberzon 0.0060685682065855 0.0147875967918264 4545 3195.36363636364 3395 0.000553215720097671 412 1.05480686573183 -0.99444593017649 -1 2.89650497987786 4542 4100 3173 4128 2855 4504 3508 412 1974 3395 2558 3901 M4669 REACTOME_INFLUENZA_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INFLUENZA_LIFE_CYCLE.html Genes involved in Influenza Life Cycle 163/257 Reactome 0.00471606214787384 0.0127053729097971 705 2893.63636363636 3396 0.000429654749841375 697 0.657712584408919 0.642001398681364 1 1.87108971914574 705 4377 4167 4546 697 1372 911 3396 4517 4469 2673 3902 M3873 BIOCARTA_CHEMICAL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CHEMICAL_PATHWAY.html Apoptotic Signaling in Response to DNA Damage 29/34 BioCarta 0.0163698018342216 0.0323557222183945 3400 2988.72727272727 3398 0.00149935370244126 1075 0.785245963215937 -0.650093581640446 -1 1.75558500905749 3398 2020 3180 3432 1075 4174 2686 2009 3588 3775 3539 3903 M2291 PASINI_SUZ12_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PASINI_SUZ12_TARGETS_UP.html Genes up-regulated in ES (embryonic stem cells) with defficient SUZ12 [GeneID=23512]. 17339329 117/167 Arthur Liberzon 0.0530433868598572 0.0848981980259498 4420 2700.18181818182 3398 0.0049424730311929 646 1.13556045926017 -1.12499873964845 -1 1.82497754623812 4420 646 1089 940 4044 3398 4674 4714 1268 958 3551 3904 M13720 KEGG_LYSINE_DEGRADATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LYSINE_DEGRADATION.html Lysine degradation 47/50 KEGG 0.68618940391 0.690284310838704 4510 3444.54545454545 3399 0.1 1262 1.02574300510841 -1.26585502168549 -1 0.247653894436781 4510 3747 3399 3607 4054 3275 4628 3035 1262 3283 3090 3905 M1180 OHASHI_AURKA_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/OHASHI_AURKA_TARGETS.html Candidate substrate proteins of AURKA [GeneID=6790]. 16785988 8/8 Arthur Liberzon 0.6513215599 0.690284310838704 3190 3539.27272727273 3401 0.1 2035 0.536745947469269 0.536745947469269 1 0.129540707679541 3188 3123 4380 3342 3425 3988 3161 4238 2035 4651 3401 3906 M17261 KAYO_AGING_MUSCLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KAYO_AGING_MUSCLE_DN.html Downregulated in the vastus lateralis muscle of aged vs young adult rhesus monkeys 11309484 174/237 John Newman 0.68618940391 0.690284310838704 4405 3031.18181818182 3401 0.1 605 1.06771815150454 -0.941980768328627 -1 0.257792643183829 4401 1229 2879 605 4380 3401 4401 4131 902 3294 3720 3907 M223 PID_BETA_CATENIN_NUC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BETA_CATENIN_NUC_PATHWAY.html Regulation of nuclear beta catenin signaling and target gene transcription 18832364 96/123 Pathway Interaction Database 0.0935422420560709 0.136566465358693 4270 3010.81818181818 3403 0.00888852044368933 1617 1.14513138526424 -1.26626466072964 -1 1.48562608165978 4270 2360 1617 3600 1795 4062 4013 3667 3403 1989 2343 3908 M1088 REACTOME_METABOLISM_OF_PORPHYRINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_PORPHYRINS.html Genes involved in Metabolism of porphyrins 15/22 Reactome 0.000590265961877212 0.00262093635000982 4110 2967.63636363636 3403 5.36749446679495e-05 329 0.776744208542917 -0.729305173270506 -1 3.00873548805649 4106 2624 3114 3536 329 1449 1690 3953 4163 3403 4277 3909 M12490 ONKEN_UVEAL_MELANOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/ONKEN_UVEAL_MELANOMA_UP.html Genes up-regulated in uveal melanoma: class 2 vs class 1 tumors. 16651410 1064/1255 Arthur Liberzon 0.174543246267786 0.230124056531829 3405 2915 3405 0.0189990396784956 421 0.979104867628568 -0.937560162943802 -1 0.937278198958747 3405 465 4277 421 2197 4664 3856 3740 1982 2845 4213 3910 M1116 CAIRO_PML_TARGETS_BOUND_BY_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_PML_TARGETS_BOUND_BY_MYC_UP.html Genes up-regulated in MEF cells (embryonic fibroblasts) after knockout of PML [GeneID=5371] and whose promoters were bound by MYC [GeneID=4609]. 15735755 31/35 Lauren Kazmierski 0.68618940391 0.690284310838704 2865 3414.54545454545 3405 0.1 2580 0.869952550511236 0.836720957614708 1 0.210024001227055 2863 3405 2580 2950 4685 2774 2601 3965 4429 3490 3818 3911 M258 PID_BARD1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_BARD1_PATHWAY.html BARD1 signaling events 18832364 34/36 Pathway Interaction Database 0.68618940391 0.690284310838704 4520 3500.09090909091 3406 0.1 2323 0.575363242261559 -0.551054567050255 -1 0.138868395199549 2614 3406 3945 4118 3172 2323 3809 3317 4518 4516 2763 3912 M13809 LIAO_METASTASIS http://www.broadinstitute.org/gsea/msigdb/cards/LIAO_METASTASIS.html Genes up-regulated in the samples with intrahepatic metastatic hepatocellular carcinoma (HCC) vs primary HCC. 18504433 725/853 Jessica Robertson 0.6513215599 0.690284310838704 2915 3508 3406 0.1 2284 1.04168116455526 1.14270761550484 1 0.251503624765225 2913 3964 4436 2969 3406 4636 3636 3099 2284 2996 4249 3913 M4282 BHATTACHARYA_EMBRYONIC_STEM_CELL http://www.broadinstitute.org/gsea/msigdb/cards/BHATTACHARYA_EMBRYONIC_STEM_CELL.html The 'stemnes' signature: genes up-regulated and common to 6 human embryonic stem cell lines tested. 15070671 151/195 Kate Stafford 0.231490351514128 0.291992105597724 1890 3189.09090909091 3406 0.0236523528117426 1889 1.18354329929537 1.12146092960559 1 0.949357910005618 1889 4363 3469 4661 3984 3406 2690 1901 1928 3683 3106 3914 M655 REACTOME_SYNTHESIS_OF_PIPS_AT_THE_LATE_ENDOSOME_MEMBRANE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_PIPS_AT_THE_LATE_ENDOSOME_MEMBRANE.html Genes involved in Synthesis of PIPs at the late endosome membrane 13/13 Reactome 0.00797167909182566 0.0181945480238961 3410 2766.18181818182 3409 0.000727337434726009 125 1.13908472099615 -1.32851274258939 -1 2.97403645411838 3409 4245 3236 3554 837 4530 3895 1173 125 3843 1581 3915 M6752 TENEDINI_MEGAKARYOCYTE_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/TENEDINI_MEGAKARYOCYTE_MARKERS.html Genes essential to the development of megakaryocytes, as expressed in normal cells and essential thrombocythemic cells (ET). 15271793 79/96 Kate Stafford 0.0475056309467963 0.0770538068965218 4665 3256.09090909091 3410 0.00441486966173478 1072 1.21340819060987 -1.08924903058614 -1 2.02675640232124 4662 1869 1072 3201 4517 4712 3410 3751 2740 2233 3650 3916 M12243 SCHUHMACHER_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHUHMACHER_MYC_TARGETS_UP.html Genes up-regulated in P493-6 cells (Burkitt's lymphoma) induced to express MYC [GeneID=4609]. 11139609 105/115 Yujin Hoshida 0.481018260372246 0.550802083686803 1720 3138.27272727273 3411 0.0578832302989523 1103 0.967260785051422 1.13987759441003 1 0.375811698330296 1720 3665 3819 3422 4590 3253 3265 2415 1103 3858 3411 3917 M18750 CAMPS_COLON_CANCER_COPY_NUMBER_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAMPS_COLON_CANCER_COPY_NUMBER_UP.html Genes from chromosomal copy number gains in a panel of 51 primary colon carcinoma samples. 18316590 87/166 Jessica Robertson 0.280343671751944 0.344273836957841 2995 3055 3412 0.0294646081047431 1537 0.94404896483673 0.887522310840066 1 0.655899459824217 2994 4394 3412 2160 3996 1818 1561 4181 1537 3768 3784 3918 M30 PID_HDAC_CLASSII_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HDAC_CLASSII_PATHWAY.html Signaling events mediated by HDAC Class II 18832364 50/63 Pathway Interaction Database 0.00360995909882067 0.0103959773925769 3870 3048.45454545455 3413 0.000328717844553367 312 1.17662369915604 -1.24124176053425 -1 3.50121258602429 3867 4473 2755 4504 2134 3472 3542 312 3413 2434 2627 3919 M17042 CAFFAREL_RESPONSE_TO_THC_24HR_5_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_5_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated with 5 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 76/97 Jessica Robertson 0.68618940391 0.690284310838704 4125 3208.72727272727 3413 0.1 735 1.01579334532677 -1.07193683414755 -1 0.245250636573363 4124 735 3186 2398 3463 4154 4209 2940 2663 3413 4011 3920 M2203 PHESSE_TARGETS_OF_APC_AND_MBD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/PHESSE_TARGETS_OF_APC_AND_MBD2_DN.html Genes down-regulated in small intestine upon loss of both APC and MBD2 [GeneID=324, 8932]. 18644872 17/22 Arthur Liberzon 0.68618940391 0.690284310838704 3730 3223.81818181818 3413 0.1 503 1.1233014462881 -0.89715069543653 -1 0.271218327397655 3730 3882 2827 3043 3349 3487 3413 4228 503 2995 4005 3921 M1275 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM2.html Cluster PAM2: genes up-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 222/290 Leona Saunders 0.00170190932772344 0.00591532549842021 3925 3021.36363636364 3415 0.000154838849472728 668 1.12624856183364 -1.17227440560503 -1 3.7651579505454 3923 3184 668 3305 2010 3602 4245 4050 3527 1306 3415 3922 M10739 CROONQUIST_NRAS_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_SIGNALING_DN.html Genes down-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing a constantly active form of NRAS [GeneID=4893] off a plasmid vector compared to those grown in the presence of IL6 [GeneID=3569]. 12791645 90/102 Arthur Liberzon 0.68618940391 0.690284310838704 1905 3063.45454545455 3416 0.1 1644 0.990363473201559 -0.995107021805505 -1 0.239108261709108 1903 1852 3593 2472 3171 3681 3433 4461 1644 4072 3416 3923 M16120 BIOCARTA_SALMONELLA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SALMONELLA_PATHWAY.html How does salmonella hijack a cell 20/24 BioCarta 0.180376491383745 0.236856964274484 3260 3513.72727272727 3417 0.0179202318542742 2176 0.920970405888712 0.88344322836142 1 0.864313377816916 3257 4216 3248 3885 2176 4517 3338 3800 4087 2710 3417 3924 M1060 REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYTOKINE_SIGNALING_IN_IMMUNE_SYSTEM.html Genes involved in Cytokine Signaling in Immune system 294/406 Reactome 0.68618940391 0.690284310838704 3020 3598.09090909091 3417 0.1 3019 0.950662875043552 -0.96192319189293 -1 0.229518911238882 3019 3614 3260 3247 3528 3417 3283 4495 3303 3697 4716 3925 M3697 GOUYER_TATI_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GOUYER_TATI_TARGETS_DN.html Genes down-regulated in constitutively invasive HT-29 5M21 cells (colon cancer) vs those expressing functionally inactive TATI [GeneID=6690]. 18317448 19/22 Jessica Robertson 0.0324817305470525 0.0560640205418186 4430 3163.09090909091 3417 0.00299740524772027 997 1.35019509558567 1.54419427428523 1 2.5350534439766 4429 3499 997 3932 3000 3923 3417 2742 4417 1273 3165 3926 M4519 CHESLER_BRAIN_HIGHEST_EXPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/CHESLER_BRAIN_HIGHEST_EXPRESSION.html Neurologically relevant transcripts with highest abundance fold range in brain tissue among mouse strains. 15711545 63/83 Jean Junior 0.431407640547711 0.499814448548158 1610 3458.27272727273 3418 0.0500315463046817 1610 0.913151385450579 0.850531184171654 1 0.412586941948612 1610 4433 3098 4589 4022 3344 1867 4591 3705 3418 3364 3927 M1703 HOWLIN_CITED1_TARGETS_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOWLIN_CITED1_TARGETS_1_DN.html Genes down-regulated in mammary glands from the CITED1 [GeneID=4435] knockout mice: homozygotic vs. heterozygotic animals. 16278680 56/75 Arthur Liberzon 0.174886596714324 0.230512353111312 4040 3406.72727272727 3418 0.0173240413555155 1725 1.1118933249061 -1.12794589298952 -1 1.06318679201211 4040 3318 2089 3557 2945 4639 3418 1725 4046 3102 4595 3928 M2367 PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_DN http://www.broadinstitute.org/gsea/msigdb/cards/PURBEY_TARGETS_OF_CTBP1_NOT_SATB1_DN.html Genes down-regulated in HEK-293 cells (fibroblast) upon knockdown of CTBP1 but not of SATB1 [GeneID=1487, 6304] by RNAi. 19103759 519/815 Arthur Liberzon 0.0889923104004125 0.130813984767969 3420 2925.54545454545 3418 0.00927709384891369 500 1.07001078939371 -1.0806551324885 -1 1.41817008114623 3418 500 4691 840 1815 4198 3745 3639 2913 2132 4290 3929 M767 REACTOME_HOMOLOGOUS_RECOMBINATION_REPAIR_OF_REPLICATION_INDEPENDENT_DOUBLE_STRAND_BREAKS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HOMOLOGOUS_RECOMBINATION_REPAIR_OF_REPLICATION_INDEPENDENT_DOUBLE_STRAND_BREAKS.html Genes involved in Homologous recombination repair of replication-independent double-strand breaks 20/26 Reactome 0.426151390962625 0.497141513925751 2100 3106.54545454545 3421 0.0492365347660435 1941 0.945157386765561 -1.00348883461949 -1 0.430354578378982 2099 4548 3440 4420 3526 2502 2366 3421 2164 3745 1941 3930 M2881 REACTOME_LYSOSOME_VESICLE_BIOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LYSOSOME_VESICLE_BIOGENESIS.html Genes involved in Lysosome Vesicle Biogenesis 40/42 Reactome 0.228229272524229 0.288572774260477 4505 3247.45454545455 3421 0.0232764396150783 614 0.71850197126768 0.790352816349833 1 0.581807246431303 4501 857 3338 614 2313 4382 4309 3395 4538 4054 3421 3931 M2475 LIU_IL13_MEMORY_MODEL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIU_IL13_MEMORY_MODEL_DN.html Genes down-regulated in BEAS-2B cells (bronchial epithelium) stimulated with IL13 [GeneID=3596] on days 1 to 3 and then rested for the next 3 days (repeated-stimulation or memory model) 20123980 9/9 Arthur Liberzon 0.00301173367283809 0.00909926003110916 3425 3338.09090909091 3421 0.00030158232183946 608 1.08158224229559 -1.33421601077032 -1 3.31229640280598 3421 4276 4706 4012 608 3222 4653 2757 2813 2768 3483 3932 M6698 RAMASWAMY_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMASWAMY_METASTASIS_UP.html Up-regulated genes in metastatic vs primary solid tumors. 12469122 92/101 John Newman 0.206941444538522 0.266511219160115 3035 3399.63636363636 3423 0.0208574310821213 1847 0.927515068795554 0.90296307392855 1 0.79915748777645 3031 1847 2987 3413 2249 4484 3886 3789 3423 3871 4416 3933 M13736 PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP.html Up-regulated genes in head and neck cancer compared to cervical carcinoma samples. 17510386 240/306 Arthur Liberzon 0.68618940391 0.690284310838704 2900 3296.45454545455 3424 0.1 1222 0.956256543200145 0.846296843712702 1 0.230870015425127 2897 3178 3997 2191 3891 3424 2720 3804 1222 4264 4673 3934 M745 REACTOME_MRNA_CAPPING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_CAPPING.html Genes involved in mRNA Capping 29/31 Reactome 0.0287461197636658 0.0508361503501321 2190 3257.81818181818 3425 0.00264806786749164 1294 0.536497143939578 -0.592131707001487 -1 1.04145718275832 2188 4175 4058 4098 1294 2374 2883 2981 3813 4547 3425 3935 M14601 CAIRO_HEPATOBLASTOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_HEPATOBLASTOMA_UP.html Genes up-regulated in hepatoblastoma samples compared to normal liver tissue. 19061838 299/338 Arthur Liberzon 0.68618940391 0.690284310838704 4530 3173.36363636364 3425 0.1 1182 0.995400760382348 -0.985834170537656 -1 0.2403249766816 4530 1182 2882 2940 3978 2336 3929 3714 3454 3425 2537 3936 M585 REACTOME_PRE_NOTCH_TRANSCRIPTION_AND_TRANSLATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRE_NOTCH_TRANSCRIPTION_AND_TRANSLATION.html Genes involved in Pre-NOTCH Transcription and Translation 31/31 Reactome 0.507320222242145 0.576167336136411 2555 3394.54545454545 3426 0.0623271535127906 2030 0.874027816919608 0.96755410879807 1 0.313933748340741 2554 4509 3671 4278 2973 2349 2030 3020 4453 4077 3426 3937 M4288 SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_UP.html Genes up-regulated in MCF10A cells (breast cancer) grown at low (mesenchymal phenotype) compared to those grown at high (epithelial, basal-like phenotype) confluency. 18281472 224/277 Jessica Robertson 0.68618940391 0.690284310838704 2515 3494.18181818182 3426 0.1 2515 1.10611850248629 -1.17973515322592 -1 0.267067929724301 2515 4341 3426 4146 4037 3403 2808 4109 2908 3572 3171 3938 M16498 REACTOME_SEMA3A_PAK_DEPENDENT_AXON_REPULSION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SEMA3A_PAK_DEPENDENT_AXON_REPULSION.html Genes involved in Sema3A PAK dependent Axon repulsion 32/35 Reactome 0.515661198083614 0.584049956666007 2455 3229.54545454545 3428 0.0637815279038035 2046 1.11840274980269 1.29680358317986 1 0.391834465786132 2453 3808 2119 3205 3428 3525 2046 4478 4259 2736 3468 3939 M1 PID_FANCONI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FANCONI_PATHWAY.html Fanconi anemia pathway 18832364 55/62 Pathway Interaction Database 0.68618940391 0.690284310838704 3000 3548.18181818182 3429 0.1 1916 0.979813681198901 -1.05666427953948 -1 0.236560046881239 3000 3323 3823 3429 4381 3192 4694 4314 1916 4015 2943 3940 M17068 BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_TUMOR_SAMPLE_DN.html Down-regulated genes in tumor samples from colon cancer patients who developed recurrence of the disease. 16091735 14/17 Leona Saunders 0.837214300393669 0.840061968082083 3925 3267.27272727273 3429 0.15213101315851 1263 0.727101056830485 0.570004880548669 1 0.0824727684798848 3921 2120 3019 1263 3696 2733 3429 2979 4526 3882 4372 3941 M19208 RADAEVA_RESPONSE_TO_IFNA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/RADAEVA_RESPONSE_TO_IFNA1_DN.html Genes down-regulated in primary hepatocytes and Hep3B (hepatocyte) cells in response to IFNA [GeneID=3439]. 11910354 15/16 Yujin Hoshida 0.631702161117386 0.690284310838704 4175 3263.90909090909 3431 0.08680492427451 1469 1.31174480503045 -1.39286737555661 -1 0.316735258995886 4173 4586 2413 3547 3030 4201 3583 3245 1469 2225 3431 3942 M891 REACTOME_RECYCLING_PATHWAY_OF_L1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECYCLING_PATHWAY_OF_L1.html Genes involved in Recycling pathway of L1 35/41 Reactome 0.68618940391 0.690284310838704 3190 3181.72727272727 3433 0.1 778 0.917875287340358 -0.598754553109412 -1 0.221599341153115 3187 3789 3459 3594 3115 2486 3180 3433 778 3954 4024 3943 M5583 REACTOME_MRNA_SPLICING_MINOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_SPLICING_MINOR_PATHWAY.html Genes involved in mRNA Splicing - Minor Pathway 47/59 Reactome 0.106727071265894 0.152421112367631 2250 3327.54545454545 3434 0.0102078259048528 1858 0.492546523076403 -0.514783577966805 -1 0.603685865384956 2250 4122 4119 4135 1858 2489 3242 2640 3760 4554 3434 3944 M17753 BENPORATH_MYC_MAX_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_MYC_MAX_TARGETS.html Set 'Myc targets2': targets of c-Myc [GeneID=4609] and Max [GeneID=4149] identified by ChIP on chip in a Burkitt's lymphoma cell line; overlap set. 18443585 1015/1222 Jessica Robertson 0.229595994705693 0.290067744917256 3435 3359 3434 0.0257467724893557 2119 0.888357627103498 -0.896898834857473 -1 0.716381586309738 3434 4300 4454 4347 2373 2119 3788 3106 2425 4465 2138 3945 M228 PID_SMAD2_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_SMAD2_3PATHWAY.html Regulation of cytoplasmic and nuclear SMAD2/3 signaling 18832364 19/22 Pathway Interaction Database 0.0363684760501843 0.0615045528329881 1800 2869.54545454545 3435 0.00336218008146333 573 0.659743227732926 0.824933349977544 1 1.19882505742561 1800 4576 3938 4475 1893 1307 573 3661 3435 4031 1876 3946 M19076 GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_20Q13_AMPLIFICATION_UP.html Genes up-regulated in metastatic breast cancer tumors having type 2 amplification in the 20q13 region; involves MYBL2, STK6 and ZNF217 [GeneID=4605;6790;7764] 16899599 183/223 Leona Saunders 0.0394533221139387 0.066011939162634 4085 3257 3435 0.0036526491940811 1427 1.07678189217315 -1.10435570093105 -1 1.90706887639953 4084 3634 3435 3216 1427 2966 4129 3996 1969 3673 3298 3947 M10100 CHOI_ATL_ACUTE_STAGE http://www.broadinstitute.org/gsea/msigdb/cards/CHOI_ATL_ACUTE_STAGE.html Acute stage-specific genes for adult T cell leukemia (ATL). 16909099 5/15 Leona Saunders 0.115938919337474 0.163401522625523 3490 3384.27272727273 3435 0.0122472961346881 1961 1.21129255789721 1.27051684071168 1 1.4298553341615 3487 3137 4354 2856 1961 4475 4558 3200 3671 2093 3435 3948 M2488 FORTSCHEGGER_PHF8_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FORTSCHEGGER_PHF8_TARGETS_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) upon knockdown of PHF8 [GeneID=23133] by RNAi. 20421419 984/1186 Arthur Liberzon 0.293882392031559 0.358060116259411 3435 2889.36363636364 3435 0.0341988812563003 468 1.02221361232326 1.01700259356605 1 0.684059750840809 3435 468 4707 842 2517 4562 3673 3534 1464 3003 3578 3949 M6489 ZHANG_BREAST_CANCER_PROGENITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_BREAST_CANCER_PROGENITORS_DN.html Genes down-regulated in cancer stem cells isolated from mammary tumors compared to the non-tumorigenic cells. 18559513 206/242 Leona Saunders 0.261405471254864 0.324266445288556 2275 3371.63636363636 3437 0.027170084942531 2273 0.985362858497019 -0.902927508985583 -1 0.723053302970138 2273 3191 2943 3437 2395 4507 3600 3462 3966 3302 4012 3950 M514 REACTOME_SPRY_REGULATION_OF_FGF_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SPRY_REGULATION_OF_FGF_SIGNALING.html Genes involved in Spry regulation of FGF signaling 21/24 Reactome 0.00911459018219016 0.0203216181671883 1470 2613.81818181818 3438 0.000832052034195469 254 0.723251764327294 0.854548024688495 1 1.83618884951804 1467 4571 3878 3692 3438 785 254 1667 4414 4091 495 3951 M2219 WIERENGA_PML_INTERACTOME http://www.broadinstitute.org/gsea/msigdb/cards/WIERENGA_PML_INTERACTOME.html Proteins identified in complex with PML [GeneID=5371] in K562 cells (lymphoblast). 18779318 74/96 Arthur Liberzon 0.151306169757866 0.203930645704491 3615 3305.72727272727 3438 0.0148035862644699 2075 1.00820597300936 -1.09800916584628 -1 1.04453204635583 3614 4071 3021 4310 2075 3438 2920 2256 3520 2783 4355 3952 M1026 REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_THE_HIV1_EARLY_ELONGATION_COMPLEX.html Genes involved in Formation of the HIV-1 Early Elongation Complex 34/36 Reactome 0.0508777471331196 0.0819041495458133 2105 3381.45454545455 3440 0.00473581104657564 1525 0.541668843471094 -0.588245173733227 -1 0.883142799892682 2105 4504 4078 4478 1525 2441 2787 3019 4218 4601 3440 3953 M136 PID_FOXO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FOXO_PATHWAY.html FoxO family signaling 18832364 57/65 Pathway Interaction Database 0.489360812870922 0.558863546274075 3915 3450.09090909091 3441 0.0592701562343865 2263 0.743490167151311 0.725815647102686 1 0.281805379877597 3911 3312 3854 3441 2796 2537 3787 3256 2263 4260 4534 3954 M1009 REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ENDOSOMAL_SORTING_COMPLEX_REQUIRED_FOR_TRANSPORT_ESCRT.html Genes involved in Endosomal Sorting Complex Required For Transport (ESCRT) 29/32 Reactome 0.00303806512499151 0.00913000143151477 3395 3052.54545454545 3441 0.000276569875966344 591 0.625710884292435 -0.606749628954348 -1 1.91479124715917 3391 3441 3972 3635 591 2394 4644 1197 4416 4594 1303 3955 M1177 KOINUMA_COLON_CANCER_MSI_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOINUMA_COLON_CANCER_MSI_DN.html Genes down-regulated in colorectal carcinoma samples positive for MSI (microsatellite instability) compared to the MSI negative ones. 16247484 11/12 Arthur Liberzon 0.227634630468814 0.288206935572104 2930 3136.54545454545 3441 0.0232080493565463 1697 0.859158333223711 -0.859158333223711 -1 0.696434752979506 2929 3933 3441 3609 3937 1875 1882 1890 4673 4636 1697 3956 M1781 MCGOWAN_RSP6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/MCGOWAN_RSP6_TARGETS_DN.html Genes down-regulated by hemizygotic cre-lox knockout of RSP6 [GeneID=81492] in keratinocytes. 18641651 6/7 Jessica Robertson 0.0807074984704681 0.120398038173391 3445 3217.54545454545 3441 0.00837978470438039 1697 0.931642227900631 -0.451270925946917 -1 1.2851403000654 3441 4287 4529 3743 1764 3916 3551 1697 2071 3240 3154 3957 M2441 LE_NEURONAL_DIFFERENTIATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LE_NEURONAL_DIFFERENTIATION_DN.html Genes down-regulated during neuronal differentiation of SH-SY5Y cells (neuroblastoma) in response to stimulation by tretinoin (all-trans retinoic acid, ATRA) [PubChem=444795] and BDNF [GeneID=627]. 19635812 22/25 Arthur Liberzon 0.68618940391 0.690284310838704 3935 3477.36363636364 3442 0.1 1128 1.19813959467055 -1.10661121829562 -1 0.28929486192557 3933 4200 3023 3317 3442 4500 4302 3275 1128 2887 4244 3958 M3812 KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_AMYOTROPHIC_LATERAL_SCLEROSIS_ALS.html Amyotrophic lateral sclerosis (ALS) 50/69 KEGG 0.448293696940057 0.516840803506856 4520 3116.63636363636 3444 0.0526315789473684 379 0.870635168934813 -0.654409927400857 -1 0.374366446986283 4519 803 2428 379 4373 4586 3491 2832 3444 3113 4315 3959 M853 REACTOME_MYOGENESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MYOGENESIS.html Genes involved in Myogenesis 29/38 Reactome 0.38032587350581 0.449009035254484 3445 3442.27272727273 3444 0.0425728024288254 1766 0.899237656906275 0.91485319955358 1 0.469114790855452 3444 3818 3029 3134 4422 2644 1766 4533 3935 3388 3752 3960 M859 REACTOME_JNK_C_JUN_KINASES_PHOSPHORYLATION_AND_ACTIVATION_MEDIATED_BY_ACTIVATED_HUMAN_TAK1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_JNK_C_JUN_KINASES_PHOSPHORYLATION_AND_ACTIVATION_MEDIATED_BY_ACTIVATED_HUMAN_TAK1.html Genes involved in JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 15/16 Reactome 0.300697054445209 0.364685456577792 2285 3106.72727272727 3444 0.0319926188286355 2076 0.6272854392874 0.655656244082532 1 0.412240360045342 2283 3535 3622 3608 3444 2158 2149 2076 4099 4576 2624 3961 M19230 EPPERT_LSC_R http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_LSC_R.html Genes up-regulated in functionally defined leukemic stem cells (LSC) from acute myeloid leukemia (AML) patients. 21873988 57/67 Kolja Eppert 0.628763848052368 0.690284310838704 4220 3308.63636363636 3444 0.0861449911007789 2130 0.88319468619398 -0.970781775590531 -1 0.213222529358312 4219 2885 3444 3735 4384 2297 2567 4229 2130 4174 2331 3962 M10791 ENK_UV_RESPONSE_KERATINOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/ENK_UV_RESPONSE_KERATINOCYTE_UP.html Genes up-regulated in NHEK cells (normal epidermal keratinocytes) after UVB irradiation. 16434974 663/936 Lauren Kazmierski 0.439733068465383 0.508586151226809 4085 3247.45454545455 3446 0.056287953197926 2036 1.06499040253401 -1.10425113255192 -1 0.469135243482209 4085 4310 4327 3883 3259 2072 4132 3446 2051 2121 2036 3963 M2029 KOYAMA_SEMA3B_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOYAMA_SEMA3B_TARGETS_DN.html Genes down-regulated in NCI-H1299 cells (large cell neuroendocrine carcinoma) stably expressing SEMA3B [GeneID=7869]. 18985860 488/616 Jessica Robertson 0.388521467349451 0.457198036870957 3660 2918.72727272727 3446 0.0437309268181067 1328 1.11498983676791 1.09050315526805 1 0.568561549447532 3658 1687 1951 1328 3977 4624 3446 4130 1744 1409 4152 3964 M5718 NIKOLSKY_BREAST_CANCER_21Q22_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_21Q22_AMPLICON.html Genes within amplicon 21q22 identified in a copy alterations study of 191 breast tumor samples. 19010930 17/21 Jessica Robertson 0.782464054186274 0.786128211102429 3270 3697.36363636364 3447 0.129486424564303 2937 1.10633768457639 -1.57855669736745 -1 0.173383717616888 4647 3889 3187 2937 3267 3447 3282 3270 4563 3978 4204 3965 M1277 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM3 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM3.html Cluster PAM3: genes most highly up-regulated in hepatocellular carcinoma (HCC) vs normal liver tissue from mice deficient for TXNIP [GeneID=10628]. 16607285 114/153 Leona Saunders 7.42818182227805e-09 1.6856258750554e-07 3175 3019.18181818182 3448 6.75289258850808e-10 169 1.41011956344995 1.33216381374196 1 14.3314762221868 3172 3658 169 3174 3008 4372 4103 3448 3468 579 4060 3966 M3900 MUNSHI_MULTIPLE_MYELOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/MUNSHI_MULTIPLE_MYELOMA_DN.html Genes down-regulated in multiple myeloma (MM) compared to normal plasma cells from the patient's identical twin. 12969976 11/14 Kevin Vogelsang 0.68618940391 0.690284310838704 3450 3279.09090909091 3448 0.1 1601 0.746193440354725 -0.584369680467244 -1 0.180131013810323 4148 1601 3448 2085 3630 3446 3649 3141 1627 4679 4616 3967 M2342 FEVR_CTNNB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FEVR_CTNNB1_TARGETS_UP.html Genes up-regulated in intestinal crypt cells upon deletion of CTNNB1 [GeneID=1499]. 17785439 861/1201 Arthur Liberzon 3.52923118051391e-11 1.14967549790324e-09 3605 2602.63636363636 3448 3.52923118056996e-12 65 1.2229854727287 -1.19527491214321 -1 16.4047598326669 3605 474 4685 243 1952 4386 3448 3728 1631 65 4412 3968 M1494 REACTOME_BASE_FREE_SUGAR_PHOSPHATE_REMOVAL_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASE_FREE_SUGAR_PHOSPHATE_REMOVAL_VIA_THE_SINGLE_NUCLEOTIDE_REPLACEMENT_PATHWAY.html Genes involved in Base-free sugar-phosphate removal via the single-nucleotide replacement pathway 10/11 Reactome 0.0656762385883862 0.101337641757824 1795 2837 3451 0.00615662991429326 805 0.677628570246197 -0.677628570246197 -1 1.01082172560763 1791 3936 3451 3994 4355 858 805 1520 4641 4541 1315 3969 M9416 JIANG_CORE_DUPLICON_GENES http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_CORE_DUPLICON_GENES.html Genes mapped to core duplicons - elements shared by a majority of segmental duplication blocks. 17922013 8/15 Leona Saunders 0.149341087163299 0.201742968348819 2385 3424.36363636364 3453 0.0160443005456689 2120 0.564736954888946 0.564736954888946 1 0.589007400855106 2383 4632 4418 4565 2120 2460 3453 2326 4071 4658 2582 3970 M1440 WANG_TARGETS_OF_MLL_CBP_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TARGETS_OF_MLL_CBP_FUSION_UP.html Top 50 genes up-regulated in granulocyte/macrophage progenitors (GMP) upon expression of MLL-CBP fusion [GeneID=4297;1387]. 15635450 59/77 Kevin Vogelsang 0.68618940391 0.690284310838704 3800 2940.45454545455 3453 0.1 717 1.14904675777978 1.1966338987778 1 0.277436894026709 3797 1383 1887 1258 3453 4393 4086 4685 717 2027 4659 3971 M13202 FOURNIER_ACINAR_DEVELOPMENT_LATE_DN http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_LATE_DN.html Genes down-regulated late in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 40/50 Arthur Liberzon 0.68618940391 0.690284310838704 2415 3211 3454 0.1 2144 1.09719116484229 1.01459102304994 1 0.264911605300835 2414 4129 2537 3836 3866 3454 2865 3696 2852 2144 3528 3972 M17836 AMUNDSON_DNA_DAMAGE_RESPONSE_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_DNA_DAMAGE_RESPONSE_TP53.html Genes discriminating TP53 [GeneID=7157] status across various genotoxic stress agents. 15824734 27/35 Leona Saunders 0.360390304826485 0.428582070743515 3455 3532.45454545455 3454 0.0398127992250083 1721 0.71353483009801 0.778628230425673 1 0.393865556948064 3356 3454 3085 4405 4347 3671 1721 3454 4063 4196 3105 3973 M2416 WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_36HR http://www.broadinstitute.org/gsea/msigdb/cards/WAKABAYASHI_ADIPOGENESIS_PPARG_BOUND_36HR.html Genes with promoters bound by PPARG [GeneID=5468] at 36 h time point of adipocyte differentiation of 3T3-L1 cells (preadipocyte). 19414603 35/37 Arthur Liberzon 0.68618940391 0.690284310838704 4560 3219.54545454545 3454 0.1 1517 0.78101770659308 -0.659157731349748 -1 0.188542526717483 4556 1978 3454 1517 4408 3980 4033 2762 1574 3710 3443 3974 M682 FARMER_BREAST_CANCER_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/FARMER_BREAST_CANCER_CLUSTER_5.html Cluster 5: selected 17q21_23 amplicon genes clustered together across breast cancer samples. 15897907 23/23 Leona Saunders 0.00896597560321601 0.0201042303312017 4235 2746.90909090909 3454 0.000818429616739592 337 0.655944757288078 0.677985345688595 1 1.66989753423123 4232 337 3569 803 864 4602 4710 2631 882 4132 3454 3975 M12674 WANG_LMO4_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LMO4_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) engineered to conditionally express LMO4 [GeneID=8543] by a Tet Off system. 17452977 465/560 Arthur Liberzon 0.480010313186295 0.549781285668361 3445 3461 3455 0.0577170365606208 1864 0.947116660457265 0.889766002728037 1 0.369127782601516 3445 3165 4102 3455 2776 4018 3057 3579 1864 4268 4342 3976 M2606 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_6HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_6HR.html Cell cycle genes significantly (p =< 0.05) changed in fibroblast cells at 6 h after exposure to ionizing radiation. 17404513 98/110 Itai Pashtan 0.182915649080024 0.239756140976871 815 3112.81818181818 3455 0.018197207561484 814 1.11529431158246 -1.06692967499638 -1 1.03786284603676 814 4048 3983 4155 4086 1862 1272 3209 3455 4276 3081 3977 M16479 FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLOTHO_PEDIATRIC_ALL_THERAPY_RESPONSE_UP.html Up-regulated genes significantly associated with positive minimal residual disease (MRD) on day 46 after chemotherapy treatment of children with acute lymphoblastic leukemia (ALL). 16627760 59/75 Arthur Liberzon 0.069051065793112 0.105749847677965 1060 2846.27272727273 3456 0.00648351379578708 824 0.753040763250437 0.712212011371482 1 1.10241197870851 1058 3735 4040 4313 3456 1046 824 2950 3887 4198 1802 3978 M1142 SCIBETTA_KDM5B_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCIBETTA_KDM5B_TARGETS_UP.html Genes up-regulated in HB2 cells (mammary epithelium) upon expression of KDM5B [GeneID=10765] off an adenoviral vector. 17709396 25/25 Leona Saunders 0.437016514150859 0.505692068348138 3735 3091.81818181818 3458 0.0508872952094941 1492 0.99046912638025 -0.856988045143921 -1 0.43998415567401 3733 3843 2932 3560 2843 3631 3458 2349 1492 2647 3522 3979 M14194 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_30 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_30.html Amplification hot spot 30: colocolized fragile sites and cancer genes in the 12q21-q24.3 region. 16751803 6/10 Arthur Liberzon 0.34655630091094 0.413484767517603 3955 3272.27272727273 3459 0.0416573476277116 1592 1.17534131453019 -1.17534131453019 -1 0.676315081217843 3955 3577 4371 3107 2621 3864 3459 2684 1592 3230 3535 3980 M3710 WALLACE_PROSTATE_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/WALLACE_PROSTATE_CANCER_UP.html Genes up-regulated in prostate tumor vs normal tissue samples. 18245496 25/27 Jessica Robertson 0.68618940391 0.690284310838704 3645 3360.18181818182 3459 0.1 1504 0.774417627440378 -0.774423285209758 -1 0.18694833229566 3642 3459 3521 3113 4705 2763 2773 3872 1504 3136 4474 3981 M12012 ST_P38_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_P38_MAPK_PATHWAY.html p38 MAPK Pathway 51/52 Signaling Transduction KE 0.190685842528389 0.248217643886927 3460 3190 3460 0.0190496815378629 1296 0.80106111902571 -0.821265686965226 -1 0.727310342396068 3460 1938 3672 2981 4540 2090 1296 4635 2409 3761 4308 3982 M71 PID_ILK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ILK_PATHWAY.html Integrin-linked kinase signaling 18832364 60/68 Pathway Interaction Database 0.0293226277338592 0.0516621138125478 1365 2707.18181818182 3461 0.00270190048540804 513 0.885324363358975 1.01399307299389 1 1.70937670753467 1362 4438 3461 4294 3596 805 513 1657 3951 4106 1596 3983 M180 PID_HIF1A_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HIF1A_PATHWAY.html Hypoxic and oxygen homeostasis regulation of HIF-1-alpha 18832364 25/30 Pathway Interaction Database 0.68618940391 0.690284310838704 3135 3423.36363636364 3461 0.1 2493 1.00682381329842 -0.761514080812808 -1 0.243084120446039 4257 3461 2880 2691 3131 2493 3622 4275 4059 3135 3653 3984 M933 REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS.html Genes involved in Regulation of Water Balance by Renal Aquaporins 35/48 Reactome 0.68618940391 0.690284310838704 3605 3236.54545454545 3463 0.1 2160 1.03677542752129 -1.18178425758186 -1 0.250318684640487 3604 2969 2388 3137 4029 3550 2372 3463 3785 2160 4145 3985 M1421 PEART_HDAC_PROLIFERATION_CLUSTER_DN http://www.broadinstitute.org/gsea/msigdb/cards/PEART_HDAC_PROLIFERATION_CLUSTER_DN.html Cell proliferation genes down-regulated by histone deacetylase (HDAC) inhibitors SAHA and depsipeptide [PubChem=5311;5352062]. 15738394 98/131 Kate Stafford 0.0904950628946411 0.132568807219958 3035 3089.09090909091 3463 0.00858609554572942 1379 1.24051442011633 -1.21581088581702 -1 1.63339657386083 3032 3677 3463 3893 2574 3883 4716 1379 1563 3703 2097 3986 M9611 MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MASRI_RESISTANCE_TO_TAMOXIFEN_AND_AROMATASE_INHIBITORS_UP.html Genes up-regulated in derivatives of MCF-7aro cells (breast cancer) that developed resistance to tamoxifen [PubChem=5376] or inhibitors of aromatase (CYP19A1) [GeneID=1588]. 18559539 21/31 Leona Saunders 0.0121551880183913 0.0254524129780691 3465 2861.81818181818 3463 0.00111117005327444 985 1.55717805135521 -1.96663379516268 -1 3.72503108059226 3463 3860 1242 2538 985 3477 4428 2117 3644 1440 4286 3987 M7371 LOPES_METHYLATED_IN_COLON_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/LOPES_METHYLATED_IN_COLON_CANCER_UP.html Genes methylated aberrantly in HCT116 and Colo320 (colon cancer) cells. 18794111 27/42 Jessica Robertson 0.00162063488089223 0.00570424805205916 2760 2872.90909090909 3464 0.000147439087077548 476 1.27244072447088 1.20330897753714 1 4.28403581817502 2756 3847 1438 3573 476 3609 3464 2070 4391 1939 4039 3988 M11428 GAURNIER_PSMD4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/GAURNIER_PSMD4_TARGETS.html Inflammatory cytokines, chemokines and their cognate receptors up-regulated in THP-1 cells (monocyte) after treatment with PSMD4 [GeneID=5710]. 18632645 62/115 Jessica Robertson 0.0030342716999938 0.00912795565581309 2365 3009.18181818182 3464 0.000276224064523972 687 1.19402385310303 1.37943344337667 1 3.6542047285455 2363 3715 722 3080 3464 3652 3423 4618 3642 687 3735 3989 M1195 PATIL_LIVER_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/PATIL_LIVER_CANCER.html Genes up-regulated in hepatocellular carcinoma (HCC) compared to normal liver samples. 15735714 912/1154 Arthur Liberzon 0.435156887550486 0.503787223261784 3685 3131.63636363636 3466 0.0555199611420182 1120 0.968650898942191 -0.905381423870298 -1 0.432672019994701 3681 1120 4384 2975 3636 1662 3466 4658 2258 3861 2747 3990 M2163 FIGUEROA_AML_METHYLATION_CLUSTER_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_2_DN.html Cluster 2 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 8/12 Arthur Liberzon 0.0128034000387447 0.0265402056139108 4640 3316.36363636364 3466 0.00128777709856076 1027 0.928612291433726 -0.484285894382347 -1 2.19602811837524 2813 4637 4665 4368 1027 3109 2667 1408 4640 3466 3680 3991 M104 SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP.html Top 50 up-regulated markers distinguishing diffuse large B-cell lymphoma (DLBCL) from follicular lymphoma (FL) samples. 11786909 81/118 Jean Junior 0.106855843956634 0.152512725574633 3825 3308.90909090909 3467 0.0102207982766662 1788 0.948010971261184 1.11802564233189 1 1.16164901866129 3822 2393 3467 3411 1859 4297 4165 3179 1788 3811 4206 3992 M205 WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEST_ADRENOCORTICAL_TUMOR_MARKERS_UP.html Top up-regulated genes in pediatric adrenocortical tumors (ACT) compared to the normal tissue. 17234769 27/28 Arthur Liberzon 0.68618940391 0.690284310838704 2910 3257.54545454545 3468 0.1 2098 1.2550233100615 1.60682512775272 1 0.303034651960003 2909 3468 2386 4062 3884 3971 4652 3511 2098 2370 2522 3993 M7079 WONG_EMBRYONIC_STEM_CELL_CORE http://www.broadinstitute.org/gsea/msigdb/cards/WONG_EMBRYONIC_STEM_CELL_CORE.html The 'core ESC-like gene module': genes coordinately up-regulated in a compendium of mouse embryonic stem cells (ESC) which are shared with the human ESC-like module. 18397753 414/477 Nikolaos Papanikolaou 0.595195412698061 0.661795606109505 1635 3341.27272727273 3468 0.0789249068719509 1634 0.748351807929586 -0.696091282903554 -1 0.201206359025029 1634 3974 4180 4533 3192 2104 2197 3468 3590 4475 3407 3994 M14339 BIOCARTA_ARENRF2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ARENRF2_PATHWAY.html Oxidative Stress Induced Gene Expression Via Nrf2 16/19 BioCarta 0.0462707627253057 0.0753616287313467 4525 3000.81818181818 3469 0.00429759933898532 195 0.970835800498975 -1.12099680030407 -1 1.63561516680012 4521 3883 2738 2204 4366 3483 3378 1082 195 3469 3690 3995 M5372 REACTOME_XENOBIOTICS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_XENOBIOTICS.html Genes involved in Xenobiotics 4/46 Reactome 0.151297187034848 0.203930645704491 3920 2737.18181818182 3469 0.0162707967536234 348 2.02417381848764 -2.30399181805524 -1 2.09721227105589 3919 1651 4224 1206 4023 3469 3683 4467 348 1108 2011 3996 M8232 KEGG_LONG_TERM_DEPRESSION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_LONG_TERM_DEPRESSION.html Long-term depression 61/94 KEGG 0.68618940391 0.690284310838704 2550 3228.18181818182 3470 0.1 2001 1.09121909074196 1.21621900932129 1 0.263469100294882 2547 3719 2001 2749 4362 4487 3618 3470 2434 3594 2529 3997 M729 REACTOME_FATTY_ACYL_COA_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FATTY_ACYL_COA_BIOSYNTHESIS.html Genes involved in Fatty Acyl-CoA Biosynthesis 16/19 Reactome 0.00904168997398569 0.0202114211853244 3800 3155.81818181818 3470 0.000825369570302452 868 0.807141979655436 1.01456857770378 1 2.05204129721007 3798 2111 2538 3057 868 4135 3949 2607 3907 3470 4274 3998 M8458 GRATIAS_RETINOBLASTOMA_16Q24 http://www.broadinstitute.org/gsea/msigdb/cards/GRATIAS_RETINOBLASTOMA_16Q24.html Genes from 16q24 region up-regulated in retinoblastoma tumors with 16q24 LOH (loss of heterozygocity) compared to those without the LOH. 17210724 21/22 Jessica Robertson 0.68618940391 0.690284310838704 4665 3345.81818181818 3470 0.1 978 0.648877659145286 -0.535040329766517 -1 0.156625193354242 4663 978 3814 2143 3288 3041 3470 4039 3014 4092 4262 3999 M17670 REACTOME_RAS_ACTIVATION_UOPN_CA2_INFUX_THROUGH_NMDA_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RAS_ACTIVATION_UOPN_CA2_INFUX_THROUGH_NMDA_RECEPTOR.html Genes involved in Ras activation uopn Ca2+ infux through NMDA receptor 16/23 Reactome 0.013332735733799 0.0274805732155158 3730 2997.63636363636 3471 0.00121947534916453 606 0.912801574563647 -1.04377995351609 -1 2.13792477612999 3728 3523 2482 3393 4127 2062 730 606 4271 3471 4581 4000 M199 PID_P38_MK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P38_MK2_PATHWAY.html p38 signaling mediated by MAPKAP kinases 18832364 22/24 Pathway Interaction Database 0.0406317290046352 0.0675050196768315 3185 3069.09090909091 3472 0.00376383188630378 1025 0.690336763497595 -0.578035504481243 -1 1.21254299190717 3181 4549 3748 4285 3472 1646 2174 1025 4340 4115 1225 4001 M928 REACTOME_INCRETIN_SYNTHESIS_SECRETION_AND_INACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INCRETIN_SYNTHESIS_SECRETION_AND_INACTIVATION.html Genes involved in Incretin Synthesis, Secretion, and Inactivation 16/29 Reactome 0.397282858640171 0.466577529928242 3495 3277.54545454545 3472 0.0449847159216798 2235 1.19697867837905 -0.828196776730061 -1 0.594536964222608 3492 3517 2235 3130 2666 2987 2827 4047 3828 3472 3852 4002 M1913 ZHANG_TLX_TARGETS_36HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_36HR_DN.html Genes down-regulated in neural stem cells (NSC) at 36 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 247/272 Jessica Robertson 0.3942743156554 0.463505546673347 1975 3301.81818181818 3472 0.0445523246289753 1975 1.02317727778764 1.03452498356012 1 0.512599374877008 1975 3625 4128 3472 4608 2834 2830 2264 2242 4377 3965 4003 M932 REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GLP1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_SECRETION_AND_INACTIVATION_OF_GLP1.html Genes involved in Synthesis, Secretion, and Inactivation of Glucagon-like Peptide-1 (GLP-1) 16/25 Reactome 0.397282858640171 0.466577529928242 3495 3278.54545454545 3473 0.0449847159216798 2236 1.19697867837905 -0.828196776730061 -1 0.594536964222608 3493 3518 2236 3131 2667 2988 2828 4048 3829 3473 3853 4004 M15047 MULLIGHAN_NPM1_SIGNATURE_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_SIGNATURE_3_DN.html The 'NPM1 signature 3': genes down-regulated in pediatric AML (acute myeloid leukemia) with mutated NPM1 [GeneID=4869] compared to the AML cases with intact NPM1 and MLL [GeneID=4297]. 17597811 229/372 Arthur Liberzon 0.111884313465856 0.158396508565939 3135 3174 3474 0.010728693210894 1213 1.18103199841729 1.22163124849086 1 1.41807477489466 3133 3180 1213 3797 3474 4689 3684 3701 2865 1483 3695 4005 M794 REACTOME_ACTIVATION_OF_CHAPERONES_BY_ATF6_ALPHA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_CHAPERONES_BY_ATF6_ALPHA.html Genes involved in Activation of Chaperones by ATF6-alpha 19/20 Reactome 0.244474775317344 0.305998658047696 4295 3165.45454545455 3475 0.0251636286668273 1603 0.717330885526434 0.717330885526434 1 0.553449936673427 1855 3886 3475 4291 2361 1603 1980 4295 4688 4032 2354 4006 M1403 PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_VS_MULTIPOTENT_PROGENITORS_DN.html Genes down-regulated in long term hematopoietic stem cells (LT-HSC) compared to multipotent progenitor (MPP) cells. 11781229 24/32 Kate Stafford 0.274889374349755 0.338325383815083 4080 3413.63636363636 3475 0.0287981991479022 2015 0.721050429754394 -0.567520091133668 -1 0.509130921492172 4079 3475 3877 3628 3134 3213 2406 2015 3056 4157 4510 4007 M3905 XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_AND_NSC682994_DN.html Genes down-regulated synergistically in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin and NSC682994 [PubChem=444795;388304]. 16140955 17/18 Kevin Vogelsang 0.0263320925348564 0.0475032222458705 3340 3154.36363636364 3475 0.00242296812678176 620 0.962577059594015 -0.989130055380917 -1 1.91119063794934 3339 4228 3511 4042 1246 3475 2264 4646 620 2993 4334 4008 M12964 XU_RESPONSE_TO_TRETINOIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_RESPONSE_TO_TRETINOIN_DN.html Genes down-regulated in NB4 cells (acute promyelocytic leukemia, APL) by tretinoin [PubChem=444795] alone. 16140955 21/22 Kevin Vogelsang 0.123039564436109 0.171818563354567 4285 3178.63636363636 3476 0.0118648150563363 302 0.90314084701324 -0.984962575823837 -1 1.03651263555703 4282 4201 3476 2908 1939 4495 4142 1774 302 3326 4120 4009 M1762 TESAR_ALK_TARGETS_EPISC_4D_UP http://www.broadinstitute.org/gsea/msigdb/cards/TESAR_ALK_TARGETS_EPISC_4D_UP.html Genes up-regulated in EpiSC cells (epiblast stem cells) after treatment with the ALK [GeneID=238] inhibitor SB-431542 [PubChem=4521392]. 17597760 3/8 Jessica Robertson 3.80583507091697e-05 0.000306022854083954 3570 3026.36363636364 3476 3.80590025220072e-06 10 1.33564828625505 1.33564828625505 1 7.04303051894355 3568 3144 4525 2064 3476 4640 3524 10 3790 2688 1861 4010 M2522 JIANG_HYPOXIA_VIA_VHL http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_HYPOXIA_VIA_VHL.html Genes up-regulated in 786-0 cells (renal carcinoma, RCC) by the loss of VHL [GeneID=7428] and in response to hypoxia. 12692265 44/50 Arthur Liberzon 0.675013513885967 0.690284310838704 3480 3444 3477 0.0971322960198491 2099 0.686894885896063 -0.668007003203428 -1 0.165807939411828 3477 4130 4011 4272 4450 2099 2653 2934 3051 4244 2563 4011 M2240 JOHNSTONE_PARVB_TARGETS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_3_UP.html Genes up-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D Matrigel only. 17998334 613/767 Arthur Liberzon 0.000242092730768955 0.00136033058241603 3765 2462.18181818182 3477 2.421191088141e-05 34 1.09287002945901 -1.04469834901718 -1 4.70035440830378 3761 483 4670 34 1550 4038 4017 3541 1185 328 3477 4012 M2556 HOLLEMAN_DAUNORUBICIN_B_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_DAUNORUBICIN_B_ALL_UP.html Genes distinguishing daunorubicin [PubChem=30323] resistant and sensitive B-lineage ALL; here - genes up-regulated in the drug resistant samples. 15295046 16/26 Arthur Liberzon 0.46205340533291 0.531276997118474 2660 3341.63636363636 3477 0.0548042894627431 1941 0.868819196654838 -0.547907739233886 -1 0.357987850706525 2658 4244 2316 4239 3864 2232 1941 4641 4369 3477 2777 4013 M1219 SMID_BREAST_CANCER_ERBB2_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_ERBB2_DN.html Genes down-regulated in the erbb2 subype of breast cancer samples, characterized by higher expression of ERBB2 [GeneID=2064]. 18451135 8/9 Jessica Robertson 8.13418960929574e-05 0.000561306651401695 4665 3164.90909090909 3478 8.13448736731803e-06 124 1.33570832517607 -1.17673565581528 -1 6.51533293127106 4664 2670 4552 3104 124 4477 3478 3754 2019 1888 4084 4014 M17200 SA_B_CELL_RECEPTOR_COMPLEXES http://www.broadinstitute.org/gsea/msigdb/cards/SA_B_CELL_RECEPTOR_COMPLEXES.html Antigen binding to B cell receptors activates protein tyrosine kinases, such as the Src family, which ultimate activate MAP kinases. 33/37 SigmaAldrich 0.0284380011555789 0.0505945591610752 3920 3295.18181818182 3480 0.00261930856876606 1283 0.845656310184383 -0.850240942712969 -1 1.64428828459081 3918 3811 3318 3670 1283 3480 3073 4094 3445 3905 2250 4015 M176 PID_FOXM1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_FOXM1_PATHWAY.html FOXM1 transcription factor network 18832364 45/51 Pathway Interaction Database 0.68618940391 0.690284310838704 4415 3177.72727272727 3480 0.1 490 1.07069061226925 1.08438569779155 1 0.258510616447567 4412 1430 2863 2419 4124 4316 4458 3480 490 2485 4478 4016 M1409 PEART_HDAC_PROLIFERATION_CLUSTER_UP http://www.broadinstitute.org/gsea/msigdb/cards/PEART_HDAC_PROLIFERATION_CLUSTER_UP.html Cell proliferation genes up-regulated by histone deacetylase (HDAC) inhibitors SAHA and depsipeptide [PubChem=5311;5352062]. 15738394 79/88 Kate Stafford 0.000330055504665091 0.00169148966560177 3720 2838.90909090909 3481 3.00095483382395e-05 241 0.950927706182097 -0.972130451870459 -1 3.95483813135193 3716 2389 3525 1585 241 4021 4374 3481 1179 3497 3220 4017 M7615 RIZKI_TUMOR_INVASIVENESS_2D_DN http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_2D_DN.html Genes down-regulated in monolayer (2D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 71/112 Jessica Robertson 0.68618940391 0.690284310838704 4720 3143.18181818182 3482 0.1 754 0.996323441835212 -1.07846062813326 -1 0.240547842739907 4718 754 2410 1572 3727 4510 4594 3482 4169 2087 2552 4018 M3548 REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEP_NS2_INTERACTS_WITH_THE_CELLULAR_EXPORT_MACHINERY.html Genes involved in NEP/NS2 Interacts with the Cellular Export Machinery 30/34 Reactome 0.379151599357884 0.44784673397628 4035 3516.72727272727 3484 0.0424080069022113 2235 0.667118526427026 -0.647946983743853 -1 0.349122261600327 4031 3420 3902 3190 2828 4220 4474 2235 2302 4598 3484 4019 M7860 BIOCARTA_NGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NGF_PATHWAY.html Nerve growth factor pathway (NGF) 31/34 BioCarta 0.356106579495993 0.423951851732903 4395 3393.18181818182 3486 0.0392299566049112 2186 0.688738946467498 -0.77451020561871 -1 0.385050088424957 4393 3826 3709 2796 3486 2742 4366 2186 3372 3851 2598 4020 M237 PID_VEGFR1_2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGFR1_2_PATHWAY.html Signaling events mediated by VEGFR1 and VEGFR2 18832364 106/133 Pathway Interaction Database 0.00577426225782821 0.0142024584976285 3290 3021.54545454545 3487 0.000526315789473684 28 0.901744067109058 0.986259612124377 1 2.49990349557675 3286 28 2641 202 3998 4032 3346 4081 3487 3722 4414 4021 M1578 BOQUEST_STEM_CELL_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOQUEST_STEM_CELL_DN.html Genes down-regulated in freshly isolated CD31- [GeneID=5175] (stromal stem cells from adipose tissue) versus the CD31+ (non-stem) counterparts. 15635089 285/359 Arthur Liberzon 3.53184210160954e-11 1.14967549790324e-09 3845 2982.09090909091 3487 3.21076554696931e-12 114 1.26032940426767 1.2717019728967 1 16.9056833463044 3842 3616 114 2523 4080 3146 4153 3181 4290 371 3487 4022 M16284 INGA_TP53_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/INGA_TP53_TARGETS.html Genes whose promoters contain TP53 [GeneID=7157] response elements. 12446780 23/27 John Newman 0.000396536266763767 0.00194592308160632 3490 3391.54545454545 3488 3.60552507264871e-05 271 0.963789128498609 0.91892942371884 1 3.92031977473225 3488 4206 2424 4630 271 3425 2838 4254 4442 2976 4353 4023 M4085 KEGG_PRIMARY_IMMUNODEFICIENCY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PRIMARY_IMMUNODEFICIENCY.html Primary immunodeficiency 21/48 KEGG 0.833296153245153 0.836308280526712 3410 3564.09090909091 3489 0.150295763144129 2092 0.830488351122008 -0.881214837894365 -1 0.0966384076858237 3410 3489 2092 3955 4261 2458 3398 4623 4660 4088 2771 4024 M1117 CAIRO_PML_TARGETS_BOUND_BY_MYC_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAIRO_PML_TARGETS_BOUND_BY_MYC_DN.html Genes down-regulated in MEF cells (embryonic fibroblasts) after knockout of PML [GeneID=5371] and whose promoters were bound by MYC [GeneID=4609]. 15735755 21/27 Lauren Kazmierski 0.000535305370045979 0.00243649117320831 4390 3160 3491 4.86759695699146e-05 318 1.04319956112054 -1.18433793045222 -1 4.0905005997073 4387 3491 1781 2765 318 4054 3861 2785 4550 2799 3969 4025 M4371 MARTINEZ_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_TP53_TARGETS_UP.html Genes up-regulated in mice with skin specific knockout of TP53 [GeneID=7157]. 18245467 770/969 Jessica Robertson 0.184193635089214 0.241293856627434 3495 3337.54545454545 3491 0.0201520035472525 1182 1.15338835474542 -1.12647435722713 -1 1.06851046815081 3491 2701 4534 2450 2405 4650 3536 4444 3429 1182 3891 4026 M6444 NUYTTEN_NIPP1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/NUYTTEN_NIPP1_TARGETS_UP.html Genes up-regulated in PC3 cells (prostate cancer) after knockdown of NIPP1 [GeneID=5511] by RNAi. 17724462 933/1265 Jessica Robertson 0.508494934944203 0.577362543405494 2975 3621.45454545455 3493 0.0685644710514663 2056 1.13762130374723 -1.11643915510771 -1 0.40710703189268 2973 4302 4428 4116 2897 4545 3493 3369 3073 2056 4584 4027 M1780 MCGOWAN_RSP6_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MCGOWAN_RSP6_TARGETS_UP.html Genes up-regulated by hemizygotic cre-lox knockout of RSP6 [GeneID=81492] in keratinocytes. 18641651 17/23 Jessica Robertson 0.68618940391 0.690284310838704 4675 3189.54545454545 3493 0.1 1775 1.2025229969545 -0.804168975101185 -1 0.29035363642024 4675 2098 1908 1775 3493 4093 2650 3590 4449 2426 3928 4028 M1972 MIKKELSEN_IPS_LCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_IPS_LCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the bivalent tri-methylation marks at H3K4 (H3K4me3) and H3K27 (H3K27me3) in MCV8.1 cells (induced pluripotent cells, iPS). 18509334 8/17 Jessica Robertson 0.264098647273727 0.326888044944004 2755 3114.90909090909 3494 0.030200490500409 1585 2.12467385106338 2.50276718102734 1 1.54804624998432 2754 3566 4626 3494 3925 1843 1585 4212 3862 1890 2507 4029 M290 PID_IL12_STAT4_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL12_STAT4_PATHWAY.html IL12 signaling mediated by STAT4 18832364 21/40 Pathway Interaction Database 0.101760234803817 0.146233294258128 3520 3163.09090909091 3495 0.00970876692588143 1059 0.708727328106252 -0.839009692854628 -1 0.887833721397292 3517 3863 3281 3820 1839 2365 1059 3443 4321 3791 3495 4030 M7250 MA_PITUITARY_FETAL_VS_ADULT_UP http://www.broadinstitute.org/gsea/msigdb/cards/MA_PITUITARY_FETAL_VS_ADULT_UP.html Up-regulated in human fetal pituitary tissue, compared to adult pituitary tissue 15894316 38/42 John Newman 0.192255069827821 0.249984553605321 3495 3437.09090909091 3495 0.0192227452886354 2209 1.16076501526222 1.09975916167867 1 1.04857962313346 3495 3377 2800 4433 2209 3827 4386 4051 3089 2382 3759 4031 M10967 VICENT_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VICENT_METASTASIS_UP.html The metastasis gene signature: genes up-regulated during metastasis of NSCLC (non-small cell lung carcinoma) tumors to bone. 18381434 20/23 Jessica Robertson 0.68618940391 0.690284310838704 3840 3626.27272727273 3495 0.1 2820 0.707899953990793 0.683077496267688 1 0.170881539532654 3838 3495 3259 3102 3457 4119 3099 2820 4440 4069 4191 4032 M2174 FIGUEROA_AML_METHYLATION_CLUSTER_5_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_5_DN.html Cluster 5 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 44/119 Arthur Liberzon 0.0460026159207533 0.07495075842111 3850 3133.27272727273 3495 0.00427215278938939 1252 1.23785799369133 -1.26359093194698 -1 2.08991978489116 3846 2473 1252 3495 1486 4437 4027 3144 3890 2059 4357 4033 M16067 REACTOME_PREFOLDIN_MEDIATED_TRANSFER_OF_SUBSTRATE_TO_CCT_TRIC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PREFOLDIN_MEDIATED_TRANSFER_OF_SUBSTRATE_TO_CCT_TRIC.html Genes involved in Prefoldin mediated transfer of substrate to CCT/TriC 31/39 Reactome 0.68618940391 0.690284310838704 3400 3669.36363636364 3496 0.1 2257 1.1441854987191 0.908367693338846 1 0.276262697187814 3399 3419 2812 3691 3496 4563 4606 4407 3291 2257 4422 4034 M2276 KIM_PTEN_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_PTEN_TARGETS_UP.html Genes up-regulated in HCT116 cells (colorectal carcinoma) upon knockout of PTEN [GeneID=5728]. 17060456 19/23 Arthur Liberzon 0.259430992153391 0.322325423259807 3200 3176.18181818182 3497 0.0269339482164628 1487 0.839009837295372 -0.850711735942941 -1 0.618927274237132 3198 3497 3060 2178 3992 2286 1487 3629 3872 3695 4044 4035 M272 PID_CD8_TCR_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CD8_TCR_DOWNSTREAM_PATHWAY.html Downstream signaling in naïve CD8+ T cells 18832364 62/117 Pathway Interaction Database 0.213657954439623 0.273667719119409 2800 3372.45454545455 3498 0.0216142105380437 1154 0.807417511464189 -0.779275752669736 -1 0.681723803071345 2797 4442 3498 4160 3484 1154 3395 3747 4311 3987 2122 4036 M29 SHEN_SMARCA2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHEN_SMARCA2_TARGETS_UP.html Genes whose expression positively correlated with that of SMARCA2 [GeneID=6595] in prostate cancer samples. 19074882 532/578 Jessica Robertson 0.187141132109877 0.244209605628593 4270 3234.45454545455 3498 0.0205065981600425 792 0.774603697847254 -0.792504770453469 -1 0.711502676078318 4268 2213 4459 1676 2244 4257 4434 3498 792 4468 3270 4037 M6023 BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_DN http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_DN.html Genes down-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes are independent of ATM [GeneID=472] signaling. 18849970 74/95 Jessica Robertson 0.262820112688221 0.325507985276411 4350 3231.45454545455 3499 0.0273396213249678 1564 1.0964371909162 -0.890823897748081 -1 0.801840428485639 4350 3273 1830 3499 3658 3508 4664 2023 4116 3061 1564 4038 M376 PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BREAST_CANCER_WITH_BRCA1_MUTATED_DN.html The XPRSS-Int network genes down-regulated in breast tumors from patients with germline mutations in BRCA1 [GeneID=672] compared to those with the wild type allele. 17922014 11/11 Arthur Liberzon 0.000459890094588011 0.00216617344782318 3475 2985.54545454545 3499 4.18169325995924e-05 296 0.814010598601068 -0.792850283646463 -1 3.2541830094558 3475 3931 3499 2154 296 3808 2093 4213 1105 3731 4536 4039 M1411 LAU_APOPTOSIS_CDKN2A_UP http://www.broadinstitute.org/gsea/msigdb/cards/LAU_APOPTOSIS_CDKN2A_UP.html Genes up-regulated by UV-irradiation in cervical cancer cells after knockdown of CDKN2A [GeneID=1029]. 17369842 67/74 Leona Saunders 0.0218021946606942 0.0406729114747001 4045 3179.81818181818 3500 0.00200193657833743 1181 0.830628560794991 0.783257995803101 1 1.7332210839971 4044 2862 3500 2743 1181 3725 4104 2293 3556 3814 3156 4040 M13022 BIOCARTA_PTC1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PTC1_PATHWAY.html Sonic Hedgehog (SHH) Receptor Ptc1 Regulates cell cycle 14/16 BioCarta 0.39691240677833 0.466374548168712 1545 3434.54545454545 3501 0.044931368360154 1543 0.653280214802867 -0.653280214802867 -1 0.324620180916447 1543 4614 3501 4480 2664 2237 3153 3510 4655 4506 2917 4041 M16617 GAJATE_RESPONSE_TO_TRABECTEDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAJATE_RESPONSE_TO_TRABECTEDIN_DN.html Genes down-regulated in HeLa cells (cervical carcinoma) by trabectedin [PubChem=3199]. 12198119 25/37 John Newman 0.171914148597746 0.226996591394182 4535 3275.90909090909 3502 0.0170027432380728 1840 0.956857250473745 0.499973534275183 1 0.924510988978478 4533 3022 3502 3368 2150 3562 3961 2555 1840 3920 3622 4042 M10762 IGARASHI_ATF4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/IGARASHI_ATF4_TARGETS_UP.html Genes up-regulated in A549 cells (lung cancer) after knockdown of ATF4 [GeneID=468] by RNAi. 17297441 4/5 Leona Saunders 0.337180036227678 0.403317225290076 2820 3636.18181818182 3503 0.0402910209991568 2484 0.3289963890228 0.396715522526911 1 0.194572829099005 2817 4298 4282 4383 2606 3091 3503 2484 4643 4628 3263 4043 M18635 CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASORELLI_ACUTE_PROMYELOCYTIC_LEUKEMIA_DN.html Genes down-regulated in APL (acute promyeolocytic leukemia) blasts expressing PML-RARA fusion [GeneID=5371;5914] compared to normal promyeloblasts. 16990782 874/1119 Leona Saunders 0.6513215599 0.690284310838704 3505 3420 3504 0.1 2407 0.994371869377876 -0.920919543740875 -1 0.240076456586304 3997 2699 4289 2490 3501 2992 3504 3796 2407 4300 3645 4044 M18085 LIANG_SILENCED_BY_METHYLATION_2 http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_SILENCED_BY_METHYLATION_2.html Genes up-regulated in T24 cells (bladder carcinoma) after treatment with decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 11861364 65/108 John Newman 1.57490226825704e-05 0.000150248278081907 4165 3034.63636363636 3504 1.43173958412629e-06 385 1.42610233591239 -1.50727479071964 -1 8.18112106997708 4163 3705 385 4026 2420 3717 3203 3169 3504 402 4687 4045 M2620 ZWANG_EGF_INTERVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZWANG_EGF_INTERVAL_DN.html Genes repressed in the time interval between two pulses of EGF [GeneID =1950] in 184A1 cells (mammary epithelium). 21596316 255/310 Yaara Zwang 0.68618940391 0.690284310838704 4395 3511.09090909091 3505 0.1 2182 1.00450192992599 -1.03523173164706 -1 0.24252328875981 4392 2742 3059 3505 4687 2182 4440 4280 2599 3152 3584 4046 M19135 REACTOME_POST_CHAPERONIN_TUBULIN_FOLDING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_CHAPERONIN_TUBULIN_FOLDING_PATHWAY.html Genes involved in Post-chaperonin tubulin folding pathway 17/22 Reactome 0.68618940391 0.690284310838704 4710 3375.81818181818 3506 0.1 1429 1.13525906247862 -1.34627870811602 -1 0.274106590490897 4708 3506 2116 3197 4693 4225 3805 2956 1429 2418 4081 4047 M10287 BIOCARTA_FMLP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FMLP_PATHWAY.html fMLP induced chemokine gene expression in HMC-1 cells 52/63 BioCarta 0.493858285343393 0.563590693138495 3250 3270.09090909091 3507 0.0600264170056351 2006 0.828691010252997 -0.706519190156321 -1 0.309562575392317 3249 4099 3507 3665 3269 3889 2006 2587 2145 3959 3596 4048 M8179 BIOCARTA_RAB_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RAB_PATHWAY.html Rab GTPases Mark Targets In The Endocytotic Machinery 24/29 BioCarta 0.68618940391 0.690284310838704 3600 3429.90909090909 3507 0.1 2428 1.08085521641832 -1.11777163017947 -1 0.260965792341608 3600 3852 3137 4234 3307 4385 2428 3891 3507 2562 2826 4049 M14529 KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/KUUSELO_PANCREATIC_CANCER_19Q13_AMPLIFICATION.html List of genes in the 19q13 amplicon region based on a copy number alterations study of a panel of 16 pancreatic cancer cell lines and 31 primary tumors. 17332321 59/72 Jessica Robertson 0.158534347512511 0.212038005174002 3725 3295.36363636364 3508 0.0155693505040594 995 1.14857746419852 -1.00659005739348 -1 1.16079558160341 3722 4443 3307 4468 4508 995 2910 4661 1513 3508 2214 4050 M14298 PETRETTO_BLOOD_PRESSURE_UP http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_BLOOD_PRESSURE_UP.html Genes that are most strongly positively correlated with systolic blood pressure (SBP). 18443592 12/17 Jessica Robertson 0.588971323972085 0.655400192246446 2420 3589.36363636364 3511 0.0776463607772399 2266 1.14249007681197 1.04351210175419 1 0.31446234317324 2417 4616 3181 4397 4326 4219 3511 3358 4064 3128 2266 4051 M18108 NIKOLSKY_MUTATED_AND_AMPLIFIED_IN_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_MUTATED_AND_AMPLIFIED_IN_BREAST_CANCER.html Genes both mutated and amplified in a panel of 191 breast tumor samples. 19010930 119/172 Jessica Robertson 0.498902600924711 0.567974017454085 3015 3507.18181818182 3513 0.0608819338108473 2151 1.03884246415367 -1.02810041967931 -1 0.382847929232229 3015 4033 2151 4029 2813 3442 2672 4379 4134 3513 4398 4052 M8240 REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL.html Genes involved in Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell 45/119 Reactome 0.190369668931388 0.247942835915053 3280 3326.90909090909 3514 0.0190148489547879 1777 1.20520618043534 -0.94847973733073 -1 1.09517064368825 3280 4471 1777 4421 2199 2927 3514 3857 4015 2486 3649 4053 M17856 MULLIGHAN_MLL_SIGNATURE_1_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_MLL_SIGNATURE_1_UP.html The 'MLL signature 1': genes up-regulated in pediatric AML (acute myeloid leukemia) with rearranged MLL [GeneID=4297] compared to all AML cases with the intact gene. 17597811 461/602 Arthur Liberzon 0.00577426225782821 0.0142024584976285 4255 2585.45454545455 3514 0.000526315789473684 93 0.917478996431033 -0.861302647258835 -1 2.54352725917098 4254 506 3514 93 3531 1016 4076 4290 1732 3616 1812 4054 M2608 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_24HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_24HR.html Cell cycle genes significantly (p =< 0.05) changed in fibroblast cells at 24 h after exposure to ionizing radiation. 17404513 153/213 Itai Pashtan 0.552012324441906 0.619619065723138 1565 3378.18181818182 3514 0.0703982874327771 1564 1.08164576609907 -1.02168171385569 -1 0.337282147854844 1564 4362 4043 4526 4639 2253 2119 3514 2653 4214 3273 4055 M4902 LUI_THYROID_CANCER_PAX8_PPARG_DN http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_PAX8_PPARG_DN.html Top down-regulated genes distinguishing between follicular thyroid carcinoma (FTC) samples by the presence or absence of the PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 61/83 Leona Saunders 0.0284534433492274 0.0506029587823487 2340 3054.45454545455 3515 0.00262074972108009 1284 0.892422869562964 0.986773604624715 1 1.73513016982244 1939 4097 3515 3861 1284 2338 2445 3734 4216 3832 2338 4056 M1526 MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_7 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_CURCUMIN_SULINDAC_7.html Cluster 7: genes up-regulated in SW260 cells (colon cancer) by curcumin and sulindac [PubChem=969516;5352]. 10969808 27/28 John Newman 0.0883000125559953 0.130039332063743 3180 3355.63636363636 3516 0.00836881252950035 1742 1.32213178577747 -1.46873240599853 -1 1.75746827284165 3176 4534 3204 4071 1763 3516 1742 2930 4286 3700 3990 4057 M17363 KIM_LRRC3B_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KIM_LRRC3B_TARGETS.html Immune response genes up-regulated in zenograft tumors formed by SNU-601 cells (gastric cancer) made to express LRRC3B [GeneID=116135]. 18757430 58/111 Jessica Robertson 0.262180041298456 0.325091520374166 4260 3253.36363636364 3517 0.0272628759634444 1437 1.27639987704928 -0.937259278977772 -1 0.93453201929066 4258 3313 1437 2741 4538 3783 3517 2515 3571 1971 4143 4058 M2537 MIZUSHIMA_AUTOPHAGOSOME_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/MIZUSHIMA_AUTOPHAGOSOME_FORMATION.html Key proteins in mammalian autophagosome formation. 20144757 22/22 Arthur Liberzon 0.0208606330852237 0.0391344150088457 2710 2916.45454545455 3517 0.00191464564887653 959 0.721570182054768 -0.853033224483077 -1 1.52377369166489 2707 2578 3688 3552 1173 3558 3812 3517 959 4119 2418 4059 M1702 CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_NEUROBLASTOMA_COPY_NUMBER_GAINS.html High-grade amplification (copy number, CN >= 5) detected in primary neuroblastoma samples. 18923524 52/69 Jessica Robertson 0.68618940391 0.690284310838704 4280 3549.81818181818 3519 0.1 2328 1.08805234550588 -1.18116748637125 -1 0.2627041992272 4277 2452 2328 3519 4382 2931 3951 4456 4104 3495 3153 4060 M6868 HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_UP.html Genes up-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with low risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 41/55 Arthur Liberzon 0.0159433919248537 0.0317656436831192 4105 3308.45454545455 3520 0.00146001087766426 1065 1.06441724857912 -1.05726330771961 -1 2.39253660254502 4105 2935 2113 3520 1065 4449 4023 3420 3756 3307 3700 4061 M13465 KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS.html Terpenoid backbone biosynthesis 15/17 KEGG 0.000505757340431549 0.00233350405360402 4290 3088 3521 4.59885132971958e-05 309 0.86512754967559 -1.08620071774055 -1 3.41659083173989 4286 3521 3125 3346 309 4478 4446 1484 1006 3913 4054 4062 M4223 TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_SUSTAINED_IN_MONOCYTE_DN.html Genes down-regulated by RUNX1-RUNX1T1 [GeneID=861;862] fusion protein in normal hematopoietic progenitors; their expression was sustained in subsequently developing monocytes. 17898786 3/14 Arthur Liberzon 0.160074558068842 0.213734629161225 3525 3094.90909090909 3521 0.0172929456187393 1620 1.24856624162813 -1.3754174228168 -1 1.25537269287789 3521 3591 4304 3950 2158 2086 1762 4106 4582 1620 2364 4063 M1140 DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_SQUAMOUS_CELL_CARCINOMA_DN.html Genes down-regulated in squamous cell carcinoma (SCC) compared to normal skin. 17525749 225/323 Arthur Liberzon 0.199230377594805 0.257705503493418 4410 3401.90909090909 3521 0.01999574191457 2076 1.15345375478116 -1.16723198130216 -1 1.01910980523349 4408 4339 2997 4121 2232 3521 4461 4201 2364 2701 2076 4064 M2221 ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACOSTA_PROLIFERATION_INDEPENDENT_MYC_TARGETS_UP.html Genes up-regulated in K562 cells (lymphoblast) by MYC [GeneID=4609] in the presence of CKN1B [GeneID=1027]. 18838534 101/112 Arthur Liberzon 0.484984294918388 0.554536306205133 3375 3359.09090909091 3521 0.0585400252024657 2070 0.881907511942035 -0.799868981005199 -1 0.338756723891522 3375 2813 3697 3521 4630 3603 3007 3778 2552 3904 2070 4065 M526 REACTOME_TETRAHYDROBIOPTERIN_BH4_SYNTHESIS_RECYCLING_SALVAGE_AND_REGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TETRAHYDROBIOPTERIN_BH4_SYNTHESIS_RECYCLING_SALVAGE_AND_REGULATION.html Genes involved in Tetrahydrobiopterin (BH4) synthesis, recycling, salvage and regulation 17/21 Reactome 0.155126397440137 0.208424877858652 2610 3267.18181818182 3523 0.0152075650570154 1647 0.899563991137351 1.16188507212347 1 0.91918547548944 2607 3891 2198 4096 4081 3686 2560 1647 4315 3523 3335 4066 M5329 KIM_MYCL1_AMPLIFICATION_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_MYCL1_AMPLIFICATION_TARGETS_UP.html Genes positively correlated with amplifications of MYCL1 [GeneID=4610] in SCLC (small cell lung cancer) cell lines. 16116477 10/19 Arthur Liberzon 0.159873574876133 0.213526676122056 3860 3148.90909090909 3524 0.0157118865634885 1236 1.72482379676729 -1.72482379676729 -1 1.73536103156504 3856 3935 1545 3929 3524 3413 3990 1669 4639 2902 1236 4067 M42 PID_DNA_PK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_DNA_PK_PATHWAY.html DNA-PK pathway in nonhomologous end joining 18832364 15/19 Pathway Interaction Database 0.000319896640050115 0.00166289883374069 1005 2393.81818181818 3526 2.9085742264776e-05 62 0.485987045136002 -0.485987045136002 -1 2.02653139526509 1005 3526 3859 3616 4570 187 96 62 4357 4511 543 4068 M926 REACTOME_PROSTACYCLIN_SIGNALLING_THROUGH_PROSTACYCLIN_RECEPTOR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROSTACYCLIN_SIGNALLING_THROUGH_PROSTACYCLIN_RECEPTOR.html Genes involved in Prostacyclin signalling through prostacyclin receptor 15/22 Reactome 0.222392129103706 0.282630815662221 4245 3555 3527 0.0226071677137654 2299 1.10764439226495 -1.0551138709485 -1 0.911990743426519 4244 4585 2731 3140 2299 3842 3386 4486 4078 2787 3527 4069 M920 REACTOME_AQUAPORIN_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_AQUAPORIN_MEDIATED_TRANSPORT.html Genes involved in Aquaporin-mediated transport 37/54 Reactome 0.68618940391 0.690284310838704 4010 3259.63636363636 3528 0.1 1943 1.04196351771486 -1.17338582293724 -1 0.251571824830953 4006 2958 2325 3528 3777 3620 2479 4261 3676 1943 3283 4070 M1235 OXFORD_RALA_OR_RALB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_OR_RALB_TARGETS_UP.html Genes up-regulated after knockdown of RALA or RALB [GeneiD=5898;5899], which were also differentially expressed in bladder cancer compared to normal bladder urothelium tissue. 17496927 65/75 Arthur Liberzon 0.68618940391 0.690284310838704 2850 3525.09090909091 3528 0.1 2227 0.865868593594004 -0.88286455730741 -1 0.209037555279093 2850 3300 3783 3238 4011 3528 4447 3827 2227 4247 3318 4071 M1949 MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3.html Genes with high-CpG-density promoters (HCP) bearing histone H3 dimethylation mark at K4 (H3K4me2) and trimethylation mark at K27 (H3K27me3) in neural precursor cells (NPC). 18600261 251/536 Arthur Liberzon 4.35901505947258e-26 9.35206867305025e-24 3530 2806.27272727273 3528 3.96274096315687e-27 15 1.53520151441639 -1.67722892559625 -1 53.0497269325983 3528 1728 15 3708 3536 4304 3602 3924 3371 71 3082 4072 M1016 REACTOME_SYNTHESIS_OF_VERY_LONG_CHAIN_FATTY_ACYL_COAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SYNTHESIS_OF_VERY_LONG_CHAIN_FATTY_ACYL_COAS.html Genes involved in Synthesis of very long-chain fatty acyl-CoAs 12/15 Reactome 0.193909679160021 0.251579575735805 4220 3483.54545454545 3530 0.0194055568432785 2214 0.823432402074168 -0.514440224623835 -1 0.740405794718354 4216 3094 2525 3530 2214 4120 3268 2773 4124 3802 4653 4073 M1678 BURTON_ADIPOGENESIS_6 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_6.html Strongly up-regulated at 96 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 223/254 John Newman 0.68618940391 0.690284310838704 4635 3123.72727272727 3532 0.1 561 0.95601990896436 -0.798743349701463 -1 0.230812858386556 4635 561 3203 762 4160 2955 4007 4524 2109 3532 3913 4074 M1382 PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_LEFT_VENTRICLE_MASS_QTL_CIS_DN.html Down-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that were identified as candidate genes for the regulation of left ventricle mass (LVM). 18443592 10/12 Jessica Robertson 0.0076385859521332 0.0176217623138166 4600 2789.18181818182 3533 0.00069683976446204 399 0.668359535448105 -0.567655194551284 -1 1.75890830662323 4597 2145 3533 1335 823 4345 1746 4546 399 3658 3554 4075 M3029 ALONSO_METASTASIS_EMT_DN http://www.broadinstitute.org/gsea/msigdb/cards/ALONSO_METASTASIS_EMT_DN.html EMT (epithelial-mesenchymal transition) genes down-regulated genes in melanoma tumous that developed metastatic disease compared to primary melanoma that did not. 17409456 9/19 Jessica Robertson 0.380028356328566 0.448770037996205 3370 3472.09090909091 3534 0.0466833402864646 1820 1.90778395196902 -0.907071623817299 -1 0.996034388387597 3367 3941 4580 3534 3923 2854 1820 3271 4307 2762 3834 4076 M13398 OHM_EMBRYONIC_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/OHM_EMBRYONIC_CARCINOMA_DN.html Genes with low to medium basal transcription state in undifferentiated embryonic carcinoma cells. 17211412 11/14 Leona Saunders 0.00121407259110762 0.00457125844069806 3475 3228.36363636364 3535 0.000110431190598279 431 1.17587072856018 1.35266365566998 1 4.12856829600841 3473 3926 1871 3535 431 4543 3011 4326 4474 2346 3576 4077 M1120 JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_GLIOMAGENESIS_BY_PDGFB_UP.html Genes up-regulated in brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 77/90 Arthur Liberzon 0.68618940391 0.690284310838704 3660 3464.90909090909 3536 0.1 2029 1.09667661972522 -0.892679669935356 -1 0.264787321192049 3660 4416 2733 4608 4446 2527 2993 3735 2029 3431 3536 4078 M4230 ZHAN_LATE_DIFFERENTIATION_GENES_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_LATE_DIFFERENTIATION_GENES_DN.html B lymphocyte late differentiation genes (LDG): top genes down-regulated in plasma cells from tonsils (TPC) compared to those from bone marrow (BPC). 12393520 16/37 Arthur Liberzon 0.0122617681629089 0.0256313311465589 2710 3123.81818181818 3537 0.0011209679611659 586 0.877033683136869 1.06678760122125 1 2.09396189358081 2708 4230 2671 4205 3816 3537 1588 586 4276 3948 2797 4079 M1995 KYNG_NORMAL_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_NORMAL_AGING_DN.html Genes distinctly down-regulated in primary fibroblast cultures from normal old donors compared to those from normal young donors. 14527998 39/60 Arthur Liberzon 0.00255321712197013 0.0080185330277533 4185 3254.90909090909 3540 0.000232380462705978 563 1.03702651135858 0.683519505494025 1 3.26128824289395 4181 4132 2958 4258 563 4413 3646 3426 1797 3540 2890 4080 M18928 BIOCARTA_IL5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL5_PATHWAY.html IL 5 Signaling Pathway 5/16 BioCarta 0.0948485537075555 0.138046615325212 3940 3262.09090909091 3541 0.00991581145158095 1846 2.09063435240514 -2.39957519539559 -1 2.69766672309278 3938 2690 4193 2106 1846 2971 3892 3915 3541 2090 4701 4081 M17394 GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARGALOVIC_RESPONSE_TO_OXIDIZED_PHOSPHOLIPIDS_LIGHTYELLOW_DN.html Genes from the lightyellow module which are down-regulated in HAEC cells (primary aortic endothelium) after exposure to the oxidized 1-palmitoyl-2-arachidonyl-sn-3-glycerophosphorylcholine (oxPAPC). 16912112 13/14 Arthur Liberzon 0.000894563102765899 0.0036399464181509 4695 3309.90909090909 3541 8.13570051685434e-05 386 0.723494217205762 -0.743474118119531 -1 2.64761235716053 4691 3915 2995 3541 386 3190 3523 1290 4438 4631 3809 4082 M1256 INAMURA_LUNG_CANCER_SCC_SUBTYPES_UP http://www.broadinstitute.org/gsea/msigdb/cards/INAMURA_LUNG_CANCER_SCC_SUBTYPES_UP.html Up-regulated genes discriminating between two subtypes of squamous cell carcinoma (SCC) type of non-small cell lung cancer: SSC-A vs SSC-B. 16007138 17/17 Arthur Liberzon 0.0233262436300682 0.0428904830284074 3955 3324.63636363636 3541 0.00214339115715563 1202 1.18118552566193 -1.35508967286893 -1 2.42388750785026 3952 4589 3410 4424 1202 3541 3563 2445 1261 3526 4658 4083 M948 REACTOME_IRAK2_MEDIATED_ACTIVATION_OF_TAK1_COMPLEX_UPON_TLR7_8_OR_9_STIMULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IRAK2_MEDIATED_ACTIVATION_OF_TAK1_COMPLEX_UPON_TLR7_8_OR_9_STIMULATION.html Genes involved in IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation 11/14 Reactome 0.000558876091961154 0.00251707552868001 1015 2743.45454545455 3542 5.08198287574375e-05 28 0.651148022032395 0.651148022032395 1 2.53937623882249 1015 4256 3542 4415 4660 640 28 1046 4696 4587 1293 4084 M1343 FUJIWARA_PARK2_IN_LIVER_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/FUJIWARA_PARK2_IN_LIVER_CANCER_UP.html Genes up-regulated in tumorous liver tissues from PARK2 [GeneID=5071] knockout mice compared to the normal, non-tumorous tissue from wild type mice. 18574468 6/9 Jessica Robertson 0.107379709100482 0.153068693048297 3545 3263.81818181818 3543 0.0112951250939211 1711 0.999087492879934 1.22087825860746 1 1.2218724441063 3543 2180 4439 3741 1914 3968 2738 3911 4522 3235 1711 4085 M1007 FERRANDO_TAL1_NEIGHBORS http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_TAL1_NEIGHBORS.html Nearest neighbors of TAL1 [GeneID=6886], based on the close agreement of their expression profiles with that of TAL1 in pediatric T cell acute lymphoblastic leukemia (T-ALL) 12086890 24/40 Jean Junior 0.0417202105958602 0.0690702890257665 3780 2748.27272727273 3543 0.00386664048386301 349 1.45058729131872 -1.40782151479633 -1 2.52633380884374 3779 349 1044 971 4555 4179 4397 4479 1605 1330 3543 4086 M502 REACTOME_METABOLISM_OF_NON_CODING_RNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_NON_CODING_RNA.html Genes involved in Metabolism of non-coding RNA 50/58 Reactome 0.68618940391 0.690284310838704 2760 3531.36363636364 3544 0.1 2757 0.628484150832818 -0.631987280014717 -1 0.15169931043058 2757 3743 4086 4066 3544 3556 3495 2859 2909 4523 3307 4087 M9183 STEGMEIER_PRE-MITOTIC_CELL_CYCLE_REGULATORS http://www.broadinstitute.org/gsea/msigdb/cards/STEGMEIER_PRE-MITOTIC_CELL_CYCLE_REGULATORS.html Pre-mitotic cell cycle regulators (CDC) identified in an shRNA screen of the ubiquitin pathway components. 17443180 10/12 Jessica Robertson 0.00160789582811588 0.00567209888543121 1665 2625.72727272727 3545 0.000146279289226097 71 1.20939121107531 1.20939121107531 1 4.0762107634565 1665 4624 3545 4572 4191 1297 71 550 3873 3659 836 4088 M85 BIOCARTA_BAD_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BAD_PATHWAY.html Regulation of BAD phosphorylation 37/40 BioCarta 0.272031489376543 0.335157564567289 3740 3111.18181818182 3546 0.0284508386082964 875 0.901712676675729 0.94405151583762 1 0.642250265392802 3737 875 2215 2729 3546 4351 4154 2011 4215 2314 4076 4089 M11563 KAUFFMANN_DNA_REPAIR_GENES http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_DNA_REPAIR_GENES.html Genes involved in DNA repair, compiled manually by the authors. 17891185 235/260 Jessica Robertson 0.428626011064927 0.499814448548158 1840 3353.36363636364 3546 0.0496099945050469 1688 0.766899445854024 -0.803691244485806 -1 0.346489338659012 1838 4699 4178 4532 3903 1688 2988 3131 3546 4437 1947 4090 M1512 RUAN_RESPONSE_TO_TNF_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_UP.html Adipocyte abundant genes up-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to TNF [GeneID=7124]. 12732648 27/34 John Newman 0.0754244128690936 0.113702207195948 4345 3428 3546 0.00710378177891824 1308 1.10583660062601 -1.08455308523278 -1 1.56668518265374 4563 3824 1308 3546 1695 4341 2899 3519 4341 3280 4392 4091 M16597 REACTOME_EGFR_DOWNREGULATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EGFR_DOWNREGULATION.html Genes involved in EGFR downregulation 32/36 Reactome 0.68618940391 0.690284310838704 4205 3484 3547 0.1 2527 0.870283718214292 -0.705441269161603 -1 0.210103992041208 4205 2527 3437 3590 3668 3490 3144 3912 2924 3547 3880 4092 M788 REACTOME_REGULATION_OF_THE_FANCONI_ANEMIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_THE_FANCONI_ANEMIA_PATHWAY.html Genes involved in Regulation of the Fanconi anemia pathway 10/13 Reactome 0.00119514976254561 0.00452365603763441 2560 2985.09090909091 3548 0.000108709047432101 54 0.258061322217867 0.208418281608278 1 0.907750018451126 2559 4625 3548 4251 4638 850 54 1269 4698 4560 1784 4093 M10237 RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP.html Genes up-regulated in anaplastic thyroid carcinoma (ATC) compared to normal thyroid tissue. 17406368 980/1173 Arthur Liberzon 0.553678054386308 0.620898174555327 1115 3218.90909090909 3549 0.0775032938306442 1112 1.06523857493691 1.02344218230508 1 0.330732846819522 1112 4301 4322 4341 4059 2738 2272 2602 2062 4050 3549 4094 M867 MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MEINHOLD_OVARIAN_CANCER_LOW_GRADE_DN.html Genes down-regulated in low grade (LMP and G1) serous ovarian carcinomas vs the higher grade invasive tumors (G2 and G3). 15558012 28/32 Arthur Liberzon 0.0135206649556823 0.02777092871066 4210 3108.72727272727 3549 0.00123677106650647 1016 0.786755012120474 -1.06510324004047 -1 1.83730057972542 4207 2548 3549 3232 1016 3672 4363 3033 1234 3735 3607 4095 M14631 KEGG_COLORECTAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_COLORECTAL_CANCER.html Colorectal cancer 72/82 KEGG 0.11749619024666 0.165103309903018 3555 3249.54545454545 3551 0.0112986106340567 1915 0.822034367623624 -0.685949719630139 -1 0.964776042276108 4694 2855 3551 2234 1915 4352 3716 3743 2154 2979 3552 4096 M54 PID_IL12_2PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_IL12_2PATHWAY.html IL12-mediated signaling events 18832364 65/119 Pathway Interaction Database 0.68618940391 0.690284310838704 2700 3491.45454545455 3552 0.1 2589 0.839256805941741 -0.876518575207625 -1 0.202609698514287 2697 3714 2962 4134 4267 2589 3552 3338 4319 4046 2788 4097 M41 PID_ER_NONGENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ER_NONGENOMIC_PATHWAY.html Plasma membrane estrogen receptor signaling 18832364 60/69 Pathway Interaction Database 0.68618940391 0.690284310838704 4395 3369.36363636364 3553 0.1 1382 0.870471140123415 -0.869211117194436 -1 0.210149262250116 4394 1382 3290 2227 3258 4674 3721 3941 3801 3553 2822 4098 M8845 CHIN_BREAST_CANCER_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIN_BREAST_CANCER_COPY_NUMBER_DN.html Genes from common regions of losses observed in more than 15% of 148 primary breast cancer tumors. 17001317 19/23 Arthur Liberzon 0.68618940391 0.690284310838704 3490 3548.18181818182 3554 0.1 2281 1.36539304230257 1.13635851674882 1 0.329693546104427 3490 4225 2990 4410 3554 4171 2520 4594 2281 3168 3627 4099 M1469 BIOCARTA_LYM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_LYM_PATHWAY.html Adhesion and Diapedesis of Lymphocytes 10/14 BioCarta 0.00435256514194288 0.0119234518107779 3625 2900.18181818182 3555 0.000396472759334799 671 2.01985968784055 -2.66396233757944 -1 5.83001192804953 3621 4620 1224 4361 671 4138 3555 1533 2658 1591 3930 4100 M14344 DASU_IL6_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/DASU_IL6_SIGNALING_UP.html Genes up-regulated in normal fibroblasts in response to IL6 [GeneID=3569]. 15095275 113/166 Arthur Liberzon 0.000239301937318288 0.00135230656797059 3555 2743.81818181818 3555 2.17570882743598e-05 280 1.28154553902272 -1.32357693729918 -1 5.51679303836706 3555 2808 529 2223 280 4501 3690 4515 3787 488 3806 4101 M1244 WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WIEMANN_TELOMERE_SHORTENING_AND_CHRONIC_LIVER_DAMAGE_DN.html Genes down-regulated by telomere shortening due to the knockout of TERC [GeneID=7012] in the presence of chronic liver damage. 15608677 6/9 Leona Saunders 0.0122712464761057 0.0256397890071796 4655 3464.81818181818 3558 0.0012339540413672 1015 0.618373391034987 -0.467228013845694 -1 1.47623331347989 3080 3953 4400 3558 1015 3102 3285 4360 4653 4655 2052 4102 M10322 REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS.html Genes involved in Glucagon-type ligand receptors 17/36 Reactome 0.45423667162107 0.522798607669215 3560 3528.72727272727 3560 0.0535638840175376 2253 1.10764439226495 -1.0551138709485 -1 0.468034372608801 3560 4233 2354 3589 2747 3512 2253 4568 4645 2988 4367 4103 M1158 CROSBY_E2F4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/CROSBY_E2F4_TARGETS.html Putative E2F4 [GeneID=1874] target genes identified as mitotic genes down-regulated in the LNCaP C4-2 cells (prostate cancer) at both 6 and 24 h following irradiation. 17043659 10/10 Leona Saunders 0.108767566236868 0.154773262779023 3625 3261.90909090909 3560 0.0104135826317275 1006 0.632750978271753 0.680622205208802 1 0.769241854192606 3623 2658 3064 3803 3435 2332 1006 3865 3560 4641 3894 4104 M14092 OXFORD_RALA_AND_RALB_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_AND_RALB_TARGETS_UP.html Genes up-regulated in the UMUC-3 cells (bladder cancer) after knockdown of both RALA and RALB [GeneID=5898;5899] by RNAi. 17496927 9/12 Arthur Liberzon 0.6513215599 0.690284310838704 4660 3405.90909090909 3561 0.1 1518 0.852595215977081 -0.902903554224272 -1 0.20583148091755 4660 2165 4398 1518 3142 4599 4336 3291 1529 3561 4266 4105 M5298 BIOCARTA_STEM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_STEM_PATHWAY.html Regulation of hematopoiesis by cytokines 6/15 BioCarta 0.0287893816464617 0.0508935885285765 3565 3376.09090909091 3564 0.00291693001921879 1338 1.99822568217325 -2.80046009529594 -1 3.87780681848947 3564 4286 4195 3959 1338 3171 3350 2636 4069 2294 4275 4106 M1606 IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR.html Genes in the expression cluster 'Early Progenitors Shared': up-regulated in hematopoietic progenitors from adult bone marrow and from fetal liver. 12228721 652/783 John Newman 0.0534585172071135 0.0854467325491282 3315 3408.18181818182 3564 0.00547898349120016 1582 0.987557279649666 -0.980642880547234 -1 1.58296073900957 3315 4669 4486 4671 1582 1868 3564 4266 2416 4396 2257 4107 M111 BIOCARTA_BARRESTIN_SRC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BARRESTIN_SRC_PATHWAY.html Roles of fl-arrestin-dependent Recruitment of Src Kinases in GPCR Signaling 30/35 BioCarta 0.373717256730133 0.442313302850107 4195 3366.90909090909 3565 0.0416490318364399 1426 0.811710028212035 -0.681912859199696 -1 0.431390491670234 4194 4501 3565 3243 3788 3265 4646 2225 1426 3825 2358 4108 M18941 KORKOLA_EMBRYONAL_CARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONAL_CARCINOMA.html Genes predicting the embryonic carcinoma (EC) subtype of nonseminomatous male germ cell tumors (NSGCT). 15870693 10/19 Leona Saunders 0.00347186203373845 0.0100906334970723 3545 3424.45454545455 3565 0.000316123016485748 625 0.97865239334512 0.814740893196307 1 2.93111511636463 4466 3565 2493 3545 625 3757 4348 3542 4587 2901 3840 4109 M6821 NIKOLSKY_BREAST_CANCER_20P13_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_20P13_AMPLICON.html Genes within amplicon 20p13 identified in a copy number alterations study of 191 breast tumor samples. 19010930 9/12 Jessica Robertson 0.209020874025231 0.268749257804165 2705 3397.45454545455 3565 0.0231755932842014 1943 1.28009934850907 1.28009934850907 1 1.09601235356482 2702 4277 4466 4038 2311 4160 3379 1947 4584 3565 1943 4110 M7218 FAELT_B_CLL_WITH_VH3_21_DN http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH3_21_DN.html Genes down-regulated in samples from B-CLL (B-cell chronic lymphocytic leukemia) with the immunoglobulin heavy chain VH3-21 gene. 15817677 63/74 Kevin Vogelsang 0.00408552408400025 0.0113566982782575 3455 3276.81818181818 3566 0.000372102810623742 656 0.828354566805251 -0.716066825991186 -1 2.41714319408116 3453 3309 3893 3648 656 3566 4299 3314 3681 4228 1998 4111 M805 REACTOME_FORMATION_OF_RNA_POL_II_ELONGATION_COMPLEX_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_RNA_POL_II_ELONGATION_COMPLEX_.html Genes involved in Formation of RNA Pol II elongation complex 45/48 Reactome 0.0435652052734224 0.0717269306412464 3060 3505.63636363636 3567 0.00404114551741352 1466 0.545209422417237 -0.618636421227355 -1 0.936057871463803 3060 4123 4108 4115 1466 2720 3567 3459 3865 4563 3516 4112 M904 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_UP.html Up-regulated genes that vary between HNSCC (head and neck squamous cell carcinoma) groups formed on the basis of their level of pathological differentiation: well vs poorly differentiated tumors. 18679425 304/403 Jessica Robertson 0.68618940391 0.690284310838704 2740 3003.18181818182 3567 0.1 1295 0.998277145235785 0.960998301556986 1 0.241019743605189 2737 2249 3580 1803 4337 3666 2438 3736 1295 3627 3567 4113 M1665 JIANG_AGING_CEREBRAL_CORTEX_DN http://www.broadinstitute.org/gsea/msigdb/cards/JIANG_AGING_CEREBRAL_CORTEX_DN.html Down-regulated in the cerebral cortex of aged (22 months) BALB/c mice, compared to young (2 months) controls 11172053 91/114 John Newman 0.355558197094624 0.423475823943131 2735 3276.18181818182 3567 0.0391555985152296 1078 0.929852697569357 -0.825638134716115 -1 0.520566252458275 2735 4050 3567 3900 2583 3708 2864 3522 1078 4084 3947 4114 M11513 SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_DN http://www.broadinstitute.org/gsea/msigdb/cards/SARRIO_EPITHELIAL_MESENCHYMAL_TRANSITION_DN.html Genes down-regulated in MCF10A cells (breast cancer) grown at low (mesenchymal phenotype) compared to those grown at high (epithelial, basal-like phenotype) confluency. 18281472 237/351 Jessica Robertson 5.40951836167879e-07 8.2899112555597e-06 3570 3030.72727272727 3567 4.91774517437323e-08 257 1.25724268794382 1.30118294452085 1 9.58614070114981 3567 2749 257 3619 3854 4615 3348 3718 3137 404 4070 4115 M943 REACTOME_GABA_A_RECEPTOR_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GABA_A_RECEPTOR_ACTIVATION.html Genes involved in GABA A receptor activation 3/15 Reactome 0.49589223018288 0.565092063366295 3760 3360.72727272727 3568 0.0662032907346954 1922 0.432521006745815 0.360910552457937 1 0.160770405510467 3756 2189 4254 2347 4556 4199 2070 3568 1922 4586 3521 4116 M1038 BOYLAN_MULTIPLE_MYELOMA_PCA1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYLAN_MULTIPLE_MYELOMA_PCA1_DN.html Top down-regulated genes from principal component 1 (PCA1) which captures variation between normal plasma cells and tumors arising from aberrant expression of BCL2L1 and MYC [GeneID=598;4609]. 17483317 8/9 Arthur Liberzon 0.306053453414135 0.369928886072911 2220 3403.90909090909 3568 0.0358766483026072 1891 1.73058221997913 1.84950793861463 1 1.12139320554664 2219 3568 4638 3532 4592 4646 2521 2130 4075 1891 3631 4117 M2156 DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP.html Genes up-regulated in MCF7 cells (breast cancer) at 24 h of estradiol [PubChem=5757] treatment. 20406972 375/447 Jessica Robertson 0.68618940391 0.690284310838704 2395 3441.36363636364 3570 0.1 1585 1.1759196447286 -1.17155675175516 -1 0.283927817162763 2392 3976 3172 3880 4310 3111 3227 4592 1585 4040 3570 4118 M5490 WELCSH_BRCA1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WELCSH_BRCA1_TARGETS_UP.html Up-regulated by induction of exogenous BRCA1 in EcR-293 cells 12032322 322/395 John Newman 0.089589867521675 0.131405896427068 4615 3266.81818181818 3572 0.00849643462516059 1772 0.964181937614864 -0.925188411741503 -1 1.27505959279449 4614 2242 3572 2484 1772 3075 4693 3777 1973 4148 3585 4119 M532 REACTOME_G0_AND_EARLY_G1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G0_AND_EARLY_G1.html Genes involved in G0 and Early G1 26/29 Reactome 0.68618940391 0.690284310838704 2685 3473.18181818182 3573 0.1 2681 0.689115555485488 -0.755489673584826 -1 0.166344323747571 2681 3838 3787 3798 3310 3654 3445 3573 2901 4178 3040 4120 M1823 HOEGERKORP_CD44_TARGETS_DIRECT_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOEGERKORP_CD44_TARGETS_DIRECT_DN.html Genes directly down-regulated by CD44 [GeneID=960] stimulation of B lymphocytes. 12411303 21/39 Kevin Vogelsang 0.0324245009858634 0.0559984063861234 3725 3113.18181818182 3573 0.00299204415685177 1349 1.31423037847699 1.09796810992336 1 2.46852813063265 3723 1525 2087 1349 1351 4539 4456 4300 3573 2801 4541 4121 M1909 BIOCARTA_EGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EGF_PATHWAY.html EGF Signaling Pathway 49/53 BioCarta 0.68618940391 0.690284310838704 3470 3329.54545454545 3574 0.1 1228 0.780812960993664 -0.784581846221866 -1 0.188493072114753 3466 2903 3658 2237 3574 4418 3079 3994 1228 3680 4388 4122 M409 LOPEZ_EPITHELIOID_MESOTHELIOMA http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_EPITHELIOID_MESOTHELIOMA.html Top 20 genes expressed higher in epithelioid than in sarcomatoid mesothelioma samples. 16540645 27/30 Arthur Liberzon 0.68618940391 0.690284310838704 4485 3267.72727272727 3574 0.1 1885 1.17799175008895 -1.10457402752384 -1 0.284428317040184 4481 2550 1885 2607 4091 4597 3704 3729 2353 2374 3574 4123 M5519 PAL_PRMT5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PAL_PRMT5_TARGETS_DN.html Genes down-regulated in NIH-3T3 cells (fibroblast) after knockdown of PRMT5 [GeneID=10419] by RNAi. 15485929 26/42 John Newman 0.595727987304435 0.662231771096781 3720 3470.36363636364 3575 0.0790351362197707 2147 1.18976471990137 -0.85241848666273 -1 0.319438882510896 3718 4541 2520 4594 4609 2147 2200 3327 4214 2729 3575 4124 M854 LINDGREN_BLADDER_CANCER_CLUSTER_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/LINDGREN_BLADDER_CANCER_CLUSTER_3_UP.html Genes whose expression profile is specific to Cluster III of urothelial cell carcinoma (UCC) tumors. 16532037 397/547 Leona Saunders 0.68618940391 0.690284310838704 3420 3470.36363636364 3576 0.1 1130 0.981706825779996 -0.921536107332197 -1 0.237017320265552 3419 2720 3924 3397 4654 3108 3576 4526 1130 4108 3612 4125 M2324 LEE_BMP2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_BMP2_TARGETS_UP.html Genes up-regulated in uterus upon knockout of BMP2 [GeneID=650]. 17515606 962/1167 Arthur Liberzon 3.88647089707512e-16 2.47893819381008e-14 3595 2768.72727272727 3576 3.88647089707512e-17 35 1.2575808857695 -1.17665981820764 -1 25.6742598033554 3593 1117 4683 916 2451 4396 3739 3576 2068 35 3882 4126 M89 BIOCARTA_CDK5_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CDK5_PATHWAY.html Phosphorylation of MEK1 by cdk5/p35 down regulates the MAP kinase pathway 15/15 BioCarta 0.200373859319935 0.258824327799352 2930 3374.09090909091 3577 0.0201230450127661 1124 0.43735358107194 -0.43735358107194 -1 0.385114172436728 2926 4603 3577 4489 4448 1124 2519 1936 4617 4502 2374 4127 M10960 REACTOME_P2Y_RECEPTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P2Y_RECEPTORS.html Genes involved in P2Y receptors 5/14 Reactome 0.00908351419454464 0.0202810723738177 3245 3505.90909090909 3578 0.000912085881744232 901 0.81899250894589 -1.0230439962772 -1 2.08033502589023 3243 3141 4237 3336 901 4028 3578 4230 4583 3078 4210 4128 M1039 REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APC_C_CDC20_MEDIATED_DEGRADATION_OF_CYCLIN_B.html Genes involved in APC/C:Cdc20 mediated degradation of Cyclin B 27/32 Reactome 0.0323872105173865 0.0559544779070514 2915 3503.27272727273 3578 0.00298855105452878 1350 0.50790275061058 -0.495950330305711 -1 0.954192112218935 2911 3845 3963 3681 1350 3509 3321 3578 4484 4610 3284 4129 M3766 SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/SOTIRIOU_BREAST_CANCER_GRADE_1_VS_3_UP.html Up-regulated genes whose expression correlated with histologic grade of invasive breast cancer tumors: comparison of grade 1 vs grade 3. 16478745 183/229 Arthur Liberzon 0.68618940391 0.690284310838704 1295 3440.63636363636 3578 0.1 1291 0.891928419693673 -0.872882903503924 -1 0.215332090305197 1291 4716 4130 4529 3578 2737 2433 3829 2704 4400 3500 4130 M15664 ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER http://www.broadinstitute.org/gsea/msigdb/cards/ROSTY_CERVICAL_CANCER_PROLIFERATION_CLUSTER.html The 'Cervical Cancer Proliferation Cluster' (CCPC): genes whose expression in cervical carcinoma positively correlates with that of the HPV E6 and E7 oncogenes; they are also differentially expressed according to disease outcome. 16007141 173/219 Leona Saunders 0.682388130361271 0.690284310838704 1525 3394.18181818182 3579 0.0990143292489911 1525 0.974044643264915 -0.939486418043256 -1 0.235166583578625 1525 4715 3975 4667 3579 2806 2355 4299 1531 4352 3532 4131 M654 REACTOME_OXYGEN_DEPENDENT_PROLINE_HYDROXYLATION_OF_HYPOXIA_INDUCIBLE_FACTOR_ALPHA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OXYGEN_DEPENDENT_PROLINE_HYDROXYLATION_OF_HYPOXIA_INDUCIBLE_FACTOR_ALPHA.html Genes involved in Oxygen-dependent Proline Hydroxylation of Hypoxia-inducible Factor Alpha 19/27 Reactome 0.0026465274032716 0.00824528669534122 4685 3267.45454545455 3581 0.000240883314596657 568 1.02933884778873 -0.745288420099354 -1 3.21840522525321 4683 3059 3270 3581 568 3612 4340 2178 2686 3685 4280 4132 M5200 VALK_AML_WITH_EVI1 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_WITH_EVI1.html Genes that best predicted acute myeloid leukemia (AML) with the up-regulated expression of EVI1 [GeneID=2122]. 15084694 29/41 Jessica Robertson 0.40254914433418 0.471940377858254 4560 3662.45454545455 3581 0.0457463380643318 2677 0.811339298412395 -0.730038311833148 -1 0.396914049894542 4557 3008 3424 4570 2677 3639 3300 3069 4437 4025 3581 4133 M608 REACTOME_SIGNALING_BY_THE_B_CELL_RECEPTOR_BCR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_THE_B_CELL_RECEPTOR_BCR.html Genes involved in Signaling by the B Cell Receptor (BCR) 136/158 Reactome 0.0047247263171593 0.0127214536320547 4120 2893 3582 0.000430445796918814 424 0.723598600591371 -0.722446690410435 -1 2.05793931945641 4119 614 3889 424 698 3055 4636 3606 2872 4328 3582 4134 M1444 STONER_ESOPHAGEAL_CARCINOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/STONER_ESOPHAGEAL_CARCINOGENESIS_DN.html Genes down-regulated in esophagus by the carcinogen NMBA [PubChem=13643] and brought back to normal by a diet with PEITC [PubChem=16741] or black raspberries. 18676871 8/8 Jessica Robertson 0.228060346964264 0.28852811467413 3255 3577.81818181818 3582 0.0255527483850452 1944 0.666052995085494 0.666052995085494 1 0.539396120823772 3254 4279 4483 4231 3221 3582 2750 1944 4024 4678 2910 4135 M6682 BIOCARTA_MCM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_MCM_PATHWAY.html CDK Regulation of DNA Replication 19/19 BioCarta 0.67197828293232 0.690284310838704 2415 3642.63636363636 3583 0.0963689504518224 2411 0.704164471700849 -0.689755347652121 -1 0.169979264742964 2411 4234 3625 4117 3090 3301 3437 3196 4581 4494 3583 4136 M564 REACTOME_MEMBRANE_BINDING_AND_TARGETTING_OF_GAG_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEMBRANE_BINDING_AND_TARGETTING_OF_GAG_PROTEINS.html Genes involved in Membrane binding and targetting of GAG proteins 14/17 Reactome 0.00366053152999866 0.0104904121564018 1990 2998 3585 0.000333330584858625 140 0.631387159561401 0.658496776342031 1 1.87501332801987 1990 4250 3585 4047 4472 1086 140 2238 4608 4529 2033 4137 M13962 REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_THE_AP1_FAMILY_OF_TRANSCRIPTION_FACTORS.html Genes involved in Activation of the AP-1 family of transcription factors 9/10 Reactome 0.44294763274605 0.511802405522976 2690 3466.45454545455 3586 0.0568308166013532 2065 0.417008300085043 -0.417008300085043 -1 0.181917378970518 2687 3939 4245 4064 3586 2364 3585 2410 4611 4575 2065 4138 M10331 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FGF3 http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_FGF3.html Genes whose expression is coregulated with that of FGF3 [GeneID=2248] in hematopoietic stem cells (HSC). 15711547 7/12 Jean Junior 0.0745243716133932 0.112525602692008 4240 3442.90909090909 3586 0.00771483478916855 1734 0.792294680064622 -0.785801517341926 -1 1.12781786696508 3586 2679 4474 2876 1734 4632 1764 4240 2980 4670 4237 4139 M1285 SCHMAHL_PDGF_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/SCHMAHL_PDGF_SIGNALING.html These genes form a a network that controls specific processes downstream of PDGF signaling. 17143286 9/11 Leona Saunders 0.0851294316639122 0.126196896185196 2005 3241.90909090909 3587 0.00885780434618162 902 0.787727899540103 0.846866081061706 1 1.06245600840669 2002 4635 4413 4402 3587 2425 1375 4031 4326 3563 902 4140 M2008 MIKKELSEN_ES_LCP_WITH_H3K4ME3_AND_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_ES_LCP_WITH_H3K4ME3_AND_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the bivalent histone H3 trimethylation mark at K4 and K27 (H3K4me3 and H3K27me3) in embryonic stem cells (ES). 17603471 3/8 Arthur Liberzon 0.0750326517609904 0.113148279971845 4380 3293 3587 0.00776934552154976 1655 1.0963257537822 1.0963257537822 1 1.55669892531944 4376 1655 4645 2521 1736 4019 4215 3587 2121 2693 4655 4141 M754 REACTOME_GLYCOPROTEIN_HORMONES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOPROTEIN_HORMONES.html Genes involved in Glycoprotein hormones 3/9 Reactome 0.6513215599 0.690284310838704 4145 3464.45454545455 3588 0.1 2193 1.59566783784311 -1.59566783784311 -1 0.385314514587301 4142 3588 4229 3522 4301 2507 2673 4445 2193 2682 3827 4142 M9703 BIOCARTA_ATRBRCA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ATRBRCA_PATHWAY.html Role of BRCA1, BRCA2 and ATR in Cancer Susceptibility 27/27 BioCarta 0.127462684756272 0.176740267934666 3135 3444.09090909091 3589 0.0123189345558205 1672 0.729385556193824 0.752348323441214 1 0.823653593604872 3135 4526 3589 4638 1969 2314 1672 3389 4487 4505 3661 4143 M270 PID_MAPK_TRK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MAPK_TRK_PATHWAY.html Trk receptor signaling mediated by the MAPK pathway 18832364 47/49 Pathway Interaction Database 0.100232065903962 0.144412500325611 2650 3290 3589 0.00955572383935521 959 0.906874025948622 -0.735125756323354 -1 1.14348941857559 2648 4469 3674 4651 3752 2935 959 2251 4025 3589 3237 4144 M756 REACTOME_PEPTIDE_HORMONE_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PEPTIDE_HORMONE_BIOSYNTHESIS.html Genes involved in Peptide hormone biosynthesis 3/11 Reactome 0.6513215599 0.690284310838704 4145 3465.45454545455 3589 0.1 2194 1.59566783784311 -1.59566783784311 -1 0.385314514587301 4143 3589 4230 3523 4302 2508 2674 4446 2194 2683 3828 4145 M588 GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAUSSMANN_MLL_AF4_FUSION_TARGETS_F_DN.html Down-regualted genes from the set F (Fig. 5a): specific signature shared by cells expressing AF4-MLL [GeneID=4299;4297] alone and those expressing both AF4-MLL and MLL-AF4 fusion proteins. 17130830 35/49 Arthur Liberzon 0.0392935134084247 0.0658145433952322 3755 2983.09090909091 3593 0.0036375807918799 1420 1.33266214919384 -1.48963103026174 -1 2.36287973448207 3752 2502 1449 2532 1420 3593 3651 4089 4037 1808 3981 4146 M8981 BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOGNI_TREATMENT_RELATED_MYELOID_LEUKEMIA_DN.html Genes down-regulated in ALL (acute lymphoblastic leukemia) patients who developed t-ML (treatment related myeloid leukemia). 16341039 46/51 Arthur Liberzon 0.00598147131867604 0.0145904623380625 3440 3267.27272727273 3594 0.000545254201672832 754 1.12065475124697 1.00214907159978 1 3.08713129178987 3440 4489 3594 4501 754 2076 1959 2996 4211 3999 3921 4147 M1742 MARSON_BOUND_BY_FOXP3_STIMULATED http://www.broadinstitute.org/gsea/msigdb/cards/MARSON_BOUND_BY_FOXP3_STIMULATED.html Genes with promoters bound by FOXP3 [GeneID=50943] in hybridoma cells stimulated by PMA [PubChem=4792] and ionomycin [PubChem=3733]. 17237765 1186/1510 Jessica Robertson 0.151529972297998 0.204115716109175 4275 3358 3594 0.0162977821632974 1801 0.989797395200835 -1.02400210130891 -1 1.0248731679275 4275 3594 4518 2773 2130 3957 4319 2792 1801 4277 2502 4148 M710 REACTOME_VEGF_LIGAND_RECEPTOR_INTERACTIONS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_VEGF_LIGAND_RECEPTOR_INTERACTIONS.html Genes involved in VEGF ligand-receptor interactions 9/10 Reactome 0.706917241711113 0.710832846373339 3130 3862 3597 0.115497576867015 3129 0.964581353577179 0.964581353577179 1 0.214442009124753 3129 4641 4221 4591 3200 3436 3264 3157 4714 4532 3597 4149 M1347 SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN.html Genes down-regulated in the urogenital sinus (UGS) of day E16 females exposed to the androgen dihydrotestosterone [PubChem=10635] for 6 h. 18794802 710/839 Jessica Robertson 0.130886161087355 0.180796804311477 4425 3475.18181818182 3597 0.0139301807022981 2021 1.01217007718834 -1.01944839371578 -1 1.12805912986806 4425 3597 4441 3870 2040 3088 4376 3266 2021 4208 2895 4150 M13515 KEGG_MISMATCH_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MISMATCH_REPAIR.html Mismatch repair 22/23 KEGG 0.68618940391 0.690284310838704 1830 3581.90909090909 3598 0.1 1829 0.580044155262994 -0.591470833178741 -1 0.139999030942435 1829 4547 3898 4441 3336 2427 3091 3598 4436 4487 3311 4151 M11480 REACTOME_MEMBRANE_TRAFFICKING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MEMBRANE_TRAFFICKING.html Genes involved in Membrane Trafficking 151/177 Reactome 0.030064654667923 0.052733247875361 4185 3005.18181818182 3598 0.00277123157463453 597 0.80937123162166 -0.741917566068629 -1 1.55189412184949 4185 604 3993 597 1318 3479 3675 4172 3188 4248 3598 4152 M19655 LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_DN.html Genes down-regulated in LSK cells (bone marrow) as a function of a QTL for the size of hematopoietic stem cell (HSC) population: comparison of congenic D.B. Chr 3 (DB, small HSC population) vs parental D2 strain (huge HSC population). 17220891 40/56 Leona Saunders 0.00750260858779277 0.0173930808125648 3765 3299.81818181818 3599 0.000684392489667413 817 0.953711387765745 -1.042773509737 -1 2.51802637180629 3763 3780 2371 4089 817 3326 3336 3749 4496 3599 2972 4153 M7899 WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_TBH http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_TBH.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to HNE and tBH [PubChem=5283344;6410]. 12419474 98/117 John Newman 0.448293696940057 0.516840803506856 4110 3071.45454545455 3599 0.0526315789473684 426 0.92123040392922 -0.92851136291859 -1 0.396128160058268 4109 1301 3237 426 4386 3673 4505 2887 1804 3859 3599 4154 M2181 FIGUEROA_AML_METHYLATION_CLUSTER_7_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_7_DN.html Cluster 7 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 3/6 Arthur Liberzon 0.814607986984079 0.818074403949968 3570 3906.90909090909 3599 0.15509262300112 3084 0.803149545101534 1.03556301286647 1 0.104991227117733 3570 3590 4666 3084 3374 3599 3319 4656 4595 4713 3810 4155 M11680 HATADA_METHYLATED_IN_LUNG_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/HATADA_METHYLATED_IN_LUNG_CANCER_DN.html Genes with unmethylated DNA in lung cancer samples. 16407832 61/217 Arthur Liberzon 0.662141640572094 0.690284310838704 3545 3581.27272727273 3600 0.093938457772873 2323 1.02695577312166 -0.989840278020072 -1 0.247946828499685 3542 4436 3056 4008 3600 3278 2323 3958 3261 3833 4099 4156 M9372 KAUFFMANN_DNA_REPLICATION_GENES http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_DNA_REPLICATION_GENES.html Genes involved in DNA replication, compiled manually by the authors. 17891185 144/171 Jessica Robertson 0.68618940391 0.690284310838704 2715 3597.36363636364 3601 0.1 2274 0.818408896526726 -0.869971359511818 -1 0.19757405877011 2713 4367 4135 4677 4297 2511 3215 3601 2274 4412 3369 4157 M19629 MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGHAN_NPM1_MUTATED_SIGNATURE_1_DN.html The 'NPM1-mutated signature 1': genes down-regulated in pediatric AML (acute myeloid leukemia) samples with mutated NPM1 [GeneID=4869] compared to all AML cases with the intact gene. 17597811 169/259 Arthur Liberzon 0.68618940391 0.690284310838704 3515 3547.63636363636 3602 0.1 1998 1.18124656194628 -1.10672115283445 -1 0.285214489870386 3514 4352 1998 4268 3602 4520 3880 3408 3050 2053 4379 4158 M633 REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SMAD2_SMAD3_SMAD4_HETEROTRIMER_REGULATES_TRANSCRIPTION.html Genes involved in SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription 33/41 Reactome 0.181682029002742 0.238337736768467 3965 3336.36363636364 3603 0.0180625445703576 1699 0.845503709619001 -0.968230041922471 -1 0.790046716167943 3961 4153 3699 4265 2179 2385 1699 3922 3292 3603 3542 4159 M18550 BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP http://www.broadinstitute.org/gsea/msigdb/cards/BHATI_G2M_ARREST_BY_2METHOXYESTRADIOL_UP.html Up-regulated genes in MDA-MB-435 cells (breast cancer) undergoing G2/M arrest after treatment with 2-methoxyestradiol (2ME2)[PubChem=1573]. 17234781 161/205 Jessica Robertson 0.291374434719203 0.35562517384168 3605 3377.27272727273 3603 0.030826504454446 1471 1.12860668784097 1.06842480836154 1 0.760287026479322 4330 3640 1471 3603 4370 3393 4096 3902 3079 1663 3603 4160 M18436 BOYAULT_LIVER_CANCER_SUBCLASS_G3_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G3_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G3, defined by unsupervised clustering. 17187432 258/323 Yujin Hoshida 0.574157562608934 0.64127394593331 2775 3498.90909090909 3605 0.0746727368460344 1285 0.878826586585744 -0.93420598356357 -1 0.254345190582862 2775 4695 4164 4690 4255 3185 3605 2573 1285 4380 2881 4161 M2248 BRUINS_UVC_RESPONSE_EARLY_LATE http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_EARLY_LATE.html Early-late response genes: differentially expressed in the first 3 h and after 12 h following UV-C irradiation of MEF cells (embryonic fibroblast). 18195040 399/493 Arthur Liberzon 0.481344055846068 0.551041460973427 2990 3413.81818181818 3605 0.057937011311408 1553 1.00524808198647 0.961400257162222 1 0.390290494576156 2986 4322 3863 3605 2778 3843 2860 3226 1553 3819 4697 4162 M15347 BIOCARTA_AKAPCENTROSOME_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAPCENTROSOME_PATHWAY.html Protein Kinase A at the Centrosome 24/25 BioCarta 0.43119990772354 0.499814448548158 3610 3026 3607 0.05 108 0.924415597697599 0.748493161674068 1 0.417677728672722 3607 336 3093 411 4698 4463 4341 4653 108 3048 4528 4163 M2831 BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP http://www.broadinstitute.org/gsea/msigdb/cards/BREDEMEYER_RAG_SIGNALING_VIA_ATM_NOT_VIA_NFKB_UP.html Genes up-regulated in pre B lymphocyte after induction of physiological DNA double-strand breaks (DSB) by RAG2 [GeneID=5897]; the changes depend on ATM [GeneID=472] but not NFKB signaling. 18849970 60/75 Jessica Robertson 0.158246069978836 0.211832515683524 4610 3299.90909090909 3607 0.0155386956518977 1838 0.98348778366553 -0.844575938573395 -1 0.994555945334452 4610 1910 2867 2036 2103 4561 3607 4695 1838 3817 4255 4164 M5039 NAGY_PCAF_COMPONENTS_HUMAN http://www.broadinstitute.org/gsea/msigdb/cards/NAGY_PCAF_COMPONENTS_HUMAN.html Composition of the 2 MDa human PCAF complex. 17694077 10/12 Arthur Liberzon 0.68618940391 0.690284310838704 3815 3609.18181818182 3610 0.1 2714 0.603419590469004 -0.603419590469004 -1 0.145645173594803 3813 3934 3778 3610 3277 3274 2714 3889 3400 4644 3368 4165 M3695 SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/SETLUR_PROSTATE_CANCER_TMPRSS2_ERG_FUSION_UP.html Genes up-regulated in prostate cancer samples bearing the fusion of TMPRSS2 with ERG [GeneID=7113;2078]. 18505969 108/126 Jessica Robertson 0.00577426225782821 0.0142024584976285 3705 2646.72727272727 3610 0.000526315789473684 29 1.13578940213423 -1.10325576407212 -1 3.14877443465445 3701 29 1986 123 3610 4332 3629 4002 950 2277 4475 4166 M1491 LY_AGING_PREMATURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_PREMATURE_DN.html Genes down-regulated in fibroblasts from patients with Hutchinson-Gilford progeria (premature aging), compared to those from normal young individuals. 10741968 42/57 Arthur Liberzon 0.68618940391 0.690284310838704 4045 3444 3612 0.1 1853 1.58087148647387 -1.77739716828488 -1 0.381740578537382 4042 3365 1853 3612 4200 4360 3266 3835 3637 2285 3429 4167 M2529 BIOCARTA_PDGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PDGF_PATHWAY.html PDGF Signaling Pathway 48/52 BioCarta 0.68618940391 0.690284310838704 3110 3324.54545454545 3613 0.1 1572 0.798891644321833 -0.856098784076799 -1 0.192859828247345 3106 2913 3613 2236 4110 4158 2584 4587 1572 3630 4061 4168 M6312 WU_APOPTOSIS_BY_CDKN1A_NOT_VIA_TP53 http://www.broadinstitute.org/gsea/msigdb/cards/WU_APOPTOSIS_BY_CDKN1A_NOT_VIA_TP53.html Genes downstream of CDKN1A [GeneID=1026] in a TP53 [GeneID=7157] independent pathway in 2774qw1 cells (ovarian cancer). 12138103 18/19 Arthur Liberzon 0.524038546149283 0.592304103885205 2745 3455.63636363636 3614 0.0652653460013641 2220 1.12682000383001 1.03743098124945 1 0.384479169014083 2741 4584 2950 3657 2862 2220 2592 4438 4647 3614 3707 4169 M12307 NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON.html Genes within amplicon 16q24 identified in a copy number alterations study of 191 breast tumor samples. 19010930 58/71 Jessica Robertson 0.181191586772516 0.23776043635426 3615 3447.36363636364 3615 0.0180090587540612 1747 0.793031115519574 0.913663317370213 1 0.74226254788024 2506 4440 3614 4391 3422 3615 3800 1747 3846 4074 2466 4170 M9494 BIOCARTA_BCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_BCR_PATHWAY.html BCR Signaling Pathway 47/57 BioCarta 0.116158945814638 0.163613913531808 3460 3543.63636363636 3616 0.0111625076250713 1905 0.766730943809008 -0.80699812873131 -1 0.904390196123114 3585 4112 3616 3908 1905 4253 2051 3456 3457 4169 4468 4171 M19877 KEGG_ENDOMETRIAL_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_ENDOMETRIAL_CANCER.html Endometrial cancer 56/61 KEGG 0.166655706461391 0.220959251263417 3675 3446.18181818182 3617 0.0164369066257316 2135 0.738200963458006 0.800050107390832 1 0.726189960949673 3744 3311 3638 3256 2135 3544 2737 3617 3673 3675 4578 4172 M2524 VANOEVELEN_MYOGENESIS_SIN3A_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/VANOEVELEN_MYOGENESIS_SIN3A_TARGETS.html Loci bound exclusively by SIN3A [GeneID=25942] in myotubules. 20956564 279/323 Arthur Liberzon 0.213265511114903 0.273442150103529 4530 3468.18181818182 3618 0.0215698308342852 2269 0.93829853575142 -0.906595825932836 -1 0.792751441662755 4527 3618 3922 3182 2269 3890 4275 2501 2747 4211 3008 4173 M11090 DITTMER_PTHLH_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DITTMER_PTHLH_TARGETS_UP.html Genes up-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PTHLH [GeneID=5744] by RNAi. 16551631 174/198 Leona Saunders 0.68618940391 0.690284310838704 3620 3017.09090909091 3619 0.1 593 1.03757254661978 -0.857921601022876 -1 0.250511222152681 3619 593 2122 1875 4042 4244 3725 3940 1763 2747 4518 4174 M16826 ZUCCHI_METASTASIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZUCCHI_METASTASIS_DN.html The 50 most down-regulated genes in primary invasive breast dutcal carcinoma (IDC) or lymph node metastases, compared to normal mammary epithelium. 15608061 57/65 Kate Stafford 0.547305120282292 0.615359735048218 4650 3533.27272727273 3620 0.0695145244204735 2486 1.09984827894287 -1.10667779187054 -1 0.347903824775062 4649 3316 2486 3620 4699 3678 4690 2519 2745 2831 3633 4175 M5688 CADWELL_ATG16L1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/CADWELL_ATG16L1_TARGETS_UP.html Genes up-regulated in Paneth cell (part of intestiinal epithelium) of mice with hypomorphic (reduced function) form of ATG16L1 [GeneID=55054]. 18849966 80/138 Jessica Robertson 0.000204194390911674 0.00118698340117844 3200 3242.09090909091 3622 1.85648496187496e-05 524 1.48750973923133 1.58431983661683 1 6.52984552686234 3197 2844 524 3928 3309 3759 4511 4696 3622 991 4282 4176 M13038 CHASSOT_SKIN_WOUND http://www.broadinstitute.org/gsea/msigdb/cards/CHASSOT_SKIN_WOUND.html List of the transcription factors up-regulated 1 hr after wounding HDF cells (dermal fibroblasts). 17404577 13/13 Leona Saunders 0.68618940391 0.690284310838704 2505 3309.45454545455 3623 0.1 1921 1.13184490941838 -1.279650387156 -1 0.273281930113655 2504 3557 1921 3623 4219 3823 2843 4068 3757 1962 4127 4177 M9802 BROWNE_HCMV_INFECTION_1HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_1HR_DN.html Genes down-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 1 h time point that were not down-regulated at the previous time point, 30 min. 11711622 282/402 Arthur Liberzon 0.68618940391 0.690284310838704 3985 3595.63636363636 3623 0.1 1976 1.17066558980459 -1.25930288149443 -1 0.282658743738338 3985 3617 1976 3869 3623 4206 3774 4542 3374 3341 3245 4178 M495 REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_APOPTOTIC_CLEAVAGE_OF_CELLULAR_PROTEINS.html Genes involved in Apoptotic cleavage of cellular proteins 51/60 Reactome 0.68618940391 0.690284310838704 4160 2998.36363636364 3624 0.1 601 0.952333841542729 -1.04865383140917 -1 0.229922519348786 4157 798 2660 601 3993 4398 3833 3068 3683 2167 3624 4179 M550 REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANTIVIRAL_MECHANISM_BY_IFN_STIMULATED_GENES.html Genes involved in Antiviral mechanism by IFN-stimulated genes 86/100 Reactome 0.68618940391 0.690284310838704 2045 3471.54545454545 3624 0.1 2044 0.759874424122126 -0.752860758097458 -1 0.183435542059518 2044 3693 4060 4158 3624 3018 2641 3412 3883 4314 3340 4180 M2835 PIEPOLI_LGI1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PIEPOLI_LGI1_TARGETS_DN.html Down-regulated genes in U87 cells (glioblastoma multiforme, GBM) engineered to stably express LGI1 [GeneID=9211]. 16533756 20/35 Arthur Liberzon 0.0208298886591606 0.0390922761317049 4640 3473.09090909091 3624 0.00191179666049975 1171 1.16412247072553 -0.862272028974895 -1 2.45921438316716 4640 4214 2381 3587 1171 4260 3859 3624 3578 2212 4678 4181 M10828 SHEPARD_CRUSH_AND_BURN_MUTANT_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_CRUSH_AND_BURN_MUTANT_UP.html Human orthologs of genes up-regulated in the crb ('crash and burn') zebrafish mutant that represents a loss-of-function mutation in BMYB [GeneID=4605]. 16150706 236/269 Jennifer Shepard 0.623599330695802 0.688995515188246 2690 3540.27272727273 3624 0.084996484923179 2331 1.00170063539547 1.08936081043651 1 0.243066563880401 2688 4698 3624 4511 3014 3554 2331 2944 3710 3874 3995 4182 M12256 REACTOME_SIGNALLING_TO_RAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_RAS.html Genes involved in Signalling to RAS 34/36 Reactome 0.234862437612807 0.295692372774726 3350 3319.54545454545 3626 0.0240425901977158 1909 0.746261111858018 -0.737636702363836 -1 0.592436701085275 3347 4147 3762 4140 3987 3038 3626 1909 2355 3925 2279 4183 M203 PID_ALK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ALK2_PATHWAY.html ALK2 signaling events 18832364 9/13 Pathway Interaction Database 0.050085675564354 0.0808585204838208 4380 3086.90909090909 3627 0.00512516959610705 440 0.920134005458564 -0.578428569148931 -1 1.50797482672725 4379 1623 4204 2041 3627 4081 4400 1162 440 3556 4443 4184 M16066 SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN http://www.broadinstitute.org/gsea/msigdb/cards/SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_DN.html Genes down-regulated in lymphoblastoid cells from the European population compared to those from the Asian population. 17206142 795/989 Leona Saunders 0.100060606250826 0.144209484428671 4635 3425.36363636364 3627 0.0104874054459798 1837 0.907211001331004 -0.888736448728263 -1 1.14474605159737 4631 2700 4415 2495 1876 3627 4393 3985 1837 4431 3289 4185 M1456 PARK_HSC_AND_MULTIPOTENT_PROGENITORS http://www.broadinstitute.org/gsea/msigdb/cards/PARK_HSC_AND_MULTIPOTENT_PROGENITORS.html Genes commonly expressed in long term hematopoietic stem cells (HSC) and multipotent progenitors (MPP). 11781229 86/120 Kevin Vogelsang 0.320985850376121 0.385804230653244 3630 3416.54545454545 3627 0.034580077397332 1713 0.971117701731698 -0.987958024678969 -1 0.602632590133842 3627 4402 3600 4303 4624 1744 3965 3489 2366 3749 1713 4186 M2059 FERRANDO_HOX11_NEIGHBORS http://www.broadinstitute.org/gsea/msigdb/cards/FERRANDO_HOX11_NEIGHBORS.html Nearest neighbors of HOX11 [GeneID=3195], based on the close agreement of their expression profiles with that of HOX11 in pediatric T cell acute lymphoblastic leukemia (T-ALL). 12086890 23/28 Arthur Liberzon 0.376885625277061 0.445281639876778 3095 3760.45454545455 3627 0.0420908035483687 2627 0.64897489131672 -0.631944371488752 -1 0.342053562152821 3093 3859 3520 3627 2627 4529 3921 3547 4552 4701 3389 4187 M7970 PENG_GLUCOSE_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUCOSE_DEPRIVATION_DN.html Genes down-regulated in BJAB cells (B-lymphoma) after glucose [PubChem=206] deprivation. 12101249 225/285 Broad Institute 0.515869548589107 0.584049956666007 2720 3249.09090909091 3628 0.0638181476011174 2093 1.0547628374855 1.14157374536589 1 0.369532083289709 2716 3994 3684 3884 3628 2912 2697 2472 2093 3721 3939 4188 M2168 FIGUEROA_AML_METHYLATION_CLUSTER_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_3_UP.html Cluster 3 of aberrantly hypermethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 225/343 Arthur Liberzon 0.0195320688917658 0.0370842176866993 3305 3611.90909090909 3628 0.00179160593208074 1148 1.01244646184407 1.00586017591343 1 2.17357667101943 3304 3628 3550 3868 1148 4427 3620 4686 2850 4030 4620 4189 M17523 ZHAN_MULTIPLE_MYELOMA_CD2_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_CD2_DN.html Top 50 down-regulated genes in cluster CD-2 of multiple myeloma samples with the charachteristic expression spike of CCND3 [GeneID=896]. 16728703 62/72 Kevin Vogelsang 0.0174337919697825 0.0339469876639329 3695 2858.45454545455 3629 0.00159759069128014 770 0.984723569385684 -1.06783315801521 -1 2.17077855116951 3692 770 2298 990 1103 4620 3891 3873 2399 3629 4178 4190 M113 PID_NFAT_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_NFAT_3PATHWAY.html Role of Calcineurin-dependent NFAT signaling in lymphocytes 18832364 65/74 Pathway Interaction Database 0.68618940391 0.690284310838704 2880 3564.81818181818 3630 0.1 2877 0.784897777764161 -0.617313844132943 -1 0.189479725753145 2877 3295 3630 3862 4121 3117 3159 4223 3142 4047 3740 4191 M11650 BIOCARTA_NOS1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NOS1_PATHWAY.html Nitric Oxide Signaling Pathway 21/27 BioCarta 0.0289688538713984 0.0511533820699591 4690 3292.45454545455 3632 0.00266886267873833 1298 1.06935654808124 -1.47972150097966 -1 2.07162271532019 4690 4208 2375 3839 1298 3830 3632 2623 4323 3322 2077 4192 M19943 BIOCARTA_CERAMIDE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CERAMIDE_PATHWAY.html Ceramide Signaling Pathway 29/33 BioCarta 0.117163027092845 0.164782326542976 4230 3292 3633 0.011264684191618 1279 0.740474422670101 -0.492000886088957 -1 0.869982211572045 4228 3415 3537 3633 1912 1696 4298 4700 1279 3776 3738 4193 M7248 RASHI_RESPONSE_TO_IONIZING_RADIATION_3 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_3.html Cluster 3: genes activated by ionizing radiation regardless of ATM [GeneID=472] status. 16314843 66/83 Arthur Liberzon 0.68618940391 0.690284310838704 3715 3629.18181818182 3635 0.1 2713 0.865052312056268 -0.953300050173281 -1 0.208840389238507 3711 4076 3635 4094 3555 3352 2713 3303 3593 3929 3960 4194 M2325 LEE_BMP2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_BMP2_TARGETS_DN.html Genes down-regulated in uterus upon knockout of BMP2 [GeneID=650]. 17515606 1059/1243 Arthur Liberzon 0.6513215599 0.690284310838704 1350 3533.72727272727 3635 0.1 1350 0.995929889970968 1.05697269220034 1 0.240452783548621 1350 4664 4684 4697 3635 3273 3001 2798 2691 4423 3655 4195 M11520 BIOCARTA_TPO_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TPO_PATHWAY.html TPO Signaling Pathway 37/42 BioCarta 0.599151410401566 0.665430043573571 4460 3221.09090909091 3638 0.0797468653783195 540 0.776839942958581 -0.876188208275509 -1 0.206097317173705 4460 2956 3711 1679 2983 4231 3902 3545 540 3787 3638 4196 M2303 VANDESLUIS_NORMAL_EMBRYOS_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANDESLUIS_NORMAL_EMBRYOS_UP.html Genes up-regulated in normal 9.5 days post coitus (dpc) embryos compared to normal 8.5 dpc and 9.5 dpc embryos. 17371845 5/13 Arthur Liberzon 0.00809054795755032 0.0184302057720258 1835 2903.63636363636 3639 0.000812015541437335 179 1.37405725641633 1.21759451542167 1 3.5760248868619 1834 3960 4681 3639 4230 3999 1221 2242 4628 1327 179 4197 M17600 NAGASHIMA_NRG1_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAGASHIMA_NRG1_SIGNALING_DN.html Genes down-regulated in MCF7 cells (breast cancer) after stimulation with NRG1 [GeneID=3084]. 17142811 76/84 Arthur Liberzon 0.68618940391 0.690284310838704 4320 3627.63636363636 3640 0.1 2018 1.1245534910479 -1.08301461594542 -1 0.271520748433186 4316 3269 2018 3497 3293 3749 4615 4462 3337 3640 3708 4198 M15589 PENG_GLUTAMINE_DEPRIVATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUTAMINE_DEPRIVATION_UP.html Genes up-regulated in BJAB cells (B-lymphoma) after glutamine [PubChem=738] deprivation. 12101249 68/87 Broad Institute 0.0700000679847045 0.106960285169247 4245 3219.27272727273 3640 0.00657562767409541 789 0.938846720469958 -0.946416748790406 -1 1.36748500373753 4241 1892 3596 3640 1657 4248 4204 4488 789 3963 2694 4199 M17225 BROWNE_HCMV_INFECTION_14HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BROWNE_HCMV_INFECTION_14HR_UP.html Genes up-regulated in primary fibroblast cell culture after infection with HCMV (AD169 strain) at 14 h time point that were not up-regulated at the previous time point, 12 h. 11711622 228/312 John Newman 0.00760608981153629 0.0175671011637266 3865 3391.27272727273 3640 0.000693864949019799 821 1.08849518769399 -1.15726567238653 -1 2.86684107175896 3861 3185 3390 3696 821 4527 4015 4097 2972 3100 3640 4200 M1096 KOINUMA_COLON_CANCER_MSI_UP http://www.broadinstitute.org/gsea/msigdb/cards/KOINUMA_COLON_CANCER_MSI_UP.html Genes up-regulated in colorectal carcinoma samples positive for MSI (microsatellite instability) compared to the MSI negative ones. 16247484 18/21 Arthur Liberzon 0.0255437860416147 0.0462827908316397 3710 3315.45454545455 3641 0.00234957113982992 845 0.989623214974409 -1.23980727917927 -1 1.98167875371112 3708 3880 2918 4014 4626 3641 3252 845 3132 4008 2446 4201 M1330 MANTOVANI_VIRAL_GPCR_SIGNALING_DN http://www.broadinstitute.org/gsea/msigdb/cards/MANTOVANI_VIRAL_GPCR_SIGNALING_DN.html Down-regulated genes in the expression signature of direct and paracrine viral GPCR signaling in endothelial cells. 17906691 76/105 Jessica Robertson 0.68618940391 0.690284310838704 4185 3522.81818181818 3641 0.1 2407 1.05463294198733 1.0264735729422 1 0.254632019267346 4184 2407 2533 2700 3847 3921 4669 3214 3236 3641 4399 4202 M7747 BIOCARTA_IL2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL2_PATHWAY.html IL 2 signaling pathway 34/41 BioCarta 0.398795822294994 0.468005042573937 2715 3290.81818181818 3642 0.0452029028038575 1730 0.799551764073939 -0.820458988223143 -1 0.395508942088786 2715 4499 3536 3689 4025 1730 3642 3760 2587 4125 1891 4203 M17541 REACTOME_REGULATION_OF_BETA_CELL_DEVELOPMENT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_BETA_CELL_DEVELOPMENT.html Genes involved in Regulation of beta-cell development 8/32 Reactome 0.0848210188507404 0.125897864457703 3190 3490 3643 0.00882439693298858 934 0.636148739463174 -0.524542925164156 -1 0.858975198701094 3189 3942 4225 4375 2646 3643 934 3264 4681 4544 2947 4204 M14897 REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REGULATION_OF_GLUCOKINASE_BY_GLUCOKINASE_REGULATORY_PROTEIN.html Genes involved in Regulation of Glucokinase by Glucokinase Regulatory Protein 28/32 Reactome 0.68618940391 0.690284310838704 4610 3560 3643 0.1 1926 0.668848315380046 -0.647058111900683 -1 0.16144893986288 4609 3437 3892 2726 3797 3595 3643 2822 1926 4609 4104 4205 M4144 SAGIV_CD24_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAGIV_CD24_TARGETS_UP.html Genes up-regulated in HT29 cells (colon cancer) after knockdown of CD24 [GeneID=100133941] by both RNAi and monoclonal antibodies. 18413748 30/39 Jessica Robertson 0.68618940391 0.690284310838704 4485 3565.45454545455 3643 0.1 2556 1.29601673337432 -1.50221923564074 -1 0.312936273632211 4484 3840 2556 4030 3643 4411 3178 2872 4256 2597 3353 4206 M1559 MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_REGULATED_BY_HISTONE_ACETYLATION_UP.html Cluster 9: genes up-regulated in SW260 cells (colon cancer) by sodium butyrate and TSA [PubChem=5222465;5562] with the same kinetics with which each alters the level of histone H4 acetylation. 10969808 108/120 John Newman 0.68618940391 0.690284310838704 3710 3324.09090909091 3646 0.1 1822 1.16159020286612 1.03786492557266 1 0.280466659234734 3710 1822 2547 2901 3853 3646 4168 3695 3034 3186 4003 4207 M2080 KARLSSON_TGFB1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/KARLSSON_TGFB1_TARGETS_UP.html Genes up-regulated by TGFB1 [GeneID=7040] in MEF cells (embryonic fibroblast) via TGFB1R [GeneID=7046]. 15769904 181/201 Arthur Liberzon 0.68618940391 0.690284310838704 1690 3350 3647 0.1 1686 0.967874694019432 0.984369005590453 1 0.233676283471232 1686 4005 3725 3911 3647 3093 2707 3719 3155 3763 3439 4208 M213 PID_AR_NONGENOMIC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_AR_NONGENOMIC_PATHWAY.html Nongenotropic Androgen signaling 18832364 43/48 Pathway Interaction Database 0.0134141615772338 0.0275905044694181 4300 3187 3649 0.00122696885790889 1014 0.662790054135445 -0.613403302869376 -1 1.55060513960222 4296 1956 3649 1675 1014 3684 3854 3619 3213 4120 3977 4209 M2480 ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ACEVEDO_NORMAL_TISSUE_ADJACENT_TO_LIVER_TUMOR_UP.html Genes up-regulated in normal tissue adjacent to liver tumor, compared to the normal liver samples. 18413731 260/382 Jessica Robertson 0.0265390149603951 0.0478289998522584 4450 3462.09090909091 3649 0.00244224303937521 1253 1.01737450212464 -0.935143948662041 -1 2.0154653642304 4449 2741 3222 3649 1253 3816 4184 4674 3055 3857 3183 4210 M1832 MATZUK_SPERMATID_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_SPERMATID_DIFFERENTIATION.html Genes important for spermatid differentiation, based on mouse models with male reproductive defects. 18989307 41/62 Jessica Robertson 0.244417697414652 0.305998658047696 3650 3592.72727272727 3649 0.0251569337811671 2091 1.01767007328454 -1.07876932058026 -1 0.785218137382215 3413 4121 3133 4369 2360 3901 4179 2091 3648 3649 4656 4211 M5500 KEGG_BASE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_BASE_EXCISION_REPAIR.html Base excision repair 33/35 KEGG 0.32004029423924 0.384765712890783 2595 3399.81818181818 3650 0.0344579375636621 2265 0.763504836853885 -0.916953325657468 -1 0.475115753686708 2592 4163 3894 4438 2522 2667 3040 3650 4055 4112 2265 4212 M14591 WEIGEL_OXIDATIVE_STRESS_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_RESPONSE.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to HNE, tBH and H2O2 [PubChem=5283344;6410;784]. 12419474 86/100 John Newman 0.68618940391 0.690284310838704 4640 3345.36363636364 3651 0.1 813 1.12525648895815 -0.944399340977992 -1 0.271690551752382 4638 4054 2780 3651 4289 2973 4404 2889 813 2551 3757 4213 M10189 REACTOME_SIGNALING_BY_NOTCH http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALING_BY_NOTCH.html Genes involved in Signaling by NOTCH 116/129 Reactome 0.248583210913095 0.310564519722025 3970 3270.27272727273 3652 0.0256467346517476 1517 1.07708831461278 -1.01081477883655 -1 0.820674629116833 3968 3652 2619 3768 3685 2936 4081 4513 2648 2586 1517 4214 M2891 ROETH_TERT_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ROETH_TERT_TARGETS_DN.html Genes down-regulated in T lymphocytes overexpressing TERT [GeneID=7015] off a retrovirus vector. 15741219 6/14 Kevin Vogelsang 0.00388227676468333 0.0109268612577849 3680 2857 3656 0.000388907592103743 453 0.909716970463016 -0.993645660903683 -1 2.67744318464295 3677 2177 4484 1897 668 4265 3656 1460 453 4680 4010 4215 M7857 KEGG_NON_HOMOLOGOUS_END_JOINING http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NON_HOMOLOGOUS_END_JOINING.html Non-homologous end-joining 12/13 KEGG 0.0670024222225439 0.103047061873707 2080 2826.81818181818 3659 0.00628495509744491 810 0.618810338914531 -0.528675562632931 -1 0.916327450885496 2077 3928 3659 4040 3906 1101 810 1615 4399 4489 1071 4216 M14046 DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_COMMON_UP.html Common up-regulated transcripts in fibroblasts expressing either XP/CS or TDD mutant forms of ERCC3 [GeneID=2071], after UVC irradiation. 15608684 128/179 Arthur Liberzon 0.211583016394226 0.271599629420927 4140 3344.63636363636 3659 0.0213797926508868 1607 1.04491840081165 0.966871688123263 1 0.887448526768049 4137 4028 2770 3659 2265 4272 3685 4631 2929 2808 1607 4217 M9664 BIOCARTA_GPCR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_GPCR_PATHWAY.html Signaling Pathway from G-Protein Families 51/55 BioCarta 0.500520301238146 0.569403668798276 4175 3717.63636363636 3660 0.0611579544550691 2820 0.678609344193147 -0.75824168073264 -1 0.24894163460482 4174 4107 3950 3468 2820 3660 3409 3597 3287 4207 4215 4218 M1157 KONG_E2F3_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KONG_E2F3_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblasts) at 16 hr after serum stimulation and knockdown of E2F3 [GeneID=1871] by RNAi. 16909124 118/175 Arthur Liberzon 0.262499016695759 0.325366428257349 1065 3056.90909090909 3661 0.0273011139443332 1062 1.0364749932137 -1.12582996264767 -1 0.758277213865295 1062 3661 3749 4321 4481 1365 1497 3770 2707 4288 2725 4219 M2112 KIM_ALL_DISORDERS_DURATION_CORR_UP http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_DURATION_CORR_UP.html Genes whose expression in brain significantly and positively correlated with the duration of all psychiatric disorders studied. 18762803 10/16 Jessica Robertson 0.221306613886989 0.281402806451128 3225 3553.36363636364 3661 0.0224832092125151 1388 1.05782032985789 0.64051550363744 1 0.873964500095129 3224 4255 2712 4020 4644 3396 1388 3316 4062 3661 4409 4220 M6231 BIOCARTA_NO2IL12_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NO2IL12_PATHWAY.html NO2-dependent IL 12 Pathway in NK cells 9/23 BioCarta 0.0181598057018207 0.0350856663579999 3665 3525 3662 0.00183099356241582 1151 0.856670691135302 -0.93958370655631 -1 1.87005943796796 3386 2665 4194 4005 1151 3665 3501 4503 4488 3555 3662 4221 M16123 EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/EBAUER_MYOGENIC_TARGETS_OF_PAX3_FOXO1_FUSION.html Muscle development genes up-regulated in Rh4 cells (alveolar rhabdomyosarcoma, ARMS) but not in the RD cells (embryonal rhabdomyosarcoma, ERMS) after knockdown of PAX3-FOXO1 [GeneID=5077;2308] fusion by RNAi for 72 hr. 17525748 59/86 Leona Saunders 0.00651582050970009 0.0155956758650023 3665 3002.27272727273 3663 0.000594109004846461 798 1.3512553410279 -1.44554380700432 -1 3.6637331192042 3663 4096 798 3538 2561 3774 4282 2061 3703 878 3671 4222 M11629 MONTERO_THYROID_CANCER_POOR_SURVIVAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MONTERO_THYROID_CANCER_POOR_SURVIVAL_UP.html Up-regulated genes predicting poor survival of patients with thyroid carcinoma. 17873908 14/14 Arthur Liberzon 0.0174701325473593 0.0340021990173493 925 3070.81818181818 3663 0.00160094768275179 384 0.720232557615325 -0.720232557615325 -1 1.58692892494062 925 4612 3663 4452 3763 2219 384 2557 4304 4704 2196 4223 M7738 PYEON_HPV_POSITIVE_TUMORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PYEON_HPV_POSITIVE_TUMORS_UP.html Up-regulated genes in cervical carcinoma and head and neck tumors positive for human papilloma virus (HPV) compared to those negative for HPV. 17510386 105/125 Arthur Liberzon 0.68618940391 0.690284310838704 2925 3535.72727272727 3666 0.1 2386 0.952826058551559 0.809941303253673 1 0.230041410288068 2923 3666 3680 3842 3482 3202 2386 4680 2814 3957 4261 4224 M5489 BIOCARTA_IL6_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_IL6_PATHWAY.html IL 6 signaling pathway 34/36 BioCarta 0.00516121053430154 0.0136782221908497 4155 3548.36363636364 3667 0.000470305334285663 717 0.832886275235759 -0.844354796650654 -1 2.32941454406651 4020 4155 3646 4152 717 3546 4620 3816 3543 3667 3150 4225 M16458 RIZ_ERYTHROID_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION.html Selected gradually up-regulated genes in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 93/104 Leona Saunders 0.68618940391 0.690284310838704 3325 3669.18181818182 3668 0.1 1781 0.797681169552053 -0.739772179135691 -1 0.192567448098396 3668 4047 4022 4275 3322 3321 4527 3655 1781 4249 3494 4226 M12363 REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE_FROM_THE_C_STRAND http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REMOVAL_OF_THE_FLAP_INTERMEDIATE_FROM_THE_C_STRAND.html Genes involved in Removal of the Flap Intermediate from the C-strand 10/11 Reactome 0.68618940391 0.690284310838704 3540 3794.27272727273 3669 0.1 3334 0.65762889080014 -0.642835775103537 -1 0.158738980835492 3539 3561 3334 3550 3419 3669 4060 4344 3719 4618 3924 4227 M16347 WANG_PROSTATE_CANCER_ANDROGEN_INDEPENDENT http://www.broadinstitute.org/gsea/msigdb/cards/WANG_PROSTATE_CANCER_ANDROGEN_INDEPENDENT.html Genes changed in prostate cancer: androgen independent vs androgen dependent samples. 19047173 100/131 Jessica Robertson 0.0332533402696067 0.0571163631996156 3280 3275.09090909091 3669 0.00306971545495904 947 1.20390811599608 -1.16001697646042 -1 2.24579168545007 3279 3669 1578 4010 4526 3817 4311 947 3497 2165 4227 4228 M18694 LIU_COMMON_CANCER_GENES http://www.broadinstitute.org/gsea/msigdb/cards/LIU_COMMON_CANCER_GENES.html Low abundance transcripts common to nasopharyngeal carcinoma (NPC), breast and liver tumors. 18332864 138/184 Jessica Robertson 0.0666599399470958 0.102620651190571 2130 3439.18181818182 3670 0.00625179969442124 1637 0.912897696028751 0.999307742277138 1 1.35432586381825 2127 4022 3621 4666 1637 3868 3572 2653 3670 4301 3694 4229 M13396 MORI_SMALL_PRE_BII_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_SMALL_PRE_BII_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: the Small Pre-BII stage. 18922927 117/154 Jessica Robertson 0.254424680208657 0.316688947939046 4655 3640.18181818182 3671 0.0263377767315117 2386 1.00043581703052 -0.920598415192352 -1 0.749531078852917 4655 3653 2744 3427 2386 3862 4049 4460 3172 3671 3963 4230 M13334 WU_ALZHEIMER_DISEASE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_ALZHEIMER_DISEASE_DN.html Genes down-regulated in brain endothelial cells from patients with Alzheimer disease. 16116430 29/44 Jessica Robertson 0.190651577077278 0.248217643886927 3675 3284.18181818182 3671 0.0190459059438769 1393 1.27707042465323 1.23142931345883 1 1.15955809204555 3671 4514 1651 3602 3253 4466 3758 1778 3982 1393 4058 4231 M810 REACTOME_ELONGATION_ARREST_AND_RECOVERY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ELONGATION_ARREST_AND_RECOVERY.html Genes involved in Elongation arrest and recovery 34/37 Reactome 0.088829635889619 0.130685311445815 3530 3640 3672 0.00842119516657775 1767 0.540156798272694 -0.615152771808007 -1 0.716206612386543 3527 4152 4063 4097 1767 3045 3672 3495 4030 4566 3626 4232 M6302 LIANG_SILENCED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIANG_SILENCED_BY_METHYLATION_DN.html Genes down-regulated in LD419 cells (fibroblast) after treatment with decitabine (5-aza-2'-deoxycytidine) [PubChem=451668]. 11861364 12/16 John Newman 0.592626611708769 0.659094629421628 2445 3478.90909090909 3673 0.0783950751838057 2189 0.302806382149674 -0.384712001054649 -1 0.08215833926229 2443 4259 3673 4106 4170 2605 2189 2756 4492 4682 2893 4233 M953 REACTOME_TRAF3_DEPENDENT_IRF_ACTIVATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRAF3_DEPENDENT_IRF_ACTIVATION_PATHWAY.html Genes involved in TRAF3-dependent IRF activation pathway 14/18 Reactome 0.91410065408 0.91526412542588 4210 3752.18181818182 3674 0.2 2628 0.568744472811433 -0.584753076934492 -1 0.0327109207746458 4208 2628 3210 3308 4049 3674 4463 3324 4596 4588 3226 4234 M347 WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_H2O2 http://www.broadinstitute.org/gsea/msigdb/cards/WEIGEL_OXIDATIVE_STRESS_BY_HNE_AND_H2O2.html Oxidative stress genes down-regulated in ARPE-19 cells (retinal pigmented epithelium) in response to HNE and H2O2 [PubChem=5283344;784]. 12419474 54/62 John Newman 0.217238837668804 0.27727618004239 3675 3450.81818181818 3675 0.0220200896965386 2285 1.07642755102805 1.15516199938972 1 0.899702438486657 3675 3726 2857 3829 2285 4338 4208 3649 2349 2366 4677 4235 M2503 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_OLD http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_OLD.html Human environmental stress response (H-ESR) genes not changed in primary fibroblasts from old donors in response to gamma radiation. 15897889 36/42 Jessica Robertson 0.68618940391 0.690284310838704 4515 3375.18181818182 3675 0.1 883 0.921054343447664 1.05689424624682 1 0.222367215809717 4515 883 2631 3076 3177 2694 4224 4307 3675 3759 4186 4236 M1487 MORI_PLASMA_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/MORI_PLASMA_CELL_UP.html Up-regulated genes in the B lymphocyte developmental signature, based on expression profiling of lymphomas from the Emu-myc transgenic mice: plasma cell. 18922927 60/65 Jessica Robertson 0.0266437866750018 0.0479445951605065 3430 3434.45454545455 3676 0.00245200398994045 1255 0.666075507084893 -0.617613038705404 -1 1.31844167491613 3427 2438 4005 2739 1255 3676 3930 4504 3650 4381 3774 4237 M19360 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_11 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_11.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 11. 12554760 146/171 Arthur Liberzon 0.143432101482131 0.195213240771527 2820 3412.72727272727 3676 0.0139761135731364 1929 1.0350204593523 0.933433710904397 1 1.10178220818094 2816 4019 3676 3006 2041 4587 3692 4045 1929 3544 4185 4238 M3155 GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_UP http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_DIVIDING_VS_NORMAL_QUIESCENT_UP.html Genes up-regulated in quiescent CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors compared to the dividing cells from CML (chronic myeloid leukemia) patients. 17717066 228/341 Arthur Liberzon 0.68618940391 0.690284310838704 2550 3564.90909090909 3677 0.1 2548 1.16077410472738 -1.29839485713978 -1 0.280269537492658 2548 4340 3124 3897 4652 3693 3051 3677 2861 3665 3706 4239 M622 REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROLONGED_ERK_ACTIVATION_EVENTS.html Genes involved in Prolonged ERK activation events 25/26 Reactome 0.68618940391 0.690284310838704 2450 3488.81818181818 3678 0.1 2448 0.650916087852245 0.779053591920427 1 0.157117558915129 2448 4529 3795 3678 3118 3964 2645 3726 3647 3918 2909 4240 M3231 SEIDEN_ONCOGENESIS_BY_MET http://www.broadinstitute.org/gsea/msigdb/cards/SEIDEN_ONCOGENESIS_BY_MET.html Genes changed in xenograft tumors formed by DLD-1 or DKO-4 cells (colon cancer) overexpressing MET [GeneID=4233]. 16158056 131/151 Arthur Liberzon 0.132313593150523 0.182448191548487 4590 3212.54545454545 3678 0.0128193873308391 512 1.00413474399324 -1.12863760572573 -1 1.1131531731377 4586 3645 3746 2470 1987 4625 3912 2444 512 3678 3733 4241 M11302 SMID_BREAST_CANCER_RELAPSE_IN_LUNG_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LUNG_DN.html Genes down-regulated in lung relapse of breast cancer. 18451135 44/60 Jessica Robertson 1.90096975354894e-05 0.000176973909995089 4305 3283.90909090909 3678 1.72816925417557e-06 392 1.47289073658004 -1.36152908236063 -1 8.2923978623412 4005 2949 392 3559 3678 4706 3103 4606 4305 515 4305 4242 M983 REACTOME_INTERFERON_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERFERON_SIGNALING.html Genes involved in Interferon Signaling 180/246 Reactome 0.158963653446554 0.212551967214655 4375 3525.18181818182 3679 0.0156150197325799 1810 0.943456918262967 -0.909438129965043 -1 0.951985675473444 4373 4004 3471 3679 2108 4415 4621 1810 3202 3736 3358 4243 M2532 BOSCO_INTERFERON_INDUCED_ANTIVIRAL_MODULE http://www.broadinstitute.org/gsea/msigdb/cards/BOSCO_INTERFERON_INDUCED_ANTIVIRAL_MODULE.html Genes representing interferon-induced antiviral module in sputum during asthma exacerbations. 20336062 90/139 Antony Bosco 0.68618940391 0.690284310838704 4370 3343.63636363636 3679 0.1 1199 1.04819402010463 1.15474243591596 1 0.253076751048519 4369 2829 2658 3503 3859 3831 4387 3679 1199 2464 4002 4244 M13936 PENG_GLUTAMINE_DEPRIVATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_GLUTAMINE_DEPRIVATION_DN.html Genes down-regulated in BJAB cells (B-lymphoma) after glutamine [PubChem=738] deprivation. 12101249 453/542 Broad Institute 0.644685210859093 0.690284310838704 3625 3532.81818181818 3681 0.0897793957389848 2017 0.932598517898597 -0.914520929774322 -1 0.225155615477119 3625 4319 4153 3922 3787 2962 3681 2688 2017 4275 3432 4245 M81 PID_CDC42_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_CDC42_PATHWAY.html CDC42 signaling events 18832364 97/107 Pathway Interaction Database 0.68618940391 0.690284310838704 3675 3271.09090909091 3682 0.1 668 1.00737032096632 -1.09778236235832 -1 0.243216124844091 4367 3673 3682 1392 3746 4221 3740 2980 668 3674 3839 4246 M6423 REACTOME_LOSS_OF_NLP_FROM_MITOTIC_CENTROSOMES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LOSS_OF_NLP_FROM_MITOTIC_CENTROSOMES.html Genes involved in Loss of Nlp from mitotic centrosomes 85/107 Reactome 0.68618940391 0.690284310838704 3415 3592.63636363636 3683 0.1 1878 0.960373625774761 -1.25676863443564 -1 0.231864462601104 3412 4407 3683 3459 3401 3723 2945 4139 1878 3872 4600 4247 M16108 CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN.html Genes down-regulated in SH-SY5Y cells (neuroblastoma) after treatment with epoxomicin [PubChem=3035402], a protease inhibitor causing apoptosis. 16983338 203/279 Leona Saunders 0.00735659625065586 0.017121861096201 4170 3211 3683 0.000671028346367309 816 1.25571757787708 -1.1402173320954 -1 3.32828941593777 4167 3189 816 2555 4703 3327 4161 4001 3830 889 3683 4248 M7339 FURUKAWA_DUSP6_TARGETS_PCI35_DN http://www.broadinstitute.org/gsea/msigdb/cards/FURUKAWA_DUSP6_TARGETS_PCI35_DN.html Genes down-regulated in PCI-35 cells (pancreatic cancer, lack endogenous DUSP6 [GeneID=1848]) upon expression of DUSP6 off an adenoviral vector. 16532023 84/97 Arthur Liberzon 0.68618940391 0.690284310838704 3940 3497.63636363636 3683 0.1 787 1.23441767694851 1.09390645653242 1 0.298057532048737 3939 4056 3387 3375 3683 3243 3817 4426 787 3452 4309 4249 M17830 TOMIDA_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOMIDA_METASTASIS_UP.html Up-regulated genes associated with the acquision of metastatic potential in LNM35 cells (large cell lung cancer). 17260014 46/61 Arthur Liberzon 0.628202993348581 0.690284310838704 3685 3651.63636363636 3684 0.0860195653634754 2313 1.12644732766688 -1.2165572009845 -1 0.271978188973515 3684 4468 3006 4654 3022 4667 3923 3120 2313 2859 4452 4250 M748 REACTOME_RECRUITMENT_OF_MITOTIC_CENTROSOME_PROTEINS_AND_COMPLEXES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RECRUITMENT_OF_MITOTIC_CENTROSOME_PROTEINS_AND_COMPLEXES.html Genes involved in Recruitment of mitotic centrosome proteins and complexes 93/115 Reactome 0.68618940391 0.690284310838704 3645 3630.81818181818 3685 0.1 1997 0.960373625774761 -1.25676863443564 -1 0.231864462601104 3643 4398 3818 3465 3163 3685 3023 4287 1997 3991 4469 4251 M7257 REACTOME_NRIF_SIGNALS_CELL_DEATH_FROM_THE_NUCLEUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NRIF_SIGNALS_CELL_DEATH_FROM_THE_NUCLEUS.html Genes involved in NRIF signals cell death from the nucleus 19/23 Reactome 0.141601194097348 0.192943890340497 3530 3415 3686 0.013784697789309 1598 0.870985789564817 -0.994784002689364 -1 0.933786978963758 3529 4220 3200 3985 4151 2613 4069 1598 4358 3686 2156 4252 M10633 BASSO_B_LYMPHOCYTE_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/BASSO_B_LYMPHOCYTE_NETWORK.html Genes which comprise the top 1% of highly interconnected genes (major hubs) that account for most of gene interactions in the reconstructed regulatory networks from expression profiles in B lymphocytes. 15778709 193/235 Jean Junior 0.0561586852531416 0.0889379778651781 1585 2754.63636363636 3686 0.005240513596074 540 0.902714920883099 -0.799611905647593 -1 1.42339947715225 1585 4709 4021 3699 3686 540 900 2307 3715 4073 1066 4253 M4399 MOHANKUMAR_TLX1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOHANKUMAR_TLX1_TARGETS_UP.html Up-regulated in MCF7 cells (breast cancer) by TLX1 (HOX11) [GeneID=3195]. 17213808 551/650 Arthur Liberzon 0.6513215599 0.690284310838704 4710 3544 3687 0.1 1937 0.959665279108847 -0.923066478457283 -1 0.231693367334307 4709 2705 4399 1937 3268 3718 4244 4284 2464 3569 3687 4254 M10372 CHIBA_RESPONSE_TO_TSA_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHIBA_RESPONSE_TO_TSA_UP.html Cancer related genes up-regulated in any of four hepatoma cell lines following 24 h treatment with TSA [PubChem=5562]. 15452378 89/110 John Newman 0.0527009740017959 0.0844360479594286 4070 3453.90909090909 3688 0.00490976878698289 1088 1.03410982009448 -0.848672961108493 -1 1.66560355808524 4066 3688 1088 4138 2296 4313 4491 3162 4464 2664 3623 4255 M4290 LUI_THYROID_CANCER_CLUSTER_3 http://www.broadinstitute.org/gsea/msigdb/cards/LUI_THYROID_CANCER_CLUSTER_3.html Cluster 3: genes with similar expression profiles across follicular thyrorid carcinoma (FTC) samples; genes in this cluster correlated well with the presence of PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 37/55 Leona Saunders 0.51282128785363 0.581575319238138 1595 3505.09090909091 3689 0.063283807841115 1591 0.886467659724989 0.897674380965825 1 0.313006489970017 1591 4497 3689 3448 4682 2735 2637 4579 4594 3986 2118 4256 M808 REACTOME_CYCLIN_A_B1_ASSOCIATED_EVENTS_DURING_G2_M_TRANSITION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CYCLIN_A_B1_ASSOCIATED_EVENTS_DURING_G2_M_TRANSITION.html Genes involved in Cyclin A/B1 associated events during G2/M transition 16/17 Reactome 0.39874518728073 0.468005042573937 1985 3475.18181818182 3692 0.0451955925791617 1984 0.67995790344754 -0.653280214802867 -1 0.336334414852403 1984 4595 3692 4479 2668 2550 2058 3900 4462 4565 3274 4257 M13059 ZHAN_V2_LATE_DIFFERENTIATION_GENES http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_V2_LATE_DIFFERENTIATION_GENES.html The v2LDG set: 50 most variable late differentiation genes (LDG) with similar expression patterns in bone marrow plasma cells (BPC) and multiple myeloma (MM) samples. 12393520 58/77 Kevin Vogelsang 0.646310331560857 0.690284310838704 2380 3511.72727272727 3692 0.090158650374291 2378 1.05053720118511 -1.19495999410432 -1 0.253642727019624 4122 4444 3167 4250 3692 2631 4119 3968 2379 3479 2378 4258 M628 REACTOME_DOWNREGULATION_OF_TGF_BETA_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNREGULATION_OF_TGF_BETA_RECEPTOR_SIGNALING.html Genes involved in Downregulation of TGF-beta receptor signaling 27/31 Reactome 0.528613671278948 0.596903475702544 3695 3366.81818181818 3694 0.0660857578153569 1796 0.677084962382204 -0.683320650391536 -1 0.227571021527991 2663 3837 3694 3169 3694 1796 2430 4430 3962 3968 3392 4259 M19944 GEISS_RESPONSE_TO_DSRNA_DN http://www.broadinstitute.org/gsea/msigdb/cards/GEISS_RESPONSE_TO_DSRNA_DN.html Genes down-pregulated by dsRNA in GRE cells (glioma; no interferon system). 11487589 19/25 John Newman 0.0535613150331105 0.0855352980421861 2975 3345.45454545455 3694 0.00499196137866375 603 1.1233670479073 -1.24295631348924 -1 1.79990709300779 2971 4577 2794 4422 4175 3242 3957 1921 4444 3694 603 4260 M6379 KUMAMOTO_RESPONSE_TO_NUTLIN_3A_DN http://www.broadinstitute.org/gsea/msigdb/cards/KUMAMOTO_RESPONSE_TO_NUTLIN_3A_DN.html Genes down-regulated in response to nutlin-3a [PubChem=216345], an inhibitor of MDM2 [GeneID=4193], in skin fibroblast cultures after knockdown of TP53 [GeneID=7157] by RNAi. 18451145 15/17 Jessica Robertson 0.68618940391 0.690284310838704 2475 3472.72727272727 3694 0.1 1318 1.79246488353716 -1.79246488353716 -1 0.432849210038349 2474 3899 3350 3586 3901 3694 4036 4529 1318 3917 3496 4261 M861 REACTOME_THROMBIN_SIGNALLING_THROUGH_PROTEINASE_ACTIVATED_RECEPTORS_PARS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_THROMBIN_SIGNALLING_THROUGH_PROTEINASE_ACTIVATED_RECEPTORS_PARS.html Genes involved in Thrombin signalling through proteinase activated receptors (PARs) 28/35 Reactome 0.00283256670321827 0.00867083905491461 4235 3279.72727272727 3696 0.000257838209654905 583 1.09555490993193 -1.18550965124887 -1 3.38951987841979 4234 3821 2554 3555 583 4567 3696 4528 1754 2871 3914 4262 M7927 REACTOME_NUCLEOTIDE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NUCLEOTIDE_EXCISION_REPAIR.html Genes involved in Nucleotide Excision Repair 51/54 Reactome 0.52249331251591 0.59084054505872 1905 3450.18181818182 3700 0.0649898736681461 1780 0.565529170883044 -0.560805382147216 -1 0.193821712143053 1904 4467 4106 4492 3210 1780 2572 3700 4070 4559 3092 4263 M825 REACTOME_SHC_RELATED_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SHC_RELATED_EVENTS.html Genes involved in SHC-related events 21/25 Reactome 0.419441555727794 0.490283343990884 3065 3052.90909090909 3700 0.0482312315474705 552 0.84538914379346 -0.801122681378655 -1 0.392569211961595 3062 4561 3789 3700 3969 2125 2246 3855 552 3793 1930 4264 M8365 RHODES_UNDIFFERENTIATED_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/RHODES_UNDIFFERENTIATED_CANCER.html Genes commonly up-regulated in undifferentiated cancer relative to well-differentiated cancer, based on the meta-analysis of the OncoMine gene expression database. 15184677 117/172 John Newman 0.68618940391 0.690284310838704 4135 3672.54545454545 3701 0.1 2451 1.12962451466631 1.09804874172742 1 0.2727456121626 4134 4038 2451 3701 4271 3613 3472 3786 3066 3672 4194 4265 M15327 AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_2G http://www.broadinstitute.org/gsea/msigdb/cards/AMUNDSON_POOR_SURVIVAL_AFTER_GAMMA_RADIATION_2G.html Genes with basal expression distinguishing NCI-60 cell lines with poor survival after 2 Gy gamma irradiation. 18199535 228/292 Jessica Robertson 0.68618940391 0.690284310838704 4365 3504.63636363636 3701 0.1 2170 0.917144245067213 -0.91613585346875 -1 0.221422763950479 4361 2267 3579 2170 4120 4092 3701 4588 2759 3930 2984 4266 M16807 FIRESTEIN_CTNNB1_PATHWAY_AND_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/FIRESTEIN_CTNNB1_PATHWAY_AND_PROLIFERATION.html Genes required for both proliferation and CTNNB1 [GeneID=1499] activity in DLD-1 cell (colon cancer with APC [GeneID=324] deletions). 18794900 14/14 Jessica Robertson 0.239296064433394 0.300299682615965 3475 3275.27272727273 3701 0.0245580613863523 888 1.03864232913968 -1.03864232913968 -1 0.814126814170815 3471 4593 3701 4380 2349 4068 4163 2423 888 3886 2106 4267 M18799 REACTOME_DIABETES_PATHWAYS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DIABETES_PATHWAYS.html Genes involved in Diabetes pathways 158/214 Reactome 0.00494464054416576 0.0132155738213264 3750 3560.45454545455 3702 0.000450526275927721 710 0.984810443093789 0.955147687431378 1 2.77641765065319 3748 3206 3149 2978 710 4703 4128 4647 3552 3702 4642 4268 M12661 MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOLENAAR_TARGETS_OF_CCND1_AND_CDK4_DN.html Genes commonly down-regulated in SK-N-BE cells (neuroblastoma) after RNAi knockdown of CCND1 and CDK4 [GeneID=595;1019]. 18413728 72/103 Jessica Robertson 0.207697273969677 0.267338732788894 2545 3276.27272727273 3702 0.0209423022159792 948 1.16410713413479 1.20656874319651 1 1.00068305854112 2542 3702 3336 3789 4534 3983 4350 1828 948 3739 3288 4269 M1179 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_6 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_6.html Amplification hot spot 6: colocolized fragile sites and cancer genes in the 17p13-p11.1 region. 16751803 9/9 Arthur Liberzon 0.479803494210123 0.549677789483441 3235 3691 3703 0.0632650094210779 2117 0.969942888137241 -0.433645448318504 -1 0.378145591968012 3232 4626 4373 4222 3189 3703 2969 3988 4623 3559 2117 4270 M1335 CAFFAREL_RESPONSE_TO_THC_8HR_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_8HR_3_UP.html Genes up-regulated in EVSA-T cells (breast cancer) treated with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 8 h. 18454173 9/10 Jessica Robertson 0.0163697152255329 0.0323557222183945 3900 3234.27272727273 3703 0.00164915658316251 921 0.956499530130135 0.74111950664763 1 2.1384820022012 3899 2162 4437 2152 1117 4659 4637 3703 921 3564 4326 4271 M9678 STEIN_ESR1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/STEIN_ESR1_TARGETS.html Genes regulated by ESR1 [GeneID=2099] in MCF-7 cells (breast cancer). 18974123 97/113 Arthur Liberzon 0.68618940391 0.690284310838704 3250 3453.90909090909 3704 0.1 1913 1.07917555194978 -1.19226223622088 -1 0.260560083309286 4239 3249 2276 3961 3870 4369 3855 3307 1913 3250 3704 4272 M9648 REACTOME_FORMATION_OF_TUBULIN_FOLDING_INTERMEDIATES_BY_CCT_TRIC http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_TUBULIN_FOLDING_INTERMEDIATES_BY_CCT_TRIC.html Genes involved in Formation of tubulin folding intermediates by CCT/TriC 20/26 Reactome 0.68618940391 0.690284310838704 3990 3490.63636363636 3705 0.1 1424 1.25276212733905 0.871484505431882 1 0.302488482012727 3988 3054 2864 3676 4171 4406 3706 3705 1424 2711 4692 4273 M18917 MORI_IMMATURE_B_LYMPHOCYTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_IMMATURE_B_LYMPHOCYTE_DN.html Down-regulated genes in the B lymphocyte developmental signature based on expression profiling of lymphomas from the Emu-myc transgenic mice: the immature B stage. 18922927 137/197 Jessica Robertson 0.561598203623437 0.628883397651868 2145 3440.45454545455 3706 0.0722244170529249 2137 0.901175901735773 -0.914338248985036 -1 0.27227419475151 2144 4024 3735 3706 4575 2703 2137 3876 3254 4209 3482 4274 M17646 JAIN_NFKB_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/JAIN_NFKB_SIGNALING.html Genes abnormally regulated in response to CD40L and IL4 [GeneID=959;3565] stimulation of B lymphocytes from patients with a hypomorphic mutation of IKBKG [GeneID=8517]. 15578091 105/119 Kevin Vogelsang 0.0844201449603336 0.125460668832738 4305 3444.09090909091 3707 0.00798591389665334 1748 0.754477125885382 -0.71519133441638 -1 1.02048099414381 3707 2812 4000 3224 1748 2635 3992 4301 4303 4313 2850 4275 M7912 DELLA_RESPONSE_TO_TSA_AND_BUTYRATE http://www.broadinstitute.org/gsea/msigdb/cards/DELLA_RESPONSE_TO_TSA_AND_BUTYRATE.html Genes up-regulated in HT-29 cells (colon cancer) by the combination of trichostatin A (TSA) and sodium butyrate [PubChem=5562;5222465]. 11423116 41/46 John Newman 0.000351483483425165 0.00178387316319008 3760 2934.63636363636 3707 3.19581500749606e-05 248 1.10202207451868 1.09081310476873 1 4.54505585737376 3760 1440 1441 2449 248 4086 4416 4421 3707 1878 4435 4276 M15896 MARTINEZ_RB1_AND_TP53_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RB1_AND_TP53_TARGETS_UP.html Genes up-regulated in mice with skin specific double knockout of both RB1 and TP53 [GeneID=5925;7157] by Cre-lox. 18245467 754/970 Jessica Robertson 0.00989964452586083 0.0216726911697881 3780 3080.63636363636 3709 0.000994402436406646 608 1.16857330965445 -1.13320231207074 -1 2.91781725814615 3780 1665 4536 1352 2493 4302 3857 4244 3341 608 3709 4277 M665 REACTOME_TRANSCRIPTIONAL_ACTIVITY_OF_SMAD2_SMAD3_SMAD4_HETEROTRIMER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTIONAL_ACTIVITY_OF_SMAD2_SMAD3_SMAD4_HETEROTRIMER.html Genes involved in Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer 49/61 Reactome 0.0921288372199999 0.134586230788734 2175 3126.54545454545 3710 0.0087481288152426 930 0.864207633139479 -0.973831078968051 -1 1.12937209616418 2172 4458 3941 4618 2460 1217 930 4012 2973 3901 3710 4278 M6387 WINNEPENNINCKX_MELANOMA_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WINNEPENNINCKX_MELANOMA_METASTASIS_UP.html Genes from the 254-gene classifier which were up-regulated in melanoma patients with a reported distant metastasis within 4 years. 16595783 211/263 Arthur Liberzon 0.68618940391 0.690284310838704 2435 3685.54545454545 3711 0.1 2431 0.824855001397049 -0.819808964259256 -1 0.19913106198007 2431 4705 4110 4681 3941 2713 3088 3354 3711 4399 3408 4279 M3845 GALE_APL_WITH_FLT3_MUTATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/GALE_APL_WITH_FLT3_MUTATED_UP.html Genes up-regulated in acute promyelocytic leukemia (APL) patients with mutated FLT3 [GeneID=2322]. 16105978 79/92 Kevin Vogelsang 0.0744718880927117 0.112482339775232 3955 3423.45454545455 3712 0.00701083341662722 1284 0.992827737923927 -0.96643210687003 -1 1.41354881410412 3951 3698 3712 4429 3313 4397 4415 1284 2859 3740 1860 4280 M5989 IVANOV_MUTATED_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/IVANOV_MUTATED_IN_COLON_CANCER.html Genes mutated in colon cancer cell lines, identified using the GINI method described in the paper. 17086209 17/17 Leona Saunders 0.68618940391 0.690284310838704 4350 3457.81818181818 3713 0.1 963 0.829322881448621 -0.889366223087885 -1 0.200210241379406 4348 2609 3713 2714 4148 4049 3928 3332 963 3525 4707 4281 M12851 BIOCARTA_CELL2CELL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CELL2CELL_PATHWAY.html Cell to Cell Adhesion Signaling 14/19 BioCarta 0.297756392327138 0.361846079244101 3715 3834.90909090909 3714 0.0316232697188459 2466 0.424018333781001 -0.416186031104331 -1 0.280782484845727 3714 3901 3640 4602 2466 3371 3352 3527 4661 4495 4455 4282 M3492 REACTOME_MTORC1_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MTORC1_MEDIATED_SIGNALLING.html Genes involved in mTORC1-mediated signalling 12/12 Reactome 0.0400321408102497 0.0667673867930666 1920 2713.54545454545 3714 0.00370724523452619 632 0.438502609403297 0.438502609403297 1 0.773309612885102 1916 3930 3832 4242 3714 814 632 1019 4101 4615 1034 4283 M1270 CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_DN http://www.broadinstitute.org/gsea/msigdb/cards/CALVET_IRINOTECAN_SENSITIVE_VS_RESISTANT_DN.html Genes down-regulated in neuroblastoma xenografts: sensitive vs resistant to the topoisomerase inhibitor irinotecan [GeneID=3750]. 16501609 6/7 Arthur Liberzon 0.494080994671815 0.563708555680679 2385 3636.45454545455 3716 0.0658683231973435 2066 1.82760750553349 1.82760750553349 1 0.682592440301729 2382 4651 4409 4434 3784 3591 2066 3049 4686 3233 3716 4284 M4455 EGUCHI_CELL_CYCLE_RB1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/EGUCHI_CELL_CYCLE_RB1_TARGETS.html RB1 [GeneID=5925] target genes involved in cell cycle regulation: genes down-regulated by doxorubicin [PubChem=31703] only in cells expressing RB1. 16862181 24/25 Leona Saunders 0.68618940391 0.690284310838704 1965 3755.45454545455 3718 0.1 1963 0.744417619564926 -0.689755347652121 -1 0.179702079015489 1963 4543 3718 4466 3735 3580 3208 3581 4410 4640 3466 4285 M68 PID_RHOA_REG_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RHOA_REG_PATHWAY.html Regulation of RhoA activity 18832364 56/59 Pathway Interaction Database 0.43119990772354 0.499814448548158 4540 2855.81818181818 3719 0.05 137 0.982198515198046 0.977143471580227 1 0.443792338628638 4490 137 2394 288 4107 4207 4537 4540 222 2773 3719 4286 M18058 WILCOX_RESPONSE_TO_PROGESTERONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WILCOX_RESPONSE_TO_PROGESTERONE_UP.html Genes up-regulated in primary cultures of ovarian surface epithlium cells exposed to progesterone [PubChem=5994] for 5 days. 18070364 188/235 Arthur Liberzon 0.68618940391 0.690284310838704 3720 3442.63636363636 3720 0.1 1256 1.15790115504038 1.17384849231516 1 0.279575600305052 3720 4345 2594 3171 4566 4129 3832 3496 1256 2300 4460 4287 M3694 LIN_MELANOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LIN_MELANOMA_COPY_NUMBER_DN.html Candidate genes in significant regions of chromosomal copy number losses in a panel of melanoma samples. 18245465 55/59 Jessica Robertson 0.0423560639535635 0.0699512322816025 2785 3205.90909090909 3723 0.00392674684847071 1292 0.803097686937212 -0.920214762508565 -1 1.39198991207917 2781 4447 3929 4601 1454 2933 2443 3723 1292 3864 3798 4288 M780 REACTOME_CDC6_ASSOCIATION_WITH_THE_ORC_ORIGIN_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CDC6_ASSOCIATION_WITH_THE_ORC_ORIGIN_COMPLEX.html Genes involved in CDC6 association with the ORC:origin complex 11/11 Reactome 0.68618940391 0.690284310838704 3725 3898.45454545455 3724 0.1 2629 1.23159250987085 -1.23159250987085 -1 0.297375136354425 3724 4636 3554 4068 4338 3445 2629 4675 4424 3724 3666 4289 M2114 BENPORATH_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_PROLIFERATION.html Set 'Proliferation Cluster': genes defined in human breast tumor expression data. 18443585 178/210 Jessica Robertson 0.68618940391 0.690284310838704 2670 3634.09090909091 3725 0.1 2670 0.758466947913189 -0.636491023126121 -1 0.183095577845571 2670 4006 4142 3703 4115 2999 2829 4245 3108 4433 3725 4290 M16801 SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES http://www.broadinstitute.org/gsea/msigdb/cards/SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES.html Genes related to regulation of the actin cytoskeleton 45/63 Signaling Gateway 0.68618940391 0.690284310838704 3495 3681.54545454545 3726 0.1 2892 0.839159586382087 -0.859269111918794 -1 0.202586215935351 3895 3345 2892 3207 3726 4055 3794 3493 4004 3493 4593 4291 M6139 STARK_BRAIN_22Q11_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/STARK_BRAIN_22Q11_DELETION.html Genes located outside the microdeletion region in 22q11 which were differentially expressed in the same manner both in hyppocampus and prefrontal cortex. 18469815 11/17 Jessica Robertson 0.134221923404833 0.184469445828226 4630 3627.45454545455 3726 0.0130169610739846 2002 0.997707658517675 0.453121236867733 1 1.09886427458265 4626 3559 3032 4196 2002 4696 4055 3335 2402 3726 4273 4292 M1008 REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTIONAL_REGULATION_OF_WHITE_ADIPOCYTE_DIFFERENTIATION.html Genes involved in Transcriptional Regulation of White Adipocyte Differentiation 83/93 Reactome 0.00923154296720917 0.0205006564524236 4005 3506.72727272727 3727 0.000842773551330956 883 0.963277970669986 1.07156709944756 1 2.44009530539217 4003 4406 3443 4615 883 4537 3872 3386 3727 2928 2774 4293 M827 REACTOME_REPAIR_SYNTHESIS_FOR_GAP_FILLING_BY_DNA_POL_IN_TC_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_REPAIR_SYNTHESIS_FOR_GAP_FILLING_BY_DNA_POL_IN_TC_NER.html Genes involved in Repair synthesis for gap-filling by DNA polymerase in TC-NER 14/15 Reactome 0.679156103746895 0.690284310838704 2345 3574.09090909091 3728 0.098184663997946 2342 0.610478557240943 -0.642835775103537 -1 0.147350208518066 2342 4243 3728 4035 3100 2689 3024 3920 4294 4569 3371 4294 M1560 RASHI_RESPONSE_TO_IONIZING_RADIATION_6 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_6.html Cluster 6: late responding genes activated in ATM [GeneID=472] deficient but not in the wild type tissues. 16314843 81/120 Arthur Liberzon 0.584302219261224 0.651063851490316 4100 3223.72727272727 3731 0.0766987408790853 2002 1.11026518020841 -1.00307235996164 -1 0.310392657986654 4099 2378 2002 2307 3867 3826 4370 2590 3731 2051 4240 4295 M8801 NICK_RESPONSE_TO_PROC_TREATMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/NICK_RESPONSE_TO_PROC_TREATMENT_DN.html Genes down-regulated in neutrophils upon treatment with activated protein C (PROC) [GeneID=5624] of pulmonary inflammation induced by bacterial lipopolysaccharide (LPS). 15339848 57/68 Arthur Liberzon 0.545602839875514 0.614030854604775 2100 3456.27272727273 3733 0.0691969823606968 2097 0.740658725491405 0.685316846952879 1 0.235293930757218 2097 3733 3984 4110 3802 3076 2101 3684 3322 4173 3937 4296 M5316 MODY_HIPPOCAMPUS_PRENATAL http://www.broadinstitute.org/gsea/msigdb/cards/MODY_HIPPOCAMPUS_PRENATAL.html Genes highly expressed in prenatal hippocampus (cluster 1). 11438693 63/88 John Newman 0.262707237864179 0.325507985276411 2135 3423.81818181818 3734 0.0273260830938386 1562 0.887162635318997 -0.94737300446329 -1 0.648774710023234 2134 4449 3734 4520 4401 2749 3678 2190 4234 4011 1562 4297 M1383 SHIN_B_CELL_LYMPHOMA_CLUSTER_1 http://www.broadinstitute.org/gsea/msigdb/cards/SHIN_B_CELL_LYMPHOMA_CLUSTER_1.html Cluster 1 of genes distinguishing among different B lymphocyte neoplasms. 19010892 11/18 Jessica Robertson 0.559054664145611 0.626386908095247 3495 3689.72727272727 3736 0.0717363563987562 2446 0.392555794509633 0.392555794509633 1 0.119561527490616 3494 4638 2647 4457 3736 3335 2446 2548 4711 4665 3910 4298 M16561 JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAZAERI_BREAST_CANCER_BRCA1_VS_BRCA2_DN.html Down-regulated genes distinguishing between breast cancer tumors with mutated BRCA1 [GeneID=672] from those with mutated BRCA2 [GeneID=675]. 12096084 52/68 John Newman 0.0483136285410708 0.0783374533541237 2095 3244.09090909091 3738 0.00449167667628611 1505 1.05555355513647 1.24745614973786 1 1.75171305954005 2094 3738 2540 3991 1505 3855 2677 4573 4122 3785 2805 4299 M11338 GENTILE_RESPONSE_CLUSTER_D3 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_RESPONSE_CLUSTER_D3.html Cluster d3: genes progressively down-regulated in WS1 cells (fibroblast) through 12 h irradiation with high dose UV-C. 12907719 72/80 John Newman 0.362039751601962 0.430218435941908 2880 3357.45454545455 3738 0.040038169228833 853 0.897962753443606 0.823980617007769 1 0.493465668713807 2880 4068 3803 4584 2603 3071 3302 3818 853 3738 4212 4300 M16584 LIU_BREAST_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LIU_BREAST_CANCER.html Low abundance transcripts specific for breast cancer. 18332864 41/57 Jessica Robertson 0.68618940391 0.690284310838704 3580 3848.45454545455 3739 0.1 3024 1.2269587374271 -1.54285800087784 -1 0.296255887022576 3577 4498 3739 4502 3857 3143 3615 4304 3024 3646 4428 4301 M3494 BIOCARTA_PAR1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PAR1_PATHWAY.html Thrombin signaling and protease-activated receptors 53/59 BioCarta 0.00577426225782821 0.0142024584976285 4700 2879.18181818182 3741 0.000526315789473684 155 0.959732547692825 -1.0056344226873 -1 2.66067166405159 4699 155 2994 187 3138 4435 3867 4253 381 3821 3741 4302 M9473 RAMALHO_STEMNESS_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMALHO_STEMNESS_UP.html Genes enriched in embryonic, neural and hematopoietic stem cells. 12228720 260/297 John Newman 0.446889646599134 0.515895373146812 3235 3635 3741 0.0524126520661588 1552 0.795343725135273 -0.846114582945477 -1 0.342931518911449 3233 3620 4158 3439 2740 4040 3741 4570 1552 4428 4464 4303 M1211 YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP http://www.broadinstitute.org/gsea/msigdb/cards/YORDY_RECIPROCAL_REGULATION_BY_ETS1_AND_SP100_UP.html Genes up-regulated in HUVEC cells (endothelium) by ETS1 [GeneID=2113] which were down-regulated by SP100 [GeneID=6672]. 15592518 31/37 Arthur Liberzon 0.68618940391 0.690284310838704 3745 3678.36363636364 3742 0.1 2011 0.853013868696289 -0.763499515498036 -1 0.205932603012331 3742 2011 3159 3548 4094 4416 4277 3515 4230 3853 3617 4304 M1957 MIKKELSEN_MCV6_LCP_WITH_H3K27ME3 http://www.broadinstitute.org/gsea/msigdb/cards/MIKKELSEN_MCV6_LCP_WITH_H3K27ME3.html Genes with low-CpG-density promoters (LCP) bearing the tri-methylation mark at H3K27 (H3K27me3) in MCV6 cells (embryonic fibroblasts trapped in a differentiated state). 18509334 19/57 Jessica Robertson 0.00687898965914066 0.0162506662618338 4440 3540.27272727273 3742 0.000627326691657253 793 0.982982947826037 -1.06820135284077 -1 2.63883350367664 4439 4554 2466 4351 793 3235 3199 4424 4569 3171 3742 4305 M3256 HASLINGER_B_CLL_WITH_17P13_DELETION http://www.broadinstitute.org/gsea/msigdb/cards/HASLINGER_B_CLL_WITH_17P13_DELETION.html Genes changed in the B cell chronic lymphocytic leukemia (B-CLL) with deletions in the 17p13 region. 15459216 34/36 Kevin Vogelsang 0.333839192652707 0.3998277059936 4210 3625.45454545455 3747 0.0362558955002922 2512 0.693728542069008 -0.775662883672782 -1 0.414326025605004 4210 2512 3516 3092 2548 4089 3747 3930 4413 4126 3697 4306 M4965 VALK_AML_CLUSTER_6 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_6.html Top 40 genes from cluster 6 of acute myeloid leukemia (AML) expression profile; all samples are FAB M1 or M2 subtypes and all samples have internal tundem duplication of FLT3 [GeneID=2322]. 15084694 42/55 Jessica Robertson 0.68618940391 0.690284310838704 3965 3518.45454545455 3747 0.1 1959 1.22087065201149 -1.31655338118995 -1 0.294785360444851 3964 4119 1959 3525 3148 4470 4100 2781 3747 2286 4604 4307 M164 PID_ERBB1_DOWNSTREAM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ERBB1_DOWNSTREAM_PATHWAY.html ErbB1 downstream signaling 18832364 147/159 Pathway Interaction Database 0.68618940391 0.690284310838704 3795 3312.36363636364 3748 0.1 572 0.928265847512396 -0.897344460150616 -1 0.224109094851916 3793 2782 3678 1395 4672 4467 3070 3849 572 3748 4410 4308 M17481 YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_7 http://www.broadinstitute.org/gsea/msigdb/cards/YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_7.html Genes co-regulated in uterus during a time course response to progesterone [PubChem=5994]: SOM cluster 7. 12554760 104/120 Arthur Liberzon 0.00542671818349898 0.0141680697019049 2590 3473.09090909091 3748 0.000494559147774368 729 0.779355164622974 0.706137458262685 1 2.16182182841874 2587 3243 4016 3456 729 3838 3748 4470 3626 4370 4121 4309 M18705 JAZAG_TGFB1_SIGNALING_VIA_SMAD4_DN http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_VIA_SMAD4_DN.html Genes down-regulated in PANC-1-S4KD cells (pancreatic cancer; SMAD4 [GeneID=4089] knocked down by RNAi) after stimulation by TGF1B [GeneID=7040] for 2 h. 15592526 77/105 Leona Saunders 0.0187168128021868 0.0359411539570064 4480 3255 3750 0.00171617923277397 727 1.259122808794 -1.17667051320944 -1 2.72887057002026 4477 4417 1473 3996 4629 3197 3724 727 3750 1243 4172 4310 M15657 SAGIV_CD24_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAGIV_CD24_TARGETS_DN.html Genes down-regulated in HT29 cells (colon cancer) after knockdown of CD24 [GeneID=100133941] by both RNAi and monoclonal antibodies. 18413748 49/67 Jessica Robertson 0.261115427439609 0.324076996454103 3825 3178.09090909091 3750 0.027135361382383 1549 1.21980684546311 -1.34106688312447 -1 0.895576612819056 3821 3750 1549 4381 4457 2492 3993 1981 4370 1774 2391 4311 M934 REACTOME_DESTABILIZATION_OF_MRNA_BY_BRF1 http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_BRF1.html Genes involved in Destabilization of mRNA by Butyrate Response Factor 1 (BRF1) 21/22 Reactome 0.559103399111287 0.626386908095247 3675 3498.45454545455 3752 0.0717456837082282 1531 0.607844732313351 -0.565736300391128 -1 0.185190562011322 3673 1531 3752 2696 2923 3814 4407 3801 2875 4585 4426 4312 M9044 HEIDENBLAD_AMPLIFIED_IN_PANCREATIC_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLIFIED_IN_PANCREATIC_CANCER.html Genes amplified and up-regulated more than twofold in at least two out of 10 pancreatic cancer cell lines studied. 15688027 49/53 Leona Saunders 0.550919496143238 0.618686657576989 3755 3279.36363636364 3754 0.0701923624591045 662 0.960350142880919 1.03879177751235 1 0.300389964047902 3754 1942 3438 3776 2912 3920 3899 4225 662 3681 3864 4313 M17580 ST_IL_13_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_IL_13_PATHWAY.html Interleukin 13 (IL-13) Pathway 5/7 Signaling Transduction KE 5.70420361030755e-06 6.27595362252952e-05 4145 2815.72727272727 3755 5.70421825243291e-07 20 0.892557376644453 -0.955141282527556 -1 5.62806279266734 4141 1646 4200 1064 20 4145 3755 4103 170 3077 4652 4314 M8273 CROONQUIST_NRAS_VS_STROMAL_STIMULATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/CROONQUIST_NRAS_VS_STROMAL_STIMULATION_UP.html Genes up-regulated in ANBL-6 cell line (multiple myeloma, MM) expressing an activated form of NRAS [GeneID=4893] off a plasmid vector compared to those co-cultured with bone marrow stromal cells. 12791645 47/67 Arthur Liberzon 0.490644934583168 0.560059030527825 4140 3664.18181818182 3755 0.0594854647576571 2432 0.86079550167427 -0.831484298955271 -1 0.32508569431457 4138 3755 2777 3799 3220 3979 4682 2432 4184 3593 3747 4315 M74 REACTOME_POST_NMDA_RECEPTOR_ACTIVATION_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POST_NMDA_RECEPTOR_ACTIVATION_EVENTS.html Genes involved in Post NMDA receptor activation events 36/45 Reactome 0.401412678164231 0.470841908781106 3450 3522.27272727273 3756 0.0455814647905365 1804 0.850530570718034 0.844682138312771 1 0.417383447881954 3450 4493 3112 4629 4134 2925 1804 2291 4003 3756 4148 4316 M1133 DARWICHE_PAPILLOMA_RISK_LOW_UP http://www.broadinstitute.org/gsea/msigdb/cards/DARWICHE_PAPILLOMA_RISK_LOW_UP.html Genes up-regulated during skin tumor progression from low risk papilloma vs normal skin. 17525749 179/307 Arthur Liberzon 0.446927156948584 0.515895373146812 4125 3403.36363636364 3757 0.0524184943046055 1484 1.28318922987266 -1.20807930403282 -1 0.553342718765822 4121 4002 1611 3757 3755 4534 4109 3192 1484 2210 4662 4317 M16858 OSMAN_BLADDER_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/OSMAN_BLADDER_CANCER_DN.html Genes down-regulated in blood samples from bladder cancer patients. 16740760 561/764 Leona Saunders 0.13659861555441 0.187208323291758 4305 3594.72727272727 3758 0.0145802231840222 1809 0.927311731656769 -1.03266876461768 -1 1.0124172379663 3647 4675 4301 4514 2062 3505 2793 4175 1809 4303 3758 4318 M1577 BURTON_ADIPOGENESIS_3 http://www.broadinstitute.org/gsea/msigdb/cards/BURTON_ADIPOGENESIS_3.html Strongly up-regulated at 16-24 h during differentiation of 3T3-L1 cells (fibroblast) into adipocytes. 15033539 132/152 John Newman 0.68618940391 0.690284310838704 3760 3711.63636363636 3758 0.1 2519 1.24861093150293 1.18402984719826 1 0.301485795061142 3758 3215 3263 2992 4283 4542 4488 4108 2519 3706 3954 4319 M17138 BYSTRYKH_SCP2_QTL http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_SCP2_QTL.html Genes that physically map to the hematopoietic stem cell (HSC) proliferation QTL (quantitative trait locus) Scp2. 15711547 6/8 Jean Junior 0.200636467121411 0.259027386436833 4685 3703.54545454545 3760 0.02214506208226 1859 0.538486426048405 0.538486426048405 1 0.473916544114898 4685 3131 4473 3760 2981 4557 3680 1859 2795 4669 4149 4320 M2125 CHICAS_RB1_TARGETS_SENESCENT http://www.broadinstitute.org/gsea/msigdb/cards/CHICAS_RB1_TARGETS_SENESCENT.html Genes up-regulated in senescent IMR90 cells (fibroblast) after knockdown of RB1 [GeneID=5925] by RNAi. 20385362 733/946 Arthur Liberzon 0.321294796507172 0.385978986895864 2420 3372.90909090909 3760 0.0380154039290844 1783 1.17635000662168 1.22953697392035 1 0.729665864277115 2418 4307 4661 4224 4227 3760 2911 2167 2836 1783 3808 4321 M5756 REACTOME_E2F_ENABLED_INHIBITION_OF_PRE_REPLICATION_COMPLEX_FORMATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_E2F_ENABLED_INHIBITION_OF_PRE_REPLICATION_COMPLEX_FORMATION.html Genes involved in E2F-enabled inhibition of pre-replication complex formation 13/13 Reactome 0.60444709862021 0.670660626583778 2590 3798.09090909091 3761 0.0808587989728025 2590 0.275838831971406 -0.353922767499965 -1 0.0717049545837561 2590 4615 3761 4476 2991 3427 3276 4345 4458 4539 3301 4322 M2048 KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_DN http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_DN.html Genes down-regulated in response to hydorgen peroxyde [PubChem=784] in CS-B cells (Cockaine syndrome fibroblast, CS) with defficient ERCC6 [GeneID=2074]. 12606941 61/81 Arthur Liberzon 0.530376493971017 0.598750789653958 3700 3656.90909090909 3761 0.066403800438973 2604 0.729440068435355 -0.535558479014562 -1 0.243707106989839 3700 3306 3845 4233 2869 4110 4116 3469 2604 4213 3761 4323 M6438 WONG_IFNA2_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/WONG_IFNA2_RESISTANCE_DN.html Genes down-regulated in hepatocellular carcinoma (HCC) cell lines resistant to IFNA2 [GeneID=3440]. 15709204 37/93 Yujin Hoshida 0.350800633959201 0.418126008153391 4320 3780.63636363636 3763 0.0385128985565691 2575 0.798661357533177 -0.644273972549694 -1 0.453722445597265 4317 3383 3763 4571 2575 4607 4518 3079 3467 3789 3518 4324 M14265 APPIERTO_RESPONSE_TO_FENRETINIDE_DN http://www.broadinstitute.org/gsea/msigdb/cards/APPIERTO_RESPONSE_TO_FENRETINIDE_DN.html Genes down-regulated in A2780 cells (ovarian carcinoma) exposed to fenretinide [PubChem=1744]. 17213814 81/108 Arthur Liberzon 0.68618940391 0.690284310838704 4335 3332.81818181818 3764 0.1 1328 1.09540532529112 -1.04513994697996 -1 0.264480250557222 4334 1328 1913 3410 4089 3144 3968 3764 4052 2837 3822 4325 M13314 LUI_TARGETS_OF_PAX8_PPARG_FUSION http://www.broadinstitute.org/gsea/msigdb/cards/LUI_TARGETS_OF_PAX8_PPARG_FUSION.html Genes down-regulated in follicular thyroid carcinoma (FTC) samples that bear PAX8-PPARG [GeneID=7849;5468] fusion protein. 15608688 61/93 Leona Saunders 0.615605757413181 0.681279994136041 4515 3731.27272727273 3764 0.0832467819786825 2440 0.775381175262059 0.846525531197183 1 0.193815630345312 4513 4452 3764 3470 3552 3324 4164 2644 4509 4212 2440 4326 M1221 YAN_ESCAPE_FROM_ANOIKIS http://www.broadinstitute.org/gsea/msigdb/cards/YAN_ESCAPE_FROM_ANOIKIS.html Genes up-regulated in IEC-18 cells (intestinal epithelial cells) which avoided anoikis (a form of apoptosis) after detachment. 16007176 46/64 Arthur Liberzon 0.0132289180498939 0.0272801152459194 4215 3237.81818181818 3764 0.0012099219653461 1011 1.22222502383741 -1.29772900345692 -1 2.86851028483322 4211 3764 1122 3617 1011 3752 4156 4556 4023 1321 4083 4327 M2076 WHITFIELD_CELL_CYCLE_G2 http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_G2.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the G2 phase of cell cycle. 12058064 236/299 Jessica Robertson 0.68618940391 0.690284310838704 4415 3779.63636363636 3764 0.1 2244 1.0184033727786 -0.925545293409337 -1 0.245881067074006 4414 4337 3665 4311 3432 3058 3764 4663 2244 4009 3679 4328 M14804 REACTOME_EXTENSION_OF_TELOMERES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTENSION_OF_TELOMERES.html Genes involved in Extension of Telomeres 27/29 Reactome 0.68618940391 0.690284310838704 2665 3680.18181818182 3765 0.1 2664 0.641068110287994 -0.62539116218362 -1 0.154738861548639 2664 3839 3869 4017 3765 2995 2771 4648 3636 4619 3659 4329 M19742 REACTOME_COPI_MEDIATED_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_COPI_MEDIATED_TRANSPORT.html Genes involved in COPI Mediated Transport 14/14 Reactome 2.62699630595699e-06 3.19572746497861e-05 4000 2893.54545454545 3766 2.38818131166385e-07 14 0.665325797898627 0.71559883261553 1 4.48783825142979 3998 2117 3766 1326 14 3848 3759 3960 43 4525 4473 4330 M17723 CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_DN.html Genes down-regulated by 2-methoxyestradiol (2ME2) [PubChem=1573] in the MM.1S cell line (multiple myeloma) sensitive to dexamethasone [PubChem=5743]. 12480690 157/223 Arthur Liberzon 0.0270625681761566 0.0485501033034812 4265 3495.63636363636 3769 0.00249102888530556 1263 0.978370002307086 -1.0408921242361 -1 1.92865087146395 4263 4359 3695 4498 1263 3030 3769 3824 3153 3903 2695 4331 M1359 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX4_DN.html Early prostate development genes (down-regulated at 6 hr dihydrotestosterone [PubChem=10635]) which are also down-regulated in localized vs metastatic prostate cancers. 18794802 43/46 Jessica Robertson 0.194003825302869 0.251579575735805 4710 3603.45454545455 3770 0.0194159689503381 2216 0.656242639004685 -0.651670230314051 -1 0.590052271598811 4710 3770 4013 4249 2216 4046 3700 2926 3028 4236 2744 4332 M14990 REACTOME_FANCONI_ANEMIA_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FANCONI_ANEMIA_PATHWAY.html Genes involved in Fanconi Anemia pathway 24/27 Reactome 0.147123360359555 0.199432010596525 3515 3351.45454545455 3772 0.0143631569678863 1523 0.860754851853852 -0.964382204032829 -1 0.904265067805026 3515 4542 3772 4583 2052 2351 1523 1756 4359 4154 4259 4333 M13172 TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_DN http://www.broadinstitute.org/gsea/msigdb/cards/TURASHVILI_BREAST_NORMAL_DUCTAL_VS_LOBULAR_DN.html Genes down-regulated in normal ductal and normal lobular breast cells. 17389037 19/23 Arthur Liberzon 0.68618940391 0.690284310838704 4670 3958.63636363636 3773 0.1 3128 1.18511026376171 -1.1729346722256 -1 0.286147735023851 4667 3870 3445 3773 3599 3761 4572 4624 3128 3688 4418 4334 M4253 VALK_AML_CLUSTER_4 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_4.html Top 40 genes from cluster 4 of acute myeloid leukemia (AML) expression profile; 87% of the samples are FAB M1 subtype, 53% bear mutations in CEBPA [GeneID=1050]. 15084694 39/59 Jessica Robertson 0.00674211015229888 0.0159993765303422 1210 3180.45454545455 3775 0.00061480555255708 788 1.17066419285662 1.14671034926853 1 3.15457592494479 4468 3775 1210 3564 788 4210 4146 4490 3780 1208 3346 4335 M4762 WEBER_METHYLATED_LCP_IN_SPERM_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_LCP_IN_SPERM_DN.html Unmethylated germline-specific genes with low-CpG-density promoters (LCP) in sperm. 17334365 3/9 Arthur Liberzon 0.0708017208070412 0.107766566336419 3780 3609.90909090909 3777 0.00731641675428522 1309 1.61491156444995 -1.61491156444995 -1 2.34438581069683 3777 4653 4635 4555 1942 3683 4681 1309 4520 2692 3262 4336 M5113 REACTOME_GLYCOLYSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLYCOLYSIS.html Genes involved in Glycolysis 29/44 Reactome 0.00157725227898862 0.00558486928494095 4080 3167.45454545455 3778 0.000143489472658618 471 0.847517465178868 -0.734382438789317 -1 2.86505594629074 4077 3834 3681 3843 471 2569 3119 3980 1618 3778 3872 4337 M2355 YUAN_ZNF143_PARTNERS http://www.broadinstitute.org/gsea/msigdb/cards/YUAN_ZNF143_PARTNERS.html Proteins associated with ZNF143 [GeneID=7702] in HeLa cells, based on MudPIT analysis. 17938208 31/39 Arthur Liberzon 0.0134025717951991 0.0275883728187265 3935 3320.09090909091 3780 0.0012259022318396 1013 0.839858204416698 0.529153478886382 1 1.96492872244267 3935 3828 3780 4087 1013 3050 2999 3773 2014 3855 4187 4338 M207 PID_RETINOIC_ACID_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_RETINOIC_ACID_PATHWAY.html Retinoic acid receptors-mediated signaling 18832364 38/42 Pathway Interaction Database 0.68618940391 0.690284310838704 4040 3792 3781 0.1 2870 0.613925074073851 -0.534190935535476 -1 0.148182686096382 4038 3781 3981 3684 4541 2870 3635 3435 3548 4295 3904 4339 M1881 MARSHALL_VIRAL_INFECTION_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARSHALL_VIRAL_INFECTION_RESPONSE_UP.html Genes up-regulated in the influenza-specific CD8+ [GeneID=925] T lymphocytes from bronchoalveolar lavage (BAL) compared to those from spleen. 15831586 7/8 Arthur Liberzon 0.0294600719784578 0.0518655500702428 2910 3465.09090909091 3783 0.00298580713684861 938 0.702997717303609 -0.702997717303609 -1 1.3555197283942 2906 3950 4596 3106 3783 4424 3711 938 4554 4696 1452 4340 M1752 VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP http://www.broadinstitute.org/gsea/msigdb/cards/VANHARANTA_UTERINE_FIBROID_WITH_7Q_DELETION_UP.html Genes up-regulated in uterine fibroids with deletions in the 7q region vs those without the deletion. 15940248 80/102 Leona Saunders 0.68618940391 0.690284310838704 3185 3446.45454545455 3784 0.1 502 0.779212592396044 0.67190085995774 1 0.188106516342896 3182 3263 4033 3784 4112 3458 2598 4501 502 4280 4198 4341 M139 PID_MYC_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MYC_PATHWAY.html C-MYC pathway 18832364 34/39 Pathway Interaction Database 0.155845507027029 0.209271918397604 4155 3278.27272727273 3785 0.0152837946210812 1032 0.710575010099365 -0.76413164505958 -1 0.724173931634062 4153 2517 3932 2986 2092 4101 3973 3785 1032 3924 3566 4342 M3844 TONG_INTERACT_WITH_PTTG1 http://www.broadinstitute.org/gsea/msigdb/cards/TONG_INTERACT_WITH_PTTG1.html Proteins that interact with PTTG1 [GeneID=9232], based on protein array. 18663361 64/83 Jessica Robertson 0.68618940391 0.690284310838704 4680 3615.45454545455 3788 0.1 1359 0.789789832509664 -0.950979157461589 -1 0.190661361034494 4677 3296 4003 3815 3157 3420 4630 3788 1359 4237 3388 4343 M19436 FUNG_IL2_TARGETS_WITH_STAT5_BINDING_SITES http://www.broadinstitute.org/gsea/msigdb/cards/FUNG_IL2_TARGETS_WITH_STAT5_BINDING_SITES.html Genes with putative STAT5 [GeneID=6777] binding sites; up-regulated by IL2 [Gene D=3558] in both primary thymocytes and T1 cells (primary thymocytes immortalized by Tax, an HTLV-1 encoded gene). 15735688 6/9 Arthur Liberzon 0.162174950866765 0.216050174454172 1985 3437.90909090909 3789 0.0175389671251542 1268 1.66861465693178 1.66861465693178 1 1.66602951050893 1982 4647 4394 4407 4633 3789 2165 2648 4652 3232 1268 4344 M13678 JEON_SMAD6_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/JEON_SMAD6_TARGETS_DN.html Genes down-regulated in H1299 cells (lung cancer) upon knockdown of SMAD6 [GeneID=4091] by RNAi. 19047146 27/32 Jessica Robertson 0.0825645962504224 0.1229740909757 4585 3427.90909090909 3790 0.00780331357241904 1336 1.2451980073637 1.23330443934637 1 1.7005269970192 4583 4522 2543 4102 3790 3847 3588 1336 2002 2814 4580 4345 M539 REACTOME_TRANS_GOLGI_NETWORK_VESICLE_BUDDING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANS_GOLGI_NETWORK_VESICLE_BUDDING.html Genes involved in trans-Golgi Network Vesicle Budding 84/96 Reactome 0.00331849644490475 0.00980425330377675 3960 2597.27272727273 3791 0.000302137516918111 65 0.729871333724959 -0.68920619987286 -1 2.199670039174 3956 65 3791 559 610 4173 4688 2428 3968 4095 237 4346 M4671 BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_DN http://www.broadinstitute.org/gsea/msigdb/cards/BARRIER_CANCER_RELAPSE_NORMAL_SAMPLE_DN.html Down-regulated genes in non-neoplastic mucosa samples from colon cancer patients who developed recurrence of the disease. 16091735 51/54 Leona Saunders 0.91410065408 0.91526412542588 3725 3715.63636363636 3791 0.2 2213 0.669020383964039 0.662724658393254 1 0.038496874769564 3725 2459 3887 2213 4244 3791 3441 3721 4577 4357 4457 4347 M9375 DAZARD_UV_RESPONSE_CLUSTER_G1 http://www.broadinstitute.org/gsea/msigdb/cards/DAZARD_UV_RESPONSE_CLUSTER_G1.html Cluster G1: genes most highly up-regulated in NHEK cells (normal keratinocyte) between 6 h and 12 h after UV-B irradiation. 12771951 114/137 John Newman 0.249443705874495 0.311474680351221 3975 3513.45454545455 3791 0.0257482232761044 1919 1.06284116629217 -1.04719364573953 -1 0.807790917879961 3975 2809 1919 4108 2374 3821 4576 3727 3791 3377 4171 4348 M10986 CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHIANG_LIVER_CANCER_SUBCLASS_UNANNOTATED_DN.html Marker genes down-regulated in the 'unannotated' subclass of hepatocellular carcinoma (HCC) samples. 18701503 246/288 Yujin Hoshida 0.306223967988667 0.370040227574631 720 3058.36363636364 3792 0.0326906399444635 716 0.769386829882141 -0.759686522097628 -1 0.498342300381001 716 3992 4147 3913 4618 1450 1823 2585 3792 4429 2177 4349 M5042 CHANG_CORE_SERUM_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_CORE_SERUM_RESPONSE_UP.html Up-regulated genes in the canonical gene expression signature of the fibroblast core serum response (CSR) defined by the Stanford group. 14737219 273/318 Arthur Liberzon 0.68618940391 0.690284310838704 2955 3520.09090909091 3793 0.1 2149 0.89110852317757 -0.877856794094106 -1 0.215134051096545 2955 4330 4093 4129 3793 2545 2795 4043 2149 4302 3587 4350 M6659 FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP http://www.broadinstitute.org/gsea/msigdb/cards/FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP.html Genes up-regulated in monocyte-derived dendritic cells (MDDC) after stimulation with galecin-1 (lectin, LGALS1) [GeneID=3956] compared to that with bacterial lipopolysaccharide (LPS). 16785517 680/844 Arthur Liberzon 1.7873583143e-07 3.09023122472381e-06 3960 2605 3795 1.78735845805925e-08 137 1.12810470597491 -1.11268387072434 -1 9.32692751530915 3960 481 4283 224 1522 3795 4392 4651 1133 137 4077 4351 M504 REACTOME_ANDROGEN_BIOSYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ANDROGEN_BIOSYNTHESIS.html Genes involved in Androgen biosynthesis 2/16 Reactome 0.230323368356646 0.290908830249764 3645 3402.7 3797 0.0286682405697519 369 0.240372862232231 -0.0780360434238418 -1 0.193308640030311 3644 3592 4206 NA 2422 4422 3956 2942 369 4524 3950 4352 M1045 REACTOME_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IMMUNE_SYSTEM.html Genes involved in Immune System 856/1251 Reactome 0.41764334677006 0.488423339136443 3290 3286.18181818182 3797 0.0526315789473684 425 1.00536478332564 1.08772347537161 1 0.469366585063183 3290 1122 4258 425 4441 4323 3797 3722 2380 3863 4527 4353 M2509 ABDELMOHSEN_ELAVL4_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ABDELMOHSEN_ELAVL4_TARGETS.html Major ELAVL4 [GeneID=1996] associated mRNAs encoding proteins with functions in neuronal physiology. 20584986 29/33 Arthur Liberzon 0.68618940391 0.690284310838704 4515 3658.36363636364 3797 0.1 2488 1.36729477490577 1.35452783524593 1 0.330152893854306 3403 4512 2488 4065 4514 3797 2768 4519 3281 2529 4366 4354 M1265 STANHILL_HRAS_TRANSFROMATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/STANHILL_HRAS_TRANSFROMATION_UP.html Selected genes up-regulated in Rat1Ras cells (fibroblasts) which were transformed by expression of an oncogenic activated form of HRAS [GeneID=3265] compared to the parental Rat1 cells. 16278678 14/14 Leona Saunders 0.185721422043772 0.242894184551567 3155 3709 3799 0.0185041776338596 2187 0.824433643073444 0.888005834066886 1 0.760181890152865 3152 4627 2674 4656 2187 3234 3279 4602 4706 3883 3799 4355 M224 WEBER_METHYLATED_HCP_IN_FIBROBLAST_UP http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_HCP_IN_FIBROBLAST_UP.html Methylated germline-specific genes with high-CpG-density promoters (HCP) in primary fibroblasts. 17334365 3/7 Jessica Robertson 0.000363877377375993 0.00182712895873903 4570 3042.72727272727 3802 3.63936974146459e-05 275 0.481958101904498 0.481958101904498 1 1.98014929141952 4570 1652 4558 2322 275 3802 4297 1896 1167 4689 4242 4356 M1883 BOYAULT_LIVER_CANCER_SUBCLASS_G1_DN http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G1_DN.html Down-regulated genes in hepatocellular carcinoma (HCC) subclass G1, defined by unsupervised clustering 17187432 56/75 Yujin Hoshida 0.68618940391 0.690284310838704 4275 3436.72727272727 3802 0.1 1920 1.0254097657198 -1.24664538814676 -1 0.247573403224154 4271 1920 2361 3802 3540 3981 3371 3841 3904 2776 4037 4357 M2474 LIU_IL13_MEMORY_MODEL_UP http://www.broadinstitute.org/gsea/msigdb/cards/LIU_IL13_MEMORY_MODEL_UP.html Genes up-regulated in BEAS-2B cells (bronchial epithelium) stimulated with IL13 [GeneID=3596] on days 1 to 3 and then rested for the next 3 days (repeated-stimulation or memory model) 20123980 25/35 Arthur Liberzon 0.254130793420751 0.316406580043773 3970 3409.90909090909 3803 0.0263028927238033 1157 1.04017684103022 -0.858866792965711 -1 0.779914096662658 3969 3844 2953 3958 2384 4498 3363 4441 1157 3139 3803 4358 M4517 MUNSHI_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MUNSHI_MULTIPLE_MYELOMA_UP.html Genes up-regulated in multiple myeloma (MM) compared to normal plasma cells from the patient's identical twin. 12969976 146/189 Kevin Vogelsang 0.68618940391 0.690284310838704 4165 3765.63636363636 3805 0.1 2713 0.96928858066728 -0.934201698896718 -1 0.234017796073572 4162 4016 3358 4301 4269 3805 3793 4645 2713 3543 2817 4359 M15123 MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN.html Genes down-regulated in at least 8 of 11 sarcoma cell lines by trabectedin [PubChem=3199]. 15897246 377/435 John Newman 0.68618940391 0.690284310838704 3260 3700.90909090909 3806 0.1 2661 0.904402296484091 -0.9354474685004 -1 0.218345051867884 3256 3169 4124 3909 3519 3806 2880 4475 2661 4338 4573 4360 M14594 LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN http://www.broadinstitute.org/gsea/msigdb/cards/LASTOWSKA_NEUROBLASTOMA_COPY_NUMBER_DN.html Genes with copy number losses in primary neuroblastoma tumors. 17533364 1015/1145 Arthur Liberzon 0.474753161528981 0.54455283655329 2835 3496.63636363636 3807 0.0623595282577608 2197 0.943516548005998 -0.927360680692069 -1 0.373599602953682 4422 2197 4356 2485 2835 3807 4140 4365 2607 4416 2833 4361 M19048 RUIZ_TNC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/RUIZ_TNC_TARGETS_DN.html Genes down-regulated in T98G cells (glioblastoma) by TNC [GeneID=3371]. 15492259 190/241 Arthur Liberzon 0.68618940391 0.690284310838704 3170 3481.81818181818 3807 0.1 1805 1.22951697745792 1.12191329322845 1 0.296873808700855 3170 4708 1826 4633 3807 4004 4424 3560 1805 1852 4511 4362 M16853 KEGG_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_DNA_REPLICATION.html DNA replication 35/36 KEGG 0.419726590960216 0.490495050589804 1470 3425.27272727273 3809 0.0482737217012754 1470 0.5699458461425 -0.575465343322529 -1 0.264468133469985 1470 4148 3949 4435 3518 2585 1840 3809 3996 4484 3444 4363 M9461 REACTOME_LAGGING_STRAND_SYNTHESIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LAGGING_STRAND_SYNTHESIS.html Genes involved in Lagging Strand Synthesis 19/20 Reactome 0.68618940391 0.690284310838704 3065 3908.54545454545 3809 0.1 3061 0.634036195547143 -0.608445654914076 -1 0.153040360819295 3061 4210 3738 4006 3774 3607 3693 4509 3809 4595 3992 4364 M9583 SANA_RESPONSE_TO_IFNG_DN http://www.broadinstitute.org/gsea/msigdb/cards/SANA_RESPONSE_TO_IFNG_DN.html Genes down-regulated in five primary endothelial cell types (lung, aortic, iliac, dermal, and colon) by IFNG [GeneID=3458]. 15749026 119/144 Yujin Hoshida 0.219419309363884 0.279409886568529 3810 3466.45454545455 3810 0.022268065301782 2288 1.00934913754618 -0.984117592373793 -1 0.838587946467881 3810 2335 2848 4227 2288 4395 4040 4541 2375 2703 4569 4365 M1260 WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP http://www.broadinstitute.org/gsea/msigdb/cards/WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_UP.html Genes up-regulated in rectal cancer patients resistant to radiotherapy (non-responders) relative to the sensitive ones (responders). 16585155 140/172 Arthur Liberzon 0.68618940391 0.690284310838704 4600 3686.54545454545 3811 0.1 2898 0.833803504794954 -0.743463361020015 -1 0.201292498815983 4599 3211 4077 4304 3292 3811 3822 3077 2898 4270 3191 4366 M3045 CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_UP.html Genes up-regulated in CD4+ [GeneID=920] T lymphocytes after stimulation with prostaglandin E2 [PubChem=5280360]. 16424048 177/192 Arthur Liberzon 0.68618940391 0.690284310838704 3065 3740.81818181818 3811 0.1 2805 0.887710908002516 -0.902379158482201 -1 0.214313385308416 3063 4714 3917 4470 3821 2805 3105 3811 3783 4364 3296 4367 M5443 HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_HIGH_RISK_DN.html Genes down-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 31/43 Arthur Liberzon 0.68618940391 0.690284310838704 4675 3607.90909090909 3814 0.1 2117 1.32633521065693 1.20894386751269 1 0.320259450558398 4671 3816 2117 3814 3197 4208 4583 2946 3087 3109 4139 4368 M2136 QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2 http://www.broadinstitute.org/gsea/msigdb/cards/QI_HYPOXIA_TARGETS_OF_HIF1A_AND_FOXA2.html Genes up-regulated by hypoxia in TRAMP-C cells (prostatic cancer) expressing HIF1A and FOXA2 [GeneID=3091,3170] off plasmid vectors. 20609350 53/57 Arthur Liberzon 0.249203036474268 0.31125650493743 4535 3574.18181818182 3814 0.0257198275594025 2372 0.958909868234899 -0.885520147707884 -1 0.729227553604047 4531 4102 2851 4256 2372 3930 4022 3814 3114 3542 2782 4369 M101 PID_HDAC_CLASSI_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_HDAC_CLASSI_PATHWAY.html Signaling events mediated by HDAC Class I 18832364 80/88 Pathway Interaction Database 0.423410991168262 0.494433418682384 4240 3561.90909090909 3815 0.0488246691672262 2108 0.794709484303325 0.786643426104089 1 0.364663727192931 4238 4063 4057 4318 2708 3815 3749 2962 2108 4027 3136 4370 M6327 BIOCARTA_CSK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_CSK_PATHWAY.html Activation of Csk by cAMP-dependent Protein Kinase Inhibits Signaling through the T Cell Receptor 23/36 BioCarta 0.911213833453923 0.913536383581673 3450 3830 3818 0.197592410542457 2635 0.929811819376558 0.581418241996037 1 0.0546895189783951 3818 3861 2635 4277 3521 3250 3447 4555 4659 3447 4660 4371 M14242 BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/BYSTRYKH_HEMATOPOIESIS_STEM_CELL_AND_BRAIN_QTL_TRANS.html Genes trans-regulated by the same QTL (quantitative trait loci) in brain and hematopoietic stem cells (HSC). 15711547 217/280 Jean Junior 0.0404577662413212 0.0672870530863411 4385 3496.27272727273 3818 0.00374741069075385 1437 0.902291683314873 -0.853680298807821 -1 1.58676564840798 4385 3629 3951 3860 1437 3598 4231 4074 2509 3818 2967 4372 M1593 MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_UP http://www.broadinstitute.org/gsea/msigdb/cards/MULLIGAN_NTF3_SIGNALING_VIA_INSR_AND_IGF1R_UP.html Genes similarly up-regulated in 3T3-L1 cells (fibroblasts able to differentiate to adipocytes) upon stimulation of INSR or IGFR1 by NTF3 [GeneID=3643;3480;4908]. 12213819 31/39 John Newman 0.68618940391 0.690284310838704 3265 3723.09090909091 3819 0.1 2334 1.0118791932288 0.951316515398305 1 0.244305205572253 3264 3819 3242 3580 4647 4250 4294 4442 2334 3107 3975 4373 M243 PID_ARF_3PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ARF_3PATHWAY.html Arf1 pathway 18832364 30/33 Pathway Interaction Database 0.00792808690699944 0.018121341501713 3885 2958.54545454545 3820 0.000723345649078001 518 0.724301197459546 0.791971347979135 1 1.89294251693702 3882 2007 3820 1348 835 4118 4264 3242 518 4043 4467 4374 M824 REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_FORMATION_OF_TRANSCRIPTION_COUPLED_NER_TC_NER_REPAIR_COMPLEX.html Genes involved in Formation of transcription-coupled NER (TC-NER) repair complex 31/33 Reactome 0.63491690188687 0.690284310838704 3360 3767.63636363636 3820 0.0875324476300763 2649 0.578594725034136 -0.57230987484379 -1 0.139648933082666 3357 4517 4044 4462 3033 2649 3633 3842 3820 4567 3520 4375 M17040 CASTELLANO_HRAS_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/CASTELLANO_HRAS_TARGETS_DN.html Genes down-regulated in MEF cells (embryonic fibroblast) isolated from HRAS [GeneID=3265] knockout mice. 16909116 8/10 Leona Saunders 0.0681360052984495 0.104589723757225 2165 3128.63636363636 3822 0.00703199930732723 843 0.54906666670015 0.54906666670015 1 0.807723006156606 2165 4281 4332 3822 4661 1822 843 2244 3895 4635 1715 4376 M17517 WU_HBX_TARGETS_2_DN http://www.broadinstitute.org/gsea/msigdb/cards/WU_HBX_TARGETS_2_DN.html Genes down-regulated by expression of HBV X protein (HBVgp3) [GeneID=944566] in primary hepatocytes. 11439330 19/22 John Newman 0.68618940391 0.690284310838704 3825 3786.09090909091 3824 0.1 2774 0.761898134907155 -0.778425123626841 -1 0.183924352628336 3824 3055 2774 4200 3848 3534 3267 4593 4489 3693 4370 4377 M14308 GRASEMANN_RETINOBLASTOMA_WITH_6P_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/GRASEMANN_RETINOBLASTOMA_WITH_6P_AMPLIFICATION.html Genes changed in retinoblastoma tumors with respect to chromosome 6p amplifications. 16007192 16/23 Leona Saunders 0.68618940391 0.690284310838704 2075 3718.72727272727 3825 0.1 2072 0.765380019698191 0.765380019698191 1 0.184765373043829 2072 4611 3825 4477 3541 3439 2540 4055 4468 4650 3228 4378 M3334 SHIPP_DLBCL_CURED_VS_FATAL_UP http://www.broadinstitute.org/gsea/msigdb/cards/SHIPP_DLBCL_CURED_VS_FATAL_UP.html Top 50 up-regulated markers for the diffused large B-cell lymphoma (DLBCL) that distinguished between cured and fatal/refractory clinical outcomes. 11786909 81/144 Jean Junior 0.0602345251412229 0.0942037636403486 3920 3358.54545454545 3825 0.00563180248591437 1523 1.24813608688025 -1.41316948880158 -1 1.92131377378628 3920 4058 1523 4386 1593 4588 3825 3132 3539 2052 4328 4379 M1895 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_OLD http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_OLD.html Human environmental etress response genes not changed in primary fibroblasts from old donors in response to 4NQO treatment. 15897889 17/20 Jessica Robertson 0.68618940391 0.690284310838704 3345 3530.63636363636 3825 0.1 1565 1.02336977279526 -0.803085973073834 -1 0.247080659839473 3344 1565 2339 3083 3825 4643 3925 4436 4076 3528 4073 4380 M2843 REACTOME_ACTIVATION_OF_NMDA_RECEPTOR_UPON_GLUTAMATE_BINDING_AND_POSTSYNAPTIC_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_NMDA_RECEPTOR_UPON_GLUTAMATE_BINDING_AND_POSTSYNAPTIC_EVENTS.html Genes involved in Activation of NMDA receptor upon glutamate binding and postsynaptic events 38/49 Reactome 0.494721837811329 0.56413406247857 3540 3644.18181818182 3826 0.06017232416453 2313 0.850530570718034 0.844682138312771 1 0.317189546187443 3540 4486 2924 4628 4161 3354 2313 2436 4041 3826 4377 4381 M12972 MATHEW_FANCONI_ANEMIA_GENES http://www.broadinstitute.org/gsea/msigdb/cards/MATHEW_FANCONI_ANEMIA_GENES.html Genes identified with the Fanconi anemia (FA) and the FA pathway. 16998502 11/11 Arthur Liberzon 0.23388509799228 0.294540464920908 3830 3505.90909090909 3826 0.0239293261340084 2000 0.645517317350081 -0.637534487204263 -1 0.5140865617101 3826 4262 3639 4046 2333 2897 2000 2116 4237 4645 4564 4382 M4888 ZHAN_MULTIPLE_MYELOMA_PR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHAN_MULTIPLE_MYELOMA_PR_UP.html Top 50 up-regulated genes in cluster PR of multiple myeloma samples characterized by increased expression of proliferation and cell cycle genes. 16728703 48/61 Kevin Vogelsang 0.227844663631308 0.288395498079854 895 3237.72727272727 3826 0.0232321999692425 891 1.053654261297 -1.09260232668899 -1 0.853668247975904 891 4475 3826 4499 3896 1848 1404 3633 4033 4039 3071 4383 M6981 KEGG_PROTEIN_EXPORT http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_PROTEIN_EXPORT.html Protein export 33/39 KEGG 0.232721536520795 0.293388261853139 2130 3358.72727272727 3827 0.0237946519446444 1903 0.626446094932896 -0.60422842555907 -1 0.500495306078199 2130 4511 3827 4139 3999 1965 3071 1903 4692 4485 2224 4384 M985 REACTOME_NEGATIVE_REGULATORS_OF_RIG_I_MDA5_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_NEGATIVE_REGULATORS_OF_RIG_I_MDA5_SIGNALING.html Genes involved in Negative regulators of RIG-I/MDA5 signaling 38/48 Reactome 0.0158668142047048 0.0316264202053238 4165 3606.18181818182 3827 0.0014529470553562 1064 1.09547403575288 -0.834489884635084 -1 2.46548308593576 4165 3803 3489 4050 1064 3386 4236 3365 3844 3827 4439 4385 M2065 HOFFMAN_CLOCK_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMAN_CLOCK_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) upon knockdown of CLOCK [GeneID=9575] by RNAi that also belong to the highest confidence network (according to Ingenuity Pathway Analysis). 20124474 6/13 Jessica Robertson 0.116117815419905 0.163604802621478 4485 3459.09090909091 3827 0.0122672858374307 1440 1.95333012416066 -3.00721536782147 -1 2.30426664433972 4485 3140 4653 1440 1963 2025 3827 4600 4669 3244 4004 4386 M12153 HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_RISK_DN.html Genes down-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with high risk of myelodysplastic syndrom (MDS) compared to the low risk patients. 12411319 38/55 Arthur Liberzon 0.68618940391 0.690284310838704 3850 3339.09090909091 3828 0.1 1656 1.57302912514047 1.58189599218843 1 0.379846321150106 3848 3784 1858 2747 3887 4327 3931 3828 1656 2383 4481 4387 M964 REACTOME_DESTABILIZATION_OF_MRNA_BY_TRISTETRAPROLIN_TTP http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DESTABILIZATION_OF_MRNA_BY_TRISTETRAPROLIN_TTP.html Genes involved in Destabilization of mRNA by Tristetraprolin (TTP) 20/20 Reactome 0.68618940391 0.690284310838704 4340 3667.81818181818 3829 0.1 2590 0.577416816491358 -0.575494625677117 -1 0.13936441903596 4336 2590 3829 2695 3158 3248 3546 4125 3906 4591 4322 4388 M11068 KORKOLA_CHORIOCARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CHORIOCARCINOMA_DN.html Genes from the 12p region that were down-regulated in choriocarcinoma cells compared to normal testis. 16424014 31/69 Arthur Liberzon 0.0141739183486352 0.0288988745596364 4315 3313.90909090909 3830 0.00129691534247258 620 1.23593522277228 1.25121199784975 1 2.85426068024199 4314 4159 1658 3830 3730 4195 4566 620 2894 1862 4625 4389 M6979 GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_MYELOID_DN.html Genes down-regulated in myeloid progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 74/110 Arthur Liberzon 0.0603573475363768 0.0943645844225566 2865 3485.27272727273 3831 0.00564361761357943 1204 0.888803165354382 0.972636740584633 1 1.3671575220558 2862 4423 3828 4483 1717 4642 3195 1204 3849 4304 3831 4390 M2558 HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLEMAN_PREDNISOLONE_RESISTANCE_ALL_UP.html Genes distinguishing prednisolone [PubChem=5755] resistant and sensitive ALL (B- and T-lineage ALL); here - genes up-regulated in the drug resistant samples. 15295046 26/27 Arthur Liberzon 0.000859492063131984 0.00352765438085475 4370 3303 3831 7.8166184702307e-05 378 0.635784339643059 -0.673912860426142 -1 2.33961006343544 4366 4178 3905 2941 378 4328 3687 3831 758 4181 3780 4391 M48 PID_MET_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_MET_PATHWAY.html Signaling events mediated by Hepatocyte Growth Factor Receptor (c-Met) 18832364 101/111 Pathway Interaction Database 0.158526804901874 0.212038005174002 4170 3341.45454545455 3833 0.0155685483164161 1731 0.846101772902297 -0.787479620541196 -1 0.855074402796017 4166 3239 3833 2232 2105 3989 3875 3956 1731 3770 3860 4392 M19148 TOMLINS_PROSTATE_CANCER_UP http://www.broadinstitute.org/gsea/msigdb/cards/TOMLINS_PROSTATE_CANCER_UP.html Genes up-regulated in prostate cancer vs benign prostate tissue, based on a meta-analysis of five gene expression profiling studies. 17173048 58/64 Leona Saunders 0.68618940391 0.690284310838704 3255 3851.81818181818 3833 0.1 3252 0.821860807002037 0.835956940753267 1 0.198407839138049 3252 4095 3602 4229 3479 4409 4113 3524 3833 4188 3646 4393 M14951 ZUCCHI_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZUCCHI_METASTASIS_UP.html The 50 most up-regulated genes in primary invasive breast dutcal carcinoma (IDC) or lymph node metastases, compared to normal mammary epithelium. 15608061 60/78 Kate Stafford 0.217012588761021 0.277137288677494 3835 3723.72727272727 3834 0.0219943953593714 1854 0.845829121287129 -0.907551104672889 -1 0.707216568441658 3834 4456 3395 4508 3539 3822 2992 1854 4589 4107 3865 4394 M17956 ZERBINI_RESPONSE_TO_SULINDAC_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZERBINI_RESPONSE_TO_SULINDAC_DN.html Selected genes down-regulated in DU145 and PC-3 cells (prostate cancer) after treatment with the NSAID (non-steroid anti-inflammatory drug) sulindac [PubChem=5352]. 17178890 7/8 Arthur Liberzon 0.6513215599 0.690284310838704 2880 3914.54545454545 3836 0.1 2878 0.405140017887182 0.405140017887182 1 0.0977523860603122 2878 3567 4281 3625 3522 4700 4047 3836 4383 4627 3594 4395 M11844 KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_CYTOSOLIC_DNA_SENSING_PATHWAY.html Cytosolic DNA-sensing pathway 42/60 KEGG 0.371136000005102 0.439588938525491 4000 3810.90909090909 3838 0.0412906216015068 2218 0.987682690886696 0.791967404653884 1 0.52891233734025 4000 4483 3348 4626 4209 3553 3838 2218 3558 3372 4715 4396 M1486 KAMMINGA_EZH2_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KAMMINGA_EZH2_TARGETS.html Putative targets or partners of EZH2 [GeneID=2146] in hematopoietic stem cells. 16293602 49/56 Kevin Vogelsang 0.68618940391 0.690284310838704 3610 3691.09090909091 3838 0.1 2356 0.72462821729033 -0.723442521209287 -1 0.174922112898804 3610 3341 3992 3431 3339 4134 4272 4007 2356 4282 3838 4397 M1588 MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_4 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_SULINDAC_4.html Cluster 4: genes down-regulated in SW260 cells (colon cancer) by sodium butyrate and sulindac [PubChem=5222465;5352]. 10969808 25/34 John Newman 0.68618940391 0.690284310838704 3600 4018.09090909091 3839 0.1 3163 1.04795610253206 0.950686964605033 1 0.253019284030584 3596 4525 3490 4575 4658 3839 3702 4390 3163 3582 4679 4398 M15973 SHEPARD_BMYB_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_BMYB_TARGETS.html Human orthologs of BMYB [GeneID=4605] target genes in zebra fish, identified as commonly changed in the BMYB loss of function mutant crb ('crush and burn') and after knockdown of BMYB by morpholino. 16150706 100/158 Jennifer Shepard 0.193241919639088 0.251129366931854 4060 3317.27272727273 3840 0.0193317375895491 1340 1.61751177031124 1.59153041372309 1 1.45640827026056 4060 4042 1340 3840 4287 2785 3708 3893 1636 2401 4498 4399 M1667 VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_DN http://www.broadinstitute.org/gsea/msigdb/cards/VISALA_RESPONSE_TO_HEAT_SHOCK_AND_AGING_DN.html Genes down-regulated after heat shock in peripheral lympocytes from old donors, compared to those from the young ones. 12618007 25/28 John Newman 0.774005644362877 0.777795750775554 4240 3854 3841 0.12646240784786 2907 0.679164452653274 -0.706877172580599 -1 0.111113061919775 4236 4528 3311 3841 3252 3298 3037 2907 4663 4684 4637 4400 M17857 KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SNARE_INTERACTIONS_IN_VESICULAR_TRANSPORT.html SNARE interactions in vesicular transport 34/39 KEGG 0.68618940391 0.690284310838704 3595 3768.27272727273 3842 0.1 2876 0.629409663616868 0.571159405076468 1 0.15192286037347 3591 3805 3953 4414 4387 2876 2913 4211 3842 4490 2969 4401 M5198 GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_NORMAL_QUIESCENT_VS_NORMAL_DIVIDING_DN.html Genes down-regulated in quiescent vs dividing CD34+ [GeneID=8842] cells isolated from peripheral blood of normal donors. 17717066 105/155 Arthur Liberzon 0.68618940391 0.690284310838704 2355 3793.45454545455 3844 0.1 2352 0.921596891704906 -0.892218349172221 -1 0.222498263844938 2352 4382 3633 4640 3573 3145 3087 4597 4209 4266 3844 4402 M2078 WHITFIELD_CELL_CYCLE_M_G1 http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_M_G1.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the M/G1 phase of cell cycle. 12058064 212/254 Jessica Robertson 0.307339983504151 0.371198751826918 3395 3801.27272727273 3844 0.0328322002218171 2494 0.94612255500121 0.913055365768059 1 0.610913433507966 3393 4702 3844 4648 2494 3539 3292 4138 3126 4114 4524 4403 M13336 PETRETTO_HEART_MASS_QTL_CIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_HEART_MASS_QTL_CIS_DN.html Down-regulated cis-regulated expression quantitative loci (cis-eQTL) in the heart that colocalize with previously mapped cardiac mass QTLs. 18443592 39/74 Jessica Robertson 0.236712396927916 0.297560786540552 3175 3611.90909090909 3848 0.0242573428814393 2337 0.85092234522107 -0.661321552234727 -1 0.67204643761817 3175 4139 3333 4080 2337 4531 4114 3370 4231 3848 2573 4404 M10514 NAGY_STAGA_COMPONENTS_HUMAN http://www.broadinstitute.org/gsea/msigdb/cards/NAGY_STAGA_COMPONENTS_HUMAN.html Composition of the 2 MDa human STAGA complex containing KAT2A [GeneID=2648]. 17694077 16/18 Arthur Liberzon 0.0470283114730537 0.0763845939961505 4175 3485 3850 0.0043695242293547 1214 0.894226366905197 -0.603419590469004 -1 1.49868217290713 4172 3516 3850 3800 1497 4576 4692 2490 1214 3943 4585 4405 M10243 FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP.html Genes up-regulated in peripheral blood lymphocytes (PBL) from patients with acute transplant rejection compared to those from patients with well functioning kidneys more than 1-year post transplant. 15307835 84/112 Jean Junior 0.345137897702278 0.412104952480332 4575 3755.90909090909 3850 0.0377534764589553 2568 0.884833076620331 -0.944594854512376 -1 0.511052040205344 4574 3260 3641 3850 2568 4568 4183 4499 2885 4097 3190 4406 M11537 CHANG_CYCLING_GENES http://www.broadinstitute.org/gsea/msigdb/cards/CHANG_CYCLING_GENES.html Fibroblast serum response genes showing periodic expression during the cell cycle; excluded from the core serum response signature. 14737219 202/262 Arthur Liberzon 0.68618940391 0.690284310838704 2540 3678.54545454545 3851 0.1 2325 1.04761850355019 -0.999035001517148 -1 0.252937739794332 2536 4707 3851 4530 4435 2940 2946 4465 2325 4230 3499 4407 M40 PID_E2F_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_E2F_PATHWAY.html E2F transcription factor network 18832364 85/115 Pathway Interaction Database 0.68618940391 0.690284310838704 2995 3524.45454545455 3853 0.1 2165 0.810821260240175 0.809068289296405 1 0.19574132810689 2995 2833 3788 3853 4537 2165 2420 4030 4007 3983 4158 4408 M9267 TAGHAVI_NEOPLASTIC_TRANSFORMATION http://www.broadinstitute.org/gsea/msigdb/cards/TAGHAVI_NEOPLASTIC_TRANSFORMATION.html Genes that cooperate with MYC and TBX2 [GeneID=4609;6909] to transform MEF cells (embryo fibroblasts). 18762810 20/23 Jessica Robertson 0.0795032068288336 0.118902134420816 3855 3538.81818181818 3854 0.00750278183614165 1320 0.756808657021567 -0.895159899081081 -1 1.0501148884537 3854 4562 3586 4403 1847 4610 4254 1320 3100 4068 3323 4409 M3592 GOLDRATH_HOMEOSTATIC_PROLIFERATION http://www.broadinstitute.org/gsea/msigdb/cards/GOLDRATH_HOMEOSTATIC_PROLIFERATION.html Up-regulated in CD8+ [GeneID=925] T lymphocytes undergoing homeostatic proliferation (HP) versus the naive cells; these genes are not up-regulated versus effector or memory cell population. 15548615 217/249 Kate Stafford 0.592028845811792 0.658584999347551 4440 3085.45454545455 3854 0.0782722178497822 517 0.922545248997074 -0.860973170021374 -1 0.250989385419936 4436 1740 3996 1331 2971 3116 3938 4149 517 3892 3854 4410 M15565 ZHU_CMV_24_HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_24_HR_UP.html Up-regulated at 24 h following infection of primary human foreskin fibroblasts with CMV 9826724 163/221 John Newman 0.282424520634718 0.346335083760943 3470 3691.90909090909 3855 0.0297200578960169 2032 0.937365834996298 0.978922357860733 1 0.647609054160898 3470 4011 3356 3912 3549 4718 4339 2032 3855 3483 3886 4411 M3218 MOSERLE_IFNA_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/MOSERLE_IFNA_RESPONSE.html Top 50 genes up-regulated in ovarian cancer progenitor cells (also known as side population, SP, cells) in response to interferon alpha (IFNA). 18632618 49/74 Jessica Robertson 0.119061330271083 0.16705394734825 3855 3042.18181818182 3855 0.0114581469015711 1025 1.35968766589933 1.44505025896995 1 1.58545186811569 3855 1936 1397 2589 4675 3959 3999 4449 1085 1025 4495 4412 M8525 KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_24HR_DN.html Genes down-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 24 h. 18701491 1166/1371 Jessica Robertson 0.175736919226394 0.231310166968372 4640 3608.18181818182 3859 0.0191409922420815 1647 0.974358862773706 -0.905500061138239 -1 0.929470117542834 4636 3148 4504 3680 2205 3351 4051 4311 1647 4298 3859 4413 M2066 WHITFIELD_CELL_CYCLE_LITERATURE http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_LITERATURE.html A list of known cell cycle regulated genes that was compiled from the literature by the authors. 12058064 49/52 Jessica Robertson 0.68618940391 0.690284310838704 2215 3646.27272727273 3860 0.1 2212 0.676683498076109 -0.678949909345934 -1 0.1633414633098 2212 2463 3860 3873 4424 3997 3143 4389 3620 4351 3777 4414 M18448 REACTOME_GLUCOSE_TRANSPORT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLUCOSE_TRANSPORT.html Genes involved in Glucose transport 35/44 Reactome 0.68618940391 0.690284310838704 4370 3584.09090909091 3861 0.1 1187 0.834049899310939 -0.816080936630607 -1 0.201352013369349 4368 3394 3729 3191 4007 4241 4378 2927 1187 4142 3861 4415 M13766 NIKOLSKY_BREAST_CANCER_5P15_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_5P15_AMPLICON.html Genes within amplicon 5p15 identified in a copy number alterations study of 191 breast tumor samples. 19010930 27/36 Jessica Robertson 0.353708803418028 0.421379493218852 4030 3599 3861 0.0389052527798907 1788 0.721487385577666 -0.672890898547932 -1 0.406225118376906 4028 3018 3111 3343 4298 3861 4227 3398 4320 4197 1788 4416 M19630 ZHU_CMV_ALL_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHU_CMV_ALL_UP.html Up-regulated at any timepoint following infection of primary human foreskin fibroblasts with CMV 9826724 199/272 John Newman 0.161389871140373 0.21518649485383 3865 3399.63636363636 3862 0.0158735178859795 2117 1.03768908319456 1.03377163370224 1 1.03875010051454 3862 4343 2239 3906 2117 4390 4250 2485 3224 2462 4118 4417 M9389 FINETTI_BREAST_CANCER_KINOME_RED http://www.broadinstitute.org/gsea/msigdb/cards/FINETTI_BREAST_CANCER_KINOME_RED.html Genes in the red cluster of protein kinases distinguishing between luminal A and basal breast cancer subtypes. 18245477 29/55 Jessica Robertson 0.0951879422826655 0.138369906859926 3905 3592 3863 0.00905223663917364 1798 0.904652695125843 -0.694890791349328 -1 1.16588677786194 3904 3426 3439 3863 1798 3493 4233 4582 2036 4218 4520 4418 M14775 ST_G_ALPHA_S_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_G_ALPHA_S_PATHWAY.html G alpha s Pathway 19/21 Signaling Transduction KE 0.68618940391 0.690284310838704 3870 3871.72727272727 3866 0.1 2861 1.12239431291511 -0.9838384347441 -1 0.27099921684919 3866 4564 2861 4425 3803 4442 4160 3840 4150 3163 3315 4419 M2439 HUANG_GATA2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HUANG_GATA2_TARGETS_DN.html Genes down-regulated in G1ME cells (megakaryocyte/erythroid progenitor lacking GATA1 [GeneID=2623]) upon knockdown of GATA2 [GeneID=2624] by RNAi. 19620289 82/97 Arthur Liberzon 0.68618940391 0.690284310838704 4405 3713.72727272727 3866 0.1 2100 1.02349363086415 -1.06030527614185 -1 0.247110576729552 4402 3690 2100 3795 4328 3340 3866 4352 4017 2853 4108 4420 M1571 YAMAZAKI_TCEB3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/YAMAZAKI_TCEB3_TARGETS_DN.html Genes down-regulated in embryonic stem cells from TCEB3 [GeneID=6924] knockout mice. 12604609 301/568 John Newman 0.68618940391 0.690284310838704 3655 3565 3867 0.1 2116 1.15355704247065 -1.21866400594437 -1 0.278526315915243 3653 3986 2527 3867 3256 4456 4011 4455 2116 2256 4632 4421 M720 REACTOME_METABOLISM_OF_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_PROTEINS.html Genes involved in Metabolism of proteins 467/627 Reactome 0.291591424348974 0.355727971808518 4620 3711.90909090909 3868 0.0308534875307709 1937 0.959282841170767 -0.966928941886782 -1 0.646025293555679 4617 4317 4107 3460 2453 3771 4460 3467 1937 4374 3868 4422 M8410 REACTOME_ERKS_ARE_INACTIVATED http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ERKS_ARE_INACTIVATED.html Genes involved in ERKs are inactivated 15/15 Reactome 0.022511521954054 0.0416847326885582 3335 3490.27272727273 3871 0.00206774783586635 1187 0.601283830425451 0.771039411310237 1 1.24500397236808 3331 3902 3802 3871 1187 4284 4495 4609 2283 3915 2714 4423 M16381 SCHLOSSER_SERUM_RESPONSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_SERUM_RESPONSE_UP.html Cluster 1: genes up-regulated in B493-6 cells (B lymphocytes) upon serum stimulation but not by affected by MYC [GeneID=4609]. 15516975 208/270 Leona Saunders 0.547269988786066 0.615359735048218 4135 3668.27272727273 3871 0.0695079600564282 1843 0.924113250114745 -0.903047381498069 -1 0.292298440394876 4135 3188 3737 3848 2905 4176 4548 3917 1843 4183 3871 4424 M1944 IRITANI_MAD1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/IRITANI_MAD1_TARGETS_DN.html Genes down-regulated by overexpression of MAD1 [GeneID=4084] in primary thymocytes from RAG2 [GeneID=5897] knockout mice. 12234922 73/109 Jessica Robertson 0.0871747522666711 0.128654689382336 3880 3665.90909090909 3871 0.00825760991169926 1363 0.880327411956421 -0.843857889464057 -1 1.17629746260541 3876 4077 3870 3683 4447 3871 3658 1363 4156 4042 3282 4425 M609 CHOI_ATL_CHRONIC_VS_ACUTE_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHOI_ATL_CHRONIC_VS_ACUTE_DN.html Genes down-regulated in adult T-cell leukemia (ATL), chronic vs acute clinical condition. 16909099 33/34 Arthur Liberzon 0.68618940391 0.690284310838704 3635 3922.36363636364 3874 0.1 3175 0.755195267927477 -0.816604001520338 -1 0.182305330658752 4259 3397 3874 3631 4125 3175 4242 3853 3633 4630 4327 4426 M2974 NAGY_TFTC_COMPONENTS_HUMAN http://www.broadinstitute.org/gsea/msigdb/cards/NAGY_TFTC_COMPONENTS_HUMAN.html Composition of the 2 MDa human TFTC complex containing KAT2A [GeneID=2648]. 17694077 20/22 Arthur Liberzon 0.0703881578448884 0.107282390003735 3855 3642 3874 0.00661332181906863 1664 0.894226366905197 -0.603419590469004 -1 1.30073558038364 3852 3874 3911 3837 1664 4612 4520 2958 2373 4067 4394 4427 M3721 ST_JNK_MAPK_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_JNK_MAPK_PATHWAY.html JNK MAPK Pathway 48/52 Signaling Transduction KE 0.41169362182622 0.481823430453697 4675 3588.45454545455 3875 0.0470834520166578 1914 0.982742711066713 -1.02856539741857 -1 0.467515631002788 4673 4110 3450 3653 4141 2877 2133 4694 3953 3875 1914 4428 M1415 BYSTROEM_CORRELATED_WITH_IL5_UP http://www.broadinstitute.org/gsea/msigdb/cards/BYSTROEM_CORRELATED_WITH_IL5_UP.html Genes whose expression in bone marrow samples correlated directly with increased levels of serum IL5 [GeneID=3567]. 14525773 72/96 Kate Stafford 0.68618940391 0.690284310838704 4090 3698.72727272727 3876 0.1 2761 1.12244095256099 -1.37015686045893 -1 0.27101048226913 4089 4420 2982 4411 4030 4022 3876 2761 3355 3737 3003 4429 M2505 RATTENBACHER_BOUND_BY_CELF1 http://www.broadinstitute.org/gsea/msigdb/cards/RATTENBACHER_BOUND_BY_CELF1.html Transcripts bound by CELF1 [GeneID=10658] in HeLa cells (cervical carcinoma). 20547756 545/748 Arthur Liberzon 0.6513215599 0.690284310838704 3605 3746 3877 0.1 1969 1.16381976629286 -1.22071038279395 -1 0.281005191803175 3601 4315 4710 4590 3877 4461 3650 3848 2209 1969 3976 4430 M5731 BIOCARTA_AKAP95_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_AKAP95_PATHWAY.html AKAP95 role in mitosis and chromosome dynamics 20/20 BioCarta 0.271685594853164 0.33490624385138 4440 3688.81818181818 3879 0.0284088811270981 2022 0.813689802539046 0.551775098150404 1 0.57994287993235 4440 3875 3723 3879 2419 4014 3947 3600 2022 4060 4598 4431 M4735 WANG_LMO4_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_LMO4_TARGETS_UP.html Genes up-regulated in MCF7 cells (breast cancer) engineered to conditionally express LMO4 [GeneID=8543] by a Tet Off system. 17452977 475/584 Arthur Liberzon 0.68618940391 0.690284310838704 4300 3676.27272727273 3880 0.1 1119 1.00083059344151 -0.98931928724457 -1 0.241636507857827 4300 3606 3880 3428 4533 4275 3981 4713 1119 3634 2970 4432 M1156 KONG_E2F1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KONG_E2F1_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblast) at 16 h after serum stimulation and knockdown of E2F1 [GeneID=1869] by RNAi. 16909124 15/22 Arthur Liberzon 0.579170230734064 0.646566577356855 3900 3441.27272727273 3880 0.0756682744362557 1856 1.39633520383793 -1.24392420763013 -1 0.396702780116189 3896 4602 1856 3997 3880 3270 2427 2582 4342 2788 4214 4433 M7721 BIOCARTA_EIF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_EIF_PATHWAY.html Eukaryotic protein translation 21/40 BioCarta 0.418422589767542 0.489213431682635 1350 3322.63636363636 3881 0.0480794893863192 1348 0.656692051857193 0.757284765135751 1 0.305856142818654 1348 3881 3935 4104 3497 2265 1836 4056 4287 4498 2842 4434 M2478 FU_INTERACT_WITH_ALKBH8 http://www.broadinstitute.org/gsea/msigdb/cards/FU_INTERACT_WITH_ALKBH8.html Proteins identified by mass spectrometry in complexes containing ALKBH8 [GeneID=91801]. 20308323 15/18 Arthur Liberzon 0.68618940391 0.690284310838704 3345 3885.36363636364 3882 0.1 3154 0.975750328799779 0.975750328799779 1 0.235578577783869 3343 3909 3882 3875 3154 4095 3582 3858 4244 4719 4078 4435 M11675 KEGG_HOMOLOGOUS_RECOMBINATION http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_HOMOLOGOUS_RECOMBINATION.html Homologous recombination 27/27 KEGG 0.451322829025478 0.519952099829206 2870 3485.72727272727 3884 0.0531056274549934 1640 0.646390565900991 -0.642835775103537 -1 0.275387585758898 2870 4190 3907 4090 3041 1640 2631 3884 4368 4488 3234 4436 M669 REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DOWNREGULATION_OF_SMAD2_3_SMAD4_TRANSCRIPTIONAL_ACTIVITY.html Genes involved in Downregulation of SMAD2/3:SMAD4 transcriptional activity 28/39 Reactome 0.033315722085042 0.0572026948859216 1260 2803.63636363636 3885 0.00307556376208535 545 0.791077718263098 -0.934714582234924 -1 1.47487558212818 1256 4176 3904 4442 1714 636 545 3885 4274 4204 1804 4437 M2148 SHEPARD_CRUSH_AND_BURN_MUTANT_DN http://www.broadinstitute.org/gsea/msigdb/cards/SHEPARD_CRUSH_AND_BURN_MUTANT_DN.html Human orthologs of genes down-regulated in the crb ('crash and burn') zebrafish mutant that represents a loss-of-function mutation in BMYB [GeneID=4605]. 16150706 255/352 Jennifer Shepard 0.68618940391 0.690284310838704 4460 3574.45454545455 3885 0.1 1790 1.35643072051167 -1.36052828409573 -1 0.327528771550203 4458 4334 2061 4257 3885 4292 3803 4040 1790 2843 3556 4438 M1058 REACTOME_ADAPTIVE_IMMUNE_SYSTEM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADAPTIVE_IMMUNE_SYSTEM.html Genes involved in Adaptive Immune System 520/690 Reactome 0.6513215599 0.690284310838704 4295 3237.27272727273 3886 0.1 891 0.939053444192609 -0.887753008084122 -1 0.226714749428864 4295 1143 4261 891 4611 3013 3927 3886 2319 4286 2978 4439 M2257 SONG_TARGETS_OF_IE86_CMV_PROTEIN http://www.broadinstitute.org/gsea/msigdb/cards/SONG_TARGETS_OF_IE86_CMV_PROTEIN.html Cellular genes up-regulated in forskin fibroblasts by expression of CMV EI86 protein off an adenovirus vector. 11867723 71/80 John Newman 0.68618940391 0.690284310838704 2235 3586.90909090909 3890 0.1 1900 1.02198599575533 -1.01561461432645 -1 0.246746419963395 2235 4078 3895 4323 3931 3653 3545 4459 1900 3890 3547 4440 M5588 HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOFFMANN_LARGE_TO_SMALL_PRE_BII_LYMPHOCYTE_UP.html Genes up-regulated during differentiation from large pre-BII to small pre-BII lymphocyte. 11779835 223/286 Arthur Liberzon 0.68618940391 0.690284310838704 3305 3909.27272727273 3890 0.1 3078 0.947576239278309 0.931161703604187 1 0.228773359949981 3301 4342 3890 4165 4276 3844 3456 4636 3078 4189 3825 4441 M18667 DITTMER_PTHLH_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/DITTMER_PTHLH_TARGETS_DN.html Genes down-regulated in MDA-MB-231 cells (breast cancer) after knockdown of PTHLH [GeneID=5744] by RNAi. 16551631 117/141 Leona Saunders 0.331921931042908 0.397632364092011 3800 3766.72727272727 3894 0.0360040675885833 2546 0.942041811414853 -0.849291780010706 -1 0.56604783842035 3796 4037 3156 3894 2546 4616 4335 3066 4267 3670 4051 4442 M13404 BIOCARTA_VDR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VDR_PATHWAY.html Control of Gene Expression by Vitamin D Receptor 15/17 BioCarta 0.335935197884897 0.401988114345051 3990 3724.18181818182 3895 0.0365319559898161 1746 0.568696405968299 -0.644746261052403 -1 0.337635016155908 3987 3895 3868 3833 2552 4357 4077 3854 1746 4496 4301 4443 M1150 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_SMAD4_UP.html Apoptotic genes dependent on SMAD4 [GeneID=4089] and up-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 7/7 Arthur Liberzon 0.6513215599 0.690284310838704 3545 3676.45454545455 3895 0.1 2474 0.778200167764535 0.722049659535645 1 0.187861973563526 3544 3126 4352 3050 3182 4458 4039 3926 4395 2474 3895 4444 M2431 KAUFFMANN_MELANOMA_RELAPSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KAUFFMANN_MELANOMA_RELAPSE_UP.html DNA repair and replication genes up-regulated in melanoma patients who will relapse vs patients who will not. 17891185 69/74 Jessica Robertson 0.68618940391 0.690284310838704 4090 3893 3896 0.1 2874 0.655533917364968 -0.664926079580098 -1 0.158232957364115 2874 4089 4090 4163 4491 3585 3654 3896 3834 4402 3745 4445 M599 ST_PAC1_RECEPTOR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/ST_PAC1_RECEPTOR_PATHWAY.html PAC1 Receptor Pathway 6/9 Signaling Transduction KE 0.000305912946552038 0.00161511085875349 4690 3305 3898 3.05955066941767e-05 243 0.44611190305066 -0.453603399821149 -1 1.86872314678039 4688 1642 4202 2116 243 3898 2411 3676 4555 4509 4415 4446 M15555 CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHNG_MULTIPLE_MYELOMA_HYPERPLOID_UP.html Protein biosynthesis, transport or catabolism genes up-regulated in hyperploid multiple myeloma (MM) compared to the non-hyperploid MM samples. 17409404 63/115 Jessica Robertson 0.278934552378925 0.342857053965761 1180 3176.81818181818 3898 0.0292920024150923 1176 0.717276716819355 -0.87522717308683 -1 0.500246426302689 1176 4451 4109 4164 2510 1635 1555 3898 4376 4349 2722 4447 M7507 CHOI_ATL_STAGE_PREDICTOR http://www.broadinstitute.org/gsea/msigdb/cards/CHOI_ATL_STAGE_PREDICTOR.html Genes used to predict the clinical stages of acute T-cell leukemia (ATL): chronic vs acute. 16909099 86/133 Leona Saunders 0.68618940391 0.690284310838704 2740 3826.54545454545 3900 0.1 2738 0.835044174185273 0.895082817686025 1 0.201592172225288 2738 4409 4041 4634 3581 3900 3124 4237 3835 4003 3590 4448 M13881 REACTOME_SIGNALLING_TO_ERKS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNALLING_TO_ERKS.html Genes involved in Signalling to ERKs 43/46 Reactome 0.68618940391 0.690284310838704 3050 3577.72727272727 3903 0.1 1905 0.72565957022586 -0.737636702363836 -1 0.175171227653144 3048 3361 3855 3903 4290 3919 2759 4086 1905 3936 4293 4449 M15356 PUJANA_BREAST_CANCER_LIT_INT_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BREAST_CANCER_LIT_INT_NETWORK.html Genes constituting the LIT-Int network of proteins interacting with breast cancer reference proteins BRCA1, BRCA2, ATM, and CHEK2 [GeneID=672;675;472;11200]; the interactions were manually curated from the literature. 17922014 130/143 Leona Saunders 0.68618940391 0.690284310838704 3905 3438.81818181818 3903 0.1 1540 0.877129863840248 -0.8709602416945 -1 0.211757621780393 4127 2323 3903 2488 3728 4098 3903 4066 1540 3994 3657 4450 M19256 SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_UP.html Genes up-regulated in pleura relapse of breast cancer. 18451135 9/11 Jessica Robertson 0.6513215599 0.690284310838704 4360 3790.45454545455 3903 0.1 2759 1.72824296770969 -1.12787952227744 -1 0.417336938503097 4360 3943 4550 3713 3611 3903 2761 3512 4008 2759 4575 4451 M2427 NAKAMURA_CANCER_MICROENVIRONMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/NAKAMURA_CANCER_MICROENVIRONMENT_DN.html Genes down-regulated in pancreatic cancer cells grown in orthotopic xenograft tumors compared to those grown in vitro. 17210693 54/56 Arthur Liberzon 0.68618940391 0.690284310838704 4660 3767 3906 0.1 1770 0.875322049713459 0.906592245392857 1 0.211320959260151 4658 3315 3609 3571 3709 4258 3966 3906 1770 4137 4538 4452 M18000 GOERING_BLOOD_HDL_CHOLESTEROL_QTL_TRANS http://www.broadinstitute.org/gsea/msigdb/cards/GOERING_BLOOD_HDL_CHOLESTEROL_QTL_TRANS.html Top scoring trans-regulated expression quantitative trait loci (eQTL) influencing blood levels of high-density lipoprotein (HDL) cholesterol. 17873875 13/31 Leona Saunders 0.153534127179228 0.206514634856169 2870 3475.54545454545 3906 0.0150389853439489 1536 1.05600868239537 0.968264698815142 1 1.08539720050296 4591 3906 2869 2868 4199 4329 4543 1638 1536 3219 4533 4453 M2106 KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_DN.html Genes whose expression was significantly and negatively correlated with the number of perineuronal oligodendrocytes in the layer III of BA9 brain region. 18762803 55/111 Jessica Robertson 0.639930077646135 0.690284310838704 3055 3760.54545454545 3906 0.0886786782592069 2923 1.12755245538758 1.08120116681745 1 0.272245123415811 3051 4446 2923 4409 3043 3906 3341 4398 3963 3357 4529 4454 M5570 HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_DN.html Genes down-regulated in lesional skin biopsies from mycosis fundoides patients compared to the normal skin samples. 16914566 33/50 Arthur Liberzon 0.68618940391 0.690284310838704 3585 3907.72727272727 3907 0.1 3198 1.07933229111123 -1.30165621204213 -1 0.260597942354776 3584 4503 3367 4436 3222 4585 4328 3383 4472 3907 3198 4455 M5792 LI_AMPLIFIED_IN_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LI_AMPLIFIED_IN_LUNG_CANCER.html Genes with increased copy number that correlates with increased expression across six different lung adenocarcinoma cell lines. 16369491 260/356 Arthur Liberzon 0.17806867220189 0.234118142839253 3335 3500.18181818182 3907 0.0176691668092021 1317 1.2195719712511 -1.16413908659451 -1 1.15382308662003 3332 3991 1317 3907 2742 4358 4422 4472 3192 2083 4686 4456 M4324 LOPEZ_MBD_TARGETS_IMPRINTED_AND_X_LINKED http://www.broadinstitute.org/gsea/msigdb/cards/LOPEZ_MBD_TARGETS_IMPRINTED_AND_X_LINKED.html X chromosome and imprinted genes up-regulated in HeLa cells (cervical cancer) after knockdown of the MBD (methyl-CpG binding domain) proteins by RNAi. 18223687 25/54 Jessica Robertson 0.126140169923694 0.1753701331487 2950 3696.45454545455 3907 0.0121829337257049 1539 0.737698504173179 -1.09284399226828 -1 0.836783431116437 2949 4198 3308 4461 3907 4716 3399 1539 4649 4165 3370 4457 M4383 BIOCARTA_NO1_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_NO1_PATHWAY.html Actions of Nitric Oxide in the Heart 37/50 BioCarta 0.0687166657603791 0.105340260600516 4140 3508.90909090909 3908 0.00645107595435775 1132 1.20973040632201 -1.43077525872588 -1 1.77410503175833 4532 4140 1132 4432 3908 3150 4157 3208 4140 2313 3486 4458 M1284 SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6 http://www.broadinstitute.org/gsea/msigdb/cards/SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM6.html Cluster PAM6: genes changed exclusively in normal liver tissue adjacent to hepatocellular carcinoma (HCC) from mice deficient for TXNIP [GeneID=10628]. 16607285 50/57 Leona Saunders 0.68618940391 0.690284310838704 3585 3821.63636363636 3910 0.1 3020 0.908825671301017 0.872161412331282 1 0.219413481396624 3582 4111 3020 4210 4389 3179 3160 4184 3910 3719 4574 4459 M9379 REACTOME_SIGNAL_AMPLIFICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SIGNAL_AMPLIFICATION.html Genes involved in Signal amplification 28/36 Reactome 0.68618940391 0.690284310838704 4470 3532.45454545455 3911 0.1 1478 0.799701565352938 -0.748422789706377 -1 0.193055457960266 4467 1478 2934 2110 4183 4536 3744 4220 3937 3337 3911 4460 M1239 JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_UP http://www.broadinstitute.org/gsea/msigdb/cards/JOHANSSON_BRAIN_CANCER_EARLY_VS_LATE_UP.html Genes up-regulated in early vs late brain tumors induced by retroviral delivery of PDGFB [GeneID=5155]. 15750623 15/20 Leona Saunders 0.367972331926228 0.436389298163768 4420 3570.63636363636 3911 0.0408531625563179 2213 1.27553506709323 -1.12397649364366 -1 0.689162904735983 4419 3911 2475 4384 3301 3949 2803 2213 3955 3406 4461 4461 M6171 TANG_SENESCENCE_TP53_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/TANG_SENESCENCE_TP53_TARGETS_DN.html Genes down-regulated in WI-38 cells (senescent primary fibroblasts) after inactivation of TP53 [GeneID=7157] by GSE56 polypeptide. 17533371 65/94 Leona Saunders 0.68618940391 0.690284310838704 3580 3907.81818181818 3912 0.1 2983 1.11875928526911 -1.00083611610814 -1 0.270121206046235 3578 4093 3770 4126 4710 4136 3879 3970 2983 3912 3829 4462 M1441 REACTOME_P38MAPK_EVENTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_P38MAPK_EVENTS.html Genes involved in p38MAPK events 15/15 Reactome 0.68618940391 0.690284310838704 4580 3708.54545454545 3914 0.1 1756 0.67212500223019 -0.674150723349016 -1 0.162240396416309 4578 3082 3627 2971 4281 4337 4108 4406 1756 3914 3734 4463 M14954 KIM_RESPONSE_TO_TSA_AND_DECITABINE_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_RESPONSE_TO_TSA_AND_DECITABINE_DN.html Genes down-regulated in glioma cell lines treated with both decitabine [PubChem=451668] and TSA [PubChem=5562]. 16885346 13/19 Arthur Liberzon 0.138020488329382 0.188773313507587 2025 3644.09090909091 3916 0.0134114162374541 2022 0.540365987341026 0.584318356157077 1 0.586983262597154 3502 3916 3535 4032 2022 4447 4450 2024 4693 4626 2838 4464 M5040 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_WS http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_4NQO_IN_WS.html Human environmental stress response genes not changed in primary fibroblasts from Wilmor syndrom (WS) patients in response to 4NQO treatment. 15897889 54/61 Jessica Robertson 0.558088984587398 0.625547377642489 3785 3766.81818181818 3917 0.0715517294878388 2543 1.02562305190344 1.20883094527906 1 0.313443187170647 3785 3329 2740 4580 4460 3917 3976 2543 4318 3299 4488 4465 M10688 PAL_PRMT5_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/PAL_PRMT5_TARGETS_UP.html Genes up-regulated in NIH-3T3 cells (fibroblast) after knockdown of PRMT5 [GeneID=10419] by RNAi. 15485929 279/323 John Newman 0.68618940391 0.690284310838704 3715 3820.90909090909 3918 0.1 2838 0.957398739184793 -0.826456988579562 -1 0.231145903399381 3713 4332 4070 3918 4168 2838 3439 4682 3116 4135 3619 4466 M975 REACTOME_ADVANCED_GLYCOSYLATION_ENDPRODUCT_RECEPTOR_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ADVANCED_GLYCOSYLATION_ENDPRODUCT_RECEPTOR_SIGNALING.html Genes involved in Advanced glycosylation endproduct receptor signaling 12/16 Reactome 0.0715890960475701 0.108754597149833 4320 3073.72727272727 3920 0.00673005647775664 287 1.68741541349183 -0.628953952833833 -1 2.43960945549835 4320 3920 2171 3977 1672 4230 4444 2195 287 2454 4141 4467 M6451 ODONNELL_TFRC_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ODONNELL_TFRC_TARGETS_DN.html Genes down-regulated in P493-6 cells (B lymphocyte, Burkitt's lymphoma model) upon knockdown of TFRC [GeneID=7037] by RNAi. 16508012 145/184 Leona Saunders 0.68618940391 0.690284310838704 4525 3849.27272727273 3922 0.1 2261 1.23245552983111 1.24323485808428 1 0.297583591673633 4524 4365 3305 4286 3832 3112 4432 3771 2261 3922 4532 4468 M15164 FAELT_B_CLL_WITH_VH3_21_UP http://www.broadinstitute.org/gsea/msigdb/cards/FAELT_B_CLL_WITH_VH3_21_UP.html Genes up-regulated in samples from B-CLL (B-cell chronic lymphocytic leukemia) with the immunoglobulin heavy chain VH3-21 gene. 15817677 63/70 Kevin Vogelsang 0.68618940391 0.690284310838704 3945 3442.36363636364 3922 0.1 1367 0.791547231460365 -0.728880804890294 -1 0.191085846186763 3922 1908 3942 3430 3804 4289 3945 2800 1367 4229 4230 4469 M734 REACTOME_RNA_POL_II_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_II_TRANSCRIPTION.html Genes involved in RNA Polymerase II Transcription 114/152 Reactome 0.0997367563949767 0.143830580563486 3870 3785.81818181818 3929 0.00950617027821949 1829 0.559477994928884 -0.576597856896594 -1 0.706884764869677 3870 4384 4171 4531 1829 2781 3846 3945 3929 4543 3815 4470 M1452 NEMETH_INFLAMMATORY_RESPONSE_LPS_DN http://www.broadinstitute.org/gsea/msigdb/cards/NEMETH_INFLAMMATORY_RESPONSE_LPS_DN.html Genes down-regulated in RAW 264.7 cells (macrophage) 3 hr after stimulation with bacterial lipopolysaccharide (LPS). 12766259 43/60 Kevin Vogelsang 0.0848908399855465 0.125926261892128 4345 2593 3931 0.00803228741431824 211 1.3160304095823 1.01018954003081 1 1.77692152507911 4342 211 1227 334 4341 4608 4167 4093 339 930 3931 4471 M14808 SESTO_RESPONSE_TO_UV_C7 http://www.broadinstitute.org/gsea/msigdb/cards/SESTO_RESPONSE_TO_UV_C7.html Cluster 7: genes changed in primary keratinocytes by UVB irradiation. 11867738 86/113 John Newman 0.68618940391 0.690284310838704 3905 3788 3931 0.1 2161 1.14743976844599 -1.11125627778905 -1 0.2770487390709 3901 4397 2161 4002 4503 3931 3729 4705 4249 2288 3802 4472 M12812 GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_DN.html Genes down-regulated in common hematopoietic progenitor cells isolated from bone marrow of patients with Diamond-Blackfan anemia (DBA) and mutated RPS19 [GeneID=6223]. 16741228 92/122 Arthur Liberzon 0.68618940391 0.690284310838704 3935 3979.36363636364 3932 0.1 2937 0.908315110144356 -0.8496277953094 -1 0.219290159580458 3932 4389 3916 4280 3327 3745 4634 3880 2937 4175 4558 4473 M7160 JAZAG_TGFB1_SIGNALING_UP http://www.broadinstitute.org/gsea/msigdb/cards/JAZAG_TGFB1_SIGNALING_UP.html Genes up-regulated in PANC-1-puro cells (pancreatic cancer) stimulated by TGF1B [GeneID=7040] for 2 h. 15592526 160/228 Leona Saunders 0.225406176571869 0.285922373936904 3085 3696.54545454545 3932 0.0229521781867389 1884 0.929015527060799 1.06843748981892 1 0.757887766927803 3084 4720 3419 4627 3179 3985 4198 1884 4105 3932 3529 4474 M2534 PECE_MAMMARY_STEM_CELL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PECE_MAMMARY_STEM_CELL_UP.html The '3/3 signature': genes consistently up-regulated in all three pools of normal mammary stem cells (defined by their ability to retain the dye PKH26). 20074520 188/297 Arthur Liberzon 0.283298916063868 0.347136781885113 4310 3689.90909090909 3933 0.0298276016830145 2035 1.06167723028392 -1.18389954219535 -1 0.731907905540983 4308 4349 2710 4131 4407 3741 4329 2035 3933 3333 3313 4475 M9746 SU_TESTIS http://www.broadinstitute.org/gsea/msigdb/cards/SU_TESTIS.html Genes up-regulated specifically in human testis tissue. 11904358 79/176 John Newman 0.625585825324099 0.690284310838704 3230 3629.09090909091 3936 0.0854365441951935 2539 0.804375212840022 0.768117230415863 1 0.194184338778373 3229 4059 3936 3859 4361 2743 4065 2658 2539 4272 4199 4476 M15377 CREIGHTON_AKT1_SIGNALING_VIA_MTOR_DN http://www.broadinstitute.org/gsea/msigdb/cards/CREIGHTON_AKT1_SIGNALING_VIA_MTOR_DN.html Genes in the AKT1 [GeneID=207] pathway which depend on MTOR [GeneID=2475], sensitive to RAD001 (everolimus) [PubChem=6442177]. 17213801 38/43 Arthur Liberzon 0.024024768602892 0.0439863878222073 4210 3413.54545454545 3940 0.00220829181514403 811 1.04583174529908 0.9521237790736 1 2.12892326432688 4209 4488 3432 4269 1213 4644 3940 3328 811 2744 4471 4477 M7813 PETRETTO_BLOOD_PRESSURE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PETRETTO_BLOOD_PRESSURE_DN.html Genes that are most strongly negatively correlated with systolic blood pressure (SBP). 18443592 10/14 Jessica Robertson 0.68618940391 0.690284310838704 3580 3915.63636363636 3940 0.1 2719 0.595090330767975 0.595090330767975 1 0.143633309941948 3580 4618 3768 4243 3415 4025 4414 3686 3940 4664 2719 4478 M580 REACTOME_ASSOCIATION_OF_LICENSING_FACTORS_WITH_THE_PRE_REPLICATIVE_COMPLEX http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ASSOCIATION_OF_LICENSING_FACTORS_WITH_THE_PRE_REPLICATIVE_COMPLEX.html Genes involved in Association of licensing factors with the pre-replicative complex 16/19 Reactome 0.686414893435339 0.690364009591903 3695 3764.72727272727 3941 0.100058809905514 2494 1.23159250987085 -1.23159250987085 -1 0.29728247650007 3694 4260 3618 4123 4305 3153 2494 2749 4679 3941 4396 4479 M4072 REACTOME_OLFACTORY_SIGNALING_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_OLFACTORY_SIGNALING_PATHWAY.html Genes involved in Olfactory Signaling Pathway 7/764 Reactome 0.0210033257297009 0.0393708091517825 3775 3927.72727272727 3941 0.00212045201104983 1199 0.220134868142303 0.24060660411176 1 0.463931671133854 3775 4649 4232 4471 1199 3859 3939 3869 4720 4551 3941 4480 M11594 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_22 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_22.html Amplification hot spot 22: colocolized fragile sites and cancer genes in the 22q11.1-q13s region. 16751803 16/25 Arthur Liberzon 0.664752565618942 0.690284310838704 4250 3725.90909090909 3944 0.0945772433837917 2432 0.627069539825426 -0.621991527073506 -1 0.151357622865195 4249 3505 3074 3747 4615 4072 4029 2719 4599 3944 2432 4481 M1875 JU_AGING_TERC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/JU_AGING_TERC_TARGETS_UP.html Cytokines, growth factors, and secreted proteins that show increased expression on a protein array of samples from aged TERC [GeneID=7012] knockout mice. 17486088 9/12 Jessica Robertson 0.105588701389207 0.151039204473101 3350 3683.09090909091 3944 0.0110969242179887 1904 2.25878631120482 -2.80046009529594 -1 2.78224997373498 3349 3944 4592 3989 1904 4269 3677 3717 3991 2763 4319 4482 M17700 BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP http://www.broadinstitute.org/gsea/msigdb/cards/BANDRES_RESPONSE_TO_CARMUSTIN_WITHOUT_MGMT_48HR_UP.html Genes up-regulated in A172 cells (glioma, does not express MGMT [GeneID=4255]) by carmustine [PubChem=2578] at 48 h. 15980968 16/24 John Newman 0.68618940391 0.690284310838704 4415 3989.09090909091 3946 0.1 3278 0.670930069631614 -0.541302462582252 -1 0.16195177035001 4415 3520 3278 3981 3916 4399 4603 3742 4263 3946 3817 4483 M7854 WHITEFORD_PEDIATRIC_CANCER_MARKERS http://www.broadinstitute.org/gsea/msigdb/cards/WHITEFORD_PEDIATRIC_CANCER_MARKERS.html Differentially expressed genes in a panel of xenografts representing 8 common pediatric tumors compared to the normal tissues. 17210681 148/222 Jessica Robertson 0.68618940391 0.690284310838704 4025 3657.09090909091 3946 0.1 2487 0.936452874068862 -1.00249075822967 -1 0.226086603267445 2487 4023 4025 4342 4210 3345 3030 3946 2897 4337 3586 4484 M19907 KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_DN.html Genes down-regulated in HL-60 cells (acute promyelocytic leukemia, APL) after treatment with the aminopeptidase inhibitor tosedostat (CHR-2797) [PubChem=15547703] for 6 h. 18701491 1042/1244 Jessica Robertson 0.232703459546752 0.293388261853139 4385 3630.90909090909 3948 0.0261404577301939 1918 0.977228458190627 -0.891831816041874 -1 0.780810005423067 4382 3596 4502 3660 2381 3259 3995 3948 1918 4278 4021 4485 M2249 BRUINS_UVC_RESPONSE_MIDDLE http://www.broadinstitute.org/gsea/msigdb/cards/BRUINS_UVC_RESPONSE_MIDDLE.html Middle response genes: differentially expressed in the period between 3 h and 12 h after UV-C irradiation of MEF cells (embryonic fibroblast). 18195040 119/136 Arthur Liberzon 0.255018128164463 0.31734394013611 2580 3466.81818181818 3948 0.0264082564123568 1965 0.85484134507587 0.967089359256467 1 0.639284659305358 2577 4373 3959 4611 2628 4454 3948 1965 2020 4200 3400 4486 M14781 REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_LATE_PHASE_OF_HIV_LIFE_CYCLE.html Genes involved in Late Phase of HIV Life Cycle 110/125 Reactome 0.12269977875728 0.171394778258172 3545 3741.36363636364 3949 0.01183001561485 1937 0.611308912100494 -0.608460244843644 -1 0.702533854967734 3541 4381 4159 4519 1937 3385 3998 3172 3949 4604 3510 4487 M15434 REACTOME_DNA_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DNA_REPAIR.html Genes involved in DNA Repair 114/127 Reactome 0.68618940391 0.690284310838704 4385 3607.54545454545 3950 0.1 2133 0.772555817139997 -0.810101440706142 -1 0.186498627447175 2133 4383 4132 4524 3976 2172 3714 3950 3851 4385 2463 4488 M13715 LANDIS_ERBB2_BREAST_TUMORS_65_DN http://www.broadinstitute.org/gsea/msigdb/cards/LANDIS_ERBB2_BREAST_TUMORS_65_DN.html Down-regulated genes from the 65 most significantly changed (p<0.01) genes identified by two analytical methods in the mammary tumors induced by transgenic expression of ERBB2 [GeneID=2064]. 15897883 49/55 Leona Saunders 0.00462548731322562 0.012532893294159 4590 3076.27272727273 3951 0.000421385554173684 693 1.2827167460866 -1.27367538862496 -1 3.66065505478482 4589 4113 938 3951 693 4322 4313 3158 4013 826 2923 4489 M6564 HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP http://www.broadinstitute.org/gsea/msigdb/cards/HAHTOLA_MYCOSIS_FUNGOIDES_SKIN_UP.html Genes up-regulated in lesional skin biopsies from mycosis fundoides patients compared to the normal skin samples. 16914566 217/264 Arthur Liberzon 0.469791037635701 0.53977938111989 2150 3650.45454545455 3952 0.0560483865113734 2149 0.904730476209766 1.01582357055314 1 0.36342829424885 2149 4701 3719 4658 2761 4029 2710 3952 4338 4149 2989 4490 M19957 FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP http://www.broadinstitute.org/gsea/msigdb/cards/FERREIRA_EWINGS_SARCOMA_UNSTABLE_VS_STABLE_UP.html Genes up-regulated in genomically unstable Ewing's sarcoma tumors compared to the stable ones. 17952124 245/318 Jessica Robertson 0.68618940391 0.690284310838704 4710 3893.45454545455 3954 0.1 2028 1.00595806402531 1.02864694163903 1 0.242875005883931 3481 4336 3954 4305 4707 3856 3623 3499 2028 4333 4706 4491 M19443 GUTIERREZ_MULTIPLE_MYELOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/GUTIERREZ_MULTIPLE_MYELOMA_UP.html Genes exclusively up-regulated in plasma cells from MM (multiple myeloma) patients but with a similiar expression pattern in the normal cells and in the cells from WM (Waldenstroem's macroblobulinemia) patients. 17252022 43/48 Arthur Liberzon 0.00734234892198476 0.017102237254964 4305 3393.54545454545 3955 0.000669724419776513 811 0.786703904888462 0.817534132578544 1 2.08571334447136 4302 2934 3955 2774 811 4476 4357 4703 1007 3732 4278 4492 M18501 DANG_REGULATED_BY_MYC_UP http://www.broadinstitute.org/gsea/msigdb/cards/DANG_REGULATED_BY_MYC_UP.html Genes up-regulated by MYC [GeneID=4609], according to the MYC Target Gene Database. 14519204 97/109 Chi Dang 0.129472420173301 0.179001119864669 3070 3663.18181818182 3955 0.0125259649170778 1977 0.765230604286656 0.850064178206174 1 0.857797986394389 3069 4388 4031 4300 1977 4242 3566 3339 3277 4151 3955 4493 M12458 KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_ENVIRONMENTAL_STRESS_RESPONSE_NOT_BY_GAMMA_IN_WS.html Human environmental stress response genes not changed in primary fibroblasts from Werner syndrom (WS) patients in response to gamma radiation. 15897889 43/47 Jessica Robertson 0.011272419622105 0.023925789237578 3990 3211 3956 0.00103005411785488 847 0.817005826468204 -0.594134845328182 -1 1.98729654187663 3986 847 2948 2894 955 3056 4008 4551 3956 4121 3999 4494 M2331 BILANGES_RAPAMYCIN_SENSITIVE_VIA_TSC1_AND_TSC2 http://www.broadinstitute.org/gsea/msigdb/cards/BILANGES_RAPAMYCIN_SENSITIVE_VIA_TSC1_AND_TSC2.html Genes translationally repressed by rapamycin (sirolimus) [PubChem=6610346] in MEF cells (embryonic fibroblast) lacking either TSC1 or TSC2 [GeneID=7248, 7249] but not in the wild type cells. 17562867 105/145 Arthur Liberzon 0.68618940391 0.690284310838704 3005 3874.45454545455 3958 0.1 3005 0.953701436819133 0.959696681386734 1 0.230252850653989 3005 3672 3750 3698 4072 3962 3638 4183 4194 3958 4487 4495 M1945 ISHIDA_E2F_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/ISHIDA_E2F_TARGETS.html Genes up-regulated in MEF cells (embryonic fibroblast) after expression of E2F1 or E2F2 [GeneID=1869;1870]. 11416145 57/63 Arthur Liberzon 0.68618940391 0.690284310838704 2435 3601.18181818182 3959 0.1 1736 0.94752450085778 1.14526958309815 1 0.228760862963279 2433 2893 3876 2989 4404 4362 4030 4670 1736 4261 3959 4496 M18184 REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_RIBONUCLEOPROTEINS_INTO_THE_HOST_NUCLEUS.html Genes involved in Transport of Ribonucleoproteins into the Host Nucleus 31/33 Reactome 0.68618940391 0.690284310838704 4655 3845.54545454545 3960 0.1 2382 0.668848315380046 -0.647058111900683 -1 0.16144893986288 4654 3430 3960 3634 4374 3837 4453 2840 2382 4599 4138 4497 M864 REACTOME_MITOTIC_G2_G2_M_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MITOTIC_G2_G2_M_PHASES.html Genes involved in Mitotic G2-G2/M phases 105/128 Reactome 0.68618940391 0.690284310838704 3900 3899.45454545455 3961 0.1 2589 0.941679244286279 -1.21653607312679 -1 0.227348989680428 3898 4387 3920 4680 3299 3961 3369 4306 2589 4152 4333 4498 M11891 MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP http://www.broadinstitute.org/gsea/msigdb/cards/MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP.html The postradiation tumor escape signature: genes up-regulated in tumors from irradiated stroma vs those from non-irradiated stroma. 18794119 499/559 Jessica Robertson 0.68618940391 0.690284310838704 3540 3772.27272727273 3961 0.1 2556 1.0102644388971 -0.995408782700028 -1 0.243915175045551 3538 3967 3961 4312 3458 4113 3842 4256 2556 3430 4062 4499 M1107 GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN.html Genes down-regulated in ME-A cells (breast cancer, sensitive to apoptotic stimuli) exposed to doxorubicin [PubChem=31703] in the presence of medium concentrate (MC) from ME-C cells (breast cancer, resistant to apoptotic stimuli). 17160024 1007/1118 Arthur Liberzon 0.137979388072683 0.188771800493641 4620 3615.18181818182 3962 0.0147379274395984 1986 0.885166008171078 -0.814701051961661 -1 0.961601268905697 4618 3962 4340 3263 2071 2740 4442 4690 1986 4462 3193 4500 M1581 RUAN_RESPONSE_TO_TNF_TROGLITAZONE_UP http://www.broadinstitute.org/gsea/msigdb/cards/RUAN_RESPONSE_TO_TNF_TROGLITAZONE_UP.html Adipocyte abundant genes up-regulated in 3T3-L1 cells (fibroblasts induced to differentiate to adipocytes) in response to troglitazone [PubChem=5591] and TNF [GeneID=7124]. 12732648 32/42 John Newman 0.0164623520600635 0.0324941630478106 4170 3521.90909090909 3962 0.00150789492167523 1077 1.04627564625636 -0.975358002221749 -1 2.33629667207485 4170 3395 1723 3962 1077 4533 2939 4296 4425 3878 4343 4501 M725 REACTOME_TRANSPORT_OF_MATURE_TRANSCRIPT_TO_CYTOPLASM http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_MATURE_TRANSCRIPT_TO_CYTOPLASM.html Genes involved in Transport of Mature Transcript to Cytoplasm 63/92 Reactome 0.580518416954631 0.647306148836725 3260 3738.27272727273 3964 0.0759378694490441 2557 0.610191013149632 -0.661652665056848 -1 0.172842830583361 3259 4441 4123 4500 2957 3342 2557 3964 3111 4538 4329 4502 M13072 SMID_BREAST_CANCER_LUMINAL_A_DN http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_LUMINAL_A_DN.html Genes down-regulated in the luminal A subtype of breast cancer. 18451135 23/24 Jessica Robertson 0.68618940391 0.690284310838704 3965 4007.90909090909 3964 0.1 3226 1.44343038467864 1.77498105005911 1 0.348542819428491 3376 4550 3226 4472 3961 4305 3743 4277 3964 3868 4345 4503 M10973 MATTIOLI_MGUS_VS_PCL http://www.broadinstitute.org/gsea/msigdb/cards/MATTIOLI_MGUS_VS_PCL.html Genes changed in MGUS (monoclonal gammopathy of undetermined significance) compared to PCL (plasma cell leukemia) samples. 15735737 135/226 Leona Saunders 0.68618940391 0.690284310838704 3430 3574.72727272727 3966 0.1 988 0.9866994313936 1.04485193548531 1 0.238223242775785 3428 3213 3417 1927 4304 4464 4477 4450 988 3966 4688 4504 M12975 BIOCARTA_VEGF_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_VEGF_PATHWAY.html VEGF, Hypoxia, and Angiogenesis 40/64 BioCarta 0.68618940391 0.690284310838704 3145 3922 3967 0.1 3143 0.978157530253343 0.866641572437338 1 0.236160017345529 3143 3787 3220 4314 4217 4489 4120 3936 4352 3597 3967 4505 M11153 REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ACTIVATION_OF_ATR_IN_RESPONSE_TO_REPLICATION_STRESS.html Genes involved in Activation of ATR in response to replication stress 40/40 Reactome 0.635022260042058 0.690284310838704 2635 3814.54545454545 3967 0.0875563895046062 2631 0.66733426165536 -0.658475632619732 -1 0.161083232733255 2631 4143 3967 4333 3034 3600 4059 3458 4250 4607 3878 4506 M13492 REACTOME_DEADENYLATION_OF_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEADENYLATION_OF_MRNA.html Genes involved in Deadenylation of mRNA 25/27 Reactome 0.0284964468957019 0.0506107131215275 2220 3617.36363636364 3969 0.00262476316351058 1285 0.592537180805916 0.660938823619053 1 1.15197025568529 2218 4537 3969 4458 1285 3689 3889 3972 4166 4570 3038 4507 M10236 BORCZUK_MALIGNANT_MESOTHELIOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BORCZUK_MALIGNANT_MESOTHELIOMA_UP.html Genes up-regulated in biphasic (mixed) vs epithelial subtypes of malignant peritoneal mesothelioma. 16862182 420/473 Arthur Liberzon 0.68618940391 0.690284310838704 4410 3755 3971 0.1 1951 0.86438307310162 -0.839092183322621 -1 0.208678740115264 4442 3971 4154 1951 4263 3818 4408 3528 2584 4410 3776 4508 M1353 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX1_UP.html Early prostate development genes (up-regulated at 6 h dihydrotestosterone [PubChem=10635]) which are also up-regulated in normal epithelium vs high grade prostatic intraepithelial neoplasia (PIN). 18794802 27/30 Jessica Robertson 0.065867269719288 0.101532825955271 3975 3741.81818181818 3971 0.00617510440086214 1633 0.690883552708651 -0.617818294575086 -1 1.02972997824705 4482 4165 3539 3972 1633 3860 4678 3501 4175 3971 3184 4509 M3621 MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_DN http://www.broadinstitute.org/gsea/msigdb/cards/MORI_EMU_MYC_LYMPHOMA_BY_ONSET_TIME_DN.html Genes correlated with the late tumor onset in the Emu-myc transgenic mouse lymphoma model. 18922927 28/33 Jessica Robertson 0.68618940391 0.690284310838704 3705 3793.45454545455 3971 0.1 2642 1.00289289888367 1.10374492862824 1 0.242134640646226 3705 4182 2642 4099 4696 3872 3971 3410 2963 4205 3983 4510 M1236 OXFORD_RALA_OR_RALB_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/OXFORD_RALA_OR_RALB_TARGETS_DN.html Genes down-regulated after knockdown of RALA or RALB [GeneiD=5898;5899], which were also differentially expressed in bladder cancer compared to normal bladder urothelium tissue. 17496927 38/43 Arthur Liberzon 0.68618940391 0.690284310838704 2165 3665.72727272727 3973 0.1 2164 1.33266992630613 1.41429220064561 1 0.321789548625123 2164 4496 2326 4593 4656 4551 4061 3254 3973 3148 3101 4511 M1586 CHEN_ETV5_TARGETS_SERTOLI http://www.broadinstitute.org/gsea/msigdb/cards/CHEN_ETV5_TARGETS_SERTOLI.html Genes down-regulated in Sertoli cells from both 4 and 10 week old ETV5 [GeneID=2119] knockout mice. 16107850 18/29 John Newman 0.0465483100290545 0.0757875209855596 4580 3612.45454545455 3973 0.00432394482653113 1065 1.41250365583713 -1.60048346271112 -1 2.37457573284681 4158 4580 1065 4393 1681 3893 4666 3675 4579 3074 3973 4512 M17864 GENTILE_UV_LOW_DOSE_UP http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_LOW_DOSE_UP.html Selected genes up-regulated in WS1 (fibroblast) in response to irradiation with low dose UV-C. 12907719 41/54 John Newman 0.157151216740755 0.210605832770121 4285 3650.27272727273 3974 0.0154223580538135 2098 0.963225764396888 -1.03791704371278 -1 0.977709194588497 4284 3796 2548 4124 2098 4193 3974 4414 4562 3306 2854 4513 M3990 GENTILE_UV_RESPONSE_CLUSTER_D1 http://www.broadinstitute.org/gsea/msigdb/cards/GENTILE_UV_RESPONSE_CLUSTER_D1.html Cluster d1: genes down-regulated in WS1 cells (fibroblast) at 6 h after irradiation with high dose UV-C. 12907719 31/39 John Newman 0.68618940391 0.690284310838704 4475 3959.27272727273 3975 0.1 2812 0.800049758900619 0.84226634863848 1 0.193139561226089 4471 3429 3810 4306 4598 3934 3975 2812 4084 4240 3893 4514 M10142 KALMA_E2F1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/KALMA_E2F1_TARGETS.html DNA replication genes up-regulated in a Rat-1a cell line (fibroblast) by expression of E2F1 [GeneID=1869]. 11313881 12/13 John Newman 0.448191482178795 0.516840803506856 2675 3719.54545454545 3977 0.052615624002011 1910 0.628169809176214 0.672422006496743 1 0.27007872918943 2675 4610 3564 4401 4062 3216 1910 4249 3977 4683 3568 4515 M493 REACTOME_EXTRINSIC_PATHWAY_FOR_APOPTOSIS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_EXTRINSIC_PATHWAY_FOR_APOPTOSIS.html Genes involved in Extrinsic Pathway for Apoptosis 14/17 Reactome 0.68618940391 0.690284310838704 3980 3909.45454545455 3978 0.1 3145 0.914399401344781 -0.604423215160408 -1 0.22075976969695 3978 4601 3145 4377 3591 4595 3631 3146 4314 3310 4316 4516 M11063 REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_DECAY_BY_5_TO_3_EXORIBONUCLEASE.html Genes involved in mRNA Decay by 5' to 3' Exoribonuclease 13/14 Reactome 0.305458906808649 0.369494115873097 4235 3890.45454545455 3978 0.0325937157975941 2485 0.486681624241932 -0.486681624241932 -1 0.315659821078243 4235 3543 3861 3613 2485 4212 4342 4392 3563 4571 3978 4517 M19489 REACTOME_SOS_MEDIATED_SIGNALLING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_SOS_MEDIATED_SIGNALLING.html Genes involved in SOS-mediated signalling 19/20 Reactome 0.499930244709199 0.568869516641133 4455 3897.36363636364 3978 0.0610571818390636 2817 0.63363825959857 -0.43735358107194 -1 0.232824929706768 4452 4573 3807 4154 2817 3478 4484 3711 3978 4033 3384 4518 M1303 GROSS_HYPOXIA_VIA_ELK3_UP http://www.broadinstitute.org/gsea/msigdb/cards/GROSS_HYPOXIA_VIA_ELK3_UP.html Genes up-regulated in SEND cells (skin endothelium) at hypoxia with ELK3 [GeneID=2004] knockdown by RNAi. 17704799 314/372 Jessica Robertson 0.68618940391 0.690284310838704 3985 3009.09090909091 3982 0.1 537 1.02486399604802 1.0140761019494 1 0.247441577082948 3982 537 2392 892 4174 4243 4573 4297 1999 1900 4111 4519 M901 REACTOME_GLOBAL_GENOMIC_NER_GG_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GLOBAL_GENOMIC_NER_GG_NER.html Genes involved in Global Genomic NER (GG-NER) 33/34 Reactome 0.68618940391 0.690284310838704 2550 3656.09090909091 3983 0.1 2214 0.561043590003954 -0.550794179499174 -1 0.135409601869448 2549 4156 4006 4086 3589 2214 3197 4505 3983 4582 3350 4520 M7700 KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_UP http://www.broadinstitute.org/gsea/msigdb/cards/KUROKAWA_LIVER_CANCER_EARLY_RECURRENCE_UP.html Genes up-regulated in hepatocellular carcinoma (HCC) with early recurrence. 15288478 23/24 Yujin Hoshida 0.68618940391 0.690284310838704 3785 3661.54545454545 3984 0.1 2378 1.15240818072017 1.110633328931 1 0.278248817880495 3781 4558 2378 4426 4345 2697 3984 2997 4451 2499 4161 4521 M1029 REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTERACTIONS_OF_VPR_WITH_HOST_CELLULAR_PROTEINS.html Genes involved in Interactions of Vpr with host cellular proteins 36/39 Reactome 0.422952717610907 0.49414277899096 4630 3831.36363636364 3986 0.0487559671507108 2614 0.668848315380046 -0.647058111900683 -1 0.307150071146698 4629 3804 3986 4070 2707 3929 4288 3449 2614 4605 4064 4522 M17423 LAIHO_COLORECTAL_CANCER_SERRATED_DN http://www.broadinstitute.org/gsea/msigdb/cards/LAIHO_COLORECTAL_CANCER_SERRATED_DN.html Genes down-regulated in serrated vs conventional colorectal carcinoma (CRC) samples. 16819509 124/154 Arthur Liberzon 0.00774762208218939 0.0178029200994471 4435 3529.36363636364 3986 0.000706821977322332 828 0.887651889038402 -0.847914112812357 -1 2.330133945652 4431 4029 3933 3672 828 3986 4410 4525 1730 4020 3259 4523 M744 REACTOME_PROCESSIVE_SYNTHESIS_ON_THE_LAGGING_STRAND http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSIVE_SYNTHESIS_ON_THE_LAGGING_STRAND.html Genes involved in Processive synthesis on the lagging strand 15/16 Reactome 0.68618940391 0.690284310838704 3795 3996.63636363636 3988 0.1 3590 0.634036195547143 -0.608445654914076 -1 0.153040360819295 3792 3893 3590 3988 3985 4006 4041 4121 3832 4546 4169 4524 M6693 POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/POMEROY_MEDULLOBLASTOMA_PROGNOSIS_DN.html Top marker genes in medulloblastoma associated with poor response to treatment (poor outcome). 11807556 54/80 Jean Junior 0.478017410699991 0.548030648167102 4455 3792 3988 0.0573893002355616 2006 1.05468607944421 -1.11406516355023 -1 0.413255778551346 3765 4454 3652 4455 2772 4007 4523 3644 2006 3988 4446 4525 M2428 WELCSH_BRCA1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WELCSH_BRCA1_TARGETS_DN.html Down-regulated by induction of exogenous BRCA1 in EcR-293 cells 12032322 189/216 John Newman 0.165061429023367 0.21915328973004 4720 3762 3989 0.0162659949987677 2129 0.938203269601793 -1.0416469578814 -1 0.927984422224565 4720 4346 3989 3463 2129 4267 4324 2909 3569 4105 3561 4526 M13831 BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP http://www.broadinstitute.org/gsea/msigdb/cards/BOYAULT_LIVER_CANCER_SUBCLASS_G123_UP.html Up-regulated genes in hepatocellular carcinoma (HCC) subclass G123, defined by unsupervised clustering. 17187432 58/69 Yujin Hoshida 0.68618940391 0.690284310838704 4095 3699.63636363636 3993 0.1 2101 0.916196775361398 -0.909475385034699 -1 0.221193910495102 4094 3727 3742 4076 4236 4153 4098 3993 2101 3480 2996 4527 M8692 NIKOLSKY_BREAST_CANCER_19Q13.1_AMPLICON http://www.broadinstitute.org/gsea/msigdb/cards/NIKOLSKY_BREAST_CANCER_19Q13.1_AMPLICON.html Genes within amplicon 19q13.1 identified in a copy number alterations study of 191 breast tumor samples. 19010930 73/126 Jessica Robertson 0.678206451170546 0.690284310838704 2255 3731.72727272727 3994 0.0979423311361058 2254 0.832551266212237 0.814613749637041 1 0.200990030964133 2254 4428 3994 4488 4073 4056 2348 3520 3889 4233 3766 4528 M1345 RHODES_CANCER_META_SIGNATURE http://www.broadinstitute.org/gsea/msigdb/cards/RHODES_CANCER_META_SIGNATURE.html Genes commonly up-regulated in cancer relative to normal tissue, according to the meta-analysis of the OncoMine gene expression database. 15184677 111/130 John Newman 0.541213024026409 0.609381076670956 2135 3650.27272727273 3994 0.0683830727244143 2135 0.96827418232677 1.07829738402575 1 0.31243218963848 2135 4379 3560 4169 2893 4161 3941 2700 4020 4201 3994 4529 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 0.370304691871545 0.438824540706426 3960 3874.72727272727 3995 0.0451986030601056 2096 1.76591828933178 -1.75014306924887 -1 0.947750236523486 3995 3957 4631 3956 2669 4371 4581 4363 3506 2096 4497 4530 M9503 BIOCARTA_FAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_FAS_PATHWAY.html FAS signaling pathway ( CD95 ) 31/35 BioCarta 0.68618940391 0.690284310838704 4540 3697.81818181818 3997 0.1 680 0.790949625816867 -0.571817031587196 -1 0.190941499496175 4538 4154 3722 3399 3965 3734 4252 3997 680 4076 4159 4531 M5091 EINAV_INTERFERON_SIGNATURE_IN_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/EINAV_INTERFERON_SIGNATURE_IN_CANCER.html A gene expression signature found in a subset of cancer patients suggestive of a deregulated immune or inflammatory response. 16007187 37/53 Leona Saunders 0.68618940391 0.690284310838704 4355 3798.54545454545 3997 0.1 2699 0.910026102455583 -0.824925716576266 -1 0.219703435593553 4351 3800 3138 4577 4245 4185 4468 3476 3997 2699 2848 4532 M2075 WHITFIELD_CELL_CYCLE_S http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_S.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the S phase of cell cycle. 12058064 199/285 Jessica Robertson 0.523416298439579 0.591742497876602 4455 3642.54545454545 3998 0.0651543188386323 2146 1.12754310867997 -1.34374277220161 -1 0.385422996808134 4453 3998 2351 4317 3695 4376 4482 4150 2805 3295 2146 4533 M1014 REACTOME_IL_6_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_IL_6_SIGNALING.html Genes involved in Interleukin-6 signaling 11/11 Reactome 0.00211827912540478 0.00698203734071965 4340 3361.18181818182 4000 0.000192756497532151 522 0.911576283688157 -0.995139621413437 -1 2.9489783879478 4340 2139 2650 3156 522 4340 4305 4372 4000 3018 4131 4534 M1447 BROWN_MYELOID_CELL_DEVELOPMENT_DN http://www.broadinstitute.org/gsea/msigdb/cards/BROWN_MYELOID_CELL_DEVELOPMENT_DN.html Genes defining proliferation and self renewal potential of the bipotential myeloid cell line FDB. 16769770 141/182 Kevin Vogelsang 0.68618940391 0.690284310838704 3810 3885.54545454545 4004 0.1 2818 1.18516399213392 -1.24498910873215 -1 0.286160712666891 3809 4021 2818 3790 4214 4374 4427 4004 3288 3420 4576 4535 M10279 HORIUCHI_WTAP_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HORIUCHI_WTAP_TARGETS_DN.html Genes down-regulated in primary endothelial cells (HUVEC) after knockdown of WTAP [GeneID=9589] by RNAi. 17088532 419/539 Leona Saunders 0.68618940391 0.690284310838704 3295 3912.45454545455 4007 0.1 3086 0.982431598689914 -0.939222448808584 -1 0.237192383155457 3291 4680 4007 4660 4233 3086 3756 4288 3272 4299 3465 4536 M19232 EPPERT_PROGENITOR http://www.broadinstitute.org/gsea/msigdb/cards/EPPERT_PROGENITOR.html Genes up-regulated in human hematopoietic lineage committed progenitor cells versus hematopoietic stem cells (HSC) and mature cells. 21873988 164/189 Kolja Eppert 0.68618940391 0.690284310838704 4010 3735.18181818182 4007 0.1 1739 0.996005534787833 -0.904227016711537 -1 0.240471054927236 4067 4007 3822 2958 4009 4402 4568 3810 1739 3370 4335 4537 M14473 WEBER_METHYLATED_IN_COLON_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_IN_COLON_CANCER.html Genes identified as hypermethylated in SW48 cells (colon cancer). 16007088 16/24 John Newman 0.000303711784563309 0.00160528513229431 3270 3429.90909090909 4008 2.76139745751568e-05 222 1.01210932650588 1.09680112532819 1 4.24379512255106 3268 4581 2203 4353 222 4515 4180 2479 4446 3474 4008 4538 M13611 WEBER_METHYLATED_LCP_IN_FIBROBLAST_DN http://www.broadinstitute.org/gsea/msigdb/cards/WEBER_METHYLATED_LCP_IN_FIBROBLAST_DN.html Unmethylated germline-specific genes with low-CpG-density promoters (LCP) in primary fibroblasts. 17334365 4/15 Arthur Liberzon 0.0483499254689402 0.0783693846886667 4520 3618.09090909091 4008 0.00494352839589759 1137 1.61491156444995 -1.61491156444995 -1 2.67960650156709 4516 4652 4632 4561 2476 4008 2758 1137 4521 2917 3621 4539 M14796 MAYBURD_RESPONSE_TO_L663536_DN http://www.broadinstitute.org/gsea/msigdb/cards/MAYBURD_RESPONSE_TO_L663536_DN.html Genes down-regulated in H720 cells (lung cancer) after treatment with L663536 (MK886) [PubChem=105049], an inhibitor of leukotriene biosynthesis. 16551867 90/107 Arthur Liberzon 0.134442312039778 0.184628371494836 2630 3289.54545454545 4010 0.0130398039020621 900 0.86626481699738 -0.776526070504749 -1 0.953594490242901 2628 4403 4061 4517 4016 900 1687 3630 4010 4223 2110 4540 M11171 DACOSTA_UV_RESPONSE_VIA_ERCC3_UP http://www.broadinstitute.org/gsea/msigdb/cards/DACOSTA_UV_RESPONSE_VIA_ERCC3_UP.html Genes up-regulated in fibroblasts expressing mutant forms of ERCC3 [GeneID=2071] after UV irradiation. 15608684 427/511 Arthur Liberzon 0.68618940391 0.690284310838704 4685 3968.72727272727 4010 0.1 2797 0.902685744448823 -0.887229525994397 -1 0.217930432949522 4682 4320 4010 4170 3502 2797 3757 4702 3655 4238 3823 4541 M12804 LE_EGR2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LE_EGR2_TARGETS_UP.html Genes up-regulated in P14 nerves of transgenic mice having hypomorhic (reduced function) allele of EGR2 [GeneID=1959]. 15695336 158/189 Kate Stafford 0.68618940391 0.690284310838704 4420 3735.18181818182 4010 0.1 2700 1.16680570992048 -1.08003278435106 -1 0.281726421740709 4417 4010 2700 3666 4177 4236 4402 3558 2853 2820 4248 4542 M19283 REACTOME_METABOLISM_OF_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_MRNA.html Genes involved in Metabolism of mRNA 247/349 Reactome 0.0115843543471056 0.0244754487548517 2555 3608.63636363636 4015 0.00105870969106962 965 0.641127249944012 -0.609203735670104 -1 1.54997443648413 2553 3995 4174 3707 965 4044 3126 4015 4374 4471 4271 4543 M14427 DODD_NASOPHARYNGEAL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/DODD_NASOPHARYNGEAL_CARCINOMA_DN.html Genes down-regulated in nasopharyngeal carcinoma (NPC) compared to the normal tissue. 17119049 1648/1982 Arthur Liberzon 0.6513215599 0.690284310838704 2395 3804.09090909091 4016 0.1 2391 0.967928728395305 1.05489969655433 1 0.23368933502692 2391 4660 4319 4708 3994 4016 3723 2904 2521 4474 4135 4544 M15606 MARKEY_RB1_ACUTE_LOF_UP http://www.broadinstitute.org/gsea/msigdb/cards/MARKEY_RB1_ACUTE_LOF_UP.html Genes up-regulated in adult fibroblasts with inactivated RB1 [GeneID=5925] by Cre-lox: acute loss of function (LOF) of RB1. 17452985 299/356 Arthur Liberzon 0.68618940391 0.690284310838704 3715 3965.18181818182 4017 0.1 2368 1.07029671067795 -0.977334376359105 -1 0.258415472782607 3712 4688 3704 4162 4390 4017 4010 4707 2368 4130 3729 4545 M7465 CAFFAREL_RESPONSE_TO_THC_24HR_3_UP http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_24HR_3_UP.html Genes up-regulated in EVSA-T cells (breast cancer) after treatment with 3 micromolar THC (delta-9-tetrahydrocannabinol) [PubChem=6610319] for 24 h. 18454173 14/23 Jessica Robertson 0.109773741255434 0.15582919059418 4355 3527.18181818182 4020 0.0105151996756994 1560 0.799320457579352 -0.93401378929505 -1 0.968228267629808 4354 4252 3483 4100 1877 4020 3002 1560 4045 3884 4222 4546 M2228 PILON_KLF1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PILON_KLF1_TARGETS_DN.html Genes down-regulated in erythroid progenitor cells from fetal livers of E13.5 embryos with KLF1 [GeneID=10661] knockout compared to those from the wild type embryos. 18852285 2428/2834 Arthur Liberzon 0.6513215599 0.690284310838704 3505 3552.63636363636 4020 0.1 1400 0.890480323823628 -0.887042589922164 -1 0.214982314748741 3501 2195 4669 1400 4376 4384 3991 4020 1722 4477 4344 4547 M79 PID_TRAIL_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TRAIL_PATHWAY.html TRAIL signaling pathway 18832364 28/31 Pathway Interaction Database 0.207309539689686 0.266912446081647 4380 3729.18181818182 4021 0.0208987548327408 1374 0.587482814395564 -0.530111304182159 -1 0.505567120074112 4377 4505 3753 4093 4021 3584 4019 2703 4389 4203 1374 4548 M771 REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSCRIPTION_COUPLED_NER_TC_NER.html Genes involved in Transcription-coupled NER (TC-NER) 46/49 Reactome 0.635452154310757 0.690284310838704 2480 3694.54545454545 4022 0.0876541450171393 2479 0.588159874696178 -0.592460132060861 -1 0.141959315713286 2479 4478 4098 4490 3036 2549 3368 4022 4108 4552 3460 4549 M832 REACTOME_ZINC_TRANSPORTERS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ZINC_TRANSPORTERS.html Genes involved in Zinc transporters 12/15 Reactome 0.456750230429972 0.525563405077881 4190 3953.81818181818 4022 0.0539609788265019 2748 0.798827762949146 -0.544143079090582 -1 0.334768855664144 4190 4254 3109 4022 2748 4496 4649 4590 4009 3800 3625 4550 M1201 TERAMOTO_OPN_TARGETS_CLUSTER_5 http://www.broadinstitute.org/gsea/msigdb/cards/TERAMOTO_OPN_TARGETS_CLUSTER_5.html Cluster 5: genes whose up-regulation peaked 5 days after knockdown of OPN [GeneID=6696] by RNAi in the NIH3T3 cells (fibroblasts) transformed by activated HRAS [GeneID=3265]. 15516973 7/8 Arthur Liberzon 0.474128082741888 0.544100304046125 4025 3681.72727272727 4024 0.0622480024971924 2029 0.343741735596472 -0.224643206533122 -1 0.136228679938912 4024 4272 4387 3984 3533 2040 2029 4180 4634 4654 2762 4551 M2077 WHITFIELD_CELL_CYCLE_G2_M http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_G2_M.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the G2/M phase of cell cycle. 12058064 297/356 Jessica Robertson 0.68618940391 0.690284310838704 3980 3976.09090909091 4024 0.1 2742 0.952844873027276 0.927824017084797 1 0.230045954768755 3977 4326 3781 4287 4680 3489 3808 4024 2742 4199 4424 4552 M2368 GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP http://www.broadinstitute.org/gsea/msigdb/cards/GOBERT_OLIGODENDROCYTE_DIFFERENTIATION_UP.html Genes up-regulated during later stage of differentiation of Oli-Neu cells (oligodendroglial precursor) in response to PD174265 [PubChem=4709]. 19139271 661/745 Arthur Liberzon 0.6513215599 0.690284310838704 3485 3964.27272727273 4026 0.1 1691 1.02462218097542 -0.985265643597903 -1 0.24738316865618 3484 4670 4692 4682 4628 3635 4026 3892 1691 4391 3816 4553 M7870 HEIDENBLAD_AMPLIFIED_IN_BONE_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLIFIED_IN_BONE_CANCER.html Genes from selected recurrently amplified regions in bone tissue tumors with supernumerary ring chromosomes. 16732325 8/11 Arthur Liberzon 0.6513215599 0.690284310838704 4385 4075.90909090909 4028 0.1 3367 0.93908488690517 1.12789597791861 1 0.226722344155505 4381 3940 4379 3367 3972 4420 4028 3820 4505 3460 4563 4554 M14340 FUJII_YBX1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FUJII_YBX1_TARGETS_DN.html Genes down-regulated in MCF-7 cells (breast cancer) after knockdown of YBX1 [GeneID=4904] by RNAi. 18316615 266/317 Jessica Robertson 0.615300862792241 0.681102268381655 3355 3939.36363636364 4029 0.0831807010530747 2643 1.01840740141043 1.06507981184716 1 0.254769211503857 3353 4693 3651 4675 3739 4156 4582 2643 3253 4029 4559 4555 M1529 SA_G1_AND_S_PHASES http://www.broadinstitute.org/gsea/msigdb/cards/SA_G1_AND_S_PHASES.html Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition. 20/30 SigmaAldrich 0.68618940391 0.690284310838704 4250 3507.72727272727 4033 0.1 994 0.761845430419174 -0.818561638993111 -1 0.183911622296047 4248 994 3158 1646 4469 4315 4516 3530 4423 3253 4033 4556 M795 REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_TRANSPORT_OF_MATURE_MRNA_DERIVED_FROM_AN_INTRONLESS_TRANSCRIPT.html Genes involved in Transport of Mature mRNA Derived from an Intronless Transcript 38/59 Reactome 0.68618940391 0.690284310838704 4040 3864 4036 0.1 2530 0.668848315380046 -0.647058111900683 -1 0.16144893986288 4036 4136 4018 3854 4300 4273 4185 2982 2530 4561 3629 4557 M5669 KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY.html Natural killer cell mediated cytotoxicity 99/188 KEGG 0.68618940391 0.690284310838704 4045 3945.72727272727 4041 0.1 3095 0.889730313631639 -0.945259235952397 -1 0.214801156002503 3666 4041 3095 4145 4593 3812 3406 4160 4043 3870 4572 4558 M3427 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_11 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_11.html Amplification hot spot 11: colocolized fragile sites and cancer genes in the 11q3 region. 16751803 3/3 Arthur Liberzon 0.806825204764821 0.810430935622463 3895 4106.18181818182 4041 0.151610966537855 3364 0.170030864498033 -0.0881883951907461 -1 0.0231838878162655 3893 4299 4368 4041 3364 3882 3481 4716 4575 4648 3901 4559 M6907 BIOCARTA_RARRXR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_RARRXR_PATHWAY.html Nuclear receptors coordinate the activities of chromatin remodeling complexes and coactivators to facilitate initiation of transcription in carcinoma cells 17/21 BioCarta 0.68618940391 0.690284310838704 4310 4040.90909090909 4042 0.1 2986 0.570752862147558 -0.557115068511834 -1 0.137754796091088 4306 4587 3966 4450 4551 2986 3737 3508 3816 4501 4042 4560 M14449 BIOCARTA_ETS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_ETS_PATHWAY.html METS affect on Macrophage Differentiation 26/27 BioCarta 0.68618940391 0.690284310838704 3185 3916.18181818182 4043 0.1 3078 0.871740724818982 -0.694033277683609 -1 0.210455919911771 3185 4553 3782 4491 3121 3511 3078 4717 4420 4177 4043 4561 M12016 OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_UP http://www.broadinstitute.org/gsea/msigdb/cards/OUELLET_OVARIAN_CANCER_INVASIVE_VS_LMP_UP.html Genes up-regulated in epithelial ovarian cancer (EOC) biopsies: invasive (TOV) vs low malignant potential (LMP) tumors. 15940270 174/234 Leona Saunders 0.68618940391 0.690284310838704 4550 3756.54545454545 4050 0.1 1155 0.842648257926271 -0.652840731855984 -1 0.203428875634823 4549 3637 4050 3904 4589 2849 3613 4523 1155 4279 4174 4562 M11318 MITSIADES_RESPONSE_TO_APLIDIN_DN http://www.broadinstitute.org/gsea/msigdb/cards/MITSIADES_RESPONSE_TO_APLIDIN_DN.html Genes down-regulated in the MM1S cells (multiple myeloma) after treatment with aplidin [PubChem=44152164], a marine-derived compound with potential anti-cancer properties. 18593922 353/406 Jessica Robertson 0.68618940391 0.690284310838704 4050 3791.27272727273 4050 0.1 1301 0.919318664739438 -0.94864365908448 -1 0.221947977002013 4050 3978 4101 3704 4363 4287 4626 3645 1301 4274 3375 4563 M4242 RIZKI_TUMOR_INVASIVENESS_2D_UP http://www.broadinstitute.org/gsea/msigdb/cards/RIZKI_TUMOR_INVASIVENESS_2D_UP.html Genes up-regulated in monolayer (2D) cultures of preinvasive (S3-C) vs invasive (T4-2) breast cancer cells. 18316601 95/114 Jessica Robertson 0.0107708980448274 0.0231380297147379 3825 3417 4051 0.00098399956186589 935 1.17304741889142 -1.20299605125022 -1 2.87897612708586 3825 4051 1945 4292 935 3300 4073 4167 4109 2669 4221 4564 M2138 SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN.html Cluster 6: genes down-regulated in B493-6 cells (B lymphocytes) by MYC [GeneID=4609] in combination with serum but not affected by serum alone; they are also up-regulated by MYC alone. 15516975 70/92 Leona Saunders 0.91410065408 0.91526412542588 4335 4036.81818181818 4053 0.2 3282 0.725610109980179 -0.663782277954473 -1 0.0417621211039115 3282 4091 4028 4335 3575 3657 3919 4053 4576 4335 4554 4565 M3909 UDAYAKUMAR_MED1_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/UDAYAKUMAR_MED1_TARGETS_UP.html Genes up-regulated in HeLa cells after knockdown of MED1 [GeneID=5469] by RNAi. 16574658 170/176 Leona Saunders 0.680251813118466 0.690284310838704 4435 3618.72727272727 4055 0.0984650792489514 1009 0.902244549617603 0.896138410867015 1 0.2178238659944 4025 2771 4055 2429 3102 4601 4657 4432 1009 4293 4432 4566 M3134 HUMMEL_BURKITTS_LYMPHOMA_UP http://www.broadinstitute.org/gsea/msigdb/cards/HUMMEL_BURKITTS_LYMPHOMA_UP.html Up-regulated genes constituting the molecular signature of Burkitt 's lymphoma. 16760442 57/71 Arthur Liberzon 0.00754612376701338 0.01746822176572 2840 3247.27272727273 4055 0.000688375670680018 819 1.16120696500847 1.14084998422146 1 3.06262527564139 2837 4437 2401 4576 819 4472 4486 4206 1203 2228 4055 4567 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 0.470944069479079 0.540840877844587 4245 3669.45454545455 4056 0.0616817599348791 2023 1.19160112598794 -1.16974346865645 -1 0.477171603435287 4245 4297 4406 4018 4128 3292 2023 3133 4672 2094 4056 4568 M18789 LY_AGING_OLD_DN http://www.broadinstitute.org/gsea/msigdb/cards/LY_AGING_OLD_DN.html Genes down-regulated in fibroblasts from old individuals, compared to those from young donors. 10741968 77/99 Arthur Liberzon 0.68618940391 0.690284310838704 4195 3845.09090909091 4062 0.1 2878 1.22990316796563 -1.39198324769151 -1 0.296967089817477 3523 4062 2878 4113 4195 4191 3726 4458 4106 3679 3365 4569 M1148 MOTAMED_RESPONSE_TO_ANDROGEN_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOTAMED_RESPONSE_TO_ANDROGEN_UP.html Genes up-regulated in ovarian epithelial cells in response to dihydrotestosterone (DHT) [PubChem=10635]. 16832351 4/6 Arthur Liberzon 0.00544400759944295 0.0141965281046247 4065 3466.72727272727 4065 0.000545739051353799 755 0.48319420485024 0.48319420485024 1 1.33964083592885 4065 1098 4350 2063 755 3664 3922 4298 4695 4638 4586 4570 M1976 OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/OKAMOTO_LIVER_CANCER_MULTICENTRIC_OCCURRENCE_DN.html Genes down-regulated in both the patients in the multicentric hepatocellular carcinoma (HCC) group and those with multicentric recurrence. 16788756 5/13 Yujin Hoshida 0.00218275957220078 0.00713478198115489 2050 3106.90909090909 4067 0.000218490653849995 240 0.407654095021935 -0.407654095021935 -1 1.31296649115436 2046 4293 4628 4204 4067 1759 1591 240 4684 4706 1958 4571 M19965 NGO_MALIGNANT_GLIOMA_1P_LOH http://www.broadinstitute.org/gsea/msigdb/cards/NGO_MALIGNANT_GLIOMA_1P_LOH.html Proteins with reduced expression in mulignant glioma cell line (A172) which bears loss of heterozygosity (LOH) in the 1p region. 17440165 29/43 Jessica Robertson 0.077412395040933 0.116180128646488 3355 3902.63636363636 4068 0.00729805192360613 1710 0.616040691364874 -0.561199949049201 -1 0.864068918085942 3354 4545 3792 4523 1710 3283 3637 4610 4700 4707 4068 4572 M739 REACTOME_RNA_POL_III_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION.html Genes involved in RNA Polymerase III Transcription 34/37 Reactome 0.392593639351564 0.461874869825369 3170 3847.81818181818 4069 0.0443116251238983 1787 0.634298729117889 -0.559997112803548 -1 0.319192522201323 3168 4524 4069 4665 4260 3650 1787 3862 4495 4267 3579 4573 M11829 MENSSEN_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/MENSSEN_MYC_TARGETS.html Genes up-regulated by adenoviral expression of c-MYC [GeneID=4609] in HUVEC cells (umbilical vein endothelium). 11983916 81/88 Yujin Hoshida 0.91410065408 0.91526412542588 4340 4103.90909090909 4070 0.2 3665 0.756164882716145 -0.60250976142317 -1 0.0435251418268689 4220 4070 4026 4340 4053 3894 3665 3698 4573 4336 4268 4574 M6705 BIOCARTA_TH1TH2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_TH1TH2_PATHWAY.html Th1/Th2 Differentiation 7/21 BioCarta 0.0765235127605049 0.115065619697223 3980 3756.45454545455 4071 0.00792938922674321 1343 0.785009608368205 0.778286854807451 1 1.10602766260741 3979 3129 4199 3307 4449 3874 4243 1343 4220 4507 4071 4575 M13893 GARY_CD5_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARY_CD5_TARGETS_DN.html Genes down-regulated in Daudi cells (B lymphocytes) stably expressing CD5 [GeneID=921] off a plasmid vector. 17878328 524/626 Arthur Liberzon 0.6513215599 0.690284310838704 3030 3856.54545454545 4071 0.1 2427 0.829414510698886 0.783039329944929 1 0.200232373665439 3030 3605 4286 3921 4083 4080 3789 4071 2427 4463 4667 4576 M10994 BIOCARTA_SRCRPTP_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_SRCRPTP_PATHWAY.html Activation of Src by Protein-tyrosine phosphatase alpha 17/18 BioCarta 0.68618940391 0.690284310838704 4660 4059.18181818182 4072 0.1 3159 0.993169384389505 0.993169384389505 1 0.23978600630284 4657 4221 3644 4625 3159 3918 4072 3248 4058 4492 4557 4577 M8779 LI_LUNG_CANCER http://www.broadinstitute.org/gsea/msigdb/cards/LI_LUNG_CANCER.html Proteins showing significant overexpression in lung cancer cell lines relative to normal bronchial epithelial cell lines. 16369491 69/87 Arthur Liberzon 0.661062687238665 0.690284310838704 4075 3696.09090909091 4072 0.0936757920472676 2427 1.09703212188838 -1.21414855256399 -1 0.264873189793372 4104 4072 2427 4119 3076 3530 4074 4612 3446 2835 4362 4578 M1858 MALONEY_RESPONSE_TO_17AAG_DN http://www.broadinstitute.org/gsea/msigdb/cards/MALONEY_RESPONSE_TO_17AAG_DN.html Down-regulated genes in A2780 cells (ovarian cancer) treated with 17AAG [PubChem=6440175], a chemical with anticancer properties. 17409432 130/188 Jessica Robertson 0.68618940391 0.690284310838704 4075 4013.90909090909 4073 0.1 3122 0.836019205446322 -0.777957008522786 -1 0.201827682945918 4206 4372 4072 4521 3952 3492 4152 4073 3122 4361 3830 4579 M5635 BUSA_SAM68_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/BUSA_SAM68_TARGETS_DN.html Genes down-regulated in LNCaP cells (prostate cancer) after knockdown of SAM68 [GeneID=10657] by RNAi. 17237817 6/7 Arthur Liberzon 0.0500339351572817 0.0808214147646713 4680 3648.18181818182 4079 0.00511975079509204 1551 0.77979917991579 0.77979917991579 1 1.27820219354704 4679 2684 4347 4559 1551 3139 3500 2333 4622 4637 4079 4580 M105 PID_TELOMERASE_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TELOMERASE_PATHWAY.html Regulation of Telomerase 18832364 83/89 Pathway Interaction Database 0.68618940391 0.690284310838704 4300 3861.81818181818 4080 0.1 2238 0.832208311123644 -0.815877206839001 -1 0.200907193004691 4298 4408 4059 4332 3399 4570 4539 3441 2238 4080 3116 4581 M10294 REACTOME_UNFOLDED_PROTEIN_RESPONSE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_UNFOLDED_PROTEIN_RESPONSE.html Genes involved in Unfolded Protein Response 99/108 Reactome 0.00146524241599582 0.00527129893559473 4080 3436.72727272727 4080 0.000133292655145644 460 0.801635504745922 0.796226966959333 1 2.74013146455088 4080 2362 4023 2478 460 4653 4273 4368 2533 4167 4407 4582 M837 REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_RAS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_RAS.html Genes involved in CREB phosphorylation through the activation of Ras 28/35 Reactome 0.198813825797971 0.257237186887725 4085 3679.81818181818 4082 0.0199494085292137 1802 0.760907508080001 -0.810761570941302 -1 0.67314973112145 4082 4520 3409 4308 4426 3434 2118 1802 4272 3992 4115 4583 M15501 MOREIRA_RESPONSE_TO_TSA_UP http://www.broadinstitute.org/gsea/msigdb/cards/MOREIRA_RESPONSE_TO_TSA_UP.html Up-regulated in CD4+ [GeneID=920] T lymphocytes after 4 h treatment with 100 nM TSA [PubChem=5562]. 14606959 42/46 John Newman 0.742460205708481 0.746413667932701 4550 3839.18181818182 4085 0.116024161004418 2917 0.678524169622727 -0.674556281396028 -1 0.129218629238303 4548 4470 3346 4085 3203 3191 4708 2917 4650 4103 3010 4584 M11159 SMID_BREAST_CANCER_RELAPSE_IN_LIVER_UP http://www.broadinstitute.org/gsea/msigdb/cards/SMID_BREAST_CANCER_RELAPSE_IN_LIVER_UP.html Genes up-regulated in liver relapse of breast cancer. 18451135 5/6 Jessica Robertson 0.13962650429007 0.190528216319495 4475 3720.54545454545 4085 0.0149263496414588 1325 1.81247108286932 1.83874400188035 1 1.95815230588653 4475 3579 4549 3940 2079 4141 4717 4085 4572 1325 3464 4585 M6506 DANG_MYC_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/DANG_MYC_TARGETS_UP.html Genes up-regulated by MYC [GeneID=4609] and whose promoters are bound by MYC, according to MYC Target Gene Database. 14519204 185/250 Chi Dang 0.49426018781857 0.563776724626305 1600 3583.09090909091 4085 0.0600942948925475 1597 0.846538278999589 0.843247812783365 1 0.316049746699365 1597 4360 4085 4701 4242 2706 2007 3227 4299 4386 3804 4586 M2486 GUILLAUMOND_KLF10_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GUILLAUMOND_KLF10_TARGETS_DN.html Genes down-regulated in the liver tissue from 10 week old male mice with KLF10 [GeneID=7071] compared to wild-type littermates. 20385766 32/42 Arthur Liberzon 0.68618940391 0.690284310838704 3980 4073.90909090909 4093 0.1 2909 0.78426562670913 -0.763287283558754 -1 0.189327034904693 3980 4510 2909 4581 4075 4317 3770 3622 4497 4093 4459 4587 M8577 WANG_CLIM2_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/WANG_CLIM2_TARGETS_DN.html Genes down-regulated in MCF7 cells (breast cancer) engineered to conditionally express a dominant negative form of CLIM2 [GeneID=8861] by a Tet Off system. 17452977 290/317 Arthur Liberzon 0.536236888993201 0.604643601540351 2630 3701.45454545455 4096 0.0674689719570446 2462 0.836150527596913 0.87756933803098 1 0.274038199428495 2626 4328 4121 4652 2881 3914 2462 4497 2731 4408 4096 4588 M261 PID_P53_REGULATION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_P53_REGULATION_PATHWAY.html p53 pathway 18832364 81/90 Pathway Interaction Database 0.274013511050777 0.337335360500695 2875 3571.36363636364 4097 0.0286916106055745 1539 0.612815789583264 0.612529719765912 1 0.433861290846874 2872 3261 4097 4316 4123 2116 1539 4506 4161 4368 3926 4589 M15866 BIDUS_METASTASIS_UP http://www.broadinstitute.org/gsea/msigdb/cards/BIDUS_METASTASIS_UP.html Genes up-regulated in endometroid endometrial tumors from patients with lymph node metastases compared to those without the metastases. 16397028 283/314 Arthur Liberzon 0.68618940391 0.690284310838704 4430 4042.90909090909 4098 0.1 2739 0.729639796686066 -0.788799983748298 -1 0.176132618368868 4430 3988 4177 3919 3905 4295 4479 4098 2739 4460 3982 4590 M17998 CAFFAREL_RESPONSE_TO_THC_DN http://www.broadinstitute.org/gsea/msigdb/cards/CAFFAREL_RESPONSE_TO_THC_DN.html Genes down-regulated in EVSA-T cells (breast cancer) treated THC (delta-9-tetrahydrocannabinol) [PubChem=6610319]. 18454173 60/72 Jessica Robertson 0.68618940391 0.690284310838704 4400 3888.63636363636 4098 0.1 2570 1.09254921356353 0.774789515507469 1 0.263790380439169 4399 4098 2570 3469 4327 3460 4346 3361 4306 3816 4623 4591 M18260 HEIDENBLAD_AMPLICON_8Q24_UP http://www.broadinstitute.org/gsea/msigdb/cards/HEIDENBLAD_AMPLICON_8Q24_UP.html Up-regulated genes whose expression is associated with amplification of the 8q24 chromosome region in pancreatic cancer cell lines. 15688027 51/65 Arthur Liberzon 0.489130452353306 0.558847054119529 4305 3997.18181818182 4100 0.059231583795085 2794 0.913898173068471 -0.973867746191852 -1 0.346437026523589 4305 4462 3506 4631 2794 4480 4695 3611 3900 4100 3485 4592 M13108 LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN http://www.broadinstitute.org/gsea/msigdb/cards/LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN.html Genes down-regulated in Wilm's tumor samples compared to fetal kidney. 12057921 229/287 Kevin Vogelsang 0.429877490309214 0.499814448548158 2705 3826.90909090909 4101 0.0497994229211622 2340 1.04036620447066 1.16340090526667 1 0.470080843659202 2705 4697 3400 4507 4352 4011 4270 2340 3580 4133 4101 4593 M19381 REACTOME_G2_M_CHECKPOINTS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G2_M_CHECKPOINTS.html Genes involved in G2/M Checkpoints 46/46 Reactome 0.684449063834691 0.690284310838704 3215 4065.18181818182 4103 0.0995473901159818 3109 0.719707948031481 0.765632184590292 1 0.173733662635581 3214 4127 3931 4664 3109 4249 4670 3937 4103 4620 4093 4594 M8214 CHNG_MULTIPLE_MYELOMA_HYPERPLOID_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHNG_MULTIPLE_MYELOMA_HYPERPLOID_DN.html Protein biosynthesis, transport or catabolism genes down-regulated in hyperploid multiple myeloma (MM) compared to the non-hyperploid MM samples. 17409404 36/41 Jessica Robertson 0.68618940391 0.690284310838704 3695 4093.09090909091 4103 0.1 3360 0.68432281313912 -0.52021964323478 -1 0.165186676553191 3691 3801 3990 3817 4103 4574 4472 4532 3360 4284 4400 4595 M13844 GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN http://www.broadinstitute.org/gsea/msigdb/cards/GARCIA_TARGETS_OF_FLI1_AND_DAX1_DN.html Genes down-regulated in the A673 cells (Ewing sarcoma) after double knockdown of both FLI1 and DAX1 [GeneID=2313;190] by RNAi. 18591936 215/270 Jessica Robertson 0.300710973940841 0.364685456577792 4660 3981.27272727273 4104 0.0319943704815442 2475 0.876187674645841 -0.985440669322102 -1 0.575856285816569 4656 4704 4104 4674 2475 3695 4709 4037 2639 4371 3730 4596 M1055 REACTOME_RNA_POL_III_CHAIN_ELONGATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_CHAIN_ELONGATION.html Genes involved in RNA Polymerase III Chain Elongation 18/20 Reactome 0.999384223365488 0.999384223365488 3875 4236 4106 0.489342890865098 3813 0.493030227130129 -0.660384168726014 -1 9.20772312915086e-05 3871 4609 3940 4657 4106 3813 4365 4009 4703 4616 3907 4597 M12977 KORKOLA_EMBRYONAL_CARCINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_EMBRYONAL_CARCINOMA_DN.html Genes from the 12p region that were down-regulated in embryonic carcinoma tumors compared to normal tissue. 16424014 32/70 Arthur Liberzon 0.0286803997365472 0.0507389380646563 4550 3377.81818181818 4107 0.00264193296932672 885 1.23593522277228 1.25121199784975 1 2.40089763886939 4397 4157 1705 4252 3613 4107 4546 885 2999 1947 4548 4598 M632 KORKOLA_SEMINOMA_DN http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_SEMINOMA_DN.html Genes from the 12p region that were down-regulated in seminoma tumors compared to normal testis. 16424014 32/69 Arthur Liberzon 0.0286803997365472 0.0507389380646563 4550 3378.81818181818 4108 0.00264193296932672 886 1.23593522277228 1.25121199784975 1 2.40089763886939 4398 4158 1706 4253 3614 4108 4547 886 3000 1948 4549 4599 M13007 GLINSKY_CANCER_DEATH_UP http://www.broadinstitute.org/gsea/msigdb/cards/GLINSKY_CANCER_DEATH_UP.html Genes whose over-expression is associated with the risk of death in multiple cancer types 15931389 9/12 Yujin Hoshida 0.1069293645433 0.152571523773996 2455 3631.81818181818 4111 0.0112452543025802 1035 0.321150913900704 -0.313448750503353 -1 0.39337290445149 2455 4271 4627 4069 4154 3430 1035 4111 4236 4705 2857 4600 M3141 RASHI_RESPONSE_TO_IONIZING_RADIATION_4 http://www.broadinstitute.org/gsea/msigdb/cards/RASHI_RESPONSE_TO_IONIZING_RADIATION_4.html Cluster 4: genes repressed by ionizing radiation regardless of ATM [GeneID=472] status. 16314843 76/108 Arthur Liberzon 0.68618940391 0.690284310838704 4420 3611.09090909091 4114 0.1 915 1.31485877746979 -1.33317226220258 -1 0.317487413231867 4418 4066 2259 4237 4523 4114 4481 4203 915 2598 3908 4601 M11961 PUJANA_CHEK2_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_CHEK2_PCC_NETWORK.html Genes constituting the CHEK2-PCC network of transcripts whose expression positively correlates (Pearson correlation coefficient, PCC >= 0.4) with that of CHEK2 [GeneID=11200]. 17922014 959/1174 Leona Saunders 0.6513215599 0.690284310838704 3950 4158.90909090909 4114 0.1 2893 0.794205240478523 -0.790277563970166 -1 0.191727866237109 3949 4666 4422 4709 4632 3845 4070 4114 2893 4660 3788 4602 M2935 LAMB_CCND1_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/LAMB_CCND1_TARGETS.html The cyclin D1 signature: genes whose expression correlated with the levels of CCND1 [GeneID=595]. 12914697 33/36 Jean Junior 0.306431738242248 0.370196520220991 4540 3913.36363636364 4117 0.0327169787398694 2490 0.888958142332648 -0.706220360350147 -1 0.575562082879111 4540 4149 3050 3424 2490 4594 4379 3843 4553 3908 4117 4603 M11690 KORKOLA_CHORIOCARCINOMA http://www.broadinstitute.org/gsea/msigdb/cards/KORKOLA_CHORIOCARCINOMA.html Genes predicting the choriocarcinoma (CC) of nonseminomatous male germ cell tumors (NSGCT). 15870693 2/12 Leona Saunders 0.308857412739223 0.372745330639002 3450 3920.1 4118 0.0402145015440863 1726 0.747847027473552 0.747847027473552 1 0.480838018934565 3449 4657 4385 NA 3616 3792 1726 4278 4687 4653 3958 4604 M14670 DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_EXPRESSION_BY_COPY_NUMBER.html The lung adenocarcinoma TSP (tumor sequencing project) genes showing strong correlation between DNA copy number variation and gene expression. 18948947 130/141 Jessica Robertson 0.68618940391 0.690284310838704 4480 3771.90909090909 4118 0.1 739 0.864986184346663 -1.04093355909031 -1 0.208824416638279 4478 3647 4118 4297 3964 4380 4395 4036 739 4360 3077 4605 M2074 WHITFIELD_CELL_CYCLE_G1_S http://www.broadinstitute.org/gsea/msigdb/cards/WHITFIELD_CELL_CYCLE_G1_S.html Genes periodically expressed in synchronized HeLa cells (cervical carcinoma), with peak during the G1/S phase of cell cycle. 12058064 168/193 Jessica Robertson 0.68618940391 0.690284310838704 2935 3930.36363636364 4120 0.1 2931 0.880427478568795 0.900849740878577 1 0.212554133289412 3533 4357 3888 4295 4667 3705 2931 2932 4120 4254 4552 4606 M1173 HESSON_TUMOR_SUPPRESSOR_CLUSTER_3P21_3 http://www.broadinstitute.org/gsea/msigdb/cards/HESSON_TUMOR_SUPPRESSOR_CLUSTER_3P21_3.html Genes in the tumor suppressor cluster of the 3p21.3 region. 17533367 6/8 Leona Saunders 0.000298157645310387 0.00158174292324708 4640 3620.90909090909 4124 2.98197656957775e-05 238 0.657056482740827 0.657056482740827 1 2.76134013967119 4639 3573 4360 3533 238 3545 1960 4554 4658 4646 4124 4607 M1836 LABBE_WNT3A_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/LABBE_WNT3A_TARGETS_UP.html Up-regulated genes in NMuMG cells (mammary epithelium) after stimulation with WNT3A [GeneID=89780]. 17210685 148/192 Jessica Robertson 4.8824986034514e-05 0.000374113529355367 4130 2606.09090909091 4128 4.438733604515e-06 254 1.31255853858743 -1.19674169634478 -1 6.74943395709634 4128 608 557 585 4246 4556 4258 4394 731 254 4350 4608 M17794 ASGHARZADEH_NEUROBLASTOMA_POOR_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/ASGHARZADEH_NEUROBLASTOMA_POOR_SURVIVAL_DN.html Down-regulated genes associated with poor survival prognosis of patients with metastatic neuroblastoma that lack MYCN [GeneID=4613] amplification. 16954472 94/116 Jessica Robertson 0.330941796554776 0.396659542848792 3055 3723.45454545455 4130 0.035875582854145 2543 0.976162169527765 1.04194209558432 1 0.58811191479003 3052 4395 3245 4451 2543 4555 4130 2776 4235 3369 4207 4609 M9193 MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_B_LYMPHOCYTE_MATURATION_BY_TACI_DN.html Genes down-regulated in normal bone marrow plasma cells (BMPC) compared to polyclonal plasmablasts (PPC) that also distinguished multiple myeloma (MM) samples by expression of levels of TACI [GeneID=23495]. 15827134 82/89 Kevin Vogelsang 0.68618940391 0.690284310838704 4135 3876.18181818182 4131 0.1 2462 0.692441035367557 0.662717368020166 1 0.167147565853494 4131 4410 4129 4497 4558 3063 3389 3345 2462 4419 4235 4610 M18912 XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/XU_HGF_TARGETS_INDUCED_BY_AKT1_48HR_DN.html Genes down-regulated in DU-145 cells (prostate cancer) in the absence but not in the presence of a dominant negative form of AKT1 [GeneID=207] upon exposure to HGF [GeneID=3082] for 48 h. 17099727 44/54 Arthur Liberzon 0.68618940391 0.690284310838704 3930 4152.54545454545 4133 0.1 3850 0.898701210827428 0.925875635943503 1 0.216968001874709 3927 4482 3978 4133 4203 4388 3850 3888 4079 4243 4507 4611 M1859 RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN http://www.broadinstitute.org/gsea/msigdb/cards/RHEIN_ALL_GLUCOCORTICOID_THERAPY_DN.html Genes down-regulated in ALL (acute lymphoblastic leukemia) blasts after 1 week of treatment with glucocorticoids. 17330098 474/606 Arthur Liberzon 0.68618940391 0.690284310838704 3070 3825.90909090909 4134 0.1 2499 0.843161210266585 -0.782630679313696 -1 0.203552775021583 3067 4678 4134 4336 4165 2499 3327 4190 3775 4407 3507 4612 M18833 HU_ANGIOGENESIS_DN http://www.broadinstitute.org/gsea/msigdb/cards/HU_ANGIOGENESIS_DN.html Down-regulated genes that separate angiogenic from non-angiogenic non-small cell lung carcinoma (NSCLC) samples. 15592519 57/71 Leona Saunders 0.68618940391 0.690284310838704 4100 4166.18181818182 4134 0.1 3423 0.648097432404627 -0.556782946181036 -1 0.156436736051089 4097 4439 3909 4643 4090 3423 4557 4134 4380 4375 3781 4613 M3682 FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN http://www.broadinstitute.org/gsea/msigdb/cards/FLECHNER_PBL_KIDNEY_TRANSPLANT_REJECTED_VS_OK_DN.html Genes down-regulated in peripheral blood lymphocytes (PBL) from patients with acute transplant rejection compared to those from patients with well functioning kidneys more than 1-year post transplant. 15307835 75/112 Jean Junior 0.104837373171821 0.150085654040338 4425 3795.54545454545 4142 0.0100176557610427 1851 0.675064980774043 0.636927519264184 1 0.834220204637733 4421 4422 3915 4647 1851 4142 4046 2841 4366 4307 2793 4614 M839 REACTOME_DEADENYLATION_DEPENDENT_MRNA_DECAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_DEADENYLATION_DEPENDENT_MRNA_DECAY.html Genes involved in Deadenylation-dependent mRNA decay 49/52 Reactome 0.145103068892888 0.197259932365907 3845 4014.54545454545 4149 0.0141511330328277 2046 0.561740778512007 -0.512141755958484 -1 0.594108235031461 3843 3753 4103 4460 2046 4149 4228 4604 3912 4573 4489 4615 M802 RIZ_ERYTHROID_DIFFERENTIATION_HBZ http://www.broadinstitute.org/gsea/msigdb/cards/RIZ_ERYTHROID_DIFFERENTIATION_HBZ.html Selected gradually up-regulated genes whose expression profile follows that of HBZ [GeneID=3050] in the TLX1 [GeneID=3195] Tet On iEBHX15-4 cells (pro-erythroblasts). 17213805 42/65 Leona Saunders 0.68618940391 0.690284310838704 4315 3686.18181818182 4150 0.1 1329 1.11288155530784 1.17752237745608 1 0.268701489085207 4315 4124 2743 4192 4150 3037 4715 4186 1329 3375 4382 4616 M18811 PUJANA_XPRSS_INT_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_XPRSS_INT_NETWORK.html Genes constituting the XPRSS-Int network: intersection of genes whose expression correlates with BRCA1, BRCA2, ATM, and CHEK2 [GeneID=672;675;472;11200] in a compendium of normal tissues. 17922014 243/283 Leona Saunders 0.68618940391 0.690284310838704 4435 3925 4150 0.1 1989 0.84209555317256 0.850614647292961 1 0.203295374382051 3709 4696 4150 4338 4172 3754 3818 4434 1989 4434 3681 4617 M1916 ZHANG_TLX_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_DN.html Genes down-regulated in neural stem cells (NSC) at both 36 h and 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 100/112 Jessica Robertson 0.68618940391 0.690284310838704 4035 3973.81818181818 4150 0.1 2165 1.11933977006036 -1.16649896215476 -1 0.270261417336851 4035 4052 4020 4150 4348 4628 4333 3333 2165 4359 4289 4618 M18810 REACTOME_PD1_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PD1_SIGNALING.html Genes involved in PD-1 signaling 11/21 Reactome 0.68603159398234 0.690284310838704 4155 3547.81818181818 4151 0.0999588644518117 1806 1.52641947280689 1.70195855194524 1 0.368588145901883 4151 2142 1806 2132 4720 4704 4247 4319 3194 3017 4594 4619 M4076 REACTOME_HIV_LIFE_CYCLE http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_HIV_LIFE_CYCLE.html Genes involved in HIV Life Cycle 123/144 Reactome 0.116379289424513 0.16382649748992 4095 3951.81818181818 4152 0.0111849210253896 1906 0.675985280396462 -0.608198051497898 -1 0.796767492151428 4092 4378 4152 4525 1906 3820 4391 4553 3345 4457 3851 4620 M9695 HOLLMANN_APOPTOSIS_VIA_CD40_UP http://www.broadinstitute.org/gsea/msigdb/cards/HOLLMANN_APOPTOSIS_VIA_CD40_UP.html Genes up-regulated in DLBCL (diffuse large B-cell lymphoma) cell lines sensitive to stimulation of CD40 [GeneID=958] relative to the resistant ones. 16585179 281/339 Arthur Liberzon 0.68618940391 0.690284310838704 4155 4167.90909090909 4154 0.1 3713 0.96725681755157 0.987432740166677 1 0.233527040531011 3734 4689 3790 4512 4317 3713 4524 4154 3745 4153 4516 4621 M496 REACTOME_RNA_POL_I_TRANSCRIPTION_TERMINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_TRANSCRIPTION_TERMINATION.html Genes involved in RNA Polymerase I Transcription Termination 20/20 Reactome 0.68618940391 0.690284310838704 4080 4202.09090909091 4155 0.1 3662 0.594508171273336 -0.644369672076643 -1 0.143492694140609 4076 4572 3987 4620 3662 4333 3796 3838 4155 4518 4666 4622 M8256 REACTOME_GENERIC_TRANSCRIPTION_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_GENERIC_TRANSCRIPTION_PATHWAY.html Genes involved in Generic Transcription Pathway 356/490 Reactome 0.68547293345684 0.690284310838704 4535 4012.72727272727 4155 0.0998133920160406 2306 0.967001412920764 -0.985590185536475 -1 0.233465349659081 4535 4684 4136 4528 3111 4096 3906 4333 2306 4350 4155 4623 M2531 REACTOME_MRNA_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_PROCESSING.html Genes involved in mRNA Processing 181/233 Reactome 0.68618940391 0.690284310838704 4155 4077.81818181818 4155 0.1 3458 0.590868302672541 -0.620288215384031 -1 0.142613514045143 4155 4358 4172 4538 3545 3877 4610 3697 3458 4467 3979 4624 M18854 PENG_RAPAMYCIN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/PENG_RAPAMYCIN_RESPONSE_DN.html Genes down-regulated in BJUB cells (B-lymphoma) in response to rapamycin (sirolimus) [PubChem=6610346] treatment. 12101249 314/354 Broad Institute 0.68618940391 0.690284310838704 4335 3998.90909090909 4155 0.1 2820 0.796262840815459 -0.715747672884778 -1 0.192224862546333 4335 3985 4155 3471 4395 3880 4512 3769 2820 4355 4311 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 336/395 Kate Stafford 0.68618940391 0.690284310838704 3005 3738.90909090909 4156 0.1 1455 0.920159087117893 -0.903613744748706 -1 0.222150974062611 3004 4685 4156 4343 4616 3126 3120 4454 1455 4426 3743 4626 M787 REACTOME_POL_SWITCHING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_POL_SWITCHING.html Genes involved in Polymerase switching 13/14 Reactome 0.68618940391 0.690284310838704 4110 4181.81818181818 4162 0.1 3733 0.542714768025455 -0.539665414535155 -1 0.130982426818868 4107 4246 3733 4016 4070 4162 4344 4153 4301 4558 4310 4627 M12967 REACTOME_MRNA_3_END_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_3_END_PROCESSING.html Genes involved in mRNA 3'-end processing 44/71 Reactome 0.151501104573958 0.204115716109175 3445 4022.09090909091 4162 0.0148241600330753 2076 0.556865905122708 0.541866641020124 1 0.576553455198234 3443 4484 4105 4503 2076 4417 4032 4435 4022 4564 4162 4628 M2178 FIGUEROA_AML_METHYLATION_CLUSTER_6_DN http://www.broadinstitute.org/gsea/msigdb/cards/FIGUEROA_AML_METHYLATION_CLUSTER_6_DN.html Cluster 6 of aberrantly hypomethylated genes in blasts from AML (acute myeloid leukemia) patients. 20060365 25/107 Arthur Liberzon 0.284089753232149 0.348015477616336 4525 3611.45454545455 4165 0.0299249712335871 1861 0.866079226569724 -0.8873315307974 -1 0.595618593869824 4525 2566 1861 4551 3027 4400 4616 2037 4394 3584 4165 4629 M2879 BLUM_RESPONSE_TO_SALIRASIB_DN http://www.broadinstitute.org/gsea/msigdb/cards/BLUM_RESPONSE_TO_SALIRASIB_DN.html Selected genes down-regulated in response to the Ras inhibitor salirasib [PubChem=5469318] in a panel of cancer cell lines with constantly active HRAS [GeneID=3265]. 17409441 494/576 Jessica Robertson 0.68618940391 0.690284310838704 4705 4140.36363636364 4167 0.1 3353 1.03592741487343 -1.01066165479424 -1 0.250113854213219 4704 4677 3518 4167 4237 3841 4569 4492 3353 4037 3949 4630 M13087 REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PROCESSING_OF_CAPPED_INTRON_CONTAINING_PRE_MRNA.html Genes involved in Processing of Capped Intron-Containing Pre-mRNA 163/214 Reactome 0.68618940391 0.690284310838704 4325 4123.72727272727 4170 0.1 3422 0.604851871590675 -0.631952563273572 -1 0.145991129229853 4325 4364 4170 4536 3823 3978 4683 3509 3422 4461 4090 4631 M2158 REACTOME_BASE_EXCISION_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_BASE_EXCISION_REPAIR.html Genes involved in Base Excision Repair 19/21 Reactome 0.68618940391 0.690284310838704 4175 4077.72727272727 4171 0.1 3509 0.674157527746561 0.672422006496743 1 0.162731336110431 4171 4218 3703 4394 3509 3833 4237 4032 4465 4522 3771 4632 M16374 IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_DN http://www.broadinstitute.org/gsea/msigdb/cards/IIZUKA_LIVER_CANCER_PROGRESSION_G1_G2_DN.html Genes down-regulated during transition from G1 (well differentiated tumor, infected with HCV) to G2 (moderately differentiated tumor, infected with HCV) in the development of hepatocellular carcinoma. 15710396 66/76 Yujin Hoshida 0.61408997307851 0.680240477101752 3540 4000.45454545455 4172 0.0829187296565478 2641 0.751660557400939 0.685505220715933 1 0.188631117944231 3537 4435 3883 4662 3298 4365 4166 2641 4212 4172 4634 4633 M14033 REACTOME_MRNA_SPLICING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_MRNA_SPLICING.html Genes involved in mRNA Splicing 129/178 Reactome 0.68618940391 0.690284310838704 4205 4083.27272727273 4173 0.1 3460 0.566143935956506 -0.586568045593463 -1 0.136641548165666 4202 4380 4173 4535 3460 3581 4609 3607 3794 4447 4128 4634 M17094 GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN http://www.broadinstitute.org/gsea/msigdb/cards/GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN.html Genes down-regulated in non-metastatic breast cancer tumors having type 1 amplification in the 20q13 region; involves ZNF217 [GeneID=7764] locus only. 16899599 407/460 Leona Saunders 0.344218795194281 0.411111516527582 4565 3757.54545454545 4176 0.0376307803312739 2211 0.817789986422598 -0.803586911189268 -1 0.473608265583365 4562 4321 4176 4516 2567 3256 4490 3907 2211 4422 2905 4635 M46 PID_ATR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATR_PATHWAY.html ATR signaling pathway 18832364 50/52 Pathway Interaction Database 0.68618940391 0.690284310838704 4535 3945.72727272727 4177 0.1 2317 0.842022053336685 0.88908082204268 1 0.203277621105818 4534 3342 3934 3887 3625 4686 4238 4177 2317 4290 4373 4636 M13045 SAMOLS_TARGETS_OF_KHSV_MIRNAS_UP http://www.broadinstitute.org/gsea/msigdb/cards/SAMOLS_TARGETS_OF_KHSV_MIRNAS_UP.html Genes up-regulated in 293 cells (embryonic kidney) upon expression of KHSV (Kaposi sarcoma-associated herpesvirus) microRNAs. 17500590 35/44 Arthur Liberzon 0.68618940391 0.690284310838704 3940 4009.27272727273 4179 0.1 2290 1.61827845318105 -1.29018439221761 -1 0.390775921338909 3940 4500 2290 4465 4179 3355 4629 4321 4411 3955 4057 4637 M17193 MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN http://www.broadinstitute.org/gsea/msigdb/cards/MOREAUX_MULTIPLE_MYELOMA_BY_TACI_DN.html Down-regulated genes distinguishing in multiple myeloma (MM) samples with lower expression of TACI [GeneID=23495]. 15827134 199/217 Kevin Vogelsang 0.68618940391 0.690284310838704 4645 4068.72727272727 4179 0.1 2693 0.72000923620068 0.701055627001872 1 0.173806436295955 4643 4706 4179 4686 4051 3251 3452 4502 2693 4464 4129 4638 M8560 BIOCARTA_G2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_G2_PATHWAY.html Cell Cycle: G2/M Checkpoint 38/43 BioCarta 0.68618940391 0.690284310838704 4580 3949.09090909091 4180 0.1 3013 0.727690277072802 0.60432058549367 1 0.175661728062738 4579 3375 3470 4299 4397 3515 3013 4076 4242 4294 4180 4639 M18312 KEGG_MATURITY_ONSET_DIABETES_OF_THE_YOUNG http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_MATURITY_ONSET_DIABETES_OF_THE_YOUNG.html Maturity onset diabetes of the young 4/27 KEGG 0.515846473132714 0.584049956666007 4005 3993.90909090909 4184 0.06996710438307 2115 0.348769434686892 -0.118239343308935 -1 0.122119188836155 4004 4656 4184 4418 3151 4012 2115 3564 4716 4491 4622 4640 M1364 SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_UP http://www.broadinstitute.org/gsea/msigdb/cards/SCHAEFFER_PROSTATE_DEVELOPMENT_AND_CANCER_BOX6_UP.html Early prostate development genes (up-regulated at 48 hr dihydrotestosterone [PubChem=10635]) which are also up-regulated in high grade prostatic intraepithelial neoplasia (PIN) vs invasive cancer. 18794802 14/15 Jessica Robertson 0.00369630791677268 0.0105736808285861 2605 3108.72727272727 4185 0.000336593898061466 738 1.65149319502974 1.74027320159783 1 4.89605663114347 2605 4594 738 4362 4185 4321 4685 1023 4455 1162 2066 4641 M1629 KYNG_RESPONSE_TO_H2O2_VIA_ERCC6 http://www.broadinstitute.org/gsea/msigdb/cards/KYNG_RESPONSE_TO_H2O2_VIA_ERCC6.html Genes down-regulated in CS-B cells (Cockayne syndrome fibroblast, CS) with defficient ERCC6 [GeneID=2074] in response to hydrogen peroxide [PubChem=784]. 12606941 25/42 John Newman 0.68618940391 0.690284310838704 4510 4004.81818181818 4189 0.1 2947 0.627747040481178 -0.529742647560793 -1 0.151521267533871 4506 4189 3361 4592 4243 2947 4289 4133 4247 4166 3380 4642 M7987 LEE_LIVER_CANCER_SURVIVAL_DN http://www.broadinstitute.org/gsea/msigdb/cards/LEE_LIVER_CANCER_SURVIVAL_DN.html Genes highly expressed in hepatocellular carcinoma with poor survival. 15349906 237/330 Yujin Hoshida 0.68618940391 0.690284310838704 4315 3928.81818181818 4190 0.1 1833 0.927935104495738 -1.04950622245767 -1 0.224029206617242 4313 3179 3976 3890 4222 4710 4496 4322 1833 4086 4190 4643 M7739 BIOCARTA_PYK2_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_PYK2_PATHWAY.html Links between Pyk2 and Map Kinases 43/47 BioCarta 0.68618940391 0.690284310838704 4195 3814.27272727273 4191 0.1 1414 0.668994623346122 -0.656195433212955 -1 0.161484279339573 4191 3360 3872 3693 4462 4553 3344 4265 1414 4235 4568 4644 M621 REACTOME_ARMS_MEDIATED_ACTIVATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_ARMS_MEDIATED_ACTIVATION.html Genes involved in ARMS-mediated activation 22/23 Reactome 0.678462839170864 0.690284310838704 4215 4060.09090909091 4192 0.0980076922303051 3098 0.733683951658881 -0.43735358107194 -1 0.177109450487011 4215 4556 3773 4493 3098 4444 4192 3491 3974 3835 4590 4645 M1507 ZAMORA_NOS2_TARGETS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZAMORA_NOS2_TARGETS_UP.html Up-regulated in hepatocytes upon expression of NOS2 [GeneID=4843]. 12381414 104/123 John Newman 0.27595520486137 0.339460142545131 4390 4086.36363636364 4192 0.0289280638169947 2426 0.965103340938879 1.0375093763027 1 0.67938563952503 4389 4393 3526 4693 2426 4131 4382 4182 4192 4048 4588 4646 M6866 MISSIAGLIA_REGULATED_BY_METHYLATION_DN http://www.broadinstitute.org/gsea/msigdb/cards/MISSIAGLIA_REGULATED_BY_METHYLATION_DN.html Genes down-regulated in PaCa44 and CFPAC1 cells (pancreatic cancer) after treatment with decitabine [PubChem=451668], a DNA hypomethylating agent similar to azacitidine [PubChem=9444]. 15637593 152/203 Leona Saunders 0.68618940391 0.690284310838704 4370 4081.27272727273 4196 0.1 3167 0.955182302464519 -1.00152386750014 -1 0.230610541478102 3167 4369 4051 4692 4657 3746 4358 3609 4196 4367 3682 4647 M1757 SANSOM_APC_TARGETS_REQUIRE_MYC http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_TARGETS_REQUIRE_MYC.html Genes up-regulated after Cre-lox knockout of APC [GeneID=324] in the small intestine that require functional MYC [GeneID=4609]. 17377531 255/287 Jessica Robertson 0.68618940391 0.690284310838704 4695 4104.09090909091 4200 0.1 2828 0.952018785284213 -0.921593967955863 -1 0.22984642012054 4693 4694 3958 4635 3510 3829 4561 4200 2828 4320 3917 4648 M19472 HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN http://www.broadinstitute.org/gsea/msigdb/cards/HOFMANN_MYELODYSPLASTIC_SYNDROM_LOW_RISK_DN.html Genes down-regulated in bone marrow hematopoietic stem cells (HSC, CD34+ [GeneID=947]) from patients with low risk of myelodysplastic syndrome (MDS) compared with healthy controls. 12411319 42/59 Arthur Liberzon 0.68618940391 0.690284310838704 4205 3918.54545454545 4201 0.1 2559 0.98252514991959 -1.01040003846459 -1 0.237214979679689 4201 4472 3150 3647 4131 4614 4713 4637 2559 2641 4339 4649 M1654 SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_DN http://www.broadinstitute.org/gsea/msigdb/cards/SARTIPY_NORMAL_AT_INSULIN_RESISTANCE_DN.html Genes down-regulated in 3T3-L1 cells (adipocyte) by insulin [GeneID=3630] which continued to respond normally to insulin in the insulin resistant cells. 14530283 23/28 John Newman 0.743842316895878 0.747643896028224 4315 3849.63636363636 4204 0.116456483746228 2720 1.10343845295795 -1.20904449883028 -1 0.209021689343688 4311 4204 2720 3089 3204 4263 3676 4510 4605 3450 4314 4650 M114 CHEOK_RESPONSE_TO_HD_MTX_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_HD_MTX_UP.html Genes specifically up-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by high-dose methotrexate (HDMTX) [PubChem=4112]. 12704389 15/79 Jean Junior 0.161620943931169 0.215372912296758 4040 3663.90909090909 4213 0.0158981726777785 1289 1.14103200372805 -1.23956782557649 -1 1.14156534284011 4039 3073 1289 3509 4475 4457 4213 4259 4418 2224 4347 4651 M84 PID_ATM_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_ATM_PATHWAY.html ATM pathway 18832364 41/48 Pathway Interaction Database 0.430550678760602 0.499814448548158 3805 3872.09090909091 4216 0.0499014755695323 2424 0.830982640139383 0.650062463040493 1 0.375451317317816 3805 4491 3962 4487 2716 4259 4705 2424 2907 4216 4621 4652 M1590 LEE_AGING_NEOCORTEX_UP http://www.broadinstitute.org/gsea/msigdb/cards/LEE_AGING_NEOCORTEX_UP.html Upregulated in the neocortex of aged adult mice (30-month) vs young adult (5-month) 10888876 152/194 John Newman 0.68618940391 0.690284310838704 4685 3783.63636363636 4216 0.1 2212 1.13029035498639 -0.9367199519839 -1 0.272906440373828 4684 4018 2449 4485 4216 2212 4426 4718 2574 3517 4321 4653 M1865 WANG_TUMOR_INVASIVENESS_UP http://www.broadinstitute.org/gsea/msigdb/cards/WANG_TUMOR_INVASIVENESS_UP.html Up-regulated genes in the subpopulation of invasive PyMT cells (breast cancer) compared to the general population of PyMT cells. 17440055 520/637 Jessica Robertson 0.6513215599 0.690284310838704 3085 3945.09090909091 4222 0.1 2687 0.92711209388962 -0.903383756454074 -1 0.223830415225955 3082 3602 4585 3920 4440 4414 3645 4248 2687 4222 4551 4654 M6562 CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_UP http://www.broadinstitute.org/gsea/msigdb/cards/CHAUHAN_RESPONSE_TO_METHOXYESTRADIOL_UP.html Genes up-regulated by 2-methoxyestradiol (2ME2) [PubChem=1573] in the MM.1S cell line (multiple myeloma) sensitive to dexamethasone [PubChem=5743]. 12480690 73/89 Arthur Liberzon 0.68618940391 0.690284310838704 4225 4056.81818181818 4222 0.1 3002 0.970401920845121 -0.844322891283701 -1 0.234286714166831 4222 4073 3117 4132 4691 4353 4249 4384 3002 3769 4633 4655 M8180 SAKAI_TUMOR_INFILTRATING_MONOCYTES_DN http://www.broadinstitute.org/gsea/msigdb/cards/SAKAI_TUMOR_INFILTRATING_MONOCYTES_DN.html Selected genes down-regulated in inflammatory monocytes infiltrating hepatocellular carcinoma (HCC). 19074895 100/137 Jessica Robertson 0.562487730722088 0.629580765712178 4225 4109.90909090909 4223 0.0723957094104744 2926 0.816297239763897 0.871201662750933 1 0.246030099418608 4223 4391 4052 4157 2926 3866 4229 4562 4248 4358 4197 4656 M16010 KOBAYASHI_EGFR_SIGNALING_24HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/KOBAYASHI_EGFR_SIGNALING_24HR_DN.html Genes down-regulated in H1975 cells (non-small cell lung cancer, NSCLC) resistant to gefitinib [PubChem=123631] after treatment with EGFR inhibitor CL-387785 [PubChem=2776] for 24h. 17145885 303/370 Arthur Liberzon 0.68618940391 0.690284310838704 4690 4201 4223 0.1 2383 1.07278528113589 1.04365419401593 1 0.25901656635294 4018 4692 4034 4534 4690 4687 4170 4561 2383 4219 4223 4657 M2394 JUBAN_TARGETS_OF_SPI1_AND_FLI1_DN http://www.broadinstitute.org/gsea/msigdb/cards/JUBAN_TARGETS_OF_SPI1_AND_FLI1_DN.html Genes down-regulated in 745A cells (erythroleukemia) upon knockdown of FLI1 [GeneID=2313] by RNAi and down-regulation of SPI1 [GeneID=6688] by HMBA [PubChem=3616]. 19289502 137/161 Arthur Liberzon 0.68618940391 0.690284310838704 3305 4021.63636363636 4223 0.1 3305 0.967040672885573 0.979088570099981 1 0.233474832578217 3305 4370 3815 4334 4223 4355 4293 3308 4098 3911 4226 4658 M1819 MATZUK_MEIOTIC_AND_DNA_REPAIR http://www.broadinstitute.org/gsea/msigdb/cards/MATZUK_MEIOTIC_AND_DNA_REPAIR.html Meitic and DNA repair genes important for female fertility, based on mouse models with female fertility defects. 18989307 41/156 Jessica Robertson 0.155703857227138 0.209141208341518 4400 3737.81818181818 4224 0.0152687742968938 1650 0.872022947004695 0.827059934534882 1 0.889090738231794 4224 4480 3484 4440 4308 3389 2266 1650 4396 4082 4397 4659 M6515 SPIRA_SMOKERS_LUNG_CANCER_DN http://www.broadinstitute.org/gsea/msigdb/cards/SPIRA_SMOKERS_LUNG_CANCER_DN.html Down-regulated genes that distinguished smokers with and without lung cancer. 17334370 53/87 Jessica Robertson 0.68618940391 0.690284310838704 4715 4057.45454545455 4226 0.1 3362 0.799243406736388 -0.686169664836096 -1 0.192944793543384 4713 4453 3839 4448 3383 3465 4570 3362 3668 4226 4505 4660 M15969 VERNELL_RETINOBLASTOMA_PATHWAY_UP http://www.broadinstitute.org/gsea/msigdb/cards/VERNELL_RETINOBLASTOMA_PATHWAY_UP.html Cluster 1: genes up-regulated by RB1, CDNK2A [GeneID=1029;5925], and one of the E2Fs (E2F1, E2F2, or E2F3 [GeneID=1869;1870;1871]). 12923195 91/123 Kevin Vogelsang 0.68618940391 0.690284310838704 3680 3979.18181818182 4234 0.1 1934 0.939694482288774 0.961703543559877 1 0.226869586868452 3678 4399 3856 4649 4240 4167 3882 4347 1934 4234 4385 4661 M541 REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RESOLUTION_OF_AP_SITES_VIA_THE_MULTIPLE_NUCLEOTIDE_PATCH_REPLACEMENT_PATHWAY.html Genes involved in Resolution of AP sites via the multiple-nucleotide patch replacement pathway 17/19 Reactome 0.68618940391 0.690284310838704 3195 3812.09090909091 4238 0.1 2403 0.674157527746561 0.672422006496743 1 0.162731336110431 3191 4238 3642 4413 4303 2403 2819 4697 4480 4528 3219 4662 M123 MUELLER_PLURINET http://www.broadinstitute.org/gsea/msigdb/cards/MUELLER_PLURINET.html Genes constituting the PluriNet protein-protein network shared by the pluripotent cells (embryonic stem cells, embryonical carcinomas and induced pluripotent cells). 18724358 364/443 Arthur Liberzon 0.68618940391 0.690284310838704 3850 4165.90909090909 4243 0.1 3162 0.901939791938352 -0.928726920264555 -1 0.217750254302627 3850 4683 4140 4541 4400 4043 4661 4243 3162 4427 3675 4663 M14019 DING_LUNG_CANCER_MUTATED_RECURRENTLY http://www.broadinstitute.org/gsea/msigdb/cards/DING_LUNG_CANCER_MUTATED_RECURRENTLY.html The lung adenocarcinoma TSP (tumor sequencing project) genes bearing recurrent somatic mutations. 18948947 12/13 Arthur Liberzon 0.508897177769726 0.57768029799738 4255 3679.45454545455 4252 0.0626003946258751 2455 1.03200530132133 -0.691074975821989 -1 0.368931636219394 4427 4253 2501 3443 4309 4252 2561 2455 4486 3130 4657 4664 M8822 LU_TUMOR_ENDOTHELIAL_MARKERS_DN http://www.broadinstitute.org/gsea/msigdb/cards/LU_TUMOR_ENDOTHELIAL_MARKERS_DN.html Genes specifically down-regulated in tumor endothelium. 17308118 5/6 Jessica Robertson 0.8926258176 0.895281313019974 4625 4069.18181818182 4258 0.2 3065 1.95020623816708 1.95020623816708 1 0.140476163587841 4621 3578 4577 3065 4258 3970 4500 4193 4615 3093 4291 4665 M15409 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_3 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_3.html Amplification hot spot 3: colocolized fragile sites and cancer genes in the 15q21-q26 region. 16751803 6/7 Arthur Liberzon 0.0497369353087903 0.0804532234759996 4375 3835.90909090909 4260 0.00508865097671844 1546 0.918370460797434 -0.59689274331028 -1 1.50809175212984 4083 4288 4372 4372 1546 4232 2724 4527 4560 3231 4260 4666 M7239 BIOCARTA_DNAFRAGMENT_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/BIOCARTA_DNAFRAGMENT_PATHWAY.html Apoptotic DNA fragmentation and tissue homeostasis 9/18 BioCarta 0.6513215599 0.690284310838704 4050 4100.90909090909 4266 0.1 2822 0.514085722149576 -0.502780383724814 -1 0.124067318047979 4047 4266 4186 4588 4464 3548 2822 4318 4469 4493 3909 4667 M1370 COURTOIS_SENESCENCE_TRIGGERS http://www.broadinstitute.org/gsea/msigdb/cards/COURTOIS_SENESCENCE_TRIGGERS.html Genes that trigger senescence in vitro and in vivo. 18193093 8/8 Jessica Robertson 0.433121610182905 0.501553974500322 2640 3726.36363636364 4267 0.0551801908612997 2392 0.520838450338861 -0.524542925164156 -1 0.234104463432033 3437 4267 4446 4595 4716 2639 2636 2392 4408 4662 2792 4668 M7910 CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_DN http://www.broadinstitute.org/gsea/msigdb/cards/CHEOK_RESPONSE_TO_MERCAPTOPURINE_AND_HD_MTX_DN.html Genes specifically down-regulated in pediatric acute lymphoblastic leukemia (ALL) patients by mercaptopurine [PubChem=667490] and high dose methotrexate (HDMTX) [PubChem=4112]. 12704389 27/33 Arthur Liberzon 0.68618940391 0.690284310838704 4270 4279.36363636364 4267 0.1 3819 0.650818116700326 -0.676807460586885 -1 0.157093894795309 4267 4531 3957 4456 4583 3904 4223 3819 4132 4702 4499 4669 M5223 BRUNEAU_SEPTATION_ATRIAL http://www.broadinstitute.org/gsea/msigdb/cards/BRUNEAU_SEPTATION_ATRIAL.html Genes for which mutations result in atrial septation defects, a major class of congenital heart disease. 18288184 4/18 Jessica Robertson 0.27756396514991 0.341350160371959 4390 3883.90909090909 4268 0.0319897855073735 2474 0.714901730449635 -0.951278974518823 -1 0.50064180000833 4386 3583 4604 2667 2474 4268 4574 2954 4666 4698 3849 4670 M7982 ISHIKAWA_STING_SIGNALING http://www.broadinstitute.org/gsea/msigdb/cards/ISHIKAWA_STING_SIGNALING.html Prmary innate immune response genes induced in 293T cells (embryonic kidney) by overexpression of STING (TMEM173) [GeneID=340061]. 18724357 8/9 Jessica Robertson 0.900202646349007 0.902688865682454 4140 4233.27272727273 4273 0.205832879968908 3165 0.431854853836452 -0.445108080194422 -1 0.0287057984806285 4136 4273 4584 4564 4055 3809 4718 3165 4701 4691 3870 4671 M2421 PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_UP http://www.broadinstitute.org/gsea/msigdb/cards/PARK_OSTEOBLAST_DIFFERENTIATION_BY_PHENYLAMIL_UP.html Genes up-regulated in M2-10B4 cells (osteoblast) in response to phenylamil [PubChem=4755]. 19433444 16/19 Arthur Liberzon 0.046770369392133 0.0760965679182584 1715 3088.54545454545 4277 0.00434502828026542 553 1.59719351799639 1.53568615094681 1 2.68083805633825 1714 4592 1146 4553 4452 4277 4383 1576 4397 2331 553 4672 M629 GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_DN http://www.broadinstitute.org/gsea/msigdb/cards/GRAHAM_CML_QUIESCENT_VS_CML_DIVIDING_DN.html Genes down-regulated in quiescent (G0) vs dividing (M) CD34+ [GeneID=8842] cells isolated from peripheral blood of CML (chronic myeloid leukemia) patients. 17717066 8/35 Arthur Liberzon 0.0724305025194844 0.109856032098961 4280 3920.45454545455 4278 0.0074905606053719 1720 0.518592512319147 0.518592512319147 1 0.746285174208936 3808 4280 4315 4445 1720 4088 4278 2935 4691 4633 3932 4673 M1152 RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_UP http://www.broadinstitute.org/gsea/msigdb/cards/RAMJAUN_APOPTOSIS_BY_TGFB1_VIA_MAPK1_UP.html Apoptotic genes dependent on MAPK1 [GeneID=5594] and up-regulated in AML12 cells (hepatocytes) after stimulation with TGFB1 [GeneID=7040]. 16909112 12/12 Arthur Liberzon 0.265347135517617 0.328121163123698 4625 3848.81818181818 4278 0.0276432074231376 2403 0.674002044667155 0.63935919090241 1 0.489354680880573 4278 4621 2765 4622 2403 2708 3621 3401 4709 4639 4570 4674 M4077 FOURNIER_ACINAR_DEVELOPMENT_LATE_2 http://www.broadinstitute.org/gsea/msigdb/cards/FOURNIER_ACINAR_DEVELOPMENT_LATE_2.html Genes identified by method 2 as coordinately down-regulated late in HMEC cells (mammary epithelium) during acinar development in vitro. 16849555 391/454 Arthur Liberzon 0.68618940391 0.690284310838704 3380 3971.90909090909 4281 0.1 2215 0.907502891133232 0.999137548501531 1 0.219093974809508 3377 4323 4029 3916 4329 4441 4598 3497 2215 4281 4685 4675 M1051 REACTOME_INTEGRATION_OF_PROVIRUS http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_INTEGRATION_OF_PROVIRUS.html Genes involved in Integration of provirus 10/13 Reactome 0.0535864144726153 0.0855352980421861 4290 3940.63636363636 4287 0.00499436027057148 1541 0.604875514932958 -0.604002957965959 -1 0.969108770793339 4287 4261 3479 4044 1541 4651 4361 3129 4351 4614 4629 4676 M679 REICHERT_G1S_REGULATORS_AS_PI3K_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/REICHERT_G1S_REGULATORS_AS_PI3K_TARGETS.html G1 to S phase regulators significantly changed in DanG cells (pancreatic cancer) treated with Ly294002 [PubChem=3973], a phosphoinositide 3-kinase (PI3K) inhibitor. 17483325 10/11 Jessica Robertson 0.997861233174923 0.998284234969402 4495 4199.36363636364 4287 0.428142810693228 3397 0.405140017887182 0.405140017887182 1 0.000347551835440856 4494 3562 3397 4081 4467 4254 4287 3763 4708 4694 4486 4677 M1040 REACTOME_G1_S_SPECIFIC_TRANSCRIPTION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_G1_S_SPECIFIC_TRANSCRIPTION.html Genes involved in G1/S-Specific Transcription 20/22 Reactome 0.68618940391 0.690284310838704 2795 4048.09090909091 4291 0.1 2794 0.580789125746408 -0.592464127156626 -1 0.140178972388833 2794 4555 3720 4617 4438 3951 3476 4291 4409 4611 3667 4678 M2045 MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_1 http://www.broadinstitute.org/gsea/msigdb/cards/MARIADASON_RESPONSE_TO_BUTYRATE_CURCUMIN_SULINDAC_TSA_1.html Cluster 1: genes up-regulated in SW260 cells (colon cancer) by sodium butyrate, curcumin, sulindac and TSA [PubChem=5222465;969516;5352;5562]. 10969808 14/24 Arthur Liberzon 0.848884724037993 0.851591051532269 4715 3966.54545454545 4295 0.15784570117614 2721 0.675497186233548 0.565720909449678 1 0.0706117368161347 3546 3531 3012 3408 4712 4581 2721 4508 4607 4711 4295 4679 M6768 REACTOME_E2F_MEDIATED_REGULATION_OF_DNA_REPLICATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_E2F_MEDIATED_REGULATION_OF_DNA_REPLICATION.html Genes involved in E2F mediated regulation of DNA replication 38/40 Reactome 0.68618940391 0.690284310838704 3735 4115.81818181818 4296 0.1 2422 0.828891341426492 -0.579264449001258 -1 0.200106006463407 3732 4495 3873 4641 4019 4482 4635 4440 2422 4296 4239 4680 M18855 VECCHI_GASTRIC_CANCER_EARLY_UP http://www.broadinstitute.org/gsea/msigdb/cards/VECCHI_GASTRIC_CANCER_EARLY_UP.html Up-regulated genes distinguishing between early gastric cancer (EGC) and normal tissue samples. 17297478 529/656 Arthur Liberzon 0.6513215599 0.690284310838704 4225 4082.54545454545 4298 0.1 2135 1.14250272868523 -1.0344285225033 -1 0.275856238031925 4221 4676 4298 4672 4525 3679 4327 3927 2135 3964 4484 4681 M16189 BERENJENO_TRANSFORMED_BY_RHOA_UP http://www.broadinstitute.org/gsea/msigdb/cards/BERENJENO_TRANSFORMED_BY_RHOA_UP.html Genes up-regulated in NIH3T3 cells (fibroblasts) transformed by expression of contitutively active (Q63L) form of RHOA [GeneID=387] off plasmid vector. 17213802 675/796 Leona Saunders 0.6513215599 0.690284310838704 4410 4116.09090909091 4303 0.1 2444 1.02626990457261 -0.968531870447687 -1 0.247781162635731 4407 4311 4341 3914 4296 4240 4438 4396 2444 4187 4303 4682 M2099 MARTENS_TRETINOIN_RESPONSE_DN http://www.broadinstitute.org/gsea/msigdb/cards/MARTENS_TRETINOIN_RESPONSE_DN.html Genes down-regulated in NB4 cells (acute promyelocytic leukemia, APL) in response to tretinoin [PubChem=444795]; based on Chip-seq data. 20159609 922/1412 Arthur Liberzon 0.296443036263837 0.36062142555807 4085 4033 4303 0.0345496894015002 2525 0.912076378394678 -0.909959109718937 -1 0.606108541784481 4081 4303 4657 4694 2525 3779 4420 3744 3354 4442 4364 4683 M2044 KEGG_SPLICEOSOME http://www.broadinstitute.org/gsea/msigdb/cards/KEGG_SPLICEOSOME.html Spliceosome 141/188 KEGG 0.68618940391 0.690284310838704 4645 4200.63636363636 4306 0.1 3484 0.598188945432935 -0.630429323606555 -1 0.144381754634802 4645 4376 4168 4171 3665 4306 4430 3484 4398 4445 4119 4684 M2343 FEVR_CTNNB1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/FEVR_CTNNB1_TARGETS_DN.html Genes down-regulated in intestinal crypt cells upon deletion of CTNNB1 [GeneID=1499]. 17785439 720/1027 Arthur Liberzon 0.6513215599 0.690284310838704 4350 3752.54545454545 4308 0.1 1342 1.0493428292727 0.934837701149381 1 0.253354236382421 3065 4308 4686 4346 4559 3499 3230 3388 1342 4346 4509 4685 M1756 SANSOM_APC_MYC_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/SANSOM_APC_MYC_TARGETS.html Genes down-regulated after double Cre-lox knockout of both APC and MYC [GeneID=324;4609] in small intestine. 17377531 278/308 Arthur Liberzon 0.68618940391 0.690284310838704 4420 4140.54545454545 4309 0.1 3605 0.902243131059535 -0.91915620947908 -1 0.217823523353455 4416 4331 4036 4309 4604 4311 3763 4070 3605 4319 3782 4686 M16843 REACTOME_METABOLISM_OF_RNA http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_METABOLISM_OF_RNA.html Genes involved in Metabolism of RNA 292/402 Reactome 0.0530103510873947 0.0848741035049197 3290 3964.90909090909 4310 0.00493931727820375 1537 0.639254198223835 -0.613388468304829 -1 1.02742773357264 3288 4691 4175 4539 1537 4391 3674 3715 4310 4574 4720 4687 M17859 KIM_WT1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/KIM_WT1_TARGETS_DN.html Genes down-regulated in UB27 cells (osteosarcoma) at any time point after inducing the expression of a mutant form of WT1 [GeneID=7490]. 17430890 592/683 Arthur Liberzon 0.236724735902494 0.297560786540552 4315 3850.90909090909 4313 0.0266520493630908 1971 0.999109468852455 -0.899410954501526 -1 0.789100962510477 3499 4313 4313 4166 4518 4379 3898 1971 2625 4326 4352 4688 M11197 HSIAO_HOUSEKEEPING_GENES http://www.broadinstitute.org/gsea/msigdb/cards/HSIAO_HOUSEKEEPING_GENES.html Housekeeping genes identified as expressed across 19 normal tissues. 11773596 560/786 Arthur Liberzon 0.6513215599 0.690284310838704 4390 3947.09090909091 4314 0.1 2895 0.851019492766735 -0.862821054585508 -1 0.205450878034743 4388 4316 4611 4348 4060 3194 4314 2895 3728 4438 3126 4689 M9841 TURJANSKI_MAPK8_AND_MAPK9_TARGETS http://www.broadinstitute.org/gsea/msigdb/cards/TURJANSKI_MAPK8_AND_MAPK9_TARGETS.html Examples of transcription factors whose activities are regulated by MAPK8 and MAPK9 [GeneID=5599;5601]. 17496919 11/11 Arthur Liberzon 0.822641705376249 0.825966570809592 3985 4059.36363636364 4318 0.145496643235138 3324 0.27935448980869 -0.40507048034073 -1 0.0347015962956875 3984 4630 3326 4454 3337 3370 4318 4550 4718 4642 3324 4690 M1019 REACTOME_CLEAVAGE_OF_GROWING_TRANSCRIPT_IN_THE_TERMINATION_REGION_ http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_CLEAVAGE_OF_GROWING_TRANSCRIPT_IN_THE_TERMINATION_REGION_.html Genes involved in Cleavage of Growing Transcript in the Termination Region 53/83 Reactome 0.381200378863713 0.449816447059182 4025 4164.27272727273 4328 0.0426957134804307 2636 0.549344394434605 0.541866641020124 1 0.285897943083484 4023 4465 4122 4510 2636 4084 4356 4328 4005 4596 4682 4691 M1024 REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION_TERMINATION.html Genes involved in RNA Polymerase III Transcription Termination 20/22 Reactome 0.607553512780094 0.673474067713021 4325 4133.90909090909 4331 0.0815173654770721 2971 0.692528286530158 0.70860034543223 1 0.178294977194782 4323 4591 3901 4650 2997 4575 2971 4331 4610 4066 4458 4692 M19927 TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C http://www.broadinstitute.org/gsea/msigdb/cards/TOYOTA_TARGETS_OF_MIR34B_AND_MIR34C.html Genes down-regulated in HCT116 cells (colon cancer) upon expression of MIR34B or MIR34C [GeneID=407041;407042] microRNAs. 18519671 589/723 Leona Saunders 0.6513215599 0.690284310838704 4020 4068.09090909091 4334 0.1 1511 0.952710455883372 0.971430953046206 1 0.230013487421613 4019 4672 4560 4678 4000 4334 4381 3903 1511 4421 4270 4693 M137 PID_VEGF_VEGFR_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_VEGF_VEGFR_PATHWAY.html VEGF and VEGFR signaling network 18832364 9/10 Pathway Interaction Database 0.912598658030873 0.914730445085096 3905 4247.63636363636 4335 0.216296457109018 3571 0.365742946233989 0.356392270595408 1 0.0211366796042131 3905 4643 4203 4453 3571 4005 3950 4335 4715 4513 4431 4694 M18784 VALK_AML_CLUSTER_10 http://www.broadinstitute.org/gsea/msigdb/cards/VALK_AML_CLUSTER_10.html Top 40 genes from cluster 10 of acute myeloid leukemia (AML) expression profile; 41% of the samples are FAB M1 subtype, 45% have up-regulated EVI1 [GeneID=2122] expression; indicate poor survival. 15084694 38/54 Jessica Robertson 0.0475000194466681 0.0770538068965218 4340 3984.81818181818 4337 0.00441433644826273 1500 0.710630170587831 -0.700603350672552 -1 1.18692213487964 4337 3793 3583 4603 1500 4688 3475 4531 4463 4184 4676 4695 M8520 SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6 http://www.broadinstitute.org/gsea/msigdb/cards/SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6.html Cluster 6 of method A: up-regulation of these genes in patients with non-small cell lung cancer (NSCLC) predicts poor survival outcome. 18641660 580/733 Arthur Liberzon 0.6513215599 0.690284310838704 4720 4220.45454545455 4344 0.1 2328 1.01602769511583 -0.968487711668452 -1 0.24530724182276 4719 4674 4603 4344 4645 4130 4399 4065 2328 4315 4203 4696 M5611 PUJANA_BRCA1_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BRCA1_PCC_NETWORK.html Genes constituting the BRCA1-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC >= 0.4) with that of BRCA1 [GeneID=672] across a compendium of normal tissues. 17922014 1946/2578 Leona Saunders 0.6513215599 0.690284310838704 4660 4169.72727272727 4351 0.1 2966 0.896662694679953 -0.900623542018885 -1 0.21647561519329 4447 4658 4419 4710 4130 3656 4351 4227 2966 4659 3644 4697 M9585 PUJANA_ATM_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_ATM_PCC_NETWORK.html Genes constituting the ATM-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC >= 0.4) with that of ATM [GeneID=472] across a compendium of normal tissues. 17922014 1698/2334 Leona Saunders 0.6513215599 0.690284310838704 3250 4017.09090909091 4357 0.1 3179 0.995094949256622 0.984725592437325 1 0.240251110538561 3179 4659 4421 4704 3246 4104 3257 4357 3250 4444 4567 4698 M607 REACTOME_PRE_NOTCH_EXPRESSION_AND_PROCESSING http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_PRE_NOTCH_EXPRESSION_AND_PROCESSING.html Genes involved in Pre-NOTCH Expression and Processing 51/53 Reactome 0.68618940391 0.690284310838704 4505 4188 4361 0.1 3393 0.981331020577861 -0.907721038046997 -1 0.236926547633425 4504 4455 3393 4599 4476 4361 4281 3570 4121 3934 4374 4699 M1175 IWANAGA_E2F1_TARGETS_NOT_INDUCED_BY_SERUM http://www.broadinstitute.org/gsea/msigdb/cards/IWANAGA_E2F1_TARGETS_NOT_INDUCED_BY_SERUM.html Genes up-regulated in REF52 cells (embryonic fibroblast) by expression of E2F1 [GeneID=1869] that were not induced at all at 16 hr after serum stimulation. 16288221 6/8 Arthur Liberzon 0.943330082867228 0.944330432902082 4650 4133.45454545455 4361 0.249526679199807 2914 0.178640318508838 -0.136155537055892 -1 0.00656227203283357 3973 4648 4361 4597 4344 2914 3237 3643 4662 4647 4442 4700 M4364 PASTURAL_RIZ1_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/PASTURAL_RIZ1_TARGETS_DN.html Genes down-regulated in K562 (chronic myelogenous leukemia, CML) cells engineered to stably express RIZ1 [GeneID=7799]. 16953217 5/6 Aravind Subramanian 0.329948100602171 0.395669470234311 3595 4155 4365 0.0392490020144139 2187 0.904500810850656 0.904500810850656 1 0.546403152238537 3595 4650 4325 4365 4520 4564 4177 2187 4717 4634 3971 4701 M1295 GALIE_TUMOR_STEMNESS_GENES http://www.broadinstitute.org/gsea/msigdb/cards/GALIE_TUMOR_STEMNESS_GENES.html Stemness-related genes changed in A17 carcinomas (MTC, mesenchymal tumor cells) compared with the mesenchymal stem cells (MSC). 17998939 11/11 Jessica Robertson 0.580104085775973 0.646996995477928 4370 3990.45454545455 4367 0.0758549324531518 1722 1.26217514041041 1.55494916676097 1 0.358029991875279 4666 4617 1722 4367 3837 4367 4544 3815 4428 3020 4512 4702 M1176 MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_2 http://www.broadinstitute.org/gsea/msigdb/cards/MYLLYKANGAS_AMPLIFICATION_HOT_SPOT_2.html Amplification hot spot 2: colocolized fragile sites and cancer genes in the 12p13-p11.1 region. 16751803 8/9 Arthur Liberzon 0.146557256606399 0.198893114198449 4650 3872 4369 0.0157227685653777 1202 0.120582367416659 0.137585448450052 1 0.126799293545475 3186 4646 4369 4645 4129 3246 1202 4620 4719 4649 3181 4703 M10501 RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP http://www.broadinstitute.org/gsea/msigdb/cards/RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP.html Genes up-regulated in poorly differentiated thyroid carcinoma (PDTC) compared to normal thyroid tissue. 17406368 798/909 Arthur Liberzon 0.6513215599 0.690284310838704 4375 4153.27272727273 4372 0.1 1665 1.03302976920642 -1.06326065180408 -1 0.249413951916308 4372 4304 4320 4337 4499 4540 4405 4668 1665 4392 4184 4704 M1731 GAVIN_FOXP3_TARGETS_CLUSTER_T7 http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_FOXP3_TARGETS_CLUSTER_T7.html Cluster T7 of genes with similar expression profiles in thymic T lymphocytes after FOXP3 [GeneID=50943] loss of function (LOF). 17220874 126/151 Jessica Robertson 0.68618940391 0.690284310838704 3500 4264.18181818182 4374 0.1 3497 0.762577535400917 0.761450778020753 1 0.184088456187138 3497 4374 4114 4505 4666 4589 4234 4418 3697 4193 4619 4705 M9516 PUJANA_BRCA2_PCC_NETWORK http://www.broadinstitute.org/gsea/msigdb/cards/PUJANA_BRCA2_PCC_NETWORK.html Genes constituting the BRCA2-PCC network of transcripts whose expression positively correlated (Pearson correlation coefficient, PCC >= 0.4) with that of BRCA2 [GeneID=675] across a compendium of normal tissues. 17922014 585/743 Leona Saunders 0.6513215599 0.690284310838704 4025 4080.81818181818 4387 0.1 1971 0.93858193279854 -0.968434054502705 -1 0.226600859759231 4021 4673 4420 4700 4010 4106 4647 4387 1971 4439 3515 4706 M14865 PALOMERO_GSI_SENSITIVITY_DN http://www.broadinstitute.org/gsea/msigdb/cards/PALOMERO_GSI_SENSITIVITY_DN.html Down-regulated genes associated with sensitivity and resistance to gamma-secretase (GSI) in T-cell acute lymphoblastic leukemia (T-ALL) cell lines. 17873882 9/9 Jessica Robertson 0.00224755853867479 0.00730020588604876 4360 4038.90909090909 4387 0.000224983496345169 552 0.349999153689015 -0.349999153689015 -1 1.12202945142016 4357 4631 4595 4387 552 3995 4502 3794 4614 4695 4306 4707 M134 PID_TCR_RAS_PATHWAY http://www.broadinstitute.org/gsea/msigdb/cards/PID_TCR_RAS_PATHWAY.html Ras signaling in the CD4+ TCR pathway 18832364 15/17 Pathway Interaction Database 0.00760674078828451 0.0175671011637266 4700 3929.09090909091 4394 0.000693924540940595 822 0.576307531901331 -0.43735358107194 -1 1.51780909778417 4700 4607 3806 4149 822 2861 4394 4457 4333 4512 4579 4708 M12113 WEI_MYCN_TARGETS_WITH_E_BOX http://www.broadinstitute.org/gsea/msigdb/cards/WEI_MYCN_TARGETS_WITH_E_BOX.html Genes whose promoters contain E-box motifs and whose expression changed in MYCN-3 cells (neuroblastoma) upon induction of MYCN [GeneID=4613]. 18504438 947/1100 Jessica Robertson 0.6513215599 0.690284310838704 4620 4125.72727272727 4414 0.1 1688 0.936064840473107 -0.902916533491655 -1 0.225992876968181 4619 4665 4435 4689 3868 3937 4367 4585 1688 4414 4116 4709 M15774 DANG_BOUND_BY_MYC http://www.broadinstitute.org/gsea/msigdb/cards/DANG_BOUND_BY_MYC.html Genes whose promoters are bound by MYC [GeneID=4609], according to MYC Target Gene Database. 14519204 1400/1799 Chi Dang 0.488879040809154 0.558718903781891 4445 3966.63636363636 4429 0.0649122469840983 2370 0.958817250505565 -0.962936837428542 -1 0.363613277740695 4443 4662 4641 4702 2858 3201 4489 4429 2370 4388 3450 4710 M80 KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP http://www.broadinstitute.org/gsea/msigdb/cards/KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_UP.html Genes up-regulated in TC71 and EWS502 cells (Ewing's sarcoma) by EWSR1-FLI1 [GeneID=2130;2314] as inferred from RNAi knockdown of this fusion protein. 17114343 1535/1883 Leona Saunders 0.6513215599 0.690284310838704 4665 4180.45454545455 4441 0.1 1873 0.981660100841179 -1.00394676803421 -1 0.237006034243809 4441 4661 4312 4698 3997 4148 4663 4652 1873 4455 4085 4711 M1915 ZHANG_TLX_TARGETS_60HR_DN http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_TLX_TARGETS_60HR_DN.html Genes down-regulated in neural stem cells (NSC) at 60 h after cre-lox knockout of TLX (NR2E1) [GeneID=7101]. 18235445 324/374 Jessica Robertson 0.68618940391 0.690284310838704 4705 4266.09090909091 4445 0.1 2808 0.968912459846709 0.912048214481335 1 0.233926947206428 4705 4687 4139 4696 4050 4609 4531 3817 2808 4440 4445 4712 M15150 ZHANG_BREAST_CANCER_PROGENITORS_UP http://www.broadinstitute.org/gsea/msigdb/cards/ZHANG_BREAST_CANCER_PROGENITORS_UP.html Genes up-regulated in cancer stem cells isolated from mammary tumors compared to the non-tumorigenic cells. 18559513 606/696 Leona Saunders 0.6513215599 0.690284310838704 3365 4117.27272727273 4451 0.1 2794 0.943675312400524 -0.854155886798293 -1 0.227831123391203 3364 4671 4561 4699 3779 4582 4035 3671 2794 4451 4683 4713 M8156 BENPORATH_CYCLING_GENES http://www.broadinstitute.org/gsea/msigdb/cards/BENPORATH_CYCLING_GENES.html Genes showing cell-cycle stage-specific expression [PMID=12058064]. 18443585 832/1017 Jessica Robertson 0.6513215599 0.690284310838704 4570 4260 4455 0.1 2944 0.976848488796884 0.957012570994043 1 0.235843829230275 4567 4667 4455 4695 4567 4497 4334 3986 2944 4373 3775 4714 M1740 GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_DN http://www.broadinstitute.org/gsea/msigdb/cards/GAVIN_IL2_RESPONSIVE_FOXP3_TARGETS_DN.html FOXP3 [GeneID=50943] target genes down-regulated in T lymphocytes after stimulation with IL2 [GeneID=3558]. 17220874 8/8 Jessica Robertson 0.034271962882486 0.0585675832025105 2025 3303.36363636364 4463 0.00348122837305174 585 0.443305047455102 -0.494981253805008 -1 0.819633894393261 2022 4640 4516 4585 2934 1595 585 4463 4606 4685 1706 4715 M2241 JOHNSTONE_PARVB_TARGETS_3_DN http://www.broadinstitute.org/gsea/msigdb/cards/JOHNSTONE_PARVB_TARGETS_3_DN.html Genes down-regulated upon overexpression of PARVB [GeneID=29780] in MDA-MB-231 cells (breast cancer) cultured in 3D Matrigel only. 17998334 1117/1358 Arthur Liberzon 0.6513215599 0.690284310838704 4515 4202.90909090909 4514 0.1 2679 0.865470526380609 0.842685041094901 1 0.208941405442641 3598 4663 4671 4705 4637 4514 4004 3533 2679 4715 4513 4716 M486 REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_2_PROMOTER.html Genes involved in RNA Polymerase III Transcription Initiation From Type 2 Promoter 24/27 Reactome 0.830335186076103 0.833513840552787 4265 4333.36363636364 4538 0.148934688393329 2666 0.481890170380447 -0.559997112803548 -1 0.0570809978840817 4262 4569 4027 4509 4576 4720 2666 4538 4668 4517 4615 4717 M1022 REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_III_TRANSCRIPTION_INITIATION_FROM_TYPE_3_PROMOTER.html Genes involved in RNA Polymerase III Transcription Initiation From Type 3 Promoter 27/30 Reactome 0.99637202944 0.997005719515964 4595 4407.81818181818 4543 0.4 3958 0.493030227130129 -0.660384168726014 -1 0.000857653305203567 4592 4566 4054 4676 4543 4042 3958 4530 4690 4597 4238 4718 M1095 REACTOME_RNA_POL_I_TRANSCRIPTION_INITIATION http://www.broadinstitute.org/gsea/msigdb/cards/REACTOME_RNA_POL_I_TRANSCRIPTION_INITIATION.html Genes involved in RNA Polymerase I Transcription Initiation 25/25 Reactome 0.91410065408 0.91526412542588 4230 4423.36363636364 4568 0.2 4073 0.565419918995408 -0.636054668324094 -1 0.0325190928948286 4226 4568 4073 4663 4274 4255 4592 4088 4600 4625 4693 4719 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 0.961369535458467 0.962184946430018 4345 4351.54545454545 4582 0.277740948750326 3211 0.14140190074053 0.0399839887709557 1 0.00344631102265705 4345 4655 4696 4582 3849 4202 3211 4598 4713 4718 4298 4720 M2604 ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_2HR http://www.broadinstitute.org/gsea/msigdb/cards/ZHOU_CELL_CYCLE_GENES_IN_IR_RESPONSE_2HR.html Cell cycle genes significantly (p =< 0.05) changed in fibroblast cells at 2 h after exposure to ionizing radiation. 17404513 9/9 Itai Pashtan 0.9990234375 0.99923513986014 4645 4526.72727272727 4641 0.5 3943 0.212238944364834 0.177688811130576 1 0 4641 4645 4716 4464 4286 4356 3943 4708 4705 4720 4610